Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003333.1 Hibiscus syriacus cultivar Beakdansim tig00007016_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: 168441
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1595 original size:28 final size:28
Alignment explanation
Indices: 1534--1601 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
1524 TTTCATTACC
* * *
1534 ATTTATTAC-TATTTTTCTATTTATATT
1 ATTTATTACTTATTCTTATATTTATACT
*
1561 ATATATTACTTATTCTTATATTCTAT-CT
1 ATTTATTACTTATTCTTATATT-TATACT
*
1589 ATTTATTATTTAT
1 ATTTATTACTTAT
1602 ATATTTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.24
28 22 0.67
29 3 0.09
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTATTACTTATTCTTATATTTATACT
Found at i:1828 original size:15 final size:17
Alignment explanation
Indices: 1809--1846 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1799 CTTTTTCGTA
*
1809 TTTTTATTT-TTTTTTG
1 TTTTTATTTATTTGTTG
1825 TTTTTATTTCATTTGTTG
1 TTTTTATTT-ATTTGTTG
1843 TTTT
1 TTTT
1847 ACTCTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.82
Consensus pattern (17 bp):
TTTTTATTTATTTGTTG
Found at i:3241 original size:21 final size:20
Alignment explanation
Indices: 3185--3248 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
3175 AATATTAAAA
*
3185 ATTAGGGTT-TAATTTTGGG
1 ATTAGGGTTCTAATTTAGGG
3204 ATTAGGGTTCTAATTTAGGG
1 ATTAGGGTTCTAATTTAGGG
*
3224 ATTA-GGTTACTCAATTTAGGA
1 ATTAGGGTT-CT-AATTTAGGG
3245 ATTA
1 ATTA
3249 AAATTCTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.32
20 15 0.38
21 12 0.30
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (20 bp):
ATTAGGGTTCTAATTTAGGG
Found at i:3644 original size:13 final size:13
Alignment explanation
Indices: 3628--3653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3618 TTGATCCAAG
3628 TATTATTAAAAAT
1 TATTATTAAAAAT
3641 TATTATTAAAAAT
1 TATTATTAAAAAT
3654 AATGTAATTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTATTAAAAAT
Found at i:4988 original size:6 final size:6
Alignment explanation
Indices: 4971--5019 Score: 89
Period size: 6 Copynumber: 8.0 Consensus size: 6
4961 TAACGTAATC
4971 CAAAACT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
1 CAAAA-T CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
5020 TCAATGGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 37 0.88
7 5 0.12
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.16
Consensus pattern (6 bp):
CAAAAT
Found at i:5621 original size:13 final size:12
Alignment explanation
Indices: 5594--5625 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
5584 ATTTTTATTG
5594 TTATAATATATA
1 TTATAATATATA
5606 TTATAATATAATA
1 TTATAATAT-ATA
5619 TTATAAT
1 TTATAAT
5626 TTTGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTATAATATATA
Found at i:5982 original size:24 final size:22
Alignment explanation
Indices: 5932--5990 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
5922 GTATTAAGTA
* *
5932 AATATTATAATATTTTAAAAAT
1 AATATTATTATTTTTTAAAAAT
5954 AATATTATTATTTTATTAATAAAT
1 AATATTATTATTTT-TTAA-AAAT
5978 AATATTATT-TTTT
1 AATATTATTATTTT
5991 GTATTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 12 0.36
23 8 0.24
24 13 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTATTATTTTTTAAAAAT
Found at i:5983 original size:21 final size:21
Alignment explanation
Indices: 5923--5988 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
5913 GCATAAATAG
*
5923 TATTAAGTAAATATTATAATATTT
1 TATTAA-TAAATA--ATATTATTT
** *
5947 TAAAAAT-AATATTATTATTT
1 TATTAATAAATAATATTATTT
5967 TATTAATAAATAATATTATTT
1 TATTAATAAATAATATTATTT
5988 T
1 T
5989 TTGTATTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 12 0.35
21 13 0.38
22 4 0.12
23 1 0.03
24 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTAATAAATAATATTATTT
Found at i:6410 original size:17 final size:18
Alignment explanation
Indices: 6380--6414 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
6370 TAGATTTTCC
6380 TTAATATATTCATTTAAAA
1 TTAATATA-TCATTTAAAA
6399 TTAATATA-CATTTAAA
1 TTAATATATCATTTAAA
6415 TACAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATATATCATTTAAAA
Found at i:10390 original size:12 final size:10
Alignment explanation
Indices: 10361--10385 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10351 TTCATCACAC
10361 CAAATTCTCT
1 CAAATTCTCT
10371 CAAATTCTCT
1 CAAATTCTCT
10381 CAAAT
1 CAAAT
10386 ATTCTATCTG
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:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:12159 original size:18 final size:18
Alignment explanation
Indices: 12136--12189 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
12126 GTATCAGCCA
12136 CCGCAACCATTTATGATG
1 CCGCAACCATTTATGATG
12154 CCGCAACCATTTATGATG
1 CCGCAACCATTTATGATG
* *
12172 CCGCAGCCATATATGATG
1 CCGCAACCATTTATGATG
12190 TCGCCATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (18 bp):
CCGCAACCATTTATGATG
Found at i:23090 original size:14 final size:13
Alignment explanation
Indices: 23071--23101 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
23061 CAAATAGCCC
23071 TTTTTTCTCTGTGT
1 TTTTTTCTC-GTGT
23085 TTTTTTCTCGTGT
1 TTTTTTCTCGTGT
23098 TTTT
1 TTTT
23102 GCTTTCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (13 bp):
TTTTTTCTCGTGT
Found at i:24374 original size:13 final size:13
Alignment explanation
Indices: 24356--24381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24346 TATGTGTCAC
24356 CCTCTCATTGAAA
1 CCTCTCATTGAAA
24369 CCTCTCATTGAAA
1 CCTCTCATTGAAA
24382 GAAAACAAAT
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:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
CCTCTCATTGAAA
Found at i:24605 original size:27 final size:26
Alignment explanation
Indices: 24542--24612 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 26
24532 TTAAATTCAT
*
24542 AATATTTTATATATATTAACTTA--A
1 AATATTTTTTATATATTAACTTATTA
* *
24566 AAAATATTTT-TATATTAACTTATTA
1 AATATTTTTTATATATTAACTTATTA
24591 AATATTTTTTAT-TATTAACTTA
1 AATATTTTTTATATATTAACTTA
24613 ATTTAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 12 0.31
24 7 0.18
25 19 0.49
26 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTTTTTATATATTAACTTATTA
Found at i:24618 original size:27 final size:26
Alignment explanation
Indices: 24542--24630 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 26
24532 TTAAATTCAT
* *
24542 AATATTTTATATATATTAACTTAA-AA
1 AATATTTTTTAT-TATTAACTTAATTA
24568 AATA-TTTTTA-TATTAACTT-ATTA
1 AATATTTTTTATTATTAACTTAATTA
24591 AATATTTTTTATTATTAACTTAATTTA
1 AATATTTTTTATTATTAACTTAA-TTA
* *
24618 AAAATATTTTATT
1 AATATTTTTTATT
24631 TTTTATTTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.02
23 14 0.26
24 6 0.11
25 14 0.26
26 5 0.09
27 14 0.26
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTTTTTATTATTAACTTAATTA
Found at i:24825 original size:31 final size:31
Alignment explanation
Indices: 24790--24854 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
24780 TGATGACCAC
*
24790 ATCTTAATTAAATAAAAATGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
24821 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
24852 ATC
1 ATC
24855 ATATGTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTGATCAT
Found at i:37795 original size:41 final size:41
Alignment explanation
Indices: 37738--37821 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
37728 GGCTGCATCG
37738 TCACTAGGTTGTGTCGAAGCTGGGCTTTCAAAGATTCATGC
1 TCACTAGGTTGTGTCGAAGCTGGGCTTTCAAAGATTCATGC
37779 TCACTAGGTTGTGTCGAAGCTGGGCTTTCAAAGATTCATGC
1 TCACTAGGTTGTGTCGAAGCTGGGCTTTCAAAGATTCATGC
37820 TC
1 TC
37822 TGAATGCAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (41 bp):
TCACTAGGTTGTGTCGAAGCTGGGCTTTCAAAGATTCATGC
Found at i:46425 original size:22 final size:21
Alignment explanation
Indices: 46386--46426 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
46376 TATGATTTTG
46386 AAAAAAATAAAAATTAGGTGA
1 AAAAAAATAAAAATTAGGTGA
46407 AAAAAAACTACAAAA-TAGGT
1 AAAAAAA-TA-AAAATTAGGT
46427 AGATGACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAAAAATAAAAATTAGGTGA
Found at i:47594 original size:19 final size:20
Alignment explanation
Indices: 47556--47596 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
47546 TCAAGATAGA
47556 ACATGATTGGCTTTGGTCTGC
1 ACATGATT-GCTTTGGTCTGC
*
47577 ACATGATT-CTTTGTTCTGC
1 ACATGATTGCTTTGGTCTGC
47596 A
1 A
47597 GACTGAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
ACATGATTGCTTTGGTCTGC
Found at i:57460 original size:16 final size:16
Alignment explanation
Indices: 57428--57468 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
57418 GTTTATTTCA
*
57428 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
57443 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
57459 GAATGATTCA
1 GAATGATTCA
57469 GAGGCTCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:57578 original size:23 final size:25
Alignment explanation
Indices: 57521--57584 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 25
57511 TTTACTGGCT
*
57521 CTGAATCATTCAGAATATATTTTTTG
1 CTGAATCATTCAG-ATATATGTTTTG
57547 CATTGAATCATTCAG-TAT-TGTTTTG
1 C--TGAATCATTCAGATATATGTTTTG
*
57572 CTGAATCAGTCAG
1 CTGAATCATTCAG
57585 CGCTGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 11 0.32
25 7 0.21
26 4 0.12
28 12 0.35
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (25 bp):
CTGAATCATTCAGATATATGTTTTG
Found at i:57591 original size:15 final size:15
Alignment explanation
Indices: 57571--57614 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
57561 GTATTGTTTT
*
57571 GCTGAATCAGTCAGC
1 GCTGAATCATTCAGC
57586 GCTGAATCATTCAGC
1 GCTGAATCATTCAGC
*
57601 ACTGAATCATTCAG
1 GCTGAATCATTCAG
57615 AGGTGCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (15 bp):
GCTGAATCATTCAGC
Found at i:63271 original size:118 final size:118
Alignment explanation
Indices: 63131--63347 Score: 371
Period size: 118 Copynumber: 1.8 Consensus size: 118
63121 TCTGTGATAG
* * * * *
63131 AATTTTCACTTCTTTTCTTGGATTTGTGATAGAATTTTCATAGTTCCATGCGAGTATTATTTTGA
1 AATTTTCACTTATTTTCCTGGATTTGTGATAGAAATTTCATAATTCCATGCGAGTATTATTTTAA
* *
63196 AAGGGAATTTGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
66 AAGGGAATTCGTTATTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
63249 AATTTTCACTTATTTTCCTGGATTTGTGATAGAAATTTCATAATTCCATGCGAGTATTATTTTAA
1 AATTTTCACTTATTTTCCTGGATTTGTGATAGAAATTTCATAATTCCATGCGAGTATTATTTTAA
63314 AAGGGAATTCGTTATTTTTGTTGAAATTTATTGA
66 AAGGGAATTCGTTATTTTTGTTGAAATTTATTGA
63348 TCAACATAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 92 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (118 bp):
AATTTTCACTTATTTTCCTGGATTTGTGATAGAAATTTCATAATTCCATGCGAGTATTATTTTAA
AAGGGAATTCGTTATTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
Found at i:64747 original size:24 final size:23
Alignment explanation
Indices: 64711--64756 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
64701 AGTTTCCACA
*
64711 ATGTAAACATTTAGTTAAATGTTG
1 ATGTAAACATTTA-ATAAATGTTG
64735 ATGTAAA-ATTTTAATAAATGTT
1 ATGTAAACA-TTTAATAAATGTT
64757 TACATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (23 bp):
ATGTAAACATTTAATAAATGTTG
Found at i:64881 original size:15 final size:16
Alignment explanation
Indices: 64845--64878 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
64835 ATCAACAGAT
64845 ATAA-TTTTTATATAA
1 ATAATTTTTTATATAA
*
64860 ATAATTTTTTATTTAA
1 ATAATTTTTTATATAA
64876 ATA
1 ATA
64879 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAATTTTTTATATAA
Found at i:65499 original size:2 final size:2
Alignment explanation
Indices: 65494--65550 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
65484 ACCAGATTAG
65494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65536 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
65551 AGGGTAAACT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67884 original size:16 final size:16
Alignment explanation
Indices: 67856--67908 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 16
67846 CAAAATACAA
67856 TATTCCC-GGTAATCT
1 TATTCCCTGGTAATCT
67871 TATTCCCTGGTAATCT
1 TATTCCCTGGTAATCT
67887 TACATTCCCACTGGTAATCT
1 T--ATT-CC-CTGGTAATCT
67907 TA
1 TA
67909 CATTCCGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 7 0.21
16 9 0.27
18 4 0.12
19 2 0.06
20 11 0.33
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (16 bp):
TATTCCCTGGTAATCT
Found at i:67902 original size:20 final size:20
Alignment explanation
Indices: 67877--67914 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
67867 ATCTTATTCC
67877 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
67897 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
67915 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:69962 original size:149 final size:149
Alignment explanation
Indices: 69721--70026 Score: 549
Period size: 149 Copynumber: 2.1 Consensus size: 149
69711 ACCGAAGTGT
*
69721 CGCGTAGAATTGCACCCTAGTGCCATATAATGATGTCGATAAGGACCACATAGAATTCCTTAAGA
1 CGCGTAGAATTGCACCCTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
* *
69786 ATCATATACATATGCTAGGGATCAAGTATGTGTCTTCCAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTGTCTTCCAAGACTTCACACATGTTCCAAAGAATA
*
69851 TATATATATCCCGAAGGAC
131 TACATATATCCCGAAGGAC
*
69870 CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
1 CGCGTAGAATTGCACCCTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
*
69935 ATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTGTCTTCCAAGACTTCACACATGTTCCAAAGAATA
*
70000 TACATATGTCCCGAAGGAC
131 TACATATATCCCGAAGGAC
70019 CGCGTAGA
1 CGCGTAGA
70027 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (149 bp):
CGCGTAGAATTGCACCCTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGA
ATCATATACATATACTAGGGATCAAGTATGTGTCTTCCAAGACTTCACACATGTTCCAAAGAATA
TACATATATCCCGAAGGAC
Found at i:71670 original size:21 final size:21
Alignment explanation
Indices: 71646--71690 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
71636 TGTTGTTCGT
* *
71646 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
71667 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
71688 TTG
1 TTG
71691 CCTAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:80342 original size:14 final size:15
Alignment explanation
Indices: 80314--80342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
80304 TAATGAATAT
80314 TATTTTAACAAATTA
1 TATTTTAACAAATTA
80329 TATTTTAA-AAATTA
1 TATTTTAACAAATTA
80343 ATTAGTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTTAACAAATTA
Found at i:81706 original size:24 final size:24
Alignment explanation
Indices: 81679--81737 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
81669 GTTTTCATTT
81679 GACGGTGGCGGTGGTGGAGATGGC
1 GACGGTGGCGGTGGTGGAGATGGC
81703 GACGGTGGCGGTGGTGGAGATGGC
1 GACGGTGGCGGTGGTGGAGATGGC
*
81727 GACGGAGGCGG
1 GACGGTGGCGG
81738 CGGTAGTGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.14, G:0.59, T:0.14
Consensus pattern (24 bp):
GACGGTGGCGGTGGTGGAGATGGC
Found at i:82021 original size:54 final size:51
Alignment explanation
Indices: 81949--82131 Score: 207
Period size: 54 Copynumber: 3.6 Consensus size: 51
81939 TGGTGGAGGA
81949 GACTGATGCTCATAAGATGACGGTGGTGGATGGTATTCTACTGATGGAGGTGG
1 GACTGATGCTCATAAGATGACGGTGGTGGATGGTATTCTACTG-T-GAGGTGG
*
82002 CGACTGATGCTCATAAGATGACGGTGGTGGATGGTATTCAAC--T--GGT-G
1 -GACTGATGCTCATAAGATGACGGTGGTGGATGGTATTCTACTGTGAGGTGG
* * **
82049 GA-GGATGCTCAAAAGATGGTGGTGGTGGATGGTATTCTACTGGTGAAGGTGG
1 GACTGATGCTCATAAGATGACGGTGGTGGATGGTATTCTACT-GTG-AGGTGG
* *
82101 AGACTGATGCTCATAAGTTGACGGAGGTGGA
1 -GACTGATGCTCATAAGATGACGGTGGTGGA
82132 GGGGGGCTTG
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
45 33 0.31
46 2 0.02
47 1 0.01
48 4 0.04
51 4 0.04
52 1 0.01
53 2 0.02
54 61 0.56
ACGTcount: A:0.24, C:0.11, G:0.38, T:0.27
Consensus pattern (51 bp):
GACTGATGCTCATAAGATGACGGTGGTGGATGGTATTCTACTGTGAGGTGG
Found at i:82027 original size:27 final size:28
Alignment explanation
Indices: 81949--82029 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 28
81939 TGGTGGAGGA
*
81949 GACTGATGCTCATAAGATGACGGTGGTG
1 GACTGATGCTCATAAGATGACGGTGGTC
* ** *
81977 GA-TGGTATTC-TACTGATGGA-GGTGG-C
1 GACTGATGCTCATA-AGAT-GACGGTGGTC
82003 GACTGATGCTCATAAGATGACGGTGGT
1 GACTGATGCTCATAAGATGACGGTGGT
82030 GGATGGTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 12
0.64 0.15 0.20
Matches are distributed among these distances:
26 6 0.16
27 26 0.68
28 6 0.16
ACGTcount: A:0.23, C:0.14, G:0.36, T:0.27
Consensus pattern (28 bp):
GACTGATGCTCATAAGATGACGGTGGTC
Found at i:82065 original size:45 final size:45
Alignment explanation
Indices: 82007--82093 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
81997 GGTGGCGACT
*
82007 GATGCTCATAAGATGACGGTGGTGGATGGTATTCAACTGGTGGAG
1 GATGCTCAAAAGATGACGGTGGTGGATGGTATTCAACTGGTGGAG
** *
82052 GATGCTCAAAAGATGGTGGTGGTGGATGGTATTCTACTGGTG
1 GATGCTCAAAAGATGACGGTGGTGGATGGTATTCAACTGGTG
82094 AAGGTGGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.29
Consensus pattern (45 bp):
GATGCTCAAAAGATGACGGTGGTGGATGGTATTCAACTGGTGGAG
Found at i:82077 original size:99 final size:99
Alignment explanation
Indices: 81953--82131 Score: 286
Period size: 99 Copynumber: 1.8 Consensus size: 99
81943 GGAGGAGACT
* * *
81953 GATGCTCATAAGATGACGGTGGTGGATGGTATTCTACTGATGGAGGTGGCGACTGATGCTCATAA
1 GATGCTCAAAAGATGACGGTGGTGGATGGTATTCTACTGATGAAGGTGGAGACTGATGCTCATAA
*
82018 GATGACGGTGGTGGATGGTATTCAACTGGTGGAG
66 GATGACGGAGGTGGATGGTATTCAACTGGTGGAG
** *
82052 GATGCTCAAAAGATGGTGGTGGTGGATGGTATTCTACTGGTGAAGGTGGAGACTGATGCTCATAA
1 GATGCTCAAAAGATGACGGTGGTGGATGGTATTCTACTGATGAAGGTGGAGACTGATGCTCATAA
*
82117 GTTGACGGAGGTGGA
66 GATGACGGAGGTGGA
82132 GGGGGGCTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 72 1.00
ACGTcount: A:0.24, C:0.11, G:0.38, T:0.27
Consensus pattern (99 bp):
GATGCTCAAAAGATGACGGTGGTGGATGGTATTCTACTGATGAAGGTGGAGACTGATGCTCATAA
GATGACGGAGGTGGATGGTATTCAACTGGTGGAG
Found at i:82438 original size:27 final size:27
Alignment explanation
Indices: 82402--82457 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
82392 TGGTGGTGAG
*
82402 GGTGGTGTATTGTG-GTAATGGCTT-GGT
1 GGTGGAGTATTG-GAGTAATGG-TTAGGT
82429 GGTGGAGTATTGGAGTAATGGTTAGGT
1 GGTGGAGTATTGGAGTAATGGTTAGGT
82456 GG
1 GG
82458 CGGTGGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.16, C:0.02, G:0.46, T:0.36
Consensus pattern (27 bp):
GGTGGAGTATTGGAGTAATGGTTAGGT
Found at i:86122 original size:13 final size:14
Alignment explanation
Indices: 86104--86137 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
86094 ATATAAGTGT
86104 ATAATAAATTTATA
1 ATAATAAATTTATA
*
86118 A-AATATATTTATA
1 ATAATAAATTTATA
86131 ATAATAA
1 ATAATAA
86138 TAATCATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAAATTTATA
Found at i:98224 original size:21 final size:21
Alignment explanation
Indices: 98198--98237 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
98188 TCTGCTGAAA
*
98198 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGTGGAGTATG
98219 CTCCACCTGTTGTGGAGTA
1 CTCCACCTGTTGTGGAGTA
98238 CTACTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (21 bp):
CTCCACCTGTTGTGGAGTATG
Found at i:99436 original size:23 final size:23
Alignment explanation
Indices: 99400--99472 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
99390 CACCACAGCT
*
99400 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
*
99421 CATATAGAATTGCACCGTAGTGT
1 CATATAGAATTGCACCGTAGTGC
*** *
99444 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
99467 CATATA
1 CATATA
99473 ATAATGTCCA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 6 0.15
22 2 0.05
23 32 0.80
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Found at i:99655 original size:103 final size:103
Alignment explanation
Indices: 99484--99701 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
99474 TAATGTCCAT
99484 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
99549 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
99587 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
99652 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
99690 AAGGACCACATA
1 AAGGACCACATA
99702 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:101162 original size:21 final size:21
Alignment explanation
Indices: 101136--101179 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
101126 ATTTTATTCG
* *
101136 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
101157 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
101178 CT
1 CT
101180 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:104226 original size:23 final size:23
Alignment explanation
Indices: 104196--104241 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
104186 GCTTGCCAAT
*
104196 CTTGCCAACTTGCAAGCCTTCAA
1 CTTGCCAACCTGCAAGCCTTCAA
104219 CTTGCCAACCTGCAAGCCTTCAA
1 CTTGCCAACCTGCAAGCCTTCAA
104242 GTCACACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (23 bp):
CTTGCCAACCTGCAAGCCTTCAA
Found at i:106169 original size:14 final size:15
Alignment explanation
Indices: 106143--106178 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
106133 TATTAGATGA
106143 AATTTTATTAATTTT
1 AATTTTATTAATTTT
106158 AATTTT-TTAA-TTT
1 AATTTTATTAATTTT
106171 -ATTTTATT
1 AATTTTATT
106179 TTAATCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.25
13 5 0.25
14 4 0.20
15 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AATTTTATTAATTTT
Found at i:107196 original size:21 final size:20
Alignment explanation
Indices: 107133--107196 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
107123 TTAATATAAT
*
107133 AATAAATTTTAATTTTTTAAA
1 AATAAA-TTTAATATTTTAAA
* **
107154 AATAAATTTGATATGTAGAAA
1 AATAAATTTAATAT-TTTAAA
107175 AATAAATTTAATATTCTTAAA
1 AATAAATTTAATATT-TTAAA
107196 A
1 A
107197 TAATTTTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (20 bp):
AATAAATTTAATATTTTAAA
Found at i:108974 original size:15 final size:15
Alignment explanation
Indices: 108954--108982 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
108944 TGTGGTTGTT
108954 TTATCTAATATTACA
1 TTATCTAATATTACA
108969 TTATCTAATATTAC
1 TTATCTAATATTAC
108983 TATTTGCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATCTAATATTACA
Found at i:110912 original size:24 final size:24
Alignment explanation
Indices: 110876--110930 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
110866 ACAATAATAG
*
110876 ATATGTTCATGAATATATTTATTTA
1 ATAT-TTCATGAATATATTCATTTA
*
110901 TATATTTC-TGAATATGTTCATTTA
1 -ATATTTCATGAATATATTCATTTA
110925 ATATTT
1 ATATTT
110931 GTTTAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 14 0.52
25 3 0.11
26 4 0.15
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (24 bp):
ATATTTCATGAATATATTCATTTA
Found at i:110971 original size:22 final size:22
Alignment explanation
Indices: 110945--110986 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
110935 AATAAATATG
110945 TTTATTTAATATTTGTTTAGTA
1 TTTATTTAATATTTGTTTAGTA
110967 TTTATTTAATATTTGTTTAG
1 TTTATTTAATATTTGTTTAG
110987 CGTTGGTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (22 bp):
TTTATTTAATATTTGTTTAGTA
Found at i:111584 original size:9 final size:9
Alignment explanation
Indices: 111572--111605 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
111562 TAAATAAACT
111572 ATTAAATAA
1 ATTAAATAA
111581 ATTAAA-AA
1 ATTAAATAA
*
111589 TTTAAATAA
1 ATTAAATAA
111598 ATTAAATA
1 ATTAAATA
111606 TAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:111586 original size:17 final size:16
Alignment explanation
Indices: 111556--111612 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
111546 CTGTAAAAAA
*
111556 ATTAATTAAA-TAAACT
1 ATTAAATAAATTAAA-T
*
111572 ATTAAATAAATTAAAA
1 ATTAAATAAATTAAAT
111588 ATTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
111605 ATAAAATA
1 ATTAAATA
111613 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 16 0.46
17 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:111588 original size:33 final size:31
Alignment explanation
Indices: 111551--111619 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
111541 TATATCTGTA
*
111551 AAAAAATTAATTAAA-TAAACTATTAAATAAATT
1 AAAAAATTAAATAAATTAAA-TA-TAAA-AAATT
* *
111584 AAAAATTTAAATAAATTAAATATAAAATATT
1 AAAAAATTAAATAAATTAAATATAAAAAATT
111615 AAAAA
1 AAAAA
111620 TATAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.28
32 4 0.12
33 15 0.47
34 4 0.12
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAAAATTAAATAAATTAAATATAAAAAATT
Found at i:118084 original size:24 final size:24
Alignment explanation
Indices: 118052--118104 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
118042 TGCCCCACCG
118052 TTAAAAACTTAACGCATTTAGTAC
1 TTAAAAACTTAACGCATTTAGTAC
118076 TTAAAAACTTAACGCATTTAGTAC
1 TTAAAAACTTAACGCATTTAGTAC
118100 TTAAA
1 TTAAA
118105 CTATCAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAACTTAACGCATTTAGTAC
Found at i:124874 original size:20 final size:20
Alignment explanation
Indices: 124845--124883 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
124835 AGAGCTCATA
*
124845 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
124865 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
124884 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:125225 original size:25 final size:27
Alignment explanation
Indices: 125197--125246 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
125187 AGCTGCCCAT
*
125197 GAGGGGATCA-TGCC-CAGCTGCTCTG
1 GAGGGGACCACTGCCACAGCTGCTCTG
125222 GAGGGGACCACTGCCACAGCTGCTC
1 GAGGGGACCACTGCCACAGCTGCTC
125247 ACCCCCTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 4 0.18
27 9 0.41
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (27 bp):
GAGGGGACCACTGCCACAGCTGCTCTG
Found at i:125748 original size:21 final size:20
Alignment explanation
Indices: 125710--125748 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
125700 CAATGGATGG
*
125710 TTGTTTTTGTATGCTTTTAT
1 TTGTTTTTGTATGATTTTAT
*
125730 TTGTTTTGTTTATGATTTT
1 TTGTTTT-TGTATGATTTT
125749 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTGTTTTTGTATGATTTTAT
Found at i:148241 original size:20 final size:19
Alignment explanation
Indices: 148190--148241 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
148180 ATATACGTAT
*
148190 ATAATAATA-AAATATATA
1 ATAATAATATAAATAAATA
148208 ATAGCATAA-ATAAATAAATA
1 ATA--ATAATATAAATAAATA
148228 ATAATAATAGTAAA
1 ATAATAATA-TAAA
148242 AAGTAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 19 0.68
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATAATATAAATAAATA
Found at i:148646 original size:18 final size:17
Alignment explanation
Indices: 148624--148672 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
148614 TAAAAATAGT
148624 AATAATAGAAATAATAAG
1 AATAATA-AAATAATAAG
* * *
148642 GATAATATAAAGAATAAT
1 AATAATA-AAATAATAAG
148660 AATAATAAAATAA
1 AATAATAAAATAA
148673 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AATAATAAAATAATAAG
Found at i:148667 original size:21 final size:21
Alignment explanation
Indices: 148624--148673 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
148614 TAAAAATAGT
*
148624 AATAATAGAAATAATAAGGATAA
1 AATAA-AG-AATAATAAGAATAA
* *
148647 TATAAAGAATAATAATAATAA
1 AATAAAGAATAATAAGAATAA
148668 AATAAA
1 AATAAA
148674 AATGGTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AATAAAGAATAATAAGAATAA
Found at i:148747 original size:34 final size:32
Alignment explanation
Indices: 148696--148760 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 32
148686 TATAAAAAGA
*
148696 AATAAAATATATATATATATACGTATAATAAT
1 AATAAAATATATATATATATACATATAATAAT
*
148728 AATAACAATAATATATATATATATATATAATAA
1 AATAA-AAT-ATATATATATATACATATAATAA
148761 CGTAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.17
33 3 0.10
34 21 0.72
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (32 bp):
AATAAAATATATATATATATACATATAATAAT
Found at i:165131 original size:17 final size:18
Alignment explanation
Indices: 165109--165153 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
165099 TTCTTGAAGG
165109 ATAATTTAAAC-AAATTA
1 ATAATTTAAACTAAATTA
*
165126 ATAATTTAAACTTAATTA
1 ATAATTTAAACTAAATTA
*
165144 ATCATTTAAA
1 ATAATTTAAA
165154 AAAGTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATTTAAACTAAATTA
Found at i:165534 original size:76 final size:76
Alignment explanation
Indices: 165444--165607 Score: 285
Period size: 76 Copynumber: 2.1 Consensus size: 76
165434 TTAATTAAAA
*
165444 TATTAAAATTAATTAAATTCACCCTCCAATCATATAGTGACACATAACA-CATCTGGATTGGAGG
1 TATT-AAATTAATTAAATTCACCCTCCAATCATATAGTGACACATAACATC-TCCGGATTGGAGG
165508 ACTAAATTTATTT
64 ACTAAATTTATTT
*
165521 TATTAAATTAATTAAATTCACCCTCCAATCATATAGTGACACATGACATCTCCGGATTGGAGGAC
1 TATTAAATTAATTAAATTCACCCTCCAATCATATAGTGACACATAACATCTCCGGATTGGAGGAC
165586 TAAATTTATTT
66 TAAATTTATTT
165597 TATTAAATTAA
1 TATTAAATTAA
165608 AATAGTGATT
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
76 79 0.94
77 5 0.06
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (76 bp):
TATTAAATTAATTAAATTCACCCTCCAATCATATAGTGACACATAACATCTCCGGATTGGAGGAC
TAAATTTATTT
Found at i:167216 original size:23 final size:23
Alignment explanation
Indices: 167190--167244 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
167180 TATTACATGG
167190 AGACGAGAAGTAAGAGAGCCTAA
1 AGACGAGAAGTAAGAGAGCCTAA
167213 AGACGAGAAGTAAGAGAGCCTAA
1 AGACGAGAAGTAAGAGAGCCTAA
167236 AGACGAGAA
1 AGACGAGAA
167245 CCGGAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.49, C:0.13, G:0.31, T:0.07
Consensus pattern (23 bp):
AGACGAGAAGTAAGAGAGCCTAA
Done.