Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004601.1 Hibiscus syriacus cultivar Beakdansim tig00010281_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: 96793
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1689 original size:18 final size:18
Alignment explanation
Indices: 1668--1702 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1658 CTTGTTTGGT
*
1668 TGTTCATCTTTTTTGAGG
1 TGTTCATCTTCTTTGAGG
1686 TGTTCATCTTCTTTGAG
1 TGTTCATCTTCTTTGAG
1703 TTAAGGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.54
Consensus pattern (18 bp):
TGTTCATCTTCTTTGAGG
Found at i:1764 original size:26 final size:26
Alignment explanation
Indices: 1708--1764 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1698 TTGAGTTAAG
*
1708 GACTTCAATTAAGTTATAAAATAGTC
1 GACTTCAATCAAGTTATAAAATAGTC
* * * *
1734 AACTTCAATCAAGTTATCAAGTATTC
1 GACTTCAATCAAGTTATAAAATAGTC
1760 GACTT
1 GACTT
1765 TTAGTTTCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (26 bp):
GACTTCAATCAAGTTATAAAATAGTC
Found at i:2197 original size:6 final size:6
Alignment explanation
Indices: 2186--2439 Score: 78
Period size: 6 Copynumber: 41.8 Consensus size: 6
2176 TCTGTTAACC
* * * *
2186 CTTCTT CTTCTT CTT-TT CCTCCTC CTCCTT C-TATT CTTTCTT C-TCTT
1 CTTCTT CTTCTT CTTCTT -CTTCTT CTTCTT CTTCTT C-TTCTT CTTCTT
* * * * * *
2233 CATTCTC CTCCTT CTCCTT C-TCATT TTTCTC CTTCTT CTT-TT CCTTCTC
1 C-TTCTT CTTCTT CTTCTT CTTC-TT CTTCTT CTTCTT CTTCTT -CTTCTT
* * * *
2282 CTGCTT CTTCTT CTTTCCT CTTCTCT CTTTCTT C-TCATT CTCCTT CTCCTT
1 CTTCTT CTTCTT C-TTCTT CTTCT-T C-TTCTT CTTC-TT CTTCTT CTTCTT
* * * * *
2333 CTCCTT C-TCATT CTACTT CTTCTT C-TCATT CTACTT AC-TATT CTCCTT
1 CTTCTT CTTC-TT CTTCTT CTTCTT CTTC-TT CTTCTT -CTTCTT CTTCTT
* * * * * * *
2381 CTTTTT CTTCTT CTCCTC CTCCTT CTTATT CTTCTC CTT-TT CATTTTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT C-TTCTT
*
2429 CTCCTT CTTCT
1 CTTCTT CTTCT
2440 CATTCTTTTC
Statistics
Matches: 182, Mismatches: 43, Indels: 46
0.67 0.16 0.17
Matches are distributed among these distances:
5 21 0.12
6 129 0.71
7 28 0.15
8 4 0.02
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (6 bp):
CTTCTT
Found at i:2216 original size:21 final size:21
Alignment explanation
Indices: 2192--2334 Score: 54
Period size: 21 Copynumber: 6.2 Consensus size: 21
2182 AACCCTTCTT
2192 CTTCTTCTTTTCCTCCTCCTC
1 CTTCTTCTTTTCCTCCTCCTC
2213 CTTCTATTCTTTCTTCTCTTCATTCTCCTC
1 CTTC--TTC-TT-TTC-C-TC---CTCCTC
* * * ** *
2243 CTTCTCCTTCTCATTTTTCTC
1 CTTCTTCTTTTCCTCCTCCTC
* *
2264 CTTCTTCTTTTCCTTCTCCTG
1 CTTCTTCTTTTCCTCCTCCTC
*
2285 CTTCTTCTTCTTTCCTCTTCTCTC
1 CTTCTTC-T-TTTCCTCCTC-CTC
* * *
2309 TTTCTTCTCATT-CTCCTTCTC
1 CTTCTTCT-TTTCCTCCTCCTC
2330 CTTCT
1 CTTCT
2335 CCTTCTCATT
Statistics
Matches: 90, Mismatches: 20, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
21 37 0.41
22 5 0.06
23 15 0.17
24 11 0.12
25 3 0.03
26 3 0.03
27 4 0.04
28 2 0.02
30 10 0.11
ACGTcount: A:0.03, C:0.40, G:0.01, T:0.57
Consensus pattern (21 bp):
CTTCTTCTTTTCCTCCTCCTC
Found at i:2248 original size:18 final size:17
Alignment explanation
Indices: 2246--2466 Score: 81
Period size: 18 Copynumber: 12.1 Consensus size: 17
2236 TCTCCTCCTT
*
2246 CTCCTTCTCATTTTTCTC
1 CTCCTTCTC-TTCTTCTC
* *
2264 CTTCTTCTTTTCCTTCTC
1 CTCCTTCTCTT-CTTCTC
*
2282 CTGCTTCTTCTTCTT-TC
1 CTCCTTC-TCTTCTTCTC
*
2299 CTCTTCTCTCTTTCTTCTC
1 CTCCT-TCTC-TTCTTCTC
* *
2318 ATTCTCCTTCTCCTTCTCCTT
1 ---CTCCTTCT-CTTCTTCTC
* *
2339 CTCATTCTACTTCTTCTT
1 CTCCTTCT-CTTCTTCTC
*
2357 CTCATTCTACTTACTATTCTC
1 CTCCTTCT-CTT-C--TTCTC
* *
2378 CTTCTTTTTCTTCTTCTC
1 C-TCCTTCTCTTCTTCTC
* * *
2396 CTCCTCCTTCTTATTCTT
1 CTCCTTC-TCTTCTTCTC
* *
2414 CTCCTTTTCATTTTTCTC
1 CTCCTTCTC-TTCTTCTC
*
2432 CTTCTTCTCATTCTT-T-
1 CTCCTTCTC-TTCTTCTC
2448 -TCCTTCTCATTCTTCTC
1 CTCCTTCTC-TTCTTCTC
2465 CT
1 CT
2467 TATTTTCCTC
Statistics
Matches: 156, Mismatches: 29, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
15 13 0.08
16 1 0.01
17 15 0.10
18 93 0.60
19 6 0.04
20 1 0.01
21 17 0.11
22 10 0.06
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.57
Consensus pattern (17 bp):
CTCCTTCTCTTCTTCTC
Found at i:2269 original size:42 final size:41
Alignment explanation
Indices: 2185--2451 Score: 149
Period size: 42 Copynumber: 6.5 Consensus size: 41
2175 TTCTGTTAAC
* *
2185 CCTTCTTCTTCTTCTTTTCCTCCTCCTCCTTCT-A---TTCT
1 CCTTCTTC-TCTTCTTCTCCTCCTTCTCCTTCTCATTTTTCT
2223 --TTCTTCTCTTCATTCTCCTCCTTCTCCTTCTCATTTTTCT
1 CCTTCTTCTCTTC-TTCTCCTCCTTCTCCTTCTCATTTTTCT
* * * * *
2263 CCTTCTTCTTTTCCTTCTCCTGCTTCTTCTTCTTTCCTCTTCTCT
1 CCTTCTTCTCTT-CTTCTCCTCCTTCTCCTTC--TCAT-TTTTCT
* * * * *
2308 CTTTCTTCTCATTCTCCTTCTCCTTCTCCTTCTCATTCTACT
1 CCTTCTTCTC-TTCTTCTCCTCCTTCTCCTTCTCATTTTTCT
* * * *
2350 TCTTCTTCTCATTCTACTTACT-ATTCTCC-T-TC-TTTTTCT
1 CCTTCTTCTC-TTCTTC-TCCTCCTTCTCCTTCTCATTTTTCT
* * * ** * *
2389 TCTTCTCCTCCTCCTTCTTATTCTTCTCCTTTTCATTTTTCT
1 CCTTCTTCT-CTTCTTCTCCTCCTTCTCCTTCTCATTTTTCT
*
2431 CCTTCTTCTCATTCTTTTCCT
1 CCTTCTTCTC-TTCTTCTCCT
2452 TCTCATTCTT
Statistics
Matches: 174, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
35 5 0.03
36 23 0.13
37 1 0.01
38 2 0.01
39 23 0.13
40 8 0.05
41 4 0.02
42 68 0.39
43 7 0.04
44 3 0.02
45 28 0.16
46 2 0.01
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (41 bp):
CCTTCTTCTCTTCTTCTCCTCCTTCTCCTTCTCATTTTTCT
Found at i:2344 original size:24 final size:25
Alignment explanation
Indices: 2259--2406 Score: 98
Period size: 24 Copynumber: 6.2 Consensus size: 25
2249 CTTCTCATTT
*
2259 TTCTCCTTCTTC-TTTTCCTTCTCC
1 TTCTCCTTCTTCATTCTCCTTCTCC
* * *
2283 TGCTTCTTCTTCTTTC-CTCTTCTCTC
1 TTCTCCTTCTTCATTCTC-CTTCTC-C
2309 TT-T-CTTC-TCATTCTCCTTCTCC
1 TTCTCCTTCTTCATTCTCCTTCTCC
* *
2331 TTCTCCTTC-TCATTCTACTTCTTC
1 TTCTCCTTCTTCATTCTCCTTCTCC
* * *
2355 TTCTCATTCTAC-TTACT-ATTCTCC
1 TTCTCCTTCTTCATT-CTCCTTCTCC
** *
2379 TTCTTTTTCTTC-TTCTCCTCCTCC
1 TTCTCCTTCTTCATTCTCCTTCTCC
2403 TTCT
1 TTCT
2407 TATTCTTCTC
Statistics
Matches: 99, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
22 3 0.03
23 14 0.14
24 68 0.69
25 12 0.12
26 2 0.02
ACGTcount: A:0.05, C:0.39, G:0.01, T:0.56
Consensus pattern (25 bp):
TTCTCCTTCTTCATTCTCCTTCTCC
Found at i:2439 original size:33 final size:33
Alignment explanation
Indices: 2187--2467 Score: 121
Period size: 33 Copynumber: 8.3 Consensus size: 33
2177 CTGTTAACCC
* * * * *
2187 TTCTTCTTCTTCTTTTCCTCCTCCTCCTTCT-A
1 TTCTTCTCCTTCTTCTCATTCTTCTCCTTCTCA
* *
2219 TTCTTTCTTCTCTTCATTCTCCTCCTTCTCCTTCTCA
1 TTC-TTC-TC-CTTC-TTCTCATTCTTCTCCTTCTCA
* * *
2256 TTTTTCTCCTTCTTCT-TTTCCTTCTCCTGCTTC-
1 TTCTTCTCCTTCTTCTCATT-CTTCTCCTTC-TCA
* * *
2289 TTCTTCTTTCC-TCTTCTCTCTTTCTTCTCATTCTCC
1 TTCTTC--TCCTTC-T-TCTCATTCTTCTCCTTCTCA
* * * *
2325 TTCTCCTTCTCCTTCTCATTCTACTTCTTCTTCTCA
1 TTCTTCTCCTTCTTCTCA-T-T-CTTCTCCTTCTCA
* * * *
2361 TTCTACTTAC-TATTCTCCTTCTT-T--TTCTTC-
1 TTCTTC-TCCTTCTTCTCATTCTTCTCCTTC-TCA
* * * *
2391 TTCTCCTCCTCCTTCTTATTCTTCTCCTTTTCA
1 TTCTTCTCCTTCTTCTCATTCTTCTCCTTCTCA
* *
2424 TTTTTCTCCTTCTTCTCATTCTTTTCCTTCTCA
1 TTCTTCTCCTTCTTCTCATTCTTCTCCTTCTCA
2457 TTCTTCTCCTT
1 TTCTTCTCCTT
2468 ATTTTCCTCC
Statistics
Matches: 189, Mismatches: 36, Indels: 47
0.69 0.13 0.17
Matches are distributed among these distances:
29 2 0.01
30 17 0.09
31 3 0.02
32 7 0.04
33 67 0.35
34 14 0.07
35 15 0.08
36 56 0.30
37 8 0.04
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTTCTCCTTCTTCTCATTCTTCTCCTTCTCA
Found at i:2454 original size:24 final size:24
Alignment explanation
Indices: 2427--2481 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2417 CTTTTCATTT
*
2427 TTCTCCTTCTTCTCATTCTTTTCC
1 TTCTCCTTCTTCTCATTATTTTCC
* *
2451 TTCTCATTCTTCTCCTTATTTTCC
1 TTCTCCTTCTTCTCATTATTTTCC
*
2475 TCCTCCT
1 TTCTCCT
2482 GCCACATTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (24 bp):
TTCTCCTTCTTCTCATTATTTTCC
Found at i:2461 original size:15 final size:15
Alignment explanation
Indices: 2243--2467 Score: 86
Period size: 15 Copynumber: 14.6 Consensus size: 15
2233 CATTCTCCTC
2243 CTTCTCCTTCTCATT
1 CTTCTCCTTCTCATT
*
2258 TTTCTCC-T-TC-TT
1 CTTCTCCTTCTCATT
* * *
2270 CTTTTCCTTCTCCTG
1 CTTCTCCTTCTCATT
*
2285 CTTCTTCTTCT--TT
1 CTTCTCCTTCTCATT
* * *
2298 CCTCTTC-TCTCTTT
1 CTTCTCCTTCTCATT
* *
2312 CTTCTCATTCTCCTTCT
1 CTTCTCCTTCT-CAT-T
2329 CCTTCTCCTTCTCATTCT
1 -CTTCTCCTTCTCA-T-T
*
2347 ACTTCTTCTTCTCATT
1 -CTTCTCCTTCTCATT
* * *
2363 CTACTTACTATTCTCCTT
1 CTTC-T-C-CTTCTCATT
* * *
2381 CTTTTTCTTCTTC-TC
1 CTTCTCCTTC-TCATT
* *
2396 CTCCTCCTTCTTATT
1 CTTCTCCTTCTCATT
*
2411 CTTCTCCTTTTCATT
1 CTTCTCCTTCTCATT
*
2426 TTTCTCCTTCTTCTCATT
1 CTTCT-C--CTTCTCATT
*
2444 CTTTTCCTTCTCATT
1 CTTCTCCTTCTCATT
2459 CTTCTCCTT
1 CTTCTCCTT
2468 ATTTTCCTCC
Statistics
Matches: 155, Mismatches: 37, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
12 10 0.06
13 10 0.06
14 10 0.06
15 67 0.43
16 8 0.05
17 5 0.03
18 45 0.29
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTCTCCTTCTCATT
Found at i:4503 original size:21 final size:19
Alignment explanation
Indices: 4479--4805 Score: 222
Period size: 21 Copynumber: 15.7 Consensus size: 19
4469 CATATTCGCA
4479 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
** *
4500 TTGCGATAGTTGAAGTTCTCA
1 TTGCGATAGTCCAAG-T-TCG
* *
4521 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
4542 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
4563 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAAG-TT-CG
*
4584 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
4605 TTGTGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTT--CG
* * *
4626 TTGCAATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
4647 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
4668 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
4689 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
4710 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
4731 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
4752 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
4771 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
4792 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
4806 AATGCAACGA
Statistics
Matches: 260, Mismatches: 28, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
19 53 0.20
20 2 0.01
21 171 0.66
22 4 0.02
23 30 0.12
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:4565 original size:63 final size:61
Alignment explanation
Indices: 4479--4806 Score: 326
Period size: 63 Copynumber: 5.2 Consensus size: 61
4469 CATATTCGCA
* ** *
4479 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTTGAAGTTCTCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAATTC-CGTTGCGATAGTCCAAGTT-TCGTTGCGATTTATTCCAAATTCG
* *
4542 TTGCGATTTATTCCAAATT-CGTTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAATTCCGTTGCGATAGTCCAAGTTT-CGTTGCGATTTATTCCAAATTCG
* * * * * *
4605 TTGTGATAGTCGAAGTTCACGTTGCAATTTATTCCAA-ATTCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAATTC-CGTTGCGA--TAGTCCAAGTTTCGTTGCGATTTATTCCAAATTCG
* * *
4668 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAATTC-CGTTGCGATAGTCCAAGTT-TCGTTGCGATTTATTCCAAATTCG
* * *
4731 TTGCGATTTATTCCAAATT-CGTTGCGATAGTCCAAG-TTCGTTGCGA--TAGTCCAAGTTCGCG
1 TTGCGA--TAGTCCAAATTCCGTTGCGATAGTCCAAGTTTCGTTGCGATTTATTCCAAATT--CG
4792 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
4807 ATGCAACGAC
Statistics
Matches: 223, Mismatches: 29, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
59 17 0.08
61 30 0.13
62 3 0.01
63 146 0.65
64 2 0.01
65 25 0.11
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (61 bp):
TTGCGATAGTCCAAATTCCGTTGCGATAGTCCAAGTTTCGTTGCGATTTATTCCAAATTCG
Found at i:4628 original size:84 final size:81
Alignment explanation
Indices: 4540--4798 Score: 376
Period size: 84 Copynumber: 3.1 Consensus size: 81
4530 ATTCCAAATT
* * *
4540 CGTTGCGATTTATTCCAAATTCGTTGCGA-TAGTCCAAGTTTGCGTTGCGATTTATTCCAAGTTC
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTATTCCAA-ATT-CGTTGCGA--TAGTCCAAGTTC
* *
4604 GTTGTGATAGTCGAAGTTCA
62 GTTGCGATAGTCGAAGTTCG
*
4624 CGTTGCAATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCCAAGTT--CG
4689 TTGCGATAGTCGAAGTTCG
63 TTGCGATAGTCGAAGTTCG
4708 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTT
*
4773 GCGATAGTCCAAGTTCG
65 GCGATAGTCGAAGTTCG
4790 CGTTGCGAT
1 CGTTGCGAT
4799 AGTCCAAAAT
Statistics
Matches: 163, Mismatches: 8, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
82 39 0.24
84 115 0.71
85 2 0.01
86 7 0.04
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (81 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTG
CGATAGTCGAAGTTCG
Found at i:5530 original size:21 final size:21
Alignment explanation
Indices: 5504--5615 Score: 83
Period size: 21 Copynumber: 5.4 Consensus size: 21
5494 ATTTTGGACT
5504 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
5525 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
5546 ATCACAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
5567 ATCGCAACGTGAACTTCGACT--
1 ATCGCAAC--GAATTTGGAATAA
5588 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
5607 ATCGCAACG
1 ATCGCAACG
5616 CGAACTTCGA
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
19 24 0.35
21 28 0.41
23 17 0.25
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:5631 original size:21 final size:21
Alignment explanation
Indices: 5525--5661 Score: 129
Period size: 21 Copynumber: 6.6 Consensus size: 21
5515 TTTGGAATAA
5525 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * * *
5546 ATCACAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
5565 AAATCGCAACGTGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
5588 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
5607 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
5628 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
5649 ATCGCAATGCGAA
1 ATCGCAACGCGAA
5662 TATGTAAATC
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
19 23 0.26
21 59 0.66
23 8 0.09
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:5646 original size:42 final size:42
Alignment explanation
Indices: 5500--5636 Score: 242
Period size: 42 Copynumber: 3.3 Consensus size: 42
5490 TGCGATTTTG
5500 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
5542 GACTATCACAACGAATTTGGAATAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
5584 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
5624 GACTATCGCAACG
1 GACTATCGCAACG
5637 CGAACTTGGA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 31 0.34
41 1 0.01
42 59 0.65
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:5653 original size:82 final size:83
Alignment explanation
Indices: 5500--5655 Score: 237
Period size: 82 Copynumber: 1.9 Consensus size: 83
5490 TGCGATTTTG
*
5500 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAAT
5565 AAATCGCAACGTGAACTTC
66 -AATCGCAACGTGAACTTC
*
5584 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAA--CGAACTTGGA
*
5647 CT-ATCGCAA
64 ATAATCGCAA
5656 TGCGAATATG
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
82 36 0.54
83 1 0.01
84 30 0.45
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (83 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAAT
AATCGCAACGTGAACTTC
Found at i:5742 original size:21 final size:21
Alignment explanation
Indices: 5718--5793 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
5708 AATTTGGAAA
* *
5718 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTGGACT
5739 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
* *
5760 ATCCCAATGAGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
5781 ATCGCAATGCGAA
1 ATCGCAATGCGAA
5794 TATGTAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGGACT
Found at i:5812 original size:111 final size:110
Alignment explanation
Indices: 5595--5820 Score: 296
Period size: 111 Copynumber: 2.0 Consensus size: 110
5585 ACTATCGCAA
* *
5595 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCG
1 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCCCAATGAG
* * * * **
5660 AATATGTAAATCGCAATGTGATAGTCGAAGTTCGCGTTGCGATAGT
66 AATATGGAAATCGCAATGCGATAGTC-AAGATCACAATGCGATAGT
*
5706 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCCCAATGAG
1 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCCCAATGAG
*
5771 AACT-TGGACTATCGCAATGCGAATATGT-AA-ATCACAATGCGATAGT
66 AA-TATGGA-AATCGCAATGCG-ATA-GTCAAGATCACAATGCGATAGT
5817 CGAA
1 CGAA
5821 GTTCGCGTTG
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
111 83 0.82
112 13 0.13
113 3 0.03
114 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (110 bp):
CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCCCAATGAG
AATATGGAAATCGCAATGCGATAGTCAAGATCACAATGCGATAGT
Found at i:5834 original size:21 final size:21
Alignment explanation
Indices: 5808--5854 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
5798 TAAATCACAA
5808 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
5829 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
5850 TGCGA
1 TGCGA
5855 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:15591 original size:22 final size:21
Alignment explanation
Indices: 15549--15588 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15539 AAGATTATTT
*
15549 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
15570 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
15589 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:18788 original size:20 final size:20
Alignment explanation
Indices: 18763--18812 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
18753 ATATATTATA
18763 TTTTCGAG-CTGCTCACGAAC
1 TTTTCGAGTC-GCTCACGAAC
18783 TTTTCGAGTCGCTCACGAAC
1 TTTTCGAGTCGCTCACGAAC
18803 TTTTCGAGTC
1 TTTTCGAGTC
18813 AAATATCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (20 bp):
TTTTCGAGTCGCTCACGAAC
Found at i:20104 original size:22 final size:20
Alignment explanation
Indices: 20061--20105 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
20051 ATGTGAAAAA
**
20061 TAAAATATTAAATTTATTTT
1 TAAAATATTAAATTTAAATT
20081 TAAAATATATAAATTTTAAATT
1 TAAAATAT-TAAA-TTTAAATT
20103 TAA
1 TAA
20106 TTTCTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATATTAAATTTAAATT
Found at i:24840 original size:22 final size:21
Alignment explanation
Indices: 24815--24859 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
24805 TTTATTTGAC
*
24815 ATCAGATTCAGTTCGAGTTTGG
1 ATCAGATTAAGTTC-AGTTTGG
* *
24837 ATCAGGTTAATTTCAGTTTGG
1 ATCAGATTAAGTTCAGTTTGG
24858 AT
1 AT
24860 TGATGTTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (21 bp):
ATCAGATTAAGTTCAGTTTGG
Found at i:25502 original size:2 final size:2
Alignment explanation
Indices: 25495--25576 Score: 82
Period size: 2 Copynumber: 42.0 Consensus size: 2
25485 GAAGTAAGGG
*
25495 AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AC AT A- AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
* * *
25537 GT AT AT -T CT -T AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25577 TAAGTCAACG
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.06
2 62 0.91
3 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:25743 original size:2 final size:2
Alignment explanation
Indices: 25738--25769 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25728 TGAGAGATAC
25738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25770 CTTAAACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29971 original size:2 final size:2
Alignment explanation
Indices: 29964--30009 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
29954 ATAACTTAGC
29964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30006 AT AT
1 AT AT
30010 GAGTTCCGTT
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):
AT
Found at i:35311 original size:27 final size:28
Alignment explanation
Indices: 35260--35317 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
35250 TTTTTTGAAA
* * *
35260 TTTTGGCTTTTTTGTTTTTTGTTTTTTT
1 TTTTGCCTTTTTTGTTTTTTCTTTTGTT
35288 TTTTGCCTTTTTTG-TTTTTCTTTTGTT
1 TTTTGCCTTTTTTGTTTTTTCTTTTGTT
35315 TTT
1 TTT
35318 GAAATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (28 bp):
TTTTGCCTTTTTTGTTTTTTCTTTTGTT
Found at i:35312 original size:20 final size:21
Alignment explanation
Indices: 35274--35312 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35264 GGCTTTTTTG
*
35274 TTTTTTGTTTTTTTTTTTGCC
1 TTTTTTGTTTTTTCTTTTGCC
35295 TTTTTTG-TTTTTCTTTTG
1 TTTTTTGTTTTTTCTTTTG
35313 TTTTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (21 bp):
TTTTTTGTTTTTTCTTTTGCC
Found at i:35316 original size:28 final size:28
Alignment explanation
Indices: 35260--35317 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
35250 TTTTTTGAAA
* *
35260 TTTTGGCTTTTTTGTTTTTTGTTTTTTT
1 TTTTGCCTTTTTTGTTTTTTGTTTGTTT
35288 TTTTGCCTTTTTTGTTTTTCT-TTTGTTT
1 TTTTGCCTTTTTTGTTTTT-TGTTTGTTT
35316 TT
1 TT
35318 GAAATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (28 bp):
TTTTGCCTTTTTTGTTTTTTGTTTGTTT
Found at i:41189 original size:52 final size:52
Alignment explanation
Indices: 41020--41236 Score: 224
Period size: 51 Copynumber: 4.2 Consensus size: 52
41010 CGACTAACCG
* * * * ** *
41020 TTAACACATACTTACACTGATGTAATTGAACAAAA-TAAAAAAATACAACAC
1 TTAACACATACTTACACTGGTGTAAGTGAATAAAATTAAAAAAGTGTAGCAC
* *
41071 TTAACACATACTTACACTGGTGTAAGTGGATAAAA-TAAAAAAGTATAGCAC
1 TTAACACATACTTACACTGGTGTAAGTGAATAAAATTAAAAAAGTGTAGCAC
* *
41122 TTAACACATACTTACACCGGTATAAGTGAATAAAATTTAAAAAA-TGTAGCAC
1 TTAACACATACTTACACTGGTGTAAGTGAATAAAA-TTAAAAAAGTGTAGCAC
** * * * *
41174 TTAATGCATAGTTACACTTGCGTAAGTGAATAAAATAAAAAAAAACGTGTAGCAC
1 TTAACACATACTTACACTGGTGTAAGTGAATAAAAT--TAAAAAA-GTGTAGCAC
41229 TTAACACA
1 TTAACACA
41237 GAGTTACATC
Statistics
Matches: 139, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
51 77 0.55
52 35 0.25
53 13 0.09
55 14 0.10
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (52 bp):
TTAACACATACTTACACTGGTGTAAGTGAATAAAATTAAAAAAGTGTAGCAC
Found at i:41200 original size:103 final size:102
Alignment explanation
Indices: 41020--41215 Score: 248
Period size: 103 Copynumber: 1.9 Consensus size: 102
41010 CGACTAACCG
* * *
41020 TTAACACATACTTACACTGATGTAATTGAACAAAATAAAAAAATACAACACTTAACACATACTTA
1 TTAACACATACTTACACCGATATAAGTGAACAAAATAAAAAAATACAACACTTAACACATACTTA
* *
41085 CACTGGTGTAAGTGGATAAAATAAAAAAGTATAGCAC
66 CACTGGCGTAAGTGAATAAAATAAAAAAGTATAGCAC
* * * ** * ** *
41122 TTAACACATACTTACACCGGTATAAGTGAATAAAATTTAAAAAATGTAGCACTTAATGCATAGTT
1 TTAACACATACTTACACCGATATAAGTGAACAAAA-TAAAAAAATACAACACTTAACACATACTT
*
41187 ACACTTGCGTAAGTGAATAAAATAAAAAA
65 ACACTGGCGTAAGTGAATAAAATAAAAAA
41216 AAACGTGTAG
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
102 30 0.38
103 48 0.62
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (102 bp):
TTAACACATACTTACACCGATATAAGTGAACAAAATAAAAAAATACAACACTTAACACATACTTA
CACTGGCGTAAGTGAATAAAATAAAAAAGTATAGCAC
Found at i:44051 original size:22 final size:21
Alignment explanation
Indices: 44009--44048 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43999 AAGATTATTT
44009 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
44030 TCATTTTTTTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
44049 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:44688 original size:23 final size:23
Alignment explanation
Indices: 44662--44706 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44652 CACCACAGCT
*
44662 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
44685 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
44707 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:44955 original size:149 final size:149
Alignment explanation
Indices: 44685--44988 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
44675 CGAAGTGCCC
44685 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
44750 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
44815 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
*
44834 CGTAGAATTGCACCTTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
44899 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
44964 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
44983 CGTAGA
1 CGTAGA
44989 CCCTCTACCC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:45552 original size:66 final size:67
Alignment explanation
Indices: 45444--45588 Score: 256
Period size: 67 Copynumber: 2.2 Consensus size: 67
45434 TTATGGGGAA
45444 ATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGG-AATTCATATTCGTTGAGGG
1 ATCGGTT-CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTGAGGG
45508 GGT
65 GGT
* *
45511 ATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTGAGGGG
1 ATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTGAGGGG
45576 GT
66 GT
45578 ATCGGTTCCCC
1 ATCGGTTCCCC
45589 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 35 0.47
67 40 0.53
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.31
Consensus pattern (67 bp):
ATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTGAGGGG
GT
Found at i:51699 original size:23 final size:23
Alignment explanation
Indices: 51673--51717 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
51663 CACCACAGCT
*
51673 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
51696 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
51718 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:51966 original size:149 final size:149
Alignment explanation
Indices: 51696--51999 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
51686 CGAAGTGCCC
51696 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
51761 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
51826 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
51845 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
51910 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
51975 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
51994 CGTAGA
1 CGTAGA
52000 CCCTCTACCC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:52563 original size:66 final size:67
Alignment explanation
Indices: 52449--52599 Score: 259
Period size: 67 Copynumber: 2.3 Consensus size: 67
52439 TTTTTCTCAT
*
52449 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGG-AATTCATATTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGT
52513 TGA
65 TGA
* *
52516 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTT
52581 GA
66 GA
52583 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
52600 TTGAATGGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
66 35 0.44
67 45 0.56
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTT
GA
Found at i:55446 original size:65 final size:65
Alignment explanation
Indices: 55311--55454 Score: 157
Period size: 65 Copynumber: 2.2 Consensus size: 65
55301 TGGATGGTCT
* * *** *
55311 GTGCATCGGTACACAAAATGCATTTGATATTAAAAAATATTCAGGAGTGCATTGATGCATGCCTT
1 GTGCATCGGTACACAAAATGCATTTGATAATAAAAAATATTCAGGAGTGCATCGATGCATAAATG
* * **
55376 ATGCATCGGTACACAAAATGCATTTGA-AATACAATTTATTCAAGG-GTGCATCGATGCATTAAA
1 GTGCATCGGTACACAAAATGCATTTGATAATAAAAAATATTC-AGGAGTGCATCGATGCA-TAAA
55439 TG
64 TG
*
55441 GTGCATCAGTACAC
1 GTGCATCGGTACAC
55455 TACTTTGAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
64 22 0.34
65 43 0.66
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTTGATAATAAAAAATATTCAGGAGTGCATCGATGCATAAATG
Found at i:65638 original size:13 final size:13
Alignment explanation
Indices: 65620--65646 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65610 GTCAAAAAGA
65620 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
65633 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
65646 G
1 G
65647 CAATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:66095 original size:16 final size:17
Alignment explanation
Indices: 66074--66108 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
66064 CACTATTCAC
*
66074 GTGAATAGT-GAATTTT
1 GTGAATAGTAAAATTTT
66090 GTGAATAGTAAAATTTT
1 GTGAATAGTAAAATTTT
66107 GT
1 GT
66109 CGGCGATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
GTGAATAGTAAAATTTT
Found at i:72009 original size:30 final size:31
Alignment explanation
Indices: 71941--72012 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
71931 TTAAAAAAAA
*
71941 GTTATATTTCAATCACTAACATTATTAATTT
1 GTTATATTTTAATCACTAACATTATTAATTT
* * *
71972 ATTATATTTTAATCACTTACACTT-TTGA-TT
1 GTTATATTTTAATCACTAACA-TTATTAATTT
72002 GTTATATTTTA
1 GTTATATTTTA
72013 GACAATGAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 12 0.34
31 21 0.60
32 2 0.06
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (31 bp):
GTTATATTTTAATCACTAACATTATTAATTT
Found at i:80806 original size:16 final size:17
Alignment explanation
Indices: 80779--80814 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
80769 TATATGAGAA
80779 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
80796 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
80812 AAA
1 AAA
80815 ATAAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:80899 original size:2 final size:2
Alignment explanation
Indices: 80892--80930 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
80882 ATTATTAATG
*
80892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80931 ATCCAGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:81475 original size:14 final size:14
Alignment explanation
Indices: 81456--81483 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
81446 TTCCAGGCAT
81456 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
81470 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
81484 AAGCATCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:81497 original size:20 final size:20
Alignment explanation
Indices: 81472--81523 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
81462 CCATCCGACC
81472 GAGGCCATCCGAAAGCATCT
1 GAGGCCATCCGAAAGCATCT
*
81492 GAGGCCATCCGAGAGCATCT
1 GAGGCCATCCGAAAGCATCT
81512 GAGGCCATCCGA
1 GAGGCCATCCGA
81524 CCGAGCTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.13
Consensus pattern (20 bp):
GAGGCCATCCGAAAGCATCT
Found at i:81549 original size:10 final size:10
Alignment explanation
Indices: 81451--81590 Score: 64
Period size: 10 Copynumber: 13.0 Consensus size: 10
81441 CGACCTTCCA
81451 GGCATCCGAG
1 GGCATCCGAG
*
81461 GCCATCCGACCG
1 GGCATCCGA--G
*
81473 AGGCCATCCGAA
1 -GG-CATCCGAG
* *
81485 AGCATCTGAG
1 GGCATCCGAG
*
81495 GCCATCCGAG
1 GGCATCCGAG
* *
81505 AGCATCTGAG
1 GGCATCCGAG
*
81515 GCCATCCGACCG
1 GGCATCCGA--G
* *
81527 AGCTATGCGAG
1 GGC-ATCCGAG
81538 GGCATCCGAG
1 GGCATCCGAG
*
81548 GGCAACCGAG
1 GGCATCCGAG
*
81558 CGAGCTATGCGAG
1 -G-GC-ATCCGAG
*
81571 GGAATCCGAG
1 GGCATCCGAG
*
81581 GGCAACCGAG
1 GGCATCCGAG
81591 CGAGGGTAGG
Statistics
Matches: 93, Mismatches: 27, Indels: 20
0.66 0.19 0.14
Matches are distributed among these distances:
10 63 0.68
11 6 0.06
12 6 0.06
13 11 0.12
14 7 0.08
ACGTcount: A:0.25, C:0.31, G:0.34, T:0.11
Consensus pattern (10 bp):
GGCATCCGAG
Found at i:81562 original size:33 final size:33
Alignment explanation
Indices: 81501--81594 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
81491 TGAGGCCATC
* * * * *
81501 CGAGAGCATCTGAGGCCATCCGACCGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
81534 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
*
81567 CGAGGGAATCCGAGGGCAACCGAGCGAG
1 CGAGGGCATCCGAGGGCAACCGAGCGAG
81595 GGTAGGTCGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.26, C:0.28, G:0.37, T:0.10
Consensus pattern (33 bp):
CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
Found at i:81668 original size:33 final size:33
Alignment explanation
Indices: 81627--81701 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
81617 GCGACCTACC
*
81627 CTCGCTCGGTTGCCCTCAGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCAGATGCCCTCGCATAG
* *
81660 CTCGCTCGGTTTCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCAGATGCCCTCGCATAG
*
81693 CTCGTTCGG
1 CTCGCTCGG
81702 ATGGCCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.09, C:0.39, G:0.24, T:0.28
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCAGATGCCCTCGCATAG
Found at i:81710 original size:33 final size:33
Alignment explanation
Indices: 81627--81711 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
81617 GCGACCTACC
* * *
81627 CTCGCTCGGTTGCCCTCAGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* *
81660 CTCGCTCGGTTTCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* *
81693 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGATGCCCTCGG
81712 TCGGATGGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.38, G:0.26, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
Found at i:81715 original size:14 final size:14
Alignment explanation
Indices: 81693--81725 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
81683 CCTCGCATAG
*
81693 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
81707 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
81721 CTCGG
1 CTCGG
81726 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:81750 original size:44 final size:46
Alignment explanation
Indices: 81673--81761 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 46
81663 GCTCGGTTTC
81673 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGGCCTCGGTCGGATGG
1 CCTCGGATGCCCTCGCATAGCTC-TTCGGATGGCCTCGGTCGGATGG
* *
81720 CCTCGGATGCTCTCGGAT-GCT-TTCGGATGGCCTCGGTCGGAT
1 CCTCGGATGCCCTCGCATAGCTCTTCGGATGGCCTCGGTCGGAT
81762 AAACAAGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
44 21 0.52
46 3 0.08
47 16 0.40
ACGTcount: A:0.10, C:0.30, G:0.34, T:0.26
Consensus pattern (46 bp):
CCTCGGATGCCCTCGCATAGCTCTTCGGATGGCCTCGGTCGGATGG
Found at i:85382 original size:30 final size:28
Alignment explanation
Indices: 85341--85437 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 28
85331 CTTCATCAAC
85341 CTTTAAATTTTAGATAGAATACTAATTTGA
1 CTTTAAATTTTAGATA-AATA-TAATTTGA
* * *
85371 CTTTGAATTTTAGATAAATATCATTTTAA
1 CTTTAAATTTTAGATAAATAT-AATTTGA
*
85400 C-ATAAATTTTAGATAAAATATTAATTTGA
1 CTTTAAATTTTAGAT-AAATA-TAATTTGA
85429 CTTATAAAT
1 CTT-TAAAT
85438 CATATAAAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
28 12 0.22
29 21 0.39
30 16 0.30
31 5 0.09
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (28 bp):
CTTTAAATTTTAGATAAATATAATTTGA
Found at i:89392 original size:16 final size:16
Alignment explanation
Indices: 89371--89401 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
89361 TCTCCATTAC
89371 TTTAACACTTCTCCCA
1 TTTAACACTTCTCCCA
89387 TTTAACACTTCTCCC
1 TTTAACACTTCTCCC
89402 CTTTTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.39, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTAACACTTCTCCCA
Found at i:91665 original size:19 final size:19
Alignment explanation
Indices: 91638--91721 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 19
91628 AATTCCAGAA
*
91638 CCCCAAGGGGGTATCGATT
1 CCCCAAGGGGGAATCGATT
* *
91657 CCCCTAGGGGGAATCGGTT
1 CCCCAAGGGGGAATCGATT
*
91676 CCCATTCAAAGGGGGAATCGGTT
1 CCC---C-AAGGGGGAATCGATT
* * *
91699 CCCTCATGAGGGTATCGATT
1 CCC-CAAGGGGGAATCGATT
91719 CCC
1 CCC
91722 TCTGCACCAA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 19 0.36
20 14 0.26
21 2 0.04
22 1 0.02
23 17 0.32
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (19 bp):
CCCCAAGGGGGAATCGATT
Found at i:95695 original size:15 final size:15
Alignment explanation
Indices: 95675--95728 Score: 108
Period size: 15 Copynumber: 3.6 Consensus size: 15
95665 TTCTTGTTCC
95675 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
95690 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
95705 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
95720 TCTTCATCG
1 TCTTCATCG
95729 CTCCATGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.35
Consensus pattern (15 bp):
TCTTCATCGGAACCT
Done.