Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008414.1 Hibiscus syriacus cultivar Beakdansim tig00111192_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: 209268
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:279 original size:23 final size:25
Alignment explanation
Indices: 253--299 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
243 AATTGTAAAA
*
253 AAATCAGCAC-AAATAAT-TTTTAT
1 AAATCAACACTAAATAATATTTTAT
*
276 AAATCAACCCTAAATAATATTTTA
1 AAATCAACACTAAATAATATTTTA
300 GAGTTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATCAACACTAAATAATATTTTAT
Found at i:3437 original size:69 final size:69
Alignment explanation
Indices: 3326--3465 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
3316 TTGAATACAA
3326 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
1 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
3391 TAAG
66 TAAG
3395 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
1 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
3460 TAAG
66 TAAG
3464 AG
1 AG
3466 AGTACAATTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (69 bp):
AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
TAAG
Found at i:13588 original size:17 final size:18
Alignment explanation
Indices: 13566--13601 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13556 CTCAAAATCA
*
13566 TCTC-TTTGTTTTTGTTT
1 TCTCTTTTGTTTTTATTT
13583 TCTCTTTTGTTTTTATTT
1 TCTCTTTTGTTTTTATTT
13601 T
1 T
13602 GCATATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.78
Consensus pattern (18 bp):
TCTCTTTTGTTTTTATTT
Found at i:22732 original size:36 final size:37
Alignment explanation
Indices: 22685--22759 Score: 116
Period size: 36 Copynumber: 2.0 Consensus size: 37
22675 TGTCAGGATA
22685 TTGTGCATCGGGTTTGAGAGAACAA-AAGATTCTTTC
1 TTGTGCATCGGGTTTGAGAGAACAACAAGATTCTTTC
* *
22721 TTGTGCATCGGGTTTGGGAGAATAACGAAGATTCTTTC
1 TTGTGCATCGGGTTTGAGAGAACAAC-AAGATTCTTTC
22759 T
1 T
22760 CTGTCAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 23 0.66
38 12 0.34
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (37 bp):
TTGTGCATCGGGTTTGAGAGAACAACAAGATTCTTTC
Found at i:26013 original size:31 final size:31
Alignment explanation
Indices: 25975--26039 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
25965 GAGTTTCAGG
25975 ACAAACAAAATTTAAATAAAATAGACAACAA
1 ACAAACAAAATTTAAATAAAATAGACAACAA
26006 ACAAACAAAATTTAAATAAAATAGACAACAA
1 ACAAACAAAATTTAAATAAAATAGACAACAA
26037 ACA
1 ACA
26040 TTGATGAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.68, C:0.14, G:0.03, T:0.15
Consensus pattern (31 bp):
ACAAACAAAATTTAAATAAAATAGACAACAA
Found at i:26362 original size:14 final size:14
Alignment explanation
Indices: 26343--26370 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
26333 ATGAAGCAAT
26343 TATAATATATATAA
1 TATAATATATATAA
26357 TATAATATATATAA
1 TATAATATATATAA
26371 ACTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAATATATATAA
Found at i:26471 original size:49 final size:50
Alignment explanation
Indices: 26395--26505 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 50
26385 GTATAGTTTA
* * * * * * * *
26395 TATATAAACTATTTAGTTTATATTTATATATTATG-TACAAACTATATAG
1 TATATAAATTATATAATTTAAATTTATATACTATGCAAAAAACCATATAG
*
26444 TATGTAAATTATATAATTTAAATTTATATACTATGCAAAAAACCATATAG
1 TATATAAATTATATAATTTAAATTTATATACTATGCAAAAAACCATATAG
26494 TATATAAATTAT
1 TATATAAATTAT
26506 GCATAAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 29 0.57
50 22 0.43
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (50 bp):
TATATAAATTATATAATTTAAATTTATATACTATGCAAAAAACCATATAG
Found at i:26584 original size:9 final size:9
Alignment explanation
Indices: 26572--26649 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
26562 TGTTTATATT
26572 TATATACTA
1 TATATACTA
**
26581 TATATAAAA
1 TATATACTA
*
26590 CTATATAGT-
1 -TATATACTA
26599 T-TATA-TA
1 TATATACTA
* *
26606 TAAAAACTA
1 TATATACTA
26615 TATATACTA
1 TATATACTA
26624 TATATAAACTA
1 TATAT--ACTA
*
26635 CATATACTA
1 TATATACTA
26644 TATATA
1 TATATA
26650 AACTATATAG
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 5 0.09
8 3 0.06
9 30 0.57
10 6 0.11
11 8 0.15
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (9 bp):
TATATACTA
Found at i:26595 original size:34 final size:33
Alignment explanation
Indices: 26536--26666 Score: 105
Period size: 34 Copynumber: 4.1 Consensus size: 33
26526 ATTTATATAT
* * *
26536 TATTTATAAATATATA-AAAATTATATTGTTTA
1 TATTTATAACTATATATAAAACTATATAGTTTA
26568 TATTTATATACTATATATAAAACTATATAGTTTA
1 TATTTATA-ACTATATATAAAACTATATAGTTTA
* * **
26602 TATATAAAAACTATATAT---ACTATATA-TAAA
1 TAT-TTATAACTATATATAAAACTATATAGTTTA
**
26632 CTACATAT-ACTATATAT-AAACTATATAGTTTA
1 -TATTTATAACTATATATAAAACTATATAGTTTA
26664 TAT
1 TAT
26667 ATAAATTATA
Statistics
Matches: 78, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
29 9 0.12
30 3 0.04
31 20 0.26
32 10 0.13
33 7 0.09
34 26 0.33
35 3 0.04
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (33 bp):
TATTTATAACTATATATAAAACTATATAGTTTA
Found at i:26665 original size:20 final size:20
Alignment explanation
Indices: 26579--26720 Score: 123
Period size: 20 Copynumber: 7.0 Consensus size: 20
26569 ATTTATATAC
26579 TATATATAAAACTATATAGTT
1 TATATAT-AAACTATATAGTT
*
26600 TATATATAAAAACTATATA-TAC
1 TATATAT--AAACTATATAGT-T
* *
26622 TATATATAAACTACATA-TAC
1 TATATATAAACTATATAGT-T
26642 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
26662 TATATATAAATTATATAGTT
1 TATATATAAACTATATAGTT
* * *
26682 TATATTTATA-TACTAT-GTA
1 TATATATAAACTA-TATAGTT
26701 TA-ATTATAAACTATATAGTT
1 TATA-TATAAACTATATAGTT
26721 ACAAACTATA
Statistics
Matches: 103, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 13 0.13
20 62 0.60
21 9 0.09
22 18 0.17
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:26785 original size:14 final size:14
Alignment explanation
Indices: 26766--26796 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
26756 TTAAAAAAAC
26766 TATAATATATTATA
1 TATAATATATTATA
26780 TATAATATATTATA
1 TATAATATATTATA
26794 TAT
1 TAT
26797 GTATGATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATAATATATTATA
Found at i:26864 original size:5 final size:5
Alignment explanation
Indices: 26854--27034 Score: 362
Period size: 5 Copynumber: 36.2 Consensus size: 5
26844 ATGCATCCAT
26854 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
26904 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
26954 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
27004 TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
27035 TATGTACTTT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 176 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:27222 original size:20 final size:19
Alignment explanation
Indices: 27174--27224 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
27164 AAATGTCCAA
* *
27174 CAAAATCGCAACGCGATCT
1 CAAATTCGCAACGCGAACT
*
27193 TAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
*
27212 CCAACTTCGCAAC
1 -CAAATTCGCAAC
27225 TCAGTTTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.18
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:27255 original size:21 final size:21
Alignment explanation
Indices: 27229--27372 Score: 114
Period size: 21 Copynumber: 7.0 Consensus size: 21
27219 CGCAACTCAG
*
27229 TTTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
*
27250 TTTCC-ATTTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
** *
27270 AGTCGAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
* *
27291 TTTTC-ATTTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
** * *
27311 AGTCGAAATTCACGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
** * *
27332 AGTCGAAATTCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
* *
27353 TTTCC-ATTTCGTGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
27373 AGTCCAAAAT
Statistics
Matches: 96, Mismatches: 25, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
20 42 0.44
21 54 0.56
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:27282 original size:41 final size:41
Alignment explanation
Indices: 27234--27331 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
27224 CTCAGTTTCC
*
27234 AAATTCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTCG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCG
*
27275 AAATTCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTCG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCG
*
27316 AAATTCACGTTGCGAT
1 AAATTCGCGTTGCGAT
27332 AGTCGAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (41 bp):
AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCG
Found at i:28380 original size:13 final size:13
Alignment explanation
Indices: 28362--28386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28352 AAGCTTGGCT
28362 TTGTCGAAGGGAG
1 TTGTCGAAGGGAG
28375 TTGTCGAAGGGA
1 TTGTCGAAGGGA
28387 TAATTATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.44, T:0.24
Consensus pattern (13 bp):
TTGTCGAAGGGAG
Found at i:30557 original size:19 final size:19
Alignment explanation
Indices: 30533--30572 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
30523 ATTATTGAAG
30533 ACAATCATAATGATATTCA
1 ACAATCATAATGATATTCA
30552 ACAATCATAATGATATTCA
1 ACAATCATAATGATATTCA
30571 AC
1 AC
30573 GAGTATTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (19 bp):
ACAATCATAATGATATTCA
Found at i:34548 original size:21 final size:21
Alignment explanation
Indices: 34506--34548 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
34496 TTATACGAGG
*
34506 AAATACATTTTTAAAATTAAA
1 AAATACATTTTTAAAATAAAA
*
34527 AAATACATATTTT-CAATAAAA
1 AAATACAT-TTTTAAAATAAAA
34548 A
1 A
34549 TATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATACATTTTTAAAATAAAA
Found at i:37140 original size:22 final size:21
Alignment explanation
Indices: 37115--37156 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
37105 GAATTCTACC
37115 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
37137 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
37157 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:37380 original size:16 final size:16
Alignment explanation
Indices: 37359--37407 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
37349 AATGGACATG
37359 ATTAATAAAATATAAT
1 ATTAATAAAATATAAT
*
37375 ATTAATTAAATA-AATT
1 ATTAATAAAATATAA-T
37391 ATTAATAAAAATATAAT
1 ATTAAT-AAAATATAAT
37408 TATATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 18 0.64
17 6 0.21
18 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAATAAAATATAAT
Found at i:40894 original size:17 final size:17
Alignment explanation
Indices: 40874--40907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40864 ATTGGCATGA
*
40874 CTTTCAAATAAGGTTAG
1 CTTTCAAAGAAGGTTAG
*
40891 CTTTTAAAGAAGGTTAG
1 CTTTCAAAGAAGGTTAG
40908 GCTTGAAGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (17 bp):
CTTTCAAAGAAGGTTAG
Found at i:51960 original size:18 final size:18
Alignment explanation
Indices: 51918--51960 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
51908 AAAAATTTAA
**
51918 AAAAGTTATATATTAATTT
1 AAAA-TTATATATTAAACT
51937 AAAATTATATATTAAACT
1 AAAATTATATATTAAACT
*
51955 ATAATT
1 AAAATT
51961 GTGATTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATTATATATTAAACT
Found at i:59992 original size:19 final size:19
Alignment explanation
Indices: 59961--60001 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
59951 GTTATTTTTC
59961 AAATTATTGTGTT-TTGATT
1 AAATTATTGTGTTGTT-ATT
59980 AAATTA-TGTTGTTGTTATT
1 AAATTATTG-TGTTGTTATT
59999 AAA
1 AAA
60002 AACTATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.10
19 16 0.80
20 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
AAATTATTGTGTTGTTATT
Found at i:71644 original size:23 final size:23
Alignment explanation
Indices: 71593--71675 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
71583 AAAATTCACG
*
71593 AGGGTATCGATACTTC--C-CCT
1 AGGGTATCGATACTTCATCTTCT
*
71613 GGGGTATCGATACTTCATCTTCT
1 AGGGTATCGATACTTCATCTTCT
71636 AGGGTATCGATACTTCATCTTCT
1 AGGGTATCGATACTTCATCTTCT
71659 AGGGTATCGATACTTCA
1 AGGGTATCGATACTTCA
71676 ATGAGTATTG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.26
22 1 0.02
23 41 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (23 bp):
AGGGTATCGATACTTCATCTTCT
Found at i:72173 original size:19 final size:20
Alignment explanation
Indices: 72151--72193 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
72141 AAAAGTTTTT
*
72151 TTAAAATAAAA-AATAAGAA
1 TTAAAATAAAAGAAAAAGAA
*
72170 TT-AAATAAAAGAAAAATAA
1 TTAAAATAAAAGAAAAAGAA
72189 TTAAA
1 TTAAA
72194 CAAACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 10 0.50
20 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
TTAAAATAAAAGAAAAAGAA
Found at i:72342 original size:14 final size:14
Alignment explanation
Indices: 72323--72350 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
72313 ATCTTACAAG
72323 AACAATTCTTCGCT
1 AACAATTCTTCGCT
72337 AACAATTCTTCGCT
1 AACAATTCTTCGCT
72351 GCCAACTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
AACAATTCTTCGCT
Found at i:72977 original size:72 final size:64
Alignment explanation
Indices: 72804--72982 Score: 209
Period size: 64 Copynumber: 2.7 Consensus size: 64
72794 TAAAACATCT
* **
72804 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAAAATAATAAAATATAA
*
72868 TAAATCCTAATTAAAACACTAAAACCTATTTCAACTAAAATACCTAAAACAA-AGATAAAATATA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAA-AATA-ATAAAATAT-
72932 AAA
63 -AA
*
72935 TAATATCCTAAAACTTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 TAA-ATCCT--AA-TTAAAACACT-AAAACCTATTTAAACTAAAATAC
72983 AAAGATAAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
63 5 0.05
64 43 0.43
65 10 0.10
67 3 0.03
68 5 0.05
70 2 0.02
71 9 0.09
72 22 0.22
ACGTcount: A:0.56, C:0.16, G:0.01, T:0.28
Consensus pattern (64 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAATAATAAAATATAA
Found at i:74687 original size:27 final size:27
Alignment explanation
Indices: 74634--74708 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
74624 CTGTTCAGAG
** *
74634 AAAAATAAAATAAAATTGAGTATATGA
1 AAAAATAAAATAAAATAAAGGATATGA
*
74661 TAAAATAAAATAAAATAAATGGA-ATGA
1 AAAAATAAAATAAAATAAA-GGATATGA
*
74688 AATAAATACAATGAAAATAAA
1 AA-AAATAAAAT-AAAATAAA
74709 ACGAAATGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 21 0.54
28 10 0.26
29 8 0.21
ACGTcount: A:0.67, C:0.01, G:0.09, T:0.23
Consensus pattern (27 bp):
AAAAATAAAATAAAATAAAGGATATGA
Found at i:74690 original size:14 final size:15
Alignment explanation
Indices: 74663--74708 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
74653 GTATATGATA
*
74663 AAATAAAAT-AAAAT
1 AAATACAATGAAAAT
**
74677 AAATGGAATG-AAAT
1 AAATACAATGAAAAT
74691 AAATACAATGAAAAT
1 AAATACAATGAAAAT
74706 AAA
1 AAA
74709 ACGAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (15 bp):
AAATACAATGAAAAT
Found at i:76653 original size:16 final size:16
Alignment explanation
Indices: 76632--76663 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
76622 TACTGTTGTT
76632 GGGGTCATGTTGACTA
1 GGGGTCATGTTGACTA
76648 GGGGTCATGTTGACTA
1 GGGGTCATGTTGACTA
76664 ATGCTCCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (16 bp):
GGGGTCATGTTGACTA
Found at i:77730 original size:18 final size:18
Alignment explanation
Indices: 77707--77748 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
77697 TGTGAAAGCA
77707 GCCTCAGACTTTAGCTTC
1 GCCTCAGACTTTAGCTTC
77725 GCCTCAGACTTTAGCTTC
1 GCCTCAGACTTTAGCTTC
77743 GCCTCA
1 GCCTCA
77749 AATTCCTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.36, G:0.17, T:0.31
Consensus pattern (18 bp):
GCCTCAGACTTTAGCTTC
Found at i:86731 original size:20 final size:19
Alignment explanation
Indices: 86706--86744 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
86696 TGCTTTCTTT
86706 TCAAATAACTAAAGAAATAA
1 TCAAATAAC-AAAGAAATAA
*
86726 TCAAATAACAAATAAATAA
1 TCAAATAACAAAGAAATAA
86745 ACCTGCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (19 bp):
TCAAATAACAAAGAAATAA
Found at i:87132 original size:6 final size:6
Alignment explanation
Indices: 87121--87145 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
87111 CGGCCACCAT
87121 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
87146 CCTCTCCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:101002 original size:23 final size:23
Alignment explanation
Indices: 100971--101019 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
100961 AGTTAAGTTA
*
100971 TTTTTAAAAATA-TACATTTAAC
1 TTTTTAAAAATATTACATTCAAC
*
100993 TTTTTAAAAATATTATATTCAAC
1 TTTTTAAAAATATTACATTCAAC
101016 TTTT
1 TTTT
101020 AACTAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTTAAAAATATTACATTCAAC
Found at i:102802 original size:2 final size:2
Alignment explanation
Indices: 102795--102825 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
102785 AGTTGGACTG
102795 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 T
102826 GAACTCTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103415 original size:30 final size:27
Alignment explanation
Indices: 103381--103436 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
103371 CCGATCCGAT
103381 CCGACCCGACCCGATATATAACTTAAAAAC
1 CCGACCCGACCCGA-A-ATAA-TTAAAAAC
* *
103411 CCGACCGGATCCGAAATAATTAAAAA
1 CCGACCCGACCCGAAATAATTAAAAA
103437 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 4 0.17
29 1 0.04
30 12 0.50
ACGTcount: A:0.43, C:0.29, G:0.12, T:0.16
Consensus pattern (27 bp):
CCGACCCGACCCGAAATAATTAAAAAC
Found at i:106634 original size:18 final size:18
Alignment explanation
Indices: 106611--106653 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
106601 ACCGGTCACA
106611 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
106629 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
106647 ACTCGAC
1 ACCCGAC
106654 ACGTTGACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:107984 original size:18 final size:18
Alignment explanation
Indices: 107958--107992 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
107948 TCGAAAGGAC
*
107958 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
107976 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
107993 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:111794 original size:13 final size:13
Alignment explanation
Indices: 111775--111810 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
111765 GTCACAACCC
111775 GACCCGACCCGTT
1 GACCCGACCCGTT
*
111788 TACCCGACCCGTT
1 GACCCGACCCGTT
111801 GACCCGACCC
1 GACCCGACCC
111811 CAACCCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.50, G:0.19, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:111828 original size:32 final size:31
Alignment explanation
Indices: 111771--111838 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
111761 ACCGGTCACA
* *
111771 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCAACCCGTTGACCCGACCCGTTG
*
111802 ACCCGACCCCAACCCGTTGACTCGACCCGTTG
1 ACCCGA-CCCAACCCGTTGACCCGACCCGTTG
111834 ACCCG
1 ACCCG
111839 TTGACCGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 6 0.18
32 27 0.82
ACGTcount: A:0.18, C:0.49, G:0.19, T:0.15
Consensus pattern (31 bp):
ACCCGACCCAACCCGTTGACCCGACCCGTTG
Found at i:113158 original size:18 final size:18
Alignment explanation
Indices: 113132--113167 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
113122 TCGAAAGGAC
*
113132 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
113150 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
113168 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:117650 original size:25 final size:24
Alignment explanation
Indices: 117621--117667 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
117611 ACTAACCCAT
*
117621 CAAATTAGGGTTTTAAACCCTAAAA
1 CAAATTAAGG-TTTAAACCCTAAAA
*
117646 CAAATTAAGGTTTCAACCCTAA
1 CAAATTAAGGTTTAAACCCTAA
117668 TCCCCTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.28
Consensus pattern (24 bp):
CAAATTAAGGTTTAAACCCTAAAA
Found at i:125127 original size:21 final size:21
Alignment explanation
Indices: 125098--125143 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
125088 TCCAAGTGAG
* *
125098 GATGCAGGCGAAAGCATGGGT
1 GATGAAGGCGAAAGCATCGGT
125119 GATGAAGGCGAAAGCATCGGT
1 GATGAAGGCGAAAGCATCGGT
125140 GATG
1 GATG
125144 CACCTGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.41, T:0.15
Consensus pattern (21 bp):
GATGAAGGCGAAAGCATCGGT
Found at i:130353 original size:45 final size:45
Alignment explanation
Indices: 130261--130354 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
130251 TTTGTGTCAA
* * * *
130261 TTTATTTTATATTACTAATATATAAGTTCGTCTTTAAAACCATTT
1 TTTATTTTATATTACTAACATATAAGTTCATCATTAAAACAATTT
*
130306 TTTATTTTATATTATTAACATATAAGTTCATCATTAAAA-AATATT
1 TTTATTTTATATTACTAACATATAAGTTCATCATTAAAACAAT-TT
130351 TTTA
1 TTTA
130355 GATCCATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 2 0.05
45 41 0.95
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (45 bp):
TTTATTTTATATTACTAACATATAAGTTCATCATTAAAACAATTT
Found at i:138458 original size:36 final size:36
Alignment explanation
Indices: 138418--138486 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
138408 TATTTCGAAA
*
138418 AAAAAAGTATTTATAACAAATCTAAATAAATTCTCT
1 AAAAAAGTATTTATAACAAACCTAAATAAATTCTCT
* *
138454 AAAAAAGTTTTTATAACAAACCTAATTAAATTC
1 AAAAAAGTATTTATAACAAACCTAAATAAATTC
138487 AAAATGAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (36 bp):
AAAAAAGTATTTATAACAAACCTAAATAAATTCTCT
Found at i:140208 original size:86 final size:86
Alignment explanation
Indices: 140066--140231 Score: 235
Period size: 86 Copynumber: 1.9 Consensus size: 86
140056 GAATTAGCAC
* * * *
140066 CTATCATTCAAGTTGCGGCTACAATTCGTTGTTATTGGTGTTATTCCACTTCACACCGTTATTTT
1 CTATCATTCAAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTCCACTTCACACCGTTATTTT
* *
140131 TTGTAATAATGGTTTTAGCCT
66 CTATAATAATGGTTTTAGCCT
* *
140152 CTATCCATT-AAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTTCACTTTACACCGTTATTT
1 CTAT-CATTCAAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTCCACTTCACACCGTTATTT
*
140216 TCTATAATAGTGGTTT
65 TCTATAATAATGGTTT
140232 CGGACACTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
86 66 0.94
87 4 0.06
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (86 bp):
CTATCATTCAAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTCCACTTCACACCGTTATTTT
CTATAATAATGGTTTTAGCCT
Found at i:143067 original size:19 final size:19
Alignment explanation
Indices: 143045--143082 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
143035 GTTCGTTTTT
143045 ATTGAATCGGTTCCAGGAA
1 ATTGAATCGGTTCCAGGAA
143064 ATTGAATCGGTTCCAGGAA
1 ATTGAATCGGTTCCAGGAA
143083 TGTTCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
ATTGAATCGGTTCCAGGAA
Found at i:143832 original size:13 final size:13
Alignment explanation
Indices: 143814--143839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
143804 AAGCAAGGTA
143814 AACAAATACATAT
1 AACAAATACATAT
143827 AACAAATACATAT
1 AACAAATACATAT
143840 GCATACATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AACAAATACATAT
Found at i:146276 original size:26 final size:26
Alignment explanation
Indices: 146232--146282 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
146222 AAATAATACA
*
146232 ATAATATATTTTCTATGAATTTTTAT
1 ATAATATATTTTCTATGAATATTTAT
*
146258 ATAA-ATATTTTCATTTGAATATTTA
1 ATAATATATTTTC-TATGAATATTTA
146283 GAATTCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
ATAATATATTTTCTATGAATATTTAT
Found at i:154705 original size:2 final size:2
Alignment explanation
Indices: 154700--154726 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
154690 AAACCATAGG
154700 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 T
154727 TTGATTCTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:154744 original size:39 final size:39
Alignment explanation
Indices: 154725--154804 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
154715 ATATATATAT
*
154725 ATTTGATTCTCTTAAATATAGTGTATAATAAATTATTAA
1 ATTTGATTCTCTTAAATATAGTATATAATAAATTATTAA
* ** * *
154764 ATTTGATTCTCTTAAAAACCGTGTATAATAAAATATTAA
1 ATTTGATTCTCTTAAATATAGTATATAATAAATTATTAA
154803 AT
1 AT
154805 GTAATCTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (39 bp):
ATTTGATTCTCTTAAATATAGTATATAATAAATTATTAA
Found at i:154825 original size:38 final size:39
Alignment explanation
Indices: 154745--154826 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
154735 CTTAAATATA
* * * *
154745 GTGTATAATAAATTATTAAATTTGATTCTCTTAAAAACC
1 GTGTATAATAAAATATTAAATGTGAATCTCTCAAAAACC
154784 GTGTATAATAAAATATTAAATGT-AATCTCTCACAAAA-C
1 GTGTATAATAAAATATTAAATGTGAATCTCTCA-AAAACC
154822 GTGTA
1 GTGTA
154827 ATTAAAACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (39 bp):
GTGTATAATAAAATATTAAATGTGAATCTCTCAAAAACC
Found at i:159555 original size:15 final size:16
Alignment explanation
Indices: 159523--159555 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
159513 AAAATCTTTC
159523 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
159539 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
159554 TT
1 TT
159556 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:160324 original size:16 final size:16
Alignment explanation
Indices: 160303--160334 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
160293 TCGCCGACCA
160303 AAATTCACTATTCACG
1 AAATTCACTATTCACG
160319 AAATTCACTATTCACG
1 AAATTCACTATTCACG
160335 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (16 bp):
AAATTCACTATTCACG
Found at i:166670 original size:14 final size:14
Alignment explanation
Indices: 166647--166679 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
166637 CGTTCGGTAA
*
166647 TATGTTCGTTCATT
1 TATGTGCGTTCATT
166661 TATGTGCGTTCATT
1 TATGTGCGTTCATT
166675 TATGT
1 TATGT
166680 TTAGCACAAT
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:0.15, C:0.12, G:0.18, T:0.55
Consensus pattern (14 bp):
TATGTGCGTTCATT
Found at i:166866 original size:10 final size:10
Alignment explanation
Indices: 166843--166877 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
166833 GGAAAAAAAT
*
166843 TTTATTTTCA
1 TTTATGTTCA
*
166853 TTTATGTTCG
1 TTTATGTTCA
166863 TTTATGTTCA
1 TTTATGTTCA
166873 TTTAT
1 TTTAT
166878 TGTGTTCGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:166931 original size:24 final size:24
Alignment explanation
Indices: 166849--166934 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 24
166839 AAATTTTATT
* *
166849 TTCATTTATGTTCGTTTATGTTCA
1 TTCATTTGTGTTCGTTTAAGTTCA
*
166873 TTTA-TTGTGTTCG-TTAACGTTCA
1 TTCATTTGTGTTCGTTTAA-GTTCA
* ** * *
166896 TTTACATCTGTTCGTTTAAGTTCG
1 TTCATTTGTGTTCGTTTAAGTTCA
166920 TTCATTTGTGTTCGT
1 TTCATTTGTGTTCGT
166935 CCATTTGTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
22 3 0.06
23 17 0.35
24 25 0.51
25 4 0.08
ACGTcount: A:0.15, C:0.14, G:0.16, T:0.55
Consensus pattern (24 bp):
TTCATTTGTGTTCGTTTAAGTTCA
Found at i:166932 original size:14 final size:14
Alignment explanation
Indices: 166915--166949 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
166905 GTTCGTTTAA
166915 GTTCGTTCATTTGT
1 GTTCGTTCATTTGT
*
166929 GTTCGTCCATTTGT
1 GTTCGTTCATTTGT
166943 GTTCGTT
1 GTTCGTT
166950 TGTCATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.23, T:0.54
Consensus pattern (14 bp):
GTTCGTTCATTTGT
Found at i:167851 original size:17 final size:16
Alignment explanation
Indices: 167829--167872 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
167819 TTATAATTTT
167829 TATTTTTAAAAATAAAA
1 TATTTTTAAAAA-AAAA
167846 TA-TTTTAAAAAAAAA
1 TATTTTTAAAAAAAAA
167861 TATTTTTTAAAA
1 TA-TTTTTAAAA
167873 CAATTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
16 9 0.36
17 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTTTAAAAAAAAA
Found at i:167853 original size:16 final size:15
Alignment explanation
Indices: 167832--167866 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
167822 TAATTTTTAT
167832 TTTTAAAAATAAAATA
1 TTTTAAAAA-AAAATA
167848 TTTTAAAAAAAAATA
1 TTTTAAAAAAAAATA
167863 TTTT
1 TTTT
167867 TTAAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTTAAAAAAAAATA
Found at i:167855 original size:15 final size:16
Alignment explanation
Indices: 167832--167872 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
167822 TAATTTTTAT
*
167832 TTTTAAAAATAAAATA
1 TTTTAAAAAAAAAATA
*
167848 TTTTAAAAAAAAATATT
1 TTTTAAAAAAAAA-ATA
167865 TTTTAAAA
1 TTTTAAAA
167873 CAATTTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTAAAAAAAAAATA
Found at i:174416 original size:21 final size:19
Alignment explanation
Indices: 174390--174567 Score: 140
Period size: 19 Copynumber: 8.7 Consensus size: 19
174380 CATATTCACA
174390 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
174411 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
174432 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
174453 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
*
174474 TTGCAATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
*
174493 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* * * **
174514 TTGCGATTTATTCTAAATTTA
1 TTGCGA--TAGTCCAAGTTCG
*
174535 TTGCGATATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
174554 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
174568 AATCGTAACG
Statistics
Matches: 126, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
19 57 0.45
21 43 0.34
23 26 0.21
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:174441 original size:42 final size:42
Alignment explanation
Indices: 174390--174499 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
174380 CATATTCACA
*
174390 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
174432 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
174474 TTGCAATAGTCCAAGTT--CGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT
174500 AGTCGAAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 9 0.14
42 55 0.86
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:174495 original size:61 final size:61
Alignment explanation
Indices: 174422--174564 Score: 241
Period size: 61 Copynumber: 2.3 Consensus size: 61
174412 TGCGATTTAT
*
174422 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCAATAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCAATAG
* * * *
174483 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTTATTGCGATAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCAATAG
174544 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
174565 CAAAATCGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 77 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCAATAG
Found at i:174573 original size:19 final size:19
Alignment explanation
Indices: 174535--174573 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
174525 TCTAAATTTA
* **
174535 TTGCGATATTCCAAGTTCG
1 TTGCGATAGTCCAAAATCG
174554 TTGCGATAGTCCAAAATCG
1 TTGCGATAGTCCAAAATCG
174573 T
1 T
174574 AACGACGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TTGCGATAGTCCAAAATCG
Found at i:180070 original size:18 final size:18
Alignment explanation
Indices: 180047--180081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
180037 TTCCATCCGG
*
180047 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
180065 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
180082 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:183831 original size:38 final size:38
Alignment explanation
Indices: 183789--183866 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 38
183779 GTATATAAAA
* * * *
183789 GAGAACAATATTTTCTTTAACTATTTATATCACTTTAC
1 GAGAACAATATTTTATTTAACCATTAATATCACTTGAC
* *
183827 GAGAATAATGTTTTATTTAACCATTAATATCACTTGAC
1 GAGAACAATATTTTATTTAACCATTAATATCACTTGAC
183865 GA
1 GA
183867 ATTTAATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (38 bp):
GAGAACAATATTTTATTTAACCATTAATATCACTTGAC
Found at i:184034 original size:16 final size:15
Alignment explanation
Indices: 184001--184030 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
183991 CATTATTAAT
184001 TATTTCTTAAAATAA
1 TATTTCTTAAAATAA
*
184016 TATTTTTTAAAATAA
1 TATTTCTTAAAATAA
184031 ATATAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTCTTAAAATAA
Found at i:184505 original size:19 final size:18
Alignment explanation
Indices: 184472--184515 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
184462 ATTAAAAAAA
*
184472 TAAATATTAAATTATATTT
1 TAAA-ATTAAATTATATAT
184491 TAAAATTAAACTTATATAT
1 TAAAATTAAA-TTATATAT
184510 TAAAAT
1 TAAAAT
184516 AATTTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTAAATTATATAT
Found at i:184927 original size:17 final size:18
Alignment explanation
Indices: 184905--184950 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
184895 AAATTCCAAA
184905 AATAAAAATTAAAT-TAC
1 AATAAAAATTAAATATAC
*
184922 AATAAAAATTTAATATAC
1 AATAAAAATTAAATATAC
184940 ATATTAAAAAT
1 A-A-TAAAAAT
184951 ATTAAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 13 0.52
18 4 0.16
19 1 0.04
20 7 0.28
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAAAATTAAATATAC
Found at i:184934 original size:18 final size:19
Alignment explanation
Indices: 184905--184956 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 19
184895 AAATTCCAAA
184905 AATAAAAA-TTAAAT-TAC
1 AATAAAAATTTAAATATAC
184922 AATAAAAATTT-AATATAC
1 AATAAAAATTTAAATATAC
184940 ATATTAAAAATATTAAA
1 A-A-TAAAAAT-TTAAA
184957 ACTATTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.38
18 6 0.21
19 1 0.03
20 7 0.24
21 2 0.07
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAAATTTAAATATAC
Found at i:185323 original size:25 final size:25
Alignment explanation
Indices: 185295--185345 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
185285 AAGTTTTGAC
*
185295 TAATCTAAAATTTGTAAGTCTCGAT
1 TAATCTAAAATTTATAAGTCTCGAT
* *
185320 TAATTTAAATTTTATAAGTCTCGAT
1 TAATCTAAAATTTATAAGTCTCGAT
185345 T
1 T
185346 TGTCTAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (25 bp):
TAATCTAAAATTTATAAGTCTCGAT
Found at i:186552 original size:25 final size:25
Alignment explanation
Indices: 186524--186578 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
186514 ATAGCTTAAG
*
186524 ATAAAATCCTAAAAATATACAAATA
1 ATAAAATCCTAAAAATAAACAAATA
* *
186549 ATAAAATCCTAAAGATAAACAAATG
1 ATAAAATCCTAAAAATAAACAAATA
186574 ATAAA
1 ATAAA
186579 TCCCAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.22
Consensus pattern (25 bp):
ATAAAATCCTAAAAATAAACAAATA
Found at i:187058 original size:20 final size:21
Alignment explanation
Indices: 187016--187062 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
187006 TGTATATTCA
*
187016 ATTTTTAGTAATTTAATTTTT
1 ATTTTTAGTAATTTAATTATT
* *
187037 ATTTTTAGTATTTTTA-TATT
1 ATTTTTAGTAATTTAATTATT
187057 ATTTTT
1 ATTTTT
187063 TTAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
ATTTTTAGTAATTTAATTATT
Found at i:187149 original size:23 final size:24
Alignment explanation
Indices: 187062--187139 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
187052 ATATTATTTT
187062 TTTAAATATTT-AAATAATTTTATA
1 TTTAAA-ATTTAAAATAATTTTATA
187086 TTTAAAATTTAAAATAATTTTATA
1 TTTAAAATTTAAAATAATTTTATA
187110 TTTAAAATTTAAAATAATTTT-TA
1 TTTAAAATTTAAAATAATTTTATA
187133 TTTAAAA
1 TTTAAAA
187140 AATTAAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
23 13 0.25
24 40 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAAATTTAAAATAATTTTATA
Found at i:188912 original size:23 final size:23
Alignment explanation
Indices: 188867--188913 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
188857 GATTAACTTA
*
188867 ATTTATTTATTTTATATACTTTT
1 ATTTATTTATTTTAAATACTTTT
*
188890 ATTTTTTTATTTTTAAATA-TTTT
1 ATTTATTTA-TTTTAAATACTTTT
188913 A
1 A
188914 GATGACCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTATTTATTTTAAATACTTTT
Found at i:191037 original size:23 final size:23
Alignment explanation
Indices: 191011--191070 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
191001 ATCAAACACA
* *
191011 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCACTTAT
* * *
191034 ATAATGTAATATGTATCACTTAT
1 ATAATATAATAGGTACCACTTAT
*
191057 ATAATAAAATAGGT
1 ATAATATAATAGGT
191071 TAATTACTGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTACCACTTAT
Found at i:191068 original size:87 final size:87
Alignment explanation
Indices: 190923--191157 Score: 402
Period size: 87 Copynumber: 2.7 Consensus size: 87
190913 ATTAACAAGT
190923 ACAATAACATATTAGGTACCGC-T-TATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
190986 ATCACTGGAAACATTATCAAAC
66 ATCACTGGAAACATTATCAAAC
* * *
191008 ACAATAATATATTAGGTACCGCTTATATAATGTAATATGTATCACTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
*
191073 ATTACTGGAAACATTATCAAAC
66 ATCACTGGAAACATTATCAAAC
* *
191095 ACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
1 ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGT
191158 AGCGCTTATA
Statistics
Matches: 139, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
85 21 0.15
86 1 0.01
87 117 0.84
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (87 bp):
ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
ATCACTGGAAACATTATCAAAC
Found at i:191124 original size:23 final size:23
Alignment explanation
Indices: 191098--191180 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
191088 ATCAAACACA
* *
191098 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
191121 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
191144 ATAATAAAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
191167 ATAATAAAATAGGT
1 ATAATATAATAGGT
191181 TAATTACTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:191141 original size:110 final size:110
Alignment explanation
Indices: 191011--191264 Score: 373
Period size: 110 Copynumber: 2.3 Consensus size: 110
191001 ATCAAACACA
* * * ** * *
191011 ATAATATATTAGGTACCGCTTATATAATGTAATATGTATCACTTATATAATAAAATAGGTTAATT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
* * *
191076 ACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTAT
66 ACTAGAAACATTATCAAACACAATAACATATTAGGTACCACTTAT
* *
191121 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
* *
191186 ACTAGAAATATTATCAAGCACAATAACATATTAGGTACCACTTAT
66 ACTAGAAACATTATCAAACACAATAACATATTAGGTACCACTTAT
*
191231 ATAATGTAATAGGTAACACTTATATAATAAAATA
1 ATAATGTAATAGGTAACGCTTATATAATAAAATA
191265 AGTTAATTAT
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 129 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (110 bp):
ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
ACTAGAAACATTATCAAACACAATAACATATTAGGTACCACTTAT
Found at i:191230 original size:87 final size:87
Alignment explanation
Indices: 191130--191362 Score: 358
Period size: 87 Copynumber: 2.7 Consensus size: 87
191120 TATAATGTAA
* ** *
191130 TAGGTAGCGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAT
1 TAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
191195 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* * * * * *
191217 TAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAAGTTAATTATTGGAAAC
1 TAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
191282 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* *
191304 TAAGTAGCACTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT
1 TAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT
191363 TAATTTGTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 129 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (87 bp):
TAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
ATTATCAAGCACAATAACATAT
Found at i:191264 original size:23 final size:23
Alignment explanation
Indices: 191217--191264 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
191207 AATAACATAT
* **
191217 TAGGTACCACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
191240 TAGGTAACACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
191263 TA
1 TA
191265 AGTTAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:191289 original size:197 final size:197
Alignment explanation
Indices: 190954--191354 Score: 667
Period size: 197 Copynumber: 2.0 Consensus size: 197
190944 CTTATAATGT
* *
190954 AATAGGTAGCACTTATATAATAAAATAGGTTAATCACTGGAAACATTATCAAACACAATAATATA
1 AATAGGTAGCACTTATATAATAAAATAGGTTAATCACTAGAAACATTATCAAACACAATAACATA
* * * *
191019 TTAGGTACCGCTTATATAATGTAATATGTATCACTTATATAATAAAATAGGTTAATTACTGGAAA
66 TTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAAGTTAATTACTGGAAA
* * *
191084 CATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAAT
131 CATTATCAAACACAATAACATATTAAGTAGCACTTATATAACGTAATAGGTAGCGCTTATATAAT
191149 AA
196 AA
* * * *
191151 AATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAATATTATCAAGCACAATAACATA
1 AATAGGTAGCACTTATATAATAAAATAGGTTAATCACTAGAAACATTATCAAACACAATAACATA
*
191216 TTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAAGTTAATTATTGGAAA
66 TTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAAGTTAATTACTGGAAA
*
191281 CATTATCAAGCACAATAACATATTAAGTAGCACTTATATAACGTAATAGGTAGCGCTTATATAAT
131 CATTATCAAACACAATAACATATTAAGTAGCACTTATATAACGTAATAGGTAGCGCTTATATAAT
191346 AA
196 AA
191348 AATAGGT
1 AATAGGT
191355 TAATTACTTA
Statistics
Matches: 189, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 189 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (197 bp):
AATAGGTAGCACTTATATAATAAAATAGGTTAATCACTAGAAACATTATCAAACACAATAACATA
TTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAAGTTAATTACTGGAAA
CATTATCAAACACAATAACATATTAAGTAGCACTTATATAACGTAATAGGTAGCGCTTATATAAT
AA
Found at i:191351 original size:23 final size:23
Alignment explanation
Indices: 191307--191354 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
191297 AACATATTAA
**
191307 GTAGCACTTATATAACGTAATAG
1 GTAGCACTTATATAACAAAATAG
* *
191330 GTAGCGCTTATATAATAAAATAG
1 GTAGCACTTATATAACAAAATAG
191353 GT
1 GT
191355 TAATTACTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (23 bp):
GTAGCACTTATATAACAAAATAG
Found at i:192327 original size:200 final size:198
Alignment explanation
Indices: 191924--192366 Score: 656
Period size: 200 Copynumber: 2.2 Consensus size: 198
191914 TTTAAAATAA
*
191924 ACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
*
191989 TAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAATATCGACAC
66 TAAATGTATCGACACTTTATGTGTGCACCTCATTGGGCATTCATTCTGGAAAAAAATATCGACAC
* *
192054 AAACTTAAAATGTGTCGATACATTATGTAGACATATTTTCTCATAAAACCGGTATATTTATACCG
131 AAACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACAG
192119 AGT
196 AGT
* *
192122 ACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* * * * **
192186 AATAAATGTATCGACATTTTATGTGTGCACCTCATTTGGCATTCATTTTGGGCAAAATGTATCGA
66 --TAAATGTATCGACACTTTATGTGTGCACCTCATTGGGCATTCATTCT-GGAAAAAAATATCGA
*** * * * *
192251 CAC-TTTTTAAATTTGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATCGGTATATTTAT
128 CACAAACTTAAA-ATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTAT
*
192315 ACAGATT
192 ACAGAGT
192322 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
192367 AACATATGTG
Statistics
Matches: 220, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
197 3 0.01
198 58 0.26
199 48 0.22
200 111 0.50
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (198 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
TAAATGTATCGACACTTTATGTGTGCACCTCATTGGGCATTCATTCTGGAAAAAAATATCGACAC
AAACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACAG
AGT
Found at i:192508 original size:31 final size:30
Alignment explanation
Indices: 192467--192552 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
192457 TTATAATAAA
*
192467 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
192497 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
*
192527 TTATAAAATTATAGAT-ATAAT-ATTTT
1 TAATAAAA-TATA-ATAATAATAATTTT
192553 AATAGTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.04
30 28 0.58
31 16 0.33
32 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:192809 original size:21 final size:21
Alignment explanation
Indices: 192770--192810 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
192760 CGGTAAAAAT
* *
192770 TACCTAAAACATTATTATTTA
1 TACCTAAAACATCAATATTTA
192791 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
192811 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTA
Found at i:197918 original size:15 final size:14
Alignment explanation
Indices: 197881--197951 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 14
197871 GTTATTAAAA
197881 TATCTCAACATCTC
1 TATCTCAACATCTC
* *
197895 TACCATCAACCTCCTC
1 TATC-TCAACAT-CTC
197911 TATCTCAACATCTC
1 TATCTCAACATCTC
197925 TATCATCATCATCATCTTC
1 TATC-TCA--A-CATC-TC
197944 TATCTCAA
1 TATCTCAA
197952 TCTTCTCGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
14 10 0.22
15 15 0.33
16 7 0.15
17 1 0.02
18 7 0.15
19 6 0.13
ACGTcount: A:0.28, C:0.37, G:0.00, T:0.35
Consensus pattern (14 bp):
TATCTCAACATCTC
Found at i:197946 original size:33 final size:30
Alignment explanation
Indices: 197881--197951 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 30
197871 GTTATTAAAA
*
197881 TATCTCAACATCTCTACCATCAACCTCCTC
1 TATCTCAACATCTCTACCATCAACATCCTC
* *
197911 TATCTCAACATCTCTATCATCATCATCATCTTC
1 TATCTCAACATCTCTA-C--CATCAACATCCTC
197944 TATCTCAA
1 TATCTCAA
197952 TCTTCTCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 16 0.46
31 1 0.03
33 18 0.51
ACGTcount: A:0.28, C:0.37, G:0.00, T:0.35
Consensus pattern (30 bp):
TATCTCAACATCTCTACCATCAACATCCTC
Found at i:200609 original size:32 final size:32
Alignment explanation
Indices: 200573--200646 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
200563 CTGTTAACTG
*
200573 GGATATGCATATAGTTTCCATTACTTTAACCC
1 GGATATCCATATAGTTTCCATTACTTTAACCC
**
200605 GGATATCCATATAGTTTCCATTACTTTAACTG
1 GGATATCCATATAGTTTCCATTACTTTAACCC
200637 GGATATCCAT
1 GGATATCCAT
200647 TTGACTGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (32 bp):
GGATATCCATATAGTTTCCATTACTTTAACCC
Found at i:200909 original size:24 final size:24
Alignment explanation
Indices: 200871--200960 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 24
200861 TTTAAAATGA
* *
200871 TAAACGAACACAAATGAACGAACG
1 TAAACAAACATAAATGAACGAACG
* *
200895 TAAACAAAAATAAATGAATGAACG
1 TAAACAAACATAAATGAACGAACG
* * * *
200919 TAAACGAACACAAACGAACGAACA
1 TAAACAAACATAAATGAACGAACG
*
200943 TAAACAAACGTAAATGAA
1 TAAACAAACATAAATGAA
200961 ACATAAAAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (24 bp):
TAAACAAACATAAATGAACGAACG
Found at i:201084 original size:17 final size:16
Alignment explanation
Indices: 201057--201098 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
201047 GTATTTTTAT
201057 TTGGGTTTAAAATTAC
1 TTGGGTTTAAAATTAC
201073 TTGGGTTTTAAAATTA-
1 TTGGG-TTTAAAATTAC
*
201089 ATGGGTTTAA
1 TTGGGTTTAA
201099 GGTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 10 0.42
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (16 bp):
TTGGGTTTAAAATTAC
Found at i:208147 original size:4 final size:4
Alignment explanation
Indices: 208138--208169 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
208128 TTTATTCATG
*
208138 AAAT AAAT AAAT AAAT AAAT AAAT AAAG AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
208170 TCATGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Done.