Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005453.1 Hibiscus syriacus cultivar Beakdansim tig00012492_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: 68648
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:4750 original size:18 final size:18
Alignment explanation
Indices: 4679--4751 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
4669 AGGGATTATC
*
4679 AGTGATCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
4697 AGTGGTTCGTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
* *
4716 CAGTGGTCTTTTGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
4735 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
4752 AATATTCAGT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
18 26 0.63
19 4 0.10
20 11 0.27
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:14770 original size:64 final size:67
Alignment explanation
Indices: 14700--14827 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 67
14690 ATTTAAAAAG
14700 AAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT-CC-CCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGCATACCTCCATTAAA
14761 TAC
65 TAC
*
14764 AAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAA
14828 AGATGAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.56
65 15 0.25
66 2 0.03
67 8 0.14
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (67 bp):
AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAAT
AC
Found at i:15434 original size:23 final size:23
Alignment explanation
Indices: 15401--15463 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
15391 ATTATTATAT
15401 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
15424 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
15447 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
15464 ATATGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:19309 original size:20 final size:21
Alignment explanation
Indices: 19255--19317 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
19245 GATTCCCCTG
19255 TGGGGGGAATCGGTTCCCATTCAA
1 TGGGGGG-ATCGGTTCCC--TCAA
* *
19279 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
19299 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
19318 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
23 10 0.29
24 5 0.15
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:25990 original size:35 final size:35
Alignment explanation
Indices: 25944--26014 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
25934 TCAATGGTTA
25944 GTATAGGAGGGAGTGTCTCGACCATTAAGTATCAT
1 GTATAGGAGGGAGTGTCTCGACCATTAAGTATCAT
25979 GTATAGGAGGGAGTGTCTCGACCATTAAGTATCAT
1 GTATAGGAGGGAGTGTCTCGACCATTAAGTATCAT
26014 G
1 G
26015 GACAGGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (35 bp):
GTATAGGAGGGAGTGTCTCGACCATTAAGTATCAT
Found at i:26022 original size:35 final size:35
Alignment explanation
Indices: 25948--26022 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
25938 TGGTTAGTAT
* *
25948 AGGAGGGAGTGTCTCGACCATTAAGTATCATGTAT
1 AGGAGGGAGTGTCTCGACCATTAAGTATCATGGAC
25983 AGGAGGGAGTGTCTCGACCATTAAGTATCATGGAC
1 AGGAGGGAGTGTCTCGACCATTAAGTATCATGGAC
26018 AGGAG
1 AGGAG
26023 AAATTTGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (35 bp):
AGGAGGGAGTGTCTCGACCATTAAGTATCATGGAC
Found at i:29130 original size:26 final size:26
Alignment explanation
Indices: 29100--29150 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
29090 TTATTTTTAT
*
29100 TTCTTAAAATTTTATAAATTTGTCCA
1 TTCTTAAAATTTTAGAAATTTGTCCA
29126 TTCTTAAAATTTTAGAAATTTGTCC
1 TTCTTAAAATTTTAGAAATTTGTCC
29151 CTCCTTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (26 bp):
TTCTTAAAATTTTAGAAATTTGTCCA
Found at i:29157 original size:26 final size:26
Alignment explanation
Indices: 29102--29157 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
29092 ATTTTTATTT
* *
29102 CTTAAAATTTTATAAATTTGTCCATT
1 CTTAAAATTTTAGAAATTTGTCCATC
*
29128 CTTAAAATTTTAGAAATTTGTCCCTC
1 CTTAAAATTTTAGAAATTTGTCCATC
29154 CTTA
1 CTTA
29158 GATAAAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (26 bp):
CTTAAAATTTTAGAAATTTGTCCATC
Found at i:29906 original size:16 final size:16
Alignment explanation
Indices: 29887--29919 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29877 TTAAAATACT
29887 TTTTTCTAAAA-AATTA
1 TTTTT-TAAAACAATTA
29903 TTTTTTAAAACAATTA
1 TTTTTTAAAACAATTA
29919 T
1 T
29920 CATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTTAAAACAATTA
Found at i:30664 original size:91 final size:91
Alignment explanation
Indices: 30338--30710 Score: 464
Period size: 92 Copynumber: 4.1 Consensus size: 91
30328 GGTATGTTTG
* * *
30338 AAATTTTATGTTTCAGTGGAGGGAAATTGGAGGAAATGAGCAGGTAAGTAAAAAACCTCTAAATT
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGC-GGTAATTAAAAAAACTCTAAATT
* *
30403 TTGTGACGAAACATATGAACCCGTCAC
65 TTGTGACGGAACATATGGACCCGTCAC
* * *
30430 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGTTGGTAATTGAAAAAAACT-AAAAA
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAG-CGGTAATT-AAAAAAACTCTAAAT
* *
30494 ATTGTGACGGAACA-AGTGGACTCGTCAC
64 TTTGTGACGGAACATA-TGGACCCGTCAC
* * * *
30522 AAATTTTATGTTTCAATGAATGGAAATTGGAGGAAATGAGCAGATAATTAAAAACACTCTAAATT
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGC-GGTAATTAAAAAAACTCTAAATT
* *
30587 TTGTGACAGAACACATGGACCCGTCAC
65 TTGTGACGGAACATATGGACCCGTCAC
* * * *
30614 AAATTTTATGTTTTAATAGA-GGAAATTGGAGGTAATGAGCGGATAATTAAAAAAACTATAAATT
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCGG-TAATTAAAAAAACTCTAAATT
* * *
30678 TTGTGGCGGAACATGTGGACTCGTCAC
65 TTGTGACGGAACATATGGACCCGTCAC
30705 AAATTT
1 AAATTT
30711 GTGAGAGCCC
Statistics
Matches: 242, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
90 1 0.00
91 75 0.31
92 157 0.65
93 9 0.04
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (91 bp):
AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCGGTAATTAAAAAAACTCTAAATTT
TGTGACGGAACATATGGACCCGTCAC
Found at i:44180 original size:24 final size:26
Alignment explanation
Indices: 44141--44221 Score: 89
Period size: 24 Copynumber: 3.3 Consensus size: 26
44131 TATATTATAG
* *
44141 ATATTAATTTTAATATTAATTTTTTA
1 ATATTAAATTAAATATTAATTTTTTA
*
44167 A-A-TAAATTAAATATTAATGTTTTA
1 ATATTAAATTAAATATTAATTTTTTA
* *
44191 ATATTATATTAGATATTAA--TTTTA
1 ATATTAAATTAAATATTAATTTTTTA
44215 ATATTAA
1 ATATTAA
44222 TTTTTAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 31 0.66
25 2 0.04
26 14 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTAAATTAAATATTAATTTTTTA
Found at i:44251 original size:61 final size:63
Alignment explanation
Indices: 44123--44276 Score: 251
Period size: 61 Copynumber: 2.5 Consensus size: 63
44113 AGGTTTTATA
*
44123 TTTAATTTTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATGT
1 TTTAATATTATA-TATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATGT
*
44187 TTTAATATTATAT-TAGATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATGT
44248 TTTAATATTAT-TATAGATATTTAATTTTA
1 TTTAATATTATATATAGATA-TTAATTTTA
44277 TCATATAAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
60 1 0.01
61 42 0.49
62 31 0.36
63 1 0.01
64 11 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (63 bp):
TTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATGT
Found at i:44667 original size:28 final size:28
Alignment explanation
Indices: 44636--44724 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
44626 TAATTGCATA
44636 TTTAATAATAGTTTAATGATAATTAATG
1 TTTAATAATAGTTTAATGATAATTAATG
* *** * *
44664 TTTAAAAATAGGAGAGATG-TGCGATTCATTG
1 TTTAATAATAGTTTA-ATGAT--AATT-AATG
*
44695 ATTAATAATAGTTTAATGATAATTAATG
1 TTTAATAATAGTTTAATGATAATTAATG
44723 TT
1 TT
44725 GTTGTGCCAT
Statistics
Matches: 42, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
28 16 0.38
29 6 0.14
30 6 0.14
31 14 0.33
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTAATAATAGTTTAATGATAATTAATG
Found at i:44976 original size:31 final size:31
Alignment explanation
Indices: 44939--44998 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
44929 TAGTTGTATG
* *
44939 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGAATTGTAAAACTAA
44970 AATTATTTAAATCTCAGAATTGTAAAACT
1 AATTATTTAAATCTCAGAATTGTAAAACT
44999 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGAATTGTAAAACTAA
Found at i:46052 original size:36 final size:36
Alignment explanation
Indices: 45925--46339 Score: 374
Period size: 36 Copynumber: 11.6 Consensus size: 36
45915 ATACATACAT
* *
45925 ATATATTATATAG-TTTGAAAACATTTTTAAAATATA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATA-A
* * **
45961 CATATAATATATAGTTTTGAAAACATGTTTGAAAACATTT
1 -ATATATTATATAGTTTTTAAAACAT-TTTG-AAA-ATAA
*
46001 ATATATTATATAGTTTTTAAAATATTTTGAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * * *
46037 ATATAATATACAGTTTTTAAATCGTTTTTGAAAAT--
1 ATATATTATATAGTTTTTAAAAC-ATTTTGAAAATAA
*
46072 ATATATTATATAGTTTTTAAAACATATTGAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * * *
46108 ATATAATATATAATTTTTAAAACGTTTTTGAAAA-AT
1 ATATATTATATAGTTTTTAAAAC-ATTTTGAAAATAA
46144 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * *
46180 ATATAATATATAATTTTTAAAATATTTTTGAAAAT--
1 ATATATTATATAGTTTTTAAAACA-TTTTGAAAATAA
*
46215 ATATATTATGTAGTTTTTAAAACATTTTG-----AA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* *
46246 A-ATA-TATATAGTTTTTAAAAAACATTTTTGAAAACAT
1 ATATATTATATAGTTTTT--AAAACA-TTTTGAAAATAA
* * * *
46283 ATATACTATATAGTTTTGAAATCATTTTGAAAACT-T
1 ATATATTATATAGTTTTTAAAACATTTTGAAAA-TAA
*
46319 ATATAGTATATAG-TTTTAAAA
1 ATATATTATATAGTTTTTAAAA
46340 TTTTTTTTGA
Statistics
Matches: 312, Mismatches: 43, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
29 11 0.04
30 3 0.01
31 7 0.02
32 5 0.02
34 14 0.04
35 55 0.18
36 108 0.35
37 50 0.16
38 18 0.06
39 36 0.12
40 3 0.01
41 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:46102 original size:71 final size:72
Alignment explanation
Indices: 45923--46440 Score: 500
Period size: 71 Copynumber: 7.3 Consensus size: 72
45913 ATATACATAC
* * * *
45923 ATATATATTATATAG-TTTGAAAACATTTTTAAAATATACATATAATATATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATA-A-ATATAATATATAATTTTTAAAACAT
*
45987 GTTTGAAAA
64 TTTTGAAAA
* * * * *
45996 CATTTATATATTATATAGTTTTTAAAATATTTTGAAAATAAATATAATATACAGTTTTTAAATCG
1 -A--TATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACA
46061 TTTTTG-AAA
63 TTTTTGAAAA
* *
46070 ATATATATTATATAGTTTTTAAAACATATTGAAAATAAATATAATATATAATTTTTAAAACGTTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
46135 TTGAAAA
66 TTGAAAA
*
46142 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAATATTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
46207 TTG-AAA
66 TTGAAAA
* **
46213 ATATATATTATGTAGTTTTTAAAACATTTTGAAAAT--ATAT-ATAGT-T--TTTAAAAAACATT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATA-TATAATTTTTAAAACATT
46272 TTTGAAAA
65 TTTGAAAA
* * * * * * **
46280 CATATATACTATATAGTTTTGAAATCATTTTGAAAACT-TATATAGTATAT-AGTTTTAAAATTT
1 -ATATATATTATATAGTTTTTAAAACATTTTGAAAA-TAAATATAATATATAATTTTTAAAA-CA
46343 TTTTTG----
63 TTTTTGAAAA
* * * * *
46349 A-A-A-ACTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAA-TTTTAAAATAT
1 ATATATATTATATAGTTTTTAAAACA-TTTTGAAAATAA-ATATAATATATAATTTTTAAAACA-
46410 TTTTTTG-AAA
63 -TTTTTGAAAA
*
46420 ATATATATTGTATAGATTTTT
1 ATATATATTATATAG-TTTTT
46441 GGAAAATATT
Statistics
Matches: 378, Mismatches: 40, Indels: 51
0.81 0.09 0.11
Matches are distributed among these distances:
65 18 0.05
66 24 0.06
67 22 0.06
68 43 0.11
69 6 0.02
70 5 0.01
71 104 0.28
72 75 0.20
73 8 0.02
74 11 0.03
75 29 0.08
76 15 0.04
77 18 0.05
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (72 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
TTGAAAA
Found at i:46285 original size:66 final size:66
Alignment explanation
Indices: 46185--46325 Score: 180
Period size: 68 Copynumber: 2.1 Consensus size: 66
46175 AATAAATATA
* * * * *
46185 ATATATAATTTTTAAAATATTTTTGAAAATATATAT-TATGTAGTTTTTAAAACATTTTGAAAA-
1 ATATATAGTTTTTAAAACATTTTTGAAAACATATATATATATAGTTTTGAAAACATTTTGAAAAC
46248 T
66 T
*
46249 ATATATAGTTTTTAAAAAACATTTTTGAAAACATATATACTATATAGTTTTGAAATCATTTTGAA
1 ATATATAGTTTTT--AAAACATTTTTGAAAACATATATA-TATATAGTTTTGAAAACATTTTGAA
46314 AACT
63 AACT
46318 -TATATAGT
1 ATATATAGT
46326 ATATAGTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
64 12 0.18
66 21 0.32
68 32 0.48
69 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (66 bp):
ATATATAGTTTTTAAAACATTTTTGAAAACATATATATATATAGTTTTGAAAACATTTTGAAAAC
T
Found at i:46375 original size:29 final size:29
Alignment explanation
Indices: 46325--46388 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
46315 ACTTATATAG
** *
46325 TATATAGTTTTAAAATTTTTTTTGAAAAC
1 TATATAGTTTTAAAATCATTTTTCAAAAC
46354 TATATAGTTTTCAAAA-CATTTTTCAAAAC
1 TATATAGTTTT-AAAATCATTTTTCAAAAC
*
46383 AATATA
1 TATATA
46389 TAATATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAGTTTTAAAATCATTTTTCAAAAC
Found at i:46375 original size:65 final size:68
Alignment explanation
Indices: 46287--46426 Score: 198
Period size: 67 Copynumber: 2.1 Consensus size: 68
46277 AAACATATAT
* * * * * *
46287 ACTATATAGTTTTGAAATCA-TTTTGAAAAC-TTATATAGTATATAGTTTTAAAAT-TTTTTTTG
1 ACTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTG
46349 AAA
66 AAA
46352 ACTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTG
1 ACTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTG
46417 AAA
66 AAA
46420 A-TATATA
1 ACTATATA
46427 TTGTATAGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 18 0.27
66 9 0.14
67 27 0.41
68 12 0.18
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (68 bp):
ACTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTG
AAA
Found at i:46395 original size:36 final size:36
Alignment explanation
Indices: 45925--46413 Score: 282
Period size: 36 Copynumber: 13.8 Consensus size: 36
45915 ATACATACAT
* * *
45925 ATATATTATATAG-TTTGAAAACATTTTT-AAAATA
1 ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
* * *
45959 TACATATAATATATAGTTTTGAAAACATGTTTGAAAACA
1 -ATATAT-A-ATATAGTTTTTAAAACATTTTTGAAAACA
* * *
45998 TTTATATATTATATAGTTTTTAAAATA-TTTTGAAAATA
1 ---ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
* * *
46036 A-ATATAATATACAGTTTTTAAATCGTTTTTGAAAA-T
1 ATATATAATAT--AGTTTTTAAAACATTTTTGAAAACA
* * *
46072 ATATATTATATAGTTTTTAAAACA-TATTGAAAATA
1 ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
* *
46107 A-ATATAATATATAATTTTTAAAACGTTTTTGAAAA-A
1 ATATAT-A-ATATAGTTTTTAAAACATTTTTGAAAACA
* *
46143 TATATATTATATAGTTTTTAAAACA-TTTTGAAAATA
1 -ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
* * *
46179 A-ATATAATATATAATTTTTAAAATATTTTTGAAAA-T
1 ATATAT-A-ATATAGTTTTTAAAACATTTTTGAAAACA
* *
46215 ATATATTATGTAGTTTTTAAAACA-TTTTG---A-A
1 ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
46246 A-ATAT-ATATAGTTTTTAAAAAACATTTTTGAAAAC-
1 ATATATAATATAGTTTTT--AAAACATTTTTGAAAACA
* *
46281 ATATATACTATATAGTTTTGAAATCA-TTTTGAAAAC-
1 ATATATA--ATATAGTTTTTAAAACATTTTTGAAAACA
* **
46317 TTATATAGTATATAG-TTTTAAAATTTTTTTTGAAAAC-
1 ATATATA--ATATAGTTTTTAAAA-CATTTTTGAAAACA
* *
46354 -----T-ATATAGTTTTCAAAACATTTTTCAAAACA
1 ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
*
46384 ATATATAATATA-TAATTTTAAAATATTTTT
1 ATATATAATATAGT--TTTTAAAACATTTTT
46414 TTGAAAATAT
Statistics
Matches: 359, Mismatches: 51, Indels: 86
0.72 0.10 0.17
Matches are distributed among these distances:
29 26 0.07
30 11 0.03
31 8 0.02
32 6 0.02
34 29 0.08
35 52 0.14
36 91 0.25
37 73 0.20
38 27 0.08
39 30 0.08
41 6 0.02
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATAATATAGTTTTTAAAACATTTTTGAAAACA
Found at i:46434 original size:139 final size:136
Alignment explanation
Indices: 45931--46439 Score: 431
Period size: 139 Copynumber: 3.6 Consensus size: 136
45921 ACATATATAT
* * * * * *
45931 TATATAGTTTGAAAACATTTTTAAAATATACATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 TATATAGTTTTAAAACATTTTTAAAACA-ATATATAATATATAATTTTAAAAACATTTTTGAAAA
* * * *
45996 CATTTATATATTATATAGTTTTTAAAATATTTTGAAAATAAATATAATATA-CAGTTTTTAAATC
65 -A--TATATATTATATAGTTTTGAAAACATTTTGAAAATAAATATAATATATAAGTTTTAAAAT-
*
46060 GTTTTTGAAAATATATA
126 ATTTTTG---A-A-A-A
* * * * *
46077 TTATATAGTTTTTAAAACATATTGAAAATAA-ATATAATATATAATTTTTAAAACGTTTTTGAAA
1 -TATATAG-TTTTAAAACATTTTTAAAACAATATATAATATATAATTTTAAAAACATTTTTGAAA
* *
46141 AATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAATATT
64 AATATATATTATATAGTTTTGAAAACATTTTGAAAATAAATATAATATATAAGTTTTAAAATATT
46206 TTTGAAAA
129 TTTGAAAA
* ** * * * *
46214 TATATA-TTAT-GTA-GTTTTTAAAACATTTTGAAAATATATATAGTTTTTAAAAAACATTTTTG
1 TATATAGTTTTAAAACATTTTTAAAACAATAT-ATAATATATA-A--TTTT-AAAAACATTTTTG
* * * *
46276 AAAACATATATACTATATAGTTTTGAAATCATTTTGAAAACT-TATATAGTATAT-AGTTTTAAA
61 AAAA-ATATATATTATATAGTTTTGAAAACATTTTGAAAA-TAAATATAATATATAAGTTTTAAA
*
46339 ATTTTTTTTGAAAA
124 A-TATTTTTGAAAA
**
46353 CTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTG-
1 -TATATAGTTTT-AAAACATTTTT-AAAACAATATATAATATATAATTTTAAAA-ACATTTTTGA
*
46417 AAAATATATATTGTATAGATTTT
62 AAAATATATATTATATAG-TTTT
46440 TGGAAAATAT
Statistics
Matches: 301, Mismatches: 42, Indels: 45
0.78 0.11 0.12
Matches are distributed among these distances:
132 8 0.03
133 2 0.01
134 12 0.04
135 1 0.00
136 6 0.02
137 5 0.02
138 25 0.08
139 67 0.22
140 19 0.06
141 14 0.05
143 54 0.18
144 23 0.08
145 9 0.03
146 30 0.10
147 8 0.03
148 18 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (136 bp):
TATATAGTTTTAAAACATTTTTAAAACAATATATAATATATAATTTTAAAAACATTTTTGAAAAA
TATATATTATATAGTTTTGAAAACATTTTGAAAATAAATATAATATATAAGTTTTAAAATATTTT
TGAAAA
Found at i:47794 original size:14 final size:14
Alignment explanation
Indices: 47777--47876 Score: 62
Period size: 14 Copynumber: 6.9 Consensus size: 14
47767 AACTCTTCAT
*
47777 TTTTTATTATTTTG
1 TTTTTATTATTTTA
47791 TTTTT-TTATTTTA
1 TTTTTATTATTTTA
* *
47804 TTTTTATTATTCGTC
1 TTTTTATTATT-TTA
*
47819 TTTTTATCAAATTTTA
1 TTTTTAT--TATTTTA
47835 TTTTCTATCT-TATTTA
1 TTTT-TAT-TAT-TTTA
* *
47851 -TTTCATTACTTTA
1 TTTTTATTATTTTA
*
47864 TTATTATTATTTT
1 TTTTTATTATTTT
47877 TCTTATTTCA
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
13 17 0.26
14 21 0.32
15 12 0.18
16 9 0.14
17 6 0.09
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:48033 original size:4 final size:4
Alignment explanation
Indices: 48010--48053 Score: 63
Period size: 4 Copynumber: 11.0 Consensus size: 4
48000 TTCCCCTTTG
*
48010 ATTT A-TT ATTT TTCTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
48054 TCCCTCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:48052 original size:33 final size:32
Alignment explanation
Indices: 48010--48088 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 32
48000 TTCCCCTTTG
**
48010 ATTTA-TTATTTTTCT-TATTTATTTATTTATTT
1 ATTTATTTATTTTTCTCT-TTTA-TTATTTAAGT
* *
48042 ATTTATTTATTTTCCCTCTTTTATTGTTTAAGT
1 ATTTATTTATTTT-TCTCTTTTATTATTTAAGT
48075 ATTTATTTATTTTT
1 ATTTATTTATTTTT
48089 ATCTAACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
32 5 0.13
33 27 0.69
34 6 0.15
35 1 0.03
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (32 bp):
ATTTATTTATTTTTCTCTTTTATTATTTAAGT
Found at i:48168 original size:13 final size:13
Alignment explanation
Indices: 48150--48179 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
48140 TGAATCAGGT
48150 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
48163 TTTTAATTTTTAA
1 TTTTAAATTTTAA
48176 TTTT
1 TTTT
48180 CACGATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:51852 original size:67 final size:67
Alignment explanation
Indices: 51744--51888 Score: 254
Period size: 67 Copynumber: 2.2 Consensus size: 67
51734 TGGTAGTAGC
* *
51744 TCAACTTCACAGCGAAGGGGCGACTGACTGTTAATAAATAACTTTTCAGTTTCATTCAAAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAAAGTCAA
51809 TT
66 TT
* *
51811 TCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAAAGTCAA
51876 TT
66 TT
51878 TCAACTTCACA
1 TCAACTTCACA
51889 ATGAAGAATA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (67 bp):
TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAAAGTCAA
TT
Found at i:52010 original size:110 final size:110
Alignment explanation
Indices: 51806--52084 Score: 414
Period size: 110 Copynumber: 2.5 Consensus size: 110
51796 CATTCAAAGT
* * *
51806 CAATTTCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGA
1 CAATCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGA
* * *
51871 GTCAATTTCAACTTCACAATGAAGAATATTGGACTCGAGACAACA
66 GGCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACA
* *
51916 CAATCTCAACTTCACAGCGAAGGAGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGA
1 CAATCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGA
* * *
51981 GGCAATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACA
66 GGCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACA
* * * * *
52026 CAAGCTCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAGCTTTCCAGTTTCA
1 CAATCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
52085 GAGTCAATTT
Statistics
Matches: 151, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 151 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (110 bp):
CAATCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGA
GGCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACA
Found at i:52399 original size:84 final size:84
Alignment explanation
Indices: 52184--52547 Score: 484
Period size: 84 Copynumber: 4.3 Consensus size: 84
52174 AAGGGATTTT
* * * * * *
52184 TGCCCACC-AAAGACCTTCGAGTTCGACTACGCTTAGCTCAAAGGCACAATATTTGCAGCATAGC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-TATATTTGCAACATAAC
52248 TTAAGTCGAGAAGGGCTATC
65 TTAAGTCGAGAAGGGCTATC
52268 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT-ATTTGCAACATAAC
*
52333 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGCTATC
* * *
52353 TGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCATATAGTTTGCAGCATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATA-TTTGCAACATAAC
* * * *
52417 TTAAGTCAATAAGGGTTATA
65 TTAAGTCGAGAAGGGCTATC
* * *
52437 TGCCAACC-AAAGACCGTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAACATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT-ATTTGCAACATAAC
*
52501 TTAAGTTGAGAAGGGCTATC
65 TTAAGTCGAGAAGGGCTATC
*
52521 TGCCAACCGAAA-ACCTTTCGAGTTCGA
1 TGCCAACCAAAAGACC-TTCGAGTTCGA
52548 TTCAATTCAG
Statistics
Matches: 248, Mismatches: 25, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
83 1 0.00
84 159 0.64
85 88 0.35
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (84 bp):
TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATATTTGCAACATAACT
TAAGTCGAGAAGGGCTATC
Found at i:52503 original size:168 final size:170
Alignment explanation
Indices: 52184--52547 Score: 524
Period size: 169 Copynumber: 2.2 Consensus size: 170
52174 AAGGGATTTT
* * * *
52184 TGCCCACC-AAAGACCTTCGAGTTCGACTACGCTTAGCTCAAAGGCACAATATTTGCAGCATAGC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACAATATTTGCAGCATAAC
* * *
52248 TTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
66 TTAAGTCAAGAAGGGCTATATGCCAACCAAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
52313 CATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATC
131 AACATCATTTGCAACATAACTTAAGTCGAGAAGGGCTATC
*
52353 TGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCA-TATAGTTTGCAGCATA
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAAC-TCAAAGGCACAATA-TTTGCAGCATA
* *
52415 ACTTAAGTCAATAAGGGTTATATGCCAACC-AAAGACCGTCGAGTTCGACTACGCTCAGCTCCAA
64 ACTTAAGTCAAGAAGGGCTATATGCCAACCAAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAA
*
52479 GGAACATCATTTGCAACATAACTTAAGTTGAGAAGGGCTATC
129 GGAACATCATTTGCAACATAACTTAAGTCGAGAAGGGCTATC
*
52521 TGCCAACCGAAA-ACCTTTCGAGTTCGA
1 TGCCAACCAAAAGACC-TTCGAGTTCGA
52548 TTCAATTCAG
Statistics
Matches: 175, Mismatches: 15, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
168 84 0.48
169 89 0.51
170 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (170 bp):
TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACAATATTTGCAGCATAAC
TTAAGTCAAGAAGGGCTATATGCCAACCAAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAAGG
AACATCATTTGCAACATAACTTAAGTCGAGAAGGGCTATC
Found at i:53279 original size:71 final size:71
Alignment explanation
Indices: 53100--53615 Score: 524
Period size: 71 Copynumber: 7.3 Consensus size: 71
53090 ATATACATAC
* * *
53100 ATATATATTATATAG-TTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATA-A-ATATAATATATAGTTTTTAAAACAT
*
53164 GTTTGAAAA
64 TTTTG-AAA
*
53173 CATTAATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTTAAACA
1 -A-T-ATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACA
53238 TTTTTGAAA
63 TTTTTGAAA
* *
53247 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACGTTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTT
53312 TTGAAA
66 TTGAAA
* ** *
53318 ATATATATTATATATTTTTTAAAACATTTTGAAAATAAATATAATATATAAATTTTAAAATATTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTT
53383 TTGAAA
66 TTGAAA
* * **
53389 ATATATATTATATAGTTTTTAAAACATTTTGAAAAT--ATAT-ATA-GT--TTTTTAAAAAAAAT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTT
53448 TTGAAAA
66 TTG-AAA
* ** * * * *
53455 CATATATATTATATAGTTTTGAACTCAATTTT-AAAACT-TATATAGTATATAGTTTTAAAAATA
1 -ATATATATTATATAGTTTTTAAAAC-ATTTTGAAAA-TAAATATAATATATAGTTTTTAAAACA
53518 TTTTTG---
63 TTTTTGAAA
* * * * * *
53524 A-A-A-ACTATATAGTTTTGAAAACAATTTTCAAAACAATATATAATATATA-ATTTTAAAATAT
1 ATATATATTATATAGTTTTTAAAAC-ATTTTGAAAATAA-ATATAATATATAGTTTTTAAAACA-
53585 TTTTTTGAAA
63 -TTTTTGAAA
*
53595 ATATATATTGTATAGATTTTT
1 ATATATATTATATAG-TTTTT
53616 GGAAAATATT
Statistics
Matches: 380, Mismatches: 38, Indels: 47
0.82 0.08 0.10
Matches are distributed among these distances:
65 35 0.09
66 17 0.04
67 39 0.10
68 16 0.04
69 8 0.02
70 2 0.01
71 170 0.45
72 2 0.01
73 15 0.04
74 11 0.03
75 32 0.08
76 14 0.04
77 19 0.05
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (71 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTT
TTGAAA
Found at i:53436 original size:29 final size:31
Alignment explanation
Indices: 53397--53462 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
53387 AAATATATAT
* * *
53397 TATATAG-TTTTT-AAAACATTTTGAAAATA
1 TATATAGTTTTTTAAAAAAAATTTGAAAACA
53426 TATATAGTTTTTTAAAAAAAATTTGAAAACA
1 TATATAGTTTTTTAAAAAAAATTTGAAAACA
53457 TATATA
1 TATATA
53463 TTATATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 7 0.22
30 5 0.16
31 20 0.62
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (31 bp):
TATATAGTTTTTTAAAAAAAATTTGAAAACA
Found at i:53536 original size:36 final size:35
Alignment explanation
Indices: 53100--53534 Score: 413
Period size: 36 Copynumber: 12.2 Consensus size: 35
53090 ATATACATAC
* *
53100 ATATATATTATATAG-TTTGAAAACATTTTTAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
53134 TATATATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 -ATATATAT--TATATAGTTTTTAAAACATTTTTG-AAA
53173 CATTAATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 -A-T-ATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
53210 ATAAATATAATATATAGTTTTTTAAACATTTTTGAAA
1 AT--ATATATTATATAGTTTTTAAAACATTTTTGAAA
53247 ATATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
53281 ATAAATATAATATATAATTTTTAAAACGTTTTTGAAA
1 AT--ATATATTATATAGTTTTTAAAACATTTTTGAAA
*
53318 ATATATATTATATATTTTTTAAAACA-TTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* ** *
53352 ATAAATATAATATATAAATTTTAAAATATTTTTGAAA
1 AT--ATATATTATATAGTTTTTAAAACATTTTTGAAA
53389 ATATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * **
53423 ATATATA-TA-GT--TTTTTAAAAAAAATTTGAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTG-AAA
* ** *
53455 CATATATATTATATAGTTTTGAACTCAATTTT-AAA
1 -ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
53490 ACTTATATAGTATATAGTTTTAAAAATATTTTTGAAA
1 A--TATATATTATATAGTTTTTAAAACATTTTTGAAA
53527 ACTATATA
1 A-TATATA
53535 GTTTTGAAAA
Statistics
Matches: 337, Mismatches: 39, Indels: 47
0.80 0.09 0.11
Matches are distributed among these distances:
30 10 0.03
31 4 0.01
32 4 0.01
33 9 0.03
34 38 0.11
35 76 0.23
36 95 0.28
37 55 0.16
38 18 0.05
39 21 0.06
40 1 0.00
41 6 0.02
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (35 bp):
ATATATATTATATAGTTTTTAAAACATTTTTGAAA
Found at i:53541 original size:65 final size:67
Alignment explanation
Indices: 53464--53601 Score: 192
Period size: 67 Copynumber: 2.1 Consensus size: 67
53454 ACATATATAT
** * * *
53464 TATATAGTTTTGAACTCAATTTT-AAAAC-TTATATAGTATATAGTTTTAAAA-ATATTTTTGAA
1 TATATAGTTTTGAAAACAATTTTCAAAACAATATATAATATATAATTTTAAAATATATTTTTGAA
53526 AA
66 AA
*
53528 CTATATAGTTTTGAAAACAATTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTGA
1 -TATATAGTTTTGAAAACAATTTTCAAAACAATATATAATATATAATTTTAAAATATATTTTTGA
53593 AAA
65 AAA
53596 TATATA
1 TATATA
53602 TTGTATAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
65 21 0.33
66 5 0.08
67 26 0.41
68 12 0.19
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (67 bp):
TATATAGTTTTGAAAACAATTTTCAAAACAATATATAATATATAATTTTAAAATATATTTTTGAA
AA
Found at i:53544 original size:29 final size:29
Alignment explanation
Indices: 53500--53563 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
53490 ACTTATATAG
* * *
53500 TATATAGTTTTAAAAATATTTTTGAAAAC
1 TATATAGTTTTAAAAACAATTTTCAAAAC
*
53529 TATATAGTTTTGAAAACAATTTTCAAAAC
1 TATATAGTTTTAAAAACAATTTTCAAAAC
*
53558 AATATA
1 TATATA
53564 TAATATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (29 bp):
TATATAGTTTTAAAAACAATTTTCAAAAC
Found at i:53609 original size:103 final size:101
Alignment explanation
Indices: 53108--53614 Score: 370
Period size: 103 Copynumber: 4.8 Consensus size: 101
53098 ACATATATAT
* * * * * *
53108 TATATAG-TTTGAAAAC-ATTTTTAAAATATATATATAATATATAGTTTTGAAAACATGTTTGAA
1 TATATAGTTTTTAAAACAATTTTGAAAACA-ATATATAATATATAATTTT-AAAATATTTTTG-A
*
53171 AACATTAATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAA
63 AA-A-T-ATATATTATATAGTTTTAAAAACATTTTG-----AAA-AT-A
* * * * *
53220 TATATAGTTTTTTAAACATTTTTG--AA-AATATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 TATATAGTTTTTAAAACAATTTTGAAAACAATATATAATATATA-ATTTTAAAATATTTTTGAAA
* * * *
53281 ATAAATATAATATATAATTTTTAAAACGTTTTTGAAAATATATA
65 AT--ATATATTATATAGTTTTAAAAAC-ATTTTG--AA-A-ATA
* *
53325 TTATATATTTTTTAAAAC-ATTTTGAAAATAA-ATATAATATATAAATTTTAAAATATTTTTGAA
1 -TATATAGTTTTTAAAACAATTTTGAAAACAATATATAATATAT-AATTTTAAAATATTTTTGAA
*
53388 AATATATATTATATAGTTTTTAAAACATTTTGAAAATA
64 AATATATATTATATAGTTTTAAAAACATTTTGAAAATA
* * * * * * *
53426 TATATAGTTTTTTAAAAAAAATTTGAAAAC-ATATATATTATATAGTTTTGAACTCAATTTT-AA
1 TATATAG-TTTTTAAAACAATTTTGAAAACAATATATAATATATAATTTTAAAAT-ATTTTTGAA
* * *
53489 AACTTATATAGTATATAGTTTTAAAAATATTTTTGAAAA-C
64 AA--TATATATTATATAGTTTTAAAAACA-TTTTGAAAATA
* *
53529 TATATAGTTTTGAAAACAATTTTCAAAACAATATATAATATATAATTTTAAAATATTTTTTTGAA
1 TATATAGTTTTTAAAACAATTTTGAAAACAATATATAATATATAATTTTAAAATA--TTTTTGAA
*
53594 AATATATATTGTATAGATTTT
64 AATATATATTATATAG-TTTT
53615 TGGAAAATAT
Statistics
Matches: 327, Mismatches: 44, Indels: 56
0.77 0.10 0.13
Matches are distributed among these distances:
100 6 0.02
101 25 0.08
102 44 0.13
103 63 0.19
104 17 0.05
105 18 0.06
106 41 0.13
107 44 0.13
108 21 0.06
109 4 0.01
110 19 0.06
111 5 0.02
112 9 0.03
113 7 0.02
114 4 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (101 bp):
TATATAGTTTTTAAAACAATTTTGAAAACAATATATAATATATAATTTTAAAATATTTTTGAAAA
TATATATTATATAGTTTTAAAAACATTTTGAAAATA
Found at i:53634 original size:3 final size:3
Alignment explanation
Indices: 53622--53669 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
53612 TTTTGGAAAA
* * *
53622 TAT T-T TAT TAT TAT TAT TAT TAT TAT TCT TTT TTT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53668 TA
1 TA
53670 ATTTCATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:53673 original size:9 final size:8
Alignment explanation
Indices: 53622--53669 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
53612 TTTTGGAAAA
53622 TATTTTAT
1 TATTTTAT
53630 TA--TTAT
1 TATTTTAT
53636 TATTATTAT
1 TATT-TTAT
53645 TATTCTT-T
1 TATT-TTAT
53653 T-TTTTAT
1 TATTTTAT
53660 TATTTTAT
1 TATTTTAT
53668 TA
1 TA
53670 ATTTCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
6 8 0.24
7 4 0.12
8 12 0.35
9 10 0.29
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTTTAT
Found at i:54844 original size:33 final size:34
Alignment explanation
Indices: 54778--54846 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
54768 GCATGTTAAA
54778 ATTTGGCCATTGGTTTTTTTTCTCTTTTCTTTTG
1 ATTTGGCCATTGGTTTTTTTTCTCTTTTCTTTTG
54812 ATTTGGCCATT-GTTTTTTTAT-T-TTTTCGTTTTG
1 ATTTGGCCATTGGTTTTTTT-TCTCTTTTC-TTTTG
54845 AT
1 AT
54847 CCTTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 5 0.15
33 16 0.48
34 12 0.36
ACGTcount: A:0.09, C:0.12, G:0.14, T:0.65
Consensus pattern (34 bp):
ATTTGGCCATTGGTTTTTTTTCTCTTTTCTTTTG
Found at i:55299 original size:7 final size:7
Alignment explanation
Indices: 55277--55318 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
55267 TCAAATCAGG
55277 TTTTTAA
1 TTTTTAA
*
55284 ATTTT-A
1 TTTTTAA
55290 TTTTTAA
1 TTTTTAA
55297 TTTTTAA
1 TTTTTAA
55304 --TTTAA
1 TTTTTAA
55309 TTTTTAA
1 TTTTTAA
55316 TTT
1 TTT
55319 CCGATTAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 5 0.17
6 5 0.17
7 20 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:55300 original size:19 final size:19
Alignment explanation
Indices: 55278--55318 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
55268 CAAATCAGGT
*
55278 TTTTAAATTTTATTTTTAA
1 TTTTAAATTTAATTTTTAA
*
55297 TTTTTAATTTAATTTTTAA
1 TTTTAAATTTAATTTTTAA
55316 TTT
1 TTT
55319 CCGATTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTAAATTTAATTTTTAA
Found at i:61817 original size:14 final size:14
Alignment explanation
Indices: 61798--61825 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61788 TCCCTGGCAC
61798 GAGGACGGTACGGG
1 GAGGACGGTACGGG
61812 GAGGACGGTACGGG
1 GAGGACGGTACGGG
61826 ACGGCCGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.57, T:0.07
Consensus pattern (14 bp):
GAGGACGGTACGGG
Found at i:64782 original size:12 final size:12
Alignment explanation
Indices: 64761--64790 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
64751 GATTCTCTAA
64761 ATAA-TTTTAAT
1 ATAATTTTTAAT
64772 ATAATTTTTAAT
1 ATAATTTTTAAT
64784 ATAATTT
1 ATAATTT
64791 ATATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATAATTTTTAAT
Found at i:64976 original size:118 final size:116
Alignment explanation
Indices: 64725--64976 Score: 330
Period size: 118 Copynumber: 2.2 Consensus size: 116
64715 TTAATTTAAT
* * *
64725 TTAAA-TTATTTTTATTTTATTATTTGGATTCTCTAAATAATTTTAATATAATTTTTAATATAAT
1 TTAAACTTATTTTTATTTTATGATTTGAATTCTCTAAATAAATTTAATATAATTTTTAATATAAT
*
64789 TTATATATTTTATTTAGAAAATAATTTTAAAAAATAATTTAAATAAAAATA
66 TTATATATTTTATTTAGAAAATAATTCTAAAAAATAATTTAAATAAAAATA
* * * * **
64840 TTAATCTCATTTTCATTTTGTGATTTGAATTCTCTAAA-AAATTTAATATAATTTTATTTTATAA
1 TTAAACTTATTTTTATTTTATGATTTGAATTCTCTAAATAAATTTAATATAATTTT-TAATAT-A
* *
64904 TATTTATATATTATTATTT-TAAAGTAATTCTAAAAAATAATTTAAATAAAAATA
64 -ATTTATATATT-TTATTTAGAAAATAATTCTAAAAAATAATTTAAATAAAAATA
*
64958 TTAAACTTGTTTTTATTTT
1 TTAAACTTATTTTTATTTT
64977 TAAGTTTTAC
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
115 20 0.17
116 31 0.27
117 1 0.01
118 58 0.50
119 6 0.05
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (116 bp):
TTAAACTTATTTTTATTTTATGATTTGAATTCTCTAAATAAATTTAATATAATTTTTAATATAAT
TTATATATTTTATTTAGAAAATAATTCTAAAAAATAATTTAAATAAAAATA
Found at i:65021 original size:118 final size:117
Alignment explanation
Indices: 64757--65024 Score: 273
Period size: 118 Copynumber: 2.3 Consensus size: 117
64747 TTTGGATTCT
*
64757 CTAAATAATTTTAATATAATT-T-TTA-AT-ATAATTTATATATTTTATTTAGAAAATAATTTTA
1 CTAAA-AA-TTTAATATAATTATATTATATAAT-ATTTATATATTTTATTTAGAAAATAATTCTA
* * **
64818 AAAAATAATTTAAATAAAAATATTAATCTCATTTTCATTTTGTGATTTGAATTCT
63 AAAAATAATTTAAATAAAAATATTAAACTCATTTTCATTTTGTAATTTGAATTAA
* * * *
64873 CTAAAAAATTTAATATAATTTTATTTTATAATATTTATATATTATTATTT-TAAAGTAATTCTAA
1 CT-AAAAATTTAATATAATTATATTATATAATATTTATATATT-TTATTTAGAAAATAATTCTAA
** * *
64937 AAAATAATTTAAATAAAAATATTAAACTTGTTTTTATTTT-TAAGTTTTACATTAA
64 AAAATAATTTAAATAAAAATATTAAACTCATTTTCATTTTGTAA-TTTGA-ATTAA
*
64992 CT-ATAATTTAATAT-ATATATATATATATAATAT
1 CTAAAAATTTAATATAAT-TATAT-TATATAATAT
65025 AATTTACTCA
Statistics
Matches: 127, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
115 12 0.09
116 7 0.06
117 22 0.17
118 73 0.57
119 13 0.10
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (117 bp):
CTAAAAATTTAATATAATTATATTATATAATATTTATATATTTTATTTAGAAAATAATTCTAAAA
AATAATTTAAATAAAAATATTAAACTCATTTTCATTTTGTAATTTGAATTAA
Done.