Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001227.1 Hibiscus syriacus cultivar Beakdansim tig00002416_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: 56878
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4359 original size:2 final size:2
Alignment explanation
Indices: 4352--4388 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4342 CTGTAACTGT
4352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4389 GAGGATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5850 original size:16 final size:16
Alignment explanation
Indices: 5829--5870 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
5819 TTAAACAATG
5829 TATTTATTATTATCTA
1 TATTTATTATTATCTA
5845 TATTTA--ATTATCTA
1 TATTTATTATTATCTA
5859 TATTT-TTATTAT
1 TATTTATTATTAT
5871 TTATTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 13 0.54
15 5 0.21
16 6 0.25
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATTATTATCTA
Found at i:5946 original size:2 final size:2
Alignment explanation
Indices: 5939--5984 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
5929 TTAATCTATG
*
5939 TA TA TA TA TA TA TA TA T- TA TA TCA CTA -A TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA TA TA
5981 TA TA
1 TA TA
5985 CCACTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 2 0.05
2 33 0.87
3 2 0.05
4 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5993 original size:28 final size:26
Alignment explanation
Indices: 5940--5996 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
5930 TAATCTATGT
*
5940 ATATATATATATATATTATATCACTA
1 ATATATATATATATATTATAACACTA
*
5966 ATATATATATATAT-TTATACCACTA
1 ATATATATATATATATTATAACACTA
*
5991 CTATAT
1 ATATAT
5997 TTTATCGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATATATATATATTATAACACTA
Found at i:6127 original size:27 final size:27
Alignment explanation
Indices: 6097--6149 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
6087 ATATATGTAT
*
6097 ATTTTTCT-TTCTTTTTACTTTCTTTTA
1 ATTTTT-TATTCTTTTTACTTTATTTTA
6124 ATTTTTTATTCTTTTTACTTTATTTT
1 ATTTTTTATTCTTTTTACTTTATTTT
6150 TTTGATGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.75
Consensus pattern (27 bp):
ATTTTTTATTCTTTTTACTTTATTTTA
Found at i:6228 original size:12 final size:12
Alignment explanation
Indices: 6208--6247 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
6198 TATATAGATT
*
6208 TTTACTATTTTA
1 TTTATTATTTTA
6220 TTTATTATTTTA
1 TTTATTATTTTA
*
6232 TGTTTTTATTTTA
1 T-TTATTATTTTA
6245 TTT
1 TTT
6248 TTTGTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:6247 original size:18 final size:18
Alignment explanation
Indices: 6224--6259 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6214 ATTTTATTTA
6224 TTATTTTATGTTTTTATT
1 TTATTTTATGTTTTTATT
*
6242 TTATTTTTTGTTTTTATT
1 TTATTTTATGTTTTTATT
6260 CCTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (18 bp):
TTATTTTATGTTTTTATT
Found at i:6259 original size:13 final size:12
Alignment explanation
Indices: 6213--6255 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
6203 AGATTTTTAC
*
6213 TATTTTATTTAT
1 TATTTTATTTTT
6225 TATTTTATGTTTT
1 TATTTTAT-TTTT
6238 TATTTTATTTTT
1 TATTTTATTTTT
*
6250 TGTTTT
1 TATTTT
6256 TATTCCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:10204 original size:95 final size:95
Alignment explanation
Indices: 10029--10289 Score: 346
Period size: 95 Copynumber: 2.7 Consensus size: 95
10019 AGATTATACT
*
10029 ATTATAA-ATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
1 ATTATAATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
*
10093 GGATAAGATTCAGCTAGCATGATAAAAGTG
66 GGATAAGATTCAGCTAGCATGATAAAAGTC
* * *
10123 ATTATAATATACGATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCAGCTTTAT
1 ATTATAATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
* * *
10188 GGATAATATTCAGCTAGCCTGATAAAGGTC
66 GGATAAGATTCAGCTAGCATGATAAAAGTC
* * * * * *
10218 ATTATAATATA-TATACAATGATATTAAGCTGTCTCTCTAAAGCAATTGGTTAAACGCCCCGGCT
1 ATTATAATATACAATA-AA--A-CTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCT
10282 TTATGGAT
62 TTATGGAT
10290 TCAGCTAGCC
Statistics
Matches: 146, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
94 10 0.07
95 92 0.63
97 1 0.01
98 43 0.29
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
ATTATAATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
GGATAAGATTCAGCTAGCATGATAAAAGTC
Found at i:11674 original size:84 final size:84
Alignment explanation
Indices: 11532--11823 Score: 433
Period size: 84 Copynumber: 3.5 Consensus size: 84
11522 GAAACTATTG
11532 GCAGCATAACTCAAGGCTAGAAGGGCTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCA
*
11597 GCTCCAAGGTATATCATTT
66 GCTCCAAGGCATATCATTT
* *
11616 ACAGCATAACTCAAGGCTAGAAGGGTTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCA
11681 GCTCCAAGGCATATCATTT
66 GCTCCAAGGCATATCATTT
* * * * * *
11700 GCATCATAACTCATGGCTAGAAGGGTTATGTGCCAACC-AAAGACCTTTGAGTTTGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGCTATATGCC-ACCAAAAGACCTTCGAGTTCGACTACGCTC
*
11764 AGCTCCAAGGCACATCATTT
65 AGCTCCAAGGCATATCATTT
* * * * *
11784 GCAGCGTAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATATGCCACCAAA
11824 CAAGTTTCAA
Statistics
Matches: 188, Mismatches: 18, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
83 2 0.01
84 183 0.97
85 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCTAGAAGGGCTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGGCATATCATTT
Found at i:12020 original size:43 final size:43
Alignment explanation
Indices: 11959--12085 Score: 191
Period size: 43 Copynumber: 3.0 Consensus size: 43
11949 CGAAGGGGTC
*
11959 ATCCACGATTTCAACTCCACGACAGAGGATATCGTACCCATAA
1 ATCCACGATTTCAACTCCACGACAAAGGATATCGTACCCATAA
* * *
12002 ATCCACGATTTCAACTCCACGACATAGGATATCATACCCACAA
1 ATCCACGATTTCAACTCCACGACAAAGGATATCGTACCCATAA
* * *
12045 ATCCACGATTTCAATTTCACGACAAAGGATATCGTGCCCAT
1 ATCCACGATTTCAACTCCACGACAAAGGATATCGTACCCAT
12086 CTCTAGATTG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACAAAGGATATCGTACCCATAA
Found at i:14145 original size:16 final size:16
Alignment explanation
Indices: 14124--14165 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
14114 TTAAACAATG
14124 TATTTATTATTATCTA
1 TATTTATTATTATCTA
14140 TATTTA--ATTATCTA
1 TATTTATTATTATCTA
14154 TATTT-TTATTAT
1 TATTTATTATTAT
14166 TTATTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 13 0.54
15 5 0.21
16 6 0.25
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATTATTATCTA
Found at i:14234 original size:2 final size:2
Alignment explanation
Indices: 14227--14311 Score: 118
Period size: 2 Copynumber: 41.5 Consensus size: 2
14217 TGGTATTTTA
* *
14227 AT AT AT AT AT AT AT AT -T AT GT CACT GCT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -A-T -AT AT AT AT AT AT AT AT
14269 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
14311 A
1 A
14312 CCACTACTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
1 1 0.01
2 72 0.96
3 1 0.01
4 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14428 original size:4 final size:4
Alignment explanation
Indices: 14413--14476 Score: 51
Period size: 4 Copynumber: 15.2 Consensus size: 4
14403 TGTATATATG
* *
14413 TATT TTTT TATT TATT T-TT TACTT TATTT TCATT T-TT TATT CTTTT
1 TATT TATT TATT TATT TATT TA-TT TA-TT T-ATT TATT TATT -TATT
14459 TATT TATT TAATT TATT T
1 TATT TATT T-ATT TATT T
14477 TTTTGATGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 6 0.12
4 25 0.51
5 17 0.35
6 1 0.02
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:14431 original size:13 final size:13
Alignment explanation
Indices: 14415--14480 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
14405 TATATATGTA
14415 TTTTTTTATTTA-
1 TTTTTTTATTTAT
14427 -TTTTTTACTTTAT
1 TTTTTTTA-TTTAT
*
14440 TTTCATTT-TTTAT
1 TTT-TTTTATTTAT
*
14453 TCTTTTTATTTAT
1 TTTTTTTATTTAT
**
14466 TTAATTTATTT-T
1 TTTTTTTATTTAT
14478 TTT
1 TTT
14481 GATGTTCATG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 7 0.17
12 10 0.24
13 20 0.48
14 2 0.05
15 3 0.07
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTATTTAT
Found at i:14459 original size:17 final size:17
Alignment explanation
Indices: 14419--14477 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
14409 TATGTATTTT
14419 TTTA-TTTATTTTTTAC
1 TTTATTTTATTTTTTAC
14435 TTTATTTTCATTTTTTA-
1 TTTATTTT-ATTTTTTAC
*
14452 TTCT-TTTTATTTATTTAA
1 TT-TATTTTATTT-TTTAC
14470 TTTATTTT
1 TTTATTTT
14478 TTTGATGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
16 8 0.22
17 14 0.38
18 15 0.41
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTTTTAC
Found at i:14554 original size:21 final size:21
Alignment explanation
Indices: 14530--14591 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
14520 TTGTATATAG
14530 ATTTTTA-CTATTTTATTTATT
1 ATTTTTATCTATTTTATTT-TT
* *
14551 A-TTTTATGTTTTTTATTTTT
1 ATTTTTATCTATTTTATTTTT
14571 ATTTTTATTCCT-TTTTATTTT
1 ATTTTTA-T-CTATTTTATTTT
14592 CTTTATCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 8 0.24
21 15 0.44
22 10 0.29
23 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTTTATCTATTTTATTTTT
Found at i:16985 original size:14 final size:14
Alignment explanation
Indices: 16966--17018 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
16956 AGTCAACGAG
16966 TTGACTCAACTGGT
1 TTGACTCAACTGGT
**
16980 TTGACTCTATTTGAG-
1 TTGACTC-AACTG-GT
16995 TTGACTCAACTGGT
1 TTGACTCAACTGGT
17009 TTGACTCAAC
1 TTGACTCAAC
17019 GAGTTGACGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 1 0.03
14 20 0.62
15 10 0.31
16 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (14 bp):
TTGACTCAACTGGT
Found at i:19310 original size:7 final size:7
Alignment explanation
Indices: 19278--19309 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
19268 TTTAATTACG
19278 AAAAATT
1 AAAAATT
19285 AAAAATT
1 AAAAATT
19292 AAAAATT
1 AAAAATT
19299 AAAATATT
1 AAAA-ATT
19307 AAA
1 AAA
19310 TTCAAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:19431 original size:35 final size:36
Alignment explanation
Indices: 19392--19482 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 36
19382 ATAAATATTG
*
19392 AATAAATCAAAGAAAAAAA-ACAAACAAATAAAAAT
1 AATAAATCAAAGAAAAAAAGACAAAAAAATAAAAAT
*
19427 AATAAATCAAAGGAAAAAAAGAGAAAAAAATAAAAAT
1 AATAAATCAAA-GAAAAAAAGACAAAAAAATAAAAAT
*
19464 AAAAAAGTCAAAGAAAAAA
1 AATAAA-TCAAAGAAAAAA
19483 CTAAATAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 11 0.22
36 8 0.16
37 26 0.52
38 5 0.10
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (36 bp):
AATAAATCAAAGAAAAAAAGACAAAAAAATAAAAAT
Found at i:19480 original size:25 final size:26
Alignment explanation
Indices: 19451--19525 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 26
19441 AAAAAAGAGA
19451 AAAAAATAAAAATAAAAAAGTCAAA-G
1 AAAAAATAAAAATAAAAAAGT-AAAGG
19477 AAAAAACT--AAAT-AAAAAGTAAAGG
1 AAAAAA-TAAAAATAAAAAAGTAAAGG
*
19501 AAAAAATAAAAATAAGAAAAATAAA
1 AAAAAATAAAAATAA-AAAAGTAAA
19526 CAAATAAGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
23 4 0.10
24 14 0.33
25 8 0.19
26 7 0.17
27 9 0.21
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (26 bp):
AAAAAATAAAAATAAAAAAGTAAAGG
Found at i:19530 original size:17 final size:15
Alignment explanation
Indices: 19502--19666 Score: 79
Period size: 15 Copynumber: 10.7 Consensus size: 15
19492 AAGTAAAGGA
19502 AAAAATAAAAATAAG
1 AAAAATAAAAATAAG
19517 AAAAATAAACAAATAAG
1 AAAAAT-AA-AAATAAG
* **
19534 TCAAAGGAAAAATAA-
1 -AAAAATAAAAATAAG
19549 AATAAATAAAAAT-AG
1 AA-AAATAAAAATAAG
19564 AAAAATATAAAATAA-
1 AAAAATA-AAAATAAG
* * * *
19579 AAATATTAATATAAT
1 AAAAATAAAAATAAG
*
19594 AATAAT-AAAATAA-
1 AAAAATAAAAATAAG
*
19607 AATAAATAGATAAATAAA
1 AA-AAATA-A-AAATAAG
* *
19625 AATAAATAAAATTTAG
1 AA-AAATAAAAATAAG
* *
19641 TAAAAAGAAAAATAAT
1 -AAAAATAAAAATAAG
*
19657 ACAAATAAAA
1 AAAAATAAAA
19667 TAAAATAAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
13 2 0.02
14 22 0.19
15 38 0.33
16 23 0.20
17 18 0.16
18 11 0.10
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAATAAG
Found at i:19573 original size:25 final size:25
Alignment explanation
Indices: 19541--19712 Score: 92
Period size: 25 Copynumber: 6.8 Consensus size: 25
19531 AAGTCAAAGG
19541 AAAA-ATAAAATAAATAAAAATAGA
1 AAAATATAAAATAAATAAAAATAGA
*
19565 AAAATATAAAATAAA-AATATTAATATA
1 AAAATATAAAATAAATAA-A--AATAGA
* *
19592 ATAATAATAAAATAAA-ATAAATAGA
1 AAAAT-ATAAAATAAATAAAAATAGA
* *
19617 TAAATA-AAAATAAATAAAATTTAGTA
1 AAAATATAAAATAAATAAAA-ATAG-A
* *
19643 AAAAGA-AAAAT-AATACAAATA-A
1 AAAATATAAAATAAATAAAAATAGA
* *
19665 AATAAAATAAAA-AGATAAAAA-ACGA
1 AA-AATATAAAATAAATAAAAATA-GA
* *
19690 AATAAAATAAAAAAAATTAAAAA
1 AA-AATATAAAATAAA-TAAAAA
19713 AGGTTAAATA
Statistics
Matches: 117, Mismatches: 16, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
22 3 0.03
23 12 0.10
24 22 0.19
25 41 0.35
26 12 0.10
27 16 0.14
28 11 0.09
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.21
Consensus pattern (25 bp):
AAAATATAAAATAAATAAAAATAGA
Found at i:19609 original size:27 final size:26
Alignment explanation
Indices: 19544--19636 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 26
19534 TCAAAGGAAA
* *
19544 AATAAAAT-AAATAAAAATAGAAAAAT
1 AATAAAATAAAATAATAATA-AATAAT
*
19570 -ATAAAATAAAAATATTAATATAATAAT
1 AATAAAAT-AAAATAATAATA-AATAAT
*
19597 AATAAAATAAAATAAATAGATAAATAAA
1 AATAAAATAAAAT-AATA-ATAAATAAT
19625 AAT-AAATAAAAT
1 AATAAAATAAAAT
19637 TTAGTAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
25 7 0.12
27 28 0.50
28 18 0.32
29 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (26 bp):
AATAAAATAAAATAATAATAAATAAT
Found at i:19609 original size:63 final size:60
Alignment explanation
Indices: 19542--19705 Score: 147
Period size: 63 Copynumber: 2.6 Consensus size: 60
19532 AGTCAAAGGA
* *
19542 AAAATAAAATAAATAAAAATAGAA-AAATATAAAATAAAAATATTAATATAATA-ATAATAAAAT
1 AAAATAAAATAAATAAAAATA-AATAAA-ATAAAATAAAAAGA--AAAATAATACA-AATAAAAT
** *
19605 AAAATAAATAGATAAATAAAAATAAATAAAATTTAGTAAAAAGAAAAATAATACAAATAAAAT
1 AAAAT-AA-A-ATAAATAAAAATAAATAAAATAAAATAAAAAGAAAAATAATACAAATAAAAT
* *
19668 AAAATAAAA-AGATAAAAAACGAAATAAAATAAAA-AAAA
1 AAAATAAAATAAAT-AAAAA-TAAATAAAATAAAATAAAA
19706 TTAAAAAAGG
Statistics
Matches: 84, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
59 3 0.04
60 10 0.12
61 11 0.13
62 2 0.02
63 26 0.31
64 3 0.04
65 13 0.15
66 16 0.19
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (60 bp):
AAAATAAAATAAATAAAAATAAATAAAATAAAATAAAAAGAAAAATAATACAAATAAAAT
Found at i:19712 original size:10 final size:9
Alignment explanation
Indices: 19477--19713 Score: 54
Period size: 9 Copynumber: 24.6 Consensus size: 9
19467 AAAGTCAAAG
*
19477 AAAAAACTA
1 AAAAAAATA
19486 AATAAAAAGTA
1 AA-AAAAA-TA
*
19497 AAGGAAAA-A
1 AA-AAAAATA
*
19506 ATAAAAATA
1 AAAAAAATA
*
19515 AGAAAAATA
1 AAAAAAATA
19524 AACAAATAAGTCA
1 AA-AAA-AA-T-A
19537 AAGGAAAAATA
1 AA--AAAAATA
*
19548 AAATAAATA
1 AAAAAAATA
19557 AAAATAGAA-A
1 AAAA-A-AATA
19567 AATATAAAATA
1 AA-A-AAAATA
19578 AAAATATTAATA
1 AAAA-A--AATA
*
19590 TAATAATAATA
1 -AA-AAAAATA
19601 AAATAAAAT-
1 AAA-AAAATA
* *
19610 AAATAGATA
1 AAAAAAATA
19619 AATAAAAATA
1 AA-AAAAATA
* *
19629 AATAAAATT
1 AAAAAAATA
* **
19638 TAGTAAA-A
1 AAAAAAATA
*
19646 AGAAAAATA
1 AAAAAAATA
* *
19655 ATACAAATA
1 AAAAAAATA
19664 AAATAAAAT-
1 AAA-AAAATA
*
19673 AAAAAGAT-
1 AAAAAAATA
**
19681 AAAAAACGA
1 AAAAAAATA
*
19690 AATAAAATA
1 AAAAAAATA
19699 AAAAAAATTA
1 AAAAAAA-TA
19709 AAAAA
1 AAAAA
19714 GGTTAAATAT
Statistics
Matches: 165, Mismatches: 38, Indels: 49
0.65 0.15 0.19
Matches are distributed among these distances:
8 19 0.12
9 64 0.39
10 39 0.24
11 24 0.15
12 7 0.04
13 7 0.04
14 5 0.03
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (9 bp):
AAAAAAATA
Found at i:19876 original size:27 final size:27
Alignment explanation
Indices: 19808--19865 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
19798 ATCAAAACAT
* *
19808 AAAAATTAAAATAATAGTGGCTAAATC
1 AAAAATGAAAAAAATAGTGGCTAAATC
*
19835 AAAAATGAAAAAAATAGTGGCTAAATT
1 AAAAATGAAAAAAATAGTGGCTAAATC
19862 AAAA
1 AAAA
19866 TTTGCATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.22
Consensus pattern (27 bp):
AAAAATGAAAAAAATAGTGGCTAAATC
Found at i:20861 original size:16 final size:16
Alignment explanation
Indices: 20840--20873 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20830 CTGCACAAAA
20840 AAATAA-AATATATAAT
1 AAATAATAATA-ATAAT
20856 AAATAATAATAATAAT
1 AAATAATAATAATAAT
20872 AA
1 AA
20874 TATTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:20924 original size:26 final size:25
Alignment explanation
Indices: 20895--20944 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
20885 TTATTATTAT
*
20895 TATATAAAAAATATATTTCCAAAAAC
1 TATATAAAAAATAT-TTTCAAAAAAC
* *
20921 TATATAATATATATTTTCAAAAAA
1 TATATAAAAAATATTTTCAAAAAA
20945 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (25 bp):
TATATAAAAAATATTTTCAAAAAAC
Found at i:20962 original size:37 final size:37
Alignment explanation
Indices: 20916--21272 Score: 427
Period size: 37 Copynumber: 9.8 Consensus size: 37
20906 TATATTTCCA
*
20916 AAAACTATATA--ATATATATTTTCAAAAAATATTTT-
1 AAAACTATATATTATATATATTTTC-AAAAATGTTTTC
*
20951 AAAACTATATA-T-TATATA-TTTAAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
*
20985 AAAACTATATATTATATA-GTTTTCAAAAATGTTTT-
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
* *
21020 AAAACTATATATTATATATGTTTTCGAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
21057 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
* *
21094 AAAATTATATATTATATA-AGTTTTC-AAAATGATTTC
1 AAAACTATATATTATATATA-TTTTCAAAAATGTTTTC
* *
21130 AAAACTATATATTATATA-AGTTTTTC-AAAACGATTTC
1 AAAACTATATATTATATATA--TTTTCAAAAATGTTTTC
* **
21167 AAAATTATATATTATATA-AGTTTTTTAAAATGTTTTC
1 AAAACTATATATTATATATA-TTTTCAAAAATGTTTTC
*
21204 AAAAACTATATATTATATATATATTT-TAAAATGTTTTC
1 -AAAACTATATATTATATATAT-TTTCAAAAATGTTTTC
21242 AAAAACTATATATTATATATATTTTCAAAAA
1 -AAAACTATATATTATATATATTTTCAAAAA
21273 GCATTTTTAA
Statistics
Matches: 289, Mismatches: 19, Indels: 25
0.87 0.06 0.08
Matches are distributed among these distances:
33 10 0.03
34 14 0.05
35 36 0.12
36 67 0.23
37 102 0.35
38 56 0.19
39 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAAATGTTTTC
Found at i:21251 original size:25 final size:26
Alignment explanation
Indices: 21223--21284 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
21213 ATATTATATA
*
21223 TATATTTTAAAATGTTTTCAAAAA-C
1 TATATTTTAAAATATTTTCAAAAAGC
* *
21248 TATATATTATATATATTTTCAAAAAGC
1 TATATTTTA-AAATATTTTCAAAAAGC
21275 -AT-TTTTAAAA
1 TATATTTTAAAA
21285 AAAAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 2 0.07
25 12 0.40
26 15 0.50
27 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (26 bp):
TATATTTTAAAATATTTTCAAAAAGC
Found at i:21251 original size:27 final size:26
Alignment explanation
Indices: 21221--21272 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
21211 ATATATTATA
* *
21221 TATATATTTTAAAATGTTTTCAAAAAC
1 TATATATTAT-AAATATTTTCAAAAAC
*
21248 TATATATTATATATATTTTCAAAAA
1 TATATATTATAAATATTTTCAAAAA
21273 GCATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
TATATATTATAAATATTTTCAAAAAC
Found at i:21299 original size:17 final size:18
Alignment explanation
Indices: 21279--21317 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
21269 AAAAGCATTT
21279 TTAAAAAAAAATA-TATA
1 TTAAAAAAAAATACTATA
**
21296 TTAAAAAATTATACTATA
1 TTAAAAAAAAATACTATA
21314 TTAA
1 TTAA
21318 TATATATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAAAAAATACTATA
Found at i:24787 original size:29 final size:31
Alignment explanation
Indices: 24724--24789 Score: 102
Period size: 29 Copynumber: 2.2 Consensus size: 31
24714 GGCTGCTGGA
24724 AACCGGTTTAACCGATTTTCAACCGGTTCTG
1 AACCGGTTTAACCGATTTTCAACCGGTTCTG
*
24755 -ACCGGTTTGACCGA-TTTCAACCGGTTC-G
1 AACCGGTTTAACCGATTTTCAACCGGTTCTG
24783 AACCGGT
1 AACCGGT
24790 CTGAACCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 19 0.58
30 13 0.39
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (31 bp):
AACCGGTTTAACCGATTTTCAACCGGTTCTG
Found at i:24832 original size:17 final size:17
Alignment explanation
Indices: 24810--24848 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
24800 TTGACCGGTC
*
24810 TGACCCGACCCGACCGT
1 TGACCCAACCCGACCGT
24827 TGACCCAACCCGACCGT
1 TGACCCAACCCGACCGT
24844 TGACC
1 TGACC
24849 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.46, G:0.21, T:0.13
Consensus pattern (17 bp):
TGACCCAACCCGACCGT
Found at i:28971 original size:9 final size:9
Alignment explanation
Indices: 28957--29000 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
28947 AGCTGCTGGA
28957 AACCGGTTT
1 AACCGGTTT
28966 AACCGGTTT
1 AACCGGTTT
* *
28975 GACCGGTCTG
1 AACCGGT-TT
28985 AACCGGTTT
1 AACCGGTTT
*
28994 GACCGGT
1 AACCGGT
29001 CTGACCCGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:28990 original size:19 final size:19
Alignment explanation
Indices: 28966--29004 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28956 AAACCGGTTT
28966 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
28985 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
29004 A
1 A
29005 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:29005 original size:9 final size:9
Alignment explanation
Indices: 28967--29006 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
28957 AACCGGTTTA
*
28967 ACCGGTTTG
1 ACCGGTCTG
28976 ACCGGTCTG
1 ACCGGTCTG
*
28985 AACCGGTTTG
1 -ACCGGTCTG
28995 ACCGGTCTG
1 ACCGGTCTG
29004 ACC
1 ACC
29007 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:29025 original size:12 final size:12
Alignment explanation
Indices: 29008--29045 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28998 GGTCTGACCC
29008 GACCCGACCGTT
1 GACCCGACCGTT
*
29020 GACCCGA-C-AT
1 GACCCGACCGTT
29030 GACCCGACCGTT
1 GACCCGACCGTT
29042 GACC
1 GACC
29046 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:30947 original size:78 final size:78
Alignment explanation
Indices: 30849--31005 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
30839 GAAACATGCG
*
30849 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATTGTTGAA
1 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
30914 CCAATTCTGCAAA
66 CCAATTCTGCAAA
30927 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
1 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
30992 CCAATTCTGCAAA
66 CCAATTCTGCAAA
31005 A
1 A
31006 GTATGCCTAA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (78 bp):
ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
CCAATTCTGCAAA
Found at i:39126 original size:57 final size:56
Alignment explanation
Indices: 39064--39171 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
39054 ATGCACATAA
* *
39064 CATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCACCAGC
1 CATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCACCAGC
* * *
39121 CATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCA
39172 TCGGTGCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 22 0.49
57 20 0.44
58 3 0.07
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (56 bp):
CATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCACCAGC
Found at i:40577 original size:20 final size:20
Alignment explanation
Indices: 40523--40590 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
40513 ATCGATTTTC
* * *
40523 TTTTGAAA-ACAAAATTAGA
1 TTTTGAAAGCCAAAATGAAA
40542 TTTTGAAAGCCCAAAATGAAA
1 TTTTGAAAG-CCAAAATGAAA
40563 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAGCCAAAATGAAA
40583 TTTTGAAA
1 TTTTGAAA
40591 AAGGATTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.18
20 19 0.43
21 17 0.39
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (20 bp):
TTTTGAAAGCCAAAATGAAA
Found at i:41865 original size:34 final size:30
Alignment explanation
Indices: 41827--41895 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
41817 CGATATAACA
41827 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
41861 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
41890 AATTTA
1 AATTTA
41896 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:41906 original size:29 final size:30
Alignment explanation
Indices: 41836--41895 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
41826 AAATTTAAGG
41836 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
41867 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
41896 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:41999 original size:21 final size:21
Alignment explanation
Indices: 41973--42029 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
41963 AGGGTGTCAA
41973 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
41994 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCACCCCTGC
42015 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
42030 TTGCACTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:42042 original size:22 final size:20
Alignment explanation
Indices: 42014--42072 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
42004 TGCATCCCTG
42014 TAGTGCATCCATGCACTTGCAC
1 TAGTGCATCCATGCACTT--AC
* *
42036 TAGTGCATCGATGCATCATAC
1 TAGTGCATCCATGCA-CTTAC
42057 -AGTGCATCCATGCACT
1 TAGTGCATCCATGCACT
42073 CAAACACCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 2 0.06
22 14 0.44
23 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (20 bp):
TAGTGCATCCATGCACTTAC
Found at i:42117 original size:20 final size:20
Alignment explanation
Indices: 42092--42159 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
42082 AATACAATTA
*
42092 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
42112 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
42133 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
42153 GTGCATC
1 GTGCATC
42160 CATACACGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:42172 original size:41 final size:41
Alignment explanation
Indices: 42092--42174 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
42082 AATACAATTA
* * *
42092 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATACATCAAGGCT
42133 GTGCATCGATGCATCCTGCTGTGCATCCATACA-CGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATACATC-AAGGCT
42174 G
1 G
42175 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATACATCAAGGCT
Found at i:42559 original size:34 final size:32
Alignment explanation
Indices: 42520--42589 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
42510 TTTTGTAAAG
* * *
42520 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
42554 GGGAAATGTTATAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
42586 GGGA
1 GGGA
42590 GTTGTAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:43808 original size:18 final size:20
Alignment explanation
Indices: 43785--43823 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
43775 ACCAATTTCG
*
43785 TCAAAAACAAA-C-AATTTT
1 TCAAAAAAAAATCGAATTTT
43803 TCAAAAAAAAATCGAATTTT
1 TCAAAAAAAAATCGAATTTT
43823 T
1 T
43824 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (20 bp):
TCAAAAAAAAATCGAATTTT
Found at i:45514 original size:2 final size:2
Alignment explanation
Indices: 45507--45532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45497 CAGCTTAAGC
45507 TA 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
45533 ATCAATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46073 original size:64 final size:64
Alignment explanation
Indices: 45978--46182 Score: 236
Period size: 65 Copynumber: 3.2 Consensus size: 64
45968 TTTCAGAGTA
* *
45978 ATGCACCGATGCACCGATCCATGCATCGATGCACTATGAATTAAATTG-AACATCGAATGCATTT
1 ATGCATCGATGCACC-ATCCATGCATCGATGCACTATG-ATTATATTGAAACATCGAATGCATTT
*
46042 C
64 G
* * *
46043 ATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATTTTA-TGAAAACATCGAATGCATT
1 ATGCATCGATGCACCAT-CCATGCATCGATGCACT-ATGATTATATTG-AAACATCGAATGCATT
46106 TG
63 TG
* * ** * *
46108 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACCATCCATGCATCGATGCACTATGATTATATTGAAACATCGAATGCATTTG
46172 ATGCATCGATG
1 ATGCATCGATG
46183 TACTCTTAGT
Statistics
Matches: 119, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
63 4 0.03
64 52 0.44
65 61 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACCATCCATGCATCGATGCACTATGATTATATTGAAACATCGAATGCATTTG
Found at i:49759 original size:29 final size:29
Alignment explanation
Indices: 49704--49763 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
49694 TTAAAAATAT
*
49704 ATATTTTTTTAAATAAAAATAAGAGTAAA
1 ATATATTTTTAAATAAAAATAAGAGTAAA
* * * *
49733 ATATATTTTTATATTAAATTAATAGTAAA
1 ATATATTTTTAAATAAAAATAAGAGTAAA
49762 AT
1 AT
49764 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
ATATATTTTTAAATAAAAATAAGAGTAAA
Found at i:49892 original size:28 final size:28
Alignment explanation
Indices: 49834--49909 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
49824 AATATATATC
* *
49834 AATAAATTAAAA-TAAAA-GAAATATTT
1 AATAAATTAAAACAAAAATAAAATATTT
*
49860 AATAAATTAAGACAAAAATAAAATATTT
1 AATAAATTAAAACAAAAATAAAATATTT
*
49888 AATAACTTAAAACAAAAATAAA
1 AATAAATTAAAACAAAAATAAA
49910 GAGATAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 11 0.26
27 4 0.09
28 28 0.65
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (28 bp):
AATAAATTAAAACAAAAATAAAATATTT
Done.