Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015349.1 Kokia drynarioides strain JFW-HI SEQ_130396, whole genome shotgun sequence
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: 220987
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:4161 original size:25 final size:24
Alignment explanation
Indices: 4132--4201 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 24
4122 GATACAAAAC
* *
4132 TTTTGTTGCTATCTTTTTTCGACCT
1 TTTTGTTGATATC-CTTTTCGACCT
4157 TTTTGTTGATATCCTTTTCGACCT
1 TTTTGTTGATATCCTTTTCGACCT
4181 TTTCAT-TTGATATCCTTTTCG
1 TTT--TGTTGATATCCTTTTCG
4202 GATACATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.32
25 27 0.66
26 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTTGTTGATATCCTTTTCGACCT
Found at i:5461 original size:17 final size:17
Alignment explanation
Indices: 5432--5522 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
5422 ATTGTTTTTA
*
5432 AAATTTTAATTTATTCT
1 AAATTTAAATTTATTCT
* ***
5449 AAGTTTAAATTTAAAAT
1 AAATTTAAATTTATTCT
*
5466 AAATTTAAACTTA--CT
1 AAATTTAAATTTATTCT
* *
5481 AGGAGTTTAAATTTATTTT
1 A--AATTTAAATTTATTCT
*
5500 AATATTTAAATTTATTTT
1 AA-ATTTAAATTTATTCT
5518 AAATT
1 AAATT
5523 AAAAATTAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
15 2 0.04
17 37 0.65
18 16 0.28
19 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTCT
Found at i:5529 original size:18 final size:18
Alignment explanation
Indices: 5489--5526 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5479 CTAGGAGTTT
*
5489 AAATTTATTTTAATATTT
1 AAATTTATTTTAATATTA
5507 AAATTTATTTTAA-ATTA
1 AAATTTATTTTAATATTA
5524 AAA
1 AAA
5527 ATTAAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTATTTTAATATTA
Found at i:5650 original size:18 final size:18
Alignment explanation
Indices: 5629--5674 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
5619 AAACCTAATA
5629 CAAACCCAAATGCTAA-CC
1 CAAACCCAAAT-CTAAGCC
5647 CAAACCCAAAATCTAAGCC
1 CAAACCC-AAATCTAAGCC
5666 CAAACCCAA
1 CAAACCCAA
5675 CCCCAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.48, C:0.39, G:0.04, T:0.09
Consensus pattern (18 bp):
CAAACCCAAATCTAAGCC
Found at i:5667 original size:19 final size:19
Alignment explanation
Indices: 5629--5674 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5619 AAACCTAATA
5629 CAAACCC-AAATGCTAACC
1 CAAACCCAAAATGCTAACC
5647 CAAACCCAAAAT-CTAAGCC
1 CAAACCCAAAATGCTAA-CC
5666 CAAACCCAA
1 CAAACCCAA
5675 CCCCAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.48, C:0.39, G:0.04, T:0.09
Consensus pattern (19 bp):
CAAACCCAAAATGCTAACC
Found at i:7371 original size:29 final size:28
Alignment explanation
Indices: 7324--7582 Score: 256
Period size: 29 Copynumber: 9.0 Consensus size: 28
7314 GAGGTCCCTG
* *
7324 AACTTTCTAAAATTCCATTTTTACCTCA
1 AACTTTCCAAAATTACATTTTTACCTCA
* *
7352 AATTTTCCAAAAATTACATTTTTACC-CTG
1 AACTTTCC-AAAATTACATTTTTACCTC-A
*
7381 AACTTTCCAAAATTCCATTTTTACC-CTA
1 AACTTTCCAAAATTACATTTTTACCTC-A
*
7409 AATTTTCCAAAAATTACA-TTTTACCCTCA
1 AACTTTCC-AAAATTACATTTTTA-CCTCA
* *
7438 GACTTTCCAAAATTCCATTTTTAACCTCA
1 AACTTTCCAAAATTACATTTTT-ACCTCA
* * *
7467 AAATTTCCAAAAATTACAATTTTACCCTCG
1 AACTTTCC-AAAATTACATTTTTA-CCTCA
* *
7497 AACTTTCCAAAATTCCATTTTAGACCTCA
1 AACTTTCCAAAATTACATTTT-TACCTCA
* *
7526 AAATTTCCAAAATTACATTTTTACCCCTA
1 AACTTTCCAAAATTACATTTTTACCTC-A
7555 AACTTTCCAAAATTACCA-TTTTACCTCA
1 AACTTTCCAAAATTA-CATTTTTACCTCA
7583 GAATGTTTAA
Statistics
Matches: 191, Mismatches: 28, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
28 50 0.26
29 113 0.59
30 28 0.15
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (28 bp):
AACTTTCCAAAATTACATTTTTACCTCA
Found at i:7384 original size:57 final size:57
Alignment explanation
Indices: 7319--7683 Score: 390
Period size: 59 Copynumber: 6.3 Consensus size: 57
7309 CCTTGGAGGT
*
7319 CCCTGAACTTTCTAAAATTCCATTTTTACCTCAAATTTTCCAAAAATTACATTTTTA
1 CCCTGAACTTTCCAAAATTCCATTTTTACCTCAAATTTTCCAAAAATTACATTTTTA
7376 CCCTGAACTTTCCAAAATTCCATTTTTACC-CTAAATTTTCCAAAAATTACA-TTTTA
1 CCCTGAACTTTCCAAAATTCCATTTTTACCTC-AAATTTTCCAAAAATTACATTTTTA
* * *
7432 CCCTCAGACTTTCCAAAATTCCATTTTTAACCTCAAAATTTCCAAAAATTACAATTTTA
1 CCCTGA-ACTTTCCAAAATTCCATTTTT-ACCTCAAATTTTCCAAAAATTACATTTTTA
* *
7491 CCCTCGAACTTTCCAAAATTCCATTTTAGACCTCAAAATTTCC-AAAATTACATTTTTA
1 CCCT-GAACTTTCCAAAATTCCATTTT-TACCTCAAATTTTCCAAAAATTACATTTTTA
*
7549 CCCCTAAACTTTCCAAAATTACCA-TTTTACCTCAGAATGTTT--AAAAATT-CTATTTTTAA
1 -CCCTGAACTTTCCAAAATT-CCATTTTTACCTCA-AAT-TTTCCAAAAATTAC-ATTTTT-A
* * * * * *
7608 CCCCGAATCCTTCCAAAATTACCATTTTAACC-CTAAA-TGTCTAAAAACTT-CATTTTAA
1 CCCTGAA-CTTTCCAAAATT-CCATTTTTACCTC-AAATTTTCCAAAAA-TTACATTTTTA
*
7666 ACCTCGAACTTTCCAAAA
1 CCCT-GAACTTTCCAAAA
7684 ATCACCATTA
Statistics
Matches: 269, Mismatches: 18, Indels: 41
0.82 0.05 0.12
Matches are distributed among these distances:
56 11 0.04
57 78 0.29
58 83 0.31
59 86 0.32
60 11 0.04
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (57 bp):
CCCTGAACTTTCCAAAATTCCATTTTTACCTCAAATTTTCCAAAAATTACATTTTTA
Found at i:7518 original size:58 final size:58
Alignment explanation
Indices: 7319--7683 Score: 371
Period size: 58 Copynumber: 6.3 Consensus size: 58
7309 CCTTGGAGGT
* * * *
7319 CCCT-GAACTTTCTAAAATTCCATTTTTACCTCAAATTTTCCAAAAATTACATTTTTA
1 CCCTCGAACTTTCCAAAATTCCATTTTAACCTCAAAATTTCCAAAAATTACAATTTTA
* *
7376 CCCT-GAACTTTCCAAAATTCCATTTTTACC-CTAAATTTTCCAAAAATTAC-ATTTTA
1 CCCTCGAACTTTCCAAAATTCCATTTTAACCTC-AAAATTTCCAAAAATTACAATTTTA
7432 CCCTC-AGACTTTCCAAAATTCCATTTTTAACCTCAAAATTTCCAAAAATTACAATTTTA
1 CCCTCGA-ACTTTCCAAAATTCCA-TTTTAACCTCAAAATTTCCAAAAATTACAATTTTA
*
7491 CCCTCGAACTTTCCAAAATTCCATTTTAGACCTCAAAATTTCC-AAAATTACATTTTTA
1 CCCTCGAACTTTCCAAAATTCCATTTTA-ACCTCAAAATTTCCAAAAATTACAATTTTA
* * * *
7549 CCC-CTAAACTTTCCAAAATTACCATTTT-ACCTCAGAATGTT-TAAAAATT-CTATTTTTAA
1 CCCTC-GAACTTTCCAAAATT-CCATTTTAACCTCAAAAT-TTCCAAAAATTAC-AATTTT-A
* * * *
7608 CCC-CGAATCCTTCCAAAATTACCATTTTAACC-CTAAATGTCTAAAAACTT-C-ATTTTAA
1 CCCTCGAA-CTTTCCAAAATT-CCATTTTAACCTCAAAATTTCCAAAAA-TTACAATTTT-A
*
7666 ACCTCGAACTTTCCAAAA
1 CCCTCGAACTTTCCAAAA
7684 ATCACCATTA
Statistics
Matches: 273, Mismatches: 16, Indels: 37
0.84 0.05 0.11
Matches are distributed among these distances:
56 11 0.04
57 74 0.27
58 94 0.34
59 87 0.32
60 7 0.03
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
CCCTCGAACTTTCCAAAATTCCATTTTAACCTCAAAATTTCCAAAAATTACAATTTTA
Found at i:7683 original size:29 final size:28
Alignment explanation
Indices: 7323--7741 Score: 228
Period size: 29 Copynumber: 14.5 Consensus size: 28
7313 GGAGGTCCCT
* * *
7323 GAACTTTCTAAAATTCCATTTTTACCTC
1 GAACTTTCCAAAATTACATTTTAACCTC
* * *
7351 AAATTTTCCAAAAATTACATTTTTACC-C
1 GAACTTTCC-AAAATTACATTTTAACCTC
* *
7379 TGAACTTTCCAAAATTCCATTTTTACC-C
1 -GAACTTTCCAAAATTACATTTTAACCTC
* * *
7407 TAAATTTTCCAAAAATTACATTTTACCCTC
1 -GAACTTTCC-AAAATTACATTTTAACCTC
*
7437 -AGACTTTCCAAAATTCCATTTTTAACCTC
1 GA-ACTTTCCAAAATTACA-TTTTAACCTC
* * *
7466 AAAATTTCCAAAAATTACAATTTTACCCTC
1 GAACTTTCC-AAAATTAC-ATTTTAACCTC
*
7496 GAACTTTCCAAAATTCCATTTTAGACCTC
1 GAACTTTCCAAAATTACATTTTA-ACCTC
* * * *
7525 AAAATTTCCAAAATTACATTTTTACCCC
1 GAACTTTCCAAAATTACATTTTAACCTC
*
7553 TAAACTTTCCAAAATTACCATTTT-ACCTC
1 -GAACTTTCCAAAATTA-CATTTTAACCTC
** *
7582 AGAA-TGTTTAAAAATT-CTATTTTTAACCCC
1 -GAACT-TTCCAAAATTAC-A-TTTTAACCTC
*
7612 GAATCCTTCCAAAATTACCATTTTAACC-C
1 GAA-CTTTCCAAAATTA-CATTTTAACCTC
* * * *
7641 TAAATGTCTAAAAACTT-CATTTTAAACCTC
1 GAACTTTC-CAAAA-TTACATTTT-AACCTC
* * *
7671 GAACTTTCCAAAAATCACCATTATACCCTC
1 GAACTTTCC-AAAATTA-CATTTTAACCTC
* * * *
7701 GAAC-ATCTAAAATTTCGTCTTTAA-CTC
1 GAACTTTCCAAAATTACAT-TTTAACCTC
7728 TGAACTTTCCAAAA
1 -GAACTTTCCAAAA
7742 ATTGCCATTT
Statistics
Matches: 303, Mismatches: 58, Indels: 59
0.72 0.14 0.14
Matches are distributed among these distances:
27 6 0.02
28 73 0.24
29 144 0.48
30 72 0.24
31 7 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
GAACTTTCCAAAATTACATTTTAACCTC
Found at i:19690 original size:49 final size:48
Alignment explanation
Indices: 19628--19900 Score: 196
Period size: 49 Copynumber: 5.6 Consensus size: 48
19618 GAAGATATGG
* **
19628 AGGGAAAGGTTTAAGTCGCAACAACGAACCTTGTACCTCAGAGACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TGTACCTCAGAGACATGA
* *** * *
19677 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAACACCAC-GAAGATAT-A
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTGTACCTCAG-AGACATGA
* * * *
19725 GAGGGAAAGGTTTAAATCGCAATGGCGAACCATGTACCTCAGAAACATGA
1 -AGGGAAAGATTTAAGTCGCAACGGCGAACC-TGTACCTCAGAGACATGA
* * **
19775 AGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCAC-GAAGACACAAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTGTACCTCAG-AGACA-TGA
* * * * *
19825 AGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAGA-AGCACGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TGTACCTCAGAGA-CATGA
* * *
19874 AAGGAAA-ATTTAAGCCGCGACGGCGAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA
19901 TTTAGTACCA
Statistics
Matches: 173, Mismatches: 39, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
48 22 0.13
49 110 0.64
50 40 0.23
51 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTGTACCTCAGAGACATGA
Found at i:19782 original size:98 final size:98
Alignment explanation
Indices: 19613--19901 Score: 391
Period size: 98 Copynumber: 2.9 Consensus size: 98
19603 AGGTCTCAGT
* *** *
19613 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAACGAACCTTGTACCTCAGAGACATGAA
1 ACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAA
19678 GGGAAAGATTTAAGCCGCAACGGCGAATCCAAC
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAAC
* *
19711 ACCACGAAGATATAGAGGGAAAGGTTTAAATCGCAATGGCGAACCATGTACCTCAGAAACATGAA
1 ACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAA
* **
19776 GGGAAAGATTTAAGTCGCAACGGCGAATCCAGT
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAAC
* * * * * * *
19809 ACCACGAAGACACAAAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAGAAGCACGA
1 ACCACGAAGATA-TAGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGA
* *
19874 AAGGAAA-ATTTAAGCCGCGACGGCGAAT
65 AGGGAAAGATTTAAGCCGCAACGGCGAAT
19902 TTAGTACCAT
Statistics
Matches: 168, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
98 118 0.70
99 50 0.30
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (98 bp):
ACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAA
GGGAAAGATTTAAGCCGCAACGGCGAATCCAAC
Found at i:20389 original size:27 final size:27
Alignment explanation
Indices: 20357--20418 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
20347 TGTTTTTAAA
* * *
20357 ATTTTAATTTATTTTAAGTTTAAATTT
1 ATTTTAAATTACTTGAAGTTTAAATTT
*
20384 ATTTTAAATTACTTGGAGTTTAAATTT
1 ATTTTAAATTACTTGAAGTTTAAATTT
20411 ATTTTAAA
1 ATTTTAAA
20419 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (27 bp):
ATTTTAAATTACTTGAAGTTTAAATTT
Found at i:20425 original size:18 final size:18
Alignment explanation
Indices: 20402--20436 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20392 TTACTTGGAG
20402 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
20420 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
20437 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:20445 original size:18 final size:18
Alignment explanation
Indices: 20405--20442 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20395 CTTGGAGTTT
*
20405 AAATTTATTTTAAAATTT
1 AAATTTATTTTAAAATTA
20423 AAATTTATTTT-AAATTA
1 AAATTTATTTTAAAATTA
20440 AAA
1 AAA
20443 ATTAAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTATTTTAAAATTA
Found at i:21222 original size:3 final size:3
Alignment explanation
Indices: 21216--21255 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
21206 AGTAATAAAT
21216 ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21256 AAAGTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21222 original size:9 final size:10
Alignment explanation
Indices: 21208--21251 Score: 58
Period size: 9 Copynumber: 4.7 Consensus size: 10
21198 TTATTAGTAG
21208 TAATAAAT-A
1 TAATAAATAA
*
21217 TAATAATTAA
1 TAATAAATAA
21227 TAAT-AATAA
1 TAATAAATAA
21236 TAAT-AATAA
1 TAATAAATAA
21245 TAATAAA
1 TAATAAA
21252 ATAAAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 24 0.77
10 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TAATAAATAA
Found at i:21225 original size:22 final size:22
Alignment explanation
Indices: 21208--21255 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
21198 TTATTAGTAG
21208 TAATAA-ATATAATAATTAATAA
1 TAATAATA-ATAATAATTAATAA
21230 TAATAATAATAATAA-TAATAA
1 TAATAATAATAATAATTAATAA
21251 -AATAA
1 TAATAA
21256 AAAGTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.20
21 6 0.24
22 13 0.52
23 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAATTAATAA
Found at i:22390 original size:29 final size:30
Alignment explanation
Indices: 22314--22635 Score: 269
Period size: 29 Copynumber: 10.9 Consensus size: 30
22304 CCCTGAAGGT
*
22314 CCCT-AAACTTTCCAAAATTTCATTTTTGA
1 CCCTCAAACTTTCCAAAATTACATTTTTGA
** * *
22343 -TATCAAATTTTCCAAAAATTATATTTTT-A
1 CCCTCAAACTTTCC-AAAATTACATTTTTGA
* *
22372 CCCTCAAACTTTCCAAAATTCCATTTTTAA
1 CCCTCAAACTTTCCAAAATTACATTTTTGA
* *
22402 CCCT-AAATTTTCCAAAAATTAC-TTTTTTA
1 CCCTCAAACTTTCC-AAAATTACATTTTTGA
* *
22431 CCCCTCGAACTTTCCAAAATTCCATTTTTGA
1 -CCCTCAAACTTTCCAAAATTACATTTTTGA
* *
22462 -CTTCAAATTTTCCAAAAATTACATTTTT-A
1 CCCTCAAACTTTCC-AAAATTACATTTTTGA
*
22491 CCCTCAAACTTT-CAAAATT-CAATTTTTAA
1 CCCTCAAACTTTCCAAAATTAC-ATTTTTGA
* *
22520 CCCT-AAATTTTCCAAAAATTATATTTTT-A
1 CCCTCAAACTTTCC-AAAATTACATTTTTGA
* *
22549 CCC-CTATACTTTCCAAAATTCCATTTTTGA
1 CCCTC-AAACTTTCCAAAATTACATTTTTGA
*
22579 -CCTCAAATTTTCCAAAATTACATTTTT-A
1 CCCTCAAACTTTCCAAAATTACATTTTTGA
*
22607 CGCCT-AAACTTACCAAAAATTACCATTTT
1 C-CCTCAAACTTTCC-AAAATTA-CATTTT
22636 AGCCCCAGAT
Statistics
Matches: 236, Mismatches: 34, Indels: 44
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.00
28 20 0.08
29 98 0.42
30 98 0.42
31 19 0.08
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAATTACATTTTTGA
Found at i:22390 original size:59 final size:58
Alignment explanation
Indices: 22314--22635 Score: 372
Period size: 59 Copynumber: 5.5 Consensus size: 58
22304 CCCTGAAGGT
*
22314 CCCT-AAACTTTCCAAAATTTCATTTTTGATATCAAATTTTCCAAAAATTATATTTTTA
1 CCCTCAAACTTTCCAAAATTCCATTTTTGA-ATCAAATTTTCCAAAAATTATATTTTTA
*
22372 CCCTCAAACTTTCCAAAATTCCATTTTT-AACCCTAAATTTTCCAAAAATTACT-TTTTTA
1 CCCTCAAACTTTCCAAAATTCCATTTTTGAA-TC-AAATTTTCCAAAAATTA-TATTTTTA
* * *
22431 CCCCTCGAACTTTCCAAAATTCCATTTTTGACTTCAAATTTTCCAAAAATTACATTTTTA
1 -CCCTCAAACTTTCCAAAATTCCATTTTTGA-ATCAAATTTTCCAAAAATTATATTTTTA
* *
22491 CCCTCAAACTTT-CAAAATTCAATTTTT-AACCCTAAATTTTCCAAAAATTATATTTTTA
1 CCCTCAAACTTTCCAAAATTCCATTTTTGAA-TC-AAATTTTCCAAAAATTATATTTTTA
* * *
22549 CCC-CTATACTTTCCAAAATTCCATTTTTGACCTCAAATTTTCC-AAAATTACATTTTTA
1 CCCTC-AAACTTTCCAAAATTCCATTTTTGA-ATCAAATTTTCCAAAAATTATATTTTTA
*
22607 CGCCT-AAACTTACCAAAAATTACCATTTT
1 C-CCTCAAACTTTCC-AAAATT-CCATTTT
22636 AGCCCCAGAT
Statistics
Matches: 228, Mismatches: 18, Indels: 34
0.81 0.06 0.12
Matches are distributed among these distances:
57 4 0.02
58 75 0.33
59 87 0.38
60 60 0.26
61 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (58 bp):
CCCTCAAACTTTCCAAAATTCCATTTTTGAATCAAATTTTCCAAAAATTATATTTTTA
Found at i:22628 original size:30 final size:28
Alignment explanation
Indices: 22314--22635 Score: 258
Period size: 30 Copynumber: 10.9 Consensus size: 28
22304 CCCTGAAGGT
*
22314 CCCTAAACTTTCCAAAATTTCATTTTTGA
1 CCCTAAACTTTCCAAAATTACATTTTT-A
** * *
22343 -TATCAAATTTTCCAAAAATTATATTTTTA
1 CCCT-AAACTTTCC-AAAATTACATTTTTA
*
22372 CCCTCAAACTTTCCAAAATTCCATTTTTAA
1 CCCT-AAACTTTCCAAAATTACATTTTT-A
* *
22402 CCCTAAATTTTCCAAAAATTACTTTTTTA
1 CCCTAAACTTTCC-AAAATTACATTTTTA
* *
22431 CCCCTCGAACTTTCCAAAATTCCATTTTTGA
1 -CCCT-AAACTTTCCAAAATTACATTTTT-A
* *
22462 -CTTCAAATTTTCCAAAAATTACATTTTTA
1 CCCT-AAACTTTCC-AAAATTACATTTTTA
22491 CCCTCAAACTTT-CAAAATT-CAATTTTTAA
1 CCCT-AAACTTTCCAAAATTAC-ATTTTT-A
* *
22520 CCCTAAATTTTCCAAAAATTATATTTTTA
1 CCCTAAACTTTCC-AAAATTACATTTTTA
* *
22549 CCCCTATACTTTCCAAAATTCCATTTTTGA
1 -CCCTAAACTTTCCAAAATTACATTTTT-A
*
22579 -CCTCAAATTTTCCAAAATTACATTTTTA
1 CCCT-AAACTTTCCAAAATTACATTTTTA
*
22607 CGCCTAAACTTACCAAAAATTACCATTTT
1 C-CCTAAACTTTCC-AAAATTA-CATTTT
22636 AGCCCCAGAT
Statistics
Matches: 237, Mismatches: 34, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
27 1 0.00
28 23 0.10
29 88 0.37
30 111 0.47
31 14 0.06
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTACATTTTTA
Found at i:22712 original size:59 final size:57
Alignment explanation
Indices: 22613--22800 Score: 141
Period size: 59 Copynumber: 3.2 Consensus size: 57
22603 TTTACGCCTA
* * * * *
22613 AACTTACCAAAAATTACCATTTTAGCCCC-AGATGTTTAAAAATTCTATTTTTAACCTTG
1 AACTTTCC-AAAATCACCATTATA-CCCCTAAATGTCTAAAAATTC-ATTTTTAACCTTG
* * * *
22672 AAACCTTT-TAAAATCACCATTATACCCCTAAATGTCTAAAAACTCCATTTTAAAGCTTG
1 -AA-CTTTCCAAAATCACCATTATACCCCTAAATGTCTAAAAA-TTCATTTTTAACCTTG
* * * * *
22731 TACTTTCCCAAAATCACCATTATA-CCCTCGAACGTCTAAAATTTCATTTTTAA-CTCTA
1 AACTTT-CCAAAATCACCATTATACCCCT-AAATGTCTAAAAATTCATTTTTAACCT-TG
22789 AACTTTCCAAAA
1 AACTTTCCAAAA
22801 ATTATCATTT
Statistics
Matches: 103, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
57 12 0.12
58 24 0.23
59 60 0.58
60 4 0.04
61 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (57 bp):
AACTTTCCAAAATCACCATTATACCCCTAAATGTCTAAAAATTCATTTTTAACCTTG
Found at i:33871 original size:18 final size:18
Alignment explanation
Indices: 33848--33884 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
33838 TATGGAAAAC
33848 CAGAAGATGATTATTGAA
1 CAGAAGATGATTATTGAA
33866 CAGAAGATGATTATTGAA
1 CAGAAGATGATTATTGAA
33884 C
1 C
33885 TTCCATGGAC
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:0.08, G:0.22, T:0.27
Consensus pattern (18 bp):
CAGAAGATGATTATTGAA
Found at i:38755 original size:29 final size:29
Alignment explanation
Indices: 38677--38748 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
38667 ATTTTAGCCA
*
38677 ATTTATTCCATATCTATATTTCCTAATAG
1 ATTTATTCCATATCTATATTTCCCAATAG
38706 ATTTATTCCATATCTATATTTCCCAATAG
1 ATTTATTCCATATCTATATTTCCCAATAG
*
38735 ATTTATTCAATATC
1 ATTTATTCCATATC
38749 CTCATTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (29 bp):
ATTTATTCCATATCTATATTTCCCAATAG
Found at i:40100 original size:17 final size:18
Alignment explanation
Indices: 40073--40106 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40063 GCTTCGGGGA
*
40073 ATATGCCAAAATTTTCAC
1 ATATGCCAAAATCTTCAC
40091 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
40107 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:42690 original size:28 final size:28
Alignment explanation
Indices: 42659--42712 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
42649 TTTCTCGATT
*
42659 TATT-TAAAAAAAATTTATTTGATTAAAA
1 TATTATAAAAAAAATTTAATT-ATTAAAA
* *
42687 TATTATTAAAAAAGTTTAATTATTAA
1 TATTATAAAAAAAATTTAATTATTAA
42713 TGTTATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 9 0.41
29 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
TATTATAAAAAAAATTTAATTATTAAAA
Found at i:45758 original size:17 final size:16
Alignment explanation
Indices: 45719--45752 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
45709 TTAATTTGAG
45719 TTAAATTTAAATATTAA
1 TTAAA-TTAAATATTAA
45736 TTAAATTAAAT-TTAA
1 TTAAATTAAATATTAA
45751 TT
1 TT
45753 GTAAATCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTAAATATTAA
Found at i:51234 original size:18 final size:18
Alignment explanation
Indices: 51208--51242 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
51198 CTGGCTAGGG
*
51208 AGCTGAAAAAGGAAAGGA
1 AGCTAAAAAAGGAAAGGA
51226 AGCTAAAAAAGGAAAGG
1 AGCTAAAAAAGGAAAGG
51243 GCCCTGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.06, G:0.31, T:0.06
Consensus pattern (18 bp):
AGCTAAAAAAGGAAAGGA
Found at i:55435 original size:29 final size:28
Alignment explanation
Indices: 55330--55493 Score: 152
Period size: 28 Copynumber: 5.8 Consensus size: 28
55320 AATTATGTGA
* * *
55330 AAAAGATATATCTGTAAGGATATCATTG
1 AAAAGGTATATCCGTAAGGATATCAATG
* *
55358 AAAAAGG-ATATCCGCAAGCATATCAATG
1 -AAAAGGTATATCCGTAAGGATATCAATG
* *
55386 AAAAGGAATATCCGTAAGGATATTAATG
1 AAAAGGTATATCCGTAAGGATATCAATG
* *
55414 AAAAGGTTATATTCGTAAGGATAT-TATG
1 AAAAGG-TATATCCGTAAGGATATCAATG
* * * *
55442 AAAAGGGATTTCCGGAAGGATATCATTG
1 AAAAGGTATATCCGTAAGGATATCAATG
**
55470 AAAAGGTTATATCCCAAAGGATAT
1 AAAAGG-TATATCCGTAAGGATAT
55494 TTGAAAATGT
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 19 0.17
28 58 0.53
29 33 0.30
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.27
Consensus pattern (28 bp):
AAAAGGTATATCCGTAAGGATATCAATG
Found at i:55519 original size:27 final size:27
Alignment explanation
Indices: 55467--55519 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
55457 AAGGATATCA
* *
55467 TTGAAAAGGTTATATCCCAAAGGATAT
1 TTGAAAAGGTTATATCCAAAAAGATAT
* *
55494 TTGAAAATGTTATATCTAAAAAGATA
1 TTGAAAAGGTTATATCCAAAAAGATA
55520 ATAAATGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (27 bp):
TTGAAAAGGTTATATCCAAAAAGATAT
Found at i:64771 original size:3 final size:3
Alignment explanation
Indices: 64763--64827 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
64753 GTCGAGGCAA
* *
64763 TTC TTC TTC TTC TTC TTC TTC TTT TTCC TTC -TC CTC TT- TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC -TTC
*
64808 TTA TTC -TC TTGC TTC TTC TT
1 TTC TTC TTC TT-C TTC TTC TT
64828 TTGCTTCAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
2 6 0.12
3 37 0.73
4 8 0.16
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:73368 original size:23 final size:23
Alignment explanation
Indices: 73342--73442 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 23
73332 AGCACGTTTC
*
73342 GTGCCCTCTGATCAGCACTTTGT
1 GTGCTCTCTGATCAGCACTTTGT
* *
73365 GTGCTTTCTGATTAGCACTTTGT
1 GTGCTCTCTGATCAGCACTTTGT
* * * *
73388 GTGCTCTCTAATTAGTATTTTGT
1 GTGCTCTCTGATCAGCACTTTGT
* * * * *
73411 GTACTCTCTGTTTAACACTGTGT
1 GTGCTCTCTGATCAGCACTTTGT
73434 GTGCTCTCT
1 GTGCTCTCT
73443 ATTGCCCAGC
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATCAGCACTTTGT
Found at i:75196 original size:18 final size:18
Alignment explanation
Indices: 75158--75195 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
75148 TCACTGGAAA
**
75158 TTTCAGATCTTCCTCCCT
1 TTTCAGATCTAACTCCCT
75176 TTTCAGATCTAACT-CCT
1 TTTCAGATCTAACTCCCT
75193 TTT
1 TTT
75196 TGCAATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.32, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTCAGATCTAACTCCCT
Found at i:77516 original size:128 final size:129
Alignment explanation
Indices: 77269--77518 Score: 283
Period size: 128 Copynumber: 1.9 Consensus size: 129
77259 GATGCGAGTT
* * * * *
77269 TAAAAAAAAGAAGAGATCGAGATGAAAATCCGTAAATGACATCTTGAAACCTAAGGAGTTTTTAT
1 TAAAAAAAAGAAGAGATCGAGATGAAAATCCGTAAAGGACATCTCGAAACCTAAGGAGATTTGAG
** * * * **
77334 TTGAAAACCCAAAAAGTGCGGCTCAAATTTGAACCAAAGAATTGGCATGTAATGGTCATTTCCC
66 TCAAAAACCCAAAAAGGGCGACTCAAATTTGAACCAAAGAATGGGCATCAAATGGTCATTTCCC
* * *
77398 TAAAAAAAAGAA-AGGTTGAGATGAAAA-CTCGTAAAAGGGCATCTCGAAACCTAAGGAGATTTG
1 TAAAAAAAAGAAGAGATCGAGATGAAAATC-CGT-AAAGGACATCTCGAAACCTAAGGAGATTTG
* * *
77461 AGTCAAAAACCC-AAAAGGGCGACTCAAATTT-AGATCGAAGAATGGGTATCAAATGGTC
64 AGTCAAAAACCCAAAAAGGGCGACTCAAATTTGA-ACCAAAGAATGGGCATCAAATGGTC
77519 TTCTCTCTCA
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
127 2 0.02
128 52 0.52
129 46 0.46
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (129 bp):
TAAAAAAAAGAAGAGATCGAGATGAAAATCCGTAAAGGACATCTCGAAACCTAAGGAGATTTGAG
TCAAAAACCCAAAAAGGGCGACTCAAATTTGAACCAAAGAATGGGCATCAAATGGTCATTTCCC
Found at i:79260 original size:63 final size:63
Alignment explanation
Indices: 79189--79315 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
79179 TAAATTACAG
*
79189 AATAAAAGGAAAGAAAAAGAAAATCTTAGTTTGAAATTTTGAATGAAGTACGCGACCAAACAT
1 AATAAAAGGAAAGAAAAAGAAAATCTTAGTTTAAAATTTTGAATGAAGTACGCGACCAAACAT
*
79252 AATAAAAGGAAAGAAAAAGAAAATCTTAGTTTAAAATTTTGAATGAAGTATGCGACCAAACAT
1 AATAAAAGGAAAGAAAAAGAAAATCTTAGTTTAAAATTTTGAATGAAGTACGCGACCAAACAT
79315 A
1 A
79316 CCTTAAATTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.23
Consensus pattern (63 bp):
AATAAAAGGAAAGAAAAAGAAAATCTTAGTTTAAAATTTTGAATGAAGTACGCGACCAAACAT
Found at i:79421 original size:24 final size:25
Alignment explanation
Indices: 79394--79442 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
79384 TGCTTGCTGG
*
79394 TTCAGTGC-AGAGTAGCCACAACAA
1 TTCAGTGCGAGAGCAGCCACAACAA
79418 TTCAGTGCGAGAGCAGCCACAACAA
1 TTCAGTGCGAGAGCAGCCACAACAA
79443 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (25 bp):
TTCAGTGCGAGAGCAGCCACAACAA
Found at i:82619 original size:9 final size:9
Alignment explanation
Indices: 82605--82658 Score: 74
Period size: 9 Copynumber: 5.9 Consensus size: 9
82595 GGCAACACAA
82605 TTATTTTTT
1 TTATTTTTT
82614 TTATTTTTT
1 TTATTTTTT
82623 TTATTTTTT
1 TTATTTTTT
82632 TCTATTTTATT
1 T-TATTTT-TT
*
82643 TTA-TTTTC
1 TTATTTTTT
82651 TTATTTTT
1 TTATTTTT
82659 CCTAGAAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
8 4 0.10
9 26 0.63
10 8 0.20
11 3 0.07
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (9 bp):
TTATTTTTT
Found at i:82629 original size:5 final size:5
Alignment explanation
Indices: 82605--82649 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
82595 GGCAACACAA
82605 TTATT TT-TT TTATT TT-TT TTATT TT-TT TCTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TT
82650 CTTATTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 11 0.31
5 22 0.61
6 3 0.08
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.84
Consensus pattern (5 bp):
TTATT
Found at i:92303 original size:20 final size:21
Alignment explanation
Indices: 92260--92306 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
92250 TAATAACCTT
**
92260 AATTAA-TTAAATTAATCTTT
1 AATTAACTTAAATTAATCTAA
92280 AATTAACTTAAATTAAT-TAA
1 AATTAACTTAAATTAATCTAA
92300 AATTAAC
1 AATTAAC
92307 CTATTTAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAACTTAAATTAATCTAA
Found at i:95340 original size:5 final size:5
Alignment explanation
Indices: 95322--95367 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
95312 GCCTTCGCTT
* *
95322 CTCTC CGCTT CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC C
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC C
95368 ATTACCCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.59, G:0.02, T:0.39
Consensus pattern (5 bp):
CTCTC
Found at i:99466 original size:61 final size:61
Alignment explanation
Indices: 99366--99495 Score: 251
Period size: 61 Copynumber: 2.1 Consensus size: 61
99356 TTTTTAATTT
*
99366 CCCCTTCATATACCTGAAGAATGAAAAAGTCATTACTGAATTGAGAATCCATCAAACCTTA
1 CCCCATCATATACCTGAAGAATGAAAAAGTCATTACTGAATTGAGAATCCATCAAACCTTA
99427 CCCCATCATATACCTGAAGAATGAAAAAGTCATTACTGAATTGAGAATCCATCAAACCTTA
1 CCCCATCATATACCTGAAGAATGAAAAAGTCATTACTGAATTGAGAATCCATCAAACCTTA
99488 CCCCATCA
1 CCCCATCA
99496 ATCTTTCACT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (61 bp):
CCCCATCATATACCTGAAGAATGAAAAAGTCATTACTGAATTGAGAATCCATCAAACCTTA
Found at i:100039 original size:2 final size:2
Alignment explanation
Indices: 100034--100060 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
100024 GAATGACTAG
100034 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
100061 AATAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:105489 original size:23 final size:23
Alignment explanation
Indices: 105444--105581 Score: 147
Period size: 23 Copynumber: 6.0 Consensus size: 23
105434 CTTACTGATC
* *
105444 AGCATTGTGTGTG-CTTCTGTTT
1 AGCACTGTGTGTGCCCTCTGTTT
*
105466 AGCACTGTGTGTGCTCTCTGTTT
1 AGCACTGTGTGTGCCCTCTGTTT
* * *
105489 AGCA-TGTTTCATGCCATCTGTTT
1 AGCACTGTGT-GTGCCCTCTGTTT
105512 AGCACTGTGTGTGCCCTCTGTTATT
1 AGCACTGTGTGTGCCCTCTG-T-TT
*
105537 AGCACT-TCGTGTGCCCTCTGATT
1 AGCACTGT-GTGTGCCCTCTGTTT
*
105560 AGCACTTTGTGTGCCCTCTGTT
1 AGCACTGTGTGTGCCCTCTGTT
105582 ACCCAGCACT
Statistics
Matches: 97, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
22 16 0.16
23 54 0.56
24 7 0.07
25 20 0.21
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (23 bp):
AGCACTGTGTGTGCCCTCTGTTT
Found at i:105548 original size:25 final size:24
Alignment explanation
Indices: 105510--105607 Score: 119
Period size: 25 Copynumber: 4.0 Consensus size: 24
105500 TGCCATCTGT
105510 TTAGCACTGTGTGTGCCCTCTGTTA
1 TTAGCACT-TGTGTGCCCTCTGTTA
105535 TTAGCACTTCGTGTGCCCTCTG--A
1 TTAGCACTT-GTGTGCCCTCTGTTA
105558 TTAGCACTTTGTGTGCCCTCTGTTA
1 TTAGCAC-TTGTGTGCCCTCTGTTA
** *
105583 CCCAGCACTTATGTGCCCTCTGTTA
1 -TTAGCACTTGTGTGCCCTCTGTTA
105608 AGTACTTCGG
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
23 20 0.31
24 3 0.05
25 37 0.57
26 5 0.08
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (24 bp):
TTAGCACTTGTGTGCCCTCTGTTA
Found at i:105562 original size:48 final size:47
Alignment explanation
Indices: 105459--105606 Score: 158
Period size: 48 Copynumber: 3.1 Consensus size: 47
105449 TGTGTGTGCT
* * * *
105459 TCTGTTTAGCACTGTGTGTGCTCTCTG-T-TTAGCA-TGTTTCATGCCA
1 TCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCACT-TAT-GTGCCC
*
105505 TCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCACTTCGTGTGCCC
1 TCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCACTT-ATGTGCCC
* * **
105553 TCTGATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTTATGTGCCC
1 TCTGTTTAGCACTGTGTGTGCCCTCTGTTA-TTAGCACTTATGTGCCC
105601 TCTGTT
1 TCTGTT
105607 AAGTACTTCG
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
46 26 0.30
47 1 0.01
48 51 0.59
49 9 0.10
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (47 bp):
TCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCACTTATGTGCCC
Found at i:109478 original size:24 final size:24
Alignment explanation
Indices: 109442--109569 Score: 184
Period size: 24 Copynumber: 5.3 Consensus size: 24
109432 CAGAGAACAG
* *
109442 GAAGTTGGCAAGAGTACGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
*
109466 GAAGGTGGTAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
*
109490 GAAGGTGACAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
*
109514 GAAAGTGGCAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
* * *
109538 GAAGGTAGTAAGAGTAGGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
109562 GAAGGTGG
1 GAAGGTGG
109570 AAACAAGACT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 92 1.00
ACGTcount: A:0.45, C:0.11, G:0.33, T:0.11
Consensus pattern (24 bp):
GAAGGTGGCAAGAGTAAGACACAA
Found at i:112603 original size:29 final size:28
Alignment explanation
Indices: 112530--112606 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
112520 TTGGATTTTC
*
112530 ATTTTTAAATATAAATATAAAGAGTTAA
1 ATTTTTAAATATAAAAATAAAGAGTTAA
* *
112558 ATTTTCTGAA-ATAAAAATAAATAGATTAA
1 ATTTT-TAAATATAAAAATAAAGAG-TTAA
*
112587 ATTTTAAATATATAAAAATA
1 ATTTTTAA-ATATAAAAATA
112607 TAAAGGATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 18 0.45
29 13 0.32
30 9 0.22
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (28 bp):
ATTTTTAAATATAAAAATAAAGAGTTAA
Found at i:116782 original size:375 final size:375
Alignment explanation
Indices: 116091--116842 Score: 1495
Period size: 375 Copynumber: 2.0 Consensus size: 375
116081 TATGCTGCAA
116091 AAACAGAGGCACCAACTTTTCTATTGGAGGCTAAAAATTTCTAGCACAGCTTGCTTAGCATTGCC
1 AAACAGAGGCACCAACTTTTCTATTGGAGGCTAAAAATTTCTAGCACAGCTTGCTTAGCATTGCC
116156 ATTAAATTCAGCCTAAGTAGGAATTGTGCTCCTCCTGCAACTTAAGTTTCCCCAGTCCCCTTTAG
66 ATTAAATTCAGCCTAAGTAGGAATTGTGCTCCTCCTGCAACTTAAGTTTCCCCAGTCCCCTTTAG
116221 TTTAAAAAAATATTTCATTTCTTTTGAAGATATTGTAAAACTGTTGGTACCGACTTCATTCTTTT
131 TTTAAAAAAATATTTCATTTCTTTTGAAGATATTGTAAAACTGTTGGTACCGACTTCATTCTTTT
116286 CCGTGTCAATGCCACCATCCATCATCACTAACGCCAGATTTTAACTTCTGCAAAAACAGAAAATT
196 CCGTGTCAATGCCACCATCCATCATCACTAACGCCAGATTTTAACTTCTGCAAAAACAGAAAATT
*
116351 CCTTCAAATATTTTATCCTTGGAACGAACGTGGTGGTGTTAGGATTGACGGCGAGCCAAAAGCTT
261 CCTTCAAATATTTTATCCTTGGAACGAACGTGGTGGTGTTAGGATTGACAGCGAGCCAAAAGCTT
116416 TAGACTTTTTGTAAAGCTGAAAAAAAATCTCAGATAGCCGTTGATGAAGC
326 TAGACTTTTTGTAAAGCTGAAAAAAAATCTCAGATAGCCGTTGATGAAGC
116466 AAACAGAGGCACCAACTTTTCTATTGGAGGCTAAAAATTTCTAGCACAGCTTGCTTAGCATTGCC
1 AAACAGAGGCACCAACTTTTCTATTGGAGGCTAAAAATTTCTAGCACAGCTTGCTTAGCATTGCC
116531 ATTAAATTCAGCCTAAGTAGGAATTGTGCTCCTCCTGCAACTTAAGTTTCCCCAGTCCCCTTTAG
66 ATTAAATTCAGCCTAAGTAGGAATTGTGCTCCTCCTGCAACTTAAGTTTCCCCAGTCCCCTTTAG
116596 TTTAAAAAAATATTTCATTTCTTTTGAAGATATTGTAAAACTGTTGGTACCGACTTCATTCTTTT
131 TTTAAAAAAATATTTCATTTCTTTTGAAGATATTGTAAAACTGTTGGTACCGACTTCATTCTTTT
116661 CCGTGTCAATGCCACCATCCATCATCACTAACGCCAGATTTTAACTTCTGCAAAAACAGAAAATT
196 CCGTGTCAATGCCACCATCCATCATCACTAACGCCAGATTTTAACTTCTGCAAAAACAGAAAATT
116726 CCTTCAAATATTTTATCCTTGGAACGAACGTGGTGGTGTTAGGATTGACAGCGAGCCAAAAGCTT
261 CCTTCAAATATTTTATCCTTGGAACGAACGTGGTGGTGTTAGGATTGACAGCGAGCCAAAAGCTT
116791 TAGACTTTTTGTAAAGCTGAAAAAAAATCTCAGATAGCCGTTGATGAAGC
326 TAGACTTTTTGTAAAGCTGAAAAAAAATCTCAGATAGCCGTTGATGAAGC
116841 AA
1 AA
116843 TAAGAGGAAA
Statistics
Matches: 376, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
375 376 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (375 bp):
AAACAGAGGCACCAACTTTTCTATTGGAGGCTAAAAATTTCTAGCACAGCTTGCTTAGCATTGCC
ATTAAATTCAGCCTAAGTAGGAATTGTGCTCCTCCTGCAACTTAAGTTTCCCCAGTCCCCTTTAG
TTTAAAAAAATATTTCATTTCTTTTGAAGATATTGTAAAACTGTTGGTACCGACTTCATTCTTTT
CCGTGTCAATGCCACCATCCATCATCACTAACGCCAGATTTTAACTTCTGCAAAAACAGAAAATT
CCTTCAAATATTTTATCCTTGGAACGAACGTGGTGGTGTTAGGATTGACAGCGAGCCAAAAGCTT
TAGACTTTTTGTAAAGCTGAAAAAAAATCTCAGATAGCCGTTGATGAAGC
Found at i:117610 original size:302 final size:298
Alignment explanation
Indices: 117042--117626 Score: 936
Period size: 302 Copynumber: 1.9 Consensus size: 298
117032 AACTCCCTTC
* * * *
117042 CACCTTTCTTCGTCTCTGTGAGTACTTTTCAATTTCGTGACATGCAACACAAGATTTATTAAAAG
1 CACCTTTCTTCGTCTCTCTGAGTACTTTCCAATTTCGTGACATACAACACAAAATTTATTAAAAG
* *
117107 TATAGACGTGTCGAAGATTTCAATAAAGAATATTTCAAAATTTAGAGAGAAAATAGGGTTTAAGA
66 TATAGACGTATCGAAGATTTAAATAAAGAATATTTCAAAATTTAGAGAGAAAATAGGGTTTAAGA
*
117172 GGTGAAAAGTTGAGAAGAGAAGAAGAGAATTGTAGAGAAAGGACATTTGCTGATTAGGATTCTCC
131 CGTGAAAAGTTGAGAAGAGAAGAAGAGAATTGTAGAGAAAGGACATTTGCTGATTAGGATTCTCC
*
117237 TCCAATTTCCTTCAAATATTTTATCCTTAGAACGAACGTGACGGTGTTAGGATTGACGGCGAGCC
196 TCCAATTTCCTTAAAATATTTTATCCTTAGAACGAACGTGACGGTGTTAGGATTGACGGCGAGCC
117302 AAAAGCTTTACACTTTTTGTAAAGCTGGAAAAAAAAAT
261 AAAAGCTTTACACTTTTTGTAAAGCTGGAAAAAAAAAT
**
117340 CACCTTTCTTCGTCTCTCTGAGTACTTTCCAATTTCGTGACATACTGCACAAAATTTATTAAAAG
1 CACCTTTCTTCGTCTCTCTGAGTACTTTCCAATTTCGTGACATACAACACAAAATTTATTAAAAG
* * * *
117405 TATAGGCGTATCGAAGATTTGAAATAAGGAATATTTTAAAATTTAGAGAGAAAATAGGGTTTGAG
66 TATAGACGTATCGAAGATTT-AAATAAAGAATATTTCAAAATTTAGAGAGAAAATAGGGTTTAAG
* *
117470 ACGTGAAAAGATTGAGAAGAGAAGAAGAGAATTGTAGAGGAAGGACATTTGCTGATTAGGGTTCT
130 ACGTGAAAAG-TTGAGAAGAGAAGAAGAGAATTGTAGAGAAAGGACATTTGCTGATTAGGATTC-
* * **
117535 TTCCTCCAATTTCCTTAAAATATTTTATCTTTGGAACGAACGTGGTGGTGTTAGGATTGACGGCG
193 -TCCTCCAATTTCCTTAAAATATTTTATCCTTAGAACGAACGTGACGGTGTTAGGATTGACGGCG
**
117600 AGCCAAAAGCTTTAGGCTTTTTGTAAA
257 AGCCAAAAGCTTTACACTTTTTGTAAA
117627 TCTTCGACAC
Statistics
Matches: 261, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
298 77 0.30
299 49 0.19
300 51 0.20
302 84 0.32
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (298 bp):
CACCTTTCTTCGTCTCTCTGAGTACTTTCCAATTTCGTGACATACAACACAAAATTTATTAAAAG
TATAGACGTATCGAAGATTTAAATAAAGAATATTTCAAAATTTAGAGAGAAAATAGGGTTTAAGA
CGTGAAAAGTTGAGAAGAGAAGAAGAGAATTGTAGAGAAAGGACATTTGCTGATTAGGATTCTCC
TCCAATTTCCTTAAAATATTTTATCCTTAGAACGAACGTGACGGTGTTAGGATTGACGGCGAGCC
AAAAGCTTTACACTTTTTGTAAAGCTGGAAAAAAAAAT
Found at i:147847 original size:21 final size:21
Alignment explanation
Indices: 147823--147866 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
147813 GATTGGATTG
147823 GCTGGAGTTTTAGTTATGTCA
1 GCTGGAGTTTTAGTTATGTCA
147844 GCTGGAGTTTTAGTTATGTCA
1 GCTGGAGTTTTAGTTATGTCA
147865 GC
1 GC
147867 CTTTCCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.30, T:0.41
Consensus pattern (21 bp):
GCTGGAGTTTTAGTTATGTCA
Found at i:152140 original size:3 final size:3
Alignment explanation
Indices: 152132--152162 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
152122 GCTTCTCAAA
152132 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
152163 GATAGCTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:160426 original size:31 final size:29
Alignment explanation
Indices: 160361--160432 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
160351 CTTAGGTTAT
*
160361 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTGAAATGTAAC
***
160390 ATTTTAGTCACTTATGTTGTCGTGTTGTAAC
1 ATTTTAGTCACTTATGTT-T-GAAATGTAAC
160421 ATTTTAGTCACT
1 ATTTTAGTCACT
160433 GAGCGTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 18 0.49
30 1 0.03
31 18 0.49
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTGAAATGTAAC
Found at i:171332 original size:19 final size:19
Alignment explanation
Indices: 171305--171345 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
171295 CAATTTTTTT
*
171305 AAAATTTTTAATATTTAA-A
1 AAAAATTTTAAT-TTTAATA
171324 AAAAATTTTAATTTTAATA
1 AAAAATTTTAATTTTAATA
171343 AAA
1 AAA
171346 TTATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATTTTAATTTTAATA
Found at i:171337 original size:17 final size:17
Alignment explanation
Indices: 171317--171355 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
171307 AATTTTTAAT
*
171317 ATTTAAAAAAAATTTTA
1 ATTTAAAAAAAATTATA
* *
171334 ATTTTAATAAAATTATA
1 ATTTAAAAAAAATTATA
171351 ATTTA
1 ATTTA
171356 GGACCCTCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAAAAAAATTATA
Found at i:187305 original size:2 final size:2
Alignment explanation
Indices: 187298--187324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
187288 CCAGCATCGT
187298 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 T
187325 TTTTAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:190330 original size:21 final size:21
Alignment explanation
Indices: 190300--190341 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
190290 AGCTATAAAA
*
190300 GTTTTGCTGTTTGAATTGATT
1 GTTTTGCTGTTTGAATCGATT
*
190321 GTTTTTCTGTTTGAATCGATT
1 GTTTTGCTGTTTGAATCGATT
190342 CATTTTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (21 bp):
GTTTTGCTGTTTGAATCGATT
Found at i:190347 original size:21 final size:21
Alignment explanation
Indices: 190301--190357 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
190291 GCTATAAAAG
* **
190301 TTTTGCTGTTTGAATTGATTGT
1 TTTT-CTGTTTGAATCGATTCA
190323 TTTTCTGTTTGAATCGATTCA
1 TTTTCTGTTTGAATCGATTCA
*
190344 TTTTC-GTTTAAATC
1 TTTTCTGTTTGAATC
190358 AATTTTGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.26
21 19 0.61
22 4 0.13
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.56
Consensus pattern (21 bp):
TTTTCTGTTTGAATCGATTCA
Found at i:191608 original size:23 final size:23
Alignment explanation
Indices: 191582--191638 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
191572 AAAATTAAAT
191582 TATAATTTTTACGATAATAAAAA
1 TATAATTTTTACGATAATAAAAA
191605 TATAATTTTTACGATAATAAAAA
1 TATAATTTTTACGATAATAAAAA
191628 TATAATTTTTA
1 TATAATTTTTA
191639 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (23 bp):
TATAATTTTTACGATAATAAAAA
Found at i:191648 original size:23 final size:23
Alignment explanation
Indices: 191572--191638 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
191562 TTTAAGAGTC
* *
191572 AAAATTAAATTATAATTTTTACG
1 AAAATAAAAATATAATTTTTACG
*
191595 ATAATAAAAATATAATTTTTACG
1 AAAATAAAAATATAATTTTTACG
*
191618 ATAATAAAAATATAATTTTTA
1 AAAATAAAAATATAATTTTTA
191639 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (23 bp):
AAAATAAAAATATAATTTTTACG
Found at i:198489 original size:3 final size:3
Alignment explanation
Indices: 198481--198514 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
198471 AACAAAAATA
198481 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
198515 TAAGCAGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:209047 original size:16 final size:16
Alignment explanation
Indices: 209026--209057 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
209016 GAACGACTTC
209026 ATGGTTAAATAATATT
1 ATGGTTAAATAATATT
209042 ATGGTTAAATAATATT
1 ATGGTTAAATAATATT
209058 GTAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
ATGGTTAAATAATATT
Found at i:210235 original size:34 final size:35
Alignment explanation
Indices: 210197--210289 Score: 111
Period size: 34 Copynumber: 2.7 Consensus size: 35
210187 ATATACCCTT
210197 TTTAAATTTATTTTAAGATTAAATTTAT-TTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATCTTTAAA
* * *
210231 TTTAAATTTAATTCAAG-TTAAATTTATCTTTGAA
1 TTTAAATTTATTTTAAGATTAAATTTATCTTTAAA
* *
210265 TTTAAAATTATTATAA-ATTTAAATT
1 TTTAAATTTATTTTAAGA-TTAAATT
210290 AAAAGTCCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
33 10 0.20
34 32 0.65
35 7 0.14
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTATCTTTAAA
Found at i:210285 original size:17 final size:17
Alignment explanation
Indices: 210197--210289 Score: 100
Period size: 17 Copynumber: 5.5 Consensus size: 17
210187 ATATACCCTT
210197 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
210215 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
210231 TTTAAATTTA-ATTCAA
1 TTTAAATTTATTTTAAA
* *
210247 GTTAAATTTATCTTTGAA
1 TTTAAATTTAT-TTTAAA
* *
210265 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
210282 TTTAAATT
1 TTTAAATT
210290 AAAAGTCCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
16 14 0.23
17 35 0.56
18 13 0.21
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:212122 original size:29 final size:29
Alignment explanation
Indices: 212070--212677 Score: 288
Period size: 29 Copynumber: 20.8 Consensus size: 29
212060 TTTAACCCAT
* *
212070 AAACTTTTCC-AAAATTATATTTTTCACCCC
1 AAAC-TTTCCAAAAATTACA-TTTTGACCCC
212100 AAACTTTCCAAAAATTACATTTT-ACCCC
1 AAACTTTCCAAAAATTACATTTTGACCCC
* * *
212128 TAAATTTTCC-AAAATTCCATTTTGACCTC
1 -AAACTTTCCAAAAATTACATTTTGACCCC
* * * *
212157 GAACTTACCAAAAATTACATTTTTACCCT
1 AAACTTTCCAAAAATTACATTTTGACCCC
* * **
212186 AAATTTTCC-AAAATTCCATTTTTGACCTT
1 AAACTTTCCAAAAATTACA-TTTTGACCCC
* * ** * *
212215 AAACTTTCCAAAAAATAAATTTACATCACT
1 AAACTTTCCAAAAATTACATTTTGA-CCCC
* * * * *
212245 GAATTTTCC-AAAATTCCCTTTTTAACCCC
1 AAACTTTCCAAAAATT-ACATTTTGACCCC
*
212274 AAACTTTCCAAAAATTACATTTTTACCCTC
1 AAACTTTCCAAAAATTACATTTTGACCC-C
* * * * **
212304 GAATTTTCC-AAAATTCCATTTTTTAACCAT
1 AAACTTTCCAAAAATTACA--TTTTGACCCC
* *
212334 AAACTTTCC-AAAATTACATTTTTACCACT
1 AAACTTTCCAAAAATTACATTTTGACC-CC
* *
212363 AAAC-TTCCAAAAATTCCATTTTTGACCCT
1 AAACTTTCCAAAAATTACA-TTTTGACCCC
* * *
212392 GAAC-TTCCAAAAATTACCATTTTAACCTC
1 AAACTTTCCAAAAATTA-CATTTTGACCCC
*
212421 AAACTTT-CAAAAATT-CTATTTTTGTCCCC
1 AAACTTTCCAAAAATTAC-A-TTTTGACCCC
*
212450 AAAC-TTCTCGAAAATTACCATTTT-ACCCC
1 AAACTTTC-CAAAAATTA-CATTTTGACCCC
* * *
212479 GAAC-TTCTAAAAATT-CTATTTTTGACCTC
1 AAACTTTCCAAAAATTAC-A-TTTTGACCCC
* * *
212508 GAAC-TTCTCGAAAGTTACCATTTT-ACCCTC
1 AAACTTTC-CAAAAATTA-CATTTTGACCC-C
* * *
212538 GAAC-TTCCAAAAATTTCATTTTTGACCTC
1 AAACTTTCCAAAAATTACA-TTTTGACCCC
* *
212567 GAACTTCCCAAAAATTAACATTTT-ACCCC
1 AAACTTTCCAAAAATT-ACATTTTGACCCC
* **
212596 TAAAC-TTCCAAAAATTCCATTTTTGACCTT
1 -AAACTTTCCAAAAATTACA-TTTTGACCCC
* *
212626 GAACTTCCCAAAAATTACCATTTT-ACCCTC
1 AAACTTTCCAAAAATTA-CATTTTGACCC-C
* * *
212656 GAAC-TTCCAAAGATTCCATTTT
1 AAACTTTCCAAAAATTACATTTT
212678 TAGCCACGAA
Statistics
Matches: 446, Mismatches: 92, Indels: 82
0.72 0.15 0.13
Matches are distributed among these distances:
26 1 0.00
27 2 0.00
28 65 0.15
29 223 0.50
30 140 0.31
31 13 0.03
32 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTTCCAAAAATTACATTTTGACCCC
Found at i:212142 original size:58 final size:58
Alignment explanation
Indices: 212058--212678 Score: 477
Period size: 59 Copynumber: 10.6 Consensus size: 58
212048 TAGAAATCAA
* ** * *
212058 ATTTTAACCCATAAACTTTTCCAAAATTATATTTTTCACCCCAAACTTTCCAAAAATTAC
1 ATTTT-ACCCCTAAA-TTTTCCAAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTAC
* *
212118 ATTTTACCCCTAAATTTTCCAAAATTCCA-TTTTGACCTCGAACTTACCAAAAATTAC
1 ATTTTACCCCTAAATTTTCCAAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTAC
* *
212175 ATTTTTA-CCCTAAATTTTCCAAAATTCCATTTTTGACCTTAAACTTTCCAAAAAATA-
1 A-TTTTACCCCTAAATTTTCCAAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTAC
* * * * * *
212232 AATTTACATCACTGAATTTTCCAAAATTCCCTTTTTAACCCCAAACTTTCCAAAAATTAC
1 ATTTTAC--CCCTAAATTTTCCAAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTAC
* *
212292 ATTTTTA-CCCTCGAATTTTCCAAAATTCCATTTTTTAACCAT-AAACTTTCC-AAAATTAC
1 A-TTTTACCCCT-AAATTTTCCAAAATTCCA-TTTTTGACC-TCAAACTTTCCAAAAATTAC
* * *
212351 ATTTTTACCACTAAA-CTTCCAAAAATTCCATTTTTGACC-CTGAAC-TTCCAAAAATTACC
1 A-TTTTACCCCTAAATTTTCC-AAAATTCCATTTTTGACCTC-AAACTTTCCAAAAATTA-C
* * * * * * *
212410 ATTTTA-ACCTCAAACTTTCAAAAATTCTATTTTTGTCCCCAAAC-TTCTCGAAAATTACC
1 ATTTTACCCCT-AAATTTTCCAAAATTCCATTTTTGACCTCAAACTTTC-CAAAAATTA-C
* * * * * * * *
212469 ATTTTACCCCGAACTTCT-AAAAATTCTATTTTTGACCTCGAAC-TTCTCGAAAGTTACC
1 ATTTTACCCCTAAATTTTCCAAAATTCCATTTTTGACCTCAAACTTTC-CAAAAATTA-C
* * * * *
212527 ATTTTA-CCCTCGAA-CTTCCAAAAATTTCATTTTTGACCTCGAACTTCCCAAAAATTAAC
1 ATTTTACCCCT-AAATTTTCC-AAAATTCCATTTTTGACCTCAAACTTTCCAAAAATT-AC
* ** *
212586 ATTTTACCCCTAAA-CTTCCAAAAATTCCATTTTTGACCTTGAACTTCCCAAAAATTACC
1 ATTTTACCCCTAAATTTTCC-AAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTA-C
* *
212645 ATTTTA-CCCTCGAA-CTTCCAAAGATTCCATTTTT
1 ATTTTACCCCT-AAATTTTCCAAA-ATTCCATTTTT
212679 AGCCACGAAC
Statistics
Matches: 471, Mismatches: 60, Indels: 61
0.80 0.10 0.10
Matches are distributed among these distances:
56 4 0.01
57 58 0.12
58 147 0.31
59 222 0.47
60 36 0.08
61 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
ATTTTACCCCTAAATTTTCCAAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTAC
Found at i:212678 original size:29 final size:29
Alignment explanation
Indices: 212134--212688 Score: 339
Period size: 29 Copynumber: 19.0 Consensus size: 29
212124 CCCCTAAATT
*
212134 TTCC-AAAATTCCATTTTGA-CCTCGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
* * *
212161 TTACCAAAAATTACATTTTTACCCT-AAATT
1 TT-CCAAAAATTCCATTTTTACCCTCGAA-C
**
212191 TTCC-AAAATTCCATTTTTGA-CCTTAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
* ** ** * *
212219 TTTCCAAAAAATAAATTTACATCACT-GAATT
1 -TTCCAAAAATTCCATTTTTA-CCCTCGAA-C
* *
212250 TTCC-AAAATTCCCTTTTTAACCC-CAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
* *
212278 TTTCCAAAAATTACATTTTTACCCTCGAATT
1 -TTCCAAAAATTCCATTTTTACCCTCGAA-C
* *
212309 TTCC-AAAATTCCATTTTTTAACCAT-AAAC
1 TTCCAAAAATTCCA-TTTTT-ACCCTCGAAC
* *
212338 TTTCC-AAAATTACATTTTTACCACT-AAAC
1 -TTCCAAAAATTCCATTTTTACC-CTCGAAC
212367 TTCCAAAAATTCCATTTTTGACCCT-GAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
* *
212396 TTCCAAAAATTACCA-TTTTAACCTCAAAC
1 TTCCAAAAATT-CCATTTTTACCCTCGAAC
* * * *
212425 TTTCAAAAATTCTATTTTTGTCCC-CAAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
*
212454 TTCTCGAAAATTACCA-TTTTACCC-CGAAC
1 TTC-CAAAAATT-CCATTTTTACCCTCGAAC
* *
212483 TTCTAAAAATTCTATTTTTGA-CCTCGAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
* *
212512 TTCTCGAAAGTTACCA-TTTTACCCTCGAAC
1 TTC-CAAAAATT-CCATTTTTACCCTCGAAC
*
212542 TTCCAAAAATTTCATTTTTGA-CCTCGAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
* *
212571 TTCCCAAAAATTAACA-TTTTACCC-CTAAAC
1 TT-CCAAAAATT-CCATTTTTACCCTC-GAAC
*
212601 TTCCAAAAATTCCATTTTTGA-CCTTGAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAC
212630 TTCCCAAAAATTACCA-TTTTACCCTCGAAC
1 TT-CCAAAAATT-CCATTTTTACCCTCGAAC
* * *
212660 TTCCAAAGATTCCATTTTTAGCCACGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAC
212689 CTTTCGAAAA
Statistics
Matches: 415, Mismatches: 65, Indels: 94
0.72 0.11 0.16
Matches are distributed among these distances:
27 4 0.01
28 50 0.12
29 204 0.49
30 142 0.34
31 15 0.04
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTCGAAC
Done.