Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009288.1 Hibiscus syriacus cultivar Beakdansim tig00112981_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: 633898
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 3
Found at i:3908 original size:7 final size:7
Alignment explanation
Indices: 3896--3938 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
3886 CAATATGGCC
3896 TTGCAAG
1 TTGCAAG
3903 TTGCAAG
1 TTGCAAG
3910 TTGCAAG
1 TTGCAAG
*
3917 TTGTAAG
1 TTGCAAG
3924 TTGCAAG
1 TTGCAAG
3931 TTGCAAG
1 TTGCAAG
3938 T
1 T
3939 AGAACGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (7 bp):
TTGCAAG
Found at i:15689 original size:15 final size:17
Alignment explanation
Indices: 15664--15700 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
15654 AGTAACTTTC
15664 AAAATTGA-TTTCAAAA
1 AAAATTGATTTTCAAAA
*
15680 AAAATT-ATTTTCAAAG
1 AAAATTGATTTTCAAAA
15696 AAAAT
1 AAAAT
15701 CTTAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATTGATTTTCAAAA
Found at i:19407 original size:41 final size:40
Alignment explanation
Indices: 19305--19489 Score: 136
Period size: 41 Copynumber: 4.4 Consensus size: 40
19295 ACTAGCTGTC
* * * *
19305 GTCATAGTTGTCATATACTGAATTTAGAATTCTTTATGGTA
1 GTCATTGTCGTCATA-ACTGAATTTAGAATTCGTCATGGTA
* * *
19346 GTCGTTATAGTCATTAACTGAATTTAGAATTCGTCATGGTA
1 GTCATTGTCGTCA-TAACTGAATTTAGAATTCGTCATGGTA
* * *
19387 GTCATTGTCTTCATACACTGAATTTAGAGTCCGTCATGATCGTCA
1 GTCATTGTCGTCATA-ACTGAATTTAGAATTCGTCATG---GT-A
* * * * *
19432 TTGTCATTATCATCATAGATTGAATTTAGAGTTCATCATGGTA
1 --GTCATTGTCGTCATA-ACTGAATTTAGAATTCGTCATGGTA
*
19475 ATCATTGTCGTCATA
1 GTCATTGTCGTCATA
19490 GTTGTCATGA
Statistics
Matches: 115, Mismatches: 21, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
40 2 0.02
41 73 0.63
42 2 0.02
43 1 0.01
44 4 0.03
45 1 0.01
47 32 0.28
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (40 bp):
GTCATTGTCGTCATAACTGAATTTAGAATTCGTCATGGTA
Found at i:19480 original size:47 final size:47
Alignment explanation
Indices: 19387--19483 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 47
19377 CGTCATGGTA
* * * **
19387 GTCATTGTCTTCATACACTGAATTTAGAGTCCGTCATGATCGTCATT
1 GTCATTATCATCATACACTGAATTTAGAGTCCATCATGATAATCATT
* * * *
19434 GTCATTATCATCATAGATTGAATTTAGAGTTCATCATGGTAATCATT
1 GTCATTATCATCATACACTGAATTTAGAGTCCATCATGATAATCATT
19481 GTC
1 GTC
19484 GTCATAGTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (47 bp):
GTCATTATCATCATACACTGAATTTAGAGTCCATCATGATAATCATT
Found at i:27291 original size:157 final size:159
Alignment explanation
Indices: 26983--27300 Score: 532
Period size: 157 Copynumber: 2.0 Consensus size: 159
26973 CTTGAGATGG
26983 ATGGATAATTAGATGAAGCCCACATAATTCATGTTGCTTAATTAGTAAAACAAAGTTAAGTTTTA
1 ATGGATAATTAGATGAAGCCCACATAATTCATGTTGCTTAATTAGTAAAACAAAGTTAAGTTTTA
* * * * *
27048 GGGTACGAATCAAGCGATCTCGATGGTAAATAATTTTTATTATTACTTGAGGTCCTGGGTTCAAG
66 GGATACGAATCAAGCGATCTCAATGGTAAATAATTGTTATTATAACTTGAGGTCATGGGTTCAAG
27113 CGTCGAGAATGCTAGGGTATAAACGTTAA
131 CGTCGAGAATGCTAGGGTATAAACGTTAA
*
27142 ATGGATAATTAGATGAAG-CC-CATAATTCATGTTGCTTAATTAGTAAAACCAAGTTAAGTTTTA
1 ATGGATAATTAGATGAAGCCCACATAATTCATGTTGCTTAATTAGTAAAACAAAGTTAAGTTTTA
* *
27205 GGATACGAATTAAGCGATCTCAATGGTAAATAATTGTTATTATAACTTGAGGTCATGGGTTCGAG
66 GGATACGAATCAAGCGATCTCAATGGTAAATAATTGTTATTATAACTTGAGGTCATGGGTTCAAG
* *
27270 CGTCGGGAATGCTAGGGTATAAGCGTTAA
131 CGTCGAGAATGCTAGGGTATAAACGTTAA
27299 AT
1 AT
27301 ATCAATTGGT
Statistics
Matches: 149, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
157 129 0.87
158 2 0.01
159 18 0.12
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (159 bp):
ATGGATAATTAGATGAAGCCCACATAATTCATGTTGCTTAATTAGTAAAACAAAGTTAAGTTTTA
GGATACGAATCAAGCGATCTCAATGGTAAATAATTGTTATTATAACTTGAGGTCATGGGTTCAAG
CGTCGAGAATGCTAGGGTATAAACGTTAA
Found at i:32330 original size:7 final size:7
Alignment explanation
Indices: 32318--32392 Score: 150
Period size: 7 Copynumber: 10.7 Consensus size: 7
32308 CGAAACACTA
32318 AGAGAAG
1 AGAGAAG
32325 AGAGAAG
1 AGAGAAG
32332 AGAGAAG
1 AGAGAAG
32339 AGAGAAG
1 AGAGAAG
32346 AGAGAAG
1 AGAGAAG
32353 AGAGAAG
1 AGAGAAG
32360 AGAGAAG
1 AGAGAAG
32367 AGAGAAG
1 AGAGAAG
32374 AGAGAAG
1 AGAGAAG
32381 AGAGAAG
1 AGAGAAG
32388 AGAGA
1 AGAGA
32393 GAAGTGACCT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 68 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AGAGAAG
Found at i:35496 original size:20 final size:20
Alignment explanation
Indices: 35471--35509 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35461 TTCATCCCAA
*
35471 TTTATCCAGTATTGATATTG
1 TTTATCCAGTATCGATATTG
*
35491 TTTATCTAGTATCGATATT
1 TTTATCCAGTATCGATATT
35510 TGAACCCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTATCCAGTATCGATATTG
Found at i:37829 original size:20 final size:20
Alignment explanation
Indices: 37804--37847 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
37794 AGTAGTACCA
37804 ATACCATGGTAGGGGTATCG
1 ATACCATGGTAGGGGTATCG
37824 ATACCATGGTAGGGGTATCG
1 ATACCATGGTAGGGGTATCG
37844 ATAC
1 ATAC
37848 TATTGAGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (20 bp):
ATACCATGGTAGGGGTATCG
Found at i:38262 original size:55 final size:55
Alignment explanation
Indices: 38173--38465 Score: 383
Period size: 55 Copynumber: 5.3 Consensus size: 55
38163 CTATGTGTAC
* *
38173 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * *
38228 CACATGCACTATGTGTGCAAATCCACGGATTTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * * *
38283 TACATGCACCATATGTGAAAATCCACTGAATTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * * *
38338 TACATGCACTATATGTGGAAATCCACAGAATTCATCATGAGTTGATGAAAAACAG
1 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * * *
38393 TACAAGCACGATGTGTGC-AACCCGCAGAATTCATCATGAGTTGATGAACT-ACCG
1 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAA-TAACCG
* * *
38447 TATAGGCACTACGTGTGCA
1 TACATGCACTATGTGTGCA
38466 TCTTAATACA
Statistics
Matches: 210, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
54 45 0.21
55 165 0.79
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (55 bp):
TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
Found at i:44622 original size:36 final size:36
Alignment explanation
Indices: 44581--44656 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
44571 ATTTTCGGGA
*
44581 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
44617 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
44653 TTTT
1 TTTT
44657 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:50138 original size:60 final size:61
Alignment explanation
Indices: 50074--50201 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 61
50064 AGAAAGAGGG
* * ** *
50074 TCATAGTTT-AGGGATGAGATTAGAATGTTCAAGAGTTTAAAGACTAATTTAAAATGAG-AT
1 TCATAGTTTGA-GGATGAAATTAAAATAATCAAAAGTTTAAAGACTAATTTAAAATGAGAAT
* *
50134 TCATAGTTTGAGGATGAAATTAAAATAATCAAAAGTTTAAGGATTAATTTAAAATGAGAAT
1 TCATAGTTTGAGGATGAAATTAAAATAATCAAAAGTTTAAAGACTAATTTAAAATGAGAAT
50195 T-ATAGTT
1 TCATAGTT
50202 GGGAGAAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 55 0.93
61 4 0.07
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (61 bp):
TCATAGTTTGAGGATGAAATTAAAATAATCAAAAGTTTAAAGACTAATTTAAAATGAGAAT
Found at i:50142 original size:31 final size:30
Alignment explanation
Indices: 50107--50201 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 30
50097 AATGTTCAAG
*
50107 AGTTTAAAGACTAATTTAAAATGAGATTCAT
1 AGTTTAAGGA-TAATTTAAAATGAGATTCAT
* * *
50138 AGTTTGAGGATGAAATTAAAAT-A-A-TCAAA
1 AGTTTAAGGAT-AATTTAAAATGAGATTC-AT
50167 AGTTTAAGGATTAATTTAAAATGAGAATT-AT
1 AGTTTAAGGA-TAATTTAAAATGAG-ATTCAT
50198 AGTT
1 AGTT
50202 GGGAGAAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
28 2 0.04
29 20 0.40
30 4 0.08
31 22 0.44
32 1 0.02
33 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.35
Consensus pattern (30 bp):
AGTTTAAGGATAATTTAAAATGAGATTCAT
Found at i:51166 original size:31 final size:31
Alignment explanation
Indices: 51124--51196 Score: 128
Period size: 31 Copynumber: 2.3 Consensus size: 31
51114 AGCTCAGCTT
*
51124 GAACTCGAAATATAATATTGAAACTCGACTC
1 GAACTCAAAATATAATATTGAAACTCGACTC
51155 GAACTCAAAATATAATATTGAAACTCGACTC
1 GAACTCAAAATATAATATTGAAACTCGACTC
51186 GAACTCGAAAA
1 GAACTC-AAAA
51197 GACTCGAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.23
Consensus pattern (31 bp):
GAACTCAAAATATAATATTGAAACTCGACTC
Found at i:51212 original size:16 final size:16
Alignment explanation
Indices: 51181--51212 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51171 ATTGAAACTC
*
51181 GACTCGAACTCGAAAA
1 GACTCGAACTCAAAAA
51197 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
51213 AATTTCAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:51301 original size:29 final size:29
Alignment explanation
Indices: 51226--51308 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
51216 TTCAGGAGCT
* * *
51226 CGATTGAAGCTCGAGACTCGAGCTCGAAGA
1 CGATTGAAGCTCGA-ACTCAAACTCGAACA
** * *
51256 -TTTTG-AGCTCG-ATTCAATCTCGAACA
1 CGATTGAAGCTCGAACTCAAACTCGAACA
51282 CGATTGAAGCTCGAACTCAAACTCGAA
1 CGATTGAAGCTCGAACTCAAACTCGAA
51309 TTTGAACCTA
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
26 11 0.28
27 3 0.08
28 12 0.30
29 14 0.35
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (29 bp):
CGATTGAAGCTCGAACTCAAACTCGAACA
Found at i:53765 original size:2 final size:2
Alignment explanation
Indices: 53758--53801 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
53748 GCAATGTAAT
53758 TA TA TA TA 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 TA
53800 TA
1 TA
53802 CTATCTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54426 original size:10 final size:10
Alignment explanation
Indices: 54411--54435 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54401 AATGTTGTTG
54411 GGAAGCTTAA
1 GGAAGCTTAA
54421 GGAAGCTTAA
1 GGAAGCTTAA
54431 GGAAG
1 GGAAG
54436 AGTTTAGAAC
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (10 bp):
GGAAGCTTAA
Found at i:64251 original size:40 final size:42
Alignment explanation
Indices: 64207--64311 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 42
64197 TAAAAATGCA
* *
64207 ACTAAGGTACATGTCTATTGCGGCATTTATT-C-AAAACGCC
1 ACTAAAGTACATGTCTATTGCGGCATTTATTACAAAAACACC
* ** *
64247 ACTAAATTACATGAT-TATTGCATCGTTTATTACAAAAACACC
1 ACTAAAGTACATG-TCTATTGCGGCATTTATTACAAAAACACC
* *
64289 ACTAAAGTACAAGACTATTGCGG
1 ACTAAAGTACATGTCTATTGCGG
64312 AGTTTGAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
40 24 0.48
41 2 0.04
42 24 0.48
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (42 bp):
ACTAAAGTACATGTCTATTGCGGCATTTATTACAAAAACACC
Found at i:64308 original size:42 final size:40
Alignment explanation
Indices: 64232--64309 Score: 102
Period size: 42 Copynumber: 1.9 Consensus size: 40
64222 TATTGCGGCA
* * * *
64232 TTTATTCAAAACGCCACTAAATTACATGATTATTGCATCG
1 TTTATTCAAAACACCACTAAAGTACAAGACTATTGCATCG
64272 TTTATTACAAAAACACCACTAAAGTACAAGACTATTGC
1 TTTATT-C-AAAACACCACTAAAGTACAAGACTATTGC
64310 GGAGTTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.19
41 1 0.03
42 25 0.78
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (40 bp):
TTTATTCAAAACACCACTAAAGTACAAGACTATTGCATCG
Found at i:64400 original size:41 final size:41
Alignment explanation
Indices: 64355--64433 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
64345 TCTATAGCGA
* **
64355 CGTTTGTAA-ACAAACGCCACTAAAGTCTGAGTCTTTTGTGG
1 CGTTTG-AATACAAACACCACTAAAGTAAGAGTCTTTTGTGG
*
64396 CGTTTGAATACAAACACCACTAACGTAAGAGTCTTTTG
1 CGTTTGAATACAAACACCACTAAAGTAAGAGTCTTTTG
64434 CAGCGTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
CGTTTGAATACAAACACCACTAAAGTAAGAGTCTTTTGTGG
Found at i:64656 original size:42 final size:40
Alignment explanation
Indices: 64564--64658 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 40
64554 CGCCGCTAAA
* *
64564 GTACCACTATTGTGGAGATTTTTGAAAAAAGCCACTATATAT
1 GTACC-CTATTGT-GAGATTTTTGAAAAAAGACACTATATAC
* *
64606 GAATCCTATTGT-AGCATTTATTGAAAAAATGACACTATATAC
1 GTACCCTATTGTGAG-ATTT-TTGAAAAAA-GACACTATATAC
64648 GTACCCTATTG
1 GTACCCTATTG
64659 CGGTGTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
39 2 0.05
40 4 0.09
41 16 0.36
42 22 0.50
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (40 bp):
GTACCCTATTGTGAGATTTTTGAAAAAAGACACTATATAC
Found at i:73108 original size:29 final size:29
Alignment explanation
Indices: 73054--73129 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
73044 GGTGACATTT
** * *
73054 TGGTAATTATTTTGGAAATGGTGCTATTC
1 TGGTAATTATTTTAAAAAGGGAGCTATTC
*
73083 TGGTAATTATTTTAAAAAGGGAGCTATTT
1 TGGTAATTATTTTAAAAAGGGAGCTATTC
* * *
73112 TTGTAATTTTTTTTAAAA
1 TGGTAATTATTTTAAAAA
73130 TATGACAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.47
Consensus pattern (29 bp):
TGGTAATTATTTTAAAAAGGGAGCTATTC
Found at i:73179 original size:29 final size:29
Alignment explanation
Indices: 73147--73233 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
73137 ATTTCATAAA
* * *
73147 ATTTTTAAAAGAGTGATATTTTAGTAATT
1 ATTTTGAAAAGAGTGCTATTTTGGTAATT
*
73176 ATTTTGAAAATGA-TGCCATTTTGGTAATT
1 ATTTTGAAAA-GAGTGCTATTTTGGTAATT
* * *
73205 AATTTCAAAATGA-TGCTATTTTCGTAATT
1 ATTTTGAAAA-GAGTGCTATTTTGGTAATT
73234 TAAAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 47 0.96
30 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (29 bp):
ATTTTGAAAAGAGTGCTATTTTGGTAATT
Found at i:74384 original size:117 final size:117
Alignment explanation
Indices: 74174--74465 Score: 503
Period size: 117 Copynumber: 2.5 Consensus size: 117
74164 GGAAGTATTT
*
74174 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGT
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
*
74239 GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGGAAGTTATTACTG
66 GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGAAAGTTATTACTG
*
74291 CAGGCTCCTTTACTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
74356 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGAAAGTTATTACTG
66 GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGAAAGTTATTACTG
** * *
74408 CAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
74466 TTTCGGGAAA
Statistics
Matches: 165, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 165 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGAAAGTTATTACTG
Found at i:75458 original size:20 final size:21
Alignment explanation
Indices: 75413--75464 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
75403 CGGAAATATT
* *
75413 CATTTTATGTAGTAAAATTAA
1 CATTTTAGGTAGTAAAAATAA
* *
75434 TATTTTCGGTAG-AAAAATAA
1 CATTTTAGGTAGTAAAAATAA
75454 CATTTTAGGTA
1 CATTTTAGGTA
75465 TTGTCTGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (21 bp):
CATTTTAGGTAGTAAAAATAA
Found at i:92761 original size:21 final size:21
Alignment explanation
Indices: 92737--92776 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
92727 AAATGAATTA
92737 TAATCATTATTA-TATATTTTT
1 TAAT-ATTATTATTATATTTTT
*
92758 TAATATTTTTATTATATTT
1 TAATATTATTATTATATTT
92777 GGAGAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TAATATTATTATTATATTTTT
Found at i:93705 original size:2 final size:2
Alignment explanation
Indices: 93698--93727 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
93688 AAATTAAAAT
93698 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93728 TAACTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:100424 original size:248 final size:248
Alignment explanation
Indices: 99986--100482 Score: 940
Period size: 248 Copynumber: 2.0 Consensus size: 248
99976 AGTACACCCG
99986 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
1 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
*
100051 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAGTCATGAACAT
66 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
100116 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
131 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
100181 TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
196 TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
100234 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
1 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
* * *
100299 ACAAGGGATTCGTGATATACCTTAGTTTATTAGAATAATAGCAAATCAGCAGCAATCATGAACAT
66 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
100364 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
131 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
* *
100429 TCTTTTCTCAAAATGGTTTTGAGAAATATTGTCAAGAGGATTTAAACGGCTGC
196 TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
100482 T
1 T
100483 AGGGCATCAT
Statistics
Matches: 243, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
248 243 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (248 bp):
TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
Found at i:107845 original size:56 final size:57
Alignment explanation
Indices: 107752--107859 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 57
107742 ATATTCTCTC
*
107752 CCCATTACGATACTTTCATACTAATTTTATATA-TTTT-TTCACGTTATCTCACTAAT
1 CCCATTACGATACTTTCATACTAATTTTACATATTTTTCTTCACG-TATCTCACTAAT
* * * *
107808 CCCATTACGGTATTTTCAT-GTCAATTTTACATGTTTTTCTTCACGTATCTCA
1 CCCATTACGATACTTTCATACT-AATTTTACATATTTTTCTTCACGTATCTCA
107860 TAGTTCTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
55 1 0.02
56 26 0.59
57 11 0.25
58 6 0.14
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.46
Consensus pattern (57 bp):
CCCATTACGATACTTTCATACTAATTTTACATATTTTTCTTCACGTATCTCACTAAT
Found at i:108150 original size:11 final size:12
Alignment explanation
Indices: 108134--108159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
108124 GGTAATGTAA
108134 TTTTTTCATTTT
1 TTTTTTCATTTT
108146 TTTTTTCATTTT
1 TTTTTTCATTTT
108158 TT
1 TT
108160 CTTAACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCATTTT
Found at i:109474 original size:37 final size:37
Alignment explanation
Indices: 109375--109668 Score: 340
Period size: 37 Copynumber: 8.0 Consensus size: 37
109365 TTAAATCGGT
109375 TTTTGAAATATATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAA-A-AT-TATATAATATATAGTTTTTGAAAACA
* *
109415 TTTTG--AAA--ACAT-ATATATAGTTTTTAAAAACA
1 TTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
109447 TTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
109484 TTTTG-AAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAAAT-TATATAATATATAGTTTTTGAAAACA
* ***
109521 TTTT-AAATATATATATAATATATAGTTTTTGAAATTT
1 TTTTGAAAAAT-TATATAATATATAGTTTTTGAAAACA
* *
109558 TTTTGAAAACTTATATAATATACAGTTTTTGAAAACA
1 TTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
109595 TTTT-AAAAACTTATATAATATATAG-TTTTGAAAACA
1 TTTTGAAAAA-TTATATAATATATAGTTTTTGAAAACA
* **
109631 TTTTTGAAAGCA-TATATAATAT-TTTTTTTTGAAAACA
1 -TTTTGAAA-AATTATATAATATATAGTTTTTGAAAACA
109668 T
1 T
109669 ATATAATATA
Statistics
Matches: 222, Mismatches: 19, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
32 24 0.11
33 3 0.01
34 3 0.01
36 26 0.12
37 152 0.68
38 8 0.04
39 1 0.00
40 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
Found at i:109476 original size:111 final size:107
Alignment explanation
Indices: 109375--109744 Score: 376
Period size: 111 Copynumber: 3.5 Consensus size: 107
109365 TTAAATCGGT
109375 TTTTGAAATATATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAGTTTTT
1 TTTTGAAA-A-ATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAGTTTTT
109440 AAAAACATTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
64 AAAAACATTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
* *
109484 TTTTG-AAAATATATATAATATATAGTTTTTGAAAACATTTTAAATATATATATAATATATAGTT
1 TTTTGAAAAATATATATAATATATAGTTTTTGAAAACATTTT-GA-A-A-ACAT-ATATATAGTT
* *** * *
109548 TTTGAAATTTTTTTGAAAACTTATATAATATACAGTTTTTGAAAACA
61 TTTAAAAACATTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
*
109595 TTTT-AAAAACT-TATATAATATATAG-TTTTGAAAACATTTTTGAAAGCATATATAATA-TTTT
1 TTTTGAAAAA-TATATATAATATATAGTTTTTGAAAACA-TTTTGAAAACATATAT-ATAGTTTT
* *
109656 T-------TTTTGAAAACA-TATATAATATATAG-TTTTAAAAATA
63 TAAAAACATTTTGAAAA-ATTATATAATATATAGTTTTTGAAAACA
* * * *
109693 TTTTTGAAAAA-ATATATATTATATAGTTTTGGAAATA-TTTTTGAAAATATAT
1 -TTTTGAAAAATATATATAATATATAGTTTTTGAAA-ACATTTTGAAAACATAT
109745 TATTATTATT
Statistics
Matches: 226, Mismatches: 20, Indels: 40
0.79 0.07 0.14
Matches are distributed among these distances:
98 9 0.04
99 51 0.23
100 12 0.05
101 1 0.00
106 42 0.19
107 7 0.03
108 4 0.02
109 7 0.03
110 15 0.07
111 77 0.34
112 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (107 bp):
TTTTGAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATATAGTTTTTAA
AAACATTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
Found at i:109685 original size:25 final size:25
Alignment explanation
Indices: 109632--109693 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
109622 TTGAAAACAT
* * **
109632 TTTTGAAAGCATATATAATATTTTT
1 TTTTGAAAACATATATAATATATAG
109657 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
109682 TTTT-AAAA-ATAT
1 TTTTGAAAACATAT
109694 TTTTGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 4 0.12
24 4 0.12
25 25 0.76
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:109723 original size:62 final size:62
Alignment explanation
Indices: 109595--109723 Score: 168
Period size: 62 Copynumber: 2.1 Consensus size: 62
109585 TTTGAAAACA
* * * ** * **
109595 TTTTAAAAACTTATATAATATATAGTTTTGAAAACATTTTTGAAAGCATATATAATATTTTT
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTGAAAAAATATATAATATATAG
* *
109657 TTTTGAAAACATATATAATATATAGTTTTAAAAATATTTTTGAAAAAATATATATTATATAG
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTGAAAAAATATATAATATATAG
109719 TTTTG
1 TTTTG
109724 GAAATATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (62 bp):
TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTGAAAAAATATATAATATATAG
Found at i:109750 original size:3 final size:3
Alignment explanation
Indices: 109742--109784 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
109732 TTTGAAAATA
* *
109742 TAT TAT TAT TAT TAT TAT TAT TAT CTCT TCT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT T
109785 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:109753 original size:39 final size:37
Alignment explanation
Indices: 109656--109750 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
109646 ATAATATTTT
* *
109656 TTTTTGAAAACATATATAATATATAGTTTTAAAAATA
1 TTTTTGAAAAAATATATATTATATAGTTTTAAAAATA
**
109693 TTTTTGAAAAAATATATATTATATAGTTTTGGAAATA
1 TTTTTGAAAAAATATATATTATATAGTTTTAAAAATA
*
109730 TTTTTGAAAATATAT-TATTAT
1 TTTTTGAAAAAATATATATTAT
109751 TATTATTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 6 0.11
37 47 0.89
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAAAATATATATTATATAGTTTTAAAAATA
Found at i:109793 original size:18 final size:18
Alignment explanation
Indices: 109750--109793 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
109740 TATATTATTA
109750 TTATTATTATTATTATCTC
1 TTATT-TTATTATTATCTC
* * *
109769 TTCTTTTATTATTATTTT
1 TTATTTTATTATTATCTC
109787 TTATTTT
1 TTATTTT
109794 TTTCTTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTTATTATTATCTC
Found at i:110922 original size:24 final size:24
Alignment explanation
Indices: 110865--110923 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 24
110855 TTTTAGCATT
110865 TTTTTA-TTTTATTTTTTAAATCA
1 TTTTTATTTTTATTTTTTAAATCA
* **
110888 TTATTTGTTTTATATTTTTTACTTC-
1 TT-TTTATTTT-TATTTTTTAAATCA
110913 TTTTTATTTTT
1 TTTTTATTTTT
110924 TTTATTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
23 3 0.10
24 10 0.34
25 5 0.17
26 11 0.38
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTTATTTTTATTTTTTAAATCA
Found at i:110962 original size:5 final size:5
Alignment explanation
Indices: 110952--111025 Score: 66
Period size: 5 Copynumber: 15.2 Consensus size: 5
110942 AAATTTAAAA
** *
110952 TATTT TATTT TATTT TATTT TATTT TA-TT CCTTT GA-TT TATTT AATATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT --TATTT
*
111002 T-TAT T-TTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
111026 TTCCTTTGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 11 0.19
5 41 0.72
7 5 0.09
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:111032 original size:47 final size:49
Alignment explanation
Indices: 110959--111053 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 49
110949 AAATATTTTA
110959 TTTTATTTTATTTTATTTTATTCCTTTGATTTATTTAATATTT-TTATT
1 TTTTATTTTATTTTATTTTATTCCTTTGATTTATTTAATATTTCTTATT
*
111007 TTTTATTTTATTTTATTTT-TTCCTTTGATTTATTTATTATTTCTTAT
1 TTTTATTTTATTTTATTTTATTCCTTTGATTTATTTAATATTTCTTAT
111054 CTAACATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 22 0.49
48 23 0.51
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (49 bp):
TTTTATTTTATTTTATTTTATTCCTTTGATTTATTTAATATTTCTTATT
Found at i:112345 original size:23 final size:23
Alignment explanation
Indices: 112319--112378 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
112309 TTAATTTTTA
*
112319 AAATCATATTATTTATTTATTTG
1 AAATAATATTATTTATTTATTTG
*
112342 AAATAATATTAATTATTTATTTG
1 AAATAATATTATTTATTTATTTG
112365 AAATAATATTATTT
1 AAATAATATTATTT
112379 TTAAATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (23 bp):
AAATAATATTATTTATTTATTTG
Found at i:112375 original size:19 final size:19
Alignment explanation
Indices: 112331--112411 Score: 64
Period size: 23 Copynumber: 4.2 Consensus size: 19
112321 ATCATATTAT
112331 TTATTTATTTGAAATAATATTAA
1 TTATTTATTTGAAAT-A-A-T-A
112354 TTATTTATTTGAAATAATA
1 TTATTTATTTGAAATAATA
112373 TTA-TT-TTT-AAAT--TA
1 TTATTTATTTGAAATAATA
*
112387 TCTATTTAATTTTAAATAATA
1 T-TATTT-ATTTGAAATAATA
112408 TTAT
1 TTAT
112412 ACAGAACCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.06
15 2 0.04
16 6 0.12
17 3 0.06
18 5 0.10
19 8 0.16
20 4 0.08
21 4 0.08
22 1 0.02
23 15 0.29
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTTATTTGAAATAATA
Found at i:113001 original size:144 final size:146
Alignment explanation
Indices: 112800--113068 Score: 382
Period size: 144 Copynumber: 1.9 Consensus size: 146
112790 AAGTATGAAA
* *
112800 TTTATCTTTTTATCCACATAGGTGGTGACACATGTCACCACCTAATCAGCTGAATAAAATTAATT
1 TTTATCTTTTTATCCACATAGGTAGTCACACATGTCACCACCTAATCAGCTGAATAAAATTAATT
*
112865 AAAACATATCAACCAATAAA-AATAAA-GTGAC-TAGTAATTGAAAAATAAAAATAATTGAGTTC
66 AAAACATATCAACCAATAAAGAA-AAAGGTGACGTAGTAATTGAAAAATAAAAAAAATTGAGTTC
112927 TCATGTCCGTTAATGGT
130 TCATGTCCGTTAATGGT
* * * * *
112944 TTTATCTTTTTATCCCCATAGGTAGTCACACGTGTCACCACCTAATCGGTTGGATAAAATTAATT
1 TTTATCTTTTTATCCACATAGGTAGTCACACATGTCACCACCTAATCAGCTGAATAAAATTAATT
* * ** * *
113009 AAAAGATGTTGACGAATAAAGAAAAAGGTGACGTGGTAATTGAAAAATAAAAAAAATTGA
66 AAAACATATCAACCAATAAAGAAAAAGGTGACGTAGTAATTGAAAAATAAAAAAAATTGA
113069 CATGTCATGT
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
144 76 0.70
145 7 0.06
146 25 0.23
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (146 bp):
TTTATCTTTTTATCCACATAGGTAGTCACACATGTCACCACCTAATCAGCTGAATAAAATTAATT
AAAACATATCAACCAATAAAGAAAAAGGTGACGTAGTAATTGAAAAATAAAAAAAATTGAGTTCT
CATGTCCGTTAATGGT
Found at i:113483 original size:21 final size:20
Alignment explanation
Indices: 113454--113496 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
113444 TATATTTTTA
*
113454 TTATACATTTTTGTCTATCT
1 TTATACATTTTTATCTATCT
*
113474 TTATGACATTTTTATTTATCT
1 TTAT-ACATTTTTATCTATCT
113495 TT
1 TT
113497 TGGCATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.63
Consensus pattern (20 bp):
TTATACATTTTTATCTATCT
Found at i:114381 original size:21 final size:19
Alignment explanation
Indices: 114343--114383 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
114333 TAAAATTAAT
*
114343 TATATTAATTTAAACAAAA
1 TATATTAATATAAACAAAA
114362 TATATTAATAATATAACAAAA
1 TATATTAAT-ATA-AACAAAA
114383 T
1 T
114384 GAAATTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATTAATATAAACAAAA
Found at i:114746 original size:15 final size:15
Alignment explanation
Indices: 114723--114753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
114713 AAATCAACTA
114723 ACTTCAACAATTAAG
1 ACTTCAACAATTAAG
*
114738 ACTTTAACAATTAAG
1 ACTTCAACAATTAAG
114753 A
1 A
114754 TTAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (15 bp):
ACTTCAACAATTAAG
Found at i:128670 original size:20 final size:21
Alignment explanation
Indices: 128645--128737 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
128635 TTTTCCCAAT
*
128645 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
128665 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
128686 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
128706 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
128727 TCGCAATGCGA
1 TCGCAATGCGA
128738 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:128690 original size:41 final size:41
Alignment explanation
Indices: 128645--128737 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
128635 TTTTCCCAAT
128645 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
128686 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
128727 TCGCAATGCGA
1 TCGCAATGCGA
128738 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:128750 original size:41 final size:41
Alignment explanation
Indices: 128664--128798 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
128654 GAATAAGTAA
** *
128664 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
128705 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
128746 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
128787 TTCGCAACGCGA
1 ATCGCAACGCGA
128799 TTCTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:128816 original size:20 final size:20
Alignment explanation
Indices: 128768--128820 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
128758 TAATACAAAA
* *
128768 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
128788 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
128808 TTGCAACGCGATT
1 TCGCAACGCGATT
128821 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:129378 original size:19 final size:19
Alignment explanation
Indices: 129354--129398 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
129344 GCAACGAGAT
*
129354 AATCGCAACACGAAATAAA
1 AATCGCAACACGAAACAAA
* *
129373 AATCGCAACGCGAAACCAA
1 AATCGCAACACGAAACAAA
129392 AATCGCA
1 AATCGCA
129399 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.13, T:0.09
Consensus pattern (19 bp):
AATCGCAACACGAAACAAA
Found at i:129416 original size:19 final size:19
Alignment explanation
Indices: 129394--129545 Score: 188
Period size: 19 Copynumber: 8.1 Consensus size: 19
129384 GAAACCAAAA
*
129394 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
129413 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
129432 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
129451 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
129471 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
**
129487 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
129504 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
129524 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
129544 TC
1 TC
129546 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
14 11 0.09
16 1 0.01
17 1 0.01
19 54 0.47
20 48 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:129471 original size:39 final size:38
Alignment explanation
Indices: 129394--129545 Score: 188
Period size: 39 Copynumber: 4.1 Consensus size: 38
129384 GAAACCAAAA
*
129394 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
129432 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
**
129471 TCGCGTTGCGATTTTC---T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
129504 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
129544 TC
1 TC
129546 AACCAAAAGA
Statistics
Matches: 98, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
33 14 0.14
34 15 0.15
36 1 0.01
38 22 0.22
39 31 0.32
40 15 0.15
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:129511 original size:20 final size:19
Alignment explanation
Indices: 129464--129545 Score: 75
Period size: 20 Copynumber: 4.5 Consensus size: 19
129454 CGGTTGCGAT
129464 TTTCATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
129483 TTTC---T--CGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
**
129497 AGTCATTTCCGCGTTGCGAT
1 TTTCATTT-CGCGTTGCGAT
* *
129517 TCTCATTATCTCGTTGCGAT
1 TTTCATT-TCGCGTTGCGAT
129537 TTTCATTTC
1 TTTCATTTC
129546 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 11 0.22
16 1 0.02
17 1 0.02
19 6 0.12
20 30 0.60
21 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTTCATTTCGCGTTGCGAT
Found at i:131604 original size:42 final size:42
Alignment explanation
Indices: 131544--131666 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
131534 GCCCGACTCG
* * *
131544 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
131586 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
131628 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
131667 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:131624 original size:21 final size:21
Alignment explanation
Indices: 131600--131666 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
131590 TCATTCCTCG
131600 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
131621 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
131642 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
131663 AGAG
1 AGAG
131667 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:133043 original size:14 final size:14
Alignment explanation
Indices: 133024--133059 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
133014 ATTGTTTAAT
133024 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
133038 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
133052 TGATTTGT
1 TGATTTGT
133060 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:133242 original size:19 final size:20
Alignment explanation
Indices: 133198--133237 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
133188 GCAACGAGAG
133198 AATCGCAACGCGAAAATAAA
1 AATCGCAACGCGAAAATAAA
*
133218 AATCGCAACGCGAAATTAAA
1 AATCGCAACGCGAAAATAAA
133238 TTCGCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.15, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAAAATAAA
Found at i:133284 original size:33 final size:32
Alignment explanation
Indices: 133242--133368 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
133232 ATTAAATTCG
*
133242 CGTTGCGATTTTCATTTTGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
133275 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
133308 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
133341 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
133369 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:133299 original size:19 final size:19
Alignment explanation
Indices: 133238--133368 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
133228 CGAAATTAAA
*
133238 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
133257 TTTGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
133273 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
133290 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
133304 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
133323 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
133339 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
133356 TTCGCATTGCGAT
1 TTCGCATTGCGAT
133369 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 23 0.28
16 12 0.15
17 13 0.16
19 34 0.41
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:133331 original size:66 final size:66
Alignment explanation
Indices: 133235--133367 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
133225 ACGCGAAATT
* *
133235 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
133300 G
66 G
*
133301 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
133366 G
66 G
133367 A
1 A
133368 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:135679 original size:12 final size:12
Alignment explanation
Indices: 135662--135686 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
135652 TCTTCGGGGA
135662 CTTTTTCTTCTT
1 CTTTTTCTTCTT
135674 CTTTTTCTTCTT
1 CTTTTTCTTCTT
135686 C
1 C
135687 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:137054 original size:14 final size:16
Alignment explanation
Indices: 137034--137107 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
137024 TGAAAATCGC
137034 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
137049 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
137066 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
137085 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
137101 -TTGCGAT
1 ATTGCGAT
137108 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:137071 original size:19 final size:19
Alignment explanation
Indices: 137030--137097 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
137020 GAAATGAAAA
137030 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
137046 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137063 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137082 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
137098 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:137073 original size:52 final size:52
Alignment explanation
Indices: 137011--137125 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
137001 AACGAGAAAA
* ***
137011 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
137063 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
137115 TCGCGTTGCGA
1 TCGCATTGCGA
137126 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:139151 original size:20 final size:19
Alignment explanation
Indices: 139120--139171 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
139110 CTTAAAATCA
*
139120 CAACGTGAAATGACTATCG
1 CAACGCGAAATGACTATCG
*
139139 CAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGACTATCG
*
139159 CAATGCGAAATGA
1 CAACGCGAAATGA
139172 AAATTGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (19 bp):
CAACGCGAAATGACTATCG
Found at i:139194 original size:14 final size:14
Alignment explanation
Indices: 139171--139228 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
139161 ATGCGAAATG
*
139171 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
139185 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
139201 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
139217 AAAATCGCAACG
1 AAAATCGCAACG
139229 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:139218 original size:32 final size:33
Alignment explanation
Indices: 139155--139233 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
139145 GGAAATGGCT
* *
139155 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
139188 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
139220 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
139234 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:139262 original size:19 final size:19
Alignment explanation
Indices: 139240--139336 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
139230 GAAACACAAA
139240 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
139259 TCGCGTTGCGATTTT--TT
1 TCGCATTGCGATTTTCATT
139276 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
139292 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
139308 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
139325 TCGCATTGCGAT
1 TCGCATTGCGAT
139337 AGCCATTCCG
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
14 9 0.14
15 9 0.14
16 9 0.14
17 9 0.14
18 9 0.14
19 21 0.32
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:139282 original size:15 final size:15
Alignment explanation
Indices: 139262--139320 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
139252 TTTCATTTCG
139262 CGTTGCGATTTTTTT
1 CGTTGCGATTTTTTT
*
139277 CGTTGCGATTTCATTT
1 CGTTGCGATTT-TTTT
*
139293 CGCATTGCGA-TTTTGT
1 CG--TTGCGATTTTTTT
139309 CGTTGCGATTTT
1 CGTTGCGATTTT
139321 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.16
15 14 0.38
16 9 0.24
17 2 0.05
18 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (15 bp):
CGTTGCGATTTTTTT
Found at i:139293 original size:33 final size:34
Alignment explanation
Indices: 139245--139336 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 34
139235 ACAAATCGCA
* *
139245 TTGCGATTTTCATTTCGCGTTGCGATTTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTTGTCG
139279 TTGCGA-TTTCATTTCGCATTGCGA-TTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTTGTCG
139311 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
139337 AGCCATTCCG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 13 0.24
33 35 0.65
34 6 0.11
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTTGTCG
Found at i:139343 original size:19 final size:19
Alignment explanation
Indices: 139321--139363 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
139311 TTGCGATTTT
139321 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* * *
139340 CATTCCGCGTTGCGATAGT
1 CATTTCGCATTGCGATAGC
139359 CATTT
1 CATTT
139364 TCGTGTTGCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:139881 original size:18 final size:18
Alignment explanation
Indices: 139855--139899 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
139845 GTCGATCAGA
*
139855 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
139873 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
139891 TGATGGCTC
1 TGATGGCTC
139900 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:141776 original size:20 final size:20
Alignment explanation
Indices: 141751--141844 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
141741 GATTATGTAT
141751 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
141771 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
141791 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
141812 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
141832 TATCGCATTGCGA
1 TATCGCGTTGCGA
141845 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:141845 original size:20 final size:19
Alignment explanation
Indices: 141731--141845 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
141721 CGCTTTGAAA
*
141731 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
141752 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* *
141772 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
141792 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
141813 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
141833 ATCGCATTGCGAT
1 ATCGCATTGCGAT
141846 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.06
20 48 0.62
21 23 0.29
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:141863 original size:21 final size:21
Alignment explanation
Indices: 141834--141909 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
141824 ATAGTCAGTA
141834 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
141855 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
141875 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
141896 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
141910 ACTTATTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:141864 original size:41 final size:41
Alignment explanation
Indices: 141773--141907 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
141763 AAAGTCAGTA
* * * ** *
141773 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
141813 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
141855 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
141896 TCGCGTTGCGAT
1 TCGCGTTGCGAT
141908 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:141878 original size:20 final size:20
Alignment explanation
Indices: 141853--141919 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
141843 GATTTTCCCA
141853 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
141873 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
141894 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
141914 ATTCGC
1 ATTCGC
141920 ATTACGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:141908 original size:41 final size:41
Alignment explanation
Indices: 141834--141922 Score: 178
Period size: 41 Copynumber: 2.2 Consensus size: 41
141824 ATAGTCAGTA
141834 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
141875 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
141916 TCGCATT
1 TCGCATT
141923 ACGAATTGCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:147080 original size:16 final size:16
Alignment explanation
Indices: 147059--147099 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
147049 TTTACTTTTA
147059 TCCGATTATTCGTTTC
1 TCCGATTATTCGTTTC
* *
147075 TCCGATTACTCTTTTC
1 TCCGATTATTCGTTTC
147091 TCCG-TTATT
1 TCCGATTATT
147100 TTCGATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.51
Consensus pattern (16 bp):
TCCGATTATTCGTTTC
Found at i:148678 original size:42 final size:42
Alignment explanation
Indices: 148619--148699 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
148609 CGTAATTCAT
148619 TGTTTTCCCGCGTTTGTTTCACGTAATTCGTTTTTCGGAAAA
1 TGTTTTCCCGCGTTTGTTTCACGTAATTCGTTTTTCGGAAAA
* *
148661 TGTTTTCCCGTGTTTGTTTCACGTAATTGGTTTTTCGGA
1 TGTTTTCCCGCGTTTGTTTCACGTAATTCGTTTTTCGGA
148700 TGTAATTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (42 bp):
TGTTTTCCCGCGTTTGTTTCACGTAATTCGTTTTTCGGAAAA
Found at i:148967 original size:30 final size:32
Alignment explanation
Indices: 148901--148980 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
148891 ATTATTTATT
148901 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
148932 TATTATATTT-TTAATA-TTAT-ATAA-ATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
148960 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
148981 AAGTTATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 12 0.29
31 11 0.26
32 10 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:149092 original size:23 final size:23
Alignment explanation
Indices: 149064--149114 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
149054 ATGTTTAAAT
*
149064 AATATTTTAATAAAGATATTTAA
1 AATATTCTAATAAAGATATTTAA
* * *
149087 AATATTCTAATTAATATTTTTAA
1 AATATTCTAATAAAGATATTTAA
149110 AATAT
1 AATAT
149115 AATATAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATTCTAATAAAGATATTTAA
Found at i:149221 original size:29 final size:32
Alignment explanation
Indices: 149155--149224 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 32
149145 AATATAATTT
*
149155 ATAATA-TTTTATTTCACTAAAATATACAAAA
1 ATAATATTTTTATTTCAATAAAATATACAAAA
*
149186 ATTAATATTTTTA-TT-AATAAAAT-TATAAAA
1 A-TAATATTTTTATTTCAATAAAATATACAAAA
149216 ATAATATTT
1 ATAATATTT
149225 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 8 0.23
30 7 0.20
31 8 0.23
32 7 0.20
33 5 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (32 bp):
ATAATATTTTTATTTCAATAAAATATACAAAA
Found at i:149470 original size:20 final size:20
Alignment explanation
Indices: 149430--149471 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
149420 TTTACAGAAA
**
149430 TCATTTTCCAGAAATGTAAT
1 TCATTTTCCAGAAATCAAAT
*
149450 TCATTTTCCAGAATTCAAAT
1 TCATTTTCCAGAAATCAAAT
149470 TC
1 TC
149472 CAATTATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (20 bp):
TCATTTTCCAGAAATCAAAT
Found at i:149473 original size:34 final size:34
Alignment explanation
Indices: 149407--149473 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
149397 TTTTTCAGAA
**
149407 AAATGTAATTCATTTTACAGAAATCATTTTCCAG
1 AAATGTAATTCATTTTACAGAAATCAAATTCCAG
* *
149441 AAATGTAATTCATTTTCCAGAATTCAAATTCCA
1 AAATGTAATTCATTTTACAGAAATCAAATTCCA
149474 ATTATTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.37
Consensus pattern (34 bp):
AAATGTAATTCATTTTACAGAAATCAAATTCCAG
Found at i:158441 original size:23 final size:22
Alignment explanation
Indices: 158355--158473 Score: 102
Period size: 23 Copynumber: 5.3 Consensus size: 22
158345 GTTGAGGTTT
***
158355 CTATGTGGTCCTTTAAGACAAA
1 CTATGTGGTCCTTCGGGACAAA
158377 CCTATGTGGTCCTTCGGGACAAAA
1 -CTATGTGGTCCTTCGGGAC-AAA
158401 CTATGTGGT-CTTCCGGGACAAA
1 CTATGTGGTCCTT-CGGGACAAA
* *
158423 GCTATGTGGTTCTTTGGGACAAA
1 -CTATGTGGTCCTTCGGGACAAA
158446 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTC-CTTCGG-GACAAA
*
158467 TTATGTG
1 CTATGTG
158474 AGTTGTGGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
21 16 0.19
22 13 0.16
23 48 0.58
24 6 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:163814 original size:24 final size:24
Alignment explanation
Indices: 163787--163834 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
163777 TTGGGTTATT
163787 GGAAGGGCATTATGATCTTTTCAA
1 GGAAGGGCATTATGATCTTTTCAA
* *
163811 GGAAGGGTATTATGGTCTTTTCAA
1 GGAAGGGCATTATGATCTTTTCAA
163835 ATAAAGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.35
Consensus pattern (24 bp):
GGAAGGGCATTATGATCTTTTCAA
Found at i:165197 original size:23 final size:23
Alignment explanation
Indices: 165148--165223 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 23
165138 GTTGAGGGTT
* *
165148 CTATGTGGTCATTTGAGACAAAC
1 CTATGTGGTCATTCGAGACAAAA
* * *
165171 CTATTTGGTCATTCGGGATAAAA
1 CTATGTGGTCATTCGAGACAAAA
* *
165194 CTATGTGGTCCTTCAAGAC-AAA
1 CTATGTGGTCATTCGAGACAAAA
165216 -TATGTGGT
1 CTATGTGGT
165224 ACTTCGATGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 8 0.19
22 3 0.07
23 32 0.74
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (23 bp):
CTATGTGGTCATTCGAGACAAAA
Found at i:165236 original size:21 final size:22
Alignment explanation
Indices: 165195--165243 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
165185 GGGATAAAAC
*
165195 TATGTGGTCCTTCAAGACAAA-
1 TATGTGGTACTTCAAGACAAAT
*
165216 TATGTGGTACTTCGATG-CAAAT
1 TATGTGGTACTTC-AAGACAAAT
165238 TATGTG
1 TATGTG
165244 AGCTATGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (22 bp):
TATGTGGTACTTCAAGACAAAT
Found at i:166032 original size:30 final size:30
Alignment explanation
Indices: 165996--166057 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
165986 TCTTAAATTT
* *
165996 TTTAGGGATTAAATTGAAATT-TTAGTTAAA
1 TTTAGGGACTAAAAT-AAATTCTTAGTTAAA
*
166026 TTTAGGGACTAAAATAAATTCTTATTTAAA
1 TTTAGGGACTAAAATAAATTCTTAGTTAAA
166056 TT
1 TT
166058 CAGATCCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTAGGGACTAAAATAAATTCTTAGTTAAA
Found at i:169251 original size:24 final size:23
Alignment explanation
Indices: 169210--169256 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
169200 CTCATTATTC
*
169210 TTCTTATTTTTGTTTTCTTCATT
1 TTCTTATTTTTGTATTCTTCATT
169233 TTCTTATTCTTTGTATTCTTCATT
1 TTCTTATT-TTTGTATTCTTCATT
169257 CTTTACCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.70
Consensus pattern (23 bp):
TTCTTATTTTTGTATTCTTCATT
Found at i:171585 original size:31 final size:32
Alignment explanation
Indices: 171527--171586 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
171517 ATTAAATATT
* * *
171527 TTGATTTCATGATATTTGTTTTTCCGTATGCA
1 TTGATTTCATGATATCTGATTTACCGTATGCA
171559 TTGATTTC-TGATATCTGATTTACCGTAT
1 TTGATTTCATGATATCTGATTTACCGTAT
171587 ACTTTTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (32 bp):
TTGATTTCATGATATCTGATTTACCGTATGCA
Found at i:177335 original size:56 final size:56
Alignment explanation
Indices: 177269--177376 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
177259 ACTTAGGCTT
*
177269 ATTTTAATGTTTCTGCTACAAAACTGATGCTATGACATTGTTAATCTTGTAGTCTG
1 ATTTTAATGTTTCTACTACAAAACTGATGCTATGACATTGTTAATCTTGTAGTCTG
* * * * *
177325 ATTTTAATGTTTCTATTACAAAACTGATGTTGTGACTTTGTTAATGTTGTAG
1 ATTTTAATGTTTCTACTACAAAACTGATGCTATGACATTGTTAATCTTGTAG
177377 CCGTTGCTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (56 bp):
ATTTTAATGTTTCTACTACAAAACTGATGCTATGACATTGTTAATCTTGTAGTCTG
Found at i:179745 original size:18 final size:18
Alignment explanation
Indices: 179722--179756 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
179712 ATCCACAAAA
*
179722 ACAACATTGCAATCAGCC
1 ACAACATTACAATCAGCC
179740 ACAACATTACAATCAGC
1 ACAACATTACAATCAGC
179757 AGTAGACGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (18 bp):
ACAACATTACAATCAGCC
Found at i:182360 original size:86 final size:86
Alignment explanation
Indices: 182215--182386 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
182205 CTCAAGTTGC
182215 CCGAAATTGGCTCTAGTGAAAAAAGAGAAAAAAAGAAGAAAAAATACTTTCCAAATTTCCAATGT
1 CCGAAATTGGCTCTAGTGAAAAAAGAGAAAAAAAGAAGAAAAAATACTTTCCAAATTTCCAATGT
182280 AATACCCCAAATTTTGGACTA
66 AATACCCCAAATTTTGGACTA
182301 CCGAAATTGGCTCTAGTGAAAAAAGAGAAAAAAAGAAGAAAAAATACTTTCCAAATTTCCAATGT
1 CCGAAATTGGCTCTAGTGAAAAAAGAGAAAAAAAGAAGAAAAAATACTTTCCAAATTTCCAATGT
*
182366 TATACCCCAAATTTTGGACTA
66 AATACCCCAAATTTTGGACTA
182387 GACTAAAATA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (86 bp):
CCGAAATTGGCTCTAGTGAAAAAAGAGAAAAAAAGAAGAAAAAATACTTTCCAAATTTCCAATGT
AATACCCCAAATTTTGGACTA
Found at i:189423 original size:20 final size:20
Alignment explanation
Indices: 189398--189436 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
189388 TACAAGTATC
189398 GATACTACAAGAACAATATT
1 GATACTACAAGAACAATATT
*
189418 GATACTATAAGAACAATAT
1 GATACTACAAGAACAATAT
189437 CATTAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (20 bp):
GATACTACAAGAACAATATT
Found at i:203449 original size:18 final size:18
Alignment explanation
Indices: 203426--203460 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
203416 ATGAAAGGAG
203426 TAAGAATCAACAAAAAAA
1 TAAGAATCAACAAAAAAA
203444 TAAGAATCAACAAAAAA
1 TAAGAATCAACAAAAAA
203461 TGAATAGAAA
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:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (18 bp):
TAAGAATCAACAAAAAAA
Found at i:211255 original size:2 final size:2
Alignment explanation
Indices: 211248--211273 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
211238 TAACGTGAAA
211248 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
211274 TTGAGTAAAA
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):
AT
Found at i:215006 original size:44 final size:45
Alignment explanation
Indices: 214923--215009 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
214913 TCATACTTAT
* *
214923 AATGCCCCATTATGCATTTTCATTTATGGCATTATTTCATGCCAA
1 AATGCCCCATTATGCATTTTCATTGATGGCATCATTTCATGCCAA
*
214968 AATGCACCCATT-TGCATTTT-ATTGATGGCATCCTTTCATGCC
1 AATGC-CCCATTATGCATTTTCATTGATGGCATCATTTCATGCC
215010 TTTTTTACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 19 0.50
45 13 0.34
46 6 0.16
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (45 bp):
AATGCCCCATTATGCATTTTCATTGATGGCATCATTTCATGCCAA
Found at i:215031 original size:45 final size:45
Alignment explanation
Indices: 214929--215096 Score: 160
Period size: 45 Copynumber: 3.7 Consensus size: 45
214919 TTATAATGCC
* ** *** *
214929 CCATTATGCATTTTCATTTATGGCATTATTTCATGCC-AAAATGCA
1 CCATTATACA-TTTCATTTATGGCATCCTTTCATGCCTTTTATACA
* * * *
214974 CCCATT-TGCATTTTATTGATGGCATCCTTTCATGCCTTTTTTACA
1 -CCATTATACATTTCATTTATGGCATCCTTTCATGCCTTTTATACA
* * * *
215019 CCGTTATACATTTCCTTTATGGAATCCATTCATGCCTTTTATACA
1 CCATTATACATTTCATTTATGGCATCCTTTCATGCCTTTTATACA
*
215064 CTATTATACATTTCATTTATGGCATCCTTTCAT
1 CCATTATACATTTCATTTATGGCATCCTTTCAT
215097 ACCCATTATG
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
44 26 0.27
45 67 0.68
46 5 0.05
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.44
Consensus pattern (45 bp):
CCATTATACATTTCATTTATGGCATCCTTTCATGCCTTTTATACA
Found at i:215151 original size:46 final size:46
Alignment explanation
Indices: 215074--215247 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 46
215064 CTATTATACA
* * * * *
215074 TTTCATTTATGGCATCCTTTCATACCCATTATGTATTGTTTATGTT
1 TTTCCTTTATGACATCCATTCATACCAATTATGTATTGTTTACGTT
* *
215120 TTTCCTTTATGACATTCATTCATACCGATTATGTATTGTTTACGTT
1 TTTCCTTTATGACATCCATTCATACCAATTATGTATTGTTTACGTT
* *
215166 TTTCCTTTATGACATCCATTCATACCAATTATGCATTGTTGTACATT
1 TTTCCTTTATGACATCCATTCATACCAATTATGTATTGTT-TACGTT
* * * *
215213 TTATATCTATATGACATCCTTTCATACCACTTATG
1 TT-T-CCTTTATGACATCCATTCATACCAATTATG
215248 CACCGTTTAT
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
46 77 0.69
47 7 0.06
48 1 0.01
49 26 0.23
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.48
Consensus pattern (46 bp):
TTTCCTTTATGACATCCATTCATACCAATTATGTATTGTTTACGTT
Found at i:215386 original size:81 final size:81
Alignment explanation
Indices: 215279--215844 Score: 642
Period size: 81 Copynumber: 7.0 Consensus size: 81
215269 TTATAATTCC
* * * * * *
215279 TTTAGTCTTTTACCCAAAGG-CATTTAACCTTTCATCTAACTTGCTTGATTGACACTTTTCTGCC
1 TTTA-TCTTTTACTCAACGGTC-TTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGCC
* *
215343 AAATGCATAGTTAGGCCA
64 AAATGCACAGCTAGGCCA
* * *
215361 TTTATCTTTTACTCAACGGTCTTTAACTGTTCATCT-A-TATGACATAATTGATACCTTTCTACC
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-TG-CATAATTGACACCTTTCTGCC
* *
215424 AAATACACAGCTAGGTCA
64 AAATGCACAGCTAGGCCA
* * *
215442 TTTATCTTTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGCCAA
215507 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * * *
215523 TTTATCTTTAAATCAACGGTCTTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCAAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGCCAA
** * * **
215588 ATAAATAACTACTCCA
66 ATGCACAGCTAGGCCA
* * * *
215604 TTTATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTAT-CATAATTGACACCTTTTTTTCC
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-TGCATAATTGACACC-TTTCTGCC
* *
215668 AAATGCACAACAAGGCCA
64 AAATGCACAGCTAGGCCA
* * *
215686 TTTATCTTTCACTCAATGGTCTTTAACCGTTCATCTAA-TTGGCATAATTGACACCTTTCTACCA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTT-GCATAATTGACACCTTTCTGCCA
* *
215750 AAAGCACAACTAGGCCA
65 AATGCACAGCTAGGCCA
* *
215767 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAAC-TGCATAATTGACACTTTTCTGTC-A
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGCCAA
* *
215830 ATACACAGTTAGGCC
66 ATGCACAGCTAGGCC
215845 TCAAAGGCAC
Statistics
Matches: 409, Mismatches: 65, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
79 13 0.03
80 23 0.06
81 301 0.74
82 71 0.17
83 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (81 bp):
TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGCCAA
ATGCACAGCTAGGCCA
Found at i:215773 original size:244 final size:241
Alignment explanation
Indices: 215301--215826 Score: 730
Period size: 244 Copynumber: 2.2 Consensus size: 241
215291 CCCAAAGGCA
* * * * * ** ** **
215301 TTTAACCTTTCATCTAACTTGCTTGATTGACACTTTTCTGCCAAATGCATAGTTAGGCCATTTAT
1 TTTAACCGTTCATCTAAC-TGCATAATTGACACCTTTCTGCAAAATAAATAACTACTCCATTTAT
* *
215366 CTTTTACTCAACGGTCTTTAACTGTTCATCTATATGACATAATTGATACCTTTCTACCAAATACA
65 CTTTTACTCAACAGTCTTTAACTGTTCATCTATAT-ACATAATTGACACCTTTCTACCAAATACA
* * * *
215431 CAGCTAGGTCATTTATCTTTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACAC
129 CAACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACAC
* * *
215496 CTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTAAATCAACGGTC
194 CTTTCTACCAAAAGCACAACTAGGCCATTTATCTTTAAATCAACGGTC
*
215544 TTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCAAAATAAATAACTACTCCATTTAT
1 TTTAACCGTTCATCTAACT-GCATAATTGACACCTTTCTGCAAAATAAATAACTACTCCATTTAT
* * *
215609 CTTTTACTCAACAGTCTTTAACTGTTCATCTA-ACTATCATAATTGACACCTTTTTTTCCAAATG
65 CTTTTACTCAACAGTCTTTAACTGTTCATCTATA-TA-CATAATTGACACC-TTTCTACCAAATA
* *
215673 CACAACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCGTTCATCTAATTGGCATAATTGAC
127 CACAACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGAC
* *
215738 ACCTTTCTACCAAAAGCACAACTAGGCCATTTATCTTTTACTCAACGGTC
192 ACCTTTCTACCAAAAGCACAACTAGGCCATTTATCTTTAAATCAACGGTC
*
215788 TTTAACCGTTCATCTAACTGCATAATTGACACTTTTCTG
1 TTTAACCGTTCATCTAACTGCATAATTGACACCTTTCTG
215827 TCAATACACA
Statistics
Matches: 249, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
242 3 0.01
243 114 0.46
244 132 0.53
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (241 bp):
TTTAACCGTTCATCTAACTGCATAATTGACACCTTTCTGCAAAATAAATAACTACTCCATTTATC
TTTTACTCAACAGTCTTTAACTGTTCATCTATATACATAATTGACACCTTTCTACCAAATACACA
ACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACCT
TTCTACCAAAAGCACAACTAGGCCATTTATCTTTAAATCAACGGTC
Found at i:216059 original size:67 final size:67
Alignment explanation
Indices: 215796--216046 Score: 360
Period size: 67 Copynumber: 3.8 Consensus size: 67
215786 TCTTTAACCG
215796 TTCATCTAACT-GCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
215860 CT
66 CT
* * * * *
215862 TTCATCTAACTGGCATAATTGACATTTTTCAGTCAATAAACAGTTATGTCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
215927 CT
66 CT
* ** * * * *
215929 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGTACAGTGAGGCCTTAAAGGCATTTATC
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
215994 CT
66 CT
* * *
215996 TTCATTTAACTGGTATAATTGACACTTTTCTGTCAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCT
216047 TATAAACTTT
Statistics
Matches: 163, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 11 0.07
67 152 0.93
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:216749 original size:19 final size:20
Alignment explanation
Indices: 216680--216750 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
216670 TGGCTCCTCA
* * *
216680 GTATCGATATTCGTACCATG
1 GTATCGATACTCATACTATG
216700 GTATCGATACTACTATACTATG
1 GTATCGATACT-C-ATACTATG
*
216722 TTA-CTGATACTC-TACTATG
1 GTATC-GATACTCATACTATG
216741 GTATCGATAC
1 GTATCGATAC
216751 CATTTTTGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 14 0.33
20 11 0.26
21 3 0.07
22 14 0.33
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
GTATCGATACTCATACTATG
Found at i:220650 original size:32 final size:32
Alignment explanation
Indices: 220609--220680 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
220599 TCATGGCATT
**
220609 CTTTCATGCCTTTTTTACAAGATTATACATTTC
1 CTTT-ATGCCTTTTACACAAGATTATACATTTC
**
220642 CTTTATGCCTTTTACACACTATTATACATTTC
1 CTTTATGCCTTTTACACAAGATTATACATTTC
*
220674 ATTTATG
1 CTTTATG
220681 GCATTCTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.49
Consensus pattern (32 bp):
CTTTATGCCTTTTACACAAGATTATACATTTC
Found at i:220947 original size:81 final size:80
Alignment explanation
Indices: 220829--221311 Score: 523
Period size: 81 Copynumber: 6.0 Consensus size: 80
220819 TTATAATTCC
* * *
220829 TTTAGTCTTTTACTCAAAGG-CATTTAA-CATCTCATCTAACTTGAGTGATTGACACTTTTCTGC
1 TTTA-TCTTTTACTCAACGGTC-TTTAACCGT-TCATCTAACTTGA-TAATTGACACTTTTCTGC
* *
220892 CAAATTCACAGTTAGGCCA
62 CAAATGCACAGCTAGGCCA
* * * *
220911 TTTATATTTTACTCAACGGTTTTTAACCGTTCATCTAA-TTGGCATAATTAACACCTTTT-TGTC
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTT-G-ATAATTGACA-CTTTTCTGCC
*
220974 AAATGCACATCTAGGCCA
63 AAATGCACAGCTAGGCCA
* * * * * *
220992 TTTATATTTTACTCAACGATCTTTAACCGTGCATCTAACTGGCATAA-TGTACACATTTCTACCA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTG-ATAATTG-ACACTTTTCTGCCA
221056 AATGCACAGCTAGGCCA
64 AATGCACAGCTAGGCCA
* * * * *
221073 TTTATCTTTTACTCAACGGTCTTTAACTGTTCATCTGACTGGCATAATTGACACATTTCTGCTAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTG-ATAATTGACACTTTTCTGCCAA
* *
221138 ATACACAGCTAGGTCA
65 ATGCACAGCTAGGCCA
* * *
221154 TTTATCTTTTACTCAATGGTCTTTAACCGTTCATCTAAC-TGACATAATTGCCACCTTTCTGCCA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTG--ATAATTGACACTTTTCTGCCA
*
221218 AATGCACACCTAGGCCA
64 AATGCACAGCTAGGCCA
* *
221235 TTTATCCTTTACTCAACGGTCTTTAACCGTTCATCTAACTAT-ATAATTGACACTTTTCTGTC-A
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-TGATAATTGACACTTTTCTGCCAA
*
221298 ATGCACAGTTAGGC
65 ATGCACAGCTAGGC
221312 ATCAAAGGAA
Statistics
Matches: 344, Mismatches: 45, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
79 13 0.04
80 25 0.07
81 290 0.84
82 15 0.04
83 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (80 bp):
TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGATAATTGACACTTTTCTGCCAAA
TGCACAGCTAGGCCA
Found at i:221516 original size:67 final size:67
Alignment explanation
Indices: 221264--221514 Score: 335
Period size: 67 Copynumber: 3.8 Consensus size: 67
221254 TCTTTAACCG
** * * *
221264 TTCATCTAACT-ATATAATTGACACTTTTCTGTCAATGCACAGTTAGGCATCAAAGGAACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
221328 CT
66 CT
* * *
221330 TTCATCTAACTGGCATAATTGATACCTTTCTGTCAATGCAAAGTTAGGCCTCAACGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
221395 CT
66 CT
* * * * *
221397 TTCCTCTAACTCGCATAATTGACACATTTCT-TCCAATGCACAGTTAGGCCTTAAAGGCACTTGG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGT-CAATGCACAGTTAGGCCTCAAAGGCACTTAG
221461 CCT
65 CCT
* * *
221464 GTCATCTAATTGGCATAATTGACACCTTTCTGTCAATGCACAGTTATGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCT
221515 TATAATCTTT
Statistics
Matches: 160, Mismatches: 22, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
66 12 0.08
67 147 0.92
68 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:221785 original size:57 final size:57
Alignment explanation
Indices: 221724--221832 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
221714 GTTATTAGAC
*
221724 GGAAATTCATAAACAAATTATGAATTTCTTAACTCTTTGCACACTCAGTGCCCATAT
1 GGAAATTCATAAACAAATTATGAATTTCTTAACTCTTTGCACACTAAGTGCCCATAT
* * *
221781 GGAAATTGATAAACAAATTATGAATTTCTTAACTTTTTGCGCACTAAGTGCC
1 GGAAATTCATAAACAAATTATGAATTTCTTAACTCTTTGCACACTAAGTGCC
221833 ATTATGTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (57 bp):
GGAAATTCATAAACAAATTATGAATTTCTTAACTCTTTGCACACTAAGTGCCCATAT
Found at i:222147 original size:22 final size:20
Alignment explanation
Indices: 222117--222175 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 20
222107 TTCTAAAACA
*
222117 ATACCATGGTATCGATACTAC
1 ATACTATGGTATCGATACT-C
222138 TATACTATGGTATCGATACTC
1 -ATACTATGGTATCGATACTC
222159 -TACTATGGTATCGATAC
1 ATACTATGGTATCGATAC
222176 CATTTTTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 17 0.47
21 1 0.03
22 18 0.50
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (20 bp):
ATACTATGGTATCGATACTC
Found at i:226530 original size:20 final size:19
Alignment explanation
Indices: 226486--226858 Score: 234
Period size: 20 Copynumber: 18.5 Consensus size: 19
226476 AATGACCAAC
226486 AAAATCGCAACGCGATATC-
1 AAAATCGCAACGCGAT-TCA
*
226505 AAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGATTCA
* **
226524 GAAAATCGCAACGTTGA-AAA
1 -AAAATCGCAACG-CGATTCA
*
226544 GAAAATCGCAACGGTCGA--AA
1 -AAAATCGCAAC-G-CGATTCA
226564 GAAAATCGCAACGCGATCTTCCA
1 -AAAATCGCAACGCGA--TT-CA
* * *
226587 AGAATCGCAATGCGATCCA
1 AAAATCGCAACGCGATTCA
* *
226606 AAGAATCGCAATGCGATCCA
1 AA-AATCGCAACGCGATTCA
* *
226626 AAGAATCGCAATGCGATCCA
1 AA-AATCGCAACGCGATTCA
* **
226646 AAGAATCGCAATGCGAGCCA
1 AA-AATCGCAACGCGATTCA
*
226666 AAGAATCGCAATGCGATTCCA
1 AA-AATCGCAACGCGATT-CA
* *
226687 AGAATCGCAATGCGATTCCA
1 AAAATCGCAACGCGATT-CA
* *
226707 AGAATCGCAATGCGATCTTCGA
1 AAAATCGCAACGCGA--TTC-A
*
226729 AGAATCGCAACGCGA-TCGA
1 AAAATCGCAACGCGATTC-A
226748 GAAAATCGCAACGCGATTCCA
1 -AAAATCGCAACGCGATT-CA
* *
226769 ATAATCGCAACGCGATTGA
1 AAAATCGCAACGCGATTCA
226788 GAAAATCGCAACGCGATTCCA
1 -AAAATCGCAACGCGATT-CA
* *
226809 AGAATCGCAACGCGATTGA
1 AAAATCGCAACGCGATTCA
*
226828 GAAAATCGCAATGCGATTCCA
1 -AAAATCGCAACGCGATT-CA
*
226849 AGAATCGCAA
1 AAAATCGCAA
226859 AACGGCAAAA
Statistics
Matches: 307, Mismatches: 26, Indels: 41
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.01
19 26 0.08
20 231 0.75
21 14 0.05
22 31 0.10
23 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACGCGATTCA
Found at i:226639 original size:40 final size:40
Alignment explanation
Indices: 226567--226858 Score: 326
Period size: 40 Copynumber: 7.2 Consensus size: 40
226557 GTCGAAAGAA
*
226567 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-TCCAAAG
1 AATCGCAACGCGATC--CAAAGAATCGCAATGCGATTCC-AAG
*
226609 AATCGCAATGCGATCCAAAGAATCGCAATGCGA-TCCAAAG
1 AATCGCAACGCGATCCAAAGAATCGCAATGCGATTCC-AAG
* *
226649 AATCGCAATGCGAGCCAAAGAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATCCAAAGAATCGCAATGCGATTCCAAG
* *
226689 AATCGCAATGCGATTCC-AAGAATCGCAATGCGATCTTCGAAG
1 AATCGCAACGCGA-TCCAAAGAATCGCAATGCGA--TTCCAAG
* * *
226731 AATCGCAACGCGATCGAGAA-AATCGCAACGCGATTCCAAT
1 AATCGCAACGCGATCCA-AAGAATCGCAATGCGATTCCAAG
** *
226771 AATCGCAACGCGATTGAGAA-AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATCCA-AAGAATCGCAATGCGATTCCAAG
**
226811 AATCGCAACGCGATTGAGAA-AATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATCCA-AAGAATCGCAATGCGATTCCAAG
226851 AATCGCAA
1 AATCGCAA
226859 AACGGCAAAA
Statistics
Matches: 231, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
40 178 0.77
41 7 0.03
42 44 0.19
43 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (40 bp):
AATCGCAACGCGATCCAAAGAATCGCAATGCGATTCCAAG
Found at i:226668 original size:60 final size:59
Alignment explanation
Indices: 226567--226858 Score: 304
Period size: 60 Copynumber: 4.8 Consensus size: 59
226557 GTCGAAAGAA
*
226567 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATCCAAAGAATCGCAATGCGA-TCCAAAG
1 AATCGCAACGCGA---TCCAAGAATCGCAATGCGATCCAAAGAATCGCAACGCGATTCC-AAG
* * *
226629 AATCGCAATGCGATCCAAAGAATCGCAATGCGAGCCAAAGAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATCC-AAGAATCGCAATGCGATCCAAAGAATCGCAACGCGATTCCAAG
* * * *
226689 AATCGCAATGCGATTCCAAGAATCGCAATGCGATCTTCGAAGAATCGCAACGCGA-TCGAGAA
1 AATCGCAACGCGA-TCCAAGAATCGCAATGCGATC--CAAAGAATCGCAACGCGATTCCA-AG
* * **
226751 AATCGCAACGCGATTCCAATAATCGCAACGCGATTGAGAA-AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGA-TCCAAGAATCGCAATGCGATCCA-AAGAATCGCAACGCGATTCCAAG
** *
226811 AATCGCAACGCGATTGAGAAAATCGCAATGCGATTCC-AAGAATCGCAA
1 AATCGCAACGCGATCCA-AGAATCGCAATGCGA-TCCAAAGAATCGCAA
226859 AACGGCAAAA
Statistics
Matches: 198, Mismatches: 21, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
59 7 0.04
60 116 0.59
61 15 0.08
62 60 0.30
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (59 bp):
AATCGCAACGCGATCCAAGAATCGCAATGCGATCCAAAGAATCGCAACGCGATTCCAAG
Found at i:226979 original size:6 final size:6
Alignment explanation
Indices: 226968--227007 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
226958 AGACACGTAT
226968 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
227008 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:227760 original size:5 final size:5
Alignment explanation
Indices: 227750--227778 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
227740 CCGCCGCCGC
227750 CGTCT CGTCT CGTCT CGTCT CGTCT CGTC
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTC
227779 GTGGTCGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.21, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:227787 original size:6 final size:6
Alignment explanation
Indices: 227776--227819 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
227766 GTCTCGTCTC
227776 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
227820 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:227961 original size:22 final size:20
Alignment explanation
Indices: 227943--227998 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
227933 CGATTCTTGG
*
227943 AATCGCGTTGCGATTTTCTC
1 AATCGCATTGCGATTTTCTC
*
227963 AATCGCATTGCGATTTT-TG
1 AATCGCATTGCGATTTTCTC
**
227982 TTTCGCATTGCGATTTT
1 AATCGCATTGCGATTTT
227999 GTTGGTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.45
Consensus pattern (20 bp):
AATCGCATTGCGATTTTCTC
Found at i:229967 original size:20 final size:21
Alignment explanation
Indices: 229907--229971 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
229897 GTTTCGTTAT
*
229907 TCTACTTTCTAAAAAATAATCA
1 TCTACTTT-TAAAAAAAAATCA
*
229929 ACTACTTTTAAAAAGAAAATCA
1 TCTACTTTTAAAAA-AAAATCA
*
229951 TCTTC-TTTAAAAAAAAATCA
1 TCTACTTTTAAAAAAAAATCA
229971 T
1 T
229972 GACCTTGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.21
21 14 0.37
22 16 0.42
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (21 bp):
TCTACTTTTAAAAAAAAATCA
Found at i:230412 original size:38 final size:38
Alignment explanation
Indices: 230363--230439 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
230353 GTTATTTAAG
** *
230363 ATAAATATTAGTACAATGGTTAATGAAAGATGTTCAAA
1 ATAAATATTAGTACAATAATTAATGAAAGATGTTAAAA
230401 ATAAATATTAGTACAATAATTAATGAAAGATGTTAAAA
1 ATAAATATTAGTACAATAATTAATGAAAGATGTTAAAA
230439 A
1 A
230440 ATTTTGATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.31
Consensus pattern (38 bp):
ATAAATATTAGTACAATAATTAATGAAAGATGTTAAAA
Done.