Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000176.1 Hibiscus syriacus cultivar Beakdansim tig00000308_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: 117385
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2205 original size:18 final size:18
Alignment explanation
Indices: 2182--2216 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2172 AGAAAAAGAC
*
2182 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2200 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2217 CAACCGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2439 original size:20 final size:19
Alignment explanation
Indices: 2385--2569 Score: 93
Period size: 20 Copynumber: 9.9 Consensus size: 19
2375 TTACACATTC
2385 ATTTGAATATCGCAACGCA
1 ATTTGAATATCGCAACGCA
* * *
2404 AGTTTGACTATTGCAATGCGA
1 A-TTTGAATATCGCAACGC-A
* *
2425 ATTTGATTATCGCAACTCA
1 ATTTGAATATCGCAACGCA
2444 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGC-A
*
2459 ATTTGACTATCGCAACG-A
1 ATTTGAATATCGCAACGCA
*
2477 A----AAAATCGCAACGCGA
1 ATTTGAATATCGCAACGC-A
* * *
2493 ATTTGACTATAGCAACGAGA
1 ATTTGAATATCGCAACG-CA
* *
2513 ATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACG-CA
* **
2533 ATTTGATTATCGCAACGGGT
1 ATTTGAATATCGCAAC-GCA
*
2553 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
2570 AGAAAATCAC
Statistics
Matches: 129, Mismatches: 21, Indels: 32
0.71 0.12 0.18
Matches are distributed among these distances:
14 19 0.15
15 3 0.02
16 2 0.02
18 2 0.02
19 5 0.04
20 95 0.74
21 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (19 bp):
ATTTGAATATCGCAACGCA
Found at i:2459 original size:34 final size:34
Alignment explanation
Indices: 2416--2510 Score: 145
Period size: 34 Copynumber: 2.8 Consensus size: 34
2406 TTTGACTATT
* * **
2416 GCAATGCGAATTTGATTATCGCAACTCAAAAATC
1 GCAACGCGAATTTGACTATCGCAACGAAAAAATC
2450 GCAACGCGAATTTGACTATCGCAACGAAAAAATC
1 GCAACGCGAATTTGACTATCGCAACGAAAAAATC
*
2484 GCAACGCGAATTTGACTATAGCAACGA
1 GCAACGCGAATTTGACTATCGCAACGA
2511 GAATTTGACT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (34 bp):
GCAACGCGAATTTGACTATCGCAACGAAAAAATC
Found at i:2536 original size:40 final size:40
Alignment explanation
Indices: 2447--2569 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 40
2437 CAACTCAAAA
* *
2447 ATCGCAACGCGAATTTGACTATCGCAACGA-AA----A-A
1 ATCGCAACGCGAATTTGACTATAGCAACGAGAATTTGACT
2481 ATCGCAACGCGAATTTGACTATAGCAACGAGAATTTGACT
1 ATCGCAACGCGAATTTGACTATAGCAACGAGAATTTGACT
* * * * *
2521 ATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACT
1 ATCGCAACGCGAATTTGACTATAGCAACGAGAATTTGACT
2561 ATCGCAACG
1 ATCGCAACG
2570 AGAAAATCAC
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
34 29 0.38
35 2 0.03
39 1 0.01
40 44 0.58
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (40 bp):
ATCGCAACGCGAATTTGACTATAGCAACGAGAATTTGACT
Found at i:2595 original size:94 final size:93
Alignment explanation
Indices: 2447--2618 Score: 245
Period size: 94 Copynumber: 1.8 Consensus size: 93
2437 CAACTCAAAA
* * *
2447 ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATAGCAACGAG
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCACAAAGCGAATTAGACTATAGCAACGAG
2512 AATTTGACTATCGCAACGTGAATTTGATT
66 AA-TTGACTATCGCAACGTGAATTTGATT
* * * * * *
2541 ATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCACAAAGCGTATTAGACTATCGCAACGTG
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCACAAAGCGAATTAGACTATAGCAACGAG
*
2606 AATTGACTTTCGC
66 AATTGACTATCGC
2619 GTTGCGATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
93 10 0.15
94 58 0.85
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCACAAAGCGAATTAGACTATAGCAACGAG
AATTGACTATCGCAACGTGAATTTGATT
Found at i:2663 original size:20 final size:21
Alignment explanation
Indices: 2612--2665 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2602 CGTGAATTGA
2612 CTTTC-GCGTTGCGATTTTGG
1 CTTTCAGCGTTGCGATTTTGG
*
2632 CTTTCA-CATTGCGATTTTGAG
1 CTTTCAGCGTTGCGATTTTG-G
2653 -TTT-AGCGTTGCGA
1 CTTTCAGCGTTGCGA
2666 AAGTGTACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (21 bp):
CTTTCAGCGTTGCGATTTTGG
Found at i:4286 original size:21 final size:21
Alignment explanation
Indices: 4205--4291 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 21
4195 GAATGTTGGG
* * *
4205 AGGGACCTCTTCAATGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
4226 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* * ** *
4247 ATGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
4268 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
4289 AGG
1 AGG
4292 TGAGTCGGGC
Statistics
Matches: 46, Mismatches: 20, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:4806 original size:20 final size:19
Alignment explanation
Indices: 4770--4835 Score: 98
Period size: 20 Copynumber: 3.5 Consensus size: 19
4760 GAAACTTAAA
*
4770 ATCGCAACACG-AATGACT
1 ATCGCAACGCGAAATGACT
4788 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
4808 ATCGCAACGCGAATTGACT
1 ATCGCAACGCGAAATGACT
4827 ATCGCAACG
1 ATCGCAACG
4836 AGAGAATCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 10 0.23
19 16 0.36
20 18 0.41
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4903 original size:20 final size:20
Alignment explanation
Indices: 4878--4925 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4868 GTGATTCTTT
4878 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
4898 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
4918 CGTTGCGA
1 CGTTGCGA
4926 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:5096 original size:18 final size:18
Alignment explanation
Indices: 5073--5122 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
5063 TTTACTAAGC
*
5073 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGATT
5091 AATCTAAGTGAAATGATT
1 AATCTAAGTGAAATGATT
5109 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
5123 TACGAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGATT
Found at i:6793 original size:20 final size:20
Alignment explanation
Indices: 6770--6837 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
6760 TCTGAAACTT
6770 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
6790 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
6810 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
6829 AAAATCGCA
1 AAAATCGCA
6838 TTACGATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.17
20 35 0.83
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:7458 original size:20 final size:20
Alignment explanation
Indices: 7424--7557 Score: 196
Period size: 20 Copynumber: 6.7 Consensus size: 20
7414 GCGCTTTGAA
*
7424 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
7444 CATCGCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
7464 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
7484 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
7504 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
7524 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
7544 AATTGCATTGCGAT
1 AATCGCGTTGCGAT
7558 TTACATATTC
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:20773 original size:21 final size:22
Alignment explanation
Indices: 20747--20810 Score: 78
Period size: 24 Copynumber: 2.9 Consensus size: 22
20737 TTGTGCATAA
20747 TGCATCGATACA-CTATGAAAG
1 TGCATCGATACATCTATGAAAG
* *
20768 TGCATCGATGCATTCCTATGAATG
1 TGCATCGATACA-T-CTATGAAAG
20792 TGCATCGATACATC-ATGAA
1 TGCATCGATACATCTATGAA
20811 GATGCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.43
22 1 0.03
23 1 0.03
24 19 0.51
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (22 bp):
TGCATCGATACATCTATGAAAG
Found at i:20816 original size:21 final size:22
Alignment explanation
Indices: 20746--20816 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 22
20736 TTTGTGCATA
20746 ATGCATCGATACA-CTATGAA-
1 ATGCATCGATACATCTATGAAG
*
20766 AGTGCATCGATGCATTCCTATGAATG
1 A-TGCATCGATACA-T-CTATGAA-G
20792 -TGCATCGATACATC-ATGAAG
1 ATGCATCGATACATCTATGAAG
20812 ATGCA
1 ATGCA
20817 CTAATGCACG
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
20 2 0.05
21 20 0.48
22 1 0.02
23 1 0.02
24 18 0.43
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
ATGCATCGATACATCTATGAAG
Found at i:23614 original size:65 final size:64
Alignment explanation
Indices: 23486--23621 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 64
23476 TTTTGTGTAC
* * * **
23486 CGATGCGCATACCATGCATCGATGCACTCCATATATATTAAAACATCGAATTAATTTTATGCAT
1 CGATGCACAAACCATGCATCGATGCACTCCAGATATATTAAAACATCGAAGCAATTTTATGCAT
* * *
23550 TGATGCACAAACCATGCATCGATGCAC-CCAGGATTTTTTTAAAACATCGAAGC-ATATTTATGC
1 CGATGCACAAACCATGCATCGATGCACTCCA-GA-TATATTAAAACATCGAAGCAAT-TTTATGC
23613 AT
63 AT
23615 CGATGCA
1 CGATGCA
23622 ATATCAGTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.05
64 27 0.45
65 30 0.50
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (64 bp):
CGATGCACAAACCATGCATCGATGCACTCCAGATATATTAAAACATCGAAGCAATTTTATGCAT
Found at i:27596 original size:20 final size:21
Alignment explanation
Indices: 27537--27597 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
27527 CAGAACCCCA
*
27537 GGGGGTATCGATTCCC-CTGT
1 GGGGGGATCGATTCCCTCTGT
*
27557 GGGGGGAATCGGTTCCCTCT-T
1 GGGGGG-ATCGATTCCCTCTGT
27578 GGGGGGATCGATTCCCTCTG
1 GGGGGGATCGATTCCCTCTG
27598 CACCAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 17 0.49
21 16 0.46
22 2 0.06
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (21 bp):
GGGGGGATCGATTCCCTCTGT
Found at i:37120 original size:19 final size:20
Alignment explanation
Indices: 37085--37124 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
37075 TAAGTCAAAG
37085 AAAGAAAAAACAAAAAGAAA
1 AAAGAAAAAACAAAAAGAAA
*
37105 AAAGAACAAA-AAAAAGAAA
1 AAAGAAAAAACAAAAAGAAA
37124 A
1 A
37125 GAAAATAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAACAAAAAGAAA
Found at i:38050 original size:110 final size:110
Alignment explanation
Indices: 37853--38307 Score: 663
Period size: 110 Copynumber: 4.2 Consensus size: 110
37843 GGTTTTAGCT
* *
37853 AGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* *
37918 CGAAGGGGCGACTGACTATCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
37963 AGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* *
38028 AGAAGGGGTAACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* *
38073 AGAGTCAATTTTAACTTCAC-GTCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACA
1 AGAGTCAATTTCAACTTCACAG-CGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACA
*
38137 GCGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATGC
65 GCGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * * * * *
38183 AAAGTCAATTTCAACTTCACAACGAATGATATTGGACTCGAGATAACACAGGCTCAACTTCGCAG
1 AGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* * * *
38248 CGAATGGGCG-CTGGCTGTCAACAAACAA-TTTCCTAG-TTC---C
66 CGAAGGGGTGACTGACTGTCAACAAACAACTTTTC-AGTTTCATTC
*
38288 AGAGCCAATTTCAACTTCAC
1 AGAGTCAATTTCAACTTCAC
38308 GGCAGAGGAT
Statistics
Matches: 317, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
105 19 0.06
108 7 0.02
109 20 0.06
110 271 0.85
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
CGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:39122 original size:2 final size:2
Alignment explanation
Indices: 39110--39178 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
39100 TGAAATAAAC
39110 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39179 TGTATAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40256 original size:20 final size:20
Alignment explanation
Indices: 40228--40302 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
40218 TCCCTTTTAA
*
40228 TTTAATTATTTTTTATTATT
1 TTTATTTATTTTTTATTATT
40248 TTTATTTATTTATTTATTTTATT
1 TTTATTTATTT-TTTA--TTATT
* *
40271 CTTATTATATTTCTTATTATT
1 TTTATT-TATTTTTTATTATT
40292 TTGT-TTTATTT
1 TT-TATTTATTT
40303 ATACGATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
20 15 0.33
21 12 0.26
22 1 0.02
23 13 0.28
24 5 0.11
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTATTTATTTTTTATTATT
Found at i:40281 original size:28 final size:28
Alignment explanation
Indices: 40227--40305 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
40217 TTCCCTTTTA
*
40227 ATTTAATTATTTTTTATTATTTTTATTT
1 ATTTAATTATTTTTTATTATTTATATTT
* *
40255 ATTTATTTATTTTATTCTTA-TTATATTT
1 ATTTAATTATTTT-TTATTATTTATATTT
*
40283 -CTT-ATTATTTTGTT-TTATTTATA
1 ATTTAATTATTTT-TTATTATTTATA
40306 CGATATTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
25 3 0.07
26 14 0.33
27 2 0.05
28 19 0.44
29 5 0.12
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (28 bp):
ATTTAATTATTTTTTATTATTTATATTT
Found at i:40304 original size:26 final size:27
Alignment explanation
Indices: 40232--40305 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 27
40222 TTTTAATTTA
* *
40232 ATTATTTTTTATTATTTTTATTTATTT
1 ATTATTTTTTATTATTTATATTTACTT
*
40259 ATTTATTTTATTCTTA-TTATATTT-CTT
1 A-TTATTTT-TTATTATTTATATTTACTT
40286 ATTATTTTGTT-TTATTTATA
1 ATTATTTT-TTATTATTTATA
40306 CGATATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.08
26 14 0.35
27 4 0.10
28 14 0.35
29 5 0.12
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (27 bp):
ATTATTTTTTATTATTTATATTTACTT
Found at i:40449 original size:22 final size:23
Alignment explanation
Indices: 40414--40456 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40404 TGCATATATA
*
40414 TATATGTATATTTT-TTATTTGT
1 TATATATATATTTTATTATTTGT
*
40436 TATATATATTTTTTATTATTT
1 TATATATATATTTTATTATTT
40457 ATGGTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (23 bp):
TATATATATATTTTATTATTTGT
Found at i:42945 original size:31 final size:31
Alignment explanation
Indices: 42910--42982 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
42900 CGATTACGTC
*
42910 GGGACCATATTGCAAACAGACTAAATGTTGG
1 GGGACTATATTGCAAACAGACTAAATGTTGG
* *
42941 GGGACTGTACTGCAAACAGACTAAATGTTGG
1 GGGACTATATTGCAAACAGACTAAATGTTGG
42972 GGGACTATATT
1 GGGACTATATT
42983 ATAAGTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (31 bp):
GGGACTATATTGCAAACAGACTAAATGTTGG
Found at i:43440 original size:77 final size:76
Alignment explanation
Indices: 43325--43613 Score: 303
Period size: 77 Copynumber: 3.8 Consensus size: 76
43315 CCTAAAAATG
* * * * *
43325 TCATGGTTCACTAAAAAATAGGTTGTGATCTGAAATGTTAACATTTTTATTAATAAAATGGGTTG
1 TCATGGTTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTTATTAATAAAATGGGTTG
*
43390 TGTCCAAGAATA
66 CG-CCAAGAATA
* * ** * * *
43402 TCACGGTTCACTAAGAAATAAATTGTTATATGGAATGTTAATATTTTTATTAATAAAATGGATTA
1 TCATGGTTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTTATTAATAAAATGGGTTG
*
43467 CGCCTAAGAATG
66 CGCC-AAGAATA
* * * * * *
43479 TCATTGTTCGCTAAGTAATAGGTTACGATCTGGAACGTTAATATTTTTATTAATAAAATGGGTTG
1 TCATGGTTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTTATTAATAAAATGGGTTG
* *
43544 CGCCAAAAAAA
66 CGCCAAGAATA
* *
43555 GTTATGGTTCACTAAGAAAGTAGGA-TGCAATCTGGAATGTTAATATTTTTATT-ATAAAA
1 -TCATGGTTCACTAAGAAA-TA-GATTGCGATCTGGAATGTTAATATTTTTATTAATAAAA
43614 AATTTGAAAG
Statistics
Matches: 172, Mismatches: 36, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
76 6 0.03
77 138 0.80
78 27 0.16
79 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (76 bp):
TCATGGTTCACTAAGAAATAGATTGCGATCTGGAATGTTAATATTTTTATTAATAAAATGGGTTG
CGCCAAGAATA
Found at i:43612 original size:154 final size:154
Alignment explanation
Indices: 43314--43613 Score: 381
Period size: 154 Copynumber: 1.9 Consensus size: 154
43304 ATACAGTTGT
** *
43314 GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTGTGATCTGAAATGTTAACATTTTTATTAAT
1 GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTACGATCTGAAACGTTAACATTTTTATTAAT
* * * **
43379 AAAATGGGTTGTGTCCAAGAATATCACGGTTCACTAAGAAATAAATTGTTATATGGAATGTTAAT
66 AAAATGGGTTGCGTCCAAAAAAATCACGGTTCACTAAGAAATAAATTGCAATATGGAATGTTAAT
43444 ATTTTTATTAATAAAATGGATTAC
131 ATTTTTATTAATAAAATGGATTAC
* * * ** * *
43468 GCCTAAGAATGTCATTGTTCGCTAAGTAATAGGTTACGATCTGGAACGTTAATATTTTTATTAAT
1 GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTACGATCTGAAACGTTAACATTTTTATTAAT
* * * *
43533 AAAATGGGTTGCG-CCAAAAAAAGTTATGGTTCACTAAGAAAGTAGGA-TGCAATCTGGAATGTT
66 AAAATGGGTTGCGTCCAAAAAAA-TCACGGTTCACTAAGAAA-TA-AATTGCAATATGGAATGTT
43596 AATATTTTTATT-ATAAAA
128 AATATTTTTATTAATAAAA
43614 AATTTGAAAG
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
153 7 0.06
154 89 0.72
155 27 0.22
156 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (154 bp):
GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTACGATCTGAAACGTTAACATTTTTATTAAT
AAAATGGGTTGCGTCCAAAAAAATCACGGTTCACTAAGAAATAAATTGCAATATGGAATGTTAAT
ATTTTTATTAATAAAATGGATTAC
Found at i:44180 original size:101 final size:98
Alignment explanation
Indices: 43853--44207 Score: 317
Period size: 101 Copynumber: 3.6 Consensus size: 98
43843 TTTTGTTATG
* * * * * *
43853 CTCATGATAAAGTAGTAGGTAACGT-TTTTTTAATGTCAATTGTTTAATTTACAAATATCAAATT
1 CTCATGATAACGTAGTAGGTAGCGTCTTTTTTAATGTCAATCGTTTAAATTATAAGTA-CAAATT
* * *
43917 GTTTATATGATGCATAAGTAAGATAAAACATGTTT
65 GTTTATATTATGCAAAAGTAAGATAAAA-AAGTTT
* * * * * *
43952 CTCATGATAACGAAGTAGTTAGCG-CATTTTTT-ATGTCAATC-ATTAAGTTATAAGTATAAAAC
1 CTCATGATAACGTAGTAGGTAGCGTC-TTTTTTAATGTCAATCGTTTAAATTATAAGTA-CAAAT
* * * *
44014 CGTTTATATTATGCAAAAGAAAGATAAAACATTTT
64 TGTTTATATTATGCAAAAGTAAGATAAAAAAGTTT
* ** *
44049 GCTCATTATAACGTA-TCAGGTAGCACCTTTTTTAAATGTCAGTCGTTTAAATTATAAGTACGAA
1 -CTCATGATAACGTAGT-AGGTAGCGTCTTTTTT-AATGTCAATCGTTTAAATTATAAGTAC-AA
* *
44113 ATTGTTTATATTATGTAAAAGTAAGACAAAATAAGTTT
62 ATTGTTTATATTATGCAAAAGTAAGATAAAA-AAGTTT
* * * * *
44151 ATCATGATAACGTAGTATGTAGCGTCTTTTTT-ATGTTAATAGTTTAAGTTATAAGTA
1 CTCATGATAACGTAGTAGGTAGCGTCTTTTTTAATGTCAATCGTTTAAATTATAAGTA
44208 TGTGACCTAT
Statistics
Matches: 203, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
97 4 0.02
98 64 0.32
99 50 0.25
100 14 0.07
101 66 0.33
102 5 0.02
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (98 bp):
CTCATGATAACGTAGTAGGTAGCGTCTTTTTTAATGTCAATCGTTTAAATTATAAGTACAAATTG
TTTATATTATGCAAAAGTAAGATAAAAAAGTTT
Found at i:44832 original size:43 final size:43
Alignment explanation
Indices: 44777--44945 Score: 227
Period size: 43 Copynumber: 4.0 Consensus size: 43
44767 GACATATAGT
*
44777 GGCGTTTGTCTTTACAAACGCCGCTATTGAATGTGTATTTAGC
1 GGCGTTTTTCTTTACAAACGCCGCTATTGAATGTGTATTTAGC
* **
44820 GGCGTTTTTCTTTACAAACGCCGTTATTGTCTGTGTATTTAGC
1 GGCGTTTTTCTTTACAAACGCCGCTATTGAATGTGTATTTAGC
** *
44863 GGTATTTTTCTTTACAAACGCCGCTATTG-A-CTGTATTTAGC
1 GGCGTTTTTCTTTACAAACGCCGCTATTGAATGTGTATTTAGC
* *
44904 GACGTTTTTCTTTACAAACGCCGCTATT-AACTGTATATTTAG
1 GGCGTTTTTCTTTACAAACGCCGCTATTGAA-TGTGTATTTAG
44946 TGACATTTGT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 36 0.33
43 73 0.67
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (43 bp):
GGCGTTTTTCTTTACAAACGCCGCTATTGAATGTGTATTTAGC
Found at i:44916 original size:84 final size:86
Alignment explanation
Indices: 44785--44945 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 86
44775 GTGGCGTTTG
* * * **
44785 TCTTTACAAACGCCGCTATTGAATGTGTATTTAGCGGCGTTTTTCTTTACAAACGCCGTTATTGT
1 TCTTTACAAACGCCGCTATTGAATCTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAA
*
44850 CTGTGTATTTAGCGGTATTTT
66 CTGTATATTTAGCGGTATTTT
44871 TCTTTACAAACGCCGCTATTG-A-CTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAA
1 TCTTTACAAACGCCGCTATTGAATCTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAA
44934 CTGTATATTTAG
66 CTGTATATTTAG
44946 TGACATTTGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
84 47 0.68
85 1 0.01
86 21 0.30
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (86 bp):
TCTTTACAAACGCCGCTATTGAATCTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAA
CTGTATATTTAGCGGTATTTT
Found at i:44966 original size:43 final size:41
Alignment explanation
Indices: 44878--44970 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 41
44868 TTTTCTTTAC
* * * ** *
44878 AAACGCCGCTATTGACTGTATTTAGCGACGTTTTTCTTTAC
1 AAACGCCGCTATTAACTGTATTTAGCGACATTTGTAATTAA
*
44919 AAACGCCGCTATTAACTGTATATTTAGTGACATTTGTAATTAA
1 AAACGCCGCTATTAACTG--TATTTAGCGACATTTGTAATTAA
44962 AAACGCCGC
1 AAACGCCGC
44971 AAATAAGCCC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 17 0.40
43 26 0.60
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTATTAACTGTATTTAGCGACATTTGTAATTAA
Found at i:44966 original size:84 final size:86
Alignment explanation
Indices: 44792--44970 Score: 227
Period size: 84 Copynumber: 2.1 Consensus size: 86
44782 TTGTCTTTAC
* * * ** *
44792 AAACGCCGCTATTGAATGTGTATTTAGCGGCGTTTTTCTTTACAAACGCCGTTATTGTCTGTGTA
1 AAACGCCGCTATTGAATCTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAACTGTATA
** * ** *
44857 TTTAGCGGTATTTTTCTTTAC
66 TTTAGCGACATTTGTAATTAA
44878 AAACGCCGCTATTG-A-CTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAACTGTATA
1 AAACGCCGCTATTGAATCTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAACTGTATA
*
44941 TTTAGTGACATTTGTAATTAA
66 TTTAGCGACATTTGTAATTAA
44962 AAACGCCGC
1 AAACGCCGC
44971 AAATAAGCCC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 65 0.81
85 1 0.01
86 14 0.17
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (86 bp):
AAACGCCGCTATTGAATCTGTATTTAGCGACGTTTTTCTTTACAAACGCCGCTATTAACTGTATA
TTTAGCGACATTTGTAATTAA
Found at i:46338 original size:21 final size:21
Alignment explanation
Indices: 46312--46353 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
46302 AAGCTTAAAT
46312 GTGTTATAGCCGGCAGCACCG
1 GTGTTATAGCCGGCAGCACCG
46333 GTGTTATAGCCGGCAGCACCG
1 GTGTTATAGCCGGCAGCACCG
46354 AGCCTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (21 bp):
GTGTTATAGCCGGCAGCACCG
Found at i:47723 original size:22 final size:22
Alignment explanation
Indices: 47696--47747 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
47686 TATTTTGATA
47696 AATTTAATGTTTATTTTATAAT
1 AATTTAATGTTTATTTTATAAT
47718 AATTTAATGTTTATTTTATAAT
1 AATTTAATGTTTATTTTATAAT
47740 AATTTAAT
1 AATTTAAT
47748 AAAATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
AATTTAATGTTTATTTTATAAT
Found at i:47753 original size:10 final size:11
Alignment explanation
Indices: 47708--47772 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
47698 TTTAATGTTT
*
47708 ATTTTATAATA
1 ATTTAATAATA
** *
47719 ATTTAATGTTT
1 ATTTAATAATA
*
47730 ATTTTATAATA
1 ATTTAATAATA
47741 ATTTAATAA-A
1 ATTTAATAATA
*
47751 ATTTAATAATC
1 ATTTAATAATA
47762 A-TTAATAATA
1 ATTTAATAATA
47772 A
1 A
47773 ATTGATTAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 19 0.45
11 23 0.55
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:48229 original size:41 final size:41
Alignment explanation
Indices: 48181--48719 Score: 681
Period size: 41 Copynumber: 13.2 Consensus size: 41
48171 TTGTAAACAC
** *
48181 AAACGCCACTAAAACACGAGTCTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
48222 AAACGCCACTAAATCATGAGTCTATAGCGACGTTTGTA-AA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
48262 AAATGCCACTAAATCACGAGTCTATAGCGGCGTTTGTA-ACA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATA-A
* * * *
48303 AACACGCCACTAAAGTATGAGTCTTTAGCGGCGATTGTATAA
1 AA-ACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
48345 AAACGCCACTAAAGTACGAGTCTTTAGCGGTGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
48386 AAACGCCACTAAATCATGAGTCTATAGCGACGTTTATATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
48427 AAACACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
48468 AAACGCCACTAAATCATGAGTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
48509 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
48550 AAACGCCACTAAATCATGAGTCTATAGCGGCGTTTGTATTAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTA-TAA
* * *
48592 AAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
48633 AAATGCCACTAGATTAC-AGACTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *
48673 AAACGCCACTAAATTAC-ATTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
48713 AAACGCC
1 AAACGCC
48720 GTTATAGTAG
Statistics
Matches: 434, Mismatches: 60, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
40 101 0.23
41 263 0.61
42 69 0.16
43 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:48392 original size:82 final size:82
Alignment explanation
Indices: 48181--48719 Score: 766
Period size: 82 Copynumber: 6.6 Consensus size: 82
48171 TTGTAAACAC
** * *
48181 AAACGCCACTAAAACACGAGTCTATAGCGGTGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
48246 TAGCGACGTTTGTA-AA
66 TAGCGACGTTTGTATAA
* *
48262 AAATGCCACTAAA-TCACGAGTCTATAGCGGCGTTTGTA-ACAAACACGCCACTAAAGT-ATGAG
1 AAACGCCACTAAAGT-ACGAGTCTTTAGCGGCGTTTGTATA-AAA-ACGCCACTAAA-TCATGAG
* * *
48324 TCTTTAGCGGCGATTGTATAA
62 TCTATAGCGACGTTTGTATAA
*
48345 AAACGCCACTAAAGTACGAGTCTTTAGCGGTGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
*
48410 TAGCGACGTTTATATAA
66 TAGCGACGTTTGTATAA
*
48427 AAACACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
48492 TAGCGACGTTTGTATAA
66 TAGCGACGTTTGTATAA
48509 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
*
48574 TAGCGGCGTTTGTATTAA
66 TAGCGACGTTTGTA-TAA
* * * * * * * * *
48592 AAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATAAAAATGCCACTAGATTA-CAGACTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
*
48656 TAGCGGCGTTTGTATAA
66 TAGCGACGTTTGTATAA
* *
48673 AAACGCCACTAAATTAC-ATTCTTTAGCGGCGTTTGTATAAAAACGCC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
48720 GTTATAGTAG
Statistics
Matches: 417, Mismatches: 32, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
80 27 0.06
81 57 0.14
82 238 0.57
83 93 0.22
84 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTA
TAGCGACGTTTGTATAA
Found at i:49101 original size:2 final size:2
Alignment explanation
Indices: 49094--49125 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49084 AACATATTTC
49094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49126 TCATAACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50090 original size:21 final size:21
Alignment explanation
Indices: 50064--50108 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
50054 GTTTTGCCCC
*
50064 TAAAATTTTAATTCGTCACCT
1 TAAAATTTTAATTCATCACCT
*
50085 TAAAATTTTAGTTCATCACCT
1 TAAAATTTTAATTCATCACCT
50106 TAA
1 TAA
50109 GTTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (21 bp):
TAAAATTTTAATTCATCACCT
Found at i:68783 original size:21 final size:20
Alignment explanation
Indices: 68697--68854 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
68687 AAATGACCAA
**
68697 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
68716 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
68736 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
68756 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
68777 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
68798 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
68818 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
68839 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
68855 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:68883 original size:20 final size:20
Alignment explanation
Indices: 68821--69090 Score: 262
Period size: 20 Copynumber: 13.5 Consensus size: 20
68811 CGATTTTCCA
* ** *
68821 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
68841 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
68861 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
68881 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
68901 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
68921 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
68941 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
68961 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
68981 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
69001 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
69021 AAATCGCAACG-ATAATCTGT
1 AAATCGCAACGCGT-ATCCGT
*
69041 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
69061 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
69081 AAATCACAAC
1 AAATCGCAAC
69091 ACTGAAATTT
Statistics
Matches: 216, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 212 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:68907 original size:40 final size:40
Alignment explanation
Indices: 68860--69090 Score: 290
Period size: 40 Copynumber: 5.8 Consensus size: 40
68850 CGCGAACACA
*
68860 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAT-AATCCG
*
68900 TATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAA--CGATAATCCG
*
68940 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
* * *
68980 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
* *
69020 TAAATCGCAACG-ATAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGT-ATCCGTAAATCGCAACGATAATCCG
* * * *
69060 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGCGTATCCGTAAATCGCAAC
69091 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 169 0.97
42 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
Found at i:69804 original size:24 final size:24
Alignment explanation
Indices: 69765--69811 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
69755 AAATTTGGTC
69765 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
69789 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
69812 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:72209 original size:19 final size:18
Alignment explanation
Indices: 72159--72442 Score: 251
Period size: 19 Copynumber: 16.7 Consensus size: 18
72149 GCAACGAGAG
72159 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
72178 AATCCCAA--C---ATGA
1 AATCGCAATGCGAAATGA
72191 AATCGCAATGCGGAAATGA
1 AATCGCAATGC-GAAATGA
72210 AATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGA
72228 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
72247 AATCGCAA--CG--A-G-
1 AATCGCAATGCGAAATGA
72259 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
72278 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
72297 AATCGCAA--CGAGA-G-
1 AATCGCAATGCGAAATGA
72311 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
72330 AATCGCAATGCGAAA-GAA
1 AATCGCAATGCGAAATG-A
*
72348 AATCGC-A--CG-GA-G-
1 AATCGCAATGCGAAATGA
72360 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
72379 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
72398 AATCGCAA--CGAGA-G-
1 AATCGCAATGCGAAATGA
*
72412 AATCGCAATGCGAAATTA
1 AATCGCAATGCGAAATGA
*
72430 AATCGCATTGCGA
1 AATCGCAATGCGA
72443 TTCTCCCGTT
Statistics
Matches: 225, Mismatches: 10, Indels: 61
0.76 0.03 0.21
Matches are distributed among these distances:
12 14 0.06
13 9 0.04
14 24 0.11
15 6 0.03
16 12 0.05
17 15 0.07
18 45 0.20
19 100 0.44
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:72383 original size:120 final size:119
Alignment explanation
Indices: 72159--72405 Score: 335
Period size: 120 Copynumber: 2.1 Consensus size: 119
72149 GCAACGAGAG
72159 AATCGCAATGCGAAATGAAAATCCCAACATGAAATCGCAATGCGGAAATGAAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAATCGCAATGCGGAAATGAAATCGCAATGCGAA
* * *
72224 ATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAATCGCAATGCGAAATGAA
66 ATGAAATCGCAACGCGAAATGAAAATCGAAACGAAAATCGCAATGCGAAATGAA
*
72278 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGA-AATCGCAATGCGGAAATG-AAATCGCAATGC
* *
72341 GAAA-GAAAATCGC-ACG-GAGAATCG-CAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 GAAATG-AAATCGCAACGCGA-AAT-GAAAAT-CGAAACGAAAATCGCAATGCGAAATGAA
72398 AATCGCAA
1 AATCGCAA
72406 CGAGAGAATC
Statistics
Matches: 115, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
118 2 0.02
119 44 0.38
120 69 0.60
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (119 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAATCGCAATGCGGAAATGAAATCGCAATGCGAA
ATGAAATCGCAACGCGAAATGAAAATCGAAACGAAAATCGCAATGCGAAATGAA
Found at i:72545 original size:52 final size:53
Alignment explanation
Indices: 72432--72548 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
72422 CGAAATTAAA
*
72432 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
*
72485 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTACGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
72537 TCGCATTGCGAT
1 TCGCATTGCGAT
72549 AGTCATTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
Found at i:72556 original size:19 final size:19
Alignment explanation
Indices: 72451--72548 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
72441 GATTCTCCCG
72451 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
72471 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
72490 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
72504 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
72523 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72542 TTGCGAT
1 TTGCGAT
72549 AGTCATTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 34 0.49
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:72680 original size:14 final size:14
Alignment explanation
Indices: 72647--72682 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
72637 CATCAATTAC
72647 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
72661 AC-AATCATCTTTT
1 ACAAATCAACTTTT
72674 ACAAATCAA
1 ACAAATCAA
72683 TTAACAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:73353 original size:137 final size:137
Alignment explanation
Indices: 73101--73371 Score: 510
Period size: 137 Copynumber: 2.0 Consensus size: 137
73091 TCCCGTCGTC
73101 AACGCTCAACGCCAAGCATACGAGAGGACCACAATCTCCTCTGGCTCCGCTCGTTTGTTGTGGCG
1 AACGCTCAACGCCAAGCATACGAGAGGACCACAATCTCCTCTGGCTCCGCTCGTTTGTTGTGGCG
73166 CGTCTCGTCTCTATAACTGTAATATTGAGCTTCTTTGGCTTCTTGTTTCCAG-ACGAGTCCAATA
66 CGTCTCGTCTCTATAACTGTAATATTGAGCTTCTTTGGCTTCTTGTTTCCAGAACGAGTCCAATA
73230 ATTGTCA
131 ATTGTCA
73237 AACGCTCCAACGCCAAGCATACGAGAGGACCACAATCTCCTCTGGCTCCGCTCGTTTGTTGTGGC
1 AACGCT-CAACGCCAAGCATACGAGAGGACCACAATCTCCTCTGGCTCCGCTCGTTTGTTGTGGC
73302 GCGTCTCGTCTCTAATAACTGTAATATTGAGCTTCTTTGGCTT-TTGTTTCCAGAACGAGTCCAA
65 GCGTCTCGTCTCT-ATAACTGTAATATTGAGCTTCTTTGGCTTCTTGTTTCCAGAACGAGTCCAA
73366 TAATTG
129 TAATTG
73372 ATCGCATCCA
Statistics
Matches: 132, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
136 6 0.05
137 81 0.61
138 45 0.34
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (137 bp):
AACGCTCAACGCCAAGCATACGAGAGGACCACAATCTCCTCTGGCTCCGCTCGTTTGTTGTGGCG
CGTCTCGTCTCTATAACTGTAATATTGAGCTTCTTTGGCTTCTTGTTTCCAGAACGAGTCCAATA
ATTGTCA
Found at i:74789 original size:14 final size:14
Alignment explanation
Indices: 74770--74826 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
74760 GCGAAATGAA
*
74770 AATCGCAACGACAG
1 AATCGCAACGAAAG
74784 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
74801 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
74817 AATCGCAACG
1 AATCGCAACG
74827 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:74797 original size:33 final size:33
Alignment explanation
Indices: 74751--74843 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
74741 GCGAAACCAA
*
74751 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
74784 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
74817 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
74844 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:74808 original size:19 final size:19
Alignment explanation
Indices: 74715--74848 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
74705 ATAGTTACTT
*
74715 TCGCAACACGAAACT-AAAA
1 TCGCAACGCGAAA-TGAAAA
**
74734 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
74753 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
74772 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
74786 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
74805 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
74819 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
74838 TCGCAATGCGA
1 TCGCAACGCGA
74849 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 7, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 59 0.61
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:74866 original size:19 final size:19
Alignment explanation
Indices: 74844--74972 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
74834 AAAATCGCAA
74844 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
74863 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
74877 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
74896 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
74910 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
74929 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
74948 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
74968 TGCGA
1 TGCGA
74973 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:74886 original size:33 final size:33
Alignment explanation
Indices: 74844--74935 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
74834 AAAATCGCAA
74844 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
74877 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
74910 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
74936 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:75257 original size:93 final size:93
Alignment explanation
Indices: 75020--75486 Score: 879
Period size: 93 Copynumber: 5.1 Consensus size: 93
75010 ATGGATTGCA
75020 TTAC-TTCAACCAAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACC-AAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGT
75083 TTAGCAGAATTGGCAGCAACCGAACAAA-
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
75111 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
75176 TAGCAGAATTGGCAGCAACTGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
75204 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
75269 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
75297 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC-GTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
75361 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
75389 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
75454 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
75482 TTACT
1 TTACT
75487 AAGCAATCTA
Statistics
Matches: 369, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 30 0.08
92 151 0.41
93 188 0.51
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:75364 original size:185 final size:186
Alignment explanation
Indices: 75020--75486 Score: 879
Period size: 185 Copynumber: 2.5 Consensus size: 186
75010 ATGGATTGCA
75020 TTAC-TTCAACCAAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACC-AAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGT
75083 TTAGCAGAATTGGCAGCAACCGAACAAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
65 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
*
75147 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACTGAACAAAT
130 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
75204 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
75269 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
75334 ATTTCACAGTGTTAAAGAATACAC-GTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
75389 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
75454 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
75487 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
184 30 0.11
185 187 0.67
186 61 0.22
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:77281 original size:33 final size:33
Alignment explanation
Indices: 77233--77313 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
77223 AAAATCGCAA
**
77233 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
77266 TGTGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
77299 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
77314 TCTCGTTGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:77301 original size:14 final size:14
Alignment explanation
Indices: 77249--77305 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
77239 TTTGGTTTCG
77249 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
77263 CGTTGTGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
77282 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
77296 CGTTGCGATT
1 CGTTGCGATT
77306 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:77346 original size:41 final size:41
Alignment explanation
Indices: 77289--77366 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
77279 TCGCGTTGCG
*
77289 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
77330 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
77367 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:77351 original size:20 final size:21
Alignment explanation
Indices: 77290--77365 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
77280 CGCGTTGCGA
77290 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
77311 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
77331 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
77352 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
77366 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:77487 original size:33 final size:33
Alignment explanation
Indices: 77445--77515 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
77435 AATACTAACT
*
77445 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
77478 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
77511 TGAAA
1 TGAAA
77516 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:77925 original size:20 final size:20
Alignment explanation
Indices: 77900--78012 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
77890 CTTTAAATAT
77900 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
**
77920 CGCGTTGCGAAATACGGATA
1 CGCGTTGCGATTTACGGATA
*
77940 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
77960 GGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
77980 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
78000 CGCGTTGCGATTT
1 CGCGTTGCGATTT
78013 TGGAAACTGA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 76 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:81496 original size:31 final size:31
Alignment explanation
Indices: 81461--81582 Score: 165
Period size: 31 Copynumber: 3.9 Consensus size: 31
81451 GAATGACCAA
* * *
81461 TCCATAAATCCCGAATAATC-TAGGTAATCAG
1 TCCATATATCCCGAAGAA-CATAGGTAAACAG
* *
81492 TCCATATGTCCCAAAGAACATAGGTAAACAG
1 TCCATATATCCCGAAGAACATAGGTAAACAG
81523 TCCATATATCCCGAAGAACATAGGTAAACAG
1 TCCATATATCCCGAAGAACATAGGTAAACAG
* *
81554 TCTATATGTCCCGAAGAACATAGGTAAAC
1 TCCATATATCCCGAAGAACATAGGTAAAC
81583 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 1 0.01
31 80 0.99
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (31 bp):
TCCATATATCCCGAAGAACATAGGTAAACAG
Found at i:81561 original size:62 final size:62
Alignment explanation
Indices: 81461--81582 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
81451 GAATGACCAA
* *
81461 TCCATAAATCCCGAATAATCTAGGTAATCAGTCCATATGTCCCAAAGAACATAGGTAAACAG
1 TCCATAAATCCCGAAGAATCTAGGTAAACAGTCCATATGTCCCAAAGAACATAGGTAAACAG
* * *
81523 TCCATATATCCCGAAGAA-CATAGGTAAACAGTCTATATGTCCCGAAGAACATAGGTAAAC
1 TCCATAAATCCCGAAGAATC-TAGGTAAACAGTCCATATGTCCCAAAGAACATAGGTAAAC
81583 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 1 0.02
62 53 0.98
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (62 bp):
TCCATAAATCCCGAAGAATCTAGGTAAACAGTCCATATGTCCCAAAGAACATAGGTAAACAG
Found at i:83758 original size:29 final size:29
Alignment explanation
Indices: 83704--83760 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
83694 TGCATGTTTT
*
83704 TCCAGTTTAGTGCATAACGTTTATTTCGG
1 TCCAGTTTAGTGCACAACGTTTATTTCGG
* *
83733 TCCAGTTTGGTGC-CAACTTTTCATTTCG
1 TCCAGTTTAGTGCACAACGTTT-ATTTCG
83761 TTACTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (29 bp):
TCCAGTTTAGTGCACAACGTTTATTTCGG
Found at i:84764 original size:17 final size:18
Alignment explanation
Indices: 84734--84769 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
84724 ACTGGTTTTT
84734 AAAAATAATTAAAATTAAA
1 AAAAATAA-TAAAATTAAA
84753 AAAAATAA-AAAATTAAA
1 AAAAATAATAAAATTAAA
84770 CCTTTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAATAATAAAATTAAA
Found at i:84850 original size:29 final size:29
Alignment explanation
Indices: 84808--84867 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
84798 ATGCTTGTTT
* *
84808 TTCCAGTTTAGTGCATAACGTTT-ATTTCG
1 TTCCAGTTTAGTGC-CAACATTTCATTTCG
*
84837 TTCCAGTTTGGTGCCAACATTTCATTTCG
1 TTCCAGTTTAGTGCCAACATTTCATTTCG
84866 TT
1 TT
84868 ACTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (29 bp):
TTCCAGTTTAGTGCCAACATTTCATTTCG
Found at i:85956 original size:18 final size:18
Alignment explanation
Indices: 85935--85979 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
85925 AAGTTTTTTT
*
85935 TTAAATAAAAGATAAGAA
1 TTAAATAAAAGAAAAGAA
*
85953 TTAAATAAAAGAAAATAA
1 TTAAATAAAAGAAAAGAA
*
85971 CTAAATAAA
1 TTAAATAAA
85980 TAATCTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (18 bp):
TTAAATAAAAGAAAAGAA
Found at i:87115 original size:18 final size:18
Alignment explanation
Indices: 87077--87117 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
87067 AATAACCATT
* * *
87077 TTTTTAAAACAATTTTTA
1 TTTTAAAAACAATTATGA
87095 TTTTAAAAACAATTATGA
1 TTTTAAAAACAATTATGA
87113 TTTTA
1 TTTTA
87118 TTTGAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTAAAAACAATTATGA
Found at i:87899 original size:31 final size:31
Alignment explanation
Indices: 87861--87935 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
87851 ATGTAATAAA
* * *
87861 AACATCATATATTTAATCAACCAGAACATAT
1 AACATCATACATTTAACCAACAAGAACATAT
* * *
87892 ATCATCATGCATTTAACCAAGAAGAACATAT
1 AACATCATACATTTAACCAACAAGAACATAT
*
87923 AACATCATGCATT
1 AACATCATACATT
87936 GTTCATTCAT
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:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (31 bp):
AACATCATACATTTAACCAACAAGAACATAT
Found at i:88068 original size:24 final size:24
Alignment explanation
Indices: 88041--88090 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
88031 CAGCTCGTAT
88041 AAATTGCACCGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
*
88065 AAATTGCACTGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
88089 AA
1 AA
88091 GTGTCCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAG
Found at i:91294 original size:3 final size:3
Alignment explanation
Indices: 91279--91320 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
91269 GTAATATGAA
* * *
91279 AAT AAT AAA AAT AAT ATT AGT -AT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
91321 TCATAATCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:91295 original size:20 final size:20
Alignment explanation
Indices: 91270--91314 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
91260 GGGCCAACTG
91270 TAATATGAAAATAATAAAAA
1 TAATATGAAAATAATAAAAA
* ** *
91290 TAATATTAGTATAATAATAA
1 TAATATGAAAATAATAAAAA
91310 TAATA
1 TAATA
91315 ATAATATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TAATATGAAAATAATAAAAA
Found at i:91326 original size:20 final size:20
Alignment explanation
Indices: 91280--91327 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
91270 TAATATGAAA
* * *
91280 ATAATAAAAATAATATTAGT
1 ATAATAATAATAATAATAAT
91300 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
*
91320 ATCATAAT
1 ATAATAAT
91328 CCAAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:91809 original size:2 final size:2
Alignment explanation
Indices: 91802--91827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
91792 ATTGAATTTA
91802 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
91828 GAACCGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98431 original size:55 final size:56
Alignment explanation
Indices: 98371--98529 Score: 137
Period size: 55 Copynumber: 2.8 Consensus size: 56
98361 ATGTACTTTC
98371 TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCACCTATCATATGTA
1 TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCACCTATCATATGTA
* * * * * ** * *
98427 -CTTTC-TCTTTCACTTA-CACGTAAAAT-ATTTTCATATGATTCACCTATCATATGTA
1 TCTTTCATATATCTCATATCACAT-AGCTCATATT-AT-TCATTCACCTATCATATGTA
98482 CTTTCTCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCA
1 -----TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCA
98530 AATCATGTCA
Statistics
Matches: 73, Mismatches: 18, Indels: 19
0.66 0.16 0.17
Matches are distributed among these distances:
53 8 0.11
54 11 0.15
55 24 0.33
61 11 0.15
62 11 0.15
63 8 0.11
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (56 bp):
TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCACCTATCATATGTA
Found at i:98438 original size:25 final size:25
Alignment explanation
Indices: 98410--98493 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
98400 ATATTATTCA
98410 TTCACCTATCATATGTACTTTCTCT
1 TTCACCTATCATATGTACTTTCTCT
* ** * *
98435 TTCACTTA-CACGTAAAATATTTTCATAT
1 TTCACCTATCA--T-ATGTACTTTC-TCT
98463 GATTCACCTATCATATGTACTTTCTCT
1 --TTCACCTATCATATGTACTTTCTCT
98490 TTCA
1 TTCA
98494 TATATCTCAT
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 1 0.02
27 9 0.21
28 9 0.21
29 1 0.02
30 7 0.17
31 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (25 bp):
TTCACCTATCATATGTACTTTCTCT
Found at i:109527 original size:18 final size:19
Alignment explanation
Indices: 109498--109533 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
109488 TATTAATATA
*
109498 TTTATGTAAATATTATTTT
1 TTTATGTAAATAATATTTT
109517 TTTAT-TAAATAATATTT
1 TTTATGTAAATAATATTT
109534 ATATAATTAT
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:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATGTAAATAATATTTT
Found at i:109532 original size:33 final size:31
Alignment explanation
Indices: 109476--109553 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 31
109466 TTTAAATAGT
* *
109476 TATTATATTTTATATTAATATATTTATGTAAA
1 TATTAT-TTTTTTATTAATATATTTATATAAA
*
109508 TATTATTTTTTTATTAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAT-ATATTTATATAAA
*
109541 TATTATTTATTTA
1 TATTATTTTTTTA
109554 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.20
32 9 0.22
33 23 0.57
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
TATTATTTTTTTATTAATATATTTATATAAA
Found at i:111385 original size:21 final size:21
Alignment explanation
Indices: 111323--111412 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
111313 CCATCTCCGT
*
111323 AGGGTTACATTCCGAGCCCGT
1 AGGGTTACATTCCGAGCCCGC
111344 AGGGTTACATTCCGAGCCCGC
1 AGGGTTACATTCCGAGCCCGC
*
111365 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATTCCGAGCCCG-C
* * *
111387 A-GGTTACATGCCTAGCACGC
1 AGGGTTACATTCCGAGCCCGC
111407 AGGGTT
1 AGGGTT
111413 TTATACCATA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (21 bp):
AGGGTTACATTCCGAGCCCGC
Found at i:111636 original size:9 final size:9
Alignment explanation
Indices: 111622--111648 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
111612 TTTATACAGG
111622 CCCTTCAGC
1 CCCTTCAGC
111631 CCCTTCAGC
1 CCCTTCAGC
111640 CCCTTCAGC
1 CCCTTCAGC
111649 GTCATCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.56, G:0.11, T:0.22
Consensus pattern (9 bp):
CCCTTCAGC
Found at i:111971 original size:28 final size:28
Alignment explanation
Indices: 111939--112033 Score: 118
Period size: 28 Copynumber: 3.2 Consensus size: 28
111929 GATAAATGTT
* *
111939 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
111967 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
111995 TTTAAAATTAAAATATAAATTATAGTATTCGAAA
1 TTTAAAA-TAAAA-AT-AA-TAT--TATTCGAAA
112029 TTTAA
1 TTTAA
112034 CATTAAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
28 33 0.56
29 5 0.08
30 2 0.03
31 2 0.03
32 3 0.05
34 14 0.24
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:112006 original size:34 final size:34
Alignment explanation
Indices: 111968--112040 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
111958 TATTCGAAAT
*
111968 TTAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATAATAGTATTCGAAATTTAAAA
* * *
112002 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATAATAGTATTCGAAATTTAAAA
112036 TTAAA
1 TTAAA
112041 TTTCAACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATAATAGTATTCGAAATTTAAAA
Found at i:112665 original size:125 final size:127
Alignment explanation
Indices: 112434--113047 Score: 968
Period size: 125 Copynumber: 4.7 Consensus size: 127
112424 ACAATCCATC
112434 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC-AAATAAT
*
112499 GGAAGGTGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
65 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
112562 TAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATGTTCT-TGACAAATAATG
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATG
* *
112625 GAAGGGGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
112687 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATG
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAAT-
*
112752 GAAGGCGCGCCCCCGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGG
65 --------------GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
112817 TACTGATATGAA
116 TACTGATATGAA
*
112829 TAGTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATG
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATG
*
112894 GAAGGCGCGTCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAAT-ATA-GTACTGATATGAA
66 GAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
112954 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC-AAATAAT
*
113019 GGAAGGCGC-CCCCCCGGAACGCGCCTTCA
65 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
113048 TGTGAATAGT
Statistics
Matches: 455, Mismatches: 13, Indels: 39
0.90 0.03 0.08
Matches are distributed among these distances:
125 161 0.35
126 67 0.15
127 98 0.22
128 6 0.01
142 123 0.27
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (127 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATG
GAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:112790 original size:16 final size:15
Alignment explanation
Indices: 112751--112782 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
112741 GACAAATAAT
112751 GGAAGGCGCGCCCCC
1 GGAAGGCGCGCCCCC
112766 GGAAGGCGCGCCCCC
1 GGAAGGCGCGCCCCC
112781 GG
1 GG
112783 GAACGCGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.44, G:0.44, T:0.00
Consensus pattern (15 bp):
GGAAGGCGCGCCCCC
Found at i:112880 original size:142 final size:142
Alignment explanation
Indices: 112624--112909 Score: 527
Period size: 142 Copynumber: 2.0 Consensus size: 142
112614 GACAAATAAT
* *
112624 GGAAGGGGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
1 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
*
112689 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATGGA
66 GTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATGGA
112754 AGGCGCGCCCCC
131 AGGCGCGCCCCC
*
112766 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATGAATA
1 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
112831 GTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATGGA
66 GTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATGGA
*
112896 AGGCGCGTCCCC
131 AGGCGCGCCCCC
112908 GG
1 GG
112910 GAACGCGCCT
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.19
Consensus pattern (142 bp):
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
GTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATGGA
AGGCGCGCCCCC
Found at i:112981 original size:267 final size:268
Alignment explanation
Indices: 112499--113042 Score: 970
Period size: 267 Copynumber: 2.0 Consensus size: 268
112489 ACAAAATAAT
*
112499 GGAAGGTGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
1 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
* *
112564 GTGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATGTTCTTGACAAATAATGGAAG
66 GTGTCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTTGACAAATAATGGAAG
*
112629 GGGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTC
131 GCGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTC
112694 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC-AAATAATGGAAGGC
196 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
*
112758 GCGCCCCC
261 GCCCCCCC
*
112766 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATGAATA
1 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
112831 GTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAATAATGGA
66 GTGT-CCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCT-TGACAAATAATGGA
112896 AGGCGCGTCCC-CGGGAACGCGCCTTCAAGTCCCCTGAGAAAT-ATA-GTACTGATATGAATAGT
129 AGGCGCG-CCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGT
112958 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
193 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
113023 GGCGCCCCCCC
258 GGCGCCCCCCC
*
113034 GGAACGCGC
1 GGAAGGCGC
113043 CTTCATGTGA
Statistics
Matches: 266, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
267 137 0.52
268 75 0.28
269 51 0.19
270 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (268 bp):
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
GTGTCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTTGACAAATAATGGAAG
GCGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTGTC
CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
GCCCCCCC
Found at i:113142 original size:8 final size:8
Alignment explanation
Indices: 113129--113169 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
113119 TCACAAGCTT
113129 TCAAATTC
1 TCAAATTC
113137 TCAAATTC
1 TCAAATTC
* *
113145 CCAAACTC
1 TCAAATTC
113153 T-AAATTC
1 TCAAATTC
113160 TCAAATTC
1 TCAAATTC
113168 TC
1 TC
113170 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:116155 original size:13 final size:13
Alignment explanation
Indices: 116132--116172 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
116122 AAATACATAA
*
116132 ATATTTTTAATAT
1 ATATATTTAATAT
*
116145 ATTTATTTAATAT
1 ATATATTTAATAT
116158 A-ATA-TTAATAT
1 ATATATTTAATAT
116169 ATAT
1 ATAT
116173 TAGTTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATTTAATAT
Done.