Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 20 of 250
Found at i:5627887 original size:20 final size:20
Alignment explanation
Indices: 5627858--5627896 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5627848 TCAAACAAAT
*
5627858 AAAATTTATATAAAA-TAAAC
1 AAAATGTATA-AAAACTAAAC
5627878 AAAATGTATAAAAACTAAA
1 AAAATGTATAAAAACTAAA
5627897 TTTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATGTATAAAAACTAAAC
Found at i:5640677 original size:18 final size:18
Alignment explanation
Indices: 5640654--5640746 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
5640644 CCCAACTACT
*
5640654 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
5640672 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
*
5640690 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
5640708 GTATACATAAATAGTGCC
1 GTATACGTGAATAGTACC
*
5640726 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
5640744 GTA
1 GTA
5640747 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5643109 original size:77 final size:77
Alignment explanation
Indices: 5643025--5643180 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
5643015 TTCTATGTAA
5643025 CTACTACTACATAGATATATATGTCCTTGAGATGTATTAATAAAATTCAAGTGATTACCCTATTC
1 CTACTACTACATAGATATATATGTCCTTGAGATGTATTAATAAAATTCAAGTGATTACCCTATTC
5643090 TTATCATGACGT
66 TTATCATGACGT
5643102 CTACTACTACATAGATATATATGTCCTTGAGATGTATTAATAAAATTCAAGTGATTACCCTATTC
1 CTACTACTACATAGATATATATGTCCTTGAGATGTATTAATAAAATTCAAGTGATTACCCTATTC
5643167 TTATCATGACGT
66 TTATCATGACGT
5643179 CT
1 CT
5643181 GAGCAAGGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (77 bp):
CTACTACTACATAGATATATATGTCCTTGAGATGTATTAATAAAATTCAAGTGATTACCCTATTC
TTATCATGACGT
Found at i:5645862 original size:32 final size:32
Alignment explanation
Indices: 5645821--5645885 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
5645811 GTAGAATTAT
*
5645821 ATTAATATCCCTTTTGAGAGTAAAAATAACTG
1 ATTAATATCCCTTTCGAGAGTAAAAATAACTG
5645853 ATTAATATCCCTTTCGAGAGTAAAAATAACTG
1 ATTAATATCCCTTTCGAGAGTAAAAATAACTG
5645885 A
1 A
5645886 CTCTAGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (32 bp):
ATTAATATCCCTTTCGAGAGTAAAAATAACTG
Found at i:5646161 original size:20 final size:20
Alignment explanation
Indices: 5646136--5646177 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5646126 CTCTCGGCCC
5646136 TTAGTTTCATTAGCGGCGTT
1 TTAGTTTCATTAGCGGCGTT
5646156 TTAGTTTCATTAGCGGCGTT
1 TTAGTTTCATTAGCGGCGTT
5646176 TT
1 TT
5646178 GCGGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (20 bp):
TTAGTTTCATTAGCGGCGTT
Found at i:5646343 original size:28 final size:29
Alignment explanation
Indices: 5646298--5646352 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
5646288 CGCAAAATTT
*
5646298 TTTATCTATATATTTATT-ATTTAAATGG
1 TTTATCTATATATTTATTGATTAAAATGG
*
5646326 TTTATTTATAT-TTATATTGATTAAAAT
1 TTTATCTATATATT-TATTGATTAAAAT
5646353 ACAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTATCTATATATTTATTGATTAAAATGG
Found at i:5646732 original size:22 final size:22
Alignment explanation
Indices: 5646707--5646762 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
5646697 TGGGTAAAGG
*
5646707 TTAAGGGTTATGGATTATGGGT
1 TTAAGGGTTAAGGATTATGGGT
* *
5646729 TTAAGGATTAAGGGTTATGGGT
1 TTAAGGGTTAAGGATTATGGGT
*
5646751 TTAATGGTTAAG
1 TTAAGGGTTAAG
5646763 AGGATATGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (22 bp):
TTAAGGGTTAAGGATTATGGGT
Found at i:5646745 original size:29 final size:28
Alignment explanation
Indices: 5646690--5646748 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
5646680 TAAAGTTTAG
5646690 GGATTAGTGGGTAAAGGTTAAGGGTTAT
1 GGATTAGTGGGTAAAGGTTAAGGGTTAT
*
5646718 GGATTA-TGGGTTTAAGGATTAAGGGTTAT
1 GGATTAGTGGG-TAAAGG-TTAAGGGTTAT
5646747 GG
1 GG
5646749 GTTTAATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 4 0.14
28 11 0.39
29 13 0.46
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.34
Consensus pattern (28 bp):
GGATTAGTGGGTAAAGGTTAAGGGTTAT
Found at i:5648306 original size:49 final size:49
Alignment explanation
Indices: 5648244--5648432 Score: 287
Period size: 49 Copynumber: 3.9 Consensus size: 49
5648234 TAGTATGGCG
5648244 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5648293 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
5648342 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
5648389 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
5648433 TCCCGAATGG
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
47 48 0.37
48 1 0.01
49 80 0.62
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:5650086 original size:40 final size:40
Alignment explanation
Indices: 5649815--5650074 Score: 358
Period size: 40 Copynumber: 6.5 Consensus size: 40
5649805 TGAAATGTCT
* *
5649815 GGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
5649855 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
5649895 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCT
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
5649935 GGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
* * * *
5649975 AGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
** ** * * * *
5650015 ATGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
5650055 GGGCTAGGTCCCGAAGAGCA
1 GGGCTAAGTCCCGAAGAGCA
5650075 ATCATGCTGG
Statistics
Matches: 197, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 197 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
Found at i:5652957 original size:49 final size:49
Alignment explanation
Indices: 5652895--5653460 Score: 900
Period size: 49 Copynumber: 11.9 Consensus size: 49
5652885 TAGTATGGCG
5652895 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5652944 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
5652993 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGTC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5653042 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5653089 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
5653138 TAAAGGCC--------G-ATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
5653176 TAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5653225 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5653272 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
5653321 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * *
5653370 TAATGACCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
5653417 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
5653461 TCCCGAATGG
Statistics
Matches: 483, Mismatches: 17, Indels: 36
0.90 0.03 0.07
Matches are distributed among these distances:
38 25 0.05
40 11 0.02
41 1 0.00
46 1 0.00
47 150 0.31
48 1 0.00
49 294 0.61
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:5653100 original size:96 final size:96
Alignment explanation
Indices: 5652895--5653460 Score: 911
Period size: 96 Copynumber: 6.0 Consensus size: 96
5652885 TAGTATGGCG
5652895 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5652960 GAATGTGAAAGTGTATATATATGTGATAAGGCC
66 GAATGTGAAAGTG--TATATATGTGATAAGGCC
*
5652993 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5653058 GAATGTGAAAGTGTATATATGTGATAAGGCC
66 GAATGTGAAAGTGTATATATGTGATAAGGCC
*
5653089 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAAGGCC--------
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5653146 G-ATGTGAAAGTGTATATATGTGATAAGGCC
66 GAATGTGAAAGTGTATATATGTGATAAGGCC
*
5653176 TAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5653241 GAATGTGAAAGTGTATATATGTGATAAGGCC
66 GAATGTGAAAGTGTATATATGTGATAAGGCC
5653272 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5653337 GAATGTGAAAGTGTATATATATGTGATAAGGCC
66 GAATGTGAAAGTG--TATATATGTGATAAGGCC
* * * * * * *
5653370 TAATGACCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
5653433 GGATGTGAAAGTGTATAAATGTGATAAG
66 GAATGTGAAAGTGTATATATGTGATAAG
5653461 TCCCGAATGG
Statistics
Matches: 442, Mismatches: 15, Indels: 26
0.92 0.03 0.05
Matches are distributed among these distances:
87 84 0.19
88 1 0.00
94 14 0.03
95 1 0.00
96 219 0.50
98 123 0.28
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (96 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
GAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:5653332 original size:232 final size:232
Alignment explanation
Indices: 5652913--5653460 Score: 861
Period size: 232 Copynumber: 2.3 Consensus size: 232
5652903 GATGTGATGA
5652913 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
5652978 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGTCT
65 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCT
5653043 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
129 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
*
5653108 TGTGAAAGTGTATATATATGTGATAAGGCCTAAAGGCCG
194 TGTGAAAGTGTATATATATGTGATAAGGCCTAAAGACCG
*
5653147 ATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTA
1 ATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
5653211 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAA
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAA
5653275 TGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
131 TGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
*
5653340 TGTGAAAGTGTATATATATGTGATAAGGCCTAATGACCG
194 TGTGAAAGTGTATATATATGTGATAAGGCCTAAAGACCG
* * * * * * *
5653379 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGA--AA-GTG--A---TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
5653444 TGTATA-A-ATGTGATAAG
58 TGTATATATATGTGATAAG
5653461 TCCCGAATGG
Statistics
Matches: 291, Mismatches: 12, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
230 46 0.16
232 175 0.60
234 13 0.04
235 3 0.01
239 10 0.03
240 1 0.00
241 43 0.15
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (232 bp):
ATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAA
TGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
TGAAAGTGTATATATATGTGATAAGGCCTAAAGACCG
Found at i:5653424 original size:145 final size:146
Alignment explanation
Indices: 5652895--5653460 Score: 896
Period size: 145 Copynumber: 4.0 Consensus size: 146
5652885 TAGTATGGCG
5652895 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5652960 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
66 GAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
5653025 ATATATGTGATAAGGTC
130 ATATATGTGATAAGGCC
5653042 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
5653105 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAAAGGCC--------G-ATGTGAAAGTG--T
66 GAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
5653159 ATATATGTGATAAGGCC
130 ATATATGTGATAAGGCC
*
5653176 TAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
5653241 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
66 GAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
5653305 TATATGTGATAAGGCC
131 TATATGTGATAAGGCC
*
5653321 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGACCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * * * * * *
5653386 GAATGTGAAAGTG-TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA
66 GAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
5653450 -A-ATGTGATAAG
131 TATATGTGATAAG
5653461 TCCCGAATGG
Statistics
Matches: 393, Mismatches: 13, Indels: 30
0.90 0.03 0.07
Matches are distributed among these distances:
134 71 0.18
136 57 0.15
137 1 0.00
142 1 0.00
143 21 0.05
144 1 0.00
145 212 0.54
147 29 0.07
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (146 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
GAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TATATGTGATAAGGCC
Found at i:5654410 original size:16 final size:16
Alignment explanation
Indices: 5654386--5654416 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5654376 ACAATATGGG
5654386 TTAAGGGTTAAGGGGT
1 TTAAGGGTTAAGGGGT
*
5654402 TTAATGGTTAAGGGG
1 TTAAGGGTTAAGGGG
5654417 ACATGGGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32
Consensus pattern (16 bp):
TTAAGGGTTAAGGGGT
Found at i:5654439 original size:7 final size:7
Alignment explanation
Indices: 5654429--5654561 Score: 61
Period size: 7 Copynumber: 17.9 Consensus size: 7
5654419 ATGGGTAAAG
5654429 GGTTTAT
1 GGTTTAT
5654436 GGTTTAT
1 GGTTTAT
*
5654443 GAGTTAAT
1 G-GTTTAT
* *
5654451 GTTTTAA
1 GGTTTAT
5654458 GGTTTAT
1 GGTTTAT
* *
5654465 TGATTAT
1 GGTTTAT
**
5654472 GGGTTTCG
1 -GGTTTAT
5654480 GGATTT-T
1 GG-TTTAT
5654487 GGTTTAT
1 GGTTTAT
*
5654494 GGTTTAA
1 GGTTTAT
*
5654501 GGTTTAG
1 GGTTTAT
*
5654508 GGGTTAGT
1 GGTTTA-T
5654516 GGTTAATTAT
1 GG-T--TTAT
*
5654526 GGTTTAA
1 GGTTTAT
5654533 GGTTTTAT
1 GG-TTTAT
*
5654541 GGTTTAGG
1 GGTTTA-T
*
5654549 GGTTTAA
1 GGTTTAT
5654556 GGTTTA
1 GGTTTA
5654562 AGATTTTGAG
Statistics
Matches: 94, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
6 3 0.03
7 58 0.62
8 26 0.28
9 1 0.01
10 3 0.03
11 3 0.03
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.49
Consensus pattern (7 bp):
GGTTTAT
Found at i:5654542 original size:15 final size:15
Alignment explanation
Indices: 5654489--5654568 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
5654479 GGGATTTTGG
5654489 TTTATGGTTTAAGG-
1 TTTATGGTTTAAGGT
* * *
5654503 TTTAGGGGTTAGTGGT
1 TTTATGGTTTA-AGGT
5654519 TAATTATGGTTTAAGGT
1 T--TTATGGTTTAAGGT
* *
5654536 TTTATGGTTTAGGGG
1 TTTATGGTTTAAGGT
* *
5654551 TTTAAGGTTTAAGAT
1 TTTATGGTTTAAGGT
5654566 TTT
1 TTT
5654569 GAGGGTATGG
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
14 9 0.18
15 28 0.56
16 1 0.02
17 4 0.08
18 8 0.16
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:5654978 original size:15 final size:15
Alignment explanation
Indices: 5654955--5654984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5654945 TAGCTGATTG
5654955 TTTTCTAATTTATAT
1 TTTTCTAATTTATAT
*
5654970 TTTTTTAATTTATAT
1 TTTTCTAATTTATAT
5654985 ATTAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCTAATTTATAT
Found at i:5656057 original size:32 final size:32
Alignment explanation
Indices: 5656016--5656080 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5656006 ATATGCACAG
5656016 TAGTGCATTGGTCTCTATTCTAAATTCTTTCA
1 TAGTGCATTGGTCTCTATTCTAAATTCTTTCA
5656048 TAGTGCATTGGTCTCTATTCTAAATTCTTTCA
1 TAGTGCATTGGTCTCTATTCTAAATTCTTTCA
5656080 T
1 T
5656081 CTGTTTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (32 bp):
TAGTGCATTGGTCTCTATTCTAAATTCTTTCA
Found at i:5657625 original size:9 final size:9
Alignment explanation
Indices: 5657613--5657756 Score: 77
Period size: 9 Copynumber: 16.6 Consensus size: 9
5657603 TATATCATAT
5657613 CATAACTTA
1 CATAACTTA
5657622 CATAACTTA
1 CATAACTTA
*
5657631 CAAAACTTA
1 CATAACTTA
5657640 CATAA--TA
1 CATAACTTA
*
5657647 CATAA-ATA
1 CATAACTTA
*
5657655 TATAACTTA
1 CATAACTTA
5657664 CATAACTTA
1 CATAACTTA
*
5657673 CGTAA--TA
1 CATAACTTA
* *
5657680 AATAA-ATA
1 CATAACTTA
* ** *
5657688 TATTTCATA
1 CATAACTTA
*
5657697 TCATAATTTA
1 -CATAACTTA
5657707 CATAACTTA
1 CATAACTTA
*
5657716 CATACCTTA
1 CATAACTTA
*
5657725 CATAAATT-
1 CATAACTTA
* * *
5657733 TATATCATA
1 CATAACTTA
5657742 TCATAACTTA
1 -CATAACTTA
5657752 CATAA
1 CATAA
5657757 TACATAAATA
Statistics
Matches: 101, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
7 12 0.12
8 14 0.14
9 65 0.64
10 10 0.10
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:5657660 original size:33 final size:33
Alignment explanation
Indices: 5657623--5657690 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
5657613 CATAACTTAC
*
5657623 ATAACTTACAAAACTTACATAATACATAAATAT
1 ATAACTTACAAAACTTACATAATAAATAAATAT
* *
5657656 ATAACTTACATAACTTACGTAATAAATAAATAT
1 ATAACTTACAAAACTTACATAATAAATAAATAT
5657689 AT
1 AT
5657691 TTCATATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (33 bp):
ATAACTTACAAAACTTACATAATAAATAAATAT
Found at i:5657699 original size:85 final size:88
Alignment explanation
Indices: 5657597--5657756 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 88
5657587 ATCTTAATGT
5657597 TAAATATATATCATATCATAACTTACATAACTTACAAAACTTACAT-AATACATA-AATAT-ATA
1 TAAATATATATCATATCATAACTTACATAACTTACAAAACTTACATAAATACATATAATATCATA
5657659 ACTTACATAACTTACGTAATAAA
66 ACTTACATAACTTACGTAATAAA
* * * * ** *
5657682 TAAATATATTTCATATCATAATTTACATAACTTACATACCTTACATAAATTTATATCATATCATA
1 TAAATATATATCATATCATAACTTACATAACTTACAAAACTTACATAAATACATATAATATCATA
5657747 ACTTACATAA
66 ACTTACATAA
5657757 TACATAAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 42 0.65
86 6 0.09
87 4 0.06
88 13 0.20
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (88 bp):
TAAATATATATCATATCATAACTTACATAACTTACAAAACTTACATAAATACATATAATATCATA
ACTTACATAACTTACGTAATAAA
Found at i:5659431 original size:26 final size:26
Alignment explanation
Indices: 5659402--5659509 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
5659392 TGGTACAAAT
5659402 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5659428 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5659454 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5659480 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5659506 TGAT
1 TGAT
5659510 GGCCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5669992 original size:14 final size:15
Alignment explanation
Indices: 5669968--5669996 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5669958 TTTTAAGCTA
5669968 AGAATAAAGAACAAT
1 AGAATAAAGAACAAT
5669983 AGAA-AAAGAACAAT
1 AGAATAAAGAACAAT
5669997 GGACACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (15 bp):
AGAATAAAGAACAAT
Found at i:5670884 original size:20 final size:20
Alignment explanation
Indices: 5670855--5670905 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5670845 TCACTTCTTC
* **
5670855 CACGCTCGTGTAACCTTCCA
1 CACGCCCGTGTAACCTAACA
*
5670875 CACGCCCGTGTGACCTAACA
1 CACGCCCGTGTAACCTAACA
*
5670895 CACGGCCGTGT
1 CACGCCCGTGT
5670906 GCCTTGCTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.39, G:0.22, T:0.20
Consensus pattern (20 bp):
CACGCCCGTGTAACCTAACA
Found at i:5686213 original size:10 final size:10
Alignment explanation
Indices: 5686194--5686253 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
5686184 TGAAATTCTA
5686194 AAAGATAAAT
1 AAAGATAAAT
5686204 ACAA-ATAAAT
1 A-AAGATAAAT
*
5686214 AAAGATAATT
1 AAAGATAAAT
5686224 AAAGATAAAT
1 AAAGATAAAT
5686234 AAAGATAAAT
1 AAAGATAAAT
5686244 GAAA-ATAAAT
1 -AAAGATAAAT
5686254 TCTTAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5693264 original size:76 final size:75
Alignment explanation
Indices: 5693181--5693410 Score: 291
Period size: 76 Copynumber: 3.0 Consensus size: 75
5693171 GTAATTGCCA
* * * *
5693181 ATATTAATTGTGTGGCCAGCACCAGTCAAATAAATAGATAAAGATTTGCACTCAGTGCTAGTTGG
1 ATATTAATTGTGTGACCAGCACTAGTCGAATAAATCGATAAAGATTTGCACTCAGTGCTAGTTGG
5693246 ATAAATCGACG
66 ATAAA-CGACG
* * * * **
5693257 ATATTAATTGTATGCCCAGCACTAGTCGAATAAATCGATAAAGATTTGCCCCCAGTGCTAGTCAG
1 ATATTAATTGTGTGACCAGCACTAGTCGAATAAATCGATAAAGATTTGCACTCAGTGCTAGTTGG
5693322 ATAAACTGACG
66 ATAAAC-GACG
* * * *
5693333 ATATTAAGTGTGTGACCATCACTAGTCGAATAAATCGACAAAGATTTG-AGCTCAGCGCTAGTTG
1 ATATTAATTGTGTGACCAGCACTAGTCGAATAAATCGATAAAGATTTGCA-CTCAGTGCTAGTTG
5693397 GATAAACCGACG
65 GATAAA-CGACG
5693409 AT
1 AT
5693411 CGCATATGTA
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 1 0.01
76 130 0.98
77 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (75 bp):
ATATTAATTGTGTGACCAGCACTAGTCGAATAAATCGATAAAGATTTGCACTCAGTGCTAGTTGG
ATAAACGACG
Found at i:5693408 original size:152 final size:152
Alignment explanation
Indices: 5693128--5693410 Score: 372
Period size: 152 Copynumber: 1.9 Consensus size: 152
5693118 TGCCCTGCAA
** * * *
5693128 AGTCGAATAAATCAACAAAAATTTGTGCCCAATGCTAGTCAGAGTAATTGCCAATATTAATTGTG
1 AGTCGAATAAATCAACAAAAATTTGCCCCCAATGCTAGTCAGAGTAACTGACAATATTAAGTGTG
* * * *
5693193 TGGCCAGCACCAGTCAAATAAATAGATAAAGATTTGCACTCAGTGCTAGTTGGATAAATCGACGA
66 TGACCAGCACCAGTCAAATAAATAGACAAAGATTTGCACTCAGCGCTAGTTGGATAAACCGACGA
5693258 TATTAATTGTATGCCCAGCACT
131 TATTAATTGTATGCCCAGCACT
* * * * *
5693280 AGTCGAATAAATCGATAAAGATTTGCCCCCAGTGCTAGTCAGA-TAAACTGACGATATTAAGTGT
1 AGTCGAATAAATCAACAAAAATTTGCCCCCAATGCTAGTCAGAGT-AACTGACAATATTAAGTGT
* * * *
5693344 GTGACCATCACTAGTCGAATAAATCGACAAAGATTTG-AGCTCAGCGCTAGTTGGATAAACCGAC
65 GTGACCAGCACCAGTCAAATAAATAGACAAAGATTTGCA-CTCAGCGCTAGTTGGATAAACCGAC
5693408 GAT
129 GAT
5693411 CGCATATGTA
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
151 2 0.02
152 109 0.98
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (152 bp):
AGTCGAATAAATCAACAAAAATTTGCCCCCAATGCTAGTCAGAGTAACTGACAATATTAAGTGTG
TGACCAGCACCAGTCAAATAAATAGACAAAGATTTGCACTCAGCGCTAGTTGGATAAACCGACGA
TATTAATTGTATGCCCAGCACT
Found at i:5697444 original size:144 final size:144
Alignment explanation
Indices: 5697207--5697631 Score: 629
Period size: 144 Copynumber: 3.0 Consensus size: 144
5697197 CTTATTGGAG
* * * * * *
5697207 GATAGATCCAGTGTAACCAAA-TTCGTTAGCCTACCAATGTCTTGTGGAATGGATCCATTAAGTT
1 GATAGAGCCAATGTAATCAAATTTC-TTAGTCTCCCAATTTCTTGTGGAATGGATCCATTAAGTT
* ** * ** *
5697271 GGTTGTGC-TGAAGGAGCAACGACCCTAGATTGGTTACATTGCTGATAGAAGATGGGATTGGACC
65 GGTTG-CCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGATAGAAGATGGGATTGGACC
5697335 AACAAGCATATTAAAC
129 AACAAGCATATTAAAC
*
5697351 GATAGAGCCAATGTAATCAAATTTCTTAGTCTCCCAATTTCTTGTGGAATGGGTCCATTAAGTTG
1 GATAGAGCCAATGTAATCAAATTTCTTAGTCTCCCAATTTCTTGTGGAATGGATCCATTAAGTTG
* *
5697416 GTTGCCTTGAAGGAGCAACGATTGTAGATTAGTTAGGTTGGTAATAGAAGATGGGATTGGACCAA
66 GTTGCCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGATAGAAGATGGGATTGGACCAA
*
5697481 CAAGCATATTAGAC
131 CAAGCATATTAAAC
* * * *
5697495 GATAGAGCCAATGTAATCAAATTTGTCAATCTCCCAATTTCTCGTGGAATGGATCCATTAAGTTG
1 GATAGAGCCAATGTAATCAAATTTCTTAGTCTCCCAATTTCTTGTGGAATGGATCCATTAAGTTG
5697560 GTTGCCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGATAGAAGATGGGATTGGACCAA
66 GTTGCCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGATAGAAGATGGGATTGGACCAA
5697625 CAAGCAT
131 CAAGCAT
5697632 GTTGCTTGAG
Statistics
Matches: 255, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
143 1 0.00
144 251 0.98
145 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (144 bp):
GATAGAGCCAATGTAATCAAATTTCTTAGTCTCCCAATTTCTTGTGGAATGGATCCATTAAGTTG
GTTGCCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGATAGAAGATGGGATTGGACCAA
CAAGCATATTAAAC
Found at i:5699667 original size:2 final size:2
Alignment explanation
Indices: 5699660--5699691 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5699650 GGAGCTGAAC
*
5699660 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5699692 CTCTATGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5700729 original size:40 final size:40
Alignment explanation
Indices: 5700685--5700792 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
5700675 TTACATTAGT
5700685 GGCGTTTTCAAT-AAAACGCCGCTAAAAACAGAGCAATAGC
1 GGCGTTTTCAATCAAAACGCCGCT-AAAACAGAGCAATAGC
** * * *
5700725 GGCGTTTTTTATCCAAACGCTGCTAAAACTGAGCAATAGC
1 GGCGTTTTCAATCAAAACGCCGCTAAAACAGAGCAATAGC
****
5700765 GGCGTTTTTGGCCAAAACGCCGCTAAAA
1 GGCGTTTTCAATCAAAACGCCGCTAAAA
5700793 ACTGAACAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 48 0.84
41 9 0.16
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (40 bp):
GGCGTTTTCAATCAAAACGCCGCTAAAACAGAGCAATAGC
Found at i:5700815 original size:40 final size:41
Alignment explanation
Indices: 5700697--5700829 Score: 110
Period size: 40 Copynumber: 3.3 Consensus size: 41
5700687 CGTTTTCAAT
* * * * **
5700697 AAAACGCCGCTAAAAACAGAGCAATAGCGGCGTTTTTTATCC
1 AAAACGCCGCTAAAAACTGAACAACAGCGGCG-TCTTTGGCC
* * * *
5700739 -AAACGCTGCT-AAAACTGAGCAATAGCGGCGTTTTTGGCC
1 AAAACGCCGCTAAAAACTGAACAACAGCGGCGTCTTTGGCC
* **
5700778 AAAACGCCGCTAAAAACTGAACAACAGGGGCG-CTTTGGGG
1 AAAACGCCGCTAAAAACTGAACAACAGCGGCGTCTTTGGCC
*
5700818 AAAATGCCGCTA
1 AAAACGCCGCTA
5700830 TAGGTCGAGG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 7 0.09
40 44 0.57
41 26 0.34
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACTGAACAACAGCGGCGTCTTTGGCC
Found at i:5701197 original size:18 final size:18
Alignment explanation
Indices: 5701168--5701218 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
5701158 TTGTCCCTTG
5701168 TTATATATATATATTAA-A
1 TTATA-ATATATATTAAGA
*
5701186 CTTCTAATATATATTAAGA
1 -TTATAATATATATTAAGA
5701205 TTATAATATATATT
1 TTATAATATATATT
5701219 TAGGGTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATAATATATATTAAGA
Found at i:5701659 original size:15 final size:15
Alignment explanation
Indices: 5701639--5701669 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5701629 TTTAATGTAG
*
5701639 AAGATAAATGTATAT
1 AAGATAAATATATAT
5701654 AAGATAAATATATAT
1 AAGATAAATATATAT
5701669 A
1 A
5701670 TAAATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:5708126 original size:36 final size:36
Alignment explanation
Indices: 5708079--5708173 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
5708069 ATCCCAACTA
* * *
5708079 CTGTATACGTGAACAGTATCGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACCATATACGTGAATAGTG
*
5708115 CTGTATACGTGAATAGTACCATATATGTGAATAGTG
1 CTGTATACGTGAATAGTACCATATACGTGAATAGTG
*
5708151 -TCATATACGTGAATAGTACCATA
1 CT-GTATACGTGAATAGTACCATA
5708174 AACGGTCGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
35 1 0.02
36 52 0.98
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (36 bp):
CTGTATACGTGAATAGTACCATATACGTGAATAGTG
Found at i:5708173 original size:18 final size:18
Alignment explanation
Indices: 5708082--5708173 Score: 103
Period size: 18 Copynumber: 5.1 Consensus size: 18
5708072 CCAACTACTG
* * *
5708082 TATACGTGAACAGTATCG
1 TATACGTGAATAGTACCA
* **
5708100 TATACGTGAATAGTGCTG
1 TATACGTGAATAGTACCA
5708118 TATACGTGAATAGTACCA
1 TATACGTGAATAGTACCA
* **
5708136 TATATGTGAATAGTGTCA
1 TATACGTGAATAGTACCA
5708154 TATACGTGAATAGTACCA
1 TATACGTGAATAGTACCA
5708172 TA
1 TA
5708174 AACGGTCGTA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (18 bp):
TATACGTGAATAGTACCA
Found at i:5708794 original size:20 final size:20
Alignment explanation
Indices: 5708769--5708808 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5708759 ACATGGCTGA
*
5708769 TTTGATGCTTATGTGATCCC
1 TTTGATGCTTATATGATCCC
5708789 TTTGATGCTTATATGATCCC
1 TTTGATGCTTATATGATCCC
5708809 CTGCAAGATC
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:0.20, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTGATGCTTATATGATCCC
Found at i:5712077 original size:9 final size:9
Alignment explanation
Indices: 5712054--5712181 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
5712044 ATTGATCATT
*
5712054 ACTTAAATA
1 ACTTACATA
*
5712063 AATTACATA
1 ACTTACATA
5712072 ACTTACATA
1 ACTTACATA
* *
5712081 ACTCATATA
1 ACTTACATA
5712090 ACTTACATA
1 ACTTACATA
*
5712099 ATTTACATAA
1 ACTTACAT-A
5712109 CCACTTACATA
1 --ACTTACATA
*
5712120 ACTCACATA
1 ACTTACATA
5712129 ACTTACATA
1 ACTTACATA
*
5712138 ATTTACATA
1 ACTTACATA
*
5712147 ACTCACATA
1 ACTTACATA
*
5712156 ACGTACATAACA
1 ACTTACAT---A
5712168 ACTTACATA
1 ACTTACATA
5712177 ACTTA
1 ACTTA
5712182 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
10 1 0.01
11 1 0.01
12 15 0.16
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:5712124 original size:39 final size:39
Alignment explanation
Indices: 5712072--5712148 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
5712062 AAATTACATA
*
5712072 ACTTACATAACTCATATAACTTACATAATTTACATAACC
1 ACTTACATAACTCACATAACTTACATAATTTACATAACC
5712111 ACTTACATAACTCACATAACTTACATAATTTACATAAC
1 ACTTACATAACTCACATAACTTACATAATTTACATAAC
5712149 TCACATAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.32
Consensus pattern (39 bp):
ACTTACATAACTCACATAACTTACATAATTTACATAACC
Found at i:5712148 original size:57 final size:57
Alignment explanation
Indices: 5712067--5712179 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
5712057 TAAATAAATT
* * ** *
5712067 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACCACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
5712124 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
5712180 TAACTAATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:5717741 original size:15 final size:16
Alignment explanation
Indices: 5717716--5717746 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5717706 GCAACAACTT
5717716 AGAGCGGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
5717732 AGAG-GGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
5717747 CTGCAGCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (16 bp):
AGAGCGGAGGCAGCAG
Found at i:5718190 original size:43 final size:42
Alignment explanation
Indices: 5718143--5718286 Score: 164
Period size: 43 Copynumber: 3.4 Consensus size: 42
5718133 ATCTGCCAAA
*
5718143 TTTAGCGGCG-TTTGTAAAAAAAGCGCCGCTAAAAGGCTTGACC
1 TTTAGCGGCGCTTT-TACAAAAA-CGCCGCTAAAAGGCTTGACC
* * *
5718186 TTTAGCGGCGCTTTTCCCATAAACGTCGCTAAAAGGCTTGACC
1 TTTAGCGGCGCTTTT-ACAAAAACGCCGCTAAAAGGCTTGACC
* * **
5718229 TTTAGCGGCGCTTTCACCACAAACGCCGCTAAAAACCTTGACC
1 TTTAGCGGCGCTTTTA-CAAAAACGCCGCTAAAAGGCTTGACC
*
5718272 TTTAGCGGCGTTTTT
1 TTTAGCGGCGCTTTT
5718287 TCCAATAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
43 79 0.92
44 7 0.08
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (42 bp):
TTTAGCGGCGCTTTTACAAAAACGCCGCTAAAAGGCTTGACC
Found at i:5719022 original size:55 final size:56
Alignment explanation
Indices: 5718931--5719052 Score: 167
Period size: 55 Copynumber: 2.2 Consensus size: 56
5718921 TTGCTAAAAT
* * *
5718931 ATAATATCCTATAATATCCCTTCAGGAATCAAATTGCTAAGAGATAGTAT-CCACA
1 ATAATATCCTATAATATCCATTCAGGAATCAAATTGCTAAAAGATAATATCCCACA
* * *
5718986 ATAGTATCCTATAATATCTCATT-AGGAATCAGATTGCTAAAAGATAATATCCCATA
1 ATAATATCCTATAATATC-CATTCAGGAATCAAATTGCTAAAAGATAATATCCCACA
5719042 ATAATATCCTA
1 ATAATATCCTA
5719053 ATAGACTTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
55 41 0.71
56 17 0.29
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (56 bp):
ATAATATCCTATAATATCCATTCAGGAATCAAATTGCTAAAAGATAATATCCCACA
Found at i:5724914 original size:9 final size:9
Alignment explanation
Indices: 5724900--5724936 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
5724890 TGCGTTGACA
5724900 TTCTTTTCT
1 TTCTTTTCT
5724909 TTC-TTTCT
1 TTCTTTTCT
*
5724917 TTATTTTCT
1 TTCTTTTCT
5724926 TTCTTTTCT
1 TTCTTTTCT
5724935 TT
1 TT
5724937 TGATTAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:5724918 original size:13 final size:13
Alignment explanation
Indices: 5724900--5724936 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
5724890 TGCGTTGACA
5724900 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
5724913 TTCTTTAT-TTTCT
1 TTCTTT-TCTTTCT
5724926 TTCTTTTCTTT
1 TTCTTTTCTTT
5724937 TGATTAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:5725574 original size:16 final size:16
Alignment explanation
Indices: 5725539--5725579 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5725529 GACGTTCCTC
*
5725539 TTCTTCTTTCTTTTTA
1 TTCTTCTTTATTTTTA
5725555 TTCTTCTTTATTATTT-
1 TTCTTCTTTATT-TTTA
5725571 TTC-TCTTTA
1 TTCTTCTTTA
5725580 AAAAAAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 14 0.61
17 3 0.13
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTCTTTATTTTTA
Found at i:5726634 original size:48 final size:48
Alignment explanation
Indices: 5726580--5726676 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
5726570 ACGTGTCTAC
* * * *
5726580 TTCCATTTGATTGTCCGTTGACGTGTACAATATTTCTGTGGATTTGTA
1 TTCCATTTGATTATCCATTGACATGTACAATATTTCTGTAGATTTGTA
5726628 TTCCATTTGATTATCCATTGACATGTACAATATTTCTGTAGATTTGTA
1 TTCCATTTGATTATCCATTGACATGTACAATATTTCTGTAGATTTGTA
5726676 T
1 T
5726677 GCATACATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.46
Consensus pattern (48 bp):
TTCCATTTGATTATCCATTGACATGTACAATATTTCTGTAGATTTGTA
Found at i:5733775 original size:104 final size:105
Alignment explanation
Indices: 5733577--5733776 Score: 235
Period size: 104 Copynumber: 1.9 Consensus size: 105
5733567 CATCATGCCG
* * * *
5733577 ATGTCCTTACTTGTGTGGCTCACACGGCCTGGAGACACACCCATGTCCTCTGTCCGTGTGGTTCT
1 ATGTCCTTACCTGTATGGCTCACACGGCCTGGAGACACACCCATGTCCTCTGGCCGTGTGGTCCT
* * *
5733642 AAATCGCAAACAGTAAGTTACACAGCCTAGATACACGCTC
66 AAATCACAAACAATAAGTTACACAACCTAGATACACGCTC
* * * *
5733682 ATGTCCTTGCCTGTATGGTTCACACGGCCTAGG-TACA-AGCCCGTGTCC-CTGGCCGTGTGGTC
1 ATGTCCTTACCTGTATGGCTCACACGGCCT-GGAGACACA-CCCATGTCCTCTGGCCGTGTGGTC
* * *
5733744 CTAGATCATAAACAATGAGTTACACAACCTAGA
64 CTAAATCACAAACAATAAGTTACACAACCTAGA
5733777 CACATGCCCG
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
104 40 0.51
105 37 0.47
106 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (105 bp):
ATGTCCTTACCTGTATGGCTCACACGGCCTGGAGACACACCCATGTCCTCTGGCCGTGTGGTCCT
AAATCACAAACAATAAGTTACACAACCTAGATACACGCTC
Found at i:5734936 original size:18 final size:19
Alignment explanation
Indices: 5734921--5734956 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5734911 AGAAAAAGAG
5734921 GAAAAA-TGCAAAAAAGTA
1 GAAAAAGTGCAAAAAAGTA
5734939 GAAAAAGTGCAAAAAAGT
1 GAAAAAGTGCAAAAAAGT
5734957 GGGATTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.64, C:0.06, G:0.19, T:0.11
Consensus pattern (19 bp):
GAAAAAGTGCAAAAAAGTA
Found at i:5734944 original size:19 final size:19
Alignment explanation
Indices: 5734913--5734956 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5734903 ATTGCTGAAG
*
5734913 AAAAAG-AGGAAAAATGCA
1 AAAAAGTAGAAAAAATGCA
*
5734931 AAAAAGTAGAAAAAGTGCA
1 AAAAAGTAGAAAAAATGCA
5734950 AAAAAGT
1 AAAAAGT
5734957 GGGATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.66, C:0.05, G:0.20, T:0.09
Consensus pattern (19 bp):
AAAAAGTAGAAAAAATGCA
Found at i:5736401 original size:24 final size:24
Alignment explanation
Indices: 5736373--5736420 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5736363 ATCAAATATA
*
5736373 TATTTA-AAATTTATAAAAATAAAT
1 TATTTAGAAACTTA-AAAAATAAAT
5736397 TATTTAGTAAACTTAAAAAATAAA
1 TATTTAG-AAACTTAAAAAATAAA
5736421 CAAGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 9 0.43
26 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TATTTAGAAACTTAAAAAATAAAT
Found at i:5736983 original size:23 final size:23
Alignment explanation
Indices: 5736940--5736984 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
5736930 ACTAAAAAAA
*
5736940 ATGTATTTATCATTTATTAATAT
1 ATGTATTTATCATTAATTAATAT
*
5736963 ATGT-TTTATTATTAATGTAATA
1 ATGTATTTATCATTAAT-TAATA
5736985 GTTAATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (23 bp):
ATGTATTTATCATTAATTAATAT
Found at i:5742073 original size:44 final size:44
Alignment explanation
Indices: 5742023--5742113 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
5742013 GAGACAACCT
* *
5742023 TCTGTGATAATATTATTATGTAGTACATCCCTTTCTCCTTTATA
1 TCTGTGATAATATTATTATGTAGTACATCACTTTCTCCTTGATA
5742067 TCTGTGATAATATTATTATGTAGTACATCACTTTCTCCTTGATA
1 TCTGTGATAATATTATTATGTAGTACATCACTTTCTCCTTGATA
5742111 TCT
1 TCT
5742114 ACATTTAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (44 bp):
TCTGTGATAATATTATTATGTAGTACATCACTTTCTCCTTGATA
Found at i:5746757 original size:21 final size:22
Alignment explanation
Indices: 5746728--5746774 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5746718 CAGAAGGAGT
*
5746728 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5746750 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5746771 GAGT
1 GAGT
5746775 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:5752525 original size:6 final size:6
Alignment explanation
Indices: 5752507--5752536 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5752497 TAAATACACA
5752507 ATAAAT A-AAAT ATAAAT ATAAAT ATAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A
5752537 ATATAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
ATAAAT
Found at i:5752531 original size:12 final size:11
Alignment explanation
Indices: 5752507--5752558 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
5752497 TAAATACACA
5752507 ATAAATAAAAT
1 ATAAATAAAAT
5752518 ATAAATATAAAT
1 ATAAATA-AAAT
5752530 ATAAAT--AAT
1 ATAAATAAAAT
**
5752539 ATAGTTAAAAAT
1 ATAAAT-AAAAT
5752551 ATAAATAA
1 ATAAATAA
5752559 CATAATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 7 0.21
11 9 0.27
12 17 0.52
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:5752539 original size:21 final size:21
Alignment explanation
Indices: 5752515--5752563 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5752505 CAATAAATAA
*
5752515 AATATAAATATAAATATAAAT
1 AATATAAATAAAAATATAAAT
**
5752536 AATATAGTTAAAAATATAAAT
1 AATATAAATAAAAATATAAAT
*
5752557 AACATAA
1 AATATAA
5752564 TTCAAGGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AATATAAATAAAAATATAAAT
Found at i:5755487 original size:13 final size:13
Alignment explanation
Indices: 5755469--5755497 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5755459 AATCAATATT
5755469 TTAAAATTATAAA
1 TTAAAATTATAAA
5755482 TTAAAATTATAAA
1 TTAAAATTATAAA
5755495 TTA
1 TTA
5755498 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAATTATAAA
Found at i:5755490 original size:6 final size:7
Alignment explanation
Indices: 5755472--5755501 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5755462 CAATATTTTA
5755472 AAATTAT
1 AAATTAT
5755479 AAATTA-
1 AAATTAT
5755485 AAATTAT
1 AAATTAT
5755492 AAATTAT
1 AAATTAT
5755499 AAA
1 AAA
5755502 AATTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATTAT
Found at i:5758627 original size:6 final size:6
Alignment explanation
Indices: 5758616--5758643 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5758606 AAATAACGCA
5758616 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
5758644 GCAATGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:5759647 original size:13 final size:13
Alignment explanation
Indices: 5759626--5759668 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
5759616 TGACGAGATA
*
5759626 CAAATGTGCAAAC
1 CAAAAGTGCAAAC
5759639 CAAAAGTGCAAAC
1 CAAAAGTGCAAAC
* *
5759652 CAAAAATGTAAAC
1 CAAAAGTGCAAAC
5759665 CAAA
1 CAAA
5759669 GTGACGGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (13 bp):
CAAAAGTGCAAAC
Found at i:5759722 original size:29 final size:29
Alignment explanation
Indices: 5759664--5759728 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
5759654 AAAATGTAAA
* * *
5759664 CCAAAGTGACGGACAAGCCAAAGAATAAG
1 CCAAAGTGACGAACAAACCAAAGAACAAG
*
5759693 CCAAAGTGGCGAACAAACCAAA-AGACAAG
1 CCAAAGTGACGAACAAACCAAAGA-ACAAG
*
5759722 CTAAAGT
1 CCAAAGT
5759729 ACTACAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.49, C:0.22, G:0.22, T:0.08
Consensus pattern (29 bp):
CCAAAGTGACGAACAAACCAAAGAACAAG
Found at i:5759859 original size:28 final size:28
Alignment explanation
Indices: 5759827--5759882 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5759817 GCAAGTTGTC
*
5759827 AACTTGTTAGAAAAAGTTGTCAAATTAT
1 AACTTGCTAGAAAAAGTTGTCAAATTAT
5759855 AACTTGCTAGAAAAAGTTGTCAAATTAT
1 AACTTGCTAGAAAAAGTTGTCAAATTAT
5759883 TTATCTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (28 bp):
AACTTGCTAGAAAAAGTTGTCAAATTAT
Found at i:5761538 original size:9 final size:9
Alignment explanation
Indices: 5761509--5761565 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
5761499 TTTTGTTTCT
5761509 TTATTAAATA
1 TTATT-AATA
*
5761519 TTATTATTA
1 TTATTAATA
5761528 TT-TCTAATA
1 TTAT-TAATA
5761537 TTATTAATA
1 TTATTAATA
*
5761546 TTATAAATA
1 TTATTAATA
*
5761555 TTATTATTA
1 TTATTAATA
5761564 TT
1 TT
5761566 TATATATTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 33 0.82
10 6 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTAATA
Found at i:5761538 original size:18 final size:17
Alignment explanation
Indices: 5761512--5761574 Score: 81
Period size: 18 Copynumber: 3.6 Consensus size: 17
5761502 TGTTTCTTTA
5761512 TTAAATATTATTATTAT
1 TTAAATATTATTATTAT
* *
5761529 TTCTAATATTATTAATAT
1 TT-AAATATTATTATTAT
5761547 TATAAATATTATTATTAT
1 T-TAAATATTATTATTAT
*
5761565 TTATATATTA
1 TTAAATATTA
5761575 GTGTATGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 10 0.26
18 28 0.72
19 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTATTATTAT
Found at i:5761661 original size:3 final size:3
Alignment explanation
Indices: 5761648--5761809 Score: 52
Period size: 3 Copynumber: 53.0 Consensus size: 3
5761638 TTTAATTTCA
* * * * * **
5761648 TAT TGT TAT TAT TAG TAT TA- TAA TAT TAT AAT TAT TAT TAA TAT TGG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5761695 TAT ATAT T-T TAT TAT ATAT GTAT ATAT ACACT TTT TAT ATAG TAT TAT
1 TAT -TAT TAT TAT TAT -TAT -TAT -TAT -TA-T TAT TAT -TAT TAT TAT
* *
5761743 CAT T-T CTAT TAT TA- TATT TAT TAT TAT GT-T TAT TAT T-T TCAC TAT
1 TAT TAT -TAT TAT TAT TA-T TAT TAT TAT -TAT TAT TAT TAT T-AT TAT
*
5761788 TAT TAT T-T T-T TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
5761810 ACATATACAT
Statistics
Matches: 117, Mismatches: 27, Indels: 30
0.67 0.16 0.17
Matches are distributed among these distances:
2 14 0.12
3 81 0.69
4 21 0.18
5 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5761717 original size:20 final size:21
Alignment explanation
Indices: 5761657--5761769 Score: 66
Period size: 20 Copynumber: 5.6 Consensus size: 21
5761647 ATATTGTTAT
*
5761657 TATTAGTATTATAATAT-TATA
1 TATTATTATTAT-ATATGTATA
5761678 -ATTATTATTA-ATATTGGTATA
1 TATTATTATTATATA-T-GTATA
5761699 TATT-TTATTATATATGTATA
1 TATTATTATTATATATGTATA
* *
5761719 TATACACTTTTTATATA-GTAT-
1 TAT-TA-TTATTATATATGTATA
*
5761740 TATCATT-TCTAT-TAT-TATA
1 TATTATTAT-TATATATGTATA
5761759 T-TTATTATTAT
1 TATTATTATTAT
5761770 GTTTATTATT
Statistics
Matches: 76, Mismatches: 4, Indels: 27
0.71 0.04 0.25
Matches are distributed among these distances:
18 16 0.21
19 8 0.11
20 19 0.25
21 14 0.18
22 10 0.13
23 9 0.12
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTATTATTATATATGTATA
Found at i:5761982 original size:26 final size:26
Alignment explanation
Indices: 5761953--5762024 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
5761943 CATATATTTT
5761953 ATTATGTATATATTTTTAATAACTAC
1 ATTATGTATATATTTTTAATAACTAC
* * * * *
5761979 ATTATGTCTGTATTTGTAA-CACTAT
1 ATTATGTATATATTTTTAATAACTAC
* *
5762004 ATTATGTACATACTTTTAATA
1 ATTATGTATATATTTTTAATA
5762025 TTATTATGTA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
25 18 0.53
26 16 0.47
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.49
Consensus pattern (26 bp):
ATTATGTATATATTTTTAATAACTAC
Found at i:5762060 original size:20 final size:21
Alignment explanation
Indices: 5762001--5762061 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
5761991 TTTGTAACAC
5762001 TATATTATGTACATACTTTTAA
1 TATATTATGTACATA-TTTTAA
**
5762023 TATTATTATGTATTTATTTTAA
1 TA-TATTATGTACATATTTTAA
5762045 TATA-TATGTACATATTT
1 TATATTATGTACATATTT
5762062 ATGTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.32
21 2 0.06
22 10 0.29
23 11 0.32
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TATATTATGTACATATTTTAA
Found at i:5762060 original size:24 final size:24
Alignment explanation
Indices: 5762017--5762140 Score: 92
Period size: 26 Copynumber: 5.0 Consensus size: 24
5762007 ATGTACATAC
*
5762017 TTTTAATAT-TAT-TATGTATTTA
1 TTTTAATATATATGTATATATTTA
*
5762039 TTTTAATATATATGTACATATTTA
1 TTTTAATATATATGTATATATTTA
* * **
5762063 -TGTAGTATTATATACATATATTAGTA
1 TTTTAATA-TATATGTATATATT--TA
* *
5762089 TTTCTAATATATATTGTATATGTTCA
1 TTT-TAATATATA-TGTATATATTTA
5762115 TTTTATATATATTATGTATATATTTA
1 TTTTA-ATATA-TATGTATATATTTA
5762141 ATATTATTAT
Statistics
Matches: 77, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
22 9 0.12
23 8 0.10
24 19 0.25
25 2 0.03
26 21 0.27
27 7 0.09
28 11 0.14
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTTAATATATATGTATATATTTA
Found at i:5762148 original size:21 final size:22
Alignment explanation
Indices: 5762114--5762155 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5762104 GTATATGTTC
*
5762114 ATTTTATATATATTATGTATAT
1 ATTTAATATATATTATGTATAT
5762136 ATTTAATAT-TATTATGTATA
1 ATTTAATATATATTATGTATA
5762156 CACTTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTAATATATATTATGTATAT
Found at i:5765547 original size:72 final size:72
Alignment explanation
Indices: 5765468--5765624 Score: 199
Period size: 72 Copynumber: 2.2 Consensus size: 72
5765458 TTTGATTAAA
* *
5765468 GGATAAGTCCAACAATTCCAAATTGGTTAAGTT-GCCTAATGTAGAAGGGACAGGACCAATAATT
1 GGATAAGTCCAACAATTCCAAATTGGTTAAGTTGGCC-AAGGTAGAAGGGACAGGACCAAGAATT
*
5765532 TGGTTTTT
65 TGGTTATT
* * ** * * *
5765540 GGATAAGTTCAACATTTTTAAATTGGTTAAGTTGGCCAAGGTAGGAGGGATAGGACCACGAATTT
1 GGATAAGTCCAACAATTCCAAATTGGTTAAGTTGGCCAAGGTAGAAGGGACAGGACCAAGAATTT
5765605 GGTTATT
66 GGTTATT
*
5765612 GGATAGGTCCAAC
1 GGATAAGTCCAAC
5765625 TGTTTCAACC
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 69 0.96
73 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (72 bp):
GGATAAGTCCAACAATTCCAAATTGGTTAAGTTGGCCAAGGTAGAAGGGACAGGACCAAGAATTT
GGTTATT
Found at i:5766646 original size:20 final size:19
Alignment explanation
Indices: 5766613--5766657 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5766603 ATTGTTTGCG
*
5766613 TTTTATTTTGTTTATTAAAA
1 TTTTATTTTGTTTA-AAAAA
5766633 TTTTGATTTT-TTTAAAAAA
1 TTTT-ATTTTGTTTAAAAAA
5766652 TTTTAT
1 TTTTAT
5766658 CACTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 8 0.35
20 8 0.35
21 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTATTTTGTTTAAAAAA
Found at i:5776982 original size:94 final size:99
Alignment explanation
Indices: 5776778--5777012 Score: 268
Period size: 94 Copynumber: 2.4 Consensus size: 99
5776768 AAAAGATGTG
* * *
5776778 ATATGTG-TTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATGTGATAAGGTGCTTC
1 ATATGTGCTT-CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGA-GTGATAAGGAGCTTC
*
5776842 CGTATAAGACCATGTCTGGGACATGACATCGCTATC
64 CGTATAAGACCATATCTGGGACATGACATCGCTATC
* * *
5776878 ATATGAGCTTCCGTATAAGACCATATCTGGGATATGGCATC-G-GTGA-T-AT-ATGAGCTTTCG
1 ATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGTGTGAGTGATAAGGAGCTTCCG
* * * *
5776938 TATAAGACCATATCTGGGATAT-AGCATCGGTGTT
66 TATAAGACCATATCTGGGACATGA-CATCGCTATC
* * *
5776972 ATATGTGCTTCTGTGTAAGACCATATTTGGGATATGGCATC
1 ATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATC
5777013 AATATGATAT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
93 1 0.01
94 72 0.61
95 2 0.02
96 1 0.01
98 4 0.03
99 1 0.01
100 35 0.30
101 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (99 bp):
ATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGTGTGAGTGATAAGGAGCTTCCG
TATAAGACCATATCTGGGACATGACATCGCTATC
Found at i:5777023 original size:47 final size:46
Alignment explanation
Indices: 5776835--5777041 Score: 227
Period size: 47 Copynumber: 4.4 Consensus size: 46
5776825 ATGTGATAAG
* * * *
5776835 GTGCTTCCGTATAAGACCATGTCTGGGACATGACATCGCTATCATAT
1 GTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGTAT-ATAT
*
5776882 GAGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGTGATATAT
1 GTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGT-ATATAT
* * * *
5776929 GAGCTTTCGTATAAGACCATATCTGGGATATAGCATCGGTGTTATAT
1 GTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGT-ATATAT
* * * **
5776976 GTGCTTCTGTGTAAGACCATATTTGGGATATGGCATCAATATGATAT
1 GTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGTAT-ATAT
* *
5777023 GTG-ATCCGTGTAAGACCAT
1 GTGCTTCCGTATAAGACCAT
5777042 GGCTAGGCTA
Statistics
Matches: 139, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
46 15 0.11
47 122 0.88
48 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (46 bp):
GTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGGTATATAT
Found at i:5777210 original size:42 final size:42
Alignment explanation
Indices: 5777163--5777248 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
5777153 ATGAAAGTAA
5777163 ATGAAAAATAGGCCCAAGAGTTCTAAAATTTGGTGAATAGTG
1 ATGAAAAATAGGCCCAAGAGTTCTAAAATTTGGTGAATAGTG
*
5777205 ATGAAAAATGGGCCCAAGAGTTCTAAAATTTGGTGAATAGTG
1 ATGAAAAATAGGCCCAAGAGTTCTAAAATTTGGTGAATAGTG
5777247 AT
1 AT
5777249 ATCGAAATCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (42 bp):
ATGAAAAATAGGCCCAAGAGTTCTAAAATTTGGTGAATAGTG
Found at i:5784579 original size:41 final size:43
Alignment explanation
Indices: 5784475--5784642 Score: 123
Period size: 41 Copynumber: 3.9 Consensus size: 43
5784465 TTGCACAATA
* * *
5784475 CCAATGTCCCAGATGTGGTCTTACA-TATGATCAAATATCTATG
1 CCAATGTCCCAGATATGGTCTTACACGA-GATCAAATATCGATG
* * * * *
5784518 CCACTGTCCCTGACAGGGTCTTACACGA-ATCATATA-CGATG
1 CCAATGTCCCAGATATGGTCTTACACGAGATCAAATATCGATG
* *
5784559 CCAATGTCCCAGATATGGTCTTACACATACATCTCAAATA--GATG
1 CCAATGTCCCAGATATGGTCTTACAC-GAGA--TCAAATATCGATG
* * * *
5784603 CCAACGTCCCAG-TCGTGGTCTTACACGAAATCACATATCG
1 CCAATGTCCCAGAT-ATGGTCTTACACGAGATCAAATATCG
5784643 GAATCCTATG
Statistics
Matches: 98, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
41 32 0.33
42 8 0.08
43 25 0.26
44 27 0.28
45 6 0.06
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
CCAATGTCCCAGATATGGTCTTACACGAGATCAAATATCGATG
Found at i:5787695 original size:18 final size:18
Alignment explanation
Indices: 5787672--5787733 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
5787662 TCAAAATATT
5787672 AAAATTATAAAAATACAA
1 AAAATTATAAAAATACAA
*
5787690 AAAATTATAAAATATA-GA
1 AAAATTATAAAA-ATACAA
* *
5787708 AAATTTATAAAGAAT-CAT
1 AAAATTATAAA-AATACAA
5787726 AAAATTAT
1 AAAATTAT
5787734 TAGACATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 32 0.89
19 4 0.11
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAATACAA
Found at i:5787718 original size:36 final size:34
Alignment explanation
Indices: 5787664--5787733 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
5787654 TTGAATATTC
*
5787664 AAAATATTAAAATTATAAA-AATACAAAAAATTAT
1 AAAATATGAAAATTATAAAGAAT-CAAAAAATTAT
*
5787698 AAAATATAGAAAATTTATAAAGAATCATAAAATTAT
1 AAAATAT-GAAAA-TTATAAAGAATCAAAAAATTAT
5787734 TAGACATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 7 0.23
35 4 0.13
36 17 0.55
37 3 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (34 bp):
AAAATATGAAAATTATAAAGAATCAAAAAATTAT
Found at i:5791704 original size:72 final size:71
Alignment explanation
Indices: 5791544--5791712 Score: 180
Period size: 72 Copynumber: 2.3 Consensus size: 71
5791534 TACCCCAGTG
* * * * *
5791544 ATTTGATTAAAGGATAAGTCCAAC-TGTTTTAAATTGGTTAATTTGCCTAAGGTAGAAGGGAAAG
1 ATTTGATT-ATGGATAGGTCCAACAT-TTTTAAAGTGGTTAAGTTGCCCAAGGTAGAAGGGAAAG
5791608 GACCACTA
64 GACCACTA
* * * *
5791616 ATTTGGTTTTTGGATAGGTTCAACATTTTTAAAGTGGTTAAGTTGCCCAAGGTAGAAGGGATAGG
1 ATTT-GATTATGGATAGGTCCAACATTTTTAAAGTGGTTAAGTTGCCCAAGGTAGAAGGGAAAGG
* *
5791681 GCCAGTA
65 ACCACTA
5791688 ATTCT-ATTATGCGATAGGTCCAACA
1 ATT-TGATTATG-GATAGGTCCAACA
5791713 GCTTCAAACT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
71 4 0.05
72 70 0.89
73 5 0.06
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (71 bp):
ATTTGATTATGGATAGGTCCAACATTTTTAAAGTGGTTAAGTTGCCCAAGGTAGAAGGGAAAGGA
CCACTA
Found at i:5792548 original size:16 final size:15
Alignment explanation
Indices: 5792517--5792547 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5792507 TTTGATTTGT
*
5792517 ATTTTTTTATTGAAA
1 ATTTTTCTATTGAAA
5792532 ATTTTTCTATTGAAA
1 ATTTTTCTATTGAAA
5792547 A
1 A
5792548 AATATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTTCTATTGAAA
Found at i:5793253 original size:17 final size:19
Alignment explanation
Indices: 5793221--5793260 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5793211 AAATGTGAAA
5793221 AATAACAACAAAATTA-AC
1 AATAACAACAAAATTATAC
*
5793239 AATAA-AACAAGATTATAC
1 AATAACAACAAAATTATAC
5793257 AATA
1 AATA
5793261 TTCAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (19 bp):
AATAACAACAAAATTATAC
Found at i:5801345 original size:17 final size:17
Alignment explanation
Indices: 5801313--5801345 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5801303 TTAAAAAATC
5801313 ATATTTTTTTATATTTA
1 ATATTTTTTTATATTTA
5801330 ATATATTTTTTA-ATTT
1 ATAT-TTTTTTATATTT
5801346 CAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTTTTTATATTTA
Found at i:5801353 original size:18 final size:18
Alignment explanation
Indices: 5801317--5801358 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5801307 AAAATCATAT
*
5801317 TTTTTTATATTTAATATA
1 TTTTTTATATTTAAAATA
5801335 TTTTTTA-ATTTCAAAATA
1 TTTTTTATATTT-AAAATA
5801353 TATTTT
1 T-TTTT
5801359 GACAAGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTTATATTTAAAATA
Found at i:5804198 original size:12 final size:12
Alignment explanation
Indices: 5804181--5804213 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5804171 CTCGTTGAGT
5804181 TATATATATATG
1 TATATATATATG
*
5804193 TATATATATATT
1 TATATATATATG
5804205 TATATATAT
1 TATATATAT
5804214 CATCTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
TATATATATATG
Found at i:5809715 original size:52 final size:53
Alignment explanation
Indices: 5809648--5809752 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
5809638 ATCCTCAATA
* *
5809648 AATTTCATTCCTATTGCA-TTGCTATCTTTGATTAACTTATTCATTTTGAGTT
1 AATTTCATTCCTATTGCATTTGCAATCTTTGATTAACTTATTCATTTCGAGTT
* * * * *
5809700 AATTTCCTTCTTATTGTATTTGCAATCTTTGATTGATTTATTCATTTCGAGTT
1 AATTTCATTCCTATTGCATTTGCAATCTTTGATTAACTTATTCATTTCGAGTT
5809753 TTGCTCTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 15 0.33
53 30 0.67
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (53 bp):
AATTTCATTCCTATTGCATTTGCAATCTTTGATTAACTTATTCATTTCGAGTT
Found at i:5810199 original size:64 final size:64
Alignment explanation
Indices: 5810123--5810314 Score: 339
Period size: 64 Copynumber: 3.0 Consensus size: 64
5810113 TCATTCATAA
5810123 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
* * * *
5810187 CATATCTAGTTAGGGGAATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGTAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
*
5810251 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
5810315 AGATACATGA
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 119 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:5810565 original size:45 final size:45
Alignment explanation
Indices: 5810384--5810570 Score: 130
Period size: 45 Copynumber: 4.2 Consensus size: 45
5810374 AATTTTACAG
* * *
5810384 ATCTTGCCTCCCTGAAGTTGCAGTGGAACAGATCAAAGACGACGA
1 ATCTTGTCTCTCTGAAGTTGCAGTGGAACAGATCGAAGACGACGA
* ** * *
5810429 ATCTTGTCTCTCTGAAGTTGCAGTGGAGCAGATTTAAG-CCAC-C
1 ATCTTGTCTCTCTGAAGTTGCAGTGGAACAGATCGAAGACGACGA
* * * ** * ** * * * *
5810472 ATCCTATCT-TCTTAAGCAGTAGTGGAGTAGGTTGAAGATTG-CGG
1 ATCTTGTCTCTCTGAAGTTGCAGTGGAACAGATCGAAGA-CGACGA
* *
5810516 ATCTTGTCTCTCTGAAGTTGCAGTGGAACAAATCGAAGACGGCGA
1 ATCTTGTCTCTCTGAAGTTGCAGTGGAACAGATCGAAGACGACGA
*
5810561 ATCTTATCTC
1 ATCTTGTCTC
5810571 CCTAACCAGT
Statistics
Matches: 104, Mismatches: 33, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
42 21 0.20
43 8 0.08
44 11 0.11
45 64 0.62
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (45 bp):
ATCTTGTCTCTCTGAAGTTGCAGTGGAACAGATCGAAGACGACGA
Found at i:5810716 original size:131 final size:131
Alignment explanation
Indices: 5810381--5810718 Score: 435
Period size: 131 Copynumber: 2.6 Consensus size: 131
5810371 GGTAATTTTA
* * * *
5810381 CAGATCTTGCCTCCCTGAAGTTGCAGTGGAACAGATCAAAGACGACGAATCTTGTCTCTCTGAAG
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGACGAATCTTATCTC-CCGAAG
* * * * *
5810446 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTTCTTAAGCAGTAGTGGAGTAGGTTGAAGAT
65 TTGCAGTGGAGCAAATTTAAGCCACCATCCTATCTTCCTAAGAAGTAGTGGAGTAGGCTAAAGAT
5810511 TG
130 TG
* * * * * **
5810513 CGGATCTTGTCTCTCTGAAGTTGCAGTGGAACAAATCGAAGACGGCGAATCTTATCTCCCTAACC
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGACGAATCTTATCTCCCGAAGT
* *
5810578 AGTAGTGGAGCAAATTTAAGCCACCATCCTATCTTCCTAAGAAGTAGTGGAGTAGGCTAAAGATT
66 TGCAGTGGAGCAAATTTAAGCCACCATCCTATCTTCCTAAGAAGTAGTGGAGTAGGCTAAAGATT
5810643 G
131 G
* * * * * *
5810644 TAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CCACTAACCTTATCTTCCCGAAG
1 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGACGAATCTTATC-TCCCGAAG
5810708 TTGCAGTGGAG
65 TTGCAGTGGAG
5810719 TAGGTTGAAG
Statistics
Matches: 172, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
130 10 0.06
131 111 0.65
132 51 0.30
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (131 bp):
CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGACGAATCTTATCTCCCGAAGT
TGCAGTGGAGCAAATTTAAGCCACCATCCTATCTTCCTAAGAAGTAGTGGAGTAGGCTAAAGATT
G
Found at i:5810763 original size:44 final size:44
Alignment explanation
Indices: 5810647--5810766 Score: 145
Period size: 44 Copynumber: 2.7 Consensus size: 44
5810637 AAGATTGTAG
* *
5810647 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTA
* * **
5810691 ACCTTATCTTCCC-GAAGTTGCAGTGGAGTAGGTTGAAGTTAC-A
1 ATCTTATC-TCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTA
*
5810734 AGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGA
5810767 CTCATGATAG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.09
44 54 0.84
45 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTA
Found at i:5811984 original size:19 final size:18
Alignment explanation
Indices: 5811955--5812004 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5811945 GTATATATTT
5811955 TAAATTTATTTAGGTAAA
1 TAAATTTATTTAGGTAAA
* *
5811973 TAAATCTTATTTGGGTAGA
1 TAAAT-TTATTTAGGTAAA
*
5811992 TAAGTTTTATTTA
1 TAA-ATTTATTTA
5812005 TATTCTAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (18 bp):
TAAATTTATTTAGGTAAA
Found at i:5812071 original size:43 final size:43
Alignment explanation
Indices: 5812024--5812108 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
5812014 AATTTTTTTA
5812024 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
1 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
* * *
5812067 TTTTATGTTTTAGTAGTTTATTAGAATAATGGAACTATTTTC
1 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTC
5812109 CTAATTAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (43 bp):
TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
Found at i:5815721 original size:46 final size:45
Alignment explanation
Indices: 5815668--5815843 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
5815658 TATTTGGGCA
5815668 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
5815714 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
5815761 TCCGAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
5815807 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5815844 GCAGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 65 0.60
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:5815823 original size:93 final size:93
Alignment explanation
Indices: 5815664--5815836 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
5815654 GGGATATTTG
* *
5815664 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
5815729 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
5815757 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGTCC-GAACTCGTTGA
5815821 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
5815837 CTTATGGGCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:5819520 original size:19 final size:19
Alignment explanation
Indices: 5819474--5819521 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
5819464 GTATATATTT
5819474 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
* *
5819492 TAAATCTTATTTGGGTAGA
1 TAAATTTTATTTAGGTAGA
*
5819511 TAAGTTTTATT
1 TAAATTTTATT
5819522 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:5822683 original size:15 final size:17
Alignment explanation
Indices: 5822638--5822691 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 17
5822628 TATATTATAC
5822638 ATTATAA-GATTA-TTTT
1 ATTATAATG-TTATTTTT
5822654 ATTATAAATGTTATTTTT
1 ATTAT-AATGTTATTTTT
*
5822672 ATTAT-ATG-TATTATT
1 ATTATAATGTTATTTTT
5822687 ATTAT
1 ATTAT
5822692 TTATTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 11 0.32
16 8 0.24
17 5 0.15
18 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTATAATGTTATTTTT
Found at i:5822685 original size:18 final size:18
Alignment explanation
Indices: 5822646--5822692 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
5822636 ACATTATAAG
5822646 ATTA-TTTTATTATAAAT
1 ATTATTTTTATTATAAAT
* **
5822663 GTTATTTTTATTATATGT
1 ATTATTTTTATTATAAAT
*
5822681 ATTATTATTATT
1 ATTATTTTTATT
5822693 TATTATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
ATTATTTTTATTATAAAT
Found at i:5822785 original size:20 final size:19
Alignment explanation
Indices: 5822726--5822786 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 19
5822716 TTTATATCAT
*
5822726 TTTTATATATATATTGTTATA
1 TTTT-TATATATATTATT-TA
* *
5822747 TTTTCACATATATTATATTTA
1 TTTTTATATATA-T-TATTTA
5822768 TTATTTATATATATTATTT
1 TT-TTTATATATATTATTT
5822787 TACATATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 11 0.34
21 10 0.31
22 11 0.34
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATATATATTATTTA
Found at i:5826676 original size:25 final size:25
Alignment explanation
Indices: 5826648--5826697 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5826638 CTACTATTTA
5826648 AGAAAAGAGTATGACAAGTGAAGAC
1 AGAAAAGAGTATGACAAGTGAAGAC
5826673 AGAAAAGAGTATGACAAGTGAAGAC
1 AGAAAAGAGTATGACAAGTGAAGAC
5826698 TAAGTCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (25 bp):
AGAAAAGAGTATGACAAGTGAAGAC
Found at i:5833310 original size:31 final size:30
Alignment explanation
Indices: 5833275--5833371 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 30
5833265 AACAACCCAA
5833275 TGACTTAAATAAAAACTTTTTAATAGTTTAG
1 TGACTTAAAT-AAAACTTTTTAATAGTTTAG
**
5833306 TGACTTAAATAAATTTTTTTGAATAGTTTAG
1 TGACTTAAATAAAACTTTTT-AATAGTTTAG
* * *
5833337 TGACTTAAATGAAAGCTTTTGAATAATTTAG
1 TGACTTAAAT-AAAACTTTTTAATAGTTTAG
5833368 TGAC
1 TGAC
5833372 CAAATTGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 8 0.14
31 43 0.74
32 7 0.12
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (30 bp):
TGACTTAAATAAAACTTTTTAATAGTTTAG
Found at i:5833432 original size:34 final size:34
Alignment explanation
Indices: 5833394--5833458 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
5833384 TTTTCTAGTT
5833394 AAATGACCAAAACAAAAACTTACTCATAATTAAG
1 AAATGACCAAAACAAAAACTTACTCATAATTAAG
*
5833428 AAATGACCAAAATAAAAACTTACTCATAATT
1 AAATGACCAAAACAAAAACTTACTCATAATT
5833459 TAGTGACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.23
Consensus pattern (34 bp):
AAATGACCAAAACAAAAACTTACTCATAATTAAG
Found at i:5836886 original size:2 final size:2
Alignment explanation
Indices: 5836881--5836949 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
5836871 CTCTTTCTCT
5836881 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5836923 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
5836950 GAGAGACACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5844175 original size:10 final size:10
Alignment explanation
Indices: 5844136--5844185 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
5844126 TGAAATTCTA
5844136 AAAGATAAAT
1 AAAGATAAAT
*
5844146 ACAA-ATAAAA
1 A-AAGATAAAT
5844156 AAAGATAAAT
1 AAAGATAAAT
5844166 AAAGATAAAT
1 AAAGATAAAT
5844176 GAAA-ATAAAT
1 -AAAGATAAAT
5844186 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5845053 original size:41 final size:40
Alignment explanation
Indices: 5844945--5845054 Score: 93
Period size: 41 Copynumber: 2.8 Consensus size: 40
5844935 TCTGATAATT
* *
5844945 CGAAGTAACAGTTTGACACCCAGTGTCTCATCGGCCATGC
1 CGAAGTAACAATTTGACACCCAGTGTCTCATCAGCCATGC
** ** ***
5844985 CGAAGT---AATTTGGTACCCAGTACCTCATCAAATTTAT-C
1 CGAAGTAACAATTTGACACCCAGTGTCTCATC--AGCCATGC
5845023 CGAAGTAACAATTTGACACCCAGTGTCTCATC
1 CGAAGTAACAATTTGACACCCAGTGTCTCATC
5845055 GACTCGAGGT
Statistics
Matches: 52, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
37 18 0.35
38 7 0.13
39 2 0.04
40 6 0.12
41 19 0.37
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (40 bp):
CGAAGTAACAATTTGACACCCAGTGTCTCATCAGCCATGC
Found at i:5847202 original size:27 final size:27
Alignment explanation
Indices: 5847164--5847218 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5847154 TTTGGGGTGC
*
5847164 TTTCATTGCATTTTTGGGCTTAAGTTG
1 TTTCATTGCATTTTTGAGCTTAAGTTG
*
5847191 TTTCATTGCATTTTTGAGCTTGAGTTG
1 TTTCATTGCATTTTTGAGCTTAAGTTG
5847218 T
1 T
5847219 GAACTTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.11, G:0.22, T:0.53
Consensus pattern (27 bp):
TTTCATTGCATTTTTGAGCTTAAGTTG
Found at i:5847587 original size:15 final size:15
Alignment explanation
Indices: 5847567--5847616 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
5847557 ATGTGAGTAA
5847567 AAATACAACCTAAAG
1 AAATACAACCTAAAG
**
5847582 AAATAC-A--TAACTC
1 AAATACAACCTAA-AG
5847595 AAATACAACCTAAAG
1 AAATACAACCTAAAG
5847610 AAATACA
1 AAATACA
5847617 TAACTCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.11
13 6 0.22
14 2 0.07
15 13 0.48
16 3 0.11
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (15 bp):
AAATACAACCTAAAG
Found at i:5847599 original size:28 final size:28
Alignment explanation
Indices: 5847567--5847626 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
5847557 ATGTGAGTAA
5847567 AAATACAACCTAAAGAAATACATAACTC
1 AAATACAACCTAAAGAAATACATAACTC
5847595 AAATACAACCTAAAGAAATACATAACTC
1 AAATACAACCTAAAGAAATACATAACTC
5847623 AAAT
1 AAAT
5847627 TGACATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.58, C:0.20, G:0.03, T:0.18
Consensus pattern (28 bp):
AAATACAACCTAAAGAAATACATAACTC
Found at i:5861577 original size:47 final size:48
Alignment explanation
Indices: 5861494--5861587 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 48
5861484 GCTTAAAAAG
5861494 GTCACCCATCTATGCATAAATGTTCAAAAGAATGAATTCACTTTTAAT
1 GTCACCCATCTATGCATAAATGTTCAAAAGAATGAATTCACTTTTAAT
*
5861542 GTCACCCATCTATGCA-AAATGTTCAAAAGATTGAATTCACTTTTAA
1 GTCACCCATCTATGCATAAATGTTCAAAAGAATGAATTCACTTTTAA
5861588 GTATGATTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 29 0.64
48 16 0.36
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (48 bp):
GTCACCCATCTATGCATAAATGTTCAAAAGAATGAATTCACTTTTAAT
Found at i:5875002 original size:60 final size:60
Alignment explanation
Indices: 5874925--5875040 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
5874915 CCTCAACAAC
* *
5874925 CTGAGTACTGTCAGGAGCTGAATGGGAATCT-GAACATGCAGCAACTGGAGAAGAATCAAT
1 CTGAGTACTGCCAGGAGCTGAATGGGAAT-TAGAACAAGCAGCAACTGGAGAAGAATCAAT
* * **
5874985 CTGAGTATTGCCAGGAGCTGAATGGGAATTAGAACAAGCATCAGTTGGAGAAGAAT
1 CTGAGTACTGCCAGGAGCTGAATGGGAATTAGAACAAGCAGCAACTGGAGAAGAAT
5875041 GTGGTGTAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (60 bp):
CTGAGTACTGCCAGGAGCTGAATGGGAATTAGAACAAGCAGCAACTGGAGAAGAATCAAT
Found at i:5881553 original size:15 final size:15
Alignment explanation
Indices: 5881541--5881593 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
5881531 GACTTCATGC
*
5881541 TTTGACTTGTCATCT
1 TTTGATTTGTCATCT
*
5881556 TTTGATTTGTCGTCT
1 TTTGATTTGTCATCT
5881571 TTTGATTTGTCATCT
1 TTTGATTTGTCATCT
5881586 TTTGATTT
1 TTTGATTT
5881594 TTTGCCATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.60
Consensus pattern (15 bp):
TTTGATTTGTCATCT
Found at i:5888136 original size:9 final size:9
Alignment explanation
Indices: 5888118--5888148 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5888108 ACTATGAATT
5888118 TTTTTAAAAA
1 TTTTT-AAAA
5888128 TTTTTAAAA
1 TTTTTAAAA
5888137 TTTTTAAAA
1 TTTTTAAAA
5888146 TTT
1 TTT
5888149 ATTCTTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:5894722 original size:27 final size:26
Alignment explanation
Indices: 5894682--5894796 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
5894672 AGCATGGCTG
* *
5894682 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
5894708 CCAGATACAGTTAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5894736 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
5894763 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
5894790 CCAGAAC
1 CCAGAAC
5894797 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.06
27 56 0.72
28 17 0.22
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5894746 original size:54 final size:54
Alignment explanation
Indices: 5894682--5894796 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
5894672 AGCATGGCTG
* *
5894682 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGTTAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
5894736 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5894790 CCAGAAC
1 CCAGAAC
5894797 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5896449 original size:26 final size:26
Alignment explanation
Indices: 5896413--5896522 Score: 161
Period size: 26 Copynumber: 4.2 Consensus size: 26
5896403 CATGAAATTC
5896413 TTATCATGAAACATTTACCTAACAC-A
1 TTATCATGAAACATTTACCTAAC-CTA
*
5896439 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5896465 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5896491 TTATCATTG-AACAATTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCTA
5896517 TTATCA
1 TTATCA
5896523 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
25 1 0.01
26 76 0.96
27 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5900139 original size:25 final size:25
Alignment explanation
Indices: 5900104--5900165 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
5900094 ATTTTTGTCT
* *
5900104 TTTTTGTTCACCCAACTATCTTGGA
1 TTTTTGGTCACCAAACTATCTTGGA
5900129 TTTTTGGTCACCAAACTATCTTGGA
1 TTTTTGGTCACCAAACTATCTTGGA
5900154 TTTTTGGTCACC
1 TTTTTGGTCACC
5900166 TATAACCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTTTGGTCACCAAACTATCTTGGA
Found at i:5909623 original size:32 final size:32
Alignment explanation
Indices: 5909582--5909647 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
5909572 ATCAATTAAC
5909582 ATTATTTTATTCTCAATTTATCATATAACACA
1 ATTATTTTATTCTCAATTTATCATATAACACA
5909614 ATTATTTTATTCTCAATTTATCATATAACACA
1 ATTATTTTATTCTCAATTTATCATATAACACA
5909646 AT
1 AT
5909648 ATGCTTCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTATTTTATTCTCAATTTATCATATAACACA
Found at i:5912438 original size:13 final size:14
Alignment explanation
Indices: 5912420--5912497 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 14
5912410 GAAAAAAATT
*
5912420 TTATAT-GAATTAG
1 TTATATGGAAATAG
*
5912433 TTATATGGAAATAA
1 TTATATGGAAATAG
* *
5912447 ATATATGG-AATGG
1 TTATATGGAAATAG
*
5912460 TTATAT-G-AATCGG
1 TTATATGGAAAT-AG
5912473 TTATATGGAAATAG
1 TTATATGGAAATAG
*
5912487 ATATAT-GAAAT
1 TTATATGGAAAT
5912498 GGAACATTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
12 4 0.08
13 27 0.51
14 19 0.36
15 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATATGGAAATAG
Found at i:5912476 original size:40 final size:40
Alignment explanation
Indices: 5912420--5912499 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
5912410 GAAAAAAATT
* *
5912420 TTATATGAATTAGTTATATGGAAATAAATATATGGAATGG
1 TTATATGAATCAGTTATATGGAAATAAATATATGAAATGG
* *
5912460 TTATATGAATCGGTTATATGGAAATAGATATATGAAATGG
1 TTATATGAATCAGTTATATGGAAATAAATATATGAAATGG
5912500 AACATTGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.36
Consensus pattern (40 bp):
TTATATGAATCAGTTATATGGAAATAAATATATGAAATGG
Found at i:5917776 original size:7 final size:7
Alignment explanation
Indices: 5917764--5917806 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
5917754 TTCAAACTAC
5917764 TTTTTAT
1 TTTTTAT
5917771 TTTTTAAT
1 TTTTT-AT
5917779 TTTTTAAT
1 TTTTT-AT
*
5917787 TTTTTAA
1 TTTTTAT
5917794 TTTTTAT
1 TTTTTAT
5917801 TTTTTA
1 TTTTTA
5917807 GCAGATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 18 0.55
8 15 0.45
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:5917780 original size:8 final size:8
Alignment explanation
Indices: 5917764--5917806 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
5917754 TTCAAACTAC
5917764 TTTTT-AT
1 TTTTTAAT
5917771 TTTTTAAT
1 TTTTTAAT
5917779 TTTTTAAT
1 TTTTTAAT
5917787 TTTTTAA-
1 TTTTTAAT
5917794 TTTTT-AT
1 TTTTTAAT
5917801 TTTTTA
1 TTTTTA
5917807 GCAGATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 1 0.03
7 15 0.45
8 17 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTAAT
Done.