Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007719.1 Hibiscus syriacus cultivar Beakdansim tig00109951_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: 308719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:185476 original size:32 final size:32
Alignment explanation
Indices: 185439--185503 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
185429 TTTGAAATTT
185439 ATTTGAGAAA-AATCAAGAAACTTCCGAAAATC
1 ATTTGA-AAATAATCAAGAAACTTCCGAAAATC
* *
185471 ATTTGAAAATCATCAAGAAACTTCTGAAAATC
1 ATTTGAAAATAATCAAGAAACTTCCGAAAATC
185503 A
1 A
185504 GACTTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (32 bp):
ATTTGAAAATAATCAAGAAACTTCCGAAAATC
Found at i:188027 original size:8 final size:8
Alignment explanation
Indices: 188014--188068 Score: 83
Period size: 8 Copynumber: 6.8 Consensus size: 8
188004 ATTCTTTCTT
188014 TTTTTTCC
1 TTTTTTCC
**
188022 TTTTTTTAT
1 -TTTTTTCC
188031 TTTTTTCC
1 TTTTTTCC
188039 TTTTTTCC
1 TTTTTTCC
188047 TTTTTTCC
1 TTTTTTCC
188055 TTTTTTCC
1 TTTTTTCC
188063 TTTTTT
1 TTTTTT
188069 TTCTTCTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
8 36 0.86
9 6 0.14
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:188031 original size:25 final size:24
Alignment explanation
Indices: 188002--188071 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
187992 TTTTTATTAC
188002 TTATTCTTTCTTTTTTTTCCTTTTT
1 TTATT-TTTCTTTTTTTTCCTTTTT
188027 TTATTTTT-TTCCTTTTTTCCTTTTT
1 TTATTTTTCTT--TTTTTTCCTTTTT
188052 TCCT-TTTTTCCTTTTTTTTC
1 T--TATTTTT-CTTTTTTTTC
188072 TTCTTCCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
23 2 0.05
24 3 0.08
25 19 0.49
26 12 0.31
27 1 0.03
28 2 0.05
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (24 bp):
TTATTTTTCTTTTTTTTCCTTTTT
Found at i:188067 original size:17 final size:17
Alignment explanation
Indices: 188008--188069 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
187998 TTACTTATTC
*
188008 TTTCTTTTTTTTCCTTT
1 TTTCCTTTTTTTCCTTT
**
188025 TTTTATTTTTTTCCTTT
1 TTTCCTTTTTTTCCTTT
188042 TTTCC-TTTTTTCCTTT
1 TTTCCTTTTTTTCCTTT
188058 TTTCCTTTTTTT
1 TTTCCTTTTTTT
188070 TCTTCTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.40
17 24 0.60
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTCCTTTTTTTCCTTT
Found at i:188799 original size:170 final size:170
Alignment explanation
Indices: 188513--188855 Score: 632
Period size: 170 Copynumber: 2.0 Consensus size: 170
188503 ACATTATACA
188513 TATATGTTTTATACATAATAAGGAAGACTTGTGATAAGTCAACCTTGTTTATATTATCATGATAA
1 TATATGTTTTATACATAATAAGGAAGACTTGTGATAAGTCAACCTTGTTTATATTATCATGATAA
* * *
188578 TATGTCATTTTTATAACTTTGATATGGCATTGATATGTTATAGTGTGAAATTATAATGCATTGAT
66 TATGTCATTTTTATAACTTTGATATGACATTGATATGTTATAGTATGAAATTATAATGCATTCAT
188643 CATGAATAATATGATATTTTACCATTAATGTTATTTTGGG
131 CATGAATAATATGATATTTTACCATTAATGTTATTTTGGG
* *
188683 TATATGTTTTATACATCATAAGGAAGACTTGTGATAAGTCAGCCTTGTTTATATTATCATGATAA
1 TATATGTTTTATACATAATAAGGAAGACTTGTGATAAGTCAACCTTGTTTATATTATCATGATAA
*
188748 TATTTCATTTTTATAACTTTGATATGACATTGATATGTTATAGTATGAAATTATAATGCATTCAT
66 TATGTCATTTTTATAACTTTGATATGACATTGATATGTTATAGTATGAAATTATAATGCATTCAT
188813 CATGAATAATATGATATTTTACCATTAATGTTATTTTGGG
131 CATGAATAATATGATATTTTACCATTAATGTTATTTTGGG
188853 TAT
1 TAT
188856 GAACTGCCCA
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
170 167 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (170 bp):
TATATGTTTTATACATAATAAGGAAGACTTGTGATAAGTCAACCTTGTTTATATTATCATGATAA
TATGTCATTTTTATAACTTTGATATGACATTGATATGTTATAGTATGAAATTATAATGCATTCAT
CATGAATAATATGATATTTTACCATTAATGTTATTTTGGG
Found at i:189211 original size:20 final size:20
Alignment explanation
Indices: 189175--189214 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
189165 ATATATTGGA
*
189175 CTATTGTCTATTATTTATGG
1 CTATTGTCTATGATTTATGG
*
189195 CTATTGTCTATGGTTTATGG
1 CTATTGTCTATGATTTATGG
189215 TTTATTGCTT
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:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (20 bp):
CTATTGTCTATGATTTATGG
Found at i:189274 original size:45 final size:45
Alignment explanation
Indices: 189225--189443 Score: 357
Period size: 45 Copynumber: 4.8 Consensus size: 45
189215 TTTATTGCTT
* *
189225 AATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGTAAGTGTATTGATAAAATAAGCTTACGAGCTTATGG
* *
189270 AATAAATGGCAAGTGTATTGATAAAATAAGCTTACAAGCTTATGG
1 AATAAATGGTAAGTGTATTGATAAAATAAGCTTACGAGCTTATGG
* *
189315 AATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGTAAGTGTATTGATAAAATAAGCTTACGAGCTTATGG
*
189360 AATAAATGGAAAGTGTATTGATAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGTAAGTGTATTGATAAAATAAGCTTACGAGCTTATGG
*
189405 AAATAAATGGTAAGTGTATTGACAAAATAAGCTTACGAG
1 -AATAAATGGTAAGTGTATTGATAAAATAAGCTTACGAG
189444 TTTTTAGGAT
Statistics
Matches: 160, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 124 0.77
46 36 0.22
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29
Consensus pattern (45 bp):
AATAAATGGTAAGTGTATTGATAAAATAAGCTTACGAGCTTATGG
Found at i:190279 original size:15 final size:15
Alignment explanation
Indices: 190259--190315 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
190249 AACCGGGTAA
190259 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
190274 CGGGTACTCGCAAAATC
1 CGGGTACCCG-ATTA-C
* *
190291 CAGGTACCCGATTAT
1 CGGGTACCCGATTAC
190306 CGGGTACCCG
1 CGGGTACCCG
190316 TAACATCCAG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
15 18 0.58
16 4 0.13
17 9 0.29
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:190302 original size:32 final size:32
Alignment explanation
Indices: 190261--190327 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
190251 CCGGGTAACG
*
190261 GGTACCCGATTACCGGGTACTCGCAAAATCCA
1 GGTACCCGATTACCGGGTACCCGCAAAATCCA
* * *
190293 GGTACCCGATTATCGGGTACCCGTAACATCCA
1 GGTACCCGATTACCGGGTACCCGCAAAATCCA
190325 GGT
1 GGT
190328 TGGGACACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.21
Consensus pattern (32 bp):
GGTACCCGATTACCGGGTACCCGCAAAATCCA
Found at i:190386 original size:15 final size:16
Alignment explanation
Indices: 190366--190407 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
190356 CGGAAGTTTT
190366 GGGTACCCGGAAAT-C
1 GGGTACCCGGAAATCC
*
190381 GGGTACCCGAAAATCC
1 GGGTACCCGGAAATCC
190397 GGGTACCCGGA
1 GGGTACCCGGA
190408 TTTGCACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.26, C:0.29, G:0.33, T:0.12
Consensus pattern (16 bp):
GGGTACCCGGAAATCC
Found at i:191735 original size:89 final size:89
Alignment explanation
Indices: 191609--191828 Score: 291
Period size: 89 Copynumber: 2.5 Consensus size: 89
191599 CATTTCTTAT
* * * *
191609 CAATATATTTACCA-TATATCCCATAAGCTTGTAAGCTTATTTTACCAACATACTTATCA-TTAT
1 CAATATACTTACCATTA-AT-CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTAA
191672 TCCATAAGCTCATAAGCTTAATTTAC
64 TCCATAAGCTCATAAGCTTAATTTAC
* * *
191698 CAATATACTTATCATTTAATCCATAAGATCGTAAGCTTATTTTACCAATATACTTACCATTTAAT
1 CAATATACTTACCA-TTAATCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTAAT
* *
191763 CCATAAGCTCTTAAGCTTATTTTAC
65 CCATAAGCTCATAAGCTTAATTTAC
* * *
191788 CAATATACTTGCCATTATTCAATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTAATCCATAAGCTCGTAAGCTTATTT
191829 GCATGCTTAC
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
89 71 0.62
90 41 0.36
91 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (89 bp):
CAATATACTTACCATTAATCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTAATC
CATAAGCTCATAAGCTTAATTTAC
Found at i:191736 original size:45 final size:44
Alignment explanation
Indices: 191609--191828 Score: 280
Period size: 45 Copynumber: 4.9 Consensus size: 44
191599 CATTTCTTAT
* *
191609 CAATATATTTACCA-TATATCCCATAAGCTTGTAAGCTTATTTTAC
1 CAATATACTTACCATTA-AT-CCATAAGCTCGTAAGCTTATTTTAC
* * * * *
191654 CAACATACTTATCATTATTCCATAAGCTCATAAGCTTAATTTAC
1 CAATATACTTACCATTAATCCATAAGCTCGTAAGCTTATTTTAC
* *
191698 CAATATACTTATCATTTAATCCATAAGATCGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTAATCCATAAGCTCGTAAGCTTATTTTAC
*
191743 CAATATACTTACCATTTAATCCATAAGCTCTTAAGCTTATTTTAC
1 CAATATACTTACCA-TTAATCCATAAGCTCGTAAGCTTATTTTAC
* * *
191788 CAATATACTTGCCATTATTCAATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTAATCCATAAGCTCGTAAGCTTATTT
191829 GCATGCTTAC
Statistics
Matches: 154, Mismatches: 19, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
44 59 0.38
45 93 0.60
46 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (44 bp):
CAATATACTTACCATTAATCCATAAGCTCGTAAGCTTATTTTAC
Found at i:194406 original size:20 final size:21
Alignment explanation
Indices: 194383--194429 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
194373 GTAAACCATG
194383 TATAGTATATAT-AAACTATA
1 TATAGTATATATAAAACTATA
194403 TATA-TATATATAAAACTATA
1 TATAGTATATATAAAACTATA
*
194423 TAAAGTA
1 TATAGTA
194430 AATTACTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 15 0.62
21 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
TATAGTATATATAAAACTATA
Found at i:194515 original size:7 final size:7
Alignment explanation
Indices: 194499--194570 Score: 54
Period size: 7 Copynumber: 10.3 Consensus size: 7
194489 TTGTTTATAG
*
194499 AAACCTT
1 AAACCCT
194506 AAACCCT
1 AAACCCT
* *
194513 AAATCAT
1 AAACCCT
*
194520 AAATCCT
1 AAACCCT
**
194527 AAACTTT
1 AAACCCT
194534 AAACCCT
1 AAACCCT
**
194541 AAATGCT
1 AAACCCT
*
194548 AAACACT
1 AAACCCT
*
194555 AAACCAT
1 AAACCCT
194562 AAACCCT
1 AAACCCT
194569 AA
1 AA
194571 TATAAATGGA
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:194536 original size:21 final size:21
Alignment explanation
Indices: 194505--194570 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
194495 ATAGAAACCT
* *
194505 TAAACCCTAAATCATAAATCC
1 TAAACACTAAACCATAAATCC
** * *
194526 TAAACTTTAAACCCTAAATGC
1 TAAACACTAAACCATAAATCC
*
194547 TAAACACTAAACCATAAACCC
1 TAAACACTAAACCATAAATCC
194568 TAA
1 TAA
194571 TATAAATGGA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAACACTAAACCATAAATCC
Found at i:194539 original size:28 final size:29
Alignment explanation
Indices: 194499--194577 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
194489 TTGTTTATAG
194499 AAACCTTAAACCCTAAATCATAAATC-CT
1 AAACCTTAAACCCTAAATCATAAATCACT
*
194527 AAACTTTAAACCCTAAATGC-TAAA-CACT
1 AAACCTTAAACCCTAAAT-CATAAATCACT
*
194555 AAACCATAAACCCT-AAT-ATAAAT
1 AAACCTTAAACCCTAAATCATAAAT
194578 GGATTAGCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.09
27 4 0.09
28 35 0.80
29 1 0.02
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.24
Consensus pattern (29 bp):
AAACCTTAAACCCTAAATCATAAATCACT
Found at i:194550 original size:14 final size:14
Alignment explanation
Indices: 194505--194570 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 14
194495 ATAGAAACCT
194505 TAAACCCTAAATCA
1 TAAACCCTAAATCA
* *
194519 TAAATCCTAAA-CTT
1 TAAACCCTAAATC-A
194533 TAAACCCTAAATGC-
1 TAAACCCTAAAT-CA
* *
194547 TAAACACTAAACCA
1 TAAACCCTAAATCA
194561 TAAACCCTAA
1 TAAACCCTAA
194571 TATAAATGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.05
14 39 0.93
16 1 0.02
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:201710 original size:22 final size:22
Alignment explanation
Indices: 201667--201707 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
201657 AAGAATATTT
*
201667 TCATTTTTTTAATTTTGAAATA
1 TCATTTTTCTAATTTTGAAATA
201689 TCATTTTTCT-ATTTTGAAA
1 TCATTTTTCTAATTTTGAAA
201708 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (22 bp):
TCATTTTTCTAATTTTGAAATA
Found at i:204118 original size:23 final size:24
Alignment explanation
Indices: 204088--204133 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
204078 TTTTTCTTTA
204088 TATAAATTAAACTATA-TAATTTT
1 TATAAATTAAACTATATTAATTTT
204111 TATAAATTAAACTATATTAATTT
1 TATAAATTAAACTATATTAATTT
204134 CCTTTGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAAATTAAACTATATTAATTTT
Found at i:204182 original size:25 final size:22
Alignment explanation
Indices: 204154--204206 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
204144 ATTAATCATG
204154 TTTTATCTAATTTACATTTAAATAA
1 TTTTAT-TAATTT-CA-TTAAATAA
*
204179 TTTTATTAATTTTATTAAATAA
1 TTTTATTAATTTCATTAAATAA
204201 TTTTAT
1 TTTTAT
204207 ATAACAGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.52
23 1 0.04
24 6 0.22
25 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTAATTTCATTAAATAA
Found at i:209006 original size:39 final size:39
Alignment explanation
Indices: 208948--209023 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
208938 CTATACACCT
* * *
208948 GGTAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCCTGC
1 GGTAAGATCTTATCATGTGCACAAAGAAGAGGAGCCTGC
*
208987 GGTAAGATCTTATCATGTGCACAAAGAAGATGAGCCT
1 GGTAAGATCTTATCATGTGCACAAAGAAGAGGAGCCT
209024 ATGGTAACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (39 bp):
GGTAAGATCTTATCATGTGCACAAAGAAGAGGAGCCTGC
Found at i:209066 original size:44 final size:44
Alignment explanation
Indices: 209018--209132 Score: 194
Period size: 44 Copynumber: 2.6 Consensus size: 44
209008 CAAAGAAGAT
* * *
209018 GAGCCTATGGTAACGGTAAGGACTTACCTTTGCACATAGCAAAG
1 GAGCCTACGGTAACGGTAAGGACTTACCCTTGCACACAGCAAAG
*
209062 GAGCCTACGGTAACGGTAAGGACTTACCCTTGCACACAGCAGAG
1 GAGCCTACGGTAACGGTAAGGACTTACCCTTGCACACAGCAAAG
209106 GAGCCTACGGTAACGGTAAGGACTTAC
1 GAGCCTACGGTAACGGTAAGGACTTAC
209133 AAGTCATAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.19
Consensus pattern (44 bp):
GAGCCTACGGTAACGGTAAGGACTTACCCTTGCACACAGCAAAG
Found at i:215840 original size:44 final size:44
Alignment explanation
Indices: 215792--215899 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 44
215782 ATCATGACGA
* ** *
215792 CGGTAACGATAAGGACTTACCTTTACACATATCAGAGGAGCCCG
1 CGGTAACGATAAGGACTTACCCTTACACATAGAAGAGGAGCCAG
* * *
215836 CGGTAACGGTAAGGATTTACCCTTGCACATAGAAGAGGAGCCAG
1 CGGTAACGATAAGGACTTACCCTTACACATAGAAGAGGAGCCAG
*
215880 CGATAAC-AGTAAGGACTTAC
1 CGGTAACGA-TAAGGACTTAC
215900 AAATCATAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (44 bp):
CGGTAACGATAAGGACTTACCCTTACACATAGAAGAGGAGCCAG
Found at i:217457 original size:3 final size:3
Alignment explanation
Indices: 217449--217486 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
217439 GCTTATATTT
217449 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
217487 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:217491 original size:3 final size:3
Alignment explanation
Indices: 217485--217529 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
217475 GATGATGATG
217485 ATT ATT ATT ATT ATT ATT 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
217530 CAGGTTGTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:217732 original size:3 final size:3
Alignment explanation
Indices: 217718--217761 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
217708 AAAAAGAGAT
*
217718 GAA GAT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
217762 CAATGGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:219521 original size:33 final size:33
Alignment explanation
Indices: 219484--219615 Score: 205
Period size: 33 Copynumber: 4.0 Consensus size: 33
219474 ATTTGGCAAG
219484 TTGGAAAATTT-ATCTTGGTTGGTGGCCAACTTA
1 TTGG-AAATTTCATCTTGGTTGGTGGCCAACTTA
219517 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
219550 TTGGAAATTTCATCTTGGTTAGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
219583 TTGG-AATATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAT-TTCATC-TTGGTTGGTGGCCAACTT
219616 TGCACATGGG
Statistics
Matches: 93, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
32 9 0.10
33 68 0.73
34 16 0.17
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.39
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:224314 original size:34 final size:33
Alignment explanation
Indices: 224229--224327 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
224219 ATTTGGCAAG
* *
224229 TTGGAAACTTCATCTTGGTTGGTAGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
224262 TTGGAAATTTCATCTTGGTTGGTGGCCATCTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
224295 TTGGAAAATTCATCTTTGGTAT-GTGGCCAACTT
1 TTGGAAAATTCATC-TTGGT-TGGTGGCCAACTT
224328 TGCACATGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
33 43 0.73
34 15 0.25
35 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:227338 original size:11 final size:11
Alignment explanation
Indices: 227322--227351 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
227312 TATTTTTCAT
227322 TTTATTTACTC
1 TTTATTTACTC
*
227333 TTTATTTACTG
1 TTTATTTACTC
227344 TTTATTTA
1 TTTATTTA
227352 ACATTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTATTTACTC
Found at i:227922 original size:2 final size:2
Alignment explanation
Indices: 227915--227991 Score: 74
Period size: 2 Copynumber: 41.0 Consensus size: 2
227905 ATAATTATTT
227915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
227954 AA TT TA -A TT TA AA T- TA AA 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
227992 AAGGAGATTA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
1 5 0.08
2 55 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:228174 original size:32 final size:32
Alignment explanation
Indices: 228106--228195 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
228096 CTGGTGACTT
* * *
228106 CACTTCGTCGGCCGATCTT-CCTTTCCCTCGC
1 CACTTCGACGGCCGATCTTCCCCTTCCCTAGC
* * *
228137 CACTTCGCCGGTCGATCTTCCCCTTCCCTAGT
1 CACTTCGACGGCCGATCTTCCCCTTCCCTAGC
* *
228169 TACTTCTACGGCCGATCTTCCCCTTCC
1 CACTTCGACGGCCGATCTTCCCCTTCC
228196 GAGTTCCGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 17 0.35
32 32 0.65
ACGTcount: A:0.09, C:0.44, G:0.14, T:0.32
Consensus pattern (32 bp):
CACTTCGACGGCCGATCTTCCCCTTCCCTAGC
Found at i:230098 original size:25 final size:25
Alignment explanation
Indices: 230068--230144 Score: 118
Period size: 25 Copynumber: 3.1 Consensus size: 25
230058 CTCATATAAA
230068 TTGCACCGAAGTGCCGCGTAGAATT
1 TTGCACCGAAGTGCCGCGTAGAATT
* *
230093 TTGCACTGAAGTGCCGCGTAGATTT
1 TTGCACCGAAGTGCCGCGTAGAATT
* *
230118 TTGGACCGAAGTGTCGCGTAGAATT
1 TTGCACCGAAGTGCCGCGTAGAATT
230143 TT
1 TT
230145 ATCCCGAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (25 bp):
TTGCACCGAAGTGCCGCGTAGAATT
Found at i:230151 original size:25 final size:24
Alignment explanation
Indices: 230068--230153 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 24
230058 CTCATATAAA
230068 TTGCACCGAAGTGCCGCGTAGAATT
1 TTGC-CCGAAGTGCCGCGTAGAATT
* *
230093 TTGCACTGAAGTGCCGCGTAGATTT
1 TTGC-CCGAAGTGCCGCGTAGAATT
* *
230118 TTGGACCGAAGTGTCGCGTAGAATT
1 TT-GCCCGAAGTGCCGCGTAGAATT
*
230143 TTATCCCGAAG
1 TT-GCCCGAAG
230154 GACCACATAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
25 50 0.98
26 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (24 bp):
TTGCCCGAAGTGCCGCGTAGAATT
Found at i:231885 original size:21 final size:21
Alignment explanation
Indices: 231861--231913 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
231851 TCGGTTGAGG
231861 GGGTATCGATTCCCATTGAAT
1 GGGTATCGATTCCCATTGAAT
*
231882 GGGTATCGATTCTCATTGAAT
1 GGGTATCGATTCCCATTGAAT
*
231903 GGGTACCGATT
1 GGGTATCGATT
231914 GCCCTAGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (21 bp):
GGGTATCGATTCCCATTGAAT
Found at i:236580 original size:23 final size:22
Alignment explanation
Indices: 236533--236603 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
236523 CCTATAACTT
* * * *
236533 ATATCTCATGTTCATATAGCTC
1 ATATATCATTTTCATATAACAC
* *
236555 ATATATCATTTTTCCTATAATAC
1 ATATATCA-TTTTCATATAACAC
*
236578 ATAAATCATTTTCATATAACAC
1 ATATATCATTTTCATATAACAC
236600 ATAT
1 ATAT
236604 CATAAAAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 22 0.58
23 16 0.42
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
ATATATCATTTTCATATAACAC
Found at i:236972 original size:20 final size:22
Alignment explanation
Indices: 236947--236993 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
236937 TAATCACTTT
236947 TTCCCT-TT-AGGGGGAATCGG
1 TTCCCTATTGAGGGGGAATCGG
*
236967 TTCCCTATTGTGGGGGAATCGG
1 TTCCCTATTGAGGGGGAATCGG
236989 TTCCC
1 TTCCC
236994 CCATGACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.25
21 2 0.08
22 16 0.67
ACGTcount: A:0.13, C:0.23, G:0.32, T:0.32
Consensus pattern (22 bp):
TTCCCTATTGAGGGGGAATCGG
Found at i:237046 original size:21 final size:21
Alignment explanation
Indices: 237022--237061 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
237012 TCTGGTTCCG
*
237022 TTGAGGGGGTATCGATTCCTA
1 TTGAAGGGGTATCGATTCCTA
*
237043 TTGAATGGGTATCGATTCC
1 TTGAAGGGGTATCGATTCC
237062 CCTAGCCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCTA
Found at i:238762 original size:31 final size:30
Alignment explanation
Indices: 238727--238873 Score: 97
Period size: 30 Copynumber: 4.9 Consensus size: 30
238717 TAATAATTAA
*
238727 TTTATTTTAACTTTAAAAAATATATTTTATT
1 TTTATCTTAAC-TTAAAAAATATATTTTATT
**
238758 TTTATCTTAACTTATTAAATATATTTTATT
1 TTTATCTTAACTTAAAAAATATATTTTATT
* * ** * *
238788 ATCAAATTAAATTAAAATATATATTTTATT
1 TTTATCTTAACTTAAAAAATATATTTTATT
**
238818 CAT-TCTT-A-TTAAAAATATATATTTTTTATT
1 TTTATCTTAACTTAAAAA-ATATA--TTTTATT
*
238848 CTTATC-TAA-TATAAAAATATATATTT
1 TTTATCTTAACT-TAAAAA-ATATATTT
238874 CGTCTCATGC
Statistics
Matches: 92, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
27 6 0.07
28 6 0.07
29 2 0.02
30 52 0.57
31 14 0.15
32 12 0.13
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTATCTTAACTTAAAAAATATATTTTATT
Found at i:240775 original size:2 final size:2
Alignment explanation
Indices: 240760--240805 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
240750 GTACATGAAA
*
240760 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
240800 AT AT AT
1 AT AT AT
240806 GTTAATATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:240813 original size:12 final size:13
Alignment explanation
Indices: 240769--240813 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
240759 AATATTATAA
*
240769 TATATATATATAT
1 TATATATATATGT
240782 ATATATATATATG-
1 -TATATATATATGT
240795 TATATATATATGT
1 TATATATATATGT
240808 TA-ATAT
1 TATATAT
240814 TGTTAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 16 0.55
13 2 0.07
14 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (13 bp):
TATATATATATGT
Found at i:245386 original size:30 final size:30
Alignment explanation
Indices: 245347--245413 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
245337 GTGTCGATTA
245347 ATAA-ATTGGCATAATTATATATTTGGTCC
1 ATAATATTGGCATAATTATATATTTGGTCC
*
245376 TTAATATTGGCATAATTATATATTTGGTCC
1 ATAATATTGGCATAATTATATATTTGGTCC
245406 ATAATATT
1 ATAATATT
245414 TACATATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (30 bp):
ATAATATTGGCATAATTATATATTTGGTCC
Found at i:245398 original size:16 final size:16
Alignment explanation
Indices: 245351--245399 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
245341 CGATTAATAA
245351 ATTGGCATAATTATAT
1 ATTGGCATAATTATAT
**
245367 ATTTGG--TCCTTA-AT
1 A-TTGGCATAATTATAT
245381 ATTGGCATAATTATAT
1 ATTGGCATAATTATAT
245397 ATT
1 ATT
245400 TGGTCCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
13 4 0.16
14 3 0.12
15 8 0.32
16 6 0.24
17 4 0.16
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (16 bp):
ATTGGCATAATTATAT
Found at i:245410 original size:19 final size:19
Alignment explanation
Indices: 245356--245410 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
245346 AATAAATTGG
245356 CATAATTATATATTTGGTC
1 CATAATTATATATTTGGTC
245375 C----TTA-ATA-TTGG--
1 CATAATTATATATTTGGTC
245386 CATAATTATATATTTGGTC
1 CATAATTATATATTTGGTC
245405 CATAAT
1 CATAAT
245411 ATTTACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 1 0.04
13 4 0.14
14 3 0.11
15 6 0.21
16 3 0.11
17 4 0.14
19 7 0.25
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
CATAATTATATATTTGGTC
Found at i:245770 original size:17 final size:17
Alignment explanation
Indices: 245748--245795 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
245738 GGATAAAACC
**
245748 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAA
245765 TTAAACAAATTATTTAA
1 TTAAACAAATTATTTAA
*
245782 TTAAATAAATTATT
1 TTAAACAAATTATT
245796 CACGACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (17 bp):
TTAAACAAATTATTTAA
Found at i:245925 original size:29 final size:29
Alignment explanation
Indices: 245891--245946 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
245881 AAAATTTATC
*
245891 TGAAAATTATTAACCGAACTGAATTAATT
1 TGAAAATTATTAACCGAACCGAATTAATT
245920 TGAAAATTATTAACCGAACCGAATTAA
1 TGAAAATTATTAACCGAACCGAATTAA
245947 CCGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (29 bp):
TGAAAATTATTAACCGAACCGAATTAATT
Found at i:245999 original size:127 final size:127
Alignment explanation
Indices: 245849--246211 Score: 550
Period size: 128 Copynumber: 2.9 Consensus size: 127
245839 TAGAGAAAAC
* * * * *
245849 AATTCGGTTAATTCGGTTTGGTTAATTGAACAAAAATTTATCTGAAAATTATTAACCGAACTGAA
1 AATTCGGTTAATTTGGCTAGGTTAATCGAACAAAAATTTATCTGAAAATTATTAACCGAACTAAA
245914 TTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTAATTATTAATCGAAGCAAA
66 TTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTAATTATTAATCGAAGCAAA
* * *
245976 AATTTGGTTAATTTGGCTCGGTTAATCGAACCAAAATTTATCTGAAAATTATTAACCGAA-TCAA
1 AATTCGGTTAATTTGGCTAGGTTAATCGAACAAAAATTTATCTGAAAATTATTAACCGAACT-AA
246040 ATTAATTTGAAAATTATTAACCGAACCGAATTAACCGAATTTTTTAATTATTAATCGAAGCAAA
65 ATTAATTTGAAAATTATTAACCGAACCGAATTAACCG-ATTTTTTAATTATTAATCGAAGCAAA
** * * * *
246104 AATTCAATTAA-TTGGGTAAAGTTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACCAA
1 AATTCGGTTAATTTGGCT-AGGTTAATCGAACAAAAATTTATCTGAAAATTATTAACCGAACTAA
*
246168 ATTAATTTGAAAATTATTAACCGAACCGAATTAACCGGTTTTTT
65 ATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTT
246212 TTCTTTAACC
Statistics
Matches: 215, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
126 1 0.00
127 103 0.48
128 111 0.52
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (127 bp):
AATTCGGTTAATTTGGCTAGGTTAATCGAACAAAAATTTATCTGAAAATTATTAACCGAACTAAA
TTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTTTTTAATTATTAATCGAAGCAAA
Found at i:246051 original size:29 final size:29
Alignment explanation
Indices: 245997--246073 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
245987 TTTGGCTCGG
* *
245997 TTAATCGAACCAAAATTTATCTGAAAATTA
1 TTAACCGAACC-AAATTAATCTGAAAATTA
* *
246027 TTAACCGAATCAAATTAATTTGAAAATTA
1 TTAACCGAACCAAATTAATCTGAAAATTA
*
246056 TTAACCGAACCGAATTAA
1 TTAACCGAACCAAATTAA
246074 CCGAATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 32 0.78
30 9 0.22
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (29 bp):
TTAACCGAACCAAATTAATCTGAAAATTA
Found at i:246164 original size:30 final size:29
Alignment explanation
Indices: 246125--246193 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
246115 TTGGGTAAAG
* *
246125 TTAATCGAACAAAAATTTATTTGAAAATTA
1 TTAACCGAAC-AAAATTAATTTGAAAATTA
*
246155 TTAACCGAACCAAATTAATTTGAAAATTA
1 TTAACCGAACAAAATTAATTTGAAAATTA
246184 TTAACCGAAC
1 TTAACCGAAC
246194 CGAATTAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (29 bp):
TTAACCGAACAAAATTAATTTGAAAATTA
Found at i:246169 original size:29 final size:29
Alignment explanation
Indices: 246137--246201 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
246127 AATCGAACAA
*
246137 AAATTTATTTGAAAATTATTAACCGAACC
1 AAATTAATTTGAAAATTATTAACCGAACC
246166 AAATTAATTTGAAAATTATTAACCGAACC
1 AAATTAATTTGAAAATTATTAACCGAACC
*
246195 GAATTAA
1 AAATTAA
246202 CCGGTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (29 bp):
AAATTAATTTGAAAATTATTAACCGAACC
Found at i:246388 original size:16 final size:17
Alignment explanation
Indices: 246369--246404 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
246359 ACAATTAATA
246369 TAAAT-AATAATTTGTT
1 TAAATAAATAATTTGTT
246385 TAAATAAATAATTTGTT
1 TAAATAAATAATTTGTT
246402 TAA
1 TAA
246405 GGTTTTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TAAATAAATAATTTGTT
Found at i:246702 original size:30 final size:30
Alignment explanation
Indices: 246666--246724 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
246656 AAAATATGTA
* *
246666 AATATTAAGGACTAAATGTATAATTATGCT
1 AATATTAAGGACCAAATATATAATTATGCT
246696 AATATTAAGGACCAAATATATAATTATGC
1 AATATTAAGGACCAAATATATAATTATGC
246725 AATTTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATTATGCT
Found at i:249111 original size:33 final size:34
Alignment explanation
Indices: 249071--249137 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
249061 ACTCACAAAG
249071 AAAGACTTATATTGCAAATTAAAAAGGA-ATAAC
1 AAAGACTTATATTGCAAATTAAAAAGGATATAAC
249104 AAAGACTTATATTGCAAATTAAAAAGGATATAAC
1 AAAGACTTATATTGCAAATTAAAAAGGATATAAC
249138 CTTTCTGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (34 bp):
AAAGACTTATATTGCAAATTAAAAAGGATATAAC
Found at i:255512 original size:2 final size:2
Alignment explanation
Indices: 255502--255532 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
255492 TATGAAAAAA
255502 AT AT A- 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
255533 TGTATATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:266098 original size:76 final size:75
Alignment explanation
Indices: 265990--266179 Score: 213
Period size: 76 Copynumber: 2.5 Consensus size: 75
265980 TTTAGAAGTA
* * * * *
265990 TCAAATTGAGGTTACT-GGAGAAACGATCTTAAGAAATAATAGATTGAACCTTCTAGTATATAAG
1 TCAAATTGAGGTTTCTAGG-GAAACGATCTTAAGAAAGAATAGATGGAACCTTCTAGAATACAAG
*
266054 TCCTAAAAGAG
65 TCCTAAAACAG
* ** * *
266065 TCAATATTGAGGTTTCTAGGGAAACGATATTAAGAAAGGCTAGATGGAGCTTTCTAGAATACAAG
1 TCAA-ATTGAGGTTTCTAGGGAAACGATCTTAAGAAAGAATAGATGGAACCTTCTAGAATACAAG
*
266130 TCCTAAGACAG
65 TCCTAAAACAG
* *
266141 TCAAAATCGAGGTTTCTA-GGAAATGATCTTAAGAAAGAA
1 TC-AAATTGAGGTTTCTAGGGAAACGATCTTAAGAAAGAA
266180 AAAAATTAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
75 21 0.22
76 70 0.74
77 4 0.04
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (75 bp):
TCAAATTGAGGTTTCTAGGGAAACGATCTTAAGAAAGAATAGATGGAACCTTCTAGAATACAAGT
CCTAAAACAG
Found at i:270076 original size:17 final size:17
Alignment explanation
Indices: 270051--270101 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
270041 CAGAAGTTAG
* *
270051 TAAAAAAAGAAATATAA
1 TAAATAAAGAAATAAAA
*
270068 TAAATAAAGTAATAAAA
1 TAAATAAAGAAATAAAA
* *
270085 TAAATATATAAATAAAA
1 TAAATAAAGAAATAAAA
270102 AGGACCAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
TAAATAAAGAAATAAAA
Found at i:270079 original size:26 final size:25
Alignment explanation
Indices: 270049--270100 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
270039 AACAGAAGTT
270049 AGTAAAAAAAGAAATATAATAAATAA
1 AGTAAAAAAAGAAATAT-ATAAATAA
* *
270075 AGTAATAAAATAAATATATAAATAA
1 AGTAAAAAAAGAAATATATAAATAA
270100 A
1 A
270101 AAGGACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (25 bp):
AGTAAAAAAAGAAATATATAAATAA
Found at i:273034 original size:33 final size:34
Alignment explanation
Indices: 272958--273043 Score: 120
Period size: 36 Copynumber: 2.5 Consensus size: 34
272948 AACTCGAATG
* * *
272958 TTTTGTGTTTCAAGAGAAATATTTTCAAAGATTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAG--TGTT
272994 TTTTGTGTTTCAAGAGAAACAATTTCAAAG-GTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGTGTT
273027 TTTTGTGTTTCAAGAGA
1 TTTTGTGTTTCAAGAGA
273044 GACTGTCTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
33 19 0.40
36 28 0.60
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (34 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGTGTT
Found at i:273076 original size:37 final size:36
Alignment explanation
Indices: 273032--273479 Score: 246
Period size: 36 Copynumber: 12.1 Consensus size: 36
273022 AGGTTTTTTG
*
273032 TGTTTCAAGAGAGACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
273069 TGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* ** *
273105 TGTTTCCAGAGATCCTGTCTCAAGAGAAACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
273142 AGTTCCAACAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
273178 TGTTTCAAG-GAAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* * * * *
273207 TGTTTCAGGGGAAATTATCTCAAGAGATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
273243 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
273279 TGTTTCAAGAGAGACAAAACTTAGT-TCCAA-A-AG--AAAA--
1 TGTTTC-A-AGAG---AAAC-T-GTCT-CAAGAGAGACAAAATT
* * * *
273316 TGTCTCAAGGGAAACGAAATTTGTTTCAA-AGAAAACATATTCAATGATTT
1 TGTTTCAA--G--A-GAAA-CTGTCTCAAGAG-AGAC--A---AA--A-TT
* *
273366 TGTTTCAAGGGAAACTGTCTCAAGTGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
273402 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
273438 TGTTTAAAGAGAAACTGTCTCAATAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
273475 TGTTT
1 TGTTT
273480 TGAGTAAATT
Statistics
Matches: 316, Mismatches: 52, Indels: 86
0.70 0.11 0.19
Matches are distributed among these distances:
28 2 0.01
29 16 0.05
30 2 0.01
31 1 0.00
32 1 0.00
33 2 0.01
35 3 0.01
36 157 0.50
37 78 0.25
38 4 0.01
39 7 0.02
40 1 0.00
41 6 0.02
42 5 0.02
43 5 0.02
44 10 0.03
45 7 0.02
47 1 0.00
48 1 0.00
50 7 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:273123 original size:73 final size:73
Alignment explanation
Indices: 273032--273186 Score: 211
Period size: 73 Copynumber: 2.1 Consensus size: 73
273022 AGGTTTTTTG
* * * **
273032 TGTTTCAAGAGAGACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAAAG
1 TGTTTCAAGAGAGACTGTCTCAAGAGAAACAAAACTTAGTTCCAACAGAAACTGTCTCAAGAAAG
273097 ACAAAATT
66 ACAAAATT
* ** **
273105 TGTTTCCAGAGATCCTGTCTCAAGAGAAACAAAACTTAGTTCCAACAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAGACTGTCTCAAGAGAAACAAAACTTAGTTCCAACAGAAACTGTCTCAAGAAAG
*
273170 ACGAAATT
66 ACAAAATT
273178 TGTTTCAAG
1 TGTTTCAAG
273187 GAAAACAAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (73 bp):
TGTTTCAAGAGAGACTGTCTCAAGAGAAACAAAACTTAGTTCCAACAGAAACTGTCTCAAGAAAG
ACAAAATT
Found at i:273251 original size:21 final size:21
Alignment explanation
Indices: 273226--273297 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
273216 GGAAATTATC
*
273226 TCAAGAGATACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
273247 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
273262 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
273283 TCAAGAGAGACAAAA
1 TCAAGAGAGACAAAA
273298 CTTAGTTCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
15 8 0.20
16 4 0.10
17 1 0.03
20 4 0.10
21 23 0.57
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.24
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:273336 original size:58 final size:57
Alignment explanation
Indices: 273226--273344 Score: 148
Period size: 58 Copynumber: 2.1 Consensus size: 57
273216 GGAAATTATC
* * * ** * *
273226 TCAAGAGATACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTAGTTCCAAAAGAAAATGTCTCAAGAGAAACAAAATTTGTT
* *
273283 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAAACGAAATTTGTT
1 TCAAGAGAGACAAAA-TTAGTTCCAAAAGAAAATGTCTCAAGAGAAACAAAATTTGTT
273341 TCAA
1 TCAA
273345 AGAAAACATA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
57 14 0.27
58 38 0.73
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (57 bp):
TCAAGAGAGACAAAATTAGTTCCAAAAGAAAATGTCTCAAGAGAAACAAAATTTGTT
Found at i:273378 original size:159 final size:159
Alignment explanation
Indices: 273124--273452 Score: 514
Period size: 159 Copynumber: 2.1 Consensus size: 159
273114 AGATCCTGTC
* * * *
273124 TCAAGAGAAACAAAACTTAGTTCCAACAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
1 TCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAAACGAAATTTGTTTCAAAGA
* * * *
273189 AAACAAATTCAAAGATTTTGTTTCAGGGGAAATTATCTCAAGAGATACAAAATTTGTTTCAAGGG
66 AAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAG
* *
273254 AAACTGTCTCAAGAGAGACAAAATTTGTT
131 AAACTATCTCAAGAGAGACAAAACTTGTT
*
273283 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAAACGAAATTTGTTTCAAAGA
1 TCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAAACGAAATTTGTTTCAAAGA
* * * *
273348 AAACATATTCAATGATTTTGTTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGAG
66 AAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAG
273413 AAACTATCTCAAGAGAGACAAAACTTGTT
131 AAACTATCTCAAGAGAGACAAAACTTGTT
*
273442 TAAAGAGAAAC
1 TCAAGAGAAAC
273453 TGTCTCAATA
Statistics
Matches: 153, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
159 153 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (159 bp):
TCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAAACGAAATTTGTTTCAAAGA
AAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAG
AAACTATCTCAAGAGAGACAAAACTTGTT
Found at i:273504 original size:37 final size:37
Alignment explanation
Indices: 273364--273504 Score: 150
Period size: 36 Copynumber: 3.9 Consensus size: 37
273354 ATTCAATGAT
* *
273364 TTTGTTTCAAGGGAAACT-GTCTCAAGTGAGACAAAA-
1 TTTGTTT-AAGAGAAACTAGTCTCAAGAGAGACAAAAC
273400 TTTGTTTCAAGAGAAACTA-TCTCAAGAGAGACAAAAC
1 TTTGTTT-AAGAGAAACTAGTCTCAAGAGAGACAAAAC
*
273437 -TTGTTTAAAGAGAAACT-GTCTCAATAGAGACAAAAC
1 TTTGTTT-AAGAGAAACTAGTCTCAAGAGAGACAAAAC
* * *
273473 TTTGTTT-TGAGTAAATTAGTCTCAAGCGAGAC
1 TTTGTTTAAGAG-AAACTAGTCTCAAGAGAGAC
273505 GATCCCTTGT
Statistics
Matches: 91, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
35 3 0.03
36 70 0.77
37 18 0.20
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (37 bp):
TTTGTTTAAGAGAAACTAGTCTCAAGAGAGACAAAAC
Found at i:274016 original size:32 final size:32
Alignment explanation
Indices: 273971--274054 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 32
273961 TAAGGGTGTC
* *
273971 GAATCCCCGAAGATG-CCCAAATATTCGATGAT
1 GAATCTCCAAAGATGCCCCAAA-ATTCGATGAT
* *
274003 GAATCTCCAAAGATGCCCCCAAAATTTGATGTT
1 GAATCTCCAAAGATG-CCCCAAAATTCGATGAT
*
274036 GAATCTTCAAATG-TGCCCC
1 GAATCTCCAAA-GATGCCCC
274055 CATTATTCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 17 0.39
33 20 0.45
34 7 0.16
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (32 bp):
GAATCTCCAAAGATGCCCCAAAATTCGATGAT
Found at i:274053 original size:33 final size:34
Alignment explanation
Indices: 273986--274056 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
273976 CCCGAAGATG
273986 CCCAAATATTCGATGATGAATCTCCAAAGATGCC
1 CCCAAATATTCGATGATGAATCTCCAAAGATGCC
* * *
274020 CCCAAA-ATTTGATGTTGAATCTTCAAATG-TGCC
1 CCCAAATATTCGATGATGAATCTCCAAA-GATGCC
274053 CCCA
1 CCCA
274057 TTATTCCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (34 bp):
CCCAAATATTCGATGATGAATCTCCAAAGATGCC
Found at i:275128 original size:14 final size:13
Alignment explanation
Indices: 275111--275158 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
275101 TTCTTCTTTG
*
275111 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
275124 TTTTTATTTTCTCT
1 TTTTT-TTTTCTCT
275138 TTGCTTTTTTTCT-T
1 TT--TTTTTTTCTCT
275152 TTTTTTT
1 TTTTTTT
275159 CTTTTTGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 12 0.39
15 6 0.19
16 3 0.10
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:275146 original size:13 final size:13
Alignment explanation
Indices: 275130--275171 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
275120 CTCTTTTTTA
275130 TTTTCTCTTTGCT
1 TTTTCTCTTTGCT
* *
275143 TTTTTTCTTT-TT
1 TTTTCTCTTTGCT
*
275155 TTTTCTTTTTGCT
1 TTTTCTCTTTGCT
275168 TTTT
1 TTTT
275172 GTTCTGATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTTCTCTTTGCT
Found at i:275159 original size:25 final size:27
Alignment explanation
Indices: 275124--275176 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
275114 TTGTTTCTCT
275124 TTTTTATTTTCTCTTTGCTTTTT-TTC
1 TTTTTATTTTCTCTTTGCTTTTTGTTC
*
275150 TTTTT-TTTTCTTTTTGCTTTTTGTTC
1 TTTTTATTTTCTCTTTGCTTTTTGTTC
275176 T
1 T
275177 GATTGGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (27 bp):
TTTTTATTTTCTCTTTGCTTTTTGTTC
Found at i:278405 original size:17 final size:17
Alignment explanation
Indices: 278385--278420 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
278375 AAAGAAAAAT
278385 AATAAATAAAGT-AATAA
1 AATAAATAAA-TAAATAA
278402 AATAAATAAATAAATAA
1 AATAAATAAATAAATAA
278419 AA
1 AA
278421 AAGATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AATAAATAAATAAATAA
Found at i:282029 original size:2 final size:2
Alignment explanation
Indices: 282022--282052 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
282012 AAAAACAATA
282022 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 A
282053 AGTGCAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:285395 original size:22 final size:21
Alignment explanation
Indices: 285369--285436 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
285359 AGTTCTAATA
285369 AAATAATCAAACTAAAAATCCT
1 AAATAATCAAACTAAAAAT-CT
** * * *
285391 AAATAAAAAAAGTAATAAT-A
1 AAATAATCAAACTAAAAATCT
285411 AAATAATCAAACTAAAAATCTT
1 AAATAATCAAACTAAAAATC-T
285433 AAAT
1 AAAT
285437 CTAAAAGGTT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 15 0.44
22 19 0.56
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.24
Consensus pattern (21 bp):
AAATAATCAAACTAAAAATCT
Found at i:292583 original size:20 final size:21
Alignment explanation
Indices: 292552--292662 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 21
292542 GTCATTTTCG
292552 CAAATT-GCAACACAT-AA-GT
1 CAAATTCGCAACAC-TGAATGT
*
292571 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACACTGAATGT
*
292592 CAAATTCGC-A-ACTGAATTT
1 CAAATTCGCAACACTGAATGT
* * *
292611 CAAA-TCTGCAACTC-GATTTT
1 CAAATTC-GCAACACTGAATGT
*
292631 CGAATTCGCAACAC-GAAT-T
1 CAAATTCGCAACACTGAATGT
* *
292650 TAATTTCGCAACA
1 CAAATTCGCAACA
292663 GGTTTTAGTT
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 33 0.43
20 28 0.37
21 13 0.17
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (21 bp):
CAAATTCGCAACACTGAATGT
Found at i:292607 original size:19 final size:19
Alignment explanation
Indices: 292570--292661 Score: 89
Period size: 19 Copynumber: 4.7 Consensus size: 19
292560 AACACATAAG
292570 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
292591 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
292610 TCAAA-TCTGCAACTCGATTT
1 TCAAATTC-GCAACT-GAATT
* *
292630 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
292650 T-AATTTCGCAAC
1 TCAAATTCGCAAC
292662 AGGTTTTAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.03
19 28 0.46
20 19 0.31
21 12 0.20
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:292614 original size:40 final size:40
Alignment explanation
Indices: 292570--292662 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 40
292560 AACACATAAG
*
292570 TCAAATTCGCAACACTGAATTTCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACACGAATT
* * *
292610 TCAAA-TCTGCAACTCGATTTTCGAATTCGCAACACGAATT
1 TCAAATTC-GCAACACGAATTTCAAATTCGCAACACGAATT
*
292650 T-AATTTCGCAACA
1 TCAAATTCGCAACA
292663 GGTTTTAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
39 25 0.57
40 19 0.43
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (40 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACACGAATT
Found at i:292844 original size:16 final size:16
Alignment explanation
Indices: 292823--292853 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
292813 ATCTCTACTT
292823 TTTTTACATAATTTTA
1 TTTTTACATAATTTTA
*
292839 TTTTTATATAATTTT
1 TTTTTACATAATTTT
292854 CAATGATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTA
Found at i:295881 original size:18 final size:18
Alignment explanation
Indices: 295858--295893 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
295848 AAGCAAAAGG
295858 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
295876 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
295894 CAACAGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:296690 original size:24 final size:25
Alignment explanation
Indices: 296663--296714 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
296653 TTTCAAATTC
*
296663 ATTTTATATGT-AATTGGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
* *
296687 A-TTTAAATTTCAATTTGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
296711 ATTT
1 ATTT
296715 CAATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (25 bp):
ATTTTAAATGTCAATTGGAGTTTGA
Found at i:296703 original size:18 final size:18
Alignment explanation
Indices: 296682--296718 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
296672 GTAATTGGAG
296682 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
296700 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
296718 T
1 T
296719 ATATATAAAT
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:297858 original size:20 final size:20
Alignment explanation
Indices: 297833--297870 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
297823 TGCGATTATT
*
297833 GCGAAAGTCAAATTCGCGAC
1 GCGAAAATCAAATTCGCGAC
297853 GCGAAAATCAAATTCGCG
1 GCGAAAATCAAATTCGCG
297871 TTGCGATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCGAC
Found at i:297876 original size:20 final size:20
Alignment explanation
Indices: 297831--297876 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
297821 GTTGCGATTA
*
297831 TTGCGAAAGTCAAATTCGCG
1 TTGCGAAAATCAAATTCGCG
**
297851 ACGCGAAAATCAAATTCGCG
1 TTGCGAAAATCAAATTCGCG
297871 TTGCGA
1 TTGCGA
297877 TTGTTGCGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGCGAAAATCAAATTCGCG
Found at i:297941 original size:20 final size:20
Alignment explanation
Indices: 297918--298079 Score: 184
Period size: 20 Copynumber: 8.1 Consensus size: 20
297908 TCGCAACGCC
*
297918 AATTTGACTTTCGCGTTGTG
1 AATTTGACTTTCGCGTTGCG
*
297938 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCGTTGCG
* *
297958 AATTTGACTATGGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
*
297978 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCGTTGCG
* * *
297998 AATTTGACTATGGCGTTGTG
1 AATTTGACTTTCGCGTTGCG
298018 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
* * **
298038 AATTCGACTAT--CGTAACG
1 AATTTGACTTTCGCGTTGCG
298056 TAAATTTGACTTTCGCGTTGCG
1 --AATTTGACTTTCGCGTTGCG
298078 AA
1 AA
298080 AGTGTATCTT
Statistics
Matches: 115, Mismatches: 23, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
18 5 0.04
20 105 0.91
22 5 0.04
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCG
Found at i:297974 original size:40 final size:40
Alignment explanation
Indices: 297918--298079 Score: 220
Period size: 40 Copynumber: 4.0 Consensus size: 40
297908 TCGCAACGCC
* *
297918 AATTTGACTTTCGCGTTGTGAATTTGACTTTCACGTTGCG
1 AATTTGACTATGGCGTTGTGAATTTGACTTTCACGTTGCG
*
297958 AATTTGACTATGGCGTTGCGAATTTGACTTTCACGTTGCG
1 AATTTGACTATGGCGTTGTGAATTTGACTTTCACGTTGCG
*
297998 AATTTGACTATGGCGTTGTGAATTTGACTTTCGCGTTGCG
1 AATTTGACTATGGCGTTGTGAATTTGACTTTCACGTTGCG
* * * *
298038 AATTCGACTAT--CGTAACGTAAATTTGACTTTCGCGTTGCG
1 AATTTGACTATGGCGT--TGTGAATTTGACTTTCACGTTGCG
298078 AA
1 AA
298080 AGTGTATCTT
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
38 3 0.03
40 109 0.97
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (40 bp):
AATTTGACTATGGCGTTGTGAATTTGACTTTCACGTTGCG
Found at i:298221 original size:14 final size:14
Alignment explanation
Indices: 298202--298238 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
298192 CATCAATTAA
298202 ACAAATCAACTTTT
1 ACAAATCAACTTTT
298216 ACAAATCAACTTTT
1 ACAAATCAACTTTT
298230 ACAAATCAA
1 ACAAATCAA
298239 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:298268 original size:71 final size:72
Alignment explanation
Indices: 298138--298323 Score: 254
Period size: 71 Copynumber: 2.5 Consensus size: 72
298128 AATTAAAACA
298138 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGC--AAAA-AA---TTATTTACACATCAATTAAA
298203 CAAATCAACTTTT
60 CAAATCAACTTTT
* *
298216 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA-TATTTCCTCATCAATTAAACAAATC
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATTATTTACACATCAATTAAACAAATC
298280 AACTTTT
66 AACTTTT
*
298287 ACAAATCAA--TGTA-AAATTCAATTAAACAAGCAAAAAA
1 ACAAATCAACTTTTACAAA-TCAATTAAACAAGCAAAAAA
298324 AGTATACCCC
Statistics
Matches: 104, Mismatches: 3, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
68 3 0.03
69 23 0.22
71 39 0.38
75 2 0.02
76 4 0.04
78 33 0.32
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.28
Consensus pattern (72 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATTATTTACACATCAATTAAACAAATC
AACTTTT
Found at i:299687 original size:21 final size:21
Alignment explanation
Indices: 299657--299732 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
299647 GTGAATCAGG
* *
299657 CTCTTAAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
299678 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * * *
299699 CTCTTGAATGATAGAAGGCGC
1 CTCTTGAACGATGGGAGGGGC
299720 CTCTTGAACGATG
1 CTCTTGAACGATG
299733 ACGGGTGAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:301791 original size:20 final size:21
Alignment explanation
Indices: 301768--301806 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
301758 TCGCGTTGCG
*
301768 ATTTTGGTGTTGC-AATTTTC
1 ATTTTCGTGTTGCGAATTTTC
301788 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
301807 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTTC
Found at i:302177 original size:22 final size:22
Alignment explanation
Indices: 302147--302197 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
302137 GATGGAGATA
302147 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
302169 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
302191 GACGGAT
1 GACGGAT
302198 GTCACCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:302379 original size:20 final size:20
Alignment explanation
Indices: 302351--302412 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
302341 TAAACGCGCT
302351 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* *
302371 TTGCAAATTTGAATTTTGTG
1 TTGCGAATTTGACTTTTGTG
302391 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
302411 TT
1 TT
302413 TCGATTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.52
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:302434 original size:40 final size:40
Alignment explanation
Indices: 302351--302440 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
302341 TAAACGCGCT
* * * *
302351 TTGCGAATTTGACTTTTGTGTTGCAAATTTGAATTTTGTG
1 TTGCGAATTTGACTTTTGTGTTGCAAATTTCAAATTCGCG
* *
302391 TTGCGAATTTGACTTTTGTGTTTC-GATTTACAAATTCGCG
1 TTGCGAATTTGACTTTTGTGTTGCAAATTT-CAAATTCGCG
302431 TTGCGAATTT
1 TTGCGAATTT
302441 CGAAAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.20, C:0.11, G:0.21, T:0.48
Consensus pattern (40 bp):
TTGCGAATTTGACTTTTGTGTTGCAAATTTCAAATTCGCG
Found at i:302450 original size:21 final size:21
Alignment explanation
Indices: 302432--302478 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
302422 AAATTCGCGT
302432 TGCGAATTTCGAAAATCGCAA
1 TGCGAATTTCGAAAATCGCAA
* *
302453 CGCGAATTTGGAAAATCGCAA
1 TGCGAATTTCGAAAATCGCAA
302474 TGCGA
1 TGCGA
302479 TTTACATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
TGCGAATTTCGAAAATCGCAA
Found at i:302550 original size:19 final size:19
Alignment explanation
Indices: 302513--302562 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
302503 GGAAACTGGG
* *
302513 TTGCGAAATTGGAGTTCGCA
1 TTGCG-AATTTGAGATCGCA
*
302533 TTGCGAATTTGAGATCGCG
1 TTGCGAATTTGAGATCGCA
*
302552 TTGCAAATTTG
1 TTGCGAATTTG
302563 TTGGTCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (19 bp):
TTGCGAATTTGAGATCGCA
Found at i:303545 original size:21 final size:21
Alignment explanation
Indices: 303521--303561 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
303511 GTTATCTGAT
303521 TCGACTCATAATTTTATAAAG
1 TCGACTCATAATTTTATAAAG
303542 TCGACTCATAATTTTATAAA
1 TCGACTCATAATTTTATAAA
303562 TTTGATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (21 bp):
TCGACTCATAATTTTATAAAG
Found at i:303718 original size:2 final size:2
Alignment explanation
Indices: 303713--303755 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
303703 AAATATGAAG
303713 AT AT AT AT AT AT AT AT -T 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
303754 AT
1 AT
303756 TATTGAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.