Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004682.1 Hibiscus syriacus cultivar Beakdansim tig00010496_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: 61604
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:4686 original size:22 final size:22
Alignment explanation
Indices: 4655--4704 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
4645 GTCGAAGAAG
*
4655 AAGAAGAAAAAAATAAAAAG-GA
1 AAGAA-AAAAAAAAAAAAAGAGA
*
4677 AAGAAAAAAACAAAAAAAGAGA
1 AAGAAAAAAAAAAAAAAAGAGA
4699 AA-AAAA
1 AAGAAAA
4705 CTTTGGGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAAAAAAAAAAGAGA
Found at i:4691 original size:18 final size:17
Alignment explanation
Indices: 4658--4705 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
4648 GAAGAAGAAG
*
4658 AAGAAAAAAATAAAAAGGA
1 AAGAAAAAAACAAAAA--A
4677 AAGAAAAAAACAAAAAA
1 AAGAAAAAAACAAAAAA
4694 AGAGAAAAAAAC
1 A-AGAAAAAAAC
4706 TTTGGGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 2 0.07
18 10 0.37
19 15 0.56
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAACAAAAAA
Found at i:4763 original size:20 final size:19
Alignment explanation
Indices: 4740--4810 Score: 76
Period size: 19 Copynumber: 3.6 Consensus size: 19
4730 CCTTAAATTA
4740 AAAAAGAGAACAAAGAAAAG
1 AAAAAGAGAA-AAAGAAAAG
4760 AAAAAAGAGAAAAAGAACAA-
1 -AAAAAGAGAAAAAGAA-AAG
4780 ATAAAAGA-AAAAGAGAAAAG
1 A-AAAAGAGAAAA-AGAAAAG
4800 AAAAAGA-AAAA
1 AAAAAGAGAAAA
4811 TAAGGTGGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
19 17 0.37
20 17 0.37
21 12 0.26
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (19 bp):
AAAAAGAGAAAAAGAAAAG
Found at i:4785 original size:27 final size:27
Alignment explanation
Indices: 4741--4800 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
4731 CTTAAATTAA
4741 AAAAGAGAACAAAGAAAAGAAAAAAGAG
1 AAAAGAGAACAAAGAAAAG-AAAAAGAG
*
4769 AAAA-AGAACAAATAAAAGAAAAAGAG
1 AAAAGAGAACAAAGAAAAGAAAAAGAG
4795 AAAAGA
1 AAAAGA
4801 AAAAGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 12 0.40
27 14 0.47
28 4 0.13
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (27 bp):
AAAAGAGAACAAAGAAAAGAAAAAGAG
Found at i:6049 original size:123 final size:121
Alignment explanation
Indices: 5704--6053 Score: 393
Period size: 120 Copynumber: 2.9 Consensus size: 121
5694 ACAATACTTG
* * *
5704 GATTTCAAATTCACGACGAAGGATATTGTGCCTACCAA-CAACATTCATCATTATATTGGATTTC
1 GATTTCAACTTCACGACGAAGGATATTGTGCCCA-CAAGCAACATCCATC-TTA-A-TGGATTTC
* * * * * *
5768 AACTTCATAATGAAGGATATTCAATTCGAGGTTGAACTTCACCACAAATGGGCCATCCAC
62 AACTTCATAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCATCCAC
* * * * * * * *
5828 GATTTCAACTTCATGATGAATGAT-TTCATGTCCACAAGCAACATACAATATT--TGGATTTTAA
1 GATTTCAACTTCACGACGAAGGATATT-GTGCCCACAAGCAACAT-CCATCTTAATGGATTTCAA
* * *
5890 CTTCATGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCAT
64 CTTCATAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCATCCAC
5948 GATTTCAACTTCACGACGAAGGATATTGTGCCCACAAGCAACATCCATCTCTAGATGGATTTCAA
1 GATTTCAACTTCACGACGAAGGATATTGTGCCCACAAGCAACATCCATCT-TA-ATGGATTTCAA
* * *
6013 CTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
64 CTTCATAATGAAGGATATCCAATTCAAGGCTCAACTTCACA
6054 GTAAAGGAGA
Statistics
Matches: 186, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
119 4 0.02
120 95 0.51
121 2 0.01
123 51 0.27
124 32 0.17
125 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (121 bp):
GATTTCAACTTCACGACGAAGGATATTGTGCCCACAAGCAACATCCATCTTAATGGATTTCAACT
TCATAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCATCCAC
Found at i:7709 original size:13 final size:13
Alignment explanation
Indices: 7693--7733 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
7683 TTAATATATA
*
7693 TTTATTTGTTTCT
1 TTTATTTGTTTAT
*
7706 TTTATTTTTTTAT
1 TTTATTTGTTTAT
7719 TTTATTT-TTTAT
1 TTTATTTGTTTAT
7731 TTT
1 TTT
7734 CTTTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTATTTGTTTAT
Found at i:7728 original size:12 final size:12
Alignment explanation
Indices: 7693--7806 Score: 70
Period size: 12 Copynumber: 8.7 Consensus size: 12
7683 TTAATATATA
*
7693 TTTATTTGTTTCT
1 TTTATTT-TTTAT
7706 TTTATTTTTTTAT
1 TTTA-TTTTTTAT
7719 TTTATTTTTTAT
1 TTTATTTTTTAT
*
7731 TTTCTTTAATTATTAT
1 TTT-ATT--TT-TTAT
7747 TATTATTTTCTTA-
1 T-TTATTTT-TTAT
*
7760 TTTATTATTTAT
1 TTTATTTTTTAT
7772 TTTATCCTATTTT-T
1 TTTAT--T-TTTTAT
*
7786 TACTATTTTTTAT
1 T-TTATTTTTTAT
7799 TTTATTTT
1 TTTATTTT
7807 ATATATTATA
Statistics
Matches: 81, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
11 3 0.04
12 32 0.40
13 18 0.22
14 11 0.14
15 8 0.10
16 7 0.09
17 2 0.02
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:7747 original size:3 final size:3
Alignment explanation
Indices: 7739--7869 Score: 59
Period size: 3 Copynumber: 44.0 Consensus size: 3
7729 ATTTTCTTTA
*
7739 ATT ATT ATT ATT ATT -TT CTT ATTT ATT ATTT ATT -TT ATCCT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT AT--T ATT ATT
*
7785 -TT ACT ATT -TT -TT ATT -TT ATT -TT ATAT ATT ATAT ATAT ATGT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T AT-T AT-T ATT
* *
7828 ATAT ATT -TT A-T CTT ATTT GTT ATT ATT ATT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
7870 TCTAGTATTT
Statistics
Matches: 103, Mismatches: 8, Indels: 34
0.71 0.06 0.23
Matches are distributed among these distances:
2 21 0.20
3 56 0.54
4 23 0.22
5 3 0.03
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:7766 original size:21 final size:20
Alignment explanation
Indices: 7705--7774 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
7695 TATTTGTTTC
*
7705 TTTTATTTTTTTATTTTATT-
1 TTTTATTTTCTTA-TTTATTA
*
7725 TTTTATTTTCTTTAATTATTA
1 TTTTATTTTC-TTATTTATTA
7746 TTATTATTTTCTTATTTATTA
1 TT-TTATTTTCTTATTTATTA
7767 -TTTATTTT
1 TTTTATTTT
7775 ATCCTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.16
20 15 0.34
21 14 0.32
22 8 0.18
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTTCTTATTTATTA
Found at i:8094 original size:12 final size:11
Alignment explanation
Indices: 8072--8145 Score: 54
Period size: 10 Copynumber: 7.3 Consensus size: 11
8062 GCTATTTGTT
8072 TTTTATCTTTA
1 TTTTATCTTTA
8083 TTTTATCTTT-
1 TTTTATCTTTA
*
8093 TATTA-C-TTA
1 TTTTATCTTTA
*
8102 TTTCATCTTT-
1 TTTTATCTTTA
8112 TTTCT-TCTTTA
1 TTT-TATCTTTA
8123 TTTTAT-TTT-
1 TTTTATCTTTA
* *
8132 CTTTATTTTTA
1 TTTTATCTTTA
8143 TTT
1 TTT
8146 ATTTTCATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 20 0.41
11 18 0.37
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATCTTTA
Found at i:8133 original size:14 final size:15
Alignment explanation
Indices: 8116--8145 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8106 ATCTTTTTTC
8116 TTCTTTA-TTTTATT
1 TTCTTTATTTTTATT
8130 TTCTTTATTTTTATT
1 TTCTTTATTTTTATT
8145 T
1 T
8146 ATTTTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCTTTATTTTTATT
Found at i:16998 original size:27 final size:26
Alignment explanation
Indices: 16939--16994 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
16929 TACATGGATG
*
16939 TTTTATACAACATGATTTTACCATGA
1 TTTTATACAACATGATTTTACCATCA
* *
16965 TTTTATATCGACATGATTTTA-TATCA
1 TTTTATA-CAACATGATTTTACCATCA
16991 TTTT
1 TTTT
16995 TATAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (26 bp):
TTTTATACAACATGATTTTACCATCA
Found at i:17576 original size:47 final size:45
Alignment explanation
Indices: 17481--17607 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 45
17471 GGTAACCATG
* * *
17481 AAAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGA
* *
17525 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGA
*
17572 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
17608 AGATTTTATA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.31
45 11 0.15
46 1 0.01
47 39 0.53
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGA
Found at i:24737 original size:47 final size:45
Alignment explanation
Indices: 24643--24768 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
24633 GTAACCATGC
* * *
24643 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
24687 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
* * *
24734 AAATAAGCTTGCAAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
24769 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:25243 original size:22 final size:22
Alignment explanation
Indices: 25215--25267 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
25205 AAAGTGGTAC
25215 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
25237 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
25259 CGATTCCCC
1 CGATTCCCC
25268 CACTGTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAT
Found at i:25283 original size:7 final size:7
Alignment explanation
Indices: 25268--25297 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
25258 TCGATTCCCC
*
25268 CACTGTT
1 CACTATT
25275 CACTATT
1 CACTATT
25282 CACTATT
1 CACTATT
25289 CACTATT
1 CACTATT
25296 CA
1 CA
25298 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.40
Consensus pattern (7 bp):
CACTATT
Found at i:28709 original size:18 final size:18
Alignment explanation
Indices: 28683--28718 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28673 AGATTTAATT
*
28683 TAGATACACGGTTTGATA
1 TAGAAACACGGTTTGATA
28701 TAGAAACACGGTTTGATA
1 TAGAAACACGGTTTGATA
28719 GGTTTCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
TAGAAACACGGTTTGATA
Found at i:29967 original size:75 final size:76
Alignment explanation
Indices: 29881--30068 Score: 272
Period size: 75 Copynumber: 2.5 Consensus size: 76
29871 GAAAATCGAT
* *
29881 TTTTGGAAAATATATAAAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAG
1 TTTT-GAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATAAATATAATATATAG
*
29946 TTTTTGAAAATA
65 TTTTTGAAAACA
* * * *
29958 TTTTG-AAATATATATAATACATTGTTTTCGAAAACATTTTGAAAACATAAATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATAAATATAATATATAGT
30022 TTTTGAAAACA
66 TTTTGAAAACA
30033 TTTTGAAAAAATATATATAATATATAG-TTTTGAAAA
1 TTTTG--AAAATATATATAATATATAGTTTTTGAAAA
30069 TGTTTTTGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
75 68 0.69
76 1 0.01
77 12 0.12
78 17 0.17
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (76 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATAAATATAATATATAGT
TTTTGAAAACA
Found at i:30079 original size:39 final size:39
Alignment explanation
Indices: 29887--30068 Score: 273
Period size: 39 Copynumber: 4.8 Consensus size: 39
29877 CGATTTTTGG
*
29887 AAAATATATAAAATATATAGTTTTTGAAAACATTTTGAA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGAA
*
29926 AAAATATATATAATATATAGTTTTTGAAAATATTTTG--
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGAA
* * *
29963 -AAATATATATAATACATTGTTTTCGAAAACATTTTGAA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGAA
* *
30001 AACATAAATATAATATATAGTTTTTGAAAACATTTTGAA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGAA
30040 AAAATATATATAATATATAG-TTTTGAAAA
1 AAAATATATATAATATATAGTTTTTGAAAA
30069 TGTTTTTGAA
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
36 32 0.25
38 9 0.07
39 86 0.68
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (39 bp):
AAAATATATATAATATATAGTTTTTGAAAACATTTTGAA
Found at i:30085 original size:20 final size:20
Alignment explanation
Indices: 30060--30099 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
30050 TAATATATAG
*
30060 TTTTGAAAATGTTTTTGAAA
1 TTTTGAAAATGTTTTGGAAA
30080 TTTTGAAAATGTTTTGGAAA
1 TTTTGAAAATGTTTTGGAAA
30100 ATATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.47
Consensus pattern (20 bp):
TTTTGAAAATGTTTTGGAAA
Found at i:30146 original size:4 final size:4
Alignment explanation
Indices: 30121--30184 Score: 59
Period size: 4 Copynumber: 16.8 Consensus size: 4
30111 ATATGTTTTA
30121 ATTT -TTT ACTTT -TTT A-TT ATTT ATTT A-TT ATTT ATTT -TCCTT -TTT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT--TT ATTT
30166 ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATT
30185 ATGTCCTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
3 15 0.29
4 31 0.60
5 6 0.12
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:30149 original size:11 final size:11
Alignment explanation
Indices: 30133--30186 Score: 65
Period size: 11 Copynumber: 4.7 Consensus size: 11
30123 TTTTTACTTT
30133 TTTATTATTTA
1 TTTATTATTTA
30144 TTTATTATTTA
1 TTTATTATTTA
*
30155 TTT-TCCTTTTTA
1 TTTAT--TATTTA
30167 TTTATTTATTTA
1 TTTA-TTATTTA
30179 TTTATTAT
1 TTTATTAT
30187 GTCCTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 1 0.03
11 18 0.49
12 17 0.46
14 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:30196 original size:31 final size:28
Alignment explanation
Indices: 30132--30196 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 28
30122 TTTTTTACTT
30132 TTTTATTATTTATTTATTATTTATTTTCC
1 TTTT-TTATTTATTTATTATTTATTTTCC
30161 -TTTTTATTTATTTATTTATTTATTATGTCC
1 TTTTTTATTTATTTA-TTATTTATT-T-TCC
30191 TTTTTT
1 TTTTTT
30197 CATATTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 11 0.34
28 12 0.38
29 1 0.03
30 3 0.09
31 5 0.16
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTTTATTTATTTATTATTTATTTTCC
Found at i:31515 original size:12 final size:12
Alignment explanation
Indices: 31498--31524 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31488 ATTCTCCCAC
31498 TTTTTTATTTTA
1 TTTTTTATTTTA
31510 TTTTTTATTTTA
1 TTTTTTATTTTA
31522 TTT
1 TTT
31525 GTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:31641 original size:4 final size:4
Alignment explanation
Indices: 31632--31675 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
31622 TTCTTCTTTG
* * *
31632 ATTT ATTT ATTT AATT ATTT ATCT ATTT ATTT AATT -TTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
31676 ATATTTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 2 0.06
4 31 0.94
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:31651 original size:12 final size:12
Alignment explanation
Indices: 31632--31681 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
31622 TTCTTCTTTG
*
31632 ATTTATTTATTT
1 ATTTATTTAATT
*
31644 AATTATTT-ATCT
1 ATTTATTTAAT-T
31656 ATTTATTTAATT
1 ATTTATTTAATT
31668 -TTTATTTAA-T
1 ATTTATTTAATT
31678 ATTT
1 ATTT
31682 CTTTTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 1 0.03
11 13 0.41
12 16 0.50
13 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTATTTAATT
Found at i:31658 original size:20 final size:19
Alignment explanation
Indices: 31635--31672 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
31625 TTCTTTGATT
31635 TATTTATTTAATTATTTATC
1 TATTTATTTAATT-TTTATC
31655 TATTTATTTAATTTTTAT
1 TATTTATTTAATTTTTAT
31673 TTAATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTATTTAATTTTTATC
Found at i:37235 original size:66 final size:62
Alignment explanation
Indices: 37150--37350 Score: 260
Period size: 66 Copynumber: 3.1 Consensus size: 62
37140 AAAAAAATCG
*
37150 ATTTTTGAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATATATAATTCA
1 ATTTTTG-AAAACATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATATA-AA-T-A
37215 T
62 T
* *
37216 ATTTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATA-ACATAT
1 A-TTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATATAAATAT
* *
37278 AGTTTTGAAAACATATATATAATATATAGTTTTTGGAAACATTTTGAAAATATATATATAATATA
1 ATTTTTGAAAAC--ATATATAATATATAG-TTTTGAAAACATTTTGAAAATATATATATAA-ATA
37343 T
62 T
37344 AGTTTTT
1 A-TTTTT
37351 TTTAAAACAT
Statistics
Matches: 120, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
61 10 0.08
62 3 0.03
63 16 0.13
64 27 0.22
65 2 0.02
66 52 0.43
67 10 0.08
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (62 bp):
ATTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATATAAATAT
Found at i:37247 original size:26 final size:25
Alignment explanation
Indices: 37203--37255 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
37193 GAAAATATAT
*
37203 ATATATAATTCATATTTTTTGAAAAC
1 ATATATAATTCATA-GTTTTGAAAAC
37229 ATATATAATAT-ATAGTTTTGAAAAC
1 ATATATAAT-TCATAGTTTTGAAAAC
37254 AT
1 AT
37256 TTTGAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 12 0.48
26 12 0.48
27 1 0.04
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (25 bp):
ATATATAATTCATAGTTTTGAAAAC
Found at i:37297 original size:29 final size:28
Alignment explanation
Indices: 37255--37319 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
37245 TTTGAAAACA
37255 TTTTGAAAAC--ATATATAACATATAG-
1 TTTTGAAAACATATATATAACATATAGT
*
37280 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATATAACATATAGT
*
37308 TTTTGGAAACAT
1 TTTTGAAAACAT
37320 TTTGAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 10 0.29
27 14 0.40
28 11 0.31
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTTGAAAACATATATATAACATATAGT
Found at i:37352 original size:41 final size:40
Alignment explanation
Indices: 37280--37387 Score: 143
Period size: 39 Copynumber: 2.8 Consensus size: 40
37270 TAACATATAG
*
37280 TTTTGAAAACATATATATAATATATAG--TTTTTGGAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTTTGAAAACA
*
37319 TTTTGAAAATATATATATAATATATAGTTTTTTTTAAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTTTGAAAACA
*
37360 TTTT--TAAATATATATAATATATAGTTTT
1 TTTTGAAAAATATATATAATATATAGTTTT
37388 GAAAATGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
38 21 0.33
39 28 0.44
41 14 0.22
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (40 bp):
TTTTGAAAAATATATATAATATATAGTTTTTTTGAAAACA
Found at i:37371 original size:66 final size:66
Alignment explanation
Indices: 37151--37373 Score: 248
Period size: 66 Copynumber: 3.4 Consensus size: 66
37141 AAAAAATCGA
37151 TTTTTGAAAA-ATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAT-ATA-ATT
1 TTTTTGAAAACAT-T-TATAATATATAGTTTTGAAAACATTTTGAAAATATATATATAATATA-T
37213 CA-TAT
63 -AGT-T
* * *
37218 TTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTG-AAA-ACATATATAACATATAG-
1 TTTTTGAAAACATTTATAATATATAGTTTTGAAAACATTTTGAAAATATATATATAATATATAGT
37280 -
66 T
*
37280 -TTTTGAAAACATATATATAATATATAGTTTTTGGAAACATTTTGAAAATATATATATAATATAT
1 TTTTTGAAAACAT-T-TATAATATATAG-TTTTGAAAACATTTTGAAAATATATATATAATATAT
37344 AGTT
63 AGTT
* *
37348 TTTTTTAAAACATTTTTAAATATATA
1 TTTTTGAAAACATTTAT-AATATATA
37374 TAATATATAG
Statistics
Matches: 134, Mismatches: 9, Indels: 25
0.80 0.05 0.15
Matches are distributed among these distances:
61 12 0.09
63 12 0.09
64 23 0.17
65 9 0.07
66 44 0.33
67 12 0.09
68 11 0.08
69 11 0.08
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (66 bp):
TTTTTGAAAACATTTATAATATATAGTTTTGAAAACATTTTGAAAATATATATATAATATATAGT
T
Found at i:37409 original size:20 final size:20
Alignment explanation
Indices: 37384--37423 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
37374 TAATATATAG
* *
37384 TTTTGAAAATGTTTTTGAAA
1 TTTTGAAAACGTTTTAGAAA
*
37404 TTTTGATAACGTTTTAGAAA
1 TTTTGAAAACGTTTTAGAAA
37424 ATATATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTTGAAAACGTTTTAGAAA
Found at i:41609 original size:23 final size:23
Alignment explanation
Indices: 41579--41633 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
41569 TACAATGGAC
41579 GACTAAGATCAATCTAGATCAAT
1 GACTAAGATCAATCTAGATCAAT
41602 GACTAAGATCAATCTAGATCAAT
1 GACTAAGATCAATCTAGATCAAT
*
41625 GGCTAAGAT
1 GACTAAGAT
41634 TATCCCTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (23 bp):
GACTAAGATCAATCTAGATCAAT
Found at i:41612 original size:13 final size:12
Alignment explanation
Indices: 41581--41633 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 12
41571 CAATGGACGA
41581 CTAAGATCAAT-
1 CTAAGATCAATG
41592 CT-AGATCAATG
1 CTAAGATCAATG
41603 ACTAAGATCAAT-
1 -CTAAGATCAATG
41615 CT-AGATCAATGG
1 CTAAGATCAAT-G
41627 CTAAGAT
1 CTAAGAT
41634 TATCCCTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 16 0.44
11 4 0.11
12 4 0.11
13 12 0.33
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (12 bp):
CTAAGATCAATG
Found at i:43528 original size:33 final size:33
Alignment explanation
Indices: 43456--43519 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
43446 TCAAAAGGAT
*
43456 AAAATAAAATAAATAATTATAATTTAAAAGAAA
1 AAAATAAAATAAATAATAATAATTTAAAAGAAA
*
43489 AAAATAAAAT-AATAAATAATAATTTTAAAGA
1 AAAATAAAATAAAT-AATAATAATTTAAAAGA
43520 TGATAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (33 bp):
AAAATAAAATAAATAATAATAATTTAAAAGAAA
Found at i:44114 original size:12 final size:12
Alignment explanation
Indices: 44093--44124 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
44083 AGATATATGT
44093 GAAAAATAGAGG
1 GAAAAATAGAGG
*
44105 GAAAACTAGAGG
1 GAAAAATAGAGG
44117 GAAAAATA
1 GAAAAATA
44125 AGATTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.28, T:0.09
Consensus pattern (12 bp):
GAAAAATAGAGG
Found at i:46604 original size:40 final size:40
Alignment explanation
Indices: 46549--46670 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
46539 TGCAGGTTTA
46549 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
46589 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
46629 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
46669 TA
1 TA
46671 GCACTACGAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:46869 original size:47 final size:45
Alignment explanation
Indices: 46775--46900 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
46765 GTAACCATGC
* *
46775 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
46819 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTATGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
46866 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAG
46901 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:53732 original size:40 final size:40
Alignment explanation
Indices: 53616--53733 Score: 218
Period size: 40 Copynumber: 3.0 Consensus size: 40
53606 GGTTTATAAC
*
53616 ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGAAAT
1 ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
53656 ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
1 ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
*
53696 ACACTTCGGTGTTTATGGTGGGCACGACCTTATGTGTA
1 ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTA
53734 GCACTACGGT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (40 bp):
ACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
Found at i:53943 original size:47 final size:45
Alignment explanation
Indices: 53849--53974 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
53839 GTAACCATGC
* * *
53849 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
53893 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
53940 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
53975 AGATTTTAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:58439 original size:5 final size:5
Alignment explanation
Indices: 58429--58534 Score: 81
Period size: 5 Copynumber: 21.0 Consensus size: 5
58419 AAGATCTGTT
* * *
58429 TAAAA TAAAA T-AAA TCAAAA TAAAA TAAAA T-AAA TAGAA TGAAA TAAAG
1 TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
**** * * *
58478 TTTGC TAAAAA TAAAA TGAAAA TAAAA CAAAA TGAAA TAAAA TGAAA TAAAA
1 TAAAA T-AAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
58530 TAAAA
1 TAAAA
58535 ATAGAACGAA
Statistics
Matches: 77, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
4 8 0.10
5 59 0.77
6 10 0.13
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:58535 original size:26 final size:26
Alignment explanation
Indices: 58486--58536 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
58476 AGTTTGCTAA
*
58486 AAATAAAATGAAAATAAAACAAAATG
1 AAATAAAATGAAAATAAAAAAAAATG
58512 AAATAAAATG-AAATAAAATAAAAAT
1 AAATAAAATGAAAATAAAA-AAAAAT
58537 AGAACGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATAAAATGAAAATAAAAAAAAATG
Done.