Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001901.1 Hibiscus syriacus cultivar Beakdansim tig00003852_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: 41925
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1219 original size:21 final size:20
Alignment explanation
Indices: 1152--1290 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 20
1142 AAATGACCAA
***
1152 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1172 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1192 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1213 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1234 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1254 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1275 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1291 ACACATAAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.01
20 42 0.47
21 47 0.52
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1469 original size:20 final size:20
Alignment explanation
Indices: 1257--1482 Score: 210
Period size: 20 Copynumber: 11.5 Consensus size: 20
1247 CGATTTTCCA
** *
1257 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1277 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
1297 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1317 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
1337 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
1357 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1377 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
1397 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
1417 AAATCGCAA--CGAAT-CGT
1 AAATCGCAACGCGAATCCGT
**
1434 AAATCGC-ACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1453 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1473 AAATCACAAC
1 AAATCGCAAC
1483 ACTGAAATTT
Statistics
Matches: 172, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
16 1 0.01
17 10 0.06
18 6 0.03
19 10 0.06
20 144 0.84
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:2188 original size:21 final size:22
Alignment explanation
Indices: 2145--2188 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2135 AAATTTGGTC
2145 TTGGTCAATATCCGGACTTTGA
1 TTGGTCAATATCCGGACTTTGA
2167 TTGGTCAATA-CACGGA-TTTGA
1 TTGGTCAATATC-CGGACTTTGA
2188 T
1 T
2189 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (22 bp):
TTGGTCAATATCCGGACTTTGA
Found at i:2379 original size:12 final size:12
Alignment explanation
Indices: 2362--2386 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2352 CATATAATCT
2362 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2374 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2386 G
1 G
2387 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4677 original size:19 final size:19
Alignment explanation
Indices: 4655--4941 Score: 320
Period size: 19 Copynumber: 16.4 Consensus size: 19
4645 CGGAAATTAC
*
4655 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4674 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
4688 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
4708 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4722 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4741 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4760 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4774 AATCGCAATGC-AAATGAA
1 AATCGCAATGCGAAATGAA
4792 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4811 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4825 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4844 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
4863 AATCGCAA----ATA-GAG
1 AATCGCAATGCGAAATGAA
4877 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4896 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4915 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4934 AATCGCAA
1 AATCGCAA
4942 CGAGAGAATC
Statistics
Matches: 229, Mismatches: 12, Indels: 54
0.78 0.04 0.18
Matches are distributed among these distances:
14 52 0.23
15 5 0.02
16 6 0.03
17 7 0.03
18 18 0.08
19 128 0.56
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4742 original size:33 final size:34
Alignment explanation
Indices: 4655--4941 Score: 238
Period size: 33 Copynumber: 8.2 Consensus size: 34
4645 CGGAAATTAC
* *
4655 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
4688 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
4722 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* * *
4760 AATCGCAACGAGAGAATCG-CAAT-GCAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCAACGATGAA
*
4792 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
4825 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
4863 AATCGCAA----ATA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
4896 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
4934 AATCGCAA
1 AATCGCAA
4942 CGAGAGAATC
Statistics
Matches: 215, Mismatches: 16, Indels: 41
0.79 0.06 0.15
Matches are distributed among these distances:
30 1 0.00
31 6 0.03
32 20 0.09
33 84 0.39
34 32 0.15
35 5 0.02
37 4 0.02
38 56 0.26
39 6 0.03
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:4819 original size:103 final size:104
Alignment explanation
Indices: 4683--4922 Score: 446
Period size: 103 Copynumber: 2.3 Consensus size: 104
4673 AAATCCCAAC
4683 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
*
4748 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-AA
65 ATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
4787 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
*
4852 TGCGAAATGAAAATCGCAAATAGAGAATCGCAATGCGAA
66 TGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
4891 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
4923 TGCGAAATGA
Statistics
Matches: 133, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
103 83 0.62
104 50 0.38
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
Found at i:4963 original size:52 final size:52
Alignment explanation
Indices: 4683--4922 Score: 446
Period size: 52 Copynumber: 4.6 Consensus size: 52
4673 AAATCCCAAC
4683 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4736 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-AA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4787 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
**
4839 ATGAAAATCGCAATGCGAAATGAAAATCGCAAATAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4891 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
4923 TGCGAAATGA
Statistics
Matches: 184, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
51 51 0.28
52 117 0.64
53 16 0.09
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4979 original size:71 final size:71
Alignment explanation
Indices: 4683--4963 Score: 300
Period size: 71 Copynumber: 4.0 Consensus size: 71
4673 AAATCCCAAC
* * *
4683 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAAT-GCGAAATGA-A-AAT
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGA-AAT-GAAAATCGC-AAA-GAGAGAAT
4744 CGCAATGCGAA
61 CGCAATGCGAA
* * * *
4755 ATGAAAATCGCAA--CG--A-GAGAATCGCAATGC-AAATGAAAATCGCAATGCGA-AAT-GAAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCG-CA
*
4812 AT-CGCA
65 ATGCGAA
* *
4818 ACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAATAGAGAATCGC
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGC
4883 AATGCGAA
64 AATGCGAA
*
4891 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAA
4956 TGCGAA
66 TGCGAA
4962 AT
1 AT
4964 TATAAACGCA
Statistics
Matches: 176, Mismatches: 18, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
63 9 0.05
64 16 0.09
65 11 0.06
66 11 0.06
67 3 0.02
69 2 0.01
70 14 0.08
71 83 0.47
72 20 0.11
73 7 0.04
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (71 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAA
TGCGAA
Found at i:5012 original size:52 final size:52
Alignment explanation
Indices: 4950--5085 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
4940 AACGAGAGAA
*
4950 TCGCAATGCGAAATT-ATAAACGCATTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGAAATTCAT-AACGCATTGCGATTCTCTCGTTGCGATTTTCATT
** **
5001 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATTCATAACGCATTGCGATTCTCTCGTTGCGATTTTCATT
** **
5054 TCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGAAATTCATAACGCATTGCGATT
5086 TTCATTTCGC
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
51 1 0.01
52 66 0.86
53 10 0.13
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (52 bp):
TCGCATTGCGAAATTCATAACGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:5111 original size:19 final size:19
Alignment explanation
Indices: 4988--5103 Score: 172
Period size: 19 Copynumber: 6.4 Consensus size: 19
4978 GATTCTCTCG
4988 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5007 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5026 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5040 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5059 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5078 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5097 TTGCGAT
1 TTGCGAT
5104 AGTCATTTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 7 0.08
19 61 0.69
20 8 0.09
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5228 original size:14 final size:14
Alignment explanation
Indices: 5209--5244 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5199 CATCAATTAC
5209 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5223 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5237 AC-AATCAA
1 ACAAATCAA
5245 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6664 original size:22 final size:22
Alignment explanation
Indices: 6633--6697 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
6623 GTGAATCGGG
6633 CTCTTGAATGGTGGGAGGGGAC
1 CTCTTGAATGGTGGGAGGGGAC
* * ** *
6655 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAGGGGAC
*
6676 CTCTTGAACGGTGGGAGGGGAC
1 CTCTTGAATGGTGGGAGGGGAC
6698 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (22 bp):
CTCTTGAATGGTGGGAGGGGAC
Found at i:6700 original size:21 final size:21
Alignment explanation
Indices: 6633--6700 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
6623 GTGAATCGGG
6633 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
* * ** * *
6654 CCTCTTCAATGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
*
6676 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
6697 CTCT
1 CTCT
6701 CGAGGAATGA
Statistics
Matches: 33, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:7226 original size:14 final size:14
Alignment explanation
Indices: 7207--7263 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
7197 GCGAAATGAA
*
7207 AATCGCAACGACAG
1 AATCGCAACGAAAG
7221 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
7238 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
7254 AATCGCAACG
1 AATCGCAACG
7264 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:7234 original size:33 final size:33
Alignment explanation
Indices: 7188--7280 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
7178 GCGAAACCAA
*
7188 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
7221 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
7254 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
7281 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:7245 original size:19 final size:19
Alignment explanation
Indices: 7151--7285 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
7141 TAGTTTACTT
* *
7151 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
7171 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
7190 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
7209 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
7223 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
7242 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
7256 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
7275 TCGCAATGCGA
1 TCGCAACGCGA
7286 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:7334 original size:18 final size:18
Alignment explanation
Indices: 7281--7390 Score: 96
Period size: 18 Copynumber: 6.4 Consensus size: 18
7271 AAAATCGCAA
7281 TGCGATTTTGGTTTCGCGT
1 TGCGA-TTTGGTTTCGCGT
7300 TGCGATCTT-G--T--CGT
1 TGCGAT-TTGGTTTCGCGT
7314 TGCGATTTGGTTTCGCGT
1 TGCGATTTGGTTTCGCGT
7332 TGCGATTCT-G--T--CGT
1 TGCGATT-TGGTTTCGCGT
**
7346 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTGGTTTCGCGT
7365 TGCGATTTGGTTTCGCGT
1 TGCGATTTGGTTTCGCGT
7383 TGCGATTT
1 TGCGATTT
7391 TAAGTTTCGT
Statistics
Matches: 75, Mismatches: 3, Indels: 27
0.71 0.03 0.26
Matches are distributed among these distances:
13 2 0.03
14 19 0.25
15 2 0.03
16 3 0.04
17 1 0.01
18 32 0.43
19 16 0.21
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.46
Consensus pattern (18 bp):
TGCGATTTGGTTTCGCGT
Found at i:7366 original size:33 final size:34
Alignment explanation
Indices: 7281--7371 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 34
7271 AAAATCGCAA
7281 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
7314 TGCGA-TTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
7346 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
7372 TGGTTTCGCG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.08, C:0.18, G:0.29, T:0.46
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:7571 original size:93 final size:93
Alignment explanation
Indices: 7455--7829 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
7445 ATGGATTGCA
7455 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
7519 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
7547 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
7612 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
7640 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
7705 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
7733 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
7797 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
7825 TTACT
1 TTACT
7830 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 37 0.13
93 243 0.87
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:9547 original size:14 final size:14
Alignment explanation
Indices: 9528--9616 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
9518 TTGAAATGAA
9528 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
9542 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
9561 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
9575 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
9592 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
9607 AATCGCAACG
1 AATCGCAACG
9617 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 28 0.45
15 2 0.03
16 10 0.16
17 3 0.05
18 9 0.15
19 10 0.16
ACGTcount: A:0.43, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:9602 original size:32 final size:33
Alignment explanation
Indices: 9520--9633 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
9510 TCTTTTGGTT
9520 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
9553 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
9586 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
9618 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
9634 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 31 0.40
33 47 0.60
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:9669 original size:14 final size:14
Alignment explanation
Indices: 9650--9706 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
9640 TTTGGTTTCG
9650 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
9664 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
9683 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
9697 CGTTGCGATT
1 CGTTGCGATT
9707 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:9684 original size:33 final size:33
Alignment explanation
Indices: 9647--9711 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
9637 GATTTTGGTT
9647 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
9680 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
9712 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:9747 original size:41 final size:41
Alignment explanation
Indices: 9690--9767 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
9680 TCGCGTTGCG
*
9690 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
9731 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
9768 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:9752 original size:20 final size:21
Alignment explanation
Indices: 9691--9766 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
9681 CGCGTTGCGA
9691 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
9712 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
9732 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
9753 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
9767 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:9888 original size:33 final size:33
Alignment explanation
Indices: 9846--9916 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
9836 AATACTAACT
*
9846 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
9879 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
9912 TGAAA
1 TGAAA
9917 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:10148 original size:22 final size:22
Alignment explanation
Indices: 10096--10150 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
10086 TGGTTGTGAG
**
10096 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
10118 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
10140 GGATTTCTTCG
1 GGATTTCTTCG
10151 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:10322 original size:20 final size:20
Alignment explanation
Indices: 10297--10490 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
10287 CTTTAAATAT
10297 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
10317 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
10339 -TCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
10358 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
10378 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
*
10398 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
10418 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
10438 CGAGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
10458 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
10478 CGCGTTGCGATTT
1 CGCGTTGCGATTT
10491 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:10464 original size:60 final size:60
Alignment explanation
Indices: 10299--10490 Score: 217
Period size: 60 Copynumber: 3.2 Consensus size: 60
10289 TTAAATATCG
* *
10299 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATT-ATCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACGAGTTGCGA-TTTATGTATTCA-CGTTGCGATTTACAGATACA
* *** * *
10360 CGTTGCGATATACGGATACGCA-TTGCGATTTACCCATACACGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG-AGTTGCGATTTATGTATTCACGTTGCGATTTACAGATACA
* * * * * *
10420 CGTTGCGATTTACGGATACGAGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCACGTTGCGATTTACAGATACA
10480 CGTTGCGATTT
1 CGTTGCGATTT
10491 TGGAAAATCG
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.01
60 81 0.75
61 26 0.24
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCACGTTGCGATTTACAGATACA
Found at i:10507 original size:21 final size:21
Alignment explanation
Indices: 10477--10559 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
10467 ATTTTCATAT
*
10477 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
10498 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
10519 TCGCATTGCAATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
10540 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
10560 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:12302 original size:24 final size:24
Alignment explanation
Indices: 12275--12350 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
12265 TATATCAAAA
*
12275 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
12299 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
12323 AACAGATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
12347 ATCA
1 ATCA
12351 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:12352 original size:24 final size:24
Alignment explanation
Indices: 12292--12407 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
12282 CATAAATCAG
* *
12292 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
12316 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
12340 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
12364 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
12388 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
12408 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 77 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:12423 original size:48 final size:48
Alignment explanation
Indices: 12325--12425 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
12315 GGTCAAGTAA
** *
12325 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* *
12373 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
12421 CAGAT
1 CAGAT
12426 AAAATATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:13874 original size:30 final size:30
Alignment explanation
Indices: 13832--13890 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
13822 AATTTAAGGC
13832 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAATGGTTTTTGGACTT-AATTGAATTTAA
13863 AAAAT-GTTTTTGGACTTAATTGAATTTA
1 AAAATGGTTTTTGGACTTAATTGAATTTA
13891 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGGTTTTTGGACTTAATTGAATTTAA
Found at i:14005 original size:21 final size:21
Alignment explanation
Indices: 13980--14058 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
13970 TTCAAGATTG
* *
13980 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
14001 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
14019 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
*
14037 CCTAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
14058 C
1 C
14059 TGCAAGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.22
18 7 0.14
21 31 0.63
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:14026 original size:36 final size:36
Alignment explanation
Indices: 13986--14057 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
13976 ATTGCCCAGG
* *
13986 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
*
14022 GGGTACAGATACCCCCCTAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
14058 CTGCAAGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:14027 original size:15 final size:15
Alignment explanation
Indices: 14007--14036 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13997 CCCCCCCAGG
14007 GGGTACAGATACCCC
1 GGGTACAGATACCCC
14022 GGGTACAGATACCCC
1 GGGTACAGATACCCC
14037 CCTAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:14175 original size:21 final size:21
Alignment explanation
Indices: 14149--14191 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
14139 ATTTGAATAT
*
14149 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
14170 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
14191 T
1 T
14192 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:14257 original size:20 final size:22
Alignment explanation
Indices: 14219--14258 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
14209 TTTGAGTATA
14219 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
14241 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
14259 ATATGCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:17339 original size:36 final size:36
Alignment explanation
Indices: 17299--17370 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
17289 ATTGCCCAGG
* *
17299 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
17335 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
17371 CTGCAGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.14
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:17340 original size:15 final size:15
Alignment explanation
Indices: 17320--17349 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17310 CCCCCCCAGG
17320 GGGTACAGATACCCC
1 GGGTACAGATACCCC
17335 GGGTACAGATACCCC
1 GGGTACAGATACCCC
17350 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:17377 original size:22 final size:21
Alignment explanation
Indices: 17293--17371 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
17283 TTCAAGATTG
* *
17293 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
17314 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
17332 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
17350 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
17371 C
1 C
17372 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 31 0.62
ACGTcount: A:0.23, C:0.37, G:0.28, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:17445 original size:20 final size:21
Alignment explanation
Indices: 17405--17447 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17395 AACAGAATGT
17405 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
17426 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
17447 C
1 C
17448 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:17512 original size:21 final size:21
Alignment explanation
Indices: 17486--17526 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17476 TGAATATTTT
*
17486 TGAAGGGGTATCGATTCCCTA
1 TGAAGGGGTACCGATTCCCTA
17507 TGAAGGGGTACCGATTCCCT
1 TGAAGGGGTACCGATTCCCT
17527 CTATTCTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (21 bp):
TGAAGGGGTACCGATTCCCTA
Found at i:17592 original size:20 final size:22
Alignment explanation
Indices: 17554--17593 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
17544 TTTGAGTATA
17554 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
17576 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
17594 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:17847 original size:34 final size:32
Alignment explanation
Indices: 17808--17877 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
17798 TTTTGTAAAG
* *
17808 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
17842 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
17874 GGGA
1 GGGA
17878 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:26849 original size:16 final size:16
Alignment explanation
Indices: 26825--26855 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26815 ATAAATTAAT
*
26825 TTAATGGTACCCATCG
1 TTAACGGTACCCATCG
26841 TTAACGGTACCCATC
1 TTAACGGTACCCATC
26856 CTTGCTCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAACGGTACCCATCG
Found at i:31908 original size:31 final size:31
Alignment explanation
Indices: 31870--32029 Score: 153
Period size: 32 Copynumber: 5.1 Consensus size: 31
31860 GAACCTCAAT
* *
31870 AACTGTCCATAGGTCCCGTAGAACCTAGGTA
1 AACTGTCCATATGTCCCGTAGAACATAGGTA
* *
31901 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGTAGAACATAGGTA
* *
31932 TACTGTCCATATGTCCCG-AAAGACATAGGTA
1 AACTGTCCATATGTCCCGTAGA-ACATAGGTA
* * *
31963 ATTCTGTCCATATGTCTCG-AAAGACATAGGTA
1 A-ACTGTCCATATGTCCCGTAGA-ACATAGGTA
** * *
31995 ATTTTGTCCATATGTTCTGTAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGTAGAACATAGGTA
32027 AAC
1 AAC
32030 CCTCGACTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
30 2 0.02
31 51 0.47
32 53 0.49
33 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGTAGAACATAGGTA
Found at i:33757 original size:23 final size:23
Alignment explanation
Indices: 33731--33780 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
33721 TTTGTTTCCT
33731 TTAAAATTTTATAAA-TTCATCTC
1 TTAAAATTTTA-AAAGTTCATCTC
*
33754 TTAAAATTTTAAAAGTTCGTCTC
1 TTAAAATTTTAAAAGTTCATCTC
33777 TTAA
1 TTAA
33781 TATAAGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (23 bp):
TTAAAATTTTAAAAGTTCATCTC
Found at i:40019 original size:23 final size:21
Alignment explanation
Indices: 39988--40060 Score: 53
Period size: 23 Copynumber: 3.4 Consensus size: 21
39978 TATAATTTAA
*
39988 TTTATATGACTATGATAGTTGTT
1 TTTAGATGA-TAT-ATAGTTGTT
*
40011 TTTAGATGATATA-A-TT-TAA
1 TTTAGATGATATATAGTTGT-T
*
40030 TTTATATGATTATTATAGTTGTT
1 TTTAGATGA-TA-TATAGTTGTT
40053 TTTAGATG
1 TTTAGATG
40061 CATACATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 1 0.03
19 10 0.26
20 3 0.08
21 3 0.08
22 4 0.10
23 17 0.44
24 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.53
Consensus pattern (21 bp):
TTTAGATGATATATAGTTGTT
Found at i:40034 original size:42 final size:42
Alignment explanation
Indices: 39975--40060 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
39965 ATTTAACTAC
39975 TGATATAATTTAATTTATATGACTATGATAGTTGTTTTTAGA
1 TGATATAATTTAATTTATATGACTATGATAGTTGTTTTTAGA
* *
40017 TGATATAATTTAATTTATATGATTATTATAGTTGTTTTTAGA
1 TGATATAATTTAATTTATATGACTATGATAGTTGTTTTTAGA
40059 TG
1 TG
40061 CATACATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.52
Consensus pattern (42 bp):
TGATATAATTTAATTTATATGACTATGATAGTTGTTTTTAGA
Found at i:40038 original size:19 final size:19
Alignment explanation
Indices: 39975--40039 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
39965 ATTTAACTAC
39975 TGATATAATTTAATTTATA
1 TGATATAATTTAATTTATA
* *
39994 TGACTATGATAGTTGT-TTTTAGA
1 TGA-TAT-A-A-TT-TAATTTATA
40017 TGATATAATTTAATTTATA
1 TGATATAATTTAATTTATA
40036 TGAT
1 TGAT
40040 TATTATAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
18 1 0.03
19 14 0.39
20 4 0.11
21 2 0.06
22 4 0.11
23 10 0.28
24 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (19 bp):
TGATATAATTTAATTTATA
Done.