Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006685.1 Hibiscus syriacus cultivar Beakdansim tig00016600_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: 67190
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2262 original size:21 final size:21
Alignment explanation
Indices: 2236--2286 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2226 AGAAAACGGA
2236 AGCTCTTCTAACGTCTGCGCG
1 AGCTCTTCTAACGTCTGCGCG
2257 AGCTCTTCTAACGTCTGCGCG
1 AGCTCTTCTAACGTCTGCGCG
2278 AGCTCTTCT
1 AGCTCTTCT
2287 TGGTGCAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.33, G:0.22, T:0.31
Consensus pattern (21 bp):
AGCTCTTCTAACGTCTGCGCG
Found at i:2409 original size:14 final size:15
Alignment explanation
Indices: 2390--2424 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
2380 TAATAAGGTT
2390 ATTTATTTTTAAA-A
1 ATTTATTTTTAAATA
2404 ATTTA-TTTTAAATA
1 ATTTATTTTTAAATA
2418 ATTTATT
1 ATTTATT
2425 AGTATGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 11 0.58
15 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTTTTAAATA
Found at i:2440 original size:32 final size:31
Alignment explanation
Indices: 2404--2501 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
2394 ATTTTTAAAA
2404 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
2436 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
2458 ATTTATTTTAAATAATTTATTACTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
2490 ATTTATTTTAAA
1 ATTTATTTTAAA
2502 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.25
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 26 0.46
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTATATGGATTG
Found at i:2443 original size:22 final size:22
Alignment explanation
Indices: 2427--2469 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2417 AATTTATTAG
2427 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2449 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2470 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2471 original size:54 final size:54
Alignment explanation
Indices: 2404--2518 Score: 221
Period size: 54 Copynumber: 2.1 Consensus size: 54
2394 ATTTTTAAAA
*
2404 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTACTATGGATTGATTTATTTTAAAATATGGATTG
2458 ATTTATTTTAAATAATTTATTACTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTACTATGGATTGATTTATTTTAAAATATGGATTG
2512 ATTTATT
1 ATTTATT
2519 ATTGTAGTTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTACTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2494 original size:72 final size:68
Alignment explanation
Indices: 2418--2593 Score: 192
Period size: 72 Copynumber: 2.5 Consensus size: 68
2408 ATTTTAAATA
*
2418 ATTTATT-AGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTACT
1 ATTTATTAAATATGGATTGATTTATTTTAAAAT-T-GA-TGA-TTATTTTAAATAA-TTATTACT
*
2482 ATGGATTG
61 ATGAATTG
** *
2490 ATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGATGATTATTTTAAATAATTATTACTA
1 ATTTA--TT-AAATATGGATTGATTTATT-TTAAAATTGATGATTATTTTAAATAATTATTACTA
2555 TGAATTG
62 TGAATTG
* *
2562 ATTTTTTAAAATATGGATTGATTTGTTTTAAA
1 ATTTATT-AAATATGGATTGATTTATTTTAAA
2594 TAATTTATTA
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
69 3 0.03
70 21 0.23
72 24 0.27
73 13 0.14
74 5 0.06
75 2 0.02
76 18 0.20
77 4 0.04
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (68 bp):
ATTTATTAAATATGGATTGATTTATTTTAAAATTGATGATTATTTTAAATAATTATTACTATGAA
TTG
Found at i:2495 original size:18 final size:18
Alignment explanation
Indices: 2472--2519 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
2462 ATTTTAAATA
*
2472 ATTTATTACTATGGATTG
1 ATTTATTAATATGGATTG
2490 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
2512 ATTTATTA
1 ATTTATTA
2520 TTGTAGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:2581 original size:20 final size:21
Alignment explanation
Indices: 2553--2595 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2543 TAATTATTAC
2553 TATGAATTGATTT-TTTAAAA
1 TATGAATTGATTTGTTTAAAA
* *
2573 TATGGATTGATTTGTTTTAAA
1 TATGAATTGATTTGTTTAAAA
2594 TA
1 TA
2596 ATTTATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (21 bp):
TATGAATTGATTTGTTTAAAA
Found at i:2615 original size:52 final size:51
Alignment explanation
Indices: 2536--2637 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
2526 TTGATGATTA
2536 TTTTAAATAATTATTACTATGAATTGATT-TTTTAAA-ATATGGATTGATTTG
1 TTTTAAATAATTATTACTATGAATTGATTATTTTAAACATA--GATTGATTTG
* *
2587 TTTTAAATAATTTATTAGTATGGATTGATTATTTTAAACATAGATTGATTT
1 TTTTAAATAA-TTATTACTATGAATTGATTATTTTAAACATAGATTGATTT
2638 ATTATTGTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
51 10 0.22
52 26 0.57
53 7 0.15
54 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (51 bp):
TTTTAAATAATTATTACTATGAATTGATTATTTTAAACATAGATTGATTTG
Found at i:2708 original size:20 final size:21
Alignment explanation
Indices: 2683--2725 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2673 AATTTATTAG
2683 TATGGA-TGATTTATTTAAAA
1 TATGGATTGATTTATTTAAAA
*
2703 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
2724 TA
1 TA
2726 ATTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:5832 original size:2 final size:2
Alignment explanation
Indices: 5825--5858 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5815 GTTTGCATTG
*
5825 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5859 GCTTTTCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:17115 original size:5 final size:5
Alignment explanation
Indices: 17099--17225 Score: 194
Period size: 5 Copynumber: 26.2 Consensus size: 5
17089 ATGTCATACC
17099 TATAA TAT-A TATAA TAT-A -ATAA TATAATA TATAA TATAA TAT-A -ATAA
1 TATAA TATAA TATAA TATAA TATAA TAT-A-A TATAA TATAA TATAA TATAA
17146 TATAA TATAA TAT-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
17195 TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
17226 TGAATCACAC
Statistics
Matches: 114, Mismatches: 0, Indels: 16
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.04
4 12 0.11
5 92 0.81
6 2 0.02
7 4 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:22087 original size:26 final size:27
Alignment explanation
Indices: 22054--22113 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
22044 AAATTATAAT
22054 TTAAAATACTCC-AAAAGGAATAAAAA
1 TTAAAATACTCCAAAAAGGAATAAAAA
22080 TTAAAATACTCCAAAAAGGAATAAAAA
1 TTAAAATACTCCAAAAAGGAATAAAAA
22107 TTAAAAT
1 TTAAAAT
22114 GATCGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.22
Consensus pattern (27 bp):
TTAAAATACTCCAAAAAGGAATAAAAA
Found at i:36123 original size:63 final size:64
Alignment explanation
Indices: 36044--36165 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 64
36034 TAATTAATAA
* * * * * * *
36044 TTATTAATTTTCTAATAGATAATAAGAAAGATATTGAATTACTAATTAATAA-TTACTATTAAT
1 TTATTAATTCTATAATAAACAATAAGAAAGATACTAAATTACTAACTAATAATTTACTATTAAT
*
36107 TTATTAATTCTATAATAAACAATAAGAAAGATACTAAATTATTAACTAATAATTTACTA
1 TTATTAATTCTATAATAAACAATAAGAAAGATACTAAATTACTAACTAATAATTTACTA
36166 GATTTTACAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
63 44 0.88
64 6 0.12
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (64 bp):
TTATTAATTCTATAATAAACAATAAGAAAGATACTAAATTACTAACTAATAATTTACTATTAAT
Found at i:40944 original size:3 final size:3
Alignment explanation
Indices: 40938--40991 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
40928 TCAATTCTTC
40938 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40986 TAT TAT
1 TAT TAT
40992 GTCTTCAACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42561 original size:16 final size:17
Alignment explanation
Indices: 42540--42576 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42530 CCATGACTCC
*
42540 AAGCCAA-CTTAACCTA
1 AAGCCAACCCTAACCTA
42556 AAGCCAACCCTAACCTA
1 AAGCCAACCCTAACCTA
42573 AAGC
1 AAGC
42577 AGTCCCCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.43, C:0.35, G:0.08, T:0.14
Consensus pattern (17 bp):
AAGCCAACCCTAACCTA
Found at i:44035 original size:20 final size:20
Alignment explanation
Indices: 43941--44309 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
43931 GATTTTCCAT
* ** *
43941 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
43961 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
43981 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44001 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
44021 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
44041 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44061 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
44081 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
44101 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
44121 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44141 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
44161 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44181 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
44201 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44221 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
44241 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
44261 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
44281 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
44301 AATCACAAC
1 AATCGCAAC
44310 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:45030 original size:24 final size:24
Alignment explanation
Indices: 44991--45037 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44981 AAATTTGGTC
44991 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
45015 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
45038 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:47535 original size:19 final size:19
Alignment explanation
Indices: 47513--47797 Score: 302
Period size: 19 Copynumber: 16.4 Consensus size: 19
47503 CGGAAAATAC
*
47513 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47532 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
47546 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
47566 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
47580 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47599 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
47617 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
47631 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47650 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
47668 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
* *
47682 AATCGTAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
47701 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47720 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47739 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
47753 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
47771 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
47790 AATCGCAA
1 AATCGCAA
47798 CGAGATAATC
Statistics
Matches: 227, Mismatches: 12, Indels: 54
0.77 0.04 0.18
Matches are distributed among these distances:
13 1 0.00
14 46 0.20
15 2 0.01
16 21 0.09
17 8 0.04
18 38 0.17
19 98 0.43
20 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:47585 original size:14 final size:15
Alignment explanation
Indices: 47566--47643 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
47556 CGGAAATGAA
47566 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
47580 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCG--A-GAG
*
47599 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
47616 AAATCGCAA-CGAGAG
1 -AATCGCAAGCGAGAG
47631 AATCGCAATGCGA
1 AATCGCAA-GCGA
47644 AATGAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 16 0.31
15 1 0.02
16 10 0.20
17 1 0.02
18 9 0.18
19 14 0.27
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:47632 original size:51 final size:51
Alignment explanation
Indices: 47541--47778 Score: 333
Period size: 51 Copynumber: 4.6 Consensus size: 51
47531 AAATCCCAAC
47541 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
47594 ATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
* *
47645 ATGAAAATCGCAATGCGAAATGAAATCGCAACGACAGAATCGTAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
* *
47696 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATG-AAATCGCAA--CG--A-GAGAATCGCAATGCGAA
47751 A-G--AATCGCAATGCGAAATGAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAATCGCAA
47779 TGCGAAATGA
Statistics
Matches: 172, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
51 108 0.63
52 32 0.19
53 16 0.09
54 2 0.01
55 5 0.03
56 1 0.01
57 8 0.05
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (51 bp):
ATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:47663 original size:70 final size:68
Alignment explanation
Indices: 47580--47819 Score: 250
Period size: 70 Copynumber: 3.5 Consensus size: 68
47570 GCAACGAGAG
47580 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AATCGCAACGA-AGAATCGCAATGCGAA
47645 ATGAA
64 ATGAA
* * **
47650 AATCGCAATGCGAAATG-AAATCGCAACGAC-AGAATCGTAATGCGAAATTAA-AATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAATG-CGA-AAT-G-AAT-CGCAACGAAGAATCGCAATGC
47712 GAAATGAA
61 GAAATGAA
47720 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAATCGCAATGCGAAATGAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAATCGCAA--CG-AA-G-AATCGCAATGC
47782 GAAATGAA
61 GAAATGAA
*
47790 AATCGCAA--CG--A-GATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
47820 TATAAACGCA
Statistics
Matches: 146, Mismatches: 9, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
64 4 0.03
65 13 0.09
66 2 0.01
67 7 0.05
68 5 0.03
69 12 0.08
70 84 0.58
71 14 0.10
72 5 0.03
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (68 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAATCGCAACGAAGAATCGCAATGCGAAAT
GAA
Found at i:47789 original size:51 final size:49
Alignment explanation
Indices: 47546--47819 Score: 240
Period size: 51 Copynumber: 5.3 Consensus size: 49
47536 CCAACATGAA
*
47546 AATCGCAATGCGGAAATGAAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 AATCGCAATGC-GAAATG-AAATCGCAACGAAAGAAAATCGCAA-GCGAAA-G
*
47597 AAAATCGCAATGCGAAATGAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 --AATCGCAATGCGAAATGAAATCGCAACGAAAGAAAATCGCAA-GCGAAA-G
* * *
47648 AAAATCGCAATGCGAAATGAAATCGCAACGACAG--AATCGTAATGCGAAATTAA
1 --AATCGCAATGCGAAATGAAATCGCAACGAAAGAAAATCGCAA-GCG-AA--AG
47701 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAAG
1 AATCGCAATGCGAAATG-AAATCGCAA--CGAAA-GAAAATCGCAAGCGAAAG
* *
47753 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT
1 AATCGCAATGCGAAATGAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAAG
47804 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
47820 TATAAACGCA
Statistics
Matches: 203, Mismatches: 7, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
51 138 0.68
52 35 0.17
53 13 0.06
54 7 0.03
55 3 0.01
57 7 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (49 bp):
AATCGCAATGCGAAATGAAATCGCAACGAAAGAAAATCGCAAGCGAAAG
Found at i:47935 original size:19 final size:19
Alignment explanation
Indices: 47826--47927 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
47816 AAATTATAAA
47826 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
47845 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
47865 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
47881 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
47898 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
47917 CGCATTGCGAT
1 CGCATTGCGAT
47928 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:48053 original size:14 final size:14
Alignment explanation
Indices: 48034--48070 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
48024 CATCAATTAC
48034 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
48048 ACAAATCATCTTTT
1 ACAAATCAACTTTT
48062 ACAAATCAA
1 ACAAATCAA
48071 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:50007 original size:19 final size:19
Alignment explanation
Indices: 49967--50082 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
49957 TAGTTTACTT
* *
49967 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
49987 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
50006 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
50020 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
50039 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
50053 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
50072 TCGCAATGCGA
1 TCGCAACGCGA
50083 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:50023 original size:14 final size:14
Alignment explanation
Indices: 50004--50060 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
49994 GCGAAATGAA
*
50004 AATCGCAACGACAG
1 AATCGCAACGAAAG
50018 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
50035 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
50051 AATCGCAACG
1 AATCGCAACG
50061 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:50031 original size:33 final size:33
Alignment explanation
Indices: 49985--50077 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
49975 CGAAACTTAA
*
49985 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
50018 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
50051 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
50078 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:50100 original size:19 final size:19
Alignment explanation
Indices: 50078--50206 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
50068 AAAATCGCAA
50078 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
50097 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
50111 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
50130 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
50144 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
50163 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
50182 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
50202 TGCGA
1 TGCGA
50207 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:50120 original size:33 final size:33
Alignment explanation
Indices: 50078--50169 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
50068 AAAATCGCAA
50078 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
50111 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
50144 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
50170 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:50574 original size:185 final size:186
Alignment explanation
Indices: 50250--50906 Score: 1284
Period size: 185 Copynumber: 3.5 Consensus size: 186
50240 TTGAATGGAT
50250 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50315 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
50379 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
50435 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50499 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
50564 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
50620 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50685 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
50750 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
50805 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
50870 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
50907 AAGCAATCTA
Statistics
Matches: 469, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
184 87 0.19
185 290 0.62
186 92 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:50633 original size:93 final size:93
Alignment explanation
Indices: 50250--50906 Score: 1284
Period size: 93 Copynumber: 7.1 Consensus size: 93
50240 TTGAATGGAT
50250 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50315 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50343 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50407 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50435 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50499 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50527 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50592 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50620 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50685 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50713 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50777 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50805 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
50870 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50898 AAATTTACT
1 AAATTTACT
50907 AAGCAATCTA
Statistics
Matches: 560, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
92 276 0.49
93 284 0.51
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:52629 original size:14 final size:14
Alignment explanation
Indices: 52610--52732 Score: 93
Period size: 14 Copynumber: 7.7 Consensus size: 14
52600 TTGAAATGAA
52610 AATCGCAACGAGAG
1 AATCGCAACGAGAG
52624 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
52641 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
52657 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
52676 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
52690 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
52709 AATCGCAACGAGAG
1 AATCGCAACGAGAG
52723 AATCGCAACG
1 AATCGCAACG
52733 CGAAATGAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
14 38 0.42
15 2 0.02
16 10 0.11
17 10 0.11
18 2 0.02
19 28 0.31
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:52647 original size:33 final size:33
Alignment explanation
Indices: 52602--52749 Score: 278
Period size: 33 Copynumber: 4.5 Consensus size: 33
52592 TCTTTTGGTT
52602 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
52635 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
52668 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
52701 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
52734 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
52750 TGCGATTTTG
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 111 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:52648 original size:19 final size:18
Alignment explanation
Indices: 52609--52754 Score: 108
Period size: 19 Copynumber: 8.8 Consensus size: 18
52599 GTTGAAATGA
52609 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
52624 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
52641 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
52657 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
52674 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
52690 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
52707 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
52723 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
52740 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
52755 TTTTGGTTTC
Statistics
Matches: 105, Mismatches: 6, Indels: 36
0.71 0.04 0.24
Matches are distributed among these distances:
14 32 0.30
16 20 0.19
17 17 0.16
19 36 0.34
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:52785 original size:14 final size:14
Alignment explanation
Indices: 52766--52820 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
52756 TTTGGTTTCG
52766 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
52780 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
52799 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
52813 CGTTGCGA
1 CGTTGCGA
52821 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:52798 original size:33 final size:33
Alignment explanation
Indices: 52750--52820 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
52740 AAAATCGCAA
**
52750 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
52783 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
52816 TGCGA
1 TGCGA
52821 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:52828 original size:33 final size:33
Alignment explanation
Indices: 52761--52842 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
52751 GCGATTTTGG
***
52761 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
52794 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
* *
52827 TTCTCTCGTTGTGATT
1 TT-TCGCGTTGCGATT
52843 TTCATTTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 32 0.74
34 11 0.26
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:52983 original size:33 final size:33
Alignment explanation
Indices: 52941--53011 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
52931 AATACTAACT
*
52941 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
52974 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
53007 TGAAA
1 TGAAA
53012 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:53245 original size:22 final size:22
Alignment explanation
Indices: 53193--53247 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
53183 TGGTTGTGAG
**
53193 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
53215 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
53237 GGATTTCTTCG
1 GGATTTCTTCG
53248 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:53418 original size:20 final size:20
Alignment explanation
Indices: 53393--53585 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
53383 CTTTAAATAT
53393 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
53413 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
53435 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
53454 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
53474 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
53494 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
53514 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
53534 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
53554 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
53574 CGCGTTGCGATT
1 CGCGTTGCGATT
53586 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:53580 original size:60 final size:60
Alignment explanation
Indices: 53393--53585 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
53383 CTTTAAATAT
**
53393 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
53454 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
53514 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
53574 CGCGTTGCGATT
1 CGCGTTGCGATT
53586 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:53666 original size:20 final size:20
Alignment explanation
Indices: 53641--53692 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
53631 AAGAATCGCG
*
53641 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
53661 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
*
53681 TTACGATTCTGG
1 TTGCGATTCTGG
53693 GGATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:60660 original size:21 final size:21
Alignment explanation
Indices: 60611--60660 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
60601 GTTTGTTTGT
*
60611 TAAAATGATAAACGAACACAAA
1 TAAAAT-ATAAAAGAACACAAA
60633 T-AAATATAAAAGAACA-AATA
1 TAAAATATAAAAGAACACAA-A
60653 TAAAATAT
1 TAAAATAT
60661 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 12 0.48
21 10 0.40
22 1 0.04
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.20
Consensus pattern (21 bp):
TAAAATATAAAAGAACACAAA
Done.