Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004687.1 Hibiscus syriacus cultivar Beakdansim tig00010514_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: 69855
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:716 original size:5 final size:5
Alignment explanation
Indices: 703--767 Score: 55
Period size: 5 Copynumber: 13.2 Consensus size: 5
693 ATAGAACAAG
* * *
703 ATAAA ATAAT ATAAAA ATAAA AGGAAA AGAAA ATAAA ATAAA AT-AA ATAAA
1 ATAAA ATAAA AT-AAA ATAAA A-TAAA ATAAA ATAAA ATAAA ATAAA ATAAA
*
754 GT-AA A-AAA ATAAA A
1 ATAAA ATAAA ATAAA A
768 ATAACAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
4 9 0.18
5 32 0.65
6 8 0.16
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:752 original size:14 final size:13
Alignment explanation
Indices: 732--777 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
722 AAAGGAAAAG
732 AAAATAAAATAAA
1 AAAATAAAATAAA
*
745 ATAAATAAAGTAAA
1 A-AAATAAAATAAA
759 AAAATAAAAATAACA
1 AAAAT-AAAATAA-A
774 AAAA
1 AAAA
778 AATGTAGCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 5 0.18
14 18 0.64
15 5 0.18
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:2152 original size:29 final size:28
Alignment explanation
Indices: 2102--2163 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
2092 TAAAAATTAG
*
2102 TAGACCCTTATTTAAATATTTTAGAAGGT
1 TAGACCCTTATTTAAATATTTTA-AACGT
* * * *
2131 TAGATCCTTATTTGATTGTTTTAAACGT
1 TAGACCCTTATTTAAATATTTTAAACGT
2159 TAGAC
1 TAGAC
2164 TCGTGTCGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (28 bp):
TAGACCCTTATTTAAATATTTTAAACGT
Found at i:5321 original size:2 final size:2
Alignment explanation
Indices: 5314--5340 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5304 TGTTGCATTA
5314 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 A
5341 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5772 original size:4 final size:4
Alignment explanation
Indices: 5749--5787 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
5739 ATATACGTAT
* *
5749 ATAC ATGC ATAC ATAA ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
5788 TATATGTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:8990 original size:21 final size:24
Alignment explanation
Indices: 8966--9019 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
8956 TCATTGAATC
8966 ATTAAAAATAAAT-A-ATAT-TGT
1 ATTAAAAATAAATAATATATATGT
*
8987 ATTATCAAA-AAATAATATATATGT
1 ATTA-AAAATAAATAATATATATGT
9011 ATTAAAAAT
1 ATTAAAAAT
9020 GGTAATTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
21 8 0.31
22 4 0.15
23 7 0.27
24 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
ATTAAAAATAAATAATATATATGT
Found at i:18321 original size:21 final size:20
Alignment explanation
Indices: 18295--18413 Score: 96
Period size: 21 Copynumber: 5.8 Consensus size: 20
18285 ATCAGTTTCC
18295 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
*
18316 AAAATCGCAATGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
18337 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
18356 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* * *
18379 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
18399 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
18414 ACACATAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
19 1 0.01
20 18 0.22
21 59 0.73
22 2 0.02
23 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:18406 original size:20 final size:20
Alignment explanation
Indices: 18381--18574 Score: 196
Period size: 20 Copynumber: 9.7 Consensus size: 20
18371 GATTTTCCAG
** *
18381 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
*
18401 AATCGCAACGCGAA-CACATA
1 AATCGCAACGCGAATC-CGTA
* *
18421 AATCGCAACGCGTAGT-TGTA
1 AATCGCAACGCG-AATCCGTA
* *
18441 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
18461 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
18481 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
18501 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
18521 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
18542 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
18562 AATCGCAACGCGA
1 AATCGCAACGCGA
18575 TTTTTAAAGC
Statistics
Matches: 146, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
19 1 0.01
20 127 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:18464 original size:60 final size:60
Alignment explanation
Indices: 18381--18573 Score: 230
Period size: 60 Copynumber: 3.2 Consensus size: 60
18371 GATTTTCCAG
* ** * * *
18381 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTAGT-TGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTA-TCCGTA
* * *
18441 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA
* *
18501 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAACACGT-AAATCGCAACGCGTATCCGTA
18562 AATCGCAACGCG
1 AATCGCAACGCG
18574 ATTTTTAAAG
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.02
60 77 0.68
61 34 0.30
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:18992 original size:33 final size:33
Alignment explanation
Indices: 18953--19023 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
18943 TTCACTTAGA
18953 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
18986 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
19019 TTTCA
1 TTTCA
19024 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:19129 original size:21 final size:20
Alignment explanation
Indices: 19103--19209 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
19093 TGCAGAAGAG
19103 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* * **
19124 TCGCAACGTGAAAATCACTA
1 TCGCAACGAGAAAATGAAAA
19144 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
19166 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
19180 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
19199 TCGCAACGAGA
1 TCGCAACGAGA
19210 GAATCGCAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 8 0.12
21 25 0.37
22 9 0.13
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:19183 original size:14 final size:14
Alignment explanation
Indices: 19164--19220 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
19154 GAAAAATGAA
19164 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
19178 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
19197 AATCGCAACGAGAG
1 AATCGCAACGAGAG
19211 AATCGCAACG
1 AATCGCAACG
19221 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:19195 original size:33 final size:33
Alignment explanation
Indices: 19157--19236 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
19147 GCAACGAGAA
19157 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
19190 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
19223 AAACCAAAATCGCA
1 AAATGAAAATCGCA
19237 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:19273 original size:14 final size:14
Alignment explanation
Indices: 19254--19310 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
19244 TTTCATTTCG
19254 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
19268 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
19287 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
19301 CGTTGCGATT
1 CGTTGCGATT
19311 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:19279 original size:33 final size:33
Alignment explanation
Indices: 19237--19318 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
19227 CAAAATCGCA
19237 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19270 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19303 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
19319 TCTCATTGCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:19321 original size:21 final size:21
Alignment explanation
Indices: 19295--19359 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
19285 CGCGTTGCGA
19295 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
19316 TTCTCTCATTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
19336 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
19357 TTC
1 TTC
19360 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:21201 original size:93 final size:93
Alignment explanation
Indices: 21042--21264 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
21032 TAGATTGCTT
*
21042 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21107 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21135 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21200 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21228 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
21265 AATACCCTGA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:21418 original size:14 final size:14
Alignment explanation
Indices: 21397--21455 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
21387 ACGCGAAATG
21397 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21411 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
21430 AAAATCGCAACGAC
1 AAAATCGCAACGAC
21444 AAAATCGCAACG
1 AAAATCGCAACG
21456 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:21422 original size:33 final size:33
Alignment explanation
Indices: 21378--21467 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
21368 CACGAAACTT
**
21378 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
21411 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
21444 AAAATCGCAACGCGAAACCAAAAT
1 AAAATCGCAACGCGAAACCAAAAT
21468 TGCATTGCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:21467 original size:19 final size:19
Alignment explanation
Indices: 21362--21467 Score: 88
Period size: 19 Copynumber: 6.1 Consensus size: 19
21352 TAGTTTACTT
* *
21362 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
21382 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
21401 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
21415 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
21434 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
21448 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
21467 T
1 T
21468 TGCATTGCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 26 0.37
20 12 0.17
ACGTcount: A:0.47, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:21494 original size:19 final size:19
Alignment explanation
Indices: 21472--21620 Score: 138
Period size: 19 Copynumber: 8.3 Consensus size: 19
21462 CAAAATTGCA
21472 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
21491 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
21505 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
21524 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
21538 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
** *
21557 TTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCG
*
21576 TTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
21595 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
21615 TTGCGA
1 TTGCGA
21621 AAGTAAACTA
Statistics
Matches: 103, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
14 17 0.17
16 8 0.08
17 8 0.08
19 58 0.56
20 12 0.12
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:21508 original size:14 final size:14
Alignment explanation
Indices: 21489--21545 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
21479 TTTCATTTCG
21489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21503 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
21520 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
21536 CGTTGCGATT
1 CGTTGCGATT
21546 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21514 original size:33 final size:33
Alignment explanation
Indices: 21472--21602 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
21462 CAAAATTGCA
21472 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
21505 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
21538 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
21576 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
21603 TTAAGTTTCG
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 56 0.64
35 1 0.01
36 1 0.01
38 29 0.33
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:23565 original size:14 final size:14
Alignment explanation
Indices: 23546--23581 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
23536 ATTGTTTAAT
23546 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
23560 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
23574 TGATTTGT
1 TGATTTGT
23582 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:23756 original size:20 final size:19
Alignment explanation
Indices: 23688--23766 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
23678 AAAAATGATT
23688 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
23707 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
23721 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
23740 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
23760 ATCGCAA
1 ATCGCAA
23767 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:23810 original size:19 final size:19
Alignment explanation
Indices: 23775--23963 Score: 203
Period size: 19 Copynumber: 10.7 Consensus size: 19
23765 AACGAGAGAA
*
23775 TCGCAATGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
23793 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23812 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
23828 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
23845 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23864 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
23881 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
23898 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23917 TCCGCATTACGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
23935 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
23951 TCGCATTGCGATT
1 TCGCATTGCGATT
23964 CTCTCGTTGC
Statistics
Matches: 144, Mismatches: 9, Indels: 35
0.77 0.05 0.19
Matches are distributed among these distances:
14 22 0.15
16 14 0.10
17 14 0.10
18 14 0.10
19 55 0.38
20 25 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:23893 original size:53 final size:53
Alignment explanation
Indices: 23781--23963 Score: 309
Period size: 53 Copynumber: 3.5 Consensus size: 53
23771 AGAATCGCAA
23781 TGCGA-TTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
23832 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
23885 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
*
23938 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
23964 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
51 5 0.04
52 27 0.21
53 93 0.74
54 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:23900 original size:86 final size:84
Alignment explanation
Indices: 23798--23977 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
23788 TCATTTCGCA
*
23798 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTACGATTTTCA--T-G--TTGCGATTT
23859 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
23884 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTACGATTTTCATGTTGCGATTTTCA
23949 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
23970 TTGCGATT
1 TTGCGATT
23978 GTAATTTCCG
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 51 0.60
87 14 0.16
88 3 0.04
89 3 0.04
90 3 0.04
92 11 0.13
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTACGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:23985 original size:33 final size:33
Alignment explanation
Indices: 23798--23977 Score: 152
Period size: 33 Copynumber: 5.2 Consensus size: 33
23788 TCATTTCGCA
23798 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
23831 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
23868 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* *
23903 TTGCGATTTTCATTTCCGCATTACGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
23937 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
23970 TTGCGATT
1 TTGCGATT
23978 GTAATTTCCG
Statistics
Matches: 116, Mismatches: 16, Indels: 30
0.72 0.10 0.19
Matches are distributed among these distances:
31 4 0.03
32 7 0.06
33 58 0.50
34 16 0.14
35 4 0.03
36 3 0.03
37 2 0.02
38 2 0.02
39 8 0.07
40 3 0.03
41 9 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:26275 original size:12 final size:12
Alignment explanation
Indices: 26258--26282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26248 TCTTCGGGGA
26258 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26270 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26282 C
1 C
26283 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:26491 original size:24 final size:24
Alignment explanation
Indices: 26457--26503 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26447 CTGAAACATC
26457 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
26481 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
26504 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:27223 original size:20 final size:20
Alignment explanation
Indices: 27195--27423 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
27185 AAATTTCAGT
* * *
27195 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27215 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27235 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27255 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
**
27275 GTTGCGATTTACGGATAAGC
1 GTTGCGATTTACGGATTCGC
* *
27295 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27315 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
27335 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
27355 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27375 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27395 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27415 GTTGCGATT
1 GTTGCGATT
27424 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:31250 original size:21 final size:21
Alignment explanation
Indices: 31224--31300 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
31214 GACCCGACCT
*
31224 AAAATAATATATTTATTTAAA
1 AAAATAATATATTTATTAAAA
* * *
31245 AAAATATTATGTTTATTCAATA
1 AAAATAATATATTTATT-AAAA
31267 AAAAT-ATATATTTAATTAAAA
1 AAAATAATATATTT-ATTAAAA
31288 GAAAATAATATAT
1 -AAAATAATATAT
31301 AGAAGAGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 24 0.53
22 15 0.33
23 6 0.13
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAATAATATATTTATTAAAA
Found at i:36031 original size:29 final size:29
Alignment explanation
Indices: 35989--36077 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
35979 CTACAGTGGT
35989 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
36018 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
36047 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
36076 CT
1 CT
36078 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:36122 original size:18 final size:18
Alignment explanation
Indices: 36099--36135 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
36089 AGAATAGGGC
36099 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
36117 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
36135 C
1 C
36136 GTGGGAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:36165 original size:44 final size:44
Alignment explanation
Indices: 36117--36252 Score: 272
Period size: 44 Copynumber: 3.1 Consensus size: 44
36107 CAACATGGGA
36117 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
36161 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
36205 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
36249 CATG
1 CATG
36253 GGGTGGGAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 92 1.00
ACGTcount: A:0.27, C:0.14, G:0.43, T:0.16
Consensus pattern (44 bp):
CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
Found at i:36264 original size:15 final size:15
Alignment explanation
Indices: 36224--36403 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
36214 AACATGGGAC
36224 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
36240 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
36255 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
36270 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
36287 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
36305 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
36320 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
36337 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
36353 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
36373 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
36388 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
36403 G
1 G
36404 GAGGGGATGG
Statistics
Matches: 131, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.01
15 52 0.40
16 27 0.21
17 30 0.23
18 3 0.02
19 15 0.11
20 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:36285 original size:65 final size:66
Alignment explanation
Indices: 36211--36337 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
36201 GATGCATGCA
36211 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
36275 G
66 G
*
36276 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
36338 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:36340 original size:82 final size:83
Alignment explanation
Indices: 36226--36402 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 83
36216 CATGGGACGT
* * *
36226 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
36288 TGTGGGAATGCATGGGGGA
66 CGTGGGAATGCAT-GGGGA
* *** *
36307 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
36372 CGTGGGAATGCATGGGGT
66 CGTGGGAATGCATGGGGA
36390 GGGAATGCATGGG
1 GGGAATGCATGGG
36403 GGAGGGGATG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 12 0.15
82 31 0.38
83 21 0.26
84 18 0.22
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (83 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
CGTGGGAATGCATGGGGA
Found at i:36350 original size:65 final size:64
Alignment explanation
Indices: 36214--36407 Score: 207
Period size: 65 Copynumber: 3.0 Consensus size: 64
36204 GCATGCAATC
*
36214 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT
1 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
*
36278 CAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGGTG-GG
1 -AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG--GTGGGAATGCATGGGG-GAGG
36342 AAT
62 AAT
* * ** * *
36345 -GCATGGGGGA-G-GGGATGGTGCATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAG
1 AACAT--GGGACGTGGGA--ATGCA-TGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAG
36407 G
61 G
36408 GGATGGTGCA
Statistics
Matches: 112, Mismatches: 8, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
65 48 0.43
66 19 0.17
67 28 0.25
68 17 0.15
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.17
Consensus pattern (64 bp):
AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
Found at i:36388 original size:51 final size:51
Alignment explanation
Indices: 36289--36430 Score: 254
Period size: 51 Copynumber: 2.8 Consensus size: 51
36279 AACATGGGAT
*
36289 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
36337 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
36388 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
36431 CTGTGCATGG
Statistics
Matches: 90, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
48 23 0.26
51 67 0.74
ACGTcount: A:0.20, C:0.08, G:0.54, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:36544 original size:32 final size:32
Alignment explanation
Indices: 36503--36566 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
36493 AAGGTCCTGC
36503 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
36535 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
36567 CAGAGATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:36924 original size:21 final size:21
Alignment explanation
Indices: 36876--36924 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
36866 ACTAAAATCT
*
36876 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
36898 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
36919 AGTTAT
1 AGTTAT
36925 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:36934 original size:28 final size:28
Alignment explanation
Indices: 36901--36961 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
36891 TAGTATAAAT
*
36901 TATTAGTTTGTAAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
*
36929 TATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
36957 TATTA
1 TATTA
36962 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
TATTAGTTTATAAGTTTAAGTTATATTA
Found at i:37511 original size:20 final size:21
Alignment explanation
Indices: 37467--37511 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
37457 AAATATTGTG
**
37467 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
37488 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
37508 TTTA
1 TTTA
37512 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:38980 original size:47 final size:47
Alignment explanation
Indices: 38877--38967 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
38867 CAACAAACAA
38877 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
* *
38925 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
38968 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
Found at i:39036 original size:41 final size:40
Alignment explanation
Indices: 38898--39036 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 40
38888 CTATTTAACT
* * *
38898 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATT
1 AACATAAACTAATTAAAT-ATTTTTTAACTAT-A-TAACTATA
*
38940 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATATTTTTTAACTATATAACTAT-A
* * *
38984 AACATATACTAATTAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATATTTTTTAA-CTATATA-ACTATA
*
39025 AACTTAAACTAA
1 AACATAAACTAA
39037 CAATCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
41 30 0.38
42 8 0.10
43 15 0.19
44 12 0.15
45 15 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (40 bp):
AACATAAACTAATTAAATATTTTTTAACTATATAACTATA
Found at i:39201 original size:4 final size:4
Alignment explanation
Indices: 39173--39230 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
39163 TTTCGAATTC
* ** **
39173 TTCT TACT TTCCT TTCT CCCT TTCT TTCT TTCT TTCAT TTCT CACT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT
39223 TTCT TTCT
1 TTCT TTCT
39231 CGGCTGCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (4 bp):
TTCT
Found at i:39207 original size:25 final size:25
Alignment explanation
Indices: 39173--39230 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
39163 TTTCGAATTC
* * *
39173 TTCTTACTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCATTTCTCACTTTCT
39198 TTCTTTCTTTCATTTCTCACTTTCT
1 TTCTTTCTTTCATTTCTCACTTTCT
39223 TTCTTTCT
1 TTCTTTCT
39231 CGGCTGCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTCTTTCATTTCTCACTTTCT
Found at i:39320 original size:25 final size:25
Alignment explanation
Indices: 39292--39343 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
39282 TTTCTTTTAT
*
39292 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
39317 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
39342 AA
1 AA
39344 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:39491 original size:23 final size:23
Alignment explanation
Indices: 39464--39510 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
39454 GAATCTATAT
39464 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
*
39487 GGCTGCATTTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
39510 G
1 G
39511 AATGGACGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.43, T:0.28
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:39515 original size:13 final size:13
Alignment explanation
Indices: 39497--39528 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39487 GGCTGCATTT
*
39497 GAATGGATGATGG
1 GAATGGACGATGG
39510 GAATGGACGATGG
1 GAATGGACGATGG
39523 GAATGG
1 GAATGG
39529 CGCCGGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (13 bp):
GAATGGACGATGG
Found at i:39630 original size:29 final size:29
Alignment explanation
Indices: 39529--39619 Score: 164
Period size: 29 Copynumber: 3.1 Consensus size: 29
39519 ATGGGAATGG
*
39529 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
39558 CGCCGGGAGTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
39587 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
39616 CGCC
1 CGCC
39620 TAGGCTGCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.23, C:0.31, G:0.32, T:0.14
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:39635 original size:29 final size:29
Alignment explanation
Indices: 39529--39637 Score: 139
Period size: 29 Copynumber: 3.8 Consensus size: 29
39519 ATGGGAATGG
* *
39529 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCAGGACTACATGGCGACCTACAAGGT
* *
39558 CGCCGGGAGTACATGGCGACCTACAAGGT
1 CGCCAGGACTACATGGCGACCTACAAGGT
*
39587 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCAGGACTACATGGCGACCTACAAGGT
* *
39616 CGCCTAGG-CTGCATGACGACCT
1 CGCC-AGGACTACATGGCGACCT
39638 CTCTATTCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
29 71 0.97
30 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.16
Consensus pattern (29 bp):
CGCCAGGACTACATGGCGACCTACAAGGT
Found at i:39692 original size:43 final size:43
Alignment explanation
Indices: 39631--39879 Score: 216
Period size: 43 Copynumber: 5.9 Consensus size: 43
39621 AGGCTGCATG
39631 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGA
1 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGA
***
39674 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCG-
1 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGA
* * **
39716 -C-A-CTC-GTATGGCTCGTA-TGCATGGGGACCTCGCATGGGGAGA
1 ACGACCTCTCTAT---TC-CACTGCATGGCCACCTCGCATGGGGAGA
***
39758 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCG-
1 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGA
* * **
39800 -C-A-CTC-GTATGGCTCGTA-TGCATGGGGACCTCGCATGGGGAGA
1 ACGACCTCTCTAT---TC-CACTGCATGGCCACCTCGCATGGGGAGA
39842 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGG
1 ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGG
39880 CTCGCACTCG
Statistics
Matches: 158, Mismatches: 28, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
38 6 0.04
39 6 0.04
40 2 0.01
41 44 0.28
42 4 0.03
43 82 0.52
44 2 0.01
45 6 0.04
46 6 0.04
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.22
Consensus pattern (43 bp):
ACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGA
Found at i:39749 original size:41 final size:41
Alignment explanation
Indices: 39692--39907 Score: 142
Period size: 41 Copynumber: 5.2 Consensus size: 41
39682 TCTATTCCAC
39692 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
39733 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
39775 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
39817 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
39859 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
39901 TGCATGG
1 TGCATGG
39908 GGAGAACCAT
Statistics
Matches: 127, Mismatches: 28, Indels: 40
0.65 0.14 0.21
Matches are distributed among these distances:
38 6 0.05
39 6 0.05
40 2 0.02
41 51 0.40
42 4 0.03
43 44 0.35
44 2 0.02
45 6 0.05
46 6 0.05
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:39790 original size:84 final size:84
Alignment explanation
Indices: 39649--39910 Score: 506
Period size: 84 Copynumber: 3.1 Consensus size: 84
39639 TCTATTCCAC
**
39649 TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
39714 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
39733 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
39798 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
39817 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
39882 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
39901 TGCATGGGGA
1 TGCATGGGGA
39911 GAACCATTGG
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 176 1.00
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (84 bp):
TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
CGCACTCGTATGGCTCGTA
Found at i:39932 original size:35 final size:35
Alignment explanation
Indices: 39886--39998 Score: 226
Period size: 35 Copynumber: 3.2 Consensus size: 35
39876 ATGGCTCGCA
39886 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
39921 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
39956 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
39991 CTCGTATG
1 CTCGTATG
39999 TTCCCGTATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
Found at i:49232 original size:29 final size:30
Alignment explanation
Indices: 49168--49225 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
49158 GCTCCAATGA
*
49168 TATAATTGAAGTTAAAATCAAAGTTTAGTGT
1 TATAATTGAAG-TAAAATAAAAGTTTAGTGT
*
49199 TATAATTGAA-TAAATTAAAAGTTTAGT
1 TATAATTGAAGTAAAATAAAAGTTTAGT
49226 TGTATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
31 10 0.40
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.40
Consensus pattern (30 bp):
TATAATTGAAGTAAAATAAAAGTTTAGTGT
Found at i:54498 original size:85 final size:82
Alignment explanation
Indices: 54351--54569 Score: 255
Period size: 83 Copynumber: 2.6 Consensus size: 82
54341 TGATACGCCC
* * * * *
54351 TTGAGCTGAATGTAATCGAACTCGAGG-GTTTATTGACAGATAACCCTTCTGGCCTTAAGTTATG
1 TTGAGCTGAATGTAATCGAACTCAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* *
54415 ATTCAAAT-ATGGTATGCTT
66 ATGCAAATGAT-G--TGCCT
* *
54434 TTGAGCTGAATGTAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTTTAGCCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTC-AAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTAAGTTAT
*
54499 GCTGCAAATGATGTGCCT
65 GATGCAAATGATGTGCCT
*
54517 TTGAGCT-AAGTGTAATCGAGCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 TTGAGCTGAA-TGTAATCGAACTC-AAGGTCTTT-GTTGGCAGATAACCCTTCT
54570 CGACTTTGAG
Statistics
Matches: 118, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
82 2 0.02
83 55 0.47
84 21 0.18
85 38 0.32
86 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (82 bp):
TTGAGCTGAATGTAATCGAACTCAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
ATGCAAATGATGTGCCT
Found at i:54605 original size:58 final size:58
Alignment explanation
Indices: 54515--54625 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
54505 AATGATGTGC
*
54515 CTTTGAGCTAAGTGTAATCGAGCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
1 CTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
* *
54573 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT
1 CTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
54626 ATAGCCTTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (58 bp):
CTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
Found at i:54690 original size:142 final size:141
Alignment explanation
Indices: 54433--54717 Score: 489
Period size: 142 Copynumber: 2.0 Consensus size: 141
54423 ATGGTATGCT
*
54433 TTTGAGCTGAATGTAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTTTAGCCTTGAGTTA
1 TTTGAGCTGAATGTAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTA
* *
54498 TGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAGCTCGAAGGTCTTTGGTTGGCAGATAA
66 TGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATAA
*
54563 CCCTTCTCGAC
131 CACTTCTCGAC
* *
54574 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATAGCCTTGAGTT
1 TTTGAGCTGAATGTAATCGAACTCAAAGGTC-TTTGTTGGCAGATAACCCTTATAGCCTTGAGTT
* *
54639 ATGCTGCAAATGATGTGTCTTTGAGCTAAGTGTAATCGAACTCGAATGTCTTTGGTTGGAAGATA
65 ATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATA
54704 ACACTTCTCGAC
130 ACACTTCTCGAC
54716 TT
1 TT
54718 AAGCTATACT
Statistics
Matches: 135, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
141 29 0.21
142 106 0.79
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (141 bp):
TTTGAGCTGAATGTAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTA
TGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATAA
CACTTCTCGAC
Found at i:54836 original size:83 final size:84
Alignment explanation
Indices: 54573--54902 Score: 396
Period size: 84 Copynumber: 3.9 Consensus size: 84
54563 CCCTTCTCGA
* * *
54573 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATAGCCTTGAGT
1 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGT
*
54638 TATGCTGCAAATGATGTGT
66 TATGCTGCAAATGATGTGC
* * * * * *
54657 CTTTGAGCTAAGTGTAATCGAACTCGAATGTCTTTGGTTGGA-AGATAACACTTCTCGACTTAAG
1 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTT-GACAGATAACCCTTCTAGCCTTAAG
* *
54721 CTATACTGCAAATGATGTGC
65 TTATGCTGCAAATGATGTGC
* * * *
54741 CTTTGAGTTGAGTATAATCGAACTCGAAGGT-TTTTGTTGACATATAACCCTTCTAGCCTTTAGT
1 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGT
* *
54805 TATGCTGTAAATAATGTGC
66 TATGCTGCAAATGATGTGC
* * * * *
54824 CTTTAAGCTGAGTGTAATAGAACTCGAAGGTCTTTTGTT-AGCAGATATCCCTTCTTGCCTTGAG
1 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGA-CAGATAACCCTTCTAGCCTTAAG
* *
54888 CTAAGCTGCAAATGA
65 TTATGCTGCAAATGA
54903 GCACGATATC
Statistics
Matches: 204, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
82 2 0.01
83 67 0.33
84 134 0.66
85 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (84 bp):
CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGT
TATGCTGCAAATGATGTGC
Found at i:54850 original size:167 final size:168
Alignment explanation
Indices: 54573--54902 Score: 448
Period size: 167 Copynumber: 2.0 Consensus size: 168
54563 CCCTTCTCGA
* *
54573 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATAGCCTTGAGT
1 CTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTATAGCCTTGAGT
* * * * * *
54638 TATGCTGCAAATGATGTGTCTTTGAGCTAAGTGTAATCGAACTCGAATGTCTTTGGTTGGAAGAT
66 TATGCTGCAAATAATGTGCCTTTAAGCTAAGTGTAATAGAACTCGAAGGTCTTTGGTTAGAAGAT
54703 AACACTTCTCGACTTAAGCTATA-CTGCAAATGATGTGC
131 AACACTTCTCGACTTAAGCTA-AGCTGCAAATGATGTGC
* * * *
54741 CTTTGAGTTGAGTATAATCGAACTCGAAGGT-TTTTGTTGACATATAACCCTTCTAGCCTTTAGT
1 CTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTATAGCCTTGAGT
* * * *
54805 TATGCTGTAAATAATGTGCCTTTAAGCTGAGTGTAATAGAACTCGAAGGTCTTTTGTTAGCAGAT
66 TATGCTGCAAATAATGTGCCTTTAAGCTAAGTGTAATAGAACTCGAAGGTCTTTGGTTAGAAGAT
* * * * *
54870 ATCCCTTCTTGCCTTGAGCTAAGCTGCAAATGA
131 AACACTTCTCGACTTAAGCTAAGCTGCAAATGA
54903 GCACGATATC
Statistics
Matches: 140, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
166 1 0.01
167 110 0.79
168 29 0.21
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (168 bp):
CTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTATAGCCTTGAGT
TATGCTGCAAATAATGTGCCTTTAAGCTAAGTGTAATAGAACTCGAAGGTCTTTGGTTAGAAGAT
AACACTTCTCGACTTAAGCTAAGCTGCAAATGATGTGC
Found at i:55679 original size:43 final size:43
Alignment explanation
Indices: 55630--55739 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
55620 GATTCCCTTC
* * *
55630 ATTGTGGAGTTTAAACCGTGGATGTATGGGCACGATATCCTCCT
1 ATTGTGGAGTTGAAATCGTGGATGTATGGGCACAATATCCT-CT
* * * *
55674 -TTGTGGAGTTGAAATCGTGGATCTGTTGGTACAATATCCTCT
1 ATTGTGGAGTTGAAATCGTGGATGTATGGGCACAATATCCTCT
55716 ATTGTGGAGTTGAAATCGTGGATG
1 ATTGTGGAGTTGAAATCGTGGATG
55740 ACCCCTTCGT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 2 0.04
43 55 0.96
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.35
Consensus pattern (43 bp):
ATTGTGGAGTTGAAATCGTGGATGTATGGGCACAATATCCTCT
Found at i:56397 original size:32 final size:33
Alignment explanation
Indices: 56329--56400 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
56319 CATCAGGATG
* *
56329 TTGAAT-TCTCAAATATGCCACAATATTCAATG
1 TTGAATCTCTCAAATATGCCACAACATTCAATA
* * *
56361 TTGAATCTC-CAAATATGCCCCAACATTTACTA
1 TTGAATCTCTCAAATATGCCACAACATTCAATA
56393 TTGAATCT
1 TTGAATCT
56401 TTAAAGATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (33 bp):
TTGAATCTCTCAAATATGCCACAACATTCAATA
Found at i:67399 original size:27 final size:27
Alignment explanation
Indices: 67364--67419 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
67354 GAGGTGGCGT
*
67364 TTGGGGGCTGGCTT-CTGCTGCTGTGGA
1 TTGGCGGCTGG-TTGCTGCTGCTGTGGA
*
67391 TTGGCGGCTGGTTGCTGCTGTTGTGGA
1 TTGGCGGCTGGTTGCTGCTGCTGTGGA
67418 TT
1 TT
67420 CGTGACATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.04, C:0.16, G:0.43, T:0.38
Consensus pattern (27 bp):
TTGGCGGCTGGTTGCTGCTGCTGTGGA
Done.