Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004335.1 Hibiscus syriacus cultivar Beakdansim tig00009503_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: 108622
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3331 original size:33 final size:33
Alignment explanation
Indices: 3289--3389 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
3279 ACCTAGTGTA
3289 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
*
3322 TATGGTGGACACGACCTTATGTGTCATACGAAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
3355 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
3388 TA
1 TA
3390 GCACTACGGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (33 bp):
TATGGTGGACACGACCTTATGTGTCATACGGAT
Found at i:3352 original size:17 final size:17
Alignment explanation
Indices: 3299--3384 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 17
3289 TATGGTGGAC
3299 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
* *
3316 ACGGA--TTATG-GTGGAC
1 AC-GACCTTATGTGT-CAT
3332 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
* * *
3349 ACGA-ATTATG-GTGGAC
1 ACGACCTTATGTGT-CAT
3365 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
3382 ACG
1 ACG
3385 GATTAGCACT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
15 6 0.12
16 18 0.35
17 21 0.41
18 6 0.12
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (17 bp):
ACGACCTTATGTGTCAT
Found at i:3368 original size:16 final size:17
Alignment explanation
Indices: 3289--3375 Score: 56
Period size: 17 Copynumber: 5.2 Consensus size: 17
3279 ACCTAGTGTA
*
3289 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
* * *
3306 TAT-GTGTCATACG-GAT
1 TATGGTG-GACACGACAT
*
3322 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
* *
3339 TAT-GTGTCATACGA-AT
1 TATGGTG-GACACGACAT
*
3355 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
3372 TATG
1 TATG
3376 TGTCATACGG
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
16 23 0.46
17 27 0.54
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (17 bp):
TATGGTGGACACGACAT
Found at i:8256 original size:34 final size:33
Alignment explanation
Indices: 8180--8286 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
8170 GTGGTAAGAA
* *
8180 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
8214 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
8249 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
8283 ATTT
1 ATTT
8287 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:8268 original size:36 final size:34
Alignment explanation
Indices: 8213--8291 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
8203 TTTAAATAGT
*
8213 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
8245 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
8279 TATTATTTATTTA
1 TATTATTTTTTTA
8292 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:8453 original size:17 final size:17
Alignment explanation
Indices: 8431--8484 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
8421 AATGTTAATA
8431 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
8448 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
8465 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
8482 TTT
1 TTT
8485 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:10096 original size:21 final size:21
Alignment explanation
Indices: 10066--10142 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
10056 TATGCCATCT
* *
10066 CCGCATGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
*
10087 CCGCAGGGTTATATATATTCCTAGC
1 CCGCAGGG---T-TACATTCCTAGC
*
10112 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
10133 CCGCAGGGTT
1 CCGCAGGGTT
10143 TTATACCATA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.04
21 24 0.53
22 1 0.02
24 1 0.02
25 15 0.33
26 2 0.04
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:10701 original size:34 final size:34
Alignment explanation
Indices: 10651--10748 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
10641 AAATGTTTTT
*
10651 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
10685 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
10719 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
10749 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:11439 original size:128 final size:128
Alignment explanation
Indices: 11149--11773 Score: 1082
Period size: 128 Copynumber: 4.9 Consensus size: 128
11139 TTACCTGATT
*
11149 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * *** *
11214 TGACAAAATAATGGAAGGCGC-CCCCCGGGAACGTGCCTTCAAGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
11276 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
*
11340 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCTCCTTCATGTGAATAGTGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
11404 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
11469 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
11532 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
11597 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
11660 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
11725 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
11774 ACTCCGATTA
Statistics
Matches: 479, Mismatches: 15, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
125 47 0.10
127 83 0.17
128 349 0.73
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:11857 original size:8 final size:8
Alignment explanation
Indices: 11844--11884 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
11834 TCACAAGCTT
11844 TCAAATTC
1 TCAAATTC
11852 TCAAATTC
1 TCAAATTC
* *
11860 CCAAACTC
1 TCAAATTC
11868 T-AAATTC
1 TCAAATTC
11875 TCAAATTC
1 TCAAATTC
11883 TC
1 TC
11885 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:14902 original size:12 final size:12
Alignment explanation
Indices: 14885--14923 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
14875 TACATAAATA
14885 TATTTAATATAT
1 TATTTAATATAT
*
14897 TATTTAATATAA
1 TATTTAATATAT
*
14909 TAATTAATATTAT
1 TATTTAATA-TAT
14922 TA
1 TA
14924 GTTATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:16718 original size:59 final size:58
Alignment explanation
Indices: 16654--16767 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 58
16644 TTTAAGTCTG
* * * *
16654 AAATATATTTTA-T-TTTTACTTCAACTTTAAAATGTATTTTGTTATTATCTTAACTTTAA
1 AAATATATTTTATTATTTTA-TT-AAATTAAAAATGTAGTTT-TTATCATCTTAACTTTAA
16713 AAATATATTTTATTATTTTATTAAATTAAAAATGTAGTTTTTATCATCTTAACTT
1 AAATATATTTTATTATTTTATTAAATTAAAAATGTAGTTTTTATCATCTTAACTT
16768 CAAATAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 14 0.29
59 27 0.55
60 3 0.06
61 5 0.10
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.54
Consensus pattern (58 bp):
AAATATATTTTATTATTTTATTAAATTAAAAATGTAGTTTTTATCATCTTAACTTTAA
Found at i:16722 original size:30 final size:30
Alignment explanation
Indices: 16654--16767 Score: 110
Period size: 29 Copynumber: 3.9 Consensus size: 30
16644 TTTAAGTCTG
*
16654 AAATATATTTTATTTTTA-CTTCAACTTT-A
1 AAATATATTTTATTATTATCTT-AACTTTAA
* *
16683 AAATGTATTTTGTTATTATCTTAACTTTAA
1 AAATATATTTTATTATTATCTTAACTTTAA
* * *
16713 AAATATATTTTATTATTTTATTAA-ATTAA
1 AAATATATTTTATTATTATCTTAACTTTAA
* * *
16742 AAATGTAGTTT-TTATCATCTTAACTT
1 AAATATATTTTATTATTATCTTAACTT
16768 CAAATAAAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
28 9 0.13
29 35 0.51
30 24 0.35
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.54
Consensus pattern (30 bp):
AAATATATTTTATTATTATCTTAACTTTAA
Found at i:16812 original size:29 final size:28
Alignment explanation
Indices: 16780--16899 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 28
16770 AATAAAAGAA
*
16780 TTTTAAGTTAATA-AAAGATTAGAATATAT
1 TTTTAAGTTAATATAAA-A-TAAAATATAT
* *
16809 TTTTAAAATTAAGATAAACATAAAATATAT
1 TTTT-AAGTTAATATAAA-ATAAAATATAT
*
16839 TTTAAAGTTAATATAAAAATAAAATATAT
1 TTTTAAGTTAATAT-AAAATAAAATATAT
*
16868 TTAATACA-TTAA-ATGAAAATAAAATATAT
1 TT-TTA-AGTTAATAT-AAAATAAAATATAT
16897 TTT
1 TTT
16900 CTTAAAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
29 43 0.57
30 27 0.36
31 5 0.07
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (28 bp):
TTTTAAGTTAATATAAAATAAAATATAT
Found at i:16838 original size:30 final size:28
Alignment explanation
Indices: 16802--16914 Score: 113
Period size: 29 Copynumber: 3.8 Consensus size: 28
16792 AAAAGATTAG
16802 AATATATTTTTAAAATTAAGATAAACATAA
1 AATATA-TTTTAAAATTAAGATAAA-ATAA
* *
16832 AATATATTTTAAAGTTAATATAAAAATAA
1 AATATATTTTAAAATTAAGAT-AAAATAA
16861 AATATA-TTTAATACATTAA-ATGAAAATAA
1 AATATATTTTAA-A-ATTAAGAT-AAAATAA
16890 AATATATTTTCTTAAAATTAAGATA
1 AATATA--TT-TTAAAATTAAGATA
16915 TGAATTTAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
28 5 0.07
29 39 0.55
30 13 0.18
31 6 0.08
32 4 0.06
33 4 0.06
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (28 bp):
AATATATTTTAAAATTAAGATAAAATAA
Found at i:16865 original size:59 final size:57
Alignment explanation
Indices: 16769--16899 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 57
16759 TCTTAACTTC
* * *
16769 AAATAAAAGA-ATTTTAAGTTAATAAAAGATTAGAATATATTTTTAA-A-ATTAAGAT-A
1 AAATAAAATATATTTTAAGTTAATAAAAGAATA-AA-ATATATTTAATACATTAA-ATGA
16825 AACATAAAATATATTTTAAAGTTAATATAAA-AATAAAATATATTTAATACATTAAATGA
1 AA-ATAAAATATATTTT-AAGTTAATA-AAAGAATAAAATATATTTAATACATTAAATGA
16884 AAATAAAATATATTTT
1 AAATAAAATATATTTT
16900 CTTAAAATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
56 2 0.03
57 16 0.25
58 24 0.37
59 20 0.31
60 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (57 bp):
AAATAAAATATATTTTAAGTTAATAAAAGAATAAAATATATTTAATACATTAAATGA
Found at i:17227 original size:16 final size:16
Alignment explanation
Indices: 17206--17292 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
17196 TAACCAAAAT
17206 CAACCCGAACTGAAAG
1 CAACCCGAACTGAAAG
* *
17222 CAACCCAAACTGAAAAT
1 CAACCCGAACTG-AAAG
* *
17239 CAACCCGAACCGAAAT
1 CAACCCGAACTGAAAG
*** * *
17255 CAATTAGAACTAAAAA
1 CAACCCGAACTGAAAG
* *
17271 TAACCCGAACTAAAAG
1 CAACCCGAACTGAAAG
17287 CAACCC
1 CAACCC
17293 AAATTTAAGT
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
16 41 0.76
17 13 0.24
ACGTcount: A:0.49, C:0.30, G:0.10, T:0.10
Consensus pattern (16 bp):
CAACCCGAACTGAAAG
Found at i:17243 original size:33 final size:33
Alignment explanation
Indices: 17201--17295 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
17191 TAGTTTAACC
*
17201 AAAATCAACCCGAACTGAAAGCAACCCAAACTG
1 AAAATCAACCCGAACTGAAAGCAACCCAAACTA
* * **
17234 AAAATCAACCCGAACCGAAATCAA-TTAGAACTA
1 AAAATCAACCCGAACTGAAAGCAACCCA-AACTA
*
17267 AAAAT-AACCCGAACTAAAAGCAACCCAAA
1 AAAATCAACCCGAACTGAAAGCAACCCAAA
17296 TTTAAGTTAC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 18 0.36
33 32 0.64
ACGTcount: A:0.53, C:0.27, G:0.09, T:0.11
Consensus pattern (33 bp):
AAAATCAACCCGAACTGAAAGCAACCCAAACTA
Found at i:17977 original size:46 final size:46
Alignment explanation
Indices: 17887--17977 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
17877 TAAACAAAAA
* * * *
17887 CAACCTGAATTGACCCGAAAATCTAAAGGTTAATCTCAATCGAAAT
1 CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCCAACCGAAAT
*
17933 CAACCCGAATTGACCCGAAAATCTAAAGCTTGA-CCCGAACCGAAA
1 CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCC-AACCGAAA
17978 CTAACTGATC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.05
46 37 0.95
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (46 bp):
CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCCAACCGAAAT
Found at i:18019 original size:32 final size:31
Alignment explanation
Indices: 17972--18031 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
17962 TTGACCCGAA
*
17972 CCGAAACTAACTGATCCGAGATTAACCCAAC
1 CCGAAACCAACTGATCCGAGATTAACCCAAC
**
18003 CCGAACACCAACTGATCCGATTTTAACCC
1 CCGAA-ACCAACTGATCCGAGATTAACCC
18032 GACTCGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.35, C:0.35, G:0.12, T:0.18
Consensus pattern (31 bp):
CCGAAACCAACTGATCCGAGATTAACCCAAC
Found at i:19220 original size:20 final size:20
Alignment explanation
Indices: 19175--19220 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
19165 GACCAACAAA
*
19175 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
19195 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
19214 ATCGCAA
1 ATCGCAA
19221 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:19285 original size:21 final size:21
Alignment explanation
Indices: 19255--19307 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
19245 ATTATGACTA
19255 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
19276 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
19297 TCGCAATGCGA
1 TCGCAATGCGA
19308 ATAAGTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:19340 original size:21 final size:21
Alignment explanation
Indices: 19297--19369 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
19287 TTTTCCCAAT
** *
19297 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
19317 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
19338 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
19359 TCGCAACGCGA
1 TCGCAATGCGA
19370 TACTGACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 12 0.25
21 36 0.75
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:19382 original size:41 final size:41
Alignment explanation
Indices: 19355--19492 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
19345 GCGAATTTGG
19355 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
19396 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * *
19436 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
19477 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
19493 TTTCAAAGCG
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.41
41 47 0.59
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:19383 original size:20 final size:20
Alignment explanation
Indices: 19358--19472 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
19348 AATTTGGAAA
19358 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
19378 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
19399 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
19419 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
19439 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
19459 TTCGCAACGAGATA
1 ATCGCAACGCGATA
19473 ATACATAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:19687 original size:22 final size:22
Alignment explanation
Indices: 19659--19702 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19649 CACTCTCTCA
19659 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
19681 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
19703 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:20216 original size:25 final size:24
Alignment explanation
Indices: 20162--20216 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
20152 TGTTTATTAT
* *
20162 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
20186 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
20212 TGTTT
1 TGTTT
20217 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:21581 original size:19 final size:20
Alignment explanation
Indices: 21527--21593 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
21517 TAGTTTACTT
* *
21527 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
21547 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
21567 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
21586 TCGCAACG
1 TCGCAACG
21594 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:21601 original size:14 final size:14
Alignment explanation
Indices: 21582--21640 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
21572 ATGCGAAATG
21582 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21596 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
21615 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21629 AAAATTGCAACG
1 AAAATCGCAACG
21641 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:21608 original size:33 final size:33
Alignment explanation
Indices: 21566--21656 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
21556 GGAAATGGCT
21566 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
21599 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
21632 ATTGCAACGCGAAATGAAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCA
21657 TTGCGATAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:21620 original size:19 final size:19
Alignment explanation
Indices: 21566--21662 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
21556 GGAAATGGCT
21566 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
21585 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
21599 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
21618 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
21632 ATTGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
21651 ATCGCATTGCGA
1 ATCGCAATGCGA
21663 TAGTCATTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 29 0.48
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:21682 original size:20 final size:20
Alignment explanation
Indices: 21657--21702 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
21647 GAAAATCGCA
21657 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
21677 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
21697 TTGCGA
1 TTGCGA
21703 AAGTAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:21713 original size:20 final size:20
Alignment explanation
Indices: 21673--21728 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
21663 TAGTCATTTC
* * *
21673 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
21693 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
21713 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
21729 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:22121 original size:21 final size:20
Alignment explanation
Indices: 22069--22129 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
22059 GACTCACCTG
22069 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
22089 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
22110 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
22130 CCACCATTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:22128 original size:42 final size:40
Alignment explanation
Indices: 22069--22185 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 40
22059 GACTCACCTG
* * *
22069 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ACCATTCAAGAGGCCACTA
*
22111 TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCACTA
** * *
22151 TCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGA-GTCCC-CCCACCATTCAAGAG
22186 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
40 25 0.38
41 7 0.11
42 33 0.51
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCACTA
Found at i:23594 original size:14 final size:14
Alignment explanation
Indices: 23560--23598 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23550 TTGATTGTTT
23560 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
23574 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
23588 TGTTGATTTGT
1 AATTGATTTGT
23599 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:23757 original size:19 final size:17
Alignment explanation
Indices: 23732--23781 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
23722 TATCGCAACT
23732 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
23750 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
23765 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
23782 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:23825 original size:20 final size:20
Alignment explanation
Indices: 23800--23852 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
23790 TCGCATTACA
*
23800 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
23820 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
23840 ATTTTCGCGTTGC
1 ATTTTCGAGTTGC
23853 AATTTCCCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:24107 original size:20 final size:20
Alignment explanation
Indices: 24082--24194 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
24072 TGATTTTCAA
*
24082 AATCTCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* * *
24102 AATCTCGTTACAAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
24122 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
24142 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
24162 TATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
24182 TATCGCGTTGCGA
1 AATCGCGTTGCGA
24195 TTTTGTATTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:24225 original size:41 final size:41
Alignment explanation
Indices: 24123--24239 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
24113 AAAAGTCAGA
* * ** *
24123 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGT-ATT
*
24163 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
24204 ATCTCGTTGCGATAGTTAGTATCGCATTGCGATTTT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT
24240 CCAAATTTGC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 31 0.46
41 34 0.51
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:24273 original size:20 final size:21
Alignment explanation
Indices: 24225--24276 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
24215 ATAGTTAGTA
*
24225 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
24246 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
24266 TCGCATTGCGA
1 TCGCATTGCGA
24277 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:25086 original size:24 final size:24
Alignment explanation
Indices: 25059--25112 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
25049 GTATTTGAAA
*
25059 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
25083 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
25107 TTTGAT
1 TTTGAT
25113 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:25303 original size:12 final size:12
Alignment explanation
Indices: 25286--25310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25276 ATATAATCCT
25286 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25298 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25310 G
1 G
25311 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:27650 original size:19 final size:19
Alignment explanation
Indices: 27628--27719 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
27618 GGAAATTACT
27628 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27647 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
27661 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27680 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
27694 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27713 ATCGCAA
1 ATCGCAA
27720 CGAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 26 0.46
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27665 original size:33 final size:33
Alignment explanation
Indices: 27632--27754 Score: 210
Period size: 33 Copynumber: 3.7 Consensus size: 33
27622 ATTACTATCG
* *
27632 CAATGCGAAATGAAAATCGCAACGAGATAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
27665 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
*
27698 CAATGCGAAATGAAAATCGCAACGAGGGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
*
27731 CAAAGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
27755 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:27757 original size:19 final size:18
Alignment explanation
Indices: 27628--27758 Score: 79
Period size: 19 Copynumber: 7.7 Consensus size: 18
27618 GGAAATTACT
27628 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
27647 ATCGCAA-CG--A-GATA
1 ATCGCAAGCGAAATGAAA
27661 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
27680 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
27694 ATCACAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
27713 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
27727 ATCACAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
27746 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
27759 TTTAGTTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 32
0.66 0.09 0.25
Matches are distributed among these distances:
14 25 0.30
15 5 0.06
16 6 0.07
17 6 0.07
18 5 0.06
19 37 0.44
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:27808 original size:33 final size:33
Alignment explanation
Indices: 27764--27876 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
27754 GCGAATTTAG
* * * *
27764 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTTA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
27797 TTTCGCATTGCGATTCCCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
27830 TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
27863 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
27877 AGTAATTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:27842 original size:19 final size:19
Alignment explanation
Indices: 27785--27876 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
27775 GATTTTGTCG
*
27785 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
27804 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
27818 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
27837 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
27851 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27870 TTGCGAT
1 TTGCGAT
27877 AGTAATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
14 16 0.29
16 9 0.16
17 8 0.14
19 23 0.41
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:28002 original size:14 final size:15
Alignment explanation
Indices: 27983--28019 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
27973 CATCAATTAA
27983 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
27997 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
28011 ACAAATCAA
1 ACAAATCAA
28020 TTAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:29433 original size:21 final size:21
Alignment explanation
Indices: 29367--29433 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
29357 GTGAATCGGG
*
29367 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
29387 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
29409 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
29430 CTCT
1 CTCT
29434 CGAGGAATTA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:29890 original size:91 final size:90
Alignment explanation
Indices: 29707--29891 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
29697 ATTTCAAACT
*
29707 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
29772 AGAATTGACAATAACCGAATAAATTTAC
63 AGAATTGACAATAACCGAATAAATTTAC
29800 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* * *
29864 GTATTGGCAGTAACCGAATAAATTTAC
64 GAATTGACAATAACCGAATAAATTTAC
29891 T
1 T
29892 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGACAATAACCGAATAAATTTAC
Found at i:31617 original size:20 final size:19
Alignment explanation
Indices: 31590--31744 Score: 106
Period size: 19 Copynumber: 8.8 Consensus size: 19
31580 TCTTTTGGTT
31590 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
31609 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
31630 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
31649 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
31663 GAAATGACTATCGCAAC--
1 GAAATGAAAATCGCAACGA
* *
31680 G--AT-AGAATCGCAACGT
1 GAAATGAAAATCGCAACGA
31696 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
31715 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
31729 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
31745 TGCGATTTTG
Statistics
Matches: 107, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
14 30 0.28
15 2 0.02
16 5 0.05
17 5 0.05
18 2 0.02
19 31 0.29
20 30 0.28
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:31658 original size:14 final size:14
Alignment explanation
Indices: 31639--31727 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
31629 GGAAATGACT
31639 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
31653 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
*
31670 CTATCGCAACGATAGA
1 --ATCGCAACGAGAGA
*
31686 ATCGCAACGTGAAATGAAA
1 ATCGCAAC--G--A-GAGA
31705 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
31719 ATCGCAACG
1 ATCGCAACG
31728 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 27 0.45
15 1 0.02
16 7 0.12
17 7 0.12
18 1 0.02
19 17 0.28
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:31672 original size:33 final size:33
Alignment explanation
Indices: 31590--31744 Score: 193
Period size: 33 Copynumber: 4.5 Consensus size: 33
31580 TCTTTTGGTT
31590 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
**
31629 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
** * *
31663 GAAATGACTATCGCAACGATAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31696 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31729 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
31745 TGCGATTTTG
Statistics
Matches: 107, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
33 76 0.71
34 11 0.10
36 1 0.01
37 1 0.01
40 18 0.17
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:31793 original size:33 final size:32
Alignment explanation
Indices: 31745--31837 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 32
31735 AAAATCGCAA
* *
31745 TGCGATTTTGGTTTCGCGTTGCGATTATCTTGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
31778 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
31811 TGCGATAGTTATTTCCGCGTTGCGATT
1 TGCGAT-TTTATTT-CGCGTTGCGATT
31838 TTCATTCTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTATCTCGT
Found at i:31800 original size:19 final size:19
Alignment explanation
Indices: 31776--31843 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
31766 CGATTATCTT
31776 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGC
*
31795 GTTGCGA--TTC---TCTC
1 GTTGCGATTTTCATTTCGC
*
31809 GTTGCGATAGTT-ATTTCCGC
1 GTTGCGAT-TTTCATTT-CGC
31829 GTTGCGATTTTCATT
1 GTTGCGATTTTCATT
31844 CTCGAAACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 15
0.68 0.05 0.27
Matches are distributed among these distances:
14 10 0.26
17 5 0.13
19 10 0.26
20 13 0.34
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGC
Found at i:32387 original size:20 final size:20
Alignment explanation
Indices: 32362--32453 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
32352 GCTATGTAAA
32362 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
32382 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
32403 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
32423 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
32443 TCGCATTGCGA
1 TCGCATTGCGA
32454 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:32432 original size:41 final size:40
Alignment explanation
Indices: 32362--32453 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
32352 GCTATGTAAA
* *
32362 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT-AT
* * *
32403 TCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAT
32443 TCGCATTGCGA
1 TCGCATTGCGA
32454 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.28
41 33 0.72
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAT
Found at i:32466 original size:41 final size:41
Alignment explanation
Indices: 32382--32591 Score: 135
Period size: 41 Copynumber: 5.1 Consensus size: 41
32372 ATTTACGTAT
* * * *
32382 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGAATTA-TGAAAA
*
32423 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
** * * * *
32464 TCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAA
* * * * * *
32505 TTGCAATGCGATAGT-CAGTA-TCGCATTGCG-ATTTTCCAAAT
1 TCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTAT-GAAAA
* * **
32546 TCGCATTGCGATTTACTTATTCGTATTGCGAATTGGGAAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
32587 TCGCA
1 TCGCA
32592 ACGCGAAATT
Statistics
Matches: 130, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
39 1 0.01
40 27 0.21
41 94 0.72
42 5 0.04
43 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
Found at i:32474 original size:21 final size:21
Alignment explanation
Indices: 32443--32515 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
32433 ATTTACGTAT
* *
32443 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
32464 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
32484 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
32505 TTGCAATGCGA
1 TCGCAATGCGA
32516 TAGTCAGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:32486 original size:61 final size:62
Alignment explanation
Indices: 32357--32494 Score: 156
Period size: 61 Copynumber: 2.3 Consensus size: 62
32347 ATGGCGCTAT
* * * ** *
32357 GTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTAC
1 GTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATAC
* * *
32419 -TTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATAC
1 GTAAATCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC
*
32479 GTAAATCGCAATGCGA
1 GTAAATCGCATTGCGA
32495 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
60 3 0.05
61 55 0.89
62 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (62 bp):
GTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATAC
Found at i:32618 original size:21 final size:22
Alignment explanation
Indices: 32570--32618 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
32560 ACTTATTCGT
32570 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
32591 AACGCGAAATT-GGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
32612 ATTGCGA
1 ATTGCGA
32619 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:36140 original size:21 final size:21
Alignment explanation
Indices: 36114--36172 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
36104 ATTATCCAAT
*
36114 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
36135 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
36156 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
36173 TAATAAATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:41845 original size:19 final size:19
Alignment explanation
Indices: 41823--41861 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41813 GAAAACATGA
41823 AAAAACCGGAAAAATCGGG
1 AAAAACCGGAAAAATCGGG
*
41842 AAAAACCGGGAAAATCGGG
1 AAAAACCGGAAAAATCGGG
41861 A
1 A
41862 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.28, T:0.05
Consensus pattern (19 bp):
AAAAACCGGAAAAATCGGG
Found at i:45277 original size:3 final size:3
Alignment explanation
Indices: 45269--45293 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45259 GATGGAAATA
45269 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
45294 CGAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47291 original size:22 final size:20
Alignment explanation
Indices: 47255--47299 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
47245 ATTAATTATT
47255 TAAAAAAATTAAATAAAAATA
1 TAAAAAAATTAAATAAAAA-A
*
47276 TAAAAAACATTTAATAAAAAA
1 TAAAAAA-ATTAAATAAAAAA
47297 TAA
1 TAA
47300 TTTTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAAAATTAAATAAAAAA
Found at i:51940 original size:2 final size:2
Alignment explanation
Indices: 51933--51997 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
51923 GGTCACTATC
51933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
51975 AT AT AT AT AT -T GT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
51998 TGATACTATT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:59193 original size:14 final size:14
Alignment explanation
Indices: 59174--59213 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
59164 TGAAAATACC
59174 CTAAAGTGCAATGA
1 CTAAAGTGCAATGA
59188 CTAAAGTGCAATGA
1 CTAAAGTGCAATGA
59202 CTAAAGTGCAAT
1 CTAAAGTGCAAT
59214 TTACCCATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (14 bp):
CTAAAGTGCAATGA
Found at i:69998 original size:17 final size:17
Alignment explanation
Indices: 69972--70034 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
69962 TTATTTTCAA
69972 TATTAAAAAAATAAAAT
1 TATTAAAAAAATAAAAT
*
69989 TATTATAAAAATAAAA-
1 TATTAAAAAAATAAAAT
* *
70005 CA-TAAAAAAATAGAAT
1 TATTAAAAAAATAAAAT
*
70021 TA-CAAAAAAATAAA
1 TATTAAAAAAATAAA
70035 GATATTTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 11 0.29
16 12 0.32
17 15 0.39
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (17 bp):
TATTAAAAAAATAAAAT
Found at i:72122 original size:21 final size:21
Alignment explanation
Indices: 72096--72144 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
72086 CCCACAAGCG
72096 ATACCCCTTTACTCCATCAGC
1 ATACCCCTTTACTCCATCAGC
72117 ATACCCCTTTACTCCATCAGC
1 ATACCCCTTTACTCCATCAGC
72138 ATACCCC
1 ATACCCC
72145 AAAAATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.45, G:0.04, T:0.27
Consensus pattern (21 bp):
ATACCCCTTTACTCCATCAGC
Found at i:77864 original size:17 final size:17
Alignment explanation
Indices: 77842--77880 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
77832 TAAATCAAAT
77842 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
77859 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
77876 -AATTA
1 TAATTA
77881 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:87669 original size:15 final size:15
Alignment explanation
Indices: 87651--87686 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
87641 AATTTAAAGA
87651 ACCTCATGTGTCACC
1 ACCTCATGTGTCACC
87666 ACCTCATGTGTCACC
1 ACCTCATGTGTCACC
87681 ACCTCA
1 ACCTCA
87687 ATAGTAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.42, G:0.11, T:0.25
Consensus pattern (15 bp):
ACCTCATGTGTCACC
Found at i:89633 original size:31 final size:31
Alignment explanation
Indices: 89582--89653 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
89572 TTAACCCATG
*
89582 GTGACCACATCTTAAATAAATAAAAACAAAA
1 GTGACCATATCTTAAATAAATAAAAACAAAA
* * * *
89613 GTGATCATATCTTAATTAAATAAAAACGAAG
1 GTGACCATATCTTAAATAAATAAAAACAAAA
89644 GTGACCATAT
1 GTGACCATAT
89654 ATAATGTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (31 bp):
GTGACCATATCTTAAATAAATAAAAACAAAA
Found at i:99605 original size:2 final size:2
Alignment explanation
Indices: 99598--99624 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
99588 ACTCTAGTTG
99598 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
99625 ATGTACTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.