Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002085.1 Hibiscus syriacus cultivar Beakdansim tig00004257_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: 92238
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:492 original size:35 final size:35
Alignment explanation
Indices: 434--549 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
424 CCCATTATCA
* * *
434 TTTTTC-AACAAACATCTATCAAACTTTGAAAAAC
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
*
468 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
* * *
503 ATTTTCAAAGAAACATTTTCCAAACTTTGAAAACCAT
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAA--AC
540 TTTTTCAAAG
1 TTTTTCAAAG
550 TTAGTTACCA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
34 6 0.09
35 55 0.79
37 9 0.13
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (35 bp):
TTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
Found at i:561 original size:35 final size:36
Alignment explanation
Indices: 453--576 Score: 134
Period size: 35 Copynumber: 3.6 Consensus size: 36
443 AAACATCTAT
* *
453 CAAACTTTGAAAA--ACTTTTTCAAAGAAACATTTAC
1 CAAACTTTGAAAACCATTTTTTCAAAG-AACAGTTAC
* *
488 CAAACTTTGAAAACCA--TTTTCAAAGAAACATTTTC
1 CAAACTTTGAAAACCATTTTTTCAAAG-AACAGTTAC
**
523 CAAACTTTGAAAACCATTTTTTCAAAG-TTAGTTAC
1 CAAACTTTGAAAACCATTTTTTCAAAGAACAGTTAC
558 CAAAC-TTGAAAACCATTTT
1 CAAACTTTGAAAACCATTTT
577 ATAATTTCAA
Statistics
Matches: 80, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
34 14 0.17
35 56 0.70
37 10 0.12
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
CAAACTTTGAAAACCATTTTTTCAAAGAACAGTTAC
Found at i:3837 original size:46 final size:46
Alignment explanation
Indices: 3787--3885 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 46
3777 CGAAGTGCCA
* * *
3787 CGTAGAAATGTTCCGAAA-GACCACATA-AATATGTCTCGAAAGACCG
1 CGTAGAAAAG-TCCCAAAGGACCACATAGAAT-TGTCCCGAAAGACCG
* * *
3833 CGTAGAAAAGTCCCAAAGGACCACGTAGAATTGTCCCGAAGGACTG
1 CGTAGAAAAGTCCCAAAGGACCACATAGAATTGTCCCGAAAGACCG
3879 CGTAGAA
1 CGTAGAA
3886 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 6 0.13
46 36 0.80
47 3 0.07
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (46 bp):
CGTAGAAAAGTCCCAAAGGACCACATAGAATTGTCCCGAAAGACCG
Found at i:3874 original size:23 final size:23
Alignment explanation
Indices: 3745--3885 Score: 83
Period size: 23 Copynumber: 6.1 Consensus size: 23
3735 TGCTCATATA
* *
3745 AATTGTACCGAAGTG-CCGCGTAG
1 AATTGTCCCGAAG-GACCACGTAG
3768 AATATG-CACCGAAGTG-CCACGTAG
1 AAT-TGTC-CCGAAG-GACCACGTAG
* * * *
3792 AAATGTTCCGAAAGACCACATA-
1 AATTGTCCCGAAGGACCACGTAG
* * *
3814 AATATGTCTCGAAAGACCGCGTAG
1 AAT-TGTCCCGAAGGACCACGTAG
** *
3838 AAAAGTCCCAAAGGACCACGTAG
1 AATTGTCCCGAAGGACCACGTAG
**
3861 AATTGTCCCGAAGGACTGCGTAG
1 AATTGTCCCGAAGGACCACGTAG
3884 AA
1 AA
3886 CCCTCGACTC
Statistics
Matches: 90, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
22 3 0.03
23 66 0.73
24 21 0.23
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACGTAG
Found at i:6221 original size:32 final size:32
Alignment explanation
Indices: 6135--6242 Score: 96
Period size: 32 Copynumber: 3.4 Consensus size: 32
6125 ATAGGTCCCG
* * * **
6135 AAGAACCTAGGTAA-ACTGTCCATATATTCCT
1 AAGAACATAGGTAATTCTGTCCATATGTTCGA
* * *
6166 TAGAACATA-GTTATACTGTCCATATGTGTCGA
1 AAGAACATAGGTAATTCTGTCCATATGT-TCGA
*
6198 AAG-ACATAGGTAATTCTGTCCATATGTTCTA
1 AAGAACATAGGTAATTCTGTCCATATGTTCGA
*
6229 TAGAACATAGGTAA
1 AAGAACATAGGTAA
6243 ACCCTCGACT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
30 3 0.05
31 29 0.47
32 30 0.48
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (32 bp):
AAGAACATAGGTAATTCTGTCCATATGTTCGA
Found at i:9682 original size:12 final size:12
Alignment explanation
Indices: 9665--9696 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
9655 ATCGGGTAAT
9665 CGGGGAAAATCG
1 CGGGGAAAATCG
9677 CGGGGAAAATCG
1 CGGGGAAAATCG
*
9689 TGGGGAAA
1 CGGGGAAA
9697 CAGGTATCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.44, T:0.09
Consensus pattern (12 bp):
CGGGGAAAATCG
Found at i:9757 original size:4 final size:4
Alignment explanation
Indices: 9748--9833 Score: 53
Period size: 4 Copynumber: 23.5 Consensus size: 4
9738 TTGGGCTGAG
* * *
9748 TATA TATA TATT TAAA T-TA AATA TATA T-TA TATA TATA TATA TAT-
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
9793 TA-A TTTA AAT- TAAA TTTA T-TA -ATA T-TA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
9834 ATAATAATTA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
3 15 0.25
4 46 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:9787 original size:6 final size:6
Alignment explanation
Indices: 9748--9833 Score: 53
Period size: 6 Copynumber: 15.7 Consensus size: 6
9738 TTGGGCTGAG
* * *
9748 TATATA TATATT TAAAT- TAAATA TATAT- TATATA TATATA TATAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
9793 TA-ATT TAAAT- TAAATT TAT-TA -ATAT- TATATA TATATA TATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATA
9834 ATAATAATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
4 4 0.06
5 25 0.37
6 38 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:9799 original size:38 final size:40
Alignment explanation
Indices: 9748--9838 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 40
9738 TTGGGCTGAG
9748 TATATATAT-ATTTAAATTAAA-TA-T-ATATTATATATA
1 TATATATATAATTTAAATTAAATTATTAATATTATATATA
9784 TATATATATTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATA-TAATTTAAATTAAA-TTATTAATATTATATATA
9826 TATATATAATAAT
1 TATATAT-ATAAT
9839 AATTATTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
36 8 0.17
37 1 0.02
38 12 0.25
40 2 0.04
41 1 0.02
42 23 0.48
43 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
TATATATATAATTTAAATTAAATTATTAATATTATATATA
Found at i:9851 original size:36 final size:40
Alignment explanation
Indices: 9748--9854 Score: 113
Period size: 42 Copynumber: 2.8 Consensus size: 40
9738 TTGGGCTGAG
* *
9748 TATATAT-ATATTTAAATTAA-ATA-T-ATATTATATATA
1 TATATATAATAATTAAATTAATTTATTAATATTATATATA
*
9784 TATATATATTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATAATAA-TTAAATT-AATTTATTAATATTATATATA
9826 TATATATAATAA-T-AATT-ATTT-TTAATATT
1 TATATATAATAATTAAATTAATTTATTAATATT
9855 TATCAGGCCG
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
36 15 0.25
37 6 0.10
38 7 0.11
39 6 0.10
40 3 0.05
41 1 0.02
42 23 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
TATATATAATAATTAAATTAATTTATTAATATTATATATA
Found at i:13143 original size:8 final size:7
Alignment explanation
Indices: 13130--13202 Score: 50
Period size: 7 Copynumber: 10.9 Consensus size: 7
13120 CTATTTTAAT
13130 TTATATA
1 TTATATA
13137 GTTATATA
1 -TTATATA
13145 TTAT-TAA
1 TTATAT-A
* *
13152 TTATTTC
1 TTATATA
13159 TTATAT-
1 TTATATA
13165 TTA-ATA
1 TTATATA
13171 TTACTA-A
1 TTA-TATA
13178 TTAT-TA
1 TTATATA
13184 TTATAT-
1 TTATATA
*
13190 TTATTTA
1 TTATATA
13197 TTATAT
1 TTATAT
13203 TCATTTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
5 2 0.04
6 18 0.34
7 24 0.45
8 9 0.17
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:13157 original size:26 final size:26
Alignment explanation
Indices: 13128--13200 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
13118 ATCTATTTTA
*
13128 ATTTATATAGTTATATATTATTAATT
1 ATTTATATATTTATATATTATTAATT
* *
13154 ATTTCTTATATTTA-ATATTACTAATT
1 ATTT-ATATATTTATATATTATTAATT
*
13180 A-TTATTATATTTATTTATTAT
1 ATTTA-TATATTTATATATTAT
13201 ATTCATTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 10 0.26
26 21 0.55
27 7 0.18
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (26 bp):
ATTTATATATTTATATATTATTAATT
Found at i:13165 original size:19 final size:19
Alignment explanation
Indices: 13141--13203 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 19
13131 TATATAGTTA
13141 TATATTATTAATTATTTCT
1 TATATTATTAATTATTTCT
*
13160 TATA-T-TTAA-TATTACT
1 TATATTATTAATTATTTCT
* *
13176 AATTATTATTATATTTATTTAT
1 TA-TATTATTA-A-TTATTTCT
13198 TATATT
1 TATATT
13204 CATTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
18 2 0.06
19 7 0.21
20 1 0.03
21 4 0.12
22 6 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTATTAATTATTTCT
Found at i:13197 original size:13 final size:13
Alignment explanation
Indices: 13128--13209 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 13
13118 ATCTATTTTA
*
13128 ATTTA-TATAGTT
1 ATTTATTATATTT
* *
13140 ATATATTATTAATT
1 ATTTATTA-TATTT
*
13154 ATTTCTTATATTT
1 ATTTATTATATTT
* *
13167 A-ATATTACTAATT
1 ATTTATTA-TATTT
13180 A-TTATTATATTT
1 ATTTATTATATTT
*
13192 ATTTATTATATTC
1 ATTTATTATATTT
13205 ATTTA
1 ATTTA
13210 ATTTCTACGT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
12 13 0.24
13 32 0.58
14 10 0.18
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (13 bp):
ATTTATTATATTT
Found at i:14957 original size:2 final size:2
Alignment explanation
Indices: 14950--14988 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14940 ATAATCATTC
14950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14989 ATCATATTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16730 original size:18 final size:18
Alignment explanation
Indices: 16707--16741 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16697 ACTGAAAATC
16707 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
16725 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
16742 TATAATCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:18694 original size:20 final size:21
Alignment explanation
Indices: 18663--18708 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
18653 ACCGGAAACA
* *
18663 TTATTATTTCTACCGGTTTTG
1 TTATTATTTCTACCGATTATG
18684 TTATT-TTTCTACCGATTATG
1 TTATTATTTCTACCGATTATG
18704 TTATT
1 TTATT
18709 GTTGGGCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (21 bp):
TTATTATTTCTACCGATTATG
Found at i:21740 original size:25 final size:26
Alignment explanation
Indices: 21689--21741 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
21679 TTTTTCATTT
* *
21689 TTAAAAGTAAAAATTAAAATTATATG
1 TTAAAAATAAAAATTAAAAATATATG
21715 TTAAAAAT-AAAATTATAAAATA-ATG
1 TTAAAAATAAAAATTA-AAAATATATG
21740 TT
1 TT
21742 TGTTTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (26 bp):
TTAAAAATAAAAATTAAAAATATATG
Found at i:22031 original size:22 final size:22
Alignment explanation
Indices: 22003--22074 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
21993 TTCCATTTCG
22003 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
22025 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
22044 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
22066 CGTTGCGAT
1 CGTTGCGAT
22075 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:22048 original size:19 final size:19
Alignment explanation
Indices: 22024--22089 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
22014 TCTACAGTTG
22024 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
22043 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
22064 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
22084 TCGTTG
1 TCGTTG
22090 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:22048 original size:41 final size:41
Alignment explanation
Indices: 21983--22096 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
21973 TTGAAAATCG
*
21983 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
22025 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
22066 CGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
22097 TAAAAAAAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 52 0.75
42 14 0.20
43 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:22868 original size:20 final size:20
Alignment explanation
Indices: 22843--23047 Score: 122
Period size: 20 Copynumber: 10.1 Consensus size: 20
22833 ACTGTAGACT
*
22843 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
22863 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** **
22883 AGCGCAACGCGATTTTCATCT
1 ATCGCAACGCGAAATGGA-AA
*
22904 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
22924 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
**
22945 ATCGCAACGCGAAATTAAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
22965 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATGGAA-A
*
22986 ATCGCAACGCGAAATGGGAA
1 ATCGCAACGCGAAATGGAAA
** ** *
23006 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
23027 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
23047 A
1 A
23048 GCACAACGCA
Statistics
Matches: 131, Mismatches: 50, Indels: 8
0.69 0.26 0.04
Matches are distributed among these distances:
20 75 0.57
21 56 0.43
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:22911 original size:21 final size:21
Alignment explanation
Indices: 22885--23079 Score: 121
Period size: 21 Copynumber: 9.5 Consensus size: 21
22875 AATGGAAAAG
*
22885 CGCAACGCGATTTTCATCTAT
1 CGCAACGCGATTTTCAACTAT
* ** ** * *
22906 CGCAACGTGAAATGGAA-AAG
1 CGCAACGCGATTTTCAACTAT
22926 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
** **
22947 CGCAACGCGAAATT-AAAAAT
1 CGCAACGCGATTTTCAACTAT
*
22967 CGCAACGCGATTTCCAACTAT
1 CGCAACGCGATTTTCAACTAT
* ***
22988 CGCAACGCGAAATGGGAA--AT
1 CGCAACGCG-ATTTTCAACTAT
23008 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
** ** * *
23029 CGCAACGCGAAATGGAA-AAG
1 CGCAACGCGATTTTCAACTAT
* *
23049 CACAACGCAATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
23070 CGCAACGCGA
1 CGCAACGCGA
23080 AATGGTTGTT
Statistics
Matches: 120, Mismatches: 48, Indels: 12
0.67 0.27 0.07
Matches are distributed among these distances:
19 4 0.03
20 51 0.43
21 61 0.51
22 4 0.03
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:22918 original size:41 final size:41
Alignment explanation
Indices: 22863--23084 Score: 354
Period size: 41 Copynumber: 5.4 Consensus size: 41
22853 GAAATGGAAA
*
22863 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCATCT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
*
22904 ATCGCAACGTGAAATGGAAAAGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
** * *
22945 ATCGCAACGCGAAATTAAAAATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
* *
22986 ATCGCAACGCGAAATGGGAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
* *
23027 ATCGCAACGCGAAATGGAAAAGCACAACGCAATTTTCAACT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
23068 ATCGCAACGCGAAATGG
1 ATCGCAACGCGAAATGG
23085 TTGTTCCCAA
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 166 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
Found at i:23456 original size:6 final size:6
Alignment explanation
Indices: 23445--23484 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
23435 TCTCGGGTCA
* * *
23445 GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG GGTC
23485 ATACGTGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.25
Consensus pattern (6 bp):
GGTCGG
Found at i:23462 original size:12 final size:12
Alignment explanation
Indices: 23445--23484 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
23435 TCTCGGGTCA
*
23445 GGTCGGGGTCGG
1 GGTCGGGGTCGT
23457 GGTCGGGGTCGT
1 GGTCGGGGTCGT
*
23469 GGTCGTGGTCGT
1 GGTCGGGGTCGT
23481 GGTC
1 GGTC
23485 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.25
Consensus pattern (12 bp):
GGTCGGGGTCGT
Found at i:23613 original size:22 final size:22
Alignment explanation
Indices: 23583--23654 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
23573 AATTTGGAAA
*
23583 ATCGAAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
23605 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
23624 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
23646 ATCGCAACG
1 ATCGCAACG
23655 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:23618 original size:41 final size:41
Alignment explanation
Indices: 23561--23654 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
23551 TTTTTTTTTA
*
23561 ACTATCACAACGAATTTGGAAAATCGAAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGAAACGACAACTGTAG
*
23602 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGAAACGACAACTGTAG
23643 ACTATCGCAACG
1 ACTATCGCAACG
23655 CGAAATGGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGAAACGACAACTGTAG
Found at i:23629 original size:19 final size:19
Alignment explanation
Indices: 23568--23633 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
23558 TTAACTATCA
23568 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * * **
23587 AAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
23609 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
23628 CAACGA
1 CAACGA
23634 CAACTGTAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 18 0.53
20 2 0.06
21 2 0.06
22 12 0.35
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:23671 original size:20 final size:20
Alignment explanation
Indices: 23646--23783 Score: 141
Period size: 20 Copynumber: 6.8 Consensus size: 20
23636 ACTGTAGACT
23646 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
23666 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
23686 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
23707 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
23727 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
23748 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
23768 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
23784 CAACGCGAAT
Statistics
Matches: 91, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
20 63 0.69
21 28 0.31
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:23714 original size:21 final size:21
Alignment explanation
Indices: 23688--23759 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
23678 AATAGAAAAG
23688 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
** ** * *
23709 CGCAACGCGAAATGGAA-AAG
1 CGCAACGCGATTTTCAACTAT
23729 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
23750 CGCAACGCGA
1 CGCAACGCGA
23760 AATGGAAAAT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:23716 original size:41 final size:41
Alignment explanation
Indices: 23666--23779 Score: 210
Period size: 41 Copynumber: 2.8 Consensus size: 41
23656 GAAATGGAAA
*
23666 ATCGCAACGCGAAATAGAAAAGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
23707 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
*
23748 ATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ATCGCAACGCGAAATGGAAAAGCGCAACGCGA
23780 AATGCAACGC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.15
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACT
Found at i:23876 original size:754 final size:749
Alignment explanation
Indices: 22362--23787 Score: 2291
Period size: 754 Copynumber: 1.9 Consensus size: 749
22352 ATTGAGCCTT
*
22362 AAATAGTGATATTATTTTTGAATGTTTTGCTTAAAATTGCAATAATCGCGATTGATTGTAGATTG
1 AAATAGTGATATTATTTTTGAATGTTTTGCTTAAAATTGCAATAATCGCGATTGATTATAGATTG
22427 ACTTTTAATTATGACATATTTAATTGTATAATACTAATGCAATTAGTTGCTGATTCAGTTGTTTT
66 ACTTTTAATTATGACATATTTAATTGTATAATACTAATGCAATTAGTTGCTGATTCAGTTGTTTT
22492 AAGGTGCATGATTGTTAATTGTTTCCTGAATAATCACATTGTATTGGAAACAAGTGTTGGTAATG
131 AAGGTGCATGATTGTTAATTGTTTCCTGAATAATCACATTGTATTGGAAACAAGTGTTGGTAATG
22557 CTTAATCCCACATAGTATTGGAAACACTATTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTC
196 CTTAATCCCACATAGTATTGGAAACACTATTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTC
22622 CTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGCCGTCGCCGCCGTCCGTCTCGTCTCGG
261 CTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGCCGTCGCCGCCGTCCGTCTCGTCTCGG
* *
22687 GTCGGGTCGGGGTCGGGGTCGTGGTTGTGGTCGTGGTCATACATGTCTTTGACACGTCCGCGCGG
326 GTCGGGTCGGGGTCGGGGTCGTGGTCGTGGTCGTGGTCATACATGTCTTTGACACGTCCACGCGG
22752 ATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATCTTTTTTTAACTATCACAACGAATTTG
391 ATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATCTTTTTTTAACTATCACAACGAATTTG
*
22817 GAAAATCGCAACGACAACTGTAGACTATCGCAATGCGAAATGGAAAATCGCAACGCGAAATGGAA
456 GAAAATCGAAACGACAACTGTAGACTATCGCAA-GCGAAATGGAAAATCGCAACGCGAAATGGAA
** * ** * *
22882 AAGCGCAACGCGATTTTCATCTATCGCAACGTGAAATGGAAAAGCGCAACGCGATTTTCAACTAT
520 AAGCGCAACGCGAAATGCATAAATCGCAACGCGAAATAGAAAAGCGCAACGCGATTTTCAACTAT
* * *
22947 CGCAACGCGAAATTAAAAATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGGAAATCGCA
585 CGCAACGCGAAATGAAAAAGCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAATCGCA
** * * *
23012 ACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAGCACAACGCAATTTTCAACTATCGCAACG
650 ACGCGAAATGCAAC-AGCGCAACGCGAAATGGAAAAGCACAACGCAA-TTTCAACGATCGCAACG
* ** ** *****
23077 CGAAATGGTTGTTCCCAATACTATGTGGGATTGAGCCTT
713 CGAAATGGTTGGT-CCAATA-TATGTGAAATCAAAAAAA
23116 AAATAGTGATATTATTTTTGAATGTTTTGCTTAAAATTGCAATAATCGCGATTGATTATAGATTG
1 AAATAGTGATATTATTTTTGAATGTTTTGCTTAAAATTGCAATAATCGCGATTGATTATAGATTG
23181 ACTTTTAATTATGACATATTTAATTGTATAATACTAATGCAATTAGTTGCTGATTCAGTTGTTTT
66 ACTTTTAATTATGACATATTTAATTGTATAATACTAATGCAATTAGTTGCTGATTCAGTTGTTTT
23246 AAGGTGCATGATTGTTAATTGTTTCCTGAATAATCACATTGTATTGGAAACAAGTGTTGGTAATG
131 AAGGTGCATGATTGTTAATTGTTTCCTGAATAATCACATTGTATTGGAAACAAGTGTTGGTAATG
*
23311 CTTAATCCCACATAGTATTGGAAACACTATTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTT
196 CTTAATCCCACATAGTATTGGAAACACTATTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTC
* * * *
23376 CTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGTCGTCGTCGCTGTCTGTCTCGTCTCGG
261 CTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGCCGTCGCCGCCGTCCGTCTCGTCTC--
*
23441 GTCAGGTCGGGGTCGGGGTCGGGGTCGTGGTCGTGGTCGTGGTCATACGTGTCTTTGACACGTCC
324 G---GGTC-GGGTCGGGGTCGGGGTCGTGGTCGTGGTCGTGGTCATACATGTCTTTGACACGTCC
23506 ACGCGGATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATCTTTTTTTTTAACTATCACAA
385 ACGCGGATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATC--TTTTTTTAACTATCACAA
*
23571 CGAATTTGGAAAATCGAAACGACAACTGTAGACTATCGCAA-CGAATTTGGAAAATCGCAACGAC
448 CGAATTTGGAAAATCGAAACGACAACTGTAGACTATCGCAAGCGAA-ATGGAAAATCGCAACG-C
* ** * *
23635 -AACTGTAGACTATCGCAACGCGAAATGGA-AAATCGCAACGCGAAATAGAAAAGCGCAACGCGA
511 GAAATG--GAAAAGCGCAACGCGAAATGCATAAATCGCAACGCGAAATAGAAAAGCGCAACGCGA
* *
23698 TTTTCAACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATCGCAACGCGAAAT
574 TTTTCAACTATCGCAACGCGAAATGAAAAAGCGCAACGCGATTTCCAACTATCGCAACGCGAAAT
23763 GGAAAATCGCAACGCGAAATGCAAC
639 GGAAAATCGCAACGCGAAATGCAAC
23788 GCGAATTTGC
Statistics
Matches: 629, Mismatches: 31, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
754 317 0.50
756 1 0.00
759 4 0.01
760 102 0.16
761 19 0.03
762 171 0.27
763 15 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (749 bp):
AAATAGTGATATTATTTTTGAATGTTTTGCTTAAAATTGCAATAATCGCGATTGATTATAGATTG
ACTTTTAATTATGACATATTTAATTGTATAATACTAATGCAATTAGTTGCTGATTCAGTTGTTTT
AAGGTGCATGATTGTTAATTGTTTCCTGAATAATCACATTGTATTGGAAACAAGTGTTGGTAATG
CTTAATCCCACATAGTATTGGAAACACTATTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTC
CTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGCCGTCGCCGCCGTCCGTCTCGTCTCGG
GTCGGGTCGGGGTCGGGGTCGTGGTCGTGGTCGTGGTCATACATGTCTTTGACACGTCCACGCGG
ATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAAATCTTTTTTTAACTATCACAACGAATTTG
GAAAATCGAAACGACAACTGTAGACTATCGCAAGCGAAATGGAAAATCGCAACGCGAAATGGAAA
AGCGCAACGCGAAATGCATAAATCGCAACGCGAAATAGAAAAGCGCAACGCGATTTTCAACTATC
GCAACGCGAAATGAAAAAGCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAATCGCAA
CGCGAAATGCAACAGCGCAACGCGAAATGGAAAAGCACAACGCAATTTCAACGATCGCAACGCGA
AATGGTTGGTCCAATATATGTGAAATCAAAAAAA
Found at i:24568 original size:39 final size:39
Alignment explanation
Indices: 24476--24575 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
24466 CATTTATGGG
* * * *
24476 GTATTCTTAATTTGCTTGAAGATGCCATACAATTGTGAA
1 GTATTCATCATTTGCTTGAAGACGCCATACAATCGTGAA
* *
24515 GTATTCTTCATTTGCTTGAAGACGTCATACAATCGTAGAA
1 GTATTCATCATTTGCTTGAAGACGCCATACAATCGT-GAA
*
24555 -TCTTCAT-ATTTTGCTTGAAGA
1 GTATTCATCA-TTTGCTTGAAGA
24576 AGCATGGTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.02
39 49 0.92
40 3 0.06
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (39 bp):
GTATTCATCATTTGCTTGAAGACGCCATACAATCGTGAA
Found at i:31964 original size:6 final size:6
Alignment explanation
Indices: 31955--31993 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
31945 TAAATTAAAC
31955 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
31994 TTAACCTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTAAT
Found at i:35147 original size:19 final size:19
Alignment explanation
Indices: 35123--35161 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35113 TTAGAAAATG
*
35123 AAATATTCTA-AATTACAAT
1 AAATATT-TACAATCACAAT
35142 AAATATTTACAATCACAAT
1 AAATATTTACAATCACAAT
35161 A
1 A
35162 GTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATTTACAATCACAAT
Found at i:39145 original size:30 final size:30
Alignment explanation
Indices: 39074--39136 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
39064 TTTTTTAATA
* **
39074 TTTTCAGAT-ATTTTTTAGCGTCTAGTAATG
1 TTTTCAG-TCATTTTTTAGCGCCTAACAATG
39104 TTTTCAGTCATTTTTTAGCGCCTAACAATG
1 TTTTCAGTCATTTTTTAGCGCCTAACAATG
39134 TTT
1 TTT
39137 CTGGTCATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (30 bp):
TTTTCAGTCATTTTTTAGCGCCTAACAATG
Found at i:39649 original size:2 final size:2
Alignment explanation
Indices: 39642--39696 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
39632 TTGTCCTTAT
39642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39684 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
39697 TTTTTTAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39812 original size:37 final size:37
Alignment explanation
Indices: 39738--39812 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
39728 TACTATAATT
**
39738 AATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
* * *
39775 AATTTATATAATTTTTTTTACAAAA-TTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTTAAAAACATAA
39812 A
1 A
39813 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.59
38 13 0.41
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
Found at i:40456 original size:21 final size:20
Alignment explanation
Indices: 40370--40526 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
40360 AAATGACCAA
**
40370 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
40389 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
40409 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
40429 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
40450 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
40470 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
40490 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
40511 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
40527 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:40479 original size:41 final size:41
Alignment explanation
Indices: 40370--40526 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
40360 AAATGACCAA
* **
40370 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
40409 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
40450 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
40491 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
40527 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:40536 original size:20 final size:20
Alignment explanation
Indices: 40513--40686 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
40503 GCGAATATGA
40513 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
40533 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
40553 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
40573 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
40593 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
40613 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
40633 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
40653 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
40674 AAATCGCAACGCG
1 AAATCGCAACGCG
40687 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:40557 original size:40 final size:39
Alignment explanation
Indices: 40493--40687 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
40483 CGATTTTCCA
* ** *
40493 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
40533 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
40573 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
40613 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
40653 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
40688 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:40578 original size:60 final size:60
Alignment explanation
Indices: 40493--40686 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
40483 CGATTTTCCA
* ** * *
40493 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
40553 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
40613 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
40674 AAATCGCAACGCG
1 AAATCGCAACGCG
40687 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:41108 original size:33 final size:33
Alignment explanation
Indices: 41069--41139 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
41059 TTCACTTAGA
41069 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
41102 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
41135 TTTCA
1 TTTCA
41140 AGTTAGTATT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:41276 original size:19 final size:20
Alignment explanation
Indices: 41219--41293 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
41209 TGCAGAAGAG
* *
41219 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
41240 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
41260 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
41279 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
41294 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:41296 original size:14 final size:14
Alignment explanation
Indices: 41277--41333 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41267 GCGAAATGAC
41277 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
41291 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
41310 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41324 AATCGCAACG
1 AATCGCAACG
41334 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:41302 original size:33 final size:33
Alignment explanation
Indices: 41231--41349 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
41221 GCAACGAGAT
41231 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
*
41270 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
41303 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
41336 AAACCAAAATCGCA
1 AAATGAAAATCGCA
41350 TTGCGATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 54 0.71
36 1 0.01
38 1 0.01
39 20 0.26
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:41315 original size:19 final size:19
Alignment explanation
Indices: 41231--41319 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
41221 GCAACGAGAT
*
41231 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
***
41250 AGAATGACTGTCGCAACGCG
1 A-AATGAAAATCGCAACGCG
*
41270 AAATGACAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
41287 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
41303 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
41320 AGAGAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 25 0.45
20 15 0.27
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:41386 original size:14 final size:14
Alignment explanation
Indices: 41367--41423 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41357 TTTTATTTCG
41367 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
41381 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
41400 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41414 CGTTGCGATT
1 CGTTGCGATT
41424 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41398 original size:33 final size:33
Alignment explanation
Indices: 41350--41431 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
41340 CAAAATCGCA
*
41350 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
41383 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
41416 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
41432 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:41405 original size:19 final size:18
Alignment explanation
Indices: 41345--41409 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
41335 GAAACCAAAA
* *
41345 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGA-TTTCATT
41364 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
41378 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCATT
41397 TCGCGTTGCGATT
1 TCGCGTTGCGATT
41410 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:43288 original size:93 final size:93
Alignment explanation
Indices: 43129--43419 Score: 573
Period size: 93 Copynumber: 3.1 Consensus size: 93
43119 TAGATTGCTT
*
43129 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43194 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43222 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43287 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43315 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43380 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43408 AGTAAATTTGTT
1 AGTAAATTTGTT
43420 TCAGTCCATG
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 197 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:44950 original size:12 final size:12
Alignment explanation
Indices: 44933--44957 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44923 TTCTTCGGGA
44933 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44945 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44957 C
1 C
44958 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:45165 original size:24 final size:24
Alignment explanation
Indices: 45131--45177 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
45121 ATGAAACATC
45131 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
45155 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
45178 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:45886 original size:20 final size:20
Alignment explanation
Indices: 45858--46067 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
45848 AAATTTCAGT
* * *
45858 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
45878 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
45898 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
45918 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
45938 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
45958 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
45978 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
45998 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
46018 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
46038 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
46058 GTTGCGATTT
1 GTTGCGATTT
46068 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:46084 original size:21 final size:20
Alignment explanation
Indices: 46034--46131 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
46024 ATTTATGTGT
* * * *
46034 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
46054 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
46075 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
46095 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
46116 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
46132 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:46126 original size:41 final size:41
Alignment explanation
Indices: 46034--46190 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
46024 ATTTATGTGT
* * *
46034 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
46075 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
46116 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
46156 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
46191 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:48951 original size:18 final size:18
Alignment explanation
Indices: 48864--48952 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 18
48854 TATCAAATTT
*
48864 TAAAATTATTTAAATATAA
1 TAAAATTATTAAAATAT-A
48883 TAAAATTATTTAAAATGA-A
1 TAAAATTA-TTAAAAT-ATA
*
48902 -AAATTTATTAATAAATATA
1 TAAAATTATT-A-AAATATA
**
48921 TTTAATT-TATAAAATATA
1 TAAAATTAT-TAAAATATA
48939 TAAAATTATTAAAA
1 TAAAATTATTAAAA
48953 AGAAAAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
17 2 0.04
18 25 0.45
19 17 0.31
20 10 0.18
21 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAAATTATTAAAATATA
Found at i:49229 original size:41 final size:41
Alignment explanation
Indices: 49184--49315 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
49174 CTGGTTCTCC
49184 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
* * *** **
49225 CCATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCC
1 CCATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGG
49268 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
49309 CCATGCA
1 CCATGCA
49316 GAGGAATAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 3 0.04
41 27 0.40
42 2 0.03
43 20 0.30
44 3 0.04
45 3 0.04
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (41 bp):
CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
Found at i:49330 original size:55 final size:55
Alignment explanation
Indices: 49270--49435 Score: 323
Period size: 55 Copynumber: 3.0 Consensus size: 55
49260 CGAGGTCCCC
49270 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
49325 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
*
49380 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
49435 A
1 A
49436 GAGGTCGTTC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 110 1.00
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.15
Consensus pattern (55 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
Found at i:49507 original size:41 final size:41
Alignment explanation
Indices: 49380--49509 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
49370 AGAGGAATAG
49380 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
* * *** **
49421 ATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCCCC
1 ATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGGCC
49464 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
49505 ATGCA
1 ATGCA
49510 GAGGAATAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 3 0.05
41 25 0.38
42 2 0.03
43 20 0.31
44 3 0.05
45 3 0.05
46 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (41 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
Found at i:49590 original size:28 final size:29
Alignment explanation
Indices: 49523--49602 Score: 153
Period size: 29 Copynumber: 2.8 Consensus size: 29
49513 GAATAGGGTG
49523 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
49552 TAGGTCGCCATGTAGTCCCGGCGACC-TA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
49580 TAGGTCGCCATGTAGTCCCGGCG
1 TAGGTCGCCATGTAGTCCCGGCG
49603 CCATTCCATC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 25 0.49
29 26 0.51
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGTAGTCCCGGCGACCTTA
Found at i:49645 original size:23 final size:23
Alignment explanation
Indices: 49618--49669 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
49608 CCATCCATTC
49618 CCATTCACATGCAGCCCCATCAT
1 CCATTCACATGCAGCCCCATCAT
49641 CCATTCACATGCAGCCCCATCAT
1 CCATTCACATGCAGCCCCATCAT
49664 CCATTC
1 CCATTC
49670 CTTCACGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.23
Consensus pattern (23 bp):
CCATTCACATGCAGCCCCATCAT
Found at i:49808 original size:25 final size:25
Alignment explanation
Indices: 49780--49831 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
49770 TGTACAATTA
*
49780 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
49805 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
49830 TT
1 TT
49832 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:49902 original size:4 final size:4
Alignment explanation
Indices: 49893--49950 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
49883 ATTGCAGCCG
** **
49893 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA
*
49943 AGTA AGAA
1 AGAA AGAA
49951 GAATTCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:49920 original size:17 final size:16
Alignment explanation
Indices: 49892--49923 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
49882 GATTGCAGCC
49892 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
49908 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
49924 AAAGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:49921 original size:25 final size:25
Alignment explanation
Indices: 49893--49950 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
49883 ATTGCAGCCG
49893 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
49918 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
*
49943 AGTAAGAA
1 AGAAAGAA
49951 GAATTCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGGGAGAAAGGAA
Found at i:50218 original size:44 final size:46
Alignment explanation
Indices: 50155--50245 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
50145 GTTATATAGT
50155 TAAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATA
1 TAAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATA
* *
50198 TAAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 TAAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATA
50245 T
1 T
50246 TTGTTTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.17
44 17 0.40
45 3 0.07
46 7 0.17
47 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (46 bp):
TAAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATA
Found at i:51704 original size:26 final size:24
Alignment explanation
Indices: 51646--51704 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
51636 CTAATAAACC
*
51646 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
51670 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
51698 TAATAAT
1 TAATAAT
51705 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:52548 original size:28 final size:30
Alignment explanation
Indices: 52508--52570 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
52498 ATTTTTTATA
*
52508 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
52538 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
52566 TAATA
1 TAATA
52571 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:52577 original size:28 final size:28
Alignment explanation
Indices: 52512--52577 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
52502 TTTATATAAT
*
52512 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
52540 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
52568 ATAATTTATA
1 ATAATATATA
52578 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:52580 original size:21 final size:21
Alignment explanation
Indices: 52547--52595 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
52537 CTAATATAAT
52547 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
52568 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
52589 ATTAACT
1 A-TAACT
52596 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:52965 original size:16 final size:16
Alignment explanation
Indices: 52944--52976 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52934 GGGTGCAGGA
52944 ATCTCAGCTATGATGC
1 ATCTCAGCTATGATGC
52960 ATCTCAGCTATGATGC
1 ATCTCAGCTATGATGC
52976 A
1 A
52977 ACGCATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (16 bp):
ATCTCAGCTATGATGC
Found at i:53148 original size:25 final size:25
Alignment explanation
Indices: 53094--53151 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
53084 GTTCCCACGT
* *
53094 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
53119 ACCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
53144 CCCATGCA
1 CCCATGCA
53152 TTCCCACCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:53151 original size:16 final size:18
Alignment explanation
Indices: 53130--53172 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
53120 CCATGCACAG
53130 CATGCAT-C-CCCTCCCC
1 CATGCATCCACCCTCCCC
53146 CATGCATTCCCACCCTCCCC
1 CATGCA-T-CCACCCTCCCC
53166 CATGCAT
1 CATGCAT
53173 TCCCACGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 1 0.04
19 2 0.09
20 14 0.61
ACGTcount: A:0.16, C:0.56, G:0.07, T:0.21
Consensus pattern (18 bp):
CATGCATCCACCCTCCCC
Found at i:53161 original size:20 final size:20
Alignment explanation
Indices: 53138--53178 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
53128 AGCATGCATC
53138 CCCTCCCCCATGCATTCCCA
1 CCCTCCCCCATGCATTCCCA
53158 CCCTCCCCCATGCATTCCCA
1 CCCTCCCCCATGCATTCCCA
53178 C
1 C
53179 GGCCCATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.61, G:0.05, T:0.20
Consensus pattern (20 bp):
CCCTCCCCCATGCATTCCCA
Found at i:53249 original size:29 final size:29
Alignment explanation
Indices: 53217--53300 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
53207 TATACCTTGG
*
53217 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
53246 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
53275 AGGTCGCCTGGATTGCATGGCGACCT
1 AGGTCGCCTGGATTGCATGGCGACCT
53301 ATGGCTATCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.17, C:0.31, G:0.32, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:53629 original size:41 final size:41
Alignment explanation
Indices: 53584--53715 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
53574 CTGGTTCTCC
53584 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
* * *** **
53625 CCATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCC
1 CCATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGG
53668 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
53709 CCATGCA
1 CCATGCA
53716 GAGGAATAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 3 0.04
41 27 0.40
42 2 0.03
43 20 0.30
44 3 0.04
45 3 0.04
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (41 bp):
CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
Found at i:53730 original size:55 final size:55
Alignment explanation
Indices: 53670--53835 Score: 323
Period size: 55 Copynumber: 3.0 Consensus size: 55
53660 CGAGGTCCCC
53670 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
53725 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
*
53780 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
53835 A
1 A
53836 GAGGTCGTTC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 110 1.00
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.15
Consensus pattern (55 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
Found at i:53907 original size:41 final size:41
Alignment explanation
Indices: 53780--53909 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
53770 AGAGGAATAG
53780 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
* * *** **
53821 ATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCCCC
1 ATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGGCC
53864 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
53905 ATGCA
1 ATGCA
53910 GAGGAATAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 3 0.05
41 25 0.38
42 2 0.03
43 20 0.31
44 3 0.05
45 3 0.05
46 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (41 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
Found at i:53957 original size:29 final size:29
Alignment explanation
Indices: 53923--54032 Score: 220
Period size: 29 Copynumber: 3.8 Consensus size: 29
53913 GAATAGGGTG
53923 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
53952 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
53981 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
54010 TAGGTCGCCATGTAGTCCCGGCG
1 TAGGTCGCCATGTAGTCCCGGCG
54033 CCATTCCATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTAGTCCCGGCGACCTTA
Found at i:54075 original size:23 final size:23
Alignment explanation
Indices: 54048--54099 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
54038 CCATCCATTC
54048 CCATTCACATGCAGCCCCATCAT
1 CCATTCACATGCAGCCCCATCAT
54071 CCATTCACATGCAGCCCCATCAT
1 CCATTCACATGCAGCCCCATCAT
54094 CCATTC
1 CCATTC
54100 CTTCACGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.23
Consensus pattern (23 bp):
CCATTCACATGCAGCCCCATCAT
Found at i:54238 original size:25 final size:25
Alignment explanation
Indices: 54210--54261 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
54200 TGTACAATTA
*
54210 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
54235 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
54260 TT
1 TT
54262 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:54332 original size:4 final size:4
Alignment explanation
Indices: 54323--54380 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
54313 ATTGCAGCCG
** **
54323 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA
*
54373 AGTA AGAA
1 AGAA AGAA
54381 GAATTCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:54350 original size:17 final size:16
Alignment explanation
Indices: 54322--54353 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54312 GATTGCAGCC
54322 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
54338 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
54354 AAAGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:54351 original size:25 final size:25
Alignment explanation
Indices: 54323--54380 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
54313 ATTGCAGCCG
54323 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
54348 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
*
54373 AGTAAGAA
1 AGAAAGAA
54381 GAATTCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGGGAGAAAGGAA
Found at i:54590 original size:41 final size:40
Alignment explanation
Indices: 54545--54648 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 40
54535 TACATAAATT
*
54545 AAAAAA-TATTTAATTAGTATATGTTTGATAGTTA-TAGT-TA
1 AAAAAATTATTTAATTAGTAT-TG-TTAATAGTTAGTA-TATA
* * *
54585 AAAAAATTAATTAGTTTGTATTGTTAATAGTTAGTTATATA
1 AAAAAATTATTTAATTAGTATTGTTAATAGTTAG-TATATA
54626 AAAAAATTATTTAATTAGT-TTGT
1 AAAAAATTATTTAATTAGTATTGT
54649 GTTAGTTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
39 9 0.17
40 13 0.25
41 31 0.58
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (40 bp):
AAAAAATTATTTAATTAGTATTGTTAATAGTTAGTATATA
Found at i:54615 original size:39 final size:43
Alignment explanation
Indices: 54543--54669 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 43
54533 TATACATAAA
* **
54543 TTAAAAAATATTTAATTAG--TATA-T-GTTTGATAGTTATAG
1 TTAAAAAATATTTAATTAGTTTGTATTAGTTAAATAGTTATAG
54582 TTAAAAAA-A-TTAATTAGTTTGTATT-GTTAATAGTTAGTTATA-
1 TTAAAAAATATTTAATTAGTTTGTATTAGTTAA-A--TAGTTATAG
* *
54624 TAAAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTA-AG
1 TTAAAAAA-TATTTAATTAGTTTGTATTAGTTAAATAGTTATAG
54667 TTA
1 TTA
54670 TATTTGTTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
37 8 0.11
38 1 0.01
39 11 0.15
40 4 0.06
41 1 0.01
42 8 0.11
43 16 0.23
44 1 0.01
45 16 0.23
46 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (43 bp):
TTAAAAAATATTTAATTAGTTTGTATTAGTTAAATAGTTATAG
Found at i:56124 original size:26 final size:24
Alignment explanation
Indices: 56066--56124 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
56056 CTAATAAACC
*
56066 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
56090 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
56118 TAATAAT
1 TAATAAT
56125 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:56970 original size:28 final size:30
Alignment explanation
Indices: 56930--56992 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
56920 ATTTTTTATA
*
56930 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
56960 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
56988 TAATA
1 TAATA
56993 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:56999 original size:28 final size:28
Alignment explanation
Indices: 56934--56999 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
56924 TTTATATAAT
*
56934 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
56962 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
56990 ATAATTTATA
1 ATAATATATA
57000 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:57002 original size:21 final size:21
Alignment explanation
Indices: 56969--57017 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
56959 CTAATATAAT
56969 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
56990 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
57011 ATTAACT
1 A-TAACT
57018 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:57389 original size:16 final size:16
Alignment explanation
Indices: 57368--57400 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
57358 GGGTGCAGGA
57368 ATCTCAGCTATGATGC
1 ATCTCAGCTATGATGC
57384 ATCTCAGCTATGATGC
1 ATCTCAGCTATGATGC
57400 A
1 A
57401 ACGCATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (16 bp):
ATCTCAGCTATGATGC
Found at i:57572 original size:25 final size:25
Alignment explanation
Indices: 57518--57575 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
57508 GTTCCCACGT
* *
57518 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
57543 ACCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
57568 CCCATGCA
1 CCCATGCA
57576 TTCCCACCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:57575 original size:16 final size:18
Alignment explanation
Indices: 57554--57596 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
57544 CCATGCACAG
57554 CATGCAT-C-CCCTCCCC
1 CATGCATCCACCCTCCCC
57570 CATGCATTCCCACCCTCCCC
1 CATGCA-T-CCACCCTCCCC
57590 CATGCAT
1 CATGCAT
57597 TCCCACGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 1 0.04
19 2 0.09
20 14 0.61
ACGTcount: A:0.16, C:0.56, G:0.07, T:0.21
Consensus pattern (18 bp):
CATGCATCCACCCTCCCC
Found at i:57585 original size:20 final size:20
Alignment explanation
Indices: 57562--57602 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57552 AGCATGCATC
57562 CCCTCCCCCATGCATTCCCA
1 CCCTCCCCCATGCATTCCCA
57582 CCCTCCCCCATGCATTCCCA
1 CCCTCCCCCATGCATTCCCA
57602 C
1 C
57603 GGCCCATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.61, G:0.05, T:0.20
Consensus pattern (20 bp):
CCCTCCCCCATGCATTCCCA
Found at i:57673 original size:29 final size:29
Alignment explanation
Indices: 57641--57724 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
57631 TATACCTTGG
*
57641 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
57670 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
57699 AGGTCGCCTGGATTGCATGGCGACCT
1 AGGTCGCCTGGATTGCATGGCGACCT
57725 ATGGCTATCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.17, C:0.31, G:0.32, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:68020 original size:35 final size:35
Alignment explanation
Indices: 67974--68043 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
67964 TCACGAACCT
67974 CAGCAAGCCAACCTTTCACTCATATCCTCCTTATA
1 CAGCAAGCCAACCTTTCACTCATATCCTCCTTATA
*
68009 CAGCAAGCCAACTTTTCACTCATATCCTCCTTATA
1 CAGCAAGCCAACCTTTCACTCATATCCTCCTTATA
68044 GAACTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.36, G:0.06, T:0.30
Consensus pattern (35 bp):
CAGCAAGCCAACCTTTCACTCATATCCTCCTTATA
Found at i:77819 original size:7 final size:7
Alignment explanation
Indices: 77809--77858 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
77799 AGATCTCTCA
77809 TCTGCTG
1 TCTGCTG
77816 TCTGCTG
1 TCTGCTG
77823 TCTGCTG
1 TCTGCTG
77830 TCTGCTG
1 TCTGCTG
77837 TCTGCTG
1 TCTGCTG
77844 TCTGCTG
1 TCTGCTG
77851 TCTGCTG
1 TCTGCTG
77858 T
1 T
77859 ATCTAATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.00, C:0.28, G:0.28, T:0.44
Consensus pattern (7 bp):
TCTGCTG
Found at i:81277 original size:15 final size:16
Alignment explanation
Indices: 81257--81287 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
81247 AATGGGCAGT
81257 AATCCCTGC-AAAAAA
1 AATCCCTGCGAAAAAA
81272 AATCCCTGCGAAAAAA
1 AATCCCTGCGAAAAAA
81288 TCTCTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
AATCCCTGCGAAAAAA
Found at i:81854 original size:2 final size:2
Alignment explanation
Indices: 81847--81899 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
81837 TGTACGAACA
81847 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
81889 AT CAT AT AT AT
1 AT -AT AT AT AT
81900 TGATGGGGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82259 original size:67 final size:65
Alignment explanation
Indices: 82169--82295 Score: 164
Period size: 65 Copynumber: 1.9 Consensus size: 65
82159 TCTCTAATTT
* * * *
82169 AATATTCGTCTATTATTCCTTTTTTTTATACCATACATACAGTTCAATTCATTAAAATTCAAAAA
1 AATATTCGTCAATTATT-C-ATTTTTTATACCATACACACAATTCAATTCATTAAAATTCAAAAA
82234 GA
64 GA
* * * *
82236 AATATTCTTCAATTATTTATTTTTTATACCATACCCACAATTCAATTCATTCAAATTCAA
1 AATATTCGTCAATTATTCATTTTTTATACCATACACACAATTCAATTCATTAAAATTCAA
82296 GAAGGAAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 37 0.71
67 15 0.29
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (65 bp):
AATATTCGTCAATTATTCATTTTTTATACCATACACACAATTCAATTCATTAAAATTCAAAAAGA
Found at i:85043 original size:64 final size:65
Alignment explanation
Indices: 84936--85065 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 65
84926 AACGTTCTCC
* * * *
84936 TTCTTCTTAAATTTGAATGAATTGAATTGTAGGTATGGTATAAAAAA-TAAATAATTGAAGAATA
1 TTCTTCTTAAATTTGAATGAATTGAACTGTAGGTATGGCATAAAAAAGGAAA-AAGTGAAGAATA
85000 T
65 T
85001 TTCTT-TTAAATTTGAATGAATTGAACTGTAGGTATGGCATAAAAAAGGAAAAAGTGAAGAATAT
1 TTCTTCTTAAATTTGAATGAATTGAACTGTAGGTATGGCATAAAAAAGGAAAAAGTGAAGAATAT
85065 T
1 T
85066 AAATTAGGGA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 52 0.87
65 8 0.13
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (65 bp):
TTCTTCTTAAATTTGAATGAATTGAACTGTAGGTATGGCATAAAAAAGGAAAAAGTGAAGAATAT
Done.