Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006646.1 Hibiscus syriacus cultivar Beakdansim tig00016363_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: 69663
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:15612 original size:160 final size:153
Alignment explanation
Indices: 15321--15848 Score: 534
Period size: 156 Copynumber: 3.4 Consensus size: 153
15311 TGTGGTATAT
* * *
15321 GAGCATGTGGTTCAAATTTGGT-AAAAA-AATGGACTTGAAATAAAGGATGAATTGAAGAAATAA
1 GAGCATGTGGTTCAAATTTTGTAAAAAATAATAGACTTGAAATAAAGGAGGAATTGAAGAAATAA
* ** ** * **
15384 GAAAATTACGA-AAAATTGATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAGTAC
66 GGAAATTAATAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAGTAC
*
15448 ATATGTATTAGACA-ATGGTTTAG
131 ATATGTATTATA-AGATGGTTTAG
* * *
15471 GAGCATGTGGTTCAAATTTTGTAAAAAA-AATGGACTTGAAATAAAGGATG-ATTGAAGAAATAC
1 GAGCATGTGGTTCAAATTTTGTAAAAAATAATAGACTTGAAATAAAGGAGGAATTGAAGAAATAA
* * * * *
15534 GGAAATTATGAAAAAAATAAGGGACTAAATTGAAAAAAAGAAAATTTGTTATCATAAAGGGGCAT
66 GGAAA-T-T------AAT-AGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAAT
* * *
15599 TGAAAGCACATATGTATTTTAAGATAGTTTAG
122 TGAAAGTACATATGTATTATAAGATGGTTTAG
* *
15631 GAGCATGTAGTTCAAATTTTGTAAAAAAAAATAATAGACTTGAAATAAAGGAGGAATTGAATAAA
1 GAGCATGTGGTTCAAATTTTGT---AAAAAATAATAGACTTGAAATAAAGGAGGAATTGAAGAAA
* * ***
15696 TAAGTAAATTAATAGGGACTAAATTGAAAAATTGAAAAAAAATTATCAAAAAGAGGAATTGAAAG
63 TAAGGAAATTAATAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAG
* *
15761 TACATATGTATTCTAAGATGATTTAG
128 TACATATGTATTATAAGATGGTTTAG
* * * * * *
15787 GAGCATGTGGTTCAAATTTGGT-AAAAAT--TATACTTAAAATGAAGGAGGAATTAAAGGAATAA
1 GAGCATGTGGTTCAAATTTTGTAAAAAATAATAGACTTGAAATAAAGGAGGAATTGAAGAAATAA
15849 TAAAATCAGG
Statistics
Matches: 315, Mismatches: 46, Indels: 34
0.80 0.12 0.09
Matches are distributed among these distances:
150 65 0.21
151 28 0.09
152 7 0.02
156 85 0.27
157 3 0.01
158 1 0.00
159 2 0.01
160 81 0.26
163 7 0.02
164 21 0.07
165 15 0.05
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (153 bp):
GAGCATGTGGTTCAAATTTTGTAAAAAATAATAGACTTGAAATAAAGGAGGAATTGAAGAAATAA
GGAAATTAATAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAGTAC
ATATGTATTATAAGATGGTTTAG
Found at i:16621 original size:25 final size:25
Alignment explanation
Indices: 16572--16645 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 25
16562 TAAATGAAAA
* *
16572 AATAAAATATTTTTAAATAACTTAAT
1 AATAAAATATATTT-AATAAGTTAAT
16598 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
*
16623 -ATAAAA-ATATTT-TTAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
16645 A
1 A
16646 TATATAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
22 9 0.20
23 6 0.14
24 6 0.14
25 10 0.23
26 13 0.30
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:16639 original size:22 final size:24
Alignment explanation
Indices: 16573--16647 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 24
16563 AAATGAAAAA
* *
16573 ATAAAATATTTTTAAATAACTTAAT
1 ATAAAATATATTT-AATAAGTTAAT
16598 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATATATTTAATAAGTTAAT
*
16623 ATAAAA-ATATTT-TTAAGTTAAT
1 ATAAAATATATTTAATAAGTTAAT
16645 ATA
1 ATA
16648 TATAAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 12 0.26
23 6 0.13
24 6 0.13
25 10 0.22
26 12 0.26
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:16654 original size:25 final size:25
Alignment explanation
Indices: 16573--16655 Score: 68
Period size: 25 Copynumber: 3.3 Consensus size: 25
16563 AAATGAAAAA
*
16573 ATAAAATATTTTTAA-ATAACT-TAAT
1 ATAAAATATTTTTAAGTTAA-TAT-AT
16598 AATAAAATATATTTAATAAGTT-A-ATAT
1 -ATAAAATAT-TTT--TAAGTTAATATAT
16625 A-AAAATATTTTTAAGTTAATATAT
1 ATAAAATATTTTTAAGTTAATATAT
16649 ATAAAAT
1 ATAAAAT
16656 TATATTATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
22 6 0.12
23 1 0.02
24 8 0.17
25 12 0.25
26 10 0.21
27 5 0.10
28 1 0.02
29 4 0.08
30 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (25 bp):
ATAAAATATTTTTAAGTTAATATAT
Found at i:16856 original size:21 final size:22
Alignment explanation
Indices: 16816--16870 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
16806 AAAAATTCAA
*
16816 ATTAAATAAATAAGATAAATTT
1 ATTAAATAAATAAAATAAATTT
* **
16838 ATTAAA-AATTAAAATAAATAA
1 ATTAAATAAATAAAATAAATTT
16859 ATTAAATTAAAT
1 ATTAAA-TAAAT
16871 TTCAAATGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 17 0.65
22 6 0.23
23 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTAAATAAATAAAATAAATTT
Found at i:17466 original size:31 final size:31
Alignment explanation
Indices: 17416--17490 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
17406 TAACTTGGGG
* * *
17416 TGATCACATCTTAAATAAATAAAAACGAAAG
1 TGATCATATCTTAAATAAATAAAAACAAAAA
* *
17447 TGGTCATATCTTAATTAAATAAAAACAAAAA
1 TGATCATATCTTAAATAAATAAAAACAAAAA
*
17478 TGATTATATCTTA
1 TGATCATATCTTA
17491 TGTTTTTTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (31 bp):
TGATCATATCTTAAATAAATAAAAACAAAAA
Found at i:19324 original size:24 final size:25
Alignment explanation
Indices: 19288--19335 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
19278 TTCTCCTTGT
*
19288 AAATTTTAAATATAAATA-ATATAA
1 AAATATTAAATATAAATATATATAA
* *
19312 AAATATTATATATATATATATATA
1 AAATATTAAATATAAATATATATA
19336 TAATACACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATTAAATATAAATATATATAA
Found at i:20946 original size:8 final size:8
Alignment explanation
Indices: 20933--20963 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
20923 CATGATTTGA
20933 CATCCATT
1 CATCCATT
20941 CATCCATT
1 CATCCATT
*
20949 CATCCATA
1 CATCCATT
20957 CATCCAT
1 CATCCAT
20964 GCATGCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (8 bp):
CATCCATT
Found at i:25173 original size:24 final size:25
Alignment explanation
Indices: 25134--25182 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
25124 GATCCCAAAC
*
25134 TTTTAATTCACTTTTTCTCTATCAT
1 TTTTAATTCACTTTTTCTATATCAT
*
25159 TTTTTATTCACTTTTT-TATATCAT
1 TTTTAATTCACTTTTTCTATATCAT
25183 GAATGCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTAATTCACTTTTTCTATATCAT
Found at i:26124 original size:59 final size:59
Alignment explanation
Indices: 26042--26155 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
26032 CACAAATGCT
* * ** * *
26042 CCCAACTATAGGATAATGTTTTATCGAGTCCCTTGATTATTAAATGTTACAAAATGATC
1 CCCAACTATAGGATAATGCTTTATCGAATCCCTCAACTATTAAAAGTTACAAAATGATC
* *
26101 CCCAACTATAAGGAT-TTGCTTTATTGAATCCCTCAACTATTAAAAGTTACAAAAT
1 CCCAACTAT-AGGATAATGCTTTATCGAATCCCTCAACTATTAAAAGTTACAAAAT
26156 AGTCACTCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 41 0.89
60 5 0.11
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (59 bp):
CCCAACTATAGGATAATGCTTTATCGAATCCCTCAACTATTAAAAGTTACAAAATGATC
Found at i:26739 original size:25 final size:25
Alignment explanation
Indices: 26711--26758 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
26701 AAAAGCTACT
*
26711 CCATATCAAAATTTCATTTCTAAAC
1 CCATATCAAAATTTCATCTCTAAAC
* * *
26736 CCATTTTACAATTTCATCTCTAA
1 CCATATCAAAATTTCATCTCTAA
26759 TTTATTTCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
CCATATCAAAATTTCATCTCTAAAC
Found at i:33690 original size:20 final size:20
Alignment explanation
Indices: 33645--33690 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
33635 GACCAACAAA
* *
33645 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
33665 -TCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATCTCCAAT
33684 ATCGCAA
1 ATCGCAA
33691 ATTCGCGCTG
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:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:33748 original size:41 final size:41
Alignment explanation
Indices: 33701--33923 Score: 240
Period size: 41 Copynumber: 5.5 Consensus size: 41
33691 ATTCGCGCTG
33701 CATTTCGCGTTGCGATAGT-TAAAAATCG-CGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTGT-AAAAT-GTCGTTGCGATTTTC
* * * * *
33742 CTTTTCGTGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTGTAAAATGTCGTTGCGATTTTC
* * * *
33783 CATTTCGCGTTGCGATAGTGTACAGTGTCATTACGATTTT-
1 CATTTCGCGTTGCGATAGTGTAAAATGTCGTTGCGATTTTC
* *
33823 CTTTTCCCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTGT-AAAAT-GTCGTTGCGATTTTC
* * * *
33864 CATTTCGCGTTGCGGTAGTGTACATTGTTGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTGTAAAATGTCGTTGCGATTTTC
33905 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
33924 CTACAGTAAA
Statistics
Matches: 153, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 32 0.21
41 118 0.77
42 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTGTAAAATGTCGTTGCGATTTTC
Found at i:33795 original size:20 final size:20
Alignment explanation
Indices: 33726--33798 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
33716 TAGTTAAAAA
*
33726 TCGCGTTGCGATTTTCCTTT
1 TCGCGTTGCGATTTTCCATT
* * * *
33746 TCGTGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
33767 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
33787 TCGCGTTGCGAT
1 TCGCGTTGCGAT
33799 AGTGTACAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
19 4 0.10
20 22 0.56
21 10 0.26
22 3 0.08
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:33860 original size:81 final size:82
Alignment explanation
Indices: 33770--33923 Score: 238
Period size: 81 Copynumber: 1.9 Consensus size: 82
33760 TCTACAGTGT
*
33770 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGTCATTACGATTTT-CTTTTCCCGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGTCATTACGATTTTCCATTTCCCGTT
33834 GCGATAGTTGAAAATCG
66 GCGATAGTTGAAAATCG
* * ** * *
33851 CGTTGCGATTTTCCATTTCGCGTTGCGGTAGTGTACATTGTTGTTGCGATTTTCCATTTCGCGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGTCATTACGATTTTCCATTTCCCGTT
33916 GCGATAGT
66 GCGATAGT
33924 CTACAGTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 48 0.74
82 17 0.26
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (82 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGTCATTACGATTTTCCATTTCCCGTT
GCGATAGTTGAAAATCG
Found at i:33873 original size:20 final size:20
Alignment explanation
Indices: 33848--33920 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
33838 TAGTTGAAAA
33848 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
33868 TCGCGTTGCGGTAGTGTACA-T
1 TCGCGTTGC-G-ATTTTCCATT
*
33889 T-GTTGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
33909 TCGCGTTGCGAT
1 TCGCGTTGCGAT
33921 AGTCTACAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 5 0.12
20 21 0.52
21 9 0.22
22 5 0.12
ACGTcount: A:0.11, C:0.21, G:0.26, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:33897 original size:122 final size:122
Alignment explanation
Indices: 33703--33930 Score: 375
Period size: 122 Copynumber: 1.9 Consensus size: 122
33693 TCGCGCTGCA
* * *
33703 TTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCTTTTCGTGTTGCGATAGTCTACAGT
1 TTTCCCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
*
33768 GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGTCATTACGATTTTCT
66 GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCATTACGATTTTCT
* * * *
33825 TTTCCCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGGTAGTGTACATT
1 TTTCCCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
*
33890 GTTGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
66 GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
33931 AAATTAAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 97 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (122 bp):
TTTCCCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCATTACGATTTTCT
Found at i:35137 original size:21 final size:21
Alignment explanation
Indices: 35111--35204 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
35101 GAAATGAAAA
35111 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * *
35132 ATCGCAACGCGA-AATGAA-A
1 ATCGCAACGCGATTTTCAACT
* *
35151 ATCGCAACGAC-ACTGT-AGACT
1 ATCGCAACG-CGATTTTCA-ACT
35172 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
35193 ATCGCAACGCGA
1 ATCGCAACGCGA
35205 AATGTAACGC
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
19 11 0.19
20 7 0.12
21 39 0.67
22 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:35173 original size:40 final size:41
Alignment explanation
Indices: 35090--35183 Score: 131
Period size: 40 Copynumber: 2.3 Consensus size: 41
35080 TAAGAAACAA
* *
35090 TATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGAAAAATCGCAACGCGACTGTCAAC
35131 TATCGCAACGCGAAATG-AAAATCGCAACGAC-ACTGT-AGAC
1 TATCGCAACGCGAAATGAAAAATCGCAACG-CGACTGTCA-AC
35171 TATCGCAACGCGA
1 TATCGCAACGCGA
35184 TTTTCAACTA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
39 1 0.02
40 30 0.61
41 18 0.37
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
TATCGCAACGCGAAATGAAAAATCGCAACGCGACTGTCAAC
Found at i:35257 original size:19 final size:19
Alignment explanation
Indices: 35233--35301 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
35223 GATACTGAAA
35233 ATCGCGTTGCGAATTAGAG
1 ATCGCGTTGCGAATTAGAG
35252 ATCGCGTTGCGAATTAGAG
1 ATCGCGTTGCGAATTAGAG
35271 ATCGCGTTGCGAATTAGAG
1 ATCGCGTTGCGAATTAGAG
*
35290 ATCGCATTGCGA
1 ATCGCGTTGCGA
35302 TTTTGTTGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
ATCGCGTTGCGAATTAGAG
Found at i:43154 original size:20 final size:20
Alignment explanation
Indices: 43124--43190 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
43114 AATTTTAATT
43124 TTTATATTATTAAATATATTA
1 TTTA-ATTATTAAATATATTA
**
43145 TTTAATTATTAAATATAAAA
1 TTTAATTATTAAATATATTA
*
43165 TATT-ATTATAAAATATATTAA
1 T-TTAATTATTAAATATATT-A
43186 TTTAA
1 TTTAA
43191 CCGTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 29 0.76
21 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAATTATTAAATATATTA
Found at i:43176 original size:13 final size:13
Alignment explanation
Indices: 43127--43184 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
43117 TTTAATTTTT
*
43127 ATATTATTA-AAT
1 ATATTATTATAAA
43139 ATATTATT-T-AA
1 ATATTATTATAAA
* *
43150 TTATTAAATATAAA
1 ATATT-ATTATAAA
43164 ATATTATTATAAA
1 ATATTATTATAAA
43177 ATA-TATTA
1 ATATTATTA
43185 ATTTAACCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 5 0.14
12 15 0.41
13 11 0.30
14 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTATTATAAA
Found at i:43232 original size:20 final size:20
Alignment explanation
Indices: 43125--43232 Score: 57
Period size: 20 Copynumber: 5.3 Consensus size: 20
43115 ATTTTAATTT
43125 TTAT-ATTATTAAATATATTA
1 TTATAATTA-TAAATATATTA
*
43145 TT-TAATTATTAAATATA-AA
1 TTATAATTA-TAAATATATTA
* *
43164 ATATTATTATAAAATATATTAA
1 TTATAATTAT-AAATATATT-A
*
43186 TT-TAACCGTT-TAAA-ATATAA
1 TTATAA---TTATAAATATATTA
*
43206 TAAATAATTATAAATATATTA
1 T-TATAATTATAAATATATTA
43227 TTATAA
1 TTATAA
43233 AATATATGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 24
0.66 0.10 0.24
Matches are distributed among these distances:
19 6 0.09
20 37 0.56
21 12 0.18
22 8 0.12
23 1 0.02
24 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (20 bp):
TTATAATTATAAATATATTA
Found at i:43237 original size:15 final size:14
Alignment explanation
Indices: 43128--43239 Score: 56
Period size: 14 Copynumber: 8.0 Consensus size: 14
43118 TTAATTTTTA
43128 TATTATTAAATATAT
1 TATTA-TAAATATAT
43143 TATT-T-AAT-TAT
1 TATTATAAATATAT
*
43154 TAAATATAAA-ATAT
1 T-ATTATAAATATAT
43168 TATTATAAAATATAT
1 TATTAT-AAATATAT
***
43183 TAATT-TAACCGT-T
1 T-ATTATAAATATAT
** *
43196 TAAAATATAATAAAT
1 TATTATA-AATATAT
*
43211 AATTATAAATATAT
1 TATTATAAATATAT
43225 TATTATAAAATATAT
1 TATTAT-AAATATAT
43240 GTTTTTAATT
Statistics
Matches: 70, Mismatches: 16, Indels: 22
0.65 0.15 0.20
Matches are distributed among these distances:
11 4 0.06
12 6 0.09
13 10 0.14
14 24 0.34
15 23 0.33
16 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (14 bp):
TATTATAAATATAT
Found at i:47170 original size:2 final size:2
Alignment explanation
Indices: 47165--47214 Score: 57
Period size: 2 Copynumber: 24.5 Consensus size: 2
47155 TCTCTCTCTC
* *
47165 TA TA TA TA TA TA TA TA T- TGG TA TA AA TGA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA TA
47208 TA TA TA T
1 TA TA TA T
47215 TGGTATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:48663 original size:18 final size:17
Alignment explanation
Indices: 48630--48663 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
48620 GAATAATTAA
48630 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
48647 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
48664 AAACAAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:55748 original size:18 final size:18
Alignment explanation
Indices: 55714--55748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55704 TCTCGAAACT
**
55714 GGAGGAAGAGGTGGAGGC
1 GGAGGAAGAGGAAGAGGC
55732 GGAGGAAGAGGAAGAGG
1 GGAGGAAGAGGAAGAGG
55749 AGGTGTTACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.60, T:0.03
Consensus pattern (18 bp):
GGAGGAAGAGGAAGAGGC
Found at i:56746 original size:18 final size:17
Alignment explanation
Indices: 56713--56746 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56703 GAATAATTAA
56713 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
56730 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
56747 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:57752 original size:20 final size:20
Alignment explanation
Indices: 57727--57778 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
57717 GTTCACGGAA
57727 TAAGATTACCAGTGGGAATG
1 TAAGATTACCAGTGGGAATG
57747 TAAGATTACCAGTGGGAATG
1 TAAGATTACCAGTGGGAATG
57767 TAAGATTACCAG
1 TAAGATTACCAG
57779 GGAATAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (20 bp):
TAAGATTACCAGTGGGAATG
Found at i:60531 original size:21 final size:21
Alignment explanation
Indices: 60507--60577 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
60497 CCAGGGAGAG
*
60507 TATCTATACTCAGGGTGACAA
1 TATCGATACTCAGGGTGACAA
60528 TATCGATACTCAGGGTGACAA
1 TATCGATACTCAGGGTGACAA
*
60549 TATCGATACTCAGGGTGACAG
1 TATCGATACTCAGGGTGACAA
60570 TATCGATA
1 TATCGATA
60578 TTGAGGCCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (21 bp):
TATCGATACTCAGGGTGACAA
Found at i:64850 original size:2 final size:2
Alignment explanation
Indices: 64845--64881 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
64835 ACACACACAC
64845 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64882 CCTAAGCACG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64869 original size:19 final size:19
Alignment explanation
Indices: 64845--64881 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
64835 ACACACACAC
64845 ATATATATATATAATATAT
1 ATATATATATATAATATAT
*
64864 ATATATATATATATTATA
1 ATATATATATATAATATA
64882 CCTAAGCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATATAATATAT
Found at i:65604 original size:18 final size:19
Alignment explanation
Indices: 65577--65614 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
65567 ATTTAATTAA
* *
65577 ATATTTTTTTTAAT-TTTT
1 ATATTATTTTCAATATTTT
65595 ATATTATTTTCAATATTTT
1 ATATTATTTTCAATATTTT
65614 A
1 A
65615 ACCTCTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTATTTTCAATATTTT
Found at i:68308 original size:19 final size:20
Alignment explanation
Indices: 68271--68311 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
68261 ATATGTAGAA
68271 AAAAAATTTATCAATAAAAT
1 AAAAAATTTATCAATAAAAT
*
68291 AAAAAATTTATTAA-AAAAT
1 AAAAAATTTATCAATAAAAT
68310 AA
1 AA
68312 TACATAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATTTATCAATAAAAT
Done.