Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006295.1 Hibiscus syriacus cultivar Beakdansim tig00015048_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: 80382
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1045 original size:24 final size:23
Alignment explanation
Indices: 1008--1060 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 23
998 CTGAAAAATC
1008 ATCAAAATCGAGTATTGACCAAG
1 ATCAAAATCGAGTATTGACCAAG
*
1031 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAAT-CGAGTATTGACCAAG
1055 ATCAAA
1 ATCAAA
1061 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (23 bp):
ATCAAAATCGAGTATTGACCAAG
Found at i:1938 original size:39 final size:40
Alignment explanation
Indices: 1890--2042 Score: 177
Period size: 39 Copynumber: 3.9 Consensus size: 40
1880 TCGAATCTTG
*
1890 TTGCAATTTACAG-ATTCGCATTGCGA-TTACGTAATCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACGTAATCGCA
1929 TTGCGATTTACGTATTCGCATTGCGATTTACGTAAATCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGT-AATCGCA
* * * * *
1970 ATGCGATTTACGTACTAGCATTGCGA-TTATGTACTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
* ** *
2009 TTGCGATTTTCCAATTCGCGTTGCGATTTACGTA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTA
2043 TTCGTTGCGA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.01
39 48 0.50
40 17 0.18
41 30 0.31
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
Found at i:2045 original size:20 final size:20
Alignment explanation
Indices: 1890--2046 Score: 167
Period size: 20 Copynumber: 7.9 Consensus size: 20
1880 TCGAATCTTG
*
1890 TTGCAATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
1910 TTGCGA-TTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
1929 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
1949 TTGCGATTTACGTAAATCGCA
1 TTGCGATTTACGT-ATTCGCA
* * *
1970 ATGCGATTTACGTACTAGCA
1 TTGCGATTTACGTATTCGCA
* *
1990 TTGCGA-TTATGTACTCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
2009 TTGCGATTTTCCAATTCGCG
1 TTGCGATTTACGTATTCGCA
2029 TTGCGATTTACGTATTCG
1 TTGCGATTTACGTATTCG
2047 TTGCGAATTA
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
18 1 0.01
19 33 0.29
20 62 0.54
21 18 0.16
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2075 original size:21 final size:21
Alignment explanation
Indices: 2049--2094 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2039 CGTATTCGTT
2049 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2070 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2091 GCGA
1 GCGA
2095 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:4088 original size:2 final size:2
Alignment explanation
Indices: 4081--4133 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
4071 CTATAAAATA
4081 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4122 GT AT AT A- AT AT A
1 AT AT AT AT AT AT A
4134 AACATGTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16599 original size:11 final size:11
Alignment explanation
Indices: 16583--16607 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16573 TGAATTTAAC
16583 TTTTTTGTTTT
1 TTTTTTGTTTT
16594 TTTTTTGTTTT
1 TTTTTTGTTTT
16605 TTT
1 TTT
16608 GTTTTTCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:16644 original size:12 final size:12
Alignment explanation
Indices: 16629--16673 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 12
16619 TTTTCTCAAG
16629 TCTTTTTTGTTT
1 TCTTTTTTGTTT
16641 TC--TTTTGTTT
1 TCTTTTTTGTTT
16651 TCTCTATTTTGTTT
1 TCT-T-TTTTGTTT
16665 TCTTTTTTG
1 TCTTTTTTG
16674 ATCTGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.34
12 7 0.24
13 1 0.03
14 11 0.38
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.78
Consensus pattern (12 bp):
TCTTTTTTGTTT
Found at i:16684 original size:24 final size:24
Alignment explanation
Indices: 16629--16689 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
16619 TTTTCTCAAG
*
16629 TCTTTTTTGTTTTCTTTTGTTTTC
1 TCTTTTTTGTTTTCTTTTGTTATC
*
16653 TCTATTTTGTTTTCTTTT-TTGATC
1 TCTTTTTTGTTTTCTTTTGTT-ATC
* *
16677 TGTTTTTTTTTTT
1 TCTTTTTTGTTTT
16690 TGAAGAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.03, C:0.10, G:0.08, T:0.79
Consensus pattern (24 bp):
TCTTTTTTGTTTTCTTTTGTTATC
Found at i:16973 original size:21 final size:21
Alignment explanation
Indices: 16933--16972 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16923 AGTGGTTATT
16933 ATTTTAATAAAAACAATTTTA
1 ATTTTAATAAAAACAATTTTA
*
16954 ATTTT-ATTAAAACAATTTT
1 ATTTTAATAAAAACAATTTT
16973 TTTAGGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTAATAAAAACAATTTTA
Found at i:19893 original size:128 final size:128
Alignment explanation
Indices: 19741--20041 Score: 363
Period size: 128 Copynumber: 2.4 Consensus size: 128
19731 GTGAAAGCTA
* * * * *
19741 AATCAGGGTTGACTTGCTTCACTGCTCTTCAAGAAGATCAAATCTGGAA-AA-AGGATCTATTTT
1 AATCAAGGTTGATTTGCTTCACTGCTCTTCAAGAAGATCAAATCT--AAGAACAGGACCTACTTC
* * * * * * *
19804 ACTGCTCTTCAGGAATGATAGATCTGGAAACTTTGATTCACTTCGCTTCTCTTCAGGGAATGTTG
64 ACTACTCTTCAGGAAGGATACATCTGGAAACTTCGATTCACTTCGCTACTCTTCAAGGAAGGTTG
* * * * **
19869 AATCGAGTTTGATTTGCTTTACTGCTCTTCAAAAAGATCAAATCTAAGAACTTGACCTACTTCAC
1 AATCAAGGTTGATTTGCTTCACTGCTCTTCAAGAAGATCAAATCTAAGAACAGGACCTACTTCAC
* *
19934 TACTTTTCAGGAAGGTTACATCTGGAAACTTCGATTCACTTCGCTACTCTTCAAGGAAGGTTG
66 TACTCTTCAGGAAGGATACATCTGGAAACTTCGATTCACTTCGCTACTCTTCAAGGAAGGTTG
* * *
19997 AATCAAGGTTGGTTTGCTTCACTGTTCTTCAGGAAGATCAAATCT
1 AATCAAGGTTGATTTGCTTCACTGCTCTTCAAGAAGATCAAATCT
20042 TAAAATTAAA
Statistics
Matches: 144, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
126 2 0.01
127 2 0.01
128 140 0.97
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (128 bp):
AATCAAGGTTGATTTGCTTCACTGCTCTTCAAGAAGATCAAATCTAAGAACAGGACCTACTTCAC
TACTCTTCAGGAAGGATACATCTGGAAACTTCGATTCACTTCGCTACTCTTCAAGGAAGGTTG
Found at i:32776 original size:20 final size:20
Alignment explanation
Indices: 32753--32808 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
32743 TATTGTTCAC
32753 ACAGTATCGATACTATTTAT
1 ACAGTATCGATACTATTTAT
* *
32773 ACAGCATCGGTACTATTTAT
1 ACAGTATCGATACTATTTAT
*
32793 ACAGTA-CAATACTATT
1 ACAGTATCGATACTATT
32809 CATAAAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
ACAGTATCGATACTATTTAT
Found at i:34227 original size:19 final size:19
Alignment explanation
Indices: 34203--34240 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34193 ATTTATTTTC
*
34203 AATTTTTAGTTTTGAAATT
1 AATTTTTAGATTTGAAATT
*
34222 AATTTTTAGATTTGGAATT
1 AATTTTTAGATTTGAAATT
34241 CATGGTCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTTAGATTTGAAATT
Found at i:35917 original size:40 final size:41
Alignment explanation
Indices: 35856--35942 Score: 149
Period size: 40 Copynumber: 2.1 Consensus size: 41
35846 AGAGGATGAA
* *
35856 AATAATAATGAAAAACTTCTTCTCTTGTGTTTGAATGCTTG
1 AATAGTAATGAAAAACTTCTTCTCTTGTGTTTGAATGCTTC
35897 AATAGTAATG-AAAACTTCTTCTCTTGTGTTTGAATGCTTC
1 AATAGTAATGAAAAACTTCTTCTCTTGTGTTTGAATGCTTC
35937 AATAGT
1 AATAGT
35943 TGTTCTCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 35 0.80
41 9 0.20
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (41 bp):
AATAGTAATGAAAAACTTCTTCTCTTGTGTTTGAATGCTTC
Found at i:36158 original size:20 final size:20
Alignment explanation
Indices: 36133--36177 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
36123 GGCTTGATTA
* *
36133 CTGTAGCAGTATTGGTACCC
1 CTGTAGCAGTATCGATACCC
*
36153 CTGTAGCATTATCGATACCC
1 CTGTAGCAGTATCGATACCC
36173 CTGTA
1 CTGTA
36178 ACATTCTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (20 bp):
CTGTAGCAGTATCGATACCC
Found at i:36257 original size:20 final size:20
Alignment explanation
Indices: 36219--36282 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
36209 TTCATTATTC
* *
36219 TTCACATAGTATC-AGTACTG
1 TTCACACAGTATCGA-TACTA
36239 TTCACACAGTATCGATACTA
1 TTCACACAGTATCGATACTA
* *
36259 TTCATACAATATCGATACTA
1 TTCACACAGTATCGATACTA
36279 TTCA
1 TTCA
36283 TACAATACAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 38 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (20 bp):
TTCACACAGTATCGATACTA
Found at i:36283 original size:20 final size:20
Alignment explanation
Indices: 36234--36303 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
36224 ATAGTATCAG
* * *
36234 TACTGTTCACACAGTATCGA
1 TACTATTCATACAATATCGA
36254 TACTATTCATACAATATCGA
1 TACTATTCATACAATATCGA
36274 TACTATTCATACAATA-C-A
1 TACTATTCATACAATATCGA
36292 GTACTATTCATA
1 -TACTATTCATA
36304 AAAACATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 12 0.26
20 33 0.72
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATATCGA
Found at i:36561 original size:18 final size:18
Alignment explanation
Indices: 36514--36570 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
36504 ATATTTAATG
* *
36514 AAAAATATACTAATTGTTT
1 AAAAAGATACCAATTG-TT
36533 ACAAAAGGATACCAATTGTT
1 A-AAAA-GATACCAATTGTT
36553 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
36571 GCGAATTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.38
19 5 0.15
20 7 0.21
21 9 0.26
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:39187 original size:33 final size:33
Alignment explanation
Indices: 39142--39211 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
39132 CATTTACAAC
* * *
39142 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACATT
*
39175 TCCCTAGCTTTTCACGGGATCAACTAGAACATT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACATT
39208 TCCC
1 TCCC
39212 CTTTACAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACATT
Found at i:39575 original size:20 final size:20
Alignment explanation
Indices: 39550--39591 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
39540 TTGAAATTAT
* *
39550 TGTAGCAGTATTGGTACCCC
1 TGTAGCAGTATCGATACCCC
39570 TGTAGCAGTATCGATACCCC
1 TGTAGCAGTATCGATACCCC
39590 TG
1 TG
39592 CAACATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (20 bp):
TGTAGCAGTATCGATACCCC
Found at i:39672 original size:19 final size:20
Alignment explanation
Indices: 39629--39675 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
39619 TACTGTTTAT
*
39629 TACTATTCACACAGTATCGG
1 TACTATTCACACAGTATCAG
*
39649 TACTATTCATACAGTA-CAG
1 TACTATTCACACAGTATCAG
39668 TACTATTC
1 TACTATTC
39676 CTAAAAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (20 bp):
TACTATTCACACAGTATCAG
Found at i:42217 original size:24 final size:24
Alignment explanation
Indices: 42190--42238 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42180 TGCATGACAT
42190 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
42214 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
42238 T
1 T
42239 CAGGAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:42900 original size:24 final size:24
Alignment explanation
Indices: 42873--42945 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
42863 AGCTTATGGG
42873 ATAAATTGTAAGTATATTGGTAAA
1 ATAAATTGTAAGTATATTGGTAAA
* * *
42897 ATAAGCTTATGAGCT-TA-TGG---A
1 ATAA-ATTGTAAG-TATATTGGTAAA
*
42918 ATAAATGGTAAGTATATTGGTAAA
1 ATAAATTGTAAGTATATTGGTAAA
42942 ATAA
1 ATAA
42946 GATTACGAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 14
0.62 0.12 0.25
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 8 0.23
24 12 0.34
25 7 0.20
26 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (24 bp):
ATAAATTGTAAGTATATTGGTAAA
Found at i:42901 original size:45 final size:45
Alignment explanation
Indices: 42806--42981 Score: 282
Period size: 45 Copynumber: 3.9 Consensus size: 45
42796 GTAACCATGC
*
42806 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
42850 AAATAAGCTTACGAGCTTATGGGATAAATTGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
42895 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
42940 AAATAAGATTACGAGCTTATGGGATAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTG
42982 ATAAGAAATT
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
44 24 0.20
45 97 0.80
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:45697 original size:12 final size:11
Alignment explanation
Indices: 45680--45866 Score: 120
Period size: 11 Copynumber: 17.0 Consensus size: 11
45670 AAAATAGGAA
45680 AAAACAGAAAAG
1 AAAACA-AAAAG
*
45692 AAAACAAAAACA
1 AAAACAAAAA-G
*
45704 AAAACAAAACG
1 AAAACAAAAAG
*
45715 AAAGAAGAAAAAG
1 -AA-AACAAAAAG
* *
45728 AAGACAAAAACA
1 AAAACAAAAA-G
*
45740 AAAACAAAAAC
1 AAAACAAAAAG
*
45751 AAAA-ACAAAAC
1 AAAACA-AAAAG
45762 AAAACAAAAAG
1 AAAACAAAAAG
*
45773 AAAGA-AAGAAG
1 AAA-ACAAAAAG
*
45784 -AAA-AAGAAG
1 AAAACAAAAAG
45793 AAAACAAAAAG
1 AAAACAAAAAG
*
45804 AAAATAAAAAG
1 AAAACAAAAAG
45815 AAAACAAAAA-
1 AAAACAAAAAG
* *
45825 AAAA-GAAGA-
1 AAAACAAAAAG
*
45834 AAAAGAAAAAG
1 AAAACAAAAAG
*
45845 AAAAAGAAAAAG
1 -AAAACAAAAAG
45857 AAAA-AAAAAG
1 AAAACAAAAAG
45867 GAGTGGAAAA
Statistics
Matches: 144, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
9 14 0.10
10 19 0.13
11 63 0.44
12 41 0.28
13 7 0.05
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (11 bp):
AAAACAAAAAG
Found at i:45703 original size:6 final size:6
Alignment explanation
Indices: 45679--45865 Score: 95
Period size: 6 Copynumber: 31.7 Consensus size: 6
45669 GAAAATAGGA
* *
45679 AAAAAC AGAAAA- GAAAAC AAAAAC AAAAAC -AAAAC GAAAGAAG AAAAA-
1 AAAAAC A-AAAAC AAAAAC AAAAAC AAAAAC AAAAAC -AAA-AAC AAAAAC
* * *
45727 GAAGAC AAAAAC AAAAAC AAAAAC AAAAAC -AAAAC -AAAAC AAAAAG
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
* * * * * * *
45773 AAAGA- AAGAAG AAAAAGA AGAAAAC AAAAA- GAAAAT AAAAA- GAAAAC
1 AAAAAC AAAAAC AAAAA-C A-AAAAC AAAAAC AAAAAC AAAAAC AAAAAC
* * * * * *
45820 AAAAAA AAAGAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAC AAA-AAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
45866 GGAGTGGAAA
Statistics
Matches: 148, Mismatches: 20, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
5 37 0.25
6 89 0.60
7 16 0.11
8 6 0.04
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.01
Consensus pattern (6 bp):
AAAAAC
Found at i:45737 original size:1 final size:1
Alignment explanation
Indices: 45733--45865 Score: 59
Period size: 1 Copynumber: 133.0 Consensus size: 1
45723 AAAAGAAGAC
* * * * * * * * * * * * *
45733 AAAAACAAAAACAAAAACAAAAACAAAACAAAACAAAAAGAAAGAAAGAAGAAAAAGAAGAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * *
45798 AAAAAGAAAATAAAAAGAAAACAAAAAAAAAGAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45863 AAA
1 AAA
45866 GGAGTGGAAA
Statistics
Matches: 86, Mismatches: 46, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.01
Consensus pattern (1 bp):
A
Found at i:45890 original size:53 final size:55
Alignment explanation
Indices: 45681--45866 Score: 188
Period size: 53 Copynumber: 3.4 Consensus size: 55
45671 AAATAGGAAA
* * **
45681 AAACAGAAAAGAAAACAAAAACAAAAACAAAACGAAAGAAGAAAAAG---AAGACA-A
1 AAACA-AAAAGAAAATAAAAA-GAAAACAAAAAAAAAGAAGAAAAAGAAAAAGA-AGA
* * *
45735 AAACAAAAACAAAAACAAAAACAAAACAAAACAAAAAGAAAGAAAGAAGAAAAAGAAGA
1 AAACAAAAA-GAAAATAAAAAGAAAACAAAA-AAAAAG-AAGAAA-AAGAAAAAGAAGA
45794 AAACAAAAAGAAAATAAAAAGAAAACAAAAAAAAAGAAGAAAAAGAAAAAG-A-A
1 AAACAAAAAGAAAATAAAAAGAAAACAAAAAAAAAGAAGAAAAAGAAAAAGAAGA
*
45847 AAAGAAAAAGAAAA-AAAAAG
1 AAACAAAAAGAAAATAAAAAG
45867 GAGTGGAAAA
Statistics
Matches: 116, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
52 6 0.05
53 27 0.23
54 20 0.17
55 15 0.13
56 9 0.08
57 6 0.05
58 19 0.16
59 14 0.12
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.01
Consensus pattern (55 bp):
AAACAAAAAGAAAATAAAAAGAAAACAAAAAAAAAGAAGAAAAAGAAAAAGAAGA
Found at i:49175 original size:24 final size:24
Alignment explanation
Indices: 49143--49191 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
49133 TGCATGACAT
*
49143 TGTACATAGATGTTTTATATATCA
1 TGTACATAGATGTTTTATAAATCA
49167 TGTACATAGATGTTTTATAAATCA
1 TGTACATAGATGTTTTATAAATCA
49191 T
1 T
49192 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (24 bp):
TGTACATAGATGTTTTATAAATCA
Found at i:49843 original size:45 final size:45
Alignment explanation
Indices: 49748--50013 Score: 426
Period size: 45 Copynumber: 5.9 Consensus size: 45
49738 GTAACCATGT
* * *
49748 AAATAAGCTTACGAGCTTATGGAAT-CATGGCAAGTATATTGGTC
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
49792 ATATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* **
49837 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTAATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
49882 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
49927 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
49972 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTG
50014 ATAAGAAATT
Statistics
Matches: 203, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
44 23 0.11
45 180 0.89
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:66352 original size:14 final size:15
Alignment explanation
Indices: 66333--66361 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
66323 CCCTATATTT
66333 TGATGAAG-AAAACA
1 TGATGAAGCAAAACA
66347 TGATGAAGCAAAACA
1 TGATGAAGCAAAACA
66362 AACAGCTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (15 bp):
TGATGAAGCAAAACA
Found at i:66385 original size:21 final size:22
Alignment explanation
Indices: 66361--66401 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
66351 GAAGCAAAAC
*
66361 AAACAGCTAGAAGA-GAAATGG
1 AAACAACTAGAAGAGGAAATGG
66382 AAACAACTAGAAGAGGAAAT
1 AAACAACTAGAAGAGGAAAT
66402 TAGGGCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.56, C:0.10, G:0.24, T:0.10
Consensus pattern (22 bp):
AAACAACTAGAAGAGGAAATGG
Found at i:68730 original size:6 final size:6
Alignment explanation
Indices: 68719--68755 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
68709 TAGATTCTCC
68719 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA T
68756 ATATCTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TGTATA
Found at i:74357 original size:20 final size:20
Alignment explanation
Indices: 74332--74397 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
74322 TGTGTGTCTA
*
74332 TATATATATATATTATTTTT
1 TATATATATATATTATTATT
* ** *
74352 TATATATTTATATGGTTATG
1 TATATATATATATTATTATT
**
74372 TATACGTATATATTATTATT
1 TATATATATATATTATTATT
74392 TATATA
1 TATATA
74398 CTTATATGGT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
TATATATATATATTATTATT
Found at i:74403 original size:20 final size:20
Alignment explanation
Indices: 74340--74404 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
74330 TATATATATA
* *
74340 TATATTATTTTTTATATATT
1 TATATTATTATTTATATACT
** *
74360 TATATGGTTA--TGTATACGT
1 TATATTATTATTTATATAC-T
74379 ATATATTATTATTTATATACT
1 -TATATTATTATTTATATACT
74400 TATAT
1 TATAT
74405 GGTTATGCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 20 0.61
21 1 0.03
22 6 0.18
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (20 bp):
TATATTATTATTTATATACT
Found at i:74410 original size:20 final size:20
Alignment explanation
Indices: 74350--74410 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
74340 TATATTATTT
*
74350 TTTATATATTTATATGGTTA
1 TTTATATACTTATATGGTTA
* **
74370 --TGTATACGTATATATTATTA
1 TTTATATAC-T-TATATGGTTA
74390 TTTATATACTTATATGGTTA
1 TTTATATACTTATATGGTTA
74410 T
1 T
74411 GCTTAAATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
18 5 0.17
19 1 0.03
20 17 0.57
21 1 0.03
22 6 0.20
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTATATACTTATATGGTTA
Found at i:74436 original size:40 final size:40
Alignment explanation
Indices: 74332--74437 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 40
74322 TGTGTGTCTA
* * * *
74332 TATATATATATATTATTTTTTATATATTTATATGGTTATG
1 TATAAATATATATTATTATATATATACTTATATGGTTATG
** *
74372 TATACGTATATATTATTATTTATATACTTATATGGTTATG
1 TATAAATATATATTATTATATATATACTTATATGGTTATG
*
74412 CT-TAAATA-ATGTTATATATATATATA
1 -TATAAATATATATTAT-TATATATATA
74438 AGAAGGTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 6 0.11
40 49 0.88
41 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (40 bp):
TATAAATATATATTATTATATATATACTTATATGGTTATG
Found at i:74524 original size:2 final size:2
Alignment explanation
Indices: 74460--74505 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
74450 GGCGTGTGTT
74460 TA TA T- TA 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 TA TA TA TA
74501 TA TA T
1 TA TA T
74506 GCGAGTGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76311 original size:17 final size:17
Alignment explanation
Indices: 76285--76328 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
76275 CATTTGGTGA
*
76285 ATATTATTCAAAACATT
1 ATATTGTTCAAAACATT
76302 ATATTGTTCAAAACATT
1 ATATTGTTCAAAACATT
76319 ATATTGTTCA
1 ATATTGTTCA
76329 CGAAATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (17 bp):
ATATTGTTCAAAACATT
Done.