Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011669.1 Kokia drynarioides strain JFW-HI SEQ_126661, 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: 73930
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:9759 original size:49 final size:49
Alignment explanation
Indices: 9706--10039 Score: 144
Period size: 49 Copynumber: 6.8 Consensus size: 49
9696 TAAGATATGG
**
9706 AGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCAAAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACC-TGTACCTCAAAAGACACAA
* * ** *
9755 AGGGAAAGATTTAAG-CTGCAATGGCGAATCCAATACCAC-AAAGACACAA
1 AGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCTGTACCTCAAAAGACACAA
* * * * * *
9804 AGAGAAGGGTTTAAGTCACAACGACGAACCTTGTACCTC-AGAGACATGAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACC-TGTACCTCAAAAGACA-CAA
** * * * * * * * *
9854 A-GGAAATATCTAAGCCGTAACAGCGGATCCAGTACCGT-AAAGATACAAAA
1 AGGGAAAGGTTTAAGTCGCAACGGC-GAACCTGTACC-TCAAA-AGACACAA
* * * ** * * **
9904 AAGAAAAGGTTTAAGTCACAACGATGAACCTAGTACCT-TAGAGACATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCT-GTACCTCAAAAGACACAA
* * * * * *
9953 AGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAAG-CACAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCT-GTACCTCAAAAGACACAA
* * *
10002 AGAGAAAGGTTTAAGTCACAATGGCGAACCTTGTACCT
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACC-TGTACCT
10040 TAGAAACCTA
Statistics
Matches: 201, Mismatches: 70, Indels: 28
0.67 0.23 0.09
Matches are distributed among these distances:
48 7 0.03
49 147 0.73
50 25 0.12
51 22 0.11
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (49 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTGTACCTCAAAAGACACAA
Found at i:9826 original size:98 final size:98
Alignment explanation
Indices: 9651--10039 Score: 424
Period size: 98 Copynumber: 3.9 Consensus size: 98
9641 GTACCACGAA
** * *** *
9651 ACATGAAGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCA-ATAAGATATGGAGGGAAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA-AAGACACAAAGAGAAAGG
* * * *
9715 TTTAAGTCGCAACGGCGAACCGTGTACCTCA-AA
65 TTTAAGTCACAACGACGAACCTTGTACCTCAGAG
* * * *
9748 AGCATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCCAATACCACAAAGACACAAAGAGAAGGG
1 A-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGAGAAAGG
9813 TTTAAGTCACAACGACGAACCTTGTACCTCAGAG
65 TTTAAGTCACAACGACGAACCTTGTACCTCAGAG
* * * * * * ** * *
9847 ACATGAAAGGAAATATCTAAGCCGTAACAGCGGATCCAGTACCGTAAAGATACAAAAAAGAAAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACAC-AAAGAG-AAAG
* * *
9912 GTTTAAGTCACAACGATGAACCTAGTACCTTAGAG
64 GTTTAAGTCACAACGACGAACCTTGTACCTCAGAG
* *
9947 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAAG-CACAAAGAGAAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAAGACACAAAGAGAAAGG
* *
10011 TTTAAGTCACAATGGCGAACCTTGTACCT
65 TTTAAGTCACAACGACGAACCTTGTACCT
10040 TAGAAACCTA
Statistics
Matches: 238, Mismatches: 48, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
97 1 0.00
98 148 0.62
99 13 0.05
100 72 0.30
101 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (98 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGAGAAAGGT
TTAAGTCACAACGACGAACCTTGTACCTCAGAG
Found at i:10752 original size:17 final size:17
Alignment explanation
Indices: 10732--10809 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
10722 AATGGACCCA
*
10732 ATTTTAAATTTTAATTT
1 ATTTTAAATTTGAATTT
10749 ATTTT-AATTTGAATTT
1 ATTTTAAATTTGAATTT
* * *
10765 ACTTTAAATTATAAACTT
1 ATTTTAAATT-TGAATTT
* *
10783 ATTATAAGTTTGAATTT
1 ATTTTAAATTTGAATTT
*
10800 ATTCTAAATT
1 ATTTTAAATT
10810 AAAATTAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
16 14 0.29
17 22 0.46
18 12 0.25
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTGAATTT
Found at i:11402 original size:3 final size:3
Alignment explanation
Indices: 11394--11503 Score: 71
Period size: 3 Copynumber: 36.7 Consensus size: 3
11384 ACGTTAATTT
* * * * ** *
11394 ATA ATA ATA TTA ATA ATA ATGA A-G ATA ATA CTA ATG GCA CTA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * *
11439 ATA ATA ATA ATA ATA ACA ATA ATA A-A GATC ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * *
11484 TTA ATA ATA TTA ATA TTA AT
1 ATA ATA ATA ATA ATA ATA AT
11504 TTTAAATAAA
Statistics
Matches: 78, Mismatches: 25, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
2 2 0.03
3 74 0.95
4 2 0.03
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12615 original size:29 final size:29
Alignment explanation
Indices: 12577--12835 Score: 132
Period size: 29 Copynumber: 8.9 Consensus size: 29
12567 AAGGTCCCTA
12577 AACTATCCAAAAATTACATTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTACCCTCG
* *
12607 AACTTCC-AAAATTCCATTTTTTA-CCT-T
1 AACTTCCAAAAATTACA-TTTTTACCCTCG
** * * *
12634 ATTTTTTCAAAAATTATATTTTTACCCTCA
1 A-ACTTCCAAAAATTACATTTTTACCCTCG
* *
12664 AACTTTCC-AAATTTCCATTTTTTACCCT--
1 AAC-TTCCAAAAATTACA-TTTTTACCCTCG
* *
12692 AATTTTTCCAAAAATTACCA-TTTTACCC-CA
1 AA--CTTCCAAAAATTA-CATTTTTACCCTCG
*
12722 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACATTTTT-ACCCTCG
** *
12751 ATTTTTCCAAAAATTACCA--TTTACCCCCG
1 A-ACTTCCAAAAATTA-CATTTTTACCCTCG
12780 AACTTCCAAAAATT-CTATTTTTGACCC-CG
1 AACTTCCAAAAATTAC-ATTTTT-ACCCTCG
* *
12809 ATTCTTCCAAAAAGTACCA-TTTTACCC
1 A-ACTTCCAAAAATTA-CATTTTTACCC
12836 CCGGATGTCT
Statistics
Matches: 175, Mismatches: 28, Indels: 53
0.68 0.11 0.21
Matches are distributed among these distances:
26 1 0.01
27 4 0.02
28 51 0.29
29 58 0.33
30 55 0.31
31 5 0.03
32 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.39
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:12724 original size:58 final size:57
Alignment explanation
Indices: 12582--12917 Score: 297
Period size: 58 Copynumber: 5.8 Consensus size: 57
12572 CCCTAAACTA
* * *
12582 TCCAAAAATTA-CATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTTACCTTATTTT
1 TCCAAAAATTACCA-TTTTACCC-CAAACTTCCAAAAATTCCATTTTTGACCTGATTTT
* * * * *
12639 TTCAAAAATTA-TATTTTTACCCTCAAACTTTCC-AAATTTCCATTTTTTACCCTAATTTT
1 TCCAAAAATTACCA-TTTTACCC-CAAAC-TTCCAAAAATTCCATTTTTGA-CCTGATTTT
12698 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCT-GATTTT
* * * *
12756 TCCAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCGATTCT
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATTCCATTTTTGA-CCTGATTTT
* ** * * ** *
12814 TCCAAAAAGTACCATTTTACCCCCGGA-TGTCTAAAAATTTCATTTTTGACCACAATTT
1 TCCAAAAATTACCATTTTA-CCCCAAACT-TCCAAAAATTCCATTTTTGACCTGATTTT
* * * * *
12872 TCCCAAAATTACCATTTTGCCCCTAAGTTACAAAAATTACCATTTT
1 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATT-CCATTTT
12918 GCCCTCGGGT
Statistics
Matches: 237, Mismatches: 31, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
57 49 0.21
58 131 0.55
59 56 0.24
60 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCTGATTTT
Found at i:12776 original size:116 final size:115
Alignment explanation
Indices: 12582--12917 Score: 331
Period size: 116 Copynumber: 2.9 Consensus size: 115
12572 CCCTAAACTA
* * *
12582 TCCAAAAATTA-CATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTTACCTTATTTTTTCAAA
1 TCCAAAAATTACCA-TTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCTCATTTTTCCAAA
* * * * * *
12645 AATTA-TATTTTTACCCTCAAACTTTCC-AAATTTCCATTTTTTACCCTAATTTT
64 AATTACCA--TTTACCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCAATTCT
*
12698 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCCAAAA
1 TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTC-ATTTTTCCAAAA
* * *
12763 ATTACCATTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCGATTCT
65 ATTACCATTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATTCT
* * * * * * *
12814 TCCAAAAAGTACCATTTTACCCCCGGA-TGTCTAAAAATTTCATTTTTGACCACAATTTTCCCAA
1 TCCAAAAATTACCATTTTA-CCCCGAACT-TCCAAAAATTCCATTTTTGACCTCATTTTTCCAAA
** * * *
12878 AATTACCATTTTGCCCCTAAGTTACAAAAATTACCATTTT
64 AATTACCATTTACCCCCAAACTTCCAAAAATT-CCATTTT
12918 GCCCTCGGGT
Statistics
Matches: 185, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
115 12 0.06
116 123 0.66
117 49 0.26
118 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (115 bp):
TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTCATTTTTCCAAAAA
TTACCATTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATTCT
Found at i:19702 original size:49 final size:49
Alignment explanation
Indices: 19649--19982 Score: 144
Period size: 49 Copynumber: 6.8 Consensus size: 49
19639 TAAGATATGG
**
19649 AGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCAAAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACC-TGTACCTCAAAAGACACAA
* * ** *
19698 AGGGAAAGATTTAAG-CTGCAATGGCGAATCCAATACCAC-AAAGACACAA
1 AGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCTGTACCTCAAAAGACACAA
* * * * * *
19747 AGAGAAGGGTTTAAGTCACAACGACGAACCTTGTACCTC-AGAGACATGAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACC-TGTACCTCAAAAGACA-CAA
** * * * * * * * *
19797 A-GGAAATATCTAAGCCGTAACAGCGGATCCAGTACCGT-AAAGATACAAAA
1 AGGGAAAGGTTTAAGTCGCAACGGC-GAACCTGTACC-TCAAA-AGACACAA
* * * ** * * **
19847 AAGAAAAGGTTTAAGTCACAACGATGAACCTAGTACCT-TAGAGACATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCT-GTACCTCAAAAGACACAA
* * * * * *
19896 AGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAAG-CACAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCT-GTACCTCAAAAGACACAA
* * *
19945 AGAGAAAGGTTTAAGTCACAATGGCGAACCTTGTACCT
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACC-TGTACCT
19983 TAGAAACCTA
Statistics
Matches: 201, Mismatches: 70, Indels: 28
0.67 0.23 0.09
Matches are distributed among these distances:
48 7 0.03
49 147 0.73
50 25 0.12
51 22 0.11
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (49 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTGTACCTCAAAAGACACAA
Found at i:19769 original size:98 final size:98
Alignment explanation
Indices: 19594--19982 Score: 424
Period size: 98 Copynumber: 3.9 Consensus size: 98
19584 GTACCACGAA
** * *** *
19594 ACATGAAGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCA-ATAAGATATGGAGGGAAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA-AAGACACAAAGAGAAAGG
* * * *
19658 TTTAAGTCGCAACGGCGAACCGTGTACCTCA-AA
65 TTTAAGTCACAACGACGAACCTTGTACCTCAGAG
* * * *
19691 AGCATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCCAATACCACAAAGACACAAAGAGAAGGG
1 A-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGAGAAAGG
19756 TTTAAGTCACAACGACGAACCTTGTACCTCAGAG
65 TTTAAGTCACAACGACGAACCTTGTACCTCAGAG
* * * * * * ** * *
19790 ACATGAAAGGAAATATCTAAGCCGTAACAGCGGATCCAGTACCGTAAAGATACAAAAAAGAAAAG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACAC-AAAGAG-AAAG
* * *
19855 GTTTAAGTCACAACGATGAACCTAGTACCTTAGAG
64 GTTTAAGTCACAACGACGAACCTTGTACCTCAGAG
* *
19890 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAAG-CACAAAGAGAAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAAGACACAAAGAGAAAGG
* *
19954 TTTAAGTCACAATGGCGAACCTTGTACCT
65 TTTAAGTCACAACGACGAACCTTGTACCT
19983 TAGAAACCTA
Statistics
Matches: 238, Mismatches: 48, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
97 1 0.00
98 148 0.62
99 13 0.05
100 72 0.30
101 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (98 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAAGAGAAAGGT
TTAAGTCACAACGACGAACCTTGTACCTCAGAG
Found at i:20695 original size:17 final size:17
Alignment explanation
Indices: 20675--20752 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
20665 AATGGACCCA
*
20675 ATTTTAAATTTTAATTT
1 ATTTTAAATTTGAATTT
20692 ATTTT-AATTTGAATTT
1 ATTTTAAATTTGAATTT
* * *
20708 ACTTTAAATTATAAACTT
1 ATTTTAAATT-TGAATTT
* *
20726 ATTATAAGTTTGAATTT
1 ATTTTAAATTTGAATTT
*
20743 ATTCTAAATT
1 ATTTTAAATT
20753 AAAATTAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
16 14 0.29
17 22 0.46
18 12 0.25
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTGAATTT
Found at i:21345 original size:3 final size:3
Alignment explanation
Indices: 21337--21446 Score: 71
Period size: 3 Copynumber: 36.7 Consensus size: 3
21327 ACGTTAATTT
* * * * ** *
21337 ATA ATA ATA TTA ATA ATA ATGA A-G ATA ATA CTA ATG GCA CTA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * *
21382 ATA ATA ATA ATA ATA ACA ATA ATA A-A GATC ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * *
21427 TTA ATA ATA TTA ATA TTA AT
1 ATA ATA ATA ATA ATA ATA AT
21447 TTTAAATAAA
Statistics
Matches: 78, Mismatches: 25, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
2 2 0.03
3 74 0.95
4 2 0.03
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:22558 original size:29 final size:29
Alignment explanation
Indices: 22520--22778 Score: 132
Period size: 29 Copynumber: 8.9 Consensus size: 29
22510 AAGGTCCCTA
22520 AACTATCCAAAAATTACATTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTACCCTCG
* *
22550 AACTTCC-AAAATTCCATTTTTTA-CCT-T
1 AACTTCCAAAAATTACA-TTTTTACCCTCG
** * * *
22577 ATTTTTTCAAAAATTATATTTTTACCCTCA
1 A-ACTTCCAAAAATTACATTTTTACCCTCG
* *
22607 AACTTTCC-AAATTTCCATTTTTTACCCT--
1 AAC-TTCCAAAAATTACA-TTTTTACCCTCG
* *
22635 AATTTTTCCAAAAATTACCA-TTTTACCC-CA
1 AA--CTTCCAAAAATTA-CATTTTTACCCTCG
*
22665 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACATTTTT-ACCCTCG
** *
22694 ATTTTTCCAAAAATTACCA--TTTACCCCCG
1 A-ACTTCCAAAAATTA-CATTTTTACCCTCG
22723 AACTTCCAAAAATT-CTATTTTTGACCC-CG
1 AACTTCCAAAAATTAC-ATTTTT-ACCCTCG
* *
22752 ATTCTTCCAAAAAGTACCA-TTTTACCC
1 A-ACTTCCAAAAATTA-CATTTTTACCC
22779 CCGGATGTCT
Statistics
Matches: 175, Mismatches: 28, Indels: 53
0.68 0.11 0.21
Matches are distributed among these distances:
26 1 0.01
27 4 0.02
28 51 0.29
29 58 0.33
30 55 0.31
31 5 0.03
32 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.39
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:22667 original size:58 final size:57
Alignment explanation
Indices: 22525--22860 Score: 297
Period size: 58 Copynumber: 5.8 Consensus size: 57
22515 CCCTAAACTA
* * *
22525 TCCAAAAATTA-CATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTTACCTTATTTT
1 TCCAAAAATTACCA-TTTTACCC-CAAACTTCCAAAAATTCCATTTTTGACCTGATTTT
* * * * *
22582 TTCAAAAATTA-TATTTTTACCCTCAAACTTTCC-AAATTTCCATTTTTTACCCTAATTTT
1 TCCAAAAATTACCA-TTTTACCC-CAAAC-TTCCAAAAATTCCATTTTTGA-CCTGATTTT
22641 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCT-GATTTT
* * * *
22699 TCCAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCGATTCT
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATTCCATTTTTGA-CCTGATTTT
* ** * * ** *
22757 TCCAAAAAGTACCATTTTACCCCCGGA-TGTCTAAAAATTTCATTTTTGACCACAATTT
1 TCCAAAAATTACCATTTTA-CCCCAAACT-TCCAAAAATTCCATTTTTGACCTGATTTT
* * * * *
22815 TCCCAAAATTACCATTTTGCCCCTAAGTTACAAAAATTACCATTTT
1 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATT-CCATTTT
22861 GCCCTCGGGT
Statistics
Matches: 237, Mismatches: 31, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
57 49 0.21
58 131 0.55
59 56 0.24
60 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCTGATTTT
Found at i:22719 original size:116 final size:115
Alignment explanation
Indices: 22525--22860 Score: 331
Period size: 116 Copynumber: 2.9 Consensus size: 115
22515 CCCTAAACTA
* * *
22525 TCCAAAAATTA-CATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTTACCTTATTTTTTCAAA
1 TCCAAAAATTACCA-TTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCTCATTTTTCCAAA
* * * * * *
22588 AATTA-TATTTTTACCCTCAAACTTTCC-AAATTTCCATTTTTTACCCTAATTTT
64 AATTACCA--TTTACCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCAATTCT
*
22641 TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTTCCAAAA
1 TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTC-ATTTTTCCAAAA
* * *
22706 ATTACCATTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCGATTCT
65 ATTACCATTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATTCT
* * * * * * *
22757 TCCAAAAAGTACCATTTTACCCCCGGA-TGTCTAAAAATTTCATTTTTGACCACAATTTTCCCAA
1 TCCAAAAATTACCATTTTA-CCCCGAACT-TCCAAAAATTCCATTTTTGACCTCATTTTTCCAAA
** * * *
22821 AATTACCATTTTGCCCCTAAGTTACAAAAATTACCATTTT
64 AATTACCATTTACCCCCAAACTTCCAAAAATT-CCATTTT
22861 GCCCTCGGGT
Statistics
Matches: 185, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
115 12 0.06
116 123 0.66
117 49 0.26
118 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (115 bp):
TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTCATTTTTCCAAAAA
TTACCATTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATTCT
Found at i:25181 original size:2 final size:2
Alignment explanation
Indices: 25176--25200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25166 ATTTTTAAAT
25176 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25201 TTAATTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29708 original size:210 final size:210
Alignment explanation
Indices: 29346--29766 Score: 770
Period size: 210 Copynumber: 2.0 Consensus size: 210
29336 GTCCTCAACA
* * * *
29346 GCTCGTGTGAGCAACATCGAGTACTAGTAACAGAAAAGTTATAGACAGGAAAGTGAAAGTTTGTA
1 GCTCGTGTGAACAACATCGAGTACCAGTAACAGAAAAGTTATAAACAGGAAAATGAAAGTTTGTA
29411 AAGGACTCGAGAAAGCAATGGAACTATCTTGGCTCGGTTGAGTTATAGCTGCTTTATACAAATGT
66 AAGGACTCGAGAAAGCAATGGAACTATCTTGGCTCGGTTGAGTTATAGCTGCTTTATACAAATGT
*
29476 TTGGTAATTCTTTAAAACTATCGAACTTACTAAGCTATGAAGCTTACCAAAGATGTTGTTGTTTT
131 TTGGTAATTCTTTAAAACTATCGAACTTAATAAGCTATGAAGCTTACCAAAGATGTTGTTGTTTT
29541 ATAGATTATTTTGTT
196 ATAGATTATTTTGTT
*
29556 GCTCGTGTGAACAACATCGAGTACCGGTAACAGAAAAGTTATAAACAGGAAAATGAAAGTTTGTA
1 GCTCGTGTGAACAACATCGAGTACCAGTAACAGAAAAGTTATAAACAGGAAAATGAAAGTTTGTA
* *
29621 AAGGACTCGAGAAAGCAATGGGACTATCTTGGCTCGGTTGAGTTATATCTGCTTTATACAAATGT
66 AAGGACTCGAGAAAGCAATGGAACTATCTTGGCTCGGTTGAGTTATAGCTGCTTTATACAAATGT
29686 TTGGTAATTCTTTAAAACTATCGAACTTAATAAGCTATGAAGCTTACCAAAGATGTTGTTGTTTT
131 TTGGTAATTCTTTAAAACTATCGAACTTAATAAGCTATGAAGCTTACCAAAGATGTTGTTGTTTT
29751 ATAGATTATTTTGTT
196 ATAGATTATTTTGTT
29766 G
1 G
29767 ATTGAAGATC
Statistics
Matches: 203, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
210 203 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (210 bp):
GCTCGTGTGAACAACATCGAGTACCAGTAACAGAAAAGTTATAAACAGGAAAATGAAAGTTTGTA
AAGGACTCGAGAAAGCAATGGAACTATCTTGGCTCGGTTGAGTTATAGCTGCTTTATACAAATGT
TTGGTAATTCTTTAAAACTATCGAACTTAATAAGCTATGAAGCTTACCAAAGATGTTGTTGTTTT
ATAGATTATTTTGTT
Found at i:31769 original size:32 final size:32
Alignment explanation
Indices: 31729--31795 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
31719 TCGAAACTTA
* *
31729 AATTACTTATTCAAGTTTACACGAATAATTTG
1 AATTACTTATTCAAGTTGACACGAATAATTCG
* *
31761 AATTACTTATTCGAGTTGACTCGAATAATTCG
1 AATTACTTATTCAAGTTGACACGAATAATTCG
31793 AAT
1 AAT
31796 AACTCGATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (32 bp):
AATTACTTATTCAAGTTGACACGAATAATTCG
Found at i:33044 original size:56 final size:56
Alignment explanation
Indices: 32972--33083 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
32962 CGTATGATTA
32972 CAACTTTTTAAAAGAAATATATATATTTAGGAGATTGAATGGTAGTTGAATGAGGG
1 CAACTTTTTAAAAGAAATATATATATTTAGGAGATTGAATGGTAGTTGAATGAGGG
33028 CAACTTTTTAAAAGAAATATATATATTTAGGAGATTGAATGGTAGTTGAATGAGGG
1 CAACTTTTTAAAAGAAATATATATATTTAGGAGATTGAATGGTAGTTGAATGAGGG
33084 GCAAATGCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (56 bp):
CAACTTTTTAAAAGAAATATATATATTTAGGAGATTGAATGGTAGTTGAATGAGGG
Found at i:33509 original size:53 final size:53
Alignment explanation
Indices: 33442--33543 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
33432 CTTAGGTTGT
* *
33442 CAATTACTTGAATAAAAGAGAGTTATTGTAGAATTTAACTACTCCATTTGATC
1 CAATTACTTGAATAAAAGAGAGTTATTGTAAAATTTAACTACTCAATTTGATC
*
33495 CAATTACATT-AATAAAAGAGAGTTCTTGTAAAATTTAACTACTCAATTT
1 CAATTAC-TTGAATAAAAGAGAGTTATTGTAAAATTTAACTACTCAATTT
33544 AGTTGTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 43 0.96
54 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (53 bp):
CAATTACTTGAATAAAAGAGAGTTATTGTAAAATTTAACTACTCAATTTGATC
Found at i:33986 original size:29 final size:30
Alignment explanation
Indices: 33937--34005 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
33927 AACCTTTACA
*
33937 AAAGTGCACAAATGGAAGCCAAAA-TTTTC
1 AAAGTGCTCAAATGGAAGCCAAAACTTTTC
* *
33966 AAAGTGCTCAAATAGG-GGCCAAAACTTTTTG
1 AAAGTGCTCAAAT-GGAAGCCAAAAC-TTTTC
33997 AAAGTGCTC
1 AAAGTGCTC
34006 GTATAAGAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.56
30 2 0.06
31 13 0.38
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (30 bp):
AAAGTGCTCAAATGGAAGCCAAAACTTTTC
Found at i:34018 original size:31 final size:29
Alignment explanation
Indices: 33953--34024 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
33943 CACAAATGGA
*
33953 AGCCAAAATTTTCAAAGTGCTCAAATAGG
1 AGCCAAAATTTTCAAAGTGCTCAAATAAG
* * **
33982 GGCCAAAACTTTTTGAAAGTGCTCGTATAAG
1 AGCCAAAA--TTTTCAAAGTGCTCAAATAAG
*
34013 AGCCAAATTTTT
1 AGCCAAAATTTT
34025 TTTTGAATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
29 11 0.32
31 23 0.68
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (29 bp):
AGCCAAAATTTTCAAAGTGCTCAAATAAG
Found at i:35047 original size:5 final size:6
Alignment explanation
Indices: 35031--35057 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35021 ATTTGTTTAA
35031 ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATT
35058 CAACAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:37220 original size:6 final size:6
Alignment explanation
Indices: 37209--37244 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
37199 ATCTTTCAAT
37209 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
37245 TTTCCTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTCTC
Found at i:43247 original size:15 final size:15
Alignment explanation
Indices: 43229--43263 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43219 GTATTTAAAA
*
43229 TTTCAATACTTAATT
1 TTTCAACACTTAATT
*
43244 TTTCAACACTTACTT
1 TTTCAACACTTAATT
43259 TTTCA
1 TTTCA
43264 GTATGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTCAACACTTAATT
Found at i:52330 original size:29 final size:29
Alignment explanation
Indices: 52288--52756 Score: 429
Period size: 29 Copynumber: 16.1 Consensus size: 29
52278 CTTTAGAGGT
*
52288 TTCG-GGGTCAAAAATGGAATATTTGGAAG
1 TTCGAGGGT-AAAAATGGAATTTTTGGAAG
*
52317 TTCGAGGCTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
52346 TTCGAGGGTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
*
52375 TTCGAGGGTAAAAATGGAATTTTTAGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
* * *
52404 TTTTG-GGGTTAAAAATGGGATTTTTAGAAG
1 -TTCGAGGG-TAAAAATGGAATTTTTGGAAG
* *
52434 TTCG-GGATAAAAATGGAATTTTTAGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
*
52462 TTTC-AGGGTTAAAATGTG-ATTTTTGGAAG
1 -TTCGAGGGTAAAAATG-GAATTTTTGGAAG
* *
52491 TTCGAGGGTAAAAATGAAATTTTTAGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
* *
52520 TTTCG-GGGTCAAAATGGGATTTTTGGAAG
1 -TTCGAGGGTAAAAATGGAATTTTTGGAAG
* * *
52549 TTTTGA-GGTCAAAATGGGATTTTTGGAAG
1 -TTCGAGGGTAAAAATGGAATTTTTGGAAG
** *
52578 TTTTAGGGTCAAAAATAGG-ATTTTTGAAAG
1 TTCGAGGGT-AAAAAT-GGAATTTTTGGAAG
* *
52608 TT-TAGGTGTAAAAATGGAATTTTTAGAAG
1 TTCGAGG-GTAAAAATGGAATTTTTGGAAG
**
52637 TTTTAGGGTCAAAAAT-GAGATTTTTGGAAG
1 TTCGAGGGT-AAAAATGGA-ATTTTTGGAAG
* *
52667 TT-TAGGGGTAAAAATGGAAGTTTTGGAAG
1 TTCGA-GGGTAAAAATGGAATTTTTGGAAG
*** * **
52696 TTTTTGGGTTAAAAATGGGATTTTTTTAAG
1 TTCGAGGG-TAAAAATGGAATTTTTGGAAG
* * *
52726 TTCGAGGGTAAAAAAGAAATTTTTAGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
52755 TT
1 TT
52757 TCGGGGACCT
Statistics
Matches: 378, Mismatches: 40, Indels: 44
0.82 0.09 0.10
Matches are distributed among these distances:
28 29 0.08
29 246 0.65
30 101 0.27
31 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAG
Found at i:52622 original size:59 final size:57
Alignment explanation
Indices: 52292--52757 Score: 481
Period size: 59 Copynumber: 8.0 Consensus size: 57
52282 AGAGGTTTCG
* * * * **
52292 GGGTCAAAAATGGAATATTTGGAAGTTCGAGGCTAAAAATGGAATTTTTGGAAGTTCGA
1 GGGTCAAAAATGG-ATTTTTGGAAGTT-TAGGGTAAAAATGGAATTTTTAGAAGTTTTA
* *
52351 GGGT-AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTG
1 GGGTCAAAAATGG-ATTTTTGGAAGTT-TAGGGTAAAAATGGAATTTTTAGAAGTTTTA
* * * *
52409 GGGTTAAAAATGGGATTTTTAGAAG-TTCGGGATAAAAATGGAATTTTTAGAAGTTTCA
1 GGGTCAAAAAT-GGATTTTTGGAAGTTTAGGG-TAAAAATGGAATTTTTAGAAGTTTTA
* * * **
52467 GGGT-TAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTAGAAGTTTCG
1 GGGTCAAAAATG-GATTTTTGGAAGTT-TAGGGTAAAAATGGAATTTTTAGAAGTTTTA
* * * *
52525 GGGTC-AAAATGGGATTTTTGGAAGTTTTGAGGTCAAAATGGGATTTTTGGAAGTTTTA
1 GGGTCAAAAAT-GGATTTTTGGAAGTTTAG-GGTAAAAATGGAATTTTTAGAAGTTTTA
*
52583 GGGTCAAAAATAGGATTTTTGAAAGTTTAGGTGTAAAAATGGAATTTTTAGAAGTTTTA
1 GGGTCAAAAAT-GGATTTTTGGAAGTTTAGG-GTAAAAATGGAATTTTTAGAAGTTTTA
* * *
52642 GGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTAAAAATGGAAGTTTTGGAAGTTTTT
1 GGGTCAAAAATG-GATTTTTGGAAGTTTA-GGGTAAAAATGGAATTTTTAGAAGTTTTA
* ** * * *
52701 GGGTTAAAAATGGGATTTTTTTAAGTTCGAGGGTAAAAAAGAAATTTTTAGAAGTTT
1 GGGTCAAAAAT-GGATTTTTGGAAGTT-TAGGGTAAAAATGGAATTTTTAGAAGTTT
52758 CGGGGACCTC
Statistics
Matches: 349, Mismatches: 43, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.00
57 20 0.06
58 158 0.45
59 164 0.47
60 6 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (57 bp):
GGGTCAAAAATGGATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTAGAAGTTTTA
Found at i:53650 original size:261 final size:258
Alignment explanation
Indices: 53200--53709 Score: 817
Period size: 261 Copynumber: 2.0 Consensus size: 258
53190 AACGGTGTCA
*
53200 TTTTGGGGTTTAAAAGCCTGAACCAAAACGGCACCGTTTTGACCCATTATAAAAGACTTTCTAAC
1 TTTTGGGGTTTAAAAGCCTGAACCAAAACGACACCGTTTTGACCCATTATAAAAGACTTTCTAAC
53265 CCCTTTTTTTTTTCATTTTTTTTCTTTTTACAAAAAAAAAAATCAAAAACTCTCTCACTTTCTCT
66 CCCTTTTTTTTTTCA-TTTTTTTCTTTTTAC-AAAAAAAAAATCAAAAACTCTCTCACTTTCTCT
*
53330 CCTTCTCTCATGGGCGACCACCGATCGGTCGTCCGATGTCCAGCCCGTCTTCGCCACACGCGCGC
129 CCTTCTCTCATGGGCGACCACCGATCGGCCGTCCGATGTCCAGCCCGTCTTCGCCACACGCGCGC
* * * * * *
53395 CGTCGATCGCCGCGCGTGGTCACCACGCGTCACCGCTTGGAGTCTTTCGGTGCAAAACGATGCCG
194 CGCCGATCGCCGCACGTGGTCACCACGCGTCACCACCTGGAGTCCTCCGGTGCAAAACGATGCCG
* * *
53460 TTTTGGGGTTTAAAAGCCTGAACCAAAACGACATCGTTTTGGCCCCTTATAAAAGACTTTCTAAC
1 TTTTGGGGTTTAAAAGCCTGAACCAAAACGACACCGTTTTGACCCATTATAAAAGACTTTCTAAC
53525 CCCTTTTTTTTCATTTC-TTTTTTTCTTTTTAC-AAAAAAAAATCAAAAACTCTCTCTCACTTTC
66 CCC-TTTTTTT--TTTCATTTTTTTCTTTTTACAAAAAAAAAATCAAAAA--CTCTCTCACTTTC
* *
53588 TCTCGTTCTCTCATGGGCGACCACCGATCGGCCGTCCGGTGTCCAGCCCGTCTTCGCCACACGCG
126 TCTCCTTCTCTCATGGGCGACCACCGATCGGCCGTCCGATGTCCAGCCCGTCTTCGCCACACGCG
*
53653 CGCCGCCGATCGCCGCACGTGGTCACCACGTGTCACCACCTGGAGTCCTCCGGTGCA
191 CGCCGCCGATCGCCGCACGTGGTCACCACGCGTCACCACCTGGAGTCCTCCGGTGCA
53710 CGCGCCGCTG
Statistics
Matches: 231, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
259 16 0.07
260 64 0.28
261 147 0.64
263 4 0.02
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.30
Consensus pattern (258 bp):
TTTTGGGGTTTAAAAGCCTGAACCAAAACGACACCGTTTTGACCCATTATAAAAGACTTTCTAAC
CCCTTTTTTTTTTCATTTTTTTCTTTTTACAAAAAAAAAATCAAAAACTCTCTCACTTTCTCTCC
TTCTCTCATGGGCGACCACCGATCGGCCGTCCGATGTCCAGCCCGTCTTCGCCACACGCGCGCCG
CCGATCGCCGCACGTGGTCACCACGCGTCACCACCTGGAGTCCTCCGGTGCAAAACGATGCCG
Found at i:54855 original size:17 final size:16
Alignment explanation
Indices: 54825--54865 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
54815 TTAAATTTTG
*
54825 AAATTAAATTTAAAAT
1 AAATTAAATCTAAAAT
54841 AAATCTAAATCTAAAAT
1 AAAT-TAAATCTAAAAT
54858 AAATTAAA
1 AAATTAAA
54866 AAGGGGGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAAATCTAAAAT
Found at i:56667 original size:23 final size:26
Alignment explanation
Indices: 56591--56668 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 26
56581 GCTATATCCT
*
56591 TTAT-TATATA-TAATATA-ATAATA
1 TTATATATATATTCATATATATAATA
*
56614 GTTATATATATATTCATATTTATAA-A
1 -TTATATATATATTCATATATATAATA
*
56640 ATATAT-TAT-TTCAT-TATATAATA
1 TTATATATATATTCATATATATAATA
56663 TTATAT
1 TTATAT
56669 CTGATACTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
22 6 0.13
23 11 0.24
24 7 0.16
25 11 0.24
26 6 0.13
27 4 0.09
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (26 bp):
TTATATATATATTCATATATATAATA
Found at i:64318 original size:5 final size:5
Alignment explanation
Indices: 64302--64332 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
64292 AAATGATGAT
*
64302 ATAAA ATGAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
64333 AAATCAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:69933 original size:28 final size:28
Alignment explanation
Indices: 69872--69929 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
69862 CTTTTCACTT
*
69872 AAATAATATGAAAAATAATTAATTATGA
1 AAATAATATGAAAAATAATTAATTATAA
69900 AAATAATAT-AAAACAT-ATTAATTATAA
1 AAATAATATGAAAA-ATAATTAATTATAA
69927 AAA
1 AAA
69930 ATAAGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATAATATGAAAAATAATTAATTATAA
Found at i:72743 original size:29 final size:28
Alignment explanation
Indices: 72705--73048 Score: 227
Period size: 30 Copynumber: 11.8 Consensus size: 28
72695 TTCGGATGCA
* *
72705 CGGGGGCAAAATGGTAGTTTTGGAAGGTT
1 CGGGGTCAAAATGGTATTTTTGGAA-GTT
* *
72734 CAGAGTCAAAAATGAG-ATTTTTGGAAGTT
1 CGGGGTC-AAAATG-GTATTTTTGGAAGTT
72763 CGGAGGT-AAAATGGTAATTTTTGGAAAGTT
1 CGG-GGTCAAAATGGT-ATTTTTGG-AAGTT
* * *
72793 TGGGGTTTAAAATGATATTTTTGGAAGTT
1 CGGGG-TCAAAATGGTATTTTTGGAAGTT
*
72822 CGGCGGT-AAAATGGTAATTTTT-AAAGGTT
1 CGG-GGTCAAAATGGT-ATTTTTGGAA-GTT
* * *
72851 AGAGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGTT
*
72880 CGAGGGT-AAAATGGTAATTTTTAGAAGGTT
1 CG-GGGTCAAAATGGT-ATTTTTGGAA-GTT
* *
72910 CGGGGTCAAAAATGGGATTTTTGAAAGTTT
1 CGGGGTC-AAAATGGTATTTTTGGAAG-TT
* *
72940 AGGGGT-AAAATGGTAATTTTTAGAAGGTT
1 CGGGGTCAAAATGGT-ATTTTTGGAA-GTT
* **
72969 CGGGGGT-AAAATGATAATTTTTATAAGGTT
1 C-GGGGTCAAAATGGT-ATTTTTGGAA-GTT
* *
72999 CGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGTT
*
73028 CGGGGGT-AAAATGGTAATTTT
1 C-GGGGTCAAAATGGTATTTTT
73049 CAAAAAGTTT
Statistics
Matches: 252, Mismatches: 37, Indels: 53
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.00
28 44 0.17
29 79 0.31
30 107 0.42
31 21 0.08
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
CGGGGTCAAAATGGTATTTTTGGAAGTT
Found at i:72819 original size:89 final size:88
Alignment explanation
Indices: 72722--73048 Score: 339
Period size: 89 Copynumber: 3.7 Consensus size: 88
72712 AAAATGGTAG
* * * *
72722 TTTTGGAAGGTTCAGAGTCAAAAATGAGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTGG
1 TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGAAAGTTCGGAGGTAAAATGGTAATTTTTGG
*
72787 AAAGTTTGGGGTTTAAAATGAT-AT
66 AAAGTTCGGGG--TAAAATGATAAT
* * * * *
72811 TTTTGGAA-GTTCGGCGGT--AAAATGGTAATTTTT-AAAGGTT-AGAGGTCAAAAATGG-GATT
1 TTTTAGAAGGTTCGG-AGTCAAAAATGG-GATTTTTGAAA-GTTCGGAGGT--AAAATGGTAATT
*
72870 TTTGG-AAGTTCGAGGGTAAAATGGTAAT
61 TTTGGAAAGTTCG-GGGTAAAATGATAAT
* * *
72898 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGAAAGTTTAGG-GGTAAAATGGTAATTTTTA
1 TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGAAAG-TTCGGAGGTAAAATGGTAATTTTTG
*
72962 GAAGGTTCGGGGGTAAAATGATAAT
65 GAAAGTTC-GGGGTAAAATGATAAT
* * *
72987 TTTTATAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTT
1 TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGAAAGTTCGGAGGTAAAATGGTAATTTT
73049 CAAAAAGTTT
Statistics
Matches: 201, Mismatches: 20, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
86 8 0.04
87 38 0.19
88 49 0.24
89 104 0.52
90 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (88 bp):
TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGAAAGTTCGGAGGTAAAATGGTAATTTTTGG
AAAGTTCGGGGTAAAATGATAAT
Found at i:72922 original size:117 final size:117
Alignment explanation
Indices: 72707--72969 Score: 343
Period size: 117 Copynumber: 2.2 Consensus size: 117
72697 CGGATGCACG
* * **
72707 GGGGCAAAATGGTAGTTTTGGAAGGTTCAGAGTCAAAAATGAGATTTTTGGAAGTTCGGAGGTAA
1 GGGGTAAAATGGTAATTTTTAAAGGTTCAGAGTCAAAAATGAGATTTTTGGAAGTTCGGAGGTAA
* * ** * * *
72772 AATGGTAATTTTTGGAAAGTTTGGGGTTTAAAATGATATTTTTGGAAG-TTC
66 AATGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGAGATTTTTGAAAGTTTA
*
72823 GGCGGTAAAATGGTAATTTTTAAAGGTT-AGAGGTCAAAAATGGGATTTTTGGAAGTTC-GAGGG
1 GG-GGTAAAATGGTAATTTTTAAAGGTTCAGA-GTCAAAAATGAGATTTTTGGAAGTTCGGA-GG
* *
72886 TAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGAAAGTTTA
63 TAAAATGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGAGATTTTTGAAAGTTTA
72941 GGGGTAAAATGGTAATTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTA-AAGGTTC
72970 GGGGGTAAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
116 7 0.06
117 110 0.87
118 10 0.08
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTAAAGGTTCAGAGTCAAAAATGAGATTTTTGGAAGTTCGGAGGTAA
AATGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGAGATTTTTGAAAGTTTA
Found at i:72970 original size:59 final size:58
Alignment explanation
Indices: 72707--72973 Score: 331
Period size: 59 Copynumber: 4.6 Consensus size: 58
72697 CGGATGCACG
* * * * *
72707 GGGGCAAAATGGT-AGTTTTGGAAGGTTCAGAGTCAAAAATGAGATTTTTGGAAGTTC
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTC
* * * ** *
72764 GGAGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTTTAAAATGATATTTTTGGAAGTTC
1 GG-GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTC
* * *
72823 GGCGGTAAAATGGTAATTTTTA-AAGGTTAGAGGTCAAAAATGGGATTTTTGGAAGTTC
1 GG-GGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTC
* * *
72881 GAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAG-TTC
72941 GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGG
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGG
72974 GTAAAATGAT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
57 2 0.01
58 59 0.32
59 119 0.65
60 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTC
Found at i:72989 original size:59 final size:58
Alignment explanation
Indices: 72742--73040 Score: 267
Period size: 59 Copynumber: 5.1 Consensus size: 58
72732 TTCAGAGTCA
* * * * *
72742 AAAATGA-GATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTTT
1 AAAATGATGATTTTTGAAAGTTCGG-GGTAAAATGGTAATTTTTAGAAGGTTCGGGG-GT
* * *
72801 AAAATGAT-ATTTTTGGAAGTTCGGCGGTAAAATGGTAATTTTTA-AAGGTT-AGAGGT
1 AAAATGATGATTTTTGAAAGTTCGG-GGTAAAATGGTAATTTTTAGAAGGTTCGGGGGT
* *
72857 CAAAAATG-GGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTC-GGGGT
1 --AAAATGATGATTTTTGAAAGTTCG-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGGT
* *
72916 CAAAAATG-GGATTTTTGAAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGGT
1 --AAAATGATGATTTTTGAAAG-TTCGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGGT
* * * *
72976 AAAATGATAATTTTT-ATAAGGTTCGGAGTCAAAAATGG-GATTTTTGGAA-GTTCGGGGGT
1 AAAATGATGATTTTTGA-AA-GTTCGGGGT--AAAATGGTAATTTTTAGAAGGTTCGGGGGT
73035 AAAATG
1 AAAATG
73041 GTAATTTTCA
Statistics
Matches: 210, Mismatches: 16, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
56 1 0.00
57 2 0.01
58 52 0.25
59 130 0.62
60 18 0.09
61 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (58 bp):
AAAATGATGATTTTTGAAAGTTCGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGGT
Done.