Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011227.1 Corchorus capsularis cultivar CVL-1 contig11248, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47816
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:583 original size:15 final size:14
Alignment explanation
Indices: 549--579 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
539 TAGTTTTTAG
*
549 TTTAATTGTTTTCT
1 TTTAATTGATTTCT
563 TTTAATTGATTTCT
1 TTTAATTGATTTCT
577 TTT
1 TTT
580 TAATCCCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTAATTGATTTCT
Found at i:1958 original size:58 final size:58
Alignment explanation
Indices: 1891--2067 Score: 336
Period size: 58 Copynumber: 3.1 Consensus size: 58
1881 AACTACTTAC
1891 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
1949 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
* *
2007 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAACTTAGGCAAAAGTTAGAGCAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
2065 AAA
1 AAA
2068 AAAAAAACCC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 117 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (58 bp):
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
Found at i:3907 original size:13 final size:14
Alignment explanation
Indices: 3884--3912 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3874 TTTTATATAT
3884 AATTCTAGATCTAC
1 AATTCTAGATCTAC
3898 AATT-TAGATCTAC
1 AATTCTAGATCTAC
3911 AA
1 AA
3913 AATAACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (14 bp):
AATTCTAGATCTAC
Found at i:4859 original size:16 final size:16
Alignment explanation
Indices: 4838--4871 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4828 TCTGAAATAT
4838 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
4854 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
4870 TT
1 TT
4872 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Found at i:14887 original size:16 final size:16
Alignment explanation
Indices: 14868--14900 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14858 AACCCACCTG
14868 AACCCGAA-CTCGAAAA
1 AACCCGAATCT-GAAAA
14884 AACCCGAATCTGAAAA
1 AACCCGAATCTGAAAA
14900 A
1 A
14901 TCTCAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (16 bp):
AACCCGAATCTGAAAA
Found at i:15095 original size:17 final size:16
Alignment explanation
Indices: 15073--15137 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 16
15063 GATTTGGCTA
15073 AAACCCAAATTGAACCT
1 AAACCCAAATT-AACCT
*
15090 AAACCCGAATTAACCT
1 AAACCCAAATTAACCT
* *
15106 -GACCCAAATTCAACCC
1 AAACCCAAATT-AACCT
*
15122 AAACCCGAATTAACCT
1 AAACCCAAATTAACCT
15138 GATCTAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 8 0.21
16 13 0.33
17 18 0.46
ACGTcount: A:0.43, C:0.34, G:0.06, T:0.17
Consensus pattern (16 bp):
AAACCCAAATTAACCT
Found at i:15126 original size:32 final size:32
Alignment explanation
Indices: 15075--15153 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
15065 TTTGGCTAAA
* *
15075 ACCCAAATTGAACCTAAACCCGAATTAACCTG
1 ACCCAAATTCAACCCAAACCCGAATTAACCTG
15107 ACCCAAATTCAACCCAAACCCGAATTAACCTG
1 ACCCAAATTCAACCCAAACCCGAATTAACCTG
* *
15139 ATCTAAATTCAACCC
1 ACCCAAATTCAACCC
15154 GACCTGACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.41, C:0.34, G:0.06, T:0.19
Consensus pattern (32 bp):
ACCCAAATTCAACCCAAACCCGAATTAACCTG
Found at i:16598 original size:39 final size:38
Alignment explanation
Indices: 16544--16653 Score: 123
Period size: 39 Copynumber: 2.8 Consensus size: 38
16534 AGAAGAAAAT
* * *
16544 TGCCTTTGTCTTATATGTGTTTAGGGACTTT-AGTATAGA
1 TGCCTCTGTGTTATATGTGTTT-GGGACTTTGAG-AGAGA
*
16583 TGCCTCTGTGTTATATGTGTTTGAGGACTTTGAGAGAGT
1 TGCCTCTGTGTTATATGTGTTTG-GGACTTTGAGAGAGA
* *
16622 TGCCCCTTTGTTATATGTGTTTGGGGACTTTG
1 TGCCTCTGTGTTATATGTGTTT-GGGACTTTG
16654 GGGAGAGAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 58 0.94
40 3 0.05
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.45
Consensus pattern (38 bp):
TGCCTCTGTGTTATATGTGTTTGGGACTTTGAGAGAGA
Found at i:18466 original size:20 final size:20
Alignment explanation
Indices: 18441--18480 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18431 TGCCATGCTT
*
18441 TTGTCTCTGCCGCAACTATG
1 TTGTCTCTACCGCAACTATG
18461 TTGTCTCTACCGCAACTATG
1 TTGTCTCTACCGCAACTATG
18481 ATACTTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTCTCTACCGCAACTATG
Found at i:18860 original size:19 final size:19
Alignment explanation
Indices: 18827--18863 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18817 GCCTCCATTT
*
18827 TGTGATAGTGAGCTTCGAA
1 TGTGATAGTCAGCTTCGAA
*
18846 TGTGATAGTCTGCTTCGA
1 TGTGATAGTCAGCTTCGA
18864 CCTTTGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
TGTGATAGTCAGCTTCGAA
Found at i:23853 original size:47 final size:46
Alignment explanation
Indices: 23699--24180 Score: 156
Period size: 47 Copynumber: 10.9 Consensus size: 46
23689 AGATCTGGAA
* * * * *
23699 AACTAAACAGCACCTTCCGATGGAGAAGGGC-AAACGAG-AATGAGAC
1 AACTAAACAACACCTTCTG-TGGGGAAGGGCAAAACGGGAAAT-AGGC
** * * *
23745 AAAGAAACAACACCTTCTGACT-GGGAAGGGCGAAACAGGAAATTGGC
1 AACTAAACAACACCTTCTG--TGGGGAAGGGCAAAACGGGAAATAGGC
* *
23792 AACTAGACAGCACCTTCTGTGGGGAAGGGCAAAACGGG-AATAAGGC
1 AACTAAACAACACCTTCTGTGGGGAAGGGCAAAACGGGAAAT-AGGC
* * *
23838 TACTTAAACAACACCTTCCGGTGGGGAAGGGCAAAATGGG----A---
1 AAC-TAAACAACACCTT-CTGTGGGGAAGGGCAAAACGGGAAATAGGC
* * * *
23879 AACTAAATAATACCTACCGATGGGGAAGGGC-AAACTGGG--A-A---
1 AACTAAACAACACCTTCTG-TGGGGAAGGGCAAAAC-GGGAAATAGGC
* * * * *
23920 AACTAACCAACACCTTCCGGTGGGGAAGGGC-AAACTGGTAATTAGAC
1 AACTAAACAACACCTT-CTGTGGGGAAGGGCAAAAC-GGGAAATAGGC
* * *
23967 AACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGG-AAT----
1 AACTAAACAACACCTT-CTGTGGGGAAGGGCAAAACGGGAAATAGGC
* * * *
24009 --CTAAACAACACCTTCCGGTGAGGAAGGGC--AA---G-ACT-GGA
1 AACTAAACAACACCTT-CTGTGGGGAAGGGCAAAACGGGAAATAGGC
* * **
24047 AACTAAACAACACCTTCCGAT-GGGATAGGTCAAATTGGGAAATA-GC
1 AACTAAACAACACCTTCTG-TGGGGA-AGGGCAAAACGGGAAATAGGC
* * * *
24093 AACT-AACAAACACCTTGCGGTGGGGAAGGGC-AAACTGGTAATTAGAC
1 AACTAAAC-AACACCTT-CTGTGGGGAAGGGCAAAAC-GGGAAATAGGC
* * *
24140 AACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGAA
1 AACTAAACAACACCTT-CTGTGGGGAAGGGCAAAACGGGAA
24181 TCTACACAAC
Statistics
Matches: 339, Mismatches: 58, Indels: 77
0.72 0.12 0.16
Matches are distributed among these distances:
35 3 0.01
38 2 0.01
39 10 0.03
40 72 0.21
41 33 0.10
42 3 0.01
44 2 0.01
45 10 0.03
46 71 0.21
47 99 0.29
48 34 0.10
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.15
Consensus pattern (46 bp):
AACTAAACAACACCTTCTGTGGGGAAGGGCAAAACGGGAAATAGGC
Found at i:23918 original size:40 final size:40
Alignment explanation
Indices: 23842--24522 Score: 471
Period size: 40 Copynumber: 15.9 Consensus size: 40
23832 TAAGGCTACT
*
23842 TAAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAC
* * * *
23882 TAAATAATACCTACCGATGGGGAAGGGCAAACTGGGAAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AAAC
*
23923 TAACCAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTAGACAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGG------GA-AAC
* *
23970 TAAACAACACCTTCCGGTGAGGAAGGGCAAAACT-GGAATC
1 TAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAAAC
*
24010 TAAACAACACCTTCCGGTGAGGAAGGGCAAGACT-GGAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAA-ACTGGGAAAC
* * *
24050 TAAACAACACCTTCCGAT-GGGATAGGTCAAATTGGGAAATAGC
1 TAAACAACACCTTCCGGTGGGGA-AGGGCAAACTGGG-AA-A-C
* *
24093 AACTAACAAACACCTTGCGGTGGGGAAGGGCAAACTGGTAATTAGACAAC
1 TA--AAC-AACACCTTCCGGTGGGGAAGGGCAAACTGG------GA-AAC
* *
24143 TAAACAACACCTTCCGGTGAGGAAGGGCAAAACT-GGAATC
1 TAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAAAC
* *
24183 TACACAACACCTTCCGGTGAGGAAGGGCAAGACT-GGAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAA-ACTGGGAAAC
* * *
24223 TAAACAACACCTTCCAGTGGGGAAGTGCAAGACT-GCAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAA-ACTGGGAAAC
* * *
24263 TAAACAACACTTTCCGATGGGGAAGGGCAAATTGGGAATTTAACAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG------A-AAC
* * * *
24310 TAGACAACACCTTCCGCTTGGGAAGGGCAAGACTGGAAAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAA-ACTGG-GAAAC
* *
24352 TAAACAACACCTTCCGGTGAGGAAGGGCAAATTGGGAATTTGACAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACT-GG-----GA-AAC
* **
24399 TAGACAACACCTTCCAACT-GGGAAGGGCAAGA-TGGGAAAAGC
1 TAAACAACACCTTCC-GGTGGGGAAGGGCAA-ACTGGG-AAA-C
* * *
24441 TTAACAACACCTTCCGGTGGGGAAGGGTAAATTGGTAATTAGACAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGG------GA-AAC
*
24488 TAAACAACACCTTCCGACT-GGGAAGGGCAAACTGG
1 TAAACAACACCTTCCG-GTGGGGAAGGGCAAACTGG
24523 AAATTAGACA
Statistics
Matches: 517, Mismatches: 66, Indels: 109
0.75 0.10 0.16
Matches are distributed among these distances:
39 11 0.02
40 193 0.37
41 47 0.09
42 60 0.12
43 3 0.01
45 3 0.01
46 26 0.05
47 145 0.28
48 23 0.04
50 2 0.00
51 2 0.00
52 2 0.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (40 bp):
TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAC
Found at i:24148 original size:173 final size:171
Alignment explanation
Indices: 23664--24524 Score: 761
Period size: 173 Copynumber: 5.0 Consensus size: 171
23654 ACAAAATTAC
* *
23664 ACAACACCTTCCGGT-AGGGAAGGGC-AGATCTGGAAAACTAAACAGCACCTTCCGA-TGGAGAA
1 ACAACACCTTCCGGTGA-GGAAGGGCAAGA-CTGG-AAACTAAACAACACCTTCCGACTGGGGAA
* * ** * * * *
23726 GGGCAAACGAGAATGAGACAAAGAA-ACAACACCTTCTGACT-GGGAAGGGCGAAACAGGAAATT
63 GGGCAAATGGGAA--AG-CAACTAACA-AACACCTTCCG-GTGGGGAAGGGC-AAACTGGTAATT
* * * * * *
23789 -GGCAACTAGACAGCACCTTCTGTG-GGGAAGGGCAAAACGGGAATAAGGCTACTTAA
122 AGACAACTAAACAACACCTTCCGAGTGGGAAGGGCAAAACTGG---AA---T-C-TAA
* * * * *
23845 ACAACACCTTCCGGTGGGGAAGGGCAA-AATGGGAAACTAAATAATACCTACCGA-TGGGGAAGG
1 ACAACACCTTCCGGTGAGGAAGGGCAAGACT-GGAAACTAAACAACACCTTCCGACTGGGGAAGG
*
23908 GCAAACTGGG-AA--AACTAACCAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTAGACAAC
65 GCAAA-TGGGAAAGCAACTAACAAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTAGACAAC
23970 TAAACAACACCTTCCG-GTGAGGAAGGGCAAAACTGGAATCTAA
129 TAAACAACACCTTCCGAGTG-GGAAGGGCAAAACTGGAATCTAA
24013 ACAACACCTTCCGGTGAGGAAGGGCAAGACTGGAAACTAAACAACACCTTCCGA-T-GGGATAGG
1 ACAACACCTTCCGGTGAGGAAGGGCAAGACTGGAAACTAAACAACACCTTCCGACTGGGGA-AGG
* *
24076 TCAAATTGGGAAATAGCAACTAACAAACACCTTGCGGTGGGGAAGGGCAAACTGGTAATTAGACA
65 GCAAA-TGGG-AA-AGCAACTAACAAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTAGACA
*
24141 ACTAAACAACACCTTCCG-GTGAGGAAGGGCAAAACTGGAATCTAC
127 ACTAAACAACACCTTCCGAGTG-GGAAGGGCAAAACTGGAATCTAA
* *
24186 ACAACACCTTCCGGTGAGGAAGGGCAAGACTGGAAACTAAACAACACCTTCC-AGTGGGGAAGTG
1 ACAACACCTTCCGGTGAGGAAGGGCAAGACTGGAAACTAAACAACACCTTCCGACTGGGGAAGGG
** * * * *
24250 C-AA---GACTGCAAACTAA-ACAACACTTTCCGATGGGGAAGGGCAAATTGGGAATTTA-ACAA
66 CAAATGGGAAAGC-AACTAACA-AACACCTTCCGGTGGGGAAGGGCAAACTGGTAA-TTAGACAA
* ** * *
24309 CTAGACAACACCTTCCGCTTGGGAAGGGCAAGACTGGAAAAACTAA
128 CTAAACAACACCTTCCGAGTGGGAAGGGCAAAACTGG--AATCTAA
* * * *
24355 ACAACACCTTCCGGTGAGGAAGGGCAAATTGGGAATTTGACAACTAGACAACACCTTCCAACT-G
1 ACAACACCTTCCGGTGAGGAAGGGC-AA----G-ACTGGA-AACTAAACAACACCTTCCGACTGG
* * *
24419 GGAAGGGCAAGATGGGAAAAGC--TTAAC-AACACCTTCCGGTGGGGAAGGGTAAATTGGTAATT
59 GGAAGGGCAA-ATGGG-AAAGCAACTAACAAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATT
*
24481 AGACAACTAAACAACACCTTCCGACTGGGAAGGGC-AAACTGGAA
122 AGACAACTAAACAACACCTTCCGAGTGGGAAGGGCAAAACTGGAA
24525 ATTAGACAAA
Statistics
Matches: 579, Mismatches: 61, Indels: 86
0.80 0.08 0.12
Matches are distributed among these distances:
166 3 0.01
167 74 0.13
168 67 0.12
169 33 0.06
170 4 0.01
171 1 0.00
172 3 0.01
173 148 0.26
174 17 0.03
175 48 0.08
176 40 0.07
177 12 0.02
178 61 0.11
179 3 0.01
180 32 0.06
181 29 0.05
182 4 0.01
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (171 bp):
ACAACACCTTCCGGTGAGGAAGGGCAAGACTGGAAACTAAACAACACCTTCCGACTGGGGAAGGG
CAAATGGGAAAGCAACTAACAAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTAGACAACTA
AACAACACCTTCCGAGTGGGAAGGGCAAAACTGGAATCTAA
Found at i:24211 original size:213 final size:212
Alignment explanation
Indices: 23842--24382 Score: 639
Period size: 213 Copynumber: 2.6 Consensus size: 212
23832 TAAGGCTACT
* * * * *
23842 TAAACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAA-ACT-A-AA-T----AATACCTACCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAATTGGGAATA-TAACAACTAGACAACACCTTCCGC
* * *
23899 TGGGGAAGGGCAA-ACTGGGAAAACTAACCAACACCTTCCGGTGGGGAAGGGC-AAACTGGTAAT
65 TGGGGAAGGGCAAGACTGGAAAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGTAAT
* *
23962 TAGACAACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGAATCTAAACAACACCTTCCGG
130 T-----ACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGAAACTAAACAACACCTTCCAG
*
24027 TGAGGAAGGGCAAGACTGGAAAC
190 TGAGGAAGGGCAAGACTGCAAAC
* * *
24050 TAAACAACACCTTCCGAT-GGGATAGGTCAAATTGGGAA-ATAGCAACTA-ACAAACACCTTGCG
1 TAAACAACACCTTCCGATGGGGA-AGGGCAAATTGGGAATATAACAACTAGAC-AACACCTTCCG
*
24112 GTGGGGAAGGGCAA-ACTGGTAATTAGACAACTAAACAACACCTTCCGGTGAGGAAGGGCAAAAC
64 CTGGGGAAGGGCAAGACTGG--A--A-A-AACTAAACAACACCTTCCGGTGAGGAAGGGCAAAAC
* *
24176 TGG-AA-T-CTACACAACACCTTCCGGTGAGGAAGGGCAAGACTGGAAACTAAACAACACCTTCC
123 TGGTAATTACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGAAACTAAACAACACCTTCC
* *
24238 AGTGGGGAAGTGCAAGACTGCAAAC
188 AGTGAGGAAGGGCAAGACTGCAAAC
* *
24263 TAAACAACACTTTCCGATGGGGAAGGGCAAATTGGGAATTTAACAACTAGACAACACCTTCCGCT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAATTGGGAATATAACAACTAGACAACACCTTCCGCT
*
24328 TGGGAAGGGCAAGACTGGAAAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAA
66 GGGGAAGGGCAAGACTGGAAAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAA
24383 TTGGGAATTT
Statistics
Matches: 289, Mismatches: 25, Indels: 37
0.82 0.07 0.11
Matches are distributed among these distances:
207 5 0.02
208 31 0.11
209 36 0.12
210 2 0.01
211 1 0.00
213 106 0.37
214 60 0.21
215 7 0.02
218 1 0.00
219 2 0.01
220 31 0.11
221 7 0.02
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (212 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAATTGGGAATATAACAACTAGACAACACCTTCCGCT
GGGGAAGGGCAAGACTGGAAAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGTAATT
ACTAAACAACACCTTCCGGTGAGGAAGGGCAAAACTGGAAACTAAACAACACCTTCCAGTGAGGA
AGGGCAAGACTGCAAAC
Found at i:24278 original size:80 final size:81
Alignment explanation
Indices: 23842--24521 Score: 436
Period size: 89 Copynumber: 7.9 Consensus size: 81
23832 TAAGGCTACT
* * * * *
23842 TAAACAACACCTTCCGGTGGGGAAGGGCAAAATGGG-A-AACTAAATAATACCTACCGATGGGGA
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAACAACTAAACAACACCTTCCG-TGGGGA
23905 AGGGCAA-ACTGGGAAAAC
65 AGGGCAAGACT--GAAAAC
* * *
23923 TAACCAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTAGACAACTAAACAACACCTTCCGGT
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG----GA-ACAACTAAACAACACCTTCC-GT
* * * *
23988 GAGGAAGGGCAAAACTGGAATC
60 GGGGAAGGGCAAGACTGAAAAC
24010 TAAACAACACCTTCCGGTGAGGAAGGGCAAGACT-GG-A-AACTAAACAACACCTTCCGAT-GGG
1 TAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGGGAACAACTAAACAACACCTTCCG-TGGGG
* *
24071 ATAGGTCAA-ATTGGGAAATAGC
64 A-AGGGCAAGACT--GAAA-A-C
* * * *
24093 AACTAACAAACACCTTGCGGTGGGGAAGGGCAAACTGGTAATTAGACAACTAAACAACACCTTCC
1 TA--AAC-AACACCTTCCGGTGAGGAAGGGCAAACTGG----GA-ACAACTAAACAACACCTTCC
* * * *
24158 GGTGAGGAAGGGCAAAACTGGAATC
58 -GTGGGGAAGGGCAAGACTGAAAAC
*
24183 TACACAACACCTTCCGGTGAGGAAGGGCAAGACT-GG-A-AACTAAACAACACCTTCCAGTGGGG
1 TAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGGGAACAACTAAACAACACCTTCC-GTGGGG
* *
24245 AAGTGCAAGACTGCAAAC
64 AAGGGCAAGACTGAAAAC
* * * * *
24263 TAAACAACACTTTCCGATGGGGAAGGGCAAATTGGGAATTTAACAACTAGACAACACCTTCCGCT
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG-----AACAACTAAACAACACCTTCCG-T
*
24328 TGGGAAGGGCAAGACTGGAAAAAC
60 GGGGAAGGGCAAGACT-G-AAAAC
* * *
24352 TAAACAACACCTTCCGGTGAGGAAGGGCAAATTGGGAATTTGACAACTAGACAACACCTTCCAAC
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG-A----ACAACTAAACAACACCTTCC--G
24417 T-GGGAAGGGCAAGA-TGGGAAAAGC
59 TGGGGAAGGGCAAGACT--GAAAA-C
* * * * *
24441 TTAACAACACCTTCCGGTGGGGAAGGGTAAATTGGTAATTAGACAACTAAACAACACCTTCCGAC
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGG----GA-ACAACTAAACAACACCTTCCG--
24506 T-GGGAAGGGCAA-ACTG
59 TGGGGAAGGGCAAGACTG
24522 GAAATTAGAC
Statistics
Matches: 485, Mismatches: 57, Indels: 108
0.75 0.09 0.17
Matches are distributed among these distances:
79 8 0.02
80 90 0.19
81 38 0.08
83 2 0.00
85 7 0.01
86 26 0.05
87 91 0.19
88 42 0.09
89 142 0.29
90 3 0.01
92 5 0.01
93 25 0.05
94 6 0.01
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (81 bp):
TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAACAACTAAACAACACCTTCCGTGGGGAA
GGGCAAGACTGAAAAC
Found at i:24333 original size:47 final size:46
Alignment explanation
Indices: 24260--24533 Score: 223
Period size: 47 Copynumber: 6.0 Consensus size: 46
24250 CAAGACTGCA
* * *
24260 AACTAAACAACACTTTCCGATGGGGAAGGGCAAATTGGGAATTTAAC
1 AACTAAACAACACCTTCCGCTTGGGAAGGGCAAATTGGGAA-TTAAC
* *
24307 AACTAGACAACACCTTCCGCTTGGGAAGGGCAAGACT-GG-A--AA-
1 AACTAAACAACACCTTCCGCTTGGGAAGGGCAA-ATTGGGAATTAAC
* *
24349 AACTAAACAACACCTTCCG-GTGAGGAAGGGCAAATTGGGAATTTGAC
1 AACTAAACAACACCTTCCGCTTG-GGAAGGGCAAATTGGGAA-TTAAC
* *
24396 AACTAGACAACACCTTCCAAC-TGGGAAGGGCAAGA-TGGG-A--AA-
1 AACTAAACAACACCTTCC-GCTTGGGAAGGGCAA-ATTGGGAATTAAC
* * * * * *
24438 AGCTTAACAACACCTTCCGGTGGGGAAGGGTAAATTGGTAATTAGAC
1 AACTAAACAACACCTTCCGCTTGGGAAGGGCAAATTGGGAATTA-AC
* *
24485 AACTAAACAACACCTTCCGAC-TGGGAAGGGCAAACTGGAAATTAGAC
1 AACTAAACAACACCTTCCG-CTTGGGAAGGGCAAATTGGGAATTA-AC
24532 AA
1 AA
24534 AGCTAGTCTT
Statistics
Matches: 181, Mismatches: 27, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
41 5 0.03
42 58 0.32
43 5 0.03
45 1 0.01
46 4 0.02
47 103 0.57
48 5 0.03
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (46 bp):
AACTAAACAACACCTTCCGCTTGGGAAGGGCAAATTGGGAATTAAC
Found at i:25121 original size:50 final size:49
Alignment explanation
Indices: 25018--25114 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
25008 CACTTAAGAG
* *
25018 TTTTATTTCAAATTTATCAAAAGTCAATCTTTTAGCTTAAAGACTTCAC
1 TTTTATTTCAAATTGATCAAAAGTCAACCTTTTAGCTTAAAGACTTCAC
*
25067 TTTTATTTCAAATTGATCAAAATTTCAACCTTTTA-CATTAAAGACTTC
1 TTTTATTTCAAATTGATCAAAA-GTCAACCTTTTAGC-TTAAAGACTTC
25115 GTTTTTAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 22 0.51
50 21 0.49
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (49 bp):
TTTTATTTCAAATTGATCAAAAGTCAACCTTTTAGCTTAAAGACTTCAC
Found at i:25150 original size:50 final size:50
Alignment explanation
Indices: 25096--25273 Score: 146
Period size: 50 Copynumber: 3.5 Consensus size: 50
25086 AAATTTCAAC
* *
25096 CTTTTACATTAAAGACTTCGTTTTTAATCACCAATTATTCAAGAGTACAT
1 CTTTTACATTAAAGATTTCATTTTTAATCACCAATTATTCAAGAGTACAT
* * * * * *
25146 CTTTTAGC-TTAAAGGTTTCATCTTT-ATCACCAATTAATCAAAAATTTCAT
1 CTTTTA-CATTAAAGATTTCATTTTTAATCACCAATTATTC-AAGAGTACAT
* * * * * * *
25196 CTCTTAGATTAAAGATTTCATTTTTTAATTACAAATTATTTAAGAGTTCCCT
1 CTTTTACATTAAAGATTTCA-TTTTTAATCACCAATTATTCAAGAG-TACAT
*
25248 CATTTA-ATTCAAAGATTTCATTTTTA
1 CTTTTACATT-AAAGATTTCATTTTTA
25274 TTTACAAATC
Statistics
Matches: 99, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
49 13 0.13
50 42 0.42
51 17 0.17
52 27 0.27
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.44
Consensus pattern (50 bp):
CTTTTACATTAAAGATTTCATTTTTAATCACCAATTATTCAAGAGTACAT
Found at i:25220 original size:100 final size:101
Alignment explanation
Indices: 25044--25242 Score: 233
Period size: 100 Copynumber: 2.0 Consensus size: 101
25034 TCAAAAGTCA
** * *
25044 ATCTTTTAGCTTAAAGACTTCACTTTTATTTCAAATTGATCAAAATTTCAACCTTTTACATTAAA
1 ATCTTTTAGCTTAAAGACTTCACTTTTATCACAAATTAATCAAAATTTCAACCTCTTACATTAAA
* *
25109 GACTTC-GTTTTTAATCACCAATTATTCAAGAGTAC
66 GACTTCATTTTTTAATCACAAATTATTCAAGAGTAC
** * * *
25144 ATCTTTTAGCTTAAAGGTTTCA-TCTTTATCACCAATTAATCAAAAATTTC-ATCTCTTAGATTA
1 ATCTTTTAGCTTAAAGACTTCACT-TTTATCACAAATTAATC-AAAATTTCAACCTCTTACATTA
* * *
25207 AAGATTTCATTTTTTAATTACAAATTATTTAAGAGT
64 AAGACTTCATTTTTTAATCACAAATTATTCAAGAGT
25243 TCCCTCATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
99 1 0.01
100 50 0.61
101 31 0.38
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.43
Consensus pattern (101 bp):
ATCTTTTAGCTTAAAGACTTCACTTTTATCACAAATTAATCAAAATTTCAACCTCTTACATTAAA
GACTTCATTTTTTAATCACAAATTATTCAAGAGTAC
Found at i:25295 original size:51 final size:51
Alignment explanation
Indices: 25181--25427 Score: 273
Period size: 51 Copynumber: 4.8 Consensus size: 51
25171 ATCACCAATT
* * * * *
25181 AATCAAAAATTTCATC-TCTTAGATT-AAAGATTTCATTTTTTAATTACAAATT
1 AATCAAAAGTTCCATCAT-TTA-ATTCAAAGATCTCA-TTTTTATTTACAAATC
* * * * *
25233 ATTTAAGAGTTCCCTCATTTAATTCAAAGATTTCATTTTTATTTACAAATC
1 AATCAAAAGTTCCATCATTTAATTCAAAGATCTCATTTTTATTTACAAATC
**
25284 AATCAAAAGTTCCATCATTTGGTTCAAAGATCTCATTTTTATTTACAAATC
1 AATCAAAAGTTCCATCATTTAATTCAAAGATCTCATTTTTATTTACAAATC
** * *
25335 AATCAAAAGTTCCATCATTTGGTTCAATGATCTCATTTTTATTTACAAATT
1 AATCAAAAGTTCCATCATTTAATTCAAAGATCTCATTTTTATTTACAAATC
** * *
25386 AATCAAAAGTTTAATCTTTTAATTCAAAGGTCTCATTTTTAT
1 AATCAAAAGTTCCATCATTTAATTCAAAGATCTCATTTTTAT
25428 CACAAAAATT
Statistics
Matches: 169, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
51 145 0.86
52 23 0.14
53 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (51 bp):
AATCAAAAGTTCCATCATTTAATTCAAAGATCTCATTTTTATTTACAAATC
Found at i:26964 original size:11 final size:11
Alignment explanation
Indices: 26947--26976 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
26937 TTGCTCTTGC
26947 ATTTTGAAAGA
1 ATTTTGAAAGA
*
26958 GTTTTGAAAGA
1 ATTTTGAAAGA
26969 ATTTTGAA
1 ATTTTGAA
26977 TTGAGCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
ATTTTGAAAGA
Found at i:28151 original size:72 final size:72
Alignment explanation
Indices: 28022--28209 Score: 263
Period size: 72 Copynumber: 2.6 Consensus size: 72
28012 TGTCTACAAT
* *
28022 TGCC-AATGTGGGAACTGTCTAGGCTACAATCGCAATGAGGAAGATAATCACATAAGGATTGTGC
1 TGCCAAATGTGGGAACTGTCTCGGCTACAATCGCAATGAGGAAGATAATCACAGAAGGATTGTGC
28086 GAAGGAC
66 GAAGGAC
* * **
28093 TGCCAAATGTGGGAACTGTCTCGGCTACAACCGCAAT-ATGGAAGATTATCATGGAAGGATTGTG
1 TGCCAAATGTGGGAACTGTCTCGGCTACAATCGCAATGA-GGAAGATAATCACAGAAGGATTGTG
*
28157 CGAAGGAT
65 CGAAGGAC
** *
28165 TGCCAAATGTGGGAACTACCTCGGCTACAATCGCAATGAAGAAGA
1 TGCCAAATGTGGGAACTGTCTCGGCTACAATCGCAATGAGGAAGA
28210 AGACCATGGG
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
71 5 0.05
72 97 0.94
73 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (72 bp):
TGCCAAATGTGGGAACTGTCTCGGCTACAATCGCAATGAGGAAGATAATCACAGAAGGATTGTGC
GAAGGAC
Found at i:32561 original size:39 final size:38
Alignment explanation
Indices: 32510--32619 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 38
32500 AGAAGAAAAT
* *
32510 TGCCCTTGTGTTATATGTGTTTAGGGACTTT-AGTATAGA
1 TGCCCCTGTGTTATATGTGTTT-GGGACTTTGAG-AGAGA
* * *
32549 TGCCTCTGTGTTATATATGTTTGAGGACTTTGAGAGAGT
1 TGCCCCTGTGTTATATGTGTTTG-GGACTTTGAGAGAGA
32588 TGCCCCTGTGTTATATGTGTTTGGGGACTTTG
1 TGCCCCTGTGTTATATGTGTTT-GGGACTTTG
32620 GGGAGAGAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
38 1 0.02
39 57 0.93
40 3 0.05
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.43
Consensus pattern (38 bp):
TGCCCCTGTGTTATATGTGTTTGGGACTTTGAGAGAGA
Found at i:36873 original size:92 final size:92
Alignment explanation
Indices: 36716--36900 Score: 343
Period size: 92 Copynumber: 2.0 Consensus size: 92
36706 TCAAAGATAT
*
36716 CAGATTGCTTGAATACAAGTGAACAAAGGGAAAATGCTATGTTAAAGAACTACTCCTAAGTTACA
1 CAGATTGCTTGAATACAAGTGAACAAAGGGAAAATGCTAAGTTAAAGAACTACTCCTAAGTTACA
36781 AGATTACTCTAATTCTAAGGGTTACTC
66 AGATTACTCTAATTCTAAGGGTTACTC
*
36808 CAGATTGCTTGAATACAAGTGAACAAAGGGAAAATGCTAAGTTAAAGAACTACTCGTAAGTTACA
1 CAGATTGCTTGAATACAAGTGAACAAAGGGAAAATGCTAAGTTAAAGAACTACTCCTAAGTTACA
*
36873 AGATTACTCTAATTCTAATGGTTACTC
66 AGATTACTCTAATTCTAAGGGTTACTC
36900 C
1 C
36901 TACAAATCTA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (92 bp):
CAGATTGCTTGAATACAAGTGAACAAAGGGAAAATGCTAAGTTAAAGAACTACTCCTAAGTTACA
AGATTACTCTAATTCTAAGGGTTACTC
Found at i:41331 original size:10 final size:10
Alignment explanation
Indices: 41312--41361 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
41302 CAACTCAAAG
*
41312 AAAAGGAAAA
1 AAAAGAAAAA
41322 AAAAG-AAAA
1 AAAAGAAAAA
*
41331 AAAA-AAAGA
1 AAAAGAAAAA
* *
41340 AGAAGAAAGA
1 AAAAGAAAAA
41350 AAAAGAAAAA
1 AAAAGAAAAA
41360 AA
1 AA
41362 CTCAGCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 14 0.41
10 20 0.59
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:43238 original size:54 final size:54
Alignment explanation
Indices: 43116--43437 Score: 531
Period size: 54 Copynumber: 5.9 Consensus size: 54
43106 TTCAGAAGAA
* * *
43116 TAAGTATATCTTCAAGTGA-CCTAGTGCGGTCAATCAA-AGAAGTATCCAATGGTAT
1 TAAGTTTATCTTCAAGTGATCC-AGTGCGGTCAATCAAGA-AAGTTTCCAGTGGT-T
*
43171 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGGTTCCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
*
43225 TATGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
*
43279 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGCT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
43333 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
* *
43387 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTGCAGTG
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTG
43438 CGGTCAACTA
Statistics
Matches: 254, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
54 207 0.81
55 44 0.17
56 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (54 bp):
TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
Found at i:43516 original size:43 final size:42
Alignment explanation
Indices: 43453--43877 Score: 260
Period size: 43 Copynumber: 10.5 Consensus size: 42
43443 AACTAGGTTT
* *
43453 ATCTTCAAG-TGG-TTCGGTGAATTAGATGACTCAGTGAAGC
1 ATCTTCAAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* *
43493 ATCTTCTAAGTTGGATTTGGTGAATCAGATGAATCAGTGTAGC
1 ATCTTC-AAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* * *
43536 ATCCTCATAGGTT-GATTCGGTGAATCAAATGACTCAGTGTAGA
1 ATCTTCA-A-GTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* * * * * *
43579 ATCTTCAAGCTGGATTCGGTAAATCAGATGGCACGGTGCAGC
1 ATCTTCAAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
*
43621 ATCTTCGAAGTTGGA-----T---TCAGATGACTCAGTGCAGC
1 ATCTTC-AAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* *
43656 ATCTTCAAAGTTGGA-----T---TCAGATGACTCGGTGCAGC
1 ATCTTC-AAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* *
43691 ATCTTCAAAGTTGGATAT-GGTGAATCAGATGACTCGGTGTAGA
1 ATCTTC-AAGTTGGAT-TCGGTGAATCAGATGACTCAGTGTAGC
* * * * * * *
43734 ATCTTCAAGCTGGATTCGGTAAATCAAATGGCTCGGTGCAAC
1 ATCTTCAAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* * *
43776 ATCTTCGAAGTT-GA-------ATTCAGATGACTCGGTGCAGC
1 ATCTTC-AAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
* * *
43811 ATCTTCAAAGTTGGATAT-GGTGGATCAGATAACTCGGTGTAGC
1 ATCTTC-AAGTTGGAT-TCGGTGAATCAGATGACTCAGTGTAGC
*
43854 ATCTTAAAAGTTGGATTCGGTGAA
1 ATCTT-CAAGTTGGATTCGGTGAA
43878 CTAGGTGAGC
Statistics
Matches: 313, Mismatches: 45, Indels: 51
0.77 0.11 0.12
Matches are distributed among these distances:
35 92 0.29
36 2 0.01
38 1 0.00
40 7 0.02
41 6 0.02
42 70 0.22
43 132 0.42
44 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (42 bp):
ATCTTCAAGTTGGATTCGGTGAATCAGATGACTCAGTGTAGC
Found at i:43653 original size:35 final size:35
Alignment explanation
Indices: 43614--43706 Score: 168
Period size: 35 Copynumber: 2.7 Consensus size: 35
43604 AGATGGCACG
*
43614 GTGCAGCATCTTCGAAGTTGGATTCAGATGACTCA
1 GTGCAGCATCTTCAAAGTTGGATTCAGATGACTCA
*
43649 GTGCAGCATCTTCAAAGTTGGATTCAGATGACTCG
1 GTGCAGCATCTTCAAAGTTGGATTCAGATGACTCA
43684 GTGCAGCATCTTCAAAGTTGGAT
1 GTGCAGCATCTTCAAAGTTGGAT
43707 ATGGTGAATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (35 bp):
GTGCAGCATCTTCAAAGTTGGATTCAGATGACTCA
Found at i:43796 original size:120 final size:121
Alignment explanation
Indices: 43649--43874 Score: 373
Period size: 120 Copynumber: 1.9 Consensus size: 121
43639 AGATGACTCA
* *
43649 GTGCAGCATCTTCAAAGTTGGATTCAGATGACTCGGTGCAGCATCTTCAAAGTTGGATATGGTGA
1 GTGCAACATCTTCAAAGTTGAATTCAGATGACTCGGTGCAGCATCTTCAAAGTTGGATATGGTGA
* *
43714 ATCAGATGACTCGGTGTAGAATCTT-CAAGCTGGATTCGGTAAATCAAATGGCTCG
66 ATCAGATAACTCGGTGTAGAATCTTAAAAGCTGGATTCGGTAAATCAAATGGCTCG
* *
43769 GTGCAACATCTTCGAAGTTGAATTCAGATGACTCGGTGCAGCATCTTCAAAGTTGGATATGGTGG
1 GTGCAACATCTTCAAAGTTGAATTCAGATGACTCGGTGCAGCATCTTCAAAGTTGGATATGGTGA
* *
43834 ATCAGATAACTCGGTGTAGCATCTTAAAAGTTGGATTCGGT
66 ATCAGATAACTCGGTGTAGAATCTTAAAAGCTGGATTCGGT
43875 GAACTAGGTG
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
120 84 0.87
121 13 0.13
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (121 bp):
GTGCAACATCTTCAAAGTTGAATTCAGATGACTCGGTGCAGCATCTTCAAAGTTGGATATGGTGA
ATCAGATAACTCGGTGTAGAATCTTAAAAGCTGGATTCGGTAAATCAAATGGCTCG
Found at i:43803 original size:77 final size:77
Alignment explanation
Indices: 43556--43858 Score: 264
Period size: 78 Copynumber: 3.9 Consensus size: 77
43546 GTTGATTCGG
* * *
43556 TGAA-TCAAATGACTCAGTGTAGAATCTTCAAGCTGGATTCGGTAAATCAGATGGCACGGTGCAG
1 TGAATTCAGATGACTCAGTGCAGAATCTTCAAGCTGGATTCGGTAAATCAGATGGCTCGGTGCAG
43620 CATCTTCGAAGT
66 CATCTTCGAAGT
* * * * *
43632 TGGATTCAGATGACTCAGTGCAGCATCTTCAA---AG-TT-GG--ATTCAGATGACTCGGTGCAG
1 TGAATTCAGATGACTCAGTGCAGAATCTTCAAGCTGGATTCGGTAAATCAGATGGCTCGGTGCAG
*
43690 CATCTTCAAAGT
66 CATCTTCGAAGT
* * *
43702 TGGATATGGTGAATCAGATGACTCGGTGTAGAATCTTCAAGCTGGATTCGGTAAATCAAATGGCT
1 T-GA-A---T---TCAGATGACTCAGTGCAGAATCTTCAAGCTGGATTCGGTAAATCAGATGGCT
*
43767 CGGTGCAACATCTTCGAAGT
58 CGGTGCAGCATCTTCGAAGT
* * * ** ** *
43787 TGAATTCAGATGACTCGGTGCAGCATCTTCAAAGTTGGATAT-GGTGGATCAGATAACTCGGTGT
1 TGAATTCAGATGACTCAGTGCAGAATCTTC-AAGCTGGAT-TCGGTAAATCAGATGGCTCGGTGC
43851 AGCATCTT
64 AGCATCTT
43859 AAAAGTTGGA
Statistics
Matches: 180, Mismatches: 29, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
70 29 0.16
71 1 0.01
72 3 0.02
73 2 0.01
74 1 0.01
75 1 0.01
76 3 0.02
77 47 0.26
78 55 0.31
79 1 0.01
80 1 0.01
81 1 0.01
82 2 0.01
83 3 0.02
84 2 0.01
85 28 0.16
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (77 bp):
TGAATTCAGATGACTCAGTGCAGAATCTTCAAGCTGGATTCGGTAAATCAGATGGCTCGGTGCAG
CATCTTCGAAGT
Found at i:44389 original size:25 final size:27
Alignment explanation
Indices: 44348--44437 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
44338 TTTTCTACCT
44348 TCTTCTTTTACTAATTACCA-GTCTTAC
1 TCTT-TTTTACTAATTACCATGTCTTAC
* * * *
44375 TC-TTTTTACTGATTACAATTTTTTAC
1 TCTTTTTTACTAATTACCATGTCTTAC
* *
44401 TCTTTTTTACTTATTACCATTTTCTTAC
1 TCTTTTTTACTAATTACCA-TGTCTTAC
44429 TCTTCTTTT
1 TCTT-TTTT
44438 CTTCTTTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.25
26 8 0.15
27 16 0.31
28 11 0.21
29 4 0.08
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (27 bp):
TCTTTTTTACTAATTACCATGTCTTAC
Found at i:44416 original size:27 final size:28
Alignment explanation
Indices: 44369--44437 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
44359 TAATTACCAG
44369 TCTTACTC-TTTTTACTGATTACAATTT
1 TCTTACTCTTTTTTACTGATTACAATTT
* *
44396 T-TTACTCTTTTTTACTTATTACCATTT
1 TCTTACTCTTTTTTACTGATTACAATTT
44423 TCTTACTCTTCTTTT
1 TCTTACTCTT-TTTT
44438 CTTCTTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 6 0.16
27 19 0.51
28 8 0.22
29 4 0.11
ACGTcount: A:0.17, C:0.20, G:0.01, T:0.61
Consensus pattern (28 bp):
TCTTACTCTTTTTTACTGATTACAATTT
Found at i:44505 original size:26 final size:25
Alignment explanation
Indices: 44450--44591 Score: 97
Period size: 26 Copynumber: 5.2 Consensus size: 25
44440 TCTTTCTTTT
* *
44450 TTTTTACTGATTATCCTTTTCTTACT-
1 TTTTTACTGAATA-CCATTT-TTACTC
44476 TTTTTACTGAATACCATTCTTTACTC
1 TTTTTACTGAATACCATT-TTTACTC
* *
44502 TTTTTTCCTTTACTGAATACCATTTTTTCTAT
1 ----TT--TTTACTGAATACCATTTTTACT-C
* *
44534 TTTTTACTAAATACCGTTTTTACTC
1 TTTTTACTGAATACCATTTTTACTC
*
44559 TTTTTACTCTTGAATACCATTTTTAATC
1 TTTTTA--C-TGAATACCATTTTTACTC
44587 TTTTT
1 TTTTT
44592 TTTCTAATTA
Statistics
Matches: 93, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
25 15 0.16
26 32 0.34
27 1 0.01
28 22 0.24
30 2 0.02
31 5 0.05
32 16 0.17
ACGTcount: A:0.20, C:0.19, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTTACTGAATACCATTTTTACTC
Found at i:44517 original size:32 final size:29
Alignment explanation
Indices: 44478--44591 Score: 112
Period size: 28 Copynumber: 4.0 Consensus size: 29
44468 TTCTTACTTT
44478 TTTACTGAATACCATTCTTTACTCTTTTTTCC
1 TTTACTGAATACCATT-TTTACTC-TTTTT-C
*
44510 TTTACTGAATACCATTTTT--TCTATTT-
1 TTTACTGAATACCATTTTTACTCTTTTTC
* *
44536 TTTACTAAATACCGTTTTTACTCTTTTTAC
1 TTTACTGAATACCATTTTTACTCTTTTT-C
* *
44566 TCT--TGAATACCATTTTTAATCTTTTT
1 TTTACTGAATACCATTTTTACTCTTTTT
44592 TTTCTAATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
26 17 0.24
28 30 0.43
29 2 0.03
30 2 0.03
31 3 0.04
32 16 0.23
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (29 bp):
TTTACTGAATACCATTTTTACTCTTTTTC
Found at i:44615 original size:7 final size:7
Alignment explanation
Indices: 44605--44687 Score: 58
Period size: 7 Copynumber: 11.4 Consensus size: 7
44595 CTAATTACAA
44605 TTTACTT
1 TTTACTT
*
44612 TTTACAACT
1 TTTAC--TT
44621 TTTACTT
1 TTTACTT
*
44628 TTTACTG
1 TTTACTT
* *
44635 ATTACTC
1 TTTACTT
44642 TTTACTT
1 TTTACTT
*
44649 TTTACCAT
1 TTTA-CTT
*
44657 TTTACTC
1 TTTACTT
*
44664 TTTACTG
1 TTTACTT
* *
44671 ATTACTC
1 TTTACTT
44678 TTTACTT
1 TTTACTT
44685 TTT
1 TTT
44688 TTACCATTTT
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
7 46 0.79
8 6 0.10
9 6 0.10
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.59
Consensus pattern (7 bp):
TTTACTT
Found at i:44653 original size:14 final size:14
Alignment explanation
Indices: 44606--44687 Score: 65
Period size: 14 Copynumber: 5.6 Consensus size: 14
44596 TAATTACAAT
*
44606 TTACTTTTTACAACTT
1 TTACTTTTTAC-TC-T
**
44622 TTACTTTTTACTGA
1 TTACTTTTTACTCT
* *
44636 TTACTCTTTACTTT
1 TTACTTTTTACTCT
*
44650 TTACCATTTTACTCT
1 TTA-CTTTTTACTCT
**
44665 TTACTGATTACTCT
1 TTACTTTTTACTCT
44679 TTACTTTTT
1 TTACTTTTT
44688 TTACCATTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
14 29 0.57
15 11 0.22
16 11 0.22
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.59
Consensus pattern (14 bp):
TTACTTTTTACTCT
Found at i:44661 original size:22 final size:22
Alignment explanation
Indices: 44636--44707 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
44626 TTTTTACTGA
44636 TTACTCTTTACTTTTTACCATT
1 TTACTCTTTACTTTTTACCATT
**
44658 TTACTCTTTACTGATTA-C-TCT
1 TTACTCTTTACTTTTTACCAT-T
44679 TTA--C-TT--TTTTTACCATT
1 TTACTCTTTACTTTTTACCATT
44696 TTACTCTTTACT
1 TTACTCTTTACT
44708 GATTACTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
16 4 0.11
17 5 0.13
18 3 0.08
19 2 0.05
20 3 0.08
21 5 0.13
22 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.01, T:0.58
Consensus pattern (22 bp):
TTACTCTTTACTTTTTACCATT
Found at i:44698 original size:38 final size:36
Alignment explanation
Indices: 44605--44719 Score: 185
Period size: 38 Copynumber: 3.1 Consensus size: 36
44595 CTAATTACAA
* *
44605 TTTACTTTTTACAACTTTTACTTTTTACTGATTACTC
1 TTTACTTTTTACCA-TTTTACTCTTTACTGATTACTC
44642 TTTACTTTTTACCATTTTACTCTTTACTGATTACTC
1 TTTACTTTTTACCATTTTACTCTTTACTGATTACTC
44678 TTTACTTTTTTTACCATTTTACTCTTTACTGATTACTC
1 TTTAC--TTTTTACCATTTTACTCTTTACTGATTACTC
44716 TTTA
1 TTTA
44720 TTCTTTTCTC
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
36 26 0.35
37 13 0.18
38 35 0.47
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTACTTTTTACCATTTTACTCTTTACTGATTACTC
Found at i:44792 original size:26 final size:27
Alignment explanation
Indices: 44742--44857 Score: 90
Period size: 32 Copynumber: 3.9 Consensus size: 27
44732 TACTGGTTAC
**
44742 TATTTTACTCTCTTGAATTTAATTACTA
1 TATTTTACTCT-TTGAATTGGATTACTA
*
44770 T-TTTTACTCTTTGAATTGGATTACCATCTG
1 TATTTTACTCTTTGAATTGGATT---A-CTA
*
44800 TCATTTTACTCTTTGAATTGGATTACCATCTG
1 T-ATTTTACTCTTTGAATTGGATT---A-CTA
44832 TCATTTTACTCTTTGAATTGGATTAC
1 T-ATTTTACTCTTTGAATTGGATTAC
44858 CATCTTACCA
Statistics
Matches: 79, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.13
27 9 0.11
28 2 0.03
29 2 0.03
30 3 0.04
32 53 0.67
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.50
Consensus pattern (27 bp):
TATTTTACTCTTTGAATTGGATTACTA
Found at i:44807 original size:32 final size:32
Alignment explanation
Indices: 44771--44862 Score: 184
Period size: 32 Copynumber: 2.9 Consensus size: 32
44761 TAATTACTAT
44771 TTTTACTCTTTGAATTGGATTACCATCTGTCA
1 TTTTACTCTTTGAATTGGATTACCATCTGTCA
44803 TTTTACTCTTTGAATTGGATTACCATCTGTCA
1 TTTTACTCTTTGAATTGGATTACCATCTGTCA
44835 TTTTACTCTTTGAATTGGATTACCATCT
1 TTTTACTCTTTGAATTGGATTACCATCT
44863 TACCATTTCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTTACTCTTTGAATTGGATTACCATCTGTCA
Found at i:44947 original size:30 final size:30
Alignment explanation
Indices: 44913--44978 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
44903 AGTTTCATTC
* * *
44913 TTTACTGATTTACTGATTACTTCTTTTACT
1 TTTACTAACTTACTAATTACTTCTTTTACT
*
44943 TTTACCAACTTACTAATTACTTCTTTTACT
1 TTTACTAACTTACTAATTACTTCTTTTACT
44973 TTTACT
1 TTTACT
44979 CTTAATTACC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTACTAACTTACTAATTACTTCTTTTACT
Found at i:44963 original size:45 final size:45
Alignment explanation
Indices: 44875--44963 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 45
44865 CCATTTCACT
** * **
44875 ATTTACTGATTACTCTTTACTTTTTACCAGTTTCATTCTTTACTG
1 ATTTACTGATTACTCTTTACTTTTTACCAACTTCACTAATTACTG
44920 ATTTACTGATTACTTCTTTTAC-TTTTACCAACTT-ACTAATTACT
1 ATTTACTGATTAC-TC-TTTACTTTTTACCAACTTCACTAATTACT
44964 TCTTTTACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
45 20 0.54
46 12 0.32
47 5 0.14
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (45 bp):
ATTTACTGATTACTCTTTACTTTTTACCAACTTCACTAATTACTG
Found at i:44976 original size:36 final size:38
Alignment explanation
Indices: 44935--45014 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 38
44925 CTGATTACTT
44935 CTTTTA-CTT-TTACCAACTTACTAATTACTTCTTTTA
1 CTTTTACCTTATTACCAACTTACTAATTACTTCTTTTA
* * *
44971 CTTTTACTCTTAATTACCAACTTGCTGATTACTTCTTTTG
1 CTTTTAC-CTT-ATTACCAACTTACTAATTACTTCTTTTA
45011 CTTT
1 CTTT
45015 CCCTCCATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 6 0.16
38 3 0.08
40 28 0.76
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.53
Consensus pattern (38 bp):
CTTTTACCTTATTACCAACTTACTAATTACTTCTTTTA
Found at i:46939 original size:22 final size:23
Alignment explanation
Indices: 46892--46940 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
46882 TTATGAACAC
*
46892 AATTTACTAAATGTCAAAGAGTG
1 AATTTACTAAATGCCAAAGAGTG
46915 AATTTACTAAATGCCAAA-AGTG
1 AATTTACTAAATGCCAAAGAGTG
46937 AATT
1 AATT
46941 AGAAAATGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (23 bp):
AATTTACTAAATGCCAAAGAGTG
Found at i:47322 original size:79 final size:78
Alignment explanation
Indices: 47217--47445 Score: 300
Period size: 79 Copynumber: 2.9 Consensus size: 78
47207 ATCAAATCTT
*
47217 ACATTAACTTGATTCACCGAATCACCTTGAACTGTTTGAGAGTATGCTGCATCGAGCTCACCGAG
1 ACATTAACTTGATTCACCGAATCACCTTGAACTGTTTGAGAGTATGCTGCA-CGAGCTCACCGAA
47282 TCCAATAATGCACC
65 TCCAATAATGCACC
* * * *
47296 GCATTAACTTGATTCACCGAATCACCTTGAACTGTTTGAGAATGTGCTGCACCGAGCGCACCGAA
1 ACATTAACTTGATTCACCGAATCACCTTGAACTGTTTGAGAGTATGCTGCA-CGAGCTCACCGAA
*
47361 TACAATAATGCACC
65 TCCAATAATGCACC
* * * *
47375 ACATTTAACTTGATTCACCGAATAATCC-TAAACTGTTTGA-AGATTTGCTACACTGAGCTCACC
1 ACA-TTAACTTGATTCACCGAATCA-CCTTGAACTGTTTGAGAG-TATGCTGCAC-GAGCTCACC
47438 GAATCCAA
62 GAATCCAA
47446 CCTTGAAGAA
Statistics
Matches: 131, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
79 76 0.58
80 53 0.40
81 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (78 bp):
ACATTAACTTGATTCACCGAATCACCTTGAACTGTTTGAGAGTATGCTGCACGAGCTCACCGAAT
CCAATAATGCACC
Found at i:47495 original size:90 final size:90
Alignment explanation
Indices: 47381--47580 Score: 292
Period size: 90 Copynumber: 2.2 Consensus size: 90
47371 CACCACATTT
* * * * * *
47381 AACTTGATTCACCGAATAATCCTAAACTGTTTGAAGATTTGCTACACTGAGCTCACCGAATCCAA
1 AACTTGATTCACCGAATCACCCTAAACTGTCTGAAAATGTGCTACACCGAGCTCACCGAATCCAA
*
47446 CCTTGAAGAAGTAAGGCACCGCCTC
66 CCTTGAAGAACTAAGGCACCGCCTC
* * *
47471 AGCTTGATTCACCGAATCACCCTAAACTGTCTGAAAATGTGCTGCACCGAGCTCACTGAATCCAA
1 AACTTGATTCACCGAATCACCCTAAACTGTCTGAAAATGTGCTACACCGAGCTCACCGAATCCAA
*
47536 TCTTGAAGAACTAAGGCACCGCCTC
66 CCTTGAAGAACTAAGGCACCGCCTC
*
47561 AACTTGATTCACTGAATCAC
1 AACTTGATTCACCGAATCAC
47581 TTAAAGATAA
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 97 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (90 bp):
AACTTGATTCACCGAATCACCCTAAACTGTCTGAAAATGTGCTACACCGAGCTCACCGAATCCAA
CCTTGAAGAACTAAGGCACCGCCTC
Found at i:47692 original size:55 final size:54
Alignment explanation
Indices: 47605--47806 Score: 230
Period size: 54 Copynumber: 3.7 Consensus size: 54
47595 AATTGACCGT
* * * *
47605 ACTGCAAACTTTCTTGACTAACTGCACTGGATCACTGGAAGATAAACTTAAACC
1 ACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACTTAAACC
* *
47659 ACTGGAAACTTTTTTTGACTGACCGCACTGGATCACTTGAAGATAAACCTAAACC
1 ACTGGAAAC-TTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACTTAAACC
* * * *
47714 ACTACG-AACTTTCTTAATTGACCGCACTGGATCACTTGAA-AAAAACTTAATACC
1 ACT-GGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACTTAA-ACC
* * **
47768 ACTGGAAACTTT-TTAATTGACCGCACCAGATCACTTGAA
1 ACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAA
47807 ACCCGACTAA
Statistics
Matches: 129, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
53 34 0.26
54 48 0.37
55 46 0.36
56 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (54 bp):
ACTGGAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACTTAAACC
Found at i:47807 original size:53 final size:53
Alignment explanation
Indices: 47628--47806 Score: 227
Period size: 53 Copynumber: 3.3 Consensus size: 53
47618 TTGACTAACT
* * *
47628 GCACTGGATCACTGGAAGATAAACTTAAACCACTGGAAACTTTTTTTGACTGACC
1 GCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAAC--TTTTTAATTGACC
* *
47683 GCACTGGATCACTTGAAGATAAACCTAAACCACTACG-AACTTTCTTAATTGACC
1 GCACTGGATCACTTGAAGATAAACTTAAACCACT-GGAAACTTT-TTAATTGACC
*
47737 GCACTGGATCACTTGAA-AAAAACTTAATACCACTGGAAACTTTTTAATTGACC
1 GCACTGGATCACTTGAAGATAAACTTAA-ACCACTGGAAACTTTTTAATTGACC
**
47790 GCACCAGATCACTTGAA
1 GCACTGGATCACTTGAA
47807 ACCCGACTAA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
53 37 0.34
54 37 0.34
55 35 0.32
56 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (53 bp):
GCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTTTAATTGACC
Done.