Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000923.1 Hibiscus syriacus cultivar Beakdansim tig00001841_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: 75927
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:237 original size:19 final size:18
Alignment explanation
Indices: 199--245 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
189 ATTTAACCTA
*
199 AAATATATAAACATATAT
1 AAATATATAAACATAGAT
217 AACATATATAAACAGT-GAT
1 AA-ATATATAAACA-TAGAT
236 AAAT-TATAAA
1 AAATATATAAA
246 AATATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 4 0.15
19 15 0.58
20 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (18 bp):
AAATATATAAACATAGAT
Found at i:1438 original size:14 final size:14
Alignment explanation
Indices: 1410--1453 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1400 TTTAATATAT
1410 ATAATAT-AT-ATA
1 ATAATATAATAATA
**
1422 ATAATATTTTAATA
1 ATAATATAATAATA
1436 ATAATATAATAATA
1 ATAATATAATAATA
1450 ATAA
1 ATAA
1454 ATTGAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 7 0.26
13 1 0.04
14 19 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATAATAATA
Found at i:1450 original size:11 final size:11
Alignment explanation
Indices: 1402--1452 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
1392 ATATTTTGTT
1402 TAATATATATAA
1 TAATATA-ATAA
1414 TATATATAATAA
1 TA-ATATAATAA
* *
1426 TATTTTAATAA
1 TAATATAATAA
1437 TAATATAATAA
1 TAATATAATAA
1448 TAATA
1 TAATA
1453 AATTGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 21 0.62
12 8 0.24
13 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATATAATAA
Found at i:5333 original size:41 final size:41
Alignment explanation
Indices: 5219--5333 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
5209 GGTTGATAAT
* *
5219 TAGCGGCGTTTTCATATAAACGCCGCTAAA-GTTCAGTATA
1 TAGCGGCGTTTTTATACAAACGCCGCTAAATGTTCAGTATA
* * *
5259 TAGCGGCGTTTCTAGTATACAAACACAGCTAAATGTAT-GGTATA
1 TAGCGGCGTTT-T--TATACAAACGCCGCTAAATGT-TCAGTATA
* *
5303 TTGCGGCGTTTTTTTACAAACGCCGCTAAAT
1 TAGCGGCGTTTTTATACAAACGCCGCTAAAT
5334 AACACAGAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
40 11 0.18
41 17 0.28
43 15 0.25
44 17 0.28
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
TAGCGGCGTTTTTATACAAACGCCGCTAAATGTTCAGTATA
Found at i:5672 original size:21 final size:21
Alignment explanation
Indices: 5648--5717 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
5638 GCTGATATGA
*
5648 TGCTTCTCTCAGTGCTGCCAT
1 TGCTTCTCTCAGTGCTGCCAC
**
5669 TGCTTCTCTCTA-TGCTATCAC
1 TGCTTCTCTC-AGTGCTGCCAC
* *
5690 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCAGTGCTGCCAC
5711 TGCTTCT
1 TGCTTCT
5718 TTCTCTGCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.07, C:0.34, G:0.17, T:0.41
Consensus pattern (21 bp):
TGCTTCTCTCAGTGCTGCCAC
Found at i:5694 original size:42 final size:42
Alignment explanation
Indices: 5648--5740 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
5638 GCTGATATGA
*
5648 TGCTTCTCTCAGTGCTGCCATTGCTTCTCTCTATGCTATCAC
1 TGCTTCTCTCAGTGCTGCCACTGCTTCTCTCTATGCTATCAC
* * * * * *
5690 TGCTTCTCTCTGTGCTGCCGCTGCTTCTTTCTCTGCTTTCGC
1 TGCTTCTCTCAGTGCTGCCACTGCTTCTCTCTATGCTATCAC
*
5732 TGCTGCTCT
1 TGCTTCTCT
5741 GGCTACTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.05, C:0.34, G:0.17, T:0.43
Consensus pattern (42 bp):
TGCTTCTCTCAGTGCTGCCACTGCTTCTCTCTATGCTATCAC
Found at i:5726 original size:21 final size:21
Alignment explanation
Indices: 5648--5768 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 21
5638 GCTGATATGA
** **
5648 TGCTTCTCTCAGTGCTGCCAT
1 TGCTTCTCTCTCTGCTGCCGC
* ** *
5669 TGCTTCTCTCTATGCTATCAC
1 TGCTTCTCTCTCTGCTGCCGC
*
5690 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCTCTGCTGCCGC
* **
5711 TGCTTCTTTCTCTGCTTTCGC
1 TGCTTCTCTCTCTGCTGCCGC
* ** * * *
5732 TGCTGCTCTGGCTACTTCTGC
1 TGCTTCTCTCTCTGCTGCCGC
*
5753 TGCTGCTCTCTCTGCT
1 TGCTTCTCTCTCTGCT
5769 TCCCTTGCTT
Statistics
Matches: 77, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.05, C:0.35, G:0.18, T:0.42
Consensus pattern (21 bp):
TGCTTCTCTCTCTGCTGCCGC
Found at i:7304 original size:17 final size:17
Alignment explanation
Indices: 7250--7298 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
7240 ATGATATCTA
7250 TAATAAAAAAACATGAG
1 TAATAAAAAAACATGAG
7267 TAATAAAAAAACATGAG
1 TAATAAAAAAACATGAG
7284 TAATAAAAAAA-ATGA
1 TAATAAAAAAACATGA
7299 ATTAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.18
Consensus pattern (17 bp):
TAATAAAAAAACATGAG
Found at i:9406 original size:18 final size:18
Alignment explanation
Indices: 9383--9417 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9373 ATAAGCACGC
*
9383 ATAATTTAATTTCACATA
1 ATAATTTAAGTTCACATA
9401 ATAATTTAAGTTCACAT
1 ATAATTTAAGTTCACAT
9418 TTATTTGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (18 bp):
ATAATTTAAGTTCACATA
Found at i:9593 original size:24 final size:24
Alignment explanation
Indices: 9566--9640 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
9556 CATAATAAGT
*
9566 TTGTCTCTTAAAACAATACTTCAG
1 TTGTCTCTTAAAACAACACTTCAG
*
9590 TTGTCTCTTAAAACAACACTTCATTAT
1 TTGTCTCTTAAAACAACACTTC---AG
*
9617 TTGTCTATTAAAAACAACACTTCA
1 TTGTCTCTT-AAAACAACACTTCA
9641 TGCATCCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 21 0.48
25 1 0.02
27 9 0.20
28 13 0.30
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (24 bp):
TTGTCTCTTAAAACAACACTTCAG
Found at i:13583 original size:22 final size:22
Alignment explanation
Indices: 13553--13601 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
13543 CACGTTTTGA
*
13553 AAAGTTATTATTATCATATTCG
1 AAAGCTATTATTATCATATTCG
* **
13575 AAAGCTATTATTTTTGTATTCG
1 AAAGCTATTATTATCATATTCG
13597 AAAGC
1 AAAGC
13602 AGAAAAACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
AAAGCTATTATTATCATATTCG
Found at i:14215 original size:81 final size:82
Alignment explanation
Indices: 14062--14242 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 82
14052 TTTGTTTGAT
* * * * * * *
14062 AAACGCCGCTAAATTAATTCTCTATAGCGTCATTTGTTGGATAAATGCCACTATAAACAACCCTG
1 AAACGCCGCTAAATTACTACTCTATAGCGGCATTTATTGGAAAAATGCCACTATAAACAAACCTA
*
14127 TTGCGGCGTTTTTA-TAC
66 TTCCGGCG-TTTTACTAC
* * * *
14144 AAACGCCGCTAAATTACTACTCTATTGCGGCGTTTATT-GAAAAATGCCACTGTAAACAAATCTA
1 AAACGCCGCTAAATTACTACTCTATAGCGGCATTTATTGGAAAAATGCCACTATAAACAAACCTA
*
14208 TTCCGGCGTTTTAGCTAT
66 TTCCGGCGTTTTA-CTAC
14226 AAACGCCGCTAAATTAC
1 AAACGCCGCTAAATTAC
14243 CACTGTTACT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 5 0.06
81 28 0.33
82 51 0.61
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (82 bp):
AAACGCCGCTAAATTACTACTCTATAGCGGCATTTATTGGAAAAATGCCACTATAAACAAACCTA
TTCCGGCGTTTTACTAC
Found at i:16945 original size:23 final size:23
Alignment explanation
Indices: 16918--16963 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16908 ATTAGAAATG
16918 ATTAAGAACATGTTTGAAATTAT
1 ATTAAGAACATGTTTGAAATTAT
16941 ATTAAGAACATGTTTGAAATTAT
1 ATTAAGAACATGTTTGAAATTAT
16964 GGTATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTAAGAACATGTTTGAAATTAT
Found at i:20074 original size:2 final size:2
Alignment explanation
Indices: 20067--20199 Score: 230
Period size: 2 Copynumber: 66.5 Consensus size: 2
20057 GATGGTGTCC
* *
20067 TA TA TA TA TG TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
20109 TA TG TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20193 TA TA TA T
1 TA TA TA T
20200 TATTCAAAGT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 123 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20334 original size:19 final size:19
Alignment explanation
Indices: 20312--20363 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
20302 GAATATAGGA
20312 AAATTGAG-AATTTAGAGGG
1 AAATTGAGAAATTTAGA-GG
*
20331 AAATTGGGAAATTTAGAGG
1 AAATTGAGAAATTTAGAGG
* *
20350 AAATAGAAAAATTT
1 AAATTGAGAAATTT
20364 GGGAAGTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (19 bp):
AAATTGAGAAATTTAGAGG
Found at i:20343 original size:46 final size:46
Alignment explanation
Indices: 20273--20362 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
20263 TTTTATTTGG
* *
20273 GAATTTAGAGGGAAATCAACAAATTTTGA-GAATATAGGAAAATTGA
1 GAATTTAGAGGGAAATCAACAAATTTAGAGGAA-ATAGAAAAATTGA
****
20319 GAATTTAGAGGGAAATTGGGAAATTTAGAGGAAATAGAAAAATT
1 GAATTTAGAGGGAAATCAACAAATTTAGAGGAAATAGAAAAATT
20363 TGGGAAGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
46 34 0.92
47 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (46 bp):
GAATTTAGAGGGAAATCAACAAATTTAGAGGAAATAGAAAAATTGA
Found at i:20845 original size:14 final size:14
Alignment explanation
Indices: 20826--20872 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
20816 ATTTTTTCTT
20826 TATATAAATTAAAC
1 TATATAAATTAAAC
20840 TATAT-AATT----
1 TATATAAATTAAAC
20849 TATATAAATTAAAC
1 TATATAAATTAAAC
*
20863 TATATTAATT
1 TATATAAATT
20873 TTCCTTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:20850 original size:23 final size:24
Alignment explanation
Indices: 20824--20873 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
20814 TTATTTTTTC
20824 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
20847 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
20871 TTT
1 TTT
20874 TCCTTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:21150 original size:16 final size:16
Alignment explanation
Indices: 21129--21180 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
21119 TGGATCATTT
21129 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
21145 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
21161 ACAGGTCAAGTTGAAA
1 ACAGGTCAGGTTGAAA
21177 ACAG
1 ACAG
21181 ATCGAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.17
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:21974 original size:53 final size:53
Alignment explanation
Indices: 21905--22011 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 53
21895 CTGGCTTGAC
*
21905 TTGCCTAATTTCCCAAGATGTAACGCAACTTATTATC-GCCGTAGATTATGGAT
1 TTGCCTAATTTCCCAAGATGTAACGCAACTTATTATCAG-CGTACATTATGGAT
* * *
21958 TTGCCTAATTTTCCAAGATGTAACGCAAGTTATTTTCAGCGTACATTATGGAT
1 TTGCCTAATTTCCCAAGATGTAACGCAACTTATTATCAGCGTACATTATGGAT
22011 T
1 T
22012 GGGACTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 48 0.98
54 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (53 bp):
TTGCCTAATTTCCCAAGATGTAACGCAACTTATTATCAGCGTACATTATGGAT
Found at i:28967 original size:26 final size:26
Alignment explanation
Indices: 28938--28990 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28928 TTAGTATACC
28938 ATACCATTTTATTTAATAAAAAACTA
1 ATACCATTTTATTTAATAAAAAACTA
28964 ATACCATTTTATTTAATAAAAAACTA
1 ATACCATTTTATTTAATAAAAAACTA
28990 A
1 A
28991 CTTTTTGTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
ATACCATTTTATTTAATAAAAAACTA
Found at i:32523 original size:15 final size:14
Alignment explanation
Indices: 32502--32540 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
32492 TCTGTCTGTA
32502 TGCAGAGATTT-TT
1 TGCAGAGATTTATT
32515 TACGCAGAGATTTATT
1 T--GCAGAGATTTATT
32531 TGCAGAGATT
1 TGCAGAGATT
32541 ACTTTCCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 9 0.39
15 10 0.43
16 3 0.13
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (14 bp):
TGCAGAGATTTATT
Found at i:32926 original size:2 final size:2
Alignment explanation
Indices: 32919--32954 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
32909 AACCTTGAGA
32919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32955 AGTTTGACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36591 original size:37 final size:36
Alignment explanation
Indices: 36519--36944 Score: 342
Period size: 37 Copynumber: 11.4 Consensus size: 36
36509 AACGTATATA
36519 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAAC--ATATAAT
*
36557 ATATAGTTTTGAAAATATTTTTTTTGAAACATATATAAT
1 ATATAGTTTTGAAAATA--TTTTTTGAAA-ACATATAAT
*
36596 ATATAGTTTTGAAAACATTTTTTG-AAACGTATATAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAAC--ATATAAT
* * *
36633 ATATAATTTTGAAAACATTTTTTGTAACAA-AAATAAT
1 ATATAGTTTTGAAAATATTTTTTG-AA-AACATATAAT
* * *
36670 ATATAATTTTGAAAA-ATACTTTTGAAAACGTATAAT
1 ATATAGTTTTGAAAATAT-TTTTTGAAAACATATAAT
* * * *
36706 ATATAGTTTTTAAAATA-CTTTTGAAAACGTACAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAACATATAAT
* *
36741 ATAT-GATTTTAAAAACATTTTTTGAAAACATATAAT
1 ATATAG-TTTTGAAAATATTTTTTGAAAACATATAAT
* * * *
36777 ATATAGTTTTTAAAAAAAATATTTTTAAAAACTTATAAT
1 ATATAG-TTTT-GAAAATAT-TTTTTGAAAACATATAAT
* * * * * *
36816 ATGTAGTTTTTAAAA-ATAATTTGGAAATATATAAAAT
1 ATATAGTTTTGAAAATAT-TTTTTGAAA-ACATATAAT
*
36853 ATAATGGTTTTGAAAATATTTTTTGAAAACATATAAT
1 AT-ATAGTTTTGAAAATATTTTTTGAAAACATATAAT
* * * *
36890 ATATAGTTTTTTTAAAAAAATATTTTTAAAAACTTATAAT
1 ATATAG---TTTTGAAAATAT-TTTTTGAAAACATATAAT
* *
36930 ATGTAGTTTTTAAAA
1 ATATAGTTTTGAAAA
36945 AGAATTTGGA
Statistics
Matches: 323, Mismatches: 42, Indels: 47
0.78 0.10 0.11
Matches are distributed among these distances:
34 1 0.00
35 33 0.10
36 55 0.17
37 98 0.30
38 45 0.14
39 57 0.18
40 33 0.10
41 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
ATATAGTTTTGAAAATATTTTTTGAAAACATATAAT
Found at i:36929 original size:114 final size:113
Alignment explanation
Indices: 36524--37012 Score: 488
Period size: 114 Copynumber: 4.4 Consensus size: 113
36514 ATATAATATA
* * * * **
36524 GTTTTGAAAATATTTTTTGAAAACGTATATAATATATAG--TTTTGAAAATATTTTTTTTGAAAC
1 GTTTTGAAAACATTTTTTGAAAAC--ATATAATATATAGTTTTTTAAAAAAATATTTTTAAAAAC
* * * *
36587 ATATATAATATATAGTTTTGAAAACAT-TTTTTGAAACGTATATAATATATAA--
64 -T-TATAATATATAGTTTTTAAAA-ATAATTTGGAAA--TATATAAAATATAATG
* * * * *
36639 -TTTTGAAAACATTTTTTGTAACAA-AAATAATATATA--ATTTT-GAAAAATACTTTTGAAAAC
1 GTTTTGAAAACATTTTTTG-AA-AACATATAATATATAGTTTTTTAAAAAAATATTTTTAAAAAC
* * * ** *
36699 GTATAATATATAGTTTTT-AAAATACTTTTGAAA-ACGTACAATAT-ATG
64 TTATAATATATAGTTTTTAAAAATAATTTGGAAATATATAAAATATAATG
* * *
36746 ATTTTAAAAACATTTTTTGAAAACATATAATATATAGTTTTTAAAAAAAATATTTTTAAAAACTT
1 GTTTTGAAAACATTTTTTGAAAACATATAATATATAGTTTTTTAAAAAAATATTTTTAAAAACTT
*
36811 ATAATATGTAGTTTTTAAAAATAATTTGGAAATATATAAAATATAATG
66 ATAATATATAGTTTTTAAAAATAATTTGGAAATATATAAAATATAATG
*
36859 GTTTTGAAAATATTTTTTGAAAACATATAATATATAGTTTTTTTAAAAAAATATTTTTAAAAACT
1 GTTTTGAAAACATTTTTTGAAAACATATAATATATAG-TTTTTTAAAAAAATATTTTTAAAAACT
* * *
36924 TATAATATGTAGTTTTTAAAAAGAATTTGGAAACATATAAAATATAATG
65 TATAATATATAGTTTTTAAAAATAATTTGGAAATATATAAAATATAATG
**
36973 GTTTTGAAAACA--TTTAAAAAACATAT-ATCATATAGTTTTT
1 GTTTTGAAAACATTTTTTGAAAACATATAAT-ATATAGTTTTT
37013 CATTATTATT
Statistics
Matches: 320, Mismatches: 38, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
105 1 0.00
106 9 0.03
107 13 0.04
108 19 0.06
109 14 0.04
110 48 0.15
111 20 0.06
112 39 0.12
113 52 0.16
114 101 0.32
115 2 0.01
116 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (113 bp):
GTTTTGAAAACATTTTTTGAAAACATATAATATATAGTTTTTTAAAAAAATATTTTTAAAAACTT
ATAATATATAGTTTTTAAAAATAATTTGGAAATATATAAAATATAATG
Found at i:36968 original size:37 final size:38
Alignment explanation
Indices: 36813--36969 Score: 124
Period size: 38 Copynumber: 4.2 Consensus size: 38
36803 AAAAACTTAT
*
36813 AATAT-GTAGTTTTTAAAAATAATTTGGAAATATATAA
1 AATATAGTAGTTTTTAAAAATAATTTGGAAACATATAA
* * * ** *
36850 AATATAATGGTTTTGAAAATATTTTTTGAAAACATATAA
1 AATATAGTAGTTTTTAAAA-ATAATTTGGAAACATATAA
* * * ** * *
36889 TATATAGT-TTTTTTAAAAAAATATTTTTAAAAACT-TAT
1 AATATAGTAGTTTTTAAAAATA-ATTTGGAAACA-TATAA
*
36927 AATAT-GTAGTTTTTAAAAAGAATTTGGAAACATATAA
1 AATATAGTAGTTTTTAAAAATAATTTGGAAACATATAA
36964 AATATA
1 AATATA
36970 ATGGTTTTGA
Statistics
Matches: 88, Mismatches: 25, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
36 1 0.01
37 23 0.26
38 42 0.48
39 22 0.25
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (38 bp):
AATATAGTAGTTTTTAAAAATAATTTGGAAACATATAA
Found at i:37058 original size:16 final size:15
Alignment explanation
Indices: 37039--37072 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
37029 TTTATATTGT
*
37039 TTATTTATTTTATTTA
1 TTATTTATTCT-TTTA
37055 TTATTTATTCTTTTA
1 TTATTTATTCTTTTA
37070 TTA
1 TTA
37073 GGGGTCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATTCTTTTA
Found at i:47334 original size:38 final size:38
Alignment explanation
Indices: 47291--47752 Score: 476
Period size: 38 Copynumber: 12.4 Consensus size: 38
47281 AACATATATA
47291 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
* *
47329 ATATAGTTTTGAAAACATTTTTTG-AAACATATATAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
* *
47366 ATATAGTTTTGAAAACATTTTTTGAAAACATATATAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
* * *
47404 TTATAGTTTTGAAAACATTTTTTTG-AAATGTATATAAT
1 ATATAGTTTTGAAAATA-TTTTTTGAAAACGTATATAAT
** * * *
47442 ATATAGTTTTGAATTTTTTTTTTG-AAACATATATAAC
1 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
* *
47479 ATATAGTTTTGAAAACATTTTTTTTTG-AAATGTATATAAT
1 ATATAGTTTTG-AAA-A-TATTTTTTGAAAACGTATATAAT
*
47519 ATATAGTTTTGAAAACATTTTTTTG-AAACGTATATAAT
1 ATATAGTTTTGAAAATA-TTTTTTGAAAACGTATATAAT
* * *
47557 ATATAGTTTTGAAAACATTTTTT-TAAACATATATAAT
1 ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
* *
47594 ATATAGTTTTGAAAA-ATACTTTTGAAAAAG--TATAAT
1 ATATAGTTTTGAAAATAT-TTTTTGAAAACGTATATAAT
* *
47630 ATATAGTTTCTAAAAATA-CTTTTGAAAAC--ATATAAT
1 ATATAGTTT-TGAAAATATTTTTTGAAAACGTATATAAT
* *
47666 ATAT-GATTTTG-AAATTTTTTTTGAAAAC--AAATAAT
1 ATATAG-TTTTGAAAATATTTTTTGAAAACGTATATAAT
*
47701 ATATAGTTTT-AAAAAATATTTTTGAAAAC-T-TATAAT
1 ATATAGTTTTGAAAATAT-TTTTTGAAAACGTATATAAT
*
47737 ATATAGTTTTTAAAAT
1 ATATAGTTTTGAAAAT
47753 GAATTTGGAA
Statistics
Matches: 369, Mismatches: 36, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
34 4 0.01
35 30 0.08
36 67 0.18
37 110 0.30
38 118 0.32
39 10 0.03
40 30 0.08
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (38 bp):
ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAAT
Found at i:47362 original size:37 final size:37
Alignment explanation
Indices: 47281--47812 Score: 526
Period size: 37 Copynumber: 14.4 Consensus size: 37
47271 TAGTATATAT
*
47281 AACATATAT-A-ATATAGTTTTGAAAATATTTTTTGAA
1 AACATATATAATATATAGTTTTGAAAACATTTTTTG-A
*
47317 AACGTATATAATATATAGTTTTGAAAACATTTTTTGA
1 AACATATATAATATATAGTTTTGAAAACATTTTTTGA
47354 AACATATATAATATATAGTTTTGAAAACATTTTTTGAA
1 AACATATATAATATATAGTTTTGAAAACATTTTTTG-A
*
47392 AACATATATAATTTATAGTTTTGAAAACATTTTTTTGA
1 AACATATATAATATATAGTTTTGAAAACA-TTTTTTGA
** ****
47430 AATGTATATAATATATAGTTTTGAATTTTTTTTTTGA
1 AACATATATAATATATAGTTTTGAAAACATTTTTTGA
*
47467 AACATATATAACATATAGTTTTGAAAACATTTTTTTTTGA
1 AACATATATAATATATAGTTTTGAAAACA---TTTTTTGA
**
47507 AATGTATATAATATATAGTTTTGAAAACATTTTTTTGA
1 AACATATATAATATATAGTTTTGAAAACA-TTTTTTGA
* *
47545 AACGTATATAATATATAGTTTTGAAAACATTTTTTTA
1 AACATATATAATATATAGTTTTGAAAACATTTTTTGA
*
47582 AACATATATAATATATAGTTTTGAAAA-ATACTTTTGA
1 AACATATATAATATATAGTTTTGAAAACAT-TTTTTGA
*
47619 AA-A-AGTATAATATATAGTTTCT-AAAA-ATACTTTTGA
1 AACATA-TATAATATATAGTTT-TGAAAACAT-TTTTTGA
* **
47655 AA-ACATATAATATAT-GATTTTG-AAATTTTTTTTGAA
1 AACATATATAATATATAG-TTTTGAAAACATTTTTTG-A
*
47691 AACA-A-ATAATATATAGTTTT-AAAAAATATTTTTGA
1 AACATATATAATATATAGTTTTGAAAACAT-TTTTTGA
* * * *
47726 AA-ACT-TATAATATATAGTTTTTAAAATGA-ATTTGGA
1 AACA-TATATAATATATAGTTTTGAAAA-CATTTTTTGA
* **
47762 AACATATAAAATATA-ATGATTTTGAAAACA--TTTAAA
1 AACATATATAATATATA-G-TTTTGAAAACATTTTTTGA
47798 AACATATATAATATA
1 AACATATATAATATA
47813 GTTTTTCATT
Statistics
Matches: 429, Mismatches: 39, Indels: 56
0.82 0.07 0.11
Matches are distributed among these distances:
34 1 0.00
35 31 0.07
36 110 0.26
37 125 0.29
38 121 0.28
39 7 0.02
40 34 0.08
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
AACATATATAATATATAGTTTTGAAAACATTTTTTGA
Found at i:47386 original size:75 final size:75
Alignment explanation
Indices: 47281--47812 Score: 532
Period size: 75 Copynumber: 7.2 Consensus size: 75
47271 TAGTATATAT
47281 AACATATAT-A-ATATAGTTTTGAAAATATTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
1 AACATATATAATATATAGTTTTGAAAATATTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
47344 CATTTTTTGA
66 CATTTTTTGA
* * *
47354 AACATATATAATATATAGTTTTGAAAACATTTTTTGAAAACATATATAATTTATAGTTTTGAAAA
1 AACATATATAATATATAGTTTTGAAAATATTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
47419 CATTTTTTTGA
66 CA-TTTTTTGA
** ** * * *
47430 AATGTATATAATATATAGTTTTGAATTTTTTTTTTG-AAACATATATAACATATAGTTTTGAAAA
1 AACATATATAATATATAGTTTTGAAAATATTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
47494 CATTTTTTTTTGA
66 CA---TTTTTTGA
** *
47507 AATGTATATAATATATAGTTTTGAAAACATTTTTTTG-AAACGTATATAATATATAGTTTTGAAA
1 AACATATATAATATATAGTTTTGAAAATA-TTTTTTGAAAACGTATATAATATATAGTTTTGAAA
*
47571 ACATTTTTTTA
65 ACATTTTTTGA
* *
47582 AACATATATAATATATAGTTTTGAAAA-ATACTTTTGAAAAAG--TATAATATATAGTTTCT-AA
1 AACATATATAATATATAGTTTTGAAAATAT-TTTTTGAAAACGTATATAATATATAGTTT-TGAA
*
47643 AA-ATACTTTTGA
64 AACAT-TTTTTGA
* * *
47655 AA-ACATATAATATAT-GATTTTG-AAATTTTTTTTGAAAAC--AAATAATATATAGTTTT-AAA
1 AACATATATAATATATAG-TTTTGAAAATATTTTTTGAAAACGTATATAATATATAGTTTTGAAA
*
47714 AAATATTTTTGA
65 ACAT-TTTTTGA
* * * * *
47726 AA-ACT-TATAATATATAGTTTTTAAAATGA--ATTTGGAAACATATAAAATATA-ATGATTTTG
1 AACA-TATATAATATATAGTTTTGAAAAT-ATTTTTTGAAAACGTATATAATATATA-G-TTTTG
**
47786 AAAACA--TTTAAA
62 AAAACATTTTTTGA
47798 AACATATATAATATA
1 AACATATATAATATA
47813 GTTTTTCATT
Statistics
Matches: 394, Mismatches: 40, Indels: 50
0.81 0.08 0.10
Matches are distributed among these distances:
70 5 0.01
71 61 0.15
72 33 0.08
73 55 0.14
74 12 0.03
75 121 0.31
76 38 0.10
77 34 0.09
78 35 0.09
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (75 bp):
AACATATATAATATATAGTTTTGAAAATATTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
CATTTTTTGA
Found at i:47390 original size:13 final size:13
Alignment explanation
Indices: 47372--47396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47362 TAATATATAG
47372 TTTTGAAAACATT
1 TTTTGAAAACATT
47385 TTTTGAAAACAT
1 TTTTGAAAACAT
47397 ATATAATTTA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:47800 original size:107 final size:106
Alignment explanation
Indices: 47550--47817 Score: 269
Period size: 107 Copynumber: 2.5 Consensus size: 106
47540 TTTGAAACGT
** *
47550 ATATAATATAT-AGTTTTGAAA-ACATTTTTTTAAACATATATAATATATAGTTTTGAAAAATAC
1 ATATAATATATGA-TTTTGAAATACA--TTTAAAAACA-A-ATAATATATAGTTTTAAAAAATAC
*
47613 TTTTGAAAAAGTATAATATATAGTTTCTAAAAATACTTTTGAAAAC
61 TTTTGAAAAAGTATAATATATAGTTTCTAAAAATACATTTGAAAAC
*** * *
47659 ATATAATATATGATTTTGAAATTTTTTTTGAAAACAAATAATATATAGTTTTAAAAAATATTTTT
1 ATATAATATATGATTTTGAAA-TACATTTAAAAACAAATAATATATAGTTTTAAAAAATACTTTT
** * *
47724 GAAAACTTATAATATATAGTTT-TTAAAATGA-ATTTGGAAAC
65 GAAAAAGTATAATATATAGTTTCTAAAAAT-ACATTTGAAAAC
*
47765 ATATAAAATATAATGATTTTGAAA-ACATTTAAAAACATAT-ATAATATAGTTTT
1 ATAT--AATAT-ATGATTTTGAAATACATTTAAAAACAAATAAT-ATATAGTTTT
47818 TCATTATTAT
Statistics
Matches: 134, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
106 20 0.15
107 68 0.51
108 6 0.04
109 39 0.29
110 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (106 bp):
ATATAATATATGATTTTGAAATACATTTAAAAACAAATAATATATAGTTTTAAAAAATACTTTTG
AAAAAGTATAATATATAGTTTCTAAAAATACATTTGAAAAC
Found at i:47837 original size:21 final size:21
Alignment explanation
Indices: 47808--47859 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
47798 AACATATATA
*
47808 ATATAGTTTTTCATTA-TTATT
1 ATATAGTTTAT-ATTATTTATT
*
47829 ATATTGTTTATATTATTTATT
1 ATATAGTTTATATTATTTATT
*
47850 ATTTA-TTTAT
1 ATATAGTTTAT
47860 TTTTTTAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
ATATAGTTTATATTATTTATT
Found at i:47858 original size:20 final size:20
Alignment explanation
Indices: 47820--47859 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
47810 ATAGTTTTTC
*
47820 ATTATTATTATATTGTTTAT
1 ATTATTATTATATTATTTAT
47840 ATTATTTATTAT-TTATTTAT
1 ATTA-TTATTATATTATTTAT
47860 TTTTTTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTATTATTATATTATTTAT
Found at i:52434 original size:90 final size:89
Alignment explanation
Indices: 52282--52454 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 89
52272 ACACACCCTT
52282 TTATAGCCAAGTTACACTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACACTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
52347 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* * *
52371 TTATATCCAAGTTACCCTAAT-ATTATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATT
1 TTATAGCCAAGTTACACTAATCA-TATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATT
52435 TAATTAATTGAAATTAAATA
64 TAATTAATTGAAATTAAATA
52455 TTCATGATTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
88 1 0.01
89 26 0.34
90 50 0.65
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACACTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:59215 original size:90 final size:89
Alignment explanation
Indices: 59063--59235 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 89
59053 ACACACCCTT
59063 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAAGTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAAGTAATTAAATCTATATTTA
* *
59128 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
59152 TTATATCCAAGTTACCCTAATCATATT-GGAGATTTTATTATTTCAAATTAATTAAATCTATATT
1 TTATAGCCAAGTTACCCTAATCATATTAGG-G-TTTTATTATTTCAAAGTAATTAAATCTATATT
59216 TAATTAATTGAAATTAAATA
64 TAATTAATTGAAATTAAATA
59236 TTCTGTATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
88 2 0.03
89 27 0.35
90 49 0.63
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAAGTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:60232 original size:12 final size:12
Alignment explanation
Indices: 60215--60442 Score: 348
Period size: 12 Copynumber: 19.0 Consensus size: 12
60205 ATACTCTAAC
*
60215 ATATATATACAT
1 ATATATATATAT
*
60227 ATATATATACAT
1 ATATATATATAT
* *
60239 ATATGTATATAC
1 ATATATATATAT
60251 ATATATATATAT
1 ATATATATATAT
60263 ATATATATATAT
1 ATATATATATAT
*
60275 ATATATGTATAT
1 ATATATATATAT
*
60287 ATACATATATAT
1 ATATATATATAT
*
60299 ATATATATATAC
1 ATATATATATAT
60311 ATATATATATAT
1 ATATATATATAT
60323 ATATATATATAT
1 ATATATATATAT
*
60335 ATACATATATAT
1 ATATATATATAT
60347 ATATATATATAT
1 ATATATATATAT
*
60359 ATATATATACAT
1 ATATATATATAT
60371 ATATATATATAT
1 ATATATATATAT
60383 ATATATATATAT
1 ATATATATATAT
*
60395 ATACATATATAT
1 ATATATATATAT
*
60407 ATACATATATAT
1 ATATATATATAT
*
60419 ATATACATATAT
1 ATATATATATAT
60431 ATATATATATAT
1 ATATATATATAT
60443 GATCAACCAT
Statistics
Matches: 197, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 197 1.00
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (12 bp):
ATATATATATAT
Found at i:60234 original size:14 final size:14
Alignment explanation
Indices: 60215--60442 Score: 298
Period size: 14 Copynumber: 16.0 Consensus size: 14
60205 ATACTCTAAC
60215 ATATATATAC--AT
1 ATATATATACATAT
60227 ATATATATACATAT
1 ATATATATACATAT
*
60241 ATGTATATACATAT
1 ATATATATACATAT
*
60255 ATATATATATATAT
1 ATATATATACATAT
*
60269 ATATATATATATGTAT
1 ATATATATACA--TAT
*
60285 ATATACATATATATAT
1 ATAT--ATATACATAT
60301 ATATATATACATAT
1 ATATATATACATAT
*
60315 ATATATATATATAT
1 ATATATATACATAT
60329 ATATATATACATATAT
1 ATATATATAC--ATAT
*
60345 ATATATATATATAT
1 ATATATATACATAT
60359 ATATATATACATAT
1 ATATATATACATAT
*
60373 ATATATATATATAT
1 ATATATATACATAT
* *
60387 ATATATATATACAT
1 ATATATATACATAT
60401 ATATATATACATAT
1 ATATATATACATAT
60415 ATATATATACATAT
1 ATATATATACATAT
*
60429 ATATATATATATAT
1 ATATATATACATAT
60443 GATCAACCAT
Statistics
Matches: 195, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
12 10 0.05
14 151 0.77
16 27 0.14
18 7 0.04
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:60253 original size:26 final size:26
Alignment explanation
Indices: 60215--60442 Score: 348
Period size: 26 Copynumber: 8.8 Consensus size: 26
60205 ATACTCTAAC
* *
60215 ATATATATACATATATATATACATAT
1 ATATATATATATATATATATATATAT
* *
60241 ATGTATATACATATATATATATATAT
1 ATATATATATATATATATATATATAT
* *
60267 ATATATATATATATGTATATATACAT
1 ATATATATATATATATATATATATAT
*
60293 ATATATATATATATATACATATATAT
1 ATATATATATATATATATATATATAT
*
60319 ATATATATATATATATATACATATAT
1 ATATATATATATATATATATATATAT
*
60345 ATATATATATATATATATATATACAT
1 ATATATATATATATATATATATATAT
60371 ATATATATATATATATATATATATAT
1 ATATATATATATATATATATATATAT
* *
60397 ACATATATATATACATATATATATAT
1 ATATATATATATATATATATATATAT
*
60423 ACATATATATATATATATAT
1 ATATATATATATATATATAT
60443 GATCAACCAT
Statistics
Matches: 185, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 185 1.00
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (26 bp):
ATATATATATATATATATATATATAT
Found at i:60259 original size:30 final size:30
Alignment explanation
Indices: 60215--60442 Score: 352
Period size: 30 Copynumber: 7.7 Consensus size: 30
60205 ATACTCTAAC
* * * *
60215 ATATATATACATATATATATACATATATGT
1 ATATACATATATATATATATATATATATAT
60245 ATATACATATATATATATATATATATATAT
1 ATATACATATATATATATATATATATATAT
** *
60275 ATATATGTATATATACATATATATATATAT
1 ATATACATATATATATATATATATATATAT
60305 ATATAC--ATATATATATATATATATATAT
1 ATATACATATATATATATATATATATATAT
60333 ATATACATATATATATATATATATATATAT
1 ATATACATATATATATATATATATATATAT
60363 ATATACATATATATATATATATATATATAT
1 ATATACATATATATATATATATATATATAT
*
60393 ATATACATATATATATACATATATATATAT
1 ATATACATATATATATATATATATATATAT
* *
60423 ACATATATATATATATATAT
1 ATATACATATATATATATAT
60443 GATCAACCAT
Statistics
Matches: 183, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
28 27 0.15
30 156 0.85
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATACATATATATATATATATATATATAT
Found at i:64970 original size:3 final size:3
Alignment explanation
Indices: 64956--65012 Score: 80
Period size: 3 Copynumber: 18.3 Consensus size: 3
64946 TGTAAAACAC
64956 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
65002 AATT AAT AAT A
1 AA-T AAT AAT A
65013 TTTTTTCGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 1 0.02
3 42 0.84
4 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:65538 original size:44 final size:44
Alignment explanation
Indices: 65363--65682 Score: 178
Period size: 44 Copynumber: 7.6 Consensus size: 44
65353 GTCAGGGATG
* * * *
65363 ACACTACTAATACTATGATGAATCTTGACCGTCTAAGGGTGATA
1 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
* ** * *
65407 ACACTGCTCAAACTATGATGAATCTTGGTTATC-CAGGGT--TC
1 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
* * * * *
65448 ACACGGCTCCTACGTAATGAGGAGATC-TAG---TC--AGGG-GATG
1 ACACTGCTCATAC-T-ATGATGA-ATCTTGGCCATCTAAGGGTGATA
*
65488 ACACTGCACATACTATGATGAATCTTGGCCATCTAAGGGTGATA
1 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
* * ** * * *
65532 ACACTGCTCATACTATGATGAGTCTCGGTTATCCAA-AGT--TG
1 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
* * * *
65573 ACAC-GACTCCTACGTGATGAGGAGATC-AGG---TC---GGGTGATG
1 ACACTG-CTCATAC-T-ATGATGA-ATCTTGGCCATCTAAGGGTGATA
65613 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
1 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
* *
65657 ATATTGCTCATACTATGATGAATCTT
1 ACACTGCTCATACTATGATGAATCTT
65683 ACTTATCCAG
Statistics
Matches: 209, Mismatches: 40, Indels: 54
0.69 0.13 0.18
Matches are distributed among these distances:
37 6 0.03
38 18 0.09
39 6 0.03
40 28 0.13
41 27 0.13
42 2 0.01
43 27 0.13
44 95 0.45
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
Found at i:65538 original size:125 final size:124
Alignment explanation
Indices: 65188--65772 Score: 717
Period size: 125 Copynumber: 4.7 Consensus size: 124
65178 CGGGTTGTCT
* * * * * * **
65188 AAGGGTGACACAGCTCCTACGTGACGAGGAGATCTGGTTATGGGATGACATTGCTCATA-TGCGA
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTAGTCA-GGGATGACACTGCTCATACTATGA
* * *
65252 TGAGTCTTGGCCATCTTTAGGAAGGGTGATAAAACTGCTCATACTATGATGAATCCTGGTTATCC
65 TGAATCTTGGCCATC--T---AAGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCC
* * * * * *
65317 AAGGTTGACACGGTTCCTCCGTGATGAGAAAATC-AGGTCAGGGATGACACTACTAATACTATGA
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTA-GTCAGGGATGACACTGCTCATACTATGA
* * *
65381 TGAATCTTGACCGTCTAAGGGTGATAACACTGCTCAAACTATGATGAATCTTGGTTATCC
65 TGAATCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCC
* * * *
65441 AGGGTTCACACGGCTCCTACGTAATGAGGAGATCTAGTCAGGGGATGACACTGCACATACTATGA
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTAGTCA-GGGATGACACTGCTCATACTATGA
* *
65506 TGAATCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAGTCTCGGTTATCC
65 TGAATCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCC
* * *
65566 AAAGTTGACACGACTCCTACGTGATGAGGAGATC-AGGTCGGGTGATGACACTGCTCATACTATG
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTA-GTCAGG-GATGACACTGCTCATACTATG
* * **
65630 ATGAATCTTGGCCATCTAAGGGTGATAATATTGCTCATACTATGATGAATCTTACTTATCC
64 ATGAATCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCC
* ** * *
65691 AGGGTTGACATAGCTCCTACGTGATGAGGAGATATGGTCAGGGATGACACTGCTCATACTATGAT
1 AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTAGTCAGGGATGACACTGCTCATACTATGAT
65756 GAATCTTGGCCATCTAA
66 GAATCTTGGCCATCTAA
65773 AGATTTTGAT
Statistics
Matches: 393, Mismatches: 56, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
124 115 0.29
125 217 0.55
127 1 0.00
128 15 0.04
129 45 0.11
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (124 bp):
AAGGTTGACACGGCTCCTACGTGATGAGGAGATCTAGTCAGGGATGACACTGCTCATACTATGAT
GAATCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTATCC
Found at i:65740 original size:249 final size:249
Alignment explanation
Indices: 65189--65772 Score: 789
Period size: 249 Copynumber: 2.3 Consensus size: 249
65179 GGGTTGTCTA
* * * * **
65189 AGGG-TGACACAGCTCCTACGTGACGAGGAGATCTGGTTATGGGATGACATTGCTCATA-TGCGA
1 AGGGTTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACTATGA
*
65252 TGAGTCTTGGCCATCTTTAGGAAGGGTGATAAAACTGCTCATACTATGATGAATCCTGGTTATCC
66 TGAATCTTGGCCATC--T---AAGGGTGATAAAACTGCTCATACTATGATGAATCCTGGTTATCC
* ** *
65317 AAGGTTGACACGGTTCCTCCGTGATGAGAAAATCAGGTCAGGGATGACACTACTAATACTATGAT
126 AAAGTTGACACGACTCCTACGTGATGAGAAAATCAGGTCAGGGATGACACTACTAATACTATGAT
* **
65382 GAATCTTGACCGTCTAAGGGTGATAACACTGCTCAAACTATGATGAATCTTGGTTATCC
191 GAATCTTGACCATCTAAGGGTGATAACACTGCTCAAACTATGATGAATCTTACTTATCC
* * * * *
65441 AGGGTTCACACGGCTCCTACGTAATGAGGAGATCTAGTCAGGGGATGACACTGCACATACTATGA
1 AGGGTTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACTATGA
* *
65506 TGAATCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAGT-CTCGGTTATCCAAAG
66 TGAATCTTGGCCATCTAAGGGTGATAAAACTGCTCATACTATGATGAATCCT-GGTTATCCAAAG
* * * * *
65570 TTGACACGACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACTGCTCATACTATGATGAA
130 TTGACACGACTCCTACGTGATGAGAAAATCAGGTCAGG-GATGACACTACTAATACTATGATGAA
* * * *
65635 TCTTGGCCATCTAAGGGTGATAATATTGCTCATACTATGATGAATCTTACTTATCC
194 TCTTGACCATCTAAGGGTGATAACACTGCTCAAACTATGATGAATCTTACTTATCC
* *
65691 AGGGTTGACATAGCTCCTACGTGATGAGGAGATATGGTCA-GGGATGACACTGCTCATACTATGA
1 AGGGTTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACTATGA
65755 TGAATCTTGGCCATCTAA
66 TGAATCTTGGCCATCTAA
65773 AGATTTTGAT
Statistics
Matches: 291, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
248 2 0.01
249 115 0.40
250 107 0.37
252 5 0.02
253 45 0.15
254 17 0.06
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (249 bp):
AGGGTTGACACAGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACTATGA
TGAATCTTGGCCATCTAAGGGTGATAAAACTGCTCATACTATGATGAATCCTGGTTATCCAAAGT
TGACACGACTCCTACGTGATGAGAAAATCAGGTCAGGGATGACACTACTAATACTATGATGAATC
TTGACCATCTAAGGGTGATAACACTGCTCAAACTATGATGAATCTTACTTATCC
Found at i:72156 original size:293 final size:284
Alignment explanation
Indices: 71637--72212 Score: 843
Period size: 293 Copynumber: 2.0 Consensus size: 284
71627 TTTTGATGGG
*
71637 ATTTGGGTGGGATTTAGTGAATGATTTGCTTTGTTTTTAATGGATTTGTTTGCAGGTGGATGATG
1 ATTTGGGTGGGATTTAGTGAATGATTTGCTTTGTTTTTAATGGATTTGTTTGCAAGTGGATGATG
** * * *
71702 ACGATGGTGGCTCGGCGGTTGACTCACACGTTGGTGAAATTGAGCGGTGATGTGCACACGCGCTA
66 ACGATGGTGGCTCGGCGGCAGACTCACACGCTGGTGAAACTGAGCGGTGATGTGCACACGCGCCA
* * * *
71767 ATGGAAGTTGGAGGGTTGTTGGCGGTCGGTTCGATGTAATCGGGTCAGAGTTGGATTCGAATTTA
131 ATGAAAATTGGAGGGTTGTTGGCGGTCGGTTCGATGTAATCGGGTCAGAGTTGGATCCAAATTTA
*
71832 GGCCGAAACCGGGTCTTCAGACTAGCTGTTGGGTCTTGTAAATTTGGGTCCAACTTCGGGCCTAC
196 GGCCGAAACCGGGTCTTCAGACTAACTGTTGGGTCTTGTAAATTTGGGTCCAACTTCGGGCCTAC
*
71897 AAAACATAAATGTAAAATGCAATA
261 AAAACATAAATGTAAAACGCAATA
*
71921 ATTTGGGTGGGATTTAGTTAATGATTTGCTTTGTTTTTTTAATGGATTTGTTTGCAAGTGGATGA
1 ATTTGGGTGGGATTTAGTGAATGATTTGCTTTG--TTTTTAATGGATTTGTTTGCAAGTGGATGA
* *
71986 TGACGATGGTGGCTCGGTAGCTCGGCAGACGGCTCACGCGCT-GTGGAACTGAGCGGTGATGTGC
64 TGACGATGGTGGCTC-G--G--CGGCAGA---CTCACACGCTGGTGAAACTGAGCGGTGATGTGC
* *
72050 ACACGCGCCAATGAAAATTGGAGGGTTGTTGGTGGTTGGTTCGATGTAATCGGGTCAGAGTTGGA
121 ACACGCGCCAATGAAAATTGGAGGGTTGTTGGCGGTCGGTTCGATGTAATCGGGTCAGAGTTGGA
* *
72115 TCCAAATTT-GGCCCGAAATCC-GGTCTTCGGGCTAACTGTTGGGTCTTGTAAATTTGGGTCCAA
186 TCCAAATTTAGG-CCGAAA-CCGGGTCTTCAGACTAACTGTTGGGTCTTGTAAATTTGGGTCCAA
*
72178 CTTTGGGCCTACAAAACATAAATGTAAAACGCAAT
249 CTTCGGGCCTACAAAACATAAATGTAAAACGCAAT
72213 TAATAATAAT
Statistics
Matches: 260, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
284 32 0.12
286 44 0.17
287 1 0.00
289 1 0.00
291 5 0.02
292 2 0.01
293 165 0.63
294 10 0.04
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (284 bp):
ATTTGGGTGGGATTTAGTGAATGATTTGCTTTGTTTTTAATGGATTTGTTTGCAAGTGGATGATG
ACGATGGTGGCTCGGCGGCAGACTCACACGCTGGTGAAACTGAGCGGTGATGTGCACACGCGCCA
ATGAAAATTGGAGGGTTGTTGGCGGTCGGTTCGATGTAATCGGGTCAGAGTTGGATCCAAATTTA
GGCCGAAACCGGGTCTTCAGACTAACTGTTGGGTCTTGTAAATTTGGGTCCAACTTCGGGCCTAC
AAAACATAAATGTAAAACGCAATA
Found at i:72468 original size:7 final size:7
Alignment explanation
Indices: 72456--72480 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
72446 AAAGGAACTG
72456 TTTGGTA
1 TTTGGTA
72463 TTTGGTA
1 TTTGGTA
72470 TTTGGTA
1 TTTGGTA
72477 TTTG
1 TTTG
72481 TCCTAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TTTGGTA
Found at i:73062 original size:25 final size:25
Alignment explanation
Indices: 73009--73065 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
72999 TGCACATCAT
* * *
73009 CTTTAATCTCTTACATAACAGACAA
1 CTTTCATCTCTTACACAACACACAA
**
73034 CTTTCATCTCTTACACAACACACTC
1 CTTTCATCTCTTACACAACACACAA
73059 CTTTCAT
1 CTTTCAT
73066 ATTCAATCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.35
Consensus pattern (25 bp):
CTTTCATCTCTTACACAACACACAA
Found at i:73084 original size:32 final size:32
Alignment explanation
Indices: 73039--73163 Score: 214
Period size: 32 Copynumber: 3.9 Consensus size: 32
73029 GACAACTTTC
* * *
73039 ATCTCTTACACAACACACTCCTTTCATATTCA
1 ATCTCTTATACAACAAACTCCTTTCATCTTCA
*
73071 ATCTCTTATACAACACACTCCTTTCATCTTCA
1 ATCTCTTATACAACAAACTCCTTTCATCTTCA
73103 ATCTCTTATACAACAAACTCCTTTCATCTTCA
1 ATCTCTTATACAACAAACTCCTTTCATCTTCA
73135 ATCTCTTATACAACAAACTCCTTTCATCT
1 ATCTCTTATACAACAAACTCCTTTCATCT
73164 AACCAAAAAC
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 90 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (32 bp):
ATCTCTTATACAACAAACTCCTTTCATCTTCA
Done.