Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 5 of 211
Found at i:1651442 original size:51 final size:51
Alignment explanation
Indices: 1651366--1651468 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1651356 ATTGGTTCTT
*
1651366 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCGCCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1651417 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1651468 T
1 T
1651469 AGAGCTATGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (51 bp):
TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
Found at i:1655085 original size:17 final size:17
Alignment explanation
Indices: 1655058--1655224 Score: 64
Period size: 17 Copynumber: 8.7 Consensus size: 17
1655048 CTGATATAAT
* * *
1655058 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
1655075 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
1655092 AAATATTTTTAAAATACTTTTTA
1 AAATATTTTT---A-A--TTTTA
* *
1655115 AATTTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
* *
1655132 AAATATTTTAAAATACTTTTT
1 AAATATTTT----TAATTTTA
*
1655153 AAATTTTTTTAATTTTATA
1 AAATATTTTTAA-TTT-TA
1655172 AAATATTTTTTAAATACTTTTTAA
1 AAATA-TTTTT--A-A--TTTT-A
*
1655196 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
1655213 TAATATTTTTAA
1 AAATATTTTTAA
1655225 AATACATTTT
Statistics
Matches: 114, Mismatches: 18, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
17 47 0.41
18 7 0.06
19 6 0.05
20 8 0.07
21 16 0.14
22 1 0.01
23 20 0.18
24 9 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:1655101 original size:11 final size:11
Alignment explanation
Indices: 1655087--1655228 Score: 87
Period size: 11 Copynumber: 13.9 Consensus size: 11
1655077 ATTTTTTTAA
1655087 TTTTAAAATAT
1 TTTTAAAATAT
1655098 TTTTAAAATACT
1 TTTTAAAATA-T
1655110 TTTT-AAAT-T
1 TTTTAAAATAT
* *
1655119 TTTT---TTAA
1 TTTTAAAATAT
1655127 TTTTAAAATA-
1 TTTTAAAATAT
1655137 TTTTAAAATACT
1 TTTTAAAATA-T
1655149 TTTT-AAAT-T
1 TTTTAAAATAT
*
1655158 TTTT-TAAT-T
1 TTTTAAAATAT
*
1655167 TTATAAAATAT
1 TTTTAAAATAT
*
1655178 TTTTTAAATACT
1 TTTTAAAATA-T
1655190 TTTTAAAA-AT
1 TTTTAAAATAT
* *
1655200 TTTT---TTAA
1 TTTTAAAATAT
*
1655208 TTTTATAATAT
1 TTTTAAAATAT
1655219 TTTTAAAATA
1 TTTTAAAATA
1655229 CATTTTTTAA
Statistics
Matches: 103, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
7 1 0.01
8 9 0.09
9 17 0.17
10 18 0.17
11 41 0.40
12 17 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1655124 original size:40 final size:39
Alignment explanation
Indices: 1655070--1655243 Score: 260
Period size: 40 Copynumber: 4.3 Consensus size: 39
1655060 ATATATTTAT
1655070 TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1655109 TTTTTAAATTTTTTTTAATTTTAAAATA-TTTTAAAATAC
1 TTTTTAAA-TTTTTTTAATTTTAAAATATTTTTAAAATAC
*
1655148 TTTTTAAATTTTTTTAATTTTATAAAATATTTTTTAAATAC
1 TTTTTAAATTTTTTTAA-TTT-TAAAATATTTTTAAAATAC
*
1655189 TTTTTAAAAATTTTTTTAATTTTATAATATTTTTAAAATAC
1 TTTTT--AAATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
1655230 ATTTTTTAATTTTT
1 -TTTTTAAATTTTT
1655244 AAAATAAAAT
Statistics
Matches: 124, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
38 9 0.07
39 30 0.24
40 33 0.27
41 32 0.26
42 8 0.06
43 12 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (39 bp):
TTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:1655130 original size:29 final size:29
Alignment explanation
Indices: 1655098--1655186 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
1655088 TTTAAAATAT
* * *
1655098 TTTTAAAATACTTTTTAAAT-TTTTTTTAA
1 TTTTAAAATA-TTTTAAAATACTTTTTAAA
1655127 TTTTAAAATATTTTAAAATACTTTTTAAA
1 TTTTAAAATATTTTAAAATACTTTTTAAA
** *
1655156 TTTTTTTAAT-TTTATAAAATATTTTTTAAA
1 -TTTTAAAATATTT-TAAAATACTTTTTAAA
1655186 T
1 T
1655187 ACTTTTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
28 8 0.16
29 21 0.41
30 22 0.43
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAATATTTTAAAATACTTTTTAAA
Found at i:1655211 original size:31 final size:32
Alignment explanation
Indices: 1655176--1655249 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
1655166 TTTATAAAAT
*
1655176 ATTTTTTAAATACTTTTTAAAA-A-TTTTTTTA
1 ATTTTTTAAATA-TTTTTAAAATACATTTTTTA
*
1655207 ATTTTAT-AATATTTTTAAAATACATTTTTTA
1 ATTTTTTAAATATTTTTAAAATACATTTTTTA
*
1655238 ATTTTTAAAATA
1 ATTTTTTAAATA
1655250 AAATTTTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 9 0.25
30 5 0.14
31 18 0.50
32 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTTTTAAATATTTTTAAAATACATTTTTTA
Found at i:1655239 original size:23 final size:21
Alignment explanation
Indices: 1655207--1655249 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1655197 AATTTTTTTA
1655207 ATTTTATAATATTTTTAAAATAC
1 ATTTTAT-A-ATTTTTAAAATAC
*
1655230 ATTTTTTAATTTTTAAAATA
1 ATTTTATAATTTTTAAAATA
1655250 AAATTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTATAATTTTTAAAATAC
Found at i:1655256 original size:21 final size:21
Alignment explanation
Indices: 1655217--1655257 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1655207 ATTTTATAAT
* *
1655217 ATTTTTAAAATACATTTTTTA
1 ATTTTTAAAATAAAATTTTTA
1655238 ATTTTTAAAATAAAATTTTT
1 ATTTTTAAAATAAAATTTTT
1655258 GGTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTAAAATAAAATTTTTA
Found at i:1657198 original size:26 final size:26
Alignment explanation
Indices: 1657157--1657207 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1657147 CAGTTTGCAT
*
1657157 ATTGAGCTTGTATATCGAGCTCGCAC
1 ATTGAGCTCGTATATCGAGCTCGCAC
* *
1657183 ATTGAGCTCGTGTATCGGGCTCGCA
1 ATTGAGCTCGTATATCGAGCTCGCA
1657208 TGATACTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (26 bp):
ATTGAGCTCGTATATCGAGCTCGCAC
Found at i:1657339 original size:13 final size:13
Alignment explanation
Indices: 1657321--1657347 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1657311 CAAACTCCCA
1657321 TCGTATAAATACG
1 TCGTATAAATACG
1657334 TCGTATAAATACG
1 TCGTATAAATACG
1657347 T
1 T
1657348 GTTAAGTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TCGTATAAATACG
Found at i:1662581 original size:189 final size:190
Alignment explanation
Indices: 1662259--1662636 Score: 557
Period size: 189 Copynumber: 2.0 Consensus size: 190
1662249 GACCGATAAT
** *** *
1662259 GAGGATGAATTTTGATGTTTCCGGTATGATCATGTCCGCGAGGGCTTAATTTAAGCTCTCATGAA
1 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCTCTCATGAA
*
1662324 TATGATCATATCAGTTTCATGCCTAGAAAACCAGAGGAATCATGACAATTAGTTGAATGAACAGA
66 TATGATCATATCAGTTTCATGCCTAGAAAACCAGAGGAATCATGAAAATTAGTTGAATGAACAGA
*
1662389 GTTTAAACAAGCTAGAACTAGTGAACT-AGACTGATTT-CCGGTCATGCCTTGTGTGACCG
131 GTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCCAGTC-TGCCTTGTGTGACCG
* *
1662448 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTTCGCGAGGGCTTAATTTAAGCGT-TCTTGA
1 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGC-TCTCATGA
* * * *
1662512 ATATGATCATATCAGTTTCATGCTTAGAAAACTAGATGAATCATGAAAAATT-GTTGAATGAATA
65 ATATGATCATATCAGTTTCATGCCTAGAAAACCAGAGGAATCATG-AAAATTAGTTGAATGAACA
* *
1662576 GAGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCCATTCTGCCTTGTGTGACC
129 GAGTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCCAGTCTGCCTTGTGTGACC
1662637 AATCTTTTGA
Statistics
Matches: 169, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
189 135 0.80
190 30 0.18
191 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (190 bp):
GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCTCTCATGAA
TATGATCATATCAGTTTCATGCCTAGAAAACCAGAGGAATCATGAAAATTAGTTGAATGAACAGA
GTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCCAGTCTGCCTTGTGTGACCG
Found at i:1663052 original size:406 final size:401
Alignment explanation
Indices: 1662256--1663080 Score: 929
Period size: 406 Copynumber: 2.0 Consensus size: 401
1662246 TGTGACCGAT
* * * **
1662256 AATGAGGATGAATTTTGATGTTTCCGGTATGATCATGTCCGCGAGGGCTTAATTTAAGCTCTCAT
1 AATGAGGATAAATTTTGATGTTTCCGGTATGATCATATCCACGAGGGCTTAATTTAAGCGATCAT
*
1662321 GAATATGATCATATCAGTTTCATGCCTAGAAAACCAGAGGAATCATGACAATTAGTTGAATGAAC
66 GAATATGATCATATCAGTTTCATGCCT---AAACCAGAGGAATCATAACAATTAGTTGAATGAAC
* * *
1662386 AGAGTTTAAACAAGCTAGAACTAGTGAACTAGACTGATTTCCGGTCATGCCTTGTGTGACCGGAG
128 AGAGTTTAAACAAGCTAGAACTAGTGAACTAGACTAATTTCCAGTCATGCCATGTGTGACCGGAG
* * *
1662451 GATGAATTTCAATGTTTCCAACATGAGCATGTTCGCGAGGGCTTAATTTAAGCGTTCTTGAATAT
193 GATG----T-AATGTTTCCAACA-GACCATGTTCGCAAGGGCTTAATTTAAGCGTTCGTGAATAT
* *
1662516 GATCATATCAGTTTCATGCTTAGAAAACTAGATGAATCATGAAAAATTGTTGAATGAATAGAGTT
252 GATCATATCAGTTTCATGCTTAGAAAACTAGAGGAATCATGAAAAATAGTTGAATGAATAGAGTT
* * ** *
1662581 TGAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCCATTCTGCCTTGTGTGACCAATCTTTTG
317 TGAACAAGCTAGAACTAATGAACCGAGACTGACATCCCATTCTGCCTTGTGCGACCAATCTTTTG
1662646 AAAA-TCATATAGAACCATTG
382 AAAACT-ATATAGAACCATTG
* * *
1662666 AATGAGGATAAATTTTGATGTTTCCTGTATGATCATATGCACGAGGGCTTAATTTAAGCGATCTT
1 AATGAGGATAAATTTTGATGTTTCCGGTATGATCATATCCACGAGGGCTTAATTTAAGCGATCAT
* * * * * * *
1662731 GAATATGATCGTATCAGTTTCTTG-CT-TACTAGAGGAATCATAATAATTAGTCT-ATTGAATTA
66 GAATATGATCATATCAGTTTCATGCCTAAACCAGAGGAATCATAACAATTAGT-TGAATGAA-CA
* * *
1662793 -AGTTTGAACAAGCTAGAACTAGTGAACTGAGACTAATTTCCAATTCTACCTTGTGTCATGTGTG
129 GAGTTTAAACAAGCTAGAACTAGTGAACT-AGACTAATTTCC-AGTC-A-----TGCCATGTGTG
*
1662857 ACCGGAGGATG-AAT-TTTCCGATACA-ACCATGTTCGCAAGGGCTTAA-TTAAGCAG-TGGTGA
186 ACCGGAGGATGTAATGTTTCC-A-ACAGACCATGTTCGCAAGGGCTTAATTTAAGC-GTTCGTGA
* * * *
1662917 ATATGATCGTATCAGTTTCATGCTTTAGGAAACTAGAGGAATCCT-AAAAACTAGTTGATTGAAT
248 ATATGATCATATCAGTTTCATGC-TTAGAAAACTAGAGGAATCATGAAAAA-TAGTTGAATGAAT
* * **
1662981 AGAGTTTGAGCAAAGCTAGAACTAATGACCCGAGACT-ACCATCTGATT-TGCCTTGTGCGACCA
311 AGAGTTTGAAC-AAGCTAGAACTAATGAACCGAGACTGA-CATCCCATTCTGCCTTGTGCGACCA
* *
1663044 ATCTTTTGAAAACTGTATAGAATCATTG
374 ATCTTTTGAAAACTATATAGAACCATTG
1663072 AATGAGGAT
1 AATGAGGAT
1663081 GAATGATGCT
Statistics
Matches: 354, Mismatches: 43, Indels: 40
0.81 0.10 0.09
Matches are distributed among these distances:
405 90 0.25
406 125 0.35
407 34 0.10
408 4 0.01
409 2 0.01
410 79 0.22
413 20 0.06
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (401 bp):
AATGAGGATAAATTTTGATGTTTCCGGTATGATCATATCCACGAGGGCTTAATTTAAGCGATCAT
GAATATGATCATATCAGTTTCATGCCTAAACCAGAGGAATCATAACAATTAGTTGAATGAACAGA
GTTTAAACAAGCTAGAACTAGTGAACTAGACTAATTTCCAGTCATGCCATGTGTGACCGGAGGAT
GTAATGTTTCCAACAGACCATGTTCGCAAGGGCTTAATTTAAGCGTTCGTGAATATGATCATATC
AGTTTCATGCTTAGAAAACTAGAGGAATCATGAAAAATAGTTGAATGAATAGAGTTTGAACAAGC
TAGAACTAATGAACCGAGACTGACATCCCATTCTGCCTTGTGCGACCAATCTTTTGAAAACTATA
TAGAACCATTG
Found at i:1665142 original size:21 final size:21
Alignment explanation
Indices: 1665118--1665162 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1665108 CGATTCAACT
1665118 TTCGATTTGTTTTGTTTTTCA
1 TTCGATTTGTTTTGTTTTTCA
1665139 TTCGATTTGTTTTGTTTTTCA
1 TTCGATTTGTTTTGTTTTTCA
1665160 TTC
1 TTC
1665163 ATGATGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.09, C:0.11, G:0.13, T:0.67
Consensus pattern (21 bp):
TTCGATTTGTTTTGTTTTTCA
Found at i:1699839 original size:4 final size:4
Alignment explanation
Indices: 1699825--1699891 Score: 125
Period size: 4 Copynumber: 16.8 Consensus size: 4
1699815 AGAAAATTGA
*
1699825 TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1699873 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
1699892 ATGCGTGTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1705893 original size:23 final size:22
Alignment explanation
Indices: 1705866--1705917 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1705856 CCAAACAATT
1705866 ATATGCAATATTCACTTCAGGGA
1 ATATGC-ATATTCACTTCAGGGA
*
1705889 ATATGTCATATTCGCTTCAGGGA
1 ATATG-CATATTCACTTCAGGGA
1705912 ATATGC
1 ATATGC
1705918 CAAAATCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (22 bp):
ATATGCATATTCACTTCAGGGA
Found at i:1712781 original size:3 final size:3
Alignment explanation
Indices: 1712773--1712797 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1712763 GAATTAATGT
1712773 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
1712798 AATGATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1727933 original size:17 final size:17
Alignment explanation
Indices: 1727911--1727946 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1727901 TAAAAACACT
1727911 AAAAATGAAAATCCAAC
1 AAAAATGAAAATCCAAC
1727928 AAAAATGAAAATCCAAC
1 AAAAATGAAAATCCAAC
1727945 AA
1 AA
1727947 TTTGACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAATCCAAC
Found at i:1732987 original size:19 final size:19
Alignment explanation
Indices: 1732941--1732988 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1732931 GTATATATTT
1732941 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1732959 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1732978 TAAGTTTTATT
1 TAAATTTTATT
1732989 CATATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:1733037 original size:42 final size:42
Alignment explanation
Indices: 1732991--1733080 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
1732981 GTTTTATTCA
* *
1732991 TATTTTATT-TTATCTTTTAGTAGTTTATTAGAATAAGGGAAT
1 TATTTT-TTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
* *
1733033 TATTTTTTCTTATGTTTTAGTAGTTGATTAGAATAAATGAAT
1 TATTTTTTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
1733075 TATTTT
1 TATTTT
1733081 CCTAATTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (42 bp):
TATTTTTTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
Found at i:1737669 original size:19 final size:19
Alignment explanation
Indices: 1737623--1737670 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1737613 AGGGAGGGTT
1737623 TAAA-TTTATTTAGGCAGA
1 TAAATTTTATTTAGGCAGA
* *
1737641 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGCAGA
*
1737660 TAAGTTTTATT
1 TAAATTTTATT
1737671 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (19 bp):
TAAATTTTATTTAGGCAGA
Found at i:1748244 original size:48 final size:48
Alignment explanation
Indices: 1748151--1748618 Score: 335
Period size: 48 Copynumber: 9.8 Consensus size: 48
1748141 AATTGGAGCA
* ** * **
1748151 CCAATAGGTGCACCACCTCCCAGTGCATCAGCTGCAGTACCAGGCACT-
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCA-TG
* ** * **
1748199 CCAATAGGAGCACCAACTCCAAGTGCACCAGCTGCAACACAAGGCACA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
** * * * * * * * **
1748247 CCGGTAGGAGCAGCACCTCCTGGGGAAGCAGTTGCAAAACAAGGCACA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* * * * ***
1748295 CCAATAGGAGCGCCATCTCCAGGTGCAACAGCTGCAACATTGGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
** * * **
1748343 CCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACACCGGGCACA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* *** *
1748391 CCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* **
1748439 GCAATAGGAGCACCACCTCCTGGCACACCAGCTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* * * * * * *
1748487 GCAATAGGCGCACCATCTCTTGGTACATCAGCTGGAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* ** * * * * *
1748535 CCAATTGGAGCACCACCTCCCAGTACATCAGTTGCAACACCTGACATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* * * ** *
1748583 CCAATTGGAGCAACTCCTCCCAGTGCAGCAGCTGCA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCA
1748619 GCTGCAGCAC
Statistics
Matches: 341, Mismatches: 78, Indels: 2
0.81 0.19 0.00
Matches are distributed among these distances:
48 341 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (48 bp):
CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
Found at i:1748871 original size:48 final size:48
Alignment explanation
Indices: 1748819--1748913 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
1748809 TGCCAACAAG
*
1748819 AGCACCAACTCCTGATGCACCAGATGCAACACCTGGCAAGCCAATAGA
1 AGCACCAACTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAGA
* * * * * *
1748867 AGCACCACCTCCTGGTGCACCAGCTGCAAGACCAGGTACGCCAATAG
1 AGCACCAACTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAG
1748914 GTTCAGCGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.13
Consensus pattern (48 bp):
AGCACCAACTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAGA
Found at i:1749121 original size:33 final size:33
Alignment explanation
Indices: 1749052--1749122 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
1749042 CAAGGCTCAC
* **
1749052 CAATAGGAGCACCAGCAGCAACACCAGGAATGT
1 CAATAGGAGCACCAGCAGCAACACCAAGAACAT
* *
1749085 CAATTGGAGCACCAGCTA-CAACACCAAGCACAT
1 CAATAGGAGCACCAGC-AGCAACACCAAGAACAT
1749118 CAATA
1 CAATA
1749123 AGAATGCCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.30, G:0.18, T:0.11
Consensus pattern (33 bp):
CAATAGGAGCACCAGCAGCAACACCAAGAACAT
Found at i:1749181 original size:48 final size:48
Alignment explanation
Indices: 1749129--1749241 Score: 118
Period size: 48 Copynumber: 2.4 Consensus size: 48
1749119 AATAAGAATG
* * *
1749129 CCACCTCCTGGTGCACCGGCCACAACACCAAGCACGCCAAAAGGAGCA
1 CCACCTCCTGGTGCACCAGCCACAACACCAAGAAAGCCAAAAGGAGCA
*** ** * * **
1749177 CCACCTCCCAATGCACCAGCTGCAACACTAGGAAAGCCAATTGGAGCA
1 CCACCTCCTGGTGCACCAGCCACAACACCAAGAAAGCCAAAAGGAGCA
1749225 CCACCTCCTGGTGCACC
1 CCACCTCCTGGTGCACC
1749242 TGCTGTAGCA
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.29, C:0.41, G:0.19, T:0.11
Consensus pattern (48 bp):
CCACCTCCTGGTGCACCAGCCACAACACCAAGAAAGCCAAAAGGAGCA
Found at i:1752286 original size:32 final size:32
Alignment explanation
Indices: 1752221--1752286 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1752211 TGGCAAACTC
*
1752221 AAATGACCCTAAACCAAAACAACCCGAACATG
1 AAATGACCCTAAACCAAAACAACACGAACATG
* * *
1752253 AAATGACCC-AAACCCGAAACAACATGAATATG
1 AAATGACCCTAAA-CCAAAACAACACGAACATG
1752285 AA
1 AA
1752287 TTGGCCTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.52, C:0.27, G:0.11, T:0.11
Consensus pattern (32 bp):
AAATGACCCTAAACCAAAACAACACGAACATG
Found at i:1763408 original size:22 final size:21
Alignment explanation
Indices: 1763379--1763424 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
1763369 TGGGAACAAG
1763379 TTTCTTGTCCATACTTTATAT
1 TTTCTTGTCCATACTTTATAT
1763400 TTTCATTGTCCATACTTTATAT
1 TTTC-TTGTCCATACTTTATAT
1763422 TTT
1 TTT
1763425 GTTAATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.20, C:0.17, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTCTTGTCCATACTTTATAT
Found at i:1765116 original size:25 final size:24
Alignment explanation
Indices: 1765081--1765128 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1765071 TTGTTTTGGA
* *
1765081 GGAGGTTTTTTTTTTTTTGTTTTTT
1 GGAGGTGTTTTTTTTGTT-TTTTTT
1765106 GGAGGTGTTTTTTTTGTTTTTTT
1 GGAGGTGTTTTTTTTGTTTTTTT
1765129 GGAAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.04, C:0.00, G:0.23, T:0.73
Consensus pattern (24 bp):
GGAGGTGTTTTTTTTGTTTTTTTT
Found at i:1765473 original size:3 final size:3
Alignment explanation
Indices: 1765459--1765543 Score: 63
Period size: 3 Copynumber: 28.3 Consensus size: 3
1765449 GAGCTTTGTT
* *
1765459 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
1765503 TT- TCTCA TGTA TATA TTA TTT TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1765544 ATATGCCCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.12
3 50 0.76
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1765494 original size:24 final size:23
Alignment explanation
Indices: 1765462--1765543 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
1765452 CTTTGTTTTA
*
1765462 TTATTTTATTATTTTTACTATTAT
1 TTATATTATTATTTTTA-TATTAT
* *
1765486 TTATATTATTATTATTATTTCTCAT
1 TTATATTATTATTTTTATAT-T-AT
*
1765511 GTATA-TATTATTTTTATATTATT
1 TTATATTATTATTTTTATATTA-T
1765534 ATTATATTAT
1 -TTATATTAT
1765544 ATATGCCCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 32 0.70
25 9 0.20
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATATTATTATTTTTATATTAT
Found at i:1765530 original size:11 final size:11
Alignment explanation
Indices: 1765459--1765543 Score: 64
Period size: 11 Copynumber: 7.4 Consensus size: 11
1765449 GAGCTTTGTT
1765459 TTATTATTT-TA
1 TTATT-TTTATA
1765470 TTATTTTTACTA
1 TTATTTTTA-TA
*
1765482 TTATTTATATTA
1 TTATTTTTA-TA
* *
1765494 TTATTATTATT
1 TTATTTTTATA
* *
1765505 TCTCATGTATATA
1 T-T-ATTTTTATA
1765518 TTATTTTTATA
1 TTATTTTTATA
*
1765529 TTATTATTATA
1 TTATTTTTATA
1765540 TTAT
1 TTAT
1765544 ATATGCCCTC
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
10 3 0.05
11 28 0.48
12 21 0.36
13 6 0.10
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:1765784 original size:18 final size:19
Alignment explanation
Indices: 1765748--1765806 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
1765738 ACTATTACTA
*
1765748 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
1765768 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
1765785 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
1765803 TTAT
1 TTAT
1765807 TACTTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 2 0.06
20 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:1765788 original size:17 final size:18
Alignment explanation
Indices: 1765748--1765803 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
1765738 ACTATTACTA
*
1765748 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATA-TT
*
1765768 TTATGTATA-TATATATT
1 TTATATATAGTATATATT
1765785 TTATATATAGTAT-TATT
1 TTATATATAGTATATATT
1765802 TT
1 TT
1765804 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 16 0.50
18 8 0.25
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (18 bp):
TTATATATAGTATATATT
Found at i:1778338 original size:132 final size:132
Alignment explanation
Indices: 1778096--1778808 Score: 1192
Period size: 132 Copynumber: 5.4 Consensus size: 132
1778086 TGAAGTCATT
*
1778096 AAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
1778161 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
1778226 AG
131 AG
* * *
1778228 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * *
1778293 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTAGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
1778358 AG
131 AG
*
1778360 AAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
1778425 TATTGATAGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
1778490 AG
131 AG
*
1778492 AAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
1778557 TATTGATAGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
1778622 AG
131 AG
1778624 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * * *
1778689 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
1778754 AG
131 AG
** * * * * * *
1778756 ATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAG
1 AAAGCAGATCTTGTCTTCATGTA-TTGGC-GTGAAGTAGATCGAAGATAGCAG
1778809 ATTTTACCTC
Statistics
Matches: 549, Mismatches: 30, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
132 525 0.96
133 5 0.01
134 19 0.03
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
AG
Found at i:1778936 original size:46 final size:46
Alignment explanation
Indices: 1778881--1779093 Score: 134
Period size: 46 Copynumber: 4.7 Consensus size: 46
1778871 GCAGTGGAAT
* *
1778881 AGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGC
1 AGATTGAAGATGGCAGATCTTACCTTCCTGTATTAGGCAGCGAAGC
* * * * * * *
1778927 AGATCGAAGATGGCAGATTTTACCTCCCTGTGACTA--CAGTGGAGT
1 AGATTGAAGATGGCAGATCTTACCTTCCTGT-ATTAGGCAGCGAAGC
* ** * * * * *
1778972 ACATTGAAG-CCG-ATAACTCTATC-TCACTGTATCT-GGCAGTGGAA-T
1 AGATTGAAGATGGCAGATCT-TACCTTC-CTGTAT-TAGGCAG-CGAAGC
* *
1779017 AGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGC
1 AGATTGAAGATGGCAGATCTTACCTTCCTGTATTAGGCAGCGAAGC
* * *
1779063 AGATCGAAGATGGCAGATTTTACCTCCCTGT
1 AGATTGAAGATGGCAGATCTTACCTTCCTGT
1779094 GACTACAGTG
Statistics
Matches: 120, Mismatches: 35, Indels: 24
0.67 0.20 0.13
Matches are distributed among these distances:
43 5 0.04
44 9 0.08
45 29 0.24
46 68 0.57
47 9 0.08
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (46 bp):
AGATTGAAGATGGCAGATCTTACCTTCCTGTATTAGGCAGCGAAGC
Found at i:1779036 original size:136 final size:136
Alignment explanation
Indices: 1778746--1779186 Score: 814
Period size: 136 Copynumber: 3.3 Consensus size: 136
1778736 GGTGGTGAAG
* *
1778746 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
*
1778811 TTTACCTCCC--TGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
66 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
1778874 GTGGAA
131 GTGGAA
1778880 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1778945 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
66 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
1779010 GTGGAA
131 GTGGAA
1779016 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
*
1779081 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
66 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
1779146 GTGGAA
131 GTGGAA
* *
1779152 TAGATTGAAGATTGCAGATCCTGCCTTCCTATATT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATT
1779187 GGTAGGAAGT
Statistics
Matches: 299, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
134 73 0.24
136 226 0.76
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (136 bp):
TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
GTGGAA
Found at i:1779401 original size:40 final size:40
Alignment explanation
Indices: 1779349--1779500 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
1779339 AAGATTACAA
* *
1779349 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
* *** *
1779389 TCTTATCTCCCTAAGCAGTAATGGAGCAGATAAAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCA-AG
* * *
1779430 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
1779471 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1779501 CTAAAAACAC
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
40 57 0.63
41 4 0.04
42 30 0.33
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:1779444 original size:82 final size:83
Alignment explanation
Indices: 1779347--1779516 Score: 252
Period size: 82 Copynumber: 2.1 Consensus size: 83
1779337 CAAAGATTAC
* * * *
1779347 AATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTAATG
1 AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAATG
*
1779412 GAGCAGA-TAAAACCACA
66 GAGCAGACTAAAAACACA
* * * *
1779429 GATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAATG
1779494 GAGCAGACTAAAAACACA
66 GAGCAGACTAAAAACACA
1779512 AATCT
1 AATCT
1779517 CATCCCCATG
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 64 0.83
83 13 0.17
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (83 bp):
AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAATG
GAGCAGACTAAAAACACA
Found at i:1780001 original size:23 final size:23
Alignment explanation
Indices: 1779972--1780021 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1779962 TTTTGGGTTT
1779972 TTTTGGAGAAGGATTATTCTTTG
1 TTTTGGAGAAGGATTATTCTTTG
* * * *
1779995 TTTTGGAGGAGGTTTTTTTTTTG
1 TTTTGGAGAAGGATTATTCTTTG
1780018 TTTT
1 TTTT
1780022 TTGGAGGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.26, T:0.58
Consensus pattern (23 bp):
TTTTGGAGAAGGATTATTCTTTG
Found at i:1780388 original size:3 final size:3
Alignment explanation
Indices: 1780374--1780458 Score: 63
Period size: 3 Copynumber: 28.3 Consensus size: 3
1780364 GAGCTTTGTT
* *
1780374 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
1780418 TT- TCTCA TGTA TATA TTA TTT TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1780459 ATATGCCCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.12
3 50 0.76
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1780409 original size:24 final size:23
Alignment explanation
Indices: 1780377--1780458 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
1780367 CTTTGTTTTA
*
1780377 TTATTTTATTATTTTTACTATTAT
1 TTATATTATTATTTTTA-TATTAT
* *
1780401 TTATATTATTATTATTATTTCTCAT
1 TTATATTATTATTTTTATAT-T-AT
*
1780426 GTATA-TATTATTTTTATATTATT
1 TTATATTATTATTTTTATATTA-T
1780449 ATTATATTAT
1 -TTATATTAT
1780459 ATATGCCCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 32 0.70
25 9 0.20
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATATTATTATTTTTATATTAT
Found at i:1780445 original size:11 final size:11
Alignment explanation
Indices: 1780374--1780458 Score: 64
Period size: 11 Copynumber: 7.4 Consensus size: 11
1780364 GAGCTTTGTT
1780374 TTATTATTT-TA
1 TTATT-TTTATA
1780385 TTATTTTTACTA
1 TTATTTTTA-TA
*
1780397 TTATTTATATTA
1 TTATTTTTA-TA
* *
1780409 TTATTATTATT
1 TTATTTTTATA
* *
1780420 TCTCATGTATATA
1 T-T-ATTTTTATA
1780433 TTATTTTTATA
1 TTATTTTTATA
*
1780444 TTATTATTATA
1 TTATTTTTATA
1780455 TTAT
1 TTAT
1780459 ATATGCCCTC
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
10 3 0.05
11 28 0.48
12 21 0.36
13 6 0.10
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:1780701 original size:16 final size:17
Alignment explanation
Indices: 1780675--1780716 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1780665 ATATATTAGT
* *
1780675 GTATATTTTTATGTATA
1 GTATATATTTATATATA
1780692 -TATATATTTATATATA
1 GTATATATTTATATATA
1780708 GTAT-TATTT
1 GTATATATTT
1780717 TTTATTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
GTATATATTTATATATA
Found at i:1780821 original size:12 final size:12
Alignment explanation
Indices: 1780804--1780833 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1780794 GTATTTCTAT
1780804 TATATACATATA
1 TATATACATATA
*
1780816 TATATACATTTA
1 TATATACATATA
1780828 TATATA
1 TATATA
1780834 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:1785155 original size:29 final size:30
Alignment explanation
Indices: 1785079--1785155 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
1785069 GTCACTACAC
1785079 TTTTTACAAATTT-AAAATTTAGTCATTGTA
1 TTTTTA-AAATTTCAAAATTTAGTCATTGTA
* *
1785109 TTTTT--ATTTTCAAGAATTTAGTC-TTTTA
1 TTTTTAAAATTTCAA-AATTTAGTCATTGTA
1785137 TTTTTAAAATTTCAAAATT
1 TTTTTAAAATTTCAAAATT
1785156 GAATTCTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 13 0.32
30 12 0.30
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (30 bp):
TTTTTAAAATTTCAAAATTTAGTCATTGTA
Found at i:1792894 original size:21 final size:21
Alignment explanation
Indices: 1792862--1792902 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1792852 AGGCTCGAGG
1792862 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
1792883 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
1792903 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:1800656 original size:30 final size:30
Alignment explanation
Indices: 1800589--1800658 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1800579 TTCTATCTTA
*
1800589 TTTTAATTTAATCCTTTAAGTTTCGTTTCT
1 TTTTAATTTAATCCTTTAAGTTTCGTTTAT
** * *
1800619 TCATAATTTAA-CCTTTTAGTTTTGTTATAT
1 TTTTAATTTAATCCTTTAAGTTTCGTT-TAT
1800649 TTTTAATTTA
1 TTTTAATTTA
1800659 TTCCCTTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (30 bp):
TTTTAATTTAATCCTTTAAGTTTCGTTTAT
Found at i:1801438 original size:106 final size:106
Alignment explanation
Indices: 1801324--1801521 Score: 283
Period size: 106 Copynumber: 1.9 Consensus size: 106
1801314 ATTTTCGGGA
* * * * **
1801324 ATTCGAGAC-TTCGTGCCCTAACTTACGGGGCATGTTTTTC-TTCACAATTAACTTGAAATACGA
1 ATTCGAGACATT-GTACCCTAACTTACGAGACATGATTTTCTTTC-CAATTAACTCAAAATACGA
1801387 AGACATTCTTCATAAAATTTGATTTAATTTCTTATTTTTGGAG
64 AGACATTCTTCATAAAATTTGATTTAATTTCTTATTTTTGGAG
*
1801430 ATTCGAGACATTGTACCCTAACTTACGAGACATGATTTTCTTTCCTATTAACTCAAAATACGAAG
1 ATTCGAGACATTGTACCCTAACTTACGAGACATGATTTTCTTTCCAATTAACTCAAAATACGAAG
* *
1801495 ATATTTTTCATAAAATTTGATTTAATT
66 ACATTCTTCATAAAATTTGATTTAATT
1801522 AGCGATATTT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
106 76 0.94
107 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (106 bp):
ATTCGAGACATTGTACCCTAACTTACGAGACATGATTTTCTTTCCAATTAACTCAAAATACGAAG
ACATTCTTCATAAAATTTGATTTAATTTCTTATTTTTGGAG
Found at i:1802534 original size:12 final size:12
Alignment explanation
Indices: 1802517--1802541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1802507 AATAATAAAT
1802517 TATTTTTAAAAA
1 TATTTTTAAAAA
1802529 TATTTTTAAAAA
1 TATTTTTAAAAA
1802541 T
1 T
1802542 TTCTATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTTTAAAAA
Found at i:1803872 original size:3 final size:3
Alignment explanation
Indices: 1803857--1803914 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
1803847 GTGTATATGT
* * *
1803857 ATA ATA GTA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1803905 ATA ATG ATA A
1 ATA ATA ATA A
1803915 ATATTTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1807259 original size:21 final size:22
Alignment explanation
Indices: 1807237--1807276 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1807227 AATTTTATTA
1807237 AAATA-ATTTAT-CATATTTTT
1 AAATACATTTATGCATATTTTT
*
1807257 AAATACTTTTATGCATATTT
1 AAATACATTTATGCATATTT
1807277 ATTTGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (22 bp):
AAATACATTTATGCATATTTTT
Found at i:1807364 original size:29 final size:29
Alignment explanation
Indices: 1807327--1807388 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1807317 TTCTTACATC
*
1807327 CTTTGAATTTTTAA-AATTTAATCCTTATA
1 CTTTGAA-TTCTAAGAATTTAATCCTTATA
* *
1807356 CTTTTAATTCTAAGAATTTAATCTTTATA
1 CTTTGAATTCTAAGAATTTAATCCTTATA
1807385 -TTTG
1 CTTTG
1807389 TTTGATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (29 bp):
CTTTGAATTCTAAGAATTTAATCCTTATA
Found at i:1808526 original size:6 final size:6
Alignment explanation
Indices: 1808515--1808544 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1808505 GTTCAAACTG
1808515 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
1808545 GATTTCCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
CTTTTC
Found at i:1808550 original size:18 final size:18
Alignment explanation
Indices: 1808515--1808551 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1808505 GTTCAAACTG
*
1808515 CTTTTCCTTTTCCTTTTC
1 CTTTTCCTTTTCCATTTC
*
1808533 CTTTTCCTTTTCGATTTC
1 CTTTTCCTTTTCCATTTC
1808551 C
1 C
1808552 AGAAATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.32, G:0.03, T:0.62
Consensus pattern (18 bp):
CTTTTCCTTTTCCATTTC
Found at i:1812836 original size:72 final size:72
Alignment explanation
Indices: 1812717--1812857 Score: 169
Period size: 72 Copynumber: 2.0 Consensus size: 72
1812707 TTGATCACAC
* * * ** *
1812717 CACTCAAGTTGTTTGATGACAAATCAAGATAACTCATGTTCGTAAGATCAAAAAGGGAAT-CGGG
1 CACTCAAGTTGTTTGAAGACAAATCAAGATAACTAAGGTTCACAAGATAAAAAAGGGAATAC-GG
1812781 TATTGGAT
65 TATTGGAT
* * *
1812789 CACTCAAGTTGTTTGAAGACAAGTCAAG-TAAAGTAAGGTTCACAAGATAAAAAATGGAATACGG
1 CACTCAAGTTGTTTGAAGACAAATCAAGAT-AACTAAGGTTCACAAGATAAAAAAGGGAATACGG
1812853 TATTG
65 TATTG
1812858 AACCACCGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
71 1 0.02
72 56 0.97
73 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (72 bp):
CACTCAAGTTGTTTGAAGACAAATCAAGATAACTAAGGTTCACAAGATAAAAAAGGGAATACGGT
ATTGGAT
Found at i:1816807 original size:16 final size:16
Alignment explanation
Indices: 1816783--1816814 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1816773 ACCATATATA
*
1816783 AAATTCTCATATGAAG
1 AAATCCTCATATGAAG
1816799 AAATCCTCATATGAAG
1 AAATCCTCATATGAAG
1816815 GCATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (16 bp):
AAATCCTCATATGAAG
Found at i:1818679 original size:44 final size:42
Alignment explanation
Indices: 1818610--1818707 Score: 135
Period size: 44 Copynumber: 2.3 Consensus size: 42
1818600 ATATAAGTTA
**
1818610 TCGTGTAAGACCATGTATGGGACATCGGCATCA-ATTTGAGATT
1 TCGTGTAAGACCATGTATGAAACATCGGCATCATATTT--GATT
*
1818653 TACGTGTAAGACCATGTCTGAAACATCGGCATCATATTTGATT
1 T-CGTGTAAGACCATGTATGAAACATCGGCATCATATTTGATT
1818696 TCGTGTAAGACC
1 TCGTGTAAGACC
1818708 CTATTTGGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 11 0.22
43 6 0.12
44 29 0.58
45 4 0.08
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCATGTATGAAACATCGGCATCATATTTGATT
Found at i:1821902 original size:63 final size:63
Alignment explanation
Indices: 1821803--1821928 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
1821793 GTGCACGAAC
1821803 CCGTTGCAAAAAGAAGATAAATTGATGGTGAATCTTGGTGGCTTGAGCGACGGCACACAAGGG
1 CCGTTGCAAAAAGAAGATAAATTGATGGTGAATCTTGGTGGCTTGAGCGACGGCACACAAGGG
*
1821866 CCGTTGCAAAAAGAAGATAAATTGATGGTGAATCTTGGTGGCTTGAGCGGCGGCACACAAGGG
1 CCGTTGCAAAAAGAAGATAAATTGATGGTGAATCTTGGTGGCTTGAGCGACGGCACACAAGGG
1821929 AAGAAAGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.21
Consensus pattern (63 bp):
CCGTTGCAAAAAGAAGATAAATTGATGGTGAATCTTGGTGGCTTGAGCGACGGCACACAAGGG
Found at i:1826056 original size:34 final size:34
Alignment explanation
Indices: 1826013--1826077 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1826003 ACGACTGTTT
* * *
1826013 ACGATACTATTTACGTATACGGTATTGTTCATCC
1 ACGATACTATTCACGTAGACGGTACTGTTCATCC
1826047 ACGATACTATTCACGTAGACGGTACTGTTCA
1 ACGATACTATTCACGTAGACGGTACTGTTCA
1826078 CATATACAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (34 bp):
ACGATACTATTCACGTAGACGGTACTGTTCATCC
Found at i:1833122 original size:72 final size:72
Alignment explanation
Indices: 1832974--1833132 Score: 205
Period size: 72 Copynumber: 2.2 Consensus size: 72
1832964 ACTTGATCAC
* * *
1832974 ACCACTCAAGTTATTTGGTGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGGAATATG
1 ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGGAACACG
* * *
1833039 TTATTGG
66 GTATCGA
* * *
1833046 ACCACTCAAGTTGTTTGATGACAAATCAAG-TGAAGTAAGGTTCACAAGATCAAAAATGGAACAC
1 ACCACTCAAGTTATTTGATGACAAATCAAGAT-AACTAAGGTACACAAGATCAAAAATGGAACAC
1833110 GGTATCGA
65 GGTATCGA
1833118 ACCAC-CAATGTTATT
1 ACCACTCAA-GTTATT
1833133 ATAACTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
71 4 0.05
72 71 0.95
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGGAACACG
GTATCGA
Found at i:1842823 original size:42 final size:42
Alignment explanation
Indices: 1842764--1842858 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
1842754 TAGTTGGATT
* *
1842764 TTAATCATGGATTATGAATGTTAAATAAAATTTGATGGTATC
1 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
*
1842806 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATT
1 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
*
1842848 TTAATAATGAA
1 TTAATCATGAA
1842859 AATACTGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (42 bp):
TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
Found at i:1843453 original size:20 final size:20
Alignment explanation
Indices: 1843430--1843493 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
1843420 TCCAAAAATA
1843430 TATATATATTTAATAAAAAG
1 TATATATATTTAATAAAAAG
* *
1843450 TATATTTGATTAAAAATAAAAA-
1 TATATAT-ATT--TAATAAAAAG
1843472 TATATATATTTAATATAAAAG
1 TATATATATTTAATA-AAAAG
1843493 T
1 T
1843494 CTTACCCGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
19 4 0.11
20 10 0.29
21 7 0.20
22 6 0.17
23 8 0.23
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TATATATATTTAATAAAAAG
Found at i:1846716 original size:21 final size:21
Alignment explanation
Indices: 1846690--1846744 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1846680 ACCATTGTTT
*
1846690 CTAATCTCACCGCTACAGTGTA
1 CTAATCTCACCGCTACAGT-AA
1846712 C-AATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
1846732 CTAATCTCACCGC
1 CTAATCTCACCGC
1846745 CACCGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:1848522 original size:11 final size:11
Alignment explanation
Indices: 1848508--1848533 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1848498 TTTTGTTTCG
1848508 TTTTTTATTTA
1 TTTTTTATTTA
1848519 TTTTTTATTTA
1 TTTTTTATTTA
1848530 TTTT
1 TTTT
1848534 GAAATACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:1849240 original size:3 final size:3
Alignment explanation
Indices: 1849232--1849262 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1849222 AAATTTGATG
*
1849232 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1849263 AATTGCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1849300 original size:22 final size:21
Alignment explanation
Indices: 1849272--1849326 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1849262 TAATTGCTCT
** *
1849272 TATATATGTATATTTTTTTGTA
1 TATATATACATATATTTTT-TA
1849294 TATATATACATATATTTTTTA
1 TATATATACATATATTTTTTA
1849315 TATACT-TACATA
1 TATA-TATACATA
1849327 CATACTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (21 bp):
TATATATACATATATTTTTTA
Found at i:1850913 original size:22 final size:22
Alignment explanation
Indices: 1850870--1850913 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1850860 TCGTAGACCA
* *
1850870 AAATCGTTGTTTTAATAAAATC
1 AAATCGTTGTATTAAAAAAATC
1850892 AAATCGTT-TATTAAAAATAATC
1 AAATCGTTGTATTAAAAA-AATC
1850914 GTTTTTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (22 bp):
AAATCGTTGTATTAAAAAAATC
Found at i:1852984 original size:13 final size:13
Alignment explanation
Indices: 1852968--1852993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1852958 CTTTGCATAT
1852968 TGTCTTCAACAGG
1 TGTCTTCAACAGG
1852981 TGTCTTCAACAGG
1 TGTCTTCAACAGG
1852994 CTCGCACTTT
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:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:1855006 original size:39 final size:39
Alignment explanation
Indices: 1854963--1855044 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
1854953 TCAGAACCTT
1854963 CATGTTCCACCACCAATGGTAGACTTAGTTCAGCATTCC
1 CATGTTCCACCACCAATGGTAGACTTAGTTCAGCATTCC
1855002 CATGTTCCACCACCAATGGTAGACTTAGTTCAGCATTCC
1 CATGTTCCACCACCAATGGTAGACTTAGTTCAGCATTCC
1855041 CATG
1 CATG
1855045 GTCGACGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (39 bp):
CATGTTCCACCACCAATGGTAGACTTAGTTCAGCATTCC
Found at i:1856554 original size:72 final size:72
Alignment explanation
Indices: 1856437--1856585 Score: 199
Period size: 72 Copynumber: 2.1 Consensus size: 72
1856427 ACTTGATCAC
* **
1856437 ACCACTCAAGTTGTTGGGTGACAAATAAAGTGAACAAAGGTTCACAAGATCAAAAATGGAACCTG
1 ACCACTCAAGTTGTTGGATGACAAATAAAGCCAACAAAGGTTCACAAGATCAAAAATGGAACCTG
1856502 GTATTGG
66 GTATTGG
* * * ** * **
1856509 ACCACTCAAGTTGTTTGATGACAAATCAAGCCTAGTAAGGTTCACAAGATTAAAAATGGAATTTG
1 ACCACTCAAGTTGTTGGATGACAAATAAAGCCAACAAAGGTTCACAAGATCAAAAATGGAACCTG
1856574 GTATTGG
66 GTATTGG
1856581 ACCAC
1 ACCAC
1856586 CAATGTTATT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTGTTGGATGACAAATAAAGCCAACAAAGGTTCACAAGATCAAAAATGGAACCTG
GTATTGG
Found at i:1856606 original size:72 final size:71
Alignment explanation
Indices: 1856473--1856609 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 71
1856463 AAAGTGAACA
* *
1856473 AAGGTTCACAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTGTTTGATGACAAATCAA
1 AAGGTTCACAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTATTTAAT-ACAAATCAA
1856538 GCCTAGT
65 GCCTAGT
* **
1856545 AAGGTTCACAAGATTAAAAATGGAATTTGGTATTGGACCAC-CAATGTTATTATAACT-CAAATC
1 AAGGTTCACAAGATCAAAAATGGAACCTGGTATTGGACCACTCAA-GTTATT-TAA-TACAAATC
1856608 AA
63 AA
1856610 CCTCTTGGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
71 3 0.05
72 51 0.89
73 2 0.04
74 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (71 bp):
AAGGTTCACAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTATTTAATACAAATCAAG
CCTAGT
Found at i:1864385 original size:17 final size:17
Alignment explanation
Indices: 1864355--1864387 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1864345 TTTTTATAAA
1864355 AATTATATTAAAAAATT
1 AATTATATTAAAAAATT
1864372 AATTA-ATTACAAAAAT
1 AATTATATTA-AAAAAT
1864388 GAGGTGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATATTAAAAAATT
Found at i:1867389 original size:39 final size:39
Alignment explanation
Indices: 1867340--1867419 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
1867330 AGCACTGGCA
* *
1867340 GTCATTGAATTTATAACAAAGGCCTATCCATCATAACAT
1 GTCATAGAATTTATAACAAAGGCCCATCCATCATAACAT
* * * *
1867379 GTCATAGAATTTATACCATAGGCCCATGCATTATAACAT
1 GTCATAGAATTTATAACAAAGGCCCATCCATCATAACAT
1867418 GT
1 GT
1867420 TTGCATTTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (39 bp):
GTCATAGAATTTATAACAAAGGCCCATCCATCATAACAT
Found at i:1869283 original size:9 final size:9
Alignment explanation
Indices: 1869269--1869327 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
1869259 TTTTGGTTAA
1869269 GAATTAACC
1 GAATTAACC
*
1869278 GAATTACCC
1 GAATTAACC
1869287 GAATTAACC
1 GAATTAACC
*
1869296 GAATTACCC
1 GAATTAACC
*
1869305 GAATTACCC
1 GAATTAACC
1869314 GAATTAACC
1 GAATTAACC
1869323 GAATT
1 GAATT
1869328 GAATCACTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (9 bp):
GAATTAACC
Found at i:1869300 original size:27 final size:27
Alignment explanation
Indices: 1869269--1869327 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1869259 TTTTGGTTAA
1869269 GAATTAACCGAATTACCCGAATTAACC
1 GAATTAACCGAATTACCCGAATTAACC
*
1869296 GAATTACCCGAATTACCCGAATTAACC
1 GAATTAACCGAATTACCCGAATTAACC
1869323 GAATT
1 GAATT
1869328 GAATCACTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (27 bp):
GAATTAACCGAATTACCCGAATTAACC
Found at i:1874780 original size:14 final size:14
Alignment explanation
Indices: 1874742--1874780 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1874732 AAGGTTCGAG
* *
1874742 GTTTATGATTCGAA
1 GTTTAGGATTTGAA
*
1874756 GTTTAGGATTTGAT
1 GTTTAGGATTTGAA
1874770 GTTTAGGATTT
1 GTTTAGGATTT
1874781 AAGGTTCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTTAGGATTTGAA
Found at i:1888744 original size:19 final size:19
Alignment explanation
Indices: 1888695--1888750 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1888685 AATAGGTTTG
* *
1888695 TAAATTTTTTAATATTTTT
1 TAAATTTTTTATTAATTTT
***
1888714 TAAATAACTTATTAATTTT
1 TAAATTTTTTATTAATTTT
1888733 TAAATTTTTTATTTAATT
1 TAAATTTTTTA-TTAATT
1888751 AATATTCGGT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAATTTTTTATTAATTTT
Found at i:1891016 original size:36 final size:36
Alignment explanation
Indices: 1890968--1891039 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1890958 GCTAATGGGG
*
1890968 GAGTTAATGACCGAGGCTTTGAAAATAGTTTTGGTT
1 GAGTTAAAGACCGAGGCTTTGAAAATAGTTTTGGTT
1891004 GAGTTAAAGACCGAGGCTTTGAAAATAGTTTTGGTT
1 GAGTTAAAGACCGAGGCTTTGAAAATAGTTTTGGTT
1891040 TTACATACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.28, T:0.35
Consensus pattern (36 bp):
GAGTTAAAGACCGAGGCTTTGAAAATAGTTTTGGTT
Found at i:1903267 original size:20 final size:21
Alignment explanation
Indices: 1903223--1903267 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
1903213 ATGTATCCAT
1903223 TTATTTTCCTATATATATGTA
1 TTATTTTCCTATATATATGTA
*
1903244 -TATTTT-CTATAATGTAT-TA
1 TTATTTTCCTAT-ATATATGTA
1903263 TTATT
1 TTATT
1903268 ATTTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATTTTCCTATATATATGTA
Found at i:1904963 original size:21 final size:21
Alignment explanation
Indices: 1904934--1905000 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1904924 ATATTAATGT
1904934 ATTACTGTAATATGTAGCTCAA
1 ATTA-TGTAATATGTAGCTCAA
*
1904956 ATTATGT-AT-TGTAG-TTAA
1 ATTATGTAATATGTAGCTCAA
1904974 TATTCA--TAATATTGTAGCTCAA
1 -ATT-ATGTAATA-TGTAGCTCAA
1904996 ATTAT
1 ATTAT
1905001 CAATCCGTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
18 4 0.11
19 10 0.28
20 4 0.11
21 11 0.31
22 7 0.19
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (21 bp):
ATTATGTAATATGTAGCTCAA
Found at i:1905639 original size:39 final size:41
Alignment explanation
Indices: 1905583--1905688 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 41
1905573 CATGTCAGCC
* * * * *
1905583 AATCGCGCTTACGTGGACGCGATTTGTTGCCACGT-AAGT-
1 AATCGCGCTGACATGGACGCGATTTGCTGACACATCAAGTG
***
1905622 AATCGCGCTGACATGGACGCGATTTGCTGACACATCCCTTG
1 AATCGCGCTGACATGGACGCGATTTGCTGACACATCAAGTG
1905663 ACATCGCGCTGACATGGACGCGATTT
1 A-ATCGCGCTGACATGGACGCGATTT
1905689 CGGGGAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 30 0.54
40 1 0.02
41 1 0.02
42 24 0.43
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (41 bp):
AATCGCGCTGACATGGACGCGATTTGCTGACACATCAAGTG
Found at i:1906217 original size:20 final size:19
Alignment explanation
Indices: 1906180--1906225 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1906170 CACATTAAAC
*
1906180 AATATAAAAAATAGAAATA
1 AATATAAAAAATACAAATA
*
1906199 AATATATAAAAATTCAAATA
1 AATATA-AAAAATACAAATA
*
1906219 TATATAA
1 AATATAA
1906226 TCTAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AATATAAAAAATACAAATA
Found at i:1906384 original size:22 final size:23
Alignment explanation
Indices: 1906359--1906437 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 23
1906349 AAAAAACTGT
1906359 AAAAAATATTTTA-AAAAGTT-TA
1 AAAAAATATTTTATAAAA-TTCTA
* *
1906381 AAAATATTTTTTATAAAATTCT-
1 AAAAAATATTTTATAAAATTCTA
** * *
1906403 AAAATTTATAATTCTAAAATTCTA
1 AAAAAATAT-TTTATAAAATTCTA
*
1906427 AAAAATTATTT
1 AAAAAATATTT
1906438 AAATTTCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
22 20 0.44
23 17 0.38
24 8 0.18
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (23 bp):
AAAAAATATTTTATAAAATTCTA
Found at i:1906407 original size:8 final size:8
Alignment explanation
Indices: 1906394--1906429 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1906384 ATATTTTTTA
1906394 TAAAATTC
1 TAAAATTC
1906402 TAAAATT-
1 TAAAATTC
*
1906409 TATAATTC
1 TAAAATTC
1906417 TAAAATTC
1 TAAAATTC
1906425 TAAAA
1 TAAAA
1906430 AATTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAAATTC
Found at i:1906496 original size:28 final size:28
Alignment explanation
Indices: 1906465--1906548 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 28
1906455 CAATTACTTG
1906465 AATTT-TAATTACTTTTTAATTTTTTTTAA
1 AATTTATAATTA-TTTTTAA-TTTTTTTAA
*
1906494 ATTTTATATATTATTTTTAA--TTTTTAA
1 AATTTATA-ATTATTTTTAATTTTTTTAA
1906521 AATTTATAATTATATATTTTAATTTTTT
1 AATTTATAA-T-TAT-TTTTAATTTTTT
1906549 AAATAATGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
26 1 0.02
27 15 0.33
28 3 0.07
29 10 0.22
30 9 0.20
31 8 0.17
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (28 bp):
AATTTATAATTATTTTTAATTTTTTTAA
Found at i:1906527 original size:20 final size:19
Alignment explanation
Indices: 1906477--1906527 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1906467 TTTTAATTAC
*
1906477 TTTTTAATTT-TTTTTAAA
1 TTTTAAATTTATTTTTAAA
* *
1906495 TTTTATATATTATTTTTAAT
1 TTTTAAAT-TTATTTTTAAA
1906515 TTTTAAAATTTAT
1 TTTT-AAATTTAT
1906528 AATTATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.23
19 2 0.08
20 15 0.58
21 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAAATTTATTTTTAAA
Found at i:1911710 original size:36 final size:37
Alignment explanation
Indices: 1911644--1911723 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
1911634 TCTCCACCTT
*
1911644 CCCCT-CCCACAACCCAATCCTCCGCCCCTTCACCC-G
1 CCCCTCCCCACAACCCAATCCCCCGCCCCTTC-CCCTG
** *
1911680 -CCCTCCCCACAACCCCTTCCCCCGCTCCTTCCCCTG
1 CCCCTCCCCACAACCCAATCCCCCGCCCCTTCCCCTG
1911716 CCCCTCCC
1 CCCCTCCC
1911724 AAAACACCCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 7 0.19
36 23 0.62
37 7 0.19
ACGTcount: A:0.11, C:0.68, G:0.05, T:0.16
Consensus pattern (37 bp):
CCCCTCCCCACAACCCAATCCCCCGCCCCTTCCCCTG
Found at i:1914201 original size:22 final size:24
Alignment explanation
Indices: 1914157--1914202 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1914147 ATCAAATACA
1914157 CTAAAAACATTGAAAGAAATGTTT
1 CTAAAAACATTGAAAGAAATGTTT
*
1914181 CTAAATACATT-AAA-AAATGTTT
1 CTAAAAACATTGAAAGAAATGTTT
1914203 AATACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (24 bp):
CTAAAAACATTGAAAGAAATGTTT
Found at i:1914356 original size:21 final size:22
Alignment explanation
Indices: 1914332--1914387 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1914322 GCAATATAAT
1914332 AACAACAAAACAACA-TAAAGA-
1 AACAACAAAACAACAGTAAA-AC
*
1914353 AACAAC-AAACAATAGTAAAAC
1 AACAACAAAACAACAGTAAAAC
*
1914374 AACAGCAAAACAAC
1 AACAACAAAACAAC
1914388 CGTGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 8 0.28
21 15 0.52
22 6 0.21
ACGTcount: A:0.68, C:0.21, G:0.05, T:0.05
Consensus pattern (22 bp):
AACAACAAAACAACAGTAAAAC
Found at i:1915575 original size:36 final size:36
Alignment explanation
Indices: 1915528--1915600 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
1915518 ATACTCCCTT
*
1915528 CCTAGCATTGATACCAATATTTACACAGTCACACAG
1 CCTAGCATTGATACCAATATTTACACAATCACACAG
* *
1915564 CCTAGCATTGATACCAATGTTTACATAATCACACAG
1 CCTAGCATTGATACCAATATTTACACAATCACACAG
1915600 C
1 C
1915601 TTGGCGGCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (36 bp):
CCTAGCATTGATACCAATATTTACACAATCACACAG
Found at i:1917367 original size:3 final size:3
Alignment explanation
Indices: 1917359--1917404 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1917349 AGTAAAATCT
1917359 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1917405 AGATTAGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1918168 original size:15 final size:15
Alignment explanation
Indices: 1918148--1918176 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1918138 TTTGAATTTT
1918148 TTTAAAAAATTAATA
1 TTTAAAAAATTAATA
1918163 TTTAAAAAATTAAT
1 TTTAAAAAATTAAT
1918177 TAAATACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAAAAATTAATA
Found at i:1918498 original size:9 final size:9
Alignment explanation
Indices: 1918485--1918544 Score: 68
Period size: 9 Copynumber: 6.7 Consensus size: 9
1918475 TTTGGTTAAA
*
1918485 AATTAACCA
1 AATTAACCG
1918494 AATTAA-CG
1 AATTAACCG
*
1918502 TAATTACCCG
1 -AATTAACCG
1918512 AATTAACCG
1 AATTAACCG
*
1918521 AATTACCCG
1 AATTAACCG
*
1918530 AATTAACGG
1 AATTAACCG
1918539 AATTAA
1 AATTAA
1918545 TCAAATTGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
8 1 0.02
9 40 0.93
10 2 0.05
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:1918533 original size:27 final size:27
Alignment explanation
Indices: 1918485--1918551 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1918475 TTTGGTTAAA
*
1918485 AATTAACCAAATTAACGTAATTACCCG
1 AATTAACCAAATTAACGTAATTAACCG
* * *
1918512 AATTAACCGAATTACCCG-AATTAACGG
1 AATTAACCAAATTA-ACGTAATTAACCG
*
1918539 AATTAATCAAATT
1 AATTAACCAAATT
1918552 GAATCACTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (27 bp):
AATTAACCAAATTAACGTAATTAACCG
Found at i:1918551 original size:18 final size:18
Alignment explanation
Indices: 1918485--1918551 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1918475 TTTGGTTAAA
*
1918485 AATTAACCAAATTAACGT
1 AATTAACCAAATTAACGG
* * *
1918503 AATTACCCGAATTAACCG
1 AATTAACCAAATTAACGG
* *
1918521 AATTACCCGAATTAACGG
1 AATTAACCAAATTAACGG
*
1918539 AATTAATCAAATT
1 AATTAACCAAATT
1918552 GAATCACTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (18 bp):
AATTAACCAAATTAACGG
Found at i:1918694 original size:18 final size:18
Alignment explanation
Indices: 1918654--1918697 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1918644 AATTTTTATG
*
1918654 ATTGGGTTGAGTTTGATA
1 ATTGGGTTGAGGTTGATA
1918672 ATTGGGTTG-GGTTGAATA
1 ATTGGGTTGAGGTTG-ATA
*
1918690 CTTGGGTT
1 ATTGGGTT
1918698 TGGATTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGAGGTTGATA
Found at i:1941311 original size:14 final size:13
Alignment explanation
Indices: 1941266--1941312 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1941256 AAAACATTTC
*
1941266 TTTATTTT-TAAT
1 TTTATTTTAAAAT
1941278 TTTATTTTAAAAT
1 TTTATTTTAAAAT
*
1941291 ATTATTTTAAAATT
1 TTTATTTTAAAA-T
1941305 TTTATTTT
1 TTTATTTT
1941313 TTATAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 8 0.27
13 14 0.47
14 8 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTTTAAAAT
Found at i:1958766 original size:16 final size:15
Alignment explanation
Indices: 1958740--1958771 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1958730 CGTGCGTTTA
1958740 CTGAAAAGAACAATG
1 CTGAAAAGAACAATG
1958755 CTGAAGAAGAACAATG
1 CTGAA-AAGAACAATG
1958771 C
1 C
1958772 AATGAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (15 bp):
CTGAAAAGAACAATG
Found at i:1959022 original size:16 final size:15
Alignment explanation
Indices: 1958996--1959027 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1958986 CGTGCGTTTA
1958996 CTGAAAAGAACAATG
1 CTGAAAAGAACAATG
1959011 CTGAAGAAGAACAATG
1 CTGAA-AAGAACAATG
1959027 C
1 C
1959028 AATGAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (15 bp):
CTGAAAAGAACAATG
Found at i:1961851 original size:11 final size:11
Alignment explanation
Indices: 1961835--1961863 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1961825 AAAAAACTTG
1961835 TATATAAATTT
1 TATATAAATTT
1961846 TATATAAATTT
1 TATATAAATTT
1961857 TAT-TAAA
1 TATATAAA
1961864 CATGTATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATAAATTT
Found at i:1971736 original size:28 final size:28
Alignment explanation
Indices: 1971703--1971767 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
1971693 AGAACAATGA
1971703 ATTGGATTGACTCGACAAGAGAATGCTT
1 ATTGGATTGACTCGACAAGAGAATGCTT
1971731 ATTGGATTGACTCGACAAGAGAATGCTT
1 ATTGGATTGACTCGACAAGAGAATGCTT
1971759 ATTGGATTG
1 ATTGGATTG
1971768 TTATGTGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (28 bp):
ATTGGATTGACTCGACAAGAGAATGCTT
Found at i:1973741 original size:123 final size:123
Alignment explanation
Indices: 1973522--1973767 Score: 474
Period size: 123 Copynumber: 2.0 Consensus size: 123
1973512 GGCAAACTTG
*
1973522 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAAGTAAAATACTGAA
1 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAAGGGTAAGGGCAAAAGTAAAATACTGAA
*
1973587 AAGATAGTGCTAACGGCAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGA
66 AAGATAGTGCTAACGACAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGA
1973645 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAAGGGTAAGGGCAAAAGTAAAATACTGAA
1 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAAGGGTAAGGGCAAAAGTAAAATACTGAA
1973710 AAGATAGTGCTAACGACAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGA
66 AAGATAGTGCTAACGACAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGA
1973768 TGTGGTTAAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (123 bp):
AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAAGGGTAAGGGCAAAAGTAAAATACTGAA
AAGATAGTGCTAACGACAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGA
Found at i:1976923 original size:16 final size:16
Alignment explanation
Indices: 1976904--1976945 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1976894 TATAAGATCC
1976904 TTATATTATTAGAAAA
1 TTATATTATTAGAAAA
* * *
1976920 TTATATTTTTATACAA
1 TTATATTATTAGAAAA
1976936 TTATA-TATTA
1 TTATATTATTA
1976946 AATGTAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATATTATTAGAAAA
Found at i:1977310 original size:19 final size:21
Alignment explanation
Indices: 1977286--1977332 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1977276 ATAATGAGCA
1977286 ATAAAATAT-GAAA-AAAATG
1 ATAAAATATAGAAATAAAATG
*
1977305 ATAAAAT-TAGAAATATAATG
1 ATAAAATATAGAAATAAAATG
1977325 A-AAAATAT
1 ATAAAATAT
1977333 TAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 16 0.67
20 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (21 bp):
ATAAAATATAGAAATAAAATG
Found at i:1982159 original size:16 final size:15
Alignment explanation
Indices: 1982133--1982162 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1982123 TGATGATCTT
1982133 TAAATTATTTTTTTA
1 TAAATTATTTTTTTA
1982148 TAAATGTATTTTTTT
1 TAAAT-TATTTTTTT
1982163 TAATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TAAATTATTTTTTTA
Found at i:1985176 original size:89 final size:89
Alignment explanation
Indices: 1985073--1985251 Score: 331
Period size: 89 Copynumber: 2.0 Consensus size: 89
1985063 AAGTAGTGAT
*
1985073 ATGAAGGGGGCTCTAACCTTCATTCAGAAAAACCATATACTAGAAATATCTTTGGGATATGGAAC
1 ATGAAGGGGGCTCTAACCTTCATTCAGAAAAACCATATACTAGAAATATCTTCGGGATATGGAAC
* *
1985138 AGTGATGGCAGATTGATGCTCTGC
66 ACTGATAGCAGATTGATGCTCTGC
1985162 ATGAAGGGGGCTCTAACCTTCATTCAGAAAAACCATATACTAGAAATATCTTCGGGATATGGAAC
1 ATGAAGGGGGCTCTAACCTTCATTCAGAAAAACCATATACTAGAAATATCTTCGGGATATGGAAC
1985227 ACTGATAGCAGATTGATGCTCTGC
66 ACTGATAGCAGATTGATGCTCTGC
1985251 A
1 A
1985252 GCTGCATGAA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (89 bp):
ATGAAGGGGGCTCTAACCTTCATTCAGAAAAACCATATACTAGAAATATCTTCGGGATATGGAAC
ACTGATAGCAGATTGATGCTCTGC
Found at i:1990579 original size:14 final size:15
Alignment explanation
Indices: 1990560--1990588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1990550 TTATGGAGTA
1990560 TCTTGC-TGCTCTAT
1 TCTTGCATGCTCTAT
1990574 TCTTGCATGCTCTAT
1 TCTTGCATGCTCTAT
1990589 GTGTGAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.10, C:0.28, G:0.14, T:0.48
Consensus pattern (15 bp):
TCTTGCATGCTCTAT
Found at i:1993107 original size:20 final size:20
Alignment explanation
Indices: 1993070--1993108 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1993060 CATCCAAATA
**
1993070 CAAAAAAAAATTAATTTTTC
1 CAAAAAAAAAGCAATTTTTC
*
1993090 CAAAAAAAAAGCACTTTTT
1 CAAAAAAAAAGCAATTTTT
1993109 AAAAACCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (20 bp):
CAAAAAAAAAGCAATTTTTC
Found at i:1996117 original size:60 final size:60
Alignment explanation
Indices: 1996052--1996183 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
1996042 GTTATCTAAT
* * * * * *
1996052 TATGAAAAGTTATAAAATAATCA-CTCAACTATTAGTACATTTCTTTTTTGGTCACCCAAA
1 TATGAAAAGTTAGAAAATAACCACCT-AACTATCAGTAAATTTCCTTTTTGATCACCCAAA
* * *
1996112 TATGAAAAGTTAGAAAATGACCACCTAACTATCAGTAAATTTCCTTTTTGATCATCTAAA
1 TATGAAAAGTTAGAAAATAACCACCTAACTATCAGTAAATTTCCTTTTTGATCACCCAAA
1996172 TATGAAAAGTTA
1 TATGAAAAGTTA
1996184 CAATATGGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 60 0.97
61 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (60 bp):
TATGAAAAGTTAGAAAATAACCACCTAACTATCAGTAAATTTCCTTTTTGATCACCCAAA
Found at i:2023254 original size:58 final size:60
Alignment explanation
Indices: 2023143--2023264 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 60
2023133 TACAAAACCA
2023143 ATTCAATCAATAAATTCCGAAAAAAAAAACATAATCAAACAAGAAATCCTATATCACTC-G
1 ATTCAATCAATAAATTCCG-AAAAAAAAACATAATCAAACAAGAAATCCTATATCACTCTG
* * * * * *
2023203 ATTCAATTAATAAATTTCG-AAGAAAAACATGATCAAACAAG-AATACTTATATTACTCTG
1 ATTCAATCAATAAATTCCGAAAAAAAAACATAATCAAACAAGAAAT-CCTATATCACTCTG
2023262 ATT
1 ATT
2023265 TGGGTGTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 3 0.06
58 30 0.56
59 4 0.07
60 17 0.31
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (60 bp):
ATTCAATCAATAAATTCCGAAAAAAAAACATAATCAAACAAGAAATCCTATATCACTCTG
Found at i:2028199 original size:31 final size:32
Alignment explanation
Indices: 2028164--2028223 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2028154 TTTTAGCTAA
*
2028164 ATTTGACGC-TCAA-CTTTTTAAAAAGAGTCGG
1 ATTTGAC-CATCAACCTTTTAAAAAAGAGTCGG
2028195 ATTTGACCATCAACCTTTTAAAAAAGAGT
1 ATTTGACCATCAACCTTTTAAAAAAGAGT
2028224 TGAAATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 1 0.04
31 11 0.42
32 14 0.54
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (32 bp):
ATTTGACCATCAACCTTTTAAAAAAGAGTCGG
Found at i:2029121 original size:25 final size:25
Alignment explanation
Indices: 2029071--2029122 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2029061 AACTTGACTA
* * *
2029071 ATTTAAAATATATTATAAAATGTAT
1 ATTTAAAATATATAAAAAAATATAT
2029096 ATTTAAAATA-ATAAAAATAATATAT
1 ATTTAAAATATATAAAAA-AATATAT
2029121 AT
1 AT
2029123 GTTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTTAAAATATATAAAAAAATATAT
Found at i:2029478 original size:15 final size:16
Alignment explanation
Indices: 2029458--2029487 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2029448 TTTCTTTATT
2029458 TTTTAAAA-ATTTTTA
1 TTTTAAAATATTTTTA
2029473 TTTTAAAATATTTTT
1 TTTTAAAATATTTTT
2029488 TGATTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAAAATATTTTTA
Found at i:2030566 original size:19 final size:18
Alignment explanation
Indices: 2030511--2030566 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
2030501 AACTTGTCTA
*
2030511 AAAAAAATTGTAATTTTTT
1 AAAATAATT-TAATTTTTT
*
2030530 AAATTAATTT-ATATTTTT
1 AAAATAATTTAAT-TTTTT
*
2030548 AAAATATTTTTAATTTTTT
1 AAAATA-ATTTAATTTTTT
2030567 TAATTTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.07
18 11 0.37
19 15 0.50
20 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AAAATAATTTAATTTTTT
Found at i:2035046 original size:3 final size:3
Alignment explanation
Indices: 2035038--2035111 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
2035028 GACTTCTATT
* * * * * *
2035038 ATA ATA ATA ATA ATA ATA ATA ATT AGA CTT CT- ATA ATA ATA ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2035085 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2035112 TTATTATTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 1 0.02
3 60 0.98
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2035069 original size:35 final size:35
Alignment explanation
Indices: 2035023--2035095 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2035013 GAGCTGCCCG
*
2035023 AATTAGACTTCTATTATAATAATAATAATAATAAT
1 AATTAGACTTCTATAATAATAATAATAATAATAAT
*
2035058 AATTAGACTTCTATAATAATAATACTAATAATAAT
1 AATTAGACTTCTATAATAATAATAATAATAATAAT
2035093 AAT
1 AAT
2035096 AATAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (35 bp):
AATTAGACTTCTATAATAATAATAATAATAATAAT
Found at i:2035116 original size:3 final size:3
Alignment explanation
Indices: 2035110--2035137 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2035100 ATAATAATAA
2035110 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2035138 TACCTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2043390 original size:72 final size:71
Alignment explanation
Indices: 2043302--2043444 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 71
2043292 AAAGAAAATA
*
2043302 ACTCTTAAATTTTATCAAACTGTCCATGCCATAAGTACACAAGTACTT-AGACTTCAGAGTTCGA
1 ACTCTTAAATTTTATCAAACTGTCCATGCCATAACTACACAAGTACTTAAGAC-T-AGAGTTCGA
2043366 TTCACGTG
64 TTCACGTG
*
2043374 ACTCTTAAATTTTATCAAACTGTCCATGCCATAACTACACAAGTACTTAAGACTAGAGTTTGATT
1 ACTCTTAAATTTTATCAAACTGTCCATGCCATAACTACACAAGTACTTAAGACTAGAGTTCGATT
2043439 CACGTG
66 CACGTG
2043445 CTTCAAGTTC
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
71 16 0.24
72 48 0.71
73 4 0.06
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (71 bp):
ACTCTTAAATTTTATCAAACTGTCCATGCCATAACTACACAAGTACTTAAGACTAGAGTTCGATT
CACGTG
Found at i:2050322 original size:129 final size:128
Alignment explanation
Indices: 2050093--2050352 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 128
2050083 ACGGTGGTTT
2050093 TGAGCTGCTTGCATCAGCCTGAAAAAACCAGATTTCTCCCACCAAGCATACCATCTAAACATACA
1 TGAGCTGCTTGCATCAGCCTGAAAAAACCAGATTTCTCCCACCAAGCATACCATCTAAACATACA
2050158 GAGACAAAGAATGCAATAGTTGAAACAAAAATTAACTTTAAAACATATCTAATCTACCAATTG
66 GAGACAAAGAATGCAATAGTTGAAACAAAAATTAACTTTAAAACATATCTAATCTACCAATTG
2050221 TGAGCTGCTTGCATCAGCCTGAAAAAACCCAGATTTCTCCCACCAAGCATACCATCTAAACATAC
1 TGAGCTGCTTGCATCAGCCTGAAAAAA-CCAGATTTCTCCCACCAAGCATACCATCTAAACATAC
2050286 AGAGACAAAGAATGCAATAGTTGAAACAAAAATTAACTTTAAAACATATCTAATCTACCAATTG
65 AGAGACAAAGAATGCAATAGTTGAAACAAAAATTAACTTTAAAACATATCTAATCTACCAATTG
2050350 TGA
1 TGA
2050353 ACTTTTTCAA
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 27 0.21
129 104 0.79
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (128 bp):
TGAGCTGCTTGCATCAGCCTGAAAAAACCAGATTTCTCCCACCAAGCATACCATCTAAACATACA
GAGACAAAGAATGCAATAGTTGAAACAAAAATTAACTTTAAAACATATCTAATCTACCAATTG
Found at i:2051098 original size:20 final size:20
Alignment explanation
Indices: 2051073--2051112 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2051063 AATTTAATCC
*
2051073 AAAAAAATTACAA-GAAATGA
1 AAAAAAAAT-CAATGAAATGA
2051093 AAAAAAAATCAATGAAATGA
1 AAAAAAAATCAATGAAATGA
2051113 GAGAATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAAAAAATCAATGAAATGA
Found at i:2052194 original size:24 final size:23
Alignment explanation
Indices: 2052167--2052211 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2052157 TAAATTTTAA
2052167 AAATTAAAAAAATTTAAAAAAACC
1 AAATT-AAAAAATTTAAAAAAACC
**
2052191 AAATTAAATTATTTAAAAAAA
1 AAATTAAAAAATTTAAAAAAA
2052212 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATTAAAAAATTTAAAAAAACC
Done.