Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009614.1 Hibiscus syriacus cultivar Beakdansim tig00117000_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: 2129691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:181791 original size:107 final size:106
Alignment explanation
Indices: 181476--181799 Score: 486
Period size: 106 Copynumber: 3.0 Consensus size: 106
181466 ATATCGTGCC
* *
181476 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
181541 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
181582 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
181647 AATTTCGGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
* * * * *
181688 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAAGGGGCGGCTGGCTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACG-AAGGGACGGCTGGTTGTCAACAAACAATTTCC
* * * * * * * *
181753 TAGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
181795 ACTCG
1 ACTCG
181800 GAACAATACA
Statistics
Matches: 198, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
106 131 0.66
107 67 0.34
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
Found at i:182124 original size:102 final size:102
Alignment explanation
Indices: 181946--182132 Score: 252
Period size: 102 Copynumber: 1.8 Consensus size: 102
181936 GACAGTTTCC
* * * *
181946 AAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAACATCTTTTCCTTGAAAC
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCATTGAACAACTTTCCCTTGAAAC
182011 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
66 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
* *
182048 AAGTTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAA-CATTGAA-AACATTTCCCTTGAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA-AAATCATTGAACAAC-TTTCCCTTGAA
** * *
182111 ATGAATTTTGTCTCTCTTGAGA
64 ACAAATTTCGTCTCCCTTGAGA
182133 TAGTTTCCCT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
101 2 0.03
102 68 0.93
103 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (102 bp):
AAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCATTGAACAACTTTCCCTTGAAAC
AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
Found at i:183562 original size:2 final size:2
Alignment explanation
Indices: 183555--183641 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
183545 TTCCGTCCCC
*
183555 TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
183597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
183639 TA T
1 TA T
183642 GTGTGTGTGT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:183646 original size:2 final size:2
Alignment explanation
Indices: 183641--183665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
183631 TATATATATA
183641 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
183666 ATAGATGTAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:183739 original size:37 final size:34
Alignment explanation
Indices: 183698--183800 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 34
183688 ATTTACTATG
183698 TATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATTTTTTCTTAATATTATATTTT-T--GTTTT
* *
183735 TATATATATTTTCTTAATATTTTATTTTTGTTTT
1 TATATATTTTTTCTTAATATTATATTTTTGTTTT
* * *
183769 TATTTATTTATATATATATATATTATATTTTT
1 TATATATTT-TTTCT-TA-ATATTATATTTTT
183801 ACTTTACTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 12 0.21
35 3 0.05
36 3 0.05
37 38 0.68
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (34 bp):
TATATATTTTTTCTTAATATTATATTTTTGTTTT
Found at i:183893 original size:38 final size:38
Alignment explanation
Indices: 183808--183905 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 38
183798 TTTACTTTAC
* *
183808 TTTATTTATTTTATTATTTTTCTTCTTAATATCATGTATA
1 TTTA-TTATTTTTTTATTTTTCTTCTTAATAT-ATATATA
*
183848 TCT-TTATTTTTTTATTTGTT-TTACTTAATAT-TATATA
1 TTTATTATTTTTTTATTT-TTCTT-CTTAATATATATATA
183885 TTTATTATTTTTATTTATTTT
1 TTTATTA-TTTT-TTTATTTT
183906 AGTAAATACT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
37 7 0.14
38 18 0.37
39 15 0.31
40 9 0.18
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.69
Consensus pattern (38 bp):
TTTATTATTTTTTTATTTTTCTTCTTAATATATATATA
Found at i:191590 original size:10 final size:10
Alignment explanation
Indices: 191575--191633 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
191565 TTCATTTTTT
191575 TAAAAATAAA
1 TAAAAATAAA
*
191585 TAAAAATGTAA
1 TAAAAAT-AAA
*
191596 TAAAAATGAAT
1 TAAAAAT-AAA
*
191607 TAAAAATGAA
1 TAAAAATAAA
* *
191617 TAAAATTCAA
1 TAAAAATAAA
191627 TAAAAAT
1 TAAAAAT
191634 TTAATGTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 22 0.55
11 18 0.45
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:191597 original size:11 final size:11
Alignment explanation
Indices: 191583--191638 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
191573 TTTAAAAATA
191583 AATAAAAATGT
1 AATAAAAATGT
191594 AATAAAAATG-
1 AATAAAAATGT
191604 AATTAAAAATG-
1 AA-TAAAAATGT
191615 AAT-AAAAT-T
1 AATAAAAATGT
*
191624 CAATAAAAATTT
1 -AATAAAAATGT
191636 AAT
1 AAT
191639 GTAAAGCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 5 0.12
10 6 0.15
11 28 0.70
12 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (11 bp):
AATAAAAATGT
Found at i:191600 original size:21 final size:21
Alignment explanation
Indices: 191575--191638 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
191565 TTCATTTTTT
191575 TAAAAATAAATAAAAATGTAA
1 TAAAAATAAATAAAAATGTAA
*
191596 TAAAAATGAATTAAAAATG-AA
1 TAAAAAT-AAATAAAAATGTAA
* * *
191617 TAAAATTCAATAAAAATTTAA
1 TAAAAATAAATAAAAATGTAA
191638 T
1 T
191639 GTAAAGCTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.22
21 18 0.50
22 10 0.28
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAATAAATAAAAATGTAA
Found at i:192936 original size:21 final size:22
Alignment explanation
Indices: 192912--192959 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
192902 TTTTATTGAA
*
192912 TTTTATT-TAATTTTAATTCTT
1 TTTTATTGTAATTTTAATTATT
* *
192933 TTTTATTGTATTTTTATTTATT
1 TTTTATTGTAATTTTAATTATT
192955 TTTTA
1 TTTTA
192960 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTATTGTAATTTTAATTATT
Found at i:192959 original size:11 final size:10
Alignment explanation
Indices: 192899--192957 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
192889 TTTTACATTA
192899 TATTTTTATT
1 TATTTTTATT
* *
192909 GAATTTTATT
1 TATTTTTATT
*
192919 TAATTTTAATT
1 T-ATTTTTATT
192930 CT-TTTTTATT
1 -TATTTTTATT
192940 GTATTTTTATT
1 -TATTTTTATT
192951 TATTTTT
1 TATTTTT
192958 TAAAAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
10 23 0.59
11 15 0.38
12 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (10 bp):
TATTTTTATT
Found at i:199876 original size:207 final size:209
Alignment explanation
Indices: 199502--199919 Score: 813
Period size: 207 Copynumber: 2.0 Consensus size: 209
199492 GATGTAGAAG
199502 TATACATAGAAGGACACGTTCTCCCCTCAAAGGATTATTTCAAGTACCTAGGGTCTATGATACAT
1 TATACATAGAAGGACACGTTCTCCCCTCAAAGGATTATTTCAAGTACCTAGGGTCTATGATACAT
199567 AAAGATGGGGGTGTAGATGATGACGTTACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGC
66 AAAGATGGGGGTGTA-ATGATGACGTTACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGC
199632 CGCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAGAATGG
130 CGCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAGAATGG
199697 CAATAAGACCAGCGT
195 CAATAAGACCAGCGT
199712 TATACATAGAAGGACACGTTCTCCCCTCAAAGGATTATTTCAAGTACCTAGGGTCTATGATACAT
1 TATACATAGAAGGACACGTTCTCCCCTCAAAGGATTATTTCAAGTACCTAGGGTCTATGATACAT
199777 AAAGATGGGGGTGT-A-GATGACGTTACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCC
66 AAAGATGGGGGTGTAATGATGACGTTACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCC
199840 GCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAGAATGGC
131 GCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAGAATGGC
199905 AATAAGACCAGCGT
196 AATAAGACCAGCGT
199919 T
1 T
199920 GTTGTATGGA
Statistics
Matches: 208, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
207 128 0.62
208 1 0.00
210 79 0.38
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (209 bp):
TATACATAGAAGGACACGTTCTCCCCTCAAAGGATTATTTCAAGTACCTAGGGTCTATGATACAT
AAAGATGGGGGTGTAATGATGACGTTACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCC
GCTACTGGAGTTTTGTGTGACAAGAAGGTGCCTCTAAAACTTAAGGGAAAATTTTATAGAATGGC
AATAAGACCAGCGT
Found at i:203029 original size:288 final size:287
Alignment explanation
Indices: 202513--203087 Score: 1114
Period size: 288 Copynumber: 2.0 Consensus size: 287
202503 AAATATATAG
202513 TTGGACATTATTTATATGCAGTCTTCATATGCACGTCTGTAATGAGAATTAATCCTTGCAAATAA
1 TTGGACATTATTTATATGCAGTCTTCATATGCACGTCTGTAATGAGAATTAATCCTTGCAAATAA
202578 ATCCCTACGTAAAAATCTCTGAATATCGACAAAAACGTAAGTCCCGACTAAATTTAAAAAGAGGG
66 ATCCCTACGTAAAAATCTCTGAATATCGACAAAAACGTAAGTCCCGACTAAATTTAAAAAGAGGG
202643 AACATGAAGAGAATGATGCACAGAAGTCAGAAATAGAAAGATACGAGAAGGAATAAAGTCAAATG
131 AACATGAAGAGAATGATGCACAGAAGTCAGAAATAGAAAGATACGAGAAGGAATAAAGTCAAATG
*
202708 AGTTAAAACCTAAACTAAGGCAACACTACTCCGTTACCCTAGTTCTAAGTCTTCATAATTTTCAA
196 AGTTAAAACCTAAACTAAGGCAACACTACTCCGTTACCCTAGTTCTAAGCCTTCATAATTTTCAA
202773 TGACAGAAACATATAAAAAGTAGAAGTC
261 TGACAGAAACATAT-AAAAGTAGAAGTC
*
202801 TTGGACATTATTTATATGCAGTCTTCATATGCGCGTCTGTAATGAGAATTAATCCTTGCAAATAA
1 TTGGACATTATTTATATGCAGTCTTCATATGCACGTCTGTAATGAGAATTAATCCTTGCAAATAA
202866 ATCCCTACGTAAAAATCTCTGAATATCGACAAAAACGTAAGTCCCGACTAAATTTAAAAAGAGGG
66 ATCCCTACGTAAAAATCTCTGAATATCGACAAAAACGTAAGTCCCGACTAAATTTAAAAAGAGGG
*
202931 AACATGAAGAGAATGATGCACAGAAGTCAGAAATAGCAAGATACGAGAAGGAATAAAGTCAAATG
131 AACATGAAGAGAATGATGCACAGAAGTCAGAAATAGAAAGATACGAGAAGGAATAAAGTCAAATG
202996 AGTTAAAACCTAAACTAAGGCAACACTACTCCGTTACCCTAGTTCTAAGCCTTCATAATTTTCAA
196 AGTTAAAACCTAAACTAAGGCAACACTACTCCGTTACCCTAGTTCTAAGCCTTCATAATTTTCAA
203061 TGACAGAAACATATAAAAGTAGAAGTC
261 TGACAGAAACATATAAAAGTAGAAGTC
203088 ATAGAAAATT
Statistics
Matches: 284, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
287 13 0.05
288 271 0.95
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (287 bp):
TTGGACATTATTTATATGCAGTCTTCATATGCACGTCTGTAATGAGAATTAATCCTTGCAAATAA
ATCCCTACGTAAAAATCTCTGAATATCGACAAAAACGTAAGTCCCGACTAAATTTAAAAAGAGGG
AACATGAAGAGAATGATGCACAGAAGTCAGAAATAGAAAGATACGAGAAGGAATAAAGTCAAATG
AGTTAAAACCTAAACTAAGGCAACACTACTCCGTTACCCTAGTTCTAAGCCTTCATAATTTTCAA
TGACAGAAACATATAAAAGTAGAAGTC
Found at i:204309 original size:227 final size:227
Alignment explanation
Indices: 203896--204342 Score: 781
Period size: 227 Copynumber: 2.0 Consensus size: 227
203886 GTAAATTATC
* * *
203896 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
203961 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
204026 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
204091 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
204124 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
204189 TTAATATTGTTAAATTTAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAAT-ATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
204252 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
204317 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
204343 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
226 4 0.02
227 89 0.43
228 61 0.29
229 55 0.26
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:204431 original size:20 final size:19
Alignment explanation
Indices: 204408--204453 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
204398 CGATATACCA
204408 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
204428 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
204448 GGTAAA
1 GGTAAA
204454 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:204598 original size:20 final size:19
Alignment explanation
Indices: 204575--204621 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
204565 CGATATAACA
204575 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
204595 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
204615 GGTAAAA
1 GGTAAAA
204622 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:204623 original size:17 final size:18
Alignment explanation
Indices: 204579--204626 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
204569 ATAACAGGTA
204579 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
204598 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
204618 -AAAATGATA
1 AAAAATGATA
204627 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:206898 original size:21 final size:21
Alignment explanation
Indices: 206851--206915 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
206841 AAGACAATCA
* *
206851 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
206873 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
206893 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
206914 AG
1 AG
206916 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:207001 original size:18 final size:18
Alignment explanation
Indices: 206980--207016 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
206970 GTAATTGGAG
206980 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
206998 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
207016 T
1 T
207017 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:207024 original size:24 final size:24
Alignment explanation
Indices: 206972--207018 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
206962 CAAATCATGT
* *
206972 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
206996 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
207019 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:207318 original size:39 final size:39
Alignment explanation
Indices: 207275--207400 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
207265 TCCGATGCTC
* *
207275 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
207314 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
207353 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
207392 ATCAAAATC
1 ATCAAAATC
207401 TACAACTTGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:207829 original size:23 final size:23
Alignment explanation
Indices: 207798--207861 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
207788 ATAGGTAAAC
*
207798 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
207821 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
207844 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
207862 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:207868 original size:23 final size:23
Alignment explanation
Indices: 207798--207870 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
207788 ATAGGTAAAC
* **
207798 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
207821 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
207844 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
207867 ATAT
1 ATAT
207871 TTAGTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:217963 original size:20 final size:20
Alignment explanation
Indices: 217938--217986 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
217928 AATTAAATTT
217938 ATTCAAAGTTTTCAAAAATA
1 ATTCAAAGTTTTCAAAAATA
217958 ATTCAAAGTTTTCAAAAATA
1 ATTCAAAGTTTTCAAAAATA
217978 ATTCAAAGT
1 ATTCAAAGT
217987 CCATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (20 bp):
ATTCAAAGTTTTCAAAAATA
Found at i:218396 original size:20 final size:21
Alignment explanation
Indices: 218362--218401 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
218352 GCAGAAAAAA
*
218362 CATCCTCAAATGGCTAGAAAT
1 CATCCTCAAACGGCTAGAAAT
218383 CATCC-CAAACGGCTAGAAA
1 CATCCTCAAACGGCTAGAAA
218402 CGGTCACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (21 bp):
CATCCTCAAACGGCTAGAAAT
Found at i:221880 original size:20 final size:21
Alignment explanation
Indices: 221841--221886 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
221831 ATTTTTGCAG
221841 AGAAAACATCCTCAAACGGCT
1 AGAAAACATCCTCAAACGGCT
* *
221862 AGAAATCATCC-CCAACGGCT
1 AGAAAACATCCTCAAACGGCT
221882 AGAAA
1 AGAAA
221887 CGACCCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.13
Consensus pattern (21 bp):
AGAAAACATCCTCAAACGGCT
Found at i:221961 original size:97 final size:97
Alignment explanation
Indices: 221795--221988 Score: 336
Period size: 97 Copynumber: 2.0 Consensus size: 97
221785 TCGATACTCT
*
221795 CTATAAGAGTACCGATACCCATGTACTGGGCAGTTGATTTTTGCAGAGAAAACATCCTCAAACGG
1 CTATAAGAGTACCGATACCCATGTAATGGGCAGTTGATTTTTGCAGAGAAAACATCCTCAAACGG
221860 CTAGAAATCATCCCCAACGGCTAGAAACGACC
66 CTAGAAATCATCCCCAACGGCTAGAAACGACC
* *
221892 CTATAAGAGTACTGATACCCTCTGTAAT-GGCAGTTGATTTTTGCAGAGAAAACATCCTCAAACG
1 CTATAAGAGTACCGATACCC-ATGTAATGGGCAGTTGATTTTTGCAGAGAAAACATCCTCAAACG
*
221956 GCTAGAAATTATCCCCAACGGCTAGAAACGACC
65 GCTAGAAATCATCCCCAACGGCTAGAAACGACC
221989 AACACCTCAT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 87 0.95
98 5 0.05
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (97 bp):
CTATAAGAGTACCGATACCCATGTAATGGGCAGTTGATTTTTGCAGAGAAAACATCCTCAAACGG
CTAGAAATCATCCCCAACGGCTAGAAACGACC
Found at i:221969 original size:21 final size:20
Alignment explanation
Indices: 221945--221983 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
221935 CAGAGAAAAC
221945 ATCCTCAAACGGCTAGAAATT
1 ATCC-CAAACGGCTAGAAATT
*
221966 ATCCCCAACGGCTAGAAA
1 ATCCCAAACGGCTAGAAA
221984 CGACCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCCCAAACGGCTAGAAATT
Found at i:231208 original size:12 final size:12
Alignment explanation
Indices: 231191--231221 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
231181 GTTTATATAC
231191 TTCTCTAACTAT
1 TTCTCTAACTAT
231203 TTCTCTAACTAT
1 TTCTCTAACTAT
*
231215 TTATCTA
1 TTCTCTA
231222 TGGGTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCTCTAACTAT
Found at i:234292 original size:31 final size:31
Alignment explanation
Indices: 234225--234284 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
234215 CAATTTAAGG
*
234225 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
234256 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
234285 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:234474 original size:21 final size:21
Alignment explanation
Indices: 234448--234489 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
234438 ATTTGAATAT
*
234448 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
234469 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
234490 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:248826 original size:22 final size:22
Alignment explanation
Indices: 248798--248840 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
248788 CCGAAAATGT
* *
248798 TAAAAAACATTAATGTTTTAGG
1 TAAAAAACAATAATATTTTAGG
*
248820 TAAAAAATAATAATATTTTAG
1 TAAAAAACAATAATATTTTAG
248841 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAAAAACAATAATATTTTAGG
Found at i:265542 original size:17 final size:19
Alignment explanation
Indices: 265520--265559 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
265510 AATGTCTTTT
265520 AAAAAT-AATTTTAAGA-A
1 AAAAATCAATTTTAAGACA
*
265537 AAAAATCATTTTTAAGACA
1 AAAAATCAATTTTAAGACA
265556 AAAA
1 AAAA
265560 GTTAGTCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAATCAATTTTAAGACA
Found at i:267604 original size:3 final size:3
Alignment explanation
Indices: 267596--267650 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
267586 ATAAACTAAT
* * *
267596 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TATA TTA TAG TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A
267642 TAA TAA TAA
1 TAA TAA TAA
267651 ATATAATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.88
4 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:272919 original size:13 final size:13
Alignment explanation
Indices: 272901--272943 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
272891 ATTTATATAT
272901 AATCATTAAATTA
1 AATCATTAAATTA
272914 AATCATTAAATTA
1 AATCATTAAATTA
* *
272927 AATTCTTTAATTTA
1 AA-TCATTAAATTA
272941 AAT
1 AAT
272944 AATAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AATCATTAAATTA
Found at i:285317 original size:21 final size:21
Alignment explanation
Indices: 285256--285323 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
285246 TTTTAATAGC
285256 ATTTAAGTTTATAACAATTTGATTT
1 ATTTAAGTTTATAACAA---G-TTT
* *
285281 TTTTAA-TTTACAAACAAGTTT
1 ATTTAAGTTTA-TAACAAGTTT
*
285302 ATTTAAGTTTATAACAACTTT
1 ATTTAAGTTTATAACAAGTTT
285323 A
1 A
285324 GTTCCCTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 17 0.47
22 5 0.14
24 4 0.11
25 10 0.28
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTTAAGTTTATAACAAGTTT
Found at i:287035 original size:3 final size:3
Alignment explanation
Indices: 287027--287051 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
287017 AAACAGGCGG
287027 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
287052 GTAACTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:289091 original size:9 final size:9
Alignment explanation
Indices: 289077--289103 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
289067 AGTTGGTCCT
289077 GGAGGAGGG
1 GGAGGAGGG
289086 GGAGGAGGG
1 GGAGGAGGG
289095 GGAGGAGGG
1 GGAGGAGGG
289104 CTAGTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (9 bp):
GGAGGAGGG
Found at i:291287 original size:141 final size:140
Alignment explanation
Indices: 291135--291417 Score: 397
Period size: 141 Copynumber: 2.0 Consensus size: 140
291125 CTTAATATAT
* *
291135 ATATATATAAGATTTAATAATTTCATTTAATTTGATTAATTAACCGATTTCGAATCGAATTAACC
1 ATATATATAAGATGTAATAATTTCATTTAATTAGATTAATTAACCGATTTCGAATCGAATTAACC
* * ** * * *
291200 GTCAATCGAATATTAAAAAAATGTTAATTGTTTCTCAACCGAATTAATTCGGTGGA-CGACCGAA
66 ATCAATCGAAT-TTAAAAAAATATTAATCATTTCTCAACCGAACTAATTCAGT-GACCGACCAAA
*
291264 TTAACTGAATTA
129 TTAACTGAACTA
* *
291276 ATATATATAAGATGTAATAATTTTATTTAATTAGATTAATTAACCGATTTCGAATCGAATTAATC
1 ATATATATAAGATGTAATAATTTCATTTAATTAGATTAATTAACCGATTTCGAATCGAATTAACC
* * * *
291341 ATTAATCGAATTTAAAAAAATATTAATCATTTCTCGACCTAACTAATTCAGTGACCGATCAAATT
66 ATCAATCGAATTTAAAAAAATATTAATCATTTCTCAACCGAACTAATTCAGTGACCGACCAAATT
291406 AACTGAACTA
131 AACTGAACTA
291416 AT
1 AT
291418 TTGATTAAGT
Statistics
Matches: 125, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
139 2 0.02
140 53 0.42
141 70 0.56
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (140 bp):
ATATATATAAGATGTAATAATTTCATTTAATTAGATTAATTAACCGATTTCGAATCGAATTAACC
ATCAATCGAATTTAAAAAAATATTAATCATTTCTCAACCGAACTAATTCAGTGACCGACCAAATT
AACTGAACTA
Found at i:293364 original size:289 final size:289
Alignment explanation
Indices: 292845--293404 Score: 1021
Period size: 289 Copynumber: 1.9 Consensus size: 289
292835 GGGGTTAAAG
* *
292845 TAAAAAAATTAAACCCTTTTACTAATGTGTTGTGTTAGAAAATCATTAAAGGTTTAATGATCGTT
1 TAAAAAAATTAAACCCTTTTACTAATGTGTCGTGTCAGAAAATCATTAAAGGTTTAATGATCGTT
* * *
292910 TACGTTAAGTGACCAATCTTAATTAAAACGAAATTAAAATGGTTACGAATTATGTTTTTTTAATG
66 TACGTTAAATGACCAATCTTAATTAAAACGAAATTAAAATGATTACGAATTATATTTTTTTAATG
*
292975 TAGTGATCATACGTTGTAAAACTGAAATAAAAATGACCAACTCTGTAATCTATCTAAAATTTTAC
131 TAGTGATCATACGTTGTAAAACTGAAATAAAAATGAACAACTCTGTAATCTATCTAAAATTTTAC
*
293040 TACTAATGAATATTGAATCTACAACTTAAAGGAGAGAAGAGATGTCAATAGATGGATATTAATAA
196 TACTAATGAATATTGAATCTACAACTTAAAGGAGAGAAGAGATGTCAACAGATGGATATTAATAA
293105 CCTCATTTAGAGTCAGAAAATCTACAACT
261 CCTCATTTAGAGTCAGAAAATCTACAACT
* *
293134 TAAAAAAATTAAACCCTTTTACTAATGTGTCGTGTCAGAAAATCGTTAAAGGTTTAATGATTGTT
1 TAAAAAAATTAAACCCTTTTACTAATGTGTCGTGTCAGAAAATCATTAAAGGTTTAATGATCGTT
*
293199 TACGTTAAATGACCAATCTTAATTAAAACGAAATTAAAATGATTATGAATTATATTTTTTTAATG
66 TACGTTAAATGACCAATCTTAATTAAAACGAAATTAAAATGATTACGAATTATATTTTTTTAATG
*
293264 TAGTGATCATTCGTTGTAAAACTGAAATAAAAATGAACAACTCTGTAATCTATCTAAAATTTTAC
131 TAGTGATCATACGTTGTAAAACTGAAATAAAAATGAACAACTCTGTAATCTATCTAAAATTTTAC
293329 TACTAATGAATATTGAATCTACAACTTAAAGGAGAGAAGAGATGTCAACAGATGGATATTAATAA
196 TACTAATGAATATTGAATCTACAACTTAAAGGAGAGAAGAGATGTCAACAGATGGATATTAATAA
293394 CCTCATTTAGA
261 CCTCATTTAGA
293405 ATTTATTAAA
Statistics
Matches: 260, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
289 260 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (289 bp):
TAAAAAAATTAAACCCTTTTACTAATGTGTCGTGTCAGAAAATCATTAAAGGTTTAATGATCGTT
TACGTTAAATGACCAATCTTAATTAAAACGAAATTAAAATGATTACGAATTATATTTTTTTAATG
TAGTGATCATACGTTGTAAAACTGAAATAAAAATGAACAACTCTGTAATCTATCTAAAATTTTAC
TACTAATGAATATTGAATCTACAACTTAAAGGAGAGAAGAGATGTCAACAGATGGATATTAATAA
CCTCATTTAGAGTCAGAAAATCTACAACT
Found at i:295055 original size:150 final size:151
Alignment explanation
Indices: 294784--295084 Score: 595
Period size: 150 Copynumber: 2.0 Consensus size: 151
294774 GTAGTTTCCT
294784 CCTGAGACATAAACCAAAATTATTCAGTCGTTAAGGACATTCCATGTCAAGCAAGTCAATATTTT
1 CCTGAGACATAAACCAAAATTATTCAGTCGTTAAGGACATTCCATGTCAAGCAAGTCAATATTTT
294849 GGTAAAATTTTGCTCCTGTGCAAAGGCGACAGTACAGATTACAATCAAATGGTTGAAAAAATCTA
66 GGTAAAATTTTGCTCCTGTGCAAAGGCGACAGTACAGATTACAATCAAATGGTTGAAAAAATCTA
294914 T-AAAACTCGAAGATGGAAGA
131 TAAAAACTCGAAGATGGAAGA
294934 CCTGAGACATAAACCAAAATTATTCAGTCGTTAAGGACATTCCATGTCAAGCAAGTCAATATTTT
1 CCTGAGACATAAACCAAAATTATTCAGTCGTTAAGGACATTCCATGTCAAGCAAGTCAATATTTT
294999 GGTAAAATTTTGCTCCTGTGCAAAGGCGACAGTACAGATTACAATCAAATGGTTGAAAAAATCTA
66 GGTAAAATTTTGCTCCTGTGCAAAGGCGACAGTACAGATTACAATCAAATGGTTGAAAAAATCTA
295064 TAAAAACTCGAAGATGGAAGA
131 TAAAAACTCGAAGATGGAAGA
295085 TGAATAGTTC
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
150 131 0.87
151 19 0.13
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (151 bp):
CCTGAGACATAAACCAAAATTATTCAGTCGTTAAGGACATTCCATGTCAAGCAAGTCAATATTTT
GGTAAAATTTTGCTCCTGTGCAAAGGCGACAGTACAGATTACAATCAAATGGTTGAAAAAATCTA
TAAAAACTCGAAGATGGAAGA
Found at i:296070 original size:13 final size:13
Alignment explanation
Indices: 296052--296077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
296042 GCAGCTAGAA
296052 AATATTATATATT
1 AATATTATATATT
296065 AATATTATATATT
1 AATATTATATATT
296078 TTTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTATATATT
Found at i:298461 original size:15 final size:15
Alignment explanation
Indices: 298441--298471 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
298431 GGATTTTCAA
298441 GTAATAATTGAAGGG
1 GTAATAATTGAAGGG
298456 GTAATAATTGAAGGG
1 GTAATAATTGAAGGG
298471 G
1 G
298472 GAGTACCGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (15 bp):
GTAATAATTGAAGGG
Found at i:302909 original size:45 final size:45
Alignment explanation
Indices: 302824--302909 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
302814 TTTATACCAA
* * * * * *
302824 CCACCTCCTCCTCCTCCCCATCCCCATCCACCACCTCCACCTCCT
1 CCACCTCCACCACCACCCCATCCCCAACCACAAACTCCACCTCCT
302869 CCACCTCCACCACCACCCCATCCCCAACCA-AAACTGCCACC
1 CCACCTCCACCACCACCCCATCCCCAACCACAAACT-CCACC
302910 AACTCCCCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.21, C:0.64, G:0.01, T:0.14
Consensus pattern (45 bp):
CCACCTCCACCACCACCCCATCCCCAACCACAAACTCCACCTCCT
Found at i:308927 original size:14 final size:15
Alignment explanation
Indices: 308905--308951 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
308895 TGTAAGGTAA
*
308905 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
308919 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
308934 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
308950 TT
1 TT
308952 GAAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:311791 original size:519 final size:519
Alignment explanation
Indices: 310811--312368 Score: 2981
Period size: 519 Copynumber: 3.0 Consensus size: 519
310801 GGTCCAGATC
310811 GACGGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
1 GACGGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
310876 TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
66 TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
*
310941 TCCTCCGAAACTTACGTGTACATGTTATCACGAGGGAAAAAAATATGTGTCATTTCAGATCGCGG
131 TCCTCCGAAACTTACGTGCACATGTTATCACGAGGG-AAAAAATATGTGTCATTTCAGATCGCGG
*
311006 AGCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGTAACCACCCTTTGTCCAACATA
195 AGCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGCAACCACCCTTTGTCCAACATA
* *
311071 GGTATTATCTCCGACACATTGTTGCGAACTACCATAGAAGGTACAAGAAGAATGATGAGCGTCAA
260 GGTATTGTCTCCGACACATTGTTGCGAACTACCATGGAAGGTACAAGAAGAATGATGAGCGTCAA
*
311136 TTAATTGTGCGCATGAGTAAGTGAAACTGATGTAGTTTGTTTTCTTTCGATCATTTTAATTTTGC
325 TTAATTGTGCGCATGGGTAAGTGAAACTGATGTAGTTTGTTTTCTTTCGATCATTTTAATTTTGC
311201 AAAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTG
390 AAAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTG
*
311266 AATCAATGCTTCAAGATCTGCGGGTGAAGAACGAGGAATGATACGATTACATCAGCCTCATCGAT
455 AATCAATGCTTCAAGATCTGCGGGCGAAGAACGAGGAATGATACGATTACATCAGCCTCATCGAT
311331 GACGGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
1 GACGGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
311396 TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
66 TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
*
311461 TCCTCTGAAACTTACGTGCACATGTTATCACGAGGGAAAAAATATGTGTCATTTCAGATCGCGGA
131 TCCTCCGAAACTTACGTGCACATGTTATCACGAGGGAAAAAATATGTGTCATTTCAGATCGCGGA
311526 GCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGCAACCACCCTTTGTCCAACATAG
196 GCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGCAACCACCCTTTGTCCAACATAG
311591 GTATTGTCTCCGACACATTGTTGCGAACTACCATGGAAGGTACAAGAAGAATGATGAGCGTCAAT
261 GTATTGTCTCCGACACATTGTTGCGAACTACCATGGAAGGTACAAGAAGAATGATGAGCGTCAAT
311656 TAATTGTGCGCATGGGTAAGTGAAACTGATGTAGTTTGTTTTCTTTCGATCATTTTAATTTTGCA
326 TAATTGTGCGCATGGGTAAGTGAAACTGATGTAGTTTGTTTTCTTTCGATCATTTTAATTTTGCA
311721 AAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTGA
391 AAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTGA
311786 ATCAATGCTTCAAGATCTGCGGGCGAAGAACGAGGAATGATACGATTACATCAGCCTCATCGAT
456 ATCAATGCTTCAAGATCTGCGGGCGAAGAACGAGGAATGATACGATTACATCAGCCTCATCGAT
*
311850 GACAGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
1 GACGGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
311915 TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
66 TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
*
311980 TCCTCCGAAACTTAAGTGCACATGTTATCACGAGGGAAAAAATATGTGTCATTTCAGATCGCGGA
131 TCCTCCGAAACTTACGTGCACATGTTATCACGAGGGAAAAAATATGTGTCATTTCAGATCGCGGA
312045 GCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGCAACCACCCTTTGTCCAACATAG
196 GCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGCAACCACCCTTTGTCCAACATAG
312110 GTATTGTCTCCGACACATTGTTGCGAACTACCATGGAAGGTACAAGAAGAATGATGAGCGTCAAT
261 GTATTGTCTCCGACACATTGTTGCGAACTACCATGGAAGGTACAAGAAGAATGATGAGCGTCAAT
* *
312175 TAATTGTGCGCATGGGTAAGTGAAACGGATGTAGTTTGTTTTCTTTCGATTATTTTAATTTTGCA
326 TAATTGTGCGCATGGGTAAGTGAAACTGATGTAGTTTGTTTTCTTTCGATCATTTTAATTTTGCA
312240 AAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTGA
391 AAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTGA
* * *
312305 ATTAATGCTTCAAGATCTACGGGCGAAGAACGAGGAATCATACGATTACATCAGCCTCATCGAT
456 ATCAATGCTTCAAGATCTGCGGGCGAAGAACGAGGAATGATACGATTACATCAGCCTCATCGAT
312369 AAAGAAATGT
Statistics
Matches: 1023, Mismatches: 15, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
519 859 0.84
520 164 0.16
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (519 bp):
GACGGGACTTTCTTGTATGGAAAATACAAACAAGTTTTATTATTGGCAGTTGTCCAAGATGGCAA
TCGCAACATTCTTCCAGTTGCTTTTGCTCTTATCGAAGGAGAATTTACAGATTCTTGGGCTTTTT
TCCTCCGAAACTTACGTGCACATGTTATCACGAGGGAAAAAATATGTGTCATTTCAGATCGCGGA
GCTGGGATCAAAGCAGCAATGGAGTCTTTGGGTCTAATGTGGCAACCACCCTTTGTCCAACATAG
GTATTGTCTCCGACACATTGTTGCGAACTACCATGGAAGGTACAAGAAGAATGATGAGCGTCAAT
TAATTGTGCGCATGGGTAAGTGAAACTGATGTAGTTTGTTTTCTTTCGATCATTTTAATTTTGCA
AAGAAAGCAAGTTAGTAAGTTATACATTTTTTATCAGGTTACGAACTACTTCCTCGAAAGTTTGA
ATCAATGCTTCAAGATCTGCGGGCGAAGAACGAGGAATGATACGATTACATCAGCCTCATCGAT
Found at i:313710 original size:3 final size:3
Alignment explanation
Indices: 313704--313729 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
313694 GCTGTCATCA
313704 TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
313730 CTAAGCAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:315805 original size:16 final size:16
Alignment explanation
Indices: 315747--315810 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
315737 TGCAAAAAAA
*
315747 ATTAATTAAA-TATAAT
1 ATTAAATAAATTA-AAT
*
315763 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
315779 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
315796 ATTAAATAAAATAAA
1 ATTAAATAAATTAAA
315811 ATATACCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
16 25 0.60
17 17 0.40
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:315812 original size:17 final size:16
Alignment explanation
Indices: 315742--315814 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
315732 ATATCTGCAA
* *
315742 AAAAAATTAATTAAAT
1 AAAATATTAAATAAAT
* *
315758 ATAATATTAAATAATT
1 AAAATATTAAATAAAT
*
315774 TAAATACTTAAATAAAT
1 AAAATA-TTAAATAAAT
*
315791 TAAATATTAAATAAAAT
1 AAAATATTAAAT-AAAT
315808 AAAATAT
1 AAAATAT
315815 ACCTTAAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 22 0.47
17 25 0.53
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:315864 original size:20 final size:20
Alignment explanation
Indices: 315839--315883 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
315829 ATATAAAAGT
* *
315839 ATTTGAGAGAGGTTGAGAGA
1 ATTTGAGAAAAGTTGAGAGA
*
315859 ATTTGAGAAAAGTTGAGAGG
1 ATTTGAGAAAAGTTGAGAGA
315879 ATTTG
1 ATTTG
315884 GTATGATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (20 bp):
ATTTGAGAAAAGTTGAGAGA
Found at i:316153 original size:15 final size:13
Alignment explanation
Indices: 316122--316153 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
316112 TCAACGTAAA
316122 GCGCGCTGCAGGG
1 GCGCGCTGCAGGG
316135 GCGCGCTGCAGGG
1 GCGCGCTGCAGGG
316148 GCGCGC
1 GCGCGC
316154 CTTACTGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.34, G:0.53, T:0.06
Consensus pattern (13 bp):
GCGCGCTGCAGGG
Found at i:325515 original size:87 final size:87
Alignment explanation
Indices: 325368--325540 Score: 301
Period size: 87 Copynumber: 2.0 Consensus size: 87
325358 CAACAACAAC
325368 GGATATCCTGCGCTTGCAGAGGATCCTGAAGAGGATTTTCTACTCAATGGCATGAACCCGAAGTT
1 GGATATCCTGCGCTTGCAGAGGATCCTGAAGAGGATTTTCTACTCAATGGCATGAACCCGAAGTT
*
325433 TATTGGACCTGATCCGAGCAAA
66 TATTGGACCTGATCCAAGCAAA
* * * *
325455 GGATATCCTGGGCTTGCAGAGGATCCTGAAGAGGATTTTCTACTCGATGGCTTGACCCCGAAGTT
1 GGATATCCTGCGCTTGCAGAGGATCCTGAAGAGGATTTTCTACTCAATGGCATGAACCCGAAGTT
325520 TATTGGACCTGATCCAAGCAA
66 TATTGGACCTGATCCAAGCAA
325541 CGGTTGGGAG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (87 bp):
GGATATCCTGCGCTTGCAGAGGATCCTGAAGAGGATTTTCTACTCAATGGCATGAACCCGAAGTT
TATTGGACCTGATCCAAGCAAA
Found at i:328709 original size:64 final size:64
Alignment explanation
Indices: 328631--328758 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
328621 GTTAGTTGCC
328631 GCTGGACTAATTTCTTTACCATTCACCGATGAACTAGATCTGCCAGGTAAAAACTTTAAACCAA
1 GCTGGACTAATTTCTTTACCATTCACCGATGAACTAGATCTGCCAGGTAAAAACTTTAAACCAA
328695 GCTGGACTAATTTCTTTACCATTCACCGATGAACTAGATCTGCCAGGTAAAAACTTTAAACCAA
1 GCTGGACTAATTTCTTTACCATTCACCGATGAACTAGATCTGCCAGGTAAAAACTTTAAACCAA
328759 CCAACGTCAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (64 bp):
GCTGGACTAATTTCTTTACCATTCACCGATGAACTAGATCTGCCAGGTAAAAACTTTAAACCAA
Found at i:332076 original size:23 final size:24
Alignment explanation
Indices: 332050--332110 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
332040 TCTACAAAAA
332050 TATTTTATTATATT-ATATTTATT
1 TATTTTATTATATTAATATTTATT
*
332073 TATTTATTATTATTATTAATATTTTTT
1 TA-TT-TTATTA-TATTAATATTTATT
*
332100 TATTTTTTTAT
1 TATTTTATTAT
332111 TTTTACAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 11 0.34
26 6 0.19
27 10 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTTTATTATATTAATATTTATT
Found at i:332207 original size:33 final size:33
Alignment explanation
Indices: 332161--332246 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
332151 TTCAGAAAAT
*
332161 AAATCGACGTATTTGAGTCCTATTGAAACACTA
1 AAATCAACGTATTTGAGTCCTATTGAAACACTA
*
332194 AAATCAACTTATTTGAGTCCTATTGAAACACTA
1 AAATCAACGTATTTGAGTCCTATTGAAACACTA
* *
332227 AAACTGAA-GCATTTGAGTCC
1 AAA-TCAACGTATTTGAGTCC
332247 AAGTATGACT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 44 0.94
34 3 0.06
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (33 bp):
AAATCAACGTATTTGAGTCCTATTGAAACACTA
Found at i:332730 original size:7 final size:7
Alignment explanation
Indices: 332718--332787 Score: 63
Period size: 7 Copynumber: 10.0 Consensus size: 7
332708 ATGATAATAC
332718 ATTATTT
1 ATTATTT
332725 ATTATTT
1 ATTATTT
332732 ATTTATTTT
1 A-TTA-TTT
332741 ATTATTT
1 ATTATTT
*
332748 ATTATTC
1 ATTATTT
332755 ATT-TTT
1 ATTATTT
*
332761 -TTCTTT
1 ATTATTT
*
332767 TTTATTT
1 ATTATTT
*
332774 AGTATTT
1 ATTATTT
*
332781 AATATTT
1 ATTATTT
332788 CATTTTGTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 2 0.04
6 5 0.09
7 36 0.68
8 6 0.11
9 4 0.08
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:332745 original size:23 final size:22
Alignment explanation
Indices: 332718--332772 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
332708 ATGATAATAC
*
332718 ATTATTTATTATTTATTTATTTT
1 ATTATTTATTATTCATTT-TTTT
332741 ATTATTTATTATTCATTTTTTT
1 ATTATTTATTATTCATTTTTTT
* *
332763 CTTTTTTATT
1 ATTATTTATT
332773 TAGTATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
ATTATTTATTATTCATTTTTTT
Found at i:332752 original size:19 final size:19
Alignment explanation
Indices: 332730--332774 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
332720 TATTTATTAT
332730 TTATTTATTTTATTATTTA
1 TTATTTATTTTATTATTTA
* * * *
332749 TTATTCATTTTTTTCTTTT
1 TTATTTATTTTATTATTTA
332768 TTATTTA
1 TTATTTA
332775 GTATTTAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATTTATTTTATTATTTA
Found at i:332771 original size:26 final size:26
Alignment explanation
Indices: 332723--332779 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
332713 AATACATTAT
332723 TTATTATTTATTTATTTTATTATTTA
1 TTATTATTTATTTATTTTATTATTTA
* *
332749 TTATTCATTTTTTTCTTTT-TTATTTA
1 TTATT-ATTTATTTATTTTATTATTTA
*
332775 GTATT
1 TTATT
332780 TAATATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (26 bp):
TTATTATTTATTTATTTTATTATTTA
Found at i:334146 original size:14 final size:15
Alignment explanation
Indices: 334123--334173 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
334113 TAACCGAAAT
* *
334123 TATTAAATATTTA-A
1 TATTATATATATATA
334137 TATTATATATATATA
1 TATTATATATATATA
334152 TA-TATATATATATA
1 TATTATATATATATA
334166 TA-TATATA
1 TATTATATA
334174 ATTTAGCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 31 0.91
15 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTATATATATATA
Found at i:334147 original size:2 final size:2
Alignment explanation
Indices: 334136--334173 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
334126 TAAATATTTA
334136 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
334174 ATTTAGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334566 original size:24 final size:24
Alignment explanation
Indices: 334539--334584 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
334529 ATGATAAAAG
* *
334539 AACACAAATGAACGAACATAAATA
1 AACACAAACGAACAAACATAAATA
*
334563 AACACAAACGAACAAATATAAA
1 AACACAAACGAACAAACATAAA
334585 ATTAATTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.65, C:0.17, G:0.07, T:0.11
Consensus pattern (24 bp):
AACACAAACGAACAAACATAAATA
Found at i:335516 original size:10 final size:10
Alignment explanation
Indices: 335497--335526 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
335487 CGTTAAATTG
335497 AAAATAAAATA
1 AAAAT-AAATA
335508 AAAATAAATA
1 AAAATAAATA
335518 AAAATAAAT
1 AAAATAAAT
335527 TAAATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATAAATA
Found at i:341307 original size:30 final size:30
Alignment explanation
Indices: 341240--341298 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
341230 GTCGAGCGGC
* *
341240 CATTTTTTAACATACGATAACGTTAGTGAT
1 CATTTTGTAACAAACGATAACGTTAGTGAT
*
341270 CATTTTGTAACAAACGCTAACGTTAGTGA
1 CATTTTGTAACAAACGATAACGTTAGTGA
341299 CTGATTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (30 bp):
CATTTTGTAACAAACGATAACGTTAGTGAT
Found at i:342225 original size:112 final size:112
Alignment explanation
Indices: 342074--342549 Score: 670
Period size: 112 Copynumber: 4.3 Consensus size: 112
342064 TTCTAAAAGT
* * * * * * *
342074 ATCGATAC-TTATAATAAAGTATCGACACTATCAACATATCTGGTAGCTCTTTACC-GATTTTAT
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTG-TTTTGT
* * * *
342137 CATTTCGAGATCGATTTTGTCATATTTTTACCTATTATATTGTTATGG
65 CATTTAGAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGG
* *
342185 ATCGATACTTTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTC
* * *
342250 ATTT-GTAAACCGGTTTTATCATTTTTTTACCTGTTATATTGTTATGG
66 ATTTAG-AGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGG
*
342297 ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTC
* *
342362 ATTTATAGATCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGG
66 ATTTAGAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGG
* *
342409 ATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTC
* * * *
342474 ATTTATAGACCGGTTTTGTCATTTATTTACTTGTTATATTGTTATGG
66 ATTTAGAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGG
* *
342521 ATCAATATATTTTTATAAAGTATCGACAC
1 ATCGATACATTTTTATAAAGTATCGACAC
342550 AAACCGACAA
Statistics
Matches: 329, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
111 9 0.03
112 319 0.97
113 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTC
ATTTAGAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGG
Found at i:343997 original size:14 final size:14
Alignment explanation
Indices: 343967--344010 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
343957 ATATTTTATT
**
343967 TTTAGG-TTTATAA
1 TTTAGGATTTATGG
343980 TTTAGGATTTATGG
1 TTTAGGATTTATGG
*
343994 TTTAAGATTTATGG
1 TTTAGGATTTATGG
344008 TTT
1 TTT
344011 GTGTTTGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (14 bp):
TTTAGGATTTATGG
Found at i:344708 original size:12 final size:12
Alignment explanation
Indices: 344691--344715 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
344681 CAAAATTTTA
344691 AAAAATTTAGTT
1 AAAAATTTAGTT
344703 AAAAATTTAGTT
1 AAAAATTTAGTT
344715 A
1 A
344716 GACCCTAATT
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAAATTTAGTT
Found at i:348472 original size:39 final size:39
Alignment explanation
Indices: 348382--348472 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 39
348372 TTCAGCACAG
* *
348382 TGAAGAAAAACCTCAGGTGAAGACACCAAATGAGTACCT
1 TGAAGAAAAATCTAAGGTGAAGACACCAAATGAGTACCT
* * * *
348421 TGAAGTAGAATCTAAGAGTGTAG-CACCAAATGAGTTCAC-
1 TGAAGAAAAATCTAAG-GTGAAGACACCAAATGAGTAC-CT
348460 TGAAGAAAAATCT
1 TGAAGAAAAATCT
348473 CAGTTGCTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
39 36 0.86
40 6 0.14
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (39 bp):
TGAAGAAAAATCTAAGGTGAAGACACCAAATGAGTACCT
Found at i:350640 original size:30 final size:30
Alignment explanation
Indices: 350604--350663 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
350594 TCAGAATGAA
**
350604 TGATTCTTCTCTGTCTACTGATGATCAGCC
1 TGATTCTTCTCCATCTACTGATGATCAGCC
* *
350634 TGATTCTTCTCCATCTATTGCTGATCAGCC
1 TGATTCTTCTCCATCTACTGATGATCAGCC
350664 CAAGAAACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.17, C:0.28, G:0.15, T:0.40
Consensus pattern (30 bp):
TGATTCTTCTCCATCTACTGATGATCAGCC
Found at i:353954 original size:23 final size:22
Alignment explanation
Indices: 353928--353992 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
353918 CAGCTCATAT
353928 AATTGCACCTAAGTGCCATGTAG
1 AATTGCACCT-AGTGCCATGTAG
* **
353951 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCATGTAG
353974 AATTGCACCGTAGTGCCAT
1 AATTGCACC-TAGTGCCAT
353993 ATAATAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (22 bp):
AATTGCACCTAGTGCCATGTAG
Found at i:354132 original size:103 final size:103
Alignment explanation
Indices: 354007--354327 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
353997 TAATGTCCAT
*
354007 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
354072 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
354110 AAGGACCACATATCATTCCTTAAGAATCATATATATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
354175 GACCTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
354213 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
354278 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
354316 AAGGACCACATA
1 AAGGACCACATA
354328 GACCCTCTAC
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:354847 original size:19 final size:20
Alignment explanation
Indices: 354810--354847 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
354800 TTTTTTATTA
*
354810 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
354830 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
354848 TCTAGCGTTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:360983 original size:23 final size:22
Alignment explanation
Indices: 360957--361020 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
360947 CAGCTCATAT
360957 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACC-AAGTGCCACGTAG
* *
360980 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-AAGTGCCACGTAG
361003 AATTGCACCATAGTGCCA
1 AATTGCACCA-AGTGCCA
361021 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCAAGTGCCACGTAG
Found at i:361161 original size:103 final size:103
Alignment explanation
Indices: 361036--361356 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
361026 TAATGTCCAT
*
361036 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
361101 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
361139 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
361204 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
361242 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
361307 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
361345 AAGGACCACATA
1 AAGGACCACATA
361357 GATCCTCTAC
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:361877 original size:19 final size:20
Alignment explanation
Indices: 361839--361876 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
361829 TTTTTTATTA
*
361839 TGGGGGAATCGGTTCCCCCT
1 TGGGGGAATCGATTCCCCCT
*
361859 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
361877 TCTAGCGTTC
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:0.11, C:0.29, G:0.34, T:0.26
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCT
Found at i:365971 original size:737 final size:738
Alignment explanation
Indices: 364557--366028 Score: 2856
Period size: 737 Copynumber: 2.0 Consensus size: 738
364547 ATGGGGGTAA
*
364557 TAGTGGTTCTGTTTGGTTTTGAAGATAATTGTGATTAATATATAATATTCTGGGTTTTTTATGAT
1 TAGTGGTTCTGTTTGGTTTTGAAGATAATTGCGATTAATATATAATATTCTGGGTTTTTTATGAT
364622 CAAATCGATAGGCTGAGTTCATCCCCAGTAGGTGACGCCGGAATAAATCAGTCAATAGAGCCAGG
66 CAAATCGATAGGCTGAGTTCATCCCCAGTAGGTGACGCCGGAATAAATCAGTCAATAGAGCCAGG
364687 AATTGTCATGCTAGTTAGCTACAAATATTAGGGGACGATAATGGTAAAGTATTTTGATTTTTAAC
131 AATTGTCATGCTAGTTAGCTACAAATATTAGGGGACGATAATGGTAAAGTATTTTGATTTTTAAC
364752 TGGTTCAAAATTGCTAATGAAGATAAAGAACCCGGCTTGTCAATTCACGGTGCTTCATTTCATAG
196 TGGTTCAAAATTGCTAATGAAGATAAAGAACCCGGCTTGTCAATTCACGGTGCTTCATTTCATAG
364817 CAGCGCATTCCTGCTTCATATCATGTTCATTGTGCAGATTGCAGACCACAATAAAAAAAAGTAGC
261 CAGCGCATTCCTGCTTCATATCATGTTCATTGTGCAGATTGCAGACCACAATAAAAAAAAGTAGC
*
364882 AATTGTGCCACAATAAAATCTCCGTGAAGTTTGATTAGGTTGCACATTAAGTTCATGAATGTTTG
326 AATTGTGCCACAATAAAATCTCCGAGAAGTTTGATTAGGTTGCACATTAAGTTCATGAATGTTTG
* *
364947 TCTTATCTCTTTAGCTTTTAATAATCAGAAAGCTCAGAATTTGTGGTCTGTCCTTTTTCATTTAT
391 TCTTATCGCTTTAGCTTTTAATAATCAGAAAGCTCAAAATTTGTGGTCTGTCCTTTTTCATTTAT
365012 ATTCATACCCTTCTCCTTTTAGGATAGCCAATTGTTTCTCCAAAGAGGCTTTAAGCATACAGACT
456 ATTCATACCCTTCTCCTTTTAGGATAGCCAATTGTTTCTCCAAAGAGGCTTTAAGCATACAGACT
*
365077 CCGAAATAATTTGAAAGGATCTTCAGTTTTAGTTTCTATAACTCTTAGATGTATGAAGTTCTGAA
521 CCGAAATAATTCGAAAGGATCTTCAGTTTTAGTTTCTATAACTCTTAGATGTATGAAGTTCTGAA
365142 CTAAAATGAAGCACTTCTCTGCTTTGAAGTAGGATTCTGAAATGTCCTTTGCCAAAGGTCTCTGC
586 CTAAAATGAAGCACTTCTCTGCTTTGAAGTAGGATTCTGAAATGTCCTTTGCCAAAGGTCTCTGC
365207 GACTAAAAGTGGCAATCTACTTCACTGCTGTCAAGCTAGTAAGAAAGGAACTGGTCCTTTCAAAT
651 GACTAAAAGTGGCAATCTACTTCACTGCTGTCAAGCTAGTAAGAAAGGAACTGGTCCTTTCAAAT
365272 ATTAAAGATATTTGCGACTTGGT
716 ATTAAAGATATTTGCGACTTGGT
365295 TAGTGGTTCTGTTTGGTTTTGAAGATAATTGCGATTAATATATAATATTCTGGGTTTTTTATGAT
1 TAGTGGTTCTGTTTGGTTTTGAAGATAATTGCGATTAATATATAATATTCTGGGTTTTTTATGAT
*
365360 CAAATCGATAGGCTGAGTTCATCCCCAGTAGGTGACGCCGGAATAAATCAGTCAATAGATCCAGG
66 CAAATCGATAGGCTGAGTTCATCCCCAGTAGGTGACGCCGGAATAAATCAGTCAATAGAGCCAGG
365425 AATTGTCATGCTAGTTAGCTACAAATATTAGGGGACGATAATGGTAAAGTATTTTGATTTTTAAC
131 AATTGTCATGCTAGTTAGCTACAAATATTAGGGGACGATAATGGTAAAGTATTTTGATTTTTAAC
365490 TGGTTCAAAATTGCTAATGAAGATAAAGAACCCGGCTTGTCAATTCACGGTGCTTCATTTCATAG
196 TGGTTCAAAATTGCTAATGAAGATAAAGAACCCGGCTTGTCAATTCACGGTGCTTCATTTCATAG
365555 CAGCGCATTCCTGCTTCATATCATGTTCATTGTGCAGATTGCAGACCACAATAAAAAAAA-TAGC
261 CAGCGCATTCCTGCTTCATATCATGTTCATTGTGCAGATTGCAGACCACAATAAAAAAAAGTAGC
*
365619 AATTGTGCCACAATAAAATCTCCGAGGAGTTTGATTAGGTTGCACATTAAGTTCATGAATGTTTG
326 AATTGTGCCACAATAAAATCTCCGAGAAGTTTGATTAGGTTGCACATTAAGTTCATGAATGTTTG
365684 TCTTATCGCTTTAGCTTTTAATAATCAGAAAGCTCAAAATTTGTGGTCTGTCCTTTTTCATTTAT
391 TCTTATCGCTTTAGCTTTTAATAATCAGAAAGCTCAAAATTTGTGGTCTGTCCTTTTTCATTTAT
365749 ATTCATACCCTTCTCCTTTTAGGATAGCCAATTGTTTCTCCAAAGAGGCTTTAAGCATACAGACT
456 ATTCATACCCTTCTCCTTTTAGGATAGCCAATTGTTTCTCCAAAGAGGCTTTAAGCATACAGACT
365814 CCGAAATAATTCGAAAGGATCTTCAGTTTTAGTTTCTATAACTCTTAGATGTATGAAGTTCTGAA
521 CCGAAATAATTCGAAAGGATCTTCAGTTTTAGTTTCTATAACTCTTAGATGTATGAAGTTCTGAA
365879 CTAAAATGAAGCACTTCTCTGCTTTGAAGTAGGATTCTGAAATGTCCTTTGCCAAAGGTCTCTGC
586 CTAAAATGAAGCACTTCTCTGCTTTGAAGTAGGATTCTGAAATGTCCTTTGCCAAAGGTCTCTGC
* *
365944 GACTAAATGTGGCAATCTACTTCACTGCTGTCAAGCTAGTAAGAAAGGAATTGGTCCTTTCAAAT
651 GACTAAAAGTGGCAATCTACTTCACTGCTGTCAAGCTAGTAAGAAAGGAACTGGTCCTTTCAAAT
366009 ATTAAAGATATTTGCGACTT
716 ATTAAAGATATTTGCGACTT
366029 AGTATCTATT
Statistics
Matches: 725, Mismatches: 9, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
737 407 0.56
738 318 0.44
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (738 bp):
TAGTGGTTCTGTTTGGTTTTGAAGATAATTGCGATTAATATATAATATTCTGGGTTTTTTATGAT
CAAATCGATAGGCTGAGTTCATCCCCAGTAGGTGACGCCGGAATAAATCAGTCAATAGAGCCAGG
AATTGTCATGCTAGTTAGCTACAAATATTAGGGGACGATAATGGTAAAGTATTTTGATTTTTAAC
TGGTTCAAAATTGCTAATGAAGATAAAGAACCCGGCTTGTCAATTCACGGTGCTTCATTTCATAG
CAGCGCATTCCTGCTTCATATCATGTTCATTGTGCAGATTGCAGACCACAATAAAAAAAAGTAGC
AATTGTGCCACAATAAAATCTCCGAGAAGTTTGATTAGGTTGCACATTAAGTTCATGAATGTTTG
TCTTATCGCTTTAGCTTTTAATAATCAGAAAGCTCAAAATTTGTGGTCTGTCCTTTTTCATTTAT
ATTCATACCCTTCTCCTTTTAGGATAGCCAATTGTTTCTCCAAAGAGGCTTTAAGCATACAGACT
CCGAAATAATTCGAAAGGATCTTCAGTTTTAGTTTCTATAACTCTTAGATGTATGAAGTTCTGAA
CTAAAATGAAGCACTTCTCTGCTTTGAAGTAGGATTCTGAAATGTCCTTTGCCAAAGGTCTCTGC
GACTAAAAGTGGCAATCTACTTCACTGCTGTCAAGCTAGTAAGAAAGGAACTGGTCCTTTCAAAT
ATTAAAGATATTTGCGACTTGGT
Found at i:375191 original size:21 final size:21
Alignment explanation
Indices: 375165--375212 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
375155 TTTTATGTTT
375165 GTTGCTTATGTATAACTTAAG
1 GTTGCTTATGTATAACTTAAG
375186 GTTGCTTATGTATAACTTAAG
1 GTTGCTTATGTATAACTTAAG
375207 GTTGCT
1 GTTGCT
375213 GTCATGCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (21 bp):
GTTGCTTATGTATAACTTAAG
Found at i:378416 original size:17 final size:18
Alignment explanation
Indices: 378391--378427 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
378381 TCCATTGAAA
378391 ATTTAAAATTATA-ATAT
1 ATTTAAAATTATATATAT
*
378408 ATTTTAAATTATATATAT
1 ATTTAAAATTATATATAT
378426 AT
1 AT
378428 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAAAATTATATATAT
Found at i:400951 original size:27 final size:27
Alignment explanation
Indices: 400915--400983 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
400905 ATATTTTAAT
400915 ATATTTTTAAATAAAAATAAAAATAAA
1 ATATTTTTAAATAAAAATAAAAATAAA
* * * *
400942 TTATTTTTAAATTAAATTAATAATAAA
1 ATATTTTTAAATAAAAATAAAAATAAA
*
400969 ATATTTATTTAATAA
1 ATATTT-TTAAATAA
400984 GTTAATATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 28 0.82
28 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATTTTTAAATAAAAATAAAAATAAA
Found at i:400988 original size:27 final size:26
Alignment explanation
Indices: 400936--401014 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
400926 TAAAAATAAA
* * *
400936 AATAAATTATTTTTAAATTAAATTAAT
1 AATAAAATATTTTTTAA-TAAGTTAAT
400963 AATAAAATATTTATTTAATAAGTTAAT
1 AATAAAATATTT-TTTAATAAGTTAAT
400990 -ATAAAAATATTTTTT-A-AAGTTAAT
1 AAT-AAAATATTTTTTAATAAGTTAAT
401014 A
1 A
401015 TATTTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 8 0.17
25 1 0.02
26 5 0.11
27 28 0.61
28 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
AATAAAATATTTTTTAATAAGTTAAT
Found at i:401009 original size:24 final size:26
Alignment explanation
Indices: 400953--401017 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
400943 TATTTTTAAA
400953 TTAAA-TTAATA-ATAAAATATTTAT
1 TTAAAGTTAATATATAAAATATTTAT
400977 TTAATAAGTTAATATA-AAAATATTT-T
1 TT-A-AAGTTAATATATAAAATATTTAT
401003 TTAAAGTTAATATAT
1 TTAAAGTTAATATAT
401018 TTATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
24 13 0.36
25 2 0.06
26 5 0.14
27 15 0.42
28 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
TTAAAGTTAATATATAAAATATTTAT
Found at i:402156 original size:16 final size:16
Alignment explanation
Indices: 402124--402153 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
402114 ATCTCACAAG
402124 ATTAATATTTGAAAAT
1 ATTAATATTTGAAAAT
402140 ATTAA-ATTTGAAAA
1 ATTAATATTTGAAAA
402154 ATAAATTCAA
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:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTAATATTTGAAAAT
Found at i:403881 original size:19 final size:19
Alignment explanation
Indices: 403857--403906 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
403847 TGTTCTGCCT
403857 AGTTTCAAAACTTTTTGGG
1 AGTTTCAAAACTTTTTGGG
403876 AGTTTCAAAACTTTTTGGG
1 AGTTTCAAAACTTTTTGGG
*
403895 AGTTTCGAAACT
1 AGTTTCAAAACT
403907 ATGACCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (19 bp):
AGTTTCAAAACTTTTTGGG
Found at i:412727 original size:25 final size:26
Alignment explanation
Indices: 412699--412760 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
412689 AATTACAAAA
* *
412699 TTTGAATTACTCTATACTTATAAT-T
1 TTTGAATTACTCGAAACTTATAATGT
* *
412724 TTTGAATTAGTCGAAACTTATTATGT
1 TTTGAATTACTCGAAACTTATAATGT
*
412750 TTTTAATTACT
1 TTTGAATTACT
412761 TTTTGTAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (26 bp):
TTTGAATTACTCGAAACTTATAATGT
Found at i:412878 original size:26 final size:25
Alignment explanation
Indices: 412849--412897 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
412839 TAAATTTCGT
412849 CTAATATAAAATTTAT-TAAGTCTCGA
1 CTAAT-TAAAATTT-TGTAAGTCTCGA
*
412875 CTAATTTAAATTTTGTAAGTCTC
1 CTAATTAAAATTTTGTAAGTCTC
412898 AATTAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 15 0.71
26 5 0.24
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (25 bp):
CTAATTAAAATTTTGTAAGTCTCGA
Found at i:412904 original size:25 final size:25
Alignment explanation
Indices: 412857--412904 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
412847 GTCTAATATA
*
412857 AAATTTATTAAGTCTCGACTAATTT
1 AAATTTATTAAGTCTCAACTAATTT
*
412882 AAATTT-TGTAAGTCTCAATTAAT
1 AAATTTAT-TAAGTCTCAACTAAT
412905 CTAATAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (25 bp):
AAATTTATTAAGTCTCAACTAATTT
Found at i:413571 original size:19 final size:19
Alignment explanation
Indices: 413547--413584 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
413537 AGGGTGAGAA
413547 ACTTATGGTGGAGACTGAG
1 ACTTATGGTGGAGACTGAG
413566 ACTTATGGTGGAGACTGAG
1 ACTTATGGTGGAGACTGAG
413585 TAAGCCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (19 bp):
ACTTATGGTGGAGACTGAG
Found at i:418503 original size:20 final size:20
Alignment explanation
Indices: 418474--418521 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
418464 CGTACCTTTT
*
418474 CGACCCCCTAAACATGATTC
1 CGACCTCCTAAACATGATTC
418494 CGACCTCCTAAACATGATTC
1 CGACCTCCTAAACATGATTC
*
418514 CAACCTCC
1 CGACCTCC
418522 GTTTCGTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.42, G:0.08, T:0.21
Consensus pattern (20 bp):
CGACCTCCTAAACATGATTC
Found at i:418651 original size:20 final size:20
Alignment explanation
Indices: 418626--418666 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
418616 TAAAATGGAC
418626 TATGTTGATTTACTCGTCAT
1 TATGTTGATTTACTCGTCAT
*
418646 TATGTTGATTTACTTGTCAT
1 TATGTTGATTTACTCGTCAT
418666 T
1 T
418667 CTCCCGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.54
Consensus pattern (20 bp):
TATGTTGATTTACTCGTCAT
Found at i:440097 original size:24 final size:24
Alignment explanation
Indices: 440027--440097 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
440017 CAATCTTATA
* *
440027 TGGCACTACGGTGC-ATTTCTACA
1 TGGCACTTCGGTGCAATTTCTACG
* * *
440050 CGACACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
440074 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
440098 AGCTGTGGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:446027 original size:15 final size:15
Alignment explanation
Indices: 446007--446045 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
445997 GCAACGGCAA
446007 TTTTCTTTCATTTAC
1 TTTTCTTTCATTTAC
446022 TTTTCTTTCATTTAC
1 TTTTCTTTCATTTAC
446037 TTTTCTTTC
1 TTTTCTTTC
446046 GAAAGGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTCTTTCATTTAC
Found at i:447145 original size:20 final size:20
Alignment explanation
Indices: 447107--447146 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
447097 GACCCGAACT
*
447107 CGACGGGGAAACCCCAAACC
1 CGACGGGGAAACCCAAAACC
*
447127 CGACGGGGAAACCTAAAACC
1 CGACGGGGAAACCCAAAACC
447147 TGGCTAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.25, T:0.03
Consensus pattern (20 bp):
CGACGGGGAAACCCAAAACC
Found at i:447268 original size:2 final size:2
Alignment explanation
Indices: 447261--447295 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
447251 TCCTGCCCCG
447261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
447296 TTTACATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:447320 original size:34 final size:33
Alignment explanation
Indices: 447282--447360 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 33
447272 TATATATATA
447282 TATATATATAATATTTTACATATTTTATATTAAT
1 TATATATATAATATTTTACAT-TTTTATATTAAT
**
447316 TATATATATAATATTTTTTATTTTTATATTAAT
1 TATATATATAATATTTTACATTTTTATATTAAT
447349 TATATAATATAA
1 TATAT-ATATAA
447361 ACCCTAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 17 0.40
34 25 0.60
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATATATAATATTTTACATTTTTATATTAAT
Found at i:447336 original size:18 final size:18
Alignment explanation
Indices: 447262--447336 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
447252 CCTGCCCCGA
*
447262 TATATATATATATATATATA
1 TATATATATA-ATAT-TATT
447282 TATATATATAATA-T-TT
1 TATATATATAATATTATT
* * * *
447298 TACATATTTTATATTAAT
1 TATATATATAATATTATT
*
447316 TATATATATAATATTTTT
1 TATATATATAATATTATT
447334 TAT
1 TAT
447337 TTTTATATTA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
16 11 0.26
17 2 0.05
18 17 0.40
19 3 0.07
20 10 0.23
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATATAATATTATT
Found at i:459878 original size:34 final size:34
Alignment explanation
Indices: 459815--459897 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
459805 TCCCGCCCCG
459815 ATTATATATATATATATTTTACATATTTTATATTA
1 ATTATATATATA-ATATTTTACATATTTTATATTA
** *
459850 ATTATATATATAATATTTTTTATTTTTTATATTA
1 ATTATATATATAATATTTTACATATTTTATATTA
459884 ATTATATAATATAA
1 ATTATAT-ATATAA
459898 ACCCTAAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 26 0.59
35 18 0.41
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTATATATATAATATTTTACATATTTTATATTA
Found at i:463110 original size:28 final size:28
Alignment explanation
Indices: 463029--463100 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
463019 AGTCGCCGAT
* * *
463029 TAAATAAAATT-AAAAAAAATAGATTGA
1 TAAATAAAATTGACACAAAATAAATTGA
* *
463056 TTAATAAAATTTACACAAAATAAATTGA
1 TAAATAAAATTGACACAAAATAAATTGA
463084 TAAATAAAATTGACACA
1 TAAATAAAATTGACACA
463101 TCTTATATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (28 bp):
TAAATAAAATTGACACAAAATAAATTGA
Found at i:465230 original size:12 final size:12
Alignment explanation
Indices: 465213--465237 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
465203 AAGAAATCTT
465213 GGACTGTTATTG
1 GGACTGTTATTG
465225 GGACTGTTATTG
1 GGACTGTTATTG
465237 G
1 G
465238 AGAGGAATCT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GGACTGTTATTG
Found at i:466691 original size:34 final size:34
Alignment explanation
Indices: 466652--466736 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
466642 CGATTATATA
466652 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
466686 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
466720 TATATATAAAATATTTT
1 TATATATATAATATTTT
466737 CGGGTTCGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:468309 original size:60 final size:59
Alignment explanation
Indices: 468217--468396 Score: 193
Period size: 60 Copynumber: 3.0 Consensus size: 59
468207 TATGTCCTCG
* * *
468217 AACTAT-ACTCTCATTTTAAATTGATCCTTAAACATTTGAATATTCTAATTTCATCCCTA
1 AACTATGACTCTCATTCTAAATTGATCCATAAAC-TTTGAATATTCTAATTTCATCCCGA
* * ** * *
468276 AACTATGACTCTCATTCTAAAATGGTCCATAAACTTTTGACCATT-TCATTTCCAACCCGA
1 AACTATGACTCTCATTCTAAATTGATCCATAAAC-TTTGAATATTCTAATTT-CATCCCGA
** * * *
468336 AACTATGACTCTCATTCTAAATTGATCCCCAAACTTTGAATTTTCCAAATTCATCCCGA
1 AACTATGACTCTCATTCTAAATTGATCCATAAACTTTGAATATTCTAATTTCATCCCGA
468395 AA
1 AA
468397 TTCATCCAAA
Statistics
Matches: 97, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
59 27 0.28
60 70 0.72
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (59 bp):
AACTATGACTCTCATTCTAAATTGATCCATAAACTTTGAATATTCTAATTTCATCCCGA
Found at i:468643 original size:58 final size:62
Alignment explanation
Indices: 468531--468752 Score: 200
Period size: 58 Copynumber: 3.7 Consensus size: 62
468521 TAGTTTGGAT
* *
468531 TGAAATTGAAATGTTAAAAAAAGTTTGAGGACCCATTTAGAATGAAGGTCATAGTTTGTAGA
1 TGAAATTGAAATGTTAAAAAAAGTTTGAGGACCAATTTAGAATGAAGGCCATAGTTTGTAGA
* **
468593 TGAAATTGGAATGTT-AAAAAAG-TT-A-GACCAATTTAGAATGAAGGCCATAGTTTGGGGA
1 TGAAATTGAAATGTTAAAAAAAGTTTGAGGACCAATTTAGAATGAAGGCCATAGTTTGTAGA
* * * ** * *
468651 TAAAATTGAAATGCT---CAAAGTTTGAGGATTAATTTAGAATGATAGG-CATAATTTAG-GGA
1 TGAAATTGAAATGTTAAAAAAAGTTTGAGGACCAATTTAGAATGA-AGGCCATAGTTT-GTAGA
*
468710 TGAAATTAGAATAT-TT--AAAAA-TTTAAGGACCAATTTAGAATGA
1 TGAAATT-GAA-ATGTTAAAAAAAGTTTGAGGACCAATTTAGAATGA
468753 TGACCATACT
Statistics
Matches: 134, Mismatches: 18, Indels: 18
0.79 0.11 0.11
Matches are distributed among these distances:
56 4 0.03
57 2 0.01
58 42 0.31
59 31 0.23
60 29 0.22
61 12 0.09
62 14 0.10
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (62 bp):
TGAAATTGAAATGTTAAAAAAAGTTTGAGGACCAATTTAGAATGAAGGCCATAGTTTGTAGA
Found at i:469285 original size:17 final size:17
Alignment explanation
Indices: 469263--469300 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
469253 GTGGTCGTTC
469263 GGTCCCAAAATAGGATG
1 GGTCCCAAAATAGGATG
469280 GGTCCCAAAATAGGATG
1 GGTCCCAAAATAGGATG
469297 GGTC
1 GGTC
469301 GGTTCGTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (17 bp):
GGTCCCAAAATAGGATG
Found at i:470038 original size:15 final size:16
Alignment explanation
Indices: 470010--470042 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
470000 GTTCATTTGA
470010 CATCATCAAATGTTCC
1 CATCATCAAATGTTCC
*
470026 CATC-TCAATTGTTCC
1 CATCATCAAATGTTCC
470041 CA
1 CA
470043 CTGTAGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.33
Consensus pattern (16 bp):
CATCATCAAATGTTCC
Found at i:484286 original size:7 final size:8
Alignment explanation
Indices: 484261--484285 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
484251 CGTTCGTCAG
484261 TTATTTTT
1 TTATTTTT
484269 TTATTTTT
1 TTATTTTT
484277 TTATTTTT
1 TTATTTTT
484285 T
1 T
484286 AATAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:489318 original size:31 final size:31
Alignment explanation
Indices: 489283--489361 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
489273 ATAACGGTTG
*
489283 AGTGACCATTTTGTTACAAATTGATAAAGTT
1 AGTGACCATTTTGTTACAAATCGATAAAGTT
* *
489314 AGTGAACATTTTGTTACAAATCGATAATGTT
1 AGTGACCATTTTGTTACAAATCGATAAAGTT
* *
489345 AGCGACCAATTTGTTAC
1 AGTGACCATTTTGTTAC
489362 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCGATAAAGTT
Found at i:492107 original size:25 final size:25
Alignment explanation
Indices: 492079--492128 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
492069 CACACTTACA
492079 CAGTTACCAAGTGCAGTTAGGGTGT
1 CAGTTACCAAGTGCAGTTAGGGTGT
492104 CAGTTACCAAGTGCAGTTAGGGTGT
1 CAGTTACCAAGTGCAGTTAGGGTGT
492129 TGTTCTGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (25 bp):
CAGTTACCAAGTGCAGTTAGGGTGT
Found at i:496219 original size:220 final size:218
Alignment explanation
Indices: 495837--496277 Score: 823
Period size: 220 Copynumber: 2.0 Consensus size: 218
495827 TCTGATACTA
495837 TCCATAGTACCAGTTCAAGATCCATAAGGACCGCACGAGGAACGTACCTTCCACCGGAAGCCTCA
1 TCCATAGTACCAGTTCAAGATCCATAAGGACCGCACGAGGAACGTACCTTCCACCGGAAGCCTCA
495902 TTGTAATACACATCAATCCGCTCTAGTTGCATATCGATGTTCCATCTCCAGTGTACCTTCCGTAG
66 TTGTAATACACATCAATCCGCTCTAGTTGCATATCGATGTTCCATCTCCAGTGTACCTTCCGTA-
495967 GATCACACCGTGCTCGCCGCATATCACTTCCCAAAAACTTGGATCCGATTTGGTTCCCGCATTGA
130 GATCACACCGTGCTCGCCGCATATCACTTCCC-AAAACTTGGATCCGATTTGGTTCCCGCATTGA
496032 CCTCCTTGAACATGAAGGATTTCTC
194 CCTCCTTGAACATGAAGGATTTCTC
496057 TCCATAGTACCAGGTTCAAGATCCATAAGGACCGCACGA-GAACGTACCTTCCACCGGAAGCCTC
1 TCCATAGTACCA-GTTCAAGATCCATAAGGACCGCACGAGGAACGTACCTTCCACCGGAAGCCTC
496121 ATTGTAATACACATCAATCCGCTCTAGTTGCATATCGATGTTCCATCTCCAGTGTACCTTCCGGT
65 ATTGTAATACACATCAATCCGCTCTAGTTGCATATCGATGTTCCATCTCCAGTGTACCTTCC-GT
496186 A-ATCAACACCGTGCTCGCCGCATATCACTTCCCAAAACTTGGATCCGATTTGGTTCCCGCATTG
129 AGATC-ACACCGTGCTCGCCGCATATCACTTCCCAAAACTTGGATCCGATTTGGTTCCCGCATTG
496250 ACCTCCTTGAACATGAAGGATTTCTC
193 ACCTCCTTGAACATGAAGGATTTCTC
496276 TC
1 TC
496278 ATTGTTTAAA
Statistics
Matches: 218, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
219 62 0.28
220 127 0.58
221 29 0.13
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (218 bp):
TCCATAGTACCAGTTCAAGATCCATAAGGACCGCACGAGGAACGTACCTTCCACCGGAAGCCTCA
TTGTAATACACATCAATCCGCTCTAGTTGCATATCGATGTTCCATCTCCAGTGTACCTTCCGTAG
ATCACACCGTGCTCGCCGCATATCACTTCCCAAAACTTGGATCCGATTTGGTTCCCGCATTGACC
TCCTTGAACATGAAGGATTTCTC
Found at i:497024 original size:21 final size:20
Alignment explanation
Indices: 497000--497061 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
496990 GGTAAAAAAA
497000 TATTTAAAATATTATTATTTT
1 TATTTAAAATA-TATTATTTT
497021 TATTT-AAATACTATTATTTT
1 TATTTAAAATA-TATTATTTT
* *
497041 TACTTAAAATATAATATTTT
1 TATTTAAAATATATTATTTT
497061 T
1 T
497062 TAATATTTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 27 0.73
21 10 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTAAAATATATTATTTT
Found at i:501616 original size:62 final size:60
Alignment explanation
Indices: 501518--501634 Score: 198
Period size: 62 Copynumber: 1.9 Consensus size: 60
501508 GTCCCCGAAT
*
501518 AATAGATCTATGTTGACCATTTTTATTGTCATTAATATGACTCGTCATCTCAACGTGATA
1 AATAGATCCATGTTGACCATTTTTATTGTCATTAATATGACTCGTCATCTCAACGTGATA
*
501578 AATAGGTCCATGTTGACCATTGTTTTATTGTCATTAATATGACTCGTCATCTCAACG
1 AATAGATCCATGTTGACCA-T-TTTTATTGTCATTAATATGACTCGTCATCTCAACG
501635 AGACAAATCT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 17 0.32
61 1 0.02
62 35 0.66
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (60 bp):
AATAGATCCATGTTGACCATTTTTATTGTCATTAATATGACTCGTCATCTCAACGTGATA
Found at i:501834 original size:15 final size:15
Alignment explanation
Indices: 501814--501843 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
501804 TATTCGGTCG
501814 ATTAAAATTTAAAAA
1 ATTAAAATTTAAAAA
501829 ATTAAAATTTAAAAA
1 ATTAAAATTTAAAAA
501844 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAAAATTTAAAAA
Found at i:502831 original size:15 final size:16
Alignment explanation
Indices: 502800--502832 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
502790 AAACTGTAAA
502800 TAGTAAATATCAAAGT
1 TAGTAAATATCAAAGT
*
502816 TAGTATATAT-AAAGT
1 TAGTAAATATCAAAGT
502831 TA
1 TA
502833 AAAAATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (16 bp):
TAGTAAATATCAAAGT
Found at i:503042 original size:25 final size:25
Alignment explanation
Indices: 502996--503049 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
502986 TATAAACAAA
**
502996 TAAAAAATAATTAAATTTATGAAAT
1 TAAAAAATAATTAAATAAATGAAAT
*
503021 TAAAAAA-AAGTTAAATAAATGAAGT
1 TAAAAAATAA-TTAAATAAATGAAAT
503046 TAAA
1 TAAA
503050 CAATTACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (25 bp):
TAAAAAATAATTAAATAAATGAAAT
Found at i:503860 original size:15 final size:15
Alignment explanation
Indices: 503840--503869 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
503830 TGGACATTAT
*
503840 CCAAGTGGTCGTTGC
1 CCAAGTGATCGTTGC
503855 CCAAGTGATCGTTGC
1 CCAAGTGATCGTTGC
503870 ATTTGCTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (15 bp):
CCAAGTGATCGTTGC
Found at i:506293 original size:21 final size:21
Alignment explanation
Indices: 506269--506312 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
506259 GATAAAAATC
*
506269 ATTTATTAATATGTTGTCTTG
1 ATTTATTAATATATTGTCTTG
* *
506290 ATTTATTACTATATTGTGTTG
1 ATTTATTAATATATTGTCTTG
506311 AT
1 AT
506313 AATGTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTTATTAATATATTGTCTTG
Found at i:507342 original size:20 final size:21
Alignment explanation
Indices: 507312--507350 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
507302 ATTACAGGTA
507312 CAAATATGACAAAACCGGTCT
1 CAAATATGACAAAACCGGTCT
507333 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
507351 AAAACGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCT
Found at i:508031 original size:183 final size:183
Alignment explanation
Indices: 507299--508148 Score: 1048
Period size: 183 Copynumber: 4.7 Consensus size: 183
507289 GTTCCATAGC
* * * * * *
507299 AATATTACAGGTACAAATATGACAAAACCGGTCTC-AAAATGACAAAACC-GGTAAAACGCTACC
1 AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCAGG-AAAAAGTTACC
* * * *
507362 GAATATGTT-ATCGAGTGTCGATAATTTAATATAAATATCGAAACTTTCTGAATTTAAAAGAGAA
65 GGATATGTTGA--AAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAA
* * * * * *
507426 TAAGTTATAGCACCTATAAAGTGTCGACACTTTAAAAAAATATATCGATCCACAAC
128 GAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCACAAT
* * * *
507482 AATATAATAGGTAAAAATATGATAAAACTGGTCTAAAAAATGAC-AAACC-GGAAAAAGTTACCA
1 AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCAGGAAAAAGTTACCG
* *
507545 GATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
* ** **
507610 GTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTACC
131 GTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCACAAT
* * * **
507663 AATATAATAGGTAAAAATATGATAAAACATGTCTCAAAAATGACAAAACC-GGAAAAATTTACTA
1 AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCAGGAAAAAGTTACCG
* * * * *
507727 GATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGATAATTTCTAAATTTAAAAGAGAAAAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
* * * * *
507792 GTTATTGCGCTTAAAAAATGTCGACACTTTATGAAAATGTATCGATCCATAAT
131 GTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCACAAT
* * * *
507845 AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCG
1 AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCAGGAAAAAGTTACCG
* * * * *
507910 GATATATTGAAAGTGTCGATAATTTAATATAAGTATCAAAACTTTCTGAATTTTAAAGAAAAGAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
* * * *
507975 GTTATAGTGCCTATAAAGTGTCGATACTTT-TAAAAAATATATCGATCCACAAT
131 GTTATAGCGCCTAAAAAGTGTCGACACTTTAT-AAAAATGTATCGATCCACAAT
* * * * * * *
508028 AATATAACAGGTAAAAATATGATAAAACAGATCCCAAAATTGACAAAACCAGTAAAACGATATCG
1 AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCAGGAAAAAGTTACCG
*
508093 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAAATTAAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAA
508149 CTAAAAAGTG
Statistics
Matches: 584, Mismatches: 78, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
181 136 0.23
182 185 0.32
183 255 0.44
184 8 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (183 bp):
AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCAGGAAAAAGTTACCG
GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
GTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCACAAT
Found at i:508482 original size:182 final size:182
Alignment explanation
Indices: 508150--508648 Score: 695
Period size: 182 Copynumber: 2.7 Consensus size: 182
508140 GAAATTAAAC
* *
508150 TAAAAAGTGTCTACACTTTATGAAAATGTATCGATCCATAACAATATAA-AAGGTAAAAATATGA
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTAACAATATAACAA-GTAAAAATATGA
* * *
508214 TAAAA-TTGGTCTCAAAAATGACAAAATC-GGAAAAAGTTACCGAATATATTGAAAGTGTCGATA
65 TAAAACAT-GTCTCAAAAATGACAAAA-CAGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATA
* * *
508277 ATTTAATATTAGTATCAACACTTTCTGAATTTAAAAGAGAATAAGTTATAGCGCT
128 ATTTAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
* * * *
508332 TAAAAAATGTCGACACTTTATTAAAATGTATCGATCCTTACCAATATAACAAGTAAAAATATAAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTAACAATATAACAAGTAAAAATATGAT
*
508397 AAAACATGTCTCAAAAATGACAAAACAGGAAAAAGTTATCGGATATGTTGAAAGTGTCGATAATT
66 AAAACATGTCTCAAAAATGACAAAACAGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
*
508462 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
131 TAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
* * *
508514 TAAAAAGTATCGACACTTTATGAAAATGTATCGAT-CTAGAATAATATAAC-AGATAAAAATATG
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCT-TAACAATATAACAAG-TAAAAATATG
** * * *
508577 ATAAAACCGGTCTC-AAAATGACAAAACAGGTAAATAGATACCGGATATGTTGAAAGTGTAGATA
64 ATAAAACATGTCTCAAAAATGACAAAACAGG-AAAAAGTTACCGGATATGTTGAAAGTGTCGATA
*
508641 CTTTAATA
128 ATTTAATA
508649 AGTACGCGTA
Statistics
Matches: 283, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
181 21 0.07
182 259 0.92
183 3 0.01
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.28
Consensus pattern (182 bp):
TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTAACAATATAACAAGTAAAAATATGAT
AAAACATGTCTCAAAAATGACAAAACAGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
TAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
Found at i:509059 original size:18 final size:19
Alignment explanation
Indices: 509036--509080 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
509026 TAGTTAATAT
509036 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
509054 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
509073 TTTTAGGT
1 TTATAGGT
509081 TGTATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:509361 original size:18 final size:18
Alignment explanation
Indices: 509326--509364 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
509316 TTGAAATGGT
509326 AATTGGATTAAAACTTTA
1 AATTGGATTAAAACTTTA
*
509344 AATT-GATTACAAATTTTA
1 AATTGGATTA-AAACTTTA
509362 AAT
1 AAT
509365 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTGGATTAAAACTTTA
Found at i:514826 original size:22 final size:22
Alignment explanation
Indices: 514775--514830 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
514765 ATGTTTTTGT
*
514775 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
514798 TAGTTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
514820 CTTTTATTATA
1 -TTTTATTATA
514831 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 17 0.61
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Done.