Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005056.1 Hibiscus syriacus cultivar Beakdansim tig00011350_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: 63383
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2682 original size:42 final size:41
Alignment explanation
Indices: 2634--2721 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 41
2624 ATAATAAATT
2634 AATATATTATCGATGAAGTTT-TATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAA-TTTGTATAGAAATAA-TTTTATTTA
2676 AATATATTATCGATGAATTTGTATAGAAATAATTTTATTTA
1 AATATATTATCGATGAATTTGTATAGAAATAATTTTATTTA
2717 AATAT
1 AATAT
2722 TTAGAATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 17 0.38
42 28 0.62
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (41 bp):
AATATATTATCGATGAATTTGTATAGAAATAATTTTATTTA
Found at i:13814 original size:23 final size:23
Alignment explanation
Indices: 13780--13862 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
13770 AATCAGAATA
*
13780 AAAAAACCCTGTTTACCATAGTC
1 AAAAAACTCTGTTTACCATAGTC
13803 AAAAAACTCTGTTTACCATAGTC
1 AAAAAACTCTGTTTACCATAGTC
* *
13826 AGAAAACTCTGTTTACCAGA-TCC
1 AAAAAACTCTGTTTACCATAGT-C
*
13849 AGAAAACTCTGTTT
1 AAAAAACTCTGTTT
13863 CTATATGGTA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 1 0.02
23 55 0.98
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (23 bp):
AAAAAACTCTGTTTACCATAGTC
Found at i:18949 original size:35 final size:35
Alignment explanation
Indices: 18910--18976 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
18900 TTTATTCAAG
* *
18910 GGGTATCGATACCA-GAAGGGTAGTATCGATACCCA
1 GGGTACCGATACCATGAAGCG-AGTATCGATACCCA
*
18945 GGGTACCGATACCATTAAGCGAGTATCGATAC
1 GGGTACCGATACCATGAAGCGAGTATCGATAC
18977 TAATTTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (35 bp):
GGGTACCGATACCATGAAGCGAGTATCGATACCCA
Found at i:19880 original size:21 final size:21
Alignment explanation
Indices: 19804--19881 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
19794 CCTTCGTGAT
*
19804 ATATATGTAATCCTTTGGAAC
1 ATATATGTGATCCTTTGGAAC
* * **
19825 ATATATGCGGTTTTTCTGGACAC
1 ATATATGTGATCCTT-TGGA-AC
* *
19848 ATAT-T-TGGTCCTTTGGAAT
1 ATATATGTGATCCTTTGGAAC
19867 ATATATGTGATCCTT
1 ATATATGTGATCCTT
19882 AAGGAGTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 5 0.12
20 5 0.12
21 22 0.51
22 5 0.12
23 6 0.14
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (21 bp):
ATATATGTGATCCTTTGGAAC
Found at i:19965 original size:21 final size:21
Alignment explanation
Indices: 19887--19955 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
19877 TCCTTAAGGA
19887 GTGGTCATTCGGGACATATAT
1 GTGGTCATTCGGGACATATAT
*
19908 GTGGTCATTCGGGACATCTAT
1 GTGGTCATTCGGGACATATAT
* * *
19929 GTGGTCCTTTGGGATATATAT
1 GTGGTCATTCGGGACATATAT
*
19950 ATGGTC
1 GTGGTC
19956 CTTCAGGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.36
Consensus pattern (21 bp):
GTGGTCATTCGGGACATATAT
Found at i:23270 original size:33 final size:33
Alignment explanation
Indices: 23233--23297 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
23223 TGGAAATTTC
*
23233 ATCTTGATTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGATTGGTGGCCAACTCATTGAAAAATTA
* *
23266 ATCTTGGTTGGTGGCCAACTCATTGGAAAATT
1 ATCTTGATTGGTGGCCAACTCATTGAAAAATT
23298 CTTTGGTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (33 bp):
ATCTTGATTGGTGGCCAACTCATTGAAAAATTA
Found at i:23310 original size:31 final size:33
Alignment explanation
Indices: 23233--23316 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
23223 TGGAAATTTC
* * *
23233 ATCTTGATTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGGTAGGTGGCCAACTCATTGAAAAATTA
* *
23266 ATCTTGGTTGGTGGCCAACTCATTGGAAAATT-
1 ATCTTGGTAGGTGGCCAACTCATTGAAAAATTA
* *
23298 CT-TTGGTAGGTGGCTAACT
1 ATCTTGGTAGGTGGCCAACT
23317 TATTTTTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 15 0.33
32 1 0.02
33 29 0.64
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (33 bp):
ATCTTGGTAGGTGGCCAACTCATTGAAAAATTA
Found at i:25329 original size:2 final size:2
Alignment explanation
Indices: 25322--25367 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
25312 TATCTTATTC
25322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25364 AT AT
1 AT AT
25368 CCGCAAACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25886 original size:24 final size:20
Alignment explanation
Indices: 25832--25887 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
25822 CCCCTTGAAT
25832 TGCATCGATGCATTCTACAG
1 TGCATCGATGCATTCTACAG
*
25852 TACATCGATGCATTCTTTAACATG
1 TGCATCGATGCATTC--T-ACA-G
25876 TGCATCGATGCA
1 TGCATCGATGCA
25888 CTACTCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
22 1 0.03
23 3 0.10
24 12 0.40
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (20 bp):
TGCATCGATGCATTCTACAG
Found at i:30559 original size:33 final size:33
Alignment explanation
Indices: 30522--30586 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
30512 TAGAAATTTC
*
30522 ATCTTGGGTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGGGTGGTGGCCAACTCATTGAAAAATTA
*
30555 ATCTTGGTTGGTGGCCAACTCATTGAAAAATT
1 ATCTTGGGTGGTGGCCAACTCATTGAAAAATT
30587 CTTTGATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (33 bp):
ATCTTGGGTGGTGGCCAACTCATTGAAAAATTA
Found at i:47677 original size:63 final size:63
Alignment explanation
Indices: 47578--47739 Score: 245
Period size: 63 Copynumber: 2.6 Consensus size: 63
47568 TAACCTAATT
* *
47578 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTGCAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAATTGAA
47641 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAATTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAATTGAA
** * *
47704 CGAGCATTATACAATACTC-AATTTGAGCATTATCAA
1 TTAGCATTAT-CATTA-TCAAAATTGAGCATTATCAA
47740 CATTCCCCCA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
63 69 0.76
64 20 0.22
65 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAATTGAA
Found at i:53130 original size:63 final size:63
Alignment explanation
Indices: 53031--53168 Score: 258
Period size: 63 Copynumber: 2.2 Consensus size: 63
53021 TAACCTAATT
*
53031 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGTTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
53094 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTATAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
53157 TTAGCATTATCA
1 TTAGCATTATCA
53169 AGAAATGACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:53175 original size:41 final size:41
Alignment explanation
Indices: 53113--53248 Score: 245
Period size: 41 Copynumber: 3.3 Consensus size: 41
53103 TCATTATCAA
*
53113 AATTGAGCATTATCAAGAAATGACAATTTATAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
53155 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
53196 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
*
53237 AATGAGCATTAT
1 AATTAGCATTAT
53249 ACAATACTCA
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
41 88 0.96
42 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:60618 original size:21 final size:21
Alignment explanation
Indices: 60592--60633 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
60582 AGGCAAAGGT
60592 AAAGCCTTTTTCGCACCCAAG
1 AAAGCCTTTTTCGCACCCAAG
60613 AAAGCCTTTTTCGCACCCAAG
1 AAAGCCTTTTTCGCACCCAAG
60634 TCAAAGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGCCTTTTTCGCACCCAAG
Found at i:62604 original size:31 final size:31
Alignment explanation
Indices: 62552--62612 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
62542 TAAAACTTAT
* *
62552 TAAATTTATTAAAAGATTATAAAATTATTAA
1 TAAATTTATTAAAAGACTATAAAATAATTAA
*
62583 TAAATTTATCT-AAATACTATAAAATAATTA
1 TAAATTTAT-TAAAAGACTATAAAATAATTA
62613 TTATATTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (31 bp):
TAAATTTATTAAAAGACTATAAAATAATTAA
Found at i:63148 original size:23 final size:23
Alignment explanation
Indices: 63117--63168 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
63107 TGTTCTTTGC
* *
63117 CTTTATGACACGTTTATGTCTGT
1 CTTTGTGACACGTTTATCTCTGT
*
63140 CTTTGTGACACGTTTTTCTCTGT
1 CTTTGTGACACGTTTATCTCTGT
*
63163 TTTTGT
1 CTTTGT
63169 TAGCATACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (23 bp):
CTTTGTGACACGTTTATCTCTGT
Done.