Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002102.1 Hibiscus syriacus cultivar Beakdansim tig00004300_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: 61869
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:938 original size:34 final size:38
Alignment explanation
Indices: 872--951 Score: 114
Period size: 36 Copynumber: 2.2 Consensus size: 38
862 ATATTATTTC
*
872 CATCACCATAATCCATCTTCCATTATCACGCCTAT-AT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAAT
*
909 CATC-CCATAGTCCATC-ACCA-TATCACGCCTATAAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAAT
944 CATCACCA
1 CATCACCA
952 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 12 0.31
35 9 0.23
36 14 0.36
37 4 0.10
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (38 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAAT
Found at i:10260 original size:932 final size:932
Alignment explanation
Indices: 8449--11126 Score: 5196
Period size: 932 Copynumber: 2.9 Consensus size: 932
8439 TAGTTCTATT
8449 GCATCCCT-TGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCAC
1 GCAT-CCTATGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCAC
* * *
8513 ATGGCAGCCTACTTGAATGCACATGGCTCTTATTGTAATTCTTTGGTGAGGTTGCAACAATAGGA
65 ATGGCAGCCTACTTGAATGCACATGGCTGTTATTGCAATTCTTTGGTGAGGTTGCAACCATAGGA
8578 TGATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGC
130 TGATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGC
8643 ATCTAGGTGACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGA
195 ATCTAGGTGACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGA
* * * *
8708 GTGTCTTGGTAGCTAACTAGGTGAGTTATAGCTTGATGAACTCAAGCTAGTTAGCTTTGGTCTTC
260 GTGTCTTGGTAGCTAACTAGGTGAGTTATTGCTTAATGAACTCAATCTAGTTACCTTTGGTCTTC
* *
8773 TCAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTTAGCAATTTGGT
325 TCAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTCAACAATTTGGT
8838 CCAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAACTAAGTTGAAGCTCCTTA
390 CCAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAACTAAGTTGAAGCTCCTTA
8903 TGTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGC
455 TGTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGC
8968 TAACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATT
520 TAACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATT
9033 AAGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGC
585 AAGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGC
9098 TATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCT
650 TATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCT
9163 AGGAGCTAAAATAAATGCATATGAGCTAACAAATGAATGATTAAGCATGCTGCCATTTCATGAAT
715 AGGAGCTAAAATAAATGCATATGAGCTAACAAATGAATGATTAAGCATGCTGCCATTTCATGAAT
9228 GTAATGAATCATGCTTAAATGGATGTGAGATTAATAAATACATGGTTTTGGCCGAATGGTTATGT
780 GTAATGAATCATGCTTAAATGGATGTGAGATTAATAAATACATGGTTTTGGCCGAATGGTTATGT
9293 GTTGGTTCGACCCTAAGGATGATTTGAATGTATTTGGAAGTTATTTGGTGCCAAAATGAAGAGGA
845 GTTGGTTCGACCCTAAGGATGATTTGAATGTATTTGGAAGTTATTTGGTGCCAAAATGAAGAGGA
9358 AAGTGTCTTTGGCCGAATAGGAA
910 AAGTGTCTTTGGCCGAATAGGAA
9381 GCATCCTATGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCACA
1 GCATCCTATGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCACA
9446 TGGCAGCCTACTTGAATGCACATGGCTGTTATTGCAATTCTTTGGTGAGGTTGCAACCATAGGAT
66 TGGCAGCCTACTTGAATGCACATGGCTGTTATTGCAATTCTTTGGTGAGGTTGCAACCATAGGAT
9511 GATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGCA
131 GATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGCA
*
9576 TCTAGGTAACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGAG
196 TCTAGGTGACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGAG
9641 TGTCTTGGTAGCTAACTAGGTGAGTTATTGCTTAATGAACTCAATCTAGTTACCTTTGGTCTTCT
261 TGTCTTGGTAGCTAACTAGGTGAGTTATTGCTTAATGAACTCAATCTAGTTACCTTTGGTCTTCT
9706 CAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTCAACAATTTGGTC
326 CAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTCAACAATTTGGTC
*
9771 CAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAGCTAAGTTGAAGCTCCTTAT
391 CAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAACTAAGTTGAAGCTCCTTAT
9836 GTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGCT
456 GTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGCT
9901 AACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATTA
521 AACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATTA
9966 AGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGCT
586 AGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGCT
10031 ATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCTA
651 ATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCTA
10096 GGAGCTAAAATAAATGCATATGAGCTAACAAATGAATGATTAAGCATGCTGCCATTTCATGAATG
716 GGAGCTAAAATAAATGCATATGAGCTAACAAATGAATGATTAAGCATGCTGCCATTTCATGAATG
10161 TAATGAATCATGCTTAAATGGATGTGAGATTAATAAATACATGGTTTTGGCCGAATGGTTATGTG
781 TAATGAATCATGCTTAAATGGATGTGAGATTAATAAATACATGGTTTTGGCCGAATGGTTATGTG
10226 TTGGTTCGACCCTAAGGATGATTTGAATGTATTTGGAAGTTATTTGGTGCCAAAATGAAGAGGAA
846 TTGGTTCGACCCTAAGGATGATTTGAATGTATTTGGAAGTTATTTGGTGCCAAAATGAAGAGGAA
10291 AGTGTCTTTGGCCGAATAGGAA
911 AGTGTCTTTGGCCGAATAGGAA
10313 GCATCCTATGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCACA
1 GCATCCTATGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCACA
10378 TGGCAGCCTACTTGAATGCACATGGCTGTTATTGCAATTCTTTGGTGAGGTTGCAACCATAGGAT
66 TGGCAGCCTACTTGAATGCACATGGCTGTTATTGCAATTCTTTGGTGAGGTTGCAACCATAGGAT
10443 GATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGCA
131 GATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGCA
10508 TCTAGGTGACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGAG
196 TCTAGGTGACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGAG
10573 TGTCTTGGTAGCTAACTAGGTGAGTTATTGCTTAATGAACTCAATCTAGTTACCTTTGGTCTTCT
261 TGTCTTGGTAGCTAACTAGGTGAGTTATTGCTTAATGAACTCAATCTAGTTACCTTTGGTCTTCT
10638 CAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTCAACAATTTGGTC
326 CAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTCAACAATTTGGTC
10703 CAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAACTAAGTTGAAGCTCCTTAT
391 CAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAACTAAGTTGAAGCTCCTTAT
10768 GTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGCT
456 GTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGCT
10833 AACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATTA
521 AACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATTA
10898 AGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGCT
586 AGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGCT
10963 ATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCTA
651 ATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCTA
* * * *
11028 GGAGATAAAATAAATGCTTATGAGCTAACAAATTAATGATTAAGCATGCTACCATTTCATGAATG
716 GGAGCTAAAATAAATGCATATGAGCTAACAAATGAATGATTAAGCATGCTGCCATTTCATGAATG
*
11093 TAATGAATCATGCTAAAATGGATGTGAGATTAAT
781 TAATGAATCATGCTTAAATGGATGTGAGATTAAT
11127 CTAACATATT
Statistics
Matches: 1727, Mismatches: 18, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
931 3 0.00
932 1724 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (932 bp):
GCATCCTATGGAGTTTTGGCGCCAATTTGATGTCACATGGAGTGCACATGCTTGAATGATGCACA
TGGCAGCCTACTTGAATGCACATGGCTGTTATTGCAATTCTTTGGTGAGGTTGCAACCATAGGAT
GATGTCTTGAAGTCCATGGAATGGAGATAGGCAGCAACTAGGCGTGACTTAGCTTCCAACGTGCA
TCTAGGTGACGTGGCATCCATTGGATAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGATGAG
TGTCTTGGTAGCTAACTAGGTGAGTTATTGCTTAATGAACTCAATCTAGTTACCTTTGGTCTTCT
CAGCTCCTCAGCTACTCTCTGAGCTTCTTCCAGCTACCTCTAGTCCACTTTTCAACAATTTGGTC
CAAAGCTCTCCTCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAACTAAGTTGAAGCTCCTTAT
GTGATGAAATGAGTTGCCATAATGTTCATGAGCTAGTGTTAACTGATATGCTTATCCTTTTAGCT
AACCAAGCTACCATAATATGCCTTGCTTTGTGTTTTAGCTATAGGAATAACAAACAAACAAATTA
AGCAACGTGTGAGCTCATTTAAGGTAAAATGCATGCTTTCGTGAGGTATTTGAGTGATGTAAGCT
ATGAATGCATGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTGTAAGACCTA
GGAGCTAAAATAAATGCATATGAGCTAACAAATGAATGATTAAGCATGCTGCCATTTCATGAATG
TAATGAATCATGCTTAAATGGATGTGAGATTAATAAATACATGGTTTTGGCCGAATGGTTATGTG
TTGGTTCGACCCTAAGGATGATTTGAATGTATTTGGAAGTTATTTGGTGCCAAAATGAAGAGGAA
AGTGTCTTTGGCCGAATAGGAA
Found at i:14792 original size:17 final size:17
Alignment explanation
Indices: 14730--14782 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
14720 AATTAAGAGT
**
14730 TAGTTTAAGAAATGAAC
1 TAGTTTAATTAATGAAC
* *
14747 TAGTTTGATTTATGAAC
1 TAGTTTAATTAATGAAC
14764 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
14781 TA
1 TA
14783 ACTTTATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:14810 original size:18 final size:17
Alignment explanation
Indices: 14789--14848 Score: 70
Period size: 16 Copynumber: 3.5 Consensus size: 17
14779 ACTAACTTTA
14789 TTAAATGAAATAG-ATGC
1 TTAAATGAAAT-GCATGC
*
14806 TTTAAATGCAATGCATGC
1 -TTAAATGAAATGCATGC
*
14824 TTAAATGAACT-CATGC
1 TTAAATGAAATGCATGC
14840 TTAAATGAA
1 TTAAATGAA
14849 GTAGCATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 14 0.37
17 10 0.26
18 14 0.37
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
TTAAATGAAATGCATGC
Found at i:18030 original size:17 final size:17
Alignment explanation
Indices: 18008--18075 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
17998 AATTAAGAGT
18008 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* **
18025 TAGTTTGATTTATGAAC
1 TAGTTTAATAAATGAAC
*
18042 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
18059 TAACTTTATTAAATGAA
1 T-AGTTTAATAAATGAA
18076 ATAGATGCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:18088 original size:18 final size:17
Alignment explanation
Indices: 18067--18125 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 17
18057 ACTAACTTTA
18067 TTAAATGAAATAG-ATGC
1 TTAAATGAAAT-GCATGC
*
18084 TTTAAATGCAATGCATGC
1 -TTAAATGAAATGCATGC
*
18102 TTAAATGAACT-CATGC
1 TTAAATGAAATGCATGC
18118 TTAAATGA
1 TTAAATGA
18126 TATAACATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 13 0.35
17 10 0.27
18 14 0.38
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
TTAAATGAAATGCATGC
Found at i:18811 original size:22 final size:21
Alignment explanation
Indices: 18774--18814 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18764 CCATCTCCAT
18774 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
18795 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
18815 TTTCTGTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:26750 original size:12 final size:12
Alignment explanation
Indices: 26733--26778 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
26723 TTGGTGCTGG
26733 AAATAAGATAAA
1 AAATAAGATAAA
*
26745 AAATAAGAT-TA
1 AAATAAGATAAA
*
26756 AAACAAGATAAA
1 AAATAAGATAAA
*
26768 GAA-AAGATAAA
1 AAATAAGATAAA
26779 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (12 bp):
AAATAAGATAAA
Found at i:29978 original size:178 final size:178
Alignment explanation
Indices: 29679--30034 Score: 703
Period size: 178 Copynumber: 2.0 Consensus size: 178
29669 TTCTAAAGGT
29679 CCTAAATAACTAATGAATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCTAATAAAA
1 CCTAAATAACTAATGAATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCTAATAAAA
29744 TAAAAATAACTAAAAATAATATTTTAACCCAACCTTAATTCCTAGTAAAATAATAAATCTAATAC
66 TAAAAATAACTAAAAATAATATTTTAACCCAACCTTAATTCCTAGTAAAATAATAAATCTAATAC
29809 TATAAGATAATTCATTATCCAATATTAAATTATATTACAAATAATCAA
131 TATAAGATAATTCATTATCCAATATTAAATTATATTACAAATAATCAA
*
29857 CCTAAATAACTAATGAATAAAATAATAATAAACTAAACATGTCTTAACTTTAATTCCTAATAAAA
1 CCTAAATAACTAATGAATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCTAATAAAA
29922 TAAAAATAACTAAAAATAATATTTTAACCCAACCTTAATTCCTAGTAAAATAATAAATCTAATAC
66 TAAAAATAACTAAAAATAATATTTTAACCCAACCTTAATTCCTAGTAAAATAATAAATCTAATAC
29987 TATAAGATAATTCATTATCCAATATTAAATTATATTACAAATAATCAA
131 TATAAGATAATTCATTATCCAATATTAAATTATATTACAAATAATCAA
30035 TATAAATATT
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 177 1.00
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (178 bp):
CCTAAATAACTAATGAATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCTAATAAAA
TAAAAATAACTAAAAATAATATTTTAACCCAACCTTAATTCCTAGTAAAATAATAAATCTAATAC
TATAAGATAATTCATTATCCAATATTAAATTATATTACAAATAATCAA
Found at i:34994 original size:16 final size:16
Alignment explanation
Indices: 34955--34999 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
34945 GATGTAGGAG
*
34955 TCTTTTTCTTTTCTCTT
1 TCTTTTTGTTTT-TCTT
*
34972 T-TGTTTGTTTTTCTT
1 TCTTTTTGTTTTTCTT
34987 TCTTTTTGTTTTT
1 TCTTTTTGTTTTT
35000 ATTGCAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 18 0.75
17 1 0.04
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (16 bp):
TCTTTTTGTTTTTCTT
Found at i:35234 original size:20 final size:20
Alignment explanation
Indices: 35196--35235 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35186 AGAAGTGAAT
*
35196 GAAAGAAATGAAATGAAAGG
1 GAAAGAAATGAAATCAAAGG
**
35216 GAAAGAAATGTTATCAAAGG
1 GAAAGAAATGAAATCAAAGG
35236 TAGGAAAGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.28, T:0.15
Consensus pattern (20 bp):
GAAAGAAATGAAATCAAAGG
Found at i:49007 original size:90 final size:89
Alignment explanation
Indices: 48891--49063 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
48881 TAATCCTGAA
* * *
48891 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAA-CCCTAATATGAT
*
48956 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGATAACTTGGATATAAGAGGAT
48981 TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAACCCTAATATGATT
*
49046 AGGATAACTTGGCTATAA
66 AGGATAACTTGGATATAA
49064 AAGAGTGTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 29 0.37
90 49 0.63
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAACCCTAATATGATT
AGGATAACTTGGATATAAGAGGAT
Found at i:53232 original size:22 final size:21
Alignment explanation
Indices: 53195--53235 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
53185 CCATCTCCAT
53195 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
53216 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
53236 ATTTCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:55605 original size:17 final size:17
Alignment explanation
Indices: 55583--55620 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
55573 TTTCTTGAAA
55583 TTTTGCCTTTTTTGTTT
1 TTTTGCCTTTTTTGTTT
55600 TTTTGCCTTTTTTGTTT
1 TTTTGCCTTTTTTGTTT
55617 TTTT
1 TTTT
55621 TTTTGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (17 bp):
TTTTGCCTTTTTTGTTT
Done.