Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000729.1 Hibiscus syriacus cultivar Beakdansim tig00001416_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: 80539
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:490 original size:16 final size:16
Alignment explanation
Indices: 471--565 Score: 57
Period size: 16 Copynumber: 5.9 Consensus size: 16
461 AACCATAACT
471 GAAATTAACCCGAACC
1 GAAATTAACCCGAACC
** * *
487 GAAAGCAACCCCAACT
1 GAAATTAACCCGAACC
* * *
503 GAATTTTAACTCGATCC
1 GAA-ATTAACCCGAACC
* *
520 GAAAATAACCCGAACT
1 GAAATTAACCCGAACC
* *
536 GAATTTAA-CCGACCC
1 GAAATTAACCCGAACC
**
551 GAAAGCAACCCGAAC
1 GAAATTAACCCGAAC
566 AAATTGAAAT
Statistics
Matches: 53, Mismatches: 24, Indels: 4
0.65 0.30 0.05
Matches are distributed among these distances:
15 10 0.19
16 34 0.64
17 9 0.17
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.15
Consensus pattern (16 bp):
GAAATTAACCCGAACC
Found at i:496 original size:32 final size:32
Alignment explanation
Indices: 467--561 Score: 111
Period size: 33 Copynumber: 3.0 Consensus size: 32
457 AATCAACCAT
*
467 AACTGAAATTAACCCGAACCGAAAGCAACCCC
1 AACTGAATTTAACCCGAACCGAAAGCAACCCC
* * ** *
499 AACTGAATTTTAACTCGATCCGAAAATAACCCG
1 AACTGAA-TTTAACCCGAACCGAAAGCAACCCC
*
532 AACTGAATTTAA-CCGACCCGAAAGCAACCC
1 AACTGAATTTAACCCGAACCGAAAGCAACCC
562 GAACAAATTG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 14 0.27
32 12 0.23
33 26 0.50
ACGTcount: A:0.41, C:0.31, G:0.13, T:0.16
Consensus pattern (32 bp):
AACTGAATTTAACCCGAACCGAAAGCAACCCC
Found at i:5844 original size:59 final size:59
Alignment explanation
Indices: 5752--5922 Score: 227
Period size: 59 Copynumber: 2.9 Consensus size: 59
5742 ATAGTCCCTT
* * * *
5752 GACTATAAGATAA-TACTTTATTGAGTCCCTTGACTATTAAGAGTTATAAAATGATCCCC
1 GACTATAAGA-AATTGCTTTCTTTAGTCCCTTGACTATTAAGAGTTACAAAATGATCCCC
* *
5811 GACTATAGGAAATTGCTTTCTTTAGTCCCTTGACTATTAAGAGTTACAAAATGATCCTC
1 GACTATAAGAAATTGCTTTCTTTAGTCCCTTGACTATTAAGAGTTACAAAATGATCCCC
* ** * *
5870 GACTATAAGAAATTGTTTTCTTTAGTCCCTCAACTATCAAAAGTTACAAAATG
1 GACTATAAGAAATTGCTTTCTTTAGTCCCTTGACTATTAAGAGTTACAAAATG
5923 GTCACCCAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
58 2 0.02
59 97 0.98
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (59 bp):
GACTATAAGAAATTGCTTTCTTTAGTCCCTTGACTATTAAGAGTTACAAAATGATCCCC
Found at i:6290 original size:20 final size:20
Alignment explanation
Indices: 6265--6311 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
6255 ACCATTTATG
6265 TACTTTACCCATTAAACATA
1 TACTTTACCCATTAAACATA
6285 TACTTTACCCATTAAACATA
1 TACTTTACCCATTAAACATA
6305 TACTTTA
1 TACTTTA
6312 ACGGATCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
TACTTTACCCATTAAACATA
Found at i:9746 original size:32 final size:32
Alignment explanation
Indices: 9687--9748 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
9677 TTTTTTCTAA
*
9687 GTCCATGGTGTTTTTTCGGTTGCCCTCCCGGT
1 GTCCATGGTGTTTTTTCGGGTGCCCTCCCGGT
*
9719 GTCCATGGTGTTTTCTT-GGGTGTCCTCCCG
1 GTCCATGGTGTTTT-TTCGGGTGCCCTCCCG
9749 ATTCTCTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.03, C:0.27, G:0.29, T:0.40
Consensus pattern (32 bp):
GTCCATGGTGTTTTTTCGGGTGCCCTCCCGGT
Found at i:11245 original size:29 final size:28
Alignment explanation
Indices: 11183--11246 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
11173 TCACATATTT
* *
11183 TAAACCCTAAACTTTAAATTCTAAATCA
1 TAAACCCTAAACTTGAAATACTAAATCA
*
11211 TAAAACCCTAAACTTGAAGTACTTAAATTC-
1 T-AAACCCTAAACTTGAAATAC-TAAA-TCA
11241 TAAACC
1 TAAACC
11247 ATATATATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 22 0.73
30 5 0.17
31 2 0.07
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (28 bp):
TAAACCCTAAACTTGAAATACTAAATCA
Found at i:12194 original size:36 final size:37
Alignment explanation
Indices: 12137--12210 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
12127 CGGGCCTGAT
* *
12137 TCGGGTTGGGTTAAGGGTATAC-ATTTTCAGGTCGGG
1 TCGGGTTGGGTGAAGGATATACAATTTTCAGGTCGGG
*
12173 TCGGGTTGGGTGAAGGATATACAATTTTCGGGTCGGG
1 TCGGGTTGGGTGAAGGATATACAATTTTCAGGTCGGG
12210 T
1 T
12211 TGGTCCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 20 0.59
37 14 0.41
ACGTcount: A:0.18, C:0.11, G:0.39, T:0.32
Consensus pattern (37 bp):
TCGGGTTGGGTGAAGGATATACAATTTTCAGGTCGGG
Found at i:12519 original size:40 final size:40
Alignment explanation
Indices: 12475--12604 Score: 106
Period size: 40 Copynumber: 3.1 Consensus size: 40
12465 AGTCACTCAA
12475 TTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAAT
1 TTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAAT
* * * * * *
12515 TTAAAACACATGTTCAA-CATAACATAA-TAATAT-TAGTCTTTCAA-
1 TT--AA-A-ATATT-AATTATAA-AGAATTTAT-TCTA-TCGTTAAAT
12559 TTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAAT
1 TTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAAT
12599 TTAAAA
1 TTAAAA
12605 CACATGTTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 24
0.65 0.12 0.24
Matches are distributed among these distances:
39 12 0.18
40 21 0.32
41 1 0.02
42 4 0.06
43 1 0.02
44 15 0.23
45 12 0.18
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (40 bp):
TTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAAT
Found at i:12564 original size:84 final size:84
Alignment explanation
Indices: 12458--12639 Score: 339
Period size: 84 Copynumber: 2.2 Consensus size: 84
12448 AATAAAAATT
**
12458 ATAAT-TTAGTCACTCAATTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAATTTAAAAC
1 ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAATTTAAAAC
12522 ACATGTTCAACATAACATA
66 ACATGTTCAACATAACATA
12541 ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAATTTAAAAC
1 ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAATTTAAAAC
12606 ACATGTTCAACATAACATA
66 ACATGTTCAACATAACATA
12625 ATAATATTAGTCTTT
1 ATAATATTAGTCTTT
12640 AAAAGTGATA
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 5 0.05
84 91 0.95
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.40
Consensus pattern (84 bp):
ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAATTTAAAAC
ACATGTTCAACATAACATA
Found at i:13193 original size:29 final size:30
Alignment explanation
Indices: 13161--13224 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
13151 CACAAATCGG
* *
13161 TCACTAATGTTAT-TTTTATTACAAAATGA
1 TCACTAAAGTTATCGTTTATTACAAAATGA
* *
13190 TCACTAAAGTTATCGTTTGTTACAAAATGG
1 TCACTAAAGTTATCGTTTATTACAAAATGA
13220 TCACT
1 TCACT
13225 CAACGTTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (30 bp):
TCACTAAAGTTATCGTTTATTACAAAATGA
Found at i:14341 original size:3 final size:3
Alignment explanation
Indices: 14335--14369 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
14325 GGAGGAGGAG
14335 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
14370 GTTAAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22211 original size:17 final size:18
Alignment explanation
Indices: 22189--22235 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
22179 TATGGAATTG
22189 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTGACA
*
22206 GATTCCAATTCCTTTACA
1 GATTCCAATTCCTTGACA
22224 GATTCCAATTCC
1 GATTCCAATTCC
22236 CTCAAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTGACA
Found at i:26014 original size:28 final size:28
Alignment explanation
Indices: 25982--26037 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
25972 CACCCGAACA
25982 ACGAATCAATGTAACGAAGTATGTTATT
1 ACGAATCAATGTAACGAAGTATGTTATT
26010 ACGAATCAATGTAACGAAGTATGTTATT
1 ACGAATCAATGTAACGAAGTATGTTATT
26038 TACTTTAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (28 bp):
ACGAATCAATGTAACGAAGTATGTTATT
Found at i:33455 original size:2 final size:2
Alignment explanation
Indices: 33448--33479 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33438 CATTCCATCC
33448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33480 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33824 original size:17 final size:17
Alignment explanation
Indices: 33775--33824 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
33765 TTGTTCATGT
33775 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
33792 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
33806 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
33823 TT
1 TT
33825 AGAAGAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:34715 original size:9 final size:10
Alignment explanation
Indices: 34701--34725 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34691 AAAAAATAAA
34701 GAAAAAGAAG
1 GAAAAAGAAG
34711 GAAAAAGAAG
1 GAAAAAGAAG
34721 GAAAA
1 GAAAA
34726 CATATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAG
Found at i:34774 original size:2 final size:2
Alignment explanation
Indices: 34769--34841 Score: 87
Period size: 2 Copynumber: 37.0 Consensus size: 2
34759 AATAAAAAAT
* * *
34769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA TA AA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
34810 TA -A TA GTA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
34842 AATTAATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
1 2 0.03
2 57 0.93
3 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:35248 original size:37 final size:37
Alignment explanation
Indices: 35198--35302 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
35188 GTGCTTGTGG
* * *
35198 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
35235 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
35272 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
35303 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:36351 original size:106 final size:105
Alignment explanation
Indices: 36033--37196 Score: 1644
Period size: 106 Copynumber: 11.0 Consensus size: 105
36023 GCATTGTTAT
* * * ***
36033 GAGTCCAATATCCTCCGTCGTGATGTTGAAATTGGCTCTGGAAGCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAATTGTTTGTTGACAA
* * * * *
36098 ACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
36139 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T-GAAA-T-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAAC
* * *
36199 CAGTC-GCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
36240 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* *
36304 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
36345 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTGTTGACAA
*
36410 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
36451 GAGTCCAATATACTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
*
36516 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
36557 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* * *
36622 CTAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
36663 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
36728 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
36769 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
* * *
36834 CCAGTGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
36875 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
36940 CCAGCGGTCCCTTCGTTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
*
36982 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* *
37047 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
37088 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTGTTGACAA
* * * *
37152 CCAGTC-GTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTT
65 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
37193 GAGT
1 GAGT
37197 GGCACGATAT
Statistics
Matches: 962, Mismatches: 78, Indels: 37
0.89 0.07 0.03
Matches are distributed among these distances:
100 79 0.08
101 6 0.01
102 5 0.01
104 4 0.00
105 56 0.06
106 708 0.74
107 104 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:38041 original size:22 final size:22
Alignment explanation
Indices: 38015--38113 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
38005 TTATGTTTGG
38015 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
38037 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
38059 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
38081 TCATAGGTTTGGCATTTGATGG
1 TCAAAGGTTTGGCATTTGATGC
*
38103 TCAACGGTTTG
1 TCAAAGGTTTG
38114 ATGGGGTAGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:38787 original size:13 final size:12
Alignment explanation
Indices: 38757--38820 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
38747 TTTCTTTCAG
38757 TTTTTGTTCTTT
1 TTTTTGTTCTTT
38769 CTTTTTGTTCTTT
1 -TTTTTGTTCTTT
* *
38782 TGTTTTTTTCCTT
1 T-TTTTGTTCTTT
**
38795 TTTTCCTTCTTT
1 TTTTTGTTCTTT
38807 TCTTTT-TTCTTT
1 T-TTTTGTTCTTT
38819 TT
1 TT
38821 GCCCTTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 1 0.02
12 17 0.40
13 25 0.58
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (12 bp):
TTTTTGTTCTTT
Found at i:38826 original size:24 final size:25
Alignment explanation
Indices: 38776--38826 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
38766 TTTCTTTTTG
* *
38776 TTCTTTTGTTTTTTTCCTTTTTTCC
1 TTCTTTTGCTTTTTTCCTTTTTCCC
38801 TTCTTTT-CTTTTTT-CTTTTTGCCC
1 TTCTTTTGCTTTTTTCCTTTTT-CCC
38825 TT
1 TT
38827 TTTGTTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 10 0.43
25 7 0.30
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.75
Consensus pattern (25 bp):
TTCTTTTGCTTTTTTCCTTTTTCCC
Found at i:41938 original size:10 final size:10
Alignment explanation
Indices: 41923--41971 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
41913 AATAAATATA
41923 AAAAATAAAG
1 AAAAATAAAG
41933 AAAAATAAAG
1 AAAAATAAAG
* *
41943 AAAAAGAAGG
1 AAAAATAAAG
*
41953 AAAACATATA-
1 AAAA-ATAAAG
41963 AAAAATAAA
1 AAAAATAAA
41972 ACAAGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 4 0.12
10 26 0.81
11 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:41994 original size:9 final size:9
Alignment explanation
Indices: 41910--41999 Score: 56
Period size: 9 Copynumber: 9.2 Consensus size: 9
41900 AAATAGTAAG
*
41910 TAAAATAAA
1 TAAAAAAAA
*
41919 TATAAAAAA
1 TAAAAAAAA
41928 TAAAGAAAAA
1 TAAA-AAAAA
41938 TAAAGAAAAA
1 TAAA-AAAAA
* *
41948 GAAGGAAAACA
1 TAA--AAAAAA
*
41959 TATAAAAAA
1 TAAAAAAAA
41968 TAAAACAAGTAA
1 TAAAA-AA--AA
41980 -ATAAAAAAA
1 TA-AAAAAAA
41989 TAAAAAAAA
1 TAAAAAAAA
41998 TA
1 TA
42000 TATATATATA
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
9 30 0.47
10 20 0.31
11 8 0.12
12 6 0.09
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:41996 original size:30 final size:29
Alignment explanation
Indices: 41913--41999 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
41903 TAGTAAGTAA
*
41913 AATAAATATAAAAAATAAAGAAAAAT-AAAG
1 AATAAATA-AAAAAATAAA-AAAAATAAAAC
* *
41943 AA-AAAGAAGGAAAACATATAAAAAATAAAAC
1 AATAAATAA--AAAA-ATAAAAAAAATAAAAC
41974 AAGTAAATAAAAAAATAAAAAAAATA
1 AA-TAAATAAAAAAATAAAAAAAATA
42000 TATATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 23 0.50
31 13 0.28
33 5 0.11
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (29 bp):
AATAAATAAAAAAATAAAAAAAATAAAAC
Found at i:42002 original size:2 final size:2
Alignment explanation
Indices: 41997--42058 Score: 74
Period size: 2 Copynumber: 31.5 Consensus size: 2
41987 AATAAAAAAA
* * *
41997 AT AT AT AT AT AT A- AT AA AT AA AT A- AT AGT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
42038 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
42059 AATTAATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:42473 original size:37 final size:37
Alignment explanation
Indices: 42432--42536 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
42422 GTGCTTGTGG
* *
42432 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
42469 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* *
42506 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
42537 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:44020 original size:30 final size:30
Alignment explanation
Indices: 43984--44044 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
43974 ATGCCCTACA
*
43984 CTTCACATTTTAGTACTTTTTAACTAAATT
1 CTTCACATTTTAGTACCTTTTAACTAAATT
44014 CTTCACATTTTAGTACCTTTTAACTAAATT
1 CTTCACATTTTAGTACCTTTTAACTAAATT
44044 C
1 C
44045 ATTAAGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.48
Consensus pattern (30 bp):
CTTCACATTTTAGTACCTTTTAACTAAATT
Found at i:45856 original size:2 final size:2
Alignment explanation
Indices: 45849--45893 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
45839 CATATCTGTT
* *
45849 TA TA TA TA TA TA TA TA TA AA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45891 TA T
1 TA T
45894 TGTTCAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:46820 original size:20 final size:20
Alignment explanation
Indices: 46795--46852 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
46785 TGGGTTCAAG
*
46795 TATCGATACTAGATGAATAA
1 TATCGATACTGGATGAATAA
*
46815 TATCGATACTGGATGAACAA
1 TATCGATACTGGATGAATAA
*
46835 TATCGAAACTGGATGAAT
1 TATCGATACTGGATGAAT
46853 TGAGACAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (20 bp):
TATCGATACTGGATGAATAA
Found at i:48666 original size:14 final size:14
Alignment explanation
Indices: 48647--48711 Score: 76
Period size: 15 Copynumber: 4.4 Consensus size: 14
48637 TTATATAAAA
48647 ATGTGATATAAGCT
1 ATGTGATATAAGCT
* *
48661 ATGTGATAATGATCT
1 ATGTGAT-ATAAGCT
*
48676 ATGTGATTATATGTCT
1 ATGTGA-TATAAG-CT
48692 ATGTGATATAAGCT
1 ATGTGATATAAGCT
48706 ATGTGA
1 ATGTGA
48712 AATGTTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 15 0.36
15 18 0.43
16 9 0.21
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (14 bp):
ATGTGATATAAGCT
Found at i:48679 original size:15 final size:15
Alignment explanation
Indices: 48647--48711 Score: 73
Period size: 14 Copynumber: 4.4 Consensus size: 15
48637 TTATATAAAA
*
48647 ATGTGATATAAG-CT
1 ATGTGATATATGTCT
48661 ATGTGATA-ATGATCT
1 ATGTGATATATG-TCT
48676 ATGTGATTATATGTCT
1 ATGTGA-TATATGTCT
*
48692 ATGTGATATAAG-CT
1 ATGTGATATATGTCT
48706 ATGTGA
1 ATGTGA
48712 AATGTTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 2 0.04
14 16 0.36
15 13 0.29
16 11 0.24
17 3 0.07
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (15 bp):
ATGTGATATATGTCT
Found at i:48832 original size:23 final size:23
Alignment explanation
Indices: 48796--48868 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
48786 GGTTCTACGC
* *
48796 GGTCATTTGAGACAATTTTATGT
1 GGTCATTCGGGACAATTTTATGT
* * *
48819 GGTCATTCGGGACATTTTTACGC
1 GGTCATTCGGGACAATTTTATGT
* * **
48842 GGTCTTTCGGGATAATACTATGT
1 GGTCATTCGGGACAATTTTATGT
48865 GGTC
1 GGTC
48869 CTTTGGGATA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (23 bp):
GGTCATTCGGGACAATTTTATGT
Found at i:48885 original size:23 final size:23
Alignment explanation
Indices: 48810--48886 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
48800 ATTTGAGACA
* * *
48810 ATTT-TATGTGGTCATTCGGGAC
1 ATTTCTATGTGGTCCTTTGGGAT
* * *
48832 ATTTTTACGCGGT-CTTTCGGGAT
1 ATTTCTATGTGGTCCTTT-GGGAT
* *
48855 AATACTATGTGGTCCTTTGGGAT
1 ATTTCTATGTGGTCCTTTGGGAT
48878 ATTTCTATG
1 ATTTCTATG
48887 CGGTACTTCG
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
22 6 0.15
23 30 0.75
24 4 0.10
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (23 bp):
ATTTCTATGTGGTCCTTTGGGAT
Found at i:48906 original size:24 final size:24
Alignment explanation
Indices: 48878--48929 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
48868 CCTTTGGGAT
**
48878 ATTTCTATGCGGTACTTCGGTACA
1 ATTTCTACACGGTACTTCGGTACA
*
48902 ATTTCTACACGGTACTTCGGTGCA
1 ATTTCTACACGGTACTTCGGTACA
48926 ATTT
1 ATTT
48930 ATACGAGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (24 bp):
ATTTCTACACGGTACTTCGGTACA
Found at i:50191 original size:3 final size:3
Alignment explanation
Indices: 50185--50212 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
50175 GTTACATGTG
50185 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
50213 CTTATGAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:55776 original size:31 final size:32
Alignment explanation
Indices: 55723--55840 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
55713 GTTCTACGGA
55723 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
* *
55755 ACATATGGACAGTA-TACCTATGT-TCTACG-G
1 ACATATGGACAGAATTACCTATGTCT-TTCGAG
55785 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAATTACCTATGTCTTTCGAG
* *
55818 ACATATAGACAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
55841 TCTAAGGAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
30 2 0.03
31 34 0.45
32 37 0.49
33 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:55781 original size:63 final size:63
Alignment explanation
Indices: 55703--55868 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
55693 AGAGTCGAGG
*
55703 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
55766 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
* *
55829 GTATACCTATGTTCTAAGGAACATATGGACA-ATTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
55869 GGTTCTTCGG
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 8 0.08
63 92 0.92
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
Found at i:55853 original size:31 final size:31
Alignment explanation
Indices: 55703--55896 Score: 191
Period size: 31 Copynumber: 6.2 Consensus size: 31
55693 AGAGTCGAGG
55703 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
55734 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
55766 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
55797 GAATTACCTATG-TCTTTC-GAGACATATAGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
55829 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * * * *
55860 ATTTACCTAGGTTCTTCGGAACCTATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
55891 GT-TACC
1 GTATACC
55897 GAGGATCTTT
Statistics
Matches: 134, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
30 4 0.03
31 77 0.57
32 53 0.40
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:68569 original size:23 final size:23
Alignment explanation
Indices: 68543--68597 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
68533 AACGATTGAG
*
68543 AAAGA-AAACAAAAAACGTGTTAC
1 AAAGACAAA-AAAAAACGTGTCAC
* *
68566 AAAGACATATAAAAACGTGTCAC
1 AAAGACAAAAAAAAACGTGTCAC
*
68589 AAAGGCAAA
1 AAAGACAAA
68598 TTATTCTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
AAAGACAAAAAAAAACGTGTCAC
Found at i:69880 original size:21 final size:22
Alignment explanation
Indices: 69847--69887 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
69837 GGTTAAAATA
69847 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
69869 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
69888 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:70564 original size:19 final size:19
Alignment explanation
Indices: 70510--70570 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
70500 CTATTTAAAC
70510 TAAAATACCTAAAA--TAAT
1 TAAAATA-CTAAAACCTAAT
* * *
70528 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
70548 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
70567 TAAA
1 TAAA
70571 CTAAAATACA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.15
19 24 0.73
20 4 0.12
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:70678 original size:74 final size:75
Alignment explanation
Indices: 70544--70689 Score: 233
Period size: 74 Copynumber: 2.0 Consensus size: 75
70534 TTCTAAATCC
*
70544 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGTTAAAATATAAAAATA-TA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAAAATATTA
70608 TCCTAAAACT
66 TCCTAAAACT
* * *
70618 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATATAATGTTTAAAATATT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATATT
70682 ATCCTAAA
65 ATCCTAAA
70690 TTTGAGTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
73 5 0.08
74 52 0.79
75 9 0.14
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAAAATATTA
TCCTAAAACT
Found at i:75091 original size:453 final size:453
Alignment explanation
Indices: 74245--75153 Score: 1782
Period size: 453 Copynumber: 2.0 Consensus size: 453
74235 CATAGCAGAA
*
74245 AGGAGTTGATTATGATGAAATCTTTTCTCATGTGGTCAGTCACACTTCAATCCGAGCAGTACTTG
1 AGGAGTTGATTATGATGAAATATTTTCTCATGTGGTCAGTCACACTTCAATCCGAGCAGTACTTG
74310 CATTGGTGGCTAGTTGGGATTTGCATTTAGAGCAGATGAATGTTAAAACTGCTTTTTTGCATGGT
66 CATTGGTGGCTAGTTGGGATTTGCATTTAGAGCAGATGAATGTTAAAACTGCTTTTTTGCATGGT
74375 GATTTAGAGGAGCAGATCTACATACGGCAACCTGAAGGCTTCACTCAACCTGGAAACGAGCATTT
131 GATTTAGAGGAGCAGATCTACATACGGCAACCTGAAGGCTTCACTCAACCTGGAAACGAGCATTT
74440 AGTTTGTAGATTGAAGAAATTTTTGTACGGGTTGAAACAGTCTCCGAGATAGTGGTATAAACGGT
196 AGTTTGTAGATTGAAGAAATTTTTGTACGGGTTGAAACAGTCTCCGAGATAGTGGTATAAACGGT
74505 TTGACTCCTATATGATCAAGATTGGCTACAACCGTTGTGAGTATGATTGGTGTGTCTATGTTAAA
261 TTGACTCCTATATGATCAAGATTGGCTACAACCGTTGTGAGTATGATTGGTGTGTCTATGTTAAA
74570 AGCTTTGATGATAGTTCTTTTATTTTTCTGTTATTGTATGTTGATGATATGTTGATTGCTGCGAA
326 AGCTTTGATGATAGTTCTTTTATTTTTCTGTTATTGTATGTTGATGATATGTTGATTGCTGCGAA
* *
74635 GAACATGGATGATGTTATTGGTTTGAAAACCTTTTTGAGTCAGGAATTTGATATGGATGATTT
391 GAACATGGATGATGTTATTGGTTTGAAAACCTTTTTGAGTCAGGAATTTGATATGAAAGATTT
74698 AGGAGTTGATTATGATGAAATATTTTCTCATGTGGTCAGTCACACTTCAATCCGAGCAGTACTTG
1 AGGAGTTGATTATGATGAAATATTTTCTCATGTGGTCAGTCACACTTCAATCCGAGCAGTACTTG
74763 CATTGGTGGCTAGTTGGGATTTGCATTTAGAGCAGATGAATGTTAAAACTGCTTTTTTGCATGGT
66 CATTGGTGGCTAGTTGGGATTTGCATTTAGAGCAGATGAATGTTAAAACTGCTTTTTTGCATGGT
74828 GATTTAGAGGAGCAGATCTACATACGGCAACCTGAAGGCTTCACTCAACCTGGAAACGAGCATTT
131 GATTTAGAGGAGCAGATCTACATACGGCAACCTGAAGGCTTCACTCAACCTGGAAACGAGCATTT
74893 AGTTTGTAGATTGAAGAAATTTTTGTACGGGTTGAAACAGTCTCCGAGATAGTGGTATAAACGGT
196 AGTTTGTAGATTGAAGAAATTTTTGTACGGGTTGAAACAGTCTCCGAGATAGTGGTATAAACGGT
74958 TTGACTCCTATATGATCAAGATTGGCTACAACCGTTGTGAGTATGATTGGTGTGTCTATGTTAAA
261 TTGACTCCTATATGATCAAGATTGGCTACAACCGTTGTGAGTATGATTGGTGTGTCTATGTTAAA
*
75023 AGCTTTGATGATGGTTCTTTTATTTTTCTGTTATTGTATGTTGATGATATGTTGATTGCTGCGAA
326 AGCTTTGATGATAGTTCTTTTATTTTTCTGTTATTGTATGTTGATGATATGTTGATTGCTGCGAA
75088 GAACATGGATGATGTTATTGGTTTGAAAACCTTTTTGAGTCAGGAATTTGATATGAAAGATTT
391 GAACATGGATGATGTTATTGGTTTGAAAACCTTTTTGAGTCAGGAATTTGATATGAAAGATTT
75151 AGG
1 AGG
75154 TGCTACAAAG
Statistics
Matches: 452, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
453 452 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (453 bp):
AGGAGTTGATTATGATGAAATATTTTCTCATGTGGTCAGTCACACTTCAATCCGAGCAGTACTTG
CATTGGTGGCTAGTTGGGATTTGCATTTAGAGCAGATGAATGTTAAAACTGCTTTTTTGCATGGT
GATTTAGAGGAGCAGATCTACATACGGCAACCTGAAGGCTTCACTCAACCTGGAAACGAGCATTT
AGTTTGTAGATTGAAGAAATTTTTGTACGGGTTGAAACAGTCTCCGAGATAGTGGTATAAACGGT
TTGACTCCTATATGATCAAGATTGGCTACAACCGTTGTGAGTATGATTGGTGTGTCTATGTTAAA
AGCTTTGATGATAGTTCTTTTATTTTTCTGTTATTGTATGTTGATGATATGTTGATTGCTGCGAA
GAACATGGATGATGTTATTGGTTTGAAAACCTTTTTGAGTCAGGAATTTGATATGAAAGATTT
Found at i:76365 original size:22 final size:21
Alignment explanation
Indices: 76340--76382 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
76330 TAGGTTGATT
*
76340 TTAAAATATACACATATAAATA
1 TTAAAATATAAACATA-AAATA
* *
76362 TTAAGATTTAAACATAAAATA
1 TTAAAATATAAACATAAAATA
76383 ATACCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Done.