Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005860.1 Hibiscus syriacus cultivar Beakdansim tig00013773_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: 375081
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:5156 original size:21 final size:22
Alignment explanation
Indices: 5116--5158 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5106 AAAAAGACTA
5116 AAAAAATAGAAAAACATAATAT
1 AAAAAATAGAAAAACATAATAT
5138 AAAAAATA-AGAAAAC-TAATAT
1 AAAAAATAGA-AAAACATAATAT
5159 TCATCGGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAAATAGAAAAACATAATAT
Found at i:7384 original size:38 final size:38
Alignment explanation
Indices: 7331--7410 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
7321 TCAAAGGAGA
* ** *
7331 GATATATACATACATATGTGTGTGTGTTCATAAAGAGG
1 GATACATACATACATACATATGTGTGTTCATAAAGAGG
*
7369 GATACATACATACATACATATGTGTGTTCATAAGGAGG
1 GATACATACATACATACATATGTGTGTTCATAAAGAGG
7407 GATA
1 GATA
7411 TATTCATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (38 bp):
GATACATACATACATACATATGTGTGTTCATAAAGAGG
Found at i:11486 original size:7 final size:7
Alignment explanation
Indices: 11476--11504 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
11466 TGTTGTTATT
11476 TGTTAAG
1 TGTTAAG
11483 TGTTAAG
1 TGTTAAG
11490 TGTTAAG
1 TGTTAAG
11497 TGTTAAG
1 TGTTAAG
11504 T
1 T
11505 TTGAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (7 bp):
TGTTAAG
Found at i:11907 original size:21 final size:21
Alignment explanation
Indices: 11858--11909 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
11848 ATTTCTAGAA
*
11858 TGCTACAGGGGTATCGATACCC
1 TGCTACA-GTGTATCGATACCC
**
11880 TAATACAGTGTATCGATACCC
1 TGCTACAGTGTATCGATACCC
11901 TGCTACAGT
1 TGCTACAGT
11910 AATTTCGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGTATCGATACCC
Found at i:12496 original size:22 final size:22
Alignment explanation
Indices: 12455--12496 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12445 TATGAAATTT
* *
12455 TGTCCCGAAGGACTTGTGAAGG
1 TGTCCCGAAGGACCTATGAAGG
12477 TGTCCCGAAGGACCTATGAA
1 TGTCCCGAAGGACCTATGAA
12497 ACCCTCGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGAAGG
Found at i:12836 original size:2 final size:2
Alignment explanation
Indices: 12829--12856 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12819 GATTACGTTC
12829 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
12857 ATAATACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14593 original size:19 final size:19
Alignment explanation
Indices: 14569--14615 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
14559 TCTGATCCGT
14569 TGACTTTGACCCAAACCGC
1 TGACTTTGACCCAAACCGC
* *
14588 TGAC-TTGACCCAACCCGT
1 TGACTTTGACCCAAACCGC
14606 TGACTTTGAC
1 TGACTTTGAC
14616 TAGAGTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (19 bp):
TGACTTTGACCCAAACCGC
Found at i:15114 original size:13 final size:13
Alignment explanation
Indices: 15098--15122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15088 TGTGCAATAT
15098 ATATGTTTGAAAC
1 ATATGTTTGAAAC
15111 ATATGTTTGAAA
1 ATATGTTTGAAA
15123 TATCATGTGC
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:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
ATATGTTTGAAAC
Found at i:17661 original size:27 final size:26
Alignment explanation
Indices: 17634--17699 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
17624 TATTAACTTA
*
17634 AAAAATATTTTTTATATTAACTT-ATT
1 AAAAATATTTTAT-TATTAACTTAATT
17660 -AAAATATTTTATTATTAACTTAATTT
1 AAAAATATTTTATTATTAACTTAA-TT
*
17686 AAAATTATTTTATT
1 AAAAATATTTTATT
17700 GTATTTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 9 0.26
25 12 0.34
26 2 0.06
27 12 0.34
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (26 bp):
AAAAATATTTTATTATTAACTTAATT
Found at i:17663 original size:26 final size:26
Alignment explanation
Indices: 17620--17698 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 26
17610 TATATATATA
17620 TATATATTAACTTA--AAAAATATTT
1 TATATATTAACTTATTAAAAATATTT
*
17644 TTTATATTAACTTATT-AAAATATTT
1 TATATATTAACTTATTAAAAATATTT
*
17669 TAT-TATTAACTTAATTTAAAATTATTT
1 TATATATTAACTT-A-TTAAAAATATTT
17696 TAT
1 TAT
17699 TGTATTTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 22 0.47
25 12 0.26
26 2 0.04
27 11 0.23
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
TATATATTAACTTATTAAAAATATTT
Found at i:18602 original size:2 final size:2
Alignment explanation
Indices: 18595--18629 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18585 AACATTTTAT
18595 TA TA TA 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 TA TA TA T
18630 TACAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20502 original size:13 final size:13
Alignment explanation
Indices: 20481--20540 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
20471 ATTTTGTTAG
20481 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
20494 TATTGTA-TTATT
1 TATTTTATTTAAT
20506 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
20518 TATTTTATTTAAT
1 TATTTTATTTAAT
20531 TATTTTATTT
1 TATTTTATTT
20541 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:20506 original size:21 final size:20
Alignment explanation
Indices: 20481--20545 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
20471 ATTTTGTTAG
20481 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
20502 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
20518 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
20539 TTTTTTA
1 TATTTTA
20546 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:20516 original size:29 final size:29
Alignment explanation
Indices: 20483--20545 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
20473 TTTGTTAGTA
20483 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
20512 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
20541 TTTTA
1 TTTTA
20546 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:20527 original size:16 final size:16
Alignment explanation
Indices: 20485--20527 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
20475 TGTTAGTATT
* *
20485 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
20501 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
20517 TTATTTTATTT
1 TTATTTAATTT
20528 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:21879 original size:45 final size:45
Alignment explanation
Indices: 21815--21900 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
21805 ATAAAAGAAA
*
21815 AACATAGTACAAGATAAAGTTTCATGTAATGACATGTATCCCACT
1 AACATAGTACAAGATAAAGTTTCATGCAATGACATGTATCCCACT
21860 AACATAGTACAAGATAAAGTTTCATGCAATGACATGTATCC
1 AACATAGTACAAGATAAAGTTTCATGCAATGACATGTATCC
21901 AACTTTTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (45 bp):
AACATAGTACAAGATAAAGTTTCATGCAATGACATGTATCCCACT
Found at i:23329 original size:21 final size:21
Alignment explanation
Indices: 23305--23345 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23295 AAAAATTACA
23305 TAAAAAATTATTATTTTTATC
1 TAAAAAATTATTATTTTTATC
* *
23326 TAAAATATTATTTTTTTTAT
1 TAAAAAATTATTATTTTTAT
23346 ATTTTCAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TAAAAAATTATTATTTTTATC
Found at i:23400 original size:29 final size:29
Alignment explanation
Indices: 23358--23421 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
23348 TTTCAGTTAT
23358 TTTTTAACACCTAAAAATATTTTCGATCA
1 TTTTTAACACCTAAAAATATTTTCGATCA
*
23387 TTTTTAACACCTAATAATATTTTCGATCA
1 TTTTTAACACCTAAAAATATTTTCGATCA
23416 TATTTT
1 T-TTTT
23422 TTTAACTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTTTAACACCTAAAAATATTTTCGATCA
Found at i:31420 original size:29 final size:29
Alignment explanation
Indices: 31344--31420 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
31334 GCTTCCATCA
*
31344 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
31373 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
31402 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
31421 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:31527 original size:14 final size:14
Alignment explanation
Indices: 31480--31520 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
31470 GCTCGAATGG
31480 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
31494 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
31508 CCTCGGTCGGATG
1 CCTCGGTCGGATG
31521 GCTTCGGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.07, C:0.34, G:0.37, T:0.22
Consensus pattern (14 bp):
CCTCGGTCGGATGC
Found at i:34149 original size:19 final size:19
Alignment explanation
Indices: 34113--34176 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
34103 GGACCTGGAG
* *
34113 AAAA-AAAATATATGAAAT
1 AAAATAAAATAAATAAAAT
* * *
34131 TAAATTAAATTAATAAAAT
1 AAAATAAAATAAATAAAAT
*
34150 AAAATAAAATAAATAATAT
1 AAAATAAAATAAATAAAAT
*
34169 AATATAAA
1 AAAATAAA
34177 CTATATAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
18 3 0.09
19 32 0.91
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAAATAAATAAAAT
Found at i:34184 original size:19 final size:19
Alignment explanation
Indices: 34137--34192 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
34127 AAATTAAATT
* * *
34137 AAATTAATAAAATAAAATA
1 AAATAAATAATATAATATA
34156 AAATAAATAATATAATATA
1 AAATAAATAATATAATATA
* *
34175 AACTATATAATAT-ATATA
1 AAATAAATAATATAATATA
34193 TTTCAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 5 0.16
19 27 0.84
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAAATAATATAATATA
Found at i:34217 original size:39 final size:37
Alignment explanation
Indices: 34174--34400 Score: 156
Period size: 36 Copynumber: 6.2 Consensus size: 37
34164 AATATAATAT
34174 AAACTATATAATATATATATTTCAAAAATACATTTTAGA
1 AAACTATATAATATATATATTTCAAAAAT-CATTTTA-A
* * *
34213 AAACTATATATTACATAGT-TTTC-AAAA-CGTTTTAA
1 AAACTATATAATATATA-TATTTCAAAAATCATTTTAA
* *
34248 AAA-TAT-T-ATATA-AGT-TTTCAAAAAT-GTTTTCA
1 AAACTATATAATATATA-TATTTCAAAAATCATTTTAA
* *
34280 AAACTATATATTATATATATTTTAAAAAT-ATTTTCAA
1 AAACTATATAATATATATATTTCAAAAATCATTTT-AA
* * *
34317 AAACTATATAATATATAAATTTTCGAAAATCATTTTCTGA
1 AAACTATATAATATATATA-TTTCAAAAATCA-TTT-TAA
* * *
34357 AAATTATAT-AT-TATATTTTGTCAAAAA-CATTTTTAC
1 AAACTATATAATATATATATT-TCAAAAATCA-TTTTAA
34393 AAACTATA
1 AAACTATA
34401 ATAAAAAAAC
Statistics
Matches: 152, Mismatches: 22, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
31 7 0.05
32 16 0.11
33 4 0.03
34 4 0.03
35 9 0.06
36 28 0.18
37 26 0.17
38 22 0.14
39 22 0.14
40 13 0.09
41 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (37 bp):
AAACTATATAATATATATATTTCAAAAATCATTTTAA
Found at i:34291 original size:37 final size:38
Alignment explanation
Indices: 34250--34372 Score: 144
Period size: 37 Copynumber: 3.2 Consensus size: 38
34240 CGTTTTAAAA
*
34250 ATATTATATAAGTTTTCAAAAATGTTTTC-AAAACTAT
1 ATATTATATAAGTTTTCAAAAATATTTTCAAAAACTAT
34287 ATATTATATATA-TTTT-AAAAATATTTTCAAAAACTAT
1 ATATTATATA-AGTTTTCAAAAATATTTTCAAAAACTAT
* * * * *
34324 ATAATATATAAATTTTCGAAAATCATTTTCTGAAAATTAT
1 ATATTATATAAGTTTTCAAAAAT-ATTTTC-AAAAACTAT
34364 ATATTATAT
1 ATATTATAT
34373 TTTGTCAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
36 12 0.16
37 35 0.47
38 6 0.08
39 6 0.08
40 15 0.20
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
ATATTATATAAGTTTTCAAAAATATTTTCAAAAACTAT
Found at i:35293 original size:84 final size:84
Alignment explanation
Indices: 34938--36059 Score: 1290
Period size: 84 Copynumber: 13.6 Consensus size: 84
34928 AACTCGGTAA
* * * * * * * * *
34938 TTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCTC-TAGAGCTGAT
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC-CGTTGAGCTGAG
* **
35002 CGTAATCGAACTCGGGGGTC
65 CGTAGTCGAACTCGAAGGTC
* *
35022 ---T-TTGGCAGATAGCCCTTCTCGAGTTAA-TCTATGCTGCAAATGATGTGCCGTTGA---GAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGT-TATGCTGCAAATGATGTGCCGTTGAGCTGAG
35079 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * *
35099 TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGTTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTG-AGCTGAG
* * **
35164 TGTAATCGAACTCGGGGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
35184 ---T-TTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
35245 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
35264 TTTTGTTGGAAGATAACCATTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTG-AGCTGAG
* * **
35329 TGTAATCGAACTCGGGGGTC
65 CGTAGTCGAACTCGAAGGTC
* *
35349 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
35410 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
35429 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCC-TTGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGCTGAG
35493 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * *
35513 TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTG-AGCTGAG
* * **
35578 TGTAATCGAACTCGGGGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
35598 ---T-TTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
*
35659 GTAGTCGAACTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
35678 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCC-TTGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGCTGAG
35742 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * *
35762 TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTG-AGCTGAG
* * **
35827 TGTAATCGAACTCGGGGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
35847 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
*
35908 GTAGTCAAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
35927 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
35992 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* *
36011 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
36060 ATTTAAAAAA
Statistics
Matches: 872, Mismatches: 132, Indels: 68
0.81 0.12 0.06
Matches are distributed among these distances:
77 19 0.02
79 1 0.00
80 131 0.15
81 226 0.26
82 3 0.00
83 8 0.01
84 394 0.45
85 90 0.10
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:35320 original size:165 final size:165
Alignment explanation
Indices: 34938--36059 Score: 1377
Period size: 165 Copynumber: 6.8 Consensus size: 165
34928 AACTCGGTAA
* * * * * * * * * *
34938 TTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCTCTAG-AGCTGAT
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *
35002 CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGAGTTAATCTATGCTGCAAATGATG
66 CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
35067 TGCCGTTGA---GAGCGTAGTCGAACTCGAAGGTC
131 TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * *
35099 TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGTTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *
35164 TGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
66 CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
35229 TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
131 TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * *
35264 TTTTGTTGGAAGATAACCATTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
*
35329 TGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
66 CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
35394 TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
131 TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * *
35429 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* ** * * *
35493 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAAT
66 CGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
* * * * **
35558 GATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
127 GATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * * *
35598 ---T-TTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *** * * * * *
35658 CGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAAT
66 CGTAATCGAACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
*
35723 GATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
127 GATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC
* * *
35762 TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *
35827 TGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATG
66 CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
*
35892 TGCCGTTGAGCTGAGCGTAGTCAAACTCGAAGGTC
131 TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * *
35927 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCGTTG-AGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* ** * * *
35991 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAAT
66 CGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
36056 GATG
127 GATG
36060 ATTTAAAAAA
Statistics
Matches: 840, Mismatches: 99, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
161 47 0.06
162 75 0.09
164 74 0.09
165 454 0.54
166 13 0.02
168 132 0.16
169 45 0.05
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (165 bp):
TTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
CGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
TGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
Found at i:35529 original size:249 final size:249
Alignment explanation
Indices: 35023--36059 Score: 1574
Period size: 249 Copynumber: 4.2 Consensus size: 249
35013 TCGGGGGTCT
* * * * * *
35023 TTGGCAGATAGCCCTTCTCGAGTTAA-TCTATGCTGCAAATGATGTGCCGTTG-A---GAGCGTA
1 TTGGCAGATAACCCTTCTCGACTTAAGT-TATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
* ** * * * *
35083 GTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATG
65 ATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * * * * ** * * * *
35148 TGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTC---T-TTGGTAGATAGCCCTTCTCGACTT
126 TGCCGTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTT
* * * *
35209 AAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
190 AAGTTGTGCTGCAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
35269 TTGGAAGATAACCATTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
35334 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
35399 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
131 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
35464 TGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
196 TGCTGCAAATGATATGCCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
35518 TTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
35583 TCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
*
35648 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
131 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
35713 TGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
196 TGCTGCAAATGATATGCCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * *
35767 TTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
35832 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCG
66 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
*
35897 TTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
131 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
35962 TGCTGCAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
196 TGCTGCAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
36016 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATG
36060 ATTTAAAAAA
Statistics
Matches: 736, Mismatches: 44, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
245 22 0.03
246 89 0.12
247 2 0.00
248 4 0.01
249 598 0.81
250 21 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCG
TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
TGCTGCAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:39151 original size:19 final size:19
Alignment explanation
Indices: 39127--39172 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
39117 AGTTAATGTG
39127 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
39146 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
39165 AATGCAAA
1 AATGCAAA
39173 ATGTCTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:40973 original size:20 final size:20
Alignment explanation
Indices: 40949--41023 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
40939 AACAAAATGC
40949 TAATAAATAAAAAATGAATAA
1 TAATAAATAAAAAAT-AATAA
*
40970 -AATATATAAAAAATAATAA
1 TAATAAATAAAAAATAATAA
*
40989 TAAT-AATGAAAGAAA-GA-AA
1 TAATAAAT-AAA-AAATAATAA
*
41008 TAATAAAAAAAAAATA
1 TAATAAATAAAAAATA
41024 TGAAATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 3 0.07
19 16 0.36
20 22 0.50
21 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
TAATAAATAAAAAATAATAA
Found at i:41069 original size:19 final size:18
Alignment explanation
Indices: 40949--41086 Score: 61
Period size: 19 Copynumber: 7.6 Consensus size: 18
40939 AACAAAATGC
* * *
40949 TAATAAATAAAAAATGAA
1 TAATATATATAAAATAAA
* *
40967 TAAAATATATAAAAAATAA
1 TAATATATATAAAATA-AA
* *
40986 TAATA-ATAATGAAAGAAA
1 TAATATAT-ATAAAATAAA
*
41004 GAA-ATA-ATAAAA-AAA
1 TAATATATATAAAATAAA
* * *
41019 AAATATGAAATTAAATTAAA
1 TAATAT-ATA-TAAAATAAA
*
41039 TTAATA-AAATAAAATAAA
1 -TAATATATATAAAATAAA
* *
41057 TAATATGATATAAACTATA
1 TAATAT-ATATAAAATAAA
41076 TAATATATATA
1 TAATATATATA
41087 TTTCAAAAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
15 5 0.05
16 7 0.08
17 7 0.08
18 32 0.35
19 34 0.37
20 3 0.03
21 4 0.04
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
TAATATATATAAAATAAA
Found at i:41185 original size:37 final size:36
Alignment explanation
Indices: 41068--41266 Score: 153
Period size: 37 Copynumber: 5.4 Consensus size: 36
41058 AATATGATAT
* *
41068 AAACTATATAATATAT-ATATTTCAAAAATACGTTTTAGA
1 AAACTATATATTATATAAT-TTTCAAAAAT--GTTTT-CA
* * *
41107 AAACTATATATTACATAGTTTTC-AAAACGTTTT--
1 AAACTATATATTATATAATTTTCAAAAATGTTTTCA
41140 AAA--A-ATATTATATAAGTTTTCAAAAATGTTTTCA
1 AAACTATATATTATATAA-TTTTCAAAAATGTTTTCA
*
41174 AAACTATATATTATATATATTTT-AAAAATATTTTCAA
1 AAACTATATATTATATA-ATTTTCAAAAATGTTTTC-A
* * *
41211 AAACTATATAATATATAAATTTTCGAAAATCATTTTCTGA
1 AAACTATATATTATAT-AATTTTCAAAAAT-GTTTTC--A
*
41251 AAATTATATATTATAT
1 AAACTATATATTATAT
41267 TTTGTCAAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 27
0.77 0.08 0.16
Matches are distributed among these distances:
30 9 0.07
31 6 0.05
32 9 0.07
33 3 0.02
34 3 0.02
36 17 0.13
37 35 0.26
38 11 0.08
39 24 0.18
40 16 0.12
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
AAACTATATATTATATAATTTTCAAAAATGTTTTCA
Found at i:41219 original size:67 final size:69
Alignment explanation
Indices: 41087--41221 Score: 159
Period size: 67 Copynumber: 2.0 Consensus size: 69
41077 AATATATATA
* * * * *
41087 TTTCAAAAATACGTTTTAGAAAACTATATATTACATAGTTTTCAAAACGTTTTAAAAATATTATA
1 TTTCAAAAATA-GTTTTACAAAACTATATATTACATAATTTTAAAAACATTTTAAAAATACTATA
41152 TAAGT
65 TAAGT
* * *
41157 TTTCAAAAAT-GTTTT-CAAAACTATATATTATATATATTTTAAAAATATTTTCAAAA-ACTATA
1 TTTCAAAAATAGTTTTACAAAACTATATATTACATA-ATTTTAAAAACATTTTAAAAATACTATA
41219 TAA
65 TAA
41222 TATATAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
67 25 0.45
68 21 0.38
70 10 0.18
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (69 bp):
TTTCAAAAATAGTTTTACAAAACTATATATTACATAATTTTAAAAACATTTTAAAAATACTATAT
AAGT
Found at i:41295 original size:74 final size:73
Alignment explanation
Indices: 41068--41297 Score: 185
Period size: 74 Copynumber: 3.2 Consensus size: 73
41058 AATATGATAT
* * *
41068 AAACTATATAATATATATA-TTTCAAAAATACGTTTTAGAAAACTATATATTACATAGT-TTTC-
1 AAAC-ATATAATATATAAATTTTCAAAAATA--TTTT-CAAAACTATATATTATATA-TATTTCA
*
41130 AAAACGTTTT--A
61 AAAACATTTTCAA
* * * *
41141 AAA-ATAT--TATATAAGTTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAAT
1 AAACATATAATATATAAATTTTCAAAAATATTTTCAAAACTATATATTATATATATTTCAAAAAC
41203 ATTTTCAA
66 ATTTTCAA
* *
41211 AAACTATATAATATATAAATTTTCGAAAATCATTTTCTGAAAATTATATATTATAT-T-TTGTCA
1 AAAC-ATATAATATATAAATTTTCAAAAAT-ATTTTC--AAAACTATATATTATATATATT-TCA
* *
41274 AAAACATTTTTAC
61 AAAACATTTTCAA
41287 AAAC-TATAATA
1 AAACATATAATA
41298 AAAAAACACA
Statistics
Matches: 128, Mismatches: 16, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
66 1 0.01
67 20 0.16
68 12 0.09
69 6 0.05
70 14 0.11
71 4 0.03
72 4 0.03
73 3 0.02
74 24 0.19
75 7 0.05
76 17 0.13
77 16 0.12
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (73 bp):
AAACATATAATATATAAATTTTCAAAAATATTTTCAAAACTATATATTATATATATTTCAAAAAC
ATTTTCAA
Found at i:43602 original size:5 final size:5
Alignment explanation
Indices: 43580--43614 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
43570 CGTATTATCA
43580 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
43615 GACGAGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:44135 original size:12 final size:11
Alignment explanation
Indices: 44105--44138 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
44095 CCGTCTCGTC
44105 TCGGGTCG-GG
1 TCGGGTCGTGG
44115 TCGGGTCGTGG
1 TCGGGTCGTGG
44126 TCGTGGTCGTGG
1 TCG-GGTCGTGG
44138 T
1 T
44139 AATACGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:44207 original size:42 final size:42
Alignment explanation
Indices: 44148--44287 Score: 167
Period size: 42 Copynumber: 3.3 Consensus size: 42
44138 TAATACGTAT
* *
44148 CTTCGACTATTGCAACGAATTTGGAATAAATCGTAACGCGAA
1 CTTCGACTATCGCAACGAATTTGGAATAAATCGTAATGCGAA
* *
44190 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAATGCTAA
1 CTTCGACTATCGCAACGAATTTGGAATAAATCGTAATGCGAA
* * * * *
44232 CTTGGACTATCGTAATGCGAACTTCGACT--ATCGTAATGCGAA
1 CTTCGACTATCGCAA--CGAATTTGGAATAAATCGTAATGCGAA
44274 CTTCGACTATCGCA
1 CTTCGACTATCGCA
44288 TTGCGATTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 74 0.89
44 9 0.11
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
CTTCGACTATCGCAACGAATTTGGAATAAATCGTAATGCGAA
Found at i:44292 original size:21 final size:21
Alignment explanation
Indices: 44185--44293 Score: 114
Period size: 21 Copynumber: 5.2 Consensus size: 21
44175 AAATCGTAAC
44185 GCGAACTTCGACTATCGCAA-
1 GCGAACTTCGACTATCGCAAT
* * *
44205 -CGAATTTGGAATAAATCGCAAT
1 GCGAACTTCGACT--ATCGCAAT
* * *
44227 GCTAACTTGGACTATCGTAAT
1 GCGAACTTCGACTATCGCAAT
*
44248 GCGAACTTCGACTATCGTAAT
1 GCGAACTTCGACTATCGCAAT
*
44269 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCAAT
44290 GCGA
1 GCGA
44294 TTTACATATT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
19 9 0.12
21 56 0.76
23 9 0.12
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:44328 original size:21 final size:21
Alignment explanation
Indices: 44302--44397 Score: 174
Period size: 21 Copynumber: 4.6 Consensus size: 21
44292 GATTTACATA
44302 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
44323 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
44344 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
44365 TTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
44386 TTCGCGTTGCGA
1 TTCGCATTGCGA
44398 ATCTGGAAAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:46142 original size:28 final size:28
Alignment explanation
Indices: 46109--46182 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 28
46099 CCTAAACCCG
* *
46109 AACCCGACCCGAATTTCACACTTAAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
46137 AACCCGACATGACCTGAATATCAAACTTAAAAA
1 AACCCGAC----CC-GAATATCAAACTTAAAAA
*
46170 AACCCAACCCGAA
1 AACCCGACCCGAA
46183 CCCGATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
28 11 0.29
29 2 0.05
32 2 0.05
33 23 0.61
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACTTAAAAA
Found at i:50174 original size:40 final size:35
Alignment explanation
Indices: 50099--50210 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
50089 AAAACAGTCC
*
50099 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* *
50134 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* * * * * *
50169 TTAATTTAATTTTAAACCTCAAATTCTAAAGTACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
*
50204 CCAATTT
1 TCAATTT
50211 AAGGTTTAGA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
Found at i:50280 original size:35 final size:35
Alignment explanation
Indices: 50206--50280 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
50196 AAAGTACTCC
* * *
50206 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* * *
50241 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTTA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
50276 AATTT
1 AATTT
50281 TGAACATGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:51984 original size:18 final size:18
Alignment explanation
Indices: 51963--52009 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
51953 TTTTTTTGAA
*
51963 AAATTATTAT-TTTATCAT
1 AAATTATTATATATAT-AT
51981 AAATTATATATATATATAT
1 AAATTAT-TATATATATAT
52000 AAA-TATTATA
1 AAATTATTATA
52010 AAATAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 8 0.31
20 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTATTATATATATAT
Found at i:52031 original size:17 final size:19
Alignment explanation
Indices: 51996--52035 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
51986 ATATATATAT
51996 ATATAAATATTATAAAATA
1 ATATAAATATTATAAAATA
52015 ATATAAATA-TA-AAAATA
1 ATATAAATATTATAAAATA
52032 ATAT
1 ATAT
52036 TAAACAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAATATTATAAAATA
Found at i:52075 original size:2 final size:2
Alignment explanation
Indices: 52068--52095 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52058 TCGTTATTTA
52068 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
52096 TAGTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59595 original size:16 final size:16
Alignment explanation
Indices: 59576--59606 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59566 TTCAAAAATA
*
59576 TATAATATATATAGTT
1 TATAAGATATATAGTT
59592 TATAAGATATATAGT
1 TATAAGATATATAGT
59607 ATAGTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
TATAAGATATATAGTT
Found at i:59609 original size:25 final size:24
Alignment explanation
Indices: 59537--59609 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 24
59527 TTTATTACAT
*
59537 TATATAG--TATATGATA-ATATA
1 TATATAGTTTATAAGATATATATA
* *
59558 TATATAATTTCA-AAAATATATAATA
1 TATATAGTTT-ATAAGATATAT-ATA
59583 TATATAGTTTATAAGATATATAGTA
1 TATATAGTTTATAAGATATATA-TA
59608 TA
1 TA
59610 GTTTTTGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
21 6 0.15
23 5 0.12
24 5 0.12
25 24 0.60
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (24 bp):
TATATAGTTTATAAGATATATATA
Found at i:86462 original size:2 final size:2
Alignment explanation
Indices: 86455--86488 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
86445 CTGTTTAGTT
* *
86455 TA TA TA TA TA TA TA TA TC TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86489 CACACTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88357 original size:17 final size:18
Alignment explanation
Indices: 88335--88368 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88325 TTAGCCGATC
88335 CGGTTCGAA-CGGTTCAG
1 CGGTTCGAATCGGTTCAG
*
88352 CGGTTCTAATCGGTTCA
1 CGGTTCGAATCGGTTCA
88369 CTAGTAGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (18 bp):
CGGTTCGAATCGGTTCAG
Found at i:88796 original size:59 final size:59
Alignment explanation
Indices: 88733--88844 Score: 152
Period size: 59 Copynumber: 1.9 Consensus size: 59
88723 GATATGTTTA
* * *
88733 TCATTCTAAAAAAATCCTCAAACTTTTGAACATTTCAATTTCATTCCAAACTATGACCT
1 TCATTCTAAAAAAATCCCCAAACTTTTGAACATTCCAATTTCATACCAAACTATGACCT
** * * *
88792 TCATTCTAAATCAGTCCCCAAATTTTTTAACATTCCAATTTCATACCAAACTA
1 TCATTCTAAAAAAATCCCCAAACTTTTGAACATTCCAATTTCATACCAAACTA
88845 CATGCATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
TCATTCTAAAAAAATCCCCAAACTTTTGAACATTCCAATTTCATACCAAACTATGACCT
Found at i:91934 original size:30 final size:30
Alignment explanation
Indices: 91898--91957 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
91888 AGTGCTCCAT
* *
91898 AGGTCGTCGTGTGCTCTTGGAAACCTATGG
1 AGGTCGTCATGTGCTCTTAGAAACCTATGG
* *
91928 AGGTCGTCATGTGTTCTTAGAGACCTATGG
1 AGGTCGTCATGTGCTCTTAGAAACCTATGG
91958 TGGTTACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (30 bp):
AGGTCGTCATGTGCTCTTAGAAACCTATGG
Found at i:93177 original size:25 final size:25
Alignment explanation
Indices: 93149--93198 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
93139 CTTTCAACCA
*
93149 TTTGACATTGAATACTAACACCCCT
1 TTTGACATTGAACACTAACACCCCT
93174 TTTGACATTGAACACTAACACCCCT
1 TTTGACATTGAACACTAACACCCCT
93199 ATCATTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (25 bp):
TTTGACATTGAACACTAACACCCCT
Found at i:94624 original size:33 final size:33
Alignment explanation
Indices: 94587--94652 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
94577 TGTTATAAGC
* *
94587 ATTGTTTGGGCAACTCTTTTGATTTTTAGCATA
1 ATTGTTTGGGCAACTCTTCTGATTTTCAGCATA
94620 ATTGTTTGGGCAACTCTTCTGATTTTCAGCATA
1 ATTGTTTGGGCAACTCTTCTGATTTTCAGCATA
94653 CGCTTGAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (33 bp):
ATTGTTTGGGCAACTCTTCTGATTTTCAGCATA
Found at i:106999 original size:21 final size:21
Alignment explanation
Indices: 106969--107029 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
106959 ACTATTTAGC
*
106969 CTTTTTACTTTTTCCATCAAT
1 CTTTTAACTTTTTCCATCAAT
106990 CTTTTAACTTTTTCCATCAAT
1 CTTTTAACTTTTTCCATCAAT
* *
107011 CTTTTAATTTTTTCAATCA
1 CTTTTAACTTTTTCCATCA
107030 CACCACATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (21 bp):
CTTTTAACTTTTTCCATCAAT
Found at i:111902 original size:21 final size:22
Alignment explanation
Indices: 111853--111902 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
111843 TAATTATTAA
111853 ATTTATTAAAATATTACAAAAT
1 ATTTATTAAAATATTACAAAAT
* * * *
111875 ATATATTAAATTTTTA-AAATT
1 ATTTATTAAAATATTACAAAAT
111896 ATTTATT
1 ATTTATT
111903 TATAAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTATTAAAATATTACAAAAT
Found at i:117783 original size:20 final size:20
Alignment explanation
Indices: 117745--117784 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
117735 TAATTCAAAT
*
117745 TAATTATAAACCAAATATTA
1 TAATTATAAACAAAATATTA
117765 TAATTATAAA-AAAATTATTA
1 TAATTATAAACAAAA-TATTA
117785 ATTATTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTATAAACAAAATATTA
Found at i:117788 original size:18 final size:20
Alignment explanation
Indices: 117743--117789 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
117733 CTTAATTCAA
117743 ATTAATTATAAACCAAATATT
1 ATTAATTATAAA-CAAATATT
117764 A-TAATTATAAA-AAA-ATT
1 ATTAATTATAAACAAATATT
117781 ATTAATTAT
1 ATTAATTAT
117790 TTCCTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
20 10 0.40
21 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAATTATAAACAAATATT
Found at i:119985 original size:157 final size:155
Alignment explanation
Indices: 119676--120144 Score: 678
Period size: 157 Copynumber: 3.0 Consensus size: 155
119666 TCATAAACCA
* * *
119676 TGATAATAAATTTTTATTTTTCAATTTAGT-CCTTAATTTTTCATAATTTCGTTATTTAGTCAAT
1 TGATAATAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTC-TTATTTATTCAAT
* **
119740 ACATCATTTATTTTAAG-TCCTTTTTACCAAATTTGAA-CACATGCTCATATACCACAATAGAAT
65 TCATCATTTATTTTAAGTTGTTTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAAT
*
119803 ACCTATGTAACTTCAATTCATCTTTT
130 ACCTATGTAACTTCAATTCCTCTTTT
* *
119829 TGATAATAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTTATAATTTCTTATTTCTTCAATT
1 TGATAATAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCTTATTTATTCAATT
*
119894 CATCCTTTATTTTAAGTTTGTTCTTTTACCAAATTTGAACCACATGCTCATATGA-CACAATAGA
66 CATCATTTATTTTAAG-TTGTT-TTTTACCAAATTTGAACCACATGCTCATAT-ACCACAATAGA
119958 ATACCTATGTAACTTCAATTCCTCTTTT
128 ATACCTATGTAACTTCAATTCCTCTTTT
* * *
119986 TAACAATAGTTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCCTTATTTATTCAAT
1 TGATAATAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTT-CTTATTTATTCAAT
* *
120051 TCATCATTTATTTTCAGTACGGTTTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGA
65 TCATCATTTATTTTAAGT--TGTTTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGA
* *
120116 ATA-TTATGTAACTTCAATTTCTACTTTT
128 ATACCTATGTAACTTCAATTCCT-CTTTT
120144 T
1 T
120145 TTAAAAAAAT
Statistics
Matches: 285, Mismatches: 20, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
153 55 0.19
154 18 0.06
155 2 0.01
156 16 0.06
157 114 0.40
158 77 0.27
159 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (155 bp):
TGATAATAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCTTATTTATTCAATT
CATCATTTATTTTAAGTTGTTTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATA
CCTATGTAACTTCAATTCCTCTTTT
Found at i:127116 original size:20 final size:20
Alignment explanation
Indices: 127093--127227 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
127083 AAATAAGTAA
127093 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
127113 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
127133 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
127154 ATCACAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
127174 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* ** *
127194 TTCGCAACACGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
127214 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
127228 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.70
21 22 0.24
22 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:127168 original size:61 final size:61
Alignment explanation
Indices: 127103--127217 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 61
127093 ATCGCAATGC
* * **
127103 GATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAATCACAACGA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACACGATAATACAAAATCACAACGA
* * * *
127164 GATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACACGATAATACATAATC
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACACGATAATACAAAATC
127218 GCAATGCGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (61 bp):
GATACTGACTATCGCAACGCGATACTGACTATCGCAACACGATAATACAAAATCACAACGA
Found at i:127741 original size:20 final size:20
Alignment explanation
Indices: 127682--127745 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
127672 GCGATTTTAG
*
127682 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
127702 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
127722 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
127742 TTTC
1 TTTC
127746 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:127936 original size:25 final size:24
Alignment explanation
Indices: 127882--127936 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
127872 TGTTTATTAT
* *
127882 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
127906 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
127932 TGTTT
1 TGTTT
127937 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:129085 original size:18 final size:18
Alignment explanation
Indices: 129064--129108 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
129054 TCCACTTCGG
*
129064 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
129082 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
129100 GAGCCATCA
1 GAGCCATCA
129109 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:129615 original size:20 final size:20
Alignment explanation
Indices: 129590--129635 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
129580 TAGTTTACTT
129590 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
129610 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
129630 TCGCAA
1 TCGCAA
129636 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:129644 original size:19 final size:19
Alignment explanation
Indices: 129601--129659 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
129591 CGCAACACGA
*
129601 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAATGC-G
*
129621 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
129640 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
129659 A
1 A
129660 TTTGTGTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:129690 original size:14 final size:14
Alignment explanation
Indices: 129671--129761 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
129661 TTGTGTTTCG
129671 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
129685 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
129701 CGCATTGTGATTTTGT
1 CG--TTGCGATTTTGT
* *
129717 CATTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
129734 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
129750 CGTTGCGATTTT
1 CGTTGCGATTTT
129762 CATTTCACAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 26 0.43
15 3 0.05
16 11 0.18
17 3 0.05
18 11 0.18
19 6 0.10
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:129735 original size:33 final size:33
Alignment explanation
Indices: 129666--129777 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
129656 GCGATTTGTG
*
129666 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
129698 TTTCGCATTGTGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
129731 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
129764 TTTCACATTGCGAT
1 TTTCGCATTGCGAT
129778 AGCCATTTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 24 0.33
33 49 0.67
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:129741 original size:19 final size:19
Alignment explanation
Indices: 129717--129777 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
129707 GTGATTTTGT
129717 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
129736 CATTGCGA-TTT--TGTCG
1 CATTGCGATTTTCATTTCG
*
129752 --TTGCGATTTTCATTTCA
1 CATTGCGATTTTCATTTCG
129769 CATTGCGAT
1 CATTGCGAT
129778 AGCCATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 3 0.09
18 3 0.09
19 15 0.44
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:129784 original size:19 final size:19
Alignment explanation
Indices: 129762--129805 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
129752 TTGCGATTTT
129762 CATTTCACATTGCGATAGC
1 CATTTCACATTGCGATAGC
* * *
129781 CATTTTCGCGTTGCGATAGT
1 CA-TTTCACATTGCGATAGC
129801 CATTT
1 CATTT
129806 TCGCGTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (19 bp):
CATTTCACATTGCGATAGC
Found at i:129794 original size:20 final size:20
Alignment explanation
Indices: 129771--129814 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
129761 TCATTTCACA
129771 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
*
129791 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
129811 TTGC
1 TTGC
129815 AATTTTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:130279 original size:41 final size:41
Alignment explanation
Indices: 130183--130270 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
130173 GACTCACCTG
* * *
130183 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
130225 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
130266 TCATC
1 TCATC
130271 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:131707 original size:14 final size:14
Alignment explanation
Indices: 131688--131723 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
131678 ATTGTTTAAT
131688 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
131702 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
131716 TGATTTGT
1 TGATTTGT
131724 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:131918 original size:20 final size:20
Alignment explanation
Indices: 131901--131988 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
131891 CGATTTTCTA
131901 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
131921 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
131941 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
131961 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
131981 GTTGCGAT
1 GTTGCGAT
131989 TTCCCCGTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:131926 original size:34 final size:36
Alignment explanation
Indices: 131881--131968 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
131871 GCGATTTTCA
* *
131881 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
131915 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
131955 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
131969 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:132227 original size:20 final size:20
Alignment explanation
Indices: 132202--132293 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
132192 TTGAAGATAA
132202 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
132222 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
132242 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
132263 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
132283 TTGCGATTTTC
1 TTGCGATTTTC
132294 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:132545 original size:12 final size:12
Alignment explanation
Indices: 132526--132559 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
132516 CTCTCCGGCG
132526 ACATCCGTTCCT
1 ACATCCGTTCCT
*
132538 ATATCCGTTCCT
1 ACATCCGTTCCT
132550 ACATCC-TTCC
1 ACATCCGTTCC
132560 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:133358 original size:12 final size:12
Alignment explanation
Indices: 133341--133365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
133331 ATATAATCCT
133341 GAAGAAGAAAAA
1 GAAGAAGAAAAA
133353 GAAGAAGAAAAA
1 GAAGAAGAAAAA
133365 G
1 G
133366 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:135667 original size:19 final size:19
Alignment explanation
Indices: 135642--135772 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
135632 GGAAATTACT
135642 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
135661 ATTGCAA--CGAGA-G-AA
1 ATCGCAATGCGAAATGAAA
135676 A-CGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
135694 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
135708 TTTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
135727 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
135741 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
135760 ATCGCAACGCGAA
1 ATCGCAATGCGAA
135773 TTTAATTTCG
Statistics
Matches: 80, Mismatches: 17, Indels: 30
0.63 0.13 0.24
Matches are distributed among these distances:
14 20 0.25
15 5 0.06
16 9 0.11
17 9 0.11
18 5 0.06
19 32 0.40
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:135686 original size:33 final size:33
Alignment explanation
Indices: 135642--135768 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
135632 GGAAATTACT
*
135642 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
135675 AACGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
135707 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
135741 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
135769 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:135751 original size:66 final size:66
Alignment explanation
Indices: 135645--135775 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
135635 AATTACTATC
* *
135645 GCAATGCGAAATGAAAATTGCAACGAGAGAAACGCAATGCGAAATGAAAATCGCAACGCTAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAAACGCAATGCGAAATGAAAATCGCAACGCGAATTT
135710 T
66 T
* *
135711 GCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAAACGCAATGCGAAATGAAAATCGCAACGCGAATTT
135776 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (66 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAAACGCAATGCGAAATGAAAATCGCAACGCGAATTT
T
Found at i:135843 original size:19 final size:20
Alignment explanation
Indices: 135799--135843 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
135789 GATTCTCTCG
135799 TTGCGATTTTCATTTCGCGA
1 TTGCGATTTTCATTTCGCGA
*
135819 -TACGATTTTCATTTCGC-A
1 TTGCGATTTTCATTTCGCGA
135837 TTGCGAT
1 TTGCGAT
135844 AGTACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (20 bp):
TTGCGATTTTCATTTCGCGA
Found at i:135969 original size:14 final size:14
Alignment explanation
Indices: 135950--135986 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
135940 CATCAATTAA
135950 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
135964 ACAAATCACCTTTT
1 ACAAATCAACTTTT
135978 ACAAATCAA
1 ACAAATCAA
135987 TTAAACAATA
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:137428 original size:42 final size:42
Alignment explanation
Indices: 137382--137545 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
137372 CGATGACAGT
* * *
137382 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * * **
137424 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAAT
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
137466 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
137508 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
137546 CAGGCGAGTC
Statistics
Matches: 98, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:137484 original size:84 final size:84
Alignment explanation
Indices: 137373--137547 Score: 341
Period size: 84 Copynumber: 2.1 Consensus size: 84
137363 CCTCTTCAAC
*
137373 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
137438 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
137457 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
137522 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
137541 GATGACA
1 GATGACA
137548 GGCGAGTCAG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (84 bp):
GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:137942 original size:91 final size:90
Alignment explanation
Indices: 137767--137951 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
137757 ATTTCAAACT
*
137767 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
137832 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
137860 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
137924 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
137951 T
1 T
137952 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:139756 original size:19 final size:19
Alignment explanation
Indices: 139734--139936 Score: 363
Period size: 19 Copynumber: 10.7 Consensus size: 19
139724 GCGACGAGAG
139734 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139753 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139772 AATCGCAACG-GTAAATGAA
1 AATCGCAACGCG-AAATGAA
139791 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139810 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139829 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139848 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139867 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
139886 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
139905 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATGAA
*
139924 AATCGCAATGCGA
1 AATCGCAACGCGA
139937 TTTTGGTTTC
Statistics
Matches: 179, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
18 1 0.01
19 177 0.99
20 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:139776 original size:38 final size:38
Alignment explanation
Indices: 139639--139936 Score: 375
Period size: 38 Copynumber: 8.1 Consensus size: 38
139629 TCTTTTGGTT
* *
139639 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** * *
139678 GGAAATGACTATTGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
139712 GAAATGACTATCGCGA--CG--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139745 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACG-
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139782 GTAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 G-AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139821 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139859 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** *
139897 GAAATGAAAATCGCAACGCGAAACCAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139935 GA
1 GA
139937 TTTTGGTTTC
Statistics
Matches: 238, Mismatches: 13, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
33 44 0.18
34 14 0.06
35 3 0.01
37 2 0.01
38 161 0.68
39 1 0.00
40 13 0.05
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:139813 original size:57 final size:57
Alignment explanation
Indices: 139639--139936 Score: 375
Period size: 57 Copynumber: 5.4 Consensus size: 57
139629 TCTTTTGGTT
* * ** *
139639 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGCGGAAATGACTATTGCAA--C
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGC
* ** * *
139696 G--A-GAGAATCGCAACGCGAAATGACTATCGCGA--CG--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139745 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACG-GTAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCG-AAATGAAAATCGCAACGC
139802 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
139859 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** *
139916 GAAACCAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
139937 TTTTGGTTTC
Statistics
Matches: 213, Mismatches: 16, Indels: 24
0.84 0.06 0.09
Matches are distributed among these distances:
47 8 0.04
48 1 0.00
49 2 0.01
50 1 0.00
51 2 0.01
52 26 0.12
53 12 0.06
54 14 0.07
55 1 0.00
56 1 0.00
57 144 0.68
58 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (57 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:140593 original size:20 final size:20
Alignment explanation
Indices: 140568--140621 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
140558 GATTTTGTAT
140568 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
140588 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
140608 TATCGTATTGCGAT
1 TATCGCATTGCGAT
140622 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:140732 original size:21 final size:21
Alignment explanation
Indices: 140692--140732 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
140682 ACTGTAGACC
**
140692 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
140713 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
140733 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:141434 original size:17 final size:18
Alignment explanation
Indices: 141397--141437 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
141387 ATATTATGTA
*
141397 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
141415 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
141432 TTTACT
1 TTTACT
141438 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:143145 original size:18 final size:18
Alignment explanation
Indices: 143119--143153 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
143109 CAATAGCCAT
*
143119 CGCATCCATATATGATGC
1 CGCAACCATATATGATGC
143137 CGCAACCATATATGATG
1 CGCAACCATATATGATG
143154 TCACCATCGC
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:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (18 bp):
CGCAACCATATATGATGC
Found at i:147440 original size:41 final size:41
Alignment explanation
Indices: 147380--147489 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
147370 CGCGGTCGCA
*
147380 CTATAGCCCTACGTGGCGTATAGCGCGGCCTCTGATCCGCG
1 CTATAGCCCTACGTGGCGTATAGCGCGGCCCCTGATCCGCG
* * *
147421 CTATAGTCCTACGTTGCGTATAGCACGGCCCCTGATCCGCG
1 CTATAGCCCTACGTGGCGTATAGCGCGGCCCCTGATCCGCG
*
147462 CTATACCCCTACGTGGCGTATAGCGCGG
1 CTATAGCCCTACGTGGCGTATAGCGCGG
147490 ATCAGGGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.16, C:0.34, G:0.27, T:0.23
Consensus pattern (41 bp):
CTATAGCCCTACGTGGCGTATAGCGCGGCCCCTGATCCGCG
Found at i:175869 original size:18 final size:19
Alignment explanation
Indices: 175846--175895 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
175836 TAACAATTTT
175846 AGTATCGATACTCAAGG-G
1 AGTATCGATACTCAAGGAG
*
175864 AGTATCGATAC-CCAGGTAG
1 AGTATCGATACTCAAGG-AG
175883 AGTATCGATACTC
1 AGTATCGATACTC
175896 CCCATATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 12 0.43
20 1 0.04
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
AGTATCGATACTCAAGGAG
Found at i:175977 original size:263 final size:263
Alignment explanation
Indices: 175506--176030 Score: 942
Period size: 263 Copynumber: 2.0 Consensus size: 263
175496 TACTCATCCT
175506 AAGAGTATCGATACTCAAGGTTCAATTTTGAAACCCGAGAAGAGGGTATCGAGATCGTTTTTCCA
1 AAGAGTATCGATACTCAAGGTTCAATTTTGAAACCCGAGAAGAGGGTATCGAGATCGTTTTTCCA
*
175571 TATAACAATTTTAGTATCGGTACTCAAGGGAGTATCGATACCCAGGTAGAGTATCGATACTCCCC
66 TATAACAATTTTAGTATCGATACTCAAGGGAGTATCGATACCCAGGTAGAGTATCGATACTCCCC
* * *
175636 ATATGAGTAGTGATACCACTCATTTTCTTTTGAGTAGAAAGTAGCTAGAGAGTATTGATACCCTG
131 ATATGAGTAGTGATACCACTCATTTTATTTTAAGTAGAAAGTAGCTAGAGAGTATCGATACCCTG
*
175701 ATAGTAGTATCGATACTCAAGAGGCAGTACTGATACTAATAGTCTTAGTATCAATACTTAAGTGC
196 ATAGTAATATCGATACTCAAGAGGCAGTACTGATACTAATAGTCTTAGTATCAATACTTAAGTGC
175766 TAG
261 TAG
* *
175769 AAGAGTATCGATACTCAAGGTTCAGTTTTGAAACCCGAGAAGAGGGTATTGAGATCGTTTTTCCA
1 AAGAGTATCGATACTCAAGGTTCAATTTTGAAACCCGAGAAGAGGGTATCGAGATCGTTTTTCCA
175834 TATAACAATTTTAGTATCGATACTCAAGGGAGTATCGATACCCAGGTAGAGTATCGATACTCCCC
66 TATAACAATTTTAGTATCGATACTCAAGGGAGTATCGATACCCAGGTAGAGTATCGATACTCCCC
* **
175899 ATATGAGTAGTGATACCACTCATTTTATTTTAAGTATAATTTAGCTAGAGAGTATCGATACCCTG
131 ATATGAGTAGTGATACCACTCATTTTATTTTAAGTAGAAAGTAGCTAGAGAGTATCGATACCCTG
* *
175964 ATAGTAATATCGATACTCAAGAGGCAGTACTGATATTAATTGTCTTAGTATCAATACTTAAGTGC
196 ATAGTAATATCGATACTCAAGAGGCAGTACTGATACTAATAGTCTTAGTATCAATACTTAAGTGC
176029 TA
261 TA
176031 TGTTGGGGCA
Statistics
Matches: 250, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
263 250 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (263 bp):
AAGAGTATCGATACTCAAGGTTCAATTTTGAAACCCGAGAAGAGGGTATCGAGATCGTTTTTCCA
TATAACAATTTTAGTATCGATACTCAAGGGAGTATCGATACCCAGGTAGAGTATCGATACTCCCC
ATATGAGTAGTGATACCACTCATTTTATTTTAAGTAGAAAGTAGCTAGAGAGTATCGATACCCTG
ATAGTAATATCGATACTCAAGAGGCAGTACTGATACTAATAGTCTTAGTATCAATACTTAAGTGC
TAG
Found at i:177246 original size:12 final size:14
Alignment explanation
Indices: 177210--177263 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
177200 AGTATCTGTT
*
177210 TTATATAGTATATCA
1 TTATATATTATAT-A
*
177225 TTATGT-TTATAT-
1 TTATATATTATATA
177237 TTAT-TATTATATA
1 TTATATATTATATA
*
177250 TTTTATATTATATA
1 TTATATATTATATA
177264 GTGTTGAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 1 0.03
12 10 0.30
13 3 0.09
14 14 0.42
15 5 0.15
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (14 bp):
TTATATATTATATA
Found at i:179669 original size:20 final size:19
Alignment explanation
Indices: 179641--179727 Score: 59
Period size: 20 Copynumber: 4.5 Consensus size: 19
179631 AATCCCAACG
179641 TATAGTATAGTATTATATT
1 TATAGTATAGTATTATATT
* *
179660 ATATATTATA-TAATATATT
1 -TATAGTATAGTATTATATT
* *
179679 TATAGCATATTATATATATT
1 TATAGTATAGTAT-TATATT
* * * *
179699 ACATAGTGTAGTCTAATATT
1 -TATAGTATAGTATTATATT
*
179719 TATATTATA
1 TATAGTATA
179728 TAGGTAGTAT
Statistics
Matches: 50, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
18 7 0.14
19 16 0.32
20 19 0.38
21 8 0.16
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (19 bp):
TATAGTATAGTATTATATT
Found at i:179776 original size:23 final size:24
Alignment explanation
Indices: 179744--179789 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
179734 GTATATTTTT
179744 TATAAATATTAT-TAT-TATATAA
1 TATAAATATTATATATATATATAA
179766 TATAACATATTATATATATATATA
1 TATAA-ATATTATATATATATATA
179790 TTATCATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 7 0.33
24 3 0.14
25 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAAATATTATATATATATATAA
Found at i:180518 original size:32 final size:32
Alignment explanation
Indices: 180425--180522 Score: 124
Period size: 32 Copynumber: 3.1 Consensus size: 32
180415 GACTATGCTA
* ** * * *
180425 TGCATTATCTAAATGTGATACTGGCTCTATCG
1 TGCATTATCTGAATGCAATACTGACTCTGTTG
* *
180457 TGCATTATATGAATGCAATACTGATTCTGTTG
1 TGCATTATCTGAATGCAATACTGACTCTGTTG
180489 TGCATTATCTGAATGCAATACTGACTCTGTTG
1 TGCATTATCTGAATGCAATACTGACTCTGTTG
180521 TG
1 TG
180523 ACTCATACAC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (32 bp):
TGCATTATCTGAATGCAATACTGACTCTGTTG
Found at i:183947 original size:20 final size:21
Alignment explanation
Indices: 183890--183964 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
183880 TAACATAAAC
* *
183890 ATAAAATTTATAAATTCAAATT
1 ATAAAA-TTATAAAATAAAATT
*
183912 ATATAATCTA-AAAATAAAATT
1 ATAAAAT-TATAAAATAAAATT
* *
183933 TTAAAA-TATAAAATAGAATT
1 ATAAAATTATAAAATAAAATT
183953 ATAAAATTATAA
1 ATAAAATTATAA
183965 CTAAATTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 15 0.35
21 19 0.44
22 7 0.16
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAAAATTATAAAATAAAATT
Found at i:194888 original size:18 final size:18
Alignment explanation
Indices: 194865--194900 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
194855 AGGCAACAAC
194865 TGTAAGTATTTATTTGTT
1 TGTAAGTATTTATTTGTT
194883 TGTAAGTATTTATTTGTT
1 TGTAAGTATTTATTTGTT
194901 ATCTGTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (18 bp):
TGTAAGTATTTATTTGTT
Found at i:205243 original size:86 final size:86
Alignment explanation
Indices: 205098--205260 Score: 326
Period size: 86 Copynumber: 1.9 Consensus size: 86
205088 TTCGATCAAC
205098 CTTGTTCAACGTACCATTCCGTGTTCGTTCGACACATACTCGTATCCGACATACATTTCGAGATA
1 CTTGTTCAACGTACCATTCCGTGTTCGTTCGACACATACTCGTATCCGACATACATTTCGAGATA
205163 GAGTATCCTTTTCGAAATAAT
66 GAGTATCCTTTTCGAAATAAT
205184 CTTGTTCAACGTACCATTCCGTGTTCGTTCGACACATACTCGTATCCGACATACATTTCGAGATA
1 CTTGTTCAACGTACCATTCCGTGTTCGTTCGACACATACTCGTATCCGACATACATTTCGAGATA
205249 GAGTATCCTTTT
66 GAGTATCCTTTT
205261 TTTAAATAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (86 bp):
CTTGTTCAACGTACCATTCCGTGTTCGTTCGACACATACTCGTATCCGACATACATTTCGAGATA
GAGTATCCTTTTCGAAATAAT
Found at i:206525 original size:13 final size:13
Alignment explanation
Indices: 206507--206532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
206497 TCCGAAGGTC
206507 GTGTCATGCCTTT
1 GTGTCATGCCTTT
206520 GTGTCATGCCTTT
1 GTGTCATGCCTTT
206533 CTTCGTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (13 bp):
GTGTCATGCCTTT
Found at i:210251 original size:42 final size:42
Alignment explanation
Indices: 210192--210277 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
210182 AGGTAGATGC
210192 TCTTGCGATATTACAACTGATAGATGTTGGTGATGTTTATTT
1 TCTTGCGATATTACAACTGATAGATGTTGGTGATGTTTATTT
210234 TCTTGCGATATTACAACTGATAGATGTTGGTGATGTTTATTT
1 TCTTGCGATATTACAACTGATAGATGTTGGTGATGTTTATTT
210276 TC
1 TC
210278 ATATAGGGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.45
Consensus pattern (42 bp):
TCTTGCGATATTACAACTGATAGATGTTGGTGATGTTTATTT
Found at i:216148 original size:14 final size:14
Alignment explanation
Indices: 216129--216217 Score: 73
Period size: 14 Copynumber: 6.6 Consensus size: 14
216119 CTCGAGTACA
216129 TATTTAATAATAAT
1 TATTTAATAATAAT
*
216143 TATTTAA-ATTTAAT
1 TATTTAATA-ATAAT
*
216157 TATTT-A-ACTAAT
1 TATTTAATAATAAT
*
216169 GATTTAATAATAAT
1 TATTTAATAATAAT
216183 TATTTAACT--TAAT
1 TATTTAA-TAATAAT
*
216196 GATTTAAT-ATAAT
1 TATTTAATAATAAT
216209 TACTTTAAT
1 TA-TTTAAT
216218 GATTTACTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
12 9 0.15
13 19 0.31
14 33 0.53
15 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (14 bp):
TATTTAATAATAAT
Found at i:216203 original size:27 final size:26
Alignment explanation
Indices: 216139--216265 Score: 113
Period size: 26 Copynumber: 4.9 Consensus size: 26
216129 TATTTAATAA
* *
216139 TAATTATTTAAATTTAATTATTTAAC-
1 TAATGATTT-AATATAATTATTTAACT
216165 TAATGATTTAATAATAATTATTTAACT
1 TAATGATTTAAT-ATAATTATTTAACT
*
216192 TAATGATTTAATATAATTA-CT---T
1 TAATGATTTAATATAATTATTTAACT
* * *
216214 TAATGATTTACTTTAATGATTTAACTT
1 TAATGATTTAATATAATTATTTAAC-T
216241 TAATGA-TTAATAATAATTACTTTAA
1 TAATGATTTAAT-ATAATTA-TTTAA
216266 TGATTTAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
22 17 0.21
23 1 0.01
25 4 0.05
26 31 0.38
27 24 0.29
28 5 0.06
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.50
Consensus pattern (26 bp):
TAATGATTTAATATAATTATTTAACT
Found at i:216236 original size:8 final size:8
Alignment explanation
Indices: 216225--217465 Score: 442
Period size: 8 Copynumber: 167.5 Consensus size: 8
216215 AATGATTTAC
216225 TTTAATGA
1 TTTAATGA
*
216233 TTTAA--C
1 TTTAATGA
216239 TTTAATGA
1 TTTAATGA
216247 -TTAAT-A
1 TTTAATGA
* *
216253 -ATAATTA
1 TTTAATGA
216260 CTTTAATGA
1 -TTTAATGA
216269 TTTAAT--
1 TTTAATGA
216275 TTTAATGA
1 TTTAATGA
216283 TTTAAT-A
1 TTTAATGA
*
216290 --TAATTA
1 TTTAATGA
216296 CTTTAATGA
1 -TTTAATGA
216305 TTT-AT--
1 TTTAATGA
216310 TTTAATGA
1 TTTAATGA
216318 TTTAATGA
1 TTTAATGA
*
216326 TTTAA--C
1 TTTAATGA
216332 TTTAATGA
1 TTTAATGA
216340 TTTAAT-A
1 TTTAATGA
*
216347 --TAATTA
1 TTTAATGA
216353 CTTTAATGA
1 -TTTAATGA
216362 TTTAAT-A
1 TTTAATGA
* *
216369 -ATAATTA
1 TTTAATGA
216376 CTTTAATGA
1 -TTTAATGA
*
216385 TTTAA--C
1 TTTAATGA
216391 TTTAATGA
1 TTTAATGA
*
216399 TTTAATAA
1 TTTAATGA
* *
216407 TAATTATTAA
1 T--TTAATGA
216417 CTTTAATGA
1 -TTTAATGA
216426 TTTAAT-A
1 TTTAATGA
216433 --TAA--A
1 TTTAATGA
216437 CTTTAATGA
1 -TTTAATGA
*
216446 TTTAA--C
1 TTTAATGA
216452 TTT-ATGA
1 TTTAATGA
216459 TTTAAT-A
1 TTTAATGA
* *
216466 -ATAATTA
1 TTTAATGA
216473 CTTTAATGA
1 -TTTAATGA
*
216482 TTTAATAA
1 TTTAATGA
*
216490 TATT-A--C
1 T-TTAATGA
216496 TTTAATGA
1 TTTAATGA
216504 TTT-A--A
1 TTTAATGA
216509 TTTAATGA
1 TTTAATGA
216517 TTT-ATGA
1 TTTAATGA
*
216524 TTT-A--C
1 TTTAATGA
216529 TTTAATGA
1 TTTAATGA
216537 TTTAAT-A
1 TTTAATGA
*
216544 --TAATTA
1 TTTAATGA
*
216550 CTTAATGA
1 TTTAATGA
216558 TTTAATGA
1 TTTAATGA
216566 TTTAATGA
1 TTTAATGA
216574 TTTAATGA
1 TTTAATGA
216582 TTTAAT-A
1 TTTAATGA
* *
216589 -ATAATTA
1 TTTAATGA
216596 CTTTAATGA
1 -TTTAATGA
*
216605 TTT-A--C
1 TTTAATGA
216610 TTTAATGA
1 TTTAATGA
216618 TTTAAT-A
1 TTTAATGA
* *
216625 -ATAATTA
1 TTTAATGA
*
216632 TTTAA--C
1 TTTAATGA
216638 TTTAATGA
1 TTTAATGA
216646 TTTAAT-A
1 TTTAATGA
* *
216653 -ATAATTA
1 TTTAATGA
216660 CTTTAATGA
1 -TTTAATGA
*
216669 TTTAA--C
1 TTTAATGA
216675 TTTAATGA
1 TTTAATGA
216683 TTTAAT-A
1 TTTAATGA
* *
216690 -ATAATTA
1 TTTAATGA
216697 CTTTAATGA
1 -TTTAATGA
216706 TTTAAT--
1 TTTAATGA
216712 TTTAATGA
1 TTTAATGA
216720 TTTAAT-A
1 TTTAATGA
* *
216727 -ATAATTA
1 TTTAATGA
216734 CTTTAATGA
1 -TTTAATGA
216743 TTTAAT--
1 TTTAATGA
216749 TTTAATGA
1 TTTAATGA
216757 TTTAATGA
1 TTTAATGA
*
216765 TTTAA--C
1 TTTAATGA
216771 TTTAATGA
1 TTTAATGA
216779 TTTAAT-A
1 TTTAATGA
* *
216786 -ATAATTA
1 TTTAATGA
216793 CTTTAATGA
1 -TTTAATGA
216802 TTTAATGA
1 TTTAATGA
*
216810 TTTAATAA
1 TTTAATGA
216818 TTTAATGA
1 TTTAATGA
216826 TTTAAT-A
1 TTTAATGA
* *
216833 -ATAATTA
1 TTTAATGA
216840 CTTTAATGA
1 -TTTAATGA
*
216849 TTTAA--C
1 TTTAATGA
216855 TTTAATGA
1 TTTAATGA
216863 TTTAAT-A
1 TTTAATGA
* *
216870 -ATAATTA
1 TTTAATGA
*
216877 TTTAA--C
1 TTTAATGA
216883 TTTAATGA
1 TTTAATGA
216891 TTTAAT-A
1 TTTAATGA
* *
216898 -ATAATTA
1 TTTAATGA
216905 CTTTAATGA
1 -TTTAATGA
*
216914 TTTAA--C
1 TTTAATGA
216920 TTTAATGA
1 TTTAATGA
*
216928 CTTAAT-A
1 TTTAATGA
* *
216935 -ATAATTA
1 TTTAATGA
216942 CTTTAATGA
1 -TTTAATGA
216951 TTTAAT--
1 TTTAATGA
*
216957 TTTAATAA
1 TTTAATGA
216965 TTTAAT-A
1 TTTAATGA
* *
216972 -ATAATTA
1 TTTAATGA
216979 CTTTAATGA
1 -TTTAATGA
*
216988 TTTAA--C
1 TTTAATGA
*
216994 TTTAATGC
1 TTTAATGA
217002 TTTAAT-A
1 TTTAATGA
** *
217009 -ACAATTA
1 TTTAATGA
217016 CTTTAATGA
1 -TTTAATGA
217025 TTTAATGA
1 TTTAATGA
217033 TTTAATGA
1 TTTAATGA
217041 TTTAATGA
1 TTTAATGA
217049 TTTAATGA
1 TTTAATGA
217057 TTTAAT-A
1 TTTAATGA
* *
217064 -ATAATTA
1 TTTAATGA
217071 CTTTAATGA
1 -TTTAATGA
*
217080 TTTAA--C
1 TTTAATGA
*
217086 TTTAATGC
1 TTTAATGA
217094 TTTAAT-A
1 TTTAATGA
* *
217101 -ATAATTA
1 TTTAATGA
217108 CTTTAATGA
1 -TTTAATGA
217117 TTTAATGA
1 TTTAATGA
217125 TTTAAT-A
1 TTTAATGA
* *
217132 -ATAATTA
1 TTTAATGA
217139 CTTTAATGA
1 -TTTAATGA
217148 TTTAAT--
1 TTTAATGA
217154 TTTAATGA
1 TTTAATGA
217162 TTTAAT-A
1 TTTAATGA
* *
217169 -ATAATTA
1 TTTAATGA
217176 CTTTAATGA
1 -TTTAATGA
*
217185 TTTACT--
1 TTTAATGA
217191 TTTAATGA
1 TTTAATGA
217199 TTTAATGA
1 TTTAATGA
*
217207 TTTAA--C
1 TTTAATGA
217213 TTTAATGA
1 TTTAATGA
217221 TTTAAT-A
1 TTTAATGA
* *
217228 -ATAATTA
1 TTTAATGA
217235 CTTTAATGA
1 -TTTAATGA
*
217244 TTTAA--C
1 TTTAATGA
*
217250 TTTAATGC
1 TTTAATGA
217258 TTTAAT-A
1 TTTAATGA
** *
217265 -ACAATTA
1 TTTAATGA
217272 CTTTAAT-A
1 -TTTAATGA
217280 TTTAATGA
1 TTTAATGA
217288 TTTAATGA
1 TTTAATGA
217296 TTTAAT-A
1 TTTAATGA
* *
217303 -ATAATTA
1 TTTAATGA
217310 CTTTAATGA
1 -TTTAATGA
*
217319 TTTAA--C
1 TTTAATGA
*
217325 TTTAA-GCT
1 TTTAATG-A
*
217333 TTAATAATTA
1 TT--TAATGA
217343 CTTTAATGA
1 -TTTAATGA
217352 TTTAATGA
1 TTTAATGA
217360 -TTAAT-A
1 TTTAATGA
* *
217366 -ATAATTA
1 TTTAATGA
217373 CTTTAATGA
1 -TTTAATGA
217382 TTTAAT--
1 TTTAATGA
*
217388 TTTAATAA
1 TTTAATGA
217396 TTTAAT-A
1 TTTAATGA
* *
217403 -ATAATTA
1 TTTAATGA
*
217410 CTTAAT--
1 TTTAATGA
*
217416 TTTAATAA
1 TTTAATGA
217424 TTTAAT--
1 TTTAATGA
217430 TTTAATGA
1 TTTAATGA
*
217438 TTTAATAA
1 TTTAATGA
*
217446 TATTAATTA
1 T-TTAATGA
*
217455 CTT-ATGA
1 TTTAATGA
217462 TTTA
1 TTTA
217466 TATTTACTGA
Statistics
Matches: 942, Mismatches: 131, Indels: 320
0.68 0.09 0.23
Matches are distributed among these distances:
4 1 0.00
5 31 0.03
6 231 0.25
7 86 0.09
8 450 0.48
9 131 0.14
10 9 0.01
11 3 0.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:216242 original size:14 final size:14
Alignment explanation
Indices: 216139--217442 Score: 470
Period size: 14 Copynumber: 99.8 Consensus size: 14
216129 TATTTAATAA
* *
216139 TAATTATTTAAATT
1 TAATGATTTAACTT
*
216153 TAATTATTTAAC--
1 TAATGATTTAACTT
*
216165 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
216179 TAATTATTTAAC-T
1 TAATGATTTAACTT
216192 TAATGATTTAA---
1 TAATGATTTAACTT
*
216203 T-AT-AATT-ACTT
1 TAATGATTTAACTT
216214 TAATGATTT-ACTT
1 TAATGATTTAACTT
216227 TAATGATTTAACTT
1 TAATGATTTAACTT
216241 TAATGA-TTAA---
1 TAATGATTTAACTT
*
216251 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
216263 TAATGATTTAATTT
1 TAATGATTTAACTT
*
216277 TAATGATTTAA-TA
1 TAATGATTTAACTT
*
216290 TAATTACTTTAA-TGAT
1 TAATGA-TTTAACT--T
* *
216306 TTAT--TTTAATGATT
1 TAATGATTTAA--CTT
216320 TAATGATTTAACTT
1 TAATGATTTAACTT
216334 TAATGATTTAA---
1 TAATGATTTAACTT
*
216345 T-AT-AATT-ACTT
1 TAATGATTTAACTT
216356 TAATGATTTAA---
1 TAATGATTTAACTT
*
216367 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216379 TAATGATTTAACTT
1 TAATGATTTAACTT
*
216393 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
216407 TAATTA-TTAACTT
1 TAATGATTTAACTT
216420 TAATGATTTAATATAAACTT
1 TAATGA--T--T-T-AACTT
216440 TAATGATTTAACTT
1 TAATGATTTAACTT
216454 T-ATGATTTAA---
1 TAATGATTTAACTT
*
216464 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216476 TAATGATTTAA---
1 TAATGATTTAACTT
216487 TAAT-A-TT-ACTT
1 TAATGATTTAACTT
216498 TAATGATTTAA-TT
1 TAATGATTTAACTT
216511 TAATGATTTATGATTTACTT
1 TAATGA-TT-T-A---ACTT
*
216531 TAATGATTTAA-TA
1 TAATGATTTAACTT
* * *
216544 TAATTACTTAATGATT
1 TAATGATTTAA--CTT
*
216560 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
216576 TAATGATTTAA---
1 TAATGATTTAACTT
*
216587 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216599 TAATGATTT-ACTT
1 TAATGATTTAACTT
*
216612 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
216626 TAATTATTTAACTT
1 TAATGATTTAACTT
216640 TAATGATTTAA---
1 TAATGATTTAACTT
*
216651 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216663 TAATGATTTAACTT
1 TAATGATTTAACTT
216677 TAATGATTTAA---
1 TAATGATTTAACTT
*
216688 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
216700 TAATGATTTAATTT
1 TAATGATTTAACTT
216714 TAATGATTTAA---
1 TAATGATTTAACTT
*
216725 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
216737 TAATGATTTAATTT
1 TAATGATTTAACTT
216751 TAATG-----A-TT
1 TAATGATTTAACTT
216759 TAATGATTTAACTT
1 TAATGATTTAACTT
*
216773 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
* *
216787 TAATTACTTTAATGATT
1 TAATGA-TTTAA--CTT
*
216804 TAATGATTTAATAATT
1 TAATGATTT-A-ACTT
216820 TAATGATTTAA---
1 TAATGATTTAACTT
*
216831 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216843 TAATGATTTAACTT
1 TAATGATTTAACTT
*
216857 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
216871 TAATTATTTAACTT
1 TAATGATTTAACTT
216885 TAATGATTTAA---
1 TAATGATTTAACTT
*
216896 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216908 TAATGATTTAACTT
1 TAATGATTTAACTT
*
216922 TAATGACTTAA---
1 TAATGATTTAACTT
*
216933 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
216945 TAATGATTTAATTT
1 TAATGATTTAACTT
*
216959 TAATAATTTAA---
1 TAATGATTTAACTT
*
216970 TAAT-AATT-ACTT
1 TAATGATTTAACTT
216982 TAATGATTTAACTT
1 TAATGATTTAACTT
*
216996 TAATGCTTTAA---
1 TAATGATTTAACTT
* *
217007 TAA-CAATT-ACTT
1 TAATGATTTAACTT
*
217019 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
*
217035 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
217051 TAATGATTTAA---
1 TAATGATTTAACTT
*
217062 TAAT-AATT-ACTT
1 TAATGATTTAACTT
217074 TAATGATTTAACTT
1 TAATGATTTAACTT
*
217088 TAATGCTTTAA---
1 TAATGATTTAACTT
*
217099 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
217111 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
*
217127 TAATAATAATT-ACTT
1 TAATGAT--TTAACTT
*
217142 TAATGATTTAATTT
1 TAATGATTTAACTT
217156 TAATGATTTAA---
1 TAATGATTTAACTT
*
217167 TAAT-AATT-ACTT
1 TAATGATTTAACTT
217179 TAATGATTT-ACTTT
1 TAATGATTTAAC-TT
217193 TAATG-----A-TT
1 TAATGATTTAACTT
217201 TAATGATTTAACTT
1 TAATGATTTAACTT
217215 TAATGATTTAA---
1 TAATGATTTAACTT
*
217226 TAAT-AATT-ACTT
1 TAATGATTTAACTT
217238 TAATGATTTAACTT
1 TAATGATTTAACTT
*
217252 TAATGCTTTAA---
1 TAATGATTTAACTT
* *
217263 TAA-CAATT-ACTT
1 TAATGATTTAACTT
*
217275 TAAT-ATTTAATGATT
1 TAATGATTTAA--CTT
217290 TAATGATTTAA---
1 TAATGATTTAACTT
*
217301 TAAT-AATT-ACTT
1 TAATGATTTAACTT
217313 TAATGATTTAACTT
1 TAATGATTTAACTT
*
217327 TAA-GCTTTAATAATTACTT
1 TAATG-ATT--T-A--ACTT
217346 TAATGATTTAA-TGAT
1 TAATGATTTAACT--T
*
217361 TAATAATAATT-ACTT
1 TAATGAT--TTAACTT
*
217376 TAATGATTTAATTT
1 TAATGATTTAACTT
* *
217390 TAATAATTTAA-TAA
1 TAATGATTTAACT-T
* * *
217404 TAATTACTTAATTT
1 TAATGATTTAACTT
* *
217418 TAATAATTTAATTT
1 TAATGATTTAACTT
217432 TAATGATTTAA
1 TAATGATTTAA
217443 TAATATTAAT
Statistics
Matches: 994, Mismatches: 107, Indels: 378
0.67 0.07 0.26
Matches are distributed among these distances:
8 17 0.02
9 28 0.03
10 61 0.06
11 76 0.08
12 88 0.09
13 162 0.16
14 372 0.37
15 39 0.04
16 98 0.10
17 13 0.01
18 7 0.01
19 13 0.01
20 20 0.02
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (14 bp):
TAATGATTTAACTT
Found at i:216393 original size:37 final size:37
Alignment explanation
Indices: 216151--217447 Score: 619
Period size: 37 Copynumber: 33.9 Consensus size: 37
216141 ATTATTTAAA
* *
216151 TTTAATTATTTAAC--TAATGATTTAATAATAATTATT
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTA-C
* * *
216187 TAACTTAATGATTTAA-TATAATTACTTTAATGAT--TTAC
1 T---TTAATGATTTAACTTTAATGA-TTTAATAATAATTAC
216225 TTTAATGATTTAACTTTAATGA-TTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
216261 TTTAATGATTTAATTTTAATGATTTAAT-ATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
* *
216297 TTTAATGATTT-ATTTTAATGATTTAATGAT--TTAAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATT-AC
216332 TTTAATGATTTAATATAATTACTTTAATGATTTAATAATAATTAC
1 TTTAATGA--T--T-T-A--ACTTTAATGATTTAATAATAATTAC
216377 TTTAATGATTTAACTTTAATGATTTAATAATAATTATTAAC
1 TTTAATGATTTAACTTTAATGATTTAATAAT-A--ATT-AC
* *
216418 TTTAATGATTTAATATAAACTTTAATGATTTAACT--TTATGA-
1 TTTAATGA--T--T-T-AACTTTAATGATTTAA-TAATAATTAC
*
216459 TTTAATAATAATT-ACTTTAATGATTTAATAAT-ATTAC
1 TTTAATGAT--TTAACTTTAATGATTTAATAATAATTAC
*
216496 TTTAATGATTTAA-TTTAATGATTT-ATGAT--TTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
* * *
216529 TTTAATGATTTAA---T-AT-AATTACT--TAATGA-
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
216558 TTTAATGATTTAATGATTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAA--CTTTAATGATTTAATAATAATTAC
216597 TTTAATGATTT-ACTTTAATGATTTAATAATAATTATTTAAC
1 TTTAATGATTTAACTTTAATGATTTAATAAT-A--A-TT-AC
* * *
216638 TTTAATGATTTAA-TAATAATTACTTTAATGAT--TTAAC
1 TTTAATGATTTAACT-TTAATGA-TTTAATAATAATT-AC
** *
216675 TTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGA-
1 TTTAATGA--T--T--T-A--ACTTTAATGATTTAATAATAATTAC
* ** *
216720 TTTAATAATAATT-ACTTTAATGATTTAATTTTAATGA-
1 TTTAATGAT--TTAACTTTAATGATTTAATAATAATTAC
216757 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
216794 TTTAATGATTTAATGATTTAATAATTTAATGATTTAATAATAATTAC
1 --------TTTAATGATTT-A-ACTTTAATGATTTAATAATAATTAC
216841 TTTAATGATTTAACTTTAATGATTTAATAATAATTATTTAAC
1 TTTAATGATTTAACTTTAATGATTTAATAAT-A--A-TT-AC
* * *
216883 TTTAATGATTTAA-TAATAATTACTTTAATGAT--TTAAC
1 TTTAATGATTTAACT-TTAATGA-TTTAATAATAATT-AC
* * * * *
216920 TTTAATGACTTAA-TAATAATTACTTTAATGAT--TTAAT
1 TTTAATGATTTAACT-TTAATGA-TTTAATAATAATT-AC
* * * *
216957 TTTAATAATTTAA-TAATAATTACTTTAATGAT--TTAAC
1 TTTAATGATTTAACT-TTAATGA-TTTAATAATAATT-AC
* ** * * *
216994 TTTAATGCTTTAA-TAACAATTACTTTAATGATTTAATGA-
1 TTTAATGATTTAACT-TTAATGA-TTTAAT-A-ATAATTAC
*
217033 TTTAATGATTTAATGATTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAA--CTTTAATGATTTAATAATAATTAC
*
217072 TTTAATGATTTAACTTTAATGCTTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
217109 TTTAATG-----A-TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
217140 TTTAATGATTTAATTTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
*
217177 TTTAATGATTT-ACTTTTAATGATTTAATGAT--TTAAC
1 TTTAATGATTTAAC-TTTAATGATTTAATAATAATT-AC
* * *
217213 TTTAATGATTTAA-TAATAATTACTTTAATGAT--TTAAC
1 TTTAATGATTTAACT-TTAATGA-TTTAATAATAATT-AC
* ** * * *
217250 TTTAATGCTTTAA-TAACAATTACTTTAATATTTAATGA-
1 TTTAATGATTTAACT-TTAATGA-TTTAATA-ATAATTAC
* * *
217288 TTTAATGATTTAA-TAATAATTACTTTAATGATTTAACTTTAAGC
1 TTTAATGATTTAACT-TTAATGA-TTTAAT-A-ATAA--TT-A-C
* *
217332 TTTAATAATTACTTTAATGATTTAATGA-TTAATAATAATTAC
1 -TT--TAATGA-TTTAA--CTTTAATGATTTAATAATAATTAC
* *
217374 TTTAATGATTTAATTTTAATAATTTAATAATAATTAC
1 TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
* *
217411 TTAATTTTAATAATTTAATTTTAATGATTTAATAATA
1 -----TTTAATGATTTAACTTTAATGATTTAATAATA
217448 TTAATTACTT
Statistics
Matches: 1048, Mismatches: 82, Indels: 256
0.76 0.06 0.18
Matches are distributed among these distances:
28 1 0.00
29 16 0.02
30 5 0.00
31 30 0.03
32 1 0.00
33 17 0.02
34 14 0.01
35 59 0.06
36 142 0.14
37 333 0.32
38 49 0.05
39 83 0.08
40 21 0.02
41 53 0.05
42 60 0.06
43 26 0.02
44 20 0.02
45 38 0.04
46 15 0.01
47 48 0.05
48 11 0.01
50 5 0.00
51 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (37 bp):
TTTAATGATTTAACTTTAATGATTTAATAATAATTAC
Found at i:216418 original size:27 final size:26
Alignment explanation
Indices: 216263--217084 Score: 154
Period size: 23 Copynumber: 30.9 Consensus size: 26
216253 ATAATTACTT
*
216263 TAATGATTTAATTTTAATGATTTAATA
1 TAAT-ATTTAACTTTAATGATTTAATA
*
216290 TAATTACTTTAA-TGATTTAT--TTTAATGA
1 TAA-TA-TTTAACT--TTAATGATTTAAT-A
216318 TTTAATGATTTAACTTTAATGATTTAATA
1 --TAAT-ATTTAACTTTAATGATTTAATA
216347 T-A-A-TT-ACTTTAATGATTT-A-A
1 TAATATTTAACTTTAATGATTTAATA
* *
216367 TAATAATT-ACTTTAATGATTTAACTT
1 TAATATTTAACTTTAATGATTTAA-TA
* * *
216393 TAATGATTTAATAATAATTATTAACTTTAATGA
1 TAAT-ATTT-A-ACT--TTAATGA-TTTAAT-A
*
216426 TTTAATA-TAAACTTTAATGATTTAACT-
1 --TAATATTTAACTTTAATGATTTAA-TA
* * *
216453 TTATGATTTAA-TAATAATTACTTTAATGA
1 TAAT-ATTTAACT-TTAATGA-TTTAAT-A
*
216482 TTTAATAATATT-ACTTTAATGATTTAATT
1 --TAAT-AT-TTAACTTTAATGATTTAATA
216511 TAATGATTTATGATTTACTTTAATGATTTAATA
1 TAAT-A-TT-T-A---ACTTTAATGATTTAATA
* *
216544 TAATTACTTAATGATTTAATGATTTAATGA
1 TAA-TATTTAA--CTTTAATGATTTAAT-A
* * *
216574 TTTAATGATTTAA---TAAT-AATTACTT
1 --TAAT-ATTTAACTTTAATGATTTAATA
216599 TAATGATTT-ACTTTAATGATTTAATAA
1 TAAT-ATTTAACTTTAATGATTTAAT-A
216626 TAATTATTTAACTTTAATGATTT-A-A
1 TAA-TATTTAACTTTAATGATTTAATA
* *
216651 TAATAATT-ACTTTAATGATTTAACTT
1 TAATATTTAACTTTAATGATTTAA-TA
* * *
216677 TAATGATTTAA---TAAT-AATTACTT
1 TAAT-ATTTAACTTTAATGATTTAATA
*
216700 TAATGATTTAATTTTAATGATTT-A-A
1 TAAT-ATTTAACTTTAATGATTTAATA
*
216725 TAATAATT-ACTTTAATGATTTAAT-
1 TAATATTTAACTTTAATGATTTAATA
* * * *
216749 T-TTA-ATGA-TTTAATGATTTAACTT
1 TAATATTTAACTTTAATGATTTAA-TA
* *
216773 TAATGATTTAA-TAATAATTACTTTAATGA
1 TAAT-ATTTAACT-TTAATGA-TTTAAT-A
*
216802 TTTAATGATTTAATAATTTAATGATTT-A-A
1 --TAAT-ATTT-A-ACTTTAATGATTTAATA
* *
216831 TAATAATT-ACTTTAATGATTTAACTT
1 TAATATTTAACTTTAATGATTTAA-TA
* * *
216857 TAATGATTTAA-TAATAATTATTTAACTT
1 TAAT-ATTTAACT-TTAATGATTTAA-TA
* * *
216885 TAATGATTTAA---TAAT-AATTACTT
1 TAAT-ATTTAACTTTAATGATTTAATA
*
216908 TAATGATTTAACTTTAATGACTT-A-A
1 TAAT-ATTTAACTTTAATGATTTAATA
* *
216933 TAATAATT-ACTTTAATGATTTAATTT
1 TAATATTTAACTTTAATGATTTAA-TA
* * *
216959 TAATAATTTAA---TAAT-AATTACTT
1 TAAT-ATTTAACTTTAATGATTTAATA
*
216982 TAATGATTTAACTTTAATGCTTTAATA
1 TAAT-ATTTAACTTTAATGATTTAATA
217009 -ACA-A-TT-ACTTTAATGATTTAATGA
1 TA-ATATTTAACTTTAATGATTTAAT-A
*
217033 TTTAATGATTTAATGATTTAATGATTT-A-A
1 --TAAT-ATTTAA--CTTTAATGATTTAATA
*
217062 TAATAATT-ACTTTAATGATTTAA
1 TAATATTTAACTTTAATGATTTAA
217085 CTTTAATGCT
Statistics
Matches: 602, Mismatches: 78, Indels: 233
0.66 0.09 0.26
Matches are distributed among these distances:
20 2 0.00
21 2 0.00
22 29 0.05
23 143 0.24
24 34 0.06
25 34 0.06
26 50 0.08
27 76 0.13
28 71 0.12
29 40 0.07
30 22 0.04
31 26 0.04
32 34 0.06
33 32 0.05
34 3 0.00
35 4 0.01
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (26 bp):
TAATATTTAACTTTAATGATTTAATA
Found at i:217308 original size:75 final size:72
Alignment explanation
Indices: 217213--217429 Score: 299
Period size: 75 Copynumber: 3.1 Consensus size: 72
217203 ATGATTTAAC
217213 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAACAATTACTTTAA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAA-AATTAC-TTAA
217278 TATTTAATGA
64 T-TTTAATGA
217288 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAA-GCTTTAAT--AATTAC-----T
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAAAATTACTTAATT
217345 TTAATGA
66 TTAATGA
* **
217352 TTTAATGA-TTAATAATAATTACTTTAATGATTTAATTTTAATAATTTAATAATAATTACTTAAT
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAA-AATTACTTAAT
*
217416 TTTAATAA
65 TTTAATGA
217424 TTTAAT
1 TTTAAT
217430 TTTAATGATT
Statistics
Matches: 129, Mismatches: 4, Indels: 21
0.84 0.03 0.14
Matches are distributed among these distances:
63 32 0.25
64 22 0.17
67 6 0.05
71 6 0.05
72 13 0.10
74 8 0.06
75 42 0.33
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (72 bp):
TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAAAATTACTTAATT
TTAATGA
Found at i:217343 original size:33 final size:28
Alignment explanation
Indices: 217280--217471 Score: 139
Period size: 28 Copynumber: 6.6 Consensus size: 28
217270 TACTTTAATA
217280 TTTAATGATTTAATGATTTAATAATAATTAC
1 TTTAATGATTT-A--ATTTAATAATAATTAC
217311 TTTAATGATTTAACTTTAAGCTTTAATAATTAC
1 TTTAATGATTTAA-TTTAA----TAATAATTAC
217344 TTTAATGATTTAATGATTAATAATAATTAC
1 TTTAATGATTTAAT--TTAATAATAATTAC
*
217374 TTTAATGATTTAATTT--TAATAATTTAA
1 TTTAATGATTTAATTTAATAATAA-TTAC
* * * *
217401 TAATAATTACTTAATTT--TAATAATTTAAT
1 T-TTAATGATTTAATTTAATAATAA-TT-AC
*
217430 TTTAATGATTTAA--TAATATTAATTAC
1 TTTAATGATTTAATTTAATAATAATTAC
217456 -TT-ATGATTTATATTTA
1 TTTAATGATTTA-ATTTA
217472 CTGATATCAT
Statistics
Matches: 136, Mismatches: 10, Indels: 34
0.76 0.06 0.19
Matches are distributed among these distances:
24 8 0.06
25 3 0.02
26 8 0.06
27 8 0.06
28 38 0.28
29 7 0.05
30 25 0.18
31 11 0.08
32 1 0.01
33 23 0.17
34 4 0.03
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (28 bp):
TTTAATGATTTAATTTAATAATAATTAC
Found at i:218139 original size:28 final size:29
Alignment explanation
Indices: 218103--218160 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
218093 TGGCAAGTAT
218103 GAACCCCTGTTGTT-CAATGATTGATATG
1 GAACCCCTGTTGTTCCAATGATTGATATG
218131 GAACCCCTGTTGTTCCAATGATTGATATG
1 GAACCCCTGTTGTTCCAATGATTGATATG
218160 G
1 G
218161 TTAGCAGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (29 bp):
GAACCCCTGTTGTTCCAATGATTGATATG
Found at i:220337 original size:41 final size:41
Alignment explanation
Indices: 220277--220354 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
220267 CCCTCTCAGG
*
220277 CTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCAAA
1 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCCCAAA
220318 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCC
1 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCC
220355 GAGCAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (41 bp):
CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCCCAAA
Found at i:220535 original size:23 final size:23
Alignment explanation
Indices: 220509--220552 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
220499 AGTTGCATGC
220509 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
220532 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
220553 CCCTGCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:221152 original size:35 final size:35
Alignment explanation
Indices: 221112--221180 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
221102 ACTTTTAATT
*
221112 TTTTTTCAAAACTATACT-TAAAGTTTAGTTTTTTA
1 TTTTTTCAAAACCATA-TATAAAGTTTAGTTTTTTA
221147 TTTTTTCAAAACCATATATAAAGTTTAGTTTTTT
1 TTTTTTCAAAACCATATATAAAGTTTAGTTTTTT
221181 GTTTCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.54
Consensus pattern (35 bp):
TTTTTTCAAAACCATATATAAAGTTTAGTTTTTTA
Found at i:221955 original size:24 final size:27
Alignment explanation
Indices: 221917--221965 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
221907 TTTTAATAAT
221917 AAAAATATTATTTTTAATTA-AAAACA
1 AAAAATATTATTTTTAATTACAAAACA
*
221943 AAAAAT-TTA-TTTTATTTACAAAA
1 AAAAATATTATTTTTAATTACAAAA
221966 GAACCCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 7 0.33
26 6 0.29
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAATATTATTTTTAATTACAAAACA
Found at i:225279 original size:5 final size:5
Alignment explanation
Indices: 225269--225294 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
225259 ACCTGTCAAA
225269 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
225295 GAAAACACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:225339 original size:2 final size:2
Alignment explanation
Indices: 225332--225360 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
225322 TTCGGCCTAT
225332 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
225361 TATTATAAAT
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:234859 original size:20 final size:20
Alignment explanation
Indices: 234834--234873 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
234824 TCCAACATGA
234834 ACATGATTAAAATATTCTAT
1 ACATGATTAAAATATTCTAT
*
234854 ACATGATTAATATATTCTAT
1 ACATGATTAAAATATTCTAT
234874 CTTTTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (20 bp):
ACATGATTAAAATATTCTAT
Found at i:235288 original size:38 final size:40
Alignment explanation
Indices: 235246--235324 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
235236 TTTCAATCGC
*
235246 ACAATCATGTAAGGAACG-A-AAGAATGGTTGAAGAACCT
1 ACAATCATGCAAGGAACGAAGAAGAATGGTTGAAGAACCT
235284 ACAATCATGCAAGGAACGAAAGAAGAATGGTTGAAGAACCT
1 ACAATCATGCAAGGAACG-AAGAAGAATGGTTGAAGAACCT
235325 TACTTGTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 17 0.46
40 1 0.03
41 19 0.51
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (40 bp):
ACAATCATGCAAGGAACGAAGAAGAATGGTTGAAGAACCT
Done.