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 55 of 120
Found at i:16204991 original size:22 final size:22
Alignment explanation
Indices: 16204966--16205013 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
16204956 AGAAATATAT
* **
16204966 AAAAATACATTAATATTTTTTA
1 AAAAATACAATAATAAATTTTA
*
16204988 AAAAATATAATAATAAATTTTA
1 AAAAATACAATAATAAATTTTA
16205010 AAAA
1 AAAA
16205014 TATGTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATACAATAATAAATTTTA
Found at i:16205008 original size:23 final size:23
Alignment explanation
Indices: 16204982--16205056 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 23
16204972 ACATTAATAT
16204982 TTTTTAAAAAATATAATAATAAA
1 TTTTTAAAAAATATAATAATAAA
*
16205005 -TTTTAAAAATATGTAAAAATAAATAAA
1 TTTTTAAAAA-A--T-ATAAT-AATAAA
*
16205032 TATTTTCACAAAATATAATAATAAA
1 T-TTTT-AAAAAATATAATAATAAA
16205057 AATAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
22 9 0.22
23 1 0.02
25 7 0.17
26 8 0.20
27 7 0.17
29 5 0.12
30 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (23 bp):
TTTTTAAAAAATATAATAATAAA
Found at i:16205045 original size:31 final size:31
Alignment explanation
Indices: 16204988--16205047 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
16204978 ATATTTTTTA
16204988 AAAAATATAATAATAAATTTTAAAAATATGT
1 AAAAATATAATAATAAATTTTAAAAATATGT
*
16205019 AAAAATA-AATAA-ATATTTTCACAAAATAT
1 AAAAATATAATAATAAATTTT-A-AAAATAT
16205048 AATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 6 0.23
31 14 0.54
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (31 bp):
AAAAATATAATAATAAATTTTAAAAATATGT
Found at i:16208456 original size:20 final size:20
Alignment explanation
Indices: 16208412--16208509 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
16208402 AAAATGATAA
* *
16208412 TAATAAAAATAAATAAAA-GT
1 TAATAAAAAT-TATAAAATTT
*
16208432 T-ATAAAAATTATTAAATTT
1 TAATAAAAATTATAAAATTT
*
16208451 TAATAAAAA-TATTTAAATTT
1 TAATAAAAATTA-TAAAATTT
* * *
16208471 TATTAAAATTTATAAAAATTG
1 TAATAAAAATTAT-AAAATTT
*
16208492 TAAAAAAAATTATAAAAT
1 TAATAAAAATTATAAAAT
16208510 ATAGAAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.08
19 12 0.19
20 29 0.46
21 17 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATAAAAATTATAAAATTT
Found at i:16208497 original size:19 final size:18
Alignment explanation
Indices: 16208474--16208586 Score: 54
Period size: 18 Copynumber: 5.9 Consensus size: 18
16208464 TAAATTTTAT
*
16208474 TAAAATTTATAAAAATTG
1 TAAAAATTATAAAAATTG
*
16208492 TAAAAAAAATTATAAAATATAG
1 T---AAAAATTATAAAA-ATTG
* *
16208514 -AAAAATT-TATAAAGTCG
1 TAAAAATTATA-AAAATTG
*
16208531 TAAGAAAATTATAAATAAATG
1 T-A-AAAATTATAAA-AATTG
*
16208552 TAAATAAATAT-AAAATTCG
1 TAAA-AATTATAAAAATT-G
16208571 T-AAAATTATAAAAATT
1 TAAAAATTATAAAAATT
16208587 ATTGTACCAA
Statistics
Matches: 72, Mismatches: 10, Indels: 26
0.67 0.09 0.24
Matches are distributed among these distances:
17 9 0.12
18 22 0.31
19 7 0.10
20 14 0.19
21 17 0.24
22 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (18 bp):
TAAAAATTATAAAAATTG
Found at i:16208498 original size:10 final size:10
Alignment explanation
Indices: 16208426--16208526 Score: 66
Period size: 10 Copynumber: 10.2 Consensus size: 10
16208416 AAAAATAAAT
*
16208426 AAAAGTTATA
1 AAAATTTATA
*
16208436 AAAA-TTATT
1 AAAATTTATA
*
16208445 AAATTTTAATA
1 AAAATTT-ATA
16208456 AAAATATT-T-
1 AAAAT-TTATA
* *
16208465 AAATTTTATT
1 AAAATTTATA
16208475 AAAATTTATA
1 AAAATTTATA
*
16208485 AAAATTGTAAA
1 AAAATT-TATA
*
16208496 AAAAATTAT-
1 AAAATTTATA
* *
16208505 AAAATATAGA
1 AAAATTTATA
16208515 AAAATTTATA
1 AAAATTTATA
16208525 AA
1 AA
16208527 GTCGTAAGAA
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
8 2 0.03
9 18 0.26
10 33 0.48
11 14 0.20
12 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAATTTATA
Found at i:16208499 original size:21 final size:19
Alignment explanation
Indices: 16208435--16208575 Score: 63
Period size: 19 Copynumber: 7.1 Consensus size: 19
16208425 TAAAAGTTAT
* *
16208435 AAAAATTATTAAATTTTAA
1 AAAAATTATAAAATTGTAA
* * *
16208454 TAAAAA-TATTTAAATTTTATT
1 -AAAAATTA-TAAAATTGTA-A
*
16208475 AAAATTTATAAAAATTGTAAA
1 AAAAATTAT-AAAATTGT-AA
*
16208496 AAAAATTATAAAA-TATAGA
1 AAAAATTATAAAATTGTA-A
* * *
16208515 AAAATTTATAAAGTCGTAA
1 AAAAATTATAAAATTGTAA
* *
16208534 GAAAATTATAAATAAATGTAA
1 AAAAATTAT-AA-AATTGTAA
*
16208555 ATAAA-TATAAAATTCGTAA
1 AAAAATTATAAAATT-GTAA
16208574 AA
1 AA
16208576 TTATAAAAAT
Statistics
Matches: 91, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
18 4 0.04
19 31 0.34
20 31 0.34
21 24 0.26
22 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (19 bp):
AAAAATTATAAAATTGTAA
Found at i:16208773 original size:9 final size:10
Alignment explanation
Indices: 16208756--16208807 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
16208746 TTTTGACTCA
16208756 TTTTATATATT
1 TTTTATA-ATT
*
16208767 TTTTATAATC
1 TTTTATAATT
*
16208777 TTTTATGA-T
1 TTTTATAATT
*
16208786 TTTTATATTT
1 TTTTATAATT
*
16208796 TTTTCTAATT
1 TTTTATAATT
16208806 TT
1 TT
16208808 AATAACATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 6 0.18
10 20 0.61
11 7 0.21
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATAATT
Found at i:16222946 original size:27 final size:27
Alignment explanation
Indices: 16222785--16222947 Score: 103
Period size: 27 Copynumber: 6.0 Consensus size: 27
16222775 TTAATCTATG
* * *
16222785 TTTGACTCGAATGAGCAATACTCTGAA
1 TTTGGCTCGAATGAGCAATATTCTGTA
* * * * * * *
16222812 CTTGACTTGAAAGAGTAATACTCTGTG
1 TTTGGCTCGAATGAGCAATATTCTGTA
* *
16222839 TCTGGCTCGAATGAGCAATATTCTGAA
1 TTTGGCTCGAATGAGCAATATTCTGTA
* * * * * * *
16222866 CTCGGCTCGAATAAGCCATTTTTTGCA
1 TTTGGCTCGAATGAGCAATATTCTGTA
* *
16222893 TCTGGCTCGAATGAGCGAA-ATTATGTA
1 TTTGGCTCGAATGAGC-AATATTCTGTA
* *
16222920 TTTGGCTCAAATGAGCTATATTCTGTA
1 TTTGGCTCGAATGAGCAATATTCTGTA
16222947 T
1 T
16222948 CTTACTCGAG
Statistics
Matches: 99, Mismatches: 35, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
26 1 0.01
27 97 0.98
28 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (27 bp):
TTTGGCTCGAATGAGCAATATTCTGTA
Found at i:16230318 original size:10 final size:10
Alignment explanation
Indices: 16230303--16230329 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16230293 GAGTGAAATA
16230303 ATATATGTAT
1 ATATATGTAT
16230313 ATATATGTAT
1 ATATATGTAT
16230323 ATATATG
1 ATATATG
16230330 ATTGGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (10 bp):
ATATATGTAT
Found at i:16232133 original size:23 final size:23
Alignment explanation
Indices: 16232107--16232151 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16232097 AATTTTGAAT
**
16232107 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
16232130 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
16232152 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:16232472 original size:57 final size:58
Alignment explanation
Indices: 16232372--16232489 Score: 193
Period size: 57 Copynumber: 2.1 Consensus size: 58
16232362 ACCCATCAAC
* *
16232372 AAACTAAACCTAAATATTTTTAAACTCAAATATAATTTCATTCTTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
* *
16232430 AAACTAAACCCAAATA-TTTTAAACCCAAATATAATTTTATTCTTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
16232487 AAA
1 AAA
16232490 TAATTCTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
57 41 0.73
58 15 0.27
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
Found at i:16233097 original size:21 final size:20
Alignment explanation
Indices: 16233073--16233121 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
16233063 TGTTGTGTTG
*
16233073 TCATTGTTTACTTGAATTTTT
1 TCATTGTTTACTTCAA-TTTT
* *
16233094 TCATTTATTTATTTCAATTTT
1 TCA-TTGTTTACTTCAATTTT
16233115 TCATTGT
1 TCATTGT
16233122 ATAGTCATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 10 0.43
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.63
Consensus pattern (20 bp):
TCATTGTTTACTTCAATTTT
Found at i:16233104 original size:22 final size:21
Alignment explanation
Indices: 16233079--16233119 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16233069 GTTGTCATTG
*
16233079 TTTACTTGAATTTTTTCATTTA
1 TTTACTTCAA-TTTTTCATTTA
*
16233101 TTTATTTCAATTTTTCATT
1 TTTACTTCAATTTTTCATT
16233120 GTATAGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTACTTCAATTTTTCATTTA
Found at i:16238331 original size:26 final size:26
Alignment explanation
Indices: 16238295--16238354 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
16238285 TATTTTCTTG
*
16238295 AAATTTTACCAAGGAAAAAATTACCA
1 AAATTTTACCAAGGAAAAAATCACCA
* *
16238321 AAATTTTACCAAGGATAAAATCATCA
1 AAATTTTACCAAGGAAAAAATCACCA
16238347 AAATTTTA
1 AAATTTTA
16238355 TGGGGAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (26 bp):
AAATTTTACCAAGGAAAAAATCACCA
Found at i:16275164 original size:3 final size:3
Alignment explanation
Indices: 16275156--16275187 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16275146 CACCTCAAAT
16275156 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16275188 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16281869 original size:71 final size:71
Alignment explanation
Indices: 16281702--16281855 Score: 247
Period size: 71 Copynumber: 2.2 Consensus size: 71
16281692 CATCCCTTGG
* * *
16281702 TTCTACCGATACAACCAAAACTTCTATCGGTAGAACAAACTACAGAGAGCAAAGAAGTTGTGGCT
1 TTCTACCGATACAACCAAGACTTCTATCGATAGAACAAACTACAGAGAGCAAAGAAGTTGTGGCC
16281767 TGGGAC
66 TGGGAC
* *
16281773 TTCTACCGATACAACCAAGACTTCTATCGATAGAACAAAC-ACTATAGAGTAAAGAAGTTGTGGC
1 TTCTACCGATACAACCAAGACTTCTATCGATAGAACAAACTAC-AGAGAGCAAAGAAGTTGTGGC
16281837 CTGGGAC
65 CTGGGAC
16281844 TTCTACCGATAC
1 TTCTACCGATAC
16281856 TTGGAAGGCT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
70 2 0.03
71 75 0.97
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (71 bp):
TTCTACCGATACAACCAAGACTTCTATCGATAGAACAAACTACAGAGAGCAAAGAAGTTGTGGCC
TGGGAC
Found at i:16283454 original size:12 final size:12
Alignment explanation
Indices: 16283439--16283468 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16283429 AGTAACCAAT
16283439 GAAGTGCCAAAG
1 GAAGTGCCAAAG
16283451 GAAGTGCCAAAG
1 GAAGTGCCAAAG
*
16283463 AAAGTG
1 GAAGTG
16283469 GGAGTTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.13, G:0.33, T:0.10
Consensus pattern (12 bp):
GAAGTGCCAAAG
Found at i:16283744 original size:28 final size:29
Alignment explanation
Indices: 16283704--16283763 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
16283694 GATTGTCCAT
* *
16283704 AATTGAAGAAGAAAGGGGCATCAAAA-AA
1 AATTAAAGAAGAAAAGGGCATCAAAACAA
16283732 AATTAAAGAAGAAAAGGGCATCAAAACAA
1 AATTAAAGAAGAAAAGGGCATCAAAACAA
16283761 AAT
1 AAT
16283764 GATGGCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.60, C:0.08, G:0.20, T:0.12
Consensus pattern (29 bp):
AATTAAAGAAGAAAAGGGCATCAAAACAA
Found at i:16288158 original size:30 final size:27
Alignment explanation
Indices: 16288119--16288173 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 27
16288109 GAACTTAGAT
16288119 TTGTAATTTTATATACATATTTTTTTAAA
1 TTGTAA-TTT-TATACATATTTTTTTAAA
16288148 TTGTATATTTTATACATATTTTTTTA
1 TTGTA-ATTTTATACATATTTTTTTA
16288174 CATATATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 16 0.64
29 8 0.32
30 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (27 bp):
TTGTAATTTTATACATATTTTTTTAAA
Found at i:16288189 original size:30 final size:28
Alignment explanation
Indices: 16288130--16288191 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
16288120 TGTAATTTTA
*
16288130 TATACATATTTTTTTAAATTGTATATTT
1 TATACATATTTTTTTAAATTATATATTT
* *
16288158 TATACATATTTTTTTACATATATACTGTTT
1 TATACATATTTTTTTAAAT-TATA-TATTT
16288188 TATA
1 TATA
16288192 TATAGAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 18 0.62
29 3 0.10
30 8 0.28
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (28 bp):
TATACATATTTTTTTAAATTATATATTT
Found at i:16288237 original size:15 final size:15
Alignment explanation
Indices: 16288219--16288253 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16288209 ACATATATAC
16288219 TATATTATATTTACA
1 TATATTATATTTACA
* *
16288234 TATATTGTTTTTACA
1 TATATTATATTTACA
16288249 TATAT
1 TATAT
16288254 ATTGATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (15 bp):
TATATTATATTTACA
Found at i:16292187 original size:12 final size:11
Alignment explanation
Indices: 16292158--16292183 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16292148 CTGAGAAAAC
16292158 TTTTCTTCGCT
1 TTTTCTTCGCT
16292169 TTTTCTTCGCT
1 TTTTCTTCGCT
16292180 TTTT
1 TTTT
16292184 TCTTTAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCGCT
Found at i:16306005 original size:6 final size:6
Alignment explanation
Indices: 16305989--16306023 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16305979 TTTCTTCCCC
*
16305989 CCCTCA TCCTCA CCCTCA CCCTCA CCCTCA CCCTC
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTC
16306024 GCTTTCTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.20
Consensus pattern (6 bp):
CCCTCA
Found at i:16311100 original size:2 final size:2
Alignment explanation
Indices: 16311088--16311116 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16311078 AAGAACTATC
16311088 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16311117 ACTGCTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16311261 original size:39 final size:39
Alignment explanation
Indices: 16311216--16311294 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
16311206 TAAACTATTA
*
16311216 GTTTAAAAGTTTTAAAATTTTTAATATTAGAATTGATAT
1 GTTTAAAAGTTTTAAAATTTTTAATACTAGAATTGATAT
16311255 GTTTAAAAGTTTTAAAATTTTTAATACTAGAATTGATAT
1 GTTTAAAAGTTTTAAAATTTTTAATACTAGAATTGATAT
16311294 G
1 G
16311295 GCTTAATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (39 bp):
GTTTAAAAGTTTTAAAATTTTTAATACTAGAATTGATAT
Found at i:16311630 original size:6 final size:6
Alignment explanation
Indices: 16311619--16311669 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
16311609 TAGATTATAA
16311619 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
16311667 ATA
1 ATA
16311670 TTAATGTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:16317362 original size:3 final size:3
Alignment explanation
Indices: 16317356--16317382 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16317346 ACAACATGCT
16317356 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
16317383 ATAAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:16319040 original size:19 final size:19
Alignment explanation
Indices: 16319001--16319061 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
16318991 AAATACAAAT
*
16319001 TTTAGAATTTTTATAAA-TA
1 TTTAGAATTTTGA-AAATTA
16319020 TTTAGAATTTTGAAAATTA
1 TTTAGAATTTTGAAAATTA
**
16319039 TTTTTAATTTTTGAAAATTA
1 TTTAGAA-TTTTGAAAATTA
16319059 TTT
1 TTT
16319062 TGATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.08
19 19 0.51
20 15 0.41
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTAGAATTTTGAAAATTA
Found at i:16320564 original size:31 final size:31
Alignment explanation
Indices: 16320508--16320567 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
16320498 ATAAAATGAC
* *
16320508 CATTTAATTATTTAAAATTTTTTATTTAAGT
1 CATTGAATTATTTAAAAGTTTTTATTTAAGT
* *
16320539 CATTGAATTGTTTAGAAGTTTTTATTTAA
1 CATTGAATTATTTAAAAGTTTTTATTTAA
16320568 TTCACTAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.55
Consensus pattern (31 bp):
CATTGAATTATTTAAAAGTTTTTATTTAAGT
Found at i:16321763 original size:49 final size:49
Alignment explanation
Indices: 16321710--16321809 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
16321700 AGTTTACCCT
16321710 TAAATTTATTCTATCAATTTATATACAAGATTTTTGCCATGGAAAAAAA
1 TAAATTTATTCTATCAATTTATATACAAGATTTTTGCCATGGAAAAAAA
*
16321759 TAAATTTATTCTATCAATTTATATACAAGATTTTTGCTATGGAAAAAAA
1 TAAATTTATTCTATCAATTTATATACAAGATTTTTGCCATGGAAAAAAA
16321808 TA
1 TA
16321810 TTTATTTCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (49 bp):
TAAATTTATTCTATCAATTTATATACAAGATTTTTGCCATGGAAAAAAA
Found at i:16323965 original size:5 final size:5
Alignment explanation
Indices: 16323955--16323979 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16323945 AATCCTTAAA
16323955 ATGAG ATGAG ATGAG ATGAG ATGAG
1 ATGAG ATGAG ATGAG ATGAG ATGAG
16323980 GTTGCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
ATGAG
Found at i:16333420 original size:31 final size:31
Alignment explanation
Indices: 16333382--16333483 Score: 123
Period size: 31 Copynumber: 3.1 Consensus size: 31
16333372 AATGCACCAG
16333382 CACAAAGCCTACTAGGCACATAGCCCGAAAA
1 CACAAAGCCTACTAGGCACATAGCCCGAAAA
*
16333413 CACAAAGCCTACTAGGCACATAGCCTGAATACACCGA
1 CACAAAGCCTACTAGGCACATAGCCCG-A-A-A---A
* *
16333450 CACAAAGCCTACTAGGTACGTAGCCCGAAAA
1 CACAAAGCCTACTAGGCACATAGCCCGAAAA
16333481 CAC
1 CAC
16333484 TGGCACAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
31 30 0.49
32 1 0.02
33 1 0.02
34 2 0.03
35 1 0.02
36 1 0.02
37 25 0.41
ACGTcount: A:0.39, C:0.32, G:0.17, T:0.12
Consensus pattern (31 bp):
CACAAAGCCTACTAGGCACATAGCCCGAAAA
Found at i:16333457 original size:68 final size:68
Alignment explanation
Indices: 16333348--16333483 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 68
16333338 ACACCGGCAT
*
16333348 AAAGCCTACTAGACACATAGCCTGAATGCACCAGCACAAAGCCTACTAGGCACATAGCCCGAAAA
1 AAAGCCTACTAGACACATAGCCTGAATACACCAGCACAAAGCCTACTAGGCACATAGCCCGAAAA
16333413 CAC
66 CAC
* * *
16333416 AAAGCCTACTAGGCACATAGCCTGAATACACC-GACACAAAGCCTACTAGGTACGTAGCCCGAAA
1 AAAGCCTACTAGACACATAGCCTGAATACACCAG-CACAAAGCCTACTAGGCACATAGCCCGAAA
16333480 ACAC
65 ACAC
16333484 TGGCACAAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 1 0.02
68 62 0.98
ACGTcount: A:0.39, C:0.32, G:0.17, T:0.12
Consensus pattern (68 bp):
AAAGCCTACTAGACACATAGCCTGAATACACCAGCACAAAGCCTACTAGGCACATAGCCCGAAAA
CAC
Found at i:16333474 original size:37 final size:37
Alignment explanation
Indices: 16333302--16333501 Score: 189
Period size: 37 Copynumber: 5.6 Consensus size: 37
16333292 CTTCTTGATT
* * ***
16333302 CACCGATACAAAGCCTACTAGGCACACAATTCGAATA
1 CACCGACACAAAGCCTACTAGGCACATAGCCCGAATA
* * * * *
16333339 CACCGGCATAAAGCCTACTAGACACATAGCCTGAATG
1 CACCGACACAAAGCCTACTAGGCACATAGCCCGAATA
16333376 CACC-AGCACAAAGCCTACTAGGCACATAGCCCG-A-A
1 CACCGA-CACAAAGCCTACTAGGCACATAGCCCGAATA
*
16333411 -A---ACACAAAGCCTACTAGGCACATAGCCTGAATA
1 CACCGACACAAAGCCTACTAGGCACATAGCCCGAATA
* * *
16333444 CACCGACACAAAGCCTACTAGGTACGTAGCCCGAAAA
1 CACCGACACAAAGCCTACTAGGCACATAGCCCGAATA
* * *
16333481 CACTGGCACAAAGCCTTCTAG
1 CACCGACACAAAGCCTACTAG
16333502 TTACAAAGCC
Statistics
Matches: 133, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
31 26 0.20
32 2 0.02
33 1 0.01
34 2 0.02
36 1 0.01
37 101 0.76
ACGTcount: A:0.38, C:0.32, G:0.17, T:0.14
Consensus pattern (37 bp):
CACCGACACAAAGCCTACTAGGCACATAGCCCGAATA
Found at i:16333491 original size:105 final size:105
Alignment explanation
Indices: 16333309--16333501 Score: 244
Period size: 105 Copynumber: 1.8 Consensus size: 105
16333299 ATTCACCGAT
* * * *
16333309 ACAAAGCCTACTAGGCACACAATTCGAATACACCGGCATAAAGCCTACTAGACACATAGCCTGAA
1 ACAAAGCCTACTAGGCACACAACTCGAATACACCGACACAAAGCCTACTAGACACATAGCCCGAA
**
16333374 TGCACCAGCACAAAGCCTACTAGGCACATAGCCCGAAAAC
66 AACACCAGCACAAAGCCTACTAGGCACATAGCCCGAAAAC
* * ** *
16333414 ACAAAGCCTACTAGGCACATAGC-CTGAATACACCGACACAAAGCCTACTAGGTACGTAGCCCGA
1 ACAAAGCCTACTAGGCACACAACTC-GAATACACCGACACAAAGCCTACTAGACACATAGCCCGA
** *
16333478 AAACACTGGCACAAAGCCTTCTAG
65 AAACACCAGCACAAAGCCTACTAG
16333502 TTACAAAGCC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
104 1 0.01
105 72 0.99
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.14
Consensus pattern (105 bp):
ACAAAGCCTACTAGGCACACAACTCGAATACACCGACACAAAGCCTACTAGACACATAGCCCGAA
AACACCAGCACAAAGCCTACTAGGCACATAGCCCGAAAAC
Found at i:16347132 original size:20 final size:19
Alignment explanation
Indices: 16347092--16347133 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
16347082 CCTTTTATAA
*
16347092 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
16347111 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
16347131 TTA
1 TTA
16347134 TTACGTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Found at i:16361036 original size:21 final size:21
Alignment explanation
Indices: 16361012--16361054 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16361002 TCTGAAAACT
*
16361012 TCATACTTGT-TTCGGTAGAAC
1 TCATACATGTATT-GGTAGAAC
*
16361033 TCATGCATGTATTGGTAGAAC
1 TCATACATGTATTGGTAGAAC
16361054 T
1 T
16361055 ATAGGGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (21 bp):
TCATACATGTATTGGTAGAAC
Found at i:16361979 original size:27 final size:30
Alignment explanation
Indices: 16361940--16362014 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 30
16361930 CCACTTCTCT
*
16361940 CAGATTGGCACCTAA-AGTTTTTT-GTCC-
1 CAGATTGGTACCTAACAGTTTTTTCGTCCA
*
16361967 CAGATTGGTACCTGAACATTTTTTTCGTCCA
1 CAGATTGGTACCT-AACAGTTTTTTCGTCCA
*
16361998 CTAGTTTGGTACCTAAC
1 C-AGATTGGTACCTAAC
16362015 CCTAACATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.30
28 2 0.05
29 7 0.17
30 4 0.10
31 4 0.10
32 11 0.28
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (30 bp):
CAGATTGGTACCTAACAGTTTTTTCGTCCA
Found at i:16362917 original size:10 final size:10
Alignment explanation
Indices: 16362902--16362961 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 10
16362892 TGTATGTATG
16362902 TATGTATAAT
1 TATGTATAAT
*
16362912 TATGTAT-GT
1 TATGTATAAT
16362921 TATGTACTATTAT
1 TATGTA-TA--AT
16362934 GTATGTATAAT
1 -TATGTATAAT
*
16362945 CATGTAT-AT
1 TATGTATAAT
16362954 TATGTATA
1 TATGTATA
16362962 TATAATTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
9 15 0.38
10 14 0.35
11 2 0.05
13 3 0.08
14 6 0.15
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (10 bp):
TATGTATAAT
Found at i:16362935 original size:33 final size:34
Alignment explanation
Indices: 16362898--16363073 Score: 133
Period size: 37 Copynumber: 5.3 Consensus size: 34
16362888 TTTGTGTATG
16362898 TATGTATGTATAATTATGTATGTTATG-TACTAT
1 TATGTATGTATAATTATGTATGTTATGTTACTAT
*
16362931 TATGTATG--T-A-TA---A--TCATG-TA-TAT
1 TATGTATGTATAATTATGTATGTTATGTTACTAT
* *
16362954 TATGTATATATAATTATGTATGTTATGTTTACTGT
1 TATGTATGTATAATTATGTATGTTATG-TTACTAT
* *
16362989 TATGTTTGTATATTTGTATGTATGTTATGTTTACTAT
1 TATGTATGTATA-AT-TATGTATGTTATG-TTACTAT
* *
16363026 TATGTTTGTATATTTTTATGTATGTTATGTTTACTAT
1 TATGTATGTATA--ATTATGTATGTTATG-TTACTAT
*
16363063 TATGTTTGTAT
1 TATGTATGTAT
16363074 GACTATTTAT
Statistics
Matches: 120, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
23 10 0.08
24 6 0.05
25 1 0.01
26 2 0.02
27 2 0.02
29 2 0.02
30 2 0.02
31 1 0.01
32 4 0.03
33 8 0.07
34 2 0.02
35 12 0.10
36 1 0.01
37 64 0.53
38 3 0.03
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (34 bp):
TATGTATGTATAATTATGTATGTTATGTTACTAT
Found at i:16362994 original size:17 final size:17
Alignment explanation
Indices: 16362972--16363031 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
16362962 TATAATTATG
16362972 TATGTTATGTTTACTGT
1 TATGTTATGTTTACTGT
* *
16362989 TATGTT-TGTATATTTGTAT
1 TATGTTATGTTTA-CTG--T
*
16363008 GTATGTTATGTTTACTAT
1 -TATGTTATGTTTACTGT
16363026 TATGTT
1 TATGTT
16363032 TGTATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 5 0.15
17 14 0.42
18 1 0.03
19 1 0.03
20 7 0.21
21 5 0.15
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (17 bp):
TATGTTATGTTTACTGT
Found at i:16363001 original size:37 final size:36
Alignment explanation
Indices: 16362967--16363073 Score: 187
Period size: 37 Copynumber: 2.9 Consensus size: 36
16362957 GTATATATAA
*
16362967 TTATGTATGTTATGTTTACTGTTATGTTTGTATATT
1 TTATGTATGTTATGTTTACTATTATGTTTGTATATT
16363003 TGTATGTATGTTATGTTTACTATTATGTTTGTATATTT
1 T-TATGTATGTTATGTTTACTATTATGTTTGTATA-TT
16363041 TTATGTATGTTATGTTTACTATTATGTTTGTAT
1 TTATGTATGTTATGTTTACTATTATGTTTGTAT
16363074 GACTATTTAT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
36 1 0.01
37 64 0.94
38 3 0.04
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.61
Consensus pattern (36 bp):
TTATGTATGTTATGTTTACTATTATGTTTGTATATT
Found at i:16363007 original size:56 final size:56
Alignment explanation
Indices: 16362888--16363007 Score: 154
Period size: 56 Copynumber: 2.1 Consensus size: 56
16362878 TTCTTTACTG
* *
16362888 TTTGTGTATGTATGTATGTATAATTATGTATGTTATGTACTATTATGTATGTATAA
1 TTTGTATATGTATGTATATATAATTATGTATGTTATGTACTATTATGTATGTATAA
* * *
16362944 TCATGTATAT-TATGTATATATAATTATGTATGTTATGTTTACTGTTATGTTTGTAT-A
1 T-TTGTATATGTATGTATATATAATTATGTATGTTATG--TACTATTATGTATGTATAA
16363001 TTTGTAT
1 TTTGTAT
16363008 GTATGTTATG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
56 32 0.58
57 8 0.15
58 15 0.27
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.54
Consensus pattern (56 bp):
TTTGTATATGTATGTATATATAATTATGTATGTTATGTACTATTATGTATGTATAA
Found at i:16363009 original size:74 final size:73
Alignment explanation
Indices: 16362931--16363073 Score: 182
Period size: 74 Copynumber: 1.9 Consensus size: 73
16362921 TATGTACTAT
*
16362931 TATGTATGTATAATCATGTA-TATTATG-TATATATAATTATGTATGTTATGTTTACTGTTATGT
1 TATGTATGT-T-AT-ATGTACTATTATGTTATATATAATTATGTATGTTATGTTTACTATTATGT
16362994 TTGTATATTTG
63 TTGTATATTTG
* * * **
16363005 TATGTATGTTATGTTTACTATTATGTTTGTATATTTTTATGTATGTTATGTTTACTATTATGTTT
1 TATGTATGTTATATGTACTATTATG-TTATATATAATTATGTATGTTATGTTTACTATTATGTTT
16363070 GTAT
65 GTAT
16363074 GACTATTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 3 0.05
72 9 0.15
73 1 0.02
74 47 0.78
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (73 bp):
TATGTATGTTATATGTACTATTATGTTATATATAATTATGTATGTTATGTTTACTATTATGTTTG
TATATTTG
Found at i:16363010 original size:12 final size:13
Alignment explanation
Indices: 16362916--16363073 Score: 83
Period size: 12 Copynumber: 12.8 Consensus size: 13
16362906 TATAATTATG
16362916 TATGTTATGTACTAT
1 TATG-TATGTA-TAT
16362931 TATGTATGTATA-
1 TATGTATGTATAT
*
16362943 -AT-CATGTATAT
1 TATGTATGTATAT
16362954 TATGTA--TATAT
1 TATGTATGTATAT
* *
16362965 AAT-TATGTATGT
1 TATGTATGTATAT
*
16362977 TATGT-T-TACTGT
1 TATGTATGTA-TAT
*
16362989 TATGTTTGTATAT
1 TATGTATGTATAT
*
16363002 T-TGTATGTATGT
1 TATGTATGTATAT
16363014 TATGT-T-TACTAT
1 TATGTATGTA-TAT
*
16363026 TATGTTTGTATAT
1 TATGTATGTATAT
* *
16363039 T-TTTATGTATGT
1 TATGTATGTATAT
16363051 TATGT-T-TACTAT
1 TATGTATGTA-TAT
*
16363063 TATGTTTGTAT
1 TATGTATGTAT
16363074 GACTATTTAT
Statistics
Matches: 112, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
10 9 0.08
11 15 0.13
12 52 0.46
13 20 0.18
14 12 0.11
15 4 0.04
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (13 bp):
TATGTATGTATAT
Found at i:16363072 original size:25 final size:25
Alignment explanation
Indices: 16362970--16363074 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 25
16362960 TATATAATTA
*
16362970 TGTATGTTATGTT-TACTGTTATGTT
1 TGTATGTTATGTTGTA-TATTATGTT
* *
16362995 TGTATATT-TGTATGTATGTTATG-T
1 TGTATGTTATGT-TGTATATTATGTT
*
16363019 T-TACTATTATGTTTGTATATT-T-TT
1 TGTA-TGTTATG-TTGTATATTATGTT
16363043 ATGTATGTTATGTT-TACTATTATGTT
1 -TGTATGTTATGTTGTA-TATTATGTT
16363069 TGTATG
1 TGTATG
16363075 ACTATTTATT
Statistics
Matches: 66, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
23 4 0.06
24 17 0.26
25 38 0.58
26 7 0.11
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (25 bp):
TGTATGTTATGTTGTATATTATGTT
Found at i:16363078 original size:17 final size:17
Alignment explanation
Indices: 16363021--16363080 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 17
16363011 TGTTATGTTT
16363021 ACTATTATGTTTGTAT-
1 ACTATTATGTTTGTATG
* * *
16363037 ATTTTTATGTATGTTATG
1 ACTATTATGTTTG-TATG
16363055 TTTACTATTATGTTTGTATG
1 ---ACTATTATGTTTGTATG
16363075 ACTATT
1 ACTATT
16363081 TATTACTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
16 10 0.30
17 9 0.27
20 4 0.12
21 10 0.30
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.58
Consensus pattern (17 bp):
ACTATTATGTTTGTATG
Found at i:16367638 original size:127 final size:125
Alignment explanation
Indices: 16367410--16367658 Score: 354
Period size: 127 Copynumber: 2.0 Consensus size: 125
16367400 GGGTAATCTG
* * *
16367410 AGCTCACCAGATTGCGACACGTGGTGACGTGTGATTGCCAGCGCTGCCACATCATAAAAAATAAA
1 AGCTCACCAGATTACGACACGTAGTGACATGTGATTGCCAGCGCTGCCACATCATAAAAAATAAA
* *
16367475 CGGAGTTAGGGTCAAGAACCAAACCAGTGGACGGAAAAAAAGTTTCGGTGCCAATCTCTA
66 CGGAGTTAGAGTCAAGAACCAAACCAGTCGACGGAAAAAAAGTTTCGGTGCCAATCTCTA
* * * *
16367535 AGCTCACCAGATTATGACACGTAGTGGCATGTGATTGGCCAGCGTTGCCACATCATCAAAAATTA
1 AGCTCACCAGATTACGACACGTAGTGACATGTGATT-GCCAGCGCTGCCACATCAT-AAAAAATA
* * * * *
16367600 AACGGAGTTAGAGTCAAGTATCAAACCAGTCGATGGAAAAAAGGTTTGGGTGCCAATCT
64 AACGGAGTTAGAGTCAAGAACCAAACCAGTCGACGGAAAAAAAGTTTCGGTGCCAATCT
16367659 AGGACAAAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
125 31 0.29
126 18 0.17
127 59 0.55
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (125 bp):
AGCTCACCAGATTACGACACGTAGTGACATGTGATTGCCAGCGCTGCCACATCATAAAAAATAAA
CGGAGTTAGAGTCAAGAACCAAACCAGTCGACGGAAAAAAAGTTTCGGTGCCAATCTCTA
Found at i:16373166 original size:24 final size:24
Alignment explanation
Indices: 16373138--16373208 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
16373128 AGAAATAATC
16373138 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
16373162 TTTCAATTAAACTCTATTTTTTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
16373186 TTTGAGTCAAACTCT-TATTATTT
1 TTTCAGTTAAACTCTAT-TTATTT
16373209 TAGATTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:16374495 original size:13 final size:13
Alignment explanation
Indices: 16374477--16374502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16374467 TTTAATCAAC
16374477 ATGAACTTTTAAT
1 ATGAACTTTTAAT
16374490 ATGAACTTTTAAT
1 ATGAACTTTTAAT
16374503 CTACAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGAACTTTTAAT
Found at i:16375244 original size:31 final size:30
Alignment explanation
Indices: 16375209--16375268 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
16375199 TTTGTACATC
* * *
16375209 ATTTGGTACTTTAACTTGACATTTCTTTCTA
1 ATTTGGTACCTAAACTTGACACTT-TTTCTA
16375240 ATTTGGTACCTAAACTTGACACTTTTTCT
1 ATTTGGTACCTAAACTTGACACTTTTTCT
16375269 TCAGTTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.48
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTA
Found at i:16375277 original size:31 final size:31
Alignment explanation
Indices: 16375211--16375279 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
16375201 TGTACATCAT
* * * *
16375211 TTGGTACTTTAACTTGACATTTCTTTCTAAT
1 TTGGTACCTAAACTTGACACTTCTTTCTAAG
*
16375242 TTGGTACCTAAACTTGACACTT-TTTCTTCAG
1 TTGGTACCTAAACTTGACACTTCTTTC-TAAG
16375273 TTGGTAC
1 TTGGTAC
16375280 TTAATCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTCTTTCTAAG
Found at i:16375319 original size:60 final size:60
Alignment explanation
Indices: 16375236--16375351 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
16375226 GACATTTCTT
* * *
16375236 TCTAATTTGGTACCTAAACTTGACACTTTTTCTTCAG-TTGGTACTTAATCTTTTTTGGGG
1 TCTAATTTGGTACATAAACTTGACACTTTTTCCT-AGTTTGGTACTTAATATTTTTTGGGG
* * * * *
16375296 TCTAATTTTGTACATGAATTTGACTCTTTTTCCTAGTTTGGTTCTTAATATTTTTT
1 TCTAATTTGGTACATAAACTTGACACTTTTTCCTAGTTTGGTACTTAATATTTTTT
16375352 TTGTTCGATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.52
Consensus pattern (60 bp):
TCTAATTTGGTACATAAACTTGACACTTTTTCCTAGTTTGGTACTTAATATTTTTTGGGG
Found at i:16375860 original size:30 final size:29
Alignment explanation
Indices: 16375785--16375871 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
16375775 AAAAAATACC
16375785 AAGTTCAAGTACCAAATTGAGACAAAAAA
1 AAGTTCAAGTACCAAATTGAGACAAAAAA
* *
16375814 AAGTTTAAGTATCAAATT-AGA-AAAAGTATTA
1 AAGTTCAAGTACCAAATTGAGACAAAA--A--A
16375845 AA-TTCAAGTACCAAATTGA-ACAAAAAA
1 AAGTTCAAGTACCAAATTGAGACAAAAAA
16375872 GAATTAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 18 0.38
30 14 0.29
31 8 0.17
ACGTcount: A:0.55, C:0.10, G:0.11, T:0.23
Consensus pattern (29 bp):
AAGTTCAAGTACCAAATTGAGACAAAAAA
Found at i:16376356 original size:27 final size:27
Alignment explanation
Indices: 16376326--16376380 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
16376316 GTCCCAATTC
16376326 TAAA-AAATTCAAAAATATAAAAATACA
1 TAAATAAATTCAAAAATAT-AAAATACA
** *
16376353 TAAATATTTTCAAAAATATATAATACA
1 TAAATAAATTCAAAAATATAAAATACA
16376380 T
1 T
16376381 TGTATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAATAAATTCAAAAATATAAAATACA
Found at i:16377379 original size:29 final size:29
Alignment explanation
Indices: 16377337--16377395 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
16377327 CATCCACATC
16377337 AAACATGAACGAACCTTTTGGACACCTAT
1 AAACATGAACGAACCTTTTGGACACCTAT
*
16377366 AAACATGAACGAACCTTTTGGTCACCTAT
1 AAACATGAACGAACCTTTTGGACACCTAT
16377395 A
1 A
16377396 GTCAGCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (29 bp):
AAACATGAACGAACCTTTTGGACACCTAT
Found at i:16378861 original size:21 final size:21
Alignment explanation
Indices: 16378835--16378876 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16378825 AAAGAAGAAG
16378835 AGAAAACTAAAAG-AAAAACTA
1 AGAAAACT-AAAGCAAAAACTA
16378856 AGAAAACTAAAGCAAAAACTA
1 AGAAAACTAAAGCAAAAACTA
16378877 TCCTAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.69, C:0.12, G:0.10, T:0.10
Consensus pattern (21 bp):
AGAAAACTAAAGCAAAAACTA
Found at i:16380860 original size:30 final size:30
Alignment explanation
Indices: 16380824--16380948 Score: 137
Period size: 30 Copynumber: 4.1 Consensus size: 30
16380814 CAAAATGAAA
*
16380824 TTTTGGAAAGTTTTAGGGTCAAAACATAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACATAAT
* *
16380854 TTTTGGAAAGTTTG-GGAGTTAAAACATATT
1 TTTTGGAAAGTTTGAGG-GTCAAAACATAAT
* *
16380884 TTTTGGAAAGTTCGAGGGTCAAATAC-GAAT
1 TTTTGGAAAGTTTGAGGGTCAAA-ACATAAT
* * *
16380914 TTTTGGATAGTTTGGGGGTCCAAAACATAAA
1 TTTTGGAAAGTTTGAGGGT-CAAAACATAAT
16380945 TTTT
1 TTTT
16380949 AAATAAAATA
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
29 2 0.03
30 62 0.79
31 14 0.18
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAGTTTGAGGGTCAAAACATAAT
Found at i:16381745 original size:14 final size:14
Alignment explanation
Indices: 16381728--16381754 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16381718 TGGATTTTCC
16381728 TTTTTATGTATATA
1 TTTTTATGTATATA
16381742 TTTTTATGTATAT
1 TTTTTATGTATAT
16381755 TTTCTTTTCG
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:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTATGTATATA
Found at i:16382597 original size:78 final size:79
Alignment explanation
Indices: 16382475--16383040 Score: 497
Period size: 80 Copynumber: 7.1 Consensus size: 79
16382465 GAATGGTGTA
* * *
16382475 TCTTCAATCTGCCCTCCGATTAGGGTAAAAGATTGGAT-GCTTCAATCTACCCCATGATTGAGGT
1 TCTTCAATCTG-CCTCTGATTAGGGTAAAAGATTGGATGGTTTCAATCTACCCCATGATCGAGGT
*
16382539 AAGAGATTGG-TGTA
65 AAGAGATTGGATGTG
* * * * *
16382553 TCTTCAATCTGCCTTCTGATTAAGGTAAAATATTGGAT-GTTTCAATCTGCCCTATGATCGGGGT
1 TCTTCAATCTGCC-TCTGATTAGGGTAAAAGATTGGATGGTTTCAATCTACCCCATGATCGAGGT
*
16382617 AAGAGATTGGTTGATG
65 AAGAGATTGGATG-TG
* * * *
16382633 TCTTCAATTTGCCCCATGA-TCGGGATAAGAGATTGGATGGTCTTCAATCTACCCCATGATC-AG
1 TCTTCAATCTGCCTC-TGATTAGGG-TAAAAGATTGGATGGT-TTCAATCTACCCCATGATCGA-
16382696 GGTAAGAGATTGGATGATG
62 GGTAAGAGATTGGATG-TG
* * * * * **
16382715 TCTTCAATCTGTCCTATGATCAAGGTAAAAGATTTGATGGTCTTCAATCTGCCCCACAATCGAGG
1 TCTTCAATCTG-CCTCTGATTAGGGTAAAAGATTGGATGGT-TTCAATCTACCCCATGATCGAGG
*
16382780 TAAGATATTGGATG-G
64 TAAGAGATTGGATGTG
* * * * * * * *
16382795 TCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGTGTC-TTC-AACCTA-GATCGGGGT
1 TCTTCAATCTGCCTC-TGATTAGGGTAAAAGATTGGATGGTTTCAATCTACCCCATGATCGAGGT
*
16382857 AAGAGATTAGATGGTG
65 AAGAGATTGGAT-GTG
* * * *
16382873 TCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGAT-GCTTCATTCTGCCCCATGATCGGGGT
1 TCTTCAATCTG-CCTCTGATTAGGGTAAAAGATTGGATGGTTTCAATCTACCCCATGATCGAGGT
*
16382937 AAGAGATTGGATGGTA
65 AAGAGATTGGAT-GTG
* * * * * *
16382953 TCTTCAATCTGCCCCATGA-TCGGGGAAAGAGATTGTATGATGTCTACAATCTGCCCCATGATCG
1 TCTTCAATCTGCCTC-TGATTAGGGTAAA-AGATTGGATG--GT-TTCAATCTACCCCATGATCG
16383017 AGGTAAGAGATTGGATGATG
61 AGGTAAGAGATTGGATG-TG
16383037 TCTT
1 TCTT
16383041 TAATTTGCTC
Statistics
Matches: 399, Mismatches: 64, Indels: 44
0.79 0.13 0.09
Matches are distributed among these distances:
76 17 0.04
77 9 0.02
78 100 0.25
79 26 0.07
80 106 0.27
81 2 0.01
82 94 0.24
83 7 0.02
84 38 0.10
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (79 bp):
TCTTCAATCTGCCTCTGATTAGGGTAAAAGATTGGATGGTTTCAATCTACCCCATGATCGAGGTA
AGAGATTGGATGTG
Found at i:16382646 original size:42 final size:42
Alignment explanation
Indices: 16382510--16383040 Score: 500
Period size: 42 Copynumber: 13.2 Consensus size: 42
16382500 TAAAAGATTG
* * *
16382510 GATG-CTTCAATCTACCCCATGATTGAGGTAAGAGATTGG-T
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * *** * *
16382550 G-TATCTTCAATCTGCCTTC-TGATTAAGGTAAAATATT-G--
1 GATGTCTTCAATCTGCC-CCATGATCGGGGTAAGAGATTGGAT
* *
16382588 GATGT-TTCAATCTGCCCTATGATCGGGGTAAGAGATTGGTT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* *
16382629 GATGTCTTCAATTTGCCCCATGATCGGGATAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* *
16382671 G--GTCTTCAATCTACCCCATGATCAGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * ** * *
16382711 GATGTCTTCAATCTGTCCTATGATCAAGGTAAAAGATTTGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
** * *
16382753 G--GTCTTCAATCTGCCCCACAATCGAGGTAAGATATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
*
16382793 G--GTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * *
16382833 GGTGTCTTCAA-----CCTA-GATCGGGGTAAGAGATTAGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* ** *
16382869 GGTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATT-G--
1 GATGTCTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGAT
*
16382908 GATG-CTTCATTCTGCCCCATGATCGGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * * *
16382949 GGTATCTTCAATCTGCCCCATGATCGGGGAAAGAGATTGTAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* *
16382991 GATGTCTACAATCTGCCCCATGATCGAGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
16383033 GATGTCTT
1 GATGTCTT
16383041 TAATTTGCTC
Statistics
Matches: 402, Mismatches: 65, Indels: 46
0.78 0.13 0.09
Matches are distributed among these distances:
36 30 0.07
37 4 0.01
38 52 0.13
39 9 0.02
40 130 0.32
41 11 0.03
42 166 0.41
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
GATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
Found at i:16382792 original size:122 final size:122
Alignment explanation
Indices: 16382475--16383033 Score: 512
Period size: 122 Copynumber: 4.6 Consensus size: 122
16382465 GAATGGTGTA
** ** * * * *
16382475 TCTTCAATCTGCCCTCCGATTAGGGTAAAAGATTGGA--TG-CTTCAATCTACCCCATGATTGAG
1 TCTTCAATCTGCCCTATGATCGGGGTAAAAGATTTGATGTGTCTTCAATCTGCCCCATAATCG-G
* * * * * *
16382537 GTAAGAGATTGG-TGTATCTTCAATCTGCCTTC-TGATTAAGGTAAAATATT-G--GATG
65 GTAAGAGATTGGATG-GTCTTCAATCTGCC-CCATGATCAGGGTAAGAGATTGGATGATG
* * * * *
16382592 T-TTCAATCTGCCCTATGATCGGGGTAAGAGATTGGTTGATGTCTTCAATTTGCCCCATGATCGG
1 TCTTCAATCTGCCCTATGATCGGGGTAAAAGATTTGATG-TGTCTTCAATCTGCCCCATAATCGG
*
16382656 GATAAGAGATTGGATGGTCTTCAATCTACCCCATGATCAGGGTAAGAGATTGGATGATG
65 G-TAAGAGATTGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATG
* ** *
16382715 TCTTCAATCTGTCCTATGATCAAGGTAAAAGATTTGATG-GTCTTCAATCTGCCCCACAATCGAG
1 TCTTCAATCTGCCCTATGATCGGGGTAAAAGATTTGATGTGTCTTCAATCTGCCCCATAATCG-G
* *
16382779 GTAAGATATTGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGTG
65 GTAAGAGATTGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATG
* * * *
16382837 TCTTCAA-----CCTA-GATCGGGGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTC-TGATTA
1 TCTTCAATCTGCCCTATGATCGGGGTAAAAGATTTGAT-GTGTCTTCAATCTGCCC-CAT-AATC
* * * * *
16382895 GGGTAAAAGATTGGAT-G-CTTCATTCTGCCCCATGATCGGGGTAAGAGATTGGATGGTA
63 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATG
* * *
16382953 TCTTCAATCTGCCCCATGATCGGGG-AAAGAGA-TTGTATGATGTCTACAATCTGCCCCATGATC
1 TCTTCAATCTGCCCTATGATCGGGGTAAA-AGATTTG-ATG-TGTCTTCAATCTGCCCCATAATC
16383016 GAGGTAAGAGATTGGATG
63 G-GGTAAGAGATTGGATG
16383034 ATGTCTTTAA
Statistics
Matches: 366, Mismatches: 48, Indels: 50
0.79 0.10 0.11
Matches are distributed among these distances:
116 91 0.25
117 7 0.02
118 28 0.08
119 9 0.02
120 55 0.15
121 14 0.04
122 124 0.34
123 7 0.02
124 31 0.08
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (122 bp):
TCTTCAATCTGCCCTATGATCGGGGTAAAAGATTTGATGTGTCTTCAATCTGCCCCATAATCGGG
TAAGAGATTGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATG
Found at i:16383576 original size:99 final size:99
Alignment explanation
Indices: 16383424--16384080 Score: 667
Period size: 99 Copynumber: 6.6 Consensus size: 99
16383414 CGCTGTTATG
* * * * *
16383424 GCCTCGATCTTTCCCATCA-AGTC-TCTAAGGTACTA-GGTTCGCCATTGCAGCCTCAACCTTTC
1 GCCTCAATCCTTCCCATCACA-TCTTCTAAGGTAC-AGGGTTCGTCGTTGCGGCCTCAACCTTTC
* * *
16383486 CCTTCATATCTTCATAGTACCGAATTTGCCGTTGCG
64 CCTTCATATCTTCATGGTACCGAATTCGCCGTTGCA
* *
16383522 GCCTCAATCCTTCCCATCACATCTTCTTAGGTACAGGGTTCGTCGTTACGGCCTCAACCTTTCCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCC
* * * * **
16383587 TTTATATCTTCATGGTATCGGATTTGTTGTTGCA
66 TTCATATCTTCATGGTACCGAATTCGCCGTTGCA
* * * * * *
16383621 ACCTCAATCCTTCTCATCACATCTTCTAAGGTATAGGGTTTGCCGTTGCAGCCTCAACCTTTCCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCC
*
16383686 TTCATATCTTCATGGTACC-AGATTAGCCGTTGCA
66 TTCATATCTTCATGGTACCGA-ATTCGCCGTTGCA
** * *
16383720 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAACGATCATCGTTGCGGCCTCAACCTTTCCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCC
* * * * * * *
16383785 TTTATATCTTCATGATATCGGATTCACTGTTGTA
66 TTCATATCTTCATGGTACCGAATTCGCCGTTGCA
* * * * *
16383819 GCCTCAATCCTTCCCATCACATCTTTTAAGGTACAGGGTTTGCCGTTACGGCCTCAACCTTTCCT
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCC
* ** *
16383884 TTCATATCTTCATGGTACCAAATTCATCGTTGCG
66 TTCATATCTTCATGGTACCGAATTCGCCGTTGCA
* ** * * * ** * *
16383918 GGCTCAATCCTTCTAATCACATCTTTTAAGGTATAGGGTTTGTTATTGTGGCATCAACCTTTCCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCC
* * ** * *
16383983 TTCATATCTTCATGGTATCGGATTCGTTGTTACG
66 TTCATATCTTCATGGTACCGAATTCGCCGTTGCA
* * ** *
16384017 GCCTTAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCACCATTGTC-GCCTCAACCTTTCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTG-CGGCCTCAACCTTTCC
16384081 TTTTATTTCC
Statistics
Matches: 461, Mismatches: 92, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
98 20 0.04
99 441 0.96
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (99 bp):
GCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCC
TTCATATCTTCATGGTACCGAATTCGCCGTTGCA
Found at i:16383675 original size:198 final size:197
Alignment explanation
Indices: 16383424--16384080 Score: 822
Period size: 198 Copynumber: 3.3 Consensus size: 197
16383414 CGCTGTTATG
* *
16383424 GCCTCGATCTTTCCCATCA-AGTC-TCTAAGGTACTA-GGTTCGCCATTGCAGCCTCAACCTTTC
1 GCCTCAATCCTTCCCATCACA-TCTTCTAAGGTA-TAGGGTTCGCCATTGCAGCCTCAACCTTTC
* *
16383486 CCTTCATATCTTCATAGTACCGAATTTGCCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTTA
64 CCTTCATATCTTCATGGTACC-AATTAGCCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTTA
* *
16383551 GGTACAGGGTTCGTCGTTACGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCGGATTTGTTG
128 GGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCGGATTCGTTG
16383616 TTGCA
193 TTGCA
* * * *
16383621 ACCTCAATCCTTCTCATCACATCTTCTAAGGTATAGGGTTTGCCGTTGCAGCCTCAACCTTTCCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCGCCATTGCAGCCTCAACCTTTCCC
* *
16383686 TTCATATCTTCATGGTACCAGATTAGCCGTTGCAGCCTCAATCCTTCCCATCACATCTTCTAAGG
66 TTCATATCTTCATGGTACCA-ATTAGCCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTTAGG
** * * * **
16383751 TACAACGATCATCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGATATCGGATTCACTGTT
130 TACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCGGATTCGTTGTT
*
16383816 GTA
195 GCA
* * * * * * *
16383819 GCCTCAATCCTTCCCATCACATCTTTTAAGGTACAGGGTTTGCCGTTACGGCCTCAACCTTTCCT
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCGCCATTGCAGCCTCAACCTTTCCC
* * **
16383884 TTCATATCTTCATGGTACCAAATTCA-TCGTTGCGGGCTCAATCCTTCTAATCACATCTT-TTAA
66 TTCATATCTTCATGGTACC-AATT-AGCCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTT-A
* * ** * * *
16383947 GGTATAGGGTTTGTTATTGTGGCATCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCGTTG
128 GGTACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCGGATTCGTTG
* *
16384012 TTACG
193 TTGCA
* *
16384017 GCCTTAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCACCATTGTC-GCCTCAACCTTTCC
1 GCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCGCCATTG-CAGCCTCAACCTTTCC
16384081 TTTTATTTCC
Statistics
Matches: 395, Mismatches: 57, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
197 21 0.05
198 371 0.94
199 3 0.01
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (197 bp):
GCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCGCCATTGCAGCCTCAACCTTTCCC
TTCATATCTTCATGGTACCAATTAGCCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTTAGGT
ACAGGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCGGATTCGTTGTTG
CA
Found at i:16384073 original size:297 final size:296
Alignment explanation
Indices: 16383377--16384086 Score: 811
Period size: 297 Copynumber: 2.4 Consensus size: 296
16383367 CCATTGTGCT
* * * * ** * ** * *
16383377 TCAATCTTTCCCATTTATATTTTCATGGTACTAGATCCGCTGTTATGGCCTCGATCTTTCCCATC
1 TCAACCTTTCCC-TTCATATCTTCATGGTACCAGATTAGCCGTTACAGCCTCAATCCTTCCCATC
* *
16383442 A-AGTC-TCTAAGGTACTAGGTTCGCCATTGCAGCCTCAACCTTTCCCTTCATATCTTCATAGTA
65 ACA-TCTTCTAAGGTA-TAGGTTCACCATTGCAGCCTCAACCTTTCCCTTTATATCTTCATAGTA
** * *
16383505 CCGAATTTGCCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTTAGGTACAGGGTTCGTCGTTA
128 CCGAATTCACCGTTGCAGCCTCAATCCTTCCCATCACATCTTCTTAGGTACAGGGTTCGCCGTTA
* ** ** *
16383570 CGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCGGATTTGTTGTTGCAACCTCAATCCTTCT
193 CGGCCTCAACCTTTCCCTTTATATCTTCATGGTACCAAATTCATCGTTGCAACCTCAATCCTTCT
* * *
16383635 CATCACATCTTCTAAGGTATAGGGTTTGCCGTTGCAGCC
258 AATCACATCTTCTAAGGTATAGGGTTTGCCATTGCAGCA
*
16383674 TCAACCTTTCCCTTCATATCTTCATGGTACCAGATTAGCCGTTGCAGCCTCAATCCTTCCCATCA
1 TCAACCTTTCCCTTCATATCTTCATGGTACCAGATTAGCCGTTACAGCCTCAATCCTTCCCATCA
* * * * * * *
16383739 CATCTTCTAAGGTACAACGATCATCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCAT-GATAT
66 CATCTTCTAAGGTA-TAGGTTCACCATTGCAGCCTCAACCTTTCCCTTTATATCTTCATAG-TAC
* * * *
16383803 CGGATTCACTGTTGTAGCCTCAATCCTTCCCATCACATCTT-TTAAGGTACAGGGTTTGCCGTTA
129 CGAATTCACCGTTGCAGCCTCAATCCTTCCCATCACATCTTCTT-AGGTACAGGGTTCGCCGTTA
***
16383867 CGGCCTCAACCTTT-CCTTTCATATCTTCATGGTACCAAATTCATCGTTGCGGGCTCAATCCTTC
193 CGGCCTCAACCTTTCCCTTT-ATATCTTCATGGTACCAAATTCATCGTTGCAACCTCAATCCTTC
* ** **
16383931 TAATCACATCTTTTAAGGTATAGGGTTTGTTATTGTGGCA
257 TAATCACATCTTCTAAGGTATAGGGTTTGCCATTGCAGCA
* * * ** * *
16383971 TCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCGTTGTTACGGCCTTAATCCTTCCCATCA
1 TCAACCTTTCCCTTCATATCTTCATGGTACCAGATTAGCCGTTACAGCCTCAATCCTTCCCATCA
*
16384036 CATCTTCTAAGGTATAGGGTTCACCATTGTC-GCCTCAACCTTTCCTTTTAT
66 CATCTTCTAAGGTATA-GGTTCACCATTG-CAGCCTCAACCTTTCCCTTTAT
16384087 TTCCATTGTG
Statistics
Matches: 346, Mismatches: 60, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
296 53 0.15
297 292 0.84
298 1 0.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.36
Consensus pattern (296 bp):
TCAACCTTTCCCTTCATATCTTCATGGTACCAGATTAGCCGTTACAGCCTCAATCCTTCCCATCA
CATCTTCTAAGGTATAGGTTCACCATTGCAGCCTCAACCTTTCCCTTTATATCTTCATAGTACCG
AATTCACCGTTGCAGCCTCAATCCTTCCCATCACATCTTCTTAGGTACAGGGTTCGCCGTTACGG
CCTCAACCTTTCCCTTTATATCTTCATGGTACCAAATTCATCGTTGCAACCTCAATCCTTCTAAT
CACATCTTCTAAGGTATAGGGTTTGCCATTGCAGCA
Found at i:16384797 original size:112 final size:115
Alignment explanation
Indices: 16384592--16384802 Score: 320
Period size: 112 Copynumber: 1.9 Consensus size: 115
16384582 CCTTATATCG
* * *
16384592 TTAGACCACTAACTGTTATTTCAAAAGCAAAAAATGCTTGAATCAAGATTGTGAGGTGGATGAAA
1 TTAGACCACTAACTGTTATTTCAAAAGCAAAAAATACTTGAACCAAGATTGTGAGGTGGATAAAA
* *
16384657 TTGAATTTGATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCA
66 TTAAATTTGATTAGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCA
* * *
16384707 TTAGTCCACTAACTGTTATTTC-AATGC-AAAAATACTTG-ACCATGATTGTGAGGTGGATAAAA
1 TTAGACCACTAACTGTTATTTCAAAAGCAAAAAATACTTGAACCAAGATTGTGAGGTGGATAAAA
*
16384769 TTAAATTTTATTAGAGGCAAAGCTCGCATGAATG
66 TTAAATTTGATTAGAGGCAAAGCTCGCATGAATG
16384803 CAAACATTGA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 52 0.60
113 10 0.11
114 4 0.05
115 21 0.24
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (115 bp):
TTAGACCACTAACTGTTATTTCAAAAGCAAAAAATACTTGAACCAAGATTGTGAGGTGGATAAAA
TTAAATTTGATTAGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCA
Found at i:16385149 original size:18 final size:17
Alignment explanation
Indices: 16385113--16385165 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
16385103 TACCTCTCCC
*
16385113 TTTT-TTTTCCTTCTTT
1 TTTTCTTTTCCTTTTTT
16385129 TTTTCTTTTCCTTTTTAT
1 TTTTCTTTTCCTTTTT-T
*
16385147 TTTTCTCTTCCCTTTTTT
1 TTTTCT-TTTCCTTTTTT
16385165 T
1 T
16385166 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
18 9 0.28
19 9 0.28
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTCCTTTTTT
Found at i:16385160 original size:19 final size:18
Alignment explanation
Indices: 16385128--16385163 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16385118 TTTCCTTCTT
*
16385128 TTTTTCTTTTCCTTTTTA
1 TTTTTCTTTCCCTTTTTA
16385146 TTTTTCTCTTCCCTTTTT
1 TTTTTCT-TTCCCTTTTT
16385164 TTATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCTTTCCCTTTTTA
Found at i:16386042 original size:14 final size:14
Alignment explanation
Indices: 16386025--16386066 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16386015 TTCATCTTGA
16386025 CTTTTCTTTCTTTT
1 CTTTTCTTTCTTTT
16386039 CTTTTC-TTCTTCTT
1 CTTTTCTTTCTT-TT
* *
16386053 CTTCTCTTTATTTT
1 CTTTTCTTTCTTTT
16386067 GATCTCCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 15 0.62
15 4 0.17
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTTCTTTCTTTT
Found at i:16389955 original size:104 final size:106
Alignment explanation
Indices: 16389679--16389977 Score: 302
Period size: 109 Copynumber: 2.8 Consensus size: 106
16389669 GAAATATCTG
* * * * *
16389679 ATTACTTAGGTTCAAGGCAAAATCATACCCAACACATTAGGGCACAATCTTTCGAGTCCCCTAAA
1 ATTACTTAGGTTCAAGGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTTCCCTAAA
* * *
16389744 ATAACAGAATATTGAGCATTAATTGATTCTGAATAGGATATTCA
66 ATAAAAGAACATT--GCCTTAATT-ATTCTGAATAGGATATTCA
* * * ** * *
16389788 ATTATTTAGGTTCAAGGAAAAATCATACCCAACACGTTAGGGCATAATTCCTCAACTTCCCTAAA
1 ATTACTTAGGTTCAAGGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTTCCCTAAA
* *
16389853 ATAAAAGAACATTGCCTTGATT-TT-TTAATAGGATATTCA
66 ATAAAAGAACATTGCCTTAATTATTCTGAATAGGATATTCA
* *** * *
16389892 ATTACTTAGGTTCGAA-GAAAAATCGTACCCTGTATGTTTGAGCACAATTTTTCGAGTTCCCT-A
1 ATTACTTAGGTTC-AAGGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTTCCCTAA
*
16389955 AAT-AAAGAAACATTGCCTCAATT
65 AATAAAAG-AACATTGCCTTAATT
16389978 TTGAAAATAT
Statistics
Matches: 158, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
102 4 0.03
103 17 0.11
104 60 0.38
105 4 0.03
107 7 0.04
109 66 0.42
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (106 bp):
ATTACTTAGGTTCAAGGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTTCCCTAAA
ATAAAAGAACATTGCCTTAATTATTCTGAATAGGATATTCA
Found at i:16390224 original size:15 final size:15
Alignment explanation
Indices: 16390204--16390233 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16390194 CAAAATTATC
16390204 GAAAAATAAAATAAA
1 GAAAAATAAAATAAA
16390219 GAAAAATAAAATAAA
1 GAAAAATAAAATAAA
16390234 TAAATATACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
GAAAAATAAAATAAA
Found at i:16390382 original size:30 final size:30
Alignment explanation
Indices: 16390339--16390502 Score: 163
Period size: 30 Copynumber: 5.5 Consensus size: 30
16390329 AAAGGGGTCA
*
16390339 AAAACA-AAATTTTGGAAAGTTCGGGGGTT
1 AAAACATAATTTTTGGAAAGTTCGGGGGTT
* * *
16390368 AAAACTTAATTTTTGGAAAGTTTGGGGGTC
1 AAAACATAATTTTTGGAAAGTTCGGGGGTT
* *
16390398 AAAACATAATTTTTAGAAAGTTCGAGGGTT
1 AAAACATAATTTTTGGAAAGTTCGGGGGTT
* *
16390428 AAAACATAATTTTTGGAAAGCTT-GAGGGTC
1 AAAACATAATTTTTGGAAAG-TTCGGGGGTT
* * * * *
16390458 AAATAC-GAATTTTTGGATAGTTTGAGGGTCC
1 AAA-ACATAATTTTTGGAAAGTTCGGGGGT-T
16390489 AAAACATAATTTTT
1 AAAACATAATTTTT
16390503 AAATGAAACA
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.06
30 93 0.81
31 15 0.13
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAACATAATTTTTGGAAAGTTCGGGGGTT
Found at i:16390396 original size:60 final size:60
Alignment explanation
Indices: 16390332--16390502 Score: 218
Period size: 60 Copynumber: 2.8 Consensus size: 60
16390322 TAAGGAAAAA
* * * *
16390332 GGGGTCAAAAACAAAATTTTGGAAAGTTCGGGGGTTAAAACTTAATTTTTGGAAAGTTTG
1 GGGGTCAAAAACAAATTTTTGGAAAGTTCGAGGGTTAAAACATAATTTTTGGAAAGCTTG
*
16390392 GGGGTC-AAAACATAATTTTTAGAAAGTTCGAGGGTTAAAACATAATTTTTGGAAAGCTTG
1 GGGGTCAAAAACA-AATTTTTGGAAAGTTCGAGGGTTAAAACATAATTTTTGGAAAGCTTG
* * * * * *
16390452 AGGGTCAAATACGAATTTTTGGATAGTTTGAGGGTCCAAAACATAATTTTT
1 GGGGTCAAAAACAAATTTTTGGAAAGTTCGAGGGT-TAAAACATAATTTTT
16390503 AAATGAAACA
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
59 6 0.06
60 72 0.75
61 18 0.19
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (60 bp):
GGGGTCAAAAACAAATTTTTGGAAAGTTCGAGGGTTAAAACATAATTTTTGGAAAGCTTG
Found at i:16391294 original size:14 final size:14
Alignment explanation
Indices: 16391277--16391303 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16391267 TGTATTTTCC
16391277 TTTTTATGTATATA
1 TTTTTATGTATATA
16391291 TTTTTATGTATAT
1 TTTTTATGTATAT
16391304 TTTCTTTTCG
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:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTATGTATATA
Found at i:16392171 original size:11 final size:10
Alignment explanation
Indices: 16392147--16392171 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16392137 TTGAAAACTT
16392147 AAAAACTACG
1 AAAAACTACG
16392157 AAAAACTACG
1 AAAAACTACG
16392167 AAAAA
1 AAAAA
16392172 TGCATGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAACTACG
Found at i:16394180 original size:6 final size:6
Alignment explanation
Indices: 16394171--16394210 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
16394161 GATTACGATT
16394171 ACAATC ACAATC ACAATC ACAATC ACAATC ACAATC ACAA
1 ACAATC ACAATC ACAATC ACAATC ACAATC ACAATC ACAA
16394211 ATACATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.15
Consensus pattern (6 bp):
ACAATC
Found at i:16395710 original size:30 final size:29
Alignment explanation
Indices: 16395676--16395732 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
16395666 CATATTGACA
16395676 AATTAGTTAAATTAATAATTTGTATTAAAT
1 AATTAGTTAAATTAAT-ATTTGTATTAAAT
* * *
16395706 AATTATTTAATTTAGTATTTGTATTAA
1 AATTAGTTAAATTAATATTTGTATTAA
16395733 TTGTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (29 bp):
AATTAGTTAAATTAATATTTGTATTAAAT
Found at i:16396468 original size:16 final size:15
Alignment explanation
Indices: 16396447--16396477 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
16396437 AAAATTTATG
16396447 AATTTTTTTAATTTTT
1 AATTTTTTT-ATTTTT
16396463 AATTTTTTTATTTTT
1 AATTTTTTTATTTTT
16396478 GGATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
AATTTTTTTATTTTT
Found at i:16397029 original size:31 final size:31
Alignment explanation
Indices: 16396994--16397053 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
16396984 CTTATAGAAA
16396994 GAAAATTCATTTTAATATCAACCATCACAAT
1 GAAAATTCATTTTAATATCAACCATCACAAT
16397025 GAAAATTCATTTTAATATCAACCATCACA
1 GAAAATTCATTTTAATATCAACCATCACA
16397054 TATATTATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (31 bp):
GAAAATTCATTTTAATATCAACCATCACAAT
Found at i:16397437 original size:11 final size:11
Alignment explanation
Indices: 16397423--16397449 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16397413 TTAAAACTGT
16397423 AAAAAATTATA
1 AAAAAATTATA
16397434 AAAAAATTATA
1 AAAAAATTATA
16397445 AAAAA
1 AAAAA
16397450 TAACTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:16397597 original size:18 final size:17
Alignment explanation
Indices: 16397561--16397602 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
16397551 AATTATTTTA
*
16397561 AAAATTATAAGATAGTT
1 AAAATTATAAAATAGTT
16397578 AACAATTATAAAATTA-TT
1 AA-AATTATAAAA-TAGTT
16397596 AAAATTA
1 AAAATTA
16397603 ATAATGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
AAAATTATAAAATAGTT
Found at i:16398221 original size:27 final size:26
Alignment explanation
Indices: 16398187--16398238 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
16398177 TTTTTATAAG
16398187 TTTTTAGAACTTCTATAAATTATTTAA
1 TTTTTAGAACTTCTAT-AATTATTTAA
** *
16398214 TTTTTAGATTTTTTATAATTATTTA
1 TTTTTAGAACTTCTATAATTATTTA
16398239 GAATGTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTTTAGAACTTCTATAATTATTTAA
Found at i:16398935 original size:20 final size:22
Alignment explanation
Indices: 16398910--16398951 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16398900 AAAGTTGTAC
16398910 TTTTTA-AAAACT-TAAAATAT
1 TTTTTATAAAACTCTAAAATAT
*
16398930 TTTTTATAAAATTCTAAAATAT
1 TTTTTATAAAACTCTAAAATAT
16398952 ATAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTTATAAAACTCTAAAATAT
Found at i:16399303 original size:21 final size:20
Alignment explanation
Indices: 16399260--16399312 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
16399250 TTTTACTAGA
* *
16399260 TTTTATATTTTTTTTGAATT
1 TTTTATATTTTATTTCAATT
*
16399280 TTTTATATATTTATTTCCATT
1 TTTTATAT-TTTATTTCAATT
*
16399301 TTTTATTTTTTA
1 TTTTATATTTTA
16399313 ATGTGTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTATATTTTATTTCAATT
Found at i:16402215 original size:25 final size:25
Alignment explanation
Indices: 16402178--16402226 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16402168 TAGCAATTTT
16402178 TTTCTTCTTTTC-TCTTTTTCTTTAC
1 TTTCTTCTTTTCTTCTTTTT-TTTAC
16402203 TTTCTT-TTCTTCTTCTTTTTTTTA
1 TTTCTTCTT-TTCTTCTTTTTTTTA
16402227 TATGTGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 13 0.59
26 7 0.32
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTCTTCTTTTCTTCTTTTTTTTAC
Found at i:16402822 original size:17 final size:17
Alignment explanation
Indices: 16402802--16402844 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
16402792 AAATGAACTA
*
16402802 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
*
16402819 ACAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
16402836 ACAATTAAA
1 ACAACTAAA
16402845 TGAGCTGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:16407821 original size:13 final size:12
Alignment explanation
Indices: 16407794--16407818 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16407784 CTTAATGATC
16407794 TCTTTTTTCATT
1 TCTTTTTTCATT
16407806 TCTTTTTTCATT
1 TCTTTTTTCATT
16407818 T
1 T
16407819 TCTCATTCAG
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTTTCATT
Found at i:16409523 original size:18 final size:18
Alignment explanation
Indices: 16409500--16409543 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16409490 CTTGTGGTTA
16409500 CATCTGGTTGTATAATTG
1 CATCTGGTTGTATAATTG
* * * *
16409518 CATCTGATTTTGTGATTG
1 CATCTGGTTGTATAATTG
16409536 CATCTGGT
1 CATCTGGT
16409544 CTGATTGCAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (18 bp):
CATCTGGTTGTATAATTG
Found at i:16428241 original size:17 final size:17
Alignment explanation
Indices: 16428197--16428244 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
16428187 TATCATATAG
*
16428197 TTGTCATTGCATTTTAC
1 TTGTCAATGCATTTTAC
* ** *
16428214 TTATCTCTGCATTTTAT
1 TTGTCAATGCATTTTAC
16428231 TTGTCAATGCATTT
1 TTGTCAATGCATTT
16428245 GCATTGTAGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (17 bp):
TTGTCAATGCATTTTAC
Found at i:16433687 original size:31 final size:31
Alignment explanation
Indices: 16433582--16433716 Score: 97
Period size: 28 Copynumber: 4.5 Consensus size: 31
16433572 TTAATATAAT
* *
16433582 ATTTGGTACTTGAACTTGACACTTTTACCTA
1 ATTTGGTACTTAAACTTGACACTTTTTCCTA
* * * **
16433613 ATTTGGCACCTAAACTT----TTTTTTGTTCA
1 ATTTGGTACTTAAACTTGACACTTTTTCCT-A
16433641 ATTTGGTA-TTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACTT-AAACTTGACACTTTTTCCTA
* **
16433672 ATTTGGTACATAAACTTG--A-TTTTTTTTA
1 ATTTGGTACTTAAACTTGACACTTTTTCCTA
*
16433700 AGTTGGTACTTAAACTT
1 ATTTGGTACTTAAACTT
16433717 TTTTGGATCC
Statistics
Matches: 80, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
27 6 0.08
28 36 0.45
29 1 0.01
31 30 0.38
32 7 0.09
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACACTTTTTCCTA
Found at i:16433706 original size:59 final size:59
Alignment explanation
Indices: 16433584--16433716 Score: 173
Period size: 59 Copynumber: 2.3 Consensus size: 59
16433574 AATATAATAT
* * *
16433584 TTGGTACTTGAACTTGACACTTTTACCTAATTTGGCACCTAAACTTTTTTTTGTTCAAT
1 TTGGTACTTAAACTTGACACTTTTACCTAATTTGGCACATAAACTTTTTTTTGTTCAAG
* *
16433643 TTGGTA-TTCAAACTTGACACTTTTTCCTAATTTGGTACATAAACTTGATTTTTT-TT-AAG
1 TTGGTACTT-AAACTTGACACTTTTACCTAATTTGGCACATAAACTT--TTTTTTGTTCAAG
16433702 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
16433717 TTTTGGATCC
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
58 2 0.03
59 53 0.82
60 4 0.06
61 6 0.09
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (59 bp):
TTGGTACTTAAACTTGACACTTTTACCTAATTTGGCACATAAACTTTTTTTTGTTCAAG
Found at i:16433984 original size:31 final size:27
Alignment explanation
Indices: 16433937--16434074 Score: 118
Period size: 31 Copynumber: 4.8 Consensus size: 27
16433927 AATTGAATCT
16433937 AAAAAAA-TATTAGGTACCAAATTAGGA
1 AAAAAAAGT-TTAGGTACCAAATTAGGA
*
16433964 AAAAATGTCAAGTTTAGGTACCAGATTAGGTA
1 AAAAA----AAGTTTAGGTACCAAATTAGG-A
* *
16433996 AAAAAAAGTTCAGGTACCAAATTAGGT
1 AAAAAAAGTTTAGGTACCAAATTAGGA
* * *
16434023 AAAAAAA-TTTAGATATCAAATTAAGA
1 AAAAAAAGTTTAGGTACCAAATTAGGA
16434049 AAAAATGTCAAGTTTAGGTACCAAAT
1 AAAAA----AAGTTTAGGTACCAAAT
16434075 GTTATTTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
26 19 0.21
27 12 0.13
28 19 0.21
30 2 0.02
31 30 0.34
32 7 0.08
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (27 bp):
AAAAAAAGTTTAGGTACCAAATTAGGA
Found at i:16434013 original size:28 final size:28
Alignment explanation
Indices: 16433936--16434029 Score: 104
Period size: 28 Copynumber: 3.3 Consensus size: 28
16433926 AAATTGAATC
16433936 TAAAAAAATA-TT-AGGTACCAAATTAGG
1 TAAAAAAA-AGTTCAGGTACCAAATTAGG
* *
16433963 -AAAAAATGTCAAGTTTAGGTACCAGATTAGG
1 TAAAAAA----AAGTTCAGGTACCAAATTAGG
16433994 TAAAAAAAAGTTCAGGTACCAAATTAGG
1 TAAAAAAAAGTTCAGGTACCAAATTAGG
16434022 TAAAAAAA
1 TAAAAAAA
16434030 TTTAGATATC
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
26 6 0.11
28 27 0.47
29 1 0.02
30 3 0.05
31 14 0.25
32 6 0.11
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (28 bp):
TAAAAAAAAGTTCAGGTACCAAATTAGG
Found at i:16434042 original size:26 final size:27
Alignment explanation
Indices: 16433973--16434053 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
16433963 AAAAAATGTC
* * *
16433973 AAGTTTAGGTACCAGATTAGGTAAAAAA
1 AAGTTCAGATACCAAATTAGGT-AAAAA
*
16434001 AAGTTCAGGTACCAAATTAGGTAAAAA
1 AAGTTCAGATACCAAATTAGGTAAAAA
* * *
16434028 AA-TTTAGATATCAAATTAAG-AAAAA
1 AAGTTCAGATACCAAATTAGGTAAAAA
16434053 A
1 A
16434054 TGTCAAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.13
26 14 0.30
27 7 0.15
28 20 0.43
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (27 bp):
AAGTTCAGATACCAAATTAGGTAAAAA
Found at i:16434755 original size:18 final size:18
Alignment explanation
Indices: 16434734--16434784 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
16434724 TGATTTTTTT
16434734 ATTTTTAATTTTTTAAAA
1 ATTTTTAATTTTTTAAAA
16434752 ATTTCTT-ATTTTTTAAAA
1 ATTT-TTAATTTTTTAAAA
* *
16434770 ATTTTGAATTATTTA
1 ATTTTTAATTTTTTA
16434785 TTGAAGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 26 0.90
19 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTTAATTTTTTAAAA
Found at i:16436488 original size:31 final size:31
Alignment explanation
Indices: 16436448--16436530 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
16436438 AAGGAATAAG
* *
16436448 AAAGATATATAATATATTCTTAAATATATGA
1 AAAGATATATAATATATTCCTAAACATATGA
* *
16436479 AAAGGTATATAATATATTCCTAAACATATACCTA
1 AAAGATATATAATATATTCCTAAACATAT---GA
*
16436513 AAAGATATACAATATATT
1 AAAGATATATAATATATT
16436531 TAGATATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
31 26 0.60
34 17 0.40
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (31 bp):
AAAGATATATAATATATTCCTAAACATATGA
Found at i:16449352 original size:31 final size:31
Alignment explanation
Indices: 16449317--16449413 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
16449307 ATTTGCTATT
*
16449317 TAAACTTGACTTTTTTTCTTAATTTGATACC
1 TAAACTTGACTTTTTTTCCTAATTTGATACC
** *
16449348 TAAACTT---TTTTTGACCTAATTTGATACT
1 TAAACTTGACTTTTTTTCCTAATTTGATACC
**
16449376 TAAACTTGACACTTTTTCCTAATTTGATACC
1 TAAACTTGACTTTTTTTCCTAATTTGATACC
*
16449407 TGAACTT
1 TAAACTT
16449414 TTTGTGGGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 24 0.45
31 29 0.55
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (31 bp):
TAAACTTGACTTTTTTTCCTAATTTGATACC
Found at i:16449367 original size:28 final size:26
Alignment explanation
Indices: 16449325--16449416 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 26
16449315 TTTAAACTTG
*
16449325 ACTTTTTTTCTTAATTTGATACCTAA
1 ACTTTTTTTCCTAATTTGATACCTAA
*
16449351 ACTTTTTTTGACCTAATTTGATACTTAA
1 ACTTTTTTT--CCTAATTTGATACCTAA
*
16449379 ACTTGACACTTTTTCCTAATTTGATACCTGA
1 ACTT-----TTTTTCCTAATTTGATACCTAA
16449410 ACTTTTT
1 ACTTTTT
16449417 GTGGGCCCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
26 12 0.22
28 19 0.35
31 19 0.35
33 5 0.09
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (26 bp):
ACTTTTTTTCCTAATTTGATACCTAA
Found at i:16449459 original size:60 final size:59
Alignment explanation
Indices: 16449307--16449478 Score: 177
Period size: 59 Copynumber: 2.9 Consensus size: 59
16449297 TTAATATAAC
* * * * *
16449307 ATTTGCTATTTAAACTTGACTTTTTTTCTTAATTTGATACCTAAACTTTTTTTGACCTA
1 ATTTGATACTTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTGGACCCA
* * * *
16449366 ATTTGATACTTAAACTTGACACTTTTTCCTAATTTGATACCTGAACTTTTTGTGGGCCCA
1 ATTTGATACTTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTT-TGGACCCA
* * * *
16449426 ATTTGGTA-TCTGAACTT-ATCATTTTTTCTTAATTTGGTACCTAAGCCTTTTTT
1 ATTTGATACT-TAAACTTGA-CATTTTTTCTTAATTTGATACCTAA-ACTTTTTT
16449479 CAGATTCAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
59 47 0.51
60 40 0.43
61 6 0.06
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (59 bp):
ATTTGATACTTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTGGACCCA
Found at i:16449756 original size:31 final size:29
Alignment explanation
Indices: 16449701--16449759 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
16449691 ATCCCAAAAA
*
16449701 GTTTACATACCAAGTTAAAAAAATGTCAT
1 GTTTACATACCAAATTAAAAAAATGTCAT
*
16449730 GTTTAGATACCAAATTAGGAAAAAATGTCA
1 GTTTACATACCAAATTA--AAAAAATGTCA
16449760 AATTCAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
31 11 0.42
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (29 bp):
GTTTACATACCAAATTAAAAAAATGTCAT
Found at i:16450484 original size:21 final size:19
Alignment explanation
Indices: 16450447--16450498 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
16450437 AAATTATAAA
**
16450447 AATAAAAATTATTAAATTTT
1 AATAAAAA-TATTAAATTAG
16450467 AATAAAAATATTAAAAATTAG
1 AATAAAAATATT--AAATTAG
16450488 AATAAAAATAT
1 AATAAAAATAT
16450499 ATATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 8 0.29
21 16 0.57
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATAAAAATATTAAATTAG
Found at i:16450535 original size:20 final size:20
Alignment explanation
Indices: 16450518--16450554 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
16450508 TTGTAAAATT
16450518 TTATAAAAT-CA-TAAAAAA
1 TTATAAAATACATTAAAAAA
16450536 TTATAAAATACATTAAAAA
1 TTATAAAATACATTAAAAA
16450555 GTCCTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
TTATAAAATACATTAAAAAA
Found at i:16450762 original size:10 final size:9
Alignment explanation
Indices: 16450748--16450845 Score: 56
Period size: 9 Copynumber: 10.3 Consensus size: 9
16450738 CTTTAAGTAA
16450748 TTTTATATT
1 TTTTATATT
*
16450757 TCTTTACATT
1 T-TTTATATT
16450767 TTTTATAATT
1 TTTTAT-ATT
* *
16450777 TTCTTACAAGT
1 TT-TTA-TATT
* * *
16450788 TTATAAAAT
1 TTTTATATT
16450797 -TTTATGATT
1 TTTTAT-ATT
16450806 TTTT-TATAT
1 TTTTATAT-T
*
16450815 TTTTATATA
1 TTTTATATT
16450824 TTTTATATT
1 TTTTATATT
16450833 TTTTATGATT
1 TTTTAT-ATT
16450843 TTT
1 TTT
16450846 ATAAAATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 5 0.07
9 30 0.43
10 27 0.39
11 7 0.10
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:16450827 original size:18 final size:18
Alignment explanation
Indices: 16450796--16450848 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
16450786 GTTTATAAAA
*
16450796 TTTTATGATTTTTTTATAT
1 TTTTAT-ATATTTTTATAT
16450815 TTTTATATA-TTTTATAT
1 TTTTATATATTTTTATAT
16450832 TTTT-TATGATTTTTATA
1 TTTTATAT-ATTTTTATA
16450849 AAATTTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 13 0.42
18 9 0.29
19 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTATATATTTTTATAT
Found at i:16450855 original size:19 final size:19
Alignment explanation
Indices: 16450787--16450875 Score: 74
Period size: 19 Copynumber: 4.6 Consensus size: 19
16450777 TTCTTACAAG
16450787 TTTATAAAATTTTATGATT
1 TTTATAAAATTTTATGATT
* * *
16450806 TTTTTATATTTTTAT-ATAT
1 TTTATAAAATTTTATGAT-T
**
16450825 TTTAT-ATTTTTTATGATT
1 TTTATAAAATTTTATGATT
**
16450843 TTTATAAAATTTTACAATTT
1 TTTATAAAATTTTATGA-TT
16450863 TGTTATAAAATTT
1 T-TTATAAAATTT
16450876 ACTTTTTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 15 0.27
19 26 0.47
20 3 0.05
21 11 0.20
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTATAAAATTTTATGATT
Found at i:16454873 original size:7 final size:7
Alignment explanation
Indices: 16454861--16454897 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
16454851 TTATTTCTAA
16454861 TTGTAAT
1 TTGTAAT
16454868 TTGTAAT
1 TTGTAAT
16454875 TTGTAAT
1 TTGTAAT
16454882 TTGTAAT
1 TTGTAAT
16454889 TTGTAAT
1 TTGTAAT
16454896 TT
1 TT
16454898 TTCTAGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TTGTAAT
Found at i:16454887 original size:21 final size:20
Alignment explanation
Indices: 16454834--16454897 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
16454824 GCTAAGAAAG
*
16454834 TTCTAATT-TAATTTGTTTTAT
1 TTCTAATTGTAATTTG--TAAT
16454855 TTCTAATTGTAATTTGTAAT
1 TTCTAATTGTAATTTGTAAT
*
16454875 TTGTAATTTGTAATTTGTAAT
1 TTCTAA-TTGTAATTTGTAAT
16454896 TT
1 TT
16454898 TTCTAGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.21
21 24 0.62
22 7 0.18
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (20 bp):
TTCTAATTGTAATTTGTAAT
Found at i:16455904 original size:24 final size:24
Alignment explanation
Indices: 16455877--16455930 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
16455867 GTTGCTATTG
* *
16455877 CATCTTGAATT-TCTCTTCCTTGTT
1 CATCTTAAATTAT-TCTTCCTTGAT
*
16455901 CATCTAAAATTATTCTTCCTTGAT
1 CATCTTAAATTATTCTTCCTTGAT
16455925 CATCTT
1 CATCTT
16455931 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.50
Consensus pattern (24 bp):
CATCTTAAATTATTCTTCCTTGAT
Found at i:16458385 original size:9 final size:9
Alignment explanation
Indices: 16458363--16458432 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
16458353 CAAATTGAAT
16458363 ATTTTTATA
1 ATTTTTATA
* *
16458372 TTTTTTGTA
1 ATTTTTATA
16458381 ATTTTTATTAA
1 ATTTTTA-T-A
* *
16458392 ATTTTAACA
1 ATTTTTATA
*
16458401 ATTTTAATA
1 ATTTTTATA
16458410 ATTTTTAT-
1 ATTTTTATA
* *
16458418 TTTTTTATC
1 ATTTTTATA
16458427 ATTTTT
1 ATTTTT
16458433 TTCCACATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
8 7 0.15
9 33 0.69
10 1 0.02
11 7 0.15
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:16460209 original size:41 final size:41
Alignment explanation
Indices: 16460141--16460262 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 41
16460131 CGGCGATTGG
* * * * * *
16460141 ACAGAAAACGCCGCAAAAGAT-ACAGCAATAGCGGCGTTTTT
1 ACAGAAAACGTCGCTAAAGGTCAGAGCAATAGCGGCG-CTTA
* * *
16460182 ACA-TAAACG-CTGCTAAAGGTCAGAGCAATGGCGGTGCTTA
1 ACAGAAAACGTC-GCTAAAGGTCAGAGCAATAGCGGCGCTTA
*
16460222 AGAGAAAACGTCGCTAAAGGTCAGAGCAATAGCGGCGCTTA
1 ACAGAAAACGTCGCTAAAGGTCAGAGCAATAGCGGCGCTTA
16460263 TGGGCAGAGC
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
39 1 0.02
40 16 0.25
41 47 0.72
42 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.17
Consensus pattern (41 bp):
ACAGAAAACGTCGCTAAAGGTCAGAGCAATAGCGGCGCTTA
Found at i:16460260 original size:24 final size:24
Alignment explanation
Indices: 16460233--16460284 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16460223 GAGAAAACGT
*
16460233 CGCTAAAGGTCAGAGCAATAGCGG
1 CGCTAAAGGGCAGAGCAATAGCGG
* *
16460257 CGCTTATGGGCAGAGCAATAGCGG
1 CGCTAAAGGGCAGAGCAATAGCGG
16460281 CGCT
1 CGCT
16460285 TATGGAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.35, T:0.15
Consensus pattern (24 bp):
CGCTAAAGGGCAGAGCAATAGCGG
Found at i:16460285 original size:24 final size:24
Alignment explanation
Indices: 16460243--16460289 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
16460233 CGCTAAAGGT
16460243 CAGAGCAATAGCGGCGCTTATGGG
1 CAGAGCAATAGCGGCGCTTATGGG
16460267 CAGAGCAATAGCGGCGCTTATGG
1 CAGAGCAATAGCGGCGCTTATGG
16460290 AAAGTGCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.36, T:0.17
Consensus pattern (24 bp):
CAGAGCAATAGCGGCGCTTATGGG
Found at i:16460356 original size:41 final size:41
Alignment explanation
Indices: 16460269--16460630 Score: 381
Period size: 41 Copynumber: 8.9 Consensus size: 41
16460259 CTTATGGGCA
* **
16460269 GAGCAATAGCGGCGCTTATGGA-AAGTGCCGCTAAATATCT
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTCT
* * * *
16460309 GAGCAATAGCGACACTTATAGACAAGCGCCACTAAAGGTCT
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTCT
* *
16460350 GAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCA
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTCT
* * * * *
16460391 GACCAATAGCGACGCTTATGGGCAAGCGTCGCTAAAGATCT
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTCT
* * * *
16460432 GAGCAATAGCGGCGCTTATAGACAAGCACCGCTTAAGGTTT
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTCT
* * * *
16460473 GAGCAATAGCGGCGCTTATGGGCAGGTGCCGCTAAAGGGCAT
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC-T
* * * *
16460515 -AACAATAGCGACGCTTATTGGA-AAGCACCGCTAAAGGTCA
1 GAGCAATAGCGGCGCTTA-TGGACAAGCGCCGCTAAAGGTCT
* * * *
16460555 AAGCAATAGCGGCGCTTATGGAAAAGCGTCACTAAAGGTCAT
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC-T
* *
16460597 -AGCAATAGCGGCGCTTATTGAAAAGCGCCGCTAA
1 GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAA
16460631 TTTATTTAAA
Statistics
Matches: 264, Mismatches: 52, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
40 23 0.09
41 237 0.90
42 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (41 bp):
GAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTCT
Found at i:16460490 original size:123 final size:122
Alignment explanation
Indices: 16460264--16460630 Score: 448
Period size: 123 Copynumber: 3.0 Consensus size: 122
16460254 CGGCGCTTAT
* * * * * *
16460264 GGGCAGAGCAATAGCGGCGCTTATGGAAAGTGCCGCTAAATATCTGAGCAATAGCGACACTTATA
1 GGGCAGAACAATAGCGACGCTTATGGAAAGCGCCGCTAAAGATCTGAGCAATAGCGGCGCTTATA
*
16460329 GACAAGCGCCACTAAAGGTCTGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAA
66 GACAAGCGCCACTAAAGGTATGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAA
* * * *
16460386 GGTCAGACCAATAGCGACGCTTATGGGCAAGCGTCGCTAAAGATCTGAGCAATAGCGGCGCTTAT
1 GGGCAGAACAATAGCGACGCTTAT-GGAAAGCGCCGCTAAAGATCTGAGCAATAGCGGCGCTTAT
* * * * * *
16460451 AGACAAGCACCGCTTAAGGTTTGAGCAATAGCGGCGCTTATGGGCAGGTGCCGCTAAA
65 AGACAAGCGCCACTAAAGGTATGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAA
* * * **
16460509 GGGCATAACAATAGCGACGCTTATTGGAAAGCACCGCTAAAGGTCAAAGCAATAGCGGCGCTTAT
1 GGGCAGAACAATAGCGACGCTTA-TGGAAAGCGCCGCTAAAGATCTGAGCAATAGCGGCGCTTAT
* * * * **
16460574 GGAAAAGCGTCACTAAAGGTCAT-AGCAATAGCGGCGCTTATTGAAAAGCGCCGCTAA
65 AGACAAGCGCCACTAAAGGT-ATGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAA
16460631 TTTATTTAAA
Statistics
Matches: 206, Mismatches: 36, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
122 21 0.10
123 183 0.89
124 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.18
Consensus pattern (122 bp):
GGGCAGAACAATAGCGACGCTTATGGAAAGCGCCGCTAAAGATCTGAGCAATAGCGGCGCTTATA
GACAAGCGCCACTAAAGGTATGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAA
Found at i:16466088 original size:43 final size:43
Alignment explanation
Indices: 16465999--16466256 Score: 335
Period size: 43 Copynumber: 6.1 Consensus size: 43
16465989 GATAGTGGCA
*
16465999 TTTGT-GGAAAAGCGCCGCTAAAGACCAT-TTCTTTAGCGGTG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
16466040 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
* * * *
16466083 TTTGTGGTAAAAGCGCCGCTAAAGATCATTTTCTTTAGCAGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
** *
16466126 TTTGTGGGAAAAGCGCCGCTAAAGAATATGGTCTTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
* * * *
16466169 TTTGTGGGTAAAGCGTCGCTAAAGAACATGGTT-TTTAGCGGCA
1 TTTGTGGGAAAAGCGCCGCTAAAGACCAT-GTTCTTTAGCGGCG
* * * *
16466212 TTTGT-GGATAAGCCCCACTAAAGACCATGGTCTTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
16466254 TTT
1 TTT
16466257 TTATTCATAA
Statistics
Matches: 189, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
41 7 0.04
42 52 0.28
43 128 0.68
44 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (43 bp):
TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
Found at i:16468003 original size:21 final size:21
Alignment explanation
Indices: 16467955--16468004 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
16467945 AGTCATGATG
* *
16467955 TTGAAGACTAGTGTAGCGACG
1 TTGAAGGCTAGTGTAGCGACA
*
16467976 TTGAAGGCTAGTGTCGCGACA
1 TTGAAGGCTAGTGTAGCGACA
16467997 TTGAAGGC
1 TTGAAGGC
16468005 AGATTCCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (21 bp):
TTGAAGGCTAGTGTAGCGACA
Found at i:16470145 original size:5 final size:5
Alignment explanation
Indices: 16470135--16470160 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16470125 TGAGCTCCAA
16470135 GTGAT GTGAT GTGAT GTGAT GTGAT G
1 GTGAT GTGAT GTGAT GTGAT GTGAT G
16470161 AGAGGTCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTGAT
Found at i:16470484 original size:22 final size:22
Alignment explanation
Indices: 16470434--16470512 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
16470424 AGTACTTAAT
*
16470434 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACACAGTGCAAT-C
16470457 AGTAGGCACACACAGTGCAATC
1 AGTAGGCACACACAGTGCAATC
* * *
16470479 AGTAGGCGCACATAGCGCAAATC
1 AGTAGGCACACACAGTGC-AATC
*
16470502 AATAGGCACAC
1 AGTAGGCACAC
16470513 GAGGTGCGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.38, C:0.28, G:0.22, T:0.13
Consensus pattern (22 bp):
AGTAGGCACACACAGTGCAATC
Found at i:16470537 original size:23 final size:23
Alignment explanation
Indices: 16470507--16470554 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
16470497 AAATCAATAG
*
16470507 GCACACGAGGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
16470530 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
16470553 GC
1 GC
16470555 GCGCTAGCGT
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:0.40, C:0.23, G:0.29, T:0.08
Consensus pattern (23 bp):
GCACACGAAGTGCGAAACAGTAA
Done.