Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 26
Found at i:5138064 original size:110 final size:110
Alignment explanation
Indices: 5137923--5138126 Score: 309
Period size: 110 Copynumber: 1.9 Consensus size: 110
5137913 CTGGAAATTA
* * * * *
5137923 TTTGTTGACAGTCAGCCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATAACC
1 TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATAACC
*
5137988 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
66 CTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
* * * *
5138033 TTTGTTGACAATCAGTCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCC
1 TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATAACC
*
5138098 CTCGCTGTGAAGTTGAAATTGGCTCTGAA
66 CTCGCTGTGAAGTTGAAATTGACTCTGAA
5138127 ACAGGGAAAC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 83 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (110 bp):
TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATAACC
CTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
Found at i:5139224 original size:20 final size:18
Alignment explanation
Indices: 5139201--5139243 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
5139191 TTGAACCCAC
*
5139201 CTTTTTGTTATTTTTCTTTT
1 CTTTTTGTT-TTTTT-TTCT
5139221 C-TTTTGTTTTTTTTTCT
1 CTTTTTGTTTTTTTTTCT
5139238 CTTTTT
1 CTTTTT
5139244 CAATTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 7 0.33
20 1 0.05
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (18 bp):
CTTTTTGTTTTTTTTTCT
Found at i:5139227 original size:19 final size:17
Alignment explanation
Indices: 5139203--5139242 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
5139193 GAACCCACCT
*
5139203 TTTTGTTATTTTTCTTTTC
1 TTTTGTT-TTTTT-TTCTC
5139222 TTTTGTTTTTTTTTCTC
1 TTTTGTTTTTTTTTCTC
5139239 TTTT
1 TTTT
5139243 TCAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTGTTTTTTTTTCTC
Found at i:5149311 original size:16 final size:16
Alignment explanation
Indices: 5149290--5149320 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5149280 ATATAAAAAT
*
5149290 AAAAATAGAAGATAAC
1 AAAAATAAAAGATAAC
5149306 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
5149321 AATGAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAATAAAAGATAAC
Found at i:5149313 original size:36 final size:36
Alignment explanation
Indices: 5149251--5149322 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
5149241 AATAAAATAC
* * *
5149251 ATAAAATAAAGAAGATAATAACAATAACAATATAAAA
1 ATAAAATAAAGAAGATAACAAAAATAA-AAGATAAAA
*
5149288 ATAAAA-ATAGAAGATAACAAAAATAAAAGATAAAA
1 ATAAAATAAAGAAGATAACAAAAATAAAAGATAAAA
5149323 TGAAATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 8 0.26
36 17 0.55
37 6 0.19
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (36 bp):
ATAAAATAAAGAAGATAACAAAAATAAAAGATAAAA
Found at i:5149391 original size:22 final size:22
Alignment explanation
Indices: 5149310--5149393 Score: 57
Period size: 22 Copynumber: 3.7 Consensus size: 22
5149300 GATAACAAAA
5149310 ATAAAAGATAA-AATG-AAATAT
1 ATAAAA-ATAATAATGAAAATAT
* *
5149331 ATAAAATAATAAATATAT-ATAACAT
1 AT-AAA-AAT-AATA-ATGAAAATAT
** *
5149356 ATAATTATAGTAATGAAAATAT
1 ATAAAAATAATAATGAAAATAT
5149378 ATAAAAATAATAATGA
1 ATAAAAATAATAATGA
5149394 TATATGAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
21 4 0.09
22 26 0.57
23 5 0.11
24 3 0.07
25 8 0.17
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (22 bp):
ATAAAAATAATAATGAAAATAT
Found at i:5149400 original size:29 final size:31
Alignment explanation
Indices: 5149341--5149403 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5149331 ATAAAATAAT
* *
5149341 AAATATATATAACATATAATTATAGTAATGA
1 AAATATATATAAAATATAATGATAGTAATGA
5149372 AAATATATA-AAAATAATAATGATA-T-ATGA
1 AAATATATATAAAAT-ATAATGATAGTAATGA
5149401 AAA
1 AAA
5149404 AGAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 7 0.24
30 5 0.17
31 17 0.59
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (31 bp):
AAATATATATAAAATATAATGATAGTAATGA
Found at i:5149410 original size:48 final size:46
Alignment explanation
Indices: 5149321--5149410 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 46
5149311 TAAAAGATAA
* *
5149321 AATGAAATATATAAAATAATAAATATATATAACATATAATTATAGT
1 AATGAAATATATAAAATAATAAATATATATAACAAAGAATTATAGT
5149367 AATGAAAATATATAAAAATAAT-AATGATATATGAA-AAAGAATTA
1 AATG-AAATATAT-AAAATAATAAAT-ATATAT-AACAAAGAATTA
5149411 AATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
46 4 0.11
47 11 0.29
48 21 0.55
49 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (46 bp):
AATGAAATATATAAAATAATAAATATATATAACAAAGAATTATAGT
Found at i:5150554 original size:11 final size:11
Alignment explanation
Indices: 5150499--5150555 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
5150489 TTTATAATAC
*
5150499 AAATTAAATTA
1 AAATTTAATTA
5150510 ACATATTTAATTA
1 A-A-ATTTAATTA
**
5150523 AAAAGTAATTA
1 AAATTTAATTA
* *
5150534 AAAATAAATTA
1 AAATTTAATTA
5150545 AAATTTAATTA
1 AAATTTAATTA
5150556 TGAGAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 26 0.70
12 2 0.05
13 9 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (11 bp):
AAATTTAATTA
Found at i:5154036 original size:17 final size:17
Alignment explanation
Indices: 5154001--5154056 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
5153991 TTACCCATAG
*
5154001 TTTTGTTTTTA-TATATA
1 TTTTATTTTTATTAT-TA
5154018 TTTTATTTTTATTATTA
1 TTTTATTTTTATTATTA
5154035 --TTATTTTTACTTA--A
1 TTTTATTTTTA-TTATTA
5154049 TTTTATTT
1 TTTTATTT
5154057 ATCTTCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
16 9 0.26
17 12 0.35
18 3 0.09
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTATTATTA
Found at i:5159667 original size:17 final size:17
Alignment explanation
Indices: 5159647--5159682 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5159637 TCGCTCTCAC
5159647 TCTTCCT-TTCCTCTTCT
1 TCTTCCTCTT-CTCTTCT
5159664 TCTTCCTCTTCTCTTCT
1 TCTTCCTCTTCTCTTCT
5159681 TC
1 TC
5159683 CTCATTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (17 bp):
TCTTCCTCTTCTCTTCT
Found at i:5161090 original size:37 final size:37
Alignment explanation
Indices: 5161014--5161090 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
5161004 TTTTTATATT
*
5161014 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
5161051 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
5161088 TTT
1 TTT
5161091 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:5161970 original size:14 final size:16
Alignment explanation
Indices: 5161940--5161976 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5161930 GTATGTAAAA
5161940 ATAATAAAATTATATT
1 ATAATAAAATTATATT
5161956 ATAA-AAAATTA-ATT
1 ATAATAAAATTATATT
5161970 ATCAATA
1 AT-AATA
5161977 TTAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
15 9 0.47
16 5 0.26
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATAAAATTATATT
Found at i:5162292 original size:25 final size:25
Alignment explanation
Indices: 5162258--5162315 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
5162248 CTAAAGCTTA
5162258 TTTCGTTCCAGTTTAGTGCGTAACG
1 TTTCGTTCCAGTTTAGTGCGTAACG
5162283 TTTCGTTCCAGTTTAGTGCGTAACG
1 TTTCGTTCCAGTTTAGTGCGTAACG
5162308 TTTCGTTC
1 TTTCGTTC
5162316 TGTTACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (25 bp):
TTTCGTTCCAGTTTAGTGCGTAACG
Found at i:5163148 original size:34 final size:34
Alignment explanation
Indices: 5163079--5163148 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
5163069 GGTTTATTAA
**
5163079 TGACAGATATAATGAATATTGATTATTTGGTTTG
1 TGACAGATATAATGAATATTGATTATTTGACTTG
* *
5163113 TGACAGCTATAATGAATATTGGTTATTTGACTTG
1 TGACAGATATAATGAATATTGATTATTTGACTTG
5163147 TG
1 TG
5163149 GTTATTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (34 bp):
TGACAGATATAATGAATATTGATTATTTGACTTG
Found at i:5164828 original size:31 final size:31
Alignment explanation
Indices: 5164793--5164857 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
5164783 TATTTTTTAA
* *
5164793 TTTAAATTGTTTTCCAATTTGGTGCCCAACC
1 TTTAAATTGCTTTACAATTTGGTGCCCAACC
*
5164824 TTTAAATTGCTTTACACTTTGGTGCCCAACC
1 TTTAAATTGCTTTACAATTTGGTGCCCAACC
5164855 TTT
1 TTT
5164858 GTCTCTGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTAAATTGCTTTACAATTTGGTGCCCAACC
Found at i:5165688 original size:81 final size:81
Alignment explanation
Indices: 5165572--5166388 Score: 1238
Period size: 81 Copynumber: 10.1 Consensus size: 81
5165562 AAGCATTTAG
* * * * * * *
5165572 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACACATTTCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5165637 ACAGCTATGCCATTAA
66 ACAGCTAGGCCATTAA
* *
5165653 TCTTTTACTCAATGGTATTTAACCTTTCATCTAACTGGCATAATTGACATCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
5165718 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * * *
5165734 TGTTTTACTCAAAGGCATTTAATCTTTCATCTAACTGGCATAATTGACGCTTTTCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5165799 ACAGCTAGTCCATTAA
66 ACAGCTAGGCCATTAA
*
5165815 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5165880 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
5165896 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACATTTCTGACAATTGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
5165961 ACATCTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* *
5165977 TCTTTTACTCTAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTCCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5166042 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
5166058 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5166123 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
5166139 TCTTTTACTCAAAGGTTTTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
5166204 ACAGGTAGACCATTAA
66 ACAGCTAGGCCATTAA
* * * *
5166220 TCTTTTACTCAAAGGCATTGAACATTTCATCTAACTGGCATAATTGACATCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
**
5166285 ACAATTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
5166301 TCTTTTACTCAAAGGTATTTAACTTTTCATCTAACTGGCATAATTGACACCTTCCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
5166366 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
5166382 TCTTTTA
1 TCTTTTA
5166389 TTTTAGAATA
Statistics
Matches: 666, Mismatches: 70, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 666 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:5166878 original size:12 final size:12
Alignment explanation
Indices: 5166861--5166891 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5166851 ACTATTATTT
5166861 CAATTTCTATAA
1 CAATTTCTATAA
5166873 CAATTTCTATAA
1 CAATTTCTATAA
5166885 CAATTTC
1 CAATTTC
5166892 AACCTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (12 bp):
CAATTTCTATAA
Found at i:5166945 original size:20 final size:21
Alignment explanation
Indices: 5166920--5166972 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
5166910 AAGCTCGATA
5166920 GTATCGATACCCT-TACCATG
1 GTATCGATACCCTATACCATG
* *
5166940 GTATCGATACTTCTATACTATG
1 GTATCGATAC-CCTATACCATG
*
5166962 GTACCGATACC
1 GTATCGATACC
5166973 TTTCTCTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 2 0.07
22 15 0.56
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (21 bp):
GTATCGATACCCTATACCATG
Found at i:5169001 original size:2 final size:2
Alignment explanation
Indices: 5168994--5169068 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
5168984 CTATAAAAGC
5168994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5169036 TA TA TA TA TA TA TA TA TA TG TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5169069 CTTTCTGACA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5170924 original size:28 final size:29
Alignment explanation
Indices: 5170879--5170934 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
5170869 ACATCACTTT
5170879 TTAAAATATTTTTACAAT-TTAAAAACCC
1 TTAAAATATTTTTACAATGTTAAAAACCC
*
5170907 TTAAAAT-TTTGTTTCAATGTTAAAAACC
1 TTAAAATATTT-TTACAATGTTAAAAACC
5170935 AGAAACGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 13 0.52
29 9 0.36
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (29 bp):
TTAAAATATTTTTACAATGTTAAAAACCC
Found at i:5171434 original size:46 final size:45
Alignment explanation
Indices: 5171380--5171482 Score: 152
Period size: 46 Copynumber: 2.3 Consensus size: 45
5171370 TTATTCATTA
* * *
5171380 ATTTCATTTATGGCATCTTTTCATGCCTTTAATGCACCGTTAAGC
1 ATTTCATTTATGGCATCCTCTCATGCCTTTAATGCACCATTAAGC
* *
5171425 ATTTTCATTTATGGCATCCTCTCATGCCTTTTATGCACCATTATGC
1 A-TTTCATTTATGGCATCCTCTCATGCCTTTAATGCACCATTAAGC
5171471 ATTTCATTTATG
1 ATTTCATTTATG
5171483 TCAAATTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 12 0.23
46 40 0.77
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTCTCATGCCTTTAATGCACCATTAAGC
Found at i:5171596 original size:81 final size:81
Alignment explanation
Indices: 5171508--5171919 Score: 565
Period size: 81 Copynumber: 5.1 Consensus size: 81
5171498 AAGCATTTAG
* * * * *
5171508 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5171573 ACAGCTAGTCCATTAA
66 ACAGCTAGGCCATTAA
*
5171589 TCTTTTACT-AAATGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCTAATG
1 TCTTTTACTCAAA-GGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATG
*
5171653 CACAGCTAGACCATTAA
65 CACAGCTAGGCCATTAA
* * * * * *
5171670 TCTTTTACTCAAAGGCATTTAGCATTTCATCTAACTGGCATATTTGACACCTTTCTACCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
5171735 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
5171751 TATTTTACTCAAAGGTATTTAACCTTTCACCTAATTGGCATAATTGACACGTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
5171816 ACAGCCAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * * *
5171832 TCTTTTACTCAAAGATGTTTAACCTTTCACCTAACAGGCATAATTGGCACCTTTCTGCCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
5171897 ACAACTAAGCCATTAA
66 ACAGCTAGGCCATTAA
5171913 TCTTTTA
1 TCTTTTA
5171920 TTTTAGAATA
Statistics
Matches: 292, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
80 3 0.01
81 286 0.98
82 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:5172498 original size:42 final size:41
Alignment explanation
Indices: 5172452--5172544 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
5172442 CCTTACCATG
* * * **
5172452 GTATCGATACTTCTATACTATAGTATTGATATCTTTCTTTCA
1 GTATCGATACTACTACACTATAGTACTGATA-CTCCCTTTCA
* *
5172494 GTATCGATACTACTACACTATGGTACTGATACTCCCTTTCG
1 GTATCGATACTACTACACTATAGTACTGATACTCCCTTTCA
5172535 GTATCGATAC
1 GTATCGATAC
5172545 CATTTTGTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 17 0.39
42 27 0.61
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.40
Consensus pattern (41 bp):
GTATCGATACTACTACACTATAGTACTGATACTCCCTTTCA
Found at i:5172884 original size:20 final size:20
Alignment explanation
Indices: 5172837--5172887 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5172827 AACTTCTTAT
* *
5172837 AACATCTAAAATCTCTCAAG
1 AACATCTCAAATCTCCCAAG
5172857 AACATCTCAAATCTCCCAAG
1 AACATCTCAAATCTCCCAAG
5172877 AACATCTCAAA
1 AACATCTCAAA
5172888 CCAAGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.29, G:0.04, T:0.22
Consensus pattern (20 bp):
AACATCTCAAATCTCCCAAG
Found at i:5172893 original size:16 final size:17
Alignment explanation
Indices: 5172853--5172894 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 17
5172843 TAAAATCTCT
5172853 CAAGAACATCTCAAATCTCC
1 CAAGAACATCTCAAA---CC
5172873 CAAGAACATCTCAAA-C
1 CAAGAACATCTCAAACC
5172889 CAAGAA
1 CAAGAA
5172895 TCATTCCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
20 15 0.68
ACGTcount: A:0.48, C:0.31, G:0.07, T:0.14
Consensus pattern (17 bp):
CAAGAACATCTCAAACC
Found at i:5181267 original size:2 final size:2
Alignment explanation
Indices: 5181260--5181302 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5181250 ACTTTATTTA
5181260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5181301 AT
1 AT
5181303 TCAGTTTACG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5182036 original size:51 final size:51
Alignment explanation
Indices: 5181969--5182134 Score: 255
Period size: 51 Copynumber: 3.3 Consensus size: 51
5181959 ATGACTAATG
5181969 AATAAAATAATAATAAACTAAAGATAATGTTTTGATTCTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATGTTTTGATTCTATCCTAATTCCT
5182020 AATAAAATAATAATAAACTAAAGATAATGTTTTGATTCTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATGTTTTGATTCTATCCTAATTCCT
* * * * *
5182071 AATAAAATAATAATAAACT-AAGAATATTGTTTTAACTT-GATCTTAATTCTT
1 AATAAAATAATAATAAACTAAAG-ATAATGTTTTGA-TTCTATCCTAATTCCT
5182122 AATAAAATAATAA
1 AATAAAATAATAA
5182135 ATCTAATTCT
Statistics
Matches: 108, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
50 3 0.03
51 103 0.95
52 2 0.02
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATGTTTTGATTCTATCCTAATTCCT
Found at i:5182907 original size:16 final size:16
Alignment explanation
Indices: 5182883--5182925 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
5182873 ATCAAAATTT
5182883 TATAATTAAAATACATC
1 TATAATTAAAATA-ATC
*
5182900 TA-AATTAATTATAATC
1 TATAATTAA-AATAATC
5182916 TATAATTAAA
1 TATAATTAAA
5182926 GTAAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAATTAAAATAATC
Found at i:5184950 original size:20 final size:20
Alignment explanation
Indices: 5184927--5184969 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5184917 CTCGGTTCAG
* *
5184927 TTCGTGTTGACTCAGACCAA
1 TTCGAGTTGACTCAAACCAA
*
5184947 TTCGAGTTGACTTAAACCAA
1 TTCGAGTTGACTCAAACCAA
5184967 TTC
1 TTC
5184970 TAGGAGGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (20 bp):
TTCGAGTTGACTCAAACCAA
Found at i:5185913 original size:18 final size:18
Alignment explanation
Indices: 5185890--5185926 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5185880 GGTGTGACAA
*
5185890 ATCTTTTAAATATCTATT
1 ATCTTTTAAATATCAATT
5185908 ATCTTTTAAATATCAATT
1 ATCTTTTAAATATCAATT
5185926 A
1 A
5185927 AATATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
ATCTTTTAAATATCAATT
Found at i:5188438 original size:41 final size:41
Alignment explanation
Indices: 5188381--5188463 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5188371 CAATCAGTAC
5188381 ATTCAATATAACTATAATCAAAATTAATCATTATTACACAT
1 ATTCAATATAACTATAATCAAAATTAATCATTATTACACAT
5188422 ATTCAATATAACTATAATCAAAATTAATCATTATTACACAT
1 ATTCAATATAACTATAATCAAAATTAATCATTATTACACAT
5188463 A
1 A
5188464 CATGTTTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.36
Consensus pattern (41 bp):
ATTCAATATAACTATAATCAAAATTAATCATTATTACACAT
Found at i:5190495 original size:27 final size:25
Alignment explanation
Indices: 5190444--5190497 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
5190434 TACTAATTTG
*
5190444 AAACCTAAGTTTTATCTAAATTATT
1 AAACCTAAGTTTTATCTAAAATATT
* *
5190469 AAACCTAAAGTATTTTTTTAAAATATT
1 AAACCT-AAGT-TTTATCTAAAATATT
5190496 AA
1 AA
5190498 TTATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 4 0.17
27 14 0.58
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (25 bp):
AAACCTAAGTTTTATCTAAAATATT
Found at i:5190534 original size:13 final size:13
Alignment explanation
Indices: 5190516--5190541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5190506 AAAATTTAAA
5190516 ATTCGAGTAATCG
1 ATTCGAGTAATCG
5190529 ATTCGAGTAATCG
1 ATTCGAGTAATCG
5190542 GCCATCTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
ATTCGAGTAATCG
Found at i:5191214 original size:127 final size:127
Alignment explanation
Indices: 5191013--5191359 Score: 482
Period size: 139 Copynumber: 2.6 Consensus size: 127
5191003 ACAGAGTTAT
* * * *
5191013 AACCATAATAATGCGGATCATACCTCGGATCAGGTCACCACAGGGTCGAATCAAATATTAGAAAT
1 AACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGATCGAATCAAATATTAGAAAT
5191078 AATAAATAAATAAATAAAAGTTAGAATGCAATAAAATAAAAGTCACTAGTTAGCAGAGCCCG
66 AATAAATAAATAAATAAAAGTTAGAATGCAATAAAATAAAAGTCACTAGTTAGCAGAGCCCG
5191140 AACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGATCGAATCAAATATGAGAAAT
1 AACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGATCGAATCAAATAT------T
* *
5191205 GATAAATAAATAAATAAATAAATAAACAAAAGTTAGAATGCAATAAAATAAAAGTCATTAGTTAG
60 -AGAAAT-AATAAATAAATAAAT----AAAAGTTAGAATGCAATAAAATAAAAGTCACTAGTTAG
* *
5191270 CAGAGTCTG
119 CAGAGCCCG
*
5191279 AACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAA-AGTCGAATC-GATATTAGAAA
1 AACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGA-TCGAATCAAATATTAGAAA
5191342 TAATAAATAAATAAATAA
65 TAATAAATAAATAAATAA
5191360 CAATGATTAA
Statistics
Matches: 197, Mismatches: 10, Indels: 27
0.84 0.04 0.12
Matches are distributed among these distances:
126 2 0.01
127 54 0.27
130 15 0.08
131 5 0.03
132 1 0.01
133 1 0.01
134 5 0.03
135 15 0.08
138 5 0.03
139 94 0.48
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (127 bp):
AACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGATCGAATCAAATATTAGAAAT
AATAAATAAATAAATAAAAGTTAGAATGCAATAAAATAAAAGTCACTAGTTAGCAGAGCCCG
Found at i:5191215 original size:4 final size:4
Alignment explanation
Indices: 5191206--5191230 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5191196 ATGAGAAATG
5191206 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5191231 CAAAAGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5191519 original size:4 final size:4
Alignment explanation
Indices: 5191510--5191534 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5191500 ATGAGAAATG
5191510 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5191535 CAAAAGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5191520 original size:304 final size:310
Alignment explanation
Indices: 5191194--5191809 Score: 1181
Period size: 304 Copynumber: 2.0 Consensus size: 310
5191184 ATCGAATCAA
5191194 ATATGAGAAATGATAAATAAATAAATAAATAAATAAACAAAAGTTAGAATGCAATAAAATAAAAG
1 ATATGAGAAATGATAAATAAATAAATAAATAAATAAACAAAAGTTAGAATGCAATAAAATAAAAG
5191259 TCATTAGTTAGCAGAGTCTGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAAG
66 TCATTAGTTAGCAGAGTCTGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAAG
5191324 TCGAATCGA-TATTAGAAATAATAAATAAATAAATAACAATGATTAAAGTACGATAAAATAAAAG
131 TCGAATCGATTATTAGAAATAATAAATAAATAAATAACAATGATTAAAGTACGATAAAATAAAAG
5191388 -TAATAG-TAGAAATAAATAACATAGCAGAAAAGTGAACAAATTAAAAAG-T-TAAAATTTGCAT
196 TTAATAGTTAGAAATAAATAACATAGCAGAAAAGTGAACAAATTAAAAAGTTATAAAATTTGCAT
5191449 GGATATTCG-AATAAATAAAAAAAATAAGTGACTAAAGTGCCAAAGGAGT
261 GGATATTCGAAATAAATAAAAAAAATAAGTGACTAAAGTGCCAAAGGAGT
5191498 ATATGAGAAATGATAAATAAATAAATAAATAAATAAACAAAAGTTAGAATGCAATAAAATAAAAG
1 ATATGAGAAATGATAAATAAATAAATAAATAAATAAACAAAAGTTAGAATGCAATAAAATAAAAG
5191563 TCATTAGTTAGCAGAGTCTGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAAG
66 TCATTAGTTAGCAGAGTCTGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAAG
5191628 TCGAATCGATTATTAGAAATAATAAATAAATAAATAACAATGATTAAAGTACGATAAAATAAAAG
131 TCGAATCGATTATTAGAAATAATAAATAAATAAATAACAATGATTAAAGTACGATAAAATAAAAG
5191693 TTAATAGTTAGAAATAAATAACATAGCAGAAAAGTGAACAAATTAAAAAGTTAATAAAATTTGCA
196 TTAATAGTTAGAAATAAATAACATAGCAGAAAAGTGAACAAATTAAAAAGTT-ATAAAATTTGCA
5191758 TGGATATTCGAAATAAATAAAAAAAATAAGTGACTAAAGTGCCAAAGGAGT
260 TGGATATTCGAAATAAATAAAAAAAATAAGTGACTAAAGTGCCAAAGGAGT
5191809 A
1 A
5191810 AAATACAGGG
Statistics
Matches: 305, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
304 139 0.46
305 55 0.18
306 6 0.02
307 42 0.14
308 1 0.00
310 21 0.07
311 41 0.13
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (310 bp):
ATATGAGAAATGATAAATAAATAAATAAATAAATAAACAAAAGTTAGAATGCAATAAAATAAAAG
TCATTAGTTAGCAGAGTCTGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAAG
TCGAATCGATTATTAGAAATAATAAATAAATAAATAACAATGATTAAAGTACGATAAAATAAAAG
TTAATAGTTAGAAATAAATAACATAGCAGAAAAGTGAACAAATTAAAAAGTTATAAAATTTGCAT
GGATATTCGAAATAAATAAAAAAAATAAGTGACTAAAGTGCCAAAGGAGT
Found at i:5193105 original size:117 final size:117
Alignment explanation
Indices: 5192952--5193401 Score: 611
Period size: 117 Copynumber: 3.9 Consensus size: 117
5192942 CATATGGGAT
* * * *
5192952 GAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCGGATGAGTTC
1 GAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTCGGATGAGTTC
* * *
5193017 TTCTCATTATGAACTCTCCATTCGAAATGATGATCCACCTCCTTCTGTGATA
66 TTCTCATTATGAACTCTCCATTGGAAATGATGATCCACCTCATTCTGTGATG
* * * **
5193069 GAATCGAACAAAGATTGAACCAA-TTCTTCTCATTATGAACTTTTTTTATCT-TATCGGATGAGT
1 GAATCGAACCAAGGTTGAA-CAAGTTCTTCTCATTATGAACTTTTTCTCCCTCT-TCGGATGAGT
* * **
5193132 TCTTCTCATTATGAACTCTCCACTGGAAAT-ATTGATACACCTTTTTCTGTGATG
64 TCTTCTCATTATGAACTCTCCATTGGAAATGA-TGATCCACCTCATTCTGTGATG
* * * * *
5193186 GAATTGAACCAAGGTTGAACAAGTTTTTCTCATTATGAACTTTTTCCCCCTCATCAGATGAGTTC
1 GAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTCGGATGAGTTC
* * *
5193251 TTCTCATTATGAACTCTCTATAGGAAATGTTGATCCACCTCATTCTGTGATG
66 TTCTCATTATGAACTCTCCATTGGAAATGATGATCCACCTCATTCTGTGATG
*
5193303 GAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT-CCTCTTCGGATGAGTTA
1 GAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTCGGATGAGTTC
*
5193367 TTCTCATTATGAACTCTCCATTGGAAATGTTGATC
66 TTCTCATTATGAACTCTCCATTGGAAATGATGATC
5193402 AATTTATCTT
Statistics
Matches: 288, Mismatches: 39, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
116 52 0.18
117 233 0.81
118 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (117 bp):
GAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTCGGATGAGTTC
TTCTCATTATGAACTCTCCATTGGAAATGATGATCCACCTCATTCTGTGATG
Found at i:5193494 original size:14 final size:14
Alignment explanation
Indices: 5193475--5193512 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
5193465 TGTTTGAAGT
5193475 ACCCGAAGGTATTG
1 ACCCGAAGGTATTG
5193489 ACCCGAAGGTATTG
1 ACCCGAAGGTATTG
5193503 ACCCGAAGGT
1 ACCCGAAGGT
5193513 TCTCGAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (14 bp):
ACCCGAAGGTATTG
Found at i:5193797 original size:73 final size:73
Alignment explanation
Indices: 5193693--5194228 Score: 611
Period size: 73 Copynumber: 7.3 Consensus size: 73
5193683 AGAGAAGCTC
* * * *
5193693 TCTCTAGTGAGATAAATTTTGTTTCGAGGGAAAACTGCCTCAAGCGAGACGGAGTTGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAG
5193758 AAAAACCA
66 AAAAACCA
* *
5193766 TCTCGAGTTAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAG
5193831 AAAAACCA
66 AAAAACCA
* *
5193839 TCTCAAGTGAGATACATTTTGTTTCAATGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAG
*
5193904 GAAAACCA
66 AAAAACCA
* * * * **
5193912 TCTCGAGTGAGATAAAATTTTTTGTTTCAAGGG-AAACTGTCTCCAGTGAAACGAAACTGGTTTT
1 TCTCAAGTGAGAT-AAA--TTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTT
5193976 AAGAAAAACCA
63 AAGAAAAACCA
* * * * *
5193987 TCTCAAGTAAGATAAAATTTCTTGTTTTAAGGG-AAACTGTCTCCAGTGAGACGAAACTT-GTTT
1 TCTCAAGTGAGAT-AAA-TT-TTGTTTCAAGGGAAAACTGTCTCAAGCGAGACG-AAGTTGGTTT
* *
5194050 TGAGAAAAACAA
62 TAAGAAAAACCA
* * * *
5194062 TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCCAGTGAGACAAAACTT-GTTTTAA
1 TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGAC-GAAGTTGGTTTTAA
5194126 GAAAAA-CA
65 GAAAAACCA
* * * *
5194134 CTCTCAAGTGAGATAAATTTTCTTGTTTCAAGGG-AAACTGTTTCCAGTGAGACAAAAGTT-GTT
1 -TCTCAAGTGAGATAAA--TT-TTGTTTCAAGGGAAAACTGTCTCAAGCGAGAC-GAAGTTGGTT
5194197 TTAAGAAAAA-CA
61 TTAAGAAAAACCA
*
5194209 CTTTCAAGTGAGATAAATTT
1 -TCTCAAGTGAGATAAATTT
5194229 CTTATCTTTG
Statistics
Matches: 417, Mismatches: 35, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
72 13 0.03
73 204 0.49
74 8 0.02
75 164 0.39
76 28 0.07
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (73 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAG
AAAAACCA
Found at i:5193880 original size:37 final size:36
Alignment explanation
Indices: 5193701--5194228 Score: 178
Period size: 36 Copynumber: 14.3 Consensus size: 36
5193691 TCTCTCTAGT
* *
5193701 GAGATAAATTTTGTTTCGAGGGAAAACTGCCTCAAGC
1 GAGATAAATTTTGTTTC-AAGGAAAACTGTCTCAAGC
*** * * * * ** * *
5193738 GAGACGGAGTTGGTTTTAAGAAAAACCATCTCGAGT
1 GAGATAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
*
5193774 TAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGC
1 GAGATAAATTTTGTTTCAA-GGAAAACTGTCTCAAGC
** * * * * ** *
5193811 GAGACGAAGTTGGTTTTAAGAAAAACCATCTCAAGT
1 GAGATAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
*
5193847 GAGATACATTTTGTTTCAATGGAAAACTGTCTCAAGC
1 GAGATAAATTTTGTTTCAA-GGAAAACTGTCTCAAGC
** * * * ** * *
5193884 GAGACGAAGTTGGTTTTAAGGAAAACCATCTCGAGT
1 GAGATAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
* * *
5193920 GAGATAAAATTTTTTGTTTCAAGGGAAACTGTCTCCAGT
1 GAGAT-AAA--TTTTGTTTCAAGGAAAACTGTCTCAAGC
* * * * * * ** *
5193959 GAAACGAAA-CTGGTTTTAAGAAAAACCATCTCAAGT
1 GAGA-TAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
* * * * *
5193995 AAGATAAAATTTCTTGTTTTAAGGGAAACTGTCTCCAGT
1 GAGAT-AAA-TT-TTGTTTCAAGGAAAACTGTCTCAAGC
* * ** * ** *
5194034 GAGACGAAA-CTTGTTTTGAGAAAAACAATCTCAAGT
1 GAGA-TAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
* *
5194070 GAGATAAATTTTGTTTCAAGGGAAAACTGTCTCCAGT
1 GAGATAAATTTTGTTTCAA-GGAAAACTGTCTCAAGC
* ** * * ** *
5194107 GAGACAAAACTTGTTTTAAGAAAAACACTCTCAAGT
1 GAGATAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
* * * *
5194143 GAGATAAATTTTCTTGTTTCAAGGGAAACTGTTTCCAGT
1 GAGATAAA--TT-TTGTTTCAAGGAAAACTGTCTCAAGC
* ** * * ** * *
5194182 GAGACAAAAGTTGTTTTAAGAAAAACACTTTCAAGT
1 GAGATAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
5194218 GAGATAAATTT
1 GAGATAAATTT
5194229 CTTATCTTTG
Statistics
Matches: 344, Mismatches: 131, Indels: 33
0.68 0.26 0.06
Matches are distributed among these distances:
35 3 0.01
36 170 0.49
37 92 0.27
39 79 0.23
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
GAGATAAATTTTGTTTCAAGGAAAACTGTCTCAAGC
Found at i:5194097 original size:148 final size:148
Alignment explanation
Indices: 5193693--5194228 Score: 642
Period size: 148 Copynumber: 3.6 Consensus size: 148
5193683 AGAGAAGCTC
* * * * * *
5193693 TCTCTAGTGAGAT-AAA-TT-TTGTTTCGAGGGAAAACTGCCTCAAGCGAGACG-GAGTTGGTTT
1 TCTCAAGTGAGATAAAATTTCTTGTTTCAAGGG-AAACTGTCTCCAGTGAGACGAAAGTT-GTTT
* * * * *
5193754 TAAGAAAAACCATCTCGAGTTAGATAAATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAA
64 TAAGAAAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCCAGTGAGACGAA
**
5193819 GTTGGTTTTAAGAAAAACCA
129 ACTGGTTTTAAGAAAAACCA
* * * *
5193839 TCTCAAGTGAGAT-ACA-TT-TTGTTTCAATGGAAAACTGTCTCAAGCGAGACG-AAGTTGGTTT
1 TCTCAAGTGAGATAAAATTTCTTGTTTCAA-GGGAAACTGTCTCCAGTGAGACGAAAGTT-GTTT
* * * *
5193900 TAAGGAAAACCATCTCGAGTGAGATAAAATTTTTTGTTTCAAGGG-AAACTGTCTCCAGTGAAAC
64 TAAGAAAAACAATCTCAAGTGAGAT-AAA--TTTTGTTTCAAGGGAAAACTGTCTCCAGTGAGAC
5193964 GAAACTGGTTTTAAGAAAAACCA
126 GAAACTGGTTTTAAGAAAAACCA
* * * *
5193987 TCTCAAGTAAGATAAAATTTCTTGTTTTAAGGGAAACTGTCTCCAGTGAGACGAAACTTGTTTTG
1 TCTCAAGTGAGATAAAATTTCTTGTTTCAAGGGAAACTGTCTCCAGTGAGACGAAAGTTGTTTTA
*
5194052 AGAAAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCCAGTGAGACAAAAC
66 AGAAAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCCAGTGAGACGAAAC
*
5194117 TTGTTTTAAGAAAAA-CA
131 TGGTTTTAAGAAAAACCA
* * *
5194134 CTCTCAAGTGAGATAAATTTTCTTGTTTCAAGGGAAACTGTTTCCAGTGAGACAAAAGTTGTTTT
1 -TCTCAAGTGAGATAAAATTTCTTGTTTCAAGGGAAACTGTCTCCAGTGAGACGAAAGTTGTTTT
* *
5194199 AAGAAAAACACTTTCAAGTGAGATAAATTT
65 AAGAAAAACAATCTCAAGTGAGATAAATTT
5194229 CTTATCTTTG
Statistics
Matches: 344, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
146 75 0.22
147 21 0.06
148 170 0.49
149 19 0.06
150 47 0.14
151 12 0.03
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (148 bp):
TCTCAAGTGAGATAAAATTTCTTGTTTCAAGGGAAACTGTCTCCAGTGAGACGAAAGTTGTTTTA
AGAAAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTCCAGTGAGACGAAAC
TGGTTTTAAGAAAAACCA
Found at i:5196175 original size:8 final size:8
Alignment explanation
Indices: 5196159--5196264 Score: 52
Period size: 8 Copynumber: 12.0 Consensus size: 8
5196149 GATCTGTCTA
*
5196159 TTTTCTTC
1 TTTTTTTC
5196167 TTTTTTTC
1 TTTTTTTC
5196175 TTTTTTCTCTC
1 -TTTTT-T-TC
5196186 TTTTTTTTCC
1 -TTTTTTT-C
5196196 TTATTTTTC
1 TT-TTTTTC
*
5196205 -CTTTTTC
1 TTTTTTTC
*
5196212 CTTTTTTC
1 TTTTTTTC
5196220 TTTTTCTCTC
1 TTTTT-T-TC
5196230 TTTCTTTTTC
1 -TT-TTTTTC
*
5196240 CTTTTTTC
1 TTTTTTTC
**
5196248 CCTTTTTC
1 TTTTTTTC
5196256 TATTTTTTC
1 T-TTTTTTC
5196265 CTATCTTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
7 6 0.08
8 30 0.38
9 17 0.22
10 12 0.15
11 11 0.14
12 3 0.04
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5196203 original size:14 final size:14
Alignment explanation
Indices: 5196168--5196247 Score: 74
Period size: 14 Copynumber: 5.5 Consensus size: 14
5196158 ATTTTCTTCT
*
5196168 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTCC
*
5196182 TCTCTTT-TTTTTCC
1 T-TTTTTCTTTTTCC
5196196 TTATTTTTCCTTTTTCC
1 -T-TTTTT-CTTTTTCC
5196213 TTTTTTCTTTTT-C
1 TTTTTTCTTTTTCC
*
5196226 TCTCTTTCTTTTTCC
1 T-TTTTTCTTTTTCC
5196241 TTTTTTC
1 TTTTTTC
5196248 CCTTTTTCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.04
14 28 0.52
15 16 0.30
16 1 0.02
17 7 0.13
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTTTTCC
Found at i:5196226 original size:44 final size:46
Alignment explanation
Indices: 5196164--5196264 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 46
5196154 GTCTATTTTC
*
5196164 TTCT-TTTTTTCTTTTTTCTCTCTTT-TTTTTCCTTATTTTTCCTTT
1 TTCTATTTTTTCTTTTTTCTCTCTTTCTTTTTCCTT-TTTTCCCTTT
*
5196209 TTC-CTTTTTTC-TTTTTCTCTCTTTCTTTTTCCTTTTTTCCCTTT
1 TTCTATTTTTTCTTTTTTCTCTCTTTCTTTTTCCTTTTTTCCCTTT
5196253 TTCTATTTTTTC
1 TTCTATTTTTTC
5196265 CTATCTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
44 25 0.49
45 26 0.51
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (46 bp):
TTCTATTTTTTCTTTTTTCTCTCTTTCTTTTTCCTTTTTTCCCTTT
Found at i:5196254 original size:36 final size:36
Alignment explanation
Indices: 5196199--5196277 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
5196189 TTTTTCCTTA
* *
5196199 TTTTTCC-TTTTTCCTTTTTTCT-TTTTCTCTCTTTC
1 TTTTTCCTTTTTTCCCTTTTTCTATTTTCTC-CTATC
*
5196234 TTTTTCCTTTTTTCCCTTTTTCTATTTTTTCCTATC
1 TTTTTCCTTTTTTCCCTTTTTCTATTTTCTCCTATC
5196270 TTTTTCCT
1 TTTTTCCT
5196278 ATCTTTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 7 0.18
36 26 0.67
37 6 0.15
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (36 bp):
TTTTTCCTTTTTTCCCTTTTTCTATTTTCTCCTATC
Found at i:5196275 original size:11 final size:11
Alignment explanation
Indices: 5196249--5196285 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5196239 CCTTTTTTCC
5196249 CTTTTT-CTAT
1 CTTTTTCCTAT
5196259 -TTTTTCCTAT
1 CTTTTTCCTAT
5196269 CTTTTTCCTAT
1 CTTTTTCCTAT
5196280 CTTTTT
1 CTTTTT
5196286 TGTTGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.20
10 4 0.16
11 16 0.64
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTTTTCCTAT
Found at i:5199815 original size:25 final size:26
Alignment explanation
Indices: 5199771--5199824 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
5199761 GACTAATTTG
5199771 AAACCTAAGTTTTATCT-AAATTATT
1 AAACCTAAGTTTTATCTAAAATTATT
5199796 AAACCTAAAGTATTT-T-TAAAAATTATT
1 AAACCT-AAGT-TTTATCT-AAAATTATT
5199823 AA
1 AA
5199825 TTATTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
25 7 0.28
26 5 0.20
27 13 0.52
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (26 bp):
AAACCTAAGTTTTATCTAAAATTATT
Found at i:5200039 original size:13 final size:13
Alignment explanation
Indices: 5200021--5200089 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 13
5200011 AAACTTAATT
5200021 AAAATAAAATAAA
1 AAAATAAAATAAA
5200034 AAAATACAATAATAAA
1 AAAAT--AA-AATAAA
5200050 AAACAGTAAAA-AAA
1 AAA-A-TAAAATAAA
*
5200064 ACAAT-AAATAAA
1 AAAATAAAATAAA
*
5200076 AAACTTAAAATAAA
1 AAA-ATAAAATAAA
5200090 CATAAATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
11 3 0.07
12 6 0.13
13 7 0.16
14 12 0.27
15 4 0.09
16 11 0.24
17 1 0.02
18 1 0.02
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.16
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:5200050 original size:26 final size:26
Alignment explanation
Indices: 5200020--5200096 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
5200010 TAAACTTAAT
5200020 TAAAATAA-AATAAAAAAATACAAT-AA
1 TAAAA-AACAATAAAAAAA-ACAATAAA
*
5200046 TAAAAAACAGTAAAAAAAACAATAAA
1 TAAAAAACAATAAAAAAAACAATAAA
* *
5200072 TAAAAAAC-TTAAAATAAAC-ATAAA
1 TAAAAAACAATAAAAAAAACAATAAA
5200096 T
1 T
5200097 TAAAGGTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.13
25 16 0.35
26 24 0.52
ACGTcount: A:0.74, C:0.06, G:0.01, T:0.18
Consensus pattern (26 bp):
TAAAAAACAATAAAAAAAACAATAAA
Found at i:5200084 original size:25 final size:26
Alignment explanation
Indices: 5200030--5200096 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
5200020 TAAAATAAAA
5200030 TAAAAAAATACAAT-AATAAAAAACAG
1 TAAAAAAA-ACAATAAATAAAAAACAG
*
5200056 TAAAAAAAACAATAAATAAAAAAC-T
1 TAAAAAAAACAATAAATAAAAAACAG
*
5200081 TAAAATAAAC-ATAAAT
1 TAAAAAAAACAATAAAT
5200097 TAAAGGTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 6 0.16
25 14 0.37
26 18 0.47
ACGTcount: A:0.73, C:0.07, G:0.01, T:0.18
Consensus pattern (26 bp):
TAAAAAAAACAATAAATAAAAAACAG
Found at i:5200100 original size:25 final size:25
Alignment explanation
Indices: 5199979--5200096 Score: 73
Period size: 26 Copynumber: 4.6 Consensus size: 25
5199969 TAAATCTAAG
5199979 AAAATAAATCATGAAATAAAACAA-TT
1 AAAATAAA-CAT-AAATAAAACAACTT
* * * **
5200005 AATAATAAACTTAATTAAAATAAAAT
1 AA-AATAAACATAAATAAAACAACTT
* *
5200031 AAAAAAATACA-ATAATAAAA-AACAGT
1 AAAATAA-ACATA-AATAAAACAAC-TT
*
5200057 AAAAAAAACAATAAATAAAA-AACTT
1 AAAATAAAC-ATAAATAAAACAACTT
5200082 AAAATAAACATAAAT
1 AAAATAAACATAAAT
5200097 TAAAGGTGAA
Statistics
Matches: 74, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
24 6 0.08
25 27 0.36
26 34 0.46
27 7 0.09
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (25 bp):
AAAATAAACATAAATAAAACAACTT
Found at i:5200482 original size:139 final size:128
Alignment explanation
Indices: 5200328--5200710 Score: 391
Period size: 127 Copynumber: 2.9 Consensus size: 128
5200318 CGATTAACAT
* * * * *
5200328 AGTCTGAACCATAATAATGTGAATCATACCCCGGATTAGGTCACTATAATGTCAAATCAAATATT
1 AGTCTGAACCATAATAATG-GAATCATACCCTGGATCAGGTCACCACAA-GTCGAATCAAATATT
5200393 AGAAATAATAAATAAATAAACAAACAAACAAACAAAAGTTAGAATGCAATAAAATAAAAGT-AAG
64 AGAAATAATAAATAAAT--------AAA-AAACAAAAGTTAGAATGCAATAAAATAAAAGTCAA-
5200457 AAGTTAGCAA
119 AAGTTAGCAA
* * * *
5200467 AGTCCGAACCATAATAATGCAGATCATACCCTGAATCGGGTCACCACAAGATCGAATCAAATATT
1 AGTCTGAACCATAATAATGGA-ATCATACCCTGGATCAGGTCACCACAAG-TCGAATCAAATATT
* * * *
5200532 AGAAATAATAAATAAAT---AAACAAAAGTTAGAATGTAATAAAATAAAAGTCAATAGTTAGTAG
64 AGAAATAATAAATAAATAAAAAACAAAAGTTAGAATGCAATAAAATAAAAGTCAAAAGTTAGCAA
* * *
5200594 AGTCTGAACCATAATAATACGAATCATACCCTGGATCAGGTCACCACAAGGCCGAATCGAATATT
1 AGTCTGAACCATAATAAT-GGAATCATACCCTGGATCAGGTCACCACAA-GTCGAATCAAATATT
* * *
5200659 AGAAACAATAAATAAATAAATAAC-AATGATTA-AAGTGCAATAAAATAAAAGT
64 AGAAATAATAAATAAATAAAAAACAAAAG-TTAGAA-TGCAATAAAATAAAAGT
5200711 TAGTAGTTAC
Statistics
Matches: 210, Mismatches: 24, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
127 108 0.51
128 4 0.02
129 5 0.02
130 22 0.10
138 2 0.01
139 69 0.33
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.22
Consensus pattern (128 bp):
AGTCTGAACCATAATAATGGAATCATACCCTGGATCAGGTCACCACAAGTCGAATCAAATATTAG
AAATAATAAATAAATAAAAAACAAAAGTTAGAATGCAATAAAATAAAAGTCAAAAGTTAGCAA
Found at i:5200565 original size:127 final size:127
Alignment explanation
Indices: 5200422--5200723 Score: 396
Period size: 127 Copynumber: 2.4 Consensus size: 127
5200412 ACAAACAAAC
* *
5200422 AAACAAAAGTTAGAATGCAATAAAATAAAAGTAAGAAGTTAGCAAAGTCCGAACCATAATAATGC
1 AAACAAAAGTTAGAATGCAATAAAATAAAAGTAAGTAGTTAGCAAAGTCCGAACCATAATAATAC
* * *
5200487 -AGATCATACCCTGAATCGGGTCACCACAAGATCGAATCAAATATTAGAAATAATAAATAAAT
66 GA-ATCATACCCTGAATCAGGTCACCACAAGACCGAATCAAATATTAGAAACAATAAATAAAT
* * * *
5200549 AAACAAAAGTTAGAATGTAATAAAATAAAAGTCAA-TAGTTAGTAGAGTCTGAACCATAATAATA
1 AAACAAAAGTTAGAATGCAATAAAATAAAAGT-AAGTAGTTAGCAAAGTCCGAACCATAATAATA
* * *
5200613 CGAATCATACCCTGGATCAGGTCACCACAAGGCCGAATCGAATATTAGAAACAATAAATAAAT
65 CGAATCATACCCTGAATCAGGTCACCACAAGACCGAATCAAATATTAGAAACAATAAATAAAT
* *
5200676 AAATAACAATGATTA-AAGTGCAATAAAATAAAAGTTAGTAGTTA-CAAA
1 AAACAA-AA-G-TTAGAA-TGCAATAAAATAAAAGTAAGTAGTTAGCAAA
5200724 AAAATAACAA
Statistics
Matches: 151, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
127 115 0.76
128 5 0.03
129 6 0.04
130 25 0.17
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (127 bp):
AAACAAAAGTTAGAATGCAATAAAATAAAAGTAAGTAGTTAGCAAAGTCCGAACCATAATAATAC
GAATCATACCCTGAATCAGGTCACCACAAGACCGAATCAAATATTAGAAACAATAAATAAAT
Found at i:5202559 original size:3 final size:3
Alignment explanation
Indices: 5202551--5202604 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
5202541 TGTTAAGAAA
5202551 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5202598 TAT TAT T
1 TAT TAT T
5202605 TTAATGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5206935 original size:14 final size:14
Alignment explanation
Indices: 5206916--5206949 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5206906 ATTTTCTTTC
5206916 TTTTTCTATTATTT
1 TTTTTCTATTATTT
* *
5206930 TTTTTCTCTTCTTT
1 TTTTTCTATTATTT
5206944 TTTTTC
1 TTTTTC
5206950 CAATTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTATTATTT
Found at i:5206941 original size:25 final size:25
Alignment explanation
Indices: 5206895--5206945 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
5206885 TTCATGTTCA
5206895 TCTATTCATTTATTTTCTTTCTTTT
1 TCTATTCATTTATTTTCTTTCTTTT
*
5206920 TCTATT-ATTTTTTTTCTCTTCTTTT
1 TCTATTCATTTATTTTCT-TTCTTTT
5206945 T
1 T
5206946 TTTCCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (25 bp):
TCTATTCATTTATTTTCTTTCTTTT
Found at i:5207279 original size:44 final size:44
Alignment explanation
Indices: 5207189--5207280 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
5207179 AAGAATGAAA
* * * *
5207189 ATGTTGATCTACCTCCATCTTTGATAGAATTGAACAAAATGTTG
1 ATGTCGATCTACCTCCATCTGTGATAGAATTCAACAAAATGGTG
* * *
5207233 ATGTCGATCTATCTCCTTCTGTGATAGAA-TCAAGCAACATGGTG
1 ATGTCGATCTACCTCCATCTGTGATAGAATTCAA-CAAAATGGTG
5207277 ATGT
1 ATGT
5207281 TTATCCAACT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.08
44 37 0.93
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (44 bp):
ATGTCGATCTACCTCCATCTGTGATAGAATTCAACAAAATGGTG
Found at i:5207847 original size:102 final size:102
Alignment explanation
Indices: 5207497--5207903 Score: 597
Period size: 103 Copynumber: 4.0 Consensus size: 102
5207487 GAGATAAAAT
* * *
5207497 TTTGAGTG-AACAATTTCAAATTTTGTGTTCCAAGGGAAAACTTTCTCAATG-AAGACGAAATTG
1 TTTGAGTGAAACAATTTCAAATTTTATGTTCCAAGGGAAAACTGTCTCAA-GCGAGACGAAATTG
* * * *
5207560 ATTTTAAGAAAAACCATTTCAAATTAGATAAATTTTTG
65 ATTTAAAGAAAAATCATCTCAAATGAGATAAATTTTTG
5207598 TTTCGAGTGAAACAATTTCAAATTTTATGTTCCAAGGGAAAACTGTCTCAAGCGAGACGAAATTG
1 TTT-GAGTGAAACAATTTCAAATTTTATGTTCCAAGGGAAAACTGTCTCAAGCGAGACGAAATTG
* *
5207663 ATTTTAAGAAAAATCATCTCAAGTGAGATAAATTTTTG
65 ATTTAAAGAAAAATCATCTCAAATGAGATAAATTTTTG
* * *
5207701 TTTTGAGTGAAACAATTTCAAAATTTATGTTCTAAGGGAAAACTGTCTCAAGCGAGATGAAATTG
1 -TTTGAGTGAAACAATTTCAAATTTTATGTTCCAAGGGAAAACTGTCTCAAGCGAGACGAAATTG
5207766 ATTTAAAGAAAAATCATCTCAAATGAGATAAATTTTT-
65 ATTTAAAGAAAAATCATCTCAAATGAGATAAATTTTTG
* * *
5207803 TTATGAGTGAAACAATTTCAAAATTTT-TGTTTCAAGGGAAAACTGTCTCAAGCGAGACAAAATC
1 TT-TGAGTGAAACAATTTC-AAATTTTATGTTCCAAGGGAAAACTGTCTCAAGCGAGACGAAATT
*
5207867 GATTTAAAGAAAAATCATCTCAAGTGAGATAAATTTT
64 GATTTAAAGAAAAATCATCTCAAATGAGATAAATTTT
5207904 GATCATTGCT
Statistics
Matches: 281, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
101 5 0.02
102 90 0.32
103 183 0.65
104 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (102 bp):
TTTGAGTGAAACAATTTCAAATTTTATGTTCCAAGGGAAAACTGTCTCAAGCGAGACGAAATTGA
TTTAAAGAAAAATCATCTCAAATGAGATAAATTTTTG
Found at i:5207879 original size:205 final size:205
Alignment explanation
Indices: 5207496--5207903 Score: 626
Period size: 205 Copynumber: 2.0 Consensus size: 205
5207486 TGAGATAAAA
* * *
5207496 TTTTGAGTGAACAATTTCAAATTTTGTGTTCCAAGGGAAAACTTTCTCAATGAAGACGAAATTGA
1 TTTTGAGTGAACAATTTCAAAATTTATGTTCCAAGGGAAAACTGTCTCAATGAAGACGAAATTGA
* * *
5207561 TTTTAAGAAAAACCATTTCAAATTAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTAT
66 TTTAAAGAAAAACCATCTCAAATGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTAT
* * *
5207626 GTTCCAAGGGAAAACTGTCTCAAGCGAGACGAAATTGATTTTAAGAAAAATCATCTCAAGTGAGA
131 GTTCCAAGGGAAAACTGTCTCAAGCGAGACAAAATCGATTTAAAGAAAAATCATCTCAAGTGAGA
5207691 TAAATTTTTG
196 TAAATTTTTG
* * *
5207701 TTTTGAGTGAAACAATTTCAAAATTTATGTTCTAAGGGAAAACTGTCTCAA-GCGAGATGAAATT
1 TTTTGAGTG-AACAATTTCAAAATTTATGTTCCAAGGGAAAACTGTCTCAATG-AAGACGAAATT
*
5207765 GATTTAAAGAAAAATCATCTCAAATGAGATAAATTTTT-TTAT-GAGTGAAACAATTTCAAAATT
64 GATTTAAAGAAAAACCATCTCAAATGAGATAAATTTTTGTT-TCGAGTGAAACAATTTC-AAATT
*
5207828 TT-TGTTTCAAGGGAAAACTGTCTCAAGCGAGACAAAATCGATTTAAAGAAAAATCATCTCAAGT
127 TTATGTTCCAAGGGAAAACTGTCTCAAGCGAGACAAAATCGATTTAAAGAAAAATCATCTCAAGT
5207892 GAGATAAATTTT
192 GAGATAAATTTT
5207904 GATCATTGCT
Statistics
Matches: 185, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
205 97 0.52
206 88 0.48
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (205 bp):
TTTTGAGTGAACAATTTCAAAATTTATGTTCCAAGGGAAAACTGTCTCAATGAAGACGAAATTGA
TTTAAAGAAAAACCATCTCAAATGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAATTTTAT
GTTCCAAGGGAAAACTGTCTCAAGCGAGACAAAATCGATTTAAAGAAAAATCATCTCAAGTGAGA
TAAATTTTTG
Found at i:5232890 original size:17 final size:18
Alignment explanation
Indices: 5232860--5232896 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5232850 ATAAATATAT
5232860 ATATATATATAATTTAAA
1 ATATATATATAATTTAAA
*
5232878 ATATATA-ATAATTTTAA
1 ATATATATATAATTTAAA
5232895 AT
1 AT
5232897 TTTCGGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATATAATTTAAA
Found at i:5236220 original size:19 final size:20
Alignment explanation
Indices: 5236181--5236220 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5236171 TAAGTGTTAA
*
5236181 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
5236201 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
5236220 T
1 T
5236221 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:5250957 original size:25 final size:24
Alignment explanation
Indices: 5250927--5250975 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
5250917 TTTAATTGAA
*
5250927 TTAAATATAAATATTAATTTTTTAT
1 TTAAATATAAATA-TAATTATTTAT
*
5250952 TTAAATTTAAATATAATTATTTAT
1 TTAAATATAAATATAATTATTTAT
5250976 AATAGTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAATATAAATATAATTATTTAT
Found at i:5252504 original size:43 final size:44
Alignment explanation
Indices: 5252395--5252529 Score: 184
Period size: 45 Copynumber: 3.1 Consensus size: 44
5252385 ACCATAAATT
**
5252395 TTTTTTTCAATTCCTCTTTTTATATTTATAATTGATGACTTTAA
1 TTTTTTTCAATTCCTCTTTTTATATTTATAATTGATGACCCTAA
*
5252439 TGTTTTTTCAATCCCTCTTTTTATATTTATAATTGATGACCCTAA
1 T-TTTTTTCAATTCCTCTTTTTATATTTATAATTGATGACCCTAA
* * *
5252484 TTTTTTTCAATTCCAC-TTTTACT-TTTATAATTGAAGCCCCTAA
1 TTTTTTTCAATTCCTCTTTTTA-TATTTATAATTGATGACCCTAA
5252527 TTT
1 TTT
5252530 AATCAATTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
43 26 0.32
44 15 0.18
45 41 0.50
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (44 bp):
TTTTTTTCAATTCCTCTTTTTATATTTATAATTGATGACCCTAA
Found at i:5253422 original size:10 final size:10
Alignment explanation
Indices: 5253407--5253444 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
5253397 TTTTTATAAT
5253407 AAAATATTTC
1 AAAATATTTC
5253417 AAAATATTAAT-
1 AAAATATT--TC
5253428 AAAATATTTC
1 AAAATATTTC
5253438 AAAATAT
1 AAAATAT
5253445 AATATTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.04
10 15 0.60
11 8 0.32
12 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATATTTC
Found at i:5253428 original size:21 final size:20
Alignment explanation
Indices: 5253401--5253448 Score: 87
Period size: 21 Copynumber: 2.4 Consensus size: 20
5253391 AATAGTTTTT
5253401 TATAATAAAATATTTCAAAA
1 TATAATAAAATATTTCAAAA
5253421 TATTAATAAAATATTTCAAAA
1 TA-TAATAAAATATTTCAAAA
5253442 TATAATA
1 TATAATA
5253449 TTCATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TATAATAAAATATTTCAAAA
Found at i:5257678 original size:23 final size:23
Alignment explanation
Indices: 5257648--5257697 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
5257638 CCAAACATGA
5257648 GAATGTGGATTCCATTCCTATGG
1 GAATGTGGATTCCATTCCTATGG
5257671 GAATGTGGATTCCATTCCTATGG
1 GAATGTGGATTCCATTCCTATGG
5257694 GAAT
1 GAAT
5257698 CCTACATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (23 bp):
GAATGTGGATTCCATTCCTATGG
Found at i:5263632 original size:14 final size:14
Alignment explanation
Indices: 5263600--5263656 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
5263590 TCAAATCATC
5263600 CATAACATCCAAAA
1 CATAACATCCAAAA
5263614 CATAA-ATCCAAACA
1 CATAACATCCAAA-A
* *
5263628 TATAAGCATCCAAATT
1 CATAA-CATCCAAA-A
5263644 CA-AACATCCAAAA
1 CATAACATCCAAAA
5263657 TGTTAAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 7 0.20
14 18 0.51
15 2 0.06
16 8 0.23
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.18
Consensus pattern (14 bp):
CATAACATCCAAAA
Found at i:5265629 original size:22 final size:23
Alignment explanation
Indices: 5265583--5265637 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
5265573 AATTCCCCTG
5265583 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
5265606 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
*
5265628 GGGGGTATCG
1 GGGGGAATCG
5265638 ATTCTCTCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.22
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:5269504 original size:22 final size:21
Alignment explanation
Indices: 5269462--5269501 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5269452 AAGACTATTT
5269462 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
5269483 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
5269502 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:5274669 original size:16 final size:17
Alignment explanation
Indices: 5274638--5274673 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5274628 TTTTTACATG
5274638 AATCAAAAATATTATTA
1 AATCAAAAATATTATTA
*
5274655 AATCAAAATTA-TATTA
1 AATCAAAAATATTATTA
5274671 AAT
1 AAT
5274674 TTGTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AATCAAAAATATTATTA
Found at i:5275324 original size:31 final size:31
Alignment explanation
Indices: 5275275--5275349 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
5275265 TCAAGTTTTG
*
5275275 ATAAATTTAAGGATTATTTTATAATAGTTTA
1 ATAAATTTAAGGATTATTTTATAATAATTTA
* * * *
5275306 GTAAAATTAATGATTATTTTTTAATAATTTA
1 ATAAATTTAAGGATTATTTTATAATAATTTA
5275337 ATAAATTTAAGGA
1 ATAAATTTAAGGA
5275350 CTAACCTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (31 bp):
ATAAATTTAAGGATTATTTTATAATAATTTA
Found at i:5276132 original size:26 final size:28
Alignment explanation
Indices: 5276071--5276133 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
5276061 CGAGTATTGT
*
5276071 TGAGCTCGACTCGACTCGAAAACTCTGAAA
1 TGAGCTCGACTCGACTCAAAAACTCTG--A
5276101 TAGAGCTCGACTCGACTCAAAAACTC-G-
1 T-GAGCTCGACTCGACTCAAAAACTCTGA
5276128 TGAGCT
1 TGAGCT
5276134 TAAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 5 0.16
27 1 0.03
30 2 0.06
31 23 0.74
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCAAAAACTCTGA
Found at i:5277572 original size:15 final size:16
Alignment explanation
Indices: 5277533--5277572 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
5277523 GGATAGGTTC
*
5277533 TTTATTTTTCTTTCTT
1 TTTATTTTTCTTTATT
*
5277549 TTAATTTTT-TTTATT
1 TTTATTTTTCTTTATT
5277564 TTTATTTTT
1 TTTATTTTT
5277573 ATAGGGATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTATTTTTCTTTATT
Found at i:5280311 original size:2 final size:2
Alignment explanation
Indices: 5280304--5280334 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5280294 AATTTGAAAT
5280304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5280335 TCATTACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5280585 original size:20 final size:20
Alignment explanation
Indices: 5280560--5280599 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5280550 TAACGGTCGT
5280560 TAGTTTTCTCCATTAAGTGA
1 TAGTTTTCTCCATTAAGTGA
*
5280580 TAGTTTTCTCTATTAAGTGA
1 TAGTTTTCTCCATTAAGTGA
5280600 CATGTGTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (20 bp):
TAGTTTTCTCCATTAAGTGA
Found at i:5281910 original size:20 final size:20
Alignment explanation
Indices: 5281885--5281937 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
5281875 TGATCGTATA
** *
5281885 ATATAATTATAATTAATTAT
1 ATATAATTATAAAAAAATAT
5281905 ATATAAATTTATAAAAAAATAT
1 ATAT-AA-TTATAAAAAAATAT
5281927 AT-TAATTATAA
1 ATATAATTATAA
5281938 CATAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 3 0.11
22 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATTATAAAAAAATAT
Found at i:5282099 original size:33 final size:31
Alignment explanation
Indices: 5282033--5282094 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5282023 TTTTAGTTAG
5282033 TTTTTTTCAACTATAACTCTTTATTATTTAA
1 TTTTTTTCAACTATAACTCTTTATTATTTAA
*
5282064 TTTTTTTTAACTATAACTCTTTATTATTTAA
1 TTTTTTTCAACTATAACTCTTTATTATTTAA
5282095 AATTTATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (31 bp):
TTTTTTTCAACTATAACTCTTTATTATTTAA
Found at i:5296333 original size:15 final size:15
Alignment explanation
Indices: 5296315--5296347 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5296305 TTCGTTGACC
5296315 CCCTTTTGTTTAAGT
1 CCCTTTTGTTTAAGT
*
5296330 CCC-TTTGTTTAATT
1 CCCTTTTGTTTAAGT
5296344 CCCT
1 CCCT
5296348 AACATGGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.12, C:0.27, G:0.09, T:0.52
Consensus pattern (15 bp):
CCCTTTTGTTTAAGT
Found at i:5297097 original size:30 final size:30
Alignment explanation
Indices: 5297061--5297120 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5297051 GCGTAGAAGA
*
5297061 ATGAGAAACCCATCGGCTCGCCCTCCTCGT
1 ATGAGAAACCCATCGACTCGCCCTCCTCGT
5297091 ATGAGAAACCCATCGACTCGCCCTCCTCGT
1 ATGAGAAACCCATCGACTCGCCCTCCTCGT
5297121 TTTGACACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (30 bp):
ATGAGAAACCCATCGACTCGCCCTCCTCGT
Found at i:5299429 original size:36 final size:36
Alignment explanation
Indices: 5299377--5299491 Score: 151
Period size: 36 Copynumber: 3.2 Consensus size: 36
5299367 GAAGTCTTTG
* * **
5299377 TAGGTTCAGCTTTGATCAAGCGGGTAATTCCTTATA
1 TAGGTTCAACTCTGATCAAGTTGGTAATTCCTTATA
*
5299413 TAAGTTCAACTCTGATCAAGTTGGTAATTCCTTATA
1 TAGGTTCAACTCTGATCAAGTTGGTAATTCCTTATA
* * *
5299449 CAGGTTCAACACTGATC-GGTTGGTAATTCCTTATA
1 TAGGTTCAACTCTGATCAAGTTGGTAATTCCTTATA
5299484 TAGGTTCA
1 TAGGTTCA
5299492 GTACCAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
35 24 0.35
36 45 0.65
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (36 bp):
TAGGTTCAACTCTGATCAAGTTGGTAATTCCTTATA
Found at i:5301601 original size:5 final size:5
Alignment explanation
Indices: 5301591--5301636 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
5301581 GAATATGACA
* * *
5301591 AATAT AATAT ATTTT AATAT AA-A- AAAAT AATAT AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
5301637 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 30 0.88
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:5305335 original size:15 final size:15
Alignment explanation
Indices: 5305315--5305357 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5305305 TCATTCAAAC
5305315 ATTAAAAAATAATTA
1 ATTAAAAAATAATTA
* *
5305330 ATTAAAAATTTTATTA
1 ATTAAAAA-ATAATTA
5305346 ATTAAAATAATA
1 ATTAAAA-AATA
5305358 TAACAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 8 0.36
16 13 0.59
17 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAAAAAATAATTA
Found at i:5306760 original size:31 final size:31
Alignment explanation
Indices: 5306725--5306785 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5306715 ATAAATTTAT
* * *
5306725 TATCAATTGTTTAATCACTAATTATTTAAAA
1 TATCAAATATTTAAACACTAATTATTTAAAA
5306756 TATCAAATATTTAAACACTAATTATTTAAA
1 TATCAAATATTTAAACACTAATTATTTAAA
5306786 TGAATTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (31 bp):
TATCAAATATTTAAACACTAATTATTTAAAA
Found at i:5306785 original size:15 final size:15
Alignment explanation
Indices: 5306729--5306785 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5306719 ATTTATTATC
* *
5306729 AATTGTTTAATCACT
1 AATTATTTAAACACT
*
5306744 AATTATTTAAA-ATAT
1 AATTATTTAAACA-CT
*
5306759 CAAATATTTAAACACT
1 -AATTATTTAAACACT
5306775 AATTATTTAAA
1 AATTATTTAAA
5306786 TGAATTAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 11 0.33
17 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTATTTAAACACT
Found at i:5309027 original size:2 final size:2
Alignment explanation
Indices: 5308984--5309015 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5308974 CACACGTGTG
5308984 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5309016 TGAGAGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5311134 original size:17 final size:17
Alignment explanation
Indices: 5311112--5311149 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5311102 AAAGTTGAGT
5311112 AAAACAGGACTTGATAC
1 AAAACAGGACTTGATAC
*
5311129 AAAACAGGACTTGATGC
1 AAAACAGGACTTGATAC
5311146 AAAA
1 AAAA
5311150 TTGAGGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (17 bp):
AAAACAGGACTTGATAC
Found at i:5314151 original size:10 final size:10
Alignment explanation
Indices: 5314136--5314162 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5314126 TTTGTCTCAC
5314136 CACAACTCCA
1 CACAACTCCA
5314146 CACAACTCCA
1 CACAACTCCA
5314156 CACAACT
1 CACAACT
5314163 TCTTTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.48, G:0.00, T:0.11
Consensus pattern (10 bp):
CACAACTCCA
Found at i:5319932 original size:41 final size:41
Alignment explanation
Indices: 5319874--5319955 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
5319864 TTGAGAGTCA
5319874 AAGGTAAAATTGACATGCTATGAAGTGGAGTGATTATCTGT
1 AAGGTAAAATTGACATGCTATGAAGTGGAGTGATTATCTGT
* *
5319915 AAGGTAAAATTGGCATGCTATGAAGTGGTGTGATTATCTGT
1 AAGGTAAAATTGACATGCTATGAAGTGGAGTGATTATCTGT
5319956 TCTGATTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (41 bp):
AAGGTAAAATTGACATGCTATGAAGTGGAGTGATTATCTGT
Found at i:5321262 original size:33 final size:33
Alignment explanation
Indices: 5321204--5321284 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
5321194 TTTAATTTTA
* * *
5321204 TCTATTTTTTATTTTGGTACCTAAATTACTATTT
1 TCTA-TTTTAATTTAGGTACATAAATTACTATTT
5321238 TCTATTTTAATTTAGGTACATAAATTACTATTT
1 TCTATTTTAATTTAGGTACATAAATTACTATTT
* *
5321271 TCTATCTTATTTTA
1 TCTATTTTAATTTA
5321285 CCTTTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 38 0.90
34 4 0.10
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (33 bp):
TCTATTTTAATTTAGGTACATAAATTACTATTT
Found at i:5327240 original size:111 final size:110
Alignment explanation
Indices: 5326977--5327452 Score: 690
Period size: 110 Copynumber: 4.4 Consensus size: 110
5326967 TTGCAGCTTT
** *
5326977 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTTGAGACAACACAAGCTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
* *
5327042 CGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTA
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * *
5327087 AGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCATAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
*
5327152 GGAAGGGGCGACTGACTGTCAACAAACAACTTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAAC-TTTTCAGTTTCATTC
* * *
5327198 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGTTCAATTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
*
5327263 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * * * * *
5327308 AGAGTCAATTTCAACTTCACAACGAATGATATTAGACTCGAGATAACACAAGCTCAACTTCAAAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
* * * **
5327373 CGAAGGGGTGGCTGGCTGTCAACAAACAACTTCCCAG---C-TTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
*
5327414 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC
5327453 GAAACAATAC
Statistics
Matches: 329, Mismatches: 36, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
106 38 0.12
110 189 0.57
111 102 0.31
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:5327360 original size:221 final size:216
Alignment explanation
Indices: 5326970--5327452 Score: 716
Period size: 221 Copynumber: 2.2 Consensus size: 216
5326960 ACAATTTTTG
* **
5326970 CAGCTTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTTGAGACAACACAAGCTCAAC
1 CAGCTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAAC
*
5327035 TTCACAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTAAGAGTCAATTTCA
66 TTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAAGAGTCAATTTCA
* *
5327100 ACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCATAGGGAAGGGGCGACT
131 ACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCAAAGCGAAGGGGCGACT
**
5327165 GACTGTCAACAAACAACTTTTT
196 GACTGTCAACAAACAAC-TTCC
* *
5327187 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGTT
1 CAG---C-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
* * * *
5327252 CAATTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGTCAAT
62 CAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAAGAGTCAAT
* * *
5327317 TTCAACTTCACAACGAATGATATT-AGACTCGAGATAACACAAGCTCAACTTCAAAGCGAAGGGG
127 TTCAACTTCACAACGAAGGATATTGA-ACTCAAGACAACACAAGCTCAACTTCAAAGCGAAGGGG
* * *
5327381 TGGCTGGCTGTCAACAAACAACTTCC
191 CGACTGACTGTCAACAAACAACTTCC
*
5327407 CAGCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 CAGCTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC
5327453 GAAACAATAC
Statistics
Matches: 239, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
216 40 0.17
217 4 0.02
220 7 0.03
221 188 0.79
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (216 bp):
CAGCTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAAC
TTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAAGAGTCAATTTCA
ACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCAAAGCGAAGGGGCGACT
GACTGTCAACAAACAACTTCC
Found at i:5327673 original size:85 final size:85
Alignment explanation
Indices: 5327564--5328155 Score: 592
Period size: 85 Copynumber: 7.0 Consensus size: 85
5327554 AAGGGAATCG
* * * * *
5327564 TGCCCACC-AAAGGCCTTCGAGTTCGACTACACTCAACTCCAAGGCACATTATTTGCAGTATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAAC
5327628 TTAAGTCGAGAAGGGTTATC
66 TTAAGTCGAGAAGGGTTATC
* * *
5327648 TTCCAACCAAAAGACCTTCGAGTTCGACGA-AGCTCAGCTCCAAGGTACATCATTTGCAGCATAA
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACA-CTCAGCTCCAAGGCACATCATTTGCAGCATAA
* * * *
5327712 ATCAAGGCTAGAAGGGTTATC
65 CTTAAGTCGAGAAGGGTTATC
* * * *
5327733 TGCCAA-CAAAA-ACCTTCAAGTTCGACTACACTTAGCTCCATGGCATATCATTTGCAGCATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
5327796 TTAAGACGAGAAGGGTTATC
66 TTAAGTCGAGAAGGGTTATC
* * * * * * *
5327816 TGCCAA-CAAAAAACCTTTGAGTTCGACTACACTC-GGTTCAACGGTATATCATTTGCAGCATAG
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAA
* *
5327879 CTTAAGTCGATAAGGGCTATC
65 CTTAAGTCGAGAAGGGTTATC
* * * * * * *
5327900 TGCCAGCC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAA
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAA
* * * *
5327964 CTCAAGGCTATAAGGGTTATC
65 CTTAAGTCGAGAAGGGTTATC
* * * *
5327985 T-CTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGTATAG
1 TGC-CAACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAA
5328048 CTTAAGTCGAGAAGGGTTATC
65 CTTAAGTCGAGAAGGGTTATC
* * * * * * * * *
5328069 TTCCAACC-GAAGACCTTCGAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAACATAG
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAA
* * *
5328133 CTTAAGGCAAGAAGGGCTATC
65 CTTAAGTCGAGAAGGGTTATC
5328154 TG
1 TG
5328156 TCAAAAAAAT
Statistics
Matches: 414, Mismatches: 81, Indels: 25
0.80 0.16 0.05
Matches are distributed among these distances:
83 75 0.18
84 162 0.39
85 175 0.42
86 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (85 bp):
TGCCAACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAAC
TTAAGTCGAGAAGGGTTATC
Found at i:5328009 original size:169 final size:167
Alignment explanation
Indices: 5327567--5328154 Score: 626
Period size: 169 Copynumber: 3.5 Consensus size: 167
5327557 GGAATCGTGC
* * * * * **
5327567 CCACCAAAGGCCTTCGAGTTCGACTACACTCAACTCCAAGGCACATTATTTGCAGTATAACTTAA
1 CCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAGGGCACATCATTTACAACATAACTTAA
* *
5327632 GTCGAGAAGGGTTATCT-TCCAACCAAAAGACCTTCGAGTTCGACGA-AGCTCAGCTCCAAGGTA
66 GGCGAGAAGGGTTATCTCT-C-ACCAAAAGACCTTCGAGTTCGACTACA-CTCAGCTCCAAGGTA
** * * *
5327695 CATCATTTGCAGCATAAATCAAGGCTAGAAGGGTTATCTG
128 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
* * * * * * * *
5327735 CCAACAAAAACCTTCAAGTTCGACTACACTTAGCTCCATGGCATATCATTTGCAGCATAACTTAA
1 CCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAGGGCACATCATTTACAACATAACTTAA
* * * * * * *
5327800 GACGAGAAGGGTTATCTGC-CAACAAAAAACCTTTGAGTTCGACTACACTC-GGTTCAACGGTAT
66 GGCGAGAAGGGTTATCT-CTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGTAC
* *
5327863 ATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTG
129 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
* * * *
5327902 CCAGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTC
1 CCA-CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAGGGCACATCATTTACAACATAACTT
* * * * *
5327967 AAGGCTATAAGGGTTATCTCTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCAC
64 AAGGCGAGAAGGGTTATCTCTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTAC
* *
5328032 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGTTATCTT
129 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
* * * * *
5328071 CCAACCGAAGACCTTCGAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAACATAGCTT
1 CC-ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAGGGCACATCATTTACAACATAACTT
* *
5328136 AAGGCAAGAAGGGCTATCT
64 AAGGCGAGAAGGGTTATCT
5328155 GTCAAAAAAA
Statistics
Matches: 350, Mismatches: 61, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
166 5 0.01
167 63 0.18
168 99 0.28
169 178 0.51
170 5 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (167 bp):
CCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAGGGCACATCATTTACAACATAACTTAA
GGCGAGAAGGGTTATCTCTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTACAT
CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
Found at i:5331364 original size:32 final size:32
Alignment explanation
Indices: 5331323--5331389 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
5331313 TTAAGGATTT
5331323 GCAGAGATAAATTCATCAAAGACGAGACTCAA
1 GCAGAGATAAATTCATCAAAGACGAGACTCAA
5331355 GCAGAGATAAATTCATCAAAGACGAGACTCAA
1 GCAGAGATAAATTCATCAAAGACGAGACTCAA
5331387 GCA
1 GCA
5331390 TGTGTCTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.15
Consensus pattern (32 bp):
GCAGAGATAAATTCATCAAAGACGAGACTCAA
Found at i:5334043 original size:59 final size:59
Alignment explanation
Indices: 5333919--5334043 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 59
5333909 TAGTCGGATG
* * * *
5333919 ACCATTTTGTAACTTTTAATAGTAGAAGACTCAATAAAGCAACATCCTTTAATTGAGGG
1 ACCATTTTATAACTTTTAATAGTAGAAGACTCAATAAAACAACATCCTATAATTGAGGA
* * * *
5333978 AGCATTTTATAACTTTTAATAATTA-AGAGACTCAATAAAACAATA-CTCTATAGTTG-GGA
1 ACCATTTTATAACTTTTAAT-AGTAGA-AGACTCAATAAAACAACATC-CTATAATTGAGGA
5334037 ACCATTT
1 ACCATTT
5334044 ATGTATTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
59 28 0.52
60 26 0.48
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (59 bp):
ACCATTTTATAACTTTTAATAGTAGAAGACTCAATAAAACAACATCCTATAATTGAGGA
Found at i:5335925 original size:48 final size:48
Alignment explanation
Indices: 5335854--5335949 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
5335844 ATGTCAAAAC
*
5335854 ACTCTTGGTACCTCCTAAACCAATGTCATTTATGAACTCCAAAGCATA
1 ACTCTTGGTACCTCCTAAACCAATGTCATTTATGAACCCCAAAGCATA
5335902 ACTCTTGGTACCTCCTAAACCAATGTCATTTATGAACCCCAAAGCATA
1 ACTCTTGGTACCTCCTAAACCAATGTCATTTATGAACCCCAAAGCATA
5335950 CTTTCTTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (48 bp):
ACTCTTGGTACCTCCTAAACCAATGTCATTTATGAACCCCAAAGCATA
Found at i:5336848 original size:18 final size:18
Alignment explanation
Indices: 5336822--5336872 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
5336812 ATTAAATATT
*
5336822 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
5336840 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5336858 TGACCCGAAGGACCA
1 TGTCCCGAAGGACCA
5336873 TTGAAAATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5337058 original size:18 final size:18
Alignment explanation
Indices: 5337035--5337081 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
5337025 TTGATTCTCT
*
5337035 TATAATGTCATTCATTCA
1 TATAATATCATTCATTCA
5337053 TATAATATCATTCATTCA
1 TATAATATCATTCATTCA
5337071 TATAATATCAT
1 TATAATATCAT
5337082 GTTAAAGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (18 bp):
TATAATATCATTCATTCA
Found at i:5344252 original size:20 final size:23
Alignment explanation
Indices: 5344227--5344305 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 23
5344217 TTTAAGGTAG
5344227 GTATCGGTACA-C-TCAA-GAGT
1 GTATCGGTACATCATCAACGAGT
* *
5344247 GTATCGATACATTCATTAACGAGT
1 GTATCGGTACA-TCATCAACGAGT
* *
5344271 GTATCGGTACATTCCTTAACGAGT
1 GTATCGGTACA-TCATCAACGAGT
*
5344295 GTATCGATACA
1 GTATCGGTACA
5344306 CTACATGTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 10 0.20
22 1 0.02
23 3 0.06
24 36 0.72
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (23 bp):
GTATCGGTACATCATCAACGAGT
Found at i:5344275 original size:24 final size:24
Alignment explanation
Indices: 5344243--5344305 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
5344233 GTACACTCAA
5344243 GAGTGTATCGATACATTCATTAAC
1 GAGTGTATCGATACATTCATTAAC
* *
5344267 GAGTGTATCGGTACATTCCTTAAC
1 GAGTGTATCGATACATTCATTAAC
5344291 GAGTGTATCGATACA
1 GAGTGTATCGATACA
5344306 CTACATGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (24 bp):
GAGTGTATCGATACATTCATTAAC
Found at i:5344394 original size:62 final size:64
Alignment explanation
Indices: 5344295--5344430 Score: 161
Period size: 62 Copynumber: 2.2 Consensus size: 64
5344285 CTTAACGAGT
* * * * *
5344295 GTATCGATACACTACATGTGTATCGGTGCTCAAATTACATTCGATGTTTTCATT-TT-AAGGGG
1 GTATCGATACACTACATGTGTATCGATACACAAATTACATTCGATATTTTCATTATTCAAGAGG
** * *
5344357 GTATCGATACACTA-ATTGTGTATCGATACACTTATTACATTCGATATTTTCTTTATTCAAGAGT
1 GTATCGATACACTACA-TGTGTATCGATACACAAATTACATTCGATATTTTCATTATTCAAGAGG
5344421 GTATCGATAC
1 GTATCGATAC
5344431 CTGTTGAACG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
61 1 0.02
62 45 0.73
63 2 0.03
64 14 0.23
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (64 bp):
GTATCGATACACTACATGTGTATCGATACACAAATTACATTCGATATTTTCATTATTCAAGAGG
Found at i:5348046 original size:2 final size:2
Alignment explanation
Indices: 5348041--5348082 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5348031 AAAAAAGGAA
5348041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5348083 CAAAGTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5348588 original size:18 final size:17
Alignment explanation
Indices: 5348565--5348607 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5348555 ATATATACAT
5348565 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
5348583 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
5348600 ATAA-AATA
1 ATAATAATA
5348608 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:5349075 original size:34 final size:34
Alignment explanation
Indices: 5349021--5349089 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
5349011 GAATCCTAGC
*
5349021 AAAATTCTATCATATCTTTAGGAGTTTAAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTAAATCCT
* * *
5349055 AAAATTATATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTAAATCCT
5349089 A
1 A
5349090 GTAGGACGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (34 bp):
AAAATTATATCATATCTTTAGGAGTTTAAATCCT
Found at i:5349854 original size:98 final size:98
Alignment explanation
Indices: 5349685--5349943 Score: 286
Period size: 98 Copynumber: 2.6 Consensus size: 98
5349675 TGGAACCGGA
* * *
5349685 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCAAGTCCA
1 AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCAAGTCCA
* * *
5349750 ATATCCTTCGTTGTGAAGTTGAGATTGGCTCCG
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
** * ***
5349783 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCA
1 AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCAAGTCCA
5349848 ATATCCTCCGCTGTGAAGTTGAAATTGGC-CCTG
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC-G
* * * * *
5349881 AAACTGGGAAATTGTTGTTGATAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAA-T-TG----T-TTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTC
5349944 ATAGGTAGCA
Statistics
Matches: 133, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
97 2 0.02
98 86 0.65
99 1 0.01
100 1 0.01
104 1 0.01
105 42 0.32
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (98 bp):
AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCAAGTCCA
ATATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
Found at i:5349937 original size:105 final size:102
Alignment explanation
Indices: 5349685--5350077 Score: 316
Period size: 105 Copynumber: 3.8 Consensus size: 102
5349675 TGGAACCGGA
***
5349685 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCAAGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* * ** * ** ** **
5349749 A-ATATCCTTCGTTGT-GAAGTTGAG-ATTG-GCTCCG
65 AGATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
** * * * *
5349783 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* **
5349847 A-ATATCCTCCG-CTGTGAAGTTGAAATTGGCCCTGAAACTGGG
65 AGATATCCTCCGTC-GTG--G--AAAATCAGCCCTGAAA-TGGG
* * * *
5349889 AAATTGTTGTTGATAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCATAGGTAGCA
1 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
** *
5349954 TGATATCCTCCGTCGTGGAAAATCAGCTTTGAAATTGG
66 -GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
* **
5349992 AAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGG
1 AAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAC
*
5350057 CACGATATCCTCCATCGTGGA
64 CA-GATATCCTCCGTCGTGGA
5350078 GTTGAAATCG
Statistics
Matches: 235, Mismatches: 45, Indels: 23
0.78 0.15 0.08
Matches are distributed among these distances:
98 67 0.29
101 1 0.00
103 9 0.04
104 18 0.08
105 115 0.49
106 11 0.05
108 13 0.06
109 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (102 bp):
AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
Found at i:5350972 original size:65 final size:65
Alignment explanation
Indices: 5350868--5351048 Score: 299
Period size: 65 Copynumber: 2.8 Consensus size: 65
5350858 GACAAAATTT
5350868 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
5350933 TGTTTCAAGAGAAACTATCTCAAGAGAGATGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
5350998 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
5351049 CTATCTCAAG
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 93 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:5351049 original size:37 final size:37
Alignment explanation
Indices: 5350998--5351102 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 37
5350988 TCAATGTTTA
* * *
5350998 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAGTT
*
5351035 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAGTT
*
5351071 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
5351103 TGGTGAGCAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 33 0.54
37 28 0.46
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAGTT
Found at i:5351994 original size:22 final size:22
Alignment explanation
Indices: 5351968--5352022 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
5351958 TTGTGTTTGG
5351968 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
5351990 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
5352012 TCAAAGGTTTG
1 TCAAAGGTTTG
5352023 ATGGGATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:5352666 original size:22 final size:22
Alignment explanation
Indices: 5352632--5352711 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 22
5352622 TTGCATGTGC
*
5352632 TTTTTGTCCCTTTTTCTTT-TTGA
1 TTTTTG-CTCTTTTTCTTTGTT-A
*
5352655 TTTTTGCTCTTTTT-TTTGTTC
1 TTTTTGCTCTTTTTCTTTGTTA
*
5352676 TTGTTT-CTCTTTTTCTTTGTTTT
1 TT-TTTGCTCTTTTTCTTTG-TTA
5352699 TTTTTGCT-TTTTT
1 TTTTTGCTCTTTTT
5352712 GCTTCTTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
21 13 0.27
22 24 0.49
23 12 0.24
ACGTcount: A:0.01, C:0.14, G:0.09, T:0.76
Consensus pattern (22 bp):
TTTTTGCTCTTTTTCTTTGTTA
Found at i:5352672 original size:19 final size:18
Alignment explanation
Indices: 5352648--5352699 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 18
5352638 TCCCTTTTTC
5352648 TTTTTGATTTTTGCTCTTT
1 TTTTTG-TTTTTGCTCTTT
*
5352667 TTTTTGTTCTTGTTTCTCTTT
1 TTTTTG-T-TT-TTGCTCTTT
5352688 TTCTTTGTTTTT
1 TT-TTTGTTTTT
5352700 TTTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.32
20 4 0.14
21 11 0.39
22 4 0.14
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.77
Consensus pattern (18 bp):
TTTTTGTTTTTGCTCTTT
Found at i:5352726 original size:16 final size:16
Alignment explanation
Indices: 5352683--5352733 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
5352673 TTCTTGTTTC
*
5352683 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
5352699 T-TTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
5352715 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
5352730 TCTT
1 TCTT
5352734 GATTGGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 11 0.35
17 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:5355263 original size:5 final size:5
Alignment explanation
Indices: 5355253--5355281 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5355243 GCAAGTGATG
5355253 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
5355282 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5357008 original size:18 final size:16
Alignment explanation
Indices: 5356987--5357027 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
5356977 ATATATACAT
5356987 ATAAAAATAATAACATGA
1 ATAAAAA-AATAA-ATGA
5357005 ATAATAAAAATAAATGA
1 ATAA-AAAAATAAATGA
5357022 ATAAAA
1 ATAAAA
5357028 TATCCATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 9 0.41
19 3 0.14
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (16 bp):
ATAAAAAAATAAATGA
Found at i:5357487 original size:34 final size:34
Alignment explanation
Indices: 5357444--5357512 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
5357434 GAATCCTAGC
5357444 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
5357478 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
5357512 A
1 A
5357513 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:5359434 original size:22 final size:22
Alignment explanation
Indices: 5359409--5359451 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5359399 ACTTCATTCC
* * *
5359409 TTGCTTGTTTTTATTGTTGTTA
1 TTGCTAGTTCTTATTGGTGTTA
5359431 TTGCTAGTTCTTATTGGTGTT
1 TTGCTAGTTCTTATTGGTGTT
5359452 TGTGACTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.07, G:0.21, T:0.63
Consensus pattern (22 bp):
TTGCTAGTTCTTATTGGTGTTA
Found at i:5360621 original size:17 final size:17
Alignment explanation
Indices: 5360601--5360663 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 17
5360591 TAAAAAGAGA
5360601 AAAAAGAGAAAAT-AAAT
1 AAAAAGA-AAAATAAAAT
*
5360618 AAAAGGAAAAATAAAAT
1 AAAAAGAAAAATAAAAT
*
5360635 AAATAAATAAAAAATAAAAT
1 -AA-AAA-GAAAAATAAAAT
5360655 AAAACAGAA
1 AAAA-AGAA
5360664 TGTCGGATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 5 0.14
17 10 0.27
18 6 0.16
19 5 0.14
20 11 0.30
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAAGAAAAATAAAAT
Found at i:5360649 original size:20 final size:20
Alignment explanation
Indices: 5360609--5360657 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
5360599 GAAAAAAGAG
5360609 AAAATAAATAAAAGGAAAAAT
1 AAAATAAATAAAA-GAAAAAT
5360630 AAAATAAATAAATA-AAAAAT
1 AAAATAAATAAA-AGAAAAAT
5360650 AAAATAAA
1 AAAATAAA
5360658 ACAGAATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.52
21 12 0.44
22 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (20 bp):
AAAATAAATAAAAGAAAAAT
Done.