Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006235.1 Hibiscus syriacus cultivar Beakdansim tig00014862_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: 996025
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:829107 original size:9 final size:9
Alignment explanation
Indices: 829086--829190 Score: 105
Period size: 9 Copynumber: 11.7 Consensus size: 9
829076 CTTAAAGATA
829086 AAAAAAATG
1 AAAAAAATG
829095 --AAAAATG
1 AAAAAAATG
829102 AAAAAAAATG
1 -AAAAAAATG
829112 AAAAAAATG
1 AAAAAAATG
829121 AAAAAAATG
1 AAAAAAATG
829130 AAAAAAATG
1 AAAAAAATG
829139 AAATAGAAAAAT-
1 --A-A-AAAAATG
829151 AGAAAAAATG
1 A-AAAAAATG
*
829161 GAAAAAAT-
1 AAAAAAATG
829169 AAAAAAAT-
1 AAAAAAATG
829177 AAAAAAAT-
1 AAAAAAATG
829185 AAAAAA
1 AAAAAA
829191 GAAGAAGAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 17
0.81 0.03 0.16
Matches are distributed among these distances:
7 7 0.08
8 21 0.25
9 40 0.47
10 9 0.11
11 1 0.01
12 1 0.01
13 6 0.07
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:829107 original size:17 final size:17
Alignment explanation
Indices: 829085--829134 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
829075 GCTTAAAGAT
829085 AAAAAAAATGAAAAATG
1 AAAAAAAATGAAAAATG
829102 AAAAAAAATGAAAAAAATG
1 AAAAAAAATG--AAAAATG
829121 -AAAAAAATGAAAAA
1 AAAAAAAATGAAAAA
829135 AATGAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.16
17 10 0.32
18 9 0.29
19 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAAAATGAAAAATG
Found at i:829108 original size:18 final size:18
Alignment explanation
Indices: 829085--829183 Score: 66
Period size: 17 Copynumber: 5.3 Consensus size: 18
829075 GCTTAAAGAT
829085 AAAAAAAATGAAAAATG-
1 AAAAAAAATGAAAAATGA
829102 AAAAAAAATGAAAAA--A
1 AAAAAAAATGAAAAATGA
829118 ATGAAAAAAATGAAAAAAATGA
1 A--AAAAAAATG--AAAAATGA
829140 AATAGAAAAATAGAAAAAATGGA
1 AA-A-AAAAAT-G-AAAAAT-GA
*
829163 AAAAATAA--AAAAAT-A
1 AAAAAAAATGAAAAATGA
829178 AAAAAA
1 AAAAAA
829184 TAAAAAAGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
15 6 0.09
16 1 0.01
17 21 0.30
18 9 0.13
20 6 0.09
21 5 0.07
22 16 0.23
23 5 0.07
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (18 bp):
AAAAAAAATGAAAAATGA
Found at i:830455 original size:55 final size:55
Alignment explanation
Indices: 830371--830650 Score: 483
Period size: 55 Copynumber: 5.1 Consensus size: 55
830361 TGAAGCAAAA
830371 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
830426 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
830481 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
830534 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
830589 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
830644 GGAGATT
1 GAAGATT
830651 ATTGTTCGAG
Statistics
Matches: 210, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
53 47 0.22
54 6 0.03
55 157 0.75
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:830574 original size:108 final size:110
Alignment explanation
Indices: 830371--830653 Score: 507
Period size: 108 Copynumber: 2.6 Consensus size: 110
830361 TGAAGCAAAA
830371 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
830436 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
830481 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
830544 CGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
*
830589 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
830654 GTTCGAGTTC
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
108 101 0.62
109 6 0.04
110 57 0.35
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:830706 original size:52 final size:52
Alignment explanation
Indices: 830646--831094 Score: 727
Period size: 52 Copynumber: 8.6 Consensus size: 52
830636 CGATCGTTGG
*
830646 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCACACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
830698 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGTAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
830750 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
830802 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * *
830854 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
830906 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
830958 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
831010 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
831062 AGATTATCGTTCGAGTTCTACTTCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
831095 TAGAGAGCGA
Statistics
Matches: 372, Mismatches: 25, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 372 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:831177 original size:55 final size:53
Alignment explanation
Indices: 830963--831165 Score: 175
Period size: 52 Copynumber: 3.8 Consensus size: 53
830953 TAGGAAGATT
* * * **
830963 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-GA-C-AGACCCGTAGAAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * * * * **
831015 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GC-AGTCTCGTAGAAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * *
831067 ATCGTTCGAGTTCTACTTCCTGAAGAAATAGAGAGCGAACCCGTAAAAAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAAAAAGAAG
831120 ATTGTTCGAGTTCTATACTCCCTGAAGAAAAAGAGAGCGAACCCGT
1 ATTGTTCGAGTTC--TACTCCCTGAAGAAAAAGAGAGCGAACCCGT
831166 TTGCAGAAGA
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
51 1 0.01
52 75 0.58
53 24 0.18
54 1 0.01
55 29 0.22
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAAAAAGAAG
Found at i:831376 original size:3 final size:3
Alignment explanation
Indices: 831364--831406 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
831354 TTATATTTAA
831364 ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT A-T ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
831407 ATGTTACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:831378 original size:11 final size:11
Alignment explanation
Indices: 831371--831404 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
831361 TAAATTATAT
831371 TATTATTATTA
1 TATTATTATTA
831382 TATTATTATTA
1 TATTATTATTA
831393 TATTATTATTA
1 TATTATTATTA
831404 T
1 T
831405 TAATGTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:831381 original size:14 final size:14
Alignment explanation
Indices: 831364--831406 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
831354 TTATATTTAA
831364 ATTATATTATTATT
1 ATTATATTATTATT
831378 ATTATATTATTATT
1 ATTATATTATTATT
831392 A-TATTATTATTATT
1 ATTA-TATTATTATT
831406 A
1 A
831407 ATGTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 2 0.07
14 26 0.93
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATATTATTATT
Found at i:832206 original size:146 final size:146
Alignment explanation
Indices: 831777--832431 Score: 1084
Period size: 146 Copynumber: 4.5 Consensus size: 146
831767 TCGGATCACC
*
831777 ATTCGGAACGGTC-AAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
1 ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
831841 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
66 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
831906 GGAATATTTGATCAAT
131 GGAATATTTGATCAAT
831922 A-TCCGAACGGTC-AAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
1 ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
831985 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
66 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
832050 GGAATATTTGATCAAT
131 GGAATATTTGATCAAT
832066 ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
1 ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
* *
832131 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCAGTTTTTAGCCTCTTGCCGGTTATC
66 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
* *
832196 AGAATCTTTGATCAAT
131 GGAATATTTGATCAAT
*
832212 ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCG
1 ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
* * ** *
832277 GACGGTGGACGGTGACGGATCGGAGAAAATAATTCCGTACTGTTTTTAGCCTCTTGCCGGTGATC
66 GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
* **
832342 GGAATCTGCGATCAAT
131 GGAATATTTGATCAAT
* * * * * *
832358 ATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAAAATCAGGACAATC
1 ATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATC
*
832422 GGACGGTGGA
65 AGACGGTGGA
832432 TGACGGCAGA
Statistics
Matches: 486, Mismatches: 21, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
144 143 0.29
145 12 0.02
146 330 0.68
147 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (146 bp):
ATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGATCA
GACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCCGGTGATC
GGAATATTTGATCAAT
Found at i:838375 original size:102 final size:102
Alignment explanation
Indices: 838199--838399 Score: 402
Period size: 102 Copynumber: 2.0 Consensus size: 102
838189 CAACAAGATC
838199 ATATATTTTGAAAGCAATTTTTAATTACCAAATTTCATTCTTTAACTAAGGAAAACCTAGTACTA
1 ATATATTTTGAAAGCAATTTTTAATTACCAAATTTCATTCTTTAACTAAGGAAAACCTAGTACTA
838264 TAAGATAAAGTTGAACTCACACTAGTAACATGAAACT
66 TAAGATAAAGTTGAACTCACACTAGTAACATGAAACT
838301 ATATATTTTGAAAGCAATTTTTAATTACCAAATTTCATTCTTTAACTAAGGAAAACCTAGTACTA
1 ATATATTTTGAAAGCAATTTTTAATTACCAAATTTCATTCTTTAACTAAGGAAAACCTAGTACTA
838366 TAAGATAAAGTTGAACTCACACTAGTAACATGAA
66 TAAGATAAAGTTGAACTCACACTAGTAACATGAA
838400 CCTAGTAAAC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (102 bp):
ATATATTTTGAAAGCAATTTTTAATTACCAAATTTCATTCTTTAACTAAGGAAAACCTAGTACTA
TAAGATAAAGTTGAACTCACACTAGTAACATGAAACT
Found at i:839760 original size:219 final size:224
Alignment explanation
Indices: 839381--839825 Score: 837
Period size: 219 Copynumber: 2.0 Consensus size: 224
839371 GTTAACCATA
839381 AATAAACTAGATAACAATAGAAAGTTGAAAGACTTGACCTTTAGTAAGGGCATTTCTATAAAAAA
1 AATAAACTAGATAACAATAGAAAGTTGAAAGACTTGACCTTTAGTAAGGGCATTTCTATAAAAAA
839446 AATAATAAATTAAAATCCTTGTAGCAGATAGAAATGAATTTAGACAACAAGGAAGTCGAACTCAT
66 AATAATAAATTAAAATCCTTGTAGCAGATAGAAATGAATTTAGACAACAAGGAAGTCGAACTCAT
839511 ATGGCACTAGAAGTTCACCTGCACAATTAAATA-TCA-GGCCCTATGAAAGTTCGAATCCAGCA-
131 ATGGCACTAGAAGTTCACCTGCACAATTAAATACTCAGGGCCCTATGAAAGTTCGAATCCAGCAT
839573 TAGAATTG-TGCATAACGAAGC-TTGCTT
196 TAGAATTGATGCATAACGAAGCTTTGCTT
839600 AATAAACTAGATAACAATAGAAAGTTGAAAGACTTGACCTTTAGTAAGGGCATTTCTATAAAAAA
1 AATAAACTAGATAACAATAGAAAGTTGAAAGACTTGACCTTTAGTAAGGGCATTTCTATAAAAAA
839665 AATAATAAATTAAAATCCTTGTAGCAGATAGAAATGAATTTAGACAACAAGGAAGTCGAACTCAT
66 AATAATAAATTAAAATCCTTGTAGCAGATAGAAATGAATTTAGACAACAAGGAAGTCGAACTCAT
839730 ATGGCACTAGAAGTTCACCTGCACAATTAAATATCTCAGGGCCCTATGAAAGTTCGAATCCAGCA
131 ATGGCACTAGAAGTTCACCTGCACAATTAAATA-CTCAGGGCCCTATGAAAGTTCGAATCCAGCA
839795 TTAGAATTGATTGCATAACGAAGCTTTGCTT
195 TTAGAATTGA-TGCATAACGAAGCTTTGCTT
839826 TCAGAGTGCT
Statistics
Matches: 219, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
219 163 0.74
221 3 0.01
222 26 0.12
223 8 0.04
225 13 0.06
226 6 0.03
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.26
Consensus pattern (224 bp):
AATAAACTAGATAACAATAGAAAGTTGAAAGACTTGACCTTTAGTAAGGGCATTTCTATAAAAAA
AATAATAAATTAAAATCCTTGTAGCAGATAGAAATGAATTTAGACAACAAGGAAGTCGAACTCAT
ATGGCACTAGAAGTTCACCTGCACAATTAAATACTCAGGGCCCTATGAAAGTTCGAATCCAGCAT
TAGAATTGATGCATAACGAAGCTTTGCTT
Found at i:849152 original size:18 final size:18
Alignment explanation
Indices: 849129--849201 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
849119 AGGGATATAC
849129 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
849147 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
849166 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
849185 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
849202 AATACTGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 31 0.63
19 4 0.08
20 14 0.29
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:849179 original size:38 final size:38
Alignment explanation
Indices: 849128--849202 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
849118 GAGGGATATA
*
849128 CAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAAT
*
849166 CAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAA
1 CAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAA
849203 ATACTGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.27
Consensus pattern (38 bp):
CAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAAT
Found at i:855868 original size:20 final size:20
Alignment explanation
Indices: 855823--855877 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
855813 ATGATACAGG
*
855823 TATGTGAATATTGAAAAGAAT
1 TATGTGTATA-TGAAAAGAAT
*
855844 CATGTGTATATGAAATA-AAT
1 TATGTGTATATGAAA-AGAAT
855864 TATGTGCTATATGA
1 TATGTG-TATATGA
855878 GAAGTGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (20 bp):
TATGTGTATATGAAAAGAAT
Found at i:856004 original size:18 final size:18
Alignment explanation
Indices: 855981--856053 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
855971 AGGGATATAC
855981 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
855999 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
856018 CAGTGGTCCTTCGGGAAAT
1 -AGTGGTCCTTCGGGACAT
856037 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
856054 AATACTGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:856031 original size:38 final size:38
Alignment explanation
Indices: 855980--856054 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
855970 GAGGGATATA
* *
855980 CAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGAAATAGTGGTCCTTCGGAACAAT
*
856018 CAGTGGTCCTTCGGGAAATAGTGGTCCTTCGGGACAA
1 CAGTGGTCCTTCGGGAAATAGTGGTCCTTCGGAACAA
856055 ATACTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (38 bp):
CAGTGGTCCTTCGGGAAATAGTGGTCCTTCGGAACAAT
Found at i:859200 original size:55 final size:54
Alignment explanation
Indices: 859095--859336 Score: 272
Period size: 55 Copynumber: 4.4 Consensus size: 54
859085 CTCACTACCA
* * * * * *
859095 ATACGAAAATTCAC-CAACTTATTATGAATTT-TTTATGTCTGTACATATAGTTCTC
1 ATACGAAAATTCACAC-ACTTAGTATGAATTTCTTAAT-TTTGCACACATAGTGC-C
* * *
859150 ATACAAAAATTCACACATTTAGTATGAATTTCTTACTTTTGCACACATAGTGTCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTG-CC
* * *
859205 ATCCGGAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATGGTGCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCC
*
859259 TATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCC
1 -ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTG-CC
* * *
859315 ATACGGAAATTCATACATTTAG
1 ATACGAAAATTCACACACTTAG
859337 GTGGCGTTTG
Statistics
Matches: 161, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
54 2 0.01
55 152 0.94
56 7 0.04
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (54 bp):
ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCC
Found at i:859391 original size:18 final size:17
Alignment explanation
Indices: 859368--859416 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
859358 TGTTTCCGAG
859368 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
859386 GGAATTGAAATCTGTCA
1 GGAATTGGAATCTGTAA
*
859403 GAAATTGGAATCTG
1 GGAATTGGAATCTG
859417 AATCTGAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:859414 original size:17 final size:18
Alignment explanation
Indices: 859370--859416 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
859360 TTTCCGAGGG
*
859370 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGA
* *
859388 AATTGAAATCTGT-CAGA
1 AATTGGAATCTGTGAAGA
859405 AATTGGAATCTG
1 AATTGGAATCTG
859417 AATCTGAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGA
Found at i:860163 original size:24 final size:25
Alignment explanation
Indices: 860123--860182 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
860113 AAAGGCAATG
* *
860123 AAAATAAA-TAAACTAAAGACAAAT
1 AAAATAAAGGAAACTAAAAACAAAT
*
860147 AAAATAAAGGAAA-TAAAAATAAAT
1 AAAATAAAGGAAACTAAAAACAAAT
*
860171 GAAA-AAAGGAAA
1 AAAATAAAGGAAA
860183 ATAAGATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 8 0.26
24 20 0.65
25 3 0.10
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (25 bp):
AAAATAAAGGAAACTAAAAACAAAT
Found at i:860216 original size:25 final size:22
Alignment explanation
Indices: 860157--860292 Score: 85
Period size: 25 Copynumber: 5.5 Consensus size: 22
860147 AAAATAAAGG
**
860157 AAATAAAAATAAATGAAAAAAGGA
1 AAAT-AAAATAAA-GAAAAAAAAA
*
860181 AAATAAGATAAAGAAAAGACATAAA
1 AAATAAAATAAAGAAAA-A-A-AAA
860206 AAATAAAATAAAGATAAAAAAAA
1 AAATAAAATAAAGA-AAAAAAAA
860229 CTAAATAAAATAAAGAACATAAAAAA
1 --AAATAAAATAAAGAA-A-AAAAAA
*
860255 CAAA-AGAAATAAAAAATGAAGAAAAA
1 -AAATA-AAATAAAGAA--AA-AAAAA
860281 TAAATAAAATAA
1 -AAATAAAATAA
860293 TCAAAATAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.05
23 11 0.12
24 8 0.09
25 43 0.47
26 24 0.26
27 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (22 bp):
AAATAAAATAAAGAAAAAAAAA
Found at i:860238 original size:10 final size:9
Alignment explanation
Indices: 860123--860302 Score: 51
Period size: 10 Copynumber: 19.9 Consensus size: 9
860113 AAAGGCAATG
860123 AAAATAAAT
1 AAAATAAAT
* *
860132 AAACTAAAG
1 AAAATAAAT
860141 ACAAATAAAAT
1 A-AAAT-AAAT
**
860152 AAAGGAAAT
1 AAAATAAAT
860161 AAAAATAAAT
1 -AAAATAAAT
**
860171 GAAAA-AAGG
1 -AAAATAAAT
860180 AAAATAAGAT
1 AAAATAA-AT
860190 AAAGA-AAA-
1 AAA-ATAAAT
* *
860198 GACAT-AA-
1 AAAATAAAT
860205 AAAATAAAAT
1 AAAAT-AAAT
*
860215 AAAGATAAAA
1 AAA-ATAAAT
860225 AAAACTAAAT
1 AAAA-TAAAT
*
860235 AAAATAAAG
1 AAAATAAAT
*
860244 AACATAAA-
1 AAAATAAAT
860252 AAACA-AAA-
1 AAA-ATAAAT
*
860260 GAAAT-AA-
1 AAAATAAAT
860267 AAAATGAAGA-
1 AAAAT-AA-AT
860277 AAAATAAAT
1 AAAATAAAT
860286 AAAAT-AAT
1 AAAATAAAT
860294 CAAAATAAA
1 -AAAATAAA
860303 GATAACGAGC
Statistics
Matches: 127, Mismatches: 24, Indels: 39
0.67 0.13 0.21
Matches are distributed among these distances:
7 13 0.10
8 16 0.13
9 45 0.35
10 46 0.36
11 7 0.06
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (9 bp):
AAAATAAAT
Found at i:860395 original size:17 final size:18
Alignment explanation
Indices: 860373--860410 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
860363 TATACATAAT
860373 AAACAAAT-AAAAAAAGA
1 AAACAAATGAAAAAAAGA
*
860390 AAACAAATGAAAATAAGA
1 AAACAAATGAAAAAAAGA
860408 AAA
1 AAA
860411 AAAAACCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (18 bp):
AAACAAATGAAAAAAAGA
Found at i:860424 original size:22 final size:24
Alignment explanation
Indices: 860377--860438 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
860367 CATAATAAAC
860377 AAATAA-AAAAAGAAAACAAATGA
1 AAATAAGAAAAAGAAAACAAATGA
*
860400 AAATAAGAAAAA-AAAACCAAT-A
1 AAATAAGAAAAAGAAAACAAATGA
*
860422 AAATAAGAAAAATAAAA
1 AAATAAGAAAAAGAAAA
860439 AGTAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 13 0.36
23 18 0.50
24 5 0.14
ACGTcount: A:0.79, C:0.05, G:0.06, T:0.10
Consensus pattern (24 bp):
AAATAAGAAAAAGAAAACAAATGA
Found at i:860742 original size:55 final size:55
Alignment explanation
Indices: 860676--860863 Score: 304
Period size: 55 Copynumber: 3.4 Consensus size: 55
860666 AAACGCCTCA
* *
860676 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATATGGAAATTCACACAT
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATATGGAAATTCATACAC
* **
860731 TTAGTATGAATTTCTTAATTTTGCACACATAGTGTCCATACAGAAATTCATACAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATATGGAAATTCATACAC
* *
860786 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCTTATGGAAATTCATATAC
1 TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATATGGAAATTCATACAC
860841 TTAGTATGAATTTCTTAACTTTT
1 TTAGTATGAATTTCTTAA-TTTT
860864 TATACACAAA
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
55 118 0.97
56 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (55 bp):
TTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATATGGAAATTCATACAC
Found at i:860763 original size:28 final size:28
Alignment explanation
Indices: 860732--860818 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 28
860722 TTCACACATT
860732 TAGTATGAATTTCTTAATTTTGCACACA
1 TAGTATGAATTTCTTAATTTTGCACACA
* ** * ** * *** *
860760 TAGTGTCCA-TACAGAAATTCATACACT
1 TAGTATGAATTTCTTAATTTTGCACACA
860787 TAGTATGAATTTCTTAATTTTGCACACA
1 TAGTATGAATTTCTTAATTTTGCACACA
860815 TAGT
1 TAGT
860819 GCCCTTATGG
Statistics
Matches: 36, Mismatches: 22, Indels: 2
0.60 0.37 0.03
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (28 bp):
TAGTATGAATTTCTTAATTTTGCACACA
Found at i:861335 original size:21 final size:21
Alignment explanation
Indices: 861309--861365 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
861299 CCCCTTTCGG
* *
861309 TATCGATACTTCTTACATCAA
1 TATCGATACTTCTCACACCAA
* *
861330 TATCGATACTTCTCGCACCAG
1 TATCGATACTTCTCACACCAA
861351 TATCGATACTTCTCA
1 TATCGATACTTCTCA
861366 ACTGATTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (21 bp):
TATCGATACTTCTCACACCAA
Found at i:863401 original size:30 final size:32
Alignment explanation
Indices: 863339--863412 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
863329 ATCGGGCCCG
*
863339 ATATATATATTTAAATTAAATATATAAATATT
1 ATATATATATTTAAATTAAATATACAAATATT
* **
863371 ATATATAT-TTTAATTTAAAT-TACATTTATT
1 ATATATATATTTAAATTAAATATACAAATATT
863401 AATATTATATAT
1 -ATA-TATATAT
863413 ATATATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 7 0.20
31 14 0.40
32 13 0.37
33 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATATATATTTAAATTAAATATACAAATATT
Found at i:868423 original size:6 final size:6
Alignment explanation
Indices: 868412--868436 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
868402 TTTTTTTAGA
868412 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
868437 AAATTCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:868692 original size:42 final size:42
Alignment explanation
Indices: 868637--868753 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
868627 CCCCGAATTT
* * *
868637 CCGTGTTTATTTCAAGTAATTCGTTTTCTGGAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAACGTTTTC
* *
868679 CCGTGTTTGTTTCACGTAATTTGTTTT-TCGAAAAACGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCT-GGAAAACGTTTTC
*
868721 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTCTGGAA
868754 TGTAATTCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
41 1 0.02
42 64 0.98
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAACGTTTTC
Found at i:868959 original size:12 final size:12
Alignment explanation
Indices: 868938--868970 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
868928 ATATTAATTA
868938 TTAA-AATATTT
1 TTAATAATATTT
*
868949 TTATTAATATTT
1 TTAATAATATTT
868961 TTAATAATAT
1 TTAATAATAT
868971 AATATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTAATAATATTT
Found at i:868976 original size:23 final size:23
Alignment explanation
Indices: 868950--869039 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
868940 AAAATATTTT
868950 TATTA-ATATTTTTAATAATATAA
1 TATTATAT-TTTTTAATAATATAA
868973 TATTATATTTTTTAATATTATATAA
1 TATTATATTTTTTAATA--ATATAA
* *
868998 AATAATCAATTATATTATAATAATATAAGA
1 TATTAT--ATT-T-TT-TAATAATAT-A-A
869028 TATTATATTTTT
1 TATTATATTTTT
869040 ATTTTAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
23 14 0.26
24 2 0.04
25 10 0.19
26 2 0.04
27 4 0.08
28 8 0.15
29 3 0.06
30 10 0.19
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
TATTATATTTTTTAATAATATAA
Found at i:868990 original size:20 final size:22
Alignment explanation
Indices: 868950--868995 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
868940 AAAATATTTT
868950 TATTAATATTTTTAATAATATAA
1 TATTAATATTTTT-ATAATATAA
*
868973 TATT-ATATTTTT-TAATATTA
1 TATTAATATTTTTATAATATAA
868993 TAT
1 TAT
868996 AAAATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTAATATTTTTATAATATAA
Found at i:869211 original size:10 final size:10
Alignment explanation
Indices: 869196--869220 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
869186 ATTAATATAA
869196 TTTATAATAT
1 TTTATAATAT
869206 TTTATAATAT
1 TTTATAATAT
869216 TTTAT
1 TTTAT
869221 TTCACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:869311 original size:27 final size:27
Alignment explanation
Indices: 869258--869328 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
869248 TTTTTATTAA
* * *
869258 TAAAATTATAAAATAATATTTAATA-TT
1 TAAAATAATAATATTAT-TTTAATATTT
869285 TAATAATAAATAA-ATTATTTTAATATTT
1 TAA-AAT-AATAATATTATTTTAATATTT
869313 TAAAATAATAATATTA
1 TAAAATAATAATATTA
869329 AGTTTTATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 5 0.13
27 17 0.45
28 12 0.32
29 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAATAATAATATTATTTTAATATTT
Found at i:869563 original size:20 final size:20
Alignment explanation
Indices: 869445--869554 Score: 202
Period size: 20 Copynumber: 5.5 Consensus size: 20
869435 TTTCCAGATG
869445 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
869465 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
869485 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
869505 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
869525 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
869545 TTTTCCAGAA
1 TTTTCCAGAA
869555 TTTAAATTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:869570 original size:29 final size:30
Alignment explanation
Indices: 869537--869608 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
869527 TTACAGAAAT
*
869537 GTAATTCATTTTCCAG-AATTTAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
869566 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
869596 GTAATTCATTTTC
1 GTAATTCATTTTC
869609 TGGAAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:869579 original size:15 final size:15
Alignment explanation
Indices: 869537--869608 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
869527 TTACAGAAAT
869537 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* **
869552 G-AATTTAAATTCCA
1 GTAATTCATTTTCCA
869566 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
869581 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
869596 GTAATTCATTTTC
1 GTAATTCATTTTC
869609 TGGAAAACCA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
14 11 0.24
15 35 0.76
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:870091 original size:26 final size:26
Alignment explanation
Indices: 870018--870093 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
870008 GATTCATTTT
* *
870018 TAAAATCATAAATGGTTTTTTTAATTA
1 TAAAATTATAAAT-ATTTTTTTAATTA
** * * *
870045 TAACTTTATAAATAATCTTTTAATTC
1 TAAAATTATAAATATTTTTTTAATTA
*
870071 TAAAATTATAATTATTTTTTTAA
1 TAAAATTATAAATATTTTTTTAA
870094 ATGAATGTAT
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
26 27 0.73
27 10 0.27
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (26 bp):
TAAAATTATAAATATTTTTTTAATTA
Found at i:870672 original size:16 final size:18
Alignment explanation
Indices: 870641--870673 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
870631 TAAGTTTTTA
870641 TCATAATAATTTTAAATC
1 TCATAATAATTTTAAATC
870659 TCAT-ATAA-TTTAAAT
1 TCATAATAATTTTAAAT
870674 ATATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (18 bp):
TCATAATAATTTTAAATC
Found at i:871674 original size:2 final size:2
Alignment explanation
Indices: 871661--871696 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
871651 ACTACAAATA
* *
871661 AT AT AA AT AT AT AT GT 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
871697 TGATTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:872732 original size:15 final size:15
Alignment explanation
Indices: 872712--872745 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
872702 TTGGATCACT
872712 TTTGTAATCCATATA
1 TTTGTAATCCATATA
* *
872727 TTTGTAATCTATATG
1 TTTGTAATCCATATA
872742 TTTG
1 TTTG
872746 AAAATGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTGTAATCCATATA
Found at i:875799 original size:149 final size:149
Alignment explanation
Indices: 875614--875926 Score: 565
Period size: 149 Copynumber: 2.1 Consensus size: 149
875604 GTCGAGGGTT
* *
875614 TACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
*
875679 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGATATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
*
875744 TGGCACTACGGTGCAATTC
131 TGGAACTACGGTGCAATTC
*
875763 TACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
875828 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
875893 TGGAACTACGGTGCAATTC
131 TGGAACTACGGTGCAATTC
875912 TACGCGG-CACTTCGG
1 TACGCGGTC-CTTCGG
875927 TGCAATTATA
Statistics
Matches: 158, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
TGGAACTACGGTGCAATTC
Found at i:880774 original size:151 final size:149
Alignment explanation
Indices: 880576--880890 Score: 551
Period size: 151 Copynumber: 2.1 Consensus size: 149
880566 GTCGAGGGTT
* *
880576 TACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACATATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
880641 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
*
880706 TGGCACTACGGTGTAATTC
131 TGGCACTACGGTGCAATTC
* *
880725 TACGCGGTCCTTCGGGATATATATATATATTTTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TACGCGGTCCTTCGGGACATATATATAT-TCTT-TGGAACATGTGTGAAGTCTTGAAAGACACAT
880790 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
64 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
880855 TATGGCACTACGGTGCAATTC
129 TATGGCACTACGGTGCAATTC
880876 TACGCGG-CACTTCGG
1 TACGCGGTC-CTTCGG
880891 TGCAATTATA
Statistics
Matches: 158, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
149 26 0.16
150 4 0.03
151 128 0.81
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
TGGCACTACGGTGCAATTC
Found at i:880891 original size:23 final size:23
Alignment explanation
Indices: 880858--880902 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
880848 ATTATTATAT
*
880858 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
880881 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
880903 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:881753 original size:236 final size:236
Alignment explanation
Indices: 881340--881810 Score: 897
Period size: 236 Copynumber: 2.0 Consensus size: 236
881330 AAGACAGGTC
881340 AGTTCTCCTTACCAAATGTCAGATCAGAAAATATATGTTCTGGTTATAGAGTGTAGTTGGCATGT
1 AGTTCTCCTTACCAAATGTCAGATCAGAAAATATATGTTCTGGTTATAGAGTGTAGTTGGCATGT
881405 AGTCTAAAAATATAAATTGTATGAACTCTGATATATTTTGTAAACGTTTTGAATAAGTTAAATGT
66 AGTCTAAAAATATAAATTGTATGAACTCTGATATATTTTGTAAACGTTTTGAATAAGTTAAATGT
*
881470 TATTAAAGTTTTTAAATTACTCACTATTTTATACGAATAAATGTTTGAAAAGTCAATGTGACACT
131 TATCAAAGTTTTTAAATTACTCACTATTTTATACGAATAAATGTTTGAAAAGTCAATGTGACACT
881535 TCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGTGTTAT
196 TCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGTGTTAT
*
881576 AGTTCTCTTTACCAAATGTCAGATCAGAAAATATATGTTCTGGTTATAGAGTGTAGTTGGCATGT
1 AGTTCTCCTTACCAAATGTCAGATCAGAAAATATATGTTCTGGTTATAGAGTGTAGTTGGCATGT
*
881641 AGTCTAAAGATATAAATTGTATGAACTCTGATATATTTTGTAAACGTTTTGAATAAGTTAAATGT
66 AGTCTAAAAATATAAATTGTATGAACTCTGATATATTTTGTAAACGTTTTGAATAAGTTAAATGT
*
881706 TATCAAAGTTTTTAAATTACTCACTATTTTATACGAATAAATGTTTGAAAAGTTAATGTGACACT
131 TATCAAAGTTTTTAAATTACTCACTATTTTATACGAATAAATGTTTGAAAAGTCAATGTGACACT
*
881771 TCGGACTCGTATCCGGGTTGGATACGGGTTGGGGGTGTTA
196 TCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGTGTTA
881811 CACATGGGTA
Statistics
Matches: 230, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
236 230 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (236 bp):
AGTTCTCCTTACCAAATGTCAGATCAGAAAATATATGTTCTGGTTATAGAGTGTAGTTGGCATGT
AGTCTAAAAATATAAATTGTATGAACTCTGATATATTTTGTAAACGTTTTGAATAAGTTAAATGT
TATCAAAGTTTTTAAATTACTCACTATTTTATACGAATAAATGTTTGAAAAGTCAATGTGACACT
TCGGACTCGTATCCGGGTCGGATACGGGTTGGGGGTGTTAT
Found at i:887303 original size:22 final size:22
Alignment explanation
Indices: 887275--887321 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
887265 TCCGACCTAT
887275 ATATCTAATTTATTTTTATTAG
1 ATATCTAATTTATTTTTATTAG
887297 ATATCTAATTTATTTTTATTAG
1 ATATCTAATTTATTTTTATTAG
887319 ATA
1 ATA
887322 AAATAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
ATATCTAATTTATTTTTATTAG
Found at i:899110 original size:3 final size:3
Alignment explanation
Indices: 899102--899145 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
899092 CTCACTGTCA
* *
899102 TCG TCG TCG TCG TCG TCA TCA TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
899146 CTGAGCAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.05, C:0.34, G:0.27, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:899125 original size:21 final size:21
Alignment explanation
Indices: 899099--899139 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
899089 CTCCTCACTG
899099 TCATCGTCGTCGTCGTCGTCA
1 TCATCGTCGTCGTCGTCGTCA
899120 TCATCGTCGTCGTCGTCGTC
1 TCATCGTCGTCGTCGTCGTC
899140 GTCGTCCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.34, G:0.24, T:0.34
Consensus pattern (21 bp):
TCATCGTCGTCGTCGTCGTCA
Found at i:901216 original size:111 final size:108
Alignment explanation
Indices: 900965--901292 Score: 552
Period size: 111 Copynumber: 3.0 Consensus size: 108
900955 ATTACAAAAA
900965 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
901030 AATTAAAACGTTAAAATGTTACGTATCAGCAAA-GTG-GATAT
66 AATTAAAACGTTAAAATGTTACGTATCAGCAAATGTGAGATAT
901071 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
901136 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTA-CGTATCAGCAAA-TGT-GAGATAT
* * *
901182 TTAATTCTTAATCTAATATTCATGCATTACATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
901247 AATTAAAACGTTAAAATGTTATCGTATCAGCAAACTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTA-CGTATCAGCAAA-TGT-GAGATAT
901293 ATGATTTCCA
Statistics
Matches: 209, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
106 86 0.41
107 11 0.05
109 2 0.01
110 1 0.00
111 109 0.52
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (108 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACGTATCAGCAAATGTGAGATAT
Found at i:901374 original size:17 final size:18
Alignment explanation
Indices: 901354--901389 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
901344 GAATTATATT
901354 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
901371 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
901389 A
1 A
901390 TTATATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:901649 original size:47 final size:47
Alignment explanation
Indices: 901598--901718 Score: 147
Period size: 48 Copynumber: 2.5 Consensus size: 47
901588 AGATACCTAG
*
901598 GTATAGCGCGGATCAGGGG-GCGCTATACCCACGTGA-GCCAAATCATC
1 GTATA-CGCGG-TCAGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
*
901645 GTATATCGCCGGGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
1 GTATA-CG-CGGTCA-GGGGCGCGCTATACCCACGTGACGCCAAATCAAC
*
901695 GTATACACGGTTCAGGGGCGCGCT
1 GTATACGCGG-TCAGGGGCGCGCT
901719 TTACTGCTAC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
47 9 0.14
48 20 0.31
49 20 0.31
50 15 0.23
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.17
Consensus pattern (47 bp):
GTATACGCGGTCAGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
Found at i:901711 original size:49 final size:48
Alignment explanation
Indices: 901611--901718 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 48
901601 TAGCGCGGAT
* *
901611 CAGGGG-GCGCTATACCCACGTGAGCCAAATCATCGTATATCGCCGGG
1 CAGGGGCGCGCTATACCCACGTGAGCCAAATCAACGTATATCGACGGG
*
901658 CAGGGGGCGCGCTATACCCACGTGACGCCAAATCAACGTATA-C-ACGGTT
1 CA-GGGGCGCGCTATACCCACGTGA-GCCAAATCAACGTATATCGACGG-G
901707 CAGGGGCGCGCT
1 CAGGGGCGCGCT
901719 TTACTGCTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
47 2 0.04
48 17 0.31
49 20 0.37
50 15 0.28
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.16
Consensus pattern (48 bp):
CAGGGGCGCGCTATACCCACGTGAGCCAAATCAACGTATATCGACGGG
Found at i:909679 original size:60 final size:54
Alignment explanation
Indices: 909586--909748 Score: 173
Period size: 55 Copynumber: 2.9 Consensus size: 54
909576 ATCCCTATTT
* * *
909586 TAAATTGTCCCTAAACTTTTAAATATTTCAATTTCATCCCTAAACTATAACTATCATTC
1 TAAATTGTCCC-AAACTTTTGAACATTTTAATTTCATCCC-AAACTATAAC---CATTC
*
909645 TAAATTAGTCCGCAAACTTTTGAACATTTTAATTTCATCCCAAACTATAACCATTT
1 TAAATT-GTCC-CAAACTTTTGAACATTTTAATTTCATCCCAAACTATAACCATTC
* * * * *
909701 TAAACTGGTTCCAAACTTTTGAACATTCTAATTGCATCACAAACTATA
1 TAAA-TTGTCCCAAACTTTTGAACATTTTAATTTCATCCCAAACTATA
909749 CGCATATACT
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
55 34 0.37
56 11 0.12
57 1 0.01
59 16 0.17
60 29 0.32
61 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (54 bp):
TAAATTGTCCCAAACTTTTGAACATTTTAATTTCATCCCAAACTATAACCATTC
Found at i:909688 original size:28 final size:28
Alignment explanation
Indices: 909657--909745 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
909647 AATTAGTCCG
909657 CAAACTTTTGAACATTTTAATTTCATCC
1 CAAACTTTTGAACATTTTAATTTCATCC
* ** ** *
909685 CAAAC-TAT-AACCATTTTAAACTGGTTC
1 CAAACTTTTGAA-CATTTTAATTTCATCC
* * *
909712 CAAACTTTTGAACATTCTAATTGCATCA
1 CAAACTTTTGAACATTTTAATTTCATCC
909740 CAAACT
1 CAAACT
909746 ATACGCATAT
Statistics
Matches: 43, Mismatches: 15, Indels: 6
0.67 0.23 0.09
Matches are distributed among these distances:
26 2 0.05
27 18 0.42
28 21 0.49
29 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (28 bp):
CAAACTTTTGAACATTTTAATTTCATCC
Found at i:910012 original size:60 final size:59
Alignment explanation
Indices: 909860--910026 Score: 178
Period size: 60 Copynumber: 2.8 Consensus size: 59
909850 ATTGGATAAA
* *
909860 TTTGGGGATGAAATTGGAATATTTGAAAGTTT-GGGATTAATTTAGAAAGAGAGTCATAG
1 TTTGGGGATGAAATTGGAATA-TTAAAAGTTTAAGGATTAATTTAGAAAGAGAGTCATAG
* * * * * *
909919 TTTAGGGATGGAATTAGAATATTCAAAATTTTAAGGACTAATTTA-AAATGAGTGTCATAG
1 TTTGGGGATGAAATTGGAATATT-AAAAGTTTAAGGATTAATTTAGAAA-GAGAGTCATAG
* * *
909979 TTTGGGGAAGAAATTGGAGTACATAAAAGTTTAAGGATTAATTT-GAAA
1 TTTGGGGATGAAATTGGAATA-TTAAAAGTTTAAGGATTAATTTAGAAA
910027 CGAGGGTTAT
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.02
59 27 0.31
60 57 0.66
61 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
TTTGGGGATGAAATTGGAATATTAAAAGTTTAAGGATTAATTTAGAAAGAGAGTCATAG
Found at i:917697 original size:92 final size:92
Alignment explanation
Indices: 917540--917725 Score: 347
Period size: 92 Copynumber: 2.0 Consensus size: 92
917530 GTTAATCATT
917540 GACACCGCATACATACCCTGTAGAAGCAGTTGTTCGAATCCATAACCTCTAAGAAAAATAATACT
1 GACACCGCATACATACCCTGTAGAAGCAGTTGTTCGAATCCATAACCTCTAAGAAAAATAATACT
917605 T-CGTTTAATCATTGAGGTTACATAATA
66 TCCG-TTAATCATTGAGGTTACATAATA
*
917632 GACACCGCATACATACCCTGTAGACGCAGTTGTTCGAATCCATAACCTCTAAGAAAAATAATACT
1 GACACCGCATACATACCCTGTAGAAGCAGTTGTTCGAATCCATAACCTCTAAGAAAAATAATACT
917697 TCCGTTAATCATTGAGGTTACATAATA
66 TCCGTTAATCATTGAGGTTACATAATA
917724 GA
1 GA
917726 TTTTTTTTAA
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 90 0.98
93 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (92 bp):
GACACCGCATACATACCCTGTAGAAGCAGTTGTTCGAATCCATAACCTCTAAGAAAAATAATACT
TCCGTTAATCATTGAGGTTACATAATA
Found at i:917757 original size:20 final size:20
Alignment explanation
Indices: 917732--917784 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
917722 TAGATTTTTT
917732 TTAATTTTAAAAATTAAAAA
1 TTAATTTTAAAAATTAAAAA
* *
917752 TTAATTTT-TAATTTAAAAA
1 TTAATTTTAAAAATTAAAAA
*
917771 ATAA-TTTAAAAATT
1 TTAATTTTAAAAATT
917785 CTCAATTTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 3 0.11
19 16 0.59
20 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTTTAAAAATTAAAAA
Found at i:919740 original size:6 final size:6
Alignment explanation
Indices: 919729--919793 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
919719 TGAAGAAGAG
* * * *** *
919729 GATGAT GATGAT GACGAC GATGAC GATGAC GATGAC GATTTT GATGGC
1 GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC
*
919777 GATGAA GATGAC GATGA
1 GATGAC GATGAC GATGA
919794 TGAAGAAGCA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (6 bp):
GATGAC
Found at i:922620 original size:59 final size:59
Alignment explanation
Indices: 922540--922749 Score: 276
Period size: 59 Copynumber: 3.5 Consensus size: 59
922530 AAAAGTTTGG
* * *
922540 GGACCAATTTAGTATAAGAGTCATAGTTTGGGATGAAACTGAAATGTTCAAACGTTTAA
1 GGACCAATTTAGAATGAGAGTCATAGTTTGGGATGAAATTGAAATGTTCAAACGTTTAA
*
922599 GGACTAATTTAGAATGAGAGTCATAGTTTGGGATGAAATTGAAATGTTCAAACGTTTAA
1 GGACCAATTTAGAATGAGAGTCATAGTTTGGGATGAAATTGAAATGTTCAAACGTTTAA
* * * * * * * *
922658 GGACTAATTTAGAATGAGAGTCTTAGTTTACGGATAAAATTGGAATATTTAAAAGTTTAA
1 GGACCAATTTAGAATGAGAGTCATAGTTT-GGGATGAAATTGAAATGTTCAAACGTTTAA
* * *
922718 GGACCAATTTAAAATGAGGGTCATAATTTGGG
1 GGACCAATTTAGAATGAGAGTCATAGTTTGGG
922750 GATTTATGAT
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
59 85 0.64
60 48 0.36
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (59 bp):
GGACCAATTTAGAATGAGAGTCATAGTTTGGGATGAAATTGAAATGTTCAAACGTTTAA
Found at i:922875 original size:19 final size:20
Alignment explanation
Indices: 922841--922881 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
922831 ATGCTAATTA
*
922841 ATGGACTAAGATTTACAGAG
1 ATGGACTAAGATTTACAAAG
922861 ATGGACTAA-ATTTACAAAG
1 ATGGACTAAGATTTACAAAG
922880 AT
1 AT
922882 TAAAAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (20 bp):
ATGGACTAAGATTTACAAAG
Found at i:923847 original size:16 final size:16
Alignment explanation
Indices: 923760--923857 Score: 106
Period size: 16 Copynumber: 6.1 Consensus size: 16
923750 GGTAAACTAA
923760 ATTCAAGTTACTTTCG
1 ATTCAAGTTACTTTCG
* ** * *
923776 GTTCGGGTTGCTTTCA
1 ATTCAAGTTACTTTCG
*
923792 ATTCGAGTTACTTTCG
1 ATTCAAGTTACTTTCG
923808 ATTCAAGTTACTTTCG
1 ATTCAAGTTACTTTCG
* *
923824 ATTGAAGTTACTTTTG
1 ATTCAAGTTACTTTCG
* *
923840 GTTCAAGTTGCTTTCG
1 ATTCAAGTTACTTTCG
923856 AT
1 AT
923858 CCAACTAAAT
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 65 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (16 bp):
ATTCAAGTTACTTTCG
Found at i:923855 original size:32 final size:33
Alignment explanation
Indices: 923760--923857 Score: 121
Period size: 32 Copynumber: 3.1 Consensus size: 33
923750 GGTAAACTAA
** *
923760 ATTC-AAGTTACTTTCGGTTCGGGTTGCTTTCA
1 ATTCGAAGTTACTTTCGGTTCAAGTTGCTTTCG
* *
923792 ATTCG-AGTTACTTTCGATTCAAGTTACTTTCG
1 ATTCGAAGTTACTTTCGGTTCAAGTTGCTTTCG
*
923824 ATT-GAAGTTACTTTTGGTTCAAGTTGCTTTCG
1 ATTCGAAGTTACTTTCGGTTCAAGTTGCTTTCG
923856 AT
1 AT
923858 CCAACTAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 55 0.98
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (33 bp):
ATTCGAAGTTACTTTCGGTTCAAGTTGCTTTCG
Found at i:930270 original size:48 final size:48
Alignment explanation
Indices: 930214--930310 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
930204 GTTGGATACA
930214 TCGATGTTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTT
1 TCGATGTTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTT
930262 TCGATGTTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTT
1 TCGATGTTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTT
930310 T
1 T
930311 ATTATTATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (48 bp):
TCGATGTTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTT
Found at i:930328 original size:43 final size:45
Alignment explanation
Indices: 930220--930328 Score: 132
Period size: 48 Copynumber: 2.4 Consensus size: 45
930210 TACATCGATG
**
930220 TTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTTTCGA
1 TTTATAATTTTAAAGTTAGGATAAACTATTAATATTTCCTTTTC-A
**
930266 TGTTTATAATTTTTTAGTTAGGATAAACTATTAATATTTCCTTTT-A
1 --TTTATAATTTTAAAGTTAGGATAAACTATTAATATTTCCTTTTCA
*
930312 -TTATTATTTTAAAGTTA
1 TTTATAATTTTAAAGTTA
930329 AATCGTCAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
43 14 0.24
46 1 0.02
48 43 0.74
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.54
Consensus pattern (45 bp):
TTTATAATTTTAAAGTTAGGATAAACTATTAATATTTCCTTTTCA
Found at i:932278 original size:19 final size:19
Alignment explanation
Indices: 932240--932277 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
932230 TTAAAATTTT
932240 ATTTTTAGAAAAGCTTAAA
1 ATTTTTAGAAAAGCTTAAA
*
932259 ATTTTT-GAAAATCTTAAA
1 ATTTTTAGAAAAGCTTAAA
932277 A
1 A
932278 AAACACAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (19 bp):
ATTTTTAGAAAAGCTTAAA
Found at i:934747 original size:40 final size:40
Alignment explanation
Indices: 934692--934813 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
934682 TGTAGGTTTA
*
934692 TAATACACTTCGGTGTTTATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
934732 TAATACACTTCGGTGTATATGGTGGGCACGACCCTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
934772 TAATACACTTCGGTGTATATGGTGGGCACGACTTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
934812 TA
1 TA
934814 GCACTACGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:935049 original size:46 final size:45
Alignment explanation
Indices: 934918--935042 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 45
934908 GTAACCATGC
* * * *
934918 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
* *
934962 AAATAAGCTTACGAACTTATGGAATTTAAAT-GTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGGAA
*
935008 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
935043 AGATTTTATA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 26 0.38
45 5 0.07
46 35 0.51
47 3 0.04
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
Found at i:936682 original size:228 final size:232
Alignment explanation
Indices: 936282--936743 Score: 896
Period size: 228 Copynumber: 2.0 Consensus size: 232
936272 AAGAATTGAT
936282 AGATTAAGGATGTTTTAGACCGAGTAGTTCACATTGGGGTGAACTGGTGTTATTTATATAAAAAA
1 AGATTAAGGATGTTTTAGACCGAGTAGTTCACATTGGGGTGAACTGGTGTTATTTATATAAAAAA
936347 ATGGATATGTGTGGTTATGCATAAATTATCGATAGTTAAATAGAGTAACTATCAAGAATAAATAT
66 ATGGATATGTGTGGTTATGCATAAATTATCGATAGTTAAATAGAGTAACTATCAAGAATAAATAT
936412 CCTATTTTGAGGATTGATGATTTGTTTTATCAGCTTAAAAGGAGCAACAATGTTTTTTGAAAGTT
131 CCTATTTTGAGGATTGATGATTTGTTTTATCAGCTTAAAAGGAGCAACAATGTTTTTTGAAAGTT
936477 TATATTCGAATGGGATATTACGAGTTAAATA-TAAAG
196 TATATTCGAATGGGATATTACGAGTTAAATATTAAAG
936513 AGATTAAGGATGTTTTAGACCGAGTAGTTCACATTGGGGTGAACTGGTGTTATTTATAT-AAAAA
1 AGATTAAGGATGTTTTAGACCGAGTAGTTCACATTGGGGTGAACTGGTGTTATTTATATAAAAAA
936577 ATGGATATGTGTGGTTATGCATAAA-T-TCGATAGTTAAATAGAGTAACTATCAAGAATAAATAT
66 ATGGATATGTGTGGTTATGCATAAATTATCGATAGTTAAATAGAGTAACTATCAAGAATAAATAT
936640 CCTATTTTGAGGATTGATGATTTGTTTTATCAGCTTAAAAGGAGCAACAATGTTTTTTGAAAGTT
131 CCTATTTTGAGGATTGATGATTTGTTTTATCAGCTTAAAAGGAGCAACAATGTTTTTTGAAAGTT
936705 TATATTCGAATGGGATATTACGAGTTAAATATTAAAG
196 TATATTCGAATGGGATATTACGAGTTAAATATTAAAG
936742 AG
1 AG
936744 GAAGATGTTC
Statistics
Matches: 230, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
228 133 0.58
229 8 0.03
230 30 0.13
231 59 0.26
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (232 bp):
AGATTAAGGATGTTTTAGACCGAGTAGTTCACATTGGGGTGAACTGGTGTTATTTATATAAAAAA
ATGGATATGTGTGGTTATGCATAAATTATCGATAGTTAAATAGAGTAACTATCAAGAATAAATAT
CCTATTTTGAGGATTGATGATTTGTTTTATCAGCTTAAAAGGAGCAACAATGTTTTTTGAAAGTT
TATATTCGAATGGGATATTACGAGTTAAATATTAAAG
Found at i:940876 original size:17 final size:17
Alignment explanation
Indices: 940854--940897 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
940844 TTCATAAATC
940854 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
940871 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
940888 -AAATATCCAA
1 CAAA-ATCCAA
940898 AAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:940889 original size:9 final size:8
Alignment explanation
Indices: 940849--940900 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
940839 CACTATTCAT
940849 AAATCC-A
1 AAATCCAA
940856 AAATCCAA
1 AAATCCAA
*
940864 CAATCCACA
1 AAATCCA-A
940873 AAAT-CAA
1 AAATCCAA
940880 ACAATCCAA
1 A-AATCCAA
940889 AATATCCAA
1 AA-ATCCAA
940898 AAA
1 AAA
940901 GTTGAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 8 0.21
8 14 0.37
9 16 0.42
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATCCAA
Found at i:942876 original size:20 final size:21
Alignment explanation
Indices: 942830--942890 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
942820 ATCCCCTGTG
942830 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
942853 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
942873 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
942891 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:944888 original size:12 final size:12
Alignment explanation
Indices: 944871--944895 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
944861 ATGATGATTC
944871 TCTAACGTCATT
1 TCTAACGTCATT
944883 TCTAACGTCATT
1 TCTAACGTCATT
944895 T
1 T
944896 GCTTGTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTAACGTCATT
Found at i:949218 original size:18 final size:18
Alignment explanation
Indices: 949171--949223 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
949161 AGGGATTATC
* * *
949171 AGTGGTCCTTCAGGAAAT
1 AGTGGTTCTTCGGGACAT
949189 AGTGG-TCTTTCGGGACAT
1 AGTGGTTC-TTCGGGACAT
949207 AGTGGTTCTTCGGGACA
1 AGTGGTTCTTCGGGACA
949224 AATATTCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.90
19 2 0.07
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTTCTTCGGGACAT
Found at i:976810 original size:2 final size:2
Alignment explanation
Indices: 976803--976828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
976793 ACTTAAAAAT
976803 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
976829 ACATCCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:978682 original size:31 final size:31
Alignment explanation
Indices: 978644--978784 Score: 201
Period size: 31 Copynumber: 4.5 Consensus size: 31
978634 GAGTCGAGGG
* * *
978644 TTACCTATGTTCTTCGAGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGAACTGT
* * *
978675 TTACCTATGTTCTTCGGGATATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGAACTGT
*
978706 TTACCTATGTTCTTCGGGACATATGAATTGT
1 TTACCTATGTTCTTCGGGACATATGAACTGT
*
978737 TTACCTATGTTATTCGGGACATATGAACTGT
1 TTACCTATGTTCTTCGGGACATATGAACTGT
*
978768 TTACCTAGGTTCTTCGG
1 TTACCTATGTTCTTCGG
978785 AATCTATGGA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGAACTGT
Found at i:979540 original size:21 final size:21
Alignment explanation
Indices: 979514--979557 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
979504 TTGCTGAAAT
*
979514 CACTGTAGCAGTGCATCGATA
1 CACTGTAGCAGTACATCGATA
979535 CACTGTAGCAGTACATCGATA
1 CACTGTAGCAGTACATCGATA
979556 CA
1 CA
979558 TAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
CACTGTAGCAGTACATCGATA
Found at i:980632 original size:16 final size:15
Alignment explanation
Indices: 980579--980659 Score: 51
Period size: 16 Copynumber: 5.3 Consensus size: 15
980569 TTTTTAGTAA
980579 TTTAAATTTAA-A-T
1 TTTAAATTTAATATT
** *
980592 TTTATTTTTAGTATT
1 TTTAAATTTAATATT
*
980607 ATTTATATTTAATATT
1 -TTTAAATTTAATATT
*
980623 TTTGAAATTT-TTATAT
1 TTT-AAATTTAATAT-T
980639 TTTAAATTTAGAATATT
1 TTTAAATTT--AATATT
980656 TTTA
1 TTTA
980660 TTTTTTCTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
13 8 0.15
14 1 0.02
15 13 0.25
16 22 0.42
17 5 0.10
18 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (15 bp):
TTTAAATTTAATATT
Found at i:980647 original size:24 final size:25
Alignment explanation
Indices: 980603--980665 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
980593 TTATTTTTAG
*
980603 TATTATTTATA-TTTAATATTTTTGAA
1 TATT-TTTATATTTTAATA-TTTAGAA
980629 -ATTTTTATATTTTAA-ATTTAGAA
1 TATTTTTATATTTTAATATTTAGAA
*
980652 TATTTTTATTTTTT
1 TATTTTTATATTTT
980666 CTTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 6 0.18
24 19 0.58
25 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (25 bp):
TATTTTTATATTTTAATATTTAGAA
Found at i:988669 original size:83 final size:83
Alignment explanation
Indices: 988530--988696 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
988520 CTCCTAGTTT
988530 AGGACTTTGGTATCCTAGAGACTCTAGCTTTAGCTTGCATGCTTTTTCTGATGCGGATTATGGAG
1 AGGACTTTGGTATCCTAGAGACTCTAGCTTTAGCTTGCATGCTTTTTCTGATGCGGATTATGGAG
988595 GATGCAAATTAGATAGGA
66 GATGCAAATTAGATAGGA
988613 AGGACTTTGGTATCCTAGAGACTCTAGCTTTAGCTTGCATGCTTTTTCTGATGCGGATTATGGAG
1 AGGACTTTGGTATCCTAGAGACTCTAGCTTTAGCTTGCATGCTTTTTCTGATGCGGATTATGGAG
988678 GATGCAAATTAGATAGGA
66 GATGCAAATTAGATAGGA
988696 A
1 A
988697 AAGCACCTCT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (83 bp):
AGGACTTTGGTATCCTAGAGACTCTAGCTTTAGCTTGCATGCTTTTTCTGATGCGGATTATGGAG
GATGCAAATTAGATAGGA
Found at i:989400 original size:20 final size:20
Alignment explanation
Indices: 989375--989414 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
989365 TTTTGGTGCA
*
989375 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
989395 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCTT
989415 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:989427 original size:23 final size:21
Alignment explanation
Indices: 989375--989436 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
989365 TTTTGGTGCA
*
989375 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
989395 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
*
989416 GAAGGGGAACCGTTTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
989437 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:994782 original size:3 final size:3
Alignment explanation
Indices: 994776--994860 Score: 68
Period size: 3 Copynumber: 28.0 Consensus size: 3
994766 TAATATTATT
* * * *
994776 TAA TAA TAA TAT TAT TATA TAA TAA TAT TATA TAA TAA TAA -CA TATA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TA-A
*
994823 TAA TAA TAA T-A TAA TAAA TAA TAG TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
994861 GTAAGATCGG
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 5 0.07
3 52 0.78
4 10 0.15
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:994783 original size:13 final size:13
Alignment explanation
Indices: 994781--994859 Score: 77
Period size: 13 Copynumber: 5.7 Consensus size: 13
994771 TTATTTAATA
*
994781 ATAATATTATTAT
1 ATAATAATATTAT
994794 ATAATAATATTAT
1 ATAATAATATTAT
*
994807 ATAATAATAACATAT
1 ATAATAAT-A-TTAT
*
994822 ATAATAATAATAT
1 ATAATAATATTAT
*
994835 AATAAATAATAGTAAT
1 -AT-AATAATA-TTAT
994851 ATAATAATA
1 ATAATAATA
994860 AGTAAGATCG
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
13 24 0.42
14 11 0.19
15 20 0.35
16 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (13 bp):
ATAATAATATTAT
Found at i:994786 original size:16 final size:16
Alignment explanation
Indices: 994765--994860 Score: 112
Period size: 16 Copynumber: 6.2 Consensus size: 16
994755 ATTGGACTTT
*
994765 ATAATATTATTTAATA
1 ATAATATTATATAATA
994781 ATAATATTAT-TATATA
1 ATAATATTATATA-ATA
994797 ATAATATTATATAATA
1 ATAATATTATATAATA
*
994813 ATAACA-TATATAATA
1 ATAATATTATATAATA
*
994828 ATAATATAATA-AATA
1 ATAATATTATATAATA
*
994843 ATAGTA--ATATAATA
1 ATAATATTATATAATA
994857 ATAA
1 ATAA
994861 GTAAGATCGG
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
13 3 0.04
14 7 0.10
15 25 0.35
16 34 0.48
17 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
ATAATATTATATAATA
Found at i:994804 original size:29 final size:28
Alignment explanation
Indices: 994764--994859 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
994754 AATTGGACTT
* *
994764 TATAATATTATTTAATAATAATATTATTA
1 TATAATAATATTTAATAATAATAATA-TA
*
994793 TATAATAATA-TTATATAATAATAACATA
1 TATAATAATATTTA-ATAATAATAATATA
* *
994821 TATAATAATAATATAATAAATAATAGTA-A
1 TATAATAAT-ATTTAAT-AATAATAATATA
994850 TATAATAATA
1 TATAATAATA
994860 AGTAAGATCG
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
28 15 0.26
29 32 0.56
30 10 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
TATAATAATATTTAATAATAATAATATA
Found at i:994864 original size:15 final size:14
Alignment explanation
Indices: 994776--994859 Score: 77
Period size: 15 Copynumber: 6.0 Consensus size: 14
994766 TAATATTATT
*
994776 TAATAATAATATTA
1 TAATAATAATAATA
*
994790 TTAT-ATAATAATA
1 TAATAATAATAATA
*
994803 TTATATAATAATAACA
1 -TA-ATAATAATAATA
994819 TATATAATAATAATA
1 TA-ATAATAATAATA
994834 TAAT-A-AATAATA
1 TAATAATAATAATA
994846 GTAAT-ATAATAATA
1 -TAATAATAATAATA
994860 AGTAAGATCG
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.12
13 14 0.23
14 13 0.22
15 18 0.30
16 8 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (14 bp):
TAATAATAATAATA
Done.