Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001532.1 Hibiscus syriacus cultivar Beakdansim tig00003005_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: 105789
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8035 original size:15 final size:15
Alignment explanation
Indices: 7998--8026 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7988 TCGTTTAGAA
7998 TAAGGATTTAAAATG
1 TAAGGATTTAAAATG
8013 TAAGGATTTAAAAT
1 TAAGGATTTAAAAT
8027 TTAGTGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
TAAGGATTTAAAATG
Found at i:8826 original size:20 final size:20
Alignment explanation
Indices: 8797--8848 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
8787 GATTGAAGTA
*
8797 GTATCAATACTAA-TGTGGAG
1 GTATCAATACTAAGAGT-GAG
* *
8817 GTATCGATACCAAGAGTGAG
1 GTATCAATACTAAGAGTGAG
8837 GTATCAATACTA
1 GTATCAATACTA
8849 TAATTGAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (20 bp):
GTATCAATACTAAGAGTGAG
Found at i:9342 original size:15 final size:15
Alignment explanation
Indices: 9324--9370 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9314 GAATATGCTA
9324 TATGTGAATGTGTTC
1 TATGTGAATGTGTTC
**
9339 TATGTGAAAATGCTT-
1 TATGTGAATGTG-TTC
*
9354 TATGTGAATGTGCTC
1 TATGTGAATGTGTTC
9369 TA
1 TA
9371 CGCAAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (15 bp):
TATGTGAATGTGTTC
Found at i:9352 original size:30 final size:30
Alignment explanation
Indices: 9313--9370 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9303 TATTAGTATA
* *
9313 TGAATATGCTATATGTGAATGTGTTCTATG
1 TGAAAATGCTATATGTGAATGTGCTCTATG
*
9343 TGAAAATGCTTTATGTGAATGTGCTCTA
1 TGAAAATGCTATATGTGAATGTGCTCTA
9371 CGCAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (30 bp):
TGAAAATGCTATATGTGAATGTGCTCTATG
Found at i:9514 original size:25 final size:24
Alignment explanation
Indices: 9480--9529 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
9470 AAGTTGAGGG
9480 TTCTACGCGGTCCATCGGGACAAAT
1 TTCTACGCGGTCCATCGGGA-AAAT
*
9505 TTCTACGCGGTCCTTCGGGAAAAT
1 TTCTACGCGGTCCATCGGGAAAAT
9529 T
1 T
9530 CTATGTGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (24 bp):
TTCTACGCGGTCCATCGGGAAAAT
Found at i:22598 original size:21 final size:21
Alignment explanation
Indices: 22574--22667 Score: 188
Period size: 21 Copynumber: 4.5 Consensus size: 21
22564 AGATGAACAT
22574 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
22595 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
22616 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
22637 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
22658 TATCGATACT
1 TATCGATACT
22668 AATGTAGAGG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (21 bp):
TATCGATACTGATTGAAGTAG
Found at i:22785 original size:22 final size:23
Alignment explanation
Indices: 22760--22802 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
22750 ACTGAAGTGG
*
22760 GTATTAGTACCATA-GAAGAGAA
1 GTATCAGTACCATAGGAAGAGAA
*
22782 GTATCAGTACTATAGGAAGAG
1 GTATCAGTACCATAGGAAGAG
22803 TATCGATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.42, C:0.09, G:0.26, T:0.23
Consensus pattern (23 bp):
GTATCAGTACCATAGGAAGAGAA
Found at i:23228 original size:30 final size:30
Alignment explanation
Indices: 23166--23229 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
23156 TATTAGTATA
* * **
23166 TGAATATGCTATATGTGAATGTGTTCTACG
1 TGAAAATGCTATATGTGAATATACTCTACG
* *
23196 TGAAAATGCTTTATGTGAATATACTCTGCG
1 TGAAAATGCTATATGTGAATATACTCTACG
23226 TGAA
1 TGAA
23230 TAAAATATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (30 bp):
TGAAAATGCTATATGTGAATATACTCTACG
Found at i:23381 original size:24 final size:24
Alignment explanation
Indices: 23351--23414 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 24
23341 GGTTCTTCGA
23351 GACAAATTCTACGTGGTCCTTCAG
1 GACAAATTCTACGTGGTCCTTCAG
* * * *
23375 GATAAATTTCTACGCGGTTCTTCGG
1 GACAAA-TTCTACGTGGTCCTTCAG
*
23400 GACAAA-TCTATGTGG
1 GACAAATTCTACGTGG
23415 CACTTCGGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 7 0.22
24 5 0.16
25 20 0.62
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (24 bp):
GACAAATTCTACGTGGTCCTTCAG
Found at i:23397 original size:25 final size:24
Alignment explanation
Indices: 23340--23406 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
23330 GGGTTTTACA
23340 CGGTTCTTCGAGACAAA-TTCTACG
1 CGGTTCTTCG-GACAAATTTCTACG
* * *
23364 TGGTCCTTCAGGATAAATTTCTACG
1 CGGTTCTTC-GGACAAATTTCTACG
23389 CGGTTCTTCGGGACAAAT
1 CGGTTCTTC-GGACAAAT
23407 CTATGTGGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (24 bp):
CGGTTCTTCGGACAAATTTCTACG
Found at i:23420 original size:23 final size:24
Alignment explanation
Indices: 23394--23438 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
23384 CTACGCGGTT
23394 CTTCGG-GACAAA-TCTATGTGGCA
1 CTTCGGTG-CAAATTCTATGTGGCA
23417 CTTCGGTGCAAATTCTATGTGG
1 CTTCGGTGCAAATTCTATGTGG
23439 AAGTGGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTATGTGGCA
Found at i:27619 original size:20 final size:18
Alignment explanation
Indices: 27569--27620 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
27559 CTTTAAATTA
27569 TTAGTATCGATACTCAAG
1 TTAGTATCGATACTCAAG
*
27587 -TAGGGTATTGATACTCTTAAG
1 TTA--GTATCGATACTC--AAG
27608 TTAGTATCGATAC
1 TTAGTATCGATAC
27621 CAATGTACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.07
19 11 0.41
20 9 0.33
21 3 0.11
22 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (18 bp):
TTAGTATCGATACTCAAG
Found at i:30145 original size:17 final size:17
Alignment explanation
Indices: 30123--30163 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
30113 ACTAAAATGG
30123 AATAGTACAGGAAAAGA
1 AATAGTACAGGAAAAGA
*
30140 AATAGTATAGGAAAAGA
1 AATAGTACAGGAAAAGA
*
30157 AACAGTA
1 AATAGTA
30164 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.22, T:0.15
Consensus pattern (17 bp):
AATAGTACAGGAAAAGA
Found at i:30935 original size:15 final size:15
Alignment explanation
Indices: 30912--30945 Score: 59
Period size: 15 Copynumber: 2.2 Consensus size: 15
30902 CCTGGTAATT
30912 TTAAAAAAATTTAAAA
1 TTAAAAAAA-TTAAAA
30928 TTAAAAAAATTAAAA
1 TTAAAAAAATTAAAA
30943 TTA
1 TTA
30946 TATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAAAATTAAAA
Found at i:33040 original size:20 final size:21
Alignment explanation
Indices: 32994--33041 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
32984 TTTTTTTAAA
32994 TAAAATTTATGAAGAAATTAT
1 TAAAATTTATGAAGAAATTAT
*
33015 T-TAATTTATGAA-ATAATT-T
1 TAAAATTTATGAAGA-AATTAT
33034 TAAAATTT
1 TAAAATTT
33042 CTAGAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (21 bp):
TAAAATTTATGAAGAAATTAT
Found at i:36754 original size:22 final size:20
Alignment explanation
Indices: 36715--36764 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
36705 AACTTGAGAC
36715 TTCCTTTTATTTTCTTTATT
1 TTCCTTTTATTTTCTTTATT
*
36735 TTCCTTTTTTTCTTCTTTTATT
1 TTCCTTTTATT-TTC-TTTATT
*
36757 TTCATTTT
1 TTCCTTTT
36765 CATCTCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 3 0.12
22 13 0.50
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCCTTTTATTTTCTTTATT
Found at i:36803 original size:15 final size:16
Alignment explanation
Indices: 36774--36868 Score: 68
Period size: 15 Copynumber: 5.8 Consensus size: 16
36764 TCATCTCTTC
*
36774 TTCCATTTTTCATTTT
1 TTCCCTTTTTCATTTT
36790 TTCCCTTTTT-ATTTT
1 TTCCCTTTTTCATTTT
*
36805 TTCCTTTTTTTTCATTTT
1 TTCC--CTTTTTCATTTT
* * *
36823 TTATCTTTTTATCTTTTT
1 TT-CCCTTTT-TCATTTT
* * *
36841 TTTCGTTTTTC-GTTT
1 TTCCCTTTTTCATTTT
36856 TTCCCTTTTTCAT
1 TTCCCTTTTTCAT
36869 CATTTTTTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
15 21 0.33
16 11 0.17
17 16 0.25
18 15 0.23
19 1 0.02
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (16 bp):
TTCCCTTTTTCATTTT
Found at i:36816 original size:33 final size:32
Alignment explanation
Indices: 36779--36893 Score: 108
Period size: 33 Copynumber: 3.4 Consensus size: 32
36769 TCTTCTTCCA
36779 TTTTTCATTTTTTCCCTTTTTAT-TTTTTCCTTT
1 TTTTTC-TTTTTTCCCTTTTTATCTTTTT-CTTT
**
36812 TTTTTCATTTTTTATCTTTTTATCTTTTT-TTT
1 TTTTTC-TTTTTTCCCTTTTTATCTTTTTCTTT
*
36844 CGTTTTTCGTTTTTCCCTTTTTCATCATTTTTTCTTT
1 --TTTTTCTTTTTTCCCTTTTT-ATC--TTTTTCTTT
*
36881 TTTCTCTTTTTTC
1 TTTTTCTTTTTTC
36894 ATTTCTTCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
32 3 0.04
33 32 0.47
34 14 0.21
35 11 0.16
36 5 0.07
37 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (32 bp):
TTTTTCTTTTTTCCCTTTTTATCTTTTTCTTT
Found at i:36857 original size:42 final size:42
Alignment explanation
Indices: 36811--36893 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
36801 TTTTTTCCTT
* * *
36811 TTTTTTCATTTTTTATC-TTTTTATCTTTTTTTTCGTTTTTCG
1 TTTTTCCATTTTTCATCATTTTT-TCTTTTTTCTCGTTTTTCG
* *
36853 TTTTTCCCTTTTTCATCATTTTTTCTTTTTTCTCTTTTTTC
1 TTTTTCCATTTTTCATCATTTTTTCTTTTTTCTCGTTTTTC
36894 ATTTCTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (42 bp):
TTTTTCCATTTTTCATCATTTTTTCTTTTTTCTCGTTTTTCG
Found at i:36883 original size:9 final size:9
Alignment explanation
Indices: 36801--36893 Score: 56
Period size: 8 Copynumber: 10.8 Consensus size: 9
36791 TCCCTTTTTA
36801 TTTTTTC-C
1 TTTTTTCTC
*
36809 TTTTTTTTC
1 TTTTTTCTC
*
36818 ATTTTTTATC
1 -TTTTTTCTC
36828 TTTTTATCT-
1 TTTTT-TCTC
36837 TTTTTT-TC
1 TTTTTTCTC
*
36845 -GTTTT-TC
1 TTTTTTCTC
*
36852 GTTTTTC-C
1 TTTTTTCTC
*
36860 CTTTTTCATC
1 TTTTTTC-TC
*
36870 ATTTTT-TC
1 TTTTTTCTC
36878 TTTTTTCTC
1 TTTTTTCTC
36887 TTTTTTC
1 TTTTTTC
36894 ATTTCTTCTT
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
7 7 0.10
8 25 0.37
9 20 0.29
10 16 0.24
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:45112 original size:51 final size:51
Alignment explanation
Indices: 44995--45242 Score: 219
Period size: 51 Copynumber: 4.7 Consensus size: 51
44985 AAACGGGTCC
* * * * *
44995 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGT-T
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCG----ATCTCCAACAAACATGTCT
* *
45049 CGCTCCCTATTCCTTCATAGAGTATAGGACTCGATCTCCAACAAACATGTTT
1 -GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTCCAACAAACATGTCT
** * * * *
45101 TTTCCCTATTCCTTCAGAGAGCATAGGACTCGATCTTCAATAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTCCAACAAACATGTCT
* * * * * *
45152 GCTACCTATTCCTTCAGAGAGTATAGGGCTTGAATAATATTCAACAAACTTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCG----ATCTCCAACAAACATGTCT
* *
45207 GCTCCCTATTCCTTCAGAGAGTATATGACTCAATCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCT
45243 TCATAAAATG
Statistics
Matches: 159, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
51 87 0.55
52 1 0.01
55 71 0.45
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTCCAACAAACATGTCT
Found at i:45219 original size:55 final size:54
Alignment explanation
Indices: 44834--45237 Score: 362
Period size: 55 Copynumber: 7.5 Consensus size: 54
44824 AAGTCCGCTT
* *
44834 CCTATTCCTTCA-AGGAGTATAAGACTCGAACAATCTTCAACAAACGTGT-TCGCTT
1 CCTATTCCTTCAGA-GAGTATAGGACTCGAA-AATCTTCAACAAACGTGTCT-GCTC
* * * * * *
44889 CCTATTCATTCAGGGAGTATAAGACTCGAAAAATCTTCATA-AAATGGGTCAGCTC
1 CCTATTCCTTCAGAGAGTATAGGACTCG-AAAATCTTCA-ACAAACGTGTCTGCTC
* * * * * *
44944 TCTATTCGTTCAGGGAGTATAGAACTCGAATAATCTTCATA-AAACGGGTCCGCTC
1 CCTATTCCTTCAGAGAGTATAGGACTCGAA-AATCTTCA-ACAAACGTGTCTGCTC
* * *
44999 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGT-TCGCTC
1 CCTATTCCTTCAGAGAGTATAGGACTCGAA-AATCTTCAACAAACGTGTCT-GCTC
* * * * **
45054 CCTATTCCTTCATAGAGTATAGGACTCG---ATCTCCAACAAACATGTTTTTTC
1 CCTATTCCTTCAGAGAGTATAGGACTCGAAAATCTTCAACAAACGTGTCTGCTC
* * *
45105 CCTATTCCTTCAGAGAGCATAGGACTCG---ATCTTCAATAAACGTGTCTGCTA
1 CCTATTCCTTCAGAGAGTATAGGACTCGAAAATCTTCAACAAACGTGTCTGCTC
* * * *
45156 CCTATTCCTTCAGAGAGTATAGGGCTTGAATAATATTCAACAAACTTGTCTGCTC
1 CCTATTCCTTCAGAGAGTATAGGACTCGAA-AATCTTCAACAAACGTGTCTGCTC
*
45211 CCTATTCCTTCAGAGAGTATATGACTC
1 CCTATTCCTTCAGAGAGTATAGGACTC
45238 AATCTTCATA
Statistics
Matches: 292, Mismatches: 45, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
51 84 0.29
52 1 0.00
54 3 0.01
55 201 0.69
56 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (54 bp):
CCTATTCCTTCAGAGAGTATAGGACTCGAAAATCTTCAACAAACGTGTCTGCTC
Found at i:45296 original size:37 final size:36
Alignment explanation
Indices: 45250--45359 Score: 141
Period size: 37 Copynumber: 3.0 Consensus size: 36
45240 TCTTCATAAA
45250 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAG
1 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AG
* *
45288 ATGATTTGCTTCACTACTCTTCTGTGAAAGCTTAAG
1 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
* *
45324 ATTGAATTT-CTTCACTGCTCTTTCGTGAAGGCTTAA
1 A-TG-ATTTGCTTCACTACTCTTCCGTGAAGGCTTAA
45360 TATTGACTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
36 3 0.05
37 53 0.83
38 8 0.12
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (36 bp):
ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
Found at i:47066 original size:19 final size:19
Alignment explanation
Indices: 47042--47092 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
47032 CTGGACAATT
47042 ATATTAATAATTATTTATA
1 ATATTAATAATTATTTATA
* *
47061 ATATTAATATATTAATTATG
1 ATATTAATA-ATTATTTATA
47081 AT-TTAA-AATTAT
1 ATATTAATAATTAT
47093 AATTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.14
18 1 0.04
19 13 0.46
20 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTAATAATTATTTATA
Found at i:48531 original size:20 final size:21
Alignment explanation
Indices: 48506--48550 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
48496 GAAGAATGAA
48506 GAAGGGG-AGGGGGAGCA-GGG
1 GAAGGGGAAGGGGGA-CATGGG
48526 GAAGGGGAAGGGGGACATGGG
1 GAAGGGGAAGGGGGACATGGG
48547 GAAG
1 GAAG
48551 AAAGGGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.29, C:0.04, G:0.64, T:0.02
Consensus pattern (21 bp):
GAAGGGGAAGGGGGACATGGG
Found at i:50160 original size:24 final size:24
Alignment explanation
Indices: 50133--50242 Score: 93
Period size: 24 Copynumber: 4.6 Consensus size: 24
50123 GTAAACGGAG
*
50133 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * *
50157 ATATCAGATATCAGAATAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
50181 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
50204 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
50228 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
50243 TAAAATATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 15 0.22
24 49 0.72
25 2 0.03
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:50205 original size:12 final size:12
Alignment explanation
Indices: 50137--50228 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
50127 ACGGAGATAT
* *
50137 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
50149 CAGAATTCATAT
1 CAGAATTCAGAA
50161 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
50173 TAGAATCCAGAT
1 CAGAATTCAGAA
50185 CAGAA-TCAGAA
1 CAGAATTCAGAA
50196 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
50210 C-GTA-TCAGAA
1 CAGAATTCAGAA
50220 CAGAATTCA
1 CAGAATTCA
50229 ATTCGGAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 35 0.58
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:50216 original size:47 final size:48
Alignment explanation
Indices: 50135--50225 Score: 116
Period size: 47 Copynumber: 1.9 Consensus size: 48
50125 AAACGGAGAT
* *
50135 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAATAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
50183 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
50226 TCAATTCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
47 29 0.76
48 6 0.16
49 3 0.08
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:54891 original size:24 final size:23
Alignment explanation
Indices: 54855--54926 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
54845 GTAAACGGAG
* *
54855 ATATCAGAAATCAAAATAGAATTC
1 ATATCAG-AATCAGAACAGAATTC
*
54879 ATATCAGATATCAGAACAGAATCC
1 ATATCAGA-ATCAGAACAGAATTC
*
54903 AGATCAGAATCAGAACAGAATTC
1 ATATCAGAATCAGAACAGAATTC
54926 A
1 A
54927 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 16 0.38
24 26 0.62
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (23 bp):
ATATCAGAATCAGAACAGAATTC
Found at i:54905 original size:12 final size:11
Alignment explanation
Indices: 54883--54923 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
54873 GAATTCATAT
54883 CAGATATCAGAA
1 CAGA-ATCAGAA
*
54895 CAGAATCCAGAT
1 CAGAAT-CAGAA
54907 CAGAATCAGAA
1 CAGAATCAGAA
54918 CAGAAT
1 CAGAAT
54924 TCAGGTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (11 bp):
CAGAATCAGAA
Found at i:54927 original size:12 final size:12
Alignment explanation
Indices: 54889--54927 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
54879 ATATCAGATA
54889 TCAGAACAGAAT
1 TCAGAACAGAAT
* *
54901 CCAGATCAGAA-
1 TCAGAACAGAAT
54912 TCAGAACAGAAT
1 TCAGAACAGAAT
54924 TCAG
1 TCAG
54928 GTAACGTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (12 bp):
TCAGAACAGAAT
Found at i:57401 original size:15 final size:15
Alignment explanation
Indices: 57371--57414 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
57361 GGTCAACAGT
57371 GGTCAACGACGGTCAAC
1 GGTCAACG--GGTCAAC
57388 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
*
57403 AGTCAACGGGTC
1 GGTCAACGGGTC
57415 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 18 0.69
17 8 0.31
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:57436 original size:13 final size:13
Alignment explanation
Indices: 57414--57449 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
57404 GTCAACGGGT
*
57414 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
57427 CGGGTTGGGTAAA
1 CGGGTCGGGTAAA
57440 CGGGTCGGGT
1 CGGGTCGGGT
57450 TATGACCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:58742 original size:11 final size:11
Alignment explanation
Indices: 58726--58758 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
58716 ATTGATGTGC
58726 TTGTTATATTT
1 TTGTTATATTT
58737 TTGTTATATTT
1 TTGTTATATTT
58748 TTGTTATATTT
1 TTGTTATATTT
58759 GACACCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTGTTATATTT
Found at i:59537 original size:24 final size:24
Alignment explanation
Indices: 59504--59558 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
59494 TATTCTTTCA
59504 CTTCAATTGAGCTCAAATTTTAGG
1 CTTCAATTGAGCTCAAATTTTAGG
*
59528 TTTCAATTGAGCTCAAATTTTAGG
1 CTTCAATTGAGCTCAAATTTTAGG
59552 CTTCAAT
1 CTTCAAT
59559 CGAACTTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (24 bp):
CTTCAATTGAGCTCAAATTTTAGG
Found at i:59818 original size:30 final size:30
Alignment explanation
Indices: 59782--59839 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
59772 AGTGAACCGG
*
59782 CGGTTCAAACCGGTTTTGCCAGTTTTCAGC
1 CGGTTCAAACCGGTTTTCCCAGTTTTCAGC
** *
59812 CGGTTCACCCCGGTTTTCCCGGTTTTCA
1 CGGTTCAAACCGGTTTTCCCAGTTTTCA
59840 ACCGATTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.31, G:0.22, T:0.34
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTCCCAGTTTTCAGC
Found at i:60595 original size:182 final size:182
Alignment explanation
Indices: 60041--60696 Score: 833
Period size: 182 Copynumber: 3.7 Consensus size: 182
60031 TTGTCAGTAC
* * *
60041 GTATCAATACTATTA-AAATATGTATCGATACATAACAATATATA-AGGTAAAAATATGAGAAAA
1 GTATCGATACT-TTATAAACATGTATCGATACATAACAATATA-ACAGGTAAAAATATGACAAAA
* * * * *
60104 TC-GATTCA-ATATGACAAAACTGGTAAAGCGCTACCGGATATGTTGAAGGTATCGATTCCATTA
64 CCGGTTTCATA-ATGACAAAACCGGTAAA-AGCTACCGGATATGTTGAAGGTATCGATTCCATTC
* * *
60167 AAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGTGCCTATAAA
127 AAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAA
* *
60223 GTATCGATACTTTATAAACATATATCGATACATAACAATATAACAGGTAGAAATATGAC-AAACT
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAC-
* *
60287 CGGTTTCATAATAACAAAACC-G----A--TACCGGATATGTTGAATGGTATTGATTCCATTCAA
65 CGGTTTCATAATGACAAAACCGGTAAAAGCTACCGGATATGTTGAA-GGTATCGATTCCATTCAA
* * * *
60345 AT-A-TATTGATACTTTTGGCATTTAAAAGAAAAGTAATAATAGCGCCTATAAA
129 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAA
* * * ** *
60397 ATATCGGTACTTTATAAACATGTATCTATGTATAACAATATAACATGTAAAAATATGACAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACC
*
60462 GGTTTCATAATGACAAAACCGGTAAAACGCTACCGGATATGTTGAAGGTATCGATTTCATTCAAA
66 GGTTTCATAATGACAAAACCGGTAAAA-GCTACCGGATATGTTGAAGGTATCGATTCCATTCAAA
*
60527 TAAGTATCGACACTTTT-GAATTTAAAAGAATAGCAATAATAGCGCCTATAAA
130 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAA
* * *
60579 GCATCGATAATTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATGACAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACC
* *
60644 GGTTTCATAATGACAAAACCGGTAATGAGCTACCAGATATGTT--AGGTATCGAT
66 GGTTTCATAATGACAAAACCGGTAA-AAGCTACCGGATATGTTGAAGGTATCGAT
60697 ACTTTAATAA
Statistics
Matches: 412, Mismatches: 44, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
174 113 0.27
175 22 0.05
176 18 0.04
179 1 0.00
180 10 0.02
181 25 0.06
182 196 0.48
183 26 0.06
184 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.29
Consensus pattern (182 bp):
GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACC
GGTTTCATAATGACAAAACCGGTAAAAGCTACCGGATATGTTGAAGGTATCGATTCCATTCAAAT
AAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGCCTATAAA
Found at i:63368 original size:11 final size:11
Alignment explanation
Indices: 63352--63381 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
63342 AAGAAAAGAT
63352 GGAGGAAGTGA
1 GGAGGAAGTGA
63363 GGAGGAAGTGA
1 GGAGGAAGTGA
63374 GGAGGAAG
1 GGAGGAAG
63382 GATATGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.57, T:0.07
Consensus pattern (11 bp):
GGAGGAAGTGA
Found at i:68689 original size:200 final size:199
Alignment explanation
Indices: 67608--68961 Score: 2097
Period size: 200 Copynumber: 6.8 Consensus size: 199
67598 TGAGGTATCA
* *
67608 ATACATTTATTGTAAGTATCGATCCTAAAAACATCGAAACCGATAATTATAAAGAAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* * * *
67673 TTTACAATGTAACAGGTAAAAATATGTCAGTTTAATGAGAAAATAGGTCCACATAATGTATCGAT
66 TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
*
67738 ACGTTTTTAAAATGTATCGATATTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
131 AC-TTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
67803 TGTCG
195 TGTCG
* * * *
67808 ATACATTTATTGTACGCATCGATCCCAAAAATATCGAAACAGATAATTATAAAGTAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* * *
67873 TTAACAATGTAACCGGTAAAAATATATC-GTTTTATGAGAAAGTAGGTTCACATAATGTATCGAT
66 TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
*
67937 ACTTTTTAAAATTGTATCGATACTTTTGGTCCAGATTGAATGCCCAACGAGGTGCACGCATAAAG
131 ACTTTTTAAAA-TGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
68002 TGTCG
195 TGTCG
* * *
68007 ATACATTTATTGTAAGTATCGATCCCAAGAACTTCGAAACCGATAATTATAAAGCAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* * * *
68072 TTTACAATGTAACAAGTAAAAATATATTGGTTTTACGAGAAAGTAGGTCCACATAATGTATTGAT
66 TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
* * *
68137 AC-TTTTAAAATTGTATCGATACTTTTGGTTCAGAATGAATGCTCAACGAGGTGCACGTATAAAG
131 ACTTTTTAAAA-TGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
*
68201 TGTTG
195 TGTCG
* * * * *
68206 ATACATTTATTATAATTATCGATCCCAAAAACATCAAAACCGATCATTATTAAGTAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* *
68271 TTTACAATGTAACCA-GTAAAAATGTACCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGA
66 TTTACAATGTAA-CAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGA
** *
68335 TACTTTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTTTACTCAT--A
130 TAC-TTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAA
*
68398 TTGTCG
194 GTGTCG
*
68404 ATACATTTATTGTAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAAAGTAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* * *
68469 TTTACAATGTAACCGGTAAAAATATATCGGTTTAATGAGAAAGTAGATCCACATAATGTATCGAT
66 TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
*
68534 ACTTTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAAGTGCACGCATAAAG
131 AC-TTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
68599 TGTCG
195 TGTCG
* * *
68604 ATATATTTATTATAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAAAGTAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* * *
68669 TTTACAATGTAACAGGTAAAAATATACCGTTTTTATGAGAAAGTTGGTCCACATAATGTATCGAT
66 TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
68734 ACTTTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
131 AC-TTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAG
*
68799 TGTCA
195 TGTCG
68804 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
1 ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
* * * * **
68869 TTAAAAATGTAACAAGTAAAAATATACCAATTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
66 TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
68934 ACTTTTTAAAATTGTATCGATACATTTT
131 ACTTTTTAAAA-TGTATCGATAC-TTTT
68962 TTAAATTAAG
Statistics
Matches: 1053, Mismatches: 91, Indels: 19
0.91 0.08 0.02
Matches are distributed among these distances:
197 1 0.00
198 188 0.18
199 360 0.34
200 492 0.47
201 12 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (199 bp):
ATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAA
TTTACAATGTAACAGGTAAAAATATATCGGTTTTATGAGAAAGTAGGTCCACATAATGTATCGAT
ACTTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGT
GTCG
Found at i:68799 original size:598 final size:596
Alignment explanation
Indices: 67605--68961 Score: 2155
Period size: 598 Copynumber: 2.3 Consensus size: 596
67595 ACTTGAGGTA
* *
67605 TCAATACATTTATTGTAAGTATCGATCCTAAAAACATCGAAACCGATAATTATAAAGAAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
** * *
67670 AAATTTACAATGTAA-CAGGTAAAAATATGTCAGTTTAATGAGAAAATAGGTCCACATAATGTAT
66 AAATTTACAATGTAACCA-GTAAAAATATACCAGTTTTATGAGAAAGTAGGTCCACATAATGTAT
*
67734 CGATACGTTTTTAAAATGTATCGATATTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCAT
130 CGATAC-TTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCAT
*
67799 AAAGTGTCGATACATTTATTGTACGCATCGATCCCAAAAATATCGAAACAGATAATTATAAAGTA
194 -AAGTGTCGATACATTTATTGTAAGCATCGATCCCAAAAATATCGAAACAGATAATTATAAAGTA
* * *
67864 ATAGGTAAATTAACAATGTAACCGGTAAAAATATATCGTTTTATGAGAAAGTAGGTTCACATAAT
258 ATAGGTAAATTAACAATGTAACCGGTAAAAATATATCGTTTAATGAGAAAGTAGATCCACATAAT
* *
67929 GTATCGATACTTTTTAAAATTGTATCGATACTTTTGGTCCAGATTGAATGCCCAACGAGGTGCAC
323 GTATCGATACTTTTTAAAATTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAAGTGCAC
* * * *
67994 GCATAAAGTGTCGATACATTTATTGTAAGTATCGATCCCAAGAACTTCGAAACCGATAATTATAA
388 GCATAAAGTGTCGATACATTTATTATAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAA
**
68059 AGCAATAGGTAAATTTACAATGTAACAAGTAAAAATATATTGGTTTTACGAGAAAGTAGGTCCAC
453 AGCAATAGGTAAATTTACAATGTAACAAGTAAAAATATACCGGTTTTACGAGAAAGTAGGTCCAC
* * *
68124 ATAATGTATTGATACTTTTAAAATTGTATCGATACTTTTGGTTCAGAATGAATGCTCAACGAGGT
518 ATAATGTATCGATACTTTTAAAATTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGT
*
68189 GCACGTATAAAGTG
583 GCACGCATAAAGTG
** * * * * *
68203 TTGATACATTTATTATAATTATCGATCCCAAAAACATCAAAACCGATCATTATTAAGTAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* *
68268 AAATTTACAATGTAACCAGTAAAAATGTACCGGTTTTATGAGAAAGTAGGTCCACATAATGTATC
66 AAATTTACAATGTAACCAGTAAAAATATACCAGTTTTATGAGAAAGTAGGTCCACATAATGTATC
** *
68333 GATACTTTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTTTACTCAT-
131 GATAC-TTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATA
* * *
68397 ATTGTCGATACATTTATTGTAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAAAGTAAT
195 AGTGTCGATACATTTATTGTAAGCATCGATCCCAAAAATATCGAAACAGATAATTATAAAGTAAT
*
68462 AGGTAAATTTACAATGTAACCGGTAAAAATATATCGGTTTAATGAGAAAGTAGATCCACATAATG
260 AGGTAAATTAACAATGTAACCGGTAAAAATATATC-GTTTAATGAGAAAGTAGATCCACATAATG
68527 TATCGATACTTTTTTAAAA-TGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAAGTGCAC
324 TATCGATAC-TTTTTAAAATTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAAGTGCAC
*
68591 GCATAAAGTGTCGATATATTTATTATAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAA
388 GCATAAAGTGTCGATACATTTATTATAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAA
* * * * *
68656 AGTAATAGGTAAATTTACAATGTAACAGGTAAAAATATACCGTTTTTATGAGAAAGTTGGTCCAC
453 AGCAATAGGTAAATTTACAATGTAACAAGTAAAAATATACCGGTTTTACGAGAAAGTAGGTCCAC
68721 ATAATGTATCGATACTTTTTTAAAA-TGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAG
518 ATAATGTATCGATAC--TTTTAAAATTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAG
68785 GTGCACGCATAAAGTG
581 GTGCACGCATAAAGTG
68801 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * *
68866 AAATTAAAAATGTAACAAGTAAAAATATACCAATTTTATGAGAAAGTAGGTCCACATAATGTATC
66 AAATTTACAATGTAACCAGTAAAAATATACCAGTTTTATGAGAAAGTAGGTCCACATAATGTATC
68931 GATACTTTTTAAAATTGTATCGATACATTTT
131 GATACTTTTTAAAA-TGTATCGATAC-TTTT
68962 TTAAATTAAG
Statistics
Matches: 693, Mismatches: 59, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
596 95 0.14
597 219 0.32
598 365 0.53
599 14 0.02
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (596 bp):
TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
AAATTTACAATGTAACCAGTAAAAATATACCAGTTTTATGAGAAAGTAGGTCCACATAATGTATC
GATACTTTTTAAAATGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAA
GTGTCGATACATTTATTGTAAGCATCGATCCCAAAAATATCGAAACAGATAATTATAAAGTAATA
GGTAAATTAACAATGTAACCGGTAAAAATATATCGTTTAATGAGAAAGTAGATCCACATAATGTA
TCGATACTTTTTAAAATTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAAGTGCACGCA
TAAAGTGTCGATACATTTATTATAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAAAGC
AATAGGTAAATTTACAATGTAACAAGTAAAAATATACCGGTTTTACGAGAAAGTAGGTCCACATA
ATGTATCGATACTTTTAAAATTGTATCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCA
CGCATAAAGTG
Found at i:68951 original size:21 final size:22
Alignment explanation
Indices: 68925--68968 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
68915 GTCCACATAA
68925 TGTATCGATAC-TTTTTAAAAT
1 TGTATCGATACATTTTTAAAAT
*
68946 TGTATCGATACATTTTTTAAAT
1 TGTATCGATACATTTTTAAAAT
68968 T
1 T
68969 AAGTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
TGTATCGATACATTTTTAAAAT
Found at i:69276 original size:15 final size:15
Alignment explanation
Indices: 69250--69309 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 15
69240 TGGGTCTTCT
69250 CAACCTTCTTCTCAAC
1 CAACC-TCTTCTCAAC
*
69266 CAAGCTCTTCTCAAC
1 CAACCTCTTCTCAAC
*
69281 GACAACCTTTATCTCAAC
1 --CAACCTCT-TCTCAAC
69299 CAACCTCTTCT
1 CAACCTCTTCT
69310 TCTGAACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.35
16 11 0.30
17 6 0.16
18 7 0.19
ACGTcount: A:0.27, C:0.40, G:0.03, T:0.30
Consensus pattern (15 bp):
CAACCTCTTCTCAAC
Found at i:70455 original size:18 final size:18
Alignment explanation
Indices: 70432--70471 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
70422 CAAGCGCTCA
70432 ATGAAGATGAAAATGAAG
1 ATGAAGATGAAAATGAAG
* *
70450 ATGAAGATGATAATGATG
1 ATGAAGATGAAAATGAAG
70468 ATGA
1 ATGA
70472 TGATCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (18 bp):
ATGAAGATGAAAATGAAG
Found at i:71924 original size:18 final size:18
Alignment explanation
Indices: 71903--71939 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
71893 TTAATTGGAG
71903 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
71921 TTTGATTTTTAATTTCAA
1 TTTGAATTTAAATTTCAA
71939 T
1 T
71940 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:73211 original size:21 final size:21
Alignment explanation
Indices: 73181--73224 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
73171 GCGTGCAAAT
73181 GTATCAAAACACATTATTAAA
1 GTATCAAAACACATTATTAAA
*
73202 GTATCGAAACACATTATTAAA
1 GTATCAAAACACATTATTAAA
73223 GT
1 GT
73225 GTCGTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (21 bp):
GTATCAAAACACATTATTAAA
Found at i:76816 original size:20 final size:20
Alignment explanation
Indices: 76771--76816 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
76761 GTTTACATAA
*
76771 AGTATCGATACATTTTGTAT
1 AGTATCGATACATTTTGTAC
* *
76791 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACATTTTGTAC
76812 AGTAT
1 AGTAT
76817 GATTCTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (20 bp):
AGTATCGATACATTTTGTAC
Found at i:82993 original size:13 final size:13
Alignment explanation
Indices: 82975--82999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82965 AAAACACAAA
82975 ACCCAATGTCTGT
1 ACCCAATGTCTGT
82988 ACCCAATGTCTG
1 ACCCAATGTCTG
83000 GTCGCCTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (13 bp):
ACCCAATGTCTGT
Found at i:84262 original size:2 final size:2
Alignment explanation
Indices: 84255--84322 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
84245 ATCATAATTG
84255 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
84297 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
84323 GTGTGTGTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84337 original size:12 final size:12
Alignment explanation
Indices: 84322--84346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84312 TATATATATA
84322 TGTGTGTGTGTT
1 TGTGTGTGTGTT
84334 TGTGTGTGTGTT
1 TGTGTGTGTGTT
84346 T
1 T
84347 TTTAAAAATA
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:0.00, G:0.40, T:0.60
Consensus pattern (12 bp):
TGTGTGTGTGTT
Found at i:85019 original size:45 final size:45
Alignment explanation
Indices: 84955--85043 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
84945 CTCACGGGAA
84955 AAAGTATGTTGGAACCGCCTTTTACTTCATATTTCAATTACTTTG
1 AAAGTATGTTGGAACCGCCTTTTACTTCATATTTCAATTACTTTG
85000 AAAGTATGTTGGAACCGCCTTTTACTTCATATTTCAATTACTTT
1 AAAGTATGTTGGAACCGCCTTTTACTTCATATTTCAATTACTTT
85044 CCAACGAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (45 bp):
AAAGTATGTTGGAACCGCCTTTTACTTCATATTTCAATTACTTTG
Found at i:85237 original size:15 final size:16
Alignment explanation
Indices: 85217--85246 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
85207 AATCTGGTGA
85217 TTTTAAAAT-TTATTT
1 TTTTAAAATATTATTT
85232 TTTTAAAATATTATT
1 TTTTAAAATATTATT
85247 ATATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAAAATATTATTT
Found at i:85257 original size:19 final size:16
Alignment explanation
Indices: 85216--85258 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
85206 TAATCTGGTG
85216 ATTTTAAAATTTATTT
1 ATTTTAAAATTTATTT
85232 -TTTTAAAATATTATTAT
1 ATTTTAAAAT-TTATT-T
85249 ATTTATAAAA
1 ATTT-TAAAA
85259 AACTCTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.39
16 5 0.22
17 1 0.04
18 3 0.13
19 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTAAAATTTATTT
Found at i:92632 original size:19 final size:20
Alignment explanation
Indices: 92605--92643 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
92595 CAACTCGAAG
*
92605 TCAATTCGAG-TCGAATTTT
1 TCAAGTCGAGATCGAATTTT
*
92624 TCAAGTCGAGATCGAGTTTT
1 TCAAGTCGAGATCGAATTTT
92644 GCTCACCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
TCAAGTCGAGATCGAATTTT
Found at i:97534 original size:14 final size:14
Alignment explanation
Indices: 97515--97545 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
97505 GTTCTAAATC
97515 AAACCAAGAAAACT
1 AAACCAAGAAAACT
97529 AAACCAAGAAAACT
1 AAACCAAGAAAACT
97543 AAA
1 AAA
97546 TCAAATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.19, G:0.06, T:0.06
Consensus pattern (14 bp):
AAACCAAGAAAACT
Found at i:98791 original size:21 final size:21
Alignment explanation
Indices: 98765--98809 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
98755 GATTTCTGGG
* *
98765 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
98786 CAAGGGGAACCGATACCCATT
1 CAAGGGGAACCGATACCCATT
98807 CAA
1 CAA
98810 ACGAACAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:99300 original size:2 final size:2
Alignment explanation
Indices: 99293--99361 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
99283 CATGAGTTAG
99293 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
99335 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 A
99362 GGAATTGTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:100236 original size:32 final size:32
Alignment explanation
Indices: 100195--100291 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
100185 GAGTCGAGGG
100195 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
100227 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
100258 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
100290 TT
1 TT
100292 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:100267 original size:31 final size:31
Alignment explanation
Indices: 100194--100294 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
100184 AGAGTCGAGG
100194 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
100225 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
100257 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
100288 GTTTACC
1 GTTTACC
100295 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:100326 original size:30 final size:30
Alignment explanation
Indices: 100282--100375 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
100272 AAGGAACATA
100282 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
100313 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
100343 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
100372 TGGA
1 TGGA
100376 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:101416 original size:75 final size:75
Alignment explanation
Indices: 101284--101451 Score: 246
Period size: 75 Copynumber: 2.2 Consensus size: 75
101274 GATTGCTCAT
* ** *
101284 AGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTTTGGCTCCGAGATTTCC
1 AGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCC
101349 AGAATGCTCGG
65 AGAATGCTCGG
* * *
101360 AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTTTTGTTCCGAGAATTCCA
1 AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCA
*
101425 GTATGCTCGG
66 GAATGCTCGG
*
101435 AGGGAACCGATCCCCCC
1 AGGGAACCGATTCCCCC
101452 CCCAAGGGGG
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 71 0.86
76 12 0.14
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCA
GAATGCTCGG
Done.