Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005965.1 Hibiscus syriacus cultivar Beakdansim tig00014014_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: 56130
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4067 original size:24 final size:24
Alignment explanation
Indices: 4035--4083 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4025 GAAACAACTT
4035 GTAACAGATGAGATTAAAAGAGTA
1 GTAACAGATGAGATTAAAAGAGTA
4059 GTAACAGATGAGATTAAAAGAGTA
1 GTAACAGATGAGATTAAAAGAGTA
4083 G
1 G
4084 CAAGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (24 bp):
GTAACAGATGAGATTAAAAGAGTA
Found at i:4597 original size:20 final size:20
Alignment explanation
Indices: 4569--4834 Score: 201
Period size: 20 Copynumber: 13.3 Consensus size: 20
4559 AATTTGTAAA
4569 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
4589 TTACAACACA-AACGTCAAAT
1 TCGCAACACAGAA-GTCAAAT
** *
4609 TTACAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
4629 TCGTAACAC-GAATTTGT-AAA-
1 TCGCAACACAGAA---GTCAAAT
*
4649 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
4669 TCGCAACGC-GATA-TCCAAAT
1 TCGCAACACAGA-AGT-CAAAT
4689 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
** *
4709 TCATAAC-GAGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
4729 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
** *
4749 TCATAAC-GAGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
4769 TCGCAACGCGGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
4789 TCGCAACGCGGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
4809 TCGCAACGC-GAAAGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
4829 TCGCAA
1 TCGCAA
4835 TGCGGAACAA
Statistics
Matches: 203, Mismatches: 25, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.01
19 15 0.07
20 170 0.84
21 14 0.07
22 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:4831 original size:40 final size:41
Alignment explanation
Indices: 4569--4834 Score: 232
Period size: 40 Copynumber: 6.6 Consensus size: 41
4559 AATTTGTAAA
** *
4569 TCGCAACACAGAAGTCAAATTTACAACACA-A-ACGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCAGATA-GTCAAAT
** * * * *
4609 TTACAACGC-GATAGTCAAATTCGTAACAC-GAATTTGT-AAA-
1 TCGCAACACAGA-AGTCAAATTCGCAACGCAG-A-TAGTCAAAT
*
4649 TCGCAACACATAAGTCAAATTCGCAACGC-GATA-TCCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCAGATAGT-CAAAT
**
4689 TCGCAACACAGAAGTCAAATTCATAACG-AGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCAGATAGTCAAAT
**
4729 TCGCAACACAGAAGTCAAATTCATAACG-AGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCAGATAGTCAAAT
* * *
4769 TCGCAACGCGGAAGTCAAATTCGCAACGCGGA-AGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCAGATAGTCAAAT
*
4809 TCGCAACGC-GAAAGTCAAATTCGCAA
1 TCGCAACACAG-AAGTCAAATTCGCAA
4835 TGCGGAACAA
Statistics
Matches: 191, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 7 0.04
40 172 0.90
41 8 0.04
42 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.20
Consensus pattern (41 bp):
TCGCAACACAGAAGTCAAATTCGCAACGCAGATAGTCAAAT
Found at i:7008 original size:22 final size:22
Alignment explanation
Indices: 6944--7009 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
6934 CCATCACCTG
*
6944 ATCGAGCCTCTTCTCCACCTACC
1 ATCGAGCCTCTTCTCCACC-ATC
*
6967 ATC-A-CCT-AT-TCCATCACATC
1 ATCGAGCCTCTTCTCCA-C-CATC
6987 ATCGAGCCTCTTCTCCACCATC
1 ATCGAGCCTCTTCTCCACCATC
7009 A
1 A
7010 CCTCATGACA
Statistics
Matches: 34, Mismatches: 3, Indels: 13
0.68 0.06 0.26
Matches are distributed among these distances:
19 4 0.12
20 7 0.21
21 5 0.15
22 9 0.26
23 5 0.15
24 4 0.12
ACGTcount: A:0.23, C:0.44, G:0.06, T:0.27
Consensus pattern (22 bp):
ATCGAGCCTCTTCTCCACCATC
Found at i:7599 original size:21 final size:21
Alignment explanation
Indices: 7573--7663 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
7563 CTCCTATCGT
*
7573 TCAAGAGGCCCCTCTCACC-A
1 TCAAGAGGCCCCTCCCACCGA
* *
7593 TCGAAGAAGCCCCTCCCACCGT
1 TC-AAGAGGCCCCTCCCACCGA
** * *
7615 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCCCACCGA
* * * *
7636 TCAAGAGGTCCCGCCCGCCGT
1 TCAAGAGGCCCCTCCCACCGA
7657 TCAAGAG
1 TCAAGAG
7664 CTCGATTCAC
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.22, C:0.40, G:0.22, T:0.16
Consensus pattern (21 bp):
TCAAGAGGCCCCTCCCACCGA
Found at i:7657 original size:42 final size:42
Alignment explanation
Indices: 7570--7663 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
7560 CGTCTCCTAT
*
7570 CGTTCAAGAGGCCCCTCTCACCATCGAAGAAGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCACCATCGAAGAAGCCCCGCCCAC
* ** * * *
7612 CGTTCAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCGCCCGC
1 CGTTCAAGAGGCCCCTCTCA-CCATCGAAGAAGCCCCGCCCAC
7654 CGTTCAAGAG
1 CGTTCAAGAG
7664 CTCGATTCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 41 0.93
43 3 0.07
ACGTcount: A:0.21, C:0.39, G:0.22, T:0.17
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCACCATCGAAGAAGCCCCGCCCAC
Found at i:9150 original size:66 final size:65
Alignment explanation
Indices: 8991--9166 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
8981 GGTGTACACT
8991 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
9055 TAATTA
60 TAATTA
* *
9061 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAATAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAATAATT
9125 A
65 A
9126 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
9167 GTTTTAAATT
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 17 0.17
65 19 0.19
66 40 0.40
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTA
Found at i:12004 original size:24 final size:24
Alignment explanation
Indices: 11970--12023 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
11960 CCATCACATC
11970 ATCAAAATCCGAGTATTAACTAAG
1 ATCAAAATCCGAGTATTAACTAAG
* * *
11994 ATCAAAGTCCGGGTATTGACTAAG
1 ATCAAAATCCGAGTATTAACTAAG
12018 ATCAAA
1 ATCAAA
12024 TTTCGAATAC
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:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACTAAG
Found at i:12170 original size:12 final size:12
Alignment explanation
Indices: 12149--12182 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12139 GGTTGTGGGT
*
12149 TTTGAGATTGTG
1 TTTGATATTGTG
12161 TTTGATATTGTG
1 TTTGATATTGTG
*
12173 TTTGGTATTG
1 TTTGATATTG
12183 AAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:13081 original size:40 final size:40
Alignment explanation
Indices: 13007--13179 Score: 174
Period size: 40 Copynumber: 4.3 Consensus size: 40
12997 CGAAAATCTA
* * *
13007 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGACTATCGC
* *
13048 GTTGCGAATTTGACTTCTGTATTGCGAATTTGACTATCGT
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATCGC
*
13088 GTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-TA-TCGC
* ** * *
13128 GTTGCGAAATTGGA-AACTGTGTTGCGAAATTGGAAT-TCGC
1 GTTGCG-AATTTGACTTCTGTGTTGCG-AATTTGACTATCGC
13168 GTTGCGAATTTG
1 GTTGCGAATTTG
13180 TTGGTCATTT
Statistics
Matches: 111, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.02
39 10 0.09
40 77 0.69
41 18 0.16
42 3 0.03
43 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATCGC
Found at i:13109 original size:20 final size:19
Alignment explanation
Indices: 12967--13114 Score: 127
Period size: 20 Copynumber: 7.4 Consensus size: 19
12957 AACTAAAACC
* * *
12967 TGTTGCGAAATTAAATTCG
1 TGTTGCGAATTTGACTTCG
* **
12986 TGTTGCGAATTCGAAAATC-
1 TGTTGCGAATTTG-ACTTCG
*
13005 TAGTTGCGAATTTGAAATTCCG
1 T-GTTGCGAATTTG-ACTT-CG
*
13027 CGTTGCGAATTTGACTATCG
1 TGTTGCGAATTTGACT-TCG
*
13047 CGTTGCGAATTTGACTTCTG
1 TGTTGCGAATTTGACTTC-G
*
13067 TATTGCGAATTTGACTATCG
1 TGTTGCGAATTTGACT-TCG
13087 TGTTGCGAATTTGACTTCTG
1 TGTTGCGAATTTGACTTC-G
13107 TGTTGCGA
1 TGTTGCGA
13115 TTTACAAATT
Statistics
Matches: 110, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
19 15 0.14
20 79 0.72
21 16 0.15
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (19 bp):
TGTTGCGAATTTGACTTCG
Found at i:13171 original size:20 final size:20
Alignment explanation
Indices: 13121--13175 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
13111 GCGATTTACA
13121 AATTCGCGTTGCGAAATTGG
1 AATTCGCGTTGCGAAATTGG
* *
13141 AA-ACTGTGTTGCGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
13161 AATTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
13176 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:15522 original size:2 final size:2
Alignment explanation
Indices: 15515--15542 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15505 AAAACGAGCG
15515 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
15543 AACTTAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16654 original size:19 final size:19
Alignment explanation
Indices: 16630--16678 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
16620 AAATGACCAA
16630 CAAAATCGCAATGCGATCG
1 CAAAATCGCAATGCGATCG
16649 CAAAATCGCAATGCGATCG
1 CAAAATCGCAATGCGATCG
* *
16668 CTAATTCGCAA
1 CAAAATCGCAA
16679 CACGATCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (19 bp):
CAAAATCGCAATGCGATCG
Found at i:16684 original size:19 final size:19
Alignment explanation
Indices: 16630--16685 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
16620 AAATGACCAA
**
16630 CAAAATCGCAATGCGATCG
1 CAAAATCGCAACACGATCG
**
16649 CAAAATCGCAATGCGATCG
1 CAAAATCGCAACACGATCG
* *
16668 CTAATTCGCAACACGATC
1 CAAAATCGCAACACGATC
16686 TCCATTATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (19 bp):
CAAAATCGCAACACGATCG
Found at i:16802 original size:20 final size:20
Alignment explanation
Indices: 16777--16869 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
16767 TTTTCCCAAT
16777 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
16797 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
16817 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
16838 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
16859 TCGCAATGCGA
1 TCGCAATGCGA
16870 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:16819 original size:41 final size:41
Alignment explanation
Indices: 16774--16869 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
16764 CGATTTTCCC
*
16774 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
16815 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
16856 AAATCGCAATGCGA
1 AATTCGCAATGCGA
16870 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:16904 original size:21 final size:20
Alignment explanation
Indices: 16855--16905 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
16845 GCGAATTGAG
* *
16855 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
16875 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
16896 AAAATCGCAA
1 AAAATCGCAA
16906 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:16928 original size:20 final size:20
Alignment explanation
Indices: 16903--16947 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
16893 TAAAAAATCG
*
16903 CAACGAGATACTTACTTTCA
1 CAACGAGATACTGACTTTCA
* *
16923 CAACGATATACTGACTTTCG
1 CAACGAGATACTGACTTTCA
16943 CAACG
1 CAACG
16948 CGATTTACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (20 bp):
CAACGAGATACTGACTTTCA
Found at i:17541 original size:19 final size:19
Alignment explanation
Indices: 17519--17650 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
17509 GAAACCAAAA
*
17519 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17538 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17557 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17576 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
17590 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
17609 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
17629 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
17649 TC
1 TC
17651 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.10
16 2 0.02
17 3 0.03
19 51 0.54
20 28 0.30
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:17608 original size:33 final size:34
Alignment explanation
Indices: 17562--17625 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
17552 TCATTTCGCG
** *
17562 TTGCGATTTTCATTT-CGCGTTGCGATTCTCTCA
1 TTGCGATAGTCATTTCCGCGTTGCAATTCTCTCA
17595 TTGCGATAGTCATTTCCGCGTTGCAATTCTC
1 TTGCGATAGTCATTTCCGCGTTGCAATTCTC
17626 ATTATCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCAATTCTCTCA
Found at i:17627 original size:20 final size:20
Alignment explanation
Indices: 17604--17650 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17594 ATTGCGATAG
17604 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
17624 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
17644 TCATTTC
1 TCATTTC
17651 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:19712 original size:42 final size:42
Alignment explanation
Indices: 19652--19774 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
19642 GCCCGACTCG
* * *
19652 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
19694 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
19736 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
19775 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:19732 original size:21 final size:21
Alignment explanation
Indices: 19708--19774 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
19698 TCATTCCTCG
19708 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
19729 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
19750 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
19771 AGAG
1 AGAG
19775 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:21150 original size:14 final size:14
Alignment explanation
Indices: 21131--21166 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21121 ATTGTTTAAT
21131 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
21145 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
21159 TGATTTGT
1 TGATTTGT
21167 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:21367 original size:19 final size:19
Alignment explanation
Indices: 21345--21442 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
21335 CGAAATTAAA
*
21345 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
21364 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
21380 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
21397 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
21413 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
21430 TTCGCATTGCGAT
1 TTCGCATTGCGAT
21443 AGTAATTTCC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.19
16 13 0.21
17 13 0.21
19 24 0.39
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:21391 original size:33 final size:33
Alignment explanation
Indices: 21349--21442 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
21339 ATTAAATTCG
21349 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
21382 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
21415 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
21443 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:23753 original size:12 final size:12
Alignment explanation
Indices: 23736--23760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23726 TCTTCGGGGA
23736 CTTTTTCTTCTT
1 CTTTTTCTTCTT
23748 CTTTTTCTTCTT
1 CTTTTTCTTCTT
23760 C
1 C
23761 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:23969 original size:24 final size:24
Alignment explanation
Indices: 23935--23993 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
23925 CTGAAACATC
* *
23935 ATCAAAATTCGTGTATTGACCAAT
1 ATCAAAATTCGGGTATTGACCAAG
*
23959 ATCAAAGTTCGGGTATTGACCAAG
1 ATCAAAATTCGGGTATTGACCAAG
*
23983 ATCAAATTTCG
1 ATCAAAATTCG
23994 AATACTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (24 bp):
ATCAAAATTCGGGTATTGACCAAG
Found at i:24002 original size:24 final size:24
Alignment explanation
Indices: 23951--24002 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
23941 ATTCGTGTAT
* ** *
23951 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
23975 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
23999 TGAC
1 TGAC
24003 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:25257 original size:14 final size:14
Alignment explanation
Indices: 25238--25274 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
25228 CATCAATTAA
25238 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
25252 ACAAATCATCTTTT
1 ACAAATCAACATTT
25266 ACAAATCAA
1 ACAAATCAA
25275 TTAAACAATC
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:25695 original size:20 final size:20
Alignment explanation
Indices: 25641--25697 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
25631 TTCATTTGAC
* *
25641 TATCGCAATGCGAAAATGGT
1 TATCGCAACGAGAAAATGGT
25661 TATCGCAAC-ACGAAAATGGT
1 TATCGCAACGA-GAAAATGGT
25681 TATCGCAACGAGAAAAT
1 TATCGCAACGAGAAAAT
25698 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
TATCGCAACGAGAAAATGGT
Found at i:25740 original size:14 final size:16
Alignment explanation
Indices: 25720--25793 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
25710 TGAAAATCGC
25720 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
25735 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
25752 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
25771 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
25787 -TTGCGAT
1 ATTGCGAT
25794 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:25757 original size:19 final size:19
Alignment explanation
Indices: 25716--25783 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
25706 GAAATGAAAA
25716 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
25732 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25749 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25768 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
25784 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:25900 original size:14 final size:14
Alignment explanation
Indices: 25881--25917 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
25871 CATCAATTAA
25881 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
25895 ACAAATCATCTTTT
1 ACAAATCAACATTT
25909 ACAAATCAA
1 ACAAATCAA
25918 TTAAACAATC
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:27858 original size:14 final size:14
Alignment explanation
Indices: 27839--27929 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
27829 ATGCGAAATG
27839 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
27853 AAAATCGCAACGCGAAATG
1 AAAATCGCAA--CG--A-C
27872 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
27886 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
27902 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
27918 AAAATCGCAACG
1 AAAATCGCAACG
27930 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.25, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:27877 original size:19 final size:19
Alignment explanation
Indices: 27765--27915 Score: 117
Period size: 19 Copynumber: 8.4 Consensus size: 19
27755 TAGTTTACTT
* *
27765 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
27785 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
27804 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
27824 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
27843 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
27857 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
27876 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
27890 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
27908 TCGCAACG
1 TCGCAACG
27916 ACAAAATCGC
Statistics
Matches: 107, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.19
15 2 0.02
16 4 0.04
17 4 0.04
18 13 0.12
19 35 0.33
20 29 0.27
ACGTcount: A:0.43, C:0.25, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:27914 original size:32 final size:33
Alignment explanation
Indices: 27823--27934 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
27813 GGAAATGGCT
*
27823 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
27856 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
27889 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
27921 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
27935 CACAAATCGC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 30 0.38
33 48 0.62
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:27942 original size:65 final size:66
Alignment explanation
Indices: 27823--27945 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
27813 GGAAATGGCT
* *
27823 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATCGCAACGACAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
27888 A
66 A
27889 ATCGCAACGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
27946 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 38 0.70
66 15 0.28
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (66 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:27963 original size:19 final size:17
Alignment explanation
Indices: 27941--28036 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
27931 GAAACACAAA
27941 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
27960 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
27976 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
27992 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
28008 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
28025 TCGCATTGCGAT
1 TCGC-TTGCGAT
28037 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:27982 original size:14 final size:14
Alignment explanation
Indices: 27963--28020 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
27953 TTTCATTTCG
27963 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
27977 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
27993 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
28009 CGTTGCGATTTT
1 CGTTGCGATTTT
28021 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:28027 original size:33 final size:33
Alignment explanation
Indices: 27946--28036 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
27936 ACAAATCGCA
27946 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
27979 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
28011 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
28037 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:28055 original size:20 final size:19
Alignment explanation
Indices: 28021--28075 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
28011 TTGCGATTTT
*
28021 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
28040 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
28060 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
28076 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:28574 original size:18 final size:18
Alignment explanation
Indices: 28548--28592 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28538 GTCGATCAGA
*
28548 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
28566 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
28584 TGATGGCTC
1 TGATGGCTC
28593 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:30236 original size:22 final size:22
Alignment explanation
Indices: 30211--30254 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30201 GATTTAGATA
30211 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
30233 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
30255 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:30467 original size:20 final size:20
Alignment explanation
Indices: 30442--30494 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
30432 GATTATGTAT
*
30442 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
30462 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
30482 TATCTCGTTGCGA
1 TATCGCGTTGCGA
30495 TTTTTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:30529 original size:20 final size:20
Alignment explanation
Indices: 30422--30537 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
30412 CGCTTTGAAA
*
30422 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
30443 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
30463 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
30483 ATCTCGTTGCGATTTTTTTATT
1 ATCGCATTGCGA--TAGTCAGT
30505 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
30525 ATCGCATTGCGAT
1 ATCGCATTGCGAT
30538 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 11 0.14
22 13 0.17
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:30574 original size:41 final size:41
Alignment explanation
Indices: 30526--30621 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
30516 ATAGTCAGTA
* *
30526 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
30567 TCTCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
30608 TCGCATTGCGAATT
1 TCGCATTGCGAATT
30622 GGGAAAATCG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:30575 original size:20 final size:20
Alignment explanation
Indices: 30526--30618 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
30516 ATAGTCAGTA
*
30526 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
30547 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* * *
30567 TCTCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
30588 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
30608 TCGCATTGCGA
1 TCGCATTGCGA
30619 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:31260 original size:21 final size:21
Alignment explanation
Indices: 31230--31282 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
31220 TTTAAACAAT
*
31230 AACTAAAATAAATGAAAT-TAA
1 AACTATAATAAATGAAATAT-A
*
31251 AACTATAAT-ATTGAAATATA
1 AACTATAATAAATGAAATATA
*
31271 AACAATAATAAA
1 AACTATAATAAA
31283 ATTTGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (21 bp):
AACTATAATAAATGAAATATA
Found at i:32659 original size:3 final size:3
Alignment explanation
Indices: 32653--32704 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
32643 ATTTATTATT
* * *
32653 TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA -AA TAA TAA -AA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32699 TAA TAA
1 TAA TAA
32705 ATCAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:32701 original size:22 final size:21
Alignment explanation
Indices: 32653--32705 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
32643 ATTTATTATT
32653 TAATAATAAAAAAAATAATAA
1 TAATAATAAAAAAAATAATAA
32674 TAATAATAAAATAATAA-AATAA
1 TAATAATAAAA-AA-AATAATAA
*
32696 TTATAATAAA
1 TAATAATAAA
32706 TCAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.38
22 16 0.55
23 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TAATAATAAAAAAAATAATAA
Found at i:32701 original size:25 final size:26
Alignment explanation
Indices: 32660--32718 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
32650 ATTTAATAAT
32660 AAAA-AAAATAATAATAAT-AAT-AA
1 AAAATAAAATAATAATAATAAATCAA
*
32683 AATAATAAAATAATTATAATAAATCAA
1 AA-AATAAAATAATAATAATAAATCAA
32710 AAAATAAAA
1 AAAATAAAA
32719 CACAAATGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 13 0.42
26 10 0.32
27 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAATAAAATAATAATAATAAATCAA
Found at i:33919 original size:80 final size:79
Alignment explanation
Indices: 33823--33982 Score: 248
Period size: 80 Copynumber: 2.0 Consensus size: 79
33813 TGCGCGTTCT
*
33823 TGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTTGGGTTAGATTTAAGTAATGT
1 TGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAA-TTAGGTTAGATTTAAGTAATGT
* *
33888 TTGCATTTTGGTTAC
65 TTACATTGTGGTTAC
* * *
33903 TGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATGTAAAATTAGGTTTGATTTACGTAATGTT
1 TGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTAGGTTAGATTTAAGTAATGTT
*
33968 TACATTGTGTTTAC
66 TACATTGTGGTTAC
33982 T
1 T
33983 AATCCGAGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 32 0.44
80 41 0.56
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (79 bp):
TGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTAGGTTAGATTTAAGTAATGTT
TACATTGTGGTTAC
Found at i:36264 original size:18 final size:18
Alignment explanation
Indices: 36232--36266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36222 TTCATTGTCA
**
36232 TGGATTACATGACTGTTC
1 TGGATTACAAAACTGTTC
36250 TGGATTACAAAACTGTT
1 TGGATTACAAAACTGTT
36267 TTTGCATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
TGGATTACAAAACTGTTC
Found at i:40811 original size:34 final size:34
Alignment explanation
Indices: 40768--40834 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
40758 GATGAACTAT
*
40768 CAATTTAGGGCATTGAATATCGGAACTCTATGTC
1 CAATTTAGGGCATTGAATATCGGAACCCTATGTC
*
40802 CAATTTAGGGTATTGAATATCGGAACCCTATGT
1 CAATTTAGGGCATTGAATATCGGAACCCTATGT
40835 GCTTGCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (34 bp):
CAATTTAGGGCATTGAATATCGGAACCCTATGTC
Found at i:53976 original size:18 final size:18
Alignment explanation
Indices: 53950--53995 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
53940 TCACGGAATG
* *
53950 TAAGATTACTGGCGTGAA
1 TAAGATTACTGACGAGAA
* *
53968 TAGGATTACCGACGAGAA
1 TAAGATTACTGACGAGAA
53986 TAAGATTACT
1 TAAGATTACT
53996 AGGAATGTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (18 bp):
TAAGATTACTGACGAGAA
Done.