Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002836.1 Hibiscus syriacus cultivar Beakdansim tig00005835_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: 115481
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:843 original size:13 final size:13
Alignment explanation
Indices: 825--850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
815 AAAGTTTCAA
825 AGTTTTTTAAAAT
1 AGTTTTTTAAAAT
838 AGTTTTTTAAAAT
1 AGTTTTTTAAAAT
851 TAACAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AGTTTTTTAAAAT
Found at i:3074 original size:2 final size:2
Alignment explanation
Indices: 3067--3094 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3057 AACTACATGA
3067 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
3095 TAAATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12091 original size:21 final size:21
Alignment explanation
Indices: 12065--12104 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12055 TCAATTGTGT
12065 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
*
12086 ATCGATGTACTGCTACAGT
1 ATCGATGCACTGCTACAGT
12105 AACTTTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:15187 original size:42 final size:42
Alignment explanation
Indices: 15101--15416 Score: 221
Period size: 43 Copynumber: 7.3 Consensus size: 42
15091 TAAGGGCTTA
* * *
15101 AATTATAAAAATAAAAAGT-ATTATTGAAAAAATTACGGACCTC
1 AATTAT-AAAGTAAAAAGTGA-GATTGAAAAAATTAGGGACCTC
* * *
15144 AATTATAAAGATAAAAAGTGATATTTAAAAAA-TAGGGGCCTC
1 AATTATAAAG-TAAAAAGTGAGATTGAAAAAATTAGGGACCTC
* * * * *
15186 AATTTTAAAGTAAAAAATGAGATTGAAAAACTAAGGG-CCTA
1 AATTATAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTC
* * *
15227 AATTATGTAAGTAAAAAGTGGGATTGAAAAAATTAGGGACCTT
1 AATTAT-AAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTC
* * ** *
15270 AATTATGAAGGTAAAAAGTGAGACTGGAAAAAATTA-CAAGCTC
1 AATTAT-AAAGTAAAAAGTGAGA-TTGAAAAAATTAGGGACCTC
* * * * *
15313 AATTATAAAGGTACAAAGTGAGAATGAAAAACTTA-GAATCATC
1 AATTATAAA-GTAAAAAGTGAGATTGAAAAAATTAGGGA-CCTC
* **
15356 AATCATAAATGTAAAAAGT-ATGATTGGAAAAAAAATTAAAGACCTC
1 AATTATAAA-GTAAAAAGTGA-GATT-G--AAAAAATTAGGGACCTC
15402 AATTATAAAGATAAA
1 AATTATAAAG-TAAA
15417 TTAAATTAAA
Statistics
Matches: 216, Mismatches: 43, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
41 25 0.12
42 64 0.30
43 89 0.41
44 13 0.06
45 1 0.00
46 23 0.11
47 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (42 bp):
AATTATAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTC
Found at i:15434 original size:15 final size:16
Alignment explanation
Indices: 15407--15436 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15397 ACCTCAATTA
15407 TAAAGATAAATTAAAT
1 TAAAGATAAATTAAAT
15423 TAAAGA-AAATTAAA
1 TAAAGATAAATTAAA
15437 GGACTCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
TAAAGATAAATTAAAT
Found at i:27657 original size:3 final size:3
Alignment explanation
Indices: 27645--27682 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
27635 CTATATCATC
* *
27645 ATT ATT -TT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27683 TACAAACCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:27829 original size:12 final size:12
Alignment explanation
Indices: 27807--27848 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
27797 AATAAACCAC
27807 ACCC-AAACCCA
1 ACCCAAAACCCA
* *
27818 ACCTATAACCCA
1 ACCCAAAACCCA
27830 ACCCAAAACCCA
1 ACCCAAAACCCA
27842 A-CCAAAA
1 ACCCAAAA
27849 TCCGACCGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.50, C:0.45, G:0.00, T:0.05
Consensus pattern (12 bp):
ACCCAAAACCCA
Found at i:27838 original size:24 final size:24
Alignment explanation
Indices: 27798--27844 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27788 AAAACCAAAA
27798 ATAAACCACACCCAAACCCAACCT
1 ATAAACCACACCCAAACCCAACCT
*
27822 ATAACCCA-ACCCAAAACCCAACC
1 ATAAACCACACCC-AAACCCAACC
27845 AAAATCCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.47, C:0.47, G:0.00, T:0.06
Consensus pattern (24 bp):
ATAAACCACACCCAAACCCAACCT
Found at i:32918 original size:14 final size:14
Alignment explanation
Indices: 32890--32929 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
32880 TGTTTTTTTT
*
32890 GTTTGTGTT-GTTC
1 GTTTATGTTCGTTC
*
32903 GTTTATTTTCGTTC
1 GTTTATGTTCGTTC
32917 GTTTATGTTCGTT
1 GTTTATGTTCGTT
32930 TATCATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.05, C:0.10, G:0.23, T:0.62
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:33457 original size:2 final size:2
Alignment explanation
Indices: 33452--33479 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33442 AAACATAAAG
33452 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
33480 GTACTTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33936 original size:247 final size:251
Alignment explanation
Indices: 33482--33973 Score: 704
Period size: 247 Copynumber: 2.0 Consensus size: 251
33472 ATATATATGT
* *
33482 ACTTCTAAAATTTTAGGAGAGGCTAACTTATAAAATTATAGAGGGACGAAAACATACTATTAATA
1 ACTTCTAAAATTTTAGGAGAGACTAACTTATAAAATTATAGAGGGAAGAAAACATACTATTAATA
* * *
33547 CAAAATACATAAAAGAATATCTAAAATATATGTTAATTTAAAATTTTTAAAAATAAAAACTACCC
66 AAAAATACATAAAAGAATATCTAAAATATATGATAATTTAAAACTTTTAAAAATAAAAACTACCC
* **
33612 CGATTGTCGCCTGGGTCCATCCCTACCTACACAATCATCTTCCGATGAGATTATATTAGTGAAAC
131 CGATTGTCCCCTAAGTCCATCCCTACCTACACAATCATCTTCCGATGAGATTATATTAGTGAAAC
* *
33677 ACACCACACCATTTTCAAACCAAAGTGAAATGGGAAAGGAATAATGCTAGAGGAGA
196 ACACCACACCATTTGCAAACCAAAGTGAAATGGGAAAGAAATAATGCTAGAGGAGA
* * * * * *
33733 ACTTCTGAAATTTTAGGAGATACTAACTTATTAAATTTTAGATGGAAGAAAACATATTA-TAA-A
1 ACTTCTAAAATTTTAGGAGAGACTAACTTATAAAATTATAGAGGGAAGAAAACATACTATTAATA
* * * * *
33796 AAAAATACATAAAA-AA-ATCTAAAATATTTGATAATTTAAAACTTTTAAAGATGACAACTACCT
66 AAAAATACATAAAAGAATATCTAAAATATATGATAATTTAAAACTTTTAAAAATAAAAACTACCC
* * *
33859 CGGTTGTCCCCTAAGTCCATCCCTACCTACACTATCATCTTCCGGTGAGATTATATTAGTGAAAC
131 CGATTGTCCCCTAAGTCCATCCCTACCTACACAATCATCTTCCGATGAGATTATATTAGTGAAAC
* * * *
33924 ACACCTCACCATTTGCAAACCAAATTGCAATGGGAAATAAATAATGCTAG
196 ACACCACACCATTTGCAAACCAAAGTGAAATGGGAAAGAAATAATGCTAG
33974 GATTAGCACC
Statistics
Matches: 213, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
247 143 0.67
248 2 0.01
249 14 0.07
250 3 0.01
251 51 0.24
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (251 bp):
ACTTCTAAAATTTTAGGAGAGACTAACTTATAAAATTATAGAGGGAAGAAAACATACTATTAATA
AAAAATACATAAAAGAATATCTAAAATATATGATAATTTAAAACTTTTAAAAATAAAAACTACCC
CGATTGTCCCCTAAGTCCATCCCTACCTACACAATCATCTTCCGATGAGATTATATTAGTGAAAC
ACACCACACCATTTGCAAACCAAAGTGAAATGGGAAAGAAATAATGCTAGAGGAGA
Found at i:36410 original size:15 final size:15
Alignment explanation
Indices: 36392--36422 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
36382 TCTGGGCTGT
36392 TGAGTTCGGGCTTGG
1 TGAGTTCGGGCTTGG
36407 TGAGTTCGGGCTTGG
1 TGAGTTCGGGCTTGG
36422 T
1 T
36423 TCAAGCCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.45, T:0.35
Consensus pattern (15 bp):
TGAGTTCGGGCTTGG
Found at i:36979 original size:107 final size:106
Alignment explanation
Indices: 36857--37843 Score: 1518
Period size: 107 Copynumber: 9.3 Consensus size: 106
36847 TCACTTCCTC
* * ** *
36857 TTTCTTCAGAGAGTAGAACTCGAACATTCTTCTTCCTACGTG-CTCGCTCTCTCTTTTCTTCAGG
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCT-TTTTCTTCAGG
* * * * *
36921 GAGTAGAACTCAAACAATCATCTTCCTATGGGTCTGCTCTCTC
64 GAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * * *
36964 TTCCTTCAAGGAGTAGAACTCGAACAATCATCTTCCTACGGGTCCGCTCTCTCTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
* *
37029 GTAGAACTAGAACAATAATCTTCCTACGGGTCCGCTATCTA
66 GTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37070 TTTCTTCAGGGAGTAGAACTCAAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
37135 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
66 GT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37177 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
37242 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
66 GT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
37284 TTTCTTTAGGGAGTAGAACTCGAACAATAATCTTCATACGGGTCCGCTCTCTTTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
*
37349 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
66 GT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
37391 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCT-TTATTTCTTCAGG
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT-TTTCTTCAGG
* ** *
37455 GAGTAGAACTCGAACAATGATCTTCCTACGGGTCCATTCTCTT
64 GAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
37498 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTACTACGGGTCCGCTCTCTATTTCTTCAGGG
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGG
*
37563 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
65 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37605 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGCCCGCTCTCTTTTTCTTCAGGG
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGG
37670 AGTAGAACTCGAACAATAATCTTCCTACGGGAT-CGCTCTCTA
65 AGTAGAACTCGAACAATAATCTTCCTACGGG-TCCGCTCTCTA
* * * *
37712 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCTTACGGGTCCAC-C-CTATTTCTTCAAGG
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGG
* *
37775 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCCCTGT-
65 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
37816 TTTCTTCAGGGAGTAGAACTCGAACAAT
1 TTTCTTCAGGGAGTAGAACTCGAACAAT
37844 CTTATGTTGC
Statistics
Matches: 825, Mismatches: 48, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
103 14 0.02
104 15 0.02
105 49 0.06
106 109 0.13
107 586 0.71
108 52 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (106 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
GTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
Found at i:36990 original size:53 final size:53
Alignment explanation
Indices: 36857--37843 Score: 1498
Period size: 53 Copynumber: 18.5 Consensus size: 53
36847 TCACTTCCTC
* * ** * *
36857 TTTCTTCAGAGAGTAGAACTCGAACATTCTTCTTCCTACGTG-CTCGCTCTCTCT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCT-A
* * * * *
36911 TTTCTTCAGGGAGTAGAACTCAAACAATCATCTTCCTATGGGTCTGCTCTCTC
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * * *
36964 TTCCTTCAAGGAGTAGAACTCGAACAATCATCTTCCTACGGGTCCGCTCTCTC
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
37017 TTTCTTCAGGGAGTAGAACTAGAACAATAATCTTCCTACGGGTCCGCTATCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
37070 TTTCTTCAGGGAGTAGAACTCAAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
37123 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
37177 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
37230 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * *
37284 TTTCTTTAGGGAGTAGAACTCGAACAATAATCTTCATACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37337 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37391 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTTTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* ** *
37445 TTTCTTCAGGGAGTAGAACTCGAACAATGATCTTCCTACGGGTCCATTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37498 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTACTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
37552 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
37605 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGCCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
37659 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGAT-CGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCCGCTCTCTA
* *
37712 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCTTACGGGTCCAC-C-CTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * *
37764 TTTCTTCAAGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCCCTGT-
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
37816 TTTCTTCAGGGAGTAGAACTCGAACAAT
1 TTTCTTCAGGGAGTAGAACTCGAACAAT
37844 CTTATGTTGC
Statistics
Matches: 864, Mismatches: 58, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
51 31 0.04
52 44 0.05
53 411 0.48
54 377 0.44
55 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (53 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
Found at i:39207 original size:8 final size:8
Alignment explanation
Indices: 39194--39281 Score: 53
Period size: 8 Copynumber: 10.9 Consensus size: 8
39184 TGTTTTATTT
39194 ATTTTTTC
1 ATTTTTTC
39202 ATTTTTTTC
1 A-TTTTTTC
39211 ATTTATTT-
1 ATTT-TTTC
39219 -TTTCATTT-
1 ATTT--TTTC
39227 ATTTTTTC
1 ATTTTTTC
*
39235 A-TTTAT-
1 ATTTTTTC
39241 -TTTTTTC
1 ATTTTTTC
39248 ATTTTTTTTC
1 A--TTTTTTC
*
39258 ATTTTTTAT
1 ATTTTTT-C
39267 ATTTTTTC
1 ATTTTTTC
39275 ATTTTTT
1 ATTTTTT
39282 TTTCTTTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
6 4 0.06
7 10 0.15
8 22 0.34
9 21 0.32
10 8 0.12
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTC
Found at i:39208 original size:25 final size:24
Alignment explanation
Indices: 39180--39284 Score: 110
Period size: 27 Copynumber: 4.4 Consensus size: 24
39170 CTTTTATTTG
*
39180 TTTTTGTTTT-ATTTATTTTTTCA
1 TTTTTTTTTTCATTTATTTTTTCA
39203 ---TTTTTTTCATTTATTTTTTCA
1 TTTTTTTTTTCATTTATTTTTTCA
*
39224 TTTATTTTTTCATTTATTTTTTTCA
1 TTTTTTTTTTCATTTA-TTTTTTCA
**
39249 TTTTTTTTCATTTTTTATATTTTTTCA
1 TTTTTTTT--TTCATT-TATTTTTTCA
39276 TTTTTTTTT
1 TTTTTTTTT
39285 CTTTTTTTCA
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
20 6 0.09
21 13 0.19
24 12 0.17
25 16 0.23
27 20 0.29
28 2 0.03
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.79
Consensus pattern (24 bp):
TTTTTTTTTTCATTTATTTTTTCA
Found at i:39219 original size:12 final size:12
Alignment explanation
Indices: 39186--39285 Score: 102
Period size: 12 Copynumber: 8.4 Consensus size: 12
39176 TTTGTTTTTG
39186 TTTT-ATTTATT
1 TTTTCATTTATT
39197 TTTTCA--T-TT
1 TTTTCATTTATT
39206 TTTTCATTTATT
1 TTTTCATTTATT
39218 TTTTCATTTATT
1 TTTTCATTTATT
39230 TTTTCATTTATTT
1 TTTTCATTTA-TT
*
39243 TTTTCATTTTTT
1 TTTTCATTTATT
**
39255 TTCATTTTTTATATT
1 TT--TTCATT-TATT
39270 TTTTCATTT-TT
1 TTTTCATTTATT
39281 TTTTC
1 TTTTC
39286 TTTTTTTCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
9 8 0.11
10 1 0.01
11 12 0.16
12 30 0.40
13 15 0.20
14 4 0.05
15 5 0.07
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCATTTATT
Found at i:39242 original size:64 final size:61
Alignment explanation
Indices: 39172--39292 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 61
39162 GAACCCCCCT
**
39172 TTTATTTGTTTTTGTTTTATTT-ATTTTTTCAT-TTTTTTCATTTATTTTTTCATTTATTTTTTC
1 TTTATTT-TTTTCATTTTATTTCATTTTTT-ATATTTTTTCATTT-TTTTTTC-TTT-TTTTTTC
39235 A
61 A
*
39236 TTTATTTTTTTCATTTTTTTTCATTTTTTATATTTTTTCATTTTTTTTTCTTTTTTT
1 TTTATTTTTTTCATTTTATTTCATTTTTTATATTTTTTCATTTTTTTTTCTTTTTTT
39293 CATCTTCAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
61 4 0.08
62 3 0.06
63 20 0.38
64 25 0.48
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (61 bp):
TTTATTTTTTTCATTTTATTTCATTTTTTATATTTTTTCATTTTTTTTTCTTTTTTTTTCA
Found at i:39289 original size:25 final size:25
Alignment explanation
Indices: 39171--39289 Score: 106
Period size: 25 Copynumber: 4.8 Consensus size: 25
39161 TGAACCCCCC
* *
39171 TTTT-ATTTGTTTTTGTTTTATTTATT
1 TTTTCATTTTTTTTTCTTTTA--TATT
*
39197 TTTTCA--TTTTTTTC-ATT-TATT
1 TTTTCATTTTTTTTTCTTTTATATT
*
39218 TTTTCATTTATTTTTTCATTTAT-TT
1 TTTTCATTT-TTTTTTCTTTTATATT
*
39243 TTTTCATTTTTTTTCATTTTTTATATT
1 TTTTCATTTTTTTT--TCTTTTATATT
39270 TTTTCATTTTTTTTTCTTTT
1 TTTTCATTTTTTTTTCTTTT
39290 TTTCATCTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
21 10 0.13
23 1 0.01
24 14 0.18
25 24 0.31
26 11 0.14
27 17 0.22
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTCATTTTTTTTTCTTTTATATT
Found at i:51878 original size:23 final size:23
Alignment explanation
Indices: 51851--51919 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
51841 GTTTGGACGA
51851 TTTATAATTTATAATTTATAATT
1 TTTATAATTTATAATTTATAATT
* *
51874 TTTAT-TTATTATAATTTCT--TT
1 TTTATAAT-TTATAATTTATAATT
*
51895 TTAAATTAATTTATAA-TTATAATT
1 TT-TA-TAATTTATAATTTATAATT
51919 T
1 T
51920 GTTTAATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 22 0.63
24 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTATAATTTATAATTTATAATT
Found at i:51885 original size:7 final size:7
Alignment explanation
Indices: 51850--51874 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51840 TGTTTGGACG
51850 ATTTATA
1 ATTTATA
51857 ATTTATA
1 ATTTATA
51864 ATTTATA
1 ATTTATA
51871 ATTT
1 ATTT
51875 TTATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTATA
Found at i:52523 original size:18 final size:19
Alignment explanation
Indices: 52497--52559 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 19
52487 GTTATAATAA
52497 AATATTAATTATGATAATT
1 AATATTAATTATGATAATT
* *
52516 AA-ATTAATAAAT-ATACTT
1 AATATTAAT-TATGATAATT
52534 AATATATTAATTATGATAATT
1 -A-ATATTAATTATGATAATT
52555 AATAT
1 AATAT
52560 ACTTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 11 0.31
19 9 0.26
20 4 0.11
21 11 0.31
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (19 bp):
AATATTAATTATGATAATT
Found at i:52556 original size:21 final size:21
Alignment explanation
Indices: 52490--52560 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
52480 TTTAAATGTT
*
52490 ATAA-TAAAATATTAATTATG
1 ATAATTAATATATTAATTATG
*
52510 ATAATT-A-A-ATTAATAAAT-
1 ATAATTAATATATTAAT-TATG
*
52528 ATACTTAATATATTAATTATG
1 ATAATTAATATATTAATTATG
52549 ATAATTAATATA
1 ATAATTAATATA
52561 CTTTATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 11 0.27
19 4 0.10
20 8 0.20
21 18 0.44
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (21 bp):
ATAATTAATATATTAATTATG
Found at i:52577 original size:14 final size:15
Alignment explanation
Indices: 52556--52662 Score: 66
Period size: 15 Copynumber: 7.3 Consensus size: 15
52546 ATGATAATTA
52556 ATATACTTTATATTT
1 ATATACTTTATATTT
52571 A-ATAC-TTATATTT
1 ATATACTTTATATTT
*
52584 ATATACTTTAATACTT
1 ATATACTTT-ATATTT
*** *
52600 ATAT-CCAAACACTTT
1 ATATACTTTATA-TTT
52615 AT-TACTTTATA-TT
1 ATATACTTTATATTT
* *
52628 ATATA-TATATATACT
1 ATATACTTTATAT-TT
52643 A-ATACTTTATAGTTT
1 ATATACTTTATA-TTT
52658 ATATA
1 ATATA
52663 TGTAGATAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 21
0.66 0.14 0.21
Matches are distributed among these distances:
13 18 0.27
14 16 0.24
15 20 0.30
16 13 0.19
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:52581 original size:13 final size:14
Alignment explanation
Indices: 52556--52591 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52546 ATGATAATTA
52556 ATATACTTTATATTT
1 ATATAC-TTATATTT
52571 A-ATACTTATATTT
1 ATATACTTATATTT
52584 ATATACTT
1 ATATACTT
52592 TAATACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 10 0.50
15 1 0.05
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATACTTATATTT
Found at i:52613 original size:22 final size:22
Alignment explanation
Indices: 52568--52626 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
52558 ATACTTTATA
** * *
52568 TTTAATACTTATATTTATATAC
1 TTTAATACTTATATCCAAACAC
52590 TTTAATACTTATATCCAAACAC
1 TTTAATACTTATATCCAAACAC
*
52612 TTTATTACTTTATAT
1 TTTAATAC-TTATAT
52627 TATATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAATACTTATATCCAAACAC
Found at i:53093 original size:2 final size:2
Alignment explanation
Indices: 53081--53120 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
53071 CATTATACTT
*
53081 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53121 ATGTACATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:53210 original size:6 final size:6
Alignment explanation
Indices: 53201--54036 Score: 1193
Period size: 6 Copynumber: 139.7 Consensus size: 6
53191 TTATATATAT
* * * *
53201 ACATAC ACATAC GCATAC ACATAT ACATAC GCATAC ACACAC ACGCATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC A--CATAC
*
53251 ACATAC ACATAC ACATAC ACATAC AC--AC ACATAC ACAT-- ATATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * *
53295 ACATAC ACATAC ACATAC ACATGC ACATGC ACATAC ACATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
53343 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
53391 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * *
53439 ACATGC ACATGC ACATAC ACATAC ACATAC ACATCC ACATCC ACATCC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53487 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53535 ACATAC ACATACAC ACATAC ACATACAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACAT--AC ACATAC ACAT--AC ACATAC ACATAC ACATAC ACATAC
53587 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53635 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53683 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53731 ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53777 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53825 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53871 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
53919 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
53967 ACATCC ACATCC ACATCC ACATCC ACATCC ACATCC ACATCC ACAAAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * *
54015 ACATCC ACACAC ACACAC ACAT
1 ACATAC ACATAC ACATAC ACAT
54037 CTTTTCATCT
Statistics
Matches: 792, Mismatches: 24, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
4 15 0.02
6 760 0.96
8 17 0.02
ACGTcount: A:0.46, C:0.35, G:0.03, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:56878 original size:183 final size:179
Alignment explanation
Indices: 56532--56885 Score: 568
Period size: 183 Copynumber: 2.0 Consensus size: 179
56522 TTTAATTCAA
* *
56532 AAAAACAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAATTTAAT
1 AAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATAAAATTTAAT
* *
56597 TAATTAATATTGATTTAGGTTTAAAGTTATTGGATCTTAAATTATTAATTAGGTTTTAAATGGTT
66 TAATTAATAATGATTTAGGTTTAAAGTTATTGGATCTTAAATTATTAATTAGGTTTTAAATGATT
56662 TGGGCTGAGCCCATATGTTATATATAATATATTTAATATTTTTTTATTT
131 TGGGCTGAGCCCATATGTTATATATAATATATTTAATATTTTTTTATTT
*
56711 AAAAACAGTTTACAATTAATTTAACTAATATATAATTA-AAAATTAAAAATTTAATATAAAATTT
1 AAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAA-TAAAAATTT--TATAAAA--T
* *
56775 TTAATTATTTAATAATGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAA
61 TTAATTAATTAATAATGATTTAGGTTT-AAAGTTATTGGATCTTAAATTATTAATTAGGTTTTAA
*
56840 AT-ATTTGGGTTGAGCCCATATGTTATATATAATATATTTAATATTT
125 ATGATTTGGGCTGAGCCCATATGTTATATATAATATATTTAATATTT
56886 AAAATTTAAT
Statistics
Matches: 161, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
178 4 0.02
179 45 0.28
181 6 0.04
183 68 0.42
184 38 0.24
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (179 bp):
AAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATAAAATTTAAT
TAATTAATAATGATTTAGGTTTAAAGTTATTGGATCTTAAATTATTAATTAGGTTTTAAATGATT
TGGGCTGAGCCCATATGTTATATATAATATATTTAATATTTTTTTATTT
Found at i:58706 original size:88 final size:88
Alignment explanation
Indices: 58557--58733 Score: 327
Period size: 88 Copynumber: 2.0 Consensus size: 88
58547 ATTTTAGTGA
* *
58557 CCAAATTTTAAAATTACAAACTACAGGGGTTGCGGGGATGATTTACCCACACGCAAAATACACAG
1 CCAAATTGTAAAATTACAAACTACAGGGGTTGCGGGGATGATTTACCAACACGCAAAATACACAG
58622 ATAACCCCTCCTTGAAACGACGT
66 ATAACCCCTCCTTGAAACGACGT
*
58645 CCAAATTGTAAAATTACAAACTACAGGGGTTGCGGGGATGATTTACCAACGCGCAAAATACACAG
1 CCAAATTGTAAAATTACAAACTACAGGGGTTGCGGGGATGATTTACCAACACGCAAAATACACAG
58710 ATAACCCCTCCTTGAAACGACGT
66 ATAACCCCTCCTTGAAACGACGT
58733 C
1 C
58734 GTTTCAAGGA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (88 bp):
CCAAATTGTAAAATTACAAACTACAGGGGTTGCGGGGATGATTTACCAACACGCAAAATACACAG
ATAACCCCTCCTTGAAACGACGT
Found at i:60688 original size:19 final size:19
Alignment explanation
Indices: 60666--60709 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
60656 CGATTTATTT
60666 TTATTAAAAA-TATATAAAA
1 TTATTAAAAACTAT-TAAAA
*
60685 TTATTAAAAACTGTTAAAA
1 TTATTAAAAACTATTAAAA
60704 TTATTA
1 TTATTA
60710 TTTTTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
TTATTAAAAACTATTAAAA
Found at i:65429 original size:11 final size:11
Alignment explanation
Indices: 65413--65437 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65403 CAGTTGCCCC
65413 TCTTTGCTCAT
1 TCTTTGCTCAT
65424 TCTTTGCTCAT
1 TCTTTGCTCAT
65435 TCT
1 TCT
65438 AATTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (11 bp):
TCTTTGCTCAT
Found at i:67313 original size:16 final size:16
Alignment explanation
Indices: 67294--67368 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
67284 TTGTTTTTCA
67294 TTTTTCTTTTCATTTT
1 TTTTTCTTTTCATTTT
**
67310 TTTTGATTTTCATTTT
1 TTTTTCTTTTCATTTT
*
67326 TTTCTCTTTTC-TTTT
1 TTTTTCTTTTCATTTT
* *
67341 TTCTCTCTTTTTATTTT
1 TT-TTTCTTTTCATTTT
67358 TTCTTT-TTTTC
1 TT-TTTCTTTTC
67369 TTCAGGCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.12
16 34 0.69
17 9 0.18
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTCATTTT
Found at i:67340 original size:14 final size:13
Alignment explanation
Indices: 67322--67367 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
67312 TTGATTTTCA
67322 TTTTTTTCTCTTT
1 TTTTTTTCTCTTT
67335 TCTTTTTTCTCTCTT
1 T-TTTTTTCTCT-TT
*
67350 TTTATTTTTTCTTT
1 TTT-TTTTCTCTTT
67364 TTTT
1 TTTT
67368 CTTCAGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 2 0.07
14 17 0.59
15 10 0.34
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:67340 original size:28 final size:28
Alignment explanation
Indices: 67278--67341 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
67268 TTGAACCCCC
* * *
67278 TTTTATTTGTTTTTCATTTTTCTTTTCA
1 TTTTTTTTGATTTTCATTTTTCTTCTCA
*
67306 TTTTTTTTGATTTTCATTTTT-TTCTCT
1 TTTTTTTTGATTTTCATTTTTCTTCTCA
67333 TTTCTTTTT
1 TTT-TTTTT
67342 TCTCTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (28 bp):
TTTTTTTTGATTTTCATTTTTCTTCTCA
Found at i:85360 original size:42 final size:41
Alignment explanation
Indices: 85307--85409 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 41
85297 TTCTAAAATC
* *
85307 GATAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGAT
1 GATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGAT
* * * *
85348 GATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGAT
1 GA-TAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGAT
*
85390 GATAAGTCCTTCGGGCCATC
1 GATAAATCCTTCGGGCCATC
85410 TATAAGACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 18 0.34
42 35 0.66
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
GATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGAT
Found at i:85392 original size:249 final size:249
Alignment explanation
Indices: 84967--85421 Score: 766
Period size: 249 Copynumber: 1.8 Consensus size: 249
84957 ATTTCCAAAA
*
84967 TTTCCCATTCATTGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTC
1 TTTCCCATTCACTGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTC
* * * *
85032 TTACCCAGTAAACTATTTCTAAAATTGGTAAGTCATTCGGGTCATCAGTAAGTCTTTCGAGCATG
66 TTACCCAGTAAACTATTTCTAAAATCGATAAGTCATTCGGGCCATCAGTAAGCCTTTCGAGCATG
*
85097 ACGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCTAGATGATAAGTCATTCGGGCCATCC
131 ACGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCC
*
85162 ATGAGACCTTCGAGTAGGATGTTTTCACATGAATTGAGAAAAAGAATTCTAAAG
196 ATAAGACCTTCGAGTAGGATGTTTTCACATGAATTGAGAAAAAGAATTCTAAAG
* *
85216 TTTCTCATTCACTGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTC
1 TTTCCCATTCACTGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTC
*
85281 TTACCCAGTAAACTATTTCTAAAATCGATAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATG
66 TTACCCAGTAAACTATTTCTAAAATCGATAAGTCATTCGGGCCATCAGTAAGCCTTTCGAGCATG
* * * * * *
85346 ATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCT
131 ACGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCC
85411 ATAAGACCTTC
196 ATAAGACCTTC
85422 AGGCAAGATG
Statistics
Matches: 190, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
249 190 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (249 bp):
TTTCCCATTCACTGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTC
TTACCCAGTAAACTATTTCTAAAATCGATAAGTCATTCGGGCCATCAGTAAGCCTTTCGAGCATG
ACGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCC
ATAAGACCTTCGAGTAGGATGTTTTCACATGAATTGAGAAAAAGAATTCTAAAG
Found at i:85428 original size:41 final size:40
Alignment explanation
Indices: 85307--85431 Score: 128
Period size: 41 Copynumber: 3.0 Consensus size: 40
85297 TTCTAAAATC
*
85307 GATAAGTCCTTCGGGCCATC-AGTAAGCCTTTCGAGCATGAT
1 GATAAGTCCTTCGGGCCATCTA-TAAGCC-TTCGAGCAAGAT
* * * * *
85348 GATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGAT
1 GA-TAAGTCCTTCGGGCCATCTATAAG-CCTTCGAGCAAGAT
85390 GATAAGTCCTTCGGGCCATCTATAAGACCTTC-AGGCAAGAT
1 GATAAGTCCTTCGGGCCATCTATAAG-CCTTCGA-GCAAGAT
85431 G
1 G
85432 CTTTCATATG
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
40 1 0.01
41 34 0.50
42 32 0.47
43 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (40 bp):
GATAAGTCCTTCGGGCCATCTATAAGCCTTCGAGCAAGAT
Found at i:85516 original size:17 final size:17
Alignment explanation
Indices: 85494--85532 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
85484 TTTAAAATAT
*
85494 TAAAAAAATAATAAAAA
1 TAAAAAAAGAATAAAAA
* *
85511 TAAAAATAGAATAATAA
1 TAAAAAAAGAATAAAAA
85528 TAAAA
1 TAAAA
85533 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAAAAAGAATAAAAA
Found at i:90074 original size:18 final size:19
Alignment explanation
Indices: 90038--90075 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
90028 TCATACAAAA
90038 ATCATTACCATGTTTTTTT
1 ATCATTACCATGTTTTTTT
90057 ATCATTACCATGTTTTTTT
1 ATCATTACCATGTTTTTTT
90076 CTTAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (19 bp):
ATCATTACCATGTTTTTTT
Found at i:91208 original size:17 final size:17
Alignment explanation
Indices: 91174--91225 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
91164 ACCGGATAAA
* *
91174 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
91191 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
91208 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
91223 TTT
1 TTT
91226 CTACTGTAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:91912 original size:11 final size:11
Alignment explanation
Indices: 91896--91920 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
91886 TATTCCCTTC
91896 TTTTTTCTTTT
1 TTTTTTCTTTT
91907 TTTTTTCTTTT
1 TTTTTTCTTTT
91918 TTT
1 TTT
91921 GGTTCCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:94665 original size:35 final size:34
Alignment explanation
Indices: 94580--94666 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
94570 AAAATAATTT
*
94580 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
94614 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
94652 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
94667 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:104708 original size:91 final size:90
Alignment explanation
Indices: 104471--104739 Score: 297
Period size: 91 Copynumber: 3.0 Consensus size: 90
104461 TAATATTGAT
* * * * * * * * * *
104471 ACTACTATACAACATACAAACTGAGGTAGGCATCATAGTGTGGCTAAGGTGCTATATCACGGAGC
1 ACTACTATGCAACACACAAACTGAGATAGGCATCATGGTGCGGCTGAGGGGCTACATCTCAGAGC
*
104536 TCACACACCCCTCTAGCCTACCTAT
66 TCACACACCCCTCTAGCCTACCTAC
* * *
104561 ACTACTATGCAACACACACAAACCGAGATAGGAATCATGGTACGGCTGAGGGGCTACATCTCAGA
1 ACTACTATGC-A-ACACACAAACTGAGATAGGCATCATGGTGCGGCTGAGGGGCTACATCTCAGA
* *
104626 GCTCATATACCCCCTCTAGCCTACCTAC
64 GCTCACACA-CCCCTCTAGCCTACCTAC
* * *
104654 ACTACTATGCAACACACGAACTGAGATAGGCATCATGGTGCGACTGAGGGGCTACATCT-TGAAG
1 ACTACTATGCAACACACAAACTGAGATAGGCATCATGGTGCGGCTGAGGGGCTACATCTCAG-AG
** *
104718 CTCGTACACCCCTCTAACCTAC
65 CTCACACACCCCTCTAGCCTAC
104740 TTATACCCGT
Statistics
Matches: 150, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
90 23 0.15
91 52 0.35
92 48 0.32
93 27 0.18
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (90 bp):
ACTACTATGCAACACACAAACTGAGATAGGCATCATGGTGCGGCTGAGGGGCTACATCTCAGAGC
TCACACACCCCTCTAGCCTACCTAC
Found at i:111296 original size:19 final size:19
Alignment explanation
Indices: 111259--111297 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
111249 AAATAAAAAT
*
111259 AATATATATATATATATTA
1 AATATATATAGATATATTA
111278 AATATATAATAGATA-ATTA
1 AATATAT-ATAGATATATTA
111297 A
1 A
111298 TTACGAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AATATATATAGATATATTA
Found at i:111441 original size:18 final size:18
Alignment explanation
Indices: 111420--111458 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
111410 CCGAGACGAT
111420 AAAATAATATT-TATAATA
1 AAAAT-ATATTATATAATA
*
111438 AAAATATATTATTTAATA
1 AAAATATATTATATAATA
111456 AAA
1 AAA
111459 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATATTATATAATA
Found at i:113103 original size:30 final size:30
Alignment explanation
Indices: 113069--113160 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
113059 TGAAAAATAA
*
113069 TTTACGTAAAAT-AGATTACCTGAAAACTGT
1 TTTACGTAAAATGA-ATTACATGAAAACTGT
* *
113099 TTTACATAAAATGAATTACATGAAAATTGT
1 TTTACGTAAAATGAATTACATGAAAACTGT
* * *
113129 TTTATGTAAAATGAATTAC-TTAAAACTAT
1 TTTACGTAAAATGAATTACATGAAAACTGT
113158 TTT
1 TTT
113161 GCATATTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 10 0.19
30 42 0.79
31 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACATGAAAACTGT
Found at i:113792 original size:19 final size:18
Alignment explanation
Indices: 113754--113788 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
113744 ATAAAGAAAA
113754 TAGAAAAATTAATTACAT
1 TAGAAAAATTAATTACAT
113772 TAGAAAAATTAATTACA
1 TAGAAAAATTAATTACA
113789 ATTATCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
TAGAAAAATTAATTACAT
Found at i:114314 original size:14 final size:14
Alignment explanation
Indices: 114279--114316 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
114269 TATATTTCGG
114279 TTTGAATTA-AAAA
1 TTTGAATTATAAAA
*
114292 TTT-AATTATAAGA
1 TTTGAATTATAAAA
114305 TTTGAATTATAA
1 TTTGAATTATAA
114317 CATTCCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 5 0.23
13 9 0.41
14 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (14 bp):
TTTGAATTATAAAA
Done.