Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007135.1 Hibiscus syriacus cultivar Beakdansim tig00018661_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: 71651
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3178 original size:13 final size:13
Alignment explanation
Indices: 3160--3186 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3150 TAGAATGCTT
3160 AACATTTATCTTC
1 AACATTTATCTTC
3173 AACATTTATCTTC
1 AACATTTATCTTC
3186 A
1 A
3187 CTTTGTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (13 bp):
AACATTTATCTTC
Found at i:10033 original size:24 final size:23
Alignment explanation
Indices: 10006--10121 Score: 135
Period size: 24 Copynumber: 4.9 Consensus size: 23
9996 TTGATTTGAT
10006 TTCTGATATGATACTAGACATGGA
1 TTCTGATATGATACT-GACATGGA
*
10030 TTCTGATATGATATCTGTCATGGA
1 TTCTGATATGATA-CTGACATGGA
* *
10054 TTCTGATCTGATAC-GACTTGGA
1 TTCTGATATGATACTGACATGGA
* *
10076 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATAC-TGACATGGA
*
10100 TTTTGATATGATACTTGACATG
1 TTCTGATATGATAC-TGACATG
10122 AATTATGGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
22 20 0.25
23 1 0.01
24 58 0.72
25 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (23 bp):
TTCTGATATGATACTGACATGGA
Found at i:10100 original size:46 final size:47
Alignment explanation
Indices: 10006--10113 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 47
9996 TTGATTTGAT
*
10006 TTCTGATATGATACTAGACATGGATTCTGATATGATATCTGTCATGGA
1 TTCTGATATGATAC-AGACATGGATTCTGATATGATATCTGACATGGA
* * * *
10054 TTCTGATCTGATAC-GACTTGGATTCTGATCTGATA-CTTGACCTGGA
1 TTCTGATATGATACAGACATGGATTCTGATATGATATC-TGACATGGA
*
10100 TTTTGATATGATAC
1 TTCTGATATGATAC
10114 TTGACATGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 1 0.02
46 38 0.73
48 13 0.25
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (47 bp):
TTCTGATATGATACAGACATGGATTCTGATATGATATCTGACATGGA
Found at i:11526 original size:56 final size:56
Alignment explanation
Indices: 11453--11608 Score: 161
Period size: 56 Copynumber: 2.8 Consensus size: 56
11443 TTCCCCAGAA
* *
11453 GTTTTGTTAATGAGGTTGTGAGAGTGAAATGAGTAATATTCACTCTCTTACTCGCTT
1 GTTTTGTT-ATGAGGTTGTGAGAGTGAAATGAGTAATACTCACTATCTTACTCGCTT
* *** * *
11510 GTTTTGTTTTGAGGTTGTGAGAGTG-AATCGAACGATACTCACTATCTTGCTCTCTT
1 GTTTTGTTATGAGGTTGTGAGAGTGAAAT-GAGTAATACTCACTATCTTACTCGCTT
* * * * * *
11566 ATTTTGTTGTGAGGTTATAAGAGTGAAATGGGTAATACCCACT
1 GTTTTGTTATGAGGTTGTGAGAGTGAAATGAGTAATACTCACT
11609 CTATTGTTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
55 3 0.04
56 66 0.82
57 11 0.14
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (56 bp):
GTTTTGTTATGAGGTTGTGAGAGTGAAATGAGTAATACTCACTATCTTACTCGCTT
Found at i:12184 original size:13 final size:13
Alignment explanation
Indices: 12166--12192 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12156 TTACAGACAC
12166 GCATATGAAGACT
1 GCATATGAAGACT
12179 GCATATGAAGACT
1 GCATATGAAGACT
12192 G
1 G
12193 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:15983 original size:3 final size:3
Alignment explanation
Indices: 15977--16295 Score: 620
Period size: 3 Copynumber: 105.7 Consensus size: 3
15967 TAGTAATAAT
15977 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16025 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16073 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16121 AAC AAC AAC AAC AAC AAC AAC AAC AAC ACAC ACAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A-AC A-AC AAC AAC AAC AAC
16168 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16216 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16264 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
16296 TAATAATAAT
Statistics
Matches: 315, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 308 0.98
4 7 0.02
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:16300 original size:3 final size:3
Alignment explanation
Indices: 16294--16322 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16284 CAACAACAAC
16294 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16323 ACCCGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21888 original size:59 final size:57
Alignment explanation
Indices: 21825--22100 Score: 204
Period size: 58 Copynumber: 4.7 Consensus size: 57
21815 CCCTTTTCGA
* *
21825 AAATCCATACCATT-AGTATGACTTTGTTACCATTTTAGCATATAATATGCCCTATCTGG
1 AAATCCATA-CATTCAGTATGA-TTTCTTACCATTTTAGCACAT-ATATGCCCTATCTGG
** * * * **
21884 AAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACCCT-TAGTGCTTTATCTGG
1 AAATCCATACATTCAGTATGATTT-CTTACCATTTTAGCA-CATATA-TGCCCTATCTGG
* *
21942 AAACCCATACATTCAGTATGATTCCCTTACCATTTTAGCACATATTATGCCCTATCTGG
1 AAATCCATACATTCAGTATGATT-TCTTACCATTTTAGCACATA-TATGCCCTATCTGG
** * * * *
22001 AAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACACTCA-GTGCTCC-ATATGG
1 AAATCCATACATTCAGTATGATTT-CTTACCATTTTAGCACA-T-ATATGC-CCTATCTGG
* * * *
22059 AAATCTACACACTCAGTATGATTTCTTTATCATTTTAGCACA
1 AAATCCATACATTCAGTATGATTTC-TTACCATTTTAGCACA
22101 CAAAGTGCCA
Statistics
Matches: 171, Mismatches: 32, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
57 3 0.02
58 90 0.53
59 75 0.44
60 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (57 bp):
AAATCCATACATTCAGTATGATTTCTTACCATTTTAGCACATATATGCCCTATCTGG
Found at i:21950 original size:58 final size:58
Alignment explanation
Indices: 21876--22101 Score: 238
Period size: 58 Copynumber: 3.9 Consensus size: 58
21866 ATAATATGCC
*
21876 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCT
1 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCT
* * ** * * * * *
21934 TTATCTGGAAACCCATACATTCAGTATGATTCCCTTACCATTTTAGCACATATTA-TGCC
1 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACA-CTTAGTGCT
*
21993 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCT
1 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCT
* * * * *** * *
22051 CCATATGGAAATCTACACACTCAGTATGATTTCTTTATCATTTTAGCACAC
1 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACAC
22102 AAAGTGCCAT
Statistics
Matches: 135, Mismatches: 29, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
57 2 0.01
58 76 0.56
59 54 0.40
60 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (58 bp):
CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTTAGTGCT
Found at i:21972 original size:117 final size:117
Alignment explanation
Indices: 21851--22100 Score: 374
Period size: 117 Copynumber: 2.1 Consensus size: 117
21841 TATGACTTTG
*
21851 TTACCATTTTAGCATATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* * ** * * *
21916 TTTAGCACCCTTAGTGCTTTATCTGGAAACCCATACATTCAGTATGATTCCC
66 TTTAGCACACTCAGTGCTCCATATGGAAACCCACACACTCAGTATGATTCCC
*
21968 TTACCATTTTAGCACATATTATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* * * *
22033 TTTAGCACACTCAGTGCTCCATATGGAAATCTACACACTCAGTATGATTTCT
66 TTTAGCACACTCAGTGCTCCATATGGAAACCCACACACTCAGTATGATTCCC
*
22085 TTATCATTTTAGCACA
1 TTACCATTTTAGCACA
22101 CAAAGTGCCA
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 119 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (117 bp):
TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAACCCACACACTCAGTATGATTCCC
Found at i:22548 original size:17 final size:16
Alignment explanation
Indices: 22506--22553 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 16
22496 ATCTTAAGGG
22506 AGTGCATCGATACACT
1 AGTGCATCGATACACT
22522 ACCTGTGCATCGATACACTT
1 A---GTGCATCGATACAC-T
22542 AGTGCATTCGAT
1 AGTGCA-TCGAT
22554 GTTTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 5 0.19
19 14 0.52
20 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (16 bp):
AGTGCATCGATACACT
Found at i:29105 original size:116 final size:117
Alignment explanation
Indices: 28958--29215 Score: 331
Period size: 117 Copynumber: 2.2 Consensus size: 117
28948 ATTCGAAAAT
** * * *
28958 CCATATCA-TTAGTATGATTTTGTTACCATTTTAGCATATAATATTCCCTAT-TGGAAATCCATA
1 CCATA-CACTTAGTATGATTTCCTTACCATTTTAGCAAATAATATGCCCTATCTAGAAATCCATA
* * * * ** *
29021 TTTTTAATATGATTTCATTATCATTTAGAACCCTTAGTGCTTTATTTGGAAAC
65 ATTTCAATATGATTTCATTATCATTTAGAACACTCAGTGCTCCATATGGAAAC
*
29074 CCATACACTTAGTATGATTCCCTTACCATTTTAGCAAATAATATGCCCTATCTAGAAATCCATAA
1 CCATACACTTAGTATGATTTCCTTACCATTTTAGCAAATAATATGCCCTATCTAGAAATCCATAA
* * *
29139 TTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAAT
66 TTTCAATATGATTTCATTATCATTTAGAACACTCAGTGCTCCATATGGAAAC
* *
29191 CTATACACTCAGTATGATTTCCTTA
1 CCATACACTTAGTATGATTTCCTTA
29216 TCGATTTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
115 2 0.02
116 43 0.36
117 76 0.63
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (117 bp):
CCATACACTTAGTATGATTTCCTTACCATTTTAGCAAATAATATGCCCTATCTAGAAATCCATAA
TTTCAATATGATTTCATTATCATTTAGAACACTCAGTGCTCCATATGGAAAC
Found at i:29255 original size:58 final size:57
Alignment explanation
Indices: 29076--29237 Score: 141
Period size: 58 Copynumber: 2.8 Consensus size: 57
29066 TTGGAAACCC
* * * * * *
29076 ATACACTTAGTATGATTCCCTTACCATTTTAGCAAATAATA-TGCCC-TATCTAGAAATCC
1 ATACACTCAGTATGATTTCCTTATCA-TTTAGCACACAA-AGTGCCCATATC--GAAATCT
* * ** *
29135 ATA-ATTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCT
1 ATACA-CTCAGTATGATTTCCTTATCATTTAGCACACAAAGTGC-CCATATCGAAATCT
29193 ATACACTCAGTATGATTTCCTTATCGATTTAGCACACAAAGTGCC
1 ATACACTCAGTATGATTTCCTTATC-ATTTAGCACACAAAGTGCC
29238 ATTCGTAATC
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
57 1 0.01
58 40 0.49
59 38 0.46
60 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (57 bp):
ATACACTCAGTATGATTTCCTTATCATTTAGCACACAAAGTGCCCATATCGAAATCT
Found at i:29661 original size:17 final size:18
Alignment explanation
Indices: 29619--29666 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
29609 ATCTTAAGGG
29619 AGTGCATCGATACACTACT
1 AGTGCATCGATACACTA-T
*
29638 TGTGCATCGATACACT-T
1 AGTGCATCGATACACTAT
29655 AGTGCATTCGAT
1 AGTGCA-TCGAT
29667 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 15 0.58
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (18 bp):
AGTGCATCGATACACTAT
Found at i:29708 original size:63 final size:64
Alignment explanation
Indices: 29577--29711 Score: 161
Period size: 63 Copynumber: 2.1 Consensus size: 64
29567 CACAGCCTAC
* *
29577 GCATCGATGCACTATATGCATTCGATGTTTTAATCTTAAGGGAGTGCATCGATACACTACTTGT
1 GCATCGATACACTATATGCATTCGATGTTTTAATCTTAAGGGAGTGCATCGATACACTACTTAT
* * * *
29641 GCATCGATACACT-TAGTGCATTCGATGTTTATTTAT-TT-A-GGTGTGCATCGGTGCACTACTT
1 GCATCGATACACTATA-TGCATTCGATG-TT-TTAATCTTAAGGGAGTGCATCGATACACTACTT
29702 AT
63 AT
29704 GCATCGAT
1 GCATCGAT
29712 GCACCTTGCC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
63 30 0.48
64 24 0.39
65 4 0.06
66 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (64 bp):
GCATCGATACACTATATGCATTCGATGTTTTAATCTTAAGGGAGTGCATCGATACACTACTTAT
Found at i:38373 original size:14 final size:15
Alignment explanation
Indices: 38356--38384 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38346 TATATATTGA
38356 ATAATAA-AATATTT
1 ATAATAATAATATTT
38370 ATAATAATAATATTT
1 ATAATAATAATATTT
38385 TAAATCCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATAATAATATTT
Found at i:39760 original size:3 final size:3
Alignment explanation
Indices: 39752--39791 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
39742 ATGTAACAAT
39752 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39792 ACCCGGACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45735 original size:20 final size:20
Alignment explanation
Indices: 45710--45747 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
45700 ATTGCTTAGT
45710 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
*
45730 AGTATCGATACTGAAGGG
1 AGTATCGATACCGAAGGG
45748 AAGGTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.37, T:0.18
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:45754 original size:20 final size:20
Alignment explanation
Indices: 45710--45761 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
45700 ATTGCTTAGT
* *
45710 AGTATCGATACCGAAGGGGG
1 AGTATCGATACTGAAGGGAG
45730 AGTATCGATACTGAAGGGA-
1 AGTATCGATACTGAAGGGAG
*
45749 AGGTATCAATACT
1 A-GTATCGATACT
45762 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (20 bp):
AGTATCGATACTGAAGGGAG
Found at i:45817 original size:19 final size:19
Alignment explanation
Indices: 45789--45841 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
45779 AAAAATGGTT
45789 TCGATACCATAGTATAATA
1 TCGATACCATAGTATAATA
* *
45808 TCGGTACCATAGTATAGTA
1 TCGATACCATAGTATAATA
45827 TCGATACCATAGTAT
1 TCGATACCATAGTAT
45842 GGTAGTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (19 bp):
TCGATACCATAGTATAATA
Found at i:46364 original size:45 final size:45
Alignment explanation
Indices: 46288--46559 Score: 422
Period size: 45 Copynumber: 6.0 Consensus size: 45
46278 TGAAAATAAT
* *
46288 AATGTATATGGGTGAATTAT-AGACATG-AAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCA-ACA-GAAAAGTATGCTATAGTTGA
* *
46333 AATGGATATGGGTGTATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
46378 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
46423 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
** *
46468 AGGGCATATGGGTGCATTATCAACAGAAAAGTATGTTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
** *
46513 AATGCATATGGGTGCATTATCAACATTAAAGTATGATATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
46558 AA
1 AA
46560 ATGTTTAATG
Statistics
Matches: 213, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
44 1 0.00
45 211 0.99
46 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
Found at i:52073 original size:54 final size:54
Alignment explanation
Indices: 51917--52143 Score: 260
Period size: 54 Copynumber: 4.2 Consensus size: 54
51907 GTACTATTGT
* ** * *
51917 CACTATCTGTGCAACCCCACGGAGTTCATAATGAGTTTATGAATGACCGTATCGG
1 CACTATGTGTGCAA-CCCACATAATTCATAATAAGTTTATGAATGACCGTATCGG
* * *
51972 CACTATGTGTACAA-CCACAAAATTCAGAATAAGTTTATGAATGACCGTATCGG
1 CACTATGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGACCGTATCGG
* * *
52025 CACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTAT-GG
1 CACTATGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGACCGTATCGG
* * * * * *
52078 ACACTATGTTTGCAACCTAAATAATTCATAACAAGTTTGTGAATTACCGTATCGG
1 -CACTATGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGACCGTATCGG
52133 CACATATGTGT
1 CAC-TATGTGT
52144 AATCTATGGA
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
53 49 0.33
54 80 0.54
55 20 0.13
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGACCGTATCGG
Found at i:52157 original size:107 final size:106
Alignment explanation
Indices: 51917--52175 Score: 272
Period size: 107 Copynumber: 2.4 Consensus size: 106
51907 GTACTATTGT
* * * *
51917 CACTATCTGTGCAACCCCACGGAGTTCATAATGAGTTTATGAATGACCGTATCGGCACTATGTGT
1 CACTATGTGT-CAA-CCCACAGAATTCATAATGAGTTTATGAATTACCGTATCGGCACTATGTGT
*
51982 ACAACCACAAAATTCAGAATAAGTTTATGAATGACCGTATCGG
64 ACAACCACAAAATTCAGAACAAGTTTATGAATGACCGTATCGG
* * *
52025 CACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTAT-GGACACTATGTTT
1 CACTATGTGT-CAACCCACAGAATTCATAATGAGTTTATGAATTACCGTATCGG-CACTATGTGT
* * * *
52089 GCAACCTA-AATAATTCATAACAAGTTTGTGAATTACCGTATCGG
64 ACAACC-ACAA-AATTCAGAACAAGTTTATGAATGACCGTATCGG
* * ** **
52133 CACATATGTGT-AATCTATGGAATTCATAACAAGTTTATGAATT
1 CAC-TATGTGTCAACCCACAGAATTCATAATGAGTTTATGAATT
52176 CCCATTTCAG
Statistics
Matches: 127, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
106 2 0.02
107 72 0.57
108 46 0.36
109 7 0.06
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (106 bp):
CACTATGTGTCAACCCACAGAATTCATAATGAGTTTATGAATTACCGTATCGGCACTATGTGTAC
AACCACAAAATTCAGAACAAGTTTATGAATGACCGTATCGG
Found at i:52174 original size:53 final size:52
Alignment explanation
Indices: 51941--52175 Score: 229
Period size: 54 Copynumber: 4.4 Consensus size: 52
51931 CCCCACGGAG
* * * *
51941 TTCATAATGAGTTTATGAATGACCGTATCGGCACTATGTGTACAACCACAAAA
1 TTCATAATAAGTTTATGAATTACCGTATCGGCACTATGTGTA-ACCCACATAA
* *
51994 TTCAGAATAAGTTTATGAATGACCGTATCGGCACTATGTGTGCAACCCACATAA
1 TTCATAATAAGTTTATGAATTACCGTATCGGCACTATGTGT--AACCCACATAA
* * * * *
52048 TTCATAATGAGTTTGTGAATTACCGTAT-GGACACTATGTTTGCAACCTAAATAA
1 TTCATAATAAGTTTATGAATTACCGTATCGG-CACTATG--TGTAACCCACATAA
* * * * ***
52102 TTCATAACAAGTTTGTGAATTACCGTATCGGCACATATGTGTAATCTATGGAA
1 TTCATAATAAGTTTATGAATTACCGTATCGGCAC-TATGTGTAACCCACATAA
*
52155 TTCATAACAAGTTTATGAATT
1 TTCATAATAAGTTTATGAATT
52176 CCCATTTCAG
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
53 70 0.45
54 77 0.49
55 7 0.04
56 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (52 bp):
TTCATAATAAGTTTATGAATTACCGTATCGGCACTATGTGTAACCCACATAA
Found at i:57571 original size:54 final size:54
Alignment explanation
Indices: 57498--57703 Score: 245
Period size: 54 Copynumber: 3.8 Consensus size: 54
57488 ACCTACGGAG
* * * *
57498 TTCATTATGAATTTATGAATGATCGTATCAGCACTATGTGTACAACCCATATAA
1 TTCATAATGAATTTGTGAATGACCGTATCAGCACTATGTGTACAACCCATGTAA
* * * ** * * *
57552 TTCAAAATGAGTTTTTGAATGACCGTATTGGCACTATGTGTGCAACCCACGGAA
1 TTCATAATGAATTTGTGAATGACCGTATCAGCACTATGTGTACAACCCATGTAA
* * *
57606 TTCATAATGAGTTTGTGAATTACCGTATCA-CACTATGTGTCCAACCCATGTAA
1 TTCATAATGAATTTGTGAATGACCGTATCAGCACTATGTGTACAACCCATGTAA
*
57659 TTCATAATGAATTTGTGAATTACCGTATC-GACACTATGTGTACAA
1 TTCATAATGAATTTGTGAATGACCGTATCAG-CACTATGTGTACAA
57704 TCTATGAAAT
Statistics
Matches: 129, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
53 48 0.37
54 81 0.63
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (54 bp):
TTCATAATGAATTTGTGAATGACCGTATCAGCACTATGTGTACAACCCATGTAA
Found at i:57678 original size:107 final size:108
Alignment explanation
Indices: 57469--57699 Score: 311
Period size: 107 Copynumber: 2.1 Consensus size: 108
57459 CTATGTGTAC
* * * * *
57469 TATCGACATTATGTGTGCAACCTACGGAGTTCATTATGAATTTATGAATGATCGTATCAGCACTA
1 TATCGACACTATGTGTGCAACCCACGGAATTCATAATGAATTTATGAATGACCGTATCAGCACTA
* *
57534 TGTGTACAACCCATATAATTCAAAATGAGTTTTTGAATGACCG
66 TGTGTACAACCCATATAATTCAAAATGAATTTGTGAATGACCG
* * * * *
57577 TATTGGCACTATGTGTGCAACCCACGGAATTCATAATGAGTTTGTGAATTACCGTATCA-CACTA
1 TATCGACACTATGTGTGCAACCCACGGAATTCATAATGAATTTATGAATGACCGTATCAGCACTA
* * * *
57641 TGTGTCCAACCCATGTAATTCATAATGAATTTGTGAATTACCG
66 TGTGTACAACCCATATAATTCAAAATGAATTTGTGAATGACCG
57684 TATCGACACTATGTGT
1 TATCGACACTATGTGT
57700 ACAATCTATG
Statistics
Matches: 105, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
107 56 0.53
108 49 0.47
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (108 bp):
TATCGACACTATGTGTGCAACCCACGGAATTCATAATGAATTTATGAATGACCGTATCAGCACTA
TGTGTACAACCCATATAATTCAAAATGAATTTGTGAATGACCG
Found at i:57720 original size:54 final size:53
Alignment explanation
Indices: 57504--57733 Score: 214
Period size: 54 Copynumber: 4.3 Consensus size: 53
57494 GGAGTTCATT
* *
57504 ATGAATTTATGAATGATCGTATCAGCACTATGTGTACAACCCAT-ATAATTCAA-A
1 ATGAATTTATGAATTACCGTATCA-CACTATGTGTACAACCCATGA-AATT-AATA
* * * ** * * * *
57558 ATGAGTTTTTGAATGACCGTATTGGCACTATGTGTGCAACCCACGGAATTCATA
1 ATGAATTTATGAATTACCGTA-TCACACTATGTGTACAACCCATGAAATTAATA
* * * * *
57612 ATGAGTTTGTGAATTACCGTATCACACTATGTGTCCAACCCATGTAATTCATA
1 ATGAATTTATGAATTACCGTATCACACTATGTGTACAACCCATGAAATTAATA
* * *
57665 ATGAATTTGTGAATTACCGTATCGACACTATGTGTACAATCTATGAAATTAATA
1 ATGAATTTATGAATTACCGTATC-ACACTATGTGTACAACCCATGAAATTAATA
57719 AT-AAGTTTATGAATT
1 ATGAA-TTTATGAATT
57734 TCCATTTCGG
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
53 52 0.35
54 95 0.64
55 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (53 bp):
ATGAATTTATGAATTACCGTATCACACTATGTGTACAACCCATGAAATTAATA
Found at i:57720 original size:107 final size:108
Alignment explanation
Indices: 57469--57733 Score: 282
Period size: 107 Copynumber: 2.5 Consensus size: 108
57459 CTATGTGTAC
* * * * * * * * *
57469 TATCGACATTATGTGTGCAACCTACGGAGTTCATTATGAA-TTTATGAATGATCGTATCAGCACT
1 TATCGACACTATGTGTACAACCCACGAAATTAATAAT-AAGTTTATGAATTACCGTATCAGCACT
* *
57533 ATGTGTACAACCCATATAATTCAAAATGAGTTTTTGAATGACCG
65 ATGTGTACAACCCATATAATTCAAAATGAATTTGTGAATGACCG
* * * * * * *
57577 TATTGGCACTATGTGTGCAACCCACGGAATTCATAATGAGTTTGTGAATTACCGTATCA-CACTA
1 TATCGACACTATGTGTACAACCCACGAAATTAATAATAAGTTTATGAATTACCGTATCAGCACTA
* * * *
57641 TGTGTCCAACCCATGTAATTCATAATGAATTTGTGAATTACCG
66 TGTGTACAACCCATATAATTCAAAATGAATTTGTGAATGACCG
* * *
57684 TATCGACACTATGTGTACAATCTATGAAATTAATAATAAGTTTATGAATT
1 TATCGACACTATGTGTACAACCCACGAAATTAATAATAAGTTTATGAATT
57734 TCCATTTCGG
Statistics
Matches: 130, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
107 83 0.64
108 47 0.36
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (108 bp):
TATCGACACTATGTGTACAACCCACGAAATTAATAATAAGTTTATGAATTACCGTATCAGCACTA
TGTGTACAACCCATATAATTCAAAATGAATTTGTGAATGACCG
Found at i:67424 original size:31 final size:32
Alignment explanation
Indices: 67389--67462 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
67379 GATTGGGCCT
*
67389 ATGCAATGGACTATAT-AATGGACTCTTTTAA
1 ATGCAATGGACTATATAAATGGACTCTTGTAA
** *
67420 ATGCAATATACTATGTAAATGGACTCTTGTAA
1 ATGCAATGGACTATATAAATGGACTCTTGTAA
67452 ATGCAATGGAC
1 ATGCAATGGAC
67463 CTTTATTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 13 0.36
32 23 0.64
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (32 bp):
ATGCAATGGACTATATAAATGGACTCTTGTAA
Found at i:67572 original size:15 final size:15
Alignment explanation
Indices: 67543--67600 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
67533 GATTACTATT
* *
67543 TATAATATGCAACTA
1 TATAATATACTACTA
67558 TATAATATACTACTA
1 TATAATATACTACTA
* * *
67573 TGTAACATAATAACTA
1 TATAATATACT-ACTA
*
67589 TATAGTATACTA
1 TATAATATACTA
67601 ATTACTTAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (15 bp):
TATAATATACTACTA
Done.