Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002134.1 Hibiscus syriacus cultivar Beakdansim tig00004367_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: 129190
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:24808 original size:52 final size:52
Alignment explanation
Indices: 24730--24833 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
24720 AGACCTTTAA
24730 CCCGAGATGGAGTTAAGATTAAATATTGATAGAGTCAGAATATTATATTATT
1 CCCGAGATGGAGTTAAGATTAAATATTGATAGAGTCAGAATATTATATTATT
24782 CCCGAGATGGAGTTAAGATTAAATATTGATAGAGTCAGAATATTATATTATT
1 CCCGAGATGGAGTTAAGATTAAATATTGATAGAGTCAGAATATTATATTATT
24834 TAAGAAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (52 bp):
CCCGAGATGGAGTTAAGATTAAATATTGATAGAGTCAGAATATTATATTATT
Found at i:31313 original size:18 final size:18
Alignment explanation
Indices: 31292--31330 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31282 TATTTAAAAA
31292 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* * *
31310 TTTAAATTTTTTATTTAT
1 TTTAAAATTATTATATAT
31328 TTT
1 TTT
31331 TTATTATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:37303 original size:62 final size:62
Alignment explanation
Indices: 37227--37350 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
37217 CTGTCATTTT
37227 TTATGCACAAATTTTGTAATTCTGAAAACTAACATACCACTTCATCTTGGCTTCCAATACGA
1 TTATGCACAAATTTTGTAATTCTGAAAACTAACATACCACTTCATCTTGGCTTCCAATACGA
37289 TTATGCACAAATTTTGTAATTCTGAAAACTAACATACCACTTCATCTTGGCTTCCAATACGA
1 TTATGCACAAATTTTGTAATTCTGAAAACTAACATACCACTTCATCTTGGCTTCCAATACGA
37351 CGCTCAAACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (62 bp):
TTATGCACAAATTTTGTAATTCTGAAAACTAACATACCACTTCATCTTGGCTTCCAATACGA
Found at i:40741 original size:17 final size:17
Alignment explanation
Indices: 40709--40741 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40699 GATACATATA
40709 TATATATAATTAATTAC
1 TATATATAATTAATTAC
40726 TATAT-TAATTATATTA
1 TATATATAATTA-ATTA
40742 ACGTTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATAATTAATTAC
Found at i:44370 original size:42 final size:42
Alignment explanation
Indices: 44323--44430 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 42
44313 AATCAATTCT
* *
44323 GTGTTTGTTTCATATAATTCGTTTTTTGGAAAATATTTTACC
1 GTGTTTGTTTCATGTAATTCGTTTTTTCGAAAATATTTTACC
* * * *
44365 GTGTTTGTTTTATGTAATTTG-TTTTTCGAAAATGTTTTTCC
1 GTGTTTGTTTCATGTAATTCGTTTTTTCGAAAATATTTTACC
* * *
44406 GTTTTTATTTCACGTAATTCGTTTT
1 GTGTTTGTTTCATGTAATTCGTTTT
44431 CCGGAATGTA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 33 0.61
42 21 0.39
ACGTcount: A:0.19, C:0.09, G:0.15, T:0.56
Consensus pattern (42 bp):
GTGTTTGTTTCATGTAATTCGTTTTTTCGAAAATATTTTACC
Found at i:44693 original size:23 final size:23
Alignment explanation
Indices: 44642--44697 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
44632 AAAATATATT
44642 TATTAATATTTATAATAAATAATCA
1 TATT-ATA-TTATAATAAATAATCA
*
44667 -ATTATATTATAATAATATAA-GA
1 TATTATATTATAATAA-ATAATCA
44689 TATTATATT
1 TATTATATT
44698 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 10 0.36
23 15 0.54
24 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATATTATAATAAATAATCA
Found at i:44735 original size:29 final size:29
Alignment explanation
Indices: 44668--44778 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 29
44658 AAATAATCAA
*
44668 TTATATTATAATAATATA-AGAT-ATTATAT
1 TTATATTTTAATAATATATA-ATAATTAT-T
*
44697 TTTTATTTTAATAATATATAATAATT-TT
1 TTATATTTTAATAATATATAATAATTATT
44725 TTATATCTTTAATAATGA-ATAAT-ATTATT
1 TTATAT-TTTAATAAT-ATATAATAATTATT
* *
44754 TATATATTTTAATAATTTTTAATAA
1 T-TATATTTTAATAATATATAATAA
44779 AGATATTTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
28 9 0.13
29 49 0.71
30 11 0.16
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (29 bp):
TTATATTTTAATAATATATAATAATTATT
Found at i:44739 original size:58 final size:57
Alignment explanation
Indices: 44668--44778 Score: 129
Period size: 58 Copynumber: 1.9 Consensus size: 57
44658 AAATAATCAA
*
44668 TTATATTATAATAAT--ATAAGATATTATATT-TTTATTTTAATAATATATAATAATTTT
1 TTATATTATAATAATGAAT-A-ATATTAT-TTATATATTTTAATAATATATAATAATTTT
* * *
44725 TTATATCTTTAATAATGAATAATATTATTTATATATTTTAATAATTTTTAATAA
1 TTATAT-TATAATAATGAATAATATTATTTATATATTTTAATAATATATAATAA
44779 AGATATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
57 8 0.17
58 35 0.76
59 1 0.02
60 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (57 bp):
TTATATTATAATAATGAATAATATTATTTATATATTTTAATAATATATAATAATTTT
Found at i:45179 original size:14 final size:15
Alignment explanation
Indices: 45158--45198 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
45148 TTCCAGAAAT
45158 GTAATTCATTTTTCA
1 GTAATTCATTTTTCA
**
45173 G-AATTCAAATTTCA
1 GTAATTCATTTTTCA
45187 GTAATTCATTTT
1 GTAATTCATTTT
45199 CTAATAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:45194 original size:15 final size:15
Alignment explanation
Indices: 45158--45224 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
45148 TTCCAGAAAT
**
45158 GTAATTCATTTTTCA
1 GTAATTCAAATTTCA
45173 G-AATTCAAATTTCA
1 GTAATTCAAATTTCA
*
45187 GTAATTC-ATTTTCTA
1 GTAATTCAAATTTC-A
* *
45202 ATAATTCAAATTACA
1 GTAATTCAAATTTCA
*
45217 ATAATTCA
1 GTAATTCA
45225 TTTTCTGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 17 0.40
15 22 0.51
16 4 0.09
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (15 bp):
GTAATTCAAATTTCA
Found at i:45210 original size:30 final size:30
Alignment explanation
Indices: 45158--45230 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
45148 TTCCAGAAAT
* *
45158 GTAATTCATTTT-TCAGAATTCAAATTTCA
1 GTAATTCATTTTCTAAGAATTCAAATTACA
*
45187 GTAATTCATTTTCTAATAATTCAAATTACA
1 GTAATTCATTTTCTAAGAATTCAAATTACA
*
45217 ATAATTCATTTTCT
1 GTAATTCATTTTCT
45231 GAAAAATCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 12 0.31
30 27 0.69
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.47
Consensus pattern (30 bp):
GTAATTCATTTTCTAAGAATTCAAATTACA
Found at i:46026 original size:36 final size:35
Alignment explanation
Indices: 45966--46044 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
45956 GATTACTAAA
*
45966 CCCGTCCCATCCCCGTTTAACATAAAAGGGTTTTC
1 CCCGTCCCATCCCCATTTAACATAAAAGGGTTTTC
* * * *
46001 CCCGTCCCTGTCCCCATTTAGCATAAACGGTTTTTC
1 CCCGTCCC-ATCCCCATTTAACATAAAAGGGTTTTC
46037 CCCGTCCC
1 CCCGTCCC
46045 CGTTTAATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.18, C:0.39, G:0.14, T:0.29
Consensus pattern (35 bp):
CCCGTCCCATCCCCATTTAACATAAAAGGGTTTTC
Found at i:49473 original size:18 final size:19
Alignment explanation
Indices: 49438--49475 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
49428 CACGGAATGT
49438 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
49458 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
49476 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:49488 original size:15 final size:16
Alignment explanation
Indices: 49437--49481 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
49427 TCACGGAATG
49437 TAAGATTACCAGTGGGAA
1 TAAGATTACCA--GGGAA
49455 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
49473 TAAGATTAC
1 TAAGATTAC
49482 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 7 0.28
20 10 0.40
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:53444 original size:22 final size:22
Alignment explanation
Indices: 53416--53471 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
53406 TCGGGCATGG
*
53416 ACAAAAATGGCAGGACGACGAA
1 ACAAAAATGGCAGGACAACGAA
53438 ACAAAAATGGCAGGACAACGAA
1 ACAAAAATGGCAGGACAACGAA
53460 ACAAAAATGGCA
1 ACAAAAATGGCA
53472 AAAGGTCACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.54, C:0.18, G:0.23, T:0.05
Consensus pattern (22 bp):
ACAAAAATGGCAGGACAACGAA
Found at i:63614 original size:25 final size:26
Alignment explanation
Indices: 63563--63615 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
63553 ATATCTACTT
* * *
63563 TAAAATTTTATTTTTGTTTATTCATA
1 TAAAAATTTATTTATGTTTATTAATA
63589 TAAAAATTTATTTAT-TTTATTAATA
1 TAAAAATTTATTTATGTTTATTAATA
63614 TA
1 TA
63616 CGTGTATCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TAAAAATTTATTTATGTTTATTAATA
Found at i:64070 original size:70 final size:71
Alignment explanation
Indices: 63994--64138 Score: 231
Period size: 71 Copynumber: 2.1 Consensus size: 71
63984 TAATAAAATA
63994 AAATTAAAAATTATTGAATATGACTATTAGA-GGTGTTTGGATAAAGGAATGTGA-GATTCTCAT
1 AAATTAAAAATTATTGAATATGACTATTAGAGGGTGTTTGGATAAAGGAATGT-ATGATTCTCAT
*
64057 GAGAATT
65 GAGAATG
* *
64064 AAATTAAAAATTATTGAATATGACTATTAGAGGGTGTTTGGATCAAGGAATGTATGATTCTTATG
1 AAATTAAAAATTATTGAATATGACTATTAGAGGGTGTTTGGATAAAGGAATGTATGATTCTCATG
*
64129 GGAATG
66 AGAATG
64135 AAAT
1 AAAT
64139 CCACATTCCC
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
70 32 0.46
71 37 0.54
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (71 bp):
AAATTAAAAATTATTGAATATGACTATTAGAGGGTGTTTGGATAAAGGAATGTATGATTCTCATG
AGAATG
Found at i:64530 original size:37 final size:36
Alignment explanation
Indices: 64461--64535 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
64451 TCATTAAACC
* *
64461 ATTTTATATTTTCAATTTTGTAAAAAATATATATAA
1 ATTTTATAATTTAAATTTTGTAAAAAATATATATAA
*
64497 ATTTTATGAATTTAAATTTTTTAAAGAAA-ATATATAA
1 ATTTTAT-AATTTAAATTTTGTAAA-AAATATATATAA
64534 AT
1 AT
64536 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 7 0.21
37 24 0.71
38 3 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
ATTTTATAATTTAAATTTTGTAAAAAATATATATAA
Found at i:65130 original size:14 final size:14
Alignment explanation
Indices: 65113--65146 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
65103 ATATATATAT
65113 ATATATATTTCT-TC
1 ATATATATTT-TGTC
65127 ATATATATTTTGTC
1 ATATATATTTTGTC
65141 ATATAT
1 ATATAT
65147 TATATATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (14 bp):
ATATATATTTTGTC
Found at i:65134 original size:2 final size:2
Alignment explanation
Indices: 65071--65120 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
65061 TTTCTATAAT
*
65071 TA TA TA CA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65112 TA TA TA TA T
1 TA TA TA TA T
65121 TTCTTCATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72146 original size:23 final size:23
Alignment explanation
Indices: 72117--72163 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
72107 TAGAAGGTAT
72117 TAGTACTTTATGTATTTAGTTTA
1 TAGTACTTTATGTATTTAGTTTA
72140 TAGTACTTTATGTATTTAGTTTA
1 TAGTACTTTATGTATTTAGTTTA
72163 T
1 T
72164 CTTTTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (23 bp):
TAGTACTTTATGTATTTAGTTTA
Found at i:83826 original size:31 final size:29
Alignment explanation
Indices: 83785--83843 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
83775 TATATGTATT
* *
83785 TAATTAATTTTTGTAGCTAAGTTCGAGGACC
1 TAATTAATTTTT-TAG-AAAGATCGAGGACC
*
83816 TAATTGATTTTTTAGAAAGATCGAGGAC
1 TAATTAATTTTTTAGAAAGATCGAGGAC
83844 TTTTACAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 3 0.12
31 11 0.44
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (29 bp):
TAATTAATTTTTTAGAAAGATCGAGGACC
Found at i:83935 original size:113 final size:113
Alignment explanation
Indices: 83737--83958 Score: 426
Period size: 113 Copynumber: 2.0 Consensus size: 113
83727 GGAAAATTAT
*
83737 AATATTGATGCAACAATACACGATGGAGAATGATGTGGTATATGTATTTAATTAATTTTTGTAGC
1 AATATTGATGCAACAATACACGATGGAGAATGATGTGGTAGATGTATTTAATTAATTTTTGTAGC
83802 TAAGTTCGAGGACCTAATTGATTTTTTAGAAAGATCGAGGACTTTTAC
66 TAAGTTCGAGGACCTAATTGATTTTTTAGAAAGATCGAGGACTTTTAC
*
83850 AATATTGATGCAACAATGCACGATGGAGAATGATGTGGTAGATGTATTTAATTAATTTTTGTAGC
1 AATATTGATGCAACAATACACGATGGAGAATGATGTGGTAGATGTATTTAATTAATTTTTGTAGC
83915 TAAGTTCGAGGACCTAATTGATTTTTTAGAAAGATCGAGGACTT
66 TAAGTTCGAGGACCTAATTGATTTTTTAGAAAGATCGAGGACTT
83959 GTTTAATTTA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (113 bp):
AATATTGATGCAACAATACACGATGGAGAATGATGTGGTAGATGTATTTAATTAATTTTTGTAGC
TAAGTTCGAGGACCTAATTGATTTTTTAGAAAGATCGAGGACTTTTAC
Found at i:83939 original size:31 final size:29
Alignment explanation
Indices: 83898--83956 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
83888 TAGATGTATT
* *
83898 TAATTAATTTTTGTAGCTAAGTTCGAGGACC
1 TAATTAATTTTT-TAG-AAAGATCGAGGACC
*
83929 TAATTGATTTTTTAGAAAGATCGAGGAC
1 TAATTAATTTTTTAGAAAGATCGAGGAC
83957 TTGTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 3 0.12
31 11 0.44
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (29 bp):
TAATTAATTTTTTAGAAAGATCGAGGACC
Found at i:84035 original size:24 final size:25
Alignment explanation
Indices: 83997--84056 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
83987 AAATATAAAC
*
83997 AATTATT-AAGATATT-CAATACATTA
1 AATTATTAAAAATATTACAA-A-ATTA
84022 AA-TA-TAAAAATATTACAAAATTA
1 AATTATTAAAAATATTACAAAATTA
84045 AATTATTAAAAA
1 AATTATTAAAAA
84057 AATCAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
23 7 0.23
24 12 0.40
25 11 0.37
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (25 bp):
AATTATTAAAAATATTACAAAATTA
Found at i:90415 original size:36 final size:36
Alignment explanation
Indices: 90375--90470 Score: 149
Period size: 35 Copynumber: 2.7 Consensus size: 36
90365 GATGTAACTT
*
90375 AAAATATTATATTTTTTAAATATTTTTATTGAATCG
1 AAAATATTATATTTTTTAAATATTTTTATTGAATCA
*
90411 AAAATTTTATATTTTTT-AATATTTTTATTGAATCA
1 AAAATATTATATTTTTTAAATATTTTTATTGAATCA
*
90446 AAAATATTATCTTTTTTATAATATT
1 AAAATATTATATTTTTTA-AATATT
90471 ATTTTATTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
35 32 0.59
36 16 0.30
37 6 0.11
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (36 bp):
AAAATATTATATTTTTTAAATATTTTTATTGAATCA
Found at i:90468 original size:17 final size:17
Alignment explanation
Indices: 90448--90487 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
90438 TTGAATCAAA
90448 AATATTATCTTT-TTTAT
1 AATATTAT-TTTATTTAT
*
90465 AATATTATTTTATTTGT
1 AATATTATTTTATTTAT
90482 AATATT
1 AATATT
90488 TTAGGGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
AATATTATTTTATTTAT
Found at i:103471 original size:52 final size:51
Alignment explanation
Indices: 103415--103513 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 51
103405 ATGTACATAT
*
103415 TTACACCGGTATAAGTATGTGTTAAGTGCTATATATTTTTTATTTTATCCAC
1 TTACACCGGTATAAGTATGTGTTAAGTGCTACA-ATTTTTTATTTTATCCAC
*
103467 TTACACCGGTATAAGTATGTGTTAAGTGCTACACTTTTTTATTTTAT
1 TTACACCGGTATAAGTATGTGTTAAGTGCTACAATTTTTTATTTTAT
103514 TCATATTACA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 13 0.29
52 32 0.71
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (51 bp):
TTACACCGGTATAAGTATGTGTTAAGTGCTACAATTTTTTATTTTATCCAC
Found at i:103523 original size:52 final size:53
Alignment explanation
Indices: 103410--103523 Score: 169
Period size: 52 Copynumber: 2.2 Consensus size: 53
103400 GAGAGATGTA
*
103410 CATATTTACACCGGTATAAGTATGTGTTAAGTGCTATATATTTTTTATTTTATC
1 CATA-TTACACCGGTATAAGTATGTGTTAAGTGCTACATATTTTTTATTTTATC
* * *
103464 CA-CTTACACCGGTATAAGTATGTGTTAAGTGCTACA-CTTTTTTATTTTATT
1 CATATTACACCGGTATAAGTATGTGTTAAGTGCTACATATTTTTTATTTTATC
103515 CATATTACA
1 CATATTACA
103524 TATATGAGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 15 0.28
52 37 0.69
54 2 0.04
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (53 bp):
CATATTACACCGGTATAAGTATGTGTTAAGTGCTACATATTTTTTATTTTATC
Found at i:104155 original size:17 final size:17
Alignment explanation
Indices: 104135--104186 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 17
104125 TTCATTTAAT
104135 TAAAATATTGTTATAAA
1 TAAAATATTGTTATAAA
104152 TAAAATATTTACAGTTATAAA
1 TAAAATA-TT---GTTATAAA
*
104173 TAAATTATTGTTAT
1 TAAAATATTGTTAT
104187 TCTTTGAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 12 0.40
18 2 0.07
20 2 0.07
21 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATATTGTTATAAA
Found at i:110648 original size:43 final size:43
Alignment explanation
Indices: 110600--110685 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
110590 TATTCCATGT
* *
110600 AAGAGACTGAAATGATATAGCATTTAGAATTGATTATAACCCA
1 AAGAGACTGAAATGATATAACATTTAGAATTGACTATAACCCA
* *
110643 AAGAGATTGAAATGATATAACATTTAGAATTGACTATTACCCA
1 AAGAGACTGAAATGATATAACATTTAGAATTGACTATAACCCA
110686 TAAATCTCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (43 bp):
AAGAGACTGAAATGATATAACATTTAGAATTGACTATAACCCA
Found at i:116336 original size:21 final size:23
Alignment explanation
Indices: 116296--116337 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
116286 CTTTGTTATC
116296 ATTTTATAAAATAGAAATTAATT
1 ATTTTATAAAATAGAAATTAATT
*
116319 ATTTTATTAAA-A-AAATTAA
1 ATTTTATAAAATAGAAATTAA
116338 AATTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTTATAAAATAGAAATTAATT
Found at i:116438 original size:2 final size:2
Alignment explanation
Indices: 116431--116463 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
116421 AATGAAACAT
116431 TA TA 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 TA TA T
116464 TAAATTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117021 original size:20 final size:21
Alignment explanation
Indices: 116996--117088 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
116986 TTTTCCCAAT
*
116996 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
117016 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
117037 TTGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
117057 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
117078 TCGCAATGCGA
1 TCGCAATGCGA
117089 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:117102 original size:41 final size:41
Alignment explanation
Indices: 116996--117088 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
116986 TTTTCCCAAT
116996 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
117037 TTGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
117078 TCGCAATGCGA
1 TCGCAATGCGA
117089 TACTTACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:117729 original size:19 final size:19
Alignment explanation
Indices: 117669--117749 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
117659 TTCGAGAATG
117669 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
117689 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
117705 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
117722 AAAATCGCAACACGAAACC
1 AAAATCGCAACGCGAAATA
117741 AAAATCGCA
1 AAAATCGCA
117750 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
16 5 0.10
17 4 0.08
18 1 0.02
19 23 0.48
20 8 0.17
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:117767 original size:19 final size:19
Alignment explanation
Indices: 117745--117853 Score: 173
Period size: 19 Copynumber: 5.7 Consensus size: 19
117735 GAAACCAAAA
* **
117745 TCGCATTGCGATTTTCGTT
1 TCGCGTTGCGATTTTTATT
117764 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
117783 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
117802 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
*
117821 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTTATT
117841 TCGCGTTGCGATT
1 TCGCGTTGCGATT
117854 GTCTGGTCGC
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
19 67 0.79
20 18 0.21
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:117873 original size:33 final size:33
Alignment explanation
Indices: 117836--117923 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
117826 GTTGCGATTT
* *
117836 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
117869 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
117902 TCATTTCCGCATTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
117924 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:117925 original size:20 final size:19
Alignment explanation
Indices: 117888--117948 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
117878 GTTGCGATTC
**
117888 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
117907 TC-CGCATTGCGATTCTCATT
1 TCTCG--TTGCGATTCTCATT
*
117927 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
117947 TC
1 TC
117949 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 2 0.06
22 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:120029 original size:21 final size:21
Alignment explanation
Indices: 120005--120071 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
119995 TCATTCCTCG
120005 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
120026 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
120047 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
120068 AGAG
1 AGAG
120072 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:120029 original size:42 final size:42
Alignment explanation
Indices: 119949--120071 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
119939 GCCCGACTCG
* * * * * *
119949 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
119991 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
120033 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
120072 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:121463 original size:14 final size:14
Alignment explanation
Indices: 121428--121464 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
121418 GATTGTTTAA
*
121428 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
*
121442 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
121456 TTGATTTGT
1 TTGATTTGT
121465 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:123012 original size:12 final size:12
Alignment explanation
Indices: 122995--123019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122985 TCTTCGGGGA
122995 CTTTTTCTTCTT
1 CTTTTTCTTCTT
123007 CTTTTTCTTCTT
1 CTTTTTCTTCTT
123019 C
1 C
123020 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:124330 original size:20 final size:20
Alignment explanation
Indices: 124305--124361 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
124295 ATTCATTTGA
124305 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
124325 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
124345 TTATCGCAACGAGAAAA
1 CTATCGCAACGCGAAAA
124362 CCGCAATGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:124422 original size:19 final size:19
Alignment explanation
Indices: 124381--124448 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
124371 GAAATGAAAA
124381 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
124397 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
124414 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
124433 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
124449 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:126546 original size:19 final size:19
Alignment explanation
Indices: 126434--126555 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
126424 TAGTTTACTT
* *
126434 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
126454 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
126473 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
126493 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
126512 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
126526 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
126545 TCGCAATGCGA
1 TCGCAACGCGA
126556 TTGTGTTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 39 0.46
20 29 0.35
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:126587 original size:14 final size:14
Alignment explanation
Indices: 126568--126623 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
126558 GTGTTTCGCG
126568 TGCGATTTTGTCGT
1 TGCGATTTTGTCGT
*
126582 TGCGATTTTCATTTCGCAT
1 TGCGA-TTT--TGTCG--T
126601 TGCGATTTTGTCGT
1 TGCGATTTTGTCGT
126615 TGCGATTTT
1 TGCGATTTT
126624 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 15 0.43
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
TGCGATTTTGTCGT
Found at i:126605 original size:19 final size:19
Alignment explanation
Indices: 126581--126639 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
126571 GATTTTGTCG
126581 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
126600 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
126614 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
126633 TTGCGAT
1 TTGCGAT
126640 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 13 0.39
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:126607 original size:33 final size:33
Alignment explanation
Indices: 126568--126639 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
126558 GTGTTTCGCG
126568 TGCGATTTTGTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTGTCGTTGCGATTTTCATTTCGCAT
126601 TGCGATTTTGTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTGTCGTTGCGATTTTCATTTCGCAT
126634 TGCGAT
1 TGCGAT
126640 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGTCGTTGCGATTTTCATTTCGCAT
Found at i:126658 original size:20 final size:19
Alignment explanation
Indices: 126624--126678 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
126614 TTGCGATTTT
*
126624 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
126643 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
126663 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
126679 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:127186 original size:18 final size:18
Alignment explanation
Indices: 127160--127204 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
127150 GTCGATCAGA
*
127160 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
127178 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
127196 TGATGGCTC
1 TGATGGCTC
127205 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:128538 original size:20 final size:19
Alignment explanation
Indices: 128504--128556 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
128494 GAATAGTTTT
128504 GAAAATGAAATCGCAACAC
1 GAAAATGAAATCGCAACAC
* *
128523 GAAAATGACTATCGCAACGC
1 GAAAATGA-AATCGCAACAC
* *
128543 GAAACTAAAATCGC
1 GAAAATGAAATCGC
128557 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (19 bp):
GAAAATGAAATCGCAACAC
Found at i:128811 original size:21 final size:21
Alignment explanation
Indices: 128787--128829 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
128777 GATTTAGATA
128787 GACGAATTTCGCCGGAGATGG
1 GACGAATTTCGCCGGAGATGG
* *
128808 GACGGATTTCGTCGGAGATGG
1 GACGAATTTCGCCGGAGATGG
128829 G
1 G
128830 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (21 bp):
GACGAATTTCGCCGGAGATGG
Found at i:129047 original size:19 final size:19
Alignment explanation
Indices: 129023--129068 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
129013 TGTATTAACG
*
129023 CGTTGCGAAAGTCGTATCA
1 CGTTGCGAAAGTAGTATCA
*
129042 CGTTGCGAAAGTAGTATCT
1 CGTTGCGAAAGTAGTATCA
129061 CGTTGCGA
1 CGTTGCGA
129069 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (19 bp):
CGTTGCGAAAGTAGTATCA
Found at i:129087 original size:21 final size:21
Alignment explanation
Indices: 129054--129115 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
129044 TTGCGAAAGT
* * *
129054 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
129075 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
129095 AGTATCGCATTGCGATTTTTC
1 AGTATCGCATTGCGATTTTTC
129116 CCCAATCGCG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:129149 original size:20 final size:20
Alignment explanation
Indices: 129121--129190 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
129111 TTTTCCCCAA
*
129121 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* * **
129141 TCGCATTGCGGTTTTCCCAT
1 TCGCATTGCGATTTACTTAT
*
129161 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
129181 TCGCATTGCG
1 TCGCATTGCG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:129174 original size:40 final size:42
Alignment explanation
Indices: 129099--129190 Score: 152
Period size: 40 Copynumber: 2.2 Consensus size: 42
129089 ATAGTCAGTA
*
129099 TCGCATTGCGATTTTTCCCCAATCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAGTTTTCCCCAATCGCGTTGCGATTTACTTAT
*
129141 TCGCATTGCG-GTTTT-CCCATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAGTTTTCCCCAATCGCGTTGCGATTTACTTAT
129181 TCGCATTGCG
1 TCGCATTGCG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 34 0.71
41 4 0.08
42 10 0.21
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (42 bp):
TCGCATTGCGAGTTTTCCCCAATCGCGTTGCGATTTACTTAT
Done.