Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005651.1 Hibiscus syriacus cultivar Beakdansim tig00013206_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: 57114
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1391 original size:21 final size:21
Alignment explanation
Indices: 1365--1404 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1355 GAAAAAATCA
*
1365 TTAAAAAAAGTTTTTTTGTAT
1 TTAAAAAAAGGTTTTTTGTAT
*
1386 TTAAAAAAGGGTTTTTTGT
1 TTAAAAAAAGGTTTTTTGT
1405 TTCAGTGGCA
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:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (21 bp):
TTAAAAAAAGGTTTTTTGTAT
Found at i:1980 original size:11 final size:11
Alignment explanation
Indices: 1964--1993 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1954 CCATATGTAT
1964 GAGGTAAGGGA
1 GAGGTAAGGGA
1975 GAGGTAAGGGA
1 GAGGTAAGGGA
1986 GAGGTAAG
1 GAGGTAAG
1994 ATAGTAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.53, T:0.10
Consensus pattern (11 bp):
GAGGTAAGGGA
Found at i:7780 original size:29 final size:29
Alignment explanation
Indices: 7746--7804 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
7736 CCTAAATTAA
7746 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
7775 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
7804 T
1 T
7805 AGGTGGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:12453 original size:29 final size:29
Alignment explanation
Indices: 12419--12506 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
12409 CCTAAATTAA
12419 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12448 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12477 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12506 T
1 T
12507 AGGTGAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:19331 original size:21 final size:21
Alignment explanation
Indices: 19270--19323 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
19260 TTCTTGAAAA
*
19270 TCGCAATGCGATAGTACAAAT
1 TCGCATTGCGATAGTACAAAT
19291 TCGCATTGCGATAGTACAAAT
1 TCGCATTGCGATAGTACAAAT
19312 TCGCATTGCGAT
1 TCGCATTGCGAT
19324 TTTCCAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTACAAAT
Found at i:19336 original size:21 final size:21
Alignment explanation
Indices: 19244--19343 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 21
19234 AATCAGTTTC
*
19244 CAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAATGCGATT-TTA
* **
19265 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAATGCGATTTTA
* * **
19286 CAAATTCGCATTGCGATAGTA
1 CAAAATCGCAATGCGATTTTA
* * *
19307 CAAATTCGCATTGCGATTTTC
1 CAAAATCGCAATGCGATTTTA
*
19328 CAAAATCGCAACGCGA
1 CAAAATCGCAATGCGA
19344 ATATGAAAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 1 0.02
21 64 0.98
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (21 bp):
CAAAATCGCAATGCGATTTTA
Found at i:19392 original size:20 final size:20
Alignment explanation
Indices: 19330--19559 Score: 241
Period size: 20 Copynumber: 11.5 Consensus size: 20
19320 CGATTTTCCA
* ** *
19330 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
19350 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
19370 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19390 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19410 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19430 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19450 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19470 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
19490 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
19510 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
19530 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
19550 AAATCACAAC
1 AAATCGCAAC
19560 ACTGAAATTT
Statistics
Matches: 178, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 174 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:20286 original size:24 final size:24
Alignment explanation
Indices: 20242--20288 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20232 AAATTTGGTC
*
20242 TTGGTCAATATCTGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
20266 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
20289 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:22767 original size:33 final size:33
Alignment explanation
Indices: 22716--22861 Score: 168
Period size: 33 Copynumber: 4.2 Consensus size: 33
22706 CGGAAATTAC
*
22716 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAAC-ATGAAAATCGCAATGCGAAATGAA
*
22749 AATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACATGAAAATCGCAATGC-GAAATGAA
*
22783 AATCGCAATGCGAAATGAAAATCGCAATGCAAAATGAA
1 AATCGCAA--C---ATGAAAATCGCAATGCGAAATGAA
** *
22821 AATCGCAACGGGAGAATCGCAATGCGAAATGAA
1 AATCGCAACATGAAAATCGCAATGCGAAATGAA
22854 AATCGCAA
1 AATCGCAA
22862 TGCGAAATGA
Statistics
Matches: 98, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
32 1 0.01
33 49 0.50
34 15 0.15
36 2 0.02
38 15 0.15
39 16 0.16
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACATGAAAATCGCAATGCGAAATGAA
Found at i:22799 original size:19 final size:19
Alignment explanation
Indices: 22730--22918 Score: 201
Period size: 19 Copynumber: 10.7 Consensus size: 19
22720 GCAACGAGAG
22730 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
22749 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
22763 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
22783 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
22802 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
* *
22821 AATCGCAA--CG---GGAG
1 AATCGCAATGCGAAATGAA
22835 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
22854 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
22873 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
22887 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
22906 AATCGCATTGCGA
1 AATCGCAATGCGA
22919 TTCTCCCGTT
Statistics
Matches: 142, Mismatches: 12, Indels: 32
0.76 0.06 0.17
Matches are distributed among these distances:
14 32 0.23
15 1 0.01
16 5 0.04
17 4 0.03
18 1 0.01
19 83 0.58
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:22918 original size:52 final size:52
Alignment explanation
Indices: 22716--22918 Score: 263
Period size: 52 Copynumber: 3.9 Consensus size: 52
22706 CGGAAATTAC
*
22716 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
22763 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCAAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
22821 AATCGCAACGGGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
22873 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
22919 TTCTCCCGTT
Statistics
Matches: 137, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 83 0.61
53 28 0.20
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:22967 original size:19 final size:19
Alignment explanation
Indices: 22927--23024 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
22917 GATTCTCCCG
22927 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
22947 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22966 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22980 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22999 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23018 TTGCGAT
1 TTGCGAT
23025 AGTCAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 34 0.49
20 15 0.22
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:23021 original size:52 final size:53
Alignment explanation
Indices: 22908--23024 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
22898 GAAATTAAAA
22908 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
22961 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGTGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
23013 TCGCATTGCGAT
1 TCGCATTGCGAT
23025 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:23150 original size:14 final size:14
Alignment explanation
Indices: 23131--23167 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
23121 CATCAATTAC
23131 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
23145 ACAAATCATCTTTT
1 ACAAATCAACTTTT
23159 ACAAATCAA
1 ACAAATCAA
23168 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:25154 original size:14 final size:14
Alignment explanation
Indices: 25135--25191 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
25125 ACGAAATGAA
*
25135 AATCGCAACGACAG
1 AATCGCAACGAAAG
25149 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
25166 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
25182 AATCGCAACG
1 AATCGCAACG
25192 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:25163 original size:33 final size:33
Alignment explanation
Indices: 25116--25208 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
25106 GCGAAACCAA
* *
25116 AATCGCAACACGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
25149 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
25182 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
25209 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:25173 original size:19 final size:19
Alignment explanation
Indices: 25079--25213 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
25069 TAGTTTACTT
* *
25079 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
25099 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
25118 TCGCAACACGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
25137 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
25151 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
25170 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
25184 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
25203 TCGCAATGCGA
1 TCGCAACGCGA
25214 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.11
17 11 0.11
19 46 0.48
20 12 0.12
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:25231 original size:19 final size:19
Alignment explanation
Indices: 25209--25336 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
25199 AAAATCGCAA
25209 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
25228 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
25242 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
25260 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
25274 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
25293 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
25312 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
25332 TGCGA
1 TGCGA
25337 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 20 0.23
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:25294 original size:33 final size:34
Alignment explanation
Indices: 25209--25299 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 34
25199 AAAATCGCAA
25209 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
25242 TGCGA-TTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
25274 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
25300 TTGGTTTCGC
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:0.19, G:0.29, T:0.45
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:25500 original size:93 final size:93
Alignment explanation
Indices: 25384--25944 Score: 1081
Period size: 93 Copynumber: 6.1 Consensus size: 93
25374 ATGGATTGCA
25384 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25448 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
25476 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25541 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
25569 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCATAGTGTTAAAGAATACACAATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25633 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
25661 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25726 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
25754 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25819 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
25847 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
25912 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
25940 TTACT
1 TTACT
25945 AAGCAATCTA
Statistics
Matches: 462, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 94 0.20
93 368 0.80
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:25701 original size:185 final size:186
Alignment explanation
Indices: 25384--25944 Score: 1081
Period size: 185 Copynumber: 3.0 Consensus size: 186
25374 ATGGATTGCA
25384 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25448 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
25513 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
* *
25569 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCATAGTGTTAAAGAATACACAATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25633 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
25698 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
25754 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25819 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
25884 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
25940 TTACT
1 TTACT
25945 AAGCAATCTA
Statistics
Matches: 369, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
185 187 0.51
186 182 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:25885 original size:278 final size:279
Alignment explanation
Indices: 25384--25944 Score: 1081
Period size: 278 Copynumber: 2.0 Consensus size: 279
25374 ATGGATTGCA
25384 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25448 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
25513 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
*
25578 ACCAAAAGACAAAACAAAGACAAATACTA-TTCATAGTGTTAAAGAATACACAATTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAATTTAGCAGAAT
25642 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
25661 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
25726 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
25791 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
*
25856 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAATTTAGCAGAAT
*
25921 TGGCAGCAACCGAATAAAT
261 TGGCAGCAACCGAACAAAT
25940 TTACT
1 TTACT
25945 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
277 4 0.01
278 219 0.78
279 56 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAATTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:27666 original size:14 final size:14
Alignment explanation
Indices: 27647--27736 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
27637 TTGAAATGAA
27647 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
27661 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
27680 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
27694 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
27713 AATCGCAACGAGAG
1 AATCGCAACGAGAG
27727 AATCGCAACG
1 AATCGCAACG
27737 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:27679 original size:33 final size:33
Alignment explanation
Indices: 27639--27753 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
27629 TCTTTTGGTT
27639 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
27672 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
27705 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
27738 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
27754 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:27685 original size:19 final size:19
Alignment explanation
Indices: 27661--27758 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
27651 GCAACGAGAG
27661 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
27680 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
27694 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
27713 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
27727 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
27746 AATCGCAATGCGA
1 AATCGCAACGCGA
27759 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:27789 original size:14 final size:14
Alignment explanation
Indices: 27770--27826 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
27760 TTTGGTTTCG
27770 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
27784 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
27803 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
27817 CGTTGCGATT
1 CGTTGCGATT
27827 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:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:27802 original size:33 final size:33
Alignment explanation
Indices: 27754--27834 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
27744 AAAATCGCAA
**
27754 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
27787 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
27820 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
27835 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:27837 original size:21 final size:21
Alignment explanation
Indices: 27811--27886 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
27801 CGCGTTGCGA
27811 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
27832 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
27852 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
27873 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
27887 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:27867 original size:41 final size:41
Alignment explanation
Indices: 27810--27887 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
27800 TCGCGTTGCG
*
27810 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
27851 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
27888 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:28008 original size:33 final size:33
Alignment explanation
Indices: 27966--28036 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
27956 AATACTAACT
*
27966 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
27999 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
28032 TGAAA
1 TGAAA
28037 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:28270 original size:22 final size:22
Alignment explanation
Indices: 28218--28272 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
28208 TGGTTGTGAG
**
28218 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
28240 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
28262 GGATTTCTTCG
1 GGATTTCTTCG
28273 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:28444 original size:20 final size:20
Alignment explanation
Indices: 28419--28572 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
28409 CTTTAAATAT
28419 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
28439 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
28461 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
28480 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
28500 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
28520 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
28540 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
28560 CGCGTTGCGATTT
1 CGCGTTGCGATTT
28573 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:28546 original size:40 final size:40
Alignment explanation
Indices: 28418--28572 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
28408 GCTTTAAATA
*
28418 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
28459 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
28499 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
28539 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
28573 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:28589 original size:21 final size:21
Alignment explanation
Indices: 28559--28641 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
28549 ATTTTCATAT
*
28559 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
28580 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
28601 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
28622 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
28642 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:28632 original size:42 final size:43
Alignment explanation
Indices: 28539--28637 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
28529 ATTTATGTGT
* *
28539 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
28580 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
28622 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
28638 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:28834 original size:22 final size:22
Alignment explanation
Indices: 28806--28858 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
28796 TTATTGGTAG
28806 GGTAAAATTATATAAGTTTATA
1 GGTAAAATTATATAAGTTTATA
28828 GGTAAAATTATATAAGTTTATA
1 GGTAAAATTATATAAGTTTATA
*
28850 GTTAAAATT
1 GGTAAAATT
28859 TAAAAATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
GGTAAAATTATATAAGTTTATA
Found at i:29990 original size:2 final size:2
Alignment explanation
Indices: 29977--30008 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
29967 CATTATATTT
29977 TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30009 AAACTAACCG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31598 original size:18 final size:17
Alignment explanation
Indices: 31571--31630 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 17
31561 TCAGTATTCG
*
31571 TCCCGTAGGACTCCTACA
1 TCCCGAAGGACT-CTACA
31589 TCCCGAAGGA--CTACA
1 TCCCGAAGGACTCTACA
*
31604 TCCCGAAGGA--CTACG
1 TCCCGAAGGACTCTACA
31619 TCCCGAAGGACT
1 TCCCGAAGGACT
31631 ATTATACCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 29 0.76
18 9 0.24
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.17
Consensus pattern (17 bp):
TCCCGAAGGACTCTACA
Found at i:31604 original size:15 final size:15
Alignment explanation
Indices: 31584--31631 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
31574 CGTAGGACTC
31584 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
31599 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
31614 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
31629 CTA
1 CTA
31632 TTATACCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:31810 original size:12 final size:12
Alignment explanation
Indices: 31776--31810 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31766 TATCATGTTC
**
31776 TCATATCACAGG
1 TCATATCACATA
31788 TCATATCACATA
1 TCATATCACATA
31800 TCATATCACAT
1 TCATATCACAT
31811 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:31822 original size:2 final size:2
Alignment explanation
Indices: 31815--31866 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
31805 TCACATGAAC
31815 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
31857 AT AT AT AT AT
1 AT AT AT AT AT
31867 CTTATGCATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32269 original size:64 final size:63
Alignment explanation
Indices: 32161--32386 Score: 195
Period size: 64 Copynumber: 3.5 Consensus size: 63
32151 TAATGAAGGT
** * ** * ** **
32161 ATGCATCGATGCACTACAGATGCATCGGTGCATAAAATGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGT-TTATTATTAATGGG
** * *
32225 ATGCATTTATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTT-ATTATTAATGGG
* ** **
32289 ATGCATCGATGGACTACTTATGCATCGATGCATGAATTACATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTATTA--TTAATGGG
** *
32352 AGTGCATCGATGCACTACCAATGCATCGATACACC
1 A-TGCATCGATGCACTACTTATGCATCGATGCACC
32387 TTCAAACAAT
Statistics
Matches: 131, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 124 0.95
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTATTATTAATGGG
Found at i:34258 original size:13 final size:13
Alignment explanation
Indices: 34232--34266 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
34222 CAATCCAGGC
34232 GACATACG-GGGT
1 GACATACGAGGGT
34244 GACATACGAGGGT
1 GACATACGAGGGT
34257 GACATACGAG
1 GACATACGAG
34267 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:34447 original size:93 final size:91
Alignment explanation
Indices: 34280--34475 Score: 365
Period size: 93 Copynumber: 2.1 Consensus size: 91
34270 TATACGAGTC
34280 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
1 ATACGAGCC-ATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
34345 GCCAATGGGGAGCATGCAACGAGCCAT
65 GCCAATGGGGAGCATGCAACGAGCCAT
34372 ATACGAGCCATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGAG
1 ATACGAGCCATGGGGAGCATGCAACGAGCC--ATACGAGCCAATGGGGAGCATGCAGGAATAGAG
34437 AGCCAATGGGGAGCATGCAACGAGCCAT
64 AGCCAATGGGGAGCATGCAACGAGCCAT
34465 ATACGAGCCAT
1 ATACGAGCCAT
34476 ACGAGCCAAT
Statistics
Matches: 102, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 21 0.21
92 9 0.09
93 72 0.71
ACGTcount: A:0.34, C:0.22, G:0.33, T:0.12
Consensus pattern (91 bp):
ATACGAGCCATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGAG
CCAATGGGGAGCATGCAACGAGCCAT
Found at i:34461 original size:61 final size:64
Alignment explanation
Indices: 34280--34474 Score: 257
Period size: 61 Copynumber: 3.2 Consensus size: 64
34270 TATACGAGTC
* *
34280 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGC-A-G-G-AAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
*
34340 AGA-GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCC-ATGGGGAGCATGCAACGAGCCA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-A-GAGCCAATGGGGAGCATGCAACGAGCCA
34403 T
64 T
*
34404 ATACGAGCCAATGGGGAGCATGC-A-G-G-AATAGAGAGCCAATGGGGAGCATGCAACGAGCCAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-AGAGCCAATGGGGAGCATGCAACGAGCCAT
34465 ATACGAGCCA
1 ATACGAGCCA
34475 TACGAGCCAA
Statistics
Matches: 121, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
59 30 0.25
60 20 0.17
61 43 0.36
62 2 0.02
63 2 0.02
64 5 0.04
65 19 0.16
ACGTcount: A:0.34, C:0.22, G:0.33, T:0.11
Consensus pattern (64 bp):
ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
Found at i:34555 original size:29 final size:29
Alignment explanation
Indices: 34506--34614 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
34496 AGGAATAGAG
*
34506 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-AGGCGACCTTGT
34535 AGGTCGCCATGTAGTCCAGGCGACCTTGT
1 AGGTCGCCATGTAGTCCAGGCGACCTTGT
*
34564 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCAGGCGACCTTGT
*
34593 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCAGGCG
34615 CCATTCCCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCAGGCGACCTTGT
Found at i:34721 original size:18 final size:18
Alignment explanation
Indices: 34698--34732 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34688 CCCAATGCAT
34698 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
34716 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
34733 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:34862 original size:23 final size:23
Alignment explanation
Indices: 34834--34879 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
34824 AAAAGAAAGA
34834 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
34857 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
34880 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:34892 original size:4 final size:4
Alignment explanation
Indices: 34883--34948 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
34873 ATTGCAGCCG
** **
34883 AGAA AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA
*
34933 AGTA AG-A AG-A AGAA AG
1 AGAA AGAA AGAA AGAA AG
34949 GGAGATAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 6 0.12
4 36 0.72
5 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:34894 original size:25 final size:23
Alignment explanation
Indices: 34834--34894 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
34824 AAAAGAAAGA
**
34834 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
34857 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
34880 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
34895 AGAAAGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:34914 original size:21 final size:21
Alignment explanation
Indices: 34882--34940 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
34872 GATTGCAGCC
34882 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
34902 GAGAAAGGAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
34923 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
34941 GAAGAAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:35118 original size:41 final size:41
Alignment explanation
Indices: 35073--35161 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
35063 TATATGATTG
* *
35073 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
35114 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
35155 TTAGTTT
1 TTAGTTT
35162 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:35205 original size:46 final size:48
Alignment explanation
Indices: 35142--35233 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
35132 TTATATAGTT
35142 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
35187 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
35234 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:35310 original size:32 final size:33
Alignment explanation
Indices: 35274--35350 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
35264 TTAGTTAGTA
35274 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
35306 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
35340 ATTTTATTAGT
1 AGTTTATTAGT
35351 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:35428 original size:16 final size:16
Alignment explanation
Indices: 35396--35442 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
35386 TTTAAAAAGT
*
35396 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
35412 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
35428 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
35443 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:35437 original size:15 final size:14
Alignment explanation
Indices: 35417--35447 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
35407 GTTTATTAGT
35417 TTATTATATTATAAG
1 TTATTATATTA-AAG
35432 TTATTATATTAAAG
1 TTATTATATTAAAG
35446 TT
1 TT
35448 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:38503 original size:26 final size:24
Alignment explanation
Indices: 38445--38503 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
38435 CTAATAAACC
*
38445 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
38469 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
38497 TAATAAT
1 TAATAAT
38504 ATGATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:39337 original size:8 final size:8
Alignment explanation
Indices: 39324--39378 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
39314 ATATATAACT
39324 TAAACTAA
1 TAAACTAA
39332 TAAACTAA
1 TAAACTAA
39340 TAAACTAA
1 TAAACTAA
39348 T--A-TAA
1 TAAACTAA
39353 TATAACT--
1 TA-AACTAA
39360 TAAACTAA
1 TAAACTAA
*
39368 CAAACTAA
1 TAAACTAA
39376 TAA
1 TAA
39379 TTTATACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
5 4 0.10
6 5 0.13
7 2 0.05
8 27 0.69
9 1 0.03
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAACTAA
Found at i:39363 original size:36 final size:38
Alignment explanation
Indices: 39307--39378 Score: 121
Period size: 36 Copynumber: 1.9 Consensus size: 38
39297 ATTTTTTATA
*
39307 TAATATAATATATAACTTAAACTAATAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAACTAATAAAC
39345 TAATAT-A-ATATAACTTAAACTAACAAACTAATAA
1 TAATATAATATATAACTTAAACTAACAAACTAATAA
39379 TTTATACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 26 0.79
37 1 0.03
38 6 0.18
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (38 bp):
TAATATAATATATAACTTAAACTAACAAACTAATAAAC
Found at i:39387 original size:21 final size:21
Alignment explanation
Indices: 39354--39402 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39344 CTAATATAAT
39354 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
39375 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
39396 ATTAACT
1 A-TAACT
39403 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:39958 original size:25 final size:25
Alignment explanation
Indices: 39904--39961 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
39894 GTTCCCACGT
* *
39904 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
39929 GCCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
39954 CCCATGCA
1 CCCATGCA
39962 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:40052 original size:29 final size:29
Alignment explanation
Indices: 40020--40099 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
40010 TCCACCTTGG
* *
40020 AGGTCGCCCGGATTGCATGGTGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
*
40049 AGGTCGCCTGGATTGCATGGCGACCTCTA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
40078 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
40100 TCCTATGGCG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.16, C:0.28, G:0.34, T:0.23
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:42368 original size:30 final size:30
Alignment explanation
Indices: 42332--42401 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
42322 TAGTCGCGAC
42332 CAACTCTATCAATGTTAAATATCATAGAAA
1 CAACTCTATCAATGTTAAATATCATAGAAA
42362 CAACTCTATCAATGTTAAATATCATAGAAA
1 CAACTCTATCAATGTTAAATATCATAGAAA
42392 CAACTCTATC
1 CAACTCTATC
42402 GAGTATTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (30 bp):
CAACTCTATCAATGTTAAATATCATAGAAA
Found at i:42453 original size:102 final size:102
Alignment explanation
Indices: 42272--42463 Score: 375
Period size: 102 Copynumber: 1.9 Consensus size: 102
42262 TAATCTTCGT
42272 TGTTAAATATCATAGAAACAACTCTATCGAGTATTGATAAAGCAGTACCCTAGTCGCGACCAACT
1 TGTTAAATATCATAGAAACAACTCTATCGAGTATTGATAAAGCAGTACCCTAGTCGCGACCAACT
*
42337 CTATCAATGTTAAATATCATAGAAACAACTCTATCAA
66 CTATCAATGCTAAATATCATAGAAACAACTCTATCAA
42374 TGTTAAATATCATAGAAACAACTCTATCGAGTATTGATAAAGCAGTACCCTAGTCGCGACCAACT
1 TGTTAAATATCATAGAAACAACTCTATCGAGTATTGATAAAGCAGTACCCTAGTCGCGACCAACT
42439 CTATCAATGCTAAATATCATAGAAA
66 CTATCAATGCTAAATATCATAGAAA
42464 ATGAATTATT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (102 bp):
TGTTAAATATCATAGAAACAACTCTATCGAGTATTGATAAAGCAGTACCCTAGTCGCGACCAACT
CTATCAATGCTAAATATCATAGAAACAACTCTATCAA
Found at i:43312 original size:60 final size:59
Alignment explanation
Indices: 43241--43409 Score: 212
Period size: 60 Copynumber: 2.8 Consensus size: 59
43231 AATGACCATC
* * *
43241 TTATAATTTTTAATAGTCAAGGAACTCAACAAAGCAGCGTCATATAGTCAAGAGATCATT
1 TTATAATTTTTAATAGTCAAGG-ACTCAACAAAGCAACATCATATAGTCAAGAGATCAGT
* * *
43301 TTATAACTTTTAATAGTCGAGTGACTCAACAAAGCAACATCCTATAGTCAAGAGATCAGT
1 TTATAATTTTTAATAGTCAAG-GACTCAACAAAGCAACATCATATAGTCAAGAGATCAGT
* * * * *
43361 TTGTAATTTTTAATAGTCAATGGACTCAATAAAACATCATCTTATAGTC
1 TTATAATTTTTAATAGTCAA-GGACTCAACAAAGCAACATCATATAGTC
43410 GGATGACCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
60 92 0.98
61 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (59 bp):
TTATAATTTTTAATAGTCAAGGACTCAACAAAGCAACATCATATAGTCAAGAGATCAGT
Found at i:45320 original size:340 final size:340
Alignment explanation
Indices: 44635--45472 Score: 1375
Period size: 341 Copynumber: 2.5 Consensus size: 340
44625 TAAATTTTGA
* * *
44635 AAAAATTATTGAATAATAATTCATTTGATCCCTCAATAGAAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
* *
44700 TTATATTTTTAAACAACTAATTTTAAAAGGTAATATTTTTTTCAAAAATATATGAAATTTATAAT
66 TTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAAT
* * * * *
44765 TTTTTAAGTTATAAAATATTTATCATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATA
131 TTTTAAAATTATAAAATATTTATTATTATCATCATCATCATCTTGTAAAAGAAATACTAGTTATA
44830 AAACTTTTATAAAATTATTCATATTTTAAAATACTTATCCTCAAAGTTTTTATATACTAGATTAT
196 AAACTTTTATAAAATTATTCATATTTTAAAATACTTATCCTCAAAGTTTTTATATACTAGATTAT
* **
44895 ATGTATTGTGTAATTTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAA
261 ACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAA
*
44960 CTGTTGTTAAAAATT
326 CTATTGTTAAAAATT
44975 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
45040 TTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAAATATATGAAATTTATAA
66 TTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTC-AAAAATATATGAAATTTATAA
*
45105 TTATTAAAATTATAAAATATTTATTATTATCATCATCATCATCTTGTAAAAGAAATACTAGTTAT
130 TTTTTAAAATTATAAAATATTTATTATTATCATCATCATCATCTTGTAAAAGAAATACTAGTTAT
* *
45170 AAAACTTTTATAAAATTATTCATATTTTAAAATACTTA-CTCTCAAAGTTTTTCTATATTATG-T
195 AAAACTTTTATAAAATTATTCATATTTTAAAATACTTATC-CTCAAAGTTTTTATATACTA-GAT
45233 TATACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTAT
258 TATACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTAT
45298 TAACTATTGTTAAAAA-T
323 TAACTATTGTTAAAAATT
* * *
45315 AAAAATTAATGAATAATAATTCATTTAATCCCTTAATTATAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATA-TTT
*
45380 TTTAAATATTTTTAAACAATTAATTTTAAAA--AAATAATTTTTTC-AAAATATATGAAATTTAT
65 TTT--ATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTAT
*
45442 AATTTTTAAAATTATAAAA-AATTATTATTAT
128 AATTTTTAAAATTATAAAATATTTATTATTAT
45473 TAAAAATAAA
Statistics
Matches: 469, Mismatches: 23, Indels: 14
0.93 0.05 0.03
Matches are distributed among these distances:
338 11 0.02
339 36 0.08
340 163 0.35
341 232 0.49
342 1 0.00
343 26 0.06
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (340 bp):
AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
TTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAAT
TTTTAAAATTATAAAATATTTATTATTATCATCATCATCATCTTGTAAAAGAAATACTAGTTATA
AAACTTTTATAAAATTATTCATATTTTAAAATACTTATCCTCAAAGTTTTTATATACTAGATTAT
ACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAA
CTATTGTTAAAAATT
Found at i:46165 original size:2 final size:2
Alignment explanation
Indices: 46158--46191 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46148 TTGAACTTGA
46158 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
46192 GTTAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46500 original size:16 final size:16
Alignment explanation
Indices: 46475--46519 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
46465 TAATAAATAA
46475 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
46491 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
46507 ACGAACATAAACG
1 ACGAACATAAACG
46520 TTGGAGACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:54516 original size:18 final size:19
Alignment explanation
Indices: 54493--54563 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 19
54483 TGAATATTTT
54493 TCCCGAAAG-ACCACTATG
1 TCCCGAAAGAACCACTATG
* * *
54511 TCCCGAATG-ATCACTGATTA
1 TCCCGAAAGAACCACT-A-TG
*
54531 TTCCG-AAGAACCACTATG
1 TCCCGAAAGAACCACTATG
54549 TCCC-AAAGAACCACT
1 TCCCGAAAGAACCACT
54564 GATAATCCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 27 0.66
19 4 0.10
20 10 0.24
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (19 bp):
TCCCGAAAGAACCACTATG
Found at i:55256 original size:64 final size:62
Alignment explanation
Indices: 55134--55267 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 62
55124 CCCTTGACGG
* **
55134 GTGCATCGATGCACTTCCTATGCATCAGTGCATAAATCCCATTCGATGTTTGTAATTTAAGCA
1 GTGCATCGATGCACTTCCTATGCATCAGTGCATAAATCCCATTCAATGTTCATAATTTAAG-A
** *
55197 GTTGCATCGATGCAC-TCCTTATGCATC-GATGCACT-AATGGCATTCAATGTTCATTATTTAAG
1 G-TGCATCGATGCACTTCC-TATGCATCAG-TGCA-TAAATCCCATTCAATGTTCATAATTTAAG
55259 A
62 A
55260 GTGCATCG
1 GTGCATCG
55268 GTACACATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
62 7 0.11
63 7 0.11
64 46 0.75
65 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTTCCTATGCATCAGTGCATAAATCCCATTCAATGTTCATAATTTAAGA
Found at i:56313 original size:24 final size:24
Alignment explanation
Indices: 56262--56313 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
56252 GAATGATCAT
* * *
56262 AAACGAACATAACTGGACGAACAT
1 AAACGAACATAACCGAACGAACAC
**
56286 AAACGAACATAACCGAACGTTCAC
1 AAACGAACATAACCGAACGAACAC
56310 AAAC
1 AAAC
56314 ATAAATGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.25, G:0.13, T:0.12
Consensus pattern (24 bp):
AAACGAACATAACCGAACGAACAC
Done.