Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005107.1 Hibiscus syriacus cultivar Beakdansim tig00011479_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: 93050
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2958 original size:15 final size:15
Alignment explanation
Indices: 2933--2968 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2923 CTTTTATTAC
2933 CAGAAACAAATAAA-
1 CAGAAACAAATAAAG
2947 CAGAATACAAATAAAG
1 CAGAA-ACAAATAAAG
2963 CAGAAA
1 CAGAAA
2969 TCTCCCTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.67, C:0.14, G:0.11, T:0.08
Consensus pattern (15 bp):
CAGAAACAAATAAAG
Found at i:11127 original size:2 final size:2
Alignment explanation
Indices: 11120--11154 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11110 CCCACATGTA
*
11120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11155 ACACATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14157 original size:12 final size:12
Alignment explanation
Indices: 14134--14159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14124 CGGAGCCGGA
14134 GCTGGTGCCGCT
1 GCTGGTGCCGCT
14146 GCTGGTGCCGCT
1 GCTGGTGCCGCT
14158 GC
1 GC
14160 ACTTGCCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.35, G:0.42, T:0.23
Consensus pattern (12 bp):
GCTGGTGCCGCT
Found at i:21992 original size:14 final size:14
Alignment explanation
Indices: 21965--22000 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
21955 TACTATCTTA
* *
21965 TATTTATTACAAAT
1 TATTTTTTAAAAAT
21979 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
21993 TATTTTTT
1 TATTTTTT
22001 TTAAAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:23454 original size:2 final size:2
Alignment explanation
Indices: 23447--23480 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23437 GCGAGAAAGC
23447 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23481 GAACGATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30053 original size:19 final size:18
Alignment explanation
Indices: 30004--30103 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 18
29994 CACATACTTT
30004 TCATCTCAAAAAAAATTA
1 TCATCTCAAAAAAAATTA
***
30022 TCATAAAAGAAAATAAATTA
1 TCATCTCA-AAAA-AAATTA
*
30042 TCATCTCAAAAATAAATTT
1 TCATCTCAAAAA-AAATTA
30061 TCATCTCAAAAAAAATTA
1 TCATCTCAAAAAAAATTA
30079 TTTTCATCTCAAAAAAAAATTA
1 ---TCATCTC-AAAAAAAATTA
30101 TCA
1 TCA
30104 ATATTCTCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
18 10 0.15
19 29 0.43
20 11 0.16
21 7 0.10
22 11 0.16
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (18 bp):
TCATCTCAAAAAAAATTA
Found at i:30091 original size:40 final size:38
Alignment explanation
Indices: 30001--30103 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 38
29991 TTACACATAC
30001 TTTTCATCTCAAAAAAAATTATCATAAAAGAAAATAAA
1 TTTTCATCTCAAAAAAAATTATCATAAAAGAAAATAAA
* * *
30039 TTATCATCTCAAAAATAAATTTTCATCTCAAAA-AAAAT-TA
1 TTTTCATCTCAAAAA-AAATTATCA--T-AAAAGAAAATAAA
30079 TTTTCATCTCAAAAAAAAATTATCA
1 TTTTCATCTC-AAAAAAAATTATCA
30104 ATATTCTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
38 14 0.25
39 8 0.15
40 18 0.33
41 11 0.20
42 4 0.07
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (38 bp):
TTTTCATCTCAAAAAAAATTATCATAAAAGAAAATAAA
Found at i:32329 original size:36 final size:36
Alignment explanation
Indices: 32288--32366 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
32278 CGAATTAAAT
*
32288 GAGGACAGAGG-AAAATCGTTTATGCTAAACGGAGAC
1 GAGGAC-GAGGAAAAACCGTTTATGCTAAACGGAGAC
* * *
32324 GAGGACGGGGAAAAACCGTTTATGTTAAACGGGGAC
1 GAGGACGAGGAAAAACCGTTTATGCTAAACGGAGAC
*
32360 GGGGACG
1 GAGGACG
32367 GGTTTGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.08
36 34 0.92
ACGTcount: A:0.34, C:0.14, G:0.37, T:0.15
Consensus pattern (36 bp):
GAGGACGAGGAAAAACCGTTTATGCTAAACGGAGAC
Found at i:32367 original size:36 final size:36
Alignment explanation
Indices: 32299--32368 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
32289 AGGACAGAGG
*
32299 AAAATCGTTTATGCTAAACGGAGACGAGGACGGGGA
1 AAAACCGTTTATGCTAAACGGAGACGAGGACGGGGA
* * *
32335 AAAACCGTTTATGTTAAACGGGGACGGGGACGGG
1 AAAACCGTTTATGCTAAACGGAGACGAGGACGGG
32369 TTTGATAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.36, T:0.17
Consensus pattern (36 bp):
AAAACCGTTTATGCTAAACGGAGACGAGGACGGGGA
Found at i:32430 original size:4 final size:4
Alignment explanation
Indices: 32421--32556 Score: 71
Period size: 4 Copynumber: 37.0 Consensus size: 4
32411 AAATAATTAT
* * * *
32421 TATA TATA TATA TATA TATA TA-A TAT- TA-A TAAA TTTA -ATT TAAA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
32465 T-TA -AAA TATA TATA TA-A TATT TATA TATT TAT- TTTA AAT- TA-A
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
32507 TATA TATA TATA TATA -ATA TTTA TATA TTTA -ATT TAAA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
32553 TATA
1 TATA
32557 CCCGACCCGA
Statistics
Matches: 96, Mismatches: 24, Indels: 24
0.67 0.17 0.17
Matches are distributed among these distances:
3 22 0.23
4 74 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:32552 original size:42 final size:41
Alignment explanation
Indices: 32425--32556 Score: 200
Period size: 38 Copynumber: 3.3 Consensus size: 41
32415 AATTATTATA
* *
32425 TATATATATATATATATAATATTAATAAATTTAATTTAAAT
1 TATATATATATATATATAATATTTATATATTTAATTTAAAT
*
32466 TA-A-A-ATATATATATAATATTTATATATTTATTTTAAAT
1 TATATATATATATATATAATATTTATATATTTAATTTAAAT
32504 TAATATATATATATATATAATATTTATATATTTAATTTAAA-
1 T-ATATATATATATATATAATATTTATATATTTAATTTAAAT
32545 TATATATATATA
1 TATATATATATA
32557 CCCGACCCGA
Statistics
Matches: 83, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
38 32 0.39
39 2 0.02
40 13 0.16
41 4 0.05
42 32 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (41 bp):
TATATATATATATATATAATATTTATATATTTAATTTAAAT
Found at i:35310 original size:17 final size:17
Alignment explanation
Indices: 35253--35314 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
35243 TATCTTTAAA
* *
35253 TTTATATATTTTAATTTT
1 TTTA-ATATTTTTATATT
*
35271 TTTTATATTTTTA-ATT
1 TTTAATATTTTTATATT
***
35287 AAAAATATTTTTATATT
1 TTTAATATTTTTATATT
35304 TTTAATATTTT
1 TTTAATATTTT
35315 ATAAATTTAT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
16 11 0.33
17 19 0.58
18 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATATTTTTATATT
Found at i:37022 original size:31 final size:31
Alignment explanation
Indices: 36981--37045 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
36971 ATTTATTATT
* *
36981 TAATAGTTTATTTTAATTATCTAAAAATAAA
1 TAATAATTTATTTTAATCATCTAAAAATAAA
*
37012 TAATAATTTATTTTAATCATCTAAAAGTAAA
1 TAATAATTTATTTTAATCATCTAAAAATAAA
37043 TAA
1 TAA
37046 AGTTGATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
TAATAATTTATTTTAATCATCTAAAAATAAA
Found at i:38580 original size:31 final size:30
Alignment explanation
Indices: 38539--38599 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
38529 GTTATATGAA
* *
38539 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATATGATAAAAGTATGG-AAATGAAATGT
*
38570 TTATATGATAAAAGTATGGAAATGATATGT
1 TTATATGATAAAAGTATGGAAATGAAATGT
38600 CCATGCGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (30 bp):
TTATATGATAAAAGTATGGAAATGAAATGT
Found at i:45334 original size:31 final size:30
Alignment explanation
Indices: 45298--45368 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
45288 GTTATATGAA
45298 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTATGG-AAATGAAATGT
*
45329 TTATGTGATAAAGGTATGGAAATGATATGT
1 TTATGTGATAAAGGTATGGAAATGAAATGT
* *
45359 CTATGCGATA
1 TTATGTGATA
45369 TAAATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
TTATGTGATAAAGGTATGGAAATGAAATGT
Found at i:45582 original size:24 final size:25
Alignment explanation
Indices: 45546--45604 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
45536 ATTCTTAAGG
* *
45546 AATTTATATGTGGTCCTTCGGGACA
1 AATTTCTACGTGGTCCTTCGGGACA
45571 AA-TTCTACGTGGTCCTTCGGGACA
1 AATTTCTACGTGGTCCTTCGGGACA
45595 AATTTCTACG
1 AATTTCTACG
45605 CGGCACTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (25 bp):
AATTTCTACGTGGTCCTTCGGGACA
Found at i:45613 original size:25 final size:24
Alignment explanation
Indices: 45561--45641 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 24
45551 ATATGTGGTC
*
45561 CTTCGGGACAAATTCTACGTGGTC-
1 CTTCGGGACAAATTCTACGCGG-CA
45585 CTTCGGGACAAATTTCTACGCGGCA
1 CTTCGGGACAAA-TTCTACGCGGCA
* * *
45610 CTTCGGTGCAAAAACTCTACGCTGCA
1 CTTCGG-G-ACAAATTCTACGCGGCA
45636 CTTCGG
1 CTTCGG
45642 TGCAATTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.27
25 15 0.31
26 17 0.35
27 4 0.08
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.26
Consensus pattern (24 bp):
CTTCGGGACAAATTCTACGCGGCA
Found at i:46477 original size:10 final size:10
Alignment explanation
Indices: 46446--46478 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
46436 ATTTTTTTAG
46446 AAATATATAA
1 AAATATATAA
*
46456 AAATA-ATTA
1 AAATATATAA
46465 AAATATATAA
1 AAATATATAA
46475 AAAT
1 AAAT
46479 CTAATAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATATATAA
Found at i:47101 original size:7 final size:7
Alignment explanation
Indices: 47089--47118 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
47079 TAAATTTAAA
47089 AAAACTC
1 AAAACTC
47096 AAAACTC
1 AAAACTC
47103 AAAACTC
1 AAAACTC
*
47110 AAAAATC
1 AAAACTC
47117 AA
1 AA
47119 CTTCTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAACTC
Found at i:47304 original size:16 final size:16
Alignment explanation
Indices: 47280--47313 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47270 TTTTTACATG
47280 AACTAAAATAATATTA
1 AACTAAAATAATATTA
* *
47296 AACTGAAATTATATTA
1 AACTAAAATAATATTA
47312 AA
1 AA
47314 TATATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
AACTAAAATAATATTA
Found at i:48012 original size:15 final size:15
Alignment explanation
Indices: 47992--48021 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47982 TTTAAGAATT
*
47992 TAAAATTAAATATTA
1 TAAAATAAAATATTA
48007 TAAAATAAAATATTA
1 TAAAATAAAATATTA
48022 GAAGAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATAAAATATTA
Found at i:51791 original size:19 final size:22
Alignment explanation
Indices: 51755--51799 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
51745 AATTTTTTCA
51755 TAATAATAATTATAATTATTAT
1 TAATAATAATTATAATTATTAT
*
51777 TAAT-ATAATATATTATTATTAT
1 TAATAATAAT-TATAATTATTAT
51799 T
1 T
51800 TATTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATAATAATTATAATTATTAT
Found at i:53439 original size:122 final size:119
Alignment explanation
Indices: 53288--53529 Score: 283
Period size: 122 Copynumber: 2.0 Consensus size: 119
53278 TATTTTAATC
* * * *
53288 TTGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGC-AGTCTTAAAACAACTGGATGT
1 TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCTA-TCTTAAAACAACTAGAAGT
* *
53350 CCATTTTCTAAATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATATTAA
65 -CATTTTCT-AATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATAAATTAA
* * ** *
53409 TTGTTTTAATTATTTATTTATTTTTTAATATCGAGGAAAAGAGCTATCTTAAGGCACCTAGAAGT
1 TTGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGT
* **
53474 CATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAA
65 CATTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAA
53529 T
1 T
53530 ATATATTTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
120 12 0.12
121 17 0.17
122 43 0.42
123 10 0.10
124 20 0.19
125 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (119 bp):
TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTC
ATTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAA
Found at i:59399 original size:7 final size:7
Alignment explanation
Indices: 59387--59502 Score: 70
Period size: 7 Copynumber: 14.3 Consensus size: 7
59377 TCCAGCAAAG
59387 AAAGAAA
1 AAAGAAA
59394 AAAGAAA
1 AAAGAAA
59401 AAAGATAAAA
1 AAAG---AAA
59411 AAAGAAA
1 AAAGAAA
59418 AATGAGGAAA
1 AA--A-GAAA
*
59428 AAGGAAA
1 AAAGAAA
59435 AAAGATGAA
1 AAAGA--AA
59444 AAAGGAAA
1 AAA-GAAA
59452 AAAGATGAA
1 AAAGA--AA
59461 AAAGGAAA
1 AAA-GAAA
59469 AATGAGAAA
1 AA--AGAAA
59478 AAAGAAAA
1 AAAG-AAA
*
59486 AAAGGGAA
1 AAA-GAAA
59494 AAAGAAA
1 AAAGAAA
59501 AA
1 AA
59503 GGGGAGAAAT
Statistics
Matches: 89, Mismatches: 4, Indels: 32
0.71 0.03 0.26
Matches are distributed among these distances:
7 33 0.37
8 20 0.22
9 18 0.20
10 18 0.20
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:59413 original size:17 final size:17
Alignment explanation
Indices: 59390--59502 Score: 131
Period size: 17 Copynumber: 6.8 Consensus size: 17
59380 AGCAAAGAAA
59390 GAAAAAAGAAAAAAGAT
1 GAAAAAAGAAAAAAGAT
* * *
59407 AAAAAAAGAAAAATGAG
1 GAAAAAAGAAAAAAGAT
*
59424 GAAAAAGGAAAAAAGAT
1 GAAAAAAGAAAAAAGAT
*
59441 GAAAAAGGAAAAAAGAT
1 GAAAAAAGAAAAAAGAT
* *
59458 GAAAAAGGAAAAATGA-
1 GAAAAAAGAAAAAAGAT
*
59474 GAAAAAAGAAAAAA-AG
1 GAAAAAAGAAAAAAGAT
*
59490 GGAAAAAGAAAAA
1 GAAAAAAGAAAAA
59503 GGGGAGAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
15 1 0.01
16 24 0.29
17 59 0.70
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (17 bp):
GAAAAAAGAAAAAAGAT
Found at i:59487 original size:51 final size:49
Alignment explanation
Indices: 59392--59502 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 49
59382 CAAAGAAAGA
* * *
59392 AAAAAGAAAAAAGATAAAAAAAGAAAAATGAGGAAAAAGGAAAAAAGATG
1 AAAAAGAAAAAAGATAAAAAAAGAAAAATGAGAAAAAAGAAAAAAAG-GG
* *
59442 AAAAAGGAAAAAAGATGAAAAAGGAAAAATGAGAAAAAAGAAAAAAAGGG
1 AAAAA-GAAAAAAGATAAAAAAAGAAAAATGAGAAAAAAGAAAAAAAGGG
59492 AAAAAGAAAAA
1 AAAAAGAAAAA
59503 GGGGAGAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 6 0.11
50 11 0.20
51 38 0.69
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.05
Consensus pattern (49 bp):
AAAAAGAAAAAAGATAAAAAAAGAAAAATGAGAAAAAAGAAAAAAAGGG
Found at i:61862 original size:114 final size:114
Alignment explanation
Indices: 61662--61881 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
61652 CATGTTCTCG
* * * * *
61662 TAGTAGAAATAAGGAGGCCCAACAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTT
1 TAGTAGAAATAAAGAGACCCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* *
61727 GATAGGAACCCTTAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GATAAGAACCCTAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
*
61776 TAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAAGAGACCCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
*
61841 GGTAAGAATCCC-AAAACCAATCATTGGATTTGAAAGATGAA
66 GATAAGAA-CCCTAAAACCAATCATTGGATTTGAAAGATGAA
61882 CATGATCATC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 93 0.97
115 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAAGAGACCCAACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
GATAAGAACCCTAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
Found at i:64099 original size:50 final size:52
Alignment explanation
Indices: 63958--64111 Score: 170
Period size: 50 Copynumber: 2.9 Consensus size: 52
63948 TGAGAAATCT
* *
63958 GAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATTT
1 GAGCAGAAGCCACAGAAAA-GATGAATGTGTTGTCAAATGTTTTACGAACA-TC
* * * * *
64012 GAGCAGAAGCTACAAGAAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATC-TC
1 GAGCAGAAGCCAC-AGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATC
* *
64063 GA-CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 GAGCAGAAGCCACA-GAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
64112 CAGTGATTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 35 0.42
51 5 0.06
53 2 0.02
54 35 0.42
55 5 0.06
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (52 bp):
GAGCAGAAGCCACAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATC
Found at i:65328 original size:76 final size:76
Alignment explanation
Indices: 65184--65676 Score: 844
Period size: 76 Copynumber: 6.5 Consensus size: 76
65174 CTATTTCCCA
65184 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
65249 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
65261 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
65326 AGCCTTAGGGT
66 AGCCTTAGGGT
*
65337 CATCTGTAAGTCCTGCAGCGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
65402 AGCCTTAGGGT
66 AGCCTTAGGGT
*
65413 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
65478 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
65490 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
65555 A-CCTTCGGGT
66 AGCCTTAGGGT
*
65565 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
65630 AAACCTTCGGGT
65 AAGCCTTAGGGT
* * * *
65642 CATCTGTAAGCCCTTCTGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
65677 CATTTTTATC
Statistics
Matches: 399, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
75 69 0.17
76 185 0.46
77 145 0.36
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:65644 original size:229 final size:229
Alignment explanation
Indices: 65184--65676 Score: 862
Period size: 229 Copynumber: 2.2 Consensus size: 229
65174 CTATTTCCCA
*
65184 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
* *
65249 AAGCCTTAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
65314 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGCGCATGATGTTTCCAAAAAGCCTT
131 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGCGCATGATGTTTCCAAAAAGCCTT
*
65379 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
196 CGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGT
65413 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
65478 AAGCCTTAGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
65543 TGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
131 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGCGCATGATGTTTCCAAAAAGCCTT
*
65607 CGGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
196 CGGGAGCTTTTTGATGTTTTC-AAAACCTTAGGGT
* * * *
65642 CATCTGTAAGCCCTTCTGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
65677 CATTTTTATC
Statistics
Matches: 251, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 69 0.27
229 182 0.73
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (229 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGCGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGT
Found at i:65816 original size:3 final size:3
Alignment explanation
Indices: 65804--65849 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
65794 CATAATAATA
* *
65804 ATT ATA ATT ATT ATT AAT A-T ATT A-T ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
65848 AT
1 AT
65850 ATATATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:65831 original size:16 final size:16
Alignment explanation
Indices: 65812--65861 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
65802 TAATTATAAT
65812 TATTATTAATATATTA
1 TATTATTAATATATTA
65828 TATTATT-AT-TATT-
1 TATTATTAATATATTA
65841 TATTATTATATATATATA
1 TATTATTA-ATATAT-TA
65859 TAT
1 TAT
65862 ATATATTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.24
14 4 0.14
15 4 0.14
16 10 0.34
17 1 0.03
18 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATTAATATATTA
Found at i:65844 original size:13 final size:14
Alignment explanation
Indices: 65806--65868 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
65796 TAATAATAAT
*
65806 TATAATTATTATTAA
1 TATATTTATTATT-A
65821 TATATTATATTATTA
1 TATATT-TATTATTA
65836 T-TATTTATTATTA
1 TATATTTATTATTA
*
65849 TATATATA-TATATA
1 TATATTTATTAT-TA
65863 TATATT
1 TATATT
65869 ACAAATTACA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.29
14 16 0.38
15 7 0.17
16 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATTTATTATTA
Found at i:67458 original size:20 final size:19
Alignment explanation
Indices: 67433--67474 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
67423 CTATTTTATA
67433 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
67453 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
67472 AAT
1 AAT
67475 ATCGAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:67470 original size:120 final size:119
Alignment explanation
Indices: 67327--67566 Score: 288
Period size: 120 Copynumber: 2.0 Consensus size: 119
67317 TATTTTAATC
* * * *
67327 TTGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAATGA-CAGTCTTAAAACAACTGGATGTC
1 TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-
* *
67390 CATTTTCTAAATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAA
65 CATTTTCT-AATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATAAATTAA
* * * ** *
67446 TTGTTTTAATTATTTATTTATTTTTTAATATCGAGGAAAAGAGCTGTCTTAAGGCACCTAGAAGT
1 TTGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT
* **
67511 CATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAA
65 CATTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAA
67566 T
1 T
67567 ATATATTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
119 18 0.18
120 53 0.52
121 15 0.15
122 16 0.16
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (119 bp):
TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
ATTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAA
Found at i:75383 original size:11 final size:11
Alignment explanation
Indices: 75353--75386 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
75343 CGATTTACAC
75353 TGTTTTTTTACT
1 TGTTTTTTT-CT
75365 TG-TTTTTTCT
1 TGTTTTTTTCT
75375 TGTTTTTTTCT
1 TGTTTTTTTCT
75386 T
1 T
75387 CAAAAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 15 0.71
12 2 0.10
ACGTcount: A:0.03, C:0.09, G:0.09, T:0.79
Consensus pattern (11 bp):
TGTTTTTTTCT
Found at i:75928 original size:132 final size:133
Alignment explanation
Indices: 75714--76140 Score: 556
Period size: 132 Copynumber: 3.2 Consensus size: 133
75704 TGACAATATT
* * * * *
75714 GATCCACCTCCTTCTGTGATGGAAT-GAATATA-ATGTCAGTGTTGATCTACATCCTTCTGTGAT
1 GATCCACCTCATTCTGTGATGGAATCGAACA-AGATGTCAGTGCTGATCTACCTTCTTCTGTGAT
* * * *
75777 AGAATCGAGCAAAATGTTGATGTTGATCCAACTCCTTCTGTGATGGATTTGAGTG-AAATAAAAA
65 AGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAA
75841 TGTC
130 TGTC
*
75845 GATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCAGTGCTGATCTACCTTATTCTGTGATA
1 GATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCAGTGCTGATCTACCTTCTTCTGTGATA
* * * * **
75910 GAATTGAGCTAAAGGTTGACACTGATCCAACTATTTCTGTGATGGATTTGAGCGAAAATAAAAAA
66 GAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAAT-AAAAA
75975 TGTC
130 TGTC
* * * * * *
75979 AATCCACCTCATTTTGTGATGGAATCAAACGAGATGTCAATGCTGATCTACC-TCCTCTGTGATA
1 GATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCAGTGCTGATCTACCTTCTTCTGTGATA
* * *
76043 GAATCGAGCAAAAAGTTGACGCTGATCTAACTCCTTCTGCGATGAATTTGAGCGAAAATAAAAAT
66 GAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAAT
*
76108 GTT
131 GTC
* *
76111 GATCCACCTCCTTCTGTGATTGAATCGAAC
1 GATCCACCTCATTCTGTGATGGAATCGAAC
76141 CAAGGTTAAA
Statistics
Matches: 255, Mismatches: 37, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
131 25 0.10
132 110 0.43
133 64 0.25
134 56 0.22
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (133 bp):
GATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCAGTGCTGATCTACCTTCTTCTGTGATA
GAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAAT
GTC
Found at i:77250 original size:31 final size:31
Alignment explanation
Indices: 77214--77368 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
77204 CCCGAAGGAT
* *
77214 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
77245 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
77276 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
77307 CAGTCCATATG-TCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
77337 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
77368 C
1 C
77369 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 30 0.27
31 82 0.73
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:77354 original size:61 final size:62
Alignment explanation
Indices: 77214--77368 Score: 242
Period size: 61 Copynumber: 2.5 Consensus size: 62
77204 CCCGAAGGAT
* * *
77214 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
77276 CAGTCCGTATGTTCCGAAGAACATAGGTAAACAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
77337 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 CAGTCCATATGTTCCGAAGAACATAGGTAAAC
77369 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
61 47 0.55
62 38 0.44
63 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:78159 original size:21 final size:21
Alignment explanation
Indices: 78129--78173 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
78119 ATTCTGTCGT
* *
78129 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
78150 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
78171 TTG
1 TTG
78174 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:81191 original size:31 final size:31
Alignment explanation
Indices: 81153--81308 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
81143 CCCGAAGGAC
* * *
81153 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
81184 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
81215 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
81246 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
81277 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
81308 C
1 C
81309 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:82115 original size:20 final size:21
Alignment explanation
Indices: 82075--82118 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
82065 ATTCTGTCGT
*
82075 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
82096 TTGAATGGGTA-CGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
82116 TTG
1 TTG
82119 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:83235 original size:42 final size:41
Alignment explanation
Indices: 83106--83235 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 41
83096 ATGTTGAAAA
* * * * *
83106 CATCATGCCCAAAGGTCTTATGGATGACCCGAAGGTCTTAT
1 CATCATGCTCAAAAGACTTATAGATGACCCGAAGGACTTAT
* * * *
83147 CATCTTACTCGAAAA-ACTTATAGATGACCCGAAGGATTTAAG
1 CATCATGCTC-AAAAGACTTATAGATGACCCGAAGGACTT-AT
*
83189 CATCATGCTCAAAAGACTTACT-GATGGCCCGAAGGACTTACT
1 CATCATGCTCAAAAGACTTA-TAGATGACCCGAAGGACTTA-T
83231 CATCA
1 CATCA
83236 AGAAACCCTT
Statistics
Matches: 70, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
41 32 0.46
42 37 0.53
43 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CATCATGCTCAAAAGACTTATAGATGACCCGAAGGACTTAT
Found at i:83376 original size:43 final size:43
Alignment explanation
Indices: 83272--83527 Score: 424
Period size: 43 Copynumber: 6.0 Consensus size: 43
83262 TTCTTAGTTG
* * * *
83272 TCATCAAGGAACCCCTAAATATCACATTGGTCCCTCTAG-TTG
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
* *
83314 TCATCAAAGAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
*
83357 TTATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
83400 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
*
83443 TCATCAAAGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
*
83486 TCATCAAGGAACCCTTACATATCACGTTGGTCCCTCAAGCTT
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTT
83528 AGTTTCTTAT
Statistics
Matches: 201, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
42 35 0.17
43 166 0.83
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.27
Consensus pattern (43 bp):
TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
Found at i:85535 original size:10 final size:10
Alignment explanation
Indices: 85522--85552 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
85512 CTCTTTTTTA
85522 TTTTTTATTT
1 TTTTTTATTT
85532 TTTTTTATTT
1 TTTTTTATTT
85542 TTTTCTTATTT
1 TTTT-TTATTT
85553 CTTTGTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:85561 original size:13 final size:11
Alignment explanation
Indices: 85513--85563 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
85503 CGGTTTTCTC
85513 TCTT-TTTTATT
1 TCTTATTTT-TT
*
85524 TTTTATTTTTT
1 TCTTATTTTTT
85535 T-TTATTTTTT
1 TCTTATTTTTT
85545 TCTTATTTCTTT
1 TCTTATTT-TTT
85557 GTCTTAT
1 -TCTTAT
85564 CAACTTGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 10 0.29
11 12 0.34
12 7 0.20
13 6 0.17
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (11 bp):
TCTTATTTTTT
Found at i:90935 original size:14 final size:15
Alignment explanation
Indices: 90913--90959 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
90903 TTATAGGTAA
*
90913 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
90927 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
90942 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
90958 TT
1 TT
90960 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:92535 original size:64 final size:66
Alignment explanation
Indices: 92398--92557 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 66
92388 GAATTAAATT
* * * *
92398 AAACATCGAATACATTTCAT-CCTCGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATG
1 AAACATCGAATGCATTTAATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATG
92461 A
66 A
* * * * *
92462 AAACATCGAATGTATTTGATGCATCGATGCACCAT-CCATGCATCGATGCACTCTGGCTATTT-T
1 AAACATCGAATGCATTTAATGCATCGATGCACCATACCATGCACCGATGCACTCAGGAT-TTTAT
92525 G-
65 GA
*
92526 AAACATCGAATGCACTTAATGCATCGATGCAC
1 AAACATCGAATGCATTTAATGCATCGATGCAC
92558 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 46 0.56
65 30 0.37
66 6 0.07
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (66 bp):
AAACATCGAATGCATTTAATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATG
A
Done.