Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1896
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: 235474
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 1 of 2
Found at i:9802 original size:17 final size:19
Alignment explanation
Indices: 9768--9814 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
9758 TATGCATGGT
*
9768 AAATAATAAAAGTTAACAA
1 AAATAATAAAAGTAAACAA
9787 AAATAA-AAAA-TAAACAA
1 AAATAATAAAAGTAAACAA
*
9804 ACAAGAATAAA
1 A-AATAATAAA
9815 GACATTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.15
Consensus pattern (19 bp):
AAATAATAAAAGTAAACAA
Found at i:10273 original size:14 final size:14
Alignment explanation
Indices: 10256--10293 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
10246 ATAAGCACAT
10256 ATATAAAAATAATA
1 ATATAAAAATAATA
*
10270 ATATAATAATAATA
1 ATATAAAAATAATA
10284 A-ATAATAAAT
1 ATATAA-AAAT
10294 GAGCAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAAAAATAATA
Found at i:10279 original size:11 final size:10
Alignment explanation
Indices: 10258--10291 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
10248 AAGCACATAT
10258 ATAA-AAATA
1 ATAATAAATA
10267 ATAATATAATA
1 ATAATA-AATA
10278 ATAATAAATA
1 ATAATAAATA
10288 ATAA
1 ATAA
10292 ATGAGCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.17
10 9 0.39
11 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATAAATA
Found at i:16816 original size:19 final size:19
Alignment explanation
Indices: 16792--16829 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16782 AATTCTTCAG
16792 TTACTTTCATGGATTCAAC
1 TTACTTTCATGGATTCAAC
16811 TTACTTTCATGGATTCAAC
1 TTACTTTCATGGATTCAAC
16830 ATTGGAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (19 bp):
TTACTTTCATGGATTCAAC
Found at i:18549 original size:38 final size:40
Alignment explanation
Indices: 18477--18559 Score: 125
Period size: 38 Copynumber: 2.1 Consensus size: 40
18467 ATATTTTAGC
*
18477 AGTAGTTTATTTATGTTAAAAGTTTATTTTGTATTAAGGTT
1 AGTAGTTTATTTATGTT-AAAGTTTATTTAGTATTAAGGTT
*
18518 AGTA-TTTATTTTTGTT-AAGTTTATTTAGTATTAAGGTT
1 AGTAGTTTATTTATGTTAAAGTTTATTTAGTATTAAGGTT
18556 AGTA
1 AGTA
18560 CTAATTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 25 0.62
40 11 0.28
41 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (40 bp):
AGTAGTTTATTTATGTTAAAGTTTATTTAGTATTAAGGTT
Found at i:18556 original size:22 final size:22
Alignment explanation
Indices: 18496--18556 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 22
18486 TTTATGTTAA
*
18496 AAGTTTATTTTGTATTAAGGTT
1 AAGTTTATTTAGTATTAAGGTT
**
18518 -AG--TATTTA-T-TT-TTGTT
1 AAGTTTATTTAGTATTAAGGTT
18534 AAGTTTATTTAGTATTAAGGTT
1 AAGTTTATTTAGTATTAAGGTT
18556 A
1 A
18557 GTACTAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 12
0.62 0.11 0.27
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 1 0.04
19 11 0.39
20 1 0.04
21 4 0.14
22 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (22 bp):
AAGTTTATTTAGTATTAAGGTT
Found at i:25957 original size:47 final size:46
Alignment explanation
Indices: 25847--26164 Score: 216
Period size: 47 Copynumber: 6.7 Consensus size: 46
25837 TATTTGTGTA
*
25847 CCAGTGTAAGACATGTCTAGGACAT-GCATCGGCCAT-ATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGGCATCGG-CATGA-TATGAGAG
* * * *
25893 CCAGTATAAGACCATGTCTGGGAGATGGCATCAGCATTGATACGAGAG
1 CCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCA-TGATATGAGAG
* * *
25941 CTAGTGTAAGACATGTCTGGGACAT-GCATCGGCACG-TATAGAGGTG
1 CCAGTGTAAGACATGTCTGGGACATGGCATCGGCATGATAT-GA-GAG
* *
25987 CCAGTGTAAGGCCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAG
1 CCAGTGTAA-GACATGTCTGGGACATGGCATCGGCA-TGATA--TGAGAG
* * * * * *
26037 CTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATGTCAATAG
1 CCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCAT-GATAT-GAGAG
** ** * * * * *
26086 TTAGTGTAAGACCATGTCAAGAAAATGGCATCGACTTGAT-GGATGAG
1 CCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATGATATGA-GAG
*
26133 CCAATGTAAGACCATGTCTGGGA-ATGGCATCG
1 CCAGTGTAAGA-CATGTCTGGGACATGGCATCG
26165 ACATTATACC
Statistics
Matches: 215, Mismatches: 41, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
44 2 0.01
45 3 0.01
46 38 0.18
47 61 0.28
48 36 0.17
49 35 0.16
50 37 0.17
51 2 0.01
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGGCATCGGCATGATATGAGAG
Found at i:26015 original size:94 final size:95
Alignment explanation
Indices: 25849--26072 Score: 283
Period size: 94 Copynumber: 2.3 Consensus size: 95
25839 TTTGTGTACC
*
25849 AGTGTAAGACATGTCTAGGACATGCATCGGCCATATTATGAGAGCCAGTATAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCCAGTATAAGACCATGTCTGG
* **
25914 GAGATGGCATCAGCATTGATA-CGAGAGCT
66 GACATGGCATCAGCACAGATAGCGAGAGCT
* * * *
25943 AGTGTAAGACATGTCTGGGACATGCATCGGCACGTA-TA-GAGGTGCCAGTGTAAGGCCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-CATATTATGA-GAGCCAGTATAAGACCATGTCT
* *
26006 GGGACATGGCATCGGCACAGATATGTGAGAGCT
64 GGGACATGGCATCAGCACAGATA-GCGAGAGCT
*
26039 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCC
26073 TCGATGTCAA
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
93 2 0.02
94 70 0.62
95 3 0.03
96 16 0.14
97 15 0.13
98 7 0.06
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (95 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCCAGTATAAGACCATGTCTGG
GACATGGCATCAGCACAGATAGCGAGAGCT
Found at i:26054 original size:50 final size:49
Alignment explanation
Indices: 25847--26071 Score: 234
Period size: 47 Copynumber: 4.7 Consensus size: 49
25837 TATTTGTGTA
* *
25847 CCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGC-CATAT-TATGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATAT-TGAGAG
* * * ** *
25893 CCAGTATAAGACCATGTCTGGGAGATGGCATCAGCATTGATA-CGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATTGAGAG
* * *
25941 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAC-G-TATAGAGGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATTGA-GAG
*
25987 CCAGTGTAAGGCCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATAT-TGAGAG
* *
26037 CTAGTGTAAGACCATGTCTGGGACATGGCGTCGGC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
26072 CTCGATGTCA
Statistics
Matches: 146, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 29 0.20
47 39 0.27
48 31 0.21
49 3 0.02
50 37 0.25
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (49 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATTGAGAG
Found at i:27342 original size:21 final size:21
Alignment explanation
Indices: 27318--27363 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
27308 CCATACCGGT
*
27318 GTGTTGCCCTTTTACACGGGC
1 GTGTTGCCCTCTTACACGGGC
*
27339 GTGTTGCCCTCTTACACGGGT
1 GTGTTGCCCTCTTACACGGGC
27360 GTGT
1 GTGT
27364 GCCTTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.26, G:0.30, T:0.35
Consensus pattern (21 bp):
GTGTTGCCCTCTTACACGGGC
Found at i:28207 original size:45 final size:45
Alignment explanation
Indices: 28143--28242 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
28133 TAGTATAGAA
*
28143 AAGTCTGTAAGAGTTTGGAATCATCGTGTAACCCGAAGAAACAAG
1 AAGTCTGTAAGAGTCTGGAATCATCGTGTAACCCGAAGAAACAAG
* *
28188 AAGTCTGTAAGAGTCTGGAATCATTGTGTAACCTGAAGAAACAAG
1 AAGTCTGTAAGAGTCTGGAATCATCGTGTAACCCGAAGAAACAAG
28233 AAGTCTGTAA
1 AAGTCTGTAA
28243 CCACTACGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (45 bp):
AAGTCTGTAAGAGTCTGGAATCATCGTGTAACCCGAAGAAACAAG
Found at i:35637 original size:48 final size:48
Alignment explanation
Indices: 35585--35801 Score: 175
Period size: 48 Copynumber: 4.5 Consensus size: 48
35575 ATGTCGATGC
*
35585 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGACGT
1 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCCGACGT
* * * * * ** *
35633 CATGTCGCAGACATGGTCTTACACTAGCACACATATTG-ACGCTAATGT
1 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTA-GCCGACGT
* * * ** * ** * *
35681 CATGTCCCAGATATGATCTTACACTGGCTCTCACAACATTGTTGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCCGACGT
* * * * * *
35729 CATTTTCCAAATATGGTCTTACACTGGCTCTCATATTGTAGCCGGCGT
1 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCCGACGT
* *
35777 CATGTCCTAGACATGGTTTTACACT
1 CATGTCCCAGACATGGTCTTACACT
35802 AGCGCATATA
Statistics
Matches: 124, Mismatches: 43, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
48 124 1.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCCGACGT
Found at i:37424 original size:30 final size:30
Alignment explanation
Indices: 37389--37448 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
37379 GTGGACTTAA
37389 TTTTCCTTTCTTACCGAATCTGAGGACTTT
1 TTTTCCTTTCTTACCGAATCTGAGGACTTT
37419 TTTTCCTTTCTTACCGAATCTGAGGACTTT
1 TTTTCCTTTCTTACCGAATCTGAGGACTTT
37449 CTTCTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (30 bp):
TTTTCCTTTCTTACCGAATCTGAGGACTTT
Found at i:43305 original size:48 final size:48
Alignment explanation
Indices: 43151--43470 Score: 240
Period size: 48 Copynumber: 6.7 Consensus size: 48
43141 GGGTGAATTA
*
43151 CCGATGCCATGTCCCAGATATGGTCTTACACTGG--CTCAT-ATGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT---GG
* * * *
43199 CTGATGCCGTGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAAT-T--
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--AT-AATGTGG
* * * * *
43247 TCGATACCATGTCCCAAATATGGTCTTACACTGGCTCTTATAATGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGG
* * * * * **
43295 CCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACAT-ATCGACG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGG
* * * * ** *
43343 CCGATGTCATGTCCTAGACATGGTCTTACACTGACTCTCACAACATTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGG
* * * *
43391 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATTGTTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGG
* * * *
43439 CTGACGCCATGTCTCAGATATGGTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
43471 AGGTTCAACC
Statistics
Matches: 209, Mismatches: 52, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
45 3 0.01
46 2 0.01
47 2 0.01
48 194 0.93
49 1 0.00
50 3 0.01
52 1 0.00
53 1 0.00
54 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGG
Found at i:43321 original size:96 final size:96
Alignment explanation
Indices: 43151--43470 Score: 302
Period size: 96 Copynumber: 3.3 Consensus size: 96
43141 GGGTGAATTA
* * * * * *
43151 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCATAT-GTCGAGGCTGATGCCGTGTCCCA
1 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTTATAAT-GTGGCCGATGCCATGTCTCA
* * * **
43215 GACATGGTCTTACACTAGCTCTCGTCTCAATT
65 AACATGGTCTTACACTAGCTCTCATATCAACG
* * *
43247 TCGATACCATGTCCCAAATATGGTCTTACACTGGCTCTTATAATGTGGCCGATGCCATGTCTCAA
1 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTTATAATGTGGCCGATGCCATGTCTCAA
* * *
43312 ACATGGTCTTACACTAGCACACATATCGACG
66 ACATGGTCTTACACTAGCTCTCATATCAACG
* * * * * * ** *
43343 CCGATGTCATGTCCTAGACATGGTCTTACACTGACTCTCACAACATTGCCGATGCCATGT-TCCA
1 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTTATAATGTGGCCGATGCCATGTCT-CA
* ****
43407 AACATGGTCTTACACTGGCTCTCATATTGTTG
65 AACATGGTCTTACACTAGCTCTCATATCAACG
* * *
43439 CTGACGCCATGTCTCAGATATGGTCTTACACT
1 CCGATGCCATGTCCCAGATATGGTCTTACACT
43471 AGGTTCAACC
Statistics
Matches: 181, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
95 1 0.01
96 179 0.99
97 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTTATAATGTGGCCGATGCCATGTCTCAA
ACATGGTCTTACACTAGCTCTCATATCAACG
Found at i:43414 original size:144 final size:144
Alignment explanation
Indices: 43151--43472 Score: 389
Period size: 144 Copynumber: 2.2 Consensus size: 144
43141 GGGTGAATTA
* * * * * * * *
43151 CCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCATATGTCGAGGCTGATGCCGTGTCCCAG
1 CCGATGCCATGTCTCAGATATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGTCCCAG
* * * *
43216 ACATGGTCTTACACTAGCTCTCGTCTCAATTTCGATACCATGTCCCAAATATGGTCTTACACTGG
66 ACATGGTCTTACACTAGCTCTCGACACAATTCCGATACCATGTCCCAAACATGGTCTTACACTGG
*
43281 CTCTTATAATGTGG
131 CTCTCATAATGTGG
* * * *
43295 CCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCGACGCCGATGTCATGTCCTAG
1 CCGATGCCATGTCTCAGATATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGTCCCAG
* *
43360 ACATGGTCTTACACT-GACTCTC-ACA-ACATTGCCGATGCCATGTTCCAAACATGGTCTTACAC
66 ACATGGTCTTACACTAG-CTCTCGACACA-ATT-CCGATACCATGTCCCAAACATGGTCTTACAC
* *
43422 TGGCTCTCATATTGTTG
128 TGGCTCTCATAATGTGG
* *
43439 CTGACGCCATGTCTCAGATATGGTCTTACACTAG
1 CCGATGCCATGTCTCAGATATGGTCTTACACTAG
43473 GTTCAACCGG
Statistics
Matches: 150, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
142 1 0.01
143 5 0.03
144 144 0.96
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (144 bp):
CCGATGCCATGTCTCAGATATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTCGACACAATTCCGATACCATGTCCCAAACATGGTCTTACACTGG
CTCTCATAATGTGG
Found at i:45727 original size:14 final size:15
Alignment explanation
Indices: 45696--45728 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
45686 TATTTTTGTT
45696 TTAT-TTTATTTAAG
1 TTATATTTATTTAAG
45710 TTATATTTATTTAA-
1 TTATATTTATTTAAG
45724 TTATA
1 TTATA
45729 AAATTTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTATATTTATTTAAG
Found at i:50223 original size:155 final size:155
Alignment explanation
Indices: 49935--50552 Score: 1173
Period size: 155 Copynumber: 4.0 Consensus size: 155
49925 TGTATGGTAA
49935 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
* *
50000 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTCTAA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
50065 ATTCGATTCTCATCATGACCATTAC
131 ATTCGATTCTCATCATGACCATTAC
50090 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
*
50155 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATAAGAAAATGAAACAATTGCTATGA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
*
50220 ATTCGATTCTCATCATGACCATTAG
131 ATTCGATTCTCATCATGACCATTAC
50245 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
50310 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
*
50375 ATTCGATCCTCATCATGACCATTAC
131 ATTCGATTCTCATCATGACCATTAC
*
50400 GTTCTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
1 GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
*
50465 ACTTACTTGTGAATTACGGATTAAACCATTAAGATATACATATGAAAATGAAACAATTGCTATGA
66 ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
50530 ATTCGATTCTCATCATGACCATT
131 ATTCGATTCTCATCATGACCATT
50553 CTTGCAACCC
Statistics
Matches: 453, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 453 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (155 bp):
GTTGTGACAATCTTATGCTTCACTTCATGTTTGTTGAGCAACCATTTCAACCCAAAAGAAACTCT
ACTTACTTGTGAATTACGGATTAAACCATGAAGATATACATATGAAAATGAAACAATTGCTATGA
ATTCGATTCTCATCATGACCATTAC
Found at i:52529 original size:25 final size:22
Alignment explanation
Indices: 52476--52531 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
52466 GATGAGATTG
52476 ATTTTTTATAAATTTGATATTA
1 ATTTTTTATAAATTTGATATTA
* *
52498 TTATTTTTAGCTAAATTTTGCTATTA
1 AT-TTTTTA--TAAA-TTTGATATTA
52524 ATTTTTTA
1 ATTTTTTA
52532 AAAAAATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.04
23 6 0.22
25 10 0.37
26 10 0.37
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (22 bp):
ATTTTTTATAAATTTGATATTA
Found at i:58483 original size:60 final size:60
Alignment explanation
Indices: 58359--58485 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
58349 GTGTCAAGAT
* * * * * * * *
58359 TAAAATTTTAAAATTTGATAAATATAAGGACTTAGAATTATCTAATTAGAGAATATGGAC
1 TAAATTTTTAAAATTTGAAAAATATAAGGACTTAAAATTAACTAATTAAAGAAAAAGGAA
*
58419 TAAATTTTTAAATTTTGAAAAATATAAGGAC-TAAAATTAACTAATTCAAAGAAAAAGGAA
1 TAAATTTTTAAAATTTGAAAAATATAAGGACTTAAAATTAACTAATT-AAAGAAAAAGGAA
58479 TAAATTT
1 TAAATTT
58486 AGTCAAATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 13 0.23
60 44 0.77
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (60 bp):
TAAATTTTTAAAATTTGAAAAATATAAGGACTTAAAATTAACTAATTAAAGAAAAAGGAA
Found at i:59489 original size:16 final size:16
Alignment explanation
Indices: 59452--59487 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
59442 AGAGGGGAAA
59452 GAAAATTAAAAGGATT
1 GAAAATTAAAAGGATT
*
59468 GAAAATTAGAAGGA-T
1 GAAAATTAAAAGGATT
59483 GAAAA
1 GAAAA
59488 ATATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
GAAAATTAAAAGGATT
Found at i:60880 original size:22 final size:22
Alignment explanation
Indices: 60855--60896 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
60845 AAACAAGGAT
* * *
60855 TAAATAAATATGATTATTTTAA
1 TAAAAAAATATAAATATTTTAA
60877 TAAAAAAATATAAATATTTT
1 TAAAAAAATATAAATATTTT
60897 TATTGGGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAAAATATAAATATTTTAA
Found at i:61103 original size:17 final size:17
Alignment explanation
Indices: 61083--61118 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61073 TGATTGATTA
*
61083 AATTTAATTAATTTCTT
1 AATTAAATTAATTTCTT
*
61100 AATTAAATTATTTTCTT
1 AATTAAATTAATTTCTT
61117 AA
1 AA
61119 CTCAATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTAAATTAATTTCTT
Found at i:61104 original size:22 final size:22
Alignment explanation
Indices: 61055--61108 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
61045 TTCTCAAAAT
61055 ATTAATT-AA-TTAATTAATTG
1 ATTAATTAAATTTAATTAATTG
* *
61075 ATTGATTAAATTTAATTAATTT
1 ATTAATTAAATTTAATTAATTG
*
61097 CTTAATTAAATT
1 ATTAATTAAATT
61109 ATTTTCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 20 0.71
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTAATTAAATTTAATTAATTG
Found at i:61675 original size:16 final size:16
Alignment explanation
Indices: 61627--61678 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
61617 CTTAGAAGAA
*
61627 AATATATATACACAA-
1 AATATATATACATAAT
*
61642 AATA-ATATAAAATCAAT
1 AATATATAT-ACAT-AAT
61659 AATATATATACATAAT
1 AATATATATACATAAT
61675 AATA
1 AATA
61679 AAAAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 9 0.30
17 7 0.23
18 4 0.13
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATATATACATAAT
Found at i:61685 original size:23 final size:20
Alignment explanation
Indices: 61648--61699 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
61638 ACAAAATAAT
* *
61648 ATAAAATCAATAATATATATAC
1 ATAAAAT-AA-AAAATATTTAC
61670 ATAATAATAAAAAATATTTAC
1 ATAA-AATAAAAAATATTTAC
61691 ATAAAATAA
1 ATAAAATAA
61700 TAGGAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 13 0.48
22 6 0.22
23 3 0.11
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAATAAAAAATATTTAC
Found at i:61989 original size:18 final size:18
Alignment explanation
Indices: 61968--62007 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
61958 AATAAGGAAT
61968 AAAACATAAATTGAAGTAA
1 AAAAC-TAAATTGAAGTAA
*
61987 AAAACTCAATTGAAGTAA
1 AAAACTAAATTGAAGTAA
62005 AAA
1 AAA
62008 TAAAACCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (18 bp):
AAAACTAAATTGAAGTAA
Found at i:62344 original size:40 final size:38
Alignment explanation
Indices: 62300--62405 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 38
62290 TAAATTGAAT
62300 ATTAGCGGCGTTTTTTCAAAAACGCCGCTATAGATCGAGA
1 ATTAGCGGCGTTTTTT-AAAAACGCCGCTATAGATCGA-A
** * *
62340 ATTAGCGGCG-TTTTTAAGGAAGTGCCGCTATAGGTCGAC
1 ATTAGCGGCGTTTTTTAA--AAACGCCGCTATAGATCGAA
62379 ATATAGCGGCGTTTTTATAAAAACGCC
1 AT-TAGCGGCGTTTTT-TAAAAACGCC
62406 ACTAAAAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
38 2 0.04
39 7 0.13
40 39 0.71
41 4 0.07
42 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (38 bp):
ATTAGCGGCGTTTTTTAAAAACGCCGCTATAGATCGAA
Found at i:62619 original size:155 final size:153
Alignment explanation
Indices: 62315--62680 Score: 453
Period size: 154 Copynumber: 2.4 Consensus size: 153
62305 CGGCGTTTTT
* * * * *
62315 TCAAAAACGCCGCTATAGATCGAGAATTAGCGGCGTTTTTAAGGAAGTGCCGCTATAGGTCGACA
1 TCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGTTTTTTAGAAAGCGCCGCTATAGGTCGACA
* * ** *
62380 TATAGCGGCGTTTTTATAAAAACGCCACTAAAAGATTAGGCGAACGGCGTCGTTTATTGTGAGCT
66 TATAACGGCGTTTTTATAAAAACGCCACTAAAAAATTAACCAAACGGCGTCGTTTATTGTGAGCT
** *
62445 TCAGTGGCAATAGTGGCGCTTTA
131 TCAGTGGCAATAGCAGCGCTTGA
* * * * *
62468 TCAAAAACACCGCTATAGGTTTGAGTATTAACGGCATTTTTTAGAAAGCGCCGCTATAGGTCGGC
1 TCAAAAACGCCGCTATA-GATTGAGTATTAGCGGCGTTTTTTAGAAAGCGCCGCTATAGGTCGAC
* * * *
62533 CTATAACGGCGTTTTTATAGAAACGCCGCTAAAAAATTAAACCAAACGGCGTCGTTTATTTTGAG
65 ATATAACGGCGTTTTTATAAAAACGCCACTAAAAAATT-AACCAAACGGCGTCGTTTATTGTGAG
* *
62598 CTTCATTGGCAATAGCAGCGCTTGC
129 CTTCAGTGGCAATAGCAGCGCTTGA
* * * * *
62623 GCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGCTTTCTAGAAAACGCCGCAATAG
1 TCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGTTTTTTAGAAAGCGCCGCTATAG
62681 ATATGAGTTT
Statistics
Matches: 178, Mismatches: 33, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
153 16 0.09
154 105 0.59
155 57 0.32
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (153 bp):
TCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGTTTTTTAGAAAGCGCCGCTATAGGTCGACA
TATAACGGCGTTTTTATAAAAACGCCACTAAAAAATTAACCAAACGGCGTCGTTTATTGTGAGCT
TCAGTGGCAATAGCAGCGCTTGA
Found at i:62670 original size:40 final size:42
Alignment explanation
Indices: 62611--62724 Score: 128
Period size: 40 Copynumber: 2.8 Consensus size: 42
62601 CATTGGCAAT
* *
62611 AGCAGCGCTTGC-GCAAAAACGCCGCTATAGAT-TGAGTATT-
1 AGCAGCGCTTTCTGAAAAAACGCCGCTATAGATATGAGT-TTC
* * *
62651 AGCGGCGCTTTCT-AGAAAACGCCGCAATAGATATGAGTTTC
1 AGCAGCGCTTTCTGAAAAAACGCCGCTATAGATATGAGTTTC
* *
62692 AGCAGCGCTTTTTGAAAAAACGCCGCTAAAGAT
1 AGCAGCGCTTTCTGAAAAAACGCCGCTATAGAT
62725 CTAAACTATT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 28 0.47
41 16 0.27
42 16 0.27
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (42 bp):
AGCAGCGCTTTCTGAAAAAACGCCGCTATAGATATGAGTTTC
Found at i:63033 original size:15 final size:15
Alignment explanation
Indices: 62991--63047 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
62981 ACACCATGTT
* *
62991 TTAAACCCTAACCCA
1 TTAAACCCTAAACTA
* *
63006 CTAAACCCTTAAATTA
1 TTAAACCC-TAAACTA
* *
63022 TTAAATCCTAAACTC
1 TTAAACCCTAAACTA
63037 TTAAACCCTAA
1 TTAAACCCTAA
63048 GTCTCAACCC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (15 bp):
TTAAACCCTAAACTA
Found at i:63441 original size:23 final size:21
Alignment explanation
Indices: 63415--63461 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
63405 AGGTTTATGC
*
63415 ATGGTTTAGGGTATATATGGTTT
1 ATGGTTTAGGGT-T-TATGGATT
*
63438 ATGGTTTATGGTTTATGGATT
1 ATGGTTTAGGGTTTATGGATT
63459 ATG
1 ATG
63462 ACAAGTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 11 0.50
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (21 bp):
ATGGTTTAGGGTTTATGGATT
Found at i:63442 original size:7 final size:7
Alignment explanation
Indices: 63415--63461 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
63405 AGGTTTATGC
63415 ATGGTTT
1 ATGGTTT
*
63422 AGGGTATAT
1 ATGGT-T-T
63431 ATGGTTT
1 ATGGTTT
63438 ATGGTTT
1 ATGGTTT
63445 ATGGTTT
1 ATGGTTT
*
63452 ATGGATT
1 ATGGTTT
63459 ATG
1 ATG
63462 ACAAGTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 28 0.80
8 2 0.06
9 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (7 bp):
ATGGTTT
Found at i:63511 original size:87 final size:79
Alignment explanation
Indices: 63436--63609 Score: 196
Period size: 80 Copynumber: 2.2 Consensus size: 79
63426 TATATATGGT
* ** *
63436 TTATGGTTTATGGTTTATGGATT-A-TGACAAGTTAATATT-TTAATTAAGGTTTATGGATTA-T
1 TTATGGTTTATGGTTTATGG-TTAATTTATGAGTCAATATTATT--TTAAGGTTTATGGATTATT
63497 GCA-TGTGGGTTTAGGGA
63 G-ATTGTGGGTTTAGGGA
* *
63514 TTATGGGTTTAGGGGTTTATGGTTAATTTATGGGTCAATATTATTTTAAGGTTTATGGATTATTG
1 TTAT-GGTTTA-TGGTTTATGGTTAATTTATGAGTCAATATTATTTTAAGGTTTATGGATTATTG
*
63579 ATTGTGGATTTAGGGA
64 ATTGTGGGTTTAGGGA
63595 TTATGGTTTATGGTT
1 TTATGGTTTATGGTT
63610 CAAGGGCTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
78 4 0.05
79 12 0.15
80 34 0.42
81 29 0.36
82 2 0.02
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (79 bp):
TTATGGTTTATGGTTTATGGTTAATTTATGAGTCAATATTATTTTAAGGTTTATGGATTATTGAT
TGTGGGTTTAGGGA
Found at i:63840 original size:73 final size:72
Alignment explanation
Indices: 63675--63842 Score: 194
Period size: 73 Copynumber: 2.3 Consensus size: 72
63665 GGGTCAAAGG
* * * *
63675 TTAGGAGTTAAGGGGTTGAGGGGATATAGTTTAAGGTTTAGTGTTCAAAGTCTATGGATTAAGGG
1 TTAGG-GTTTAGGGGTTAAGGGGACATAGTTTAAGGTTTAGTGTTCAAAGTCTAGGGATTAAGGG
*
63740 TTTAGGGT
65 TTAAGGGT
* * * * *
63748 TTATGGGTTT-GGAAGTTAAGGGGACATTGTTTAAGGTTTAGTGTTTAAATTTTAGGGATTAAGG
1 TTA-GGGTTTAGG-GGTTAAGGGGACATAGTTTAAGGTTTAGTGTTCAAAGTCTAGGGATTAAGG
*
63812 GTTAATGGT
64 GTTAAGGGT
63821 TTAGGGTTTAGGGGTTTAAGGG
1 TTAGGGTTTAGGGG-TTAAGGG
63843 TTAATGGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
72 9 0.11
73 68 0.86
74 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.35, T:0.38
Consensus pattern (72 bp):
TTAGGGTTTAGGGGTTAAGGGGACATAGTTTAAGGTTTAGTGTTCAAAGTCTAGGGATTAAGGGT
TAAGGGT
Found at i:64008 original size:16 final size:16
Alignment explanation
Indices: 63983--64035 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
63973 ACATATATTA
63983 AATAATTTCAAATTTT
1 AATAATTTCAAATTTT
* *
63999 AATGATTTCAAATTGTC
1 AATAATTTCAAATT-TT
64016 AATAATTTTCAAGATTTT
1 AATAA-TTTCAA-ATTTT
64034 AA
1 AA
64036 ATTTTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 13 0.43
17 5 0.17
18 9 0.30
19 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (16 bp):
AATAATTTCAAATTTT
Found at i:64186 original size:18 final size:17
Alignment explanation
Indices: 64148--64183 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
64138 CTATATAACT
64148 TATTGTTTTTTAATTTA
1 TATTGTTTTTTAATTTA
64165 TATTGTTTTTT-ATTTA
1 TATTGTTTTTTAATTTA
64181 TAT
1 TAT
64184 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TATTGTTTTTTAATTTA
Found at i:66190 original size:15 final size:16
Alignment explanation
Indices: 66164--66193 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
66154 GTAGTTATGA
66164 ATGAGTTTTTCAGTGC
1 ATGAGTTTTTCAGTGC
66180 ATGAG-TTTTCAGTG
1 ATGAGTTTTTCAGTG
66194 TATAACCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (16 bp):
ATGAGTTTTTCAGTGC
Found at i:67906 original size:14 final size:13
Alignment explanation
Indices: 67883--67912 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
67873 ATTACCATAA
67883 TAATTATATGAAG
1 TAATTATATGAAG
67896 TAATATATATGAAG
1 TAAT-TATATGAAG
67910 TAA
1 TAA
67913 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:68389 original size:15 final size:15
Alignment explanation
Indices: 68369--68397 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
68359 GGAGTAGACC
68369 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
68384 AGGTACGTTTTATT
1 AGGTACGTTTTATT
68398 TCAAAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:69301 original size:358 final size:358
Alignment explanation
Indices: 68621--69302 Score: 1321
Period size: 358 Copynumber: 1.9 Consensus size: 358
68611 CTTGTCCATT
68621 AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
68686 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
68751 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
68816 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
196 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
*
68881 ATTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
261 ATTATTATATTCAAATTACTATTTTTTTACATTAATAATGTTTGATTTTAATATTTAATATTTTT
68946 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
326 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
*
68979 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
69044 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
69109 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
69174 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTC-TTTTTTAT
196 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
*
69238 ATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTTTAATATTTAAATATTTT
261 ATTATTATATTCAAATTACTATTTTTTTACATTAATAATGTTTGATTTTAATATTT-AATATTTT
69303 AAAGATTCAA
Statistics
Matches: 320, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
357 62 0.19
358 258 0.81
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (358 bp):
AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
ATTATTATATTCAAATTACTATTTTTTTACATTAATAATGTTTGATTTTAATATTTAATATTTTT
AAATGTCTTTAAAAGTTATAACTAATTTTTATC
Found at i:71205 original size:13 final size:14
Alignment explanation
Indices: 71189--71217 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71179 TTCTAAATAT
71189 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
71202 TTATAATTGTTTAA
1 TTATAATTGTTTAA
71216 TT
1 TT
71218 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:72211 original size:42 final size:43
Alignment explanation
Indices: 72024--72209 Score: 302
Period size: 43 Copynumber: 4.3 Consensus size: 43
72014 TCTGCCAAAA
72024 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
72067 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
* * **
72110 TTAGTGGCGTTTTTTCTTCAAACGCCGCTAAAGGCCTTGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
* *
72153 TTAGCGGCGCTTTTT-TTCAAACGCCGCTAAAGGCCATGAATT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
*
72195 TTTGCGGCGCTTTTT
1 TTAGCGGCGCTTTTT
72210 TTTAATAAAC
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 39 0.29
43 95 0.71
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (43 bp):
TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
Found at i:73112 original size:19 final size:19
Alignment explanation
Indices: 73088--73124 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
73078 TTTTATGTAA
* *
73088 TTGGGCTGTAATTGGGTAT
1 TTGGGCTGAAATTAGGTAT
73107 TTGGGCTGAAATTAGGTA
1 TTGGGCTGAAATTAGGTA
73125 GCCCGGGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (19 bp):
TTGGGCTGAAATTAGGTAT
Found at i:73479 original size:88 final size:87
Alignment explanation
Indices: 73360--73785 Score: 509
Period size: 88 Copynumber: 4.8 Consensus size: 87
73350 CGTTTCAATT
* * * * * *
73360 TGCTCCACTACTGTTTAGGGAGATATGATTTGTAATCTTCAGCC-ATCT-CCACTGCTGGTCAG-
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TTCAGCCTAT-TACC-CTACTGCTTAGA
* *
73422 GGAGATAAGGCTCACTGTCTTCGATC
63 GG-GTTAAGGCTCACCGTCTTCGATC
* * * * *
73448 TGCTCCGCTATTGCTTAGGGAGATAAGATTTGTAGTTTCCAGCCTGTTACCCTACTGCTTAGAGG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT-CAGCCTATTACCCTACTGCTTAGAGG
* *
73513 GTTAAGACTCACCGTCCTCGATC
65 GTTAAGGCTCACCGTCTTCGATC
* * *
73536 TGTTCCACTATTGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTACTGCTTAG-GA
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTATTACCCTACTGCTTAGAG-
73600 GGTTAAGGCTCACCGTCTTCGATC
64 GGTTAAGGCTCACCGTCTTCGATC
* * *
73624 TACTCCACTACTACTTAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTAATGCTTAGAGG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT-CAGCCTATTACCCTACTGCTTAGAGG
* **
73689 GTTAAGGCTCACCGTTTTTTATC
65 GTTAAGGCTCACCGTCTTCGATC
* *
73712 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTATTACCCTACTGCTTAGAGG
73777 GTTAAGGCT
65 GTTAAGGCT
73786 GGTCGAGATT
Statistics
Matches: 294, Mismatches: 35, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
87 6 0.02
88 276 0.94
89 12 0.04
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (87 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCAGCCTATTACCCTACTGCTTAGAGGG
TTAAGGCTCACCGTCTTCGATC
Found at i:73595 original size:44 final size:44
Alignment explanation
Indices: 73547--73773 Score: 121
Period size: 44 Copynumber: 5.2 Consensus size: 44
73537 GTTCCACTAT
73547 TGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTAC
1 TGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTAC
* * * * * * *
73591 TGCTTAG-GAGGTTAAG-GCT-CACCGTCTTC-GATCTACT-CCACTAC
1 TGCTTAGAGA-GATAAGATCTGTA--ATTTTCAG-CCTATTACC-CTAC
* * * *
73635 TACTTAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTAA
1 TGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTAC
* * * * * * **
73679 TGCTTAGAGGGTTAAGGCTCACCGT--TTTTTA-TCTGCT-CCACTAC
1 TGCTTAGAGAGATAA-GAT--CTGTAATTTTCAGCCTATTACC-CTAC
* *
73723 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
1 TGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTAC
73767 TGCTTAG
1 TGCTTAG
73774 GGGGTTAAGG
Statistics
Matches: 128, Mismatches: 37, Indels: 36
0.64 0.18 0.18
Matches are distributed among these distances:
41 3 0.02
42 1 0.01
43 16 0.12
44 89 0.70
45 15 0.12
46 1 0.01
47 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (44 bp):
TGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTAC
Found at i:77845 original size:19 final size:19
Alignment explanation
Indices: 77821--77866 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
77811 TGTGAAGTTT
*
77821 AATGCACATG-ATGCAATG
1 AATGCAAATGCATGCAATG
*
77839 CAATGCAAATGCATGGAATG
1 -AATGCAAATGCATGCAATG
77859 AATGCAAA
1 AATGCAAA
77867 AGAAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGCAAATGCATGCAATG
Found at i:79935 original size:15 final size:14
Alignment explanation
Indices: 79901--79945 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
79891 AAATAAATCA
*
79901 AAATAATAAGA-AT
1 AAATAATAATATAT
79914 AAA-AATAATATAT
1 AAATAATAATATAT
79927 GAAATAATAATATAT
1 -AAATAATAATATAT
79942 AAAT
1 AAAT
79946 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.21
13 5 0.18
14 7 0.25
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:79949 original size:19 final size:18
Alignment explanation
Indices: 79891--79950 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 18
79881 TGAAAGTTCG
*
79891 AAAT-AAATCAAAATAAT
1 AAATGAAATAAAAATAAT
79908 -AA-G-AATAAAAATAAT
1 AAATGAAATAAAAATAAT
* *
79923 ATATGAAATAATAATATAT
1 AAATGAAATAAAAATA-AT
79942 AAATGAAAT
1 AAATGAAAT
79951 TTCAAAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 11 0.32
16 3 0.09
17 1 0.03
18 9 0.26
19 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATGAAATAAAAATAAT
Found at i:80164 original size:30 final size:29
Alignment explanation
Indices: 80130--80221 Score: 86
Period size: 30 Copynumber: 3.3 Consensus size: 29
80120 AAAAGAAAAT
80130 ATATATACACAAAATAATATAAAATCAATA
1 ATATATACACAAAATAATA-AAAATCAATA
* *
80160 ATATATATACATAATAATAAAAA--AAT-
1 ATATATACACAAAATAATAAAAATCAATA
* *
80186 AT-T-TACATAAAATAATAGGAAATCAATA
1 ATATATACACAAAATAATA-AAAATCAATA
*
80214 ATGTATAC
1 ATATATAC
80222 TTAGAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
24 11 0.22
25 4 0.08
26 2 0.04
27 6 0.12
28 2 0.04
29 5 0.10
30 20 0.40
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (29 bp):
ATATATACACAAAATAATAAAAATCAATA
Found at i:80175 original size:16 final size:16
Alignment explanation
Indices: 80127--80178 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
80117 CTTAAAAGAA
*
80127 AATATATATACACAA-
1 AATATATATACATAAT
*
80142 AATA-ATATAAAATCAAT
1 AATATATAT-ACAT-AAT
80159 AATATATATACATAAT
1 AATATATATACATAAT
80175 AATA
1 AATA
80179 AAAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 9 0.30
17 7 0.23
18 4 0.13
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATATATACATAAT
Found at i:80492 original size:18 final size:18
Alignment explanation
Indices: 80471--80510 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
80461 AATAAGGAAT
80471 AAAACATAAATTGAAGTAA
1 AAAAC-TAAATTGAAGTAA
*
80490 AAAACTCAATTGAAGTAA
1 AAAACTAAATTGAAGTAA
80508 AAA
1 AAA
80511 TAAAACCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (18 bp):
AAAACTAAATTGAAGTAA
Found at i:85704 original size:25 final size:25
Alignment explanation
Indices: 85637--85707 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
85627 AATACAAACA
* *
85637 CAACCCAATTACAAAACCCAAAACCTAT
1 CAACCCAATTAC--AACCC-AAACCAAG
* *
85665 CAACCTAATTA-AACCCAAATCAAG
1 CAACCCAATTACAACCCAAACCAAG
85689 CAACCCAATTACAACCCAA
1 CAACCCAATTACAACCCAA
85708 CCTACCCCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 15 0.41
25 12 0.32
28 10 0.27
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.14
Consensus pattern (25 bp):
CAACCCAATTACAACCCAAACCAAG
Found at i:86716 original size:3 final size:3
Alignment explanation
Indices: 86708--86992 Score: 145
Period size: 3 Copynumber: 95.7 Consensus size: 3
86698 TTTAACTACT
* * * *
86708 TTA TTA TTA -AA TTA GTTAA TT- TTA TTA TTA TTA CTA TTA TTT TTT
1 TTA TTA TTA TTA TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** *
86753 TTCA CTA TTA TTA TTCA TTA TCA TTA CTA CCA TTA TTA TTA CTA TTA
1 TT-A TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * * * *
86800 TTT TTA TTT TTA TCA CTA TCA CTC TCA GTA TTA TTA TTT TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
86848 TTA CTA TTA TCA TTA TTA TTA TTC TTA TTA TTA GTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
86896 TGC TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TT- TTG TT- TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * *
86943 ATA TTT TTA TT- TTA TT- TTA TT- TTA TTT TTA GTT- TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
86985 TTT TTA TT
1 TTA TTA TT
86993 TTACAATTAG
Statistics
Matches: 205, Mismatches: 63, Indels: 28
0.69 0.21 0.09
Matches are distributed among these distances:
2 15 0.07
3 176 0.86
4 13 0.06
5 1 0.00
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:86952 original size:23 final size:21
Alignment explanation
Indices: 86909--86994 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 21
86899 TTATTATTAC
*
86909 TATTATTATTATTATTATTATTT
1 TATT-TTATT-TTATTTTTATTT
*
86932 TGTTTTATTTAATATTTTTATTT
1 TATTTTATTT--TATTTTTATTT
86955 TATTTTATTTTATTTTTAGTTT
1 TATTTTATTTTATTTTTA-TTT
86977 TATTTTTATTTTTATTTT
1 TA-TTTTA-TTTTATTTT
86995 ACAATTAGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
21 9 0.16
22 10 0.18
23 27 0.49
24 9 0.16
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TATTTTATTTTATTTTTATTT
Found at i:86958 original size:28 final size:27
Alignment explanation
Indices: 86915--86995 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
86905 TTACTATTAT
* *
86915 TATTATTATTATTATTTTGTTTTATTTAA
1 TATTTTTATT-TTATTTTATTTTATTT-A
*
86944 TATTTTTATTTTATTTTATTTTATTTT
1 TATTTTTATTTTATTTTATTTTATTTA
*
86971 TAGTTTTATTTTTATTTTTATTTTA
1 TATTTTTA-TTTTA-TTTTATTTTA
86996 CAATTAGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.15
28 20 0.43
29 19 0.41
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.75
Consensus pattern (27 bp):
TATTTTTATTTTATTTTATTTTATTTA
Found at i:87052 original size:21 final size:22
Alignment explanation
Indices: 87011--87052 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
87001 AGCTTGCTTT
87011 TCATTTATTCATTTACTTTATCG
1 TCATTTATT-ATTTACTTTATCG
*
87034 TCATTTATT-TTTGCTTTAT
1 TCATTTATTATTTACTTTAT
87053 TGTCGCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
23 9 0.50
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (22 bp):
TCATTTATTATTTACTTTATCG
Found at i:89984 original size:53 final size:53
Alignment explanation
Indices: 89904--90007 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
89894 GCTCCCAATC
* * *
89904 AATTTCCTTTTTATCGCATTTGCTATCTTTGATTAACTTGTTCATTTCGAGTT
1 AATTTCCTTCTTATCACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
* *
89957 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAATTTATTCATTTCGAG
1 AATTTCCTTCTTATCACATTTGCTATCTTTGATTAACTTATTCATTTCGAG
90008 CTATGATCCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (53 bp):
AATTTCCTTCTTATCACATTTGCTATCTTTGATTAACTTATTCATTTCGAGTT
Found at i:90868 original size:44 final size:44
Alignment explanation
Indices: 90797--91216 Score: 198
Period size: 44 Copynumber: 9.4 Consensus size: 44
90787 CAGAGCAAAC
* * * *
90797 CTTATCTCCCTGAAGTTGTAGTAGAGCACGTTGAAGTTATAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATATAAGT
**
90841 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATATCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATAT--AAGT
* * * * *
90886 CTTATTTCCTTGAAGTTACAGTGGA-AAAGATTGAAACTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTG-AA-GAT--A-TA-AG-T
* ** * * * **
90937 CTTATCTCTCTGAAGTTGCAGTAAAGC-AGAT-AA-AAACAAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATATAAGT
* *
90978 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAG-TCACT-AGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGAT-A-TAAGT
** * *
91022 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAGACA-ATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATATA-AG-T
* ** * * * **
91067 CTTATCTCCTTGAAGTTATAGTGGAG-TAGATCGAAGATAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATA-TAAGT
** * * * * *
91112 CTTATCTATCTAAAGTAGCAGTAGAGCAGGTTGAA-ATTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGA-TATAAGT
* *
91156 CTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTGAAGATACCAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATA-TAAGT
*
91200 CTTATTTCCCTGAAGTT
1 CTTATCTCCCTGAAGTT
91217 ACAGCAGAGC
Statistics
Matches: 274, Mismatches: 73, Indels: 58
0.68 0.18 0.14
Matches are distributed among these distances:
41 23 0.08
42 3 0.01
43 4 0.01
44 123 0.45
45 82 0.30
46 7 0.03
47 3 0.01
48 3 0.01
49 2 0.01
50 2 0.01
51 22 0.08
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATATAAGT
Found at i:90958 original size:96 final size:95
Alignment explanation
Indices: 90659--90967 Score: 255
Period size: 96 Copynumber: 3.3 Consensus size: 95
90649 GAAGTTAAAG
** * * *
90659 TCTTATCTCCCTGAAGTTATAGTGGAGTAGATTGAAGATAGT-GAATCTCATTTCCTTAAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAGATA-TCGAATCTTATTTCCTTGAAGTTG
* *
90723 CAGTGGAACAGATTGAAGCTATAAATTACAGA
64 CAGTGGAAAAGATTGAAACTATAAATTACAGA
* * * * * * * * * * *
90755 CCTTATCTCTCTGAAGTTGTAGTAGAGCAGAT-CAG--AGCAAACCTTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGATATCGAATCTTATTTCCTTGAAGTTGCA
* * * *
90817 GTAGAGCACG-TTG-AAGT-T--A-TA-AG-
66 GTGGA-AAAGATTGAAACTATAAATTACAGA
* *
90840 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATATCGAATCTTATTTCCTTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAGATATCGAATCTTATTTCCTTGAAGTTGC
90905 AGTGGAAAAGATTGAAACTATAAATTACAGA
65 AGTGGAAAAGATTGAAACTATAAATTACAGA
* **
90936 TCTTATCTCTCTGAAGTTGCAGTAAAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
90968 AAAAACAAAA
Statistics
Matches: 158, Mismatches: 41, Indels: 29
0.69 0.18 0.13
Matches are distributed among these distances:
85 26 0.16
86 3 0.02
87 4 0.03
88 3 0.02
89 27 0.17
90 4 0.03
91 3 0.02
92 25 0.16
93 2 0.01
94 4 0.03
95 4 0.03
96 53 0.34
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (95 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGATATCGAATCTTATTTCCTTGAAGTTGCA
GTGGAAAAGATTGAAACTATAAATTACAGA
Found at i:91071 original size:181 final size:179
Alignment explanation
Indices: 90570--91091 Score: 650
Period size: 181 Copynumber: 2.9 Consensus size: 179
90560 ATAATGGCGA
* * ** * *
90570 ATCTTATCTCCCTGTAGTTGCAGTAGAGCAGATTGAAGCCACTAAACCTTATCTCCCTGAAATAG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-AA-AAAC-AAACCTTATCTCCCTGAAGTTG
* * ** * * * *
90635 CAGTGGAGCAGGTTGAAGTTAAAGTCTTATCTCCCTGAAGTTATAGTGGAGTAGATTGAAGATAG
62 TAGTGGAGCAGGTTGAAGTTATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGA-AA
* * * * *
90700 TGAATCTCATTTCCTTAAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAG
126 TGAATCTTATTTCCTTGAAGTTACAGTGGAAAAGATTGAAACTATAAATTACAG
* * * * *
90754 ACCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGCAAACCTTATCTCCCTGAAGTTGTAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAAACCTTATCTCCCTGAAGTTGTAGT
* * *
90819 AGAGCACGTTGAAGTTATAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATATCGA
66 GGAGCAGGTTGAAGTTAT-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGAAAT-GA
90884 ATCTTATTTCCTTGAAGTTACAGTGGAAAAGATTGAAACTATAAATTACAG
129 ATCTTATTTCCTTGAAGTTACAGTGGAAAAGATTGAAACTATAAATTACAG
* *
90935 ATCTTATCTCTCTGAAGTTGCAGTAAAGCAGATAAAAACAAAACTTATCTCCCTGAAGTTGTAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAAACCTTATCTCCCTGAAGTTGTAGT
* *
91000 GGAGCAGGTTGAAGTCACTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAGACAAT-A
66 GGAGCAGGTTGAAGTTA-TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGA-AATGA
* *
91064 GATCTTATCTCCTTGAAGTTATAGTGGA
129 -ATCTTATTTCCTTGAAGTTACAGTGGA
91092 GTAGATCGAA
Statistics
Matches: 293, Mismatches: 40, Indels: 13
0.85 0.12 0.04
Matches are distributed among these distances:
180 40 0.14
181 220 0.75
182 4 0.01
183 1 0.00
184 28 0.10
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (179 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAAACCTTATCTCCCTGAAGTTGTAGT
GGAGCAGGTTGAAGTTATAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGAAATGAAT
CTTATTTCCTTGAAGTTACAGTGGAAAAGATTGAAACTATAAATTACAG
Found at i:92776 original size:3 final size:3
Alignment explanation
Indices: 92768--93073 Score: 187
Period size: 3 Copynumber: 102.3 Consensus size: 3
92758 TTTAGCTACT
* * * * *
92768 TTA TTA TTA -AA TTA GTTAA TT- TTA TTA TTC TTA CTA TTA TTT TTT
1 TTA TTA TTA TTA TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
92813 TTCA CTA TTA TTA TTCA TTA TCA TTA TTA CCA TTA TTA TTA CTA TTA
1 TT-A TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
92860 TTT TTA TTT TTA TCA CTA TTA CTC TTA CTT- TTT TTA TT- TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * * *
92904 TTA CTA TTA TCA TTA TTA TTA CTA TTA TTA TT- TTC TT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
92950 TTTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TCA TTA TTC TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** * *
92996 TTA TTG GTA TTA TTA TCA TGC TTA TTA TTA CTA TTA TTA TTA -TG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
93043 TTA TTCT TTA TT- TTA TTA TTA TTA TTA TTA T
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T
93074 CATCATCATT
Statistics
Matches: 227, Mismatches: 61, Indels: 30
0.71 0.19 0.09
Matches are distributed among these distances:
2 14 0.06
3 197 0.87
4 15 0.07
5 1 0.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:92933 original size:53 final size:53
Alignment explanation
Indices: 92845--93073 Score: 174
Period size: 53 Copynumber: 4.5 Consensus size: 53
92835 ATTATTACCA
* * * **
92845 TTATTATTACTATTATTTTTATTTTTA-TCACTATTACTCTTACTTTTTTTATT-T
1 TTATTATTACTATTATTATTATTATTACT-ATTATTA-T-TTACTTTTACTATTAT
* *
92899 TT-TTATTACTATTATCATTATTATTACTATTATTATTTTCTTTTACTATTAT
1 TTATTATTACTATTATTATTATTATTACTATTATTATTTACTTTTACTATTAT
* * *
92951 TTATTATTATTATTATTATTATTATTACTATTATCA-TTA-TTCT--TATTA-
1 TTATTATTACTATTATTATTATTATTACTATTATTATTTACTTTTACTATTAT
** * * ** * * *
92999 TTGGTATTATTATCATGCTTATTATTACTATTATTA-TTA-TGTTATTATTCT
1 TTATTATTACTATTATTATTATTATTACTATTATTATTTACTTTTACTATTAT
*
93050 TTATT-TTATTATTATTATTATTAT
1 TTATTATTACTATTATTATTATTAT
93074 CATCATCATT
Statistics
Matches: 143, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
48 35 0.24
49 5 0.03
50 20 0.14
51 17 0.12
52 6 0.04
53 57 0.40
54 3 0.02
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.64
Consensus pattern (53 bp):
TTATTATTACTATTATTATTATTATTACTATTATTATTTACTTTTACTATTAT
Found at i:93115 original size:5 final size:5
Alignment explanation
Indices: 93086--93148 Score: 54
Period size: 5 Copynumber: 11.6 Consensus size: 5
93076 TCATCATTTC
* * *
93086 TTATT TTGTT TTATT TAATATTT TTATT TTGTT TTATTT TTATTT TTGTT
1 TTATT TTATT TTATT T--TA-TT TTATT TTATT TTA-TT TTA-TT TTATT
93136 TTATT TTATT TTA
1 TTATT TTATT TTA
93149 CAATTAGCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.65
6 12 0.25
7 2 0.04
8 3 0.06
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:93126 original size:17 final size:17
Alignment explanation
Indices: 93104--93147 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
93094 TTTTATTTAA
93104 TATTTTTA-TTTTGTTT
1 TATTTTTATTTTTGTTT
93120 TATTTTTATTTTTGTTT
1 TATTTTTATTTTTGTTT
93137 TA-TTTTATTTT
1 TATTTTTATTTT
93148 ACAATTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.82
Consensus pattern (17 bp):
TATTTTTATTTTTGTTT
Found at i:93132 original size:22 final size:22
Alignment explanation
Indices: 93081--93147 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
93071 TATCATCATC
*
93081 ATTTCTTATTTTGTTTTATTTAAT
1 ATTT-TTATTTTGTTTTATTT-TT
93105 ATTTTTATTTTGTTTTATTTTT
1 ATTTTTATTTTGTTTTATTTTT
* *
93127 ATTTTTGTTTTATTTTATTTT
1 ATTTTTATTTTGTTTTATTTT
93148 ACAATTAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.50
23 16 0.40
24 4 0.10
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.78
Consensus pattern (22 bp):
ATTTTTATTTTGTTTTATTTTT
Found at i:105938 original size:2 final size:2
Alignment explanation
Indices: 105931--105956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
105921 TTTAAAAATA
105931 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
105957 GAGACACTTG
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:106525 original size:31 final size:31
Alignment explanation
Indices: 106490--106548 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
106480 ATGGGCATTA
*
106490 TCATTACATACTTTTATTATTTTAGTCAATG
1 TCATTACATACTTTTATCATTTTAGTCAATG
106521 TCATTACATACTTTTATCATTTTAGTCA
1 TCATTACATACTTTTATCATTTTAGTCA
106549 CCTGCCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (31 bp):
TCATTACATACTTTTATCATTTTAGTCAATG
Found at i:106730 original size:14 final size:14
Alignment explanation
Indices: 106711--106737 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
106701 TTTTACAGAG
106711 GAAAATCTGAGTTA
1 GAAAATCTGAGTTA
106725 GAAAATCTGAGTT
1 GAAAATCTGAGTT
106738 CTTACACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (14 bp):
GAAAATCTGAGTTA
Found at i:106931 original size:13 final size:13
Alignment explanation
Indices: 106899--106925 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
106889 AGACATTTCA
106899 TATTATCTAGTAT
1 TATTATCTAGTAT
106912 TATTATCTAGTAT
1 TATTATCTAGTAT
106925 T
1 T
106926 CATATCAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TATTATCTAGTAT
Found at i:109802 original size:25 final size:25
Alignment explanation
Indices: 109774--109844 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
109764 ATGCTTATAA
109774 GAGCTATGAATCAGTATGCTCTCGC
1 GAGCTATGAATCAGTATGCTCTCGC
109799 GAGCTATGAATCAGTATGCTCTCGC
1 GAGCTATGAATCAGTATGCTCTCGC
* * *
109824 GAGCTGTGAATCGGTAAGCTC
1 GAGCTATGAATCAGTATGCTC
109845 ATAAGAGCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (25 bp):
GAGCTATGAATCAGTATGCTCTCGC
Found at i:112637 original size:25 final size:25
Alignment explanation
Indices: 112609--112669 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
112599 TCAGGAATGC
112609 TCATACGAG-CATGTAAACGGGAACG
1 TCATACGAGCCATGT-AACGGGAACG
**
112634 TCATGTGAGCCATGTAACGGGAA-G
1 TCATACGAGCCATGTAACGGGAACG
*
112658 TTCATAAGAGCC
1 -TCATACGAGCC
112670 GTAATCAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 24 0.80
26 5 0.17
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
TCATACGAGCCATGTAACGGGAACG
Found at i:112791 original size:27 final size:25
Alignment explanation
Indices: 112651--112792 Score: 96
Period size: 24 Copynumber: 5.7 Consensus size: 25
112641 AGCCATGTAA
* * *
112651 CGGGAAGTTCATAAGAGCC-GTAAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* ** *
112675 CAGGAAGCTCATGCGAGCTAA-TAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* * *
112699 CGAGAAGCTTA-AAAAGCC-ATTAAT
1 CGGGAAGCTCATAAGAGCCAATT-AT
*
112723 CAGGAAGCTCATAAGAGCCAATTAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* *
112748 CGGGAAGCTCGTGAGAGCCATATATAT
1 CGGGAAGCTCATAAGAGCCA-AT-TAT
112775 CGGGACA-CTCATAAGAGC
1 CGGGA-AGCTCATAAGAGC
112793 TGTAGTGAGT
Statistics
Matches: 87, Mismatches: 23, Indels: 13
0.71 0.19 0.11
Matches are distributed among these distances:
22 1 0.01
23 4 0.05
24 34 0.39
25 25 0.29
26 5 0.06
27 17 0.20
28 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAATTAT
Found at i:113703 original size:32 final size:31
Alignment explanation
Indices: 113662--113729 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
113652 GAAAGCTTTA
**
113662 AATTAAATTTGTTTCATT-TTAATTTTTATTT
1 AATTAAATTT-TGCCATTATTAATTTTTATTT
*
113693 AATTACAATTTTGCCATTATTTATTTTTATTT
1 AATTA-AATTTTGCCATTATTAATTTTTATTT
*
113725 TATTA
1 AATTA
113730 TTTTTTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (31 bp):
AATTAAATTTTGCCATTATTAATTTTTATTT
Found at i:118178 original size:19 final size:20
Alignment explanation
Indices: 118147--118186 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
118137 TGTTTAAAAC
118147 TTTAATAATTTAAGTAATTT
1 TTTAATAATTTAAGTAATTT
*
118167 TTTAAT-ATTTAAGTTATTT
1 TTTAATAATTTAAGTAATTT
118186 T
1 T
118187 CTATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTAATAATTTAAGTAATTT
Found at i:121292 original size:22 final size:22
Alignment explanation
Indices: 121252--121294 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
121242 AGAATTTCAG
* *
121252 ATACAAATACATAATATATCAA
1 ATACAAATACAGAACATATCAA
*
121274 ATACAAATGCAGAACATATCA
1 ATACAAATACAGAACATATCA
121295 GATTCAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (22 bp):
ATACAAATACAGAACATATCAA
Found at i:126541 original size:32 final size:32
Alignment explanation
Indices: 126505--126567 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
126495 TACATGAATA
* * *
126505 ATGAATTTAGATAAATCTACATCCAAATTCAC
1 ATGAATCTAGACAAATATACATCCAAATTCAC
**
126537 ATGAATCTAGACAAATATTTATCCAAATTCA
1 ATGAATCTAGACAAATATACATCCAAATTCA
126568 TTTTGGATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGAATCTAGACAAATATACATCCAAATTCAC
Found at i:126952 original size:17 final size:19
Alignment explanation
Indices: 126929--126965 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
126919 ATGTGTCTTT
*
126929 TTTTTTATA-AAATATATA
1 TTTTTAATATAAATATATA
126947 TTTTTAATATAAATATATA
1 TTTTTAATATAAATATATA
126966 AATATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAATATAAATATATA
Found at i:129492 original size:14 final size:14
Alignment explanation
Indices: 129459--129504 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
129449 AGGAATAGGA
*
129459 AATTTTATTAGATT
1 AATTTAATTAGATT
*
129473 ATTTTAAGTTA-ATT
1 AATTTAA-TTAGATT
129487 AATTTAATTAGATT
1 AATTTAATTAGATT
129501 AATT
1 AATT
129505 AATATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
AATTTAATTAGATT
Found at i:131785 original size:17 final size:16
Alignment explanation
Indices: 131765--131797 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
131755 TATTTTATAT
131765 TAATTAAATAAAGTAAA
1 TAATTAAATAAA-TAAA
131782 TAATTAAATAAATAAA
1 TAATTAAATAAATAAA
131798 AGAAAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAATTAAATAAATAAA
Found at i:131926 original size:5 final size:4
Alignment explanation
Indices: 131912--132021 Score: 73
Period size: 4 Copynumber: 25.8 Consensus size: 4
131902 ATAGTTAAAT
* *
131912 AAAG AAAG AAAAG AAAG AAA- AAAG AATAC AAAG -AAC AAAG AATAG AAAG
1 AAAG AAAG -AAAG AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AA-AG AAAG
* *
131961 AACAG AAGGTG AAACG AAA- AACAG AGAAGG AAAG AAGG AAAG AAAG AAAG
1 AA-AG AA--AG AAA-G AAAG AA-AG A-AA-G AAAG AAAG AAAG AAAG AAAG
132011 AAAG AAAG AAA
1 AAAG AAAG AAA
132022 AGGGAAAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
3 7 0.08
4 49 0.58
5 23 0.27
6 6 0.07
ACGTcount: A:0.69, C:0.05, G:0.24, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:133280 original size:18 final size:17
Alignment explanation
Indices: 133257--133321 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
133247 TACTGTCTGT
133257 TACTGAATAATTGACTGA
1 TACTGAATAATTGA-TGA
* *
133275 TACTGAATAACTGATTGC
1 TACTGAATAATTGA-TGA
* * *
133293 CATTGAACAATTGATCGA
1 TACTGAATAATTGAT-GA
133311 TACTGAATAAT
1 TACTGAATAAT
133322 ATTGATAAAG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
17 1 0.03
18 34 0.97
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (17 bp):
TACTGAATAATTGATGA
Found at i:135676 original size:16 final size:16
Alignment explanation
Indices: 135657--135703 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
135647 TAAAAGATAT
135657 AAATATTTTTATAATA
1 AAATATTTTTATAATA
135673 AAATTTATTTTTATAA-A
1 AAA--TATTTTTATAATA
*
135690 AAACATTTTT-TAAT
1 AAATATTTTTATAAT
135704 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 3 0.11
17 4 0.15
18 11 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATTTTTATAATA
Found at i:136228 original size:2 final size:2
Alignment explanation
Indices: 136221--136245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
136211 TAGAATATGA
136221 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
136246 GAGTCTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137104 original size:10 final size:9
Alignment explanation
Indices: 137090--137174 Score: 64
Period size: 10 Copynumber: 8.9 Consensus size: 9
137080 TATTTAAGCT
137090 TAAAAATTA
1 TAAAAATTA
137099 TTAAAATATTA
1 -TAAAA-ATTA
137110 TAATAAATT-
1 TAA-AAATTA
*
137119 TAAAATTTA
1 TAAAAATTA
137128 TAAAAATTA
1 TAAAAATTA
* *
137137 AAGAAAACTA
1 TA-AAAATTA
*
137147 TAAAAAATA
1 TAAAAATTA
*
137156 TTAAAATGTTA
1 -TAAAA-ATTA
137167 TAAAAATT
1 TAAAAATT
137175 TACATTATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 4 0.07
9 20 0.33
10 28 0.47
11 8 0.13
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:137123 original size:19 final size:18
Alignment explanation
Indices: 137099--137176 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
137089 TTAAAAATTA
137099 TTAAAATATTATAATAAAT
1 TTAAAATATTATAA-AAAT
137118 TTAAAAT-TTATAAAAAT
1 TTAAAATATTATAAAAAT
* * *
137135 TAAAGAAAACTATAAAAAAT
1 TTAA-AATATTAT-AAAAAT
*
137155 ATTAAAATGTTATAAAAAT
1 -TTAAAATATTATAAAAAT
137174 TTA
1 TTA
137177 CATTATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.15
18 11 0.23
19 16 0.33
20 11 0.23
21 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (18 bp):
TTAAAATATTATAAAAAT
Found at i:137211 original size:21 final size:20
Alignment explanation
Indices: 137186--137238 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
137176 ACATTATTAA
* **
137186 ATATTATAAAAGATTATCGAT
1 ATATTATAAAA-AATATAAAT
137207 ATATTATGAAAAAATATAAAT
1 ATATTAT-AAAAAATATAAAT
137228 ATATTATAAAA
1 ATATTATAAAA
137239 TTTGTAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (20 bp):
ATATTATAAAAAATATAAAT
Found at i:140618 original size:21 final size:21
Alignment explanation
Indices: 140593--140645 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
140583 CGCTATTTCT
* *
140593 AATCTCATCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
140614 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
140635 AATCTCACCGC
1 AATCTCACCGC
140646 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:141082 original size:20 final size:20
Alignment explanation
Indices: 141057--141099 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
141047 ATTGGGATTG
141057 AAGTAAGGAAAGGAGAA-GGA
1 AAGTAAGGAAA-GAGAAGGGA
*
141077 AAGTAAGGGAAGAGAAGGGA
1 AAGTAAGGAAAGAGAAGGGA
141097 AAG
1 AAG
141100 GAATGCGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (20 bp):
AAGTAAGGAAAGAGAAGGGA
Found at i:142890 original size:17 final size:17
Alignment explanation
Indices: 142865--142897 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
142855 ATTATGATAT
142865 ATATATATATATAGACA
1 ATATATATATATAGACA
*
142882 ATATGTATATATAGAC
1 ATATATATATATAGAC
142898 TCATGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
ATATATATATATAGACA
Found at i:145195 original size:62 final size:63
Alignment explanation
Indices: 145098--145235 Score: 140
Period size: 62 Copynumber: 2.2 Consensus size: 63
145088 AATCCTAAAT
* * *
145098 AATGAGTTACACGGCCTGGATACACGTCCATGTCCTTGGC-CTGTGTGAC-CTAA-AATACAAAA
1 AATGAGTTACACGGCCTGGACACACCTCCATGTCCTTAGCTC-GTGTGACTCTAATAATA-AAAA
* ** * *
145160 AATGAGTTACACGGCTTGGACACACACTTGA-GTCCTTAGCTCGTGTGCCTCTAATTCATAAAAA
1 AATGAGTTACACGGCCTGGACACAC-CTCCATGTCCTTAGCTCGTGTGACTCTAA-TAATAAAAA
145224 AATGAGTTACAC
1 AATGAGTTACAC
145236 AACCTACCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
62 37 0.59
63 7 0.11
64 16 0.25
65 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (63 bp):
AATGAGTTACACGGCCTGGACACACCTCCATGTCCTTAGCTCGTGTGACTCTAATAATAAAAA
Found at i:145813 original size:11 final size:11
Alignment explanation
Indices: 145797--145836 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
145787 AAAAGTAAAG
145797 AAAATGAAATA
1 AAAATGAAATA
145808 AAAATGAAATAA
1 AAAATGAAAT-A
*
145820 AAAATAAAAATA
1 AAAAT-GAAATA
145832 AAAAT
1 AAAAT
145837 AAAAAGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.38
12 12 0.46
13 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATGAAATA
Found at i:145826 original size:7 final size:6
Alignment explanation
Indices: 145803--145841 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
145793 AAAGAAAATG
*
145803 AAATAA AAAT-G AAATAAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAAT-AA AAATAA AAATAA AAATAA AAA
145842 GAAGAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 21 0.72
7 4 0.14
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:145826 original size:18 final size:19
Alignment explanation
Indices: 145803--145841 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
145793 AAAGAAAATG
*
145803 AAATAAAAAT-GAAATAAA
1 AAATAAAAATAAAAATAAA
145821 AAATAAAAATAAAAATAAA
1 AAATAAAAATAAAAATAAA
145840 AA
1 AA
145842 GAAGAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (19 bp):
AAATAAAAATAAAAATAAA
Found at i:145840 original size:11 final size:11
Alignment explanation
Indices: 145797--145840 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
145787 AAAAGTAAAG
*
145797 AAAATGAAATA
1 AAAATAAAATA
*
145808 AAAATGAAATAA
1 AAAATAAAAT-A
145820 AAAATAAAAATA
1 AAAAT-AAAATA
145832 AAAATAAAA
1 AAAATAAAA
145841 AGAAGAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 14 0.47
12 12 0.40
13 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:152980 original size:16 final size:16
Alignment explanation
Indices: 152959--152989 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
152949 AATCGAAAGT
152959 AAAGAAAAAGAAAAAC
1 AAAGAAAAAGAAAAAC
*
152975 AAAGAAAATGAAAAA
1 AAAGAAAAAGAAAAA
152990 GAAATAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAC
Found at i:152989 original size:7 final size:6
Alignment explanation
Indices: 152959--153019 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
152949 AATCGAAAGT
* *
152959 AAAGAA AAAG-A AAA-AC AAAGAA AATGAA AAAGAA ATAAGAA ACAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA
*
153007 AAATAGA AAAGAA
1 AAAGA-A AAAGAA
153020 GAAGGAACGT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
5 7 0.16
6 20 0.45
7 17 0.39
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:161675 original size:29 final size:29
Alignment explanation
Indices: 161618--161675 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
161608 CCACTTTGAA
* * * * *
161618 ACGAATTCTCAACGAATAAGTTGTTCACC
1 ACGAACTCTCAACAAACAAGTTCTCCACC
161647 ACGAACTCTCAACAAACAAGTTCTCCACC
1 ACGAACTCTCAACAAACAAGTTCTCCACC
161676 TCTTCCACGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.22
Consensus pattern (29 bp):
ACGAACTCTCAACAAACAAGTTCTCCACC
Found at i:166535 original size:5 final size:5
Alignment explanation
Indices: 166525--166556 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
166515 CAATTTGAGA
166525 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
166557 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:166550 original size:9 final size:9
Alignment explanation
Indices: 166526--166556 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
166516 AATTTGAGAA
166526 AAATAAAAT
1 AAATAAAAT
166535 AAAATAAAAT
1 -AAATAAAAT
166545 AAATAAAAT
1 AAATAAAAT
166554 AAA
1 AAA
166557 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:171473 original size:17 final size:17
Alignment explanation
Indices: 171453--171559 Score: 99
Period size: 17 Copynumber: 6.3 Consensus size: 17
171443 AAGTCTACTC
*
171453 AAGTTCAGAATTTGCTT
1 AAGTTCAAAATTTGCTT
171470 AAGTTCAAAATTCT-CTT
1 AAGTTCAAAATT-TGCTT
** * *
171487 AAGCCCAGAATTTGTTT
1 AAGTTCAAAATTTGCTT
* *
171504 AAGTTCAAAATGTGTTT
1 AAGTTCAAAATTTGCTT
* *
171521 AAGTTCAAGATTTGATT
1 AAGTTCAAAATTTGCTT
*
171538 AAATTCAAAATTTGCTT
1 AAGTTCAAAATTTGCTT
*
171555 GAGTT
1 AAGTT
171560 TACAGAAAGA
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
16 1 0.01
17 69 0.97
18 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (17 bp):
AAGTTCAAAATTTGCTT
Found at i:179726 original size:16 final size:17
Alignment explanation
Indices: 179705--179737 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
179695 AATCGATGTC
179705 ACCCCT-AAAGTATCGG
1 ACCCCTAAAAGTATCGG
179721 ACCCCTAAAAGTATCGG
1 ACCCCTAAAAGTATCGG
179738 GTAAGGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (17 bp):
ACCCCTAAAAGTATCGG
Found at i:183074 original size:20 final size:23
Alignment explanation
Indices: 183034--183074 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
183024 TCACTGTCTA
183034 AACACCAAACCAAACAAAATCAC
1 AACACCAAACCAAACAAAATCAC
183057 AACA-CAAA-CAAA-AAAATC
1 AACACCAAACCAAACAAAATC
183075 TCTAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 4 0.22
23 4 0.22
ACGTcount: A:0.66, C:0.29, G:0.00, T:0.05
Consensus pattern (23 bp):
AACACCAAACCAAACAAAATCAC
Found at i:186574 original size:30 final size:30
Alignment explanation
Indices: 186538--186602 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
186528 CAACTTAACA
186538 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
*
186568 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
186598 AACAA
1 AACAA
186603 TAAAATAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.26
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:193290 original size:19 final size:21
Alignment explanation
Indices: 193266--193304 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
193256 ATTTATGCAT
193266 ATGACA-TTAAAATA-ATTAC
1 ATGACATTTAAAATATATTAC
193285 ATGACATTTAAAATATATTA
1 ATGACATTTAAAATATATTA
193305 ATCATAGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (21 bp):
ATGACATTTAAAATATATTAC
Found at i:194307 original size:40 final size:40
Alignment explanation
Indices: 194248--194491 Score: 272
Period size: 40 Copynumber: 6.1 Consensus size: 40
194238 TGTATAACTG
* * *
194248 TTCAGGGTTATCGAAGTACAAAGAGGGGCACGTATGTGCA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
* * * * *
194288 TTCAAGGGTACCGAAGTACAAACAAGAGCATGTATGTGTA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
* * * *
194328 TTCAGGGGTAACAAAGTACAAACAAGGGCACGTATGTGTA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
* * * *
194368 TTCAGGGGTACCAAAGTACAAACAGGAGCTCATATGTGCA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
*
194408 TTTAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
* * * * ***
194448 TTTAGAGGTATCGAAGTACAAATAGGGGCATAAATGTGCA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
194488 TTCA
1 TTCA
194492 TACAATAGTT
Statistics
Matches: 173, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (40 bp):
TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCA
Found at i:194533 original size:13 final size:14
Alignment explanation
Indices: 194517--194550 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
194507 TAAACATTTT
194517 AAATAAAGA-ACAA
1 AAATAAAGATACAA
194530 AAATATAAGATACAA
1 AAATA-AAGATACAA
194545 AAATAA
1 AAATAA
194551 TTTTATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 5 0.26
15 9 0.47
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (14 bp):
AAATAAAGATACAA
Found at i:201442 original size:72 final size:72
Alignment explanation
Indices: 201282--201459 Score: 205
Period size: 72 Copynumber: 2.5 Consensus size: 72
201272 GCCCGCATTT
* * * * *
201282 GAGCTACTCACGGGTCTATACACAAAGTCAGCACCCGGACCCTAAAGCATTATCATGTAATACCC
1 GAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATGTAATACCC
**
201347 GCTCATT
66 GCTCAGC
* * * * *
201354 GAGCTGCTTACAGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATG-ATATGCT
1 GAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATGTA-ATACC
*
201418 CTCTCAGC
65 CGCTCAGC
* *
201426 GAGTTACTCACGGGTTTATACACAAAGTCTGTAC
1 GAGCTACTCACGGGTTTATACACAAAGTCAGTAC
201460 TCGGACCCAC
Statistics
Matches: 87, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
71 1 0.01
72 86 0.99
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (72 bp):
GAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATGTAATACCC
GCTCAGC
Found at i:207484 original size:22 final size:22
Alignment explanation
Indices: 207458--207531 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 22
207448 AACACTAAAA
207458 TGCTATATAGAGAGCACAGATG
1 TGCTATATAGAGAGCACAGATG
207480 TGCTA-ATCAGAGAGCACCA-ATG
1 TGCTATAT-AGAGAGCA-CAGATG
* *
207502 TGCTAATAATTAGAGAGCACTGACG
1 TGCT-AT-A-TAGAGAGCACAGATG
207527 TGCTA
1 TGCTA
207532 ATAATCAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
21 2 0.05
22 20 0.47
23 3 0.07
24 2 0.05
25 15 0.35
26 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (22 bp):
TGCTATATAGAGAGCACAGATG
Found at i:207517 original size:25 final size:25
Alignment explanation
Indices: 207483--207544 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
207473 ACAGATGTGC
*
207483 TAATCAGAGAGCACCAATGTGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
* **
207508 TAATTAGAGAGCACTGACGTGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
207533 TAATCAGAGAGC
1 TAATCAGAGAGC
207545 GCGCTAAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAGCACCAACGTGCTAA
Found at i:208591 original size:13 final size:13
Alignment explanation
Indices: 208573--208597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208563 CCCAAATTTT
208573 CTTTTTTCTTTCC
1 CTTTTTTCTTTCC
208586 CTTTTTTCTTTC
1 CTTTTTTCTTTC
208598 TTTCTCTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTTTCTTTCC
Found at i:208664 original size:5 final size:5
Alignment explanation
Indices: 208650--208725 Score: 61
Period size: 5 Copynumber: 15.0 Consensus size: 5
208640 CTTTTGTTTT
* *
208650 ATATA TATATA ATATA ATATT ATAATA ATATA ATATA ATA-A CATACTT
1 ATATA -ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA -ATA-TA
208698 AT-TA AT-TA ACTA-A ATATA ATATA ATATA
1 ATATA ATATA A-TATA ATATA ATATA ATATA
208726 TATTTTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
4 9 0.15
5 39 0.66
6 11 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:208672 original size:21 final size:21
Alignment explanation
Indices: 208648--208689 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
208638 TTCTTTTGTT
208648 TTAT-ATATATATAATATAATA
1 TTATAATA-ATATAATATAATA
208669 TTATAATAATATAATATAATA
1 TTATAATAATATAATATAATA
208690 ACATACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATAATAATATAATATAATA
Found at i:208729 original size:29 final size:27
Alignment explanation
Indices: 208650--208729 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
208640 CTTTTGTTTT
208650 ATATATATATAATATAATATTA-TAATA
1 ATATA-ATATAATATAATATTATTAATA
208677 ATATAATATAATA-ACATACTTATTAATTA
1 ATATAATATAATATA-ATA-TTATTAA-TA
208706 ACTA-AATATAATATAATATATATT
1 A-TATAATATAATATAATAT-TATT
208730 TTAAATTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
25 1 0.02
26 11 0.24
27 8 0.17
28 4 0.09
29 19 0.41
30 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAATATAATATAATATTATTAATA
Found at i:209481 original size:85 final size:85
Alignment explanation
Indices: 209338--209507 Score: 234
Period size: 85 Copynumber: 2.0 Consensus size: 85
209328 GAACTTCATG
* * *
209338 TACTTGTGTTGTTGCAGGTACATCATAGGAGCATCTAAAATTGGATTCTAACTTGATCTCTGACA
1 TACTTGTGTTGTTGCAGGTACATCACAAGAGCATCTAAAATTGGATTCTAACATGATCTCTGACA
*
209403 TTGTCTTACATATGGTGAAA
66 TTATCTTACATATGGTGAAA
* ** * *
209423 TACTTGTGTTGTTGTAGGTATGTCACAAGATCAT-TCAAAATTGGATTCTGACATGATCTCTGAC
1 TACTTGTGTTGTTGCAGGTACATCACAAGAGCATCT-AAAATTGGATTCTAACATGATCTCTGAC
*
209487 ATTATCTTACCTATGGTGAAA
65 ATTATCTTACATATGGTGAAA
209508 GCGAGTTCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.01
85 73 0.99
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (85 bp):
TACTTGTGTTGTTGCAGGTACATCACAAGAGCATCTAAAATTGGATTCTAACATGATCTCTGACA
TTATCTTACATATGGTGAAA
Found at i:212519 original size:48 final size:48
Alignment explanation
Indices: 212416--212640 Score: 178
Period size: 48 Copynumber: 4.8 Consensus size: 48
212406 AAGAGGGTAA
* * * * *
212416 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTGGTTCACATGTT
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATCTC
* * * *
212464 GAGGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATCTC
* * * * * *
212512 AATGCCGATTCTATGTCCCAAACATGATCTTACACTAGCTCTCATAATG
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCAT-CTC
* * * *
212561 TA-GCCGATGCCATGT-CTCAAATATGGTCTTGCAC-A-----CATATC
1 AATGCCGATGCCATGTCCT-AAACATGGTCTTACACTAGCTCTCATCTC
* * *
212602 AATACCGATGCCATGTCCCAGACATGGTCTTACACTAGC
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGC
212641 ACACATATCA
Statistics
Matches: 137, Mismatches: 33, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
41 3 0.02
42 28 0.20
43 2 0.01
47 2 0.01
48 100 0.73
49 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATCTC
Found at i:212587 original size:96 final size:96
Alignment explanation
Indices: 212416--212647 Score: 228
Period size: 96 Copynumber: 2.5 Consensus size: 96
212406 AAGAGGGTAA
* * * * **
212416 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTGGTTCACATGTTGAGGCCGATGCCATGTC
1 AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATAATGAGGCCGATGCCATGTC
*
212481 CTAGACATGGTCTTACACTAGCTCTCGTCTC
66 CTAAACATGGTCTTACACTAGCTCTCGTCTC
* * *
212512 AATGCCGATTCTATGTCCCAAACATGATCTTACACTAGCTCTCATAATGTA-GCCGATGCCATGT
1 AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATAATG-AGGCCGATGCCATGT
* * * *
212576 -CTCAAATATGGTCTTGCAC-A-----CATATC
65 CCT-AAACATGGTCTTACACTAGCTCTCGTCTC
* * * *
212602 AATACCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATA
1 AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATA
212648 TCACATGTTC
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
90 43 0.38
95 3 0.03
96 66 0.58
97 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (96 bp):
AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATAATGAGGCCGATGCCATGTC
CTAAACATGGTCTTACACTAGCTCTCGTCTC
Found at i:214607 original size:74 final size:70
Alignment explanation
Indices: 214486--214679 Score: 237
Period size: 74 Copynumber: 2.7 Consensus size: 70
214476 TTTTTCATTT
** *
214486 TTTCCATTTTTGGGTAAATTGTAAATAAGTATATTATTTATGTAAAAATACAATATAATACAATA
1 TTTCCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATAC---AT--TACAATA
214551 AAAA-AATTG
61 AAAATAATTG
* * *
214560 TTTCCATTTTTTTGTAAATTATAAATAAGTATATTATTGATGTAAAAATACATTGCAATAAAAAT
1 TTTCCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACATTACAATAAAAAT
*
214625 AATTT
66 AATTG
* *
214630 TTTTCATTTTCTTCATAAATTGTAAATAAGTATATTATTGATGTAGAAAA
1 TTTCCATTTT-TTCGTAAATTGTAAATAAGTATATTATTGATGTA-AAAA
214680 ATAAAGAAAC
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
69 10 0.09
70 13 0.12
71 33 0.31
72 4 0.04
74 47 0.44
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (70 bp):
TTTCCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACATTACAATAAAAAT
AATTG
Found at i:216819 original size:13 final size:13
Alignment explanation
Indices: 216801--216831 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
216791 AGAACAACTT
216801 ATTAATTATATTA
1 ATTAATTATATTA
216814 ATTAATTATATTA
1 ATTAATTATATTA
216827 ATTAA
1 ATTAA
216832 AAGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAATTATATTA
Found at i:221012 original size:5 final size:5
Alignment explanation
Indices: 221002--221069 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 5
220992 TATGTCTTGC
* *
221002 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT AAAAAT CAAAAGA
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT -AAAA-T
221051 AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
221070 ATAAGACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 3 0.06
5 22 0.42
6 27 0.52
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Done.