Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004852.1 Hibiscus syriacus cultivar Beakdansim tig00010936_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: 178175
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1583 original size:16 final size:16
Alignment explanation
Indices: 1562--1604 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1552 ATGAAAGCAA
1562 AGGAAATGAAGTAAAG
1 AGGAAATGAAGTAAAG
1578 AGGAAATGAAGTAAAG
1 AGGAAATGAAGTAAAG
*
1594 AGAAAATGAAG
1 AGGAAATGAAG
1605 ATAACTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (16 bp):
AGGAAATGAAGTAAAG
Found at i:6670 original size:16 final size:16
Alignment explanation
Indices: 6649--6683 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
6639 ATTATAGACC
6649 TGTTATGAAGCTGACT
1 TGTTATGAAGCTGACT
6665 TGTTATGAAGCTGACT
1 TGTTATGAAGCTGACT
6681 TGT
1 TGT
6684 CATTGACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (16 bp):
TGTTATGAAGCTGACT
Found at i:8063 original size:17 final size:17
Alignment explanation
Indices: 8041--8083 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
8031 TATCATCATA
8041 ATTATTTT-CAACCTTTT
1 ATTATTTTAC-ACCTTTT
8058 ATTATTCTTACACCTTTT
1 ATTATT-TTACACCTTTT
8076 ATTTATTT
1 A-TTATTT
8084 ATTTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.26
18 11 0.48
19 6 0.26
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTTTACACCTTTT
Found at i:19959 original size:44 final size:43
Alignment explanation
Indices: 19894--19976 Score: 139
Period size: 44 Copynumber: 1.9 Consensus size: 43
19884 AAAATAACAT
* *
19894 AAACCAAAAACCTAAAGCACTAAGAGTCAAAGAAAAAAAGGAA
1 AAACAAAAAACCTAAAGCACTAAGAGTAAAAGAAAAAAAGGAA
19937 AAACAAAAGAACCTAAAGCACTAAGAGTAAAAGAAAAAAA
1 AAACAAAA-AACCTAAAGCACTAAGAGTAAAAGAAAAAAA
19977 AGAACCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
43 7 0.19
44 30 0.81
ACGTcount: A:0.65, C:0.14, G:0.13, T:0.07
Consensus pattern (43 bp):
AAACAAAAAACCTAAAGCACTAAGAGTAAAAGAAAAAAAGGAA
Found at i:24340 original size:24 final size:21
Alignment explanation
Indices: 24305--24347 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
24295 GGCACATTCT
*
24305 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
24328 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
24348 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:29172 original size:21 final size:21
Alignment explanation
Indices: 29148--29192 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29138 TTATTTGAAA
29148 TTTTGGCTTTTTTGGCTTTTT
1 TTTTGGCTTTTTTGGCTTTTT
**
29169 TTTTGTTTTTTTTGGCTTTTT
1 TTTTGGCTTTTTTGGCTTTTT
29190 TTT
1 TTT
29193 ACCTTTTTTT
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:0.00, C:0.07, G:0.16, T:0.78
Consensus pattern (21 bp):
TTTTGGCTTTTTTGGCTTTTT
Found at i:29177 original size:9 final size:11
Alignment explanation
Indices: 29155--29203 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
29145 AAATTTTGGC
29155 TTTTTTGGCTT
1 TTTTTTGGCTT
*
29166 TTTTTTTG-TT
1 TTTTTTGGCTT
29176 TTTTTTGGCTT
1 TTTTTTGGCTT
**
29187 TTTTTTACCTT
1 TTTTTTGGCTT
29198 TTTTTT
1 TTTTTT
29204 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.80
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:29199 original size:21 final size:21
Alignment explanation
Indices: 29155--29202 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29145 AAATTTTGGC
***
29155 TTTTTTGGCTTTTTTTTTGTT
1 TTTTTTGGCTTTTTTTTACCT
29176 TTTTTTGGCTTTTTTTTACCT
1 TTTTTTGGCTTTTTTTTACCT
29197 TTTTTT
1 TTTTTT
29203 TTTGAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.79
Consensus pattern (21 bp):
TTTTTTGGCTTTTTTTTACCT
Found at i:34172 original size:35 final size:37
Alignment explanation
Indices: 34104--34183 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
34094 ATACTATTTC
* *
34104 CATCAGCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
34141 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
34176 CATCACCA
1 CATCACCA
34184 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:34832 original size:16 final size:16
Alignment explanation
Indices: 34800--34850 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
34790 AAGTTATCTC
*
34800 CATTTTCTTACTATTT
1 CATTTTCTTATTATTT
*
34816 CATTTTCTTATTCTTT
1 CATTTTCTTATTATTT
* *
34832 CATCTT-TTCTTATTT
1 CATTTTCTTATTATTT
34847 CATT
1 CATT
34851 ACTATATCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.65
Consensus pattern (16 bp):
CATTTTCTTATTATTT
Found at i:38649 original size:35 final size:37
Alignment explanation
Indices: 38580--38659 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
38570 ATACTATTTC
* * *
38580 CATCAGCATAATCCATCTTCCATTATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
38617 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
38652 CATCACCA
1 CATCACCA
38660 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:40578 original size:11 final size:12
Alignment explanation
Indices: 40548--40594 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
40538 TTGGTACTGG
40548 AAACAAGATAAA
1 AAACAAGATAAA
* *
40560 AAATAAGAT-TA
1 AAACAAGATAAA
40571 AAACAAGATAAA
1 AAACAAGATAAA
*
40583 GAA-AAGATAAA
1 AAACAAGATAAA
40594 A
1 A
40595 GAATTGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:40578 original size:23 final size:21
Alignment explanation
Indices: 40548--40594 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
40538 TTGGTACTGG
40548 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGA-TA
*
40571 AAACAAGATAAAGAAAAGATA
1 AAACAAGATAAAAAAAAGATA
40592 AAA
1 AAA
40595 GAATTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 14 0.61
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (21 bp):
AAACAAGATAAAAAAAAGATA
Found at i:41030 original size:43 final size:43
Alignment explanation
Indices: 40983--41064 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
40973 TCCTAAATAA
40983 CTAATGAATAA-AATAATAATAATAAACTAAACAT-ATATTAACT
1 CTAATGAATAATAA-AATAATAAT-AACTAAACATAATATTAACT
** *
41026 CTAATTCATAATAAAATAATAATAACTAAAGATAATATT
1 CTAATGAATAATAAAATAATAATAACTAAACATAATATT
41065 TTTAACCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 9 0.26
43 23 0.68
44 2 0.06
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (43 bp):
CTAATGAATAATAAAATAATAATAACTAAACATAATATTAACT
Found at i:42168 original size:9 final size:9
Alignment explanation
Indices: 42154--42180 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
42144 AAGTATGGGT
42154 AGAAATATC
1 AGAAATATC
42163 AGAAATATC
1 AGAAATATC
42172 AGAAATATC
1 AGAAATATC
42181 CGAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:44759 original size:21 final size:22
Alignment explanation
Indices: 44733--44777 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
44723 TTTTTTGAAA
44733 TTTTGG-CTTT-TTTAGCTTTTT
1 TTTTGGCCTTTATTTAG-TTTTT
*
44754 TTTTGGCCTTTATTTTGTTTTT
1 TTTTGGCCTTTATTTAGTTTTT
44776 TT
1 TT
44778 GTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.04, C:0.09, G:0.13, T:0.73
Consensus pattern (22 bp):
TTTTGGCCTTTATTTAGTTTTT
Found at i:44786 original size:10 final size:10
Alignment explanation
Indices: 44771--44796 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
44761 CTTTATTTTG
44771 TTTTTTTGTT
1 TTTTTTTGTT
44781 TTTTTTTGTT
1 TTTTTTTGTT
44791 TTTTTT
1 TTTTTT
44797 AAATTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:45150 original size:11 final size:12
Alignment explanation
Indices: 45120--45166 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
45110 TTGGTGTTGG
45120 AAACAAGATAAA
1 AAACAAGATAAA
* *
45132 AAATAAGAT-TA
1 AAACAAGATAAA
45143 AAACAAGATAAA
1 AAACAAGATAAA
*
45155 GAA-AAGATAAA
1 AAACAAGATAAA
45166 A
1 A
45167 GAATTGCAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:45150 original size:23 final size:21
Alignment explanation
Indices: 45120--45166 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
45110 TTGGTGTTGG
45120 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGA-TA
*
45143 AAACAAGATAAAGAAAAGATA
1 AAACAAGATAAAAAAAAGATA
45164 AAA
1 AAA
45167 GAATTGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 14 0.61
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (21 bp):
AAACAAGATAAAAAAAAGATA
Found at i:45671 original size:25 final size:22
Alignment explanation
Indices: 45642--45687 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
45632 TTTGTAACCC
45642 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
45667 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
45688 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:50632 original size:18 final size:18
Alignment explanation
Indices: 50611--50649 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
50601 CTTTAACCTT
50611 ACAACACTTACCACAACA
1 ACAACACTTACCACAACA
* * *
50629 ACAACATTTGCCACGACA
1 ACAACACTTACCACAACA
50647 ACA
1 ACA
50650 CCATTCATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.36, G:0.05, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACAACA
Found at i:57123 original size:20 final size:20
Alignment explanation
Indices: 57098--57140 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
57088 TGCTTTTCAA
*
57098 CTTTTTCTTGCTTTTC-TTTT
1 CTTTTTC-TCCTTTTCATTTT
57118 CTTTTTCTCCTTTTCATTTT
1 CTTTTTCTCCTTTTCATTTT
57138 CTT
1 CTT
57141 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.72
Consensus pattern (20 bp):
CTTTTTCTCCTTTTCATTTT
Found at i:65101 original size:2 final size:2
Alignment explanation
Indices: 65094--65130 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
65084 ATCACCAACT
65094 TA TA TA TA 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 TA TA TA TA T
65131 TTCGCTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68761 original size:22 final size:24
Alignment explanation
Indices: 68710--68761 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
68700 TTCTTTTTCT
*
68710 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTTCTTTTTGAGTACTTTCAA
*
68734 TTTCTTC-TTTTGAGTAC-TTCGA
1 TTTCTTCTTTTTGAGTACTTTCAA
68756 TTTCTT
1 TTTCTT
68762 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTACTTTCAA
Found at i:87430 original size:19 final size:19
Alignment explanation
Indices: 87406--87457 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
87396 TGAAACCCTT
**
87406 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTAAA
87425 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
87444 TGAAGATACATGAT
1 TGAAAATACATGAT
87458 CTTGGCCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:88117 original size:26 final size:25
Alignment explanation
Indices: 88087--88135 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
88077 ATAATATAAG
*
88087 ATAAGTATATGAATTATTATAAAGTA
1 ATAAGAATATGAA-TATTATAAAGTA
* *
88113 ATAAGAATGTGCATATTATAAAG
1 ATAAGAATATGAATATTATAAAG
88136 ATGTGAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (25 bp):
ATAAGAATATGAATATTATAAAGTA
Found at i:94675 original size:18 final size:17
Alignment explanation
Indices: 94652--94727 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 17
94642 CCTTGGCTTG
94652 CTTTCTCTTTTTGAATTT
1 CTTT-TCTTTTTGAATTT
*
94670 C-TTTCTTTTTG-TTTT
1 CTTTTCTTTTTGAATTT
* *
94685 CTTTT-TTTCTAAATTT
1 CTTTTCTTTTTGAATTT
*
94701 CTTTTCTTTTTGTCATTT
1 CTTTTCTTTTTG-AATTT
94719 CTTTT-TTTT
1 CTTTTCTTTT
94728 GTACTCTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 8 0.17
16 19 0.40
17 10 0.21
18 10 0.21
ACGTcount: A:0.08, C:0.14, G:0.04, T:0.74
Consensus pattern (17 bp):
CTTTTCTTTTTGAATTT
Found at i:94703 original size:31 final size:33
Alignment explanation
Indices: 94665--94726 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
94655 TCTCTTTTTG
94665 AATTTC-TTTCTTTTTGT-TTTCTTTTTTTCTA
1 AATTTCTTTTCTTTTTGTATTTCTTTTTTTCTA
94696 AATTTCTTTTCTTTTTGTCATTTCTTTTTTT
1 AATTTCTTTTCTTTTTGT-ATTTCTTTTTTT
94727 TGTACTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 6 0.21
32 11 0.39
34 11 0.39
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (33 bp):
AATTTCTTTTCTTTTTGTATTTCTTTTTTTCTA
Found at i:95001 original size:13 final size:12
Alignment explanation
Indices: 94964--95002 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
94954 ATAAAGGAAG
94964 AATAAATGAAAT
1 AATAAATGAAAT
*
94976 AATAAATATAAAT
1 AATAAAT-GAAAT
94989 AATGAAATGAAAT
1 AAT-AAATGAAAT
95002 A
1 A
95003 GTAGGGATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (12 bp):
AATAAATGAAAT
Found at i:105140 original size:30 final size:31
Alignment explanation
Indices: 105106--105165 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
105096 CTTAGCTTTA
*
105106 TATTATGTTTACATATGATTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
105136 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
105166 GGCAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:106826 original size:19 final size:18
Alignment explanation
Indices: 106789--106831 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
106779 GGAGTGCAAC
106789 AAGAA-AGAAAAATAAAA
1 AAGAAGAGAAAAATAAAA
*
106806 AAGAAGAGAAAAATTAGAA
1 AAGAAGAGAAAAA-TAAAA
106825 AAGAAGA
1 AAGAAGA
106832 AAAGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 11 0.48
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (18 bp):
AAGAAGAGAAAAATAAAA
Found at i:109284 original size:30 final size:31
Alignment explanation
Indices: 109239--109298 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
109229 CTTAGCTTTA
**
109239 TATTATGTTCACATATGTTTTAGAT-TCATT
1 TATTATGTTCACATATCATTTAGATATCATT
**
109269 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTCACATATCATTTAGATATCAT
109299 GGCAACATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGTTCACATATCATTTAGATATCATT
Found at i:110161 original size:19 final size:21
Alignment explanation
Indices: 110137--110187 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
110127 GGCCAAGAGG
*
110137 ATGTATCTTCA-TT-AAAATC
1 ATGTATTTTCATTTAAAAATC
110156 ATGTATTTTCATTTAAAAATC
1 ATGTATTTTCATTTAAAAATC
110177 ATGTATTTTCA
1 ATGTATTTTCA
110188 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 10 0.34
20 2 0.07
21 17 0.59
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAATC
Found at i:110624 original size:19 final size:20
Alignment explanation
Indices: 110600--110639 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
110590 TATCCTTTAT
*
110600 TTATTTCTTTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
110619 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
110639 T
1 T
110640 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:110909 original size:23 final size:22
Alignment explanation
Indices: 110877--110944 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
110867 TGGCTTGCTT
110877 TTCTTTTTGAACTTTTTTTTTC
1 TTCTTTTTGAACTTTTTTTTTC
*
110899 TTCCTTTTTGAA-TTTTTTCCTTC
1 TT-CTTTTTGAACTTTTTT-TTTC
* *
110922 TTCTTTTTG-TCTTTTCTTTTC
1 TTCTTTTTGAACTTTTTTTTTC
110943 TT
1 TT
110945 TTTGCACTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.13
22 20 0.51
23 14 0.36
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (22 bp):
TTCTTTTTGAACTTTTTTTTTC
Found at i:113087 original size:21 final size:19
Alignment explanation
Indices: 113047--113097 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 19
113037 CGGCCAAGAG
*
113047 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
113066 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
113087 CATGTATTTTC
1 CATGTATTTTC
113098 GAAGAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:113533 original size:19 final size:19
Alignment explanation
Indices: 113509--113550 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
113499 ATCCTTTCCT
113509 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
113528 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
113547 TATT
1 TATT
113551 ATTATCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:117110 original size:19 final size:20
Alignment explanation
Indices: 117086--117125 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
117076 TATCCCATCC
117086 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
117105 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
117125 T
1 T
117126 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:117142 original size:12 final size:12
Alignment explanation
Indices: 117127--117168 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
117117 ATTACTTATA
117127 TTATTATCCCCT
1 TTATTATCCCCT
* *
117139 TTATTAAT-TCCA
1 TTATT-ATCCCCT
117151 TTATTATCCCCT
1 TTATTATCCCCT
117163 TTATTA
1 TTATTA
117169 ATTCCATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTATCCCCT
Found at i:117153 original size:24 final size:24
Alignment explanation
Indices: 117126--117180 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
117116 CATTACTTAT
117126 ATTATTATCCCCTTTATTAATTCC
1 ATTATTATCCCCTTTATTAATTCC
117150 ATTATTATCCCCTTTATTAATTCC
1 ATTATTATCCCCTTTATTAATTCC
117174 ATTATTA
1 ATTATTA
117181 ATCATTCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATTATCCCCTTTATTAATTCC
Found at i:117178 original size:12 final size:12
Alignment explanation
Indices: 117139--117182 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
117129 ATTATCCCCT
117139 TTATTAATTCCA
1 TTATTAATTCCA
* *
117151 TTATT-ATCCCCT
1 TTATTAAT-TCCA
117163 TTATTAATTCCA
1 TTATTAATTCCA
117175 TTATTAAT
1 TTATTAAT
117183 CATTCCTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTAATTCCA
Found at i:117451 original size:8 final size:8
Alignment explanation
Indices: 117438--117474 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
117428 GAGAAAAATC
117438 AGAAATGA
1 AGAAATGA
117446 AGAAATGA
1 AGAAATGA
*
117454 AGAAACGA
1 AGAAATGA
*
117462 AGAAAAGA
1 AGAAATGA
117470 AGAAA
1 AGAAA
117475 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (8 bp):
AGAAATGA
Found at i:141283 original size:20 final size:20
Alignment explanation
Indices: 141246--141283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
141236 GTATAAAGTC
**
141246 TATGAGCTAATATGAATGCA
1 TATGAGCTAATAAAAATGCA
141266 TATGAGCTAATAAAAATG
1 TATGAGCTAATAAAAATG
141284 AATGATAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (20 bp):
TATGAGCTAATAAAAATGCA
Found at i:147275 original size:24 final size:21
Alignment explanation
Indices: 147240--147282 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
147230 GGCATATTCT
*
147240 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
147263 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
147283 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:148584 original size:14 final size:17
Alignment explanation
Indices: 148564--148601 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
148554 AGTTCTTCAA
148564 CTTCTTT-C-TTTTCTT
1 CTTCTTTGCTTTTTCTT
148579 -TTCTTTGCTTTTTCTT
1 CTTCTTTGCTTTTTCTT
148595 CTTCTTT
1 CTTCTTT
148602 TTTAAAGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 1 0.05
16 7 0.35
17 6 0.30
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (17 bp):
CTTCTTTGCTTTTTCTT
Found at i:149452 original size:16 final size:15
Alignment explanation
Indices: 149407--149459 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
149397 ATAAGGTAAT
149407 AAATAAGAAC-AAATG
1 AAATAA-AACAAAATG
*
149422 AAACAAAACAAAATG
1 AAATAAAACAAAATG
*
149437 AAATAAAGAGAAAATG
1 AAATAAA-ACAAAATG
149453 AAGATAA
1 AA-ATAA
149460 CTTACAACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 3 0.09
15 16 0.50
16 9 0.28
17 4 0.12
ACGTcount: A:0.70, C:0.06, G:0.13, T:0.11
Consensus pattern (15 bp):
AAATAAAACAAAATG
Found at i:154895 original size:19 final size:20
Alignment explanation
Indices: 154849--154898 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
154839 AAACCCCTTT
* *
154849 GAAAATACATGATTTTTGAT
1 GAAAATACATGATTTTTAAG
154869 GAAAATACATGA-TTTTAAG
1 GAAAATACATGATTTTTAAG
*
154888 GAAGATACATG
1 GAAAATACATG
154899 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAG
Found at i:172172 original size:13 final size:13
Alignment explanation
Indices: 172154--172183 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
172144 TCATGCAAAT
*
172154 TAAATGAAAGTTA
1 TAAATGAAAATTA
172167 TAAATGAAAATTA
1 TAAATGAAAATTA
172180 TAAA
1 TAAA
172184 CAAAATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (13 bp):
TAAATGAAAATTA
Found at i:175013 original size:19 final size:20
Alignment explanation
Indices: 174966--175016 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
174956 GAAACCCCTT
**
174966 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
174986 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
175005 TGAAGATACATG
1 TGAAAATACATG
175017 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.