Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 94 of 193
Found at i:30417255 original size:74 final size:74
Alignment explanation
Indices: 30417150--30417289 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 74
30417140 ATCGGCACGA
* * *
30417150 CACGAATCCTACTAGGCACACAACCTGAAAACACCGACACAAAGCCTACAAGGTACAAAGCCTGA
1 CACGAAGCCTACTAGGCACACAACCTAAAAACACCGACACAAAGCCTACAAGGCACAAAGCCTGA
30417215 AAGCACCAG
66 AAGCACCAG
** * * *
30417224 CACGAAGCCTACTAGGCACA-AAGCCTAAAAACACCGGGACGAAGCCTACTAGGCAGAAAGCCTG
1 CACGAAGCCTACTAGGCACACAA-CCTAAAAACACCGACACAAAGCCTACAAGGCACAAAGCCTG
30417288 AA
65 AA
30417290 TTTTTAGATG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 2 0.04
74 55 0.96
ACGTcount: A:0.41, C:0.31, G:0.19, T:0.09
Consensus pattern (74 bp):
CACGAAGCCTACTAGGCACACAACCTAAAAACACCGACACAAAGCCTACAAGGCACAAAGCCTGA
AAGCACCAG
Found at i:30423844 original size:21 final size:19
Alignment explanation
Indices: 30423820--30423882 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
30423810 ACGAAAAGAC
*
30423820 TTAATTGTATAAAATTGTTAT
1 TTAATTG-ATGAAATT-TTAT
* *
30423841 TTAAGTGCTGAAATTTTA-
1 TTAATTGATGAAATTTTAT
30423859 TTAATTGAATGAAATTATTAT
1 TTAATTG-ATGAAATT-TTAT
30423880 TTA
1 TTA
30423883 GATCAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 6 0.18
19 10 0.29
20 9 0.26
21 9 0.26
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (19 bp):
TTAATTGATGAAATTTTAT
Found at i:30424223 original size:26 final size:27
Alignment explanation
Indices: 30424193--30424260 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 27
30424183 TATGAATGAA
30424193 CTAAATTGATTTATATATG-ATAATTAG
1 CTAAATTGATTTATAT-TGCATAATTAG
* * * *
30424220 -TAAATTAAATTAAATTGCATTATTAG
1 CTAAATTGATTTATATTGCATAATTAG
30424246 CTAAATTGATCTTAT
1 CTAAATTGAT-TTAT
30424261 GTTTTATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
25 2 0.06
26 19 0.61
27 7 0.23
28 3 0.10
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (27 bp):
CTAAATTGATTTATATTGCATAATTAG
Found at i:30424538 original size:21 final size:24
Alignment explanation
Indices: 30424501--30424716 Score: 183
Period size: 24 Copynumber: 9.2 Consensus size: 24
30424491 CTAGTTAGCG
*
30424501 TAAACGCATATTAGCTGGCGAGCG
1 TAAACGCATATTAGCTGGCGAGCA
* *
30424525 TAAATG-A-A-TAGCTGGCAAGCA
1 TAAACGCATATTAGCTGGCGAGCA
*
30424546 TAAA--CA-AATAGCTGGCGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
*
30424567 TAAACGCATATTAGCTGGCGAGCG
1 TAAACGCATATTAGCTGGCGAGCA
30424591 TAAACGCATATTAGCTGGCGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
* * *
30424615 TAAACGCATACTAGCTGGCAAGCG
1 TAAACGCATATTAGCTGGCGAGCA
* * * * *
30424639 TAAACGTAAAGTGGCTGACGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
** * * * *
30424663 TAAACATAAAGTGGCTGACGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
* * * *
30424687 TAAACGTATAGTGGCTGACGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
30424711 TAAACG
1 TAAACG
30424717 TAATTGAAAC
Statistics
Matches: 167, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.01
21 31 0.19
22 1 0.01
23 3 0.02
24 130 0.78
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
TAAACGCATATTAGCTGGCGAGCA
Found at i:30430484 original size:20 final size:20
Alignment explanation
Indices: 30430461--30430498 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30430451 AATTATAATT
30430461 TTTAAAAAAATAAAAAACTA
1 TTTAAAAAAATAAAAAACTA
**
30430481 TTTAAAAATCTAAAAAAC
1 TTTAAAAAAATAAAAAAC
30430499 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
TTTAAAAAAATAAAAAACTA
Found at i:30430530 original size:33 final size:33
Alignment explanation
Indices: 30430466--30430529 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
30430456 TAATTTTTAA
*
30430466 AAAAATAAAAAACTATTTAAAAATCTAAAAAAC
1 AAAAATAAAAAACTATTTAAAAATATAAAAAAC
* *
30430499 AAAAATAAAAAGCT-TTTGAAAATATAAAAAA
1 AAAAATAAAAAACTATTTAAAAATATAAAAAA
30430530 AATTCCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (33 bp):
AAAAATAAAAAACTATTTAAAAATATAAAAAAC
Found at i:30430970 original size:12 final size:13
Alignment explanation
Indices: 30430953--30430981 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30430943 AATTTTTATA
30430953 TTTTT-AAAATAT
1 TTTTTAAAAATAT
30430965 TTTTTAAAAATAT
1 TTTTTAAAAATAT
30430978 TTTT
1 TTTT
30430982 AAATTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAAAAATAT
Found at i:30430982 original size:12 final size:12
Alignment explanation
Indices: 30430950--30430984 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
30430940 TGAAATTTTT
30430950 ATATTTTT-AAA
1 ATATTTTTAAAA
30430961 ATATTTTTTAAAA
1 ATA-TTTTTAAAA
30430974 ATATTTTTAAA
1 ATATTTTTAAA
30430985 TTTGAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 13 0.59
13 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATTTTTAAAA
Found at i:30431517 original size:11 final size:11
Alignment explanation
Indices: 30431503--30431530 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30431493 TGAATTTTGA
30431503 ATTTTTTTTAT
1 ATTTTTTTTAT
30431514 ATTTTTTTTAT
1 ATTTTTTTTAT
30431525 ATTTTT
1 ATTTTT
30431531 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTTTTTAT
Found at i:30431549 original size:21 final size:20
Alignment explanation
Indices: 30431522--30431587 Score: 87
Period size: 21 Copynumber: 3.2 Consensus size: 20
30431512 ATATTTTTTT
30431522 TATATTTTTATTTTTTAAAA
1 TATATTTTTATTTTTTAAAA
*
30431542 TATGATTTTTATTTTTAAAAAA
1 TAT-ATTTTTATTTTT-TAAAA
* *
30431564 TATATATTTATTATTTAAAA
1 TATATTTTTATTTTTTAAAA
30431584 TATA
1 TATA
30431588 AAAAATTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.28
21 22 0.55
22 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATATTTTTATTTTTTAAAA
Found at i:30431587 original size:20 final size:19
Alignment explanation
Indices: 30431522--30431587 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 19
30431512 ATATTTTTTT
30431522 TATATTTTTATTTTTTAAAA
1 TATATTTTTA-TTTTTAAAA
30431542 TATGATTTTTATTTTTAAAAAA
1 TAT-ATTTTTATTTTT--AAAA
*
30431564 TATATATTTATTATTTAAAA
1 TATATTTTTATT-TTTAAAA
30431584 TATA
1 TATA
30431588 AAAAATTAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 16 0.39
21 15 0.37
22 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATTTTTATTTTTAAAA
Found at i:30433251 original size:3 final size:3
Alignment explanation
Indices: 30433245--30433282 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
30433235 TTCTTTGTCG
30433245 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
30433283 ATGGATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:30433447 original size:2 final size:2
Alignment explanation
Indices: 30433434--30433469 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30433424 TCGTAGAGCC
*
30433434 AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30433470 GTGATTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:30449239 original size:38 final size:38
Alignment explanation
Indices: 30449148--30449361 Score: 173
Period size: 38 Copynumber: 5.7 Consensus size: 38
30449138 AATCCTAATG
** * * *
30449148 AACACCGGCAC-AAAACCTACTAAGCACATAGCACGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * * * *
30449185 AACACTGACACAAAGGCTTGCTAGGCACATAGCCCAAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * ** *
30449223 AACACCGGCACGAAGGCCTGTTAGTCGTAAAGCCCGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * * * *
30449261 ATCACGGGCATGAA-GCCTACTAGGCACATAGCCTGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * * *
30449298 AACACCGACACGAA-GCCTACTAGGCACACAGTCCGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* *
30449335 ATCACTGGCACGAAGGCCTGCTAGGCA
1 AACACCGGCACGAAGGCCTGCTAGGCA
30449362 TAAAGCCTGA
Statistics
Matches: 135, Mismatches: 40, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
37 66 0.49
38 69 0.51
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.14
Consensus pattern (38 bp):
AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
Found at i:30449359 original size:75 final size:74
Alignment explanation
Indices: 30449148--30449373 Score: 211
Period size: 75 Copynumber: 3.0 Consensus size: 74
30449138 AATCCTAATG
* * * * * * * *
30449148 AACACCGGCACAAAACCTACTAAGCACATAGCACGATAACACTGACACAAAGGCTTGCTAGGCAC
1 AACACCGGCACGAAGCCTACTAGGCACAAAGC-CGATATCACTGGCACGAAGGCCTGCTAGGCAC
**
30449213 ATAGCCCAAT
65 ATAGCCTGAT
** * ** * * *
30449223 AACACCGGCACGAAGGCCTGTTAGTCGTAAAGCCCGATATCACGGGCATGAA-GCCTACTAGGCA
1 AACACCGGCACGAA-GCCTACTAGGCACAAAG-CCGATATCACTGGCACGAAGGCCTGCTAGGCA
30449287 CATAGCCTGAT
64 CATAGCCTGAT
* * *
30449298 AACACCGACACGAAGCCTACTAGGCACACAGTCCGATATCACTGGCACGAAGGCCTGCTAGGCAT
1 AACACCGGCACGAAGCCTACTAGGCACAAAG-CCGATATCACTGGCACGAAGGCCTGCTAGGCAC
*
30449363 AAAGCCTGAT
65 ATAGCCTGAT
30449373 A
1 A
30449374 TCACTTGTAT
Statistics
Matches: 117, Mismatches: 31, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
74 28 0.24
75 66 0.56
76 22 0.19
77 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (74 bp):
AACACCGGCACGAAGCCTACTAGGCACAAAGCCGATATCACTGGCACGAAGGCCTGCTAGGCACA
TAGCCTGAT
Found at i:30449367 original size:112 final size:113
Alignment explanation
Indices: 30449163--30449377 Score: 281
Period size: 112 Copynumber: 1.9 Consensus size: 113
30449153 CGGCACAAAA
* * * *
30449163 CCTACTAAGCACATAGCACGATAACACTGACACAAAGGCTTGCTAGGCACATAGCCCAATAACAC
1 CCTACTAAGCACATAGCACGATAACACCGACACAAAGGCCTACTAGGCACACAGCCCAATAACAC
* * *
30449228 CGGCACGAAGGCCTGTTAGTCGTAAAGCCCGATATCACGGGCATGAAG
66 CGGCACGAAGGCCTGCTAGGCATAAAGCCCGATATCACGGGCATGAAG
* * * * *
30449276 CCTACTAGGCACATAGC-CTGATAACACCGACACGAA-GCCTACTAGGCACACAGTCCGATATCA
1 CCTACTAAGCACATAGCAC-GATAACACCGACACAAAGGCCTACTAGGCACACAGCCCAATAACA
* *
30449339 CTGGCACGAAGGCCTGCTAGGCATAAAGCCTGATATCAC
65 CCGGCACGAAGGCCTGCTAGGCATAAAGCCCGATATCAC
30449378 TTGTATGTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
112 56 0.64
113 31 0.36
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (113 bp):
CCTACTAAGCACATAGCACGATAACACCGACACAAAGGCCTACTAGGCACACAGCCCAATAACAC
CGGCACGAAGGCCTGCTAGGCATAAAGCCCGATATCACGGGCATGAAG
Found at i:30454708 original size:30 final size:30
Alignment explanation
Indices: 30454674--30454734 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
30454664 ATTTTTAAGG
* *
30454674 AATTTAGGG-TCAAATTTGAAATTTTTGAAA
1 AATTT-GGGATCAAAGTTGAAATTTTGGAAA
* *
30454704 AATTTGGGATTAAAGTTGAACTTTTGGAAA
1 AATTTGGGATCAAAGTTGAAATTTTGGAAA
30454734 A
1 A
30454735 TTGGAGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGATCAAAGTTGAAATTTTGGAAA
Found at i:30454831 original size:30 final size:30
Alignment explanation
Indices: 30454766--30455043 Score: 232
Period size: 30 Copynumber: 9.4 Consensus size: 30
30454756 TCAGATGCTC
* *
30454766 GAGGGT-AAAATGATAATTTTTG-GAAATTC
1 GAGGGTAAAAATG-TAATTTTTGAGAAGTTT
*
30454795 AAGGGTAAAAATGTAATTTTTGAGAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTT
* * **
30454825 GGGGGTAAAAATGTGATTTTTG-GAAGTAC
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTT
* *
30454854 GAGGGTAAAAATGTGATTTTTGA-AAGTTC
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTT
* * *
30454883 GAGGGCAAAATTGTGATTTTTGAGAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTT
*
30454913 -AGGGGCAAAAATGTAATTTTTGA-AAG-TT
1 GA-GGGTAAAAATGTAATTTTTGAGAAGTTT
* * * *
30454941 CAGGGGTCAAAATGTGATTTTTAAGAAGTTT
1 GA-GGGTAAAAATGTAATTTTTGAGAAGTTT
* *
30454972 GACGGTCAAAATGTAATTTTTG-GAAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAG-AAGTTT
* * *
30455002 AAAGGTCAAAATGTAATTTTTTGGAGAA-TTT
1 GAGGGTAAAAATGTAA-TTTTT-GAGAAGTTT
*
30455033 GAGGGTCAAAA
1 GAGGGTAAAAA
30455044 CGTGATTTCG
Statistics
Matches: 210, Mismatches: 27, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.01
29 90 0.43
30 94 0.45
31 20 0.10
32 3 0.01
33 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
GAGGGTAAAAATGTAATTTTTGAGAAGTTT
Found at i:30454832 original size:88 final size:87
Alignment explanation
Indices: 30454735--30454932 Score: 213
Period size: 88 Copynumber: 2.2 Consensus size: 87
30454725 TTTTGGAAAA
* *
30454735 TTGGAGGTAAAATGGTAATTTTCAGATGCT-CGAGGGT-AAAATGATAATTTTTGGAAA-TTCAA
1 TTGGGGGTAAAAT-GTAATTTTCAGAAG-TACGAGGGTAAAAATG-TAATTTTT-GAAAGTTCAA
*
30454797 GGGTAAAAATGTAATTTTTGAGAAGT
62 GGGCAAAAATGTAATTTTTGAGAAGT
* ** * *
30454823 TTGGGGGTAAAAATGTGATTTTTGGAAGTACGAGGGTAAAAATGTGATTTTTGAAAGTTCGAGGG
1 TTGGGGGT-AAAATGTAATTTTCAGAAGTACGAGGGTAAAAATGTAATTTTTGAAAGTTCAAGGG
* *
30454888 CAAAATTGTGATTTTTGAGAAGT
65 CAAAAATGTAATTTTTGAGAAGT
**
30454911 TTAGGGGCAAAAATGTAATTTT
1 TT-GGGGGTAAAATGTAATTTT
30454933 TGAAAGTTCA
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
87 5 0.05
88 72 0.78
89 15 0.16
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (87 bp):
TTGGGGGTAAAATGTAATTTTCAGAAGTACGAGGGTAAAAATGTAATTTTTGAAAGTTCAAGGGC
AAAAATGTAATTTTTGAGAAGT
Found at i:30454844 original size:59 final size:58
Alignment explanation
Indices: 30454768--30455000 Score: 243
Period size: 59 Copynumber: 3.9 Consensus size: 58
30454758 AGATGCTCGA
* * *
30454768 GGGT-AAAATGATAATTTTTGGAAATTCAAGGGTAAAAATGTAATTTTTGAGAAGTTTGG
1 GGGTAAAAATG-TGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGA-AAGTTCGG
* * * *
30454827 GGGTAAAAATGTGATTTTTGGAAGTACGAGGGTAAAAATGTGATTTTTGAAAGTTCGA
1 GGGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAAAGTTCGG
* * * * * *
30454885 GGGCAAAATTGTGATTTTTGAGAAGTTTAGGGGCAAAAATGTAATTTTTGAAAGTTCAG
1 GGGTAAAAATGTGATTTTTG-GAAGTTCAAGGGTAAAAATGTAATTTTTGAAAGTTCGG
* * ** * *
30454944 GGGTCAAAATGTGATTTTTAAGAAGTTTGACGGTCAAAATGTAATTTTTGGAAAGTT
1 GGGTAAAAATGTGATTTTT-GGAAGTTCAAGGGTAAAAATGTAATTTTT-GAAAGTT
30455001 TAAAGGTCAA
Statistics
Matches: 144, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
58 24 0.17
59 107 0.74
60 13 0.09
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (58 bp):
GGGTAAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAAAGTTCGG
Found at i:30455064 original size:61 final size:60
Alignment explanation
Indices: 30454945--30455066 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 60
30454935 AAAGTTCAGG
* * * *
30454945 GGTCAAAATGTGATTTTTAAGAAGTTTGACGGTCAAAATGTAATTTTTGGAAAGTTTAAA
1 GGTCAAAATGTAATTTTTAAGAAGTTTGACGGTCAAAACGTAATTTTCGGAAAATTTAAA
* * *
30455005 GGTCAAAATGTAATTTTTTGGAGAA-TTTGAGGGTCAAAACGTGA-TTTCGAGAAAATTTAAA
1 GGTCAAAATGTAA-TTTTT-AAGAAGTTTGACGGTCAAAACGTAATTTTCG-GAAAATTTAAA
30455066 G
1 G
30455067 ACCTTTTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
60 16 0.31
61 32 0.62
62 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (60 bp):
GGTCAAAATGTAATTTTTAAGAAGTTTGACGGTCAAAACGTAATTTTCGGAAAATTTAAA
Found at i:30456650 original size:17 final size:17
Alignment explanation
Indices: 30456628--30456669 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
30456618 TTGGACTTTT
* *
30456628 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAACA
30456645 AATTTAAATTTAAAACA
1 AATTTAAATTTAAAACA
30456662 AATTTAAA
1 AATTTAAA
30456670 AAATGGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAACA
Found at i:30457200 original size:53 final size:53
Alignment explanation
Indices: 30457138--30457245 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
30457128 GATTTACCTT
*
30457138 AGGCTCGGGGTAAACGATTGAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAG
1 AGGCTCGGGGTAAAAGATTGAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAG
30457191 AGGCTCGGGGTAAAAGATTGAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAG
1 AGGCTCGGGGTAAAAGATTGAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAG
30457244 AG
1 AG
30457246 ATTGGCTGAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (53 bp):
AGGCTCGGGGTAAAAGATTGAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAG
Found at i:30457248 original size:39 final size:39
Alignment explanation
Indices: 30457191--30457718 Score: 272
Period size: 39 Copynumber: 13.5 Consensus size: 39
30457181 TCGGGGTAAG
*
30457191 AGGCTCGGGGTAAAAGATTGAATAGCTGCAATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
* * * **
30457230 AAGCTCGGGGTAAGAGATTGGCTGATAG-TG--ATTTGCCTT
1 AGGCTCGGGGTAAGAGATT-G--AATAGCTGCAATCTGCCCC
* ** * * *
30457269 AAGCTCGGGGTAAGAGATCAAATGGCTGTAATCTACCCC
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
* * * * **
30457308 AAGCTCGGGGTAAGGGATTGACT-GGTGGGGATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATAGCT-GCAATCTGCCCC
* * * * *
30457347 AGGTTCGAGGTAAGAGATCGAATGGCTGCAATTTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
*
30457386 AGGCTTGGGGTAAGAGATTGACTGATAG-TG--ATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGA---ATAGCTGCAATCTGCCCC
** * *
30457425 AGGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCTCC
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
** * * **
30457464 AGGCTTAGGGTAAGAGATTAGCTGATAG-T--AATCTACCTT
1 AGGCTCGGGGTAAGAGATT-G--AATAGCTGCAATCTGCCCC
* * * * * *
30457503 AGGTTTGGGGTAAGAGATCGAATGGCTACAATCTGCCCT
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
* * * * ** * **
30457542 AGGCTCGAGGTAAGGGATTGACT-GGTGGTGATTTATCCC
1 AGGCTCGGGGTAAGAGATTGAATAGCT-GCAATCTGCCCC
* *
30457581 AGGCTTGGGGTAAGAGATCGAATAGCTGCAATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
* * * **
30457620 AGGCTCAGGGTAAGAGATTGACTGATGGTG--ATCTATCCC
1 AGGCTCGGGGTAAGAGATTGAAT-A-GCTGCAATCTGCCCC
* * * * * *
30457659 AGGCTTGGGGTAAGAGATCGGATGGCTGCAATTTGCCCA
1 AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
**
30457698 AGGCTCAAGGTAAGAGATTGA
1 AGGCTCGGGGTAAGAGATTGA
30457719 CTGGTGGTGA
Statistics
Matches: 355, Mismatches: 108, Indels: 52
0.69 0.21 0.10
Matches are distributed among these distances:
36 9 0.03
37 8 0.02
38 5 0.01
39 309 0.87
40 6 0.02
41 8 0.02
42 10 0.03
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.24
Consensus pattern (39 bp):
AGGCTCGGGGTAAGAGATTGAATAGCTGCAATCTGCCCC
Found at i:30457327 original size:78 final size:78
Alignment explanation
Indices: 30457191--30457754 Score: 599
Period size: 78 Copynumber: 7.2 Consensus size: 78
30457181 TCGGGGTAAG
* * * * *
30457191 AGGCTCGGGGTAAAAGATTGAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGAT
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
* **
30457256 AGTGATTTGCCTT
66 AGTGATCTGCCCC
* * * * * * *
30457269 AAGCTCGGGGTAAGAGATCAAATGGCTGTAATCTACCCCAAGCTCGGGGTAAGGGATTGACTGGT
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
* *
30457334 GGGGATCTGCCCC
66 AGTGATCTGCCCC
* * * *
30457347 AGGTTCGAGGTAAGAGATCGAATGGCTGCAATTTGCCCCAGGCTTGGGGTAAGAGATTGACTGAT
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
30457412 AGTGATCTGCCCC
66 AGTGATCTGCCCC
* * **
30457425 AGGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCTCCAGGCTTAGGGTAAGAGATT-AGCTGA
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGA-CTGA
* * **
30457489 TAGTAATCTACCTT
65 TAGTGATCTGCCCC
* * * * * * *
30457503 AGGTTTGGGGTAAGAGATCGAATGGCTACAATCTGCCCTAGGCTCGAGGTAAGGGATTGACTGGT
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
* * **
30457568 GGTGATTTATCCC
66 AGTGATCTGCCCC
* * *
30457581 AGGCTTGGGGTAAGAGATCGAATAGCTGCAATCTGCCCCAGGCTCAGGGTAAGAGATTGACTGAT
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
* **
30457646 GGTGATCTATCCC
66 AGTGATCTGCCCC
* * * * ** *
30457659 AGGCTTGGGGTAAGAGATCGGATGGCTGCAATTTGCCCAAGGCTCAAGGTAAGAGATTGACTGGT
1 AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
* * *
30457724 GGTGATCTACTCC
66 AGTGATCTGCCCC
*
30457737 AGGCTCGGGATAAGAGAT
1 AGGCTCGGGGTAAGAGAT
30457755 TAGATCTACA
Statistics
Matches: 410, Mismatches: 74, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
77 1 0.00
78 408 1.00
79 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (78 bp):
AGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGAT
AGTGATCTGCCCC
Found at i:30458043 original size:99 final size:98
Alignment explanation
Indices: 30457932--30458649 Score: 655
Period size: 99 Copynumber: 7.3 Consensus size: 98
30457922 TGCTAGGTTT
* * * * * *
30457932 ACCGTTGCGGCCTCAACCTATCCCTTCATATCTTTATAGTATCGGGTTCACCGTTGAGGTCTCAA
1 ACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGAGGCCTCAA
* *
30457997 CCTTTCCCACCACATATTTTAAGGTACCGGATTC
66 CCTTTCCCATCACATCTTTT-AGGTACCGGATTC
* * * * * * *
30458031 ACCGTCGCGGCCTCAATCC-TTACTTTCATCTCTTCATGGTATCGGGTTCACCGTT-ACAGCCTC
1 ACCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGA-GGCCTC
* *
30458094 AACC-TTCTCATCACATCTTTTTAGGTACCGGGTTC
64 AACCTTTCCCATCACATC-TTTTAGGTACCGGATTC
* * * * *
30458129 ACCGTTGCAGCCTCAACCTTTCCATTCATATCTTCATGGTACCAGATTCGCCGTT-ACGACCTCA
1 ACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGA-GGCCTCA
*
30458193 ACCTTTCCCATCACATCTTCTAAGGTACCGGATTC
65 ACCTTTCCCATCACATCTT-TTAGGTACCGGATTC
* * * * * * ** * *
30458228 GCTGTCGCGACCTCAATCC-TTCCCTTCATCTCTTCCTGGTACTAGGTTCACCGTTGCA-GCCTT
1 ACCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTG-AGGCCTC
*
30458291 AACCTTTCCCATCACATCTTCTTAGGTATCAGG-TTC
64 AACCTTTCCCATCACATCTT-TTAGGTA-CCGGATTC
* * * * * *
30458327 GCCGTTGCGGCCTCAACCTTTCCCTTCGTATCTTTCGTGGTACCGGGTTCGTCATTGCA-ACCTC
1 ACCGTTGCGGCCTCAACCTTTCCCTTCATATC-TTCATGGTACCGGGTTCGCCGTTG-AGGCCTC
* *
30458391 AACCTTTCCTATCACATCTTCTTAGGTACCGGGTTC
64 AACCTTTCCCATCACATCTT-TTAGGTACCGGATTC
* * * * *
30458427 ACCGTTGCAGCCTCAACCTTTCCCTTTATATCTTCATGGTACCGGGTTCGCCATTGCGACCTCAA
1 ACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGAGGCCTCAA
* * *
30458492 CCTTTCCCATCACATCTTCTTAGGTATCGGGTTT
66 CCTTTCCCATCACATCTT-TTAGGTACCGGATTC
* * * * * * * *
30458526 ACTGTTACGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCGCCTTTGCGGCCTCA
1 ACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTACCGGGTTCGCCGTTGAGGCCTCA
* *
30458591 ACCTTTCCCTTCA-ATCTTTTAAGGTACCAGATTC
65 ACCTTTCCCATCACATCTTTT-AGGTACCGGATTC
* *
30458625 GCCGTCGCGGCCTCAATCC-TTCCCT
1 ACCGTTGCGGCCTCAA-CCTTTCCCT
30458650 GTCAAACCTG
Statistics
Matches: 515, Mismatches: 87, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
97 2 0.00
98 82 0.16
99 304 0.59
100 126 0.24
101 1 0.00
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (98 bp):
ACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGAGGCCTCAA
CCTTTCCCATCACATCTTTTAGGTACCGGATTC
Found at i:30458046 original size:50 final size:50
Alignment explanation
Indices: 30457927--30458645 Score: 502
Period size: 50 Copynumber: 14.5 Consensus size: 50
30457917 TAAGGTGCTA
* * * * *
30457927 GGTTTACCGTTGCGGCCTCAACCTATCCCTTCATATC-TTTATA-GTATCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTA-AGGTACCG
* * * *
30457976 GGTTCACCGTTGAGGTCTCAACCTTTCCCACCACATATTTTAAGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * * ** * * *
30458026 GATTCACCGTCGCGGCCTCAATCC-TT-AC-TTTCATCTCTTCATGGTATCG
1 GGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCACATCT-TTTAAGGTACCG
* * * *
30458075 GGTTCACCGTTACAGCCTCAACC-TTCTCATCACATCTTTTTAGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * * * *
30458124 GGTTCACCGTTGCAGCCTCAACCTTT-CCATTCATATC-TTCATGGTACCA
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCA-TCACATCTTTTAAGGTACCG
* * * * *
30458173 GATTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * * * * * * **
30458223 GATTCGCTGTCGCGACCTCAATCC-TTCCCTTCATC-TCTTCCT--GGTACTA
1 GGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCA-CATCTT-TTAAGGTACCG
* * * *
30458272 GGTTCACCGTTGCAGCCTTAACCTTTCCCATCACATCTTCTT-AGGTATCA
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAGGTACCG
* * ** ***
30458322 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCGTATCTTTCGTGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
** * ** *
30458372 GGTTCGTCATTGCAACCTCAACCTTTCCTATCACATCTTCTT-AGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAGGTACCG
* * * * * *
30458422 GGTTCACCGTTGCAGCCTCAACCTTTCCCTTTATATC-TTCATGGTACCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * * *
30458471 GGTTCGCCATTGCGACCTCAACCTTTCCCATCACATCTTCTT-AGGTATCG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAGGTACCG
* * * *
30458521 GGTTTACTGTTACGGCCTCAACCTTTCCCATCACATCTTCTT-AGGTACTG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAGGTACCG
* * * *
30458571 GGTTCGCCTTTGCGGCCTCAACCTTTCCCTTCA-ATCTTTTAAGGTACCA
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * *
30458620 GATTCGCCGTCGCGGCCTCAATCCTT
1 GGTTCACCGTTGCGGCCTCAA-CCTT
30458646 CCCTGTCAAA
Statistics
Matches: 522, Mismatches: 125, Indels: 45
0.75 0.18 0.07
Matches are distributed among these distances:
48 14 0.03
49 226 0.43
50 273 0.52
51 9 0.02
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (50 bp):
GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
Found at i:30458648 original size:149 final size:149
Alignment explanation
Indices: 30457927--30458645 Score: 615
Period size: 149 Copynumber: 4.8 Consensus size: 149
30457917 TAAGGTGCTA
* * * *
30457927 GGTTTACCGTTGCGGCCTCAACCTATCCCTTCATATCTT-TATA-GTA-TCGGGTTCACCGTTG-
1 GGTTTACTGTTGCGGCCTCAACCTTTCCCATCACATCTTCT-TAGGTACT-GGGTTCACCGTTGC
* ** * * * *
30457988 AGGTCTCAACCTTTCCCACCACATATTTTAAGGTACCGGATTCACCGTCGCGGCCTCAATCC-TT
64 A-GCCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCGTTGCGGCCTCAA-CCTTT
* ** * *
30458052 ACTTTCATC-TCTTCATGGTATCG
127 CCCATCA-CATCTTCTTGGTACCG
* * * * * * *
30458075 GGTTCACCGTTACAGCCTCAACC-TTCTCATCACATCTTTTTAGGTACCGGGTTCACCGTTGCAG
1 GGTTTACTGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCACCGTTGCAG
* * * * * *
30458139 CCTCAACCTTTCCATTCATATC-TTCATGGTACCAGATTCGCCGTTACGACCTCAACCTTTCCCA
66 CCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCGTTGCGGCCTCAACCTTTCCCA
*
30458203 TCACATCTTCTAAGGTACCG
131 TCACATCTTCT-TGGTACCG
* ** * * * * *
30458223 GATTCGCTGTCGCGACCTCAATCC-TTCCCTTCATC-TCTTCCT-GGTACTAGGTTCACCGTTGC
1 GGTTTACTGTTGCGGCCTCAA-CCTTTCCCATCA-CATCTTCTTAGGTACTGGGTTCACCGTTGC
* * * *
30458285 AGCCTTAACCTTTCCCATCACATCTTCTT-AGGTATCAGGTTCGCCGTTGCGGCCTCAACCTTTC
64 AGCCTCAACCTTTCCCTTCACATCTT-TTAAGGTACCAGATTCGCCGTTGCGGCCTCAACCTTTC
* ** *
30458349 CCTTCGTATCTTTCGTGGTACCG
128 CCATCACATC-TTCTTGGTACCG
* ** * *
30458372 GG-TT-CGTCATTGCAACCTCAACCTTTCCTATCACATCTTCTTAGGTACCGGGTTCACCGTTGC
1 GGTTTAC-T-GTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCACCGTTGC
* * * * * * * *
30458435 AGCCTCAACCTTTCCCTTTATATC-TTCATGGTACCGGGTTCGCCATTGCGACCTCAACCTTTCC
64 AGCCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCGTTGCGGCCTCAACCTTTCC
*
30458499 CATCACATCTTCTTAGGTATCG
129 CATCACATCTTCTT-GGTACCG
* * * *
30458521 GGTTTACTGTTACGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCGCCTTTGCGG
1 GGTTTACTGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCACCGTTGCAG
*
30458586 CCTCAACCTTTCCCTTCA-ATCTTTTAAGGTACCAGATTCGCCGTCGCGGCCTCAATCCTT
66 CCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCGTTGCGGCCTCAA-CCTT
30458646 CCCTGTCAAA
Statistics
Matches: 451, Mismatches: 97, Indels: 44
0.76 0.16 0.07
Matches are distributed among these distances:
146 3 0.01
147 51 0.11
148 125 0.28
149 221 0.49
150 50 0.11
151 1 0.00
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (149 bp):
GGTTTACTGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCACCGTTGCAG
CCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCGTTGCGGCCTCAACCTTTCCCA
TCACATCTTCTTGGTACCG
Found at i:30459583 original size:20 final size:20
Alignment explanation
Indices: 30459559--30459602 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
30459549 TCGACCTCTC
* *
30459559 TTTTTTTTTCCTATTTTTTTA
1 TTTTCTTTTCCT-TTTATTTA
*
30459580 TTTTCTTTTTCTTTTATTTA
1 TTTTCTTTTCCTTTTATTTA
30459600 TTT
1 TTT
30459603 ATTTATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTCCTTTTATTTA
Found at i:30465482 original size:29 final size:30
Alignment explanation
Indices: 30465450--30465791 Score: 229
Period size: 30 Copynumber: 11.6 Consensus size: 30
30465440 AGATACTCAG
30465450 GGGT-AAAATGGTGATTTTTGGAAA-TTCAA
1 GGGTAAAAAT-GTGATTTTTGGAAAGTTCAA
** * * *
30465479 GGGTAAAAAAATAATTTTT-AAGAAGTTCGA
1 GGGTAAAAATGTGATTTTTGGA-AAGTTCAA
* * *
30465509 GAGTAAAAATGTGATTTTT-AAAAGTACAA
1 GGGTAAAAATGTGATTTTTGGAAAGTTCAA
* * ***
30465538 GCGTAAAAATGTGATTCTT-GAAAGTTTGG
1 GGGTAAAAATGTGATTTTTGGAAAGTTCAA
*
30465567 GGGTAAAAATGTGATTTTT-GAGAAGTTTAA
1 GGGTAAAAATGTGATTTTTGGA-AAGTTCAA
* * **
30465597 GGGTAAAAATGTAAATTTT-GAAAGTT-TG
1 GGGTAAAAATGTGATTTTTGGAAAGTTCAA
* *
30465625 GGGTTAAAATGTGATTTTT-AAGAAGTTCAA
1 GGGTAAAAATGTGATTTTTGGA-AAGTTCAA
* *
30465655 GGGTTAAAATGTAATTTTTGGAAAGTTCAA
1 GGGTAAAAATGTGATTTTTGGAAAGTTCAA
* * * **
30465685 AGGTCAAAATGTAATTTTTGGAAAGTTTGA
1 GGGTAAAAATGTGATTTTTGGAAAGTTCAA
* *
30465715 TGGTTAAAATGTAGA-TTTTGGAAAGTT-AA
1 GGGTAAAAATGT-GATTTTTGGAAAGTTCAA
* * * * *
30465744 GGGTCAAAATGTAATTTTTTGGAGACTTTAA
1 GGGTAAAAATGTGA-TTTTTGGAAAGTTCAA
* *
30465775 GGGTCAAAACGTGATTT
1 GGGTAAAAATGTGATTT
30465792 CAAGAAAATT
Statistics
Matches: 253, Mismatches: 49, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
28 19 0.08
29 81 0.32
30 137 0.54
31 16 0.06
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
GGGTAAAAATGTGATTTTTGGAAAGTTCAA
Found at i:30465575 original size:58 final size:56
Alignment explanation
Indices: 30465449--30465762 Score: 227
Period size: 59 Copynumber: 5.4 Consensus size: 56
30465439 CAGATACTCA
* ** * *
30465449 GGGGT-AAAATGGTGATTTTTGGAAA-TTCAAGGGTAAAAAAATAATTTTTAAGAAGTTC
1 GGGGTAAAAAT-GTGATTTTT-AAAAGTTCAAGGGTAAAAATGTAA-TTTTGA-AAGTTT
* * * *
30465507 GAGAGTAAAAATGTGATTTTTAAAAGTACAAGCGTAAAAATGTGATTCTTGAAAGTTT
1 G-GGGTAAAAATGTGATTTTTAAAAGTTCAAGGGTAAAAATGTAATT-TTGAAAGTTT
* *
30465565 GGGGGTAAAAATGTGATTTTTGAGAAGTTTAAGGGTAAAAATGTAAATTTTGAAAGTTT
1 -GGGGTAAAAATGTGATTTTT-AAAAGTTCAAGGGTAAAAATGT-AATTTTGAAAGTTT
* * *
30465624 GGGGTTAAAATGTGATTTTTAAGAAGTTCAAGGGTTAAAATGTAATTTTTGGAAAGTTCA
1 GGGGTAAAAATGTGATTTTTAA-AAGTTCAAGGGTAAAAATGTAA-TTTT-GAAAGTT-T
** * * * ** * * *
30465684 AAGGTCAAAATGTAATTTTTGGAAAGTTTGATGGTTAAAATGTAGATTTTGGAAAGTTA
1 GGGGTAAAAATGTGATTTTT-AAAAGTTCAAGGGTAAAAATGTA-ATTTT-GAAAGTTT
* * *
30465743 AGGGTCAAAATGTAATTTTT
1 GGGGTAAAAATGTGATTTTT
30465763 TGGAGACTTT
Statistics
Matches: 214, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.01
58 70 0.33
59 85 0.40
60 54 0.25
61 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (56 bp):
GGGGTAAAAATGTGATTTTTAAAAGTTCAAGGGTAAAAATGTAATTTTGAAAGTTT
Found at i:30467578 original size:17 final size:17
Alignment explanation
Indices: 30467541--30467598 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
30467531 TTGGACTTTT
* *
30467541 AATTTAAA-TTAGAATA
1 AATTTAAACTTAAAACA
**
30467557 AATTTAATTTTAAAACA
1 AATTTAAACTTAAAACA
*
30467574 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAACA
30467591 AATTTAAA
1 AATTTAAA
30467599 AAATGGGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
16 7 0.20
17 28 0.80
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
AATTTAAACTTAAAACA
Found at i:30470408 original size:38 final size:38
Alignment explanation
Indices: 30470357--30470707 Score: 318
Period size: 38 Copynumber: 9.3 Consensus size: 38
30470347 CCGACACAAA
*
30470357 GCCTACTAGGCACATAGCCCGATAACACTGGCACGAAG
1 GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
* *
30470395 GCCTACTAGGCACATAGACCGATAACACCAGCACGAAG
1 GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
* * * * * * *
30470433 G-CTAGCTAGGAATAAAGCTCGATATCACTGGCAC-AAA
1 GCCTA-CTAGGCACATAGCCCGATAACACCGGCACGAAG
* * *
30470470 TCCTACTAGGCACATAGCCCGATAACATCGACACGAAG
1 GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
* * *
30470508 GCCTACTAAGCACATAGACTGATAACACCGGCACGAA-
1 GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
* * * * * *
30470545 GACTAGCTAGGCATAAAGCCTGATATCACCAGCACGAA-
1 GCCTA-CTAGGCACATAGCCCGATAACACCGGCACGAAG
* * * * *
30470583 GCTTGCTGGGCACATAGCCTGATAACACCAGCACGAAG
1 GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
* * * *
30470621 GCCTATTAGG-AGTAAAGCCCGATATCACCGGCACGAA-
1 GCCTACTAGGCA-CATAGCCCGATAACACCGGCACGAAG
* * * *
30470658 GCATGCTAGGCACATAGCCTGATAACACCGACACGAAG
1 GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
30470696 GCCTACTAGGCA
1 GCCTACTAGGCA
30470708 TAAAGCCTGA
Statistics
Matches: 244, Mismatches: 61, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
37 86 0.35
38 158 0.65
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (38 bp):
GCCTACTAGGCACATAGCCCGATAACACCGGCACGAAG
Found at i:30470551 original size:113 final size:112
Alignment explanation
Indices: 30470351--30470625 Score: 372
Period size: 113 Copynumber: 2.4 Consensus size: 112
30470341 TGAATACCGA
* *
30470351 CACAAAGCCTACTAGGCACATAGCCCGATAACACTGGCACGAAGGCCTACTAGGCACATAGACCG
1 CACAAAGCCTACTAGGCACATAGCCCGATAACAC-GACACGAAGGCCTACTAAGCACATAGACCG
* **
30470416 ATAACACCAGCACGAAGGCTAGCTAGGAATAAAG-CTCGATATCACTGG
65 ATAACACCAGCACGAAGACTAGCTAGGAATAAAGCCT-GATATCACCAG
* *
30470464 CACAAATCCTACTAGGCACATAGCCCGATAACATCGACACGAAGGCCTACTAAGCACATAGACTG
1 CACAAAGCCTACTAGGCACATAGCCCGATAACA-CGACACGAAGGCCTACTAAGCACATAGACCG
* *
30470529 ATAACACCGGCACGAAGACTAGCTAGGCATAAAGCCTGATATCACCAG
65 ATAACACCAGCACGAAGACTAGCTAGGAATAAAGCCTGATATCACCAG
* * * * * *
30470577 CACGAAGCTTGCTGGGCACATAGCCTGATAACACCAGCACGAAGGCCTA
1 CACAAAGCCTACTAGGCACATAGCCCGATAACACGA-CACGAAGGCCTA
30470626 TTAGGAGTAA
Statistics
Matches: 143, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
112 2 0.01
113 138 0.97
114 3 0.02
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (112 bp):
CACAAAGCCTACTAGGCACATAGCCCGATAACACGACACGAAGGCCTACTAAGCACATAGACCGA
TAACACCAGCACGAAGACTAGCTAGGAATAAAGCCTGATATCACCAG
Found at i:30470650 original size:113 final size:110
Alignment explanation
Indices: 30470346--30470707 Score: 365
Period size: 113 Copynumber: 3.2 Consensus size: 110
30470336 CTCGATGAAT
* * *
30470346 ACCGACACAAAGCCTACTAGGCACATAGCCCGATAACACTGGCACGAAGGCCTACTAGGCA-CAT
1 ACCG-CACGAAGCCTACTAGGCACATAGCCCGATAACAC-CGCACGAAGGCCTACTAGG-AGCAA
* *
30470410 AGACCGATAACACCAGCACGAAGGCTAGCTAGGAATAAAG-CTCGATATC
63 AGACCGATAACACCGGCACGAA-GCTAGCTAGGCATAAAGCCT-GATATC
* * * *
30470459 ACTGGCACAAATCCTACTAGGCACATAGCCCGATAACATCGACACGAAGGCCTACTA--AGCACA
1 AC-CGCACGAAGCCTACTAGGCACATAGCCCGATAACACCG-CACGAAGGCCTACTAGGAGCA-A
*
30470522 TAGACTGATAACACCGGCACGAAGACTAGCTAGGCATAAAGCCTGATATC
63 -AGACCGATAACACCGGCACGAAG-CTAGCTAGGCATAAAGCCTGATATC
* * * * * *
30470572 ACCAGCACGAAGCTTGCTGGGCACATAGCCTGATAACACCAGCACGAAGGCCTATTAGGAGTAAA
1 ACC-GCACGAAGCCTACTAGGCACATAGCCCGATAACACC-GCACGAAGGCCTACTAGGAGCAAA
* * * * *
30470637 GCCCGATATCACCGGCACGAAGC-ATGCTAGGCACATAGCCTGATAAC
64 GACCGATAACACCGGCACGAAGCTA-GCTAGGCATAAAGCCTGATATC
30470684 ACCGACACGAAGGCCTACTAGGCA
1 ACCG-CACGAA-GCCTACTAGGCA
30470708 TAAAGCCTGA
Statistics
Matches: 208, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
110 1 0.00
111 4 0.02
112 31 0.15
113 164 0.79
114 5 0.02
115 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (110 bp):
ACCGCACGAAGCCTACTAGGCACATAGCCCGATAACACCGCACGAAGGCCTACTAGGAGCAAAGA
CCGATAACACCGGCACGAAGCTAGCTAGGCATAAAGCCTGATATC
Found at i:30470712 original size:75 final size:75
Alignment explanation
Indices: 30470362--30470723 Score: 351
Period size: 75 Copynumber: 4.8 Consensus size: 75
30470352 ACAAAGCCTA
* * * * * *
30470362 CTAGGCACATAGCCCGATAACACTGGCACGAAGGCCTACTAGGCACATAGACCGATAACACCAGC
1 CTAGGCACATAGCCTGATAACACCGGCACGAAGGCCTACTAGGCATAAAGCCCGATATCACCAGC
30470427 ACGAAGGCTAG
66 ACGAAGGCT-G
* * * * * ** * * * *
30470438 CTAGGAATAAAG-CTCGATATCACTGGCAC-AAATCCTACTAGGCACATAGCCCGATAACATC-G
1 CTAGGCACATAGCCT-GATAACACCGGCACGAAGGCCTACTAGGCATAAAGCCCGATATCACCAG
*
30470500 ACACGAAGGCCTA
65 -CACGAAGG-CTG
* * * *
30470513 CTAAGCACATAGACTGATAACACCGGCACGAA-GACTAGCTAGGCATAAAGCCTGATATCACCAG
1 CTAGGCACATAGCCTGATAACACCGGCACGAAGGCCTA-CTAGGCATAAAGCCCGATATCACCAG
30470577 CACGAA-GCTTG
65 CACGAAGGC-TG
* * * *
30470588 CTGGGCACATAGCCTGATAACACCAGCACGAAGGCCTATTAGG-AGTAAAGCCCGATATCACCGG
1 CTAGGCACATAGCCTGATAACACCGGCACGAAGGCCTACTAGGCA-TAAAGCCCGATATCACCAG
30470652 CACGAA-GCATG
65 CACGAAGGC-TG
* *
30470663 CTAGGCACATAGCCTGATAACACCGACACGAAGGCCTACTAGGCATAAAGCCTGATATCAC
1 CTAGGCACATAGCCTGATAACACCGGCACGAAGGCCTACTAGGCATAAAGCCCGATATCAC
30470724 TTATATGCAA
Statistics
Matches: 237, Mismatches: 38, Indels: 23
0.80 0.13 0.08
Matches are distributed among these distances:
74 3 0.01
75 175 0.74
76 58 0.24
77 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (75 bp):
CTAGGCACATAGCCTGATAACACCGGCACGAAGGCCTACTAGGCATAAAGCCCGATATCACCAGC
ACGAAGGCTG
Found at i:30481235 original size:2 final size:2
Alignment explanation
Indices: 30481228--30481263 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
30481218 CCACATGCAT
30481228 GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30481264 GGTACAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30483739 original size:32 final size:32
Alignment explanation
Indices: 30483698--30483762 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
30483688 AATTTTAAAA
30483698 TTCCTCATTGAAACACACCCTAAGAAAGGAAC
1 TTCCTCATTGAAACACACCCTAAGAAAGGAAC
30483730 TTCCTCATTGAAACACACCCTAAGAAAGGAAC
1 TTCCTCATTGAAACACACCCTAAGAAAGGAAC
30483762 T
1 T
30483763 AAACCATGTA
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:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (32 bp):
TTCCTCATTGAAACACACCCTAAGAAAGGAAC
Found at i:30484270 original size:13 final size:13
Alignment explanation
Indices: 30484252--30484279 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30484242 AAATAAGGAC
30484252 TAGTCTTATTGCA
1 TAGTCTTATTGCA
30484265 TAGTCTTATTGCA
1 TAGTCTTATTGCA
30484278 TA
1 TA
30484280 CTATTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
TAGTCTTATTGCA
Found at i:30484547 original size:330 final size:331
Alignment explanation
Indices: 30483946--30484599 Score: 1301
Period size: 330 Copynumber: 2.0 Consensus size: 331
30483936 TACAACTAGA
30483946 CATACTATTATTCAAGTAACAACCAACCTGGCATGTGATAAAAGTTCATACTCAACAATCTCATC
1 CATACTATTATTCAAGTAACAACCAACCTGGCATGTGATAAAAGTTCATACTCAACAATCTCATC
30484011 CACAATTAATTGATCAAATCATGAATACAAGCATCAATTTTCCCCAAACCTTCTTCCTTGTATCG
66 CACAATTAATTGATCAAATCATGAATACAAGCATCAATTTTCCCCAAACCTTCTTCCTTGTATCG
30484076 TGTGTTATGACCTATCATGGCTGATGGTTCAGCTCATCAAAGGGAGACTGAAACCTTCCAGCTCA
131 TGTGTTATGACCTATCATGGCTGATGGTTCAGCTCATCAAAGGGAGACTGAAACCTTCCAGCTCA
30484141 TCAAAAGGAGACAAAACCCGTAGGACTTGGTAGTGAAAGACCCAAAACTCTATGGTTTTTGATAG
196 TCAAAAGGAGACAAAACCCGTAGGACTTGGTAGTGAAAGACCCAAAACTCTATGGTTTTTGATAG
30484206 AAATTCTGCTTCGGGTTTATTATTCCATGAGTCC-TTAAATAAGGACTAGTCTTATTGCATAGTC
261 AAATTCTGCTTCGGGTTTATTATTCCATGAGTCCTTTAAATAAGGACTAGTCTTATTGCATAGTC
30484270 TTATTG
326 TTATTG
30484276 CATACTATTATTCAAGTAACAACCAACCTGGCATGTGATAAAAGTTCATACTCAACAATCTCATC
1 CATACTATTATTCAAGTAACAACCAACCTGGCATGTGATAAAAGTTCATACTCAACAATCTCATC
30484341 CACAATTAATTGATCAAATCATGAATACAAGCATCAATTTTCCCCAAACCTTCTTCCTTGTATCG
66 CACAATTAATTGATCAAATCATGAATACAAGCATCAATTTTCCCCAAACCTTCTTCCTTGTATCG
30484406 TGTGTTATGACCTATCATGGCTGATGGTTCAGCTCATCAAAGGGAGACTGAAACCTTCCAGCTCA
131 TGTGTTATGACCTATCATGGCTGATGGTTCAGCTCATCAAAGGGAGACTGAAACCTTCCAGCTCA
30484471 TCAAAAGGAGACAAAACCCGTAGGACTTGGTAGTGAAAGACCCAAAACTCTATGGTTTTTGATAG
196 TCAAAAGGAGACAAAACCCGTAGGACTTGGTAGTGAAAGACCCAAAACTCTATGGTTTTTGATAG
30484536 AAATTCTGCTTCGGGTTTATTATTCCATGAGTCCTTTAAATAAGGACTAGTCTTATTGCATAGT
261 AAATTCTGCTTCGGGTTTATTATTCCATGAGTCCTTTAAATAAGGACTAGTCTTATTGCATAGT
30484600 TAGGAAACCT
Statistics
Matches: 323, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
330 294 0.91
331 29 0.09
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (331 bp):
CATACTATTATTCAAGTAACAACCAACCTGGCATGTGATAAAAGTTCATACTCAACAATCTCATC
CACAATTAATTGATCAAATCATGAATACAAGCATCAATTTTCCCCAAACCTTCTTCCTTGTATCG
TGTGTTATGACCTATCATGGCTGATGGTTCAGCTCATCAAAGGGAGACTGAAACCTTCCAGCTCA
TCAAAAGGAGACAAAACCCGTAGGACTTGGTAGTGAAAGACCCAAAACTCTATGGTTTTTGATAG
AAATTCTGCTTCGGGTTTATTATTCCATGAGTCCTTTAAATAAGGACTAGTCTTATTGCATAGTC
TTATTG
Found at i:30490353 original size:4 final size:4
Alignment explanation
Indices: 30490344--30490375 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
30490334 TTTATAGTCG
30490344 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
30490376 ATATGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:30495892 original size:233 final size:233
Alignment explanation
Indices: 30495476--30495937 Score: 762
Period size: 233 Copynumber: 2.0 Consensus size: 233
30495466 AAAGCCAGAA
* *
30495476 CTCACATTTGCTGAATTTTGTGTACAACTATTTTTCTCGCAAAATCTATAATACCTCTCTCAGAT
1 CTCACATTTGCTAAATTTTGTGTACAACTATTTTTCTCGCAAAATCTACAATACCTCTCTCAGAT
** *
30495541 GTTGAGTATGCTCTAACTCCGTTCTGGAATAAATCAGTATGTCATCAATAAATACAACCACAAAT
66 ACTGACTATGCTCTAACTCCGTTCTGGAATAAATCAGTATGTCATCAATAAATACAACCACAAAT
* *** * *
30495606 CTATTTAACTGAGGCTAAAACACTCATTTTATTAAATCCATAAATGCTGATAGGGTTTTAGTTAA
131 CTATTTAACTGAGGCTAAAACACTCAGTTTATTAAATCCATAAAAAATGATAGGGTGTTAGTCAA
30495671 CCCAAACGACATTACCAGAAACTCGTAATGTCCACACC
196 CCCAAACGACATTACCAGAAACTCGTAATGTCCACACC
*
30495709 CTCACATTTGCTAAATTTTGTGTGCAACTATTTTTCTCGCAAAATCTACAATACCTCTCTCAGAT
1 CTCACATTTGCTAAATTTTGTGTACAACTATTTTTCTCGCAAAATCTACAATACCTCTCTCAGAT
* *
30495774 ACTGACTATGCTCTAACTCCGTTTTGGAATAAATCAGTATGTCATCGATAAATACAACCACAAAT
66 ACTGACTATGCTCTAACTCCGTTCTGGAATAAATCAGTATGTCATCAATAAATACAACCACAAAT
* * *
30495839 CTATTTAATTGAGGCTAGAACAGTCAGTTTATTAAATCCATAAAAAATGATAGGGTGTTAGTCAA
131 CTATTTAACTGAGGCTAAAACACTCAGTTTATTAAATCCATAAAAAATGATAGGGTGTTAGTCAA
*
30495904 CCCGAACGACATTACCAGAAACTCGTAATGTCCA
196 CCCAAACGACATTACCAGAAACTCGTAATGTCCA
30495938 TACCTGGTTT
Statistics
Matches: 211, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
233 211 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (233 bp):
CTCACATTTGCTAAATTTTGTGTACAACTATTTTTCTCGCAAAATCTACAATACCTCTCTCAGAT
ACTGACTATGCTCTAACTCCGTTCTGGAATAAATCAGTATGTCATCAATAAATACAACCACAAAT
CTATTTAACTGAGGCTAAAACACTCAGTTTATTAAATCCATAAAAAATGATAGGGTGTTAGTCAA
CCCAAACGACATTACCAGAAACTCGTAATGTCCACACC
Found at i:30501979 original size:18 final size:18
Alignment explanation
Indices: 30501952--30501990 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
30501942 CAACCTAATT
30501952 CAAATACAAA-TTTAACC
1 CAAATACAAACTTTAACC
30501969 CAAATTACAAACTTTAACC
1 CAAA-TACAAACTTTAACC
30501988 CAA
1 CAA
30501991 GTCTAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
CAAATACAAACTTTAACC
Found at i:30502200 original size:18 final size:19
Alignment explanation
Indices: 30502163--30502204 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
30502153 CTCCTTAGCT
*
30502163 CCCGAGACCTTTTCCACTG
1 CCCGAGACCTCTTCCACTG
*
30502182 CCCGAGACC-CTTCCTCTG
1 CCCGAGACCTCTTCCACTG
30502200 CCCGA
1 CCCGA
30502205 AGCCTCCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.14, C:0.48, G:0.17, T:0.21
Consensus pattern (19 bp):
CCCGAGACCTCTTCCACTG
Found at i:30509240 original size:20 final size:19
Alignment explanation
Indices: 30509199--30509241 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
30509189 GCTAAAATTT
*
30509199 ATTTTAAATCTATTTAATA
1 ATTTTAAATCTATATAATA
30509218 ATTTTAAAATCTGATATAA-A
1 ATTTT-AAATCT-ATATAATA
30509238 ATTT
1 ATTT
30509242 ACCTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTAAATCTATATAATA
Found at i:30510463 original size:30 final size:31
Alignment explanation
Indices: 30510398--30510468 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
30510388 TTACCAATTA
*
30510398 TTTTCTTGCACTTTAAATTCTTGCAATTTAC
1 TTTTCTCGCACTTTAAATTCTTGCAATTTAC
*
30510429 -TTTCTCGTACTTTAAATT-TATGC-ATTTAC
1 TTTTCTCGCACTTTAAATTCT-TGCAATTTAC
*
30510458 TTTTCTTGCAC
1 TTTTCTCGCAC
30510469 CAAAACAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTTCTCGCACTTTAAATTCTTGCAATTTAC
Found at i:30510672 original size:16 final size:16
Alignment explanation
Indices: 30510599--30510722 Score: 58
Period size: 17 Copynumber: 7.4 Consensus size: 16
30510589 GTTATTTTGC
*
30510599 TTATTCTTATTCTTTA
1 TTATTTTTATTCTTTA
* *
30510615 TAATTTTTAATACGTTTTA
1 TTATTTTT-ATTC--TTTA
* *
30510634 TTATTATCATTAC-TTA
1 TTATTTTTATT-CTTTA
30510650 TTATATTTTTATTCTTTA
1 -T-TATTTTTATTCTTTA
* *
30510668 TTA-TTTT-TTATGTA
1 TTATTTTTATTCTTTA
*
30510682 TTATATTTTATAC-TTA
1 TTAT-TTTTATTCTTTA
30510698 TTATATTTTTATTCTTTA
1 -T-TATTTTTATTCTTTA
30510716 TATATTT
1 T-TATTT
30510723 ATACACTTAT
Statistics
Matches: 80, Mismatches: 15, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
14 8 0.10
15 4 0.05
16 17 0.21
17 22 0.28
18 19 0.24
19 10 0.12
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATTTTTATTCTTTA
Found at i:30510677 original size:17 final size:17
Alignment explanation
Indices: 30510647--30510722 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
30510637 TTATCATTAC
30510647 TTATTATATTTTTATTCT
1 TTATTAT-TTTTTATTCT
30510665 TTATTATTTTTTA---T
1 TTATTATTTTTTATTCT
* * *
30510679 GTATTATATTTTATAC-
1 TTATTATTTTTTATTCT
30510695 TTATTATATTTTTATTCT
1 TTATTAT-TTTTTATTCT
30510713 TTATATATTT
1 TTAT-TATTT
30510723 ATACACTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 12 0.26
16 6 0.13
17 13 0.28
18 13 0.28
19 3 0.06
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (17 bp):
TTATTATTTTTTATTCT
Found at i:30510688 original size:32 final size:31
Alignment explanation
Indices: 30510648--30510726 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
30510638 TATCATTACT
*
30510648 TATTATATTTTTATTCTTTATTAT-TTTTTATG
1 TATTATA-TTTTATAC-TTATTATATTTTTATG
30510680 TATTATATTTTATACTTATTATATTTTTAT-
1 TATTATATTTTATACTTATTATATTTTTATG
*
30510710 TCTTTATATATTTATAC
1 T-ATTATAT-TTTATAC
30510727 ACTTATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 8 0.19
31 20 0.48
32 14 0.33
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (31 bp):
TATTATATTTTATACTTATTATATTTTTATG
Found at i:30510739 original size:34 final size:33
Alignment explanation
Indices: 30510683--30510753 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
30510673 TTTTATGTAT
* * *
30510683 TATATTTTATACTTATTATATTTTTATTCTTTA
1 TATATTTTACACTTATTATATTTCTATTCCTTA
*
30510716 TATATTTATACACTTATTTTATTTCTATTCCTTA
1 TATATTT-TACACTTATTATATTTCTATTCCTTA
30510750 TATA
1 TATA
30510754 AATCTAATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (33 bp):
TATATTTTACACTTATTATATTTCTATTCCTTA
Found at i:30511916 original size:22 final size:22
Alignment explanation
Indices: 30511873--30511919 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
30511863 GCTTTGAGAG
* *
30511873 ATTTTTGAGAATTTAGTGAGAA
1 ATTTTAGAGAATTTAGTAAGAA
30511895 ATTTTAGAGAATTATAG-AAGAA
1 ATTTTAGAGAATT-TAGTAAGAA
30511917 ATT
1 ATT
30511920 AGAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (22 bp):
ATTTTAGAGAATTTAGTAAGAA
Found at i:30514032 original size:19 final size:20
Alignment explanation
Indices: 30513988--30514042 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
30513978 TTTTATGAAA
30513988 ATTTTT-AAGAATTTTAGGGT
1 ATTTTTGAAG-ATTTTAGGGT
30514008 ATTTTTGAAGATTTTAGGG-
1 ATTTTTGAAGATTTTAGGGT
*
30514027 ATTTTTGAAGTTTTTA
1 ATTTTTGAAGATTTTA
30514043 TGATTGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 15 0.45
20 15 0.45
21 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (20 bp):
ATTTTTGAAGATTTTAGGGT
Found at i:30516647 original size:13 final size:13
Alignment explanation
Indices: 30516629--30516655 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30516619 TGTTTTCTAC
30516629 ACAGTTGGAAGAA
1 ACAGTTGGAAGAA
30516642 ACAGTTGGAAGAA
1 ACAGTTGGAAGAA
30516655 A
1 A
30516656 AGCTTGTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.30, T:0.15
Consensus pattern (13 bp):
ACAGTTGGAAGAA
Found at i:30523510 original size:23 final size:25
Alignment explanation
Indices: 30523470--30523515 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
30523460 CAAAATAGTG
*
30523470 AAAAAAATAACAAGAAAATAGTAAC
1 AAAAAAATAACAAGAAAACAGTAAC
*
30523495 AAAAAAATTA-AA-AAAACAGTA
1 AAAAAAATAACAAGAAAACAGTA
30523516 TTGTTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 2 0.11
25 9 0.47
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.13
Consensus pattern (25 bp):
AAAAAAATAACAAGAAAACAGTAAC
Found at i:30525403 original size:19 final size:18
Alignment explanation
Indices: 30525368--30525421 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
30525358 TTTCCCAAAC
*
30525368 AAAAA-TTTACTAC-CCA
1 AAAAATTTTACTTCTCCA
30525384 AAAAATTTTACTCTCTCC-
1 AAAAATTTTACT-TCTCCA
*
30525402 AAAACTTTTACTTCTCCA
1 AAAAATTTTACTTCTCCA
30525420 AA
1 AA
30525422 CCACCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 11 0.34
18 14 0.44
19 2 0.06
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATTTTACTTCTCCA
Found at i:30525410 original size:18 final size:17
Alignment explanation
Indices: 30525367--30525421 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
30525357 CTTTCCCAAA
*
30525367 CAAAAA-TTTACTAC-C
1 CAAAAATTTTACTTCTC
30525382 CAAAAAATTTTACTCTCTC
1 C-AAAAATTTTACT-TCTC
*
30525401 CAAAACTTTTACTTCTC
1 CAAAAATTTTACTTCTC
30525418 CAAA
1 CAAA
30525422 CCACCAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 14 0.41
18 12 0.35
19 2 0.06
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (17 bp):
CAAAAATTTTACTTCTC
Found at i:30526237 original size:12 final size:11
Alignment explanation
Indices: 30526220--30526275 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
30526210 CACAACTTAT
30526220 TTTTAAATAAA
1 TTTTAAATAAA
30526231 GTTTTAAATAATAA
1 -TTTTAAAT-A-AA
30526245 TTTTAAATTAAA
1 TTTTAAA-TAAA
* *
30526257 TTATAAAT-AT
1 TTTTAAATAAA
30526267 TTTTAAATA
1 TTTTAAATA
30526276 TCAATCTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
12 16 0.43
13 9 0.24
14 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
TTTTAAATAAA
Found at i:30529087 original size:16 final size:15
Alignment explanation
Indices: 30529049--30529117 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
30529039 ATGTCCGTTC
30529049 ATATTATT--TTTTA
1 ATATTATTAATTTTA
* *
30529062 ATTTTTTTAATTTATA
1 ATATTATTAATTT-TA
30529078 ATATTATTAATATTTA
1 ATATTATTAAT-TTTA
*
30529094 ATATT-TTATATTTTTT
1 ATATTATTA-A-TTTTA
30529110 ATATTATT
1 ATATTATT
30529118 TATATAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.14
15 6 0.14
16 27 0.61
17 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTATTAATTTTA
Found at i:30529139 original size:30 final size:30
Alignment explanation
Indices: 30529078--30529149 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
30529068 TTAATTTATA
* *
30529078 ATATTATTAATATTTAATATTTTATATTTTTT
1 ATATTATT--TATATAATATTTAATATTTTTT
30529110 ATATTATTTATATAATATCTTAATATTTTTT
1 ATATTATTTATATAATAT-TTAATATTTTTT
*
30529141 -TAATATTTA
1 ATATTATTTA
30529150 CATTTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 17 0.47
31 11 0.31
32 8 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (30 bp):
ATATTATTTATATAATATTTAATATTTTTT
Found at i:30529140 original size:32 final size:32
Alignment explanation
Indices: 30529076--30529147 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
30529066 TTTTAATTTA
* *
30529076 TAATATTATTAATATTTAATATTTTATATTTTT
1 TAATATTATT-ATATATAATATTTAATATTTTT
30529109 T-ATATTATT-TATATAATATCTTAATATTTTTT
1 TAATATTATTATATATAATAT-TTAATA-TTTTT
30529141 TAATATT
1 TAATATT
30529148 TACATTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 9 0.26
31 5 0.15
32 14 0.41
33 6 0.18
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TAATATTATTATATATAATATTTAATATTTTT
Found at i:30529180 original size:23 final size:24
Alignment explanation
Indices: 30529152--30529212 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
30529142 AATATTTACA
*
30529152 TTTTATTATATATTAGTATAAT-T
1 TTTTATTATATATTAGCATAATAT
30529175 TTTTA-TATTATATT-GCATAATAT
1 TTTTATTA-TATATTAGCATAATAT
**
30529198 TAATATTATATATTA
1 TTTTATTATATATTA
30529213 TACTTACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 8 0.26
23 21 0.68
24 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTTATTATATATTAGCATAATAT
Found at i:30529261 original size:26 final size:25
Alignment explanation
Indices: 30529232--30529320 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 25
30529222 GTTAATTTAT
* *
30529232 TATATATATTATTTAAGATTATATTA
1 TATATATATTATATAAGATAATA-TA
* *
30529258 TATATTTATTATATAATATAATATA
1 TATATATATTATATAAGATAATATA
* *
30529283 TA-ATATATAATAATAAATATAATATA
1 TATATATATTAT-AT-AAGATAATATA
*
30529309 TATA-ATAATATA
1 TATATATATTATA
30529321 ATTAACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
24 7 0.13
25 7 0.13
26 37 0.71
27 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
TATATATATTATATAAGATAATATA
Found at i:30529281 original size:19 final size:19
Alignment explanation
Indices: 30529226--30529322 Score: 58
Period size: 19 Copynumber: 5.0 Consensus size: 19
30529216 TTACAAGTTA
30529226 ATTTATTATAT-ATAT--T
1 ATTTATTATATAATATAAT
** *
30529242 ATTTAAGATTATATTAT-AT
1 ATTTATTA-TATAATATAAT
30529261 ATTTATTATATAATATAAT
1 ATTTATTATATAATATAAT
* *
30529280 ATATAATATATAATAATAAAT
1 ATTTATTATATAAT-AT-AAT
*
30529301 ATAATATATATAATAATATAAT
1 AT-TTAT-TAT-ATAATATAAT
30529323 TAACTATGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
16 6 0.10
17 3 0.05
18 10 0.16
19 21 0.33
20 2 0.03
21 5 0.08
22 6 0.10
23 5 0.08
24 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
ATTTATTATATAATATAAT
Found at i:30529281 original size:21 final size:20
Alignment explanation
Indices: 30529252--30529322 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
30529242 ATTTAAGATT
*
30529252 ATATTATATATTTATTATATA
1 ATATAATATA-TTATTATATA
*
30529273 ATATAATATA-TAATATATA
1 ATATAATATATTATTATATA
*
30529292 ATAATAAATATAATATATATAATA
1 AT-AT-AATATATTAT-TAT-ATA
30529316 ATATAAT
1 ATATAAT
30529323 TAACTATGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 10 0.24
20 2 0.05
21 15 0.36
22 5 0.12
23 5 0.12
24 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAATATATTATTATATA
Found at i:30529284 original size:12 final size:12
Alignment explanation
Indices: 30529267--30529322 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
30529257 ATATATTTAT
30529267 TATATAATATAA
1 TATATAATATAA
30529279 TATATAATAT-A
1 TATATAATATAA
30529290 TA-ATAATA-AA
1 TATATAATATAA
30529300 TATAATATATATAA
1 TAT-ATA-ATATAA
30529314 TAATATAAT
1 T-ATATAAT
30529323 TAACTATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.24
11 3 0.08
12 13 0.34
13 5 0.13
14 6 0.16
15 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATAATATAA
Found at i:30529292 original size:7 final size:7
Alignment explanation
Indices: 30529273--30529320 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
30529263 TTATTATATA
30529273 ATATAAT
1 ATATAAT
30529280 ATATAAT
1 ATATAAT
30529287 ATATAAT
1 ATATAAT
30529294 A-ATAA-
1 ATATAAT
30529299 ATATAAT
1 ATATAAT
30529306 ATAT-AT
1 ATATAAT
30529312 A-ATAAT
1 ATATAAT
30529318 ATA
1 ATA
30529321 ATTAACTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 3 0.08
6 14 0.38
7 20 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:30529295 original size:17 final size:17
Alignment explanation
Indices: 30529268--30529322 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 17
30529258 TATATTTATT
30529268 ATATAATATAAT-ATATA
1 ATAT-ATATAATAATATA
30529285 ATATATAATAATAAATATA
1 ATATAT-ATAAT-AATATA
30529304 ATATATATAATAATATA
1 ATATATATAATAATATA
30529321 AT
1 AT
30529323 TAACTATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.06
17 17 0.49
18 5 0.14
19 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATATAATAATATA
Found at i:30529306 original size:5 final size:5
Alignment explanation
Indices: 30529268--30529322 Score: 51
Period size: 5 Copynumber: 10.4 Consensus size: 5
30529258 TATATTTATT
30529268 ATATA ATATA ATAT- ATA-A TATATA ATAATAA ATATA ATATA TATAATA
1 ATATA ATATA ATATA ATATA -ATATA AT-AT-A ATATA ATATA -AT-ATA
30529316 ATATA AT
1 ATATA AT
30529323 TAACTATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
4 3 0.07
5 25 0.58
6 9 0.21
7 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:30533272 original size:22 final size:23
Alignment explanation
Indices: 30533232--30533277 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
30533222 ACTCAAACAC
30533232 TGTGTGTTATTCTTTTCTTGCAG
1 TGTGTGTTATTCTTTTCTTGCAG
30533255 TGTGTGTTATT-TTTTCTTGCAG
1 TGTGTGTTATTCTTTTCTTGCAG
30533277 T
1 T
30533278 TTTTTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.59
Consensus pattern (23 bp):
TGTGTGTTATTCTTTTCTTGCAG
Found at i:30533637 original size:19 final size:19
Alignment explanation
Indices: 30533613--30533651 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
30533603 AGTGAATCAC
*
30533613 ACTTTATCATTTCCCAATT
1 ACTTTATCACTTCCCAATT
30533632 ACTTTATCACTTCCCAATT
1 ACTTTATCACTTCCCAATT
30533651 A
1 A
30533652 TAGAGATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (19 bp):
ACTTTATCACTTCCCAATT
Found at i:30537804 original size:42 final size:42
Alignment explanation
Indices: 30537745--30537828 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
30537735 GGTGAAATGA
30537745 AGACACTGTGATTCTCATTCTTGCACCAAAAAACAGACAAAC
1 AGACACTGTGATTCTCATTCTTGCACCAAAAAACAGACAAAC
30537787 AGACACTGTGATTCTCATTCTTGCACCAAAAAACAGACAAAC
1 AGACACTGTGATTCTCATTCTTGCACCAAAAAACAGACAAAC
30537829 TTATATCCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (42 bp):
AGACACTGTGATTCTCATTCTTGCACCAAAAAACAGACAAAC
Found at i:30543547 original size:2 final size:2
Alignment explanation
Indices: 30543540--30543574 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30543530 TTATAGAAGG
30543540 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30543575 GAAGGTGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30543611 original size:3 final size:3
Alignment explanation
Indices: 30543603--30543634 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30543593 AGGAGAGATT
30543603 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
30543635 TGGGGAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30548048 original size:27 final size:28
Alignment explanation
Indices: 30548006--30548059 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
30547996 TTTTTTTTTC
30548006 ATATTTTTTTAGTATTTATTAGCATAAT
1 ATATTTTTTTAGTATTTATTAGCATAAT
*
30548034 ATATTTTTTTA-TATTTATTAGTATAA
1 ATATTTTTTTAGTATTTATTAGCATAA
30548060 AATCTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (28 bp):
ATATTTTTTTAGTATTTATTAGCATAAT
Found at i:30553210 original size:15 final size:15
Alignment explanation
Indices: 30553190--30553220 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30553180 GTGATTATCT
30553190 TATATTAGGACATAA
1 TATATTAGGACATAA
30553205 TATATTAGGACATAA
1 TATATTAGGACATAA
30553220 T
1 T
30553221 TACACATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
TATATTAGGACATAA
Found at i:30558758 original size:38 final size:38
Alignment explanation
Indices: 30558698--30558772 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
30558688 AATGGTAATT
* *
30558698 TTTGGTGAATTGGGGTTAAAAAATGGAATTTTGGAAAC
1 TTTGGTGAACTGGGGCTAAAAAATGGAATTTTGGAAAC
30558736 TTTGGTGAAACTGGGGCT-AAAAATGGAATTTTGGAAA
1 TTTGGTG-AACTGGGGCTAAAAAATGGAATTTTGGAAA
30558773 GTTCGAGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (38 bp):
TTTGGTGAACTGGGGCTAAAAAATGGAATTTTGGAAAC
Found at i:30558845 original size:60 final size:59
Alignment explanation
Indices: 30558748--30559094 Score: 371
Period size: 60 Copynumber: 5.8 Consensus size: 59
30558738 TGGTGAAACT
* *
30558748 GGGGCTAAAAATGGAATTTTGGAAAGTTC-GAGGGTAAAATGATAATTTTTGGTAAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCAG-GGGTAAAATGGTAATTTTTGGTAAAATC
* * *
30558807 GGGGTTAAAAATAGAATTTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATAAAACC
1 GGGGTTAAAAATGGAA-TTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAATC
* * * * * *
30558867 GAGGTCAAAAATGGAGTTTTGGAGAGTTTAGGGGCAAAATGGTAATTTTTGGTAAAAT-
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAATC
* *
30558925 TGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTTAAAA-C
1 GGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGG-TAAAATC
* * * *
30558984 TGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAAAT-GTAA-TTTCGGTGAAATC
1 -GGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGT---AAAATGGTAATTTTTGGTAAAATC
* * * * ** *
30559045 AAGGGTTAAAAATGGAAATTTGAAAATTTTGGGGGTAAAATTGTAATTTT
1 -GGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTT
30559095 GGAAGTTTCG
Statistics
Matches: 244, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
58 51 0.21
59 60 0.25
60 88 0.36
61 36 0.15
62 4 0.02
63 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (59 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAATC
Found at i:30559025 original size:30 final size:29
Alignment explanation
Indices: 30558748--30559122 Score: 150
Period size: 30 Copynumber: 12.7 Consensus size: 29
30558738 TGGTGAAACT
30558748 GGGGCTAAAAATGGAATTTTGGAAAGTTC-
1 GGGG-TAAAAATGGAATTTTGGAAAGTTCA
* *
30558777 GAGGGT-AAAATGATAATTTTTGGTAAA-ATC-
1 G-GGGTAAAAATG-GAA-TTTTGG-AAAGTTCA
*
30558807 GGGGTTAAAAATAGAATTTTTGGAAAGTTCA
1 GGGG-TAAAAATGGAA-TTTTGGAAAGTTCA
* ** *
30558838 GGGGT-AAAATGGTAATTTTTGATAA-AACC
1 GGGGTAAAAATGG-AATTTTGGA-AAGTTCA
* * * *
30558867 GAGGTCAAAAATGGAGTTTTGGAGAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAGTTCA
* *
30558897 GGGG-CAAAATGGTAATTTTTGGTAAAATT--
1 GGGGTAAAAATGG-AA-TTTTGG-AAAGTTCA
* *
30558926 GGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTCA
** *
30558955 GGGGT-AAAATGGTAATTTTTGGTTAAAACTGA
1 GGGGTAAAAATGG-AA-TTTTGG--AAAGTTCA
* *
30558987 -GGTTAAAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAAATGGAATTTTGGAAAGTTCA
* *
30559015 GGGGTAAAAAAATGTAATTTCGGTGAAA--TCAA
1 GGGGT--AAAAATGGAATTT-TG-GAAAGTTC-A
* * * * **
30559047 GGGTTAAAAATGGAAATTTGAAAATTTTG
1 GGGGTAAAAATGGAATTTTGGAAAGTTCA
* *
30559076 GGGGTAAAATTGTAATTTTGG-AAGTTTC-
1 GGGGTAAAAATGGAATTTTGGAAAG-TTCA
* *
30559104 GGGGTCAAAATGTAATTTT
1 GGGGTAAAAATGGAATTTT
30559123 CTGAAATTTT
Statistics
Matches: 258, Mismatches: 55, Indels: 67
0.68 0.14 0.18
Matches are distributed among these distances:
27 5 0.02
28 52 0.20
29 62 0.24
30 76 0.29
31 42 0.16
32 17 0.07
33 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTCA
Found at i:30560788 original size:6 final size:6
Alignment explanation
Indices: 30560779--30560880 Score: 104
Period size: 6 Copynumber: 17.0 Consensus size: 6
30560769 ATTTTTAATG
* **
30560779 TTTAAA TTTAGTA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
30560827 TTTAAA TAATTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -ATAAA
1 TTTAAA T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
30560875 TTTAAA
1 TTTAAA
30560881 ATCAATTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
4 1 0.01
5 10 0.12
6 57 0.71
7 6 0.08
8 6 0.08
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:30560795 original size:13 final size:12
Alignment explanation
Indices: 30560779--30560880 Score: 104
Period size: 11 Copynumber: 8.5 Consensus size: 12
30560769 ATTTTTAATG
*
30560779 TTTAAATTTAGTA
1 TTTAAATTTA-AA
30560792 TTTAAATTTAAA
1 TTTAAATTTAAA
30560804 TTTAAATTTAAA
1 TTTAAATTTAAA
**
30560816 TTT-AAGGTAAA
1 TTTAAATTTAAA
30560827 TTTAAATAATTAAA
1 TTTAAAT--TTAAA
30560841 TTTAAATTTAAGA
1 TTTAAATTTAA-A
30560854 --TAAATTTAAA
1 TTTAAATTTAAA
*
30560864 TTTAAA-ATAAA
1 TTTAAATTTAAA
30560875 TTTAAA
1 TTTAAA
30560881 ATCAATTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
10 1 0.01
11 28 0.36
12 26 0.34
13 11 0.14
14 11 0.14
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:30560814 original size:31 final size:28
Alignment explanation
Indices: 30560779--30560878 Score: 112
Period size: 31 Copynumber: 3.4 Consensus size: 28
30560769 ATTTTTAATG
30560779 TTTAAATTTAGTATTTAAATTTAAATTTAAA
1 TTTAAATTTAG-A--TAAATTTAAATTTAAA
*
30560810 TTTAAATTTAAGGTAAATTTAAATAATTAAA
1 TTTAAATTT-AGATAAATTTAAAT--TTAAA
30560841 TTTAAATTTAAGATAAATTTAAATTTAAA
1 TTTAAATTT-AGATAAATTTAAATTTAAA
*
30560870 -ATAAATTTA
1 TTTAAATTTA
30560879 AAATCAATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 7 0.11
29 16 0.25
31 37 0.59
32 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTAAATTTAGATAAATTTAAATTTAAA
Found at i:30560828 original size:17 final size:17
Alignment explanation
Indices: 30560791--30560880 Score: 107
Period size: 17 Copynumber: 5.4 Consensus size: 17
30560781 TAAATTTAGT
30560791 ATTTAAATTTAA-ATTTAA
1 ATTTAAATTTAAGA--TAA
*
30560809 ATTTAAATTTAAGGTAA
1 ATTTAAATTTAAGATAA
*
30560826 ATTTAAA--TAA-TTAA
1 ATTTAAATTTAAGATAA
30560840 ATTTAAATTTAAGATAA
1 ATTTAAATTTAAGATAA
*
30560857 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAGATAA
30560874 ATTTAAA
1 ATTTAAA
30560881 ATCAATTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 3 0.05
17 36 0.56
18 12 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAGATAA
Found at i:30560874 original size:11 final size:11
Alignment explanation
Indices: 30560800--30560890 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
30560790 TATTTAAATT
*
30560800 TAAATTTAAATT
1 TAAATTTAAA-A
**
30560812 TAAATTTAAGG
1 TAAATTTAAAA
30560823 TAAATTTAAATAA
1 TAAATTT-AA-AA
*
30560836 TTAAATTTAAAT
1 -TAAATTTAAAA
* ** *
30560848 TTAAGATAAATT
1 TAAATTTAAA-A
30560860 TAAATTTAAAA
1 TAAATTTAAAA
30560871 TAAATTTAAAA
1 TAAATTTAAAA
*
30560882 TCAATTTAA
1 TAAATTTAA
30560891 CTCTAAATTA
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
11 33 0.53
12 20 0.32
13 2 0.03
14 7 0.11
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:30560897 original size:28 final size:28
Alignment explanation
Indices: 30560794--30560902 Score: 83
Period size: 31 Copynumber: 3.8 Consensus size: 28
30560784 ATTTAGTATT
* * **
30560794 TAAATTTAAATTTAAATTTAAATTTAAGG
1 TAAATTTAAATCTAAA-ATAAATTTAAAA
* * *
30560823 TAAATTTAAATAATTAAATTTAAATTTAAGA
1 TAAATTTAAAT--CTAAA-ATAAATTTAAAA
*
30560854 TAAATTTAAATTTAAAATAAATTTAAAA
1 TAAATTTAAATCTAAAATAAATTTAAAA
* * *
30560882 TCAATTTAACTCTAAATTAAA
1 TAAATTTAAATCTAAAATAAA
30560903 ACAAGAAGTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
28 27 0.38
29 16 0.23
31 28 0.39
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (28 bp):
TAAATTTAAATCTAAAATAAATTTAAAA
Found at i:30561409 original size:76 final size:76
Alignment explanation
Indices: 30561258--30562024 Score: 1128
Period size: 76 Copynumber: 10.0 Consensus size: 76
30561248 CTTTTTCTAA
* * * *
30561258 CTCTTACTCCAATTTCAGAAGATAAAGACTTGCTATCCAACTTTTACTTCAATTTCAAGAGGATG
1 CTCTTACTTCAATTTCAG-AGATAAAGACTTGTTATCCAAC-TCTACTTCAATTTCAAGAGGATA
*
30561323 GGAAACGATCTTG
64 GGAAATGATCTTG
* * *
30561336 CTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGGAGGAT-G
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA-GAGGATAG
30561400 GAAATGATCTTG
65 GAAATGATCTTG
* * * *
30561412 CTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGGG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
30561477 AAATGATCTTG
66 AAATGATCTTG
30561488 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
*
30561553 AAATGATGTTG
66 AAATGATCTTG
* * **
30561564 CTCTTACTTCAATTTCAAAGATAAAAAACGCGTTATCC-ACTCTACTTCAATTTCAAGAGGATAG
1 CTCTTACTTCAATTTCAGAGAT-AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
30561628 GAAAAGATCTTG
65 GAAATGATCTTG
*
30561640 CTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
30561705 AAATGATCTTG
66 AAATGATCTTG
* * *
30561716 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGAATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
*
30561781 AAATGATGTTG
66 AAATGATCTTG
* * * * *
30561792 CTCTTACTTACTTCAATTTCAGAGATCAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGA
1 --C-T-CTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
30561857 TAGGAAATGATCTTG
62 TAGGAAATGATCTTG
* * *
30561872 CTCTTACTTCAATTTCAAAGATAAGGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
30561937 -AATGA-CGTTG
66 AAATGATC-TTG
* *
30561947 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCGACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
30562012 AAATGATCTTG
66 AAATGATCTTG
30562023 CT
1 CT
30562025 GTGGTCTGAT
Statistics
Matches: 630, Mismatches: 48, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
74 1 0.00
75 85 0.13
76 419 0.67
77 40 0.06
78 19 0.03
79 1 0.00
80 65 0.10
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (76 bp):
CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
AAATGATCTTG
Found at i:30566886 original size:16 final size:16
Alignment explanation
Indices: 30566865--30566905 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
30566855 TCTTATTGTC
30566865 TCTCTCTTTCTTTCTA
1 TCTCTCTTTCTTTCTA
30566881 TCTCTCTTTC-TTCTA
1 TCTCTCTTTCTTTCTA
30566896 T-T-TCTTTCTT
1 TCTCTCTTTCTT
30566906 CCTTTCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.25
14 2 0.08
15 6 0.25
16 10 0.42
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (16 bp):
TCTCTCTTTCTTTCTA
Found at i:30568946 original size:12 final size:12
Alignment explanation
Indices: 30568929--30568954 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30568919 CTTTTTCCAC
30568929 CGTCTCCTGCAT
1 CGTCTCCTGCAT
30568941 CGTCTCCTGCAT
1 CGTCTCCTGCAT
30568953 CG
1 CG
30568955 ATTTTCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.42, G:0.19, T:0.31
Consensus pattern (12 bp):
CGTCTCCTGCAT
Found at i:30574219 original size:28 final size:28
Alignment explanation
Indices: 30574188--30574247 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
30574178 AAAATGAGAC
30574188 TTTTGGATACCCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGGGGGCAAAATGGTAA
*** *
30574216 TTTTGGATGTGCGGGGGTAAAATGGTAA
1 TTTTGGATACCCGGGGGCAAAATGGTAA
30574244 TTTT
1 TTTT
30574248 TGGTGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.33, T:0.33
Consensus pattern (28 bp):
TTTTGGATACCCGGGGGCAAAATGGTAA
Found at i:30574305 original size:38 final size:38
Alignment explanation
Indices: 30574246--30574320 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
30574236 AATGGTAATT
* *
30574246 TTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAC
1 TTTGGTGAAATCAGGGCTAAAAATGGAATTTTAGAAAC
*
30574284 TTTGGTGAAATCGGGGCTAAAAATGGAATTTTAGAAA
1 TTTGGTGAAATCAGGGCTAAAAATGGAATTTTAGAAA
30574321 GTTTAGGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (38 bp):
TTTGGTGAAATCAGGGCTAAAAATGGAATTTTAGAAAC
Found at i:30574334 original size:29 final size:28
Alignment explanation
Indices: 30574303--30574664 Score: 194
Period size: 29 Copynumber: 12.5 Consensus size: 28
30574293 ATCGGGGCTA
*
30574303 AAAATGGAATTTTAGAAAGTTTAGGGGT
1 AAAATGGAATTTTGGAAAGTTTAGGGGT
* *
30574331 AAAATGGTAATTTTGGTAAA--ATCGGGGT
1 AAAATGG-AATTTTGG-AAAGTTTAGGGGT
* *
30574359 CAAAAATGGAATTTTGGAGAGTTTAGGGGC
1 --AAAATGGAATTTTGGAAAGTTTAGGGGT
**
30574389 AAAATGGTAATTTTTGGTAAA-ACT-GGGGTT
1 AAAATGG-AA-TTTTGG-AAAGTTTAGGGG-T
* **
30574419 AAAAATGGAATTTTGGAACGTTCGGGGGGT
1 -AAAATGGAATTTTGGAAAGTT-TAGGGGT
* *
30574449 AAAATGGTAATTTTCGGTGAAA-TCTA-GGTT
1 AAAATGG-AATTTT--G-GAAAGTTTAGGGGT
* *
30574479 AAAAATGGAATTTTGAAAAGTTTGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTAGGGGT
*
30574508 AAAATGGTAATTTTGGTGAAA--TTAGGGTT
1 AAAATGG-AATTTT-G-GAAAGTTTAGGGGT
*
30574537 AAAATGGAATTTTGAAAAGTTTA-GGGT
1 AAAATGGAATTTTGGAAAGTTTAGGGGT
*
30574564 AAAATGGTAATTTTCGGTGAAA---TCGGGGTT
1 AAAATGG-AATTTT--G-GAAAGTTTAGGGG-T
* *
30574594 AAAATGGAATTTT-GAAAATTTTGGCGGT
1 AAAATGGAATTTTGGAAAGTTTAGG-GGT
*
30574622 AAAATGGTAATTTTTGG-AAGTTTTGGGGT
1 AAAATGG-AA-TTTTGGAAAGTTTAGGGGT
*
30574651 CAAAATGTAATTTT
1 -AAAATGGAATTTT
30574665 CTAAAACTTT
Statistics
Matches: 260, Mismatches: 34, Indels: 80
0.70 0.09 0.21
Matches are distributed among these distances:
25 4 0.02
26 3 0.01
27 14 0.05
28 65 0.25
29 74 0.28
30 68 0.26
31 27 0.10
32 2 0.01
33 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:30574556 original size:57 final size:57
Alignment explanation
Indices: 30574284--30574635 Score: 422
Period size: 58 Copynumber: 6.1 Consensus size: 57
30574274 TTTTGGAAAC
* *
30574284 TTTGGTGAAATCGGGGCTAAAAATGGAATTTT-AGAAAGTTTAGGGGTAAAATGGTAAT
1 TTTGGTGAAATCGGGG-TTAAAATGGAATTTTGA-AAAGTTTGGGGGTAAAATGGTAAT
* * * * * *
30574342 TTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAGAGTTTAGGGGCAAAATGGTAATT
1 TTTGGTGAAATCGGGGT-TAAAATGGAATTTTGAAAAGTTTGGGGGTAAAATGGTAA-T
* * * *
30574401 TTTGGT-AAAACTGGGGTTAAAAATGGAATTTTGGAACGTTCGGGGGGTAAAATGGTAAT
1 TTTGGTGAAATC-GGGGTT-AAAATGGAATTTTGAAAAGTT-TGGGGGTAAAATGGTAAT
**
30574460 TTTCGGTGAAATCTAGGTTAAAAATGGAATTTTGAAAAGTTTGGGGGTAAAATGGTAAT
1 TTT-GGTGAAATCGGGGTT-AAAATGGAATTTTGAAAAGTTTGGGGGTAAAATGGTAAT
** *
30574519 TTTGGTGAAATTAGGGTTAAAATGGAATTTTGAAAAGTTT-AGGGTAAAATGGTAAT
1 TTTGGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTTGGGGGTAAAATGGTAAT
* *
30574575 TTTCGGTGAAATCGGGGTTAAAATGGAATTTTGAAAATTTTGGCGGTAAAATGGTAAT
1 TTT-GGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTTGGGGGTAAAATGGTAAT
30574633 TTT
1 TTT
30574636 TGGAAGTTTT
Statistics
Matches: 258, Mismatches: 26, Indels: 20
0.85 0.09 0.07
Matches are distributed among these distances:
56 18 0.07
57 57 0.22
58 83 0.32
59 55 0.21
60 41 0.16
61 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (57 bp):
TTTGGTGAAATCGGGGTTAAAATGGAATTTTGAAAAGTTTGGGGGTAAAATGGTAAT
Found at i:30575322 original size:20 final size:20
Alignment explanation
Indices: 30575297--30575339 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
30575287 TCCCCCCCCC
*
30575297 GTCCTGCTCGTCCATCTCCG
1 GTCCTGCTCGGCCATCTCCG
*
30575317 GTCCTGCTCGGCCGTCTCCG
1 GTCCTGCTCGGCCATCTCCG
30575337 GTC
1 GTC
30575340 ATCAGTCGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.44, G:0.26, T:0.28
Consensus pattern (20 bp):
GTCCTGCTCGGCCATCTCCG
Found at i:30576488 original size:6 final size:6
Alignment explanation
Indices: 30576474--30576562 Score: 80
Period size: 6 Copynumber: 15.2 Consensus size: 6
30576464 TAAATTTTGT
* **
30576474 ATTTTA ATTTAA ATTTAA ATTTAA ATTT-A AGGTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
*
30576523 ATTTGA ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
30576563 ATCAATTTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 50 0.74
7 1 0.01
8 6 0.09
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:30576564 original size:17 final size:16
Alignment explanation
Indices: 30576474--30576562 Score: 92
Period size: 17 Copynumber: 5.4 Consensus size: 16
30576464 TAAATTTTGT
*
30576474 ATTTTAATTTAAATTTAA
1 ATTTAAATTTAAA--TAA
*
30576492 ATTTAAATTTAAGGTAA
1 ATTTAAATTTAA-ATAA
*
30576509 ATTTAAA--TAATTAA
1 ATTTAAATTTAAATAA
*
30576523 ATTTGAATTTAAGATAA
1 ATTTAAATTTAA-ATAA
30576540 ATTTAAATTTAAATAA
1 ATTTAAATTTAAATAA
30576556 ATTTAAA
1 ATTTAAA
30576563 ATCAATTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.15
15 3 0.05
16 14 0.23
17 24 0.39
18 11 0.18
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:30576579 original size:27 final size:27
Alignment explanation
Indices: 30576528--30576580 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
30576518 ATTAAATTTG
* *
30576528 AATTTAAGATAAATTTAAATTTAAATA
1 AATTTAAAATAAATTTAAATCTAAATA
* *
30576555 AATTTAAAATCAATTTAACTCTAAAT
1 AATTTAAAATAAATTTAAATCTAAAT
30576581 TAAAACAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (27 bp):
AATTTAAAATAAATTTAAATCTAAATA
Found at i:30577406 original size:15 final size:16
Alignment explanation
Indices: 30577374--30577426 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
30577364 ACGAAGGAAA
*
30577374 GAAAATTAGAAATATG
1 GAAAATTAGAAAGATG
*
30577390 GAAAATT-GAAAGGTG
1 GAAAATTAGAAAGATG
* * *
30577405 GAAAAATAGAAGGATT
1 GAAAATTAGAAAGATG
30577421 GAAAAT
1 GAAAAT
30577427 AAAATTTTTC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.21
Consensus pattern (16 bp):
GAAAATTAGAAAGATG
Found at i:30580723 original size:23 final size:24
Alignment explanation
Indices: 30580666--30580723 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
30580656 TTTATAAAAG
* *
30580666 ATTTAATATTTATTAGCATAGTAT
1 ATTTGATATTTATTAGCATAGAAT
*
30580690 ATTTGACATTTATTAGCATA-AAT
1 ATTTGATATTTATTAGCATAGAAT
* *
30580713 TTTTGTTATTT
1 ATTTGATATTT
30580724 TCTTTCCATC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (24 bp):
ATTTGATATTTATTAGCATAGAAT
Found at i:30589579 original size:24 final size:24
Alignment explanation
Indices: 30589550--30589595 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
30589540 AACTCGGTAA
**
30589550 TCCGCAACAAATGTTGGATTCCGG
1 TCCGCAACAAATACTGGATTCCGG
30589574 TCCGCAACAAATACTGGATTCC
1 TCCGCAACAAATACTGGATTCC
30589596 TATTTAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (24 bp):
TCCGCAACAAATACTGGATTCCGG
Found at i:30589823 original size:2 final size:2
Alignment explanation
Indices: 30589816--30589856 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30589806 ATAATTCAAA
30589816 AC AC AC AC AC AC AC 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 AC AC AC AC AC AC AC A
30589857 TATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30595098 original size:70 final size:71
Alignment explanation
Indices: 30595016--30595157 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
30595006 GACCGGTATG
* *
30595016 GTACATCAGTACGGGTAGAAG-AACATACCTTAGATCCAAGTTGATTAAACCGTCAGTATTGGAG
1 GTACATCAGTACGAGTAGAAGAAACATACCTTAAATCCAAGTTGATTAAACCGTCAGTATTGGAG
30595080 ACCGCA
66 ACCGCA
30595086 GTACATCAGTACGAGTAGAAGAAACATACCTTAAATCCAAGTTGATTAAACCGTCAGTATTGGAG
1 GTACATCAGTACGAGTAGAAGAAACATACCTTAAATCCAAGTTGATTAAACCGTCAGTATTGGAG
30595151 ACCGCA
66 ACCGCA
30595157 G
1 G
30595158 AAAAAAAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 20 0.29
71 49 0.71
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (71 bp):
GTACATCAGTACGAGTAGAAGAAACATACCTTAAATCCAAGTTGATTAAACCGTCAGTATTGGAG
ACCGCA
Found at i:30597084 original size:29 final size:29
Alignment explanation
Indices: 30597052--30597568 Score: 188
Period size: 29 Copynumber: 17.8 Consensus size: 29
30597042 TGGATGCCTA
*
30597052 GAGGTAAAATGGTAATTTTTGGAGGTTCG
1 GAGGTAAAATGGTAATTTTTGGAAGTTCG
* * * *
30597081 GAGGTAGAACGATAATTTTTGGACA-CTC-
1 GAGGTAAAATGGTAATTTTTGGA-AGTTCG
* ** *
30597109 GAGGGCAAAAAT-GTAATTTTT-GAACATCC
1 GA-GG-TAAAATGGTAATTTTTGGAAGTTCG
* **
30597138 GAGGGTAAAATGGTAATTTTTGAAAACTCG
1 GA-GGTAAAATGGTAATTTTTGGAAGTTCG
* *
30597168 GGGGCAAAAAT-GTAATTTTTGGACA-TTC-
1 GAGG-TAAAATGGTAATTTTTGGA-AGTTCG
* ** *
30597196 GAGGGAAAAATGGTAATACTTGG-A-TATCC
1 GA-GGTAAAATGGTAATTTTTGGAAGT-TCG
* * *
30597225 GAGGGAAAATGATAATTTTTGGATGTTCG
1 GAGGTAAAATGGTAATTTTTGGAAGTTCG
* * **
30597254 GGGGTAAAATAGTAATTTTTGGAAAGTTTA
1 GAGGTAAAATGGTAATTTTTGG-AAGTTCG
*
30597284 G-GGTAAAAAT-GTAATTTTTAGATA-TTC-
1 GAGGT-AAAATGGTAATTTTTGGA-AGTTCG
30597311 GAGGGTAAAATGGTAATTTTTTGGAAGTAT-G
1 GA-GGTAAAATGGTAA-TTTTTGGAAGT-TCG
* * * *
30597342 GGGGCAAAAAT-GTGATTTTTGGAAGTTTG
1 GAGG-TAAAATGGTAATTTTTGGAAGTTCG
* * *
30597371 GGGGTAAAAAT-GTAATTTTTGAAAAG--CAT
1 GAGGT-AAAATGGTAATTTTTG-GAAGTTC-G
* *
30597400 GAGGGTAAAATAGTAAATTTTGGAAGTTC-
1 GA-GGTAAAATGGTAATTTTTGGAAGTTCG
* *
30597429 GAGGGTAAAAAT-GTGATTTTTGGAAGTTTG
1 GA-GGT-AAAATGGTAATTTTTGGAAGTTCG
* *
30597459 G-GGTAAAATGGTAATTTTTGAAAGTTTAG
1 GAGGTAAAATGGTAATTTTTGGAAG-TTCG
** * *
30597488 G-GCAAAAAT-GTGATTTTTGGAAGTTTAG
1 GAGGTAAAATGGTAATTTTTGGAAG-TTCG
* * *
30597516 G-GATAAAAAT-GTAGTTTTTGAGAAGTT-T
1 GAGGT-AAAATGGTAATTTTTG-GAAGTTCG
30597544 GAGGGTCAAAAT-GTAATTTTTGGAA
1 GA-GGT-AAAATGGTAATTTTTGGAA
30597569 AGTTTAGGGG
Statistics
Matches: 379, Mismatches: 67, Indels: 84
0.72 0.13 0.16
Matches are distributed among these distances:
27 9 0.02
28 80 0.21
29 203 0.54
30 79 0.21
31 8 0.02
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (29 bp):
GAGGTAAAATGGTAATTTTTGGAAGTTCG
Found at i:30597145 original size:87 final size:85
Alignment explanation
Indices: 30597054--30597438 Score: 314
Period size: 87 Copynumber: 4.4 Consensus size: 85
30597044 GATGCCTAGA
* * *
30597054 GGTAAAATGGTAATTTTTGGAGGTTCGGAGGTAGAACGATAATTTTTGGACACTCGAGGGCAAAA
1 GGTAAAATGGTAATTTTTGGAAGTTCGGGGGTA-AAAGATAATTTTTGGACACTCGAGGG-AAAA
*
30597119 ATGTAATTTTTGAACATCCGAG
64 ATGTAATTTTTGAATATCCGAG
* ** * *
30597141 GGTAAAATGGTAATTTTTGAAAACTCGGGGGCAAAA-ATGTAATTTTTGGACATTCGAGGGAAAA
1 GGTAAAATGGTAATTTTTGGAAGTTCGGGGGTAAAAGA--TAATTTTTGGACACTCGAGGGAAAA
** *
30597205 ATGGTAATACTTGGATATCCGAG
64 AT-GTAATTTTTGAATATCCGAG
* * * * * **
30597228 GG-AAAATGATAATTTTTGGATGTTCGGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTAAAA
1 GGTAAAATGGTAATTTTTGGAAGTTCGGGGGTAAAAGA-TAATTTTTGGACACTCGAGGG-AAAA
*
30597292 ATGTAATTTTT-AGATATTCGAG
64 ATGTAATTTTTGA-ATATCCGAG
* * * * *
30597314 GGTAAAATGGTAATTTTTTGGAAGTAT-GGGGGCAAAA-ATGTGATTTTTGGA-AGTTTGGGGGT
1 GGTAAAATGGTAA-TTTTTGGAAGT-TCGGGGGTAAAAGA--TAATTTTTGGACA-CTCGAGGG-
* * *
30597376 AAAAATGTAATTTTTGAAAAGCATGAG
60 AAAAATGTAATTTTTGAATATC-CGAG
* * *
30597403 GGTAAAATAGTAAATTTTGGAAGTTCGAGGGTAAAA
1 GGTAAAATGGTAATTTTTGGAAGTTCGGGGGTAAAA
30597439 ATGTGATTTT
Statistics
Matches: 243, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
85 1 0.00
86 70 0.29
87 84 0.35
88 71 0.29
89 17 0.07
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.32
Consensus pattern (85 bp):
GGTAAAATGGTAATTTTTGGAAGTTCGGGGGTAAAAGATAATTTTTGGACACTCGAGGGAAAAAT
GTAATTTTTGAATATCCGAG
Found at i:30597376 original size:59 final size:56
Alignment explanation
Indices: 30597057--30597568 Score: 319
Period size: 58 Copynumber: 8.8 Consensus size: 56
30597047 GCCTAGAGGT
* * * * * *
30597057 AAAATGGTAATTTTTGGAGGTTCG-GAGGTAGAACGATAATTTTTGGACACT-CGAGGGCA
1 AAAAT-GTAATTTTTGGAAGTTCGAG-GGTAAAATG-TAATTTTTGGA-AGTATG-GGGGA
* * *
30597116 AAAATGTAATTTTT-GAACATCCGAGGGTAAAATGGTAATTTTT-GAA-AACTCGGGGGCA
1 AAAATGTAATTTTTGGAA-GTTCGAGGGTAAAAT-GTAATTTTTGGAAGTA-T-GGGGG-A
* ** *
30597174 AAAATGTAATTTTTGGACA-TTCGAGGGAAAAATGGTAATACTTGG-A-TATCCGAGGG-
1 AAAATGTAATTTTTGGA-AGTTCGAGGGTAAAAT-GTAATTTTTGGAAGTAT--GGGGGA
* * * * *
30597230 AAAATGATAATTTTTGGATGTTCGGGGGTAAAATAGTAATTTTTGGAAAGTTTAGGGTA
1 AAAATG-TAATTTTTGGAAGTTCGAGGGTAAAAT-GTAATTTTTGG-AAGTATGGGGGA
*
30597289 AAAATGTAATTTTTAGATA-TTCGAGGGTAAAATGGTAATTTTTTGGAAGTATGGGGGCA
1 AAAATGTAATTTTTGGA-AGTTCGAGGGTAAAAT-GTAA-TTTTTGGAAGTATGGGGG-A
* * * * * * *
30597348 AAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAAGCATGAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTTTG-GAAGTATGGGGGA
* * * *
30597406 AAAATAGTAAATTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGT-TTGGGGT
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTTTGGAAGTATGGGGGA
* * * * * **
30597463 AAAATGGTAATTTTTGAAAGTT-TAGGGCAAAAATGTGATTTTTGGAAGTTTAGGGATA
1 AAAAT-GTAATTTTTGGAAGTTCGAGGG-TAAAATGTAATTTTTGGAAGTAT-GGGGGA
* *
30597521 AAAATGTAGTTTTTGAGAAGTTTGAGGGTCAAAATGTAATTTTTGGAA
1 AAAATGTAATTTTTG-GAAGTTCGAGGGT-AAAATGTAATTTTTGGAA
30597569 AGTTTAGGGG
Statistics
Matches: 361, Mismatches: 62, Indels: 60
0.75 0.13 0.12
Matches are distributed among these distances:
56 31 0.09
57 74 0.20
58 133 0.37
59 115 0.32
60 8 0.02
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (56 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGGAAGTATGGGGGA
Found at i:30598441 original size:22 final size:23
Alignment explanation
Indices: 30598416--30598460 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
30598406 TTTCTCTTAG
30598416 ATCTGTTTCATTTT-TTTTTAAA
1 ATCTGTTTCATTTTATTTTTAAA
*
30598438 ATCTGTTTTATTTTAGTTTTTAA
1 ATCTGTTTCATTTTA-TTTTTAA
30598461 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (23 bp):
ATCTGTTTCATTTTATTTTTAAA
Found at i:30599397 original size:18 final size:18
Alignment explanation
Indices: 30599374--30599452 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
30599364 ATAATCTTTC
*
30599374 AAATTTTAAATTTAGAAT
1 AAATTTTAAATTTAAAAT
*
30599392 AAA-TTT-AA-TAAAAAT
1 AAATTTTAAATTTAAAAT
30599407 AAA-TTTAAATTTAAAA-
1 AAATTTTAAATTTAAAAT
*
30599423 ATAATTTTAAACTTAAAAT
1 A-AATTTTAAATTTAAAAT
*
30599442 AAATTTAAAAT
1 AAATTTTAAAT
30599453 AAAAATTAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
15 11 0.22
16 5 0.10
17 10 0.20
18 23 0.46
19 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
AAATTTTAAATTTAAAAT
Found at i:30599457 original size:17 final size:17
Alignment explanation
Indices: 30599389--30599458 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
30599379 TTAAATTTAG
30599389 AATAAATTT--AATAAA
1 AATAAATTTAAAATAAA
*
30599404 AATAAATTTAAATTTAAA
1 AATAAATTTAAA-ATAAA
* * *
30599422 AATAATTTTAAACTTAA
1 AATAAATTTAAAATAAA
30599439 AATAAATTTAAAATAAA
1 AATAAATTTAAAATAAA
30599456 AAT
1 AAT
30599459 TAGGTTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
15 9 0.20
17 21 0.47
18 15 0.33
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAATTTAAAATAAA
Found at i:30600244 original size:208 final size:208
Alignment explanation
Indices: 30599837--30600296 Score: 688
Period size: 208 Copynumber: 2.2 Consensus size: 208
30599827 CTCTCGGTTT
* **** * **
30599837 ACTTCTCTGTATCTCAT-AAGGAAGGTAACTGCCTTATTGTTTCGACCTTCTTCTCAATATATCA
1 ACTTATCTGTATCTCATCAA-GAAGGTAACCATTTTATTGCTTC-ACCCGCTTCTCAATATATCA
* * *
30599901 TCAGGAGGCTGGGGTTCAAAGATTTGCTCACTTTGAGTCTGGTTTCATTGATTTGGTCTACTTAT
64 TCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTAAGCCTGGTTTCATTGATTTGGTCTACTTAT
* * *
30599966 CGGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGGTCCACTTCTTTGTGTCTCATCAGGA
129 CAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGA
30600031 AGACGGATCTAGTTC
194 AGACGGATCTAGTTC
* * *
30600046 ACTTATCTGTATCTCGTCACGAAGGTAACCATTTTATTGCTTCACCCGCTTCTCAATATCTCATC
1 ACTTATCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCACCCGCTTCTCAATATATCATC
* * *
30600111 AGGAAGCTGGGGTTCGAAGATTTGCTCACTTTAAGCCTGGTTTCATTGATTTGGTCTATTTCTCA
66 AGGAAGCTGGGGTTCAAAGATTTGCTCACTTTAAGCCTGGTTTCATTGATTTGGTCTACTTATCA
30600176 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAG
131 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAG
*
30600241 ACGGATCTGGTTC
196 ACGGATCTAGTTC
* *
30600254 ACTTCTCTGTATCTCATCAAGAAGGTAACCGTTTTATTGCTTC
1 ACTTATCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTC
30600297 GAATGACTGT
Statistics
Matches: 225, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
208 191 0.85
209 33 0.15
210 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (208 bp):
ACTTATCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCACCCGCTTCTCAATATATCATC
AGGAAGCTGGGGTTCAAAGATTTGCTCACTTTAAGCCTGGTTTCATTGATTTGGTCTACTTATCA
GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAG
ACGGATCTAGTTC
Found at i:30600479 original size:39 final size:39
Alignment explanation
Indices: 30600311--30600496 Score: 112
Period size: 39 Copynumber: 4.8 Consensus size: 39
30600301 GACTGTAATT
* * * * * **
30600311 TGCCCCATGATCGGGGTAAGAGATTAGATGGCTGCAATC
1 TGCCCCAAGCTCGGGGTAAGAGATTAGCTGACAGTGATC
* * * * **
30600350 TACCCCATGATCGGGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAAGCTCGGGGTAAGAGATTAGCTGACAGTGATC
* * * *
30600389 TGCCCCAAGCTCGAGGTAAAAGATCAGATGGTTACA---ATC
1 TGCCCCAAGCTCGGGGTAAGAGATTAGCT-G--ACAGTGATC
* *
30600428 CG-ACC-AGACTCGGGGTAAGAGATTAGCTGACAGTGATC
1 TGCCCCAAG-CTCGGGGTAAGAGATTAGCTGACAGTGATC
* *
30600466 TGCCCCAAGCTCGGGTTAAAAGATTAGCTGA
1 TGCCCCAAGCTCGGGGTAAGAGATTAGCTGA
30600497 TGTAAGAGAT
Statistics
Matches: 110, Mismatches: 28, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
35 3 0.03
37 3 0.03
38 22 0.20
39 78 0.71
40 3 0.03
42 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (39 bp):
TGCCCCAAGCTCGGGGTAAGAGATTAGCTGACAGTGATC
Found at i:30600960 original size:50 final size:50
Alignment explanation
Indices: 30600790--30601187 Score: 183
Period size: 49 Copynumber: 8.0 Consensus size: 50
30600780 ATCGGGTTTA
* * * * * *
30600790 CCGTTGCGTCCTCAACCTTTCCCTTCAA-ATC-TTCATGGTACCGGGTTCG
1 CCGTTGCGGCCTCAACATTTCCCAT-AACATCTTTTAAGGTACCAGGTTCG
* ** * * * * *
30600839 CCGTTGCGGCCTCAACCTTTCCCATTGCATC-TCTATGGAATC-GGATTCA
1 CCGTTGCGGCCTCAACATTTCCCATAACATCTTTTAAGGTACCAGG-TTCG
* * * *
30600888 CTGTTGCAGCCTCAATC-CTTCCCATAATATCTTTTAAGGTACCAGGTTCG
1 CCGTTGCGGCCTCAA-CATTTCCCATAACATCTTTTAAGGTACCAGGTTCG
* * ** *
30600938 CCGTTACGGCCTCAACATTTCCCTTCAA-AT-TTTTGTGGTACC-GAGTTTG
1 CCGTTGCGGCCTCAACATTTCCCAT-AACATCTTTTAAGGTACCAG-GTTCG
* * * ***
30600987 CCGTTGCGGCCTCAACTTTTCCCTTCACATCTTCTT-AGGTATTGGGTTCG
1 CCGTTGCGGCCTCAACATTTCCCATAACATCTT-TTAAGGTACCAGGTTCG
* * * * * * *
30601037 CCATTGTGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCAGATTCA
1 CCGTTGCGGCCTCAACATTTCCCATAACATCTTTTAAGGTACCAGGTTCG
* * ** * * * * * *
30601087 TCGTCGCAACCTCAATC-CTTCCCTTTTA-ATC-TTCATGGTACCAGGTTCA
1 CCGTTGCGGCCTCAA-CATTTCCC-ATAACATCTTTTAAGGTACCAGGTTCG
* * *
30601136 CCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT-AGGTACCGGGTTCG
1 CCGTTGCGGCCTCAACATTTCCCATAACATCTT-TTAAGGTACCAGGTTCG
30601186 CC
1 CC
30601188 ATTTCAGTCT
Statistics
Matches: 261, Mismatches: 69, Indels: 37
0.71 0.19 0.10
Matches are distributed among these distances:
48 7 0.03
49 133 0.51
50 110 0.42
51 11 0.04
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (50 bp):
CCGTTGCGGCCTCAACATTTCCCATAACATCTTTTAAGGTACCAGGTTCG
Found at i:30601200 original size:50 final size:50
Alignment explanation
Indices: 30600776--30601219 Score: 325
Period size: 50 Copynumber: 9.0 Consensus size: 50
30600766 TCATTTTATA
* ** * * *
30600776 AGGTATCGGGTTTACCGTTGCGTCCTCAACCTTTCCCTTCAAATCTTCAT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTT
*
30600826 -GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATT-GCATC-TC-T
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC-TTCACATCTTCTT
* * * * * * * * *
30600873 ATGGAATCGGATTCACTGTTGCAGCCTCAATCC-TTCCCATAATATCTT-TT
1 A-GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCACATCTTCTT
* * * *
30600923 AAGGTACCAGGTTCGCCGTTACGGCCTCAACATTTCCCTTCAAAT-TT-TT
1 -AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTT
* * * *
30600972 GTGGTACCGAGTTTGCCGTTGCGGCCTCAACTTTTCCCTTCACATCTTCTT
1 -AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTT
** * * * *
30601023 AGGTATTGGGTTCGCCATTGTGGCCTCAACCTTTCCCATCACATCTTCTA
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTT
* * ** * ** * *
30601073 AGGTACCAGATTCATCGTCGCAACCTCAATCC-TTCCCTTTTA-ATCTTCAT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCC-TTCACATCTTCTT
* * *
30601123 -GGTACCAGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTT
* * * * *
30601172 AGGTACCGGGTTCGCCATTTCAGTCTCAACCTTTCCCTTCAAATCTTC
1 AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTC
30601220 ATGTTTTTCT
Statistics
Matches: 302, Mismatches: 76, Indels: 32
0.74 0.19 0.08
Matches are distributed among these distances:
47 1 0.00
48 7 0.02
49 142 0.47
50 145 0.48
51 7 0.02
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (50 bp):
AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTT
Found at i:30601200 original size:99 final size:98
Alignment explanation
Indices: 30600789--30601222 Score: 351
Period size: 99 Copynumber: 4.4 Consensus size: 98
30600779 TATCGGGTTT
* *
30600789 ACCGTTGC-GTCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCA
1 ACCGTTGCAG-CCTCAACC-TTCCCTTTAAATCTTCATGGTACCAGGTTCGCCGTTGCGGCCTCA
** * *
30600853 ACCTTTCCCATTGCATC-TC-TATGGAATCGGATTC
64 ACCTTTCCCATCACATCTTCTTA-GGTACCGGATTC
* * * * *
30600887 ACTGTTGCAGCCTCAATCCTTCCC-ATAATATCTTTTAAGGTACCAGGTTCGCCGTTACGGCCTC
1 ACCGTTGCAGCCTCAA-CCTTCCCTTTAA-ATC-TTCATGGTACCAGGTTCGCCGTTGCGGCCTC
* * * * *
30600951 AACATTTCCCTTCAAAT-TT-TTGTGGTACC-GAGTTT
63 AACCTTTCCCATCACATCTTCTT-AGGTACCGGA-TTC
* * * * * * *** * *
30600986 GCCGTTGCGGCCTCAACTTTTCCCTTCACATCTTCTTAGGTATTGGGTTCGCCATTGTGGCCTCA
1 ACCGTTGCAGCCTCAAC-CTTCCCTTTAAATCTTCAT-GGTACCAGGTTCGCCGTTGCGGCCTCA
* *
30601051 ACCTTTCCCATCACATCTTCTAAGGTACCAGATTC
64 ACCTTTCCCATCACATCTTCTTAGGTACCGGATTC
* * * * *
30601086 ATCGTCGCAACCTCAATCCTTCCCTTTTAATCTTCATGGTACCAGGTTCACCGTTGCGGCCTCAA
1 ACCGTTGCAGCCTCAA-CCTTCCCTTTAAATCTTCATGGTACCAGGTTCGCCGTTGCGGCCTCAA
*
30601151 CCTTTCCCATCACATCTTCTTAGGTACCGGGTTC
65 CCTTTCCCATCACATCTTCTTAGGTACCGGATTC
* * * * *
30601185 GCCATTTCAGTCTCAACCTTTCCCTTCAAATCTTCATG
1 ACCGTTGCAGCCTCAACC-TTCCCTTTAAATCTTCATG
30601223 TTTTTCTCAG
Statistics
Matches: 254, Mismatches: 66, Indels: 31
0.72 0.19 0.09
Matches are distributed among these distances:
97 2 0.01
98 28 0.11
99 184 0.72
100 36 0.14
101 4 0.02
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (98 bp):
ACCGTTGCAGCCTCAACCTTCCCTTTAAATCTTCATGGTACCAGGTTCGCCGTTGCGGCCTCAAC
CTTTCCCATCACATCTTCTTAGGTACCGGATTC
Found at i:30607277 original size:29 final size:30
Alignment explanation
Indices: 30607245--30607448 Score: 92
Period size: 29 Copynumber: 6.9 Consensus size: 30
30607235 CATCCGATGG
* **
30607245 AAAAATGGTAATTTTTGG-ATGTTGTGGGTA
1 AAAAAT-GTAATTTTTGGAAAGTTCAGGGTA
*
30607275 AAATA-GTAATTTTTGGAAAGTTCAGGGTA
1 AAAAATGTAATTTTTGGAAAGTTCAGGGTA
* *
30607304 AAAAATGTAA-TTTTAGATA-TTCGAGGGTAAA
1 AAAAATGTAATTTTTGGAAAGTTC-AGGGT--A
* *
30607335 ATTAAAAT-TAA-TTTTGG-AAGTTTAGAGG-C
1 A--AAAATGTAATTTTTGGAAAGTTCAG-GGTA
* * *
30607364 AAAAATGTGATTTTTGG-AAGTTTACGGT-
1 AAAAATGTAATTTTTGGAAAGTTCAGGGTA
* * *
30607392 AAGAATGTAATTTTTGAAAAGTACGAGGGGTA
1 AAAAATGTAATTTTTGGAAAGTTC-A-GGGTA
* *
30607424 AAATA-GTAA-TTTT-GAAAGTTTAGGG
1 AAAAATGTAATTTTTGGAAAGTTCAGGG
30607449 GGTCAAAATA
Statistics
Matches: 134, Mismatches: 24, Indels: 35
0.69 0.12 0.18
Matches are distributed among these distances:
27 8 0.06
28 33 0.25
29 48 0.36
30 13 0.10
31 12 0.09
32 15 0.11
33 5 0.04
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAAATGTAATTTTTGGAAAGTTCAGGGTA
Found at i:30607398 original size:28 final size:29
Alignment explanation
Indices: 30607338--30607407 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
30607328 GGGTAAAATT
30607338 AAAAT-TAA-TTTTGGAAGTTTAGAGGCA
1 AAAATGTAATTTTTGGAAGTTTAGAGGCA
* * *
30607365 AAAATGTGATTTTTGGAAGTTTA-CGGTA
1 AAAATGTAATTTTTGGAAGTTTAGAGGCA
*
30607393 AGAATGTAATTTTTG
1 AAAATGTAATTTTTG
30607408 AAAAGTACGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.14
28 18 0.50
29 13 0.36
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTAGAGGCA
Found at i:30615500 original size:17 final size:17
Alignment explanation
Indices: 30615478--30615518 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
30615468 TCTCTTGACT
*
30615478 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATATTC
*
30615495 TTTAACCTTTCATATTC
1 TTTAACCTTCCATATTC
30615512 TTGTAAC
1 TT-TAAC
30615519 TATTTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAACCTTCCATATTC
Found at i:30621313 original size:33 final size:33
Alignment explanation
Indices: 30621276--30621341 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
30621266 ATCAAAATGG
30621276 ATAACTCTCAAAATATAAAAAATATAAATGTCA
1 ATAACTCTCAAAATATAAAAAATATAAATGTCA
30621309 ATAACTCTCAAAATATAAAAAATATAAATGTCA
1 ATAACTCTCAAAATATAAAAAATATAAATGTCA
30621342 CTAAATTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (33 bp):
ATAACTCTCAAAATATAAAAAATATAAATGTCA
Found at i:30629334 original size:23 final size:24
Alignment explanation
Indices: 30629303--30629347 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
30629293 GTTTCTCTTT
30629303 TTCTCTTATTATTATTTTTCTTCA
1 TTCTCTTATTATTATTTTTCTTCA
* *
30629327 TTCT-TTATTCTTCTTTTTCTT
1 TTCTCTTATTATTATTTTTCTT
30629348 TCTTGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (24 bp):
TTCTCTTATTATTATTTTTCTTCA
Found at i:30630103 original size:29 final size:30
Alignment explanation
Indices: 30630033--30630103 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
30630023 GCTTAAGTGT
* *
30630033 CCTAATATGTGTTAGTCGATTGTGTATATGC
1 CCTAATATGTGTAAGTCGAATGTG-ATATGC
30630064 CCTAATATGTGTAAGTCGAATGTG-TATGC
1 CCTAATATGTGTAAGTCGAATGTGATATGC
*
30630093 CCTAATCTGTG
1 CCTAATATGTG
30630104 ACATTGTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 15 0.41
31 22 0.59
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (30 bp):
CCTAATATGTGTAAGTCGAATGTGATATGC
Found at i:30633589 original size:6 final size:6
Alignment explanation
Indices: 30633580--30633615 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
30633570 ATCATCCCTT
30633580 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA
1 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA
30633616 CCCCTTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCAAA
Found at i:30641476 original size:22 final size:20
Alignment explanation
Indices: 30641450--30641500 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
30641440 GAATTAATTT
* *
30641450 TATTTTTTTAATATTATTTAT
1 TATTTTTTTAAT-TTAATTAA
*
30641471 TGATTTTTATAATTTAATTAA
1 T-ATTTTTTTAATTTAATTAA
30641492 TATTTTTTT
1 TATTTTTTT
30641501 TATAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTTTTTTAATTTAATTAA
Found at i:30642459 original size:7 final size:7
Alignment explanation
Indices: 30642449--30642473 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30642439 GTGGATTTCA
30642449 TATTTAG
1 TATTTAG
30642456 TATTTAG
1 TATTTAG
30642463 TATTTAG
1 TATTTAG
30642470 TATT
1 TATT
30642474 GGTGTACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Done.