Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007331.1 Hibiscus syriacus cultivar Beakdansim tig00019608_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: 94710
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3852 original size:7 final size:7
Alignment explanation
Indices: 3839--3882 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
3829 GTCAAAGGAA
3839 GTCAACG
1 GTCAACG
*
3846 ATCAACG
1 GTCAACG
3853 GTC-ACG
1 GTCAACG
3859 GTCAACG
1 GTCAACG
3866 GTCAACG
1 GTCAACG
* *
3873 ATCAGCG
1 GTCAACG
3880 GTC
1 GTC
3883 GGTCGGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3864 original size:20 final size:21
Alignment explanation
Indices: 3839--3882 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3829 GTCAAAGGAA
*
3839 GTCAACGATCAACGGTCA-CG
1 GTCAACGATCAACGATCAGCG
*
3859 GTCAACGGTCAACGATCAGCG
1 GTCAACGATCAACGATCAGCG
3880 GTC
1 GTC
3883 GGTCGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (21 bp):
GTCAACGATCAACGATCAGCG
Found at i:10329 original size:19 final size:19
Alignment explanation
Indices: 10305--10349 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10295 GTCAACGGTT
10305 GGGTCAGGTCAGC-CGGGTC
1 GGGTCAGGTC-GCGCGGGTC
10324 GGGTCA-GTCGCGTCGGGTC
1 GGGTCAGGTCGCG-CGGGTC
10343 GGGTCAG
1 GGGTCAG
10350 ACCGGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.09
18 3 0.13
19 18 0.78
ACGTcount: A:0.09, C:0.24, G:0.49, T:0.18
Consensus pattern (19 bp):
GGGTCAGGTCGCGCGGGTC
Found at i:10362 original size:9 final size:9
Alignment explanation
Indices: 10344--10403 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
10334 CGTCGGGTCG
*
10344 GGTCAGACC
1 GGTCAAACC
10353 GGTCAAACC
1 GGTCAAACC
* *
10362 GGTTCAGACA
1 GG-TCAAACC
10372 GGTCAAACC
1 GGTCAAACC
*
10381 GGTTCGAACC
1 GG-TCAAACC
10391 GGTCAGAACC
1 GGTCA-AACC
10401 GGT
1 GGT
10404 TTCCAGCCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 19 0.46
10 22 0.54
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:10368 original size:19 final size:19
Alignment explanation
Indices: 10346--10404 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
10336 TCGGGTCGGG
10346 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
10365 TCAGACAGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
10384 TC-GAACCGGTCAGAACCGGT
1 TCAG-ACCGGTCA-AACCGGT
10404 T
1 T
10405 TCCAGCCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.03
19 27 0.75
20 8 0.22
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:27405 original size:18 final size:18
Alignment explanation
Indices: 27382--27448 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
27372 AGACAAGCGA
27382 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTTTGTC
*
27400 AGCCAAGTGACGTTTGTC
1 AGCCAAGTGATGTTTGTC
* *
27418 AGCCAAGTGATGTATCTC
1 AGCCAAGTGATGTTTGTC
*
27436 AGCCGAGTGATGT
1 AGCCAAGTGATGT
27449 ATCTCATCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (18 bp):
AGCCAAGTGATGTTTGTC
Found at i:27449 original size:18 final size:18
Alignment explanation
Indices: 27382--27459 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
27372 AGACAAGCGA
* *
27382 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTATCTC
* * *
27400 AGCCAAGTGACGTTTGTC
1 AGCCAAGTGATGTATCTC
27418 AGCCAAGTGATGTATCTC
1 AGCCAAGTGATGTATCTC
*
27436 AGCCGAGTGATGTATCTC
1 AGCCAAGTGATGTATCTC
*
27454 ATCCAA
1 AGCCAA
27460 TCCCTCCTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (18 bp):
AGCCAAGTGATGTATCTC
Found at i:27614 original size:42 final size:42
Alignment explanation
Indices: 27568--27775 Score: 229
Period size: 42 Copynumber: 4.9 Consensus size: 42
27558 TCATCCTCAC
* * *
27568 CCTCACCCTCACCGCCACCTCCTCCTCCACCTTCACTATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * **
27610 CCTCACCCTCGCCGCCACCTCCTCATTCACCTCCGTCATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * * *
27652 CCTCACACTCGCCACCACTTCCTACTCCACCTCCACCATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * *
27694 CCTCACCCTCACC-CTCACCTCCACCTTCTCCACCTCCACCACCAT
1 CCTCACCCTCGCCGC-CACCT---CCTCCTCCACCTCCACCATCAT
**
27739 CCTCACCCTCGCCGCCACCTCCTCCTCTGCCTCCACC
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACC
27776 TCGACCTCCA
Statistics
Matches: 137, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.01
42 98 0.72
45 37 0.27
46 1 0.01
ACGTcount: A:0.16, C:0.59, G:0.04, T:0.22
Consensus pattern (42 bp):
CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
Found at i:28210 original size:39 final size:39
Alignment explanation
Indices: 28164--28249 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
28154 TTTTCCACGT
*
28164 TCCCCATCAACACCTTGCAATTTTAGTCATCCTCTTCCC
1 TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
* * *
28203 TCTCCATCAAAACCTTGTAATTTTAGTCATCCTTTTCCC
1 TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
28242 TCCCCATC
1 TCCCCATC
28250 GAAAGAACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (39 bp):
TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
Found at i:28685 original size:36 final size:36
Alignment explanation
Indices: 28642--28775 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
28632 TCCGATGCTG
** * *
28642 CTCCACCTCCAACGTGTAATGCTCCCCCACCCGCTC
1 CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
* * *
28678 CTCCACCTCCAACGTCCGATGCTGCTTCACCCCCTC
1 CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
* *
28714 CTCCACCTCCAACTTCCAATGCTGCTCCACCCCCTC
1 CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
* *
28750 CTCCACGTCCAACGTCAAATGCTCCT
1 CTCCACCTCCAACGTCCAATGCTCCT
28776 TCTCCACTGC
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.17, C:0.51, G:0.10, T:0.22
Consensus pattern (36 bp):
CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
Found at i:28887 original size:42 final size:42
Alignment explanation
Indices: 28824--28909 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
28814 ATCTGGAGCA
* *
28824 CCACCACCACCTCCTGGTGGAGGAGCTCCTGGAGCACCACCT
1 CCACCACCACCTCCAGCTGGAGGAGCTCCTGGAGCACCACCT
28866 CCACCACCACCTCCAGCTGGAGGAGCTCCTGGAGCACCACCT
1 CCACCACCACCTCCAGCTGGAGGAGCTCCTGGAGCACCACCT
28908 CC
1 CC
28910 TGGAGGTCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.20, C:0.45, G:0.22, T:0.13
Consensus pattern (42 bp):
CCACCACCACCTCCAGCTGGAGGAGCTCCTGGAGCACCACCT
Found at i:28962 original size:27 final size:28
Alignment explanation
Indices: 28918--28995 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
28908 CCTGGAGGTC
*
28918 GAGCTCTTGGTCCCCCACCTCCA-C-CTG
1 GAGCTCCTGG-CCCCCACCTCCACCACTG
28945 GAGCTCCTGGCCCTCCACCTCCACCAGCTG
1 GAGCTCCTGGCCC-CCACCTCCACCA-CTG
*
28975 GAGCTCGTGG--CCCACCTCCAC
1 GAGCTCCTGGCCCCCACCTCCAC
28996 TAGGTGCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 3 0.07
27 28 0.62
28 2 0.04
30 12 0.27
ACGTcount: A:0.13, C:0.49, G:0.21, T:0.18
Consensus pattern (28 bp):
GAGCTCCTGGCCCCCACCTCCACCACTG
Found at i:30826 original size:31 final size:31
Alignment explanation
Indices: 30763--30831 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
30753 TCTTAGGGGC
* * *
30763 CAATTTGATCAAACTTGTCAAGTTTAGGGGT
1 CAATTTGATCAAACTTATCAAGTTCAGAGGT
30794 CAATTTGATCAAACTTATCATA-TTCAGAGGT
1 CAATTTGATCAAACTTATCA-AGTTCAGAGGT
*
30825 CATTTTG
1 CAATTTG
30832 TGTTTGAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (31 bp):
CAATTTGATCAAACTTATCAAGTTCAGAGGT
Found at i:36757 original size:30 final size:30
Alignment explanation
Indices: 36717--36785 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
36707 TTTAATTGTT
* *
36717 TTCCAATTTGGTGCCCAACCTTTGTCTCGG
1 TTCCAGTTTGGTGCCCAACATTTGTCTCGG
* *
36747 TTCCAGTTTGGTGCCTAACATTTGTCTTGG
1 TTCCAGTTTGGTGCCCAACATTTGTCTCGG
*
36777 GTCCAGTTT
1 TTCCAGTTT
36786 TGATGTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.41
Consensus pattern (30 bp):
TTCCAGTTTGGTGCCCAACATTTGTCTCGG
Found at i:39416 original size:45 final size:45
Alignment explanation
Indices: 39352--39475 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
39342 GTAATCATAC
*
39352 AAATAAGCTTACGAGCTTATGGAATAAATATTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATATTGGTA
* *
39397 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATATTGGTA
* * * *
39442 AAATAAACTCACAAGCTTAT-GAGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGA-ATAAATAGTAA
39476 ATATTTTGAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
44 2 0.03
45 70 0.97
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATATTGGTA
Found at i:42292 original size:6 final size:6
Alignment explanation
Indices: 42273--42402 Score: 83
Period size: 6 Copynumber: 21.8 Consensus size: 6
42263 TATAATATAA
*
42273 AAAAAG AAATAG AAAAAG AAAAAAG AAAAAG AAAAAAG AAAAAAG AAAAA-
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG -AAAAAG -AAAAAG AAAAAG
* * * * * * *
42323 AAAAAG CAAGAA- AAAAAG CAAGAAT AAAATG AAAACG AAAACG AAGAAG
1 AAAAAG -AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
42372 --AAAT AAATAG AAAAAG -AAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
42403 ATGAGAGATG
Statistics
Matches: 98, Mismatches: 17, Indels: 18
0.74 0.13 0.14
Matches are distributed among these distances:
4 2 0.02
5 19 0.19
6 50 0.51
7 27 0.28
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:42297 original size:7 final size:7
Alignment explanation
Indices: 42272--42338 Score: 79
Period size: 7 Copynumber: 9.9 Consensus size: 7
42262 ATATAATATA
42272 AAAAAAG
1 AAAAAAG
*
42279 -AAATAG
1 AAAAAAG
42285 -AAAAAG
1 AAAAAAG
42291 AAAAAAG
1 AAAAAAG
42298 -AAAAAG
1 AAAAAAG
42304 AAAAAAG
1 AAAAAAG
42311 AAAAAAG
1 AAAAAAG
42318 AAAAAA-
1 AAAAAAG
42324 AAAAGCAAG
1 AAAA--AAG
42333 AAAAAA
1 AAAAAA
42339 AGCAAGAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 20 0.38
7 27 0.51
8 2 0.04
9 4 0.08
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:42321 original size:12 final size:12
Alignment explanation
Indices: 42272--42403 Score: 76
Period size: 13 Copynumber: 10.5 Consensus size: 12
42262 ATATAATATA
42272 AAAAAAGAAATAG
1 AAAAAAGAAA-AG
*
42285 AAAAAGAAAAAAG
1 AAAAA-AGAAAAG
*
42298 AAAAAGAAAAAAG
1 AAAAA-AGAAAAG
42311 AAAAAAGAAAA-
1 AAAAAAGAAAAG
*
42322 AAAAAAG-CAAG
1 AAAAAAGAAAAG
*
42333 AAAAAA-AGCAAG
1 AAAAAAGA-AAAG
42345 AATAAAATGAAAACG
1 AA-AAAA-GAAAA-G
42360 AAAACGAAGAAGAA-
1 AAAA--AAGAA-AAG
*
42374 ATAAATAGAAAA-
1 A-AAAAAGAAAAG
*
42386 AGAAAAGAAAAG
1 AAAAAAGAAAAG
42398 AAAAAA
1 AAAAAA
42404 TGAGAGATGA
Statistics
Matches: 98, Mismatches: 8, Indels: 27
0.74 0.06 0.20
Matches are distributed among these distances:
10 2 0.02
11 21 0.21
12 19 0.19
13 33 0.34
14 9 0.09
15 10 0.10
16 4 0.04
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:42377 original size:28 final size:26
Alignment explanation
Indices: 42349--42404 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
42339 AGCAAGAATA
*
42349 AAAT-GAAAACGAAAACGAAGAAGAAAT
1 AAATAGAAAAAGAAAA-GAA-AAGAAAT
42376 AAATAGAAAAAGAAAAGAAAAGAAA-
1 AAATAGAAAAAGAAAAGAAAAGAAAT
42401 AAAT
1 AAAT
42405 GAGAGATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 7 0.26
28 10 0.37
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (26 bp):
AAATAGAAAAAGAAAAGAAAAGAAAT
Found at i:46326 original size:45 final size:45
Alignment explanation
Indices: 46262--46385 Score: 194
Period size: 45 Copynumber: 2.8 Consensus size: 45
46252 GTAACCATGC
*
46262 AAATAAGCTTACGAGCTTATGGAATCAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
46307 AAATAAGCTTATGAGCTTATGAAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
46352 AAATAAGCTTACAAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
46386 ATATTTTGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:48022 original size:23 final size:23
Alignment explanation
Indices: 47988--48056 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
47978 CACCATAGCT
* *
47988 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
48011 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
*
48034 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
48057 TATAAAATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:48211 original size:23 final size:23
Alignment explanation
Indices: 48169--48212 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
48159 AATACATATA
*
48169 TATCCCGAAGGACCATGTAGAAT
1 TATCCCGAAGGACCACGTAGAAT
* *
48192 TATCCTGAAGGACCGCGTAGA
1 TATCCCGAAGGACCACGTAGA
48213 CCCTCAACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
TATCCCGAAGGACCACGTAGAAT
Found at i:48478 original size:14 final size:14
Alignment explanation
Indices: 48459--48491 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
48449 TGTGTATGTA
*
48459 ATCATATAATTTGT
1 ATCATATAATTTAT
48473 ATCATATAATTTAT
1 ATCATATAATTTAT
48487 ATCAT
1 ATCAT
48492 TTCTCATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (14 bp):
ATCATATAATTTAT
Found at i:51237 original size:21 final size:21
Alignment explanation
Indices: 51211--51255 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
51201 AAGCAAGATT
* * *
51211 GCCAAATCTTCTCATCAACAG
1 GCCAAAACTTCCCATCAAAAG
51232 GCCAAAACTTCCCATCAAAAG
1 GCCAAAACTTCCCATCAAAAG
51253 GCC
1 GCC
51256 TTTCCCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.18
Consensus pattern (21 bp):
GCCAAAACTTCCCATCAAAAG
Found at i:53732 original size:17 final size:15
Alignment explanation
Indices: 53696--53734 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
53686 TTTATATACG
53696 TTATTATATATAATA
1 TTATTATATATAATA
*
53711 ATATTATAGTAGTAATA
1 TTATTATA-TA-TAATA
53728 TTATTAT
1 TTATTAT
53735 TTACAAGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTATTATATATAATA
Found at i:55034 original size:18 final size:17
Alignment explanation
Indices: 55002--55057 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
54992 ATTTCATCAT
* *
55002 TAATTATTATTTTAAGA
1 TAATTATAATATTAAGA
*
55019 CTAATTATAATATTAATA
1 -TAATTATAATATTAAGA
*
55037 TAATTATATATATTATGA
1 TAATTATA-ATATTAAGA
55055 TAA
1 TAA
55058 CTTTATATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 8 0.25
18 24 0.75
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
TAATTATAATATTAAGA
Found at i:56638 original size:2 final size:2
Alignment explanation
Indices: 56631--56668 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56621 TTTTTATCAG
56631 TA TA TA TA TA TA 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 TA TA TA TA TA TA
56669 AAAGTGCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63544 original size:22 final size:22
Alignment explanation
Indices: 63519--63572 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
63509 ACATGCTCCT
*
63519 CCATGGCCAAACTCAAGCAACA
1 CCATGCCCAAACTCAAGCAACA
63541 CCATGCCCAAACTCAAGCAACA
1 CCATGCCCAAACTCAAGCAACA
63563 CCATGCCCAA
1 CCATGCCCAA
63573 CTCTTCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.41, G:0.11, T:0.09
Consensus pattern (22 bp):
CCATGCCCAAACTCAAGCAACA
Found at i:71099 original size:32 final size:32
Alignment explanation
Indices: 71063--71135 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
71053 GTTTAAGGAT
* *
71063 CATTTTGTAGCAGTTTGATACGTTTTAACAAC
1 CATTTTGTAGCAGTTAGATAAGTTTTAACAAC
*
71095 CATTTTGTAGCAGTTAGATAAGTTTTAACGAC
1 CATTTTGTAGCAGTTAGATAAGTTTTAACAAC
71127 CATTTTGTA
1 CATTTTGTA
71136 ATAGCTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (32 bp):
CATTTTGTAGCAGTTAGATAAGTTTTAACAAC
Found at i:71147 original size:32 final size:30
Alignment explanation
Indices: 71048--71167 Score: 114
Period size: 32 Copynumber: 3.8 Consensus size: 30
71038 GATAAAATTC
* * *
71048 GATAAGTTTAAGGATCATTTTGTAGCAGTTT
1 GATAAGTTTAACGACCATTTTGTAACAG-TT
* * *
71079 GATACGTTTTAACAACCATTTTGTAGCAGTT
1 GATAAG-TTTAACGACCATTTTGTAACAGTT
*
71110 AGATAAGTTTTAACGACCATTTTGTAATAGCTT
1 -GATAAG-TTTAACGACCATTTTGTAACAG-TT
* *
71143 GATAAGTTTAATGACTATTTTGTAA
1 GATAAGTTTAACGACCATTTTGTAA
71168 TTTGTGAAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
31 24 0.32
32 50 0.66
33 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
GATAAGTTTAACGACCATTTTGTAACAGTT
Found at i:72823 original size:2 final size:2
Alignment explanation
Indices: 72816--72848 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
72806 TAATTAAATT
*
72816 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72849 TCATATCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:73808 original size:2 final size:2
Alignment explanation
Indices: 73801--73827 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
73791 ATGAAATTAA
73801 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
73828 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:73832 original size:2 final size:2
Alignment explanation
Indices: 73827--73869 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
73817 TCTCTCTCTC
73827 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
73869 T
1 T
73870 GTTGAGTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76507 original size:72 final size:72
Alignment explanation
Indices: 76390--76541 Score: 205
Period size: 72 Copynumber: 2.1 Consensus size: 72
76380 GAGACGCATT
* * * * *
76390 TGCAGCCTGAAGGTATCAAGCTCCACCACAATTCCATCCAAAGAATTTAGGAGAACCATCTCAGA
1 TGCAGCCCGAAGGTAACAACCTCCACCACAACTCCATCCAAAGAATTTACGAGAACCATCTCAGA
76455 AAAAGTG
66 AAAAGTG
* * * *
76462 TGCAGCCCGAAGTTAACAACCTCCACCACTACTCCATCCAAAGAATTTACGAGAACCATGTCGGA
1 TGCAGCCCGAAGGTAACAACCTCCACCACAACTCCATCCAAAGAATTTACGAGAACCATCTCAGA
*
76527 AAAGGTG
66 AAAAGTG
*
76534 TACAGCCC
1 TGCAGCCC
76542 CAGAGTATGC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (72 bp):
TGCAGCCCGAAGGTAACAACCTCCACCACAACTCCATCCAAAGAATTTACGAGAACCATCTCAGA
AAAAGTG
Found at i:82599 original size:9 final size:9
Alignment explanation
Indices: 82577--82610 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
82567 AAAGAGAGAA
82577 AAAT-AAAT
1 AAATAAAAT
82585 AAATAAAAT
1 AAATAAAAT
*
82594 AGATAAAAT
1 AAATAAAAT
82603 AAATAAAA
1 AAATAAAA
82611 CAAAGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:82625 original size:22 final size:20
Alignment explanation
Indices: 82538--82626 Score: 52
Period size: 22 Copynumber: 3.9 Consensus size: 20
82528 CGTATTAACA
*
82538 AAAAAAATGTAAAAAATAAAAAT
1 AAAAAAA-GGAAAAAAT--AAAT
82561 AAAAATAAAGAGAGAAAAATAAAT
1 -AAAA-AAAG-GA-AAAAATAAAT
* *
82585 AAATAAAATAGATAAAATAAAT
1 AAA-AAAA-GGAAAAAATAAAT
82607 AAAACAAAGGAAAATAATAA
1 AAAA-AAAGGAAAA-AATAA
82627 TAATGATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
21 5 0.09
22 20 0.38
23 8 0.15
24 10 0.19
25 4 0.08
26 6 0.11
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAAAAGGAAAAAATAAAT
Found at i:82694 original size:16 final size:16
Alignment explanation
Indices: 82657--82718 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
82647 TAACAACAAG
*
82657 AAGAAAAT--AAAAAT
1 AAGAAAATAAAAAAAA
*
82671 AAGTAAATAAAAAAAA
1 AAGAAAATAAAAAAAA
* *
82687 AAGAAAATATAAAGAA
1 AAGAAAATAAAAAAAA
*
82703 AATAAAATAATAAAAA
1 AAGAAAATAA-AAAAA
82719 TAATATATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 7 0.19
16 26 0.70
17 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAGAAAATAAAAAAAA
Found at i:83065 original size:2 final size:2
Alignment explanation
Indices: 83058--83086 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
83048 AATAGAAATA
83058 AT AT 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 AT AT A
83087 ATAACGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83156 original size:22 final size:21
Alignment explanation
Indices: 83117--83157 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
83107 TAGTAATAGG
83117 AAATAAGAAAAAAAAATGAAC
1 AAATAAGAAAAAAAAATGAAC
83138 AAATAA-AAATAATAAAATGA
1 AAATAAGAAA-AA-AAAATGA
83158 CTAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 8 0.44
22 7 0.39
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (21 bp):
AAATAAGAAAAAAAAATGAAC
Found at i:83567 original size:22 final size:22
Alignment explanation
Indices: 83542--83584 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
83532 TCAAAGTTTT
83542 TCAAAACCA-CTTTTTTAAAAAA
1 TCAAAA-CATCTTTTTTAAAAAA
*
83564 TCAAAACATGTTTTTTAAAAA
1 TCAAAACATCTTTTTTAAAAA
83585 TATAAATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (22 bp):
TCAAAACATCTTTTTTAAAAAA
Found at i:84885 original size:37 final size:36
Alignment explanation
Indices: 84835--85282 Score: 259
Period size: 36 Copynumber: 12.9 Consensus size: 36
84825 TGTTTCAAGG
**
84835 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAA
* * * *
84872 GAAACTGTCTCAAGGGAGACGAAATTTG-TTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* * * *
84907 GAAAACATAT-TC-----AG--AAATTTTGTTTCAAGA
1 G-AAAC-TGTCTCAAGAGAGACAAAATTTGTTTTAAAA
**
84937 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* *
84973 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAA
* * *
85010 GAAATTGTCTCAAGAGAGACGAAATTTG-TTTAAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* * * *
85045 GAAAACAGAT-TC-A-A-AG----ATTTTG-TTTCAAG
1 G-AAACTG-TCTCAAGAGAGACAAAATTTGTTTTAAAA
**
85074 GAAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGA
1 G-AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* *
85111 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAA
* *
85148 GAAACTGTCTCAAGAGAGACAAAACTTTG-TTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTAAAA
* ** ** * **
85184 GAAA-----AC-A-A-ATTCAATGTTTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAA--AATTTGTTTTAAAA
* *
85214 GAAACCGTCTCAAGAGAGACAAAATTTATTTTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
85250 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTT
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTT
85283 GAGTAAATTA
Statistics
Matches: 312, Mismatches: 62, Indels: 74
0.70 0.14 0.17
Matches are distributed among these distances:
28 7 0.02
29 37 0.12
30 14 0.04
31 4 0.01
32 2 0.01
33 2 0.01
34 3 0.01
35 12 0.04
36 123 0.39
37 101 0.32
38 7 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
Found at i:84895 original size:102 final size:101
Alignment explanation
Indices: 84765--84999 Score: 330
Period size: 102 Copynumber: 2.3 Consensus size: 101
84755 GAAACTGTCT
* * *
84765 CAAAAGAAATTGTCTCGAGTGAGACGAAATTTGTTT-AATGGAAAACATATTCA-AAGATTTTGT
1 CAAAAGAAAATGTCTCAAGAGAGACGAAATTTGTTTCAA-GGAAAACATATTCAGAA-ATTTTGT
*
84828 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAGTTC
64 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT-GTTC
* *
84867 CAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACATATTCAGAAATTTTGTTT
1 CAAAAGAAAATGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACATATTCAGAAATTTTGTTT
*
84932 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
66 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTC
* ** *
84968 TACGAGAAAATGTCTCAAGAGAGACAAAATTT
1 CAAAAGAAAATGTCTCAAGAGAGACGAAATTT
85000 AGTTCTAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
101 29 0.24
102 87 0.73
103 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (101 bp):
CAAAAGAAAATGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACATATTCAGAAATTTTGTTT
CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTC
Found at i:84975 original size:36 final size:36
Alignment explanation
Indices: 84925--85282 Score: 268
Period size: 36 Copynumber: 10.2 Consensus size: 36
84915 ATTCAGAAAT
*
84925 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
84961 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
84997 TTTAGTTCTAAAAGAAATTGTCTCAAGAGAGACGAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
85034 TTTGTTTAAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTTAAGAG-AAACTG-TCTCAAGAGAGACAAAA
*
85063 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAG-AAACTGTCTCAAGAGAGACAAAA
* *
85099 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
85135 TTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * ** **
85172 CTTTGTTTCAAG-GAAA-----AC-A-A-ATTCAATGTT
1 -TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA--AA
* * *
85202 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
85238 TTTATTTTAAAAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
85274 CTTTGTTTT
1 -TTTGTTTT
85283 GAGTAAATTA
Statistics
Matches: 253, Mismatches: 43, Indels: 51
0.73 0.12 0.15
Matches are distributed among these distances:
28 5 0.02
29 32 0.13
30 6 0.02
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 3 0.01
36 118 0.47
37 75 0.30
38 7 0.03
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:85071 original size:138 final size:137
Alignment explanation
Indices: 84835--85273 Score: 691
Period size: 138 Copynumber: 3.2 Consensus size: 137
84825 TGTTTCAAGG
* * *
84835 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTG
*
84900 TTTCAAGGAAAACATATTCAGAA-ATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
66 TTTCAAGGAAAACAAATTCA-AAGATTTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAATTT
84964 GTTTTACGA
129 GTTTTACGA
*
84973 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAATTGTCTCAAGAGAGACGAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTG
* *
85038 TTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTG
66 TTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGG-AAACTGTCTCAAGAGAGACAAAATTTG
85103 TTTTACGA
130 TTTTACGA
*
85111 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAACTTT
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAA-TTT
* * *
85176 GTTTCAAGGAAAACAAATTCAATGTTTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTT
65 GTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAATTT
* **
85241 ATTTTAAAA
129 GTTTTACGA
*
85250 GAAACTGTCTCAAGAGAGACAAAA
1 GAAAATGTCTCAAGAGAGACAAAA
85274 CTTTGTTTTG
Statistics
Matches: 280, Mismatches: 17, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
137 3 0.01
138 186 0.66
139 89 0.32
140 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (137 bp):
GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTG
TTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTTGT
TTTACGA
Found at i:86786 original size:95 final size:94
Alignment explanation
Indices: 86610--86805 Score: 277
Period size: 95 Copynumber: 2.1 Consensus size: 94
86600 GGATAACTCA
* * * * * * *
86610 ATATGTAAATACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCTGGGGTGTTTAACCAATTG
1 ATATATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG
* *
86675 CCTTATACGGATAACTCAAGCTTTATTGT
66 CCTTAGACGGACAACTCAAGCTTTATTGT
86704 ATAGTATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATA-TATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
*
86769 G-CTCTAGAGGGACAACTCAAGCTTTATTGT
65 GCCT-TAGACGGACAACTCAAGCTTTATTGT
86799 ATATATA
1 ATATATA
86806 TAATATTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
94 9 0.10
95 81 0.90
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (94 bp):
ATATATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG
CCTTAGACGGACAACTCAAGCTTTATTGT
Found at i:93295 original size:105 final size:101
Alignment explanation
Indices: 93040--93462 Score: 412
Period size: 100 Copynumber: 4.1 Consensus size: 101
93030 AAGACTTGAA
* * * * *
93040 CAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTTGAAAATCTTTA-
1 CAATCTTCAA-CAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGACAATCTTCAT
* * *
93104 ATAAACAGTCCGCTCCTATTCTTTCAGAGAGTATAGGACT
65 A-AAACGGTCCTCT-CTATTCATTCA-AGAGTATAGGACT
* * * *
93144 TAATCTTTAAC-AACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCAT
1 CAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGA-CAATCTTCAT
* *
93208 AAAACGGTCCTCTCTATTCCTTC-AGAGTATAGAACT
65 AAAACGGTCCTCTCTATTCATTCAAGAGTATAGGACT
93244 CGAACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCT
1 ----CAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG-ACAATCT
*
93309 TCATACAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGGACT
61 TCATAAAAC-GGT-C-CTCTCTATTCATTCA-AGAGTATAGGACT
* * * *
93354 CAATCTTTAACAAACATGTCCGCTC-CTATT-CTTCAGAGAGTATAGGACTCG---ATCTTTATA
1 CAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGACAATCTTCATA
* * * *
93414 AAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGTACT
66 AAACG-GTC--CTCTCTATTCATTCA-AGAGTATAGGACT
*
93454 CGATCTTCA
1 CAATCTTCA
93463 TAAGTTTGCT
Statistics
Matches: 273, Mismatches: 31, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
99 2 0.01
100 58 0.21
102 47 0.17
103 17 0.06
104 38 0.14
105 58 0.21
106 27 0.10
107 1 0.00
108 13 0.05
110 12 0.04
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (101 bp):
CAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGACAATCTTCATA
AAACGGTCCTCTCTATTCATTCAAGAGTATAGGACT
Found at i:93303 original size:55 final size:55
Alignment explanation
Indices: 92951--93456 Score: 430
Period size: 55 Copynumber: 9.7 Consensus size: 55
92941 CAAATGACGA
* * *
92951 GTCCTGCTCCCTATTCCTTCAGA-AGTATA-AGGCTCGAACAA--TTCATA-AAATGT
1 GTCC-GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCA-ACAAACGT
** ** * * *
93004 GTATGCTCTCTATTTATTCAGAGAGTA-AG-ACTTGAACAATCTTCAATAAAACGG
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-CAAACGT
* * * *
93058 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTTGAA-AATCTTTAATAAAC-A
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * * *
93111 GTCCGCTC-CTATTCTTTCAGAGAGTATAGGACT----TAATCTTTAAC-AACGT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * *
93160 GTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACG-
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGT
93214 GT-C-CTCTCTATTCCTTC--AGAGTATAGAACTCGAACAATCTTCAACAAACGT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
*
93265 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAC-AACGG
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGT
* * * *
93320 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACT----CAATCTTTAACAAACAT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * *
93371 GTCCGCTC-CTATT-CTTCAGAGAGTATAGGACTCG----ATCTTTATA-AAATGT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGT
* * *
93420 GTCTGCTCCCTATTCCTTCAGAGAGTATAGTACTCGA
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGA
93457 TCTTCATAAG
Statistics
Matches: 384, Mismatches: 38, Indels: 63
0.79 0.08 0.13
Matches are distributed among these distances:
48 3 0.01
49 53 0.14
50 66 0.17
51 49 0.13
52 54 0.14
53 33 0.09
54 40 0.10
55 77 0.20
56 9 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (55 bp):
GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
Found at i:93438 original size:260 final size:259
Alignment explanation
Indices: 92961--93456 Score: 693
Period size: 260 Copynumber: 1.9 Consensus size: 259
92951 GTCCTGCTCC
* * * *
92961 CTATTCCTTCAGAAGTATAAGGCTCGAACAATTCATAAAATGTGTATGCTCTCTATTTATTCAGA
1 CTATTCCTTCAGAAGTATAAGACTCGAACAATTCATAAAACGTGTACGCTCTCTATTCATTCAGA
* *
93026 GAGTAAGACTTGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAC
66 GAGTAAGACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGAAC
* * *
93091 TTGAAAATCTTTAATAAACAGTCCGCTCCTATTCTTTCAGAGAGTATAGGACTTAATCTTTAACA
131 TT-AAAATCTTTAACAAACAGTCCGCTCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAAAA
93156 ACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGTCCTCT
195 ACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGTCCTCT
* *
93221 CTATTCCTTCAG-AGTAT-AGAACTCGAACAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTT
1 CTATTCCTTCAGAAGTATAAG-ACTCGAACAA--TTCATA-AAACGTGTACGCTCTCTATTCATT
*
93283 CAGAGAGTATAGAACTCGAACAATCTTC-ATACAACGGGTCCGCTCTCTATTCATTCAGAGAGTA
62 CAGAGAGTA-AG-ACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGTA
* * *
93347 TAGGAC-T-CAATCTTTAACAAACATGTCCGCTCCTATTC-TTCAGAGAGTATAGGACTCGATCT
125 TAGAACTTAAAATCTTTAACAAACA-GTCCGCTCCTATTCTTTCAGAGAGTATAGGACTCAATCT
* *
93409 TTATAAAATGTG-TCTGCTCCCTATTCCTTCAGAGAGTATAGTACTCGA
189 TTA-AAAACGTGTTC-GCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
93457 TCTTCATAAG
Statistics
Matches: 210, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
258 2 0.01
259 55 0.26
260 65 0.31
261 33 0.16
262 41 0.20
263 14 0.07
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (259 bp):
CTATTCCTTCAGAAGTATAAGACTCGAACAATTCATAAAACGTGTACGCTCTCTATTCATTCAGA
GAGTAAGACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGAAC
TTAAAATCTTTAACAAACAGTCCGCTCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAAAAA
CGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGTCCTCT
Done.