Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold344
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: 1758742
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1677927 original size:79 final size:81
Alignment explanation
Indices: 1677759--1677938 Score: 240
Period size: 79 Copynumber: 2.2 Consensus size: 81
1677749 GTTATTTCCG
* *
1677759 AGGGGATACTCCAACCCCGGCTTTATATCTAAAAATGTTGTTTTTTTTCATAATCAGGGGTACTC
1 AGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTG-TATTTTTCATAATCAGGGGTACTC
**
1677824 CAACCCCGTTATTTCCA
65 CAACCCCGTTACGTCCA
* * *
1677841 AGGGGATACTCCAACCTCGGCTTTATATCT-AAAATATTG-ATTTTTCATAATCGGGGGTACTCT
1 AGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTGTATTTTTCATAATCAGGGGTACTCC
1677904 AACCCCGTTACGT-CA
66 AACCCCGTTACGTCCA
* *
1677919 TCGGGGATACTCCAATCCCG
1 -AGGGGATACTCCAACCCCG
1677939 TTATTTCCGA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 2 0.02
79 48 0.55
81 8 0.09
82 29 0.33
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (81 bp):
AGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTGTATTTTTCATAATCAGGGGTACTCC
AACCCCGTTACGTCCA
Found at i:1678071 original size:79 final size:79
Alignment explanation
Indices: 1677918--1678078 Score: 193
Period size: 79 Copynumber: 2.0 Consensus size: 79
1677908 CCGTTACGTC
*
1677918 ATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAAC
1 ATCGGGAATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAAC
* *
1677983 CCCAGTTTTTCACA
66 ACCAATTTTTCACA
* * ***
1677997 ATCGGGAATAC-CCAAATCCCGTTATTTCCGAGAGGG-TATTCCAATCCCGAA-TTTATTTTTAA
1 ATCGGGAATACTCC-AATCCCGTTATTTCCGAG-GGGATACTCCAA-CCCCAATTTTATTCCCAA
*
1678059 AATACCAATTTTTCACA
63 AACACCAATTTTTCACA
1678076 ATC
1 ATC
1678079 AGAGATATTC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 60 0.86
80 8 0.11
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (79 bp):
ATCGGGAATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAAC
ACCAATTTTTCACA
Found at i:1678103 original size:51 final size:51
Alignment explanation
Indices: 1678033--1678129 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
1678023 TCCGAGAGGG
* * *
1678033 TATTCCAATCCCGAATTTATTTTTAAAATACCAATTTTTCACAATCAGAGA
1 TATTCCAATCCCGAATTTATTTTCAAAACACCAATTTCTCACAATCAGAGA
*
1678084 TATTCCAA-CTCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
1 TATTCCAATC-CCGAATTTATTTTCAAAACACCAATTTCTCACAATC
1678130 GGGGATACTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.02
51 40 0.98
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (51 bp):
TATTCCAATCCCGAATTTATTTTCAAAACACCAATTTCTCACAATCAGAGA
Found at i:1678266 original size:121 final size:122
Alignment explanation
Indices: 1678061--1678297 Score: 325
Period size: 121 Copynumber: 2.0 Consensus size: 122
1678051 ATTTTTAAAA
*
1678061 TACCAATTTTTCACAATCAGAGATATTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCAC
1 TACCAATTTTTCACAATCAGAGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCAC
** * *
1678126 AATCGGGGATACTCTAACCCCGTTA-TTTCTAAGGGATACTCCAACCCCGACTTTAT
66 AATCAAGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTAT
* * * * *
1678182 TACCAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTTAAAATACCGATTT-TCTA
1 TACCAATTTTTCACAATCAGAGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTC-A
* * * *
1678246 TAATCAAGGATATTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGA
65 CAATCAAGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGA
1678298 TTTTTATTTC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
120 2 0.02
121 75 0.75
122 23 0.23
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (122 bp):
TACCAATTTTTCACAATCAGAGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCAC
AATCAAGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTAT
Found at i:1680424 original size:4 final size:4
Alignment explanation
Indices: 1680415--1680439 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1680405 TATTTTGAGG
1680415 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1680440 GTTTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1687927 original size:55 final size:55
Alignment explanation
Indices: 1687847--1688092 Score: 296
Period size: 55 Copynumber: 4.4 Consensus size: 55
1687837 TTTCACTTTT
*
1687847 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
* *
1687902 TAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAGCTCACACAAGTTGGTGGCACCTTTC
1 TAGTCCTCAAAGAGCAGGACA-C----C-TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
* * **
1687964 -AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTT
1 TAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
* * * * *
1688018 TTGTCCTTAAAAAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
* *
1688073 CAGTCCTCAAAGAGTAGGAC
1 TAGTCCTCAAAGAGCAGGAC
1688093 GCTCTCTCCT
Statistics
Matches: 163, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
54 3 0.02
55 106 0.65
56 2 0.01
60 2 0.01
61 46 0.28
62 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (55 bp):
TAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
Found at i:1688310 original size:56 final size:55
Alignment explanation
Indices: 1688113--1688426 Score: 331
Period size: 56 Copynumber: 5.5 Consensus size: 55
1688103 TTTGCCCTTT
* * * *
1688113 AGTCCTCAAAGAACAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCA-TTTTCC
* * * * * *
1688169 AGTCCTCAAAAAGTAGGATGCATTTTCCTATTAAAGCGCACACAAGTGGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGC-CTTT-C----AAAGCCCACACAAGTCGGTGGCATTTTCC
* * *
1688230 AATCCTCAAAAAGCAAGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCA-TTTTCC
* *
1688286 AGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCC
* * **
1688341 AGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCCACACAAGTCGGTGGCATTTTCC
1688402 AGTCCTCAAAGAGCAGGACGCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTT
1688427 TCTTTTCAAA
Statistics
Matches: 217, Mismatches: 28, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
55 44 0.20
56 71 0.33
57 4 0.02
59 3 0.01
60 7 0.03
61 67 0.31
62 21 0.10
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCC
Found at i:1688376 original size:117 final size:112
Alignment explanation
Indices: 1688115--1688426 Score: 333
Period size: 117 Copynumber: 2.7 Consensus size: 112
1688105 TGCCCTTTAG
* * *
1688115 TCCTCAAAGAA-CAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
1 TCCTCAAA-AAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
* * * * *
1688179 AAGTAGGATGCATTTTCCTATTAAAGCGCACACAAGTGGGTGGCATTTTCCAA
64 GAGCAGGATGC-CTTTCC---TAAAGCCCACACAAGTCGGTGGCATTTTCCAA
*
1688232 TCCTCAAAAAGCAAGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTTCCAGTCCTCAAAG
1 TCCTCAAAAAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
* *
1688297 AGCAGAATGCCTTT-C-AAAGCCCACACAAGTCGGTGGCATTTTCCAG
65 AGCAGGATGCCTTTCCTAAAGCCCACACAAGTCGGTGGCATTTTCCAA
* * * **
1688343 TCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCT
1 TCCTCAAAAAGCAAGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
*
1688408 CAAAGAGCAGGACGCCTTT
60 CAAAGAGCAGGATGCCTTT
1688427 TCTTTTCAAA
Statistics
Matches: 168, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
111 42 0.25
113 1 0.01
115 2 0.01
116 36 0.21
117 87 0.52
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (112 bp):
TCCTCAAAAAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA
GCAGGATGCCTTTCCTAAAGCCCACACAAGTCGGTGGCATTTTCCAA
Found at i:1688406 original size:61 final size:60
Alignment explanation
Indices: 1688134--1688477 Score: 318
Period size: 61 Copynumber: 5.8 Consensus size: 60
1688124 AACAGGACGC
* * * *
1688134 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGTAGGATGCATTT-T
1 CTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCCAGTCCTCAAAGAGCAGGATGC-TTTCT
* * * * * * *
1688195 CCTATT-AAAGCGCACACAAGTGGGTGGCATTTTCCAATCCTCAAAAAGCAAGA--C--GC-
1 -CT-TTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
* * *
1688251 CTTTCAAAGCCCACACAAGTCGGTGGCATTTTTCCAGTCCTCAAAGAGCAGAATG----C-
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
* *
1688307 CTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
* *
1688367 CTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTT-T
1 CTTT-CAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATG-CTTTCT
* * * **
1688428 CTTTTCAAAGCCCATACGAGTTGGTGGTACTTTTTAGTCCTCAAAGAGCA
1 C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCA
1688478 AGACGCACTT
Statistics
Matches: 243, Mismatches: 25, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
54 2 0.01
55 48 0.20
56 49 0.20
59 2 0.01
60 4 0.02
61 106 0.44
62 30 0.12
63 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (60 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:1688410 original size:172 final size:173
Alignment explanation
Indices: 1688113--1688426 Score: 438
Period size: 172 Copynumber: 1.8 Consensus size: 173
1688103 TTTGCCCTTT
* * * *
1688113 AGTCCTCAAAGAACAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
1 AGTCCTCAAAGAACAGAACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTTTCCAGTCCTCAA
* * **
1688178 AAAGTAGGATGCATTTTCCTATTAAAGCGCACACAAGTGGGTGGCATTTTCCAATCCTCAAAAAG
66 AAAGCAGGATGCATTTTCCTATTAAAGCCCACACAAGTGGGTGGCACCTTCCAATCCTCAAAAAG
1688243 CAAGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTTCC
131 CAAGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTTCC
* *
1688286 AGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTCGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAACAGAACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTTTCCAGTCCTCAA
* * *
1688350 AGAGCAGGATGC--TTTCTCT-TTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAA
66 AAAGCAGGATGCATTTTC-CTATT--AAAGCCCACACAAGTGGGTGGCACCTTCCAATCCTCAAA
* *
1688412 GAGCAGGACGCCTTT
128 AAGCAAGACGCCTTT
1688427 TCTTTTCAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
170 6 0.05
171 2 0.02
172 71 0.58
173 44 0.36
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (173 bp):
AGTCCTCAAAGAACAGAACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTTTCCAGTCCTCAA
AAAGCAGGATGCATTTTCCTATTAAAGCCCACACAAGTGGGTGGCACCTTCCAATCCTCAAAAAG
CAAGACGCCTTTCAAAGCCCACACAAGTCGGTGGCATTTTTCC
Found at i:1688477 original size:122 final size:116
Alignment explanation
Indices: 1688201--1688426 Score: 302
Period size: 111 Copynumber: 2.0 Consensus size: 116
1688191 TTTTCCTATT
* * * * * *
1688201 AAAGCGCACACAAGTGGGTGGCATTTTCCAATCCTCAAAAAGCAAGA--C--GC-CTTTCAAAGC
1 AAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTCAAAGC
** *
1688261 CCACACAAGTCGGTGGCATTTTTCCAGTCCTCAAAGAGCAGAATGCCTTTC
66 CCACACAAGTCGGTGGCATCCTTCCAGTCCTCAAAGAGCAGAACGCCTTTC
1688312 AAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAG
1 AAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTT-CAAAG
* *
1688377 CCCACACAAGTTGGTGGCA-CCTTCCAGTCCTCAAAGAGCAGGACGCCTTT
65 CCCACACAAGTCGGTGGCATCCTTCCAGTCCTCAAAGAGCAGAACGCCTTT
1688427 TCTTTTCAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
111 42 0.43
113 1 0.01
115 1 0.01
116 31 0.32
117 23 0.23
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (116 bp):
AAAGCCCACACAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTCAAAGC
CCACACAAGTCGGTGGCATCCTTCCAGTCCTCAAAGAGCAGAACGCCTTTC
Found at i:1688525 original size:42 final size:42
Alignment explanation
Indices: 1688459--1688623 Score: 131
Period size: 42 Copynumber: 3.8 Consensus size: 42
1688449 TGGTGGTACT
1688459 TTTTAGTCCTCAAAGAGCAAGACGCACTTT-ATTTTCC-TCTTTC
1 TTTT-GTCCTCAAAGAGCAAGACGCA-TTTCATTTTCCGT-TTTC
* * *
1688502 TTTTGTCCTCAAAGAGTAGGACGCATTTCGTTTTCCGTTTTC
1 TTTTGTCCTCAAAGAGCAAGACGCATTTCATTTTCCGTTTTC
* * **
1688544 TCTTTGTCCTCAAAGAGC-AGAACACGTTTCATTCCCTT-ATTTTCTCC
1 T-TTTGTCCTCAAAGAGCAAG-ACGCATTTCATT---TTCCGTTT-T-C
* *
1688591 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTT
1 TTTTGTCCTCAAAGAGCAAGACGCATTTCATTT
1688624 CCTTTTTTTC
Statistics
Matches: 98, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
41 3 0.03
42 31 0.32
43 30 0.31
45 3 0.03
46 28 0.29
47 3 0.03
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (42 bp):
TTTTGTCCTCAAAGAGCAAGACGCATTTCATTTTCCGTTTTC
Found at i:1688621 original size:46 final size:46
Alignment explanation
Indices: 1688501--1688679 Score: 163
Period size: 46 Copynumber: 4.0 Consensus size: 46
1688491 TTTCCTCTTT
* * *
1688501 CTTTTGTCCTCAAAGAGTAGGACGCATTTCGTTTTCC--GTTTTCT-
1 CTTTTGTCCTCAAAGAGCAGGACGCATTTC-ATTTCCTTATTTTCTC
* * * *
1688545 C-TTTGTCCTCAAAGAGCAGAACACGTTTCATTCCCTTATTTTCTC
1 CTTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTATTTTCTC
* *
1688590 CTTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTTTTTTC-C
1 CTTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTATTTTCTC
* * * * *
1688635 CTTCTAGTCCTTAAAAAGCAGGACACATTTCGTTTTCCTT-TTTTC
1 CTT-TTGTCCTCAAAGAGCAGGACGCATTTC-ATTTCCTTATTTTC
1688680 CTTTGTCCTT
Statistics
Matches: 110, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
42 4 0.04
43 24 0.22
44 7 0.06
45 5 0.05
46 63 0.57
47 7 0.06
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (46 bp):
CTTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTATTTTCTC
Found at i:1688680 original size:46 final size:43
Alignment explanation
Indices: 1688503--1688812 Score: 157
Period size: 46 Copynumber: 7.3 Consensus size: 43
1688493 TCCTCTTTCT
* * * * * *
1688503 TTTGTCCTCAAAGAGTAGGACGCATTTCGTTTTCC-GTTTTCTC
1 TTTGTCCTCAAAAAGCAGGACACATTTC-ATTTCCTTTTTTCCC
* * * *
1688546 TTTGTCCTCAAAGAGCAGAACACGTTTCATTCCCTTATTTTCTCC
1 TTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTT-TTTTC-CC
* * *
1688591 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTTTTTTCCC
1 -TTTGTCCTCAAAAAGCAGGACACATTTCATTTCC-TTTTTTCCC
* *
1688636 TTCTAGTCCTTAAAAAGCAGGACACATTTCGTTTTCCTTTTTT-CC
1 TT-T-GTCCTCAAAAAGCAGGACACATTTC-ATTTCCTTTTTTCCC
** * * * *
1688681 TTTGTCCTTGAAAAGAATG--ACA-GT-A----CTCTTTTCCAC
1 TTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTCC-C
* * *
1688717 TTTGTCCTCAAGAAGCAGGACAC-TTTCTTTTTCTTTTTT-CC
1 TTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTCCC
** * **
1688758 TTTGTCCTCAAGGAGCAAGAC-CTATTTCA-TT-CTCATTT-CC
1 TTTGTCCTCAAAAAGCAGGACAC-ATTTCATTTCCTTTTTTCCC
1688798 TTTGTCCTCAAAAAG
1 TTTGTCCTCAAAAAG
1688813 TGGGACACCC
Statistics
Matches: 208, Mismatches: 39, Indels: 43
0.72 0.13 0.15
Matches are distributed among these distances:
34 6 0.03
35 1 0.00
36 15 0.07
38 3 0.01
40 22 0.11
41 25 0.12
42 9 0.04
43 43 0.21
44 8 0.04
45 8 0.04
46 61 0.29
47 7 0.03
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (43 bp):
TTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTCCC
Found at i:1689408 original size:20 final size:20
Alignment explanation
Indices: 1689379--1689555 Score: 120
Period size: 20 Copynumber: 8.8 Consensus size: 20
1689369 TTTTCACAAT
1689379 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
1689399 TTGTACCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1689419 TTGTATCGAT--A----T-A
1 TTGTATCGATACATTGTTCA
1689432 TTGTATCGATACATTCTGGATTTACCTA
1 TTGTATCGATACA-T-T-G--TT--C-A
* *
1689460 GATATATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
* *
1689481 TTGTATCGTTACATTGCTCA
1 TTGTATCGATACATTGTTCA
* *
1689501 TTGTATCGATACATGGCTCA
1 TTGTATCGATACATTGTTCA
1689521 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
1689541 ATGTATCGATACATT
1 TTGTATCGATACATT
1689556 CAAGCATTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
13 11 0.09
14 1 0.01
15 1 0.01
18 1 0.01
19 1 0.01
20 90 0.72
21 2 0.02
22 1 0.01
23 2 0.02
24 1 0.01
27 1 0.01
28 2 0.02
29 11 0.09
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1689434 original size:13 final size:13
Alignment explanation
Indices: 1689418--1689442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1689408 TACATTGTTC
1689418 ATTGTATCGATAT
1 ATTGTATCGATAT
1689431 ATTGTATCGATA
1 ATTGTATCGATA
1689443 CATTCTGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:1692023 original size:51 final size:51
Alignment explanation
Indices: 1691891--1692023 Score: 149
Period size: 52 Copynumber: 2.6 Consensus size: 51
1691881 TTCCAACATG
** * * * *
1691891 TCAATTTTTCTTAATCGGGGATACTTCAACTCTGATTTTATTTCTAAAGCA
1 TCAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA
** * * *
1691942 TCGAATTTACCGCAATCAGGAATACTCCAACTCCGATTTTATTTCCAAAACA
1 TC-AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA
*
1691994 TCAATTTTTCACAATTGGGGATACTCCAAC
1 TCAATTTTTCACAATCGGGGATACTCCAAC
1692024 CCCGTTATTT
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
51 24 0.37
52 41 0.63
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (51 bp):
TCAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA
Found at i:1692052 original size:28 final size:26
Alignment explanation
Indices: 1692012--1692083 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 26
1692002 TCACAATTGG
1692012 GGATACTCCAACCCCGTTATTTCGTCGA
1 GGATACTCCAACCCCGTTATTTC--CGA
*
1692040 GGATACTCTAACCCCGTTATTTCCGA
1 GGATACTCCAACCCCGTTATTTCCGA
1692066 GAGAATACTCCAACCCCG
1 G-G-ATACTCCAACCCCG
1692084 GCTTTATATC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 4 0.10
27 1 0.03
28 35 0.88
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (26 bp):
GGATACTCCAACCCCGTTATTTCCGA
Found at i:1692266 original size:28 final size:28
Alignment explanation
Indices: 1692226--1692299 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
1692216 TTTCATAATC
*
1692226 AGGGG-TACTCCAACCCCGTTATGTCAT
1 AGGGGATACTCCAACCCCGTTATGTCAG
* * * *
1692253 TGGGGATACTCCAATCCCGTTATTTCCG
1 AGGGGATACTCCAACCCCGTTATGTCAG
1692281 AGGGGATACTCCAACCCCG
1 AGGGGATACTCCAACCCCG
1692300 ATTTTATTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 4 0.10
28 35 0.90
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (28 bp):
AGGGGATACTCCAACCCCGTTATGTCAG
Found at i:1692274 original size:107 final size:108
Alignment explanation
Indices: 1691997--1692299 Score: 403
Period size: 109 Copynumber: 2.8 Consensus size: 108
1691987 CAAAACATCA
* * * *
1691997 ATTTTTCACAATTGGGGATACTCCAACCCCGTTATTTCGTCGAGGATACTCTAACCCCGTTATTT
1 ATTTTTCATAATCGGGG-TACTCCAACCCCGTTATTTCATCGAGGATACTCCAACCCCGTTATTT
* * *
1692062 CCGAGAGAATACTCCAACCCCGGCTTTATATCTAAAAATGTTGG
65 CCGAGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTGG
* * * * *
1692106 TTTTTTCATAATCGAGGTTACTCCAACCCTGTTATTTTATCGACGATACTCCAACCCCGTTATTT
1 ATTTTTCATAATCG-GGGTACTCCAACCCCGTTATTTCATCGAGGATACTCCAACCCCGTTATTT
* *
1692171 CCGAGGGGATACTCTAACCCTGGCTTTATATCT-AAAATATT-G
65 CCGAGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTGG
* * * *
1692213 ATTTTTCATAATCAGGGGTACTCCAACCCCGTTATGTCATTGGGGATACTCCAATCCCGTTATTT
1 ATTTTTCATAATC-GGGGTACTCCAACCCCGTTATTTCATCGAGGATACTCCAACCCCGTTATTT
1692278 CCGAGGGGATACTCCAACCCCG
65 CCGAGGGGATACTCCAACCCCG
1692300 ATTTTATTCC
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
107 75 0.45
108 8 0.05
109 82 0.49
110 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (108 bp):
ATTTTTCATAATCGGGGTACTCCAACCCCGTTATTTCATCGAGGATACTCCAACCCCGTTATTTC
CGAGGGGATACTCCAACCCCGGCTTTATATCTAAAAATATTGG
Found at i:1692306 original size:107 final size:106
Alignment explanation
Indices: 1691963--1692306 Score: 391
Period size: 107 Copynumber: 3.2 Consensus size: 106
1691953 GCAATCAGGA
* * * * * ** * *
1691963 ATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCACAATTGGGGATACTCCAACCCCG
1 ATACTCCAACCCCGACTTTATATCTAAAATATTGATTTTTCATAATCGGGG-TACTCCAACCCCG
* * * *
1692028 TTATTTCGTCGAGGATACTCTAACCCCGTTATTTCCGAGAGA
65 TTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
* * * *
1692070 ATACTCCAACCCCGGCTTTATATCTAAAAATGTTGGTTTTTTCATAATCGAGGTTACTCCAACCC
1 ATACTCCAACCCCGACTTTATATCT-AAAATATT-GATTTTTCATAATCG-GGGTACTCCAACCC
* * *
1692135 TGTTATTTTATCGACGATACTCCAACCCCGTTATTTCCGAGGGG
63 CGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
* * *
1692179 ATACTCTAACCCTGGCTTTATATCTAAAATATTGATTTTTCATAATCAGGGGTACTCCAACCCCG
1 ATACTCCAACCCCGACTTTATATCTAAAATATTGATTTTTCATAATC-GGGGTACTCCAACCCCG
* * * *
1692244 TTATGTCATTGGGGATACTCCAATCCCGTTATTTCCGAGGGG
65 TTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
*
1692286 ATACTCCAACCCCGATTTTAT
1 ATACTCCAACCCCGACTTTAT
1692307 TCCCAAAACA
Statistics
Matches: 197, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
107 100 0.51
108 13 0.07
109 82 0.42
110 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (106 bp):
ATACTCCAACCCCGACTTTATATCTAAAATATTGATTTTTCATAATCGGGGTACTCCAACCCCGT
TATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
Found at i:1692325 original size:107 final size:108
Alignment explanation
Indices: 1691963--1692378 Score: 380
Period size: 107 Copynumber: 3.9 Consensus size: 108
1691953 GCAATCAGGA
* * * *
1691963 ATACTCCAACTCCGATTTTAT-TTCCAAAACATCA-ATTTTTCACAATTGGGGATACTCCAACCC
1 ATACTCCAACCCCGACTTTATATCCCAAAACATCAGATTTTTCACAATCGGGG-TACTCCAACCC
* * * *
1692026 CGTTATTTCGTCGAGGATACTCTAACCCCGTTATTTCCGAGAGA
65 CGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
* ** ** ** * * *
1692070 ATACTCCAACCCCGGCTTTATATCTAAAAATGTTGGTTTTTTCATAATCGAGGTTACTCCAACCC
1 ATACTCCAACCCCGACTTTATATCCCAAAACATCAGATTTTTCACAATCG-GGGTACTCCAACCC
* * *
1692135 TGTTATTTTATCGACGATACTCCAACCCCGTTATTTCCGAGGGG
65 CGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
* * * * * * *
1692179 ATACTCTAACCCTGGCTTTATAT-CTAAAATAT-TGATTTTTCATAATCAGGGGTACTCCAACCC
1 ATACTCCAACCCCGACTTTATATCCCAAAACATCAGATTTTTCACAATC-GGGGTACTCCAACCC
* * * *
1692242 CGTTATGTCATTGGGGATACTCCAATCCCGTTATTTCCGAGGGG
65 CGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
* * ** *
1692286 ATACTCCAACCCCGATTTTAT-TCCCAAAACACCAG-TTTTTCACAATCGAGAATACTCCAATCC
1 ATACTCCAACCCCGACTTTATATCCCAAAACATCAGATTTTTCACAATCG-GGGTACTCCAACCC
*
1692349 CGTTACTTC--CGAGGGGATACTCCAACCCCG
65 CGTTATTTCATCGA--GGATACTCCAACCCCG
1692379 ATTTTATTTC
Statistics
Matches: 247, Mismatches: 53, Indels: 18
0.78 0.17 0.06
Matches are distributed among these distances:
105 1 0.00
106 2 0.01
107 148 0.60
108 14 0.06
109 80 0.32
110 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (108 bp):
ATACTCCAACCCCGACTTTATATCCCAAAACATCAGATTTTTCACAATCGGGGTACTCCAACCCC
GTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGG
Found at i:1692404 original size:79 final size:79
Alignment explanation
Indices: 1692258--1692412 Score: 265
Period size: 79 Copynumber: 2.0 Consensus size: 79
1692248 GTCATTGGGG
* *
1692258 ATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAGTT
1 ATACTCCAATCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATT
1692323 TTTCACAATCGAGA
66 TTTCACAATCGAGA
* * *
1692337 ATACTCCAATCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATT
1 ATACTCCAATCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATT
1692402 TTTCACAATCG
66 TTTCACAATCG
1692413 GAGATATTCC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.30
Consensus pattern (79 bp):
ATACTCCAATCCCGTTACTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATT
TTTCACAATCGAGA
Found at i:1692424 original size:51 final size:50
Alignment explanation
Indices: 1692362--1692479 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 50
1692352 TACTTCCGAG
* * *
1692362 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
* ** *
1692412 GGAGATATTCCAACTTCGGTTTTATTTCCAAAACACCAATTTCTCACAATC
1 GG-GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1692463 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
1692480 TTATTTCTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 14 0.25
51 43 0.75
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:1693719 original size:16 final size:16
Alignment explanation
Indices: 1693694--1693728 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1693684 TTGTATCAAA
*
1693694 CTTAAATCATTTTGAG
1 CTTAAATCATTTCGAG
*
1693710 CTTAAGTCATTTCGAG
1 CTTAAATCATTTCGAG
1693726 CTT
1 CTT
1693729 GGATTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (16 bp):
CTTAAATCATTTCGAG
Found at i:1695326 original size:67 final size:67
Alignment explanation
Indices: 1695218--1695349 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 67
1695208 CATTTGATTC
*
1695218 ACTTAATACTCATTTCGACTTTGAGTAGGATACAATATTGCTTTAAGGGATTCAATCTCTTTTGT
1 ACTTAATACTCATTTCGACTTTGAGTAGGATACAAAATTGCTTTAAGGGATTCAATCTCTTTTGT
1695283 GA
66 GA
1695285 ACTTAATACTCATTTCGACTTTGAGTAGGATACAAAATTGCTTTAAGGGATTCAATCTCTTTTGT
1 ACTTAATACTCATTTCGACTTTGAGTAGGATACAAAATTGCTTTAAGGGATTCAATCTCTTTTGT
1695350 AAAGGATTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (67 bp):
ACTTAATACTCATTTCGACTTTGAGTAGGATACAAAATTGCTTTAAGGGATTCAATCTCTTTTGT
GA
Found at i:1695519 original size:37 final size:37
Alignment explanation
Indices: 1695424--1695549 Score: 119
Period size: 38 Copynumber: 3.4 Consensus size: 37
1695414 CTATTCTAAC
* * * *
1695424 TTTATTTTATTATTACAAAATAGCTATTTCATT-CTAG
1 TTTATTTCATTCTTACAAAATAGCTATTCCATTAC-AA
* *
1695461 TTCTATTCCATTCTTATAAAATAGCTATTCCATTACAA
1 TT-TATTTCATTCTTACAAAATAGCTATTCCATTACAA
* * * *
1695499 TTTATTTCATTCTCACAAAATAACTATTCTATTATAA
1 TTTATTTCATTCTTACAAAATAGCTATTCCATTACAA
*
1695536 TTTTATTTTATTCT
1 -TTTATTTCATTCT
1695550 AATCAAATAA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
37 31 0.42
38 41 0.56
39 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (37 bp):
TTTATTTCATTCTTACAAAATAGCTATTCCATTACAA
Found at i:1695558 original size:38 final size:37
Alignment explanation
Indices: 1695464--1695559 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 37
1695454 ATTCTAGTTC
* * * *
1695464 TATTCCATTCTTATAAAATAGCTATTCCATTACAATT
1 TATTTCATTCTAATCAAATAACTATTCCATTACAATT
* * *
1695501 TATTTCATTCTCA-CAAAATAACTATTCTATTATAATTT
1 TATTTCATTCTAATC-AAATAACTATTCCATTACAA-TT
*
1695539 TATTTTATTCTAATCAAATAA
1 TATTTCATTCTAATCAAATAA
1695560 ACACACTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
37 28 0.58
38 19 0.40
39 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.01, T:0.46
Consensus pattern (37 bp):
TATTTCATTCTAATCAAATAACTATTCCATTACAATT
Found at i:1696713 original size:11 final size:11
Alignment explanation
Indices: 1696699--1696724 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1696689 GCTAAATGAT
1696699 AAAATTTAATA
1 AAAATTTAATA
1696710 AAAATTTAATA
1 AAAATTTAATA
1696721 AAAA
1 AAAA
1696725 AATACAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTTAATA
Found at i:1696976 original size:5 final size:5
Alignment explanation
Indices: 1696966--1696993 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1696956 AAAGTTAGGA
1696966 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1696994 CGGCAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1701924 original size:21 final size:20
Alignment explanation
Indices: 1701900--1701940 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
1701890 TGGTTGATGG
1701900 TTTTTTTCTTTCTTTTTGAGT
1 TTTTTTTCTTT-TTTTTGAGT
1701921 TTTTTTTCTTTTTTTTGAGT
1 TTTTTTTCTTTTTTTTGAGT
1701941 CGAATCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.05, C:0.07, G:0.10, T:0.78
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTGAGT
Found at i:1707266 original size:13 final size:13
Alignment explanation
Indices: 1707248--1707273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1707238 ACATTATGCT
1707248 TTGTATCGATACA
1 TTGTATCGATACA
1707261 TTGTATCGATACA
1 TTGTATCGATACA
1707274 CACTCAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1713340 original size:13 final size:13
Alignment explanation
Indices: 1713319--1713355 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1713309 TTGATGAATT
*
1713319 TGATGTTTAATCA
1 TGATATTTAATCA
1713332 TGATATTTAATCA
1 TGATATTTAATCA
1713345 TGATGATTTAA
1 TGAT-ATTTAA
1713356 ATTAGGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (13 bp):
TGATATTTAATCA
Found at i:1713504 original size:13 final size:13
Alignment explanation
Indices: 1713486--1713511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1713476 ACAAGGATCT
1713486 TTGTATCGATACA
1 TTGTATCGATACA
1713499 TTGTATCGATACA
1 TTGTATCGATACA
1713512 AGGGTTACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1716026 original size:20 final size:20
Alignment explanation
Indices: 1716001--1716052 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1715991 ATAATCCAAA
*
1716001 GTATCGATACATATGTATTT
1 GTATCGATACATAGGTATTT
1716021 GTATCGATACATAGGTATTT
1 GTATCGATACATAGGTATTT
1716041 GTATCGATACAT
1 GTATCGATACAT
1716053 TAAGGTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
GTATCGATACATAGGTATTT
Found at i:1716153 original size:91 final size:91
Alignment explanation
Indices: 1716020--1716235 Score: 380
Period size: 91 Copynumber: 2.4 Consensus size: 91
1716010 CATATGTATT
* *
1716020 TGTATCGATACAT-AGGTATTTGTATCGATACATTAAGGTTGACTTAGGCTATAATGATCAAAAC
1 TGTATCGATACATCATG-CTTTGTATCGATACATTAAGGTTGACTTAGGCTATAATGATCAAAAC
1716084 CCTAAAAAGTATCGATACACGTCCAGA
65 CCTAAAAAGTATCGATACACGTCCAGA
*
1716111 TGTATCGATATATCATGCTTTGTATCGATACATTAAGGTTGACTTAGGCTATAATGATCAAAACC
1 TGTATCGATACATCATGCTTTGTATCGATACATTAAGGTTGACTTAGGCTATAATGATCAAAACC
1716176 CTAAAAAGTATCGATACACGTCCAGA
66 CTAAAAAGTATCGATACACGTCCAGA
*
1716202 TGTATCGATACATCATGCTTTGTATTGATACATT
1 TGTATCGATACATCATGCTTTGTATCGATACATT
1716236 GTATCAATAC
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 117 0.98
92 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (91 bp):
TGTATCGATACATCATGCTTTGTATCGATACATTAAGGTTGACTTAGGCTATAATGATCAAAACC
CTAAAAAGTATCGATACACGTCCAGA
Found at i:1718952 original size:844 final size:844
Alignment explanation
Indices: 1717327--1719018 Score: 3285
Period size: 844 Copynumber: 2.0 Consensus size: 844
1717317 GATATGTATC
1717327 GATACAAATAAGGGTTTCCAGATTTCCTTTTCTACTGCCAACTGATGTACCGATACATACATGTA
1 GATACAAATAAGGGTTTCCAGATTTCCTTTTCTACTGCCAACTGATGTACCGATACATACATGTA
1717392 ATATATTGATACATTGTGTATTGTATCGATACAAATAAGGGTTTAGGATTTCCTTAGCTACTACT
66 ATATATTGATACATTGTGTATTGTATCGATACAAATAAGGGTTTAGGATTTCCTTAGCTACTACT
*
1717457 AACAGATGTATTAATACATTTAAACCTAAGCTAGAAAAAGGATTTTTTTTTGCTTAAAAATCATT
131 AACAGATGTATTAATACATTTAAACCTAAGCTAGAAAAAGGATTTTTTTTTCCTTAAAAATCATT
1717522 TGAACTTGTCTTAAAAAATTCTAAATATGATTATTCATTTTCAAATACTATTTTTGAGAAAATAA
196 TGAACTTGTCTTAAAAAATTCTAAATATGATTATTCATTTTCAAATACTATTTTTGAGAAAATAA
1717587 AAAGTAAGAAAGTTTATTTAGTATTTTTCAAAATATTTTCAATTTAATTTAAGGAAAAAACTAAA
261 AAAGTAAGAAAGTTTATTTAGTATTTTTCAAAATATTTTCAATTTAATTTAAGGAAAAAACTAAA
1717652 TTAGAATTAATCAAATGTATCTTAATTTAGCTTGAGTTATTGTTTTATCAAAACCAAGAATAATT
326 TTAGAATTAATCAAATGTATCTTAATTTAGCTTGAGTTATTGTTTTATCAAAACCAAGAATAATT
1717717 TAAAGCTAATTAAGCTAATAAGGATGCTAATATTTGGAATAACAGATAGATTATGGGATTAGGAA
391 TAAAGCTAATTAAGCTAATAAGGATGCTAATATTTGGAATAACAGATAGATTATGGGATTAGGAA
1717782 ATGAAGTGCTAGGAAGAGATGAAGGTATAGTACAAAATAAGACCCAAATGGTAGTAGAGATATTG
456 ATGAAGTGCTAGGAAGAGATGAAGGTATAGTACAAAATAAGACCCAAATGGTAGTAGAGATATTG
1717847 GATAAAAAGAATAAGACATAAAACATAGATGGCATTAGGGATTTTTTGTCTCAGAGCTAATAGAA
521 GATAAAAAGAATAAGACATAAAACATAGATGGCATTAGGGATTTTTTGTCTCAGAGCTAATAGAA
*
1717912 AGCATTATTGGAAGTTTCAATTTGTTATCTAGGTGGGAAAGACAGATTGGTATTACCAGAGACTA
586 AGCATTATTGGAAGTTTCAATTTGCTATCTAGGTGGGAAAGACAGATTGGTATTACCAGAGACTA
1717977 ATAATGGGTAGTACTTAGTGAAATTTGAGTATTAAACACTTAAAGAATTTAGTCAATGATGTATT
651 ATAATGGGTAGTACTTAGTGAAATTTGAGTATTAAACACTTAAAGAATTTAGTCAATGATGTATT
1718042 TGAGATAAGTTCTAATTGGGTTGATAAAAAAATCTAATAGATCATATGGAGCATGATTGTCCCTA
716 TGAGATAAGTTCTAATTGGGTTGATAAAAAAATCTAATAGATCATATGGAGCATGATTGTCCCTA
*
1718107 TAAAAATCAAGAATGTCCTATGAAGGGCGTGTAATAATGTTGTGACTACCCAAAATAGTATATG
781 TAAAAATCAAGAATGTCCTATGAAGGGCGTGTAATAATGTTGTGACTACCCAAAACAGTATATG
*
1718171 GATACAAATAAGGGTTTCCAGATTTCCTTTTCTACTGCCAACTGATGTACTGATACATACATGTA
1 GATACAAATAAGGGTTTCCAGATTTCCTTTTCTACTGCCAACTGATGTACCGATACATACATGTA
*
1718236 ATATATTGATACATTGTGTATTGTATCGATACAAATAAGGGTTTAGGATTTCCTTAGCTACTGCT
66 ATATATTGATACATTGTGTATTGTATCGATACAAATAAGGGTTTAGGATTTCCTTAGCTACTACT
1718301 AACAGATGTATTAATACATTTAAACCTAAGCTAGAAAAAGGATTTTTTTTTCCTTAAAAATCATT
131 AACAGATGTATTAATACATTTAAACCTAAGCTAGAAAAAGGATTTTTTTTTCCTTAAAAATCATT
1718366 TGAACTTGTCTTAAAAAATTCTAAATATGATTATTCATTTTCAAATACTATTTTTGAGAAAATAA
196 TGAACTTGTCTTAAAAAATTCTAAATATGATTATTCATTTTCAAATACTATTTTTGAGAAAATAA
*
1718431 AAAGTAAGAAAGTTTATTTAGTATTTTTCAAAATATTTTCAATTTAATTTAAGGAAAACACTAAA
261 AAAGTAAGAAAGTTTATTTAGTATTTTTCAAAATATTTTCAATTTAATTTAAGGAAAAAACTAAA
*
1718496 TTAGAATTAATCAAATGTATCTTAATTTAGCTTGTGTTATTGTTTTATCAAAACCAAGAATAATT
326 TTAGAATTAATCAAATGTATCTTAATTTAGCTTGAGTTATTGTTTTATCAAAACCAAGAATAATT
1718561 TAAAGCTAATTAAGCTAATAAGGATGCTAATATTTGGAATAACAGATAGATTATGGGATTAGGAA
391 TAAAGCTAATTAAGCTAATAAGGATGCTAATATTTGGAATAACAGATAGATTATGGGATTAGGAA
*
1718626 ATGAAGTGCTAGGAAGAGATGAAGGTATAGTACAAAATAAGACCTAAATGGTAGTAGAGATATTG
456 ATGAAGTGCTAGGAAGAGATGAAGGTATAGTACAAAATAAGACCCAAATGGTAGTAGAGATATTG
* *
1718691 GATAAAGAGAATAAGACATAAAACATAGATGGCATTAGGGATTTTTTGTCTCAGAGGTAATAGAA
521 GATAAAAAGAATAAGACATAAAACATAGATGGCATTAGGGATTTTTTGTCTCAGAGCTAATAGAA
1718756 AGCATTATTGGAAGTTTCAATTTGCTATCTAGGTGGGAAAGACAGATTGGTATTACCAGAGACTA
586 AGCATTATTGGAAGTTTCAATTTGCTATCTAGGTGGGAAAGACAGATTGGTATTACCAGAGACTA
1718821 ATAATGGGTAGTACTTAGTGAAATTTGAGTATTAAACACTTAAAGAATTTAGTCAATGATGTATT
651 ATAATGGGTAGTACTTAGTGAAATTTGAGTATTAAACACTTAAAGAATTTAGTCAATGATGTATT
1718886 TGAGATAAGTTCTAATTGGGTTGATAAAAAAATCTAATAGATCATATGGAGCATGATTGTCCCTA
716 TGAGATAAGTTCTAATTGGGTTGATAAAAAAATCTAATAGATCATATGGAGCATGATTGTCCCTA
*
1718951 TAAAAATCAAGAATGTCCTATTAAGGGCGTGTAATAATGTTGTGACTACCCAAAACAGTATATG
781 TAAAAATCAAGAATGTCCTATGAAGGGCGTGTAATAATGTTGTGACTACCCAAAACAGTATATG
1719015 GATA
1 GATA
1719019 AGAAATATTA
Statistics
Matches: 837, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
844 837 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (844 bp):
GATACAAATAAGGGTTTCCAGATTTCCTTTTCTACTGCCAACTGATGTACCGATACATACATGTA
ATATATTGATACATTGTGTATTGTATCGATACAAATAAGGGTTTAGGATTTCCTTAGCTACTACT
AACAGATGTATTAATACATTTAAACCTAAGCTAGAAAAAGGATTTTTTTTTCCTTAAAAATCATT
TGAACTTGTCTTAAAAAATTCTAAATATGATTATTCATTTTCAAATACTATTTTTGAGAAAATAA
AAAGTAAGAAAGTTTATTTAGTATTTTTCAAAATATTTTCAATTTAATTTAAGGAAAAAACTAAA
TTAGAATTAATCAAATGTATCTTAATTTAGCTTGAGTTATTGTTTTATCAAAACCAAGAATAATT
TAAAGCTAATTAAGCTAATAAGGATGCTAATATTTGGAATAACAGATAGATTATGGGATTAGGAA
ATGAAGTGCTAGGAAGAGATGAAGGTATAGTACAAAATAAGACCCAAATGGTAGTAGAGATATTG
GATAAAAAGAATAAGACATAAAACATAGATGGCATTAGGGATTTTTTGTCTCAGAGCTAATAGAA
AGCATTATTGGAAGTTTCAATTTGCTATCTAGGTGGGAAAGACAGATTGGTATTACCAGAGACTA
ATAATGGGTAGTACTTAGTGAAATTTGAGTATTAAACACTTAAAGAATTTAGTCAATGATGTATT
TGAGATAAGTTCTAATTGGGTTGATAAAAAAATCTAATAGATCATATGGAGCATGATTGTCCCTA
TAAAAATCAAGAATGTCCTATGAAGGGCGTGTAATAATGTTGTGACTACCCAAAACAGTATATG
Found at i:1723526 original size:13 final size:13
Alignment explanation
Indices: 1723508--1723532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1723498 CATAAAGTAT
1723508 TGTATCGATACAA
1 TGTATCGATACAA
1723521 TGTATCGATACA
1 TGTATCGATACA
1723533 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1723613 original size:13 final size:13
Alignment explanation
Indices: 1723595--1723652 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
1723585 ATTACTCAAA
1723595 TGTATCGATACAT
1 TGTATCGATACAT
*
1723608 TGTATCGATACAC
1 TGTATCGATACAT
1723621 TG-ATC--T---T
1 TGTATCGATACAT
1723628 TGTATCGATACAT
1 TGTATCGATACAT
1723641 TGTATCGATACA
1 TGTATCGATACA
1723653 CTGATCTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1723632 original size:20 final size:20
Alignment explanation
Indices: 1723607--1723672 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1723597 TATCGATACA
1723607 TTGTATCGATACACTGATCT
1 TTGTATCGATACACTGATCT
1723627 TTGTATCGAT--AC--A---
1 TTGTATCGATACACTGATCT
1723640 TTGTATCGATACACTGATCT
1 TTGTATCGATACACTGATCT
1723660 TTGTATCGATACA
1 TTGTATCGATACA
1723673 TGCAGGCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 23 0.59
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACACTGATCT
Found at i:1723637 original size:33 final size:33
Alignment explanation
Indices: 1723595--1723673 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1723585 ATTACTCAAA
1723595 TGTATCGATACATTGTATCGATACACTGATCTT
1 TGTATCGATACATTGTATCGATACACTGATCTT
1723628 TGTATCGATACATTGTATCGATACACTGATCTT
1 TGTATCGATACATTGTATCGATACACTGATCTT
1723661 TGTATCGATACAT
1 TGTATCGATACAT
1723674 GCAGGCAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACACTGATCTT
Found at i:1723707 original size:22 final size:22
Alignment explanation
Indices: 1723682--1723726 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1723672 ATGCAGGCAA
*
1723682 ATTTGCCTAGATGTATCGATAC
1 ATTTGCCCAGATGTATCGATAC
1723704 ATTTGCCCAGATGTATCGATAC
1 ATTTGCCCAGATGTATCGATAC
1723726 A
1 A
1723727 CTATTAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTTGCCCAGATGTATCGATAC
Found at i:1730000 original size:22 final size:22
Alignment explanation
Indices: 1729975--1730028 Score: 54
Period size: 26 Copynumber: 2.3 Consensus size: 22
1729965 CATGTAGCAC
*
1729975 AAAATACCAATTGTGAAAGAAA
1 AAAATACCAATTCTGAAAGAAA
1729997 AAAATTGACACCAATTCTGAAAGAAA
1 AAAA-T---ACCAATTCTGAAAGAAA
*
1730023 ATAATA
1 AAAATA
1730029 ACGATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
25 1 0.04
26 19 0.73
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAATACCAATTCTGAAAGAAA
Found at i:1730846 original size:17 final size:17
Alignment explanation
Indices: 1730821--1730854 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1730811 ACTACCAAGG
*
1730821 AAATGTATCGATACATT
1 AAATATATCGATACATT
1730838 AAATATATCGATACATT
1 AAATATATCGATACATT
1730855 CATCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATATATCGATACATT
Found at i:1740368 original size:2 final size:2
Alignment explanation
Indices: 1740363--1740396 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1740353 AAAATCCTAA
1740363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1740397 TTAAATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1740950 original size:28 final size:29
Alignment explanation
Indices: 1740913--1740977 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
1740903 ATACATATTT
*
1740913 AATATTAAAA-AATTTTAAAAATAAAAATA
1 AATATTAAAAGAATTTAAAAAAT-AAAATA
* *
1740942 AATA-TAAAAGTATTTAAAAAATATAATA
1 AATATTAAAAGAATTTAAAAAATAAAATA
1740970 AATTATTA
1 AA-TATTA
1740978 TTAATTAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 12 0.40
29 16 0.53
30 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
AATATTAAAAGAATTTAAAAAATAAAATA
Found at i:1743272 original size:32 final size:31
Alignment explanation
Indices: 1743235--1743340 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 31
1743225 AAACAGTAAA
1743235 TGTATCGATACATAAGTGTTGTATCGATACAG
1 TGTATCGATACATAAGTGTTGTATCGATA-AG
* ** * **
1743267 TGTATCGCTACA-AAGCTACTGCCAAGGA-AA-
1 TGTATCGATACATAAG-TGTTG-TATCGATAAG
1743297 TGTATCGATACATAAGTGTTGTATCGATATAG
1 TGTATCGATACATAAGTGTTGTATCGATA-AG
*
1743329 TGTATCGCTACA
1 TGTATCGATACA
1743341 AAGCTACTGC
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
29 3 0.05
30 15 0.27
31 8 0.15
32 26 0.47
33 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (31 bp):
TGTATCGATACATAAGTGTTGTATCGATAAG
Found at i:1743303 original size:30 final size:30
Alignment explanation
Indices: 1743267--1743370 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
1743257 ATCGATACAG
*
1743267 TGTATCGCTACAAAGCTACTGCCAAGGAAA
1 TGTATCGATACAAAGCTACTGCCAAGGAAA
** * **
1743297 TGTATCGATACATAAG-TGTTG-TATCGATATA
1 TGTATCGATACA-AAGCTACTGCCAAGGA-A-A
* *
1743328 GTGTATCGCTACAAAGCTACTGCCAAGAAAA
1 -TGTATCGATACAAAGCTACTGCCAAGGAAA
1743359 TGTATCGATACA
1 TGTATCGATACA
1743371 TTATTCAATG
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
29 3 0.06
30 26 0.48
31 8 0.15
32 15 0.28
33 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (30 bp):
TGTATCGATACAAAGCTACTGCCAAGGAAA
Found at i:1743331 original size:62 final size:62
Alignment explanation
Indices: 1743232--1743403 Score: 263
Period size: 62 Copynumber: 2.8 Consensus size: 62
1743222 TACAAACAGT
*
1743232 AAATGTATCGATACATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGG
1 AAATGTATCGATACATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGA
*
1743294 AAATGTATCGATACATAAGTGTTGTATCGATATAGTGTATCGCTACAAAGCTACTGCCAAGA
1 AAATGTATCGATACATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGA
* * ** * *
1743356 AAATGTATCGATACATTATTCAATGTATCGATACATTGTATCGATACA
1 AAATGTATCGATACATAAGT-GTTGTATCGATACAGTGTATCGCTACA
1743404 TCGATCTTTG
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 78 0.78
63 22 0.22
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (62 bp):
AAATGTATCGATACATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGA
Found at i:1743397 original size:13 final size:13
Alignment explanation
Indices: 1743379--1743404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1743369 CATTATTCAA
1743379 TGTATCGATACAT
1 TGTATCGATACAT
1743392 TGTATCGATACAT
1 TGTATCGATACAT
1743405 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1743468 original size:20 final size:19
Alignment explanation
Indices: 1743443--1743537 Score: 109
Period size: 20 Copynumber: 4.8 Consensus size: 19
1743433 TTTACCCAGA
*
1743443 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTCT-CAT
*
1743463 TGTATCGATACATGGCTCAT
1 TGTATCGATACAT-TCTCAT
*
1743483 TGCATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
* *
1743503 TGTATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
1743523 TGTATCGATACATTC
1 TGTATCGATACATTC
1743538 AGGCATTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 62 0.97
21 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:1745901 original size:51 final size:51
Alignment explanation
Indices: 1745836--1746008 Score: 208
Period size: 51 Copynumber: 3.4 Consensus size: 51
1745826 ATTTTTCATC
* * * *
1745836 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTCAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTTTCTCAA
* * *
1745887 TCGGGGATACTCCAACTCCGATTTTATTTTTAAAACACCTATTTTCCAT-AA
1 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTC-TCAA
* * *
1745938 TCGGGGATACTCCAACTTCGATTTTATTTTCAAAACACCGACTTTTT-ACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACC-AATTTTTCTCAA
1745989 TCGGGGATACTCCAACTCCG
1 TCGGGGATACTCCAACTCCG
1746009 TTATTTTTGA
Statistics
Matches: 104, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
51 98 0.94
52 6 0.06
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCTCAA
Found at i:1746040 original size:79 final size:78
Alignment explanation
Indices: 1745940--1746212 Score: 351
Period size: 79 Copynumber: 3.5 Consensus size: 78
1745930 TTCCATAATC
** *
1745940 GGGGATACTCCAACTTCGATTTTATTT-TCAAAACACCGACTTTTTACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACC-AATTTTTACAATCGGGGATACTCCAA
* *
1746004 CTCCGTTATTTTTGA
64 CCCCGTTATTTTCGA
* * * *
1746019 GGGGACATTCCAACCCCGATTTTATTTCTAAAACACCAATTTTT-C-GTC-AGGATACTCCAACC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTACAATCGGGGATACTCCAACC
1746081 CCGTTATTTTCGA
66 CCGTTATTTTCGA
* *
1746094 GGGGATACTCCAACCCC-AGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGA-TTTTATTTCTAAAACACCAATTTTT-ACAATCGGGGATACTCCAA
1746158 CCCCGTTATTTTCGA
64 CCCCGTTATTTTCGA
* *
1746173 GGGGATACTCTAA-CCCGGTTTTATTTCTAAAACACCAATT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATT
1746213 CTCCACAATC
Statistics
Matches: 169, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
74 1 0.01
75 63 0.37
76 2 0.01
77 1 0.01
78 32 0.19
79 69 0.41
80 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTACAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:1746307 original size:28 final size:28
Alignment explanation
Indices: 1746271--1746345 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
1746261 ATTTTTCACA
* *
1746271 ATCGAGGATACTCTAACCCCGTTATTTC
1 ATCGAGGATACTCCAACCCAGTTATTTC
*
1746299 ATCGGGGATACTCCAACCCAGTTATTTCC
1 ATCGAGGATACTCCAACCCAGTTATTT-C
**
1746328 AAGGA-GATACTCCAACCC
1 ATCGAGGATACTCCAACCC
1746346 CGGCTTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 37 0.93
29 3 0.08
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCAGTTATTTC
Found at i:1746437 original size:51 final size:51
Alignment explanation
Indices: 1746333--1746447 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
1746323 TTTCCAAGGA
* * *
1746333 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTTTCACAATCAGG
1 GATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCAGG
* * **
1746384 GATAC-CTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATTGGG
1 GATACTC-CAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCAGG
1746435 GATACTCCAACCC
1 GATACTCCAACCC
1746448 TATTATTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.02
51 53 0.96
52 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCAGG
Found at i:1746447 original size:130 final size:130
Alignment explanation
Indices: 1746299--1746606 Score: 322
Period size: 130 Copynumber: 2.4 Consensus size: 130
1746289 CCGTTATTTC
* *
1746299 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAACCCCGGCTT-TATTTCCAAAA
1 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCC-GATTCTATTTCCAAAA
* * *
1746363 TAT-TGATTTT-TCACAATCAGGGATACCTCAACCC-CGACCTTATTTCTAAAAT-ATTGATTTC
65 CATCT-ATTTTCT-ACAATCAGGGACACCTCAACCCTCG-CCTTATTTCT-AAATCATCGATTTC
*
1746424 TCATA
126 TCACA
* * * * ***
1746429 ATTGGGGATACTCCAACCCTA-TTATTTTCACGGGGATACTCCAATCCCGATTCTATTTTTGAAA
1 ATCGGGGATACTCCAACCC-AGTTATTTCCAAGGGGATACTCCAACCCCGATTCTATTTCCAAAA
* * * * * *
1746493 CATCTATTTTCTATAATCGGGGACACTTCAACCCTTGCCTTATTTCTAAATCATCGATTTTTCGC
65 CATCTATTTTCTACAATCAGGGACACCTCAACCCTCGCCTTATTTCTAAATCATCGATTTCTCAC
1746558 A
130 A
* * *
1746559 ATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCC
1746607 ATTATTATCT
Statistics
Matches: 145, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
129 7 0.05
130 134 0.92
131 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCCGATTCTATTTCCAAAAC
ATCTATTTTCTACAATCAGGGACACCTCAACCCTCGCCTTATTTCTAAATCATCGATTTCTCACA
Found at i:1746447 original size:158 final size:158
Alignment explanation
Indices: 1746142--1746472 Score: 355
Period size: 158 Copynumber: 2.1 Consensus size: 158
1746132 ATTTTTCATA
* * * * * * *
1746142 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCGGTTTTATTTCTAAAACA
1 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAACCCGGCTTTATTTCCAAAACA
* * ** *
1746207 CCAATTCTCCACAATCAGGAATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCACAA
66 CCAATTCTCCACAATCAGGAATACTCCAACCCCGACCTTATTTTCAAAACACTAATTTCTCACAA
* *
1746272 TCGAGGATACTCTAACCCCGTTA-TTTC
131 TCGAGGATACTCCAACCCCATTATTTTC
*
1746299 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAA-CCCGGCTTTATTTCCAAAAC
*** * * * * * *
1746364 ATTGATTTTTCACAATCAGGGATAC-CTCAACCCCGACCTTA-TTTCTAAAATATTGATTTCTCA
65 ACCAATTCTCCACAATCAGGAATACTC-CAACCCCGACCTTATTTTC-AAAACACTAATTTCTCA
* * * *
1746427 TAATTGGGGATACTCCAACCCTATTATTTTC
128 CAATCGAGGATACTCCAACCCCATTATTTTC
1746458 A-CGGGGATACTCCAA
1 ATCGGGGATACTCCAA
1746473 TCCCGATTCT
Statistics
Matches: 142, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
157 44 0.31
158 93 0.65
159 5 0.04
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (158 bp):
ATCGGGGATACTCCAACCCAGTTATTTCCAAGGAGATACTCCAACCCGGCTTTATTTCCAAAACA
CCAATTCTCCACAATCAGGAATACTCCAACCCCGACCTTATTTTCAAAACACTAATTTCTCACAA
TCGAGGATACTCCAACCCCATTATTTTC
Done.