Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009187.1 Hibiscus syriacus cultivar Beakdansim tig00112760_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: 59302
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5315 original size:2 final size:2
Alignment explanation
Indices: 5308--5339 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5298 TGTACACGCA
5308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5340 AATTCATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8431 original size:16 final size:18
Alignment explanation
Indices: 8396--8432 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
8386 TCTCAATTAT
*
8396 TTATATTTTTTAATTTAA
1 TTATATTTTTTAATTAAA
8414 TTATA-TTTTTAA-TAAA
1 TTATATTTTTTAATTAAA
8430 TTA
1 TTA
8433 AAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTTTTAATTAAA
Found at i:9335 original size:111 final size:111
Alignment explanation
Indices: 9141--9360 Score: 404
Period size: 111 Copynumber: 2.0 Consensus size: 111
9131 GAAATCATAC
*
9141 ATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATA
1 ATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATA
*
9206 TTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAAT
66 ATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAAT
9252 ATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATA
1 ATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATA
* *
9317 ATTATTTGATTTATTTAATGCATTATTATTAGATTAAGAATTAA
66 ATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
9361 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATA
ATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAAT
Found at i:14913 original size:27 final size:27
Alignment explanation
Indices: 14838--14916 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
14828 GACTTAATTT
* *
14838 TTTTA-TATCAACTT-A-TTAAATATA
1 TTTTATTATTAACTTAATTTAAAAATA
*
14862 TTTTATTATTAACTTAATTTTAAAATA
1 TTTTATTATTAACTTAATTTAAAAATA
* ** *
14889 TTTTATTTTTATTTTCATTTAAAAATA
1 TTTTATTATTAACTTAATTTAAAAATA
14916 T
1 T
14917 ATAATTTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 5 0.11
25 8 0.18
26 1 0.02
27 30 0.68
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTATTATTAACTTAATTTAAAAATA
Found at i:15278 original size:20 final size:21
Alignment explanation
Indices: 15253--15361 Score: 107
Period size: 21 Copynumber: 5.3 Consensus size: 21
15243 TTTTCCCAAT
*
15253 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
15273 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
15294 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
15314 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
15335 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-ATTAAGAAAA
15356 TCGCAA
1 TCGCAA
15362 CGAGATACTT
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
20 27 0.39
21 41 0.59
22 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:15298 original size:41 final size:41
Alignment explanation
Indices: 15253--15363 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
15243 TTTTCCCAAT
15253 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
15294 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
15335 TCGCAATGCGATAATAA-AAAATCGCAACG
1 TCGCAATGCG--AATAAGTAAATCGCAACG
15364 AGATACTTAC
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 51 0.76
42 11 0.16
43 5 0.07
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:15404 original size:20 final size:20
Alignment explanation
Indices: 15356--15407 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
15346 TAATAAAAAA
* *
15356 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
15376 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
15396 TCGCAACGCGAT
1 TCGCAACGCGAT
15408 TTACATAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:15964 original size:19 final size:19
Alignment explanation
Indices: 15926--15981 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
15916 TTCGAGAATG
15926 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
15946 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
15965 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
15982 CCAAAATTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:16034 original size:20 final size:19
Alignment explanation
Indices: 15993--16153 Score: 135
Period size: 20 Copynumber: 8.8 Consensus size: 19
15983 CAAAATTGCA
15993 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
16012 TTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
16032 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
16051 TTGCGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
* **
16065 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
16084 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
16098 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
16118 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
16138 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
16154 AACCAAAAGA
Statistics
Matches: 115, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 37 0.32
20 49 0.43
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:16069 original size:39 final size:39
Alignment explanation
Indices: 15993--16069 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
15983 CAAAATTGCA
* **
15993 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
16032 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
16070 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:16078 original size:33 final size:33
Alignment explanation
Indices: 16041--16128 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
16031 GTTGCGATTT
* *
16041 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
16074 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
16107 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
16129 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:18212 original size:42 final size:42
Alignment explanation
Indices: 18152--18274 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
18142 GCCCGACTCG
* * *
18152 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
18194 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
18236 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
18275 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:18232 original size:21 final size:21
Alignment explanation
Indices: 18208--18274 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
18198 TCATTCCTCG
18208 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
18229 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
18250 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
18271 AGAG
1 AGAG
18275 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:19651 original size:14 final size:14
Alignment explanation
Indices: 19632--19667 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
19622 ATTGTTTAAT
19632 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
19646 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
19660 TGATTTGT
1 TGATTTGT
19668 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:19868 original size:19 final size:19
Alignment explanation
Indices: 19846--19996 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
19836 CGAAATTAAA
19846 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
19865 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
19880 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
19898 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
19912 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
19931 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
19946 -TCTCGTTGCGATTATCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
19964 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
19983 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
19997 GGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 28 0.30
16 5 0.05
17 6 0.06
19 45 0.48
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:19892 original size:33 final size:32
Alignment explanation
Indices: 19850--19976 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
19840 ATTAAATTCG
19850 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
19883 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
19916 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
19949 CGTTGCGATTATCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
19977 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:19939 original size:66 final size:66
Alignment explanation
Indices: 19843--19975 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
19833 ATGCGAAATT
* *
19843 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTATCATTTCGCATTGC
19908 G
66 G
*
19909 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTATCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTATCATTTCGCATTGC
19974 G
66 G
19975 A
1 A
19976 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTATCATTTCGCATTGC
G
Found at i:22285 original size:12 final size:12
Alignment explanation
Indices: 22268--22292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22258 TCTTCGGGGA
22268 CTTTTTCTTCTT
1 CTTTTTCTTCTT
22280 CTTTTTCTTCTT
1 CTTTTTCTTCTT
22292 C
1 C
22293 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:22501 original size:24 final size:24
Alignment explanation
Indices: 22467--22520 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22457 CTGAAACATC
* *
22467 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
22491 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
22515 ATCAAA
1 ATCAAA
22521 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:23585 original size:20 final size:20
Alignment explanation
Indices: 23560--23617 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
23550 ATTCATTTGA
*
23560 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
23580 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
23600 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
23618 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:23660 original size:14 final size:14
Alignment explanation
Indices: 23641--23694 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
23631 GAAAATCGCA
23641 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
23655 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
23672 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
23688 TTGCGAT
1 TTGCGAT
23695 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:23660 original size:33 final size:33
Alignment explanation
Indices: 23623--23693 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
23613 AAAATCGCAA
23623 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
23656 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
23689 TGCGA
1 TGCGA
23694 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:23694 original size:33 final size:33
Alignment explanation
Indices: 23636--23713 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
23626 GAAATGAAAA
***
23636 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
23669 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
23702 TCGCGTTGCGAT
1 TCGCATTGCGAT
23714 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:25730 original size:19 final size:19
Alignment explanation
Indices: 25687--25784 Score: 91
Period size: 19 Copynumber: 5.4 Consensus size: 19
25677 TAGTTTACTT
* *
25687 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
25707 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
*
25726 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
25745 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
25759 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
25777 TCGCAACG
1 TCGCAACG
25785 ACAAAATCGT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 12 0.19
19 25 0.39
20 12 0.19
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:25760 original size:14 final size:14
Alignment explanation
Indices: 25741--25798 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
25731 ATGCGAAATG
25741 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
25755 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
25771 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
25787 AAAATCGTAACG
1 AAAATCGCAACG
25799 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:25783 original size:32 final size:33
Alignment explanation
Indices: 25725--25803 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
25715 CGAAATGACT
*
25725 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
25758 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
25790 ATCGTAACGCGAAA
1 ATCGCAACGCGAAA
25804 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:25809 original size:52 final size:52
Alignment explanation
Indices: 25703--25814 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 52
25693 CACGAAACTT
* * * * *
25703 AAAATCGCAACGCGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGACAATCGCAACGCAAAATGAAAAGCGAAACGAC
* *
25755 AAAATCGCAACGCGAAATGA-AATCGCAACGACAAAATCGTAACGCGAAAC-AC
1 AAAATCGCAACGCGAAATGACAATCGCAACG-CAAAAT-GAAAAGCGAAACGAC
25807 -AAATCGCA
1 AAAATCGCA
25815 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
51 16 0.31
52 27 0.53
53 8 0.16
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (52 bp):
AAAATCGCAACGCGAAATGACAATCGCAACGCAAAATGAAAAGCGAAACGAC
Found at i:25851 original size:14 final size:14
Alignment explanation
Indices: 25832--25889 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
25822 TTTCATTTCG
25832 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
25846 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
25862 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
25878 CGTTGCGATTTT
1 CGTTGCGATTTT
25890 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:25896 original size:33 final size:33
Alignment explanation
Indices: 25815--25905 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
25805 ACAAATCGCA
*
25815 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
25848 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
25880 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
25906 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:25912 original size:19 final size:20
Alignment explanation
Indices: 25890--25927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25880 TTGCGATTTT
25890 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
25909 CATTTCCGCGTTGCGATAG
1 CATTTCCGCATTGCGATAG
25928 TTATTTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:25933 original size:20 final size:19
Alignment explanation
Indices: 25878--25944 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
25868 GCGATTTTGT
*
25878 CGTTGCGAT-TTTCATTTCG
1 CGTTGCGATAGTT-ATTTCG
* **
25897 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTTATTT-CG
25917 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTTA-TTTCG
*
25937 TGTTGCGA
1 CGTTGCGA
25945 AAGTAAACTA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
19 12 0.32
20 22 0.59
21 3 0.08
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTTATTTCG
Found at i:26443 original size:18 final size:18
Alignment explanation
Indices: 26417--26461 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
26407 GTCGATCAGA
*
26417 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
26435 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
26453 TGATGGCTC
1 TGATGGCTC
26462 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:27806 original size:20 final size:20
Alignment explanation
Indices: 27781--27818 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27771 AATAGTTTCT
27781 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
27801 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
27819 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:28338 original size:20 final size:20
Alignment explanation
Indices: 28313--28406 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
28303 GATTATGTAT
28313 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
28333 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
28353 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
28374 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
28394 TATCGCATTGCGA
1 TATCGCGTTGCGA
28407 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:28407 original size:20 final size:20
Alignment explanation
Indices: 28293--28407 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
28283 CGCTTTGAAA
*
28293 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
28314 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
28334 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
28354 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
28375 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
28395 ATCGCATTGCGAT
1 ATCGCATTGCGAT
28408 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:28425 original size:21 final size:21
Alignment explanation
Indices: 28396--28488 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
28386 ATAGTCAGTA
28396 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28417 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28437 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28458 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28478 TCGCATTGCGA
1 TCGCATTGCGA
28489 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:28426 original size:41 final size:41
Alignment explanation
Indices: 28335--28469 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
28325 AAAGTCAGTA
* * * ** *
28335 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
28375 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
28417 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
28458 TCGCGTTGCGAT
1 TCGCGTTGCGAT
28470 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:28470 original size:41 final size:41
Alignment explanation
Indices: 28396--28488 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
28386 ATAGTCAGTA
28396 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28437 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28478 TCGCATTGCGA
1 TCGCATTGCGA
28489 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:29652 original size:22 final size:23
Alignment explanation
Indices: 29617--29662 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
29607 TTAAATATAA
*
29617 AATTAATTTCAACT-ATTG-TTT
1 AATTAATTACAACTAATTGATTT
29638 AATTATATTACAACTAATTGATTT
1 AATTA-ATTACAACTAATTGATTT
29662 A
1 A
29663 GTGGGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 8 0.38
23 4 0.19
24 4 0.19
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTAATTACAACTAATTGATTT
Found at i:32872 original size:22 final size:21
Alignment explanation
Indices: 32845--32895 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
32835 AACCTGATAA
*
32845 TTTTAAAA-AATATATATAAATT
1 TTTTAAAATAAAAT-TATAAA-T
*
32867 TTTTAAAATAAAATTATATAT
1 TTTTAAAATAAAATTATAAAT
32888 TTTTAAAA
1 TTTTAAAA
32896 GAGAAAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTAAAATAAAATTATAAAT
Found at i:33063 original size:21 final size:21
Alignment explanation
Indices: 33037--33134 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
33027 ATCAGTTCCC
33037 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
33058 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** * **
33078 CA-AATTCGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
* *
33100 AGAATCGGAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
33121 A-AATCGCAACGCGA
1 AGAATCGCAACGCGA
33135 ACATATAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.02
20 17 0.29
21 37 0.64
22 3 0.05
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:33131 original size:20 final size:20
Alignment explanation
Indices: 33102--33296 Score: 106
Period size: 20 Copynumber: 9.7 Consensus size: 20
33092 GATTTTCCAG
* **
33102 AATCGGAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
**
33122 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATCCGA-A
* * * * *
33142 AATTGCAATGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * *
33162 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* *
33183 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
33203 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * * *
33223 AATCGCAATGCGTATCTGTA
1 AATCGCAACGCGAATCCGAA
*
33243 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
33264 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
33284 AATCGCAACGCGA
1 AATCGCAACGCGA
33297 TCGATAATTC
Statistics
Matches: 129, Mismatches: 40, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 94 0.73
21 34 0.26
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:33193 original size:81 final size:81
Alignment explanation
Indices: 33121--33296 Score: 230
Period size: 81 Copynumber: 2.2 Consensus size: 81
33111 GCGAATATGA
* * * ** *
33121 AAATCGCAACGCGAACATATAAATTGCAATGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAAA
1 AAATCGCAACGCGAACACATAAATCGCAATGCGTA-TCTGTA-AATCGCAACGACAATACGTAAA
33184 ATCGCAACGCGTATCCGT
64 ATCGCAACGCGTATCCGT
* * *
33202 AAATCGCAACGAGAATACGTAAATCGCAATGCGTATCTGTAAATCGCAACGACAATACGTAAAAT
1 AAATCGCAACGCGAACACATAAATCGCAATGCGTATCTGTAAATCGCAACGACAATACGTAAAAT
*
33267 CGTAACGCGTATCCGT
66 CGCAACGCGTATCCGT
33283 AAATCGCAACGCGA
1 AAATCGCAACGCGA
33297 TCGATAATTC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 80 0.98
82 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (81 bp):
AAATCGCAACGCGAACACATAAATCGCAATGCGTATCTGTAAATCGCAACGACAATACGTAAAAT
CGCAACGCGTATCCGT
Found at i:33223 original size:41 final size:41
Alignment explanation
Indices: 33163--33293 Score: 201
Period size: 41 Copynumber: 3.2 Consensus size: 41
33153 GATTCTGACT
* *
33163 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
33204 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
33244 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
33285 ATCGCAACG
1 ATCGCAACG
33294 CGATCGATAA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 37 0.46
41 44 0.54
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:33396 original size:21 final size:21
Alignment explanation
Indices: 33370--33410 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33360 GACTATAGCA
33370 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
33391 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTCCCAAATTCGC
33411 AATGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:33416 original size:21 final size:21
Alignment explanation
Indices: 33371--33417 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
33361 ACTATAGCAT
**
33371 TGCGATTTCCCAAATTCGCGT
1 TGCGATTTCCCAAATTCGCAA
* *
33392 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTCCCAAATTCGCAA
33413 TGCGA
1 TGCGA
33418 ATACATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCGATTTCCCAAATTCGCAA
Found at i:33432 original size:20 final size:20
Alignment explanation
Indices: 33407--33532 Score: 175
Period size: 20 Copynumber: 6.3 Consensus size: 20
33397 TTTTCCTAAT
* *
33407 TCGCAATGCGAATACATATA
1 TCGCAATGCGAATACGTAAA
*
33427 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
33447 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
33467 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
33487 TCGCAATGCAAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
*
33507 TCACAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
33527 TCGCAA
1 TCGCAA
33533 CGAGATTCTG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 1 0.01
20 96 0.99
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:33542 original size:20 final size:20
Alignment explanation
Indices: 33497--33542 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
33487 TCGCAATGCA
* *
33497 AATCTGTAAATCACAATGCG
1 AATCTGTAAATCACAACGAG
*
33517 AATCTGTAAATCGCAACGAG
1 AATCTGTAAATCACAACGAG
*
33537 ATTCTG
1 AATCTG
33543 ACTATCGCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (20 bp):
AATCTGTAAATCACAACGAG
Found at i:34422 original size:24 final size:24
Alignment explanation
Indices: 34395--34448 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
34385 GTATTCGAAA
34395 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
34419 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
34443 TTTGAT
1 TTTGAT
34449 GATTTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:36920 original size:20 final size:20
Alignment explanation
Indices: 36883--36971 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
36873 CAACGCGGAA
*
36883 ATCGTAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
36903 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
36923 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
36943 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
36963 ATCGCAACG
1 ATCGCAACG
36972 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:37031 original size:34 final size:33
Alignment explanation
Indices: 36943--37038 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
36933 GGAATTGACT
* **
36943 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
36977 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
37010 ATCGCAATGCGAAAATGAAAATCGTAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
37039 CGAAAGCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:37208 original size:14 final size:14
Alignment explanation
Indices: 37189--37225 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
37179 TATCAATTAA
37189 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
37203 ACAAATCATCTTTT
1 ACAAATCAACATTT
37217 ACAAATCAA
1 ACAAATCAA
37226 TTAAACAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:37289 original size:19 final size:19
Alignment explanation
Indices: 37265--37360 Score: 130
Period size: 19 Copynumber: 5.3 Consensus size: 19
37255 GCAACGAGAG
37265 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37284 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37303 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37322 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
37336 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
37356 AATCG
1 AATCG
37361 TAACACGAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 8 0.12
16 5 0.07
17 2 0.03
18 3 0.04
19 44 0.66
20 5 0.07
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:37289 original size:33 final size:33
Alignment explanation
Indices: 37243--37360 Score: 137
Period size: 38 Copynumber: 3.4 Consensus size: 33
37233 ATGCAACGCG
**
37243 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
* *
37276 GAAATGAAAATCGCAATGCGAAATGAAAATCACAATGC
1 GAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGC
*
37314 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
37347 GAAAATGAAAATCG
1 G-AAATGAAAATCG
37361 TAACACGAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
33 26 0.36
34 13 0.18
35 2 0.03
36 2 0.03
37 1 0.01
38 28 0.39
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:37442 original size:33 final size:33
Alignment explanation
Indices: 37380--37475 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
37370 ATTAGTTTCG
* *
37380 CGTTGCGATTTCCATTTTCGCATTACGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
37414 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
37447 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
37476 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 32 0.58
34 23 0.42
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.41
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:37596 original size:14 final size:14
Alignment explanation
Indices: 37577--37613 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
37567 CATCAATTAA
37577 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
37591 ACAAATCATCTTTT
1 ACAAATCAACATTT
37605 ACAAATCAA
1 ACAAATCAA
37614 TTAAACAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:39008 original size:42 final size:42
Alignment explanation
Indices: 38901--39012 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
38891 TCCATCATGT
* * *
38901 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
38943 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
*
38985 TAGGG-GATGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
39013 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:39528 original size:20 final size:20
Alignment explanation
Indices: 39492--39577 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
39482 GAAACTTAAA
* *
39492 ATCGCAACGCG-AAATGATT
1 ATCGCAATGCGAAAATGACT
*
39511 ATCGTAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
39531 ATCGCAATACGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
39551 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
39571 ATCGCAA
1 ATCGCAA
39578 CGAGAGAATC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 9 0.16
20 49 0.84
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:39634 original size:19 final size:19
Alignment explanation
Indices: 39612--39688 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
39602 AAATCGCAAC
*
39612 GCGATTATAGTTTCGTGTT
1 GCGATTATAGTTTCGCGTT
* *
39631 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
*
39650 GCGATT-T--TGT--CGTT
1 GCGATTATAGTTTCGCGTT
* *
39664 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
39683 GCGATT
1 GCGATT
39689 TTCATTTCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 32 0.67
ACGTcount: A:0.09, C:0.14, G:0.30, T:0.47
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:39670 original size:33 final size:33
Alignment explanation
Indices: 39628--39690 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
39618 ATAGTTTCGT
39628 GTTGCGATTTTGGTTTCGCGTTGCGATTTTGTC
1 GTTGCGATTTTGGTTTCGCGTTGCGATTTTGTC
39661 GTTGCGATTTTGGTTTCGCGTTGCGATTTT
1 GTTGCGATTTTGGTTTCGCGTTGCGATTTT
39691 CATTTCTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.06, C:0.14, G:0.30, T:0.49
Consensus pattern (33 bp):
GTTGCGATTTTGGTTTCGCGTTGCGATTTTGTC
Found at i:39677 original size:52 final size:52
Alignment explanation
Indices: 39612--39740 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 52
39602 AAATCGCAAC
* * ** * * *
39612 GCGATTATAGTTTCGTGTTGCGATTTTGGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTAGTTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATT
* * *
39664 GCGATTTTGGTTTCGCGTTGCGATTTTCATTTCTCGTTGTGATTCTCTCATT
1 GCGATTTTAGTTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATT
* *
39716 GCGATTTTCA-TTTCTCGTTGTGATT
1 GCGATTTT-AGTTTCGCGTTGCGATT
39741 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (52 bp):
GCGATTTTAGTTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATT
Found at i:39691 original size:14 final size:14
Alignment explanation
Indices: 39646--39672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39636 TTTGGTTTCG
39646 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
39660 CGTTGCGATTTTG
1 CGTTGCGATTTTG
39673 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:39696 original size:19 final size:19
Alignment explanation
Indices: 39621--39690 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
39611 CGCGATTATA
*
39621 GTTTCGTGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
39640 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
39658 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
39673 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
39691 CATTTCTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.64
ACGTcount: A:0.06, C:0.14, G:0.30, T:0.50
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:39701 original size:19 final size:19
Alignment explanation
Indices: 39659--39740 Score: 75
Period size: 19 Copynumber: 4.6 Consensus size: 19
39649 TGCGATTTTG
**
39659 TCGTTGCGATTTTGGTTTC
1 TCGTTGCGATTTTCATTTC
*
39678 GCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
*
39697 TCGTTGTGA--TTC---TC
1 TCGTTGCGATTTTCATTTC
*
39711 TCATTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
*
39730 TCGTTGTGATT
1 TCGTTGCGATT
39741 CTCTCGTTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
14 9 0.18
16 3 0.06
17 3 0.06
19 34 0.69
ACGTcount: A:0.10, C:0.18, G:0.21, T:0.51
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:39718 original size:33 final size:33
Alignment explanation
Indices: 39681--39754 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
39671 TGGTTTCGCG
39681 TTGCGATTTTCATTTCTCGTTGTGATTCTCTCA
1 TTGCGATTTTCATTTCTCGTTGTGATTCTCTCA
*
39714 TTGCGATTTTCATTTCTCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCTCGTTGTGATTCTCTCA
39747 TTGCGATT
1 TTGCGATT
39755 CATTTCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTCATTTCTCGTTGTGATTCTCTCA
Found at i:39764 original size:15 final size:14
Alignment explanation
Indices: 39695--39768 Score: 58
Period size: 14 Copynumber: 4.9 Consensus size: 14
39685 GATTTTCATT
*
39695 TCTCGTTGTGATTC
1 TCTCGTTGCGATTC
*
39709 TCTCATTGCGATTTTC
1 TCTCGTTGCGA--TTC
*
39725 ATTTCTCGTTGTGATTC
1 ---TCTCGTTGCGATTC
39742 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
*
39756 ATTTCGTTGCGAT
1 -TCTCGTTGCGAT
39769 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 22 0.46
15 11 0.23
16 3 0.06
17 3 0.06
19 9 0.19
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:40021 original size:94 final size:94
Alignment explanation
Indices: 39856--40235 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
39846 ATGGATTGCA
* * * *
39856 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATGCTAACTTCAGAGTATTAAATAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
39920 TTAGCAGAATTGACAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
39949 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAAATTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
40014 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
40043 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
40108 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
40137 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
40201 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
40231 TTACT
1 TTACT
40236 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
93 23 0.08
94 250 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:42016 original size:19 final size:19
Alignment explanation
Indices: 41992--42075 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
41982 GCAACGAGAG
41992 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
42011 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
*
42030 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
42044 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
42063 AATCGCAATGCGA
1 AATCGCAACGCGA
42076 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.73
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:42178 original size:41 final size:41
Alignment explanation
Indices: 42121--42230 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
42111 CGATTCTCTC
42121 GTTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTTTCGT
42162 GTTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTTTCGT
*
42203 GTTGCAATTTTCATTT-TCAT-GTTGCGAT
1 GTTGCGATTTTCATTTCTC-TCGTTGCGAT
42231 TTTAAGTTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
40 10 0.15
41 57 0.85
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (41 bp):
GTTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTTTCGT
Found at i:42232 original size:20 final size:19
Alignment explanation
Indices: 42088--42233 Score: 124
Period size: 20 Copynumber: 7.6 Consensus size: 19
42078 TTGGTTTCGC
42088 GTTGCGATTTTCA-TTTCGT
1 GTTGCGATTTTCATTTTC-T
*
42107 GTTGCGA--TTC--TCTC-
1 GTTGCGATTTTCATTTTCT
42121 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
42141 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
42162 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
42182 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
*
42203 GTTGCAATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
42223 GTTGCGATTTT
1 GTTGCGATTTT
42234 AAGTTTAGAA
Statistics
Matches: 103, Mismatches: 13, Indels: 21
0.75 0.09 0.15
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 3 0.03
18 1 0.01
19 9 0.09
20 45 0.44
21 32 0.31
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.50
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:42585 original size:25 final size:26
Alignment explanation
Indices: 42527--42578 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
42517 TTTCCATTTC
*
42527 TGAATGATTGTGAGGGATTTCTGACCG
1 TGAATGGTTGTGAGGGATTTC-GACCG
42554 TGAATGGTTGTGAGGGATTTC-ACCG
1 TGAATGGTTGTGAGGGATTTCGACCG
42579 GAGATGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
27 20 0.83
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.33
Consensus pattern (26 bp):
TGAATGGTTGTGAGGGATTTCGACCG
Found at i:42814 original size:20 final size:20
Alignment explanation
Indices: 42789--43002 Score: 234
Period size: 20 Copynumber: 10.6 Consensus size: 20
42779 CTTTAAAAAT
42789 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42809 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
42829 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
42850 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
42870 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
42890 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
42910 CTCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42930 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
42950 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
42971 CACGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
42992 CTCGTTGCGAT
1 CGCGTTGCGAT
43003 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
20 107 0.67
21 52 0.33
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:43024 original size:41 final size:41
Alignment explanation
Indices: 42791--43002 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
42781 TTAAAAATCG
*
42791 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
42832 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
42872 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
42912 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
42953 CGTTGCGATTTACGGATACACGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
42994 CGTTGCGAT
1 CGTTGCGAT
43003 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.47
41 83 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:43050 original size:22 final size:20
Alignment explanation
Indices: 43011--43063 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
43001 ATAGTCAGAA
* *
43011 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTTTATAT
43031 TCGCGTTGCGATTTTTATAT
1 TCGCGTTGCGATTTTTATAT
43051 TCGCGTTGCGATT
1 TCGCGTTGCGATT
43064 CTGGAAAATC
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:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTATAT
Found at i:43124 original size:42 final size:42
Alignment explanation
Indices: 43031--43185 Score: 103
Period size: 42 Copynumber: 3.8 Consensus size: 42
43021 ATTTATATGT
* * *
43031 TCGCGTTGCG-ATTTTTATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTGTATATTCGCATTGCGATTCTGCAAAA
** * *
43072 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTTGTA-TATTCGCATTGCGATTCTGCAAAA
* * * *
43114 TCGCGTTGCG-ATTCTGGGA-ACT-G-ATTTGCGATTCTG-GAGA
1 TCGCGTTGCGAATT-T-GTATATTCGCA-TTGCGATTCTGCAAAA
*
43154 TCGCGTTGCG-ATTTTTAT-TTCGCATTGCGATT
1 TCGCGTTGCGAATTTGTATATTCGCATTGCGATT
43186 TTGTTGGTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
38 2 0.02
39 10 0.11
40 16 0.18
41 23 0.26
42 33 0.38
43 4 0.05
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGAATTTGTATATTCGCATTGCGATTCTGCAAAA
Found at i:43162 original size:20 final size:19
Alignment explanation
Indices: 43113--43166 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
43103 ATTCTTCATA
43113 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
43132 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
43153 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
43167 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:52248 original size:93 final size:93
Alignment explanation
Indices: 52133--52313 Score: 317
Period size: 93 Copynumber: 1.9 Consensus size: 93
52123 CCTATGATCA
* *
52133 TTCGCGATTAAATTAATATTAAATTGTTTAAATTTTATTCATATATATTTTTATTGGATTGATTT
1 TTCGCGATTAAATTAATATTAAATTGTTTAAATTTTATTCATATATATTTTCATTAGATTGATTT
*
52198 TTTTATGAAATATACTCAAAATCCACCC
66 TTTCATGAAATATACTCAAAATCCACCC
* *
52226 TTCGCGATTAAATTAATATTAAATTGTTTAAATTTTATTTATATATCTTTTCATTAGATTGATTT
1 TTCGCGATTAAATTAATATTAAATTGTTTAAATTTTATTCATATATATTTTCATTAGATTGATTT
52291 TTTCATGAAATATACTCAAAATC
66 TTTCATGAAATATACTCAAAATC
52314 TACGAAAAGA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (93 bp):
TTCGCGATTAAATTAATATTAAATTGTTTAAATTTTATTCATATATATTTTCATTAGATTGATTT
TTTCATGAAATATACTCAAAATCCACCC
Done.