Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006246.1 Hibiscus syriacus cultivar Beakdansim tig00014889_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: 91082
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10549 original size:13 final size:13
Alignment explanation
Indices: 10533--10559 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10523 AGTACTTGCT
10533 AACAATACTTACA
1 AACAATACTTACA
10546 AACAATACTTACA
1 AACAATACTTACA
10559 A
1 A
10560 GCATATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
AACAATACTTACA
Found at i:12334 original size:21 final size:21
Alignment explanation
Indices: 12310--12370 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
12300 AACTTTGAAA
12310 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
12331 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
12345 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
12366 AAATG
1 AAATG
12371 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:12401 original size:37 final size:37
Alignment explanation
Indices: 12302--12420 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
12292 TGGTAACCAA
12302 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
12339 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
12374 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
12411 -GTTGAAAAAT
1 CTTTGAAAAAT
12421 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:16930 original size:21 final size:20
Alignment explanation
Indices: 16906--16966 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
16896 AACTTTGAAA
16906 AAATGGTTTTCAATGTTTGGT
1 AAATGGTTTTCAA-GTTTGGT
*
16927 AAAT-G-TTT--A-TTT-GA
1 AAATGGTTTTCAAGTTTGGT
16941 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTC-AAGTTTGGT
16962 AAATG
1 AAATG
16967 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 3 0.10
17 1 0.03
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (20 bp):
AAATGGTTTTCAAGTTTGGT
Found at i:16997 original size:37 final size:37
Alignment explanation
Indices: 16898--17016 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 37
16888 TGGTAACCAA
*
16898 CTTTGAAAAA-ATGGTTTTCAATGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
*
16935 ATTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
16970 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
17007 -GTTGAAAAAT
1 CTTTGAAAAAT
17017 GATAATGGGA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
35 28 0.38
36 18 0.25
37 27 0.37
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:21464 original size:37 final size:37
Alignment explanation
Indices: 21422--21506 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
21412 AATGTTAACC
21422 CTTATTTTCACTTTCATTTCTCGTCCTAAAATGTCTG
1 CTTATTTTCACTTTCATTTCTCGTCCTAAAATGTCTG
*
21459 CTTATTTTCGCTTTCATTTCTCGTCCTAAAATGTCTG
1 CTTATTTTCACTTTCATTTCTCGTCCTAAAATGTCTG
*
21496 CTTATTCTCAC
1 CTTATTTTCAC
21507 CTCAATATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.48
Consensus pattern (37 bp):
CTTATTTTCACTTTCATTTCTCGTCCTAAAATGTCTG
Found at i:33535 original size:22 final size:22
Alignment explanation
Indices: 33507--33556 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
33497 CGCGCTGAAT
*
33507 GCTGAACGGTTCAGTATTCATC
1 GCTGAACGGTTCAGCATTCATC
33529 GCTGAACGGTTCAGCATTCATC
1 GCTGAACGGTTCAGCATTCATC
33551 GCTGAA
1 GCTGAA
33557 TGATTCCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (22 bp):
GCTGAACGGTTCAGCATTCATC
Found at i:33742 original size:39 final size:40
Alignment explanation
Indices: 33681--33758 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
33671 TATTTATTTT
*
33681 TGCTTTGGTTCCCTAAACTTTTTATTGAAGCTTTGATTGC
1 TGCTTTGGTTCCCTAAACTTTTTATTGAAACTTTGATTGC
33721 TGCTTTGGTT-CCTAAACTTTTTATTGAAACTTTGATTG
1 TGCTTTGGTTCCCTAAACTTTTTATTGAAACTTTGATTG
33759 TTGTCCGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 27 0.73
40 10 0.27
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (40 bp):
TGCTTTGGTTCCCTAAACTTTTTATTGAAACTTTGATTGC
Found at i:33934 original size:21 final size:19
Alignment explanation
Indices: 33910--33971 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 19
33900 AAAATGATTT
33910 ATTTTAATTTATGTTATTAAA
1 ATTTT-ATTTAT-TTATTAAA
33931 ATTTTATCTATATTTATT-AA
1 ATTTTAT-T-TATTTATTAAA
33951 ATTTTATTTATATTATTAAA
1 ATTTTATTTAT-TTATTAAA
33971 A
1 A
33972 ATATGTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 14 0.38
21 11 0.30
22 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTATTTATTTATTAAA
Found at i:36783 original size:2 final size:2
Alignment explanation
Indices: 36771--36800 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
36761 GTAATAATAC
*
36771 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
36801 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:36805 original size:2 final size:2
Alignment explanation
Indices: 36800--36840 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
36790 TCTCTCTCTC
36800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36841 TTCAATTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46462 original size:21 final size:21
Alignment explanation
Indices: 46438--46511 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
46428 TATCGCAAAT
46438 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
46459 TCGCATTGCGAT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
46479 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
46500 TCGCGTTACGAT
1 TCGCGTTGCGAT
46512 TTTCCTTTTC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:46494 original size:41 final size:41
Alignment explanation
Indices: 46437--46657 Score: 297
Period size: 41 Copynumber: 5.4 Consensus size: 41
46427 GTATCGCAAA
* *
46437 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCTAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
46478 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCTT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
46519 TTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCAT
* *
46560 TTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCAT
*
46601 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
46642 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
46658 GTACAGTGTC
Statistics
Matches: 165, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.01
41 161 0.98
42 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:46547 original size:21 final size:21
Alignment explanation
Indices: 46523--46593 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
46513 TTCCTTTTCG
46523 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
46544 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
46562 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
46585 CGTTGCGAT
1 CGTTGCGAT
46594 TTTCCATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.23
21 18 0.46
22 4 0.10
23 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:46736 original size:6 final size:6
Alignment explanation
Indices: 46725--46776 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
46715 AGACACGTAT
* *
46725 GACCAC GACCAC GACCAC GACCAC GAACAC GACCAC GATCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
46773 GACC
1 GACC
46777 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.35, C:0.46, G:0.17, T:0.02
Consensus pattern (6 bp):
GACCAC
Found at i:47298 original size:6 final size:6
Alignment explanation
Indices: 47287--47319 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
47277 TCTCGTCTCG
47287 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
47320 AATGGTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:47325 original size:6 final size:6
Alignment explanation
Indices: 47316--47376 Score: 122
Period size: 6 Copynumber: 10.2 Consensus size: 6
47306 GTCGTGGTCG
47316 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
47364 TGGTAA TGGTAA T
1 TGGTAA TGGTAA T
47377 ACGTGTCTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.34
Consensus pattern (6 bp):
TGGTAA
Found at i:47325 original size:18 final size:18
Alignment explanation
Indices: 47287--47325 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
47277 TCTCGTCTCG
**
47287 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTAAT
47305 GGTCGTGGTCGTGGTAAT
1 GGTCGTGGTCGTGGTAAT
47323 GGT
1 GGT
47326 AATGGTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.13, G:0.49, T:0.33
Consensus pattern (18 bp):
GGTCGTGGTCGTGGTAAT
Found at i:47487 original size:19 final size:19
Alignment explanation
Indices: 47463--47510 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
47453 ACTATAGACT
47463 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
47482 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
47501 ATCGCAACGA
1 ATCGCAACGA
47511 CACTGTAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:47527 original size:21 final size:21
Alignment explanation
Indices: 47501--47569 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
47491 AATTTGGAAA
47501 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
47522 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
*
47542 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTGTAGACT
47563 ATCGCAA
1 ATCGCAA
47570 TGCGAGATGG
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 18 0.50
22 3 0.08
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:47545 original size:41 final size:41
Alignment explanation
Indices: 47495--47784 Score: 246
Period size: 41 Copynumber: 6.9 Consensus size: 41
47485 GCAACGAATT
47495 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
* * *
47536 TGGAAAATCGCAACGACACTGTACACTATCGCAATGCGAGA
1 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
* * * **
47577 TGGAAAATCGCAATGACACTGTACACTATCGCAATGCGATT
1 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
** * * **
47618 TCCAACTATCGCAACG-CGAAATG--GAAAATCGCAACGATCGCAATGA
1 TGGAA-AATCGCAACGAC--ACTGTAGACTATCGCAACG--CG-AA--A
* * * ** * * *
47664 CTGTACACTATTGCAACGTGATTTTCA-TCTATCGCAACGCGAAA
1 -TGGA-A-AATCGCAACGACACTGT-AGACTATCGCAACGCGAAA
47708 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
47749 TGGAAAATCGCAACGACACTGTAGACTATCGCAACG
1 TGGAAAATCGCAACGACACTGTAGACTATCGCAACG
47785 ACACTGTAGA
Statistics
Matches: 200, Mismatches: 34, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
40 1 0.00
41 152 0.76
42 9 0.05
43 8 0.04
44 2 0.01
46 2 0.01
47 6 0.03
48 11 0.05
49 9 0.05
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
Found at i:47609 original size:21 final size:21
Alignment explanation
Indices: 47542--47612 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
47532 GAAATGGAAA
*
47542 ATCGCAACGACACTGTACACT
1 ATCGCAATGACACTGTACACT
* * *
47563 ATCGCAATG-CGAGATGGA-A-A
1 ATCGCAATGAC-A-CTGTACACT
47583 ATCGCAATGACACTGTACACT
1 ATCGCAATGACACTGTACACT
47604 ATCGCAATG
1 ATCGCAATG
47613 CGATTTCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 20 0.53
22 3 0.08
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAATGACACTGTACACT
Found at i:47626 original size:62 final size:62
Alignment explanation
Indices: 47560--47833 Score: 275
Period size: 62 Copynumber: 4.3 Consensus size: 62
47550 GACACTGTAC
* * * * *
47560 ACTATCGCAATGCGAGATGGAAAATCGCAATGACACTGTACACTATCGCAATGCGATTTCCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
* *
47622 ACTATCGCAACGCGAAATGGAAAATCGCAACGATCGCAATGACTGTACACTATTGCAACGTGATT
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGA---C----ACTGTACACTATCGCAACGCGATT
47687 TTCA
59 TTCA
* * ** **
47691 TCTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
* * ** *
47753 A-AATCGCAA--CGACACTGTAGACTATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGA-AATG--GAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
47815 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
47834 CAACGCGAAT
Statistics
Matches: 173, Mismatches: 26, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
59 3 0.02
60 3 0.02
61 7 0.04
62 89 0.51
63 7 0.04
64 3 0.02
65 4 0.02
66 1 0.01
69 56 0.32
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
Found at i:47696 original size:69 final size:70
Alignment explanation
Indices: 47583--47723 Score: 221
Period size: 69 Copynumber: 2.0 Consensus size: 70
47573 GAGATGGAAA
*
47583 ATCGCAATGACACTGTACACTATCGCAATGCGATTTCCAACTATCGCAACGCGAAATGGAAAATC
1 ATCGCAATGA-ACTGTACACTATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAATC
47648 GCAACG
65 GCAACG
* * * *
47654 ATCGCAATG-ACTGTACACTATTGCAACGTGATTTTCATCTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAATGAACTGTACACTATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAATCG
47718 CAACG
66 CAACG
47723 A
1 A
47724 CACTGTAGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 56 0.86
71 9 0.14
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (70 bp):
ATCGCAATGAACTGTACACTATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAATCG
CAACG
Found at i:47719 original size:20 final size:20
Alignment explanation
Indices: 47694--47763 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
47684 ATTTTCATCT
47694 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
47714 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
47735 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
47755 ATCGCAACG
1 ATCGCAACG
47764 ACACTGTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 18 0.46
21 9 0.23
22 3 0.08
23 3 0.08
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:47740 original size:21 final size:21
Alignment explanation
Indices: 47714--47805 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
47704 GAAATGGAAA
47714 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
47735 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
47755 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
47776 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
47797 ATCGCAACG
1 ATCGCAACG
47806 CGATTTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 42 0.70
22 3 0.05
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:47837 original size:21 final size:21
Alignment explanation
Indices: 47692--47833 Score: 77
Period size: 21 Copynumber: 6.9 Consensus size: 21
47682 TGATTTTCAT
*
47692 CTATCGCAACGCGAAATGGAA
1 CTATCGCAACGCGAAATGTAA
* *
47713 -AATCGCAA--CGACACTGTAGA
1 CTATCGCAACGCGA-AATGTA-A
*
47733 CTATCGCAACGCGAAATGGAA
1 CTATCGCAACGCGAAATGTAA
* *
47754 -AATCGCAA--CGACACTGTAGA
1 CTATCGCAACGCGA-AATGTA-A
*
47774 CTATCGCAA--CGACACTGTAGA
1 CTATCGCAACGCGA-AATGTA-A
* *
47795 CTATCGCAACGCG-ATTTTCAA
1 CTATCGCAACGCGAAATGT-AA
47816 CTATCGCAACGCGAAATG
1 CTATCGCAACGCGAAATG
47834 CAACGCGAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.06
19 8 0.08
20 16 0.17
21 53 0.56
22 7 0.07
23 5 0.05
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (21 bp):
CTATCGCAACGCGAAATGTAA
Found at i:48854 original size:30 final size:30
Alignment explanation
Indices: 48820--48879 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
48810 ATCATAAAAC
48820 TCAATACCTTTGAATTAGTGCATATTGTCT
1 TCAATACCTTTGAATTAGTGCATATTGTCT
48850 TCAATACCTTTGAATTAGTGCATATTGTCT
1 TCAATACCTTTGAATTAGTGCATATTGTCT
48880 AAACTAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (30 bp):
TCAATACCTTTGAATTAGTGCATATTGTCT
Found at i:52203 original size:53 final size:53
Alignment explanation
Indices: 52101--52411 Score: 299
Period size: 53 Copynumber: 5.9 Consensus size: 53
52091 TCTTCGAATG
* * * * * ***
52101 ACGGGTCCGCTCCCTCTTG-TTCATGGATTAAGGAGCTCAAACAATCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTACTT
* * * * * * *
52155 ATGAGTTTGCTCCCTATTGCTTCAGGGAGTAGAATTCGAATAATCTTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
** *
52208 ACGGGTTCGCTCCCTCTTATTTCAGGGAGTAGAACTCGAACAATATTCTACTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
* * * *
52261 ACGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAATAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
* * **
52314 ACGGGTTCGTTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
* * * *
52367 AC-AG-TC-ATCCCTCTTGCTTCA-GGAGTAAAACTCGAAAAATCTTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
52412 GGTGTGATTC
Statistics
Matches: 216, Mismatches: 40, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
49 22 0.10
50 14 0.06
51 2 0.01
52 1 0.00
53 154 0.71
54 15 0.07
55 8 0.04
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
Found at i:52282 original size:106 final size:103
Alignment explanation
Indices: 52163--52412 Score: 331
Period size: 106 Copynumber: 2.4 Consensus size: 103
52153 AAATGAGTTT
* * * *
52163 GCTCCCTATTGCTTCAGGGAGTAGAATTCGAATAATCTTCTGCTTACGGGTTCGCTCCCTCTTAT
1 GCTCCCTCTTGCTTCA-GGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTCGCTCCCTCTTAC
** *
52228 TTCAGGGAGTAGAACTCGAACAATATTCTACTTACGGGTTC
65 TTCAGGGAGTAGAACTCGAACAATATTCTACCGAC-AG-TC
* *
52269 GCTCCCTCTTGCTTCAAGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTCGTTCCCTCTTGC
1 GCTCCCTCTTGCTTC-AGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTCGCTCCCTCTTAC
* *
52334 TTCAGGGAGTAGAACTCGAACAATCTTCTGCCGACAGTC
65 TTCAGGGAGTAGAACTCGAACAATATTCTACCGACAGTC
* * *
52373 -ATCCCTCTTGCTTCAGGAGTAAAACTCGAAAAATCTTCTG
1 GCTCCCTCTTGCTTCAGGAGTAGAACTCGAATAATCTTCTG
52413 GTGTGATTCT
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
102 24 0.19
103 13 0.10
104 2 0.02
105 1 0.01
106 88 0.68
107 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (103 bp):
GCTCCCTCTTGCTTCAGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTCGCTCCCTCTTACT
TCAGGGAGTAGAACTCGAACAATATTCTACCGACAGTC
Found at i:53073 original size:22 final size:21
Alignment explanation
Indices: 53014--53075 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
53004 AGGATTTAAG
53014 CATCATGCTCGAAAGACTTAT
1 CATCATGCTCGAAAGACTTAT
* * *
53035 --TGATGGCCCGAAGGACTTCAT
1 CATCAT-GCTCGAAAGACTT-AT
53056 CATCATGCTCGAAAGACTTA
1 CATCATGCTCGAAAGACTTA
53076 CTGATGGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
19 3 0.10
20 11 0.35
21 3 0.10
22 11 0.35
23 3 0.10
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (21 bp):
CATCATGCTCGAAAGACTTAT
Found at i:53109 original size:164 final size:164
Alignment explanation
Indices: 52816--53204 Score: 570
Period size: 164 Copynumber: 2.4 Consensus size: 164
52806 ATCATCTCGT
* ** * * *
52816 TCGAAAGATTTACAAATGACCCGAAGGATTTCATCATCATGCTTGAATGACTTAATGATGGCTCG
1 TCGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTAATGATGGCCCG
*
52881 AAGGATTTCATCATCATGTCCGAAAGACTTACTGATGGGTTTGCTTCACTACTTTTCCGTGAAGG
66 AAGGACTTCATCATCATGTCCGAAAGACTTACTGATGGGTTTGCTTCACTACTTTTCCGTGAAGG
52946 CTTACAAATTACCCTAAGA-ATTTAATCATCATGC
131 CTTACAAATTACCC-AAGAGATTTAATCATCATGC
* * * * *
52980 TCTAAAGACTTACTGATGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCG
1 TCGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTAATGATGGCCCG
*
53045 AAGGACTTCATCATCATG-CTCGAAAGACTTACTGATGGAG-TTGCTTCACTACTCTTT-GGTGA
66 AAGGACTTCATCATCATGTC-CGAAAGACTTACTGATGG-GTTTGCTTCACTACT-TTTCCGTGA
*
53107 AGGCTTACAAATTACCCGAGAGATTTAATCATCATGC
128 AGGCTTACAAATTACCCAAGAGATTTAATCATCATGC
* *
53144 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
1 TCGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTAATGATGG
53205 AGTTGTTTCA
Statistics
Matches: 201, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
163 4 0.02
164 193 0.96
165 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (164 bp):
TCGAAAGACTTACTGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTAATGATGGCCCG
AAGGACTTCATCATCATGTCCGAAAGACTTACTGATGGGTTTGCTTCACTACTTTTCCGTGAAGG
CTTACAAATTACCCAAGAGATTTAATCATCATGC
Found at i:53114 original size:122 final size:121
Alignment explanation
Indices: 53000--53417 Score: 701
Period size: 122 Copynumber: 3.4 Consensus size: 121
52990 TACTGATGAC
* *
53000 CCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTCATCATCATGCT
1 CCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCT
53065 CGAAAGACTTACTGATGGAGTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTA
66 CGAAAGACTTACTGATGGAGTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTA
** *
53121 CCCGAGAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
1 CCTAAG-GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
*
53186 TCGAAAGACTTACTGATGGAGTTGTTTCACTACTCTTTGGTGAAGGCTTACAAATTA
65 TCGAAAGACTTACTGATGGAGTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTA
* * * *
53243 TCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAAGGATTTCATCATCATGCT
1 CCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCT
**
53308 CGAAAGACTTACTGATGGAGTTGCTTCACTACTCTTCAGTGAAGGCTTACAAATTA
66 CGAAAGACTTACTGATGGAGTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTA
*
53364 CCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTT
1 CCT-AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
53418 AAATTGATTA
Statistics
Matches: 277, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
121 116 0.42
122 161 0.58
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (121 bp):
CCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCT
CGAAAGACTTACTGATGGAGTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTA
Found at i:53325 original size:42 final size:42
Alignment explanation
Indices: 52816--53325 Score: 258
Period size: 42 Copynumber: 12.5 Consensus size: 42
52806 ATCATCTCGT
* ** *
52816 TCGAAAGATTTACAAATGACCCGAAGGATTTCATCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
* * * *
52858 TTGAATGACTTAATGATGGCTCGAAGGATTTCATCATCATG-
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
*** * **
52899 TCCGAAAGACTTACTGATGG---GTTTG-CTTCA-C-T-ACTTT
1 T-CGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCA-TGC
* * ** ** * * *
52936 TCCGTGAAGGCTTACAAATTACCCTAAGAATTTAATCATCATGC
1 T-CG-AAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
* * * * *
52980 TCTAAAGACTTACTGATGACCCTAAGGATTTAAGCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
* *
53022 TCGAAAGACTTATTGATGGCCCGAAGGACTTCATCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
* ** * * *
53064 TCGAAAGACTTACTGATGG--AG-TTG-CTTCA-CTACTCTTTGG
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATC-A-TC-ATGC
* ** ** *
53104 T-G-AAGGCTTACAAATTACCCG-AGAGATTTAATCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAG-GATTTCATCATCATGC
53144 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
* ** * *
53186 TCGAAAGACTTACTGATGG--AG-TTG-TTTCA-CTACTCTTTGG
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATC-A-TC-ATGC
* ** *** *
53226 T-G-AAGGCTTACAAAT-TATCGAAGGATTTAATCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
*
53265 TCGAAAGACTTACTGATGGTCCGAAGGATTTCATCATCATGC
1 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
53307 TCGAAAGACTTACTGATGG
1 TCGAAAGACTTACTGATGG
53326 AGTTGCTTCA
Statistics
Matches: 343, Mismatches: 92, Indels: 66
0.68 0.18 0.13
Matches are distributed among these distances:
35 1 0.00
36 2 0.01
37 7 0.02
38 46 0.13
39 14 0.04
40 16 0.05
41 20 0.06
42 228 0.66
43 5 0.01
44 3 0.01
45 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
Found at i:53414 original size:42 final size:42
Alignment explanation
Indices: 52956--53419 Score: 238
Period size: 42 Copynumber: 11.4 Consensus size: 42
52946 CTTACAAATT
* * *
52956 ACCCTAAGAATTTAATCATCATGCTCTAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * *
52998 ACCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * *
53040 GCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * * * * * ** *
53082 ----G-AGTTGCTTCACT-ACTCTTTGGT-G-AAGGCTTACAAATT
1 ACCCGAAG--GATTTAATCA-TC-ATGCTCGAAAGACTTACTGATG
53120 ACCCG-AGAGATTTAATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAG-GATTTAATCATCATGCTCGAAAGACTTACTGATG
* *
53162 GCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
* * * * ** *
53204 ----G-AGTTG-TTTCA-CTACTCTTTGGT-G-AAGGCTTACAAATT
1 ACCCGAAG--GATTTAATC-A-TC-ATGCTCGAAAGACTTACTGATG
*
53242 A-TCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
** *
53283 GTCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-G
*** **** * * * * ** *
53326 AGTTGCTTCA-CTACTCTTCA-G-T-G-AAGGCTTACAAATT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
*
53363 ACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
*
53405 ACCCGAAGGACTTAA
1 ACCCGAAGGATTTAA
53420 ATTGATTACT
Statistics
Matches: 310, Mismatches: 80, Indels: 64
0.68 0.18 0.14
Matches are distributed among these distances:
37 9 0.03
38 46 0.15
39 15 0.05
40 15 0.05
41 26 0.08
42 194 0.63
43 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
Found at i:60051 original size:7 final size:8
Alignment explanation
Indices: 60036--60070 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
60026 AAATAGACAT
60036 AGAAAAAA
1 AGAAAAAA
60044 AGAAAAAAAA
1 AG--AAAAAA
60054 AGAAAAAA
1 AGAAAAAA
60062 AGAAAAAA
1 AGAAAAAA
60070 A
1 A
60071 TGGGTTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:60053 original size:10 final size:10
Alignment explanation
Indices: 60038--60070 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
60028 ATAGACATAG
60038 AAAAAAAGAA
1 AAAAAAAGAA
60048 AAAAAAAG--
1 AAAAAAAGAA
60056 AAAAAAAGAA
1 AAAAAAAGAA
60066 AAAAA
1 AAAAA
60071 TGGGTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:60057 original size:18 final size:18
Alignment explanation
Indices: 60036--60070 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
60026 AAATAGACAT
60036 AGAAAAAAAGAAAAAAAA
1 AGAAAAAAAGAAAAAAAA
60054 AGAAAAAAAGAAAAAAA
1 AGAAAAAAAGAAAAAAA
60071 TGGGTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAGAAAAAAAA
Found at i:64283 original size:14 final size:13
Alignment explanation
Indices: 64251--64284 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
64241 ATTCAGTGAC
64251 TGAAAAATCAATT
1 TGAAAAATCAATT
64264 TGAAAAATCAATT
1 TGAAAAATCAATT
64277 TGAAAAAT
1 TGAAAAAT
64285 TTTAGTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (13 bp):
TGAAAAATCAATT
Found at i:70613 original size:2 final size:2
Alignment explanation
Indices: 70606--70631 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
70596 TAAGGTAGTG
70606 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
70632 CTTTTGTACA
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:74057 original size:257 final size:257
Alignment explanation
Indices: 73601--74114 Score: 1028
Period size: 257 Copynumber: 2.0 Consensus size: 257
73591 TTTATGTGTT
73601 GAGAAGAATACATAACAGGAAAAGGAGATGTATACCTAAAAGGCGGCTTACAAATGGTTTAACAT
1 GAGAAGAATACATAACAGGAAAAGGAGATGTATACCTAAAAGGCGGCTTACAAATGGTTTAACAT
73666 CAAACACTTCAAACTCATCCATGTGCTCTCCCGTTCCTATAAATATGACAGGACTCTTAGTTGCA
66 CAAACACTTCAAACTCATCCATGTGCTCTCCCGTTCCTATAAATATGACAGGACTCTTAGTTGCA
73731 GCAACCCTGGTAGAAGCCACAGAAGAGAAAAACCAAGCAAGCATATCATGAGAACTCAACCTAAT
131 GCAACCCTGGTAGAAGCCACAGAAGAGAAAAACCAAGCAAGCATATCATGAGAACTCAACCTAAT
73796 GATAGAAATGCAAATACTATCTTGAGTAGACATACAAAATAAAGGCAAGAACAATCATTACA
196 GATAGAAATGCAAATACTATCTTGAGTAGACATACAAAATAAAGGCAAGAACAATCATTACA
73858 GAGAAGAATACATAACAGGAAAAGGAGATGTATACCTAAAAGGCGGCTTACAAATGGTTTAACAT
1 GAGAAGAATACATAACAGGAAAAGGAGATGTATACCTAAAAGGCGGCTTACAAATGGTTTAACAT
73923 CAAACACTTCAAACTCATCCATGTGCTCTCCCGTTCCTATAAATATGACAGGACTCTTAGTTGCA
66 CAAACACTTCAAACTCATCCATGTGCTCTCCCGTTCCTATAAATATGACAGGACTCTTAGTTGCA
73988 GCAACCCTGGTAGAAGCCACAGAAGAGAAAAACCAAGCAAGCATATCATGAGAACTCAACCTAAT
131 GCAACCCTGGTAGAAGCCACAGAAGAGAAAAACCAAGCAAGCATATCATGAGAACTCAACCTAAT
74053 GATAGAAATGCAAATACTATCTTGAGTAGACATACAAAATAAAGGCAAGAACAATCATTACA
196 GATAGAAATGCAAATACTATCTTGAGTAGACATACAAAATAAAGGCAAGAACAATCATTACA
74115 CTTACGCACT
Statistics
Matches: 257, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
257 257 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (257 bp):
GAGAAGAATACATAACAGGAAAAGGAGATGTATACCTAAAAGGCGGCTTACAAATGGTTTAACAT
CAAACACTTCAAACTCATCCATGTGCTCTCCCGTTCCTATAAATATGACAGGACTCTTAGTTGCA
GCAACCCTGGTAGAAGCCACAGAAGAGAAAAACCAAGCAAGCATATCATGAGAACTCAACCTAAT
GATAGAAATGCAAATACTATCTTGAGTAGACATACAAAATAAAGGCAAGAACAATCATTACA
Found at i:78019 original size:59 final size:58
Alignment explanation
Indices: 77918--78035 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 58
77908 GATCATTCCG
* * *
77918 TAACTTTTAATAGTCGAGAAACTCAACAAAATAACTCTTTATAGTTGAGAGATCATTTA
1 TAACTTTTAATAGTCGAAAAACTCAACAAAATAACTCTTTATAG-TAAGAGACCATTTA
* *
77977 TAACTTTTAATAG-CTGAAAAACTCAATAAATTAA-TAAC-TTATAGTAAGAGACCATTTA
1 TAACTTTTAATAGTC-GAAAAACTCAACAAAATAACT--CTTTATAGTAAGAGACCATTTA
78035 T
1 T
78036 GTACTTTTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
58 15 0.29
59 35 0.69
60 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (58 bp):
TAACTTTTAATAGTCGAAAAACTCAACAAAATAACTCTTTATAGTAAGAGACCATTTA
Found at i:90350 original size:2 final size:2
Alignment explanation
Indices: 90343--90379 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
90333 TACAGCCGCC
*
90343 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90380 TTCTAAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:90711 original size:13 final size:13
Alignment explanation
Indices: 90693--90717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90683 TACATATTCG
90693 CATATGAAGACTA
1 CATATGAAGACTA
90706 CATATGAAGACT
1 CATATGAAGACT
90718 GTTCAACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Done.