Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004524.1 Hibiscus syriacus cultivar Beakdansim tig00009981_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: 188642
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1039 original size:20 final size:20
Alignment explanation
Indices: 1014--1056 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1004 TGCGTAACTG
1014 TTATTAATATTATTTTTCA-A
1 TTATTAATA-TATTTTTCATA
*
1034 TTATTATTATATTTTTCATA
1 TTATTAATATATTTTTCATA
1054 TTA
1 TTA
1057 AACTGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTAATATATTTTTCATA
Found at i:3193 original size:12 final size:12
Alignment explanation
Indices: 3176--3208 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3166 ATACGGTATG
3176 AACAATACCGTA
1 AACAATACCGTA
*
3188 AACAATACCGTG
1 AACAATACCGTA
3200 AACAATACC
1 AACAATACC
3209 ATGAATAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.27, G:0.09, T:0.15
Consensus pattern (12 bp):
AACAATACCGTA
Found at i:3213 original size:12 final size:12
Alignment explanation
Indices: 3173--3213 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3163 ACTATACGGT
3173 ATGAACAATACC
1 ATGAACAATACC
* *
3185 GTAAACAATACC
1 ATGAACAATACC
*
3197 GTGAACAATACC
1 ATGAACAATACC
3209 ATGAA
1 ATGAA
3214 TAGTGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:5502 original size:11 final size:11
Alignment explanation
Indices: 5488--5518 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5478 TCCTTAAGCT
*
5488 TAAGTATCACC
1 TAAGGATCACC
5499 TAAGGATCACC
1 TAAGGATCACC
5510 TAAGGATCA
1 TAAGGATCA
5519 AAACCCACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (11 bp):
TAAGGATCACC
Found at i:8169 original size:21 final size:21
Alignment explanation
Indices: 8145--8203 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
8135 CAGCGTAGAA
* * *
8145 ATGTCTCGAAGGACCACATAT
1 ATGTCCCGAAAGACCACATAG
8166 ATGTCCCGAAAGACCACATAG
1 ATGTCCCGAAAGACCACATAG
*
8187 ATGTCCCAAAAGACCAC
1 ATGTCCCGAAAGACCAC
8204 TCCTTAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAG
Found at i:13096 original size:23 final size:24
Alignment explanation
Indices: 13019--13111 Score: 134
Period size: 24 Copynumber: 3.9 Consensus size: 24
13009 CATTGAGGTA
*
13019 TGTCCCGAAAGACCGTGTAGAATT
1 TGTCCCGAAGGACCGTGTAGAATT
*
13043 TGTCCCGAAGGACCGCGTAGAATT
1 TGTCCCGAAGGACCGTGTAGAATT
* *
13067 TGTCCCGAAGGACCATATAGAA-T
1 TGTCCCGAAGGACCGTGTAGAATT
*
13090 TGTCCCGAAGGACCGCGTAGAA
1 TGTCCCGAAGGACCGTGTAGAA
13112 CCCCCGACTC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
23 20 0.33
24 41 0.67
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (24 bp):
TGTCCCGAAGGACCGTGTAGAATT
Found at i:13104 original size:47 final size:48
Alignment explanation
Indices: 13019--13111 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 48
13009 CATTGAGGTA
* *
13019 TGTCCCGAAAGACCGTGTAGAATTTGTCCCGAAGGACCGCGTAGAATT
1 TGTCCCGAAAGACCATATAGAATTTGTCCCGAAGGACCGCGTAGAATT
*
13067 TGTCCCGAAGGACCATATAGAA-TTGTCCCGAAGGACCGCGTAGAA
1 TGTCCCGAAAGACCATATAGAATTTGTCCCGAAGGACCGCGTAGAA
13112 CCCCCGACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 23 0.55
48 19 0.45
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (48 bp):
TGTCCCGAAAGACCATATAGAATTTGTCCCGAAGGACCGCGTAGAATT
Found at i:13443 original size:39 final size:39
Alignment explanation
Indices: 13396--13737 Score: 470
Period size: 37 Copynumber: 9.0 Consensus size: 39
13386 TATATATAAA
13396 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
*
13435 ATTTTGAAAACATATATATAATATATAG-TTTTGAAAAT
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
*
13473 ATTTT--AAATATATATAT-ATAATATAGTTTTTGAAAAC
1 ATTTTGAAAACATATATATAAT-ATATAGTTTTTGAAAAC
13510 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
*
13549 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
* * * *
13588 ATTTTGAAATATATATATATAATATTTAGTTTTGGAAAAT
1 ATTTTGAAA-ACATATATATAATATATAGTTTTTGAAAAC
* **
13628 ATTTTG-AAA-ATATATATAATTTATAGTTTTTGAAAGT
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
*
13665 ATTTTG-AAA-ATATATATAATATATAGTTTTTAAAAAC
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
* * *
13702 ATCTTG-AAA-ATATATATATTATATAGTTTTTAAAAA
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAA
13738 ATATTTATAT
Statistics
Matches: 279, Mismatches: 18, Indels: 14
0.90 0.06 0.05
Matches are distributed among these distances:
35 2 0.01
36 17 0.06
37 105 0.38
38 15 0.05
39 105 0.38
40 35 0.13
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (39 bp):
ATTTTGAAAACATATATATAATATATAGTTTTTGAAAAC
Found at i:13482 original size:25 final size:27
Alignment explanation
Indices: 13436--13550 Score: 75
Period size: 25 Copynumber: 4.4 Consensus size: 27
13426 TTTGAAAACA
13436 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
* *
13463 TTTTGAAAATAT-TTTA-AATATATA-
1 TTTTGAAAACATATATATAATATATAG
* * * * * *
13487 -TAT-ATAATATAGTTTTTGAA-A-ACA-
1 TTTTGAAAACATA-TATAT-AATATATAG
13511 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
13538 TTTTTGAAAACAT
1 -TTTTGAAAACAT
13551 TTTGAAAACA
Statistics
Matches: 66, Mismatches: 12, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
22 6 0.09
23 2 0.03
24 7 0.11
25 15 0.23
26 13 0.20
27 11 0.17
28 12 0.18
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (27 bp):
TTTTGAAAACATATATATAATATATAG
Found at i:13523 original size:114 final size:115
Alignment explanation
Indices: 13396--13737 Score: 516
Period size: 114 Copynumber: 3.0 Consensus size: 115
13386 TATATATAAA
13396 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATAT
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATAT
13461 AG-TTTTGAAAATATTTTAAATATATATATATAATATAGTTTTTGAAAAC
66 AGTTTTTGAAAATATTTTAAATATATATATATAATATAGTTTTTGAAAAC
13510 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATAT
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATAT
* *
13575 AGTTTTTGAAAATATTTTGAAATATATATATATAATATTTAGTTTTGGAAAAT
66 AGTTTTTGAAAATATTTT-AAATATATATATATAATA--TAGTTTTTGAAAAC
* **
13628 ATTTTG-AAA-ATATATATAATTTATAGTTTTTGAAAGTATTTTG-AAA-ATATATATAATATAT
1 ATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATAT
* * * * *
13689 AGTTTTTAAAAACATCTTGAAA-ATATATATATTATATAGTTTTTAAAAA
66 AGTTTTTGAAAATAT-TTTAAATATATATATATAATATAGTTTTTGAAAA
13738 ATATTTATAT
Statistics
Matches: 212, Mismatches: 11, Indels: 13
0.90 0.05 0.06
Matches are distributed among these distances:
111 11 0.05
113 13 0.06
114 98 0.46
115 20 0.09
116 49 0.23
117 3 0.01
118 18 0.08
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (115 bp):
ATTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATAT
AGTTTTTGAAAATATTTTAAATATATATATATAATATAGTTTTTGAAAAC
Found at i:13772 original size:8 final size:7
Alignment explanation
Indices: 13738--13788 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
13728 TTTTTAAAAA
13738 ATAT-TT
1 ATATATT
13744 ATATATT
1 ATATATT
13751 ATATA-T
1 ATATATT
13757 -TATATT
1 ATATATT
13763 ATAGTATT
1 ATA-TATT
13771 ATATATT
1 ATATATT
* *
13778 TTTTATT
1 ATATATT
13785 ATAT
1 ATAT
13789 TATTGTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.11
6 6 0.16
7 20 0.54
8 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (7 bp):
ATATATT
Found at i:13792 original size:22 final size:19
Alignment explanation
Indices: 13742--13791 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
13732 TAAAAAATAT
13742 TTATATATTATATATTATA
1 TTATATATTATATATTATA
*
13761 TTATAGTATTATATATT-TT
1 TTATA-TATTATATATTATA
13780 TTATTATATTAT
1 TTA-TATATTAT
13792 TGTAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATATATTATATATTATA
Found at i:13808 original size:22 final size:22
Alignment explanation
Indices: 13742--13808 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
13732 TAAAAAATAT
13742 TTATA-TATTATATA-TTA-TA
1 TTATAGTATTATATATTTATTA
*
13761 TTATAGTATTATATATTTTTTA
1 TTATAGTATTATATATTTATTA
* *
13783 TTATATTATTGTA-ATTTATTA
1 TTATAGTATTATATATTTATTA
13804 GTTAT
1 -TTAT
13809 TATTTTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.12
20 9 0.22
21 9 0.22
22 17 0.43
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TTATAGTATTATATATTTATTA
Found at i:13835 original size:16 final size:17
Alignment explanation
Indices: 13811--13853 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
13801 TTAGTTATTA
*
13811 TTTTCATTTTCATT-TT
1 TTTTTATTTTCATTCTT
*
13827 TTTTTATTTTCTTTCTT
1 TTTTTATTTTCATTCTT
13844 TTTGTTATTT
1 TTT-TTATTT
13854 GGTCCAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
17 5 0.22
18 6 0.26
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTCATTCTT
Found at i:16265 original size:15 final size:15
Alignment explanation
Indices: 16230--16271 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16220 AAGCATGCAG
*
16230 TTTATCATTTTTACT
1 TTTATCATTATTACT
16245 TTTATCATTATTA-T
1 TTTATCATTATTACT
16259 TTCTATC-TTATTA
1 TT-TATCATTATTA
16272 ACTAATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATCATTATTACT
Found at i:23946 original size:15 final size:14
Alignment explanation
Indices: 23920--23949 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
23910 ATAGATATCA
23920 TCTTATATTATTAT
1 TCTTATATTATTAT
23934 TCTTATCATTATTAT
1 TCTTAT-ATTATTAT
23949 T
1 T
23950 ATTGTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (14 bp):
TCTTATATTATTAT
Found at i:23948 original size:18 final size:18
Alignment explanation
Indices: 23925--23961 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
23915 TATCATCTTA
23925 TATTATTATTCTTATCAT
1 TATTATTATTCTTATCAT
*
23943 TATTATTATTGTTATCAT
1 TATTATTATTCTTATCAT
23961 T
1 T
23962 CATATCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTATTATTCTTATCAT
Found at i:24241 original size:20 final size:21
Alignment explanation
Indices: 24207--24246 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24197 CTGCGTAGAA
24207 ATGTCCCGAAAGACCACATAG
1 ATGTCCCGAAAGACCACATAG
*
24228 ATGT-CCGAATGACCACATA
1 ATGTCCCGAAAGACCACATA
24247 TAAACATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAG
Found at i:27388 original size:34 final size:35
Alignment explanation
Indices: 27326--27393 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
27316 TTCCGATTCA
27326 AAACAGTGGAGATATTCTAACACTATTCTAACATC
1 AAACAGTGGAGATATTCTAACACTATTCTAACATC
27361 AAACAGTGGAGATATTCT-ACACTATTCTAACAT
1 AAACAGTGGAGATATTCTAACACTATTCTAACAT
27394 GGTTTCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 15 0.45
35 18 0.55
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (35 bp):
AAACAGTGGAGATATTCTAACACTATTCTAACATC
Found at i:28127 original size:18 final size:18
Alignment explanation
Indices: 28100--28143 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28090 TATCATCTTA
* * *
28100 TTATCCTTATTATTATTT
1 TTATCATTATTAGTATTG
28118 TTATCATTATTAGTATTG
1 TTATCATTATTAGTATTG
28136 TTATCATT
1 TTATCATT
28144 CATATCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (18 bp):
TTATCATTATTAGTATTG
Found at i:28423 original size:21 final size:21
Alignment explanation
Indices: 28397--28437 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28387 CTGCGTAGAA
28397 ATGTCCCGAAAGACCACATAG
1 ATGTCCCGAAAGACCACATAG
*
28418 ATGTCCCGAATGACCACATA
1 ATGTCCCGAAAGACCACATA
28438 TAACACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAG
Found at i:33481 original size:44 final size:44
Alignment explanation
Indices: 33397--33482 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
33387 ACATATTTCA
* *
33397 TACTTCATTTCATCTTCTTTTGAATTTAATTTTTCTTCATTCCG
1 TACTTCATTTCATCTTCTTTTGAATTTAATCTTTCGTCATTCCG
* *
33441 TACTTCATTTCATTTTCTTTTGAATTTAATCTTTGGTCATTC
1 TACTTCATTTCATCTTCTTTTGAATTTAATCTTTCGTCATTC
33483 TGTGTGGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.57
Consensus pattern (44 bp):
TACTTCATTTCATCTTCTTTTGAATTTAATCTTTCGTCATTCCG
Found at i:38759 original size:33 final size:32
Alignment explanation
Indices: 38710--38851 Score: 168
Period size: 33 Copynumber: 4.4 Consensus size: 32
38700 AATCTTTTGG
* *
38710 TATTCGGGATCGGGTCGTGTTTTTTAAAGTTTGA
1 TATTCGGG-TCGGGTCG-GTTTTTTTAAGTGTGA
*
38744 TATTCGGGTCGGGTCGGATTTTTTTAAGTGTGC
1 TATTCGGGTCGGGTCGG-TTTTTTTAAGTGTGA
38777 TATTCGGGTC-GG--GG-TTTTTTAAGTGTGA
1 TATTCGGGTCGGGTCGGTTTTTTTAAGTGTGA
*
38805 TAGTT-TGGTCGGGTCGGGTTTTTTTAAGTGTGA
1 TA-TTCGGGTCGGGTC-GGTTTTTTTAAGTGTGA
38838 TATTCGGGTCGGGT
1 TATTCGGGTCGGGT
38852 TTAGGGTGAA
Statistics
Matches: 94, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
28 19 0.20
29 4 0.04
30 2 0.02
32 7 0.07
33 54 0.57
34 8 0.09
ACGTcount: A:0.13, C:0.09, G:0.35, T:0.43
Consensus pattern (32 bp):
TATTCGGGTCGGGTCGGTTTTTTTAAGTGTGA
Found at i:38795 original size:61 final size:61
Alignment explanation
Indices: 38719--38850 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 61
38709 GTATTCGGGA
* * * *
38719 TCGGGTCGTGTTTTTTAAAGTTTGATA-TTCGGGTCGGGTCGGATTTTTTTAAGTGTGCTAT
1 TCGGGTCGGGGTTTTTAAAGTGTGATAGTT-GGGTCGGGTCGGATTTTTTTAAGTGTGATAT
* * *
38780 TCGGGTCGGGGTTTTTTAAGTGTGATAGTTTGGTCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGGTTTTTAAAGTGTGATAGTTGGGTCGGGTCGGATTTTTTTAAGTGTGATAT
38841 TCGGGTCGGG
1 TCGGGTCGGG
38851 TTTAGGGTGA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
61 61 0.97
62 2 0.03
ACGTcount: A:0.13, C:0.09, G:0.35, T:0.43
Consensus pattern (61 bp):
TCGGGTCGGGGTTTTTAAAGTGTGATAGTTGGGTCGGGTCGGATTTTTTTAAGTGTGATAT
Found at i:39467 original size:16 final size:17
Alignment explanation
Indices: 39446--39493 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
39436 GTTTCAGATT
39446 CAGATTCCAATTCCT-A
1 CAGATTCCAATTCCTCA
*
39462 CAGATTCCAATTGCTTCA
1 CAGATTCCAATT-CCTCA
*
39480 CAGATTCTAATTCC
1 CAGATTCCAATTCC
39494 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (17 bp):
CAGATTCCAATTCCTCA
Found at i:43889 original size:2 final size:2
Alignment explanation
Indices: 43882--43920 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
43872 TTGTATTATT
* *
43882 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43921 TATCTAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:54788 original size:11 final size:10
Alignment explanation
Indices: 54772--54797 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54762 TCTTAAGTCG
54772 AAAAAAAAAC
1 AAAAAAAAAC
54782 AAAAAAAAAC
1 AAAAAAAAAC
54792 AAAAAA
1 AAAAAA
54798 GAGAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:55485 original size:14 final size:14
Alignment explanation
Indices: 55466--55492 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55456 GATCAGAACT
55466 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
55480 TCAAGATTCCAGA
1 TCAAGATTCCAGA
55493 CAAGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:56005 original size:12 final size:12
Alignment explanation
Indices: 55984--56014 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55974 GGGGCTTCCT
*
55984 AATTTTAGAACC
1 AATTTCAGAACC
55996 AATTTCAGAACC
1 AATTTCAGAACC
56008 AATTTCA
1 AATTTCA
56015 ATTTCACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (12 bp):
AATTTCAGAACC
Found at i:56204 original size:110 final size:110
Alignment explanation
Indices: 56007--56205 Score: 301
Period size: 110 Copynumber: 1.8 Consensus size: 110
55997 ATTTCAGAAC
* * *
56007 CAATTTCAATTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCACGAAGAAG
* *
56072 GGGCGGCTGATTGTTAACAAATAACTTTTCAATTTCATTCAGAGT
66 GGGCGGCTGACTGTCAACAAATAACTTTTCAATTTCATTCAGAGT
* *
56117 CAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCAC-AACGAA
1 CAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCACGAA-GAA
* *
56181 GGGGTGGCTGACTGTCAATAAATAA
65 GGGGCGGCTGACTGTCAACAAATAA
56206 TTTCCCAGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 2 0.03
110 77 0.97
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (110 bp):
CAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCACGAAGAAG
GGGCGGCTGACTGTCAACAAATAACTTTTCAATTTCATTCAGAGT
Found at i:58380 original size:51 final size:50
Alignment explanation
Indices: 58272--58381 Score: 116
Period size: 49 Copynumber: 2.2 Consensus size: 50
58262 TACATCATAT
* * * *
58272 TATATATATATATATATTATTTTTATATTTTTTTGGACTTTTTCCTTATT
1 TATATATATATATATATTATTTTTATATATTTTTAGACTTTTTCATTATG
* *
58322 TAT-TATATATATATATATATTTTTCTCATATTTTTAGA-TATTTTATATTATG
1 TATATATATATATATAT-TATTTTTAT-ATATTTTTAGACT-TTTT-CATTATG
58374 TATATATA
1 TATATATA
58382 CACGTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
49 13 0.27
50 12 0.24
51 13 0.27
52 7 0.14
53 4 0.08
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61
Consensus pattern (50 bp):
TATATATATATATATATTATTTTTATATATTTTTAGACTTTTTCATTATG
Found at i:58812 original size:26 final size:27
Alignment explanation
Indices: 58775--58826 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
58765 GAGCTTCCCC
58775 TTATTTTAC-TTTATTTATTGTTTTCT
1 TTATTTTACTTTTATTTATTGTTTTCT
* * *
58801 TTATTTTGCTTTTGTTTATTTTTTTC
1 TTATTTTACTTTTATTTATTGTTTTC
58827 CCTAACATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.75
Consensus pattern (27 bp):
TTATTTTACTTTTATTTATTGTTTTCT
Found at i:59303 original size:17 final size:17
Alignment explanation
Indices: 59264--59320 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
59254 TGATGTTCTA
59264 GGTACCCGG-TTTT-CG
1 GGTACCCGGATTTTGCG
*
59279 GATACCCGGATTTTGCG
1 GGTACCCGGATTTTGCG
59296 GGTACCCGGATTTTGCG
1 GGTACCCGGATTTTGCG
59313 GGTACCCG
1 GGTACCCG
59321 TATGTCGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.21
16 4 0.11
17 26 0.68
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.28
Consensus pattern (17 bp):
GGTACCCGGATTTTGCG
Found at i:59330 original size:32 final size:32
Alignment explanation
Indices: 59264--59335 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
59254 TGATGTTCTA
*
59264 GGTACCCGGTTTTCGGATACCCGGATTTTGCG
1 GGTACCCGGTTTTCGGATACCCGGATTGTGCG
* *
59296 GGTACCCGGATTTTGCGGGTACCCGTA-TGT-CG
1 GGTACCCGG-TTTT-CGGATACCCGGATTGTGCG
59328 GGTACCCG
1 GGTACCCG
59336 AATACCCGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 19 0.54
33 6 0.17
34 10 0.29
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.28
Consensus pattern (32 bp):
GGTACCCGGTTTTCGGATACCCGGATTGTGCG
Found at i:61504 original size:17 final size:17
Alignment explanation
Indices: 61482--61515 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61472 TGTGTAATTT
61482 TAGAGACTAATTTATAA
1 TAGAGACTAATTTATAA
61499 TAGAGACTAATTTATAA
1 TAGAGACTAATTTATAA
61516 ATTTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
TAGAGACTAATTTATAA
Found at i:63215 original size:47 final size:46
Alignment explanation
Indices: 63135--63228 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 46
63125 TGCTTCAGGT
63135 ATCTCTCCCATTTTCTTTTGCTTCTAACACACACACACACGTACAC
1 ATCTCTCCCATTTTCTTTTGCTTCTAACACACACACACACGTACAC
63181 ATCTCTCCCATTTTCTTTTTGCTTCTAACACACACACACACGTACAC
1 ATCTCTCCCATTTTC-TTTTGCTTCTAACACACACACACACGTACAC
63228 A
1 A
63229 CATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 15 0.32
47 32 0.68
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (46 bp):
ATCTCTCCCATTTTCTTTTGCTTCTAACACACACACACACGTACAC
Found at i:68523 original size:16 final size:17
Alignment explanation
Indices: 68499--68531 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
68489 CATTTGATAT
68499 TGATATTTTTA-AAAAA
1 TGATATTTTTATAAAAA
*
68515 TGATTTTTTTATAAAAA
1 TGATATTTTTATAAAAA
68532 AATATGTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TGATATTTTTATAAAAA
Found at i:72524 original size:27 final size:27
Alignment explanation
Indices: 72474--72525 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
72464 CTTGTTATCC
*
72474 ACCATCCACGTTTTGTTAGGGATTGCA
1 ACCATCCACGTTTTGTTAAGGATTGCA
*
72501 ACCATCCACGTTTTGTTAATGATTG
1 ACCATCCACGTTTTGTTAAGGATTG
72526 TAAATTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
ACCATCCACGTTTTGTTAAGGATTGCA
Found at i:80324 original size:13 final size:13
Alignment explanation
Indices: 80285--80312 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
80275 ATAATTGTAA
80285 AAAATAATTAAAT
1 AAAATAATTAAAT
80298 AAAATAATTAAAT
1 AAAATAATTAAAT
80311 AA
1 AA
80313 TTAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATAATTAAAT
Found at i:80377 original size:10 final size:10
Alignment explanation
Indices: 80362--80405 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
80352 ATACCTTAAG
80362 TTGAGAGGAT
1 TTGAGAGGAT
*
80372 TTGAGAGAAGT
1 TTGAGAGGA-T
80383 TTGAGAGGAT
1 TTGAGAGGAT
80393 TTGAGAGGAT
1 TTGAGAGGAT
80403 TTG
1 TTG
80406 GTGTGATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.32
Consensus pattern (10 bp):
TTGAGAGGAT
Found at i:90962 original size:20 final size:22
Alignment explanation
Indices: 90934--90984 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
90924 TTATTTTCCC
90934 CTTCATTTTCCTATTT-TCTTC-T
1 CTTC-TTTTCCT-TTTCTCTTCGT
90956 -TTCTTTTCCTTTTCTCTTCGT
1 CTTCTTTTCCTTTTCTCTTCGT
90977 CTTCTTTT
1 CTTCTTTT
90985 TTCTCCATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 4 0.15
22 7 0.27
ACGTcount: A:0.04, C:0.27, G:0.02, T:0.67
Consensus pattern (22 bp):
CTTCTTTTCCTTTTCTCTTCGT
Found at i:92984 original size:34 final size:34
Alignment explanation
Indices: 92910--92992 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 34
92900 TCAGGTCAGG
92910 TATATATATATTTAAATTAAATATATAAATATTA
1 TATATATATATTTAAATTAAATATATAAATATTA
*
92944 TATATATAT-TTTAAATTAAATTAAATTTATTAATATTA
1 TATATATATATTTAAATTAAA-T--A--TATAAATATTA
92982 TATATATATAT
1 TATATATATAT
92993 ATATATATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
33 11 0.26
34 10 0.24
36 1 0.02
38 19 0.45
39 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATATATTTAAATTAAATATATAAATATTA
Found at i:96197 original size:14 final size:14
Alignment explanation
Indices: 96180--96210 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
96170 TGAGAAGAGG
96180 AAAAAAAGAAAATA
1 AAAAAAAGAAAATA
*
96194 AAAAAAATAAAATA
1 AAAAAAAGAAAATA
96208 AAA
1 AAA
96211 GGGAGGAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (14 bp):
AAAAAAAGAAAATA
Found at i:96341 original size:16 final size:16
Alignment explanation
Indices: 96322--96356 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
96312 AAAGGAAAAA
*
96322 GAAAAATTAATTAATT
1 GAAAAATTAATTAAAT
*
96338 GAAAAGTTAATTAAAT
1 GAAAAATTAATTAAAT
96354 GAA
1 GAA
96357 CGAGGGACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (16 bp):
GAAAAATTAATTAAAT
Found at i:97397 original size:5 final size:5
Alignment explanation
Indices: 97389--97441 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
97379 CTAAAAAAGA
*
97389 AAAAT AAAAT GAAAA- AAAATT AAAAT -AAAT AAAAT -GAAT AAAAT AAAAT
1 AAAAT AAAAT -AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
97438 AAAA
1 AAAA
97442 AATAATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
4 11 0.27
5 22 0.54
6 8 0.20
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:97413 original size:9 final size:9
Alignment explanation
Indices: 97390--97441 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
97380 TAAAAAAGAA
97390 AAATAAAAT
1 AAATAAAAT
*
97399 GAA-AAAA-
1 AAATAAAAT
*
97406 AATTAAAAT
1 AAATAAAAT
97415 AAATAAAAT
1 AAATAAAAT
*
97424 GAATAAAAT
1 AAATAAAAT
97433 AAAATAAAA
1 -AAATAAAA
97442 AATAATAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
7 1 0.03
8 8 0.24
9 18 0.53
10 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:97434 original size:14 final size:12
Alignment explanation
Indices: 97388--97451 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 12
97378 CCTAAAAAAG
*
97388 AAAAATAAAATG
1 AAAAATAAAATA
*
97400 AAAAA-AAATTAA
1 AAAAATAAAAT-A
97412 AATAAATAAAATGA
1 AA-AAATAAAAT-A
97426 ATAAAATAAAATA
1 A-AAAATAAAATA
97439 AAAAATAATAATA
1 AAAAATAA-AATA
97452 TACTAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 4 0.09
12 14 0.33
13 9 0.21
14 15 0.35
15 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:97451 original size:23 final size:24
Alignment explanation
Indices: 97389--97451 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
97379 CTAAAAAAGA
*
97389 AAAATAAAATGAAAAAAAATTAAAAT
1 AAAA-AAAATG-AATAAAATTAAAAT
*
97415 AAATAAAATGAATAAAA-TAAAAT
1 AAAAAAAATGAATAAAATTAAAAT
97438 AAAAAATAAT-AATA
1 AAAAAA-AATGAATA
97452 TACTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 15 0.45
24 9 0.27
25 6 0.18
26 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (24 bp):
AAAAAAAATGAATAAAATTAAAAT
Found at i:97506 original size:35 final size:33
Alignment explanation
Indices: 97466--97754 Score: 164
Period size: 32 Copynumber: 8.4 Consensus size: 33
97456 AAATATAATT
*
97466 TATATAATATATATATTTCAAAAATATTTTTTAAC
1 TATATAATATATAT-TTTCAAAAA-ATTTTTAAAC
*
97501 TATAT-AT-TATATTTT-AAAAAAGTTTTCAAAAC
1 TATATAATATATATTTTCAAAAAA-TTTT-TAAAC
**
97533 TATATGTTATATAGTTTTC--AAAATGTTTTAAA-
1 TATATAATATATA-TTTTCAAAAAAT-TTTTAAAC
* *
97565 AATATTATATA-AGTTTTCAAAAAATGTTTTTAAAAC
1 TATATAATATATA-TTTTCAAAAAA--TTTTT-AAAC
* * *
97601 TATATATTATATAATTTTTTAAAAATGTTTTTTAAAC
1 TATATAATATAT-A-TTTTCAAAAA--ATTTTTAAAC
* ** *
97638 TATATTATATAT-TTTTCAAAATGTTTTTAAAA
1 TATATAATATATATTTTCAAAAAATTTTTAAAC
*
97670 TATATTATATA-ATTTTTCAAAAAATGTTTTAAAAAC
1 TATATAATATATA-TTTTCAAAAAAT-TTTT--AAAC
* * *
97706 TATATACTATATAAGTTTTCAAAATATTTTAAAAAC
1 TATATAATATAT-A-TTTTCAAAAAATTTT-TAAAC
*
97742 TATACAATATATA
1 TATATAATATATA
97755 AATGTTTTCA
Statistics
Matches: 200, Mismatches: 29, Indels: 50
0.72 0.10 0.18
Matches are distributed among these distances:
30 1 0.00
31 16 0.08
32 38 0.19
33 24 0.12
34 29 0.14
35 14 0.07
36 34 0.17
37 17 0.09
38 27 0.14
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (33 bp):
TATATAATATATATTTTCAAAAAATTTTTAAAC
Found at i:97671 original size:103 final size:106
Alignment explanation
Indices: 97503--97745 Score: 323
Period size: 105 Copynumber: 2.3 Consensus size: 106
97493 TTTTTAACTA
* *
97503 TATATTATATTTTAAAAAAGTTTTCAAAACTATATGTTATATAGTTTTCAAAATGTTTT-AAAA-
1 TATATAATTTTTTAAAAAAGTTTTCAAAACTATA-GTTATATAGTTTTCAAAATGTTTTAAAAAT
* *
97566 ATATTATATAAGTTTTCAAAAAATGTTTTTAAAACTATATAT
65 ATATTATATAAGTTTTCAAAAAATGTTTTAAAAACTATATAC
* ** * *
97608 TATATAATTTTTTAAAAATGTTTTTTAAACTATA-TTATATATTTTTCAAAATGTTTTTAAAATA
1 TATATAATTTTTTAAAAAAGTTTTCAAAACTATAGTTATATAGTTTTCAAAATGTTTTAAAAATA
*
97672 TATTATATAATTTTTCAAAAAATGTTTTAAAAACTATATAC
66 TATTATATAAGTTTTCAAAAAATGTTTTAAAAACTATATAC
* * * *
97713 TATATAAGTTTTCAAAATA-TTTTAAAAACTATA
1 TATATAATTTTTTAAAAAAGTTTTCAAAACTATA
97746 CAATATATAA
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
103 22 0.18
104 16 0.13
105 83 0.69
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (106 bp):
TATATAATTTTTTAAAAAAGTTTTCAAAACTATAGTTATATAGTTTTCAAAATGTTTTAAAAATA
TATTATATAAGTTTTCAAAAAATGTTTTAAAAACTATATAC
Found at i:97768 original size:63 final size:61
Alignment explanation
Indices: 97691--97818 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 61
97681 ATTTTTCAAA
*
97691 AAATGTTTTAAAAACTATATACTATATAAGTTTTCAAAATATTTT-AAAAACTATACAATA-TAT
1 AAATGTTTTAAAAACTATATA-T-TAT-A-TTTTAAAAATATTTTCAAAAACTATACAATATTAT
* *
97754 AAATGTTTTCAAAACTATATATTATATTTTAAAAATATTTTCAAAAACTATATAATATTAT
1 AAATGTTTTAAAAACTATATATTATATTTTAAAAATATTTTCAAAAACTATACAATATTAT
97815 AAAT
1 AAAT
97819 TTTCGAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
59 14 0.23
60 15 0.25
61 10 0.17
62 1 0.02
63 20 0.33
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AAATGTTTTAAAAACTATATATTATATTTTAAAAATATTTTCAAAAACTATACAATATTAT
Found at i:97821 original size:27 final size:27
Alignment explanation
Indices: 97731--97827 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 27
97721 TTTTCAAAAT
*
97731 ATTTT-AAAAACTATACAATA-TATAA
1 ATTTTCAAAAACTATATAATATTATAA
*
97756 ATGTTTTC-AAAACTATATATTATATTTTAAAAA
1 A--TTTTCAAAAACTATATA--ATA--TT-ATAA
97789 TATTTTCAAAAACTATATAATATTATAA
1 -ATTTTCAAAAACTATATAATATTATAA
*
97817 ATTTTCGAAAA
1 ATTTTCAAAAA
97828 TCGTTTTCCG
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
25 1 0.02
27 24 0.42
28 3 0.05
29 5 0.09
31 3 0.05
32 6 0.11
33 14 0.25
34 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTTCAAAAACTATATAATATTATAA
Found at i:97906 original size:23 final size:23
Alignment explanation
Indices: 97892--97939 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
97882 TACTATATAC
97892 ATACATATATATATAATAAAATA
1 ATACATATATATATAATAAAATA
* *
97915 ATATATATATATATAACAAAATA
1 ATACATATATATATAATAAAATA
97938 AT
1 AT
97940 TCTGGGCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
ATACATATATATATAATAAAATA
Found at i:98534 original size:2 final size:2
Alignment explanation
Indices: 98527--98599 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
98517 TAAGATTTAG
98527 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
98569 AT AT 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 AT AT A
98600 ATGATTTAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:103653 original size:21 final size:21
Alignment explanation
Indices: 103628--103667 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
103618 TCTCAAAGAT
103628 CTTATCTTTTATATTCATAAA
1 CTTATCTTTTATATTCATAAA
103649 CTTATCTTTTATATTCATA
1 CTTATCTTTTATATTCATA
103668 TAATTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (21 bp):
CTTATCTTTTATATTCATAAA
Found at i:104664 original size:31 final size:31
Alignment explanation
Indices: 104616--104740 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
104606 CCCAAAAGAC
* *
104616 CAGTCCATA-GATTCCGAAGAACATAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
104647 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
104678 CAGTCCATATGTCCCGAAGAACATAGTTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
104709 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
104740 C
1 C
104741 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:120414 original size:59 final size:61
Alignment explanation
Indices: 120283--120416 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 61
120273 TTGTACATGA
* * * *
120283 TGTTCTCCAATTATGTCTCTCATTTTAAATTACTCTCTAAATTTTTAAAATATTTTATATC
1 TGTTCTCAAACTATGACTCTCATTTTAAATTACCCTCTAAATTTTTAAAATATTTTATATC
* * *
120344 AG-TCACAAAACTATGAC-CTCATTTTAGATTGACCCT-TAAA-TTTTAAAATATTTTATATC
1 TGTTCTC-AAACTATGACTCTCATTTTAAATT-ACCCTCTAAATTTTTAAAATATTTTATATC
120403 TGTTCTCAAACTAT
1 TGTTCTCAAACTAT
120417 CAATATCATT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
59 27 0.44
60 22 0.36
61 12 0.20
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (61 bp):
TGTTCTCAAACTATGACTCTCATTTTAAATTACCCTCTAAATTTTTAAAATATTTTATATC
Found at i:123639 original size:3 final size:3
Alignment explanation
Indices: 123631--123655 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
123621 ATACGTTAAA
123631 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
123656 TATATATATA
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:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:123660 original size:2 final size:2
Alignment explanation
Indices: 123653--123681 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123643 AATAATAATA
123653 AT 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 AT A
123682 AAATAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123685 original size:52 final size:51
Alignment explanation
Indices: 123593--123717 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 51
123583 TATAAGATTG
* * *
123593 ATAATAAAATATACATATATATATTTATATACGTTAAAAATAATAATAAT-A
1 ATAATAAAATATATATATATATATATATATAC-TTAAAAATAAAAATAATGA
* *
123644 ATAATAATAATATATATATATATATATATATA-TATATAAAATAAAAATGATGT
1 ATAATAA-AATATATATATATATATATATATACT-TA-AAAATAAAAATAATGA
123697 ATACA-AAAATATATATATATA
1 ATA-ATAAAATATATATATATA
123718 GGGAATAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
50 1 0.02
51 9 0.14
52 48 0.75
53 5 0.08
54 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (51 bp):
ATAATAAAATATATATATATATATATATATACTTAAAAATAAAAATAATGA
Found at i:126992 original size:6 final size:6
Alignment explanation
Indices: 126981--127027 Score: 58
Period size: 6 Copynumber: 7.2 Consensus size: 6
126971 ACCCACCTTA
126981 TTTTTC TTTTTC TTTTTC TTTTTC TTTTGTTC TTTTGTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTT-TTC -TTT-TTC TTTTTC T
127028 CGTTTTTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 22 0.56
7 6 0.15
8 11 0.28
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:127105 original size:18 final size:18
Alignment explanation
Indices: 127084--127118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
127074 ACCCTAAACA
127084 TTTTTTTTCTCTTTTTTC
1 TTTTTTTTCTCTTTTTTC
*
127102 TTTTTTTTTTCTTTTTT
1 TTTTTTTTCTCTTTTTT
127119 TCCTTTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTTCTCTTTTTTC
Found at i:127116 original size:27 final size:27
Alignment explanation
Indices: 127085--127142 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
127075 CCCTAAACAT
*
127085 TTTTTTTCTCTTTTTTCTTTTT-TTTTTC
1 TTTTTTTC-C-TTTTCCTTTTTCTTTTTC
127113 TTTTTTTCCTTTTCCTTTTTCTTTTTC
1 TTTTTTTCCTTTTCCTTTTTCTTTTTC
127140 TTT
1 TTT
127143 CTTCGACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.36
27 10 0.36
28 8 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTTTCCTTTTCCTTTTTCTTTTTC
Found at i:127119 original size:19 final size:20
Alignment explanation
Indices: 127084--127138 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
127074 ACCCTAAACA
127084 TTTTTTTTCTCTTTTTT-CTT
1 TTTTTTTTCT-TTTTTTCCTT
127104 TTTTTTTTCTTTTTTTCCTT
1 TTTTTTTTCTTTTTTTCCTT
*
127124 TTCCTTTTTCTTTTT
1 TT-TTTTTTCTTTTT
127139 CTTTCTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 6 0.19
20 15 0.47
21 11 0.34
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTTCCTT
Found at i:134288 original size:26 final size:28
Alignment explanation
Indices: 134247--134298 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
134237 ACGAATGTAA
134247 AAACATGGAAAATATAAAATAAAAAAAC
1 AAACATGGAAAATATAAAATAAAAAAAC
*
134275 AAACAT-G-AAATATAAAATACAAAA
1 AAACATGGAAAATATAAAATAAAAAA
134299 TATGCAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 1 0.04
28 6 0.26
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (28 bp):
AAACATGGAAAATATAAAATAAAAAAAC
Found at i:137590 original size:7 final size:7
Alignment explanation
Indices: 137580--137617 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
137570 AAAAAATAAA
137580 ATAAAAC
1 ATAAAAC
137587 ATAAAAC
1 ATAAAAC
137594 ATAAAAC
1 ATAAAAC
137601 ATAAAAC
1 ATAAAAC
137608 ATAAAAC
1 ATAAAAC
137615 ATA
1 ATA
137618 TACTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (7 bp):
ATAAAAC
Found at i:137779 original size:14 final size:14
Alignment explanation
Indices: 137760--137818 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
137750 GTAAATAAGA
137760 AAATAAATAAAATG
1 AAATAAATAAAATG
*
137774 AAATAAATAAAAAG
1 AAATAAATAAAATG
*
137788 AATACACATATAAGAATG
1 AA-ATA-A-ATAA-AATG
137806 ATAATAAATAAAA
1 A-AATAAATAAAA
137819 ATATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 15 0.42
15 4 0.11
16 5 0.14
17 5 0.14
18 6 0.17
19 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAATAAATAAAATG
Found at i:137887 original size:2 final size:2
Alignment explanation
Indices: 137875--137924 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
137865 TAATAATAGC
* * * *
137875 TA TA AA TA TA TA TA TA TA TA AA TA -A TG TA TA CA -A 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
137915 TA TA TA TA TA
1 TA TA TA TA TA
137925 AGGGAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Found at i:139446 original size:41 final size:41
Alignment explanation
Indices: 139394--139484 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
139384 CTTGATATCT
* *
139394 CGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTC
139435 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTC
139476 CAGTGTTTG
1 C-GTGTTTG
139485 GTCGAAGGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 40 0.85
42 7 0.15
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTC
Found at i:139740 original size:53 final size:53
Alignment explanation
Indices: 139683--139792 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 53
139673 TTTCATCAAG
* ** *
139683 ATATTA-ATTATTAA-AATAT-TTAAAATATATTTATTAATATTTATAATAATATA
1 ATATTATATTATTAATAATATAATAAAATA-ATCAATT-ATA-TTACAATAATATA
* *
139736 ATATTATATTTTTAATATTATAATAAAATAATCAATTATATTACAATAATATA
1 ATATTATATTATTAATAATATAATAAAATAATCAATTATATTACAATAATATA
139789 ATAT
1 ATAT
139793 ATTATATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
53 22 0.46
54 10 0.21
55 9 0.19
56 7 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (53 bp):
ATATTATATTATTAATAATATAATAAAATAATCAATTATATTACAATAATATA
Found at i:139742 original size:26 final size:24
Alignment explanation
Indices: 139689--139742 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
139679 CAAGATATTA
139689 ATTATTAAAATATTTAAAATATAT
1 ATTATTAAAATATTTAAAATATAT
*
139713 -TTATTAATAT-TTATAATAATATAAT
1 ATTATTAAAATATT-TAA-AATAT-AT
139738 ATTAT
1 ATTAT
139743 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.08
23 12 0.48
24 5 0.20
25 2 0.08
26 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTAAAATATTTAAAATATAT
Found at i:139744 original size:22 final size:23
Alignment explanation
Indices: 139697--139760 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
139687 TAATTATTAA
* *
139697 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
139718 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
139741 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
139761 AAATAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:139759 original size:30 final size:29
Alignment explanation
Indices: 139708--139856 Score: 91
Period size: 30 Copynumber: 5.1 Consensus size: 29
139698 ATATTTAAAA
139708 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TT-ATA-TTATAATAATATAATAT
*
139740 TATATTTTTAATATTATAATAAAAT-A-AT
1 TATATTTTT-ATATTATAATAATATAATAT
* *
139768 CA-A---TTATATTACAATAATATAATATAT
1 TATATTTTTATATTATAATAATAT-A-ATAT
*
139795 TATATTTTTATTTTAATAA-ATATATAATA-
1 TATATTTTTATATT-ATAATA-ATATAATAT
*
139824 AATATTTTTTATATT-TAATAATGAATAATAT
1 TATA-TTTTTATATTATAATAAT--ATAATAT
139855 TA
1 TA
139857 ATATAATAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
23 13 0.14
24 2 0.02
26 1 0.01
27 4 0.04
28 9 0.10
29 5 0.05
30 29 0.32
31 15 0.16
32 14 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
TATATTTTTATATTATAATAATATAATAT
Found at i:139783 original size:23 final size:23
Alignment explanation
Indices: 139750--139800 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
139740 TATATTTTTA
*
139750 ATATTATAATAAAATAATCA-ATT
1 ATATTACAATAAAATAAT-ATATT
*
139773 ATATTACAATAATATAATATATT
1 ATATTACAATAAAATAATATATT
139796 ATATT
1 ATATT
139801 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTACAATAAAATAATATATT
Found at i:139839 original size:32 final size:31
Alignment explanation
Indices: 139784--139861 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
139774 TATTACAATA
*
139784 ATATAATATATTATATTTTTATTTTAATAAAT
1 ATATAATATAATATATTTTTA-TTTAATAAAT
*
139816 ATATAATA-AATATTTTTTATATTTAAT-AAT
1 ATATAATATAATATATTTT-TATTTAATAAAT
139846 GA-ATAATATTAATATA
1 -ATATAATA-TAATATA
139862 ATAATCTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 9 0.23
31 15 0.38
32 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
ATATAATATAATATATTTTTATTTAATAAAT
Found at i:139899 original size:23 final size:23
Alignment explanation
Indices: 139879--139923 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
139869 AATAATATTT
139879 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
139902 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
139924 ATATAACGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:140083 original size:22 final size:21
Alignment explanation
Indices: 140029--140098 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
140019 TAAAAATAAT
*
140029 ATTTAATAATAAATAA-ATT-
1 ATTTTATAATAAATAATATTA
*
140048 ATTTTAAAAT-AATAATATTA
1 ATTTTATAATAAATAATATTA
140068 AGTTTTATAATAAATAATATTA
1 A-TTTTATAATAAATAATATTA
*
140090 TTTATTATA
1 ATT-TTATA
140099 TTTAATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 11 0.26
20 1 0.02
21 10 0.24
22 15 0.36
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
ATTTTATAATAAATAATATTA
Found at i:140094 original size:19 final size:19
Alignment explanation
Indices: 140018--140094 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 19
140008 AAATAAAATT
*
140018 ATAAA-AATAATATTTAATA
1 ATAAATAATATTATTT-ATA
140037 ATAAATAA-ATTATTT-TA
1 ATAAATAATATTATTTATA
*
140054 AAATAATAATATTAAGTTTTATA
1 ATA-AATAATATT-A--TTTATA
140077 ATAAATAATATTATTTAT
1 ATAAATAATATTATTTAT
140095 TATATTTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
17 4 0.08
18 5 0.10
19 19 0.40
20 3 0.06
21 1 0.02
22 12 0.25
23 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (19 bp):
ATAAATAATATTATTTATA
Found at i:140257 original size:14 final size:14
Alignment explanation
Indices: 140224--140257 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
140214 ATTCATTCTA
*
140224 CAGAAAACATTTTT
1 CAGAAAACATTTTC
*
140238 CGGAAAACATTTTC
1 CAGAAAACATTTTC
140252 CAGAAA
1 CAGAAA
140258 TGTAATTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (14 bp):
CAGAAAACATTTTC
Found at i:140295 original size:15 final size:15
Alignment explanation
Indices: 140275--140326 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
140265 CATTTTCCAG
140275 AATTCATATTCTAAT
1 AATTCATATTCTAAT
*
140290 AATTCAT-TTTTCAAT
1 AATTCATATTCT-AAT
* * *
140305 AATTCAAATTCCAGT
1 AATTCATATTCTAAT
140320 AATTCAT
1 AATTCAT
140327 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 3 0.10
15 24 0.83
16 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTCATATTCTAAT
Found at i:140309 original size:30 final size:30
Alignment explanation
Indices: 140260--140333 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
140250 TCCAGAAATG
* * *
140260 TAATTCA-TTTTCCAGAATTCATATTCTAA
1 TAATTCATTTTTCAAGAATTCAAATTCCAA
* *
140289 TAATTCATTTTTCAATAATTCAAATTCCAG
1 TAATTCATTTTTCAAGAATTCAAATTCCAA
140319 TAATTCATTTTTCAA
1 TAATTCATTTTTCAA
140334 AAAACCAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 7 0.18
30 32 0.82
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (30 bp):
TAATTCATTTTTCAAGAATTCAAATTCCAA
Found at i:149066 original size:15 final size:15
Alignment explanation
Indices: 149046--149088 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
149036 ATGATGGTGG
149046 TTGTGATGTTGCAGC
1 TTGTGATGTTGCAGC
* ** *
149061 TTGTGATGATGGTGT
1 TTGTGATGTTGCAGC
149076 TTGTGATGTTGCA
1 TTGTGATGTTGCA
149089 ACCTTTGATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.07, G:0.35, T:0.44
Consensus pattern (15 bp):
TTGTGATGTTGCAGC
Found at i:149105 original size:30 final size:30
Alignment explanation
Indices: 149036--149105 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
149026 GCTTGTGATA
* *
149036 ATGATGGTGGTTGTGATGTTGCAGCTTGTG
1 ATGATGGTGTTTGTGATGTTGCACCTTGTG
149066 ATGATGGTGTTTGTGATGTTGCAACCTT-TG
1 ATGATGGTGTTTGTGATGTTGC-ACCTTGTG
149096 ATGATGGTGT
1 ATGATGGTGT
149106 AATCCTTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (30 bp):
ATGATGGTGTTTGTGATGTTGCACCTTGTG
Found at i:152691 original size:23 final size:22
Alignment explanation
Indices: 152632--152692 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
152622 AGTGTTTTCA
152632 TCAAAAAAA-CCTAAAAGTATT
1 TCAAAAAAATCCTAAAAGTATT
152653 TC-AAAAAATCCCTAAAAGTATT
1 TCAAAAAAAT-CCTAAAAGTATT
*
152675 TCGAAAAAAATCTTAAAA
1 TC-AAAAAAATCCTAAAA
152693 AGCATTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 6 0.17
21 2 0.06
22 14 0.40
23 6 0.17
24 7 0.20
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (22 bp):
TCAAAAAAATCCTAAAAGTATT
Found at i:156331 original size:18 final size:20
Alignment explanation
Indices: 156308--156349 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
156298 TTAAATCCAT
*
156308 ATAAATTT-ATTTA-TTTTA
1 ATAAATTTAATTTAGTTTGA
156326 ATAAATTTAATTTAGTTTGA
1 ATAAATTTAATTTAGTTTGA
156346 ATAA
1 ATAA
156350 CTAGATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
ATAAATTTAATTTAGTTTGA
Found at i:162190 original size:16 final size:16
Alignment explanation
Indices: 162164--162214 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
162154 ACCAAAGATG
162164 TCAAC-TTGCCAACTT
1 TCAACTTTGCCAACTT
*
162179 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
162195 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
162211 TCAA
1 TCAA
162215 GCCAAACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.37
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:162210 original size:9 final size:9
Alignment explanation
Indices: 162165--162211 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
162155 CCAAAGATGT
162165 CAAC-TTGC
1 CAACTTTGC
162173 CAACTTT--
1 CAACTTTGC
*
162180 CAATTTTGC
1 CAACTTTGC
162189 CAACTTT--
1 CAACTTTGC
162196 CAACTTTGC
1 CAACTTTGC
162205 CAACTTT
1 CAACTTT
162212 CAAGCCAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
7 13 0.41
8 4 0.12
9 15 0.47
ACGTcount: A:0.26, C:0.30, G:0.06, T:0.38
Consensus pattern (9 bp):
CAACTTTGC
Found at i:166873 original size:37 final size:37
Alignment explanation
Indices: 166831--166902 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
166821 CAAATATGAA
*
166831 TTTCCAATGTGGACAAGTTGGCCA-CATACCAAAGAAT
1 TTTCCAATGTGGACAAGTTAGCCACCA-ACCAAAGAAT
* *
166868 TTTCCAATGTGTACAATTTAGCCACCAACCAAAGA
1 TTTCCAATGTGGACAAGTTAGCCACCAACCAAAGA
166903 TGTCAACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 29 0.94
38 2 0.06
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (37 bp):
TTTCCAATGTGGACAAGTTAGCCACCAACCAAAGAAT
Found at i:166929 original size:16 final size:16
Alignment explanation
Indices: 166905--166940 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
166895 ACCAAAGATG
166905 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
166921 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
166937 TCAA
1 TCAA
166941 GCCAAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:169076 original size:28 final size:30
Alignment explanation
Indices: 169016--169083 Score: 113
Period size: 28 Copynumber: 2.3 Consensus size: 30
169006 TTAAAGCCTT
*
169016 AGTTTAGTTTCCTTAATTAGAAATTAAATA
1 AGTTTAGTATCCTTAATTAGAAATTAAATA
169046 AGTTTAGTATCCTTAA-TA-AAATTAAATA
1 AGTTTAGTATCCTTAATTAGAAATTAAATA
169074 AGTTTAGTAT
1 AGTTTAGTAT
169084 ACCATTTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 20 0.54
29 2 0.05
30 15 0.41
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (30 bp):
AGTTTAGTATCCTTAATTAGAAATTAAATA
Found at i:169123 original size:2 final size:2
Alignment explanation
Indices: 169116--169145 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
169106 TAATAAATTA
169116 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
169146 CTAAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175179 original size:39 final size:39
Alignment explanation
Indices: 175135--175216 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
175125 GATGGTGAAG
*
175135 TAGGGAGTGAGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAGAGGCGAGAGGA-AAATGAAAAAGGGGAAT
* * *
175174 TAGGGATTGAGGGGCGAGAGGAAAATGAAAATGGGGAAT
1 TAGGGAGTGAGAGGCGAGAGGAAAATGAAAAAGGGGAAT
175213 TAGG
1 TAGG
175217 TATTATGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.43, T:0.15
Consensus pattern (39 bp):
TAGGGAGTGAGAGGCGAGAGGAAAATGAAAAAGGGGAAT
Found at i:177609 original size:42 final size:42
Alignment explanation
Indices: 177550--177633 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
177540 AGTAAAATAT
*
177550 AAAGTTTAAACAAGATGTCACGGTTTTTATTTTGCATAACCG
1 AAAGTTTAAACAAGATGTCACGGTTGTTATTTTGCATAACCG
* *
177592 AAAGTTTAAACACGATGTCACGGTTGTTATTTTGCATCACCG
1 AAAGTTTAAACAAGATGTCACGGTTGTTATTTTGCATAACCG
177634 GTCTTCTCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (42 bp):
AAAGTTTAAACAAGATGTCACGGTTGTTATTTTGCATAACCG
Found at i:179313 original size:19 final size:18
Alignment explanation
Indices: 179289--179325 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
179279 CAATAAAAAT
179289 ATATATAAAAATATTTAAA
1 ATATATAAAAAT-TTTAAA
*
179308 ATATATAATAATTTTAAA
1 ATATATAAAAATTTTAAA
179326 TTTTTATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATAAAAATTTTAAA
Found at i:182448 original size:31 final size:31
Alignment explanation
Indices: 182382--182451 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
182372 AATCAAGCTG
* * *
182382 CAACTTTTGGTGGAATTCGGTGCATTTATAC
1 CAACTTTCGGTGGAATTCGGTGCATTCACAC
*
182413 CAACTTTCGGTGGAATTCGGTGCATTCACAT
1 CAACTTTCGGTGGAATTCGGTGCATTCACAC
182444 CAACTTTC
1 CAACTTTC
182452 AACAATCTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (31 bp):
CAACTTTCGGTGGAATTCGGTGCATTCACAC
Found at i:187684 original size:7 final size:7
Alignment explanation
Indices: 187672--187698 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
187662 CATCACCAAA
187672 TTAATAT
1 TTAATAT
187679 TTAATAT
1 TTAATAT
187686 TTAATAT
1 TTAATAT
187693 TTAATA
1 TTAATA
187699 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAATAT
Found at i:188029 original size:53 final size:51
Alignment explanation
Indices: 187966--188092 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 51
187956 ATTTCTGATT
* * *
187966 TTTTGTTAAACGCTTCTG-TTTTTTCAAAA-AATTGTTAGTTTTTTTCTTTTAAA
1 TTTTGCTAAACGCTGCTGCTTTTTACAAAATAATTGTTAG--TTTTTC--TTAAA
188019 TTTTGCTAAACGCTGCTGCTTTTTACAAAATAATTGTTAGTTTTTCTTAAA
1 TTTTGCTAAACGCTGCTGCTTTTTACAAAATAATTGTTAGTTTTTCTTAAA
* *
188070 TTTTGCTAAAAGTTGCTGCTTTT
1 TTTTGCTAAACGCTGCTGCTTTT
188093 ATTATTCGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
51 26 0.39
53 22 0.33
54 10 0.15
55 9 0.13
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (51 bp):
TTTTGCTAAACGCTGCTGCTTTTTACAAAATAATTGTTAGTTTTTCTTAAA
Done.