Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008078.1 Hibiscus syriacus cultivar Beakdansim tig00110580_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: 1434613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:197909 original size:19 final size:19
Alignment explanation
Indices: 197879--198148 Score: 309
Period size: 19 Copynumber: 15.5 Consensus size: 19
197869 GATTATCTCG
197879 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
197897 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
197916 TTGCGA--TTC--TTCG--
1 TTGCGATTTTCATTTCGCA
197929 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
197948 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
197967 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
197986 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
198005 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
198020 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
198038 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
198057 TTGCGA--TTC-TCTCG-T
1 TTGCGATTTTCATTTCGCA
198072 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
198091 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
198109 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
*
198121 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
198140 TTGCGATTT
1 TTGCGATTT
198149 CATGTGGGAT
Statistics
Matches: 218, Mismatches: 11, Indels: 45
0.80 0.04 0.16
Matches are distributed among these distances:
12 6 0.03
13 6 0.03
14 9 0.04
15 15 0.07
16 11 0.05
17 26 0.12
18 30 0.14
19 115 0.53
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:197917 original size:51 final size:53
Alignment explanation
Indices: 197857--198116 Score: 236
Period size: 51 Copynumber: 4.9 Consensus size: 53
197847 TGCGTTTATA
197857 ATTTCGCATTGCGATTATCTCGTTGCGA-TTTCATTTCGCATTGCGATT-T-TC
1 ATTTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
197908 ATTTCGCATTGCGA-TTCTTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCGCATTGCGATTTC-TCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
* *
197959 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTATGTC
1 ATTTCGCATTGCGA-TTTC---TCG--TTGCGATTTTCATTTCGCATTGCGATTATCTC
** * * * *
198018 GGTTCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
* * * *
198070 GTTT-GCGATTTTC-ATTTCGCATTGCGA-TTTCATTTCGCATTGCGATT
1 ATTTCGC-A-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATT
198117 CTCGTTGCGA
Statistics
Matches: 186, Mismatches: 10, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
49 2 0.01
50 10 0.05
51 52 0.28
52 52 0.28
53 23 0.12
54 1 0.01
55 4 0.02
57 30 0.16
58 3 0.02
59 9 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
Found at i:198053 original size:52 final size:53
Alignment explanation
Indices: 197929--198148 Score: 297
Period size: 52 Copynumber: 4.2 Consensus size: 53
197919 CGATTCTTCG
* * *
197929 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG-GTTGCGATTTTCATTTCGCA
* *
197986 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGGTTGCGATTTTCATTTCGCA
* *
198038 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGGTTGCGATTTTCATTTCGCA
*
198091 TTGCGA-TTTCATTTCGCATTGCGA-T-TCTC-GTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGGTTGCGATTTTCATTTCGCA
198140 TTGCGATTT
1 TTGCGATTT
198149 CATGTGGGAT
Statistics
Matches: 151, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
49 24 0.16
50 6 0.04
51 1 0.01
52 65 0.43
53 24 0.16
54 5 0.03
55 2 0.01
57 24 0.16
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCGGTTGCGATTTTCATTTCGCA
Found at i:198101 original size:71 final size:70
Alignment explanation
Indices: 197879--198116 Score: 319
Period size: 71 Copynumber: 3.4 Consensus size: 70
197869 GATTATCTCG
197879 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTCGTTGCGATTTTCATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTCGTTGCGATTTTCATT
197943 TCGCA
66 TCGCA
* *
197948 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT--CTTCG--TTGCGATT
* *
198011 TT-ATGTCG-G
60 TTCATTTCGCA
198020 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCT-TCG-TTGCGATTTTCA
198084 TTTCGCA
64 TTTCGCA
198091 TTGCGA-TTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
198117 CTCGTTGCGA
Statistics
Matches: 147, Mismatches: 9, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
67 7 0.05
68 3 0.02
69 10 0.07
70 41 0.28
71 62 0.42
72 7 0.05
73 5 0.03
74 6 0.04
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (70 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTCGTTGCGATTTTCATT
TCGCA
Found at i:198127 original size:30 final size:29
Alignment explanation
Indices: 198089--198177 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 29
198079 TTTCATTTCG
*
198089 CATTGCGATTTCATTTCGCATTGCGATTCT
1 CATTGCGATTTCATTTCGCGTTGCGATT-T
*
198119 CGTTGCGATTTTCATTTCGCGTTGCGATTT
1 CATTGCGA-TTTCATTTCGCGTTGCGATTT
*
198149 CATGTGGGATTTCATTTCGCGTTGCGATT
1 CAT-TGCGATTTCATTTCGCGTTGCGATT
198178 GTATTTTCCG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 30 0.57
31 23 0.43
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.44
Consensus pattern (29 bp):
CATTGCGATTTCATTTCGCGTTGCGATTT
Found at i:201349 original size:20 final size:20
Alignment explanation
Indices: 201332--201672 Score: 364
Period size: 20 Copynumber: 17.5 Consensus size: 20
201322 TACAGATTCT
*
201332 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* * *
201352 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
**
201372 CGTTGCGA-TTACGGAT-TT
1 CGTTGCGATTTACGGATACG
201390 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
201410 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
201430 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
201450 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
201470 CATTGCGATTTA-GGATACG
1 CGTTGCGATTTACGGATACG
*
201489 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
*
201509 CGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACG
201529 CGTTGCGA-TTACGGATA-G
1 CGTTGCGATTTACGGATACG
*
201547 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
201567 CATTGCGA-TTACCCATACG
1 CGTTGCGATTTACGGATACG
* *
201586 CG-CGCGATTTA-GGATACA
1 CGTTGCGATTTACGGATACG
*
201604 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
* *
201624 CGTTGCGA-TTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
201643 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
201663 CGTTGCGATT
1 CGTTGCGATT
201673 ATGGAAAATC
Statistics
Matches: 275, Mismatches: 32, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
18 28 0.10
19 87 0.32
20 158 0.57
21 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:201376 original size:40 final size:39
Alignment explanation
Indices: 201332--201633 Score: 357
Period size: 38 Copynumber: 7.7 Consensus size: 39
201322 TACAGATTCT
* * *
201332 CGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGA-TATCGTTGCGATTTACGGATACG
*
201372 CGTTGCGA-TTACGGATTTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATATCGTTGCGATTTACGGATACG
201410 CGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGA-TATCGTTGCGATTTACGGATACG
201450 CGTTGCGATTTACGGATA-CGCATTGCGATTTA-GGATACG
1 CGTTGCGATTTACGGATATCG--TTGCGATTTACGGATACG
* *
201489 CGTTGCGATTTACGGATACACGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATA-TCGTTGCGATTTACGGATACG
* *
201529 CGTTGCGA-TTACGGATAGCGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATATCGTTGCGATTTACGGATACG
* ** ** *
201567 CATTGCGA-TTACCCATA-CGCGCGCGATTTA-GGATACA
1 CGTTGCGATTTACGGATATCG-TTGCGATTTACGGATACG
*
201604 CGTTGCGATTTACGGATACACGTTGCGATT
1 CGTTGCGATTTACGGATA-TCGTTGCGATT
201634 ATGTGTTCGC
Statistics
Matches: 230, Mismatches: 21, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
37 15 0.07
38 75 0.33
39 65 0.28
40 73 0.32
41 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (39 bp):
CGTTGCGATTTACGGATATCGTTGCGATTTACGGATACG
Found at i:201647 original size:39 final size:39
Alignment explanation
Indices: 201314--201673 Score: 319
Period size: 39 Copynumber: 9.3 Consensus size: 39
201304 AAATTTCAGT
* * * * *
201314 GTTGTGATTACAGATTCTCGTTGCGATTTACGGATTA-TC
1 GTTGCGATTACGGATACGCGTTGCGATTTACGGA-TACGC
* * * **
201353 GTTGCGATTTACAGATTCTCGTTGCGA-TTACGGAT-TTC
1 GTTGCGA-TTACGGATACGCGTTGCGATTTACGGATACGC
*
201391 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTA-TC
1 GTTGCGA-TTACGGATACGCGTTGCGATTTACGGA-TACGC
201431 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
1 GTTGCGA-TTACGGATACGCGTTGCGATTTACGGATACGC
* *
201471 ATTGCGATTTA-GGATACGCGTTGCGATTTACGGATACAC
1 GTTGCGA-TTACGGATACGCGTTGCGATTTACGGATACGC
*
201510 GTTGCGGTTTACGGATACGCGTTGCGA-TTACGGATA-GC
1 GTTGC-GATTACGGATACGCGTTGCGATTTACGGATACGC
* **
201548 GTTGCGATATACGGATACGCATTGCGA-TTACCCATACGC
1 GTTGCGAT-TACGGATACGCGTTGCGATTTACGGATACGC
* * *
201587 G-CGCGATTTA-GGATACACGTTGCGATTTACGGATACAC
1 GTTGCGA-TTACGGATACGCGTTGCGATTTACGGATACGC
* * * ** *
201625 GTTGCGATTATGTG-TTCGCGTTGCGATTTTCATATTCGC
1 GTTGCGATTACG-GATACGCGTTGCGATTTACGGATACGC
201664 GTTGCGATTA
1 GTTGCGATTA
201674 TGGAAAATCG
Statistics
Matches: 278, Mismatches: 28, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
37 15 0.05
38 76 0.27
39 102 0.37
40 85 0.31
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.34
Consensus pattern (39 bp):
GTTGCGATTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:204226 original size:18 final size:18
Alignment explanation
Indices: 204203--204237 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
204193 TATATGATAG
204203 TAAGTTCAAATTTCAAAT
1 TAAGTTCAAATTTCAAAT
204221 TAAGTTCAAATTTCAAA
1 TAAGTTCAAATTTCAAA
204238 ATTATTTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (18 bp):
TAAGTTCAAATTTCAAAT
Found at i:207892 original size:42 final size:41
Alignment explanation
Indices: 207834--207913 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
207824 CTTCCAATGT
207834 TATTTTTCGTGTTACATATACGCAGAAGATAATCTCAAAGC
1 TATTTTTCGTGTTACATATACGCAGAAGATAATCTCAAAGC
*
207875 TATTTCTTCGTGTTACATATATGCAGAAGATAATCTCAA
1 TATTT-TTCGTGTTACATATACGCAGAAGATAATCTCAA
207914 GTATTGAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 5 0.14
42 32 0.86
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (41 bp):
TATTTTTCGTGTTACATATACGCAGAAGATAATCTCAAAGC
Found at i:210617 original size:13 final size:15
Alignment explanation
Indices: 210599--210630 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
210589 TCTCCTAGAA
210599 ATTTAAA-A-TTTTT
1 ATTTAAATATTTTTT
210612 ATTTAAATATTTTTT
1 ATTTAAATATTTTTT
210627 ATTT
1 ATTT
210631 TTTTTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTAAATATTTTTT
Found at i:215146 original size:23 final size:23
Alignment explanation
Indices: 215119--215171 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
215109 AAATATTGTA
*
215119 TTTTAATTAAATTATATTTAGAT
1 TTTTAATTAAATTATAATTAGAT
* *
215142 TTTTAATTAATTTATAATTATAT
1 TTTTAATTAAATTATAATTAGAT
*
215165 GTTTAAT
1 TTTTAAT
215172 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTAATTAAATTATAATTAGAT
Found at i:215190 original size:22 final size:23
Alignment explanation
Indices: 215120--215190 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
215110 AATATTGTAT
* * * **
215120 TTTAATTAAATTATATTTAGATT
1 TTTAATTAATTTATAATTATACG
*
215143 TTTAATTAATTTATAATTATATG
1 TTTAATTAATTTATAATTATACG
*
215166 TTTAA-TATTTTATAATT-TAACG
1 TTTAATTAATTTATAATTAT-ACG
215188 TTT
1 TTT
215191 TATAAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.02
22 16 0.39
23 24 0.59
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTAATTAATTTATAATTATACG
Found at i:219331 original size:26 final size:26
Alignment explanation
Indices: 219298--219354 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
219288 AACCATAAAC
*
219298 CCCAATTA-AAAGCCCAAAACATGAGG
1 CCCAATTAGAAA-CCCAAAACAAGAGG
* *
219324 CCCAATTAGCAACCCAAAATAAGAGG
1 CCCAATTAGAAACCCAAAACAAGAGG
219350 CCCAA
1 CCCAA
219355 ACCCGACAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.46, C:0.30, G:0.14, T:0.11
Consensus pattern (26 bp):
CCCAATTAGAAACCCAAAACAAGAGG
Found at i:234268 original size:33 final size:33
Alignment explanation
Indices: 234231--234299 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
234221 TCATCCGAAT
* *
234231 GAGCTATGCGAGGGCATCCGAAGGCAA-CCGAGC
1 GAGCTATGCGAGAGAATCCG-AGGCAAGCCGAGC
*
234264 GAGCTATGCGAGAGAATCCGAGGGAAGCCGAGC
1 GAGCTATGCGAGAGAATCCGAGGCAAGCCGAGC
234297 GAG
1 GAG
234300 GGTAGGTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.29, C:0.23, G:0.39, T:0.09
Consensus pattern (33 bp):
GAGCTATGCGAGAGAATCCGAGGCAAGCCGAGC
Found at i:234335 original size:29 final size:29
Alignment explanation
Indices: 234303--234358 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
234293 GAGCGAGGGT
* *
234303 AGGTCATCCGGAGTGCATGGCGACCTACA
1 AGGTCACCCGGAGGGCATGGCGACCTACA
*
234332 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCACCCGGAGGGCATGGCGACCTA
234359 TGTGTTGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.36, T:0.14
Consensus pattern (29 bp):
AGGTCACCCGGAGGGCATGGCGACCTACA
Found at i:235875 original size:20 final size:19
Alignment explanation
Indices: 235850--235903 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
235840 GCGAAATAAA
235850 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
235870 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
235890 AATCGCAACGCGAT
1 AATCGCAACGCGAT
235904 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:235914 original size:21 final size:19
Alignment explanation
Indices: 235890--236007 Score: 65
Period size: 21 Copynumber: 5.8 Consensus size: 19
235880 CAGTTCCCAG
235890 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTAT-AA
*
235910 GAATCGCAATGCGATAGTATAA
1 -AATCGCAACGCGAT--TATAA
* * ** * *
235932 ATTAGCATTGCGATTTTCTAG
1 AATCGCAACGCGA--TTATAA
* *
235953 AATCGCAACGCAAATATGAA
1 AATCGCAACGCGATTAT-AA
**
235973 AATCGCAACGCGAACATATA
1 AATCGCAACGCGATTATA-A
235993 AATCGCAACGCGATT
1 AATCGCAACGCGATT
236008 CTGACTATCG
Statistics
Matches: 73, Mismatches: 18, Indels: 13
0.70 0.17 0.12
Matches are distributed among these distances:
19 3 0.04
20 30 0.41
21 34 0.47
22 2 0.03
23 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (19 bp):
AATCGCAACGCGATTATAA
Found at i:235978 original size:20 final size:20
Alignment explanation
Indices: 235953--236005 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
235943 GATTTTCTAG
235953 AATCGCAACGC-AA-ATATGAA
1 AATCGCAACGCGAACATAT--A
235973 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
235993 AATCGCAACGCGA
1 AATCGCAACGCGA
236006 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 25 0.81
21 2 0.06
22 4 0.13
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:236058 original size:20 final size:21
Alignment explanation
Indices: 236014--236061 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
236004 GATTCTGACT
236014 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
236035 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
236055 ATCGCAA
1 ATCGCAA
236062 TGCGAATACG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:236073 original size:20 final size:21
Alignment explanation
Indices: 236033--236120 Score: 69
Period size: 20 Copynumber: 4.4 Consensus size: 21
236023 AGTATCCGTA
* *
236033 AAATCGCAACGCG-TATCCGT
1 AAATCGCAATGCGATATACGT
236053 AAATCGCAATGCGA-ATACGT
1 AAATCGCAATGCGATATACGT
* * *
236073 -ATTCGCATTGCGATTTACGT
1 AAATCGCAATGCGATATACGT
** *
236093 -AATCGCGTTGCGATTTA-GT
1 AAATCGCAATGCGATATACGT
236112 AAATCGCAA
1 AAATCGCAA
236121 CGAGATTCTG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (21 bp):
AAATCGCAATGCGATATACGT
Found at i:237009 original size:24 final size:24
Alignment explanation
Indices: 236982--237035 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
236972 GTATTCGAAA
236982 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
237006 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
237030 TTTGAT
1 TTTGAT
237036 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:239572 original size:19 final size:19
Alignment explanation
Indices: 239550--239706 Score: 163
Period size: 19 Copynumber: 8.7 Consensus size: 19
239540 CTTAATGTCT
239550 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
239569 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
239588 ATCGCAA--CG---TGAAA
1 ATCGCAATGCGAAATGAAA
* *
239602 ATCGCAACGCGAATATGAAT
1 ATCGCAATGCGAA-ATGAAA
**
239622 ATCGCAATGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
239642 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
239661 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
239675 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
239694 ATCGCAACGCGAA
1 ATCGCAATGCGAA
239707 TTTAGTTTCG
Statistics
Matches: 118, Mismatches: 8, Indels: 24
0.79 0.05 0.16
Matches are distributed among these distances:
14 22 0.19
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 55 0.47
20 28 0.24
21 3 0.03
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:239600 original size:14 final size:14
Alignment explanation
Indices: 239583--239610 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
239573 CAATGCGAAA
239583 TGAAAATCGCAACG
1 TGAAAATCGCAACG
239597 TGAAAATCGCAACG
1 TGAAAATCGCAACG
239611 CGAATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:239606 original size:33 final size:33
Alignment explanation
Indices: 239564--239702 Score: 154
Period size: 33 Copynumber: 4.0 Consensus size: 33
239554 CAATGCGAAA
239564 TGAAAATCGCAATGCGAAATGAAAATCGCAACG
1 TGAAAATCGCAATGCGAAATGAAAATCGCAACG
* *
239597 TGAAAATCGCAACGCGAATATGAATATCGCAATGCG
1 TGAAAATCGCAATGCGAA-ATGAAAATCGCAA--CG
239633 -GAAATGACTATCGCAATGCGAAATGAAAATCGCAACG
1 TG-AA--A--ATCGCAATGCGAAATGAAAATCGCAACG
* * *
239670 AGAGAATCGCAAAGCGAAATGAAAATCGCAACG
1 TGAAAATCGCAATGCGAAATGAAAATCGCAACG
239703 CGAATTTAGT
Statistics
Matches: 91, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
33 44 0.48
34 12 0.13
35 2 0.02
36 4 0.04
37 3 0.03
38 2 0.02
39 12 0.13
40 12 0.13
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
TGAAAATCGCAATGCGAAATGAAAATCGCAACG
Found at i:239646 original size:73 final size:71
Alignment explanation
Indices: 239549--239706 Score: 235
Period size: 73 Copynumber: 2.2 Consensus size: 71
239539 TCTTAATGTC
* *
239549 TATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCGCAACGCGA
1 TATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCGA
239614 ATATGAA
66 A-ATGAA
** *
239621 TATCGCAATGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCG
1 TATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCG
239686 AAATGAA
65 AAATGAA
* *
239693 AATCGCAACGCGAA
1 TATCGCAATGCGAA
239707 TTTAGTTTCG
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 3 0.04
72 25 0.32
73 50 0.64
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (71 bp):
TATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCGA
AATGAA
Found at i:239737 original size:19 final size:19
Alignment explanation
Indices: 239702--239747 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
239692 AAATCGCAAC
*
239702 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
239721 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
239740 ACGATTTT
1 GCGATTTT
239748 GTCATTGCGA
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:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:239774 original size:19 final size:19
Alignment explanation
Indices: 239750--239810 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
239740 ACGATTTTGT
239750 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
239769 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
*
239785 --TTGTGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
239802 TATTGCGAT
1 CATTGCGAT
239811 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 5 0.15
16 7 0.21
17 7 0.21
19 14 0.42
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:239936 original size:14 final size:14
Alignment explanation
Indices: 239917--239953 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
239907 CATCAATTAA
239917 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
239931 ACAAATCATCTTTT
1 ACAAATCAACATTT
239945 ACAAATCAA
1 ACAAATCAA
239954 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:241772 original size:19 final size:19
Alignment explanation
Indices: 241732--241871 Score: 102
Period size: 19 Copynumber: 7.8 Consensus size: 19
241722 TCTGGAACTT
*
241732 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
241753 ATTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
241772 AAAATCGTAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
241786 AGAATCGCAAAGCGAAATG
1 AAAATCGCAACGCGAAATG
*
241805 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
241824 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
241838 AGAATCGTAATGCGAAATG
1 AAAATCGCAACGCGAAATG
241857 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
241872 TTATAGTTTC
Statistics
Matches: 94, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
14 18 0.19
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 53 0.56
21 11 0.12
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:241814 original size:52 final size:52
Alignment explanation
Indices: 241756--241871 Score: 196
Period size: 52 Copynumber: 2.2 Consensus size: 52
241746 AAAAATGATT
*
241756 ATCGCAACGCGAAATGAAAATCGTAACGAGAGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAA
* * *
241808 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAA
241860 ATCGCAACGCGA
1 ATCGCAACGCGA
241872 TTATAGTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAA
Found at i:242389 original size:94 final size:93
Alignment explanation
Indices: 242011--242390 Score: 634
Period size: 94 Copynumber: 4.1 Consensus size: 93
242001 ATGGATTGCA
* *
242011 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
242076 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
242104 TTAATTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TT-ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
242169 TTAGCAGAATTGGCAACAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
242198 TTACTTTCAACCAAAAGACAAAATAAAGACAAATACTAACTTCACAGTGTTAAAAAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
242263 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
242292 TTACTTCAACAAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
242357 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
242386 TTACT
1 TTACT
242391 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
93 20 0.07
94 250 0.93
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:244119 original size:20 final size:21
Alignment explanation
Indices: 244087--244144 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
244077 TCTTTTGGTT
**
244087 GAAATGAAAATCGCAACGA--
1 GAAATGACTATCGCAACGACG
244106 GAGAATGACTATCGCAAC-ACG
1 GA-AATGACTATCGCAACGACG
244127 GAAATGACTATCGCAACG
1 GAAATGACTATCGCAACG
244145 CGAAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (21 bp):
GAAATGACTATCGCAACGACG
Found at i:244214 original size:17 final size:17
Alignment explanation
Indices: 244192--244226 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
244182 ATGAAAATCG
244192 CAATGCGATTTTGGTTT
1 CAATGCGATTTTGGTTT
244209 CAATGCGATTTTGGTTT
1 CAATGCGATTTTGGTTT
244226 C
1 C
244227 GCGTTGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (17 bp):
CAATGCGATTTTGGTTT
Found at i:244313 original size:20 final size:20
Alignment explanation
Indices: 244223--244358 Score: 170
Period size: 20 Copynumber: 6.8 Consensus size: 20
244213 GCGATTTTGG
*
244223 TTTCGCGTTGCGATTTTCA-
1 TTTCGTGTTGCGATTTTCAT
*
244242 TTTCGCGTTGCGATTTTCA-
1 TTTCGTGTTGCGATTTTCAT
*
244261 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
244281 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
244302 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
244322 TTTCATGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
244342 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
244359 AAGTTTAGAA
Statistics
Matches: 107, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
19 38 0.36
20 52 0.49
21 17 0.16
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:244948 original size:20 final size:20
Alignment explanation
Indices: 244935--245125 Score: 215
Period size: 20 Copynumber: 9.4 Consensus size: 20
244925 TACGTATTGT
244935 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
244955 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * * *
244975 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
**
244995 CGTTGCGATTTATAGATACG
1 CGTTGCGATTTACGGATACG
* * *
245015 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
245035 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * *
245055 CGTTACGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
245075 TCGTAT-CGATTTACGGATACG
1 -CGT-TGCGATTTACGGATACG
*
245096 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
245117 CGTTGCGAT
1 CGTTGCGAT
245126 AGTCAGAATC
Statistics
Matches: 141, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.01
20 105 0.74
21 34 0.24
22 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:245085 original size:41 final size:40
Alignment explanation
Indices: 244935--245125 Score: 258
Period size: 40 Copynumber: 4.7 Consensus size: 40
244925 TACGTATTGT
* * *
244935 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* **
244975 CATTGCGATTTACGTATTCTCGTTGCGATTTATAGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
245015 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* *
245055 CGTTACGATTTTACGTATTGTCGTAT-CGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGT-TGCGATTTACGGATACG
* *
245096 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT
245126 AGTCAGAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
40 79 0.59
41 53 0.40
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:245996 original size:22 final size:22
Alignment explanation
Indices: 245964--246014 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
245954 TCACTTTATG
* *
245964 CGACGAAATCCATCCCCATCTC
1 CGACGACATCCATCCCCATATC
*
245986 CGACGACATCCGTCCCCATATC
1 CGACGACATCCATCCCCATATC
*
246008 CGGCGAC
1 CGACGAC
246015 CCCCCTCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.45, G:0.16, T:0.16
Consensus pattern (22 bp):
CGACGACATCCATCCCCATATC
Found at i:246191 original size:20 final size:20
Alignment explanation
Indices: 246168--246396 Score: 85
Period size: 20 Copynumber: 11.3 Consensus size: 20
246158 AGCTGTTTTA
246168 CGAAATTAAAATTCGTGTTG
1 CGAAATTAAAATTCGTGTTG
*
246188 CG-AATTCAGAAA-TCGAGTTG
1 CGAAATT-A-AAATTCGTGTTG
* * *
246208 CGAAAATAAAATTCGCGTTA
1 CGAAATTAAAATTCGTGTTG
* *
246228 CG-AATTAGAAAATCTTGTTG
1 CGAAATTA-AAATTCGTGTTG
*** **
246248 CGAAAAGGAAATTTATGTTG
1 CGAAATTAAAATTCGTGTTG
* * *
246268 CGAATTTAAAAATCGTGTTA
1 CGAAATTAAAATTCGTGTTG
* *
246288 CGAAA-AAGAAATTCGTCTTG
1 CGAAATTA-AAATTCGTGTTG
* *
246308 CGAAATCGTCAAATTCGAGTTG
1 CGAAAT--TAAAATTCGTGTTG
* ** * *
246330 TG-AATTTTACTTATGTGTTG
1 CGAAATTAAAATT-CGTGTTG
*
246350 CG-AATTCCAAATTCGTGTTG
1 CGAAATT-AAAATTCGTGTTG
* * *
246370 AGAATTTGAAAACT-GTGTTG
1 CGAAATT-AAAATTCGTGTTG
246390 CGAAATT
1 CGAAATT
246397 GGAGTTTGTG
Statistics
Matches: 146, Mismatches: 50, Indels: 26
0.66 0.23 0.12
Matches are distributed among these distances:
19 16 0.11
20 98 0.67
21 21 0.14
22 11 0.08
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
CGAAATTAAAATTCGTGTTG
Found at i:246260 original size:40 final size:40
Alignment explanation
Indices: 246176--246311 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
246166 TACGAAATTA
*
246176 AAATTCGTGTTGCGAATTCAG-AAATCGAGTTGCGAAAATA-
1 AAATTCGTGTTGCGAATT-AGAAAATCGTGTTGCGAAAA-AG
* * * *
246216 AAATTCGCGTTACGAATTAGAAAATCTTGTTGCGAAAAGG
1 AAATTCGTGTTGCGAATTAGAAAATCGTGTTGCGAAAAAG
** *
246256 AAATTTATGTTGCGAATTTA-AAAATCGTGTTACGAAAAAG
1 AAATTCGTGTTGCGAA-TTAGAAAATCGTGTTGCGAAAAAG
*
246296 AAATTCGTCTTGCGAA
1 AAATTCGTGTTGCGAA
246312 ATCGTCAAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 73 0.94
41 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (40 bp):
AAATTCGTGTTGCGAATTAGAAAATCGTGTTGCGAAAAAG
Found at i:251047 original size:23 final size:23
Alignment explanation
Indices: 251000--251049 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
250990 AATAACATAT
**
251000 TAGGTAGCGCTTAGATAATGTAA
1 TAGGTAGCGCTTAGATAATAAAA
*
251023 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTAGATAATAAAA
251046 TAGG
1 TAGG
251050 CATTTAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (23 bp):
TAGGTAGCGCTTAGATAATAAAA
Found at i:251104 original size:23 final size:23
Alignment explanation
Indices: 251078--251125 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
251068 ATCAAGTACA
251078 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
251101 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
251124 AT
1 AT
251126 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:251109 original size:87 final size:87
Alignment explanation
Indices: 250963--251125 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
250953 TATGTTATAT
*
250963 CATTTAACCAGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTAGATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGT
251028 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
251050 CATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGT
251115 AGCGCTTATAT
66 AGCGCTTATAT
251126 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:251599 original size:201 final size:197
Alignment explanation
Indices: 251153--251599 Score: 494
Period size: 197 Copynumber: 2.2 Consensus size: 197
251143 AAAACGGTAA
* * * *
251153 ATTTAAACCGGTTACATT-ATAAATTGACCTATTACATTATAAATATCGGTTTCGATGTTTTCAG
1 ATTTTAACCGGTTACATTGA-AAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTCAG
* *** *
251217 GATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCAACTCGTTTGTGTTTTATTTTGGAA
65 GATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCAACTCATTTGCCATTCATTTTGGAA
* * * * *
251282 AAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACATATTTACTAATTAACCGG
130 AAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACATATTTACTAATGAACCGA
251347 TAT
195 TAT
* * * * *
251350 ATTTTAAGCGGTTACATTGTAAATTTACCTGTTAAATAATAATTATCGATTTCGATG-TTTCGAG
1 ATTTTAACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTC-AG
* *
251414 GATCGATAC-TTTTTAAAAAATGTATCGACACTTTATGCGTAG-ACCTCATTTGCCATTCATTTT
65 GATCGATACAATTTT---AAATGTATCGACACTTTATGCGT-GCAACTCATTTGCCATTCATTTT
* * * * *
251477 -GAAAAAATGTATCGACACAAATTAAACAAAGTGTCGATACTTTATGTTGACCTATTCT-CTCAT
126 GGAAAAAA-GTATCGACACAAATTAAA-AAAGTGTCGATACATAATGTAGACATATT-TACTAAT
*
251540 GATCCCGATAT
188 GA-ACCGATAT
*
251551 ATTTCT-ACCGGTTACATTGAAAATTTACCTATTACATTATATTTATCGA
1 ATTT-TAACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGA
251600 CACAAAATCT
Statistics
Matches: 206, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
196 8 0.04
197 58 0.28
198 7 0.03
199 54 0.26
200 30 0.15
201 48 0.23
202 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (197 bp):
ATTTTAACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTCAGG
ATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCAACTCATTTGCCATTCATTTTGGAAA
AAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACATATTTACTAATGAACCGAT
AT
Found at i:256722 original size:182 final size:179
Alignment explanation
Indices: 256411--257000 Score: 829
Period size: 182 Copynumber: 3.2 Consensus size: 179
256401 ATTAAAGTAC
* * * * * * *
256411 CGACACTTTCAACATAACTGGTAGCGCTTTACCGGTTTTGTCGTTTCGATACCGGTTTTATCATA
1 CGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * * *
256476 TTTTTACCTATTATATTGTTATGGATCGATACATTTTCTTAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCGA-TATATTGCTATGGATCGATACATTTT-ATAAAGTATCGACAC-TTTTAGGCGCT
* * *
256541 ATAATTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
128 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * ** *
256593 CGACACTTTCAATATATCCGGTATCTTTTTACCGGTTTTATCATTTCGAGACCTCTTTTGTCATA
1 CGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
*
256658 TTATTACCGGATATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTCAGGCGCT
66 TTATTACC-GATATATTGCTATGGATCGATACATTT-TATAAAGTATCGACACTTTT-AGGCGCT
256723 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
128 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* ** *
256775 CGACACTTTCAATATATCTGATAGCTTTTTACCGGTTTTATCATTTCGAGATCTGTTTTGTCATA
1 CGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * * * *
256840 TTATTATCTGTTATATTGCTATAGATCGACACATTTTTATAAAGTATCGACACCTTTTAGACGCT
66 TTATTA-CCGATATATTGCTATGGATCGATACA-TTTTATAAAGTATCGACA-CTTTTAGGCGCT
*
256905 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGACACTTATATTAATTTAT
128 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
256957 CGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCAT
1 CGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCAT
257001 ATTTTTACCT
Statistics
Matches: 367, Mismatches: 35, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
181 4 0.01
182 352 0.96
183 11 0.03
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (179 bp):
CGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
TTATTACCGATATATTGCTATGGATCGATACATTTTATAAAGTATCGACACTTTTAGGCGCTATA
ACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:259794 original size:15 final size:16
Alignment explanation
Indices: 259768--259797 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
259758 GGTCAAAAAA
259768 TATTATTAAATATTAT
1 TATTATTAAATATTAT
259784 TATTA-TAAATATTA
1 TATTATTAAATATTA
259798 AATAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTAAATATTAT
Found at i:262572 original size:2 final size:2
Alignment explanation
Indices: 262560--262599 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
262550 TCATTTATCC
*
262560 AT AT AT GT 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
262600 CCATTATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265266 original size:18 final size:19
Alignment explanation
Indices: 265240--265292 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
265230 GGATAAACAA
265240 TGGTCCTTCGGGACAT-AG
1 TGGTCCTTCGGGACATCAG
* *
265258 TGGTTCTTCGGAACAATCAG
1 TGGTCCTTCGGGAC-ATCAG
265278 TGGTCCTTCGGGACA
1 TGGTCCTTCGGGACA
265293 AATATTCAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 12 0.41
19 3 0.10
20 14 0.48
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (19 bp):
TGGTCCTTCGGGACATCAG
Found at i:265666 original size:4 final size:4
Alignment explanation
Indices: 265659--266284 Score: 1150
Period size: 4 Copynumber: 159.2 Consensus size: 4
265649 GATAATGACG
265659 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265707 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265755 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265803 TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG--
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265847 TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265893 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265941 TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
265987 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
266035 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG--
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
266081 TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
266127 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
266175 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
266223 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
266271 TATA TGTA GTGTA T
1 TGTA TGTA -TGTA T
266285 TTGTTGCATG
Statistics
Matches: 607, Mismatches: 2, Indels: 26
0.96 0.00 0.04
Matches are distributed among these distances:
2 12 0.02
4 591 0.97
5 4 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:274423 original size:19 final size:20
Alignment explanation
Indices: 274379--274420 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
274369 GAATTCGTAC
*
274379 AAAATTGTTATCGGTTATTA
1 AAAATTGTTATCGGGTATTA
*
274399 ACAATT-TTAT-GGGTATTA
1 AAAATTGTTATCGGGTATTA
274417 AAAA
1 AAAA
274421 ATTCAATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
AAAATTGTTATCGGGTATTA
Found at i:274822 original size:27 final size:27
Alignment explanation
Indices: 274782--274839 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
274772 TTGCTAGGTG
*
274782 AGTGATGTTGTGGACTTTCAAGTTCAA
1 AGTGATGTTATGGACTTTCAAGTTCAA
*
274809 AGTGATGTTATGGAGTTTCAAGTTCAA
1 AGTGATGTTATGGACTTTCAAGTTCAA
274836 AGTG
1 AGTG
274840 GTGATGGCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.36
Consensus pattern (27 bp):
AGTGATGTTATGGACTTTCAAGTTCAA
Found at i:275128 original size:2 final size:2
Alignment explanation
Indices: 275121--275145 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
275111 AAAAGAGTAT
275121 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 T
275146 TAATATTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:275611 original size:61 final size:61
Alignment explanation
Indices: 275511--275638 Score: 229
Period size: 61 Copynumber: 2.1 Consensus size: 61
275501 TTCTTTTTAG
* *
275511 TAAATTACACGAGTAATACTAAATTATTATTATTTATTTTGATCATGAAATTGAATGAATT
1 TAAAGTACACGAGTAATACTAAATTACTATTATTTATTTTGATCATGAAATTGAATGAATT
*
275572 TAAAGTACACGAGTAATACTAAATTACTATTATTTATTTTGATCATGAAATTGAATGAGTT
1 TAAAGTACACGAGTAATACTAAATTACTATTATTTATTTTGATCATGAAATTGAATGAATT
275633 TAAAGT
1 TAAAGT
275639 GTACGCTGCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (61 bp):
TAAAGTACACGAGTAATACTAAATTACTATTATTTATTTTGATCATGAAATTGAATGAATT
Found at i:277852 original size:25 final size:24
Alignment explanation
Indices: 277798--277855 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
277788 TATTGATTTA
* *
277798 AAAATAATTTAAATTTTTTTATTT
1 AAAATAATTTAAATATTTTTAATT
277822 AAAAATAATTTAAAATAATTTTTAATT
1 -AAAATAATTT-AAAT-ATTTTTAATT
277849 -AAATAAT
1 AAAATAAT
277856 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 17 0.59
26 4 0.14
27 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATAATTTAAATATTTTTAATT
Found at i:282036 original size:55 final size:53
Alignment explanation
Indices: 281901--282215 Score: 303
Period size: 55 Copynumber: 5.7 Consensus size: 53
281891 CTTCAAATGG
* * *
281901 CGGGTCCGCTCCCTATTCTTTCAAGGAGTATA-AGACTCGAACAATCTTTGGA-AAA
1 CGGGTCCGCT-CCTATTCATTCAGGGAGTATAGA-ACTCGAACAATC-TT-CATAAA
* * * *
281956 TGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAATAATCTTCAATAAA
1 CGGGTCCGCT-CCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTC-ATAAA
* *
282011 CGGGTCCGCTACCTAGTCATCCAGGGAGTATAGAACTCGAACAATCTTCATAAAA
1 CGGGTCCGCT-CCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAT-AAA
* * * *
282066 CGGATCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAGAATCTTCATAAAA
1 CGGGTCCGCTC-CTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAT-AAA
* *
282121 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAA
1 CGGGTCCGCTC-CTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAT-AAA
* * * * *
282176 TGAGTCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGA
1 CGGGTCCGCTC-CTATTCATTCAGGGAGTATAGAACTCGA
282216 TCTTCATAAA
Statistics
Matches: 230, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
54 6 0.03
55 223 0.97
56 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (53 bp):
CGGGTCCGCTCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
Found at i:282082 original size:110 final size:108
Alignment explanation
Indices: 281901--282215 Score: 368
Period size: 110 Copynumber: 2.9 Consensus size: 108
281891 CTTCAAATGG
* * *** *
281901 CGGGTCCGCTCCCTATTCTTTCAAGGAGTATA-AGACTCGAACAATCTTTGGAAAATGTG-TCTG
1 CGGGTCCGCT-CCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCATAAAA-G-GATCCG
* * * *
281964 CTCCCTATTCATTCAGGGAGTATA-AGACTCGAATAATCTTCA-ATAAA
62 CTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAGAATCTTCATA-AAA
* *
282011 CGGGTCCGCTACCTAGTCATCCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGATCCGCT
1 CGGGTCCGCT-CCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAA-GGATCCGCT
282076 CTCTATTCCTTCAGAGAGTATAGAACTCGAAGAATCTTCATAAAA
64 CTCTATTCCTTCAGAGAGTATAGAACTCGAAGAATCTTCATAAAA
* * *
282121 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGAGTCCGCT
1 CGGGTCCGCTC-CTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAAGGA-TCCGCT
*
282186 CTCTATTCCTTTAGAGAGTATAGAACTCGA
64 CTCTATTCCTTCAGAGAGTATAGAACTCGA
282216 TCTTCATAAA
Statistics
Matches: 179, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
109 4 0.02
110 172 0.96
111 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (108 bp):
CGGGTCCGCTCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAAGGATCCGCTCT
CTATTCCTTCAGAGAGTATAGAACTCGAAGAATCTTCATAAAA
Found at i:282207 original size:165 final size:165
Alignment explanation
Indices: 281905--282215 Score: 362
Period size: 165 Copynumber: 1.9 Consensus size: 165
281895 AAATGGCGGG
* ** * * *
281905 TCCGCTCCCTATTCTTTCAAGGAGTATAAGACTCGAACAATCTTTGGAAAATGTGTCTGCTCCCT
1 TCCGCTCCCTATTCCTTCAAGGAGTATAAGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCT
* * *
281970 ATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAATAAACGGGTCCGCTACCTAGTCATCCAG
66 ATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGAGTCCGCTACCTAGTCATCCAG
*
282035 GGAGTATAGAACTCGAACAATCTTCATAAAACGGA
131 AGAGTATAGAACTCGAACAATCTTCATAAAACGGA
* * * *
282070 TCCGCTCTCTATTCCTTC-AGAGAGTAT-AGAACTCGAAGAATCTTCATAAAACGGGTCCGCTCT
1 TCCGCTCCCTATTCCTTCAAG-GAGTATAAG-ACTCGAACAATCTTCAGAAAACGGGTCCGCTCC
* * * *
282133 CTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-ATAAAATGAGTCCGCT-CTCTATTCC
64 CTATTCATTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAACGAGTCCGCTAC-CTAGTCA
**
282195 TTTAGAGAGTATAGAACTCGA
126 TCCAGAGAGTATAGAACTCGA
282216 TCTTCATAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
164 9 0.07
165 112 0.93
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (165 bp):
TCCGCTCCCTATTCCTTCAAGGAGTATAAGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCT
ATTCATTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGAGTCCGCTACCTAGTCATCCAG
AGAGTATAGAACTCGAACAATCTTCATAAAACGGA
Found at i:283550 original size:45 final size:45
Alignment explanation
Indices: 283483--283568 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
283473 TAAACAAAAC
*
283483 TCAAGTCGCCCTTCGCGAGTTTTCAACTTGAGA-CCTCCTTTGGTT
1 TCAAGACGCCCTTCGCGAGTTTTCAACTTGA-ACCCTCCTTTGGTT
** * *
283528 TCAAGACGCCCTTTTCGGGTTTTCATCTTGAACCCTCCTTT
1 TCAAGACGCCCTTCGCGAGTTTTCAACTTGAACCCTCCTTT
283569 TATTTCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.37
Consensus pattern (45 bp):
TCAAGACGCCCTTCGCGAGTTTTCAACTTGAACCCTCCTTTGGTT
Found at i:283599 original size:16 final size:16
Alignment explanation
Indices: 283578--283624 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
283568 TTATTTCTTT
283578 TTCTTTTCCTTTTTTC
1 TTCTTTTCCTTTTTTC
*
283594 TTCTTTCTTCTTTTTTC
1 TTCTTT-TCCTTTTTTC
* *
283611 AT-TTTTCATTTTTT
1 TTCTTTTCCTTTTTT
283625 TATTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.27
16 9 0.35
17 10 0.38
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTTCCTTTTTTC
Found at i:283629 original size:15 final size:15
Alignment explanation
Indices: 283604--283641 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
283594 TTCTTTCTTC
*
283604 TTTTTTCATTTTTCA
1 TTTTTTTATTTTTCA
283619 TTTTTTTATTTTTCA
1 TTTTTTTATTTTTCA
283634 TTTATTTT
1 TTT-TTTT
283642 TCATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTATTTTTCA
Found at i:283630 original size:7 final size:7
Alignment explanation
Indices: 283605--283650 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
283595 TCTTTCTTCT
283605 TTTTTCA
1 TTTTTCA
283612 TTTTTCA
1 TTTTTCA
*
283619 TTTTTTTA
1 -TTTTTCA
283627 TTTTTCA
1 TTTTTCA
283634 --TTT-A
1 TTTTTCA
283638 TTTTTCA
1 TTTTTCA
283645 TTTTTC
1 TTTTTC
283651 TTCAAGCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
4 1 0.03
5 3 0.09
6 3 0.09
7 20 0.61
8 6 0.18
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:283639 original size:11 final size:11
Alignment explanation
Indices: 283623--283647 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
283613 TTTTCATTTT
283623 TTTATTTTTCA
1 TTTATTTTTCA
283634 TTTATTTTTCA
1 TTTATTTTTCA
283645 TTT
1 TTT
283648 TTCTTCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTTTCA
Found at i:293365 original size:45 final size:47
Alignment explanation
Indices: 293298--293404 Score: 164
Period size: 45 Copynumber: 2.3 Consensus size: 47
293288 CCATGCTTTG
293298 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC-
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
293345 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
293391 TTTATTCGAAAAAT
1 -TTATTCAAAAAAT
293405 GAAAATAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
45 28 0.50
46 9 0.16
47 19 0.34
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (47 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:301037 original size:21 final size:21
Alignment explanation
Indices: 300995--301037 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
300985 TTTCTGGGCT
* *
300995 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
301016 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
301037 A
1 A
301038 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:301089 original size:20 final size:20
Alignment explanation
Indices: 301064--301101 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
301054 GAATGCTAGA
*
301064 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
301084 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
301102 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:301998 original size:32 final size:32
Alignment explanation
Indices: 301957--302053 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
301947 GAGTCGAGGG
301957 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
301989 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
302020 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
302052 TT
1 TT
302054 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:302029 original size:31 final size:31
Alignment explanation
Indices: 301956--302056 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
301946 AGAGTCGAGG
301956 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
301987 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
302019 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
302050 GTTTACC
1 GTTTACC
302057 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:302088 original size:30 final size:30
Alignment explanation
Indices: 302044--302137 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
302034 AAGGAACATA
302044 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
302075 TGGACAGTTACCGATGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
302105 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
302134 TGGA
1 TGGA
302138 TAGGTCCTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.28
30 34 0.60
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:306574 original size:23 final size:24
Alignment explanation
Indices: 306548--306597 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
306538 CCACTAGGGG
306548 CTATGA-AATTTGTCCCGAAGGAC
1 CTATGAGAATTTGTCCCGAAGGAC
*
306571 CTATGAGTGTATTTGTCCCGAAGGAC
1 CTATGA--GAATTTGTCCCGAAGGAC
306597 C
1 C
306598 ACTCCTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
26 17 0.74
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
CTATGAGAATTTGTCCCGAAGGAC
Found at i:314417 original size:2 final size:2
Alignment explanation
Indices: 314410--314456 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
314400 AACATGTTTG
314410 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
314452 AT AT A
1 AT AT A
314457 AGCCAAATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:321241 original size:21 final size:21
Alignment explanation
Indices: 321200--321241 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
321190 AGTCATAATC
*
321200 GTTTTTAAATTAAGATTTTATT
1 GTTTTTAAA-TAAAATTTTATT
321222 GTTTTTAAA-AAAATTGTTAT
1 GTTTTTAAATAAAATT-TTAT
321242 GATAGCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
GTTTTTAAATAAAATTTTATT
Found at i:325723 original size:20 final size:20
Alignment explanation
Indices: 325698--325736 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
325688 GTGAAACTTA
325698 GAAGAAAAACATTTTCAAAT
1 GAAGAAAAACATTTTCAAAT
*
325718 GAAGAAAAGCATTTTCAAA
1 GAAGAAAAACATTTTCAAA
325737 CAAGATAATT
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:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (20 bp):
GAAGAAAAACATTTTCAAAT
Found at i:325741 original size:19 final size:20
Alignment explanation
Indices: 325699--325741 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
325689 TGAAACTTAG
*
325699 AAGAAAAACATTTTCAAATG
1 AAGAAAAACATTTTCAAATC
*
325719 AAGAAAAGCATTTTCAAA-C
1 AAGAAAAACATTTTCAAATC
325738 AAGA
1 AAGA
325742 TAATTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (20 bp):
AAGAAAAACATTTTCAAATC
Found at i:326345 original size:35 final size:35
Alignment explanation
Indices: 326294--326397 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 35
326284 GTTTTTCTTG
*
326294 AAACAAAATTTTGTCTCGCTTGAGACAGTTTTCTAA
1 AAAC-AAATTTTGTCTCGCTTGAGACAATTTTCTAA
* *
326330 AAACAAATTTTGTCTCGCTTGAGACAATTTCTTTCA
1 AAACAAATTTTGTCTCGCTTGAGACAATTT-TCTAA
* * * *
326366 AAACAAACTTCGTCTCACTTGAGACATTTTTC
1 AAACAAATTTTGTCTCGCTTGAGACAATTTTC
326398 CTTTAAGATA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
35 26 0.44
36 33 0.56
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (35 bp):
AAACAAATTTTGTCTCGCTTGAGACAATTTTCTAA
Found at i:326475 original size:103 final size:102
Alignment explanation
Indices: 326365--326558 Score: 259
Period size: 102 Copynumber: 1.9 Consensus size: 102
326355 AATTTCTTTC
* *
326365 AAAACAAACTTCGTCTCACTTGAGACATTTTTCCT-TTAAGATACAAAATTTGAATTTGTT-TCA
1 AAAACAAACTTCGTCTCACTTGAGACATTTTTCCTATGAA-ATA-AAAATTTAAATTTGTTGT-A
* * *
326428 CATT-AAACAAAGTTGATCTCATTTGAGATCGCTTTCTCAA
63 C-TTGAAACAAAATTAATCTCACTTGAGATCGCTTTCTCAA
* * *
326468 AAAACAAACTTCGTCTCGCTTGAGACATTTTTTCTATGAAATAAAATTTTAAATTTGTTGTACTT
1 AAAACAAACTTCGTCTCACTTGAGACATTTTTCCTATGAAATAAAAATTTAAATTTGTTGTACTT
326533 GAAACAAAATTAATCTCACTTGAGAT
66 GAAACAAAATTAATCTCACTTGAGAT
326559 TTTTAAAATT
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
101 2 0.03
102 38 0.47
103 37 0.46
104 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (102 bp):
AAAACAAACTTCGTCTCACTTGAGACATTTTTCCTATGAAATAAAAATTTAAATTTGTTGTACTT
GAAACAAAATTAATCTCACTTGAGATCGCTTTCTCAA
Found at i:326698 original size:20 final size:21
Alignment explanation
Indices: 326659--326698 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
326649 TTTGAATCTT
326659 TTTCTCTTGAAACGAATTTTG
1 TTTCTCTTGAAACGAATTTTG
*
326680 TTTCTCTTGAGAC-AATTTT
1 TTTCTCTTGAAACGAATTTT
326699 CCAAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (21 bp):
TTTCTCTTGAAACGAATTTTG
Found at i:327070 original size:29 final size:29
Alignment explanation
Indices: 326977--327262 Score: 206
Period size: 29 Copynumber: 9.6 Consensus size: 29
326967 TTTAAGACAA
* * *
326977 TTTCTCTTAAAACAAACATCTTTGAGATTG
1 TTTCTTTTGAAACAAAAATCTTTGAG-TTG
** *
327007 TTTCCCTTAAAACAAAACCTATCTTTGAGTTTG
1 TTTCTTTTGAAACAAAA---ATCTTTGAG-TTG
* * *
327040 TTTCTCTTGAAACAAAAGTCTGTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
* *
327069 TTTCTTTTGAAATAAAAATCTGTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
*
327098 TTTCTTTTGAAATAAAAATCTTTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
*
327127 TTTCTTTTGAAA-AAAATTCTTTGAGTCTG
1 TTTCTTTTGAAACAAAAATCTTTGAGT-TG
* *
327156 TTTCTTTTG-AACCAAAGT-TTT--GTT-
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
* ** **
327180 TCTCTTAAGACAATTTCGTGAAAAAATCTTTGAGTCA
1 TTTCTTTTGA-AA---C----AAAAATCTTTGAGTTG
*
327217 TTTCTTTTGAAACCAAAATCTTTGAGTTTG
1 TTTCTTTTGAAACAAAAATCTTTGAG-TTG
327247 TTTCTTTTGAAACAAA
1 TTTCTTTTGAAACAAA
327263 GTTTTGTCTC
Statistics
Matches: 210, Mismatches: 27, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
24 6 0.03
25 1 0.00
26 4 0.02
28 18 0.09
29 97 0.46
30 38 0.18
33 32 0.15
34 3 0.01
36 4 0.02
37 7 0.03
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTG
Found at i:327265 original size:91 final size:90
Alignment explanation
Indices: 327111--327350 Score: 299
Period size: 91 Copynumber: 2.6 Consensus size: 90
327101 CTTTTGAAAT
* *
327111 AAAAATCTTTGAGTTGTTTCTTTTGAAAAAAATTCTTTGAGTCTGTTTCTTTTGAACCAAAGTTT
1 AAAAATCTTTGAG-TCTTTCTTTTGAAAAAAA-TCTTTGAGTCTGTTTCTTTTGAAACAAAGTTT
*
327176 TGTTTCTCTTAAGACA-ATTTCGTGA-
64 TGTCTCTCTTAAGACACATTTCGTGAG
*
327201 AAAAATCTTTGAGTCATTTCTTTTGAAACCAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAGTT
1 AAAAATCTTTGAGTC-TTTCTTTTGAAA--AAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTT
* * *
327266 TTGTCTCTCTTGAGACAGCTTTTTCTTGAG
63 TTGTCTCTCTTAAGACA-C-ATTTCGTGAG
*
327296 AAAAATCTTTGAGTCTGTTCCTTTTG--AAAAATCTTTGAGTCTGTTCCTTTTGAAA
1 AAAAATCTTTGAGTCT-TT-CTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAA
327351 AAACCAACCT
Statistics
Matches: 132, Mismatches: 9, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
89 1 0.01
90 25 0.19
91 44 0.33
92 30 0.23
94 9 0.07
95 17 0.13
96 6 0.05
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (90 bp):
AAAAATCTTTGAGTCTTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTG
TCTCTCTTAAGACACATTTCGTGAG
Found at i:327328 original size:26 final size:26
Alignment explanation
Indices: 327295--327352 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
327285 TTTTTCTTGA
327295 GAAAAATCTTTGAGTCTGTTCCTTTT
1 GAAAAATCTTTGAGTCTGTTCCTTTT
327321 GAAAAATCTTTGAGTCTGTTCCTTTT
1 GAAAAATCTTTGAGTCTGTTCCTTTT
327347 GAAAAA
1 GAAAAA
327353 ACCAACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (26 bp):
GAAAAATCTTTGAGTCTGTTCCTTTT
Found at i:327363 original size:31 final size:29
Alignment explanation
Indices: 327296--327414 Score: 104
Period size: 26 Copynumber: 4.2 Consensus size: 29
327286 TTTTCTTGAG
*
327296 AAAAATCTTTGAGTCTGTTCCTTTTG---
1 AAAAACCTTTGAGTCTGTTCCTTTTGAAA
*
327322 AAAAATCTTTGAGTCTGTTCCTTTTGAAA
1 AAAAACCTTTGAGTCTGTTCCTTTTGAAA
* *
327351 AAACCAACCTTTGAGAT-TGTTTCTTTTGAGA
1 AAA--AACCTTTGAG-TCTGTTCCTTTTGAAA
* * *
327382 AAAATCC-TTGAGTCTGTTTCTTTGGAAA
1 AAAAACCTTTGAGTCTGTTCCTTTTGAAA
*
327410 CAAAA
1 AAAAA
327415 TTTACAATCT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
26 26 0.33
27 1 0.01
28 20 0.26
29 6 0.08
31 24 0.31
32 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (29 bp):
AAAAACCTTTGAGTCTGTTCCTTTTGAAA
Found at i:327692 original size:94 final size:94
Alignment explanation
Indices: 327531--327753 Score: 281
Period size: 94 Copynumber: 2.4 Consensus size: 94
327521 TGTCATCTCT
* * * *
327531 TGACCAGATCT-CTCCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGATGCCCTCATCACG
1 TGACCAGATCTCCT-CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGATGCCCTCATCAAG
* * * *
327595 TAGGAACCGTGTTTTCTCC-CTTCCTATAGA
65 TAGGAACCGAGTTATCACCAC-TCCTAAAGA
* *
327625 TGACCAGATCTCCTCATCACGTAGGATCCGTGTCAACCATAGATAACCAG-TCGTCCTCATCAAG
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGAT-GCCCTCATCAAG
327689 TAGGAACCGAGTTATCACCACTCCTAAAGA
65 TAGGAACCGAGTTATCACCACTCCTAAAGA
* * *
327719 TGACCAGAACTCTTCATCACGTATGAGCCGTGTCA
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
327754 TCCCCCGACC
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 108 0.96
95 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (94 bp):
TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGATGCCCTCATCAAGT
AGGAACCGAGTTATCACCACTCCTAAAGA
Found at i:327776 original size:40 final size:39
Alignment explanation
Indices: 327720--327838 Score: 132
Period size: 40 Copynumber: 2.9 Consensus size: 39
327710 TCCTAAAGAT
* *
327720 GACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC-C
1 GACCAGATCTCCTCATCACGTA-GAGCCGTGTCA-CCCCAC
*
327760 GACCAGATCTCCTCATCGCGTAGGAGCCGTGTCACCCCTAGAC
1 GACCAGATCTCCTCATCACGTA-GAGCCGTGTCACCCC---AC
* *
327803 GACCAGATTTCCTCATCACGTAGAACCGTGTCACCC
1 GACCAGATCTCCTCATCACGTAGAGCCGTGTCACCC
327839 TTAGACGACC
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 4 0.06
40 30 0.44
42 13 0.19
43 21 0.31
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (39 bp):
GACCAGATCTCCTCATCACGTAGAGCCGTGTCACCCCAC
Found at i:327845 original size:42 final size:43
Alignment explanation
Indices: 327621--327862 Score: 172
Period size: 43 Copynumber: 5.5 Consensus size: 43
327611 TCCCTTCCTA
* * * *
327621 TAGATGACCAGATCTCCTCATCACGTAGGATCCGTGTCAACCA
1 TAGACGACCAGATCTCCTCATCACGTAGGAACCGTGTCACCCC
** * *
327664 TAGATAACCAG-TCGTCCTCATCAAGTAGGAACCGAGTTATCACCACTCC
1 TAGACGACCAGATC-TCCTCATCACGTAGGAACC--G-TGTCA-C-C-CC
* * * * *
327713 TAAAGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 T--AGACGACCAGATCTCCTCATCACGTAGGAACCGTGTCA-CCCC
* *
327759 ----CGACCAGATCTCCTCATCGCGTAGGAGCCGTGTCACCCC
1 TAGACGACCAGATCTCCTCATCACGTAGGAACCGTGTCACCCC
* *
327798 TAGACGACCAGATTTCCTCATCACGTA-GAACCGTGTCACCCT
1 TAGACGACCAGATCTCCTCATCACGTAGGAACCGTGTCACCCC
* * *
327840 TAGACGACCCGAACTCTTCATCA
1 TAGACGACCAGATCTCCTCATCA
327863 TGTATGAGAA
Statistics
Matches: 158, Mismatches: 27, Indels: 29
0.74 0.13 0.14
Matches are distributed among these distances:
39 4 0.03
40 30 0.19
42 34 0.22
43 48 0.30
45 1 0.01
46 6 0.04
47 1 0.01
48 6 0.04
49 3 0.02
51 24 0.15
52 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (43 bp):
TAGACGACCAGATCTCCTCATCACGTAGGAACCGTGTCACCCC
Found at i:364471 original size:158 final size:160
Alignment explanation
Indices: 364177--364474 Score: 467
Period size: 158 Copynumber: 1.9 Consensus size: 160
364167 TAGAGACTGG
**
364177 ATCCATGCAATGATGAGAAACCTTTTCAATTTGATTACCATTATACAAGTTACAAACATAAGCTA
1 ATCCATGCAATGACAAGAAACCTTTTCAATTTGATTACC----TACAAGTTACAAACATAAGCTA
* * *
364242 ATAATTACTAATTACAATGGGAGAATAAAATCTATAAAAATATGTAATTAACATGTTGAGTCACT
62 ATAATTACTAATTACAATGGAAGAATAAAAGCTATAAAAATATCTAATTAACATGTTGAGTCACT
364307 AACATGTAATATGGAATAAAAAAATGTAATTAAC
127 AACATGTAATATGGAATAAAAAAATGTAATTAAC
364341 ATCCATGCAATGACAAGAAACCTTTTCAATTTGATTA-C-ACAAGTTACAAACATAAGCT-ATGA
1 ATCCATGCAATGACAAGAAACCTTTTCAATTTGATTACCTACAAGTTACAAACATAAGCTAAT-A
* *
364403 ATTACTAATTACAATGGAAGAATGAAAGCTATACAAATATCTAATTAACATGTTGAGTCACTAAC
65 ATTACTAATTACAATGGAAGAATAAAAGCTATAAAAATATCTAATTAACATGTTGAGTCACTAAC
364468 ATGTAAT
130 ATGTAAT
364475 CTGAAAAAAA
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
157 2 0.02
158 88 0.70
163 1 0.01
164 35 0.28
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.30
Consensus pattern (160 bp):
ATCCATGCAATGACAAGAAACCTTTTCAATTTGATTACCTACAAGTTACAAACATAAGCTAATAA
TTACTAATTACAATGGAAGAATAAAAGCTATAAAAATATCTAATTAACATGTTGAGTCACTAACA
TGTAATATGGAATAAAAAAATGTAATTAAC
Found at i:368475 original size:2 final size:2
Alignment explanation
Indices: 368468--368492 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
368458 CCGATTAGTT
368468 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 T
368493 GATGGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:368507 original size:16 final size:16
Alignment explanation
Indices: 368488--368519 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
368478 TATATATATA
368488 TATATGATGGATTATT
1 TATATGATGGATTATT
*
368504 TATATTATGGATTATT
1 TATATGATGGATTATT
368520 AGATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (16 bp):
TATATGATGGATTATT
Found at i:368798 original size:27 final size:27
Alignment explanation
Indices: 368768--368823 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
368758 AACCATTAAG
*
368768 ATAAGTTAATTCGTGTAAATTTAATAA
1 ATAAGTTAATTCGTGCAAATTTAATAA
368795 ATAAGTTAATTCGTGCAAATTTAATAA
1 ATAAGTTAATTCGTGCAAATTTAATAA
368822 AT
1 AT
368824 TGAATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (27 bp):
ATAAGTTAATTCGTGCAAATTTAATAA
Found at i:372984 original size:31 final size:31
Alignment explanation
Indices: 372911--372973 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
372901 TACGTCGGGT
372911 ACCATATTGCAAACGGACTAAATGTTGAGGG
1 ACCATATTGCAAACGGACTAAATGTTGAGGG
* *
372942 ACCATATTGCAAATGGACTAAATGTTGGGGG
1 ACCATATTGCAAACGGACTAAATGTTGAGGG
372973 A
1 A
372974 TTGTATTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (31 bp):
ACCATATTGCAAACGGACTAAATGTTGAGGG
Found at i:373831 original size:2 final size:2
Alignment explanation
Indices: 373824--373861 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
373814 ATAATTACAA
373824 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
373862 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:374323 original size:31 final size:31
Alignment explanation
Indices: 374280--374340 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
374270 AGTTACATCG
* **
374280 GGGATCATATTGCAAATGGAATAAATGTTGA
1 GGGACCATATTGCAAACAGAATAAATGTTGA
*
374311 GGGACCATATTGCAAACAGATTAAATGTTG
1 GGGACCATATTGCAAACAGAATAAATGTTG
374341 GGGGGATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGAATAAATGTTGA
Found at i:380197 original size:100 final size:101
Alignment explanation
Indices: 380023--380212 Score: 337
Period size: 100 Copynumber: 1.9 Consensus size: 101
380013 TAGGGATAAC
* *
380023 AATAGTGGCGTTTTTTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGTATTTATTGGAAAAA
1 AATAGTGGCGTTTTCTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCATTTATTGGAAAAA
380088 CGCCACTATATATATACTTTTTTGGGGCTACACAAT
66 CGCCACTATATATATACTTTTTTGGGGCTACACAAT
*
380124 AATAGTGGCG-TTTCTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAA
1 AATAGTGGCGTTTTCTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCATTTATTGGAAAAA
*
380188 CGCCACTATATATATATTTTTTTGG
66 CGCCACTATATATATACTTTTTTGG
380213 TGACCCTGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
100 75 0.88
101 10 0.12
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (101 bp):
AATAGTGGCGTTTTCTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCATTTATTGGAAAAA
CGCCACTATATATATACTTTTTTGGGGCTACACAAT
Found at i:385876 original size:6 final size:6
Alignment explanation
Indices: 385865--385898 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
385855 ATTATAATAT
*
385865 ATTAAA ATTAAA ATTGAA ATTAAA ATTAAA ATTA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTA
385899 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:386642 original size:23 final size:23
Alignment explanation
Indices: 386593--386642 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
386583 AATATTGTAT
* * *
386593 TTTAATTAAATTACATTTAGATT
1 TTTAACTAAATTACAATTAGATG
* *
386616 TTTAACTAAATTATAATTATATG
1 TTTAACTAAATTACAATTAGATG
386639 TTTA
1 TTTA
386643 GTATTTTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAAATTACAATTAGATG
Found at i:386920 original size:18 final size:18
Alignment explanation
Indices: 386899--386933 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
386889 AAATATTTAT
* *
386899 AATATTTAAAATTTAAAA
1 AATAATTAAAAATTAAAA
386917 AATAATTAAAAATTAAA
1 AATAATTAAAAATTAAA
386934 TTAAATCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATTAAAAATTAAAA
Found at i:387215 original size:3 final size:3
Alignment explanation
Indices: 387207--387250 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
387197 AGCTCAATTA
387207 ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
387251 TCTAAATTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:405002 original size:21 final size:21
Alignment explanation
Indices: 404976--405033 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
404966 AGGGTGTCAA
*
404976 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACCCCTGC
404997 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
405018 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
405034 TTCCACTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:408880 original size:23 final size:23
Alignment explanation
Indices: 408850--408900 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
408840 TAAACGTTAA
408850 TTTT-TTCAATAGAAGAAGCTAG
1 TTTTATTCAATAGAAGAAGCTAG
* *
408872 TTTTATTCACTAGAAGAAGTTAG
1 TTTTATTCAATAGAAGAAGCTAG
408895 TTTTAT
1 TTTTAT
408901 GAAGTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (23 bp):
TTTTATTCAATAGAAGAAGCTAG
Found at i:411720 original size:34 final size:31
Alignment explanation
Indices: 411640--411728 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
411630 GTTAGTATTT
* * *
411640 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
411672 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
411706 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
411729 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:411890 original size:17 final size:17
Alignment explanation
Indices: 411868--411921 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
411858 AATGTTAATA
411868 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
411885 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
411902 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
411919 TTT
1 TTT
411922 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:413477 original size:21 final size:21
Alignment explanation
Indices: 413453--413500 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
413443 GCAAGGGTAC
* *
413453 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
413474 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
413495 ATGCCA
1 ATGCCA
413501 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:413530 original size:21 final size:21
Alignment explanation
Indices: 413504--413576 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
413494 TATGCCATCT
*
413504 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
413525 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
413546 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
413567 CCGCAGGGTT
1 CCGCAGGGTT
413577 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:414148 original size:34 final size:34
Alignment explanation
Indices: 414098--414195 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
414088 AAATGTTTTT
*
414098 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
414132 AAAATAAAAATAATATTATTCAAAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
414166 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
414196 CATTAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:416832 original size:3 final size:3
Alignment explanation
Indices: 416824--416855 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
416814 TTTCTAAGCT
416824 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
416856 TGGCCATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:418518 original size:2 final size:2
Alignment explanation
Indices: 418511--418535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
418501 TACGCAATAC
418511 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 T
418536 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:419161 original size:18 final size:19
Alignment explanation
Indices: 419138--419173 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
419128 CAAAACAATT
419138 TTTTAAAA-AATCTTCCGA
1 TTTTAAAATAATCTTCCGA
*
419156 TTTTAAAATCATCTTCCG
1 TTTTAAAATAATCTTCCG
419174 CGCAACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (19 bp):
TTTTAAAATAATCTTCCGA
Found at i:420853 original size:14 final size:14
Alignment explanation
Indices: 420836--420875 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
420826 TCCTCTTTTT
420836 TTATTTATATTATA
1 TTATTTATATTATA
*
420850 TTATTTTTATTATA
1 TTATTTATATTATA
420864 TATATCTTATAT
1 T-TAT-TTATAT
420876 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:420857 original size:23 final size:23
Alignment explanation
Indices: 420796--420868 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
420786 ATATATATAT
*
420796 TATTATATATATTTTATTTATTTA
1 TATTATAT-TATTTTTTTTATTTA
**
420820 CTA-TAT-TCCTCTTTTTTTATTTA
1 -TATTATATTAT-TTTTTTTATTTA
* *
420843 TATTATATTATTTTTATTATATA
1 TATTATATTATTTTTTTTATTTA
420866 TAT
1 TAT
420869 CTTATATCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 3 0.08
23 28 0.74
24 5 0.13
25 2 0.05
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTATATTATTTTTTTTATTTA
Found at i:421262 original size:19 final size:17
Alignment explanation
Indices: 421240--421276 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
421230 TTTTTTAACA
421240 TTTTATTCATTTTGTTTAT
1 TTTTATT-ATTTT-TTTAT
421259 TTTTATTATTTTTTTAT
1 TTTTATTATTTTTTTAT
421276 T
1 T
421277 ATTTTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTATTTTTTTAT
Found at i:421274 original size:11 final size:11
Alignment explanation
Indices: 421258--421283 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
421248 ATTTTGTTTA
421258 TTTTTATTATT
1 TTTTTATTATT
421269 TTTTTATTATT
1 TTTTTATTATT
421280 TTTT
1 TTTT
421284 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:423199 original size:14 final size:14
Alignment explanation
Indices: 423172--423214 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
423162 GAACATTTCA
*
423172 TGCATTTTTGCATTT
1 TGCA-TTTTACATTT
423187 TGCATTTTACATTT
1 TGCATTTTACATTT
*
423201 TGC-TTCTACATTT
1 TGCATTTTACATTT
423214 T
1 T
423215 ATTTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 10 0.38
14 12 0.46
15 4 0.15
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.58
Consensus pattern (14 bp):
TGCATTTTACATTT
Found at i:423212 original size:13 final size:14
Alignment explanation
Indices: 423182--423214 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
423172 TGCATTTTTG
*
423182 CATTTTGCATTTTA
1 CATTTTGCATTCTA
423196 CATTTTGC-TTCTA
1 CATTTTGCATTCTA
423209 CATTTT
1 CATTTT
423215 ATTTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (14 bp):
CATTTTGCATTCTA
Found at i:424617 original size:69 final size:69
Alignment explanation
Indices: 424499--424636 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
424489 GATTCAAACT
* *
424499 ATGAGATTGATCAAGCACAATCATTTCTGAATCATTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
424564 TCAA
66 TCAA
*
424568 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
424633 TCAA
66 TCAA
424637 GAGAGACATA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:426155 original size:37 final size:38
Alignment explanation
Indices: 426100--426174 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
426090 GAAGATTTTA
* * *
426100 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGAAAGTTTCCCTTGAAACATAAACATTG
*
426137 TCTCCCTTGAGAAAGTTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGAAAGTTTCCCTTGAAACATAAACATTG
426175 AAAACATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGAAAGTTTCCCTTGAAACATAAACATTG
Found at i:426343 original size:65 final size:67
Alignment explanation
Indices: 426263--426418 Score: 201
Period size: 65 Copynumber: 2.3 Consensus size: 67
426253 TGGAACTAAG
** **
426263 TTTTGTCTCTTTTGAGACAGTTTCCCTTGAAA-CAAAATCTTTGAATTTATTTCTCC-TAAAAC-
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACCAAAATCTTCAAATTTATTTC-CCTTAAAACA
*
426325 AAT
65 AAA
*
426328 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTCAAAATCTTCAAATTTATTTCCCTTAAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC-CAAAATCTTCAAATTTATTTCCCTTAAAACA
426393 AAA
65 AAA
* *
426396 TTTTGTTTCCCTTGAGACCGTTT
1 TTTTGTCTCCCTTGAGACAGTTT
426419 TTCATGAAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 29 0.37
66 2 0.03
67 25 0.32
68 23 0.29
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (67 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACCAAAATCTTCAAATTTATTTCCCTTAAAACAA
AA
Found at i:427311 original size:110 final size:106
Alignment explanation
Indices: 427113--427368 Score: 329
Period size: 110 Copynumber: 2.4 Consensus size: 106
427103 TTCCAGTTTT
* * *
427113 AGAGCCAATTTCAACTTCACAGCGAGGGATATTGAACTCAAGAGAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAA
* * *
427178 CGAAAGGGCGACTGATTGTCAACAAATAACTTT-TCAGTTTCATTC
66 CGAAAGGGCGACTGACTGTCAACAAACAA-TTTCCCAG-TTC---C
* *
427223 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAA
*
427288 CGAAGGGGCGACT-AGCTGTCAACAAACAATTTCCCAGTTCC
66 CGAAAGGGCGACTGA-CTGTCAACAAACAATTTCCCAGTTCC
* *
427329 AGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTCG
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGAACTCG
427369 GAACAATACT
Statistics
Matches: 131, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
105 1 0.01
106 36 0.27
109 7 0.05
110 87 0.66
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAA
CGAAAGGGCGACTGACTGTCAACAAACAATTTCCCAGTTCC
Found at i:428704 original size:14 final size:14
Alignment explanation
Indices: 428685--428778 Score: 67
Period size: 14 Copynumber: 7.0 Consensus size: 14
428675 GTCTCCTATA
428685 TATATATATTTTAT
1 TATATATATTTTAT
428699 TATATATATTTTAT
1 TATATATATTTTAT
**
428713 T-TAT-T-TACTA-
1 TATATATATTTTAT
*
428723 TAT-TCATCTTTTAT
1 TATAT-ATATTTTAT
*
428737 T-TATTTATTTATAT
1 TATATATATTT-TAT
428751 TATAT-TATTTTTAT
1 TATATATA-TTTTAT
*
428765 TATATATATCTTAT
1 TATATATATTTTAT
428779 AACATTATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
10 2 0.03
11 4 0.06
12 2 0.03
13 11 0.17
14 36 0.57
15 8 0.13
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
TATATATATTTTAT
Found at i:428893 original size:39 final size:36
Alignment explanation
Indices: 428839--428933 Score: 109
Period size: 39 Copynumber: 2.5 Consensus size: 36
428829 TTTTTCTCCA
* *
428839 TTTGTTATGTATATATTTTTTTTCTTAATATTATATT
1 TTTGTT-TTTATATATTTATTTTCTTAATATTATATT
* *
428876 TTATACGTTTTTATATATATATTTTCTTAATATTCTATT
1 TT-T--GTTTTTATATATTTATTTTCTTAATATTATATT
*
428915 TTTGTTTTTATTTATTTAT
1 TTTGTTTTTATATATTTAT
428934 ATATATTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
36 14 0.29
37 2 0.04
38 2 0.04
39 28 0.57
40 3 0.06
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (36 bp):
TTTGTTTTTATATATTTATTTTCTTAATATTATATT
Found at i:429029 original size:38 final size:36
Alignment explanation
Indices: 428956--429051 Score: 88
Period size: 38 Copynumber: 2.6 Consensus size: 36
428946 TTTACTTTAT
* * *
428956 TTTATTTTTTTCTA-TTTTTTTTCTTAATATCATATA
1 TTTATTATTTT-TACTTGTTTTACTTAATATCATATA
* *
428992 TATCT-TTATTTTTTACTTGTTTTACTTAGTATTATATA
1 T-T-TATTA-TTTTTACTTGTTTTACTTAATATCATATA
*
429030 TTTATTATTTTTATTTGTTTTA
1 TTTATTATTTTTACTTGTTTTA
429052 GTAAATACTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
36 16 0.33
37 9 0.18
38 24 0.49
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTATTATTTTTACTTGTTTTACTTAATATCATATA
Found at i:429193 original size:19 final size:19
Alignment explanation
Indices: 429156--429197 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
429146 TTTTTTAACA
429156 TTTTATTCATTTTGTTTAT
1 TTTTATTCATTTTGTTTAT
*
429175 TTTTATT-ATTTTTTATTAT
1 TTTTATTCATTTTGT-TTAT
429194 TTTT
1 TTTT
429198 TACGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTCATTTTGTTTAT
Found at i:429199 original size:10 final size:10
Alignment explanation
Indices: 429156--429199 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
429146 TTTTTTAACA
429156 TTTTATTCATT
1 TTTTATT-ATT
*
429167 TTGT-TTA-T
1 TTTTATTATT
429175 TTTTATTATT
1 TTTTATTATT
429185 TTTTATTATT
1 TTTTATTATT
429195 TTTTA
1 TTTTA
429200 CGTGTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 18 0.62
11 3 0.10
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTATTATT
Done.