Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007829.1 Hibiscus syriacus cultivar Beakdansim tig00110168_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: 113615
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1799 original size:22 final size:22
Alignment explanation
Indices: 1743--1800 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1733 TGCAAAAGTG
1743 AAAGAAAAA-AAAGCACTCAAA
1 AAAGAAAAAGAAAGCACTCAAA
** **
1764 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAAAGAAAGCACTCAAA
1787 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
1801 AAAGATTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.59
23 11 0.38
ACGTcount: A:0.66, C:0.09, G:0.17, T:0.09
Consensus pattern (22 bp):
AAAGAAAAAGAAAGCACTCAAA
Found at i:5531 original size:19 final size:21
Alignment explanation
Indices: 5507--5558 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5497 CGGCCAAGAG
* *
5507 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
5526 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
5547 CATGTATTTTCA
1 CATGTATTTTCA
5559 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:14820 original size:21 final size:22
Alignment explanation
Indices: 14796--14850 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
14786 AGAACTTATC
14796 TTTTTTTTTTAA-TTTTCAAAA
1 TTTTTTTTTTAATTTTTCAAAA
* *
14817 TTTTTTTTTAAATTTTTCAGAA
1 TTTTTTTTTTAATTTTTCAAAA
14839 TTCTATTTTTTT
1 TT-T-TTTTTTT
14851 CAAGATGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.39
22 10 0.36
23 1 0.04
24 6 0.21
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTTTTTAATTTTTCAAAA
Found at i:16140 original size:28 final size:28
Alignment explanation
Indices: 16108--16240 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
16098 TGAATTAACT
*
16108 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
16136 AAACAAATGATGAACATGCTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** * * * *
16162 TGAC---TGAGTGTACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* *
16187 AAACAAATGATAAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
16215 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
16241 AACCCCACGA
Statistics
Matches: 79, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
23 3 0.04
24 9 0.11
25 3 0.04
26 3 0.04
27 7 0.09
28 54 0.68
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:20375 original size:11 final size:13
Alignment explanation
Indices: 20343--20372 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20333 TGGCCAAAGA
20343 TGAAAAGGTATGT
1 TGAAAAGGTATGT
20356 TGAAAAGGTATG-
1 TGAAAAGGTATGT
20368 TGAAA
1 TGAAA
20373 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:23784 original size:21 final size:21
Alignment explanation
Indices: 23760--23812 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
23750 CATCCTTATT
23760 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
23781 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
23802 TCATTTCATTT
1 TCATTTCATTT
23813 AATCTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATTTCATTTCTTATCTTTA
Found at i:24833 original size:19 final size:21
Alignment explanation
Indices: 24790--24841 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
24780 ATGGATCCTT
24790 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
24811 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
24830 TGAAGATACATG
1 TGAAAATACATG
24842 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:34598 original size:19 final size:21
Alignment explanation
Indices: 34548--34599 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
34538 GAAACCCCTT
34548 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
34569 TTAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
34588 TGAAGATACATG
1 TGAAAATACATG
34600 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:38829 original size:13 final size:13
Alignment explanation
Indices: 38811--38843 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
38801 AATAGCTGGA
38811 TTGAGCTGAAGAT
1 TTGAGCTGAAGAT
38824 TTGAGCTGAAGAT
1 TTGAGCTGAAGAT
38837 TTGAGCT
1 TTGAGCT
38844 ACAAGATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.33
Consensus pattern (13 bp):
TTGAGCTGAAGAT
Found at i:39263 original size:30 final size:31
Alignment explanation
Indices: 39228--39287 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
39218 CTTAGCTTTA
**
39228 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
39258 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
39288 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:40687 original size:19 final size:21
Alignment explanation
Indices: 40663--40714 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
40653 CGGCCAAGAG
*
40663 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
40682 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
40703 CATGTATTTTCA
1 CATGTATTTTCA
40715 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:41145 original size:15 final size:15
Alignment explanation
Indices: 41125--41155 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41115 CAGCCATCTC
*
41125 TTTCATTTCTTTTTA
1 TTTCATTTCCTTTTA
41140 TTTCATTTCCTTTTA
1 TTTCATTTCCTTTTA
41155 T
1 T
41156 ATATATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCATTTCCTTTTA
Found at i:44812 original size:19 final size:21
Alignment explanation
Indices: 44788--44839 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
44778 CGGCCAAGAG
*
44788 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
44807 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
*
44828 CACGTATTTTCA
1 CATGTATTTTCA
44840 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:46139 original size:19 final size:20
Alignment explanation
Indices: 46115--46165 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
46105 CGGCCAAGAG
* *
46115 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
46134 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
46154 CATGTATTTTCA
1 CATGTATTTTCA
46166 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:46916 original size:12 final size:12
Alignment explanation
Indices: 46897--46933 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
46887 AGAAAAGACT
46897 AAAG-AAGAAAA
1 AAAGAAAGAAAA
46908 AAAGAAAGAAAAA
1 AAAGAAAG-AAAA
46921 AAAGAAAGAAAA
1 AAAGAAAGAAAA
46933 A
1 A
46934 GACAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
13 12 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:46925 original size:21 final size:22
Alignment explanation
Indices: 46884--46956 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 22
46874 GTGCAAAAAG
* *
46884 AAAAGAAAAGAC-TAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
46905 AAAAAAGAAAGA-AAAAA-AAG-
1 AAAAAA-AAAGACAAAAAGAAGA
*
46925 AAAGAAAAAGACAAAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
46947 ATAAAAAAAA
1 A-AAAAAAAA
46957 ATCAAAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.12
20 10 0.24
21 11 0.26
22 9 0.21
23 7 0.17
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAGACAAAAAGAAGA
Found at i:46969 original size:42 final size:40
Alignment explanation
Indices: 46878--46970 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 40
46868 ACTGGAGTGC
*
46878 AAAAAGA-AAAGAAAAGACTAAAGAAGAAAAAAAGAAAGA
1 AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
*
46917 AAAAAAAGAAAGAAAAAGACAAAAAGAAGAATAAAAA-AAA-A
1 AAAAAGAGAAAG-AAAAGAC-AAAAGAAGAA-AAAAAGAAAGA
*
46958 TCAAAAGAGAAAG
1 -AAAAAGAGAAAG
46971 CAAGCCAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
39 6 0.13
40 4 0.09
41 8 0.18
42 22 0.49
43 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (40 bp):
AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
Found at i:50006 original size:19 final size:21
Alignment explanation
Indices: 49982--50033 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
49972 CGGCCAAGAG
*
49982 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
50001 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
50022 CATGTATTTTCA
1 CATGTATTTTCA
50034 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:54096 original size:19 final size:21
Alignment explanation
Indices: 54072--54123 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
54062 CGGCCAAGAG
*
54072 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
*
54091 CATGTATTTTTATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
54112 CATGTATTTTCA
1 CATGTATTTTCA
54124 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:55375 original size:30 final size:31
Alignment explanation
Indices: 55339--55398 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
55329 CTTAGCTTTA
**
55339 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
55369 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
55399 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:56318 original size:19 final size:20
Alignment explanation
Indices: 56294--56344 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
56284 CGGCCAAGAG
* *
56294 CATGTATATTCATTAAAA-T
1 CATGTATTTTCATCAAAAGT
56313 CATGTATTTTCATCAAAAGT
1 CATGTATTTTCATCAAAAGT
56333 CATGTATTTTCA
1 CATGTATTTTCA
56345 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAGT
Found at i:57094 original size:12 final size:12
Alignment explanation
Indices: 57075--57111 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
57065 AGAAAAGACT
57075 AAAG-AAGAAAA
1 AAAGAAAGAAAA
57086 AAAGAAAGAAAAA
1 AAAGAAAG-AAAA
57099 AAAGAAAGAAAA
1 AAAGAAAGAAAA
57111 A
1 A
57112 GACAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
13 12 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:57103 original size:21 final size:22
Alignment explanation
Indices: 57062--57134 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 22
57052 GTGCAAAAAG
* *
57062 AAAAGAAAAGAC-TAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
57083 AAAAAAGAAAGA-AAAAA-AAG-
1 AAAAAA-AAAGACAAAAAGAAGA
*
57103 AAAGAAAAAGACAAAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
57125 ATAAAAAAAA
1 A-AAAAAAAA
57135 ATCAAAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.12
20 10 0.24
21 11 0.26
22 9 0.21
23 7 0.17
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAGACAAAAAGAAGA
Found at i:57147 original size:42 final size:40
Alignment explanation
Indices: 57056--57148 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 40
57046 ACTGGAGTGC
*
57056 AAAAAGA-AAAGAAAAGACTAAAGAAGAAAAAAAGAAAGA
1 AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
*
57095 AAAAAAAGAAAGAAAAAGACAAAAAGAAGAATAAAAA-AAA-A
1 AAAAAGAGAAAG-AAAAGAC-AAAAGAAGAA-AAAAAGAAAGA
*
57136 TCAAAAGAGAAAG
1 -AAAAAGAGAAAG
57149 CAAGCCAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
39 6 0.13
40 4 0.09
41 8 0.18
42 22 0.49
43 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (40 bp):
AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
Found at i:59643 original size:30 final size:31
Alignment explanation
Indices: 59607--59666 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
59597 CTTAGCTTTA
**
59607 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
59637 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
59667 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:60586 original size:19 final size:20
Alignment explanation
Indices: 60562--60612 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
60552 CGGCCAAGAG
* *
60562 CATGTATATTCATTAAAA-T
1 CATGTATTTTCATCAAAAGT
60581 CATGTATTTTCATCAAAAGT
1 CATGTATTTTCATCAAAAGT
*
60601 TATGTATTTTCA
1 CATGTATTTTCA
60613 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAGT
Found at i:65527 original size:33 final size:33
Alignment explanation
Indices: 65485--65553 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
65475 GTTGATGAAT
*
65485 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
65518 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
65551 GAA
1 GAA
65554 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:69585 original size:33 final size:33
Alignment explanation
Indices: 69543--69611 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
69533 GTTGATGAAT
*
69543 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
69576 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
69609 GAA
1 GAA
69612 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:83623 original size:19 final size:19
Alignment explanation
Indices: 83599--83648 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
83589 GAAACCCCTT
**
83599 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTAAA
83618 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
83637 TGAAGATACATG
1 TGAAAATACATG
83649 CTCTTGGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:86650 original size:28 final size:28
Alignment explanation
Indices: 86618--86751 Score: 109
Period size: 28 Copynumber: 4.9 Consensus size: 28
86608 TCGTGGGGTT
*
86618 CATAACACCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
*
86646 CATAACAGCATATT-ATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * * ** **
86673 -TTAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
*
86698 CATAACATCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
86726 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
86752 AGTTAATTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
25 6 0.08
26 16 0.20
27 15 0.19
28 42 0.53
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:86666 original size:27 final size:28
Alignment explanation
Indices: 86618--86672 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
86608 TCGTGGGGTT
*
86618 CATAACACCATGTTCATCATTTGTTTTG
1 CATAACACCATATTCATCATTTGTTTTG
*
86646 CATAACAGCATATT-ATCATTTGTTTTG
1 CATAACACCATATTCATCATTTGTTTTG
86673 TTAAATTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (28 bp):
CATAACACCATATTCATCATTTGTTTTG
Found at i:86720 original size:80 final size:80
Alignment explanation
Indices: 86618--86778 Score: 270
Period size: 80 Copynumber: 2.0 Consensus size: 80
86608 TCGTGGGGTT
*
86618 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATT-ATCATTTGTTTTGTTAAATTCA
1 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTCATCATTTGTTTAGTT-AATTCA
*
86682 CGTGCACTCACATTCA
65 CGTGCACCCACATTCA
* *
86698 CATAACATCATGTTCATCATTTGTTTTGCATAACAGCATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTCATCATTTGTTTAGTTAATTCAC
86763 GTGCACCCACATTCA
66 GTGCACCCACATTCA
86778 C
1 C
86779 TTTACAACAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
80 62 0.82
81 14 0.18
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (80 bp):
CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTCATCATTTGTTTAGTTAATTCAC
GTGCACCCACATTCA
Found at i:87736 original size:26 final size:26
Alignment explanation
Indices: 87697--87754 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
87687 TGAACGTCTA
*
87697 AGGTTCGGGTTTATACTCTTTAGTAT
1 AGGTTCGGGCTTATACTCTTTAGTAT
*
87723 AGGTTTGGGCTTATACTCTTTAGTAT
1 AGGTTCGGGCTTATACTCTTTAGTAT
87749 AGGTTC
1 AGGTTC
87755 TTCCTTGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (26 bp):
AGGTTCGGGCTTATACTCTTTAGTAT
Found at i:88045 original size:27 final size:26
Alignment explanation
Indices: 88015--88078 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
88005 ATTCATCTTG
88015 AAAAAAAAAATTCCGAAAATTAAAAA
1 AAAAAAAAAATTCCGAAAATTAAAAA
*
88041 AAAAAACAAATTCCGAAAATTAAAAA
1 AAAAAAAAAATTCCGAAAATTAAAAA
88067 AAGAAAAGAAAA
1 AA-AAAA-AAAA
88079 GAAAAGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 27 0.79
27 4 0.12
28 3 0.09
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (26 bp):
AAAAAAAAAATTCCGAAAATTAAAAA
Found at i:97028 original size:21 final size:22
Alignment explanation
Indices: 97004--97051 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
96994 TTTTTTGAAA
*
97004 TTTTGGCTCTTTTTTTG-TTTT
1 TTTTGCCTCTTTTTTTGCTTTT
*
97025 TTTTGCCTTTTTTTTTGCCTTTT
1 TTTTGCCTCTTTTTTTG-CTTTT
97048 TTTT
1 TTTT
97052 TGTTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.77
Consensus pattern (22 bp):
TTTTGCCTCTTTTTTTGCTTTT
Found at i:97050 original size:11 final size:11
Alignment explanation
Indices: 97013--97051 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
97003 ATTTTGGCTC
97013 TTTTTTTG--T
1 TTTTTTTGCCT
97022 TTTTTTTGCCTT
1 TTTTTTTGCC-T
97034 TTTTTTTGCCT
1 TTTTTTTGCCT
97045 TTTTTTT
1 TTTTTTT
97052 TGTTTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
11 8 0.30
12 11 0.41
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:97060 original size:12 final size:12
Alignment explanation
Indices: 97021--97053 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
97011 TCTTTTTTTG
97021 TTTTTTTTGCCT
1 TTTTTTTTGCCT
97033 TTTTTTTTGCCT
1 TTTTTTTTGCCT
97045 TTTTTTTTG
1 TTTTTTTTG
97054 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:101384 original size:18 final size:17
Alignment explanation
Indices: 101361--101395 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
101351 AGGTTAGGGT
101361 TGAAAAGAATAGAAGAAA
1 TGAAAAG-ATAGAAGAAA
*
101379 TGAAAAGGTAGAAGAAA
1 TGAAAAGATAGAAGAAA
101396 GGTTTTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
TGAAAAGATAGAAGAAA
Found at i:106170 original size:28 final size:28
Alignment explanation
Indices: 106137--106270 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
106127 TCGTGGGGTT
106137 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
106165 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * ** **
106193 --TAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
106217 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
*
106245 CATAACAACATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
106271 AGTTAATTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 16 0.20
27 4 0.05
28 53 0.67
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:106237 original size:80 final size:80
Alignment explanation
Indices: 106137--106297 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
106127 TCGTGGGGTT
* * *
106137 CATAACAGCATGTTCATCATTTGTTTTGCATAACAGCATATTTATCATTTGTTTTGTAAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
*
106202 GTGCACTCACATTCA
66 GTGCACCCACATTCA
* *
106217 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
106282 GTGCACCCACATTCA
66 GTGCACCCACATTCA
106297 C
1 C
106298 TTTACAACAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (80 bp):
CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
GTGCACCCACATTCA
Found at i:108023 original size:19 final size:20
Alignment explanation
Indices: 107999--108050 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
107989 CGGCCAAGAG
*
107999 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
108018 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
108039 CATGTATTTTCA
1 CATGTATTTTCA
108051 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:108618 original size:21 final size:21
Alignment explanation
Indices: 108592--108632 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
108582 TTGGTGCTGG
108592 AAACAAGATAAA-AATAAGATT
1 AAACAAGATAAAGAA-AAGATT
108613 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
108633 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAAGAAAAGATT
Found at i:112181 original size:1 final size:1
Alignment explanation
Indices: 112177--112237 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
112167 AAATTTTGGC
* * *** ** *
112177 TTTTTTGTTTTTTTTTTGTTTTTTTTTTTGCCTTTTTTTTCCTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
112238 GAAAAAATAG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (1 bp):
T
Found at i:112191 original size:11 final size:11
Alignment explanation
Indices: 112177--112238 Score: 72
Period size: 11 Copynumber: 5.6 Consensus size: 11
112167 AAATTTTGGC
112177 TTTTTTGTTTT
1 TTTTTTGTTTT
112188 TTTTTTGTTTTT
1 TTTTTTG-TTTT
**
112200 TTTTTTGCCTT
1 TTTTTTGTTTT
**
112211 TTTTTT-CCTT
1 TTTTTTGTTTT
112221 TTTTTTGTTTT
1 TTTTTTGTTTT
112232 TTTTTTG
1 TTTTTTG
112239 AAAAAATAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
10 10 0.22
11 24 0.53
12 11 0.24
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:112238 original size:32 final size:32
Alignment explanation
Indices: 112170--112237 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
112160 TTTTTTGAAA
*
112170 TTTTGGCTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTGCCTTTTTTGTTTTTTTTTTGTTTTTTT
112202 TTTTGCCTTTTTT-TTCCTTTTTTTTGTTTTTTT
1 TTTTGCCTTTTTTGTT--TTTTTTTTGTTTTTTT
112235 TTT
1 TTT
112238 GAAAAAATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 2 0.06
32 12 0.36
33 19 0.58
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (32 bp):
TTTTGCCTTTTTTGTTTTTTTTTTGTTTTTTT
Found at i:112578 original size:11 final size:11
Alignment explanation
Indices: 112554--112598 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
112544 TTGATGTTGG
112554 AAACAAGATAA
1 AAACAAGATAA
* *
112565 AAATAAGATTA
1 AAACAAGATAA
112576 AAACAAGATAA
1 AAACAAGATAA
112587 AGAA-AAGATAA
1 A-AACAAGATAA
112598 A
1 A
112599 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:112582 original size:22 final size:22
Alignment explanation
Indices: 112554--112595 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
112544 TTGATGTTGG
112554 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
112576 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
112596 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:113118 original size:22 final size:23
Alignment explanation
Indices: 113077--113119 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
113067 CAACCTTAAT
113077 TCCTAATAAAATAATAAATCAGA
1 TCCTAATAAAATAATAAATCAGA
* *
113100 TCCTAA-AAGATAATTAATCA
1 TCCTAATAAAATAATAAATCA
113120 TCCTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (23 bp):
TCCTAATAAAATAATAAATCAGA
Done.