Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007911.1 Hibiscus syriacus cultivar Beakdansim tig00110307_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: 1972160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1210067 original size:30 final size:31
Alignment explanation
Indices: 1209990--1210067 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 31
1209980 AATAATTTAA
* * * * *
1209990 AGTGAGTAAAATCGGAACAATTCGAAAGTTT
1 AGTGAGTGAAATAGGAAAAATTCGAAAATAT
*
1210021 AGTGA-TGAAATTGGAAAAATT-GAAAATAT
1 AGTGAGTGAAATAGGAAAAATTCGAAAATAT
1210050 AGTGAGTGAAATAGGAAA
1 AGTGAGTGAAATAGGAAA
1210068 TAGAGTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.28
30 24 0.60
31 5 0.12
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (31 bp):
AGTGAGTGAAATAGGAAAAATTCGAAAATAT
Found at i:1213681 original size:78 final size:81
Alignment explanation
Indices: 1213592--1213743 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 81
1213582 TGATCCTTTG
*
1213592 ATATTCAAATTTAAAGAGATAAT-A-T-CTTTTAATTAGAAATATTCAAAAGGATATAATTATCT
1 ATATTCAAATTTAAAGAGATAATAAGTACTTTTAATTAGAAATATTCAAAAGGATATAATTATCA
*
1213654 TTTTAATAACTTTTTA
66 TATTAATAACTTTTTA
** * *
1213670 ATATTCAAATTTAAAGAGATAATAAGTACCTTTTAATTTTAAATATTTAAAAGGATATGATTATC
1 ATATTCAAATTTAAAGAGATAATAAGTA-CTTTTAATTAGAAATATTCAAAAGGATATAATTATC
1213735 ATATTAATA
65 ATATTAATA
1213744 TTTAAATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
78 23 0.36
79 1 0.02
80 1 0.02
82 39 0.61
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (81 bp):
ATATTCAAATTTAAAGAGATAATAAGTACTTTTAATTAGAAATATTCAAAAGGATATAATTATCA
TATTAATAACTTTTTA
Found at i:1213705 original size:35 final size:34
Alignment explanation
Indices: 1213665--1213777 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 34
1213655 TTTAATAACT
* *
1213665 TTTTAATATTCAAATTTAAAGAGATAATAAGTACC
1 TTTTAATATTAAAATTTAAA-AGATAATAAATACC
* * * *
1213700 TTTTAATTTTAAATATTTAAAAGGAT-ATGATTATCA
1 TTTTAATATTAAA-ATTTAAAA-GATAATAAATA-CC
* * *
1213736 TATTAATATTTAAATTTAAATAGATAATAAATATC
1 TTTTAATATTAAAATTTAAA-AGATAATAAATACC
1213771 TTTTAAT
1 TTTTAAT
1213778 TTCTTTTAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
35 33 0.55
36 27 0.45
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (34 bp):
TTTTAATATTAAAATTTAAAAGATAATAAATACC
Found at i:1224659 original size:30 final size:29
Alignment explanation
Indices: 1224598--1224662 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1224588 TAAGACCCCT
* *
1224598 ACAACTTAGTGGAGCATTTTAGAAGACAA
1 ACAACTTAGTGGAGCATTTGAGAACACAA
* *
1224627 ACAACTTGGTGGAGCATTTGGGAGACACAA
1 ACAACTTAGTGGAGCATTTGAGA-ACACAA
1224657 ACAACT
1 ACAACT
1224663 CACAAGAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (29 bp):
ACAACTTAGTGGAGCATTTGAGAACACAA
Found at i:1228295 original size:23 final size:23
Alignment explanation
Indices: 1228266--1228310 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1228256 CAACAAAACT
* *
1228266 AAACATTTCACAAACTGAAATTC
1 AAACATTACACAAACTAAAATTC
*
1228289 AAACATTACACCAACTAAAATT
1 AAACATTACACAAACTAAAATT
1228311 TTGTATGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (23 bp):
AAACATTACACAAACTAAAATTC
Found at i:1228444 original size:20 final size:20
Alignment explanation
Indices: 1228421--1228478 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1228411 ACATATAAAC
*
1228421 CAAATTCAATTTAAACATTT
1 CAAATTCAATTCAAACATTT
* * *
1228441 CAAATTCCATTCATACAAGTT
1 CAAATTCAATTCAAAC-ATTT
1228462 -AAATTCAATTCAAACAT
1 CAAATTCAATTCAAACAT
1228479 CTTATTGTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.03
20 26 0.87
21 3 0.10
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (20 bp):
CAAATTCAATTCAAACATTT
Found at i:1228446 original size:40 final size:40
Alignment explanation
Indices: 1228402--1228547 Score: 115
Period size: 40 Copynumber: 3.8 Consensus size: 40
1228392 TCATCAACTA
*
1228402 AAATTCTATACATATAAACCAAATTCAATTTAAACATTTC
1 AAATTCTATACATACAAACCAAATTCAATTTAAACATTTC
* * *** *
1228442 AAATTCCATTCATACAAGTTAAATTCAATTCAAACATCTT-
1 AAATTCTATACATACAAACCAAATTCAATTTAAACAT-TTC
* * * * *
1228482 --ATTGTTTA-GT-CAAACAAAATTCAAGTTAAACA-TTC
1 AAATTCTATACATACAAACCAAATTCAATTTAAACATTTC
*
1228517 AAAATTCTATTCATACAAACCAAATTCAATT
1 -AAATTCTATACATACAAACCAAATTCAATT
1228548 AAAATATGTT
Statistics
Matches: 76, Mismatches: 23, Indels: 14
0.67 0.20 0.12
Matches are distributed among these distances:
34 2 0.03
36 17 0.22
37 1 0.01
38 9 0.12
39 1 0.01
40 44 0.58
41 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (40 bp):
AAATTCTATACATACAAACCAAATTCAATTTAAACATTTC
Found at i:1244798 original size:24 final size:24
Alignment explanation
Indices: 1244771--1244820 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1244761 TGGTGGTTGA
*
1244771 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1244795 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1244819 TT
1 TT
1244821 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1253403 original size:24 final size:21
Alignment explanation
Indices: 1253352--1253399 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1253342 CATGTATTTG
1253352 GGAGGCG-CGATTCAGTCGTC
1 GGAGGCGACGATTCAGTCGTC
1253372 GGAGGCGACGATTCAGTCGTC
1 GGAGGCGACGATTCAGTCGTC
1253393 GGAGGCG
1 GGAGGCG
1253400 GCGAGAGCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.17, C:0.23, G:0.44, T:0.17
Consensus pattern (21 bp):
GGAGGCGACGATTCAGTCGTC
Found at i:1254198 original size:51 final size:50
Alignment explanation
Indices: 1254103--1254198 Score: 174
Period size: 51 Copynumber: 1.9 Consensus size: 50
1254093 CTTCTCTCCC
1254103 TTAACCTTTTTCTAAATTATTCCTATTCGCAACGTGTCATATTCATTCAT
1 TTAACCTTTTTCTAAATTATTCCTATTCGCAACGTGTCATATTCATTCAT
*
1254153 TTAACCTTTTTCTAAATTATTCCCTATTCGCAATGTGTCATATTCA
1 TTAACCTTTTTCTAAATTATT-CCTATTCGCAACGTGTCATATTCA
1254199 AAGGTTAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 21 0.48
51 23 0.52
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (50 bp):
TTAACCTTTTTCTAAATTATTCCTATTCGCAACGTGTCATATTCATTCAT
Found at i:1258234 original size:107 final size:108
Alignment explanation
Indices: 1257957--1258245 Score: 359
Period size: 111 Copynumber: 2.6 Consensus size: 108
1257947 GGTAAATTTT
* ** * * *
1257957 ACCGGTTTTGTCATATTTATACCAATTATATTATAAAGTATCGGTCCTTTTTATAAAATGATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-CTTTTTATAAAGT-ATCGA
* *
1258022 TATTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAA
64 TACTTTCAACATATCAGGTAAATTTTACCA-GTTTGTCATAATGAA
* *
1258068 ACCGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCTTTTTAATAAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTTTTT-AT-AAAGTATCGA
1258133 TACTTTCAACATATCAGGTAAATTTTACC-GTTT-T-ATAATGAA
64 TACTTTCAACATATCAGGTAAATTTTACCAGTTTGTCATAATGAA
** * **
1258175 ATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATTAA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-C-TTTTTATAAAGTATCGA
1258240 TACTTT
64 TACTTT
1258246 ATAGGCGCTA
Statistics
Matches: 157, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
107 62 0.39
108 4 0.03
109 8 0.05
110 6 0.04
111 73 0.46
112 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (108 bp):
ACCGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTTTTTATAAAGTATCGATA
CTTTCAACATATCAGGTAAATTTTACCAGTTTGTCATAATGAA
Found at i:1258881 original size:111 final size:111
Alignment explanation
Indices: 1258678--1259160 Score: 673
Period size: 111 Copynumber: 4.3 Consensus size: 111
1258668 AACTTTCAAA
* **
1258678 AAAGTATCGATCCTTTTTATAAAAAGTATATATA-TTATCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGATCATTTTTATAAAAAG-ATCGATACTT-TCAACATATCAGGTAAATTTTACCGGT
1258742 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
64 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1258790 AAAGTATCTATCATTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTATCGTTTT
1 AAAGTATCGATCATTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
** *
1258855 TGTCATAATGAAACTAATTTTATCATATTTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * **
1258901 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAATTTTACCATTTT
1 AAAGTATCGATCATTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
* *
1258966 TGTCATAATAAAACTGGTTTTGTCATATTTTTACTTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * **
1259012 AAAGTATCGATCATTTTTATAAAAAGGATTGATACTTTTAACATATTAGGTAAATTTTATAGGTT
1 AAAGTATCGATCATTTTTATAAAAA-GATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
* * *
1259077 TTGTTATAATGAAATTGGTTTTGTCATATTTTTACCTATTATATTGT
65 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1259124 AAAATATCAATACATTTTTAT-AAAATATCGATACTTT
1 AAAGTATCGAT-CATTTTTATAAAAAGATCGATACTTT
1259161 ATATGCGCTA
Statistics
Matches: 331, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
111 210 0.63
112 112 0.34
113 9 0.03
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (111 bp):
AAAGTATCGATCATTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:1259109 original size:223 final size:222
Alignment explanation
Indices: 1258678--1259160 Score: 700
Period size: 223 Copynumber: 2.2 Consensus size: 222
1258668 AACTTTCAAA
* * ** *
1258678 AAAGTATCGATCCTTTTTATAAAAAGTATATATA-TTATCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCAATCATTTTTAT-AAAAGTATCGATACTT-TCAACATATCAGGTAAATTTTACCAGT
* *
1258742 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCATTTT
64 TTTGTCATAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTT
* *
1258807 TATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTATCGTTTTTGTCATAATGAAACTAA
129 TATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTATAGGTTTTGTCATAATGAAACTAA
*
1258872 TTTTATCATATTTTTACCTGTTATATTGT
194 TTTTATCATATTTTTACCTATTATATTGT
* * * *
1258901 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAATTTTACCATTTT
1 AAAGTATCAATCATTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCAGTTT
*
1258966 TGTCATAATAAAACTGGTTTTGTCATATTTTTACTTGTTATATTGTAAAGTATCGATCATTTTTA
66 TGTCATAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTA
* * * * * **
1259031 TAAAAAGGATTGATACTTTTAACATATTAGGTAAATTTTATAGGTTTTGTTATAATGAAATTGGT
131 TAAAAA-GATCGATACTTTCAACATATCAGGTAAATTTTATAGGTTTTGTCATAATGAAACTAAT
*
1259096 TTTGTCATATTTTTACCTATTATATTGT
195 TTTATCATATTTTTACCTATTATATTGT
*
1259124 AAAATATCAATACATTTTTATAAAA-TATCGATACTTT
1 AAAGTATCAAT-CATTTTTATAAAAGTATCGATACTTT
1259161 ATATGCGCTA
Statistics
Matches: 232, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
222 104 0.45
223 115 0.50
224 13 0.06
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (222 bp):
AAAGTATCAATCATTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCAGTTT
TGTCATAATAAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTA
TAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTATAGGTTTTGTCATAATGAAACTAATT
TTATCATATTTTTACCTATTATATTGT
Found at i:1259679 original size:20 final size:20
Alignment explanation
Indices: 1259654--1259705 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1259644 AAATTTTACC
1259654 GGTTTTGTCATAATGAAACT
1 GGTTTTGTCATAATGAAACT
1259674 GGTTTTGTCATAATGAAACT
1 GGTTTTGTCATAATGAAACT
1259694 GGTTTTGTCATA
1 GGTTTTGTCATA
1259706 TTTTTACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (20 bp):
GGTTTTGTCATAATGAAACT
Found at i:1259812 original size:111 final size:111
Alignment explanation
Indices: 1259676--1260090 Score: 624
Period size: 109 Copynumber: 3.8 Consensus size: 111
1259666 ATGAAACTGG
*
1259676 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAATATCTATCCTTT
1 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTT
* * * *
1259741 TTATAAAAGGAACAATACTTTCAACATATTAGGTAAATTTTATCGT
66 TTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGT
* * * *
1259787 TTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATTTATCTTTT
1 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTT
*
1259852 TTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTATACCGT
66 TTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGT
* *
1259898 TTTTATCATAATGAAACTGATTTTGTC--ATTTTTACCTGTTATATTGTAAAATATCTATCCTTT
1 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTT
* *
1259961 TTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGG
66 TTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGT
* * *
1260007 TTTTGTCATAATGAAATTGGTTTTGTCATA-TTTTA-CTGTTATATTGTAAAATATCAATACATT
1 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTAT-CCTT
*
1260070 TTTATAAAA-TATCGATACTTT
65 TTTATAAAAGGATCGATACTTT
1260091 ATAGGCGCTA
Statistics
Matches: 276, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
109 133 0.48
110 17 0.06
111 126 0.46
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (111 bp):
TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTT
TTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGT
Found at i:1260642 original size:23 final size:23
Alignment explanation
Indices: 1260570--1260633 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
1260560 AACATATTTT
1260570 ATTATATAAGCGCTA-CTATTAC
1 ATTATATAAGCGCTACCTATTAC
1260592 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
1260615 ATTATATAAGCGCTACCTA
1 ATTATATAAGCGCTACCTA
1260634 ATATGTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 15 0.37
23 26 0.63
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:1260667 original size:109 final size:110
Alignment explanation
Indices: 1260485--1260720 Score: 431
Period size: 109 Copynumber: 2.2 Consensus size: 110
1260475 CCTATTTTAA
**
1260485 TATATAAATGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
1 TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
1260550 TCCAGTAATTAACATATTTTATTATATAAGCGCTA-CTATTACAT
66 TCCAGTAATTAACATATTTTATTATATAAGCGCTACCTATTACAT
1260594 TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
1 TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
1260659 TCCAGTAATTAACATATTTTATTATATAAGCGCTACCTATTACAT
66 TCCAGTAATTAACATATTTTATTATATAAGCGCTACCTATTACAT
1260704 TATATAAGCAG-TACCTA
1 TATATAAGC-GCTACCTA
1260721 ATATGTTATT
Statistics
Matches: 123, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
109 98 0.80
110 24 0.20
111 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (110 bp):
TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
TCCAGTAATTAACATATTTTATTATATAAGCGCTACCTATTACAT
Found at i:1260729 original size:23 final size:23
Alignment explanation
Indices: 1260679--1260723 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1260669 AACATATTTT
*
1260679 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1260702 ATTATATAAGCAG-TACCTAATA
1 ATTATATAAGC-GCTACCTAATA
1260724 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1261467 original size:227 final size:228
Alignment explanation
Indices: 1261070--1261541 Score: 644
Period size: 227 Copynumber: 2.1 Consensus size: 228
1261060 TTGACGATAG
* *
1261070 CATAACCGGTTAATTACCGGAAACATTATCAAACATAATAACATATTAGATAACGCTTATGTAAC
1 CATAACCGGTTAATTACCAGAAACATTATCAAACATAATAACATATTAGATAACACTTATGTAAC
* * ** * * * * *
1261135 GTAATAGGTAGTGTTTTTTTTTAAAGTTGATGGTGCTTTAGAAATCCGACGATAATAGAATAAGT
66 GAAATAGGTAGCG-TCATTATTAAAGTTGATGGGGCCTTAGAAATCCGACGATAACAAAATAAGT
* * * *
1261200 TAATTACTTAATTTGTCATTATTATTATCAACATATTAGGTAACGCCTAAAGTGTTACCAAAGTT
130 TAATTACTTAATTTGTCATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAA-TT
1261265 TT-AGTTGATGGAGCCTTAAAAATCCGAAAAAAAA
194 TTAAGTTGATGGAGCCTTAAAAATCCGAAAAAAAA
* * * * * * *
1261299 CATAACCGTTTAATTACTAGAAACATTATCAAGCGTAATACCATTTTAGGTAACACTTATGTAAC
1 CATAACCGGTTAATTACCAGAAACATTATCAAACATAATAACATATTAGATAACACTTATGTAAC
*
1261364 GAAATAGGTAGCG-CATTATTAAAGTTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTT
66 GAAATAGGTAGCGTCATTATTAAAGTTGATGGGGCCTTAGAAATCCGACGATAACAAAATAAGTT
*
1261428 AATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAATTTT
131 AATTACTTAATTTGTCATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAATTTT
* ** *
1261493 AAGTTGATGGAGCCTTAGAAATCCG-ACGATAA
196 AAGTTGATGGAGCCTTAAAAATCCGAAAAAAAA
*
1261525 CATAATCGGTTAATTAC
1 CATAACCGGTTAATTAC
1261542 TTGATTTGCT
Statistics
Matches: 212, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
226 23 0.11
227 122 0.58
229 67 0.32
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (228 bp):
CATAACCGGTTAATTACCAGAAACATTATCAAACATAATAACATATTAGATAACACTTATGTAAC
GAAATAGGTAGCGTCATTATTAAAGTTGATGGGGCCTTAGAAATCCGACGATAACAAAATAAGTT
AATTACTTAATTTGTCATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAATTTT
AAGTTGATGGAGCCTTAAAAATCCGAAAAAAAA
Found at i:1261705 original size:2 final size:2
Alignment explanation
Indices: 1261700--1261732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1261690 TATATATATA
1261700 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1261733 CGTTACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1261982 original size:2 final size:2
Alignment explanation
Indices: 1261975--1262006 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1261965 TATAAGTATG
1261975 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
1262007 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1262011 original size:2 final size:2
Alignment explanation
Indices: 1262006--1262050 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1261996 TATATATATA
*
1262006 TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1262048 TG T
1 TG T
1262051 CGATATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1263387 original size:19 final size:19
Alignment explanation
Indices: 1263363--1263411 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1263353 AATGCATTTG
1263363 ATGCATCGATGTACCAGCC
1 ATGCATCGATGTACCAGCC
1263382 ATGCATCGATGTACCAGCC
1 ATGCATCGATGTACCAGCC
1263401 ATGCATCGATG
1 ATGCATCGATG
1263412 CACTCTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (19 bp):
ATGCATCGATGTACCAGCC
Found at i:1263459 original size:17 final size:19
Alignment explanation
Indices: 1263431--1263479 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1263421 TATTTTGAAA
*
1263431 CATCGAATGCACT-TGA-TT
1 CATCG-ATGCACTCTGAGTG
*
1263449 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
1263468 CATCGATGCACT
1 CATCGATGCACT
1263480 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1269711 original size:17 final size:18
Alignment explanation
Indices: 1269683--1269717 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1269673 ACCAATTTCG
1269683 TCAAAAACAAATAATTTT
1 TCAAAAACAAATAATTTT
*
1269701 TCAAAAA-AAATTATTTT
1 TCAAAAACAAATAATTTT
1269718 CGAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (18 bp):
TCAAAAACAAATAATTTT
Found at i:1271334 original size:2 final size:2
Alignment explanation
Indices: 1271327--1271353 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1271317 CAGCTTAAGC
1271327 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 T
1271354 TTAATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1271945 original size:66 final size:63
Alignment explanation
Indices: 1271858--1272018 Score: 189
Period size: 66 Copynumber: 2.5 Consensus size: 63
1271848 AATTAAATTG
* *
1271858 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCAATGAGAAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCAATCAGAATATTT-TG-
1271922 AA
63 -A
* * * * **
1271924 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCAATCAGAATATTTTGA
*
1271988 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1272019 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 30 0.36
66 48 0.57
67 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCAATCAGAATATTTTGA
Found at i:1272018 original size:17 final size:19
Alignment explanation
Indices: 1271990--1272038 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1271980 TATTTTGAAA
1271990 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1272008 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1272027 CACCGATGCACT
1 CATCGATGCACT
1272039 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1274668 original size:375 final size:375
Alignment explanation
Indices: 1273966--1274681 Score: 1062
Period size: 375 Copynumber: 1.9 Consensus size: 375
1273956 CATACAAAAA
** * * *
1273966 GTATCAATACTTTATGTTAACATATTTTGTCATTAAATTGATATGTTTTTACCACTTATATTGTA
1 GTATCAATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCACTTACATTATA
* * *
1274031 AATTTACATATTACTTGAAAGTAATCATTTTTAAAGTTTTAAGAATCGATACTTTTCATATGTGT
66 AATTTACATATTACTTGAAAGTAATCATTTTCAAAGTTTTAAGAATCGATACTTTTCATACGTCT
*
1274096 ATCGATACTTTATAGGAACAATTATTGAAATCGATTTTGTCAATTTTCAACCTGTTATGTTATTT
131 ATCGATACTTTATAGGAACAATTATTGAAATCGATTTTGTCAATTTTCAACATGTTATGTTATTT
*
1274161 ATATTTAATCGATATCATTACCCATAACAAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTT
196 ATATTTAACCGATATCATTACCCATAACAAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTT
* *
1274226 CGAGAAGTTTCATTTTTGTGTAAACCGGTATCTTTTTACTAGTTTTGTCATATTGAAACCTGTTT
261 CGAGAAGTTTCATTTTTGTGTAAACCGATATCTCTTTACTAGTTTTGTCATATTGAAACCTGTTT
1274291 TGTCAATTTTCAACCTATTATATTGTCATGTATTGATACATGTGTTTGAT
326 TGTCAATTTTCAACCTATTATATTGTCATGTATTGATACATGTGTTTGAT
* **
1274341 GTATCGATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCGTTTACATTATA
1 GTATCAATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCACTTACATTATA
* * * * *
1274406 AATTTACTTATTACTTTAGAGTAATCGTTTTCAAAGTTTTAAGAATCGATACTTTTGATACGTCT
66 AATTTACATATTACTTGAAAGTAATCATTTTCAAAGTTTTAAGAATCGATACTTTTCATACGTCT
** *
1274471 ATCGATACTTTATAGGTTCAATTATTGAAA-CAGGTTTTGTCAATTTTCAACATGTTATGTTATT
131 ATCGATACTTTATAGGAACAATTATTGAAATC-GATTTTGTCAATTTTCAACATGTTATGTTATT
* * * * *
1274535 TATATTTAACCGATATCGTTACCC-TTACTGAAGTGTCGATACTTTTTTGTAAGGTATTGATACT
195 TATATTTAACCGATATCATTACCCATAAC-AAAGTGTCGATACTTTTGTGTAAGGTATCGATACT
* * * * *
1274599 TTTGAGACGTTTCGTTTTTGTGTAAATCGATATCTCTTTAC-AGGTTTTGTCATATTGAAA-TTG
259 TTCGAGAAGTTTCATTTTTGTGTAAACCGATATCTCTTTACTA-GTTTTGTCATATTGAAACCT-
*
1274662 GTTTTGTTAATTTTCAACCT
322 GTTTTGTCAATTTTCAACCT
1274682 GTTAAAAATT
Statistics
Matches: 303, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
374 6 0.02
375 297 0.98
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (375 bp):
GTATCAATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCACTTACATTATA
AATTTACATATTACTTGAAAGTAATCATTTTCAAAGTTTTAAGAATCGATACTTTTCATACGTCT
ATCGATACTTTATAGGAACAATTATTGAAATCGATTTTGTCAATTTTCAACATGTTATGTTATTT
ATATTTAACCGATATCATTACCCATAACAAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTT
CGAGAAGTTTCATTTTTGTGTAAACCGATATCTCTTTACTAGTTTTGTCATATTGAAACCTGTTT
TGTCAATTTTCAACCTATTATATTGTCATGTATTGATACATGTGTTTGAT
Found at i:1274717 original size:157 final size:157
Alignment explanation
Indices: 1274493--1274843 Score: 447
Period size: 157 Copynumber: 2.2 Consensus size: 157
1274483 TAGGTTCAAT
* *** * *
1274493 TATTGAAACAGGTTTTGTCAATTTTCAACATGTTATGTTATTTATATTTAACCGATATCGTTACC
1 TATTGAAACAGGTTTTGTCAATTTTCAACCTGTTATAAAATTTATATTTAACCGATACCATTACC
* * * * * *
1274558 CTTACTGAAGTGTCGATACTTTTTTGTAAGGTATTGATACTTTTGAGACGTTTCGTTTTTGTGTA
66 CTTACAGAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTTCGAGACATTTCGTTTTTATGTA
* *
1274623 AATC-GATATCTCTTTACAGGTTTTGTCA
131 AACCAG-TATCGCTTTACAGGTTTT-TCA
** * *
1274651 TATTGAAATTGGTTTTGTTAATTTTCAACCTGTTA-AAAATTTATATTTAATCGATACCATTACC
1 TATTGAAACAGGTTTTGTCAATTTTCAACCTGTTATAAAATTTATATTTAACCGATACCATTACC
* *
1274715 CTTACAGAAGTGTCGATACTTTTGTGTAAGGTGTCGATACTTTCGAGACATTTTGTTTTTATGTA
66 CTTACAGAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTTCGAGACATTTCGTTTTTATGTA
*
1274780 AACCAGTATCGCTTTACCGGTTTTTCA
131 AACCAGTATCGCTTTACAGGTTTTTCA
* *
1274807 TATTGAAACCA-ATTTTGTCAGTTTTCAACCTGTTATA
1 TATTGAAA-CAGGTTTTGTCAATTTTCAACCTGTTATA
1274844 TTGTCATGTA
Statistics
Matches: 164, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
156 32 0.20
157 100 0.61
158 32 0.20
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.44
Consensus pattern (157 bp):
TATTGAAACAGGTTTTGTCAATTTTCAACCTGTTATAAAATTTATATTTAACCGATACCATTACC
CTTACAGAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTTCGAGACATTTCGTTTTTATGTA
AACCAGTATCGCTTTACAGGTTTTTCA
Found at i:1274963 original size:19 final size:20
Alignment explanation
Indices: 1274933--1274972 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1274923 ACCTGTTATA
1274933 TTTAATCGATTTTGCCAAAT
1 TTTAATCGATTTTGCCAAAT
*
1274953 TTTAATC-ATTTTGTCAAAT
1 TTTAATCGATTTTGCCAAAT
1274972 T
1 T
1274973 CGTTACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTAATCGATTTTGCCAAAT
Found at i:1276681 original size:6 final size:6
Alignment explanation
Indices: 1276670--1276714 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1276660 AGTGGAGCCA
* * * *
1276670 AAATTG AAATTG AAATTC AAACTC AAATTA AAATTG AAATTG AAA
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAA
1276715 ACTGCATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (6 bp):
AAATTG
Found at i:1277057 original size:15 final size:15
Alignment explanation
Indices: 1277033--1277062 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1277023 CCAAACATAC
1277033 ATACAAAACAATGTT
1 ATACAAAACAATGTT
*
1277048 ATACATAACAATGTT
1 ATACAAAACAATGTT
1277063 CTAATATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (15 bp):
ATACAAAACAATGTT
Found at i:1286080 original size:45 final size:46
Alignment explanation
Indices: 1285987--1286087 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
1285977 CTATAATTAT
*
1285987 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
1 ATGAAAGGATACCATAACTAAAATGCATGAACGGATGCATTAAGGC
* *
1286033 ATGAAAGGATATCATAACTAAAATGCAT-AACGGATGCATTAATGC
1 ATGAAAGGATACCATAACTAAAATGCATGAACGGATGCATTAAGGC
*
1286078 ATGAACGGAT
1 ATGAAAGGAT
1286088 GCATTAAGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 25 0.49
46 26 0.51
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (46 bp):
ATGAAAGGATACCATAACTAAAATGCATGAACGGATGCATTAAGGC
Found at i:1286125 original size:46 final size:46
Alignment explanation
Indices: 1286073--1286529 Score: 619
Period size: 46 Copynumber: 9.9 Consensus size: 46
1286063 CGGATGCATT
1286073 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* **
1286119 AATGCATGAACGGATGCATTAAGACATGAAAGGATGTAATAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * *
1286165 AATGCATGAACGGATGCATTAAGGCACGATAGGATGTCATAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * *
1286211 AATACATGAACGGATGCATTAAAGTATGAAAGGATGCCATAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
*
1286257 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCTATAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * *
1286303 AATGCATGAACGGATGCATTAAGGCATGAAAGAATTCCATAATTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* *
1286349 AATGCATGAACGGATGCAATAAGGCATGAAAGGATTCCATAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
** * *
1286395 AATGCATGAACGGATGCA-TAAGGCATGAAATAATGTCGTAACTAA
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * * * *
1286440 AATGTATGGACGGATGTATTAAGGCATAAAAAGGATGCCACAACTAA
1 AATGCATGAACGGATGCATTAAGGCAT-GAAAGGATGCCATAACTAA
* * * * * * *
1286487 AATGTATGAACGAATGTATTAAAGCTTGAAAAGAGGCCATAAC
1 AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAC
1286530 AGTAATTAAT
Statistics
Matches: 363, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 37 0.10
46 290 0.80
47 36 0.10
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (46 bp):
AATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
Found at i:1286377 original size:20 final size:20
Alignment explanation
Indices: 1286352--1286423 Score: 56
Period size: 26 Copynumber: 3.4 Consensus size: 20
1286342 TAATTAAAAT
1286352 GCATGAACGGATGCAATAAG
1 GCATGAACGGATGCAATAAG
* * *
1286372 GCATGAAAGGATTCCATAACTAAAAT
1 GCATGAACGGA-TGC--AA-T--AAG
1286398 GCATGAACGGATGC-ATAAG
1 GCATGAACGGATGCAATAAG
1286417 GCATGAA
1 GCATGAA
1286424 ATAATGTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
19 9 0.22
20 10 0.25
21 3 0.08
22 1 0.03
23 2 0.05
24 1 0.03
25 2 0.05
26 12 0.30
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (20 bp):
GCATGAACGGATGCAATAAG
Found at i:1291038 original size:12 final size:12
Alignment explanation
Indices: 1291021--1291045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1291011 ATTCTAGAAG
1291021 TTGAGGATATGC
1 TTGAGGATATGC
1291033 TTGAGGATATGC
1 TTGAGGATATGC
1291045 T
1 T
1291046 AAGGGCATGT
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:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TTGAGGATATGC
Found at i:1293680 original size:46 final size:46
Alignment explanation
Indices: 1293190--1293667 Score: 695
Period size: 46 Copynumber: 10.4 Consensus size: 46
1293180 CTACAATTAT
* * *
1293190 ATGAACGGATGCCATAACTAAAATGCATGAACAGATGCACTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
*
1293236 ATGAAAGGATGTCATAACTAAAATGCATGAACGGATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
1293282 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* *
1293328 ATGAAAGGATGCAATAACTAAAATGCATGAACGGATGCATTAAGGA
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* * *
1293374 ATGAAAGGATGTCATAACTAAAATGCATGAACAGATGCAATAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* * *
1293420 ATGAAAGGATGCCATAACTATAATGTATGAACGGGTGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* * *
1293466 ATGAAAGGATGCCATAACTAAAATGAATGAATGGGTGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* * *
1293512 ATGAAAGTATGTCATAACTAAAATGCATGAACGGGTGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* * * *
1293558 ATGAAAGGATGCCATAACTAAAATGTATGAATGGATGTATTAAGAC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* * * * *
1293604 ATGAAAGAATGCCATAACTAAATTGTATGAACGAATGTATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
* *
1293650 ATGAAAAGAGGCCATAAC
1 ATGAAAGGATGCCATAAC
1293668 AGTAATTAAT
Statistics
Matches: 392, Mismatches: 40, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 392 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGC
Found at i:1296241 original size:77 final size:77
Alignment explanation
Indices: 1296114--1296267 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 77
1296104 TTTTGGCTCT
*
1296114 AAAGATAGAGGTACTTGAATTGTCCTTGCTTGTATCCCCGTGGGCCGGCCAAACCCTCGATCCTC
1 AAAGATAGAGGTACTTGAATTGTCCTTGCCTGTATCCCCGTGGGCCGGCCAAACCCTCGATCCTC
1296179 ACCCACTATAGG
66 ACCCACTATAGG
* * * *
1296191 AAAGATATAGGTACTTGAATTGTCCTTGCCTGTGTCCTCGTGGGCCGGCCAGACCCTCGATCCTC
1 AAAGATAGAGGTACTTGAATTGTCCTTGCCTGTATCCCCGTGGGCCGGCCAAACCCTCGATCCTC
*
1296256 ACCCATTATAGG
66 ACCCACTATAGG
1296268 CTCATACAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (77 bp):
AAAGATAGAGGTACTTGAATTGTCCTTGCCTGTATCCCCGTGGGCCGGCCAAACCCTCGATCCTC
ACCCACTATAGG
Found at i:1315662 original size:19 final size:19
Alignment explanation
Indices: 1315638--1315679 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1315628 GAAAAAATCA
1315638 TAAAATAATAAAATTATCC
1 TAAAATAATAAAATTATCC
1315657 TAAAATAATAAAATTATCC
1 TAAAATAATAAAATTATCC
1315676 TAAA
1 TAAA
1315680 TAAACTACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATAATAAAATTATCC
Found at i:1318630 original size:24 final size:23
Alignment explanation
Indices: 1318603--1318690 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 23
1318593 ATCAAAACAT
* *
1318603 AATCCAGTTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATC-GATCAG
*
1318627 AATCTAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTA-TCGATCAG
1318651 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTAT-CGATCAG
*
1318675 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
1318691 TATAATCAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.02
24 54 0.95
25 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (23 bp):
AATCCAGGTCAAGTATCGATCAG
Found at i:1324552 original size:24 final size:24
Alignment explanation
Indices: 1324532--1324622 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
1324522 AAAATCAAAA
*
1324532 CATAATCCAGGTAAAGTATCAGAT
1 CATAATCCAGGTCAAGTATCAGAT
*
1324556 CAAAATCCAGGTCAAGTATTC-GAT
1 CATAATCCAGGTCAAGTA-TCAGAT
**
1324580 CATAATCCAGGTCAAGTATCCTAT
1 CATAATCCAGGTCAAGTATCAGAT
* *
1324604 CAGAATCCAGGTCAGGTAT
1 CATAATCCAGGTCAAGTAT
1324623 TATAATAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.03
24 55 0.93
25 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (24 bp):
CATAATCCAGGTCAAGTATCAGAT
Found at i:1324611 original size:48 final size:48
Alignment explanation
Indices: 1324532--1324623 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
1324522 AAAATCAAAA
1324532 CATAATCCAGGTAAAGTATCAGATCAAAATCCAGGTCAAGTATTCGAT
1 CATAATCCAGGTAAAGTATCAGATCAAAATCCAGGTCAAGTATTCGAT
* ** * *
1324580 CATAATCCAGGTCAAGTATCCTATCAGAATCCAGGTCAGGTATT
1 CATAATCCAGGTAAAGTATCAGATCAAAATCCAGGTCAAGTATT
1324624 ATAATAGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (48 bp):
CATAATCCAGGTAAAGTATCAGATCAAAATCCAGGTCAAGTATTCGAT
Found at i:1325633 original size:26 final size:26
Alignment explanation
Indices: 1325597--1325649 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1325587 TCAGATTTAT
*
1325597 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
1325623 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
1325649 T
1 T
1325650 TTTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:1329273 original size:91 final size:91
Alignment explanation
Indices: 1329118--1329299 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
1329108 GAAGCCATAG
1329118 GTATTTCGAAGGAAAAAACCTTTAGAGCACCGAATGTTGTTAGCCCAATTTTCAATGACCTCAAC
1 GTATTTCGAAGGAAAAAACCTTTAGAGCACCGAATGTTGTTAGCCCAATTTTCAATGACCTCAAC
1329183 ATCGACATGTTGGTAATACTCAATCC
66 ATCGACATGTTGGTAATACTCAATCC
*
1329209 GTATTTTGAAGGAAAAAACCTTTAGAGCACCGAATGTTGTTAGCCCAATTTTCAATGACCTCAAC
1 GTATTTCGAAGGAAAAAACCTTTAGAGCACCGAATGTTGTTAGCCCAATTTTCAATGACCTCAAC
1329274 ATCGACATGTTGGTAATACTCAATCC
66 ATCGACATGTTGGTAATACTCAATCC
1329300 CACATAGTAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (91 bp):
GTATTTCGAAGGAAAAAACCTTTAGAGCACCGAATGTTGTTAGCCCAATTTTCAATGACCTCAAC
ATCGACATGTTGGTAATACTCAATCC
Found at i:1335375 original size:14 final size:14
Alignment explanation
Indices: 1335356--1335385 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1335346 TCAATCATCG
1335356 TAGATCTACTCAAA
1 TAGATCTACTCAAA
1335370 TAGATCTACTCAAA
1 TAGATCTACTCAAA
1335384 TA
1 TA
1335386 TATGTATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (14 bp):
TAGATCTACTCAAA
Found at i:1335682 original size:36 final size:37
Alignment explanation
Indices: 1335607--1335916 Score: 252
Period size: 38 Copynumber: 8.3 Consensus size: 37
1335597 AAAAAAATAG
* *
1335607 TATTATATATATTTTCGAAAAA-CGTTTTCAAAACCATA
1 TATTATATATATTTTC-AAAAATAGTTTTC-AAACTATA
* *
1335645 TATTATATATATTTTCAAAAATATTTTTC-AATTATA
1 TATTATATATATTTTCAAAAATAGTTTTCAAACTATA
* * * *
1335681 TATTATATATGTTTTCCAAAA-CGTTTTTAAAATTCTATTATA
1 TATTATATATATTTTCAAAAATAG-TTTTCAAA--C---TATA
1335723 TATATATATATATATATTC-AAAAT-GTTTTCAAAACTATA
1 TAT-TATATATAT-T-TTCAAAAATAGTTTTC-AAACTATA
*
1335762 TATTATATATGTTTTCAAAAAT-GTTTTCAAAACTATA
1 TATTATATATATTTTCAAAAATAGTTTTC-AAACTATA
*
1335799 TATTATATATGTTTTCAAAAAATA-TTTTCTAAACTATA
1 TATTATATATATTTTC-AAAAATAGTTTTC-AAACTATA
*
1335837 TATTATAT-T-TTTTC-AAAA-CGTTTTCAAAACTATA
1 TATTATATATATTTTCAAAAATAGTTTTC-AAACTATA
*
1335871 TATTATATGT-TTTT-AAAAATA-TTTTCCAAAACTATA
1 TATTATATATATTTTCAAAAATAGTTTT-C-AAACTATA
1335907 TATTATATAT
1 TATTATATAT
1335917 GTTACATATA
Statistics
Matches: 233, Mismatches: 18, Indels: 44
0.79 0.06 0.15
Matches are distributed among these distances:
34 25 0.11
35 13 0.06
36 55 0.24
37 45 0.19
38 56 0.24
39 7 0.03
42 8 0.03
43 12 0.05
44 9 0.04
45 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (37 bp):
TATTATATATATTTTCAAAAATAGTTTTCAAACTATA
Found at i:1335745 original size:44 final size:46
Alignment explanation
Indices: 1335677--1335771 Score: 115
Period size: 44 Copynumber: 2.1 Consensus size: 46
1335667 ATTTTTCAAT
* * * *
1335677 TATATATTATATATGTTTTCCAAAACGTTTTTAAAA-T-TCTATTA
1 TATATATTATATATATATTCCAAAACGTTTTCAAAACTATATATTA
*
1335721 TATATATATATATATATATT-CAAAATGTTTTCAAAACTATATATTA
1 TATATAT-TATATATATATTCCAAAACGTTTTCAAAACTATATATTA
1335767 TATAT
1 TATAT
1335772 GTTTTCAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 21 0.49
45 11 0.26
46 11 0.26
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (46 bp):
TATATATTATATATATATTCCAAAACGTTTTCAAAACTATATATTA
Found at i:1335761 original size:25 final size:25
Alignment explanation
Indices: 1335733--1335781 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1335723 TATATATATA
1335733 TATATATTCA-AAATGTTTTCAAAAC
1 TATATATT-ATAAATGTTTTCAAAAC
*
1335758 TATATATTATATATGTTTTCAAAA
1 TATATATTATAAATGTTTTCAAAA
1335782 ATGTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (25 bp):
TATATATTATAAATGTTTTCAAAAC
Found at i:1336640 original size:199 final size:199
Alignment explanation
Indices: 1336306--1336771 Score: 540
Period size: 199 Copynumber: 2.3 Consensus size: 199
1336296 AGTTAACATT
* * * * * **
1336306 GGTCTTCTTATTGACTTAAAGGCTTCGGTTTAAAAATTCAACCGGAAAGTAGTTCCTTGCTGCTA
1 GGTCTTCTTCTTGACTTAAAGACCTCGGTTT---ACTTCAACCGAAAAGTAGTTCCTCACTGCTA
* * ** * * ** * *
1336371 CTAAGCGGTTAATATGCCTTCGAGCTGAATGGAATCGTACTCGAAAGTTTTCGTTGACATATAGC
63 CCAAGCAGTTAATACACCCTCGAGCTAAATGGAATCAAACTCAAAAGTTTTCGTTGACAGATAGC
** * * * *
1336436 CCTTCTTGCCTTGAGTTATGCTGTAGA-TTAGGCTAAG-AGATAGTTCCTTGTTGCTAAATCACA
128 CCTTCTCACCTTGAGCTATGATGTAAATTTA-GCT-AGTAGATAGTTCATTGTTGCTAAATCACA
1336499 ACCAACCTA
191 ACCAACCTA
* * *
1336508 GGTCTTCTTCTTGAGTTAAATACCTCGGTTTACTTCAATCGAAAAGTAGTTCCTCACTGCTACCA
1 GGTCTTCTTCTTGACTTAAAGACCTCGGTTTACTTCAACCGAAAAGTAGTTCCTCACTGCTACCA
* * * *
1336573 TGCAGTTAATACACCCTCGAGCTAAATGGAATCAAACTCAAAAGTTTTTGTTGATAGATATCCCT
66 AGCAGTTAATACACCCTCGAGCTAAATGGAATCAAACTCAAAAGTTTTCGTTGACAGATAGCCCT
1336638 TCTCACCTTGAGCTATGATGTAAATTTAGCTAGTAGATAGTTCATTGTTGCTAAATCACAACCAA
131 TCTCACCTTGAGCTATGATGTAAATTTAGCTAGTAGATAGTTCATTGTTGCTAAATCACAACCAA
1336703 CCTA
196 CCTA
* * ** *
1336707 GGTCTTCTTCTTGACTTAAAGACCTCGGTTTAAAATTCAACTGATTAGTAGTTCCTCGCTGCTAC
1 GGTCTTCTTCTTGACTTAAAGACCTCGGTTT--ACTTCAACCGAAAAGTAGTTCCTCACTGCTAC
1336772 TATACGGTTG
Statistics
Matches: 222, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
198 2 0.01
199 165 0.74
200 3 0.01
201 26 0.12
202 26 0.12
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (199 bp):
GGTCTTCTTCTTGACTTAAAGACCTCGGTTTACTTCAACCGAAAAGTAGTTCCTCACTGCTACCA
AGCAGTTAATACACCCTCGAGCTAAATGGAATCAAACTCAAAAGTTTTCGTTGACAGATAGCCCT
TCTCACCTTGAGCTATGATGTAAATTTAGCTAGTAGATAGTTCATTGTTGCTAAATCACAACCAA
CCTA
Found at i:1343643 original size:15 final size:16
Alignment explanation
Indices: 1343620--1343652 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1343610 TAAATAATAG
1343620 AATAGAATAAAATAAA
1 AATAGAATAAAATAAA
1343636 AATA-AATAAAATAAA
1 AATAGAATAAAATAAA
1343651 AA
1 AA
1343653 GGTTAGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AATAGAATAAAATAAA
Found at i:1345059 original size:37 final size:37
Alignment explanation
Indices: 1344869--1345063 Score: 252
Period size: 37 Copynumber: 5.2 Consensus size: 37
1344859 TAAAAAAATA
1344869 ATATTATATATATTTTCGAAAAATGTTTTCAAAACCATAT
1 ATATTATATATATTTTC-AAAAATGTTTTCAAAA-C-TAT
* *
1344909 ATATTATATATA--TTCAAAAATGTTTTCTAAATTAT
1 ATATTATATATATTTTCAAAAATGTTTTCAAAACTAT
* * ** *
1344944 ATATTATATATGTTTTTCCAAACCGTTTTTAAAACTAT
1 ATATTATATAT-ATTTTCAAAAATGTTTTCAAAACTAT
*
1344982 ATATTATATATATTTTC-AAAATATTTTCAAAACTAT
1 ATATTATATATATTTTCAAAAATGTTTTCAAAACTAT
*
1345018 ATATTATATATGTTTTCAAAAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCAAAAATGTTTTCAAAACTAT
1345055 ATATTATAT
1 ATATTATAT
1345064 TTTTTGTTGA
Statistics
Matches: 135, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
35 14 0.10
36 31 0.23
37 47 0.35
38 31 0.23
40 12 0.09
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.47
Consensus pattern (37 bp):
ATATTATATATATTTTCAAAAATGTTTTCAAAACTAT
Found at i:1345800 original size:27 final size:27
Alignment explanation
Indices: 1345765--1345824 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1345755 ATATATTAAT
*
1345765 AAAACCGGTAAAACGCCCAATAATAAC
1 AAAATCGGTAAAACGCCCAATAATAAC
*
1345792 AAAATCGGTAAAACGTCCAATAATAAC
1 AAAATCGGTAAAACGCCCAATAATAAC
1345819 AAAATC
1 AAAATC
1345825 AGTAGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.22, G:0.10, T:0.15
Consensus pattern (27 bp):
AAAATCGGTAAAACGCCCAATAATAAC
Found at i:1347175 original size:13 final size:14
Alignment explanation
Indices: 1347157--1347189 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1347147 TTTGTTTTAG
1347157 TAAAAACATA-TTT
1 TAAAAACATATTTT
*
1347170 TAAAAATATATTTT
1 TAAAAACATATTTT
1347184 TAAAAA
1 TAAAAA
1347190 AATTACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAAACATATTTT
Found at i:1349014 original size:19 final size:19
Alignment explanation
Indices: 1348990--1349043 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1348980 CTCGACGGCA
* *
1348990 AGAGTAGAGGGGCAACTCG
1 AGAGTAGAGGCGCAACACG
1349009 AGAGTAGAGGCGCAACACG
1 AGAGTAGAGGCGCAACACG
1349028 AGAGTAGAGGCGCAAC
1 AGAGTAGAGGCGCAAC
1349044 CGCTGTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.39, T:0.07
Consensus pattern (19 bp):
AGAGTAGAGGCGCAACACG
Found at i:1357630 original size:29 final size:29
Alignment explanation
Indices: 1357570--1357633 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1357560 ATTTGGTTAA
* **
1357570 TTCGATTAATGATTTTCAAATTAATTCGG
1 TTCGATTAATAATTTTCAAAAAAATTCGG
*
1357599 TTCG-TTAATAATTTTCAAAAAAATTTTGG
1 TTCGATTAATAATTTTCAAAAAAA-TTCGG
1357628 TTCGAT
1 TTCGAT
1357634 ATAACCGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.55
29 12 0.41
30 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
TTCGATTAATAATTTTCAAAAAAATTCGG
Found at i:1357879 original size:29 final size:29
Alignment explanation
Indices: 1357843--1357919 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
1357833 AAAAATTCAG
*
1357843 TTAATTCGGTTTGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
1357872 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
* *
1357901 TAAATTTTGGTTCGATTAA
1 TTAA-TTCGGTTCGATTAA
1357920 CCTAACCGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:1358226 original size:38 final size:38
Alignment explanation
Indices: 1357995--1358480 Score: 326
Period size: 38 Copynumber: 13.3 Consensus size: 38
1357985 TTATTATTAT
** **
1357995 TATATATATATATATTATAGTTTGCAAATGATTTTTG-AAA
1 TATATATATAT-TA-TATAGTTTTTAAAACA-TTTTGAAAA
*
1358035 TATATATA-ATATATATAGTTTTGAAAACGATTTTTTG-AAA
1 TATATATATAT-TATATAGTTTTTAAAAC-A--TTTTGAAAA
* * *
1358075 -ATGTATATATTATATAG--TTAAAAATATTTTGAAAA
1 TATATATATATTATATAGTTTTTAAAACATTTTGAAAA
1358110 T-TATATA-A-TATATAGTTTTTAAAAAAACATTTTGAAAA
1 TATATATATATTATATAGTTTTT---AAAACATTTTGAAAA
1358148 TATATA-ATA-TATA-A-TTTTTAAAACATTTTGAAAA
1 TATATATATATTATATAGTTTTTAAAACATTTTGAAAA
**
1358182 CGTATATATATTATATAGTTTTTAAAACATTTTGAAAA
1 TATATATATATTATATAGTTTTTAAAACATTTTGAAAA
* *
1358220 TATATATGTATAATATAAAGTTTTTAAAACATTTTGAAAA
1 TATATA--TATATTATATAGTTTTTAAAACATTTTGAAAA
* *
1358260 CATATATA-ATATATATAATTTTTAAAACA-TTT-----
1 TATATATATAT-TATATAGTTTTTAAAACATTTTGAAAA
*
1358292 TA-A-A-A-A---CATAGTTTTTAAAACATTTTGAAAA
1 TATATATATATTATATAGTTTTTAAAACATTTTGAAAA
*
1358323 TATATATATATTATATAGTTTTAAAAACATTTTTTGAAAA
1 TATATATATATTATATAGTTTTTAAAACA--TTTTGAAAA
* * *
1358363 CATATATA-A-TATATAG-TTTCAAAACATTTTTAAAA
1 TATATATATATTATATAGTTTTTAAAACATTTTGAAAA
*
1358398 -ACTATATA-A-TATATAGTTTTGAAAACA-TTT-AAAA
1 TA-TATATATATTATATAGTTTTTAAAACATTTTGAAAA
* * * * *
1358432 -AAATATATAATATATAG-TTTAAAAATATTTTTGATATA
1 TATATATATATTATATAGTTTTTAAAACA-TTTTGA-AAA
1358470 TATATATATAT
1 TATATATATAT
1358481 AGTTATATTA
Statistics
Matches: 368, Mismatches: 35, Indels: 87
0.75 0.07 0.18
Matches are distributed among these distances:
25 14 0.04
26 3 0.01
29 2 0.01
30 1 0.00
31 3 0.01
32 2 0.01
33 13 0.04
34 41 0.11
35 46 0.12
36 17 0.05
37 26 0.07
38 93 0.25
39 37 0.10
40 70 0.19
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (38 bp):
TATATATATATTATATAGTTTTTAAAACATTTTGAAAA
Found at i:1359819 original size:24 final size:24
Alignment explanation
Indices: 1359782--1359828 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1359772 CCTAATTTTT
* *
1359782 TTATTTTTATTATTATGTTTTTAA
1 TTATTATTAGTATTATGTTTTTAA
*
1359806 TTATTATTAGTATTATTTTTTTA
1 TTATTATTAGTATTATGTTTTTA
1359829 CCTCATATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TTATTATTAGTATTATGTTTTTAA
Found at i:1359890 original size:9 final size:9
Alignment explanation
Indices: 1359876--1359948 Score: 53
Period size: 9 Copynumber: 8.3 Consensus size: 9
1359866 ATTTTTTTCC
1359876 TTTAATTTA
1 TTTAATTTA
*
1359885 TTTAATTTT
1 TTTAATTTA
*
1359894 TCTTTA-TTA
1 T-TTAATTTA
1359903 TTT-A-TTA
1 TTTAATTTA
*
1359910 TTTATTTTA
1 TTTAATTTA
*
1359919 TTTATTTTA
1 TTTAATTTA
* *
1359928 TTTCATTGA
1 TTTAATTTA
*
1359937 TTTATTTTA
1 TTTAATTTA
1359946 TTT
1 TTT
1359949 TTTATTTGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
7 7 0.14
8 2 0.04
9 39 0.76
10 3 0.06
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTAATTTA
Found at i:1359907 original size:4 final size:4
Alignment explanation
Indices: 1359880--1360052 Score: 73
Period size: 4 Copynumber: 43.5 Consensus size: 4
1359870 TTTTCCTTTA
* *
1359880 ATTT ATTT AATT -TTT CTTT A-TT ATTT A-TT ATTT ATTTT ATTT ATTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT A-TTT
* * *
1359927 ATTT CATTG ATTT ATTTT ATTT -TTT ATTT GTTT ATTT -GTT AGTTT -TTT
1 ATTT -ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT
* * *
1359975 ATTT CTTTT TTTT ACTTT GATTT ATTT -TTT ATTGTT ATTT -TTT GTCTT
1 ATTT -ATTT ATTT A-TTT -ATTT ATTT ATTT A-T-TT ATTT ATTT AT-TT
* *
1360023 -TTG A-TT -TTT ATTT ATTT TTTT ATTT -TTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1360053 CTAACATTAG
Statistics
Matches: 131, Mismatches: 15, Indels: 46
0.68 0.08 0.24
Matches are distributed among these distances:
3 29 0.22
4 68 0.52
5 30 0.23
6 4 0.03
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1359940 original size:34 final size:32
Alignment explanation
Indices: 1359876--1360041 Score: 85
Period size: 34 Copynumber: 5.1 Consensus size: 32
1359866 ATTTTTTTCC
* *
1359876 TTTAATTTATTTAATTTT-TCTTTATTATTTATT
1 TTTATTTTATTT-ATTTTAT-TTCATTATTTATT
1359909 ATTTATTTTATTTATTTTATTTCATTGATTTATT
1 -TTTATTTTATTTATTTTATTTCATT-ATTTATT
* * * *
1359943 TTATTTTTTATTT-GTTTATTT-GTTAGTTTTTT
1 TT-TATTTTATTTATTTTATTTCATTA-TTTATT
* * * *
1359975 ATTTCTTTTTTTTACTTTGATTT-ATTTTTTATT
1 -TTTATTTTATTTA-TTTTATTTCATTATTTATT
* *
1360008 GTTATTTT-TTGTCTTTTGATTT--TTATTTATT
1 TTTATTTTATT-TATTTT-ATTTCATTATTTATT
1360039 TTT
1 TTT
1360042 TTATTTTTTA
Statistics
Matches: 104, Mismatches: 19, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
31 16 0.15
32 26 0.25
33 26 0.25
34 36 0.35
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (32 bp):
TTTATTTTATTTATTTTATTTCATTATTTATT
Found at i:1359962 original size:15 final size:14
Alignment explanation
Indices: 1359941--1360017 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 14
1359931 CATTGATTTA
*
1359941 TTTTATTTTTTATT
1 TTTTATTTGTTATT
1359955 TGTTTATTTGTTAGTT
1 T-TTTATTTGTTA-TT
*
1359971 TTTTATTTCTT-TT
1 TTTTATTTGTTATT
1359984 TTTTACTTTGATTTATT
1 TTTTA-TTTG--TTATT
1360001 TTTTA-TTGTTATT
1 TTTTATTTGTTATT
1360014 TTTT
1 TTTT
1360018 GTCTTTTGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
13 16 0.30
14 4 0.07
15 22 0.41
16 5 0.09
17 7 0.13
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTTATTTGTTATT
Found at i:1359975 original size:30 final size:29
Alignment explanation
Indices: 1359957--1360049 Score: 70
Period size: 31 Copynumber: 3.1 Consensus size: 29
1359947 TTTTTATTTG
1359957 TTTA-TTTG-TTAGTTTTTTATTTCTTTTT
1 TTTACTTTGATTA-TTTTTTATTTCTTTTT
1359985 TTTACTTTGATTTATTTTTTATTGT-TATTTT
1 TTTACTTTGA-TTATTTTTTATT-TCT-TTTT
*
1360016 TTGT-CTTTTGATT-TTTATTTATTTTTTTATT
1 TT-TAC-TTTGATTATTT-TTTATTTCTTT-TT
1360047 TTT
1 TTT
1360050 TATCTAACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
28 4 0.07
29 4 0.07
30 17 0.31
31 24 0.44
32 6 0.11
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (29 bp):
TTTACTTTGATTATTTTTTATTTCTTTTT
Found at i:1359976 original size:23 final size:21
Alignment explanation
Indices: 1359943--1360052 Score: 79
Period size: 23 Copynumber: 5.2 Consensus size: 21
1359933 TTGATTTATT
1359943 TTATTTTTTATTTGTTTATTTG
1 TTATTTTTTATTT-TTTATTTG
1359965 TTAGTTTTTTATTTCTTT-TTT-
1 TTA-TTTTTTATTT-TTTATTTG
1359986 TTACTTTGATTTATTTTTTA-TTG
1 TTA-TTT--TTTATTTTTTATTTG
* *
1360009 TTATTTTTTGTCTTTTGATTT-
1 TTATTTTTTAT-TTTTTATTTG
* *
1360030 TTA-TTTAT-TTTTTTATTTT
1 TTATTTTTTATTTTTTATTTG
1360049 TTAT
1 TTAT
1360053 CTAACATTAG
Statistics
Matches: 73, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
18 8 0.11
19 4 0.05
20 8 0.11
21 14 0.19
22 16 0.22
23 23 0.32
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (21 bp):
TTATTTTTTATTTTTTATTTG
Found at i:1360052 original size:53 final size:54
Alignment explanation
Indices: 1359914--1360052 Score: 124
Period size: 57 Copynumber: 2.5 Consensus size: 54
1359904 TTATTATTTA
* *
1359914 TTTTATTTATTTTATTTCATTGATTTATTTTATTTTTTATTTGTTTATTTGTTAGTT
1 TTTTATTTATTTT-TTT-ATT-TTTTATTTTATTTTTTATTTGTTTATTTGTTAGAT
* *
1359971 TTTTATTTCTTTTTTTTACTTTGATTTATTTT-TTATTGTTATTT-TTTGTCTT-TT-GAT
1 TTTTATTT-ATTTTTTTA-TTT--TTTATTTTATT-TT-TTATTTGTTTAT-TTGTTAGAT
1360028 TTTTATTTATTTTTTTATTTTTTAT
1 TTTTATTTATTTTTTTATTTTTTAT
1360053 CTAACATTAG
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
53 5 0.07
55 3 0.04
56 9 0.13
57 25 0.36
58 20 0.29
59 8 0.11
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (54 bp):
TTTTATTTATTTTTTTATTTTTTATTTTATTTTTTATTTGTTTATTTGTTAGAT
Found at i:1364114 original size:95 final size:94
Alignment explanation
Indices: 1363921--1364176 Score: 278
Period size: 95 Copynumber: 2.7 Consensus size: 94
1363911 TAATGTTATA
* * * *
1363921 TATATATATACATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCCGACTTTATGG
1 TATA-ATATACATAAAGCTTGAGTTATCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTATGG
* * *
1363986 ATAAGATTCAGCTAGCCTGACAAGGGTGGT
65 ATAAGATTCAACTAGCCTGACAAAGGTGAT
* * *
1364016 TATAATATACAATAAGGCTTGAGTTATCCCTCTAGAGCAATTAGTTAAACACCTCGACTTTATGG
1 TATAATATAC-ATAAAGCTTGAGTTATCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTATGG
* * *
1364081 ATAATATTCAACTAGCTTGATAAAGGTGAT
65 ATAAGATTCAACTAGCCTGACAAAGGTGAT
* * * * * * *
1364111 TATAATATATATACAATGATGTTGAGTTGTCCCTCTAAAGCAATTGGATAAATACCCCGGCTTTA
1 TATAATATACATA-AA-G--CTTGAGTTATCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTA
1364176 T
62 T
1364177 AGATCCTGCT
Statistics
Matches: 133, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
94 9 0.07
95 85 0.64
96 1 0.01
98 38 0.29
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (94 bp):
TATAATATACATAAAGCTTGAGTTATCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTATGGA
TAAGATTCAACTAGCCTGACAAAGGTGAT
Found at i:1365171 original size:85 final size:85
Alignment explanation
Indices: 1364971--1365853 Score: 1044
Period size: 85 Copynumber: 10.4 Consensus size: 85
1364961 AAGAACCTTT
* *
1364971 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTCGTA-A-CATAACTCAAG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATT--TACAGCATAGCTCAAG
* *
1365034 GCGAGAAGGGTTAACTG-CAAAC
64 GCGAGAAGGGCTATCTGTC-AAC
* * * * *
1365056 AAAAGACCTTCGAGTTCTATTACATTCAGCTCAAAGACATATCTAATTTACAGCATAGCTCAAGG
1 -AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGG
* *
1365121 CGAGAAGGGCTATATATCAAC
65 CGAGAAGGGCTATCTGTCAAC
* *
1365142 CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
* *
1365207 GAGAAGGTCTATCTGTCAATA
66 GAGAAGGGCTATCTGTCAA-C
* * * * * *
1365228 AAAGACCTTCGAGTTTGATTACATTCAACT-TAAGGCATATCAAGTTTACAGCATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
1365292 GAGAAGGGCTATCTGTCAAC
66 GAGAAGGGCTATCTGTCAAC
* *
1365312 CAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
1365377 GAGAAGGGCTATCTGTCAAC
66 GAGAAGGGCTATCTGTCAAC
* * * *
1365397 AAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGG
1 -AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGG
* * *
1365462 TGAAAAGGGTTATCTGTCAAC
65 CGAGAAGGGCTATCTGTCAAC
* * * *
1365483 CAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCGAATTTACAACATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
*
1365548 GAGAAGGGCTA-CTGTCAATA
66 GAGAAGGGCTATCTGTCAA-C
* * * * *
1365568 AAATACCTTCGAGTTAGATTACACTCAGCTTAAAGGCATATCAAATTTACAACATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
* *
1365633 GAGAAGGTCTATCTATCAAC
66 GAGAAGGGCTATCTGTCAAC
* * *
1365653 CAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
* * *
1365718 AAGAAGGGTTATCTGTCAGC
66 GAGAAGGGCTATCTGTCAAC
* * * * ** *
1365738 AAATACCTTCGAGTTAGATT-CTATTCAGCTCAAGGGCATGTCAGATTTACAGCATAGCTTC-AG
1 AAAGACCTTCGAGTTCGATTAC-ACTCAGCTCAAAGGCACATCAAATTTACAGCATAGC-TCAAG
* *** *
1365801 TCGAGAAAATCTATTTGTCAAC
64 GCGAGAAGGGCTATCTGTCAAC
** * *
1365823 AAA-AATTGTCGAGTTCGATTCCATTCAGCTC
1 AAAGACCT-TCGAGTTCGATTACACTCAGCTC
1365854 GACAACATAT
Statistics
Matches: 682, Mismatches: 103, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
84 36 0.05
85 465 0.68
86 180 0.26
87 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
GAGAAGGGCTATCTGTCAAC
Found at i:1365606 original size:341 final size:341
Alignment explanation
Indices: 1364972--1365793 Score: 1242
Period size: 341 Copynumber: 2.4 Consensus size: 341
1364962 AGAACCTTTA
* *
1364972 AAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTCGTA-A-CATAACTCAAGG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATT--TACAGCATAGCTCAAGG
* * *
1365035 CGAGAAGGGTTAACTG-CAAACAAAAGACCTTCGAGTTCTATTACATTCAGCTCAAAGACATATC
64 CGAGAAGGGTTATCTGTC-AACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATC
* * *
1365099 TAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATATATCAACCAAGACCTTCGAGTTCGATTAC
128 AAATTTACAGCATAACTCAAGGCGAAAAGGGCTATATATCAACCAAGACCTTCGAGTTCGATTAC
*
1365164 ACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGTCTATCTGTCAATAA
193 ACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAA
* * * *
1365229 AAGACCTTCGAGTTTGATTACATTCAACTTAAGGCATATCAAGTTTACAGCATAGCTCAAGGCGA
258 AAGACCTTCGAGTTAGATTACACTCAACTTAAGGCATATCAAATTTACAACATAGCTCAAGGCGA
*
1365294 GAAGGGCTATCTGTCAACC
323 GAAGGGCTATCTATCAACC
*
1365313 AAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCG
* *
1365378 AGAAGGGCTATCTGTCAACAAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCAAA
66 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAA
* * * * *
1365443 TTTACAGCATAACTCAAGGTGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTATACT
131 TTTACAGCATAACTCAAGGCGAAAAGGGCTATATATCAACCAAGACCTTCGAGTTCGATTACACT
* *
1365508 CAGCTCAAAGGCACATCGAATTTACAACATAGCTCAAGGCGAGAAGGGCTA-CTGTCAATAAAAT
196 CAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAAAG
*
1365572 ACCTTCGAGTTAGATTACACTCAGCTTAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGA
261 ACCTTCGAGTTAGATTACACTCAACTT-AAGGCATATCAAATTTACAACATAGCTCAAGGCGAGA
*
1365637 AGGTCTATCTATCAACC
325 AGGGCTATCTATCAACC
* **
1365654 AAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGAA
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCG
* * * * * *
1365719 AGAAGGGTTATCTGTCAGC-AAATACCTTCGAGTTAGATT-CTATTCAGCTCAAGGGCATGTCAG
66 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTAC-ATTCAGCTCAAAGGCATATCAA
1365782 ATTTACAGCATA
130 ATTTACAGCATA
1365794 GCTTCAGTCG
Statistics
Matches: 438, Mismatches: 38, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
339 3 0.01
340 85 0.19
341 349 0.80
342 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (341 bp):
AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCG
AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAA
TTTACAGCATAACTCAAGGCGAAAAGGGCTATATATCAACCAAGACCTTCGAGTTCGATTACACT
CAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAAAG
ACCTTCGAGTTAGATTACACTCAACTTAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAA
GGGCTATCTATCAACC
Found at i:1366545 original size:3 final size:3
Alignment explanation
Indices: 1366537--1366564 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1366527 TTGTCTAAAT
1366537 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1366565 ATATATATAT
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):
TTA
Found at i:1366569 original size:2 final size:2
Alignment explanation
Indices: 1366562--1366590 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1366552 TTATTATTAT
1366562 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1366591 AATAGATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1366619 original size:40 final size:42
Alignment explanation
Indices: 1366575--1366671 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 42
1366565 ATATATATAT
* *
1366575 ATATATATATATTATAAATAG-ATTGCAAATGA-TTTTTGAA
1 ATATATATATATTATAAATAGTATTGAAAACGATTTTTTGAA
* * *
1366615 ATATATATATAATATATATAGTTTTGAAAACGATTTTTTGAA
1 ATATATATATATTATAAATAGTATTGAAAACGATTTTTTGAA
*
1366657 AAAT-TATATATTATA
1 ATATATATATATTATA
1366672 TAGTTAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 19 0.40
41 18 0.38
42 11 0.23
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (42 bp):
ATATATATATATTATAAATAGTATTGAAAACGATTTTTTGAA
Found at i:1366715 original size:36 final size:35
Alignment explanation
Indices: 1366608--1367042 Score: 341
Period size: 36 Copynumber: 11.8 Consensus size: 35
1366598 TGCAAATGAT
* *
1366608 TTTTGAAATATATATATAATATATATAGTTTTGAAAACGATT
1 TTTTGAAA-AT-TATAT-A-ATATATAGTTTT-TAAA--ATA
* *
1366650 TTTTGAAAAATTATATATTATATAG--TTAAAAATA
1 TTTTG-AAAATTATATAATATATAGTTTTTAAAATA
*
1366684 TTTTGAAAATTATATAATATATAGTTTTTAAAAAACA
1 TTTTGAAAATTATATAATATATAGTTTTT--AAAATA
*
1366721 TTTTGAAAA-TATATAATATAT-GATTTTTAAAACA
1 TTTTGAAAATTATATAATATATAG-TTTTTAAAATA
*
1366755 TTTTGAAAACATATATATATATATTATATAGTTTTTAAAACA
1 TTTTG--AA-A-AT-TATATA-A-TATATAGTTTTTAAAATA
* *
1366797 TTTTGAAAATATATGTATAATATAAAGTTTTTAAAACA
1 TTTTGAAAAT-TA--TATAATATATAGTTTTTAAAATA
*
1366835 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAT-TATATAATATATAGTTTTTAAAATA
*
1366871 TTTTGAAAACATATATATATATATTATAGTTTTTAAAACATT
1 TTTTG-AAA-AT-TATATA-ATA-TATAGTTTTT-AAA-ATA
* *
1366913 TTTTGAAAAAATATATAATA-ATAG-TTTTAAAACA
1 TTTTG-AAAATTATATAATATATAGTTTTTAAAATA
* *
1366947 TTTTTGAAAACTATATAATATATAGTTTTGAAAATA
1 -TTTTGAAAATTATATAATATATAGTTTTTAAAATA
* *
1366983 TTTTTAAAAAATATATAATATATAG--TTTAAAATA
1 -TTTTGAAAATTATATAATATATAGTTTTTAAAATA
*
1367017 TTTTTG-AAA-TATATATTATATAGTTT
1 -TTTTGAAAATTATATAATATATAGTTT
1367043 ATATTATTAT
Statistics
Matches: 345, Mismatches: 20, Indels: 64
0.80 0.05 0.15
Matches are distributed among these distances:
32 13 0.04
33 21 0.06
34 46 0.13
35 15 0.04
36 85 0.25
37 24 0.07
38 45 0.13
39 15 0.04
40 29 0.08
41 10 0.03
42 38 0.11
43 4 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (35 bp):
TTTTGAAAATTATATAATATATAGTTTTTAAAATA
Found at i:1366724 original size:114 final size:108
Alignment explanation
Indices: 1366608--1367042 Score: 432
Period size: 116 Copynumber: 3.9 Consensus size: 108
1366598 TGCAAATGAT
1366608 TTTTGAAATATATATATAATATATATAGTTTTGAAAACGATTTTTTGAAAA-AT-TATATATTAT
1 TTTTGAAA-A-ATATAT-A-ATATATAGTTTTGAAAAC-A-TTTTTGAAAACATATATATATTAT
1366671 ATAG-TTAAAAATATTTTGAAAATTATATAATATATAGTTTTTAAAAAACA
60 ATAGTTTAAAAATATTTTGAAAATTATATAATATATAGTTTTT--AAAACA
*
1366721 TTTTG-AAAATATATAATATAT-GATTTTTAAAACA-TTTTGAAAACATATATATATATATTATA
1 TTTTGAAAAATATATAATATATAG-TTTTGAAAACATTTTTGAAAAC----ATATATATATTATA
* * *
1366783 TAGTTTTTAAAACATTTTGAAAATATATGTATAATATAAAGTTTTTAAAACA
61 TAG-TTTAAAAATATTTTGAAAAT-TA--TATAATATATAGTTTTTAAAACA
*
1366835 TTTTGAAAATATATATAATATATAGTTTTTAAAACA-TTTTGAAAACATATATATATATATTATA
1 TTTTGAAAA-ATATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATATAT-TA-TATA
* *
1366899 GTTTTTAAAACATTTTTTGAAAAAATATATAATA-ATAG-TTTTAAAACA
63 G--TTTAAAA-ATATTTTG-AAAATTATATAATATATAGTTTTTAAAACA
* * *
1366947 TTTTTGAAAACTATATAATATATAGTTTTGAAAATATTTTT-AAAA-A-ATATATAATATATAGT
1 -TTTTGAAAAATATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATATATTATATAGT
*
1367009 TT-AAAATATTTTTG-AAA-TATATATTATATAGTTT
65 TTAAAAATA-TTTTGAAAATTATATAATATATAGTTT
1367043 ATATTATTAT
Statistics
Matches: 282, Mismatches: 15, Indels: 59
0.79 0.04 0.17
Matches are distributed among these distances:
102 8 0.03
103 7 0.02
104 4 0.01
105 17 0.06
106 3 0.01
107 2 0.01
108 20 0.07
109 3 0.01
110 15 0.05
111 16 0.06
112 49 0.17
113 40 0.14
114 25 0.09
115 10 0.04
116 58 0.21
117 5 0.02
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (108 bp):
TTTTGAAAAATATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATATATTATATAGTT
TAAAAATATTTTGAAAATTATATAATATATAGTTTTTAAAACA
Found at i:1367058 original size:14 final size:13
Alignment explanation
Indices: 1367028--1367100 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 13
1367018 TTTTGAAATA
*
1367028 TATATTATATAGTT
1 TATATTAT-TATTT
1367042 TATATTATTATTAT
1 TATATTATTATT-T
1367056 TATTATT-TTATGATT
1 TA-TATTATTAT--TT
1367071 TAT-TTATTCATTT
1 TATATTATT-ATTT
*
1367084 TATTTTATTAATTT
1 TATATTATT-ATTT
1367098 TAT
1 TAT
1367101 TTCATTTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
13 10 0.20
14 30 0.60
15 9 0.18
16 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (13 bp):
TATATTATTATTT
Found at i:1367101 original size:14 final size:13
Alignment explanation
Indices: 1367044--1367114 Score: 60
Period size: 14 Copynumber: 5.5 Consensus size: 13
1367034 ATATAGTTTA
1367044 TATTATTATTATTAT
1 TATT-TTATTATT-T
*
1367059 TATTTTATGA-TT
1 TATTTTATTATTT
1367071 TA-TTTATTCATTT
1 TATTTTATT-ATTT
1367084 TATTTTATTAATTT
1 TATTTTATT-ATTT
*
1367098 TATTTCA-T-TTT
1 TATTTTATTATTT
1367109 TATTTT
1 TATTTT
1367115 TGGGTCCAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
11 13 0.27
12 4 0.08
13 6 0.12
14 21 0.44
15 4 0.08
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (13 bp):
TATTTTATTATTT
Found at i:1367347 original size:19 final size:18
Alignment explanation
Indices: 1367314--1367352 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1367304 GGATCTGACC
*
1367314 CAATCCAATGGCCAGAAG
1 CAATCCAACGGCCAGAAG
1367332 CAATCTCAACGGCCAGAAG
1 CAATC-CAACGGCCAGAAG
1367351 CA
1 CA
1367353 TCACGCGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (18 bp):
CAATCCAACGGCCAGAAG
Found at i:1368318 original size:3 final size:3
Alignment explanation
Indices: 1368310--1368348 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1368300 ATTTTATTGT
* *
1368310 TTA TTA TTA TTA TTA TTT TTAA TTA TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT
1368349 TTTACCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1368334 original size:19 final size:19
Alignment explanation
Indices: 1368298--1368345 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1368288 CCCCTAAAAT
1368298 TTATT-TTATTGTTTATTA
1 TTATTATTATTGTTTATTA
1368316 TTATTATTATT-TTTAATTA
1 TTATTATTATTGTTT-ATTA
*
1368335 TTATTAGTATT
1 TTATTATTATT
1368346 ATTTTTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTATTATTATTGTTTATTA
Found at i:1368338 original size:22 final size:22
Alignment explanation
Indices: 1368310--1368352 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1368300 ATTTTATTGT
*
1368310 TTATTATTATTATTATTTTTAA
1 TTATTATTAGTATTATTTTTAA
1368332 TTATTATTAGTATTATTTTTA
1 TTATTATTAGTATTATTTTTA
1368353 CCTAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTAGTATTATTTTTAA
Found at i:1368361 original size:22 final size:22
Alignment explanation
Indices: 1368314--1368361 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1368304 TATTGTTTAT
* * *
1368314 TATTATTATTATTTTTAATTAT
1 TATTAGTATTATTTTTAACTAA
*
1368336 TATTAGTATTATTTTTACCTAA
1 TATTAGTATTATTTTTAACTAA
1368358 TATT
1 TATT
1368362 GTTTCCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTAGTATTATTTTTAACTAA
Found at i:1368434 original size:3 final size:3
Alignment explanation
Indices: 1368420--1368457 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1368410 TAATTTTTAT
1368420 TTA TTA TT- TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1368458 TGTTTCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.19
3 26 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:1368445 original size:20 final size:19
Alignment explanation
Indices: 1368420--1368457 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1368410 TAATTTTTAT
1368420 TTATTATTTTATTATTATTA
1 TTATTATTTTATT-TTATTA
1368440 TTATTATTTTATTTTATT
1 TTATTATTTTATTTTATT
1368458 TGTTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTATTTTATTTTATTA
Found at i:1368458 original size:66 final size:63
Alignment explanation
Indices: 1368388--1368509 Score: 156
Period size: 66 Copynumber: 1.9 Consensus size: 63
1368378 TTTAAAATAA
* *
1368388 TATTTTTTTCCTTTGATTTATTTAATTTTTATTTATTAT-TTTATTATTATTATTATTATTTTAT
1 TATTTGTTTCCTTTGATTTATTT--TTTATATTT-TTATATTT-TTATTATTATTATTATTTTAT
1368452 TT
62 TT
* * *
1368454 TATTTGTTTCCTTTTATTTATTTTTTATATTTTTATATTTTTATTTTTATTGTTAT
1 TATTTGTTTCCTTTGATTTATTTTTTATATTTTTATATTTTTATTATTATTATTAT
1368510 GTTTTTTGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
63 18 0.36
64 11 0.22
66 21 0.42
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.74
Consensus pattern (63 bp):
TATTTGTTTCCTTTGATTTATTTTTTATATTTTTATATTTTTATTATTATTATTATTTTATTT
Found at i:1368488 original size:8 final size:7
Alignment explanation
Indices: 1368403--1368501 Score: 58
Period size: 8 Copynumber: 12.9 Consensus size: 7
1368393 TTTTCCTTTG
1368403 ATTTATTT
1 ATTT-TTT
*
1368411 AATTTTT
1 ATTTTTT
*
1368418 ATTTATT
1 ATTTTTT
1368425 ATTTTATT
1 ATTTT-TT
1368433 ATTATTATT
1 ATT-TT-TT
1368442 ATTATTTT
1 ATT-TTTT
1368450 ATTTTATT
1 ATTTT-TT
1368458 -TGTTTCCTT
1 AT-TTT--TT
*
1368467 -TTATTT
1 ATTTTTT
1368473 ATTTTTT
1 ATTTTTT
1368480 ATATTTTT
1 AT-TTTTT
1368488 ATATTTTT
1 AT-TTTTT
1368496 ATTTTT
1 ATTTTT
1368502 ATTGTTATGT
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
6 2 0.03
7 26 0.34
8 35 0.45
9 14 0.18
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.75
Consensus pattern (7 bp):
ATTTTTT
Found at i:1368500 original size:6 final size:6
Alignment explanation
Indices: 1368412--1368514 Score: 52
Period size: 6 Copynumber: 16.0 Consensus size: 6
1368402 GATTTATTTA
* *
1368412 ATTTTT ATTTATT A-TTTT ATTATT ATTATT ATTATTT -TATTTT ATTTGTT
1 ATTTTT ATTT-TT ATTTTT ATTTTT ATTTTT ATT-TTT AT-TTTT ATTT-TT
*
1368462 -TCCTTTT ATTTATT -TTTTAT ATTTTTAT ATTTTT ATTTTT ATTGTT
1 AT--TTTT ATTT-TT ATTTT-T A-TTTT-T ATTTTT ATTTTT ATTTTT
1368508 ATGTTTT
1 AT-TTTT
1368515 TTGTCTTTTG
Statistics
Matches: 79, Mismatches: 4, Indels: 27
0.72 0.04 0.25
Matches are distributed among these distances:
5 4 0.05
6 45 0.57
7 20 0.25
8 10 0.13
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:1368500 original size:14 final size:15
Alignment explanation
Indices: 1368470--1368503 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1368460 TTTCCTTTTA
*
1368470 TTTATTTTTTATATT
1 TTTATATTTTATATT
1368485 TTTATATTTT-TATT
1 TTTATATTTTATATT
1368499 TTTAT
1 TTTAT
1368504 TGTTATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATATTTTATATT
Found at i:1368513 original size:51 final size:50
Alignment explanation
Indices: 1368414--1368507 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 50
1368404 TTTATTTAAT
1368414 TTTTATTTATTATTTTATTATTATTATTATTATTTTATTTTATTTGTTTCC
1 TTTTATTTATTATTTTATTATTATTATTATTATTTTATTTTA-TTGTTTCC
*
1368465 TTTTATTTATT-TTTTA-TATTTTTA-TA-T-TTTTATTTTTATTGTT
1 TTTTATTTATTATTTTATTATTATTATTATTATTTTA-TTTTATTGTT
1368508 ATGTTTTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
46 10 0.24
47 6 0.15
48 2 0.05
49 7 0.17
50 5 0.12
51 11 0.27
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (50 bp):
TTTTATTTATTATTTTATTATTATTATTATTATTTTATTTTATTGTTTCC
Found at i:1368922 original size:15 final size:15
Alignment explanation
Indices: 1368879--1368924 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1368869 ACCAAAATTT
1368879 ATTTGAAAATTATTA
1 ATTTGAAAATTATTA
* *
1368894 A-CTGAACAA-GATTA
1 ATTTGAA-AATTATTA
1368908 ATTTGAAAATTATTA
1 ATTTGAAAATTATTA
1368923 AT
1 AT
1368925 CAAACCAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (15 bp):
ATTTGAAAATTATTA
Found at i:1368936 original size:29 final size:29
Alignment explanation
Indices: 1368861--1368937 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
1368851 TCTGACACCG
*
1368861 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAATCGAACC-AAATTAATTTGAAAATTA
1368891 TTAA-CTGAA-CAAGATTAATTTGAAAATTA
1 TTAATC-GAACCAA-ATTAATTTGAAAATTA
*
1368920 TTAATCAAACCAAATTAA
1 TTAATCGAACCAAATTAA
1368938 CCGATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 2 0.05
29 28 0.68
30 11 0.27
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (29 bp):
TTAATCGAACCAAATTAATTTGAAAATTA
Found at i:1370495 original size:45 final size:47
Alignment explanation
Indices: 1370415--1370513 Score: 148
Period size: 45 Copynumber: 2.1 Consensus size: 47
1370405 ACAATTTTTG
1370415 CATACCCATTATTTTTAAGAAAATAAAATTAAAATTAAAATTTTGGACCCT
1 CATACCCATTATTTTTAAG---A-AAAATTAAAATTAAAATTTTGGACCCT
1370466 CATACCCATTATTTTTAAG-AAAA-TAAAATTAAAATTTTGGACCCT
1 CATACCCATTATTTTTAAGAAAAATTAAAATTAAAATTTTGGACCCT
1370511 CAT
1 CAT
1370514 TCTTAAATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
45 25 0.52
46 4 0.08
51 19 0.40
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (47 bp):
CATACCCATTATTTTTAAGAAAAATTAAAATTAAAATTTTGGACCCT
Found at i:1373157 original size:16 final size:16
Alignment explanation
Indices: 1373136--1373167 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1373126 TATTTTTCTG
1373136 ATTTTCTTTCATTTTT
1 ATTTTCTTTCATTTTT
*
1373152 ATTTTCTTTTATTTTT
1 ATTTTCTTTCATTTTT
1373168 TTGTGGGTTT
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:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTCTTTCATTTTT
Found at i:1378083 original size:43 final size:43
Alignment explanation
Indices: 1378036--1378185 Score: 239
Period size: 43 Copynumber: 3.5 Consensus size: 43
1378026 ATCGAAAAAA
1378036 ATCTCTTTAAATTAATAAAATATTAATTTATCGATTAATTAGT
1 ATCTCTTTAAATTAATAAAATATTAATTTATCGATTAATTAGT
* *
1378079 ATCTCTTTAAATTAATAAATTATTAATTTATCAATTAATTAGT
1 ATCTCTTTAAATTAATAAAATATTAATTTATCGATTAATTAGT
* * *
1378122 ACCTCTGTAAATTAATAAATTATTAATTTATCGATTAATTAGT
1 ATCTCTTTAAATTAATAAAATATTAATTTATCGATTAATTAGT
1378165 A-CATCTTTAAATTAATAAAAT
1 ATC-TCTTTAAATTAATAAAAT
1378186 TACGTGATAC
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 1 0.01
43 98 0.99
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (43 bp):
ATCTCTTTAAATTAATAAAATATTAATTTATCGATTAATTAGT
Found at i:1384778 original size:20 final size:20
Alignment explanation
Indices: 1384755--1384819 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1384745 GTCAAATTCA
**
1384755 CAACGATAATATGTATTTCG
1 CAACGATAATATGTAAATCG
** *
1384775 CAACGCGAATAGGTAAATCG
1 CAACGATAATATGTAAATCG
*
1384795 CAACGATAATATGTAAATCA
1 CAACGATAATATGTAAATCG
1384815 CAACG
1 CAACG
1384820 CAAATTCTCC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (20 bp):
CAACGATAATATGTAAATCG
Found at i:1384819 original size:40 final size:40
Alignment explanation
Indices: 1384729--1384820 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
1384719 ACAGGTTCCA
1384729 AAATCGCAACGCGAAAGTCAAATTCACAACGATAATATGT
1 AAATCGCAACGCGAAAGTCAAATTCACAACGATAATATGT
** *
1384769 ATTTCGCAACGCGAATAGGT-AAA-TCGCAACGATAATATGT
1 AAATCGCAACGCGAA-A-GTCAAATTCACAACGATAATATGT
*
1384809 AAATCACAACGC
1 AAATCGCAACGC
1384821 AAATTCTCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 38 0.86
41 4 0.09
42 2 0.05
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGCGAAAGTCAAATTCACAACGATAATATGT
Found at i:1384964 original size:20 final size:20
Alignment explanation
Indices: 1384939--1385011 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1384929 TTTTTCAAAT
1384939 TCGCAACGCGAATAGGTAAA
1 TCGCAACGCGAATAGGTAAA
** *
1384959 TCGCAACGATAATATGTAAA
1 TCGCAACGCGAATAGGTAAA
* *
1384979 TCGAAACGTGAATAGGTAAA
1 TCGCAACGCGAATAGGTAAA
1384999 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1385012 TCTCCAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAGGTAAA
Found at i:1385192 original size:20 final size:20
Alignment explanation
Indices: 1385131--1385184 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1385121 CGATATAGGT
* *
1385131 AATTAGCGTTGCAAAAATGA
1 AATTCGCGTTGCGAAAATGA
*
1385151 AATTCGCGTTGCGAAAACGA
1 AATTCGCGTTGCGAAAATGA
1385171 AATTCGCGTTGCGA
1 AATTCGCGTTGCGA
1385185 TTTTGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
AATTCGCGTTGCGAAAATGA
Found at i:1385457 original size:20 final size:20
Alignment explanation
Indices: 1385429--1385475 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1385419 TGACTTCTGT
*
1385429 GTTGAGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
*
1385449 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTCGC
1385469 GTTGCGA
1 GTTGCGA
1385476 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:1385515 original size:20 final size:21
Alignment explanation
Indices: 1385465--1385541 Score: 95
Period size: 20 Copynumber: 3.8 Consensus size: 21
1385455 ATTTACCTAT
1385465 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
*
1385486 TCGCGTTGCGAATTTGGAACA
1 TCGCGTTGCGAATTTGGAAAA
* * **
1385507 T-GTGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
1385526 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
1385542 TTGGTCATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.04
20 25 0.52
21 21 0.44
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:1400013 original size:7 final size:7
Alignment explanation
Indices: 1400000--1400089 Score: 54
Period size: 7 Copynumber: 12.7 Consensus size: 7
1399990 GCAATTAGCA
1400000 CTAAACC
1 CTAAACC
*
1400007 TTAAACC
1 CTAAACC
**
1400014 CTAAATA
1 CTAAACC
*
1400021 ATAAACC
1 CTAAACC
*
1400028 ATAAAACC
1 CT-AAACC
**
1400036 CTAAATA
1 CTAAACC
* *
1400043 ATAAACT
1 CTAAACC
1400050 CTAAACC
1 CTAAACC
* *
1400057 TTAAACT
1 CTAAACC
*
1400064 CTAAACT
1 CTAAACC
*
1400071 CTAAATC
1 CTAAACC
1400078 CTAAACC
1 CTAAACC
1400085 CTAAA
1 CTAAA
1400090 TCACATGTAC
Statistics
Matches: 61, Mismatches: 21, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
7 55 0.90
8 6 0.10
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:1400037 original size:22 final size:21
Alignment explanation
Indices: 1400001--1400054 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
1399991 CAATTAGCAC
*
1400001 TAAACCTTAAACCCTAAATAA
1 TAAACCTAAAACCCTAAATAA
1400022 TAAACCATAAAACCCTAAATAA
1 TAAACC-TAAAACCCTAAATAA
1400044 TAAACTCTAAA
1 TAAAC-CTAAA
1400055 CCTTAAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 6 0.20
22 23 0.77
23 1 0.03
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCTAAAACCCTAAATAA
Found at i:1400068 original size:21 final size:21
Alignment explanation
Indices: 1400044--1400089 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1400034 CCCTAAATAA
*
1400044 TAAACTCTAAA-CCTTAAACTC
1 TAAACTCTAAATCC-TAAACCC
1400065 TAAACTCTAAATCCTAAACCC
1 TAAACTCTAAATCCTAAACCC
1400086 TAAA
1 TAAA
1400090 TCACATGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACTCTAAATCCTAAACCC
Found at i:1403224 original size:3 final size:3
Alignment explanation
Indices: 1403213--1403413 Score: 88
Period size: 3 Copynumber: 63.7 Consensus size: 3
1403203 TTAAAAAAAC
* * * * *
1403213 TAT TCT TAT TATT TAT TACT TAA TAT TAT ATAT TAT TAC TACG TAC TAT
1 TAT TAT TAT TA-T TAT TA-T TAT TAT TAT -TAT TAT TAT TA-T TAT TAT
* * * *
1403262 ATAC TAT TAT TAAT TAT TAT TAT ATAT TTT TAT TAAT TAT AAA TAT TAT
1 -TAT TAT TAT T-AT TAT TAT TAT -TAT TAT TAT T-AT TAT TAT TAT TAT
* * * *
1403311 TA- AATT TAT TAT ATAT TAT ATAT GAT GAT TAT T-T T-T TAT TAC TATT
1 TAT TA-T TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* *
1403357 TAT TA- TAT TAT TTT CTAT TAT TAT ATAT TA- TAT TAT TATT TAT TAC
1 TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TA-T TAT TAT
*
1403403 TAA TAT TAT TA
1 TAT TAT TAT TA
1403414 ATGGTGATTA
Statistics
Matches: 152, Mismatches: 27, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
2 9 0.06
3 104 0.68
4 39 0.26
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1403277 original size:7 final size:6
Alignment explanation
Indices: 1403266--1403413 Score: 81
Period size: 7 Copynumber: 23.8 Consensus size: 6
1403256 TACTATATAC
* * * *
1403266 TATTAT TAATTAT TATTAT ATATTTT TATTAAT TATAAA TATTAT TA-AATT
1 TATTAT T-ATTAT TATTAT -TATTAT TATT-AT TATTAT TATTAT TATTA-T
* * *
1403317 TATTAT ATATTAT ATATGAT GATTAT T-TT-T TATTAC TATTTAT TA-TAT
1 TATTAT -TATTAT -TATTAT TATTAT TATTAT TATTAT TA-TTAT TATTAT
* * *
1403365 TATTTT CTATTAT TATATAT TA-TAT TATTATT TATTAC TAATAT TATTA
1 TATTAT -TATTAT TAT-TAT TATTAT TATTA-T TATTAT TATTAT TATTA
1403414 ATGGTGATTA
Statistics
Matches: 108, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
4 2 0.02
5 15 0.14
6 42 0.39
7 49 0.45
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (6 bp):
TATTAT
Found at i:1403326 original size:19 final size:19
Alignment explanation
Indices: 1403261--1403329 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
1403251 CTACGTACTA
*
1403261 TATACTATTATTAATTATTAT
1 TATA-TATTATTAAAT-TTAT
*
1403282 TATATATTTTTATTAA-TTA-
1 TATATATTATTA--AATTTAT
*
1403301 TAAATATTATTAAATTTAT
1 TATATATTATTAAATTTAT
1403320 TATATATTAT
1 TATATATTAT
1403330 ATATGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.05
18 3 0.08
19 19 0.49
20 10 0.26
21 4 0.10
22 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATTATTAAATTTAT
Found at i:1403358 original size:40 final size:39
Alignment explanation
Indices: 1403314--1403427 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 39
1403304 ATATTATTAA
*
1403314 ATTTATTATATATTATATATGATGATTATTTTTTATTACT
1 ATTTATTATATATTAT-TATGATGATTATTTTATATTACT
* * *
1403354 ATTTATTATATTATT-TTCT-ATTATTATATATTATATTATT
1 ATTTATTATA-TATTATTATGATGATTAT-T-TTATATTACT
*
1403394 ATTTATTACTAATATTATTAATGGTGATTATTTT
1 ATTTATTA-T-ATATTATT-ATGATGATTATTTT
1403428 CAGAAGTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
38 7 0.12
39 3 0.05
40 27 0.46
41 9 0.15
42 5 0.08
43 2 0.03
44 6 0.10
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (39 bp):
ATTTATTATATATTATTATGATGATTATTTTATATTACT
Found at i:1403810 original size:11 final size:11
Alignment explanation
Indices: 1403787--1403815 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1403777 TGCAGACTAC
1403787 TAAAATA-AAA
1 TAAAATATAAA
1403797 TAAAATATAAA
1 TAAAATATAAA
1403808 TAAAATAT
1 TAAAATAT
1403816 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAATATAAA
Found at i:1403942 original size:22 final size:22
Alignment explanation
Indices: 1403915--1403971 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1403905 ATAATAAATT
*
1403915 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1403937 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1403959 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1403972 TTTAAAAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1404015 original size:31 final size:31
Alignment explanation
Indices: 1403980--1404039 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1403970 ATTTTAAAAG
* *
1403980 AGTTTTGCAATACTAAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
1404011 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
1404040 CATAAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:1404064 original size:147 final size:148
Alignment explanation
Indices: 1403826--1404121 Score: 470
Period size: 147 Copynumber: 2.0 Consensus size: 148
1403816 TTTTTTAAAA
* * *
1403826 TTAAAAGAGTTTTGTAATACTGAGATTTAAATAATTTTAATTTTACAATACTGAAATTTAAATAA
1 TTAAAAGAGTTTTGCAATACTAAGATTTAAATAATTTTAATTTTACAATACTAAAATTTAAATAA
* * *
1403891 TCTATACAACTACTATAATAA-ATTTTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATC
66 TCTATAAAACTACAATAATAATATTTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC
1403955 CATATTTTAAAATAAATT
131 CATATTTTAAAATAAATT
*
1403973 TTAAAAGAGTTTTGCAATACTAAGATTTAAATAATTTTAGTTTTACAATACTAAAATTTAAATAA
1 TTAAAAGAGTTTTGCAATACTAAGATTTAAATAATTTTAATTTTACAATACTAAAATTTAAATAA
* *
1404038 T-TCATAAAACTACAATAATAATTTTTTTTTTAAATAAATCAATCCATATTTTAAAATAAATCAA
66 TCT-ATAAAACTACAATAATAA-TATTTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAA
*
1404102 TCTATATTTTAAAATAAATT
129 TCCATATTTTAAAATAAATT
1404122 AATCCATATT
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
146 1 0.01
147 78 0.57
149 57 0.42
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (148 bp):
TTAAAAGAGTTTTGCAATACTAAGATTTAAATAATTTTAATTTTACAATACTAAAATTTAAATAA
TCTATAAAACTACAATAATAATATTTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC
CATATTTTAAAATAAATT
Found at i:1404094 original size:22 final size:22
Alignment explanation
Indices: 1404064--1404140 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1404054 AATAATTTTT
*
1404064 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1404086 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
1404108 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
1404130 TTTTAAAATAA
1 TTTTAAAATAA
1404141 TATTTCAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1404145 original size:13 final size:13
Alignment explanation
Indices: 1404127--1404162 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1404117 AAATTAATCC
1404127 ATATTTTAAAATA
1 ATATTTTAAAATA
*
1404140 ATATTTCAAAATA
1 ATATTTTAAAATA
1404153 A-ATTTTAAAA
1 ATATTTTAAAA
1404163 GAATTTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTTTAAAATA
Found at i:1404162 original size:12 final size:12
Alignment explanation
Indices: 1404129--1404175 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
1404119 ATTAATCCAT
1404129 ATTTTAAAATAA
1 ATTTTAAAATAA
*
1404141 TATTTCAAAATAA
1 -ATTTTAAAATAA
*
1404154 ATTTTAAAA-GA
1 ATTTTAAAATAA
*
1404165 ATTTTACAATA
1 ATTTTAAAATA
1404176 CTGAGATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 9 0.32
12 8 0.29
13 11 0.39
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1404177 original size:184 final size:182
Alignment explanation
Indices: 1403956--1404303 Score: 561
Period size: 184 Copynumber: 1.9 Consensus size: 182
1403946 AAATCAATCC
* * * *
1403956 ATATTTTAAAATAAATTTTAAAAGAGTTTTGCAATACTAAGATTTAAATAATTTTAGTTTTACAA
1 ATATTTCAAAATAAATTTTAAAAGAATTTTACAATACTAAGATTTAAATAATTTTAATTTTACAA
* * *
1404021 TACTAAAATTTAAATAATTCATAAAACTACAATAATAATTTTTTTTTTAAATAAATCAATCCATA
66 TACTAAAATTTAAATAATTCATAAAACTACAATAATAA--ATTTTTTTAAAAAAATCAATACATA
*
1404086 TTTTAAAATAAATCAATCTATATTTTAAAATAAATTAATCCATATTTTAAAATA
129 TTTTAAAATAAATCAATATATATTTTAAAATAAATTAATCCATATTTTAAAATA
*
1404140 ATATTTCAAAATAAATTTTAAAAGAATTTTACAATACTGAGATTTAAATAATTTTAATTTTACAA
1 ATATTTCAAAATAAATTTTAAAAGAATTTTACAATACTAAGATTTAAATAATTTTAATTTTACAA
* * * *
1404205 TACTGAAATTTAAATAATTCATACAACTATAATAATAAATTTTTTTAAAAAAATCAATATATATT
66 TACTAAAATTTAAATAATTCATAAAACTACAATAATAAATTTTTTTAAAAAAATCAATACATATT
1404270 TTAAAATAAATCAATATATATTTTAAAATAAATT
131 TTAAAATAAATCAATATATATTTTAAAATAAATT
1404304 TTAAAACATA
Statistics
Matches: 151, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 56 0.37
184 95 0.63
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (182 bp):
ATATTTCAAAATAAATTTTAAAAGAATTTTACAATACTAAGATTTAAATAATTTTAATTTTACAA
TACTAAAATTTAAATAATTCATAAAACTACAATAATAAATTTTTTTAAAAAAATCAATACATATT
TTAAAATAAATCAATATATATTTTAAAATAAATTAATCCATATTTTAAAATA
Found at i:1404199 original size:31 final size:31
Alignment explanation
Indices: 1404164--1404223 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1404154 ATTTTAAAAG
*
1404164 AATTTTACAATACTGAGATTTAAATAATTTT
1 AATTTTACAATACTGAAATTTAAATAATTTT
1404195 AATTTTACAATACTGAAATTTAAATAATT
1 AATTTTACAATACTGAAATTTAAATAATT
1404224 CATACAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (31 bp):
AATTTTACAATACTGAAATTTAAATAATTTT
Found at i:1404263 original size:22 final size:22
Alignment explanation
Indices: 1404247--1404302 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1404237 TAATAAATTT
1404247 TTTTAAAA-AAATCAATATATA
1 TTTTAAAATAAATCAATATATA
1404268 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATATATA
1404290 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1404303 TTTAAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 8 0.24
22 26 0.76
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATATATA
Found at i:1406467 original size:20 final size:21
Alignment explanation
Indices: 1406430--1406473 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1406420 GTCACGACGC
*
1406430 TTACATGACAGTTCACAA-AT
1 TTACATGACAATTCACAATAT
1406450 TTACATGACAA-TCTACAATAT
1 TTACATGACAATTC-ACAATAT
1406471 TTA
1 TTA
1406474 TGTGACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (21 bp):
TTACATGACAATTCACAATAT
Found at i:1407971 original size:15 final size:15
Alignment explanation
Indices: 1407951--1407982 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1407941 TTTATTCCTG
1407951 GTGACTCACACGGGA
1 GTGACTCACACGGGA
1407966 GTGACTCACACGGGA
1 GTGACTCACACGGGA
1407981 GT
1 GT
1407983 CCTGAAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.16
Consensus pattern (15 bp):
GTGACTCACACGGGA
Found at i:1408059 original size:69 final size:68
Alignment explanation
Indices: 1407966--1408254 Score: 314
Period size: 69 Copynumber: 4.2 Consensus size: 68
1407956 TCACACGGGA
* * ** * *
1407966 GTGACTCACACGGGAGTCCTGAAGGATTAGAGTGACTCGCACGAGAGTTCCTCATCATATTTTTT
1 GTGACTCCCACGGGAG-CCCGAAGGATTAGAGTGACTCGCACGAGAGCACCTAATCATATTTATT
1408031 CTGG
65 CTGG
* * *
1408035 GTGCCTCGCACGGGAGCCTTGAAGGATTAGAGTGACTCGCAC-AGGAGCACCTAATCATATTTAT
1 GTGACTCCCACGGGAGCC-CGAAGGATTAGAGTGACTCGCACGA-GAGCACCTAATCATATTTAT
1408099 TCTGG
64 TCTGG
* ** * * *
1408104 GTGATTCCCACTAGAGCCACGAATGATTAGAGTGACTCGCATGAGAGAACCTAATCATATTTATT
1 GTGACTCCCACGGGAGCC-CGAAGGATTAGAGTGACTCGCACGAGAGCACCTAATCATATTTATT
**
1408169 CCAG
65 CTGG
* * *
1408173 GTGACTCCCACGGGAGCCCGAAAGATTGGAGTGACTCGTACG-GAGCACCTAATCATATTTAATT
1 GTGACTCCCACGGGAGCCCGAAGGATTAGAGTGACTCGCACGAGAGCACCTAATCATATTT-ATT
1408237 C-GG
65 CTGG
* *
1408240 ATGACTCGCACGGGA
1 GTGACTCCCACGGGA
1408255 ACACCTAATC
Statistics
Matches: 187, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
67 31 0.17
68 27 0.14
69 128 0.68
70 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (68 bp):
GTGACTCCCACGGGAGCCCGAAGGATTAGAGTGACTCGCACGAGAGCACCTAATCATATTTATTC
TGG
Found at i:1408262 original size:38 final size:36
Alignment explanation
Indices: 1408204--1408294 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
1408194 AAGATTGGAG
* *
1408204 TGACTCGTAC-GGAGCACCTAATCATATTTAATTCGGA
1 TGACTCGCACGGGAACACCTAATCATA-TT-ATTCGGA
* *
1408241 TGACTCGCACGGGAACACCTAATCATATTATTTGGG
1 TGACTCGCACGGGAACACCTAATCATATTATTCGGA
* *
1408277 TAACTCGCACGAGAACAC
1 TGACTCGCACGGGAACAC
1408295 TGAAGAATAG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 21 0.45
37 11 0.23
38 15 0.32
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (36 bp):
TGACTCGCACGGGAACACCTAATCATATTATTCGGA
Done.