Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:3795 original size:26 final size:25
Alignment explanation
Indices: 3766--3827 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3756 TTTATATAAT
3766 TTAAAATTTTCATTTAAAATAAAAAC
1 TTAAAATTTTCATTTAAAA-AAAAAC
* * **
3792 TTAAAATTATAATTTTTAAAAAAAC
1 TTAAAATTTTCATTTAAAAAAAAAC
*
3817 TCAAAATTTTC
1 TTAAAATTTTC
3828 TGGAAATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAAATTTTCATTTAAAAAAAAAC
Found at i:15382 original size:80 final size:80
Alignment explanation
Indices: 15289--15494 Score: 324
Period size: 80 Copynumber: 2.6 Consensus size: 80
15279 ATTCTTCGTA
**
15289 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAAAT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG-AAAT
15354 -GTTATGAAGAATGAC
65 GGTTATGAAGAATGAC
*
15369 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCGAAATG
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
15434 GTTATGAAGAATGAC
66 GTTATGAAGAATGAC
* * * * *
15449 ACATTTTAAGTTGCAATCGAAAATGTTATGAAGAATGTCACATTTT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTT
15495 AGGTTGTGTC
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 4 0.03
80 112 0.97
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (80 bp):
ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
GTTATGAAGAATGAC
Found at i:15433 original size:40 final size:40
Alignment explanation
Indices: 15309--15433 Score: 137
Period size: 41 Copynumber: 3.1 Consensus size: 40
15299 TTGCAATCTA
15309 AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
1 AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
* * * * * ** *
15349 AAAATGTTATGAAGAATGACAC-ATTTTAAGTTG-CAATCTA
1 -AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATC-G
*
15389 AAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCG
1 AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
15429 AAATG
1 AAATG
15434 GTTATGAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
39 21 0.33
40 21 0.33
41 22 0.34
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (40 bp):
AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
Found at i:15495 original size:39 final size:39
Alignment explanation
Indices: 15289--15500 Score: 201
Period size: 39 Copynumber: 5.3 Consensus size: 39
15279 ATTCTTCGTA
** * * * *
15289 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTC
1 ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
* * *
15328 ACTTTTTTCGGTTGCCAATCGAAAATGTTATGAAGAATGAC
1 AC-ATTTTAGGTTG-CAATCGAAAATGTTATGAAGAATGTC
* * * * * *
15369 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTC
1 ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
* * *
15408 ACTTTTTTCGGTTGCCAATCG-AAATGGTTATGAAGAATGAC
1 AC-ATTTTAGGTTG-CAATCGAAAAT-GTTATGAAGAATGTC
*
15449 ACATTTTAAGTTGCAATCGAAAATGTTATGAAGAATGTC
1 ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
15488 ACATTTTAGGTTG
1 ACATTTTAGGTTG
15501 TGTCCAACCT
Statistics
Matches: 136, Mismatches: 31, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
39 56 0.41
40 40 0.29
41 40 0.29
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (39 bp):
ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
Found at i:15780 original size:41 final size:40
Alignment explanation
Indices: 15725--15858 Score: 153
Period size: 41 Copynumber: 3.3 Consensus size: 40
15715 AACATTTTTT
*
15725 GTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCG
1 GTTGCAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
* * * * * **
15765 GTTGTCAATCGAAAATGTTATGAAGAATGACAC-ATTTTAA
1 GTTG-CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
* *
15805 GTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCG
1 GTTGCAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
15845 GTTGCCAATCGAAA
1 GTTG-CAATCGAAA
15859 TGGTTATGAA
Statistics
Matches: 73, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
39 22 0.30
40 20 0.27
41 31 0.42
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (40 bp):
GTTGCAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
Found at i:15810 original size:80 final size:80
Alignment explanation
Indices: 15716--15929 Score: 306
Period size: 80 Copynumber: 2.7 Consensus size: 80
15706 CTTCTTCGTA
**
15716 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCGAAAAT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCG-AAAT
15781 -GTTATGAAGAATGAC
65 GGTTATGAAGAATGAC
* *
15796 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCGAAATG
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCGAAATG
15861 GTTATGAAGAATGAC
66 GTTATGAAGAATGAC
* * * * * * *
15876 ACATTTTAAGTTACAATCGAAAATGTTATGAAGAATGTCAC-ATTTTAGGTTGTC
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTC
15930 CAACCTAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 14 0.12
80 106 0.88
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (80 bp):
ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCGAAATG
GTTATGAAGAATGAC
Found at i:15893 original size:39 final size:39
Alignment explanation
Indices: 15770--15922 Score: 164
Period size: 39 Copynumber: 3.9 Consensus size: 39
15760 TTTCGGTTGT
*
15770 CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTG
1 CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTA
* * * * * * * ** *
15809 CAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGC
1 CAATCGAAAATGTTATGAAGAATGACAC-ATTTTAAGTT-A
15850 CAATCG-AAATGGTTATGAAGAATGACACATTTTAAGTTA
1 CAATCGAAAAT-GTTATGAAGAATGACACATTTTAAGTTA
*
15889 CAATCGAAAATGTTATGAAGAATGTCACATTTTA
1 CAATCGAAAATGTTATGAAGAATGACACATTTTA
15923 GGTTGTCCAA
Statistics
Matches: 89, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
39 50 0.56
40 22 0.25
41 17 0.19
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (39 bp):
CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTA
Found at i:16184 original size:39 final size:39
Alignment explanation
Indices: 16141--16345 Score: 137
Period size: 41 Copynumber: 5.2 Consensus size: 39
16131 CTTCGTAACA
16141 TTTTTT-GTTGCAATCTAAAATGTAACGAAAAATGTCAC
1 TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
* * * * * * *
16179 TTTTTTCGGTTTCCAATCGAAAATGTTATGAAGAATGACAC
1 TTTTTT-AG-TTGCAATCTAAAATGTAACGAAAAATGTCAC
* * *
16220 ATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCAC
1 TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
* * * * * *
16259 TTTTTTCGGTTGCCAATC-GAAATGGTTATGAAGAATGACAC
1 TTTTTT-AGTTG-CAATCTAAAAT-GTAACGAAAAATGTCAC
* * * * * *
16300 ATTTTAAATTGCAATCGAAAATGTTATGAAAAATGTCA-
1 TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
*
16338 TATTTTAG
1 TTTTTTAG
16346 GTTATGTCCA
Statistics
Matches: 124, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
38 10 0.08
39 47 0.38
40 17 0.14
41 50 0.40
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (39 bp):
TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
Found at i:16202 original size:41 final size:41
Alignment explanation
Indices: 16151--16280 Score: 138
Period size: 41 Copynumber: 3.2 Consensus size: 41
16141 TTTTTTGTTG
*
16151 CAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
1 CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
* * * * * ** *
16192 CAATCGAAAATGTTATGAAGAATGACAC-ATTTTAAG-TTG
1 CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
* * *
16231 CAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGC
1 CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
16272 CAATCGAAA
1 CAATCGAAA
16281 TGGTTATGAA
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
39 24 0.36
40 10 0.15
41 32 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (41 bp):
CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
Found at i:16232 original size:80 final size:80
Alignment explanation
Indices: 16138--16337 Score: 312
Period size: 80 Copynumber: 2.5 Consensus size: 80
16128 CTTCTTCGTA
** *
16138 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTCCAATCGAAAAT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG-AAAT
16203 -GTTATGAAGAATGAC
65 GGTTATGAAGAATGAC
*
16218 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCGAAATG
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
16283 GTTATGAAGAATGAC
66 GTTATGAAGAATGAC
* * * *
16298 ACATTTTAAATTGCAATCGAAAATGTTATGAAAAATGTCA
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCA
16338 TATTTTAGGT
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 4 0.04
80 106 0.96
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (80 bp):
ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
GTTATGAAGAATGAC
Found at i:16266 original size:422 final size:424
Alignment explanation
Indices: 15275--16558 Score: 2369
Period size: 422 Copynumber: 3.0 Consensus size: 424
15265 ACTTAAAATA
15275 TGACATTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGT
1 TGAC-TTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGT
*
15340 TGCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
65 TTCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
15405 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAA
130 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAA
*
15470 AATGTTATGAAGAATGTCACATTTTAGGTTGTGTCCAACCTAAAATATTATGTATTTTTATCATA
195 AATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATA
*
15535 TTTTCTGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTA
260 TTTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTA
*
15600 CCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTCCCCCCCCCAAGCGATTG
325 CCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTT--TCCCCCCAAGCGATTG
*
15665 TGCTTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCTC
388 TGCTTCATGCTGCCA-TTTTTTGTCTGTTAGGGGGCGC
*
15703 TTACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
1 TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
15768 GT-CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
66 -TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
*
15832 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTACAATCGAA
130 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAA
15897 AATGTTATGAAGAATGTCACATTTTAGG-T-TGTCCAACCTAAAATATTATGTATTTTTATCATA
195 AATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATA
15960 -TTTCGGTCGCTTCATGTATGCATCGGTTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATT
260 TTTTCGGTCGCTTCATGTATGCATCGG-TTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATT
16024 ACCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGCGATTGT
324 ACCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGCGATTGT
16089 GCTTCATGCTGCCATTTTTTGTCTGTTAGGGGGCGC
389 GCTTCATGCTGCCATTTTTTGTCTGTTAGGGGGCGC
16125 TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
1 TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
16190 TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGG
66 TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGG
*
16255 TCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAATTGCAATCGAAA
131 TCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAAA
* *
16320 ATGTTATGAAAAATGTCATATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATAT
196 ATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATAT
16385 TTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTAC
261 TTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTAC
* *
16450 CCGAGGCAATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGTGATTGTGC
326 CCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGCGATTGTGC
16515 TTCATGCTGCCATCTTTTTGTCTGTTAGGGGGCGC
391 TTCATGCTGCCAT-TTTTTGTCTGTTAGGGGGCGC
16550 TGACTTCTT
1 TGACTTCTT
16559 GCAGTAATGT
Statistics
Matches: 836, Mismatches: 13, Indels: 17
0.97 0.02 0.02
Matches are distributed among these distances:
421 1 0.00
422 236 0.28
423 31 0.04
424 174 0.21
425 175 0.21
426 1 0.00
427 215 0.26
428 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (424 bp):
TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGG
TCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAAA
ATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATAT
TTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTAC
CCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGCGATTGTGC
TTCATGCTGCCATTTTTTGTCTGTTAGGGGGCGC
Found at i:28677 original size:31 final size:31
Alignment explanation
Indices: 28642--28720 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
28632 ATTTTCAAGT
*
28642 TCGACTCGAACTCGAAAGATAATATTGAAAC
1 TCGACTCGAACTCAAAAGATAATATTGAAAC
28673 TCGACTCGAACTCAAAAGATAATATTGAAAC
1 TCGACTCGAACTCAAAAGATAATATTGAAAC
28704 TCGACTCGAACTCAAAA
1 TCGACTCGAACTCAAAA
28721 AGGCTCGAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (31 bp):
TCGACTCGAACTCAAAAGATAATATTGAAAC
Found at i:28798 original size:12 final size:12
Alignment explanation
Indices: 28781--28822 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
28771 ACTCGATTGA
28781 AGCTCGATTTTG
1 AGCTCGATTTTG
**
28793 AGCTCGA-TTCA
1 AGCTCGATTTTG
28804 AGCTCGATTTTG
1 AGCTCGATTTTG
28816 AGCTCGA
1 AGCTCGA
28823 CGGGTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:28806 original size:23 final size:23
Alignment explanation
Indices: 28772--28822 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
28762 GAAACTCGAA
*
28772 CTCGATTGAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGATTTTGAG
28795 CTCGATTCAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGATTTTGAG
28818 CTCGA
1 CTCGA
28823 CGGGTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (23 bp):
CTCGATTCAAGCTCGATTTTGAG
Found at i:30227 original size:17 final size:19
Alignment explanation
Indices: 30185--30227 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
30175 AATATTTGGG
30185 AAATTGTGAAGCAGATATC
1 AAATTGTGAAGCAGATATC
*
30204 AAGTTGTGAAGCAG-T-TC
1 AAATTGTGAAGCAGATATC
30221 AAATTGT
1 AAATTGT
30228 ACATAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 13 0.59
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (19 bp):
AAATTGTGAAGCAGATATC
Found at i:30772 original size:13 final size:13
Alignment explanation
Indices: 30736--30787 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
30726 AGTATATTTT
*
30736 TTAGGGTTTATGGT
1 TTAGGGTTTA-GGA
*
30750 TTAGGATTTAAGG-
1 TTAGGGTTT-AGGA
30763 TTAGGGTTTAGGA
1 TTAGGGTTTAGGA
*
30776 TTATGGTTTAGG
1 TTAGGGTTTAGG
30788 TTTTAGGGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 3 0.09
13 19 0.58
14 10 0.30
15 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (13 bp):
TTAGGGTTTAGGA
Found at i:30786 original size:20 final size:21
Alignment explanation
Indices: 30735--30794 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
30725 AAGTATATTT
* *
30735 TTTAGGGTTTATGGTTTAGGA
1 TTTAAGGTTTAGGGTTTAGGA
30756 TTTAAGG-TTAGGGTTTAGGA
1 TTTAAGGTTTAGGGTTTAGGA
* *
30776 -TTATGGTTTAGGTTTTAGG
1 TTTAAGGTTTAGGGTTTAGG
30795 GCCTAAGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.15
20 23 0.68
21 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAGGA
Found at i:30927 original size:11 final size:11
Alignment explanation
Indices: 30911--30973 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
30901 GTATTATAGA
30911 ATTTTTAATAT
1 ATTTTTAATAT
30922 ATTTTTAA-A-
1 ATTTTTAATAT
30931 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
30942 ATCAATAATGT
1 ATTTTTAATAT
30953 ATTTTTAATAT
1 ATTTTTAATAT
30964 ATTTTTAATA
1 ATTTTTAATA
30974 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:32914 original size:31 final size:31
Alignment explanation
Indices: 32876--33060 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
32866 CCCGAAGGAC
* * *
32876 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
32907 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
32938 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
32969 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
33000 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
33031 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
33061 CCCTCGACCC
Statistics
Matches: 148, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:37283 original size:31 final size:31
Alignment explanation
Indices: 37245--37429 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
37235 CCCGAAGGAC
* * *
37245 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
37276 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37307 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37338 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37369 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37400 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
37430 CCCTCGACCC
Statistics
Matches: 148, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:41672 original size:31 final size:31
Alignment explanation
Indices: 41634--41817 Score: 309
Period size: 31 Copynumber: 6.0 Consensus size: 31
41624 CCCGAAGGAC
* * *
41634 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
41665 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
41696 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
41727 CAGTCCATATGTCCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
41757 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
41788 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
41818 CCCTCGACCC
Statistics
Matches: 146, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
30 30 0.21
31 115 0.79
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:41787 original size:61 final size:61
Alignment explanation
Indices: 41634--41818 Score: 309
Period size: 61 Copynumber: 3.0 Consensus size: 61
41624 CCCGAAGGAC
* * * *
41634 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGT-AA
41696 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
41757 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
41818 C
1 C
41819 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
61 64 0.54
62 53 0.45
63 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (61 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:41792 original size:92 final size:93
Alignment explanation
Indices: 41634--41817 Score: 318
Period size: 92 Copynumber: 2.0 Consensus size: 93
41624 CCCGAAGGAC
* * *
41634 CAGTCCATAGATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAACAG
1 CAGTCCATAGATCCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACAG
41699 TCCATATGTCCCGAAGAACATAGGTAAA
66 TCCATATGTCCCGAAGAACATAGGTAAA
41727 CAGTCCATATG-TCCCGAAGAACATAGGTAA-CAGTCCATATGTCCCGAAGAACATAGGTAAACA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACA
41790 GTCCATATGTCCCGAAGAACATAGGTAA
65 GTCCATATGTCCCGAAGAACATAGGTAA
41818 CCCTCGACCC
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
92 60 0.69
93 26 0.30
94 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (93 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACAG
TCCATATGTCCCGAAGAACATAGGTAAA
Found at i:43286 original size:20 final size:20
Alignment explanation
Indices: 43263--43314 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
43253 AACGCGATCC
43263 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
43283 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
43303 CCAAAATCGCAA
1 CCAGAATCGCAA
43315 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:43331 original size:21 final size:20
Alignment explanation
Indices: 43304--43402 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
43294 AATCAGTTTC
43304 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
43325 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
43346 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
43366 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
43387 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
43403 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:43431 original size:20 final size:20
Alignment explanation
Indices: 43369--43562 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
43359 CGATTTTCCA
* ** *
43369 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
43389 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
43409 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
43429 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
43449 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
43469 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
43489 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
43509 AAATCGCAATG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
43529 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
43550 AAATCGCAACGCG
1 AAATCGCAACGCG
43563 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:43453 original size:60 final size:60
Alignment explanation
Indices: 43369--43562 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
43359 CGATTTTCCA
* ** * *
43369 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
43429 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
43489 ATATCGCAACGCGTATCCGTAAATCGCAATGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
43550 AAATCGCAACGCG
1 AAATCGCAACGCG
43563 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:43982 original size:33 final size:33
Alignment explanation
Indices: 43943--44013 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43933 TTCACTTAGA
*
43943 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
43976 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
44009 TTTCA
1 TTTCA
44014 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:44152 original size:14 final size:14
Alignment explanation
Indices: 44133--44187 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
44123 AGAATGACTG
44133 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
44147 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
44166 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
44180 TCGCAACG
1 TCGCAACG
44188 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:44200 original size:33 final size:33
Alignment explanation
Indices: 44133--44203 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
44123 AGAATGACTG
***
44133 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
44166 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
44199 TCGCA
1 TCGCA
44204 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:44221 original size:19 final size:19
Alignment explanation
Indices: 44199--44296 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
44189 GAAACCAAAA
*
44199 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
44218 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
44232 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
44251 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
44265 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
44284 TCGCGTTGCGATT
1 TCGCGTTGCGATT
44297 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:44240 original size:14 final size:14
Alignment explanation
Indices: 44221--44310 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
44211 TTTCATTTCG
44221 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
44235 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
44254 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
44268 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
44285 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
44301 CGTTGCGATT
1 CGTTGCGATT
44311 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:44246 original size:33 final size:33
Alignment explanation
Indices: 44204--44318 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
44194 CAAAATCGCA
44204 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
44237 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
44270 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
44303 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
44319 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:46333 original size:182 final size:184
Alignment explanation
Indices: 46016--46391 Score: 702
Period size: 182 Copynumber: 2.0 Consensus size: 184
46006 TAGATTGCTT
46016 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAA-TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
46081 TTTGTTTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
46146 GTGTATTCTTTAACACTGTG-A-AATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
46199 AGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
46264 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
46329 TGTATTCTTTAACACTGTGAAATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTG-AATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
46384 AGTAAATT
1 AGTAAATT
46392 TATCCATTCA
Statistics
Matches: 188, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 141 0.75
183 6 0.03
184 1 0.01
185 40 0.21
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:46348 original size:93 final size:93
Alignment explanation
Indices: 46016--46392 Score: 699
Period size: 93 Copynumber: 4.1 Consensus size: 93
46006 TAGATTGCTT
*
46016 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
46081 TTTGTTTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46109 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46171 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46199 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46263 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
46291 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAATA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46356 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46384 AGTAAATTT
1 AGTAAATTT
46393 ATCCATTCAA
Statistics
Matches: 277, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
89 50 0.18
90 37 0.13
91 2 0.01
92 38 0.14
93 150 0.54
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:46476 original size:19 final size:19
Alignment explanation
Indices: 46436--46564 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
46426 TAGTTTACTT
* *
46436 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
46456 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
46475 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
46494 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
46508 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
46527 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
46541 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
46560 TCGCA
1 TCGCA
46565 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:46515 original size:33 final size:32
Alignment explanation
Indices: 46472--46564 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
46462 CGCGAAACCA
**
46472 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
46504 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
46537 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
46565 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:46562 original size:52 final size:52
Alignment explanation
Indices: 46436--46564 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
46426 TAGTTTACTT
**
46436 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
46488 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
46541 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
46565 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:46582 original size:19 final size:19
Alignment explanation
Indices: 46560--46695 Score: 130
Period size: 19 Copynumber: 7.6 Consensus size: 19
46550 GAAACCAAAA
*
46560 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
46579 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
46595 T--CGTTGCGATTTTTCATT
1 TCGCGTTGCGA-TTTTCATT
*
46613 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
46629 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
46646 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
46665 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
46685 TCGTGTTGCGA
1 TCGCGTTGCGA
46696 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.16
16 8 0.08
17 11 0.11
18 3 0.03
19 39 0.40
20 20 0.21
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:46601 original size:14 final size:14
Alignment explanation
Indices: 46582--46639 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
46572 TTTCATTTCG
46582 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
46596 CGTTGCGATTTTTCATTT
1 CGTTGCGA---TTC-TTT
*
46614 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
46630 CGTTGCGATT
1 CGTTGCGATT
46640 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 18 0.49
16 2 0.05
17 6 0.16
18 3 0.08
20 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:46614 original size:34 final size:33
Alignment explanation
Indices: 46565--46658 Score: 170
Period size: 34 Copynumber: 2.8 Consensus size: 33
46555 CAAAATCGCA
*
46565 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
46598 TTGCGATTTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGA-TTTTCATTTCGCGTTGCGATTCTGTCG
46632 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
46659 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
33 27 0.46
34 32 0.54
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:48551 original size:38 final size:38
Alignment explanation
Indices: 48508--48580 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
48498 TAATTGATTG
*
48508 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
48546 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
48581 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:48567 original size:19 final size:19
Alignment explanation
Indices: 48504--48567 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
48494 AGTTTAATTG
48504 ATTG-TTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
48522 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
48540 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
48560 ATTGATTT
1 ATTGATTT
48568 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 12, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
18 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:48581 original size:14 final size:14
Alignment explanation
Indices: 48562--48597 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
48552 ATTGTTTAAT
48562 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
48576 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
48590 TGATTTGT
1 TGATTTGT
48598 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48720 original size:19 final size:19
Alignment explanation
Indices: 48704--48804 Score: 158
Period size: 19 Copynumber: 5.6 Consensus size: 19
48694 AAAAATGACT
48704 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48723 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
48742 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
48756 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48775 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48794 ATCGCAATGCG
1 ATCGCAATGCG
48805 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 59 0.79
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48838 original size:52 final size:52
Alignment explanation
Indices: 48811--49130 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
48801 TGCGTTTATA
*
48811 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
48863 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
48915 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
48972 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
49024 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
49076 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
49129 AT
1 AT
49131 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:48857 original size:19 final size:19
Alignment explanation
Indices: 48833--49158 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
48823 GATTATCTCG
48833 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48852 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48871 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
48885 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48904 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48923 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
48942 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
48961 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48980 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48994 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49013 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
49032 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
49046 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49065 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
49084 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
49098 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
49118 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
49132 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
49151 TTGCGATT
1 TTGCGATT
49159 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:49076 original size:161 final size:157
Alignment explanation
Indices: 48811--49130 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
48801 TGCGTTTATA
48811 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
48876 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
48941 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
48972 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
49037 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
49102 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
49129 AT
1 AT
49131 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:49102 original size:33 final size:33
Alignment explanation
Indices: 48852--49158 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
48842 TCATTTCGCA
*
48852 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
48885 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
48921 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
48959 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
48994 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
49030 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
49065 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
49098 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
49132 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
49159 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:51689 original size:24 final size:24
Alignment explanation
Indices: 51655--51701 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
51645 CTGAAACATC
51655 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
51679 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
51702 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:52399 original size:20 final size:20
Alignment explanation
Indices: 52371--52779 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
52361 AAATTTCAGT
* * * *
52371 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
52391 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
52411 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
52431 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
52451 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
52471 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
52491 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52511 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
52531 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
52551 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52571 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52591 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
52611 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
52631 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52651 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
52671 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
52691 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
52711 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
52731 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
52751 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
52771 GTTGCGATT
1 GTTGCGATT
52780 ATGGAAAATC
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 331 0.97
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:55454 original size:18 final size:19
Alignment explanation
Indices: 55422--55461 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
55412 TATAACTTTT
*
55422 AAAATAAATAGAATCTTAA
1 AAAATAAATAGAATCATAA
*
55441 AAAATAACTA-AATCATAA
1 AAAATAAATAGAATCATAA
55459 AAA
1 AAA
55462 TTAAGAGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATAAATAGAATCATAA
Found at i:55535 original size:72 final size:70
Alignment explanation
Indices: 55435--55567 Score: 160
Period size: 72 Copynumber: 1.9 Consensus size: 70
55425 ATAAATAGAA
* * * *
55435 TCTTAAAAAATAACTAAATCATAAAAATTAAGAGACTGTAA-GTTTAATTTCATTAATTTTAAAA
1 TCTTAAAAAATAACTAAACCAGAAAAATT-AGAGA-T-TAAGGCTTAATTCCATTAATTTTAAAA
55499 CTCAAATG
63 CTCAAATG
* * * *
55507 TCTTAAAATATAATTAAACCAGATAAATTTGAGATTAAGGCTTAATTCCATTAATTTTAAA
1 TCTTAAAAAATAACTAAACCAGAAAAATTAGAGATTAAGGCTTAATTCCATTAATTTTAAA
55568 CTTTACAGTG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
69 3 0.06
70 21 0.40
71 4 0.08
72 24 0.46
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (70 bp):
TCTTAAAAAATAACTAAACCAGAAAAATTAGAGATTAAGGCTTAATTCCATTAATTTTAAAACTC
AAATG
Found at i:55610 original size:71 final size:70
Alignment explanation
Indices: 55478--55611 Score: 166
Period size: 70 Copynumber: 1.9 Consensus size: 70
55468 GACTGTAAGT
* *
55478 TTAATTTCATTAATTTTAAAACTCAAATGTCTTAAAATATAATTAAACCAGATAAATTTGAGATT
1 TTAATTCCATTAATTTTAAAACTCAAATGTCTAAAAATATAATTAAACCAGATAAATTTGAGATT
55543 AAGGC
66 AAGGC
* * *
55548 TTAATTCCATTAATTTT-AAACTTTACAGTGTCCTAAAAAT-TAATTATACCAGA-AAATGTTGA
1 TTAATTCCATTAATTTTAAAAC-TCA-AATGT-CTAAAAATATAATTAAACCAGATAAAT-TTGA
55610 GA
62 GA
55612 GGAATAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
69 4 0.07
70 22 0.40
71 22 0.40
72 7 0.13
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (70 bp):
TTAATTCCATTAATTTTAAAACTCAAATGTCTAAAAATATAATTAAACCAGATAAATTTGAGATT
AAGGC
Found at i:56968 original size:6 final size:6
Alignment explanation
Indices: 56957--56990 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
56947 TAATTTAATT
56957 ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
56991 TTAATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:56998 original size:7 final size:7
Alignment explanation
Indices: 56986--57020 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
56976 TATAAATATA
56986 AATATTT
1 AATATTT
56993 AATATTT
1 AATATTT
57000 AATATATT
1 AATAT-TT
57008 AATTATTT
1 AA-TATTT
57016 AATAT
1 AATAT
57021 AATCAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 15 0.58
8 8 0.31
9 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATATTT
Found at i:57014 original size:16 final size:15
Alignment explanation
Indices: 56986--57021 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
56976 TATAAATATA
56986 AATAT-TTAATATTT
1 AATATATTAATATTT
57000 AATATATTAATTATTT
1 AATATATTAA-TATTT
57016 AATATA
1 AATATA
57022 ATCAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATATTAATATTT
Found at i:77174 original size:19 final size:16
Alignment explanation
Indices: 77138--77179 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 16
77128 ATATTAAGAA
77138 TAAAATATTTTTTAAT
1 TAAAATATTTTTTAAT
77154 TAAACATATATTTTTATAT
1 TAAA-ATAT-TTTTTA-AT
77173 TAAAATA
1 TAAAATA
77180 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 9 0.39
19 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATATTTTTTAAT
Found at i:84942 original size:27 final size:27
Alignment explanation
Indices: 84904--84973 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
84894 CTTAAGGAGT
*
84904 GGTCCTTCGGGACAAATACAGTACATA
1 GGTCCTTCGGGACAAATACAATACATA
84931 GGTCCTTCGGGACAAATACAATACATA
1 GGTCCTTCGGGACAAATACAATACATA
*
84958 GGTCATTCGGGACAAA
1 GGTCCTTCGGGACAAA
84974 CTTTCATAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (27 bp):
GGTCCTTCGGGACAAATACAATACATA
Found at i:91028 original size:3 final size:3
Alignment explanation
Indices: 91020--91083 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
91010 TTACTCATTT
91020 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
91066 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
91084 ACTTATGCAG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:93025 original size:2 final size:2
Alignment explanation
Indices: 93018--93051 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
93008 AAGTGAATGA
93018 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
93052 GTTTATGTGA
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:93651 original size:21 final size:21
Alignment explanation
Indices: 93621--93675 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
93611 GAATGTCCAT
93621 GGGTACAGATTCCCCCCCAGG
1 GGGTACAGATTCCCCCCCAGG
* *
93642 GGGTATAGATTCCCCCCTAGG
1 GGGTACAGATTCCCCCCCAGG
*
93663 GGGTACCGATTCC
1 GGGTACAGATTCC
93676 TCTGTCTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.33, G:0.29, T:0.20
Consensus pattern (21 bp):
GGGTACAGATTCCCCCCCAGG
Found at i:93732 original size:21 final size:21
Alignment explanation
Indices: 93708--93749 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
93698 ATTGTACTTA
* *
93708 GGGAACCGATTTCTTATGAGG
1 GGGAACCGATTCCCTATGAGG
93729 GGGAACCGATTCCCTATGAGG
1 GGGAACCGATTCCCTATGAGG
93750 TGTGCTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
GGGAACCGATTCCCTATGAGG
Found at i:96510 original size:103 final size:103
Alignment explanation
Indices: 96285--96502 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
96275 GTCGAGGGTC
96285 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
96350 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
96388 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
96453 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
96491 TATGTGGTCCTT
1 TATGTGGTCCTT
96503 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:96553 original size:23 final size:23
Alignment explanation
Indices: 96518--96581 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
96508 CATTATTATA
96518 TGGCACTAC-GGTGCAATTCTACG
1 TGGCACT-CTGGTGCAATTCTACG
96541 TGGCACTCTGGTGCAATTCTACG
1 TGGCACTCTGGTGCAATTCTACG
96564 TGGCACT-TCGGTGCAATT
1 TGGCACTCT-GGTGCAATT
96582 ATATGAGCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTCTGGTGCAATTCTACG
Found at i:100342 original size:26 final size:26
Alignment explanation
Indices: 100313--100369 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
100303 TATGTGATGT
100313 TATGTGTACTCTGTTGTGAAATTATA
1 TATGTGTACTCTGTTGTGAAATTATA
100339 TATGTGTACTCTGTTGTGAAATTATA
1 TATGTGTACTCTGTTGTGAAATTATA
100365 TATGT
1 TATGT
100370 TTTCTATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.47
Consensus pattern (26 bp):
TATGTGTACTCTGTTGTGAAATTATA
Found at i:100684 original size:74 final size:74
Alignment explanation
Indices: 100562--100709 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
100552 ATCGACTTAG
100562 CGTGTGATTGTTTCACACGTAGGTTTGGAAAGCGAAAAGAAAAGTAAAGAAGAACAAGACATGTC
1 CGTGTGATTGTTTCACACGTAGGTTTGGAAAGCGAAAAGAAAAGTAAAGAAGAACAAGACATGTC
100627 AGTTCTCCT
66 AGTTCTCCT
* *
100636 CGTGTGATTGTTTCACACGTAGGTTTGGAAAGCGAAAAGAAAATTAAAGAAGAACAAGATATGTC
1 CGTGTGATTGTTTCACACGTAGGTTTGGAAAGCGAAAAGAAAAGTAAAGAAGAACAAGACATGTC
100701 AGTTCTCCT
66 AGTTCTCCT
100710 TACCGAATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (74 bp):
CGTGTGATTGTTTCACACGTAGGTTTGGAAAGCGAAAAGAAAAGTAAAGAAGAACAAGACATGTC
AGTTCTCCT
Found at i:100936 original size:21 final size:21
Alignment explanation
Indices: 100910--100973 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
100900 CCGAAAGTTA
100910 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAGGGTATCGGTACC
**
100931 CTGTAGCAGGGTATTAGTACC
1 CTGTAGCAGGGTATCGGTACC
100952 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAGGGTATCGGTACC
100973 C
1 C
100974 CTATGGCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGTATCGGTACC
Found at i:105208 original size:16 final size:16
Alignment explanation
Indices: 105187--105219 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
105177 TATGGAGTTT
*
105187 AACACAAGAAAAGAAA
1 AACACAAAAAAAGAAA
105203 AACACAAAAAAAGAAA
1 AACACAAAAAAAGAAA
105219 A
1 A
105220 CCATTTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (16 bp):
AACACAAAAAAAGAAA
Found at i:107260 original size:19 final size:19
Alignment explanation
Indices: 107211--107262 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
107201 TAATTAAAAA
*
107211 ATTA-AAAATAAATATTAT
1 ATTATAAAATAAAAATTAT
*
107229 ATTATAATCATAATAAATTAT
1 ATTATAA-AATAA-AAATTAT
107250 -TTATAAAATAAAA
1 ATTATAAAATAAAA
107263 TAAAAATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 10 0.36
21 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTATAAAATAAAAATTAT
Found at i:115825 original size:8 final size:8
Alignment explanation
Indices: 115812--115852 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
115802 CTCATTTTCA
115812 GAGAATTT
1 GAGAATTT
115820 GAGAATTT
1 GAGAATTT
*
115828 -AGAGTTT
1 GAGAATTT
*
115835 GGGAATTT
1 GAGAATTT
115843 GAGAATTT
1 GAGAATTT
115851 GA
1 GA
115853 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:116151 original size:128 final size:128
Alignment explanation
Indices: 115923--116679 Score: 1338
Period size: 128 Copynumber: 5.9 Consensus size: 128
115913 TAATCGGAGT
115923 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
115988 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
116051 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116116 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
116179 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116244 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
116307 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116372 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
116435 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
116499 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * * *
116563 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGTGCGTCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
116627 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
116680 AATCAGGTAA
Statistics
Matches: 616, Mismatches: 12, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
127 1 0.00
128 615 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:117141 original size:33 final size:34
Alignment explanation
Indices: 117080--117179 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
117070 AAATTTAATG
*
117080 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
117114 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
117147 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
117180 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:117728 original size:21 final size:21
Alignment explanation
Indices: 117698--117791 Score: 138
Period size: 21 Copynumber: 4.5 Consensus size: 21
117688 TATGGTATAA
*
117698 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
117719 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
117740 AACCCTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
*
117761 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
117782 AACCCTGCGG
1 AACCCTGCGG
117792 AGATGGCATA
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.04
21 60 0.90
22 4 0.06
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:117821 original size:21 final size:21
Alignment explanation
Indices: 117795--117842 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
117785 CCTGCGGAGA
*
117795 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
117816 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
117837 GGGCAT
1 TGGCAT
117843 GTACCCTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:119608 original size:34 final size:31
Alignment explanation
Indices: 119565--119653 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
119555 TTAATAATTC
*
119565 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
119599 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
119630 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
119654 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:119610 original size:31 final size:33
Alignment explanation
Indices: 119568--119642 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
119558 ATAATTCTAA
* * *
119568 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
119600 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
119631 ATAAAAAATAAT
1 ATAAAAAATAAT
119643 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:119873 original size:16 final size:16
Alignment explanation
Indices: 119852--119887 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
119842 TTAATGGAAG
119852 GCGCGTCCCCGGGGAT
1 GCGCGTCCCCGGGGAT
119868 GCGCGTCCCCGGGGAT
1 GCGCGTCCCCGGGGAT
119884 GCGC
1 GCGC
119888 TTTCCACACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.39, G:0.44, T:0.11
Consensus pattern (16 bp):
GCGCGTCCCCGGGGAT
Found at i:120238 original size:3 final size:3
Alignment explanation
Indices: 120232--120284 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
120222 ATATTAAAGA
* *
120232 TAT TAT TAT TTT TAT TAAT T-T TAT TAT TAT TTT TAT TGAT T-T TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
120277 TAT TAT TA
1 TAT TAT TA
120285 GATATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:120247 original size:21 final size:21
Alignment explanation
Indices: 120223--120268 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
120213 AGTAAAAAAA
120223 TATTAAAGATATTATTATTTT
1 TATTAAAGATATTATTATTTT
***
120244 TATTAATTTTATTATTATTTT
1 TATTAAAGATATTATTATTTT
120265 TATT
1 TATT
120269 GATTTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTAAAGATATTATTATTTT
Found at i:120273 original size:21 final size:21
Alignment explanation
Indices: 120232--120283 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
120222 ATATTAAAGA
120232 TATTATTATTTTTATTAATTT
1 TATTATTATTTTTATTAATTT
*
120253 TATTATTATTTTTATTGATTT
1 TATTATTATTTTTATTAATTT
120274 TATTATTATT
1 TATTATTATT
120284 AGATATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTATTATTTTTATTAATTT
Found at i:120291 original size:18 final size:18
Alignment explanation
Indices: 120231--120294 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
120221 AATATTAAAG
*
120231 ATATTATTATTTTTATTA
1 ATATTATTATTATTATTA
* *
120249 ATTTTATTATTATTTTTA
1 ATATTATTATTATTATTA
*
120267 TTGATT-TTATTATTATTA
1 AT-ATTATTATTATTATTA
120285 GATATT-TTAT
1 -ATATTATTAT
120295 CGAAAATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 34 0.92
19 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATATTATTATTATTATTA
Found at i:120338 original size:21 final size:21
Alignment explanation
Indices: 120309--120350 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
120299 AATGTTAAAA
*
120309 AATATTAATATTTTAAATAAT
1 AATAATAATATTTTAAATAAT
120330 AATAATAATATTTTAAATAAT
1 AATAATAATATTTTAAATAAT
120351 TTTTACCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATAATATTTTAAATAAT
Found at i:131938 original size:14 final size:14
Alignment explanation
Indices: 131910--131940 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
131900 TAATATTAAA
*
131910 ATAAAAATATTTAT
1 ATAAAAATATATAT
131924 ATAAAAATATATAT
1 ATAAAAATATATAT
131938 ATA
1 ATA
131941 TTTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAAAATATATAT
Found at i:134784 original size:13 final size:13
Alignment explanation
Indices: 134766--134791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
134756 ATTTGATCAG
134766 ATATGGTATATTT
1 ATATGGTATATTT
134779 ATATGGTATATTT
1 ATATGGTATATTT
134792 TTGGCTCAAC
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATATGGTATATTT
Found at i:147660 original size:29 final size:28
Alignment explanation
Indices: 147618--147675 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 28
147608 TGTGTCCATA
147618 TAGAGTAACTTACACTAGTGCTCTCTTTT
1 TAGAGTAACTTACACTAGTGCTCT-TTTT
147647 TAGAGT-ACATTACACTAGTGCTCTTTTT
1 TAGAGTAAC-TTACACTAGTGCTCTTTTT
147675 T
1 T
147676 CAGTCTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (28 bp):
TAGAGTAACTTACACTAGTGCTCTTTTT
Found at i:148675 original size:30 final size:31
Alignment explanation
Indices: 148630--148697 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
148620 CTTTTATTAG
*
148630 ATTTAAGAGTTAAATTAATATTTTATGTAAA
1 ATTTAAGAGTTAAATTAATATTTTATCTAAA
148661 ATTTAAGA-TTAAATTAATATTTTATCTAAA
1 ATTTAAGAGTTAAATTAATATTTTATCTAAA
148691 A-TTAAGA
1 ATTTAAGA
148698 ACAATTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 6 0.17
30 22 0.61
31 8 0.22
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTTAAGAGTTAAATTAATATTTTATCTAAA
Found at i:152450 original size:130 final size:130
Alignment explanation
Indices: 152217--152470 Score: 499
Period size: 130 Copynumber: 2.0 Consensus size: 130
152207 TGTGATAGTA
*
152217 AATTTTAAGCTCATAAGATTGTACATTAGTTAAGAGACATATATTGTCTAAGTGAAAATTTGTTA
1 AATTTTAAGCTCATAAGATTGTACATTAGTTAAGAGACATATATTGTCTAAGTGAAAAATTGTTA
152282 GATTAAAATCTAGAAAATAAAACAAAAAAAATTAACAGAAAACTAAAAAAATGAATAAATAAAAG
66 GATTAAAATCTAGAAAATAAAACAAAAAAAATTAACAGAAAACTAAAAAAATGAATAAATAAAAG
152347 AATTTTAAGCTCATAAGATTGTACATTAGTTAAGAGACATATATTGTCTAAGTGAAAAATTGTTA
1 AATTTTAAGCTCATAAGATTGTACATTAGTTAAGAGACATATATTGTCTAAGTGAAAAATTGTTA
152412 GATTAAAATCTAGAAAATAAAACAAAAAAAATTAACAGAAAACTAAAAAAATGAATAAA
66 GATTAAAATCTAGAAAATAAAACAAAAAAAATTAACAGAAAACTAAAAAAATGAATAAA
152471 ATAATTTTCA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 123 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (130 bp):
AATTTTAAGCTCATAAGATTGTACATTAGTTAAGAGACATATATTGTCTAAGTGAAAAATTGTTA
GATTAAAATCTAGAAAATAAAACAAAAAAAATTAACAGAAAACTAAAAAAATGAATAAATAAAAG
Found at i:165186 original size:24 final size:26
Alignment explanation
Indices: 165154--165220 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 26
165144 AAGTTTGATG
165154 TATTTATAGATTATTACTTT-AA-TT
1 TATTTATAGATTATTACTTTGAAGTT
*
165178 TATTTATAGATTGTTACTTTGAAGTT
1 TATTTATAGATTATTACTTTGAAGTT
*
165204 TAGGTTATAGAATTATT
1 TA-TTTATAG-ATTATT
165221 TCACACACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 19 0.53
25 2 0.06
26 4 0.11
27 6 0.17
28 5 0.14
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (26 bp):
TATTTATAGATTATTACTTTGAAGTT
Found at i:196749 original size:32 final size:31
Alignment explanation
Indices: 196675--196751 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
196665 CTAATGTGAC
* *
196675 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
196706 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
196738 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
196752 CACAGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:198357 original size:20 final size:20
Alignment explanation
Indices: 198328--198379 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
198318 AAGTAAGAGA
198328 AGTATCGATACTCTCTATGT
1 AGTATCGATACTCTCTATGT
*
198348 AGTATGGATACTCTCTATGT
1 AGTATCGATACTCTCTATGT
198368 AGTATCGATACT
1 AGTATCGATACT
198380 ATCAGTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTCTCTATGT
Found at i:207246 original size:167 final size:166
Alignment explanation
Indices: 206969--207292 Score: 508
Period size: 167 Copynumber: 1.9 Consensus size: 166
206959 CCAGAGCTAC
* * *
206969 ATCACATGCAGATACTGATCTAAAATGCAGTTTCTAAATTTTACTATAGAGGATTTAACTGAATC
1 ATCACATGAAGATACTAATCTAAAATGAAGTTTCTAAATTTTACTATAGAGGATTTAACTGAATC
* ** *
207034 ACATTAATAGGAAACGTCAATGTACACTATAATATTAGCAATATCTCCAATTTCACT-CAGTTCA
66 ACATTAATAGGAAACATCAATGTACACTATAATATTAAAAATATCTCCAATTTAACTCCAGTTCA
207098 ACAAAACCATTATAAAGGCATTGTTTAACAGAATCAT
131 ACAAAACCATTATAAAGGCATT-TTTAACAGAATCAT
207135 ATCACATGAAGATACTAATCTAAAACTGAAGTTTCTAAATTTTACTATAG-GGTATTTAACTGAA
1 ATCACATGAAGATACTAATCTAAAA-TGAAGTTTCTAAATTTTACTATAGAGG-ATTTAACTGAA
* *
207199 TCACGTTAATAGGAAACATCAATGTTCACTATAATATTAAAAATATCTCCAATTTAACTCCCAGT
64 TCACATTAATAGGAAACATCAATGTACACTATAATATTAAAAATATCTCCAATTTAACT-CCAGT
*
207264 TCAACAAAACCATTATAGAGGCATTTTTA
128 TCAACAAAACCATTATAAAGGCATTTTTA
207293 TACATATAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
166 25 0.17
167 87 0.60
168 4 0.03
169 28 0.19
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (166 bp):
ATCACATGAAGATACTAATCTAAAATGAAGTTTCTAAATTTTACTATAGAGGATTTAACTGAATC
ACATTAATAGGAAACATCAATGTACACTATAATATTAAAAATATCTCCAATTTAACTCCAGTTCA
ACAAAACCATTATAAAGGCATTTTTAACAGAATCAT
Found at i:212059 original size:16 final size:14
Alignment explanation
Indices: 212038--212071 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
212028 ATTTCTTGAT
212038 TTTTTTAATATAATAA
1 TTTTTTAA-ATAA-AA
212054 TTTTTTAAATAAAA
1 TTTTTTAAATAAAA
212068 TTTT
1 TTTT
212072 CAAAATGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 4 0.22
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTTAAATAAAA
Found at i:212361 original size:22 final size:21
Alignment explanation
Indices: 212314--212363 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
212304 CCATTAATCT
* *
212314 ATTAATTTTATAAATAGGTCA
1 ATTAATTTTAAAAATAGATCA
* *
212335 TTTAATTATTAAAAATATATCA
1 ATTAATT-TTAAAAATAGATCA
212357 ATTAATT
1 ATTAATT
212364 CAAATGATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTAATTTTAAAAATAGATCA
Found at i:213752 original size:39 final size:40
Alignment explanation
Indices: 213709--213786 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
213699 ACATGACTTA
* *
213709 CACGT-GGGTATAGCG-CGCCCCCTGTTCTACGCTATACGC
1 CACGTAGGGTATAGCGCCG-CCCCTGCTCAACGCTATACGC
213748 CACGTAGGGGTATAGCGCCGCCCCTGCTCAACGCTATAC
1 CACGTA-GGGTATAGCGCCGCCCCTGCTCAACGCTATAC
213787 CTTGGTACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 5 0.15
41 27 0.79
42 2 0.06
ACGTcount: A:0.18, C:0.36, G:0.26, T:0.21
Consensus pattern (40 bp):
CACGTAGGGTATAGCGCCGCCCCTGCTCAACGCTATACGC
Found at i:214034 original size:11 final size:12
Alignment explanation
Indices: 214000--214034 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
213990 AGTTCGTGCG
214000 ATTTTTCGTTATA
1 ATTTTT-GTTATA
214013 ATTTTTGTTATA
1 ATTTTTGTTATA
214025 ATTTTT-TTAT
1 ATTTTTGTTAT
214035 TATACTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.18
12 12 0.55
13 6 0.27
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (12 bp):
ATTTTTGTTATA
Found at i:217383 original size:35 final size:34
Alignment explanation
Indices: 217298--217384 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
217288 ATTTGGTATT
*
217298 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
217332 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
217370 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
217385 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:217619 original size:9 final size:9
Alignment explanation
Indices: 217602--217645 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
217592 TTCGCTATCA
217602 TCATCGTCG
1 TCATCGTCG
**
217611 TTGTCGTCG
1 TCATCGTCG
217620 TCATCGTCG
1 TCATCGTCG
*
217629 TTATCGTCG
1 TCATCGTCG
*
217638 TCGTCGTC
1 TCATCGTC
217646 ATGAGCAGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.07, C:0.30, G:0.25, T:0.39
Consensus pattern (9 bp):
TCATCGTCG
Found at i:217625 original size:18 final size:18
Alignment explanation
Indices: 217602--217645 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
217592 TTCGCTATCA
*
217602 TCATCGTCGTTGTCGTCG
1 TCATCGTCGTTATCGTCG
217620 TCATCGTCGTTATCGTCG
1 TCATCGTCGTTATCGTCG
*
217638 TCGTCGTC
1 TCATCGTC
217646 ATGAGCAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.30, G:0.25, T:0.39
Consensus pattern (18 bp):
TCATCGTCGTTATCGTCG
Found at i:223952 original size:42 final size:42
Alignment explanation
Indices: 223891--223970 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
223881 GGTACTGCAT
* *
223891 AGGTTTCTTGATTGTGATTTT-GTTCAGTTGATTTCTTTTCTC
1 AGGTTTCTCGATTGCGATTTTAGTTCAG-TGATTTCTTTTCTC
* *
223933 AGGTTTCTCGATTGCGATTTTATTTTAGTGATTTCTTT
1 AGGTTTCTCGATTGCGATTTTAGTTCAGTGATTTCTTT
223971 AATTTCTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 29 0.88
43 4 0.12
ACGTcount: A:0.14, C:0.11, G:0.19, T:0.56
Consensus pattern (42 bp):
AGGTTTCTCGATTGCGATTTTAGTTCAGTGATTTCTTTTCTC
Found at i:231878 original size:15 final size:15
Alignment explanation
Indices: 231858--231888 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
231848 AAAGGAAGTG
231858 CAAAACATAATACAT
1 CAAAACATAATACAT
231873 CAAAACATAATACAT
1 CAAAACATAATACAT
231888 C
1 C
231889 GAAGGTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (15 bp):
CAAAACATAATACAT
Found at i:236903 original size:20 final size:22
Alignment explanation
Indices: 236858--236915 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
236848 GCATGGGTAG
236858 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
236882 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
236902 TGTATCGATGCACT
1 TGCATCGATGCACT
236916 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:238461 original size:64 final size:65
Alignment explanation
Indices: 238385--238508 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
238375 ATGCATGAAT
* * *
238385 TTAAATAGAAAACATCGAATAGGA-TTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCC
1 TTAAATAGAAAACATCGAAT-GCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCATCCCC
238449 A
65 A
*
238450 TTAAATA-AAAACATCGAATGCATTTTATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCAT
238509 ACATTCATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 2 0.04
64 45 0.83
65 7 0.13
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCATCCCCA
Found at i:239237 original size:30 final size:30
Alignment explanation
Indices: 239201--239264 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
239191 AAGGAACATA
* *
239201 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
239231 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
239261 TGGA
1 TGGA
239265 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:242703 original size:64 final size:65
Alignment explanation
Indices: 242627--242750 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
242617 ATGCATGAAT
* * *
242627 TTAAATAGAAAACATCGAATAGGA-TTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCC
1 TTAAATAGAAAACATCGAAT-GCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCATCCCC
242691 A
65 A
*
242692 TTAAATA-AAAACATCGAATGCATTTTATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCAT
242751 ACATTCATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 2 0.04
64 45 0.83
65 7 0.13
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCATCCCCA
Found at i:243461 original size:30 final size:30
Alignment explanation
Indices: 243425--243488 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
243415 AAGGAACATA
* *
243425 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
243455 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
243485 TGGA
1 TGGA
243489 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:244764 original size:2 final size:2
Alignment explanation
Indices: 244757--244798 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
244747 GAACATGTGA
244757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244799 GATAAGACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245226 original size:23 final size:23
Alignment explanation
Indices: 245190--245257 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
245180 AACCTTATAT
*
245190 GGCACTTCGGTGCATTTCTTCGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
245213 GGCACTACGATGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
245236 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
245258 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:246490 original size:16 final size:16
Alignment explanation
Indices: 246466--246496 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
246456 ATTTAGGTAA
246466 TTTTAAAAATTTTATT
1 TTTTAAAAATTTTATT
*
246482 TTTTGAAAATTTTAT
1 TTTTAAAAATTTTAT
246497 AAAGGCGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTAAAAATTTTATT
Found at i:246846 original size:21 final size:21
Alignment explanation
Indices: 246822--246862 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
246812 ATTATATTTT
246822 TAAAAATTATAAAATAATTAA
1 TAAAAATTATAAAATAATTAA
**
246843 TAAATTTTATAAAATAATTA
1 TAAAAATTATAAAATAATTA
246863 TTACGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATTATAAAATAATTAA
Found at i:252658 original size:120 final size:116
Alignment explanation
Indices: 252428--252662 Score: 416
Period size: 120 Copynumber: 2.0 Consensus size: 116
252418 TATCAAAACT
* *
252428 GCATCTAATAGGTTGGTATCATTCCCATTAAAGAATCCCCCTTCCACACAAAAAAACAAGGGAAA
1 GCATCAAATAGGTTGGTATCATTCCCATTAAAGAATCCCCCTTCCACAAAAAAAAACAAGGGAAA
252493 GAAAATAATTGTCAGCAGTGATGTTAAAGAGGTTTTATTGTTACTTGTGAG
66 GAAAATAATTGTCAGCAGTGATGTTAAAGAGGTTTTATTGTTACTTGTGAG
252544 GCATCAAATAGGTTGGTATCATTCCCATTAAAGAATCCCCCTTCACACGAAAAAAAAACAAGGGA
1 GCATCAAATAGGTTGGTATCATTCCCATTAAAGAATCCCCCTTC-CAC-AAAAAAAAACAAGGGA
252609 AAGAAAAAATAATTGTCAGCAGTGATGTTAAAGAGGTTTTATTGTTACTTGTGA
64 AAG--AAAATAATTGTCAGCAGTGATGTTAAAGAGGTTTTATTGTTACTTGTGA
252663 AGTTCCTCAT
Statistics
Matches: 113, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
116 43 0.38
117 3 0.03
118 18 0.16
120 49 0.43
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (116 bp):
GCATCAAATAGGTTGGTATCATTCCCATTAAAGAATCCCCCTTCCACAAAAAAAAACAAGGGAAA
GAAAATAATTGTCAGCAGTGATGTTAAAGAGGTTTTATTGTTACTTGTGAG
Found at i:257874 original size:16 final size:14
Alignment explanation
Indices: 257843--257879 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
257833 TTTTTTATAT
257843 TTATAAAATTAATA
1 TTATAAAATTAATA
257857 TTATAATAATTAAATA
1 TTATAA-AATT-AATA
257873 TTATAAA
1 TTATAAA
257880 TAAGTAGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATAAAATTAATA
Found at i:264485 original size:27 final size:27
Alignment explanation
Indices: 264447--264512 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
264437 AAATCCGATT
*
264447 AAAAGAAAGACCTTTTTTGTAAAACAG
1 AAAACAAAGACCTTTTTTGTAAAACAG
264474 AAAACAAAGACCTTTTTTGTAAAACAG
1 AAAACAAAGACCTTTTTTGTAAAACAG
264501 AAAACAAAGACC
1 AAAACAAAGACC
264513 CGTACTTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (27 bp):
AAAACAAAGACCTTTTTTGTAAAACAG
Found at i:266134 original size:21 final size:22
Alignment explanation
Indices: 266093--266134 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
266083 TTTATAATAT
*
266093 TAAATTTAAATTAATTGATTAA
1 TAAATTTAAATTAATTAATTAA
266115 TAAA-TTAAA-TACATTAATTA
1 TAAATTTAAATTA-ATTAATTA
266135 TGACCAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.67
22 4 0.22
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTTAAATTAATTAATTAA
Found at i:269211 original size:6 final size:6
Alignment explanation
Indices: 269200--269232 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
269190 TCTTCTTCGT
*
269200 CTAGGA CTAGGA CTAGGA CTAGGA CTATGA CTA
1 CTAGGA CTAGGA CTAGGA CTAGGA CTAGGA CTA
269233 CCACAATGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.21
Consensus pattern (6 bp):
CTAGGA
Found at i:270142 original size:72 final size:71
Alignment explanation
Indices: 269800--270142 Score: 348
Period size: 72 Copynumber: 4.8 Consensus size: 71
269790 GGGCTTGAAT
* * * * * *
269800 CAGTTGAAGAGGAAGCCAATTTGGTTGCC-CAAAGCCAAGTAGAAGCAGAAGCAGAGGATGGGGA
1 CAGTTGAAGAGGAAGCAAATATGG-T-CCTGAAAGTCAAGTACAAGCAGAAGCAGCGGA-GGGGA
* *
269864 A-AAGGAAA
63 AGCAGAAAA
* * * *
269872 CAGTTGAACAGGAAGCAAATACCGTTCCTGAAAGTCAAGTACAAGCAGAAGCAACGGAGGGGAAG
1 CAGTTGAAGAGGAAGCAAATA-TGGTCCTGAAAGTCAAGTACAAGCAGAAGCAGCGGAGGGGAAG
269937 CAGAAAA
65 CAGAAAA
* * * *** * *
269944 TAGTTGAAGAGGAAACAAATATGGCTCCCGAAAGTTGTGTACAAGAAGAAGCAGTGGAGGGGAAG
1 CAGTTGAAGAGGAAGCAAATATGG-TCCTGAAAGTCAAGTACAAGCAGAAGCAGCGGAGGGGAAG
270009 CAGAAAA
65 CAGAAAA
* * * **** *
270016 CAGTTGAAGAGGAAACAAATATAGCTCATGAAAGTTGTTTACAAGCAGAAGCAGCGCAGGGGAAG
1 CAGTTGAAGAGGAAGCAAATAT-GGTCCTGAAAGTCAAGTACAAGCAGAAGCAGCGGAGGGGAAG
270081 CAGAAAA
65 CAGAAAA
*
270088 CAATTGAAGAGGAAGCAAATATGGTCACTGAAAGTCAAGTACAAGCAGAAGCAGC
1 CAGTTGAAGAGGAAGCAAATATGGTC-CTGAAAGTCAAGTACAAGCAGAAGCAGC
270143 AAACGGGAAG
Statistics
Matches: 225, Mismatches: 40, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
71 12 0.05
72 211 0.94
73 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.14
Consensus pattern (71 bp):
CAGTTGAAGAGGAAGCAAATATGGTCCTGAAAGTCAAGTACAAGCAGAAGCAGCGGAGGGGAAGC
AGAAAA
Found at i:270151 original size:144 final size:144
Alignment explanation
Indices: 269911--270171 Score: 346
Period size: 144 Copynumber: 1.8 Consensus size: 144
269901 GAAAGTCAAG
* * *
269911 TACAAGCAGAAGCAACGGAGGGGAAGCAGAAAATAGTTGAAGAGGAAACAAATATGGCTCCCGAA
1 TACAAGCAGAAGCAACGCAGGGGAAGCAGAAAACAATTGAAGAGGAAACAAATATGGCTCCCGAA
*** *** * *
269976 AGTTGTGTACAAGAAGAAGCAGTGGAGGGGAAGCA-GAAAACAGTTGAAGAGGAAACAAATATAG
66 AGTCAAGTACAAGAAGAAGCAGCAAACGGGAAGCAGGAAAA-AGTTCAAGAGGAAACAAATATAG
270040 CTCATGAAAGTTGTT
130 CTCATGAAAGTTGTT
* * *
270055 TACAAGCAGAAGCAGCGCAGGGGAAGCAGAAAACAATTGAAGAGGAAGCAAATATGG-TCACTGA
1 TACAAGCAGAAGCAACGCAGGGGAAGCAGAAAACAATTGAAGAGGAAACAAATATGGCTC-CCGA
* *
270119 AAGTCAAGTACAAGCAGAAGCAGCAAACGGGAAGGAGGAAAAAGTTCAAGAGG
65 AAGTCAAGTACAAGAAGAAGCAGCAAACGGGAAGCAGGAAAAAGTTCAAGAGG
270172 GTGTAGATTT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
143 2 0.02
144 92 0.93
145 5 0.05
ACGTcount: A:0.44, C:0.13, G:0.30, T:0.13
Consensus pattern (144 bp):
TACAAGCAGAAGCAACGCAGGGGAAGCAGAAAACAATTGAAGAGGAAACAAATATGGCTCCCGAA
AGTCAAGTACAAGAAGAAGCAGCAAACGGGAAGCAGGAAAAAGTTCAAGAGGAAACAAATATAGC
TCATGAAAGTTGTT
Found at i:270392 original size:51 final size:51
Alignment explanation
Indices: 270294--270394 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
270284 AGAGAGGAAG
**
270294 GGCAGCGTGAGAGCACTGGTCGGGGCATTTGAATCCCATGGCAAAAACAAC
1 GGCAGCGTGAGAGCACTGGTCGGGGCATTTGAATCCCACAGCAAAAACAAC
* * *
270345 GGCAGGGTGAGAGCACTGGTTGGGGCATTTGAATCTCACAG-ATAAAACAA
1 GGCAGCGTGAGAGCACTGGTCGGGGCATTTGAATCCCACAGCA-AAAACAA
270395 ACTTCAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.02
51 43 0.98
ACGTcount: A:0.31, C:0.20, G:0.32, T:0.18
Consensus pattern (51 bp):
GGCAGCGTGAGAGCACTGGTCGGGGCATTTGAATCCCACAGCAAAAACAAC
Found at i:277286 original size:27 final size:27
Alignment explanation
Indices: 277224--277294 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 27
277214 CATGTTGAAT
277224 GAAAGAAAGAAGAAAAAAAACAGCAGTTC
1 GAAAGAAA-AAG-AAAAAAACAGCAGTTC
* *
277253 G--AG--AAAGAAAAAAATAGCTGTTC
1 GAAAGAAAAAGAAAAAAACAGCAGTTC
277276 GAAAGAAAAAGAGAAAAAA
1 GAAAGAAAAAGA-AAAAAA
277295 AGACATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
23 15 0.43
24 3 0.09
25 3 0.09
27 7 0.20
28 6 0.17
29 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.21, T:0.08
Consensus pattern (27 bp):
GAAAGAAAAAGAAAAAAACAGCAGTTC
Found at i:282551 original size:23 final size:23
Alignment explanation
Indices: 282523--282584 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 23
282513 ATTTCGTCTC
282523 CTATATATATTTTTATTTATTTA
1 CTATATATATTTTTATTTATTTA
**
282546 CTATAT-TCCTTTT-TTTATTTA
1 CTATATATATTTTTATTTATTTA
282567 -TATTATACTATTTTTATT
1 CTA-TATA-TATTTTTATT
282585 ATAAATATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
22 5 0.16
23 11 0.35
24 2 0.06
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (23 bp):
CTATATATATTTTTATTTATTTA
Done.