Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001274.1 Hibiscus syriacus cultivar Beakdansim tig00002502_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: 59741
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3353 original size:22 final size:21
Alignment explanation
Indices: 3306--3353 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
3296 TTTGTATTGA
*
3306 ACATTTTGCATTTCCATTTCT
1 ACATTTTACATTTCCATTTCT
* * *
3327 GCATTTTCACATTTGCATTTTT
1 ACATTTT-ACATTTCCATTTCT
3349 ACATT
1 ACATT
3354 CACATCATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (21 bp):
ACATTTTACATTTCCATTTCT
Found at i:5990 original size:22 final size:21
Alignment explanation
Indices: 5963--6033 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
5953 CATCGAACAA
5963 AAAGAAAAGAGAAAAAATAGA-
1 AAAGAAAAGA-AAAAAATAGAG
*
5984 AGAAGAAAAAAAAAAAATAGAG
1 A-AAGAAAAGAAAAAAATAGAG
*
6006 AAAGAAAAGAAAATAATA-AG
1 AAAGAAAAGAAAAAAATAGAG
6026 AAAGAAAA
1 AAAGAAAA
6034 AATAAGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.22
21 26 0.58
22 9 0.20
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (21 bp):
AAAGAAAAGAAAAAAATAGAG
Found at i:5993 original size:16 final size:15
Alignment explanation
Indices: 5961--6018 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
5951 CTCATCGAAC
5961 AAAAAGAAAAGAGAA
1 AAAAAGAAAAGAGAA
5976 AAAATAGAAGAAGA-AA
1 AAAA-AGAA-AAGAGAA
*
5992 AAAAAAAAATAGAGAA
1 AAAAAGAAA-AGAGAA
6008 AGAAAAGAAAA
1 A-AAAAGAAAA
6019 TAATAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 1 0.03
15 10 0.28
16 14 0.39
17 11 0.31
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAGAGAA
Found at i:6000 original size:21 final size:22
Alignment explanation
Indices: 5963--6044 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 22
5953 CATCGAACAA
*
5963 AAAGAAAAGAGAAAAAATAGAAG
1 AAAGAAAA-AAAAAAAATAGAAG
5986 -AAGAAAAAAAAAAAATAG-AG
1 AAAGAAAAAAAAAAAATAGAAG
* *
6006 AAAGAAAAGAAAATAAT--AAG
1 AAAGAAAAAAAAAAAATAGAAG
*
6026 AAAGAAAAAATAAGAAATA
1 AAAGAAAAAA-AAAAAATA
6045 AATCAAGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 13 0.27
21 29 0.59
22 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAGAAAAAAAAAAAATAGAAG
Found at i:6007 original size:17 final size:16
Alignment explanation
Indices: 5986--6042 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
5976 AAAATAGAAG
5986 AAGAAAAAAAAAAAAT
1 AAGAAAAAAAAAAAAT
*
6002 AGAGAAAGAAAAGAAAAT
1 A-AGAAA-AAAAAAAAAT
* *
6020 AATAAGAAAGAAAAAAT
1 AAGAA-AAAAAAAAAAT
6037 AAGAAA
1 AAGAAA
6043 TAAATCAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.06
17 20 0.61
18 11 0.33
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (16 bp):
AAGAAAAAAAAAAAAT
Found at i:6012 original size:43 final size:42
Alignment explanation
Indices: 5963--6044 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 42
5953 CATCGAACAA
5963 AAAGAAAAGAGAAAAAAT-AGAAGAAGAAAAAA-AAAAAATAGAG
1 AAAGAAAAGA-AAAAAATAAG-A-AAGAAAAAATAAAAAATAGAG
* *
6006 AAAGAAAAGAAAATAATAAGAAAGAAAAAATAAGAAATA
1 AAAGAAAAGAAAAAAATAAGAAAGAAAAAATAAAAAATA
6045 AATCAAGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 9 0.26
42 14 0.40
43 12 0.34
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (42 bp):
AAAGAAAAGAAAAAAATAAGAAAGAAAAAATAAAAAATAGAG
Found at i:6039 original size:14 final size:15
Alignment explanation
Indices: 6011--6042 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
6001 TAGAGAAAGA
6011 AAAGAAAATAATAAG
1 AAAGAAAATAATAAG
6026 AAAGAAAA-AATAAG
1 AAAGAAAATAATAAG
6040 AAA
1 AAA
6043 TAAATCAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAGAAAATAATAAG
Found at i:8308 original size:62 final size:62
Alignment explanation
Indices: 8220--8491 Score: 219
Period size: 62 Copynumber: 4.2 Consensus size: 62
8210 TTTAGAAATT
* * *
8220 TCAATCATTTACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTCTCGAGTAGAG
1 TCAATCCTTGACTTTCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTCTCGAGTAGAG
* * * * * **
8282 TCAATACTTGACTTTCACATGAAGAGAAGTCAA-CATTTTTTA-TCTTTGACTCCCTAACAGAG
1 TCAATCCTTGACTTTCTCATGAAGAGAAGTCAATC-TTTGTTATTC-TTGACTCTCGAGTAGAG
* * * * * *
8344 TCAATCCCTGACTTAT-TCATGAAGAGAAGTCAATCTTAGTTATCCATGACTTATTCGTGAAGTG
1 TCAATCCTTGACTT-TCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGAC-T-CTC--G-AGTA
8408 GAG
60 GAG
* * *
8411 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTT-ACTCCCTTGCGAAGAA
1 TCAATCCTTGACTTTCTCATGAAGAGAAGTCAATCTTTGTTATT-CTTGACT--C-T-CG-AGTA
8475 GAG
60 GAG
8478 TCAATCCTTGACTT
1 TCAATCCTTGACTT
8492 CCTCGTAAAG
Statistics
Matches: 162, Mismatches: 33, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
61 3 0.02
62 84 0.52
63 4 0.02
64 1 0.01
66 1 0.01
67 65 0.40
68 3 0.02
69 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (62 bp):
TCAATCCTTGACTTTCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTCTCGAGTAGAG
Found at i:8465 original size:129 final size:124
Alignment explanation
Indices: 8236--8465 Score: 284
Period size: 129 Copynumber: 1.8 Consensus size: 124
8226 ATTTACTTCC
* * * *
8236 TCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTCTCGAGTAGAGTCAATACTTGACTTTCACA
1 TCATGAAGAGAAGTCAATCTTAGTTATCCATGACTCTCGAGTAGAGTCAATACTTGACTTCCACA
* *
8301 TGAAGAGAAGTCAACATTTTTTATCTTTGACTCCCTAACAGAGTCAATCCCTGACTTAT
66 TGAAGAGAAGTCAACATTTGTTATCCTTGACTCCCTAACAGAGTCAATCCCTGACTTAT
* * *
8360 TCATGAAGAGAAGTCAATCTTAGTTATCCATGACTTATTCGTGAAGTGGAGTCAATCCTTGACTT
1 TCATGAAGAGAAGTCAATCTTAGTTATCCATGAC-T-CTC--G-AGTAGAGTCAATACTTGACTT
* *
8425 CCTCGTGAAGAGAAGTCAATC-TTTGTTATTCCTT-ACTCCCT
61 CCACATGAAGAGAAGTCAA-CATTTGTTA-TCCTTGACTCCCT
8466 TGCGAAGAAG
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
124 31 0.35
125 1 0.01
126 2 0.02
128 1 0.01
129 48 0.55
130 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (124 bp):
TCATGAAGAGAAGTCAATCTTAGTTATCCATGACTCTCGAGTAGAGTCAATACTTGACTTCCACA
TGAAGAGAAGTCAACATTTGTTATCCTTGACTCCCTAACAGAGTCAATCCCTGACTTAT
Found at i:8692 original size:89 final size:89
Alignment explanation
Indices: 8531--9434 Score: 1056
Period size: 89 Copynumber: 10.1 Consensus size: 89
8521 TTTGATTTAC
* * * * * * * *
8531 TCTTCCTGAAAGACTAACGAAGCAAAATAAATCTTGAGTCTGATCTCCTCGGAAGAGCATAGGAG
1 TCTTCCCGAAAGAGTAGCGAAGC-AAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAG
* * *
8596 CAGATTCTTCTTATGTCATATTTGC
65 CAGATTCTTCTTATTTCAGATTTGG
* * *
8621 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTTGAGTTTGATCTCCCCGGAAGAGTAGAGGAAC
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
* **
8686 AAATTCTTCTTATCCCAGATTTGG
66 AGATTCTTCTTATTTCAGATTTGG
** * * * * * *
8710 TCTTCTTGAAAGAGTA-CTGAAGAAAATCAATCTCGAGTTTAATCT-CCCAGAAGAGTAGTGGAA
1 TCTTCCCGAAAGAGTAGC-GAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAG
* * *
8773 CAGATTCCTCTTATATCAGATTTGT
65 CAGATTCTTCTTATTTCAGATTTGG
** * * * * * *
8798 TCTTCCTAAAAAAGTAACGAAGTAAATCAATCTTGAGTCTGATATCCTCGGAAGAGTAGAGGAGC
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
8863 AGATTCTTCTTATTTCAGATTTGG
66 AGATTCTTCTTATTTCAGATTTGG
* ** * * * * *
8887 TTTTATCGAAAGAGTAGAGAAGAAAATCAATCTCGAGTCTGATCTCCCCGCAAGAGTAGGGGAAC
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
*
8952 ATATTCTTCTTATTTCAGATTTGG
66 AGATTCTTCTTATTTCAGATTTGG
* * * *
8976 TCTTCCCGAAATAGTAGCGAAGCAAATTAATCTCGAGTCTGATCTCCCTGGAAGAGTAGAGGAGT
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
*
9041 TGATTCTTCTTATTTCAGATTTGG
66 AGATTCTTCTTATTTCAGATTTGG
*
9065 TCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
* *
9130 AGATTCTTCTTATTTCAGTTTTTG
66 AGATTCTTCTTATTTCAGATTTGG
* * * * * *
9154 TCTTCTCGAAAGAGTAGCGAAGAAAATCAATCTTGAGTCTAATCTCCCCGGATGAGTAGAGCAGC
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
* *
9219 AGAATCTTCATATTTCAGATTTGG
66 AGATTCTTCTTATTTCAGATTTGG
* * * * *
9243 TCTTCCCGAAAGAGTAGCAAAGCAAATCAATCTCGAATCTGATCTCCCGGGAATAGTATAGGAGC
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
* * * *
9308 AAATTCTTTTTATTTCACACTTGG
66 AGATTCTTCTTATTTCAGATTTGG
* * * * * * * * *
9332 TCTTCCCGAAAGAGTAGTGATGCAAATCAATCTCGCAGTGTGGTCTCCCCAGAAAACTAAATGAG
1 TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCG-AGTCTGATCTCCCCGGAAGAGTAGAGGAG
9397 CAGATTCTTCTTATTTCAGATTTGG
65 CAGATTCTTCTTATTTCAGATTTGG
9422 TCTTCCCGAAAGA
1 TCTTCCCGAAAGA
9435 TCAGCGTTTT
Statistics
Matches: 687, Mismatches: 123, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
88 72 0.10
89 541 0.79
90 74 0.11
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (89 bp):
TCTTCCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAGC
AGATTCTTCTTATTTCAGATTTGG
Found at i:9578 original size:82 final size:82
Alignment explanation
Indices: 9459--10234 Score: 785
Period size: 82 Copynumber: 9.4 Consensus size: 82
9449 AAATTTCTCG
* * *
9459 AGTCTTATCT-CCCTGCAA-GAATAGCGGAGCAGACTCGTCTTCCTAAATTGATCTGACTACCCG
1 AGTCTGATCTCCCCTG-AATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCG
*
9522 AAAAAGAGGAACAAATCA
65 AAAAAGAGGAACAGATCA
* *
9540 AGTCTGATCTCCCCT-AATTCAATAGTGGAGTAGACTCGTGTCTTCCAAAATTGATCTGACTACC
1 AGTCTGATCTCCCCTGAA-TGAATAGTGGAGCAGACTC--GTCTTCCAAAATTGATCTGACTACC
* *
9604 C-AAAACAAAGGAACATGTGTCA
63 CGAAAA-AGAGGAACA-G-ATCA
* * * * ** * *
9626 AGTTTGATCTCCCATGAATGAGTAGTGGAACAGACAGGTCTTCCAAAATTGACCTTACTACCCG-
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGA
9690 AAAAGAAGGAACAGATCA
66 AAAAG-AGGAACAGATCA
* * * * *
9708 AGTCTGATCTCCCCTAAATAAATAGTAGAGCAGACTCATCTTCCAAAATTGATATGACTACCCGA
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGA
9773 AAAAGAGGAACAGATCA
66 AAAAGAGGAACAGATCA
* * * *
9790 AGTCTGATCTCCTCTGAATGAATAGTGGAGTAGACTCGACTTCCAAAATTGATTTGACTACCCGA
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGA
* *
9855 AAAAGAGGAACAAATTA
66 AAAAGAGGAACAGATCA
* * * *
9872 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACCCATCTTCCAAAATTGAT-TAAACTACCTG
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCT-GACTACCCG
* *
9936 -AAAAGAGGGTACAGTTCA
65 AAAAAGA-GGAACAGATCA
* * * * ** * * *
9954 AGTATGATCTCCCCTAAATGATTAATAAAGTAGACTCGTCTTCCAAAATTGATTTGAATACCCGA
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGA
*
10019 AAAAGAGGAACATATCA
66 AAAAGAGGAACAGATCA
* ** * * * * * *
10036 AGTTTGATCTATCTTGAAAGAATAGTGGAGAACATTCGTCTTCCAAAATTGATCTGACTACCCAA
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGA
*
10101 AAAAGAGAAACAGATCA
66 AAAAGAGGAACAGATCA
* * * * * * * * *
10118 ATTATGATCTCCCCTGAAAGATTAGTGAAGCATACCCAT-TCTCCAAAATTGATTTGACTACCCG
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCT-TCCAAAATTGATCTGACTACCCG
*
10182 AAAAAAGAGGAACATATCA
65 -AAAAAGAGGAACAGATCA
* * * *
10201 AGTTTGATCTCCCCTGAAAGAAGAGTAGAGCAGA
1 AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGA
10235 TTTCCCATCA
Statistics
Matches: 567, Mismatches: 110, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
80 2 0.00
81 17 0.03
82 389 0.69
83 61 0.11
84 67 0.12
86 29 0.05
87 2 0.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (82 bp):
AGTCTGATCTCCCCTGAATGAATAGTGGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGA
AAAAGAGGAACAGATCA
Found at i:10370 original size:3 final size:3
Alignment explanation
Indices: 10357--10402 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
10347 TCGTCATAGT
10357 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10403 AATAATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:10506 original size:18 final size:18
Alignment explanation
Indices: 10485--10526 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10475 CAAAGCAGAT
* *
10485 CCAGAACCTGATGCAGGC
1 CCAGAACCCGATCCAGGC
*
10503 CCAGAACCCGGTCCAGGC
1 CCAGAACCCGATCCAGGC
10521 CCAGAA
1 CCAGAA
10527 TCCAGACCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.38, G:0.26, T:0.07
Consensus pattern (18 bp):
CCAGAACCCGATCCAGGC
Found at i:30778 original size:33 final size:35
Alignment explanation
Indices: 30737--30816 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 35
30727 TCATTTAGGG
* *
30737 AAGC-ACTTCATTTATGCATCT-AGTCATTTAATA
1 AAGCTACTTCATTCATGCATCTAAGTCATTGAATA
* *
30770 AA-CTACTTCATTCATGCATTTAATTCATTGAATA
1 AAGCTACTTCATTCATGCATCTAAGTCATTGAATA
*
30804 AAGTTACTTCATT
1 AAGCTACTTCATT
30817 AATTAAATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 1 0.03
33 17 0.44
34 12 0.31
35 9 0.23
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (35 bp):
AAGCTACTTCATTCATGCATCTAAGTCATTGAATA
Found at i:30833 original size:17 final size:17
Alignment explanation
Indices: 30811--30860 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
30801 ATAAAGTTAC
* *
30811 TTCATTAATTAAATTGG
1 TTCATTAATTAAACTAG
* *
30828 TTCATTCATCAAACTAG
1 TTCATTAATTAAACTAG
*
30845 TTCATTTATTAAACTA
1 TTCATTAATTAAACTA
30861 AGTATTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:34840 original size:17 final size:18
Alignment explanation
Indices: 34814--34851 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
34804 ATGTTGTTCA
34814 TTAAAGCATGCATTGCAT
1 TTAAAGCATGCATTGCAT
* *
34832 TTAAA-CATGTATTTCAT
1 TTAAAGCATGCATTGCAT
34849 TTA
1 TTA
34852 GGGAAGTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TTAAAGCATGCATTGCAT
Found at i:34950 original size:17 final size:17
Alignment explanation
Indices: 34926--34976 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
34916 TGAATAAAGT
34926 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
34943 TGGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
34960 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
34977 CAACTCTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:40111 original size:26 final size:26
Alignment explanation
Indices: 40082--40131 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
40072 GAACTGAGTA
*
40082 AAATTTTGTTTCATTCAAATATCACC
1 AAATTTTGTTTCATTCAAACATCACC
40108 AAATTTTGTTTCATTCAAACATCA
1 AAATTTTGTTTCATTCAAACATCA
40132 ACAGTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (26 bp):
AAATTTTGTTTCATTCAAACATCACC
Found at i:48039 original size:21 final size:21
Alignment explanation
Indices: 48001--48045 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
47991 CAATTAAAAA
* ** *
48001 TCAAGGAGCTTTGTTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
48022 TCAAGGAGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
48043 TCA
1 TCA
48046 TAGCTTGTCT
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:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:52231 original size:3 final size:3
Alignment explanation
Indices: 52223--52267 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
52213 TTCTATTGTC
* *
52223 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52268 TATTTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:59306 original size:2 final size:2
Alignment explanation
Indices: 59299--59355 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
59289 CATTAAATTA
59299 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59339 AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
59356 CGTTCATTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:59316 original size:13 final size:12
Alignment explanation
Indices: 59299--59355 Score: 93
Period size: 11 Copynumber: 5.0 Consensus size: 12
59289 CATTAAATTA
59299 ATATATATATAT
1 ATATATATATAT
59311 AT-TATATATAT
1 ATATATATATAT
59322 ATATATATATAT
1 ATATATATATAT
59334 -TATATATATA-
1 ATATATATATAT
59344 ATATATATATAT
1 ATATATATATAT
59356 CGTTCATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 31 0.74
12 11 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATATATATAT
Done.