Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004110.1 Hibiscus syriacus cultivar Beakdansim tig00008995_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: 117943
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2347 original size:15 final size:16
Alignment explanation
Indices: 2322--2352 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2312 TGAGAAAATT
2322 TTAATTTTAATTTTAA
1 TTAATTTTAATTTTAA
2338 TTAA-TTTAATTTTAA
1 TTAATTTTAATTTTAA
2353 AATAACGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTTAATTTTAA
Found at i:2887 original size:36 final size:36
Alignment explanation
Indices: 2838--2925 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
2828 GACGTAAACT
* * *
2838 AAACCAAGAAACAATGGACCATCTTCATCCAAGACC
1 AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
2874 AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
1 AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
*
2910 AAATCGAGCAACAATG
1 AAACCGAGCAACAATG
2926 CAGGATCTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.44, C:0.28, G:0.14, T:0.14
Consensus pattern (36 bp):
AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
Found at i:2990 original size:36 final size:35
Alignment explanation
Indices: 2940--3059 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 35
2930 ATCTACGCTC
* *
2940 AGGCTGAACCAAGCAGCAATGCACCACCTCGATCCA
1 AGGCTAAACCAAGCA-CAATGCACCACCTCCATCCA
* * * **
2976 ACGCTAACCCAAGCAACAATCCACCACCTCCATTAA
1 AGGCTAAACCAAGC-ACAATGCACCACCTCCATCCA
* *
3012 AGGTTAAACCAAGCACTAATGCACCATCTCCATCCA
1 AGGCTAAACCAAGCAC-AATGCACCACCTCCATCCA
3048 AGGCTAAACCAA
1 AGGCTAAACCAA
3060 TCATTAATCG
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
35 2 0.03
36 64 0.96
37 1 0.01
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.14
Consensus pattern (35 bp):
AGGCTAAACCAAGCACAATGCACCACCTCCATCCA
Found at i:3074 original size:36 final size:36
Alignment explanation
Indices: 2978--3076 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 36
2968 TCGATCCAAC
* * * *
2978 GCTAACCCAAGCAAC-AATCCACCACCTCCATTAAAG
1 GCTAAACCAAGC-ACTAATCGACCATCTCCATCAAAG
* *
3014 GTTAAACCAAGCACTAAT-GCACCATCTCCATCCAAG
1 GCTAAACCAAGCACTAATCG-ACCATCTCCATCAAAG
* *
3050 GCTAAACCAATCATTAATCGACCATCT
1 GCTAAACCAAGCACTAATCGACCATCT
3077 GAAGCTCCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
35 2 0.04
36 48 0.94
37 1 0.02
ACGTcount: A:0.37, C:0.34, G:0.09, T:0.19
Consensus pattern (36 bp):
GCTAAACCAAGCACTAATCGACCATCTCCATCAAAG
Found at i:5845 original size:5 final size:5
Alignment explanation
Indices: 5837--5862 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5827 GGGGCCTTCT
5837 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
5863 GTGATAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:11526 original size:20 final size:20
Alignment explanation
Indices: 11503--11566 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
11493 TAGTATTTAG
11503 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
11523 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
11543 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
11562 TTAAA
1 ATAAA
11567 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:11536 original size:19 final size:20
Alignment explanation
Indices: 11512--11561 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11502 GATAAATTTA
*
11512 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
11531 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
11552 TT-ATAATTTT
1 TTAATAATTTT
11562 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:11564 original size:31 final size:30
Alignment explanation
Indices: 11479--11565 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
11469 TTCGATAATA
* *
11479 TAATAACTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
11510 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
11541 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
11566 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:11840 original size:4 final size:4
Alignment explanation
Indices: 11831--11855 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
11821 CTTTATACAG
11831 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
11856 TAATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:12324 original size:31 final size:30
Alignment explanation
Indices: 12289--12375 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
12279 TCAATAAAGT
*
12289 TTAAAAAACTATAAAATACTTATTAACTTTA
1 TTAAAAAACTATAAAATA-TTATTAAATTTA
* * *
12320 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAACTATAAAA-TATTATTAAATTTA
*
12351 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAACTATAAAAT-ATTATTA
12376 TATTATCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAAACTATAAAATATTATTAAATTTA
Found at i:16703 original size:36 final size:35
Alignment explanation
Indices: 16663--16853 Score: 111
Period size: 37 Copynumber: 5.2 Consensus size: 35
16653 CCCTCAAAAT
16663 ACAAATTTTATCTCACTTGAAATAGTTTTCCTTAAA
1 ACAAATTTTATCTCACTTGAAATA-TTTTCCTTAAA
* * * *
16699 ACAAAATTTGTCTCATTTGAGACA-ATTTCTCTTTAAA
1 ACAAATTTTATCTCACTTGA-A-ATATTT-TCCTTAAA
* * * * *
16736 CAAAAAATTTATCTTACTTGAGATAGTTTTCCTCAAAA
1 -ACAAATTTTATCTCACTTGAAATA-TTTTCCT-TAAA
* * *
16774 ACAAA-TTTAGTCTCACTTGAGAA-AATCTCATTGAAA
1 ACAAATTTTA-TCTCACTTGA-AATATTTTCCTT-AAA
* * *
16810 CAAAAATTATATCTCACTTAAAATATTTTCCCTTAAA
1 -ACAAATTTTATCTCACTTGAAATATTTT-CCTTAAA
16847 A-AAATTT
1 ACAAATTT
16854 GTCTCACACG
Statistics
Matches: 116, Mismatches: 25, Indels: 29
0.68 0.15 0.17
Matches are distributed among these distances:
35 5 0.04
36 35 0.30
37 46 0.40
38 30 0.26
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (35 bp):
ACAAATTTTATCTCACTTGAAATATTTTCCTTAAA
Found at i:16707 original size:37 final size:36
Alignment explanation
Indices: 16669--16847 Score: 130
Period size: 36 Copynumber: 4.8 Consensus size: 36
16659 AAATACAAAT
16669 TTTATCTCACTTGAAATAGTTTTCCTTAAAAC-AAAA
1 TTTATCTCACTTGAAATA-TTTTCCTTAAAACAAAAA
* * * * * *
16705 TTTGTCTCATTTGAGACAATTTCTCTTTAAACAAAAAA
1 TTTATCTCACTTGAAATATTTTC-CTTAAAAC-AAAAA
* * * *
16743 TTTATCTTACTTGAGATAGTTTTCCTCAAAA-ACAAA
1 TTTATCTCACTTGAAATA-TTTTCCTTAAAACAAAAA
* * * *
16779 TTTAGTCTCACTTGAGAA-AATCTCATTGAAACAAAAA
1 TTTA-TCTCACTTGA-AATATTTTCCTTAAAACAAAAA
*
16816 TTATATCTCACTTAAAATATTTTCCCTTAAAA
1 TT-TATCTCACTTGAAATATTTT-CCTTAAAA
16848 AAATTTGTCT
Statistics
Matches: 106, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
35 4 0.04
36 38 0.36
37 28 0.26
38 32 0.30
39 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (36 bp):
TTTATCTCACTTGAAATATTTTCCTTAAAACAAAAA
Found at i:16764 original size:74 final size:70
Alignment explanation
Indices: 16669--17007 Score: 306
Period size: 72 Copynumber: 4.7 Consensus size: 70
16659 AAATACAAAT
* * * **
16669 TTTATCTCACTTGAAATAGTTTTCCTTAAAACAAAATTTGTCTCATTTGAGACAATTTCTCTTTA
1 TTTATCTCACTTGAGATA-TTTTCCTT-AAA-AAAATTTGTCTCACTCGAGACAATTTCTCTCGA
16734 AACAAAAAA
63 AAC-AAAAA
* * * * *
16743 TTTATCTTACTTGAGATAGTTTTCCTCAAAAACAAATTTAGTCTCACTTGAGA-AA-ATCTCATT
1 TTTATCTCACTTGAGATA-TTTTCCT-TAAAA-AAATTT-GTCTCACTCGAGACAATTTCTC-TC
16806 GAAACAAAAA
61 GAAACAAAAA
* * * *
16816 TTATATCTCACTTAAAATATTTTCCCTTAAAAAAATTTGTCTCACACGAGACAATTTCTCACGAA
1 TT-TATCTCACTTGAGATATTTT-CCTTAAAAAAATTTGTCTCACTCGAGACAATTTCTCTCGAA
16881 ACAAAAA
64 ACAAAAA
* * ** * *
16888 TTGCATCTCACTTGAGATATTTTCTCTTGAAAATGTTTGTCTAACTCGAGACAGTTTCTCTCGAA
1 TT-TATCTCACTTGAGATATTTTC-CTTAAAAAAATTTGTCTCACTCGAGACAATTTCTCTCGAA
16953 AC-AAAA
64 ACAAAAA
** **
16959 TTTCATCTCACTTGAGATATTTTCCCTTGCAAATTTTTGTCTCACTCGA
1 TTT-ATCTCACTTGAGATATTTT-CCTTAAAAAAATTTGTCTCACTCGA
17008 AATAGTTTTT
Statistics
Matches: 224, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
71 58 0.26
72 73 0.33
73 24 0.11
74 57 0.25
75 12 0.05
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (70 bp):
TTTATCTCACTTGAGATATTTTCCTTAAAAAAATTTGTCTCACTCGAGACAATTTCTCTCGAAAC
AAAAA
Found at i:16998 original size:71 final size:72
Alignment explanation
Indices: 16806--17060 Score: 293
Period size: 72 Copynumber: 3.6 Consensus size: 72
16796 AAATCTCATT
** * * * * * *
16806 GAAACAAAAATTATATCTCACTTAAAATATTTTCCCTTAAAAAAATTTGTCTCACACGAGACAAT
1 GAAACAAAAATTGCATCTCACTTGAGATATTTTCCCTTGAAAATATTTGTCTCACTCGAGACAGT
*
16871 TTCTCAC
66 TTCTCTC
* * *
16878 GAAACAAAAATTGCATCTCACTTGAGATATTTTCTCTTGAAAATGTTTGTCTAACTCGAGACAGT
1 GAAACAAAAATTGCATCTCACTTGAGATATTTTCCCTTGAAAATATTTGTCTCACTCGAGACAGT
16943 TTCTCTC
66 TTCTCTC
* * * * *
16950 GAAAC-AAAATTTCATCTCACTTGAGATATTTTCCCTTGCAAATTTTTGTCTCACTCGAAATAGT
1 GAAACAAAAATTGCATCTCACTTGAGATATTTTCCCTTGAAAATATTTGTCTCACTCGAGACAGT
* *
17014 TTTTCTT
66 TTCTCTC
* *
17021 GATAC---AATTGCATCTCACTTGAGATATTTTCTCTTGAAAA
1 GAAACAAAAATTGCATCTCACTTGAGATATTTTCCCTTGAAAA
17061 CATCATCTCA
Statistics
Matches: 158, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
69 32 0.20
71 61 0.39
72 65 0.41
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (72 bp):
GAAACAAAAATTGCATCTCACTTGAGATATTTTCCCTTGAAAATATTTGTCTCACTCGAGACAGT
TTCTCTC
Found at i:17003 original size:34 final size:34
Alignment explanation
Indices: 16893--17056 Score: 107
Period size: 34 Copynumber: 4.7 Consensus size: 34
16883 AAAAATTGCA
* *
16893 TCTCACTTGAGATATTTTCTCTTGAAAATGTTTG
1 TCTCACTTGAGATATTTTCTCTTGCAAATTTTTG
* * * * * * **
16927 TCTAACTCGAGACAGTTTCTCTCGAAACAAAATTTCA
1 TCTCACTTGAGATATTTTCTCTTG---CAAATTTTTG
*
16964 TCTCACTTGAGATATTTTCCCTTGCAAATTTTTG
1 TCTCACTTGAGATATTTTCTCTTGCAAATTTTTG
* * * ***
16998 TCTCACTCGAAATAGTTTT-TCTTG-ATACAATTGCA
1 TCTCACTTGAGATA-TTTTCTCTTGCA-A-ATTTTTG
17033 TCTCACTTGAGATATTTTCTCTTG
1 TCTCACTTGAGATATTTTCTCTTG
17057 AAAACATCAT
Statistics
Matches: 95, Mismatches: 28, Indels: 13
0.70 0.21 0.10
Matches are distributed among these distances:
33 1 0.01
34 47 0.49
35 24 0.25
37 23 0.24
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (34 bp):
TCTCACTTGAGATATTTTCTCTTGCAAATTTTTG
Found at i:27919 original size:12 final size:12
Alignment explanation
Indices: 27903--27943 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
27893 TCATAATCTT
27903 ATTTTTAATTT-
1 ATTTTTAATTTC
27914 ATTTTTAATTTC
1 ATTTTTAATTTC
27926 ATTTTTAATTTC
1 ATTTTTAATTTC
27938 ATTTTT
1 ATTTTT
27944 CCTTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTAATTTC
Found at i:28022 original size:25 final size:25
Alignment explanation
Indices: 27989--28038 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27979 TTTATTTTCT
27989 TTTCATTTTTACCATAACTAAACAC
1 TTTCATTTTTACCATAACTAAACAC
28014 TTTCATTTTTACCATAACTAAACAC
1 TTTCATTTTTACCATAACTAAACAC
28039 GTTGTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTCATTTTTACCATAACTAAACAC
Found at i:28053 original size:23 final size:24
Alignment explanation
Indices: 27995--28053 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
27985 TTCTTTTCAT
* *
27995 TTTTACCATAACTAAACACTTTCAT
1 TTTTACCATAACTAAACACGTT-AG
28020 TTTTACCATAACTAAACACGTT-G
1 TTTTACCATAACTAAACACGTTAG
*
28043 TTTTACTATAA
1 TTTTACCATAA
28054 GTTTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 10 0.32
25 21 0.68
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTTACCATAACTAAACACGTTAG
Found at i:33173 original size:21 final size:20
Alignment explanation
Indices: 33087--33244 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
33077 AAATGACCAA
**
33087 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
33106 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
33126 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
33146 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
33167 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
33188 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
33208 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
33229 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
33245 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:33235 original size:20 final size:20
Alignment explanation
Indices: 33211--33404 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
33201 CGATTTTCCA
** *
33211 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
33231 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
33251 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
33271 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
33291 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
33311 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
33331 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
33351 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
33371 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
33391 AAATCGCAACGCGA
1 AAATCGCAACGCGA
33405 TATTTTAAAG
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:33825 original size:33 final size:33
Alignment explanation
Indices: 33786--33856 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
33776 TTCACTTAGA
* *
33786 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
33819 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
33852 TTTCA
1 TTTCA
33857 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:33993 original size:41 final size:38
Alignment explanation
Indices: 33929--34045 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
33919 TTCAATTTGC
* *
33929 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
33967 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
34008 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
34041 AGAAT
1 AGAAT
34046 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:34009 original size:21 final size:21
Alignment explanation
Indices: 33936--34011 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
33926 TGCAGAAGAG
* *
33936 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
33957 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
33977 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
33998 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
34012 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:34015 original size:14 final size:14
Alignment explanation
Indices: 33996--34052 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
33986 GAGAAATGAC
33996 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
34010 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
34029 AATCGCAACGAGAG
1 AATCGCAACGAGAG
34043 AATCGCAACG
1 AATCGCAACG
34053 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:34033 original size:33 final size:33
Alignment explanation
Indices: 33988--34068 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
33978 CGCAACGAGA
*
33988 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34021 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
34054 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
34069 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:35208 original size:19 final size:19
Alignment explanation
Indices: 35184--35283 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
35174 AAAATTGACT
*
35184 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35203 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
35222 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35236 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35255 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
35275 ATCGCAATG
1 ATCGCAATG
35284 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35313 original size:53 final size:53
Alignment explanation
Indices: 35184--35300 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
35174 AAAATTGACT
*
35184 ATCGCAATGTGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
35236 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35289 ATCGCAATGCGA
1 ATCGCAATGCGA
35301 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 28 0.46
53 33 0.54
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:35318 original size:19 final size:19
Alignment explanation
Indices: 35290--35457 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
35280 AATGGGAGAA
* *
35290 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
35309 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
35325 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35342 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35361 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
35380 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
35396 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
35413 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
35429 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35446 TCCGCATTGCGA
1 T-CGCATTGCGA
35458 AATGTAATGG
Statistics
Matches: 126, Mismatches: 7, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 19 0.15
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:35333 original size:33 final size:33
Alignment explanation
Indices: 35296--35457 Score: 234
Period size: 33 Copynumber: 4.7 Consensus size: 33
35286 AGAATCGCAA
*
35296 TGCGATTTTAATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
35329 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG--T
*
35367 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
35400 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
35433 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
35458 AATGTAATGG
Statistics
Matches: 119, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
33 71 0.60
34 10 0.08
35 6 0.05
36 7 0.06
38 25 0.21
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:35371 original size:71 final size:68
Alignment explanation
Indices: 35290--35457 Score: 250
Period size: 71 Copynumber: 2.4 Consensus size: 68
35280 AATGGGAGAA
* *
35290 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGA--
*
35355 TTCATT
64 TTC-TC
*
35361 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
35426 CTC
66 CTC
35429 TCG--TTGCGATTTTCATTTCCGCATTGCGA
1 TCGCATTGCGATTTTCATTT-CGCATTGCGA
35458 AATGTAATGG
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
66 15 0.16
67 10 0.11
68 4 0.04
69 3 0.03
71 60 0.65
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (68 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
CTC
Found at i:35404 original size:14 final size:14
Alignment explanation
Indices: 35385--35439 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
35375 TCATTTCGCA
35385 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
35399 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
35416 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
35432 TTGCGATT
1 TTGCGATT
35440 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:35540 original size:19 final size:19
Alignment explanation
Indices: 35516--35614 Score: 100
Period size: 20 Copynumber: 5.4 Consensus size: 19
35506 AAAATTGACT
35516 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
** * *
35535 ATCGCAACACGGAAATTACA
1 ATCGCAATGC-GAAATGAAA
*
35555 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35569 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35588 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
35608 ATCGCAA
1 ATCGCAA
35615 CGAGAGAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 1 0.02
18 2 0.03
19 21 0.32
20 30 0.45
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35646 original size:53 final size:53
Alignment explanation
Indices: 35516--35633 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
35506 AAAATTGACT
** * *
35516 ATCGCAATGCGAAATGAAAATCGCAACACGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35569 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35622 ATCGCAATGCGA
1 ATCGCAATGCGA
35634 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:37969 original size:12 final size:12
Alignment explanation
Indices: 37952--37976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37942 TCTTCGGGGA
37952 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37964 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37976 C
1 C
37977 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:38185 original size:24 final size:24
Alignment explanation
Indices: 38151--38197 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38141 CTGAAACATC
38151 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
38175 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
38198 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:39130 original size:20 final size:20
Alignment explanation
Indices: 38880--39129 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
38870 AAATTTCAGT
* * *
38880 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38900 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
38920 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38940 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
38960 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
38980 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
39000 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
39020 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
39040 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
39060 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
39080 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
39100 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
39120 GTTGCGATTT
1 GTTGCGATTT
39130 TGTTGGTCAT
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:39596 original size:60 final size:61
Alignment explanation
Indices: 39486--39635 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 61
39476 ATTATGTCTC
* * * ** * * *
39486 TCATTTTAAATTGGTTCTTAAATTTTTAAATATTTTAACTTCTTCTTCAAACTATGA-TAT
1 TCATTCTAAATTGGTCCTTAAACTTTTAAATATTCCAACTTCATCCTCAAACTATAACTAT
* * *
39546 TCATTCTAAATTAGTCCTTAAACTTTTAAATATTCCAA-TTGCATCCTCAAATTATAACTCT
1 TCATTCTAAATTGGTCCTTAAACTTTTAAATATTCCAACTT-CATCCTCAAACTATAACTAT
*
39607 T-ATTCTAAATTGGTCCCTAAACTTTTAAA
1 TCATTCTAAATTGGTCCTTAAACTTTTAAA
39636 CCTTTCAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.03
60 70 0.93
61 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (61 bp):
TCATTCTAAATTGGTCCTTAAACTTTTAAATATTCCAACTTCATCCTCAAACTATAACTAT
Found at i:46744 original size:3 final size:3
Alignment explanation
Indices: 46732--46763 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
46722 CAAAACATTT
46732 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46764 AACGTTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56289 original size:27 final size:27
Alignment explanation
Indices: 56232--56290 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
56222 CCACCGCCAT
* * * *
56232 CATCACTTTGAACTTGAAACTTCATAG
1 CATCACCTTGAACTTGAAACTCCACAA
* *
56259 CATCACCTTGGACTTGAAAGTCCACAA
1 CATCACCTTGAACTTGAAACTCCACAA
56286 CATCA
1 CATCA
56291 AGATCTTCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (27 bp):
CATCACCTTGAACTTGAAACTCCACAA
Found at i:61857 original size:21 final size:21
Alignment explanation
Indices: 61831--61872 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
61821 TAATAGCCAA
61831 GCTTACCTTTTGTTCTAAAGG
1 GCTTACCTTTTGTTCTAAAGG
61852 GCTTACCTTTTGTTCTAAAGG
1 GCTTACCTTTTGTTCTAAAGG
61873 TTTTTAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (21 bp):
GCTTACCTTTTGTTCTAAAGG
Found at i:70115 original size:36 final size:36
Alignment explanation
Indices: 70054--70141 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
70044 TGAAAATACG
* *
70054 TATATGATATATAG-TTTTAAAACATTTTTTG-AAAC
1 TATATAATATATAGTTTTTAAAACA-TTTTCGAAAAC
* *
70089 TATATATTATATAGTTTTTAAAACATTTTCGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTCGAAAAC
70125 TATATAATATATAGTTT
1 TATATAATATATAGTTT
70142 ATATAGTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 17 0.37
36 29 0.63
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTCGAAAAC
Found at i:70165 original size:17 final size:17
Alignment explanation
Indices: 70143--70177 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
70133 ATATAGTTTA
**
70143 TATAGTTTTTAAAAATG
1 TATAGTTTCAAAAAATG
70160 TATAGTTTCAAAAAATG
1 TATAGTTTCAAAAAATG
70177 T
1 T
70178 TTTAAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (17 bp):
TATAGTTTCAAAAAATG
Found at i:71120 original size:7 final size:7
Alignment explanation
Indices: 71108--71138 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
71098 CATTTGATGC
71108 TGGAAAG
1 TGGAAAG
71115 TGGAAAG
1 TGGAAAG
71122 TGGAAAG
1 TGGAAAG
71129 TGGAAAG
1 TGGAAAG
71136 TGG
1 TGG
71139 GAACCATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.45, T:0.16
Consensus pattern (7 bp):
TGGAAAG
Found at i:74001 original size:6 final size:6
Alignment explanation
Indices: 73990--74030 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
73980 CAAAAGCTGT
73990 ATAATC ATAATC ATAATC ATAATC ATAATC ATAATC ATAAT
1 ATAATC ATAATC ATAATC ATAATC ATAATC ATAATC ATAAT
74031 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAATC
Found at i:84490 original size:21 final size:19
Alignment explanation
Indices: 84459--84505 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
84449 ATTTTCTCAA
*
84459 TTTATTTATTTATTTATTC
1 TTTATTTATTTATTTAATC
84478 TTCTATTTGATTTATTTAATC
1 TT-TATTT-ATTTATTTAATC
84499 TTTATTT
1 TTTATTT
84506 TTCAATCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 13 0.52
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTTATTTATTTAATC
Found at i:86213 original size:16 final size:16
Alignment explanation
Indices: 86192--86228 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
86182 TGCATTTAAA
86192 CATTTTGCATTTTGTT
1 CATTTTGCATTTTGTT
86208 CATTTTGCATTTTGTT
1 CATTTTGCATTTTGTT
86224 CATTT
1 CATTT
86229 CTTTACATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.62
Consensus pattern (16 bp):
CATTTTGCATTTTGTT
Found at i:88283 original size:106 final size:106
Alignment explanation
Indices: 88148--89102 Score: 1667
Period size: 106 Copynumber: 9.0 Consensus size: 106
88138 GAGAGTGGAT
*
88148 TTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
88213 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
88254 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
88319 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
88360 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
88425 CAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
88466 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
88531 CAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
88572 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
88637 CAACTTCACATGCAAAGGATATTGGACTCAAGACAACGCAAG
66 CAACTTCACA-GCGAAGGATATTGGACTCCAGACAACGCAAG
88679 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
88744 CAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
88785 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
88850 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
88891 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
88956 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
88997 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
89062 CAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
89103 GGACGCTGGT
Statistics
Matches: 830, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
106 729 0.88
107 101 0.12
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:88515 original size:212 final size:212
Alignment explanation
Indices: 88148--89240 Score: 1735
Period size: 212 Copynumber: 5.3 Consensus size: 212
88138 GAGAGTGGAT
* *
88148 TTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
88213 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
*
88278 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
131 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
88343 ACTCAAGACAACGCAAG
196 ACTCCAGACAACGCAAG
* *
88360 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
88425 CAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
*
88490 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
131 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
88555 ACTCAAGACAATGCAAG
196 ACTCCAGACAACGCAAG
*
88572 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
88637 CAACTTCACATGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
66 CAACTTCACA-GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
* * * *
88702 GCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTAACAACGAAGGATATTG
130 GCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
88767 GACTCCAGACAACGCAAG
195 GACTCCAGACAACGCAAG
*
88785 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
88850 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
88915 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
131 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
88980 ACTCCAGACAACGCAAG
196 ACTCCAGACAACGCAAG
*
88997 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
89062 CAACTTCACAACAAAGGATATTGGACTC----C-A-G--A---C-A----ACG-C-AAGGGA-CG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
89108 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA---CACAACGAAGGATATTGG
131 CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
89170 ACTCCAGACAACGCAAG
196 ACTCCAGACAACGCAAG
* * * * *
89187 TTCAACTTCATGACGAAGGGAGCGCTAGTTGTCAATAAACAATTTCCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
89241 CTTCACAACG
Statistics
Matches: 846, Mismatches: 34, Indels: 24
0.94 0.04 0.03
Matches are distributed among these distances:
190 83 0.10
193 43 0.05
194 6 0.01
195 1 0.00
196 3 0.00
200 1 0.00
201 1 0.00
204 1 0.00
206 1 0.00
207 1 0.00
208 1 0.00
212 503 0.59
213 201 0.24
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (212 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
ACTCCAGACAACGCAAG
Found at i:89643 original size:84 final size:83
Alignment explanation
Indices: 89440--89669 Score: 216
Period size: 81 Copynumber: 2.8 Consensus size: 83
89430 ACTTCACGAC
* * * *
89440 GAAGGGTTGTCTGCCAACACAAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGACACATCATT
1 GAAGGGTTATCTG-CACCA-AAGACCTTTGAGTTCGATTACACTCAGCTTCAACGACACATCATT
** * * *
89504 TGTAGCATAGCTTAAGTCGA
64 TACAGCATAACTCAAGGCGA
* *** * * * *
89524 GAAGGGCTATCTG--CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTA
1 GAAGGGTTATCTGCACCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAACGACACATCATTTA
* *
89587 CAGTATAACTCAAGGCTA
66 CAGCATAACTCAAGGCGA
* *
89605 GAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGATTACACTCAGC-TCAAAGACACAACATTT
1 GAAGGGTTATCTG-CACCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAACGACACATCATTT
89669 A
65 A
89670 TAGAATAGCT
Statistics
Matches: 114, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
80 23 0.20
81 39 0.34
83 13 0.11
84 39 0.34
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
GAAGGGTTATCTGCACCAAAGACCTTTGAGTTCGATTACACTCAGCTTCAACGACACATCATTTA
CAGCATAACTCAAGGCGA
Found at i:91561 original size:21 final size:19
Alignment explanation
Indices: 91530--91576 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
91520 ATTTTCTCAA
*
91530 TTTATTTATTTATTTATTC
1 TTTATTTATTTATTTAATC
91549 TTCTATTTGATTTATTTAATC
1 TT-TATTT-ATTTATTTAATC
91570 TTTATTT
1 TTTATTT
91577 TTCAATCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 13 0.52
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTTATTTATTTAATC
Found at i:102184 original size:14 final size:11
Alignment explanation
Indices: 102151--102176 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
102141 AACATTTTCC
102151 TAAAAATAATT
1 TAAAAATAATT
102162 TAAAAATAATT
1 TAAAAATAATT
102173 TAAA
1 TAAA
102177 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATAATT
Found at i:102335 original size:99 final size:101
Alignment explanation
Indices: 102215--102426 Score: 331
Period size: 99 Copynumber: 2.1 Consensus size: 101
102205 TAAAAGTAGG
* * * * *
102215 ATATTTATTTATTTAAAAATATCAGAAAAAG-ACATCTAGTTGCTTTAAGACA-TCCCTTTTTTA
1 ATATATATATATTTAAAAATATCA-AAAAAGAACATCTAGTTGCTTTAAGAAAGCCCCTTTCTTA
102278 ACATTAAAAAATAAATAAA-TATTATTTAATATATAT
65 ACATTAAAAAATAAATAAATTATTATTTAATATATAT
* *
102314 ATATATATATATTTTAAAATATCAAAAAAGAATATCTAGTTGCTTTAAGAAAGCCCCTTTCTTAA
1 ATATATATATATTTAAAAATATCAAAAAAGAACATCTAGTTGCTTTAAGAAAGCCCCTTTCTTAA
102379 CATTAAAAAATAAATAAATTATTATTTAATATATAT
66 CATTAAAAAATAAATAAATTATTATTTAATATATAT
102415 ATATATATATAT
1 ATATATATATAT
102427 ATATATTTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
98 6 0.06
99 40 0.39
100 28 0.27
101 29 0.28
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (101 bp):
ATATATATATATTTAAAAATATCAAAAAAGAACATCTAGTTGCTTTAAGAAAGCCCCTTTCTTAA
CATTAAAAAATAAATAAATTATTATTTAATATATAT
Found at i:102414 original size:2 final size:2
Alignment explanation
Indices: 102407--102432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
102397 TTATTATTTA
102407 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
102433 TTATGCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103794 original size:20 final size:20
Alignment explanation
Indices: 103763--103827 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
103753 ATGACAACAT
*
103763 TGAACAAGTTCTTCTCATTA
1 TGAACTAGTTCTTCTCATTA
** * *
103783 TGAACTTTTTCTTC-CACTC
1 TGAACTAGTTCTTCTCATTA
*
103802 TGGACTAGTTCTTCTCATTA
1 TGAACTAGTTCTTCTCATTA
103822 TGAACT
1 TGAACT
103828 CTTCCACTGG
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (20 bp):
TGAACTAGTTCTTCTCATTA
Found at i:104040 original size:134 final size:135
Alignment explanation
Indices: 103877--104483 Score: 398
Period size: 123 Copynumber: 4.7 Consensus size: 135
103867 AATCTAGCAA
* * * *
103877 AAGGTTGAACAAGTTCTTCTCAATGTGAACTTTTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
103942 GAACTCCTTCTGGAAATGATGATC-CTCAAAAGAGG-T-GTTGATTCAACTTCATATA-TGATGA
66 GAACT-CTTCTGGAAATGATGATCTC-CAAAAGAGGTTCGTTCATTCAACTTCATA-AGTGATGA
*
104003 ATTAAGGC
128 ATCAAGGC
* * * *
104011 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTTTCAGATGAGTTTTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
** * * * * * *
104076 GAACT-TTCTCTAAAATTGTTGATCTCCAAATGAGGTTATTCTTTCATTCATCTTTATAAGTGCT
66 GAACTCTTCT-GGAAA-TGATGATCTCCAAAAGAGG---TTCGTTCATTCAACTTCATAAGTGAT
**
104140 GAATCAAGTT
126 GAATCAAGGC
* * * * *
104150 AAAGTCGAACATGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGGGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
104215 GAACTACTTCTGGAAAT-ACTGGTGCT------GA---TC--T-ATCTC--CTTC-T--GTGATA
66 GAACT-CTTCTGGAAATGA-TGAT-CTCCAAAAGAGGTTCGTTCAT-TCAACTTCATAAGTGAT-
*
104262 GAATCGA-GC
126 GAATCAAGGC
*
104271 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
1 --AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
** * * *
104336 ATGAACTCTTTCTGGCGATGTTGGTGCT---------GTT--TT-A-TCTTA-TTC-T-A-TGAT
64 ATGAACTC-TTCTGGAAATGATGAT-CTCCAAAAGAGGTTCGTTCATTC-AACTTCATAAGTGAT
*
104384 AGAATCGA-GC
126 -GAATCAAGGC
*
104394 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCACT
1 --AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* *
104459 ATGAACTCTTCTGAAAATGTTGATC
64 ATGAACTCTTCTGGAAATGATGATC
104484 CATTCAGTGA
Statistics
Matches: 394, Mismatches: 53, Indels: 65
0.77 0.10 0.13
Matches are distributed among these distances:
121 7 0.02
122 19 0.05
123 172 0.44
124 3 0.01
125 2 0.01
126 3 0.01
128 2 0.01
132 4 0.01
133 3 0.01
134 79 0.20
135 1 0.00
138 2 0.01
139 88 0.22
140 5 0.01
141 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (135 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCTGGAAATGATGATCTCCAAAAGAGGTTCGTTCATTCAACTTCATAAGTGATGAATC
AAGGC
Found at i:104306 original size:123 final size:122
Alignment explanation
Indices: 104163--104476 Score: 484
Period size: 123 Copynumber: 2.6 Consensus size: 122
104153 GTCGAACATG
* *
104163 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGGGTTCTTCTCATTATGAACTACTTCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-CTTCTGG
* *
104228 AAATACTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAA
65 AAATACTGGTGCTGATCTATCTCATTCTATGATAGAATCGAGCAAAAGGTTGAACAAA
104286 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC-TTCTGG
** ** * * * *
104351 CGATGTTGGTGCTGTTTTATCTTATTCTATGATAGAATCGAGCAAAAGGTTGAACAAG
65 AAATACTGGTGCTGATCTATCTCATTCTATGATAGAATCGAGCAAAAGGTTGAACAAA
* *
104409 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCACTATGAACTCTTCTGAA
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGA
104474 AAT
66 AAT
104477 GTTGATCCAT
Statistics
Matches: 174, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
122 8 0.05
123 166 0.95
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (122 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGA
AATACTGGTGCTGATCTATCTCATTCTATGATAGAATCGAGCAAAAGGTTGAACAAA
Found at i:106164 original size:11 final size:11
Alignment explanation
Indices: 106148--106182 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
106138 TCATTTTATA
106148 TTTTCTCTTTT
1 TTTTCTCTTTT
106159 TTTTCTC-TTT
1 TTTTCTCTTTT
106169 TTTTCTTCTTTT
1 TTTTC-TCTTTT
106181 TT
1 TT
106183 CTTCAAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 9 0.41
12 5 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:113461 original size:11 final size:11
Alignment explanation
Indices: 113445--113469 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
113435 CTTTTTCATA
113445 TTATTATTTAT
1 TTATTATTTAT
113456 TTATTATTTAT
1 TTATTATTTAT
113467 TTA
1 TTA
113470 ATGAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:113517 original size:15 final size:15
Alignment explanation
Indices: 113497--113528 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
113487 TGCAATGAAT
*
113497 AATGAATGTATGTAA
1 AATGAATGTATGCAA
113512 AATGAATGTATGCAA
1 AATGAATGTATGCAA
113527 AA
1 AA
113529 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:117660 original size:93 final size:91
Alignment explanation
Indices: 117514--117711 Score: 260
Period size: 93 Copynumber: 2.1 Consensus size: 91
117504 TAAAAGTAAG
* * * *
117514 ATATTTATTTATTTAAAAATATCAGAAAATGACATCTAGTTGCTTTAAGACCCCCTTTTTTAACA
1 ATATATATATATTTAAAAATATCAGAAAAAGACA-CTAGTTGCTTTAAGA-CCCCTTTCTTAACA
117579 TT-AAAAAATAAATAATATTATTTTAATAT
64 TTAAAAAAATAAAT-ATATTA-TTTAATAT
117608 ATATATATATATTT-AAAATATCAGAAAAAGACA-TAG-TGCTTTAAGACAACCCCTTTCTTAAC
1 ATATATATATATTTAAAAATATCAGAAAAAGACACTAGTTGCTTTAAG---ACCCCTTTCTTAAC
117670 ATTAAAAAAATAAATATATTATTTAATAT
63 ATTAAAAAAATAAATATATTATTTAATAT
117699 ATATATATTATAT
1 ATATATA-TATAT
117712 GCCTAAAAAT
Statistics
Matches: 95, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
90 9 0.09
91 18 0.19
92 26 0.27
93 30 0.32
94 12 0.13
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.39
Consensus pattern (91 bp):
ATATATATATATTTAAAAATATCAGAAAAAGACACTAGTTGCTTTAAGACCCCTTTCTTAACATT
AAAAAAATAAATATATTATTTAATAT
Done.