Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010852.1 Kokia drynarioides strain JFW-HI SEQ_125820, 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: 156044
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2541 original size:49 final size:50
Alignment explanation
Indices: 2476--3007 Score: 383
Period size: 49 Copynumber: 10.9 Consensus size: 50
2466 TCGGCTCCAC
* * *
2476 GAAGACACGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCA
*
2526 GAA-ACATGAAGGGAAAGATTTAAG-CTGCAACGGCGAATCC-AGTACCAC-
1 GAAGACATGAAGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTAGTACCTCA
* * * * * * *
2574 GAAGACATAAAGGGAAAGGTTTCAGTCGCAATGGCAAACTTAATACCTCA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCA
* * ** * *
2624 -AAGACATGAAGGGAAAGATATAAGCCGCAACGGTAAATCC-AATACCAC-
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCA
* * **
2672 GAAGACA-CAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACC-GG
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCA
* * * * * *
2720 GAAGATATGAGAAGG-AAGGTTTAAGTCGCAACGACGAACCTTGTACTTCA
1 GAAGACATGA-AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCA
* * * *
2770 GAA-ATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AATACCAC-
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCA
* * * * *
2818 GAAGACA-CAAAGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCA
**
2867 G-AGACATGAAGGGAAAGATTTAAG-C-CAACGGCGAATCC-AGTACAGC-
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCA
* * ** **
2913 GAAGACA-CAAGAGGAAAGGTTTAAGTCGCAATAGTAAACCTTA-TACCTCA
1 GAAGACATGAAG-GGAAAGATTTAAGTCGCAACGGCGAACC-TAGTACCTCA
* * **
2963 GAAG-CATGAAAGGAAA-ATTTAAGCCGCAACGGCGAATTTAGTACC
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACC
3008 ATGAGGATTG
Statistics
Matches: 374, Mismatches: 79, Indels: 60
0.73 0.15 0.12
Matches are distributed among these distances:
46 4 0.01
47 35 0.09
48 112 0.30
49 201 0.54
50 22 0.06
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (50 bp):
GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCA
Found at i:2710 original size:146 final size:146
Alignment explanation
Indices: 2534--2890 Score: 420
Period size: 146 Copynumber: 2.4 Consensus size: 146
2524 CAGAAACATG
* *
2534 AAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGTTTCAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGTTTAAG
* * *
2599 TCGCAATGGC-AAACTTAATACCTCA-AAGACATGAAGGGAAAGATATAAGCCGCAACGGTAAAT
66 TCGCAACGACGAAACTT-ATACCTCAGAA-ACATGAAGGGAAAGATATAAGCCGCAACGGCAAAT
2662 CCAATACCACGAAGACAC
129 CCAATACCACGAAGACAC
** *
2680 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCGGGAAGATATGAGAA-GG-AAGGTTTA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACAT-A-AAGGGAAAGGTTTA
* * * * * *
2743 AGTCGCAACGACGAACCTTGTACTTCAGAAATATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT
64 AGTCGCAACGACGAAACTTATACCTCAGAAACATGAAGGGAAAGATATAAGCCGCAACGGCAAAT
2808 CCAATACCACGAAGACAC
129 CCAATACCACGAAGACAC
* * * * * * * *
2826 AAAGGAAAGGTTTAAGTCGCAATGGTGAA-CCTAGTACCTC-AGAGACATGAAGGGAAAGATTTA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGA-AGACATAAAGGGAAAGGTTTA
2889 AG
64 AG
2891 CCAACGGCGA
Statistics
Matches: 179, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
144 2 0.01
145 5 0.03
146 160 0.89
147 10 0.06
148 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (146 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGTTTAAG
TCGCAACGACGAAACTTATACCTCAGAAACATGAAGGGAAAGATATAAGCCGCAACGGCAAATCC
AATACCACGAAGACAC
Found at i:2882 original size:97 final size:96
Alignment explanation
Indices: 2680--3008 Score: 400
Period size: 97 Copynumber: 3.4 Consensus size: 96
2670 ACGAAGACAC
** * *
2680 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCGGGAAGATATGAGAAGG-AAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACA-CA-AAGGAAAGGTTTAA
* ** * * *
2744 GTCGCAACGACGAACCTTGTACTTCAGAAATATG
64 GTCGCAATGGTGAACCTAGTACCTCAG-AACATG
*
2778 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACACAAAGGAAAGGTTTAAGT
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGAAAGGTTTAAGT
2843 CGCAATGGTGAACCTAGTACCTCAGAGACATG
66 CGCAATGGTGAACCTAGTACCTCAGA-ACATG
2875 AAGGGAAAGATTTAAG-C-CAACGGCGAATCCAGTA-CAGCGAAGACACAAGAGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA-CGAAGACACAA-AGGAAAGGTTTAA
* *
2937 GTCGCAATAGTAAACCTTA-TACCTCAGAAGCATG
64 GTCGCAATGGTGAACC-TAGTACCTCAGAA-CATG
* **
2971 AAAGGAAA-ATTTAAGCCGCAACGGCGAATTTAGTACCA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
3009 TGAGGATTGA
Statistics
Matches: 205, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
94 2 0.01
95 35 0.17
96 54 0.26
97 69 0.34
98 45 0.22
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (96 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGAAAGGTTTAAGT
CGCAATGGTGAACCTAGTACCTCAGAACATG
Found at i:3446 original size:17 final size:18
Alignment explanation
Indices: 3409--3453 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
3399 TCAGATTGGT
* *
3409 TTTAAATTTATTTTTAAA
1 TTTAAATTTATCTTAAAA
3427 TTTAAATTTA-CTTAAAA
1 TTTAAATTTATCTTAAAA
3444 TTTAAATTTA
1 TTTAAATTTA
3454 AATTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATCTTAAAA
Found at i:3470 original size:6 final size:6
Alignment explanation
Indices: 3409--3458 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
3399 TCAGATTGGT
** * *
3409 TTTAAA TTTATT TTTAAA TTTAAA TTT-AC TTAAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3456 TTT
1 TTT
3459 GTTTTAGATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 3 0.09
6 32 0.91
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5423 original size:29 final size:29
Alignment explanation
Indices: 5375--5555 Score: 148
Period size: 28 Copynumber: 6.3 Consensus size: 29
5365 CTAAACTATT
* *
5375 CAAAAATCATATTTTGACCCTCGAACTTTC
1 CAAAAATTACATTTTGACCCTCGAAC-TTC
5405 CAAAAATTACATTTT-ACCCTCGAACTTC
1 CAAAAATTACATTTTGACCCTCGAACTTC
*
5433 CAAAAATT-CAATTTTGACCC-C-AATTTTC
1 CAAAAATTAC-ATTTTGACCCTCGAA-CTTC
*
5461 CAAAAATTACCATTTT-ACCCCCGAACTTC
1 CAAAAATTA-CATTTTGACCCTCGAACTTC
**
5490 CAAAAACTT-CATTTTTGA-CCTCGATTTTTC
1 CAAAAA-TTACA-TTTTGACCCTCGA-ACTTC
*
5520 CAAAAATTACCA-TTT-A-CCTCCAAACTTC
1 CAAAAATTA-CATTTTGACCCT-CGAACTTC
5548 CAAAAATT
1 CAAAAATT
5556 CCTTTTTTAA
Statistics
Matches: 127, Mismatches: 10, Indels: 30
0.76 0.06 0.18
Matches are distributed among these distances:
27 3 0.02
28 49 0.39
29 45 0.35
30 28 0.22
31 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
CAAAAATTACATTTTGACCCTCGAACTTC
Found at i:5446 original size:28 final size:29
Alignment explanation
Indices: 5375--5556 Score: 141
Period size: 29 Copynumber: 6.3 Consensus size: 29
5365 CTAAACTATT
5375 CAAAAA-TCATATTTTGACCCTCGAACTTTC
1 CAAAAATTCA-ATTTTGACCCTCGAAC-TTC
5405 CAAAAATT-ACATTTT-ACCCTCGAACTTC
1 CAAAAATTCA-ATTTTGACCCTCGAACTTC
*
5433 CAAAAATTCAATTTTGACCC-C-AATTTTC
1 CAAAAATTCAATTTTGACCCTCGAA-CTTC
* *
5461 CAAAAATTACCATTTT-ACCCCCGAACTTC
1 CAAAAATT-CAATTTTGACCCTCGAACTTC
* **
5490 CAAAAACTTCATTTTTGA-CCTCGATTTTTC
1 CAAAAA-TTCAATTTTGACCCTCGA-ACTTC
* *
5520 CAAAAATTACCA-TTT-A-CCTCCAAACTTC
1 CAAAAATT-CAATTTTGACCCT-CGAACTTC
5548 CAAAAATTC
1 CAAAAATTC
5557 CTTTTTTAAC
Statistics
Matches: 126, Mismatches: 14, Indels: 27
0.75 0.08 0.16
Matches are distributed among these distances:
27 3 0.02
28 47 0.37
29 48 0.38
30 27 0.21
31 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
CAAAAATTCAATTTTGACCCTCGAACTTC
Found at i:5573 original size:58 final size:57
Alignment explanation
Indices: 5375--5576 Score: 241
Period size: 58 Copynumber: 3.5 Consensus size: 57
5365 CTAAACTATT
**
5375 CAAAAA-TCATATTTTGACCCTCGAACTTTCCAAAAATTA-CATTTTACCCTCGAACTTC
1 CAAAAATTCAT-TTTTGACCC-CGATTTTTCCAAAAATTACCATTTTACCC-CGAACTTC
* *
5433 CAAAAATTCAATTTTGACCCC-AATTTTCCAAAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTA-CCCCGAACTTC
* *
5490 CAAAAACTTCATTTTTGACCTCGATTTTTCCAAAAATTACCA-TTTACCTCCAAACTTC
1 CAAAAA-TTCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTACC-CCGAACTTC
* *
5548 CAAAAATTCCTTTTTTAACCCCGATTTTT
1 CAAAAATT-CATTTTTGACCCCGATTTTT
5577 TTTTTTTCAA
Statistics
Matches: 128, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
56 15 0.12
57 26 0.20
58 66 0.52
59 21 0.16
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (57 bp):
CAAAAATTCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCCGAACTTC
Found at i:5707 original size:29 final size:29
Alignment explanation
Indices: 5645--5705 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
5635 AAACTTTCCT
*
5645 AAAATTACCATTTTGCCCCTCGAGTGTCC
1 AAAATTACCATTTTGCCCCTCGAGTATCC
*
5674 AAAATTACCATTTTG-CCCTCGGGTATCC
1 AAAATTACCATTTTGCCCCTCGAGTATCC
5702 AAAA
1 AAAA
5706 ATCACATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCCTCGAGTATCC
Found at i:5713 original size:28 final size:29
Alignment explanation
Indices: 5645--5715 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
5635 AAACTTTCCT
* *
5645 AAAATTACCATTTTGCCCCTCGAGTGTCC
1 AAAATCACCATTTTGCCCCTCGAGTATCC
* *
5674 AAAATTACCATTTTG-CCCTCGGGTATCC
1 AAAATCACCATTTTGCCCCTCGAGTATCC
5702 AAAAATCA-CATTTT
1 -AAAATCACCATTTT
5716 CAACTCCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (29 bp):
AAAATCACCATTTTGCCCCTCGAGTATCC
Found at i:7151 original size:108 final size:108
Alignment explanation
Indices: 6961--7185 Score: 432
Period size: 108 Copynumber: 2.1 Consensus size: 108
6951 AAGGGGGGAA
6961 ATGGATGGCTTATGCATGAGAGGAAGAGAAAATGATATGAAAGGAAGATGAAAGAATGTGAAGTG
1 ATGGATGGCTTATGCATGAGAGGAAGAGAAAATGATATGAAAGGAAGATGAAAGAATGTGAAGTG
* *
7026 AAGGATGATTTTGGTAAGGGGTGAAGGGTGGTATTTATAGTGG
66 AAGGATGATTTTAGTAAGGGATGAAGGGTGGTATTTATAGTGG
7069 ATGGATGGCTTATGCATGAGAGGAAGAGAAAATGATATGAAAGGAAGATGAAAGAATGTGAAGTG
1 ATGGATGGCTTATGCATGAGAGGAAGAGAAAATGATATGAAAGGAAGATGAAAGAATGTGAAGTG
7134 AAGGATGATTTTAGTAAGGGATGAAGGGTGGTATTTATAGTGG
66 AAGGATGATTTTAGTAAGGGATGAAGGGTGGTATTTATAGTGG
7177 ATGGATGGC
1 ATGGATGGC
7186 ATAAGAGTTT
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 115 1.00
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.25
Consensus pattern (108 bp):
ATGGATGGCTTATGCATGAGAGGAAGAGAAAATGATATGAAAGGAAGATGAAAGAATGTGAAGTG
AAGGATGATTTTAGTAAGGGATGAAGGGTGGTATTTATAGTGG
Found at i:10568 original size:33 final size:33
Alignment explanation
Indices: 10526--10591 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
10516 GTATCTACTT
10526 GTGTGTCATAATTTAATATTTTTTAAAATTTTA
1 GTGTGTCATAATTTAATATTTTTTAAAATTTTA
10559 GTGTGTCATAATTTAATATTTTTTAAAATTTTA
1 GTGTGTCATAATTTAATATTTTTTAAAATTTTA
10592 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (33 bp):
GTGTGTCATAATTTAATATTTTTTAAAATTTTA
Found at i:21377 original size:17 final size:17
Alignment explanation
Indices: 21355--21389 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21345 GTTAAATATG
21355 ATTGATTAAATTTTTTT
1 ATTGATTAAATTTTTTT
**
21372 ATTGATTTCATTTTTTT
1 ATTGATTAAATTTTTTT
21389 A
1 A
21390 AAAATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
ATTGATTAAATTTTTTT
Found at i:21411 original size:16 final size:16
Alignment explanation
Indices: 21390--21427 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
21380 CATTTTTTTA
*
21390 AAAATTTATAATTTCC
1 AAAATTTAAAATTTCC
*
21406 AAAA-TTAAAATTTTC
1 AAAATTTAAAATTTCC
21421 AAAATTT
1 AAAATTT
21428 TCAAAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTTAAAATTTCC
Found at i:24427 original size:15 final size:15
Alignment explanation
Indices: 24407--24436 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24397 AAAAAATTAA
*
24407 ATTAATTTTATATTT
1 ATTAATTTAATATTT
24422 ATTAATTTAATATTT
1 ATTAATTTAATATTT
24437 TAAAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTAATTTAATATTT
Found at i:24447 original size:51 final size:50
Alignment explanation
Indices: 24340--24459 Score: 118
Period size: 51 Copynumber: 2.4 Consensus size: 50
24330 GTTTTTTTAT
* * * * *
24340 AATTTTTAAAAGATTAAATTAATTTATTATTATTTTTTATTATACTTATA
1 AATTTTAAAAAAATTAAATTAATTTATTATTATTATTTAATATACTTAAA
* *
24390 ATTTTTAAAAAAATTAAATTAATTT-TATATTTATTAATTTAATAT-TTTAAA
1 AATTTTAAAAAAATTAAATTAATTTAT-TA-TTATT-ATTTAATATACTTAAA
* *
24441 AATTTTAAAATATTTAAAT
1 AATTTTAAAAAAATTAAAT
24460 AAATAATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.02
50 24 0.42
51 25 0.44
52 7 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (50 bp):
AATTTTAAAAAAATTAAATTAATTTATTATTATTATTTAATATACTTAAA
Found at i:30752 original size:20 final size:19
Alignment explanation
Indices: 30720--30770 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
30710 ACAGGAAAAA
*
30720 TTAAATTAT-TTTATATTAT
1 TTAAAATATATTTATATT-T
30739 TTAAAATATATTTATATTT
1 TTAAAATATATTTATATTT
*
30758 TATAATATATATT
1 T-TAAAATATATT
30771 ATACAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAAAATATATTTATATTT
Found at i:30764 original size:18 final size:19
Alignment explanation
Indices: 30738--30773 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30728 TTTTATATTA
30738 TTTAAAATATAT-TTATAT
1 TTTAAAATATATATTATAT
*
30756 TTTATAATATATATTATA
1 TTTAAAATATATATTATA
30774 CAAATAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAAATATATATTATAT
Found at i:47423 original size:20 final size:19
Alignment explanation
Indices: 47387--47425 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
47377 AACTTACAAC
*
47387 TAATAAAAATATTTTAATT
1 TAATAAAAATATATTAATT
47406 TAATAAAAATAATATTAATT
1 TAATAAAAAT-ATATTAATT
47426 ATGATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAAAATATATTAATT
Found at i:47585 original size:31 final size:29
Alignment explanation
Indices: 47537--47604 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
47527 ACTATTCATG
* *
47537 AATTTTATTTTAATATATAATTTTATATATT
1 AATTTTATTTTAATATAT--TTTTATACATA
*
47568 AATTTTGATTTT-GTATATTTTTATACATA
1 AATTTT-ATTTTAATATATTTTTATACATA
47597 AATTTTAT
1 AATTTTAT
47605 AAATATTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 15 0.45
31 11 0.33
32 5 0.15
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (29 bp):
AATTTTATTTTAATATATTTTTATACATA
Found at i:48866 original size:2 final size:2
Alignment explanation
Indices: 48859--48901 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
48849 TGATACCATT
48859 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
48901 T
1 T
48902 TGAGCTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:51049 original size:21 final size:19
Alignment explanation
Indices: 51023--51068 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
51013 GATAATAATC
*
51023 ATGTAATTTAAACAATAATT
1 ATGTAATTTAAA-AATAAAT
*
51043 AATGTAATTTTAAAATAAAT
1 -ATGTAATTTAAAAATAAAT
51063 ATGTAA
1 ATGTAA
51069 AATTGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (19 bp):
ATGTAATTTAAAAATAAAT
Found at i:54279 original size:31 final size:31
Alignment explanation
Indices: 54241--54305 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
54231 AATCACTTTC
* *
54241 AATCTTATTGATAGACCTCAAGAGTATACAT
1 AATCTTATTGATAAACCTCAAAAGTATACAT
*
54272 AATCTTATTGATAAACCTCAAAATTATACAT
1 AATCTTATTGATAAACCTCAAAAGTATACAT
54303 AAT
1 AAT
54306 ATTTATAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (31 bp):
AATCTTATTGATAAACCTCAAAAGTATACAT
Found at i:62569 original size:23 final size:22
Alignment explanation
Indices: 62518--62583 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
62508 AAAAATTATA
62518 TTATTGTTTTGG-TGTTGTTTT
1 TTATTGTTTTGGTTGTTGTTTT
*
62539 TTAATGTTTTGGTTGCTAT-TTTT
1 TTATTGTTTTGGTTG-T-TGTTTT
*
62562 TTATTGTTTTGG-TATTGTTTT
1 TTATTGTTTTGGTTGTTGTTTT
62583 T
1 T
62584 GTTGTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.03
21 17 0.45
22 3 0.08
23 16 0.42
24 1 0.03
ACGTcount: A:0.09, C:0.02, G:0.20, T:0.70
Consensus pattern (22 bp):
TTATTGTTTTGGTTGTTGTTTT
Found at i:62594 original size:12 final size:12
Alignment explanation
Indices: 62579--62630 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
62569 TTTGGTATTG
*
62579 TTTTTGTTGTTA
1 TTTTTATTGTTA
*
62591 -TTTTACTGTTA
1 TTTTTATTGTTA
62602 TTTTTATTGTTA
1 TTTTTATTGTTA
**
62614 TTTTGGTTGTTA
1 TTTTTATTGTTA
62626 TTTTT
1 TTTTT
62631 TATGCATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.12, C:0.02, G:0.13, T:0.73
Consensus pattern (12 bp):
TTTTTATTGTTA
Found at i:62594 original size:23 final size:23
Alignment explanation
Indices: 62555--62630 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
62545 TTTTGGTTGC
* *
62555 TATTTTT-TTATTGTTTTGGTAT
1 TATTTTTATTGTTATTTTGGTAT
* * ** *
62577 TGTTTTTGTTGTTATTTTACTGT
1 TATTTTTATTGTTATTTTGGTAT
*
62600 TATTTTTATTGTTATTTTGGTTGT
1 TATTTTTATTGTTATTTTGG-TAT
62624 TATTTTT
1 TATTTTT
62631 TATGCATTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
22 6 0.14
23 26 0.62
24 10 0.24
ACGTcount: A:0.12, C:0.01, G:0.14, T:0.72
Consensus pattern (23 bp):
TATTTTTATTGTTATTTTGGTAT
Found at i:64789 original size:43 final size:43
Alignment explanation
Indices: 64656--66467 Score: 1262
Period size: 43 Copynumber: 42.1 Consensus size: 43
64646 TAATATATCA
* * * *
64656 AAGCATCTATACTGACACCCACATAATGCATCATCTGATAAACCG
1 AAGCATCTATACTGGCA--CACACAGTGCATCATCGGATAAACCG
* * **
64701 AAGCATATATACTAGCATCCACACAGTGCATCATTAGATAAACCG
1 AAGCATCTATACTGGCA--CACACAGTGCATCATCGGATAAACCG
* * * *
64746 AATCTTCTATACTGGCACACATAGTGCATCATCGGATACACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * *
64789 AAACATTTATACTGGCACACACAGTACATCATCGGATAAACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * *
64832 AAGCATCTATACTGACACACACAGTGCATCATCGAATAAACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * * * * *
64875 AAGCATCAATATTGGAAAACACAATACATCATCGAATAAACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * * **
64918 AAGCATTTACACTGGCATACACAGTGCATCATCGAACAAAGTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
** * * **
64961 AAAAATCTATATTGGCACACACAGTGCATCATCGAATAAATTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * *
65004 AAGCATCTATACTGGCACATATAGTGCATCGTAAGG-TAAATCG
1 AAGCATCTATACTGGCACACACAGTGCATCAT-CGGATAAACCG
* * * * *
65047 AAGCATCTTTACTGGCATACACAGTGCTTCATC-AAGTAAATCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGA-TAAACCG
* * * * *
65090 AAGCATCTTTACTGGCACACACAGTGTATCCTCGGATAAATCA
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * * *
65133 AAGTATTTTTCCTAGCACACACAGTGCATCATCGAATAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * * * **
65176 AAGCATCTA-AATGGGTACACATAGTGCGTCGTCGAATAAATTG
1 AAGCATCTATACT-GGCACACACAGTGCATCATCGGATAAACCG
* * * *
65219 AAGCATCTATAC-CG-ACACACAGTGCATTATCGAATAAACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
** * * * *
65260 AAATATCTATACTAGCACACATAGTGCGTCCTCGGATAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * * *
65303 AAGCATCTATACTAGCAAACACAATACATCATCAGG-TATACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATC-GGATAAACCG
* * * * *
65346 AA-CTACCTATACTAGCACACACAGTACATCATCGGGTAAA-CT
1 AAGC-ATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * *
65388 AAGGCATTTATATTGGCACACACAGTGCATCATCGGGTATACGG
1 AA-GCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* *
65432 AGGCATCTATTA-TGGCACACACAGTGCATCATCTGATAAACCG
1 AAGCATCTA-TACTGGCACACACAGTGCATCATCGGATAAACCG
** * * * *
65475 AAAAATTTATACTAGCACACATAATGCATCATCCGG-TAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCAT-CGGATAAACCG
* ** * * *
65518 AAACATCTATACTTACACACACAATGCATTATCAGG-TAAATCG
1 AAGCATCTATACTGGCACACACAGTGCATCATC-GGATAAACCG
* * * * * *
65561 AGGCATCTATACTGACACACATAATGTA-CGATCGGGTAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATC-ATCGGATAAACCG
* *
65604 AAGCATCTATACTGGCACACACAATGCATCATCCGG-TAAATCG
1 AAGCATCTATACTGGCACACACAGTGCATCAT-CGGATAAACCG
* * * *
65647 AAGCATCTATCCAGGCACACACAGTGTACCATCGGATAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * * ** * * *
65690 AGGCATCTATATTAGCACATATAGTGCAAAATAGGGTAAGCCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * *
65733 AGGCATCTATACTGGCACATAGAGTGTA-CTGTCAGG-TAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATC-ATC-GGATAAACCG
* * * * *
65776 AGGCATCTGTACTGGCACACACAGTGCATCATTGGGTAAACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * *
65819 AAGAATCTATACTGGCACACACAGTGCATCATC-AAGTAAACCT
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGA-TAAACCG
* * * * * *
65862 AGGCATTTATACTTGCACACATAGTGCATCATCGGGTAAATC-
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * *
65904 AAGGCATCTATATTGGCACACACAATGCATCATC-GAGTAAATC-
1 AA-GCATCTATACTGGCACACACAGTGCATCATCGGA-TAAACCG
*
65947 AATGCATCTATACTGGCACACACAGTGCATCATC-GAGTAAACTG
1 AA-GCATCTATACTGGCACACACAGTGCATCATCGGA-TAAACCG
* ** * * *
65991 AGGCATCTATACTGGCACTTACAGTGCATCCTCGGGTAAATCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * *
66034 AGGCATCTATACTAGCACACACAGTGCATTATCGGGTAAACTG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* *
66077 AGGCATCTATACTGGCACACACGGTGCATCATC-GAGTAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGA-TAAACCG
* ** * * *
66120 AGGTGTTTATACTGGCACACAAAGT-CA-CAATCGGGTAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATC-ATCGGATAAACCG
* * * * * ** * **
66162 AGGCGTCTACACTGGCACATATACGATATATCATCGGGTAAATTG
1 AAGCATCTATACTGGCACACACA-G-TGCATCATCGGATAAACCG
* * * *
66207 AGGCGTCTATATTGGCACACACAGTGCATCATCGGGTAAACC-
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
** * * *
66249 AAGGTGTCTATATTGGCACACACAATGCATCATC-GAGTAAACTG
1 AA-GCATCTATACTGGCACACACAGTGCATCATCGGA-TAAACCG
* * * * * * * **
66293 AGGTATCTATGCTAGTACACACAATGCATCGTCAAATAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * **
66336 AAGCATCTATACTGGCACATACAGTGCATCATCGAATAAACTA
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
** * **
66379 AAGCATCTATACTGATACACACAGTGCATCCTCAAATAAACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
* * * * *
66422 AAGCATCTATATTGACAAACACAGTGCATCATCGAATATACCG
1 AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
66465 AAG
1 AAG
66468 TACCTGTACT
Statistics
Matches: 1412, Mismatches: 311, Indels: 90
0.78 0.17 0.05
Matches are distributed among these distances:
41 33 0.02
42 53 0.04
43 1220 0.86
44 24 0.02
45 81 0.06
46 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (43 bp):
AAGCATCTATACTGGCACACACAGTGCATCATCGGATAAACCG
Found at i:69721 original size:12 final size:12
Alignment explanation
Indices: 69704--69741 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
69694 TCATTTATAA
69704 AAATAATAATTT
1 AAATAATAATTT
69716 AAATAATAATTT
1 AAATAATAATTT
* *
69728 TAAT-TTAATTT
1 AAATAATAATTT
69739 AAA
1 AAA
69742 ACCATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATAATAATTT
Found at i:70785 original size:12 final size:12
Alignment explanation
Indices: 70768--70805 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
70758 CTCCTTTTAA
70768 CCTTTTCCTCTT
1 CCTTTTCCTCTT
*
70780 CCTTTTCCTTTT
1 CCTTTTCCTCTT
*
70792 CCTCTTCCTCTT
1 CCTTTTCCTCTT
70804 CC
1 CC
70806 GCTTACCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (12 bp):
CCTTTTCCTCTT
Found at i:70787 original size:6 final size:6
Alignment explanation
Indices: 70772--70805 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
70762 TTTTAACCTT
* *
70772 TTCCTC TTCCTT TTCCTT TTCCTC TTCCTC TTCC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCC
70806 GCTTACCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCCTC
Found at i:70791 original size:18 final size:18
Alignment explanation
Indices: 70768--70805 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
70758 CTCCTTTTAA
*
70768 CCTTTTCCTCTTCCTTTT
1 CCTTTTCCTCTTCCTCTT
70786 CCTTTTCCTCTTCCTCTT
1 CCTTTTCCTCTTCCTCTT
70804 CC
1 CC
70806 GCTTACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (18 bp):
CCTTTTCCTCTTCCTCTT
Found at i:76811 original size:2 final size:2
Alignment explanation
Indices: 76804--76832 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
76794 TAAAAACAGT
76804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76833 TAGTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77130 original size:22 final size:22
Alignment explanation
Indices: 77086--77131 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
77076 TCTTATCATA
*
77086 TTTTACATAAAAAGTATACTTT
1 TTTTAAATAAAAAGTATACTTT
*
77108 TTTTAAATGAAAAATTATA-TTT
1 TTTTAAAT-AAAAAGTATACTTT
77130 TT
1 TT
77132 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTTAAATAAAAAGTATACTTT
Found at i:77645 original size:17 final size:18
Alignment explanation
Indices: 77593--77645 Score: 83
Period size: 17 Copynumber: 3.0 Consensus size: 18
77583 TTTTTCATAT
77593 TTTAAACAAATAAAAAAT-
1 TTTAAA-AAATAAAAAATA
77611 TTTAAAAAATAAAAAATA
1 TTTAAAAAATAAAAAATA
77629 TTT-AAAAATAAAAAATA
1 TTTAAAAAATAAAAAATA
77646 AAAATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 25 0.74
18 9 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TTTAAAAAATAAAAAATA
Found at i:77648 original size:23 final size:24
Alignment explanation
Indices: 77613--77679 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 24
77603 TAAAAAATTT
77613 TAAAAAATAAAAAATATTTAAAAA
1 TAAAAAATAAAAAATATTTAAAAA
*
77637 TAAAAAAT-AAAAAT-TTTTAAAA
1 TAAAAAATAAAAAATATTTAAAAA
**
77659 -AAATTATAAAAAA-ATTTAAAA
1 TAAAAAATAAAAAATATTTAAAA
77680 TTCAATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 5 0.14
22 18 0.49
23 6 0.16
24 8 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAAATAAAAAATATTTAAAAA
Found at i:77659 original size:18 final size:18
Alignment explanation
Indices: 77592--77662 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
77582 TTTTTTCATA
* *
77592 TTTTAAACAAATAAAAAA
1 TTTTAAAAAAATAAAAAT
77610 TTTT-AAAAAATAAAAAAT
1 TTTTAAAAAAAT-AAAAAT
*
77628 ATTTAAAAATAAAAAATAAAAAT
1 -TTT---TA-AAAAAATAAAAAT
77651 TTTTAAAAAAAT
1 TTTTAAAAAAAT
77663 TATAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
17 6 0.14
18 16 0.38
19 4 0.10
22 3 0.07
23 6 0.14
24 7 0.17
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (18 bp):
TTTTAAAAAAATAAAAAT
Found at i:78144 original size:17 final size:17
Alignment explanation
Indices: 78124--78165 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
78114 TATTTTTGAA
*
78124 TTTTAAAGATTTTTATT
1 TTTTAAAGAATTTTATT
78141 TTTTAATA-AATTTTATT
1 TTTTAA-AGAATTTTATT
*
78158 TTTAAAAG
1 TTTTAAAG
78166 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTAAAGAATTTTATT
Found at i:80124 original size:23 final size:23
Alignment explanation
Indices: 80094--80197 Score: 129
Period size: 23 Copynumber: 4.4 Consensus size: 23
80084 ACACTAGCGC
*
80094 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
80117 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * * *
80142 GGTCTCTGATTAACACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
80165 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
80188 GCTCTCTGTT
1 GCTCTCTGTT
80198 GCCCAGCATT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 49 0.71
24 1 0.01
25 16 0.23
26 3 0.04
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:80215 original size:48 final size:46
Alignment explanation
Indices: 80115--80222 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 46
80105 AGCACGTCTC
* **
80115 GTGCTCTCTGTTATTAGCACTGTGTGTGGTCTCTGATTAACACTTTGT
1 GTGCTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAACACTTTAA
**
80163 GTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCATTTAA
1 GTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGATT-AACA-C-TTTAA
80211 GTGCTCTCTGTT
1 GTGCTCTCTGTT
80223 AGTACTTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
45 2 0.04
46 23 0.44
47 2 0.04
48 25 0.48
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (46 bp):
GTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAACACTTTAA
Found at i:84048 original size:15 final size:16
Alignment explanation
Indices: 84014--84045 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
84004 GGTAATTTTT
*
84014 ATGTTAAAGGATTAAA
1 ATGTTAAAGGAATAAA
84030 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
84046 TGTATAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:84500 original size:27 final size:27
Alignment explanation
Indices: 84464--84540 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
84454 TGAGGAGTAA
*
84464 TTTGATTTTGGCTCAAAAGAGCGTTAT
1 TTTGATTTTGGCTCAAAAGAGCATTAT
*
84491 TTTGATTTTGGATCGAAAA-AGCATTAT
1 TTTGATTTTGGCTC-AAAAGAGCATTAT
* * *
84518 TCTGATTCTGGGCTCATAAGAGC
1 TTTGATT-TTGGCTCAAAAGAGC
84541 TAACCATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 29 0.71
28 12 0.29
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (27 bp):
TTTGATTTTGGCTCAAAAGAGCATTAT
Found at i:84550 original size:24 final size:23
Alignment explanation
Indices: 84522--84590 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
84512 CATTATTCTG
*
84522 ATTCTGGGCTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAA-C
* *
84546 ATTCTAGGCTTGTAAGAGCTAAC
1 ATTCTGGGCTCGTAAGAGCTAAC
* *
84569 ATCCTGGGCTCGTATGAGCTAA
1 ATTCTGGGCTCGTAAGAGCTAA
84591 TTTTGTCTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (23 bp):
ATTCTGGGCTCGTAAGAGCTAAC
Found at i:92172 original size:6 final size:6
Alignment explanation
Indices: 92161--92209 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
92151 GTGAGAACCT
* ** *
92161 CACAAC CACAAC CACAGC CACAGT CACAAC CACAAC CACAAT CACAAC
1 CACAAC CACAAC CACAAC CACAAC CACAAC CACAAC CACAAC CACAAC
92209 C
1 C
92210 TCATGAACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.45, C:0.47, G:0.04, T:0.04
Consensus pattern (6 bp):
CACAAC
Found at i:92188 original size:18 final size:18
Alignment explanation
Indices: 92161--92209 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
92151 GTGAGAACCT
* *
92161 CACAACCACAACCACAGC
1 CACAATCACAACCACAAC
*
92179 CACAGTCACAACCACAAC
1 CACAATCACAACCACAAC
92197 CACAATCACAACC
1 CACAATCACAACC
92210 TCATGAACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.45, C:0.47, G:0.04, T:0.04
Consensus pattern (18 bp):
CACAATCACAACCACAAC
Found at i:96961 original size:23 final size:24
Alignment explanation
Indices: 96919--96971 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
96909 TTAATTTTTT
96919 AATTTTTATTTTTAAGAATTT-AA
1 AATTTTTATTTTTAAGAATTTCAA
* *
96942 TATTTTTATTTTTTTA-AATTTCAA
1 AATTTTTA-TTTTTAAGAATTTCAA
96966 AATTTT
1 AATTTT
96972 GGTGTTAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
AATTTTTATTTTTAAGAATTTCAA
Found at i:103868 original size:38 final size:38
Alignment explanation
Indices: 103826--103902 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
103816 TCTTTATCGG
103826 ATTGTTGATATCAAAAGCAAAGTGCAATTTGGCGATCT
1 ATTGTTGATATCAAAAGCAAAGTGCAATTTGGCGATCT
103864 ATTGTTGATATCAAAAGCAAAGTGCAATTTGGCGATCT
1 ATTGTTGATATCAAAAGCAAAGTGCAATTTGGCGATCT
103902 A
1 A
103903 CTTTTCTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (38 bp):
ATTGTTGATATCAAAAGCAAAGTGCAATTTGGCGATCT
Found at i:110297 original size:21 final size:21
Alignment explanation
Indices: 110272--110319 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
110262 AATATGAGTT
110272 AAACTCAAGCTTGAAT-ATTCA
1 AAACTCAAGCTT-AATCATTCA
*
110293 AAACTCAAGCTTAATCCTTCA
1 AAACTCAAGCTTAATCATTCA
110314 AAACTC
1 AAACTC
110320 GAACTCGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (21 bp):
AAACTCAAGCTTAATCATTCA
Found at i:118846 original size:3 final size:3
Alignment explanation
Indices: 118838--118878 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
118828 TAAACTTTAA
118838 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
118879 ATTGAAAGGT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:124479 original size:19 final size:18
Alignment explanation
Indices: 124455--124524 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 18
124445 AAATTTCATA
124455 AAAAAAAAAACAAAAAAGG
1 AAAAAAAAAA-AAAAAAGG
* *
124474 AAAAAAAAGAGAAAAAGAG
1 AAAAAAAAAAAAAAAAG-G
124493 AAAAAGAAAAGGAAAAAAA-G
1 AAAAA-AAAA--AAAAAAAGG
124513 AAAAGAAAAAAA
1 AAAA-AAAAAAA
124525 GGGAGGTCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 8 0.19
19 15 0.36
20 12 0.29
21 1 0.02
22 6 0.14
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAGG
Found at i:124502 original size:14 final size:13
Alignment explanation
Indices: 124454--124523 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
124444 GAAATTTCAT
*
124454 AAAAAA-AAAAAC
1 AAAAAAGAAAAAG
*
124466 AAAAAAGGAAAA-
1 AAAAAAGAAAAAG
*
124478 AAAAGAGAAAAAG
1 AAAAAAGAAAAAG
*
124491 AGAAAAAGAAAAGG
1 A-AAAAAGAAAAAG
124505 AAAAAA-AGAAAAG
1 AAAAAAGA-AAAAG
124518 AAAAAA
1 AAAAAA
124524 AGGGAGGTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
12 17 0.35
13 20 0.42
14 11 0.23
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:124522 original size:20 final size:20
Alignment explanation
Indices: 124454--124522 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
124444 GAAATTTCAT
124454 AAAAAAAAA-A-ACAAAAAAG
1 AAAAAAAAAGAGA-AAAAAAG
* *
124473 GAAAAAAAAGAGAAAAAGAG
1 AAAAAAAAAGAGAAAAAAAG
124493 AAAAAGAAAAG-GAAAAAAAG
1 AAAAA-AAAAGAGAAAAAAAG
124513 AAAAGAAAAA
1 AAAA-AAAAA
124523 AAGGGAGGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.19
20 27 0.64
21 7 0.17
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAAAAAG
Found at i:124524 original size:8 final size:8
Alignment explanation
Indices: 124454--124525 Score: 56
Period size: 8 Copynumber: 8.6 Consensus size: 8
124444 GAAATTTCAT
124454 AAAA-AAA
1 AAAAGAAA
*
124461 AAAACAAA
1 AAAAGAAA
*
124469 AAAGGAAAA
1 AAAAG-AAA
*
124478 AAAAGAGA
1 AAAAGAAA
*
124486 AAAAGAGA
1 AAAAGAAA
124494 AAAAGAAA
1 AAAAGAAA
*
124502 AGGAAAAAAA
1 A--AAAGAAA
124512 GAAAAGAAA
1 -AAAAGAAA
124521 AAAAG
1 AAAAG
124526 GGAGGTCGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
7 4 0.08
8 29 0.55
9 13 0.25
10 6 0.11
11 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:124524 original size:14 final size:14
Alignment explanation
Indices: 124454--124524 Score: 65
Period size: 14 Copynumber: 4.9 Consensus size: 14
124444 GAAATTTCAT
*
124454 AAAA-AAAAAAACAA
1 AAAAGAAAAAAA-AG
124468 AAAAGGAAAAAAAAG
1 AAAA-GAAAAAAAAG
124483 AGAAA-AAGAGAAAAAG
1 A-AAAGAA-A-AAAAAG
*
124499 AAAAGGAAAAAAAG
1 AAAAGAAAAAAAAG
124513 AAAAGAAAAAAA
1 AAAAGAAAAAAA
124525 GGGAGGTCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.48
15 7 0.15
16 18 0.38
ACGTcount: A:0.83, C:0.01, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:125513 original size:49 final size:49
Alignment explanation
Indices: 125372--125513 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 49
125362 ATTCTACAGG
** *
125372 TATGAAGGGAAAGATTGAAGCCGCAACGGTAAATCTGATACCCTAGAGA
1 TATGAAGGGAAAGATTGAAGCCGCAACGACAAATCTTATACCCTAGAGA
* * * *
125421 TATGAAGAGAAAGGTTGAAGCCGCAACGACAAACCTTGTACCCTAGAGA
1 TATGAAGGGAAAGATTGAAGCCGCAACGACAAATCTTATACCCTAGAGA
* ** * * *
125470 TGTGAAGGGAAAGATTGGGGCCACAACGACGAATCTTACACCCT
1 TATGAAGGGAAAGATTGAAGCCGCAACGACAAATCTTATACCCT
125514 GAAGATGAGG
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.18
Consensus pattern (49 bp):
TATGAAGGGAAAGATTGAAGCCGCAACGACAAATCTTATACCCTAGAGA
Found at i:125859 original size:20 final size:20
Alignment explanation
Indices: 125822--125859 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
125812 GGTCAAATTG
* *
125822 AAGACCATCAGATCTTTTTT
1 AAGACAATCAAATCTTTTTT
125842 AAGACAATCAAAT-TTTTT
1 AAGACAATCAAATCTTTTT
125860 ACCCTAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
AAGACAATCAAATCTTTTTT
Found at i:125886 original size:40 final size:40
Alignment explanation
Indices: 125842--125965 Score: 110
Period size: 40 Copynumber: 3.1 Consensus size: 40
125832 GATCTTTTTT
*
125842 AAGACAATCAAATTTTTTACCCTAACTAGAGGGTAGATTG
1 AAGACAATCAAATCTTTTACCCTAACTAGAGGGTAGATTG
* * * ** *
125882 AAGACCATCCAATCTCTTACCCCGA-TCATG-GGATAGATTG
1 AAGACAATCAAATCTTTTACCCTAACT-A-GAGGGTAGATTG
* * * *
125922 AAG-CAATCTAATCTTTTACCCTAGCTAGAAGGCAGATTG
1 AAGACAATCAAATCTTTTACCCTAACTAGAGGGTAGATTG
125961 AAGAC
1 AAGAC
125966 CATCCGATCT
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
38 1 0.02
39 27 0.43
40 34 0.54
41 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (40 bp):
AAGACAATCAAATCTTTTACCCTAACTAGAGGGTAGATTG
Found at i:125977 original size:79 final size:79
Alignment explanation
Indices: 125846--126179 Score: 420
Period size: 79 Copynumber: 4.2 Consensus size: 79
125836 TTTTTTAAGA
* * * * * *
125846 CAATCAAATTTTTTACCCTAACTAGAGGGTAGATTGAAGACCATCCAATCTCTTACCCCGATCAT
1 CAATCTAATCTTTTACCCTAACTAGAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAT
**
125911 GGGATAGATTGAAG
66 GGGGCAGATTGAAG
* *
125925 CAATCTAATCTTTTACCCTAGCTAGAAGGCAGATTGAAGACCATCCGATCTCTTACCTCGACCAT
1 CAATCTAATCTTTTACCCTAACTAGAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAT
*
125990 GGGGCAAATTGAAG
66 GGGGCAGATTGAAG
* * * * * * * *
126004 TAATCTAATATTTTACTCTAA-TCAGAGGGCAAATTGAAAACCATCTGATCTCTTACCCCGATCA
1 CAATCTAATCTTTTACCCTAACT-AGAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCA
126068 TGGGGCAGATTGAAG
65 TGGGGCAGATTGAAG
* * * *
126083 CAATCCAATCTTTTACTCTAACTAG-AGGACAGATTGAAGACTATCTGATCTCTTACCCCGACCA
1 CAATCTAATCTTTTACCCTAACTAGAAGG-CAGATTGAAGACCATCCGATCTCTTACCCCGACCA
*
126147 TGGGGCAGATTGAAA
65 TGGGGCAGATTGAAG
126162 CAATCTAATCTTTTACCC
1 CAATCTAATCTTTTACCC
126180 CTAAAACTAT
Statistics
Matches: 219, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
78 3 0.01
79 215 0.98
80 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (79 bp):
CAATCTAATCTTTTACCCTAACTAGAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAT
GGGGCAGATTGAAG
Found at i:126001 original size:40 final size:40
Alignment explanation
Indices: 125876--126178 Score: 151
Period size: 39 Copynumber: 7.7 Consensus size: 40
125866 ACTAGAGGGT
** * * **
125876 AGATTGAAGACCATCCAATCTCTTACCCCGATCATGGGAT
1 AGATTGAAGACCATCTGATCTCTTACCTCGACCATGGGGC
* * * * * *
125916 AGATTGAAG-CAATCTAATCTTTTACC-CTAGC-TAGAAGGC
1 AGATTGAAGACCATCTGATCTCTTACCTCGACCAT-G-GGGC
*
125955 AGATTGAAGACCATCCGATCTCTTACCTCGACCATGGGGC
1 AGATTGAAGACCATCTGATCTCTTACCTCGACCATGGGGC
* * * * * *
125995 AAATTGAAGTA--ATCTAATATTTTA-CTCTAATCA-GAGGGC
1 AGATTGAAG-ACCATCTGATCTCTTACCTC-GACCATG-GGGC
* * * *
126034 AAATTGAAAACCATCTGATCTCTTACCCCGATCATGGGGC
1 AGATTGAAGACCATCTGATCTCTTACCTCGACCATGGGGC
* ** * * * *
126074 AGATTGAAG-CAATCCAATCTTTTA-CTCTAAC-TAGAGGAC
1 AGATTGAAGACCATCTGATCTCTTACCTCGACCAT-G-GGGC
* *
126113 AGATTGAAGACTATCTGATCTCTTACCCCGACCATGGGGC
1 AGATTGAAGACCATCTGATCTCTTACCTCGACCATGGGGC
* * *
126153 AGATTGAA-ACAATCTAATCTTTTACC
1 AGATTGAAGACCATCTGATCTCTTACC
126179 CCTAAAACTA
Statistics
Matches: 197, Mismatches: 49, Indels: 35
0.70 0.17 0.12
Matches are distributed among these distances:
37 2 0.01
38 14 0.07
39 86 0.44
40 80 0.41
41 13 0.07
42 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (40 bp):
AGATTGAAGACCATCTGATCTCTTACCTCGACCATGGGGC
Found at i:128741 original size:16 final size:17
Alignment explanation
Indices: 128710--128743 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
128700 GAATAGTTTT
*
128710 TTTTTTTTAATAATAAA
1 TTTTATTTAATAATAAA
128727 TTTTATTTAAT-ATAAA
1 TTTTATTTAATAATAAA
128743 T
1 T
128744 AATTACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTATTTAATAATAAA
Found at i:137416 original size:12 final size:12
Alignment explanation
Indices: 137399--137424 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
137389 CTGCTTATAT
137399 TATATTATATTA
1 TATATTATATTA
137411 TATATTATATTA
1 TATATTATATTA
137423 TA
1 TA
137425 GATAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATTATATTA
Found at i:140388 original size:19 final size:18
Alignment explanation
Indices: 140364--140409 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
140354 AATTGATAAG
140364 CAATAAATATAATAAATTT
1 CAATAAATATAA-AAATTT
*
140383 CAATAATAAATAAAAATTT
1 CAATAA-ATATAAAAATTT
*
140402 AAATAAAT
1 CAATAAAT
140410 TCATACTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
CAATAAATATAAAAATTT
Found at i:141246 original size:17 final size:18
Alignment explanation
Indices: 141226--141259 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
141216 GGAAAAAATG
141226 ATAAAAAATA-AAAATAA
1 ATAAAAAATATAAAATAA
*
141243 ATAAAAATTATAAAATA
1 ATAAAAAATATAAAATA
141260 TTAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAAATATAAAATAA
Found at i:142555 original size:19 final size:19
Alignment explanation
Indices: 142533--142620 Score: 87
Period size: 19 Copynumber: 4.7 Consensus size: 19
142523 TTTTTGATAC
142533 ATTTTATAATTTTTATAAA
1 ATTTTATAATTTTTATAAA
* *
142552 ATTTTACAATTTTT-TATAT
1 ATTTTATAATTTTTATA-AA
142571 ATTTT-TAATATTTTATTAAA
1 ATTTTATAAT-TTTTA-TAAA
*
142591 ATTTAATAATTTTTAT---
1 ATTTTATAATTTTTATAAA
142607 ATTTTATAATTTTT
1 ATTTTATAATTTTT
142621 TCTAAATGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
16 13 0.22
18 5 0.09
19 24 0.41
20 10 0.17
21 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATAATTTTTATAAA
Found at i:142575 original size:38 final size:39
Alignment explanation
Indices: 142523--142620 Score: 116
Period size: 38 Copynumber: 2.6 Consensus size: 39
142513 TTAAAGAGCC
* * *
142523 TTTTTGATACATTTTATAATTTTTA-TAAAATTTTACAA
1 TTTTTTATATATTTTATAATTTTTATTAAAATTTAACAA
*
142561 TTTTTTATATATTTT-TAATATTTTATTAAAATTTAATAA
1 TTTTTTATATATTTTATAAT-TTTTATTAAAATTTAACAA
142600 --TTTT-TATATTTTATAATTTTT
1 TTTTTTATATATTTTATAATTTTT
142621 TCTAAATGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
36 12 0.23
37 12 0.23
38 18 0.34
39 11 0.21
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (39 bp):
TTTTTTATATATTTTATAATTTTTATTAAAATTTAACAA
Found at i:142605 original size:20 final size:20
Alignment explanation
Indices: 142533--142606 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
142523 TTTTTGATAC
142533 ATTTTATAATTTTTA-TAAA
1 ATTTTATAATTTTTATTAAA
* *
142552 ATTTTACAA-TTTT-TTATAT
1 ATTTTATAATTTTTATTA-AA
142571 ATTTT-TAATATTTTATTAAA
1 ATTTTATAAT-TTTTATTAAA
*
142591 ATTTAATAATTTTTAT
1 ATTTTATAATTTTTAT
142607 ATTTTATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
18 8 0.18
19 14 0.32
20 15 0.34
21 7 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTATAATTTTTATTAAA
Found at i:142621 original size:10 final size:9
Alignment explanation
Indices: 142534--142620 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
142524 TTTTGATACA
142534 TTTTATAAT
1 TTTTATAAT
*
142543 TTTTATAAAA
1 TTTTAT-AAT
*
142553 TTTTACAATT
1 TTTTATAA-T
142563 TTTTATATAT
1 TTTTATA-AT
*
142573 TTTTAATATT
1 TTTT-ATAAT
*
142583 TTATTA-AAA
1 TT-TTATAAT
*
142592 TTTAATAAT
1 TTTTATAAT
142601 TTTTAT-A-
1 TTTTATAAT
142608 TTTTATAAT
1 TTTTATAAT
142617 TTTT
1 TTTT
142621 TCTAAATGTC
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
7 6 0.10
8 4 0.07
9 22 0.37
10 22 0.37
11 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:146858 original size:8 final size:8
Alignment explanation
Indices: 146845--146869 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
146835 ATGGATCAAC
146845 TTGATATT
1 TTGATATT
146853 TTGATATT
1 TTGATATT
146861 TTGATATT
1 TTGATATT
146869 T
1 T
146870 CTACATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TTGATATT
Found at i:154093 original size:16 final size:16
Alignment explanation
Indices: 154072--154105 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
154062 TTATATAAAA
154072 AATTTAC-ACATAATAT
1 AATTTACTACAT-ATAT
154088 AATTTACTACATATAT
1 AATTTACTACATATAT
154104 AA
1 AA
154106 AGTTCTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTACTACATATAT
Done.