Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007238.1 Hibiscus syriacus cultivar Beakdansim tig00019169_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: 66706
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:534 original size:18 final size:19
Alignment explanation
Indices: 494--537 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
484 TTTGGTTCAC
* *
494 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAG-G
514 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
532 GGAATA
1 GGAATA
538 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:1087 original size:19 final size:19
Alignment explanation
Indices: 1063--1124 Score: 124
Period size: 19 Copynumber: 3.3 Consensus size: 19
1053 GCCAACCAAA
1063 CATGGGAATGTGGGATTCC
1 CATGGGAATGTGGGATTCC
1082 CATGGGAATGTGGGATTCC
1 CATGGGAATGTGGGATTCC
1101 CATGGGAATGTGGGATTCC
1 CATGGGAATGTGGGATTCC
1120 CATGG
1 CATGG
1125 ATGAGATCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (19 bp):
CATGGGAATGTGGGATTCC
Found at i:6603 original size:12 final size:12
Alignment explanation
Indices: 6572--6612 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
6562 TTATGTTCAG
*
6572 TTTATTTTAAAT
1 TTTATGTTAAAT
*
6584 TTTA-GTTAACT
1 TTTATGTTAAAT
6595 TTTATGTTAAA-
1 TTTATGTTAAAT
6606 TTTATGT
1 TTTATGT
6613 ATGAAATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (12 bp):
TTTATGTTAAAT
Found at i:9782 original size:30 final size:28
Alignment explanation
Indices: 9700--9783 Score: 69
Period size: 30 Copynumber: 2.9 Consensus size: 28
9690 CATTTTGGAC
* * *
9700 TTTTAAATTTCAGTTTGTGATATTTGGT
1 TTTTAAATTTCTGTTTGTGCTATTTGCT
* * * * *
9728 CTTCAAATTTTCTATTTTTACTATTCTAGCT
1 TTTTAAA-TTTCTGTTTGTGCTATT-T-GCT
9759 TTTTAAATTTCTGTTTGTGCTATTT
1 TTTTAAATTTCTGTTTGTGCTATTT
9784 TAATCCTTTA
Statistics
Matches: 40, Mismatches: 13, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
28 5 0.12
29 13 0.32
30 15 0.38
31 7 0.17
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (28 bp):
TTTTAAATTTCTGTTTGTGCTATTTGCT
Found at i:9794 original size:30 final size:30
Alignment explanation
Indices: 9760--9835 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
9750 ATTCTAGCTT
*
9760 TTTAAATTTCTGTTTGT-GCTATTTTAATCC
1 TTTAAATTTCTGTTT-TCGCTATTTTAATAC
* * *
9790 TTTAATTTTCTATTTTCGTTATTTTAATAC
1 TTTAAATTTCTGTTTTCGCTATTTTAATAC
*
9820 -TTAAAGTTTTTGTTTT
1 TTTAAA-TTTCTGTTTT
9836 TATCTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTAAATTTCTGTTTTCGCTATTTTAATAC
Found at i:14586 original size:2 final size:2
Alignment explanation
Indices: 14574--14627 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
14564 TCATTTATCC
*
14574 AT AT AT GT 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
14616 AT AT AT AT AT AT
1 AT AT AT AT AT AT
14628 CCTTTGTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14893 original size:10 final size:10
Alignment explanation
Indices: 14811--14900 Score: 65
Period size: 11 Copynumber: 8.1 Consensus size: 10
14801 AAAAAGAGGA
14811 AAAAATAAA-
1 AAAAATAAAG
*
14820 AAAAATAAAA
1 AAAAATAAAG
14830 AAAAATTAAAG
1 AAAAA-TAAAG
14841 CAAGGATAATAAAG
1 -AA--A-AATAAAG
14855 AGAAAATAAAGAG
1 A-AAAAT-AA-AG
*
14868 AAAAAACAAAG
1 -AAAAATAAAG
14879 AAAAAATAAAG
1 -AAAAATAAAG
14890 AAAAATAAAG
1 AAAAATAAAG
14900 A
1 A
14901 GCTAAAAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 19
0.76 0.03 0.21
Matches are distributed among these distances:
9 9 0.13
10 16 0.24
11 19 0.28
12 7 0.10
13 7 0.10
14 8 0.12
15 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.10
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:14923 original size:15 final size:16
Alignment explanation
Indices: 14890--14933 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
14880 AAAAATAAAG
*
14890 AAAAATAAAGAGCTAA
1 AAAAACAAAGAGCTAA
14906 AAAAACAAAGAG-TGAAA
1 AAAAACAAAGAGCT--AA
14923 AAAAACAAAGA
1 AAAAACAAAGA
14934 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 13 0.52
ACGTcount: A:0.73, C:0.07, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAACAAAGAGCTAA
Found at i:14937 original size:14 final size:14
Alignment explanation
Indices: 14904--14955 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
14894 ATAAAGAGCT
14904 AAAAAAACAAAGAGTGA
1 AAAAAAACAAAGA---A
14921 AAAAAAACAAAGAA
1 AAAAAAACAAAGAA
*
14935 AAAAAAATAAA-AA
1 AAAAAAACAAAGAA
14948 AAATAAAA
1 AAA-AAAA
14956 AAATAAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 5 0.15
14 15 0.45
17 13 0.39
ACGTcount: A:0.83, C:0.04, G:0.08, T:0.06
Consensus pattern (14 bp):
AAAAAAACAAAGAA
Found at i:14940 original size:17 final size:17
Alignment explanation
Indices: 14868--14958 Score: 53
Period size: 17 Copynumber: 5.2 Consensus size: 17
14858 AAATAAAGAG
14868 AAAAAACAAAGAAAAAA
1 AAAAAACAAAGAAAAAA
* * *
14885 TAAAGAA-AAATAAAGAGCTA
1 -AAAAAACAAAGAAA-A--AA
***
14905 AAAAAACAAAGAGTGAA
1 AAAAAACAAAGAAAAAA
14922 AAAAAACAAAGAAAAAA
1 AAAAAACAAAGAAAAAA
14939 AAATAAA-AAA-AATAAAA
1 AAA-AAACAAAGAA-AAAA
14956 AAA
1 AAA
14959 TAAAGATAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
16 2 0.04
17 34 0.62
18 9 0.16
19 5 0.09
20 5 0.09
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (17 bp):
AAAAAACAAAGAAAAAA
Found at i:14946 original size:9 final size:9
Alignment explanation
Indices: 14934--14962 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
14924 AAAACAAAGA
14934 AAAAAAAAT
1 AAAAAAAAT
14943 AAAAAAAAT
1 AAAAAAAAT
14952 -AAAAAAAT
1 AAAAAAAAT
14960 AAA
1 AAA
14963 GATAAAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:14946 original size:23 final size:23
Alignment explanation
Indices: 14920--14968 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
14910 ACAAAGAGTG
14920 AAAAAAAACAAAGAAAA-AAAAAT
1 AAAAAAAACAAA-AAAATAAAAAT
* *
14943 AAAAAAAATAAAAAAATAAAGAT
1 AAAAAAAACAAAAAAATAAAAAT
14966 AAA
1 AAA
14969 GGGGACGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.86, C:0.02, G:0.04, T:0.08
Consensus pattern (23 bp):
AAAAAAAACAAAAAAATAAAAAT
Found at i:14967 original size:14 final size:14
Alignment explanation
Indices: 14890--14968 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 14
14880 AAAAATAAAG
14890 AAAAATAAAGAGCTAA
1 AAAAATAAAGA--TAA
*
14906 AAAAACAAAGAGTGAAA
1 AAAAATAAAGA-T--AA
* *
14923 AAAAACAAAGAAAA
1 AAAAATAAAGATAA
*
14937 AAAAATAAAAAAAATAA
1 AAAAAT---AAAGATAA
14954 AAAAATAAAGATAA
1 AAAAATAAAGATAA
14968 A
1 A
14969 GGGGACGAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 15 0.29
15 1 0.02
16 10 0.20
17 25 0.49
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAATAAAGATAA
Found at i:15638 original size:32 final size:32
Alignment explanation
Indices: 15602--15685 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
15592 TAAGAAGGCT
*
15602 AAACCATTGACCAAAACCAACCTGAGACATTC
1 AAACCATTGACCAAAAACAACCTGAGACATTC
15634 AAACCATTGACCAAAAACAACCTGAGACATTC
1 AAACCATTGACCAAAAACAACCTGAGACATTC
*
15666 AAACCATTGACCAAACACAA
1 AAACCATTGACCAAAAACAA
15686 TAACCTGAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.48, C:0.30, G:0.08, T:0.14
Consensus pattern (32 bp):
AAACCATTGACCAAAAACAACCTGAGACATTC
Found at i:16122 original size:33 final size:32
Alignment explanation
Indices: 16024--16141 Score: 191
Period size: 32 Copynumber: 3.7 Consensus size: 32
16014 AAGCAATAGA
*
16024 GGGCATCTTTGGAAATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
16056 GGGCATATTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
16088 GGGCGTCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
*
16121 GGGCATCTTTAGAGATTCAAC
1 GGGCATCTTTGGAGATTCAAC
16142 GTCCTGAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 52 0.66
33 27 0.34
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:16292 original size:34 final size:34
Alignment explanation
Indices: 16250--16370 Score: 172
Period size: 34 Copynumber: 3.6 Consensus size: 34
16240 ATTTTTTTTT
*
16250 GTCTCACTTGAGATAATTTCTCAAAATAAA-TTC
1 GTCTCACTTGAGACAATTTCTCAAAATAAATTTC
*
16283 TGTCTCACTTAAGACAATTTCTCAAAATAAATTTC
1 -GTCTCACTTGAGACAATTTCTCAAAATAAATTTC
* **
16318 GTCTCGCTTGAGACAATTTCTCAAAACGAATTTC
1 GTCTCACTTGAGACAATTTCTCAAAATAAATTTC
*
16352 GTCTCGCTTGAGACAATTT
1 GTCTCACTTGAGACAATTT
16371 TTCTCTGAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
34 77 0.96
35 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (34 bp):
GTCTCACTTGAGACAATTTCTCAAAATAAATTTC
Found at i:16700 original size:40 final size:40
Alignment explanation
Indices: 16644--17186 Score: 854
Period size: 40 Copynumber: 13.6 Consensus size: 40
16634 ACATGTTTTA
*
16644 TTGAAATAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
16684 TTGAAACAGAATATTTTATCTCACTCAATATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
16724 TTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
16764 ATGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
16804 TTGAAACAGAAGATTTTATCTCACTCAAGATTATTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
16844 TTGAAATAGAAGATTTTATCTCGCTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
16884 ATGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
16924 TTGAAACATAAGATTTTATATCACTCAAGATTGATTTTT-C
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTG-TTTTTCC
*
16964 TTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTG-TTTTTCC
* *
17005 TTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTTC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* *
17045 TTGAAACAGAAGATATTATCTCATTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
17085 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
* ***
17125 TTGAAACATAAGATTTTATCTTGTTCAAGATTGTTTTTCC
1 TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
*
17165 TTGAAACAAAAGATTTTATCTC
1 TTGAAACAGAAGATTTTATCTC
17187 GCTTGAGATA
Statistics
Matches: 463, Mismatches: 38, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
40 424 0.92
41 39 0.08
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (40 bp):
TTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCC
Found at i:17137 original size:23 final size:22
Alignment explanation
Indices: 17111--17179 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 22
17101 TATCTCACTC
17111 AAGATTGTTTTTCCTTGAAACA
1 AAGATTGTTTTTCCTTGAAACA
* **
17133 TAAGA-T-TTTAT-CTTG-TTC-
1 -AAGATTGTTTTTCCTTGAAACA
17151 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAAC-A
17174 AAGATT
1 AAGATT
17180 TTATCTCGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 5 0.15
20 8 0.24
21 5 0.15
22 1 0.03
23 10 0.29
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (22 bp):
AAGATTGTTTTTCCTTGAAACA
Found at i:17306 original size:43 final size:43
Alignment explanation
Indices: 17242--17455 Score: 308
Period size: 43 Copynumber: 5.0 Consensus size: 43
17232 CCTGCTTTTC
* *
17242 AGGGGTTTCTTGAAGAAAAGCTTGAAGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
*
17285 AGGGGTTTCTTGATGATAAGCTTGAAGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* *
17328 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCATGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* *
17371 ATGGG-TTCTTTGATGACAAGCTTG-AGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGACAAGCTTGAAG-GACCATCGTGATATGT
*
17414 AGGGGTTTCTTGATGACAAG-TTTAAGGGACCATCGTGATATG
1 AGGGGTTTCTTGATGACAAGCTTGAA-GGACCATCGTGATATG
17456 CAGTGATTCC
Statistics
Matches: 154, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
42 6 0.04
43 144 0.94
44 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (43 bp):
AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
Found at i:17632 original size:90 final size:91
Alignment explanation
Indices: 17476--17701 Score: 400
Period size: 90 Copynumber: 2.5 Consensus size: 91
17466 TTGGTGACAA
* *
17476 TTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTC
17541 AGTGCAAGATGTTTTCAAATGAGATT
66 AGTGCAAGATGTTTTCAAATGAGATT
*
17567 TT-AGAAACTAAGCCTTCGGGGGTTTCTTGATTTCTAAGTCCTTCAGGCCATCCATAAGACCTTC
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTC
*
17631 AGTGCATGATGTTTTCAAATGAGATT
66 AGTGCAAGATGTTTTCAAATGAGATT
*
17657 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAATCCTTC
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTC
17702 GGGTCATCTG
Statistics
Matches: 128, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
90 86 0.67
91 42 0.33
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (91 bp):
TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTC
AGTGCAAGATGTTTTCAAATGAGATT
Found at i:17967 original size:15 final size:15
Alignment explanation
Indices: 17955--17984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17945 TATATTATAT
17955 TATGTATTATTATTA
1 TATGTATTATTATTA
*
17970 TATTTATTATTATTA
1 TATGTATTATTATTA
17985 ATAGAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TATGTATTATTATTA
Found at i:17970 original size:18 final size:18
Alignment explanation
Indices: 17947--17984 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
17937 AAAAAATATA
17947 TATTATA-TTATGTATTAT
1 TATTATATTTAT-TATTAT
17965 TATTATATTTATTATTAT
1 TATTATATTTATTATTAT
17983 TA
1 TA
17985 ATAGAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTATATTTATTATTAT
Found at i:17976 original size:12 final size:13
Alignment explanation
Indices: 17943--17982 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
17933 GATTAAAAAA
17943 TATATATTA-TAT
1 TATATATTATTAT
*
17955 TATGTATTATTAT
1 TATATATTATTAT
17968 TATAT-TTATTAT
1 TATATATTATTAT
17980 TAT
1 TAT
17983 TAATAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:17994 original size:18 final size:19
Alignment explanation
Indices: 17953--17994 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
17943 TATATATTAT
* *
17953 ATTATGTATTATTATTATA
1 ATTATGTATTATTAATAGA
*
17972 TTTAT-TATTATTAATAGA
1 ATTATGTATTATTAATAGA
17990 ATTAT
1 ATTAT
17995 AATACATGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTATGTATTATTAATAGA
Found at i:19873 original size:59 final size:59
Alignment explanation
Indices: 19810--19923 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 59
19800 CATTTTAGGA
* * * *
19810 TTTAAA-GTTCATGTTTTTGCCATTTTGGTCTTTTAAATTTCAGTTTGTGATATTTGGTC
1 TTTAAATGTTC-TATTTTTACCATTCTAGTCTTTTAAATTTCAGTTTGTGATATTTGGTC
* * * * *
19869 TTTAAATTTTCTATTTTTACTATTCTAGTTTTTTAAATTTCTGTTTGTGCTATTT
1 TTTAAATGTTCTATTTTTACCATTCTAGTCTTTTAAATTTCAGTTTGTGATATTT
19924 TAATCCTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
59 42 0.93
60 3 0.07
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.59
Consensus pattern (59 bp):
TTTAAATGTTCTATTTTTACCATTCTAGTCTTTTAAATTTCAGTTTGTGATATTTGGTC
Found at i:19922 original size:30 final size:28
Alignment explanation
Indices: 19810--19923 Score: 84
Period size: 30 Copynumber: 3.9 Consensus size: 28
19800 CATTTTAGGA
* * *
19810 TTTAAAGTTCATGTTTTTGCCATTTTGGTCT
1 TTTAAATTTC-TGTTTGTGCTA-TTTGGT-T
* * *
19841 TTTAAATTTCAGTTTGTGATATTTGGTC
1 TTTAAATTTCTGTTTGTGCTATTTGGTT
* * * *
19869 TTTAAATTTTCTATTTTTACTATTCTAGTTT
1 TTTAAA-TTTCTGTTTGTGCTATT-T-GGTT
19900 TTTAAATTTCTGTTTGTGCTATTT
1 TTTAAATTTCTGTTTGTGCTATTT
19924 TAATCCTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
28 6 0.09
29 19 0.30
30 22 0.34
31 17 0.27
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.59
Consensus pattern (28 bp):
TTTAAATTTCTGTTTGTGCTATTTGGTT
Found at i:19934 original size:30 final size:30
Alignment explanation
Indices: 19900--19975 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
19890 ATTCTAGTTT
*
19900 TTTAAATTTCTGTTTGT-GCTATTTTAATCC
1 TTTAAATTTCTGTTT-TCGCTATTTTAATAC
* * *
19930 TTTAATTTTCTATTTTCGTTATTTTAATAC
1 TTTAAATTTCTGTTTTCGCTATTTTAATAC
*
19960 -TTAAAGTTTTTGTTTT
1 TTTAAA-TTTCTGTTTT
19976 TATCTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTAAATTTCTGTTTTCGCTATTTTAATAC
Found at i:20283 original size:15 final size:16
Alignment explanation
Indices: 20245--20284 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
20235 AACACAGACC
20245 AATT-TTTTTCTTAAA
1 AATTGTTTTTCTTAAA
20260 AA-TGATTTTTC-TAAA
1 AATTG-TTTTTCTTAAA
20275 AATTGTTTTT
1 AATTGTTTTT
20285 AAAAGACGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
16 8 0.36
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (16 bp):
AATTGTTTTTCTTAAA
Found at i:21969 original size:16 final size:16
Alignment explanation
Indices: 21945--21975 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21935 TTTTTTCTTG
*
21945 TTTCTTTTCTTTTTTT
1 TTTCCTTTCTTTTTTT
21961 TTTCCTTTCTTTTTT
1 TTTCCTTTCTTTTTT
21976 CTTTGATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCCTTTCTTTTTTT
Found at i:21987 original size:12 final size:11
Alignment explanation
Indices: 21934--21979 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
21924 AATTTCACGC
21934 TTTTTTTCTTGT
1 TTTTTTTCTT-T
*
21946 TTCTTTTCTTT
1 TTTTTTTCTTT
21957 TTTTTTTCCTTT
1 TTTTTTT-CTTT
*
21969 CTTTTTTCTTT
1 TTTTTTTCTTT
21980 GATTTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:25668 original size:14 final size:15
Alignment explanation
Indices: 25649--25685 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
25639 CCTTGTTGCA
*
25649 TTTGCATCTCGTA-T
1 TTTGCATCTCCTATT
25663 TTTGCA-CTCCTATT
1 TTTGCATCTCCTATT
25677 TTTGCATCT
1 TTTGCATCT
25686 TTGCATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.14, C:0.24, G:0.11, T:0.51
Consensus pattern (15 bp):
TTTGCATCTCCTATT
Found at i:27481 original size:64 final size:63
Alignment explanation
Indices: 27395--27616 Score: 211
Period size: 64 Copynumber: 3.4 Consensus size: 63
27385 CACATTCATA
* *
27395 AGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATCGCT
1 AGTGCATCGATGCATACCTTTTAAAAGAA-AACATCGAATGCATTTGATGCATCGATGCATCG-T
* * * * *
27459 AATGCATCGATGCAT-CCTTTTAAAATAAAAACATCGAATGTAATTCG-TGCATCGATGCATAAG
1 AGTGCATCGATGCATACCTTTTAAAA-GAAAACATCGAATG-CATTTGATGCATCGATGCAT-CG
27522 T
63 T
* ** * *
27523 AGTGCATCGATGCATCCCCATTAAATA-AAAACATCGAATGCATTTTATGCACCGATGCA-CAAG
1 AGTGCATCGATGCATACCTTTTAAA-AGAAAACATCGAATGCATTTGATGCATCGATGCATC--G
27586 T
63 T
27587 AGTGCATCGATGCATACCTTCATTAAAAGA
1 AGTGCATCGATGCATACCTT--TTAAAAGA
27617 GGAAATTGGC
Statistics
Matches: 129, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
63 5 0.04
64 103 0.80
65 14 0.11
66 7 0.05
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (63 bp):
AGTGCATCGATGCATACCTTTTAAAAGAAAACATCGAATGCATTTGATGCATCGATGCATCGT
Found at i:28331 original size:30 final size:30
Alignment explanation
Indices: 28282--28340 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
28272 GGAACATATG
* *
28282 GATAGTTGCCGAGGATCTTTATGACCTCTT
1 GATAGTTACCGAGGATCTTTATAACCTCTT
* * *
28312 GATAGTTACCGGGGTTCTTTGTAACCTCT
1 GATAGTTACCGAGGATCTTTATAACCTCT
28341 GGACAGGTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (30 bp):
GATAGTTACCGAGGATCTTTATAACCTCTT
Found at i:31897 original size:15 final size:15
Alignment explanation
Indices: 31874--31922 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
31864 ACTTGATATG
*
31874 TTCTCTTTCTTCTTC
1 TTCTTTTTCTTCTTC
31889 TTCTTTTTCTTC-TC
1 TTCTTTTTCTTCTTC
*
31903 TTTTTTTTCTT-TTC
1 TTCTTTTTCTTCTTC
31917 TT-TTTT
1 TTCTTTT
31923 ATTGTTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTTTTTCTTCTTC
Found at i:31909 original size:14 final size:14
Alignment explanation
Indices: 31879--31922 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
31869 ATATGTTCTC
*
31879 TTTCTTCTTCTTCTT
1 TTTCTTC-TCTTTTT
31894 TTTCTTCTCTTTTT
1 TTTCTTCTCTTTTT
*
31908 TTTCTTTTCTTTTT
1 TTTCTTCTCTTTTT
31922 T
1 T
31923 ATTGTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTCTCTTTTT
Found at i:54282 original size:2 final size:2
Alignment explanation
Indices: 54275--54308 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54265 AATACAATTA
54275 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
54309 TTATTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55927 original size:28 final size:27
Alignment explanation
Indices: 55874--55935 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 27
55864 TGGGCCTGTA
55874 TAAATAAAAATAAAAACTAAAATTAAAAT
1 TAAA-AAAAATAAAAACTAAAATT-AAAT
55903 TAAAAAAAAT-AAAA-TAATAAGTTAAAT
1 TAAAAAAAATAAAAACTAA-AA-TTAAAT
55930 TAAAAA
1 TAAAAA
55936 TCCGGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.10
27 16 0.52
28 8 0.26
29 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (27 bp):
TAAAAAAAATAAAAACTAAAATTAAAT
Found at i:59633 original size:2 final size:2
Alignment explanation
Indices: 59628--59683 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
59618 ACACACACAC
59628 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
59670 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
59684 TAAAATTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60820 original size:2 final size:2
Alignment explanation
Indices: 60815--60869 Score: 92
Period size: 2 Copynumber: 26.5 Consensus size: 2
60805 AAACGAATTA
60815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
60858 AT AT AT AGT AT A
1 AT AT AT A-T AT A
60870 AGGTTATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 47 0.92
3 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61190 original size:3 final size:3
Alignment explanation
Indices: 61182--61222 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
61172 GACTTAATTG
61182 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61223 TTTATTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.