Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005436.1 Hibiscus syriacus cultivar Beakdansim tig00012463_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: 54411
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1750 original size:91 final size:90
Alignment explanation
Indices: 1628--1825 Score: 231
Period size: 91 Copynumber: 2.2 Consensus size: 90
1618 TGTTAATACC
* * * * *
1628 ATTTTAGTCCTTAAGTTTCTATTTTTTCTATTTTAGTCTTTTAAATGTCTGTATTTGCTA-TTTG
1 ATTTTAGTCCTTAACTTTCTATTTTTGCTATTTTAGTCATTTAAATGTCTGT-TTAGCTATTTTA
1692 GTCCTTAAAGTTTATGTTTTTTTGCT
65 GTCCTTAAAGTTTATGTTTTTTTGCT
* * *
1718 ATTTTAGTCTGTTAACTTTCTATTTTTGCTATTTTAGTCATTTAACTTTCTGTTTAGCTATTTTA
1 ATTTTAGTC-CTTAACTTTCTATTTTTGCTATTTTAGTCATTTAAATGTCTGTTTAGCTATTTTA
* * * *
1783 GTCCTTTAAGTTTCTG--TATTTGTT
65 GTCCTTAAAGTTTATGTTTTTTTGCT
*
1807 ATTTTGGTCCTTTAACTTT
1 ATTTTAGTCC-TTAACTTT
1826 ATGTATTTAC
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
89 22 0.24
90 15 0.16
91 54 0.59
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (90 bp):
ATTTTAGTCCTTAACTTTCTATTTTTGCTATTTTAGTCATTTAAATGTCTGTTTAGCTATTTTAG
TCCTTAAAGTTTATGTTTTTTTGCT
Found at i:1831 original size:30 final size:30
Alignment explanation
Indices: 1628--1848 Score: 182
Period size: 30 Copynumber: 7.4 Consensus size: 30
1618 TGTTAATACC
* * * *
1628 ATTTTAGTCC-TTAAGTTTCTATTTTTTCT
1 ATTTTAGTCCTTTAACTTTCTGTATTTGCT
* * *
1657 ATTTTAGTCTTTTAAATGTCTGTATTTGCT
1 ATTTTAGTCCTTTAACTTTCTGTATTTGCT
* * * * *
1687 A-TTTGGTCCTTAAAGTTTATGTTTTTTTGCT
1 ATTTTAGTCCTTTAACTTTCTG--TATTTGCT
* *
1718 ATTTTAGT-CTGTTAACTTTCTATTTTTGCT
1 ATTTTAGTCCT-TTAACTTTCTGTATTTGCT
* *
1748 ATTTTAGTCATTTAACTTTCTGT-TTAGCT
1 ATTTTAGTCCTTTAACTTTCTGTATTTGCT
* *
1777 ATTTTAGTCCTTTAAGTTTCTGTATTTGTT
1 ATTTTAGTCCTTTAACTTTCTGTATTTGCT
* * *
1807 ATTTTGGTCCTTTAACTTTATGTATTTACT
1 ATTTTAGTCCTTTAACTTTCTGTATTTGCT
*
1837 A-TTTAGCCCTTT
1 ATTTTAGTCCTTT
1849 TAATTTATGT
Statistics
Matches: 153, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
29 58 0.38
30 72 0.47
31 11 0.07
32 12 0.08
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (30 bp):
ATTTTAGTCCTTTAACTTTCTGTATTTGCT
Found at i:1842 original size:59 final size:59
Alignment explanation
Indices: 1650--1854 Score: 184
Period size: 59 Copynumber: 3.4 Consensus size: 59
1640 AAGTTTCTAT
* * * * *
1650 TTTTTCTATTTTAGTCTTTTAAATGTCTGTATTTGCTA-TTTGGTCCTTAAAGTTTATG
1 TTTTACTATTTTAGTCCTTTAAATTTCTGTATTTGCTATTTTGGTCCTTTAACTTTATG
* * * * * * *
1708 TTTTTTTGCTATTTTAGT-CTGTTAACTTTCTATTTTTGCTATTTTAGTCATTTAACTTTCTG
1 ---TTTTACTATTTTAGTCCT-TTAAATTTCTGTATTTGCTATTTTGGTCCTTTAACTTTATG
* *
1770 -TTTAGCTATTTTAGTCCTTTAAGTTTCTGTATTTGTTATTTTGGTCCTTTAACTTTATG
1 TTTTA-CTATTTTAGTCCTTTAAATTTCTGTATTTGCTATTTTGGTCCTTTAACTTTATG
* *
1829 TATTTACTA-TTTAGCCCTTTTAATTT
1 T-TTTACTATTTTAGTCCTTTAAATTT
1855 ATGTTAATTT
Statistics
Matches: 116, Mismatches: 22, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
58 3 0.03
59 58 0.50
60 6 0.05
61 34 0.29
62 15 0.13
ACGTcount: A:0.18, C:0.12, G:0.11, T:0.59
Consensus pattern (59 bp):
TTTTACTATTTTAGTCCTTTAAATTTCTGTATTTGCTATTTTGGTCCTTTAACTTTATG
Found at i:5588 original size:12 final size:12
Alignment explanation
Indices: 5571--5595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5561 ACAAAGCACC
5571 ATTTGGTGCCTA
1 ATTTGGTGCCTA
5583 ATTTGGTGCCTA
1 ATTTGGTGCCTA
5595 A
1 A
5596 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:10023 original size:12 final size:12
Alignment explanation
Indices: 10006--10030 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9996 ACAAAGCACC
10006 ATTTGGTGCCTA
1 ATTTGGTGCCTA
10018 ATTTGGTGCCTA
1 ATTTGGTGCCTA
10030 A
1 A
10031 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:11150 original size:21 final size:21
Alignment explanation
Indices: 11124--11168 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11114 GATTTCTGGG
* *
11124 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
11145 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
11166 CAA
1 CAA
11169 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:11874 original size:31 final size:31
Alignment explanation
Indices: 11836--11960 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
11826 AGGGTCGAGG
11836 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
11867 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
11898 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
11929 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
11960 G
1 G
11961 GTCCTTCGAG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:15317 original size:21 final size:21
Alignment explanation
Indices: 15291--15335 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
15281 GATTTCTGGG
*
15291 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
15312 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
15333 CAA
1 CAA
15336 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:16043 original size:31 final size:31
Alignment explanation
Indices: 16001--16125 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
15991 AGGGTCGAGG
16001 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
16032 GTTTACATATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16063 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
16094 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
16125 G
1 G
16126 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:19245 original size:20 final size:20
Alignment explanation
Indices: 19220--19258 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
19210 AAGGATGGAA
19220 TATATTGGTTGACTTTTAAT
1 TATATTGGTTGACTTTTAAT
19240 TATATTGGTTGACTTTTAA
1 TATATTGGTTGACTTTTAA
19259 AAGAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
TATATTGGTTGACTTTTAAT
Found at i:20762 original size:32 final size:31
Alignment explanation
Indices: 20688--20762 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
20678 CCTGAAAACG
*
20688 ACCTGAACCCGAATTGAACCGAAAATATGAT
1 ACCTGAACCCGAAATGAACCGAAAATATGAT
* * *
20719 ACATGAACCCGAAATGCATCCGACTAATATGA-
1 ACCTGAACCCGAAATG-AACCGA-AAATATGAT
20751 ACCTGAACCCGA
1 ACCTGAACCCGA
20763 GATTGACCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 14 0.38
32 16 0.43
33 7 0.19
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.17
Consensus pattern (31 bp):
ACCTGAACCCGAAATGAACCGAAAATATGAT
Found at i:20861 original size:16 final size:16
Alignment explanation
Indices: 20793--20863 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
20783 GGTATTACCC
20793 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
20809 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
20825 GGCATGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
20841 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
20857 AACCTGT
1 GACCTGT
20864 AAATGATCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:21121 original size:14 final size:14
Alignment explanation
Indices: 21099--21145 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
21089 TGCAAAGGAA
*
21099 AATTAATATAGTTT
1 AATTTATATAGTTT
21113 AATTTATATA----
1 AATTTATATAGTTT
21123 AA-TTATATAGTTT
1 AATTTATATAGTTT
21136 AATTTATATA
1 AATTTATATA
21146 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:21132 original size:23 final size:24
Alignment explanation
Indices: 21098--21147 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
21088 ATGCAAAGGA
21098 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
21122 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
21145 AAA
1 AAA
21148 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:21419 original size:17 final size:18
Alignment explanation
Indices: 21387--21426 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21377 AACTATACCG
21387 TTTATATAAATTATATAC
1 TTTATATAAATTATATAC
* *
21405 TTTAT-TAATTTATATAG
1 TTTATATAAATTATATAC
21422 TTTAT
1 TTTAT
21427 GCATAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTATATAAATTATATAC
Found at i:21633 original size:19 final size:20
Alignment explanation
Indices: 21609--21652 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
21599 CCAACTTCCC
*
21609 AAATTTTTC-TATTCCCGCT
1 AAATTTTTCAAATTCCCGCT
*
21628 AAATTTTTCAAATTCCCTCT
1 AAATTTTTCAAATTCCCGCT
21648 AAATT
1 AAATT
21653 CCCAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATTTTTCAAATTCCCGCT
Found at i:21780 original size:2 final size:2
Alignment explanation
Indices: 21773--21827 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
21763 ACTTTGAATA
* *
21773 AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AC AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
21815 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
21828 ATTAAACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.96
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:22281 original size:2 final size:2
Alignment explanation
Indices: 22274--22302 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22264 TATGTTTAAT
22274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22303 TTCAAAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22421 original size:17 final size:18
Alignment explanation
Indices: 22399--22453 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
22389 TTAAGAAATT
*
22399 TTGAGAA-TATAGGGAAA
1 TTGAGAATTAGAGGGAAA
22416 TTGAGAATTTAGAGGGAAA
1 TTGAGAA-TTAGAGGGAAA
*
22435 TTGGGAAACTTAGAGGGAA
1 TTGAG-AA-TTAGAGGGAA
22454 TAGAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.22
19 13 0.41
20 12 0.38
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.24
Consensus pattern (18 bp):
TTGAGAATTAGAGGGAAA
Found at i:22431 original size:19 final size:20
Alignment explanation
Indices: 22409--22453 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
22399 TTGAGAATAT
*
22409 AGGGAAATTGAG-AATTTAG
1 AGGGAAATTGAGAAACTTAG
*
22428 AGGGAAATTGGGAAACTTAG
1 AGGGAAATTGAGAAACTTAG
22448 AGGGAA
1 AGGGAA
22454 TAGAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.42, C:0.02, G:0.36, T:0.20
Consensus pattern (20 bp):
AGGGAAATTGAGAAACTTAG
Found at i:22692 original size:7 final size:7
Alignment explanation
Indices: 22682--22735 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
22672 ATAATTTATA
22682 TAAACCT
1 TAAACCT
22689 TAAACCT
1 TAAACCT
*
22696 TAAACCC
1 TAAACCT
*
22703 TAAACCC
1 TAAACCT
*
22710 TAAATAC-
1 TAAA-CCT
*
22717 TAAACCA
1 TAAACCT
22724 TAAACCT
1 TAAACCT
22731 TAAAC
1 TAAAC
22736 ATAAACCCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 1 0.02
7 39 0.95
8 1 0.02
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCT
Found at i:22701 original size:14 final size:14
Alignment explanation
Indices: 22681--22742 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
22671 TATAATTTAT
22681 ATAAACCTTAAACC
1 ATAAACCTTAAACC
* *
22695 TTAAACCCTAAACC
1 ATAAACCTTAAACC
* *
22709 CTAAATAC-TAAACC
1 ATAAA-CCTTAAACC
22723 ATAAACCTTAAA-C
1 ATAAACCTTAAACC
22736 ATAAACC
1 ATAAACC
22743 CTAATGTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
13 9 0.22
14 30 0.75
15 1 0.03
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACCTTAAACC
Found at i:22708 original size:21 final size:19
Alignment explanation
Indices: 22682--22746 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
22672 ATAATTTATA
22682 TAAACCTTAAACCTTAAACCC
1 TAAACCTTAAA-C-TAAACCC
* *
22703 TAAACCCTAAATACTAAACCA
1 TAAA-CCTTAA-ACTAAACCC
22724 TAAACCTTAAACATAAACCC
1 TAAACCTTAAAC-TAAACCC
22744 TAA
1 TAA
22747 TGTATGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.05
20 14 0.38
21 14 0.38
22 6 0.16
23 1 0.03
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAACCTTAAACTAAACCC
Found at i:26010 original size:18 final size:20
Alignment explanation
Indices: 25979--26035 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 20
25969 GAATCCGTGG
* *
25979 GGGGTATCGATTCCCTC-AA
1 GGGGAATCGGTTCCCTCAAA
25998 -GGGAATCGGTTCCCATTCAAA
1 GGGGAATCGGTTCCC--TCAAA
26019 GGGGGAATCGGTTCCCT
1 -GGGGAATCGGTTCCCT
26036 TATGGGGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 12 0.39
20 2 0.06
21 3 0.10
23 14 0.45
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGGAATCGGTTCCCTCAAA
Found at i:31886 original size:2 final size:2
Alignment explanation
Indices: 31879--31963 Score: 56
Period size: 2 Copynumber: 44.0 Consensus size: 2
31869 TAATACATAC
*
31879 AT AT AT AT AT AT AT AT -T AT AT A- AT AT A- AT -T AT A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
31916 AT AA ACT AT AT AT -T TT AT AT AGT TT AT AT GT AT AT AT AT AT ACT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
31960 AT AT
1 AT AT
31964 TAATATAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
1 6 0.09
2 56 0.85
3 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31950 original size:66 final size:66
Alignment explanation
Indices: 31882--32010 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
31872 TACATACATA
* *
31882 TATATATATATATTATA-TAATAT-AATTATAACATATAAACTATATA-TTTTATATAGTTTATA
1 TATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTT-TATAGTTTATA
31944 TG
65 TG
***
31946 TATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATAT
1 TATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTTTATAGTTTATAT
32011 ACTTTTTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 16 0.28
65 6 0.11
66 31 0.54
67 4 0.07
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (66 bp):
TATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTTTATAGTTTATAT
G
Found at i:32037 original size:15 final size:14
Alignment explanation
Indices: 32017--32219 Score: 77
Period size: 15 Copynumber: 14.1 Consensus size: 14
32007 ATATACTTTT
32017 TATAGTTTATACATA
1 TATAGTTTATA-ATA
*
32032 TATAGTTTAT-ATG
1 TATAGTTTATAATA
*
32045 CATAGTTTATATATA
1 TATAGTTTATA-ATA
*
32060 TATAGTTCACATAA-A
1 TATAGTT--TATAATA
* * *
32075 CACAATTTAT-ATA
1 TATAGTTTATAATA
32088 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
32106 TATAGTTTATAATA
1 TATAGTTTATAATA
* * *
32120 TA-A--ATATAGTT
1 TATAGTTTATAATA
*
32131 TATAATTT-T-ATA
1 TATAGTTTATAATA
32143 TACGTAGTTTAT-ATA
1 TA--TAGTTTATAATA
*
32158 TATAGTTCACATAA-A
1 TATAGTT--TATAATA
*
32173 TATAATTTAT-ATA
1 TATAGTTTATAATA
32186 TATAGTTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
32204 TATAGTTTATAATA
1 TATAGTTTATAATA
32218 TA
1 TA
32220 ATTATAGTTT
Statistics
Matches: 140, Mismatches: 23, Indels: 51
0.65 0.11 0.24
Matches are distributed among these distances:
11 7 0.05
12 6 0.04
13 30 0.21
14 18 0.13
15 48 0.34
16 8 0.06
17 9 0.06
18 14 0.10
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:32126 original size:18 final size:18
Alignment explanation
Indices: 32082--32236 Score: 113
Period size: 18 Copynumber: 8.2 Consensus size: 18
32072 AAACACAATT
*
32082 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
32100 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
32118 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
32136 TTTTATATACGTAGTTTATATA
1 -TATATATA--TAGTTTATA-A
* **
32158 TATAGTTCACATA-AATATAA
1 TATA--T-ATATAGTTTATAA
32178 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
32198 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
32216 TATA-ATTATAGTTTAT-A
1 TATATA-TATAGTTTATAA
32233 TATA
1 TATA
32237 ATTTTATATT
Statistics
Matches: 111, Mismatches: 11, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
17 8 0.07
18 58 0.52
19 12 0.11
20 7 0.06
21 16 0.14
22 7 0.06
23 1 0.01
24 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:32163 original size:13 final size:13
Alignment explanation
Indices: 32017--32251 Score: 74
Period size: 15 Copynumber: 17.3 Consensus size: 13
32007 ATATACTTTT
32017 TATAGTTTATACATA
1 TATAGTTTAT--ATA
*
32032 TATAGTTTATATG
1 TATAGTTTATATA
*
32045 CATAGTTTATATATA
1 TATAG-TT-TATATA
* *
32060 TATAGTTCACATAAA
1 TATAGTT--TATATA
* * *
32075 CACAATTTATATA
1 TATAGTTTATATA
32088 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
32106 TATAGTTTATA-A
1 TATAGTTTATATA
** *
32118 TATA-AATATAGTT
1 TATAGTTTATA-TA
*
32131 TATAATTT-TATA
1 TATAGTTTATATA
32143 TACGTAGTTTATATA
1 TA--TAGTTTATATA
* *
32158 TATAGTTCACATAAA
1 TATAGTT--TATATA
*
32173 TATAATTTATATA
1 TATAGTTTATATA
32186 TATAGTTTATA-A
1 TATAGTTTATATA
*
32198 TA-A-TTATATAGTT
1 TATAGTT-TATA-TA
* *
32211 TATAATATA-AT-
1 TATAGTTTATATA
32222 TATAGTTTATATA
1 TATAGTTTATATA
*
32235 TA-ATTTTATATTA
1 TATAGTTTATA-TA
32248 TATA
1 TATA
32252 TATATTATAT
Statistics
Matches: 163, Mismatches: 32, Indels: 51
0.66 0.13 0.21
Matches are distributed among these distances:
10 2 0.01
11 16 0.10
12 21 0.13
13 46 0.28
14 17 0.10
15 48 0.29
16 3 0.02
17 3 0.02
18 7 0.04
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:32163 original size:98 final size:98
Alignment explanation
Indices: 32054--32232 Score: 322
Period size: 98 Copynumber: 1.8 Consensus size: 98
32044 GCATAGTTTA
32054 TATATATATAGTTCACATAAACACAATTTATATATATAGCTTATAATAATTATATAGTTTATAAT
1 TATATATATAGTTCACATAAACACAATTTATATATATAGCTTATAATAATTATATAGTTTATAAT
32119 ATAAATATAGTTTATAATTTTATATACGTAGTT
66 ATAAATATAGTTTATAATTTTATATACGTAGTT
* * *
32152 TATATATATAGTTCACATAAATATAATTTATATATATAGTTTATAATAATTATATAGTTTATAAT
1 TATATATATAGTTCACATAAACACAATTTATATATATAGCTTATAATAATTATATAGTTTATAAT
*
32217 ATAATTATAGTTTATA
66 ATAAATATAGTTTATA
32233 TATAATTTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (98 bp):
TATATATATAGTTCACATAAACACAATTTATATATATAGCTTATAATAATTATATAGTTTATAAT
ATAAATATAGTTTATAATTTTATATACGTAGTT
Found at i:32219 original size:62 final size:65
Alignment explanation
Indices: 32118--32255 Score: 144
Period size: 62 Copynumber: 2.2 Consensus size: 65
32108 TAGTTTATAA
* *
32118 TATAAATATAGTTTATAATTTTATATACGTAGTTTATAT-A-TATAGTTCACATA-AATATAAT-
1 TATATATATAGTTTATAATATTATATACGTA-TTTATATAATTATAGTTCACATATAATATAATA
32179 T
65 T
* * * *
32180 TATATATATAGTTTATAATAATTATATA-GT-TTATAATATAATTATAGTTTATATATAATTTTA
1 TATATATATAGTTTATAAT-ATTATATACGTATT-T-ATATAATTATAGTTCACATATAATATAA
32243 TAT
63 TAT
32246 TATATATATA
1 TATATATATA
32256 TTATATTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
60 2 0.03
61 1 0.02
62 24 0.38
63 8 0.13
64 11 0.17
65 6 0.10
66 11 0.17
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (65 bp):
TATATATATAGTTTATAATATTATATACGTATTTATATAATTATAGTTCACATATAATATAATAT
Found at i:47374 original size:27 final size:31
Alignment explanation
Indices: 47341--47419 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
47331 TTTTAGACAT
47341 AATACTAATTTGACCT-T-AAATTT-TAT-A
1 AATACTAATTTGACCTCTAAAATTTATATAA
*
47368 AATACTAATTTAACCTCTAAAATTTATATAA
1 AATACTAATTTGACCTCTAAAATTTATATAA
*
47399 AATA-TCAATTTGACCCCTAAA
1 AATACT-AATTTGACCTCTAAA
47420 TCCAATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 15 0.34
28 1 0.02
29 6 0.14
30 4 0.09
31 18 0.41
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (31 bp):
AATACTAATTTGACCTCTAAAATTTATATAA
Found at i:49333 original size:23 final size:23
Alignment explanation
Indices: 49307--49368 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
49297 AAAAATTATG
49307 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
49330 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
49353 ATGTAATAGGTAGCGC
1 ATGTAATAGGTAGCGC
49369 CAGGGCCGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:51269 original size:23 final size:23
Alignment explanation
Indices: 51224--51269 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
51214 GGCCGGCCTG
**
51224 GGTAGCGCTTATATAATGTAATA
1 GGTAGCGCTTATATAATAAAATA
51247 GGTAGCGCTTATATAATAAAATA
1 GGTAGCGCTTATATAATAAAATA
51270 TGTTAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (23 bp):
GGTAGCGCTTATATAATAAAATA
Found at i:51335 original size:23 final size:23
Alignment explanation
Indices: 51309--51382 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
51299 AATAACATAT
51309 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
51332 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
* **
51355 TAAGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATGTAA
51378 TAGGT
1 TAGGT
51383 TAATTACTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:51420 original size:110 final size:110
Alignment explanation
Indices: 51224--51460 Score: 402
Period size: 110 Copynumber: 2.2 Consensus size: 110
51214 GGCCGGCCTG
* * *
51224 GGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATATGTTAATTACTGGAAATAT
1 GGTAGCGCTTATATAATGTAATAAGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACAT
* * *
51289 TATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATA
66 TATCAAACACAATAACATATTAGGAAGCGCTTATATAACGTAATA
51334 GGTAGCGCTTATATAATGTAATAAGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACAT
1 GGTAGCGCTTATATAATGTAATAAGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACAT
*
51399 TATCAAACACAATAACTTATTAGGAAGCGCTTATATAACGTAATA
66 TATCAAACACAATAACATATTAGGAAGCGCTTATATAACGTAATA
*
51444 GGTAGCACTTATATAAT
1 GGTAGCGCTTATATAAT
51461 AAATAGGTTA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 119 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (110 bp):
GGTAGCGCTTATATAATGTAATAAGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACAT
TATCAAACACAATAACATATTAGGAAGCGCTTATATAACGTAATA
Found at i:51436 original size:23 final size:23
Alignment explanation
Indices: 51410--51459 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
51400 ATCAAACACA
* * *
51410 ATAACTTATTAGGAAGCGCTTAT
1 ATAACGTAATAGGAAGCACTTAT
*
51433 ATAACGTAATAGGTAGCACTTAT
1 ATAACGTAATAGGAAGCACTTAT
51456 ATAA
1 ATAA
51460 TAAATAGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACGTAATAGGAAGCACTTAT
Found at i:51807 original size:19 final size:19
Alignment explanation
Indices: 51752--51807 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
51742 TTATTTTTAA
*
51752 AATATTAGAATAATTAT-TT
1 AATATTAAAAT-ATTATATT
** * *
51771 AATATTATTATGTAATATT
1 AATATTAAAATATTATATT
51790 AATATTAAAATATTATAT
1 AATATTAAAATATTATAT
51808 CTATAATTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
AATATTAAAATATTATATT
Found at i:51826 original size:28 final size:30
Alignment explanation
Indices: 51786--51881 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 30
51776 TATTATGTAA
*
51786 TATTAATATTAAAATATTATATCTATA-ATTT
1 TATTAA-AATAAAATATTATAT-TATATATTT
*
51817 TA-T-AAATAAAA-AATATGATTATATATTT
1 TATTAAAATAAAATATTAT-ATTATATATTT
*
51845 TATTAAAATAAAATTATTATAAATTATATTTTT
1 TATTAAAATAAAA-TATTAT--ATTATATATTT
51878 TATT
1 TATT
51882 TTTATAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.15
28 14 0.26
29 2 0.04
30 9 0.17
31 2 0.04
32 4 0.08
33 14 0.26
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TATTAAAATAAAATATTATATTATATATTT
Found at i:51832 original size:30 final size:30
Alignment explanation
Indices: 51786--51876 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 30
51776 TATTATGTAA
* * *
51786 TATTAATATTAAAATATTATATCTATAATTT
1 TATTAAAATAAAAATATTATATATAT-ATTT
*
51817 TA-T-AAATAAAAAATATGAT-TATATATTT
1 TATTAAAAT-AAAAATATTATATATATATTT
* *
51845 TATTAAAATAAAATTATTATAAATTATATTT
1 TATTAAAATAAAAATATTATATA-TATATTT
51876 T
1 T
51877 TTATTTTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.12
29 17 0.35
30 15 0.31
31 10 0.21
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TATTAAAATAAAAATATTATATATATATTT
Done.