Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003456.1 Hibiscus syriacus cultivar Beakdansim tig00007305_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: 88254
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4799 original size:21 final size:21
Alignment explanation
Indices: 4775--4838 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
4765 GCAAATTCGC
4775 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
4796 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
4816 TTTTCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
4837 GT
1 GT
4839 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:10426 original size:23 final size:23
Alignment explanation
Indices: 10398--10452 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
10388 TGTTTATATG
*
10398 TTTAGTGTTTACGAACATGTTCA
1 TTTAGTATTTACGAACATGTTCA
*
10421 TTTAGTATTTGCGAACATGTTCA
1 TTTAGTATTTACGAACATGTTCA
*
10444 TTTAATATT
1 TTTAGTATT
10453 CATGAACTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (23 bp):
TTTAGTATTTACGAACATGTTCA
Found at i:10459 original size:23 final size:23
Alignment explanation
Indices: 10408--10459 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
10398 TTTAGTGTTT
* *
10408 ACGAACATGTTCATTTAGTATTT
1 ACGAACATGTTCATTTAATATTC
*
10431 GCGAACATGTTCATTTAATATTC
1 ACGAACATGTTCATTTAATATTC
*
10454 ATGAAC
1 ACGAAC
10460 TGCTCACTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (23 bp):
ACGAACATGTTCATTTAATATTC
Found at i:11006 original size:18 final size:16
Alignment explanation
Indices: 10983--11028 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
10973 TAATTTATAG
10983 TTAATAATAATAGAAAAA
1 TTAAT-ATAATA-AAAAA
11001 TTAATATAAGTTAAAAAA
1 TTAATATAA--TAAAAAA
11019 TTAATATAAT
1 TTAATATAAT
11029 TTTATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 19 0.73
19 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
TTAATATAATAAAAAA
Found at i:12227 original size:22 final size:22
Alignment explanation
Indices: 12182--12366 Score: 229
Period size: 22 Copynumber: 8.6 Consensus size: 22
12172 CTATTTTAAA
12182 ATTTATTTTAAAATATG-ATTG
1 ATTTATTTTAAAATATGAATTG
12203 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
**
12225 A-TT-TTTTAAAATATAGAA-AA
1 ATTTATTTTAAAATAT-GAATTG
*
12245 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
**
12267 ATTTATTTTAAAATATGAA-AA
1 ATTTATTTTAAAATATGAATTG
* *
12288 ATTTTATTTT-AAATAAGCATTG
1 A-TTTATTTTAAAATATGAATTG
*
12310 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
12332 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
*
12354 ATTTACTTTAAAA
1 ATTTATTTTAAAA
12367 AAATTATTAT
Statistics
Matches: 140, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.09
21 42 0.30
22 86 0.61
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGAATTG
Found at i:12364 original size:65 final size:64
Alignment explanation
Indices: 12179--12365 Score: 256
Period size: 65 Copynumber: 2.9 Consensus size: 64
12169 AATCTATTTT
12179 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAATTGATTT-TTTAAAATATAGA
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTATTT-AAATATAGA
**
12242 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAA-AAATTTTATTTTAAATA-AG
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGA-TTTA-TTTAAATATAG
12305 CA
64 -A
***
12307 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTACTTTAAA
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTA-TTTAAA
12366 AAAATTATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
63 20 0.18
64 29 0.26
65 57 0.52
66 4 0.04
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.48
Consensus pattern (64 bp):
AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTATTTAAATATAGA
Found at i:12447 original size:31 final size:31
Alignment explanation
Indices: 12389--12448 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
12379 TAGTTGTATG
*
12389 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
12420 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
12449 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:12478 original size:18 final size:18
Alignment explanation
Indices: 12457--12495 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12447 CTCTTTTAAG
12457 TTTAAAAAATCAGTTTAT
1 TTTAAAAAATCAGTTTAT
**
12475 TTT-AAATTTCAGTTTAT
1 TTTAAAAAATCAGTTTAT
12492 TTTA
1 TTTA
12496 GTAGTATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAAAAATCAGTTTAT
Found at i:15218 original size:59 final size:59
Alignment explanation
Indices: 15137--15284 Score: 183
Period size: 59 Copynumber: 2.5 Consensus size: 59
15127 TATCATGTGT
* *
15137 TTCT-AAACTATGATCTCTATTCTAAATTAGTCCTTAATCTTTTGAATATTT-AATTTCA
1 TTCTCAAACTATGATCT-TATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
* * *
15195 TTCTCAAACTATCATTCTTATTCTAAATTAGTTCTTAAACTTTTGAACATTTCAATTTTA
1 TTCTCAAACTATGA-TCTTATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
* * *
15255 TCCTCAAACTATGACCCTCATTCTAAATTA
1 TTCTCAAACTATGA-TCTTATTCTAAATTA
15285 ACCTCCAAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 4 0.05
59 39 0.51
60 34 0.44
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (59 bp):
TTCTCAAACTATGATCTTATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
Found at i:22215 original size:60 final size:60
Alignment explanation
Indices: 22143--22276 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
22133 AAATTGGAAG
* *
22143 ATTCAAAAGTTTAGGGACCAATTTAGAAAGAGTGTCACAATTTAACGATGAAATTAAAAT
1 ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCACAATTTAACGATGAAATTAAAAT
* * * * * * * * * *
22203 GTTCAAATGTTTAATGACTAATTTTGAATGAGAGTCATATTTTGAGGATGAAATTAAAAT
1 ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCACAATTTAACGATGAAATTAAAAT
22263 ATTCAAAAGTTTAA
1 ATTCAAAAGTTTAA
22277 AAACCAAATT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (60 bp):
ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCACAATTTAACGATGAAATTAAAAT
Found at i:22913 original size:2 final size:2
Alignment explanation
Indices: 22906--22948 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
22896 ACTAAAACTT
22906 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
22948 T
1 T
22949 CTATTATTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24514 original size:29 final size:28
Alignment explanation
Indices: 24469--24523 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
24459 GATGATGTCC
**
24469 TTTTTAGACAATTGAAGTATTTAATTCA
1 TTTTTAGACAAAAGAAGTATTTAATTCA
24497 TTTTTAGTACAAAAGAAGTATTTAATT
1 TTTTTAG-ACAAAAGAAGTATTTAATT
24524 TAGGCTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTTTAGACAAAAGAAGTATTTAATTCA
Found at i:27625 original size:2 final size:2
Alignment explanation
Indices: 27618--27650 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27608 ATTATCATTC
27618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27651 GTTGAATTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27846 original size:42 final size:41
Alignment explanation
Indices: 27788--27870 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
27778 GATTATCGGA
* * * * *
27788 CCAAATTAATTTAATAATTTTGATTTAGTGATATAATAATG
1 CCAAATTAATGTAATAATTGTAAGTTACTGATATAATAATG
27829 CCAAATTTAATGTAATAATTGTAAGTTACTGATATAATAATG
1 CCAAA-TTAATGTAATAATTGTAAGTTACTGATATAATAATG
27871 GCATTTTGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (41 bp):
CCAAATTAATGTAATAATTGTAAGTTACTGATATAATAATG
Found at i:33592 original size:40 final size:40
Alignment explanation
Indices: 33537--33616 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
33527 GCAATCCACC
33537 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
1 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
33577 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
1 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
33617 TAGTTTGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (40 bp):
ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
Found at i:38938 original size:42 final size:42
Alignment explanation
Indices: 38876--38958 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
38866 TCTAAATTTA
*
38876 AATAAGTAATCGAAACAATATTTAAATTTTAATAACATATCG
1 AATAAATAATCGAAACAATATTTAAATTTTAATAACATATCG
* *
38918 AATAAATAATCGAAATAATATTTAACTTTTAATAACATATC
1 AATAAATAATCGAAACAATATTTAAATTTTAATAACATATC
38959 TAATTTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (42 bp):
AATAAATAATCGAAACAATATTTAAATTTTAATAACATATCG
Found at i:39900 original size:17 final size:18
Alignment explanation
Indices: 39854--39900 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
39844 AATGTTTGAG
39854 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
* *
39872 GGAATTAAAATCTGT-CA
1 GGAATTAGAATCTGTGAA
*
39889 GGAATTGGAATC
1 GGAATTAGAATC
39901 CAATTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:40496 original size:27 final size:28
Alignment explanation
Indices: 40434--40500 Score: 118
Period size: 27 Copynumber: 2.4 Consensus size: 28
40424 AACCCGAACT
40434 CGACCCGAATATCACACTTAAAAAAACC
1 CGACCCGAATATCACACTTAAAAAAACC
*
40462 CGATCCGAATATCACACTT-AAAAAACC
1 CGACCCGAATATCACACTTAAAAAAACC
40489 CGACCCGAATAT
1 CGACCCGAATAT
40501 ATGAATTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 19 0.51
28 18 0.49
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.16
Consensus pattern (28 bp):
CGACCCGAATATCACACTTAAAAAAACC
Found at i:40804 original size:252 final size:244
Alignment explanation
Indices: 40248--40812 Score: 692
Period size: 252 Copynumber: 2.2 Consensus size: 244
40238 ATTTTTATTC
* ** * * *
40248 AATATATAAATTAGAAACCCGACCCGATACAAAATAATTATAAAATTATTTTTATTCATTAAAAA
1 AATATATGAATTAGAAACCCGACCCGACCCGAAATAA-TAAAAAATTATTTTTATTCAATAAAAA
* *
40313 CATTGACTTAATTGAAAAAAATTATATATAGAGGAGATTTATTGTAATTATTCCTAAATATATAA
65 CAGTGACTTAATTGAAAAAAATTATATAGAGAGGAGATTTATTGTAATTATTCCTAAATATATAA
* * *
40378 GGTAAAATTATATTTTTTTTCGGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACTCGACCCGAA
130 GGTAAAATTATATATATTTTCGGGTCGGT-C--ATTTTTCACCCTAAACCCGAACTCGACCCGAA
* *
40443 TATCACACTTAAAAAAACCCGATCCGAATATCACACTTAAAAAACCCGACCCG
192 TATCACACTTAAAAAAACCCGATCCGAAAATCAAACTTAAAAAACCCGACCCG
40496 AATATATGAATTAGAAATCCGATCTGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAA-CC---C-GACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
*
40561 AAAACAGTGACTTAATTG-AAAAAATATATATAGAGAGG-GGTATTATTGTAATTATTCCTAAAT
61 AAAACAGTGACTTAATTGAAAAAAAT-TATATAGAGAGGAGAT-TTATTGTAATTATTCCTAAAT
*
40624 ATATTAGGTAAAATTATATATATTTTCGGGTCGGAT-ATTTTTCACCCTAAACCCGAACTCGACC
124 ATATAAGGTAAAATTATATATATTTTCGGGTCGG-TCATTTTTCACCCTAAACCCGAACT----C
* ****
40688 TGACCCGAATATCACACTTAAAAAACCGACCCGA-CC-AAAAT-AAAGTTTCACCCGACCCGACC
184 -GACCCGAATATCACACTTAAAAAA---ACCCGATCCGAAAATCAAA-CTT-AAAAAACCCGACC
40750 CG
243 CG
*
40752 AATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACCCGAAATAAT-AAAAAATTATTTTTATTCAATA
40813 TATGAATAAG
Statistics
Matches: 277, Mismatches: 21, Indels: 34
0.83 0.06 0.10
Matches are distributed among these distances:
248 16 0.06
249 24 0.09
251 27 0.10
252 124 0.45
253 16 0.06
254 26 0.09
255 8 0.03
256 30 0.11
257 6 0.02
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (244 bp):
AATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
AGTGACTTAATTGAAAAAAATTATATAGAGAGGAGATTTATTGTAATTATTCCTAAATATATAAG
GTAAAATTATATATATTTTCGGGTCGGTCATTTTTCACCCTAAACCCGAACTCGACCCGAATATC
ACACTTAAAAAAACCCGATCCGAAAATCAAACTTAAAAAACCCGACCCG
Found at i:45217 original size:29 final size:30
Alignment explanation
Indices: 45185--45241 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
45175 ATATATAATC
*
45185 TAATATTAATACATATAATTAA-TAAAAAA
1 TAATATTAATACATATAATAAAGTAAAAAA
45214 TAATATTAATACATATAATAAAGTAAAA
1 TAATATTAATACATATAATAAAGTAAAA
45242 GTAATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (30 bp):
TAATATTAATACATATAATAAAGTAAAAAA
Found at i:45541 original size:45 final size:45
Alignment explanation
Indices: 45482--45625 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 45
45472 ATATTATACG
* *
45482 ATAAATTATTTTAATTCAAATATACTAAGAAAAA-ATTCCTACATA
1 ATAAATAATATTAATT-AAATATACTAAGAAAAAGATTCCTACATA
* * *
45527 ATAAATAATATTAATTTAATATATTAAGAAAAAGATTCGTAC---
1 ATAAATAATATTAATTAAATATACTAAGAAAAAGATTCCTACATA
* * * * *
45569 GT-AATAATATTAATTTAATATA-TAAAGAAAAATATTCATACGTA
1 ATAAATAATATTAATTAAATATACT-AAGAAAAAGATTCCTACATA
45613 ATAATATTAATAT
1 ATAA-A-TAATAT
45626 AATATATTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
40 1 0.01
41 35 0.43
42 1 0.01
44 16 0.20
45 22 0.27
46 1 0.01
47 6 0.07
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (45 bp):
ATAAATAATATTAATTAAATATACTAAGAAAAAGATTCCTACATA
Found at i:45585 original size:41 final size:41
Alignment explanation
Indices: 45530--45639 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
45520 CTACATAATA
*
45530 AATAATATTAATTTAATATATTAAGAAAAAGATTCGTACGT
1 AATAATATTAATTTAATATATTAAGAAAAAGATTCATACGT
* *
45571 AATAATATTAATTTAATATATAAAGAAAAATATTCATACGT
1 AATAATATTAATTTAATATATTAAGAAAAAGATTCATACGT
*
45612 AATAATATTAATATAATATATTAA-AAAA
1 AATAATATTAATTTAATATATTAAGAAAA
45640 TCCTACATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
40 4 0.06
41 60 0.94
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (41 bp):
AATAATATTAATTTAATATATTAAGAAAAAGATTCATACGT
Found at i:49546 original size:10 final size:10
Alignment explanation
Indices: 49521--49568 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
49511 CGTTCGAACC
*
49521 AAACCGGATGA
1 AAACCGGA-AA
49532 AAACCGGAAA
1 AAACCGGAAA
*
49542 AAACCGGGAA
1 AAACCGGAAA
* *
49552 AAACTGGGAA
1 AAACCGGAAA
49562 AAACCGG
1 AAACCGG
49569 GATTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.50, C:0.19, G:0.27, T:0.04
Consensus pattern (10 bp):
AAACCGGAAA
Found at i:49570 original size:10 final size:10
Alignment explanation
Indices: 49531--49570 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
49521 AAACCGGATG
*
49531 AAAACCGGAA
1 AAAACCGGGA
49541 AAAACCGGGA
1 AAAACCGGGA
*
49551 AAAACTGGGA
1 AAAACCGGGA
49561 AAAACCGGGA
1 AAAACCGGGA
49571 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.53, C:0.17, G:0.28, T:0.03
Consensus pattern (10 bp):
AAAACCGGGA
Found at i:71235 original size:60 final size:61
Alignment explanation
Indices: 71161--71283 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
71151 AATTAAGTTT
* * * * * *
71161 ATCCCTAAATTATGA-ATATCATTCTAAATTAGTTCTCAAAC-TTTTAAATATTTCAATTTC
1 ATCCCCAAAATATGACAT-TCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTC
* *
71221 ATCCCCAAAATATGACATTCATTCTAAATTGGTCCCCAAACTTTTTGAACATTCCAATTTC
1 ATCCCCAAAATATGACATTCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTC
71282 AT
1 AT
71284 ACCAAACTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 33 0.62
61 20 0.38
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (61 bp):
ATCCCCAAAATATGACATTCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTC
Found at i:71289 original size:60 final size:60
Alignment explanation
Indices: 71171--71299 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
71161 ATCCCTAAAT
* * * * *
71171 TATGAATATCATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTCATCCCCAAAA
1 TATGAATATCATTCTAAATTAGTCCCCAAACTTTTAAACATTCCAATTTCATCACCAAAA
* * *
71231 TATGACAT-TCATTCTAAATTGGTCCCCAAACTTTTTGAACATTCCAATTTCAT-ACCAAAC
1 TATGA-ATATCATTCTAAATTAGTCCCCAAAC-TTTTAAACATTCCAATTTCATCACCAAAA
*
71291 TATGCATAT
1 TATGAATAT
71300 ATGCTAATCG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
59 2 0.04
60 35 0.61
61 20 0.35
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (60 bp):
TATGAATATCATTCTAAATTAGTCCCCAAACTTTTAAACATTCCAATTTCATCACCAAAA
Found at i:71500 original size:60 final size:60
Alignment explanation
Indices: 71402--71681 Score: 322
Period size: 60 Copynumber: 4.7 Consensus size: 60
71392 TTACATATTT
** * *
71402 GGATGAAATTGGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAG
1 GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAGAAAGATGGTCATAGTTTAG
** * *
71462 GGATGAAATTATAAT-TTGCAAAAGTTTAAGGATTAATTTAGAATGA-GAGTCATGGTTT-G
1 GGATGAAATTATAATATT-CAAAAGTTTAAGGACCAATTTAGAAAGATG-GTCATAGTTTAG
* *
71521 ACGATGAAATTATAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGTCATAGTTTAG
1 -GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAGAAAGATGGTCATAGTTTAG
* *
71582 GGATGAAATTATAAT-TTACAAAAGTTTAAGGACTAATTTAGAATGA-GAGTCAT-GATTT-G
1 GGATGAAATTATAATATT-CAAAAGTTTAAGGACCAATTTAGAAAGATG-GTCATAG-TTTAG
* *
71641 ACGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
1 -GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTA
71682 CAATGAGTGT
Statistics
Matches: 188, Mismatches: 21, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
59 9 0.05
60 173 0.92
61 6 0.03
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAGAAAGATGGTCATAGTTTAG
Found at i:71619 original size:120 final size:120
Alignment explanation
Indices: 71403--71681 Score: 495
Period size: 120 Copynumber: 2.3 Consensus size: 120
71393 TACATATTTG
*
71403 GATGAAATTGGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
1 GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
* * *
71468 AATTATAATTTGCAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATGGTTTGAC
66 AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
* *
71523 GATGAAATTATAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGTCATAGTTTAGGGATGA
1 GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
71588 AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
66 AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
*
71643 GATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
1 GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTA
71682 CAATGAGTGT
Statistics
Matches: 151, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 151 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (120 bp):
GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
Found at i:74018 original size:21 final size:21
Alignment explanation
Indices: 73976--74018 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
73966 TTTCTAGGCT
* * *
73976 AGGGGAATCGGTACTCATTCA
1 AGGGGAATCGATACCCACTCA
*
73997 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
74018 A
1 A
74019 TGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:74728 original size:23 final size:23
Alignment explanation
Indices: 74697--74757 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
74687 TATTATATGC
74697 CACTACGGTGCAATTCTACGCGG
1 CACTACGGTGCAATTCTACGCGG
* *
74720 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
*
74743 CACTAAGGTGCAATT
1 CACTACGGTGCAATT
74758 ATTTGAGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Found at i:75735 original size:26 final size:27
Alignment explanation
Indices: 75706--75768 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
75696 ACGTGAGAAT
75706 AATAAATAAAACAAG-AAAAAATGAA-A
1 AATAAATAAAACAAGTAAAAAAT-AATA
* *
75732 AAT-AACAAAACACGTAAAAAATAATA
1 AATAAATAAAACAAGTAAAAAATAATA
*
75758 AAAAAATAAAA
1 AATAAATAAAA
75769 ATAAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 11 0.37
26 13 0.43
27 6 0.20
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (27 bp):
AATAAATAAAACAAGTAAAAAATAATA
Found at i:75851 original size:17 final size:17
Alignment explanation
Indices: 75831--75864 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
75821 TATTAATCGA
75831 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
* *
75848 GTAAAGAAATTAAAAAG
1 GTAAAAAAATAAAAAAG
75865 AATAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:75925 original size:29 final size:30
Alignment explanation
Indices: 75896--75980 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 30
75886 GTATTTACTA
75896 AAACAAATAAAAATAATAAATATATACTAAG
1 AAACAAATAAAAATAA-AAATATATACTAAG
*
75927 TAAACAAATAAAAATAAAAATACATTATATTAAG
1 -AAACAAATAAAAATAAAAAT--A-TATACTAAG
*
75961 AAAAAAATAATAGAATAAAA
1 AAACAAATAA-A-AATAAAA
75981 TAAAATAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
31 4 0.09
32 16 0.35
33 10 0.22
34 9 0.20
35 7 0.15
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (30 bp):
AAACAAATAAAAATAAAAATATATACTAAG
Found at i:75992 original size:78 final size:80
Alignment explanation
Indices: 75900--76085 Score: 199
Period size: 78 Copynumber: 2.4 Consensus size: 80
75890 TTACTAAAAC
* * *
75900 AAATAAAA-ATAATAAATATATACTA-AGTAAACAAATAAAAATAAAAATACATTATATTAAGAA
1 AAATAAAATATAATAAAAATATAATATA-TAAACAAATAAAAAAAAAAATACA--ATATTAAGAA
*
75963 AAAA-ATA-AT-AGAATA
63 AAAATATATATAAAAATA
* * *
75978 AAATAAAATA-AATAAAAATATAATATATATATAAATAAAAAAAAAAATAGAATATTAAGAAAAA
1 AAATAAAATATAATAAAAATATAATATATAAACAAATAAAAAAAAAAATACAATATTAAGAAAAA
76042 ATATATATAAAAATA
66 ATATATATAAAAATA
* *
76057 AAATATAATATTAAGAAAAA-AT-ATATATA
1 AAATAAAATA-TAATAAAAATATAATATATA
76086 CATAGTAATA
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
76 14 0.15
77 3 0.03
78 43 0.47
79 23 0.25
80 2 0.02
81 7 0.08
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (80 bp):
AAATAAAATATAATAAAAATATAATATATAAACAAATAAAAAAAAAAATACAATATTAAGAAAAA
ATATATATAAAAATA
Found at i:75994 original size:27 final size:28
Alignment explanation
Indices: 75961--76032 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
75951 TTATATTAAG
*
75961 AAAAAAATAATAGAATA-AAATA-AAAT
1 AAAAAAAAAATAGAATATAAATATAAAT
* * *
75987 -AAATAAAAATATAATATATATATAAAT
1 AAAAAAAAAATAGAATATAAATATAAAT
76014 AAAAAAAAAAATAGAATAT
1 -AAAAAAAAAATAGAATAT
76033 TAAGAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
25 13 0.36
26 4 0.11
27 4 0.11
29 15 0.42
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (28 bp):
AAAAAAAAAATAGAATATAAATATAAAT
Found at i:76042 original size:18 final size:17
Alignment explanation
Indices: 76019--76084 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 17
76009 TAAATAAAAA
76019 AAAAAATAGAATATTAAG
1 AAAAAATA-AATATTAAG
* *
76037 AAAAAATATATA-TAAA
1 AAAAAATAAATATTAAG
76053 AATAAAATATAATATTAAG
1 AA-AAAATA-AATATTAAG
*
76072 AAAAAATATATAT
1 AAAAAATAAATAT
76085 ACATAGTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.12
17 13 0.32
18 17 0.43
19 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAAAATAAATATTAAG
Found at i:76054 original size:35 final size:35
Alignment explanation
Indices: 76006--76085 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
75996 TATAATATAT
*
76006 ATATAAATAAAAAAAAAAATAGAATATTAAGAAAAA
1 ATATATAT-AAAAAAAAAATAGAATATTAAGAAAAA
* *
76042 ATATATATAAAAATAAAATATAATATTAAGAAAAA
1 ATATATATAAAAAAAAAATAGAATATTAAGAAAAA
76077 ATATATATA
1 ATATATATA
76086 CATAGTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 34 0.83
36 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (35 bp):
ATATATATAAAAAAAAAATAGAATATTAAGAAAAA
Found at i:76063 original size:57 final size:53
Alignment explanation
Indices: 75932--76077 Score: 134
Period size: 58 Copynumber: 2.6 Consensus size: 53
75922 CTAAGTAAAC
* * *
75932 AAATAAAAATAAAA-ATACATTATATTAAGAAAAAAATAATAGAATAAAATAAAAT
1 AAATAAAAATAAAATATATA-TA-AATAA-AAAAAAATAATAGAATAAAAAAAAAT
75987 AAATAAAAATATAATATATATATAAATAAAAAAAAA-AATAGAATATTAAGAAAAAAT
1 AAATAAAAATA-AA-ATATATATAAATAAAAAAAAATAATAGAATA--AA-AAAAAAT
* *
76044 ATATATAAAAATAAAATATAATATTAAGAAAAAA
1 A-A-ATAAAAATAAAATAT-ATATAAATAAAAAA
76078 TATATATACA
Statistics
Matches: 77, Mismatches: 5, Indels: 15
0.79 0.05 0.15
Matches are distributed among these distances:
54 9 0.12
55 18 0.23
56 8 0.10
57 14 0.18
58 19 0.25
59 9 0.12
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (53 bp):
AAATAAAAATAAAATATATATAAATAAAAAAAAATAATAGAATAAAAAAAAAT
Found at i:76140 original size:16 final size:16
Alignment explanation
Indices: 76119--76161 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
76109 ACATCTATAC
*
76119 ATATATATATAATAAT
1 ATATATATAAAATAAT
*
76135 ATATATAAAAAATAAT
1 ATATATATAAAATAAT
76151 ATA-ATATAAAA
1 ATATATATAAAA
76162 AATGAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATATAAAATAAT
Found at i:76181 original size:18 final size:16
Alignment explanation
Indices: 75942--76180 Score: 81
Period size: 17 Copynumber: 14.3 Consensus size: 16
75932 AAATAAAAAT
75942 AAAAATACAT-TATATTA
1 AAAAATA-ATATATA-TA
* *
75959 AGAAAAAAATA-ATAGA
1 A-AAAATAATATATATA
* *
75975 ATAAAATAAAATAAATA
1 A-AAAATAATATATATA
75992 AAAATATAATATATAT-
1 AAAA-ATAATATATATA
*
76008 ATAAATAA-A-A-A-A
1 AAAAATAATATATATA
76020 AAAAATAGA-ATAT-TA
1 AAAAATA-ATATATATA
76035 AGAAAA-AATATATATA
1 A-AAAATAATATATATA
*
76051 AAAATAAAATATAATATTA
1 AAAA-ATAATAT-ATA-TA
76070 AGAAAA-AATATATATA
1 A-AAAATAATATATATA
* * * *
76086 CATAGTAATATAGA-A
1 AAAAATAATATATATA
76101 AAATTAATACATCTATACATATA
1 AAA--AATA-A--TAT--ATATA
*
76124 TATATAATAATATATATA
1 -A-AAAATAATATATATA
76142 AAAAATAATATAATATA
1 AAAAATAATAT-ATATA
76159 AAAAATGAATATAGTA-A
1 AAAAAT-AATATA-TATA
76176 AAAAA
1 AAAAA
76181 AGATAATTAA
Statistics
Matches: 170, Mismatches: 21, Indels: 62
0.67 0.08 0.25
Matches are distributed among these distances:
12 7 0.04
13 3 0.02
14 3 0.02
15 18 0.11
16 41 0.24
17 49 0.29
18 26 0.15
19 4 0.02
20 9 0.05
22 3 0.02
23 5 0.03
24 1 0.01
25 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (16 bp):
AAAAATAATATATATA
Found at i:86693 original size:216 final size:215
Alignment explanation
Indices: 86307--86727 Score: 632
Period size: 217 Copynumber: 2.0 Consensus size: 215
86297 ATATTTAGTT
* * * * * *
86307 CACGACTTTTTTCTTTTTCAAAATCATATATTGTTATGTTTTCGTTTCATTTTGATCACCTGCTG
1 CACGACTTCTTTCTTCTTCAAAATCATATAATGTTATATTTTCGTTTCATTTTCATCACATGCTG
* *
86372 TAAAAAACAGTGATATTGATGTGTCACCATAAGATAATATCATATAATCATTGAAAAAAATTACG
66 TAAAAAACAGTGATAATGATGTATCACCATAAGATAATATCATATAATCATTGAAAAAAATTACG
*
86437 ATGTCAACAGTTATGTTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAA-TAACGTTAGAT
131 ATGTCAACAGTTATATTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATTAACGTTAGAT
86501 ATAATTTTGAATTTTGGTCA
196 ATAATTTTGAATTTTGGTCA
* *
86521 CACGACTTCTTT-TTCTTCAAAATCATATCTAATGTTATATTTTGGTTTTATTTTCATCACATGC
1 CACGACTTCTTTCTTCTTCAAAATCATA--TAATGTTATATTTTCGTTTCATTTTCATCACATGC
* *
86585 TGTTAAAAAAACAGTGATAATGATGTATCACCATAAGATAATGTCATATAATCATTG-AAAAACT
64 TG-T-AAAAAACAGTGATAATGATGTATCACCATAAGATAATATCATATAATCATTGAAAAAAAT
* * *
86649 TACGATGTCATCAGTTATATTAATCTTTAATAGCGGGTGGCCAAAAAGAAAGCAAAATTAGCGTT
127 TACGATGTCAACAGTTATATTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATTAACGTT
*
86714 GGATATAATTTTGA
192 AGATATAATTTTGA
86728 GAGAAAAAAA
Statistics
Matches: 185, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
213 14 0.08
214 11 0.06
215 31 0.17
216 61 0.33
217 68 0.37
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (215 bp):
CACGACTTCTTTCTTCTTCAAAATCATATAATGTTATATTTTCGTTTCATTTTCATCACATGCTG
TAAAAAACAGTGATAATGATGTATCACCATAAGATAATATCATATAATCATTGAAAAAAATTACG
ATGTCAACAGTTATATTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATTAACGTTAGAT
ATAATTTTGAATTTTGGTCA
Found at i:87206 original size:42 final size:42
Alignment explanation
Indices: 87137--87479 Score: 436
Period size: 42 Copynumber: 8.1 Consensus size: 42
87127 AACAGATACT
* * * * *
87137 GCAGAATCCAAACAATCAGTA-CAGAAGCTTTCCACGGAAATC
1 GCAGAATCCAAACAATCGGTAGC-GAAGCCTTCGACGGGAACC
*
87179 GCAGAATCCAAACAATCGGTGGCGAAGCCTTCGACGGGAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
** * *
87221 GTTGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGAAATC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
*
87263 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACG
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
87305 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
* *
87347 GCAGAATCCAAACAATCGGTTGGAGAAGCCTTCGACGGGAACC
1 GCAGAATCCAAACAATCGG-TAGCGAAGCCTTCGACGGGAACC
* * * * *
87390 GCGGAATCCAAACAATCGGTGGAGAAGCCTTTGACGGAAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
* * * * * * *
87432 GCGGAATCTAAACAATCGGTTGAGAAGCCTTCGTCGGAAACA
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
87474 GCAGAA
1 GCAGAA
87480 CCAGAGTCGA
Statistics
Matches: 271, Mismatches: 28, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
42 231 0.85
43 40 0.15
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (42 bp):
GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
Found at i:87419 original size:169 final size:168
Alignment explanation
Indices: 87137--87479 Score: 490
Period size: 169 Copynumber: 2.0 Consensus size: 168
87127 AACAGATACT
* * *
87137 GCAGAATCCAAACAATCAGTACAGAAGCTTTCCACGGAAATCGCAGAATCCAAACAATCGGTGGC
1 GCAGAATCCAAACAATCAGTACAGAAGCCTTCCACGGAAACCGCAGAATCCAAACAATCGGTGGA
** * *
87202 GAAGCCTTCGACGGGAACCGTTGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGAAATCGCAG
66 GAAGCCTTCGACGGGAACCGCGGAATCCAAACAATCGGTAGAGAAGCCTTCGACGGAAACCGCAG
* * *
87267 AATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACG
131 AATCCAAACAATCGGTAGAGAAGCCTTCGACGGAAACA
* * *
87305 GCAGAATCCAAACAATCGGTAGC-GAAGCCTTCGACGGGAACCGCAGAATCCAAACAATCGGTTG
1 GCAGAATCCAAACAATCAGTA-CAGAAGCCTTCCACGGAAACCGCAGAATCCAAACAATCGG-TG
* *
87369 GAGAAGCCTTCGACGGGAACCGCGGAATCCAAACAATCGGTGGAGAAGCCTTTGACGGAAACCGC
64 GAGAAGCCTTCGACGGGAACCGCGGAATCCAAACAATCGGTAGAGAAGCCTTCGACGGAAACCGC
* * * *
87434 GGAATCTAAACAATCGGTTGAGAAGCCTTCGTCGGAAACA
129 AGAATCCAAACAATCGGTAGAGAAGCCTTCGACGGAAACA
87474 GCAGAA
1 GCAGAA
87480 CCAGAGTCGA
Statistics
Matches: 154, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
168 54 0.35
169 100 0.65
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (168 bp):
GCAGAATCCAAACAATCAGTACAGAAGCCTTCCACGGAAACCGCAGAATCCAAACAATCGGTGGA
GAAGCCTTCGACGGGAACCGCGGAATCCAAACAATCGGTAGAGAAGCCTTCGACGGAAACCGCAG
AATCCAAACAATCGGTAGAGAAGCCTTCGACGGAAACA
Done.