Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003772.1 Hibiscus syriacus cultivar Beakdansim tig00008076_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: 56000
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:568 original size:23 final size:24
Alignment explanation
Indices: 515--569 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
505 TAGAAGTTCG
*
515 ATTGAAGCCTAAAATTTTAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
539 ATTGAAGCCTAAAATTTGAGCT-A
1 ATTGAAGCCTAAAATTTGAGCTCA
562 ATTGAAGC
1 ATTGAAGC
570 GAAAGATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:5329 original size:3 final size:3
Alignment explanation
Indices: 5321--5400 Score: 67
Period size: 3 Copynumber: 26.0 Consensus size: 3
5311 CCGGGTTTTA
*
5321 TAT TAT TAT T-T ATAT TAT TAT AATT TATT TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT
* *
5367 TAT TAT TA- AAA TAT TAT TATT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT
5401 AATGCATCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
2 4 0.06
3 48 0.73
4 14 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5364 original size:34 final size:38
Alignment explanation
Indices: 5321--5400 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 38
5311 CCGGGTTTTA
*
5321 TATTATTATTTA-TATTATTATAAT-TTATT-TAT-TT
1 TATTATTATTTATTATTATTAAAATATTATTATATATT
*
5355 TATTATTA-TTATTATTATTAAAATATTATTATTTATT
1 TATTATTATTTATTATTATTAAAATATTATTATATATT
5392 TATTATTAT
1 TATTATTAT
5401 AATGCATCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
33 3 0.08
34 19 0.49
35 5 0.13
36 2 0.05
37 10 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (38 bp):
TATTATTATTTATTATTATTAAAATATTATTATATATT
Found at i:5897 original size:106 final size:106
Alignment explanation
Indices: 5764--6151 Score: 476
Period size: 106 Copynumber: 3.6 Consensus size: 106
5754 GACGAAGGGG
* *
5764 CTTCCTAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGC
5829 TCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
* * * *
5870 CTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGATAGCATAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGC
* * *
5935 TCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
*** * * * ** *
5976 CTTTTAAATTTTATTTAGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTTGAGACAACAC
1 CTTCCCAA---T-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCAC
* *
6041 AAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGTCAACAAATAA
62 AAGCTCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
* * * *
6086 -TATCCCAGTTTCAGAACCAATTTTAACTTCAC-GACGAAAGATATTAGACTCGAA-ACAGCACA
1 CT-TCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTAGACTC-AAGACAGCACA
6148 AGCT
63 AGCT
6152 TGGATTTCAA
Statistics
Matches: 240, Mismatches: 35, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
105 1 0.00
106 149 0.62
107 2 0.01
109 2 0.01
110 86 0.36
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (106 bp):
CTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGC
TCAACTTCACAACGAAGGGGCGGTTGACTGTCAACAAACAA
Found at i:6502 original size:37 final size:35
Alignment explanation
Indices: 6461--6565 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 35
6451 ACAAGGGGTC
*
6461 GTCTCGCTTGAGACTAATTTACTC-AAAACAAAGTTTT
1 GTCTCCCTTGAGAC-AATTT-CTCTAAAACAAA-TTTT
* * *
6498 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAATTTCTC-TAAAACAAATTTT
* *
6534 GTCTCCCTTGAGACAGTTTCCCTAGAAACAAA
1 GTCTCCCTTGAGACAATTTCTCTA-AAACAAA
6566 ATCTTTGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
35 4 0.07
36 35 0.59
37 20 0.34
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (35 bp):
GTCTCCCTTGAGACAATTTCTCTAAAACAAATTTT
Found at i:6544 original size:36 final size:37
Alignment explanation
Indices: 6486--6565 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 37
6476 AATTTACTCA
* * *
6486 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTAG
6523 AAACAAA-TTTTGTCTCCCTTGAGACAGTTTCCCTAG
1 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTAG
6559 AAACAAA
1 AAACAAA
6566 ATCTTTGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 33 0.82
37 7 0.17
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTAG
Found at i:6645 original size:37 final size:36
Alignment explanation
Indices: 6585--6876 Score: 250
Period size: 37 Copynumber: 8.2 Consensus size: 36
6575 TATGTTTCCC
**
6585 TTGAAAC-AAATTCCGTCTCTCTTGAGACAGTTTCT
1 TTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCT
* *
6620 TTCGAAACTAAGTTTTGTCTCTCTTGAGACAGTTTTCC
1 TT-GAAACTAAATTTTGTCTCTCTTGAGACAG-TTTCT
* *
6658 TTGAAACGAAATTTTATCTCTCTTGAGACAGTTTCT
1 TTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCT
* *
6694 TTTAGAACTAAATTTTGTCTCTCTTGAGACAGTTTCCC
1 TTGA-AACTAAATTTTGTCTCTCTTGAGACAGTTT-CT
* *
6732 TTGAAAC-AAA------ATCT-TTGA-ATATGTTTTCCT
1 TTGAAACTAAATTTTGTCTCTCTTGAGACA-G-TTT-CT
* * *
6762 TT-AAAC-AAATCTCGTCTCTCTTGAGACAATTTCT
1 TTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCT
* *
6796 TTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCT
1 TTGA-AACTAAATTTTGTCTCTCTTGAGACAGTTTCT
* *
6833 CGTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCT
1 -TTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCT
6869 CTTGAAAC
1 -TTGAAAC
6877 ACAAAAAACC
Statistics
Matches: 211, Mismatches: 27, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
28 2 0.01
29 12 0.06
30 10 0.05
34 4 0.02
35 9 0.04
36 55 0.26
37 107 0.51
38 12 0.06
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCT
Found at i:6740 original size:176 final size:174
Alignment explanation
Indices: 6485--6877 Score: 596
Period size: 176 Copynumber: 2.2 Consensus size: 174
6475 TAATTTACTC
6485 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
6550 TTTCCCTAGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAAT-TCCGTCTCTCTTGAGACA
65 TTTCCCTAGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATCT-CGTCTCTCTTGAGACA
* * *
6614 GTTTCTTTCGA-AACTAAGTTTTGTCTCTCTTGAGACAGTTTTC-CTT
129 ATTTCTTT-GAGAACTAAATTTTGTCTCTCTTGAGACA-TTTTCTCGT
* * * *
6660 GAAACGAAATTTTATCTCTCTTGAGACAGTTTCT-TTTAGAACTAAATTTTGTCTCTCTTGAGAC
1 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA-AAC-AAATTTTGTCTCCCTTGAGAC
* * *
6724 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTTAAACAAATCTCGTCTCTCTTGAGAC
63 AGTTTCCCTAGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATCTCGTCTCTCTTGAGAC
*
6789 AATTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGT
128 AATTTCTTTGAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGT
6836 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
6878 CAAAAAACCT
Statistics
Matches: 197, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
174 4 0.02
175 67 0.34
176 125 0.63
177 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (174 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGT
TTCCCTAGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATCTCGTCTCTCTTGAGACAAT
TTCTTTGAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGT
Found at i:7052 original size:84 final size:84
Alignment explanation
Indices: 6911--7098 Score: 259
Period size: 84 Copynumber: 2.2 Consensus size: 84
6901 TCTTGAAACA
*
6911 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAACATAGCTCAAGGCT
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAACATAGCTCAAGGCG
* * *
6976 AGAAGAGTTATTTGCTAAC
66 AGAAGAGCTATCTGCCAAC
** * * *
6995 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCTGAGGCACATCATTTGCAACATAGCTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAACATAGCTCAAGGCG
* *
7060 AGAAGGGCTATCTGCCAAT
66 AGAAGAGCTATCTGCCAAC
*
7079 CAAAGACCTGACGAGTTCGA
1 CAAAGACCT-TCGAGTTCGA
7099 TTTTATTCAG
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
84 82 0.90
85 9 0.10
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAACATAGCTCAAGGCG
AGAAGAGCTATCTGCCAAC
Found at i:7363 original size:19 final size:20
Alignment explanation
Indices: 7328--7369 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
7318 TTACCGGGTT
*
7328 TTATATTTTTATTTTTATTA
1 TTATAATTTTATTTTTATTA
7348 TTATAATTTT-TTTTTATTA
1 TTATAATTTTATTTTTATTA
7367 TTA
1 TTA
7370 ATATATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATAATTTTATTTTTATTA
Found at i:7367 original size:22 final size:21
Alignment explanation
Indices: 7328--7388 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
7318 TTACCGGGTT
7328 TTAT-ATTTTTATTTTTATTA
1 TTATAATTTTTATTTTTATTA
*
7348 TTATAATTTTTTTTTATTATTA
1 TTATAATTTTTATTT-TTATTA
*
7370 ATATATATTTTTCATTTTT
1 TTATA-ATTTTT-ATTTTT
7389 TTTGTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 9 0.26
22 10 0.29
23 8 0.24
24 3 0.09
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTATAATTTTTATTTTTATTA
Found at i:7380 original size:19 final size:19
Alignment explanation
Indices: 7337--7381 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
7327 TTTATATTTT
*
7337 TATTTTTATTATTATAATT
1 TATTTTTATTATTATAATA
*
7356 TTTTTTTATTATTA-ATATA
1 TATTTTTATTATTATA-ATA
7375 TATTTTT
1 TATTTTT
7382 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTATTATTATAATA
Found at i:9381 original size:18 final size:18
Alignment explanation
Indices: 9358--9392 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9348 AGGGATTAAC
*
9358 AGTGGTCTTTCGGGACAT
1 AGTGGTCATTCGGGACAT
9376 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
9393 AATATTCAGT
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:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:13546 original size:13 final size:14
Alignment explanation
Indices: 13512--13546 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
13502 TACTTGCTGG
13512 GGCAAATCTTCAGA
1 GGCAAATCTTCAGA
13526 GTGCAAATCTTCA-A
1 G-GCAAATCTTCAGA
13540 GGCAAAT
1 GGCAAAT
13547 ACTTATAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (14 bp):
GGCAAATCTTCAGA
Found at i:17362 original size:19 final size:20
Alignment explanation
Indices: 17330--17368 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
17320 GTGAGTTTAA
* *
17330 TTTTATTTTGTAAAGAAAAT
1 TTTTATATTGTAAAAAAAAT
17350 TTTTATATT-TAAAAAAAAT
1 TTTTATATTGTAAAAAAAAT
17369 AAAAAAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTATATTGTAAAAAAAAT
Found at i:25322 original size:23 final size:23
Alignment explanation
Indices: 25296--25343 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
25286 ATAAAGTACA
*
25296 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
25319 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
25342 AT
1 AT
25344 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:25746 original size:21 final size:22
Alignment explanation
Indices: 25721--25772 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
25711 ACACTTTACA
*
25721 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
25744 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
25767 ATATAA
1 ATATAA
25773 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:25757 original size:23 final size:23
Alignment explanation
Indices: 25731--25793 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
25721 ATATAACCAC
25731 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
25754 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
25777 TACCTATTACATCATAT
1 TACCTATTACATTATAT
25794 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:26251 original size:39 final size:39
Alignment explanation
Indices: 26197--26322 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
26187 TCAAGTTGTA
26197 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
26236 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
26275 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
26314 GATTTTGAT
1 GATTTTGAT
26323 GAGCATCGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:26603 original size:18 final size:18
Alignment explanation
Indices: 26580--26616 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26570 CGAAATATAT
26580 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
26598 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
26616 A
1 A
26617 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:26893 original size:25 final size:25
Alignment explanation
Indices: 26865--26915 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
26855 TTAATCCAAA
*
26865 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
26890 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
26915 T
1 T
26916 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:27164 original size:21 final size:20
Alignment explanation
Indices: 27138--27177 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27128 TCCACAGTGA
* *
27138 AAAAAGTATGGACACATTTAT
1 AAAAAGGATAGACAC-TTTAT
27159 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
27178 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:27205 original size:21 final size:22
Alignment explanation
Indices: 27180--27231 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
27170 ACACTTTACA
*
27180 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
27203 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
27226 ATATAA
1 ATATAA
27232 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:27216 original size:23 final size:23
Alignment explanation
Indices: 27190--27252 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27180 ATATAACCAC
27190 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
27213 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
27236 TACCTATTACATCATAT
1 TACCTATTACATTATAT
27253 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:27635 original size:21 final size:22
Alignment explanation
Indices: 27610--27661 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
27600 ACACTTTACA
*
27610 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
27633 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
27656 ATATAA
1 ATATAA
27662 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:27646 original size:23 final size:23
Alignment explanation
Indices: 27620--27682 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27610 ATATAACCAC
27620 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
27643 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
27666 TACCTATTACATCATAT
1 TACCTATTACATTATAT
27683 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:31002 original size:183 final size:183
Alignment explanation
Indices: 30694--31204 Score: 875
Period size: 183 Copynumber: 2.8 Consensus size: 183
30684 GTATCGACAC
30694 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
*
30759 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
30824 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCAGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCAGT
*
30877 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
30942 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
* *
31007 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCAGT
* *
31060 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTAT-AATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * *
31124 CAA--TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGA
*
31187 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
31205 GAAAACTTTG
Statistics
Matches: 313, Mismatches: 12, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
182 15 0.05
183 294 0.94
185 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCAGT
Found at i:32409 original size:3 final size:3
Alignment explanation
Indices: 32401--32475 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
32391 ACTTGTTTGG
* * * **
32401 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
32449 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
32476 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:34274 original size:197 final size:199
Alignment explanation
Indices: 33939--35098 Score: 2186
Period size: 197 Copynumber: 5.9 Consensus size: 199
33929 ATATTTAATT
33939 AGTATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34003 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
34067 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
34132 AAAA
196 AAAA
34136 AGTATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34200 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
34264 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
34328 AAAA
196 AAAA
34332 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34397 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
34461 ATCGACACTTTTTATATATGGATCGACGCTTTAT-GGTGCACCTTGTTTTCCATTCATTCTGGG-
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
34524 AAAA
196 AAAA
34528 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34593 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
34657 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG-
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
34721 AAAA
196 AAAA
34725 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34790 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
34855 ATCGACAC-TTTT-TATATGGATCGACACTTTAT-GGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
34917 AAAA
196 AAAA
34921 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34986 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
35050 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
35099 GGCCATATTG
Statistics
Matches: 947, Mismatches: 4, Indels: 22
0.97 0.00 0.02
Matches are distributed among these distances:
195 94 0.10
196 329 0.35
197 410 0.43
198 102 0.11
199 12 0.01
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (199 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
AAAA
Found at i:34664 original size:393 final size:394
Alignment explanation
Indices: 33939--35098 Score: 2192
Period size: 393 Copynumber: 3.0 Consensus size: 394
33929 ATATTTAATT
33939 AGTATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34003 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
34067 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCTTGTTTTCCATTCATTCTGGGA
34132 AAAAAGTATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACC
195 AAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
34196 GGTATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GGTATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
34261 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
34326 GAAAAA
390 G-AAAA
34332 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34397 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
34461 ATCGACACTTTTTATATATGGATCGACGCTTTATGGTGCACCTTGTTTTCCATTCATTCTGGG-A
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTCCATTCATTCTGGGAA
34525 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
196 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
34590 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTT
261 GTATAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
34654 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTG
34719 GGAAAA
389 GGAAAA
34725 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
34790 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
34855 ATCGACAC-TTTT-TATATGGATCGACACTTTATGGTGCACCTTGTTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTCCATTCATTCTGGGAA
34918 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
196 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
34983 GTATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 GTATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
* *
35048 GGATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
326 GGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
35099 GGCCATATTG
Statistics
Matches: 754, Mismatches: 4, Indels: 18
0.97 0.01 0.02
Matches are distributed among these distances:
392 110 0.15
393 413 0.55
394 194 0.26
395 37 0.05
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (394 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCTTGTTTTCCATTCATTCTGGGAA
AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
GTATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGG
AAAA
Found at i:35251 original size:19 final size:19
Alignment explanation
Indices: 35218--35266 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
35208 ATTATATTCA
35218 TATACAAAA-TATAAATCG
1 TATACAAAATTATAAATCG
*
35236 TATACAAAATTATAAATCT
1 TATACAAAATTATAAATCG
35255 TATACAAAATTA
1 TATACAAAATTA
35267 ACTCGACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:37091 original size:33 final size:33
Alignment explanation
Indices: 37054--37119 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
37044 CATCTTAATA
*
37054 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
37087 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
37120 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:37193 original size:21 final size:21
Alignment explanation
Indices: 37153--37217 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
37143 CCCCTTATTC
* *
37153 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
37174 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
37195 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
37216 CT
1 CT
37218 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:39457 original size:17 final size:18
Alignment explanation
Indices: 39435--39477 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
39425 ATATATCCGG
39435 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
39452 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
39472 TATCAT
1 TATCAT
39478 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:39467 original size:20 final size:20
Alignment explanation
Indices: 39440--39486 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
39430 TCCGGTATCA
39440 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
39459 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
39480 TTTTACC
1 TTTTACC
39487 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:39634 original size:20 final size:20
Alignment explanation
Indices: 39608--39653 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
39598 CACTTTTAAA
39608 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
39627 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
39648 TTTACC
1 TTTACC
39654 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:40154 original size:226 final size:223
Alignment explanation
Indices: 39719--40162 Score: 739
Period size: 226 Copynumber: 2.0 Consensus size: 223
39709 TTAAAACTGC
39719 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
39784 TTAATTTAATAATTTAATTTACACAAAATTATATTGATTGTTTTGATATTTATAAAATATTATTT
66 TTAATTTAATAATTTAATTAACACAAAATTATATTGATTGTTTTGATATTTATAAAATATTATTT
* * *
39849 AGAATTTAAATTTAACAATATTAACCAAATATAATAATAATATGTTTTCAACAGTGAAATAAGTA
131 AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCAACAGTAAAATAAGTA
*
39914 TGGACACTTTTATAAAAATGATATACTT
196 TGGACACTTTTATAAAAAGGATATACTT
*
39942 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
40007 ATTAATTTAATAATTTCATTAACACAAAAAATTAT-TTGATTGTTTTGATATTTTATAAAATATT
65 ATTAATTTAATAATTTAATTAACAC--AAAATTATATTGATTGTTTTGATA-TTTATAAAATATT
* * *
40071 ATTTAGATTTTAAATTTAACAATATTAACTATAGATAATAATAAATATATTTTC-ACAGTAAAAT
127 ATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT-AATATATTTTCAACAGTAAAAT
40135 AAGTATGGACACTTTTATAAAAAGGATA
191 AAGTATGGACACTTTTATAAAAAGGATA
40163 GATAATTTAC
Statistics
Matches: 206, Mismatches: 10, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
223 4 0.02
224 82 0.40
225 15 0.07
226 95 0.46
227 10 0.05
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (223 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTAACACAAAATTATATTGATTGTTTTGATATTTATAAAATATTATTT
AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCAACAGTAAAATAAGTA
TGGACACTTTTATAAAAAGGATATACTT
Found at i:41005 original size:12 final size:12
Alignment explanation
Indices: 40976--41015 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
40966 TGCGGGAAAA
40976 TTAAAA-TTA-T
1 TTAAAATTTATT
40986 TT-AAATTTATT
1 TTAAAATTTATT
40997 TTAAAATTTATT
1 TTAAAATTTATT
41009 TTAAAAT
1 TTAAAAT
41016 ATAGATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.11
10 5 0.19
11 3 0.11
12 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:41027 original size:22 final size:22
Alignment explanation
Indices: 41002--41365 Score: 491
Period size: 22 Copynumber: 16.6 Consensus size: 22
40992 TTATTTTAAA
* *
41002 ATTTATTTTAAAATATAGATTT
1 ATTTATTTTAAAATATGGATTG
41024 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
41046 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
* ***
41068 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* **
41090 AATTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
*
41111 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
41133 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
41155 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
41177 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
***
41199 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
41220 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
41243 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* **
41265 ATTTATTTTAAAATATAGA-AA
1 ATTTATTTTAAAATATGGATTG
41286 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
41309 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
41331 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
41353 ATTTATTTTAAAA
1 ATTTATTTTAAAA
41366 AACATATTAT
Statistics
Matches: 307, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
21 23 0.07
22 280 0.91
23 4 0.01
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:41870 original size:2 final size:2
Alignment explanation
Indices: 41863--41889 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41853 AAATGAACGT
41863 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 T
41890 TGTTCTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43696 original size:39 final size:40
Alignment explanation
Indices: 43653--43744 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
43643 GAGGGAGATC
* *
43653 TAGGCGTCTTCAATACAA-TTGCATGCAAA-ATCAGATCTT
1 TAGGCGTCTTCAACACAATTTGCATGCAAACAT-AGAGCTT
* *
43692 TAGGCGTCTTCAACACAATTTGCATTCAAACATAGAGGTT
1 TAGGCGTCTTCAACACAATTTGCATGCAAACATAGAGCTT
*
43732 TCGGCGTCTTCAA
1 TAGGCGTCTTCAA
43745 ATTATTTTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 17 0.37
40 27 0.59
41 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (40 bp):
TAGGCGTCTTCAACACAATTTGCATGCAAACATAGAGCTT
Found at i:44191 original size:20 final size:20
Alignment explanation
Indices: 44166--44204 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44156 TGCACGCAAA
*
44166 AGGGAATTCACGTGGTGAGC
1 AGGGAATTCACGGGGTGAGC
44186 AGGGAATTCACGGGGTGAG
1 AGGGAATTCACGGGGTGAG
44205 ATGATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.44, T:0.18
Consensus pattern (20 bp):
AGGGAATTCACGGGGTGAGC
Found at i:44559 original size:13 final size:13
Alignment explanation
Indices: 44541--44566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44531 TTAAGGTTTA
44541 GTGATTATATGTT
1 GTGATTATATGTT
44554 GTGATTATATGTT
1 GTGATTATATGTT
44567 ATTACATTAC
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:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
GTGATTATATGTT
Found at i:46934 original size:8 final size:8
Alignment explanation
Indices: 46921--47068 Score: 74
Period size: 8 Copynumber: 18.0 Consensus size: 8
46911 TATCATTACT
46921 ATTATTAA
1 ATTATTAA
46929 ATTATTAA
1 ATTATTAA
*
46937 ACT-TTAA
1 ATTATTAA
* *
46944 TATCATTACT
1 -ATTATTA-A
46954 ATTATTAA
1 ATTATTAA
46962 ATTATTAA
1 ATTATTAA
*
46970 ATCATTAA
1 ATTATTAA
46978 ATT-TT-A
1 ATTATTAA
46984 ATTATTAA
1 ATTATTAA
* *
46992 AGTGAAGTAA
1 A-T-TATTAA
47002 TTATTATTAA
1 --ATTATTAA
*
47012 ATCATTAA
1 ATTATTAA
*
47020 A--GTTAA
1 ATTATTAA
*
47026 ATCATTAA
1 ATTATTAA
*
47034 AGTTAAATAA
1 A-TT-ATTAA
47044 TTATTATTAA
1 --ATTATTAA
47054 ATTATTAA
1 ATTATTAA
47062 ATT-TTAA
1 ATTATTAA
47069 TCATTAAAAT
Statistics
Matches: 107, Mismatches: 18, Indels: 31
0.69 0.12 0.20
Matches are distributed among these distances:
6 9 0.08
7 12 0.11
8 54 0.50
9 11 0.10
10 16 0.15
11 3 0.03
12 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (8 bp):
ATTATTAA
Found at i:46958 original size:25 final size:25
Alignment explanation
Indices: 46929--46976 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
46919 CTATTATTAA
46929 ATTATTAAACT-TTAATATCATTACT
1 ATTATTAAACTATTAA-ATCATTACT
*
46954 ATTATTAAATTATTAAATCATTA
1 ATTATTAAACTATTAAATCATTA
46977 AATTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTATTAAACTATTAAATCATTACT
Found at i:46990 original size:33 final size:33
Alignment explanation
Indices: 46909--46977 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
46899 AATTGAATCG
*
46909 AATATCATTACTATTATTAAATTATTAAACTTT
1 AATATCATTACTATTATTAAATTATTAAACATT
46942 AATATCATTACTATTATTAAATTATTAAATCATT
1 AATATCATTACTATTATTAAATTATTAAA-CATT
46976 AA
1 AA
46978 ATTTTAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (33 bp):
AATATCATTACTATTATTAAATTATTAAACATT
Found at i:47015 original size:42 final size:41
Alignment explanation
Indices: 46920--47097 Score: 191
Period size: 42 Copynumber: 4.3 Consensus size: 41
46910 ATATCATTAC
* * * *
46920 TATTATTAAATTATTAAACTTTAATATCATTACTA-TTATTAA-
1 TATTATTAAATCATTAAA-TTTTA-ATCATTA-AAGTTAATAAT
* *
46962 -ATTATTAAATCATTAAATTTTAATTATTAAAGTGAAGTAAT
1 TATTATTAAATCATTAAATTTTAATCATTAAAGTTAA-TAAT
* *
47003 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAATAAT
1 TATTATTAAATCATTAAATTTTAATCATTAAAGTT-AATAAT
* *
47045 TATTATTAAATTATTAAATTTTAATCATTAAAATTTAATAAT
1 TATTATTAAATCATTAAATTTTAATCATT-AAAGTTAATAAT
47087 TATTATTAAAT
1 TATTATTAAAT
47098 ATATACTCGA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 8 0.07
40 7 0.06
41 16 0.14
42 77 0.66
43 7 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (41 bp):
TATTATTAAATCATTAAATTTTAATCATTAAAGTTAATAAT
Found at i:47018 original size:14 final size:14
Alignment explanation
Indices: 47001--47097 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 14
46991 AAGTGAAGTA
47001 ATTATTATTAAATC
1 ATTATTATTAAATC
*
47015 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
47029 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
*
47043 ATTATTATTAAATT
1 ATTATTATTAAATC
47057 ATTAAATT-TT-AATC
1 ATT--ATTATTAAATC
** * *
47071 ATTAAAATTTAATA
1 ATTATTATTAAATC
47085 ATTATTATTAAAT
1 ATTATTATTAAAT
47098 ATATACTCGA
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 56 0.85
15 3 0.05
16 3 0.05
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:47032 original size:28 final size:28
Alignment explanation
Indices: 46987--47097 Score: 77
Period size: 28 Copynumber: 4.0 Consensus size: 28
46977 AATTTTAATT
* *
46987 ATTAAAGTGAAGTAATTATTATTAAATC
1 ATTAAAGTTAAATAATTATTATTAAATC
* * *
47015 ATTAAAGTTAAATCATTA-AAGTTAAATA
1 ATTAAAGTTAAATAATTATTA-TTAAATC
* *
47043 ATTATTA-TTAAATTATTAAATT-TT-AATC
1 ATTA-AAGTTAAATAATT--ATTATTAAATC
* *
47071 ATTAAAATTTAATAATTATTATTAAAT
1 ATTAAAGTTAAATAATTATTATTAAAT
47098 ATATACTCGA
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
26 3 0.05
27 4 0.06
28 52 0.83
29 3 0.05
30 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (28 bp):
ATTAAAGTTAAATAATTATTATTAAATC
Found at i:50753 original size:172 final size:172
Alignment explanation
Indices: 50336--50845 Score: 752
Period size: 172 Copynumber: 3.0 Consensus size: 172
50326 GTTGATCATA
* *
50336 TTACTTTTTTTAATGTTTTTGTTTAGTAGTGTTACTTTATAAAATTAATACTTTTATAAATTTTC
1 TTACCTTTTTTAATGTTTTTGTTTAGTAGTGTTAGTTTATAAAATTAATACTTTTATAAATTTTC
* *
50401 TTTT---AATAACAAACTTTTC-TTTATAAAATGTGCTTCTGTTTAATATAGG-TCCCAATGATT
66 TTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTTG-TTAATGTAGGCT-CCAAT-ATT
*
50461 TTGCAAAATTTTATAAAGTGTTCGTTTTATATAAAATTTT-CATG
128 TTGCAAAATTTTATAAAGTGTACGTTTTATATAAAATTTTCCATG
*
50505 TTACCTTTTTTAATATTTTT-TTTAGTA-TGTTAGTTTATAAAATTAATACTTTTATAAATTTTC
1 TTACCTTTTTTAATGTTTTTGTTTAGTAGTGTTAGTTTATAAAATTAATACTTTTATAAATTTTC
50568 TTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTTGTTAATGTAGGCTCCAATATTTTT
66 TTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTTGTTAATGTAGGCTCCAATA-TTTT
*
50633 GC-AAATTTTATAAAGTGTGCGTTTTATATAAAATTTTCCAT-
130 GCAAAATTTTATAAAGTGTACGTTTTATATAAAATTTTCCATG
*
50674 TTACCTTTTTTAAATGTTTTTGTTTAGTAGTATTAGTTTATAAAATTAATACTTTTATAAATTTT
1 TTACCTTTTTT-AATGTTTTTGTTTAGTAGTGTTAGTTTATAAAATTAATACTTTTATAAATTTT
* * * **
50739 CTTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTTATTTAATGTAGACCCCAACGCTT
65 CTTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTT-GTTAATGTAGGCTCCAA-TATT
*
50804 TTGCAAAATTTTATAAAGTGTATGTTTTTATATAAAATTTTC
128 TTGCAAAATTTTATAAAGTGTACG-TTTTATATAAAATTTTC
50846 TTTGGCATTA
Statistics
Matches: 312, Mismatches: 15, Indels: 22
0.89 0.04 0.06
Matches are distributed among these distances:
167 39 0.12
168 7 0.02
169 64 0.21
170 46 0.15
171 26 0.08
172 76 0.24
173 20 0.06
174 17 0.05
175 17 0.05
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (172 bp):
TTACCTTTTTTAATGTTTTTGTTTAGTAGTGTTAGTTTATAAAATTAATACTTTTATAAATTTTC
TTTTAACAATAACAAACTTTTCTTTTATAAAATGTGCTTTTGTTAATGTAGGCTCCAATATTTTG
CAAAATTTTATAAAGTGTACGTTTTATATAAAATTTTCCATG
Found at i:52399 original size:23 final size:21
Alignment explanation
Indices: 52373--52427 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
52363 GATAATACTT
52373 TGTTACTAATAATATATT-TTAAA
1 TGTTA-TAA-AATA-ATTATTAAA
52396 TGTTATAAAATAATTATTAAA
1 TGTTATAAAATAATTATTAAA
*
52417 T-TTATTAAATA
1 TGTTATAAAATA
52428 TATTGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 10 0.33
22 3 0.10
23 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
TGTTATAAAATAATTATTAAA
Found at i:52415 original size:21 final size:21
Alignment explanation
Indices: 52373--52431 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
52363 GATAATACTT
52373 TGTTACTAATAATATATTTTAAA
1 TGTTA-TAA-AATATATTTTAAA
52396 TGTTATAAAATA-ATTATTAAA
1 TGTTATAAAATATATT-TTAAA
*
52417 T-TTATTAAATATATT
1 TGTTATAAAATATATT
52432 GAATTTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.36
21 13 0.39
22 3 0.09
23 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (21 bp):
TGTTATAAAATATATTTTAAA
Done.