Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002397.1 Hibiscus syriacus cultivar Beakdansim tig00004900_pilon, 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: 65048
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2512 original size:4 final size:4
Alignment explanation
Indices: 2490--2557 Score: 57
Period size: 4 Copynumber: 16.2 Consensus size: 4
2480 AACAAAATTC
* * * *
2490 TAAA TAAC TAAA T-AA TAAA TAAA TTCAAA AAAA TGAA TAAA TAATT TGAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA -T-AAA TAAA TAAA TAAA TAA-A T-AAA
2541 TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA T
2558 CGAACAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 3 0.06
6 5 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:2528 original size:22 final size:21
Alignment explanation
Indices: 2499--2557 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
2489 CTAAATAACT
2499 AAATAATAAATAAATTCAAAA
1 AAATAATAAATAAATTCAAAA
* * *
2520 AAATGAATAAATAATTTGAAAT
1 AAAT-AATAAATAAATTCAAAA
2542 AAATAAATAAATAAAT
1 AAAT-AATAAATAAAT
2558 CGAACAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
AAATAATAAATAAATTCAAAA
Found at i:2567 original size:22 final size:20
Alignment explanation
Indices: 2499--2567 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
2489 CTAAATAACT
*
2499 AAATAATAAATAAATTCAAAA
1 AAATAATAAATAAA-TCGAAA
* *
2520 AAATGAATAAATAATTTGAAA
1 AAAT-AATAAATAAATCGAAA
2541 TAAATAAATAAATAAATCGAACA
1 -AAAT-AATAAATAAATCGAA-A
2564 AAAT
1 AAAT
2568 TATTAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 8 0.21
22 30 0.77
23 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AAATAATAAATAAATCGAAA
Found at i:2609 original size:22 final size:20
Alignment explanation
Indices: 2563--2611 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
2553 TAAATCGAAC
2563 AAAATTATTAAAGAAATAAA
1 AAAATTATTAAAGAAATAAA
*
2583 TAAATTATTCAAA-ATAATTAAA
1 AAAATTATT-AAAGA-AA-TAAA
2605 AAAATTA
1 AAAATTA
2612 AAACAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 5 0.21
22 10 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATTATTAAAGAAATAAA
Found at i:5722 original size:32 final size:32
Alignment explanation
Indices: 5681--5745 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5671 GTTAGGCTAT
5681 ACAGAGAATATTATACTGAACTTTTTTTTCCA
1 ACAGAGAATATTATACTGAACTTTTTTTTCCA
5713 ACAGAGAATATTATACTGAACTTTTTTTTCCA
1 ACAGAGAATATTATACTGAACTTTTTTTTCCA
5745 A
1 A
5746 ACAAAGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (32 bp):
ACAGAGAATATTATACTGAACTTTTTTTTCCA
Found at i:7041 original size:24 final size:24
Alignment explanation
Indices: 7014--7066 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
7004 ATTTCGACGT
7014 TTGGTTCATAAAAAATATTATTCA
1 TTGGTTCATAAAAAATATTATTCA
7038 TTGGTTCATAAAAAATATTATTCA
1 TTGGTTCATAAAAAATATTATTCA
7062 TTGGT
1 TTGGT
7067 AATATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (24 bp):
TTGGTTCATAAAAAATATTATTCA
Found at i:13283 original size:22 final size:23
Alignment explanation
Indices: 13242--13302 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
13232 TTGGTGTAGA
*
13242 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
*
13262 GGGAACTGATTCCCCCCTTTGAAG
1 GGGAACCGATTCCCCCC-TTGAAG
13286 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
13303 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.21
21 7 0.21
22 3 0.09
23 1 0.03
24 16 0.47
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:17697 original size:21 final size:21
Alignment explanation
Indices: 17671--17721 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
17661 ATACACAAAT
17671 GATCAATCCTTTTGTGAAAGG
1 GATCAATCCTTTTGTGAAAGG
17692 GATCAATCCTTTTGTGAAAGG
1 GATCAATCCTTTTGTGAAAGG
*
17713 GATCGATCC
1 GATCAATCC
17722 CAAACACACA
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:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (21 bp):
GATCAATCCTTTTGTGAAAGG
Found at i:17787 original size:21 final size:21
Alignment explanation
Indices: 17741--17796 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
17731 ATGAATCCAA
* *
17741 GGGATCGATCCTTT-TTTGAG
1 GGGATCGATCCTTTGGTTAAG
*
17761 GGGATCGATCCTTTGGTTAAT
1 GGGATCGATCCTTTGGTTAAG
17782 GGGATCGATCCTTTG
1 GGGATCGATCCTTTG
17797 AGCCAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (21 bp):
GGGATCGATCCTTTGGTTAAG
Found at i:18475 original size:3 final size:3
Alignment explanation
Indices: 18469--18590 Score: 163
Period size: 3 Copynumber: 40.0 Consensus size: 3
18459 TTCATTTAAA
** * * *
18469 ATT ATT ATT ATT AAA ATT ATT ATT ATT AGT ATT ATT ATT AGT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
18517 ATT ATT ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
*
18563 ATT ATT AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT
18591 TAATAAATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
3 97 0.94
4 6 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:19384 original size:13 final size:13
Alignment explanation
Indices: 19366--19394 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19356 ACCACCGTTA
19366 CGGTGGTCGGCGG
1 CGGTGGTCGGCGG
19379 CGGTGGTCGGCGG
1 CGGTGGTCGGCGG
19392 CGG
1 CGG
19395 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.62, T:0.14
Consensus pattern (13 bp):
CGGTGGTCGGCGG
Found at i:20102 original size:35 final size:35
Alignment explanation
Indices: 20027--20102 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
20017 TAACTTAATT
*
20027 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
20062 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
20097 TTTATT
1 TTTATT
20103 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:27785 original size:114 final size:114
Alignment explanation
Indices: 27582--27807 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
27572 AAGTGCCATA
27582 TGCTCATAGCAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGCAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
* * *
27647 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
* * * *
27696 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATT
1 TGCTCATAGCAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
* * *
27761 TGGTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAGGATGAA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
27808 CTGCATGATC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TGCTCATAGCAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
Found at i:29894 original size:54 final size:54
Alignment explanation
Indices: 29830--29984 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
29820 GAAATCTTGG
29830 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
*
29884 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* * *** *
29938 CAGAAGCCACAGAAAAGGATGAATGCACTATCAAATGTTTTACGAAC
1 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
29985 CTGCTATTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (54 bp):
CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:31177 original size:76 final size:76
Alignment explanation
Indices: 31051--31918 Score: 1585
Period size: 76 Copynumber: 11.4 Consensus size: 76
31041 CTATTTCTCA
31051 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31116 AGCCTTCGGGT
66 AGCCTTCGGGT
31127 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31192 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
31203 CATCTGTAAGTTCTCCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31268 AGCCTTCGGGT
66 AGCCTTCGGGT
31279 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
31344 ATCCTTCGGGT
66 AGCCTTCGGGT
31355 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31420 AGCCTTCGGGT
66 AGCCTTCGGGT
31431 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
31496 ATCCTTCGGGT
66 AGCCTTCGGGT
31507 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31571 AGCCTTCGGGT
66 AGCCTTCGGGT
31582 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31647 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
31658 CATCTGTAAGTCCTCCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
31723 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
31735 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
31800 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
31812 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
31877 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
31889 CATCTGTAATTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
31919 TCAACGTTTC
Statistics
Matches: 771, Mismatches: 19, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
75 74 0.10
76 507 0.66
77 190 0.25
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:32056 original size:3 final size:3
Alignment explanation
Indices: 32050--32156 Score: 137
Period size: 3 Copynumber: 36.0 Consensus size: 3
32040 TTCATTTAAA
** * * *
32050 ATT ATT ATT ATT AAA ATT ATT ATT ATT ACT ATT ATT ATT AGT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
32098 ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32144 ATAT ATT ATT ATT
1 AT-T ATT ATT ATT
32157 TAATAAATAA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.04
3 83 0.92
4 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:32169 original size:18 final size:18
Alignment explanation
Indices: 32097--32169 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
32087 TTAGTATTAG
* *
32097 TATTATTATTATAT-TAT
1 TATTATTAATAAATATAT
* *
32114 TATTATT-ATTATTATTAT
1 TATTATTAATAAATA-TAT
*
32132 TATTATTAATATATATAT
1 TATTATTAATAAATATAT
32150 TATTATTTAATAAATA-AT
1 TATTA-TTAATAAATATAT
32168 TA
1 TA
32170 CAAAAATGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
16 2 0.05
17 7 0.16
18 22 0.50
19 13 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTAATAAATATAT
Found at i:32951 original size:13 final size:13
Alignment explanation
Indices: 32933--32958 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32923 ACCACCGTTA
32933 CGGTGGTCGGCGG
1 CGGTGGTCGGCGG
32946 CGGTGGTCGGCGG
1 CGGTGGTCGGCGG
32959 TGGAGTACGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.62, T:0.15
Consensus pattern (13 bp):
CGGTGGTCGGCGG
Found at i:33669 original size:35 final size:35
Alignment explanation
Indices: 33594--33669 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
33584 TAACTTAATT
*
33594 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
33629 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
33664 TTTATT
1 TTTATT
33670 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:36108 original size:31 final size:31
Alignment explanation
Indices: 36073--36147 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
36063 AATGTCCAAG
* *
36073 TGATCAAAACTTAATAAAACGATAACGTCAC
1 TGATCAAAACTTAATAAAACAATAACATCAC
* * *
36104 TGATCAAAACTAAATAAAACAATAATATCAG
1 TGATCAAAACTTAATAAAACAATAACATCAC
*
36135 TGATCAAAGCTTA
1 TGATCAAAACTTA
36148 TGTTTTTTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (31 bp):
TGATCAAAACTTAATAAAACAATAACATCAC
Found at i:43562 original size:36 final size:36
Alignment explanation
Indices: 43520--43592 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
43510 CATGTGTTTT
43520 TGAAAGTACTTGATGATTTTGGTATGTCTAAGCATG
1 TGAAAGTACTTGATGATTTTGGTATGTCTAAGCATG
43556 TGAAAGTACTTGATGATTTTGGTATGTCTAAGCATG
1 TGAAAGTACTTGATGATTTTGGTATGTCTAAGCATG
43592 T
1 T
43593 CAATCTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (36 bp):
TGAAAGTACTTGATGATTTTGGTATGTCTAAGCATG
Found at i:43653 original size:17 final size:18
Alignment explanation
Indices: 43626--43661 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43616 ACATTATGCT
*
43626 TTGGTTGCATTTTAGGCA
1 TTGGTTGCATTGTAGGCA
43644 TTGG-TGCATTGTAGGCA
1 TTGGTTGCATTGTAGGCA
43661 T
1 T
43662 AATAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.42
Consensus pattern (18 bp):
TTGGTTGCATTGTAGGCA
Found at i:49006 original size:3 final size:3
Alignment explanation
Indices: 49000--49052 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
48990 TTTTTTCGTC
**
49000 ATT ATT A-T ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T A-TT
49046 ATT ATT A
1 ATT ATT A
49053 CAAATAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 4 0.09
5 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:49121 original size:17 final size:17
Alignment explanation
Indices: 49089--49123 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49079 TTACAAAATC
* *
49089 AACCCGATTTAGGCCCA
1 AACCCGATTCAAGCCCA
49106 AACCCGATTCAAGCCCA
1 AACCCGATTCAAGCCCA
49123 A
1 A
49124 GAAGCCCAAA
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:0.34, C:0.37, G:0.14, T:0.14
Consensus pattern (17 bp):
AACCCGATTCAAGCCCA
Found at i:49755 original size:23 final size:23
Alignment explanation
Indices: 49729--49772 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
49719 CGCCGGCATA
49729 AATAGTGATCGACCGGTGATCAG
1 AATAGTGATCGACCGGTGATCAG
49752 AATAGTGATCGACCGGTGATC
1 AATAGTGATCGACCGGTGATC
49773 GGAGCTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (23 bp):
AATAGTGATCGACCGGTGATCAG
Found at i:50618 original size:19 final size:20
Alignment explanation
Indices: 50594--50644 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
50584 AATGACCAAT
50594 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
50613 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
50633 AAAATCGCAACG
1 AAAATCGCAACG
50645 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:50638 original size:20 final size:20
Alignment explanation
Indices: 50594--50851 Score: 126
Period size: 20 Copynumber: 12.6 Consensus size: 20
50584 AATGACCAAT
* *
50594 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
50613 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
50633 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
50653 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
50673 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
50694 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
50717 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
50737 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
50757 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
50777 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
50800 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
50820 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
50840 AGAATCGCAACG
1 AAAATCGCAACG
50852 TTGAAAATCG
Statistics
Matches: 184, Mismatches: 43, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
19 17 0.09
20 124 0.67
21 14 0.08
23 29 0.16
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:50754 original size:43 final size:43
Alignment explanation
Indices: 50698--50838 Score: 198
Period size: 43 Copynumber: 3.3 Consensus size: 43
50688 GCTTCCAAGT
*
50698 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
* * * *
50741 TCGCAATGCGATTT---ATATAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
*
50781 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
*
50824 TCGCAATGCGATTTA
1 TCGCAACGCGATTTA
50839 TAGAATCGCA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 35 0.42
43 49 0.58
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (43 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
Found at i:50772 original size:40 final size:40
Alignment explanation
Indices: 50717--50849 Score: 176
Period size: 40 Copynumber: 3.2 Consensus size: 40
50707 GATTTAGAAG
*
50717 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAT
1 AAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAT
* * * *
50757 ATAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTT---AT
*
50800 AAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTAT
1 AAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAT
*
50840 AGAATCGCAA
1 AAAATCGCAA
50850 CGTTGAAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 44 0.56
43 35 0.44
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (40 bp):
AAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAT
Found at i:50964 original size:6 final size:6
Alignment explanation
Indices: 50953--51033 Score: 155
Period size: 6 Copynumber: 13.7 Consensus size: 6
50943 AGACACGTAT
50953 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
51001 GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
51034 CGAGACGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 70 0.93
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:51844 original size:20 final size:19
Alignment explanation
Indices: 51819--51862 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
51809 TTTTTAACTA
*
51819 TTCTTTTGACTGTTGCGATT
1 TTCTTTTAAC-GTTGCGATT
51839 TTCTTTTTAACGTTGCGATT
1 TTC-TTTTAACGTTGCGATT
51859 TTCT
1 TTCT
51863 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (19 bp):
TTCTTTTAACGTTGCGATT
Found at i:51872 original size:20 final size:20
Alignment explanation
Indices: 51849--52145 Score: 150
Period size: 20 Copynumber: 14.6 Consensus size: 20
51839 TTCTTTTTAA
51849 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
51869 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
51889 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
51909 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
51932 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
51952 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
51972 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
51992 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
52012 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
52035 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
52056 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
52074 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
52096 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
52116 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
*
52135 CGTTACGATTT
1 CGTTGCGATTT
52146 CATTGGTCAT
Statistics
Matches: 225, Mismatches: 41, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 15 0.07
20 160 0.71
21 14 0.06
22 6 0.03
23 28 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:51895 original size:40 final size:40
Alignment explanation
Indices: 51851--52021 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
51841 CTTTTTAACG
* * * * * *
51851 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* * *
51891 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TATAAATCGCA
*
51934 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* *
51974 TTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
52014 TTGCGATT
1 TTGCGATT
52022 TTCTTCTAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
40 76 0.67
41 3 0.03
42 3 0.03
43 32 0.28
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
Found at i:51951 original size:83 final size:83
Alignment explanation
Indices: 51849--52001 Score: 225
Period size: 83 Copynumber: 1.8 Consensus size: 83
51839 TTCTTTTTAA
* * * * * * * *
51849 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
51914 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
*
51932 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
51997 CGATT
66 CGATT
52002 CTATCAATCG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
83 61 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (83 bp):
CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:52013 original size:103 final size:103
Alignment explanation
Indices: 51851--52042 Score: 321
Period size: 103 Copynumber: 1.9 Consensus size: 103
51841 CTTTTTAACG
* * * * * * *
51851 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCG
1 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCG
51916 ATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
66 ATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
51954 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCG
1 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCG
52019 ATTTTCTTCTAAATCGCGTTGCGA
66 ATTTTCTTCTAAATCGCGTTGCGA
52043 ACTTGGAAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (103 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCG
ATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
Found at i:52136 original size:19 final size:20
Alignment explanation
Indices: 52096--52145 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
52086 TTCTTTTTAA
*
52096 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
52116 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
*
52135 CGTTACGATTT
1 CGTTGCGATTT
52146 CATTGGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:52497 original size:9 final size:9
Alignment explanation
Indices: 52483--52515 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
52473 TAGCTTCTGC
52483 TAATTAATT
1 TAATTAATT
52492 TAATTAATT
1 TAATTAATT
*
52501 TTA-TAATT
1 TAATTAATT
52509 TAATTAA
1 TAATTAA
52516 GAGAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:52726 original size:22 final size:22
Alignment explanation
Indices: 52675--52733 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
52665 ACGCGATTCT
52675 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * * *
52697 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTCC
*
52718 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
52734 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:52774 original size:40 final size:40
Alignment explanation
Indices: 52718--52813 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
52708 GCGATTTTTC
52718 GACTATCGCAATGCGAATATGTAAATCACAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCACAATGCGATTAT
* * **
52758 GATTATCGCAACGCGAATATGTAAATTGCAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCACAATGCGATTAT
52798 GACTATCGCAATGCGA
1 GACTATCGCAATGCGA
52814 TTCTGACTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCACAATGCGATTAT
Found at i:52814 original size:20 final size:20
Alignment explanation
Indices: 52718--52868 Score: 117
Period size: 20 Copynumber: 7.5 Consensus size: 20
52708 GCGATTTTTC
*
52718 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
52738 GTA-AATCACAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* * *
52758 GATTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
52778 GTA-AATTGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
52798 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
* * *
52818 GACTATCGCAACGTGATTCT
1 GACTATCGCAATGCGATTAT
* * * *
52838 GATTGTCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
52858 GACTGTCGCAA
1 GACTATCGCAA
52869 CACTGAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.02
20 103 0.96
21 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:53462 original size:9 final size:9
Alignment explanation
Indices: 53448--53480 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
53438 TATATTCTGC
53448 TAATTAATT
1 TAATTAATT
53457 TAATTAATT
1 TAATTAATT
*
53466 TTA-TAATT
1 TAATTAATT
53474 TAATTAA
1 TAATTAA
53481 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:56078 original size:11 final size:11
Alignment explanation
Indices: 56062--56091 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
56052 AACACCTGGT
56062 ATTGCATTCAC
1 ATTGCATTCAC
*
56073 ATTGCATCCAC
1 ATTGCATTCAC
56084 ATTGCATT
1 ATTGCATT
56092 TACTTTTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (11 bp):
ATTGCATTCAC
Found at i:60477 original size:66 final size:67
Alignment explanation
Indices: 60245--60478 Score: 316
Period size: 67 Copynumber: 3.5 Consensus size: 67
60235 CTCTCTTTTT
* * *
60245 CAAGACTTGATATTCCC-T--GAGTGACAGTGGAACAAGTTTGTCCCGATTCAATGGATCAAACT
1 CAAGATTTGATATTCCCTTCAGAGT-A-AGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACT
60307 CCTC
64 CCTC
*
60311 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAATGGATCAAACTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
60376 TC
66 TC
** *
60378 CAAGATTTGATATTCCCTTCAGAAAAAGTGGAACAAGTCTGCCCCGATTC-A-GGAATCAAAATC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGG-ATCAAACTC
*
60441 CTT
65 CTC
* *
60444 CAAGATATGATATTCCCTTCAGAGTAAGCGGAACA
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA
60479 TGTCACTCTT
Statistics
Matches: 151, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
65 2 0.01
66 58 0.38
67 86 0.57
68 1 0.01
69 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (67 bp):
CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
TC
Found at i:60768 original size:225 final size:227
Alignment explanation
Indices: 60376--60870 Score: 748
Period size: 225 Copynumber: 2.2 Consensus size: 227
60366 ATCAAACTCC
** *
60376 TCCAAGATTTGATATTCCCTTCAGAAAAAGTGGAACAAGTCTGCCCCGATTCAGGAATCAAAATC
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACCCCGATTCAGGAATCAAAATC
* * *
60441 CTTCAAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCACTCTTTCCAAGATTTGATATTC
66 CTTCAACATATGATATTCCCTTCAGAGTAAGCGAAACAGGTCACTCTTTCCAAGATTTGATATTC
* * * * *
60506 CCTTTAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATTAATC-AATTACC-CAGATCTGATATT
131 CCTTCAGAGTAAGTGGAACAAATCTGCCCCGATTCAATGAATCAAACT-CCTCAGATATGATATT
* *
60569 CCCTTCAGAGTAAGTGGATCAGGTCTC-TCTTT
195 CCCTTCAGAGTAAGCGGAACAGGTCTCTTCTTT
* *
60601 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACCCCTATTCAAGGAATCAAACT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACCCCGATTC-AGGAATCAAAAT
* *
60666 CCTTC-ACATATGATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTTTTTCCCAAGATTTGATAT
65 CCTTCAACATATGATATTCCCTTCAGAGTAAGCGAAACAGGTCACTCTTT-CCAAGATTTGATAT
*
60730 TCCCTTCAGAGTAAGTGGAACAAATCTGCCCC-ATTCAATGGATCAAACTCCTTCAGATATGATA
129 TCCCTTCAGAGTAAGTGGAACAAATCTGCCCCGATTCAATGAATCAAACTCC-TCAGATATGATA
60794 TTCCCTTCAGAGTAAGCGGAACAGGTCTCTTCTTT
193 TTCCCTTCAGAGTAAGCGGAACAGGTCTCTTCTTT
*
60829 TTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
60871 GTCTCAATTC
Statistics
Matches: 245, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
225 99 0.40
226 63 0.26
227 37 0.15
228 46 0.19
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (227 bp):
TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACCCCGATTCAGGAATCAAAATC
CTTCAACATATGATATTCCCTTCAGAGTAAGCGAAACAGGTCACTCTTTCCAAGATTTGATATTC
CCTTCAGAGTAAGTGGAACAAATCTGCCCCGATTCAATGAATCAAACTCCTCAGATATGATATTC
CCTTCAGAGTAAGCGGAACAGGTCTCTTCTTT
Found at i:60804 original size:113 final size:113
Alignment explanation
Indices: 60376--60871 Score: 716
Period size: 114 Copynumber: 4.4 Consensus size: 113
60366 ATCAAACTCC
** *
60376 TCCAAGATTTGATATTCCCTTCAGAAAAAGTGGAACAAGTCTGCCCCGATTC-AGGAATCAAAAT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAAGGAATCAAACT
* * *
60440 CCTTCAAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCACTCTT
66 CCTTC-AGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTT
* ** *
60489 TCCAAGATTTGATATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATTAATC-AATT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAAGGAATCAAACT
* * *
60553 ACC--CAGATCTGATATTCCCTTCAGAGTAAGTGGATCAGGTCTCTCTTT
66 -CCTTCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCT-TTT
* *
60601 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACCCCTATTCAAGGAATCAAACT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAAGGAATCAAACT
* *
60666 CCTTCACATATGATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTTTT
66 CCTTCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTT
*
60714 TCCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTGCCCC-ATTCAATGG-ATCAAA
1 T-CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAA-GGAATCAAA
60777 CTCCTTCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTCTTT
64 CTCCTTCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTC-T-TTT
*
60829 TTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTG
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTG
60872 TCTCAATTCA
Statistics
Matches: 344, Mismatches: 29, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
111 35 0.10
112 60 0.17
113 115 0.33
114 130 0.38
115 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (113 bp):
TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAAGGAATCAAACT
CCTTCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTTT
Found at i:61624 original size:23 final size:23
Alignment explanation
Indices: 61598--61643 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
61588 CCGCCAGCGT
61598 AAATAGTGACCGACCGGTGATCG
1 AAATAGTGACCGACCGGTGATCG
** *
61621 AAATAGTGGTCGGCCGGTGATCG
1 AAATAGTGACCGACCGGTGATCG
61644 GAGCTCCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.20, G:0.35, T:0.20
Consensus pattern (23 bp):
AAATAGTGACCGACCGGTGATCG
Found at i:62451 original size:58 final size:59
Alignment explanation
Indices: 62361--62512 Score: 222
Period size: 58 Copynumber: 2.6 Consensus size: 59
62351 AAATAATGAC
*
62361 TAATTAAAATAATAATAAAAACCAATAGTGCTATTATTATTAATAAAAGGT-AGCATTA
1 TAATTAAAATAATAATAAAAACCAATAGTGCTATCATTATTAATAAAAGGTAAGCATTA
* *
62419 TAATTAAAATAATAATACAAATCAATAGTGCTATCATTATTAATAAAAGGTAGAAGCATTA
1 TAATTAAAATAATAATAAAAACCAATAGTGCTATCATTATTAATAAAAGGT--AAGCATTA
*
62480 T-ATTAAAATAATAAT--AAACCCATAGTGCTATCA
1 TAATTAAAATAATAATAAAAACCAATAGTGCTATCA
62513 CATATGTATA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
58 64 0.74
60 14 0.16
61 8 0.09
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (59 bp):
TAATTAAAATAATAATAAAAACCAATAGTGCTATCATTATTAATAAAAGGTAAGCATTA
Found at i:62684 original size:9 final size:9
Alignment explanation
Indices: 62670--62702 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
62660 TATCTTCTGC
62670 TAATTAATT
1 TAATTAATT
62679 TAATTAATT
1 TAATTAATT
*
62688 TTA-TAATT
1 TAATTAATT
62696 TAATTAA
1 TAATTAA
62703 AAAATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:64943 original size:17 final size:17
Alignment explanation
Indices: 64923--64956 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
64913 TTGTTTAAAT
64923 AAATAACTCATAAAGTA
1 AAATAACTCATAAAGTA
*
64940 AAATAACTCATATAGTA
1 AAATAACTCATAAAGTA
64957 TTTTACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (17 bp):
AAATAACTCATAAAGTA
Done.