Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000960.1 Hibiscus syriacus cultivar Beakdansim tig00001919_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: 71263
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3170 original size:41 final size:41
Alignment explanation
Indices: 3120--3199 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
3110 GCTACATGAG
* *
3120 TGTTGAAAAGTCAAT-GAAAGGAAAATGGTGGCTAACAAAAT
1 TGTTAAAAAGTC-ATGGAAAGGAAAATGGTGGCCAACAAAAT
3161 TGTTAAAAAGTCATGGAAAGGAAAATGGTGGCCAACAAA
1 TGTTAAAAAGTCATGGAAAGGAAAATGGTGGCCAACAAA
3200 GGTTGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.46, C:0.09, G:0.25, T:0.20
Consensus pattern (41 bp):
TGTTAAAAAGTCATGGAAAGGAAAATGGTGGCCAACAAAAT
Found at i:3721 original size:16 final size:16
Alignment explanation
Indices: 3700--3731 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3690 TACTATTCAC
3700 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
3716 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
3732 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (16 bp):
GTGAATAGTGAAATTT
Found at i:6176 original size:18 final size:18
Alignment explanation
Indices: 6153--6206 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
6143 CAATGCAGGT
*
6153 GGAGGATTCTGTTAAGTG
1 GGAGGATTCAGTTAAGTG
6171 GGAGGATTCAGTTAAGTG
1 GGAGGATTCAGTTAAGTG
* **
6189 AGAGTCTTCAGTTAAGTG
1 GGAGGATTCAGTTAAGTG
6207 AGAGTCTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.31
Consensus pattern (18 bp):
GGAGGATTCAGTTAAGTG
Found at i:6207 original size:18 final size:18
Alignment explanation
Indices: 6163--6215 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
6153 GGAGGATTCT
* **
6163 GTTAAGTGGGAGGATTCA
1 GTTAAGTGAGAGTCTTCA
6181 GTTAAGTGAGAGTCTTCA
1 GTTAAGTGAGAGTCTTCA
6199 GTTAAGTGAGAGTCTTC
1 GTTAAGTGAGAGTCTTC
6216 CATGAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.32, T:0.32
Consensus pattern (18 bp):
GTTAAGTGAGAGTCTTCA
Found at i:8098 original size:31 final size:31
Alignment explanation
Indices: 8060--8215 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
8050 CCCGAAGGAC
* * *
8060 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
8091 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
8122 CACTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
8153 CAGTCCATATGTCCCGAAGAACATAGGTAAG
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
8184 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
8215 C
1 C
8216 CCTCGACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12620 original size:31 final size:31
Alignment explanation
Indices: 12582--12675 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
12572 CCCGAAGGAC
* * *
12582 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
12613 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
12644 CAGTCCATATG-TCCCGAAGAACATAAGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
12675 C
1 C
12676 CCTCGACCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAA
Found at i:13287 original size:36 final size:36
Alignment explanation
Indices: 13240--13311 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
13230 TTTCATTTAG
13240 GGGGAATCGATACCCCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCCAGGGGGGAATCTGTTCCC
*
13276 GGGGAATCGATACCCCCTAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
13312 CATGCACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.19, C:0.31, G:0.32, T:0.18
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:14652 original size:41 final size:41
Alignment explanation
Indices: 14607--14684 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
14597 TGGGAGATTA
* *
14607 TTGAAAAGTCAACGAAAGGAAAATGATGGCTAACAAAATTG
1 TTGAAAAGTCAACGAAAGGAAAACGATGGCCAACAAAATTG
** *
14648 TTGAAAAGTCATGGAAAGGAAAACGGTGGCCAACAAA
1 TTGAAAAGTCAACGAAAGGAAAACGATGGCCAACAAA
14685 GGTTGATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.17
Consensus pattern (41 bp):
TTGAAAAGTCAACGAAAGGAAAACGATGGCCAACAAAATTG
Found at i:23445 original size:2 final size:2
Alignment explanation
Indices: 23438--23465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23428 TGATGTACAT
23438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23466 ACATCCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23996 original size:20 final size:20
Alignment explanation
Indices: 23971--24072 Score: 69
Period size: 20 Copynumber: 4.7 Consensus size: 20
23961 TTTATTTATG
23971 ACATCATTTCATGCCTTAAT
1 ACATCATTTCATGCCTTAAT
*
23991 ACATCATTTCATGCATTTTATATTT
1 ACATCATTTCATGC--CTTA-A--T
* *
24016 ATGGTATCCTTTCATGCCTTAAT
1 A---CATCATTTCATGCCTTAAT
* *
24039 GCATCCTTTCATGCCTTAAT
1 ACATCATTTCATGCCTTAAT
* *
24059 GCATCTTTTCATGC
1 ACATCATTTCATGC
24073 ATTTTATTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
20 45 0.67
22 3 0.04
23 2 0.03
25 3 0.04
26 3 0.04
28 11 0.16
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.44
Consensus pattern (20 bp):
ACATCATTTCATGCCTTAAT
Found at i:24069 original size:68 final size:66
Alignment explanation
Indices: 23972--24098 Score: 191
Period size: 68 Copynumber: 1.9 Consensus size: 66
23962 TTATTTATGA
**
23972 CATCATTTCATGCCTTAATACATCATTTCATGCATTTTATATTTATGGTATCCTTTCATGCCTTA
1 CATCATTTCATGCCTTAATACATCATTTCATGCA-TTT-TATTTATGACATCCTTTCATGCCTTA
24037 ATG
64 ATG
* * *
24040 CATCCTTTCATGCCTTAATGCATCTTTTCATGCATTTTATTTATGACATCCTTTCATGC
1 CATCATTTCATGCCTTAATACATCATTTCATGCATTTTATTTATGACATCCTTTCATGC
24099 ATTTTATTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 20 0.37
67 3 0.06
68 31 0.57
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (66 bp):
CATCATTTCATGCCTTAATACATCATTTCATGCATTTTATTTATGACATCCTTTCATGCCTTAAT
G
Found at i:24096 original size:26 final size:26
Alignment explanation
Indices: 24060--24136 Score: 145
Period size: 26 Copynumber: 3.0 Consensus size: 26
24050 TGCCTTAATG
*
24060 CATCTTTTCATGCATTTTATTTATGA
1 CATCCTTTCATGCATTTTATTTATGA
24086 CATCCTTTCATGCATTTTATTTATGA
1 CATCCTTTCATGCATTTTATTTATGA
24112 CATCCTTTCATGCATTTTATTTATG
1 CATCCTTTCATGCATTTTATTTATG
24137 TATTCGGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.52
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTATTTATGA
Found at i:35640 original size:15 final size:15
Alignment explanation
Indices: 35608--35648 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
35598 GTGCAAATCC
*
35608 GGGTACCCGGATTTTT
1 GGGTACCC-GATTCTT
35624 GGGTACCCGATTCTT
1 GGGTACCCGATTCTT
35639 GGGTACCCGA
1 GGGTACCCGA
35649 AATTTCCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (15 bp):
GGGTACCCGATTCTT
Found at i:38088 original size:19 final size:19
Alignment explanation
Indices: 38064--38128 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
38054 ACAAAGAGAG
38064 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38083 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38102 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
38116 AATCGCAATGCGA
1 AATCGCAATGCGA
38129 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:38172 original size:20 final size:20
Alignment explanation
Indices: 38147--38202 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
38137 TCGCATTGCG
38147 ATTTTCTCGTTGCGATAGCC
1 ATTTTCTCGTTGCGATAGCC
* *
38167 ATTTTCGCGTTGCGATAGTC
1 ATTTTCTCGTTGCGATAGCC
38187 ATTTT-TGCGTTGCGAT
1 ATTTTCT-CGTTGCGAT
38203 TTCCCCGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (20 bp):
ATTTTCTCGTTGCGATAGCC
Found at i:38776 original size:20 final size:20
Alignment explanation
Indices: 38751--38842 Score: 139
Period size: 20 Copynumber: 4.6 Consensus size: 20
38741 ATTCTGTATT
*
38751 ATCTCGTTGCGATAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
38771 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
*
38791 ATCGCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
* *
38811 ATATCGTTGCGAAAGTCAGT
1 ATCTCGTTGCGAAAGTCAGA
*
38831 ATCGCGTTGCGA
1 ATCTCGTTGCGA
38843 TTTTGTATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (20 bp):
ATCTCGTTGCGAAAGTCAGA
Found at i:38876 original size:20 final size:20
Alignment explanation
Indices: 38750--38884 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
38740 GATTCTGTAT
*
38750 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
38770 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
38790 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* ** *
38810 AATATCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
38830 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
38851 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
38871 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
38885 TTACTTATTC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 79 0.81
21 14 0.14
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:38945 original size:21 final size:22
Alignment explanation
Indices: 38893--38945 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
38883 ATTTACTTAT
38893 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
38914 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
38935 TCGCATTGCGA
1 TCGCATTGCGA
38946 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:39003 original size:20 final size:20
Alignment explanation
Indices: 38980--39025 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
38970 GGAAACTGAT
*
38980 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
39000 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
39019 TTGCGAT
1 TTGCGAT
39026 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:39280 original size:15 final size:17
Alignment explanation
Indices: 39257--39295 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
39247 GGTGTGCAAA
*
39257 TCCGGGTACCC-GA-TT
1 TCCGTGTACCCAGATTT
39272 TCCGTGTACCCAGATTT
1 TCCGTGTACCCAGATTT
39289 TCCGTGT
1 TCCGTGT
39296 CGATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.13, C:0.31, G:0.23, T:0.33
Consensus pattern (17 bp):
TCCGTGTACCCAGATTT
Found at i:41817 original size:19 final size:19
Alignment explanation
Indices: 41765--41810 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
41755 GCAAAGAGAG
41765 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41784 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41803 AATCGCAA
1 AATCGCAA
41811 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:41873 original size:20 final size:20
Alignment explanation
Indices: 41856--41923 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
41846 CGATTTTCTC
41856 GTTGCGATAGCCATTTTCGT
1 GTTGCGATAGCCATTTTCGT
41876 GTTGCGATAGCCATTTTCGT
1 GTTGCGATAGCCATTTTCGT
* * * *
41896 GTTGTGATAGTCATTTTTGC
1 GTTGCGATAGCCATTTTCGT
41916 GTTGCGAT
1 GTTGCGAT
41924 TTCCCCGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.15, C:0.16, G:0.26, T:0.43
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGT
Found at i:41893 original size:40 final size:40
Alignment explanation
Indices: 41848--41923 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
41838 TCGCATTGCG
*
41848 ATTTTC-TCGTTGCGATAGCCATTTTCGTGTTGCGATAGCC
1 ATTTTCGT-GTTGCGATAGCCATTTTCGCGTTGCGATAGCC
* * *
41888 ATTTTCGTGTTGTGATAGTCATTTTTGCGTTGCGAT
1 ATTTTCGTGTTGCGATAGCCATTTTCGCGTTGCGAT
41924 TTCCCCGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.97
41 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (40 bp):
ATTTTCGTGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
Found at i:42497 original size:20 final size:20
Alignment explanation
Indices: 42476--42561 Score: 136
Period size: 20 Copynumber: 4.3 Consensus size: 20
42466 TGTATTATCT
* *
42476 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
42496 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
42516 CGTTGCGAAAGTCAGAATAG
1 CGTTGCGAAAGTCAGAATCG
*
42536 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
42556 CGTTGC
1 CGTTGC
42562 AATTTTGTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:42597 original size:20 final size:20
Alignment explanation
Indices: 42471--42605 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
42461 GATTCTGTAT
*
42471 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
42491 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
42511 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
42531 AATAGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
42551 TATCGCGTTGCAATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
42572 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
42592 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
42606 TTACTTATTC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 80 0.82
21 13 0.13
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:42666 original size:21 final size:22
Alignment explanation
Indices: 42614--42666 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
42604 ATTTACTTAT
42614 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
42635 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
42656 TCGCATTGCGA
1 TCGCATTGCGA
42667 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:43001 original size:15 final size:17
Alignment explanation
Indices: 42978--43016 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
42968 GGTGTGCAAA
*
42978 TCCGGGTACCC-GA-TT
1 TCCGTGTACCCAGATTT
42993 TCCGTGTACCCAGATTT
1 TCCGTGTACCCAGATTT
43010 TCCGTGT
1 TCCGTGT
43017 CGATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.13, C:0.31, G:0.23, T:0.33
Consensus pattern (17 bp):
TCCGTGTACCCAGATTT
Found at i:45308 original size:14 final size:14
Alignment explanation
Indices: 45274--45312 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
45264 TTGATTGTTT
45274 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
45288 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
45302 TGTTGATTTGT
1 AATTGATTTGT
45313 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:45494 original size:19 final size:19
Alignment explanation
Indices: 45452--45497 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
45442 GCAAAGAGAG
*
45452 AATCACAATGCAAAATGAA
1 AATCGCAATGCAAAATGAA
*
45471 AATCGCAATGCGAAATGAA
1 AATCGCAATGCAAAATGAA
45490 AATCGCAA
1 AATCGCAA
45498 CGAGAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:45504 original size:19 final size:19
Alignment explanation
Indices: 45464--45504 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
45454 TCACAATGCA
* *
45464 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGAG
45483 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
45502 AAA
1 AAA
45505 ATCACAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.20, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGAG
Found at i:45560 original size:20 final size:20
Alignment explanation
Indices: 45535--45610 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
45525 TCACATTGCG
*
45535 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
45555 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
45575 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
45595 ATTTTTGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
45611 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:45568 original size:34 final size:34
Alignment explanation
Indices: 45530--45626 Score: 95
Period size: 40 Copynumber: 2.7 Consensus size: 34
45520 TCATTTCACA
*
45530 TTGCGATTTTCTCGTTGCGATAGCCATTTTCGCG
1 TTGCGATTTTCCCGTTGCGATAGCCATTTTCGCG
* * *
45564 TTGCGATAGCCATTTTCGCGTTGCGATAGTCATTTTTGCG
1 TTGC----G--ATTTTCCCGTTGCGATAGCCATTTTCGCG
*
45604 TTGCGATTTCCCCGTTGCGATAG
1 TTGCGATTTTCCCGTTGCGATAG
45627 TCAAATGAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
34 20 0.38
36 1 0.02
38 1 0.02
40 30 0.58
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (34 bp):
TTGCGATTTTCCCGTTGCGATAGCCATTTTCGCG
Found at i:46188 original size:20 final size:20
Alignment explanation
Indices: 46163--46250 Score: 124
Period size: 20 Copynumber: 4.4 Consensus size: 20
46153 TGTATTATCC
*
46163 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCT
*
46183 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCT
*
46203 CGTTGCGAAAGTCAGAATAT
1 CGTTGCGAAAGTCAGAATCT
*
46223 CGTTGCGAAAGTCAGTATCGT
1 CGTTGCGAAAGTCAGAATC-T
46244 -GTTGCGA
1 CGTTGCGA
46251 TTTTGTATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 60 0.98
21 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCT
Found at i:46209 original size:40 final size:40
Alignment explanation
Indices: 46163--46251 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
46153 TGTATTATCC
*
46163 CGTTGCGATAGTCAGAATCTCGTTGCGAAAGTCAGAATCG
1 CGTTGCGATAGTCAGAATATCGTTGCGAAAGTCAGAATCG
* *
46203 CGTTGCGAAAGTCAGAATATCGTTGCGAAAGTCAGTATCG
1 CGTTGCGATAGTCAGAATATCGTTGCGAAAGTCAGAATCG
*
46243 TGTTGCGAT
1 CGTTGCGAT
46252 TTTGTATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (40 bp):
CGTTGCGATAGTCAGAATATCGTTGCGAAAGTCAGAATCG
Found at i:46284 original size:20 final size:20
Alignment explanation
Indices: 46158--46292 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
46148 GATTCTGTAT
*
46158 TATCCCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
46178 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
46198 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* ** *
46218 AATATCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
46238 TATCGTGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
46259 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
46279 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
46293 TTACTTATTC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 3 0.03
20 77 0.81
21 13 0.14
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:46353 original size:21 final size:22
Alignment explanation
Indices: 46304--46353 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
46294 TACTTATTCA
46304 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
**
46325 CAACGCGAAATT-GGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
46346 CATTGCGA
1 CATTGCGA
46354 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCG
Found at i:46688 original size:15 final size:16
Alignment explanation
Indices: 46665--46703 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
46655 GGTGTGCAAA
46665 TCCGGGTACCC-GATT
1 TCCGGGTACCCAGATT
*
46680 TCCGTGTACCCAGATTT
1 TCCGGGTACCCAGA-TT
46697 TCCGGGT
1 TCCGGGT
46704 CGATGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.13, C:0.31, G:0.26, T:0.31
Consensus pattern (16 bp):
TCCGGGTACCCAGATT
Found at i:46963 original size:9 final size:9
Alignment explanation
Indices: 46949--46973 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46939 AATTATATAT
46949 AAAAAAATA
1 AAAAAAATA
46958 AAAAAAATA
1 AAAAAAATA
46967 AAAAAAA
1 AAAAAAA
46974 CTAACCGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:49037 original size:14 final size:14
Alignment explanation
Indices: 49003--49041 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
48993 TTGATTGTTT
49003 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
49017 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
49031 TGTTGATTTGT
1 AATTGATTTGT
49042 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:49233 original size:19 final size:19
Alignment explanation
Indices: 49181--49226 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
49171 GCAAAGAGAG
49181 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
49200 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
49219 AATCGCAA
1 AATCGCAA
49227 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:49289 original size:20 final size:20
Alignment explanation
Indices: 49264--49339 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
49254 TCGCATTGCG
*
49264 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
49284 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
49304 ATTTTCGCGTTGTGATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
49324 ATTTTTGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
49340 TTCCCCGTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:49297 original size:34 final size:34
Alignment explanation
Indices: 49252--49355 Score: 91
Period size: 40 Copynumber: 2.9 Consensus size: 34
49242 GCGATTTTCA
* *
49252 TTTCGCATTGCGATTTTCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCCCGTTGCGATAGCCAT
* * *
49286 TTTCGCGTTGCGATAGCCATTTTCGCGTTGTGATAGTCAT
1 TTTCGCGTTGC----G--ATTTTCCCGTTGCGATAGCCAT
* *
49326 TTTTGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCCCGTTGCGATAG
49356 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
34 25 0.45
36 1 0.02
38 1 0.02
40 29 0.52
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCCCGTTGCGATAGCCAT
Found at i:50013 original size:20 final size:20
Alignment explanation
Indices: 49887--50021 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
49877 GATTCTGTAT
*
49887 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
49907 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
49927 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
49947 AATAGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
49967 TATCGTGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
49988 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
50008 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
50022 TTACTTATTC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 80 0.82
21 13 0.13
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:50082 original size:21 final size:22
Alignment explanation
Indices: 50033--50082 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
50023 TACTTATTCA
50033 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
**
50054 CAACGCGAAATT-GGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
50075 CATTGCGA
1 CATTGCGA
50083 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCG
Found at i:50417 original size:15 final size:16
Alignment explanation
Indices: 50394--50432 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
50384 GGTGTGCAAA
50394 TCCGGGTACCC-GATT
1 TCCGGGTACCCAGATT
*
50409 TCCGTGTACCCAGATTT
1 TCCGGGTACCCAGA-TT
50426 TCCGGGT
1 TCCGGGT
50433 CGATGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.13, C:0.31, G:0.26, T:0.31
Consensus pattern (16 bp):
TCCGGGTACCCAGATT
Found at i:55237 original size:2 final size:2
Alignment explanation
Indices: 55230--55263 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55220 AATGTGAAAT
55230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55264 AATTATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57225 original size:24 final size:23
Alignment explanation
Indices: 57198--57311 Score: 68
Period size: 24 Copynumber: 5.3 Consensus size: 23
57188 GCATCACTAG
57198 TGCCTTCACTGCCAACATCTCCAT
1 TGCCTTCACT-CCAACATCTCCAT
* *
57222 TG-C--CA-T-CAGCATCACCAT
1 TGCCTTCACTCCAACATCTCCAT
*
57240 TGCCTTCAACGCCAACATCTCCAT
1 TGCCTTC-ACTCCAACATCTCCAT
* *
57264 TG-C--CA-T-CAGCATCACCAT
1 TGCCTTCACTCCAACATCTCCAT
* *
57282 TGCCTTCACCACCAACATGTCCAT
1 TGCCTTCA-CTCCAACATCTCCAT
57306 TGCCTT
1 TGCCTT
57312 TGCCTTCACA
Statistics
Matches: 66, Mismatches: 12, Indels: 24
0.65 0.12 0.24
Matches are distributed among these distances:
18 24 0.36
19 2 0.03
20 2 0.03
21 6 0.09
22 1 0.02
23 2 0.03
24 29 0.44
ACGTcount: A:0.24, C:0.40, G:0.10, T:0.26
Consensus pattern (23 bp):
TGCCTTCACTCCAACATCTCCAT
Found at i:57239 original size:18 final size:18
Alignment explanation
Indices: 57213--57285 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 18
57203 TCACTGCCAA
*
57213 CATCTCCATTGCCATCAG
1 CATCACCATTGCCATCAG
*
57231 CATCACCATTGCCTTCAACG
1 CATCACCATTGCCATC-A-G
*
57251 CCAACATCTCCATTGCCATCAG
1 ----CATCACCATTGCCATCAG
57273 CATCACCATTGCC
1 CATCACCATTGCC
57286 TTCACCACCA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 26 0.59
19 1 0.02
20 1 0.02
22 1 0.02
23 1 0.02
24 14 0.32
ACGTcount: A:0.25, C:0.41, G:0.10, T:0.25
Consensus pattern (18 bp):
CATCACCATTGCCATCAG
Found at i:57244 original size:42 final size:41
Alignment explanation
Indices: 57182--57309 Score: 184
Period size: 42 Copynumber: 3.0 Consensus size: 41
57172 ACCACGACCT
* * *
57182 CCATCGGCATCACTAGTGCCTTCACTGCCAACATCTCCATTG
1 CCATCAGCATCACCATTGCCTTCAC-GCCAACATCTCCATTG
57224 CCATCAGCATCACCATTGCCTTCAACGCCAACATCTCCATTG
1 CCATCAGCATCACCATTGCCTTC-ACGCCAACATCTCCATTG
* *
57266 CCATCAGCATCACCATTGCCTTCACCACCAACATGTCCATTG
1 CCATCAGCATCACCATTGCCTTCA-CGCCAACATCTCCATTG
57308 CC
1 CC
57310 TTTGCCTTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 76 0.96
43 2 0.03
ACGTcount: A:0.24, C:0.41, G:0.11, T:0.24
Consensus pattern (41 bp):
CCATCAGCATCACCATTGCCTTCACGCCAACATCTCCATTG
Found at i:57578 original size:45 final size:45
Alignment explanation
Indices: 57513--57646 Score: 169
Period size: 45 Copynumber: 3.0 Consensus size: 45
57503 GCGCCAACAG
57513 CACCACCATTGTTGCAGCCAAATGTAGTATCAGGAGGACCACCAA
1 CACCACCATTGTTGCAGCCAAATGTAGTATCAGGAGGACCACCAA
* * * * * ** ** *
57558 TACCACCGTTGTTACTGCCAAATGTAGTCTCAGGAAAACCATTAG
1 CACCACCATTGTTGCAGCCAAATGTAGTATCAGGAGGACCACCAA
*
57603 CACCACCTTTGTTGCAGCCAAATGTAGTATCAGGAGGACCACCA
1 CACCACCATTGTTGCAGCCAAATGTAGTATCAGGAGGACCACCA
57647 TTTCCCCCAC
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (45 bp):
CACCACCATTGTTGCAGCCAAATGTAGTATCAGGAGGACCACCAA
Found at i:59722 original size:31 final size:31
Alignment explanation
Indices: 59684--59748 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
59674 CTGGTGTTAG
*
59684 AACCTAATCGTACACTAATAAACATTTAAAT
1 AACCTAATCGCACACTAATAAACATTTAAAT
59715 AACCTAATCGCACACTAATAAACATTTAAAT
1 AACCTAATCGCACACTAATAAACATTTAAAT
59746 AAC
1 AAC
59749 GGCGAGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.26
Consensus pattern (31 bp):
AACCTAATCGCACACTAATAAACATTTAAAT
Done.