Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003499.1 Hibiscus syriacus cultivar Beakdansim tig00007397_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: 51908
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:3499 original size:15 final size:15
Alignment explanation
Indices: 3479--3540 Score: 124
Period size: 15 Copynumber: 4.1 Consensus size: 15
3469 GTAGGACCAT
3479 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
3494 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
3509 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
3524 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
3539 TA
1 TA
3541 TTATACCCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:3671 original size:29 final size:29
Alignment explanation
Indices: 3636--3702 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
3626 CATATACTTC
3636 TGTCATTTCTCTTGTGATCATGTAGCTCA
1 TGTCATTTCTCTTGTGATCATGTAGCTCA
3665 TGTCATTTCTCTTGTGATCATGTAGCTCA
1 TGTCATTTCTCTTGTGATCATGTAGCTCA
3694 TGTCATTTC
1 TGTCATTTC
3703 ATATCATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (29 bp):
TGTCATTTCTCTTGTGATCATGTAGCTCA
Found at i:3731 original size:12 final size:12
Alignment explanation
Indices: 3714--3760 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
3704 TATCATGTTC
* *
3714 TCATATTACATG
1 TCATATCACATA
3726 TCATATCACATA
1 TCATATCACATA
3738 TCATATCACATA
1 TCATATCACATA
3750 TCATATCACAT
1 TCATATCACAT
3761 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:4181 original size:64 final size:63
Alignment explanation
Indices: 4069--4245 Score: 201
Period size: 64 Copynumber: 2.8 Consensus size: 63
4059 TAATGAAGGT
* * * ** * * * **
4069 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTTGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTAGTACTATTAATGGG
* **
4133 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTAGTACTATTAATGGG
*
4197 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT
4246 CTTTATTTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 1 0.01
64 95 0.99
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTAGTACTATTAATGGG
Found at i:4266 original size:64 final size:64
Alignment explanation
Indices: 4069--4293 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 64
4059 TAATGAAGGT
* * * * ** * * ** * ** *
4069 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTTGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGAG
* *
4133 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGAG
* *
4197 ATGCATCGATGCACTACTTATGCATCGATGCA-TGAATTGCATTCGATGTCTTTA-TTTTAAAAT
1 ATGCATCGATGCACTACTTATGCATCGATGCACCG-ATTGCATTCGATGT-TTTACTATT--AAT
4260 -AG
62 GAG
** *
4262 -TGCATCGATGCACTACCAATGTATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
4294 ATTCATATAA
Statistics
Matches: 135, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 126 0.93
65 5 0.04
66 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGAG
Found at i:7975 original size:21 final size:20
Alignment explanation
Indices: 7889--8046 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
7879 AAATGACCAA
**
7889 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
7908 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
7928 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
7948 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
7969 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
7990 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
8010 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
8031 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
8047 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:8179 original size:40 final size:40
Alignment explanation
Indices: 8052--8261 Score: 264
Period size: 40 Copynumber: 5.3 Consensus size: 40
8042 CGCGAACACA
* * * *
8052 TAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCATATCCGTAAATCGCAACGAGAATCTG
** * * * *
8092 TAAATCGCAACGCATATGGGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCATATCCGTAAATCGCAACGAGAATCTG
* *
8132 TATATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCATATCCGTAAATCGCAACGAGAATCTG
8172 TAAATCGCAACG-ATAATCCGT-AATCGCAACGAGAATCTG
1 TAAATCGCAACGCAT-ATCCGTAAATCGCAACGAGAATCTG
8211 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCAT-ATCCGTAAATCGCAACGAGAATCTG
*
8251 TAAATCACAAC
1 TAAATCGCAAC
8262 ACTGAAATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 40 0.26
40 113 0.74
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGCATATCCGTAAATCGCAACGAGAATCTG
Found at i:8248 original size:20 final size:20
Alignment explanation
Indices: 8013--8261 Score: 234
Period size: 20 Copynumber: 12.5 Consensus size: 20
8003 CGATTTTCCA
* ** *
8013 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
8033 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
8053 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
8073 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* **
8093 AAATCGCAACGCA-TATGGGT
1 AAATCGCAACG-AGAATCCGT
* * *
8113 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
8133 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
8153 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
8173 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
8193 -AATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
8212 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
8232 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
8252 AAATCACAAC
1 AAATCGCAAC
8262 ACTGAAATTT
Statistics
Matches: 196, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.09
20 178 0.91
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:11544 original size:19 final size:19
Alignment explanation
Indices: 11503--11600 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
11493 GATTCTCTCG
11503 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
11523 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
11542 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
11556 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11575 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11594 TTGCGAT
1 TTGCGAT
11601 AGTCAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 6 0.09
17 7 0.10
19 35 0.51
20 15 0.22
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:11597 original size:52 final size:53
Alignment explanation
Indices: 11484--11600 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
11474 GAAATGAAAA
11484 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
11537 TTGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
11589 TCGCATTGCGAT
1 TCGCATTGCGAT
11601 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:11696 original size:14 final size:14
Alignment explanation
Indices: 11677--11731 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
11667 CGGAAATGAA
11677 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
11691 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
11710 AATCGCAACGAGAG
1 AATCGCAACGAGAG
11724 AATCGCAA
1 AATCGCAA
11732 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:11711 original size:33 final size:33
Alignment explanation
Indices: 11659--11787 Score: 188
Period size: 33 Copynumber: 3.8 Consensus size: 33
11649 CCATTACATT
11659 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
11693 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
*
11726 TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAA
11764 TCGCAATGCGAAATG-AAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
11788 TGCGAAATGA
Statistics
Matches: 89, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
33 49 0.55
34 9 0.10
35 2 0.02
37 10 0.11
38 19 0.21
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:11715 original size:19 final size:19
Alignment explanation
Indices: 11659--11844 Score: 206
Period size: 19 Copynumber: 10.6 Consensus size: 19
11649 CCATTACATT
11659 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
11679 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
11693 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
11712 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
11726 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
11745 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
11764 TCGCAATGCGAAATG-AAA
1 TCGCAATGCGAAATGAAAA
11782 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
11801 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
*
11815 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
11834 TCGCATTGCGA
1 TCGCAATGCGA
11845 TTCTCCCATT
Statistics
Matches: 142, Mismatches: 8, Indels: 33
0.78 0.04 0.18
Matches are distributed among these distances:
14 30 0.21
15 3 0.02
16 6 0.04
17 5 0.04
18 22 0.15
19 70 0.49
20 6 0.04
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:11807 original size:89 final size:85
Alignment explanation
Indices: 11659--11844 Score: 291
Period size: 89 Copynumber: 2.1 Consensus size: 85
11649 CCATTACATT
*
11659 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 TCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGAGAG
11724 AATCGCAATGCGAAATGAAAA
65 AATCGCAATGCGAAATGAAAA
11745 TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGA
1 TCGCAATGCGAAATGAAAATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAAAATCGCAACGA
* *
11810 GATAATCGCAATGCGAAATTAAAA
62 GAGAATCGCAATGCGAAATGAAAA
*
11834 TCGCATTGCGA
1 TCGCAATGCGA
11845 TTCTCCCATT
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
85 16 0.17
86 9 0.10
87 4 0.04
88 1 0.01
89 62 0.67
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (85 bp):
TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
ATCGCAATGCGAAATGAAAA
Found at i:11893 original size:19 final size:19
Alignment explanation
Indices: 11851--11950 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
11841 GCGATTCTCC
11851 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
11871 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
11890 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
11906 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
11923 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
11942 CATTGCGAT
1 CATTGCGAT
11951 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:11947 original size:52 final size:53
Alignment explanation
Indices: 11834--11950 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
11824 GAAATTAAAA
11834 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
11887 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
11939 TCGCATTGCGAT
1 TCGCATTGCGAT
11951 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:12076 original size:14 final size:14
Alignment explanation
Indices: 12057--12093 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12047 CATCAATTAC
12057 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12071 ACAAATCATCTTTT
1 ACAAATCAACTTTT
12085 ACAAATCAA
1 ACAAATCAA
12094 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:14083 original size:14 final size:14
Alignment explanation
Indices: 14064--14119 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
14054 GCGAAATGAA
*
14064 AATCGCAACGACAG
1 AATCGCAACGAAAG
14078 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
14095 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
14110 AATCGCAACG
1 AATCGCAACG
14120 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:14104 original size:32 final size:33
Alignment explanation
Indices: 14045--14136 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
14035 GCGAAACCAA
*
14045 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
14078 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
14110 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
14137 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:14134 original size:19 final size:19
Alignment explanation
Indices: 14008--14141 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
13998 TAGTTTACTT
* *
14008 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
14028 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
14047 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
14066 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
14080 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
14098 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
14112 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
14131 TCGCAATGCGA
1 TCGCAACGCGA
14142 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:14159 original size:19 final size:19
Alignment explanation
Indices: 14137--14265 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
14127 AAAATCGCAA
14137 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
14156 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
14170 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
14189 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
14203 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
14222 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
14241 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
14261 TGCGA
1 TGCGA
14266 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:14179 original size:33 final size:33
Alignment explanation
Indices: 14137--14228 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
14127 AAAATCGCAA
14137 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
14170 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
14203 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
14229 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:14639 original size:93 final size:93
Alignment explanation
Indices: 14309--14780 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
14299 TTGAATGGAT
14309 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14374 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
14402 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14466 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14494 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14558 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14586 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
14651 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14679 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
14744 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
14772 AAATTTACT
1 AAATTTACT
14781 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 19 0.05
92 142 0.38
93 213 0.57
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:16500 original size:14 final size:14
Alignment explanation
Indices: 16481--16570 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
16471 TTGAAATGAA
16481 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16495 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
16512 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
16528 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
16547 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16561 AATCGCAACG
1 AATCGCAACG
16571 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:16518 original size:33 final size:33
Alignment explanation
Indices: 16473--16587 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
16463 TCTTTTGGTT
16473 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
16506 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
16539 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
16572 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
16588 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:16519 original size:19 final size:18
Alignment explanation
Indices: 16480--16592 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
16470 GTTGAAATGA
16480 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
16495 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
16512 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
16528 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
16545 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
16561 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
16578 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
16593 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:16623 original size:14 final size:14
Alignment explanation
Indices: 16604--16660 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
16594 TTTGGTTTCG
16604 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
16618 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
16637 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
16651 CGTTGCGATT
1 CGTTGCGATT
16661 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:16636 original size:33 final size:33
Alignment explanation
Indices: 16588--16668 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
16578 AAAATCGCAA
**
16588 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
16621 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
16654 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
16669 TCTCGTTGCG
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:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:16671 original size:21 final size:21
Alignment explanation
Indices: 16645--16720 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
16635 CGCGTTGCGA
16645 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
16666 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
16686 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
16707 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
16721 CTCTTCTGCA
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:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:16701 original size:41 final size:41
Alignment explanation
Indices: 16644--16721 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
16634 TCGCGTTGCG
*
16644 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
16685 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
16722 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:16846 original size:33 final size:33
Alignment explanation
Indices: 16799--16869 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
16789 AATACTAACT
* *
16799 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
16832 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
16865 TGAAA
1 TGAAA
16870 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:17102 original size:22 final size:22
Alignment explanation
Indices: 17050--17104 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
17040 TGGTTGTGAG
**
17050 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
17072 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
17094 GGATTTCTTCG
1 GGATTTCTTCG
17105 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:17270 original size:39 final size:40
Alignment explanation
Indices: 17227--17308 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
17217 TACGCGTAGC
*
17227 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
17266 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
17306 GAT
1 GAT
17309 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:17443 original size:20 final size:20
Alignment explanation
Indices: 17250--17442 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
17240 CTTTAAATAT
17250 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
17271 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
17290 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17310 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
17330 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
17350 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17370 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
17390 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
17410 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
17430 CGCGTTGCGATTT
1 CGCGTTGCGATTT
17443 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:17459 original size:21 final size:21
Alignment explanation
Indices: 17429--17511 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
17419 ATTTTCATAT
*
17429 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
17450 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
17471 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
17492 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
17512 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:17502 original size:42 final size:43
Alignment explanation
Indices: 17409--17507 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
17399 ATTTATGTGT
* *
17409 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
17450 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
17492 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
17508 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:30525 original size:91 final size:90
Alignment explanation
Indices: 30414--30595 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 90
30404 TTGTCGGTTT
*
30414 GTGTCCATACTTTATAAAAATATAT-TGATCCATAACAATATAATAAGTAAAAAAATGACAAAAC
1 GTGTCCATACTTTATAAAAATATATCT-ATCCATAACAATATAACAAGT-AAAAAATGACAAAAC
* *
30478 CGGTTTATAAATGATAAAACAGGTAAA
64 CGGTATATAAATGACAAAACAGGTAAA
* * * *
30505 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAATGACAAAATCG
1 GTGTCCATACTTTATAAAAATATATCTATCCATAACAATATAACAAGTAAAAAATGACAAAACCG
30570 GTATATAAATGACAAAACAGGTAAA
66 GTATATAAATGACAAAACAGGTAAA
30595 G
1 G
30596 CGCTACCGGA
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 40 0.48
91 42 0.51
92 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (90 bp):
GTGTCCATACTTTATAAAAATATATCTATCCATAACAATATAACAAGTAAAAAATGACAAAACCG
GTATATAAATGACAAAACAGGTAAA
Found at i:30592 original size:20 final size:19
Alignment explanation
Indices: 30546--30594 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
30536 ATAACAATAT
30546 AACAGGTAAAAAATGACAA
1 AACAGGTAAAAAATGACAA
*
30565 AATC-GGTATATAAATGACAA
1 AA-CAGGTA-AAAAATGACAA
30585 AACAGGTAAA
1 AACAGGTAAA
30595 GCGCTACCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.57, C:0.10, G:0.16, T:0.16
Consensus pattern (19 bp):
AACAGGTAAAAAATGACAA
Found at i:30668 original size:111 final size:112
Alignment explanation
Indices: 30502--30854 Score: 555
Period size: 112 Copynumber: 3.2 Consensus size: 112
30492 TAAAACAGGT
* *
30502 AAAGTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGG-TAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAA
*
30566 ATCGGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTG
66 ATCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTG
*
30613 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAAAGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAA
*
30678 ATCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTG
66 ATCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTG
* * * *
30725 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAA
** ** * *
30790 ATCAATCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTG
66 ATCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTG
*
30837 AAAGTGTCAATACTTTAT
1 AAAGTGTCGATACTTTAT
30855 TATAAGTATC
Statistics
Matches: 223, Mismatches: 18, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
111 49 0.22
112 174 0.78
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGAAAAAAAATGACAAA
ATCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTG
Found at i:31034 original size:182 final size:182
Alignment explanation
Indices: 30725--31159 Score: 726
Period size: 182 Copynumber: 2.4 Consensus size: 182
30715 AGATATATTG
*
30725 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* ** * * *
30790 ATCAATCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCAATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
*
30855 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* *
30907 AAAGTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAAGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * *
30972 ACCGGTCTCGAAATGACAAAACCGATAAAGAGCTACCAGATATTTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
31037 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* * *
31089 AAAGTTTTGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
31154 ACCGGT
66 ACCGGT
31160 AAAGAACTAC
Statistics
Matches: 235, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 235 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:31270 original size:162 final size:162
Alignment explanation
Indices: 30984--31498 Score: 681
Period size: 162 Copynumber: 3.1 Consensus size: 162
30974 CGGTCTCGAA
* * * *
30984 ATGACAAAACCGATAAAGAGCTACCAGATATTTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
* * * *
31049 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTTTTGATATTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAAGTGTCGATACTTTATAAAAATG
31114 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
*
31146 ATGATAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
31211 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAAGTGTCGATACTTTATAAAAATG
*
31276 TATCGATCTATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
* *
31308 ATGATAAAATCGGTCTCAAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGA
1 ATGACAAAACCGG--------T----AAA---G---A-A-CTACCGGATATGTTGATAGTGTCGA
* * * *
31373 TATTTTATTATAAGTATCGACACTTTTGAAATTTAAAAGA-ATAGAAGTTATAGCATCAATAAAG
46 TACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGA-AGAAGTTATAGCGTTAATAAAG
*
31437 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAT
110 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAT
31490 ATGACAAAA
1 ATGACAAAA
31499 TGGATCTCGA
Statistics
Matches: 314, Mismatches: 18, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
162 164 0.52
170 1 0.00
174 3 0.01
177 1 0.00
180 1 0.00
181 2 0.01
182 142 0.45
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (162 bp):
ATGACAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:31436 original size:344 final size:344
Alignment explanation
Indices: 30802--31498 Score: 1166
Period size: 344 Copynumber: 2.0 Consensus size: 344
30792 CAATCTCGAA
**
30802 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGA
30867 CACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATG
*
30932 TATCGATTCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTCGAAATGACAAAACCGA
131 TATCGATTCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTCAAAATGACAAAACCGA
* *
30997 TAAAGAGCTACCAGATATTTTGATAGTGTCGATACTTTATTATAAGTATCGACACTTTTGGAATT
196 TAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGACACTTTTGAAATT
* * *
31062 TAAAAGAGAAGAAGTTATAGCGCTAATAAAGTTTTGATATTTTATAAAAATGTATCGATCCATAA
261 TAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
31127 CAATATAACAGGTAAAAAT
326 CAATATAACAGGTAAAAAT
* * *
31146 ATGATAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGA
* *
31211 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATG
* *
31276 TATCGA-TCTATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCAAAATGACAAAACCG
131 TATCGATTC-ATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTCAAAATGACAAAACCG
* * *
31340 GTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATAAGTATCGACACTTTTGAAAT
195 ATAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGACACTTTTGAAAT
*
31405 TTAAAAGA-ATAGAAGTTATAGC-ATCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
260 TTAAAAGAGA-AGAAGTTATAGCGCT-AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
31468 TAACAATATAATAGGTAAAAAT
323 TAACAATATAACAGGTAAAAAT
31490 ATGACAAAA
1 ATGACAAAA
31499 TGGATCTCGA
Statistics
Matches: 329, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
343 4 0.01
344 325 0.99
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (344 bp):
ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATG
TATCGATTCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTCAAAATGACAAAACCGA
TAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGACACTTTTGAAATT
TAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
CAATATAACAGGTAAAAAT
Found at i:31458 original size:182 final size:182
Alignment explanation
Indices: 31146--31524 Score: 636
Period size: 182 Copynumber: 2.1 Consensus size: 182
31136 AGGTAAAAAT
*
31146 ATGATAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
* * *
31211 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCATCAATAAAGTGTCGATACTTTATAAAAATG
* *
31276 TATCGATCTATAACAATATAACAGGTAAAAATATGATAAAATCGG-TCTCAAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT-GGATCTCAAA
* *
31328 ATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
31393 CACTTTTGAAATTTAAAAGA-ATAGAAGTTATAGCATCAATAAAGTGTCGATACTTTATAAAAAT
66 CACTTTTGAAATTTAAAAGAGA-AGAAGTTATAGCATCAATAAAGTGTCGATACTTTATAAAAAT
* *
31457 GTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAATGGATCTCGAA
130 GTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATGGATCTCAAA
31510 ATGACAAAACCGGTA
1 ATGACAAAACCGGTA
31525 GTATAAAAGT
Statistics
Matches: 185, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
181 3 0.02
182 182 0.98
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (182 bp):
ATGACAAAACCGGTAAAGAACTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
CACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCATCAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATGGATCTCAAA
Found at i:31743 original size:41 final size:41
Alignment explanation
Indices: 31698--31780 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
31688 ATTGGTTAAT
31698 TAGTAAATAGATTTACATTATGTATCGACACTCTTTAAATA
1 TAGTAAATAGATTTACATTATGTATCGACACTCTTTAAATA
31739 TAGTAAATAGATTTACATTATGTATCGACACTCTTTAAATA
1 TAGTAAATAGATTTACATTATGTATCGACACTCTTTAAATA
31780 T
1 T
31781 GTGTCGATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (41 bp):
TAGTAAATAGATTTACATTATGTATCGACACTCTTTAAATA
Found at i:31978 original size:23 final size:23
Alignment explanation
Indices: 31952--31999 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
31942 AAATAGGTCA
* *
31952 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
31975 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
31998 AT
1 AT
32000 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:40384 original size:5 final size:5
Alignment explanation
Indices: 40374--40400 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40364 ATCTCAGATT
40374 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
40401 AGACTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:48619 original size:18 final size:18
Alignment explanation
Indices: 48598--48661 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
48588 AAATTATAAT
48598 TATTTTATTTTATATATC
1 TATTTTATTTTATATATC
* *
48616 TATTTT-TTTAAAATTAT-
1 TATTTTATTTTATA-TATC
* *
48633 AATTTTTATTTTATTTATC
1 TA-TTTTATTTTATATATC
48652 TAATTTTATT
1 T-ATTTTATT
48662 ATCAAATTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 9
0.68 0.14 0.18
Matches are distributed among these distances:
17 6 0.18
18 16 0.47
19 11 0.32
20 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTATTTTATATATC
Found at i:48640 original size:36 final size:38
Alignment explanation
Indices: 48580--48658 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
48570 AAAGTTATTT
48580 ATTTTTTAAAATTATAATTATTTTATTTTATATATCTA
1 ATTTTTTAAAATTATAATTATTTTATTTTATATATCTA
* *
48618 TTTTTTTAAAATTATAA-T-TTTTATTTTATTTATCTA
1 ATTTTTTAAAATTATAATTATTTTATTTTATATATCTA
48654 ATTTT
1 ATTTT
48659 ATTATCAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 21 0.55
37 1 0.03
38 16 0.42
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (38 bp):
ATTTTTTAAAATTATAATTATTTTATTTTATATATCTA
Found at i:49392 original size:17 final size:17
Alignment explanation
Indices: 49370--49405 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
49360 TATCGAGTTC
49370 GAGTATTTGTATATGCA
1 GAGTATTTGTATATGCA
49387 GAGTATTTGTATATGCA
1 GAGTATTTGTATATGCA
49404 GA
1 GA
49406 AATCCGTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.39
Consensus pattern (17 bp):
GAGTATTTGTATATGCA
Done.