Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001764.1 Hibiscus syriacus cultivar Beakdansim tig00003561_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: 108777
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5150 original size:10 final size:9
Alignment explanation
Indices: 5127--5160 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
5117 AGGGCTGGAA
5127 ACCGGTTTG
1 ACCGGTTTG
5136 ACCGGTTTCG
1 ACCGGTTT-G
5146 ACCGGTTTG
1 ACCGGTTTG
5155 ACCGGT
1 ACCGGT
5161 CTAACCCGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:7181 original size:16 final size:16
Alignment explanation
Indices: 7156--7186 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7146 TATTTTTTCA
*
7156 AATAATTATAATAAAC
1 AATAAATATAATAAAC
7172 AATAAATATAATAAA
1 AATAAATATAATAAA
7187 AAAATCAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAATATAATAAAC
Found at i:7612 original size:18 final size:20
Alignment explanation
Indices: 7570--7612 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
7560 TTTGGTTCAC
*
7570 GGAATGTAAGATTACTAGTG
1 GGAATGTAAGATTACTAGAG
7590 GGAATGTAAGATTAC-A-AG
1 GGAATGTAAGATTACTAGAG
7608 GGAAT
1 GGAAT
7613 AGGATTACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 1 0.05
20 15 0.68
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACTAGAG
Found at i:7836 original size:39 final size:37
Alignment explanation
Indices: 7754--7839 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
7744 AACAAGTTGG
* * *
7754 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTA
* * *
7791 ATAAAATTTATATATTTTTTTTACAAAATTGAAAATATA
1 AAAAAATTTATATATTTTCTTTAAAAAATT-AAAAT-TA
7830 AAAAAATTTA
1 AAAAAATTTA
7840 ATGAAAGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 26 0.65
38 4 0.10
39 10 0.25
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTA
Found at i:14044 original size:9 final size:10
Alignment explanation
Indices: 14022--14046 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14012 ATAAAAATAT
14022 AAAATATACA
1 AAAATATACA
14032 AAAATATACA
1 AAAATATACA
14042 AAAAT
1 AAAAT
14047 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATATACA
Found at i:14695 original size:2 final size:2
Alignment explanation
Indices: 14688--14719 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14678 AGGCATGTAC
14688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14720 GCAAACAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19069 original size:26 final size:27
Alignment explanation
Indices: 19028--19079 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
19018 AAAGTCAATT
19028 TTTTTTCAAAAATATATAAA-ATTTATA
1 TTTTTTCAAAAATATA-AAATATTTATA
*
19055 TTTTTT-AAAATTATAAAATATTTAT
1 TTTTTTCAAAAATATAAAATATTTAT
19080 TATCATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 3 0.13
26 14 0.61
27 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTTTCAAAAATATAAAATATTTATA
Found at i:21606 original size:20 final size:20
Alignment explanation
Indices: 21581--21651 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
21571 GATTCAATCA
21581 GTATCGATACCGAAGGGGGT
1 GTATCGATACCGAAGGGGGT
*
21601 GTATCGATGCCGAAGGGGGT
1 GTATCGATACCGAAGGGGGT
**
21621 GTATCGATACCGAAGGGAAT
1 GTATCGATACCGAAGGGGGT
21641 GTATCGATACC
1 GTATCGATACC
21652 ATTTTGAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (20 bp):
GTATCGATACCGAAGGGGGT
Found at i:22335 original size:79 final size:79
Alignment explanation
Indices: 22244--22486 Score: 387
Period size: 79 Copynumber: 3.1 Consensus size: 79
22234 GAATGGATGA
* *
22244 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
22309 GGTGCATTATCGAC
66 GGTGCATTATCGAC
* *
22323 ATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
*
22388 GGTGCATTATCGGC
66 GGTGCATTATCGAC
* * **
22402 ATAAAAGAATAATGCATATGCGTGCATTATTGGCATGAAAAGATGCCAAAATTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
* *
22467 AGTGCATTATCAAC
66 GGTGCATTATCGAC
22481 ATAAAA
1 ATAAAA
22487 ATTTTGCTAT
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 151 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
GGTGCATTATCGAC
Found at i:22337 original size:34 final size:34
Alignment explanation
Indices: 22299--22442 Score: 135
Period size: 34 Copynumber: 3.9 Consensus size: 34
22289 TCATAGCTGA
*
22299 AATGCATATGGGTGCATTATCGACATAAAATAAT
1 AATGCATATGGGTGCATTATCGGCATAAAATAAT
*
22333 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--AT---A-A--T
*
22376 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAATAAT
* *
22412 AATGCATATGCGTGCATTATTGGCATGAAAA
1 AATGCATATGGGTGCATTATCGGCAT-AAAA
22443 GATGCCAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
34 48 0.52
35 7 0.08
36 1 0.01
37 2 0.02
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 3 0.03
45 25 0.27
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAATAAT
Found at i:22384 original size:45 final size:41
Alignment explanation
Indices: 22333--22476 Score: 140
Period size: 45 Copynumber: 3.5 Consensus size: 41
22323 ATAAAATAAT
22333 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCCA-A--TGA
*
22378 AATGCATATGGGTGCATTATCGGCAT-AAA-A-G--AAT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAATGA
*
22412 AATGCATATGCGTGCATTATTGGCATGAAAAGATGCCAAAATTGA
1 AATGCATATGGGTGCATTATTGGCATG-AAAGATGCC--AA-TGA
*
22457 AATGCATATGAGTGCATTAT
1 AATGCATATGGGTGCATTAT
22477 CAACATAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
34 24 0.29
36 4 0.05
37 1 0.01
38 2 0.02
39 1 0.01
41 1 0.01
42 3 0.04
43 1 0.01
44 3 0.04
45 44 0.52
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (41 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAATGA
Found at i:25338 original size:21 final size:20
Alignment explanation
Indices: 25309--25352 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
25299 ACTCCGGTCT
*
25309 TCAAATCTTTGTTTATTTAAC
1 TCAAATC-TTGTCTATTTAAC
*
25330 TCAAGTCTTGTCTATTTAAC
1 TCAAATCTTGTCTATTTAAC
25350 TCA
1 TCA
25353 CTGTCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (20 bp):
TCAAATCTTGTCTATTTAAC
Found at i:35038 original size:21 final size:21
Alignment explanation
Indices: 34996--35039 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
34986 ACTCCGGGAG
* *
34996 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
35017 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
35038 CT
1 CT
35040 CCTCCTTCTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:37083 original size:30 final size:29
Alignment explanation
Indices: 37028--37085 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
37018 AAAAAGAATC
*
37028 ATGTTGAATGAGTTAAGATAGTGGTGAGG
1 ATGTTGAATGAGTAAAGATAGTGGTGAGG
*
37057 ATGTTGAAGTTAGTAAAGAT-GATGGTGAG
1 ATGTTGAA-TGAGTAAAGATAG-TGGTGAG
37086 AAGCTTGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (29 bp):
ATGTTGAATGAGTAAAGATAGTGGTGAGG
Found at i:47388 original size:22 final size:25
Alignment explanation
Indices: 47331--47382 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
47321 TCTTAATTTA
47331 TTATGAG-AAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
*
47355 TTATGAGAAAAAAATAATCTTTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
47380 TTA
1 TTA
47383 GAAAAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:50450 original size:21 final size:21
Alignment explanation
Indices: 50426--50465 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
50416 CCCTCTAGAT
*
50426 ATTATTATTT-TTAATTAAATC
1 ATTATT-TTTATTAAATAAATC
50447 ATTATTTTTATTAAATAAA
1 ATTATTTTTATTAAATAAA
50466 AGTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTTTTATTAAATAAATC
Found at i:50459 original size:17 final size:18
Alignment explanation
Indices: 50429--50462 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50419 TCTAGATATT
50429 ATTATTTTTAATTAAATC
1 ATTATTTTTAATTAAATC
50447 ATTATTTTT-ATTAAAT
1 ATTATTTTTAATTAAAT
50463 AAAAGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTTTTAATTAAATC
Found at i:50721 original size:14 final size:14
Alignment explanation
Indices: 50698--50727 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
50688 TAAACTTTGT
50698 TGCCAAAATAAGAG
1 TGCCAAAATAAGAG
*
50712 TGCCAGAATAAGAG
1 TGCCAAAATAAGAG
50726 TG
1 TG
50728 AGAAGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.17
Consensus pattern (14 bp):
TGCCAAAATAAGAG
Found at i:60125 original size:33 final size:33
Alignment explanation
Indices: 60017--60131 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
60007 AACCATACGC
*
60017 CGGCTGATAAGGATACATGCTCATCTCGTGCGG
1 CGGCTGATAAGGATACATGCTCATCCCGTGCGG
* * * * *
60050 CGTCTGATAATGACACATGCTCATCCCATGCGA
1 CGGCTGATAAGGATACATGCTCATCCCGTGCGG
* * *
60083 TGGCGGATAAGGATACATGCACATCCCGTGCGG
1 CGGCTGATAAGGATACATGCTCATCCCGTGCGG
*
60116 CGGATGATAAGGATAC
1 CGGCTGATAAGGATAC
60132 GAATCACCGT
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (33 bp):
CGGCTGATAAGGATACATGCTCATCCCGTGCGG
Found at i:61045 original size:13 final size:13
Alignment explanation
Indices: 61027--61056 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
61017 AAAAACATCG
61027 GAATCTCAAATTT
1 GAATCTCAAATTT
61040 GAATCTCAAATTT
1 GAATCTCAAATTT
61053 GAAT
1 GAAT
61057 TTCACATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (13 bp):
GAATCTCAAATTT
Found at i:61433 original size:22 final size:22
Alignment explanation
Indices: 61405--61502 Score: 187
Period size: 22 Copynumber: 4.5 Consensus size: 22
61395 CCAAAATAAT
61405 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
61427 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
61449 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
*
61471 AATAAAAATATTATTTTTATTT
1 AATAAAAATATTATTTTTATTC
61493 AATAAAAATA
1 AATAAAAATA
61503 ATGACTTAAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAAAAATATTATTTTTATTC
Found at i:62988 original size:128 final size:128
Alignment explanation
Indices: 62760--63016 Score: 505
Period size: 128 Copynumber: 2.0 Consensus size: 128
62750 ATTCATCGGA
*
62760 GAAACTAAATTAATTCGGTTGCTAGAGTTATTCTCAGCAATATCACTCCCCTCCAACTTAGCACA
1 GAAACAAAATTAATTCGGTTGCTAGAGTTATTCTCAGCAATATCACTCCCCTCCAACTTAGCACA
62825 AGCAGTTAATTTTTTTCGTTTCGTTGGAGAAGCTATGTTAATAGACACAGTAGCTAAATTCTC
66 AGCAGTTAATTTTTTTCGTTTCGTTGGAGAAGCTATGTTAATAGACACAGTAGCTAAATTCTC
62888 GAAACAAAATTAATTCGGTTGCTAGAGTTATTCTCAGCAATATCACTCCCCTCCAACTTAGCACA
1 GAAACAAAATTAATTCGGTTGCTAGAGTTATTCTCAGCAATATCACTCCCCTCCAACTTAGCACA
62953 AGCAGTTAATTTTTTTCGTTTCGTTGGAGAAGCTATGTTAATAGACACAGTAGCTAAATTCTC
66 AGCAGTTAATTTTTTTCGTTTCGTTGGAGAAGCTATGTTAATAGACACAGTAGCTAAATTCTC
63016 G
1 G
63017 GTCAGGCAAC
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (128 bp):
GAAACAAAATTAATTCGGTTGCTAGAGTTATTCTCAGCAATATCACTCCCCTCCAACTTAGCACA
AGCAGTTAATTTTTTTCGTTTCGTTGGAGAAGCTATGTTAATAGACACAGTAGCTAAATTCTC
Found at i:66615 original size:26 final size:24
Alignment explanation
Indices: 66586--66648 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
66576 TATTATTAAG
*
66586 TATAATAATATATTAGGTAGCGCTTA
1 TATAATAATA-A-TAGGTAGCACTTA
* *
66612 TATAAT-GTAATATGTAGCACTTA
1 TATAATAATAATAGGTAGCACTTA
66635 TATAATAA-AATAGG
1 TATAATAATAATAGG
66649 CATTTAACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 22 0.71
24 1 0.03
25 2 0.06
26 6 0.19
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (24 bp):
TATAATAATAATAGGTAGCACTTA
Found at i:66708 original size:87 final size:87
Alignment explanation
Indices: 66562--66724 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
66552 TATGTTATAT
* * *
66562 CATTTAACCGAAAATATTATTAAGTATAATAATATATTAGGTAGCGCTTATATAATGTAATATGT
1 CATTTAACCGAAAATATTATCAAGTACAATAATATATTAGGTAGCGCTTATATAATGTAATAGGT
66627 AGCACTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
*
66649 CATTTAACCGGAAATATTATCAAGTACAATAATATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAATATATTAGGTAGCGCTTATATAATGTAATAGGT
*
66714 AGCGCTTATAT
66 AGCACTTATAT
66725 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAATATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCACTTATATAATAAAATAGG
Found at i:66712 original size:23 final size:23
Alignment explanation
Indices: 66677--66724 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
66667 ATCAAGTACA
*
66677 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
66700 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
66723 AT
1 AT
66725 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:67433 original size:181 final size:181
Alignment explanation
Indices: 67106--68001 Score: 1252
Period size: 181 Copynumber: 4.9 Consensus size: 181
67096 TGTTGACTTA
* * *
67106 TTTTCTCATATTTTTAGC-TGTTCTATTGTTATCGATCGATACATTTTCATAAAGTGTCGACACT
1 TTTTGTCATATTTTTA-CATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
*
67170 TTTTAGGTGCTATAACTTCTTCTCTTTTAAATTC-AGAAAGTGTCGATACTTATATTAAATTATC
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCTA-AAAGTGTCGATACTTATATTAAATTATC
* *
67234 GACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGA
129 GACACTTTCAACATATCCGGTAG-TTTTTACCGGTTTTGTCATTTTGAGACCGG
* ** * *
67288 TTTTGTAATA-TTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCAACACTT
1 TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
* * * * *
67352 TATAGGCGCTATAACTCCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATAAAAGTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATTATCGA
*
67417 CACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCCGGTAGTT-TTTACCGGTTTTGTCATTTTGAGACCGG
*
67469 TTTTGTCATATTTTTAGC-TGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACGCT
1 TTTTGTCATATTTTTA-CATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
*
67533 TTTTAGGCGC-ATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCAATACTTATATTAAATTATCG
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATTATCG
** * * * **
67597 ACACTTTCAACATATCTAGTATATTTTTACCGGTTTTATCATTTTTAGACCTC
130 ACACTTTCAACATATCCGGTA-GTTTTTACCGGTTTTGTCATTTTGAGACCGG
* * * ** *
67650 TTTTGTCATATTTTTACCTGTTATATTGTTATAGATTGATACATTTTTTTTTAAAGTATCGACAC
1 TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACA--TTTTCATAAAGTGTCGACAC
* * * *
67715 TTTATAAGCGTTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAAGTATC
64 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATTATC
*
67780 GACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGG
129 GACACTTTCAACATATCCGGTAGTT-TTTACCGGTTTTGTCATTTTGAGACCGG
* * *
67834 TTTTGTCATA-TTTTAGATGTTATATTGTTATGGAT-TATACA-TTTCATAAAGTGTCGATACTT
1 TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
*
67896 TTTAGGCGCTACAACTTCTTCTCTTTTAAATT-TAGAAAGTGTCGATACTTATATTAAATTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCTA-AAAGTGTCGATACTTATATTAAATTATCG
*
67960 ACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCAT
130 ACACTTTCAACATATCCGGTAG-TTTTTACCGGTTTTGTCAT
68002 ATTTTTACCT
Statistics
Matches: 631, Mismatches: 70, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
178 2 0.00
179 111 0.18
180 4 0.01
181 290 0.46
182 71 0.11
183 49 0.08
184 104 0.16
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (181 bp):
TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCCGGTAGTTTTTACCGGTTTTGTCATTTTGAGACCGG
Found at i:67668 original size:20 final size:20
Alignment explanation
Indices: 67617--67668 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
67607 CATATCTAGT
**
67617 ATATTTTTACCGGTTTTATC
1 ATATTTTTACCTCTTTTATC
* *
67637 AT-TTTTAGACCTCTTTTGTC
1 ATATTTT-TACCTCTTTTATC
67657 ATATTTTTACCT
1 ATATTTTTACCT
67669 GTTATATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (20 bp):
ATATTTTTACCTCTTTTATC
Found at i:68089 original size:162 final size:159
Alignment explanation
Indices: 67829--68163 Score: 467
Period size: 162 Copynumber: 2.1 Consensus size: 159
67819 TCATTTTGAG
* * * *
67829 ACCGGTTTTGTCATATTTTAGATGTTATATTGTTATGGATTATACATTTCATAAAGTGTCGATAC
1 ACCGGTTTTGTCATATTTTACATGTTATATTGTTATGGATGATACATTTCATAAAGTATCGACAC
* * * * *
67894 TTTTTAGGCGCTACAACTTCTTCTCTTTTAAATT-TAGAAAGTGTCGATACTTATATTAAATTAT
66 TTTATAGGCGCTACAACTTCTTCTCTTTTAAATTCCA-AAAGTGTAGATAATTATATTAAAGTAT
*
67958 CGACACTTTCAACATATCCGGTAGCGT-TTT
130 CGACAATTTCAACATATCCGGTAG-GTATTT
* **
67988 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATA-TTTTACATGTTATATTGTTATGGAT-GATACA-TTTCATAAAGTATCGA
*
68053 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTAGATAATTATATTAAAGT
63 CACTTTATAGGCGCTACAACTTCTTCTCTTTTAAATTCCAAAAGTGTAGATAATTATATTAAAGT
*
68118 ATCGACAATTTCAACATATCCGGTAGTTATTT
128 ATCGACAATTTCAACATATCCGGTAGGTATTT
*
68150 ACCTGTTTTGTCAT
1 ACCGGTTTTGTCAT
68164 TTTGAGACCG
Statistics
Matches: 155, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
159 15 0.10
160 23 0.15
161 6 0.04
162 110 0.71
163 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (159 bp):
ACCGGTTTTGTCATATTTTACATGTTATATTGTTATGGATGATACATTTCATAAAGTATCGACAC
TTTATAGGCGCTACAACTTCTTCTCTTTTAAATTCCAAAAGTGTAGATAATTATATTAAAGTATC
GACAATTTCAACATATCCGGTAGGTATTT
Found at i:68305 original size:182 final size:182
Alignment explanation
Indices: 67988--68345 Score: 549
Period size: 182 Copynumber: 2.0 Consensus size: 182
67978 GTAGCGTTTT
* * * ** *
67988 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
1 ACCGATTTTGTCATATTTTTACCTGTTATAATATTATGGATCGATACATTTTCATAAAATATCGA
68053 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTAGATAATTATATTAAAGT
66 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTAGATAATTATATTAAAGT
* *
68118 ATCGACAATTTCAACATATCCGGTAG-TTATTTACCTGTTTTGTCATTTTGAG
131 ATCGACAATTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAG
* *
68170 ACCGATTTTGTCATATTTTTAGCTGTTATAATATTATGGATCGATACATTTTCATAAAATTTCGA
1 ACCGATTTTGTCATATTTTTACCTGTTATAATATTATGGATCGATACATTTTCATAAAATATCGA
* * * *
68235 CACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAAT
66 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTAGATAATTATATTAAAG
*
68299 TATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCAT
130 TATCGACAATTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCAT
68346 ATTTTTACCT
Statistics
Matches: 159, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
181 2 0.01
182 156 0.98
183 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
ACCGATTTTGTCATATTTTTACCTGTTATAATATTATGGATCGATACATTTTCATAAAATATCGA
CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTAGATAATTATATTAAAGT
ATCGACAATTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
Found at i:71398 original size:24 final size:24
Alignment explanation
Indices: 71364--71482 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
71354 AAACATAATT
* *
71364 CATGTCTAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* *
71388 TAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
** *
71412 CAAATCAAGTATCATATCATAATC
1 CATGTCAAGTATCATATCAGAATC
*
71436 CATGTC-AGATATCAAATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
71460 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
71483 TCAAATCGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:74074 original size:23 final size:23
Alignment explanation
Indices: 74042--74091 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
74032 CCTCATTCTA
74042 CAAATATTTACA-AAACTAACACC
1 CAAATATTTACACAAA-TAACACC
*
74065 CAAATTTTTACACAAATAACACC
1 CAAATATTTACACAAATAACACC
74088 CAAA
1 CAAA
74092 CATAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:75969 original size:2 final size:2
Alignment explanation
Indices: 75962--76042 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
75952 CTTTTAAAAC
75962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76043 CGTTTCCCAG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76273 original size:24 final size:24
Alignment explanation
Indices: 76256--76381 Score: 132
Period size: 24 Copynumber: 5.2 Consensus size: 24
76246 ATCAAAACAT
*
76256 AATTCATGTCAAGTATCATATCA-
1 AATTCATGTCAAGTATCAGATCAG
* *
76279 AAATCTAGGTCAAGTATCAGATCAG
1 AATTC-ATGTCAAGTATCAGATCAG
* * *
76304 AATCCAAGTCAAGTATCAGATCAT
1 AATTCATGTCAAGTATCAGATCAG
*
76328 AA-TCAATGTC-AGATATCATATCAG
1 AATTC-ATGTCAAG-TATCAGATCAG
*
76352 AATCCATGTCAAGTATCAGATCAG
1 AATTCATGTCAAGTATCAGATCAG
76376 AATTCA
1 AATTCA
76382 AATCGAAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
23 7 0.08
24 70 0.84
25 6 0.07
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (24 bp):
AATTCATGTCAAGTATCAGATCAG
Found at i:76345 original size:48 final size:48
Alignment explanation
Indices: 76263--76374 Score: 154
Period size: 48 Copynumber: 2.3 Consensus size: 48
76253 CATAATTCAT
* *
76263 GTCAAGTATCATATCAAAATCTAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCAAGGTCAAGTATCAGATCAGAATCCAA
* * * *
76311 GTCAAGTATCAGATCATAATCAATGTC-AGATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCAAGGTCAAG-TATCAGATCAGAATCCAA
76359 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
76375 GAATTCAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 2 0.04
48 55 0.96
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCAAGGTCAAGTATCAGATCAGAATCCAA
Found at i:78922 original size:23 final size:23
Alignment explanation
Indices: 78890--78939 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
78880 CCACCTTCTA
78890 CAAATATTTACA-AAACTAACACC
1 CAAATATTTACACAAA-TAACACC
* *
78913 CAAATTTTTATACAAATAACACC
1 CAAATATTTACACAAATAACACC
78936 CAAA
1 CAAA
78940 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:80825 original size:2 final size:2
Alignment explanation
Indices: 80818--80847 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80808 CTTTTAAAAC
80818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80848 GTTTCCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81042 original size:24 final size:24
Alignment explanation
Indices: 81029--81147 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
81019 AAACATAATT
* *
81029 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
*
81053 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
81077 CAAGTCAAGTATCAGATCATAATC
1 CATGTCAAGTATCAGATCAGAATC
*
81101 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
81125 CATATCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
81148 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:81163 original size:72 final size:71
Alignment explanation
Indices: 81012--81165 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 71
81002 AATATATAAA
* * * *
81012 AAAATCAAAACATAATTCATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCATAATCCATGTCAAGTATCATATCAAAATCCAGATCAAGTATCAGATCAGAATC
*
81077 CAAGTC
66 CAAATC
* * *
81083 AAGTATCAGATCATAATCCATGTC-AGATATCATATCAGAATCCATATCAAGTATCAGATCAGAA
1 AA-AATCAGATCATAATCCATGTCAAG-TATCATATCAAAATCCAGATCAAGTATCAGATCAGAA
*
81147 TTCAAATC
64 TCCAAATC
81155 GAAAATCAGAT
1 -AAAATCAGAT
81166 AAAATATTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 4 0.06
72 64 0.91
73 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (71 bp):
AAAATCAGATCATAATCCATGTCAAGTATCATATCAAAATCCAGATCAAGTATCAGATCAGAATC
CAAATC
Found at i:83730 original size:21 final size:21
Alignment explanation
Indices: 83686--83730 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
83676 GATTTCTGGG
* * *
83686 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
83707 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
83728 CAA
1 CAA
83731 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:83803 original size:23 final size:22
Alignment explanation
Indices: 83760--83803 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
83750 ATGCCAGAGA
*
83760 GGAACCGATACCCCCACAGGAG
1 GGAACCGATACCCCCAAAGGAG
*
83782 GGAACCGATTCCCCCTAAAGGA
1 GGAACCGATACCCCC-AAAGGA
83804 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.32, C:0.34, G:0.25, T:0.09
Consensus pattern (22 bp):
GGAACCGATACCCCCAAAGGAG
Found at i:84664 original size:32 final size:32
Alignment explanation
Indices: 84623--84719 Score: 121
Period size: 31 Copynumber: 3.1 Consensus size: 32
84613 AGAGTCGAGG
84623 GTTTT-CCTATGTTCTACGGAACATATGGACA
1 GTTTTACCTATGTTCTACGGAACATATGGACA
*
84654 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 GTTTTACCTATGTTC-TACGGA-ACATATGGACA
* *
84686 G-TATACCTATGTTCTAAGGAACATATGGACA
1 GTTTTACCTATGTTCTACGGAACATATGGACA
84717 GTT
1 GTT
84720 ACCGAGGATC
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
31 31 0.55
32 25 0.45
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (32 bp):
GTTTTACCTATGTTCTACGGAACATATGGACA
Found at i:84836 original size:29 final size:30
Alignment explanation
Indices: 84711--84833 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
84701 AAGGAACATA
84711 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
84741 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
84771 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
84801 TGGATAGTTACCG-GGGTCATTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
84830 TGGA
1 TGGA
84834 TAGGTCCTTC
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 17 0.19
30 72 0.81
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:87927 original size:2 final size:2
Alignment explanation
Indices: 87920--87946 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
87910 ATCTTTTAAA
87920 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
87947 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:87951 original size:2 final size:2
Alignment explanation
Indices: 87946--87979 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
87936 ACACACACAC
87946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87980 GTTTCCCAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88190 original size:24 final size:24
Alignment explanation
Indices: 88163--88274 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
88153 CATAATTCAT
* *
88163 GTCAAGTATGATATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
88187 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
88211 GTCAAGTATCAGATCATAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
*
88235 GTC-AGATATCAGATCAAAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
88259 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
88275 CAATTCAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:92741 original size:2 final size:2
Alignment explanation
Indices: 92734--92789 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
92724 CTTTTAAAAC
92734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92776 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
92790 GTTTCCCAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93012 original size:24 final size:24
Alignment explanation
Indices: 92974--93084 Score: 152
Period size: 24 Copynumber: 4.6 Consensus size: 24
92964 ATAATTCATA
* * *
92974 TCAAGTATGATATCAAAATCCAGG
1 TCAAGTATCAGATCAAAATCCATG
* *
92998 TCAAGTATCAGATCAGAATCCAAG
1 TCAAGTATCAGATCAAAATCCATG
*
93022 TCAAGTATCAGATCATAATCCATG
1 TCAAGTATCAGATCAAAATCCATG
93046 TC-AGATATCAGATCAAAATCCATG
1 TCAAG-TATCAGATCAAAATCCATG
93070 TCAAGTATCAGATCA
1 TCAAGTATCAGATCA
93085 GAATTCAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.03
24 74 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
TCAAGTATCAGATCAAAATCCATG
Found at i:93104 original size:48 final size:48
Alignment explanation
Indices: 93004--93105 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
92994 CAGGTCAAGT
* * ** *
93004 ATCAGATCAGAATCCAAGTCAAGTATCAGATCATAATCCATGTCAGAT
1 ATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
* *
93052 ATCAGATCAAAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAA
1 ATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AA
93100 ATCAGA
1 ATCAGA
93106 AAAAATATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.24
Consensus pattern (48 bp):
ATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:95235 original size:23 final size:24
Alignment explanation
Indices: 95203--95253 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
95193 CCGCCTTCTA
*
95203 CAAATATTTACA-AAACTAACACC
1 CAAATATTTACACAAAATAACACC
*
95226 CAAATTTTTACACAAAATAACACC
1 CAAATATTTACACAAAATAACACC
95250 CAAA
1 CAAA
95254 CAGAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (24 bp):
CAAATATTTACACAAAATAACACC
Found at i:96870 original size:993 final size:979
Alignment explanation
Indices: 94853--96821 Score: 2898
Period size: 993 Copynumber: 2.0 Consensus size: 979
94843 GCTTATCGGG
* * * * * *
94853 TTCGAGTTTG-GCGAAACAGACCCCAAAAATAGATTC-GGGTCATCGATAACATAAAATATGACT
1 TTCGAGTTTGAAC-AAACACACCCCAAAAATAGATTCAGGAT-GTCAATAACATAAAATACGACT
* * *
94916 TTTCGAAAATTTTGACTTTTCGGTCAAAGTTAAAGTCAACGGGTTTGACTGGAAATTTCGAGGCC
64 CTTC-AAAATTTTGACTTTTCGGTCAAAGTCAAAGTCAACAGGTTTGACTGGAAATTTCGAGGCC
* *
94981 TTCTGGTCTGAATTTCGAAAAATAGACTACGGAATCGGACTCAGAACGTCGAAAAACGTCAGGAT
128 TTCTGGTCTGAATTTCGAAAAACAGACTACGGAATCGGACTCAGAACGTCGAAAAACATCAGGAT
** * *
95046 TAGTATACCCGGTCAAAGTAAAAGGTTGTTTAACTTCCGGTCAACGCCGGTCAAAGTTCTGGTTA
193 TAGTATACCCGGTCAAAGTAAAAGGTTGTTTAACACCCGGTCAACGCCAGTCAAAGTTCTGGTCA
* *
95111 ACAGTGGTAAACGTCGGTCAACGGACAACAGTCGACCGGTTTACACAAATATCACCCTAACATAA
258 ACAGTGGTAAACGCCGGTCAACAGACAACAGTCGACCGGTTTACACAAATATCACCCTAACATAA
* * *
95176 ATTAATTACAAAATTAGCCGCCTTCTACAAATATTTACAAAACTAACACCCAAATTTTTACACAA
323 ATTAATTACAAAATTAACCACATTCTACAAATATTTACAAAACTAACACCCAAATTTTTACACAA
* *
95241 AATAACACCCAAACAGAAATTAATTACAAAATTAACACCCTACGGCCAGACGATGCCCACTCTCG
388 AATAACACCCAAACAGAAATTAATTACAAAATTAACACCCTACGACCAGAAGATGCCCACTCTCG
* *
95306 GGGGATGGCGCGTGGCGCGTATGAATAGTGATACGGTGTCGGAAAATGCCATAAAAATTCCTAAA
453 GGGGATGGCGCGTGGCGCG-ATGAACAGTGATACGGTGT-----AAT-CCAGAAAAATTCCTAAA
* *
95371 AATTATTTTAAGCGATTTTGAGGCACATACAAAGCTCAGTTCACAATTTTGAACGATGGAGAGCT
511 AATTATTTTAAGCGATTTTGAGGCACATACAAAGCTCAGTTCACAATTTTAAACGATGGAGAGCA
* * * **
95436 CGATTTCACCAAATTCGAAACTTTGACCATTTTATTTCCTCACGCGCCACCGCCGCCGGAGACAA
576 CGATTTCAACAAATTCGAAAATTTGACCATTTCACCTCCTCACGCGCCACCGCCGCCGGAGACAA
* *
95501 GGAGGACACCGACAGACTCGGAAGGAACACGATGGTGCGGAAGGTGTCGAAAACAGGATACCGGA
641 GGAGGACACCGACAGACGCGGAAGGAACACGATGGTGCGGAAGGTGTCGAAAACAAGATACCGGA
*
95566 TCGTCGTGAATCGACGAAAAACCAATAGAAATCGAGTTAAAACCGACGATAATTCCGACTGAAAT
706 TCGTCGTGAATCGACGAAAAACCAATAGAAATCGAGTTAAAACCGACGATAATTCCGACTAAAAT
95631 TAACGACAAACGACGACGATTCACGACGAAAGGCTTGAGGACTTTTGTTCATCGATCGACAACGA
771 T------AAACGACGACGATTCACGACGAAAGGCTTGAGGACTTTTGTTCATCGATCGACAACGA
*
95696 ACACGATAGTGGTTTCGGTTCATCGATCAGAGGTCAGACGGTGAGTAGATCGGAGTTCAAAGAGG
830 ACACGATAGTGGTTTCAGTTCATCGATCAGAGGTCAGACGGTGAGTAGATCGGAGTTCAAAGAGG
* *
95761 GGTTGACAGAGGATGAAAACTGGGAAGAATACGCAGAAACAATCGGGGAAGGGGTTTATACTTCA
895 GGTTGACAGAGGATGAAAACTGGGAAGAATACGCAAAAACAATCGGGGAAGGGGTTTATACTCCA
* * **
95826 TCTCATAACAACTTACCGGG
960 TCTCATAAAAAATTACCGAA
** *
95846 TTCGAGTTTGGCCAAACAGACCCCAAAAATAGATTCAGGATGTCAATAACATAAAATACGACTCT
1 TTCGAGTTTGAACAAACACACCCCAAAAATAGATTCAGGATGTCAATAACATAAAATACGACTCT
*
95911 T-AAAATTTTTTGACTTTTCGGTCAAAGTCAAAGTCAACAGGTTTGACTGGCAATTTCGAGGCCT
66 TCAAAA--TTTTGACTTTTCGGTCAAAGTCAAAGTCAACAGGTTTGACTGGAAATTTCGAGGCCT
* * * * *
95975 TCTGGTCTGAATTTTGAAAAACGGAGTGCGGAATCGGACTCAGAACGTCGAAAAATATCAGGATT
129 TCTGGTCTGAATTTCGAAAAACAGACTACGGAATCGGACTCAGAACGTCGAAAAACATCAGGATT
*
96040 AGTATACCCGGTCAAAGTCAAAGGTTGTTTAACACCCGGTCAACGCCAGTCAAAGTTCTGGTCAA
194 AGTATACCCGGTCAAAGTAAAAGGTTGTTTAACACCCGGTCAACGCCAGTCAAAGTTCTGGTCAA
* * * *
96105 CAGTTGTCAACGCCGGTCAACAGTCAACAGTCGACCGTTTTACACAAATATCACCCCTAACATAA
259 CAGTGGTAAACGCCGGTCAACAGACAACAGTCGACCGGTTTACACAAATATCA-CCCTAACATAA
*
96170 ATTAATTACAAAATTAACCACATTCTACAAATATTTACAAAACTAACACCCAATTTTTTACAC-A
323 ATTAATTACAAAATTAACCACATTCTACAAATATTTACAAAACTAACACCCAAATTTTTACACAA
96234 AATAACACCCAAACAGAAATTAATTACAAAATTAACACCCTACGACCAGAAGATGCCCACTCTCG
388 AATAACACCCAAACAGAAATTAATTACAAAATTAACACCCTACGACCAGAAGATGCCCACTCTCG
*
96299 GGGGGTGGCGCGTGGGTCGCG-TGAACAGTGATAC-G-GT-AT-C-GAAAAATTCCTAAAAATTA
453 GGGGATGGCGCGT-GG-CGCGATGAACAGTGATACGGTGTAATCCAGAAAAATTCCTAAAAATTA
* ** *
96358 TTTTAAGCGATTTTGAGGCACTTACAAAGCTTGGTTCACAATTTTAAACGGTGGAGAGCACGATT
516 TTTTAAGCGATTTTGAGGCACATACAAAGCTCAGTTCACAATTTTAAACGATGGAGAGCACGATT
** *
96423 TCAACAAATTCGAAAATTTGACTGTTTCACCTCCTCACGCGCCGCCGCCGCCGGAGACAAGGAGG
581 TCAACAAATTCGAAAATTTGACCATTTCACCTCCTCACGCGCCACCGCCGCCGGAGACAAGGAGG
* * **
96488 ACACCGGCAGACCCGAAGCGGTACAAGGAACACGATGGTGTGGAAGGTGTCGAAAACAAGATGTC
646 ACACCGACAGA--C---GCGG---AAGGAACACGATGGTGCGGAAGGTGTCGAAAACAAGATACC
* *
96553 GGATCGTCGTGAATCGACGAAAAACTAATAGAAATCGAGTTAAAACCGACGATACTTCCGACTAA
703 GGATCGTCGTGAATCGACGAAAAACCAATAGAAATCGAGTTAAAACCGACGATAATTCCGACTAA
* * *
96618 AATT-AACGACGACGATTCACGGCGAAAGGCTTGAGGGCTTTTGTTCATCGATCGATAACGAACA
768 AATTAAACGACGACGATTCACGACGAAAGGCTTGAGGACTTTTGTTCATCGATCGACAACGAACA
* *
96682 CGATGGTGGTTTCAGTTCATCGATCAGAGGTCGGACGGTGAGTAGATCGGAGTTCAAAGAGGGGT
833 CGATAGTGGTTTCAGTTCATCGATCAGAGGTCAGACGGTGAGTAGATCGGAGTTCAAAGAGGGGT
* * *
96747 TGACAGGGGATGGAAACTGGGAAGAATATGCAAAAACAATCGGGGAAGGGGTTTATACTCCATCT
898 TGACAGAGGATGAAAACTGGGAAGAATACGCAAAAACAATCGGGGAAGGGGTTTATACTCCATCT
96812 CATAAAAAAT
963 CATAAAAAAT
96822 GGGTAAACCA
Statistics
Matches: 889, Mismatches: 72, Indels: 40
0.89 0.07 0.04
Matches are distributed among these distances:
982 144 0.16
983 188 0.21
984 1 0.00
985 2 0.00
987 3 0.00
990 103 0.12
991 6 0.01
992 1 0.00
993 361 0.41
994 76 0.09
995 4 0.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (979 bp):
TTCGAGTTTGAACAAACACACCCCAAAAATAGATTCAGGATGTCAATAACATAAAATACGACTCT
TCAAAATTTTGACTTTTCGGTCAAAGTCAAAGTCAACAGGTTTGACTGGAAATTTCGAGGCCTTC
TGGTCTGAATTTCGAAAAACAGACTACGGAATCGGACTCAGAACGTCGAAAAACATCAGGATTAG
TATACCCGGTCAAAGTAAAAGGTTGTTTAACACCCGGTCAACGCCAGTCAAAGTTCTGGTCAACA
GTGGTAAACGCCGGTCAACAGACAACAGTCGACCGGTTTACACAAATATCACCCTAACATAAATT
AATTACAAAATTAACCACATTCTACAAATATTTACAAAACTAACACCCAAATTTTTACACAAAAT
AACACCCAAACAGAAATTAATTACAAAATTAACACCCTACGACCAGAAGATGCCCACTCTCGGGG
GATGGCGCGTGGCGCGATGAACAGTGATACGGTGTAATCCAGAAAAATTCCTAAAAATTATTTTA
AGCGATTTTGAGGCACATACAAAGCTCAGTTCACAATTTTAAACGATGGAGAGCACGATTTCAAC
AAATTCGAAAATTTGACCATTTCACCTCCTCACGCGCCACCGCCGCCGGAGACAAGGAGGACACC
GACAGACGCGGAAGGAACACGATGGTGCGGAAGGTGTCGAAAACAAGATACCGGATCGTCGTGAA
TCGACGAAAAACCAATAGAAATCGAGTTAAAACCGACGATAATTCCGACTAAAATTAAACGACGA
CGATTCACGACGAAAGGCTTGAGGACTTTTGTTCATCGATCGACAACGAACACGATAGTGGTTTC
AGTTCATCGATCAGAGGTCAGACGGTGAGTAGATCGGAGTTCAAAGAGGGGTTGACAGAGGATGA
AAACTGGGAAGAATACGCAAAAACAATCGGGGAAGGGGTTTATACTCCATCTCATAAAAAATTAC
CGAA
Found at i:98329 original size:24 final size:24
Alignment explanation
Indices: 98299--98417 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
98289 AAACATAATT
* * *
98299 CATGTCAAGTATGATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
98323 CAGGTCAAGTATCAGATTAGAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
98347 CAAGTCAAGTATCAGATCATAATC
1 CATGTCAAGTATCAGATCAGAATC
*
98371 CATGTC-AGATATCAAATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
98395 CATGTCAAGTATCATATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
98418 TCAAATCGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 77 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:98433 original size:72 final size:71
Alignment explanation
Indices: 98282--98435 Score: 166
Period size: 72 Copynumber: 2.1 Consensus size: 71
98272 GATATATCAA
* * * * * *
98282 AAAATCAAAACATAATTCATGTCAAGTATGATATCAAAATCCAGGTCAAGTATCAGATTAGAATC
1 AAAATCAGATCATAATCCATGTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGATCAGAATC
*
98347 CAAGTC
66 CAAATC
* * * *
98353 AAGTATCAGATCATAATCCATGTC-AGATATCAAATCAGAATCCATGTCAAGTATCATATCAGAA
1 AA-AATCAGATCATAATCCATGTCAAG-TATCAAATCAAAATCCAGGTCAAGTATCAGATCAGAA
*
98417 TTCAAATC
64 TCCAAATC
98425 GAAAATCAGAT
1 -AAAATCAGAT
98436 AAAATATTCA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
71 4 0.06
72 61 0.91
73 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (71 bp):
AAAATCAGATCATAATCCATGTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGATCAGAATC
CAAATC
Found at i:104370 original size:16 final size:16
Alignment explanation
Indices: 104345--104386 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
104335 TGAAAAATTA
*
104345 GCAAAGTTGAAAGTTG
1 GCAAAATTGAAAGTTG
104361 GCAAAATTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
104377 GCAAATTTGA
1 GCAAAATTGA
104387 CATCTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (16 bp):
GCAAAATTGAAAGTTG
Found at i:106274 original size:60 final size:60
Alignment explanation
Indices: 106178--106295 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
106168 GATCGTTTGA
* * *
106178 GATGAAATTCAAATGCTCAAAAGTTTAGAGACTAATTTAGAATGAGAATTATAATTTGGG
1 GATGAAATTCAAATACTCAAAAGTTTAGAGACTAATTTAAAATGAGAATAATAATTTGGG
* * * *
106238 GATGAAATTTAAATATTTAAAAGTTTA-AGAATTAATTTAAAATGAGAATAATAATTTG
1 GATGAAATTCAAATACTCAAAAGTTTAGAG-ACTAATTTAAAATGAGAATAATAATTTG
106296 AAATGAAGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.35
Consensus pattern (60 bp):
GATGAAATTCAAATACTCAAAAGTTTAGAGACTAATTTAAAATGAGAATAATAATTTGGG
Done.