Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 3 of 128
Found at i:789126 original size:18 final size:18
Alignment explanation
Indices: 789103--789145 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
789093 ATTCAAGGTG
*
789103 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATA
789121 TAATTAATTAAAATTATA
1 TAATTAATTAAAATTATA
789139 TAATTAA
1 TAATTAA
789146 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAATTAAAATTATA
Found at i:800332 original size:11 final size:11
Alignment explanation
Indices: 800316--800341 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
800306 ATTTAGTTTG
800316 GTATCGCTACA
1 GTATCGCTACA
800327 GTATCGCTACA
1 GTATCGCTACA
800338 GTAT
1 GTAT
800342 GTAATCTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (11 bp):
GTATCGCTACA
Found at i:800364 original size:32 final size:32
Alignment explanation
Indices: 800318--800386 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
800308 TTAGTTTGGT
* * *
800318 ATCGCTACAGTATCGCTACAGTATGTAATCTC
1 ATCGTTACAGTATCGCTACAATATCTAATCTC
800350 ATCGTTACAGTATCGCTACAATATCTAATCTC
1 ATCGTTACAGTATCGCTACAATATCTAATCTC
800382 ATCGT
1 ATCGT
800387 CATCGCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (32 bp):
ATCGTTACAGTATCGCTACAATATCTAATCTC
Found at i:813993 original size:22 final size:22
Alignment explanation
Indices: 813952--813993 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
813942 GTGATTATAT
*
813952 ATAAAAATTATATAAAAAATTC
1 ATAAAAATTAGATAAAAAATTC
* *
813974 ATAAAAATTAGGTAATAAAT
1 ATAAAAATTAGATAAAAAAT
813994 ATATTTATTA
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:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (22 bp):
ATAAAAATTAGATAAAAAATTC
Found at i:819224 original size:24 final size:23
Alignment explanation
Indices: 819197--819252 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
819187 GCCCGGCCCG
819197 ATTTTTAATAAACACAAA-AAAAAT
1 ATTTTTAA-AAACA-AAATAAAAAT
*
819221 A-TTTTAAAAATAAAATTAAAAAT
1 ATTTTTAAAAACAAAA-TAAAAAT
819244 ATTTTTAAA
1 ATTTTTAAA
819253 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.11
22 4 0.14
23 13 0.46
24 8 0.29
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTTTTAAAAACAAAATAAAAAT
Found at i:819251 original size:12 final size:11
Alignment explanation
Indices: 819215--819263 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
819205 TAAACACAAA
819215 AAAAATATTTT
1 AAAAATATTTT
**
819226 AAAAATAAAATT
1 AAAAAT-ATTTT
819238 AAAAATATTTT
1 AAAAATATTTT
* *
819249 TAAAGTATTTT
1 AAAAATATTTT
819260 AAAA
1 AAAA
819264 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:820485 original size:22 final size:20
Alignment explanation
Indices: 820432--820485 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
820422 TAAACTTTCT
* *
820432 TTTTCACTAATGTTTTGTTG
1 TTTTCGCTATTGTTTTGTTG
*
820452 TTGTTCGTTATTGTTTTGTTG
1 TT-TTCGCTATTGTTTTGTTG
820473 TCATTTCGCTATT
1 T--TTTCGCTATT
820486 ATATTGTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 16 0.59
22 8 0.30
23 1 0.04
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.61
Consensus pattern (20 bp):
TTTTCGCTATTGTTTTGTTG
Found at i:825033 original size:4 final size:4
Alignment explanation
Indices: 825024--825050 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
825014 AACCCAAATA
825024 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
825051 ATTGGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:826470 original size:9 final size:9
Alignment explanation
Indices: 826456--826489 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
826446 TTTGGATCTA
826456 AATTTAATT
1 AATTTAATT
826465 AATTTAATT
1 AATTTAATT
* *
826474 AATATGATT
1 AATTTAATT
826483 AATTTAA
1 AATTTAA
826490 AATTAATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
AATTTAATT
Found at i:828061 original size:5 final size:5
Alignment explanation
Indices: 828051--828083 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
828041 TAATTAAGCT
*
828051 CAACC CAACC CAACC CAACC CAACT CAACC CAA
1 CAACC CAACC CAACC CAACC CAACC CAACC CAA
828084 ACAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.55, G:0.00, T:0.03
Consensus pattern (5 bp):
CAACC
Found at i:831978 original size:310 final size:316
Alignment explanation
Indices: 831550--832208 Score: 956
Period size: 328 Copynumber: 2.1 Consensus size: 316
831540 CTATCTAATA
*
831550 CATCTGTGCTAGCAGCTTCTTGTGAGGATTGTTCCTCAGTTTCATCATTTACAGTAATATCTTCT
1 CATCTGTACTAGCAGCTTCTTGTGAGGATTGTTCCTCAGTTTCATCATTTACAGTAATATCTTCT
* * *
831615 TCTGCACCAGTTCAATACAGTAGCATATATAAACATAATTTAGAAAAACTGATGCTGAAATATGT
66 TCTGAACCAGTTCAATACAGTAGCATATATAAACATAATTTAGAAAAACTGATGCTAAAACATGT
*
831680 TG-TTTCTGC-ATTAGTTCATTGGAATTG-TA-A-C-A-TATGTTTATTAACCTTTCTCATCAGG
131 TGTTTTCTGCTATT-GTTCATTGGAATTGATAGAGCAATTATATTTATTAACCTTTCTCATCAGG
*
831738 TGTCTGCTTATCAACACTTGGATATTCCATTCCACCACGATCACCAGAAACCTGGCCTGTCTCAG
195 TGTCTGCTTATCAACACTTGGAAATTCCATTCCACCACGATCACCAGAAACCTGGCCTGTCTCAG
* * * *
831803 TTCCACGATTACTTTCATCTCCACCTGCCGGAACTAGGCAAGCTTCTGCATTTGTTT
260 TTCCACAAGTACTTTCATCTCCACCTGCAGGAACTAGGCAAGCTTCTGCATTTGCTT
*
831860 CATCTGTATTAGCAGCTTCTTGTGAGGATTGTTCCTCAGTTTCATCATTTACAGTAATATCTTCT
1 CATCTGTACTAGCAGCTTCTTGTGAGGATTGTTCCTCAGTTTCATCATTTACAGTAATATCTTCT
* *
831925 TCTGAACC-GATTCAATACAGTAGTATATATAAACATAATTTAGAAATACTGATGCTAAAACATG
66 TCTGAACCAG-TTCAATACAGTAGCATATATAAACATAATTTAGAAAAACTGATGCTAAAACATG
831989 TTGTTTTCTGCTATTGTTCATTGGAATTGCAACATATAGGCAGCAAAATATTATATTTATTAACC
130 TTGTTTTCTGCTATTGTTCATTGGAATTG------ATA-G-AGC---A-ATTATATTTATTAACC
* * * *
832054 TTTCTCATCAGGTTTCTGCTTGTCAACACTTGGAAATTCCTTTCCACCACGATCACCGGAAACCT
183 TTTCTCATCAGGTGTCTGCTTATCAACACTTGGAAATTCCATTCCACCACGATCACCAGAAACCT
*
832119 GGCCTGTCTCGGTTCCACAAGTACTTTCATCTCCACCTGCAGGAACTAGGCAAGCTTCTGCATTT
248 GGCCTGTCTCAGTTCCACAAGTACTTTCATCTCCACCTGCAGGAACTAGGCAAGCTTCTGCATTT
832184 GCTT
313 GCTT
* *
832188 CTTCTGTCCTAGCAGCTTCTT
1 CATCTGTACTAGCAGCTTCTT
832209 TCAAGGGCAT
Statistics
Matches: 308, Mismatches: 21, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
309 1 0.00
310 123 0.40
311 21 0.07
312 3 0.01
318 2 0.01
321 1 0.00
322 1 0.00
327 1 0.00
328 155 0.50
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (316 bp):
CATCTGTACTAGCAGCTTCTTGTGAGGATTGTTCCTCAGTTTCATCATTTACAGTAATATCTTCT
TCTGAACCAGTTCAATACAGTAGCATATATAAACATAATTTAGAAAAACTGATGCTAAAACATGT
TGTTTTCTGCTATTGTTCATTGGAATTGATAGAGCAATTATATTTATTAACCTTTCTCATCAGGT
GTCTGCTTATCAACACTTGGAAATTCCATTCCACCACGATCACCAGAAACCTGGCCTGTCTCAGT
TCCACAAGTACTTTCATCTCCACCTGCAGGAACTAGGCAAGCTTCTGCATTTGCTT
Found at i:832544 original size:3 final size:3
Alignment explanation
Indices: 832538--832565 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
832528 TCTACACCAG
832538 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
832566 TACCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:839243 original size:22 final size:22
Alignment explanation
Indices: 839218--839293 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
839208 AGATAATCAC
839218 ACACAAGAGGCATAAATGGAAA
1 ACACAAGAGGCATAAATGGAAA
839240 ACACAAGA---A-AAATGAGAAAATCA
1 ACACAAGAGGCATAAATG-G--AA--A
839263 CACACAAGAGGCATAAATGGAAA
1 -ACACAAGAGGCATAAATGGAAA
839286 ACACAAGA
1 ACACAAGA
839294 AAAATGAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 20
0.69 0.00 0.31
Matches are distributed among these distances:
18 5 0.11
19 2 0.05
21 2 0.05
22 16 0.36
23 2 0.05
24 8 0.18
25 2 0.05
27 2 0.05
28 5 0.11
ACGTcount: A:0.58, C:0.16, G:0.18, T:0.08
Consensus pattern (22 bp):
ACACAAGAGGCATAAATGGAAA
Found at i:839243 original size:24 final size:24
Alignment explanation
Indices: 839216--839290 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
839206 CAAGATAATC
839216 ACACACAAGAGGCATAAATGG-AA
1 ACACACAAGAGGCATAAATGGAAA
839239 A-ACACAAGA---A-AAATGAGAAAA
1 ACACACAAGAGGCATAAATG-G-AAA
839260 TCACACACAAGAGGCATAAATGGAAA
1 --ACACACAAGAGGCATAAATGGAAA
839286 ACACA
1 ACACA
839291 AGAAAAATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 19
0.69 0.00 0.31
Matches are distributed among these distances:
18 5 0.12
19 2 0.05
21 2 0.05
22 8 0.19
23 2 0.05
24 13 0.31
26 3 0.07
27 2 0.05
28 5 0.12
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.08
Consensus pattern (24 bp):
ACACACAAGAGGCATAAATGGAAA
Found at i:839268 original size:46 final size:46
Alignment explanation
Indices: 839212--839305 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
839202 AAAACAAGAT
839212 AATCACACACAAGAGGCATAAATGGAAAACACAAGAAAAATGAGAA
1 AATCACACACAAGAGGCATAAATGGAAAACACAAGAAAAATGAGAA
839258 AATCACACACAAGAGGCATAAATGGAAAACACAAGAAAAATGAGAA
1 AATCACACACAAGAGGCATAAATGGAAAACACAAGAAAAATGAGAA
839304 AA
1 AA
839306 GCTTGGGTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.09
Consensus pattern (46 bp):
AATCACACACAAGAGGCATAAATGGAAAACACAAGAAAAATGAGAA
Found at i:840013 original size:16 final size:17
Alignment explanation
Indices: 839981--840013 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
839971 TAAGGAAAAT
839981 GGATGAATTAGGACCAA
1 GGATGAATTAGGACCAA
839998 GGATGAATTA-GACCAA
1 GGATGAATTAGGACCAA
840014 ATTGAAAAGG
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:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (17 bp):
GGATGAATTAGGACCAA
Found at i:840194 original size:11 final size:11
Alignment explanation
Indices: 840180--840229 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
840170 AGATAAATAT
840180 TATTTTATTAA
1 TATTTTATTAA
*
840191 TATTTTACTAA
1 TATTTTATTAA
* *
840202 TATTTAATGAGA
1 TATTTTATTA-A
*
840214 TATTTTATTAT
1 TATTTTATTAA
840225 TATTT
1 TATTT
840230 ATTTTTATTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:842365 original size:32 final size:32
Alignment explanation
Indices: 842327--842394 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
842317 ACATTTCCCC
* * * *
842327 AAAAGTACTTAGTTAGTACCTGAACTTGTCCA
1 AAAAGTACCTAATTAGTACCTAAACTTGTCAA
* *
842359 AAAAGTACCTAATTGGTGCCTAAACTTGTCAA
1 AAAAGTACCTAATTAGTACCTAAACTTGTCAA
842391 AAAA
1 AAAA
842395 AATTACTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (32 bp):
AAAAGTACCTAATTAGTACCTAAACTTGTCAA
Found at i:845031 original size:30 final size:31
Alignment explanation
Indices: 844997--845073 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
844987 TATAAATACC
* *
844997 AAAAAATCATTTTAAAAAT-TAAAAAAAATTA
1 AAAAAAT-ATTTTAAAAATAAAAAAAAAATTT
*
845028 AAAAAAAATTTT-AAAATAAAAAAAAAATTT
1 AAAAAATATTTTAAAAATAAAAAAAAAATTT
*
845058 AAAAAGTATTTTAAAA
1 AAAAAATATTTTAAAA
845074 GTATTTTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 5 0.13
30 25 0.64
31 9 0.23
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (31 bp):
AAAAAATATTTTAAAAATAAAAAAAAAATTT
Found at i:845047 original size:18 final size:19
Alignment explanation
Indices: 845021--845061 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
845011 AAAATTAAAA
*
845021 AAAATTAAAAAAAAATTTT
1 AAAATTAAAAAAAAAATTT
845040 AAAA-TAAAAAAAAAATTT
1 AAAATTAAAAAAAAAATTT
845058 AAAA
1 AAAA
845062 AGTATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATTAAAAAAAAAATTT
Found at i:845053 original size:10 final size:10
Alignment explanation
Indices: 845010--845034 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
845000 AAATCATTTT
845010 AAAAATTAAA
1 AAAAATTAAA
845020 AAAAATTAAA
1 AAAAATTAAA
845030 AAAAA
1 AAAAA
845035 ATTTTAAAAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:845062 original size:19 final size:19
Alignment explanation
Indices: 845020--845062 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
845010 AAAAATTAAA
*
845020 AAAAATTAAAAAAAAATTT
1 AAAAATAAAAAAAAAATTT
*
845039 TAAAATAAAAAAAAAATTT
1 AAAAATAAAAAAAAAATTT
845058 AAAAA
1 AAAAA
845063 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAAAAAATTT
Found at i:845080 original size:41 final size:41
Alignment explanation
Indices: 845035--845137 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
845025 TTAAAAAAAA
845035 ATTTTAAAATAAAAAAAAAATTTAAAAAGTATTTTAAAAGT
1 ATTTTAAAATAAAAAAAAAATTTAAAAAGTATTTTAAAAGT
* ** *
845076 ATTTTCAAATTTAAAAAAATTTTAAAAAGTATTTTAAAAGT
1 ATTTTAAAATAAAAAAAAAATTTAAAAAGTATTTTAAAAGT
845117 ATTTTAAAATAAAAAATAAAA
1 ATTTTAAAATAAAAAA-AAAA
845138 AATATATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 50 0.94
42 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (41 bp):
ATTTTAAAATAAAAAAAAAATTTAAAAAGTATTTTAAAAGT
Found at i:845086 original size:30 final size:30
Alignment explanation
Indices: 845052--845110 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
845042 AATAAAAAAA
*
845052 AAATTTAAAAAGTATTTT-AAAAGTATTTTC
1 AAATTTAAAAA-AATTTTAAAAAGTATTTTC
845082 AAATTTAAAAAAATTTTAAAAAGTATTTT
1 AAATTTAAAAAAATTTTAAAAAGTATTTT
845111 AAAAGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
AAATTTAAAAAAATTTTAAAAAGTATTTTC
Found at i:848228 original size:524 final size:525
Alignment explanation
Indices: 847555--848605 Score: 2086
Period size: 524 Copynumber: 2.0 Consensus size: 525
847545 AAATTGTTTT
847555 TAAATAATATGTTAAAAGATGTTTTAAAAGTTATATTTAAAAAAATGATTTTTAAAATAATTTCT
1 TAAATAATATG-TAAAAGATGTTTTAAAAGTTATATTTAAAAAAATGATTTTTAAAATAATTTCT
847620 CTTCACCTTATTTAATACTGTATTTTAAAACTAATTTCTTAGTAAAAAATATTTTTAGATATCTA
65 CTTCACCTTATTTAATACTGTATTTTAAAACTAATTTCTTAGTAAAAAATATTTTTAGATATCTA
847685 TTTAAAAGTGTTTGTTCATGTTTAAAAATGTTTTTATAAAATAAAATAATTCTAAAAAGAAATTT
130 TTTAAAAGTGTTTGTTCATGTTTAAAAATGTTTTTATAAAATAAAATAATTCTAAAAAGAAATTT
847750 TGTTTTAAAATATATTTTAAATATGAGTATATAACGAGGACTTATTTTTTAAAAGTAAAAATATT
195 TGTTTTAAAATATATTTTAAATATGAGTATATAACGAGGACTTATTTTTTAAAAGTAAAAATATT
847815 TAATTAAAAATTATTAACCTTAAGCTTAATTATTGAGTCAAGTTCGAGTACAAAACAAGGTGAAC
260 TAATTAAAAATTATTAACCTTAAGCTTAATTATTGAGTCAAGTTCGAGTACAAAACAAGGTGAAC
847880 AAGCTTAATCGAGTTCGAGTAGCTTAATTATATTTCAAGTCGAACTCAAATTTAAAAATAAATAT
325 AAGCTTAATCGAGTTCGAGTAGCTTAATTATATTTCAAGTCGAACTCAAATTTAAAAATAAATAT
847945 TCAATCAAACTCGAGCTGAATATTTCAAGTCAAACTTGAACCTGACAATATTTGGGCTCGACTAT
390 TCAATCAAACTCGAGCTGAATATTTCAAGTCAAACTTGAACCTGACAATATTTGGGCTCGACTAT
848010 ATTACACTCCTAATTATCATCTGACAATGTACCAAGCTCTAATTTTTTTAATGGTTTTTTAATTA
455 ATTACACTCCTAATTATCATCTGACAATGTACCAAGCTCTAATTTTTTTAATGGTTTTTTAATTA
848075 GTATGA
520 GTATGA
848081 TAAATAATATG-AAAAGATGTTTTAAAAGTTATATTTAAAAAAATGATTTTTAAAATAATTTCTC
1 TAAATAATATGTAAAAGATGTTTTAAAAGTTATATTTAAAAAAATGATTTTTAAAATAATTTCTC
848145 TTCACCTTATTTAATACTGTATTTTAAAACTAATTTCTTAGTAAAAAATATTTTTAGATATCTAT
66 TTCACCTTATTTAATACTGTATTTTAAAACTAATTTCTTAGTAAAAAATATTTTTAGATATCTAT
848210 TTAAAAGTGTTTGTTCATGTTTAAAAATGTTTTTATAAAATAAAATAATTCTAAAAAGAAATTTT
131 TTAAAAGTGTTTGTTCATGTTTAAAAATGTTTTTATAAAATAAAATAATTCTAAAAAGAAATTTT
848275 GTTTTAAAATATATTTTAAATATGAGTATATAACGAGGACTTATTTTTTAAAAGTAAAAATATTT
196 GTTTTAAAATATATTTTAAATATGAGTATATAACGAGGACTTATTTTTTAAAAGTAAAAATATTT
848340 AATTAAAAATTATTAACCTTAAGCTTAATTATTGAGTCAAGTTCGAGTACAAAACAAGGTGAACA
261 AATTAAAAATTATTAACCTTAAGCTTAATTATTGAGTCAAGTTCGAGTACAAAACAAGGTGAACA
848405 AGCTTAATCGAGTTCGAGTAGCTTAATTATATTTCAAGTCGAACTCAAATTTAAAAATAAATATT
326 AGCTTAATCGAGTTCGAGTAGCTTAATTATATTTCAAGTCGAACTCAAATTTAAAAATAAATATT
848470 CAATCAAACTCGAGCTGAATATTTCAAGTCAAACTTGAACCTGACAATATTTGGGCTCGACTATA
391 CAATCAAACTCGAGCTGAATATTTCAAGTCAAACTTGAACCTGACAATATTTGGGCTCGACTATA
848535 TTACACTCCTAATTATCATCTGACAATGTACCAAGCTCTAATTTTTTTAATGGTTTTTTAATTAG
456 TTACACTCCTAATTATCATCTGACAATGTACCAAGCTCTAATTTTTTTAATGGTTTTTTAATTAG
848600 TATGA
521 TATGA
848605 T
1 T
848606 GTTTAATACA
Statistics
Matches: 525, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
524 514 0.98
526 11 0.02
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39
Consensus pattern (525 bp):
TAAATAATATGTAAAAGATGTTTTAAAAGTTATATTTAAAAAAATGATTTTTAAAATAATTTCTC
TTCACCTTATTTAATACTGTATTTTAAAACTAATTTCTTAGTAAAAAATATTTTTAGATATCTAT
TTAAAAGTGTTTGTTCATGTTTAAAAATGTTTTTATAAAATAAAATAATTCTAAAAAGAAATTTT
GTTTTAAAATATATTTTAAATATGAGTATATAACGAGGACTTATTTTTTAAAAGTAAAAATATTT
AATTAAAAATTATTAACCTTAAGCTTAATTATTGAGTCAAGTTCGAGTACAAAACAAGGTGAACA
AGCTTAATCGAGTTCGAGTAGCTTAATTATATTTCAAGTCGAACTCAAATTTAAAAATAAATATT
CAATCAAACTCGAGCTGAATATTTCAAGTCAAACTTGAACCTGACAATATTTGGGCTCGACTATA
TTACACTCCTAATTATCATCTGACAATGTACCAAGCTCTAATTTTTTTAATGGTTTTTTAATTAG
TATGA
Found at i:854784 original size:6 final size:6
Alignment explanation
Indices: 854773--854814 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
854763 TCATTGTCAC
854773 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
854815 AGAATTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:877547 original size:127 final size:128
Alignment explanation
Indices: 877210--877926 Score: 711
Period size: 127 Copynumber: 5.6 Consensus size: 128
877200 AACCTTATTC
* * *** * * *
877210 AACCATGGATGACATGAATAAGATACCAGTGCTCGAGCAATATATCAC-AGGAATAGGAACATGT
1 AACCATGGATGATACGAATAAGATAATGGTGGTCAAGCAATATATCACTA-GAATAGAAACATGT
* * * * ** *
877274 AAAAGATAAGCTTTACTGGATTGATTTCAACTAATGCAGCTTAGCT-T-TAAAAATAC-T-ATCC
65 AAAAGAAAAGTTTTTCTGGGTCAATTTCAACTAATGCAGCTTAGCTATATAAAAA-ACATGAT-T
877335 T
128 T
* * * *
877336 -ACCATGGATGATATGAATAA-TTGAATGGTGCTCAGGCAATATATCAC-----TAGAAACATGT
1 AACCATGGATGATACGAATAAGAT-AATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGT
877394 AAAAAAGAAAAGTTTTTCTGGGTCAATTTCAAAC-AATGCAGCTTAGCTATATAAAAAACATGAT
65 --AAAAGAAAAGTTTTTCTGGGTCAATTTC-AACTAATGCAGCTTAGCTATATAAAAAACATGAT
877458 TT
127 TT
* **
877460 GACCATAAATGATACGAATAAGATAAT-GTGGTCAAGCAATATATCACTAGAATAGAAACATGTA
1 AACCATGGATGATACGAATAAGATAATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTA
* * *
877524 AAAGAAAAGTTTTTCTGGGTCAATTTCAACTGATGCAGCTTAGCTATA-GAAAAACATGATTC
66 AAAGAAAAGTTTTTCTGGGTCAATTTCAACTAATGCAGCTTAGCTATATAAAAAACATGATTT
** *
877586 AATTATGGATGATACGAATAAAGAAAATGGTGTTCAAGCTGTTCAAGCAATATATCACTAGAATA
1 AACCATGGATGATACGAAT-AAGATAAT-G-G-T---G--G-TCAAGCAATATATCACTAGAATA
* ** * *
877651 GAATCATGTAAAAGAAAAGTTTTT-TCGGGTTGATTGCAATTAATGCAGCTTAGCT-T-T-AAAA
56 GAAACATGTAAAAGAAAAGTTTTTCT-GGGTCAATTTCAACTAATGCAGCTTAGCTATATAAAAA
* *
877712 ACATGACTC
120 ACATGATTT
** * *
877721 AACCATGGATGATACGAATAAGATAATGGTTCTCAAGCAATATATCACTAGAATACAAACATGAA
1 AACCATGGATGATACGAATAAGATAATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTA
** *
877786 AAAGAAAAGTTTTTCCAGGT-AGATTTCAACTAACGCAGCTTAGCTATA-AAAAAACATGATTT
66 AAAGAAAAGTTTTTCTGGGTCA-ATTTCAACTAATGCAGCTTAGCTATATAAAAAACATGATTT
* * *
877848 GATCATGGATGACACGAATAAGATAATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTA
1 AACCATGGATGATACGAATAAGATAATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTA
877913 AAAGAAAAGTTTTT
66 AAAGAAAAGTTTTT
877927 TCAGGTTGAA
Statistics
Matches: 497, Mismatches: 60, Indels: 67
0.80 0.10 0.11
Matches are distributed among these distances:
120 10 0.02
122 36 0.07
123 6 0.01
124 27 0.05
125 127 0.26
126 31 0.06
127 134 0.27
129 11 0.02
130 1 0.00
131 2 0.00
132 1 0.00
133 1 0.00
134 8 0.02
135 29 0.06
136 3 0.01
137 70 0.14
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (128 bp):
AACCATGGATGATACGAATAAGATAATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTA
AAAGAAAAGTTTTTCTGGGTCAATTTCAACTAATGCAGCTTAGCTATATAAAAAACATGATTT
Found at i:877659 original size:137 final size:128
Alignment explanation
Indices: 877181--877926 Score: 689
Period size: 125 Copynumber: 5.9 Consensus size: 128
877171 CATCCTAGTA
** * * * * * ***
877181 AATGCAGCCAAGCTAT--AAAAACCTTATTCAACCATGGATGACATGAATAAGATACCAG-TGC-
1 AATGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGATACGAATAAGATAATGGTTGCG
* * * * * * *
877242 TCGAGCAATATATCAC-AGGAATAGGAACATGTAAAAGATAAGCTTTACTGGATTGATTTCAACT
66 TCAAGCAATATATCACTA-GAATAGAAACATGTAAAAGAAAAGTTTTTCTGG-GTAATTTCAACT
* * * * * * *
877306 AATGCAGCTTAGCTTTAAAAATAC-T-ATCCTACCATGGATGATATGAATAA-TTGAATGG-TGC
1 AATGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGATACGAATAAGAT-AATGGTTGC
*
877367 -TCAGGCAATATATCAC-----TAGAAACATGTAAAAAAGAAAAGTTTTTCTGGGTCAATTTCAA
65 GTCAAGCAATATATCACTAGAATAGAAACATGT--AAAAGAAAAGTTTTTCTGGGT-AATTTC-A
877426 AC-
126 ACT
** * **
877428 AATGCAGCTTAGCTATATAAAAAACATGATTTGACCATAAATGATACGAATAAGATAAT-G-TG-
1 AATGCAGCTTAGCTATA-AAAAAACATGATTCAATCATGGATGATACGAATAAGATAATGGTTGC
877490 GTCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTCTGGGTCAATTTCAACT
65 GTCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTCTGGGT-AATTTCAACT
* * * *
877555 GATGCAGCTTAGCTATAGAAAAACATGATTCAATTATGGATGATACGAATAAAGAAAATGGTGTT
1 AATGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGATACGAAT-AAGATAAT-G-GTT
* *
877620 CAAGCTGTTCAAGCAATATATCACTAGAATAGAATCATGTAAAAGAAAAGTTTTT-TCGGGTTGA
63 ---GC-G-TCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTCT-GGG-TAA
* *
877684 TTGCAATT
121 TTTCAACT
* * *
877692 AATGCAGCTTAGCT-T-TAAAAACATGACTCAACCATGGATGATACGAATAAGATAATGGTT-C-
1 AATGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGATACGAATAAGATAATGGTTGCG
* * **
877753 TCAAGCAATATATCACTAGAATACAAACATGAAAAAGAAAAGTTTTTCCAGGTAGATTTCAACT
66 TCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTCTGGGTA-ATTTCAACT
* ** *
877817 AACGCAGCTTAGCTATAAAAAAACATGATTTGATCATGGATGACACGAATAAGATAATGG-TG-G
1 AATGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGATACGAATAAGATAATGGTTGCG
877880 TCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTT
66 TCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTT
877927 TCAGGTTGAA
Statistics
Matches: 519, Mismatches: 65, Indels: 72
0.79 0.10 0.11
Matches are distributed among these distances:
120 10 0.02
121 1 0.00
122 37 0.07
123 9 0.02
124 21 0.04
125 142 0.27
126 33 0.06
127 138 0.27
128 1 0.00
129 11 0.02
130 1 0.00
131 1 0.00
132 3 0.01
133 1 0.00
134 8 0.02
135 29 0.06
136 3 0.01
137 69 0.13
138 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (128 bp):
AATGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGATACGAATAAGATAATGGTTGCG
TCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTCTGGGTAATTTCAACT
Found at i:877841 original size:262 final size:254
Alignment explanation
Indices: 877297--877935 Score: 708
Period size: 262 Copynumber: 2.5 Consensus size: 254
877287 TACTGGATTG
* * * * * * * * ***
877297 ATTTCAACTAATGCAGCTTAGCTTTAAAAATAC-T-ATCCTACCATGGATGATATGAATAATTGA
1 ATTTCAACTAACGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGACACGAATAAGAAA
* * **
877360 ATGGTGCTCAGGCAATATATCAC-----TAGAAACATGTAAAAAAGAAAAG-TTTTTCTGGGTCA
66 ATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGT--AAAAGAAAAGTTTTTTC-GGGTTG
* * **
877419 ATTTCAAACAATGCAGCTTAGCTATATAAAAAACATGATTTGACCATAAATGATACGAATAAGAT
128 ATTGCAAACAATGCAGCTTAGCTATATAAAAAACATGACTCAACCATAAATGATACGAATAAGAT
* * * **
877484 AATGTGGTCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTCTGGGTCA
193 AATGTGCTCAAGCAATATATCACTAGAATACAAACATGAAAAAGAAAAGTTTTTCCAGGTCA
* * * * *
877546 ATTTCAACTGATGCAGCTTAGCTATAGAAAAACATGATTCAATTATGGATGATACGAATAAAGAA
1 ATTTCAACTAACGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGACACGAAT-AAGAA
*
877611 AATGGTGTTCAAGCTGTTCAAGCAATATATCACTAGAATAGAATCATGTAAAAGAAAAGTTTTTT
65 AAT-G-G-T---G--G-TCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTT
** **
877676 CGGGTTGATTGCAATTAATGCAGCTTAGCT-T-T-AAAAACATGACTCAACCATGGATGATACGA
121 CGGGTTGATTGCAAACAATGCAGCTTAGCTATATAAAAAACATGACTCAACCATAAATGATACGA
*
877738 ATAAGATAATGGTTCTCAAGCAATATATCACTAGAATACAAACATGAAAAAGAAAAGTTTTTCCA
186 ATAAGATAAT-GTGCTCAAGCAATATATCACTAGAATACAAACATGAAAAAGAAAAGTTTTTCCA
877803 GGT-A
250 GGTCA
** *
877807 GATTTCAACTAACGCAGCTTAGCTATAAAAAAACATGATTTGATCATGGATGACACGAATAAGAT
1 -ATTTCAACTAACGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGACACGAATAAGAA
*
877872 AATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTTCAGGTTGA
65 AATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTTCGGGTTGA
877936 AAAATAAGAC
Statistics
Matches: 329, Mismatches: 41, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
249 29 0.09
250 1 0.00
251 18 0.05
252 59 0.18
253 2 0.01
254 1 0.00
255 2 0.01
258 2 0.01
259 1 0.00
260 1 0.00
261 58 0.18
262 104 0.32
263 1 0.00
264 34 0.10
265 6 0.02
266 10 0.03
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (254 bp):
ATTTCAACTAACGCAGCTTAGCTATAAAAAAACATGATTCAATCATGGATGACACGAATAAGAAA
ATGGTGGTCAAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTTTTTCGGGTTGATT
GCAAACAATGCAGCTTAGCTATATAAAAAACATGACTCAACCATAAATGATACGAATAAGATAAT
GTGCTCAAGCAATATATCACTAGAATACAAACATGAAAAAGAAAAGTTTTTCCAGGTCA
Found at i:878121 original size:224 final size:226
Alignment explanation
Indices: 877716--878147 Score: 663
Period size: 224 Copynumber: 1.9 Consensus size: 226
877706 TTAAAAACAT
*
877716 GACTCAACCATGGATGATACGAATAAGATAATGGTTCTCAAGCAATATATCACTAGAATACAAAC
1 GACTCAACCATGGATGATACGAATAAGATAATGGTGCTCAAGCAATATATCACTAGAATACAAAC
*
877781 ATGAAAAAGAAAAGTTTTTCCAGGTAGATTTCAACTAACGCAGCTTAGCTATAAAAAAACATGAT
66 ATGAAAAAGAAAAGTTTTTCCAGGTAGATTTCAACTAACGCAGCTTAGCTAT-AAAAAACAAGAT
** * * * *
877846 TTGATCATGGATGACACGAATAAGATAATGGTGGTCAAGCAATATATCACTAGAATAGAAACATG
130 TCAACCATGGATGACACAAATAAGAAAATGGTGCTCAAGCAATATATCACTAGAATAGAAACATG
877911 TAAAAGAAAAGTTTTTTCAGGTTGAAAAATAA
195 TAAAAGAAAAGTTTTTTCAGGTTGAAAAATAA
* *
877943 GACTCAACCATGGATGATATGAATAAGATAATGGTGCTCAAGCAATATA-CACTAGAATAGAAAC
1 GACTCAACCATGGATGATACGAATAAGATAATGGTGCTCAAGCAATATATCACTAGAATACAAAC
* ** * * * *
878007 ATGTAAAATTATAGTTTTTCCGGGTTGATTTCAACTAATGCAGCTTAGCGT-T-AAAAACAAGAT
66 ATGAAAAAGAAAAGTTTTTCCAGGTAGATTTCAACTAACGCAGCTTAGC-TATAAAAAACAAGAT
*
878070 TCAACCATGGATGATACAAATAAGAAAATGGTGCTCAAGCAATATATCACTAGAATAGAAACATG
130 TCAACCATGGATGACACAAATAAGAAAATGGTGCTCAAGCAATATATCACTAGAATAGAAACATG
878135 TAAAAGAAAAGTT
195 TAAAAGAAAAGTT
878148 CTTCAGGGTT
Statistics
Matches: 186, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
224 81 0.44
226 57 0.31
227 48 0.26
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (226 bp):
GACTCAACCATGGATGATACGAATAAGATAATGGTGCTCAAGCAATATATCACTAGAATACAAAC
ATGAAAAAGAAAAGTTTTTCCAGGTAGATTTCAACTAACGCAGCTTAGCTATAAAAAACAAGATT
CAACCATGGATGACACAAATAAGAAAATGGTGCTCAAGCAATATATCACTAGAATAGAAACATGT
AAAAGAAAAGTTTTTTCAGGTTGAAAAATAA
Found at i:878177 original size:125 final size:125
Alignment explanation
Indices: 877935--878246 Score: 473
Period size: 125 Copynumber: 2.5 Consensus size: 125
877925 TTTCAGGTTG
* * * *
877935 AAAAATAAGACTCAACCATGGATGATATGAATAAGATAATGGTGCTCAAGCAATATA-CACTAGA
1 AAAAACAAGATTCAACCATGGATGATACGAATAAGAAAATGGTGCTCAAGCAATATATCACTAGA
** * * *
877999 ATAGAAACATGTAAAATTATAGTTTTTCCGGGTTGATTTCAACTAATGCAGCTTAGCGTT
66 ATAGAAACATGTAAAAGAAAAGTTCTTCAGGGTTGATTTCAACTAATGCAGCTTAGCGTT
*
878059 AAAAACAAGATTCAACCATGGATGATACAAATAAGAAAATGGTGCTCAAGCAATATATCACTAGA
1 AAAAACAAGATTCAACCATGGATGATACGAATAAGAAAATGGTGCTCAAGCAATATATCACTAGA
*
878124 ATAGAAACATGTAAAAGAAAAGTTCTTCAGGGTTGATTTCAACTAATGCAGCTTAGTGTT
66 ATAGAAACATGTAAAAGAAAAGTTCTTCAGGGTTGATTTCAACTAATGCAGCTTAGCGTT
* * ** *
878184 AAAAACATGATTCGACCATGGATGATACGAATAAGTGAATGGTTCTCAAGCAATATATCACTA
1 AAAAACAAGATTCAACCATGGATGATACGAATAAGAAAATGGTGCTCAAGCAATATATCACTA
878247 AAGAAAAGTT
Statistics
Matches: 170, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
124 52 0.31
125 118 0.69
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (125 bp):
AAAAACAAGATTCAACCATGGATGATACGAATAAGAAAATGGTGCTCAAGCAATATATCACTAGA
ATAGAAACATGTAAAAGAAAAGTTCTTCAGGGTTGATTTCAACTAATGCAGCTTAGCGTT
Found at i:878359 original size:109 final size:110
Alignment explanation
Indices: 878106--878392 Score: 327
Period size: 109 Copynumber: 2.6 Consensus size: 110
878096 AATGGTGCTC
* * *
878106 AAGCAATATATCACTAGAATAGAAACATGTAAAAGAAAAGTTCTTCAGGGTTGATTTCAACTAAT
1 AAGCAATATATCACAAGAATAGAAACATGTAAAAGAAAAGTTTTTCCGGGTTGATTTCAACTAAT
878171 GCAGCTTAGTGTTAAAAACATGATTCGACCATGGATGATACGAAT
66 GCAGCTTAGTGTTAAAAACATGATTCGACCATGGATGATACGAAT
* * * * * * *
878216 AAGTGAATGGT-TCTCAAGCAATA-TATCA-CT-AAAGAAAAGTTTTTCCGGGTTGACTTCAACT
1 AAG-CAAT-ATATCACAAG-AATAGAAACATGTAAAAGAAAAGTTTTTCCGGGTTGATTTCAACT
**
878277 AATGCAGCTTAGCT-TTAAAAACATGATT-GAACCATGGATGATAC-CTT
63 AATGCAGCTTAG-TGTTAAAAACATGATTCG-ACCATGGATGATACGAAT
* * * **
878324 GAGCAATATATCACAAGAATAGAAACATGTAAAAGAAAAGCTTTACCGGGTCAATTTCAACTAAT
1 AAGCAATATATCACAAGAATAGAAACATGTAAAAGAAAAGTTTTTCCGGGTTGATTTCAACTAAT
878389 GCAG
66 GCAG
878393 ATGGTCTGAG
Statistics
Matches: 144, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
106 5 0.03
107 12 0.08
108 5 0.03
109 101 0.70
110 5 0.03
111 11 0.08
112 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (110 bp):
AAGCAATATATCACAAGAATAGAAACATGTAAAAGAAAAGTTTTTCCGGGTTGATTTCAACTAAT
GCAGCTTAGTGTTAAAAACATGATTCGACCATGGATGATACGAAT
Found at i:880564 original size:30 final size:30
Alignment explanation
Indices: 880525--880585 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
880515 TTTCTCCTAG
*
880525 TTTTAATGGCTTAACTAAAATCCTTCTTAA
1 TTTTAATGGCTCAACTAAAATCCTTCTTAA
* * *
880555 TTTTTATGGCTCAACTAAAATCTTTTTTAA
1 TTTTAATGGCTCAACTAAAATCCTTCTTAA
880585 T
1 T
880586 CCTTTTAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTTAATGGCTCAACTAAAATCCTTCTTAA
Found at i:901907 original size:7 final size:7
Alignment explanation
Indices: 901897--901932 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
901887 CCCACGTCCC
901897 CCAAATA
1 CCAAATA
901904 CCAAATA
1 CCAAATA
901911 CCAAATA
1 CCAAATA
901918 CCAAATA
1 CCAAATA
901925 CCAAATA
1 CCAAATA
901932 C
1 C
901933 TACCTTCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.14
Consensus pattern (7 bp):
CCAAATA
Found at i:905213 original size:25 final size:25
Alignment explanation
Indices: 905177--905227 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
905167 ACGCATTCTA
*
905177 AGAGGTTGCAGATTCGAGGGAGCTT
1 AGAGGTTACAGATTCGAGGGAGCTT
* *
905202 AGAGGTTACAGATTTGAGGGGGCTT
1 AGAGGTTACAGATTCGAGGGAGCTT
905227 A
1 A
905228 AAAGCTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.25
Consensus pattern (25 bp):
AGAGGTTACAGATTCGAGGGAGCTT
Found at i:915812 original size:2 final size:2
Alignment explanation
Indices: 915805--915829 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
915795 AAGGCGTGAG
915805 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
915830 TCGATTTTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:918460 original size:2 final size:2
Alignment explanation
Indices: 918455--918484 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
918445 AATAAAAAAT
918455 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
918485 CTAATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:920391 original size:22 final size:21
Alignment explanation
Indices: 920366--920407 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
920356 TGGGTTAAAC
920366 AATT-TTACTAATGTAAATATAA
1 AATTATTA-TAATG-AAATATAA
*
920388 AATTATTATTATGAAATATA
1 AATTATTATAATGAAATATA
920408 CTTTTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
AATTATTATAATGAAATATAA
Found at i:920452 original size:40 final size:38
Alignment explanation
Indices: 920408--920494 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 38
920398 ATGAAATATA
*
920408 CTTTTAAACAATGTCATCTTTAAAGCTCGAATTTGTATCT
1 CTTTTAAACAATGTCATCTTAAAAGCTCGAA-TT-TATCT
*
920448 CTTTTAAGAATAATGTCATCTTAAAAGCTCGAATTTATCT
1 CTTTT-A-AACAATGTCATCTTAAAAGCTCGAATTTATCT
920488 CTTTTAA
1 CTTTTAA
920495 GAGTGTAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 15 0.35
41 3 0.07
42 23 0.53
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (38 bp):
CTTTTAAACAATGTCATCTTAAAAGCTCGAATTTATCT
Found at i:920505 original size:42 final size:42
Alignment explanation
Indices: 920417--920496 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
920407 ACTTTTAAAC
*
920417 AATGTCATCTTTAAAGCTCGAATTTGTATCTCTTTTAAGAAT
1 AATGTCATCTTAAAAGCTCGAATTTGTATCTCTTTTAAGAAT
920459 AATGTCATCTTAAAAGCTCGAA-TT-TATCTCTTTTAAGA
1 AATGTCATCTTAAAAGCTCGAATTTGTATCTCTTTTAAGA
920497 GTGTAATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 14 0.38
41 2 0.05
42 21 0.57
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (42 bp):
AATGTCATCTTAAAAGCTCGAATTTGTATCTCTTTTAAGAAT
Found at i:929125 original size:160 final size:159
Alignment explanation
Indices: 928861--929197 Score: 593
Period size: 160 Copynumber: 2.1 Consensus size: 159
928851 TATGGGATTT
* * *
928861 TTAAGCACCCAACTTAAAGTTAATTGGCATCGCAGATAATACAAAATCGAATTAATACTCACGAA
1 TTAAGCATCCAACTTAAAGTTAATTGGCATCACAAATAATACAAAATCGAATTAATACTCACGAA
928926 GACAAAAGAGGTTATAATGTAACAAACTCGAAAGGGTTATTGGGTCAGAAAATAGACAATAACAA
66 GACAAAAGAGGTTATAATGTAACAAACTCGAAAGGGTTATT-GGTCAGAAAATAGACAATAACAA
* * *
928991 TAGAACAAAACTTGGGCGTTAAATATGATG
130 CAGAACAAAACTTGGACGTTAAATACGATG
*
929021 TTAAGCATCCAACTTAAAGTTAATTGGCATCACAAATAATACAAAATCGAATTAATACTCATGAA
1 TTAAGCATCCAACTTAAAGTTAATTGGCATCACAAATAATACAAAATCGAATTAATACTCACGAA
929086 GACAAAAGAGGTTATAATGTAACAAACTCGAAAGGGTTATTGGTCAGAAAATAGACAATAACAAC
66 GACAAAAGAGGTTATAATGTAACAAACTCGAAAGGGTTATTGGTCAGAAAATAGACAATAACAAC
*
929151 AGAACACAACTTGGACGTTAAATACGATG
131 AGAACAAAACTTGGACGTTAAATACGATG
929180 TTAAGCATCCAACTTAAA
1 TTAAGCATCCAACTTAAA
929198 ATCAATTAAC
Statistics
Matches: 169, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
159 67 0.40
160 102 0.60
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.23
Consensus pattern (159 bp):
TTAAGCATCCAACTTAAAGTTAATTGGCATCACAAATAATACAAAATCGAATTAATACTCACGAA
GACAAAAGAGGTTATAATGTAACAAACTCGAAAGGGTTATTGGTCAGAAAATAGACAATAACAAC
AGAACAAAACTTGGACGTTAAATACGATG
Found at i:933671 original size:35 final size:35
Alignment explanation
Indices: 933622--933692 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
933612 GACCAAAAAA
* *
933622 TAAACTTACTAATAATTTAGAAACATTAAATGTAG
1 TAAACTTACCAATAATTTAAAAACATTAAATGTAG
*
933657 TAAACTTACCAATAATTTAAAAACATTAAGTGTAG
1 TAAACTTACCAATAATTTAAAAACATTAAATGTAG
933692 T
1 T
933693 TTACCTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (35 bp):
TAAACTTACCAATAATTTAAAAACATTAAATGTAG
Found at i:936593 original size:17 final size:18
Alignment explanation
Indices: 936565--936600 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
936555 TATTTTACTG
*
936565 CTTTTGATTAATTTCCTC
1 CTTTTGATTAATCTCCTC
936583 CTTTT-ATTAATCTCCTC
1 CTTTTGATTAATCTCCTC
936600 C
1 C
936601 ATTCAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.28, G:0.03, T:0.53
Consensus pattern (18 bp):
CTTTTGATTAATCTCCTC
Found at i:941319 original size:155 final size:154
Alignment explanation
Indices: 941077--941745 Score: 905
Period size: 154 Copynumber: 4.4 Consensus size: 154
941067 TTTAGTGTGT
* * *
941077 TTTTTATTGAAAGTAATAAGAT-TCGAGAAAAAAATACGAACAAAGGGCCGAAAT-AAGAGTTTT
1 TTTTT-TTAAAAGTAATAAAATCTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGAG--TT
* *
941140 TTTTTAAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATATTGTACTAAAATAA
63 TTTTT-AAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAA
*
941205 TGTAAAATAATAAAATTAAAAAATAGTA
127 TGTAAAATAATAAAATTAGAAAATAGTA
* *
941233 TATTTTTT-AAAGTAATAAACTCTGGGGAAAAAAAATACGAACAAAGGGCCGAAATAAAG-GTTT
1 T-TTTTTTAAAAGTAATAAAATCTCGGG-AAAAAAATACGAACAAAGGGCCGAAATAAAGAGTTT
* *
941296 TTTTAAAAAATTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAAT
64 TTTT-AAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAAT
941361 GTAAAATAATAAAATTAGAAAATAGTA
128 GTAAAATAATAAAATTAGAAAATAGTA
* * * *
941388 TTTTTTT-AAAGTAATAAACTCTGGGGAAAAAAATACAAACAAAGGGCCGAAAT--A-CGTTTTT
1 TTTTTTTAAAAGTAATAAAATCTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGAGTTTTT
* * *
941449 TTTAAATTTATTTAAAAAACACAGTAAATTAATATATTTCAAACATAATGTACTAAAATAATGTA
66 TTAAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTA
*
941514 AAATAATAAAA-TACGAAAATAATATA
131 AAATAATAAAATTA-GAAAAT-A-GTA
* *
941540 TTTTTATTGAAAGTAATAAAAT-TCGGGAAAAAAATACGAACAAAGGGCTGAAAT-AAGAGTTTT
1 TTTTT-TTAAAAGTAATAAAATCTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGAGTTTT
* **
941603 TCT-AAATTTATTTAAAAAGTACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT
65 TTTAAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT
*
941667 AAAATAAAAAAATTAGAAAATAGTA
130 AAAATAATAAAATTAGAAAATAGTA
* * *
941692 TTTTTTTAAAAGTAATAAAATC-CGGGAAAAAAATACAAACAAATGGCCAAAATA
1 TTTTTTTAAAAGTAATAAAATCTCGGGAAAAAAATACGAACAAAGGGCCGAAATA
941746 CGAATAATTG
Statistics
Matches: 465, Mismatches: 33, Indels: 34
0.87 0.06 0.06
Matches are distributed among these distances:
149 2 0.00
150 75 0.16
151 52 0.11
152 14 0.03
153 58 0.12
154 112 0.24
155 111 0.24
156 6 0.01
157 32 0.07
158 3 0.01
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (154 bp):
TTTTTTTAAAAGTAATAAAATCTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGAGTTTTT
TTAAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTA
AAATAATAAAATTAGAAAATAGTA
Found at i:941683 original size:304 final size:306
Alignment explanation
Indices: 941077--941747 Score: 962
Period size: 304 Copynumber: 2.2 Consensus size: 306
941067 TTTAGTGTGT
* * * * * *
941077 TTTTTATTGAAAGTAATAAGATTCGAGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTT
1 TTTTT-TTAAAAGTAATAAAATCCGGGAAAAAAATACAAACAAAGGGCCGAAAT-A-CGTTTTTT
*
941142 TTTAAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATATTGTACTAAAATAATG
63 TTT-AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
* * *
941207 TAAAATAATAAAATTAAAAAATAGTATATTTTTTAAAGTAATAAACTCTGGGGAAAAAAAATACG
127 TAAAATAATAAAATTAAAAAATAATATATTTTTTAAAGTAATAAAATCTCGGGAAAAAAAATACG
*
941272 AACAAAGGGCCGAAATAAAGGTTTTTTTAAAAAATTATTTAAAAAACACACTAAATTAATACATT
192 AACAAAGGGCCGAAATAAAGGTTTTTCT-AAAAATTATTTAAAAAACACACTAAATTAATACATT
* *
941337 TCAAATATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTA
256 TCAAACATAATGTACTAAAATAATGTAAAATAAAAAAATTAGAAAATAGTA
* *
941388 TTTTTTT-AAAGTAATAAACTCTGGGGAAAAAAATACAAACAAAGGGCCGAAATACG-TTTTTTT
1 TTTTTTTAAAAGTAATAAAATC-CGGGAAAAAAATACAAACAAAGGGCCGAAATACGTTTTTTTT
* * *
941451 T-AAATTTATTTAAAAAACACAGTAAATTAATATATTTCAAACATAATGTACTAAAATAATGTAA
65 TAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
941515 AATAATAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAAT-TCGGG-AAAAAAATAC
130 AATAATAAAATTA-AAAAATAATATA-TTTT-TT-AAAGTAATAAAATCTCGGGAAAAAAAATAC
* * **
941577 GAACAAAGGGCTGAAAT-AAGAGTTTTTCT-AAATTTATTTAAAAAGTACACTAAATTAATACAT
191 GAACAAAGGGCCGAAATAAAG-GTTTTTCTAAAAATTATTTAAAAAACACACTAAATTAATACAT
941640 TTCAAACATAATGTACTAAAATAATGTAAAATAAAAAAATTAGAAAATAGTA
255 TTCAAACATAATGTACTAAAATAATGTAAAATAAAAAAATTAGAAAATAGTA
* *
941692 TTTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACAAACAAATGGCCAAAATACG
1 TTTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACAAACAAAGGGCCGAAATACG
941748 AATAATTGGT
Statistics
Matches: 327, Mismatches: 26, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
304 121 0.37
305 95 0.29
306 37 0.11
307 14 0.04
308 13 0.04
309 12 0.04
310 30 0.09
311 5 0.02
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.30
Consensus pattern (306 bp):
TTTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACAAACAAAGGGCCGAAATACGTTTTTTTTT
AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
ATAATAAAATTAAAAAATAATATATTTTTTAAAGTAATAAAATCTCGGGAAAAAAAATACGAACA
AAGGGCCGAAATAAAGGTTTTTCTAAAAATTATTTAAAAAACACACTAAATTAATACATTTCAAA
CATAATGTACTAAAATAATGTAAAATAAAAAAATTAGAAAATAGTA
Found at i:944160 original size:19 final size:19
Alignment explanation
Indices: 944122--944160 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
944112 TCCGCCCATA
* *
944122 ATTTTTTTATATTATATTT
1 ATTTTTTTACATAATATTT
*
944141 ATTTTTTTACATAATTTTT
1 ATTTTTTTACATAATATTT
944160 A
1 A
944161 AATATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTTTTACATAATATTT
Found at i:945131 original size:21 final size:19
Alignment explanation
Indices: 945102--945143 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
945092 CAGCCAGGGG
945102 TTTAAATAATTGTATAGATAT
1 TTTAAATAATT-TATAG-TAT
*
945123 TTTACATAATTTATAGTAT
1 TTTAAATAATTTATAGTAT
945142 TT
1 TT
945144 ATTCATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTAAATAATTTATAGTAT
Found at i:946085 original size:7 final size:7
Alignment explanation
Indices: 946067--946111 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
946057 GGTGGTGCTG
*
946067 TTAGGAT
1 TTAGGGT
946074 TTAGGGT
1 TTAGGGT
*
946081 CTAGGGT
1 TTAGGGT
946088 TTAGGGT
1 TTAGGGT
946095 TTAGGGT
1 TTAGGGT
*
946102 TTAAGGT
1 TTAGGGT
946109 TTA
1 TTA
946112 AGGTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:947367 original size:19 final size:19
Alignment explanation
Indices: 947328--947369 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
947318 TTAAAAATAA
* **
947328 ATAAATATTAAATATTTTT
1 ATAAATAATAAATATACTT
947347 ATAAATAATAAATATACTT
1 ATAAATAATAAATATACTT
947366 ATAA
1 ATAA
947370 GTCTTTAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAATAATAAATATACTT
Found at i:955446 original size:19 final size:18
Alignment explanation
Indices: 955398--955447 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
955388 AAATATTGTC
955398 ATTTCTATATTATTATTTA
1 ATTT-TATATTATTATTTA
*
955417 ATTTTA-A-TATTTTTTA
1 ATTTTATATTATTATTTA
*
955433 TGTTTTATATTATTA
1 -ATTTTATATTATTA
955448 AAAATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTATATTATTATTTA
Found at i:955618 original size:19 final size:20
Alignment explanation
Indices: 955593--955656 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
955583 AATTACAAAA
955593 AAAAATTT-AAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
*
955612 CAAAATTTCAAAATATTTAT
1 AAAAATTTCAAAATATTTAT
955632 AAAAATTTCAAAAT-TTATAT
1 AAAAATTTCAAAATATT-TAT
955652 AAAAA
1 AAAAA
955657 AGCTAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:956257 original size:22 final size:23
Alignment explanation
Indices: 956209--956258 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
956199 TCTCAAAGTA
*
956209 TAAA-TAACTTTCGGGTGGATTG
1 TAAATTAACTTTCAGGTGGATTG
* *
956231 GAAATTAA-TTTCAGGTGGATTT
1 TAAATTAACTTTCAGGTGGATTG
956253 TAAATT
1 TAAATT
956259 GCAGAGCAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (23 bp):
TAAATTAACTTTCAGGTGGATTG
Found at i:957705 original size:13 final size:14
Alignment explanation
Indices: 957687--957717 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
957677 TACCTATACA
957687 TATTTTTAT-ACTT
1 TATTTTTATAACTT
957700 TATTTTTATAACTT
1 TATTTTTATAACTT
957714 TATT
1 TATT
957718 ATATATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTATAACTT
Found at i:965775 original size:72 final size:72
Alignment explanation
Indices: 965506--965773 Score: 396
Period size: 72 Copynumber: 3.7 Consensus size: 72
965496 AATAGAGAGC
* *
965506 ACTCATATTGCCCAAGCAATTTGGAATTGGGCCACTCAAATTGTTATAAGATACATCGAAACTGT
1 ACTCATATTGTCCAAGCAATTTGGAATTGAGCCACTCAAATTGTTATAAGATACATCGAAACTGT
965571 CAAGTTG
66 CAAGTTG
*
965578 ACTCATATTGTCCAAGCAGTTTGGAATTGAGCCACTCAAATTGTTATAAGATACATCGAAACTGT
1 ACTCATATTGTCCAAGCAATTTGGAATTGAGCCACTCAAATTGTTATAAGATACATCGAAACTGT
965643 CAAGTTG
66 CAAGTTG
* * * ***
965650 ACTCATATTGTCCAAGCAGTTTGGAATTGAGCCACTCAAATTGTTATAAGATGCAT-TAAAAAAT
1 ACTCATATTGTCCAAGCAATTTGGAATTGAGCCACTCAAATTGTTATAAGATACATCGAAACTGT
965714 CTAAGTTG
66 C-AAGTTG
* * *
965722 ACTCATATTG-CATAACCAATTTGGAATTGGGCCACTCAAATTGTTATAAGAT
1 ACTCATATTGTC-CAAGCAATTTGGAATTGAGCCACTCAAATTGTTATAAGAT
965774 GCGTCGAATT
Statistics
Matches: 182, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
71 6 0.03
72 176 0.97
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (72 bp):
ACTCATATTGTCCAAGCAATTTGGAATTGAGCCACTCAAATTGTTATAAGATACATCGAAACTGT
CAAGTTG
Found at i:967429 original size:32 final size:33
Alignment explanation
Indices: 967371--967436 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
967361 CAGAGGTCAA
*
967371 ATTTGGAAGAGAAAGTAAAATTAGGGGCATAGT
1 ATTTGGAAGAGAAAGTAAAATGAGGGGCATAGT
967404 ATTTGGAAGAG-AAGTAAAATGAGGGGCATAGT
1 ATTTGGAAGAGAAAGTAAAATGAGGGGCATAGT
967436 A
1 A
967437 AAGATGATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 21 0.66
33 11 0.34
ACGTcount: A:0.42, C:0.03, G:0.32, T:0.23
Consensus pattern (33 bp):
ATTTGGAAGAGAAAGTAAAATGAGGGGCATAGT
Found at i:968605 original size:19 final size:18
Alignment explanation
Indices: 968557--968606 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
968547 AAATATTTTC
968557 ATTTCTATATTATTATTTA
1 ATTT-TATATTATTATTTA
*
968576 ATTTTA-A-TATTTTTTA
1 ATTTTATATTATTATTTA
*
968592 TGTTTTATATTATTA
1 -ATTTTATATTATTA
968607 AAAATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTATATTATTATTTA
Found at i:984852 original size:20 final size:21
Alignment explanation
Indices: 984808--984857 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
984798 TTTTTATTCT
*
984808 TTTATCT-AAACAAATAAATA
1 TTTATCTAAAACAAATAAACA
*
984828 ATTATCTAAAAC-AATAAACA
1 TTTATCTAAAACAAATAAACA
984848 TTTAT-TAAAA
1 TTTATCTAAAA
984858 ATATTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTATCTAAAACAAATAAACA
Found at i:985809 original size:2 final size:2
Alignment explanation
Indices: 985802--985828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
985792 GATCTTTTAC
985802 AT 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 AT A
985829 GTCCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:986079 original size:17 final size:19
Alignment explanation
Indices: 986057--986097 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
986047 TAGAAAAATC
986057 AAAAT-GATTAAAATA-AA
1 AAAATGGATTAAAATATAA
*
986074 AAAATGGTTTAAAATATAA
1 AAAATGGATTAAAATATAA
986093 AAAAT
1 AAAAT
986098 TTGTACCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAATGGATTAAAATATAA
Found at i:987054 original size:2 final size:2
Alignment explanation
Indices: 987047--987073 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
987037 TATAACATAT
987047 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
987074 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:990564 original size:45 final size:44
Alignment explanation
Indices: 990505--990595 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 44
990495 TTTGGTTCGC
* * *
990505 TGTATTGGATTAGAGGTATAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCATAATAG-AAATC-ATGTGTTTGGTTGAA
* * *
990550 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCATAATAGAAATCATGTGTTTGGTTGAA
990594 TG
1 TG
990596 AAATAGAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 1 0.03
44 18 0.46
45 20 0.51
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCATAATAGAAATCATGTGTTTGGTTGAA
Found at i:1002732 original size:711 final size:711
Alignment explanation
Indices: 1001370--1002792 Score: 2801
Period size: 711 Copynumber: 2.0 Consensus size: 711
1001360 CATATGGGTG
1001370 GTTAAAATGAAAACCTACCTGCAGGCTTTTGATCTGTTGGAGGTGGTCAACTCAGATGTTGAACC
1 GTTAAAATGAAAACCTACCTGCAGGCTTTTGATCTGTTGGAGGTGGTCAACTCAGATGTTGAACC
* * *
1001435 AGAGCCACTTAGAGCCAATCCAACAGTGGCTCAAATCAGGCAGCATGCTGATGAGAGAACCAAGA
66 AGAGCCACTTAGAGCCAATCCAACAGTGGCTCAAATCAGACAACATACTGATGAGAGAACCAAGA
1001500 GGCATAAGGCCATGTCTTGCATCCAAAACTCAGTGTCAGATGTGATCTTCACAAGGATTATGGCC
131 GGCATAAGGCCATGTCTTGCATCCAAAACTCAGTGTCAGATGTGATCTTCACAAGGATTATGGCC
1001565 TGTGAGACTCCAAAACAGGCCTGGGACAAGCTTAAAGAGGAGTTTCAAGGTACTGAGAGGACAAG
196 TGTGAGACTCCAAAACAGGCCTGGGACAAGCTTAAAGAGGAGTTTCAAGGTACTGAGAGGACAAG
1001630 GCAACAACAGCTGTTGAATTTGAGAAGGGATTTCGAGAATCTGAAGATGAAGGAAGAAGAAACAG
261 GCAACAACAGCTGTTGAATTTGAGAAGGGATTTCGAGAATCTGAAGATGAAGGAAGAAGAAACAG
1001695 TGAAGCAGTATGCAGATAGAATCATGGCAGTGGTTAACAGTATAAGGCTCTTTGGTGAGCACTTT
326 TGAAGCAGTATGCAGATAGAATCATGGCAGTGGTTAACAGTATAAGGCTCTTTGGTGAGCACTTT
1001760 GATGAGGCAAGAATAGTGGAGAAAGTCCTCTCCACTTTTCCTGAGAGATATGTGGCCAAGATATC
391 GATGAGGCAAGAATAGTGGAGAAAGTCCTCTCCACTTTTCCTGAGAGATATGTGGCCAAGATATC
1001825 CTCTCTAGATGACTCAAGAGACCTAGCTAGCATCTCCTTGGCCGAGCTAATTAACACCTTTTATG
456 CTCTCTAGATGACTCAAGAGACCTAGCTAGCATCTCCTTGGCCGAGCTAATTAACACCTTTTATG
1001890 CTCAGGAACAAAGAAGAGCTAGCAGAGCTGAAGATCACCAGGAAGGTACATTCAATGCCAAGGCC
521 CTCAGGAACAAAGAAGAGCTAGCAGAGCTGAAGATCACCAGGAAGGTACATTCAATGCCAAGGCC
1001955 ATAGAAGCCTCGAACACCAATGCTCAAAGAGGCAAAAAGCCTTGGAAAGTAGGCCTAAGCCTGAT
586 ATAGAAGCCTCGAACACCAATGCTCAAAGAGGCAAAAAGCCTTGGAAAGTAGGCCTAAGCCTGAT
1002020 GCTGCAAGGAGCAATGACCAGCCCTGCAGACATTGCAAGAGGCCAGGTCATCTAGAAGACA
651 GCTGCAAGGAGCAATGACCAGCCCTGCAGACATTGCAAGAGGCCAGGTCATCTAGAAGACA
1002081 GTTAAAATGAAAACCTACCTGCAGGCTTTTGATCTGTTGGAGGTGGTCAACTCAGATGTTGAACC
1 GTTAAAATGAAAACCTACCTGCAGGCTTTTGATCTGTTGGAGGTGGTCAACTCAGATGTTGAACC
1002146 AGAGCCACTTAGAGCCAATCCAACAGTGGCTCAAATCAGACAACATACTGATGAGAGAACCAAGA
66 AGAGCCACTTAGAGCCAATCCAACAGTGGCTCAAATCAGACAACATACTGATGAGAGAACCAAGA
* *
1002211 GGCATAAGGCCATGTCTTGCATCCAGAACTCAGTGTCAGATGTGATTTTCACAAGGATTATGGCC
131 GGCATAAGGCCATGTCTTGCATCCAAAACTCAGTGTCAGATGTGATCTTCACAAGGATTATGGCC
1002276 TGTGAGACTCCAAAACAGGCCTGGGACAAGCTTAAAGAGGAGTTTCAAGGTACTGAGAGGACAAG
196 TGTGAGACTCCAAAACAGGCCTGGGACAAGCTTAAAGAGGAGTTTCAAGGTACTGAGAGGACAAG
1002341 GCAACAACAGCTGTTGAATTTGAGAAGGGATTTCGAGAATCTGAAGATGAAGGAAGAAGAAACAG
261 GCAACAACAGCTGTTGAATTTGAGAAGGGATTTCGAGAATCTGAAGATGAAGGAAGAAGAAACAG
1002406 TGAAGCAGTATGCAGATAGAATCATGGCAGTGGTTAACAGTATAAGGCTCTTTGGTGAGCACTTT
326 TGAAGCAGTATGCAGATAGAATCATGGCAGTGGTTAACAGTATAAGGCTCTTTGGTGAGCACTTT
1002471 GATGAGGCAAGAATAGTGGAGAAAGTCCTCTCCACTTTTCCTGAGAGATATGTGGCCAAGATATC
391 GATGAGGCAAGAATAGTGGAGAAAGTCCTCTCCACTTTTCCTGAGAGATATGTGGCCAAGATATC
1002536 CTCTCTAGATGACTCAAGAGACCTAGCTAGCATCTCCTTGGCCGAGCTAATTAACACCTTTTATG
456 CTCTCTAGATGACTCAAGAGACCTAGCTAGCATCTCCTTGGCCGAGCTAATTAACACCTTTTATG
1002601 CTCAGGAACAAAGAAGAGCTAGCAGAGCTGAAGATCACCAGGAAGGTACATTCAATGCCAAGGCC
521 CTCAGGAACAAAGAAGAGCTAGCAGAGCTGAAGATCACCAGGAAGGTACATTCAATGCCAAGGCC
1002666 ATAGAAGCCTCGAACACCAATGCTCAAAGAGGCAAAAAGCCTTGGAAAGTAGGCCTAAGCCTGAT
586 ATAGAAGCCTCGAACACCAATGCTCAAAGAGGCAAAAAGCCTTGGAAAGTAGGCCTAAGCCTGAT
1002731 GCTGCAAGGAGCAATGACCAGCCCTGCAGACATTGCAAGAGGCCAGGTCATCTAGAAGACA
651 GCTGCAAGGAGCAATGACCAGCCCTGCAGACATTGCAAGAGGCCAGGTCATCTAGAAGACA
1002792 G
1 G
1002793 ATGCTGGTTC
Statistics
Matches: 707, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
711 707 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (711 bp):
GTTAAAATGAAAACCTACCTGCAGGCTTTTGATCTGTTGGAGGTGGTCAACTCAGATGTTGAACC
AGAGCCACTTAGAGCCAATCCAACAGTGGCTCAAATCAGACAACATACTGATGAGAGAACCAAGA
GGCATAAGGCCATGTCTTGCATCCAAAACTCAGTGTCAGATGTGATCTTCACAAGGATTATGGCC
TGTGAGACTCCAAAACAGGCCTGGGACAAGCTTAAAGAGGAGTTTCAAGGTACTGAGAGGACAAG
GCAACAACAGCTGTTGAATTTGAGAAGGGATTTCGAGAATCTGAAGATGAAGGAAGAAGAAACAG
TGAAGCAGTATGCAGATAGAATCATGGCAGTGGTTAACAGTATAAGGCTCTTTGGTGAGCACTTT
GATGAGGCAAGAATAGTGGAGAAAGTCCTCTCCACTTTTCCTGAGAGATATGTGGCCAAGATATC
CTCTCTAGATGACTCAAGAGACCTAGCTAGCATCTCCTTGGCCGAGCTAATTAACACCTTTTATG
CTCAGGAACAAAGAAGAGCTAGCAGAGCTGAAGATCACCAGGAAGGTACATTCAATGCCAAGGCC
ATAGAAGCCTCGAACACCAATGCTCAAAGAGGCAAAAAGCCTTGGAAAGTAGGCCTAAGCCTGAT
GCTGCAAGGAGCAATGACCAGCCCTGCAGACATTGCAAGAGGCCAGGTCATCTAGAAGACA
Found at i:1012262 original size:24 final size:24
Alignment explanation
Indices: 1012219--1012264 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1012209 ACAATCTAGC
*
1012219 CAACATTAAGACACGATTTAAATG
1 CAACATTAAGACAAGATTTAAATG
1012243 CAACATTAAGACAA-AGTTTAAA
1 CAACATTAAGACAAGA-TTTAAA
1012265 CACACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (24 bp):
CAACATTAAGACAAGATTTAAATG
Found at i:1012545 original size:36 final size:36
Alignment explanation
Indices: 1012497--1012569 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1012487 AAGGAGTGCA
*
1012497 TGCCCAAGCTCGATCAATTA-ATCCCATGACAGCTTC
1 TGCCCAAACTCGATCAATTATA-CCCATGACAGCTTC
* *
1012533 TGCCCAAACTCGATCAATTATACTCGTGACAGCTTC
1 TGCCCAAACTCGATCAATTATACCCATGACAGCTTC
1012569 T
1 T
1012570 TTAAACTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (36 bp):
TGCCCAAACTCGATCAATTATACCCATGACAGCTTC
Found at i:1013514 original size:31 final size:31
Alignment explanation
Indices: 1013476--1013551 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
1013466 TTGAAATGTT
*
1013476 ACATTTTAGTCACTTACATTAACGTGTTGTA
1 ACATTTTAGTCACTTACATTAACGTGTTATA
*
1013507 ACATTTTAGTCACTTACGTTAACGTGTTATA
1 ACATTTTAGTCACTTACATTAACGTGTTATA
1013538 ACATTTTAGTCACT
1 ACATTTTAGTCACT
1013552 AAGCCGTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (31 bp):
ACATTTTAGTCACTTACATTAACGTGTTATA
Found at i:1014422 original size:31 final size:32
Alignment explanation
Indices: 1014385--1014444 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1014375 AATGATCATT
1014385 GAACTATTCAAAAG-TTTTCATTTAAGTTACA
1 GAACTATTCAAAAGTTTTTCATTTAAGTTACA
* *
1014416 GAACTATTCGAAAGTTTTTTATTTAAGTT
1 GAACTATTCAAAAGTTTTTCATTTAAGTT
1014445 TTCAGGCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (32 bp):
GAACTATTCAAAAGTTTTTCATTTAAGTTACA
Found at i:1021954 original size:18 final size:18
Alignment explanation
Indices: 1021903--1021974 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
1021893 TTTAGAATTT
*
1021903 TTTTGAAATTTTTAT-AA
1 TTTTGAAAATTTTATAAA
* **
1021920 TTTTTAAAA-AATATAAA
1 TTTTGAAAATTTTATAAA
1021937 TTTTGAAAATTTTATAAA
1 TTTTGAAAATTTTATAAA
* *
1021955 TATTT-TAAATTTTAAAAA
1 T-TTTGAAAATTTTATAAA
1021973 TT
1 TT
1021975 ATTTTAAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 3 0.07
17 18 0.42
18 19 0.44
19 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTGAAAATTTTATAAA
Found at i:1021955 original size:9 final size:9
Alignment explanation
Indices: 1021931--1021986 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
1021921 TTTTAAAAAA
1021931 TATAAATTT
1 TATAAATTT
1021940 TGA-AAATTT
1 T-ATAAATTT
1021949 TATAAATATT
1 TATAAAT-TT
1021959 T-TAAATTT
1 TATAAATTT
*
1021967 TAAAAATTAT
1 TATAAATT-T
*
1021977 TTTAAATTT
1 TATAAATTT
1021986 T
1 T
1021987 TGAATGTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 24 0.62
10 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TATAAATTT
Found at i:1021979 original size:19 final size:18
Alignment explanation
Indices: 1021943--1021986 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
1021933 TAAATTTTGA
*
1021943 AAATTTTATAAATATTTT
1 AAATTTTAAAAATATTTT
1021961 AAATTTTAAAAATTATTTT
1 AAATTTTAAAAA-TATTTT
1021980 AAATTTT
1 AAATTTT
1021987 TGAATGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATTTTAAAAATATTTT
Found at i:1021996 original size:20 final size:20
Alignment explanation
Indices: 1021912--1022007 Score: 70
Period size: 20 Copynumber: 4.6 Consensus size: 20
1021902 TTTTTGAAAT
1021912 TTTTATAATTTTTAAAAAATATAAA
1 TTTTA-AATTTTT-AAAAAT-T--A
* *
1021937 TTTTGAAAATTTTATAAA-TA
1 TTTT-AAATTTTTAAAAATTA
1021957 TTTTAAA-TTTTAAAAATTA
1 TTTTAAATTTTTAAAAATTA
* **
1021976 TTTTAAATTTTTGAATGTTA
1 TTTTAAATTTTTAAAAATTA
*
1021996 TTTTGAATTTTT
1 TTTTAAATTTTT
1022008 CTTTGTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.13
19 12 0.20
20 25 0.41
22 1 0.02
24 4 0.07
25 10 0.16
26 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTAAATTTTTAAAAATTA
Found at i:1023473 original size:18 final size:18
Alignment explanation
Indices: 1023450--1023484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1023440 CGCTTAGGTG
*
1023450 TGGCTGATGCTGATCCTT
1 TGGCTGACGCTGATCCTT
1023468 TGGCTGACGCTGATCCT
1 TGGCTGACGCTGATCCT
1023485 GATCCTTTAC
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:0.11, C:0.26, G:0.29, T:0.34
Consensus pattern (18 bp):
TGGCTGACGCTGATCCTT
Found at i:1029512 original size:31 final size:30
Alignment explanation
Indices: 1029471--1029537 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
1029461 CCAGCCCAAA
1029471 TATATTATGTTATAA-AATAATATTATATTAAT
1 TATA-TATGTTA-AATAATAATATTAT-TTAAT
* *
1029503 TATATATGTTAAATAATAATTTTATTTATT
1 TATATATGTTAAATAATAATATTATTTAAT
1029533 TATAT
1 TATAT
1029538 TAAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 11 0.34
31 17 0.53
32 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TATATATGTTAAATAATAATATTATTTAAT
Found at i:1033521 original size:26 final size:22
Alignment explanation
Indices: 1033485--1033549 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 22
1033475 ATGTGACATT
1033485 ATTA-ATATATGATATGTGATATGA
1 ATTATATATATGATAT-TGA-AT-A
1033509 ATTATACTATATGATATTGAATA
1 ATTATA-TATATGATATTGAATA
*
1033532 TTTATATATATGTATATT
1 ATTATATATATG-ATATT
1033550 AATTGATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 6 0.16
23 11 0.30
24 6 0.16
25 4 0.11
26 10 0.27
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.48
Consensus pattern (22 bp):
ATTATATATATGATATTGAATA
Found at i:1033677 original size:20 final size:20
Alignment explanation
Indices: 1033652--1033691 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1033642 CGTAAGATGA
*
1033652 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1033672 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1033692 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1033686 original size:34 final size:35
Alignment explanation
Indices: 1033637--1033703 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1033627 CAGTAAAATA
* * *
1033637 TTTTCCGTAAGATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
1033671 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
1033704 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:1034044 original size:27 final size:28
Alignment explanation
Indices: 1034007--1034076 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1033997 ATATGGAGAT
1034007 ATATGTATAAA-TAGTAAT-AGATTGATG
1 ATATGTATAAATTAG-AATGAGATTGATG
*
1034034 ATATGTATAAATTAGATTGAGATTGATG
1 ATATGTATAAATTAGAATGAGATTGATG
*
1034062 ACATTGTATGAAATT
1 ATA-TGTAT-AAATT
1034077 GAAACACTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 13 0.35
28 14 0.38
29 5 0.14
30 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.19, T:0.39
Consensus pattern (28 bp):
ATATGTATAAATTAGAATGAGATTGATG
Found at i:1039709 original size:4 final size:4
Alignment explanation
Indices: 1039694--1039740 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1039684 GTAAGAAAAA
* * * *
1039694 AAAT AAAC AAAT AAAT GAAT GAAT AAAT AAAT AAGT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1039741 ACAAATGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1039799 original size:73 final size:72
Alignment explanation
Indices: 1039705--1040020 Score: 273
Period size: 73 Copynumber: 4.5 Consensus size: 72
1039695 AATAAACAAA
* *
1039705 TAAATGAATGAATAAATAAATAAGTAAATAAATAAAACAAATGTACATAATATTAAATTTAAGTA
1 TAAAAGAAT-AATAAATAAATAAATAAATAAATAAAACAAATGTA-ATAATATTAAATTTAAGTA
*
1039770 TTTTAGAAG
64 TTTTAAAAG
* ** * *
1039779 TAAAAGAATGATAAATAAATAAATAAATCGATAAAACAAACAG-AAGTAATATTAAATTTAAATA
1 TAAAAGAATAATAAATAAATAAATAAATAAATAAAACAAA-TGTAA-TAATATTAAATTTAAGTA
1039843 -TTTAAAAG
64 TTTTAAAAG
* * * * * * * *
1039851 TAAAAAGAATAAT-GACAAATAAATAAATAAATACAATAGATATAAATAATATTAGATTTAGGTA
1 T-AAAAGAATAATAAATAAATAAATAAATAAATAAAACAAATGT-AATAATATTAAATTTAAGTA
*
1039915 TTTAAAAAG
64 TTTTAAAAG
* * *
1039924 T-AAAGAATAATAAATAAATAAATAAATAAAT-------AT-AAATAATATTAACTTTAGGTATT
1 TAAAAGAATAATAAATAAATAAATAAATAAATAAAACAAATGTAATAATATTAAATTTAAGTATT
*
1039980 TAAAAAG
66 TTAAAAG
* *
1039987 T-GAAGAATAATAAATAAATAAATATATAAA-AAAA
1 TAAAAGAATAATAAATAAATAAATAAATAAATAAAA
1040021 TATAAATAAT
Statistics
Matches: 202, Mismatches: 29, Indels: 30
0.77 0.11 0.11
Matches are distributed among these distances:
63 55 0.27
65 2 0.01
71 10 0.05
72 61 0.30
73 65 0.32
74 9 0.04
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (72 bp):
TAAAAGAATAATAAATAAATAAATAAATAAATAAAACAAATGTAATAATATTAAATTTAAGTATT
TTAAAAG
Found at i:1039974 original size:63 final size:63
Alignment explanation
Indices: 1039868--1040016 Score: 246
Period size: 63 Copynumber: 2.3 Consensus size: 63
1039858 AATAATGACA
*
1039868 AATAAATAAATAAATACAATAGATATAAATAATATTAGATTTAGGTATTTAAAAAGTAAAGAAT
1 AATAAATAAATAAATA-AATAAATATAAATAATATTAGATTTAGGTATTTAAAAAGTAAAGAAT
*
1039932 AATAAATAAATAAATAAATAAATATAAATAATATTA-ACTTTAGGTATTTAAAAAGTGAAGAAT
1 AATAAATAAATAAATAAATAAATATAAATAATATTAGA-TTTAGGTATTTAAAAAGTAAAGAAT
*
1039995 AATAAATAAATAAATATATAAA
1 AATAAATAAATAAATAAATAAA
1040017 AAAATATAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
62 1 0.01
63 64 0.79
64 16 0.20
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.31
Consensus pattern (63 bp):
AATAAATAAATAAATAAATAAATATAAATAATATTAGATTTAGGTATTTAAAAAGTAAAGAAT
Found at i:1041819 original size:24 final size:24
Alignment explanation
Indices: 1041791--1041868 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
1041781 AAAAAGTTGA
1041791 ATTGATGTTTTTTCAATAAAAAAT
1 ATTGATGTTTTTTCAATAAAAAAT
*** *
1041815 ATTGACT-AAATTT-AA-AAAAAGTT
1 ATTGA-TGTTTTTTCAATAAAAA-AT
1041838 GAATTGATGTTTTTTCAATAAAAAAT
1 --ATTGATGTTTTTTCAATAAAAAAT
1041864 ATTGA
1 ATTGA
1041869 CTAAATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 5 0.13
23 3 0.08
24 14 0.36
25 9 0.23
26 3 0.08
27 5 0.13
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (24 bp):
ATTGATGTTTTTTCAATAAAAAAT
Found at i:1041848 original size:49 final size:49
Alignment explanation
Indices: 1041779--1041876 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1041769 CCAACCTTTA
1041779 AAAAAAAGTTGAATTGATGTTTTTTCAATAAAAAATATTGACTAAATTT
1 AAAAAAAGTTGAATTGATGTTTTTTCAATAAAAAATATTGACTAAATTT
1041828 AAAAAAAGTTGAATTGATGTTTTTTCAATAAAAAATATTGACTAAATTT
1 AAAAAAAGTTGAATTGATGTTTTTTCAATAAAAAATATTGACTAAATTT
1041877 TTATGAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (49 bp):
AAAAAAAGTTGAATTGATGTTTTTTCAATAAAAAATATTGACTAAATTT
Found at i:1045929 original size:4 final size:4
Alignment explanation
Indices: 1045910--1045951 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
1045900 TGTAAGAAAA
* *
1045910 AAAT -AAT AAGT AAAT AAAT AAAT AAAT AAGT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1045952 ACAAATGTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1045991 original size:69 final size:69
Alignment explanation
Indices: 1045917--1046159 Score: 197
Period size: 69 Copynumber: 3.4 Consensus size: 69
1045907 AAAAAATAAT
* * **
1045917 AAGTAAATA-AATAAATAAATAAGTAAATAAATAAAACAAATGTACATAATATTAAATTTAAGTA
1 AAGTAAAAAGAAT-AATAAATAAATAAATAAATAAAACAAACATACATAATATTAAATTTAAGTA
1045981 TTTAG
65 TTTAG
* ** ** * *
1045986 AAGTAAAAAGAATGATAAATAAATAAATCGATAAAACAAACATAGGTAATATTAAATTTAAATGT
1 AAGTAAAAAGAATAATAAATAAATAAATAAATAAAACAAACATACATAATATTAAATTTAAGTAT
* *
1046051 CTAA
66 TTAG
* * *
1046055 AAGGT-AAAAGAATAATGAACAAATAAATAAATAAATAAATACAATAGATATAAATAATATTAGA
1 AA-GTAAAAAGAATAAT----AAATAAATAAATAAATAAA-AC-A-A-ACATACATAATATTAAA
* *
1046119 TTTAGGTATTTAAA
57 TTTAAGTATTT-AG
1046133 AAGT--AAAGAATAATAAATAAATAAATA
1 AAGTAAAAAGAATAATAAATAAATAAATA
1046160 TAAATATTAT
Statistics
Matches: 139, Mismatches: 24, Indels: 19
0.76 0.13 0.10
Matches are distributed among these distances:
69 64 0.46
70 5 0.04
72 13 0.09
73 17 0.12
74 2 0.01
75 1 0.01
76 11 0.08
77 22 0.16
78 4 0.03
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (69 bp):
AAGTAAAAAGAATAATAAATAAATAAATAAATAAAACAAACATACATAATATTAAATTTAAGTAT
TTAG
Found at i:1046214 original size:59 final size:62
Alignment explanation
Indices: 1046080--1046238 Score: 182
Period size: 59 Copynumber: 2.5 Consensus size: 62
1046070 TGAACAAATA
*
1046080 AATAAATAAATAAATA-CAATAGATATAAATAATATTAGATTTAGGTATTTAAAAAGTAAAGAAT
1 AATAAATAAATAAATATAAATAGATATAAATAATATTA-A--TAGGTATTTAAAAAGTAAAGAAT
* * * *
1046144 AATAAATAAATAAATATAAATA-TTATAAATAATATT-A-AGGTATTTAGAAAGTGAATAAT
1 AATAAATAAATAAATATAAATAGATATAAATAATATTAATAGGTATTTAAAAAGTAAAGAAT
* *
1046203 AATAAATAAATAAATATACAAAAAAATATAAATAAT
1 AATAAATAAATAAATAT--AAATAGATATAAATAAT
1046239 GAAAATAATC
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
59 36 0.43
61 4 0.05
62 11 0.13
64 29 0.35
65 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (62 bp):
AATAAATAAATAAATATAAATAGATATAAATAATATTAATAGGTATTTAAAAAGTAAAGAAT
Found at i:1061248 original size:25 final size:25
Alignment explanation
Indices: 1061220--1061269 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1061210 CAGGTAAGGC
*
1061220 TCCTTCTCCTTCTTCCATTCTTCAT
1 TCCTTCTCATTCTTCCATTCTTCAT
* * *
1061245 TCCTTTTTATTCTTCCGTTCTTCAT
1 TCCTTCTCATTCTTCCATTCTTCAT
1061270 CTTCTATTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.08, C:0.34, G:0.02, T:0.56
Consensus pattern (25 bp):
TCCTTCTCATTCTTCCATTCTTCAT
Found at i:1069499 original size:21 final size:21
Alignment explanation
Indices: 1069473--1069526 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1069463 CCATCATGTT
* *
1069473 TCTAATCTTACTGCTACAATA
1 TCTAATCTCACCGCTACAATA
*
1069494 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAATA
*
1069515 ACTAATCTCACC
1 TCTAATCTCACC
1069527 ACCACTGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAATA
Found at i:1074931 original size:15 final size:16
Alignment explanation
Indices: 1074911--1074942 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1074901 TTAGAAAATT
1074911 AAAAAAGTA-TTTAAA
1 AAAAAAGTATTTTAAA
1074926 AAAAAAGTATTTTAAA
1 AAAAAAGTATTTTAAA
1074942 A
1 A
1074943 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAAAAGTATTTTAAA
Found at i:1075787 original size:15 final size:16
Alignment explanation
Indices: 1075767--1075798 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1075757 TTAGAAAATT
1075767 AAAAAAGTA-TTTAAA
1 AAAAAAGTATTTTAAA
1075782 AAAAAAGTATTTTAAA
1 AAAAAAGTATTTTAAA
1075798 A
1 A
1075799 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAAAAGTATTTTAAA
Found at i:1075797 original size:856 final size:856
Alignment explanation
Indices: 1074145--1075857 Score: 3417
Period size: 856 Copynumber: 2.0 Consensus size: 856
1074135 GCCTGCTGAT
1074145 ATGCTGGTGCTATACCATTACCATACCCTCCATATGCAGGATAGTTCATGGGAGCTCCAGGGTAA
1 ATGCTGGTGCTATACCATTACCATACCCTCCATATGCAGGATAGTTCATGGGAGCTCCAGGGTAA
1074210 GAACCAGCTAGCTGAGGGGCTGCTTCTGGTGAGTACATATACGGACAGGTGGGTGGGGTTTGGGT
66 GAACCAGCTAGCTGAGGGGCTGCTTCTGGTGAGTACATATACGGACAGGTGGGTGGGGTTTGGGT
1074275 TCCGTACATGGCAGGTGGGGGGGATGGGTATGCTGGGACTGCAGCAGGGTACTGAGGGTGTGAGG
131 TCCGTACATGGCAGGTGGGGGGGATGGGTATGCTGGGACTGCAGCAGGGTACTGAGGGTGTGAGG
1074340 GAGACCTGACAATTGACGGTGGTGCTGCAAAAGATGAGACGTATGCATTCGTTGAACGGCCAGCT
196 GAGACCTGACAATTGACGGTGGTGCTGCAAAAGATGAGACGTATGCATTCGTTGAACGGCCAGCT
1074405 TTAGCTGGAGGCATTGGACCGCCATTACTGGCCCGTGTTCGCTTGTTAGCAGGAACTGCAGCTGG
261 TTAGCTGGAGGCATTGGACCGCCATTACTGGCCCGTGTTCGCTTGTTAGCAGGAACTGCAGCTGG
1074470 CTTTCTCTTCTCAGTCTTGGTCTTCTCTAGCTGCTCAAGGCGTTTCTTGAGGTTTTCTGGGGGAA
326 CTTTCTCTTCTCAGTCTTGGTCTTCTCTAGCTGCTCAAGGCGTTTCTTGAGGTTTTCTGGGGGAA
1074535 ACTCTGCCTCGAGTTTGTACTCTTCGATGCACTTCATGACTGCCCGAAGTGCTGATTGCTCTTTG
391 ACTCTGCCTCGAGTTTGTACTCTTCGATGCACTTCATGACTGCCCGAAGTGCTGATTGCTCTTTG
1074600 CGTGCAGCAAGTTGCTGTATAAATCAAGAACTACTACTTATTAGTAGAAACATAACTGCTAGAAA
456 CGTGCAGCAAGTTGCTGTATAAATCAAGAACTACTACTTATTAGTAGAAACATAACTGCTAGAAA
1074665 TGAAGAATACTTTAAGGTATAGACGACCATGACCAATCAATCTCTCCCACCTATTTGTCAATAGT
521 TGAAGAATACTTTAAGGTATAGACGACCATGACCAATCAATCTCTCCCACCTATTTGTCAATAGT
1074730 CAATACCACCGGTTTCATGGTTTTTGGCATTAATTAGGAGATAAAAAGTAGAGGTGTTCATGGGC
586 CAATACCACCGGTTTCATGGTTTTTGGCATTAATTAGGAGATAAAAAGTAGAGGTGTTCATGGGC
1074795 CGGGCCGGGCCCATAAAAAATTTCAGCCCGAGTCCTAGGCCCAGGCCCGGGAGAAAATTCCTAAG
651 CGGGCCGGGCCCATAAAAAATTTCAGCCCGAGTCCTAGGCCCAGGCCCGGGAGAAAATTCCTAAG
1074860 CCCGGGCCCGGCCCATTTTTTAAATAAACACCAAAAAAATTTTAGAAAATTAAAAAAGTATTTAA
716 CCCGGGCCCGGCCCATTTTTTAAATAAACACCAAAAAAATTTTAGAAAATTAAAAAAGTATTTAA
*
1074925 AAAAAAAGTATTTTAAAATATTTTTAAAAATAAAAAATATATTTATTATATTCGGGCCGTGCCGG
781 AAAAAAAGTATTTTAAAATATTTTTAAAAATAAAAAATATATTTATTATATTCGGGCCGGGCCGG
1074990 GCCTGGGCCAA
846 GCCTGGGCCAA
1075001 ATGCTGGTGCTATACCATTACCATACCCTCCATATGCAGGATAGTTCATGGGAGCTCCAGGGTAA
1 ATGCTGGTGCTATACCATTACCATACCCTCCATATGCAGGATAGTTCATGGGAGCTCCAGGGTAA
1075066 GAACCAGCTAGCTGAGGGGCTGCTTCTGGTGAGTACATATACGGACAGGTGGGTGGGGTTTGGGT
66 GAACCAGCTAGCTGAGGGGCTGCTTCTGGTGAGTACATATACGGACAGGTGGGTGGGGTTTGGGT
1075131 TCCGTACATGGCAGGTGGGGGGGATGGGTATGCTGGGACTGCAGCAGGGTACTGAGGGTGTGAGG
131 TCCGTACATGGCAGGTGGGGGGGATGGGTATGCTGGGACTGCAGCAGGGTACTGAGGGTGTGAGG
1075196 GAGACCTGACAATTGACGGTGGTGCTGCAAAAGATGAGACGTATGCATTCGTTGAACGGCCAGCT
196 GAGACCTGACAATTGACGGTGGTGCTGCAAAAGATGAGACGTATGCATTCGTTGAACGGCCAGCT
1075261 TTAGCTGGAGGCATTGGACCGCCATTACTGGCCCGTGTTCGCTTGTTAGCAGGAACTGCAGCTGG
261 TTAGCTGGAGGCATTGGACCGCCATTACTGGCCCGTGTTCGCTTGTTAGCAGGAACTGCAGCTGG
1075326 CTTTCTCTTCTCAGTCTTGGTCTTCTCTAGCTGCTCAAGGCGTTTCTTGAGGTTTTCTGGGGGAA
326 CTTTCTCTTCTCAGTCTTGGTCTTCTCTAGCTGCTCAAGGCGTTTCTTGAGGTTTTCTGGGGGAA
1075391 ACTCTGCCTCGAGTTTGTACTCTTCGATGCACTTCATGACTGCCCGAAGTGCTGATTGCTCTTTG
391 ACTCTGCCTCGAGTTTGTACTCTTCGATGCACTTCATGACTGCCCGAAGTGCTGATTGCTCTTTG
1075456 CGTGCAGCAAGTTGCTGTATAAATCAAGAACTACTACTTATTAGTAGAAACATAACTGCTAGAAA
456 CGTGCAGCAAGTTGCTGTATAAATCAAGAACTACTACTTATTAGTAGAAACATAACTGCTAGAAA
1075521 TGAAGAATACTTTAAGGTATAGACGACCATGACCAATCAATCTCTCCCACCTATTTGTCAATAGT
521 TGAAGAATACTTTAAGGTATAGACGACCATGACCAATCAATCTCTCCCACCTATTTGTCAATAGT
1075586 CAATACCACCGGTTTCATGGTTTTTGGCATTAATTAGGAGATAAAAAGTAGAGGTGTTCATGGGC
586 CAATACCACCGGTTTCATGGTTTTTGGCATTAATTAGGAGATAAAAAGTAGAGGTGTTCATGGGC
1075651 CGGGCCGGGCCCATAAAAAATTTCAGCCCGAGTCCTAGGCCCAGGCCCGGGAGAAAATTCCTAAG
651 CGGGCCGGGCCCATAAAAAATTTCAGCCCGAGTCCTAGGCCCAGGCCCGGGAGAAAATTCCTAAG
1075716 CCCGGGCCCGGCCCATTTTTTAAATAAACACCAAAAAAATTTTAGAAAATTAAAAAAGTATTTAA
716 CCCGGGCCCGGCCCATTTTTTAAATAAACACCAAAAAAATTTTAGAAAATTAAAAAAGTATTTAA
1075781 AAAAAAAGTATTTTAAAATATTTTTAAAAATAAAAAATATATTTATTATATTCGGGCCGGGCCGG
781 AAAAAAAGTATTTTAAAATATTTTTAAAAATAAAAAATATATTTATTATATTCGGGCCGGGCCGG
1075846 GCCTGGGCCAA
846 GCCTGGGCCAA
1075857 A
1 A
1075858 AAAGTGGTGC
Statistics
Matches: 856, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
856 856 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (856 bp):
ATGCTGGTGCTATACCATTACCATACCCTCCATATGCAGGATAGTTCATGGGAGCTCCAGGGTAA
GAACCAGCTAGCTGAGGGGCTGCTTCTGGTGAGTACATATACGGACAGGTGGGTGGGGTTTGGGT
TCCGTACATGGCAGGTGGGGGGGATGGGTATGCTGGGACTGCAGCAGGGTACTGAGGGTGTGAGG
GAGACCTGACAATTGACGGTGGTGCTGCAAAAGATGAGACGTATGCATTCGTTGAACGGCCAGCT
TTAGCTGGAGGCATTGGACCGCCATTACTGGCCCGTGTTCGCTTGTTAGCAGGAACTGCAGCTGG
CTTTCTCTTCTCAGTCTTGGTCTTCTCTAGCTGCTCAAGGCGTTTCTTGAGGTTTTCTGGGGGAA
ACTCTGCCTCGAGTTTGTACTCTTCGATGCACTTCATGACTGCCCGAAGTGCTGATTGCTCTTTG
CGTGCAGCAAGTTGCTGTATAAATCAAGAACTACTACTTATTAGTAGAAACATAACTGCTAGAAA
TGAAGAATACTTTAAGGTATAGACGACCATGACCAATCAATCTCTCCCACCTATTTGTCAATAGT
CAATACCACCGGTTTCATGGTTTTTGGCATTAATTAGGAGATAAAAAGTAGAGGTGTTCATGGGC
CGGGCCGGGCCCATAAAAAATTTCAGCCCGAGTCCTAGGCCCAGGCCCGGGAGAAAATTCCTAAG
CCCGGGCCCGGCCCATTTTTTAAATAAACACCAAAAAAATTTTAGAAAATTAAAAAAGTATTTAA
AAAAAAAGTATTTTAAAATATTTTTAAAAATAAAAAATATATTTATTATATTCGGGCCGGGCCGG
GCCTGGGCCAA
Found at i:1079452 original size:16 final size:16
Alignment explanation
Indices: 1079428--1079469 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1079418 TTATTTAAAA
*
1079428 AACCGATTCACAAGTT
1 AACCAATTCACAAGTT
1079444 AACCAATTCACAAGTT
1 AACCAATTCACAAGTT
1079460 AACCAATTCA
1 AACCAATTCA
1079470 ACCACTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (16 bp):
AACCAATTCACAAGTT
Found at i:1088114 original size:16 final size:17
Alignment explanation
Indices: 1088093--1088137 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1088083 CATTAAAATC
1088093 TAATTAA-A-TAAAAAA
1 TAATTAATATTAAAAAA
1088108 TATATTAATATTAAAAAA
1 TA-ATTAATATTAAAAAA
1088126 TAATT-ATATTAA
1 TAATTAATATTAA
1088138 TATTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 4 0.15
18 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATTAATATTAAAAAA
Found at i:1088120 original size:22 final size:21
Alignment explanation
Indices: 1088095--1088148 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
1088085 TTAAAATCTA
1088095 ATTAAATAAAAAATATATTAAT
1 ATTAAA-AAAAAATATATTAAT
*
1088117 ATTAAAAAATAATTATATTAAT
1 ATTAAAAAA-AAATATATTAAT
1088139 ATTAAAAAAA
1 ATTAAAAAAA
1088149 TAAGAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAAAATATATTAAT
Found at i:1088124 original size:18 final size:16
Alignment explanation
Indices: 1088101--1088137 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1088091 TCTAATTAAA
1088101 TAAAAAATATATTAATAT
1 TAAAAAATA-ATT-ATAT
1088119 TAAAAAATAATTATAT
1 TAAAAAATAATTATAT
1088135 TAA
1 TAA
1088138 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAAATAATTATAT
Found at i:1097468 original size:21 final size:21
Alignment explanation
Indices: 1097429--1097468 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1097419 ACTTGTCCAT
* *
1097429 ATTTACAAAAAGATTTTTTTA
1 ATTTAAAAAAAGATATTTTTA
*
1097450 ATTTAAAAAAATATATTTT
1 ATTTAAAAAAAGATATTTT
1097469 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTTAAAAAAAGATATTTTTA
Found at i:1105711 original size:14 final size:13
Alignment explanation
Indices: 1105671--1105721 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
1105661 AAAAGTATAT
*
1105671 TATTATTTTATTA
1 TATTATTATATTA
* *
1105684 TATT-GTAAATTA
1 TATTATTATATTA
1105696 TATTAATTATATTA
1 TATT-ATTATATTA
1105710 TATTATTATATT
1 TATTATTATATT
1105722 TTAAATAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:1106885 original size:19 final size:19
Alignment explanation
Indices: 1106861--1106935 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 19
1106851 TTTTGTGTGA
1106861 ATATGTGAATTGTGAATTG
1 ATATGTGAATTGTGAATTG
** *
1106880 ATATGTGAATTGAAAATCG
1 ATATGTGAATTGTGAATTG
* *
1106899 AGATATGAGATT-TGAA--G
1 ATATGTGA-ATTGTGAATTG
1106916 ATATGTGAATATGTGAATTG
1 ATATGTGAAT-TGTGAATTG
1106936 TGTATTAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
16 2 0.05
17 8 0.19
18 4 0.10
19 24 0.57
20 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.36
Consensus pattern (19 bp):
ATATGTGAATTGTGAATTG
Found at i:1110445 original size:18 final size:18
Alignment explanation
Indices: 1110402--1110445 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1110392 AAATATAATA
*
1110402 AAAAG-AAATCAACAAAT
1 AAAAGTAAATAAACAAAT
1110419 AAAAGTAAATAAACAAAT
1 AAAAGTAAATAAACAAAT
*
1110437 AAAATTAAA
1 AAAAGTAAA
1110446 GCACTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAGTAAATAAACAAAT
Found at i:1110561 original size:20 final size:20
Alignment explanation
Indices: 1110536--1110573 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1110526 TAAAATTATA
1110536 ATGTATATATATATATATGC
1 ATGTATATATATATATATGC
* *
1110556 ATGTATGTATGTATATAT
1 ATGTATATATATATATAT
1110574 ATGAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (20 bp):
ATGTATATATATATATATGC
Found at i:1110723 original size:24 final size:23
Alignment explanation
Indices: 1110696--1110740 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1110686 ATTTAAGAAG
* *
1110696 AGATATAGATATATATACATAATA
1 AGATATAAAGATATATA-ATAATA
1110720 AGATATAAAGATATATAATAA
1 AGATATAAAGATATATAATAA
1110741 GGTATGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (23 bp):
AGATATAAAGATATATAATAATA
Found at i:1110753 original size:20 final size:20
Alignment explanation
Indices: 1110704--1110758 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1110694 AGAGATATAG
*
1110704 ATATATATACATAATAAGAT
1 ATATATATATATAATAAGAT
* * *
1110724 ATAAAGATATATAATAAGGT
1 ATATATATATATAATAAGAT
*
1110744 ATGTATATATA-AATA
1 ATATATATATATAATA
1110759 GTTATAATAG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.35
Consensus pattern (20 bp):
ATATATATATATAATAAGAT
Found at i:1113477 original size:20 final size:19
Alignment explanation
Indices: 1113444--1113481 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1113434 TATGGTATAT
1113444 ATTTCATGTATTATTAATAC
1 ATTTCATGTATTA-TAATAC
1113464 ATTTCAT-TATTTATAATA
1 ATTTCATGTA-TTATAATA
1113482 TGTTACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTCATGTATTATAATAC
Found at i:1117818 original size:20 final size:20
Alignment explanation
Indices: 1117793--1117833 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1117783 TTGGGCATGA
1117793 TAATTGCCACAAATTTTATT
1 TAATTGCCACAAATTTTATT
*
1117813 TAATTGCCACCAATTTTATT
1 TAATTGCCACAAATTTTATT
1117833 T
1 T
1117834 TGGAGACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (20 bp):
TAATTGCCACAAATTTTATT
Found at i:1125622 original size:2 final size:2
Alignment explanation
Indices: 1125615--1125639 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1125605 AAAATATGTG
1125615 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1125640 TCTTAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1126625 original size:19 final size:21
Alignment explanation
Indices: 1126601--1126639 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1126591 ATTGAAAATG
1126601 TGAGAA-AT-TGTGATTTAAT
1 TGAGAATATATGTGATTTAAT
1126620 TGAGAATATATGTGATTTAA
1 TGAGAATATATGTGATTTAA
1126640 ATACCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (21 bp):
TGAGAATATATGTGATTTAAT
Found at i:1130432 original size:21 final size:21
Alignment explanation
Indices: 1130405--1130455 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1130395 ACAACTGTTT
*
1130405 TTAATCTCATTGCTAGAAT-A
1 TTAATCTCATCGCTAGAATAA
*
1130425 TCTAATCTCATCGCTATAATAA
1 T-TAATCTCATCGCTAGAATAA
1130447 TTAATCTCA
1 TTAATCTCA
1130456 ATGCCACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (21 bp):
TTAATCTCATCGCTAGAATAA
Found at i:1139732 original size:9 final size:9
Alignment explanation
Indices: 1139657--1139732 Score: 100
Period size: 9 Copynumber: 8.4 Consensus size: 9
1139647 TTTGGTTAAA
1139657 AATTAACCG
1 AATTAACCG
*
1139666 AATTACCCG
1 AATTAACCG
1139675 AATTAACCG
1 AATTAACCG
*
1139684 AATTACCCG
1 AATTAACCG
1139693 AATT-ACCTG
1 AATTAACC-G
1139702 AATTAACCG
1 AATTAACCG
*
1139711 AATTACCCG
1 AATTAACCG
*
1139720 AATTAACCA
1 AATTAACCG
1139729 AATT
1 AATT
1139733 GAATCACTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
8 2 0.03
9 53 0.91
10 3 0.05
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:1139732 original size:27 final size:27
Alignment explanation
Indices: 1139657--1139724 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1139647 TTTGGTTAAA
*
1139657 AATTAACCGAATTACCCGAATTAACCG
1 AATTACCCGAATTACCCGAATTAACCG
*
1139684 AATTACCCGAATTACCTGAATTAACCG
1 AATTACCCGAATTACCCGAATTAACCG
1139711 AATTACCCGAATTA
1 AATTACCCGAATTA
1139725 ACCAAATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (27 bp):
AATTACCCGAATTACCCGAATTAACCG
Found at i:1141556 original size:18 final size:17
Alignment explanation
Indices: 1141535--1141588 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 17
1141525 CATGTGTTAT
1141535 AAATTACAAAATATATAA
1 AAATTACAAAATATA-AA
* *
1141553 AAATAACATAATATAAA
1 AAATTACAAAATATAAA
* *
1141570 ACATTACAAACTA-AAA
1 AAATTACAAAATATAAA
1141586 AAA
1 AAA
1141589 GGCTAAGTCG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 5 0.17
17 11 0.38
18 13 0.45
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATTACAAAATATAAA
Found at i:1143043 original size:17 final size:16
Alignment explanation
Indices: 1142992--1143046 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
1142982 TTTTATTTTA
1142992 TTTTAATTTTTAATATT
1 TTTTAATTTTTAA-ATT
** *
1143009 TAATAATTTTATACATT
1 TTTTAATTTT-TAAATT
1143026 TTTTAATTTTTGAAATT
1 TTTTAATTTTT-AAATT
1143043 TTTT
1 TTTT
1143047 TATATATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 1 0.03
17 27 0.90
18 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTAATTTTTAAATT
Found at i:1150275 original size:2 final size:2
Alignment explanation
Indices: 1150268--1150293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1150258 CTAGATATTG
1150268 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
1150294 AAGCAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1154134 original size:19 final size:19
Alignment explanation
Indices: 1154110--1154173 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1154100 AGATATTTTT
1154110 AAAATATTTTCAGTTGCGG
1 AAAATATTTTCAGTTGCGG
* * *
1154129 AAAATATTCTGACTGTTGCAG
1 AAAATATT-T-TCAGTTGCGG
* * *
1154150 AGAATATTTTCGGTTGAGG
1 AAAATATTTTCAGTTGCGG
1154169 AAAAT
1 AAAAT
1154174 CCTCTGCTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 18 0.53
20 2 0.06
21 14 0.41
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (19 bp):
AAAATATTTTCAGTTGCGG
Found at i:1154482 original size:3 final size:3
Alignment explanation
Indices: 1154474--1154508 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1154464 GACAAAACAT
1154474 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1154509 GTATGACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1159785 original size:3 final size:3
Alignment explanation
Indices: 1159779--1159843 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
1159769 AACAACGGAC
* ** *
1159779 TTA TTA TTT TTA TTA TTA CAA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1159827 TTAA TTA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA T
1159844 GGTTTTTCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1161212 original size:3 final size:3
Alignment explanation
Indices: 1161204--1161229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1161194 ACTTAAAAGA
1161204 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1161230 AGGCAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1173789 original size:93 final size:93
Alignment explanation
Indices: 1173685--1173872 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 93
1173675 ATATTTATTA
*
1173685 AATATTTGGGCTGGGTCGGTCCAAAAAAGTGGTTCCCGAGGCCCGCCTTGTTTTTTTGCCCAAAC
1 AATATTTGGGCTGGGTCGGGCCAAAAAAGTGGTTCCCGAGGCCCGCCTTGTTTTTTTGCCCAAAC
1173750 TCATATTTCGGGCCTATATTTTTACCCG
66 TCATATTTCGGGCCTATATTTTTACCCG
1173778 AATATTTGGGCTGGGTCGGGCCAAAAAAGTGGTTCCCGAGGCCCGCCTTGTTTTTTTGCCCAAAC
1 AATATTTGGGCTGGGTCGGGCCAAAAAAGTGGTTCCCGAGGCCCGCCTTGTTTTTTTGCCCAAAC
1173843 TCATATTTCGGGCCTATATTTTTACCCG
66 TCATATTTCGGGCCTATATTTTTACCCG
1173871 AA
1 AA
1173873 CCCTACTATA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (93 bp):
AATATTTGGGCTGGGTCGGGCCAAAAAAGTGGTTCCCGAGGCCCGCCTTGTTTTTTTGCCCAAAC
TCATATTTCGGGCCTATATTTTTACCCG
Found at i:1174260 original size:14 final size:14
Alignment explanation
Indices: 1174223--1174252 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1174213 TTTATATTAT
1174223 TTTA-AATTTAATA
1 TTTATAATTTAATA
1174236 TTTATAATTTAATA
1 TTTATAATTTAATA
1174250 TTT
1 TTT
1174253 TTTATTTATT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATAATTTAATA
Found at i:1174769 original size:34 final size:34
Alignment explanation
Indices: 1174730--1174802 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
1174720 CAAATGATAG
1174730 TGTTAATTATTTCCATTAATACATGACATGTATA
1 TGTTAATTATTTCCATTAATACATGACATGTATA
1174764 TGTTAATTATTTCCATTAATACATGACATGTATA
1 TGTTAATTATTTCCATTAATACATGACATGTATA
1174798 TGTTA
1 TGTTA
1174803 TAAACTAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (34 bp):
TGTTAATTATTTCCATTAATACATGACATGTATA
Found at i:1178301 original size:21 final size:21
Alignment explanation
Indices: 1178275--1178317 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1178265 TCTGTACTTC
*
1178275 ATAAAAAAAATTAAAAAGTTA
1 ATAAAAAAAATTAAAAAATTA
* *
1178296 ATAAAAATATTTAAAAAATTA
1 ATAAAAAAAATTAAAAAATTA
1178317 A
1 A
1178318 AAATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAAAAAAAATTAAAAAATTA
Found at i:1180663 original size:11 final size:11
Alignment explanation
Indices: 1180647--1180671 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1180637 ACTTTAATTT
1180647 TTATAATATTA
1 TTATAATATTA
1180658 TTATAATATTA
1 TTATAATATTA
1180669 TTA
1 TTA
1180672 CATAGAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATAATATTA
Found at i:1183980 original size:285 final size:286
Alignment explanation
Indices: 1183458--1184030 Score: 1130
Period size: 285 Copynumber: 2.0 Consensus size: 286
1183448 TAGTATATAT
1183458 TTATTTATTATGTGTTATAAATTACATAATATAAAGTATTATAAACTTAAAATCGGGCCAAACTC
1 TTATTTATTA-GTGTTATAAATTACATAATATAAAGTATTATAAACTTAAAATCGGGCCAAACTC
1183523 AAGCCTTGAATGTTCAAGCTCGAGTTCAGCCCGTATTTTAAATGGGTCTAATTTTTTCCCAAAAC
65 AAGCCTTGAATGTTCAAGCTCGAGTTCAGCCCGTATTTTAAATGGGTCTAATTTTTTCCCAAAAC
1183588 CCATTTTTTTGGGCTTAATATTTTTGCTTAAACCCTCCCAAATTTTGGACGAACAACCCGACTTA
130 CCATTTTTTTGGGCTTAATATTTTTGCTTAAACCCTCCCAAATTTTGGACGAACAACCCGACTTA
1183653 TGAATAGGTTTGTCTAGTCTCACTCCCACCATGTTCATATGCCATATGTGGGTTATGTCCTATTT
195 TGAATAGGTTTGTCTAGTCTCACTCCCACCATGTTCATATGCCATATGTGGGTTATGTCCTATTT
1183718 TTTTTTTCGAATTAGTCTAGATTTTTC
260 TTTTTTTCGAATTAGTCTAGATTTTTC
1183745 TTATTTATTA-TGTTATAAATTACATAATATAAAGTATTATAAACTTAAAATCGGGCCAAACTCA
1 TTATTTATTAGTGTTATAAATTACATAATATAAAGTATTATAAACTTAAAATCGGGCCAAACTCA
1183809 AGCCTTGAATGTTCAAGCTCGAGTTCAGCCCGTATTTTAAATGGGTCTAATTTTTTCCCAAAACC
66 AGCCTTGAATGTTCAAGCTCGAGTTCAGCCCGTATTTTAAATGGGTCTAATTTTTTCCCAAAACC
1183874 CATTTTTTTGGGCTTAATATTTTTGCTTAAACCCTCCCAAATTTTGGACGAACAACCCGACTTAT
131 CATTTTTTTGGGCTTAATATTTTTGCTTAAACCCTCCCAAATTTTGGACGAACAACCCGACTTAT
1183939 GAATAGGTTTGTCTAGTCTCACTCCCACCATGTTCATATGCCATATGTGGGTTATGTCCTATTTT
196 GAATAGGTTTGTCTAGTCTCACTCCCACCATGTTCATATGCCATATGTGGGTTATGTCCTATTTT
1184004 TTTTTTCGAATTAGTCTAGATTTTTC
261 TTTTTTCGAATTAGTCTAGATTTTTC
1184030 T
1 T
1184031 GATTCTTCAT
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
285 276 0.97
287 10 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (286 bp):
TTATTTATTAGTGTTATAAATTACATAATATAAAGTATTATAAACTTAAAATCGGGCCAAACTCA
AGCCTTGAATGTTCAAGCTCGAGTTCAGCCCGTATTTTAAATGGGTCTAATTTTTTCCCAAAACC
CATTTTTTTGGGCTTAATATTTTTGCTTAAACCCTCCCAAATTTTGGACGAACAACCCGACTTAT
GAATAGGTTTGTCTAGTCTCACTCCCACCATGTTCATATGCCATATGTGGGTTATGTCCTATTTT
TTTTTTCGAATTAGTCTAGATTTTTC
Done.