Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001407.1 Hibiscus syriacus cultivar Beakdansim tig00002744_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: 71090
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:16474 original size:16 final size:16
Alignment explanation
Indices: 16453--16491 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16443 GGTATTACCC
*
16453 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
*
16469 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
16485 GACCTGT
1 GACCTGT
16492 AATTGACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:16667 original size:18 final size:17
Alignment explanation
Indices: 16640--16675 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
16630 TACTTTTTGA
*
16640 AATTTAATTTTTATATT
1 AATTTAATTTGTATATT
16657 AATTATAATTTGTATATT
1 AATT-TAATTTGTATATT
16675 A
1 A
16676 TAAATTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATTTAATTTGTATATT
Found at i:17460 original size:31 final size:30
Alignment explanation
Indices: 17422--17607 Score: 128
Period size: 31 Copynumber: 5.8 Consensus size: 30
17412 TATAATTTGT
*
17422 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
*
17453 AATTAATATTAATATAAATTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
* *
17483 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAACTATAGTT-ATAA
*
17519 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAACTATAG-TTATAA
*
17548 ACTATATACTATATTTAATATAAATTATAGTTA-AGA
1 A--AT-TA--ATA-TTAATATAAACTATAGTTATA-A
*
17584 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAACTATA
17608 TAGCACATTA
Statistics
Matches: 126, Mismatches: 10, Indels: 38
0.72 0.06 0.22
Matches are distributed among these distances:
29 10 0.08
30 8 0.06
31 47 0.37
32 7 0.06
33 4 0.03
34 9 0.07
35 25 0.20
36 9 0.07
37 7 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:17502 original size:14 final size:14
Alignment explanation
Indices: 17485--17546 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
17475 ATGTTATAAA
17485 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
17499 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
17513 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
17528 TAATATAGTATAGT
1 TTATATAGTATAGT
17542 TTATA
1 TTATA
17547 AACTATATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:17512 original size:66 final size:67
Alignment explanation
Indices: 17433--17608 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 67
17423 ATTAATATTA
* * *
17433 ATATAAAATATAGTCTATAAAATTAATATTAATATAAATTATATG-TTATAAATTATATAGTATA
1 ATATAAAATATAGT-TATAAAATTAATATTAATATAAACTATATGTTTATAAACTATATACTATA
17497 GTT
65 GTT
* * *
17500 -TATAAACTATAGTTAATATAATTAATATTAATAT--AGTATA-GTTTATAAACTATATACTATA
1 ATATAAAATATAGTT-ATAAAATTAATATTAATATAAACTATATGTTTATAAACTATATACTATA
*
17561 TTT
65 GTT
* *
17564 AATATAAATTATAGTTA-AGATAATTAACATTAATATAAACTATAT
1 -ATATAAAATATAGTTATA-A-AATTAATATTAATATAAACTATAT
17609 AGCACATTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
63 1 0.01
64 25 0.28
65 2 0.02
66 57 0.63
68 5 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (67 bp):
ATATAAAATATAGTTATAAAATTAATATTAATATAAACTATATGTTTATAAACTATATACTATAG
TT
Found at i:17536 original size:43 final size:41
Alignment explanation
Indices: 17487--17578 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 41
17477 GTTATAAATT
*
17487 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATATAATTAATATAA
* *
17530 ATATAGTATAGTTTATAAACTATATACTATATTTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATAATTAATATAA
17571 ATTATAGT
1 A-TATAGT
17579 TAAGATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 15 0.33
42 6 0.13
43 24 0.53
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (41 bp):
ATATAGTATAGTTTATAAACTATATAATATAATTAATATAA
Found at i:17629 original size:132 final size:131
Alignment explanation
Indices: 17393--17642 Score: 294
Period size: 132 Copynumber: 1.9 Consensus size: 131
17383 TTTTTTACTT
** * *
17393 ATATTAATATAATATAGTTTATAATTTGTAATTAATATTAATATAAAATATAGTCTATAAAATTA
1 ATATTAATATAATATAGTTTATAAACTATAACTAATATTAATATAAAATATAGTCTATAAAATTA
* * ** *
17458 ATATTAATATAAATTATATGTTATAAATTATATAGTATAGTTTATAAACTATAGTTAATATAATT
66 ACATTAATATAAACTATATGACATAAATTATATACTATAGTTTATAAACTATAGTTAATATAATT
17523 A
131 A
* *
17524 ATATTAATATAGTATAGTTTATAAACTATATACT-ATATTTAATATAAATTATAGT-TA-AGATA
1 ATATTAATATAATATAGTTTATAAACTATA-ACTAATA-TTAATATAAAATATAGTCTATA-A-A
* *
17586 ATTAACATTAATATAAACTATATAGCACATTAA-TATA-ACTATAGTTTATAAATTATA
62 ATTAACATTAATATAAACTATAT-G-ACATAAATTATATACTATAGTTTATAAACTATA
17643 TACTATATGT
Statistics
Matches: 100, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
130 1 0.01
131 32 0.32
132 58 0.58
133 5 0.05
134 4 0.04
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (131 bp):
ATATTAATATAATATAGTTTATAAACTATAACTAATATTAATATAAAATATAGTCTATAAAATTA
ACATTAATATAAACTATATGACATAAATTATATACTATAGTTTATAAACTATAGTTAATATAATT
A
Found at i:17636 original size:66 final size:63
Alignment explanation
Indices: 17479--17642 Score: 161
Period size: 66 Copynumber: 2.5 Consensus size: 63
17469 AATTATATGT
* * * * * * *
17479 TATAAATTATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGTATAGTT
1 TATAAACTATATACTATAGTTTATAAATTATAGTTAAGATAATTAACATTAATATAG-ATACTA
*
17543 TATAAACTATATACTATATTTAATATAAATTATAGTTAAGATAATTAACATTAATATA-A-ACTA
1 TATAAACTATATACTATAGTT--TATAAATTATAGTTAAGATAATTAACATTAATATAGATACTA
*
17606 TATAGCACATTAATATAACTATAGTTTATAAATTATA
1 TATA--A-ACT-ATAT-ACTATAGTTTATAAATTATA
17643 TACTATATGT
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
63 6 0.07
64 19 0.23
65 1 0.01
66 45 0.54
67 4 0.05
68 8 0.10
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (63 bp):
TATAAACTATATACTATAGTTTATAAATTATAGTTAAGATAATTAACATTAATATAGATACTA
Found at i:17647 original size:21 final size:21
Alignment explanation
Indices: 17618--17671 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
17608 TAGCACATTA
*
17618 ATATAACTATA-GTTTATAAATT
1 ATAT-ACTATATG-TTATAAAGT
17640 ATATACTATATGTTATAAAGT
1 ATATACTATATGTTATAAAGT
*
17661 ATAAACTATAT
1 ATATACTATAT
17672 AGTACACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (21 bp):
ATATACTATATGTTATAAAGT
Found at i:17748 original size:60 final size:60
Alignment explanation
Indices: 17682--17797 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
17672 AGTACACTAA
* *
17682 TATACATACATGTACTATAAGTTACATATATAGTTTACATGTATACATATACTATAAGTT
1 TATACATACATGTACTATAAATTACATATATAGTTTACATATATACATATACTATAAGTT
17742 TATACATACATGTACTATAAATTACATATATAGTTTACATATATACATATACTATA
1 TATACATACATGTACTATAAATTACATATATAGTTTACATATATACATATACTATA
17798 GGCTACATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (60 bp):
TATACATACATGTACTATAAATTACATATATAGTTTACATATATACATATACTATAAGTT
Found at i:18621 original size:35 final size:35
Alignment explanation
Indices: 18548--18622 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
18538 CGTCACTAAC
**
18548 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
18583 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
18618 AGTAA
1 AGTAA
18623 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:18727 original size:24 final size:24
Alignment explanation
Indices: 18700--18774 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
18690 CATAATTCAA
*
18700 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
18724 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
18748 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
18771 GTCA
1 GTCA
18775 GGATCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:18780 original size:23 final size:23
Alignment explanation
Indices: 18704--18780 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
18694 ATTCAAGTCA
*
18704 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
18727 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
18751 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
18774 AGGATCA
1 AGTATCA
18781 TAATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:18807 original size:47 final size:47
Alignment explanation
Indices: 18683--18796 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
18673 TATATCAAAA
* * * * *
18683 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
18731 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
18777 ATCATAAT-AGAATTCAAGTC
1 ATCA-AATCAGAATCCAAGTC
18797 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.27
47 23 0.42
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:19954 original size:18 final size:18
Alignment explanation
Indices: 19933--19968 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19923 CTTCCATCCG
*
19933 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
19951 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
19969 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:21269 original size:7 final size:7
Alignment explanation
Indices: 21257--21296 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
21247 TGGTCAACTC
21257 CGGTCAA
1 CGGTCAA
21264 CGGTCAA
1 CGGTCAA
21271 CGGGTCAA
1 C-GGTCAA
21279 CGGTCAA
1 CGGTCAA
21286 CGGGTCAA
1 C-GGTCAA
21294 CGG
1 CGG
21297 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:21278 original size:8 final size:8
Alignment explanation
Indices: 21258--21312 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
21248 GGTCAACTCC
21258 GGTCAAC-
1 GGTCAACG
21265 GGTCAACG
1 GGTCAACG
21273 GGTCAAC-
1 GGTCAACG
21280 GGTCAACG
1 GGTCAACG
21288 GGTCAACG
1 GGTCAACG
21296 GGT---CG
1 GGTCAACG
21301 GGTCAACG
1 GGTCAACG
21309 GGTC
1 GGTC
21313 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:21278 original size:15 final size:15
Alignment explanation
Indices: 21258--21296 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
21248 GGTCAACTCC
21258 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
21273 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
21288 GGTCAACGG
1 GGTCAACGG
21297 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:21304 original size:13 final size:13
Alignment explanation
Indices: 21286--21373 Score: 95
Period size: 13 Copynumber: 6.4 Consensus size: 13
21276 CAACGGTCAA
*
21286 CGGGTCAACGGGT
1 CGGGTAAACGGGT
*
21299 CGGGTCAACGGGT
1 CGGGTAAACGGGT
* *
21312 CGGGTCGGGTCAACTGGT
1 C-----GGGTAAACGGGT
21330 CGGGTAAACGGGT
1 CGGGTAAACGGGT
21343 CGGGTAAACGGGT
1 CGGGTAAACGGGT
21356 CGGGTAAACGGGT
1 CGGGTAAACGGGT
21369 CGGGT
1 CGGGT
21374 TATGACCGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
13 55 0.82
18 12 0.18
ACGTcount: A:0.17, C:0.19, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:21317 original size:18 final size:18
Alignment explanation
Indices: 21280--21334 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
21270 ACGGGTCAAC
21280 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
21301 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
21319 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
21335 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:21324 original size:31 final size:31
Alignment explanation
Indices: 21286--21373 Score: 114
Period size: 26 Copynumber: 3.0 Consensus size: 31
21276 CAACGGTCAA
*
21286 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
21317 CGGGTCAACTGGTCGGGTAAA-----CGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
21343 CGGGTAAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
21374 TATGACCGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
26 24 0.50
31 24 0.50
ACGTcount: A:0.17, C:0.19, G:0.47, T:0.17
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:23476 original size:35 final size:35
Alignment explanation
Indices: 23403--23477 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
23393 CGTCACTAAC
**
23403 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
23438 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
23473 AGTAA
1 AGTAA
23478 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:23582 original size:24 final size:24
Alignment explanation
Indices: 23555--23629 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
23545 CATAATTCAA
*
23555 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
23579 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
23603 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
23626 GTCA
1 GTCA
23630 GGATCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:23635 original size:23 final size:23
Alignment explanation
Indices: 23559--23635 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
23549 ATTCAAGTCA
*
23559 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
23582 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
23606 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
23629 AGGATCA
1 AGTATCA
23636 TAATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:23662 original size:47 final size:47
Alignment explanation
Indices: 23538--23651 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
23528 TATATCAAAA
* * * * *
23538 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
23586 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
23632 ATCATAAT-AGAATTCAAGTC
1 ATCA-AATCAGAATCCAAGTC
23652 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.27
47 23 0.42
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:24810 original size:18 final size:18
Alignment explanation
Indices: 24789--24824 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24779 CTTCCATCCG
*
24789 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
24807 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
24825 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:26125 original size:7 final size:7
Alignment explanation
Indices: 26113--26152 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
26103 TGGTCAACTC
26113 CGGTCAA
1 CGGTCAA
26120 CGGTCAA
1 CGGTCAA
26127 CGGGTCAA
1 C-GGTCAA
26135 CGGTCAA
1 CGGTCAA
26142 CGGGTCAA
1 C-GGTCAA
26150 CGG
1 CGG
26153 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:26134 original size:8 final size:8
Alignment explanation
Indices: 26114--26168 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
26104 GGTCAACTCC
26114 GGTCAAC-
1 GGTCAACG
26121 GGTCAACG
1 GGTCAACG
26129 GGTCAAC-
1 GGTCAACG
26136 GGTCAACG
1 GGTCAACG
26144 GGTCAACG
1 GGTCAACG
26152 GGT---CG
1 GGTCAACG
26157 GGTCAACG
1 GGTCAACG
26165 GGTC
1 GGTC
26169 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:26134 original size:15 final size:15
Alignment explanation
Indices: 26114--26152 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
26104 GGTCAACTCC
26114 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
26129 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
26144 GGTCAACGG
1 GGTCAACGG
26153 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:26173 original size:18 final size:18
Alignment explanation
Indices: 26136--26209 Score: 77
Period size: 18 Copynumber: 4.2 Consensus size: 18
26126 ACGGGTCAAC
26136 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
26157 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
26175 GGTCAAC---T--GGTCG
1 GGTCAACGGGTCGGGTCG
*
26188 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
26206 GGTC
1 GGTC
26210 GGGTTATGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
13 11 0.24
15 1 0.02
16 1 0.02
18 22 0.48
21 11 0.24
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:26180 original size:31 final size:31
Alignment explanation
Indices: 26142--26209 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
26132 CAACGGTCAA
*
26142 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
26173 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
26204 CGGGTC
1 CGGGTC
26210 GGGTTATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:26190 original size:13 final size:13
Alignment explanation
Indices: 26142--26173 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
26132 CAACGGTCAA
26142 CGGGTCAACGGGT
1 CGGGTCAACGGGT
26155 CGGGTCAACGGGT
1 CGGGTCAACGGGT
26168 CGGGTC
1 CGGGTC
26174 GGGTCAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:26199 original size:13 final size:13
Alignment explanation
Indices: 26168--26203 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
26158 GTCAACGGGT
*
26168 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
26181 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
26194 CGGGTCGGGT
1 CGGGTCGGGT
26204 CGGGTCGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:26997 original size:2 final size:2
Alignment explanation
Indices: 26990--27132 Score: 54
Period size: 2 Copynumber: 73.5 Consensus size: 2
26980 TTCTATAAAC
*
26990 TA TA TA TA TA TA TA T- TA TA TA GA T- TA CT- TA TA T- TA GT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * * *
27029 TA CA TA AA TA TA TA TA CTA TA T- TA -A TA TA AA T- TA TA TT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
27069 TA AA CTA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA GTT TA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* *
27111 TA CA TA CA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
27133 TAATATAAAT
Statistics
Matches: 102, Mismatches: 23, Indels: 32
0.65 0.15 0.20
Matches are distributed among these distances:
1 10 0.10
2 85 0.83
3 7 0.07
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27008 original size:15 final size:15
Alignment explanation
Indices: 26990--27147 Score: 62
Period size: 15 Copynumber: 10.3 Consensus size: 15
26980 TTCTATAAAC
26990 TATATATATATATAT
1 TATATATATATATAT
*
27005 TATATAGATTACTTATAT
1 TATATATA-TA--TATAT
*
27023 TAGT-TATACATA-A-
1 TA-TATATATATATAT
27036 -ATATATATACTATAT
1 TATATATATA-TATAT
*
27051 TA-ATATAAATTATAT
1 TATATATATA-TATAT
*
27066 T-TATAAACTATATAT
1 TATATATA-TATATAT
* *
27081 TTTATATAGTTTATA-
1 TATATATA-TATATAT
* *
27096 CATATATAGTTTATAT
1 TATATATA-TATATAT
* *
27112 ACATACATATATATAT
1 -TATATATATATATAT
*
27128 TATAT-TAATATAAAT
1 TATATAT-ATATATAT
27143 TATAT
1 TATAT
27148 TTTATAAACT
Statistics
Matches: 110, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
11 1 0.01
12 6 0.05
13 2 0.02
14 3 0.03
15 59 0.54
16 20 0.18
17 8 0.07
18 10 0.09
19 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:27119 original size:21 final size:21
Alignment explanation
Indices: 27093--27132 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
27083 TATATAGTTT
27093 ATACATATATAGT-TTATATAC
1 ATACATATATA-TATTATATAC
27114 ATACATATATATATTATAT
1 ATACATATATATATTATAT
27133 TAATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
ATACATATATATATTATATAC
Found at i:27126 original size:82 final size:83
Alignment explanation
Indices: 27027--27191 Score: 289
Period size: 83 Copynumber: 2.0 Consensus size: 83
27017 TTATATTAGT
27027 TATACATAAATATATATACTATATTAATATAAATTATA-TTTATAAACTATATA-TTTTATATAG
1 TATACATAAATATATATACTATATTAATATAAATTATATTTTATAAACTATATACTTTT-TATAG
27090 TTTATACATATATAGTTTA
65 TTTATACATATATAGTTTA
* *
27109 TATACATACATATATATATTATATTAATATAAATTATATTTTATAAACTATATACTTTTTATAGT
1 TATACATAAATATATATACTATATTAATATAAATTATATTTTATAAACTATATACTTTTTATAGT
27174 TTATACATATATAGTTTA
66 TTATACATATATAGTTTA
27192 GGGTTTATGA
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
82 36 0.46
83 39 0.49
84 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (83 bp):
TATACATAAATATATATACTATATTAATATAAATTATATTTTATAAACTATATACTTTTTATAGT
TTATACATATATAGTTTA
Found at i:27148 original size:15 final size:14
Alignment explanation
Indices: 27119--27161 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
27109 TATACATACA
*
27119 TATATATATTATAT
1 TATATAAATTATAT
27133 TAATATAAATTATAT
1 T-ATATAAATTATAT
* *
27148 TTTATAAACTATAT
1 TATATAAATTATAT
27162 ACTTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATAAATTATAT
Found at i:27485 original size:2 final size:2
Alignment explanation
Indices: 27474--27676 Score: 151
Period size: 2 Copynumber: 105.0 Consensus size: 2
27464 ATAGTGTTTC
* *
27474 TA TA -A TA TA TA TA TA TA TA TA -A TT TA TA GA T- TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
27513 T- TA GT- TA TA CA TA CA TA TA TA TA T- TA TA T- TA -A TA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
27551 T- TA TA -A TT TA TA AA CTA TA TA T- TT TA TA TA GTT TA TA CA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
27592 TA TA GTT TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
27635 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27677 GAAAATTAAA
Statistics
Matches: 157, Mismatches: 27, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
1 12 0.08
2 140 0.89
3 5 0.03
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27914 original size:19 final size:19
Alignment explanation
Indices: 27863--27924 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
27853 ATAAAATCTC
*
27863 AATTCTCAATTTCCCTCCA
1 AATTCTCAATTTCCCTCTA
* * *
27882 AATTTTTCTA-TTCCTTCTA
1 AA-TTCTCAATTTCCCTCTA
27901 AATTCTCAATTTCCCTCTA
1 AATTCTCAATTTCCCTCTA
27920 AATTC
1 AATTC
27925 CCAAATAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 5 0.15
19 24 0.71
20 5 0.15
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTCTCAATTTCCCTCTA
Found at i:28188 original size:13 final size:13
Alignment explanation
Indices: 28054--28139 Score: 82
Period size: 13 Copynumber: 6.3 Consensus size: 13
28044 ATATACTTTG
28054 TATAGTTTATCCATA
1 TATAGTTTAT--ATA
* *
28069 TATAGTTTACATG
1 TATAGTTTATATA
28082 TATAGTTTATATA
1 TATAGTTTATATA
*
28095 TATAGTTAATATA
1 TATAGTTTATATA
*
28108 TATAGTTAATATAAA
1 TATAGTT--TATATA
* *
28123 CATAATTTATATA
1 TATAGTTTATATA
28136 TATA
1 TATA
28140 ACTTATAATA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
13 40 0.69
15 18 0.31
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:28189 original size:19 final size:19
Alignment explanation
Indices: 28153--28207 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
28143 TATAATAATT
28153 ATATAGTTTATA-ATATAA
1 ATATAGTTTATATATATAA
28171 ATATAGTTTATATATATAA
1 ATATAGTTTATATATATAA
28190 ACT-TA-TATTATATATATA
1 A-TATAGT-TTATATATATA
28208 TTATATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.38
19 20 0.59
20 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (19 bp):
ATATAGTTTATATATATAA
Found at i:34002 original size:33 final size:33
Alignment explanation
Indices: 33948--34059 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
33938 ATTTTGTTCA
*
33948 GGTCGGGTCGGG-TTTTTTAAGTGTGATATTCG
1 GGTCGGGTAGGGTTTTTTTAAGTGTGATATTCG
*
33980 GGTCGAGTAGGGTTTTTTTAAGTGTGATATTCG
1 GGTCGGGTAGGGTTTTTTTAAGTGTGATATTCG
* *
34013 GGTCGGGTCGGGTTTTTTAAAGTGTGATATTCG
1 GGTCGGGTAGGGTTTTTTTAAGTGTGATATTCG
*
34046 GGTCGGGTTGGGTT
1 GGTCGGGTAGGGTT
34060 CGGGTTTAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 10 0.14
33 63 0.86
ACGTcount: A:0.13, C:0.08, G:0.38, T:0.40
Consensus pattern (33 bp):
GGTCGGGTAGGGTTTTTTTAAGTGTGATATTCG
Found at i:34615 original size:17 final size:17
Alignment explanation
Indices: 34589--34646 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
34579 ATATGGAATT
* *
34589 AGATTCCAATTCCTGAC
1 AGATTACAATTCCTCAC
*
34606 AGATTACAATTTCTTCAC
1 AGATTACAA-TTCCTCAC
*
34624 ATATTACAATTCCTTCAC
1 AGATTACAATTCC-TCAC
34642 AGATT
1 AGATT
34647 TAATTCCCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (17 bp):
AGATTACAATTCCTCAC
Found at i:38152 original size:32 final size:31
Alignment explanation
Indices: 38114--38203 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 31
38104 GTTAAAAATT
*
38114 TAGGTACTAAAATGAAACAAAAAGTTAACAA
1 TAGGTACTAAAATGAAACAAAAAGTAAACAA
* * *
38145 TGGGGTACCAAAATGAAACAAAAAATAAACAA
1 T-AGGTACTAAAATGAAACAAAAAGTAAACAA
*
38177 TAGGTACTAAAATGAAATAAAAAGTAA
1 TAGGTACTAAAATGAAACAAAAAGTAA
38204 GTGTTAGGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
31 23 0.46
32 27 0.54
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (31 bp):
TAGGTACTAAAATGAAACAAAAAGTAAACAA
Found at i:38259 original size:31 final size:30
Alignment explanation
Indices: 38177--38278 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 30
38167 AAATAAACAA
*
38177 TAGGTACTAAAATGAAATAAAA-AGTAAGTGT
1 TAGGTACTAAAATG-AATAAAAGAGAAAGT-T
* **
38208 TAGGCA-TAATTTTGAA-AAAAGAGAAAGTT
1 TAGGTACTAA-AATGAATAAAAGAGAAAGTT
* * *
38237 TAGGTACTAAAATAGAATAAAAGTGATACTT
1 TAGGTACTAAAAT-GAATAAAAGAGAAAGTT
*
38268 TAGGTATTAAA
1 TAGGTACTAAA
38279 CATGTAATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
29 11 0.20
30 17 0.31
31 27 0.49
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (30 bp):
TAGGTACTAAAATGAATAAAAGAGAAAGTT
Found at i:39872 original size:22 final size:22
Alignment explanation
Indices: 39847--39889 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39837 AATTTGATTA
39847 AAATTAAATAATAAATATAAAC
1 AAATTAAATAATAAATATAAAC
** *
39869 AAATTATCTAATAAATTTAAA
1 AAATTAAATAATAAATATAAA
39890 AAGATAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTAAATAATAAATATAAAC
Found at i:42398 original size:2 final size:2
Alignment explanation
Indices: 42391--42419 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42381 AATGAGAAAT
42391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42420 TGAAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43762 original size:22 final size:22
Alignment explanation
Indices: 43734--43782 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
43724 TACCAGACGA
*
43734 ATTGAAAGAAATTCAACTACTC
1 ATTGAAACAAATTCAACTACTC
*
43756 ATTGAAACAAATTCGACTACTC
1 ATTGAAACAAATTCAACTACTC
43778 ATTGA
1 ATTGA
43783 TTAGAAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (22 bp):
ATTGAAACAAATTCAACTACTC
Found at i:50585 original size:20 final size:21
Alignment explanation
Indices: 50562--50605 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50552 GAGAAAAAGT
*
50562 AAAAGTTAA-AATGAAAGAGA
1 AAAAGTTAATAATAAAAGAGA
*
50582 AAAAGTTAATAATAAAAGATA
1 AAAAGTTAATAATAAAAGAGA
50603 AAA
1 AAA
50606 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (21 bp):
AAAAGTTAATAATAAAAGAGA
Found at i:50597 original size:26 final size:26
Alignment explanation
Indices: 50544--50618 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
50534 GAAGATGAAG
*
50544 AAATGAGAGAGAAAAAG-TAAAAGTTA
1 AAATGAAAGAGAAAAAGTTAAAAG-TA
50570 AAATGAAAGAGAAAAAGTTAATAA-TA
1 AAATGAAAGAGAAAAAGTTAA-AAGTA
*
50596 AAA-GATAAAAGAAAAAGTTAAAA
1 AAATGA-AAGAGAAAAAGTTAAAA
50619 ATGAGAGGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 4 0.09
26 35 0.80
27 3 0.07
28 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.16
Consensus pattern (26 bp):
AAATGAAAGAGAAAAAGTTAAAAGTA
Found at i:50606 original size:20 final size:20
Alignment explanation
Indices: 50556--50606 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
50546 ATGAGAGAGA
50556 AAAAG-TAAAAGTTAAAATG
1 AAAAGATAAAAGTTAAAATG
50575 AAAGAGA-AAAAGTTAATAAT-
1 AAA-AGATAAAAGTTAA-AATG
50595 AAAAGATAAAAG
1 AAAAGATAAAAG
50607 AAAAAGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGATAAAAGTTAAAATG
Found at i:55256 original size:25 final size:25
Alignment explanation
Indices: 55228--55284 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
55218 TGTAGTAGAT
55228 ATGAACTCTTGAATGGTAGCTTCTA
1 ATGAACTCTTGAATGGTAGCTTCTA
55253 ATGAACTCTTGAATGGTAGCTTCTA
1 ATGAACTCTTGAATGGTAGCTTCTA
55278 ATGAACT
1 ATGAACT
55285 TATGCTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (25 bp):
ATGAACTCTTGAATGGTAGCTTCTA
Found at i:67053 original size:12 final size:12
Alignment explanation
Indices: 67038--67076 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
67028 TTATGTCCCT
*
67038 CCAGATGTTCCA
1 CCAGATGTACCA
67050 CCAGATGTACCTA
1 CCAGATGTACC-A
67063 CC-GATGTACCA
1 CCAGATGTACCA
67074 CCA
1 CCA
67077 TTGGCAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (12 bp):
CCAGATGTACCA
Found at i:69951 original size:21 final size:19
Alignment explanation
Indices: 69923--69968 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
69913 TCATTGAATC
69923 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
69943 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
69962 ACTTAGT
1 A-TTAGT
69969 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Done.