Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000262.1 Hibiscus syriacus cultivar Beakdansim tig00000484_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: 63872
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:366 original size:12 final size:12
Alignment explanation
Indices: 343--381 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
333 AATAAGGGGG
343 AGTAATTTTTCAA
1 AGTAA-TTTTCAA
356 AGTAATTTTCAA
1 AGTAATTTTCAA
* *
368 AATGATTTTCAA
1 AGTAATTTTCAA
380 AG
1 AG
382 AAAATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (12 bp):
AGTAATTTTCAA
Found at i:393 original size:24 final size:24
Alignment explanation
Indices: 349--394 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
339 GGGGAGTAAT
* *
349 TTTTCAAAGTAATTTTCAAAATGA
1 TTTTCAAAGAAATCTTCAAAATGA
373 TTTTCAAAGAAAATCTT-AAAAT
1 TTTTCAAAG-AAATCTTCAAAAT
395 TTCTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTTCAAAGAAATCTTCAAAATGA
Found at i:536 original size:17 final size:19
Alignment explanation
Indices: 490--529 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
480 AAGATTGAAT
* *
490 TTTAATATTTTATATTCGA
1 TTTAAAATTATATATTCGA
509 TTTAAAATTATATATTCGA
1 TTTAAAATTATATATTCGA
528 TT
1 TT
530 CAATTATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTAAAATTATATATTCGA
Found at i:1779 original size:2 final size:2
Alignment explanation
Indices: 1772--1817 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1762 GTAATATGCT
1772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1814 TA TA
1 TA TA
1818 AGTATAATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7608 original size:6 final size:6
Alignment explanation
Indices: 7597--7626 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
7587 ATATCGAATT
7597 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
7627 ATTTTACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:8026 original size:18 final size:18
Alignment explanation
Indices: 8003--8047 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
7993 GTGATCAATG
8003 GGGGAATCGATTCCCATA
1 GGGGAATCGATTCCCATA
8021 GGGGAATCGATTCCCATA
1 GGGGAATCGATTCCCATA
8039 GGGGAATCG
1 GGGGAATCG
8048 GTACCCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (18 bp):
GGGGAATCGATTCCCATA
Found at i:8589 original size:47 final size:45
Alignment explanation
Indices: 8519--8644 Score: 168
Period size: 47 Copynumber: 2.8 Consensus size: 45
8509 TATAAAATCT
*
8519 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA-TCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATTC-AAATA
*
8564 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATTCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTATTCAAATA
* *
8611 CTTGCCA-TTATT-AATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
8645 CATACTTACC
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 21 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.49
48 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATTCAAATA
Found at i:8670 original size:43 final size:42
Alignment explanation
Indices: 8519--8660 Score: 141
Period size: 47 Copynumber: 3.3 Consensus size: 42
8509 TATAAAATCT
*
8519 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTATCAAAATA
1 CTTACCATTTATCCAATAAGCTCGTAAGCTTATTTT-TC--AATA
8564 CTTACCATTTAAATTCC-ATAAGCTCGTAAGCTTATTTTATTCATATA
1 CTTACCATTT--A-TCCAATAAGCTCGTAAGCTTA-TTT-TTCA-ATA
* *
8611 CTTGCCA-TTAT-TAATAAGCTCGTAAGCTTA-TTTTC-ATA
1 CTTACCATTTATCCAATAAGCTCGTAAGCTTATTTTTCAATA
8649 CTTACCATTTAT
1 CTTACCATTTAT
8661 TAACCAATAA
Statistics
Matches: 86, Mismatches: 3, Indels: 22
0.77 0.03 0.20
Matches are distributed among these distances:
38 9 0.10
39 4 0.05
40 3 0.03
41 2 0.02
43 18 0.21
44 1 0.01
45 10 0.12
46 3 0.03
47 27 0.31
48 8 0.09
49 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (42 bp):
CTTACCATTTATCCAATAAGCTCGTAAGCTTATTTTTCAATA
Found at i:8804 original size:40 final size:40
Alignment explanation
Indices: 8725--8808 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
8715 ATAGGAGTCA
* * *
8725 AATATTGCACCGAAGTGCTGAGGTCGAGCATTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCATTACCCACCT
* * **
8765 AATAATGCACCGTAGTGCTGAGGTCGGGTTTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCATTACCCACCT
8805 AATA
1 AATA
8809 CACTGTAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGCATTACCCACCT
Found at i:21016 original size:42 final size:43
Alignment explanation
Indices: 20957--21064 Score: 148
Period size: 43 Copynumber: 2.5 Consensus size: 43
20947 AAAGTTTTTT
*
20957 AAAAAAGTGTTTAGAGTGAAAAC-TGAAAAAAGGTGCTCTAAC-A
1 AAAAAAG-GTTTAGAGTGAAAACATG-AAAAAGGAGCTCTAACAA
* * *
21000 AAAAAAGGTTTAGAGTGAAAACATGAAGAGGGAGCTTTAACAA
1 AAAAAAGGTTTAGAGTGAAAACATGAAAAAGGAGCTCTAACAA
21043 AAAAAAGGTTTAGAGTGAAAAC
1 AAAAAAGGTTTAGAGTGAAAAC
21065 CCGAAAAGGG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 27 0.46
43 32 0.54
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.19
Consensus pattern (43 bp):
AAAAAAGGTTTAGAGTGAAAACATGAAAAAGGAGCTCTAACAA
Found at i:21087 original size:42 final size:41
Alignment explanation
Indices: 20957--21115 Score: 137
Period size: 43 Copynumber: 3.8 Consensus size: 41
20947 AAAGTTTTTT
* *
20957 AAAAAAGTGTTTAGAGTGAAAA-CTGAAAAAAGGTG-CTCTAACA
1 AAAAAAG-GTTTAGAGTGAAAACCCG--AAAAGG-GACTCTAAAA
** * *
21000 AAAAAAGGTTTAGAGTGAAAACATGAAGAGGGAGCTTTAACAA
1 AAAAAAGGTTTAGAGTGAAAACCCGAAAAGGGA-CTCTAA-AA
21043 AAAAAAGGTTTAGAGTGAAAACCCGAAAAGGGCACTCT-AAA
1 AAAAAAGGTTTAGAGTGAAAACCCGAAAAGGG-ACTCTAAAA
* * *
21084 AAAAAGGGTATA-AGATGAAAACCCGCAAAGGG
1 AAAAAAGGTTTAGAG-TGAAAACCCGAAAAGGG
21116 TATCTTTAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
40 3 0.03
41 33 0.33
42 20 0.20
43 42 0.42
44 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.24, T:0.16
Consensus pattern (41 bp):
AAAAAAGGTTTAGAGTGAAAACCCGAAAAGGGACTCTAAAA
Found at i:22712 original size:24 final size:24
Alignment explanation
Indices: 22661--22732 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 24
22651 ATATATATAT
* *
22661 ATATATATAATATAGTTTTTG-AA
1 ATATATATTATATAATTTTTGAAA
22684 A-ATATATTATATAATTTTTGAAA
1 ATATATATTATATAATTTTTGAAA
22707 ATATATAATATATATAATTTTTGAAA
1 ATATAT-AT-TATATAATTTTTGAAA
22733 GCATATTAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
22 17 0.40
23 4 0.09
24 4 0.09
25 2 0.05
26 16 0.37
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
ATATATATTATATAATTTTTGAAA
Found at i:22816 original size:16 final size:16
Alignment explanation
Indices: 22795--22831 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
22785 TATAATACAT
22795 TATATAGTTT-TGAAAA
1 TATATAGTTTCT-AAAA
22811 TATATAGTTTCTAAAA
1 TATATAGTTTCTAAAA
22827 TATAT
1 TATAT
22832 GTATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (16 bp):
TATATAGTTTCTAAAA
Found at i:22874 original size:5 final size:5
Alignment explanation
Indices: 22864--22944 Score: 71
Period size: 5 Copynumber: 16.0 Consensus size: 5
22854 ATTACTACTT
22864 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTTA TTTTTA TTCTT- TTTT-
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA TT-TTA TTTTA
* *
22910 TTTCA TTTCT- TTTTA -TTTA TTTTCA TTTTA GTTTA
1 TTTTA TTT-TA TTTTA TTTTA TTTT-A TTTTA TTTTA
22945 GGTCCAAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
4 10 0.15
5 38 0.58
6 17 0.26
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:22888 original size:11 final size:11
Alignment explanation
Indices: 22863--22939 Score: 79
Period size: 11 Copynumber: 7.0 Consensus size: 11
22853 TATTACTACT
22863 TTTTTATTTTA
1 TTTTTATTTTA
22874 -TTTTATTTTA
1 TTTTTATTTTA
22884 TTTTTATTTTA
1 TTTTTATTTTA
22895 TTTTTATTCTT-
1 TTTTTATT-TTA
* *
22906 TTTTTTTCATTTC
1 TTTTTAT--TTTA
22919 TTTTTA-TTTA
1 TTTTTATTTTA
*
22929 TTTTCATTTTA
1 TTTTTATTTTA
22940 GTTTAGGTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
10 18 0.32
11 28 0.50
12 4 0.07
13 6 0.11
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:23414 original size:19 final size:19
Alignment explanation
Indices: 23390--23428 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
23380 GAAAGAAGCC
*
23390 ATCGAAGGCACAAAAAAAG
1 ATCGAAGGAACAAAAAAAG
*
23409 ATCGAAGGAACACAAAAAG
1 ATCGAAGGAACAAAAAAAG
23428 A
1 A
23429 AAGCAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.21, T:0.05
Consensus pattern (19 bp):
ATCGAAGGAACAAAAAAAG
Found at i:25941 original size:35 final size:35
Alignment explanation
Indices: 25868--25942 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
25858 CATCACTAAC
**
25868 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
25903 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
25938 AGTAA
1 AGTAA
25943 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:26058 original size:23 final size:23
Alignment explanation
Indices: 26024--26070 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
26014 ATTCAAGTCA
* *
26024 AATATCATATCAGAATCCATGTC
1 AATATCAGATCAGAATCCAGGTC
26047 AATATCAGATCAGAATCCAGGTC
1 AATATCAGATCAGAATCCAGGTC
26070 A
1 A
26071 GGATCATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (23 bp):
AATATCAGATCAGAATCCAGGTC
Found at i:26076 original size:23 final size:23
Alignment explanation
Indices: 26027--26076 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
26017 CAAGTCAAAT
* * *
26027 ATCATATCAGAATCCATGTCAAT
1 ATCAGATCAGAATCCAGGTCAAG
*
26050 ATCAGATCAGAATCCAGGTCAGG
1 ATCAGATCAGAATCCAGGTCAAG
26073 ATCA
1 ATCA
26077 TAACATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (23 bp):
ATCAGATCAGAATCCAGGTCAAG
Found at i:28586 original size:7 final size:7
Alignment explanation
Indices: 28574--28612 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
28564 TGGTCAACGT
28574 GGTCAAC
1 GGTCAAC
28581 GGTCAAC
1 GGTCAAC
28588 GGGTCAAC
1 -GGTCAAC
28596 GGTCAAC
1 GGTCAAC
28603 GGGTCAAC
1 -GGTCAAC
28611 GG
1 GG
28613 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:28594 original size:8 final size:8
Alignment explanation
Indices: 28555--28628 Score: 86
Period size: 8 Copynumber: 9.5 Consensus size: 8
28545 TCAAAGTTTT
28555 GGTCAACAG
1 GGTCAAC-G
28564 TGGTCAACG
1 -GGTCAACG
28573 TGGTCAAC-
1 -GGTCAACG
28581 GGTCAACG
1 GGTCAACG
28589 GGTCAAC-
1 GGTCAACG
28596 GGTCAACG
1 GGTCAACG
28604 GGTCAACG
1 GGTCAACG
28612 GGT---CG
1 GGTCAACG
28617 GGTCAACG
1 GGTCAACG
28625 GGTC
1 GGTC
28629 GGGTCGGGTC
Statistics
Matches: 59, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.08
7 14 0.24
8 24 0.41
9 9 0.15
10 7 0.12
ACGTcount: A:0.23, C:0.24, G:0.36, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:28594 original size:15 final size:15
Alignment explanation
Indices: 28565--28612 Score: 87
Period size: 15 Copynumber: 3.1 Consensus size: 15
28555 GGTCAACAGT
28565 GGTCAACGTGGTCAAC
1 GGTCAACG-GGTCAAC
28581 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
28596 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
28611 GG
1 GG
28613 GTCGGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 24 0.75
16 8 0.25
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:28620 original size:13 final size:13
Alignment explanation
Indices: 28602--28677 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
28592 CAACGGTCAA
28602 CGGGTCAACGGGT
1 CGGGTCAACGGGT
28615 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
28633 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
28646 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
28659 CGGGTAAACGGGT
1 CGGGTCAACGGGT
28672 CGGGTC
1 CGGGTC
28678 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:28633 original size:18 final size:18
Alignment explanation
Indices: 28596--28650 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
28586 ACGGGTCAAC
28596 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
28617 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
28635 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
28651 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:28640 original size:31 final size:31
Alignment explanation
Indices: 28602--28663 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
28592 CAACGGTCAA
*
28602 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
28633 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
28664 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:30728 original size:35 final size:35
Alignment explanation
Indices: 30655--30729 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
30645 CATCACTAAC
**
30655 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
30690 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
30725 AGTAA
1 AGTAA
30730 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:30845 original size:23 final size:23
Alignment explanation
Indices: 30811--30857 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
30801 ATTCAAGTCA
* *
30811 AATATCATATCAGAATCCATGTC
1 AATATCAGATCAGAATCCAGGTC
30834 AATATCAGATCAGAATCCAGGTC
1 AATATCAGATCAGAATCCAGGTC
30857 A
1 A
30858 GGATCATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (23 bp):
AATATCAGATCAGAATCCAGGTC
Found at i:30863 original size:23 final size:23
Alignment explanation
Indices: 30814--30863 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
30804 CAAGTCAAAT
* * *
30814 ATCATATCAGAATCCATGTCAAT
1 ATCAGATCAGAATCCAGGTCAAG
*
30837 ATCAGATCAGAATCCAGGTCAGG
1 ATCAGATCAGAATCCAGGTCAAG
30860 ATCA
1 ATCA
30864 TAACATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (23 bp):
ATCAGATCAGAATCCAGGTCAAG
Found at i:33358 original size:10 final size:9
Alignment explanation
Indices: 33345--33406 Score: 50
Period size: 7 Copynumber: 7.6 Consensus size: 9
33335 GTCAAAGTTT
33345 TGGTCAACAG
1 TGGTCAAC-G
33355 TGGTCAACG
1 TGGTCAACG
33364 TGGGTCAAC-
1 T-GGTCAACG
33373 -GGTCAAC-
1 TGGTCAACG
33380 -GGTCAAC-
1 TGGTCAACG
33387 -GGTCAACG
1 TGGTCAACG
33395 -GGTCAACG
1 TGGTCAACG
33403 -GGTC
1 TGGTC
33407 GGGTCAACGG
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
7 21 0.42
8 12 0.24
9 2 0.04
10 15 0.30
ACGTcount: A:0.24, C:0.24, G:0.34, T:0.18
Consensus pattern (9 bp):
TGGTCAACG
Found at i:33378 original size:7 final size:7
Alignment explanation
Indices: 33366--33403 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
33356 GGTCAACGTG
33366 GGTCAAC
1 GGTCAAC
33373 GGTCAAC
1 GGTCAAC
33380 GGTCAAC
1 GGTCAAC
33387 GGTCAAC
1 GGTCAAC
33394 GGGTCAAC
1 -GGTCAAC
33402 GG
1 GG
33404 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:33411 original size:13 final size:13
Alignment explanation
Indices: 33393--33468 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
33383 CAACGGTCAA
33393 CGGGTCAACGGGT
1 CGGGTCAACGGGT
33406 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
33424 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
33437 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
33450 CGGGTAAACGGGT
1 CGGGTCAACGGGT
33463 CGGGTC
1 CGGGTC
33469 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:33411 original size:21 final size:21
Alignment explanation
Indices: 33365--33437 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
33355 TGGTCAACGT
33365 GGGTCAAC-GGTCAAC-GGTC
1 GGGTCAACGGGTCAACGGGTC
*
33384 AACGGTCAACGGGTCAACGGGTC
1 --GGGTCAACGGGTCAACGGGTC
33407 GGGTCAACGGGT---CGGGTC
1 GGGTCAACGGGTCAACGGGTC
*
33425 GGGTCAACTGGTC
1 GGGTCAACGGGTC
33438 GGGTAAACGG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 17 0.37
21 18 0.39
22 7 0.15
23 4 0.09
ACGTcount: A:0.19, C:0.25, G:0.40, T:0.16
Consensus pattern (21 bp):
GGGTCAACGGGTCAACGGGTC
Found at i:33424 original size:18 final size:18
Alignment explanation
Indices: 33387--33441 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
33377 AACGGTCAAC
33387 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
33408 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
33426 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
33442 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:33431 original size:31 final size:31
Alignment explanation
Indices: 33393--33454 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
33383 CAACGGTCAA
*
33393 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
33424 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
33455 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:35520 original size:35 final size:35
Alignment explanation
Indices: 35447--35521 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
35437 CATCACTAAC
**
35447 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
35482 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
35517 AGTAA
1 AGTAA
35522 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:35637 original size:23 final size:23
Alignment explanation
Indices: 35603--35649 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
35593 ATTCAAGTCA
* *
35603 AATATCATATCAGAATCCATGTC
1 AATATCAGATCAGAATCCAGGTC
35626 AATATCAGATCAGAATCCAGGTC
1 AATATCAGATCAGAATCCAGGTC
35649 A
1 A
35650 GGATCATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (23 bp):
AATATCAGATCAGAATCCAGGTC
Found at i:35655 original size:23 final size:23
Alignment explanation
Indices: 35606--35655 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
35596 CAAGTCAAAT
* * *
35606 ATCATATCAGAATCCATGTCAAT
1 ATCAGATCAGAATCCAGGTCAAG
*
35629 ATCAGATCAGAATCCAGGTCAGG
1 ATCAGATCAGAATCCAGGTCAAG
35652 ATCA
1 ATCA
35656 TAACATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (23 bp):
ATCAGATCAGAATCCAGGTCAAG
Found at i:38168 original size:7 final size:7
Alignment explanation
Indices: 38156--38194 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
38146 GGTCAACGTG
38156 GGTCAAC
1 GGTCAAC
38163 GGTCAAC
1 GGTCAAC
38170 GGGTCAAC
1 -GGTCAAC
38178 GGTCAAC
1 GGTCAAC
38185 GGGTCAAC
1 -GGTCAAC
38193 GG
1 GG
38195 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:38175 original size:15 final size:15
Alignment explanation
Indices: 38155--38194 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
38145 TGGTCAACGT
38155 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
38170 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
38185 GGGTCAACGG
1 GGGTCAACGG
38195 GTCGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:38176 original size:8 final size:8
Alignment explanation
Indices: 38136--38210 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
38126 TCAAAGTTTT
38136 GGTCAACAG
1 GGTCAAC-G
38145 TGGTCAACGTG
1 -GGTCAAC--G
38156 GGTCAAC-
1 GGTCAACG
38163 GGTCAACG
1 GGTCAACG
38171 GGTCAAC-
1 GGTCAACG
38178 GGTCAACG
1 GGTCAACG
38186 GGTCAACG
1 GGTCAACG
38194 GGT---CG
1 GGTCAACG
38199 GGTCAACG
1 GGTCAACG
38207 GGTC
1 GGTC
38211 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:38202 original size:13 final size:13
Alignment explanation
Indices: 38184--38259 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
38174 CAACGGTCAA
38184 CGGGTCAACGGGT
1 CGGGTCAACGGGT
38197 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
38215 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
38228 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
38241 CGGGTAAACGGGT
1 CGGGTCAACGGGT
38254 CGGGTC
1 CGGGTC
38260 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:38215 original size:18 final size:18
Alignment explanation
Indices: 38178--38232 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
38168 ACGGGTCAAC
38178 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
38199 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
38217 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
38233 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:38222 original size:31 final size:31
Alignment explanation
Indices: 38184--38245 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
38174 CAACGGTCAA
*
38184 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
38215 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
38246 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:40310 original size:35 final size:35
Alignment explanation
Indices: 40237--40311 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
40227 CATCACTAAC
**
40237 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
40272 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
40307 AGTAA
1 AGTAA
40312 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:40427 original size:23 final size:23
Alignment explanation
Indices: 40393--40439 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
40383 ATTCAAGTCA
* *
40393 AATATCATATCAGAATCCATGTC
1 AATATCAGATCAGAATCCAGGTC
40416 AATATCAGATCAGAATCCAGGTC
1 AATATCAGATCAGAATCCAGGTC
40439 A
1 A
40440 GGATCATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (23 bp):
AATATCAGATCAGAATCCAGGTC
Found at i:40445 original size:23 final size:23
Alignment explanation
Indices: 40396--40445 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
40386 CAAGTCAAAT
* * *
40396 ATCATATCAGAATCCATGTCAAT
1 ATCAGATCAGAATCCAGGTCAAG
*
40419 ATCAGATCAGAATCCAGGTCAGG
1 ATCAGATCAGAATCCAGGTCAAG
40442 ATCA
1 ATCA
40446 TAACATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (23 bp):
ATCAGATCAGAATCCAGGTCAAG
Found at i:42960 original size:7 final size:7
Alignment explanation
Indices: 42948--42986 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
42938 GGTCAACGTG
42948 GGTCAAC
1 GGTCAAC
42955 GGTCAAC
1 GGTCAAC
42962 GGGTCAAC
1 -GGTCAAC
42970 GGTCAAC
1 GGTCAAC
42977 GGGTCAAC
1 -GGTCAAC
42985 GG
1 GG
42987 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:42967 original size:15 final size:15
Alignment explanation
Indices: 42947--42986 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
42937 TGGTCAACGT
42947 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
42962 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
42977 GGGTCAACGG
1 GGGTCAACGG
42987 GTCGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:42968 original size:8 final size:8
Alignment explanation
Indices: 42928--43002 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
42918 TCAAAGTTTT
42928 GGTCAACAG
1 GGTCAAC-G
42937 TGGTCAACGTG
1 -GGTCAAC--G
42948 GGTCAAC-
1 GGTCAACG
42955 GGTCAACG
1 GGTCAACG
42963 GGTCAAC-
1 GGTCAACG
42970 GGTCAACG
1 GGTCAACG
42978 GGTCAACG
1 GGTCAACG
42986 GGT---CG
1 GGTCAACG
42991 GGTCAACG
1 GGTCAACG
42999 GGTC
1 GGTC
43003 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:42994 original size:13 final size:13
Alignment explanation
Indices: 42976--43051 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
42966 CAACGGTCAA
42976 CGGGTCAACGGGT
1 CGGGTCAACGGGT
42989 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
43007 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
43020 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
43033 CGGGTAAACGGGT
1 CGGGTCAACGGGT
43046 CGGGTC
1 CGGGTC
43052 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:43007 original size:18 final size:18
Alignment explanation
Indices: 42970--43024 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
42960 ACGGGTCAAC
42970 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
42991 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
43009 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
43025 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:43014 original size:31 final size:31
Alignment explanation
Indices: 42976--43037 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
42966 CAACGGTCAA
*
42976 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
43007 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
43038 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:46236 original size:28 final size:29
Alignment explanation
Indices: 46186--46254 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 29
46176 AATAAGTATT
**
46186 TAAATGTATCTTTTGAGTTAAAAT-TGTTATC
1 TAAA-GTAT-TTTTGAGTTAAAATATG-TAAA
46217 TAAAGTATTTTTG-GTTAAAATATGTAAA
1 TAAAGTATTTTTGAGTTAAAATATGTAAA
46245 TAAAGTATTT
1 TAAAGTATTT
46255 AGATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 20 0.57
29 7 0.20
30 4 0.11
31 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (29 bp):
TAAAGTATTTTTGAGTTAAAATATGTAAA
Found at i:46378 original size:29 final size:28
Alignment explanation
Indices: 46344--46444 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 28
46334 AATTGAGTAC
* *
46344 TTTAGATATTTATTTTGATCAAAAAATAT
1 TTTAAATATTTATTTTAAT-AAAAAATAT
* *
46373 TTTAGATATTTATTTTAACTTAAAAGATAAGT
1 TTTAAATATTTATTTTAA--TAAAAAAT-A-T
* *
46405 TTTAAATACTTATTTTAATTAAAAATAT
1 TTTAAATATTTATTTTAATAAAAAATAT
46433 TTTAAATATTTA
1 TTTAAATATTTA
46445 AATAGAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 12 0.20
29 18 0.30
30 12 0.20
31 2 0.03
32 17 0.28
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (28 bp):
TTTAAATATTTATTTTAATAAAAAATAT
Found at i:46418 original size:32 final size:28
Alignment explanation
Indices: 46365--46440 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 28
46355 ATTTTGATCA
* *
46365 AAAAATATTTTAGATATTTATTTTAACTT
1 AAAAATATTTTAAATACTTATTTTAA-TT
46394 AAAAGATAAGTTTTAAATACTTATTTTAATT
1 AAAA-AT-A-TTTTAAATACTTATTTTAATT
46425 AAAAATATTTTAAATA
1 AAAAATATTTTAAATA
46441 TTTAAATAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 9 0.21
29 5 0.12
30 4 0.10
31 7 0.17
32 17 0.40
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (28 bp):
AAAAATATTTTAAATACTTATTTTAATT
Found at i:59535 original size:15 final size:16
Alignment explanation
Indices: 59507--59539 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
59497 AAAATCTTTC
59507 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
59523 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
59538 TT
1 TT
59540 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:61331 original size:20 final size:20
Alignment explanation
Indices: 61308--61364 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
61298 GCTAGCTAAA
61308 TTCAGCT-CACCTTAGCTCCG
1 TTCAGCTCCA-CTTAGCTCCG
61328 TTCAGCTCCACTTAGCTCCG
1 TTCAGCTCCACTTAGCTCCG
61348 TTCAGCTCCAC-TAGCTC
1 TTCAGCTCCACTTAGCTC
61365 AATTCAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.17
20 28 0.78
21 2 0.06
ACGTcount: A:0.16, C:0.40, G:0.14, T:0.30
Consensus pattern (20 bp):
TTCAGCTCCACTTAGCTCCG
Found at i:61374 original size:20 final size:20
Alignment explanation
Indices: 61300--61370 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
61290 CACGTTCAGC
*
61300 TAGCTAAATTCAGCT-CACCT
1 TAGCTCAATTCAGCTCCA-CT
**
61320 TAGCTCCGTTCAGCTCCACT
1 TAGCTCAATTCAGCTCCACT
**
61340 TAGCTCCGTTCAGCTCCAC-
1 TAGCTCAATTCAGCTCCACT
61359 TAGCTCAATTCA
1 TAGCTCAATTCA
61371 AGCTAACAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.22
20 33 0.73
21 2 0.04
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.30
Consensus pattern (20 bp):
TAGCTCAATTCAGCTCCACT
Done.