Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007856.1 Hibiscus syriacus cultivar Beakdansim tig00110217_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: 65166
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3035 original size:2 final size:2
Alignment explanation
Indices: 3028--3054 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3018 CCTAAATTCA
3028 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 A
3055 ATTAAAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27698 original size:40 final size:39
Alignment explanation
Indices: 27649--27774 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 39
27639 AATAAATTTA
* *
27649 CAACACGAACTCCTATTTCGCAACATAATTTCCAAATTCG
1 CAACTCGAACT-CTATTTCGCAACACAATTTCCAAATTCG
** * *
27689 CAACTCGAACATGGAAATTTTCGCAACGCGATTT-CAAATTCG
1 CAACTCGAAC-T--CTA-TTTCGCAACACAATTTCCAAATTCG
*
27731 CAA-TACGAACTCTAATTTCGCAACACAGTTTCCAAATTCG
1 CAACT-CGAACTCT-ATTTCGCAACACAATTTCCAAATTCG
27771 CAAC
1 CAAC
27775 GCTAATTTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
39 13 0.19
40 21 0.31
41 3 0.04
42 17 0.25
43 13 0.19
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (39 bp):
CAACTCGAACTCTATTTCGCAACACAATTTCCAAATTCG
Found at i:32329 original size:16 final size:15
Alignment explanation
Indices: 32306--32348 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
32296 TTATTAATAA
32306 TTTAATTTTATATTT
1 TTTAATTTTATATTT
*
32321 TTATAATTTTACATTT
1 TT-TAATTTTATATTT
*
32337 TTTAAATTTATA
1 TTTAATTTTATA
32349 ATATAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAATTTTATATTT
Found at i:33137 original size:21 final size:20
Alignment explanation
Indices: 33070--33208 Score: 73
Period size: 21 Copynumber: 6.8 Consensus size: 20
33060 AAATGACCAA
***
33070 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
33090 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
33110 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
33131 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
33152 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
33172 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
33193 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
33209 ACACATAAAT
Statistics
Matches: 88, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 43 0.49
21 44 0.50
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:33201 original size:20 final size:20
Alignment explanation
Indices: 33176--33486 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
33166 GATTTTCAAT
* *
33176 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
33196 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
33216 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
33236 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
33256 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
33276 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
33296 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
33316 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
33337 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
33357 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
33377 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
33397 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
33417 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
33437 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
33457 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
33477 AATCGCAACG
1 AATCGCAACG
33487 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:33221 original size:40 final size:40
Alignment explanation
Indices: 33176--33565 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
33166 GATTTTCAAT
* ** * * *
33176 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
33216 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
33256 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
33296 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
33337 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
33377 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
33417 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
33457 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
33497 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
33537 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
33566 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:33493 original size:20 final size:19
Alignment explanation
Indices: 33214--33565 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
33204 CGCGAACACA
33214 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
33234 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
33254 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
33274 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
33294 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
33314 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
33334 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
33355 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
33375 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
33395 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
33415 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
33435 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
33455 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
33475 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
33495 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
33515 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
33535 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
33555 TAAATCACAAC
1 TAAATCGCAAC
33566 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:34281 original size:24 final size:24
Alignment explanation
Indices: 34242--34288 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
34232 AAATTTGGTC
34242 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
34266 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
34289 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:34480 original size:12 final size:12
Alignment explanation
Indices: 34463--34487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34453 ATATAATCCT
34463 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34475 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34487 G
1 G
34488 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:36792 original size:19 final size:19
Alignment explanation
Indices: 36770--37043 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
36760 CGGAAAATAC
*
36770 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
36789 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
36803 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
36823 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
36837 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36856 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
36875 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
36889 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36908 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
36927 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
36946 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36965 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36984 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
36998 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37017 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37036 AATCGCAA
1 AATCGCAA
37044 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 147 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:36972 original size:109 final size:105
Alignment explanation
Indices: 36798--37065 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
36788 AAATCCCAAC
36798 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
36862 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
36903 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
36968 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
37012 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
37066 TATAAACGCA
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 32 0.21
105 16 0.10
106 4 0.03
107 5 0.03
108 1 0.01
109 97 0.63
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:37081 original size:52 final size:52
Alignment explanation
Indices: 36798--37065 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
36788 AAATCCCAAC
36798 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
36851 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
36903 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
36960 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
37012 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
37064 AT
1 AT
37066 TATAAACGCA
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 134 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 46 0.22
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:37162 original size:19 final size:19
Alignment explanation
Indices: 37072--37154 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
37062 AAATTATAAA
37072 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
37091 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
37111 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
37127 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
37144 CGCATTGCGAT
1 CGCATTGCGAT
37155 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:37280 original size:14 final size:14
Alignment explanation
Indices: 37261--37297 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37251 CATCAATTAC
37261 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37275 ACAAATCATCTTTT
1 ACAAATCAACTTTT
37289 ACAAATCAA
1 ACAAATCAA
37298 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:39265 original size:14 final size:14
Alignment explanation
Indices: 39246--39302 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
39236 GCGAAATGAA
*
39246 AATCGCAACGACAG
1 AATCGCAACGAAAG
39260 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
39277 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
39293 AATCGCAACG
1 AATCGCAACG
39303 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:39273 original size:33 final size:33
Alignment explanation
Indices: 39227--39319 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
39217 GCGAAACCAA
*
39227 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
39260 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
39293 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
39320 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:39284 original size:19 final size:19
Alignment explanation
Indices: 39190--39324 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
39180 TAGTTTACTT
* *
39190 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
39210 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
39229 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
39248 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
39262 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
39281 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
39295 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
39314 TCGCAATGCGA
1 TCGCAACGCGA
39325 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:39342 original size:19 final size:19
Alignment explanation
Indices: 39320--39448 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
39310 AAAATCGCAA
39320 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
39339 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
39353 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
39372 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
39386 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
39405 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
39424 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
39444 TGCGA
1 TGCGA
39449 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:39362 original size:33 final size:33
Alignment explanation
Indices: 39320--39411 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
39310 AAAATCGCAA
39320 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
39353 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
39386 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
39412 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:39662 original size:92 final size:93
Alignment explanation
Indices: 39492--39870 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
39482 TTGAATGGAT
39492 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39557 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
39585 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39649 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
39677 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39741 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
39769 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
39834 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
39862 AAATTTACT
1 AAATTTACT
39871 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:39821 original size:185 final size:185
Alignment explanation
Indices: 39492--39870 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
39482 TTGAATGGAT
39492 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39557 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
39622 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
39677 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39741 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
39806 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
39862 AAATTTACT
1 AAATTTACT
39871 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:41596 original size:14 final size:14
Alignment explanation
Indices: 41577--41666 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
41567 TTGAAATGAA
41577 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41591 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
41608 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
41624 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
41643 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41657 AATCGCAACG
1 AATCGCAACG
41667 CGAAATTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:41614 original size:33 final size:33
Alignment explanation
Indices: 41569--41683 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
41559 TCTTTTGGTT
41569 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
41602 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
41635 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
41668 GAAATTAAAATCGCAA
1 GAAATGAAAATCGCAA
41684 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:41615 original size:19 final size:18
Alignment explanation
Indices: 41576--41688 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
41566 GTTGAAATGA
41576 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
41591 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
41608 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
41624 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
41641 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
* *
41657 -AATCGCAACGCGAAATTA
1 AAATCGCAACGCGAGA-TG
*
41675 AAATCGCAATGCGA
1 AAATCGCAACGCGA
41689 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
14 24 0.31
16 15 0.19
17 11 0.14
19 28 0.36
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:41719 original size:14 final size:14
Alignment explanation
Indices: 41700--41754 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
41690 TTTGGTTTCG
41700 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
41714 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
41733 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41747 CGTTGCGA
1 CGTTGCGA
41755 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41732 original size:33 final size:33
Alignment explanation
Indices: 41684--41754 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
41674 AAAATCGCAA
**
41684 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
41717 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
41750 TGCGA
1 TGCGA
41755 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:41762 original size:33 final size:33
Alignment explanation
Indices: 41695--41776 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
41685 GCGATTTTGG
***
41695 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
41728 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
41761 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
41777 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:41781 original size:20 final size:20
Alignment explanation
Indices: 41707--41795 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
41697 TCGCGTTGCG
41707 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
41727 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
41740 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
41760 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
41780 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
41796 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:41917 original size:33 final size:33
Alignment explanation
Indices: 41875--41945 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
41865 AATACTAACT
*
41875 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
41908 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
41941 TGAAA
1 TGAAA
41946 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:42179 original size:22 final size:22
Alignment explanation
Indices: 42127--42181 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42117 TGGTTGTGAG
**
42127 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
42149 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
42171 GGATTTCTTCG
1 GGATTTCTTCG
42182 CCGTAGAGAG
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:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:42346 original size:20 final size:20
Alignment explanation
Indices: 42321--42513 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
42311 CTTTAAATAT
42321 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42341 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
42363 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42382 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
42402 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
42422 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42442 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42462 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
42482 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
42502 CGCGTTGCGATT
1 CGCGTTGCGATT
42514 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:42508 original size:60 final size:60
Alignment explanation
Indices: 42321--42513 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
42311 CTTTAAATAT
**
42321 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
42382 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
42442 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
42502 CGCGTTGCGATT
1 CGCGTTGCGATT
42514 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:45598 original size:21 final size:21
Alignment explanation
Indices: 45568--45607 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45558 AAAAATAATA
*
45568 TTTTTGATCACTTATATCAAC
1 TTTTTAATCACTTATATCAAC
* *
45589 TTTTTAATCATTTGTATCA
1 TTTTTAATCACTTATATCA
45608 TGGATATAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTTAATCACTTATATCAAC
Found at i:45765 original size:31 final size:30
Alignment explanation
Indices: 45682--45766 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
45672 AACAAATATT
* * *
45682 AAATTTTAATTTAATCTCTAACTTTTAAATA
1 AAATATTAATTTAAT-TATAAATTTTAAATA
**
45713 AAATATTAAAATAATTAATAAATTTTAAATA
1 AAATATTAATTTAATT-ATAAATTTTAAATA
45744 AAATATTAATTTAATATATAAAT
1 AAATATTAATTTAAT-TATAAAT
45767 CTAATAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 43 0.96
32 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATATTAATTTAATTATAAATTTTAAATA
Found at i:48074 original size:37 final size:37
Alignment explanation
Indices: 48031--48105 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
48021 TTCGAAGAAA
48031 GCTCTTGTCATATTAATCCTCCATTCCCATCTACCAT
1 GCTCTTGTCATATTAATCCTCCATTCCCATCTACCAT
48068 GCTCTTGTCATATTAATCCTCCATTCCCATCTACCAT
1 GCTCTTGTCATATTAATCCTCCATTCCCATCTACCAT
48105 G
1 G
48106 AACCCAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (37 bp):
GCTCTTGTCATATTAATCCTCCATTCCCATCTACCAT
Found at i:50360 original size:2 final size:2
Alignment explanation
Indices: 50353--50391 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
50343 TTTTATGTGT
50353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50392 AACATATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51502 original size:21 final size:22
Alignment explanation
Indices: 51478--51532 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
51468 TATTTTTTCC
51478 ATATCATGTA-ATTCTATATAT
1 ATATCATGTATATTCTATATAT
* *
51499 ATAT-ACGTATTTTCTATATAT
1 ATATCATGTATATTCTATATAT
* *
51520 ATTTCATTTATAT
1 ATATCATGTATAT
51533 ACTTAGTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (22 bp):
ATATCATGTATATTCTATATAT
Found at i:51816 original size:21 final size:21
Alignment explanation
Indices: 51779--51822 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
51769 CATTCATTAA
*
51779 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
51799 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
51821 TT
1 TT
51823 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:51889 original size:28 final size:25
Alignment explanation
Indices: 51813--51877 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
51803 TTATTTCCCC
*
51813 TTTTACTTTTTACTATTATTATTATTT
1 TTTTA-TTTATACTATTA-TATTATTT
* *
51840 ATTTATTTATGCTATTATATTATTT
1 TTTTATTTATACTATTATATTATTT
51865 TTTTATTATATAC
1 TTTTATT-TATAC
51878 GTATATGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 14 0.44
26 14 0.44
27 4 0.12
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTATTTATACTATTATATTATTT
Found at i:54813 original size:17 final size:17
Alignment explanation
Indices: 54783--54825 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
54773 ATTAAAATAT
*
54783 TATTAAATAGA-AAAAAG
1 TATTAAATA-ACAAAAAA
54800 TA-TAAATAACAAAAAA
1 TATTAAATAACAAAAAA
54816 TATTAAATAA
1 TATTAAATAA
54826 GATTTAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 1 0.04
16 13 0.57
17 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
TATTAAATAACAAAAAA
Found at i:57508 original size:11 final size:12
Alignment explanation
Indices: 57485--57522 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
57475 CAAAAATAAA
*
57485 AAAATACAAGAG
1 AAAAGACAAGAG
57497 AAAAGA-AAGAG
1 AAAAGACAAGAG
*
57508 AAAGGACAAGAG
1 AAAAGACAAGAG
57520 AAA
1 AAA
57523 GATGAAAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.03
Consensus pattern (12 bp):
AAAAGACAAGAG
Found at i:57518 original size:12 final size:12
Alignment explanation
Indices: 57490--57523 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
57480 ATAAAAAAAT
*
57490 ACAAGAGAAAAG
1 ACAAGAGAAAGG
57502 A-AAGAGAAAGG
1 ACAAGAGAAAGG
57513 ACAAGAGAAAG
1 ACAAGAGAAAG
57524 ATGAAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.06, G:0.29, T:0.00
Consensus pattern (12 bp):
ACAAGAGAAAGG
Found at i:60715 original size:21 final size:18
Alignment explanation
Indices: 60639--60709 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
60629 CGTCAACCCA
60639 TCTTCTT-CTTCCTTCTT
1 TCTTCTTCCTTCCTTCTT
60656 TC--CTTCCTTCCAACTT-TT
1 TCTTCTTCCTT-C--CTTCTT
60674 TCTTCTTCCTTCCTTCTT
1 TCTTCTTCCTTCCTTCTT
*
60692 TCTTCTTCTTCTCCTTCT
1 TCTTCTTCCT-TCCTTCT
60710 CCTTCTCACA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
15 3 0.07
16 3 0.07
17 6 0.13
18 15 0.33
19 11 0.24
20 7 0.16
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (18 bp):
TCTTCTTCCTTCCTTCTT
Done.