Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004665.1 Hibiscus syriacus cultivar Beakdansim tig00010463_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: 54708
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Found at i:2929 original size:26 final size:27
Alignment explanation
Indices: 2878--2939 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
2868 TAACAGGAAT
*
2878 CATGGAATTGATGAGCCATGACATAAC
1 CATGGTATTGATGAGCCATGACATAAC
2905 CATGGTATTGATGA-CCATGACATAAC
1 CATGGTATTGATGAGCCATGACATAAC
2931 CATGGTATT
1 CATGGTATT
2940 CTCACTTAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (27 bp):
CATGGTATTGATGAGCCATGACATAAC
Found at i:5185 original size:15 final size:16
Alignment explanation
Indices: 5165--5195 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5155 AATTATACAA
5165 AAATTATA-AAAAATT
1 AAATTATACAAAAATT
5180 AAATTATACAAAAATT
1 AAATTATACAAAAATT
5196 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATACAAAAATT
Found at i:5490 original size:42 final size:41
Alignment explanation
Indices: 5367--5491 Score: 114
Period size: 42 Copynumber: 3.0 Consensus size: 41
5357 GATTTCTATG
* * *
5367 TATAGTATATTATATTTATTT-CATATATTTATAATAACACAT
1 TATAGTATATTATA-TTATTTAAATATATTT-TAATAATATAT
* *
5409 TATATTATATTATA-TATTTTAAATATAGTTTT-TTAAATATAT
1 TATAGTATATTATATTA-TTTAAATATA-TTTTAAT-AATATAT
5451 ATATA-TATATTATATTATTTGAAATATATTTTAATAATATA
1 -TATAGTATATTATATTATTT-AAATATATTTTAATAATATA
5492 CAACAATATA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
40 2 0.03
41 4 0.06
42 46 0.67
43 17 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (41 bp):
TATAGTATATTATATTATTTAAATATATTTTAATAATATAT
Found at i:6383 original size:64 final size:64
Alignment explanation
Indices: 6310--6435 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
6300 TTTCGAATGT
** * *
6310 ATTTTGTGTACTGATGCACAAG-TCATGCATCGATGCACTCTTGAATATTTTGAAACATCGAAGC
1 ATTTTGTGTACCAATGCA-AAGACCATGCATCGATGCACTCATGAATATTTTGAAACATCGAAGC
* * **
6374 ATTTTGTGTACCAATGCATAGACCGTGCATCGATGCACTCATGGCTATTTTGAAACATCGAA
1 ATTTTGTGTACCAATGCAAAGACCATGCATCGATGCACTCATGAATATTTTGAAACATCGAA
6436 CGTAATTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 2 0.04
64 51 0.96
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (64 bp):
ATTTTGTGTACCAATGCAAAGACCATGCATCGATGCACTCATGAATATTTTGAAACATCGAAGC
Found at i:6466 original size:19 final size:19
Alignment explanation
Indices: 6442--6495 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
6432 CGAACGTAAT
6442 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
6461 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
*
6480 TAGTGTATCGATGCAC
1 TAGTGTACCGATGCAC
6496 TAAGTCTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (19 bp):
TAGTGTACCGATGCACCCC
Found at i:8734 original size:16 final size:16
Alignment explanation
Indices: 8709--8739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8699 AGAGGGTTGC
*
8709 CAAAGCTAAAATTTGA
1 CAAAGATAAAATTTGA
8725 CAAAGATAAAATTTG
1 CAAAGATAAAATTTG
8740 TGATACATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (16 bp):
CAAAGATAAAATTTGA
Found at i:11586 original size:23 final size:23
Alignment explanation
Indices: 11552--11650 Score: 77
Period size: 23 Copynumber: 4.5 Consensus size: 23
11542 CTAAACAGTA
11552 CATCGATGCATCTCTTGAATGTG
1 CATCGATGCATCTCTTGAATGTG
* *
11575 CATCGATACA--TCATGAA-GATG
1 CATCGATGCATCTCTTGAATG-TG
*
11596 CACCGATGCAT-TCCTTGAATGTG
1 CATCGATGCATCT-CTTGAATGTG
* *
11619 CATAGATGCA-CTC-TG-TTGTG
1 CATCGATGCATCTCTTGAATGTG
*
11639 CATCGATACATC
1 CATCGATGCATC
11651 CGTTGGGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
20 13 0.22
21 19 0.32
22 2 0.03
23 25 0.42
24 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (23 bp):
CATCGATGCATCTCTTGAATGTG
Found at i:14211 original size:65 final size:65
Alignment explanation
Indices: 14123--14282 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 65
14113 GATGCACACC
*
14123 CATTCAAATGCATTTTTTTGTACCGATGCATAAG-CCATGCATCGATGCACTCT-TGAATATTTT
1 CATT-AAATGCA-TTTTGTGTACCGATGCA-AAGACCATGCATCGATGCACT-TATGAATATTTT
14186 GAAA
62 GAAA
* **
14190 CATTAAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTATGGCTATTTTGAAA
1 CATTAAATGCATTTTGTGTACCGATGCAAAGACCATGCATCGATGCACTTATGAATATTTTGAAA
** * * *
14255 CATCGAATGTAATTAGTGTACCGATGCA
1 CATTAAATGCATTTTGTGTACCGATGCA
14283 CCCCTAGTGT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 3 0.04
65 68 0.83
66 7 0.09
67 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (65 bp):
CATTAAATGCATTTTGTGTACCGATGCAAAGACCATGCATCGATGCACTTATGAATATTTTGAAA
Found at i:14297 original size:65 final size:64
Alignment explanation
Indices: 14141--14305 Score: 181
Period size: 65 Copynumber: 2.5 Consensus size: 64
14131 TGCATTTTTT
* * * *
14141 TGTACCGATGCATAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATTAAATGCATTTTG
1 TGTACCGATGCACAA-CCATGCATCGATGCACTCTTGAATATTTTGAAACATCAAATGCAATTAG
** * *
14206 TGTACCGATGCACAGACCATGCATCGATGCACT-TATGGCTATTTTGAAACATCGAATGTAATTA
1 TGTACCGATGCACA-ACCATGCATCGATGCACTCT-TGAATATTTTGAAACATCAAATGCAATTA
14270 G
64 G
* *
14271 TGTACCGATGCAC-CCCTAGTGTATCGATGCACTCT
1 TGTACCGATGCACAACC-A-TGCATCGATGCACTCT
14306 GTTAGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
63 2 0.02
64 2 0.02
65 79 0.93
66 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (64 bp):
TGTACCGATGCACAACCATGCATCGATGCACTCTTGAATATTTTGAAACATCAAATGCAATTAG
Found at i:16721 original size:32 final size:32
Alignment explanation
Indices: 16685--16760 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
16675 CCAACCTAAA
* * *
16685 GGAGTGCCTTAGGGCCTTAGCGCCTACCCAAT
1 GGAGTACCTTAGGGCCTAAGAGCCTACCCAAT
* *
16717 GGAGTACTTTGGGGCCTAAGAGCCTACCCAA-
1 GGAGTACCTTAGGGCCTAAGAGCCTACCCAAT
16748 GG-GTTACCTTAGG
1 GGAG-TACCTTAGG
16761 TCCATAAGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 1 0.03
31 9 0.25
32 26 0.72
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.22
Consensus pattern (32 bp):
GGAGTACCTTAGGGCCTAAGAGCCTACCCAAT
Found at i:19111 original size:51 final size:51
Alignment explanation
Indices: 19056--19193 Score: 188
Period size: 51 Copynumber: 2.7 Consensus size: 51
19046 TAGTTGATTT
* * *
19056 AATCATAAATAAACAGTGACCAAAATGCATAAATTGAAAGAACA-TGAGCCA
1 AATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAGTG-GCCA
* *
19107 AATCAGAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAGTGGCCA
1 AATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAGTGGCCA
* * *
19158 AATCAGAAATAACCATTGACTAAGATGCATAAATTA
1 AATCAGAAATAAACAGTGACTAAAATGCATAAATTA
19194 TCAAACACCA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
51 74 0.97
52 2 0.03
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.20
Consensus pattern (51 bp):
AATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAGTGGCCA
Found at i:20612 original size:38 final size:35
Alignment explanation
Indices: 20570--20671 Score: 89
Period size: 36 Copynumber: 2.8 Consensus size: 35
20560 TAAAAAGAGA
*
20570 AGATATAACAAAAAATAAAAGAAGAGAAAAAATAATAG
1 AGATAAAACAAAAAA-AAAA-AAGA-AAAAAATAATAG
* * *
20608 AGATAAAATAAAAAAAAAAAATAAAAAAATAAAAAG
1 AGATAAAACAAAAAAAAAAAAGAAAAAAAT-AATAG
* **
20644 AGAGAAAA-AAGAAAGCAAAAAGAAAAAA
1 AGATAAAACAA-AAAAAAAAAAGAAAAAA
20672 GAAGAAAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 9 0.17
36 28 0.52
37 4 0.07
38 13 0.24
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (35 bp):
AGATAAAACAAAAAAAAAAAAGAAAAAAATAATAG
Found at i:20615 original size:16 final size:17
Alignment explanation
Indices: 20579--20653 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
20569 AAGATATAAC
20579 AAAAAATAAAAGAAGAG
1 AAAAAATAAAAGAAGAG
* *
20596 AAAAAATAATAG-AGAT
1 AAAAAATAAAAGAAGAG
* * * *
20612 AAAATAAAAAAAAAAAATA
1 AAAA-AATAAAAGAAGA-G
20631 AAAAAATAAAA-AGAGAG
1 AAAAAATAAAAGA-AGAG
20648 AAAAAA
1 AAAAAA
20654 GAAAGCAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
16 7 0.16
17 23 0.52
18 10 0.23
19 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAAAATAAAAGAAGAG
Found at i:20630 original size:13 final size:14
Alignment explanation
Indices: 20612--20642 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
20602 TAATAGAGAT
20612 AAAATAAAAAAA-A
1 AAAATAAAAAAATA
20625 AAAATAAAAAAATA
1 AAAATAAAAAAATA
20639 AAAA
1 AAAA
20643 GAGAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:20634 original size:14 final size:15
Alignment explanation
Indices: 20579--20657 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 15
20569 AAGATATAAC
20579 AAAAAATAAAAGAAGAG
1 AAAAAATAAAA-AA-AG
* *
20596 AAAAAAT-AATAGAG
1 AAAAAATAAAAAAAG
*
20610 ATAAAAT-AAAAAA-
1 AAAAAATAAAAAAAG
*
20623 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAG
*
20638 AAAAAGAGAGAAAAAAG
1 AAAAA-ATA-AAAAAAG
20655 AAA
1 AAA
20658 GCAAAAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 6 0.12
14 18 0.36
15 6 0.12
16 4 0.08
17 16 0.32
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (15 bp):
AAAAAATAAAAAAAG
Found at i:20652 original size:11 final size:11
Alignment explanation
Indices: 20638--20683 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
20628 ATAAAAAAAT
*
20638 AAAAAGAGAGA
1 AAAAAGAAAGA
*
20649 AAAAAGAAAGC
1 AAAAAGAAAGA
20660 AAAAAGAAA-A
1 AAAAAGAAAGA
*
20670 AAGAAGAAAGA
1 AAAAAGAAAGA
20681 AAA
1 AAA
20684 CAGGTAAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:20652 original size:29 final size:27
Alignment explanation
Indices: 20619--20683 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
20609 GATAAAATAA
*
20619 AAAAAAAAAATAAAAAAATAAAAAGAGAG
1 AAAAAAAAAACAAAAAAA-AAAAAGA-AG
* *
20648 AAAAAAGAAAGCAAAAAGAAAAAAGAAG
1 AAAAAA-AAAACAAAAAAAAAAAAGAAG
*
20676 AAAGAAAA
1 AAAAAAAA
20684 CAGGTAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 7 0.23
29 13 0.42
30 9 0.29
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAACAAAAAAAAAAAAGAAG
Found at i:20656 original size:7 final size:7
Alignment explanation
Indices: 20612--20683 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
20602 TAATAGAGAT
*
20612 AAAATAA
1 AAAAGAA
20619 AAAA-AA
1 AAAAGAA
*
20625 AAAATAA
1 AAAAGAA
20632 AAAA-ATA
1 AAAAGA-A
20639 AAAAGAGA
1 AAAAGA-A
20647 GAAAA-AA
1 -AAAAGAA
* *
20654 GAAAGCA
1 AAAAGAA
20661 AAAAGAA
1 AAAAGAA
20668 AAAAGAA
1 AAAAGAA
*
20675 GAAAGAA
1 AAAAGAA
20682 AA
1 AA
20684 CAGGTAAAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
6 10 0.19
7 36 0.68
8 3 0.06
9 4 0.08
ACGTcount: A:0.82, C:0.01, G:0.12, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:20676 original size:21 final size:21
Alignment explanation
Indices: 20624--20683 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
20614 AATAAAAAAA
* *
20624 AAAAATAAAAAAATAAAAAGAG
1 AAAAA-AAAGAAAGAAAAAGAG
*
20646 AGAAAAAAGAAAGCAAAAAGA-
1 AAAAAAAAGAAAG-AAAAAGAG
*
20667 AAAAAGAAGAAAGAAAA
1 AAAAAAAAGAAAGAAAA
20684 CAGGTAAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.12
21 17 0.53
22 11 0.34
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAAAAAAGAAAGAAAAAGAG
Found at i:22726 original size:55 final size:55
Alignment explanation
Indices: 22626--23695 Score: 549
Period size: 55 Copynumber: 19.1 Consensus size: 55
22616 CGTGATTTTT
* * *
22626 AGAAACTAAGCCTAATTTTCAG--GTTT-TTTAT-ATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * *
22677 AGAAACTAAGTCTGATTTTTAGATGTTTCTTGATGATTTTTAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* *
22732 AGAAACTAAGTGTGATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * * ** * * *
22787 ATAAACCAAGTCTGGTTTTCAGATTTTTCTTGACT-ATCTTCAAATGAG-TTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TGATTTTTAAATGAGTTTTTAA
* * * * *
22841 AGAAA-TCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTTTCAA
1 AGAAACT-AAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * * * * * *
22896 ATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* *
22951 AGAAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* ** ** * * *
23006 AGAAACTAAGTCTTCAAATGAGTTTCA-AAGAAATCGAGTCTGATTTTTAGA--AGTTTCTTGA
1 AGAAACTAAG---TC---TGATTTTCAGAAG-TTTCTTG-ATGATTTTTAAATGAGTTT-TTAA
* *** * * ** * * * * *
23067 TGATTTTTAA-AC-GAGCTTTCA-AA-TAAACTAAGTATAATTTTCAGA--AGTTTCTTGA
1 AGA-AACTAAGTCTGA-TTTTCAGAAGT-TTCT-TG-ATGATTTTTAAATGAGTTT-TTAA
** *** * *** * *
23122 TTATTTTTAA-T-TGAGCTTTCA-AAGAAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTT
1 AGA-AACTAAGTCTGA-TTTTCAGAAGTTTCT-TG-ATGATTTT--TAA-----ATGA-G-TTTT
23184 TAAATGAGTTTTTAA
53 T------------AA
* * * *
23199 AGAAACTAAGTCTGCTTTTCAGAAGTTTCTTGACGATTTTCAAATGAATTTTTAAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTT-AA
* * ** * *
23255 AGAATCTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACAAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * * * * * *
23310 AGAAACTAAGTCTGATTTTTAAAAGTTTTTTGATGTTTTTTAAATAAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
*
23365 AGAAACCAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * *
23420 AGAAACTAAGTATGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * * **
23475 AGAAACTAAGTTTCATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGCATTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * * **
23530 AGAAACTAAGTCTGATTTTCAGAGGATTCTTGA-CATGATT--A--A-TTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
* * * * * * *
23579 AGAAGCTAAGCCTGATTTTCA-AGGGTTTCTTAATTAGTATTTTCAATGA-ATTTTAA
1 AGAAACTAAGTCTGATTTTCAGA-AGTTTCTTGATGA-T-TTTTAAATGAGTTTTTAA
* * * * * *
23635 AGAAGCTAAGTATGATTTTTAGAGGTTTCTAGATGATTATTTCCAAA-GAATTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT-TTT--AAATGAGTTTTTAA
23692 AGAA
1 AGAA
23696 GTTAAGCCTA
Statistics
Matches: 807, Mismatches: 149, Indels: 120
0.75 0.14 0.11
Matches are distributed among these distances:
48 1 0.00
49 32 0.04
50 2 0.00
51 20 0.02
52 3 0.00
53 5 0.01
54 54 0.07
55 510 0.63
56 84 0.10
57 14 0.02
58 2 0.00
60 8 0.01
61 16 0.02
62 13 0.02
64 1 0.00
65 3 0.00
66 3 0.00
67 5 0.01
69 3 0.00
74 2 0.00
76 10 0.01
77 9 0.01
78 7 0.01
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
Found at i:22982 original size:164 final size:165
Alignment explanation
Indices: 22663--23018 Score: 475
Period size: 164 Copynumber: 2.2 Consensus size: 165
22653 TTATATTTTT
* * *
22663 AAATGAGTTTTTAAAGAAACTAAGTCTGATTTTTAGATGTTTCTTGATGATTTTTAAATGAGTTT
1 AAATGAGTTTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTT
* * * * * *
22728 TCAAAGAAACTAAGTGTGATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAATAAAC
66 TCAAAGAAACTAAGTATAATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAAC
* * **
22793 CAAGTCTGGTTTTCAGATTTTTCTTGACT-ATCTTC
131 CAAGTATGATTTTCAGAAGTTTCTTGA-TGATCTTC
* *
22828 AAATGAG-TTTCAAAGAAA-TCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCT
1 AAATGAGTTTTTAAAGAAACT-AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCT
* * *
22891 TTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAGAAA
65 TTCAAAGAAACTAAGTATAATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAA
* * * *
22956 CTAAGTATGATTTTCATAAGTTTCTTGATGATTTTT
130 CCAAGTATGATTTTCAGAAGTTTCTTGATGATCTTC
22992 AAATGAGTTTTTAAAGAAACTAAGTCT
1 AAATGAGTTTTTAAAGAAACTAAGTCT
23019 TCAAATGAGT
Statistics
Matches: 163, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
163 2 0.01
164 138 0.85
165 22 0.13
166 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (165 bp):
AAATGAGTTTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTT
TCAAAGAAACTAAGTATAATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAAC
CAAGTATGATTTTCAGAAGTTTCTTGATGATCTTC
Found at i:23054 original size:193 final size:193
Alignment explanation
Indices: 22823--23211 Score: 778
Period size: 193 Copynumber: 2.0 Consensus size: 193
22813 TTCTTGACTA
22823 TCTTCAAATGAGTTTCAAAGAAATCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
1 TCTTCAAATGAGTTTCAAAGAAATCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
22888 GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAG
66 GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAG
22953 AAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
131 AAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
23016 TCTTCAAATGAGTTTCAAAGAAATCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
1 TCTTCAAATGAGTTTCAAAGAAATCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
23081 GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAG
66 GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAG
23146 AAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
131 AAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
23209 TCT
1 TCT
23212 GCTTTTCAGA
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 196 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (193 bp):
TCTTCAAATGAGTTTCAAAGAAATCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAG
AAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
Found at i:23095 original size:83 final size:84
Alignment explanation
Indices: 22940--23099 Score: 225
Period size: 83 Copynumber: 1.9 Consensus size: 84
22930 TATTTTTAAT
* * * *
22940 TGAGCTTTCAAAGAAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTA
1 TGAGCTTTCAAAGAAACTAAGTATGATTTTCAGAAGTTTCTTGATGATTTTTAAACGAGCTTTCA
23005 AAGAAACTAAGTCTTCAAA
66 AAGAAACTAAGTCTTCAAA
* * *
23024 TGAG-TTTCAAAGAAA-TCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTTTC
1 TGAGCTTTCAAAGAAACT-AAGTATGATTTTCAGAAGTTTCTTGATGATTTTTAAACGAGCTTTC
*
23087 AAATAAACTAAGT
65 AAAGAAACTAAGT
23100 ATAATTTTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 62 0.93
84 4 0.06
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (84 bp):
TGAGCTTTCAAAGAAACTAAGTATGATTTTCAGAAGTTTCTTGATGATTTTTAAACGAGCTTTCA
AAGAAACTAAGTCTTCAAA
Found at i:23170 original size:110 final size:110
Alignment explanation
Indices: 23018--23562 Score: 700
Period size: 110 Copynumber: 5.0 Consensus size: 110
23008 AAACTAAGTC
* * *
23018 TTCAAATGAG-TTTCAAAGAAA-TCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
1 TTCAAATGAGCTTTCAAAGAAACT-AAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA
* * * *
23081 GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATT
65 GCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * *
23127 TTTAATTGAGCTTTCAAAGAAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAG
1 TTCAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG
* * * *
23192 TTTTTAAAGAAACTAAGTCTGCTTTTCAGAAGTTTCTTGACGATT
66 CTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
** * * * **
23237 TTCAAATGAATTTTTAAAAGAATCTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACAA
1 TTCAAATG-AGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA
* * * *
23302 GCTTTCAAAGAAACTAAGTCTGATTTTTAAAAGTTTTTTGATGTTT
65 GCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * *
23348 TTTAAATAAGCTTTCAAAGAAACCAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG
1 TTCAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG
* * *
23413 TTTTTAAAGAAACTAAGTATGATTTTCAGAAGTTTCTTGATGATT
66 CTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * *
23458 TTCAAATGAGTTTTCAAAGAAACTAAGTTTCATTTTCAGAAGTTTCTTGATAATTTTTAAATGAG
1 TTCAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG
* *
23523 CATTT-AAAGAAACTAAGTCTGATTTTCAGAGGATTCTTGA
66 C-TTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
23563 CATGATTAAT
Statistics
Matches: 370, Mismatches: 62, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
109 8 0.02
110 267 0.72
111 95 0.26
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (110 bp):
TTCAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG
CTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
Found at i:23441 original size:221 final size:220
Alignment explanation
Indices: 23018--23550 Score: 768
Period size: 221 Copynumber: 2.4 Consensus size: 220
23008 AAACTAAGTC
* * * *
23018 TTCAAATGAG-TTTCAAAGAAA-TCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGA
1 TTCAAATGAGTTTTAAAAGAAACT-AAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACGA
* * * * * *
23081 GCTTTCAAATAAACTAAGTATAATTTTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAAAG
65 GCTTTCAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGATTATTTTTAAATAAGCTTTCAAAG
* * *
23146 AAACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTC
130 AAACCAAGTATGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTA
*
23211 TGCTTTTCAGAAGTTTCTTGACGATT
195 TGATTTTCAGAAGTTTCTTGACGATT
* * *
23237 TTCAAATGAATTTTTAAAAGAATCTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACAA
1 TTCAAATG-AGTTTTAAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACGA
* *
23302 GCTTTCAAAGAAACTAAGTCTGATTTTTAAAAGTTTTTTGATGT-TTTTTAAATAAGCTTTCAAA
65 GCTTTCAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGAT-TATTTTTAAATAAGCTTTCAAA
*
23366 GAAACCAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGT
129 GAAACCAAGTATGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGT
*
23431 ATGATTTTCAGAAGTTTCTTGATGATT
194 ATGATTTTCAGAAGTTTCTTGACGATT
* * * * *
23458 TTCAAATGAGTTTTCAAAGAAACTAAGTTTCATTTTCAGAAGTTTCTTGATAATTTTTAAATGAG
1 TTCAAATGAGTTTTAAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACGAG
23523 CATTT-AAAGAAACTAAGTCTGATTTTCA
66 C-TTTCAAAGAAACTAAGTCTGATTTTCA
23551 GAGGATTCTT
Statistics
Matches: 279, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
219 8 0.03
220 73 0.26
221 196 0.70
222 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (220 bp):
TTCAAATGAGTTTTAAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAACGAG
CTTTCAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGATTATTTTTAAATAAGCTTTCAAAGA
AACCAAGTATGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTAT
GATTTTCAGAAGTTTCTTGACGATT
Found at i:23713 original size:57 final size:57
Alignment explanation
Indices: 23570--23728 Score: 171
Period size: 56 Copynumber: 2.8 Consensus size: 57
23560 TGACATGATT
* * * * *
23570 AATTTTTAAAGAAGCTAAGCCTGATTTTCA-AGGGTTTCTTA-ATTAGTATTTTCAATG
1 AATTTTTAAAGAAGCTAAGCCTGATTTTTAGA-GGTTTC-TAGATGATTATTTCCAAAG
**
23627 AA-TTTTAAAGAAGCTAAGTATGATTTTTAGAGGTTTCTAGATGATTATTTCCAAAG
1 AATTTTTAAAGAAGCTAAGCCTGATTTTTAGAGGTTTCTAGATGATTATTTCCAAAG
* * * * *
23683 AATTTTTAAAGAAGTTAAGCCTAATTTTTAGGGGTTTATTGATGAT
1 AATTTTTAAAGAAGCTAAGCCTGATTTTTAGAGGTTTCTAGATGAT
23729 AACTATGATG
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
55 2 0.02
56 44 0.52
57 39 0.46
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (57 bp):
AATTTTTAAAGAAGCTAAGCCTGATTTTTAGAGGTTTCTAGATGATTATTTCCAAAG
Found at i:28297 original size:12 final size:12
Alignment explanation
Indices: 28280--28318 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
28270 CGCAACACGA
*
28280 CTCGACTCATGG
1 CTCGACTCGTGG
28292 CTCGACTCGTGG
1 CTCGACTCGTGG
*
28304 CTTGACTCGTGG
1 CTCGACTCGTGG
28316 CTC
1 CTC
28319 AGCTCACAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.28, T:0.28
Consensus pattern (12 bp):
CTCGACTCGTGG
Found at i:31044 original size:54 final size:54
Alignment explanation
Indices: 30986--31090 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
30976 TCGATAATAA
* * *
30986 TGTACACCCCATGGTATTCATAATGTGTTTATGAATGACCATTTCGGCACTATG
1 TGTACAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACTATG
* * ***
31040 TGTACAATCCATGGAATTCATAATGAGTTTGTGAATTTTCATTTCGGCACT
1 TGTACAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACT
31091 TTGGTGCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (54 bp):
TGTACAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACTATG
Found at i:35529 original size:24 final size:22
Alignment explanation
Indices: 35489--35571 Score: 70
Period size: 24 Copynumber: 3.9 Consensus size: 22
35479 ATGCAATTAA
35489 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTTTAAGGAG
35508 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-T-TTAAGGAG
* *
35531 ATGCATCGATACACTTT-A-GAA
1 -TGCATCGATGCACTTTAAGGAG
*
35552 TGCATCGATGCACTTCAAGG
1 TGCATCGATGCACTTTAAGG
35572 GGAAATAGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
19 12 0.24
20 15 0.29
21 2 0.04
22 3 0.06
23 2 0.04
24 17 0.33
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTTTAAGGAG
Found at i:36206 original size:65 final size:66
Alignment explanation
Indices: 36131--36290 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 66
36121 GATGCACACC
*
36131 CATTCAAATGCATTTTTTATACCGATGCGTA-AG-CCATGCATCGATGCACTCT-TGAATATTTT
1 CATTCAAATGCATTTTGTATACCGATGC--ACAGACCATGCATCGATGCACT-TATGAATATTTT
36193 GAAA
63 GAAA
* **
36197 CATT-AAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTTATGGCTATTTTGAA
1 CATTCAAATGCATTTTGTATACCGATGCACAGACCATGCATCGATGCACTTATGAATATTTTGAA
36261 A
66 A
* * * * *
36262 CA-TCGAATGTAATTAGTGTACCGATGCAC
1 CATTCAAATGCATTTTGTATACCGATGCAC
36291 CCCTAGTGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 4 0.05
65 73 0.89
66 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (66 bp):
CATTCAAATGCATTTTGTATACCGATGCACAGACCATGCATCGATGCACTTATGAATATTTTGAA
A
Found at i:36299 original size:19 final size:19
Alignment explanation
Indices: 36275--36385 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
36265 CGAATGTAAT
36275 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
36294 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
* *
36313 TAGTGTACCAATGCACCTC
1 TAGTGTACCGATGCACCCC
*
36332 TAGTGTATCGATGCACCCC
1 TAGTGTACCGATGCACCCC
* *
36351 TAGTGTACCAATGCACCTC
1 TAGTGTACCGATGCACCCC
*
36370 TAGTGTATCGATGCAC
1 TAGTGTACCGATGCAC
36386 TAATTCTTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (19 bp):
TAGTGTACCGATGCACCCC
Found at i:36327 original size:38 final size:38
Alignment explanation
Indices: 36275--36385 Score: 195
Period size: 38 Copynumber: 2.9 Consensus size: 38
36265 CGAATGTAAT
* * *
36275 TAGTGTACCGATGCACCCCTAGTGTACCGATGCACCCC
1 TAGTGTACCAATGCACCTCTAGTGTATCGATGCACCCC
36313 TAGTGTACCAATGCACCTCTAGTGTATCGATGCACCCC
1 TAGTGTACCAATGCACCTCTAGTGTATCGATGCACCCC
36351 TAGTGTACCAATGCACCTCTAGTGTATCGATGCAC
1 TAGTGTACCAATGCACCTCTAGTGTATCGATGCAC
36386 TAATTCTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 70 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (38 bp):
TAGTGTACCAATGCACCTCTAGTGTATCGATGCACCCC
Found at i:38885 original size:32 final size:32
Alignment explanation
Indices: 38849--38924 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
38839 CCAACCTAAA
* * *
38849 GGAGTGCCTTAGGGCCTTAGCGCCTACCCAAT
1 GGAGTACCTTAGGGCCTAAGAGCCTACCCAAT
*
38881 GGAGTACCTTGGGGCCTAAGAGCCTACCCAA-
1 GGAGTACCTTAGGGCCTAAGAGCCTACCCAAT
38912 GG-GTTACCTTAGG
1 GGAG-TACCTTAGG
38925 TCCATAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 1 0.03
31 10 0.26
32 27 0.71
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Consensus pattern (32 bp):
GGAGTACCTTAGGGCCTAAGAGCCTACCCAAT
Found at i:39314 original size:20 final size:22
Alignment explanation
Indices: 39272--39314 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
39262 ACGAATTTTT
* *
39272 ACTATATATGAAAGTTGAGAAA
1 ACTATATAGGAAAGTAGAGAAA
39294 ACTATATAGGAAAG-AGA-AAA
1 ACTATATAGGAAAGTAGAGAAA
39314 A
1 A
39315 TATTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 2 0.11
22 13 0.68
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTATATAGGAAAGTAGAGAAA
Found at i:43153 original size:51 final size:51
Alignment explanation
Indices: 43098--43235 Score: 179
Period size: 51 Copynumber: 2.7 Consensus size: 51
43088 TAGTTGCTTT
* * *
43098 AATCATAAATAAACAGTGACCAAAATGCATAAATTGAAAGAACA-TGAGCCA
1 AATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAGTG-GCCA
* *
43149 AATCAGAAATAAATAGTGACTAAAATGCATAAAATAAAAGAACAGTGGCCA
1 AATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAGTGGCCA
* * * *
43200 AATCAGAAATAACCATTGACTAAGATGTATAAATTA
1 AATCAGAAATAAACAGTGACTAAAATGCATAAATTA
43236 TCAAACACCA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 73 0.97
52 2 0.03
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.20
Consensus pattern (51 bp):
AATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAGTGGCCA
Found at i:45451 original size:28 final size:28
Alignment explanation
Indices: 45392--45451 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
45382 AGCAAACCCG
* * *
45392 AAACACATTGCCTCCCCAAATTGACCTG
1 AAACACATTACCTCCCCAAATTAACCTA
*
45420 AAACACATTACCTCCCCAAATTAATCTA
1 AAACACATTACCTCCCCAAATTAACCTA
45448 AAAC
1 AAAC
45452 GCTCTACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.22
Consensus pattern (28 bp):
AAACACATTACCTCCCCAAATTAACCTA
Found at i:46836 original size:55 final size:55
Alignment explanation
Indices: 46727--47416 Score: 825
Period size: 55 Copynumber: 12.6 Consensus size: 55
46717 CGTGATTTTT
* * * * * *
46727 AGAAACTAAGCCTAATTTTCAG--GTTTTTTTAT-ATTTTTAAATGGGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* *
46779 AGAAACTAAGTCTGATTTTCAGATGTTTCTTGATGATTTTTAAATGTGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * *
46834 AGAAACTAAGTGTGATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * ** * *
46889 ATAAGCCAAGTCTGGTTTTCAGATTTTTCTTGACT-ATCTTCAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TGATTTTTAAATGAGTTTTCAA
** * * *
46944 AGAAACCGAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * * *
46999 ATAAACTAAGTCTAATATTCAGAAGTTTCTTGATTATTTTTAATTGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
47054 AGAAACTAAGTATGATTTTCATAAGTTTATTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* ** **
47109 AGAAACTAAGTCTGCTTTTCAGAAGTTTCTTGATGATTTTTAAACAAACTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * *
47164 AGAAACTAAGTCTGATTTTTAGAAGTTTTTTGATGTTTTTTAAATAAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* *
47219 AGAAACCAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
47274 AGAAACTATGTATCATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * *
47329 AGAAACTAAGT-TCGATTTTCATAAGTTTCTTGATAATTTTTAAATGAGCATTT-AA
1 AGAAACTAAGTCT-GATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG-TTTTCAA
*
47384 AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
47417 CATGATTAAT
Statistics
Matches: 542, Mismatches: 88, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
52 20 0.04
54 10 0.02
55 507 0.94
56 5 0.01
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
Found at i:47564 original size:57 final size:57
Alignment explanation
Indices: 47424--47582 Score: 180
Period size: 56 Copynumber: 2.8 Consensus size: 57
47414 TGACATGATT
* * * * *
47424 AATTTTTAAAGAAGCTAAGCCTGATTTTCA-AGGGTTTATTA-ATGAGTATTTTCAATG
1 AATTTTTAAAGAAGTTAAGCCTGATTTTTAGA-GGTTTA-TAGATGATTATTTCCAAAG
** *
47481 AA-TTTTAAAGAAGTTAAGTATGATTTTTAGAGGTTTCTAGATGATTATTTCCAAAG
1 AATTTTTAAAGAAGTTAAGCCTGATTTTTAGAGGTTTATAGATGATTATTTCCAAAG
* * *
47537 AATTTTTAAAGAAGTTAAGCCTAATTTTTAGGGGTTTATTGATGAT
1 AATTTTTAAAGAAGTTAAGCCTGATTTTTAGAGGTTTATAGATGAT
47583 AACTATGATG
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
55 2 0.02
56 43 0.51
57 40 0.47
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (57 bp):
AATTTTTAAAGAAGTTAAGCCTGATTTTTAGAGGTTTATAGATGATTATTTCCAAAG
Done.