Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001422.1 Hibiscus syriacus cultivar Beakdansim tig00002760_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: 109779
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5435 original size:6 final size:6
Alignment explanation
Indices: 5424--5458 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5414 CTTTCTACAT
*
5424 CTATAC CGATAC CTATAC CTATAC CTATAC CTATA
1 CTATAC CTATAC CTATAC CTATAC CTATAC CTATA
5459 TATTCTACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (6 bp):
CTATAC
Found at i:11016 original size:39 final size:39
Alignment explanation
Indices: 10959--11038 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
10949 GCACAGCTTG
* * *
10959 CTTCTATTCCATCTTCTCCCC-AGCAAGAGCCTAATACTC
1 CTTCTACTCCATCCTCTCCCCTAGC-AGAACCTAATACTC
* *
10998 CTTCTACTCCGTCCTCTCCCCTATCAGAACCTAATACTC
1 CTTCTACTCCATCCTCTCCCCTAGCAGAACCTAATACTC
11037 CT
1 CT
11039 CAAGCTCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.21, C:0.41, G:0.06, T:0.31
Consensus pattern (39 bp):
CTTCTACTCCATCCTCTCCCCTAGCAGAACCTAATACTC
Found at i:22927 original size:15 final size:15
Alignment explanation
Indices: 22907--22936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22897 GATTAGTATC
22907 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
22922 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
22937 ATATAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:27985 original size:2 final size:2
Alignment explanation
Indices: 27980--28027 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
27970 AAAAATGCTA
27980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28022 AT AT AT
1 AT AT AT
28028 TTTTTATAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29571 original size:22 final size:22
Alignment explanation
Indices: 29543--29591 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
29533 AACGGGGAGG
29543 CGACTGCCTCTTCCATCGAAGA
1 CGACTGCCTCTTCCATCGAAGA
29565 CGACTGCCTCTTCCATCGAAGA
1 CGACTGCCTCTTCCATCGAAGA
29587 CGACT
1 CGACT
29592 CAATCCAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (22 bp):
CGACTGCCTCTTCCATCGAAGA
Found at i:37639 original size:10 final size:10
Alignment explanation
Indices: 37622--37748 Score: 85
Period size: 10 Copynumber: 12.2 Consensus size: 10
37612 AACACAAATG
37622 AACGAACATA
1 AACGAACATA
*
37632 AACAAACACAATA
1 AAC-GA-AC-ATA
*
37645 AACGAACGTA
1 AACGAACATA
* *
37655 AACAAACGTA
1 AACGAACATA
*
37665 AACGAACACA
1 AACGAACATA
*
37675 AATGAACATA
1 AACGAACATA
37685 AACGAGCACAATA
1 AACGA--AC-ATA
*
37698 AATGAACATA
1 AACGAACATA
* *
37708 AATGAACGTA
1 AACGAACATA
37718 AACG-ACATA
1 AACGAACATA
* *
37727 AATGAACGTA
1 AACGAACATA
*
37737 AACGAAAATA
1 AACGAACATA
37747 AA
1 AA
37749 TGAAAATAAT
Statistics
Matches: 91, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
9 7 0.08
10 61 0.67
11 5 0.05
12 5 0.05
13 13 0.14
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (10 bp):
AACGAACATA
Found at i:37656 original size:23 final size:24
Alignment explanation
Indices: 37605--37661 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
37595 CATTTAAATG
* *
37605 ATAAACGAACACAAATGAACGAAC
1 ATAAACAAACACAAATAAACGAAC
37629 ATAAACAAACAC-AATAAACGAAC
1 ATAAACAAACACAAATAAACGAAC
*
37652 GTAAACAAAC
1 ATAAACAAAC
37662 GTAAACGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.61, C:0.21, G:0.09, T:0.09
Consensus pattern (24 bp):
ATAAACAAACACAAATAAACGAAC
Found at i:37699 original size:53 final size:53
Alignment explanation
Indices: 37606--37742 Score: 159
Period size: 53 Copynumber: 2.5 Consensus size: 53
37596 ATTTAAATGA
* *
37606 TAAACGAACACAAATGAACGAACATAAACAAACACAATAAACGAACGTAAACAAACG
1 TAAACGAACACAAAT----GAACATAAACGAACACAATAAACGAACATAAACAAACG
* * **
37663 TAAACGAACACAAATGAACATAAACGAGCACAATAAATGAACATAAATGAACG
1 TAAACGAACACAAATGAACATAAACGAACACAATAAACGAACATAAACAAACG
* *
37716 TAAACG-ACATAAATGAACGTAAACGAA
1 TAAACGAACACAAATGAACATAAACGAA
37743 AATAAATGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
52 18 0.25
53 38 0.54
57 15 0.21
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (53 bp):
TAAACGAACACAAATGAACATAAACGAACACAATAAACGAACATAAACAAACG
Found at i:37727 original size:19 final size:20
Alignment explanation
Indices: 37696--37752 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
37686 ACGAGCACAA
*
37696 TAAATGAACATAAATGAACG
1 TAAACGAACATAAATGAACG
37716 TAAACG-ACATAAATGAACG
1 TAAACGAACATAAATGAACG
*
37735 TAAACGAAAATAAATGAA
1 TAAACGAACATAAATGAA
37753 AATAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.18
Consensus pattern (20 bp):
TAAACGAACATAAATGAACG
Found at i:42670 original size:20 final size:21
Alignment explanation
Indices: 42645--42696 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
42635 TTTTCCCAAT
*
42645 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
42665 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
42686 TCGCAATGCGA
1 TCGCAATGCGA
42697 TAATGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:43356 original size:19 final size:19
Alignment explanation
Indices: 43334--43479 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
43324 GAAACCAAAA
*
43334 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43353 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43372 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
43386 TCTCTTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
43405 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
43419 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
43438 TCCGTGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
43458 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
43478 TC
1 TC
43480 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.19
16 4 0.04
17 5 0.05
19 41 0.41
20 29 0.29
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:43404 original size:33 final size:33
Alignment explanation
Indices: 43356--43454 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
43346 TTTCATTTCG
**
43356 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
43389 CTTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
43422 CGTTGCGATAGTCATTTCCGTGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
43455 ATTATCTCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:43456 original size:20 final size:20
Alignment explanation
Indices: 43420--43479 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
43410 TTGCGATTCT
**
43420 CTCGTTGCGATAGTCATTTC
1 CTCGTTGCGATTCTCATTTC
43440 CGT-GTTGCGATTCTCATTAT-
1 C-TCGTTGCGATTCTCATT-TC
*
43460 CTCGTTGCGATTTTCATTTC
1 CTCGTTGCGATTCTCATTTC
43480 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (20 bp):
CTCGTTGCGATTCTCATTTC
Found at i:45648 original size:21 final size:21
Alignment explanation
Indices: 45624--45690 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
45614 TCATTCCTCG
45624 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
45645 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
45666 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
45687 AGAG
1 AGAG
45691 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:45648 original size:42 final size:42
Alignment explanation
Indices: 45572--45690 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
45562 GACTCGCCTG
* * * * * * *
45572 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
45614 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
45656 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
45691 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:47064 original size:14 final size:14
Alignment explanation
Indices: 47045--47080 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
47035 ATTGTTTAAT
47045 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
47059 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
47073 TGATTTGT
1 TGATTTGT
47081 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:47248 original size:19 final size:19
Alignment explanation
Indices: 47187--47239 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
47177 AAAAAGTACT
*
47187 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47206 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAA
47225 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
47240 TAAATTCGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:47290 original size:33 final size:32
Alignment explanation
Indices: 47248--47374 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
47238 ATTAAATTCG
*
47248 CGTTGCGATTTTCATTTTGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
47281 CGTTGCGATTTTCATTTCGCATTGTGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
47314 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
47347 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
47375 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:47337 original size:66 final size:66
Alignment explanation
Indices: 47241--47370 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
47231 ACGCGAAATT
*
47241 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
47306 G
66 G
*
47307 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
47371 CGATAGTAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
G
Found at i:47338 original size:19 final size:19
Alignment explanation
Indices: 47244--47374 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
47234 CGAAATTAAA
*
47244 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
47263 TTTGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
47279 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
47296 TTCGCATTGTGA-----AA
1 TTCGCATTGCGATTTTCAT
*
47310 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
47329 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
47345 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
47362 TTCGCATTGCGAT
1 TTCGCATTGCGAT
47375 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 23 0.28
16 12 0.15
17 13 0.16
19 34 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:49408 original size:20 final size:21
Alignment explanation
Indices: 49383--49434 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
49373 TTTTCCTAAT
*
49383 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
49403 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
49424 TCGCAATGCGA
1 TCGCAATGCGA
49435 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:49508 original size:20 final size:20
Alignment explanation
Indices: 49461--49510 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
49451 GAGATAATAC
49461 AAAATCGCAACGAGATTATG
1 AAAATCGCAACGAGATTATG
*** *
49481 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTATG
49501 AAAATCGCAA
1 AAAATCGCAA
49511 TCATCTTCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTATG
Found at i:49799 original size:20 final size:20
Alignment explanation
Indices: 49724--49791 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
49714 CAACGGGGAA
49724 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
49744 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
49764 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
49784 ATCGCAAC
1 ATCGCAAC
49792 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:49803 original size:34 final size:34
Alignment explanation
Indices: 49708--49811 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
49698 ATTCACTTGA
** *
49708 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
49742 CTATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
49782 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
49812 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 25 0.42
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 29 0.49
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:49842 original size:14 final size:14
Alignment explanation
Indices: 49823--49876 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
49813 GAAAATCGCA
49823 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
49837 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
49854 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
49870 TTGCGAT
1 TTGCGAT
49877 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:49842 original size:33 final size:33
Alignment explanation
Indices: 49805--49875 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
49795 AAAATCGCAA
49805 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
49838 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
49871 TGCGA
1 TGCGA
49876 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:51490 original size:21 final size:20
Alignment explanation
Indices: 51466--51525 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
51456 AACGGTGGGG
51466 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
51487 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
51508 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
51526 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:51954 original size:19 final size:18
Alignment explanation
Indices: 51890--52022 Score: 84
Period size: 20 Copynumber: 7.5 Consensus size: 18
51880 ACGAAACTTA
*
51890 AAATCGCAACGCGAAAATG
1 AAATCGCAATGCG-AAATG
* *
51909 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAATGC-GAAAT-G
**
51930 CTATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
51948 CAAATCGCAAT--GACA--
1 -AAATCGCAATGCGAAATG
51963 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
* *
51981 AAAATTGCAAT--GACA--
1 -AAATCGCAATGCGAAATG
51996 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
52014 AAATCGCAA
1 AAATCGCAA
52023 CGACAAAATC
Statistics
Matches: 90, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
14 19 0.21
16 6 0.07
17 6 0.07
18 10 0.11
19 23 0.26
20 24 0.27
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:51968 original size:14 final size:14
Alignment explanation
Indices: 51949--52036 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
51939 TGCGAAATGC
51949 AAATCGCAATGACA
1 AAATCGCAATGACA
*
51963 AAATCGCAATGCGAAATGA
1 AAATCGCAAT--G--A-CA
*
51982 AAATTGCAATGACA
1 AAATCGCAATGACA
*
51996 AAATCGCAATGCGAAA
1 AAATCGCAAT--GACA
*
52012 TGAAATCGCAACGACA
1 --AAATCGCAATGACA
52028 AAATCGCAA
1 AAATCGCAA
52037 CGCGAAACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 29 0.50
15 1 0.02
16 7 0.12
17 1 0.02
18 10 0.17
19 10 0.17
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (14 bp):
AAATCGCAATGACA
Found at i:51974 original size:33 final size:33
Alignment explanation
Indices: 51932--52054 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
51922 GGAAATGGCT
51932 ATCGCAATGCGAAATGCAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAATGACAAA
* *
51965 ATCGCAATGCGAAATGAAAATTGCAATGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAATGACAAA
*
51998 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAATGACAAA
* **
52030 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
52055 TTGCGACTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 27 0.33
33 55 0.67
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAATGACAAA
Found at i:52072 original size:19 final size:18
Alignment explanation
Indices: 52050--52113 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
52040 GAAACACAAA
52050 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
52069 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
52085 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
52102 TCGCATTGCGAT
1 TCGCATTGCGAT
52114 AGCCTTTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 4 0.11
19 17 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:52660 original size:18 final size:18
Alignment explanation
Indices: 52634--52678 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
52624 GTCGATCAGT
*
52634 TGATGGCTCTGGGTAAGG
1 TGATGGCTCTGGGCAAGG
*
52652 TGATAGCTCTGGGCAAGG
1 TGATGGCTCTGGGCAAGG
52670 TGATGGCTC
1 TGATGGCTC
52679 CCGAAGTGGA
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:0.18, C:0.16, G:0.40, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCAAGG
Found at i:54038 original size:20 final size:20
Alignment explanation
Indices: 53990--54046 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
53980 AATAGTTTCT
**
53990 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
54010 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
54030 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
54047 TGAGAGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:54339 original size:22 final size:22
Alignment explanation
Indices: 54312--54355 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54302 GATGGAGATA
54312 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
54334 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
54356 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:54553 original size:21 final size:21
Alignment explanation
Indices: 54523--54638 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 21
54513 CGCTTTGAAA
54523 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* * *
54544 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCATTGCGATTATGT-ATT
* * *
54564 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTATT
*
54585 ATCGCATTGCGA-TA-GTAAGT
1 ATCGCATTGCGATTATGT-ATT
* *
54605 ATCTCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGT-ATT
54625 ATCGCATTGCGATT
1 ATCGCATTGCGATT
54639 TTCCCAATTC
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.07
20 45 0.59
21 24 0.32
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:54586 original size:41 final size:41
Alignment explanation
Indices: 54527--54636 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
54517 TTGAAAATCG
* *
54527 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCT
1 CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
* * *
54568 CGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCT
1 CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
*
54609 CATTGCGA-TA-GTCAGTATCGCATTGCGA
1 CATTGCGATTATGT-ATTATCGCATTGCGA
54637 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.03
40 15 0.25
41 43 0.72
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
Found at i:54612 original size:20 final size:20
Alignment explanation
Indices: 54584--54637 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
54574 GATTTTGTAT
54584 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
54604 TATCTCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
54624 TATCGCATTGCGAT
1 TATCGCATTGCGAT
54638 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:54624 original size:61 final size:62
Alignment explanation
Indices: 54523--54640 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
54513 CGCTTTGAAA
* * * *
54523 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* *
54585 ATCGCATTGCGA-TA-GTAAGTATCTCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
54641 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 2 0.04
61 35 0.71
62 12 0.24
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:54748 original size:21 final size:21
Alignment explanation
Indices: 54708--54748 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54698 ACTGTAGACC
** *
54708 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
54729 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
54749 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:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:59699 original size:18 final size:18
Alignment explanation
Indices: 59662--59701 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
59652 GTCAAGTTAA
*
59662 GATGATGACGACGATAAT
1 GATGATGACGACGACAAT
* *
59680 GATGATGATGACGACGAT
1 GATGATGACGACGACAAT
59698 GATG
1 GATG
59702 GTGGTTGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.33, T:0.23
Consensus pattern (18 bp):
GATGATGACGACGACAAT
Found at i:60538 original size:2 final size:2
Alignment explanation
Indices: 60526--60590 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
60516 GTCCTCTTTT
*
60526 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60568 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
60591 TGTATAGTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:60634 original size:37 final size:36
Alignment explanation
Indices: 60581--60877 Score: 263
Period size: 37 Copynumber: 8.2 Consensus size: 36
60571 ATATATATAT
* * *
60581 ATATATATATTGTATAG-TTTGAAAACATTTTTTAAA
1 ATATATATAATATATAGTTTTGAAAACA-TTTTGAAA
60617 AGTATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 A-TATATATAATATATAGTTTTGAAAACAT-TTTGAAA
* *
60655 ATATTTATATATAATATAGTTTTTAAAACATTTTGAAA
1 ATATATATA-AT-ATATAGTTTTGAAAACATTTTGAAA
* * * * *
60693 ATAAATATAATATATAATTTTTAAAATATTTTTAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTGAAA
*
60729 A-ATATATATATCATATAGTTTTTAAAACATTTTG-AA
1 ATATATATA-AT-ATATAGTTTTGAAAACATTTTGAAA
*
60765 A-ATATAT-ATA-AT--TTTT-AAAACATTTTTAAAA
1 ATATATATAATATATAGTTTTGAAAACA-TTTTGAAA
* * *
60796 CACATATATATTATATAGTTTTGAAATCATTTTGAAA
1 -ATATATATAATATATAGTTTTGAAAACATTTTGAAA
* *
60833 ACT-TATGTAATATATAGTTTTAAAAACATTTTTGAAA
1 A-TATATATAATATATAGTTTTGAAAACA-TTTTGAAA
60870 ACTATATA
1 A-TATATA
60878 ATTTTGAAAA
Statistics
Matches: 218, Mismatches: 24, Indels: 36
0.78 0.09 0.13
Matches are distributed among these distances:
29 6 0.03
30 8 0.04
31 2 0.01
32 3 0.01
33 7 0.03
34 4 0.02
35 8 0.04
36 57 0.26
37 65 0.30
38 41 0.19
39 17 0.08
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:60779 original size:29 final size:30
Alignment explanation
Indices: 60736--60803 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
60726 AAAAATATAT
*
60736 ATATCATATAGTTTTTAAAACATTTTGAAA
1 ATATCATATAATTTTTAAAACATTTTGAAA
*
60766 ATAT-ATATAATTTTTAAAACATTTTTAAA
1 ATATCATATAATTTTTAAAACATTTTGAAA
*
60795 ACA-CATATA
1 ATATCATATA
60804 TATTATATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
ATATCATATAATTTTTAAAACATTTTGAAA
Found at i:60811 original size:38 final size:38
Alignment explanation
Indices: 60768--60879 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 38
60758 TTTTGAAAAT
* *
60768 ATATATAATTTTTAAAACATTTTTAAAACACATATATA
1 ATATATAGTTTTAAAAACATTTTTAAAACACATATATA
* * * * * *
60806 TTATATAGTTTTGAAATCA-TTTTGAAA-ACTTATGTA
1 ATATATAGTTTTAAAAACATTTTTAAAACACATATATA
*
60842 ATATATAGTTTTAAAAACATTTTTGAAA-AC-TATATA
1 ATATATAGTTTTAAAAACATTTTTAAAACACATATATA
60878 AT
1 AT
60880 TTTGAAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 30 0.48
37 17 0.27
38 15 0.24
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (38 bp):
ATATATAGTTTTAAAAACATTTTTAAAACACATATATA
Found at i:60831 original size:67 final size:66
Alignment explanation
Indices: 60702--60877 Score: 210
Period size: 67 Copynumber: 2.6 Consensus size: 66
60692 AATAAATATA
* * *
60702 ATATATAATTTTTAAAATATTTTTAAAAATATATATATCATATAGTTTTTAAAACATTTTGAAAA
1 ATATATAATTTTTAAAACATTTTTAAAAACATATATATCATATAGTTTTGAAAACATTTTGAAAA
60767 T
66 T
* *
60768 ATATATAATTTTTAAAACATTTTTAAAACACATATATATTATATAGTTTTGAAATCATTTTGAAA
1 ATATATAATTTTTAAAACATTTTTAAAA-ACATATATATCATATAGTTTTGAAAACATTTTGAAA
60833 ACTT
65 A--T
* *
60837 ATGTAATATATAGTTTTAAAAACATTTTTGAAAAC-TATATA
1 A--T-ATATA-A-TTTTTAAAACATTTTTAAAAACATATATA
60878 ATTTTGAAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
66 27 0.28
67 33 0.35
69 2 0.02
71 1 0.01
72 11 0.12
73 3 0.03
74 18 0.19
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (66 bp):
ATATATAATTTTTAAAACATTTTTAAAAACATATATATCATATAGTTTTGAAAACATTTTGAAAA
T
Found at i:60879 original size:103 final size:102
Alignment explanation
Indices: 60663--60937 Score: 298
Period size: 103 Copynumber: 2.7 Consensus size: 102
60653 AAATATTTAT
* * * * *
60663 ATATAATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAATATTTTTAA
1 ATAT-ATATAATTTTTAAAACATTTTTAAAACAAATATAATATATAAGTTTTAAAATATTTTGAA
*
60728 AAATATATATATCATATAGTTTTTAAAACATTTTGAAA
65 AAATATATATATCATATAGTTTTAAAAACATTTTGAAA
* *
60766 ATATATATAATTTTTAAAACATTTTTAAAACACATAT-ATATTATATAGTTTTGAAATCATTTTG
1 ATATATATAATTTTTAAAACATTTTTAAAACAAATATAATA-TATA-AGTTTTAAAAT-ATTTTG
* *
60830 AAAACT-TATGTAAT-ATATAGTTTTAAAAACATTTTTGAAA
63 AAAAATATATAT-ATCATATAGTTTTAAAAACA-TTTTGAAA
* * * * *
60870 A-CTATATAATTTTGAAAATATTTTTTAAAC---TATAATATATAA-TTTTAAAATATTTT-TAA
1 ATATATATAATTTTTAAAACATTTTTAAAACAAATATAATATATAAGTTTTAAAATATTTTGAAA
60929 AATATATAT
66 AATATATAT
60938 TATATGTGTT
Statistics
Matches: 147, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
96 4 0.03
97 9 0.06
98 8 0.05
99 1 0.01
100 7 0.05
101 6 0.04
102 33 0.22
103 58 0.39
104 21 0.14
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (102 bp):
ATATATATAATTTTTAAAACATTTTTAAAACAAATATAATATATAAGTTTTAAAATATTTTGAAA
AATATATATATCATATAGTTTTAAAAACATTTTGAAA
Found at i:60887 original size:29 final size:28
Alignment explanation
Indices: 60843--60936 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
60833 ACTTATGTAA
*
60843 TATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAATTTTAAAAACATTTTT-AAAAC
* * *
60872 TATATAATTTTGAAAATATTTTTTAAAC
1 TATATAATTTTAAAAACATTTTTAAAAC
* *
60900 TATAATATATAATTTTAAAATATTTTTAAAA-
1 TAT-ATA-AT--TTTAAAAACATTTTTAAAAC
60931 TATATA
1 TATATA
60937 TTATATGTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 7 0.13
29 23 0.42
30 5 0.09
31 3 0.05
32 17 0.31
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (28 bp):
TATATAATTTTAAAAACATTTTTAAAAC
Found at i:60966 original size:2 final size:2
Alignment explanation
Indices: 60955--60985 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
60945 GTTTTGGAAA
60955 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60986 TATTATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:61230 original size:16 final size:15
Alignment explanation
Indices: 61209--61238 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
61199 TCGGCCGAAG
61209 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
61225 ATCCCGGGATGACC
1 ATCCCGGGATGACC
61239 GGCCACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:62182 original size:14 final size:13
Alignment explanation
Indices: 62137--62185 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
62127 TCAACTAACC
62137 TTTTA-TTATTAT
1 TTTTATTTATTAT
*
62149 TTTTATCTTAGTAT
1 TTTTAT-TTATTAT
62163 TATTTATTTATTCAT
1 T-TTTATTTATT-AT
62178 TTTTATTT
1 TTTTATTT
62186 CGTTTTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 5 0.16
14 18 0.58
15 8 0.26
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:69058 original size:14 final size:16
Alignment explanation
Indices: 69034--69071 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
69024 TAACCATGAT
*
69034 AACTAAGAAAA-AAAC
1 AACTAAAAAAATAAAC
69049 -ACTAAAAAAATAAAC
1 AACTAAAAAAATAAAC
69064 AACTAAAA
1 AACTAAAA
69072 CGGAGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.74, C:0.13, G:0.03, T:0.11
Consensus pattern (16 bp):
AACTAAAAAAATAAAC
Found at i:69981 original size:10 final size:10
Alignment explanation
Indices: 69966--70001 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
69956 TGATGATAAT
69966 ATATTATTAA
1 ATATTATTAA
* *
69976 ATATTAATAT
1 ATATTATTAA
69986 ATATTATTAA
1 ATATTATTAA
69996 ATATTA
1 ATATTA
70002 ATATATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATTATTAA
Found at i:69989 original size:20 final size:20
Alignment explanation
Indices: 69964--70012 Score: 89
Period size: 20 Copynumber: 2.4 Consensus size: 20
69954 AATGATGATA
69964 ATATATTATTAAATATTAAT
1 ATATATTATTAAATATTAAT
69984 ATATATTATTAAATATTAAT
1 ATATATTATTAAATATTAAT
70004 ATATTATTA
1 ATA-TATTA
70013 GTAAGTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTATTAAATATTAAT
Found at i:73661 original size:2 final size:2
Alignment explanation
Indices: 73654--73685 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
73644 AAGGATATGA
73654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73686 AAAATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80756 original size:33 final size:35
Alignment explanation
Indices: 80705--80775 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 35
80695 ATTTTATATG
80705 ATATATGTATATCATGTATA-AAAAATATAAAAAAT
1 ATATATGTATAT-ATGTATATAAAAATATAAAAAAT
* ** *
80740 ATATATTTATAT-TGTATATATGATTATAAAAAAT
1 ATATATGTATATATGTATATAAAAATATAAAAAAT
80774 AT
1 AT
80776 TTAAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 6 0.19
34 14 0.45
35 11 0.35
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (35 bp):
ATATATGTATATATGTATATAAAAATATAAAAAAT
Found at i:85031 original size:16 final size:17
Alignment explanation
Indices: 85000--85032 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
84990 TCCGTATCCG
85000 ATCCGCAAAATTCGGAT
1 ATCCGCAAAATTCGGAT
*
85017 ATCCG-AAATTTCGGAT
1 ATCCGCAAAATTCGGAT
85033 CGGATATCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (17 bp):
ATCCGCAAAATTCGGAT
Found at i:85052 original size:21 final size:21
Alignment explanation
Indices: 85011--85054 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
85001 TCCGCAAAAT
*
85011 TCGGATATCCGAAATTTCGGA
1 TCGGATATCCGAAATTCCGGA
85032 TCGGATATCCG-AATATCCGGA
1 TCGGATATCCGAAAT-TCCGGA
85053 TC
1 TC
85055 CGAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TCGGATATCCGAAATTCCGGA
Found at i:92449 original size:182 final size:180
Alignment explanation
Indices: 92154--92814 Score: 941
Period size: 182 Copynumber: 3.6 Consensus size: 180
92144 GATACAAATG
* * * *
92154 AAAAATGTATCGCTCCATAGA-AATATTATAGGTAAAAATATGACAAAACCGGTCTCGAAATGAC
1 AAAAATGTATCGATCCATA-ACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
* *
92218 AAAACCGGTAAAACGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
65 AAAACTGGTAAAA-ACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* *
92283 TCT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTATCGATACTTTA
129 T-TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
* *
92335 TGAAAATGTATCGATCCATAACAATATAACAGCTAAAAATATGACAAAACCGGTCTCAAAATGAC
1 -AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
* *
92400 AAAACTGGTAAAGAACTACCGTATATGTTGAAAGTTTCGATACTTTAATATAAGTATCGACACTT
65 AAAACTGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
*
92465 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTCAAA
129 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTT--TA
** * * **
92519 AAAAAAATATCGATTCATAACAATATAACAAGTAAAAATATGACAAAACATGTCTCAAAAATGA-
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTC-AAAATGAC
* * * * *
92583 AAAAATCGGTAAAAAGATATCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACT
65 AAAACT-GGTAAAAA-CTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
92648 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
128 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
* * *
92701 AAAAATGTATCGATCCATAACAATATAGCAGGTAAAAATATGACAAAACCGGTCCCAAAATGATA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
**
92766 AAACTGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
66 AAACTGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATACTTTAATA
92815 AGTACGCATA
Statistics
Matches: 425, Mismatches: 44, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
181 46 0.11
182 215 0.51
183 56 0.13
184 108 0.25
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (180 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
AAACTGGTAAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTT
GGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
Found at i:93259 original size:19 final size:19
Alignment explanation
Indices: 93237--93343 Score: 74
Period size: 19 Copynumber: 5.6 Consensus size: 19
93227 CTTTTATTTA
*
93237 ATATTATAGGTAAAAAATG
1 ATATTATAGGTAGAAAATG
* * *
93256 ATATTACATGTAGAAAGTG
1 ATATTATAGGTAGAAAATG
*
93275 ATATTCTAGGTAGAAAAT-
1 ATATTATAGGTAGAAAATG
* * * * *
93293 A-AATATAGATACATGTATATA
1 ATATTATAGGT--A-GAAAATG
93314 ATATTATAGGTAGAAAATG
1 ATATTATAGGTAGAAAATG
*
93333 ATATTTTAGGT
1 ATATTATAGGT
93344 TGTATAAATG
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
17 6 0.09
18 1 0.02
19 44 0.69
20 5 0.08
21 1 0.02
22 7 0.11
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.35
Consensus pattern (19 bp):
ATATTATAGGTAGAAAATG
Found at i:93316 original size:77 final size:77
Alignment explanation
Indices: 93181--93337 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 77
93171 TTTGGGACCG
* *** * * * *
93181 ATTATATGTAGAAAGTGATATTCTAGGTAGATGCTAAATATCGATACTTTTATTTAATATTATAG
1 ATTACATGTAGAAAGTGATATTCTAGGTAGAAAATAAATATAGATACATGTATATAATATTATAG
93246 GTAAAAAATGAT
66 GTAAAAAATGAT
93258 ATTACATGTAGAAAGTGATATTCTAGGTAGAAAATAAATATAGATACATGTATATAATATTATAG
1 ATTACATGTAGAAAGTGATATTCTAGGTAGAAAATAAATATAGATACATGTATATAATATTATAG
*
93323 GTAGAAAATGAT
66 GTAAAAAATGAT
93335 ATT
1 ATT
93338 TTAGGTTGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.36
Consensus pattern (77 bp):
ATTACATGTAGAAAGTGATATTCTAGGTAGAAAATAAATATAGATACATGTATATAATATTATAG
GTAAAAAATGAT
Found at i:95339 original size:18 final size:18
Alignment explanation
Indices: 95316--95354 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
95306 GAAAAAATTT
*
95316 GAAGAAGATAAGATGGAG
1 GAAGAAGAAAAGATGGAG
95334 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
95352 GAA
1 GAA
95355 ATGGGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:96844 original size:19 final size:19
Alignment explanation
Indices: 96820--96865 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
96810 AAATGTAGGG
96820 TTAATTTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
96839 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
96858 ATAATTTT
1 TTAATTTT
96866 TTATGTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:97582 original size:199 final size:199
Alignment explanation
Indices: 97242--98334 Score: 1765
Period size: 199 Copynumber: 5.5 Consensus size: 199
97232 TTAGGAGTCA
* *
97242 ATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAAAATGTAATAGGTAAA
1 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
* *
97307 TTAACAATGTAACCAGTCTAAATATACC-GTTTTTTGAGAAAACATGTGTACAAAAAGTATCGAC
66 TTAACAATGTAACCGGTCTAAATATACCGGTTTTTT-AGAAAACAGGTGTACAAAAAGTATCGAC
*
97371 ACAAATAAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAG
130 ACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAG
97436 TGTCG
195 TGTCG
* *
97441 ATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATATGTAAA
1 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
*
97506 TTAACAATGTAACCGGTCTAAATATACTGGTTTTTTAGAAAACAGGTGTACAAAAAGTATCGACA
66 TTAACAATGTAACCGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTACAAAAAGTATCGACA
*
97571 CAAATAAAACAAGTGTCGATACTTTTAGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAGT
131 CAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAGT
97636 GTCG
196 GTCG
* *
97640 ATACATTTATAACAAGTATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATAGGTAAA
1 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
* * *
97705 TTAACAATGTAACTGGTCTAAATATACCGGTTTTTTAGAAAACATGTGTACAAAAAGTATCAACA
66 TTAACAATGTAACCGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTACAAAAAGTATCGACA
* *
97770 AAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAGAAGT
131 CAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAGT
97835 GTCG
196 GTCG
97839 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
1 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
* * * *
97904 TTAACAATGTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAAGTGTACAAAAAGTATCAACA
66 TTAACAATGTAACCGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTACAAAAAGTATCGACA
* * *
97969 CAAATAAAATAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAATT
131 CAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAGT
98034 GTCG
196 GTCG
* *
98038 ATACATTTATAATAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAA
1 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
* ** *
98103 TTAACAATATAACCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAGTATCGACA
66 TTAACAATGTAACCGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTACAAAAAGTATCGACA
* * * * *
98168 CAAATAAAGCAAGTGTCGATACTTTTGGTTCATAATGTATTTCCAAACCAAGTGCAGGAAAAAGT
131 CAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAGT
98233 GTCG
196 GTCG
* * * * * * * *
98237 ATACATTTATAACAAGTATTGGTCCTAATAACATCGAAACCCATAATTTTAATGTAATAGGTCAT
1 ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
* * *
98302 TTTACAATGTAATCGGTATAAATATACCGGTTT
66 TTAACAATGTAACCGGTCTAAATATACCGGTTT
98335 AATTTGAAAA
Statistics
Matches: 835, Mismatches: 58, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
199 828 0.99
200 7 0.01
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (199 bp):
ATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAA
TTAACAATGTAACCGGTCTAAATATACCGGTTTTTTAGAAAACAGGTGTACAAAAAGTATCGACA
CAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAAAAAGT
GTCG
Found at i:98702 original size:15 final size:15
Alignment explanation
Indices: 98682--98739 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
98672 TTTCTCAAAG
*
98682 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAA
*
98697 CTCTTCCCAACCCAA
1 CTCTTCTCAACCCAA
*
98712 CTCTTCTTAACCACAA
1 CTCTTCTCAACC-CAA
98728 TCTCCTTCTCAA
1 -CT-CTTCTCAA
98740 ACAATCGCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 23 0.66
16 3 0.09
17 2 0.06
18 7 0.20
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (15 bp):
CTCTTCTCAACCCAA
Found at i:99915 original size:6 final size:6
Alignment explanation
Indices: 99878--99911 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
99868 CAAGCGGTCA
* *
99878 ATGAAG ATGACG ATGAAG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
99912 TGATTCAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:101292 original size:24 final size:24
Alignment explanation
Indices: 101265--101311 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
101255 TTTCATTTAT
101265 AATTAGAGTTTGAATTTAAATTTC
1 AATTAGAGTTTGAATTTAAATTTC
* * *
101289 AATTTGAGTTTGAGTTTGAATTT
1 AATTAGAGTTTGAATTTAAATTT
101312 AAATGTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (24 bp):
AATTAGAGTTTGAATTTAAATTTC
Found at i:101929 original size:198 final size:200
Alignment explanation
Indices: 101561--102503 Score: 1291
Period size: 198 Copynumber: 4.8 Consensus size: 200
101551 TATCGGTTTT
* *
101561 TGAGAAAAACAGGT-TACATAAAGTATCAACACAAATTC-ACAAGTGTCGATACTTTTTGTCCAG
1 TGAG-AAAACATGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCAG
101624 AATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACA-TT-TAACAAGTGTCGATACTAA
65 AATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACTAA
* * *
101687 AAACATAGAAACACA-AAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACAC
130 AAACATCGAAACACATAA-TTATAATGTAATAAGTAAAATAACAATGTAACCGGCCTAAATACAC
*
101751 CAATTTC
194 CAATTTA
* *
101758 TGAGAAAACATGTATACATAAAATATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCATA
1 TGAGAAAACATGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCAGA
* * *
101823 ATGTATTTTCCAAACAAAATGCACGACAAAGTGTTGATACATTTATAACAAGTGTCGATACTAAA
66 ATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACTAAA
* * * * *
101888 ATCATC-AAACACATAATTATAA-GTAATAAGTAAATTAACAATATAACCGGTCTAAATATACCA
131 AACATCGAAACACATAATTATAATGTAATAAGTAAAATAACAATGTAACCGGCCTAAATACACCA
* *
101951 GTTTT
196 ATTTA
* * *
101956 TGAGAAAACAAGTATACATAAAGTATCGACACAAATTCAACAAGTATCGATACTTTTTGTCAAGA
1 TGAGAAAACATGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCAGA
102021 ATGTA--TTCCAAACCAAGTGCACGACAAAGTGTCGATACA-TT-TAACAAGTGTCGATACTAAA
66 ATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACTAAA
* * *
102082 AACATCAAAACACA-AAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACACC
131 AACATCGAAACACATAA-TTATAATGTAATAAGTAAAATAACAATGTAACCGGCCTAAATACACC
*
102146 AGTTTA
195 AATTTA
*
102152 TGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTTTGTCCAGA
1 TGAGAAAACATGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCAGA
* * * * * **
102217 A-GTATTTTCTAAACCAAGTGCACGAAAAAGTTTCGATACATTTATAACAGGTGTCTAT-CCCAA
66 ATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACTAAA
* * * *
102280 AACATCGAAACACATAATTATAATGCAAT-AG-ATAAATAACAATGTAACCGGTCTACATATACC
131 AACATCGAAACACATAATTATAATGTAATAAGTA-AAATAACAATGTAACCGGCCTAAATACACC
*
102343 GATTTA
195 AATTTA
102349 TGAG-AAACATGTATACATAAAGTATCGACACAAA-TCTAACAAGTGTCGATAC-TTTTGTCCA-
1 TGAGAAAACATGTATACATAAAGTATCGACACAAATTC-AACAAGTGTCGATACTTTTTGTCCAG
* * * * *
102410 AA-ATATATTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAAAAAGTGTCGAT-CCAA
65 AATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACTAA
*
102473 AAACATCGAAACTCATAATTATAATGTAATA
130 AAACATCGAAACACATAATTATAATGTAATA
102504 TGTCACTTTA
Statistics
Matches: 666, Mismatches: 64, Indels: 34
0.87 0.08 0.04
Matches are distributed among these distances:
194 110 0.17
195 27 0.04
196 187 0.28
197 93 0.14
198 195 0.29
199 28 0.04
200 26 0.04
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (200 bp):
TGAGAAAACATGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCAGA
ATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACTAAA
AACATCGAAACACATAATTATAATGTAATAAGTAAAATAACAATGTAACCGGCCTAAATACACCA
ATTTA
Found at i:102085 original size:394 final size:392
Alignment explanation
Indices: 101545--102503 Score: 1404
Period size: 394 Copynumber: 2.4 Consensus size: 392
101535 ACACTTGTTA
* * *
101545 TAAATATATCGGTTTTTGAGAAAAACAGGT-TACATAAAGTATCAACACAAATTC-ACAAGTGTC
1 TAAATATA-CCGTTTTTGAG-AAAACAAGTATACATAAAGTATCGACACAAATTCAACAAGTGTC
*
101608 GATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTAACA
64 GATACTTTTTGTCAAGAATGTA--TTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTAACA
101673 AGTGTCGATACTAAAAACATAGAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACC
127 AGTGTCGATACTAAAAACATAGAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACC
* *
101738 GGCCTAAATACACCAATTTCTGAGAAAACATGTATACATAAAATATCGACACAAATTCAACAAGT
192 GGCCTAAATACACCAATTTATGAGAAAACATGTATACATAAAATATCGACACAAATCCAACAAGT
* *
101803 GTCGATACTTTTTGTCCATAATGTATTTTCCAAACAAAATGCACGACAAAGTGTT-GATACATTT
257 GTCGATACTTTTTGTCCAGAA-GTATTTTCCAAACAAAATGCACGAAAAAGT-TTCGATACATTT
* *
101867 ATAACAAGTGTCGATACTAAAATCATC-AAACACATAATTATAA-GTAATA-AGTAAATTAACAA
320 ATAACAAGTGTCGATACCAAAA-CATCGAAACACATAATTATAATGCAATAGA-TAAA-TAACAA
101929 TATAACCGGTC
382 TATAACCGGTC
*
101940 TAAATATACCAGTTTTTGAGAAAACAAGTATACATAAAGTATCGACACAAATTCAACAAGTATCG
1 TAAATATACC-GTTTTTGAGAAAACAAGTATACATAAAGTATCGACACAAATTCAACAAGTGTCG
102005 ATACTTTTTGTCAAGAATGTATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTAACAAGT
65 ATACTTTTTGTCAAGAATGTATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTAACAAGT
102070 GTCGATACTAAAAACATCA-AAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACCGG
130 GTCGATACTAAAAACAT-AGAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACCGG
* *
102134 CCTAAATACACCAGTTTATGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGT
194 CCTAAATACACCAATTTATGAGAAAACATGTATACATAAAATATCGACACAAATCCAACAAGTGT
* * *
102199 CGATACTTTTTGTCCAGAAGTATTTTCTAAACCAAGTGCACGAAAAAGTTTCGATACATTTATAA
259 CGATACTTTTTGTCCAGAAGTATTTTCCAAACAAAATGCACGAAAAAGTTTCGATACATTTATAA
* * * *
102264 CAGGTGTCTATCCCAAAACATCGAAACACATAATTATAATGCAATAGATAAATAACAATGTAACC
324 CAAGTGTCGATACCAAAACATCGAAACACATAATTATAATGCAATAGATAAATAACAATATAACC
102329 GGTC
389 GGTC
* * *
102333 TACATATACCGATTTATGAG-AAACATGTATACATAAAGTATCGACACAAA-TCTAACAAGTGTC
1 TAAATATACCG-TTTTTGAGAAAACAAGTATACATAAAGTATCGACACAAATTC-AACAAGTGTC
* * *
102396 GATAC-TTTTGTCCAA-AATATATTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAAA
64 GATACTTTTTGT-CAAGAATGTATTCCAAACCAAGTGCACGACAAAGTGTCGATACA-TT-TAAC
* * * *
102459 AAGTGTCGAT-CCAAAAACATCGAAACTCATAA-TTATAATGTAATA
126 AAGTGTCGATACTAAAAACATAGAAACACA-AAGATATAATGTAATA
102504 TGTCACTTTA
Statistics
Matches: 518, Mismatches: 31, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
391 46 0.09
392 82 0.16
393 116 0.22
394 203 0.39
395 42 0.08
396 29 0.06
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (392 bp):
TAAATATACCGTTTTTGAGAAAACAAGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGA
TACTTTTTGTCAAGAATGTATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTAACAAGTG
TCGATACTAAAAACATAGAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCC
TAAATACACCAATTTATGAGAAAACATGTATACATAAAATATCGACACAAATCCAACAAGTGTCG
ATACTTTTTGTCCAGAAGTATTTTCCAAACAAAATGCACGAAAAAGTTTCGATACATTTATAACA
AGTGTCGATACCAAAACATCGAAACACATAATTATAATGCAATAGATAAATAACAATATAACCGG
TC
Found at i:102547 original size:196 final size:196
Alignment explanation
Indices: 101561--102723 Score: 1170
Period size: 198 Copynumber: 5.9 Consensus size: 196
101551 TATCGGTTTT
* * *
101561 TGAGAAAAACAGGT-TACATAAAGTATCAACACAAATTCACAAGTGTCGATACTTTTTGTCCAGA
1 TGAG-AAAACATGTATACATAAAGTATCGACACAAATTAACAAGTGTCGATACTTTTTGTCCAGA
* * *
101625 ATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACA-TT-TAACAAGTGTCGATACTAAA
65 A-ATATATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACCAAA
* * * *
101688 AACATAGAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACACCA
129 AACATCGAAACACAAA-TTATAATGTAATAGGTAAAATAACAATGTAACC-GCTTAAATATA-CA
*
101753 -ATTTC
191 GATTTA
* *
101758 TGAGAAAACATGTATACATAAAATATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCCATA
1 TGAGAAAACATGTATACATAAAGTATCGACACAAATT-AACAAGTGTCGATACTTTTTGTCCAGA
* * * * * *
101823 ATGTATTTTCCAAACAAAATGCACGACAAAGTGTTGATACATTTATAACAAGTGTCGATACTAAA
65 A-ATATATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACCAAA
* * * * *
101888 ATCATC-AAACACATAATTATAA-GTAATAAGTAAATTAACAATATAACCGGTCTAAATATACCA
129 AACATCGAAACACA-AATTATAATGTAATAGGTAAAATAACAATGTAACCGCT-TAAATATA-CA
*
101951 G-TTTT
191 GATTTA
* * *
101956 TGAGAAAACAAGTATACATAAAGTATCGACACAAATTCAACAAGTATCGATACTTTTTGTCAAG-
1 TGAGAAAACATGTATACATAAAGTATCGACACAAATT-AACAAGTGTCGATACTTTTTGTCCAGA
* *
102020 AATGTATTCCAAACCAAGTGCACGACAAAGTGTCGATACA-TT-TAACAAGTGTCGATACTAAAA
65 AATATATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACCAAAA
* * * *
102083 ACATCAAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACACCAG
130 ACATCGAAACACAAA-TTATAATGTAATAGGTAAAATAACAATGTAACC-GCTTAAATATA-CAG
102148 -TTTA
192 ATTTA
*
102152 TGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTTTGTCCAGA
1 TGAGAAAACATGTATACATAAAGTATCGACACAAAT-TAACAAGTGTCGATACTTTTTGTCCAGA
* * * * * * * *
102217 AGTATTTTCTAAACCAAGTGCACGAAAAAGTTTCGATACATTTATAACAGGTGTCTAT-CCCAAA
65 AATATATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACCAAAA
* * * * *
102281 ACATCGAAACACATAATTATAATGCAATAGAT-AAATAACAATGTAACCGGTCTACATATACCGA
130 ACATCGAAACACA-AATTATAATGTAATAGGTAAAATAACAATGTAACCGCT-TAAATATACAGA
102345 TTTA
193 TTTA
102349 TGAG-AAACATGTATACATAAAGTATCGACACAAATCTAACAAGTGTCGATAC-TTTTGTCCA-A
1 TGAGAAAACATGTATACATAAAGTATCGACACAAAT-TAACAAGTGTCGATACTTTTTGTCCAGA
* *
102411 AATATATTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAAAAAGTGTCGAT-CCAAAA
65 AATATATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACCAAAA
* * * ** * * * *
102475 ACATCGAAACTCATAATTATAATGTAATATGTCACTTTACAGTGTAACCGACTTAAATTTACTGG
130 ACATCGAAACACA-AATTATAATGTAATAGGTAAAATAACAATGTAACCG-CTTAAATATAC-AG
*
102540 TTTTA
192 ATTTA
* * * *
102545 TGAGAAAATA-GTTCTACATAATGTATCGACAC---TGTATACATTTGTGTCGATACTTTTTGTC
1 TGAGAAAACATG-TATACATAAAGTATCGACACAAAT-TA-ACA--AGTGTCGATACTTTTTGTC
* * * * * * * * * *
102606 TA-TAATAAATGCCAAACGATGTCCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGA-AC
61 CAGAAATATATTCCAAACCAAGTGCACG-ACAAAGTGTCGATACATTTATAACAAGTGTCGATA-
* * * * *
102669 CCAAATACATCGAGAC-CGGAAATT-TAATGTAATAGGTCAATTTACAATGTAACCG
124 CCAAAAACATCGAAACAC--AAATTATAATGTAATAGGTAAAATAACAATGTAACCG
102724 GTTGAAATTT
Statistics
Matches: 832, Mismatches: 102, Indels: 62
0.84 0.10 0.06
Matches are distributed among these distances:
194 115 0.14
195 46 0.06
196 198 0.24
197 124 0.15
198 216 0.26
199 88 0.11
200 44 0.05
201 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (196 bp):
TGAGAAAACATGTATACATAAAGTATCGACACAAATTAACAAGTGTCGATACTTTTTGTCCAGAA
ATATATTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATACCAAAAA
CATCGAAACACAAATTATAATGTAATAGGTAAAATAACAATGTAACCGCTTAAATATACAGATTT
A
Found at i:102699 original size:199 final size:196
Alignment explanation
Indices: 102195--102763 Score: 482
Period size: 194 Copynumber: 2.9 Consensus size: 196
102185 AATCCAACAA
* ** * * * *
102195 GTGTCGATACTTTTTGTCCAGAAGTATTTTCTAAACCAAGTGCACGAAAAAGTTTCGATACATTT
1 GTGTCGATAC-TTTTGTCCA-AAATAAATGCCAAACCAAGTCCACGAAAAAGTGTCGATACATTT
* * * * * * * * *
102260 ATAACAGGTGTCTATCCC-AAAACATCGAAACACATAATTATAATGCAATAGAT-AAATAACAAT
64 ATAAAAAGTATCGA-CCCAAAAACATCGAAACTCATAATTATAATGTAATAGGTCAATTTACAAT
* * * * * *
102323 GTAACCGGTCT-ACATATACCGAT-TTATGAGAAACAT--GT-ATACATAAAGTATCGACACAAA
128 GTAACCGCT-TGAAATTTACCGGTGTAAT-AGAAA-ATAGGTCA-ACATAATGTATCGACAC---
* *
102383 TCTA-ACA--A
186 TGTATACATTT
* * *
102391 GTGTCGATACTTTTGTCCAAAATATATTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTAT
1 GTGTCGATACTTTTGTCCAAAATAAATGCCAAACCAAGTCCACGAAAAAGTGTCGATACATTTAT
* * * * *
102456 AAAAAGTGTCGATCCAAAAACATCGAAACTCATAATTATAATGTAATATGTCACTTTACAGTGTA
66 AAAAAGTATCGACCCAAAAACATCGAAACTCATAATTATAATGTAATAGGTCAATTTACAATGTA
* * * * *
102521 ACCGACTT-AAATTTACTGGTTTTATGAGAAAATAGTTCTACATAATGTATCGACACTGTATACA
131 ACCG-CTTGAAATTTACCGGTGTAAT-AGAAAATAGGTCAACATAATGTATCGACACTGTATACA
102585 TTT
194 TTT
* * * * *
102588 GTGTCGATACTTTTTGTCTATAATAAATGCCAAACGATGTCCACGCATAAAGTGTCGATACATTT
1 GTGTCGATAC-TTTTGTCCAAAATAAATGCCAAACCAAGTCCACG-AAAAAGTGTCGATACATTT
* *
102653 ATAAAAAGTATCGAACCCAAATACATCGAGAC-CGGA-AATT-TAATGTAATAGGTCAATTTACA
64 ATAAAAAGTATCG-ACCCAAAAACATCGAAACTC--ATAATTATAATGTAATAGGTCAATTTACA
*
102715 ATGTAACCGGTTGAAATTTACCGGTGTAATAGAAAATAGGTCAACATAA
126 ATGTAACCGCTTGAAATTTACCGGTGTAATAGAAAATAGGTCAACATAA
102764 CGTGTCTACA
Statistics
Matches: 310, Mismatches: 47, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
193 2 0.01
194 85 0.27
195 36 0.12
196 21 0.07
197 27 0.09
198 46 0.15
199 73 0.24
200 19 0.06
201 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (196 bp):
GTGTCGATACTTTTGTCCAAAATAAATGCCAAACCAAGTCCACGAAAAAGTGTCGATACATTTAT
AAAAAGTATCGACCCAAAAACATCGAAACTCATAATTATAATGTAATAGGTCAATTTACAATGTA
ACCGCTTGAAATTTACCGGTGTAATAGAAAATAGGTCAACATAATGTATCGACACTGTATACATT
T
Done.