Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001866.1 Hibiscus syriacus cultivar Beakdansim tig00003781_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: 106955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:654 original size:20 final size:20
Alignment explanation
Indices: 626--664 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
616 CGCAGCGCGA
626 ACTTCGACTATCACAATGCT
1 ACTTCGACTATCACAATGCT
* *
646 ACTTGGACTATCGCAATGC
1 ACTTCGACTATCACAATGC
665 GAATATGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
ACTTCGACTATCACAATGCT
Found at i:681 original size:21 final size:21
Alignment explanation
Indices: 655--749 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
645 TACTTGGACT
655 ATCGCAATGCGAATATGTAAA
1 ATCGCAATGCGAATATGTAAA
**
676 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--AAA
* **
697 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTAAA
718 ATCGCAATGCGAATATGT-AA
1 ATCGCAATGCGAATATGTAAA
738 ATCGCAATGCGA
1 ATCGCAATGCGA
750 TAGTCGAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
19 2 0.03
20 16 0.26
21 41 0.66
22 1 0.02
23 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAATATGTAAA
Found at i:695 original size:62 final size:62
Alignment explanation
Indices: 629--756 Score: 222
Period size: 62 Copynumber: 2.1 Consensus size: 62
619 AGCGCGAACT
*
629 TCGACTATCACAATGC-TACTTGGACTATCGCAATGCGAATATGTAAAATCGCAATGCGATAG
1 TCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGT-AAATCGCAATGCGATAG
*
691 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
753 TCGA
1 TCGA
757 AGTTCGTGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 36 0.57
63 27 0.43
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (62 bp):
TCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
Found at i:771 original size:21 final size:21
Alignment explanation
Indices: 745--853 Score: 132
Period size: 21 Copynumber: 5.3 Consensus size: 21
735 TAAATCGCAA
*
745 TGCGATAGTCGAAGTTCGTGT
1 TGCGATAGTCGAAGTTCGCGT
* *
766 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCGT
787 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
** * *
808 TGCGATTTTCCAAATT--CGT
1 TGCGATAGTCGAAGTTCGCGT
*
827 TGCGATAGTAGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
848 TGCGAT
1 TGCGAT
854 TTATTTCAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.19
21 58 0.81
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:791 original size:42 final size:42
Alignment explanation
Indices: 739--878 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
729 AATATGTAAA
* * *
739 TCGCAATGCGATAGTCGAAGTTCGTGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAAT
**
781 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAAT
* * *
823 TCG--TTGCGATAGTAGAAGTTCGCGTTGCGATTTATTTCAAAT
1 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGA--TAGTCCAAAT
865 TCG--TTGCGATAGTC
1 TCGCATTGCGATAGTC
879 CCAAAATCGC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 26 0.30
42 61 0.70
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (42 bp):
TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAAT
Found at i:1504 original size:5 final size:5
Alignment explanation
Indices: 1494--1525 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1484 CGTCTCGCTC
*
1494 TCGGG TCGGG TCGGG TCGGG TCGGG TCCGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC
1526 AGCGGTCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.25, G:0.53, T:0.22
Consensus pattern (5 bp):
TCGGG
Found at i:1649 original size:19 final size:19
Alignment explanation
Indices: 1625--1702 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
1615 TCGTTGCGAT
*
1625 TTTGGACTATCACAACGAA
1 TTTGGACTATCGCAACGAA
*
1644 TTTGGAATAAATCGCAACGCAAA
1 TTTGGACT--ATCGCAACG--AA
* *
1667 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
**
1686 TTTGGAAAATCGCAACG
1 TTTGGACTATCGCAACG
1703 CGAACTTCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
19 22 0.48
21 17 0.37
23 7 0.15
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:1688 original size:42 final size:41
Alignment explanation
Indices: 1629--1758 Score: 176
Period size: 40 Copynumber: 3.2 Consensus size: 41
1619 TGCGATTTTG
*
1629 GACTATCACAACGAATTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCACAACGAATTTGG-ATAAATCGCAACGCGAACTTC
*
1671 GACTATCGCAACGAATTTGGA-AAATCGCAACGCGAACTTC
1 GACTATCACAACGAATTTGGATAAATCGCAACGCGAACTTC
* *
1711 GACTATCACAATGCGAATAT-G-TAAATCGCAATGCGAACTTC
1 GACTATCACAA--CGAATTTGGATAAATCGCAACGCGAACTTC
1752 GACTATC
1 GACTATC
1759 GCATTGCGAT
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
40 28 0.35
41 27 0.34
42 25 0.31
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
GACTATCACAACGAATTTGGATAAATCGCAACGCGAACTTC
Found at i:1726 original size:21 final size:21
Alignment explanation
Indices: 1654--1767 Score: 85
Period size: 21 Copynumber: 5.6 Consensus size: 21
1644 TTTGGAATAA
* *
1654 ATCGCAACGCAAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* * **
1675 ATCGCAA--CGAATTTGGAAA
1 ATCGCAATGCGAACTTCGACT
*
1694 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
1715 ATCACAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
1735 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1756 ATCGCATTGCGA
1 ATCGCAATGCGA
1768 TTACATATTC
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
19 14 0.20
20 16 0.23
21 41 0.58
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1747 original size:41 final size:42
Alignment explanation
Indices: 1651--1767 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 42
1641 GAATTTGGAA
* *
1651 TAAATCGCAACGCAAACTTCGACTATCGCAA--CGAATTTGG
1 TAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGG
* *
1691 AAAATCGCAACGCGAACTTCGACTATCACAATGCGAATAT-G
1 TAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGG
* *
1732 TAAATCGCAATGCGAACTTCGACTATCGCATTGCGA
1 TAAATCGCAACGCGAACTTCGACTATCGCAATGCGA
1768 TTACATATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 28 0.42
41 33 0.49
42 6 0.09
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (42 bp):
TAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGG
Found at i:1801 original size:21 final size:21
Alignment explanation
Indices: 1775--1952 Score: 238
Period size: 21 Copynumber: 8.6 Consensus size: 21
1765 CGATTACATA
1775 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1796 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
1816 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
*
1838 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1859 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1880 TTCGCATTGCGAT--TACATA-
1 TTCGCATTGCGATAGTCCA-AG
*
1899 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1920 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1941 TTCGCGTTGCGA
1 TTCGCATTGCGA
1953 ATCTGGAAAC
Statistics
Matches: 137, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
19 15 0.11
20 5 0.04
21 114 0.83
22 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1933 original size:82 final size:83
Alignment explanation
Indices: 1775--1952 Score: 290
Period size: 82 Copynumber: 2.1 Consensus size: 83
1765 CGATTACATA
*
1775 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCCAAGTT
1 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAG-CGACTATCGCATTGCGATAGTCCAAGTT
1840 CGCATTGCGATAGTCGAAG
65 CGCATTGCGATAGTCGAAG
*
1859 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATTA-C-A-TATTCGCATTGTGATAGTCCAAGT
1 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGA-TAGCGACTA-TCGCATTGCGATAGTCCAAGT
1921 TCGCATTGCGATAGTCGAAG
64 TCGCATTGCGATAGTCGAAG
1941 TTCGCGTTGCGA
1 TTCGCGTTGCGA
1953 ATCTGGAAAC
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
81 2 0.02
82 53 0.59
83 1 0.01
84 32 0.36
85 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (83 bp):
TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGCGACTATCGCATTGCGATAGTCCAAGTTC
GCATTGCGATAGTCGAAG
Found at i:4814 original size:28 final size:28
Alignment explanation
Indices: 4774--4828 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
4764 ATTATTTTCT
4774 TTTAAATTTGAATGGTGAGAGATTGAGG
1 TTTAAATTTGAATGGTGAGAGATTGAGG
4802 TTTAAATTTGAATGGTGAGAGATTGAG
1 TTTAAATTTGAATGGTGAGAGATTGAG
4829 AAGGAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (28 bp):
TTTAAATTTGAATGGTGAGAGATTGAGG
Found at i:5029 original size:30 final size:28
Alignment explanation
Indices: 4975--5030 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
4965 TGTTTTTTTT
*
4975 AGTTTAGTGTTAATGTTTATTTCGTTTC
1 AGTTTAGTGTTAACGTTTATTTCGTTTC
*
5003 AGTTTGGTGTCTAACGTTTCATTTCGTT
1 AGTTTAGTGT-TAACGTTT-ATTTCGTT
5031 ACTCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 7 0.29
30 8 0.33
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.54
Consensus pattern (28 bp):
AGTTTAGTGTTAACGTTTATTTCGTTTC
Found at i:8085 original size:19 final size:19
Alignment explanation
Indices: 8061--8103 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
8051 ATGAAATCAT
8061 TGTTTAAGGACTTATTTGA
1 TGTTTAAGGACTTATTTGA
8080 TGTTTAAGGACTTATTTGA
1 TGTTTAAGGACTTATTTGA
8099 TGTTT
1 TGTTT
8104 TAAATGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (19 bp):
TGTTTAAGGACTTATTTGA
Found at i:8817 original size:11 final size:11
Alignment explanation
Indices: 8801--8826 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8791 TAACAAGTTG
8801 AATTCTACTAT
1 AATTCTACTAT
8812 AATTCTACTAT
1 AATTCTACTAT
8823 AATT
1 AATT
8827 AATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTACTAT
Found at i:9527 original size:2 final size:2
Alignment explanation
Indices: 9522--9547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9512 TAAATTCATA
9522 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
9548 TTTACAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20452 original size:60 final size:60
Alignment explanation
Indices: 20364--20510 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 60
20354 TATTAAGGGT
* * * * *
20364 AAAG-TACACAAATGGTCCCCTGACTATAGGGTGTTATTTTGTTGAGTCACTCAACTATTA
1 AAAGTTACA-AAATGGTCCCCAGACTATAGGGTATTACTTTATTAAGTCACTCAACTATTA
* * *
20424 AAAGTTACAAAATGGTCCCTCAG-CTATAGGGTATTGCTTTATTAAGTCCCTCGACTATTA
1 AAAGTTACAAAATGGTCCC-CAGACTATAGGGTATTACTTTATTAAGTCACTCAACTATTA
* * *
20484 AATGTTACAAAATGGTCACCTGACTAT
1 AAAGTTACAAAATGGTCCCCAGACTAT
20511 TCATATGTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.03
60 65 0.89
61 6 0.08
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCAGACTATAGGGTATTACTTTATTAAGTCACTCAACTATTA
Found at i:22031 original size:24 final size:25
Alignment explanation
Indices: 21996--22043 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
21986 TAAATATAAT
21996 ATTTAACATG-TTGAAAAAGATTTG
1 ATTTAACATGTTTGAAAAAGATTTG
*
22020 ATTTAACGTGTTTGAAAAAGATTT
1 ATTTAACATGTTTGAAAAAGATTT
22044 TATTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.40
Consensus pattern (25 bp):
ATTTAACATGTTTGAAAAAGATTTG
Found at i:33228 original size:21 final size:21
Alignment explanation
Indices: 33188--33228 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33178 TCGATTAAAT
**
33188 AATCATTTTAATCCTTTTTTG
1 AATCATTTTAATCCAATTTTG
*
33209 AATCATTTTAATTCAATTTT
1 AATCATTTTAATCCAATTTT
33229 TTTAAAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (21 bp):
AATCATTTTAATCCAATTTTG
Found at i:33792 original size:24 final size:25
Alignment explanation
Indices: 33745--33796 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
33735 AGTGTTTTTC
*
33745 TAAGTTAAAGATTGTTTTTTTCTCA
1 TAAGTTAAAGATTGATTTTTTCTCA
*
33770 TAAGTTAGAGATT-ATTTTTTCTCA
1 TAAGTTAAAGATTGATTTTTTCTCA
33794 TAA
1 TAA
33797 TAAATTACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (25 bp):
TAAGTTAAAGATTGATTTTTTCTCA
Found at i:35951 original size:22 final size:23
Alignment explanation
Indices: 35912--35955 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
35902 TAAACTATAT
*
35912 TATATACAACACATACACACATA
1 TATATACAACACACACACACATA
35935 TATATAC-ACACACACACACAT
1 TATATACAACACACACACACAT
35956 GTTGAGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (23 bp):
TATATACAACACACACACACATA
Found at i:40464 original size:26 final size:24
Alignment explanation
Indices: 40414--40464 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
40404 TTTTACTAAG
* * *
40414 ATTTTATAATATTTATTTAATTCA
1 ATTTTATAATATTTAGTGAAATCA
40438 ATTTTATAATAAATTTAGTGAAATCA
1 ATTTTATAAT--ATTTAGTGAAATCA
40464 A
1 A
40465 ATTAGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTTATAATATTTAGTGAAATCA
Found at i:40688 original size:25 final size:25
Alignment explanation
Indices: 40635--40695 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
40625 TTTGTGGTAT
* *
40635 TTTTTA-TATTTAAATTTTTAAATA
1 TTTTTATTTTTTAAATTTATAAATA
*
40659 TTTTTGTTTTTTAAA-TTATAAATA
1 TTTTTATTTTTTAAATTTATAAATA
40683 TTTTTTATTTTTT
1 -TTTTTATTTTTT
40696 CCCTAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTTATTTTTTAAATTTATAAATA
Found at i:40693 original size:24 final size:25
Alignment explanation
Indices: 40632--40694 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
40622 TTATTTGTGG
* *
40632 TATTTTTTATATTTAAATTTTTAAA
1 TATTTTTTATTTTTAAATTTATAAA
40657 TATTTTTGT-TTTTTAAA-TTATAAA
1 TATTTTT-TATTTTTAAATTTATAAA
40681 TATTTTTTATTTTT
1 TATTTTTTATTTTT
40695 TCCCTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 18 0.53
25 14 0.41
26 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
TATTTTTTATTTTTAAATTTATAAA
Found at i:41480 original size:21 final size:20
Alignment explanation
Indices: 41450--41508 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
41440 TGCGATTTAT
*
41450 TCCAAATTCGCATTGCGATAG
1 TCCAAGTTCGC-TTGCGATAG
41471 TCCAAGTTCG-TTGCGATAG
1 TCCAAGTTCGCTTGCGATAG
*
41490 TCGAAGTTCGCGTTGCGAT
1 TCCAAGTTCGC-TTGCGAT
41509 TTAGGGTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (20 bp):
TCCAAGTTCGCTTGCGATAG
Found at i:41570 original size:15 final size:15
Alignment explanation
Indices: 41545--41616 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
41535 TGGTTTTTCA
41545 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
41560 GAATTTGAATTACTG
1 GAAAATGAATTACTG
*
41575 GAAAATGAATTACTA
1 GAAAATGAATTACTG
**
41590 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
41604 GAAAATGAATTAC
1 GAAAATGAATTAC
41617 ATTTCTGTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
14 11 0.24
15 35 0.76
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:41614 original size:29 final size:30
Alignment explanation
Indices: 41545--41616 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
41535 TGGTTTTTCA
*
41545 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTAGAATTTGAATTACTG
41575 GAAAATGAATTACTAGAATTTGAATT-CTG
1 GAAAATGAATTACTAGAATTTGAATTACTG
41604 GAAAATGAATTAC
1 GAAAATGAATTAC
41617 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTAGAATTTGAATTACTG
Found at i:41622 original size:20 final size:20
Alignment explanation
Indices: 41599--41668 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
41589 AGAATTTGAA
41599 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
41619 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
41639 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
41659 TTCTGGAAAA
1 TTCTGGAAAA
41669 CATTTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:41891 original size:30 final size:28
Alignment explanation
Indices: 41834--41937 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 28
41824 CTTTACTAAA
*
41834 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAAAAATATTAT
41863 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATAT-AAAAAA-TATTAT
41893 ATATTATTAAA-ATA-AAATTATAATATCT-T
1 ATATTATTAAATATATAAA--A-AATAT-TAT
41922 ATATTATTATAATATA
1 ATATTATTA-AATATA
41938 ATTGATTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
27 3 0.05
28 9 0.14
29 28 0.44
30 20 0.31
31 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:41953 original size:29 final size:28
Alignment explanation
Indices: 41885--41976 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
41875 ATATAAAAAA
*
41885 ATTA-TTATATATTATTAAAATAAAATT
1 ATTATTTATATATTATTAAAATATAATT
* *
41912 ATAATATCT-TATATTATTATAATATAATT
1 AT--TATTTATATATTATTAAAATATAATT
*
41941 GATTATTTATATAATATTAAAAATATATATT
1 -ATTATTTATATATTATT-AAAATATA-ATT
41972 ATTAT
1 ATTAT
41977 AAATATTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.04
28 4 0.08
29 28 0.54
30 15 0.29
31 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATTATTTATATATTATTAAAATATAATT
Found at i:41967 original size:16 final size:16
Alignment explanation
Indices: 41948--41987 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
41938 ATTGATTATT
41948 TATATAATATTAAAAA
1 TATATAATATTAAAAA
* *
41964 TATATATTATTATAAA
1 TATATAATATTAAAAA
41980 TAT-TAATA
1 TATATAATA
41988 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATAATATTAAAAA
Found at i:41977 original size:24 final size:25
Alignment explanation
Indices: 41921--41994 Score: 86
Period size: 21 Copynumber: 3.1 Consensus size: 25
41911 TATAATATCT
**
41921 TATATTATTATAATA-TAATTGAT-
1 TATATTATTATAATATTAATAAATA
41944 TAT-TTA-TATAATATTAA-AAATA
1 TATATTATTATAATATTAATAAATA
41966 TATATTATTATAAATATTAATAAATA
1 TATATTATTAT-AATATTAATAAATA
41992 TAT
1 TAT
41995 TTTAAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
21 9 0.21
22 9 0.21
23 6 0.14
24 3 0.07
25 8 0.19
26 8 0.19
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
TATATTATTATAATATTAATAAATA
Found at i:42000 original size:21 final size:22
Alignment explanation
Indices: 41962--42004 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
41952 TAATATTAAA
*
41962 AATATATATTATTATAAATATT
1 AATAAATATTATTATAAATATT
*
41984 AATAAATA-TATTTTAAATATT
1 AATAAATATTATTATAAATATT
42005 TTAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAAATATTATTATAAATATT
Found at i:42358 original size:21 final size:19
Alignment explanation
Indices: 42332--42429 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 19
42322 TAATTCCAAA
42332 TTCGTTGCGATAGTTCAAG
1 TTCGTTGCGATAGTTCAAG
*
42351 TTCGCGTTGCGATTTA-TGCCAAG
1 TT--CGTTGCGA--TAGT-TCAAG
42374 TTCGTTGCGATAG-TCGAAG
1 TTCGTTGCGATAGTTC-AAG
42393 TTCGCGTTGCGATTTA-TTCCAAG
1 TT--CGTTGCGA--TAGTT-CAAG
42416 TTCGTTGCGATAGT
1 TTCGTTGCGATAGT
42430 CCAAAATCGC
Statistics
Matches: 63, Mismatches: 2, Indels: 27
0.68 0.02 0.29
Matches are distributed among these distances:
18 1 0.02
19 11 0.17
20 1 0.02
21 32 0.51
22 1 0.02
23 16 0.25
24 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (19 bp):
TTCGTTGCGATAGTTCAAG
Found at i:42377 original size:23 final size:21
Alignment explanation
Indices: 42355--42426 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
42345 TTCAAGTTCG
42355 CGTTGCGATTTATGCCAAGTT
1 CGTTGCGATTTATGCCAAGTT
*
42376 CGTTGCGA--TA-GTCGAAGTT
1 CGTTGCGATTTATG-CCAAGTT
*
42395 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATGCCAAGTT
42418 CGTTGCGAT
1 CGTTGCGAT
42427 AGTCCAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.02
19 8 0.19
21 25 0.60
23 8 0.19
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATTTATGCCAAGTT
Found at i:42430 original size:42 final size:41
Alignment explanation
Indices: 42324--42430 Score: 178
Period size: 42 Copynumber: 2.6 Consensus size: 41
42314 CAGACCCTTA
*
42324 ATTCCAAATTCGTTGCGATAGTTCAAGTTCGCGTTGCGATTT
1 ATTCCAAGTTCGTTGCGATAG-TCAAGTTCGCGTTGCGATTT
*
42366 ATGCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 ATTCCAAGTTCGTTGCGATAGTC-AAGTTCGCGTTGCGATTT
42408 ATTCCAAGTTCGTTGCGATAGTC
1 ATTCCAAGTTCGTTGCGATAGTC
42431 CAAAATCGCA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 2 0.03
42 59 0.97
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
ATTCCAAGTTCGTTGCGATAGTCAAGTTCGCGTTGCGATTT
Found at i:43425 original size:21 final size:21
Alignment explanation
Indices: 43367--43554 Score: 117
Period size: 21 Copynumber: 9.1 Consensus size: 21
43357 AACTTCGACT
43367 AACTTCGACTATCGCAA--CG
1 AACTTCGACTATCGCAACGCG
* * *
43386 AATTTGGAATAAATCGCAACGCG
1 AACTTCGACT--ATCGCAACGCG
*
43409 AACTTCGACTATTGCAA--CG
1 AACTTCGACTATCGCAACGCG
* *
43428 AACTTAGACTATCACAA--CG
1 AACTTCGACTATCGCAACGCG
* *
43447 AA-TTTGTAATAAATCGCAACGCG
1 AACTTCG-ACT--ATCGCAACGCG
**
43470 AACTTCGACTATCGCAAATC-
1 AACTTCGACTATCGCAACGCG
**
43490 AGTTTCCAGA-T-TCGCAACGCG
1 AACTT-C-GACTATCGCAACGCG
43511 AACTTCGACTATCGCAACGCG
1 AACTTCGACTATCGCAACGCG
* *
43532 AACTTGGACTATCGCAATGCG
1 AACTTCGACTATCGCAACGCG
43553 AA
1 AA
43555 TATGTAAATC
Statistics
Matches: 129, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
18 3 0.02
19 31 0.24
20 12 0.09
21 63 0.49
22 2 0.02
23 15 0.12
24 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
AACTTCGACTATCGCAACGCG
Found at i:43445 original size:19 final size:19
Alignment explanation
Indices: 43407--43448 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
43397 AATCGCAACG
* **
43407 CGAACTTCGACTATTGCAA
1 CGAACTTAGACTATCACAA
43426 CGAACTTAGACTATCACAA
1 CGAACTTAGACTATCACAA
43445 CGAA
1 CGAA
43449 TTTGTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (19 bp):
CGAACTTAGACTATCACAA
Found at i:43462 original size:61 final size:61
Alignment explanation
Indices: 43367--43486 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
43357 AACTTCGACT
* * *
43367 AACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACG
1 AACTTAGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
*
43428 AACTTAGACTATCACAACGAATTTGTAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 AACTTAGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
43487 ATCAGTTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (61 bp):
AACTTAGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
Found at i:47397 original size:14 final size:16
Alignment explanation
Indices: 47368--47400 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
47358 TGAATACTTT
47368 ATACTAAAATAATATA
1 ATACTAAAATAATATA
47384 ATACT-AAA-AATATA
1 ATACTAAAATAATATA
47398 ATA
1 ATA
47401 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 3 0.18
16 5 0.29
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
ATACTAAAATAATATA
Found at i:47445 original size:29 final size:30
Alignment explanation
Indices: 47375--47446 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
47365 TTTATACTAA
*
47375 AATAATATAATACTAAAAATATAATATTATT
1 AATAAT-TAATATTAAAAATATAATATTATT
* * *
47406 AAAAATT-ATATTATATATATAATATT-TT
1 AATAATTAATATTAAAAATATAATATTATT
47434 AATAATTAATATT
1 AATAATTAATATT
47447 TTCATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.23
29 21 0.60
30 1 0.03
31 5 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AATAATTAATATTAAAAATATAATATTATT
Found at i:60015 original size:32 final size:32
Alignment explanation
Indices: 59937--60042 Score: 150
Period size: 32 Copynumber: 3.4 Consensus size: 32
59927 ATAAATCTTG
* *
59937 TTATTAAAATTTTA-AAAAAT-T-AT-AAATTA
1 TTATT-AAATTTTATCAAAATGTCATAAAATAA
59966 TTATTAAA-TTTATCAAAATGTCATAAAATAA
1 TTATTAAATTTTATCAAAATGTCATAAAATAA
59997 TTATTAAATTTTATCAAAATGTCATAAAATAA
1 TTATTAAATTTTATCAAAATGTCATAAAATAA
60029 TTATTAAATTTTAT
1 TTATTAAATTTTAT
60043 TAACAATCTC
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
27 4 0.06
28 8 0.11
29 6 0.09
30 2 0.03
31 13 0.19
32 37 0.53
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (32 bp):
TTATTAAATTTTATCAAAATGTCATAAAATAA
Found at i:65251 original size:28 final size:28
Alignment explanation
Indices: 65211--65266 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
65201 TGAAATTAGC
* *
65211 TTTAAGGTTTAATTTGATACCTAAAATT
1 TTTAAGGTCTAATTAGATACCTAAAATT
* * *
65239 TTTATGGTCTAATTAGGTACCTGAAATT
1 TTTAAGGTCTAATTAGATACCTAAAATT
65267 GATTTACTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (28 bp):
TTTAAGGTCTAATTAGATACCTAAAATT
Found at i:66032 original size:23 final size:23
Alignment explanation
Indices: 65953--66021 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
65943 TATTGTTTGT
* *
65953 AAACATGTTTGTTTATATGTTCAC
1 AAACATGTTCGTTTA-ACGTTCAC
65977 AAACATGTTCGTTTAACGTTCAC
1 AAACATGTTCGTTTAACGTTCAC
66000 AAACATGTTCGTTTAACGTTCA
1 AAACATGTTCGTTTAACGTTCA
66022 TTTATATGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 29 0.67
24 14 0.33
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
AAACATGTTCGTTTAACGTTCAC
Found at i:69510 original size:29 final size:29
Alignment explanation
Indices: 69473--69529 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
69463 CAAATTGTCA
*
69473 TTTTTCACAAAAATTCCCAGAATATCACC
1 TTTTCCACAAAAATTCCCAGAATATCACC
*
69502 TTTTCCACAAAAATTCCCAGAATGTCAC
1 TTTTCCACAAAAATTCCCAGAATATCAC
69530 TGGGTTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.30
Consensus pattern (29 bp):
TTTTCCACAAAAATTCCCAGAATATCACC
Found at i:73177 original size:37 final size:37
Alignment explanation
Indices: 73135--73209 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
73125 CATTAAATCT
*
73135 TTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATAAA
1 TTTTATGAATTTCAATTTTGTAAAAAAAA-TATATAAA
* * *
73172 TTTTATGAATTTGAATTTTTTAAAGAAAATATATAAA
1 TTTTATGAATTTCAATTTTGTAAAAAAAATATATAAA
73209 T
1 T
73210 ATTTTCCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTTATGAATTTCAATTTTGTAAAAAAAATATATAAA
Found at i:73383 original size:20 final size:20
Alignment explanation
Indices: 73358--73410 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
73348 ATCATATTTC
73358 CTAGTAATCTTACATTCTCA
1 CTAGTAATCTTACATTCTCA
73378 CTAGTAATCTTACATTCTCA
1 CTAGTAATCTTACATTCTCA
*
73398 CTAATAATCTTAC
1 CTAGTAATCTTAC
73411 CTTCCGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (20 bp):
CTAGTAATCTTACATTCTCA
Found at i:106831 original size:27 final size:27
Alignment explanation
Indices: 106793--106844 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
106783 CTACCGTCGC
*
106793 TTTCAAACACTAACTTGATGACATATG
1 TTTCAAACACTAACTTGACGACATATG
*
106820 TTTCAAGCACTAACTTGACGACATA
1 TTTCAAACACTAACTTGACGACATA
106845 ATGTAAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (27 bp):
TTTCAAACACTAACTTGACGACATATG
Done.