Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005059.1 Hibiscus syriacus cultivar Beakdansim tig00011355_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: 80515
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3145 original size:56 final size:56
Alignment explanation
Indices: 3074--3934 Score: 1299
Period size: 55 Copynumber: 15.6 Consensus size: 56
3064 CTATGCATGC
**
3074 AAAG-TAAGAAATTCATAATGAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* * *
3129 AAAGCTAAGAAATTCATAATGAGTTTATAAATTTCAGTATGGGCACTTTGTGTG-T
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
3184 AAAGCTAAG-AATTCATAATGA-TTTATGAATTTCTGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
3238 AAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC-
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3292 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTGCGTATGAGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3348 AAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGTTTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3403 AAAGCTAAAAAATTCATAATGAGTTTATGAATTTGCGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
**
3459 AAAGCTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCGA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC-A
* *
3516 AAA--TAAGAAATTCAAAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3570 AAA-CTAA-TAATTCATAATGAGTTTATGAATTT-TGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
3623 AAAGCTAATAAATTCATAATGAGTTTTATGAATTTCCGTATGGGCACTTTGTGTGC-
1 AAAGCTAAGAAATTCATAATGAG-TTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* * *
3679 AAAGCTAAGAAGTTCATAATGAGTTTATGAATTTCCAT-TGGGCACTTTATGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* * *
3734 AAA-CTAAGAAATTCATAATGAGCTTATTAATTTCC-TCATAGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGT-ATGGGCACTTTGTGTGCA
* * * *
3789 AAA-ATAATAAATTCATAATGAGTTTATGAATTTCTGTATGGTCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
3844 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
3900 AAA-CTAAGAAATTCATAATAAGTTTATGAATTTCC
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCC
3935 ATATTGGTAG
Statistics
Matches: 739, Mismatches: 49, Indels: 36
0.90 0.06 0.04
Matches are distributed among these distances:
53 58 0.08
54 104 0.14
55 321 0.43
56 233 0.32
57 23 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (56 bp):
AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
Found at i:3955 original size:111 final size:111
Alignment explanation
Indices: 3074--3934 Score: 1314
Period size: 111 Copynumber: 7.8 Consensus size: 111
3064 CTATGCATGC
**
3074 AAAG-TAAGAAATTCATAATGAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCAAAAGCTAAG
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CTAAG
* * *
3138 AAATTCATAATGAGTTTATAAATTTCAGTATGGGCACTTTGTGTG-T
65 AAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
3184 AAAGCTAAG-AATTCATAATGA-TTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAACTAAGA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGA
3247 AATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC-
66 AATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3292 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTGCGTATGAGCACTTTGTGTGCAAAACTAAGA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGA
* *
3357 AATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGTTTGCA
66 AATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3403 AAAGCTAAAAAATTCATAATGAGTTTATGAATTTGCGTATGGGCACTTTGTGTGCAAAAGCTAAG
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CTAAG
**
3468 AAATTCATAACAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCGA
65 AAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC-A
* * *
3516 AAA--TAAGAAATTCAAAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAA-T
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGA
*
3578 AATTCATAATGAGTTTATGAATTT-TGTATGGGCACTTTGTGTGCA
66 AATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
3623 AAAGCTAATAAATTCATAATGAGTTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAGCTAAG
1 AAAGCTAAGAAATTCATAATGAG-TTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAG
* * *
3688 AAGTTCATAATGAGTTTATGAATTTCCAT-TGGGCACTTTATGTGCA
65 AAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* * * * *
3734 AAA-CTAAGAAATTCATAATGAGCTTATTAATTTCC-TCATAGGCACTTTGTGTGCAAAAATAAT
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGT-ATGGGCACTTTGTGTGCAAAACTAAG
* *
3797 AAATTCATAATGAGTTTATGAATTTCTGTATGGTCACTTTGTGTGCA
65 AAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
3844 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGA
1 AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGA
*
3909 AATTCATAATAAGTTTATGAATTTCC
66 AATTCATAATGAGTTTATGAATTTCC
3935 ATATTGGTAG
Statistics
Matches: 685, Mismatches: 50, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
107 4 0.01
108 77 0.11
109 143 0.21
110 177 0.26
111 231 0.34
112 49 0.07
113 4 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (111 bp):
AAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGA
AATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
Found at i:4274 original size:46 final size:46
Alignment explanation
Indices: 4223--4310 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
4213 TTAGATGAAG
* *
4223 AACAGTGCATAATTGGCACGAAAGGATGCCATAAATGAAAATGTAT
1 AACAGTCCATAATTGGCACGAAAGGATGCCACAAATGAAAATGTAT
*
4269 AACAGTCCATAATTGGCATGAAAGGATGCCACAAATGAAAAT
1 AACAGTCCATAATTGGCACGAAAGGATGCCACAAATGAAAAT
4311 ACATAGCGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.20
Consensus pattern (46 bp):
AACAGTCCATAATTGGCACGAAAGGATGCCACAAATGAAAATGTAT
Found at i:7060 original size:20 final size:20
Alignment explanation
Indices: 7022--7060 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7012 CGGTCAGATA
*
7022 TTTTTCTTTTCAATTTTTAG
1 TTTTTCTTTTCAATGTTTAG
7042 TTTTTCCTTTT-AATGTTTA
1 TTTTT-CTTTTCAATGTTTA
7061 ATGGGTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTCTTTTCAATGTTTAG
Found at i:7346 original size:16 final size:18
Alignment explanation
Indices: 7321--7366 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
7311 AAGTGTCACA
*
7321 ATTATGTAATA-ATTATT
1 ATTATATAATATATTATT
7338 -TTATATAATAATATTATT
1 ATTATATAAT-ATATTATT
7356 ATTATATAATA
1 ATTATATAATA
7367 GATGTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 7 0.28
19 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTATATAATATATTATT
Found at i:7360 original size:19 final size:19
Alignment explanation
Indices: 7327--7377 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
7317 CACAATTATG
7327 TAATAATTATT-TTATATAA
1 TAAT-ATTATTATTATATAA
7346 TAATATTATTATTATATAA
1 TAATATTATTATTATATAA
*
7365 TAGATGTTATTAT
1 TA-ATATTATTAT
7378 GATAATGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 6 0.21
19 14 0.48
20 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TAATATTATTATTATATAA
Found at i:8382 original size:23 final size:24
Alignment explanation
Indices: 8349--8399 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
8339 AGAAAGGTGT
*
8349 TGATAAATGATCCACGCCTTGCGC
1 TGATAAATGATCCACGCCTTACGC
*
8373 TGAT-AATGATCCGCGCCTTACGC
1 TGATAAATGATCCACGCCTTACGC
8396 TGAT
1 TGAT
8400 GTGGCACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (24 bp):
TGATAAATGATCCACGCCTTACGC
Found at i:15194 original size:28 final size:28
Alignment explanation
Indices: 15151--15206 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
15141 TTCCATTTAC
*
15151 ATTATGTCGTCAAGTCAATACTTGAAAT
1 ATTATGTCATCAAGTCAATACTTGAAAT
* *
15179 ATTATGTCATCTAGTCAGTACTTGAAAT
1 ATTATGTCATCAAGTCAATACTTGAAAT
15207 TAAAAGTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (28 bp):
ATTATGTCATCAAGTCAATACTTGAAAT
Found at i:16643 original size:12 final size:12
Alignment explanation
Indices: 16626--16650 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16616 TTATATATTG
16626 GGGTTATTCAGA
1 GGGTTATTCAGA
16638 GGGTTATTCAGA
1 GGGTTATTCAGA
16650 G
1 G
16651 AAATCCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GGGTTATTCAGA
Found at i:18084 original size:15 final size:15
Alignment explanation
Indices: 18064--18109 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
18054 ATTAAATTCG
18064 GTTCGGGTTATTTCA
1 GTTCGGGTTATTTCA
*
18079 GTTCGGGTTATTTCG
1 GTTCGGGTTATTTCA
* *
18094 GTTTGGGTCATTTCA
1 GTTCGGGTTATTTCA
18109 G
1 G
18110 ATTTAGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.13, G:0.30, T:0.46
Consensus pattern (15 bp):
GTTCGGGTTATTTCA
Found at i:18835 original size:16 final size:15
Alignment explanation
Indices: 18778--18840 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
18768 ATTAAATTCG
18778 AGTTACTTTCAGTTC
1 AGTTACTTTCAGTTC
* *
18793 AGGTTATTTTCAATTC
1 A-GTTACTTTCAGTTC
* * *
18809 AATTGCTTTCGGTTC
1 AGTTACTTTCAGTTC
18824 GAGTTACTTTC-GTTC
1 -AGTTACTTTCAGTTC
18839 AG
1 AG
18841 GCTAAAATTC
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
14 2 0.05
15 14 0.38
16 21 0.57
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.46
Consensus pattern (15 bp):
AGTTACTTTCAGTTC
Found at i:19211 original size:25 final size:25
Alignment explanation
Indices: 19185--19233 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
19175 TACAGAATAC
19185 AATATTAAAAA-AATAACATAAAAACA
1 AATA-TAAAAACAA-AACATAAAAACA
*
19211 AATATAAAAACAAAATATAAAAA
1 AATATAAAAACAAAACATAAAAA
19234 TATATAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (25 bp):
AATATAAAAACAAAACATAAAAACA
Found at i:19219 original size:11 final size:13
Alignment explanation
Indices: 19202--19233 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19192 AAAAAATAAC
19202 ATAAAAAC-AAAT
1 ATAAAAACAAAAT
19214 ATAAAAACAAAAT
1 ATAAAAACAAAAT
19227 ATAAAAA
1 ATAAAAA
19234 TATATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAAACAAAAT
Found at i:22306 original size:78 final size:78
Alignment explanation
Indices: 22211--22371 Score: 313
Period size: 78 Copynumber: 2.1 Consensus size: 78
22201 AGATATAAAA
22211 TAAGTAGTACGATGAATATGTCAGATTCAGTGGTAGCAAAAGCATGAGCTTCGGGAATGTCTGTG
1 TAAGTAGTACGATGAATATGTCAGATTCAGTGGTAGCAAAAGCATGAGCTTCGGGAATGTCTGTG
22276 AACGCAGGAAGAG
66 AACGCAGGAAGAG
22289 TAAGTAGTACGATGAATATGTCAGATTCAGTGGTAGCAAAAGCATGAGCTTCGGGAATGTCTGTG
1 TAAGTAGTACGATGAATATGTCAGATTCAGTGGTAGCAAAAGCATGAGCTTCGGGAATGTCTGTG
*
22354 AACGCAGGAATAG
66 AACGCAGGAAGAG
22367 TAAGT
1 TAAGT
22372 CATCCTTTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (78 bp):
TAAGTAGTACGATGAATATGTCAGATTCAGTGGTAGCAAAAGCATGAGCTTCGGGAATGTCTGTG
AACGCAGGAAGAG
Found at i:31652 original size:103 final size:101
Alignment explanation
Indices: 31503--31694 Score: 350
Period size: 103 Copynumber: 1.9 Consensus size: 101
31493 GAGTGGATGG
31503 TATGTTGTACAATACTACATATGTATCGTTTGAATTTGTGATTAATACAAATTTGGATT-ATTTG
1 TATGTTGTACAATACTACATATGTATCGTTTGAATTTGTGATTAATACAAATTTGGATTGATTTG
31567 TGATCGAAGCAAGTTAAATAAAAAGGGGGATATTTT
66 TGATCGAAGCAAGTTAAATAAAAAGGGGGATATTTT
31603 TATGTTAGTACAATACTAACATATGTATCGTTATGAATTTGTGATTAATACAAATTTGGATTGAT
1 TATGTT-GTACAATACT-ACATATGTATCGTT-TGAATTTGTGATTAATACAAATTTGGATTGAT
31668 TTGTGATCGAAGCAAGTTAAATAAAAA
63 TTGTGATCGAAGCAAGTTAAATAAAAA
31695 AGGGTATACA
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
100 6 0.07
101 10 0.11
102 14 0.16
103 29 0.33
104 29 0.33
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (101 bp):
TATGTTGTACAATACTACATATGTATCGTTTGAATTTGTGATTAATACAAATTTGGATTGATTTG
TGATCGAAGCAAGTTAAATAAAAAGGGGGATATTTT
Found at i:31712 original size:104 final size:100
Alignment explanation
Indices: 31499--31712 Score: 329
Period size: 104 Copynumber: 2.1 Consensus size: 100
31489 TATGGAGTGG
31499 ATGGTATGTTGTACAATACTACATATGTATCGTTTGAATTTGTGATTAATACAAATTTGGATTAT
1 ATGG-ATGTTGTACAATACTACATATGTATCGTTTGAATTTGTGATTAATACAAATTTGGATTAT
* *
31564 TTGTGATCGAAGCAAGTTAAATAAAAAGGGGGATAT
65 TTGTGATCGAAGCAAGTTAAATAAAAAAGGGGATAC
* **
31600 TTTTATGTTAGTACAATACTAACATATGTATCGTTATGAATTTGTGATTAATACAAATTTGGATT
1 ATGGATGTT-GTACAATACT-ACATATGTATCGTT-TGAATTTGTGATTAATACAAATTTGGATT
*
31665 GATTTGTGATCGAAGCAAGTTAAATAAAAAAGGGTATAC
63 -ATTTGTGATCGAAGCAAGTTAAATAAAAAAGGGGATAC
31704 ATGGATGTT
1 ATGGATGTT
31713 TTATACATCA
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
100 5 0.05
101 11 0.11
102 14 0.14
103 29 0.29
104 41 0.41
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (100 bp):
ATGGATGTTGTACAATACTACATATGTATCGTTTGAATTTGTGATTAATACAAATTTGGATTATT
TGTGATCGAAGCAAGTTAAATAAAAAAGGGGATAC
Found at i:36403 original size:182 final size:181
Alignment explanation
Indices: 36094--36458 Score: 559
Period size: 182 Copynumber: 2.0 Consensus size: 181
36084 TGTCCGAGCC
* * *
36094 AAATTCGCTACAAAGTCATCCAAAGATGGCTTGGGGTAGGGAACTTTTCCAAATACCACCAAGCA
1 AAATTCGCTACAAAATCATCCAAAGATAGCTTGGGGCAGGGAACTTTTCCAAATACCACCAAGCA
* *
36159 ACACAATACCAGATTAGAAACAAGAGCTGAAGAAAGTCCACTCATTTATAGTTGAAGATAATCTC
66 ACACAATACCAGATCAGAAACAAGAGCTGAAGAAAGTCCACTCATTTATAGCTGAAGATAATCTC
* *
36224 ATTCCAAAACAGCCACATAGACCAAAGGATTGCAAACGACAATATTCTCCA
131 ATTCCAAAACAGCCACAGAGACCAAAGGATTGCAAACGACAACATTCTCCA
* *
36275 AAATTCGCTGCAAAATCATCCAATGATAGCTTGGGGGCAGGGAACTTTTCCAAATACCACCAAGC
1 AAATTCGCTACAAAATCATCCAAAGATAGCTT-GGGGCAGGGAACTTTTCCAAATACCACCAAGC
* * * *
36340 AACACAATACCGGATCAGAAACAAGAGCTGAAGAAAGTGCACTCATTTATTGCTGATGATAATCT
65 AACACAATACCAGATCAGAAACAAGAGCTGAAGAAAGTCCACTCATTTATAGCTGAAGATAATCT
* * * * *
36405 CATTCCAAAATAGCCACAGAGACTAAATGATTGCAAACGGCAACATTTTCCA
130 CATTCCAAAACAGCCACAGAGACCAAAGGATTGCAAACGACAACATTCTCCA
36457 AA
1 AA
36459 TCAGACTCTT
Statistics
Matches: 165, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
181 28 0.17
182 137 0.83
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (181 bp):
AAATTCGCTACAAAATCATCCAAAGATAGCTTGGGGCAGGGAACTTTTCCAAATACCACCAAGCA
ACACAATACCAGATCAGAAACAAGAGCTGAAGAAAGTCCACTCATTTATAGCTGAAGATAATCTC
ATTCCAAAACAGCCACAGAGACCAAAGGATTGCAAACGACAACATTCTCCA
Found at i:41382 original size:20 final size:20
Alignment explanation
Indices: 41353--41396 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41343 AGTGACATTA
* * *
41353 AAGATTATATGATTTAGATG
1 AAGATGATATGATTCAGATC
41373 AAGATGATATGATTCAGATC
1 AAGATGATATGATTCAGATC
41393 AAGA
1 AAGA
41397 AGACATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (20 bp):
AAGATGATATGATTCAGATC
Found at i:45794 original size:15 final size:15
Alignment explanation
Indices: 45762--45790 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
45752 ATTAGTAATA
45762 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
45777 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
45791 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:46157 original size:12 final size:11
Alignment explanation
Indices: 46123--46154 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
46113 TCTTTTCTTT
46123 TTTTTTATTTG
1 TTTTTTATTTG
*
46134 TTTTTGATTTG
1 TTTTTTATTTG
46145 TTTTTTATTT
1 TTTTTTATTT
46155 TGTACTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (11 bp):
TTTTTTATTTG
Found at i:47505 original size:17 final size:17
Alignment explanation
Indices: 47483--47515 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47473 TAATAGTTGA
47483 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
47500 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
47516 CTTCCCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:49113 original size:137 final size:137
Alignment explanation
Indices: 48903--49240 Score: 410
Period size: 137 Copynumber: 2.5 Consensus size: 137
48893 GAGACGCACC
* * * ** * * *
48903 AGTAGAATTTTTTCGACCAAAGCTCATCAATTGCAGAAGGAGTTAGACCAACATCATTTCATTTC
1 AGTAGAATTTATTCAACCAAAGCTCATCCATCACAAAAGGAGTTGGATCAACATCATTTCATTTC
* * * * * * **
48968 GCTCGATTCCATTGCAGAAGGAGGTGGACCAATATTCATTCATTTCTTGCT-CATCTTAGAAGTA
66 ACTCGATTCCATTGCAGAAGGAGGTGGACCAACATGCATCCATTAC-TCCTCCATCGCAGAAGTA
*
49032 AATTGACT
130 AATGGACT
* *
49040 AGTGGAATTTATTCAACCAAAGCTCATCCATCACATAAGGAGTTGGATCAACATCATTTCATTTC
1 AGTAGAATTTATTCAACCAAAGCTCATCCATCACAAAAGGAGTTGGATCAACATCATTTCATTTC
* *
49105 ACTCGATTCTATTGCAGAAGGAGGTGGACCAACATGCATCCATTACTCCTCCATCGCAGAAGTAG
66 ACTCGATTCCATTGCAGAAGGAGGTGGACCAACATGCATCCATTACTCCTCCATCGCAGAAGTAA
49170 ATGGACT
131 ATGGACT
* * * * *
49177 AGTAGAATTCATTTAACCAAAGCTCGTCCACCACAAAAGGAGTTGGATCAGA-ATCATCTCATTT
1 AGTAGAATTTATTCAACCAAAGCTCATCCATCACAAAAGGAGTTGGATCA-ACATCATTTCATTT
49241 TGCTCATTTC
Statistics
Matches: 172, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
136 3 0.02
137 168 0.98
138 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (137 bp):
AGTAGAATTTATTCAACCAAAGCTCATCCATCACAAAAGGAGTTGGATCAACATCATTTCATTTC
ACTCGATTCCATTGCAGAAGGAGGTGGACCAACATGCATCCATTACTCCTCCATCGCAGAAGTAA
ATGGACT
Found at i:49646 original size:12 final size:11
Alignment explanation
Indices: 49555--49670 Score: 59
Period size: 12 Copynumber: 10.4 Consensus size: 11
49545 ATTTTTAGTT
*
49555 AAAAAATGAAAT
1 AAAAAATG-AAG
*
49567 AAAAAATAAAG
1 AAAAAATGAAG
49578 AAGAAGAA-GAAG
1 AA-AA-AATGAAG
49590 AAGAAAATG-AG
1 AA-AAAATGAAG
49601 AAATGAGAAATG-AG
1 -AA--A-AAATGAAG
49615 AAAAAAT-AAG
1 AAAAAATGAAG
*
49625 GAAAAA--AAG
1 AAAAAATGAAG
49634 AAAAAATTGAAG
1 AAAAAA-TGAAG
49646 -AAAAATGAAG
1 AAAAAATGAAG
49656 -AAAAATGAATG
1 AAAAAATGAA-G
49667 AAAA
1 AAAA
49671 GAATAAAAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
9 8 0.09
10 25 0.29
11 15 0.17
12 26 0.30
13 6 0.07
14 7 0.08
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (11 bp):
AAAAAATGAAG
Found at i:49649 original size:11 final size:10
Alignment explanation
Indices: 49627--49670 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
49617 AAAATAAGGA
*
49627 AAAAAAGAA-
1 AAAAATGAAG
*
49636 AAAATTGAAG
1 AAAAATGAAG
49646 AAAAATGAAG
1 AAAAATGAAG
49656 AAAAATGAATG
1 AAAAATGAA-G
49667 AAAA
1 AAAA
49671 GAATAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 7 0.23
10 18 0.60
11 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (10 bp):
AAAAATGAAG
Found at i:49664 original size:20 final size:20
Alignment explanation
Indices: 49627--49681 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
49617 AAAATAAGGA
*
49627 AAAAAAGAAAAAATTGAA-G
1 AAAAAAGAAAAAAATGAATG
*
49646 AAAAATGAAGAAAAATGAATG
1 AAAAAAGAA-AAAAATGAATG
*
49667 AAAAGAATAAAAAAA
1 AAAA-AAGAAAAAAA
49682 GAAAAAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.28
20 8 0.28
21 10 0.34
22 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAAAAGAAAAAAATGAATG
Found at i:50000 original size:34 final size:34
Alignment explanation
Indices: 49937--50005 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
49927 CAACAATTCA
** *
49937 CTCGATTTCATCACACAAGGAGTTGGATCAACAT
1 CTCGATTTCATCACACAAAAAGTTAGATCAACAT
* * *
49971 CTCGTTTTCATCACAGAAAAAGTTAGATCATCAT
1 CTCGATTTCATCACACAAAAAGTTAGATCAACAT
50005 C
1 C
50006 ATTTCATCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (34 bp):
CTCGATTTCATCACACAAAAAGTTAGATCAACAT
Found at i:51000 original size:116 final size:115
Alignment explanation
Indices: 50781--51474 Score: 817
Period size: 116 Copynumber: 6.0 Consensus size: 115
50771 ATGATTGCAG
** * * * * *
50781 CAAAGACTCGACATGTCCATCGCACAAGAAGGTGGATCAATATTTCAGAGAAAGGGTTCAAAATG
1 CAAA-ACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAA-GGTTCATAATG
* * * * *
50846 AGAAGAACACATCCAACAAGGGATAAGAAGTTCATAATGAGAAGAATTTATT
64 AGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
50898 CAAAACTTGACACATCCATTGCACAAGGAGGTGGATCAACATTTTCT-AGGAAGGTTTCATAATG
1 CAAAACTCGACACATCCATCGCACAAGGAGGTGGATCAACA-TTTCTGAGGAAGG-TTCATAATG
* * * *
50962 ACAAGAACTCATCCAACGATGGAGAATAAGTTCATAATGAGAAGAATTTGTT
64 AGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
51014 TAGAACTCGACACGTCCATCGCACAAGGAGGCGGATCAATATTTCTGAGGAAGGTTTCATAATGA
1 CAAAACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAAGG-TTCATAATGA
* * *
51079 GAAGAAGTAATCCAACGAGGGAGAAGAATTTCATAATGAGAAGAACTTGTT
65 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
51130 CAAAACTCGACACATCCATCGCACAAGTATGTGGATCAACATTTCTGAGGAAGGGTTCATAATGA
1 CAAAACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAA-GGTTCATAATGA
* * *
51195 GAAGAACTCGTCCAATGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTT
65 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
51246 CAGAACTCGACACGTCCATCACATAAGGAGGTGGATCAATATTTTTGAGGAAGAGTTCATAATGA
1 CAAAACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAAG-GTTCATAATGA
*
51311 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT---TAGAACTTGTT
65 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * * *
51359 CATAACTCTACAAATCTATCACACAAGGAGGTTGATCAACATTTCTGAGGAATGGTTCATACTGA
1 CAAAACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAA-GGTTCATAATGA
* * * * *
51424 GAATAACTCATCCAAAGAGGAAGAA-AAGTTCAT-AT-AGGAGAGCTTGTT
65 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
51472 CAA
1 CAA
51475 CATCAACAAT
Statistics
Matches: 498, Mismatches: 71, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
111 2 0.00
112 8 0.02
113 96 0.19
114 1 0.00
115 8 0.02
116 373 0.75
117 10 0.02
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (115 bp):
CAAAACTCGACACATCCATCGCACAAGGAGGTGGATCAACATTTCTGAGGAAGGTTCATAATGAG
AAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
Found at i:51246 original size:20 final size:20
Alignment explanation
Indices: 51184--51247 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
51174 CTGAGGAAGG
*
51184 GTTCATAATGAGAAGAACTC
1 GTTCATAATGAGAAGAACTA
* **
51204 G-TC-CAATGAGAGAGAAGAA
1 GTTCATAATGAGA-AGAACTA
*
51223 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTA
51243 GTTCA
1 GTTCA
51248 GAACTCGACA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 12 0.36
21 7 0.21
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTA
Found at i:52812 original size:22 final size:23
Alignment explanation
Indices: 52759--52812 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
52749 CTTGACTTGT
*
52759 TTTCT-TTGGTTTCTTTTTTTCG
1 TTTCTATTGGTTTCTTTTTTACG
52781 TTTCTAATTGGTTT-TTTATTTAC-
1 TTTCT-ATTGGTTTCTTT-TTTACG
52804 TTTCTATTG
1 TTTCTATTG
52813 TATGTATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.32
23 8 0.29
24 11 0.39
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.69
Consensus pattern (23 bp):
TTTCTATTGGTTTCTTTTTTACG
Found at i:58153 original size:15 final size:15
Alignment explanation
Indices: 58133--58163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58123 AACACCGTAA
58133 AAGGTTAGGTCATTT
1 AAGGTTAGGTCATTT
*
58148 AAGGTTATGTCATTT
1 AAGGTTAGGTCATTT
58163 A
1 A
58164 GTGGCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (15 bp):
AAGGTTAGGTCATTT
Found at i:58215 original size:42 final size:42
Alignment explanation
Indices: 58156--58257 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
58146 TTAAGGTTAT
58156 GTCATTTAGTGGCATTTTGGGAACAAATGCCGCAAAAGATAG
1 GTCATTTAGTGGCATTTTGGGAACAAATGCCGCAAAAGATAG
*
58198 GTCATTTAGTGGCATTTTGGGAACAAATGCCGCAAAAGGTAG
1 GTCATTTAGTGGCATTTTGGGAACAAATGCCGCAAAAGATAG
*
58240 GTAATTTAGTGGCATTTT
1 GTCATTTAGTGGCATTTT
58258 TAAGTAAAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (42 bp):
GTCATTTAGTGGCATTTTGGGAACAAATGCCGCAAAAGATAG
Found at i:60526 original size:42 final size:41
Alignment explanation
Indices: 60427--60528 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 41
60417 ATCCCAAGGA
*
60427 GGCATTTTAATAACAAACGCCAATAAAGTGCGTCTCTATTGC
1 GGCA-TTTAATAACAAACGCCAATAAAGTACGTCTCTATTGC
* * *
60469 GGCATTTCAACAACAAACGCCACTAACA-TACGTCTCTATTGT
1 GGCATTT-AATAACAAACGCCAATAA-AGTACGTCTCTATTGC
*
60511 GGCGTCTTAATAACAAAC
1 GGCAT-TTAATAACAAAC
60529 TCTACTAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
41 3 0.06
42 45 0.88
43 3 0.06
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (41 bp):
GGCATTTAATAACAAACGCCAATAAAGTACGTCTCTATTGC
Found at i:65148 original size:45 final size:45
Alignment explanation
Indices: 65075--65436 Score: 483
Period size: 45 Copynumber: 8.1 Consensus size: 45
65065 TTATTTATTA
* *
65075 ATTTCATTTAT-ACATCCTTTTAAGCCTTTTATACACCATTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
* * * **
65119 ATTTTATTTATGACATCATTTCATACCTTTTATACACTTTTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
**
65164 ATTTCATTTATGGTATCCTTTCATGCCTTTTATACACCATTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
* *
65209 ATGTCATTTATGACATCCTTTCATGCATTTTATACACCATTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
* **
65254 ATTTCATTTATGACATCATTTCATTTCTTTTATACACCATTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
* * * * * *
65299 CTTTTATTTACGGCATCCTTTTATTCCTTTTATACACCATTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
**
65344 ATTTCATTTATGACATCCTTTCATGCCTTTTATACATAATTATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
* * * *
65389 CTTTCATTTATGGCATCCTTTTATGCCTTTTATACACCATTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
65434 ATT
1 ATT
65437 GCTATCTATC
Statistics
Matches: 272, Mismatches: 45, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
44 10 0.04
45 262 0.96
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.47
Consensus pattern (45 bp):
ATTTCATTTATGACATCCTTTCATGCCTTTTATACACCATTATAC
Found at i:65816 original size:55 final size:55
Alignment explanation
Indices: 65677--65807 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
65667 TTTATTAAGA
* * * * *
65677 TGCACACGTAGTGCCTATATGGTAGTTCATCAACTCATGATGAATTTCATGGATT
1 TGCACACATAGTGCCTGTACGATAGTTCATAAACTCATGATGAATTTCATGGATT
* *
65732 TGCACACATCGTGCCTGTACGATAGTTCATAAACTCATGATGAATTAT-GTGGATT
1 TGCACACATAGTGCCTGTACGATAGTTCATAAACTCATGATGAATT-TCATGGATT
* *
65787 TTCACACATAGTGCTTGTACG
1 TGCACACATAGTGCCTGTACG
65808 GTTATTCATC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 64 0.98
56 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGATAGTTCATAAACTCATGATGAATTTCATGGATT
Found at i:65866 original size:54 final size:54
Alignment explanation
Indices: 65805--66123 Score: 503
Period size: 54 Copynumber: 5.9 Consensus size: 54
65795 TAGTGCTTGT
*
65805 ACGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * * * *
65859 ACAGTTATTAATCCACATATGATGAATTTCGTGAAATGCACACTTAGTGCCAAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* *
65913 ACGGTTATTTATCCACATAGGATGAATTTCGTGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* *
65967 ACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCAAACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * ** *
66021 ACGATTATTCATCCACATAGAATGAATTCCGTGAAATAAACACTTAGTGCTGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
66075 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
66124 TCTATTTGGT
Statistics
Matches: 240, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 240 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (54 bp):
ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
Found at i:66475 original size:22 final size:19
Alignment explanation
Indices: 66450--66500 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
66440 TGGCTCCTCA
66450 GTATCGATACTACCATACTATG
1 GTATCGATACT---ATACTATG
*
66472 GTATCGATACTATGCTATG
1 GTATCGATACTATACTATG
66491 GTATCGATAC
1 GTATCGATAC
66501 CTTCCCTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.61
22 11 0.39
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (19 bp):
GTATCGATACTATACTATG
Found at i:66541 original size:20 final size:19
Alignment explanation
Indices: 66490--66541 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
66480 ACTATGCTAT
66490 GGTATCGATACCTTCCCTTC
1 GGTATCGATA-CTTCCCTTC
*
66510 GATATCGATACTTCCCCTTC
1 GGTATCGATACTT-CCCTTC
66530 GGTATCGATACT
1 GGTATCGATACT
66542 GATTGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (19 bp):
GGTATCGATACTTCCCTTC
Found at i:70874 original size:21 final size:21
Alignment explanation
Indices: 70848--70966 Score: 80
Period size: 22 Copynumber: 5.4 Consensus size: 21
70838 ATTAATTTCA
70848 TTTATACATCCTTTCATGCCT
1 TTTATACATCCTTTCATGCCT
** *
70869 TTTATACA-CCATTATACATTTCA
1 TTTATACATCC-TT-T-CATGCCT
* *
70892 TTTATGACATCATTTCATGCAT
1 TTTAT-ACATCCTTTCATGCCT
** *
70914 TTTATACA-CCATTATACATTTCA
1 TTTATACATCC-TT-T-CATGCCT
70937 TTTATAGCATCCTTTCATGCCT
1 TTTATA-CATCCTTTCATGCCT
70959 TTTATACA
1 TTTATACA
70967 CCATTATACA
Statistics
Matches: 72, Mismatches: 16, Indels: 20
0.67 0.15 0.19
Matches are distributed among these distances:
20 3 0.04
21 17 0.24
22 20 0.28
23 20 0.28
24 9 0.12
25 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (21 bp):
TTTATACATCCTTTCATGCCT
Found at i:70909 original size:45 final size:45
Alignment explanation
Indices: 70842--71203 Score: 555
Period size: 45 Copynumber: 8.1 Consensus size: 45
70832 TTATTTATTA
*
70842 ATTTCATTTAT-ACATCCTTTCATGCCTTTTATACACCATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
* * *
70886 ATTTCATTTATGACATCATTTCATGCATTTTATACACCATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
*
70931 ATTTCATTTATAGCATCCTTTCATGCCTTTTATACACCATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
* * * *
70976 ATTTTATTTATGGCATCATTTCATGCCTTTTACATACCATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
* *
71021 ATTTCATTTATGGCATCCTTTCATGACTTTTATACATCATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
* *
71066 CTTTCATTTATGGCATCCTTTTATGCCTTTTATACACCATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
*
71111 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACAATTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
* * * *
71156 CTTTCATTTATGGCATCTTTTTATGCCTTTTATACACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
71201 ATT
1 ATT
71204 GATATCCATC
Statistics
Matches: 287, Mismatches: 30, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
44 11 0.04
45 276 0.96
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTTATACACCATTATAC
Found at i:71739 original size:55 final size:55
Alignment explanation
Indices: 71470--71767 Score: 334
Period size: 55 Copynumber: 5.4 Consensus size: 55
71460 ATGGTAATTA
* * * * *
71470 ATCAATTCATGATAAATTTCATGGATTTGCACACATAGTGCCTGTACGG-TAGTTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTTA-TTC
*
71525 ATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTGCATGTACGGTTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTTATTC
*
71580 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTC-TGTACGATTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG-CATGTACGGTTATTC
* * * ** * * *
71635 ATCATCTCATGATTACTTTTGTGGATTTTCACACATAGTTCTTGTACGGTTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTTATTC
** * * *
71690 ATCAACTCATGATGAATTCCGTGGATTTATATACTTAGTGC-TGAAACGGTTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATG-TACGGTTATTC
* *
71745 ATCCACAT-AGGATGAATTCCGTG
1 ATCAAC-TCATGATGAATTCCGTG
71768 AAATGCACAC
Statistics
Matches: 209, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
54 3 0.01
55 202 0.97
56 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (55 bp):
ATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTTATTC
Found at i:73014 original size:44 final size:44
Alignment explanation
Indices: 72946--73031 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
72936 ATCTAGGCAA
72946 AAAGCTGGTGTTATCCAGGATAAAATGGGGGCATCAAGGTCAAG
1 AAAGCTGGTGTTATCCAGGATAAAATGGGGGCATCAAGGTCAAG
*
72990 AAAGGTGGTGTTATCCAGGATAAAATGGGGGCATCAAGGTCA
1 AAAGCTGGTGTTATCCAGGATAAAATGGGGGCATCAAGGTCA
73032 CAATTTTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (44 bp):
AAAGCTGGTGTTATCCAGGATAAAATGGGGGCATCAAGGTCAAG
Found at i:73699 original size:42 final size:41
Alignment explanation
Indices: 73639--73745 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 41
73629 CCCGATTTTG
* * * * * * *
73639 TAAATCCTTCGGGCCATCTTTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCAGGTCATCTATAAGCCTTTCGAACAAGATG-A
* * *
73681 TAAATCCTTCAAGTCATCTGTAAGCCTTTTGAACAAGATGA
1 TAAATCCTTCAGGTCATCTATAAGCCTTTCGAACAAGATGA
*
73722 TAAAGCCTTCAGGTCATCTATAAG
1 TAAATCCTTCAGGTCATCTATAAG
73746 ACCATCAGTA
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 21 0.40
42 32 0.60
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
TAAATCCTTCAGGTCATCTATAAGCCTTTCGAACAAGATGA
Found at i:73998 original size:45 final size:42
Alignment explanation
Indices: 73904--74004 Score: 114
Period size: 42 Copynumber: 2.3 Consensus size: 42
73894 GATTCGTAAG
* * * *
73904 TCCTTCGAGCCATCTGTAAGTCTTTCAAGCATGATGCTTAAA
1 TCCTTCGGGTCATCTGTAAGCCTTTCAAGCATGATGCATAAA
*
73946 TCCTTCGGGTCATCTGTAAGCCTTTCGAGCATGATG-ATAAA
1 TCCTTCGGGTCATCTGTAAGCCTTTCAAGCATGATGCATAAA
73987 GCCTGCCTTCGGGTCATC
1 ---T-CCTTCGGGTCATC
74005 CATAAGACCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
41 4 0.08
42 32 0.64
44 1 0.02
45 13 0.26
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGTCATCTGTAAGCCTTTCAAGCATGATGCATAAA
Found at i:74112 original size:265 final size:261
Alignment explanation
Indices: 73638--74471 Score: 965
Period size: 265 Copynumber: 3.3 Consensus size: 261
73628 TCCCGATTTT
* * *
73638 GTAAATCCTTCGGGCCATCTTTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAAGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTA
* * * * *
73703 AGCCTTTTGAACAAGATGATAAAGCCTTCAGGTCATCTATAAGACCATCAGTACTGGATGCTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGTCATCCATAAGACCATCAGTACTGGAGGCTTTA
* * * * *
73768 AAATGAGATTTTAGAAACTAAGTCTTTCAGTGGTTTCCTAATTATCTGAAAAGAGTTGTTAAATG
131 AAATGAGATTTTAGAAACTAAGCCTTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAGG
* * * * * *
73833 AAGCTAAGCCTAACAATGGGGTTCCTTGACAACTAAGAAACTAAGCTTTTGAGGGTTTCTTGATT
196 AAGCTAAGCCTAACAAAGAGGTTCCTTGACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGATT
73898 C
261 C
* * *
73899 GTAAGTCCTTCGAGCCATCTGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTA
* * * **
73964 AGCCTTTCGAGCATGATGATAAAGCCTGCCTTCGGGTCATCCATAAGACCTTCAGTGTTGGAGGC
66 AGCCTTTCGAGCAAGATGATAAA----GCCTTCAGGTCATCCATAAGACCATCAGTACTGGAGGC
*
74029 TTTAAAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTCA
127 TTTAAAATGAGATTTTAGAAACTAAGCCTTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTCA
74094 AAGGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACAAAAAAACTAAGCTTTCGAGGGTTTCAT
192 AAGGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACAAAAAAACTAAGCTTTCGAGGGTTTCAT
74159 GATTC
257 GATTC
* * * * ** *
74164 GCAAGTCCTTTGGGCCATCTGTAAGTCTTTCGAGAATGATGTTTAAATTTTTCAGGTCATCAGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTA
* * * *
74229 AGCTTTTCGAGCAAGATAAT-AAGACCTTC-GG----------G--GA--AG-A-T----GTTTT
66 AGCCTTTCGAGCAAGATGATAAAG-CCTTCAGGTCATCCATAAGACCATCAGTACTGGAGGCTTT
* * * *
74272 CAAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAG
130 AAAATGAGATTTTAGAAACTAAGCCTTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAG
* * * * * *
74337 GAAGCTAAGCCTAACAAAGGGGTTCCTTAACAACTAAGAAACTAAGCTTTTGAGGGTTTCTTGAT
195 GAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGAT
74402 TC
260 TC
* * * * * * *
74404 ATATGTCCTTGGGGCCATCTGTAAATCTTTCGAGCATGATGCTTTAATCCATCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTA
74469 AGC
66 AGC
74472 ATTTTGATAA
Statistics
Matches: 501, Mismatches: 67, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
240 182 0.36
244 1 0.00
246 2 0.00
250 1 0.00
260 3 0.01
261 84 0.17
264 2 0.00
265 226 0.45
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (261 bp):
GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGTCATCCATAAGACCATCAGTACTGGAGGCTTTA
AAATGAGATTTTAGAAACTAAGCCTTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAGG
AAGCTAAGCCTAACAAAGAGGTTCCTTGACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGATT
C
Found at i:74464 original size:240 final size:241
Alignment explanation
Indices: 74033--74476 Score: 694
Period size: 240 Copynumber: 1.8 Consensus size: 241
74023 GGAGGCTTTA
74033 AAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAGG
1 AAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAGG
*
74098 AAGCTAAGCCTAACAAAGAGGTTCCTTGACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGATT
66 AAGCTAAGCCTAACAAAGAGGTTCCTTAACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGATT
* * * ***
74163 CGCAAGTCCTTTGGGCCATCTGTAAGTCTTTCGAGAATGATGTTTAAATTTTTCAGGTCATCAGT
131 CACAAGTCCTTGGGGCCATCTGTAAATCTTTCGAGAATGATGTTTAAATCCATCAGGTCATCAGT
74228 AAGC-TTTTCGAGCAAGATAATAAGACCTTCGGGGAAGATGTTTTC
196 AAGCATTTTCGAGCAAGATAATAAGACCTTCGGGGAAGATGTTTTC
* *
74273 AAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGG
1 AAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAGG
* * * * *
74338 AAGCTAAGCCTAACAAAGGGGTTCCTTAACAACTAAGAAACTAAGCTTTTGAGGGTTTCTTGATT
66 AAGCTAAGCCTAACAAAGAGGTTCCTTAACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGATT
* * * * *
74403 CATATGTCCTTGGGGCCATCTGTAAATCTTTCGAGCATGATGCTTT-AATCCATCGGGTCATCTG
131 CACAAGTCCTTGGGGCCATCTGTAAATCTTTCGAGAATGATG-TTTAAATCCATCAGGTCATCAG
74467 TAAGCATTTT
195 TAAGCATTTT
74477 GATAAGACCT
Statistics
Matches: 183, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
240 176 0.96
241 7 0.04
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (241 bp):
AAATGAGATTTTAGAAACTAAGCCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTCAAAGG
AAGCTAAGCCTAACAAAGAGGTTCCTTAACAACAAAAAAACTAAGCTTTCGAGGGTTTCATGATT
CACAAGTCCTTGGGGCCATCTGTAAATCTTTCGAGAATGATGTTTAAATCCATCAGGTCATCAGT
AAGCATTTTCGAGCAAGATAATAAGACCTTCGGGGAAGATGTTTTC
Found at i:74954 original size:3 final size:3
Alignment explanation
Indices: 74892--74935 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
74882 TTATTTGTTT
74892 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
74936 GTTACTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:79256 original size:14 final size:14
Alignment explanation
Indices: 79237--79267 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
79227 GTAACAACTC
79237 AATCTTCTCTTAGA
1 AATCTTCTCTTAGA
79251 AATCTTCTCTTAGA
1 AATCTTCTCTTAGA
79265 AAT
1 AAT
79268 ATTTGTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (14 bp):
AATCTTCTCTTAGA
Done.