Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001314.1 Hibiscus syriacus cultivar Beakdansim tig00002561_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: 43557
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:771 original size:2 final size:2
Alignment explanation
Indices: 731--755 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
721 CATTTATCTC
731 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
756 ATAGGTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3316 original size:24 final size:26
Alignment explanation
Indices: 3295--3348 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
3285 CCCTTTTTAA
3295 TATCTATATTATATGATATTTTAAATTAG
1 TATCTATATTATATGATATTTT--A-TAG
3324 TATCTATATTATATGATATTTTATA
1 TATCTATATTATATGATATTTTATA
3349 TTTTGATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.08
27 1 0.04
29 22 0.88
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (26 bp):
TATCTATATTATATGATATTTTATAG
Found at i:3409 original size:15 final size:15
Alignment explanation
Indices: 3389--3419 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3379 AATTACATTA
3389 ATAATACTTATATTT
1 ATAATACTTATATTT
*
3404 ATAATATTTATATTT
1 ATAATACTTATATTT
3419 A
1 A
3420 AGGCTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATACTTATATTT
Found at i:3736 original size:2 final size:2
Alignment explanation
Indices: 3729--3831 Score: 199
Period size: 2 Copynumber: 52.0 Consensus size: 2
3719 TCATGTTTAA
3729 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
3771 AT -T 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
3812 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3832 TTACTTCTTT
Statistics
Matches: 100, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 99 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5307 original size:20 final size:18
Alignment explanation
Indices: 5282--5320 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5272 AGGTGTTGAT
5282 TTGAAAGAGTGTTCATCAAA
1 TTGAAA-AGTGTTCAT-AAA
*
5302 TTGAAAAGTTTTCATAAA
1 TTGAAAAGTGTTCATAAA
5320 T
1 T
5321 GGACAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (18 bp):
TTGAAAAGTGTTCATAAA
Found at i:7906 original size:19 final size:19
Alignment explanation
Indices: 7879--7918 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
7869 GGAATTCGAG
*
7879 AATTTATTGATAAATG-GAT
1 AATTAATTGA-AAATGTGAT
7898 AATTAATTGAAAATGTGAT
1 AATTAATTGAAAATGTGAT
7917 AA
1 AA
7919 ACAAAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (19 bp):
AATTAATTGAAAATGTGAT
Found at i:9132 original size:72 final size:72
Alignment explanation
Indices: 9015--9156 Score: 239
Period size: 72 Copynumber: 2.0 Consensus size: 72
9005 ACAATAAAGC
9015 TTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCT
1 TTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCT
*
9080 GTTATGA
66 ATTATGA
* * * *
9087 TTGAGTTTTCCCTCTAAAGCAATTGGTTAATTGCCCCGGCTTTATGGATAATATTCAGCTAGCCT
1 TTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCT
9152 ATTAT
66 ATTAT
9157 ATTATTATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (72 bp):
TTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCT
ATTATGA
Found at i:11601 original size:55 final size:55
Alignment explanation
Indices: 11510--11615 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
11500 GTGATGAGAA
* * *
11510 ATCTAGGCAGAAGCCACAAGAAAATATTAATGTATTGTCAAATGTTTTACGGAAC
1 ATCTAGGCAAAAGCCACAAGAAAATATGAATATATTGTCAAATGTTTTACGGAAC
* *
11565 ATCTATGCAAAAGCCACATG-AAATGATGAATATATTGTCAAATGTTTTACG
1 ATCTAGGCAAAAGCCACAAGAAAAT-ATGAATATATTGTCAAATGTTTTACG
11616 AACCAGTGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
54 4 0.09
55 41 0.91
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (55 bp):
ATCTAGGCAAAAGCCACAAGAAAATATGAATATATTGTCAAATGTTTTACGGAAC
Found at i:12904 original size:116 final size:116
Alignment explanation
Indices: 12700--12961 Score: 400
Period size: 116 Copynumber: 2.3 Consensus size: 116
12690 CCCACATCTG
* * * * *
12700 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGTTTTTTGATATTTAAAGCCTTCG
1 TAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
* * *
12765 GTTCATCTGTAAGACCTACAGTGCAAGATGATGAGACCTCAGGGTCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
12816 TAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
**
12881 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCTG
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* *
12932 TAAGACCTT-CGGTGCATGATGTTTCCAAAA
1 TAAGA-CTTACAGTGCATGATGTTTTCAAAA
12962 CTTTCGGGTC
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
116 130 0.98
117 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (116 bp):
TAAGACTTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
Found at i:12937 original size:20 final size:21
Alignment explanation
Indices: 12884--12939 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
12874 GCCTCCGGGT
*
12884 CATCTGTAAGACCTACAGTGC
1 CATCTGTAAGACCTACAGGGC
* **
12905 AAGATGATAAGACCT-CAGGGC
1 CATCTG-TAAGACCTACAGGGC
12926 CATCTGTAAGACCT
1 CATCTGTAAGACCT
12940 TCGGTGCATG
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 8 0.30
21 11 0.41
22 8 0.30
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
CATCTGTAAGACCTACAGGGC
Found at i:12981 original size:45 final size:45
Alignment explanation
Indices: 12879--13695 Score: 1031
Period size: 45 Copynumber: 18.5 Consensus size: 45
12869 TTAAAGCCTC
* * * *
12879 CGGGTCATCTGTAAGACCTACAGTGCAAGATG--AT-AAGACC-T
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* * * *
12920 CAGGGCCATCTGTAAGACCTTCGGTGCATGATGTTTCCAAAACTTT
1 C-GGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
12966 CGGGTCATTTGTAAGACCTTCAGTGCAAGATGTTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
*
13011 CGGGTCATCTGTAAGACCTTCATTGCATGAT-TTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
13055 CTGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
13100 CGGGTCATCTGTAAGACCTTCAGTGCATGATATTTCCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* * *
13145 TGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
13190 CGGGTCATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACTTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
13235 CAGGTCATCTGTAAGACCTTCAGTGCAAGATGTTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* * *
13280 CGGGTCATCTGTAAGACCTTTATTGCATGAT-TTTTAAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
*
13324 CGGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* * *
13369 CGGGTCATCTGTAAGACCTTCAGTGCATGATATTTCCAAAATCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
13414 CGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
*
13459 CGGGTCATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
* *
13504 CGGGTCATCTGTAAGACCTACAGTGCA-GTATG-TTT-AAAATCCTC
1 CGGGTCATCTGTAAGACCTTCAGTGCATG-ATGTTTTCAAAA-CCTT
* * * * * *
13548 CGTGTCATCTGTAAGACCTCCAATGCAAGATG--TT-AAATCCTC
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
** * * *
13590 CGGGTCATCCATAAGACCTCCAATGCAAGATG-TTT-AAAATCCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAA-CCTT
* * *
13634 CGGGTCATCTGTAAGACCTCCAGTGCAAGATG--TT-AAATCCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
*
13676 TGGGTCATCTGTAAG-CCTTC
1 CGGGTCATCTGTAAGACCTTC
13696 CGAGCAAGAT
Statistics
Matches: 687, Mismatches: 77, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
41 5 0.01
42 78 0.11
43 19 0.03
44 147 0.21
45 436 0.63
46 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (45 bp):
CGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT
Found at i:13250 original size:269 final size:268
Alignment explanation
Indices: 12926--13695 Score: 1164
Period size: 269 Copynumber: 2.9 Consensus size: 268
12916 ACCTCAGGGC
* * * *
12926 CATCTGTAAGACCTTCGGTGCATGATGTTTCCAAAACTTTCGGGTCATTTGTAAGACCTTCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACTTTCGGGTCATCTGTAAGACCTTCAGTG
12991 CAAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCATTGCATGATTTTTCAAAACCTTC
66 CAAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCATTGCATGATTTTT-AAAACCTTC
*
13056 TGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTC
130 GGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTC
13121 AGTGCATGATATTTCCAAAACCTTTGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAA
195 AGTGCATGATATTTCCAAAACCTTTGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAA
13186 CCTTCGGGT
260 CCTTCGGGT
*
13195 CATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACTTTCAGGTCATCTGTAAGACCTTCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACTTTCGGGTCATCTGTAAGACCTTCAGTG
*
13260 CAAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTTATTGCATGATTTTTAAAAACCTTC
66 CAAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCATTGCATGATTTTT-AAAACCTTC
13325 GGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTC
130 GGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTC
* *
13390 AGTGCATGATATTTCCAAAATCTTCGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAA
195 AGTGCATGATATTTCCAAAACCTTTGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAA
13455 CCTTCGGGT
260 CCTTCGGGT
* *
13464 CATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTG
1 CATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACTTTCGGGTCATCTGTAAGACCTTCAGTG
* * * * * * * *
13529 C-AGTATG-TTT-AAAATCCTCCGTGTCATCTGTAAGACCTCCAATGCAAGA-TGTTAAATCCTC
66 CAAG-ATGTTTTCAAAA-CCTTCGGGTCATCTGTAAGACCTTCATTGCATGATTTTTAAAACCTT
** * * *
13590 CGGGTCATCCATAAGACCTCCAATGCAAGATG-TTT-AAAATCCTTCGGGTCATCTGTAAGACCT
129 CGGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAA-CCTTCGGGTCATCTGTAAGACCT
* * * * *
13653 CCAGTGCAAGAT-GTT--AAATCCTTTGGGTCATCTGTAAG-CCTTC
193 TCAGTGCATGATATTTCCAAAACCTTTGAGTCATCTGTAAGACCTTC
13696 CGAGCAAGAT
Statistics
Matches: 464, Mismatches: 34, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
261 5 0.01
262 19 0.04
264 6 0.01
265 36 0.08
266 33 0.07
267 7 0.02
268 33 0.07
269 325 0.70
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (268 bp):
CATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACTTTCGGGTCATCTGTAAGACCTTCAGTG
CAAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCATTGCATGATTTTTAAAACCTTCG
GGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCA
GTGCATGATATTTCCAAAACCTTTGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAAAC
CTTCGGGT
Found at i:13322 original size:224 final size:220
Alignment explanation
Indices: 12879--13695 Score: 1040
Period size: 224 Copynumber: 3.7 Consensus size: 220
12869 TTAAAGCCTC
* ** * *
12879 CGGGTCATCTGTAAGACCTACAGTGCAAGATGAT-AAGACC-TCAGGGCCATCTGTAAGACCTTC
1 CGGGTCATCTGTAAGACCTTCAGTGCAAGATTTTCAAAACCTTC-GGGTCATCTGTAAGACCTTC
** * * *
12942 GGTGCATGATGTTTCCAAAACTTTCGGGTCATTTGTAAGACCTTCAGTGCAAGATGTTTTCAAAA
65 AATGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAA
* *
13007 CCTTCGGGTCATCTGTAAGACCTTCATTGCATGATTTTTCAAAACCTTCTGGTCATCTGTAAGAC
130 CCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATTTTTCAAAACCTTCGGGTCATCTGTAAGAC
*
13072 CTTCAGTGCACGATGTTTTCAAAACCTT
195 CTTCAGTGCA-GAT-TTTTAAAAACCTT
* * *
13100 CGGGTCATCTGTAAGACCTTCAGTGCATGATATTTCCAAAACCTTTGAGTCATCTGTAAGACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCAAGAT-TTT-CAAAACCTTCGGGTCATCTGTAAGACCTT
* *
13165 CAATGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATATTTTCAAA
64 CAATGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
* * *
13230 ACTTTCAGGTCATCTGTAAGACCTTCAGTGCAAGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
129 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGAT-TTTTCAAAACCTTCGGGTCATCTGTAAG
* *
13295 ACCTTTATTGCATGATTTTTAAAAACCTT
193 ACCTTCAGTGCA-GATTTTTAAAAACCTT
*
13324 CGGGTCATCTGTAAGACCTTCAGTGCACGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTT
1 CGGGTCATCTGTAAGACCTTCAGTGCAAGA--TTTTCAAAACCTTCGGGTCATCTGTAAGACCTT
* * * * *
13389 CAGTGCATGATATTTCCAAAATCTTCGAGTCATCTGTAAGACCTTCAATGCATGATGTTTTCAAA
64 CAATGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
13454 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATATTTTCAAAACCTTCGGGTCATCTGTAAG
129 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGAT-TTTTCAAAACCTTCGGGTCATCTGTAAG
* * * *
13519 ACCTACAGTGCAGTATGTTTAAAATCCTC
193 ACCTTCAGTGCAG-ATTTTTAAAAACCTT
* * * * * * ** *
13548 CGTGTCATCTGTAAGACCTCCAATGCAAGATGTT-AAATCCTCCGGGTCATCCATAAGACCTCCA
1 CGGGTCATCTGTAAGACCTTCAGTGCAAGATTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCA
* * * *
13612 ATGCAAGATGTTT--AAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG--TT-AAAT
66 ATGCATGATGTTTCCAAAA-CCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAA
*
13672 CCTTTGGGTCATCTGTAAG-CCTTC
130 CCTTCGGGTCATCTGTAAGACCTTC
13696 CGAGCAAGAT
Statistics
Matches: 523, Mismatches: 64, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
216 5 0.01
217 21 0.04
218 2 0.00
219 4 0.01
220 31 0.06
221 64 0.12
222 4 0.01
223 1 0.00
224 346 0.66
225 44 0.08
226 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (220 bp):
CGGGTCATCTGTAAGACCTTCAGTGCAAGATTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCA
ATGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAAC
CTTCGGGTCATCTGTAAGACCTTCAGTGCATGATTTTTCAAAACCTTCGGGTCATCTGTAAGACC
TTCAGTGCAGATTTTTAAAAACCTT
Found at i:14322 original size:20 final size:20
Alignment explanation
Indices: 14259--14323 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
14249 TTCCAGAAGG
14259 AGTTCATAATAAGAAGAACT
1 AGTTCATAATAAGAAGAACT
* * * **
14279 CG-TC-TCAAGAGGAAGAAAA
1 AGTTCAT-AATAAGAAGAACT
14298 AGTTCATAATAAGAAGAACT
1 AGTTCATAATAAGAAGAACT
*
14318 TGTTCA
1 AGTTCA
14324 ATATTTTGCT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 17 0.55
21 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (20 bp):
AGTTCATAATAAGAAGAACT
Found at i:14649 original size:23 final size:23
Alignment explanation
Indices: 14623--14666 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
14613 TCCAGCCGTT
*
14623 CCTCTACTCCAACTGCTCCACTG
1 CCTCTACTCCAACTACTCCACTG
14646 CCTCTACTCCAACTACTCCAC
1 CCTCTACTCCAACTACTCCAC
14667 CGTTATGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.50, G:0.05, T:0.25
Consensus pattern (23 bp):
CCTCTACTCCAACTACTCCACTG
Found at i:15623 original size:15 final size:15
Alignment explanation
Indices: 15603--15633 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15593 AATTACATTA
15603 ATAATATCTATATTT
1 ATAATATCTATATTT
*
15618 ATAATATTTATATTT
1 ATAATATCTATATTT
15633 A
1 A
15634 AGGCTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATATCTATATTT
Found at i:16277 original size:20 final size:20
Alignment explanation
Indices: 16247--16382 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
16237 GTTTCCAGAT
*
16247 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
16267 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
**
16287 TTCGCGTTGCGATTTTCTGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
16310 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
16330 TCGCAACGCGATTCTAACTA
1 TCGCAATGCGATTCTGACTA
*
16350 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
*
16370 TCGCAACGCGATT
1 TCGCAATGCGATT
16383 TTCAAAGCAC
Statistics
Matches: 89, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
19 3 0.03
20 61 0.69
21 11 0.12
22 9 0.10
23 3 0.03
24 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:17002 original size:19 final size:19
Alignment explanation
Indices: 16980--17021 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
16970 AATCGCAATG
16980 CGATTTT-AGTTTCGCGTTC
1 CGATTTTCA-TTTCGCGTTC
*
16999 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTC
17018 CGAT
1 CGAT
17022 AGTAAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTC
Found at i:17082 original size:20 final size:20
Alignment explanation
Indices: 16978--17084 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
16968 AGAATCGCAA
*
16978 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
16997 TCCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** * **
17016 TGCGATAGTAAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
17036 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
17056 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
17076 TGCGATTTT
1 TGCGATTTT
17085 AAGTTTCAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 23 0.31
20 51 0.69
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:18833 original size:18 final size:18
Alignment explanation
Indices: 18810--18859 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
18800 TTTACTCGTA
18810 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
18828 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
18846 ATTTCACTTAGATT
1 ATTTCACTTAGATT
18860 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:19032 original size:20 final size:20
Alignment explanation
Indices: 19007--19074 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
18997 TAGTTTACTT
19007 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
19027 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
19047 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
19067 TCGCAACG
1 TCGCAACG
19075 AAAGAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:19142 original size:20 final size:20
Alignment explanation
Indices: 19117--19164 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
19107 GCGATTCTCT
19117 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
19137 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
19157 CGTTGCGA
1 CGTTGCGA
19165 AAGTAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:19486 original size:18 final size:18
Alignment explanation
Indices: 19424--19490 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 18
19414 GCGATTCTCT
19424 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC--ATTCG
* *
19444 CATTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCA--TTCG
19464 CGTTGCGATAGTCATTCG
1 CGTTGCGATAGTCATTCG
*
19482 TGTTGCGAT
1 CGTTGCGAT
19491 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.32
20 27 0.68
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (18 bp):
CGTTGCGATAGTCATTCG
Found at i:21130 original size:31 final size:31
Alignment explanation
Indices: 21092--21216 Score: 214
Period size: 31 Copynumber: 4.0 Consensus size: 31
21082 CCCGAAGGAC
* *
21092 CAGTCCATACATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
*
21123 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
21154 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
*
21185 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
21216 C
1 C
21217 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (31 bp):
CAGTCCATATATCCCGAAGAACATAGGTAAA
Found at i:22539 original size:3 final size:3
Alignment explanation
Indices: 22531--22585 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
22521 TCTCGTACAT
*
22531 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
22579 GAT GAA G
1 GAA GAA G
22586 GGAATATTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:25560 original size:31 final size:31
Alignment explanation
Indices: 25522--25615 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
25512 CCCGAAGGAC
*
25522 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
25553 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25584 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25615 C
1 C
25616 CCTCGACCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:26405 original size:64 final size:64
Alignment explanation
Indices: 26267--26428 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
26257 TCTTTCAATG
* *
26267 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATGTTGTATTATTA
*** * * * * * *
26331 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATCTTTTTATT-TTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGAT-GTTGTATTATTA
* *
26395 AAAG-AGTGCATCAATGCACTACCAATGCATCGAT
1 AAAGTA-TGCATCGATGCACTACTAATGCATCGAT
26429 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 73 0.91
65 6 0.08
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATGTTGTATTATTA
Found at i:28031 original size:64 final size:64
Alignment explanation
Indices: 27963--28187 Score: 267
Period size: 64 Copynumber: 3.5 Consensus size: 64
27953 TTGTTTGAAG
** **
27963 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
28026 T
64 T
** *
28027 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
* * * * *
28091 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAATAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
* * *
28155 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
28188 ACCTTCATTA
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
63 2 0.01
64 129 0.93
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
Found at i:29062 original size:103 final size:103
Alignment explanation
Indices: 28938--29160 Score: 437
Period size: 103 Copynumber: 2.2 Consensus size: 103
28928 GTCGAGGGTC
28938 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
29003 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
29041 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
29106 TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
29144 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
29161 CATTATTATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
Found at i:29209 original size:23 final size:23
Alignment explanation
Indices: 29179--29234 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
29169 TATGGAACTA
*
29179 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACACGGCACTC
* *
29202 CGGTGCAATTCTACATGGCACTT
1 CGGTGCAATTCTACACGGCACTC
29225 CGGTGCAATT
1 CGGTGCAATT
29235 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACACGGCACTC
Found at i:31345 original size:20 final size:20
Alignment explanation
Indices: 31322--31380 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
31312 ACGTTAAACT
31322 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAATGCGAAAGA
31342 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAATGCGAAAGA
*
31362 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAATGCGAAAG
31381 TCAATTCGCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGA
Found at i:31432 original size:34 final size:34
Alignment explanation
Indices: 31389--31525 Score: 141
Period size: 34 Copynumber: 3.9 Consensus size: 34
31379 AGTCAATTCG
* *
31389 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
*
31423 CGTTGCGATAGTCAAATAC-CTGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACGC-GTTGCGAT--T----TTCT
* *
31463 CGTTGCAATAGTCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
31497 TGTTGCGATAGTCAAATACCCGTTGCGAT
1 CGTTGCGATAGTCAAATACGCGTTGCGAT
31526 AATCAAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
33 1 0.01
34 53 0.62
36 1 0.01
38 1 0.01
40 28 0.33
41 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:31449 original size:20 final size:19
Alignment explanation
Indices: 31423--31639 Score: 166
Period size: 20 Copynumber: 11.5 Consensus size: 19
31413 GCGATTTTCT
*
31423 CGTTGCGATAGTCAAATAC
1 CGTTGCGATAGTCAAATTC
*
31442 CTGTTGCGATAATCAAATTC
1 C-GTTGCGATAGTCAAATTC
*
31462 GCGTTGCAATAGTCAAATTC
1 -CGTTGCGATAGTCAAATTC
**
31482 GCGTTGCGATTTTC---TT-
1 -CGTTGCGATAGTCAAATTC
*
31498 -GTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAAT-TC
*
31517 CGTTGCGATAATCAAATTC
1 CGTTGCGATAGTCAAATTC
31536 GCGTTGCGATAGTCAAATTC
1 -CGTTGCGATAGTCAAATTC
* *
31556 GAGTTGCGATAGACAAATTC
1 -CGTTGCGATAGTCAAATTC
* *
31576 GCGTTGCGAT--T---TTTG
1 -CGTTGCGATAGTCAAATTC
*
31591 CGTTGCGATAGTCATATTC
1 CGTTGCGATAGTCAAATTC
*
31610 GTGTTGCGATAGTCAAATTC
1 -CGTTGCGATAGTCAAATTC
31630 GCGTTGCGAT
1 -CGTTGCGAT
31640 TTTTGAGTTG
Statistics
Matches: 159, Mismatches: 24, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
14 19 0.12
15 2 0.01
16 1 0.01
17 3 0.02
19 4 0.03
20 129 0.81
21 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (19 bp):
CGTTGCGATAGTCAAATTC
Found at i:31478 original size:40 final size:39
Alignment explanation
Indices: 31383--31639 Score: 181
Period size: 40 Copynumber: 6.9 Consensus size: 39
31373 CGCGAAAGTC
* *
31383 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGAT--T--
1 AATTCGCGTTGCGATAGTCAAATAC-CGTTGCGATAATCA
*
31419 --TTCTCGTTGCGATAGTCAAATACCTGTTGCGATAATCA
1 AATTCGCGTTGCGATAGTCAAATACC-GTTGCGATAATCA
* *
31457 AATTCGCGTTGCAATAGTCAAATTCGCGTTGCGAT--T--
1 AATTCGCGTTGCGATAGTCAAATAC-CGTTGCGATAATCA
**
31493 --TTCTTGTTGCGATAGTCAAATACCCGTTGCGATAATCA
1 AATTCGCGTTGCGATAGTCAAATA-CCGTTGCGATAATCA
* *
31531 AATTCGCGTTGCGATAGTCAAATTCGAGTTGCGATAGA-CA
1 AATTCGCGTTGCGATAGTCAAATAC-CGTTGCGATA-ATCA
* ** *
31571 AATTCGCGTTGCGAT--T---TTTGCGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCAAATACCGTTGCGATAATCA
* * *
31605 TATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATAC-CGTTGCGAT
31640 TTTTGAGTTG
Statistics
Matches: 175, Mismatches: 22, Indels: 44
0.73 0.09 0.18
Matches are distributed among these distances:
33 1 0.01
34 79 0.45
35 3 0.02
36 3 0.02
38 2 0.01
39 3 0.02
40 82 0.47
41 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (39 bp):
AATTCGCGTTGCGATAGTCAAATACCGTTGCGATAATCA
Found at i:31503 original size:54 final size:54
Alignment explanation
Indices: 31443--31545 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
31433 GTCAAATACC
* * *
31443 TGTTGCGATAATCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCGATTTTCT
1 TGTTGCGATAATCAAATACCCGTTGCAATAATCAAATTCGCGTTGCGATTTTCT
* *
31497 TGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGAT
1 TGTTGCGATAATCAAATACCCGTTGCAATAATCAAATTCGCGTTGCGAT
31546 AGTCAAATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (54 bp):
TGTTGCGATAATCAAATACCCGTTGCAATAATCAAATTCGCGTTGCGATTTTCT
Found at i:31521 original size:94 final size:94
Alignment explanation
Indices: 31423--31639 Score: 294
Period size: 94 Copynumber: 2.3 Consensus size: 94
31413 GCGATTTTCT
* *
31423 CGTTGCGATAGTCAAATAC-CTGTTGCGATAATCAAATTCGCGTTGCAATAGTCAAATTCGCGTT
1 CGTTGCGATAGTCAAATACGC-GTTGCGATAATCAAATTCGAGTTGCAATAGACAAATTCGCGTT
*
31487 GCGATTTTCT-TGTTGCGATAGTCAAATACC
65 GCGATTTT-TGCGTTGCGATAGTCAAATACC
* * * *
31517 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGAGTTGCGATAGACAAATTCGCGTTG
1 CGTTGCGATAGTCAAATACGCGTTGCGATAATCAAATTCGAGTTGCAATAGACAAATTCGCGTTG
* * *
31582 CGATTTTTGCGTTGCGATAGTCATATTCG
66 CGATTTTTGCGTTGCGATAGTCAAATACC
* *
31611 TGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATACGCGTTGCGAT
31640 TTTTGAGTTG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
93 1 0.01
94 107 0.98
95 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATAATCAAATTCGAGTTGCAATAGACAAATTCGCGTTG
CGATTTTTGCGTTGCGATAGTCAAATACC
Found at i:31668 original size:74 final size:74
Alignment explanation
Indices: 31383--31681 Score: 309
Period size: 74 Copynumber: 4.0 Consensus size: 74
31373 CGCGAAAGTC
* * * *
31383 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATAC-CTGTT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACGC-GTT
31447 GCGATAATCA
65 GCGATAATCA
* * *
31457 AATTCGCGTTGCAATAGTCAAATTCGCGTTGCGATTTTCTTGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACGCGTTG
31522 CGATAATCA
66 CGATAATCA
* *** * * * ** **
31531 AATTCGCGTTGCGATAGTCAAATTCGAGTTGCGATAGACAAATTCGCG-TTG-CGATTTTTGCGT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTT-GCGATAGTC-AAATACGCGT
*
31594 TGCGATAGTCA
64 TGCGATAATCA
* * * *
31605 TATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCAAATTCGCGTT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-AGTTGCGATAGTCAAATACGCGTT
* *
31669 ACGATATTCA
65 GCGATAATCA
31679 AAT
1 AAT
31682 GAATGTGTAA
Statistics
Matches: 183, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
73 4 0.02
74 174 0.95
75 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACGCGTTG
CGATAATCA
Found at i:31680 original size:54 final size:54
Alignment explanation
Indices: 31538--31681 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 54
31528 TCAAATTCGC
* *
31538 GTTGCGATAGTCAAATTCGAGTTGCGATAGACAAATTCGCGTTGCGATTTTTGC
1 GTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
* *
31592 GTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
1 GTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
* * * *
31646 GTTGCGATAATCAAATTCGCGTTACGATATTCAAAT
1 GTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAAT
31682 GAATGTGTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (54 bp):
GTTGCGATAGTCAAATTCGAGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
Found at i:31909 original size:135 final size:138
Alignment explanation
Indices: 31656--31916 Score: 465
Period size: 135 Copynumber: 1.9 Consensus size: 138
31646 GTTGCGATAA
31656 TCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACA-ATCATA-C
31721 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
64 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
31786 CACATAATAG
129 CACATAATAG
* *
31796 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAAC-A-GAT-CAA
1 TCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAATCATACAA
31858 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
31917 TACAACGTTT
Statistics
Matches: 119, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
135 62 0.52
137 2 0.02
138 1 0.01
140 54 0.45
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (138 bp):
TCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAATCATACAA
TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACA
CATAATAG
Found at i:31999 original size:18 final size:18
Alignment explanation
Indices: 31976--32010 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31966 AAGCCGGTTG
*
31976 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
31994 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
32011 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:34279 original size:24 final size:24
Alignment explanation
Indices: 34245--34298 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
34235 CTGAAACATC
34245 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
34269 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
34293 ATCAAA
1 ATCAAA
34299 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:35151 original size:20 final size:20
Alignment explanation
Indices: 35128--35227 Score: 164
Period size: 20 Copynumber: 5.0 Consensus size: 20
35118 GTGTTGTGAC
35128 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCGTTGCGAT
*
35148 AGTCAGAATCTCGTTGCGAT
1 AGTCAGAATCGCGTTGCGAT
35168 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCGTTGCGAT
*
35188 AGTCAGAATCGCATTGCGAT
1 AGTCAGAATCGCGTTGCGAT
* *
35208 AGTCATAATCGCATTGCGAT
1 AGTCAGAATCGCGTTGCGAT
35228 TTACATATTC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (20 bp):
AGTCAGAATCGCGTTGCGAT
Found at i:35255 original size:20 final size:20
Alignment explanation
Indices: 35196--35257 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
35186 ATAGTCAGAA
* *
35196 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGAT-TTACATAT
35216 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
35236 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
35256 TC
1 TC
35258 TAATTGTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:35263 original size:20 final size:20
Alignment explanation
Indices: 35220--35263 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
35210 TCATAATCGC
*
35220 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGA
*
35240 ATTGCGATTTACATATTCTA
1 ATTGCGATTTACATATTCGA
35260 ATTG
1 ATTG
35264 TGAATTCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
ATTGCGATTTACATATTCGA
Done.