Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007751.1 Hibiscus syriacus cultivar Beakdansim tig00110017_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: 1434969
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 6
Found at i:253577 original size:35 final size:36
Alignment explanation
Indices: 253510--253625 Score: 173
Period size: 35 Copynumber: 3.2 Consensus size: 36
253500 CCCATTCCTA
* * *
253510 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
253545 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
*
253580 TTTTCAAATAAACATTTACCAAACTTTGAAAACCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-T
253617 TTTTCAAAG
1 TTTTCAAAG
253626 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 39 0.53
36 26 0.36
37 8 0.11
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:253581 original size:21 final size:21
Alignment explanation
Indices: 253557--253617 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
253547 TTCAAAGAAA
253557 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
253578 CATTT-TCAAA---T--AAA-
1 CATTTACCAAACTTTGAAAAC
253592 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
253613 CATTT
1 CATTT
253618 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
17 1 0.03
18 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:255729 original size:15 final size:15
Alignment explanation
Indices: 255709--255740 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
255699 AAAATCTTTC
*
255709 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
255724 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
255739 TT
1 TT
255741 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:256978 original size:36 final size:36
Alignment explanation
Indices: 256934--257034 Score: 170
Period size: 35 Copynumber: 2.9 Consensus size: 36
256924 AAAATCTACC
*
256934 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
*
256969 AAATATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
257004 AAACATTTACCAAACTTTGAAAACCATTTTT
1 AAACATTTACCAAACTTTGAAAACCATTTTT
257035 TTTAAAGTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
35 37 0.61
36 24 0.39
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:256997 original size:21 final size:21
Alignment explanation
Indices: 256973--257032 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
256963 TCAAAGAAAT
256973 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
256994 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
257008 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
257029 ATTT
1 ATTT
257033 TTTTTAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:258191 original size:2 final size:2
Alignment explanation
Indices: 258184--258240 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
258174 ATCTATGATC
258184 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
258226 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
258241 ATAGTATTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:262956 original size:21 final size:21
Alignment explanation
Indices: 262932--262974 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
262922 CTTGCTCCAG
*
262932 CCTTTGC-TTGCGCTGCTTCTT
1 CCTTTGCTTTGCGCAGC-TCTT
262953 CCTTTGCTTTGCGCAGCTCTT
1 CCTTTGCTTTGCGCAGCTCTT
262974 C
1 C
262975 ACAAGCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.02, C:0.35, G:0.19, T:0.44
Consensus pattern (21 bp):
CCTTTGCTTTGCGCAGCTCTT
Found at i:266049 original size:33 final size:33
Alignment explanation
Indices: 266007--266075 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
265997 ATCAAGAAAG
266007 TAAGCTTGAAAACTTATGTCAACGACGTGATGA
1 TAAGCTTGAAAACTTATGTCAACGACGTGATGA
266040 TAAGCTTGAAAACTTATGTCAACGACGTGATGA
1 TAAGCTTGAAAACTTATGTCAACGACGTGATGA
266073 TAA
1 TAA
266076 ATCCAACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (33 bp):
TAAGCTTGAAAACTTATGTCAACGACGTGATGA
Found at i:266603 original size:5 final size:5
Alignment explanation
Indices: 266590--266632 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
266580 ATTTGGACCA
* * *
266590 CAACT CAGCT CAGCT CAACT CAACT CAACT CAACT CAATT CAA
1 CAACT CAACT CAACT CAACT CAACT CAACT CAACT CAACT CAA
266633 ACGGAAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.37, C:0.37, G:0.05, T:0.21
Consensus pattern (5 bp):
CAACT
Found at i:268415 original size:13 final size:13
Alignment explanation
Indices: 268373--268514 Score: 72
Period size: 13 Copynumber: 11.1 Consensus size: 13
268363 TAATATATAT
268373 TTATATTATATTA
1 TTATATTATATTA
*
268386 -TATA--GTATTA
1 TTATATTATATTA
*
268396 GTATATTATATTA
1 TTATATTATATTA
*
268409 TTATATTAACATT-
1 TTATATT-ATATTA
268422 TCT-TATTAT-TTA
1 T-TATATTATATTA
*
268434 TTAT-TTAACATTA
1 TTATATT-ATATTA
268447 TTAT-TTATTATTA
1 TTATATTA-TATTA
*
268460 TTACTATTACGTAGTA
1 TTA-TATTA--TATTA
268476 TTAT-TTATATATA
1 TTATATTATAT-TA
268489 TTATA-TATATTA
1 TTATATTATATTA
*
268501 -TAAATTATAATTA
1 TTATATTAT-ATTA
268514 T
1 T
268515 GTTATACACT
Statistics
Matches: 100, Mismatches: 11, Indels: 35
0.68 0.08 0.24
Matches are distributed among these distances:
10 5 0.05
11 12 0.12
12 16 0.16
13 47 0.47
14 9 0.09
15 4 0.04
16 7 0.07
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (13 bp):
TTATATTATATTA
Found at i:268437 original size:10 final size:10
Alignment explanation
Indices: 268391--268501 Score: 50
Period size: 10 Copynumber: 10.9 Consensus size: 10
268381 TATTATATAG
*
268391 TATTAGTATAT
1 TATTATTAT-T
268402 TA-TATTATT
1 TATTATTATT
**
268411 ATATTAACATT
1 -TATTATTATT
*
268422 TCTTATTATT
1 TATTATTATT
*
268432 TATTATT-TAA
1 TATTATTAT-T
*
268442 CATTATTATT
1 TATTATTATT
268452 TATTATTA-T
1 TATTATTATT
* **
268461 TACTATTACG
1 TATTATTATT
*
268471 TAGTATTATT
1 TATTATTATT
268481 TA-TATATATT
1 TATTAT-TATT
268491 ATATATATTAT
1 -TAT-TATTAT
268502 AAATTATAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
9 13 0.17
10 46 0.61
11 10 0.13
12 3 0.04
13 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (10 bp):
TATTATTATT
Found at i:286459 original size:28 final size:28
Alignment explanation
Indices: 286399--286460 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
286389 TTTAAATATT
286399 ATTTTTTATCTTTATAATTAAGATCTCA
1 ATTTTTTATCTTTATAATTAAGATCTCA
* * *
286427 TTTTTTTATTTTTATAATT-AGATCCTTA
1 ATTTTTTATCTTTATAATTAAGAT-CTCA
286455 ATTTTT
1 ATTTTT
286461 AAATCTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.61
Consensus pattern (28 bp):
ATTTTTTATCTTTATAATTAAGATCTCA
Found at i:294525 original size:29 final size:29
Alignment explanation
Indices: 294467--294535 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
294457 ACTTTCAATC
* *
294467 AAAAAT-AATTATACCTTCAATTTAG-TT
1 AAAAATCAATTATACCTTCAAATTAGCTA
294494 AAAAATCAATTATAACCTT-AAATTAGACTA
1 AAAAATCAATTAT-ACCTTCAAATTAG-CTA
294524 AATAAATCAATT
1 AA-AAATCAATT
294536 CACTTTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.17
28 12 0.34
29 5 0.14
30 3 0.09
31 9 0.26
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATCAATTATACCTTCAAATTAGCTA
Found at i:322239 original size:21 final size:21
Alignment explanation
Indices: 322211--322261 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
322201 AATGGCGCCC
* * *
322211 AATAGCGCTTGTGGCAGTCGT
1 AATAGCGCCTGCGACAGTCGT
*
322232 AATGGCGCCTGCGACAGTCGT
1 AATAGCGCCTGCGACAGTCGT
322253 AATAGCGCC
1 AATAGCGCC
322262 CACAATGGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (21 bp):
AATAGCGCCTGCGACAGTCGT
Found at i:322358 original size:80 final size:80
Alignment explanation
Indices: 322223--322385 Score: 290
Period size: 80 Copynumber: 2.0 Consensus size: 80
322213 TAGCGCTTGT
* * *
322223 GGCAGTCGTAATGGCGCCTGCGACAGTCGTAATAGCGCCCACAATGGTCACAATCACGATAAACC
1 GGCAGTCGTAATGGCGCCTGCGACAGTCGTAATAACGCCCACAACGGCCACAATCACGATAAACC
322288 CGAAATGACTAAAAA
66 CGAAATGACTAAAAA
*
322303 GGCAGTCGTAATGGCGCCTGCGACAGTCGTAATAACGCCCACAACGGCCATAATCACGATAAACC
1 GGCAGTCGTAATGGCGCCTGCGACAGTCGTAATAACGCCCACAACGGCCACAATCACGATAAACC
322368 CGAAATGACTAAAAA
66 CGAAATGACTAAAAA
322383 GGC
1 GGC
322386 GACTGCGATT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (80 bp):
GGCAGTCGTAATGGCGCCTGCGACAGTCGTAATAACGCCCACAACGGCCACAATCACGATAAACC
CGAAATGACTAAAAA
Found at i:326147 original size:13 final size:13
Alignment explanation
Indices: 326129--326153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326119 AAATAATGAT
326129 AGGTTTATAGCAA
1 AGGTTTATAGCAA
326142 AGGTTTATAGCA
1 AGGTTTATAGCA
326154 GTAGCAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
AGGTTTATAGCAA
Found at i:335661 original size:18 final size:19
Alignment explanation
Indices: 335631--335673 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
335621 TATTCTCTTA
*
335631 TTTT-TTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
335649 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
335667 TTTTATT
1 TTTTATT
335674 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:338038 original size:30 final size:27
Alignment explanation
Indices: 337975--338038 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
337965 ATAAATACTC
337975 AAAAAT-TATTATTTTATATATTTAAT
1 AAAAATATATTATTTTATATATTTAAT
**
338001 ATTAATATATTATTTTAATATCATTTTAAT
1 AAAAATATATTATTTT-ATAT-A-TTTAAT
338031 AAAAATAT
1 AAAAATAT
338039 TAATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 4 0.13
27 9 0.30
28 4 0.13
29 1 0.03
30 12 0.40
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAAATATATTATTTTATATATTTAAT
Found at i:338039 original size:28 final size:25
Alignment explanation
Indices: 337975--338040 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 25
337965 ATAAATACTC
337975 AAAAATTATTATTTTATATATTTAAT
1 AAAAA-TATTATTTTATATATTTAAT
*
338001 ATTAATATATTATTTTAATATCATTTTAAT
1 A--AAAATATTATTTT-ATAT-A-TTTAAT
338031 AAAAATATTA
1 AAAAATATTA
338041 ATTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 1 0.03
27 9 0.27
28 15 0.45
29 1 0.03
30 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
AAAAATATTATTTTATATATTTAAT
Found at i:338091 original size:21 final size:20
Alignment explanation
Indices: 338065--338132 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
338055 TTTATTGGTA
338065 ATTTTAATAATATAATATAAT
1 ATTTTAAT-ATATAATATAAT
* * *
338086 ATTTTATTGTTATAATTATATT
1 ATTTTAAT-ATATAA-TATAAT
*
338108 ATTATAATATATAATATAAT
1 ATTTTAATATATAATATAAT
338128 ATTTT
1 ATTTT
338133 TATTTTAATA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.24
21 17 0.46
22 11 0.30
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
ATTTTAATATATAATATAAT
Found at i:338112 original size:14 final size:13
Alignment explanation
Indices: 338071--338160 Score: 53
Period size: 14 Copynumber: 7.1 Consensus size: 13
338061 GGTAATTTTA
* *
338071 ATAATATAATATA
1 ATAATATATTATT
* * *
338084 ATATTTTATTGTT
1 ATAATATATTATT
338097 ATAATTATATTATT
1 ATAA-TATATTATT
*
338111 ATAATATA-TAAT
1 ATAATATATTATT
*
338123 ATAATATTTTTATT
1 ATAATA-TATTATT
*
338137 TTAATA-A-TA-T
1 ATAATATATTATT
*
338147 ATAATAAATTATT
1 ATAATATATTATT
338160 A
1 A
338161 ATAAAATAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
10 6 0.11
11 3 0.05
12 11 0.19
13 18 0.32
14 19 0.33
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (13 bp):
ATAATATATTATT
Found at i:338125 original size:26 final size:25
Alignment explanation
Indices: 338096--338173 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 25
338086 ATTTTATTGT
338096 TATAATTATATTATTATAATATATAA
1 TATAA-TATATTATTATAATATATAA
* *
338122 TATAATATTTTTATTTTAATA-AT-A
1 TATAATA-TATTATTATAATATATAA
* *
338146 TATAATAAATTATTAATAAAATA-AA
1 TATAATATATTATT-ATAATATATAA
338171 TAT
1 TAT
338174 TATTTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
23 5 0.12
24 12 0.29
25 9 0.21
26 16 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATAATATATTATTATAATATATAA
Found at i:338182 original size:21 final size:21
Alignment explanation
Indices: 338135--338182 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
338125 AATATTTTTA
*
338135 TTTTAATAATATATAATAAAT
1 TTTTAATAAAATATAATAAAT
* *
338156 TATTAATAAAATA-AATATTAT
1 TTTTAATAAAATATAATA-AAT
338177 TTTTAA
1 TTTTAA
338183 ATTTTATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTAATAAAATATAATAAAT
Found at i:338203 original size:26 final size:29
Alignment explanation
Indices: 338151--338203 Score: 85
Period size: 26 Copynumber: 1.9 Consensus size: 29
338141 TAATATATAA
338151 TAAATTATTAATAAAATAAATATTATTTT
1 TAAATTATTAATAAAATAAATATTATTTT
338180 TAAATT-TT-ATAAAA-AAATATTATT
1 TAAATTATTAATAAAATAAATATTATT
338204 GAATTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.42
27 6 0.25
28 2 0.08
29 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAATTATTAATAAAATAAATATTATTTT
Found at i:338299 original size:25 final size:25
Alignment explanation
Indices: 338231--338305 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
338221 ATATATACTC
* *
338231 TTTAA-AATATAATATAATATTCTTGT
1 TTTAATAA-ATAATA-AATATTATTAT
**
338257 TTTAATATTTTAAT-AATATTATTAT
1 TTTAATA-AATAATAAATATTATTAT
*
338282 TTTAATAAATAATAAATATAATTA
1 TTTAATAAATAATAAATATTATTA
338306 ATAATATATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 4 0.10
25 25 0.64
26 5 0.13
27 5 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTAATAAATAATAAATATTATTAT
Found at i:338331 original size:22 final size:23
Alignment explanation
Indices: 338280--338354 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 23
338270 TAATATTATT
* *
338280 ATTTTAATAA-ATAATAAATATA
1 ATTTTAATAATATAGTTAATATA
* * *
338302 A--TTAATAATATA-TTATTCTC
1 ATTTTAATAATATAGTTAATATA
338322 ATTTTAATAA-ATAGTTAATATA
1 ATTTTAATAATATAGTTAATATA
338344 ATTTTAATAAT
1 ATTTTAATAAT
338355 TTTATTTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 12 0.29
21 6 0.15
22 23 0.56
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTTTAATAATATAGTTAATATA
Found at i:338360 original size:42 final size:40
Alignment explanation
Indices: 338263--338361 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 40
338253 TTGTTTTAAT
*
338263 ATTTTAATAATATTA-TTATTTTAATAAATAATAAATATA
1 ATTTTAATAATTTTATTTATTTTAATAAATAATAAATATA
* *
338302 A--TTAATAATATATTATTCTCATTTTAATAAATAGTTAATATA
1 ATTTTAATAAT-T-TTATT-T-ATTTTAATAAATAATAAATATA
338344 ATTTTAATAATTTTATTT
1 ATTTTAATAATTTTATTT
338362 TAATAAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
37 8 0.16
39 4 0.08
40 1 0.02
41 2 0.04
42 26 0.52
43 1 0.02
44 8 0.16
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (40 bp):
ATTTTAATAATTTTATTTATTTTAATAAATAATAAATATA
Found at i:338464 original size:20 final size:20
Alignment explanation
Indices: 338438--338492 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
338428 ATTGACATAA
338438 ATAATATTAAATAAATTATT
1 ATAATATTAAATAAATTATT
*
338458 CTAATATTAAA-AATATTATT
1 ATAATATTAAATAA-ATTATT
*
338478 ATTATATT-AATAAAT
1 ATAATATTAAATAAAT
338493 AATATTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATAAATTATT
Found at i:338498 original size:21 final size:20
Alignment explanation
Indices: 338461--338501 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
338451 AATTATTCTA
*
338461 ATATTAAAAATATTATTATT
1 ATATTAAAAATAATATTATT
338481 ATATTAATAAATAATATTATT
1 ATATTAA-AAATAATATTATT
338502 CATTGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAAAAATAATATTATT
Found at i:338501 original size:24 final size:24
Alignment explanation
Indices: 338465--338510 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
338455 ATTCTAATAT
338465 TAAAAATATTATT-ATTATATTAA
1 TAAAAATATTATTCATTATATTAA
*
338488 TAAATAATATTATTCATTGTATT
1 TAAA-AATATTATTCATTATATT
338511 TGGTGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAAAATATTATTCATTATATTAA
Found at i:341219 original size:26 final size:25
Alignment explanation
Indices: 341156--341219 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
341146 ATTTTTTCTG
*
341156 AATATCTTATT-AATTTAAATTGTTT
1 AATAT-TTATTAAATTTAAATTGTAT
* * *
341181 AGTATTATTTTAAATTTTAATTCGTAT
1 AATATT-TATTAAATTTAAATT-GTAT
341208 AATATTTATTAA
1 AATATTTATTAA
341220 TTAGAGAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
24 1 0.03
25 7 0.23
26 14 0.47
27 8 0.27
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (25 bp):
AATATTTATTAAATTTAAATTGTAT
Found at i:343415 original size:30 final size:31
Alignment explanation
Indices: 343379--343445 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
343369 TGACCATTAC
343379 TTATGTAATTGTATTTTCTAATA-TTTCAAT
1 TTATGTAATTGTATTTTCTAATACTTTCAAT
* * **
343409 TTATGTAATTTTATTTTTTTGTACTTTCAAT
1 TTATGTAATTGTATTTTCTAATACTTTCAAT
343440 TTATGT
1 TTATGT
343446 TATTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.25, C:0.06, G:0.07, T:0.61
Consensus pattern (31 bp):
TTATGTAATTGTATTTTCTAATACTTTCAAT
Found at i:343440 original size:31 final size:30
Alignment explanation
Indices: 343379--343458 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
343369 TGACCATTAC
*
343379 TTATGTAATTGTATTTTCTAATATTTCAAT
1 TTATGTAATTTTATTTTCTAATATTTCAAT
* **
343409 TTATGTAATTTTATTTTTTTGTACTTTCAAT
1 TTATGTAATTTTATTTTCTAATA-TTTCAAT
* *
343440 TTATGTTATTTTCTTTTCT
1 TTATGTAATTTTATTTTCT
343459 TTTATAAGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.23, C:0.07, G:0.06, T:0.64
Consensus pattern (30 bp):
TTATGTAATTTTATTTTCTAATATTTCAAT
Found at i:343610 original size:26 final size:26
Alignment explanation
Indices: 343578--343645 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
343568 TTTAAACAAT
343578 AAAACCCTAAACCACTCAAGCAAATA
1 AAAACCCTAAACCACTCAAGCAAATA
343604 AAAACCCTAAACCACTCAAGCAAATA
1 AAAACCCTAAACCACTCAAGCAAATA
343630 AAAACCCTAAACCACT
1 AAAACCCTAAACCACT
343646 ATCTAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.53, C:0.32, G:0.03, T:0.12
Consensus pattern (26 bp):
AAAACCCTAAACCACTCAAGCAAATA
Found at i:352672 original size:31 final size:31
Alignment explanation
Indices: 352631--352709 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
352621 ATTCAATGTC
*
352631 CAAGTGATCAAAACTTAATAAAACGATAACG
1 CAAGTGATCAAAACTTAATAAAACAATAACG
* *
352662 TAAGTAATCAAAACTTAATAAAACAATAACG
1 CAAGTGATCAAAACTTAATAAAACAATAACG
*
352693 CAAGTGACCAAAACTTA
1 CAAGTGATCAAAACTTA
352710 TGTTTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.20
Consensus pattern (31 bp):
CAAGTGATCAAAACTTAATAAAACAATAACG
Found at i:354745 original size:3 final size:3
Alignment explanation
Indices: 354726--354790 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
354716 GATGTGGCAT
* *
354726 TTA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA TTCAA TTA ATA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA
* *
354771 TTA TTA TTA GTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TT
354791 TATAATTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
5 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:355292 original size:8 final size:8
Alignment explanation
Indices: 355280--355314 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
355270 TTTAATCTCC
*
355280 CTTGTTTC
1 CTTGTTTA
355288 CTTGTTTA
1 CTTGTTTA
355296 CTTGTTTA
1 CTTGTTTA
355304 CTTGTTTA
1 CTTGTTTA
355312 CTT
1 CTT
355315 AGGTCCTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.63
Consensus pattern (8 bp):
CTTGTTTA
Found at i:357373 original size:21 final size:21
Alignment explanation
Indices: 357347--357391 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
357337 GATTTCTGGG
* *
357347 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
357368 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
357389 CAA
1 CAA
357392 ACGACAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:357983 original size:18 final size:18
Alignment explanation
Indices: 357960--357994 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
357950 CTAGGAGATT
357960 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
357978 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
357995 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:358080 original size:21 final size:22
Alignment explanation
Indices: 358051--358094 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
358041 GTTGTATGAT
358051 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
358072 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
358094 A
1 A
358095 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:359038 original size:149 final size:148
Alignment explanation
Indices: 358858--359307 Score: 850
Period size: 149 Copynumber: 3.0 Consensus size: 148
358848 GAGTCGAGGG
*
358858 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCCGGAAAGACATAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACA-AT
358923 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
358988 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
359007 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACA-AT
359072 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
359137 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
359156 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACA--TGTGAAGTCTGGAAAGACAATA
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACAATA
*
359219 CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTAT
66 CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTAT
359284 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
359302 TCTACG
1 TCTACG
359308 GGGCACTTCG
Statistics
Matches: 298, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
146 91 0.31
147 19 0.06
149 188 0.63
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACAATA
CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:359330 original size:23 final size:23
Alignment explanation
Indices: 359286--359330 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
359276 ATCATTATAT
*
359286 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
359309 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
359331 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:366619 original size:16 final size:17
Alignment explanation
Indices: 366593--366625 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
366583 TTGATCAATG
*
366593 AAAGAAAAAAAATAATC
1 AAAGAAAAAAAAGAATC
366610 AAAG-AAAAAAAGAATC
1 AAAGAAAAAAAAGAATC
366626 TTTGGTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAGAAAAAAAAGAATC
Found at i:367511 original size:2 final size:2
Alignment explanation
Indices: 367504--367535 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
367494 CCGCCTCGAT
367504 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
367536 TTTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:367542 original size:15 final size:15
Alignment explanation
Indices: 367502--367564 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 15
367492 TCCCGCCTCG
367502 ATTATATATATATAT
1 ATTATATATATATAT
367517 ATATATAATATATATAT
1 AT-TAT-ATATATATAT
* * *
367534 ATTTTATATTTTTATT
1 ATTATATATATATA-T
367550 AATTATATATA-ATAT
1 -ATTATATATATATAT
367565 TTGGGTTCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
15 10 0.26
16 8 0.21
17 20 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATATATATATAT
Found at i:370770 original size:15 final size:15
Alignment explanation
Indices: 370754--370782 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
370744 AAAATATAAT
370754 TTTAT-TATTTTTAA
1 TTTATATATTTTTAA
370768 TTTATATATTTTTAA
1 TTTATATATTTTTAA
370783 ATAAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATATTTTTAA
Found at i:371218 original size:16 final size:17
Alignment explanation
Indices: 371199--371230 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
371189 TAATTCGACC
371199 CGAAAATTGA-CTTACT
1 CGAAAATTGACCTTACT
371215 CGAAAATTGACCTTAC
1 CGAAAATTGACCTTAC
371231 ATGTTACCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (17 bp):
CGAAAATTGACCTTACT
Found at i:374315 original size:18 final size:18
Alignment explanation
Indices: 374271--374315 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
374261 CAGTTTAAGG
* *
374271 AAAGAAACCTGATAAAAC
1 AAAGAAACTTGACAAAAC
374289 AAAGAAACTTGACAAAAC
1 AAAGAAACTTGACAAAAC
374307 AAAGAAACT
1 AAAGAAACT
374316 AGGCAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.62, C:0.16, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAGAAACTTGACAAAAC
Found at i:379076 original size:20 final size:21
Alignment explanation
Indices: 379051--379094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
379041 TAGAAGTTCT
*
379051 TTCAGTTTTGC-TTATCTTTC
1 TTCAGTTTTACGTTATCTTTC
*
379071 TTCAGTTTTACGTTCTCTTTC
1 TTCAGTTTTACGTTATCTTTC
379092 TTC
1 TTC
379095 TTTCTCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.09, C:0.23, G:0.09, T:0.59
Consensus pattern (21 bp):
TTCAGTTTTACGTTATCTTTC
Found at i:379459 original size:10 final size:11
Alignment explanation
Indices: 379444--379484 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
379434 TATAATTCAA
379444 ATTTTAT-TTT
1 ATTTTATATTT
379454 ATTTTATATTT
1 ATTTTATATTT
*
379465 ATTTT-TAATT
1 ATTTTATATTT
379475 A-TTTATATTT
1 ATTTTATATTT
379485 TTATGATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.11
10 16 0.59
11 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:379797 original size:20 final size:20
Alignment explanation
Indices: 379758--379796 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
379748 ATTTATTAAC
379758 AAAATAATAATAATAATTTT
1 AAAATAATAATAATAATTTT
*
379778 AAAATATTAA-AATAATTTT
1 AAAATAATAATAATAATTTT
379797 TTAATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAATAATAATAATTTT
Found at i:379879 original size:21 final size:22
Alignment explanation
Indices: 379851--379909 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
379841 AAAATAAAAT
379851 TATTATTAAATTATATTAAGTA
1 TATTATTAAATTATATTAAGTA
*
379873 T-TTATTACAA-TA-AAT-AGTA
1 TATTATTA-AATTATATTAAGTA
379892 TATTATT-AATTATATTAA
1 TATTATTAAATTATATTAA
379910 TTTCTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
18 2 0.07
19 7 0.23
20 9 0.30
21 9 0.30
22 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (22 bp):
TATTATTAAATTATATTAAGTA
Found at i:379918 original size:40 final size:37
Alignment explanation
Indices: 379841--379937 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 37
379831 TATAAATAGA
379841 AAAATAA-AATTATTATTAAATTATATTAAGTATTTATT
1 AAAATAATAA-TATTATT-AATTATATTAAGTATTTATT
* *
379879 ACAATAAATAGTATATTATTAATTATATTAA-TTTCTTATT
1 AAAAT-AATA--ATATTATTAATTATATTAAGTAT-TTATT
379919 AAAATAATAATATTATTAA
1 AAAATAATAATATTATTAA
379938 AATACTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
37 10 0.20
38 4 0.08
39 8 0.16
40 21 0.41
41 7 0.14
42 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (37 bp):
AAAATAATAATATTATTAATTATATTAAGTATTTATT
Found at i:379936 original size:17 final size:17
Alignment explanation
Indices: 379914--379974 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
379904 TATTAATTTC
*
379914 TTATTAAAATAATAATA
1 TTATTAAAATAAAAATA
379931 TTATTAAAATACTAAAATTA
1 TTATTAAAATA--AAAA-TA
379951 TAGTATTAAAATAAAAATA
1 T--TATTAAAATAAAAATA
379970 TTATT
1 TTATT
379975 TTATTTTGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 15 0.39
19 6 0.16
20 7 0.18
22 10 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TTATTAAAATAAAAATA
Found at i:379979 original size:22 final size:22
Alignment explanation
Indices: 379928--379979 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
379918 TAAAATAATA
*
379928 ATATTATTAAAATACTAAAATT
1 ATATTATTAAAATACAAAAATT
*
379950 ATAGTATTAAAATA-AAAATATT
1 ATATTATTAAAATACAAAA-ATT
*
379972 ATTTTATT
1 ATATTATT
379980 TTGAGGAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTATTAAAATACAAAAATT
Found at i:381518 original size:9 final size:9
Alignment explanation
Indices: 381504--381568 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
381494 ACATTAACAG
381504 ATAATGCAC
1 ATAATGCAC
381513 ATAATG-AC
1 ATAATGCAC
*
381521 ATTAA--CAG
1 A-TAATGCAC
381529 ATAATGCAC
1 ATAATGCAC
381538 ATAATG-AC
1 ATAATGCAC
*
381546 ATTAA--CAG
1 A-TAATGCAC
381554 ATAATGCAC
1 ATAATGCAC
381563 ATAATG
1 ATAATG
381569 ACAGACGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
7 6 0.14
8 10 0.23
9 28 0.64
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (9 bp):
ATAATGCAC
Found at i:381522 original size:25 final size:25
Alignment explanation
Indices: 381493--381571 Score: 158
Period size: 25 Copynumber: 3.2 Consensus size: 25
381483 ATATTTACTA
381493 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
381518 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
381543 GACATTAACAGATAATGCACATAAT
1 GACATTAACAGATAATGCACATAAT
381568 GACA
1 GACA
381572 GACGAAGTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (25 bp):
GACATTAACAGATAATGCACATAAT
Found at i:393929 original size:31 final size:32
Alignment explanation
Indices: 393869--393940 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
393859 TGGTTGAAGG
* *
393869 GATTAAAATTGAACGAGAGTTAACGATTGAGA
1 GATTAAAATTAAACGAGAGTTAACAATTGAGA
* *
393901 GATTAAAATTAAAC-AGGGTTAACAATTGAGG
1 GATTAAAATTAAACGAGAGTTAACAATTGAGA
*
393932 GACTAAAAT
1 GATTAAAAT
393941 CGAATAGATC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (32 bp):
GATTAAAATTAAACGAGAGTTAACAATTGAGA
Found at i:397214 original size:4 final size:4
Alignment explanation
Indices: 397205--397240 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
397195 AAAGAGTTAT
397205 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
397241 TTTATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:406582 original size:29 final size:29
Alignment explanation
Indices: 406539--406621 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
406529 CTCACCTAAC
406539 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
406569 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
406598 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
406622 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:409985 original size:15 final size:15
Alignment explanation
Indices: 409965--409994 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
409955 CTTTCTCATA
409965 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
409980 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
409995 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:411326 original size:29 final size:29
Alignment explanation
Indices: 411283--411365 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
411273 CTCACCTAAC
411283 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
411313 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
411342 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
411366 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:412308 original size:19 final size:19
Alignment explanation
Indices: 412284--412333 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
412274 CGCTATTGCA
412284 GCTCCATAGGTCACAAAGT
1 GCTCCATAGGTCACAAAGT
*
412303 GCTCCATAGGTCACCAAGT
1 GCTCCATAGGTCACAAAGT
* *
412322 ACTTCATAGGTC
1 GCTCCATAGGTC
412334 GTCGTGTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (19 bp):
GCTCCATAGGTCACAAAGT
Found at i:412383 original size:30 final size:30
Alignment explanation
Indices: 412329--412388 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
412319 AGTACTTCAT
* *
412329 AGGTCGTCGTGTGCTCTTTGAGACCAATGG
1 AGGTCGTCATGTGCTCTCTGAGACCAATGG
*
412359 AGGTCGTCATGTGCTC-CTGAAGACCTATGG
1 AGGTCGTCATGTGCTCTCTG-AGACCAATGG
412389 TGGTAACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (30 bp):
AGGTCGTCATGTGCTCTCTGAGACCAATGG
Found at i:412824 original size:2 final size:2
Alignment explanation
Indices: 412811--412841 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
412801 GAGTATTATT
*
412811 TA TA TT 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 TA T
412842 TATTTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:422053 original size:2 final size:2
Alignment explanation
Indices: 422046--422104 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
422036 TCTTTCCATT
422046 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
422088 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
422105 CCATTAGTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:422313 original size:17 final size:17
Alignment explanation
Indices: 422266--422307 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
422256 GAAGCAGAAA
422266 CGTTCAAGAAAAAAACT
1 CGTTCAAGAAAAAAACT
*
422283 CATTCAAGAAAAAAAACT
1 CGTTCAAG-AAAAAAACT
422301 CGTTCAA
1 CGTTCAA
422308 ACAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (17 bp):
CGTTCAAGAAAAAAACT
Found at i:424500 original size:18 final size:18
Alignment explanation
Indices: 424477--424511 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
424467 ATTAAAATGA
424477 TATATTT-TGTAATAATTT
1 TATATTTCT-TAATAATTT
424495 TATATTTCTTAATAATT
1 TATATTTCTTAATAATT
424512 AAATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATTTCTTAATAATTT
Found at i:431598 original size:31 final size:31
Alignment explanation
Indices: 431563--431649 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
431553 GTACTTTTCA
431563 TTTGATAAAATGTCCAATATGGTACAC-ATAC
1 TTTGATAAAATGTCCAATATGGTAC-CTATAC
** *
431594 TTTGATAAAATGTCCAACGTGGTGCCTATAC
1 TTTGATAAAATGTCCAATATGGTACCTATAC
*
431625 TTTG-TCAAAATGTCTAATATGGTAC
1 TTTGAT-AAAATGTCCAATATGGTAC
431650 TTGAATTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 45 0.96
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (31 bp):
TTTGATAAAATGTCCAATATGGTACCTATAC
Found at i:434555 original size:3 final size:3
Alignment explanation
Indices: 434549--434579 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
434539 GAGGAGGAAA
434549 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
434580 GTCAAACGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:434711 original size:30 final size:32
Alignment explanation
Indices: 434677--434743 Score: 111
Period size: 30 Copynumber: 2.2 Consensus size: 32
434667 GTTAACGACG
*
434677 AGTGATCATTTTGTAACAAAC-A-ATAATATT
1 AGTGATCATTTTGTAACAAACTATATAAAATT
434707 AGTGATCATTTTGTAACAAACTATATAAAATT
1 AGTGATCATTTTGTAACAAACTATATAAAATT
434739 AGTGA
1 AGTGA
434744 CTAATTTGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 21 0.62
31 1 0.03
32 12 0.35
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (32 bp):
AGTGATCATTTTGTAACAAACTATATAAAATT
Found at i:434752 original size:32 final size:30
Alignment explanation
Indices: 434677--434752 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
434667 GTTAACGACG
* *
434677 AGTGATCATTTTGTAACAAACAATAATATT
1 AGTGATCAATTTGTAACAAACAATAAAATT
*
434707 AGTGATCATTTTGTAACAAACTATATAAAATT
1 AGTGATCAATTTGTAACAAAC-A-ATAAAATT
434739 AGTGA-CTAATTTGT
1 AGTGATC-AATTTGT
434753 GACTTTTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 21 0.51
31 2 0.05
32 18 0.44
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (30 bp):
AGTGATCAATTTGTAACAAACAATAAAATT
Found at i:447004 original size:13 final size:13
Alignment explanation
Indices: 446986--447010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
446976 AAATTATAAT
446986 AAAACCGAATTAG
1 AAAACCGAATTAG
446999 AAAACCGAATTA
1 AAAACCGAATTA
447011 CAAGGCTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAACCGAATTAG
Found at i:447964 original size:3 final size:3
Alignment explanation
Indices: 447939--447990 Score: 77
Period size: 3 Copynumber: 16.7 Consensus size: 3
447929 TTGGGTTTTG
*
447939 TAA TAT TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
447986 TAA TA
1 TAA TA
447991 GATTTAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:448254 original size:76 final size:76
Alignment explanation
Indices: 448124--448992 Score: 1569
Period size: 76 Copynumber: 11.4 Consensus size: 76
448114 GATGAAAATA
448124 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
448189 CCCTAAGGCTT
66 CCCGAAGGCTT
* * *
448200 TTTAGAAACATCATGCACTGCAGGACTTACAGATGACTCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448265 CCCGAAGGCTT
66 CCCGAAGGCTT
*
448276 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
448340 CCAGAAGGCTT
66 CCCGAAGGCTT
*
448351 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATAAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448416 CCCGAAGGCTT
66 CCCGAAGGCTT
448427 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448492 CCCGAAGGCTT
66 CCCGAAGGCTT
448503 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448568 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
448579 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448644 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
448655 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448720 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
448731 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATAAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448796 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
448807 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATAAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448872 CCCGAAGGCTT
66 CCCGAAGGCTT
*
448883 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
448948 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
448959 TTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGAT
448993 ATGGGAAATA
Statistics
Matches: 770, Mismatches: 22, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 0.09
76 697 0.91
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:449878 original size:22 final size:22
Alignment explanation
Indices: 449850--449904 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
449840 CATAAAGCTT
449850 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
449872 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
449894 TCATCTTTGAA
1 TCATCTTTGAA
449905 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:451424 original size:76 final size:76
Alignment explanation
Indices: 451249--451424 Score: 212
Period size: 76 Copynumber: 2.3 Consensus size: 76
451239 AGGATGTTGT
* * * * * *
451249 GGGCCTTCAGCATGCCCCAATA-TTTGCTGATATGAGCGTTCAAAATACATCAACATTCTTCATT
1 GGGCTTTCAGCATGCCCCAACATTTTGCTGATATAAACATTCAAAATACATCAACATTCCTCATT
451313 CTGATTGAAAG
66 CTGATTGAAAG
* * * ** *
451324 GGGCTTTCAGTATGCCCTAGCATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTGATT
1 GGGCTTTCAGCATGCCCCAACATTTTGCTGATATAAACATTCAAAATACATCAACATTCCTCATT
451389 CTGATTGACAA-
66 CTGATTGA-AAG
*
451400 GGGTTTTCAGCATGCCCCAACATTT
1 GGGCTTTCAGCATGCCCCAACATTT
451425 GTTTCTTGTT
Statistics
Matches: 83, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
75 17 0.20
76 64 0.77
77 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (76 bp):
GGGCTTTCAGCATGCCCCAACATTTTGCTGATATAAACATTCAAAATACATCAACATTCCTCATT
CTGATTGAAAG
Found at i:452762 original size:114 final size:114
Alignment explanation
Indices: 452562--452892 Score: 527
Period size: 114 Copynumber: 2.9 Consensus size: 114
452552 ATCATGCAGC
* * * * *
452562 TCATCTTTTAATTCCAATGATTGGTTATGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAA
1 TCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* *
452627 TACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAAT
66 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAAT
* *
452676 TCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 TCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* * *
452741 CACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATGAGCAAAT
66 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAAT
**
452790 TCATCTTTTAAATCCAATGATTAATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 TCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
*
452855 CACTTCCAGAAGATGCTATTGGGTCTCTTTATTTCTAC
66 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAC
452893 TACGAGAACA
Statistics
Matches: 198, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 198 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAAT
Found at i:460271 original size:13 final size:13
Alignment explanation
Indices: 460253--460277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460243 AAATTATAAT
460253 AAAACCGAATTAG
1 AAAACCGAATTAG
460266 AAAACCGAATTA
1 AAAACCGAATTA
460278 CAAGGCTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAACCGAATTAG
Found at i:461023 original size:3 final size:3
Alignment explanation
Indices: 460991--461055 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
460981 TTGGGTTTTG
* * *
460991 TAA TAT TAA TAAA TAA TATA TAA TAT TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
461038 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
461056 ATTTAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:463711 original size:16 final size:15
Alignment explanation
Indices: 463671--463727 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
463661 AAAATTAATG
463671 AAAATAAATAAAT-AA
1 AAAATAAAT-AATGAA
*
463686 AAAATAAATACTGAA
1 AAAATAAATAATGAA
*
463701 AAAATATAATAATGAG
1 AAAATA-AATAATGAA
463717 AAAATAAATAA
1 AAAATAAATAA
463728 AGTAAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 2 0.05
15 22 0.59
16 13 0.35
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATAAATAATGAA
Found at i:467603 original size:41 final size:41
Alignment explanation
Indices: 467523--467606 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
467513 ATGGCCTGGT
* * *
467523 CTATTTAACTAAACAGGCCAGGCTCAGGCCTTTTTAAAAGC
1 CTATTTAACTAAACAGGCCAGGCTCAGGCATATTAAAAAGC
* *
467564 CTATTTAACTAAACAGGCCAGGCTTAGGTATATTAAAAAGC
1 CTATTTAACTAAACAGGCCAGGCTCAGGCATATTAAAAAGC
467605 CT
1 CT
467607 TATAAGCCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (41 bp):
CTATTTAACTAAACAGGCCAGGCTCAGGCATATTAAAAAGC
Found at i:467772 original size:17 final size:18
Alignment explanation
Indices: 467750--467786 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
467740 TTTTAAACAT
467750 GCTTTTAAACAGG-CCAG
1 GCTTTTAAACAGGCCCAG
467767 GCTTTTAAACAGGCCCAG
1 GCTTTTAAACAGGCCCAG
467785 GC
1 GC
467787 CAGGCCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (18 bp):
GCTTTTAAACAGGCCCAG
Found at i:475784 original size:23 final size:22
Alignment explanation
Indices: 475758--475800 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
475748 TATAAAAAAT
475758 TATTTTTTATTAAATATTTTTGA
1 TATTTTTTATTAAAT-TTTTTGA
*
475781 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
475801 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGA
Found at i:488385 original size:20 final size:20
Alignment explanation
Indices: 488324--488532 Score: 226
Period size: 20 Copynumber: 10.4 Consensus size: 20
488314 CAGTTTCCAG
* ** *
488324 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
488344 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
488364 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
488384 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
488404 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
488424 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
488444 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
488464 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
488484 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
488504 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
488524 AATCGCAAC
1 AATCGCAAC
488533 AAGAATCTGT
Statistics
Matches: 160, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 156 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:488539 original size:20 final size:20
Alignment explanation
Indices: 488362--488552 Score: 215
Period size: 20 Copynumber: 9.6 Consensus size: 20
488352 CGCGAACACA
*
488362 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
488382 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
488402 TAAATAGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
488422 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
488442 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
488462 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
488482 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
488502 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* * *
488522 TAAATCGCAACAAGAATCTG
1 TAAATCGCAACGAGTATCCG
*
488542 TAAATCACAAC
1 TAAATCGCAAC
488553 ACTGAAATTT
Statistics
Matches: 148, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 147 0.99
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:488685 original size:21 final size:21
Alignment explanation
Indices: 488650--488689 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
488640 CTCTCTCCGG
488650 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCTA-ATCCAA
488672 CGACATCC-TTCCTAATCC
1 CGACATCCGTTCCTAATCC
488690 GGCAACAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.25, C:0.40, G:0.07, T:0.28
Consensus pattern (21 bp):
CGACATCCGTTCCTAATCCAA
Found at i:489284 original size:24 final size:24
Alignment explanation
Indices: 489245--489291 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
489235 AAATTTGGTC
489245 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
489269 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
489292 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:489483 original size:12 final size:12
Alignment explanation
Indices: 489466--489490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
489456 ATATAATCCT
489466 GAAGAAGAAAAA
1 GAAGAAGAAAAA
489478 GAAGAAGAAAAA
1 GAAGAAGAAAAA
489490 G
1 G
489491 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:491839 original size:34 final size:34
Alignment explanation
Indices: 491752--491951 Score: 253
Period size: 34 Copynumber: 5.8 Consensus size: 34
491742 GCATTTGACT
** * * *
491752 ATCGCAACACGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
*
491786 ATCGCAATGC-GAAATGAAAATCCCAAC-ATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAACGA-GAAA
491819 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAAA
*
491858 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
*
491891 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
491925 ATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
491952 TGCGAAATGA
Statistics
Matches: 150, Mismatches: 8, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
32 1 0.01
33 40 0.27
34 74 0.49
36 3 0.02
38 16 0.11
39 16 0.11
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
Found at i:491848 original size:53 final size:53
Alignment explanation
Indices: 491785--492022 Score: 328
Period size: 53 Copynumber: 4.5 Consensus size: 53
491775 GCAACGAGAG
*
491785 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAAAATCGCAATGCGGAAATGAA
*
491838 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGGAAATGAA
*
491890 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGGAAATGAA
*
491944 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGGAAATGAA
491997 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
492023 TTGCGATTCT
Statistics
Matches: 169, Mismatches: 4, Indels: 24
0.86 0.02 0.12
Matches are distributed among these distances:
48 10 0.06
49 1 0.01
50 1 0.01
51 3 0.02
52 13 0.08
53 112 0.66
54 13 0.08
55 2 0.01
56 1 0.01
58 13 0.08
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGGAAATGAA
Found at i:491950 original size:87 final size:86
Alignment explanation
Indices: 491838--492004 Score: 325
Period size: 87 Copynumber: 1.9 Consensus size: 86
491828 CGGAAATGAA
491838 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
491903 AAATGAAAATCGCAACGAGAG
66 AAATGAAAATCGCAACGAGAG
491924 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
491989 GAAATGAAAATCGCAA
65 GAAATGAAAATCGCAA
492005 TGCGAAATGA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 11 0.14
87 69 0.86
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (86 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG
AAATGAAAATCGCAACGAGAG
Found at i:492062 original size:53 final size:52
Alignment explanation
Indices: 491999--492114 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
491989 GAAATGAAAA
*
491999 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
492051 TCCGCATTGCGATTTTTATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
492104 TCGCATTGCGA
1 TCGCATTGCGA
492115 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:492077 original size:19 final size:19
Alignment explanation
Indices: 492037--492154 Score: 165
Period size: 19 Copynumber: 6.4 Consensus size: 19
492027 GATTCTCTCG
492037 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
492057 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
492076 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
492090 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
492109 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
492128 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
492148 TTGCGAT
1 TTGCGAT
492155 AGTCATTTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 12
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 6 0.07
19 44 0.50
20 25 0.28
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:492099 original size:33 final size:35
Alignment explanation
Indices: 492056--492154 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 35
492046 TCATTTCCGC
*
492056 ATTGCGATTTTTATTTCGCATTGCGATTC-TCTCG
1 ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
*
492090 -TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCGCATTGCGA--TTCATCTCG
492126 CATTGCGATTTTCATTTCCGCATTGCGAT
1 -ATTGCGATTTTCATTT-CGCATTGCGAT
492155 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
33 24 0.42
35 3 0.05
36 4 0.07
37 1 0.02
38 15 0.26
39 10 0.18
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (35 bp):
ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
Found at i:492131 original size:52 final size:53
Alignment explanation
Indices: 492018--492135 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
492008 GAAATGAAAA
*
492018 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTTATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
492071 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
492123 TCGCATTGCGATT
1 TCGCATTGCGATT
492136 TTCATTTCCG
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:492280 original size:14 final size:14
Alignment explanation
Indices: 492261--492297 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
492251 CATCAATTAC
492261 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
492275 ACAAATCATCTTTT
1 ACAAATCAACTTTT
492289 ACAAATCAA
1 ACAAATCAA
492298 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:494264 original size:19 final size:19
Alignment explanation
Indices: 494222--494375 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
494212 TAGTTTACTT
* *
494222 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
494242 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
494261 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
494280 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
494299 TTGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
494313 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
494332 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
494346 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
494365 TCGCAATGCGA
1 TCGCAACGCGA
494376 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 7 0.07
17 7 0.07
18 1 0.01
19 62 0.58
20 12 0.11
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:494324 original size:33 final size:33
Alignment explanation
Indices: 494240--494370 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
494230 CGAAACTTAA
* *
494240 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
*
494278 AATCGCAACGCGAAATGAAAATTGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
494311 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
494344 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
494371 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 58 0.67
34 1 0.01
36 1 0.01
38 26 0.30
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:494367 original size:52 final size:51
Alignment explanation
Indices: 494239--494375 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 51
494229 ACGAAACTTA
* * * *
494239 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* *** * * **
494290 AAAT-GAAAATTGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
494342 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
494376 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 40 0.62
53 4 0.06
54 8 0.12
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:494406 original size:14 final size:14
Alignment explanation
Indices: 494387--494413 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
494377 TTTGGTTTCG
494387 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
494401 CGTTGCGATTTTG
1 CGTTGCGATTTTG
494414 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:494413 original size:33 final size:33
Alignment explanation
Indices: 494371--494465 Score: 145
Period size: 33 Copynumber: 2.9 Consensus size: 33
494361 AAAATCGCAA
**
494371 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTACCGT
*
494404 TGCGATTTTGGTTTCGCGTTGCGATTCTACCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTACCGT
**
494437 TGCGATTTTCATTTCGCGTTGCGATTTTA
1 TGCGATTTTGGTTTCGCGTTGCGATTTTA
494466 AGTTTCATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTACCGT
Found at i:494425 original size:19 final size:19
Alignment explanation
Indices: 494371--494429 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
494361 AAAATCGCAA
494371 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
494390 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
494404 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
494423 TGCGATT
1 TGCGATT
494430 CTACCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:494458 original size:19 final size:18
Alignment explanation
Indices: 494371--494464 Score: 69
Period size: 19 Copynumber: 5.5 Consensus size: 18
494361 AAAATCGCAA
*
494371 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-CTTTCGCGT
*
494390 TGCGA-TTT-TGT--CGT
1 TGCGATTTTCTTTCGCGT
*
494404 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-CTTTCGCGT
*
494423 TGCGA--TTC-TAC-CGT
1 TGCGATTTTCTTTCGCGT
494437 TGCGATTTTCATTTCGCGT
1 TGCGATTTTC-TTTCGCGT
494456 TGCGATTTT
1 TGCGATTTT
494465 AAGTTTCATG
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 16 0.27
15 5 0.08
16 5 0.08
17 4 0.07
18 5 0.08
19 25 0.42
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (18 bp):
TGCGATTTTCTTTCGCGT
Found at i:494477 original size:20 final size:19
Alignment explanation
Indices: 494434--494480 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
494424 GCGATTCTAC
* *
494434 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCA
494453 CGTTGCGATTTTAAGTTTCA
1 CGTTGCGATTTTAA-TTTCA
*
494473 TGTTGCGA
1 CGTTGCGA
494481 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCA
Found at i:496423 original size:20 final size:20
Alignment explanation
Indices: 496392--496488 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
496382 TTTTGGTTGA
496392 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
496412 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
496432 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
496451 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
496466 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
496486 AAT
1 AAT
496489 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:496444 original size:21 final size:21
Alignment explanation
Indices: 496390--496454 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
496380 TCTTTTGGTT
496390 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
496411 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
496431 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
496452 GAA
1 GAA
496455 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:496458 original size:14 final size:14
Alignment explanation
Indices: 496439--496495 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
496429 GAGAAATGAA
496439 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
496453 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
496472 AATCGCAACGAGAG
1 AATCGCAACGAGAG
496486 AATCGCAACG
1 AATCGCAACG
496496 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:496471 original size:33 final size:33
Alignment explanation
Indices: 496390--496512 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
496380 TCTTTTGGTT
*
496390 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
496431 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
496464 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
496497 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
496513 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:496548 original size:14 final size:14
Alignment explanation
Indices: 496529--496585 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
496519 TTTGGTTTCG
496529 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
496543 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
496562 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
496576 CGTTGCGATT
1 CGTTGCGATT
496586 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:496561 original size:33 final size:33
Alignment explanation
Indices: 496513--496592 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
496503 AAAATCGCAA
**
496513 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
496546 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
496579 TGCGATTTTCATTT
1 TGCGATTTTCATTT
496593 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:496598 original size:21 final size:21
Alignment explanation
Indices: 496573--496646 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
496563 GTTGCGATTC
496573 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
496594 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
496615 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
496636 TCTCGTTGCGA
1 TCTCGTTGCGA
496647 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:496767 original size:33 final size:33
Alignment explanation
Indices: 496725--496795 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
496715 AATACTAACT
496725 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
496758 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
496791 TGAAA
1 TGAAA
496796 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:497201 original size:20 final size:20
Alignment explanation
Indices: 497176--497368 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
497166 CTTTAAAAAT
497176 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
497196 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
497216 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
497237 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
497257 CGCATTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
497277 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
497297 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
497317 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
497337 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
497357 CGCGTTGCGATT
1 CGCGTTGCGATT
497369 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 130 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:502127 original size:13 final size:13
Alignment explanation
Indices: 502109--502136 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
502099 AGCCATCGCC
502109 ATCCGTATCAGTT
1 ATCCGTATCAGTT
502122 ATCCGTATCAGTT
1 ATCCGTATCAGTT
502135 AT
1 AT
502137 AAGGGATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (13 bp):
ATCCGTATCAGTT
Found at i:502503 original size:13 final size:13
Alignment explanation
Indices: 502485--502517 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
502475 GAAATAAATT
*
502485 TTTAAAAGTGTTG
1 TTTAAAAGTGTAG
502498 TTTAAAAGTGTAG
1 TTTAAAAGTGTAG
502511 TTTAAAA
1 TTTAAAA
502518 TTTAACTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
TTTAAAAGTGTAG
Found at i:502711 original size:15 final size:15
Alignment explanation
Indices: 502691--502733 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
502681 ATATTTTAAG
502691 ATTAATAAAAAATTT
1 ATTAATAAAAAATTT
* *
502706 ATTAATGAAATATTTT
1 ATTAAT-AAAAAATTT
*
502722 ATTAAGAAAAAA
1 ATTAATAAAAAA
502734 AATACATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (15 bp):
ATTAATAAAAAATTT
Found at i:504795 original size:38 final size:34
Alignment explanation
Indices: 504759--504823 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
504749 ATATATATAT
504759 TATAA-ATAAATGATATATTTATCCTTTTAATAA
1 TATAATATAAATGATATATTTATCCTTTTAATAA
*
504792 TATAATTTAAATGATATATTTATCCTTTTAAT
1 TATAATATAAATGATATATTTATCCTTTTAAT
504824 CTTTCAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (34 bp):
TATAATATAAATGATATATTTATCCTTTTAATAA
Found at i:504910 original size:11 final size:11
Alignment explanation
Indices: 504894--504923 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
504884 ATATCAATTT
504894 AAAATATAGTA
1 AAAATATAGTA
504905 AAAATATAGTA
1 AAAATATAGTA
*
504916 AATATATA
1 AAAATATA
504924 TATATATATA
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:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (11 bp):
AAAATATAGTA
Found at i:505333 original size:15 final size:15
Alignment explanation
Indices: 505323--505382 Score: 102
Period size: 15 Copynumber: 4.0 Consensus size: 15
505313 TAATAAGGTT
505323 ATTTATTATAAAATA
1 ATTTATTATAAAATA
505338 ATTTATTATAAAATA
1 ATTTATTATAAAATA
*
505353 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
*
505368 AATTATTATAAAATA
1 ATTTATTATAAAATA
505383 TGGATTGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATTATAAAATA
Done.