Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 9 of 120
Found at i:2446198 original size:15 final size:15
Alignment explanation
Indices: 2446144--2446198 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
2446134 AAAATGATTA
* *
2446144 AAAAATCTTAAAATT
1 AAAAATATTAAAAAT
*
2446159 ATAAATA-TAAAAAT
1 AAAAATATTAAAAAT
2446173 ATAAAATTATTAAAAAT
1 A-AAAA-TATTAAAAAT
2446190 AAAAATATT
1 AAAAATATT
2446199 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.21
15 12 0.36
16 6 0.18
17 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATATTAAAAAT
Found at i:2446479 original size:10 final size:9
Alignment explanation
Indices: 2446466--2446644 Score: 76
Period size: 10 Copynumber: 18.8 Consensus size: 9
2446456 CATAAAAAAA
2446466 ATAAAAACTT
1 ATAAAAA-TT
*
2446476 ATAAATATT
1 ATAAAAATT
2446485 ATAAAAATCT
1 ATAAAAAT-T
*
2446495 A-ATAAATT
1 ATAAAAATT
*
2446503 TTAATAAATT
1 ATAA-AAATT
***
2446513 AT-ATTTTT
1 ATAAAAATT
*
2446521 TTATAAAATT
1 ATA-AAAATT
2446531 AATAAAAATAT
1 -ATAAAAAT-T
2446542 ATAAAATATT
1 ATAAAA-ATT
*
2446552 ATAAAAACAT
1 ATAAAAA-TT
*
2446562 ATACAAATT
1 ATAAAAATT
*
2446571 CTTAAAAACTT
1 -ATAAAAA-TT
*
2446582 ATAAAAATC
1 ATAAAAATT
*
2446591 ATAAAAAAT
1 ATAAAAATT
2446600 ATTAAAAA-T
1 A-TAAAAATT
*
2446609 ATTAAAATT
1 ATAAAAATT
*
2446618 GATACAAACTT
1 -ATA-AAAATT
*
2446629 ATAAAATTT
1 ATAAAAATT
*
2446638 ACAAAAA
1 ATAAAAA
2446645 AAATCATAAA
Statistics
Matches: 125, Mismatches: 29, Indels: 31
0.68 0.16 0.17
Matches are distributed among these distances:
8 9 0.07
9 40 0.32
10 64 0.51
11 12 0.10
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2447014 original size:9 final size:9
Alignment explanation
Indices: 2447000--2447206 Score: 52
Period size: 10 Copynumber: 21.4 Consensus size: 9
2446990 ACAATTCATG
*
2447000 TTTTTATGA
1 TTTTTATAA
2447009 TTTTTATAA
1 TTTTTATAA
2447018 TTTTATATCAA
1 TTTT-TAT-AA
2447029 --TTT-TAA
1 TTTTTATAA
*
2447035 TTTTTTTAA
1 TTTTTATAA
2447044 TTTTTA-AA
1 TTTTTATAA
*
2447052 GGTTTTTTTTAA
1 ---TTTTTATAA
*
2447064 GTTTTTAAGAA
1 -TTTTT-ATAA
*
2447075 CTTTTATACATA
1 -TTTT-TATA-A
2447087 TTTTTATAA
1 TTTTTATAA
*
2447096 -ATTTATAAA
1 TTTTTAT-AA
2447105 TATGCTTTATTAA
1 T-T--TTTA-TAA
*
2447118 TTTTGTAAAA
1 TTTT-TATAA
*
2447128 TGTTTATAA
1 TTTTTATAA
*
2447137 TTTATTAAAA
1 TTT-TTATAA
2447147 TTTATTAT--
1 TTT-TTATAA
*
2447155 GTTTTATAA
1 TTTTTATAA
*
2447164 TATTTTA-AG
1 T-TTTTATAA
2447173 TTTTTATTAA
1 TTTTTA-TAA
2447183 TTTTTATAA
1 TTTTTATAA
*
2447192 GTTTATATCAA
1 -TTTTTAT-AA
2447203 TTTT
1 TTTT
2447207 AATATTCTTT
Statistics
Matches: 148, Mismatches: 23, Indels: 53
0.66 0.10 0.24
Matches are distributed among these distances:
6 2 0.01
7 5 0.03
8 18 0.12
9 36 0.24
10 51 0.34
11 23 0.16
12 5 0.03
13 7 0.05
14 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2447119 original size:21 final size:19
Alignment explanation
Indices: 2447089--2447147 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
2447079 TATACATATT
*
2447089 TTTATAAATTTATAAATATG
1 TTTATTAATTTATAAA-ATG
*
2447109 CTTTATTAATTTTGTAAAATG
1 -TTTATTAA-TTTATAAAATG
2447130 TTTA-TAATTTATTAAAAT
1 TTTATTAATTTA-TAAAAT
2447148 TTATTATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.09
19 9 0.27
20 4 0.12
21 10 0.30
22 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTATTAATTTATAAAATG
Found at i:2447179 original size:18 final size:18
Alignment explanation
Indices: 2447156--2447208 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
2447146 ATTTATTATG
2447156 TTTTATAATATTTTAAGT
1 TTTTATAATATTTTAAGT
*
2447174 TTTTATTAATTTTTATAAGT
1 TTTTA-TAATATTT-TAAGT
* *
2447194 TTATATCA-ATTTTAA
1 TTTTATAATATTTTAA
2447209 TATTCTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 8 0.28
19 9 0.31
20 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTATAATATTTTAAGT
Found at i:2447194 original size:20 final size:19
Alignment explanation
Indices: 2447156--2447206 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
2447146 ATTTATTATG
*
2447156 TTTTA-TAATATTTTAAGT
1 TTTTATTAATTTTTTAAGT
2447174 TTTTATTAATTTTTATAAGT
1 TTTTATTAATTTTT-TAAGT
* *
2447194 TTATATCAATTTT
1 TTTTATTAATTTT
2447207 AATATTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 5 0.18
19 7 0.25
20 16 0.57
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTATTAATTTTTTAAGT
Found at i:2448206 original size:18 final size:18
Alignment explanation
Indices: 2448183--2448219 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2448173 GACATACTAG
2448183 TGTAATATAAAGTGACAT
1 TGTAATATAAAGTGACAT
2448201 TGTAATATAAAGTGACAT
1 TGTAATATAAAGTGACAT
2448219 T
1 T
2448220 TATGAAATTT
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:0.05, G:0.16, T:0.35
Consensus pattern (18 bp):
TGTAATATAAAGTGACAT
Found at i:2461482 original size:18 final size:18
Alignment explanation
Indices: 2461459--2461495 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2461449 GCATCTGATA
* *
2461459 TTATTCCTTGTAATTATT
1 TTATTCCTCGTAAGTATT
2461477 TTATTCCTCGTAAGTATT
1 TTATTCCTCGTAAGTATT
2461495 T
1 T
2461496 AGCAATTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.57
Consensus pattern (18 bp):
TTATTCCTCGTAAGTATT
Found at i:2462154 original size:49 final size:49
Alignment explanation
Indices: 2461929--2462266 Score: 195
Period size: 49 Copynumber: 6.9 Consensus size: 49
2461919 CATTTCCATG
* * * * *
2461929 AAGCAGGAGGGGAAAGATTTAAGCCGTAATGGCGAATCCAGTACCACGA
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCTCAA
* * * * * * *
2461978 AGGTAATTG-AGGGAAAGGTTTAAGCCGCAACGGTGAA-CCTTGTACCTCAG
1 AAG-CA-TGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC-AGTACCTCAA
*** * * *
2462028 AAG-ATGAAGGGAAAGATTTAAATTGCAACGGCAAATCCAGTACCACAGA
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCTCA-A
* * * ** * * *
2462077 TA-CA--AAGAGAAAGATTTAAGTCACAACGGCGAACCCTGTACCTTAA
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCTCAA
* *
2462123 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAGTACCACGAA
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCTC-AA
** ** ** * * * * **
2462173 AAATACAAAGAAAAAGGTTTAAGTCGTAACGGC-AAACCTTGTACCTCCG
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC-AGTACCTCAA
* *
2462222 AAGCATAAAGGGAAAGATTTAAGCTGTAACGGCGAATCCAGTACC
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACC
2462267 ATGAAGATAC
Statistics
Matches: 210, Mismatches: 66, Indels: 26
0.70 0.22 0.09
Matches are distributed among these distances:
46 2 0.01
47 36 0.17
48 30 0.14
49 73 0.35
50 68 0.32
51 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (49 bp):
AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCTCAA
Found at i:2462340 original size:98 final size:98
Alignment explanation
Indices: 2461928--2462366 Score: 474
Period size: 98 Copynumber: 4.5 Consensus size: 98
2461918 TCATTTCCAT
* * * * * *
2461928 GAAGCAGGAGGGGAAAGATTTAAGCCGTAATGGCGAATCCAGTACCACGAAGGTA-ATTGAGGGA
1 GAAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATACA--AAGAGA
*
2461992 AAGGTTTAAGCCGCAACGGTGAACCTTGTACCTCA
64 AAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCA
*** * *
2462027 GAAG-ATGAAGGGAAAGATTTAAATTGCAACGGCAAATCCAGTACCAC--AGATACAAAGAGAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATACAAAGAGAAA
* * * * *
2462089 GATTTAAGTCACAACGGCGAACCCTGTACCTTA
66 GGTTTAAGTCGCAACGGTGAACCTTGTACCTCA
* * * *
2462122 AAAGCATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAGTACCACGAAAAATACAAAGAAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACG-AAGATACAAAGAGAA
* ** *
2462187 AGGTTTAAGTCGTAACGGCAAACCTTGTACCTCC
65 AGGTTTAAGTCGCAACGGTGAACCTTGTACCTCA
* * * *
2462221 GAAGCATAAAGGGAAAGATTTAAGCTGTAACGGCGAATCCAGTACCATGAAGATACAAAGGGAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATACAAAGAGAAA
* *
2462286 GGTTTAAGTCGCAATC-GTGAACGTTATACCTCA
66 GGTTTAAGTCGCAA-CGGTGAACCTTGTACCTCA
* * ** * *
2462319 GAAGCATGAAGGAAAATATTTAAGCCACAACGACGAATCTAGTACCAC
1 GAAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCAC
2462367 AATGACATTT
Statistics
Matches: 278, Mismatches: 56, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
95 36 0.13
96 41 0.15
97 1 0.00
98 112 0.40
99 88 0.32
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (98 bp):
GAAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATACAAAGAGAAA
GGTTTAAGTCGCAACGGTGAACCTTGTACCTCA
Found at i:2463207 original size:16 final size:16
Alignment explanation
Indices: 2463176--2463215 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2463166 CCCGAAACCA
*
2463176 CTCTGCTCGACACTCC
1 CTCTGCCCGACACTCC
* *
2463192 CTTTGCCCGACGCTCC
1 CTCTGCCCGACACTCC
2463208 CTCTGCCC
1 CTCTGCCC
2463216 AAAGCCAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.07, C:0.53, G:0.15, T:0.25
Consensus pattern (16 bp):
CTCTGCCCGACACTCC
Found at i:2463687 original size:20 final size:19
Alignment explanation
Indices: 2463659--2463696 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2463649 CAGATCTATA
2463659 GTTTAAAAAATAAAAAAGGG
1 GTTT-AAAAATAAAAAAGGG
*
2463679 GTTTCAAAATAAAAAAGG
1 GTTTAAAAATAAAAAAGG
2463697 TGTAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (19 bp):
GTTTAAAAATAAAAAAGGG
Found at i:2469123 original size:12 final size:12
Alignment explanation
Indices: 2469106--2469131 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2469096 ATCAAACCCT
2469106 AAATTTCATGTA
1 AAATTTCATGTA
2469118 AAATTTCATGTA
1 AAATTTCATGTA
2469130 AA
1 AA
2469132 TCAAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATTTCATGTA
Found at i:2474456 original size:2 final size:2
Alignment explanation
Indices: 2474449--2474481 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2474439 TTATGTTTAG
2474449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2474482 GTCTTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2479120 original size:31 final size:31
Alignment explanation
Indices: 2479081--2479171 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
2479071 CATTTCTTTA
*
2479081 AATATATACAATTAAATCAAAATCAAAATTT
1 AATATATACAATTAAATCAAAATAAAAATTT
* * *
2479112 TATATATACATTTAAATTAAAATAAAAATTT
1 AATATATACAATTAAATCAAAATAAAAATTT
* * *
2479143 AATATATATAATTGAATCAAAATTAAAAT
1 AATATATACAATTAAATCAAAATAAAAAT
2479172 ATATTTATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (31 bp):
AATATATACAATTAAATCAAAATAAAAATTT
Found at i:2479204 original size:62 final size:63
Alignment explanation
Indices: 2479081--2479215 Score: 141
Period size: 62 Copynumber: 2.2 Consensus size: 63
2479071 CATTTCTTTA
* * *
2479081 AATATATACAATTAAATCAAAATCAAAATTTTATATATACATTTAAATTAAAATAAAAA-TTT
1 AATATATATAATTAAATCAAAATCAAAATTATATATATAAATTTAAATTAAAATAAAAATTTT
* * * * * *
2479143 AATATATATAATTGAATCAAAATTAAAA-TATATTTATCAAATTATATATT-AAATTATAATTTT
1 AATATATATAATTAAATCAAAATCAAAATTATATATAT-AAATT-TAAATTAAAATAAAAATTTT
*
2479206 AATATTTATA
1 AATATATATA
2479216 CATATGGTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
61 7 0.12
62 36 0.60
63 17 0.28
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (63 bp):
AATATATATAATTAAATCAAAATCAAAATTATATATATAAATTTAAATTAAAATAAAAATTTT
Found at i:2482386 original size:6 final size:6
Alignment explanation
Indices: 2482366--2482410 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
2482356 CACATTCCTC
*
2482366 TTTTC- TTTTCT TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
2482411 TGGTAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTCA
Found at i:2492847 original size:38 final size:38
Alignment explanation
Indices: 2492805--2492879 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
2492795 AAAACACTTA
2492805 ACAAAAATTATGATTTATTCCACGTTATTAAAAAGCAG
1 ACAAAAATTATGATTTATTCCACGTTATTAAAAAGCAG
2492843 ACAAAAATTATGATTTATTCCACGTTATTAAAAAGCA
1 ACAAAAATTATGATTTATTCCACGTTATTAAAAAGCA
2492880 ATCGACCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (38 bp):
ACAAAAATTATGATTTATTCCACGTTATTAAAAAGCAG
Found at i:2495922 original size:23 final size:25
Alignment explanation
Indices: 2495875--2495924 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
2495865 TTCCAATTTG
*
2495875 GTATGTACCCTCAGAACCTTTTATA
1 GTATGTACCCTCAGAACCTTGTATA
*
2495900 GTATGTACGCT-A-AACCTTGTATA
1 GTATGTACCCTCAGAACCTTGTATA
2495923 GT
1 GT
2495925 CTATAGACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 1 0.04
25 10 0.43
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (25 bp):
GTATGTACCCTCAGAACCTTGTATA
Found at i:2498316 original size:3 final size:3
Alignment explanation
Indices: 2498310--2498339 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2498300 CGCATTAAGG
2498310 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2498340 AACTTGCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:2506633 original size:17 final size:17
Alignment explanation
Indices: 2506593--2506662 Score: 95
Period size: 17 Copynumber: 3.9 Consensus size: 17
2506583 GTAATTATAT
*
2506593 AAACTATTGATGTTATATGT
1 AAACTATTGA--TT-TATGC
2506613 AAACTATTGATTTATGC
1 AAACTATTGATTTATGC
2506630 AAACTATTGATTTATGC
1 AAACTATTGATTTATGC
2506647 AAACTATTGATGTTAT
1 AAACTATTGAT-TTAT
2506663 ATCAATTAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
17 32 0.67
18 6 0.12
20 10 0.21
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (17 bp):
AAACTATTGATTTATGC
Found at i:2508717 original size:30 final size:31
Alignment explanation
Indices: 2508681--2508747 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
2508671 GTTACGTGTA
* * * *
2508681 ACAAAACAGTCACT-CAATTTTGAAAATGTG
1 ACAAAACAGTCACTAAAATTATCAAAAAGTG
2508711 ACAAAACAGTCACTAAAATTATCAAAAAGTG
1 ACAAAACAGTCACTAAAATTATCAAAAAGTG
2508742 ACAAAA
1 ACAAAA
2508748 TAGTGCTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATCAAAAAGTG
Found at i:2509894 original size:30 final size:31
Alignment explanation
Indices: 2509830--2509896 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
2509820 AAGAGGACTA
* * *
2509830 TTTTGTCACTTTTCGATAACTTTAGTGACAG
1 TTTTGTCACATTTCCATAACTTGAGTGACAG
* *
2509861 TTTTGTCACATTTCCA-AAGTTGAGTGACCG
1 TTTTGTCACATTTCCATAACTTGAGTGACAG
2509891 TTTTGT
1 TTTTGT
2509897 TAAACATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (31 bp):
TTTTGTCACATTTCCATAACTTGAGTGACAG
Found at i:2510044 original size:30 final size:31
Alignment explanation
Indices: 2509986--2510052 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
2509976 TGACGGAAAA
* *
2509986 GGACTGTTTTGTCATATTTTCAAAAGTTGAG
1 GGACTGTTTTATCACATTTTCAAAAGTTGAG
2510017 GGACTGTTTTATCACATTTTC-AAAGTTGAG
1 GGACTGTTTTATCACATTTTCAAAAGTTGAG
2510047 GGACTG
1 GGACTG
2510053 AAATGTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (31 bp):
GGACTGTTTTATCACATTTTCAAAAGTTGAG
Found at i:2512601 original size:97 final size:96
Alignment explanation
Indices: 2512413--2512601 Score: 254
Period size: 97 Copynumber: 2.0 Consensus size: 96
2512403 TTGAAAAATA
* *
2512413 GTATTCGATTATCCCGGTTTAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAACC
1 GTATTCGATTATCCCGGTTTAAGAAAAATCGTGCCTAGAAAGTTAAGGCACAAATTTTCAAAACC
* *
2512478 CGAAATAAAGAAATATCACCTCGATTTAAGG
66 CAAAATAAAGAAATATCACATCGATTTAAGG
* ** * *
2512509 GTATTTGATTATCTTGGTTTGAAGAAAAATTGTGCCTAGAAAGTTAAGGCACGAATTTTCAAAAC
1 GTATTCGATTATCCCGGTTT-AAGAAAAATCGTGCCTAGAAAGTTAAGGCACAAATTTTCAAAAC
* *
2512574 CCAAAATAAA-AGAATATTACATTGATTT
65 CCAAAATAAAGA-AATATCACATCGATTT
2512602 TAAATATTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 18 0.22
97 62 0.77
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (96 bp):
GTATTCGATTATCCCGGTTTAAGAAAAATCGTGCCTAGAAAGTTAAGGCACAAATTTTCAAAACC
CAAAATAAAGAAATATCACATCGATTTAAGG
Found at i:2512941 original size:29 final size:29
Alignment explanation
Indices: 2512909--2513030 Score: 95
Period size: 29 Copynumber: 4.2 Consensus size: 29
2512899 GTAAATTTTG
*
2512909 ATTTTTGGAAGTTTGGAGTCAAAAATGTA
1 ATTTTTGGAAGTTTGGAGGCAAAAATGTA
* ** * * *
2512938 ATTTTTGAAAG-TTCAAGGGAAAATTTTTA
1 ATTTTTGGAAGTTTGGAGGCAAAA-ATGTA
*
2512967 ATTTTTGAGAAGTTTGGGGGCAAAAATGTA
1 ATTTTTG-GAAGTTTGGAGGCAAAAATGTA
* * * *
2512997 ATTTTTAG-AGGTTCGAGGGTAAAAATGTA
1 ATTTTTGGAAGTTTGGA-GGCAAAAATGTA
2513026 ATTTT
1 ATTTT
2513031 ACAAAAGTTC
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
28 13 0.19
29 37 0.53
30 12 0.17
31 8 0.11
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (29 bp):
ATTTTTGGAAGTTTGGAGGCAAAAATGTA
Found at i:2513028 original size:59 final size:58
Alignment explanation
Indices: 2512909--2513030 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 58
2512899 GTAAATTTTG
* * *
2512909 ATTTTTGGAAGTTTGGAGTCAAAAATGTAATTTTTGAAAGTTCAAGGGAAAATTTTTA
1 ATTTTTGGAAGTTTGGAGGCAAAAATGTAATTTTTGAAAGTTCAAGGGAAAATATGTA
* * *
2512967 ATTTTTGAGAAGTTTGGGGGCAAAAATGTAATTTTT-AGAGGTTCGAGGGTAAAA-ATGTA
1 ATTTTTG-GAAGTTTGGAGGCAAAAATGTAATTTTTGA-AAGTTCAAGGG-AAAATATGTA
2513026 ATTTT
1 ATTTT
2513031 ACAAAAGTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
58 8 0.15
59 43 0.78
60 4 0.07
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (58 bp):
ATTTTTGGAAGTTTGGAGGCAAAAATGTAATTTTTGAAAGTTCAAGGGAAAATATGTA
Found at i:2513868 original size:274 final size:274
Alignment explanation
Indices: 2513379--2513927 Score: 1089
Period size: 274 Copynumber: 2.0 Consensus size: 274
2513369 ACCCGATTGG
2513379 AAATTATGAAAAAAGCGGAAGGACCAAGGGAATAAATAGACCATTTCATGAAAGCACGCGGAATC
1 AAATTATGAAAAAAGCGGAAGGACCAAGGGAATAAATAGACCATTTCATGAAAGCACGCGGAATC
2513444 TAACTTGGAGCAAGTCGGGTCGGATCTGGTCAATCTGAAATGGTGTCATTTTGGTGTTTAAGAGC
66 TAACTTGGAGCAAGTCGGGTCGGATCTGGTCAATCTGAAATGGTGTCATTTTGGTGTTTAAGAGC
2513509 CTAGCCCAAAACGACTTCGTTTTGGTCCTTCATAAATTCTATTTCAAGCCTTTTTTTTCATTTTC
131 CTAGCCCAAAACGACTTCGTTTTGGTCCTTCATAAATTCTATTTCAAGCCTTTTTTTTCATTTTC
2513574 CTTTCTTTTCTCTCCAAAAAAAAGCTTCAAAGTTCTCTTTTCTCTCTCCCTTCTCTCCATGGCCG
196 CTTTCTTTTCTCTCCAAAAAAAAGCTTCAAAGTTCTCTTTTCTCTCTCCCTTCTCTCCATGGCCG
2513639 TTCAAGAATGGATC
261 TTCAAGAATGGATC
*
2513653 AAATTATGAAAAAAGCGGAAGGACCAAGGGAATAAATAGACCATTTCATGAAAGCATGCGGAATC
1 AAATTATGAAAAAAGCGGAAGGACCAAGGGAATAAATAGACCATTTCATGAAAGCACGCGGAATC
2513718 TAACTTGGAGCAAGTCGGGTCGGATCTGGTCAATCTGAAATGGTGTCATTTTGGTGTTTAAGAGC
66 TAACTTGGAGCAAGTCGGGTCGGATCTGGTCAATCTGAAATGGTGTCATTTTGGTGTTTAAGAGC
2513783 CTAGCCCAAAACGACTTCGTTTTGGTCCTTCATAAATTCTATTTCAAGCCTTTTTTTTCATTTTC
131 CTAGCCCAAAACGACTTCGTTTTGGTCCTTCATAAATTCTATTTCAAGCCTTTTTTTTCATTTTC
2513848 CTTTCTTTTCTCTCCAAAAAAAAGCTTCAAAGTTCTCTTTTCTCTCTCCCTTCTCTCCATGGCCG
196 CTTTCTTTTCTCTCCAAAAAAAAGCTTCAAAGTTCTCTTTTCTCTCTCCCTTCTCTCCATGGCCG
2513913 TTCAAGAATGGATC
261 TTCAAGAATGGATC
2513927 A
1 A
2513928 CCGCTCTGTC
Statistics
Matches: 274, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
274 274 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (274 bp):
AAATTATGAAAAAAGCGGAAGGACCAAGGGAATAAATAGACCATTTCATGAAAGCACGCGGAATC
TAACTTGGAGCAAGTCGGGTCGGATCTGGTCAATCTGAAATGGTGTCATTTTGGTGTTTAAGAGC
CTAGCCCAAAACGACTTCGTTTTGGTCCTTCATAAATTCTATTTCAAGCCTTTTTTTTCATTTTC
CTTTCTTTTCTCTCCAAAAAAAAGCTTCAAAGTTCTCTTTTCTCTCTCCCTTCTCTCCATGGCCG
TTCAAGAATGGATC
Found at i:2514542 original size:22 final size:22
Alignment explanation
Indices: 2514517--2514562 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2514507 GTTTTTTTAT
*
2514517 TATTTA-TTAATAGTATTTAATA
1 TATTTATTTAATA-TACTTAATA
2514539 TATTTATTTAATATACTTAATA
1 TATTTATTTAATATACTTAATA
2514561 TA
1 TA
2514563 AAATAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTTATTTAATATACTTAATA
Found at i:2515249 original size:17 final size:17
Alignment explanation
Indices: 2515227--2515283 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
2515217 ACTTTGATAT
2515227 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* * * *
2515244 TTTAAACTGAAGATGAA
1 TTTAAATTTAAAATAAA
2515261 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
2515278 TTTAAA
1 TTTAAA
2515284 AATGAATTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2515291 original size:12 final size:11
Alignment explanation
Indices: 2515229--2515284 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
2515219 TTTGATATTT
2515229 TAAATTTAAAA
1 TAAATTTAAAA
*
2515240 TAAATTTAAAC
1 TAAATTTAAAA
* **
2515251 TGAAGA-TGAATT
1 T-AA-ATTTAAAA
2515263 TAAATTTAAAA
1 TAAATTTAAAA
2515274 TAAATTTAAAA
1 TAAATTTAAAA
2515285 ATGAATTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 27 0.77
12 6 0.17
13 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:2515297 original size:34 final size:34
Alignment explanation
Indices: 2515227--2515297 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
2515217 ACTTTGATAT
* *
2515227 TTTAAATTTAAAATAAATTTAAACTGAAGATGAA
1 TTTAAATTTAAAATAAATTTAAAATGAAGATCAA
*
2515261 TTTAAATTTAAAATAAATTTAAAAATGAA-TTCAA
1 TTTAAATTTAAAATAAATTT-AAAATGAAGATCAA
2515295 TTT
1 TTT
2515298 GGGCCCGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 26 0.79
35 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAAATGAAGATCAA
Found at i:2521869 original size:16 final size:15
Alignment explanation
Indices: 2521843--2521892 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2521833 TATAGTTTTC
2521843 TTAT-ATATTTATTT
1 TTATAATATTTATTT
*
2521857 TTATAATAGTTTACCTT
1 TTATAATA-TTTA-TTT
*
2521874 TT-TAATATATATTT
1 TTATAATATTTATTT
2521888 TTATA
1 TTATA
2521893 TAATCTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
16 9 0.31
17 4 0.14
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (15 bp):
TTATAATATTTATTT
Found at i:2526435 original size:22 final size:22
Alignment explanation
Indices: 2526409--2526450 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2526399 ATCAATATAA
*
2526409 TATCATAT-AAAGATTAAGAATT
1 TATCAT-TGAAAGATAAAGAATT
2526431 TATCATTGAAAGATAAAGAA
1 TATCATTGAAAGATAAAGAA
2526451 AGGACCCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (22 bp):
TATCATTGAAAGATAAAGAATT
Found at i:2533862 original size:17 final size:16
Alignment explanation
Indices: 2533834--2533890 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
2533824 AAAATAATAG
*
2533834 TAAAATTAACAATAAA
1 TAAAAATAACAATAAA
2533850 TAAAAATATACAATATTAA
1 TAAAAATA-ACAATA--AA
*
2533869 -AAAAATAATAATAAAA
1 TAAAAATAACAAT-AAA
2533885 TAAAAA
1 TAAAAA
2533891 AAATTAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 9 0.26
17 15 0.44
18 8 0.24
19 2 0.06
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAATAACAATAAA
Found at i:2533884 original size:11 final size:11
Alignment explanation
Indices: 2533823--2533887 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
2533813 TAATTACCTC
*
2533823 TAAAATAATAG
1 TAAAATAATAA
*
2533834 TAAAATTAACAA
1 TAAAA-TAATAA
*
2533846 T-AAATAAAAA
1 TAAAATAATAA
*
2533856 TATACAATATTAA
1 TA-A-AATAATAA
*
2533869 AAAAATAATAA
1 TAAAATAATAA
2533880 TAAAATAA
1 TAAAATAA
2533888 AAAAAATTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 6 0.14
11 22 0.52
12 7 0.17
13 7 0.17
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2556468 original size:13 final size:13
Alignment explanation
Indices: 2556450--2556478 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2556440 GTCAAATCGG
2556450 TTAAGTTACCAGT
1 TTAAGTTACCAGT
2556463 TTAAGTTACCAGT
1 TTAAGTTACCAGT
2556476 TTA
1 TTA
2556479 CTGATCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (13 bp):
TTAAGTTACCAGT
Found at i:2560079 original size:17 final size:17
Alignment explanation
Indices: 2560057--2560092 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2560047 GGATTTTGAT
2560057 TTTTGGGTAAATAAAAA
1 TTTTGGGTAAATAAAAA
*
2560074 TTTTGGTTAAATAAAAA
1 TTTTGGGTAAATAAAAA
2560091 TT
1 TT
2560093 CGATTTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (17 bp):
TTTTGGGTAAATAAAAA
Found at i:2560561 original size:23 final size:24
Alignment explanation
Indices: 2560524--2560585 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
2560514 ATAAAAATTA
2560524 AAATAATTTTTAAAAACT-TAAAAT
1 AAATAA-TTTTAAAAACTCTAAAAT
*
2560548 AAATAATTTTAAAAATTCTAAAAT
1 AAATAATTTTAAAAACTCTAAAAT
**
2560572 TTAT-ATTTTAAAAA
1 AAATAATTTTAAAAA
2560586 ATTATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATAATTTTAAAAACTCTAAAAT
Found at i:2560734 original size:16 final size:16
Alignment explanation
Indices: 2560715--2560745 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2560705 TTGAAAAAAT
2560715 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
2560731 TTTCAAATTTATATG
1 TTTCAAATATATATG
2560746 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:2562932 original size:12 final size:12
Alignment explanation
Indices: 2562917--2562941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2562907 CGACAATAAC
2562917 ATCTACAAAACA
1 ATCTACAAAACA
2562929 ATCTACAAAACA
1 ATCTACAAAACA
2562941 A
1 A
2562942 CAATAACATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ATCTACAAAACA
Found at i:2563553 original size:195 final size:196
Alignment explanation
Indices: 2563112--2563553 Score: 495
Period size: 196 Copynumber: 2.3 Consensus size: 196
2563102 TACCAGTACC
*
2563112 CGATGCTGCTCACATGAGCTGTCGAGGACTCGCAACATATGCGGTACC-CTAGACATCGATACGG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTC-AGACATCGATACGG
* * * * **
2563176 TGTCTGTCTATATAACTATCTCCTAACGATGCTGCTCACATAAGCTGTCGGGTGTATGCACTTAT
65 TATCTGTCAATATAACTATCTCCTAACGATGCTGCTCACACAAGCTGTCGAGAATATGCACTTAT
* *
2563241 GGATAAGAACCAACCATCGTAGGGGCCTATAATCCATTCTAGGATTCATATATTTTTTTCTAACT
130 GCATAAGAACCAACCATCGTAGGGGCCTATAATCCATTCTAGGATTCATATATATTTTTCTAACT
2563306 CA
195 CA
* * * * * * **
2563308 CGATGCTTCTCACACGAGCTATTGAGGACTCGTAACATATGCGATACCTCAGCCATCGATGTGGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGACATCGATACGGT
* * * * * * *
2563373 ATTTGTGAATATAACTGT-TCCCTGACGATGCTGCTCACACGAGTTGTCGAGAATATGCAGTTAT
66 ATCTGTCAATATAACTATCT-CCTAACGATGCTGCTCACACAAGCTGTCGAGAATATGCACTTAT
* * * * *
2563437 GCATAA-ATCTCAGCCATCGTA-GGGCTTGTAATCCATTCTTA-GATTC-TTTACTCATTTTTC-
130 GCATAAGAAC-CAACCATCGTAGGGGCCTATAATCCATTC-TAGGATTCATATA-T-ATTTTTCT
*
2563497 GACTCA
191 AACTCA
2563503 CGATGCTGCTCACACGAGCTGTCG-GAGACTCGCAACATATGCGGTACCTCA
1 CGATGCTGCTCACACGAGCTGTCGAG-GACTCGCAACATATGCGGTACCTCA
2563554 ACTATCGTGT
Statistics
Matches: 204, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
194 4 0.02
195 73 0.36
196 126 0.62
197 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (196 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGACATCGATACGGT
ATCTGTCAATATAACTATCTCCTAACGATGCTGCTCACACAAGCTGTCGAGAATATGCACTTATG
CATAAGAACCAACCATCGTAGGGGCCTATAATCCATTCTAGGATTCATATATATTTTTCTAACTC
A
Found at i:2564061 original size:16 final size:16
Alignment explanation
Indices: 2564037--2564068 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2564027 TCCTTACAAA
*
2564037 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
2564053 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
2564069 AAAAATTATT
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:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:2566071 original size:16 final size:16
Alignment explanation
Indices: 2566050--2566082 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2566040 CAAATAGAAA
2566050 CAAAC-AAGCAAACAAT
1 CAAACAAAG-AAACAAT
2566066 CAAACAAAGAAACAAT
1 CAAACAAAGAAACAAT
2566082 C
1 C
2566083 TTTACAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.64, C:0.24, G:0.06, T:0.06
Consensus pattern (16 bp):
CAAACAAAGAAACAAT
Found at i:2566631 original size:20 final size:20
Alignment explanation
Indices: 2566606--2566657 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2566596 AGTCTTCAAG
2566606 GTATCGGTAGAACTGAAGTT
1 GTATCGGTAGAACTGAAGTT
* *
2566626 GTATCGATAGAAGTGAAGTT
1 GTATCGGTAGAACTGAAGTT
* *
2566646 CTACCGGTAGAA
1 GTATCGGTAGAA
2566658 GTCCTAGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (20 bp):
GTATCGGTAGAACTGAAGTT
Found at i:2584056 original size:26 final size:25
Alignment explanation
Indices: 2584000--2584059 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2583990 AAGCATACAC
2584000 ATTTATATATAATAATACAATAAATT
1 ATTTA-ATATAATAATACAATAAATT
**
2584026 A-TTAATATAATGAATACAATTTATT
1 ATTTAATATAAT-AATACAATAAATT
2584051 ATTTAATAT
1 ATTTAATAT
2584060 TAAAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.23
25 15 0.50
26 8 0.27
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTAATATAATAATACAATAAATT
Found at i:2584057 original size:21 final size:20
Alignment explanation
Indices: 2583994--2584058 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 20
2583984 ATTATTAAGC
2583994 ATACACATTTA-TATATAATA
1 ATACA-ATTTATTATATAATA
2584014 ATACAATAAATTATTAATATAATGA
1 ATACAAT---TTATT-ATATAAT-A
*
2584039 ATACAATTTATTATTTAATA
1 ATACAATTTATTATATAATA
2584059 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 6 0.16
22 8 0.21
23 1 0.03
24 7 0.18
25 8 0.21
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (20 bp):
ATACAATTTATTATATAATA
Found at i:2584113 original size:19 final size:18
Alignment explanation
Indices: 2584082--2584125 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2584072 TTAATATCAA
*
2584082 ATTTTAACATT-AATAATT
1 ATTTTAAAATTAAATAA-T
2584100 ATTTTAAAATTTAAATAAT
1 ATTTTAAAA-TTAAATAAT
2584119 ATTTTAA
1 ATTTTAA
2584126 TAAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAAAATTAAATAAT
Found at i:2585098 original size:389 final size:390
Alignment explanation
Indices: 2584380--2585159 Score: 1544
Period size: 389 Copynumber: 2.0 Consensus size: 390
2584370 TTGAAGAGGA
*
2584380 GCTATAGGTAATTCTAGACATTGTGTCCAAAAGAGCAGATATGATTAGAACTTACAATGAGTTTC
1 GCTATAGGTAATTCTAGACATTGTGTCCAAAAGAGCAGATATGATTAGAACCTACAATGAGTTTC
2584445 AAAAAAAATATTTTACATAAAATCATTCAAACACTAAAAAATATCAATTCATTTTTCAAAAATGA
66 AAAAAAAATATTTTACATAAAATCATTCAAACACTAAAAAATATCAATTCATTTTTCAAAAATGA
2584510 AAAAAAAAGTTCATAACTTTCCTAGTCCACCTATCGTAGTATATATTGAGAAACATTTTCCTACA
131 AAAAAAAAGTTCATAACTTTCCTAGTCCACCTATCGTAGTATATATTGAGAAACATTTTCCTACA
2584575 TTTGACATTATATGTGGTATTCAACATTGTGATGCAATAGGTCAGGGTCCATTTGCAATCACATC
196 TTTGACATTATATGTGGTATTCAACATTGTGATGCAATAGGTCAGGGTCCATTTGCAATCACATC
2584640 CAAAATTGATTTATGTACACCACATGATATGTTTTATGCTATTTATTTGAGTCGGTCGAGTTAGG
261 CAAAATTGATTTATGTACACCACATGATATGTTTTATGCTATTTATTTGAGTCGGTCGAGTTAGG
2584705 TTCGAAATTACAGAAACCAAACCCTAATGCTTCAGCTTTGCAGTGTCTATTTTATCATTTGGTGG
326 TTCGAAATTACAGAAACCAAACCCTAATGCTTCAGCTTTGCAGTGTCTATTTTATCATTTGGTGG
2584770 GCTATAGGTAATTCTAGACATTGTGTCCAAAAGAGCAGATATGATTAGAACCTACAATGAGTTTC
1 GCTATAGGTAATTCTAGACATTGTGTCCAAAAGAGCAGATATGATTAGAACCTACAATGAGTTTC
2584835 AAAAAAAATA-TTTACATAAAATCATTCAAACACTAAAAAATATCAATTCATTTTTCAAAAATGA
66 AAAAAAAATATTTTACATAAAATCATTCAAACACTAAAAAATATCAATTCATTTTTCAAAAATGA
2584899 AAAAAAAAGTTCATAACTTTCCTAGTCCACCTATCGTAGTATATATTGAGAAACATTTTCCTACA
131 AAAAAAAAGTTCATAACTTTCCTAGTCCACCTATCGTAGTATATATTGAGAAACATTTTCCTACA
2584964 TTTGACATTATATGTGGTATTCAACATTGTGATGCAATAGGTCAGGGTCCATTTGCAATCACATC
196 TTTGACATTATATGTGGTATTCAACATTGTGATGCAATAGGTCAGGGTCCATTTGCAATCACATC
2585029 CAAAATTGATTTATGTACACCACATGATATGTTTTATGCTATTTATTTGAGTCGGTCGAGTTAGG
261 CAAAATTGATTTATGTACACCACATGATATGTTTTATGCTATTTATTTGAGTCGGTCGAGTTAGG
2585094 TTCGAAATTACAGAAACCAAACCCTAATGCTTCAGCTTTGCAGTGTCTATTTTATCATTTGGTGG
326 TTCGAAATTACAGAAACCAAACCCTAATGCTTCAGCTTTGCAGTGTCTATTTTATCATTTGGTGG
2585159 G
1 G
2585160 TGTGGAAATT
Statistics
Matches: 389, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
389 315 0.81
390 74 0.19
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (390 bp):
GCTATAGGTAATTCTAGACATTGTGTCCAAAAGAGCAGATATGATTAGAACCTACAATGAGTTTC
AAAAAAAATATTTTACATAAAATCATTCAAACACTAAAAAATATCAATTCATTTTTCAAAAATGA
AAAAAAAAGTTCATAACTTTCCTAGTCCACCTATCGTAGTATATATTGAGAAACATTTTCCTACA
TTTGACATTATATGTGGTATTCAACATTGTGATGCAATAGGTCAGGGTCCATTTGCAATCACATC
CAAAATTGATTTATGTACACCACATGATATGTTTTATGCTATTTATTTGAGTCGGTCGAGTTAGG
TTCGAAATTACAGAAACCAAACCCTAATGCTTCAGCTTTGCAGTGTCTATTTTATCATTTGGTGG
Found at i:2587174 original size:29 final size:29
Alignment explanation
Indices: 2587114--2587215 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
2587104 TGGCCCAGAC
* *
2587114 CGTGTGGCCCACACAGTCTAACACAC-AGT
1 CGTGTGGCTCACACGGTCTAACACACGA-T
2587143 CGTGTGGCTCACACGGTCTAACACACGAT
1 CGTGTGGCTCACACGGTCTAACACACGAT
* * ** *
2587172 CGTGGGGCTCACATGGTCTGGCACATGAT
1 CGTGTGGCTCACACGGTCTAACACACGAT
2587201 CGTGTGGCTCACACG
1 CGTGTGGCTCACACG
2587216 ATCTGGCACA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 62 0.98
30 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (29 bp):
CGTGTGGCTCACACGGTCTAACACACGAT
Found at i:2587235 original size:29 final size:29
Alignment explanation
Indices: 2587114--2587228 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 29
2587104 TGGCCCAGAC
* * **
2587114 CGTGTGGCCCACACAGTCTAACACAC-AGT
1 CGTGTGGCTCACACGGTCTGGCACACGA-T
**
2587143 CGTGTGGCTCACACGGTCTAACACACGAT
1 CGTGTGGCTCACACGGTCTGGCACACGAT
* * *
2587172 CGTGGGGCTCACATGGTCTGGCACATGAT
1 CGTGTGGCTCACACGGTCTGGCACACGAT
*
2587201 CGTGTGGCTCACACGATCTGGCACACGA
1 CGTGTGGCTCACACGGTCTGGCACACGA
2587229 CTATGTGACA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 73 0.99
30 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (29 bp):
CGTGTGGCTCACACGGTCTGGCACACGAT
Found at i:2588402 original size:43 final size:44
Alignment explanation
Indices: 2588326--2588408 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 44
2588316 ATTGAAAAAT
* *
2588326 AGTATGCATACACGGTCTGGCACACGCTAGTGTG-CCCCTAAAC
1 AGTATGCACACACGGTCTGACACACGCTAGTGTGTCCCCTAAAC
* *
2588369 AGTATGCACACACGGTCTGACATACG-TCCGTGTGTCCCCT
1 AGTATGCACACACGGTCTGACACACGCT-AGTGTGTCCCCT
2588409 GTACCTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.03
43 28 0.82
44 5 0.15
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (44 bp):
AGTATGCACACACGGTCTGACACACGCTAGTGTGTCCCCTAAAC
Found at i:2591553 original size:29 final size:28
Alignment explanation
Indices: 2591521--2591863 Score: 132
Period size: 29 Copynumber: 11.6 Consensus size: 28
2591511 GGAAGGTTCG
*
2591521 AGGGTAAAATGGTAATTTTTTGTTAAATT-
1 AGGGTAAAATGG-AA-TTTTTGTAAAATTC
*
2591550 AGGGTCAAAAATGGAA-TTTTG-AAAGGTTC
1 AGGGT--AAAATGGAATTTTTGTAAA-ATTC
* *
2591579 GAGGGTAAAATGGTAATTTTGGTAAAATTG
1 -AGGGTAAAATGG-AATTTTTGTAAAATTC
* *
2591609 AGGTTAAAATGGAA-TTTTGGAAAGATTC
1 AGGGTAAAATGGAATTTTTGTAAA-ATTC
2591637 AAGGGTAAAATGGTAATTTTTGGTAAAATT-
1 -AGGGTAAAATGG-AATTTTT-GTAAAATTC
* * ** *
2591667 GGGGTTAAAATTGGAA-TTTTGGAAGGTTT
1 AGGG-TAAAA-TGGAATTTTTGTAAAATTC
* *
2591696 GGGGATAAAATGGTAATTTTTAGTGAAA-TC
1 AGGG-TAAAATGG-AATTTTT-GTAAAATTC
** *
2591726 AGGGTTAAAAATGGAATTTTTG-AAGGTTT
1 AGGG-T-AAAATGGAATTTTTGTAAAATTC
* *
2591755 GGGGATAAAATGGTAATTTTTGGTGAAATT-
1 AGGG-TAAAATGG-AATTTTT-GTAAAATTC
* * * *
2591785 GGGGTAAAAAATGGAA-TTTTGGAAAGTTTG
1 AGGGT--AAAATGGAATTTTTGTAAA-ATTC
* *
2591815 AAGGTAAAATGGTAATTTTTGGTGAAATT-
1 AGGGTAAAATGG-AATTTTT-GTAAAATTC
*
2591844 GGGGTAAAAAATGGAATTTT
1 AGGGT--AAAATGGAATTTT
2591864 GGAAAGTTTT
Statistics
Matches: 239, Mismatches: 42, Indels: 65
0.69 0.12 0.19
Matches are distributed among these distances:
27 9 0.04
28 45 0.19
29 72 0.30
30 60 0.25
31 49 0.21
32 4 0.02
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (28 bp):
AGGGTAAAATGGAATTTTTGTAAAATTC
Found at i:2591864 original size:29 final size:30
Alignment explanation
Indices: 2591585--2591865 Score: 150
Period size: 29 Copynumber: 9.5 Consensus size: 30
2591575 GTTCGAGGGT
* * *
2591585 AAAATGGTAATTTTGGTAAAATTGAGGT-T
1 AAAATGGTAATTTTGGTGAAATTGGGGTAA
* *
2591614 AAAATGG-AATTTTGG-AAAGATTCAAGGGT--
1 AAAATGGTAATTTTGGTGAA-ATT--GGGGTAA
* *
2591643 AAAATGGTAATTTTTGGTAAAATTGGGGTTA
1 AAAATGGTAA-TTTTGGTGAAATTGGGGTAA
* * *
2591674 AAATTGG-AATTTT-G-GAAGGTTTGGGG-AT
1 AAAATGGTAATTTTGGTGAA--ATTGGGGTAA
* ** *
2591702 AAAATGGTAATTTTTAGTGAAATCAGGGTTA
1 AAAATGGTAA-TTTTGGTGAAATTGGGGTAA
* *
2591733 AAAATGG-AATTTT--TGAAGGTTTGGGG-AT
1 AAAATGGTAATTTTGGTGAA--ATTGGGGTAA
2591761 AAAATGGTAATTTTTGGTGAAATTGGGGTAA
1 AAAATGGTAA-TTTTGGTGAAATTGGGGTAA
*
2591792 AAAATGG-AATTTT-G-GAAAGTTTGAAGGT--
1 AAAATGGTAATTTTGGTGAAA--TTG-GGGTAA
2591820 AAAATGGTAATTTTTGGTGAAATTGGGGTAA
1 AAAATGGTAA-TTTTGGTGAAATTGGGGTAA
2591851 AAAATGG-AATTTTGG
1 AAAATGGTAATTTTGG
2591866 AAAGTTTTGT
Statistics
Matches: 198, Mismatches: 23, Indels: 62
0.70 0.08 0.22
Matches are distributed among these distances:
27 13 0.07
28 33 0.17
29 58 0.29
30 41 0.21
31 39 0.20
32 14 0.07
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATTGGGGTAA
Found at i:2591868 original size:59 final size:59
Alignment explanation
Indices: 2591489--2591872 Score: 481
Period size: 59 Copynumber: 6.5 Consensus size: 59
2591479 TCAAGAAAAT
* * * * * *
2591489 TTGGGGTTAGAAATGGGATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTTGTTAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAA
* * * *
2591548 TTAGGGTCAAAAATGGAATTTT-GAAAGGTTCGAGGGTAAAATGGTAA-TTTTGGTAAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAA-GTTTGAGGGTAAAATGGTAATTTTTGGTGAAA
* ** *
2591606 TTGAGGTT-AAAATGGAATTTTGGAAAGATTCAAGGGTAAAATGGTAATTTTTGGTAAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAG-TTTGAGGGTAAAATGGTAATTTTTGGTGAAA
* * *
2591665 TTGGGGTTAAAATTGGAATTTTGGAAGGTTTG-GGGATAAAATGGTAATTTTTAGTGAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGG-TAAAATGGTAATTTTTGGTGAAA
** * *
2591724 TCAGGGTTAAAAATGGAATTTTTGAAGGTTTG-GGGATAAAATGGTAATTTTTGGTGAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGG-TAAAATGGTAATTTTTGGTGAAA
* *
2591783 TTGGGGTAAAAAATGGAATTTTGGAAAGTTTGAAGGTAAAATGGTAATTTTTGGTGAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAA
*
2591842 TTGGGGTAAAAAATGGAATTTTGGAAAGTTT
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTT
2591873 TGTTTCAAAA
Statistics
Matches: 289, Mismatches: 29, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
57 14 0.05
58 42 0.15
59 214 0.74
60 19 0.07
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (59 bp):
TTGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAA
Found at i:2593936 original size:17 final size:17
Alignment explanation
Indices: 2593916--2593978 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
2593906 TTTTAAATGT
2593916 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
2593933 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
2593949 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
2593966 ACTT-AATTTAAAA
1 ATTTAAATTTAAAA
2593979 TCCAAGTTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:2593962 original size:27 final size:27
Alignment explanation
Indices: 2593900--2593971 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
2593890 TTTAAGTTTC
* * **
2593900 AAATTATTTTAAATGTATTTAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
**
2593927 AAACAAATTTAAATTTAAATAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
* *
2593954 AAATTAATTCAAACTTAA
1 AAATTAATTTAAATTTAA
2593972 TTTAAAATCC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (27 bp):
AAATTAATTTAAATTTAAATAAATTTA
Found at i:2594889 original size:29 final size:29
Alignment explanation
Indices: 2594820--2594937 Score: 139
Period size: 29 Copynumber: 4.1 Consensus size: 29
2594810 ACTTGGCCCA
* * *
2594820 GATCGTGTGGCCCACACAGTCTAACACAC
1 GATCGTGTGGCTCACACGGTCTAGCACAC
2594849 GATCGTGTGGCTCACACGGTCTAGCACAC
1 GATCGTGTGGCTCACACGGTCTAGCACAC
* * * *
2594878 GATCGTAG-GGCTCACATGGTTTGGCACAT
1 GATCGT-GTGGCTCACACGGTCTAGCACAC
* *
2594907 GATCGTGTGCCTCACACGGTCTGGCACAC
1 GATCGTGTGGCTCACACGGTCTAGCACAC
2594936 GA
1 GA
2594938 CTATGTGACA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.01
29 74 0.97
30 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (29 bp):
GATCGTGTGGCTCACACGGTCTAGCACAC
Found at i:2599447 original size:16 final size:16
Alignment explanation
Indices: 2599422--2599462 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
2599412 AAGAATTCAA
*
2599422 GTATGCATGCATGCAT
1 GTATGTATGCATGCAT
2599438 GTATGTATGCATGCAT
1 GTATGTATGCATGCAT
*
2599454 GCATGTATG
1 GTATGTATG
2599463 TATACTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (16 bp):
GTATGTATGCATGCAT
Found at i:2599447 original size:20 final size:20
Alignment explanation
Indices: 2599422--2599465 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2599412 AAGAATTCAA
2599422 GTATGCATGCATGCATGTAT
1 GTATGCATGCATGCATGTAT
2599442 GTATGCATGCATGCATGTAT
1 GTATGCATGCATGCATGTAT
2599462 GTAT
1 GTAT
2599466 ACTACAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (20 bp):
GTATGCATGCATGCATGTAT
Found at i:2599465 original size:4 final size:4
Alignment explanation
Indices: 2599424--2599458 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2599414 GAATTCAAGT
* *
2599424 ATGC ATGC ATGC ATGT ATGT ATGC ATGC ATGC ATG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATG
2599459 TATGTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (4 bp):
ATGC
Found at i:2600231 original size:18 final size:18
Alignment explanation
Indices: 2600175--2600232 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
2600165 TTTTTCTTTC
*
2600175 AAAATCATAAAATATT-A-
1 AAAATTATAAAA-ATTCAT
*
2600192 AAAAGTTATACAAACTTC-T
1 AAAA-TTATA-AAAATTCAT
2600211 AAAATTATAAAAATTCAT
1 AAAATTATAAAAATTCAT
2600229 AAAA
1 AAAA
2600233 ACTAAAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 10 0.30
18 16 0.48
19 7 0.21
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAATTCAT
Found at i:2600234 original size:28 final size:28
Alignment explanation
Indices: 2600182--2600235 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
2600172 TTCAAAATCA
*
2600182 TAAAATATTAAAAAGTTATACAAACTTC
1 TAAAATATTAAAAAGTTATAAAAACTTC
2600210 TAAAAT-TATAAAAA-TTCATAAAAACT
1 TAAAATAT-TAAAAAGTT-ATAAAAACT
2600236 AAAGATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.31
Consensus pattern (28 bp):
TAAAATATTAAAAAGTTATAAAAACTTC
Found at i:2608077 original size:25 final size:23
Alignment explanation
Indices: 2608029--2608075 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2608019 AAAATTTAAA
*
2608029 ATATTTATAAAAATTCCAAATTT
1 ATATTTATAAAAATTCAAAATTT
2608052 ATATTTATTAAAAAATT-AAAATTT
1 ATATTTA-T-AAAAATTCAAAATTT
2608076 TAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTTATAAAAATTCAAAATTT
Found at i:2613771 original size:12 final size:11
Alignment explanation
Indices: 2613741--2613820 Score: 58
Period size: 12 Copynumber: 7.3 Consensus size: 11
2613731 AATAACATCT
*
2613741 AAACAA-AAAA
1 AAACAACAACA
2613751 AAACAACAACCA
1 AAACAACAA-CA
*
2613763 AAACTACAACAA
1 AAACAACAAC-A
* *
2613775 AAATAACAATA
1 AAACAACAACA
2613786 AAACAA-AA-A
1 AAACAACAACA
* *
2613795 AAATAGCAACA
1 AAACAACAACA
2613806 AAACTAACAACA
1 AAAC-AACAACA
2613818 AAA
1 AAA
2613821 ATAGTAGCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
9 5 0.09
10 10 0.19
11 13 0.24
12 26 0.48
ACGTcount: A:0.74, C:0.19, G:0.01, T:0.06
Consensus pattern (11 bp):
AAACAACAACA
Found at i:2613796 original size:20 final size:21
Alignment explanation
Indices: 2613718--2613823 Score: 79
Period size: 24 Copynumber: 4.8 Consensus size: 21
2613708 AACAATAGTA
* *
2613718 AAAACACATAAAAAATAACATC
1 AAAACA-AAAAAAAATAACAAC
* *
2613740 TAAACAAAAAAAAACAACAACC
1 AAAACAAAAAAAAATAACAA-C
* *
2613762 AAAACTACAACAAAAATAACAAT
1 AAAAC-A-AAAAAAAATAACAAC
*
2613785 AAAAC-AAAAAAAATAGCAAC
1 AAAACAAAAAAAAATAACAAC
2613805 AAAACTAACAACAAAAATA
1 AAAAC-AA-AA-AAAAATA
2613824 GTAGCAAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
20 17 0.26
21 11 0.17
22 11 0.17
23 8 0.12
24 19 0.29
ACGTcount: A:0.72, C:0.18, G:0.01, T:0.09
Consensus pattern (21 bp):
AAAACAAAAAAAAATAACAAC
Found at i:2613816 original size:44 final size:45
Alignment explanation
Indices: 2613728--2613823 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 45
2613718 AAAACACATA
*
2613728 AAAAATAACATCTAAACAAAAAAAAACAACAACCAAAACTACAAC
1 AAAAATAACATCAAAACAAAAAAAAACAACAACCAAAACTACAAC
* *
2613773 AAAAATAACAAT-AAAAC-AAAAAAAATAGCAA-CAAAACTAACAAC
1 AAAAATAAC-ATCAAAACAAAAAAAAACAACAACCAAAACT-ACAAC
2613817 AAAAATA
1 AAAAATA
2613824 GTAGCAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 7 0.15
44 24 0.52
45 13 0.28
46 2 0.04
ACGTcount: A:0.72, C:0.18, G:0.01, T:0.09
Consensus pattern (45 bp):
AAAAATAACATCAAAACAAAAAAAAACAACAACCAAAACTACAAC
Found at i:2613822 original size:24 final size:24
Alignment explanation
Indices: 2613761--2613907 Score: 81
Period size: 21 Copynumber: 6.7 Consensus size: 24
2613751 AAACAACAAC
*
2613761 CAAAACT-ACAACAAAAATAACAA
1 CAAAACTAACAACAAAAATAGCAA
*
2613784 TAAAAC--A-AA-AAAAATAGCAA
1 CAAAACTAACAACAAAAATAGCAA
* *
2613804 CAAAACTAACAACAAAAATAGTAG
1 CAAAACTAACAACAAAAATAGCAA
* *
2613828 CAAAAAC-AAC-ACCAAAATAGTAA
1 C-AAAACTAACAACAAAAATAGCAA
*
2613851 -AAAAC-AAC-ACCAAAATAGCAA
1 CAAAACTAACAACAAAAATAGCAA
* *
2613872 -AAAA-TAGCAAC-CAAA-A-CAA
1 CAAAACTAACAACAAAAATAGCAA
* *
2613891 CAAAAATAACAGCAAAA
1 CAAAACTAACAACAAAA
2613908 GCAACATCAA
Statistics
Matches: 101, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
19 3 0.03
20 20 0.20
21 36 0.36
22 6 0.06
23 18 0.18
24 13 0.13
25 5 0.05
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (24 bp):
CAAAACTAACAACAAAAATAGCAA
Found at i:2613848 original size:23 final size:21
Alignment explanation
Indices: 2613794--2613875 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 21
2613784 TAAAACAAAA
* *
2613794 AAAATAGCAACAAAACTAACAACA
1 AAAATAGTAA-AAAAC-AAC-ACC
2613818 AAAATAGTAGCAAAAACAACACC
1 AAAATAGTA--AAAAACAACACC
2613841 AAAATAGTAAAAAACAACACC
1 AAAATAGTAAAAAACAACACC
*
2613862 AAAATAGCAAAAAA
1 AAAATAGTAAAAAA
2613876 TAGCAACCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
21 25 0.47
23 11 0.21
24 11 0.21
25 5 0.09
26 1 0.02
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (21 bp):
AAAATAGTAAAAAACAACACC
Found at i:2613877 original size:54 final size:53
Alignment explanation
Indices: 2613817--2613949 Score: 135
Period size: 54 Copynumber: 2.5 Consensus size: 53
2613807 AACTAACAAC
* * **
2613817 AAAAATAGTAGCAAAAACAACACCAAAATAGTA-AAAAACAACACCAAAATAGCA
1 AAAAATAGCAACAAAAACAACA--AAAATAACACAAAAACAACACCAAAATAGCA
* * * *
2613871 AAAAATAGCAACCAAAACAACAAAAATAACAGCAAAAGCAACATCAAAATAGTA
1 AAAAATAGCAACAAAAACAACAAAAATAACA-CAAAAACAACACCAAAATAGCA
* *
2613925 AAAAATAGC-ACCAAAATAACAAAAA
1 AAAAATAGCAACAAAAACAACAAAAA
2613950 AATAGCCCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
52 7 0.10
53 15 0.22
54 46 0.68
ACGTcount: A:0.66, C:0.18, G:0.07, T:0.09
Consensus pattern (53 bp):
AAAAATAGCAACAAAAACAACAAAAATAACACAAAAACAACACCAAAATAGCA
Found at i:2613906 original size:75 final size:76
Alignment explanation
Indices: 2613791--2613964 Score: 224
Period size: 75 Copynumber: 2.3 Consensus size: 76
2613781 CAATAAAACA
* **
2613791 AAAAAAATAGCAACAAAACTAACAACAAAAATAGTAGCAAAAACAACACCAAAATAGTAAAAAAC
1 AAAAAAATAGCAAC-CAA--AACAACAAAAATAACAGCAAAAACAACACCAAAATAGTAAAAAAC
*
2613856 AACACCAAAATAGC
63 AACACCAAAATAAC
* * * *
2613870 -AAAAAATAGCAACCAAAACAACAAAAATAACAGCAAAAGCAACATCAAAATAGTAAAAAATAGC
1 AAAAAAATAGCAACCAAAACAACAAAAATAACAGCAAAAACAACACCAAAATAGTAAAAAACAAC
2613934 ACCAAAATAAC
66 ACCAAAATAAC
**
2613945 AAAAAAATAGCCCCCAAAAC
1 AAAAAAATAGCAACCAAAAC
2613965 GCAACCAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
75 52 0.62
76 17 0.20
77 2 0.02
78 13 0.15
ACGTcount: A:0.65, C:0.20, G:0.06, T:0.09
Consensus pattern (76 bp):
AAAAAAATAGCAACCAAAACAACAAAAATAACAGCAAAAACAACACCAAAATAGTAAAAAACAAC
ACCAAAATAAC
Found at i:2615615 original size:17 final size:17
Alignment explanation
Indices: 2615595--2615629 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2615585 ATAGAATTAT
2615595 TAAATA-TTAAAATAAAA
1 TAAATATTTAAAA-AAAA
2615612 TAAATATTTAAAAAAAA
1 TAAATATTTAAAAAAAA
2615629 T
1 T
2615630 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATATTTAAAAAAAA
Found at i:2616064 original size:3 final size:3
Alignment explanation
Indices: 2616056--2616100 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2616046 TACAACACAA
2616056 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2616101 TTCACAAGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2617641 original size:19 final size:19
Alignment explanation
Indices: 2617583--2617641 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
2617573 TAAAATAAAA
*
2617583 AATATGAAT-AAA-ACTTT
1 AATATAAATAAAATACTTT
*
2617600 AATAAATAAAGTAAGAATTCTTT
1 AAT--ATAAA-TAA-AATACTTT
2617623 AATATAAATAAAATACTTT
1 AATATAAATAAAATACTTT
2617642 CCTTCCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
17 3 0.09
19 11 0.33
20 4 0.12
21 6 0.18
22 2 0.06
23 7 0.21
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
AATATAAATAAAATACTTT
Found at i:2618419 original size:17 final size:16
Alignment explanation
Indices: 2618388--2618421 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2618378 TTTTTTCCCG
*
2618388 TTTTCTTTGCGATATT
1 TTTTCATTGCGATATT
2618404 TTTTCATTGTCGATATT
1 TTTTCATTG-CGATATT
2618421 T
1 T
2618422 AATTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTTCATTGCGATATT
Found at i:2621738 original size:7 final size:7
Alignment explanation
Indices: 2621723--2621752 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2621713 TATGATATAA
*
2621723 AATATAT
1 AATACAT
2621730 AATACAT
1 AATACAT
2621737 AATACAT
1 AATACAT
2621744 AATACAT
1 AATACAT
2621751 AA
1 AA
2621753 AAGAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACAT
Found at i:2622354 original size:3 final size:3
Alignment explanation
Indices: 2622346--2622375 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2622336 CCATGAATAA
*
2622346 GAT GAT GAT GAT GAC GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2622376 CATCTCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:2632937 original size:948 final size:948
Alignment explanation
Indices: 2631104--2633004 Score: 3802
Period size: 948 Copynumber: 2.0 Consensus size: 948
2631094 ACATTAAAGC
2631104 AAATTAAAATGTTTGGTCCACATTCTTCAACACTATCGCATAAATAGAAAGATAATGCGCTTCAT
1 AAATTAAAATGTTTGGTCCACATTCTTCAACACTATCGCATAAATAGAAAGATAATGCGCTTCAT
2631169 TATATTTTTTTTATACAATGCTTAAAAATTTCAACACATTCTAGGTAGATCCCATGCATATCAAC
66 TATATTTTTTTTATACAATGCTTAAAAATTTCAACACATTCTAGGTAGATCCCATGCATATCAAC
2631234 ACATATCTTACTCTAGATTTAACACGTATTTATGCGATCTTATACGCGATCTCACGTGTGACTTC
131 ACATATCTTACTCTAGATTTAACACGTATTTATGCGATCTTATACGCGATCTCACGTGTGACTTC
2631299 GTAAGAGAATATAGGTACTCCTCCTGCGAACATCTATTATCATGCAAACTCAATCTACGAGCTCA
196 GTAAGAGAATATAGGTACTCCTCCTGCGAACATCTATTATCATGCAAACTCAATCTACGAGCTCA
2631364 ATAGGATTCTCTCTCACACTTTGACGATTCAAATGCCCAATGGTGGGAGAGCAATCAGCTGTATT
261 ATAGGATTCTCTCTCACACTTTGACGATTCAAATGCCCAATGGTGGGAGAGCAATCAGCTGTATT
2631429 TTTTCCTATGCACATGGTCTAATGTGTGTTGTGCGATAAAATATAAAACGTAATCGGTAAGTTCT
326 TTTTCCTATGCACATGGTCTAATGTGTGTTGTGCGATAAAATATAAAACGTAATCGGTAAGTTCT
2631494 GTTTATGTTACTTTTATCCCCACAAAAGCAGGTTCCGAAAAGAATCACTTTATAACTTCTTTTTG
391 GTTTATGTTACTTTTATCCCCACAAAAGCAGGTTCCGAAAAGAATCACTTTATAACTTCTTTTTG
2631559 AACTAGATGAGAGAGAAATTGTTATGATATTTGTCATCATCGACCCAAAATCCGAATAGGTTTGG
456 AACTAGATGAGAGAGAAATTGTTATGATATTTGTCATCATCGACCCAAAATCCGAATAGGTTTGG
2631624 ATTGGATCCCATTGAGCTCGTAGACCGAGCTAACATGATAATGGGTGTTCGCAAGAGGGTTATTT
521 ATTGGATCCCATTGAGCTCGTAGACCGAGCTAACATGATAATGGGTGTTCGCAAGAGGGTTATTT
2631689 ATATTCTCTTGCGAAGTCACACGTGAGATTGCGTATAGAACTGCATAAATACGTGTTAAATTTAG
586 ATATTCTCTTGCGAAGTCACACGTGAGATTGCGTATAGAACTGCATAAATACGTGTTAAATTTAG
2631754 AGTAAGATACGTGCTGATATGCATGGAACCTACTTAATATATCATATAAATAGACAAATATCACT
651 AGTAAGATACGTGCTGATATGCATGGAACCTACTTAATATATCATATAAATAGACAAATATCACT
2631819 ATCTAAAGAAGAATAGAGAAAAATATTCAACAAAACGAAATAAAATATATTATACGAATGAAAAT
716 ATCTAAAGAAGAATAGAGAAAAATATTCAACAAAACGAAATAAAATATATTATACGAATGAAAAT
2631884 ATATATAAAAAAATGAAGTAATTTATACATAGATATCGTGTGGTAGAAAGTGTAAGCTTTCAAAG
781 ATATATAAAAAAATGAAGTAATTTATACATAGATATCGTGTGGTAGAAAGTGTAAGCTTTCAAAG
2631949 TCAAAAGTAGGTCTTATTTATGAGATTTGAACGTAGTGTTTATACATATAAAACAACATTAATAA
846 TCAAAAGTAGGTCTTATTTATGAGATTTGAACGTAGTGTTTATACATATAAAACAACATTAATAA
2632014 TTATTTATTTTTTTAAAAAAGGAAAAAGTAAAAACCCT
911 TTATTTATTTTTTTAAAAAAGGAAAAAGTAAAAACCCT
2632052 AAATTAAAATGTTTGGTCCACATTCTTCAACACTATCGCATAAATAGAAAGATAATGCGCTTCAT
1 AAATTAAAATGTTTGGTCCACATTCTTCAACACTATCGCATAAATAGAAAGATAATGCGCTTCAT
2632117 TATATTTTTTTTATACAATGCTTAAAAATTTCAACACATTCTAGGTAGATCCCATGCATATCAAC
66 TATATTTTTTTTATACAATGCTTAAAAATTTCAACACATTCTAGGTAGATCCCATGCATATCAAC
2632182 ACATATCTTACTCTAGATTTAACACGTATTTATGCGATCTTATACGCGATCTCACGTGTGACTTC
131 ACATATCTTACTCTAGATTTAACACGTATTTATGCGATCTTATACGCGATCTCACGTGTGACTTC
2632247 GTAAGAGAATATAGGTACTCCTCCTGCGAACATCTATTATCATGCAAACTCAATCTACGAGCTCA
196 GTAAGAGAATATAGGTACTCCTCCTGCGAACATCTATTATCATGCAAACTCAATCTACGAGCTCA
2632312 ATAGGATTCTCTCTCACACTTTGACGATTCAAATGCCCAATGGTGGGAGAGCAATCAGCTGTATT
261 ATAGGATTCTCTCTCACACTTTGACGATTCAAATGCCCAATGGTGGGAGAGCAATCAGCTGTATT
2632377 TTTTCCTATGCACATGGTCTAATGTGTGTTGTGCGATAAAATATAAAACGTAATCGGTAAGTTCT
326 TTTTCCTATGCACATGGTCTAATGTGTGTTGTGCGATAAAATATAAAACGTAATCGGTAAGTTCT
2632442 GTTTATGTTACTTTTATCCCCACAAAAGCAGGTTCCGAAAAGAATCACTTTATAACTTCTTTTTG
391 GTTTATGTTACTTTTATCCCCACAAAAGCAGGTTCCGAAAAGAATCACTTTATAACTTCTTTTTG
2632507 AACTAGATGAGAGAGAAATTGTTATGATATTTGTCATCATCGACCCAAAATCCGAATAGGTTTGG
456 AACTAGATGAGAGAGAAATTGTTATGATATTTGTCATCATCGACCCAAAATCCGAATAGGTTTGG
2632572 ATTGGATCCCATTGAGCTCGTAGACCGAGCTAACATGATAATGGGTGTTCGCAAGAGGGTTATTT
521 ATTGGATCCCATTGAGCTCGTAGACCGAGCTAACATGATAATGGGTGTTCGCAAGAGGGTTATTT
2632637 ATATTCTCTTGCGAAGTCACACGTGAGATTGCGTATAGAACTGCATAAATACGTGTTAAATTTAG
586 ATATTCTCTTGCGAAGTCACACGTGAGATTGCGTATAGAACTGCATAAATACGTGTTAAATTTAG
2632702 AGTAAGATACGTGCTGATATGCATGGAACCTACTTAATATATCATATAAATAGACAAATATCACT
651 AGTAAGATACGTGCTGATATGCATGGAACCTACTTAATATATCATATAAATAGACAAATATCACT
2632767 ATCTAAAGAAGAATAGAGAAAAATATTCAACAAAACGAAATAAAATATATTATACGAATGAAAAT
716 ATCTAAAGAAGAATAGAGAAAAATATTCAACAAAACGAAATAAAATATATTATACGAATGAAAAT
2632832 ATATATAAAAAAATGAAGTAATTTATACATAGATATCGTGTGGTAGAAAGTGTAAGCTTTCAAAG
781 ATATATAAAAAAATGAAGTAATTTATACATAGATATCGTGTGGTAGAAAGTGTAAGCTTTCAAAG
2632897 TCAAAAGTAGGTCTTATTTATGAGATTTGAACGTAGTGTTTATACATATAAAACAACATTAATAA
846 TCAAAAGTAGGTCTTATTTATGAGATTTGAACGTAGTGTTTATACATATAAAACAACATTAATAA
2632962 TTATTTATTTTTTTAAAAAAGGAAAAAGTAAAAACCCT
911 TTATTTATTTTTTTAAAAAAGGAAAAAGTAAAAACCCT
2633000 AAATT
1 AAATT
2633005 CACGGAGACA
Statistics
Matches: 953, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
948 953 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (948 bp):
AAATTAAAATGTTTGGTCCACATTCTTCAACACTATCGCATAAATAGAAAGATAATGCGCTTCAT
TATATTTTTTTTATACAATGCTTAAAAATTTCAACACATTCTAGGTAGATCCCATGCATATCAAC
ACATATCTTACTCTAGATTTAACACGTATTTATGCGATCTTATACGCGATCTCACGTGTGACTTC
GTAAGAGAATATAGGTACTCCTCCTGCGAACATCTATTATCATGCAAACTCAATCTACGAGCTCA
ATAGGATTCTCTCTCACACTTTGACGATTCAAATGCCCAATGGTGGGAGAGCAATCAGCTGTATT
TTTTCCTATGCACATGGTCTAATGTGTGTTGTGCGATAAAATATAAAACGTAATCGGTAAGTTCT
GTTTATGTTACTTTTATCCCCACAAAAGCAGGTTCCGAAAAGAATCACTTTATAACTTCTTTTTG
AACTAGATGAGAGAGAAATTGTTATGATATTTGTCATCATCGACCCAAAATCCGAATAGGTTTGG
ATTGGATCCCATTGAGCTCGTAGACCGAGCTAACATGATAATGGGTGTTCGCAAGAGGGTTATTT
ATATTCTCTTGCGAAGTCACACGTGAGATTGCGTATAGAACTGCATAAATACGTGTTAAATTTAG
AGTAAGATACGTGCTGATATGCATGGAACCTACTTAATATATCATATAAATAGACAAATATCACT
ATCTAAAGAAGAATAGAGAAAAATATTCAACAAAACGAAATAAAATATATTATACGAATGAAAAT
ATATATAAAAAAATGAAGTAATTTATACATAGATATCGTGTGGTAGAAAGTGTAAGCTTTCAAAG
TCAAAAGTAGGTCTTATTTATGAGATTTGAACGTAGTGTTTATACATATAAAACAACATTAATAA
TTATTTATTTTTTTAAAAAAGGAAAAAGTAAAAACCCT
Found at i:2634417 original size:14 final size:14
Alignment explanation
Indices: 2634386--2634419 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2634376 CACGTGTTTC
*
2634386 TTTTTTTTTTAATA
1 TTTTATTTTTAATA
2634400 -TTTATTTTTAATA
1 TTTTATTTTTAATA
2634413 TTTTATT
1 TTTTATT
2634420 ATACCCCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTAATA
Found at i:2657305 original size:25 final size:26
Alignment explanation
Indices: 2657268--2657324 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
2657258 TAAAAATATA
*
2657268 AAAATTATGAAAAA-TAAAA-AATCTTT
1 AAAATTAT-AAAAACAAAAATAAT-TTT
2657294 AAAATT-TAAAAACAAAAATAATTTT
1 AAAATTATAAAAACAAAAATAATTTT
2657319 AAAATT
1 AAAATT
2657325 CATTTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.18
25 14 0.50
26 9 0.32
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATTATAAAAACAAAAATAATTTT
Found at i:2658326 original size:59 final size:58
Alignment explanation
Indices: 2658239--2658364 Score: 137
Period size: 59 Copynumber: 2.2 Consensus size: 58
2658229 AGGGATTAAC
* * *
2658239 TTGAAAAATAAAAGTTAAAGTCCCAATATAGGAACAATTGTCAAGTTAAAGGTTTGAT
1 TTGAAAAAAAAAAGTTAAAGTCCCAATATAGGAACAATTGTCAAGTTAAAGGTCTAAT
* * * * * * *
2658297 TTGAAAAAAAAAATGTTCAA-TCCACAATATCGGAATACTTGTGAAGTTCAGGGTCTAAT
1 TTGAAAAAAAAAA-GTTAAAGTCC-CAATATAGGAACAATTGTCAAGTTAAAGGTCTAAT
2658356 TTGAAAAAA
1 TTGAAAAAA
2658365 GATATTTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
58 15 0.27
59 41 0.73
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (58 bp):
TTGAAAAAAAAAAGTTAAAGTCCCAATATAGGAACAATTGTCAAGTTAAAGGTCTAAT
Found at i:2660709 original size:13 final size:13
Alignment explanation
Indices: 2660693--2660717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2660683 TGAAAAGAAA
2660693 AAAGGAAAGGAAG
1 AAAGGAAAGGAAG
2660706 AAAGGAAAGGAA
1 AAAGGAAAGGAA
2660718 AGGAAAAAGG
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):
AAAGGAAAGGAAG
Found at i:2660716 original size:18 final size:17
Alignment explanation
Indices: 2660693--2660727 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2660683 TGAAAAGAAA
2660693 AAAGGAAAGGAAGAAAGG
1 AAAGGAAAGGAA-AAAGG
2660711 AAAGGAAAGGAAAAAGG
1 AAAGGAAAGGAAAAAGG
2660728 GACAGGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
AAAGGAAAGGAAAAAGG
Found at i:2667055 original size:21 final size:21
Alignment explanation
Indices: 2667031--2667072 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2667021 ATTAATTTTT
2667031 TAAACATA-AAAAAATTGAAAA
1 TAAA-ATATAAAAAATTGAAAA
* *
2667052 TAAAATATTAAAAATTTAAAA
1 TAAAATATAAAAAATTGAAAA
2667073 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAATATAAAAAATTGAAAA
Found at i:2667065 original size:9 final size:9
Alignment explanation
Indices: 2667053--2667094 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 9
2667043 AATTGAAAAT
2667053 AAAATATTA
1 AAAATATTA
2667062 AAAAT-TTA
1 AAAATATTA
2667070 AAAATATT-
1 AAAATATTA
2667078 AAAATA-TA
1 AAAATATTA
2667086 AATAATATT
1 AA-AATATT
2667095 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 1 0.03
8 16 0.55
9 11 0.38
10 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATTA
Found at i:2667075 original size:17 final size:16
Alignment explanation
Indices: 2667036--2667094 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
2667026 TTTTTTAAAC
* *
2667036 ATAAAAAAATTGAAA-
1 ATAAAAATATTAAAAT
2667051 AT-AAAATATTAAAAAT
1 ATAAAAATATT-AAAAT
*
2667067 TTAAAAATATTAAAAT
1 ATAAAAATATTAAAAT
2667083 ATAAATAATATT
1 ATAAA-AATATT
2667095 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 10 0.28
17 14 0.39
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAAAAATATTAAAAT
Found at i:2667785 original size:2 final size:2
Alignment explanation
Indices: 2667778--2667802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2667768 AAACCCTCTT
2667778 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2667803 GAAGTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2668290 original size:26 final size:26
Alignment explanation
Indices: 2668259--2668332 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
2668249 TGTTTTTTTA
2668259 AATTTGGTATCTAGATTTTTTGACAC-
1 AATTTGGTATCTAGATTTTTTGAC-CT
* * *
2668285 AATTTGGTACCTTGATATTTTT-TCCT
1 AATTTGGTATCTAGAT-TTTTTGACCT
* *
2668311 AATTTGGTGTCTAAATTTTTTG
1 AATTTGGTATCTAGATTTTTTG
2668333 GGCCTAAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
25 6 0.16
26 27 0.71
27 5 0.13
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (26 bp):
AATTTGGTATCTAGATTTTTTGACCT
Found at i:2668783 original size:33 final size:32
Alignment explanation
Indices: 2668711--2668791 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
2668701 AAACGTTTGA
*
2668711 CAAGTTCAAGAACCAAA-TA-AAAAAAAAAAG
1 CAAGTTCAAGTACCAAATTAGAAAAAAAAAAG
*
2668741 --A-TT-AGGTACCAAATTAGAAAAAAAAAAG
1 CAAGTTCAAGTACCAAATTAGAAAAAAAAAAG
2668769 TCAAGTTCAAGTACCAAATTAGA
1 -CAAGTTCAAGTACCAAATTAGA
2668792 CCCCAAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
26 8 0.20
27 4 0.10
28 12 0.29
31 1 0.02
32 2 0.05
33 14 0.34
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (32 bp):
CAAGTTCAAGTACCAAATTAGAAAAAAAAAAG
Found at i:2669747 original size:2 final size:2
Alignment explanation
Indices: 2669740--2669789 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
2669730 CATAGCTTGA
2669740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
2669783 AC AT AT A
1 AT AT AT A
2669790 CTCTGTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2675181 original size:60 final size:60
Alignment explanation
Indices: 2675065--2675186 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 60
2675055 GGTCTGATGG
* **
2675065 TAAGAGTATTCATTATCTTATGTGTGACCTGAGTTCAAACCACACTAATCGTATTATTAT
1 TAAGAGTATTCATTATCTTATGTGTGACCTGAGTTCAAACAACACTAATCACATTATTAT
* *
2675125 TAAGAGTATTCATTATCTTATGTGTGACCTGAGTTCAAACAACATTAATTACATTATTAT
1 TAAGAGTATTCATTATCTTATGTGTGACCTGAGTTCAAACAACACTAATCACATTATTAT
2675185 TA
1 TA
2675187 GAACTTTGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (60 bp):
TAAGAGTATTCATTATCTTATGTGTGACCTGAGTTCAAACAACACTAATCACATTATTAT
Found at i:2677337 original size:16 final size:16
Alignment explanation
Indices: 2677316--2677346 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2677306 AACAATGGGA
*
2677316 ATTTTCAATCAATCAT
1 ATTTTCAACCAATCAT
2677332 ATTTTCAACCAATCA
1 ATTTTCAACCAATCA
2677347 AAAAGCACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTTCAACCAATCAT
Found at i:2678124 original size:27 final size:27
Alignment explanation
Indices: 2678073--2678124 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2678063 CAGTTTAATT
** **
2678073 ATTTAGGTATCAATTTTGATCAAAAAA
1 ATTTAGGTATCAATTTAAAAAAAAAAA
2678100 ATTTAGGTATCAATTTAAAAAAAAA
1 ATTTAGGTATCAATTTAAAAAAAAA
2678125 TAGTATAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (27 bp):
ATTTAGGTATCAATTTAAAAAAAAAAA
Found at i:2685957 original size:3 final size:3
Alignment explanation
Indices: 2685935--2685975 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
2685925 CCCCTTACAA
2685935 AAT AA- AAT AA- AAT GAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
2685976 CAAATATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2687914 original size:21 final size:21
Alignment explanation
Indices: 2687874--2687923 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2687864 TTTATTTTTC
* * * *
2687874 ATATAATATAAATTACAAAAT
1 ATATAAAATAAAATAAAAAAA
2687895 ATATAAAATAAAATAAAAAAA
1 ATATAAAATAAAATAAAAAAA
2687916 AT-TAAAAT
1 ATATAAAAT
2687924 GTCAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAAAATAAAATAAAAAAA
Found at i:2692673 original size:22 final size:22
Alignment explanation
Indices: 2692644--2692688 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
2692634 TTTTATTTTC
2692644 TCTCTTAAAT-TTTTT-GAAAAT
1 TCTCTT-AATCTTTTTAGAAAAT
2692665 TCTCATTAATCTTTTTAGAAAAT
1 TCTC-TTAATCTTTTTAGAAAAT
2692688 T
1 T
2692689 TTAATTAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
TCTCTTAATCTTTTTAGAAAAT
Found at i:2696161 original size:31 final size:30
Alignment explanation
Indices: 2696096--2696167 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
2696086 ATTACGTGTA
*
2696096 ACAAAACAGTCACTCAACTTTGAAAATGTG
1 ACAAAACAGTCACTAAACTTTGAAAATGTG
* *
2696126 ACAAAACAGTCATTAAAGTTATCGAAAA-GTG
1 ACAAAACAGTCACTAAACTT-T-GAAAATGTG
*
2696157 ACAAAATAGTC
1 ACAAAACAGTC
2696168 TTCTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.47
31 14 0.39
32 5 0.14
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (30 bp):
ACAAAACAGTCACTAAACTTTGAAAATGTG
Found at i:2697530 original size:30 final size:31
Alignment explanation
Indices: 2697466--2697537 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
2697456 ACAACAAGAG
* * * *
2697466 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACATTTCCATAACTTGAGT
*
2697497 GACTGTTTTGTCACATTTCCA-AAGTTGAGT
1 GACTGTTTTGTCACATTTCCATAACTTGAGT
2697527 GACTGTTTTGT
1 GACTGTTTTGT
2697538 TAAATGTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (31 bp):
GACTGTTTTGTCACATTTCCATAACTTGAGT
Found at i:2703141 original size:20 final size:20
Alignment explanation
Indices: 2703112--2703151 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2703102 TAAATAATAG
2703112 AATTTGTTAACTCGACTCGA
1 AATTTGTTAACTCGACTCGA
* *
2703132 AATTTTTTAACTCGATTCGA
1 AATTTGTTAACTCGACTCGA
2703152 TTCGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
AATTTGTTAACTCGACTCGA
Found at i:2705054 original size:31 final size:31
Alignment explanation
Indices: 2705011--2705076 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2705001 GCATAGTTGA
*
2705011 TTGCTTTTGGATGTTCTTACTTTCATTGTTT
1 TTGCTTTGGGATGTTCTTACTTTCATTGTTT
*
2705042 TTGCTTTGGGATGTTCTTATTTTCATTGTTT
1 TTGCTTTGGGATGTTCTTACTTTCATTGTTT
2705073 TTGC
1 TTGC
2705077 ATGTTTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.09, C:0.12, G:0.18, T:0.61
Consensus pattern (31 bp):
TTGCTTTGGGATGTTCTTACTTTCATTGTTT
Found at i:2706234 original size:11 final size:11
Alignment explanation
Indices: 2706218--2706242 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2706208 ACTTATTTTC
2706218 CAATCTTTTAT
1 CAATCTTTTAT
2706229 CAATCTTTTAT
1 CAATCTTTTAT
2706240 CAA
1 CAA
2706243 ATATTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (11 bp):
CAATCTTTTAT
Found at i:2707032 original size:16 final size:17
Alignment explanation
Indices: 2707013--2707051 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2707003 GAGATTCGAG
*
2707013 ATTTTTAAGTT-TTTTT
1 ATTTTTAAGTTCTTTTA
*
2707029 ATTTTTATGTTCTTTTA
1 ATTTTTAAGTTCTTTTA
2707046 ATTTTT
1 ATTTTT
2707052 TTTCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (17 bp):
ATTTTTAAGTTCTTTTA
Found at i:2707584 original size:22 final size:22
Alignment explanation
Indices: 2707559--2707600 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2707549 CTAATTTATC
2707559 TTCCAATTTCT-TCGTTGTCTTG
1 TTCCAATTTCTGTC-TTGTCTTG
*
2707581 TTCCATTTTCTGTCTTGTCT
1 TTCCAATTTCTGTCTTGTCT
2707601 CCTACGAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.07, C:0.24, G:0.12, T:0.57
Consensus pattern (22 bp):
TTCCAATTTCTGTCTTGTCTTG
Found at i:2712293 original size:25 final size:25
Alignment explanation
Indices: 2712264--2712311 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
2712254 ATTGAATATT
*
2712264 AATTC-AATTAAAAATTAACTAAAAA
1 AATTCTAATTAAAAAGTAA-TAAAAA
*
2712289 AATTCTATTTAAAAAGTAATAAA
1 AATTCTAATTAAAAAGTAATAAA
2712312 TATTATTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (25 bp):
AATTCTAATTAAAAAGTAATAAAAA
Found at i:2727476 original size:67 final size:71
Alignment explanation
Indices: 2727333--2727477 Score: 192
Period size: 71 Copynumber: 2.1 Consensus size: 71
2727323 TTATATTTTT
* * **
2727333 ATAAATATAAAATAATATTTATTTTATTTTATTATTTATTTATTTATTATTTGTTGTATGAATAT
1 ATAAATATAAAATAATACTAATTTTATTTTATTATTTATTTATTTATTATTTGTAATATGAATAT
2727398 AAATAA
66 AAATAA
* *
2727404 ATAAATGTAAAATAATACTAATTTTGTTTTATTATTTATTTA-TTATT-TTATG-AATAT-AA-A
1 ATAAATATAAAATAATACTAATTTTATTTTATTATTTATTTATTTATTATT-TGTAATATGAATA
2727464 TAAATAA
65 TAAATAA
2727471 ATAAATA
1 ATAAATA
2727478 ACCAAAATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
67 14 0.21
68 2 0.03
69 5 0.08
70 7 0.11
71 38 0.58
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (71 bp):
ATAAATATAAAATAATACTAATTTTATTTTATTATTTATTTATTTATTATTTGTAATATGAATAT
AAATAA
Found at i:2730284 original size:31 final size:30
Alignment explanation
Indices: 2730241--2730317 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
2730231 CATTTATTCT
2730241 TTTTTTTAAAAATTAAATC-CTTCTATTTTTA
1 TTTTTTT-AAAATTAAA-CACTTCTATTTTTA
*
2730272 TTTTTGTTAAAATTAAACACTTTTATTTTTA
1 TTTTT-TTAAAATTAAACACTTCTATTTTTA
2730303 TTTCTTTTAAAATTA
1 TTT-TTTTAAAATTA
2730318 CCCTTTAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
30 1 0.02
31 37 0.88
32 4 0.10
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTTTTTAAAATTAAACACTTCTATTTTTA
Found at i:2731750 original size:53 final size:53
Alignment explanation
Indices: 2731687--2731788 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
2731677 TACTCACACC
* *
2731687 CATGTGTCAGCCCATGT-T-CCCCAAAACAATATACACATACCCTGACACACGCT
1 CATGTGTCAG-CC-TGTATGCCCCAAAACAATATACACACACACTGACACACGCT
* *
2731740 CATGTGTCAGCCTGTATGCCCCAGAACAGTATACACACACACTGACACA
1 CATGTGTCAGCCTGTATGCCCCAAAACAATATACACACACACTGACACA
2731789 TGCCCATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 3 0.07
52 3 0.07
53 37 0.86
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (53 bp):
CATGTGTCAGCCTGTATGCCCCAAAACAATATACACACACACTGACACACGCT
Found at i:2735537 original size:43 final size:44
Alignment explanation
Indices: 2735451--2735539 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
2735441 TTTGAAATAA
* * *
2735451 AATAGAAATTATGATAATTATACATTTAAAAATAATTATAACTT
1 AATAGAAATTATGATAATTACACATTTAAAAACAATTAAAACTT
* * *
2735495 AATAGAAGTTATGATAA-TCCACCTTTAAAAACAATTAAAACTT
1 AATAGAAATTATGATAATTACACATTTAAAAACAATTAAAACTT
2735538 AA
1 AA
2735540 ATTATAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 23 0.59
44 16 0.41
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.34
Consensus pattern (44 bp):
AATAGAAATTATGATAATTACACATTTAAAAACAATTAAAACTT
Found at i:2735946 original size:29 final size:29
Alignment explanation
Indices: 2735904--2735965 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
2735894 ATAAGATATC
2735904 ATTTGTTATATATAACAT-ATCAACAAATA
1 ATTTGTTATATAT-ACATCATCAACAAATA
*
2735933 ATTTGTTATATATACCTCATCAACAAATA
1 ATTTGTTATATATACATCATCAACAAATA
2735962 ATTT
1 ATTT
2735966 AAAAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTTGTTATATATACATCATCAACAAATA
Found at i:2735974 original size:12 final size:12
Alignment explanation
Indices: 2735957--2735995 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2735947 CCTCATCAAC
2735957 AAATAATTTAAA
1 AAATAATTTAAA
*
2735969 AAATAATTCATAA
1 AAATAATTTA-AA
2735982 AAAT-ATTTAAA
1 AAATAATTTAAA
2735993 AAA
1 AAA
2735996 AAAAAGCAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 13 0.54
13 6 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAATTTAAA
Found at i:2736927 original size:20 final size:21
Alignment explanation
Indices: 2736880--2736928 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2736870 TTAATTTTTA
2736880 TTATATTTGAAACATATAAAT
1 TTATATTTGAAACATATAAAT
*
2736901 TTA-ATTTGATAA-ATAT-TAT
1 TTATATTTGA-AACATATAAAT
2736920 TTATATTTG
1 TTATATTTG
2736929 TCCTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.20
20 15 0.60
21 5 0.20
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (21 bp):
TTATATTTGAAACATATAAAT
Found at i:2737430 original size:20 final size:20
Alignment explanation
Indices: 2737405--2737443 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2737395 AGTTAGAAGG
*
2737405 AAATTTCCTGATAATAGAAC
1 AAATTTCCAGATAATAGAAC
2737425 AAATTTCCAGATAATAGAA
1 AAATTTCCAGATAATAGAA
2737444 AAAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
AAATTTCCAGATAATAGAAC
Found at i:2740971 original size:24 final size:26
Alignment explanation
Indices: 2740948--2740994 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2740938 AGTTTTAACA
2740948 ACAATA-ATAAT-AG-AAAAAAGAAC
1 ACAATACATAATAAGTAAAAAAGAAC
*
2740971 ACGATACATAATAAGTAAAAAAGA
1 ACAATACATAATAAGTAAAAAAGA
2740995 TATGAACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 5 0.25
25 2 0.10
26 8 0.40
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.15
Consensus pattern (26 bp):
ACAATACATAATAAGTAAAAAAGAAC
Found at i:2743907 original size:174 final size:174
Alignment explanation
Indices: 2743545--2744069 Score: 865
Period size: 174 Copynumber: 3.0 Consensus size: 174
2743535 ACATTACTGG
* * *
2743545 CACTTCTTTGTCTTCTTCGTCTCTTGAATTTTGGTTATGGCATTGACGTCTTGTTCATCCTTTAA
1 CACTTCTTTATCTTCTCCGTCTCTTGAATTTTGGTTATGGCATTGACGTCTTGTTCATCCTTCAA
* *
2743610 TCGAA-GTGCAAAATAAAGTCATGAAGCACTGCAACAAATCT-ATTTTGTACGTCAACACATCCC
66 TC-AAGGTGCAAAATAAAGTCATGAAGCAGTGCAACAAATCTCAATTTGTACGTCAACACATCCC
* *
2743673 TTTGTGTGAAGCATGTTGTATGGGGAAGAGTAATCGTCTACCATT
130 TTTGTGTGAAGCATGTTGCATGGGGAAGAGTCATCGTCTACCATT
* *
2743718 CACTTCTTTATCTTCTCCGTCTCTTGAATTTTGGTTATGACATTGACATCTTGTTCATCCTTCAA
1 CACTTCTTTATCTTCTCCGTCTCTTGAATTTTGGTTATGGCATTGACGTCTTGTTCATCCTTCAA
*
2743783 TCAAGGTGCAAAATAAAGTCATGAAGCAGTGCAACAAATCTCAATTTGTACATCAACACATCCCT
66 TCAAGGTGCAAAATAAAGTCATGAAGCAGTGCAACAAATCTCAATTTGTACGTCAACACATCCCT
2743848 TTGTGTGAAGCATGTTGCATGGGGAAGAGTCATCGTCTACCATT
131 TTGTGTGAAGCATGTTGCATGGGGAAGAGTCATCGTCTACCATT
*
2743892 CACTTCTTTATCTTCTCCATCTCTTGAATTTTGGTTATGGCATTGACGTCTTGTTCATCCTTCAA
1 CACTTCTTTATCTTCTCCGTCTCTTGAATTTTGGTTATGGCATTGACGTCTTGTTCATCCTTCAA
* * * *
2743957 TCGAGATGCAAAATAAAGTCATGAAGCAGTGCAAAAAATCTCAATTTGTACGTCAACACATCCTT
66 TCAAGGTGCAAAATAAAGTCATGAAGCAGTGCAACAAATCTCAATTTGTACGTCAACACATCCCT
* * *
2744022 TTATGTGAAGCATGTTGCATGGGAAAGAGTCATCATCTACCATT
131 TTGTGTGAAGCATGTTGCATGGGGAAGAGTCATCGTCTACCATT
2744066 CACT
1 CACT
2744070 AGTTCTACTA
Statistics
Matches: 329, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
172 2 0.01
173 97 0.29
174 230 0.70
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (174 bp):
CACTTCTTTATCTTCTCCGTCTCTTGAATTTTGGTTATGGCATTGACGTCTTGTTCATCCTTCAA
TCAAGGTGCAAAATAAAGTCATGAAGCAGTGCAACAAATCTCAATTTGTACGTCAACACATCCCT
TTGTGTGAAGCATGTTGCATGGGGAAGAGTCATCGTCTACCATT
Found at i:2748990 original size:4 final size:4
Alignment explanation
Indices: 2748983--2749032 Score: 73
Period size: 4 Copynumber: 12.2 Consensus size: 4
2748973 AAATAAACGG
* *
2748983 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
2749032 G
1 G
2749033 GTAATGTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 39 0.91
5 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2751938 original size:28 final size:28
Alignment explanation
Indices: 2751905--2751987 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 28
2751895 TCATGTATAT
*
2751905 GATTTAGAGTTTAAGGTTTCAATTTTAG
1 GATTTAGAGTTTAAGGTTTCAAGTTTAG
* * * * *
2751933 GGTTTACAGTTTATGATTCCAAGTTTAG
1 GATTTAGAGTTTAAGGTTTCAAGTTTAG
* *
2751961 GATTTAGGGTTT-AGGTTTTAAGATTTA
1 GATTTAGAGTTTAAGGTTTCAAG-TTTA
2751988 ATGTTATGAA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
27 6 0.15
28 35 0.85
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.46
Consensus pattern (28 bp):
GATTTAGAGTTTAAGGTTTCAAGTTTAG
Found at i:2754694 original size:23 final size:23
Alignment explanation
Indices: 2754668--2754742 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
2754658 TTAAGGAACA
2754668 CTCTCTGTTTAGCATTGTGTGTG
1 CTCTCTGTTTAGCATTGTGTGTG
* *
2754691 CTCTCTGTTTAGCA-CGTCTCGTG
1 CTCTCTGTTTAGCATTGTGT-GTG
*
2754714 CTCTCTGATTAGCACTT-TGTGTG
1 CTCTCTGTTTAGCA-TTGTGTGTG
*
2754737 TTCTCT
1 CTCTCT
2754743 ATTGCCCAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 3 0.07
23 38 0.88
24 2 0.05
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCATTGTGTGTG
Found at i:2761069 original size:23 final size:23
Alignment explanation
Indices: 2760996--2761070 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
2760986 TTAAGGAACA
2760996 CTCTCTGTTTAGCA-TTATGTGTG
1 CTCTCTGTTTAGCACTT-TGTGTG
* *
2761019 CTCTCTGTTTAGCACGTCT-CGTG
1 CTCTCTGTTTAGCAC-TTTGTGTG
*
2761042 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTTTGTGTG
*
2761065 TTCTCT
1 CTCTCT
2761071 ATTGCCCAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.05
23 39 0.91
24 1 0.02
25 1 0.02
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTTTGTGTG
Found at i:2771311 original size:15 final size:15
Alignment explanation
Indices: 2771285--2771344 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
2771275 AATTAAATTG
2771285 TAATTTTAATAATTTA
1 TAATTTT-ATAATTTA
*
2771301 TAATTTTATAATTTT
1 TAATTTTATAATTTA
*
2771316 TAAAGTATTA-AA-TTA
1 T-AA-TTTTATAATTTA
*
2771331 AAATTTTATAATTT
1 TAATTTTATAATTT
2771345 TTAGGGGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 12 0.34
16 11 0.31
17 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TAATTTTATAATTTA
Found at i:2771364 original size:29 final size:28
Alignment explanation
Indices: 2771301--2771368 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
2771291 TAATAATTTA
* *
2771301 TAATTTTATAATTTTTAAAGTATTAAAT
1 TAATTTTATAATTTTTAAAGGATAAAAT
**
2771329 TAAAATTTTATAATTTTTAGGGGATAAAAT
1 T--AATTTTATAATTTTTAAAGGATAAAAT
2771359 GTAATTTTAT
1 -TAATTTTAT
2771369 TTTTATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 8 0.24
30 23 0.70
31 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (28 bp):
TAATTTTATAATTTTTAAAGGATAAAAT
Done.