Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003090.1 Hibiscus syriacus cultivar Beakdansim tig00006449_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: 172626
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3528 original size:19 final size:19
Alignment explanation
Indices: 3475--3561 Score: 129
Period size: 19 Copynumber: 4.5 Consensus size: 19
3465 TTCGAGAATG
*
3475 AAAATCGCAACGCAGAAATG
1 AAAATCGCAACGC-GAAATA
3495 AAAATCGCAACCGCGAAATA
1 AAAATCGCAA-CGCGAAATA
3515 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
3534 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
3553 AAAATCGCA
1 AAAATCGCA
3562 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
19 35 0.56
20 25 0.40
21 3 0.05
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:3579 original size:19 final size:19
Alignment explanation
Indices: 3557--3740 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
3547 GAAACCAAAA
*
3557 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3576 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
3595 TCGCGGTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3614 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
3634 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
3650 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3667 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
3681 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3700 TCCGCGTTGCGA-TCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3719 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3739 TC
1 TC
3741 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 17, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 72 0.54
20 34 0.25
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3666 original size:33 final size:33
Alignment explanation
Indices: 3629--3712 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
3619 GTTGCGATTT
* *
3629 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
3662 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
3695 TCATTTCCGCGTTGCGAT
1 TCATTT-CGCGTTGCGAT
3713 CTCATTATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 36 0.77
34 11 0.23
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:3738 original size:39 final size:36
Alignment explanation
Indices: 3570--3740 Score: 147
Period size: 39 Copynumber: 4.8 Consensus size: 36
3560 CATTGCGATT
* * *
3570 TTCATTTCGCGTTGCGATTTTTATTTCGCGGTGCGA
1 TTCATTTCTCGTTGCGATTTTCATTTCGCGTTGCGA
*
3606 TTTTCATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGA
1 --TTCATTTCTC-GTTGCGATTTTCATTTCGCGTTGCGA
* * * **
3645 -T--TGTCTGGTCGCGATAGTCATTTCGCGTTGCGA
1 TTCATTTCTCGTTGCGATTTTCATTTCGCGTTGCGA
**
3678 TTC---TCTCGTTGCGATAGTCATTTCCGCGTTGCGA
1 TTCATTTCTCGTTGCGATTTTCATTT-CGCGTTGCGA
3712 TCTCATTATCTCGTTGCGATTTTCATTTC
1 T-TCATT-TCTCGTTGCGATTTTCATTTC
3741 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
33 41 0.37
34 15 0.13
35 2 0.02
36 1 0.01
38 11 0.10
39 42 0.38
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (36 bp):
TTCATTTCTCGTTGCGATTTTCATTTCGCGTTGCGA
Found at i:5820 original size:21 final size:21
Alignment explanation
Indices: 5796--5862 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5786 TCATTCCTCG
5796 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5817 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5838 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5859 AGAG
1 AGAG
5863 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5820 original size:42 final size:42
Alignment explanation
Indices: 5769--5862 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
5759 CCACTTCTAT
* *
5769 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
5811 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
5853 CATTCAAGAG
1 CGTTCAAGAG
5863 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:7233 original size:14 final size:14
Alignment explanation
Indices: 7214--7249 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
7204 ATTGTTTAAT
7214 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
7228 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
7242 TGATTTGT
1 TGATTTGT
7250 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:7470 original size:14 final size:14
Alignment explanation
Indices: 7451--7507 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
7441 TTTCATTTCG
7451 CGTTGCGATTCCCT
1 CGTTGCGATTCCCT
**
7465 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-CCT
7482 CGCATTGCGATTCCCT
1 CG--TTGCGATTCCCT
7498 CGTTGCGATT
1 CGTTGCGATT
7508 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 16 0.47
16 6 0.18
17 6 0.18
19 6 0.18
ACGTcount: A:0.11, C:0.28, G:0.21, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCCCT
Found at i:7474 original size:33 final size:33
Alignment explanation
Indices: 7432--7591 Score: 252
Period size: 33 Copynumber: 4.8 Consensus size: 33
7422 ATTAAATTCG
*
7432 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
7465 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
**
7498 CGTTGCGATTTTCATTTCGCATTGCGAAATT--AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCCT
*
7531 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
7564 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
7592 AGTAATTTCT
Statistics
Matches: 118, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
31 3 0.03
33 112 0.95
35 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:10704 original size:20 final size:20
Alignment explanation
Indices: 10674--10751 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
10664 ATTCATTTGA
*
10674 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
10694 CTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
10714 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
10734 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
10752 TGCAATGCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:10794 original size:14 final size:14
Alignment explanation
Indices: 10775--10828 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
10765 GAAAATCGCA
10775 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
10789 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
10806 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
10822 TTGCGAT
1 TTGCGAT
10829 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:10794 original size:33 final size:33
Alignment explanation
Indices: 10757--10827 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
10747 AAAATTGCAA
10757 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
10790 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
10823 TGCGA
1 TGCGA
10828 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:10828 original size:33 final size:33
Alignment explanation
Indices: 10770--10847 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
10760 GAAATGAAAA
***
10770 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
10803 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
10836 TCGCGTTGCGAT
1 TCGCATTGCGAT
10848 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:12862 original size:19 final size:19
Alignment explanation
Indices: 12837--12922 Score: 111
Period size: 19 Copynumber: 4.5 Consensus size: 19
12827 CGAAACTTAA
12837 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
12856 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
12876 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
12895 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
12913 AATCGCAACG
1 AATCGCAACG
12923 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
18 10 0.17
19 32 0.54
20 17 0.29
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:12881 original size:39 final size:38
Alignment explanation
Indices: 12838--12911 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
12828 GAAACTTAAA
**
12838 ATCGCAACGCGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
12877 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
12912 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:12970 original size:19 final size:18
Alignment explanation
Indices: 12948--13011 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
12938 GAAACACAAA
12948 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
*
12967 TCGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
12983 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
13000 TCGCATTGCGAT
1 TCGCATTGCGAT
13012 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 6 0.16
16 7 0.18
17 4 0.11
18 4 0.11
19 17 0.45
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:13019 original size:19 final size:20
Alignment explanation
Indices: 12997--13039 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12987 TGCGATTTTT
12997 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
13016 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
13036 ATTT
1 ATTT
13040 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:13030 original size:20 final size:20
Alignment explanation
Indices: 13005--13050 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
12995 TTATTTCGCA
13005 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
13025 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
13045 TTGCGA
1 TTGCGA
13051 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:13549 original size:18 final size:18
Alignment explanation
Indices: 13523--13567 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
13513 GTCGATCAGA
*
13523 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
13541 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
13559 TGATGGCTC
1 TGATGGCTC
13568 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:14911 original size:20 final size:20
Alignment explanation
Indices: 14886--14923 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14876 AATAGTTTCT
14886 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
14906 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
14924 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:15442 original size:20 final size:20
Alignment explanation
Indices: 15417--15469 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
15407 GATTATGTAT
*
15417 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
15437 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
15457 TATCTCGTTGCGA
1 TATCGCGTTGCGA
15470 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:15506 original size:20 final size:20
Alignment explanation
Indices: 15397--15511 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
15387 CGCTTTGAAA
*
15397 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
15418 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
15438 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
15458 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
*
15479 ATCACATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
15499 ATCGCATTGCGAT
1 ATCGCATTGCGAT
15512 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.65
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:15530 original size:41 final size:41
Alignment explanation
Indices: 15503--15595 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
15493 GTCAGTATCG
* * *
15503 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTATTCA
* * *
15544 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTATTCA
15585 CATTGCGAATT
1 CATTGCGAATT
15596 GGGAAAATCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (41 bp):
CATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTATTCA
Found at i:15549 original size:20 final size:20
Alignment explanation
Indices: 15500--15592 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
15490 ATAGTCAGTA
* **
15500 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
15521 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* * **
15541 TCACATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
15562 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
15582 TCGCATTGCGA
1 TCGCATTGCGA
15593 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:22930 original size:17 final size:17
Alignment explanation
Indices: 22890--22942 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
22880 ATACACTCCT
*
22890 TTCAAACTTTAATTT-AA
1 TTCAAA-TTCAATTTAAA
*
22907 TTTAAATTCAATTTAAA
1 TTCAAATTCAATTTAAA
* *
22924 TTCAAATACATTTTAAA
1 TTCAAATTCAATTTAAA
22941 TT
1 TT
22943 ATAACATAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TTCAAATTCAATTTAAA
Found at i:64192 original size:137 final size:132
Alignment explanation
Indices: 63975--64238 Score: 334
Period size: 137 Copynumber: 2.0 Consensus size: 132
63965 TTATTCATTG
* *
63975 TAATGATTCGCTAATGATATGTAGAAAAGAAAAGAACAATGTTTTTCCCTTTTTTTCCACAAACA
1 TAATGATTCGCTAATGATATGTAGAAAAGAAAAAAACAATGTTTTTCCCTCTTTTTCCACAAACA
* * * * *
64040 TATTATGTAAAATCAAAATGTTTTAGTTTATCAAATTGAATGATAGTTATTTAATATTTTAATAT
66 TATTATATAAAATCAAAATATTTCAGTTTATCAAATTGAATGATAATTATTTAAGATTTTAATAT
64105 TA
131 TA
* *
64107 TAATGATTCGCTAATGATTTGTAGAAAAGAAAAAAAAAACAATGTTTTTTTTCTCTCCTTTTT-C
1 TAATGATTCGCTAATGATATGTAGAAAAG---AAAAAAACAATG---TTTTTCCCT-CTTTTTCC
* * * *
64171 -CAAACATATTATATAAAATCAAAATATTTCAGTTTATTAAATTGGATGGTAATTATTTGAGATT
59 ACAAACATATTATATAAAATCAAAATATTTCAGTTTATCAAATTGAATGATAATTATTTAAGATT
64235 TTAA
124 TTAA
64239 GATATACTTT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
132 28 0.25
135 11 0.10
137 59 0.53
138 9 0.08
139 5 0.04
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (132 bp):
TAATGATTCGCTAATGATATGTAGAAAAGAAAAAAACAATGTTTTTCCCTCTTTTTCCACAAACA
TATTATATAAAATCAAAATATTTCAGTTTATCAAATTGAATGATAATTATTTAAGATTTTAATAT
TA
Found at i:64819 original size:20 final size:20
Alignment explanation
Indices: 64796--64847 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
64786 AACGCGATCC
64796 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
64816 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
64836 CCAAAATCGCAA
1 CCAGAATCGCAA
64848 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:64964 original size:20 final size:20
Alignment explanation
Indices: 64903--65095 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
64893 GATTTTCCAT
* ** *
64903 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
64923 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
**
64943 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
64963 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
64983 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
65003 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
65023 TATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
65043 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
65064 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
65084 AATCGCAACGCG
1 AATCGCAACGCG
65096 ATATTTAAAG
Statistics
Matches: 140, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 121 0.86
21 16 0.11
22 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:64986 original size:60 final size:60
Alignment explanation
Indices: 64922--65093 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
64912 GCGAATATGA
* **
64922 AAATCGCAACGCGAACACATAAATCGCAACGCGTATGGGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
* *** * *
64982 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
**
65042 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACG
65094 CGATATTTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 65 0.69
61 29 0.31
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
Found at i:65516 original size:33 final size:33
Alignment explanation
Indices: 65477--65547 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
65467 TTCACTTAGA
*
65477 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
65510 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
65543 TTTCA
1 TTTCA
65548 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:65687 original size:14 final size:14
Alignment explanation
Indices: 65668--65722 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
65658 AGAATGACTG
65668 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
65682 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
65701 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
65715 TCGCAACG
1 TCGCAACG
65723 CGAAACCAAA
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:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:65705 original size:33 final size:33
Alignment explanation
Indices: 65668--65738 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
65658 AGAATGACTG
**
65668 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
65701 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
65734 TCGCA
1 TCGCA
65739 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:65756 original size:19 final size:19
Alignment explanation
Indices: 65734--65831 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
65724 GAAACCAAAA
*
65734 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
65753 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
65767 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
65786 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
65800 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
65819 TCGCGTTGCGATT
1 TCGCGTTGCGATT
65832 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:65775 original size:14 final size:14
Alignment explanation
Indices: 65756--65845 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
65746 TTTCATTTCG
65756 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
65770 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
65789 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
65803 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
65820 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
65836 CGTTGCGATT
1 CGTTGCGATT
65846 TTCATTTCAA
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:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:65781 original size:33 final size:33
Alignment explanation
Indices: 65739--65853 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
65729 CAAAATCGCA
65739 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
65772 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
65805 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
65838 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
65854 AACCAAAAGA
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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:67782 original size:185 final size:186
Alignment explanation
Indices: 67551--68017 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
67541 TAGATTGCTT
*
67551 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67616 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
67681 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
67736 AGTAAATTTGTTCGGTTGATGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67801 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
67866 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
67922 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67987 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
68018 TTCAATTTGC
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.55
186 125 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:67845 original size:93 final size:93
Alignment explanation
Indices: 67551--68017 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
67541 TAGATTGCTT
*
67551 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67616 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
67644 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67708 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
67736 AGTAAATTTGTTCGGTTGATGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67801 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
67829 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67894 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
67922 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67987 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
68015 AGT
1 AGT
68018 TTCAATTTGC
Statistics
Matches: 370, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.25
93 279 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:68089 original size:19 final size:19
Alignment explanation
Indices: 68049--68177 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
68039 TAGTTTACTT
* *
68049 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
68069 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
68088 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
68107 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
68121 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
68140 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
68154 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
68173 TCGCA
1 TCGCA
68178 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:68128 original size:33 final size:32
Alignment explanation
Indices: 68085--68177 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
68075 CGCGAAACCA
**
68085 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
68117 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
68150 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
68178 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:68175 original size:52 final size:52
Alignment explanation
Indices: 68049--68177 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
68039 TAGTTTACTT
**
68049 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
68101 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
68154 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
68178 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:68195 original size:19 final size:19
Alignment explanation
Indices: 68173--68307 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
68163 GAAACCAAAA
*
68173 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
68192 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
68208 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
68225 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
68241 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
68258 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
68277 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
68297 TCGTGTTGCGA
1 TCGCGTTGCGA
68308 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:68214 original size:14 final size:14
Alignment explanation
Indices: 68195--68251 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
68185 TTTCATTTCG
68195 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
68209 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
68226 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
68242 CGTTGCGATT
1 CGTTGCGATT
68252 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:68220 original size:33 final size:33
Alignment explanation
Indices: 68178--68270 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
68168 CAAAATCGCA
*
68178 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
68211 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
68244 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
68271 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:70252 original size:14 final size:14
Alignment explanation
Indices: 70233--70268 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
70223 ATTGTTTAAT
70233 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
70247 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
70261 TGATTTGT
1 TGATTTGT
70269 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:70391 original size:19 final size:19
Alignment explanation
Indices: 70375--70476 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
70365 AAAAATGACT
70375 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70394 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
70413 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
70427 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70446 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
70466 ATCGCAATGCG
1 ATCGCAATGCG
70477 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:70525 original size:33 final size:35
Alignment explanation
Indices: 70483--70773 Score: 253
Period size: 33 Copynumber: 8.5 Consensus size: 35
70473 TGCGTTTATA
*
70483 ATTTCGCATTGCGATT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATTTCGATTGCGATTTTC
70516 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATTTCG-ATTGCGATTTTC
70552 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATTTCG-ATTGCGATTTTC
*
70585 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TTCATTTCG-ATTGCGATTTTC
*
70620 ATTTCGCATTGCGATTC-TGTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATTTCGATTGCGATTTTC
70653 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATTTCG-ATTGCGATTTTC
*
70691 ATTTCGCATTGCGATTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATTTCGATTGCGATTTTC
*
70724 ATTTCCGCATTGCGA-T--TTTC-ATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTCATTTCGA--TTGCGATTTTC
*
70758 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
70774 GTATTTTCCG
Statistics
Matches: 229, Mismatches: 9, Indels: 39
0.83 0.03 0.14
Matches are distributed among these distances:
32 3 0.01
33 121 0.53
34 25 0.11
35 20 0.09
36 23 0.10
38 37 0.16
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCATTTCGATTGCGATTTTC
Found at i:70529 original size:19 final size:19
Alignment explanation
Indices: 70505--70773 Score: 309
Period size: 19 Copynumber: 15.4 Consensus size: 19
70495 GATTATCTCG
70505 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70524 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70543 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
70557 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70576 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
70590 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
70609 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
70628 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
70642 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70661 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70680 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
70699 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
70713 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
70733 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
70747 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
70766 TTGCGATT
1 TTGCGATT
70774 GTATTTTCCG
Statistics
Matches: 216, Mismatches: 8, Indels: 52
0.78 0.03 0.19
Matches are distributed among these distances:
14 35 0.16
16 32 0.15
17 28 0.13
18 3 0.01
19 106 0.49
20 12 0.06
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:70545 original size:52 final size:52
Alignment explanation
Indices: 70483--70745 Score: 299
Period size: 52 Copynumber: 5.0 Consensus size: 52
70473 TGCGTTTATA
70483 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
70535 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
70585 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
70641 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
70691 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
70744 AT
1 AT
70746 GTTGGGATTT
Statistics
Matches: 180, Mismatches: 15, Indels: 31
0.80 0.07 0.14
Matches are distributed among these distances:
47 6 0.03
49 7 0.04
50 17 0.09
51 5 0.03
52 113 0.63
53 17 0.09
54 2 0.01
55 1 0.01
56 4 0.02
57 4 0.02
58 1 0.01
59 3 0.02
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:70562 original size:14 final size:14
Alignment explanation
Indices: 70543--70597 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
70533 TCATTTCGCA
70543 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
70557 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
70574 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
70590 TTGCGATT
1 TTGCGATT
70598 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.39
16 8 0.22
17 8 0.22
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:70717 original size:85 final size:83
Alignment explanation
Indices: 70483--70720 Score: 322
Period size: 85 Copynumber: 2.8 Consensus size: 83
70473 TGCGTTTATA
*
70483 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATTTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC-TTTCG-ATTGC
*
70547 GATTCTTTCGTTGCGATTTTC
63 GATTCTGTCGTTGCGATTTTC
*
70568 ATTTCGCATTGCGATTC-TTTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGC
1 ATTTCGCATTGCGATTCATTTCGTTGCGATTTTCATTTCGCATTGCGA-TTT-CTTTCG-ATTGC
70632 GATTCTGTCGTTGCGATTTTC
63 GATTCTGTCGTTGCGATTTTC
*
70653 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTCTCTCG-TTG
1 ATTTCGCATTGCGA--TTCATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTCTTTCGATTG
70716 CGATT
62 CGATT
70721 TTCATTTCCG
Statistics
Matches: 141, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
85 102 0.72
87 7 0.05
88 7 0.05
90 25 0.18
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (83 bp):
ATTTCGCATTGCGATTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTTCTTTCGATTGCGAT
TCTGTCGTTGCGATTTTC
Found at i:73287 original size:24 final size:24
Alignment explanation
Indices: 73253--73299 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
73243 CTGAAACATC
73253 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
73277 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
73300 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:74010 original size:20 final size:20
Alignment explanation
Indices: 73982--74350 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
73972 AAATTTCAGT
* * * *
73982 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
74002 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
74022 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
74042 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
74062 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
74082 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
74102 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
74122 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
74142 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
74162 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
74182 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
74202 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
74222 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
74242 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
74262 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
74282 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
74302 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
74322 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
74342 GTTGCGATT
1 GTTGCGATT
74351 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:74431 original size:20 final size:20
Alignment explanation
Indices: 74406--74457 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
74396 AAGAATCGCG
*
74406 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
74426 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
74446 TTGCGATTCTGG
1 TTGCGATTCTGG
74458 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:77048 original size:24 final size:24
Alignment explanation
Indices: 77009--77107 Score: 137
Period size: 24 Copynumber: 4.2 Consensus size: 24
76999 TGTTCATTCA
* *
77009 TTTAT-TGTTCGTGAACGTGTTCG
1 TTTATATGTTCGCGAACATGTTCG
77032 TTTATATGTTCGCGAACATGTTCG
1 TTTATATGTTCGCGAACATGTTCG
*
77056 TTTATATGTTCGCAAACATGTTCG
1 TTTATATGTTCGCGAACATGTTCG
* * *
77080 CTTGTATGTTCACGAACATGTTCG
1 TTTATATGTTCGCGAACATGTTCG
77104 TTTA
1 TTTA
77108 ACGTTCATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 5 0.08
24 61 0.92
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTATATGTTCGCGAACATGTTCG
Found at i:77294 original size:35 final size:35
Alignment explanation
Indices: 77250--77320 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
77240 TTCTAGTCTT
* *
77250 CATTTTCAGCTTTGTTTCTCTCAATTCTGCGTATG
1 CATTATCAGCTTTGTTTATCTCAATTCTGCGTATG
77285 CATTATCAGCTTTGTTTATCTCAATTCTGCGTATG
1 CATTATCAGCTTTGTTTATCTCAATTCTGCGTATG
77320 C
1 C
77321 TATGTATCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (35 bp):
CATTATCAGCTTTGTTTATCTCAATTCTGCGTATG
Found at i:91751 original size:18 final size:19
Alignment explanation
Indices: 91719--91754 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
91709 TTATTAAATG
91719 TATAAAATAATTTTTTGAT
1 TATAAAATAATTTTTTGAT
91738 TATAAAAT-ATTTTTTGA
1 TATAAAATAATTTTTTGA
91755 ATTTCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATAAAATAATTTTTTGAT
Found at i:95791 original size:64 final size:63
Alignment explanation
Indices: 95695--95834 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
95685 CACATTGAAT
* *
95695 GTGCATCGATGCATTCTTTAAAGAAGAAACATCGAATGCAAATGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCATCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGCAT-AGGTA
* * * * * *
95758 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCAT-CCTTTAAAGAAG-AAACATCGAAGGCAAATGGTGCATCGATGCATAGGTA
95822 GTGCATCGATGCA
1 GTGCATCGATGCA
95835 CATGTTAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGCATAGGTA
Found at i:96869 original size:31 final size:31
Alignment explanation
Indices: 96832--96954 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
96822 GAGTCGAGGG
* * *
96832 TTTACCTATGTCTTTCGAGACATATGGACAG
1 TTTACCTAGGTCTTTCGAGACCTATGGACAA
96863 TTTACCTAGGTTCTTT-GAGACCTATGGACAA
1 TTTACCTAGG-TCTTTCGAGACCTATGGACAA
96894 TTTACCTAGGT-TCTTCTG-GACCTATGGACAA
1 TTTACCTAGGTCT-TTC-GAGACCTATGGACAA
* *
96925 TTTACCTAGGT-TCGTCGGGACCTATGGACA
1 TTTACCTAGGTCT-TTCGAGACCTATGGACA
96955 GTTGCCGAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
29 1 0.01
30 4 0.05
31 72 0.87
32 6 0.07
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (31 bp):
TTTACCTAGGTCTTTCGAGACCTATGGACAA
Found at i:97006 original size:29 final size:30
Alignment explanation
Indices: 96943--97014 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
96933 GGTTCGTCGG
* * *
96943 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTATGGATAGTTACCGAGGGTCTTTAT
96973 GACCTATGGATAGTTACCG-GGGTCTTTGA-
1 GACCTATGGATAGTTACCGAGGGTCTTT-AT
*
97002 GACCTCTGGATAG
1 GACCTATGGATAG
97015 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (30 bp):
GACCTATGGATAGTTACCGAGGGTCTTTAT
Found at i:97305 original size:2 final size:2
Alignment explanation
Indices: 97298--97357 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
97288 ACATGACATG
97298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97340 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
97358 GTTATATGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99470 original size:90 final size:89
Alignment explanation
Indices: 99316--99490 Score: 314
Period size: 90 Copynumber: 2.0 Consensus size: 89
99306 TAACACACAC
99316 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
* *
99381 TAATTAATTGGAATTTAATAATCT
66 TAATTAATTGAAATTAAATAATCT
*
99405 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
99470 TTAATTAATTGAAATTAAATA
65 TTAATTAATTGAAATTAAATA
99491 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
89 32 0.39
90 50 0.61
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
TAATTAATTGAAATTAAATAATCT
Found at i:101066 original size:64 final size:64
Alignment explanation
Indices: 100997--101153 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 64
100987 TTGAAGGTAT
*
100997 ATCGATGCACAGGTAGTGCATCGATGCACTCTT-TTAA-AATAAAAAGATCGAATGCAA-TTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCA-TCTTATTAATAAT-AAAACATCGAATGCAATTTA-T
101059 GC
63 GC
* * *
101061 ATCGATGCATAAGGCA-TGCATCGATGCATCTTATTAATAATAAAACATCGAATGCAATTTATGT
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCTTATTAATAATAAAACATCGAATGCAATTTATGC
* *
101125 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
101154 ACCTTCATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 7 0.09
64 63 0.79
65 10 0.12
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCTTATTAATAATAAAACATCGAATGCAATTTATGC
Found at i:101574 original size:29 final size:29
Alignment explanation
Indices: 101535--101673 Score: 253
Period size: 29 Copynumber: 4.8 Consensus size: 29
101525 TATGTGATAT
101535 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
101565 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
101594 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
101623 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
101652 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
101674 ACATATGAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.07
29 95 0.89
30 5 0.05
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:107453 original size:64 final size:65
Alignment explanation
Indices: 107354--107495 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 65
107344 TTTTTGAACT
** * * *
107354 GTGCATCGATGCA-CTCTTTTAAAATAAAAAGATCGAATGCAA-TTAGTGCATCGATGCATAATG
1 GTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTTA-TGCACCGATGCACAA-G
107417 CA
64 CA
*
107419 -TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTTATGCACCGATGCACAAGT
1 GTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCAATTTATGCACCGATGCACAAGC
107481 A
65 A
107482 GTGCATCGATGCAT
1 GTGCATCGATGCAT
107496 ACCTTCATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
63 2 0.03
64 58 0.87
65 7 0.10
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (65 bp):
GTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTTATGCACCGATGCACAAGCA
Found at i:107913 original size:29 final size:29
Alignment explanation
Indices: 107874--107983 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
107864 TATGTGATAT
107874 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
107904 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
107933 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
107962 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
107984 ACATATGAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:108101 original size:15 final size:15
Alignment explanation
Indices: 108067--108095 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
108057 CGAGGGTATA
108067 ATAGTCCTTCGGGAC
1 ATAGTCCTTCGGGAC
108082 ATAGTCCTTCGGGA
1 ATAGTCCTTCGGGA
108096 TGTAGTGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (15 bp):
ATAGTCCTTCGGGAC
Found at i:108230 original size:18 final size:18
Alignment explanation
Indices: 108203--108268 Score: 125
Period size: 18 Copynumber: 3.7 Consensus size: 18
108193 AGCATTAGTG
108203 CACA-ACCTCTATGTACT
1 CACATACCTCTATGTACT
108220 CACATACCTCTATGTACT
1 CACATACCTCTATGTACT
108238 CACATACCTCTATGTACT
1 CACATACCTCTATGTACT
108256 CACATACCTCTAT
1 CACATACCTCTAT
108269 TCTCAATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
17 4 0.08
18 44 0.92
ACGTcount: A:0.29, C:0.35, G:0.05, T:0.32
Consensus pattern (18 bp):
CACATACCTCTATGTACT
Found at i:117627 original size:23 final size:23
Alignment explanation
Indices: 117601--117648 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
117591 GGAAGCCAAA
117601 TTAGCGGAAAGTGTTCACAATTT
1 TTAGCGGAAAGTGTTCACAATTT
117624 TTAGCGGAAAGTGTTCACAATTT
1 TTAGCGGAAAGTGTTCACAATTT
117647 TT
1 TT
117649 TGTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (23 bp):
TTAGCGGAAAGTGTTCACAATTT
Found at i:123085 original size:23 final size:22
Alignment explanation
Indices: 123038--123096 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
123028 AAATACAGAC
* *
123038 GAAAATGTGTCAAAAAGCAAAA
1 GAAAATATGTCATAAAGCAAAA
*
123060 GAAAATATGTCATAGAGACAAAA
1 GAAAATATGTCATAAAG-CAAAA
*
123083 GAAAACATGTCATA
1 GAAAATATGTCATA
123097 CATATAGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (22 bp):
GAAAATATGTCATAAAGCAAAA
Found at i:124607 original size:21 final size:21
Alignment explanation
Indices: 124583--124627 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
124573 AACGGCTGAA
*
124583 AAACGTGCCAAAATG-CAGAAG
1 AAACGTACCAAAA-GACAGAAG
*
124604 AAACGTATCAAAAGACAGAAG
1 AAACGTACCAAAAGACAGAAG
124625 AAA
1 AAA
124628 ACATGTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.56, C:0.16, G:0.20, T:0.09
Consensus pattern (21 bp):
AAACGTACCAAAAGACAGAAG
Found at i:124650 original size:23 final size:23
Alignment explanation
Indices: 124598--124668 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
124588 TGCCAAAATG
* *
124598 CAGAAG-AAACGTATCA-AAAGA
1 CAGAAGAAAACATGTCATAAAGA
*
124619 CAGAAGAAAACATGTTATAAAGA
1 CAGAAGAAAACATGTCATAAAGA
*
124642 CA-AAGGAAAACATGTCATACAGA
1 CAGAA-GAAAACATGTCATAAAGA
124665 CAGA
1 CAGA
124669 CTTATTGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.15
22 9 0.22
23 25 0.61
24 1 0.02
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.13
Consensus pattern (23 bp):
CAGAAGAAAACATGTCATAAAGA
Found at i:124717 original size:11 final size:10
Alignment explanation
Indices: 124678--124716 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
124668 ACTTATTGAA
*
124678 AATAAAAAAC
1 AATAAAAAAG
*
124688 AAGAAAAAAG
1 AATAAAAAAG
124698 AATAAAAAAG
1 AATAAAAAAG
124708 AATAAAAAA
1 AATAAAAAA
124717 ATATCGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (10 bp):
AATAAAAAAG
Found at i:126980 original size:42 final size:42
Alignment explanation
Indices: 126929--127016 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
126919 TCGCAACGCG
* *
126929 ATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCA
1 ATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTTGCA
** * *
126971 ATAGGCGAAGTTCGTGTTGCGATTCATTTCAAATTCGTTGCG
1 ATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTTGCA
127013 ATAG
1 ATAG
127017 TCCAAATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (42 bp):
ATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTTGCA
Found at i:127105 original size:6 final size:6
Alignment explanation
Indices: 127094--127119 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
127084 GACACGTATT
127094 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
127120 ACGGGACGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:127791 original size:6 final size:5
Alignment explanation
Indices: 127748--127787 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
127738 CCGTCCAGTC
127748 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
127788 TGGTTGTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:127796 original size:6 final size:6
Alignment explanation
Indices: 127751--127797 Score: 57
Period size: 5 Copynumber: 8.5 Consensus size: 6
127741 TCCAGTCTCG
*
127751 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTTGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
127795 GGT
1 GGT
127798 AATACGTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 20 0.50
6 20 0.50
ACGTcount: A:0.00, C:0.15, G:0.55, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:127933 original size:41 final size:41
Alignment explanation
Indices: 127870--127963 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
127860 AATGTAATAT
127870 TTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAAC
1 TTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAAC
127911 TTCGCCTATCGCAAC-AATTTGGAATGAATCGCAACGCGAAC
1 TTCGCCTATCGCAACGAA-TTGGAATGAATCGCAACGCGAAC
*
127952 TTCGACTATCGC
1 TTCGCCTATCGC
127964 GTTGCGAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 2 0.04
41 49 0.96
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
TTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAAC
Found at i:136994 original size:19 final size:19
Alignment explanation
Indices: 136953--136996 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
136943 TTTATTTAAA
* *
136953 ATAATAAATATTCTAAATT
1 ATAATAAAGATTCTAAATC
136972 ATAATAAAGATT-TATAATC
1 ATAATAAAGATTCTA-AATC
136991 ATAATA
1 ATAATA
136997 GTAAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATAAAGATTCTAAATC
Found at i:150594 original size:19 final size:19
Alignment explanation
Indices: 150546--150597 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
150536 CGCATTAATC
150546 AATTATAATATTTGTGTAT
1 AATTATAATATTTGTGTAT
*
150565 -ATATATCATATTTGTGTATT
1 AAT-TATAATATTTGTGTA-T
150585 AATTATATATATT
1 AATTATA-ATATT
150598 ATGTCATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.07
19 14 0.52
20 4 0.15
21 7 0.26
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (19 bp):
AATTATAATATTTGTGTAT
Found at i:159225 original size:67 final size:67
Alignment explanation
Indices: 159153--159286 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
159143 TTGAAAAGTT
159153 TAGCACAAACTGTTTCTTTTATTCCATCTATAACCATCATTTCAGTACTATTGCCTATCGAATGC
1 TAGCACAAACTGTTTCTTTTATTCCATCTATAACCATCATTTCAGTACTATTGCCTATCGAATGC
159218 AC
66 AC
*
159220 TAGCACAAACTGTTTCTTTTATTCTATCTATAACCATCATTTCAGTACTATTGCCTATCGAATGC
1 TAGCACAAACTGTTTCTTTTATTCCATCTATAACCATCATTTCAGTACTATTGCCTATCGAATGC
159285 AC
66 AC
159287 CTCCTAAATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (67 bp):
TAGCACAAACTGTTTCTTTTATTCCATCTATAACCATCATTTCAGTACTATTGCCTATCGAATGC
AC
Found at i:159531 original size:64 final size:65
Alignment explanation
Indices: 159408--159535 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 65
159398 TTTAGTTGTA
* *
159408 GCCTGTAGAATTTTGAAATAGAATGCTTTCTCATATCTGTATTCATCGACATTATGGGTATATAT
1 GCCTGTAGAATTTTGAAATAGAATGCTTTCTCATATCTGTATTCATCAACACTATGGGTATATAT
159473 GCCTGTAGAATTTTGAAATAGAATGC-TTCTCATATCTGTATTCATCAACACTATGGGTATATA
1 GCCTGTAGAATTTTGAAATAGAATGCTTTCTCATATCTGTATTCATCAACACTATGGGTATATA
159536 CAAGTATAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 35 0.57
65 26 0.43
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (65 bp):
GCCTGTAGAATTTTGAAATAGAATGCTTTCTCATATCTGTATTCATCAACACTATGGGTATATAT
Found at i:163043 original size:71 final size:72
Alignment explanation
Indices: 162941--163081 Score: 196
Period size: 70 Copynumber: 2.0 Consensus size: 72
162931 TTTTAAATTT
* * *
162941 AATAATTAAAAAATATTTTTAAACATAATTTTTTATTTTAAACACTCAAAAATATGATAATTCAA
1 AATAATTAAAAAATATTTTTAAACATAATTTTTTA-TTAAAAAACTCAAAAACATGATAATTCAA
163006 TGGGTCCC
65 TGGGTCCC
* * * *
163014 AATAATT-AAAAATA-TTTTAAACATTATTTTTTATTAAAAAACTCGAAAACATGGTGATTCAAT
1 AATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAAT
163077 GGGTC
66 GGGTC
163082 TCATTTGTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 29 0.48
71 18 0.30
72 7 0.11
73 7 0.11
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.38
Consensus pattern (72 bp):
AATAATTAAAAAATATTTTTAAACATAATTTTTTATTAAAAAACTCAAAAACATGATAATTCAAT
GGGTCCC
Found at i:164546 original size:6 final size:6
Alignment explanation
Indices: 164532--164581 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
164522 AGATTAATCG
* * *
164532 AGAAGA AGAACA AGAACG AGAAGA AGAACA AGAACA AG-ACGA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAAC-A AGAACA
164580 AG
1 AG
164582 TTAGGCGCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 2 0.05
6 33 0.89
7 2 0.05
ACGTcount: A:0.62, C:0.12, G:0.26, T:0.00
Consensus pattern (6 bp):
AGAACA
Found at i:164553 original size:18 final size:18
Alignment explanation
Indices: 164530--164581 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
164520 TGAGATTAAT
164530 CGAGAAGAAGAACAAGAA
1 CGAGAAGAAGAACAAGAA
164548 CGAGAAGAAGAACAAGAA
1 CGAGAAGAAGAACAAGAA
* *
164566 CAAGACGAAGAACAAG
1 CGAGAAGAAGAACAAG
164582 TTAGGCGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.60, C:0.13, G:0.27, T:0.00
Consensus pattern (18 bp):
CGAGAAGAAGAACAAGAA
Found at i:171558 original size:3 final size:3
Alignment explanation
Indices: 171550--171575 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
171540 ATATTAGATA
171550 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
171576 GCCAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:171602 original size:1 final size:1
Alignment explanation
Indices: 171598--171636 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
171588 AAATAATAAT
* **
171598 AAAAAAATAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
171637 GGTAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.92, C:0.00, G:0.05, T:0.03
Consensus pattern (1 bp):
A
Done.