Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007204.1 Hibiscus syriacus cultivar Beakdansim tig00019022_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: 64636
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:821 original size:30 final size:31
Alignment explanation
Indices: 780--839 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
770 ACATGATGCC
**
780 ATGATATCTAAATTAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
811 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
840 TAAGCTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:6581 original size:19 final size:20
Alignment explanation
Indices: 6557--6602 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
6547 CAAAATGGCC
*
6557 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
6576 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
6596 TAATTTC
1 CAATTTC
6603 TAGTATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:8050 original size:9 final size:9
Alignment explanation
Indices: 8038--8072 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
8028 ACCTTATTGT
8038 AATTATTAA
1 AATTATTAA
8047 AATTATTGAA
1 AATTATT-AA
8057 ACATTATTAA
1 A-ATTATTAA
8067 AATTAT
1 AATTAT
8073 ATTTACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.50
10 6 0.25
11 6 0.25
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (9 bp):
AATTATTAA
Found at i:12241 original size:36 final size:36
Alignment explanation
Indices: 12187--12289 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
12177 GGGATTGTCC
* * *
12187 AATACACATGCAATTACACAGCAACTCAATATGACA
1 AATAAACATGCAATTACACAACAACTCAATATGAAA
* *
12223 AATAAACATGTAACTACACATA-AACTCAATATGAAA
1 AATAAACATGCAATTACACA-ACAACTCAATATGAAA
**
12259 AATGGACATGCAATTACACAACAACTCAATA
1 AATAAACATGCAATTACACAACAACTCAATA
12290 AAACAATAAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 1 0.02
36 55 0.98
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.20
Consensus pattern (36 bp):
AATAAACATGCAATTACACAACAACTCAATATGAAA
Found at i:21063 original size:49 final size:49
Alignment explanation
Indices: 21010--21108 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
21000 ATTTTATGTA
*
21010 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGTCAT
1 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
21059 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
1 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
21108 C
1 C
21109 CTATGAGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (49 bp):
CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
Found at i:22870 original size:540 final size:540
Alignment explanation
Indices: 21847--22912 Score: 2060
Period size: 540 Copynumber: 2.0 Consensus size: 540
21837 TTAGTATCAC
*
21847 AGTATAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
1 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
*
21912 AATTCACAAATTCGAAAAGCCATCGCCCTAAATTCAGCTTCTACACTGGATCTAGCCACAACATT
66 AATTCACAAATTCGAAAAGCCATCACCCTAAATTCAGCTTCTACACTGGATCTAGCCACAACATT
21977 ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
131 ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
*
22042 TTCTATCAATTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
196 TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
22107 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
261 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
*
22172 TAGGTGTGATTCTTTAGGATTGTGCCTGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
326 TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
22237 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATAAGCTTTTATCGACTGCTAC
391 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATAAGCTTTTATCGACTGCTAC
22302 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
456 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
22367 GTTTTCCAATTTATTTTCAT
521 GTTTTCCAATTTATTTTCAT
22387 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
1 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
* *
22452 AATTCACAAATTCGAAATGCCATCACCCTAAATTCAGCTTCTGCACTGGATCTAGCCACAACATT
66 AATTCACAAATTCGAAAAGCCATCACCCTAAATTCAGCTTCTACACTGGATCTAGCCACAACATT
*
22517 GTGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
131 ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
22582 TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
196 TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
22647 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
261 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
22712 TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
326 TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
22777 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATAAGCTTTTATCGACTGCTAC
391 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATAAGCTTTTATCGACTGCTAC
*
22842 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTGTTGGTTTGCACCTCA
456 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
22907 GTTTTC
521 GTTTTC
22913 TAGTTTCTGT
Statistics
Matches: 518, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
540 518 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (540 bp):
AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
AATTCACAAATTCGAAAAGCCATCACCCTAAATTCAGCTTCTACACTGGATCTAGCCACAACATT
ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATAAGCTTTTATCGACTGCTAC
ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
GTTTTCCAATTTATTTTCAT
Found at i:24461 original size:29 final size:30
Alignment explanation
Indices: 24402--24473 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
24392 TATCCCTATA
* *
24402 TTTGTTTCTTTGTTTTTGTTGAGATGAG-T
1 TTTGTTTCTTTGTTTCTGCTGAGATGAGTT
* *
24431 TTTGTTTCCTTTGTTTCTGCTGTGA-GGGTT
1 TTTGTTT-CTTTGTTTCTGCTGAGATGAGTT
24461 TTTGTTTTCTTTG
1 TTTG-TTTCTTTG
24474 GTTTGTTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 9 0.25
30 24 0.67
31 3 0.08
ACGTcount: A:0.06, C:0.08, G:0.24, T:0.62
Consensus pattern (30 bp):
TTTGTTTCTTTGTTTCTGCTGAGATGAGTT
Found at i:31734 original size:36 final size:36
Alignment explanation
Indices: 31685--31768 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
31675 GGTAGGTTCC
*
31685 GGTTCCGGATCCCAATTCTTAGGAACCGGTTG-AACA
1 GGTTCCGGTTCCCAATTCTTAGGAACCGG-TGCAACA
* *
31721 GGTTCCGGTTCCCATTTTTTAGGAACCGGTGCAACA
1 GGTTCCGGTTCCCAATTCTTAGGAACCGGTGCAACA
*
31757 GGTTCCGATTCC
1 GGTTCCGGTTCC
31769 GGTTCACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 2 0.05
36 41 0.95
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (36 bp):
GGTTCCGGTTCCCAATTCTTAGGAACCGGTGCAACA
Found at i:42218 original size:25 final size:25
Alignment explanation
Indices: 42190--42244 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
42180 CAAGGTTGGT
*
42190 TGAATATTCTAGATCATTTTGGGGC
1 TGAATATTCTAGATCATTTTGGGGA
42215 TGAATATTCTAGATCATTTTGGGGA
1 TGAATATTCTAGATCATTTTGGGGA
42240 TGAAT
1 TGAAT
42245 CTAGACAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (25 bp):
TGAATATTCTAGATCATTTTGGGGA
Found at i:42839 original size:21 final size:22
Alignment explanation
Indices: 42809--42854 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
42799 CAATTAATAG
*
42809 TTAGTTTAATAAATGAACTA-T
1 TTAGTGTAATAAATGAACTAGT
42830 TTAGTGTAATAAATGAACTAGT
1 TTAGTGTAATAAATGAACTAGT
42852 TTA
1 TTA
42855 ATTAATGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
TTAGTGTAATAAATGAACTAGT
Found at i:42856 original size:17 final size:17
Alignment explanation
Indices: 42810--42885 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
42800 AATTAATAGT
42810 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
42827 TATTTAGTGTAATAAATGAAC
1 ----TAGTTTAATAAATGAAC
*
42848 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
42865 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
42883 TAG
1 TAG
42886 ATGAATGAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 17 0.36
18 14 0.30
21 16 0.34
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:42860 original size:21 final size:20
Alignment explanation
Indices: 42814--42860 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
42804 AATAGTTAGT
*
42814 TTAATAAATGAACTATTTAG
1 TTAATAAATGAACTATTTAA
42834 TGTAATAAATGAACTAGTTTAA
1 T-TAATAAATGAACTA-TTTAA
42856 TTAAT
1 TTAAT
42861 GAACTAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (20 bp):
TTAATAAATGAACTATTTAA
Found at i:42879 original size:18 final size:19
Alignment explanation
Indices: 42839--42884 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
42829 TTTAGTGTAA
*
42839 TAAATGAACT-AGTTTAAT
1 TAAATGAACTAACTTTAAT
42857 T-AATGAACTAACTTT-AT
1 TAAATGAACTAACTTTAAT
42874 TAAATGAACTA
1 TAAATGAACTA
42885 GATGAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (19 bp):
TAAATGAACTAACTTTAAT
Found at i:44098 original size:19 final size:19
Alignment explanation
Indices: 44046--44098 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
44036 ACACTTTCAA
*
44046 TCTTTTT-AACTC-CAATT
1 TCTTTTTCAACTCTCAATG
*
44063 TCTTTTTCTTCACTCTCAATG
1 TCTTTTTC--AACTCTCAATG
44084 TCTTTTTCAACTCTC
1 TCTTTTTCAACTCTC
44099 GTTTCTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.24
19 6 0.21
20 4 0.14
21 12 0.41
ACGTcount: A:0.17, C:0.28, G:0.02, T:0.53
Consensus pattern (19 bp):
TCTTTTTCAACTCTCAATG
Found at i:47393 original size:111 final size:112
Alignment explanation
Indices: 47266--47486 Score: 306
Period size: 112 Copynumber: 2.0 Consensus size: 112
47256 GTGCATTTCA
* * * * *
47266 ACATACTTTGTGTATGATAG-TATCGATCGATTTTGTTTAATGC-ATAGC-GATGCATTTAT-GT
1 ACATACTTCGTGTATGAAAGTTATCGATCGATTTTGATTAAT-CTATAACAG-TGCATTT-TCGG
* * *
47327 CATTAAAGGTGTCATCCATGGTATTCATAATGAGGTGAATTACCATTTAG
63 CATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTACCATTTAG
47377 ACATACTTCGTGTATGAAAGTTATCGATCGATTTTGATTAATCTATAACAGTGCATTTTCGGCAT
1 ACATACTTCGTGTATGAAAGTTATCGATCGATTTTGATTAATCTATAACAGTGCATTTTCGGCAT
*
47442 AAAATGTGCCACCCATGGTATTCATAATGAGGTGAATTACCATTT
66 AAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTACCATTT
47487 TGGCACTCCG
Statistics
Matches: 97, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
111 20 0.21
112 76 0.78
113 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (112 bp):
ACATACTTCGTGTATGAAAGTTATCGATCGATTTTGATTAATCTATAACAGTGCATTTTCGGCAT
AAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTACCATTTAG
Found at i:54461 original size:111 final size:108
Alignment explanation
Indices: 54241--54466 Score: 292
Period size: 111 Copynumber: 2.1 Consensus size: 108
54231 GTTATAGGTA
* * * *
54241 CATTTCGATATAGTTTGTGTATGATAGTATCGATCAATTTTGTTTAATACATAACAGTACATATC
1 CATTTCGAAATACTTCGTGTATGAAAGTATCGATCAATTTTGTTTAATACATAACAGTACATATC
54306 GACATAAAAGGTCACCCATCGTATTCATAATGAGGTGAATTAC
66 GACATAAAAGGTCACCCATCGTATTCATAATGAGGTGAATTAC
** * * * *
54349 CATTTCGAAATACTTCGTGTATGAAAGTTATCGATTGATTTTGTTTAATGCATAACGGTGCATTT
1 CATTTCGAAATACTTCGTGTATGAAAG-TATCGATCAATTTTGTTTAATACATAACAGTACA-TA
* * *
54414 TTGGCATAAAATGTGTCA-CCATGGTATTCATAATGAGGTGAATTAC
64 TCGACATAAAA-G-GTCACCCATCGTATTCATAATGAGGTGAATTAC
54460 CATTTCG
1 CATTTCG
54467 GCACTTTGGT
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
108 23 0.23
109 29 0.29
110 10 0.10
111 35 0.35
112 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (108 bp):
CATTTCGAAATACTTCGTGTATGAAAGTATCGATCAATTTTGTTTAATACATAACAGTACATATC
GACATAAAAGGTCACCCATCGTATTCATAATGAGGTGAATTAC
Found at i:59596 original size:137 final size:138
Alignment explanation
Indices: 59283--59663 Score: 469
Period size: 137 Copynumber: 2.8 Consensus size: 138
59273 GTTCCTATGC
* * * * * * * * *
59283 GATGAGGAAATCTGGTTATCTAAGGGTGATGCTGTTTCTACATGATAAGGAGATATGGAT-GGTG
1 GATGAGGAAGTCTGGCTATCTAAGGATGATACGGCTCCTACGTGATAAGGAGATCTGG-TCGGTG
* *
59347 GATGACAGGGTTCCTACGTGATGAGGGTACGTCTGGCCATCTTTAGGGATAAATTGAGATAACAC
65 GATGACACGGTTCCTACGTGATGA-GG-ACGTCTGGCCATCTTTAGGGATAAATGGAGATAACAC
*
59412 GATTCCTACGT
128 GATTCCTACAT
* * * *
59423 GATGAGGAAGTCTGACTATCTAAGGATGACATGGCTCCTACGTGATAAGGAGATCTGGTCGATGG
1 GATGAGGAAGTCTGGCTATCTAAGGATGATACGGCTCCTACGTGATAAGGAGATCTGGTCGGTGG
* * * *
59488 ATGACACGGTTCCTACGTGATGAGGATGTTTGGTCATCTTTAGGGATAAA-GGAGATAACACGGT
66 ATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGGGATAAATGGAGATAACACGAT
59552 TCCTACAT
131 TCCTACAT
* * * *
59560 GATGAGGAAGTCTGGCTATCTAAGGATAATACGGCTCCTATGTGATGAGGAGATCTGGTCGGTGA
1 GATGAGGAAGTCTGGCTATCTAAGGATGATACGGCTCCTACGTGATAAGGAGATCTGGTCGGTGG
** * *
59625 ATGACATTGTTCCTACGTGATGAGGAAGTCTGGCTATCT
66 ATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCT
59664 AAGGATGATG
Statistics
Matches: 206, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
137 109 0.53
138 22 0.11
139 3 0.01
140 72 0.35
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (138 bp):
GATGAGGAAGTCTGGCTATCTAAGGATGATACGGCTCCTACGTGATAAGGAGATCTGGTCGGTGG
ATGACACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGGGATAAATGGAGATAACACGAT
TCCTACAT
Found at i:59689 original size:83 final size:83
Alignment explanation
Indices: 59547--59734 Score: 277
Period size: 83 Copynumber: 2.3 Consensus size: 83
59537 AGGAGATAAC
* * **
59547 ACGGTTCCTACATGATGAGGAAGTCTGGCTATCTAAGGATAATACGGCTCCTATGTGATGAGGAG
1 ACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATAATACAGCTCCTACATGATGAGGAG
*
59612 ATCTGGTCGGTGAATGAC
66 ATCTGGTCGGTGAATGAA
** * *
59630 ATTGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATGATGCAGCTCCTACATGATGAGGAG
1 ACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATAATACAGCTCCTACATGATGAGGAG
*
59695 ATCTGGTCGGTGGATGAA
66 ATCTGGTCGGTGAATGAA
*
59713 ACGGTTTCTACGTGATGAGGAA
1 ACGGTTCCTACGTGATGAGGAA
59735 TTATGGCCAT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (83 bp):
ACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATAATACAGCTCCTACATGATGAGGAG
ATCTGGTCGGTGAATGAA
Found at i:59700 original size:43 final size:43
Alignment explanation
Indices: 59552--59693 Score: 120
Period size: 43 Copynumber: 3.4 Consensus size: 43
59542 ATAACACGGT
* * *
59552 TCCTACATGATGAGGAAGTCTGGCTATCTAAGGATAATACGGC
1 TCCTACATGATGAGGAAGTCTGGCTATCTAAGGATGATGCAGC
** *
59595 TCCTATGTGATGAGG-AGATCTGG---TC---GG-TGAATGACATTGT
1 TCCTACATGATGAGGAAG-TCTGGCTATCTAAGGATG-ATG-CA--GC
*
59635 TCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATGATGCAGC
1 TCCTACATGATGAGGAAGTCTGGCTATCTAAGGATGATGCAGC
59678 TCCTACATGATGAGGA
1 TCCTACATGATGAGGA
59694 GATCTGGTCG
Statistics
Matches: 77, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
36 1 0.01
37 4 0.05
38 1 0.01
40 22 0.29
41 2 0.03
42 2 0.03
43 36 0.47
45 2 0.03
46 5 0.06
47 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (43 bp):
TCCTACATGATGAGGAAGTCTGGCTATCTAAGGATGATGCAGC
Found at i:59933 original size:68 final size:69
Alignment explanation
Indices: 59828--59958 Score: 160
Period size: 68 Copynumber: 1.9 Consensus size: 69
59818 TGCTTTTATG
* * *
59828 TTTTGAGAGAAACTGTCTAAAGAGAGACAAAACTTG-TTTTAAGAGAAACTATTTCAAGGGAGAA
1 TTTTAAGAGAAACTGTCTAAAGAGAGACAAAACTTGTTTTTAAGA-AAACAATCTCAAGGGAGAA
59892 TTTTT
65 TTTTT
* * * *
59897 TTTTAAGA-AAACTGTCTCAAGCGATAC-AAACTTTGTTTTTAAGAAAACAATCTCAAGTGAGA
1 TTTTAAGAGAAACTGTCTAAAGAGAGACAAAAC-TTGTTTTTAAGAAAACAATCTCAAGGGAGA
59959 TCAATTTTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
67 4 0.08
68 34 0.64
69 15 0.28
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (69 bp):
TTTTAAGAGAAACTGTCTAAAGAGAGACAAAACTTGTTTTTAAGAAAACAATCTCAAGGGAGAAT
TTTT
Found at i:59968 original size:36 final size:36
Alignment explanation
Indices: 59890--59970 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
59880 TTCAAGGGAG
** *
59890 AATTTT-TTTTTAAGAAAACTGTCTCAAGCGATACA
1 AATTTTGTTTTTAAGAAAACAATCTCAAGCGAGACA
* *
59925 AACTTTGTTTTTAAGAAAACAATCTCAAGTGAGATC-
1 AATTTTGTTTTTAAGAAAACAATCTCAAGCGAGA-CA
59961 AATTTTGTTT
1 AATTTTGTTT
59971 CAAATAAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 5 0.13
36 32 0.84
37 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (36 bp):
AATTTTGTTTTTAAGAAAACAATCTCAAGCGAGACA
Found at i:60775 original size:27 final size:27
Alignment explanation
Indices: 60736--60791 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
60726 AAAGGTTGGG
*
60736 CGCTGTATTACATGCGCCCGTGATGGA
1 CGCTGTATCACATGCGCCCGTGATGGA
60763 CGCTGTATCACATGCGCCCGTGATGGA
1 CGCTGTATCACATGCGCCCGTGATGGA
60790 CG
1 CG
60792 GTCCAGATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.29, G:0.30, T:0.23
Consensus pattern (27 bp):
CGCTGTATCACATGCGCCCGTGATGGA
Found at i:60995 original size:3 final size:3
Alignment explanation
Indices: 60987--61013 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
60977 ACAAAATATG
60987 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
61014 ATAGTAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:62416 original size:29 final size:29
Alignment explanation
Indices: 62382--62439 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
62372 TGAAAGAAAT
*
62382 TTTTTATTTTGTTTCAGACAATGAAATCA
1 TTTTTATTTTGTTTCAAACAATGAAATCA
62411 TTTTTATTTTGTTTCAAACAATGAAATCA
1 TTTTTATTTTGTTTCAAACAATGAAATCA
62440 GGGGGAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTTTATTTTGTTTCAAACAATGAAATCA
Found at i:62801 original size:15 final size:14
Alignment explanation
Indices: 62757--62799 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
62747 ATTTAGTCTT
*
62757 AATTTTAGTAATCTA
1 AATTTTA-TAATTTA
*
62772 AATTTCTACAATTTA
1 AATTT-TATAATTTA
62787 AATTTTATAATTT
1 AATTTTATAATTT
62800 TATTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (14 bp):
AATTTTATAATTTA
Found at i:63603 original size:21 final size:20
Alignment explanation
Indices: 63557--63596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
63547 GATCCTAGAT
63557 CCGCCTCTCCTCCCTCCCAG
1 CCGCCTCTCCTCCCTCCCAG
*
63577 CCGCCTGCTCCTTCCTCCCA
1 CCGCCT-CTCCTCCCTCCCA
63597 CGCGCCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.62, G:0.10, T:0.23
Consensus pattern (20 bp):
CCGCCTCTCCTCCCTCCCAG
Done.