Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000184.1 Hibiscus syriacus cultivar Beakdansim tig00000326_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: 104624
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:914 original size:45 final size:45
Alignment explanation
Indices: 865--1149 Score: 471
Period size: 45 Copynumber: 6.3 Consensus size: 45
855 AAGAGAAACA
* *
865 GATGTTCCGCATTCCTCTCAAAAAGCAGCTGAGGAAGAATCGGCT
1 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
* *
910 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATTGACC
1 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
*
955 GATGTTCTGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
1 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
*
1000 GATGTTCTGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
1 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
*
1045 GATGTTCCACATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
1 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
* * *
1090 GATGTTCCACATTCCTCTCAAAAAGCAACTGAGGACGAATCAACT
1 GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
*
1135 GATGTTTCGCATTCC
1 GATGTTCCGCATTCC
1150 ACAAGGGCCC
Statistics
Matches: 227, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 227 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (45 bp):
GATGTTCCGCATTCCTCTCAAAAAGCAACTGAGGAAGAATCGACT
Found at i:1911 original size:15 final size:17
Alignment explanation
Indices: 1891--1923 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1881 TGTATTGTGG
1891 TTTAAGT-AGGTT-GCA
1 TTTAAGTAAGGTTAGCA
1906 TTTAAGTAAGGTTAGCA
1 TTTAAGTAAGGTTAGCA
1923 T
1 T
1924 CAATGGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (17 bp):
TTTAAGTAAGGTTAGCA
Found at i:20782 original size:72 final size:71
Alignment explanation
Indices: 20696--20840 Score: 222
Period size: 71 Copynumber: 2.0 Consensus size: 71
20686 GAAGGTGAAT
20696 AAGAAGAACGAAAGGAAGCATTAG-CACTTTCGATTCAAAGTGAACGGAAGGAAGCAT-CGACAC
1 AAGAAGAACGAAAGGAAGCA-TAGACACTTTCGATTC-AAGTGAACGGAAGGAAGCATCCG-CAC
20759 TTTCGATTC
63 TTTCGATTC
* * *
20768 AAGAAGAACGAAAGGAAGTATCGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCCGTACTTT
1 AAGAAGAACGAAAGGAAGCATAGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCCGCACTTT
20833 CGATTC
66 CGATTC
20839 AA
1 AA
20841 TTGTTCATCT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
71 35 0.51
72 33 0.49
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATAGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCCGCACTTT
CGATTC
Found at i:20819 original size:35 final size:35
Alignment explanation
Indices: 20701--20840 Score: 176
Period size: 36 Copynumber: 3.9 Consensus size: 35
20691 TGAATAAGAA
* *
20701 GAACGAAAGGAAGCAT-TAGCACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATCGA-CACTTTCGATTC-AAGT
*
20737 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAG-T
* *
20773 GAACGAAAGGAAGTATCGACACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
*
20808 GAACGGAAGGAAGCATCCG-TACTTTCGATTCAA
1 GAACGGAAGGAAGCAT-CGACACTTTCGATTCAA
20841 TTGTTCATCT
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
35 30 0.33
36 61 0.66
37 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:20838 original size:71 final size:72
Alignment explanation
Indices: 20696--20840 Score: 224
Period size: 72 Copynumber: 2.0 Consensus size: 72
20686 GAAGGTGAAT
*
20696 AAGAAGAACGAAAGGAAGCATTAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
1 AAGAAGAACGAAAGGAAGCATGAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
20761 TCGATTC
66 TCGATTC
* *
20768 AAGAAGAACGAAAGGAAGTATCGA-CACTTTCGATTC-AAGTGAACGGAAGGAAGCATCCG-TAC
1 AAGAAGAACGAAAGGAAGCAT-GAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCAT-CGACAC
20830 TTTCGATTC
64 TTTCGATTC
20839 AA
1 AA
20841 TTGTTCATCT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
71 33 0.49
72 34 0.50
73 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATGAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
TCGATTC
Found at i:22473 original size:36 final size:35
Alignment explanation
Indices: 22426--22565 Score: 167
Period size: 36 Copynumber: 3.9 Consensus size: 35
22416 TGAATAAGAA
*
22426 GAACGAAAGGAAGCAT-TAGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTC-AAGT
* *
22462 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAG-T
* *
22498 GAACGAAAGGGAGTATCGACACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* *
22533 GAACGGAAGGAAGCATCCG-TACTTTCGATTCAA
1 GAACGAAAGGAAGCAT-CGACACTTTCGATTCAA
22566 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
35 29 0.32
36 60 0.67
37 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:22560 original size:71 final size:72
Alignment explanation
Indices: 22421--22565 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 72
22411 GAAGGTGAAT
*
22421 AAGAAGAACGAAAGGAAGCATTAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
1 AAGAAGAACGAAAGGAAGCATGAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
22486 TCGATTC
66 TCGATTC
* * *
22493 AAGAAGAACGAAAGGGAGTATCGA-CACTTTCGATTC-AAGTGAACGGAAGGAAGCATCCG-TAC
1 AAGAAGAACGAAAGGAAGCAT-GAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCAT-CGACAC
22555 TTTCGATTC
64 TTTCGATTC
22564 AA
1 AA
22566 TTGTTCATCT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
71 33 0.49
72 33 0.49
73 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATGAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
TCGATTC
Found at i:28994 original size:3 final size:3
Alignment explanation
Indices: 28986--29026 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28976 ATATGTGAAA
28986 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29027 AGATAGAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30301 original size:34 final size:34
Alignment explanation
Indices: 30262--30327 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
30252 TTTTAATTTA
** *
30262 GGGTCGGGTCGGGTTTTTTTAAGTTTGATATTCG
1 GGGTCGGGTCAAGTTTTTTTAAGTGTGATATTCG
30296 GGGTCGGGTCAAGTTTTTTTAAGTGTGATATT
1 GGGTCGGGTCAAGTTTTTTTAAGTGTGATATT
30328 AGGTCAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.15, C:0.08, G:0.33, T:0.44
Consensus pattern (34 bp):
GGGTCGGGTCAAGTTTTTTTAAGTGTGATATTCG
Found at i:30340 original size:60 final size:61
Alignment explanation
Indices: 30276--30418 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 61
30266 CGGGTCGGGT
* *
30276 TTTTTTAAGTTTGATATTCGGGGTCGGGTCAAGTTTTTTTAAGTGTGATA-TTAGGTCA-G
1 TTTTTTAAGTGTGATATTCGGGGTCAGGTCAAGTTTTTTTAAGTGTGATATTTAGGTCATG
* ** * * *
30335 ATTTTTTAAGTGTGTTATTCGGATTCAGGTCGAGTTTTTTTAAGTTTGATATTTGGGTCATG
1 -TTTTTTAAGTGTGATATTCGGGGTCAGGTCAAGTTTTTTTAAGTGTGATATTTAGGTCATG
30397 TTTTTTAAGTGTGATATTCGGG
1 TTTTTTAAGTGTGATATTCGGG
30419 TTAGGTTTCT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
60 43 0.61
61 27 0.38
62 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.48
Consensus pattern (61 bp):
TTTTTTAAGTGTGATATTCGGGGTCAGGTCAAGTTTTTTTAAGTGTGATATTTAGGTCATG
Found at i:30419 original size:27 final size:28
Alignment explanation
Indices: 30299--30419 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 28
30289 ATATTCGGGG
*
30299 TCGGGTCAAGTTTTTTTAAGTGTGATAT
1 TCGGGTCATGTTTTTTTAAGTGTGATAT
* * *
30327 T-AGGTCA-GATTTTTTAAGTGTGTTAT
1 TCGGGTCATGTTTTTTTAAGTGTGATAT
* *
30353 TCGGATTCAGGTCGAGTTTTTTTAAGTTTGATAT
1 TCGG-GTCA--T---GTTTTTTTAAGTGTGATAT
*
30387 TTGGGTCATG-TTTTTTAAGTGTGATAT
1 TCGGGTCATGTTTTTTTAAGTGTGATAT
30414 TCGGGT
1 TCGGGT
30420 TAGGTTTCTA
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
26 18 0.25
27 27 0.37
28 5 0.07
31 1 0.01
33 3 0.04
34 19 0.26
ACGTcount: A:0.20, C:0.07, G:0.26, T:0.48
Consensus pattern (28 bp):
TCGGGTCATGTTTTTTTAAGTGTGATAT
Found at i:32158 original size:21 final size:20
Alignment explanation
Indices: 32072--32229 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
32062 AAATGACCAA
**
32072 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
32091 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
32111 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
32131 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
32152 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
32173 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
32193 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
32214 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
32230 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:32222 original size:20 final size:20
Alignment explanation
Indices: 32197--32507 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
32187 GATTTTCAAT
* *
32197 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
32217 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
32237 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
32257 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
32277 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
32297 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
32317 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
32337 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
32358 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
32378 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
32398 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
32418 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
32438 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
32458 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
32478 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
32498 AATCGCAACG
1 AATCGCAACG
32508 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:32242 original size:40 final size:40
Alignment explanation
Indices: 32197--32586 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
32187 GATTTTCAAT
* ** * * *
32197 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
32237 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
32277 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
32317 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
32358 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
32398 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
32438 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
32478 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
32518 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
32558 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
32587 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:32514 original size:20 final size:19
Alignment explanation
Indices: 32235--32586 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
32225 CGCGAACACA
32235 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
32255 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
32275 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
32295 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
32315 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
32335 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
32355 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
32376 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
32396 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
32416 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
32436 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
32456 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
32476 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
32496 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
32516 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
32536 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
32556 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
32576 TAAATCACAAC
1 TAAATCGCAAC
32587 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:33301 original size:24 final size:24
Alignment explanation
Indices: 33262--33308 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33252 AAATTTGGTC
33262 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
33286 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
33309 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:33500 original size:12 final size:12
Alignment explanation
Indices: 33483--33507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33473 ATATAATCCT
33483 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33495 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33507 G
1 G
33508 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:35813 original size:19 final size:19
Alignment explanation
Indices: 35791--36064 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
35781 CGGAAAATAC
*
35791 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35810 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
35824 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
35844 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
35858 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35877 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35896 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
35910 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35929 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35948 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
35967 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35986 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36005 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
36019 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36038 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36057 AATCGCAA
1 AATCGCAA
36065 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:35993 original size:109 final size:105
Alignment explanation
Indices: 35819--36086 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
35809 AAATCCCAAC
35819 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
35883 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
35924 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
35989 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
36033 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
36087 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:36102 original size:52 final size:52
Alignment explanation
Indices: 35819--36086 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
35809 AAATCCCAAC
35819 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
35872 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
35924 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
35981 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
36033 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
36085 AT
1 AT
36087 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:36183 original size:19 final size:19
Alignment explanation
Indices: 36093--36175 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
36083 AAATTATAAA
36093 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36112 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
36132 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
36148 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36165 CGCATTGCGAT
1 CGCATTGCGAT
36176 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:36300 original size:14 final size:14
Alignment explanation
Indices: 36281--36317 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36271 CATCAATTAC
36281 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36295 ACAAATCATCTTTT
1 ACAAATCAACTTTT
36309 ACAAATCAA
1 ACAAATCAA
36318 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:38289 original size:14 final size:14
Alignment explanation
Indices: 38270--38326 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38260 GCGAAATGAA
*
38270 AATCGCAACGACAG
1 AATCGCAACGAAAG
38284 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
38301 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
38317 AATCGCAACG
1 AATCGCAACG
38327 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:38297 original size:33 final size:33
Alignment explanation
Indices: 38251--38343 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38241 GCGAAACCAA
*
38251 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
38284 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
38317 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
38344 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:38308 original size:19 final size:19
Alignment explanation
Indices: 38214--38348 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
38204 TAGTTTACTT
* *
38214 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
38234 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
38253 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38272 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
38286 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
38305 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
38319 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38338 TCGCAATGCGA
1 TCGCAACGCGA
38349 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:38366 original size:19 final size:19
Alignment explanation
Indices: 38344--38472 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
38334 AAAATCGCAA
38344 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38363 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
38377 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38396 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
38410 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
38429 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
38448 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
38468 TGCGA
1 TGCGA
38473 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:38386 original size:33 final size:33
Alignment explanation
Indices: 38344--38435 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
38334 AAAATCGCAA
38344 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
38377 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
38410 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
38436 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:38679 original size:92 final size:93
Alignment explanation
Indices: 38516--38893 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
38506 TTGAATGGAT
38516 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
38581 AG-TTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
38608 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
38672 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
38700 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
38764 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
38792 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
38857 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
38885 AAATTTACT
1 AAATTTACT
38894 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 27 0.10
92 195 0.69
93 61 0.22
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:40614 original size:14 final size:14
Alignment explanation
Indices: 40595--40684 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
40585 TTGAAATGAA
40595 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40609 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
40626 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
40642 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40661 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40675 AATCGCAACG
1 AATCGCAACG
40685 CGAAATGAAA
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:40632 original size:33 final size:33
Alignment explanation
Indices: 40587--40701 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
40577 TCTTTTGGTT
40587 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
40620 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40653 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40686 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
40702 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40633 original size:19 final size:18
Alignment explanation
Indices: 40594--40706 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
40584 GTTGAAATGA
40594 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
40609 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
40626 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
40642 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
40659 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
40675 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
40692 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
40707 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:40737 original size:14 final size:14
Alignment explanation
Indices: 40718--40772 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
40708 TTTGGTTTCG
40718 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40732 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
40751 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
40765 CGTTGCGA
1 CGTTGCGA
40773 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:40750 original size:33 final size:33
Alignment explanation
Indices: 40702--40772 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
40692 AAAATCGCAA
**
40702 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
40735 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
40768 TGCGA
1 TGCGA
40773 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:40780 original size:33 final size:33
Alignment explanation
Indices: 40713--40794 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
40703 GCGATTTTGG
***
40713 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
40746 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
40779 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
40795 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:40799 original size:20 final size:20
Alignment explanation
Indices: 40725--40813 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
40715 TCGCGTTGCG
40725 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
40745 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
40758 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
40778 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
40798 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
40814 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:40934 original size:33 final size:33
Alignment explanation
Indices: 40895--40962 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
40885 TACTAACTTG
*
40895 AAATCGCAACGAGAGAATAGCAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
* *
40928 AAATCGCAACGACAGAATCGTAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
40961 AA
1 AA
40963 TCTAAGTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (33 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATGA
Found at i:41196 original size:22 final size:22
Alignment explanation
Indices: 41144--41198 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41134 TGGTTGTGAG
**
41144 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
41166 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
41188 GGATTTCTTCG
1 GGATTTCTTCG
41199 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:41369 original size:20 final size:20
Alignment explanation
Indices: 41344--41536 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
41334 CTTTAAATAT
41344 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41364 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
41386 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41405 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
41425 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
41445 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41465 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41485 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
41505 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
41525 CGCGTTGCGATT
1 CGCGTTGCGATT
41537 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:41531 original size:60 final size:60
Alignment explanation
Indices: 41344--41536 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
41334 CTTTAAATAT
**
41344 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
41405 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
41465 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
41525 CGCGTTGCGATT
1 CGCGTTGCGATT
41537 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:51573 original size:63 final size:63
Alignment explanation
Indices: 51495--51620 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
51485 TTCTGTTTGA
51495 TAAACAGAACCCTAAGTTACCGCCGTTCATTCTCTGTTTCTTCATTTATGTTACCTTAGTTGG
1 TAAACAGAACCCTAAGTTACCGCCGTTCATTCTCTGTTTCTTCATTTATGTTACCTTAGTTGG
* *
51558 TAAACAGAACCCTAAGTTACCGCCGTTCATTCTTTGTTTCTTCATTTATGTTACCTTATTTGG
1 TAAACAGAACCCTAAGTTACCGCCGTTCATTCTCTGTTTCTTCATTTATGTTACCTTAGTTGG
51621 ACCACCGCTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (63 bp):
TAAACAGAACCCTAAGTTACCGCCGTTCATTCTCTGTTTCTTCATTTATGTTACCTTAGTTGG
Found at i:58374 original size:14 final size:14
Alignment explanation
Indices: 58355--58400 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
58345 CGTTCGTGAA
58355 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
58369 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
58383 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
58397 CGTT
1 CGTT
58401 TATGTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:58397 original size:24 final size:24
Alignment explanation
Indices: 58370--58420 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
58360 GGTTATGTTC
*
58370 GTTCGGTTATGTTCGTTCGA-TTAT
1 GTTCGGTTATGTTCATTC-ATTTAT
*
58394 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCATTTAT
58418 GTT
1 GTT
58421 TAACCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCATTTAT
Found at i:59478 original size:16 final size:16
Alignment explanation
Indices: 59457--59505 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
59447 CCAACGTTTA
59457 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
59473 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
**
59489 TGCGCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
59505 T
1 T
59506 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.06, C:0.14, G:0.27, T:0.53
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:59509 original size:10 final size:10
Alignment explanation
Indices: 59451--59489 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
59441 GGGTCTCCAA
59451 CGTTTATGTT
1 CGTTTATGTT
59461 CGTTTATGTT
1 CGTTTATGTT
59471 CG----TGTT
1 CGTTTATGTT
59477 CGTTTATGTT
1 CGTTTATGTT
59487 CGT
1 CGT
59490 GCGCGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.24
10 19 0.76
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:59596 original size:16 final size:16
Alignment explanation
Indices: 59575--59605 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59565 AAAAAAAATT
59575 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
59591 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
59606 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:61029 original size:15 final size:15
Alignment explanation
Indices: 61001--61078 Score: 88
Period size: 15 Copynumber: 5.3 Consensus size: 15
60991 AAATAATTTT
61001 AAATAATTTA--ATA
1 AAATAATTTATTATA
* *
61014 AGATTATTTATTATA
1 AAATAATTTATTATA
* *
61029 AAATAATTTATCATC
1 AAATAATTTATTATA
*
61044 AAATAAATTATTATA
1 AAATAATTTATTATA
*
61059 AAATAAATTATTATA
1 AAATAATTTATTATA
61074 AAATA
1 AAATA
61079 TGGATTGATT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
13 8 0.15
15 46 0.85
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AAATAATTTATTATA
Found at i:61115 original size:14 final size:15
Alignment explanation
Indices: 61086--61121 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
61076 ATATGGATTG
61086 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
61101 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
61115 ATTTATT
1 ATTTATT
61122 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:61149 original size:22 final size:22
Alignment explanation
Indices: 61066--61156 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
61056 ATAAAATAAA
*
61066 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
61088 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * *
61112 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
*
61135 TTATTTTAAAATATGAATTGAT
1 TTATTTTAAAATATGGATTGAT
61157 GCAATGTAGC
Statistics
Matches: 48, Mismatches: 18, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
22 22 0.46
23 12 0.25
24 12 0.25
25 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:62496 original size:22 final size:22
Alignment explanation
Indices: 62471--62513 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62461 TCTTTATTAG
62471 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
62493 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
62514 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:62527 original size:54 final size:54
Alignment explanation
Indices: 62463--63065 Score: 376
Period size: 54 Copynumber: 11.1 Consensus size: 54
62453 TGTAGAGGTC
62463 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
1 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
* *
62517 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT--ATAG
1 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAATAA
* *
62570 TTGTA-TAG-ATTG-ATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAA-ATA
1 TT-TATTAGTA-TGAATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATA-A
* * * * ** * * *
62629 TTAATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGA
1 TTTATTAGTA-TGAATTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATA---A
* * * * * ** *
62687 TTGATTTATTCT-AAATAATTTA--TT--AGCATGAATTGATTTATTTT-AA-AA
1 TTTA-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
* * * ** *
62735 --TA-T-GGATTG-ATTTA-TTATTGTAGTTATATAGATTGATTTATTTTAAATAA
1 TTTATTAGTA-TGAATTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAA
62785 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
1 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
*
62839 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
1 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
* * * * *
62893 TTTATTAGTATGAATTGATTTATTTT-AAATA---ATTTATTT-GTATAGATTGA
1 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTA-AATAA
* * *** ** *
62943 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAAATTAATTTATTTTAAATAA
1 TTTA--TT--AGTATGAATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAA
* * *
63005 TTTATTAGTATGTATTGATTTATTTTAAAATATTGATTTATTTATTTTAAATAA
1 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
63059 TTTATTA
1 TTTATTA
63066 TTGTAGTTGT
Statistics
Matches: 433, Mismatches: 66, Indels: 100
0.72 0.11 0.17
Matches are distributed among these distances:
43 3 0.01
44 5 0.01
45 1 0.00
46 1 0.00
48 16 0.04
49 5 0.01
50 16 0.04
51 1 0.00
52 11 0.03
53 21 0.05
54 240 0.55
55 17 0.04
56 6 0.01
57 10 0.02
58 43 0.10
59 17 0.04
60 3 0.01
62 14 0.03
63 3 0.01
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
Found at i:62539 original size:18 final size:18
Alignment explanation
Indices: 62516--62563 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
62506 ATTTTAAATA
*
62516 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
62534 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
62556 ATTTATTA
1 ATTTATTA
62564 TTATAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:62618 original size:32 final size:32
Alignment explanation
Indices: 62577--62953 Score: 176
Period size: 32 Copynumber: 12.5 Consensus size: 32
62567 TAGTTGTATA
62577 GATTGATTTATTTTAAATAATTTATTAATATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
62609 GATTGATTTATTTT-AA-AA--TA-T--TA--
1 GATTGATTTATTTTAAATAATTTATTAATATG
*
62632 -ATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
62663 GATTGATTTA-TTT---T-A---A--AATATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
* **
62685 GATTGATTTATTCTAAATAATTTATTAGCATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
* ** *
62717 AATTGATTTATTTTAAA-ATATGGATTGAT-T-
1 GATTGATTTATTTTAAATA-ATTTATTAATATG
* * * * * * *
62747 TATT-ATTGTA-GTTATATAGATTGATTTATTTT
1 GATTGATT-TATTTTAAATA-ATTTATTAATATG
* * * * *
62779 AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATG
1 GATTGATTTATT--T-T-AAATAATTTA--TT--AATATG
*
62819 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
62851 GATTGATTTA-TTT---T-A---A--AATATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
*
62873 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAATATG
* ** *
62905 AATTGATTTATTTTAAATAATTTATTTGTATA
1 GATTGATTTATTTTAAATAATTTATTAATATG
62937 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
62954 ATATGGATTG
Statistics
Matches: 261, Mismatches: 39, Indels: 90
0.67 0.10 0.23
Matches are distributed among these distances:
22 43 0.16
23 7 0.03
24 4 0.02
25 2 0.01
26 4 0.02
27 6 0.02
28 4 0.02
29 9 0.03
30 18 0.07
31 11 0.04
32 116 0.44
33 3 0.01
34 2 0.01
35 1 0.00
36 13 0.05
37 3 0.01
38 3 0.01
40 12 0.05
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAATATG
Found at i:62628 original size:22 final size:22
Alignment explanation
Indices: 62603--62647 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
62593 ATAATTTATT
*
62603 AATATGGATTGATTTATTTTAA
1 AATATGAATTGATTTATTTTAA
*
62625 AATATTAATTGATTTATTTTAA
1 AATATGAATTGATTTATTTTAA
62647 A
1 A
62648 TAATTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AATATGAATTGATTTATTTTAA
Found at i:62640 original size:40 final size:40
Alignment explanation
Indices: 62516--62642 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 40
62506 ATTTTAAATA
* **
62516 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTAATATGGATTGATTTATTTTAAAATATTAATTG
* * * * * *
62556 ATTTATTATTATAGTTGTATAGATTGA-TTT---ATTTTAAATA
1 ATTTATTA--ATA--TGGATTGATTTATTTTAAAATATTAATTG
62596 ATTTATTAATATGGATTGATTTATTTTAAAATATTAATTG
1 ATTTATTAATATGGATTGATTTATTTTAAAATATTAATTG
62636 ATTTATT
1 ATTTATT
62643 TTAAATAATT
Statistics
Matches: 64, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
36 9 0.14
37 3 0.05
38 3 0.05
40 35 0.55
42 2 0.03
43 3 0.05
44 9 0.14
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (40 bp):
ATTTATTAATATGGATTGATTTATTTTAAAATATTAATTG
Found at i:62650 original size:134 final size:130
Alignment explanation
Indices: 62463--63065 Score: 637
Period size: 134 Copynumber: 4.5 Consensus size: 130
62453 TGTAGAGGTC
* * **
62463 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
1 TTTATTAATATGGATTGATTTATTTTAAAATATTAATTGATTTATTTTAAATAATTTATTAGTAT
* *
62528 GGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAGTTGTA-TAG-ATTGATTTATTTT
66 GGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAATT-TATTAGCATTGATTGA-TTT
62591 AAAT
129 --AT
62595 AATTTATTAATATGGATTGATTTATTTTAAAATATTAATTGATTTATTTTAAATAATTTATTAGT
1 --TTTATTAATATGGATTGATTTATTTTAAAATATTAATTGATTTATTTTAAATAATTTATTAGT
* *
62660 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTCTAAATAATTTATTAGCA-TGAATTGAT
64 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTAT-TATAATTTATTAGCATTG-ATTGAT
62724 TTAT
127 TTAT
* * **
62728 TTTA-AAATATGGATTGATTTATTATTGTAGTTATATAGATTGATTTATTTTAAATAATTTATTA
1 TTTATTAATATGGATTGATTTATT-TT-AAAATAT-TA-ATTGATTTATTTTAAATAATTTATTA
* * *
62792 GTATGAATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAATAATTTATTAGTATGGATTG
62 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT--ATAATTTATTAGCATTGATTG
62856 ATTTAT
125 ATTTAT
*
62862 TTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAAT
1 TTTATTAATATGGATTGATTTATTTT--A-AA---A-TA-T-T-AATTGATTTATTTTAAATAAT
* * * * *
62926 TTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTA-TA-AATT
56 TTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAATT-TATTAGCATT
* *
62989 AATTTATTTTAAAT
120 GATTGA-TTT--AT
* * * *
63003 AATTTATTAGTATGTATTGATTTATTTTAAAATATTGATTTATTTATTTTAAATAATTTATTA
1 --TTTATTAATATGGATTGATTTATTTTAAAATATTAATTGATTTATTTTAAATAATTTATTA
63066 TTGTAGTTGT
Statistics
Matches: 407, Mismatches: 35, Indels: 54
0.82 0.07 0.11
Matches are distributed among these distances:
130 18 0.04
131 6 0.01
132 4 0.01
133 7 0.02
134 233 0.57
135 16 0.04
136 6 0.01
137 2 0.00
138 7 0.02
139 11 0.03
140 67 0.16
141 7 0.02
142 1 0.00
143 4 0.01
144 18 0.04
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (130 bp):
TTTATTAATATGGATTGATTTATTTTAAAATATTAATTGATTTATTTTAAATAATTTATTAGTAT
GGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAATTTATTAGCATTGATTGATTTAT
Found at i:62684 original size:22 final size:22
Alignment explanation
Indices: 62659--62701 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62649 AATTTATTAG
*
62659 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTCTAAAA
62681 TATGGATTGATTTATTCTAAA
1 TATGGATTGATTTATTCTAAA
62702 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTTATTCTAAAA
Found at i:62780 original size:188 final size:188
Alignment explanation
Indices: 62463--62921 Score: 828
Period size: 188 Copynumber: 2.4 Consensus size: 188
62453 TGTAGAGGTC
*
62463 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
1 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
* *
62528 GGATTGATTTATTTTAAAATATGGATTGATTTATTATTATAGTTGTATAGATTGATTTATTTTAA
66 GAATTGATTTATTTTAAAATATGGATTGATTTATTATTATAGTTATATAGATTGATTTATTTTAA
* *
62593 ATAATTTATTAATATGGATTGATTTATTTTAAAATATTAATTGATTTATTTTAAATAA
131 ATAATTTATTAATATGAATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAA
* *
62651 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTCTAAATAATTTATTAGCAT
1 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
*
62716 GAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTATATAGATTGATTTATTTTAA
66 GAATTGATTTATTTTAAAATATGGATTGATTTATTATTATAGTTATATAGATTGATTTATTTTAA
* *
62781 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
131 ATAATTTATTAATATGAATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAA
62839 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
1 TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
62904 GAATTGATTTATTTTAAA
66 GAATTGATTTATTTTAAA
62922 TAATTTATTT
Statistics
Matches: 259, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
188 259 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (188 bp):
TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
GAATTGATTTATTTTAAAATATGGATTGATTTATTATTATAGTTATATAGATTGATTTATTTTAA
ATAATTTATTAATATGAATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAA
Found at i:62818 original size:22 final size:22
Alignment explanation
Indices: 62793--62835 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62783 AATTTATTAG
62793 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
62815 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
62836 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:62872 original size:22 final size:22
Alignment explanation
Indices: 62847--62889 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
62837 AATTTATTAG
62847 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
62869 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
62890 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:62897 original size:14 final size:14
Alignment explanation
Indices: 62878--62931 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
62868 ATATGGATTG
62878 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
62892 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
62910 ATTTATTTTAAATA
1 ATTTATTTTAAATA
62924 ATTTATTT
1 ATTTATTT
62932 GTATAGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:63061 original size:18 final size:18
Alignment explanation
Indices: 62985--63064 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 18
62975 TAGTTGTATA
*
62985 AATTAATTTATTTTAAAT
1 AATTTATTTATTTTAAAT
* **
63003 AATTTA-TTA--GTATGT
1 AATTTATTTATTTTAAAT
*
63018 -ATTGATTTATTTTAAAAT
1 AATTTATTTATTTT-AAAT
63036 ATTGATTTATTTATTTTAAAT
1 A---ATTTATTTATTTTAAAT
63057 AATTTATT
1 AATTTATT
63065 ATTGTAGTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
14 4 0.09
15 6 0.13
17 4 0.09
18 14 0.31
21 5 0.11
22 12 0.27
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTTATTTATTTTAAAT
Found at i:63137 original size:31 final size:31
Alignment explanation
Indices: 63079--63138 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
63069 TAGTTGTATG
* **
63079 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATATCAGTATTACAAAACTAA
63110 AATTATTTAAATATCAGTATTACAAAACT
1 AATTATTTAAATATCAGTATTACAAAACT
63139 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATATCAGTATTACAAAACTAA
Found at i:65976 original size:2 final size:2
Alignment explanation
Indices: 65969--66004 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
65959 ATTCATTGCT
65969 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
66005 GGCTAAACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66254 original size:14 final size:14
Alignment explanation
Indices: 66208--66245 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
66198 CGTTGGGCAT
*
66208 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
66222 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
66236 CCGAGGCCAT
1 CCGAGGCCAT
66246 TCGAGCGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:66334 original size:29 final size:29
Alignment explanation
Indices: 66301--66377 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
66291 AAGGAGCAGG
66301 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
66330 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
* *
66359 CGGAGTGCATGACGACCTA
1 AGGAGTGCATGGCGACCTA
66378 TGCTGGGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:80141 original size:20 final size:20
Alignment explanation
Indices: 80116--80157 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
80106 TTAAAGCCGC
80116 AACACGACTAAATTGAATAG
1 AACACGACTAAATTGAATAG
80136 AACACGACTAAATTGAATAG
1 AACACGACTAAATTGAATAG
80156 AA
1 AA
80158 TTAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (20 bp):
AACACGACTAAATTGAATAG
Found at i:83255 original size:22 final size:23
Alignment explanation
Indices: 83212--83258 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
83202 TTCTATCTTA
* *
83212 TTTTATATTTATACTTTTAAATT
1 TTTTATATTTATACATTAAAATT
*
83235 TTTTA-ATTTATTCATTAAAATT
1 TTTTATATTTATACATTAAAATT
83257 TT
1 TT
83259 GAATTATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTATATTTATACATTAAAATT
Found at i:83265 original size:20 final size:21
Alignment explanation
Indices: 83228--83269 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
83218 ATTTATACTT
* *
83228 TTAAATTTTTTAATTTATTCA
1 TTAAAATTTTGAATTTATTCA
83249 TTAAAATTTTGAA-TTATTCA
1 TTAAAATTTTGAATTTATTCA
83269 T
1 T
83270 GTTTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAAAATTTTGAATTTATTCA
Found at i:83302 original size:11 final size:10
Alignment explanation
Indices: 83272--83338 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
83262 TTATTCATGT
*
83272 TTTTA-ATTG
1 TTTTATATTA
83281 TTTTATATTA
1 TTTTATATTA
83291 TTTTATTATTA
1 TTTTA-TATTA
*
83302 TTTTGATATGA
1 TTTT-ATATTA
* *
83313 TGTGATATT-
1 TTTTATATTA
83322 TTTTATCATT-
1 TTTTAT-ATTA
83332 TTTTATA
1 TTTTATA
83339 AAAATAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 10 0.21
10 21 0.45
11 15 0.32
12 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.07, T:0.66
Consensus pattern (10 bp):
TTTTATATTA
Found at i:87537 original size:16 final size:16
Alignment explanation
Indices: 87507--87537 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
87497 TAATATTGAA
*
87507 ACTTGAACTCGAAAAG
1 ACTTGAACTCAAAAAG
87523 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
87538 AATTTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:95988 original size:2 final size:2
Alignment explanation
Indices: 95981--96032 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
95971 TTGTGCTTGG
95981 AT AT AT AT AT AT 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 AT AT AT AT AT AT
96023 AT AT AT AT AT
1 AT AT AT AT AT
96033 TGATTGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97479 original size:18 final size:18
Alignment explanation
Indices: 97456--97492 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
97446 GAGGAGGGGC
97456 ACCCCTCAAGAGGATCAG
1 ACCCCTCAAGAGGATCAG
97474 ACCCCTCAAGAGGATCAG
1 ACCCCTCAAGAGGATCAG
97492 A
1 A
97493 GGCTCCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCCTCAAGAGGATCAG
Found at i:102761 original size:21 final size:21
Alignment explanation
Indices: 102710--102762 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
102700 ATTATGACTA
**
102710 TCGCAATGCGATTTTTTAATT
1 TCGCAATGCGATTTTCCAATT
**
102731 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
102752 TCGCAATGCGA
1 TCGCAATGCGA
102763 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:102817 original size:20 final size:20
Alignment explanation
Indices: 102792--102906 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
102782 AATTGGGAAA
*
102792 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
102812 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
102833 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
102853 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
102873 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
102893 TTCGCAACGAGATA
1 ATCGCAACGCGATA
102907 ATACATAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:102889 original size:40 final size:40
Alignment explanation
Indices: 102790--102926 Score: 177
Period size: 41 Copynumber: 3.4 Consensus size: 40
102780 CAAATTGGGA
* *
102790 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
102830 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
102872 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
102911 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
102927 TTTCAAAGCG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 45 0.54
42 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:103133 original size:28 final size:28
Alignment explanation
Indices: 103093--103167 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
103083 CACTCTCTCA
103093 CCCATCTCCGACGAAATCCATCCCCATC
1 CCCATCTCCGACGAAATCCATCCCCATC
103121 CCCATCTCCGACGAAATCCATCCCCATC
1 CCCATCTCCGACGAAATCCATCCCCATC
*
103149 CCCATCTCCGGCGAAATCC
1 CCCATCTCCGACGAAATCC
103168 GTCTATCTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.24, C:0.49, G:0.09, T:0.17
Consensus pattern (28 bp):
CCCATCTCCGACGAAATCCATCCCCATC
Found at i:103479 original size:20 final size:20
Alignment explanation
Indices: 103430--103488 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
103420 GATTTATTCT
* **
103430 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
103450 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
103470 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
103489 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:103679 original size:25 final size:24
Alignment explanation
Indices: 103625--103679 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
103615 TGTTTATTAT
* *
103625 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
103649 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
103675 TGTTT
1 TGTTT
103680 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Done.