Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007805.1 Hibiscus syriacus cultivar Beakdansim tig00110123_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: 2708727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:5435 original size:12 final size:11
Alignment explanation
Indices: 5369--5436 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
5359 AAAATTACAT
5369 TATTAAAAATA
1 TATTAAAAATA
5380 TATTAAAAATA
1 TATTAAAAATA
* * ***
5391 CACTATTGATA
1 TATTAAAAATA
5402 -ATTATAAAA-A
1 TATTA-AAAATA
5412 T-TTAAAAATA
1 TATTAAAAATA
5422 TATTAAAAATTA
1 TATTAAAAA-TA
5434 TAT
1 TAT
5437 AATACAATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
9 4 0.09
10 9 0.21
11 25 0.58
12 5 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:6399 original size:24 final size:25
Alignment explanation
Indices: 6356--6404 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
6346 ACTTGTTATG
6356 AGGCTTATATAATTGATTGATTGTA
1 AGGCTTATATAATTGATTGATTGTA
6381 AGGCTTATAT-ATTGATTGATTGTA
1 AGGCTTATATAATTGATTGATTGTA
6405 GGAAAACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (25 bp):
AGGCTTATATAATTGATTGATTGTA
Found at i:7176 original size:11 final size:12
Alignment explanation
Indices: 7158--7223 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
7148 CTAACTAGTT
7158 TCGAGCTTCAAA
1 TCGAGCTTCAAA
7170 T-GAGCTT-AAA
1 TCGAGCTTCAAA
7180 TCGAGC-TCAAA
1 TCGAGCTTCAAA
7191 GTCGAGC-TCAAAA
1 -TCGAGCTTC-AAA
*
7204 TCAAG-TTCAAAA
1 TCGAGCTTC-AAA
7216 TCGAGCTT
1 TCGAGCTT
7224 GAGTCTTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 23 0.50
13 5 0.11
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (12 bp):
TCGAGCTTCAAA
Found at i:7551 original size:2 final size:2
Alignment explanation
Indices: 7544--7587 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
7534 AATTCGTATG
7544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7586 TA
1 TA
7588 GTAATTGTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11663 original size:18 final size:19
Alignment explanation
Indices: 11642--11678 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
11632 CATACAAGTG
*
11642 TTTTT-TTTGAAATT-TTA
1 TTTTTATTTAAAATTATTA
11659 TTTTTATTTAAAATTATTA
1 TTTTTATTTAAAATTATTA
11678 T
1 T
11679 ACCTTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTATTTAAAATTATTA
Found at i:13027 original size:16 final size:17
Alignment explanation
Indices: 12998--13046 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
12988 TTTGACTTCA
12998 TAAAATTA-TAAATAAT
1 TAAAATTATTAAATAAT
*
13014 TAATA-TATTAAAT-AT
1 TAAAATTATTAAATAAT
*
13029 TAAAATTATAAAATAAT
1 TAAAATTATTAAATAAT
13046 T
1 T
13047 TTAAATACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 8 0.30
16 16 0.59
17 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTATTAAATAAT
Found at i:18380 original size:17 final size:17
Alignment explanation
Indices: 18358--18414 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
18348 TTGACCGAGT
*
18358 CGATCTCGAGTAGCTCA
1 CGATCTCGAATAGCTCA
*
18375 CGATCTCGAATAGCTAA
1 CGATCTCGAATAGCTCA
18392 CGATCTCGAATAGCTCA
1 CGATCTCGAATAGCTCA
18409 CGATCT
1 CGATCT
18415 ATCTCGTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (17 bp):
CGATCTCGAATAGCTCA
Found at i:19376 original size:18 final size:18
Alignment explanation
Indices: 19353--19387 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19343 AAAATTTTCT
*
19353 AAGCATGTAAATATTTTG
1 AAGCATGTAAACATTTTG
19371 AAGCATGTAAACATTTT
1 AAGCATGTAAACATTTT
19388 TTCCAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (18 bp):
AAGCATGTAAACATTTTG
Found at i:19930 original size:3 final size:3
Alignment explanation
Indices: 19919--19968 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
19909 TATAAAAAAA
*
19919 TAT TA- TAT TAT TAT TAT TAT TAT TA- TAT TAA T-T TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
19962 AAT TAT T
1 TAT TAT T
19969 TTGCGACCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.13
3 31 0.79
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:19941 original size:17 final size:17
Alignment explanation
Indices: 19919--19968 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
19909 TATAAAAAAA
19919 TATTATATTATTATTAT
1 TATTATATTATTATTAT
*
19936 TATTAT-TATATTAAT-T
1 TATTATAT-TATTATTAT
*
19952 TA-TATATTATAATTAT
1 TATTATATTATTATTAT
19968 T
1 T
19969 TTGCGACCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATATTATTATTAT
Found at i:20256 original size:23 final size:23
Alignment explanation
Indices: 20209--20257 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20199 AATAACAGAT
* **
20209 TAGGTAGAGTTTATATAATGTAA
1 TAGGTAGAGCTTATATAATAAAA
*
20232 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGAGCTTATATAATAAAA
20255 TAG
1 TAG
20258 ACATTTAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (23 bp):
TAGGTAGAGCTTATATAATAAAA
Found at i:20318 original size:87 final size:87
Alignment explanation
Indices: 20172--20334 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 87
20162 AATGTTATAT
* *
20172 CATTTAACAGGAAATATTATTAAGTACAATAACAGATTAGGTAGAGTTTATATAATGTAATAGGT
1 CATTTAACAGGAAATATTATCAAGTACAATAACAGATTAGGTAGACTTTATATAATGTAATAGGT
20237 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
* *
20259 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAG-CTCTTATATAATGTAATAGG
1 CATTTAACAGGAAATATTATCAAGTACAATAACAGATTAGGTAGACT-TTATATAATGTAATAGG
20323 TAGCGCTTATAT
65 TAGCGCTTATAT
20335 TAACCTATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
86 1 0.01
87 70 0.99
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
CATTTAACAGGAAATATTATCAAGTACAATAACAGATTAGGTAGACTTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGA
Found at i:20767 original size:200 final size:198
Alignment explanation
Indices: 20352--21061 Score: 806
Period size: 200 Copynumber: 3.5 Consensus size: 198
20342 TTTTTGAAAT
* * * * *
20352 AAACCGATATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATTATTATCGGTTACGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
*** * *
20417 TGTTTTTTACATCGATA-TAATTT-TAAATGTATCGACACTTTATGCTTGCACCTGGTTGGGCAT
66 TGTTTTTGGGATCGATACT-TTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTT-----T
** * *
20480 TCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAGAC
124 TGGTA-TTCATTCTGGACAAAAGTATCGACACAAATTAACAA-GTGTCGATACATTATGTT-GAC
*
20544 CTATTCTCTCATA
186 CTATTTTCTCATA
* *
20557 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
20622 TGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTCTATGGTTGCACCCT-TTTTGGTAT
66 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA-CCTGTTTTGGTAT
* * * *
20686 TCATTCTGGACCAAAAGTATCAACACAAATTTATCAAGTGTCGATACTTTATGCTGACCTATTTT
130 TCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGTGTCGATACATTATGTTGACCTATTTT
*
20751 ATCATA
193 CTCATA
* * * *
20757 AAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCAGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
20822 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGGGTGCACCTCG-TTTGTGCA
66 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTTTTG-GTA
* *
20886 TTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACATTATGTTGACCTGTTT
129 TTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTGTCGATACATTATGTTGACCTATTT
* *
20951 TCTAATT
192 TCTCATA
* * * * *
20958 AACCCGGTATATTTATACCAGTTACATT-ATTAATTTACCTATTACATTATAATTATTGGTTTTG
1 AAACCGGTATATTTATACCGGTTACATTGA-AAATTTACCTATTACATTATAATTATCGGTTTCG
* *
21022 ATATTTTTTGGG-TCGATAC-TTGTATAAAATGTATCGACAC
65 AT-GTTTTTGGGATCGATACTTTTTAT-AAATGTATCGACAC
21062 ATATTTAGGT
Statistics
Matches: 435, Mismatches: 56, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
199 14 0.03
200 168 0.39
201 140 0.32
202 8 0.02
205 76 0.17
206 26 0.06
207 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (198 bp):
AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCTGTTTTGGTATT
CATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACCTATTTTCTC
ATA
Found at i:23984 original size:200 final size:199
Alignment explanation
Indices: 23594--23957 Score: 516
Period size: 200 Copynumber: 1.8 Consensus size: 199
23584 TTTTTCAACA
* * * * * * * * *
23594 AAGTGTCGATACATGTTGTATACCTATTCTTTCATAAAACTGGTATATTTATACCAGTTACATTG
1 AAGTGTCGAAACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACCAGTTACATTA
* * *
23659 TAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATAGACACTTTTTAAAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATAGACACTTTTTAAAAAT
* *
23724 GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTATGGAAAAATATTATCGACACAATA
131 GTATCGACACTTTATGCGTGCACCCTTTTTGG-ATCAATTATGGAAAAATAGTATCGACACAATA
23789 TTAAT
195 TTAAT
** *
23794 AAGTGTCGAAACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACTGGTTATATTA
1 AAGTGTCGAAACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACCAGTTACATTA
* *
23859 CAAAATTACTTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGACAC-TTTTAATAAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATAGACACTTTTTAA-AAA
23923 TGTATCGACACTTTATGCGTGCAACCC-TTTTGGAT
130 TGTATCGACACTTTATGCGTGC-ACCCTTTTTGGAT
23958 GGTCACTCTA
Statistics
Matches: 144, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
199 8 0.06
200 132 0.92
201 4 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (199 bp):
AAGTGTCGAAACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACCAGTTACATTA
CAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATAGACACTTTTTAAAAAT
GTATCGACACTTTATGCGTGCACCCTTTTTGGATCAATTATGGAAAAATAGTATCGACACAATAT
TAAT
Found at i:24208 original size:251 final size:251
Alignment explanation
Indices: 23719--24189 Score: 621
Period size: 250 Copynumber: 1.9 Consensus size: 251
23709 ACACTTTTTA
*
23719 AAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTATGGAAAAATATTATCGACA
1 AAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTATGGAAAAATAGTATCGACA
** * * *
23784 CAATATTAATAAGTGTCGAAACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACT
66 CAATACAAATAAGAGTCGAAAAATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACC
* **
23849 GGTTATATTACAAAATTACTTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGACACT
131 AGTTATATTACAAAATTACCCATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGACACT
* *
23914 TTTAATAAATGTATCGACACTTTATGCGTGCAACCCTTTTGGATGGTCACTCTATG
196 TTTAATAAATGGATCGACACTTTATGCGTGAAACCCTTTTGGATGGTCACTCTATG
* * * *
23970 AAAATGTATCGACACTTTGTAG-GTTCACCCTTTTTGGCATCTATTCTGGCCAAAA-AGTATCGA
1 AAAATGTATCGACACTTTAT-GCGTTCACCCTTTTTGGCATCAATTATGG-AAAAATAGTATCGA
* * * *
24033 CACAATACAAATAAGAGTC-AATAAATGTTGTAGACATATT-TTTCATAAAACCGGTATATTTAT
64 CACAATACAAATAAGAGTCGAA-AAATATTATAGACATATTCTCTCATAAAACCGGTATATGTAT
* *
24096 ACCAGTTATATTGA-AAAATTACCCATTACATTATAATTATGGGTTTTGATGTTTTTTGGG-TCG
128 ACCAGTTATATT-ACAAAATTACCCATTACATTATAATTATGGGTTTCGAT-ATTTTTGGGATCG
** * * *
24159 TTACTTTTTATATATGGATCTACACTTTATG
191 ACACTTTTAATAAATGGATCGACACTTTATG
24190 GGAAACTTTA
Statistics
Matches: 190, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
250 94 0.49
251 91 0.48
252 5 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (251 bp):
AAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTATGGAAAAATAGTATCGACA
CAATACAAATAAGAGTCGAAAAATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACC
AGTTATATTACAAAATTACCCATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGACACT
TTTAATAAATGGATCGACACTTTATGCGTGAAACCCTTTTGGATGGTCACTCTATG
Found at i:32818 original size:21 final size:23
Alignment explanation
Indices: 32780--32821 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
32770 AAAAAATACA
*
32780 AAAATAAAAAGAATGAGAGAAAG
1 AAAATAAAAACAATGAGAGAAAG
32803 AAAA-AAAAACAA-GAGAGAA
1 AAAATAAAAACAATGAGAGAA
32822 CTTATCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (23 bp):
AAAATAAAAACAATGAGAGAAAG
Found at i:34834 original size:18 final size:18
Alignment explanation
Indices: 34811--34845 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34801 GCCCTTTTTT
*
34811 AAATAAAATGTTTTTATA
1 AAATAAAATGATTTTATA
34829 AAATAAAATGATTTTAT
1 AAATAAAATGATTTTAT
34846 TTTCCTACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATAAAATGATTTTATA
Found at i:36368 original size:18 final size:18
Alignment explanation
Indices: 36345--36381 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36335 TTTTTATGTG
*
36345 ATAAAAATTATATAATAT
1 ATAAAAATAATATAATAT
*
36363 ATAAAAATAATGTAATAT
1 ATAAAAATAATATAATAT
36381 A
1 A
36382 ATATATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAAATAATATAATAT
Found at i:42239 original size:31 final size:31
Alignment explanation
Indices: 42201--42327 Score: 209
Period size: 31 Copynumber: 4.1 Consensus size: 31
42191 GAGTCGAGGG
* *
42201 TTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATAGATAGA
*
42232 TTACCTATGTTCTTCAGGACATATAGATAGA
1 TTACCTATGTTCTTCGGGACATATAGATAGA
42263 TTACCTATGTTCTTCGGGACATATAGATAGA
1 TTACCTATGTTCTTCGGGACATATAGATAGA
* *
42294 TTACCTATGTTCTTCGGGATATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATAGATAGA
42325 TTA
1 TTA
42328 TTATATAAGT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATAGATAGA
Found at i:45466 original size:13 final size:13
Alignment explanation
Indices: 45436--45469 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
45426 TCATCTCTAC
* *
45436 TTTTATTTCTTTA
1 TTTTCTTTCATTA
45449 TTTTCTTTCATTA
1 TTTTCTTTCATTA
45462 TTTTCTTT
1 TTTTCTTT
45470 TCACAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:46503 original size:24 final size:23
Alignment explanation
Indices: 46476--46532 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
46466 TCTGTCTTTT
46476 TGGCACGTTTTAAATATGCTCTTG
1 TGGCACGTTTTAAAT-TGCTCTTG
**
46500 TGGCAC-TCTTTACGTTGCTCTTG
1 TGGCACGT-TTTAAATTGCTCTTG
*
46523 TGGCATGTTT
1 TGGCACGTTT
46533 CCTCTACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (23 bp):
TGGCACGTTTTAAATTGCTCTTG
Found at i:49930 original size:32 final size:32
Alignment explanation
Indices: 49878--49982 Score: 131
Period size: 32 Copynumber: 3.3 Consensus size: 32
49868 GCTCCTTAAA
* *
49878 ACATAGGT-ATACTGTCCATATGACTCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
* * *
49909 ACATAGGTAATTTTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
* * *
49941 ACATAGGTAATTCTGTCCATAAGTCTTAAAAT
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
49973 ACATAGGTAA
1 ACATAGGTAA
49983 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 8 0.13
32 54 0.87
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCTCAAAAG
Found at i:53687 original size:4 final size:4
Alignment explanation
Indices: 53680--53704 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
53670 ATACAGTAAG
53680 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
53705 GTCATCATTT
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:54052 original size:30 final size:31
Alignment explanation
Indices: 54013--54079 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
54003 GAAGGACCTA
* * *
54013 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCATAAAGAACCTAGGTAAACTG
* *
54043 TCCATAGGTCCTGAAGAACCTAGGTAAACTG
1 TCCATAGGTCATAAAGAACCTAGGTAAACTG
54074 TCCATA
1 TCCATA
54080 TGCTCCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (31 bp):
TCCATAGGTCATAAAGAACCTAGGTAAACTG
Found at i:54076 original size:31 final size:31
Alignment explanation
Indices: 54038--54131 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
54028 GAACCTCGGC
* *
54038 AACTGTCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTGTCCATATGCTCCT-AAGAACATAGGTA
*
54069 AACTGTCCATATGCTCCTTAGAACATAGGTA
1 AACTGTCCATATGCTCCTAAGAACATAGGTA
* * **
54100 TATTGTCCATATGTCTCAAAAG-ACATAGGTA
1 AACTGTCCATATG-CTCCTAAGAACATAGGTA
54131 A
1 A
54132 TTCTGTACAT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 42 0.81
32 10 0.19
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGCTCCTAAGAACATAGGTA
Found at i:54154 original size:32 final size:31
Alignment explanation
Indices: 54091--54195 Score: 140
Period size: 32 Copynumber: 3.3 Consensus size: 31
54081 GCTCCTTAGA
54091 ACATAGGT-ATATTGTCCATATGTCTCAAAAG
1 ACATAGGTAAT-TTGTCCATATGTCTCAAAAG
* * *
54122 ACATAGGTAATTCTGTACATATGTCCCGAAAG
1 ACATAGGTAATT-TGTCCATATGTCTCAAAAG
*
54154 ACATAGGTAATTTTGTCCATATGTCTCAAAAA
1 ACATAGGTAA-TTTGTCCATATGTCTCAAAAG
54186 ACATAGGTAA
1 ACATAGGTAA
54196 CCCTCGACTC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 9 0.14
32 53 0.83
33 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (31 bp):
ACATAGGTAATTTGTCCATATGTCTCAAAAG
Found at i:67327 original size:2 final size:2
Alignment explanation
Indices: 67320--67356 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
67310 CAATTGTAAT
67320 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67357 GTCAATGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67554 original size:27 final size:27
Alignment explanation
Indices: 67524--67579 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
67514 AATTAAATTG
*
67524 TTTTTTCTTATAATTATAATTTGAATA
1 TTTTTTCTTACAATTATAATTTGAATA
67551 TTTTTTCTTACAATTATAATTTGAATA
1 TTTTTTCTTACAATTATAATTTGAATA
67578 TT
1 TT
67580 AAATTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTTTCTTACAATTATAATTTGAATA
Found at i:68836 original size:4 final size:4
Alignment explanation
Indices: 68819--68865 Score: 62
Period size: 4 Copynumber: 12.0 Consensus size: 4
68809 TAAAGTGTAG
*
68819 AAAT AAAT ATAT AAAT AAAT AAAT AAA- ATAA- AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
68866 GTGCTGAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:68855 original size:19 final size:20
Alignment explanation
Indices: 68819--68865 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
68809 TAAAGTGTAG
*
68819 AAATAAATATATAAATAAAT
1 AAATAAATATAAAAATAAAT
68839 AAATAAA-ATAAAAATAAAT
1 AAATAAATATAAAAATAAAT
68858 AAATAAAT
1 AAATAAAT
68866 GTGCTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAATATAAAAATAAAT
Found at i:69808 original size:34 final size:31
Alignment explanation
Indices: 69735--69806 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
69725 CAAGGACAAA
*
69735 CGACCACCACACTTGGATGATTACTATACTC
1 CGACCACCACACTTGGATGATTACTATACAC
69766 CGACCACCACACTTGGATGATTACTATACAC
1 CGACCACCACACTTGGATGATTACTATACAC
69797 CGACCACCAC
1 CGACCACCAC
69807 CAGTGGTGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.21
Consensus pattern (31 bp):
CGACCACCACACTTGGATGATTACTATACAC
Found at i:71299 original size:2 final size:2
Alignment explanation
Indices: 71287--71326 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
71277 TAAAAATTAA
71287 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71327 CACTAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76634 original size:20 final size:21
Alignment explanation
Indices: 76608--76658 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
76598 CTATTTTTTC
*
76608 AAAAAAAAAAGGAAAAAAGGTA
1 AAAAAAAAAAGGAAAAAA-GCA
*
76630 AAAAAAAAAA-CAAAAAAGCA
1 AAAAAAAAAAGGAAAAAAGCA
76650 AAAAAAAAA
1 AAAAAAAAA
76659 GGCCAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 11 0.41
21 6 0.22
22 10 0.37
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAGGAAAAAAGCA
Found at i:76666 original size:21 final size:22
Alignment explanation
Indices: 76607--76666 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
76597 GCTATTTTTT
76607 CAAAAAAAAAAGG-AAAAAAGG
1 CAAAAAAAAAAGGCAAAAAAGG
* *
76628 TAAAAAAAAAA-ACAAAAAA-G
1 CAAAAAAAAAAGGCAAAAAAGG
*
76648 CAAAAAAAAAAGGCCAAAA
1 CAAAAAAAAAAGGCAAAAA
76667 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (22 bp):
CAAAAAAAAAAGGCAAAAAAGG
Found at i:83750 original size:3 final size:3
Alignment explanation
Indices: 83737--83785 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
83727 CCGGGTTTTA
* * * *
83737 ATT ATTT ATT ATT ATT ATT ATT ATT ACT AGT ATT GTT TTT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
83783 ATT
1 ATT
83786 TTCAGGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:89122 original size:6 final size:6
Alignment explanation
Indices: 89111--89158 Score: 51
Period size: 6 Copynumber: 7.2 Consensus size: 6
89101 GAACACAAAG
89111 AGAAAA AGAAAA AGGGAAAAA GAGAAAA AGAAAA AGAAAAA AGAAAA A
1 AGAAAA AGAAAA A--G-AAAA -AGAAAA AGAAAA AG-AAAA AGAAAA A
89159 AGAAGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 20 0.54
7 10 0.27
8 2 0.05
9 4 0.11
10 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:89129 original size:14 final size:14
Alignment explanation
Indices: 89107--89158 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
89097 GTGAGAACAC
89107 AAAGAGAAAAAGAA
1 AAAGAGAAAAAGAA
*
89121 AAAGGGAAAAAGAGA
1 AAAGAGAAAAAGA-A
89136 AAA-AGAAAAAGAA
1 AAAGAGAAAAAGAA
89149 AAA-AGAAAAA
1 AAAGAGAAAAA
89159 AGAAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 11 0.31
14 20 0.57
15 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAGAAAAAGAA
Found at i:89158 original size:28 final size:29
Alignment explanation
Indices: 89111--89187 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
89101 GAACACAAAG
* *
89111 AGAAAAAGAAAAAGGGAAAAAG-AGAAAA
1 AGAAAAAGAAAAAAGAAAAAAGAAGAAAA
89139 AGAAAAAGAAAAAAGAAAAAAGAAGAAAA
1 AGAAAAAGAAAAAAGAAAAAAGAAGAAAA
* * *
89168 AGGGAAAAGAAGAGAGAAAA
1 A-GAAAAAGAAAAAAGAAAA
89188 CAAATCAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 20 0.48
29 7 0.17
30 15 0.36
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (29 bp):
AGAAAAAGAAAAAAGAAAAAAGAAGAAAA
Found at i:89159 original size:14 final size:14
Alignment explanation
Indices: 89107--89167 Score: 70
Period size: 14 Copynumber: 4.2 Consensus size: 14
89097 GTGAGAACAC
89107 AAAGAGAAAAAGAAA
1 AAAGA-AAAAAGAAA
* *
89122 AAGGGAAAAAGAGAA
1 AAAGAAAAAAGA-AA
89137 AAAG-AAAAAGAAA
1 AAAGAAAAAAGAAA
89150 AAAGAAAAAAGAAGA
1 AAAGAAAAAAGAA-A
89165 AAA
1 AAA
89168 AGGGAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.15
14 22 0.55
15 12 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAGAAA
Found at i:89176 original size:16 final size:16
Alignment explanation
Indices: 89116--89180 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
89106 CAAAGAGAAA
89116 AAGAAAAAGGGAAAAAG
1 AAGAAAAA-GGAAAAAG
89133 -AGAAAAA-GAAAAAG
1 AAGAAAAAGGAAAAAG
*
89147 -A-AAAAAGAAAAAAG
1 AAGAAAAAGGAAAAAG
*
89161 AAGAAAAAGGGAAAAG
1 AAGAAAAAGGAAAAAG
89177 AAGA
1 AAGA
89181 GAGAAAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.12
14 14 0.33
15 1 0.02
16 22 0.52
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGGAAAAAG
Found at i:95451 original size:31 final size:31
Alignment explanation
Indices: 95413--95475 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
95403 AGGGTCGAGG
*
95413 GTTTACCTATGTTCTTC-GGAACATATGGACT
1 GTTTACCTAGGTTCTTCGGGAAC-TATGGACT
*
95444 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTAGGTTCTTCGGGAACTATGGACT
95475 G
1 G
95476 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGAACTATGGACT
Found at i:98747 original size:64 final size:64
Alignment explanation
Indices: 98673--98811 Score: 199
Period size: 64 Copynumber: 2.2 Consensus size: 64
98663 TACATTGAAA
* * * *
98673 CATCGATGCATCCCATTAATAATGA-AACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTG
1 CATCGATGCATCCCAGTAATAAT-ACAACATCGAATACAATTCATGCACCGATGCATAAGTAGTG
* * *
98737 CATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGCACCGATGCATCAGTAGTG
1 CATCGATGCATCCCAGTAATAATACAACATCGAATACAATTCATGCACCGATGCATAAGTAGTG
98801 CATCGATGCAT
1 CATCGATGCAT
98812 ACCTTCATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 1 0.01
64 66 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (64 bp):
CATCGATGCATCCCAGTAATAATACAACATCGAATACAATTCATGCACCGATGCATAAGTAGTG
Found at i:99506 original size:31 final size:31
Alignment explanation
Indices: 99468--99530 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
99458 AGGGTCGAGG
*
99468 GTTTACCTATGTTCTTC-GGAACATATGGACT
1 GTTTACCTAGGTTCTTCGGGAAC-TATGGACT
*
99499 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTAGGTTCTTCGGGAACTATGGACT
99530 G
1 G
99531 GTTCTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGAACTATGGACT
Found at i:99536 original size:22 final size:22
Alignment explanation
Indices: 99508--99563 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
99498 TGTTTACCTA
99508 GGTTCTTCGGGATCTATGGACT
1 GGTTCTTCGGGATCTATGGACT
99530 GGTTCTTCGGGATCTATGGACT
1 GGTTCTTCGGGATCTATGGACT
*
99552 GGTCCTTCGGGA
1 GGTTCTTCGGGA
99564 CGAATACTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.12, C:0.20, G:0.34, T:0.34
Consensus pattern (22 bp):
GGTTCTTCGGGATCTATGGACT
Found at i:107412 original size:23 final size:23
Alignment explanation
Indices: 107385--107468 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
107375 AGATCCACGA
*
107385 ATAGAGTTTTAGTACCAAAAACG
1 ATAGAGTTTCAGTACCAAAAACG
* * *
107408 ATAGAGTTCCATTACC-GAAACG
1 ATAGAGTTTCAGTACCAAAAACG
107430 AGTAGAGTTTCAGTA-CAAAAAC-
1 A-TAGAGTTTCAGTACCAAAAACG
*
107452 ATACATAGTTTCAGTAC
1 AT--AGAGTTTCAGTAC
107469 TACTGAAAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
21 1 0.02
22 8 0.17
23 39 0.81
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (23 bp):
ATAGAGTTTCAGTACCAAAAACG
Found at i:108953 original size:30 final size:30
Alignment explanation
Indices: 108914--109016 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
108904 AAAAGAATTG
* * *
108914 AAATGTAAATAAAGGGAAATAAAAGTGCTT
1 AAATATAAATAAAGGAAAATAAAAGTGCTA
* * *
108944 AAATATAAATAAAGAAAAATAAAGGTACTA
1 AAATATAAATAAAGGAAAATAAAAGTGCTA
* * * * *
108974 AAATGTAAATAAATGAAAATTAAAGTGATG
1 AAATATAAATAAAGGAAAATAAAAGTGCTA
*
109004 AAATAAAAATAAA
1 AAATATAAATAAA
109017 TAAATAAATA
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.22
Consensus pattern (30 bp):
AAATATAAATAAAGGAAAATAAAAGTGCTA
Found at i:114088 original size:102 final size:102
Alignment explanation
Indices: 113912--114117 Score: 394
Period size: 102 Copynumber: 2.0 Consensus size: 102
113902 CTTGTTTTAT
*
113912 TTTATTATCATTCATGCATTTGAACTTTAGAATGTAATTGTAATATTTCTTTATTTTGATTGGAG
1 TTTATTATCATTCATGCATTTGAACTTTAGAATGTAATTGTAATATTTCTTTATTTTAATTGGAG
*
113977 TATGAATTGATTGCCTCAGGGCTTGAGAGGTTGTTTC
66 TATGAATTGATTGCCTCAGGGCTCGAGAGGTTGTTTC
114014 TTTATTATCATTCATGCATTTGAACTTTAGAATGTAATTGTAATATTTCTTTATTTTAATTGGAG
1 TTTATTATCATTCATGCATTTGAACTTTAGAATGTAATTGTAATATTTCTTTATTTTAATTGGAG
114079 TATGAATTGATTGCCTCAGGGCTCGAGAGGTTGTTTC
66 TATGAATTGATTGCCTCAGGGCTCGAGAGGTTGTTTC
114116 TT
1 TT
114118 CTTGATAGAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (102 bp):
TTTATTATCATTCATGCATTTGAACTTTAGAATGTAATTGTAATATTTCTTTATTTTAATTGGAG
TATGAATTGATTGCCTCAGGGCTCGAGAGGTTGTTTC
Found at i:117768 original size:18 final size:20
Alignment explanation
Indices: 117734--117774 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
117724 ACACCTTGAA
*
117734 TTTTGCATCTGCATTTTA-C
1 TTTTGCATCTACATTTTATC
117753 TTTTGCAT-TACATTTTATC
1 TTTTGCATCTACATTTTATC
117772 TTT
1 TTT
117775 CACATCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTGCATCTACATTTTATC
Found at i:123130 original size:21 final size:22
Alignment explanation
Indices: 123106--123146 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
123096 TATATTAGGG
123106 TTTAAGGATT-TAAAAATATCT
1 TTTAAGGATTATAAAAATATCT
**
123127 TTTAATTATTATAAAAATAT
1 TTTAAGGATTATAAAAATAT
123147 AAGAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
TTTAAGGATTATAAAAATATCT
Found at i:124378 original size:20 final size:20
Alignment explanation
Indices: 124353--124393 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
124343 AAAATTCTTT
124353 TCGATAATTGTGTCTAATTA
1 TCGATAATTGTGTCTAATTA
124373 TCGATAATTGTGTCTAATTA
1 TCGATAATTGTGTCTAATTA
124393 T
1 T
124394 TTGCACGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TCGATAATTGTGTCTAATTA
Found at i:125415 original size:23 final size:22
Alignment explanation
Indices: 125389--125431 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
125379 TTTACGTCAT
125389 ATTAGTTAAAAAATTATTATATG
1 ATTAGTTAAAAAATT-TTATATG
* *
125412 ATTATTTTAAAAATTTTATA
1 ATTAGTTAAAAAATTTTATA
125432 ATTTATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTAGTTAAAAAATTTTATATG
Found at i:125434 original size:8 final size:8
Alignment explanation
Indices: 125423--125469 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
125413 TTATTTTAAA
125423 AATTTTAT
1 AATTTTAT
125431 AA-TTTAT
1 AATTTTAT
* *
125438 CATTGTAT
1 AATTTTAT
*
125446 AATTTCAT
1 AATTTTAT
*
125454 ATTTTTAT
1 AATTTTAT
125462 AATTTTAT
1 AATTTTAT
125470 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (8 bp):
AATTTTAT
Found at i:125511 original size:20 final size:20
Alignment explanation
Indices: 125453--125517 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
125443 TATAATTTCA
125453 TATTTTTATA-ATTT-TATT
1 TATTTTTATATATTTATATT
* *
125471 TATTTTTAAAATAATTA-ATT
1 TATTTTT-ATATATTTATATT
*
125491 TATTTTTATATTTTTATATT
1 TATTTTTATATATTTATATT
125511 TAATTTT
1 T-ATTTT
125518 CTAAAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
20 17 0.46
21 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTATATATTTATATT
Found at i:125535 original size:8 final size:8
Alignment explanation
Indices: 125491--125547 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
125481 ATAATTAATT
*
125491 TATTTTTA
1 TATTTTAA
*
125499 TATTTTTA
1 TATTTTAA
125507 TA-TTTAA
1 TATTTTAA
125514 T-TTTCTAAAA
1 TATTT-T--AA
125524 TATTTTAA
1 TATTTTAA
125532 TATTTTAA
1 TATTTTAA
125540 TATTTTAA
1 TATTTTAA
125548 ATCTTCAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
7 7 0.16
8 29 0.67
10 4 0.09
11 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:128228 original size:60 final size:60
Alignment explanation
Indices: 128156--128485 Score: 439
Period size: 60 Copynumber: 5.5 Consensus size: 60
128146 GGTTCAAACC
* * * *
128156 TTTCATGTAACTTGCATTAATGGCACTTTTCTGCCAAAATGCACTGTTAGGCATTTAACT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGGCACTTAACT
* * * *
128216 TTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGACATTTAACT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGGCACTTAACT
* **
128276 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAAATGCA-TAGTTAATCACTTAACT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACT-GTTAGGCACTTAACT
* ** * * *
128336 TTTCATCTAACTTGCATTAGTGGAACCTTTCTGAAAAAATGCACAGTTAGGAAATTAACT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGGCACTTAACT
* * *
128396 TTTCATCTAACTTACATTAGTGGCACCTTTCTACCAAAATGCA-TAATTAGGCACTTAACT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACT-GTTAGGCACTTAACT
*
128456 TTTCATCTAACTTGCATTAGTGGCGCCTTT
1 TTTCATCTAACTTGCATTAGTGGCACCTTT
128486 ATAAACTTTT
Statistics
Matches: 235, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
60 235 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGGCACTTAACT
Found at i:128465 original size:180 final size:180
Alignment explanation
Indices: 128156--128485 Score: 507
Period size: 180 Copynumber: 1.8 Consensus size: 180
128146 GGTTCAAACC
* * * ** * * *
128156 TTTCATGTAACTTGCATTAATGGCACTTTTCTGCCAAAATGCACTGTTAGGCATTTAACTTTTCA
1 TTTCATCTAACTTGCATTAATGGAACCTTTCTGAAAAAATGCACAGTTAGGAAATTAACTTTTCA
* ** *
128221 TCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGACATTTAACTTTTCATCTAA
66 TCTAACTTACATTAGTGGCACCTTTCTACCAAAATGCACAATTAGACACTTAACTTTTCATCTAA
*
128286 CTTGCATTATTGGCACCTTTCTGCCAAAATGCATAGTTAATCACTTAACT
131 CTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAATCACTTAACT
*
128336 TTTCATCTAACTTGCATTAGTGGAACCTTTCTGAAAAAATGCACAGTTAGGAAATTAACTTTTCA
1 TTTCATCTAACTTGCATTAATGGAACCTTTCTGAAAAAATGCACAGTTAGGAAATTAACTTTTCA
* *
128401 TCTAACTTACATTAGTGGCACCTTTCTACCAAAATGCATAATTAGGCACTTAACTTTTCATCTAA
66 TCTAACTTACATTAGTGGCACCTTTCTACCAAAATGCACAATTAGACACTTAACTTTTCATCTAA
*
128466 CTTGCATTAGTGGCGCCTTT
131 CTTGCATTAGTGGCACCTTT
128486 ATAAACTTTT
Statistics
Matches: 133, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
180 133 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (180 bp):
TTTCATCTAACTTGCATTAATGGAACCTTTCTGAAAAAATGCACAGTTAGGAAATTAACTTTTCA
TCTAACTTACATTAGTGGCACCTTTCTACCAAAATGCACAATTAGACACTTAACTTTTCATCTAA
CTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAATCACTTAACT
Found at i:133655 original size:17 final size:18
Alignment explanation
Indices: 133630--133667 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
133620 ATTAAAATAT
133630 TTAGATTTAGGTTT-GGG
1 TTAGATTTAGGTTTAGGG
*
133647 TTAGGTTTAGGTTTAGGG
1 TTAGATTTAGGTTTAGGG
133665 TTA
1 TTA
133668 AAATAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (18 bp):
TTAGATTTAGGTTTAGGG
Found at i:135825 original size:60 final size:60
Alignment explanation
Indices: 135732--136344 Score: 884
Period size: 60 Copynumber: 10.2 Consensus size: 60
135722 TGCACGGTTA
* * * * * *
135732 TAACTTTTCATTTAACTTGCATTAATGGCACCTTTCTACCAAAATGCACCGATAGGCATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * * *
135792 TAACTTTTCATTTAACTTGCATTAGTGGCACCTTCCTGCCAAAATGCACCGTTAGGCATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * * *
135852 TAACTTTTTATCTAACATGCATTAGTGTCACCTTTCTGCCAAAATGCACAATTAGGCACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * *
135912 TAACTTTTCATCTAACTTGCATTAGTGACACCTTTATGCCAAAATGCACAGTTAGGTACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * * *
135972 TAACTTTTCATCTAACTTGCATTAGTGGTACCTTTCTACCAAAATGCATAGTTAGGTACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* ** * * *
136032 TAACTTTTCATCTAACTTGCATTAGTGGAATTTTTCTGCCAAAATGCACTGTTAGGAATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* *
136092 TAACTTTTCATCTAACTTGCATTAGTGACACCTTTCTGCCAAAATTCACAGTTAGGCACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * *
136152 TAACTTTTCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACAGCTAGGTACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * *
136212 TAACTTTTCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATGCATAGTTAGGCACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
* * *
136272 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCGAAAATGTATAGTTAGGCACT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
136332 TAACTTTTCATCT
1 TAACTTTTCATCT
136345 TAGTGCAGTT
Statistics
Matches: 499, Mismatches: 54, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 499 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (60 bp):
TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCACT
Found at i:139160 original size:2 final size:2
Alignment explanation
Indices: 139121--139149 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
139111 TAAATGCAAG
139121 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
139150 TAAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:143677 original size:54 final size:54
Alignment explanation
Indices: 143640--144292 Score: 777
Period size: 54 Copynumber: 12.1 Consensus size: 54
143630 TAAACTCATT
*** * *
143640 ATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTATTCATCAACATGTG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* * * * *
143694 ATGAATTCCGTGA-ATTGCACACTAAGT-CTCAAAATGGTTA-T-ATCAATATATG
1 ATGAATTCCGT-ACTTTGCACACTTAGTGC-CGAAACGGTTATTCATCAACATATG
* * *
143746 ATGAATTCTGTGA--ATGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTCCGT-ACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* * * *
143799 ATGAATTCTGCACTTTGCACACTTAGTGTCGAAACGATTATTCATCAACATATG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
** *
143853 ATGAATTCTATACTTTGTACACTTAGTGCCGAAACGGTTATTCAAT-AACATATG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC-ATCAACATATG
* * *
143907 ATGAATTCCGTGA-ATTGCACACTTAATGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTCCGT-ACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* * * * * *
143961 ATGAATTTCTTACTTTGCACACTTAGTGTCGAAACAGTTTTTCATCGACATATG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* * * *
144015 ATGAATTTCGTGA-ATTGCACACTTAGTGCCGAAATGGTTATTCATTAACATATG
1 ATGAATTCCGT-ACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* **
144069 ATGAATTACGTACTTTGCACACTTAGTGCCGAAACATTTATTCATCAACATATG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* * *
144123 ATGAATTCTGTGA-ATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTCCGT-ACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
**
144177 ATGAATTCCGTACTTTGCACACTTAGTGTTGAAACGGTTATTCATCAACATATG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* *
144231 ATGAATTCCGTACTTTACACACTTAGTGTCGAAACGGTTATTCATCAACATATG
1 ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
*
144285 ATAAATTC
1 ATGAATTC
144293 TATGAATTGC
Statistics
Matches: 518, Mismatches: 66, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
51 21 0.04
52 24 0.05
53 27 0.05
54 441 0.85
55 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (54 bp):
ATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
Found at i:146017 original size:40 final size:40
Alignment explanation
Indices: 145962--146043 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
145952 TGCAGGTTTA
145962 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
146002 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
146042 TA
1 TA
146044 GCACTACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:153267 original size:40 final size:40
Alignment explanation
Indices: 153215--153376 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
153205 TGCAGGTTTA
*
153215 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTT
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
153255 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGAG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
153295 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
153335 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
153375 TA
1 TA
153377 GCACTACGGT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:159835 original size:134 final size:134
Alignment explanation
Indices: 159583--159844 Score: 416
Period size: 134 Copynumber: 2.0 Consensus size: 134
159573 CTCTTCCCTA
* * *
159583 AAGAATAACAAAATTCAGCCTAGTTTCTTTTCCAACTATGTTTTCTAAACAGAAATATCCACAAG
1 AAGAATAACAAAACTCAGCCTAGTTTCCTTTCCAACTATGTTTTCGAAACAGAAATATCCACAAG
* * * *
159648 AGGTCCCATTAATAGTAAGTTTTAAGTCAATTGATAATAGACTACAGCTTTGGAAACAAACTCGG
66 AGGTCCCATTAATAATAAGTTTGAAATCAATTGATAATAGACTACAGCATTGGAAACAAACTCGG
159713 CCTG
131 CCTG
* *
159717 AAGAATAACAAAACTCAGCCTAGTTTCCTTTGCAGCTATGTTTTCGAAACAGAAATATCCACAAG
1 AAGAATAACAAAACTCAGCCTAGTTTCCTTTCCAACTATGTTTTCGAAACAGAAATATCCACAAG
* * *
159782 AGGTCCCATTAATAATAAGTTTGAAATCAATTGATAATGGTCTATAGCATTGGAAACAAACTC
66 AGGTCCCATTAATAATAAGTTTGAAATCAATTGATAATAGACTACAGCATTGGAAACAAACTC
159845 TAGATTGAGG
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 116 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (134 bp):
AAGAATAACAAAACTCAGCCTAGTTTCCTTTCCAACTATGTTTTCGAAACAGAAATATCCACAAG
AGGTCCCATTAATAATAAGTTTGAAATCAATTGATAATAGACTACAGCATTGGAAACAAACTCGG
CCTG
Found at i:165957 original size:7 final size:7
Alignment explanation
Indices: 165947--165974 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
165937 AAAAGACAAT
165947 GAAAAGG
1 GAAAAGG
165954 GAAAAGG
1 GAAAAGG
165961 GAAAAGG
1 GAAAAGG
165968 GAAAAGG
1 GAAAAGG
165975 AAAGGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:166273 original size:16 final size:16
Alignment explanation
Indices: 166237--166273 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
166227 TTCAAAAATA
*
166237 ATAATTTATACATGAT
1 ATAATTTATACATCAT
*
166253 TTAATTTATACATCAT
1 ATAATTTATACATCAT
166269 ATAAT
1 ATAAT
166274 CTTAGTAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (16 bp):
ATAATTTATACATCAT
Found at i:166722 original size:22 final size:22
Alignment explanation
Indices: 166697--166738 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
166687 CAATGGAGGC
*
166697 TTAAT-TCAATATTCAATATTAT
1 TTAATATCAA-ATTAAATATTAT
166719 TTAATATCAAATTAAATATT
1 TTAATATCAAATTAAATATT
166739 TAATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAATATCAAATTAAATATTAT
Found at i:166740 original size:19 final size:19
Alignment explanation
Indices: 166716--166755 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
166706 TATTCAATAT
166716 TATTTAATATCAAATTAAA
1 TATTTAATATCAAATTAAA
* *
166735 TATTTAATATTAAATTTAA
1 TATTTAATATCAAATTAAA
166754 TA
1 TA
166756 AAAATGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAATATCAAATTAAA
Found at i:167189 original size:11 final size:11
Alignment explanation
Indices: 167173--167202 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
167163 TATATCCATC
167173 TTGAATGAAAA
1 TTGAATGAAAA
167184 TTGAATGAAAA
1 TTGAATGAAAA
*
167195 CTGAATGA
1 TTGAATGA
167203 TAACGCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (11 bp):
TTGAATGAAAA
Found at i:168074 original size:48 final size:48
Alignment explanation
Indices: 167945--168101 Score: 167
Period size: 49 Copynumber: 3.2 Consensus size: 48
167935 TTTCCCGAAT
* * * *
167945 ATGGTGCATTTTTGGA-AGAAAGGTGTCACTAATGCATGTTTAATACAAA
1 ATGGTGCATTTTT-GACAGAAA-GTGTCACTAATGCAAGTTAAATGCATA
* * *
167994 ATGGTGCATTTTTGGCAGAAATGTGCCACTAATGCAAGTTAAATGCCTA
1 ATGGTGCATTTTTGACAGAAA-GTGTCACTAATGCAAGTTAAATGCATA
168043 ATGGTGCA-TTTTGACAGAAAGCTGTCACTAATG-ACAGTTAAATGCATA
1 ATGGTGCATTTTTGACAGAAAG-TGTCACTAATGCA-AGTTAAATGCATA
**
168091 ATAATGCATTT
1 ATGGTGCATTT
168102 AGGTATAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 40 0.44
49 49 0.54
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (48 bp):
ATGGTGCATTTTTGACAGAAAGTGTCACTAATGCAAGTTAAATGCATA
Found at i:171569 original size:12 final size:12
Alignment explanation
Indices: 171552--171576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
171542 CTTCTTCCTT
171552 CAATACTAATTC
1 CAATACTAATTC
171564 CAATACTAATTC
1 CAATACTAATTC
171576 C
1 C
171577 TAGGAGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (12 bp):
CAATACTAATTC
Found at i:185067 original size:157 final size:156
Alignment explanation
Indices: 184715--185033 Score: 494
Period size: 157 Copynumber: 2.0 Consensus size: 156
184705 GTTGTCTTGG
* * **
184715 TCAAACAGTCAACTATAAATCACACCACGTCGTGTCTCTGCCTAGTCATGGTAATCTCATCACAA
1 TCAAACAGTCAACAACAAATCACACCACG-CGCCTCTCTGCCTAGTCATGGTAATCTCATCACAA
184780 AGTCCAAGTCATATATCCCACTTCCACTGCAGTATCAAGTCGGCGAAGTAACCCTATGGGAACTT
65 AGTCCAAGTCATATATCCCACTTCCACTGCAGTATCAAGTCGGCGAAGTAACCCTATGGGAACTT
**
184845 GATGTTCCACCTTAACTTGTGGCATGG
130 GATGTTCCACCTTAACTTGTGGCATAC
* * **
184872 TCAAACAGTCAACTATAAATCACACCACGTCGTGTCTCTGCCTAGTCATGGTAATCTCATCACAA
1 TCAAACAGTCAACAACAAATCACACCACG-CGCCTCTCTGCCTAGTCATGGTAATCTCATCACAA
184937 AGTCCAAGTCATATTATCCCACTTCCACTGCAGTATCTAAGTCGGCTGAAGTAACCCTATGGGAA
65 AGTCCAAGTCATA-TATCCCACTTCCACTGCAGTATC-AAGTCGGC-GAAGTAACCCTATGGGAA
185002 CTTGATGTTCCACCTTAACTTGCTGGCATAC
127 CTTGATGTTCCACCTTAACTTG-TGGCATAC
185033 T
1 T
185034 AATTATTTAA
Statistics
Matches: 156, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
157 78 0.50
158 23 0.15
159 8 0.05
160 40 0.26
161 7 0.04
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (156 bp):
TCAAACAGTCAACAACAAATCACACCACGCGCCTCTCTGCCTAGTCATGGTAATCTCATCACAAA
GTCCAAGTCATATATCCCACTTCCACTGCAGTATCAAGTCGGCGAAGTAACCCTATGGGAACTTG
ATGTTCCACCTTAACTTGTGGCATAC
Found at i:190609 original size:31 final size:31
Alignment explanation
Indices: 190571--190642 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
190561 TCATATCACC
* * *
190571 TGTACTTTTCACATATTCACTTCATGCAACT
1 TGTACTTTTCACATATTCACATCATACAACA
*
190602 TGTAC-TTTCACATATTCACATCATATAACA
1 TGTACTTTTCACATATTCACATCATACAACA
190632 TGTACTTTTCA
1 TGTACTTTTCA
190643 TTTCAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.42
Consensus pattern (31 bp):
TGTACTTTTCACATATTCACATCATACAACA
Found at i:193600 original size:21 final size:21
Alignment explanation
Indices: 193576--193621 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
193566 GGTGTCATAA
*
193576 AACCCTGTGGGCTCAGTATGT
1 AACCCTGTGGGCTCAATATGT
193597 AACCCTGTGGGCTCAATATGT
1 AACCCTGTGGGCTCAATATGT
193618 AACC
1 AACC
193622 TTGTAGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
AACCCTGTGGGCTCAATATGT
Found at i:202828 original size:24 final size:24
Alignment explanation
Indices: 202774--202821 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
202764 TGCATCGATA
202774 CATTT-AATAGTGCATCGATACATC
1 CATTTGAAT-GTGCATCGATACATC
* *
202798 CCTTTGAATGTGCATCGATTCATC
1 CATTTGAATGTGCATCGATACATC
202822 ATGTTGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (24 bp):
CATTTGAATGTGCATCGATACATC
Found at i:204087 original size:13 final size:12
Alignment explanation
Indices: 204056--204088 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
204046 ATTTGGAGTA
204056 ATTTCAAAATTT
1 ATTTCAAAATTT
204068 ATTTCAAAATTT
1 ATTTCAAAATTT
204080 ATTTTCAAA
1 A-TTTCAAA
204089 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTCAAAATTT
Found at i:206379 original size:2 final size:2
Alignment explanation
Indices: 206374--206415 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
206364 TAATCAAAAA
* *
206374 AT AT AT AT AT TT A- AT AT GT -T 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
206414 AT
1 AT
206416 TAAGTTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:206636 original size:20 final size:22
Alignment explanation
Indices: 206611--206658 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
206601 TGTTTGATTT
*
206611 AGTTAATATTTAA-AAAAATTG
1 AGTTAATATTAAAGAAAAATTG
206632 A-TTAA-ATTAAAGAAAAATTG
1 AGTTAATATTAAAGAAAAATTG
206652 AGTTAAT
1 AGTTAAT
206659 TCAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (22 bp):
AGTTAATATTAAAGAAAAATTG
Found at i:207340 original size:25 final size:25
Alignment explanation
Indices: 207306--207358 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
207296 GAAGAACAAG
207306 GGTTCCCTTTCTCTCAATCCCCTTA
1 GGTTCCCTTTCTCTCAATCCCCTTA
207331 GGTTCCCTTTCTCTCAATCCCCTTA
1 GGTTCCCTTTCTCTCAATCCCCTTA
207356 GGT
1 GGT
207359 GTAATAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.11, C:0.38, G:0.11, T:0.40
Consensus pattern (25 bp):
GGTTCCCTTTCTCTCAATCCCCTTA
Found at i:208446 original size:20 final size:21
Alignment explanation
Indices: 208423--208480 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
208413 TACTAGAGGC
208423 TTGGTATCCATACCAAAA-GT
1 TTGGTATCCATACCAAAAGGT
*
208443 TTGGTATCCATACTAAAAGGT
1 TTGGTATCCATACCAAAAGGT
**
208464 TTAATATCCATACCAAA
1 TTGGTATCCATACCAAA
208481 GGCTTGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (21 bp):
TTGGTATCCATACCAAAAGGT
Found at i:208457 original size:40 final size:41
Alignment explanation
Indices: 208403--208480 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
208393 ACAAGACTAA
* * **
208403 TTGGTATCCGTACT-AGAGGCTTGGTATCCATACCAAAAGT
1 TTGGTATCCATACTAAAAGGCTTAATATCCATACCAAAAGT
*
208443 TTGGTATCCATACTAAAAGGTTTAATATCCATACCAAA
1 TTGGTATCCATACTAAAAGGCTTAATATCCATACCAAA
208481 GGCTTGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 13 0.41
41 19 0.59
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (41 bp):
TTGGTATCCATACTAAAAGGCTTAATATCCATACCAAAAGT
Found at i:208471 original size:21 final size:20
Alignment explanation
Indices: 208427--208480 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
208417 AGAGGCTTGG
**
208427 TATCCATACCAAAAGTTTGG
1 TATCCATACCAAAAGTTTAA
*
208447 TATCCATACTAAAAGGTTTAA
1 TATCCATACCAAAA-GTTTAA
208468 TATCCATACCAAA
1 TATCCATACCAAA
208481 GGCTTGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (20 bp):
TATCCATACCAAAAGTTTAA
Found at i:208490 original size:20 final size:20
Alignment explanation
Indices: 208419--208491 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
208409 TCCGTACTAG
*
208419 AGGCTTGGTATCCATACCAA
1 AGGCTTGATATCCATACCAA
* * * *
208439 AAGTTTGGTATCCATACTAAA
1 AGGCTTGATATCCATAC-CAA
* *
208460 AGGTTTAATATCCATACCAA
1 AGGCTTGATATCCATACCAA
208480 AGGCTTGATATC
1 AGGCTTGATATC
208492 AATATAGAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (20 bp):
AGGCTTGATATCCATACCAA
Found at i:213385 original size:3 final size:3
Alignment explanation
Indices: 213377--213423 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
213367 TTTTTATCCA
*
213377 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
213424 AATATATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:213450 original size:14 final size:15
Alignment explanation
Indices: 213422--213456 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
213412 TTATTATTAT
213422 TAAATATATATTAAA
1 TAAATATATATTAAA
213437 TAAATATATA-TAAA
1 TAAATATATATTAAA
213451 TAAATA
1 TAAATA
213457 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:213895 original size:24 final size:23
Alignment explanation
Indices: 213868--213915 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
213858 GAACCTGAAA
213868 AAAAAAAACCAGAGAAAGAG-ACAG
1 AAAAAAAA--AGAGAAAGAGAACAG
*
213892 AAAAAAAAAGAGAAGGAGAACAG
1 AAAAAAAAAGAGAAAGAGAACAG
213915 A
1 A
213916 GAGAGATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 5 0.23
24 8 0.36
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAGAGAAAGAGAACAG
Found at i:213999 original size:9 final size:9
Alignment explanation
Indices: 213987--214035 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
213977 AGCAAAAAAC
213987 AGAAAAGAA
1 AGAAAAGAA
213996 AGAAAAGAA
1 AGAAAAGAA
*
214005 AAAGAAAGAAA
1 AGA-AAAG-AA
214016 AGAAAAAGAA
1 AG-AAAAGAA
*
214026 AGAAGAGAA
1 AGAAAAGAA
214035 A
1 A
214036 CTTACTGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 18 0.53
10 8 0.24
11 7 0.21
12 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:214002 original size:5 final size:5
Alignment explanation
Indices: 213987--214035 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
213977 AGCAAAAAAC
*
213987 AGAAA AG-AA AGAAA AGAAA A-AGAA AGAAA AGAAA A-AGAA AGAAG AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGA-AA AGAAA AGAAA AGA-AA AGAAA AGAAA
214036 CTTACTGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 6 0.16
5 29 0.78
6 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:214009 original size:15 final size:15
Alignment explanation
Indices: 213989--214035 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
213979 CAAAAAACAG
213989 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
214004 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
214019 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
214034 AA
1 AA
214036 CTTACTGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:226294 original size:15 final size:16
Alignment explanation
Indices: 226266--226300 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
226256 TGAAGAAAGG
226266 AAAGAAACAGAAAAAA
1 AAAGAAACAGAAAAAA
*
226282 AAAGAAAGA-AAAAAA
1 AAAGAAACAGAAAAAA
226297 AAAG
1 AAAG
226301 TAAAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAGAAACAGAAAAAA
Found at i:227625 original size:83 final size:83
Alignment explanation
Indices: 227478--227686 Score: 368
Period size: 83 Copynumber: 2.5 Consensus size: 83
227468 ATCTTCTGCT
227478 TGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAGCAAAACCA
1 TGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAGCAAAACCA
227543 ATCATTGAATTTGGAAGA
66 ATCATTGAATTTGGAAGA
*
227561 TGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-GCAGAACC
1 TGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGAGCAAAACC
227625 AATCATTGAATTTGGAAGA
65 AATCATTGAATTTGGAAGA
*
227644 TGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
227687 TTAAGAACTA
Statistics
Matches: 122, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
83 118 0.97
84 4 0.03
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
TGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAGCAAAACCA
ATCATTGAATTTGGAAGA
Found at i:228732 original size:112 final size:113
Alignment explanation
Indices: 228398--228798 Score: 750
Period size: 113 Copynumber: 3.6 Consensus size: 113
228388 TCGAATCCAC
* *
228398 TTGATGGATCAGTTTTTCCAGAGATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
228463 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
*
228511 TTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
228576 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
*
228624 TTGATGGATCAGTTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
228688 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
*
228736 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAA
1 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
228799 TTTGTTCAAC
Statistics
Matches: 280, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
112 111 0.40
113 169 0.60
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
Found at i:228845 original size:93 final size:92
Alignment explanation
Indices: 228700--228890 Score: 319
Period size: 93 Copynumber: 2.1 Consensus size: 92
228690 TTCATAATGA
*
228700 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATGGATCAGCTTTTCCAGAG-AAGTT
228765 CATAATGAGAAGAACTCATCTAAAGAAG
65 CATAATGAGAAGAACTCATCTAAAGAAG
* * *
228793 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAGTTC
1 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATGGATCAGCTTTTCCAGAGAAGTTC
*
228858 ATAATGAGAAGAACTCATCTGAAGAAG
66 ATAATGAGAAGAACTCATCTAAAGAAG
*
228885 AAAGAA
1 GAAGAA
228891 GAAGTTCATA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 37 0.40
93 55 0.60
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (92 bp):
GAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATGGATCAGCTTTTCCAGAGAAGTTC
ATAATGAGAAGAACTCATCTAAAGAAG
Found at i:229251 original size:3 final size:3
Alignment explanation
Indices: 229243--229316 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
229233 TTTTTATCCA
229243 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
229291 TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
229317 AATATATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:229343 original size:14 final size:15
Alignment explanation
Indices: 229315--229349 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
229305 TTATTATTAT
229315 TAAATATATATTAAA
1 TAAATATATATTAAA
229330 TAAATATATA-TAAA
1 TAAATATATATTAAA
229344 TAAATA
1 TAAATA
229350 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:229892 original size:15 final size:15
Alignment explanation
Indices: 229872--229913 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
229862 ACCACTCAGC
229872 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
229887 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
229902 AAAGAAGAGAAA
1 AAAGAAAAGAAA
229914 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:229897 original size:20 final size:20
Alignment explanation
Indices: 229872--229913 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
229862 ACCACTCAGC
*
229872 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
229892 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
229912 AA
1 AA
229914 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:240291 original size:2 final size:2
Alignment explanation
Indices: 240247--240272 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
240237 TATTCGTAAG
240247 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
240273 CCTAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247465 original size:40 final size:40
Alignment explanation
Indices: 247421--247496 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
247411 GATGAATAAT
*
247421 GGGGAAATGAGGAACGAATTAGG-GGTTTAGAAATTGAATG
1 GGGGAAATGAGGAACGAATT-GGTGATTTAGAAATTGAATG
247461 GGGGAAATGAGGAACGAATTGGTGATTTAGAAATTG
1 GGGGAAATGAGGAACGAATTGGTGATTTAGAAATTG
247497 TTACCGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.37, C:0.03, G:0.37, T:0.24
Consensus pattern (40 bp):
GGGGAAATGAGGAACGAATTGGTGATTTAGAAATTGAATG
Found at i:256805 original size:21 final size:21
Alignment explanation
Indices: 256781--256833 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
256771 GATTTGAGTA
256781 TCGGTAGTTAATCTATCGGTG
1 TCGGTAGTTAATCTATCGGTG
*
256802 TCGGTAGTTAATCTATCTGTG
1 TCGGTAGTTAATCTATCGGTG
*
256823 CCGGTAGTTAA
1 TCGGTAGTTAA
256834 GCTGCAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (21 bp):
TCGGTAGTTAATCTATCGGTG
Found at i:258678 original size:30 final size:30
Alignment explanation
Indices: 258643--258704 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
258633 AAATCTTGTG
258643 CACAATGAAGATTATGAGGAGTTCGTTGCA
1 CACAATGAAGATTATGAGGAGTTCGTTGCA
*
258673 CACAATGAAGATTATGAGGTGTTCGTTGCA
1 CACAATGAAGATTATGAGGAGTTCGTTGCA
258703 CA
1 CA
258705 AGATAGTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (30 bp):
CACAATGAAGATTATGAGGAGTTCGTTGCA
Found at i:259684 original size:169 final size:169
Alignment explanation
Indices: 259405--259742 Score: 676
Period size: 169 Copynumber: 2.0 Consensus size: 169
259395 TATAATTAAA
259405 ACATGCATTAACTTACATATGAAAATAAAAAGAGATGTTCCACATTTCACTGTTTTACAGTAGTT
1 ACATGCATTAACTTACATATGAAAATAAAAAGAGATGTTCCACATTTCACTGTTTTACAGTAGTT
259470 TAATTCAAAAGTTTCACAGAGCGTTTTTACTAAACTTATTACGTGTCGACTAAAATATATCAAAA
66 TAATTCAAAAGTTTCACAGAGCGTTTTTACTAAACTTATTACGTGTCGACTAAAATATATCAAAA
259535 GTAGATAGGTAAGTCATATTGTTACTGATTAGGTGACTC
131 GTAGATAGGTAAGTCATATTGTTACTGATTAGGTGACTC
259574 ACATGCATTAACTTACATATGAAAATAAAAAGAGATGTTCCACATTTCACTGTTTTACAGTAGTT
1 ACATGCATTAACTTACATATGAAAATAAAAAGAGATGTTCCACATTTCACTGTTTTACAGTAGTT
259639 TAATTCAAAAGTTTCACAGAGCGTTTTTACTAAACTTATTACGTGTCGACTAAAATATATCAAAA
66 TAATTCAAAAGTTTCACAGAGCGTTTTTACTAAACTTATTACGTGTCGACTAAAATATATCAAAA
259704 GTAGATAGGTAAGTCATATTGTTACTGATTAGGTGACTC
131 GTAGATAGGTAAGTCATATTGTTACTGATTAGGTGACTC
259743 TGACTTTATG
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 169 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (169 bp):
ACATGCATTAACTTACATATGAAAATAAAAAGAGATGTTCCACATTTCACTGTTTTACAGTAGTT
TAATTCAAAAGTTTCACAGAGCGTTTTTACTAAACTTATTACGTGTCGACTAAAATATATCAAAA
GTAGATAGGTAAGTCATATTGTTACTGATTAGGTGACTC
Found at i:260172 original size:55 final size:55
Alignment explanation
Indices: 260083--260419 Score: 525
Period size: 55 Copynumber: 6.2 Consensus size: 55
260073 CTGTAAATAT
* * *
260083 GTGCTTGTACTGTGATTCATCAACCCATGATGAATTCCGTGAACATGCACACAAA
1 GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
* * *
260138 GTGCCTGTACGGTGATTCATCAACTCATGATGAATTCTGTGAATATGCACAAAAA
1 GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
* * *
260193 GTGCCTGTACAGTGATTCATCAACCCATGATGAATTCTGTGAATATGCACACAAG
1 GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
*
260248 GTGCCTGTACGGTAATTCATCAACCCATGATGAATT-CGTGAATATGCACACAAA
1 GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
* *
260302 GTG-CTGTACGGTGATTCATCAACCCATGATGAATTCCGTTAATATACACACAAA
1 GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
* * *
260356 GTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGTACACAAT
1 GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
260411 GTGCCTGTA
1 GTGCCTGTA
260420 GTACACATAG
Statistics
Matches: 257, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
53 31 0.12
54 38 0.15
55 188 0.73
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (55 bp):
GTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAA
Found at i:260359 original size:163 final size:163
Alignment explanation
Indices: 259956--260419 Score: 630
Period size: 163 Copynumber: 2.9 Consensus size: 163
259946 TTTATCCACT
** * *
259956 CATGATGAATTTCGTGGGT-TGCACACATAGTGCCTGTACGGTGA-T--TCAACTCATGATAAAT
1 CATGATGAA-TTCGTGAATATGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAAT
* *
260017 TCCGTGGATTTACACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCTGT-AA-A
65 TCCGTGAATATACACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCTGTGAATA
* * *
260080 T------ATGTGCTTGTACTGTGATTCATCAACC
130 TGACACAATGTGCCTGTACGGTAATTCATCAACC
*
260108 CATGATGAATTCCGTGAACATGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAAT
1 CATGATGAATT-CGTGAATATGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAAT
* * * *
260173 TCTGTGAATATGCACAAAAAGTGCCTGTACAGTGATTCATCAACCCATGATGAATTCTGTGAATA
65 TCCGTGAATATACACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCTGTGAATA
*
260238 TGCACACAAGGTGCCTGTACGGTAATTCATCAACC
130 TG-ACACAATGTGCCTGTACGGTAATTCATCAACC
*
260273 CATGATGAATTCGTGAATATGCACACAAAGTG-CTGTACGGTGATTCATCAACCCATGATGAATT
1 CATGATGAATTCGTGAATATGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATT
* * *
260337 CCGTTAATATACACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATAT
66 CCGTGAATATACACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCTGTGAATAT
260402 GTACACAATGTGCCTGTA
131 G-ACACAATGTGCCTGTA
260420 GTACACATAG
Statistics
Matches: 272, Mismatches: 26, Indels: 17
0.86 0.08 0.05
Matches are distributed among these distances:
151 2 0.01
152 13 0.05
153 24 0.09
154 1 0.00
156 69 0.25
157 2 0.01
158 2 0.01
163 105 0.39
164 20 0.07
165 34 0.12
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (163 bp):
CATGATGAATTCGTGAATATGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATT
CCGTGAATATACACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCTGTGAATAT
GACACAATGTGCCTGTACGGTAATTCATCAACC
Found at i:260367 original size:218 final size:208
Alignment explanation
Indices: 259953--260419 Score: 589
Period size: 218 Copynumber: 2.2 Consensus size: 208
259943 TCATTTATCC
** * * *
259953 ACTCATGATGAATT-TCGTGGGT-TGCACACATAGTGCCTGTACGGTGATTCAACTCATGATAAA
1 ACTCATGATGAATTCT-GTGAATATGCACACAAAGTGCCTGTACAGTGATTCAACCCATGATAAA
* * * *
260016 TTCCGTGGATTTACACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCTGTAAAT
65 TTCCGTGAATATACACACAAAGTGCCTGTACGGTAATTCATCAACCCATGATGAATTCTGTAAAA
* * * *
260081 ATGTGCTTGTACTGTGATTCATCAACCCATGATGAATTCCGTGAACATGCACACAAAGTGCCTGT
130 AAGTGCTTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAACATACACACAAAGTGCATGT
260146 ACGGTGATTCATCA
195 ACGGTGATTCATCA
* *
260160 ACTCATGATGAATTCTGTGAATATGCACAAAAAGTGCCTGTACAGTGATTCATCAACCCATGATG
1 ACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTACAGTGA-T--TCAACCCATGATA
* * *
260225 AATTCTGTGAATATGCACACAAGGTGCCTGTACGGTAATTCATCAACCCATGATGAATTCGTGAA
63 AATTCCGTGAATATACACACAAAGTGCCTGTACGGTAATTCATCAACCCATGATGAATTC-TG--
* *
260290 TATGCACACAAAGTGC-TGTACGGTGATTCATCAACCCATGATGAATTCCGTTAATATACACACA
125 TA---A-A-AAAGTGCTTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAACATACACACA
260354 AAGTGCATGTACGGTGATTCATCA
185 AAGTGCATGTACGGTGATTCATCA
* * * *
260378 ACCCATGATGAATTCCGTGAATATGTACACAATGTGCCTGTA
1 ACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTA
260420 GTACACATAG
Statistics
Matches: 222, Mismatches: 25, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
207 18 0.08
208 23 0.10
209 1 0.00
211 65 0.29
212 2 0.01
214 2 0.01
217 1 0.00
218 105 0.47
219 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (208 bp):
ACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTACAGTGATTCAACCCATGATAAAT
TCCGTGAATATACACACAAAGTGCCTGTACGGTAATTCATCAACCCATGATGAATTCTGTAAAAA
AGTGCTTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAACATACACACAAAGTGCATGTA
CGGTGATTCATCA
Found at i:260818 original size:20 final size:22
Alignment explanation
Indices: 260793--260846 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
260783 CGATGTTGCC
260793 TGGTATCGATAC-ACT-TACCA
1 TGGTATCGATACTACTATACCA
* *
260813 TGGTATTGATACTACTATACTA
1 TGGTATCGATACTACTATACCA
*
260835 TGGTACCGATAC
1 TGGTATCGATAC
260847 CCCCTTCCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 3 0.11
22 14 0.50
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (22 bp):
TGGTATCGATACTACTATACCA
Found at i:260911 original size:95 final size:95
Alignment explanation
Indices: 260718--260923 Score: 272
Period size: 95 Copynumber: 2.2 Consensus size: 95
260708 ACTACTACCC
* * * *
260718 TGGTACCGATACTTCTATACTATGGTACCAATACCCCCATCTGGTATCGATACCAAAATTAGGTT
1 TGGTATCGATACTACTATACTATGGTACCAATACCCCCATCCGGTATCGATACCAAAATTAGATT
* *
260783 CGATGTTGCCTGGTATCGATACACTTACCA
66 CGATGTTGCCTGGTATCGATACACTGACAA
* * *
260813 TGGTATTGATACTACTATACTATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGATT
1 TGGTATCGATACTACTATACTATGGTACCAATACCCCCATCCGGTATCGATACCAAAATTAGATT
** *
260878 C-ATTGTTGTTTGGTATCGATAC-CATGATAA
66 CGA-TGTTGCCTGGTATCGATACAC-TGACAA
260908 TGGTATCGATACTACT
1 TGGTATCGATACTACT
260924 TAACTAATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
94 2 0.02
95 94 0.98
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (95 bp):
TGGTATCGATACTACTATACTATGGTACCAATACCCCCATCCGGTATCGATACCAAAATTAGATT
CGATGTTGCCTGGTATCGATACACTGACAA
Found at i:266982 original size:55 final size:55
Alignment explanation
Indices: 266861--267188 Score: 374
Period size: 55 Copynumber: 6.0 Consensus size: 55
266851 ATATACAATT
* ** * * * * * *
266861 AGTGCTTGTACGGAAATTCATAAACTCGTGATGAATTCTGTGGGT-TGCACACAT
1 AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGATATGCACACAA
* *
266915 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGGATTTGCACACAA
1 AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGATATGCACACAA
* * *
266970 AGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCAT-GACTATGCACACGA
1 AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGA-TATGCACACAA
* * * * * * *
267025 AGTGCCTGTATGGTGATTCATCAACTCATTATGAATTCTGTGAATATCCATACAA
1 AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGATATGCACACAA
* * * *
267080 GGTGCCTGTACGGTGATTCATCAACCCATAATGGATTACGT-GATATGCACACAA
1 AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGATATGCACACAA
* * *
267134 AGTGCATATACGGTGATTCATCAACCCATGATGAATTCCGTGAATATGCACACAA
1 AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGATATGCACACAA
267189 GGTCCATACA
Statistics
Matches: 230, Mismatches: 40, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
54 85 0.37
55 144 0.63
56 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (55 bp):
AGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGGATATGCACACAA
Found at i:267688 original size:94 final size:92
Alignment explanation
Indices: 267524--267742 Score: 253
Period size: 94 Copynumber: 2.4 Consensus size: 92
267514 TGTCTCCATA
* * * * * *
267524 GTATCGATACTAC-TATCATGGTATCGATACTTCTATATTATGGTACCGATACCCCCATCCAGTA
1 GTATCGATAC-ACTTATCATGGTATTGATACTACCATACTATGGTACCAAAACCCCCATCCAGTA
* * **
267588 TTGATACAGAAATTAGGTTCGATGTTG-CTG
65 TCGATACAAAAATTACATT--AT-TTGTCTG
* *
267618 GTATCGATACACTTACCATGGTATTGATACTACCATACTATGGTACCAAAACCCCCTTCCAGTAT
1 GTATCGATACACTTATCATGGTATTGATACTACCATACTATGGTACCAAAACCCCCATCCAGTAT
*
267683 CGATACAAAAATTACATTATTTGTTTG
66 CGATACAAAAATTACATTATTTGTCTG
* *
267710 GTATTGATACCCTTATCATGGTATTGATACTAC
1 GTATCGATACACTTATCATGGTATTGATACTAC
267743 TTAACTAATT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
91 3 0.03
92 34 0.32
93 2 0.02
94 68 0.64
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (92 bp):
GTATCGATACACTTATCATGGTATTGATACTACCATACTATGGTACCAAAACCCCCATCCAGTAT
CGATACAAAAATTACATTATTTGTCTG
Found at i:281253 original size:16 final size:16
Alignment explanation
Indices: 281232--281262 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
281222 ATAAATAAAT
281232 GAACATAAACGAACAC
1 GAACATAAACGAACAC
281248 GAACATAAACGAACA
1 GAACATAAACGAACA
281263 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:281353 original size:16 final size:16
Alignment explanation
Indices: 281332--281396 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
281322 TAATAAATAA
**
281332 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
281348 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
281364 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
281380 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
281396 A
1 A
281397 TAAATGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.54, C:0.25, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:282503 original size:14 final size:14
Alignment explanation
Indices: 282486--282516 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
282476 AATGAACATA
282486 AACGAACATAACCG
1 AACGAACATAACCG
282500 AACGAACATAACCG
1 AACGAACATAACCG
282514 AAC
1 AAC
282517 ATAACTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.29, G:0.13, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:282506 original size:24 final size:24
Alignment explanation
Indices: 282479--282527 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
282469 ATAAATGAAT
282479 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
* *
282503 GAACATAACCGAACATAACTGAAC
1 GAACATAAACGAACATAACCGAAC
282527 G
1 G
282528 TTCACGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.24, G:0.14, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:286088 original size:45 final size:43
Alignment explanation
Indices: 286034--286172 Score: 139
Period size: 45 Copynumber: 3.3 Consensus size: 43
286024 ATTATTCATT
*
286034 ATTTCCATTTATGTCATCATTTCATGCGTTTAATACACCGTTATGC
1 ATTT-CATTTATG-CATCATTTCATGC-TTTAATGCACCGTTATGC
* *
286080 ATTTCATTTATG--GCA--TC---CTTTAATGCACCGTCATGC
1 ATTTCATTTATGCATCATTTCATGCTTTAATGCACCGTTATGC
* *
286116 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTAT-GCATCATTTCATG-CTTTAATGCACCGTTATGC
286161 ATTTCATTTATG
1 ATTTCATTTATG
286173 GAATAAAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
36 27 0.35
37 2 0.03
39 1 0.01
40 2 0.03
41 2 0.03
42 2 0.03
44 1 0.01
45 36 0.47
46 4 0.05
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (43 bp):
ATTTCATTTATGCATCATTTCATGCTTTAATGCACCGTTATGC
Found at i:286103 original size:36 final size:36
Alignment explanation
Indices: 286062--286136 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
286052 ATTTCATGCG
*
286062 TTTAATACACCGTTATGCATTTCATTTATGGCATCC
1 TTTAATACACCGTCATGCATTTCATTTATGGCATCC
*
286098 TTTAATGCACCGTCATGCATTTCATTTATGGCATCC
1 TTTAATACACCGTCATGCATTTCATTTATGGCATCC
286134 TTT
1 TTT
286137 CATGCCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (36 bp):
TTTAATACACCGTCATGCATTTCATTTATGGCATCC
Found at i:286673 original size:95 final size:95
Alignment explanation
Indices: 286530--286729 Score: 242
Period size: 95 Copynumber: 2.1 Consensus size: 95
286520 CCTTACCATG
* * * * * *
286530 GTATTGATACTTCTATACTATGGTACCGATATCCCCTTTTAGTATCGATACTATTTCT-ACATTT
1 GTATCGATACTACTATACTATGGCACCGATATCCCCTTTCAGTATCGATACCATTT-TGACATTC
* * **
286594 TGTAATTCATGGTATCGATACTTTTCTCTCA
65 TGGAATCCATGGTATCGATACTTCCCTCTCA
* *
286625 GTATCGATACTACTATACTATGGCACTGATA-CTCCCTTTCAGTATCGATACCATTTTGGCATTC
1 GTATCGATACTACTATACTATGGCACCGATATC-CCCTTTCAGTATCGATACCATTTTGACATTC
* *
286689 TGGAATCCATGGTATCGATACTTCCCTTTTA
65 TGGAATCCATGGTATCGATACTTCCCTCTCA
286720 GTATCGATAC
1 GTATCGATAC
286730 CCCATCAATA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 2 0.02
95 87 0.98
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (95 bp):
GTATCGATACTACTATACTATGGCACCGATATCCCCTTTCAGTATCGATACCATTTTGACATTCT
GGAATCCATGGTATCGATACTTCCCTCTCA
Found at i:290324 original size:6 final size:7
Alignment explanation
Indices: 290297--290325 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
290287 TAATGTTGTT
290297 ATTTTCC
1 ATTTTCC
290304 ATTTTCC
1 ATTTTCC
290311 ATTTTCC
1 ATTTTCC
290318 A-TTTCC
1 ATTTTCC
290324 AT
1 AT
290326 CAATGGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTTCC
Found at i:291323 original size:431 final size:431
Alignment explanation
Indices: 290517--291381 Score: 1184
Period size: 431 Copynumber: 2.0 Consensus size: 431
290507 TTGTAACACT
* * *
290517 CTAATCCAGTCCGACCCGAAGATTACTGAACCACGATGTCACACGAGACTACCTAAGTGGCAAAC
1 CTAATCCAGTCCGACCCAAAGATCACTGAACCACGATGTCAAACGAGACTACCTAAGTGGCAAAC
* * *
290582 CCAAAAAAATTCTTTTTAAGTCGACTGATTATAAAGTACCGAATAAAAATCTATACATACTGAAT
66 CCAAAAAAATTCTTTTTAAGCCGACTGATTATAAAGAACCGAATAAAAATCCATACATACTGAAT
* *
290647 AAATAAAAGCATAGTAATTAAGTTTTACAAATACGTGGGAGCTCCTAAAATATTCAAAATAATAA
131 AAATAAAAGCATAGTAATTAAGTTTTACAAATACGAGGGAGCTCCCAAAATATTCAAAATAATAA
* * *
290712 TACATCACTGAGTTTAAAATCAAAGGTTATGAGTGAGTAATACAAGAGTCCATAGTAGTACATGC
196 TACATCACTGAGTTTAAAATCAAAGGTTATGACTAAGTAATACAAGAGTCCATAGAAGTACATGC
* * * * * * *
290777 CCTCTATAAGTGACTCAAGACATACTTTGAGATACTCGACTGGATCTGATTTGTTGTGATAGAAT
261 CCTCTACAAGTAACTCAAGAAATACTCTGAGATACTCGACCGGATCTGATCTGCTGTGATAGAAT
* * *
290842 ATCTGATGACGAAAACTCCCCACGAACGATCTCTTAGCCTGCGCATGGAAACACA-TGTCAAATG
326 ATCTGATGACGAAAACTCCCCAAGAACGATCTCTTAGCCTGCGCATGGAAACACACTCT-AAACG
* *
290906 CTGAGCTTACAAGCTTAGTGTCTCACTAAAAACTTTACTACA
390 CTGAGCTTACAAGCTCAGTGCCTCACTAAAAACTTTACTACA
* * **
290948 CTAATCCAGTCCGACCCAAAGATCACTGAATCACGATGTCAAATG-GGTTCACCTAAGTGG-ATA
1 CTAATCCAGTCCGACCCAAAGATCACTGAACCACGATGTCAAACGAGACT-ACCTAAGTGGCA-A
*** * * *
291011 ACCCAAAATTTTTCTTTTTAAGCCGATTGATTATAAAGAACCGGATAAAAATCCAT-CAATATTG
64 ACCCAAAAAAATTCTTTTTAAGCCGACTGATTATAAAGAACCGAATAAAAATCCATAC-ATACTG
* *
291075 AATAAATAAAAGCATAGTAATTATGTTTTACAAATACGAGGGATCTCCCAAAATCA-TCAAAATA
128 AATAAATAAAAGCATAGTAATTAAGTTTTACAAATACGAGGGAGCTCCCAAAAT-ATTCAAAATA
* * *
291139 ATAATACATCACTGAGTTTAAAATCAAAGGTTATGACTAAGTAATATAAGGGTCCGTA-AAGGTA
192 ATAATACATCACTGAGTTTAAAATCAAAGGTTATGACTAAGTAATACAAGAGTCCATAGAA-GTA
* * * *
291203 CATGCCCTTTACAAGTAACTCAAGAAATACTCTGAGATACTTGGCCGGATCTGATCTGCTGTGCT
256 CATGCCCTCTACAAGTAACTCAAGAAATACTCTGAGATACTCGACCGGATCTGATCTGCTGTGAT
* * * * * *
291268 GGAATATCTGATGATGAAAGCTCCCCAAGAACGATCTCTTAGTCTGCGTATGGAAACACACTCTG
321 AGAATATCTGATGACGAAAACTCCCCAAGAACGATCTCTTAGCCTGCGCATGGAAACACACTCTA
* *
291333 AACGTTGAGCTTACGAGCTCAGTGCCTCACTAAAAACTTTACTACA
386 AACGCTGAGCTTACAAGCTCAGTGCCTCACTAAAAACTTTACTACA
291379 CTA
1 CTA
291382 CATGCATTCA
Statistics
Matches: 378, Mismatches: 50, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
430 5 0.01
431 370 0.98
432 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (431 bp):
CTAATCCAGTCCGACCCAAAGATCACTGAACCACGATGTCAAACGAGACTACCTAAGTGGCAAAC
CCAAAAAAATTCTTTTTAAGCCGACTGATTATAAAGAACCGAATAAAAATCCATACATACTGAAT
AAATAAAAGCATAGTAATTAAGTTTTACAAATACGAGGGAGCTCCCAAAATATTCAAAATAATAA
TACATCACTGAGTTTAAAATCAAAGGTTATGACTAAGTAATACAAGAGTCCATAGAAGTACATGC
CCTCTACAAGTAACTCAAGAAATACTCTGAGATACTCGACCGGATCTGATCTGCTGTGATAGAAT
ATCTGATGACGAAAACTCCCCAAGAACGATCTCTTAGCCTGCGCATGGAAACACACTCTAAACGC
TGAGCTTACAAGCTCAGTGCCTCACTAAAAACTTTACTACA
Found at i:293393 original size:30 final size:30
Alignment explanation
Indices: 293359--293463 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
293349 ATATTTATTT
* *
293359 ATTTATTTTTATTTCAGCACTTTAATTTTC
1 ATTTATTTATATTTAAGCACTTTAATTTTC
* * *
293389 ATTTATTTACAATTTTAGTTC-CTTTATTTTTC
1 ATTTATTTA-TATTTAAG--CACTTTAATTTTC
*
293421 -TTTATTTATATTTAAGCACTTTTATTTTC
1 ATTTATTTATATTTAAGCACTTTAATTTTC
* *
293450 CTTTATTTACATTT
1 ATTTATTTATATTT
293464 CAATTCTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
28 1 0.02
29 9 0.15
30 26 0.43
31 14 0.23
32 10 0.16
33 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.03, T:0.62
Consensus pattern (30 bp):
ATTTATTTATATTTAAGCACTTTAATTTTC
Found at i:293473 original size:30 final size:29
Alignment explanation
Indices: 293378--293474 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
293368 TATTTCAGCA
* * *
293378 CTTTAATTTTCATTTATTTACAATTTTAGTT
1 CTTTTATTTTCCTTTATTTAC-A-TTTAATT
* * * **
293409 CCTTTATTTTTCTTTATTTATATTTAAGCA
1 CTTTTATTTTCCTTTATTTACATTTAA-TT
293439 CTTTTATTTTCCTTTATTTACATTTCAATT
1 CTTTTATTTTCCTTTATTTACATTT-AATT
293469 CTTTTA
1 CTTTTA
293475 AATTCCAATA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 4 0.08
30 29 0.57
31 18 0.35
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (29 bp):
CTTTTATTTTCCTTTATTTACATTTAATT
Found at i:294941 original size:23 final size:23
Alignment explanation
Indices: 294898--294979 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
294888 CCTTTTAGTA
*
294898 GTACTGAAACTATGTAT-GTTTTT
1 GTACTGAAACTCTG-ATCGTTTTT
*
294921 GTACTGAAACTCTGATCGTTTTG
1 GTACTGAAACTCTGATCGTTTTT
* * *
294944 GTATTGGAACTCT-ATCATTTTT
1 GTACTGAAACTCTGATCGTTTTT
*
294966 GGTACTAAAACTCT
1 -GTACTGAAACTCT
294980 ATTCGTGGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
22 9 0.19
23 39 0.81
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (23 bp):
GTACTGAAACTCTGATCGTTTTT
Done.