Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007016.1 Hibiscus syriacus cultivar Beakdansim tig00018121_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: 70071
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2037 original size:29 final size:29
Alignment explanation
Indices: 2004--2063 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1994 CAAAACAGAA
* *
2004 GATTTATCTCGTTTGAGGTAGTTTCCCTT
1 GATTTATCTCGCTTGAGATAGTTTCCCTT
2033 GATTTATCTCGCTTGAGATAGTTTCCCTT
1 GATTTATCTCGCTTGAGATAGTTTCCCTT
2062 GA
1 GA
2064 AACAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (29 bp):
GATTTATCTCGCTTGAGATAGTTTCCCTT
Found at i:2131 original size:71 final size:70
Alignment explanation
Indices: 2034--2237 Score: 224
Period size: 71 Copynumber: 2.9 Consensus size: 70
2024 GTTTCCCTTG
* *
2034 ATTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 ATTT-TCTCTCTTGAGA-AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
2099 AAACA-A
64 AAACACA
* * *
2105 ATTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGATAGTTTTTC-TG
1 ATTT-TCTCTCTTGAGA-AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
2169 AAACACA
64 AAACACA
** * *
2176 A----AACT-TTGAGAACGTTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAGTTTTCTCTTG
1 ATTTTCTCTCTTGAGAA-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG-TTTCTCTTG
2236 AA
64 AA
2238 GCATAAACTT
Statistics
Matches: 115, Mismatches: 14, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
64 1 0.01
65 39 0.34
66 7 0.06
67 4 0.03
70 7 0.06
71 57 0.50
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (70 bp):
ATTTTCTCTCTTGAGAAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAA
ACACA
Found at i:2173 original size:35 final size:36
Alignment explanation
Indices: 2039--2163 Score: 189
Period size: 36 Copynumber: 3.5 Consensus size: 36
2029 CCTTGATTTA
* *
2039 TCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
*
2075 TCTCTCTTGAGACAGTTTCTCTTGAAACAAA-TTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
*
2110 TCTCTCTTGAGACAGTTTCCCTCGAAACAAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
* *
2146 TCTCCCTTGAGATAGTTT
1 TCTCTCTTGAGACAGTTT
2164 TTCTGAAACA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 33 0.41
36 48 0.59
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
Found at i:2378 original size:29 final size:30
Alignment explanation
Indices: 2346--2418 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
2336 TTTTGAGACA
* * *
2346 GTTTCTCTTGAAACATAAACT-TTGAAAAT
1 GTTTCCCTTGAAACACAAAATCTTGAAAAT
* * *
2375 GTTTCCCTTGAGACACAAAATCTTGAGATT
1 GTTTCCCTTGAAACACAAAATCTTGAAAAT
2405 GTTTCCCTTGAAAC
1 GTTTCCCTTGAAAC
2419 TGTTTTATCT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (30 bp):
GTTTCCCTTGAAACACAAAATCTTGAAAAT
Found at i:2434 original size:120 final size:123
Alignment explanation
Indices: 2217--2506 Score: 339
Period size: 120 Copynumber: 2.4 Consensus size: 123
2207 TTTATCTCCC
*
2217 TTGAGACAGTTTTCTCTTGAAGCATAAACTTT-AAAATG-TTCCC-TGAGACACAAAATCTTTGA
1 TTGAGACAG-TTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAGACACAAAATCTTTGA
* ** ***
2279 GATCGTTTCCCTTGAAACGAATTTTGTCCCCTTGAGACAGTTTCAT-TTGAAACA-AGTTT
65 GATCGTTTCCCTTGAAACG-ATTTTATCCCCTTGAGACAAATT-ATCTTGAAACACAACCT
2338 TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAGACACAAAATC-TTGAG
1 TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAGACACAAAATCTTTGAG
* *
2402 ATTGTTTCCCTTGAAACTG-TTTTAT-CTCTTGAGACAAATTATCTTGAAACACCAACCT
66 ATCGTTTCCCTTGAAAC-GATTTTATCCCCTTGAGACAAATTATCTTGAAACA-CAACCT
** * *
2460 TTGAGACAG-TT-TCTTGAAACACCAACATTTGAGATTGTTTCCCTTGA
1 TTGAGACAGTTTCTCTTGAAACATAAAC-TTTGAAAATGTTTCCCTTGA
2507 ACAAGAAATT
Statistics
Matches: 148, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
119 2 0.01
120 54 0.36
121 40 0.27
122 37 0.25
123 15 0.10
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (123 bp):
TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAGACACAAAATCTTTGAG
ATCGTTTCCCTTGAAACGATTTTATCCCCTTGAGACAAATTATCTTGAAACACAACCT
Found at i:2466 original size:30 final size:28
Alignment explanation
Indices: 2430--2493 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
2420 GTTTTATCTC
*
2430 TTGAGACAAATTATCTTGAAACACCAACCT
1 TTGAGAC-AATT-TCTTGAAACACCAACAT
*
2460 TTGAGACAGTTTCTTGAAACACCAACAT
1 TTGAGACAATTTCTTGAAACACCAACAT
2488 TTGAGA
1 TTGAGA
2494 TTGTTTCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 22 0.69
29 3 0.09
30 7 0.22
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (28 bp):
TTGAGACAATTTCTTGAAACACCAACAT
Found at i:3282 original size:91 final size:91
Alignment explanation
Indices: 2923--3537 Score: 770
Period size: 91 Copynumber: 6.9 Consensus size: 91
2913 AAGGGATTGA
* * *
2923 CATTTCAAATGGAGAGTTCATAAT--G-AGAACTCATCCAACGAGGGAGAAGAAGTTCATAATAA
1 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
*
2985 GAAGAACTTGTTCAAACCTTGGCTCAG
66 GAAGAACTTGTTC-AACCTTGTCTCAG
* *
3012 CATTTCCAGCGGAGAGCTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
1 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
*
3077 GAAGAACTTGTTCAACCTTGGCTCAG
66 GAAGAACTTGTTCAACCTTGTCTCAG
* *
3103 CATTTCCAG-CGAGAGTTCATAAT--GAAG-ACTCATCCAACGA---A-AAGAAGTTTATAATGA
1 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
*
3160 GAATAACTTGTTCAACCTTGGT-TCAAG
66 GAAGAACTTGTTCAACCTT-GTCTC-AG
*
3187 -ATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
1 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
* * *
3251 GAATAATTTGTTCAACCTTATCTCAG
66 GAAGAACTTGTTCAACCTTGTCTCAG
*
3277 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
1 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
* *
3342 GAAGAACTTGTTCAACCTTATCTCAA
66 GAAGAACTTGTTCAACCTTGTCTCAG
*
3368 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATGA
1 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
* * * *
3433 GAAGAACTTATT-AGACCCTGCCT-TG
66 GAAGAACTTGTTCA-ACCTTGTCTCAG
* * * * * *
3458 ACGTTACCAGTGGAGAGTTCATCAT--G-AGAACTCATACAAC-A-AGA-AAAAAGTTCATAATG
1 -CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
*
3517 AG-AGAACTTGTTCAACTTTGT
65 AGAAGAACTTGTTCAACCTTGT
3538 TCGACTTCTT
Statistics
Matches: 470, Mismatches: 38, Indels: 41
0.86 0.07 0.07
Matches are distributed among these distances:
83 43 0.09
84 30 0.06
85 16 0.03
86 6 0.01
87 27 0.06
88 17 0.04
89 21 0.04
90 17 0.04
91 244 0.52
92 49 0.10
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (91 bp):
CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTGTCTCAG
Found at i:5713 original size:18 final size:18
Alignment explanation
Indices: 5690--5755 Score: 132
Period size: 18 Copynumber: 3.7 Consensus size: 18
5680 AAACTCAGTA
5690 TTTTATTAAAATAAAATG
1 TTTTATTAAAATAAAATG
5708 TTTTATTAAAATAAAATG
1 TTTTATTAAAATAAAATG
5726 TTTTATTAAAATAAAATG
1 TTTTATTAAAATAAAATG
5744 TTTTATTAAAAT
1 TTTTATTAAAAT
5756 TACCTGATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTTATTAAAATAAAATG
Found at i:12468 original size:31 final size:30
Alignment explanation
Indices: 12428--12521 Score: 116
Period size: 31 Copynumber: 3.1 Consensus size: 30
12418 GATCCCTGAT
12428 TTTAGATAAAAATATCAATTTAACTTTTAAA
1 TTTAGAT-AAAATATCAATTTAACTTTTAAA
* * *
12459 TTTAAATAAAATATTAATTCAACTTTTAAA
1 TTTAGATAAAATATCAATTTAACTTTTAAA
* **
12489 CTTTAGATAAAATATCAATCTAACCCTTAAA
1 -TTTAGATAAAATATCAATTTAACTTTTAAA
12520 TT
1 TT
12522 CGACCAAGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
30 23 0.43
31 30 0.57
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTAGATAAAATATCAATTTAACTTTTAAA
Found at i:14378 original size:21 final size:21
Alignment explanation
Indices: 14336--14481 Score: 204
Period size: 21 Copynumber: 6.9 Consensus size: 21
14326 TTACCTTCAA
*
14336 TATGAAGTGGTATTCAT-GTCTT
1 TATGAA-TGGTCTTC-TCGTCTT
*
14358 TATGAATGGTCTTCTCATCTT
1 TATGAATGGTCTTCTCGTCTT
* *
14379 TATGAATGATCTTCTCGTCCT
1 TATGAATGGTCTTCTCGTCTT
* *
14400 TGTGAATGGTTTTCTCGTCTT
1 TATGAATGGTCTTCTCGTCTT
*
14421 TGTGAATGGTCTTCTCGTCTT
1 TATGAATGGTCTTCTCGTCTT
14442 TATGAATGGTCTTCTCGTCTT
1 TATGAATGGTCTTCTCGTCTT
14463 TATGAATGGTCTTCTCGTC
1 TATGAATGGTCTTCTCGTC
14482 CTTGGTATGA
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
20 1 0.01
21 105 0.94
22 6 0.05
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (21 bp):
TATGAATGGTCTTCTCGTCTT
Found at i:18283 original size:17 final size:16
Alignment explanation
Indices: 18261--18293 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
18251 TAAATAACAT
18261 TAATATTATTAATAATA
1 TAATATTA-TAATAATA
18278 TAATATTATAATAATA
1 TAATATTATAATAATA
18294 ATTATATCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTATAATAATA
Found at i:21739 original size:20 final size:21
Alignment explanation
Indices: 21699--21739 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21689 ATTGAATCGA
*
21699 TTTCATCCCCAATTCCCTCTT
1 TTTCAACCCCAATTCCCTCTT
*
21720 TTTCAACCCTAATT-CCTCTT
1 TTTCAACCCCAATTCCCTCTT
21740 CCATCATGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTCAACCCCAATTCCCTCTT
Found at i:24855 original size:20 final size:21
Alignment explanation
Indices: 24815--24855 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24805 ATTAAATCGA
*
24815 TTTCATCCCCAATTCCCTCTT
1 TTTCAACCCCAATTCCCTCTT
*
24836 TTTCAACCCTAATT-CCTCTT
1 TTTCAACCCCAATTCCCTCTT
24856 CCATCATGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTCAACCCCAATTCCCTCTT
Found at i:27525 original size:20 final size:20
Alignment explanation
Indices: 27492--27529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27482 TAATAAAATT
27492 ATAAAAAAAATATTTTAACA
1 ATAAAAAAAATATTTTAACA
* *
27512 ATAAATAAATTATTTTAA
1 ATAAAAAAAATATTTTAA
27530 TATTTTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAAAAAATATTTTAACA
Found at i:27558 original size:22 final size:22
Alignment explanation
Indices: 27532--27573 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27522 TATTTTAATA
27532 TTTTAAGA-ATAATAATATTAAG
1 TTTTAAGATA-AATAATATTAAG
*
27554 TTTTATGATAAATAATATTA
1 TTTTAAGATAAATAATATTA
27574 TTTATTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTAAGATAAATAATATTAAG
Found at i:32958 original size:40 final size:40
Alignment explanation
Indices: 32914--32991 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
32904 TTTTATAACT
*
32914 TTTAATAATT-ATGAGACTT-AACAAAATAATACTCTATATA
1 TTTAATAATTGA-GAGA-TTCAACAAAATAATACCCTATATA
* *
32954 TTTAATAGTTGAGAGATTCAATAAAATAATACCCTATA
1 TTTAATAATTGAGAGATTCAACAAAATAATACCCTATA
32992 ATGAGACCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.06
40 30 0.91
41 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (40 bp):
TTTAATAATTGAGAGATTCAACAAAATAATACCCTATATA
Found at i:35307 original size:28 final size:27
Alignment explanation
Indices: 35262--35317 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
35252 ACTAGTGGCC
* *
35262 ATGTGTAGTGATATTCTAACTATATGAT
1 ATGTGTAGCGATATTCTAA-TATACGAT
35290 ATGTGTAGCGATCA-TCTAATATACGAT
1 ATGTGTAGCGAT-ATTCTAATATACGAT
35317 A
1 A
35318 ATGAGTGACG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 16 0.64
29 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (27 bp):
ATGTGTAGCGATATTCTAATATACGAT
Found at i:37698 original size:65 final size:64
Alignment explanation
Indices: 37626--37781 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 64
37616 TACACTAGGG
* * * *
37626 GTGCATCGGTACACTAATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCATGG-C
37690 T
64 T
* **
37691 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGCT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGCT
*
37755 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATACATTCGA
37782 AATAGGGTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 28 0.34
65 53 0.64
66 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGCT
Found at i:39963 original size:14 final size:13
Alignment explanation
Indices: 39930--39967 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
39920 TAATGGGAAA
39930 AATTTTGAAAACT
1 AATTTTGAAAACT
39943 AATTTTGATAAAC-
1 AATTTTGA-AAACT
39956 AATGTTTGAAAA
1 AAT-TTTGAAAA
39968 ATCAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (13 bp):
AATTTTGAAAACT
Found at i:40486 original size:23 final size:22
Alignment explanation
Indices: 40454--40525 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
40444 TAGCATAGTA
40454 CATCGATGCACATTCAAGGAATG
1 CATCGATGCACATTCAAGG-ATG
*
40477 CATCGGTGCATC-TTCAA-GATG
1 CATCGATGCA-CATTCAAGGATG
* *
40498 TATCGATGCACATTCAAGAGATA
1 CATCGATGCACATTCAAG-GATG
40521 CATCG
1 CATCG
40526 GTACACTGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
20 1 0.03
21 16 0.40
22 1 0.03
23 21 0.52
24 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGATG
Found at i:40505 original size:44 final size:44
Alignment explanation
Indices: 40455--40551 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
40445 AGCATAGTAC
* *
40455 ATCGATGCACATTCAAG-GAATGCATCGGTGCATCT-TCA-AGATGT
1 ATCGATGCACATTCAAGAG-ATACATCGGTACA-CTGTCATAG-TGT
40499 ATCGATGCACATTCAAGAGATACATCGGTACACTGTCATAGTGT
1 ATCGATGCACATTCAAGAGATACATCGGTACACTGTCATAGTGT
40543 ATCGATGCA
1 ATCGATGCA
40552 TTGCGCATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
43 2 0.04
44 43 0.90
45 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGAGATACATCGGTACACTGTCATAGTGT
Found at i:40513 original size:21 final size:21
Alignment explanation
Indices: 40454--40516 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
40444 TAGCATAGTA
40454 CATCGATGCACATTCAAGGAATG
1 CATCGATGCACATTCAA-G-ATG
*
40477 CATCGGTGCATC-TTCAAGATG
1 CATCGATGCA-CATTCAAGATG
*
40498 TATCGATGCACATTCAAGA
1 CATCGATGCACATTCAAGA
40517 GATACATCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
22 1 0.03
23 14 0.40
24 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (21 bp):
CATCGATGCACATTCAAGATG
Found at i:46392 original size:65 final size:64
Alignment explanation
Indices: 46319--46471 Score: 173
Period size: 65 Copynumber: 2.4 Consensus size: 64
46309 TACACTAGGG
* * * *
46319 GTGCATCGGTACACTAATTACATTCAATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCAAGGTC
1 GTGCATCGGTACACAAAATACATTCAATATTTCAATAA-AGCCAAGAGTGCATCGATGCAAGGT-
46383 T
64 T
* * ** *
46384 GTGCATCGGTACACAAAATGCATTCGATATTTCAATAAATTCAAGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACACAAAATACATTCAATATTTCAATAAAGCCAAGAGTGCATCGATGCAAGGTT
* * *
46448 TTGCATCAGTACACAAAATGCATT
1 GTGCATCGGTACACAAAATACATT
46472 TGAAATAGGG
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
64 23 0.30
65 51 0.67
66 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATACATTCAATATTTCAATAAAGCCAAGAGTGCATCGATGCAAGGTT
Found at i:48558 original size:18 final size:19
Alignment explanation
Indices: 48535--48577 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
48525 CAGTAATCCT
48535 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
48553 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
48573 ATTCC
1 ATTCC
48578 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:48565 original size:20 final size:20
Alignment explanation
Indices: 48540--48577 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
48530 ATCCTATTCC
48540 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
48560 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
48578 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:48961 original size:14 final size:14
Alignment explanation
Indices: 48942--48978 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
48932 AATTAATATT
48942 AAGTTAATCAATAA
1 AAGTTAATCAATAA
48956 AAGTTAATCAATAA
1 AAGTTAATCAATAA
*
48970 AAATTAATC
1 AAGTTAATC
48979 TAGGGGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (14 bp):
AAGTTAATCAATAA
Found at i:57716 original size:2 final size:2
Alignment explanation
Indices: 57709--57737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57699 AGGAAAAATG
57709 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 A
57738 GGAAGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58240 original size:23 final size:23
Alignment explanation
Indices: 58207--58274 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
58197 AATCTTATAT
58207 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
58230 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
58253 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
58275 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:60459 original size:20 final size:20
Alignment explanation
Indices: 60434--60471 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
60424 TTTGGTTCAC
60434 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
60454 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
60472 GTAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:60686 original size:23 final size:23
Alignment explanation
Indices: 60660--60711 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
60650 TTAAATTCAT
60660 AAAATTTATATAATTTTTTTTAC
1 AAAATTTATATAATTTTTTTTAC
60683 AAAATTTATATAATTTTTTTTAC
1 AAAATTTATATAATTTTTTTTAC
60706 AAAATT
1 AAAATT
60712 GAAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
AAAATTTATATAATTTTTTTTAC
Done.