Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000942.1 Hibiscus syriacus cultivar Beakdansim tig00001882_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: 96415
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3271 original size:60 final size:59
Alignment explanation
Indices: 3201--3335 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 59
3191 AAAGGATAAA
* * *
3201 TTACACAAATGATCCCCTAATTATAAAATATTATTTTATTAAATCCTTTAACTATTAAAAG
1 TTACA-AAATGATCACCTAACTATAAAAT-GTATTTTATTAAATCCTTTAACTATTAAAAG
** * * * * *
3262 TTACAAAATGATCATTTGACTATAGAATGTGTTTTGTTAAGTCCTTTAACTATTAAAAG
1 TTACAAAATGATCACCTAACTATAAAATGTATTTTATTAAATCCTTTAACTATTAAAAG
3321 TTACAAAATGATCAC
1 TTACAAAATGATCAC
3336 TCGACTATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 41 0.65
60 17 0.27
61 5 0.08
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (59 bp):
TTACAAAATGATCACCTAACTATAAAATGTATTTTATTAAATCCTTTAACTATTAAAAG
Found at i:4446 original size:20 final size:18
Alignment explanation
Indices: 4400--4446 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
4390 CCATTTTGCA
4400 TATAATAATATTAAATTT
1 TATAATAATATTAAATTT
*
4418 TAAAATAATA-TACTAATTAT
1 TATAATAATATTA--AATT-T
4438 TATAATAAT
1 TATAATAAT
4447 CATAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 9 0.38
19 4 0.17
20 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAATAATATTAAATTT
Found at i:6132 original size:28 final size:27
Alignment explanation
Indices: 6090--6153 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
6080 AAGATGTTTG
* *
6090 TGTTCACTTCATTTAACGTTCATGAACA
1 TGTTCATTTCATTT-ACGTTCATAAACA
* *
6118 TGTTCATTTCGTTTAGGTTCATAAACA
1 TGTTCATTTCATTTACGTTCATAAACA
6145 TGTTCATTT
1 TGTTCATTT
6154 AAGGTTTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (27 bp):
TGTTCATTTCATTTACGTTCATAAACA
Found at i:6158 original size:23 final size:23
Alignment explanation
Indices: 6097--6171 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
6087 TTGTGTTCAC
* *
6097 TTCATTTAACGTTCATGAACATG
1 TTCATTTAAGGTTCATAAACATG
*
6120 TTCATTTCGTTTAGGTTCATAAACATG
1 TTCA--T--TTAAGGTTCATAAACATG
* *
6147 TTCATTTAAGGTTTACAAACATG
1 TTCATTTAAGGTTCATAAACATG
6170 TT
1 TT
6172 GGACATTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 21 0.50
25 2 0.05
27 19 0.45
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (23 bp):
TTCATTTAAGGTTCATAAACATG
Found at i:10847 original size:15 final size:16
Alignment explanation
Indices: 10827--10856 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10817 TAAACCAGGC
10827 AGATAAAA-AAAGAAA
1 AGATAAAAGAAAGAAA
10842 AGATAAAAGAAAGAA
1 AGATAAAAGAAAGAA
10857 CAATAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (16 bp):
AGATAAAAGAAAGAAA
Found at i:23510 original size:16 final size:17
Alignment explanation
Indices: 23489--23526 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
23479 ACAATCCATC
*
23489 TATTTATAT-GATAATT
1 TATTTATATGGATAAAT
*
23505 TATTTATTTGGATAAAT
1 TATTTATATGGATAAAT
23522 TATTT
1 TATTT
23527 CTTTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TATTTATATGGATAAAT
Found at i:28085 original size:2 final size:2
Alignment explanation
Indices: 28078--28102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28068 GTTTTCGAGT
28078 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28103 GTGAGATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28881 original size:20 final size:20
Alignment explanation
Indices: 28853--28949 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
28843 TTTTCCGACT
*
28853 ATCGTAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
28873 ATCGCAATGCGAGTATG-ACT
1 ATCGCAATGCGAATATGTA-A
***
28893 ATCGCAACATGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * *
28913 ATTGCAACGCGATTATGTAA
1 ATCGCAATGCGAATATGTAA
*
28933 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
28950 ACTATCGCAA
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 59 0.97
21 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:28937 original size:40 final size:40
Alignment explanation
Indices: 28863--28939 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
28853 ATCGTAATGC
* *
28863 GAATATGTAAATCGCAATGCGAGTATGACTATCGCAACAT
1 GAATATGTAAATCGCAACGCGAGTATGACAATCGCAACAT
* *
28903 GAATATGTAAATTGCAACGCGATTATGTA-AATCGCAA
1 GAATATGTAAATCGCAACGCGAGTATG-ACAATCGCAA
28940 TGCGATTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (40 bp):
GAATATGTAAATCGCAACGCGAGTATGACAATCGCAACAT
Found at i:28956 original size:20 final size:20
Alignment explanation
Indices: 28791--28982 Score: 86
Period size: 20 Copynumber: 9.4 Consensus size: 20
28781 GTTTCCATAT
*
28791 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* ** *
28811 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTATGAC-TA
** *
28831 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGATTAT--GACTA
* * *
28854 TCGTAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
*
28874 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTATGACTA
*** * *
28894 TCGCAACATGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
* * *
28914 TTGCAACGCGATTATGTA-AA
1 TCGCAATGCGATTATG-ACTA
28934 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
* * *
28954 TCGCAATGTGATTCTGACTG
1 TCGCAATGCGATTATGACTA
28974 TCGCAATGC
1 TCGCAATGC
28983 TGAGTTTACA
Statistics
Matches: 130, Mismatches: 33, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
19 4 0.03
20 99 0.76
21 14 0.11
22 11 0.08
23 1 0.01
24 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:29027 original size:21 final size:21
Alignment explanation
Indices: 28995--29049 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
28985 AGTTTACATA
*
28995 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
29016 TTTGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
29037 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
29050 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:29678 original size:5 final size:5
Alignment explanation
Indices: 29664--29701 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
29654 CCGCCGCCGC
29664 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTC
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTC
29702 GTGGTCGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.00, C:0.42, G:0.21, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:29710 original size:6 final size:6
Alignment explanation
Indices: 29699--29730 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
29689 GTCTCGTCTC
29699 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
29731 AATGGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:29736 original size:6 final size:6
Alignment explanation
Indices: 29727--29751 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29717 GTCGTGGTCG
29727 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
29752 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:29736 original size:18 final size:18
Alignment explanation
Indices: 29699--29736 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29689 GTCTCGTCTC
**
29699 GTCGTGGTCGTGGTCGTG
1 GTCGTGGTCGTGGTAATG
29717 GTCGTGGTCGTGGTAATG
1 GTCGTGGTCGTGGTAATG
29735 GT
1 GT
29737 AATGGTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.13, G:0.47, T:0.34
Consensus pattern (18 bp):
GTCGTGGTCGTGGTAATG
Found at i:29871 original size:21 final size:21
Alignment explanation
Indices: 29847--29914 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
29837 TTTGGAATAA
*
29847 ATCGTAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * **
29868 ATCGCAA--CGAATTTGAAAA
1 ATCGCAACGCGAACTTGGACT
29887 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
29908 ATCGCAA
1 ATCGCAA
29915 TGTGAATATG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 15 0.42
21 21 0.58
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:29896 original size:40 final size:42
Alignment explanation
Indices: 29835--29914 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 42
29825 AGTCGTTGCT
*
29835 AATTTGGAATAAATCGTAACGCGAACTTGGACTATCGCAACG
1 AATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACG
29877 AATTT-GAA-AAATCGCAACGCGAACTTGGACTATCGCAA
1 AATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
29915 TGTGAATATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 29 0.78
41 3 0.08
42 5 0.14
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (42 bp):
AATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACG
Found at i:30393 original size:20 final size:20
Alignment explanation
Indices: 30364--30416 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
30354 CGCGAACTCT
30364 AATTTCGCAACACAGTTTCCA
1 AATTT-GCAACACAGTTTCCA
* *
30385 AATTTGCAACTCAGTTTCGA
1 AATTTGCAACACAGTTTCCA
* *
30405 AAATCGCAACAC
1 AATTTGCAACAC
30417 TATTTTCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (20 bp):
AATTTGCAACACAGTTTCCA
Found at i:30602 original size:57 final size:57
Alignment explanation
Indices: 30433--30615 Score: 249
Period size: 57 Copynumber: 3.2 Consensus size: 57
30423 CTAAATTCAT
* * *
30433 AACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGATAAGCAGTACTATCAC
1 AACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
* * * * *
30490 AACACGATTTTTAAATCCTCAACACTAATTACCGATATAGGTAAACAGTATTATCGC
1 AACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
* * **
30547 AATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATCGC
1 AACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
*
30604 AACGCGAATTTC
1 AACGCGATTTTC
30616 GTTTTCGCAC
Statistics
Matches: 107, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 107 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (57 bp):
AACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
Found at i:31041 original size:58 final size:57
Alignment explanation
Indices: 30933--31072 Score: 217
Period size: 58 Copynumber: 2.4 Consensus size: 57
30923 TGCGAAATTG
* * * *
30933 GCGAATTTGAAAATCGCGTTACGATAGTAGTGTTTACCTATGTCGGTAATTAGCGTT
1 GCGAATTTGAAAATCGCGTTGCGATAATAGTGTTTACCTATATCGGTAATTAACGTT
* *
30990 GCGAATTTGAAAATCACGTTGCGATAATATTTGTTTACCTATATCGGTAATTAACGTT
1 GCGAATTTGAAAATCGCGTTGCGATAATA-GTGTTTACCTATATCGGTAATTAACGTT
31048 GCGAATTTGAAAATCGCGTTGCGAT
1 GCGAATTTGAAAATCGCGTTGCGAT
31073 TTCCGAAACT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
57 26 0.35
58 49 0.65
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (57 bp):
GCGAATTTGAAAATCGCGTTGCGATAATAGTGTTTACCTATATCGGTAATTAACGTT
Found at i:31069 original size:20 final size:20
Alignment explanation
Indices: 31044--31158 Score: 74
Period size: 20 Copynumber: 5.7 Consensus size: 20
31034 CGGTAATTAA
31044 CGTTGCGAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCG
*
31064 CGTTGCG-ATTTCCGAAACT-G
1 CGTTGCGAATTT--GAAAATCG
* *
31084 AGTTGCGAATTTGTGAAACTCG
1 CGTTGCGAA-TT-TGAAAATCG
*
31106 CGTTGCGAATTTGGAAA-CTG
1 CGTTGCGAATTTGAAAATC-G
* * * * **
31126 TGTTACGAAATTGGAGTTCG
1 CGTTGCGAATTTGAAAATCG
31146 CGTTGCGAATTTG
1 CGTTGCGAATTTG
31159 TTGGTTATTT
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
19 5 0.07
20 42 0.57
21 15 0.20
22 11 0.15
23 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCG
Found at i:31137 original size:21 final size:21
Alignment explanation
Indices: 31077--31134 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
31067 TGCGATTTCC
31077 GAAACTGAGTTGCGAATTTGT
1 GAAACTGAGTTGCGAATTTGT
*
31098 GAAACTCGCGTTGCGAATTTG-
1 GAAACT-GAGTTGCGAATTTGT
* *
31119 GAAACTGTGTTACGAA
1 GAAACTGAGTTGCGAA
31135 ATTGGAGTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 12 0.36
22 13 0.39
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (21 bp):
GAAACTGAGTTGCGAATTTGT
Found at i:41343 original size:20 final size:20
Alignment explanation
Indices: 41307--41354 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
41297 CAAAATGACC
*
41307 CAATTTC-ACATTCTAACAT
1 CAATTTCAACATTATAACAT
41326 CAATTTCAACATTATAACAT
1 CAATTTCAACATTATAACAT
*
41346 AAATTTCAA
1 CAATTTCAA
41355 GCATAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACATTATAACAT
Found at i:44685 original size:11 final size:11
Alignment explanation
Indices: 44669--44701 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
44659 AAGATAAAAT
44669 TATTTATATTA
1 TATTTATATTA
*
44680 TATTTATTTTA
1 TATTTATATTA
44691 TATTTA-ATTA
1 TATTTATATTA
44701 T
1 T
44702 TTGACCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATATTA
Found at i:44692 original size:16 final size:15
Alignment explanation
Indices: 44666--44703 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
44656 TAGAAGATAA
44666 AATTA-TTTATATTAT
1 AATTATTTTATATT-T
*
44681 ATTTATTTTATATTT
1 AATTATTTTATATTT
44696 AATTATTT
1 AATTATTT
44704 GACCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTATTTTATATTT
Found at i:52490 original size:21 final size:20
Alignment explanation
Indices: 52405--52561 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
52395 AATGACCAAT
** *
52405 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
52424 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
52444 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
52464 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
52485 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
52506 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
52527 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
52547 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
52562 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:52552 original size:20 final size:20
Alignment explanation
Indices: 52527--52721 Score: 173
Period size: 20 Copynumber: 9.7 Consensus size: 20
52517 GCGATTTTCC
* **
52527 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGTATCCG
*
52547 AAAATCGCAACGCG-AACAC-
1 AAAATCGCAACGCGTATC-CG
52566 ATAAATCGCAACGCGTATCCG
1 A-AAATCGCAACGCGTATCCG
* *
52587 TAAATCGCAACGTGTATCCG
1 AAAATCGCAACGCGTATCCG
* *
52607 TAAATCGCAACGCGTAT-GG
1 AAAATCGCAACGCGTATCCG
*
52626 ATAAATCGCAATGCGTATCCG
1 A-AAATCGCAACGCGTATCCG
* *
52647 TATATCGCAACGCGTATCCG
1 AAAATCGCAACGCGTATCCG
* * **
52667 TAAATCGCAACG-ATAATACAT
1 AAAATCGCAACGCGT-AT-CCG
52688 AAAATCGCAACGCGTATCCG
1 AAAATCGCAACGCGTATCCG
*
52708 TAAATCGCAACGCG
1 AAAATCGCAACGCG
52722 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.03
20 121 0.85
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGTATCCG
Found at i:52577 original size:40 final size:39
Alignment explanation
Indices: 52528--52722 Score: 194
Period size: 40 Copynumber: 4.9 Consensus size: 39
52518 CGATTTTCCA
* ** *
52528 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * *
52568 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * * *
52608 AAATCGCAACGCGTAT-GGATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCG-TAAATCGCAACGCG-AACCAT
* ** *
52648 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
52688 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
52723 TATTTAAAGC
Statistics
Matches: 129, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.02
40 93 0.72
41 34 0.26
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:52612 original size:60 final size:60
Alignment explanation
Indices: 52528--52721 Score: 262
Period size: 60 Copynumber: 3.2 Consensus size: 60
52518 CGATTTTCCA
* ** * *
52528 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * ** *
52588 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
52648 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
52709 AAATCGCAACGCG
1 AAATCGCAACGCG
52722 ATATTTAAAG
Statistics
Matches: 114, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 83 0.73
61 31 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:53141 original size:33 final size:33
Alignment explanation
Indices: 53102--53172 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
53092 TTCACTTAGA
* *
53102 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCATTGCGAT
* *
53135 TTTCATTTCGCGTTGCTATTCTCTCATTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCATTGCGAT
53168 TTTCA
1 TTTCA
53173 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCATTGCGAT
Found at i:53278 original size:21 final size:21
Alignment explanation
Indices: 53252--53324 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
53242 TGCAGAAGAG
*
53252 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
*
53273 TCGCAACGAGAGAACTG----
1 TCGCAACGAGAGAAATGAAAA
53290 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
53311 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
53325 TCGCAACGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
17 16 0.36
21 29 0.64
ACGTcount: A:0.47, C:0.18, G:0.25, T:0.11
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:53306 original size:38 final size:38
Alignment explanation
Indices: 53251--53324 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
53241 TTGCAGAAGA
*
53251 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAACT
53289 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA
53325 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.46, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAACT
Found at i:53379 original size:19 final size:19
Alignment explanation
Indices: 53355--53424 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
53345 CGCATTGCGA
53355 TCATTTCGCGTTGCGATTT
1 TCATTTCGCGTTGCGATTT
53374 TCATTTCGCGTTGCGA--T
1 TCATTTCGCGTTGCGATTT
* *
53391 TC---TCTCGTTGCGATTG
1 TCATTTCGCGTTGCGATTT
53407 TCATTTCGCGTTGCGATT
1 TCATTTCGCGTTGCGATT
53425 CTCTCGTGCG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.23
16 2 0.05
17 3 0.07
19 28 0.65
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATTT
Found at i:53401 original size:14 final size:14
Alignment explanation
Indices: 53382--53437 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
53372 TTTCATTTCG
53382 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
53396 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
53415 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
53429 CG-TGCGATT
1 CGTTGCGATT
53438 TTCATTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 7 0.20
14 12 0.34
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:53402 original size:33 final size:33
Alignment explanation
Indices: 53363--53445 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
53353 GATCATTTCG
53363 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
53396 CGTTGCGATTGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
53429 CG-TGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
53446 AACCAAAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 14 0.29
33 34 0.71
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:55293 original size:93 final size:93
Alignment explanation
Indices: 55135--55507 Score: 700
Period size: 93 Copynumber: 4.1 Consensus size: 93
55125 TAGATTGCTT
*
55135 AGTAAATTTATTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55199 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55227 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55292 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55320 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55385 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
55412 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATATTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55476 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55503 AGTAA
1 AGTAA
55508 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
91 29 0.10
92 106 0.38
93 142 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:55447 original size:185 final size:183
Alignment explanation
Indices: 55135--55507 Score: 694
Period size: 185 Copynumber: 2.0 Consensus size: 183
55125 TAGATTGCTT
55135 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
55200 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
55265 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
55320 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
55385 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
55449 GTGTATTCTTTAACACTGTGAATATTATTTGTCTTTGTTTTGTCTTTTGGTTGA
130 GTGTATTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
55503 AGTAA
1 AGTAA
55508 TGCAATCCAT
Statistics
Matches: 185, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 6 0.03
184 32 0.17
185 98 0.53
186 49 0.26
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (183 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAACTGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:55592 original size:19 final size:19
Alignment explanation
Indices: 55552--55628 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
55542 TAGTTTACTT
* *
55552 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
55572 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
55591 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
55605 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
55624 TCGCA
1 TCGCA
55629 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
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 19 0.40
20 13 0.27
ACGTcount: A:0.45, C:0.30, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:55646 original size:19 final size:19
Alignment explanation
Indices: 55624--55758 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
55614 GAAACCAAAA
*
55624 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
55643 TCGCGTTGC-A-ATTC-TT
1 TCGCGTTGCGATTTTCATT
*
55659 T--CGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
55676 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
55692 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
55709 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
55728 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
55748 TCGTGTTGCGA
1 TCGCGTTGCGA
55759 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
14 12 0.13
15 1 0.01
16 11 0.12
17 11 0.12
18 1 0.01
19 43 0.47
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:55718 original size:33 final size:33
Alignment explanation
Indices: 55629--55721 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
55619 CAAAATCGCA
* *
55629 TTGCGATTTTCATTTCGCGTTGCAATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
55662 TTGTGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
55695 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
55722 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:57688 original size:14 final size:14
Alignment explanation
Indices: 57669--57704 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
57659 ATTGTTTAAT
57669 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
57683 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
57697 TGATTTGT
1 TGATTTGT
57705 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:57827 original size:19 final size:19
Alignment explanation
Indices: 57811--57904 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 19
57801 AAAAATGACT
57811 ATCACAATGCGAAATGAAA
1 ATCACAATGCGAAATGAAA
*
57830 ATCGCAATGCGAAATGAAA
1 ATCACAATGCGAAATGAAA
* *
57849 ATCGCAA--CG--A-GAGA
1 ATCACAATGCGAAATGAAA
*
57863 ATCGCAATGCGAAATGAAA
1 ATCACAATGCGAAATGAAA
*
57882 ATCGCAATGCGGAAATGAAA
1 ATCACAATGC-GAAATGAAA
57902 ATC
1 ATC
57905 GCAACGAGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 38 0.58
20 12 0.18
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCACAATGCGAAATGAAA
Found at i:57940 original size:53 final size:53
Alignment explanation
Indices: 57815--57926 Score: 217
Period size: 53 Copynumber: 2.1 Consensus size: 53
57805 ATGACTATCA
57815 CAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
57867 CAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
57920 CAATGCG
1 CAATGCG
57927 TTTATAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 25 0.42
53 34 0.58
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (53 bp):
CAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
Found at i:57970 original size:33 final size:33
Alignment explanation
Indices: 57933--58085 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
57923 TGCGTTTATA
57933 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
57966 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
58006 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
58037 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
58070 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
58086 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:57979 original size:19 final size:19
Alignment explanation
Indices: 57955--58171 Score: 249
Period size: 19 Copynumber: 12.4 Consensus size: 19
57945 GATTCTCTCG
57955 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57974 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57993 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
58007 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
58026 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
58045 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
58059 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
58078 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
58097 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
58111 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
58131 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
58145 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
58164 TTGCGATT
1 TTGCGATT
58172 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:57990 original size:52 final size:52
Alignment explanation
Indices: 57933--58143 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
57923 TGCGTTTATA
57933 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
57985 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
58037 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
58089 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
58142 AT
1 AT
58144 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:58193 original size:33 final size:33
Alignment explanation
Indices: 57974--58185 Score: 234
Period size: 33 Copynumber: 6.2 Consensus size: 33
57964 TCATTTCGCA
57974 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
58007 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
58043 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
58078 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
58111 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
58145 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
58178 TTGCGATT
1 TTGCGATT
58186 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 16, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 73 0.49
34 29 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:60490 original size:12 final size:12
Alignment explanation
Indices: 60473--60497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60463 TCTTCGGGGA
60473 CTTTTTCTTCTT
1 CTTTTTCTTCTT
60485 CTTTTTCTTCTT
1 CTTTTTCTTCTT
60497 C
1 C
60498 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:60749 original size:24 final size:24
Alignment explanation
Indices: 60685--60742 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
60675 AAAATCCGTG
60685 TATTGACCAATATCAAAGACCGGA
1 TATTGACCAATATCAAAGACCGGA
*
60709 TATTGACCAATATCAAAGTCCGGA
1 TATTGACCAATATCAAAGACCGGA
60733 TATTGACCAA
1 TATTGACCAA
60743 GACCAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
TATTGACCAATATCAAAGACCGGA
Found at i:61448 original size:20 final size:20
Alignment explanation
Indices: 61420--61649 Score: 221
Period size: 20 Copynumber: 11.5 Consensus size: 20
61410 AAATTTCAGT
* * *
61420 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
61440 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
61460 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
61480 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
61500 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
61520 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** **
61540 ATTGCGATTTACCCATAAGC
1 GTTGCGATTTACGGATTCGC
* *
61560 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
61580 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
61600 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
61620 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
61640 GTTGCGATTT
1 GTTGCGATTT
61650 TGGAAAATCG
Statistics
Matches: 181, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
19 3 0.02
20 173 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:61650 original size:20 final size:20
Alignment explanation
Indices: 61616--61713 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
61606 ATTTATGTGT
*
61616 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
61636 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
61657 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
61678 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
61699 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
61714 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:61709 original size:42 final size:43
Alignment explanation
Indices: 61616--61714 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
61606 ATTTATGTGT
* *
61616 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
61657 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
61699 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
61715 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:62004 original size:14 final size:15
Alignment explanation
Indices: 61985--62013 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
61975 TATATGCATA
61985 ATATTTTTTA-TGTT
1 ATATTTTTTAGTGTT
61999 ATATTTTTTAGTGTT
1 ATATTTTTTAGTGTT
62014 TATCGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
ATATTTTTTAGTGTT
Found at i:68455 original size:82 final size:80
Alignment explanation
Indices: 68292--68568 Score: 288
Period size: 82 Copynumber: 3.4 Consensus size: 80
68282 TAGGCCAAAT
* * * *
68292 AATAGTGATGCATTATCATCTTCTGTAA-TTTTTAGAGTGT-ATTCAATACATAATTTAAACAAT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGA-TGTCATTCAATGCATAATTTAAACAA-
* * **
68355 TTTTTAGACAAGGGGTGA
64 ATTTTA-AAAAACGGTGA
** * * *
68373 AATAACGGTGCATTATCATCTTCTGCAACTTGTCAGATGTCATTTAATGCATAATTTAAACAACT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGATGTCATTCAATGCATAATTTAAACAAAT
*
68438 TTTCAAATAACGTGTGA
66 TTT-AAAAAACG-GTGA
* * * * *
68455 AATAGTGGTGCATTATCATCTTCTGTAACTTTTCAAAGGCCATTCAATGCATAATTTAAATAAAT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGATGTCATTCAATGCATAATTTAAACAAAT
68520 TTTAAAAAACGGATGA
66 TTTAAAAAACGG-TGA
* * *
68536 CATAGTGGTGAATTATCATCTTATGCAACTTTT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTT
68569 AAGTGATGTA
Statistics
Matches: 163, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 73 0.45
82 89 0.55
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (80 bp):
AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGATGTCATTCAATGCATAATTTAAACAAAT
TTTAAAAAACGGTGA
Found at i:70231 original size:17 final size:17
Alignment explanation
Indices: 70209--70245 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
70199 TCACATAATT
70209 ATTTTTGAATTTTTAGG
1 ATTTTTGAATTTTTAGG
*
70226 ATTTTTGAGTTTTTAGG
1 ATTTTTGAATTTTTAGG
70243 ATT
1 ATT
70246 ATTGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (17 bp):
ATTTTTGAATTTTTAGG
Found at i:74108 original size:187 final size:187
Alignment explanation
Indices: 73833--74228 Score: 579
Period size: 187 Copynumber: 2.1 Consensus size: 187
73823 TTTTCTAATT
* * *
73833 TATATAA-AAATTAAATATTTTATAATTCAAAAAAAAACAGTTTATAATTAATTTAAATAATATA
1 TATATAATATATTAAATATTTTATAATTC-AAAAAAAACAATTTACAATTAATTTAAATAATATA
* **
73897 TAATTATAAAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGT
65 TAATTATAAAATAAAAAATTTATATAAATTTTTTAACTAATTAATATTGATTTAGACTTAAAAGT
*
73962 TATCGGATCTTAAATTATTAATTG-GATTTTAAAT-GATTTGGTCTGAACCCATATGTTA
130 TATCGGATCTTAAATTATTAATTGAG-TTTTAAATAG-TTTGGGCTGAACCCATATGTTA
* *
74020 TATATAATATATTTAATATTTTTTAAATTC-AAAAAAACAATTTACAATTAATTTAAATAATATA
1 TATATAATATATTAAATATTTTAT-AATTCAAAAAAAACAATTTACAATTAATTTAAATAATATA
* * * *
74084 TAATTATAAAATATAAATTTTATATAATTTTTTTAACTAATTAATATTGATTTAGACTTAAGAGT
65 TAATTATAAAATAAAAAATTTATATAAATTTTTTAACTAATTAATATTGATTTAGACTTAAAAGT
* *
74149 TATTGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTGAACTCATATGTTA
130 TATCGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTGAACCCATATGTTA
74207 TATATAATAT-TTAAA-ATTTTAT
1 TATATAATATATTAAATATTTTAT
74229 TTCGGTTAAT
Statistics
Matches: 188, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
185 6 0.03
186 4 0.02
187 158 0.84
188 15 0.08
189 5 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (187 bp):
TATATAATATATTAAATATTTTATAATTCAAAAAAAACAATTTACAATTAATTTAAATAATATAT
AATTATAAAATAAAAAATTTATATAAATTTTTTAACTAATTAATATTGATTTAGACTTAAAAGTT
ATCGGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTGAACCCATATGTTA
Found at i:78710 original size:31 final size:30
Alignment explanation
Indices: 78664--78740 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
78654 TTCAATAATA
*
78664 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
78695 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
78726 TAATAAGTATTTTAT
1 TAATAA-TATTTTAT
78741 TTTTTAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 33 0.85
32 5 0.13
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:79520 original size:31 final size:30
Alignment explanation
Indices: 79463--79529 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
79453 TCAATAAAGT
*
79463 TTAAAAAATTATAAATACTTATTAAATTTA
1 TTAAAAAATTATAAATACTTAATAAATTTA
*
79493 TTAAAAGATTATTAAATTA-TTAATAAATTTA
1 TTAAAAAATTA-TAAA-TACTTAATAAATTTA
79524 TCTAAA
1 T-TAAA
79530 TACTATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 10 0.31
31 16 0.50
32 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
TTAAAAAATTATAAATACTTAATAAATTTA
Found at i:80952 original size:30 final size:29
Alignment explanation
Indices: 80916--81108 Score: 183
Period size: 30 Copynumber: 6.4 Consensus size: 29
80906 CCTTCGTCAC
* * *
80916 CACCACCACCAGCAGCCCCCCAAAGCTCAT
1 CACCACCGCCACCA-CCCCCAAAAGCTCAT
*
80946 CACCACCGCCACCGCCACCCAAAAGCTCAT
1 CACCACCGCCACCACC-CCCAAAAGCTCAT
* *
80976 CGCCACCGCCACCAACACCC-AAAGTCTCAT
1 CACCACCGCCACC-ACCCCCAAAAG-CTCAT
*
81006 CACCACCGCCACCAACACCCAAAAGCTCAT
1 CACCACCGCCACC-ACCCCCAAAAGCTCAT
* * *
81036 CGCCACCGCCACCAACACCC-AAAGTCCCAT
1 CACCACCGCCACC-ACCCCCAAAAG-CTCAT
* *
81066 CACCACCGCCACCAACACCCAAAATCTCAT
1 CACCACCGCCACC-ACCCCCAAAAGCTCAT
*
81096 CACCACCTCCACC
1 CACCACCGCCACC
81109 GAAACAATTG
Statistics
Matches: 143, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
29 10 0.07
30 125 0.87
31 8 0.06
ACGTcount: A:0.32, C:0.53, G:0.08, T:0.08
Consensus pattern (29 bp):
CACCACCGCCACCACCCCCAAAAGCTCAT
Found at i:80982 original size:60 final size:60
Alignment explanation
Indices: 80934--81108 Score: 289
Period size: 60 Copynumber: 2.9 Consensus size: 60
80924 CCAGCAGCCC
**
80934 CCCAAAG-CTCATCACCACCGCCACCGCCACCCAAAAGCTCATCGCCACCGCCACCAACA
1 CCCAAAGTCTCATCACCACCGCCACCAACACCCAAAAGCTCATCGCCACCGCCACCAACA
80993 CCCAAAGTCTCATCACCACCGCCACCAACACCCAAAAGCTCATCGCCACCGCCACCAACA
1 CCCAAAGTCTCATCACCACCGCCACCAACACCCAAAAGCTCATCGCCACCGCCACCAACA
* * * *
81053 CCCAAAGTCCCATCACCACCGCCACCAACACCCAAAATCTCATCACCACCTCCACC
1 CCCAAAGTCTCATCACCACCGCCACCAACACCCAAAAGCTCATCGCCACCGCCACC
81109 GAAACAATTG
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 7 0.06
60 102 0.94
ACGTcount: A:0.32, C:0.52, G:0.07, T:0.09
Consensus pattern (60 bp):
CCCAAAGTCTCATCACCACCGCCACCAACACCCAAAAGCTCATCGCCACCGCCACCAACA
Found at i:81010 original size:90 final size:90
Alignment explanation
Indices: 80916--81108 Score: 262
Period size: 90 Copynumber: 2.1 Consensus size: 90
80906 CCTTCGTCAC
* * * * ** * *
80916 CACCACCACCAGCAGCCCCCCAAAGCTCATCACCACCGCCACCGCCACCCAAAAG-CTCATCGCC
1 CACCACCACCACCAACACCCAAAAGCTCATCACCACCGCCACCAACACCC-AAAGTCCCATCACC
*
80980 ACCGCCACCAACACCCAAAGTCTCAT
65 ACCGCCACCAACACCCAAAATCTCAT
* *
81006 CACCACCGCCACCAACACCCAAAAGCTCATCGCCACCGCCACCAACACCCAAAGTCCCATCACCA
1 CACCACCACCACCAACACCCAAAAGCTCATCACCACCGCCACCAACACCCAAAGTCCCATCACCA
81071 CCGCCACCAACACCCAAAATCTCAT
66 CCGCCACCAACACCCAAAATCTCAT
*
81096 CACCACCTCCACC
1 CACCACCACCACC
81109 GAAACAATTG
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
89 4 0.04
90 86 0.96
ACGTcount: A:0.32, C:0.53, G:0.08, T:0.08
Consensus pattern (90 bp):
CACCACCACCACCAACACCCAAAAGCTCATCACCACCGCCACCAACACCCAAAGTCCCATCACCA
CCGCCACCAACACCCAAAATCTCAT
Found at i:88268 original size:4 final size:4
Alignment explanation
Indices: 88261--88288 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
88251 GGACTAGGCT
88261 AGGG AGGG AGGG AGGG AGGG AGGG AGGG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG
88289 CGGGCGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:88445 original size:31 final size:31
Alignment explanation
Indices: 88373--88445 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
88363 AAAATATGTT
88373 TTCG-CCCCC-TAAAATTTTATAAGTTCAAG
1 TTCGCCCCCCTTAAAATTTTATAAGTTCAAG
** * *
88402 TTTACCCACCTTAAATTTTTATAAGTTCAAG
1 TTCGCCCCCCTTAAAATTTTATAAGTTCAAG
88433 TTCGCCCCCCTTA
1 TTCGCCCCCCTTA
88446 CATAAAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 2 0.06
30 4 0.11
31 29 0.83
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.37
Consensus pattern (31 bp):
TTCGCCCCCCTTAAAATTTTATAAGTTCAAG
Found at i:89848 original size:20 final size:21
Alignment explanation
Indices: 89813--89854 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
89803 ATATAAGATA
89813 AAAAACTTATTAAGAAAATTG
1 AAAAACTTATTAAGAAAATTG
* *
89834 AAAATCTTATT-AGAAACTTG
1 AAAAACTTATTAAGAAAATTG
89854 A
1 A
89855 TCCGACCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAACTTATTAAGAAAATTG
Found at i:93362 original size:18 final size:18
Alignment explanation
Indices: 93341--93386 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
93331 AATCAAGGTA
93341 AACGGAAGAAAAAAGGGG
1 AACGGAAGAAAAAAGGGG
93359 AACGGAAGAAAAAAGGGG
1 AACGGAAGAAAAAAGGGG
*
93377 AAAGGAAGAA
1 AACGGAAGAA
93387 TAGGGAGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.37, T:0.00
Consensus pattern (18 bp):
AACGGAAGAAAAAAGGGG
Found at i:94233 original size:33 final size:31
Alignment explanation
Indices: 94190--94251 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
94180 ACTTGAAGAG
* *
94190 TTTTAAGATTTAGAGACTAGAGAGATTGAGATA
1 TTTTAAGATTTAG-G-CTAAAGAGATCGAGATA
*
94223 TTTTAGGATTTAGGCTAAAGAGATCGAGA
1 TTTTAAGATTTAGGCTAAAGAGATCGAGA
94252 GTTGGCGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 13 0.50
32 1 0.04
33 12 0.46
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (31 bp):
TTTTAAGATTTAGGCTAAAGAGATCGAGATA
Found at i:95430 original size:30 final size:28
Alignment explanation
Indices: 95396--95457 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 28
95386 AAATACTTTT
*
95396 TCCTAGAATTTTATAACTTCGAGTTTGCCC
1 TCCTAAAATTTTATAACTTCGAG-TT-CCC
95426 TCCTAAAATTTTATAACTTCGAGTTCCC
1 TCCTAAAATTTTATAACTTCGAGTTCCC
95454 TCCT
1 TCCT
95458 TACATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 7 0.23
29 2 0.06
30 22 0.71
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (28 bp):
TCCTAAAATTTTATAACTTCGAGTTCCC
Done.