Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 90 of 161
Found at i:28488016 original size:23 final size:23
Alignment explanation
Indices: 28487984--28488641 Score: 381
Period size: 23 Copynumber: 28.7 Consensus size: 23
28487974 ATGTTTTATC
*
28487984 GTTGT-AATTGAAGTGTATAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28488006 GTTGTTAATTG-AGATG-TTAAAGT
1 GTTGTAAATTGAAG-TGTTTAAA-T
* * *
28488029 GCTGCAAATTGAAATGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28488052 GCTCTAAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
**
28488075 GTTACAAATTGAAGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28488098 GTTGTGAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* * *
28488121 GCTGCAAATTGAAGTGTTTAAGT
1 GTTGTAAATTGAAGTGTTTAAAT
** ** * **
28488144 ACTACAAACTGAAGTGTTTAGTT
1 GTTGTAAATTGAAGTGTTTAAAT
** * *
28488167 GTTGGGAATT-AAGATGTTTTATT
1 GTTGTAAATTGAAG-TGTTTAAAT
* *
28488190 GTTGT-AATTGAGGTGTATAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28488212 GTTGTTAATT-AA-TATGTTAAAGT
1 GTTGTAAATTGAAGTGT-TTAAA-T
* *
28488235 GCTGAAAATTGAAGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28488258 GTTGTGAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* *
28488281 GCTGCAAATTGAAGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28488304 GTTGTAAATTGAACTGTTTTAA-
1 GTTGTAAATTGAAGTGTTTAAAT
* **
28488326 GTACTGCAAATTGAAGTGTTTAGTT
1 GT--TGTAAATTGAAGTGTTTAAAT
* * * *
28488351 ATTGGAAATTG-AGATGTTTTATT
1 GTTGTAAATTGAAG-TGTTTAAAT
* *
28488374 GTTGT-AATTGAGGTGTATAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28488396 GTTGTTAATT-AAGATG-TTAAA-
1 GTTGTAAATTGAAG-TGTTTAAAT
*
28488417 GTTCTTCAAATTGAAGTGTTTAAAT
1 GTT-GT-AAATTGAAGTGTTTAAAT
* **
28488442 GCTACAAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* *
28488465 GTTGCAAATTGAAGTGTTTAACT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28488488 GTTGTGAATTAAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* *
28488511 GCTGCAAATTGAAGTGTTT---T
1 GTTGTAAATTGAAGTGTTTAAAT
* * *
28488531 GTCGCTATAATTGAGGTGTATAAAT
1 GTTG-TA-AATTGAAGTGTTTAAAT
* *
28488556 GTTGTTAATTG-GGATG-TTAAAGT
1 GTTGTAAATTGAAG-TGTTTAAA-T
* *
28488579 GTTGTAAGTTGAGGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28488602 GTTGTAAATTGAAGTGTTTAATT
1 GTTGTAAATTGAAGTGTTTAAAT
* * *
28488625 ATTGAAAATTGAGGTGT
1 GTTGTAAATTGAAGTGT
28488642 ACAAATGAGT
Statistics
Matches: 491, Mismatches: 102, Indels: 85
0.72 0.15 0.13
Matches are distributed among these distances:
20 3 0.01
21 6 0.01
22 102 0.21
23 307 0.63
24 64 0.13
25 9 0.02
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (23 bp):
GTTGTAAATTGAAGTGTTTAAAT
Found at i:28488384 original size:184 final size:183
Alignment explanation
Indices: 28488057--28488529 Score: 673
Period size: 184 Copynumber: 2.6 Consensus size: 183
28488047 TAAATGCTCT
**
28488057 AAATTGAAGTG-TTAAAGTGTTACAAATTGAAGTGTTTAAA-TGTTGTGAATTGAAGTG-TTAAA
1 AAATTGAAGTGTTTAAA-TGTTACAAATTGAAGTG-TTAAAGTGTTGCAAATTGAAGTGTTTAAA
* * * * * *
28488119 GTGCTGCAAATTGAAGTGTTTAAGTACTACAAACTGAAGTGTTTAGTTGTTGGGAATTAAGATGT
64 -TGTTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTAAGATGT
*
28488184 TTTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAATATGTTAAAGTGCTGA
128 TTTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGCTGA
*** *
28488240 AAATTGAAGTGTTTAAATGTTGTGAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
1 AAATTGAAGTGTTTAAATGTTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
* *
28488305 TTGTAAATTGAACTGTTTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTGAGATGTTT
66 TTGTAAATTGAAGTG-TTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTAAGATGTTT
* **
28488370 TATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTTCTTC
130 TATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGCTGA
* *
28488424 AAATTGAAGTGTTTAAATGCTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAACTG
1 AAATTGAAGTGTTTAAATGTTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
* * * *
28488489 TTGTGAATTAAAGTGTTAAAGTGCTGCAAATTGAAGTGTTT
66 TTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTT
28488530 TGTCGCTATA
Statistics
Matches: 257, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
182 5 0.02
183 77 0.30
184 175 0.68
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (183 bp):
AAATTGAAGTGTTTAAATGTTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
TTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTAAGATGTTTT
ATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGCTGA
Found at i:28493402 original size:20 final size:20
Alignment explanation
Indices: 28493366--28493408 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
28493356 TAATAAGACA
*
28493366 TTATGGACTATTTAATTGGT
1 TTATGGACTATTGAATTGGT
*
28493386 TTATGGGACT-TTGAATTGTT
1 TTAT-GGACTATTGAATTGGT
28493406 TTA
1 TTA
28493409 GAATGTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (20 bp):
TTATGGACTATTGAATTGGT
Found at i:28501282 original size:15 final size:15
Alignment explanation
Indices: 28501249--28501279 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28501239 GTCCCTTGTA
28501249 GATTTGGTTAAAATG
1 GATTTGGTTAAAATG
28501264 GATTTAGGTTAAAATG
1 GATTT-GGTTAAAATG
28501280 ATTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (15 bp):
GATTTGGTTAAAATG
Found at i:28504522 original size:16 final size:16
Alignment explanation
Indices: 28504501--28504536 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28504491 AGAATAGGTC
* *
28504501 ATTTATCCATTTGTGG
1 ATTTATCCACTTGTGA
28504517 ATTTATCCACTTGTGA
1 ATTTATCCACTTGTGA
28504533 ATTT
1 ATTT
28504537 CATAGTGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (16 bp):
ATTTATCCACTTGTGA
Found at i:28504697 original size:29 final size:29
Alignment explanation
Indices: 28504646--28504711 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
28504636 TTTGGCCCTT
* * * *
28504646 AAATTTTTTGAAATTATATTTTA-CCTCA
1 AAATTTTTCGAAATTACACTTTAGCCCCA
28504674 AAATTTTCTCGAAATTACACTTTAGCCCCA
1 AAATTTT-TCGAAATTACACTTTAGCCCCA
*
28504704 AAAGTTTT
1 AAATTTTT
28504712 ACTGTGTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.23
29 14 0.45
30 10 0.32
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (29 bp):
AAATTTTTCGAAATTACACTTTAGCCCCA
Found at i:28504972 original size:20 final size:19
Alignment explanation
Indices: 28504941--28504984 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
28504931 GAAAAAAGAA
28504941 AGAGGAAAAAGAG-AGAATG
1 AGAGGAAAAAGAGAAG-ATG
28504960 AGAGGAGAAAAGAGAAGATG
1 AGAGGA-AAAAGAGAAGATG
28504980 AGAGG
1 AGAGG
28504985 GAGGAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.41, T:0.05
Consensus pattern (19 bp):
AGAGGAAAAAGAGAAGATG
Found at i:28505085 original size:13 final size:13
Alignment explanation
Indices: 28505067--28505091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28505057 CCTAGGGCTT
28505067 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
28505080 GAAGAAGAAGAA
1 GAAGAAGAAGAA
28505092 AAAATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:28505425 original size:11 final size:11
Alignment explanation
Indices: 28505409--28505440 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28505399 CAGTCCAGAA
28505409 AAAAAAGAAAG
1 AAAAAAGAAAG
*
28505420 AAAAAAAAAAG
1 AAAAAAGAAAG
28505431 AAAAAAGAAA
1 AAAAAAGAAA
28505441 AAACTGAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:28505427 original size:15 final size:14
Alignment explanation
Indices: 28505407--28505443 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
28505397 CCCAGTCCAG
28505407 AAAAAAAAGAAAGAA
1 AAAAAAAAGAAA-AA
28505422 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
28505436 AGAAAAAA
1 A-AAAAAA
28505444 CTGAGCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:28505436 original size:7 final size:7
Alignment explanation
Indices: 28505409--28505443 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
28505399 CAGTCCAGAA
28505409 AAAAAAG
1 AAAAAAG
*
28505416 AAAGAAAA
1 AAA-AAAG
28505424 AAAAAAG
1 AAAAAAG
28505431 AAAAAAG
1 AAAAAAG
28505438 AAAAAA
1 AAAAAA
28505444 CTGAGCTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28505437 original size:18 final size:17
Alignment explanation
Indices: 28505407--28505443 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
28505397 CCCAGTCCAG
*
28505407 AAAAAAAAGAAAGAAAA
1 AAAAAAAAAAAAGAAAA
28505424 AAAAAAGAAAAAAGAAAA
1 AAAAAA-AAAAAAGAAAA
28505442 AA
1 AA
28505444 CTGAGCTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAA
Found at i:28505441 original size:13 final size:12
Alignment explanation
Indices: 28505405--28505442 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
28505395 AGCCCAGTCC
28505405 AGAAAAAAAAGAA
1 AGAAAAAAAA-AA
28505418 AG-AAAAAAAAA
1 AGAAAAAAAAAA
28505429 AGAAAAAAGAAAA
1 AGAAAAAA-AAAA
28505442 A
1 A
28505443 ACTGAGCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 12 0.52
13 7 0.30
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:28518043 original size:79 final size:77
Alignment explanation
Indices: 28517679--28518634 Score: 1182
Period size: 79 Copynumber: 12.2 Consensus size: 77
28517669 AACCATTTCT
*
28517679 ATTTCTGTTTTTTC-AAAAATCAACTCCTATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
1 ATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
28517743 GAGGTATTTTTTA
65 GAGGTATTTTTTA
* * *
28517756 ATTTCTATTTTTCAAAAAAAAATTAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACG
1 ATTTCTGTTTTTC---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACG
* *
28517821 CTGAGGTATTTTTAAA
63 CCGAGGTATTTTT-TA
* * * * * *
28517837 ATTTTTGTTTTTC-AAAAATTAACCCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCA
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28517901 AGGTA-TTTTTA
66 AGGTATTTTTTA
*
28517912 ATTCCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
1 ATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
28517976 GAGGTATTTTTTA
65 GAGGTATTTTTTA
* * * *
28517989 ATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAACCTCGGGCCACATC-
1 ATTTCTGTTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CG
* *
28518053 CCGAGGTACTTTTCA
63 CCGAGGTATTTTTTA
* * *
28518068 ATTTCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACATGCC
1 ATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
28518131 GAGGTATTTTTTTTAA
65 GAGGTA--TTTTTT-A
* * * * * *
28518147 ATTTCTATTTTTC-AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGAGTTACATGCCG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28518211 AGGTA-TTTTTA
66 AGGTATTTTTTA
*
28518222 ATTTCTGTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACATGC
1 ATTTCTG--TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC
28518285 CGAGGTATTTCTTTTAA
64 CGAGGTA-TT-TTTT-A
* *
28518302 ATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28518367 AGGTATTTTTTTA
66 AGGTA-TTTTTTA
* *
28518380 ATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGTC
1 ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
*
28518445 GAGGTACTTTTTA
65 GAGGTATTTTTTA
* * *
28518458 ATTTCTGTTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGTCTCGGGT--CACGCTG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28518521 AGGTATTTTTTTA
66 AGGTA-TTTTTTA
* * **
28518534 ATTTCTATTTTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACAC
1 ATTTC---TGTTTTT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC
* *
28518599 GCCAAGGTATTTTTCA
62 GCCGAGGTATTTTTTA
* *
28518615 ATTTATGTTTTCACAAAAAA
1 ATTTCTGTTTT-TCAAAAAA
28518635 AAAGGGATCG
Statistics
Matches: 773, Mismatches: 72, Indels: 67
0.85 0.08 0.07
Matches are distributed among these distances:
75 23 0.03
76 115 0.15
77 188 0.24
78 96 0.12
79 194 0.25
80 125 0.16
81 22 0.03
82 10 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (77 bp):
ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
AGGTATTTTTTA
Found at i:28518135 original size:155 final size:153
Alignment explanation
Indices: 28517679--28518634 Score: 1167
Period size: 155 Copynumber: 6.1 Consensus size: 153
28517669 AACCATTTCT
*
28517679 ATTTCTGTTTTTTC-AAAAATCAACTCCTATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
1 ATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC-CC
* * *
28517743 GAGGTATTTTTTAATTTCT-ATTTTTCAAAAAAAAATTAACTCATATTGCGAGAAGTGAGTTGAG
64 GAGGTATTTTTTAATTTCTGTTTTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
28517807 CCTCGGGTCACACGCTGAGGTATTTTTAAA
125 CCTCGGGTCACACGCCGAGGTATTTTT-TA
* * * * * *
28517837 ATTTTTGTTTTTC-AAAAATTAACCCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCA
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CCCG
*
28517901 AGGTA-TTTTTAATTCCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
65 AGGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
28517965 GGTCACACGCCGAGGTATTTTTTA
130 GGTCACACGCCGAGGTATTTTTTA
* * * *
28517989 ATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAACCTCGGGCCACATCC
1 ATTTCTGTTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CC
* *
28518054 CGAGGTACTTTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
63 CGAGGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
28518119 C-AGACACATGCCGAGGTATTTTTTTTAA
128 CGGGTCACACGCCGAGGTA--TTTTTT-A
* * * * * *
28518147 ATTTCTATTTTTC-AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGAGTTACATGCCG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CCCG
28518211 AGGTA-TTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
65 AGGTATTTTTTAATTTCTG-TTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
28518275 GGG-CACATGCCGAGGTATTTCTTTTAA
129 GGGTCACACGCCGAGGTA-TT-TTTT-A
* *
28518302 ATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC-CCG
*
28518367 AGGTATTTTTTTAATTTTTG-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 AGGTA-TTTTTTAATTTCTGTTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
28518431 TCGGGTCACACGTCGAGGTACTTTTTA
127 TCGGGTCACACGCCGAGGTATTTTTTA
* * * *
28518458 ATTTCTGTTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGTCTCGGGTCAC-GCTGA
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACCCGA
* *
28518522 GGTATTTTTTTAATTTCTATTTTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
66 GGTA-TTTTTTAATTTC--TGTTTTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
** * *
28518587 CTCAAGTCACACGCCAAGGTATTTTTCA
126 CTCGGGTCACACGCCGAGGTATTTTTTA
* *
28518615 ATTTATGTTTTCACAAAAAA
1 ATTTCTGTTTT-TCAAAAAA
28518635 AAAGGGATCG
Statistics
Matches: 706, Mismatches: 67, Indels: 50
0.86 0.08 0.06
Matches are distributed among these distances:
152 13 0.02
153 58 0.08
154 35 0.05
155 184 0.26
156 181 0.26
157 143 0.20
158 80 0.11
159 12 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (153 bp):
ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACCCGA
GGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
GTCACACGCCGAGGTATTTTTTA
Found at i:28519177 original size:93 final size:93
Alignment explanation
Indices: 28519018--28519204 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
28519008 CAAGATACCA
*
28519018 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACTGACTCCCGAACTCTAATTTT
1 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
28519083 CTCTGGATTTTAACGTGGACTTAAAATT
66 CTCTGGATTTTAACGTGGACTTAAAATT
28519111 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
1 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
28519176 CTCTGGATTTTAACGTGGACTTAAAATT
66 CTCTGGATTTTAACGTGGACTTAAAATT
28519204 A
1 A
28519205 CCTCTTTTTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (93 bp):
ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
CTCTGGATTTTAACGTGGACTTAAAATT
Found at i:28524794 original size:13 final size:12
Alignment explanation
Indices: 28524774--28524818 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
28524764 AAAACATTTA
28524774 TTATAAATAAAT
1 TTATAAATAAAT
*
28524786 TTCATAAATAAAA
1 TT-ATAAATAAAT
*
28524799 TTAAAAATAAATT
1 TTATAAATAAA-T
28524812 TTATAAA
1 TTATAAA
28524819 CATTTTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
TTATAAATAAAT
Found at i:28525396 original size:20 final size:21
Alignment explanation
Indices: 28525371--28525409 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28525361 ATAATTTGAA
28525371 TATTTTATATTTAA-AAAATT
1 TATTTTATATTTAATAAAATT
*
28525391 TATTTTATTTTTAATAAAA
1 TATTTTATATTTAATAAAA
28525410 AAAATCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTATATTTAATAAAATT
Found at i:28526387 original size:29 final size:28
Alignment explanation
Indices: 28526347--28526420 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
28526337 TTTACCTTAG
* *
28526347 GTTACATTTTAGTCACTTATGTTTAAAAT
1 GTTACATTTTAGTCACTTACG-CTAAAAT
*
28526376 GTTACATTTTAGTCACTTACGCTAACAT
1 GTTACATTTTAGTCACTTACGCTAAAAT
*
28526404 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
28526421 AAGCTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 21 0.51
29 20 0.49
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (28 bp):
GTTACATTTTAGTCACTTACGCTAAAAT
Found at i:28528334 original size:32 final size:33
Alignment explanation
Indices: 28528265--28528336 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
28528255 GAGCTTATTC
* *
28528265 TTTATTTTGATATTTATATTTTTGGTAATTAGG
1 TTTATTTTGATATTTATATTTTTGGTAATAAGA
*
28528298 TTTATTTTGATATTTGTA-TTTTGGT-ATAAAGA
1 TTTATTTTGATATTTATATTTTTGGTAAT-AAGA
28528330 TTTATTT
1 TTTATTT
28528337 GACCTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.06
32 16 0.46
33 17 0.49
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (33 bp):
TTTATTTTGATATTTATATTTTTGGTAATAAGA
Found at i:28528566 original size:30 final size:29
Alignment explanation
Indices: 28528531--28528611 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
28528521 ATTTTTTTAA
28528531 ATTTTAAAAAATTAAAAAATATAAAAACTT
1 ATTTTAAAAAATTAAAAAATATAAAAAC-T
* * *
28528561 ATTTTAAATAATTAAAAATTATTAAAACT
1 ATTTTAAAAAATTAAAAAATATAAAAACT
*
28528590 A-ATT-AAAAATATAAAAAATATA
1 ATTTTAAAAAAT-TAAAAAATATA
28528612 TTTTTTCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 5 0.12
28 11 0.26
29 2 0.05
30 25 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTTAAAAAATTAAAAAATATAAAAACT
Found at i:28528582 original size:20 final size:19
Alignment explanation
Indices: 28528542--28528599 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
28528532 TTTTAAAAAA
*
28528542 TTAAAAAATATAAAAACTTATT
1 TTAAATAAT-TAAAAA-TTA-T
28528564 TTAAATAATTAAAAATTAT
1 TTAAATAATTAAAAATTAT
*
28528583 TAAAACTAATTAAAAAT
1 TTAAA-TAATTAAAAAT
28528600 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 6 0.18
22 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAATAATTAAAAATTAT
Found at i:28528584 original size:10 final size:10
Alignment explanation
Indices: 28528529--28528613 Score: 54
Period size: 10 Copynumber: 8.8 Consensus size: 10
28528519 TAATTTTTTT
28528529 AAATT-TTAA
1 AAATTATTAA
28528538 AAA--ATTAA
1 AAATTATTAA
*
28528546 AAAATA-TAA
1 AAATTATTAA
**
28528555 AAACTTATTTT
1 AAA-TTATTAA
*
28528566 AAATAATTAA
1 AAATTATTAA
28528576 AAATTATTAA
1 AAATTATTAA
* *
28528586 AACTAATTAA
1 AAATTATTAA
*
28528596 AAA-TATAAA
1 AAATTATTAA
28528605 AAATATATT
1 AAAT-TATT
28528614 TTTTCATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
8 7 0.12
9 16 0.29
10 26 0.46
11 7 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:28528607 original size:20 final size:20
Alignment explanation
Indices: 28528569--28528606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28528559 TTATTTTAAA
*
28528569 TAATTAAAAATTATTAAAAC
1 TAATTAAAAATTATAAAAAC
28528589 TAATTAAAAA-TATAAAAA
1 TAATTAAAAATTATAAAAA
28528607 ATATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATTAAAAATTATAAAAAC
Found at i:28530739 original size:21 final size:21
Alignment explanation
Indices: 28530714--28530757 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28530704 ATCTTCGAGG
28530714 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28530735 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28530756 AT
1 AT
28530758 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:28530763 original size:19 final size:19
Alignment explanation
Indices: 28530713--28530768 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
28530703 AATCTTCGAG
28530713 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28530732 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
28530753 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
28530769 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28530775 original size:22 final size:23
Alignment explanation
Indices: 28530726--28530791 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
28530716 ATGCAATCTT
*
28530726 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
28530747 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
28530769 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
28530792 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:28530801 original size:22 final size:23
Alignment explanation
Indices: 28530757--28530801 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28530747 AGATATGATA
*
28530757 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
28530780 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
28530802 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:28531225 original size:3 final size:3
Alignment explanation
Indices: 28531217--28531256 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
28531207 ATTAATTTTG
*
28531217 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
28531257 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28531225 original size:15 final size:15
Alignment explanation
Indices: 28531201--28531255 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
28531191 GTTTTTAGTC
28531201 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
28531215 TGTTATTATTATTTT
1 TATTATTATTAATTT
28531230 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
28531244 ATATTATTATTA
1 -TATTATTATTA
28531256 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:28531232 original size:12 final size:12
Alignment explanation
Indices: 28531203--28531254 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
28531193 TTTTAGTCTA
28531203 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
28531215 TGTTATTATTAT
1 TTTTATTATTAT
28531227 TTTTATTATTAT
1 TTTTATTATTAT
28531239 ATTATATATTATTAT
1 -TT-T-TATTATTAT
28531254 T
1 T
28531255 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:28534213 original size:19 final size:20
Alignment explanation
Indices: 28534189--28534226 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28534179 GAAAAATGAA
28534189 AAATTATAAA-AAT-GAAAAC
1 AAATTA-AAATAATAGAAAAC
28534208 AAATTAAAATAATAGAAAA
1 AAATTAAAATAATAGAAAA
28534227 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 9 0.53
20 5 0.29
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATTAAAATAATAGAAAAC
Found at i:28541452 original size:20 final size:20
Alignment explanation
Indices: 28541427--28541468 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28541417 GAAGAAGTAT
28541427 GTTGGCCAGGTATACATTGA
1 GTTGGCCAGGTATACATTGA
*
28541447 GTTGGCCAGTTATACATTGA
1 GTTGGCCAGGTATACATTGA
28541467 GT
1 GT
28541469 GAAAGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (20 bp):
GTTGGCCAGGTATACATTGA
Found at i:28553026 original size:25 final size:26
Alignment explanation
Indices: 28552980--28553028 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28552970 GCTTAATGTC
* *
28552980 AAAAATTTAAAAATCTGATCCTTAAT
1 AAAAACTTAAAAAGCTGATCCTTAAT
*
28553006 AAAAACTTAAAAAGC-GTTCCTTA
1 AAAAACTTAAAAAGCTGATCCTTA
28553029 TTAAGCCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAACTTAAAAAGCTGATCCTTAAT
Found at i:28554635 original size:19 final size:19
Alignment explanation
Indices: 28554611--28554664 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
28554601 AATCATATCT
28554611 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28554630 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
28554649 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28554665 CTTGAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28554660 original size:38 final size:40
Alignment explanation
Indices: 28554588--28554664 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
28554578 AAATTAAATC
28554588 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
28554630 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
28554665 CTTGAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:28557474 original size:14 final size:14
Alignment explanation
Indices: 28557455--28557482 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28557445 TATATTAGTA
28557455 TTTTCTATTCTATT
1 TTTTCTATTCTATT
28557469 TTTTCTATTCTATT
1 TTTTCTATTCTATT
28557483 AGTATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:28557490 original size:6 final size:6
Alignment explanation
Indices: 28557479--28557552 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
28557469 TTTTCTATTC
*
28557479 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
28557526 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
28557553 TAGTGATCCC
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 4 0.07
5 23 0.39
6 26 0.44
8 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (6 bp):
TATTAG
Found at i:28557505 original size:11 final size:11
Alignment explanation
Indices: 28557480--28557556 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
28557470 TTTCTATTCT
28557480 ATTAGTATTAG
1 ATTAGTATTAG
28557491 ---AGTATTAG
1 ATTAGTATTAG
**
28557499 ATTAGTATTCT
1 ATTAGTATTAG
28557510 ATTAGTATTAG
1 ATTAGTATTAG
28557521 ATTAGTATTAG
1 ATTAGTATTAG
28557532 -TTAG-ATTAG
1 ATTAGTATTAG
28557541 ATTAGTATTAG
1 ATTAGTATTAG
28557552 -TTAGT
1 ATTAGT
28557557 GATCCCGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:28557510 original size:30 final size:30
Alignment explanation
Indices: 28557474--28557552 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
28557464 CTATTTTTTC
28557474 TATTCTATTAGTATTAG-AGTATTAGATTAG
1 TATTCTATTAGTATTAGTAGTATTAG-TTAG
28557504 TATTCTATTAGTATTAGATTAGTATTAGTTAG
1 TATTCTATTAGTATTAG--TAGTATTAGTTAG
**
28557536 -ATTAGATTAGTATTAGT
1 TATTCTATTAGTATTAGT
28557553 TAGTGATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 14 0.32
32 4 0.09
33 8 0.18
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (30 bp):
TATTCTATTAGTATTAGTAGTATTAGTTAG
Found at i:28557524 original size:5 final size:5
Alignment explanation
Indices: 28557494--28557555 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
28557484 GTATTAGAGT
**
28557494 ATTAG ATTAG TATTCT ATTAG TATTAG ATTAG TATTAG -TTAG ATTAG
1 ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG ATTAG
28557541 ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG
28557556 TGATCCCGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.47
Consensus pattern (5 bp):
ATTAG
Found at i:28557541 original size:20 final size:21
Alignment explanation
Indices: 28557480--28557556 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
28557470 TTTCTATTCT
28557480 ATTAGTATTAG--AGTATTAG
1 ATTAGTATTAGTTAGTATTAG
28557499 ATTAGTATTCTA-TTAGTATTAG
1 ATTAGTA-T-TAGTTAGTATTAG
28557521 ATTAGTATTAGTTAG-ATTAG
1 ATTAGTATTAGTTAGTATTAG
28557541 ATTAGTATTAGTTAGT
1 ATTAGTATTAGTTAGT
28557557 GATCCCGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.13
20 23 0.44
21 7 0.13
22 15 0.29
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (21 bp):
ATTAGTATTAGTTAGTATTAG
Found at i:28559419 original size:31 final size:31
Alignment explanation
Indices: 28559326--28559419 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
28559316 AGATAATTTT
* *
28559326 AAAGAGTTTTATTAGGATTCAATTAATCTTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28559357 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
28559389 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28559420 TAATTTGCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:28568276 original size:32 final size:31
Alignment explanation
Indices: 28568231--28568326 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
28568221 CTTAGATAAT
28568231 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28568262 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
28568294 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28568325 TT
1 TT
28568327 GTCATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:28578952 original size:10 final size:10
Alignment explanation
Indices: 28578933--28578967 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28578923 AAATCTATTG
28578933 AAAA-TAATC
1 AAAATTAATC
28578942 AAAATTAATC
1 AAAATTAATC
*
28578952 AAAATTAATT
1 AAAATTAATC
28578962 AAAATT
1 AAAATT
28578968 CAACATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTAATC
Found at i:28591434 original size:32 final size:33
Alignment explanation
Indices: 28591388--28591453 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
28591378 ATCTTTATGC
*
28591388 CTTAAATGGAAAATGATTTTTA-TATAGGGGAG
1 CTTAAATGGAAAATGACTTTTATTATAGGGGAG
* * *
28591420 CTTAAATTGCAAATGACTTTTATTATGGGGGAG
1 CTTAAATGGAAAATGACTTTTATTATAGGGGAG
28591453 C
1 C
28591454 AATCTATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (33 bp):
CTTAAATGGAAAATGACTTTTATTATAGGGGAG
Found at i:28596557 original size:101 final size:100
Alignment explanation
Indices: 28596444--28596665 Score: 236
Period size: 101 Copynumber: 2.2 Consensus size: 100
28596434 TGGCACAGAT
* *
28596444 TGTGTGTAGGCTACTATGTAAAAGTGAAAGTGAT-GGTCACATGTGCAGTACTATGTGCAGGCTA
1 TGTGTGCAGGCTACTATGTAAAA--GAAAGT-ATCGATCACATGTGCAGTACTATGTGCAGGCTA
* *
28596508 CTACGTGTACCGGAAT-G-ACA-GGTCGCATGTGTAGTAC
63 CTACATGTACCGG-ATGGTA-ATGGTCACATGTGTAGTAC
** * * * *
28596545 TGTGTGCAGGCTACTATGCGTACCAGATAGTTTCGATCACGTGTGTAGTACTATGTGCAGGCTAC
1 TGTGTGCAGGCTACTAT--GTAAAAGAAAGTATCGATCACATGTGCAGTACTATGTGCAGGCTAC
*
28596610 TACATGTATCGGATGGTAATGGTCACATGTGTAGTAC
64 TACATGTACCGGATGGTAATGGTCACATGTGTAGTAC
* *
28596647 TATGTGCAGGCTACAATGT
1 TGTGTGCAGGCTACTATGT
28596666 GAACCTAACA
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
100 5 0.05
101 61 0.60
102 32 0.31
103 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (100 bp):
TGTGTGCAGGCTACTATGTAAAAGAAAGTATCGATCACATGTGCAGTACTATGTGCAGGCTACTA
CATGTACCGGATGGTAATGGTCACATGTGTAGTAC
Found at i:28596605 original size:51 final size:51
Alignment explanation
Indices: 28596480--28596660 Score: 163
Period size: 51 Copynumber: 3.6 Consensus size: 51
28596470 AAAGTGATGG
* ** * *
28596480 TCACATGTGCAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGACA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGT-A-ATGA
* * ** *
28596530 TCGCATGTGTAGTACTGTGTGCAGGCTACTATGCGTACCAGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAAT-GA
* * * * * *
28596581 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAATGA
28596632 TCACATGTGTAGTACTATGTGCAGGCTAC
1 TCACATGTGTAGTACTATGTGCAGGCTAC
28596661 AATGTGAACC
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
50 36 0.34
51 68 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAATGA
Found at i:28596724 original size:45 final size:45
Alignment explanation
Indices: 28596673--28596760 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
28596663 TGTGAACCTA
* *
28596673 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
*
28596718 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
28596761 GAGTATCTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:28612036 original size:69 final size:69
Alignment explanation
Indices: 28611915--28612109 Score: 259
Period size: 69 Copynumber: 2.8 Consensus size: 69
28611905 ACTCTAACAT
*
28611915 TAAGACCATAGTTGGGGCTATGGCAACATATGAAGTCTGC-CAA-GACAATAAACATGGGATCAT
1 TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTC--CACAAGGACAATAAACATGGGATCAT
28611978 ATTGTG
64 ATTGTG
* * * * * * *
28611984 TAAGACCACAGCTAGGGTTATGGCAACATATAAAGTCCATAAGGACAGTAAACATGGGATCTTAT
1 TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTCCACAAGGACAATAAACATGGGATCATAT
28612049 TGTG
66 TGTG
* * *
28612053 TAAGACCATAGCTGGGGCTATGGCAACATTTGAACTCCACCAGGACAATAAACATGG
1 TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTCCACAAGGACAATAAACATGG
28612110 TAGCATATGG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 1 0.01
68 2 0.02
69 104 0.97
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (69 bp):
TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTCCACAAGGACAATAAACATGGGATCATAT
TGTG
Found at i:28614690 original size:14 final size:15
Alignment explanation
Indices: 28614673--28614705 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28614663 TTCTCATTTG
28614673 CTTTTTCTCTC-TTT
1 CTTTTTCTCTCTTTT
*
28614687 CTTTTTCTTTCTTTT
1 CTTTTTCTCTCTTTT
28614702 CTTT
1 CTTT
28614706 GATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTCTCTCTTTT
Found at i:28616999 original size:25 final size:25
Alignment explanation
Indices: 28616944--28617037 Score: 97
Period size: 25 Copynumber: 3.8 Consensus size: 25
28616934 GTTCATACCC
*
28616944 ACAGCTCGTG-TGAGCATATCGATTT
1 ACAGCTCGTGATGAGCATACCGA-TT
* *
28616969 ATAGCTTGTGA-GAGCATACCGATCT
1 ACAGCTCGTGATGAGCATACCGAT-T
*
28616994 ACAGCTCG-AATGAGCATACCGATT
1 ACAGCTCGTGATGAGCATACCGATT
28617018 CACAGCTCGT-ATGAGCATAC
1 -ACAGCTCGTGATGAGCATAC
28617038 ATGTATATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.05
25 55 0.95
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (25 bp):
ACAGCTCGTGATGAGCATACCGATT
Found at i:28622068 original size:18 final size:18
Alignment explanation
Indices: 28622045--28622081 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28622035 AATCAATTTA
28622045 TATTACGTAAAACTGAAT
1 TATTACGTAAAACTGAAT
28622063 TATTACGTAAAACTGAAT
1 TATTACGTAAAACTGAAT
28622081 T
1 T
28622082 TATATTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (18 bp):
TATTACGTAAAACTGAAT
Found at i:28622323 original size:20 final size:18
Alignment explanation
Indices: 28622272--28622320 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28622262 ATTTGGCATA
28622272 TAACAGAATAATTTTTTAT
1 TAACA-AATAATTTTTTAT
* *
28622291 AAACATATCAATTTTTTATT
1 TAACAAAT-AATTTTTTA-T
28622311 TAACAAATAA
1 TAACAAATAA
28622321 ATTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (18 bp):
TAACAAATAATTTTTTAT
Found at i:28629582 original size:63 final size:61
Alignment explanation
Indices: 28629483--28629604 Score: 226
Period size: 63 Copynumber: 2.0 Consensus size: 61
28629473 TGTCAAATGT
28629483 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTTTATTTAGAAATTTTGTTGC
1 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCA--TTTTTTATTTAGAAATTTTGTTGC
28629546 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTATTTAGAAATTTTGTT
1 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTATTTAGAAATTTTGTT
28629605 TTCACCGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 22 0.37
63 37 0.63
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.56
Consensus pattern (61 bp):
TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTATTTAGAAATTTTGTTGC
Found at i:28630626 original size:21 final size:20
Alignment explanation
Indices: 28630588--28630626 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28630578 GGTTCAACTG
*
28630588 CTAGTTCAACTGTTTGTAGC
1 CTAGTTCAACCGTTTGTAGC
28630608 CTAGTTCAACCGATTTGTA
1 CTAGTTCAACCG-TTTGTA
28630627 CTGTTCAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
CTAGTTCAACCGTTTGTAGC
Found at i:28631535 original size:6 final size:7
Alignment explanation
Indices: 28631518--28631545 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28631508 TATTATAAAT
28631518 TTTTTTA
1 TTTTTTA
28631525 TTTTTTA
1 TTTTTTA
28631532 TTTTTTA
1 TTTTTTA
28631539 TTTTTTA
1 TTTTTTA
28631546 ATAACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:28635011 original size:63 final size:63
Alignment explanation
Indices: 28634934--28635055 Score: 201
Period size: 63 Copynumber: 1.9 Consensus size: 63
28634924 AATTTATCGA
* *
28634934 TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAGAT-TTATAGTTAAAACCTTATTGC
1 TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAAATCCT-TAGTTAAAACCTTATTGC
*
28634997 TAATTTTTATTGTATGAAATATTTTATTACATAAACTTAAATCCTTAGTTAAAACCTTA
1 TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAAATCCTTAGTTAAAACCTTA
28635056 AAATATAGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 54 0.98
64 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (63 bp):
TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAAATCCTTAGTTAAAACCTTATTGC
Found at i:28635864 original size:26 final size:27
Alignment explanation
Indices: 28635831--28635881 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
28635821 TAAATATATA
28635831 TTTTTA-TTTTTTAATTTTAAAATACT
1 TTTTTATTTTTTTAATTTTAAAATACT
*
28635857 TTTTTATTTTTTTATTTTTAAAATA
1 TTTTTATTTTTTTAATTTTAAAATA
28635882 AATATTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTTTTAATTTTAAAATACT
Found at i:28646580 original size:23 final size:23
Alignment explanation
Indices: 28646526--28646580 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
28646516 GATTATGCAT
* *
28646526 TTCGATGCAATTAATATTGGCAC
1 TTCGATGCAACTAATACTGGCAC
* *
28646549 TAT-GGTGCAACTGATACTGGCAC
1 T-TCGATGCAACTAATACTGGCAC
28646572 TTCGATGCA
1 TTCGATGCA
28646581 TTACTGTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (23 bp):
TTCGATGCAACTAATACTGGCAC
Found at i:28657420 original size:12 final size:12
Alignment explanation
Indices: 28657403--28657432 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28657393 AGTCACACAC
28657403 CCGTGTGCTAGG
1 CCGTGTGCTAGG
28657415 CCGTGTGCTAGG
1 CCGTGTGCTAGG
28657427 CCGTGT
1 CCGTGT
28657433 AACAGCCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.27, G:0.40, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:28658618 original size:25 final size:24
Alignment explanation
Indices: 28658579--28658665 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 24
28658569 TCATGTACAT
* *
28658579 GTATGCTTATACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGT-AATCG
* * *
28658604 ATATGCTCACTCGAGTTGTAGATCG
1 GTATGCTCACACGAGCTGTA-ATCG
* *
28658629 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGT-AATCG
28658654 GTATGCTCACAC
1 GTATGCTCACAC
28658666 AAGTTGTGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (24 bp):
GTATGCTCACACGAGCTGTAATCG
Found at i:28664118 original size:24 final size:24
Alignment explanation
Indices: 28664074--28664119 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28664064 GGACAAGCTG
* *
28664074 AAATTTCCAACAGGGAAATTAAAC
1 AAATTTCCAACAAGCAAATTAAAC
*
28664098 AAATTTCCAACAAGCATATTAA
1 AAATTTCCAACAAGCAAATTAA
28664120 TGATGATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (24 bp):
AAATTTCCAACAAGCAAATTAAAC
Found at i:28666311 original size:49 final size:49
Alignment explanation
Indices: 28666214--28666328 Score: 117
Period size: 49 Copynumber: 2.3 Consensus size: 49
28666204 GCGGTGTGGT
* * * * ** * *
28666214 AGGCTGTGCGGAGCACACGGTCGTTTGAAACATTGTAGACTGTGTGGCC
1 AGGCCGTGTGGAGCACACGATCGTGTGAAACATTACAGACCGTATGGCC
28666263 AGGCCGTGTGGAGCACACGATCGTGTGAAAC-TCTACAGACCGTATGGCC
1 AGGCCGTGTGGAGCACACGATCGTGTGAAACAT-TACAGACCGTATGGCC
*
28666312 AGACCGTGTAGG-GCACA
1 AGGCCGTGT-GGAGCACA
28666329 TGGCCATGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.02
49 52 0.95
50 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (49 bp):
AGGCCGTGTGGAGCACACGATCGTGTGAAACATTACAGACCGTATGGCC
Found at i:28689988 original size:53 final size:53
Alignment explanation
Indices: 28689908--28690015 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
28689898 ATTGACACGG
*
28689908 CCGTGTGACAAAGCCCAGGCCATGTGGCATAGGGACATGGCCATGTGGCCAAA
1 CCGTGTGACAAAGCCCAGGCCACGTGGCATAGGGACATGGCCATGTGGCCAAA
* * *
28689961 CCGTGTGATAAAGCCCAGGCCGCGTGGCATTGGGACATGGCCATGTGGCCAAA
1 CCGTGTGACAAAGCCCAGGCCACGTGGCATAGGGACATGGCCATGTGGCCAAA
28690014 CC
1 CC
28690016 ATGTAACTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (53 bp):
CCGTGTGACAAAGCCCAGGCCACGTGGCATAGGGACATGGCCATGTGGCCAAA
Found at i:28693466 original size:27 final size:26
Alignment explanation
Indices: 28693416--28693660 Score: 238
Period size: 27 Copynumber: 9.1 Consensus size: 26
28693406 TATAATAGTT
* *
28693416 ATTTTACCCTATAGAGGTAATTCGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* * *
28693443 ATTTTACCCTATAGGCGTATTTCGATT
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* *
28693470 ATTCTACCATATGGGGGTATTTCGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* **
28693497 ATATTACCCTATGGGGGTATTTCAATC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
28693524 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* *
28693551 ATTCTACCCTATAGGGGTATTTAGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* * *
28693578 ATTTTACCCTATGGATGAATTTCAGTC
1 ATTTTACCCTATGG-GGTATTTCGGTC
*
28693605 ATTCTACCCTATGTGGGTATTTCGGTC
1 ATTTTACCCTATG-GGGTATTTCGGTC
* *
28693632 ATTTTACCCTATGGAGTTATTTTGGTC
1 ATTTTACCCTATGG-GGTATTTCGGTC
28693659 AT
1 AT
28693661 AACAGTGTAA
Statistics
Matches: 181, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.02
27 177 0.98
28 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:28693544 original size:81 final size:81
Alignment explanation
Indices: 28693419--28693661 Score: 281
Period size: 81 Copynumber: 3.0 Consensus size: 81
28693409 AATAGTTATT
* ** * * * *
28693419 TTACCCTATAGAGGTAA-TTCGGTCATTTTACCCTATAGGCGTATTTCGATTATTCTACCATATG
1 TTACCCTATGGAGG-AATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATG
*
28693483 GGGGTATTTCGGTCATA
65 GGGGTATTTAGGTCATA
* * *
28693500 TTACCCTATGGGGGTATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATAG
1 TTACCCTATGGAGGAATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGG
*
28693565 GGGTATTTAGGTCATT
66 GGGTATTTAGGTCATA
* * * * * *
28693581 TTACCCTATGGATGAATTTCAGTCATTCTACCCTATGTGGGTATTTCGGTCATTTTACCCTATGG
1 TTACCCTATGGAGGAATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGG
* * *
28693646 AGTTATTTTGGTCATA
66 GGGTATTTAGGTCATA
28693662 ACAGTGTAAA
Statistics
Matches: 136, Mismatches: 25, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
80 1 0.01
81 135 0.99
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (81 bp):
TTACCCTATGGAGGAATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGG
GGGTATTTAGGTCATA
Found at i:28702106 original size:36 final size:36
Alignment explanation
Indices: 28702056--28702133 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
28702046 TTTTGTTGAC
** *
28702056 ATAAAACTTTTGAATAACTTAGAATACTTAATAATT
1 ATAAAACTCATGAATAACTTAAAATACTTAATAATT
28702092 ATAAAACTCATGAATAACTTAAAATACTTAATAATT
1 ATAAAACTCATGAATAACTTAAAATACTTAATAATT
28702128 ATAAAA
1 ATAAAA
28702134 AATTCAGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (36 bp):
ATAAAACTCATGAATAACTTAAAATACTTAATAATT
Found at i:28707328 original size:40 final size:40
Alignment explanation
Indices: 28707284--28707547 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
28707274 GCTCCTCGTT
* *
28707284 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28707324 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28707364 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28707404 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28707444 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28707483 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
28707524 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28707548 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28714319 original size:51 final size:50
Alignment explanation
Indices: 28714226--28714362 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 50
28714216 CCACAGCTCA
*
28714226 TGAGAGCATACTGATTTAAAGCTTATGTGAGCATACTGATTTACAACTCG
1 TGAGAGCATACTGATTTAAAGCTTATGTGAGCATACTAATTTACAACTCG
* * * *
28714276 TGAGAGCATACTGATGTTACAGCTTGTGTGCGCATA-TCAATTTACAGCTCG
1 TGAGAGCATACTGAT-TTAAAGCTTATGTGAGCATACT-AATTTACAACTCG
* *
28714327 TGAGAGCATACTGATTTATAGCTCGA-GTGAGCATAC
1 TGAGAGCATACTGATTTAAAGCT-TATGTGAGCATAC
28714363 ATGTACATGA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
50 31 0.42
51 43 0.58
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (50 bp):
TGAGAGCATACTGATTTAAAGCTTATGTGAGCATACTAATTTACAACTCG
Found at i:28714351 original size:25 final size:25
Alignment explanation
Indices: 28714218--28714362 Score: 148
Period size: 25 Copynumber: 5.8 Consensus size: 25
28714208 GGTCTGACCC
*
28714218 ACAGCTCATGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* ** *
28714243 AAAGCTTATGTGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
*
28714268 ACAACTCGTGAGAGCATACTGATGTT
1 ACAGCTCGTGAGAGCATACTGAT-TT
* * * *
28714294 ACAGCTTGTGTGCGCATA-TCAATTT
1 ACAGCTCGTGAGAGCATACT-GATTT
28714319 ACAGCTCGTGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* * *
28714344 ATAGCTCGAGTGAGCATAC
1 ACAGCTCGTGAGAGCATAC
28714363 ATGTACATGA
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
25 78 0.80
26 19 0.20
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACTGATTT
Found at i:28738854 original size:29 final size:28
Alignment explanation
Indices: 28738832--28738925 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 28
28738822 TTTTATTATT
* *
28738832 TTTTATATTTTTTTATGATTTTTATAAAA
1 TTTTAAATTTTCTTAT-ATTTTTATAAAA
28738861 TTTTAAATTTTCTTATATTTTT-TAAAA
1 TTTTAAATTTTCTTATATTTTTATAAAA
* * * *
28738888 TTTT-TATTTT-TTCTAATTTTAATAAAT
1 TTTTAAATTTTCTTAT-ATTTTTATAAAA
28738915 TTTTAATATTT
1 TTTTAA-ATTT
28738926 GAATTTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.06
26 10 0.19
27 17 0.31
28 6 0.11
29 18 0.33
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTTAAATTTTCTTATATTTTTATAAAA
Found at i:28738871 original size:26 final size:26
Alignment explanation
Indices: 28738842--28738943 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 26
28738832 TTTTATATTT
*
28738842 TTTTATGATTTTTATAAAATTTTAAA
1 TTTTCTGATTTTTATAAAATTTTAAA
* * **
28738868 TTTTCTTATATTTTTTAAAATTTTTATT
1 TTTTCTGAT-TTTTATAAAA-TTTTAAA
* * *
28738896 TTTTCTAATTTTAAT-AAATTTTTAA
1 TTTTCTGATTTTTATAAAATTTTAAA
*
28738921 TATT-TGAATTTTTATTAAAATTT
1 TTTTCTG-ATTTTTA-TAAAATTT
28738944 AATAATATTA
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
24 1 0.02
25 13 0.23
26 11 0.19
27 19 0.33
28 13 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTCTGATTTTTATAAAATTTTAAA
Found at i:28738881 original size:27 final size:27
Alignment explanation
Indices: 28738840--28738925 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
28738830 TTTTTTATAT
*
28738840 TTTTTTATGATTTTTATAAAATTTTAAA
1 TTTTTTAT-AATTTTATAAAATTTTAAA
* *
28738868 TTTTCTTAT-ATTTTTTAAAATTTT-TA
1 TTTT-TTATAATTTTATAAAATTTTAAA
* *
28738894 TTTTTTCTAATTTTAATAAATTTTTAATA
1 TTTTTTATAATTTT-ATAAAATTTTAA-A
28738923 TTT
1 TTT
28738926 GAATTTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.07
26 10 0.22
27 21 0.46
28 4 0.09
29 8 0.17
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTTTATAATTTTATAAAATTTTAAA
Found at i:28738883 original size:19 final size:17
Alignment explanation
Indices: 28738861--28738899 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
28738851 TTTTATAAAA
*
28738861 TTTTAAATTTTCTTATATT
1 TTTTAAAATTT-TTAT-TT
28738880 TTTTAAAATTTTTATTT
1 TTTTAAAATTTTTATTT
28738897 TTT
1 TTT
28738900 CTAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTAAAATTTTTATTT
Found at i:28739221 original size:89 final size:90
Alignment explanation
Indices: 28739001--28739323 Score: 334
Period size: 89 Copynumber: 3.5 Consensus size: 90
28738991 AATTTTTAAT
* * *
28739001 AAAAGCATGGGCTTAATTGA-TTTTTTTGAAAAAG-TTCAAGGGTCTTTTTGATGCATTTTGAAA
1 AAAAGCAGGGGCTTAATT-ACTTTTTTTGAAAAAGTTTC-AGGGCCTTTTTGAAGCATTTTGAAA
* *
28739064 GTTCAAATACCCAATTGAGTGCAAAAAA
64 GTTCAAGTACCCAAATGAGTGC-AAAAA
* * * ** *
28739092 AAAAGTAGGGCCTTAGTTGTTTTTTTTTTTTTTGAAAAGGTTTCAGGGCCTTTTTGAAGCATTTT
1 AAAAGCAGGGGCTTA------ATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTTGAAGCATTTT
28739157 GAAAGTTCAAGTACCCAAATGAGTGCAAAAA
60 GAAAGTTCAAGTACCCAAATGAGTGCAAAAA
* * *
28739188 AAAAGCA-GGGCTTAATTACTTTTTTTGAAAAGGTTTGAGGGCGTTTTTGATA-CATTTTGAAAG
1 AAAAGCAGGGGCTTAATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTTGA-AGCATTTTGAAAG
*
28739251 TTCAAGTACCCAAATGAGTG-TAAAA
65 TTCAAGTACCCAAATGAGTGCAAAAA
* * * * *
28739276 ACAAGTAGGGGCTTAATTGCTTTGTTTGAAAAAGTTTTAGGG-CTTTTT
1 AAAAGCAGGGGCTTAATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTT
28739324 ACACCCTTAA
Statistics
Matches: 197, Mismatches: 25, Indels: 23
0.80 0.10 0.09
Matches are distributed among these distances:
88 14 0.07
89 92 0.47
90 1 0.01
91 12 0.06
95 6 0.03
96 11 0.06
97 58 0.29
98 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (90 bp):
AAAAGCAGGGGCTTAATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTTGAAGCATTTTGAAAGT
TCAAGTACCCAAATGAGTGCAAAAA
Found at i:28742512 original size:38 final size:38
Alignment explanation
Indices: 28742461--28742543 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
28742451 AAACGTACTA
* * *
28742461 TTATTTAGGCTTAGTGCCTAGCAGGCTTAGTGCTGGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTCAGTGCCGGTG
*
28742499 TTATTCAGGCTTAGTGCCTAGTAGGCTCAGTGCCGGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTCAGTGCCGGTG
28742537 TTATTCA
1 TTATTCA
28742544 AACTTATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (38 bp):
TTATTCAGGCTTAGTGCCTAGCAGGCTCAGTGCCGGTG
Found at i:28756991 original size:449 final size:448
Alignment explanation
Indices: 28756149--28757045 Score: 1546
Period size: 449 Copynumber: 2.0 Consensus size: 448
28756139 TCGGAGCGGC
28756149 GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
1 GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
28756214 TAAAGCTTTATTGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGAT
66 TAAAGCTTTATTGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGAT
* *
28756279 TTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACGGGTTTTTAAAAGAATTGC
131 TTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACGGGTTTGTAAAAGAAATGC
* *
28756344 ATATGTTTTAGCAAAATACCCACAAGAACACAAACTGTTTTAAAAAGCTTCCGCAACGTATAACA
196 ATATGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTCCGCAACGTATAACA
*
28756409 TTTTGCAAACTAATGACTGAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAGATC
261 TTTTGCAAACTAATGACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAGATC
* * *
28756474 TAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACACGAGCATCGGTTTTCAAACATACT
326 TAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACAAGAGCAGCGGTTTTCAAACACACT
* * *
28756539 ATCATGTGACATCGCCAAATTCGGCCATAACGTCTAGGCCAGTTTTGCGGTGTTACAT
391 ATCATGTGACATCACCAAATTCGGCCATAACGTCCAGGCCAGGTTTGCGGTGTTACAT
*
28756597 GGAGGACTCAGCTGTGGCCACACGACTCTTTTTTACTGTTTCATATTTAATTAGGTTTA-TTTTT
1 GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
*
28756661 TAAAGCTTTATATGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTTGA
66 TAAAGCTTTAT-TGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGA
*
28756726 TTTTATACTGCTTTATGTTTTATATCTGCTGGAGGTAGATAAAACACGAGGTTTGTAAAAGAAAT
130 TTTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACG-GGTTTGTAAAAGAAAT
* *
28756791 GCATGTGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTTCGCAACGTATAA
194 GCATATGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTCCGCAACGTATAA
*
28756856 CATTTTGCAAACTAACT-ACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAATGACGAG
259 CATTTTGCAAACTAA-TGACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAG
* *
28756920 ATTTAAACGAAAAATGTTTTAAGCAAAGTTACGGTTTTTCAACAAGAGCAGCGGTTTTCAAACAC
323 ATCTAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACAAGAGCAGCGGTTTTCAAACAC
* * * *
28756985 ACTATCATGTGACATCATCAAATTCGGCCATAATGTCCAGGCCGGGTTTGGGGTGTTACAT
388 ACTATCATGTGACATCACCAAATTCGGCCATAACGTCCAGGCCAGGTTTGCGGTGTTACAT
28757046 ATGGACTCAG
Statistics
Matches: 423, Mismatches: 23, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
447 16 0.04
448 157 0.37
449 249 0.59
450 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (448 bp):
GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
TAAAGCTTTATTGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGAT
TTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACGGGTTTGTAAAAGAAATGC
ATATGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTCCGCAACGTATAACA
TTTTGCAAACTAATGACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAGATC
TAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACAAGAGCAGCGGTTTTCAAACACACT
ATCATGTGACATCACCAAATTCGGCCATAACGTCCAGGCCAGGTTTGCGGTGTTACAT
Found at i:28758585 original size:107 final size:108
Alignment explanation
Indices: 28758372--28758585 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 108
28758362 TTGTGCAGGT
*
28758372 ACAAATCCTTGTTTGGAATTTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
28758437 CACTAACTATTTCTAGAGATTTTTTACCTCTTTCCATAAGGCC
66 CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
* *
28758480 ACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG-TTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
28758544 CTAC-AACTGTTTTTAGA-ATCTTTTTACCTATATCCATAAGGC
66 C-ACTAACTATTTCTAGAGAT-TTTTTACCTATATCCATAAGGC
28758586 TTGCTAAGAT
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
106 2 0.02
107 55 0.57
108 40 0.41
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (108 bp):
ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
Found at i:28759297 original size:107 final size:108
Alignment explanation
Indices: 28759084--28759297 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 108
28759074 TTGTGCAGGT
*
28759084 ACAAATCCTTGTTTGGAATTTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
28759149 CACTAACTATTTCTAGAGATTTTTTACCTCTTTCCATAAGGCC
66 CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
* *
28759192 ACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG-TTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
28759256 CTAC-AACTGTTTTTAGA-ATCTTTTTACCTATATCCATAAGGC
66 C-ACTAACTATTTCTAGAGAT-TTTTTACCTATATCCATAAGGC
28759298 TTGCTAAGAT
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
106 2 0.02
107 55 0.57
108 40 0.41
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (108 bp):
ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
Found at i:28759299 original size:712 final size:712
Alignment explanation
Indices: 28757936--28759902 Score: 3819
Period size: 712 Copynumber: 2.8 Consensus size: 712
28757926 CTAGGAAATA
28757936 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
* * * *
28758001 AGATACTGGAGCTACAATTAGTAGTTGTAGAAAGAATGTCATTCCGGTAGAAAAATGGGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
28758066 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
*
28758131 AATATTCCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
*
28758196 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACTATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
28758261 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
28758326 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
28758391 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
28758456 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
521 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
28758521 TTTTTTATAAACAGTAGTCCATTCTACAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGGC
586 TTTTTTATAAACAGTAGTCCATTCTACAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGGC
28758586 TTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
651 TTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
28758648 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
28758713 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
28758778 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
28758843 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
28758908 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
28758973 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
28759038 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
28759103 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
28759168 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
521 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
28759233 TTTTTTATAAACAGTAGTCCATTCTACAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGGC
586 TTTTTTATAAACAGTAGTCCATTCTACAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGGC
28759298 TTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
651 TTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
28759360 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
28759425 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
28759490 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
28759555 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
28759620 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
28759685 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
28759750 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
* * *
28759815 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACCAACTGTTTTTAGA-A
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
* *
28759879 TCTTTTTACCTATATCCATAAGGC
521 T-TTTTTACCTCTTTCCATAAGGC
28759903 TTGCTAAGAT
Statistics
Matches: 1243, Mismatches: 11, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
711 2 0.00
712 1241 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (712 bp):
TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
TTTTTTATAAACAGTAGTCCATTCTACAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGGC
TTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
Found at i:28761998 original size:24 final size:24
Alignment explanation
Indices: 28761971--28762019 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28761961 AATAAGATAC
28761971 ATACTTTTTTATACATATCTTGTA
1 ATACTTTTTTATACATATCTTGTA
28761995 ATACTTTTTTATACATATCTTGTA
1 ATACTTTTTTATACATATCTTGTA
28762019 A
1 A
28762020 CACCCCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (24 bp):
ATACTTTTTTATACATATCTTGTA
Found at i:28766358 original size:19 final size:19
Alignment explanation
Indices: 28766320--28766358 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28766310 ATTAAGTATT
**
28766320 AAATTAAATAAAATTTATA
1 AAATTAAATAAAATAAATA
*
28766339 AAATTAATTAAAATAAATA
1 AAATTAAATAAAATAAATA
28766358 A
1 A
28766359 TAAAAATGTG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTAAATAAAATAAATA
Found at i:28766937 original size:9 final size:9
Alignment explanation
Indices: 28766920--28766956 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28766910 TGAGTTTTCG
28766920 AATTCGAAT
1 AATTCGAAT
*
28766929 AACTCGAAT
1 AATTCGAAT
28766938 AATTCGAAT
1 AATTCGAAT
28766947 AATTCGAAT
1 AATTCGAAT
28766956 A
1 A
28766957 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28786985 original size:42 final size:42
Alignment explanation
Indices: 28786905--28786986 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
28786895 CGTTTTCTCT
* **
28786905 ATGCCATAGTCCAAATATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAAATATGGTCTTACACATATGCACATATTG
**
28786947 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAAATATGGTCTTACACA-TATGCACATAT
28786987 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAAATATGGTCTTACACATATGCACATATTG
Found at i:28787007 original size:47 final size:48
Alignment explanation
Indices: 28786946--28787038 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 48
28786936 TTTACATATT
* *
28786946 GATGCCATAGCCCAGCTATGGTCTTACACAG-TAGCACATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
* * *
28786993 GATGCCATATCCCAGATATGGTCTTATACAGAAATCACATATCACA
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
28787039 TGTTGCCATG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 28 0.70
48 12 0.30
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (48 bp):
GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
Found at i:28788953 original size:66 final size:66
Alignment explanation
Indices: 28788842--28788972 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
28788832 TATTCCCCTT
28788842 TTTCCGAATCACATAGCAAAATATTACAAATATGTATATATTTGAATACTATAATTATGCATCAA
1 TTTCCGAATCACATAGCAAAATATTACAAATATGTATATATTTGAATACTATAATTATGCATCAA
28788907 A
66 A
* *
28788908 TTTCTGAATCACATAGCAAAATATTACAAATATGTATATCTTTGAATACTATAATTATGCATCAA
1 TTTCCGAATCACATAGCAAAATATTACAAATATGTATATATTTGAATACTATAATTATGCATCAA
28788973 CTTACCAACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.36
Consensus pattern (66 bp):
TTTCCGAATCACATAGCAAAATATTACAAATATGTATATATTTGAATACTATAATTATGCATCAA
A
Found at i:28790328 original size:44 final size:44
Alignment explanation
Indices: 28790146--28790431 Score: 223
Period size: 44 Copynumber: 6.6 Consensus size: 44
28790136 ATTTTTAGAA
* * *
28790146 ACAAATGCCGCTAAAGAACA-AGACC-TTTAGCGACGCATTTCCC
1 ACAAACGCCGCTAAAGAACATA-ACCTTTTAGCGGCGCTTTTCCC
* *** * * **
28790189 ACAAACGCCGCAAAAG-GTTTAATC-TATAGCGGCG-TTTGTGAC
1 ACAAACGCCGCTAAAGAACATAACCTTTTAGCGGCGCTTT-TCCC
* * * *
28790231 AAAAAGCGCCGCTAAAGACCATGACC-TTTAGCGACGCTTTTCCC
1 ACAAA-CGCCGCTAAAGAACATAACCTTTTAGCGGCGCTTTTCCC
* *
28790275 ACAAACGCCGCTAAAGACCATAACCTTTTGGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGAACATAACCTTTTAGCGGCGCTTTTCCC
* **
28790319 ACAAACGCCGCTAAAGAACATGACC-TTTAGCGGCGCTTTTTGTC
1 ACAAACGCCGCTAAAGAACATAACCTTTTAGCGGCGC-TTTTCCC
* * ** * *
28790363 ACAAACACCGCTATAGATTA-AACCTTTT-GCGGCGCTTCTCGC
1 ACAAACGCCGCTAAAGAACATAACCTTTTAGCGGCGCTTTTCCC
*
28790405 AAAAACGCCGCTAAA-AACATAACCTTT
1 ACAAACGCCGCTAAAGAACATAACCTTT
28790432 AAAAAAAATT
Statistics
Matches: 190, Mismatches: 44, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
41 4 0.02
42 39 0.21
43 64 0.34
44 80 0.42
45 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (44 bp):
ACAAACGCCGCTAAAGAACATAACCTTTTAGCGGCGCTTTTCCC
Found at i:28790985 original size:84 final size:84
Alignment explanation
Indices: 28790844--28791011 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
28790834 ACTCTTTTCC
28790844 GCCTCAAGATTGGACGCAAAGTCTATGTCATCTAGGACTTTGGTGAAGAATCAGAAATTCCAGGG
1 GCCTCAAGATTGGACGCAAAGTCTATGTCATCTAGGACTTTGGTGAAGAATCAGAAATTCCAGGG
28790909 TCTGCACAAGGCTTTTGCA
66 TCTGCACAAGGCTTTTGCA
28790928 GCCTCAAGATTGGACGCAAAGTCTATGTCATCTAGGACTTTGGTGAAGAATCAGAAATTCCAGGG
1 GCCTCAAGATTGGACGCAAAGTCTATGTCATCTAGGACTTTGGTGAAGAATCAGAAATTCCAGGG
28790993 TCTGCACAAGGCTTTTGCA
66 TCTGCACAAGGCTTTTGCA
28791012 CTTCTATTGC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (84 bp):
GCCTCAAGATTGGACGCAAAGTCTATGTCATCTAGGACTTTGGTGAAGAATCAGAAATTCCAGGG
TCTGCACAAGGCTTTTGCA
Found at i:28791717 original size:5 final size:5
Alignment explanation
Indices: 28791707--28791733 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28791697 CTTTCTTGCC
28791707 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
28791734 AACAAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:28792319 original size:14 final size:14
Alignment explanation
Indices: 28792300--28792326 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28792290 ATCAAGAAAA
28792300 AAATTATGTATAAT
1 AAATTATGTATAAT
28792314 AAATTATGTATAA
1 AAATTATGTATAA
28792327 GACTTACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATTATGTATAAT
Found at i:28794953 original size:27 final size:27
Alignment explanation
Indices: 28794898--28794953 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
28794888 CTAGCTTTAC
***
28794898 AAACCTTAAACTCCATATATATTTTTT
1 AAACCTTAAACTCCATATATATGCATT
28794925 AAACCTTAAACTCCATAT-TAATGCATT
1 AAACCTTAAACTCCATATAT-ATGCATT
28794952 AA
1 AA
28794954 TTGATTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.38
Consensus pattern (27 bp):
AAACCTTAAACTCCATATATATGCATT
Found at i:28795223 original size:7 final size:7
Alignment explanation
Indices: 28795213--28795247 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
28795203 ATAAAACCTA
28795213 AACCCCT
1 AACCCCT
28795220 AACCCCT
1 AACCCCT
*
28795227 AACCCTT
1 AACCCCT
*
28795234 AACTCCT
1 AACCCCT
28795241 AACCCCT
1 AACCCCT
28795248 CTTTTACAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.51, G:0.00, T:0.20
Consensus pattern (7 bp):
AACCCCT
Found at i:28795378 original size:14 final size:14
Alignment explanation
Indices: 28795361--28795398 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28795351 CACTAACTCT
*
28795361 TAACCTCTAACCT-C
1 TAACCCCTAA-CTAC
28795375 TAACCCCTAACTAC
1 TAACCCCTAACTAC
28795389 TAACCCCTAA
1 TAACCCCTAA
28795399 ACTTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.24
Consensus pattern (14 bp):
TAACCCCTAACTAC
Found at i:28795493 original size:14 final size:14
Alignment explanation
Indices: 28795457--28795513 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
28795447 AAACCCTAAC
*
28795457 CTAACACTAAATCT
1 CTAACCCTAAATCT
*
28795471 ATAAACCCTAAATCT
1 CT-AACCCTAAATCT
*
28795486 CTAACCCTTAA-CT
1 CTAACCCTAAATCT
28795499 CCTAACCCCTAAATC
1 -CTAA-CCCTAAATC
28795514 ACAACCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.06
14 13 0.38
15 18 0.53
16 1 0.03
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAACCCTAAATCT
Found at i:28795549 original size:14 final size:15
Alignment explanation
Indices: 28795530--28795562 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28795520 CTTAAACCAG
28795530 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
28795544 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28795559 AATC
1 AATC
28795563 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28796381 original size:16 final size:16
Alignment explanation
Indices: 28796356--28796387 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28796346 TCCAGTCCAA
28796356 AAAATCACATTTTTGC
1 AAAATCACATTTTTGC
*
28796372 AAAATTACATTTTTGC
1 AAAATCACATTTTTGC
28796388 CCCTAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAATCACATTTTTGC
Found at i:28799253 original size:15 final size:15
Alignment explanation
Indices: 28799235--28799267 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28799225 TGCTTCCATA
28799235 ATTGATTACATCATC
1 ATTGATTACATCATC
*
28799250 ATTGCTTACATCATC
1 ATTGATTACATCATC
28799265 ATT
1 ATT
28799268 AGTTTGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTGATTACATCATC
Found at i:28801451 original size:17 final size:17
Alignment explanation
Indices: 28801419--28801450 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28801409 CAATTGGAGG
28801419 TTTTTGTTTCTCTTTTC
1 TTTTTGTTTCTCTTTTC
28801436 TTTTTGTTT-TCTTTT
1 TTTTTGTTTCTCTTTT
28801451 TGGGCCTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (17 bp):
TTTTTGTTTCTCTTTTC
Found at i:28805704 original size:36 final size:35
Alignment explanation
Indices: 28805664--28805734 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
28805654 AGGTCAAGAA
28805664 AGAGTGTTCTTATTGATATGGGGGAATCAGACTTGT
1 AGAGTGTTCTTATTGATAT-GGGGAATCAGACTTGT
*
28805700 AGAGTGTTCTTATTGATATGGGGCATCAGACTTGT
1 AGAGTGTTCTTATTGATATGGGGAATCAGACTTGT
28805735 TCATATTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 15 0.44
36 19 0.56
ACGTcount: A:0.24, C:0.10, G:0.30, T:0.37
Consensus pattern (35 bp):
AGAGTGTTCTTATTGATATGGGGAATCAGACTTGT
Found at i:28806158 original size:37 final size:37
Alignment explanation
Indices: 28806116--28806188 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
28806106 TAGATTGGAG
*
28806116 GAGTGTTAGGAAGACCTTATTGGAAATGCTAGAGGGA
1 GAGTGTTAGGAAGACCTCATTGGAAATGCTAGAGGGA
* *
28806153 GAGTGTTAGGAAGGCCTCATTTGAAATGCTAGAGGG
1 GAGTGTTAGGAAGACCTCATTGGAAATGCTAGAGGG
28806189 GAGACAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.25
Consensus pattern (37 bp):
GAGTGTTAGGAAGACCTCATTGGAAATGCTAGAGGGA
Found at i:28816106 original size:32 final size:32
Alignment explanation
Indices: 28816063--28816125 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
28816053 AAGTTGGAAT
28816063 TACTCACGCTTTATTTTTATATCACAATAATA
1 TACTCACGCTTTATTTTTATATCACAATAATA
*
28816095 TACTCAGGCTTTATTTTTATATCACAATAAT
1 TACTCACGCTTTATTTTTATATCACAATAAT
28816126 GCCATGGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.44
Consensus pattern (32 bp):
TACTCACGCTTTATTTTTATATCACAATAATA
Found at i:28818546 original size:23 final size:23
Alignment explanation
Indices: 28818520--28818567 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
28818510 AGGACTTAAT
*
28818520 TGCATAAAATGAAATGGTTTTAC
1 TGCATAAAAGGAAATGGTTTTAC
28818543 TGCATAAAAGGAAATGGTTTTAC
1 TGCATAAAAGGAAATGGTTTTAC
28818566 TG
1 TG
28818568 TCTTAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (23 bp):
TGCATAAAAGGAAATGGTTTTAC
Found at i:28819822 original size:20 final size:20
Alignment explanation
Indices: 28819774--28819825 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
28819764 AAGCTTATGC
*
28819774 TAAGTAAAAGGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
*
28819794 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGGAATGGAAAG
28819814 TAAGTAAATGGA
1 TAAGTAAATGGA
28819826 GTGATTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:28824031 original size:33 final size:33
Alignment explanation
Indices: 28823969--28824033 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
28823959 AAAAAATAAC
* * *
28823969 TTTCTTTTTCTCTTTTCTTCTTCTTCTTCTATA
1 TTTCTTTTTCCCTTTTCATCTTCTACTTCTATA
28824002 TTTCTTTTTCCCTTTTCAATC-TCTACTTCTAT
1 TTTCTTTTTCCCTTTTC-ATCTTCTACTTCTAT
28824034 TCCCTAGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTCTTTTTCCCTTTTCATCTTCTACTTCTATA
Found at i:28825136 original size:20 final size:20
Alignment explanation
Indices: 28825113--28825173 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
28825103 CACATTGTTG
* *
28825113 GCAGCTTGTTTGCATTACTA
1 GCAGTTTGTCTGCATTACTA
*
28825133 GCAGTTTATCTGCAATT-CTA
1 GCAGTTTGTCTGC-ATTACTA
*
28825153 GCAGTTTGTCTGCACTACTA
1 GCAGTTTGTCTGCATTACTA
28825173 G
1 G
28825174 TGGCTTGTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.85
21 3 0.09
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
GCAGTTTGTCTGCATTACTA
Found at i:28836611 original size:43 final size:44
Alignment explanation
Indices: 28836562--28836652 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 44
28836552 AAAATCACCA
*
28836562 TAAATTGTGGAAATCGAATTAGAGGATG-AAAAAAATATGGAAT
1 TAAATTGTGGAAATCAAATTAGAGGATGAAAAAAAATATGGAAT
28836605 TAAATTGTGGAAATCAAATTAGAGGATGAAAAAAAATATGGAAT
1 TAAATTGTGGAAATCAAATTAGAGGATGAAAAAAAATATGGAAT
28836649 TAAA
1 TAAA
28836653 GCTTATTTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 27 0.59
44 19 0.41
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.25
Consensus pattern (44 bp):
TAAATTGTGGAAATCAAATTAGAGGATGAAAAAAAATATGGAAT
Found at i:28840576 original size:22 final size:22
Alignment explanation
Indices: 28840550--28840596 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
28840540 ACTCTCCCCC
28840550 TCTTCTCTATTTT-TTTCTCTTT
1 TCTTCTCTATTTTATTT-TCTTT
* *
28840572 TCTTCTTTCTTTTATTTTCTTT
1 TCTTCTCTATTTTATTTTCTTT
28840594 TCT
1 TCT
28840597 CCTTCTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTTCTCTATTTTATTTTCTTT
Found at i:28845267 original size:26 final size:26
Alignment explanation
Indices: 28845145--28845292 Score: 127
Period size: 27 Copynumber: 5.6 Consensus size: 26
28845135 AGACCTCAAA
*
28845145 ATAGGGTAAAATGA-CGAAATACATCT
1 ATAGGGTAAAATGACCGAAATAC-CCT
* * * *
28845171 ATAAGGTAAAATGATCGATATACCCCC
1 ATAGGGTAAAATGACCGAAATA-CCCT
* *
28845198 ATAGGATAAATTGACCGAAATACCCT
1 ATAGGGTAAAATGACCGAAATACCCT
* * *
28845224 CATAAGGTAAAATAACCAAAATACCCT
1 -ATAGGGTAAAATGACCGAAATACCCT
* * *
28845251 ATAGGGTAAAATGACCAAAATATCTT
1 ATAGGGTAAAATGACCGAAATACCCT
*
28845277 CATGGGGTAAAATGAC
1 -ATAGGGTAAAATGAC
28845293 TATTATACCC
Statistics
Matches: 98, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
26 38 0.39
27 59 0.60
28 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (26 bp):
ATAGGGTAAAATGACCGAAATACCCT
Found at i:28849658 original size:50 final size:50
Alignment explanation
Indices: 28849542--28849731 Score: 172
Period size: 50 Copynumber: 3.8 Consensus size: 50
28849532 GATAATAACA
* * * * * *
28849542 TGCCAAAGCCATGTCCCAGACATGGTTTTACATGTGATGTTTTC-TGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-CTCTCATAT-CGG
* * *
28849591 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGT-TCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCTCATATCGG
* * * * *
28849641 TGCCCATGCCATGTCCCAGGCATGGTCTTATAGGGGATCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATATCGG
* * *
28849691 TGCCAACGTCATGTCCCAGACATGATCTTACATGGGATCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTC
28849732 ATTCTCTTAA
Statistics
Matches: 113, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
48 4 0.04
49 34 0.30
50 75 0.66
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATATCGG
Found at i:28857099 original size:27 final size:27
Alignment explanation
Indices: 28857064--28857348 Score: 297
Period size: 27 Copynumber: 10.6 Consensus size: 27
28857054 AATAAAATGA
*
28857064 CTTTGTGGCGAATCATGAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
*
28857091 CTTTATGGCGAATCATGAAA-AAAATC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* **
28857117 CTTTATGGCAAATCATGAAAGAAAAAT
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * * *
28857144 ATTTCTGGAGAATCATGAAA-AAAAAC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * *
28857170 TTTTATGGTGAAT-TTGGAAAGAAAAGC
1 CTTTATGGCGAATCAT-GAAAGAAAAGC
* * *
28857197 CTTTGTGGCAAATCCTGAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * * *
28857224 ATTTGTGGCAAATCATAAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * *
28857251 CTTTGTGGCGAATCATGAAATAAAAGT
1 CTTTATGGCGAATCATGAAAGAAAAGC
*
28857278 CTTTATGGCGAATCATGAAAGATAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * *
28857305 CTTTGTGGTGAATCATGAAAGAAAGGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
*
28857332 CCTTATGGCGAATCATG
1 CTTTATGGCGAATCATG
28857349 GAGTAAGTTA
Statistics
Matches: 215, Mismatches: 39, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
25 1 0.00
26 43 0.20
27 170 0.79
28 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (27 bp):
CTTTATGGCGAATCATGAAAGAAAAGC
Found at i:28865648 original size:20 final size:19
Alignment explanation
Indices: 28865619--28865656 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28865609 AAGTGGTGAT
28865619 AATTTATTTTCTAAGAATA
1 AATTTATTTTCTAAGAATA
*
28865638 AATTATATTTTCTAGGAAT
1 AATT-TATTTTCTAAGAAT
28865657 TACAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:28880205 original size:23 final size:20
Alignment explanation
Indices: 28880155--28880208 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
28880145 CTCATCGGGA
28880155 AATTGAATA-AGTGTAATTG
1 AATTGAATATAGTGTAATTG
28880174 AATAATGAATATAGGTGTAGAATTG
1 AAT--TGAATATA-GTGT--AATTG
28880199 AATTGAATAT
1 AATTGAATAT
28880209 CGACTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
21 6 0.21
22 1 0.03
23 11 0.38
25 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.35
Consensus pattern (20 bp):
AATTGAATATAGTGTAATTG
Found at i:28891769 original size:47 final size:47
Alignment explanation
Indices: 28891693--28892049 Score: 516
Period size: 47 Copynumber: 7.6 Consensus size: 47
28891683 TTAAACCCAT
* *
28891693 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
* * *
28891742 ATGTGAAAGTGTATATTTGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
* *
28891789 ATGTGAAAGTGTATATATATGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
*
28891836 ATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
*
28891883 ATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
*
28891930 ATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
* * ** * * *
28891977 ATGTGAAAGTGTATATGTGTGACAGGGCCGAGTGGCCAATGTGATGT
1 ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
* **
28892024 ATGTGAAAGTGCATAAATGTGATAAG
1 ATGTGAAAGTGTATATGTGTGATAAG
28892050 TCCCGAAGGG
Statistics
Matches: 286, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 275 0.96
49 11 0.04
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATGTGTGATAAGGCTTAATGGCCGATGTGATGA
Found at i:28904345 original size:30 final size:30
Alignment explanation
Indices: 28904288--28904346 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28904278 GTTTTTTAAA
* *
28904288 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
28904318 AATATTTACAAAAAGAG-CAACCAAATTTT
1 AATATTTACAAAAAGAGAC-ACCAAATTTT
28904347 CAAAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:28910398 original size:23 final size:23
Alignment explanation
Indices: 28910372--28910447 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
28910362 ATAAGTGCCA
28910372 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28910395 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28910418 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28910441 CACTGAT
1 CACTGAT
28910448 CAATAACACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28910699 original size:18 final size:17
Alignment explanation
Indices: 28910673--28910711 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28910663 ATTTTCCTTC
28910673 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
28910690 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
28910708 CACA
1 CACA
28910712 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:28916060 original size:50 final size:51
Alignment explanation
Indices: 28915933--28916124 Score: 208
Period size: 50 Copynumber: 3.7 Consensus size: 51
28915923 GGAATGAGAC
** *
28915933 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTATTGAGGTTATGAAAGGT
1 CCCATGTAAGACCATGTTTGGGACATGGCATTGGC---ACCGAGG--ATGAGAGGT
*
28915989 CCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGA-GATGAGAGGT
1 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGGATGAGAGGT
* * * * **
28916039 CCCCTGTAAGACCATGTTTGGGACATGGAATGGGCACCGATG-TGAGAACT
1 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGGATGAGAGGT
* * *
28916089 CCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCA
28916125 GTACAGGAAA
Statistics
Matches: 119, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
50 80 0.67
51 1 0.01
52 1 0.01
53 3 0.03
56 34 0.29
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (51 bp):
CCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGGATGAGAGGT
Found at i:28925751 original size:19 final size:19
Alignment explanation
Indices: 28925707--28925770 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
28925697 TTTTTATTTC
* *
28925707 TTTAATTTATATTATAATAA
1 TTTAATTTAT-TAATAATCA
*
28925727 TATAATTTATTAATAATCA
1 TTTAATTTATTAATAATCA
* * *
28925746 TTTAATTAATAAAT-ATCT
1 TTTAATTTATTAATAATCA
28925764 TTTAATT
1 TTTAATT
28925771 ATAACACAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
18 10 0.27
19 18 0.49
20 9 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATTTATTAATAATCA
Found at i:28925886 original size:12 final size:13
Alignment explanation
Indices: 28925852--28925889 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
28925842 CTTATTTATT
28925852 TTATATTTAATAAA
1 TTATATTT-ATAAA
28925866 TTAATATTTATAAA
1 TT-ATATTTATAAA
28925880 -TATATTTATA
1 TTATATTTATA
28925890 CTTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 1 0.04
14 7 0.30
15 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATTTATAAA
Done.