Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008739.1 Hibiscus syriacus cultivar Beakdansim tig00111817_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: 827959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:231968 original size:18 final size:19
Alignment explanation
Indices: 231926--231970 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
231916 GCTATCTTAA
*
231926 TAAATAAT-ATATATAAAG
1 TAAATAATAAAATATAAAG
231944 T-AATAATAAAATA-AAAG
1 TAAATAATAAAATATAAAG
231961 TAAATAATAA
1 TAAATAATAA
231971 TAAGTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
TAAATAATAAAATATAAAG
Found at i:231978 original size:10 final size:10
Alignment explanation
Indices: 231923--231983 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 10
231913 AATGCTATCT
231923 TAATAAATAATA
1 TAATAAAT-A-A
231935 TATATAAAGTAA
1 TA-ATAAA-TAA
231947 TAATAAAATAA
1 TAAT-AAATAA
231958 -AAGTAAATAA
1 TAA-TAAATAA
*
231968 TAATAAGTAA
1 TAATAAATAA
231978 TAATAA
1 TAATAA
231984 CATGAAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 20 0.47
11 8 0.19
12 8 0.19
13 6 0.14
14 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (10 bp):
TAATAAATAA
Found at i:234043 original size:2 final size:2
Alignment explanation
Indices: 234036--234068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
234026 ATTTTGTTTC
234036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
234069 TCTAATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:245203 original size:27 final size:27
Alignment explanation
Indices: 245163--245219 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
245153 CGTGGAAATG
* *
245163 GCGGTGGCTCGGGATTGGTGTAGCACA
1 GCGGTGGATCGGGATTGGTGCAGCACA
*
245190 GCGGTGGATGGGGATTGGTGCAGCACA
1 GCGGTGGATCGGGATTGGTGCAGCACA
245217 GCG
1 GCG
245220 ATAACAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.19
Consensus pattern (27 bp):
GCGGTGGATCGGGATTGGTGCAGCACA
Found at i:245443 original size:6 final size:6
Alignment explanation
Indices: 245421--245458 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
245411 AGCGTGCAGA
245421 AAATA- AAAT-T AAA-AT AAATAT AAATAT AAATAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATA
245459 ATCATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 11 0.37
6 19 0.63
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATAT
Found at i:245474 original size:3 final size:3
Alignment explanation
Indices: 245455--245488 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
245445 TATAAATATA
*
245455 AAT AAT CAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
245489 CAGGATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:249659 original size:34 final size:35
Alignment explanation
Indices: 249610--249687 Score: 133
Period size: 36 Copynumber: 2.3 Consensus size: 35
249600 AGGGAAAGCT
249610 GGGAAGG-AAGAATGATCAGAGAG-AGCGTGCAGA
1 GGGAAGGAAAGAATGATCAGAGAGAAGCGTGCAGA
249643 GGGAAGGAAAGAATGATCAGAGAGAAAGCGTGCAGA
1 GGGAAGGAAAGAATGATCAGAGAG-AAGCGTGCAGA
249679 GGGAAGGAA
1 GGGAAGGAA
249688 GAAACAACGA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
33 7 0.17
34 16 0.38
36 19 0.45
ACGTcount: A:0.42, C:0.08, G:0.42, T:0.08
Consensus pattern (35 bp):
GGGAAGGAAAGAATGATCAGAGAGAAGCGTGCAGA
Found at i:250200 original size:2 final size:2
Alignment explanation
Indices: 250193--250222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
250183 GTATCACGCA
250193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250223 TTTGAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251719 original size:2 final size:2
Alignment explanation
Indices: 251712--251771 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
251702 TAAAAGTATG
251712 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
251754 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
251772 AAGGGCTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:253588 original size:27 final size:27
Alignment explanation
Indices: 253558--253611 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
253548 TTAAATACAA
253558 TTTAGCATTAACTTAATTTAAAAATAT
1 TTTAGCATTAACTTAATTTAAAAATAT
*** **
253585 TTTATTTTTATTTTAATTTAAAAATAT
1 TTTAGCATTAACTTAATTTAAAAATAT
253612 ATTTTATGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAGCATTAACTTAATTTAAAAATAT
Found at i:254636 original size:20 final size:20
Alignment explanation
Indices: 254611--254648 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
254601 AAGTGATTTG
*
254611 ATTGATAAAATTAAAAGACC
1 ATTGATAAAAATAAAAGACC
254631 ATTGATAAAAATAAAAGA
1 ATTGATAAAAATAAAAGA
254649 TTGATAATAA
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:0.61, C:0.05, G:0.11, T:0.24
Consensus pattern (20 bp):
ATTGATAAAAATAAAAGACC
Found at i:254653 original size:17 final size:17
Alignment explanation
Indices: 254610--254655 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
254600 TAAGTGATTT
*
254610 GATTGATAAAATTAAAA
1 GATTGATAAAAATAAAA
254627 GACCATTGATAAAAATAAAA
1 G---ATTGATAAAAATAAAA
254647 GATTGATAA
1 GATTGATAA
254656 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 9 0.36
20 16 0.64
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (17 bp):
GATTGATAAAAATAAAA
Found at i:259163 original size:22 final size:22
Alignment explanation
Indices: 259138--259181 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
259128 TTTTCATTTC
*
259138 CTGTTAAGTGTGTTTTCTGGTT
1 CTGTTAAGTGTGTCTTCTGGTT
*
259160 CTGTTACGTGTGTCTTCTGGTT
1 CTGTTAAGTGTGTCTTCTGGTT
259182 GTATCTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (22 bp):
CTGTTAAGTGTGTCTTCTGGTT
Found at i:260377 original size:7 final size:7
Alignment explanation
Indices: 260365--260389 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
260355 TCAAGACACC
260365 ATTCATA
1 ATTCATA
260372 ATTCATA
1 ATTCATA
260379 ATTCATA
1 ATTCATA
260386 ATTC
1 ATTC
260390 TCACCACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTCATA
Found at i:261699 original size:19 final size:19
Alignment explanation
Indices: 261675--261713 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
261665 TGTTGGATCT
*
261675 AGCCTATAGGATATATAAA
1 AGCCTATAAGATATATAAA
261694 AGCCTATAAGATATATAAA
1 AGCCTATAAGATATATAAA
261713 A
1 A
261714 TATACGCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (19 bp):
AGCCTATAAGATATATAAA
Found at i:263626 original size:32 final size:33
Alignment explanation
Indices: 263588--263666 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 33
263578 CTTTATTTTG
*
263588 TTCGGGTCGGGTCATG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATA
*
263620 TTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTC--G--GGTCAGGTTTTTTTAAGTGTGATA
263657 TTCGGGTCGG
1 TTCGGGTCGG
263667 ATCGGGTCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
32 8 0.20
33 1 0.03
34 1 0.03
35 1 0.03
36 5 0.12
37 24 0.60
ACGTcount: A:0.13, C:0.11, G:0.35, T:0.41
Consensus pattern (33 bp):
TTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATA
Found at i:263645 original size:37 final size:38
Alignment explanation
Indices: 263604--263680 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 38
263594 TCGGGTCATG
263604 TTTTTTAAGTGTGATATTCGGGTC-GAGTC-GGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGGA-TCGGGTCGGGT
263641 TTTTTTAAGTGTGATATTCGGGTCGGATCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGGATCGGGTCGGGT
263679 TT
1 TT
263681 AGGGTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
37 26 0.68
38 12 0.32
ACGTcount: A:0.13, C:0.10, G:0.35, T:0.42
Consensus pattern (38 bp):
TTTTTTAAGTGTGATATTCGGGTCGGATCGGGTCGGGT
Found at i:263818 original size:36 final size:36
Alignment explanation
Indices: 263778--263862 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
263768 TTTTTATTAT
263778 TTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATA
1 TTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATA
*
263814 TTCGGGTCGGGTAGGGTCGGATTTCTAATTCATATA
1 TTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATA
263850 TTCGGGTCGGGTC
1 TTCGGGTCGGGTC
263863 AAATGAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.15, C:0.16, G:0.33, T:0.35
Consensus pattern (36 bp):
TTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATA
Found at i:263902 original size:257 final size:254
Alignment explanation
Indices: 263416--263936 Score: 707
Period size: 257 Copynumber: 2.0 Consensus size: 254
263406 CGGGTCGATT
* *
263416 TCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTTGGATT
1 TCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATT
263481 AAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTC
66 AAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTC
* * ***
263546 TAATTCATATATTCGGATCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCATGTTTTTTA
131 TAATTCATATATTCGGATCGGGTAGGATGAAACTTTATTTTATTCGGGTCGGGTCATGAACTTTA
* *
263611 AGTGTGATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC-GGATCGGG
196 AGTGTGATATTCGGGTC-AG-CGGTCGAG-TTTTTTAAGTGTGATATTCGGGTCAAG-TCGGG
*
263673 TCGGGTTTAGGGTGAAAAAAACCGGACCGATCCGAAAATATATATAATTCGGGTCGGGTCGGATT
1 TCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATT
*
263738 AAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTC
66 AAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTC
* * * *
263803 TAATTCATATATTCGGGTCGGGTAGGGTCG-GATTTCTAATTCATATATTCGGGTCGGGTCAAAT
131 TAATTCATATATTCGGATCGGGTAGGAT-GAAACTT-T-ATT--T-TATTCGGGTCGGGTC--AT
* * *
263867 GAAACTTT-A-T-T-TTGTTCGGGTC-G-GGTTGAGTTTTTTAAGTGTGATATTCGGGTCAAGTC
188 G-AACTTTAAGTGTGATATTCGGGTCAGCGGTCGAGTTTTTTAAGTGTGATATTCGGGTCAAGTC
263926 GGG
252 GGG
263929 TCGGGTTT
1 TCGGGTTT
263937 TTTTTAAGTG
Statistics
Matches: 236, Mismatches: 18, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
256 37 0.16
257 160 0.68
258 2 0.01
259 4 0.02
261 10 0.04
262 15 0.06
263 1 0.00
264 4 0.02
265 3 0.01
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.37
Consensus pattern (254 bp):
TCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATT
AAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTC
TAATTCATATATTCGGATCGGGTAGGATGAAACTTTATTTTATTCGGGTCGGGTCATGAACTTTA
AGTGTGATATTCGGGTCAGCGGTCGAGTTTTTTAAGTGTGATATTCGGGTCAAGTCGGG
Found at i:263949 original size:39 final size:40
Alignment explanation
Indices: 263882--263972 Score: 148
Period size: 39 Copynumber: 2.2 Consensus size: 40
263872 TTTATTTTGT
263882 TCGGGTCGGGTTGAGTTTTTTAAGTGTGATATTCGGGTCAAG
1 TCGGGTCGGGTT--GTTTTTTAAGTGTGATATTCGGGTCAAG
*
263924 TCGGGTCGGGTT-TTTTTTAAGTGTGATATTCGGGTCAGG
1 TCGGGTCGGGTTGTTTTTTAAGTGTGATATTCGGGTCAAG
263963 TCGGGTCGGG
1 TCGGGTCGGG
263973 GTCGGGTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 36 0.75
42 12 0.25
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.37
Consensus pattern (40 bp):
TCGGGTCGGGTTGTTTTTTAAGTGTGATATTCGGGTCAAG
Found at i:264529 original size:16 final size:17
Alignment explanation
Indices: 264504--264548 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
264494 TATGGAATTC
*
264504 GATTCTAATTCTT-ACA
1 GATTCCAATTCTTCACA
264520 GATTCCAATTCCTTCACA
1 GATTCCAATT-CTTCACA
*
264538 GACTCCAATTC
1 GATTCCAATTC
264549 CCTCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 12 0.48
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCTTCACA
Found at i:265423 original size:2 final size:2
Alignment explanation
Indices: 265416--265449 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
265406 AAGAAATCTG
* *
265416 AT AT AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265450 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265442 original size:16 final size:16
Alignment explanation
Indices: 265423--265455 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
265413 CTGATATATA
265423 TATATATATATATGTG
1 TATATATATATATGTG
*
265439 TATATATATATGTGTG
1 TATATATATATATGTG
265455 T
1 T
265456 GTGTGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
TATATATATATATGTG
Found at i:265450 original size:14 final size:14
Alignment explanation
Indices: 265425--265453 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
265415 GATATATATA
265425 TATATATATATGTG
1 TATATATATATGTG
265439 TATATATATATGTG
1 TATATATATATGTG
265453 T
1 T
265454 GTGTGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TATATATATATGTG
Found at i:268204 original size:18 final size:18
Alignment explanation
Indices: 268181--268220 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
268171 CTCTGCTTCT
*
268181 ATAGTAAACAAAGCTACC
1 ATAGTAAACAAAGCCACC
*
268199 ATAGTAGACAAAGCCACC
1 ATAGTAAACAAAGCCACC
268217 ATAG
1 ATAG
268221 ACTGTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.15
Consensus pattern (18 bp):
ATAGTAAACAAAGCCACC
Found at i:270549 original size:20 final size:20
Alignment explanation
Indices: 270524--270561 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
270514 ATGTAGATAC
270524 TGAGCCTAAACAAGTTCCAT
1 TGAGCCTAAACAAGTTCCAT
270544 TGAGCCTAAACAAGTTCC
1 TGAGCCTAAACAAGTTCC
270562 GAAATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
TGAGCCTAAACAAGTTCCAT
Found at i:271082 original size:31 final size:31
Alignment explanation
Indices: 271044--271103 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
271034 GAGTTGAGGG
271044 TTACCTATATTCTACGGAACAAATGGACAGT
1 TTACCTATATTCTACGGAACAAATGGACAGT
* * * *
271075 TTACCTATGTTCTTCGGAATATATGGACA
1 TTACCTATATTCTACGGAACAAATGGACA
271104 ATTACATAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (31 bp):
TTACCTATATTCTACGGAACAAATGGACAGT
Found at i:271723 original size:12 final size:12
Alignment explanation
Indices: 271706--271738 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
271696 GCACTGTAGC
271706 ACTGTTCATGGT
1 ACTGTTCATGGT
271718 ACTGTTCATGGT
1 ACTGTTCATGGT
271730 ACTGTTCAT
1 ACTGTTCAT
271739 ACCGTATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:275839 original size:4 final size:4
Alignment explanation
Indices: 275830--275863 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
275820 AGACTATCAG
* *
275830 GTAT GTAT GTAT GCAT GCAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
275864 TTATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (4 bp):
GTAT
Found at i:281351 original size:67 final size:67
Alignment explanation
Indices: 281243--281379 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
281233 ATTTCATAGT
281243 AATGAATTAAATAATCTATTATGTTAAATTTAATGTAAGAGAGCTAAGGACAAAGAAGTATTTAT
1 AATGAATTAAATAATCTATTATGTTAAATTTAATGTAAGAGAGCTAAGGACAAAGAAGTATTTAT
281308 AA
66 AA
281310 AATGAATTAAATAATCTATTATGTTAAATTTAATGTAAGAGAGCTAAGGACAAAGAAGTATTTAT
1 AATGAATTAAATAATCTATTATGTTAAATTTAATGTAAGAGAGCTAAGGACAAAGAAGTATTTAT
281375 AA
66 AA
281377 AAT
1 AAT
281380 TAATGCAGTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (67 bp):
AATGAATTAAATAATCTATTATGTTAAATTTAATGTAAGAGAGCTAAGGACAAAGAAGTATTTAT
AA
Found at i:282800 original size:3 final size:3
Alignment explanation
Indices: 282794--282859 Score: 91
Period size: 3 Copynumber: 22.3 Consensus size: 3
282784 TAATGGGCCT
*
282794 ATA ATA A-A A-A ATA AAA ATAA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
*
282838 ATA ATA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
282860 ATAGTAACAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.88
4 3 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:283453 original size:260 final size:259
Alignment explanation
Indices: 282954--283602 Score: 1052
Period size: 260 Copynumber: 2.5 Consensus size: 259
282944 AAATGACCCA
* * * *
282954 AAGGATTTAATCATCATTCTCGAAATACTTACTGATGGCCTGAAAGACTTACCAATTTTGGAAAT
1 AAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAAT
* * *
283019 AGTTTACTAGTTAAGAAACTTTGGAAATTGCTTTCTTGCTTTTCAAAAA-TTTCATTTTCTGAAA
66 AGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTTCATTTTCTGAAA
* **
283083 ATACTAATGAGAAACTTTGAAAATTGCCTTCTCATTTTTCAAATTATCACATGAAAGCATCTTGC
131 ATACTAATGAGAAACTTTGAAAATTGACTTCTCAAATTTCAAATTATCACATGAAAGCATCTTGC
* *
283148 CCGAAGGTCTTATAGATGGCCCGGAGGACTTATCATCTTGCTCGAAAGATTGACAGATAA-CTCG
196 CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACCT-G
* * *
283212 AAGGATTTAATCATGATGCTTGAAAGACTTACTGATGGCGTGAAGGACTTACCAATTTTGGTAAT
1 AAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAAT
* *
283277 AGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTTCATTTTTTGAAA
66 AGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTTCATTTTCTGAAA
* *
283342 ATACTAAATGAGAAACTTTGAAAATTGATTTCTCAAATTTCAAATTATCACATGAAAGCGTCTTG
131 ATACT-AATGAGAAACTTTGAAAATTGACTTCTCAAATTTCAAATTATCACATGAAAGCATCTTG
*
283407 CCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCTG
195 CCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACCTG
* *
283472 AAGGATTTAATCATCATGCTTGAAAGATTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAAT
1 AAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAAT
*
283537 AGTTTACTACGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTT-ATTTTCTGAAA
66 AGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTTCATTTTCTGAAA
283601 AT
131 AT
283603 CTCAATTTTA
Statistics
Matches: 360, Mismatches: 28, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
258 103 0.29
259 31 0.09
260 224 0.62
261 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (259 bp):
AAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAAT
AGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTTCATTTTCTGAAA
ATACTAATGAGAAACTTTGAAAATTGACTTCTCAAATTTCAAATTATCACATGAAAGCATCTTGC
CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACCTG
Found at i:283517 original size:42 final size:41
Alignment explanation
Indices: 283421--283522 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
283411 AAGGTCTTAT
*
283421 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
* * * * * *
283462 AGATGACCTGAAGGATTTAATCATCATGCTTGAAAGATTTAC
1 AGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTGAC
*
283504 TGATGGCCCGAAGGACTTA
1 AGATGGCCCGAAGGACTTA
283523 CCAATTTTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
Found at i:285374 original size:17 final size:17
Alignment explanation
Indices: 285339--285386 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
285329 AAGTGATTGA
285339 TCTATTTTTT-TTACTTTC
1 TCTATTTTTTCTT-C-TTC
285357 TCCT-TTTTTTCTTCTTC
1 T-CTATTTTTTCTTCTTC
285374 TCTATTTTTTCTT
1 TCTATTTTTTCTT
285387 TTTTTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 8 0.30
19 4 0.15
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (17 bp):
TCTATTTTTTCTTCTTC
Found at i:285405 original size:24 final size:23
Alignment explanation
Indices: 285361--285421 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
285351 ACTTTCTCCT
* *
285361 TTTTTTCTTCTTCTCTATTTTTTC
1 TTTTTT-TTCTTCACTATTTTCTC
*
285385 TTTTTTTTCGTTCACTTTTTTCTC
1 TTTTTTTTC-TTCACTATTTTCTC
285409 TATGTTTTTTCTT
1 T-T-TTTTTTCTT
285422 TTTCTATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 3 0.10
24 18 0.58
25 3 0.10
26 7 0.23
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (23 bp):
TTTTTTTTCTTCACTATTTTCTC
Found at i:286122 original size:33 final size:32
Alignment explanation
Indices: 286076--286162 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
286066 GACGATGATG
**
286076 TGACTTTATTGCCTCAAATAGAGGTAAGGGAA
1 TGACTTTGGTGCCTCAAATAGAGGTAAGGGAA
* * * **
286108 TGATTTTGAGTGCCTCAAAGAGAGGTAATGGTG
1 TGACTTTG-GTGCCTCAAATAGAGGTAAGGGAA
*
286141 TGACTTTGGTGACTCAAATAGA
1 TGACTTTGGTGCCTCAAATAGA
286163 TGTAGTGTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
32 18 0.41
33 26 0.59
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (32 bp):
TGACTTTGGTGCCTCAAATAGAGGTAAGGGAA
Found at i:290488 original size:27 final size:27
Alignment explanation
Indices: 290450--290521 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
290440 CAACATGGTA
*
290450 TCTACCCTGACATGCTTTTATAAAAGT
1 TCTACCCAGACATGCTTTTATAAAAGT
290477 TCTACCCAGACATGCTTTTATAAAAGT
1 TCTACCCAGACATGCTTTTATAAAAGT
290504 TCTACCCAGACATG-TTTT
1 TCTACCCAGACATGCTTTT
290522 GTACCTCCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 4 0.09
27 40 0.91
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (27 bp):
TCTACCCAGACATGCTTTTATAAAAGT
Found at i:294079 original size:3 final size:3
Alignment explanation
Indices: 294058--294119 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
294048 ATGGACTTGC
294058 AAT AA- AAT AAT AA- AA- AAT AAT AAT AAT AATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
*
294101 AAT AAAT ATT AAT AA- AAT A
1 AAT -AAT AAT AAT AAT AAT A
294120 TCCTGACGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 8 0.15
3 38 0.73
4 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:294084 original size:16 final size:16
Alignment explanation
Indices: 294058--294119 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
294048 ATGGACTTGC
*
294058 AATAA-AATAATAAAA
1 AATAATAATAATAATA
*
294073 AATAATAATAATAATT
1 AATAATAATAATAATA
294089 AATAATAATAATAATA
1 AATAATAATAATAATA
*
294105 AATATTAATAA-AATA
1 AATAATAATAATAATA
294120 TCCTGACGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.21
16 33 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:309094 original size:21 final size:20
Alignment explanation
Indices: 309065--309122 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
309055 CCAAGATAAT
*
309065 AAATCAAAAGAAAAGAGGGAAA
1 AAAT-AAAA-AAAAGAGGAAAA
*
309087 AAATAAAAAATAAAAGGAAAA
1 AAATAAAAAA-AAGAGGAAAA
309108 AAATAAAATAAAAGA
1 AAATAAAA-AAAAGA
309123 AATAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.06
21 23 0.74
22 6 0.19
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.09
Consensus pattern (20 bp):
AAATAAAAAAAAGAGGAAAA
Found at i:309101 original size:14 final size:14
Alignment explanation
Indices: 309091--309149 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
309081 GGGAAAAAAT
**
309091 AAAAAATAAAAGGA
1 AAAAAATAAAATAA
309105 AAAAAATAAAATAA
1 AAAAAATAAAATAA
*
309119 AAGAAATAATAATAA
1 AAAAAATAA-AATAA
*
309134 TAATATAATAAAATAA
1 -AA-AAAATAAAATAA
309150 CTAAATAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 20 0.54
15 5 0.14
16 7 0.19
17 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (14 bp):
AAAAAATAAAATAA
Found at i:309115 original size:19 final size:20
Alignment explanation
Indices: 309082--309130 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
309072 AAGAAAAGAG
309082 GGAAAAAATAAAAAATAAAA
1 GGAAAAAATAAAAAATAAAA
*
309102 GGAAAAAA-ATAAAATAAAA
1 GGAAAAAATAAAAAATAAAA
*
309121 -GAAATAATAA
1 GGAAAAAATAA
309131 TAATAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 11 0.44
20 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
GGAAAAAATAAAAAATAAAA
Found at i:309327 original size:12 final size:13
Alignment explanation
Indices: 309282--309332 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
309272 CCAAAAAAGT
* *
309282 ATATATATATATA
1 ATATAAATAAATA
*
309295 TATATATAATTAATA
1 -ATATA-AATAAATA
309310 ATATAAATAAATA
1 ATATAAATAAATA
309323 A-ATAAATAAA
1 ATATAAATAAA
309333 AGGGACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.28
13 8 0.25
14 10 0.31
15 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAAATAAATA
Found at i:310513 original size:36 final size:36
Alignment explanation
Indices: 310440--310799 Score: 252
Period size: 39 Copynumber: 9.7 Consensus size: 36
310430 TTAAAAATAT
* *
310440 TGTTTT-AAAACTATATATAATATATATTTCCAAAAAAAA
1 TGTTTTCAAAACTATATATTATATA-ATTTTC---AAAAA
* * * *
310479 TATTTCCAAAACAATATATTATATAATTTTAAAAAA
1 TGTTTTCAAAACTATATATTATATAATTTTCAAAAA
** * *
310515 TGTTTT-TGAACTATATGTTATATAGTTTTCAAAAA
1 TGTTTTCAAAACTATATATTATATAATTTTCAAAAA
*
310550 TGTTTT-AAAAC--TATATTATAT-GTTTTCAAAAA
1 TGTTTTCAAAACTATATATTATATAATTTTCAAAAA
* *
310582 TGTTTTTTTTTCAAAAATTATATATTATATATATTTTCAAAAT
1 TG-----TTTTC-AAAACTATATATTATATA-ATTTTCAAAAA
* *
310625 TATTTTCAAAACTATATATATTATATATATTTTCTAAAA
1 TGTTTTCAAAAC--TATATATTATATA-ATTTTCAAAAA
* *
310664 TGTTTTAAAAATCTATATATTATTTAATTTTCAAAAA
1 TGTTTTCAAAA-CTATATATTATATAATTTTCAAAAA
* *
310701 TGTTTTAAAAACTATATAATATATACATTTTC-AAAA
1 TGTTTTCAAAACTATATATTATATA-ATTTTCAAAAA
* * *
310737 TATTTTGAAAACTAT-TATTATACCTGTATTTTCAAAAA
1 TGTTTTCAAAACTATATATTATA--T-AATTTTCAAAAA
* * *
310775 CTATTTGC-AAACTATATAATATATA
1 -TGTTTTCAAAACTATATATTATATA
310800 GATATATATA
Statistics
Matches: 261, Mismatches: 38, Indels: 47
0.75 0.11 0.14
Matches are distributed among these distances:
32 13 0.05
33 9 0.03
35 38 0.15
36 38 0.15
37 43 0.16
38 28 0.11
39 55 0.21
40 17 0.07
41 10 0.04
43 10 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (36 bp):
TGTTTTCAAAACTATATATTATATAATTTTCAAAAA
Found at i:310643 original size:113 final size:111
Alignment explanation
Indices: 310404--310751 Score: 266
Period size: 113 Copynumber: 3.1 Consensus size: 111
310394 ATCATAAATA
* * * *
310404 AAAACTATATAATATATATATATTTTTTAAAAATATTGTTTTAAAACT-ATATATAATATATATT
1 AAAACTATAT-ATAT-TATATATATTTTCAAAA-A-TGTTTTAAAAATCATATATTATATA-ATT
* * ** * * * *
310468 TCCAAAAAAAATATTTCCAAAACAATATATTATATA-ATTTT-AAAAAATGTTTT
61 TTC---AAAAATGTTTTAAAAACTATATAATATATACATTTTCAAAATAT-TTTC
** * * *
310521 TGAAC--TATATGTTATATA-GTTTTCAAAAATGTTTT-AAAA-C-TATATTATAT-GTTTTCAA
1 AAAACTATATATATTATATATATTTTCAAAAATGTTTTAAAAATCATATATTATATAATTTTCAA
* * *
310579 AAATGTTTTTTTTTCAAAAATTATATATTATATATATTTTCAAAATTATTTTC
66 AAATG-----TTTT-AAAAACTATATAATATATACATTTTCAAAA-TATTTTC
* *
310632 AAAACTATATATATTATATATATTTTCTAAAATGTTTTAAAAATCTATATATTATTTAATTTTCA
1 AAAACTATATATATTATATATATTTTCAAAAATGTTTTAAAAATC-ATATATTATATAATTTTCA
*
310697 AAAATGTTTTAAAAACTATATAATATATACATTTTCAAAATATTTTG
65 AAAATGTTTTAAAAACTATATAATATATACATTTTCAAAATATTTTC
310744 AAAACTAT
1 AAAACTAT
310752 TATTATACCT
Statistics
Matches: 186, Mismatches: 27, Indels: 41
0.73 0.11 0.16
Matches are distributed among these distances:
103 6 0.03
106 4 0.02
108 12 0.06
109 19 0.10
110 11 0.06
111 11 0.06
112 24 0.13
113 45 0.24
114 22 0.12
115 7 0.04
116 1 0.01
117 3 0.02
118 9 0.05
119 12 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (111 bp):
AAAACTATATATATTATATATATTTTCAAAAATGTTTTAAAAATCATATATTATATAATTTTCAA
AAATGTTTTAAAAACTATATAATATATACATTTTCAAAATATTTTC
Found at i:310768 original size:74 final size:72
Alignment explanation
Indices: 310589--310799 Score: 205
Period size: 74 Copynumber: 2.8 Consensus size: 72
310579 AAATGTTTTT
* * *
310589 TTTTCAAAAAT-TATATATTATATATATTTTCAAAATTATTTTCAAAACTATATATATTATATAT
1 TTTT-AAAAATCTATATATTAT-T-TATTTTCAAAAAT-TTTTAAAAACTATATA-A-TATATAC
*
310653 ATTTTCTAAAATG
60 ATTTTCTAAAATA
310666 TTTTAAAAATCTATATATTATTTAATTTTCAAAAATGTTTTAAAAACTATATAATATATACATTT
1 TTTTAAAAATCTATATATTATTT-ATTTTCAAAAAT-TTTTAAAAACTATATAATATATACATTT
310731 TC-AAAATA
64 TCTAAAATA
* * **
310739 TTTTGAAAA-CTAT-TATTATACCTGTATTTTCAAAAACTATTTGCAAACTATATAATATATA
1 TTTTAAAAATCTATATATTAT---T-TATTTTCAAAAA-TTTTTAAAAACTATATAATATATA
310800 GATATATATA
Statistics
Matches: 118, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
71 6 0.05
72 4 0.03
73 13 0.11
74 44 0.37
75 4 0.03
76 33 0.28
77 14 0.12
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (72 bp):
TTTTAAAAATCTATATATTATTTATTTTCAAAAATTTTTAAAAACTATATAATATATACATTTTC
TAAAATA
Found at i:311564 original size:84 final size:84
Alignment explanation
Indices: 311381--312292 Score: 913
Period size: 84 Copynumber: 11.0 Consensus size: 84
311371 GCTATGTTGT
* * *
311381 AAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAGG--TTT--TTGGCAGATAGCCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * *
311442 TAGCCTTGAGCTATACCGC
66 TCGACTTAAGTTATGCTGC
* ** * *
311461 AAATGACGCACCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
311526 TCGACTTAAGTTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * * *
311545 AAATGATATACCTTGGAGCTGAGCGTAGTTGAACTCGAATGTCTTTGG-TGACAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * *
311609 TAGCCTTGAA-TTATGCTGT
66 TCGACTT-AAGTTATGCTGC
* * * *
311628 AAATGATGTGCCCTT-AAGCTGAGTGTAATCGAACTC-AAGGGTC--T--TTGGCAGATAGCCCT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCT
* *
311687 TCTCGACTTAAGCTATGCTAC
64 TCTCGACTTAAGTTATGCTGC
* *
311708 AAATGATGTGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGG--TTTGGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
311771 TCGACTTAAGTTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * * * *
311790 AAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTT
1 AAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
*
311851 CTCGACTTAAGTTATGTTGC
65 CTCGACTTAAGTTATGCTGC
*
311871 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
311936 TCGACTTAAGTTATGCTGC
66 TCGACTTAAGTTATGCTGC
* * * * ** * *
311955 AAATGATGTTCCTTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGGATGGAAGATAACCCT
1 AAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCT
* * *
312020 TCTTGATTTAAGCTATGCTGC
64 TCTCGACTTAAGTTATGCTGC
* * * **
312041 AAATGTTGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGG-TCACAGATAACCCTT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGTTGGCAGATAACCCTT
* *
312105 CT-AACCTTGAGTTATGCTGC
65 CTCGA-CTTAAGTTATGCTGC
* * * * * * *
312125 AAATAATGTGCCCTTGAAGCTGAGTGTAATCGAACACGAGGGTC--T--TTGGCAGATAGCCCTT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
*
312186 -TCGACTTAAGCTATGCTGC
65 CTCGACTTAAGTTATGCTGC
* * * * *
312205 AAATGATATGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAAATAGCCCTT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTT
* *
312269 CTTGACTTAAGCTATGCTGC
65 CTCGACTTAAGTTATGCTGC
312289 AAAT
1 AAAT
312293 AGTTTCTTTA
Statistics
Matches: 680, Mismatches: 117, Indels: 66
0.79 0.14 0.08
Matches are distributed among these distances:
79 33 0.05
80 140 0.21
81 59 0.09
82 49 0.07
83 95 0.14
84 181 0.27
85 74 0.11
86 49 0.07
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
TCGACTTAAGTTATGCTGC
Found at i:311812 original size:163 final size:163
Alignment explanation
Indices: 311366--312292 Score: 1039
Period size: 163 Copynumber: 5.6 Consensus size: 163
311356 CCCTTCTTTC
* * * * * *
311366 CTTAGGCTATGTTGTAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAGGTTT--TTGG
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTGGTTGG
* * * * * * * * * *
311429 CAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGA--CGCACCTTGGAGCTGAGCGTAATCG
66 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC-CCTCGAAGCTGAGTGTAATCG
* *
311492 AACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGA
130 AACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGA
* * * * * *
311530 CTTAAGTTATGCTGCAAATGATATACCTTGGAGCTGAGCGTAGTTGAACTCGAATGTCTTTGG-T
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAAG-GTTTGGTT
* * * *
311594 GACAGATAACCCTTCTAGCCTTGAA-TTATGCTGTAAATGATGTGCCCT-TAAGCTGAGTGTAAT
64 GGCAGATAACCCTTCTAGACTT-AAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* *
311657 CGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGA
128 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
* *
311693 CTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGGTTTGGTTGG
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTGGTTGG
* *
311758 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATCGA
66 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
311823 ACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
131 ACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
* *
311856 CTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTT
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGG--TTTGGTT
* * *
311921 GGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTTCCTTCGAAGCTGAGTGTAATC
64 GGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
* * *
311986 GAACTCGGGGGTCTTTTGGATGGAAGATAACCCTTCTTGA
129 GAACTCGAGGGTC--TT---TGGCAGATAACCCTTCTCGA
* * * * *
312026 TTTAAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTT-TTTGG
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTGGTTGG
* * *
312090 TCACAGATAACCCTTCTA-ACCTTGAGTTATGCTGCAAATAATGTGCCCTTGAAGCTGAGTGTAA
66 ---CAGATAACCCTTCTAGA-CTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* *
312154 TCGAACACGAGGGTCTTTGGCAGATAGCCCTT-TCGA
127 TCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
* * *
312190 CTTAAGCTATGCTGCAAATGATATGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-
1 CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGG---TTTGGT
* * * * *
312254 TGACAAATAGCCCTTCTTGACTTAAGCTATGCTGCAAAT
63 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
312293 AGTTTCTTTA
Statistics
Matches: 656, Mismatches: 81, Indels: 52
0.83 0.10 0.07
Matches are distributed among these distances:
161 7 0.01
162 44 0.07
163 164 0.25
164 125 0.19
165 100 0.15
166 3 0.00
167 67 0.10
168 9 0.01
169 3 0.00
170 134 0.20
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (163 bp):
CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTGGTTGG
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
ACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
Found at i:315377 original size:13 final size:13
Alignment explanation
Indices: 315359--315392 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
315349 AAAATGGTAA
315359 TAAATTAATTAAT
1 TAAATTAATTAAT
315372 TAAATTAATTAAT
1 TAAATTAATTAAT
315385 TAAATTAA
1 TAAATTAA
315393 AATGAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAATTAATTAAT
Found at i:315466 original size:26 final size:23
Alignment explanation
Indices: 315437--315490 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
315427 ATGAAGAAAG
315437 CAAAGATAAAATAGTAAGTAAAAAAA
1 CAAAGATAAAATA-T-A-TAAAAAAA
*
315463 CAAATAATAAAATATATAAAAAAA
1 CAAA-GATAAAATATATAAAAAAA
315487 -AAAG
1 CAAAG
315491 GAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 3 0.12
24 8 0.32
25 1 0.04
26 5 0.20
27 8 0.32
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (23 bp):
CAAAGATAAAATATATAAAAAAA
Found at i:315510 original size:29 final size:27
Alignment explanation
Indices: 315456--315516 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
315446 AATAGTAAGT
* *
315456 AAAAAAACAAATAATAAAATATATAAA
1 AAAAAAACAAATAATAAAACAAATAAA
*
315483 AAAAAAAGGAAATAAATAAAACAAATAAA
1 AAAAAAA-CAAAT-AATAAAACAAATAAA
*
315512 CAAAA
1 AAAAA
315517 TAATAATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 7 0.25
28 4 0.14
29 17 0.61
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (27 bp):
AAAAAAACAAATAATAAAACAAATAAA
Found at i:315818 original size:2 final size:2
Alignment explanation
Indices: 315811--315860 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
315801 CTTGTGTAGA
* *
315811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AA AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
315854 AT AT AT A
1 AT AT AT A
315861 ACAACAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:316044 original size:2 final size:2
Alignment explanation
Indices: 316037--316061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
316027 GAACATACGC
316037 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 A
316062 CAAAATAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:316076 original size:18 final size:17
Alignment explanation
Indices: 316053--316102 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 17
316043 ATATATATAT
316053 ATATATATACAAAATAA
1 ATATATATACAAAATAA
316070 ATA-ATATA-AAAATAA
1 ATATATATACAAAATAA
316085 ATA-ATAATACAAGAATAA
1 ATATAT-ATACAA-AATAA
316103 TAAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 12 0.40
16 8 0.27
17 5 0.17
18 5 0.17
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (17 bp):
ATATATATACAAAATAA
Found at i:316138 original size:6 final size:6
Alignment explanation
Indices: 316129--316232 Score: 50
Period size: 6 Copynumber: 18.2 Consensus size: 6
316119 GTAAAAAAAT
316129 ATAATA ATAATA A-AAT- ATAA-A A-AAT- ATACATA TATAAT- ATAAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATA-ATA -ATAATA AT-AATA
* *
316174 AGTAA-A ATAA-A ATGAA-A AT-ATA ATAGTA AAAATA ATAATA A-ATATA
1 A-TAATA ATAATA AT-AATA ATAATA ATAATA ATAATA ATAATA ATA-ATA
*
316220 ATAGTA ATAATA A
1 ATAATA ATAATA A
316233 AAATGCAAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
4 5 0.06
5 19 0.25
6 43 0.56
7 6 0.08
8 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (6 bp):
ATAATA
Found at i:316221 original size:24 final size:24
Alignment explanation
Indices: 316124--316232 Score: 82
Period size: 24 Copynumber: 4.3 Consensus size: 24
316114 AGAAAGTAAA
*
316124 AAAATATAATAAT-AATAAAATA-T
1 AAAA-ATAATAATAAATATAATAGT
*
316147 AAAAAATATACATATATAATATAAATAAGT
1 -AAAAATA-ATA-ATA-AATAT-AAT-AGT
316177 -AAAATAA-AATGAAAATATAATAGT
1 AAAAATAATAAT--AAATATAATAGT
316201 AAAAATAATAATAAATATAATAGT
1 AAAAATAATAATAAATATAATAGT
*
316225 AATAATAA
1 AAAAATAA
316233 AAATGCAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
23 3 0.04
24 28 0.39
25 14 0.20
26 9 0.13
27 6 0.08
28 9 0.13
29 1 0.01
30 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAATAATAATAAATATAATAGT
Found at i:316885 original size:37 final size:37
Alignment explanation
Indices: 316787--316888 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
316777 GTGCTTGTGG
* ** * *
316787 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
* *
316824 ATCCTATTTTCAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
316861 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
316889 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:318238 original size:106 final size:106
Alignment explanation
Indices: 317497--319266 Score: 2554
Period size: 106 Copynumber: 17.0 Consensus size: 106
317487 GCATTGTTTT
* * * *
317497 GAGTCCAAT-TCC-TCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGG-AA--G-TT-GTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * * *
317555 CCAACCGT-CCTTCGTTGTGAAGTTGAACTTGTGTTGTTTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317595 GAGTCCAATATCCTT-GTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
317659 CCAGCGGTCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317700 G-GTCCAAGATCC-T--TTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
317760 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317801 G-GTCCAATATCCTAC---GAGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
317862 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317902 GAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGGCTCT-AAATTGAG-AA--G-TTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
317962 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
318003 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
318067 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
318108 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
318173 CCAGCGGTCCCTT-GATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
318214 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
318279 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
318320 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
318385 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
318426 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
318491 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
318531 -AGTCCAATATCCTACG-TGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
318594 CCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
318634 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATT--GAGA-TGTTGT-TTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTT-TATTGACA
*
318695 ACCAGC-GTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
318736 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
318801 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
318842 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATAGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
318907 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
318948 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
319013 TCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
319054 GAGTCCAATATTCTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
319119 CCAGTGGTTCCTTCGTCGTGAAGTTAAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
319160 GAGTCCAAT-T-CTTAGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
319223 CCAGCGGT-CCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
319263 GAGT
1 GAGT
319267 TGGCACGATA
Statistics
Matches: 1536, Mismatches: 102, Indels: 63
0.90 0.06 0.04
Matches are distributed among these distances:
98 9 0.01
99 31 0.02
100 18 0.01
101 203 0.13
102 188 0.12
103 91 0.06
104 118 0.08
105 183 0.12
106 694 0.45
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:318764 original size:628 final size:630
Alignment explanation
Indices: 317497--319266 Score: 2675
Period size: 628 Copynumber: 2.8 Consensus size: 630
317487 GCATTGTTTT
* *
317497 GAGTCCAAT-TCC-TCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGG-AA--G-TTG-TGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
317554 ACCAACCGT-CCTTCGTTGTGAAGTTGAACTTGTGTTGTTTTGAGTCCAATATCCTT-GTTGTGA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGA
*
317617 AGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * * * *
317682 TTGAGCTTGTGTTGTCTTG-GTCCAAGATCCTT--TGAGAAGTTGAAATTGGCTCTGAAATTGGG
195 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
317744 AAGTTGTTT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG-GTCCA
260 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
317807 ATATCC-T-AC-GAGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGC-G
325 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
* *
317868 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAT
390 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAGTCCAATATCCTACGTTGTGAAGTTGAAA
* * *
317933 TTGGCTCT-AAATTG-AGA--AGTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTG
454 TTGGCTCTGAAATTGAAAATTATTTATTGACAACCAGCGGT-CCTTCGTCGTGAAGTTGAACTTG
* *
317994 CGTTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTT
518 TGTTGTCTGGAGTCCAATATCCTTCACTGTAAAGTTGAAATTGGCTCTGAAATTGGAAGTTG-TT
* *
318059 ATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
582 ATTGACAACCAGCGGTCCCTTCATCGTAAAGTTGAACTTGCGTTGTCTG
318108 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
318173 CCAGCGGTCCCTT-GATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGA
* * *
318237 AGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
318302 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGG
195 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGG
*
318367 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCC
259 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
318432 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCG
324 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
*
318497 GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT-AGTCCAATATCCTACG-TGTGAAGTTGAAA
389 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAGTCCAATATCCTACGTTGTGAAGTTGAAA
318560 TTGGCTCTGAAATTGGAAAATTATTTATTGACAACCAGCGGTCCTTCGTCGTGAAGTTGAACTTG
454 TTGGCTCTGAAATT-GAAAATTATTTATTGACAACCAGCGGTCCTTCGTCGTGAAGTTGAACTTG
** *
318625 TGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGATGTTG-T
518 TGTTGTCTGGAGTCCAATATCCTTCACTGTAAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTT
*
318689 -TTGACAACCAGC-GTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
582 ATTGACAACCAGCGGTCCCTTCATCGTAAAGTTGAACTTGCGTTGTCTG
* *
318736 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
318801 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGAA
* *
318866 GTTGAAATTGGCTCTGAAATTGGGAAATAGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
318931 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
196 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * *
318996 AAGTCGTTTGTTGACAATCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
260 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * *
319061 ATATTCTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGTGG
325 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
* * * *
319126 TTCCTTCGTCGTGAAGTTAAACTTGCGTTATCTGGAGTCCAAT-TCTTA-GTTGTGAAGTTGAAA
390 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAGTCCAATATCCTACGTTGTGAAGTTGAAA
* * * * *
319189 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCTTCATTGTGAAGTTGAACTTG
454 TTGGCTCTGAAATTGA-AAATTATTTATTGACAACCAGCGGTCCTTCGTCGTGAAGTTGAACTTG
*
319254 TGTTGTCTTGAGT
518 TGTTGTCTGGAGT
319267 TGGCACGATA
Statistics
Matches: 1056, Mismatches: 71, Indels: 46
0.90 0.06 0.04
Matches are distributed among these distances:
611 9 0.01
612 3 0.00
613 30 0.03
614 3 0.00
616 1 0.00
617 3 0.00
618 13 0.01
619 41 0.04
620 84 0.08
621 12 0.01
624 37 0.04
625 47 0.04
626 11 0.01
627 21 0.02
628 451 0.43
629 148 0.14
630 44 0.04
631 73 0.07
632 25 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (630 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAGTCCAATATCCTACGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAAAATTATTTATTGACAACCAGCGGTCCTTCGTCGTGAAGTTGAACTTGTGT
TGTCTGGAGTCCAATATCCTTCACTGTAAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTATTG
ACAACCAGCGGTCCCTTCATCGTAAAGTTGAACTTGCGTTGTCTG
Found at i:319348 original size:49 final size:47
Alignment explanation
Indices: 319230--319348 Score: 105
Period size: 49 Copynumber: 2.5 Consensus size: 47
319220 CAACCAGCGG
* * * * *
319230 TCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGTTGGCACGATA
1 TCCTTCGTTGTGAAGTTGAAATCGTGATGTCTTGAGTTGGCAAGATA
* * * * * *
319277 TCCTCCGTCGTGGATTTTAAATCGTGGATGT-TTGACTTTGAGCAAGATA
1 TCCTTCGTTGTGAAGTTGAAATCGT-GATGTCTTGA-GTTG-GCAAGATA
319326 TCCTTCGTTGTGAAGTTGAAATC
1 TCCTTCGTTGTGAAGTTGAAATC
319349 TACTCTCGAG
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
47 21 0.40
48 7 0.13
49 25 0.47
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (47 bp):
TCCTTCGTTGTGAAGTTGAAATCGTGATGTCTTGAGTTGGCAAGATA
Found at i:320098 original size:22 final size:22
Alignment explanation
Indices: 320072--320148 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
320062 TTATGTTTGG
320072 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
320094 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
320116 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
320138 TCAACGGTTTG
1 TCAAAGGTTTG
320149 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:320818 original size:16 final size:16
Alignment explanation
Indices: 320751--320827 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 16
320741 TTTTTGTCCC
*
320751 TTTTTC-TTTTTGATT
1 TTTTTCTTTTTTGCTT
*
320766 TTTGTTCTTGTTT-CTCT
1 TTT-TTCTTTTTTGCT-T
*
320783 TCTTTCTTTGTTT--TT
1 TTTTTCTTT-TTTGCTT
*
320798 TTTTTGTTTTTTTGCTT
1 TTTTT-CTTTTTTGCTT
320815 TTTTTCTTTTTTG
1 TTTTTCTTTTTTG
320828 TTCTTGATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 11 0.23
16 20 0.42
17 17 0.35
ACGTcount: A:0.01, C:0.10, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTTGCTT
Found at i:326077 original size:12 final size:11
Alignment explanation
Indices: 326049--326089 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
326039 TAACAAAATA
* *
326049 AATAATATAAA
1 AATAATACAAG
326060 AATAATACAAG
1 AATAATACAAG
326071 TAATAATACAAG
1 -AATAATACAAG
326083 AATAATA
1 AATAATA
326090 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:326864 original size:37 final size:37
Alignment explanation
Indices: 326766--326867 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
326756 GTGCTTGCGG
* ** *
326766 ATCCTATCTTTAGGAGTTTAAATAATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
* *
326803 ATCTTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
326840 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
326868 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:329348 original size:3 final size:3
Alignment explanation
Indices: 329336--329396 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
329326 ATACATCCAA
329336 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
329382 AAT -AT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
329397 GTGAGTAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 6 0.11
3 49 0.89
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:329464 original size:7 final size:7
Alignment explanation
Indices: 329454--329486 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
329444 GAATAAAATA
329454 AAAAAGG
1 AAAAAGG
329461 AAAAAGG
1 AAAAAGG
329468 AAAAAGG
1 AAAAAGG
329475 AAAAAGG
1 AAAAAGG
329482 AAAAA
1 AAAAA
329487 AATAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:329493 original size:14 final size:14
Alignment explanation
Indices: 329448--329487 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
329438 AAGAGGGAAT
*
329448 AAAATAAAAAAGGA
1 AAAAGAAAAAAGGA
*
329462 AAAAGGAAAAAGGA
1 AAAAGAAAAAAGGA
329476 AAAAGGAAAAAA
1 AAAA-GAAAAAA
329488 ATAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAGGA
Found at i:329493 original size:21 final size:22
Alignment explanation
Indices: 329444--329498 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
329434 AAGAAAGAGG
*
329444 GAATAAAATAAAAAAGGAAAAA
1 GAATAAAAGAAAAAAGGAAAAA
* *
329466 GGA-AAAAGGAAAAAGGAAAAA
1 GAATAAAAGAAAAAAGGAAAAA
*
329487 -AATAAAATAAAA
1 GAATAAAAGAAAA
329499 GAAATAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (22 bp):
GAATAAAAGAAAAAAGGAAAAA
Found at i:329524 original size:19 final size:19
Alignment explanation
Indices: 329500--329547 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
329490 AAAATAAAAG
329500 AAATAATAATATA-ATAATA
1 AAATAATAATATAGAT-ATA
329519 AAATAACTAA-ATAGATATA
1 AAATAA-TAATATAGATATA
*
329538 AAATGATAAT
1 AAATAATAAT
329548 GAAAATACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AAATAATAATATAGATATA
Found at i:329685 original size:4 final size:4
Alignment explanation
Indices: 329671--329707 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
329661 ACATATATAT
* *
329671 ATAA ATGA ATAA ATAA TTAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
329708 AAGGACCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:330247 original size:24 final size:26
Alignment explanation
Indices: 330196--330247 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
330186 CTCTAAGGCC
*
330196 TTTGGTTGATGCTTCGATTTTGTGTG
1 TTTGGTTGATGCTTCGAATTTGTGTG
330222 TTTGGTTG-TG-TTCGACATTTGT-TG
1 TTTGGTTGATGCTTCGA-ATTTGTGTG
330246 TT
1 TT
330248 GGCGATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.38
25 7 0.29
26 8 0.33
ACGTcount: A:0.08, C:0.08, G:0.29, T:0.56
Consensus pattern (26 bp):
TTTGGTTGATGCTTCGAATTTGTGTG
Found at i:330807 original size:35 final size:32
Alignment explanation
Indices: 330759--331076 Score: 141
Period size: 35 Copynumber: 9.4 Consensus size: 32
330749 CTATATAATA
*
330759 TATATATAAATATTTTAAAAATATTGTTTTAAAAC
1 TATATATATATATTTTAAAAA-A-T-TTTTAAAAC
* **
330794 TATATATATATATTTCAAAAAAAATTTCCAAAAC
1 TATATATATATATTT--TAAAAAATTTTTAAAAC
* **
330828 AATAT-TATATAATTTTAAAAAATATTTTCGAAC
1 TATATATATAT-ATTTTAAAAAAT-TTTTAAAAC
* * **
330861 TGTGT-TATATAGTTTTCAAAAACGTTTTAAAAC
1 TATATATATATA-TTTT-AAAAAATTTTTAAAAC
*
330894 TATAT-TATAGT-TTTTAAAAATATTTTTTCAAAAATTA
1 TATATATATA-TATTTTAAAAA-A-TTTTT--AAAA--C
* *
330931 TATATTATATATATTTTCAAAATTATTTTCAAAA-
1 TATA-TATATATATTTT-AAAA-AATTTTTAAAAC
** *
330965 T-TATATATAT-TTTCTAAAATGTTTTAAAAATC
1 TATATATATATATTT-TAAAAAATTTTTAAAA-C
*
330997 TATAT-TATATAATTTTTAAAAATATTTTAAAAAC
1 TATATATATAT-A-TTTTAAAAA-ATTTTTAAAAC
* * *
331031 TATATAATATACATTTTCAAAACTATTTTAAAAAC
1 TATAT-ATATATATTTT-AAAA-AATTTTTAAAAC
331066 TATATAT-TATA
1 TATATATATATA
331077 CCCATATTTT
Statistics
Matches: 222, Mismatches: 31, Indels: 62
0.70 0.10 0.20
Matches are distributed among these distances:
30 9 0.04
31 12 0.05
32 26 0.12
33 47 0.21
34 39 0.18
35 52 0.23
36 5 0.02
37 13 0.06
38 2 0.01
39 12 0.05
40 5 0.02
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (32 bp):
TATATATATATATTTTAAAAAATTTTTAAAAC
Found at i:330848 original size:34 final size:34
Alignment explanation
Indices: 330789--330854 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
330779 ATATTGTTTT
*
330789 AAAACTATATATATATATTTCAAAAAAAATTTCC
1 AAAACAATATATATATATTTCAAAAAAAATTTCC
* *
330823 AAAACAATAT-TATATAATTTTAAAAAATATTT
1 AAAACAATATATATAT-ATTTCAAAAAAAATTT
330855 TCGAACTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (34 bp):
AAAACAATATATATATATTTCAAAAAAAATTTCC
Found at i:330894 original size:100 final size:97
Alignment explanation
Indices: 330784--331072 Score: 276
Period size: 100 Copynumber: 2.9 Consensus size: 97
330774 TAAAAATATT
* * * *
330784 GTTTTAAAACTATATATATATATTTCAAAAAAAATTTCCAAAACAATATTATATA-ATTTTAAAA
1 GTTTTAAAACTATAT-TATATATTTTAAAAAATATTTCAAAAACAATATTATATACATTTTCAAA
* * *
330848 AATATTTTCGAACTGTGTTATATAGTTTTCAAAAAC
65 AATATTTTCAAAAT-T-ATATATA-TTTTCAAAAAC
* * *
330884 GTTTTAAAACTATATTATAGT-TTTTAAAAATATTTTTTCAAAAATTATATATTATATATATTTT
1 GTTTTAAAACTATATTATA-TATTTTAAAAA-A-TATTTCAAAAA-CA-ATATTATATACATTTT
* * *
330948 CAAAATTATTTTCAAAATTATATATATTTTCTAAAAT
61 CAAAAATATTTTCAAAATTATATATATTTTCAAAAAC
* * * *
330985 GTTTTAAAAATCTATATTATATAATTTTTAAAAATATTTTAAAAACTATATAATATACATTTTCA
1 GTTTT-AAAA-CTATATTATAT-ATTTTAAAAAATATTTCAAAAACAATATTATATACATTTTCA
* * *
331050 AAACTATTTTAAAAACTATATAT
63 AAAATATTTTCAAAATTATATAT
331073 TATACCCATA
Statistics
Matches: 157, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
99 12 0.08
100 53 0.34
101 22 0.14
102 21 0.13
103 22 0.14
104 27 0.17
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (97 bp):
GTTTTAAAACTATATTATATATTTTAAAAAATATTTCAAAAACAATATTATATACATTTTCAAAA
ATATTTTCAAAATTATATATATTTTCAAAAAC
Found at i:330959 original size:12 final size:12
Alignment explanation
Indices: 330942--330968 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
330932 ATATTATATA
330942 TATTTTCAAAAT
1 TATTTTCAAAAT
330954 TATTTTCAAAAT
1 TATTTTCAAAAT
330966 TAT
1 TAT
330969 ATATATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTTCAAAAT
Found at i:331064 original size:12 final size:12
Alignment explanation
Indices: 331010--331068 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
331000 ATTATATAAT
331010 TTTTAAAAA-TA
1 TTTTAAAAACTA
331021 TTTTAAAAACTA
1 TTTTAAAAACTA
* *
331033 -TATAATATAC-A
1 TTTTAA-AAACTA
*
331044 TTTTCAAAACTA
1 TTTTAAAAACTA
331056 TTTTAAAAACTA
1 TTTTAAAAACTA
331068 T
1 T
331069 ATATTATACC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
11 17 0.45
12 21 0.55
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTTAAAAACTA
Found at i:331077 original size:35 final size:33
Alignment explanation
Indices: 330894--331076 Score: 142
Period size: 35 Copynumber: 5.3 Consensus size: 33
330884 GTTTTAAAAC
* * *
330894 TATATTATAGTTTTTAAAAATATTTTTTCAAAAATTA
1 TATATTATA-ATTTTCAAAATA--TTTT-AAAAACTA
*
330931 TATATTATATATATTTTCAAAATTATTTTCAAAA-T-
1 TATA-T-TATA-ATTTTCAAAA-TATTTTAAAAACTA
*
330966 TATA-TAT-ATTTTCTAAAATGTTTTAAAAATCTA
1 TATATTATAATTTTC-AAAATATTTTAAAAA-CTA
*
330999 TAT-TATATAATTTTTAAAAATATTTTAAAAACTA
1 TATAT-TATAA-TTTTCAAAATATTTTAAAAACTA
*
331033 TATAATATACATTTTCAAAACTATTTTAAAAACTA
1 TATATTATA-ATTTTCAAAA-TATTTTAAAAACTA
331068 TATATTATA
1 TATATTATA
331077 CCCATATTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 30
0.75 0.07 0.19
Matches are distributed among these distances:
30 15 0.12
31 4 0.03
32 4 0.03
33 3 0.02
34 21 0.17
35 42 0.35
36 5 0.04
37 8 0.07
38 5 0.04
39 12 0.10
40 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (33 bp):
TATATTATAATTTTCAAAATATTTTAAAAACTA
Found at i:331555 original size:14 final size:15
Alignment explanation
Indices: 331521--331549 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
331511 TTTATATTTT
331521 ATAA-TTTTTTAAAA
1 ATAATTTTTTTAAAA
331535 ATAATTTTTTTAAAA
1 ATAATTTTTTTAAAA
331550 CTATTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTTTTTTAAAA
Found at i:332750 original size:6 final size:6
Alignment explanation
Indices: 332739--332770 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
332729 TAGTTGATAA
332739 ATATGT ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT ATATGT AT
332771 GGCAGGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:333869 original size:18 final size:20
Alignment explanation
Indices: 333829--333869 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
333819 ATTTTTTTAC
*
333829 TTTTTATAACATTTAATATT
1 TTTTTATAACATTTAATAAT
*
333849 TTTTTA-AAC-TTTTATAAT
1 TTTTTATAACATTTAATAAT
333867 TTT
1 TTT
333870 AAAATAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTATAACATTTAATAAT
Found at i:334707 original size:26 final size:27
Alignment explanation
Indices: 334675--334726 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
334665 TTACAGAAGG
334675 AGAATTGGGAAT-GGGGTAAGAGAGGA
1 AGAATTGGGAATCGGGGTAAGAGAGGA
334701 AGAATTGGGAATCGGGGTAAGAGAGG
1 AGAATTGGGAATCGGGGTAAGAGAGG
334727 GGATGGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.37, C:0.02, G:0.46, T:0.15
Consensus pattern (27 bp):
AGAATTGGGAATCGGGGTAAGAGAGGA
Found at i:335061 original size:19 final size:19
Alignment explanation
Indices: 335039--335081 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
335029 CTCTATTTCA
* * *
335039 TTCTCGATTCTATTTTTAT
1 TTCTCAATTCTACTTCTAT
*
335058 TTCTAAATTCTACTTCTAT
1 TTCTCAATTCTACTTCTAT
335077 TTCTC
1 TTCTC
335082 TTGACTATAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (19 bp):
TTCTCAATTCTACTTCTAT
Found at i:338537 original size:3 final size:3
Alignment explanation
Indices: 338531--338590 Score: 86
Period size: 3 Copynumber: 19.7 Consensus size: 3
338521 GTTTTTTTTA
*
338531 TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
338577 TATT TAT TA- TAT TA
1 TA-T TAT TAT TAT TA
338591 CAGGCCCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:339959 original size:19 final size:17
Alignment explanation
Indices: 339935--339985 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
339925 TAATTTCAAT
339935 TTTTATTTATTTTTACAA
1 TTTTATTTATTTTTA-AA
* *
339953 GTTTTATATAGTTTT-AA
1 -TTTTATTTATTTTTAAA
339970 TTTTATTTATTGTTTA
1 TTTTATTTATT-TTTA
339986 TTTTATTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 9 0.35
17 5 0.19
19 12 0.46
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTATTTTTAAA
Found at i:340011 original size:3 final size:3
Alignment explanation
Indices: 340003--340032 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
339993 GTTTACTTTA
*
340003 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
340033 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:340981 original size:79 final size:79
Alignment explanation
Indices: 340886--341046 Score: 274
Period size: 80 Copynumber: 2.0 Consensus size: 79
340876 TTTTTTTTAT
340886 TTTTTATTTTTTGTTAGAGGTTTGAGCATTTCT-C-CACACAC-ACACCTGCATTGCATAACATA
1 TTTTTATTTTTTGTTAGAGGTTT--GCATTTCTCCTCACACACAACACCTGCATTGCATAACATA
340948 AAGCTCTATAACTGAG
64 AAGCTCTATAACTGAG
340964 TTTTTATTTTTCTGTTAGAGGTTTGCATTTCTCCTCACACACAACACCTGCATTGCATAACATAA
1 TTTTTATTTTT-TGTTAGAGGTTTGCATTTCTCCTCACACACAACACCTGCATTGCATAACATAA
341029 AGCTCTATAACTGAG
65 AGCTCTATAACTGAG
341044 TTT
1 TTT
341047 GTCCCTTTAA
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
77 8 0.10
78 12 0.15
79 19 0.24
80 40 0.51
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (79 bp):
TTTTTATTTTTTGTTAGAGGTTTGCATTTCTCCTCACACACAACACCTGCATTGCATAACATAAA
GCTCTATAACTGAG
Found at i:342544 original size:14 final size:14
Alignment explanation
Indices: 342511--342563 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
342501 ATTTTAAATA
*
342511 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
342525 -TTTACATTTGTAT
1 ATTTACATTTGCAT
342538 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
342553 CTTTGCATTTG
1 ATTTACATTTG
342564 TATTTTTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 11 0.34
14 10 0.31
15 11 0.34
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.53
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:344402 original size:25 final size:24
Alignment explanation
Indices: 344368--344417 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
344358 TCTTATACTC
344368 ATCCAGCAAAGAAAGAAAAAAGAAA
1 ATCCAGCAAAGAAAGAAAAAA-AAA
344393 ATCCAGCAAAGAAAGAAAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAAAA
344417 A
1 A
344418 GAAAAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.04
Consensus pattern (24 bp):
ATCCAGCAAAGAAAGAAAAAAAAA
Found at i:344458 original size:21 final size:20
Alignment explanation
Indices: 344404--344471 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
344394 TCCAGCAAAG
344404 AAAGAAAAAAAAAAGA-AAA
1 AAAGAAAAAAAAAAGAGAAA
* *
344423 AAATGAAAAGGAAAATGAGAAA
1 AAA-GAAAA-AAAAAAGAGAAA
344445 AAAGAAAAAAAAAAG-GAAA
1 AAAGAAAAAAAAAAGAGAAA
344464 AAA-AAAAA
1 AAAGAAAAA
344472 GGGGAGAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 10 0.24
20 10 0.24
21 11 0.26
22 6 0.14
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAAAAAAGAGAAA
Found at i:350332 original size:54 final size:54
Alignment explanation
Indices: 350250--350389 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
350240 CATAAAAAAT
* *
350250 GATGAATGTGTTGTCAAACGCTTTACGAACTTCTGAGCAGAAACCACAAGAAAG
1 GATGAATGTGTTGTCAAATGTTTTACGAACTTCTGAGCAGAAACCACAAGAAAG
* * * *
350304 GATGAATGTGTTGTCAAATGTTTTACGAACATCTTAGCAGAAGCCACAGGAAAG
1 GATGAATGTGTTGTCAAATGTTTTACGAACTTCTGAGCAGAAACCACAAGAAAG
*
350358 GATGAAT-TCGCTGTCAAATGTTTTACGAACTT
1 GATGAATGT-GTTGTCAAATGTTTTACGAACTT
350390 GCTATTCTGA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 76 0.99
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (54 bp):
GATGAATGTGTTGTCAAATGTTTTACGAACTTCTGAGCAGAAACCACAAGAAAG
Found at i:350791 original size:22 final size:22
Alignment explanation
Indices: 350754--350808 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
350744 ATCTACACTC
*
350754 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* * *
350776 TTTAAATATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
350798 TTCAAAGATGA
1 TTCAAAGATGA
350809 AAGCTTTATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:351411 original size:113 final size:113
Alignment explanation
Indices: 351244--351768 Score: 865
Period size: 113 Copynumber: 4.6 Consensus size: 113
351234 TTCCAGAGAG
*
351244 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAATAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
351309 AACTTTTCGCTTGAATTCATCATTTGATGGATCATCATTACCAGGTCA
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTACCAGGTCA
351357 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
351422 AACTTTTCGCTTGAATTCATCATTTGATGGATCAGCATTACCAGGTCA
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTACCAGGTCA
*
351470 AGTTCATAATGAGAACAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
351535 AACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTACCAGGTCA
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTACCAGGTCA
* * *
351583 AGTTCATAATGAGAAGAACTCATCTGAAGATAGAATAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * *
351648 AATTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG--A
66 AACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTACCAG-GTCA
* *
351695 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTT
1 -AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
351760 CAATCTTTT
65 CAA-CTTTT
351769 GCATGGTTCT
Statistics
Matches: 388, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
112 1 0.00
113 382 0.98
114 5 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTTGATGGATCAACATTACCAGGTCA
Found at i:352045 original size:3 final size:3
Alignment explanation
Indices: 352039--352113 Score: 105
Period size: 3 Copynumber: 24.0 Consensus size: 3
352029 TTTTTTATAT
*
352039 TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
352085 TTA TTA ATA TTA TTA TTTA TTA TATA TTA
1 TTA TTA TTA TTA TTA -TTA TTA T-TA TTA
352114 CAGGCCCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
3 56 0.86
4 9 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:353517 original size:29 final size:29
Alignment explanation
Indices: 353485--353541 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
353475 TTTTACAAGT
*
353485 TTTATATATA-GTTTTAATTTTATTTATTG
1 TTTATATATATG-TTTAATTTTAATTATTG
* *
353514 TTTATTTATATGTTTACTTTTAATTATT
1 TTTATATATATGTTTAATTTTAATTATT
353542 ATTACTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTATATATATGTTTAATTTTAATTATTG
Found at i:353544 original size:3 final size:3
Alignment explanation
Indices: 353536--353565 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
353526 TTTACTTTTA
*
353536 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
353566 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:355668 original size:27 final size:27
Alignment explanation
Indices: 355630--355682 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
355620 TTACAGAAGG
355630 AGAATTGAGAATC-GAGGTAAGAGAGGA
1 AGAATTGAGAATCAG-GGTAAGAGAGGA
*
355657 AGAATTGGGAATCAGGGTAAGAGAGG
1 AGAATTGAGAATCAGGGTAAGAGAGG
355683 GGATGGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.40, T:0.15
Consensus pattern (27 bp):
AGAATTGAGAATCAGGGTAAGAGAGGA
Found at i:356026 original size:19 final size:19
Alignment explanation
Indices: 355993--356046 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
355983 CTCTAAATTC
*
355993 TCTATTTC-ATCTTCTCGAT
1 TCTATTTCTAT-TTCTCAAT
*
356012 TCTATTTCTATTTCTAAAT
1 TCTATTTCTATTTCTCAAT
*
356031 TCTACTTCTATTTCTC
1 TCTATTTCTATTTCTC
356047 TTGACTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.93
20 2 0.07
ACGTcount: A:0.19, C:0.24, G:0.02, T:0.56
Consensus pattern (19 bp):
TCTATTTCTATTTCTCAAT
Found at i:358598 original size:18 final size:17
Alignment explanation
Indices: 358568--358616 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
358558 AAACGACACG
* **
358568 TAAAAAAATTAAAATTA
1 TAAAAATATTAAAAAAA
358585 TAAAAATATATAAAAAAA
1 TAAAAATAT-TAAAAAAA
*
358603 TAAAAATGTTAAAA
1 TAAAAATATTAAAA
358617 TATTTTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAAATATTAAAAAAA
Found at i:360740 original size:12 final size:13
Alignment explanation
Indices: 360694--360737 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
360684 TCATTTCTTC
360694 TTTCCTTCTCATT
1 TTTCCTTCTCATT
360707 TTTCCTTCTCATT
1 TTTCCTTCTCATT
360720 TTTCC-TCTCATT
1 TTTCCTTCTCATT
*
360732 CTTCCT
1 TTTCCT
360738 CTCCAAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTCCTTCTCATT
Found at i:367525 original size:13 final size:14
Alignment explanation
Indices: 367502--367531 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
367492 TTCCCATTAC
367502 AGACGTGCATATGA
1 AGACGTGCATATGA
367516 AGAC-TGCATATGA
1 AGACGTGCATATGA
367529 AGA
1 AGA
367532 TTTTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:376063 original size:15 final size:15
Alignment explanation
Indices: 376040--376070 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
376030 TAAAGTAGAA
*
376040 ATTTTATAAATTAAT
1 ATTTGATAAATTAAT
376055 ATTTGATAAATTAAT
1 ATTTGATAAATTAAT
376070 A
1 A
376071 ATTTCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTGATAAATTAAT
Found at i:379009 original size:94 final size:96
Alignment explanation
Indices: 378833--379018 Score: 270
Period size: 94 Copynumber: 2.0 Consensus size: 96
378823 ATACCGTTGA
* *
378833 GGTAGTATCGATACCATGGTAGGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCG
* **
378898 ATATCGTAAGGGGGTATCGGTACCATAATAG
66 ATACCGTAAGGAAGTATCGGTACCATAATAG
* *
378929 GGTAGTATCGATACCATGGTAAGGGTATCGATACC-AG-GAACATCGAGCCTAATTTTGGTATCG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCG
*
378992 ATACCCG-GAGGAAGTATCGGTACCATA
66 ATA-CCGTAAGGAAGTATCGGTACCATA
379019 GTATTGAAGT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 43 0.53
95 4 0.05
96 34 0.42
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (96 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCG
ATACCGTAAGGAAGTATCGGTACCATAATAG
Found at i:379051 original size:94 final size:96
Alignment explanation
Indices: 378836--379056 Score: 234
Period size: 94 Copynumber: 2.3 Consensus size: 96
378826 CCGTTGAGGT
* * * *
378836 AGTATCGATACCATGGTAGGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCAGGGTAAGAGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCGATA
* ** *
378901 TCGTAAGGGGGTATCGGTACCATAATAGGGT
66 CCGTAAGGAAGTATCGGTACCATAATAGGGA
* * * *
378932 AGTATCGATACCATGGTAAGGGTATCGATACC-AG-GAACATCGAGCCTAATTTTGGTATCGATA
1 AGTATCGATACCAGGGTAAGAGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCGATA
* * **
378995 CCCG-GAGGAAGTATCGGTACCATAGTATTGA
66 -CCGTAAGGAAGTATCGGTACCATAATAGGGA
* *
379026 AGTATCGGTACTAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCAGGGTAAG-AGTATCGATAC
379057 TACTGAGTTT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
93 2 0.02
94 70 0.65
95 4 0.04
96 31 0.29
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (96 bp):
AGTATCGATACCAGGGTAAGAGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCGATA
CCGTAAGGAAGTATCGGTACCATAATAGGGA
Found at i:379623 original size:45 final size:45
Alignment explanation
Indices: 379466--379800 Score: 437
Period size: 45 Copynumber: 7.4 Consensus size: 45
379456 TGAAAATAAT
* * * * *
379466 AATGCATATGGGTGCATTATCGGAA-TG-AAAGGATGCCATAGTTAA
1 AATGCATATGGGTGCATTATC--AACAGAAAAGTATACTATAGTTGA
* * * *
379511 AATGTATATGGGTACATTATCAACAGAAAAATATACTATAATTG-
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
379555 AATGAATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
379600 AATGCATATGGATGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * *
379645 AATGTATATGGGTACATTATCAATAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
379690 AATGCATATGGGTGAATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
379735 AATGCATATGGGTGCATTATCAACAGAAAAGTATGA-TATAGTTGAA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTAT-ACTATAGTTG-A
379781 AATGCATAAT-GGTGCATTAT
1 AATGCAT-ATGGGTGCATTAT
379801 AAATGAATGG
Statistics
Matches: 256, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.01
44 40 0.16
45 193 0.75
46 19 0.07
47 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:379754 original size:135 final size:134
Alignment explanation
Indices: 379466--379781 Score: 483
Period size: 135 Copynumber: 2.4 Consensus size: 134
379456 TGAAAATAAT
* * * *
379466 AATGCATATGGGTGCATTATCGGAA-TG-AAAGGATGCCATAGTTAAAATGTATATGGGTACATT
1 AATGCATATGGGTGCATTATC--AACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTACATT
* *
379529 ATCAACAGAAAAATATACTATAATTGAATGAATATGGGTGCATTATCAACATAAAAGTATACTAT
64 ATCAACAGAAAAATATACTATAATTGAATGAATATGGGTGAATTATCAACAGAAAAGTATACTAT
379594 AGTTGA
129 AGTTGA
*
379600 AATGCATATGGATGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTAT
* * * *
379665 CAATAGAAAAGTATACTATAGTTGAAATGCATATGGGTGAATTATCAACAGAAAAGTATACTATA
66 CAACAGAAAAATATACTATAATTG-AATGAATATGGGTGAATTATCAACAGAAAAGTATACTATA
379730 GTTGA
130 GTTGA
*
379735 AATGCATATGGGTGCATTATCAACAGAAAAGTATGATATAGTTGAAA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAA
379782 ATGCATAATG
Statistics
Matches: 166, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
132 2 0.01
133 1 0.01
134 76 0.46
135 87 0.52
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (134 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTAT
CAACAGAAAAATATACTATAATTGAATGAATATGGGTGAATTATCAACAGAAAAGTATACTATAG
TTGA
Found at i:390136 original size:23 final size:23
Alignment explanation
Indices: 390103--390147 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
390093 ATTATTATAT
*
390103 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
390126 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
390148 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:395322 original size:149 final size:149
Alignment explanation
Indices: 395052--395366 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
395042 GAGTCGAGGG
* *
395052 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
395117 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
395182 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
395201 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
395266 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
395331 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
395350 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
395367 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:395367 original size:23 final size:23
Alignment explanation
Indices: 395334--395378 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
395324 ATTATTATAT
*
395334 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
395357 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
395379 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:397097 original size:3 final size:3
Alignment explanation
Indices: 397084--397131 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
397074 AATCATACTC
397084 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
397131 A
1 A
397132 TACAAGGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:397580 original size:25 final size:24
Alignment explanation
Indices: 397552--397601 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
397542 TGTATTGAAT
* *
397552 ATCTTAATAATTCTTTATATTTTTA
1 ATCTAAATAATTATTTA-ATTTTTA
*
397577 ATCTAAATATTTATTTAATTTTTA
1 ATCTAAATAATTATTTAATTTTTA
397601 A
1 A
397602 AAATTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
ATCTAAATAATTATTTAATTTTTA
Found at i:403160 original size:23 final size:23
Alignment explanation
Indices: 403134--403181 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
403124 ATTTATCTTT
*
403134 TAAATTTTATAAAAAATTATATA
1 TAAATTTTATAAAAAAGTATATA
**
403157 TAAATTTTATTTAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
403180 TA
1 TA
403182 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTTTATAAAAAAGTATATA
Found at i:404970 original size:12 final size:12
Alignment explanation
Indices: 404939--404981 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
404929 CATCCCGTTT
*
404939 TTATTATT-ATG
1 TTATTATTAATA
*
404950 TTTTTATTAATA
1 TTATTATTAATA
*
404962 TTATTATTAATT
1 TTATTATTAATA
404974 TTATTATT
1 TTATTATT
404982 TTTACAGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:410063 original size:20 final size:20
Alignment explanation
Indices: 410038--410092 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
410028 CTCTGGAATA
*
410038 ACACCTCTTGTATTTGTATC
1 ACACCTCTTGTATTTGCATC
410058 ACACCTCTTGTATTTGCATC
1 ACACCTCTTGTATTTGCATC
* *
410078 GCACCTCTTGCATTT
1 ACACCTCTTGTATTT
410093 CCATTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (20 bp):
ACACCTCTTGTATTTGCATC
Found at i:411669 original size:16 final size:16
Alignment explanation
Indices: 411643--411698 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
411633 AAAAATATAC
411643 ATAAATAAAAAGGAAAAT
1 ATAAA-AAAAA-GAAAAT
* *
411661 ATAAGAAAAAGAAGAAG
1 ATAAAAAAAAGAA-AAT
411678 A-AAAAAAAAGAAAAT
1 ATAAAAAAAAGAAAAT
411693 ATAAAA
1 ATAAAA
411699 GATAGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.09
16 17 0.53
17 8 0.25
18 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (16 bp):
ATAAAAAAAAGAAAAT
Found at i:411683 original size:14 final size:14
Alignment explanation
Indices: 411666--411767 Score: 74
Period size: 14 Copynumber: 7.4 Consensus size: 14
411656 AAAATATAAG
411666 AAAAAGAAGAAGAA
1 AAAAAGAAGAAGAA
411680 AAAAA-AAGAA-AA
1 AAAAAGAAGAAGAA
411692 TATAAAAGATAGAA-AA
1 -A-AAAAGA-AGAAGAA
411708 AAAAAG-AGAA-AA
1 AAAAAGAAGAAGAA
* *
411720 AGAACAAGAACAAGGA
1 A-AA-AAGAAGAAGAA
411736 AAAAAGAA-AAGAGA
1 AAAAAGAAGAAGA-A
*
411750 AAAAA-AATAAGAA
1 AAAAAGAAGAAGAA
411763 AAAAA
1 AAAAA
411768 TAAAAAGAGG
Statistics
Matches: 75, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
12 9 0.12
13 19 0.25
14 32 0.43
15 7 0.09
16 8 0.11
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (14 bp):
AAAAAGAAGAAGAA
Found at i:411698 original size:28 final size:26
Alignment explanation
Indices: 411666--411775 Score: 87
Period size: 28 Copynumber: 3.9 Consensus size: 26
411656 AAAATATAAG
411666 AAAAAGAAGAAGAAAAAAAAAGAAAA
1 AAAAAGAAGAAGAAAAAAAAAGAAAA
*
411692 TATAAAAGATAGAA-AAAAAAAGAGAAAA
1 -A-AAAAGA-AGAAGAAAAAAAAAGAAAA
*
411720 AGAACAAGAACAAGGAAAAAAGAAAAGAGAAA
1 A-AA-AAGAAGAA-G-AAAAA-AAAAGA-AAA
* *
411752 AAAAATAAGAAAAAAATAAAAAGA
1 AAAAAGAAGAAGAAAA-AAAAAGA
411776 GGGAAAATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
27 7 0.10
28 33 0.49
29 5 0.07
30 11 0.16
31 7 0.10
32 4 0.06
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (26 bp):
AAAAAGAAGAAGAAAAAAAAAGAAAA
Found at i:411700 original size:22 final size:21
Alignment explanation
Indices: 411645--411773 Score: 57
Period size: 22 Copynumber: 5.7 Consensus size: 21
411635 AAATATACAT
* *
411645 AAATAAAAAGGAAAATATAAGA
1 AAATAAAAA-GAAAAAAAAAGA
411667 AAA-AGAAGAAGAAAAAAAAAGA
1 AAATA-AA-AAGAAAAAAAAAGA
411689 AAATATAAAAGATAGAAAAAAA-A
1 AAATA-AAAAGA-A-AAAAAAAGA
* * *
411712 AGAGAAAAAGAACAAGAACAAGGA
1 AAATAAAAAGAA-AA-AA-AAAGA
* *
411736 AAAAAGAAAAGAGAAAAAAAATA
1 AAATA-AAAAGA-AAAAAAAAGA
*
411759 AGAA-AAAAATAAAAA
1 A-AATAAAAAGAAAAA
411774 GAGGGAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
21 8 0.10
22 35 0.42
23 17 0.20
24 15 0.18
25 8 0.10
26 1 0.01
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.06
Consensus pattern (21 bp):
AAATAAAAAGAAAAAAAAAGA
Found at i:411763 original size:26 final size:27
Alignment explanation
Indices: 411707--411794 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 27
411697 AAGATAGAAA
* * *
411707 AAAAAAGAGAAAAAGAACAAGAACAAGG
1 AAAAAAGAGAAAAAGAAAAAAAATAA-G
*
411735 AAAAAAGA-AAAGAGAAAAAAAATAAG
1 AAAAAAGAGAAAAAGAAAAAAAATAAG
* ***
411761 AAAAAA-ATAAAAAGAGGGAAAATAAG
1 AAAAAAGAGAAAAAGAAAAAAAATAAG
*
411787 GAAAAAGA
1 AAAAAAGA
411795 AAATAAATCA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.02
26 26 0.53
27 14 0.29
28 8 0.16
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.03
Consensus pattern (27 bp):
AAAAAAGAGAAAAAGAAAAAAAATAAG
Found at i:411796 original size:45 final size:46
Alignment explanation
Indices: 411702--411802 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 46
411692 TATAAAAGAT
*
411702 AGAAAAAAAA-AGAGAAAAAGAACAAGAACAAGGAAAAAAGAAAAG
1 AGAAAAAAAATAGAGAAAAAGAACAAAAACAAGGAAAAAAGAAAAG
* * *
411747 AGAAAAAAAATA-AGAAAAA-AATAAAAAGAGGGAAAATAAGGAAAA-
1 AGAAAAAAAATAGAGAAAAAGAACAAAAACAAGGAAAA-AA-GAAAAG
*
411792 AGAAAATAAAT
1 AGAAAAAAAAT
411803 CAAGTATTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 13 0.27
45 29 0.60
46 6 0.12
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (46 bp):
AGAAAAAAAATAGAGAAAAAGAACAAAAACAAGGAAAAAAGAAAAG
Found at i:413796 original size:38 final size:38
Alignment explanation
Indices: 413754--414265 Score: 570
Period size: 38 Copynumber: 13.1 Consensus size: 38
413744 GAGGAGTCGA
*
413754 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAA
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
413792 TCAATCTTTTAATGTTATTATTAACTTCCTCGCGAAGAGAAG
1 TCAATC--TT--TGTTATTCTTGACTTCCTCGTGAAGAGAAG
*
413834 TCAATCTTT-TCTATTCTTGACTCCCTCGTGAAGAGAAG
1 TCAATCTTTGT-TATTCTTGACTTCCTCGTGAAGAGAAG
* *
413872 TCAATCTTTGTTATTCTTGACTTTCTCGTGAAGAAAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
413910 TTAATCTTTCAATGTTATTCTTGACTTCCTCATGAAGAGAAG
1 TCAATC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
413952 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
413990 TTAATCTTTGTTTATTCTTGACTCCCTCGTGAAGA-AGAG
1 TCAATCTTTG-TTATTCTTGACTTCCTCGTGAAGAGA-AG
* * * *
414029 TCAATCTTTCAATGTTATTCTTAACTTTCTCGTGAAAAGAAA
1 TCAATC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
414071 TCAATC-TTGTTATTCTTGACTCCCTTGTGAAGAG--G
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
414106 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAAAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
414144 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAAAGGAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
414182 TCAATCTTTGTTATTCTTGAC-TCCTCGTGAAGAGGAA-
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGA-GAAG
*
414219 TCAATTTTTCAGTATTATTCTTGACTTCCTCGTGAAGAGAAG
1 TCAATCTTT--G--TTATTCTTGACTTCCTCGTGAAGAGAAG
414261 TCAAT
1 TCAAT
414266 ATTTCAGTAT
Statistics
Matches: 405, Mismatches: 42, Indels: 50
0.81 0.08 0.10
Matches are distributed among these distances:
35 6 0.01
36 26 0.06
37 41 0.10
38 163 0.40
39 35 0.09
40 7 0.02
41 16 0.04
42 108 0.27
43 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (38 bp):
TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
Done.