Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007702.1 Hibiscus syriacus cultivar Beakdansim tig00109913_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: 61708
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:99 original size:22 final size:22
Alignment explanation
Indices: 71--114 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
61 CACTCTCTCA
71 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
93 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
115 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:400 original size:20 final size:20
Alignment explanation
Indices: 375--412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
365 CGATTCTCTC
375 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
395 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
413 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1741 original size:18 final size:18
Alignment explanation
Indices: 1720--1764 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1710 TCCACTTCGG
*
1720 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1738 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1756 GAGCCATCA
1 GAGCCATCA
1765 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2259 original size:20 final size:20
Alignment explanation
Indices: 2234--2279 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2224 TAGTTTACTT
2234 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* *
2254 TCGCAACGCGAAAATGGCTA
1 TCGCAACACGAAAATGACTA
2274 TCGCAA
1 TCGCAA
2280 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2284 original size:20 final size:20
Alignment explanation
Indices: 2242--2305 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
2232 TTTCGCAACA
*
2242 CGAAAATGACTATCGCAACG
1 CGAAAATGACTATCGCAATG
*
2262 CGAAAATGGCTATCGCAATG
1 CGAAAATGACTATCGCAATG
**
2282 CG-AAATGAAAATCGCAATG
1 CGAAAATGACTATCGCAATG
2301 CGAAA
1 CGAAA
2306 TGAAATCGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 16 0.42
20 22 0.58
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
CGAAAATGACTATCGCAATG
Found at i:2313 original size:18 final size:19
Alignment explanation
Indices: 2273--2353 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
2263 GAAAATGGCT
2273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2292 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
2310 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
2324 ATCGCAACGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
2342 ATCGCAATGCGA
1 ATCGCAATGCGA
2354 TTTGTGTTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 10 0.19
16 4 0.08
17 1 0.02
18 22 0.42
19 16 0.30
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2417 original size:19 final size:19
Alignment explanation
Indices: 2360--2447 Score: 117
Period size: 18 Copynumber: 4.7 Consensus size: 19
2350 GCGATTTGTG
*
2360 TTCGCGTTGCGAT-TTCAT
1 TTCGCGTTGCGATAGTCAT
*
2378 TTCGCGTTGCGAT-TTCAT
1 TTCGCGTTGCGATAGTCAT
* *
2396 TTCGCATTGCGATAGCCAT
1 TTCGCGTTGCGATAGTCAT
2415 TTCCGCGTTGCGATAGTCAT
1 TT-CGCGTTGCGATAGTCAT
2435 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2448 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
18 30 0.48
19 16 0.25
20 17 0.27
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTCAT
Found at i:2464 original size:39 final size:37
Alignment explanation
Indices: 2360--2466 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 37
2350 GCGATTTGTG
*
2360 TTCGCGTTGCGA-TTTCATTTCGCGTTGCGATTTCAT
1 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATGTCAT
* ***
2396 TTCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCATTT-CGCGTTGCGAT-GTCAT
* *
2435 TTCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TTCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
2467 AAGTAAACTA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
36 11 0.20
37 5 0.09
38 11 0.20
39 26 0.46
40 3 0.05
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (37 bp):
TTCGCGTTGCGATTTTCATTTCGCGTTGCGATGTCAT
Found at i:4315 original size:13 final size:14
Alignment explanation
Indices: 4299--4333 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
4289 ATTGTTTAAT
4299 TGATTTGTAAA-GA
1 TGATTTGTAAATGA
*
4312 TGATTTGTAAATGT
1 TGATTTGTAAATGA
4326 TGATTTGT
1 TGATTTGT
4334 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TGATTTGTAAATGA
Found at i:4523 original size:19 final size:19
Alignment explanation
Indices: 4449--4516 Score: 118
Period size: 19 Copynumber: 3.6 Consensus size: 19
4439 ATCGCAACGA
4449 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
4468 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
4487 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
4506 GAAAATCGCAA
1 GAAAATCGCAA
4517 CGAGAAAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.18
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:4592 original size:20 final size:20
Alignment explanation
Indices: 4535--4592 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
4525 TCGCATTGCG
* *
4535 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
4555 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4575 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
4593 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:5679 original size:24 final size:24
Alignment explanation
Indices: 5652--5705 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5642 GTATTCGAAA
* *
5652 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
5676 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
5700 TTTGAT
1 TTTGAT
5706 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:8217 original size:19 final size:19
Alignment explanation
Indices: 8195--8253 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
8185 GAAAATTACT
8195 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
8214 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
8228 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
8247 ATCGCAA
1 ATCGCAA
8254 CGCTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 15 0.45
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:8218 original size:39 final size:37
Alignment explanation
Indices: 8175--8292 Score: 126
Period size: 33 Copynumber: 3.4 Consensus size: 37
8165 CTTAATGTCC
8175 ATCGCAACGCGAAAATTACTATCGCAATACGAAATGAAA
1 ATCGCAACGCG-AAATTA-TATCGCAATACGAAATGAAA
* *
8214 ATCGCAA--CGAGA-GA-ATCGCAATACGAAATGAAA
1 ATCGCAACGCGAAATTATATCGCAATACGAAATGAAA
* *
8247 ATCGCAACGC-TAATT-T-T-GCAATGCGAAATGAAA
1 ATCGCAACGCGAAATTATATCGCAATACGAAATGAAA
8280 ATCGCAACGCGAA
1 ATCGCAACGCGAA
8293 TTTAATTTCG
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
33 51 0.76
34 3 0.04
35 2 0.03
36 2 0.03
37 2 0.03
39 7 0.10
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (37 bp):
ATCGCAACGCGAAATTATATCGCAATACGAAATGAAA
Found at i:8295 original size:33 final size:33
Alignment explanation
Indices: 8196--8295 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 33
8186 AAAATTACTA
* *
8196 TCGCAATACGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATACGAAATGAAAATCGCAACGCGA-ATT
*
8229 TCGCAATACGAAATGAAAATCGCAACGCTAATT
1 TCGCAATACGAAATGAAAATCGCAACGCGAATT
* *
8262 TTGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATACGAAATGAAAATCGCAACGCGAATT
8295 T
1 T
8296 AATTTCGCGT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 1 0.02
33 59 0.98
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (33 bp):
TCGCAATACGAAATGAAAATCGCAACGCGAATT
Found at i:8310 original size:19 final size:20
Alignment explanation
Indices: 8288--8330 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
8278 AAATCGCAAC
8288 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
8307 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
8327 GCGA
1 GCGA
8331 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:8315 original size:14 final size:14
Alignment explanation
Indices: 8316--8349 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8306 TGCGATTTTC
8316 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
8330 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
8344 ATTTTC
1 ATTTTC
8350 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:8491 original size:14 final size:14
Alignment explanation
Indices: 8474--8508 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
8464 CAATTAAACA
8474 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
8488 AAATCACCTTTTAC
1 AAATCAACTTTTAC
8502 AAATCAA
1 AAATCAA
8509 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:9933 original size:21 final size:21
Alignment explanation
Indices: 9867--9933 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
9857 GTGAATCGGG
*
9867 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
9887 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
9909 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
9930 CTCT
1 CTCT
9934 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:9952 original size:42 final size:41
Alignment explanation
Indices: 9867--9989 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
9857 GTGAATCGGG
* * * * *
9867 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
9909 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
9951 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
9990 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:12022 original size:20 final size:20
Alignment explanation
Indices: 11993--12031 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11983 TTTTGGTTGA
11993 AATGAAAATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
*
12013 AATGAGAATCGCAACGAGA
1 AATGAAAATCGCAACGAGA
12032 GAATCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAT
Found at i:12035 original size:14 final size:14
Alignment explanation
Indices: 12016--12042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12006 ACGAGATAAT
12016 GAGAATCGCAACGA
1 GAGAATCGCAACGA
12030 GAGAATCGCAACG
1 GAGAATCGCAACG
12043 CGAAATGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.30, T:0.07
Consensus pattern (14 bp):
GAGAATCGCAACGA
Found at i:12057 original size:33 final size:33
Alignment explanation
Indices: 11999--12131 Score: 122
Period size: 33 Copynumber: 3.8 Consensus size: 33
11989 TTGAAATGAA
* * * *
11999 AATCGCAACGAGATAATGAGAATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACCAGAC
** *
12033 AATCGCAACGCGAAATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGAAAATCGCAACCAGAC
* *
12066 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-C-C---A-GAC
12105 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
12132 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
33 39 0.48
34 13 0.16
35 1 0.01
38 1 0.01
39 28 0.34
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACCAGAC
Found at i:12099 original size:20 final size:19
Alignment explanation
Indices: 11991--12136 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
11981 TCTTTTGGTT
*
11991 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
12010 GATAATGAGAATCGCAA--C
1 GA-AATGAAAATCGCAACGC
*
12028 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
12044 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
12062 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
12077 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
12097 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
12116 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
12135 GA
1 GA
12137 TTTTGGTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.20
15 3 0.03
16 2 0.02
18 4 0.04
19 43 0.41
20 31 0.30
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:12169 original size:19 final size:19
Alignment explanation
Indices: 12132--12198 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
12122 AAAATCGCAA
**
12132 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
12151 TGCGATTTTTATTTTGCGT
1 TGCGATTTTTATTTCGCGT
**
12170 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
12190 TGCGATTTT
1 TGCGATTTT
12199 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:12734 original size:20 final size:20
Alignment explanation
Indices: 12710--12843 Score: 162
Period size: 20 Copynumber: 6.7 Consensus size: 20
12700 CGCTATGTAA
* * *
12710 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
12730 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
12750 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
12771 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12791 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12811 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12831 ATCGCATTGCGAT
1 ATCGCATTGCGAT
12844 TTTCCCAATT
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.03
20 85 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:12862 original size:81 final size:81
Alignment explanation
Indices: 12710--12864 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
12700 CGCTATGTAA
* * * * ** *
12710 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
12775 CATTGCGATAGTCAGT
66 CATTGCGATAGTCAGT
* * *
12791 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
*
12855 GCGTTGCGAT
65 GCATTGCGAT
12865 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
81 60 0.97
82 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
CATTGCGATAGTCAGT
Found at i:12954 original size:21 final size:21
Alignment explanation
Indices: 12914--12954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12904 ATTGTATACC
**
12914 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
12935 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
12955 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:16261 original size:22 final size:23
Alignment explanation
Indices: 16229--16272 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
16219 CCTTTCAATT
*
16229 AAATACATATTTTTATTGAATAA
1 AAATACATATTTTTATTCAATAA
16252 AAATA-ATATTTTTATTCAATA
1 AAATACATATTTTTATTCAATA
16273 TATCATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATACATATTTTTATTCAATAA
Found at i:17306 original size:18 final size:19
Alignment explanation
Indices: 17271--17308 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
17261 CACGGAATGT
17271 AAGATTACCAGTGGGAATAG
1 AAGATTACCAG-GGGAATAG
17291 AAGATTACCA-GGGAATAG
1 AAGATTACCAGGGGAATAG
17309 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAG
Found at i:18056 original size:60 final size:60
Alignment explanation
Indices: 17992--18151 Score: 171
Period size: 60 Copynumber: 2.7 Consensus size: 60
17982 ACTCTTATTT
* * *
17992 TAAATTAATCCTTAAACTTTTGAATATTTTAATTTTATCGC-TAAACTGTGACT-CTCGTTC
1 TAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATC-CATAAACTAT-ACTCCTCGTTC
* * * * *
18052 TAAATCAATCCTTAAAGTTTTGAACATTCTAATTTCATCCATAAACTATATTCCTCTTTC
1 TAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCATAAACTATACTCCTCGTTC
** * **
18112 TAAATTAGCCCTCAAACTTTTGAATATTCCCATTTCATCC
1 TAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCC
18152 CCAGTTTCAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 3 0.04
60 79 0.96
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (60 bp):
TAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCATAAACTATACTCCTCGTTC
Found at i:18373 original size:60 final size:58
Alignment explanation
Indices: 18280--18448 Score: 164
Period size: 60 Copynumber: 2.8 Consensus size: 58
18270 AGTATATATG
* ** *
18280 TATAGTTTGGGATGAAGTCAAAATGTTAAAAAAGTTTAGGGGTCAATTTAGGAT-AAAGGT
1 TATAGTTTGGGATGAAATTGAAATGTT--AAAAGTTTAGGGATCAATTTAGGATGAAA-GT
* **
18340 TATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTTT-GAGGATTAATTTAGGATGGTAGT
1 TATAGTTT-GGGATGAAATTGAAATGTT-AAAAGTTTAG-GGATCAATTTAGGATGAAAGT
* *
18400 CATAGTTAGGGATGAAATTAGAATAT-TTAAAAGTTTAGGGATCAATTTA
1 TATAGTTTGGGATGAAATT-GAA-ATGTTAAAAGTTTAGGGATCAATTTA
18449 AAATAAAAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
59 30 0.33
60 43 0.47
61 19 0.21
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (58 bp):
TATAGTTTGGGATGAAATTGAAATGTTAAAAGTTTAGGGATCAATTTAGGATGAAAGT
Found at i:18671 original size:2 final size:2
Alignment explanation
Indices: 18664--18699 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18654 ATTTGTTGAT
18664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18700 TGATACATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:22747 original size:7 final size:7
Alignment explanation
Indices: 22737--22796 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
22727 CTAAATTATA
*
22737 AAACCAT
1 AAACCTT
22744 AAACCTT
1 AAACCTT
*
22751 AAGCCTT
1 AAACCTT
22758 AAACC-T
1 AAACCTT
*
22764 AAGCCTT
1 AAACCTT
* *
22771 AAACATC
1 AAACCTT
22778 AAATCC-T
1 AAA-CCTT
22785 AAACCTT
1 AAACCTT
22792 AAACC
1 AAACC
22797 CTAAGGCCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 7 0.17
7 33 0.80
8 1 0.02
ACGTcount: A:0.45, C:0.30, G:0.03, T:0.22
Consensus pattern (7 bp):
AAACCTT
Found at i:22768 original size:13 final size:14
Alignment explanation
Indices: 22743--22774 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
22733 TATAAAACCA
22743 TAAACCTTAAGCCT
1 TAAACCTTAAGCCT
22757 TAAACC-TAAGCCT
1 TAAACCTTAAGCCT
22770 TAAAC
1 TAAAC
22775 ATCAAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAGCCT
Found at i:22799 original size:14 final size:14
Alignment explanation
Indices: 22706--22800 Score: 59
Period size: 14 Copynumber: 6.8 Consensus size: 14
22696 TTCATTTTTA
22706 TTAAACCCTAAACC
1 TTAAACCCTAAACC
* * *
22720 CTAAATCCTAAA-T
1 TTAAACCCTAAACC
*
22733 TATAAAACCATAAACC
1 T-T-AAACCCTAAACC
* *
22749 TTAAGCCTTAAACC
1 TTAAACCCTAAACC
* * *
22763 -TAAGCCTTAAACA
1 TTAAACCCTAAACC
* *
22776 TCAAATCCTAAACC
1 TTAAACCCTAAACC
22790 TTAAACCCTAA
1 TTAAACCCTAA
22801 GGCCTAAAAC
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
13 12 0.20
14 38 0.63
15 9 0.15
16 1 0.02
ACGTcount: A:0.45, C:0.28, G:0.02, T:0.24
Consensus pattern (14 bp):
TTAAACCCTAAACC
Found at i:22855 original size:7 final size:7
Alignment explanation
Indices: 22845--22870 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22835 CTTAAAACAC
22845 TAAACTA
1 TAAACTA
22852 TAAACTA
1 TAAACTA
22859 TAAACTA
1 TAAACTA
22866 TAAAC
1 TAAAC
22871 CCCAAACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACTA
Found at i:22927 original size:49 final size:49
Alignment explanation
Indices: 22874--22968 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
22864 TATAAACCCC
*
22874 AAACCCCAAACCCTAAATTATAAA-C-TATAAACCTTAAACCCTAAATACT
1 AAACCCCAAA-CATAAATTATAAATCATA-AAACCTTAAACCCTAAATACT
*** *
22923 AAACCTTGAACATAAATTTTAAATCATAAAACCTTAAACCCTAAAT
1 AAACCCCAAACATAAATTATAAATCATAAAACCTTAAACCCTAAAT
22969 CCCTAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
48 11 0.28
49 26 0.67
50 2 0.05
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.25
Consensus pattern (49 bp):
AAACCCCAAACATAAATTATAAATCATAAAACCTTAAACCCTAAATACT
Found at i:25615 original size:17 final size:17
Alignment explanation
Indices: 25593--25648 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
25583 AGGTTCAAAT
25593 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
25610 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
25627 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
25644 TCGAG
1 TCGAG
25649 CTCAAATTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:25647 original size:11 final size:11
Alignment explanation
Indices: 25633--25720 Score: 68
Period size: 11 Copynumber: 7.6 Consensus size: 11
25623 TGAATCGAGT
25633 TCGAGCTTGAA
1 TCGAGCTTGAA
**
25644 TCGAGCTCAAA
1 TCGAGCTTGAA
25655 TTCGAGCTTGAA
1 -TCGAGCTTGAA
**
25667 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
25679 TCGAGCTTCAA
1 TCGAGCTTGAA
* *
25690 TCGAGCTCGAGTC
1 TCGAGCTTGA--A
*
25703 TCGAGCTTCAA
1 TCGAGCTTGAA
25714 TCGAGCT
1 TCGAGCT
25721 CCTGATTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
11 33 0.56
12 18 0.31
13 8 0.14
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:25658 original size:23 final size:23
Alignment explanation
Indices: 25632--25721 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
25622 TTGAATCGAG
*
25632 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTCAATCGAGCTCAAA
*
25655 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTCAATCGAGCTCAAA
* * *
25678 ATCGAGCTTCAATCGAGCTCGAG
1 TTCGAGCTTCAATCGAGCTCAAA
25701 TCTCGAGCTTCAATCGAGCTC
1 T-TCGAGCTTCAATCGAGCTC
25722 CTGATTTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
23 42 0.69
24 19 0.31
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (23 bp):
TTCGAGCTTCAATCGAGCTCAAA
Found at i:26309 original size:29 final size:30
Alignment explanation
Indices: 26252--26326 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
26242 TAGAACTTGA
* * * *
26252 TTTTTTTAGAATTTTAGGATTTTAGGAGTT
1 TTTTTTTGGAATTTTAGAAATTTAGGAGTG
*
26282 TTTTTTTGGAATTTTTGAAATTTA-GAGTG
1 TTTTTTTGGAATTTTAGAAATTTAGGAGTG
* *
26311 TTATTTAGGAATTTTA
1 TTTTTTTGGAATTTTA
26327 ATAATTTCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (30 bp):
TTTTTTTGGAATTTTAGAAATTTAGGAGTG
Found at i:29543 original size:30 final size:30
Alignment explanation
Indices: 29479--29553 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
29469 CAATTTATTG
* *
29479 AATTATATTAAAATTAAGAATAAATTAATA
1 AATTATATAAAAATTAAGAATAAAATAATA
*
29509 AATTATATAAATAATTAAG-ATAAAAT-ATGT
1 AATTATATAAA-AATTAAGAATAAAATAAT-A
29539 AATTATA-AAAAATTA
1 AATTATATAAAAATTA
29554 TTTAACTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 5 0.12
30 23 0.57
31 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (30 bp):
AATTATATAAAAATTAAGAATAAAATAATA
Found at i:38366 original size:30 final size:30
Alignment explanation
Indices: 38239--38363 Score: 173
Period size: 30 Copynumber: 4.2 Consensus size: 30
38229 GTCCGTCACC
*
38239 GCACCTGCGGTTCAGGGAAGTTCCGT-CACT
1 GCACCGGCGGTTCAGGGAAGTTCC-TCCACT
* * *
38269 GCACCGGCGGTTCAGGGTAGCTCCACCACT
1 GCACCGGCGGTTCAGGGAAGTTCCTCCACT
38299 GCACCGGCGGTTCAGGGAAGTTCCTCCACT
1 GCACCGGCGGTTCAGGGAAGTTCCTCCACT
*
38329 GCACCCGG-GGTTCAAGGAAGTTCCTCCACT
1 GCA-CCGGCGGTTCAGGGAAGTTCCTCCACT
38359 GCACC
1 GCACC
38364 CGGTTTAGAT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
29 2 0.02
30 79 0.93
31 4 0.05
ACGTcount: A:0.18, C:0.34, G:0.29, T:0.19
Consensus pattern (30 bp):
GCACCGGCGGTTCAGGGAAGTTCCTCCACT
Found at i:43059 original size:41 final size:42
Alignment explanation
Indices: 42969--43249 Score: 171
Period size: 42 Copynumber: 6.8 Consensus size: 42
42959 AATTGATACT
* * * * *
42969 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATATAATTGACATA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATA-GAGTGATAAA
*
43012 TT-GCGGCGTTTTTA-TAAAAACGCCGCAATAGGGTGATAAA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * ** *
43052 TTAGCGGCGTTTATA-TCACAAACGCTTCAATAGA-TTATAAA
1 TTAGCGGCGTTTTTAGT-AAAAACGCCGCAATAGAGTGATAAA
* * ** * *
43093 TTTTGCGGCG-ATTTAGCCAAAACGCCGCAATATAGTGGTAAA
1 -TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * * ** * * *
43135 CTGGCAGCGTTTTTACCACAAACGCCACAATAGAAT-ATAAA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * * * * *
43176 TTTTGCAGCG-ATTGAGTAAAAACGCCGCAATAGAGCGGTAAA
1 -TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* **
43218 TTGGCGGCGTTTTTACAAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATA
43250 TATACACATA
Statistics
Matches: 178, Mismatches: 51, Indels: 19
0.72 0.21 0.08
Matches are distributed among these distances:
40 7 0.04
41 83 0.47
42 86 0.48
43 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (42 bp):
TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
Found at i:43101 original size:42 final size:41
Alignment explanation
Indices: 42972--43249 Score: 102
Period size: 41 Copynumber: 6.7 Consensus size: 41
42962 TGATACTTTA
* * ** * *
42972 GCGGCGTTTTTAGTAAAAACGCTGCAATATAATTGACATA-TT
1 GCGGCGTTTATA-TAAAAACGCCGCAATAGGA-TGATAAATTT
* * *
43014 GCGGCGTTTTTATAAAAACGCCGCAATAGGGTGATAAATTA
1 GCGGCGTTTATATAAAAACGCCGCAATAGGATGATAAATTT
* ** *
43055 GCGGCGTTTATATCACAAACGCTTCAATA-GATTATAAATTTT
1 GCGGCGTTTATAT-AAAAACGCCGCAATAGGATGATAAA-TTT
*** * * * *
43097 GCGGCGATTTA-GCCAAAACGCCGCAATA-TAGTGGTAAACTG
1 GCGGCG-TTTATATAAAAACGCCGCAATAGGA-TGATAAATTT
* * * * * *
43138 GCAGCGTTTTTACCACAAACGCCACAATAGAAT-ATAAATTTT
1 GCGGCGTTTATA-TAAAAACGCCGCAATAGGATGATAAA-TTT
* * * * * *
43180 GCAGCGATTGA-GTAAAAACGCCGCAATA-GAGCGGTAAATTG
1 GCGGCG-TTTATATAAAAACGCCGCAATAGGA-TGATAAATTT
* *
43221 GCGGCGTTTTTACAAAAAACGCCGCAATA
1 GCGGCGTTTATA-TAAAAACGCCGCAATA
43250 TATACACATA
Statistics
Matches: 172, Mismatches: 50, Indels: 28
0.69 0.20 0.11
Matches are distributed among these distances:
40 11 0.06
41 77 0.45
42 77 0.45
43 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
GCGGCGTTTATATAAAAACGCCGCAATAGGATGATAAATTT
Found at i:43101 original size:83 final size:83
Alignment explanation
Indices: 43012--43249 Score: 271
Period size: 83 Copynumber: 2.9 Consensus size: 83
43002 AATTGACATA
* * * * *
43012 TTGCGGCGTTTTTA-TAAAAACGCCGCAATAGGGTGATAAATTAGCGGCGTTTATATCACAAACG
1 TTGCGGCG-ATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACG
** *
43076 CTTCAATAGATTATAAATT
65 CCACAATAGAATATAAATT
** * * * *
43095 TTGCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTACCACAAACGC
1 TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
43160 CACAATAGAATATAAATT
66 CACAATAGAATATAAATT
* * * * * *
43178 TTGCAGCGATTGAGTAAAAACGCCGCAATAGAGCGGTAAATTGGCGGCGTTTTTACAAAAAACGC
1 TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
*
43243 CGCAATA
66 CACAATA
43250 TATACACATA
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 4 0.03
83 125 0.97
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (83 bp):
TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
CACAATAGAATATAAATT
Found at i:51548 original size:21 final size:22
Alignment explanation
Indices: 51524--51572 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
51514 CGGAAAATGA
51524 AGCAAG-GGAAACAGAGAGAGC
1 AGCAAGCGGAAACAGAGAGAGC
* **
51545 AGC-AGCGGAAGCAGCTAGAGC
1 AGCAAGCGGAAACAGAGAGAGC
51566 AGCAAGC
1 AGCAAGC
51573 TAGAGCAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.41, C:0.20, G:0.37, T:0.02
Consensus pattern (22 bp):
AGCAAGCGGAAACAGAGAGAGC
Found at i:51575 original size:13 final size:13
Alignment explanation
Indices: 51557--51582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51547 CAGCGGAAGC
51557 AGCTAGAGCAGCA
1 AGCTAGAGCAGCA
51570 AGCTAGAGCAGCA
1 AGCTAGAGCAGCA
51583 GCGGAAGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.31, T:0.08
Consensus pattern (13 bp):
AGCTAGAGCAGCA
Found at i:51603 original size:21 final size:21
Alignment explanation
Indices: 51574--51643 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
51564 GCAGCAAGCT
* * *
51574 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAG
51595 AGAGAAGCAGCGGCAGCACAG
1 AGAGAAGCAGCGGCAGCACAG
* *
51616 AGAGAGGCAGCGGCAGAACAG
1 AGAGAAGCAGCGGCAGCACAG
51637 AGAGAAG
1 AGAGAAG
51644 TAATATATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.41, T:0.00
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAG
Found at i:52111 original size:43 final size:43
Alignment explanation
Indices: 51980--52202 Score: 149
Period size: 43 Copynumber: 5.2 Consensus size: 43
51970 CATACATTTA
* * * *
51980 GCGGCGTTTTTGATA-AAAACGCCGCAAAATCTCAATACATATT
1 GCGGCGTTTTTG-TAGAAAACGCCGCTAAATATCAACACCTATT
* * * * * *
52023 CGCAGCG--TTTGTA-AGAAACGCCAG-TAAAAATAAAAATCTACT
1 -GCGGCGTTTTTGTAGA-AAACGCC-GCTAAATATCAACACCTATT
*
52065 GCGGCGTTTTTGTAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTTTGTAGAAAACGCCGCTAAATATCAAC-ACCTATT
* * *
52108 GCGGCG--TTTGTATGCCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTTTTGTA-G-AAAACGCCGCTAAATATCAACACCTATT
** * *
52151 GCGGCGTTTTAAT-GATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTTGTAGA-AAACGCCGCTAAATATCAACACCTATT
52194 GCGGCGTTT
1 GCGGCGTTT
52203 GTTGAACTAT
Statistics
Matches: 141, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
41 14 0.10
42 24 0.17
43 93 0.66
44 7 0.05
45 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTTTGTAGAAAACGCCGCTAAATATCAACACCTATT
Found at i:52312 original size:15 final size:15
Alignment explanation
Indices: 52268--52339 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
52258 CGCCGCAAAC
* *
52268 TTTAGCGGCGCTATT
1 TTTAGCGGCGTTTTT
*
52283 TTTAGCGGCG---CT
1 TTTAGCGGCGTTTTT
52295 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
*
52310 TTTA-CGCCGTATGTGTT
1 TTTAGCGGCGT-T-T-TT
52327 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
52340 AAAAACGCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
12 11 0.24
14 5 0.11
15 16 0.35
16 2 0.04
17 7 0.15
18 5 0.11
ACGTcount: A:0.10, C:0.18, G:0.28, T:0.44
Consensus pattern (15 bp):
TTTAGCGGCGTTTTT
Found at i:54618 original size:3 final size:3
Alignment explanation
Indices: 54610--54662 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
54600 AATATATATT
*
54610 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54658 TAA TA
1 TAA TA
54663 TGGGTAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55002 original size:116 final size:116
Alignment explanation
Indices: 54798--55646 Score: 1328
Period size: 116 Copynumber: 7.4 Consensus size: 116
54788 ATTGAATAAA
* * ** * *
54798 TTCTTC-TCTTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC--TCTACCTGGCAAAGATAATC
54858 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
54911 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
54976 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
55027 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
55092 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
55143 TTCTTCTTCCTTCTTCAGATGGCGAGTTCTTCTCATTATGAACTCTTCCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
55208 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
55259 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
*
55324 TCAAATGATGAATTCAAGAAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
55375 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
* * * *
55440 TCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 TCAA-ATGATGAATTCAAG-CAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
55492 TTCTTCTTCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGACTGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGA-TAATC
* ** * *
55553 CATCAAATGATGGATTCGGGTAAAAGATTGAACAAATTCTTCTCATTATGAAC
64 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
55606 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT
55647 TTCTCTGGAA
Statistics
Matches: 701, Mismatches: 24, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
113 8 0.01
114 121 0.17
115 14 0.02
116 477 0.68
117 81 0.12
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (116 bp):
TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
Found at i:56544 original size:83 final size:83
Alignment explanation
Indices: 56405--56714 Score: 525
Period size: 83 Copynumber: 3.7 Consensus size: 83
56395 GTAGTTCTTA
*
56405 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
56470 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
56488 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
56553 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
56571 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
56636 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
56654 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTT
56715 TCATTTAATG
Statistics
Matches: 213, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
83 211 0.99
84 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:57768 original size:1 final size:1
Alignment explanation
Indices: 57759--57804 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
57749 TTTTTTCCTC
* * * *
57759 TTTTCTTTTTTCTTTTTTTTTTCTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
57805 CTTTCTTTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:57803 original size:23 final size:23
Alignment explanation
Indices: 57743--57813 Score: 90
Period size: 25 Copynumber: 3.0 Consensus size: 23
57733 CTTGACCCCC
* *
57743 TTTTCTTTTTTTCCTCTTTTCTTT
1 TTTTTTTTTTTTTCTCTTTT-TTT
57767 TTTCTTTTTTTTTTCTCTTTTTTT
1 TTT-TTTTTTTTTTCTCTTTTTTT
*
57791 TTTTTTTTTTTTT-TCTTTCTTT
1 TTTTTTTTTTTTTCTCTTTTTTT
57813 T
1 T
57814 CAAGCATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 9 0.21
23 10 0.23
24 9 0.21
25 15 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTTTTTCTCTTTTTTT
Done.