Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014166.1 Kokia drynarioides strain JFW-HI SEQ_129199, 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: 125086
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:12577 original size:49 final size:49
Alignment explanation
Indices: 12521--13082 Score: 420
Period size: 49 Copynumber: 11.5 Consensus size: 49
12511 CAAAATAGAG
* *
12521 AGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAGACATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
* * * * * * * *
12570 AGTGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCACAAAGATATGG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
* * *** * *
12619 AGAGAAAGATTTAAGTCGCAACAATGAACCTTATACCTCAGAGACATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
* * * * * * * *
12668 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
* * *
12717 AGGGAAAGGTTTAAGTCGCAACGGCAAACCCTATACCTCAAAGACATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
* * * * *
12766 AGGGAAAGATTTAAGCCGCAACGGCGAA--TTCAGTACCAT-GAAGATATGG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTT--GTACC-TCAAAGACATGA
* * * * * *
12815 AGGGAAATGTTTAAGTCACAACGGCAAACCTTATACCTCAGAGACATAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
* ** * * * * **
12864 AGGGAAAGATTTAAG-CAGCAACAACGAATCTAGTACCACGAAGACACAA
1 AGGGAAAGGTTTAAGTC-GCAACGGCGAACCTTGTACCTCAAAGACATGA
* * * *
12913 AGGGAAAGGTTGAAGTCGTAACGGCGAACATTATACCTCAGAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA-AAGACATGA
* * * *
12962 AGGG-AAGGATTTAAGTCGCAACGGCGAATCC-AGTACCACGAAGACATAA
1 AGGGAAAGG-TTTAAGTCGCAACGGCGAA-CCTTGTACCTCAAAGACATGA
* * * * * * *
13011 AAGGAAAGGTTTAAGTCGGAATGGCAAACCTAGTACCTCAGAGACATTA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
*
13060 AGGG-AGGGATTTAAGTCGCAACG
1 AGGGAAAGG-TTTAAGTCGCAACG
13083 ACAAATCCAG
Statistics
Matches: 387, Mismatches: 111, Indels: 30
0.73 0.21 0.06
Matches are distributed among these distances:
47 1 0.00
48 14 0.04
49 360 0.93
50 10 0.03
51 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (49 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAGACATGA
Found at i:12656 original size:98 final size:98
Alignment explanation
Indices: 12520--13195 Score: 694
Period size: 98 Copynumber: 6.9 Consensus size: 98
12510 ACAAAATAGA
* * * *
12520 GAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAGACATGAAGTGAAAGATTTAAG
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAAG
* * *
12585 TCGTAACGGCGAATCTAGTACCACAAAGATATG
66 CCGCAACGGCGAATCTAGTACCACGAAGATATG
* * *** *
12618 GAGAGAAAGATTTAAGTCGCAACAATGAACCTTATACCTCAGAGACATGAAGGGAAAGATTTAAG
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAAG
12683 CCGCAACGGCGAATCTAGTACCACGAAGATATG
66 CCGCAACGGCGAATCTAGTACCACGAAGATATG
* *
12716 GAGGGAAAGGTTTAAGTCGCAACGGCAAACCCTATACCTCAAAGACATGAAGGGAAAGATTTAAG
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAAG
*
12781 CCGCAACGGCGAAT-TCAGTACCATGAAGATATG
66 CCGCAACGGCGAATCT-AGTACCACGAAGATATG
* * * * *
12814 GAGGGAAATGTTTAAGTCACAACGGCAAACCTTATACCTCAGAGACATAAAGGGAAAGATTTAAG
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAAG
* ** * **
12879 CAGCAACAACGAATCTAGTACCACGAAGACACA
66 CCGCAACGGCGAATCTAGTACCACGAAGATATG
* * * * *
12912 AAGGGAAAGGTTGAAGTCGTAACGGCGAACATTATACCTCAGAAG-CATGAAGGGAAGGATTTAA
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCA-AAGACATGAAGGGAAAGATTTAA
* * * *
12976 GTCGCAACGGCGAATCCAGTACCACGAAGACATA
65 GCCGCAACGGCGAATCTAGTACCACGAAGATATG
* * * * * * * **
13010 AAAGGAAAGGTTTAAGTCGGAATGGCAAACC-TAGTACCTCAGAGACATTAAGGGAGGGATTTAA
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTA-TACCTCAAAGACATGAAGGGAAAGATTTAA
* * * * * * **
13074 GTCGCAACGACAAATCCAGTATCTCGAAGATAAA
65 GCCGCAACGGCGAATCTAGTACCACGAAGATATG
* * * * * * * ** *
13108 AAGGGAAGGGTTTAAGTAGCAATGGTGAGCCTTATACCCCAGAAG-CATGAAACGAAAAATTTAA
1 GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCA-AAGACATGAAGGGAAAGATTTAA
* * *
13172 GCCGCAATGGCTAATTTAGTACCA
65 GCCGCAACGGCGAATCTAGTACCA
13196 TGCAAATTGA
Statistics
Matches: 485, Mismatches: 86, Indels: 14
0.83 0.15 0.02
Matches are distributed among these distances:
97 5 0.01
98 473 0.98
99 7 0.01
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (98 bp):
GAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAAG
CCGCAACGGCGAATCTAGTACCACGAAGATATG
Found at i:13112 original size:49 final size:48
Alignment explanation
Indices: 12667--13129 Score: 228
Period size: 49 Copynumber: 9.4 Consensus size: 48
12657 CAGAGACATG
* * * * * * **
12667 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATG
1 AAGGG-AAGGTTTAAGTCGCAACGGCAAATCCAGTACCTCGAAGACAAA
* * * **
12716 GAGGGAAAGGTTTAAGTCGCAACGGCAAACCCTA-TACCTCAAAGACATG
1 AAGGG-AAGGTTTAAGTCGCAACGGCAAATCC-AGTACCTCGAAGACAAA
* * * * * **
12765 AAGGGAAAGATTTAAGCCGCAACGGCGAATTCAGTACCAT-GAAGATATG
1 AAGGG-AAGGTTTAAGTCGCAACGGCAAATCCAGTACC-TCGAAGACAAA
* * * *
12814 GAGGGAAATGTTTAAGTCACAACGGCAAA-CCTTA-TACCTC-AGAGACATA
1 AAGGG-AAGGTTTAAGTCGCAACGGCAAATCC--AGTACCTCGA-AGACAAA
* ** * * * *
12863 AAGGGAAAGATTTAAG-CAGCAACAACGAATCTAGTACCACGAAGACACA
1 AAGGG-AAGGTTTAAGTC-GCAACGGCAAATCCAGTACCTCGAAGACAAA
* * * **
12912 AAGGGAAAGGTTGAAGTCGTAACGGCGAACAT-TA-TACCTCAGAAG-CATG
1 AAGGG-AAGGTTTAAGTCGCAACGGC-AA-ATCCAGTACCTC-GAAGACAAA
* *
12961 AAGGGAAGGATTTAAGTCGCAACGGCGAATCCAGTACCACGAAGACATAA
1 AAGGGAAGG-TTTAAGTCGCAACGGCAAATCCAGTACCTCGAAGACA-AA
* * * **
13011 AAGGAAAGGTTTAAGTCGGAATGGCAAA-CCTAGTACCTC-AGAGACATT
1 AAGGGAAGGTTTAAGTCGCAACGGCAAATCC-AGTACCTCGA-AGACAAA
* * * *
13059 AAGGGAGGGATTTAAGTCGCAACGACAAATCCAGTATCTCGAAGATAAA
1 AAGGGAAGG-TTTAAGTCGCAACGGCAAATCCAGTACCTCGAAGACAAA
*
13108 AAGGGAAGGGTTTAAGTAGCAA
1 AAGGGAA-GGTTTAAGTCGCAA
13130 TGGTGAGCCT
Statistics
Matches: 318, Mismatches: 70, Indels: 52
0.72 0.16 0.12
Matches are distributed among these distances:
47 2 0.01
48 26 0.08
49 262 0.82
50 26 0.08
51 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (48 bp):
AAGGGAAGGTTTAAGTCGCAACGGCAAATCCAGTACCTCGAAGACAAA
Found at i:13614 original size:17 final size:17
Alignment explanation
Indices: 13592--13655 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
13582 GGCCCAACAG
13592 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
13609 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** **
13626 ATTTAAATCCATTTGGA
1 ATTTAAATTTATTTTAA
13643 ATTTAAATTTATT
1 ATTTAAATTTATT
13656 ATCAATAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:14339 original size:14 final size:13
Alignment explanation
Indices: 14316--14381 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 13
14306 AAGTACATTA
14316 AATTTATAATAAAT
1 AATTTATAAT-AAT
*
14330 AATTTTTAATAAT
1 AATTTATAATAAT
*
14343 AA-TAATAATAAT
1 AATTTATAATAAT
*
14355 AA-TAATAATAAT
1 AATTTATAATAAT
*
14367 AA-TAATAATAAT
1 AATTTATAATAAT
14379 AAT
1 AAT
14382 AATAATAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
12 34 0.71
13 5 0.10
14 9 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTTATAATAAT
Found at i:14342 original size:3 final size:3
Alignment explanation
Indices: 14336--14389 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
14326 AAATAATTTT
14336 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14384 TAA TAA
1 TAA TAA
14390 AGTATTAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:15550 original size:30 final size:30
Alignment explanation
Indices: 15483--15748 Score: 171
Period size: 30 Copynumber: 8.9 Consensus size: 30
15473 CCCTAAACGT
* *
15483 CCCTAAA-TTGTCCAAAACT-CATATTTTGA
1 CCCTAAACTTTTCCAAAATTCCAT-TTTTGA
15512 CCCTTAAACTTTTCCAAAATTCCATTTTTGA
1 CCC-TAAACTTTTCCAAAATTCCATTTTTGA
** *
15543 CCCTAAACTTTTTGAAAATTACA-TTTTG-
1 CCCTAAACTTTTCCAAAATTCCATTTTTGA
* *
15571 CCCTCGAAC-TTTCCAAAATTCCATTTTTGG
1 CCCT-AAACTTTTCCAAAATTCCATTTTTGA
* *
15601 CCTCT-AACTATTT-GAAAATTACATTTTT-A
1 CC-CTAAACT-TTTCCAAAATTCCATTTTTGA
* *
15630 CCCCCAAAAC-TTTCCAAAATTCCATTTTCGA
1 --CCCTAAACTTTTCCAAAATTCCATTTTTGA
* ** *
15661 -CCTCAAATTTTTTGAAAATTACATTTTT-A
1 CCCT-AAACTTTTCCAAAATTCCATTTTTGA
*
15690 CCTCTGAAC-TTTCCAAAAATTCCATTTTTGA
1 CC-CTAAACTTTTCC-AAAATTCCATTTTTGA
* *
15721 CCCT-GATTTTTCCAAAAGTTACCATTTT
1 CCCTAAACTTTTCCAAAA-TT-CCATTTT
15749 ATCGTCGAAC
Statistics
Matches: 185, Mismatches: 29, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
28 17 0.09
29 34 0.18
30 89 0.48
31 42 0.23
32 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTCCATTTTTGA
Found at i:15657 original size:60 final size:59
Alignment explanation
Indices: 15505--15783 Score: 275
Period size: 60 Copynumber: 4.7 Consensus size: 59
15495 CAAAACTCAT
* *
15505 ATTTTGACCCTTAAACTTTTCCAAAATTCCATTTTTGACC-CTAAACTTTTTGAAAATTAC
1 ATTTTTACCCTCAAAC-TTTCCAAAATTCCATTTTTGACCTCT-AACTTTTTGAAAATTAC
* * * *
15565 A-TTTTGCCCTCGAACTTTCCAAAATTCCATTTTTGGCCTCTAACTATTTGAAAATTAC
1 ATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCTAACTTTTTGAAAATTAC
* * * *
15623 ATTTTTACCCCCAAAACTTTCCAAAATTCCATTTTCGACCTCAAATTTTTTGAAAATTAC
1 ATTTTTACCCTC-AAACTTTCCAAAATTCCATTTTTGACCTCTAACTTTTTGAAAATTAC
* * *
15683 ATTTTTA-CCTCTGAACTTTCCAAAAATTCCATTTTTGACC-CTGA-TTTTTCCAAAAGTTACC
1 ATTTTTACCCTC-AAACTTTCC-AAAATTCCATTTTTGACCTCTAACTTTTT-GAAAA-TTA-C
* * * *
15744 A-TTTTATCGTCGAAC-TTCCTAAAATTCCATTTTTTACCTC
1 ATTTTTACCCTCAAACTTTCC-AAAATTCCATTTTTGACCTC
15784 GATTTTCCAA
Statistics
Matches: 186, Mismatches: 24, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
58 44 0.24
59 58 0.31
60 79 0.42
61 5 0.03
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (59 bp):
ATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCTAACTTTTTGAAAATTAC
Found at i:15707 original size:29 final size:28
Alignment explanation
Indices: 15522--15805 Score: 137
Period size: 30 Copynumber: 9.6 Consensus size: 28
15512 CCCTTAAACT
* *
15522 TTTCCAAAATTCCATTTTTGACC-CTAAAC
1 TTTCCAAAATTACATTTTT-ACCTC-GAAC
** **
15551 TTTTTGAAAATTACATTTTGCCCTCGAAC
1 -TTTCCAAAATTACATTTTTACCTCGAAC
* * *
15580 TTTCCAAAATTCCATTTTTGGCCTCTAAC
1 TTTCCAAAATTACATTTTT-ACCTCGAAC
** * *
15609 TATTTGAAAATTACATTTTTACCCCCAAAAC
1 T-TTCCAAAATTACATTTTTA-CCTC-GAAC
* * * *
15640 TTTCCAAAATTCCATTTTCGACCTCAAATT
1 TTTCCAAAATTACATTTT-TACCTCGAA-C
**
15670 TTTTGAAAATTACATTTTTACCTCTGAAC
1 TTTCCAAAATTACATTTTTACCTC-GAAC
* **
15699 TTTCCAAAAATTCCATTTTTGACC-CTGATT
1 TTTCC-AAAATTACATTTTT-ACCTC-GAAC
*
15729 TTTCCAAAAGTTACCA-TTTTATCGTCGAAC
1 TTTCCAAAA-TTA-CATTTTTA-CCTCGAAC
* *
15759 -TTCCTAAAATTCCATTTTTTACCTCG-AT
1 TTTCC-AAAATTACA-TTTTTACCTCGAAC
15787 TTTCCAAAATTACCATTTT
1 TTTCCAAAATTA-CATTTT
15806 ACCCCCGAAT
Statistics
Matches: 192, Mismatches: 43, Indels: 40
0.70 0.16 0.15
Matches are distributed among these distances:
28 28 0.15
29 45 0.23
30 108 0.56
31 11 0.06
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.41
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTTACCTCGAAC
Found at i:15776 original size:59 final size:58
Alignment explanation
Indices: 15522--15832 Score: 185
Period size: 60 Copynumber: 5.3 Consensus size: 58
15512 CCCTTAAACT
** ** ** *
15522 TTTCC-AAAATTCCATTTTTGACCCTAAACTTTTTGAAAATTA-CATTTTGCCCTCGAAC
1 TTTCCAAAAATTCCATTTTTGA-CCTCGA-TTTTCCAAAATTACCATTTTATCGTCGAAC
* * * * ** *
15580 TTTCC-AAAATTCCATTTTTGGCCTCTAACTATTT-GAAAATTA-CATTTTTACCCCCAAAAC
1 TTTCCAAAAATTCCATTTTTGACCTC-GA-T-TTTCCAAAATTACCA-TTTTATCGTC-GAAC
* * ** *
15640 TTTCC-AAAATTCCATTTTCGACCTCAAATTTTTTGAAAATTA-CATTTT-TACCTCTGAAC
1 TTTCCAAAAATTCCATTTTTGACCTC-GA-TTTTCCAAAATTACCATTTTAT-CGTC-GAAC
15699 TTTCCAAAAATTCCATTTTTGACC-CTGATTTTTCCAAAAGTTACCATTTTATCGTCGAAC
1 TTTCCAAAAATTCCATTTTTGACCTC-GA-TTTTCCAAAA-TTACCATTTTATCGTCGAAC
* * * **
15759 -TTCCTAAAATTCCATTTTTTACCTCGATTTTCCAAAATTACCATTTTACCCCCGAA-
1 TTTCCAAAAATTCCATTTTTGACCTCGATTTTCCAAAATTACCATTTTATCGTCGAAC
* *
15815 TGTCTAAAAATTCCATTT
1 TTTCCAAAAATTCCATTT
15833 AAACTCCAAA
Statistics
Matches: 214, Mismatches: 27, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
57 33 0.15
58 44 0.21
59 63 0.29
60 64 0.30
61 9 0.04
62 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (58 bp):
TTTCCAAAAATTCCATTTTTGACCTCGATTTTCCAAAATTACCATTTTATCGTCGAAC
Found at i:15824 original size:29 final size:29
Alignment explanation
Indices: 15792--15884 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
15782 TCGATTTTCC
15792 AAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTACCATTTTACCCCCGAATGTCTA
* * * * * *
15821 AAAATT-CCATTTAAACTCCAAACTTTCCA
1 AAAATTACCATTTTACCCCCGAA-TGTCTA
*
15850 AAAATTACCATTTTACTCCCGAATGTCTA
1 AAAATTACCATTTTACCCCCGAATGTCTA
15879 AAAATT
1 AAAATT
15885 TCGTTTTTGA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
28 12 0.24
29 26 0.53
30 11 0.22
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATGTCTA
Found at i:15892 original size:29 final size:29
Alignment explanation
Indices: 15792--15902 Score: 75
Period size: 29 Copynumber: 3.8 Consensus size: 29
15782 TCGATTTTCC
*
15792 AAAATTACCA-TTTTACCCCCGAATGTCTA
1 AAAATTA-CATTTTTACTCCCGAATGTCTA
* ** * * *
15821 AAAATTCCATTTAAACT-CCAAACTTTCCA
1 AAAATTACATTTTTACTCCCGAA-TGTCTA
15850 AAAATTACCA-TTTTACTCCCGAATGTCTA
1 AAAATTA-CATTTTTACTCCCGAATGTCTA
* * *
15879 AAAATTTCGTTTTTGACTCTCGAA
1 AAAATTACATTTTT-ACTCCCGAA
15903 CTTCCCTAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
28 7 0.12
29 39 0.65
30 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTTACTCCCGAATGTCTA
Found at i:15964 original size:27 final size:27
Alignment explanation
Indices: 15910--15967 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
15900 GAACTTCCCT
* * *
15910 AAAATTACCATTTTGCCTCGAGTGTCC
1 AAAATTACCATTTTACCCCGAGTATCC
*
15937 AAAATTACCATTTTACCCCGGGTATCC
1 AAAATTACCATTTTACCCCGAGTATCC
15964 AAAA
1 AAAA
15968 ATCTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (27 bp):
AAAATTACCATTTTACCCCGAGTATCC
Found at i:20616 original size:19 final size:19
Alignment explanation
Indices: 20592--20632 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
20582 TAATGATTTA
*
20592 ATGTGGTGTAGTACTAATT
1 ATGTGGTGTAATACTAATT
20611 ATGTGGTGTAATACTAATT
1 ATGTGGTGTAATACTAATT
20630 ATG
1 ATG
20633 CACTTGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.41
Consensus pattern (19 bp):
ATGTGGTGTAATACTAATT
Found at i:20913 original size:25 final size:24
Alignment explanation
Indices: 20885--20931 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20875 GTAAAATATA
*
20885 AATTTAATATATAAAAAATAAACTC
1 AATTAAATA-ATAAAAAATAAACTC
*
20910 AATTAAATAATGAAAAATAAAC
1 AATTAAATAATAAAAAATAAAC
20932 AAGAGTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (24 bp):
AATTAAATAATAAAAAATAAACTC
Found at i:22101 original size:25 final size:26
Alignment explanation
Indices: 22073--22132 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
22063 TATAAAAAAA
22073 CAAAATA-TGCATTTTAAATAATGTT
1 CAAAATAGTGCATTTTAAATAATGTT
* ***
22098 CAAATTAGTTTTTTTTAAATAATGTT
1 CAAAATAGTGCATTTTAAATAATGTT
*
22124 CAAATTAGT
1 CAAAATAGT
22133 TAATATTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (26 bp):
CAAAATAGTGCATTTTAAATAATGTT
Found at i:22113 original size:26 final size:26
Alignment explanation
Indices: 22084--22133 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
22074 AAAATATGCA
22084 TTTTAAATAATGTTCAAATTAGTTTT
1 TTTTAAATAATGTTCAAATTAGTTTT
22110 TTTTAAATAATGTTCAAATTAGTT
1 TTTTAAATAATGTTCAAATTAGTT
22134 AATATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (26 bp):
TTTTAAATAATGTTCAAATTAGTTTT
Found at i:23300 original size:33 final size:34
Alignment explanation
Indices: 23202--23302 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 34
23192 ACAACTCATT
* * * *
23202 TTGTAAGTTTTCAAGCTCAAGAAATCAATTTGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
23236 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
* * *
23270 TTTTAAGTTTTCAAATTGAAG-AATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
23303 AAAATGACAC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
33 12 0.20
34 48 0.80
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (34 bp):
TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
Found at i:28228 original size:17 final size:17
Alignment explanation
Indices: 28202--28241 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28192 GCGTATGCGA
28202 TGGTGGCAGAAGCGTGG
1 TGGTGGCAGAAGCGTGG
* *
28219 TGGTGTCAGACGCGTGG
1 TGGTGGCAGAAGCGTGG
*
28236 TCGTGG
1 TGGTGG
28242 TAGTGTTAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.50, T:0.23
Consensus pattern (17 bp):
TGGTGGCAGAAGCGTGG
Found at i:30401 original size:14 final size:15
Alignment explanation
Indices: 30371--30403 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
30361 TATGATAATG
30371 TTTTTTAATATAAGTA
1 TTTTTTAATAT-AGTA
30387 TTTTTTAATAT-GTA
1 TTTTTTAATATAGTA
30401 TTT
1 TTT
30404 AAAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTTAATATAGTA
Found at i:31449 original size:22 final size:22
Alignment explanation
Indices: 31412--31461 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
31402 TTTTGAGGAG
* *
31412 TTAAAAT--TAAATTATAATTT
1 TTAAAATAATAAAATATAAATT
*
31432 TTATAATAATAAAATATAAATT
1 TTAAAATAATAAAATATAAATT
31454 TTAAAATA
1 TTAAAATA
31462 TATATCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.25
22 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAAATAATAAAATATAAATT
Found at i:31658 original size:21 final size:21
Alignment explanation
Indices: 31632--31671 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31622 CTCAAGAACA
*
31632 ATCTAGAAACCCACAGTAAAT
1 ATCTAGAAACCAACAGTAAAT
*
31653 ATCTAGCAACCAACAGTAA
1 ATCTAGAAACCAACAGTAA
31672 TAAAANNNNN
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.17
Consensus pattern (21 bp):
ATCTAGAAACCAACAGTAAAT
Found at i:33669 original size:2 final size:2
Alignment explanation
Indices: 33662--33714 Score: 79
Period size: 2 Copynumber: 25.5 Consensus size: 2
33652 ATATTAATAC
*
33662 AT AT AT AT AC ACT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33706 AT AT AT AT A
1 AT AT AT AT A
33715 CATGTTTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 45 0.96
3 1 0.02
4 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:34612 original size:29 final size:30
Alignment explanation
Indices: 34566--34794 Score: 152
Period size: 30 Copynumber: 7.8 Consensus size: 30
34556 GAAATTTTAT
* * *
34566 TTTGACCCTCAAACTTCCTAAAAATAT-GA
1 TTTGACCCTAAAATTTCCTAAAAATTTAGA
* * * *
34595 TTTGACCCTGAAATTTCC-CAAAATTAAGT
1 TTTGACCCTAAAATTTCCTAAAAATTTAGA
*
34624 TTTAACCCTAAAACTTT-CTAAAAATTTAGA
1 TTTGACCCTAAAA-TTTCCTAAAAATTTAGA
* * * *
34654 TTTAACCCTTAAACTTT-CTAAAAATTCAAA
1 TTTGACCC-TAAAATTTCCTAAAAATTTAGA
** * *
34684 TTTGACCCTCGAA-CTCCTAAAAATTTGGA
1 TTTGACCCTAAAATTTCCTAAAAATTTAGA
* *
34713 TTTAAGCCCCAAAATTTCC-AAAAATTTAGA
1 TTTGA-CCCTAAAATTTCCTAAAAATTTAGA
*
34743 TTTGACCCCTAAATTTTCC-AAAAATTT-GAA
1 TTTGA-CCCTAAAATTTCCTAAAAATTTAG-A
* * *
34773 TTTGGCCCCAAACTTTCC-AAAA
1 TTTGACCCTAAAATTTCCTAAAA
34795 TTTCATTTTT
Statistics
Matches: 157, Mismatches: 35, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
28 6 0.04
29 61 0.39
30 83 0.53
31 7 0.04
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (30 bp):
TTTGACCCTAAAATTTCCTAAAAATTTAGA
Found at i:34704 original size:59 final size:57
Alignment explanation
Indices: 34566--34794 Score: 180
Period size: 59 Copynumber: 3.9 Consensus size: 57
34556 GAAATTTTAT
* * * * *
34566 TTTGACCCTCAAACTTCCTAAAAATATGATTTGACCCTGAAATTTCCCAAAATTAAGT
1 TTTGACCCTCAAACTTCCTAAAAATTTGATTTAACCCTCAAATTTCCAAAAATTAA-A
* * * * *
34624 TTTAACCCTAAAACTTTCTAAAAATTTAGATTTAACCCTTAAACTTTCTAAAAATTCAAA
1 TTTGACCCTCAAACTTCCTAAAAATTT-GATTTAACCCTCAAA-TTTCCAAAAATT-AAA
* *
34684 TTTGACCCTCGAAC-TCCTAAAAATTTGGATTTAAGCCC-CAAAATTTCCAAAAATTTAGA
1 TTTGACCCTCAAACTTCCTAAAAATTT-GATTTAA-CCCTC-AAATTTCCAAAAA-TTAAA
* **
34743 TTTGACCC-CTAAATTTTCC-AAAAATTTGAATTTGGCCC-CAAACTTTCCAAAA
1 TTTGACCCTC-AAA-CTTCCTAAAAATTTG-ATTTAACCCTCAAA-TTTCCAAAA
34795 TTTCATTTTT
Statistics
Matches: 139, Mismatches: 21, Indels: 21
0.77 0.12 0.12
Matches are distributed among these distances:
58 27 0.19
59 66 0.47
60 41 0.29
61 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (57 bp):
TTTGACCCTCAAACTTCCTAAAAATTTGATTTAACCCTCAAATTTCCAAAAATTAAA
Found at i:37670 original size:34 final size:34
Alignment explanation
Indices: 37625--37693 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
37615 CGTCGTTATC
*
37625 ACCATGGCTATTATCATGAGCACTGAGTGGTTAA
1 ACCATGACTATTATCATGAGCACTGAGTGGTTAA
*
37659 ACCATGACTATTATCATGAGCATTGAGTGGTTAA
1 ACCATGACTATTATCATGAGCACTGAGTGGTTAA
37693 A
1 A
37694 GGCTCTAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (34 bp):
ACCATGACTATTATCATGAGCACTGAGTGGTTAA
Found at i:39038 original size:3 final size:3
Alignment explanation
Indices: 39030--39070 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
39020 ATTGTATATT
39030 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
39071 TTAATAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39123 original size:19 final size:20
Alignment explanation
Indices: 39101--39139 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
39091 ATAAAATATT
39101 AAATAACAAAAT-ATTTAAA
1 AAATAACAAAATGATTTAAA
* *
39120 AAATTATAAAATGATTTAAA
1 AAATAACAAAATGATTTAAA
39140 TTTATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
AAATAACAAAATGATTTAAA
Found at i:39431 original size:40 final size:38
Alignment explanation
Indices: 39377--39526 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 38
39367 ATCTTTTTTT
*
39377 AAAAAAATTAGGATAATTTTCATTTTAAAAGTAATTTAA
1 AAAAAAATTGGGATAATTTTCATTTTAAAA-TAATTTAA
* *
39416 AAAATAAATTGGGATAACTTTCTTTTTTAAAATAATTT--
1 AAAA-AAATTGGGATAATTTTC-ATTTTAAAATAATTTAA
* *
39454 AAAAAAATTTGGATAATATTT-GTTTTAAAAATAATTTTAA
1 AAAAAAATTGGGATAAT-TTTCATTTT-AAAATAA-TTTAA
*
39494 AAAATAAATTGAGATAATTTTCATTTTAAAATA
1 AAAA-AAATTGGGATAATTTTCATTTTAAAATA
39527 TTCTTTTGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
36 4 0.04
37 18 0.19
38 10 0.11
39 4 0.04
40 34 0.37
41 23 0.25
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (38 bp):
AAAAAAATTGGGATAATTTTCATTTTAAAATAATTTAA
Found at i:39485 original size:37 final size:35
Alignment explanation
Indices: 39374--39498 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 35
39364 CATATCTTTT
*
39374 TTTAAAAAAATTAGGATAATTTTCATTTTAAAAGTAA
1 TTTAAAAAAATTAGGATAATTTT--TTTTAAAAATAA
* *
39411 TTTAAAAAATAAATTGGGATAACTTTCTTTTTTAAAATAA
1 TTT--AAAA-AAATTAGGATAA-TTT-TTTTTAAAAATAA
*
39451 TTTAAAAAAATTTGGATAATATTTGTTTTAAAAATAA
1 TTTAAAAAAATTAGGATAAT-TTT-TTTTAAAAATAA
*
39488 TTTTAAAAAAT
1 TTTAAAAAAAT
39499 AAATTGAGAT
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
36 2 0.03
37 37 0.49
38 4 0.05
39 4 0.05
40 24 0.32
41 3 0.04
42 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (35 bp):
TTTAAAAAAATTAGGATAATTTTTTTTAAAAATAA
Found at i:39521 original size:77 final size:77
Alignment explanation
Indices: 39374--39526 Score: 220
Period size: 77 Copynumber: 2.0 Consensus size: 77
39364 CATATCTTTT
* *
39374 TTTAAAAAAATTAGGATAATTTTCATTTTAAAAGTAATTTAAAAAATAAATTGGGATAACTTTCT
1 TTTAAAAAAATTAGGATAATTTTCATTTTAAAAATAATTTAAAAAATAAATTGAGATAACTTTCT
*
39439 TTTTTAAAATAA
66 ATTTTAAAATAA
* * *
39451 TTTAAAAAAATTTGGATAATATTT-GTTTTAAAAATAATTTTAAAAAATAAATTGAGATAATTTT
1 TTTAAAAAAATTAGGATAAT-TTTCATTTTAAAAATAA-TTTAAAAAATAAATTGAGATAACTTT
39515 C-ATTTTAAAATA
64 CTATTTTAAAATA
39527 TTCTTTTGGA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 40 0.59
78 28 0.41
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (77 bp):
TTTAAAAAAATTAGGATAATTTTCATTTTAAAAATAATTTAAAAAATAAATTGAGATAACTTTCT
ATTTTAAAATAA
Found at i:39631 original size:28 final size:26
Alignment explanation
Indices: 39600--39680 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 26
39590 AAAATAATTT
39600 AAATTAGATAATTTTTGTTTTAAAAATA
1 AAATTAGATAA-TTTT-TTTTAAAAATA
** * * *
39628 AAATGGGATAA-CTTTTTAAAAAAAA
1 AAATTAGATAATTTTTTTTAAAAATA
*
39653 AAAATAGATAATTTTATTTTAAAAATA
1 AAATTAGATAATTTT-TTTTAAAAATA
39680 A
1 A
39681 TTTAAAAATA
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
25 17 0.43
26 4 0.10
27 10 0.25
28 9 0.22
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.38
Consensus pattern (26 bp):
AAATTAGATAATTTTTTTTAAAAATA
Found at i:48028 original size:41 final size:41
Alignment explanation
Indices: 47983--48129 Score: 240
Period size: 41 Copynumber: 3.6 Consensus size: 41
47973 GAGAAATTTG
* *
47983 ATATTAAAGGAAGAATCATGTCTCGGGACGAGAATGAGATC
1 ATATTAAAGGAAGAATCATGTCTCGGGATGAGAATGAGATT
* *
48024 ATATTAAAGGAAGACTCATGTCTCGGGATAAGAATGAGATT
1 ATATTAAAGGAAGAATCATGTCTCGGGATGAGAATGAGATT
* *
48065 ATATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAAATT
1 ATATTAAAGGAAGAATCATGTCTCGGGATGAGAATGAGATT
48106 ATATTAAAGGAAGAATCATGTCTC
1 ATATTAAAGGAAGAATCATGTCTC
48130 AAAGTGAGCG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (41 bp):
ATATTAAAGGAAGAATCATGTCTCGGGATGAGAATGAGATT
Found at i:48211 original size:40 final size:40
Alignment explanation
Indices: 48157--48253 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
48147 TGTTTTTAAA
**
48157 AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTGAGT
1 AAAAGGAAGACTTATGACTCAATAGAGCATAAGAGTGAGT
* * *
48197 AAAAGGAAGGCTTATGACTCAATAGAGTATAAGAGTGATT
1 AAAAGGAAGACTTATGACTCAATAGAGCATAAGAGTGAGT
48237 AAAAGGAAGACTTATGA
1 AAAAGGAAGACTTATGA
48254 ACCTATGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (40 bp):
AAAAGGAAGACTTATGACTCAATAGAGCATAAGAGTGAGT
Found at i:49790 original size:20 final size:20
Alignment explanation
Indices: 49765--49804 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49755 TTGGTTAGAG
49765 AACACGCTGAGAGTTCTCAA
1 AACACGCTGAGAGTTCTCAA
*
49785 AACACGTTGAGAGTTCTCAA
1 AACACGCTGAGAGTTCTCAA
49805 TGTGATGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
AACACGCTGAGAGTTCTCAA
Found at i:54023 original size:23 final size:24
Alignment explanation
Indices: 53997--54048 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
53987 GTTTTGGTGC
53997 TTTTTTTACTG-TTTTG-GTTGAT
1 TTTTTTTACTGTTTTTGAGTTGAT
*
54019 GTTTTTTTGCTGTTTTTGAGTTGAT
1 -TTTTTTTACTGTTTTTGAGTTGAT
54044 TTTTT
1 TTTTT
54049 ATTGTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 10 0.38
25 6 0.23
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (24 bp):
TTTTTTTACTGTTTTTGAGTTGAT
Found at i:54054 original size:22 final size:21
Alignment explanation
Indices: 53998--54056 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 21
53988 TTTTGGTGCT
*
53998 TTTTTTACTG-TTTTGGTTGA
1 TTTTTTATTGTTTTTGGTTGA
*
54018 TGTTTTTTTGCTGTTTTTGAGTTGA
1 T-TTTTTAT--TGTTTTTG-GTTGA
54043 TTTTTTATTGTTTT
1 TTTTTTATTGTTTT
54057 GATTTCTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.03
21 5 0.16
22 6 0.19
23 2 0.06
24 11 0.35
25 6 0.19
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.69
Consensus pattern (21 bp):
TTTTTTATTGTTTTTGGTTGA
Found at i:54124 original size:56 final size:56
Alignment explanation
Indices: 54063--54192 Score: 138
Period size: 56 Copynumber: 2.3 Consensus size: 56
54053 TTTTGATTTC
* * * * *
54063 TGTTTTCGTGTTATTTTTGCCGTTATTTTTGTTGCTTTTTTTGTTGCTATTTTTGT
1 TGTTTTAGTGTTATTTTTACCATTATTTTTGTTGCTGTTTTGGTTGCTATTTTTGT
* * * *
54119 TGTTTTTAATGTT-GTTTTACTATTATTTTTGTTGCTGTTTTGGTTGTTATTTTTGT
1 TG-TTTTAGTGTTATTTTTACCATTATTTTTGTTGCTGTTTTGGTTGCTATTTTTGT
*
54175 TG-TTTGGATGTTATTTTT
1 TGTTTTAG-TGTTATTTTT
54193 TATGTGTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
54 3 0.05
55 4 0.07
56 44 0.75
57 8 0.14
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.68
Consensus pattern (56 bp):
TGTTTTAGTGTTATTTTTACCATTATTTTTGTTGCTGTTTTGGTTGCTATTTTTGT
Found at i:54177 original size:12 final size:12
Alignment explanation
Indices: 54071--54178 Score: 66
Period size: 12 Copynumber: 9.3 Consensus size: 12
54061 TCTGTTTTCG
*
54071 TGTTATTTTTGC
1 TGTTATTTTTGT
*
54083 CGTTATTTTTGT
1 TGTTATTTTTGT
54095 TGCTT-TTTTTGT
1 TG-TTATTTTTGT
*
54107 TGCTATTTTTGT
1 TGTTATTTTTGT
*
54119 TGTT-TTTAATGT
1 TGTTATTT-TTGT
**
54131 TG----TTTTAC
1 TGTTATTTTTGT
*
54139 TATTATTTTTGT
1 TGTTATTTTTGT
* * *
54151 TGCTGTTTTGGT
1 TGTTATTTTTGT
54163 TGTTATTTTTGT
1 TGTTATTTTTGT
54175 TGTT
1 TGTT
54179 TGGATGTTAT
Statistics
Matches: 70, Mismatches: 19, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
8 2 0.03
9 2 0.03
11 4 0.06
12 60 0.86
13 2 0.03
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:54396 original size:49 final size:47
Alignment explanation
Indices: 54303--54397 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
54293 TATCTTAATA
* * *
54303 TAATTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTTTGTTT
1 TAATTTTTTAATGTATTTGAAATTTATATATTTTTTAATATTTGTTT
*
54350 TAATGTTTTTAAGTGTATTTGATATATTATATATTTTTTAA-ATTTGTT
1 TAAT-TTTTTAA-TGTATTTGAAAT-TTATATATTTTTTAATATTTGTT
54398 GTATGTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 7 0.17
49 16 0.39
50 14 0.34
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.64
Consensus pattern (47 bp):
TAATTTTTTAATGTATTTGAAATTTATATATTTTTTAATATTTGTTT
Found at i:56088 original size:41 final size:41
Alignment explanation
Indices: 56043--56189 Score: 222
Period size: 41 Copynumber: 3.6 Consensus size: 41
56033 AAGAAATTTG
*
56043 ATATTAAAGGAAGACTCATATCTTGGGACGAGAATGAGATC
1 ATATTAAAGGAAGACTCATGTCTTGGGACGAGAATGAGATC
* *
56084 ATATTAAAGGAAGACTCATGTCTCGGAACGAGAATGAGATC
1 ATATTAAAGGAAGACTCATGTCTTGGGACGAGAATGAGATC
* * * * *
56125 ATATTAAAGGAAGACTCGTGTCTTGGGATGGGAATGAAATT
1 ATATTAAAGGAAGACTCATGTCTTGGGACGAGAATGAGATC
56166 ATATTAAAGGAAGACTCATGTCTT
1 ATATTAAAGGAAGACTCATGTCTT
56190 CAAAATGAGC
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (41 bp):
ATATTAAAGGAAGACTCATGTCTTGGGACGAGAATGAGATC
Found at i:56281 original size:40 final size:40
Alignment explanation
Indices: 56219--56311 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
56209 GTTTTTAAAA
* * * *
56219 AAAAAGAAGAATTGTGATTCGGTAGAGCATAAGAGTGAGT
1 AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTGAGT
* *
56259 AAAAGGAAGACTTATGACTCGGTAGAGTATAAGAGTGATT
1 AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTGAGT
56299 AAAAGGAAGACTT
1 AAAAGGAAGACTT
56312 GTGAACCTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.43, C:0.06, G:0.28, T:0.23
Consensus pattern (40 bp):
AAAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTGAGT
Found at i:56770 original size:21 final size:21
Alignment explanation
Indices: 56725--56775 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
56715 TTGTCCATTG
* *
56725 CACTTGTATCGGTAGATGCTA
1 CACTTGTATCAGTAGATACTA
56746 CACTTGTATCAGTAGA-ACTA
1 CACTTGTATCAGTAGATACTA
*
56766 TCACTAGTAT
1 -CACTTGTAT
56776 TGATAGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
CACTTGTATCAGTAGATACTA
Found at i:59480 original size:21 final size:21
Alignment explanation
Indices: 59454--59494 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59444 CTCAAGAACA
* *
59454 ATCTAGAAACCCACAGTAAAT
1 ATCTAGAAACCAACAATAAAT
*
59475 ATCTAGCAACCAACAATAAA
1 ATCTAGAAACCAACAATAAA
59495 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.07, T:0.17
Consensus pattern (21 bp):
ATCTAGAAACCAACAATAAAT
Found at i:76418 original size:19 final size:19
Alignment explanation
Indices: 76394--76435 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
76384 ACGGCCTTAG
76394 ATGCCTCTTGATCACTAAA
1 ATGCCTCTTGATCACTAAA
76413 ATGCCTCTTGATCACTAAA
1 ATGCCTCTTGATCACTAAA
76432 ATGC
1 ATGC
76436 TTAAGTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (19 bp):
ATGCCTCTTGATCACTAAA
Found at i:77886 original size:14 final size:15
Alignment explanation
Indices: 77863--77900 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
77853 TACAAAAAAC
77863 AAAAAAAAATAG-TG
1 AAAAAAAAATAGTTG
* *
77877 AAAAATAAATCGTTG
1 AAAAAAAAATAGTTG
77892 AAAAAAAAA
1 AAAAAAAAA
77901 GAAAAGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.16
Consensus pattern (15 bp):
AAAAAAAAATAGTTG
Found at i:81406 original size:26 final size:26
Alignment explanation
Indices: 81377--81508 Score: 156
Period size: 26 Copynumber: 5.1 Consensus size: 26
81367 CTAAAGAAAA
* * *
81377 ATACTGAATTAGCTCATAAGAGCGAT
1 ATACTGAACTGGCTCGTAAGAGCGAT
*
81403 ATACTGAACTGGCTCGTAATAGCGAT
1 ATACTGAACTGGCTCGTAAGAGCGAT
* * *
81429 ATACTGAACTGGCTAGTAATAGCTAT
1 ATACTGAACTGGCTCGTAAGAGCGAT
* * *
81455 TTATTGAACTGGTTCGTAAGAGCGAT
1 ATACTGAACTGGCTCGTAAGAGCGAT
* *
81481 ATACTGAACTAGCTCGTAAGAGAGAT
1 ATACTGAACTGGCTCGTAAGAGCGAT
81507 AT
1 AT
81509 CTTGACTAGG
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 89 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (26 bp):
ATACTGAACTGGCTCGTAAGAGCGAT
Found at i:101419 original size:22 final size:22
Alignment explanation
Indices: 101359--101437 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
101349 GCACGTTTCA
* * *
101359 TGCCTTCTATTCAGCTCTATGTG
1 TGCC-TCTGTTCAGCACTGTGTG
101382 TGTCCTCTGTTCAGCACTGTGTG
1 TG-CCTCTGTTCAGCACTGTGTG
* * *
101405 TGCTTCTGTTTAGCACTTTGTG
1 TGCCTCTGTTCAGCACTGTGTG
101427 TGCCTACTGTT
1 TGCCT-CTGTT
101438 GCCTAGCACT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 21 0.45
23 24 0.51
24 2 0.04
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (22 bp):
TGCCTCTGTTCAGCACTGTGTG
Found at i:103197 original size:16 final size:16
Alignment explanation
Indices: 103161--103215 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
103151 GTTTGGTTCA
*
103161 CTGTAATGTAATAGAG
1 CTGTAATGAAATAGAG
* *
103177 TTGTAATGAAATAGGG
1 CTGTAATGAAATAGAG
* *
103193 CTGTAATTAAATAGTG
1 CTGTAATGAAATAGAG
103209 CTGTAAT
1 CTGTAAT
103216 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (16 bp):
CTGTAATGAAATAGAG
Found at i:104376 original size:21 final size:21
Alignment explanation
Indices: 104351--104416 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
104341 ATAAATAGTC
104351 TAAAATTTGGTACCAACATAA
1 TAAAATTTGGTACCAACATAA
* * *
104372 TAAAACTAT-GTA--AATAGT-C
1 TAAAA-TTTGGTACCAACA-TAA
104391 TAAAATTTGGTACCAACATAA
1 TAAAATTTGGTACCAACATAA
104412 TAAAA
1 TAAAA
104417 CTATATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
18 2 0.06
19 11 0.33
20 2 0.06
21 16 0.48
22 2 0.06
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (21 bp):
TAAAATTTGGTACCAACATAA
Found at i:104397 original size:40 final size:40
Alignment explanation
Indices: 104340--104439 Score: 173
Period size: 40 Copynumber: 2.5 Consensus size: 40
104330 ACAACATTTG
104340 TATAAATAGTCTAAAATTTGGTACCAACATAATAAAACTA
1 TATAAATAGTCTAAAATTTGGTACCAACATAATAAAACTA
*
104380 TGTAAATAGTCTAAAATTTGGTACCAACATAATAAAACTA
1 TATAAATAGTCTAAAATTTGGTACCAACATAATAAAACTA
*
104420 TATAAAATAGTCTGAAATTT
1 TAT-AAATAGTCTAAAATTT
104440 TATTTTTCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 41 0.73
41 15 0.27
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (40 bp):
TATAAATAGTCTAAAATTTGGTACCAACATAATAAAACTA
Found at i:109010 original size:21 final size:21
Alignment explanation
Indices: 108984--109034 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
108974 CATACTTGTT
108984 TCGGTAGAACCCTTACATGTA
1 TCGGTAGAACCCTTACATGTA
109005 TCGGTAGAACCCTTACATGTA
1 TCGGTAGAACCCTTACATGTA
*
109026 TTGGTAGAA
1 TCGGTAGAA
109035 GTAATAGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TCGGTAGAACCCTTACATGTA
Found at i:119213 original size:34 final size:34
Alignment explanation
Indices: 119169--119249 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
119159 TGGGCCCAAC
* * *
119169 AAATTTAAATTTATTTTAAAATTAGGTTTATTTT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
* *
119203 GAATTTAAATTTATTTGAAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
119237 AAATTTAAATTTA
1 AAATTTAAATTTA
119250 AAATTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
Found at i:119256 original size:24 final size:25
Alignment explanation
Indices: 119215--119263 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
119205 ATTTAAATTT
*
119215 ATTTGAAATTTAAGTTTA-TTATAA
1 ATTTGAAATTTAAATTTATTTATAA
119239 ATTT-AAATTTAAAATTTATTTATAA
1 ATTTGAAATTT-AAATTTATTTATAA
119264 TGTCCAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTGAAATTTAAATTTATTTATAA
Found at i:119260 original size:17 final size:17
Alignment explanation
Indices: 119169--119249 Score: 99
Period size: 17 Copynumber: 4.8 Consensus size: 17
119159 TGGGCCCAAC
119169 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* **
119186 AAAATTAGGTTTATTTT
1 AAATTTAAATTTATTTT
* *
119203 GAATTTAAATTTATTTG
1 AAATTTAAATTTATTTT
* *
119220 AAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTT
119237 AAATTTAAATTTA
1 AAATTTAAATTTA
119250 AAATTTATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:121097 original size:30 final size:29
Alignment explanation
Indices: 121027--121378 Score: 320
Period size: 29 Copynumber: 12.0 Consensus size: 29
121017 CCCTAGAGGT
*
121027 CCCTAAACCTTCCAAAAAT-TCTATTTTTA
1 CCCTAAAACTTCCAAAAATCTC-ATTTTTA
**
121056 CCCCCAAACTTCCAAAAATCTCATTTTTAA
1 CCCTAAAACTTCCAAAAATCTCATTTTT-A
*
121086 CCTTAAAACTTCCAAAAAT-TCCATTTTTA
1 CCCTAAAACTTCCAAAAATCT-CATTTTTA
* * *
121115 CCCCAAAACTTTCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATCTCATTTTT-A
*
121145 CCCTAAAACTTCCAAAACT-TCCATTTTTA
1 CCCTAAAACTTCCAAAAATCT-CATTTTTA
** * *
121174 CCCTCGAATTTCCAAAAATCTCATTTTAA
1 CCCTAAAACTTCCAAAAATCTCATTTTTA
* * *
121203 CCCTAAAACTTCCAAAATTTTTATTTTTA
1 CCCTAAAACTTCCAAAAATCTCATTTTTA
*** *
121232 CCCCCGAAC-TCTCAAAAATCCCATTTTTGA
1 CCCTAAAACTTC-CAAAAATCTCATTTTT-A
*
121262 CCCCAAAACTTCCAAAAAT-TCTATTTTTAA
1 CCCTAAAACTTCCAAAAATCTC-ATTTTT-A
121292 CCCTAAAACTTCCAAAAAT-TCCATTTTTA
1 CCCTAAAACTTCCAAAAATCT-CATTTTTA
* * * * *
121321 CCCTCAAACTTCAAAAAAACCCATTTTAA
1 CCCTAAAACTTCCAAAAATCTCATTTTTA
* *
121350 CCCTAAAACTTCCCAAAAAACCCATTTTT
1 CCCTAAAACTT-CCAAAAATCTCATTTTT
121379 GCCCCGGATG
Statistics
Matches: 263, Mismatches: 46, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.01
29 145 0.55
30 113 0.43
31 3 0.01
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATCTCATTTTTA
Found at i:121131 original size:59 final size:59
Alignment explanation
Indices: 121027--121378 Score: 388
Period size: 59 Copynumber: 6.0 Consensus size: 59
121017 CCCTAGAGGT
* * * *
121027 CCCTAAACCTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAA
* * *
121086 CCTTAAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTTCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAA
* * * *
121145 CCCTAAAACTTCCAAAACTTCCATTTTTACCCTC-GAATTTCCAAAAATCTCA-TTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCC-CAAAACTTCCAAAAATCCCATTTTTAA
* ** ** *
121203 CCCTAAAACTTCCAAAATTTTTATTTTTACCCCCGAAC-TCTCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTC-CAAAAATCCCATTTTTAA
* * * *
121262 CCCCAAAACTTCCAAAAATTCTATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTT-A
1 CCCTAAAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATCCCATTTTTAA
* * ** * * *
121321 CCCTCAAACTTCAAAAAAACCCATTTTAACCCTAAAACTTCCCAAAAAACCCATTTTT
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCAAAACTT-CCAAAAATCCCATTTTT
121379 GCCCCGGATG
Statistics
Matches: 250, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
57 3 0.01
58 59 0.24
59 163 0.65
60 23 0.09
61 2 0.01
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAA
Found at i:121640 original size:6 final size:7
Alignment explanation
Indices: 121622--121648 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
121612 ATGCACTCGG
121622 ATTTTTT
1 ATTTTTT
121629 ATTTTTT
1 ATTTTTT
121636 ATTTTTT
1 ATTTTTT
121643 ATTTTT
1 ATTTTT
121649 CGCAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Done.