Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006839.1 Hibiscus syriacus cultivar Beakdansim tig00017390_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: 39033
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:87 original size:24 final size:26
Alignment explanation
Indices: 40--87 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
30 ATTAGTCCAT
*
40 TTTTATATATTAATATCAGCTTCACA
1 TTTTATATATTAATATCAACTTCACA
*
66 TTTTATA-ATTAAT-TCAATTTCA
1 TTTTATATATTAATATCAACTTCA
88 TCCCTCGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 6 0.30
26 7 0.35
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATATATTAATATCAACTTCACA
Found at i:228 original size:4 final size:4
Alignment explanation
Indices: 219--259 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
209 AATGTACATT
219 ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC -TAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
260 TGTATTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 6 0.17
4 30 0.83
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2708 original size:14 final size:14
Alignment explanation
Indices: 2691--2766 Score: 66
Period size: 14 Copynumber: 5.4 Consensus size: 14
2681 GTGTATATAT
2691 ATATAAAGTATAAA
1 ATATAAAGTATAAA
2705 ATATATAA-TATAAA
1 ATATA-AAGTATAAA
* * *
2719 TTATTAAACTATATA
1 ATA-TAAAGTATAAA
* *
2734 ATAT-AAGTTTTAA
1 ATATAAAGTATAAA
2747 ATATAAAGTATTAAA
1 ATATAAAGTA-TAAA
2762 ATATA
1 ATATA
2767 TAAATATAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
13 9 0.19
14 20 0.42
15 19 0.40
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (14 bp):
ATATAAAGTATAAA
Found at i:2709 original size:22 final size:22
Alignment explanation
Indices: 2684--2795 Score: 76
Period size: 22 Copynumber: 5.2 Consensus size: 22
2674 TATGTGTGTG
2684 TATATATATATAAAGTATAAAA
1 TATATATATATAAAGTATAAAA
* *
2706 TATATA-ATATAAATTATTAAAC
1 TATATATATATAAAGTA-TAAAA
* *
2728 TATATA-ATAT-AAGTTTTAAA
1 TATATATATATAAAGTATAAAA
* *
2748 TATAAAGTAT-TAAAATATATAAA
1 TATATA-TATATAAAGTATA-AAA
*
2771 TATA-AGTAT-TACA-TATAAAA
1 TATATA-TATATAAAGTATAAAA
2791 TATAT
1 TATAT
2796 TAATTATCAT
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
20 15 0.21
21 17 0.23
22 34 0.47
23 7 0.10
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (22 bp):
TATATATATATAAAGTATAAAA
Found at i:2752 original size:35 final size:36
Alignment explanation
Indices: 2689--2798 Score: 116
Period size: 36 Copynumber: 3.0 Consensus size: 36
2679 GTGTGTATAT
*
2689 ATATATAAAGTATAA-AATATATAATATAAATTATTAAA
1 ATATATAAA-TATAAGTAT-TA-AATATAAATTATTAAA
* * *
2727 CTATAT-AATATAAGTTTTAAATATAAAGTATTAAA
1 ATATATAAATATAAGTATTAAATATAAATTATTAAA
*
2762 ATATATAAATATAAGTATTACATATAAAATATATTAA
1 ATATATAAATATAAGTATTAAATAT-AAAT-TATTAA
2799 TTATCATAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
35 20 0.33
36 23 0.38
37 6 0.10
38 11 0.18
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (36 bp):
ATATATAAATATAAGTATTAAATATAAATTATTAAA
Found at i:2773 original size:36 final size:35
Alignment explanation
Indices: 2711--2824 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 35
2701 TAAAATATAT
* * *
2711 AATATAAATTATTAAACTATATAATATAAGTTTTA
1 AATATAAAGTATTAAAATATATAATATAAGTATTA
2746 AATATAAAGTATTAAAATATATAAATATAAGTATTA
1 AATATAAAGTATTAAAATATAT-AATATAAGTATTA
* * * * *
2782 CATATAAAATATATTAATTATCATAAT-TAATATATTA
1 AATATAAAGTAT-TAAAATAT-ATAATATAA-GTATTA
2819 AATATA
1 AATATA
2825 TTTATTAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
35 20 0.30
36 25 0.38
37 19 0.29
38 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (35 bp):
AATATAAAGTATTAAAATATATAATATAAGTATTA
Found at i:2806 original size:21 final size:20
Alignment explanation
Indices: 2778--2819 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2768 AAATATAAGT
2778 ATTACAT-ATAAAATATATTA
1 ATTACATAAT-AAATATATTA
*
2798 ATTATCATAATTAATATATTA
1 ATTA-CATAATAAATATATTA
2819 A
1 A
2820 ATATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 13 0.68
22 2 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTACATAATAAATATATTA
Found at i:2808 original size:73 final size:73
Alignment explanation
Indices: 2689--2824 Score: 158
Period size: 73 Copynumber: 1.9 Consensus size: 73
2679 GTGTGTATAT
2689 ATATATAAAGTATAAAATATATAATATAAATTATTAAACTATATAATATAAGT-T-TTAAATATA
1 ATATATAAAGTATAAAATATATAATATAAATTATTAAACTATATAAT-TAA-TATATTAAATATA
2752 AAGTATTAAA
64 AAGTATTAAA
* *
2762 ATATATAAA-TAT-AAGTAT-TACATATAAAATATATT-AATTATCATAATTAATATATTAAATA
1 ATATATAAAGTATAAAATATATA-ATAT-AAAT-TATTAAACTAT-ATAATTAATATATTAAATA
2823 TA
62 TA
2825 TTTATTAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
70 2 0.04
71 10 0.18
72 16 0.29
73 27 0.49
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (73 bp):
ATATATAAAGTATAAAATATATAATATAAATTATTAAACTATATAATTAATATATTAAATATAAA
GTATTAAA
Found at i:2812 original size:13 final size:13
Alignment explanation
Indices: 2794--2851 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
2784 TATAAAATAT
2794 ATTAATTATCATA
1 ATTAATTATCATA
*
2807 ATTAATATATTA-A
1 ATTAAT-TATCATA
*
2820 ATATATTTAT--TA
1 AT-TAATTATCATA
2832 ATTTAATTATCATA
1 A-TTAATTATCATA
2846 ATTAAT
1 ATTAAT
2852 ATTTTATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
12 8 0.22
13 18 0.50
14 10 0.28
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAATTATCATA
Found at i:2831 original size:21 final size:21
Alignment explanation
Indices: 2789--2853 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
2779 TTACATATAA
*
2789 AATATATTAATTATCATAATT
1 AATATATTAAATATCATAATT
2810 AATATATTAAATAT-AT--TT
1 AATATATTAAATATCATAATT
* *
2828 ATTA-ATTTAATTATCATAATT
1 AATATA-TTAAATATCATAATT
2849 AATAT
1 AATAT
2854 TTTATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.03
18 12 0.34
19 2 0.06
20 2 0.06
21 18 0.51
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATATTAAATATCATAATT
Found at i:2839 original size:30 final size:31
Alignment explanation
Indices: 2778--2860 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
2768 AAATATAAGT
* *
2778 ATTA-CATATAAAATATATTAATT-ATCATA
1 ATTATCATATTAAATATATTTATTAATCATA
*
2807 ATTAAT-ATATTAAATATATTTATTAAT-TTA
1 ATT-ATCATATTAAATATATTTATTAATCATA
2837 ATTATCATAATT-AATAT-TTTATTA
1 ATTATCAT-ATTAAATATATTTATTA
2861 TAACATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 12 0.26
30 29 0.63
31 5 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTATCATATTAAATATATTTATTAATCATA
Found at i:5846 original size:14 final size:14
Alignment explanation
Indices: 5827--5856 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5817 GGTATTTATG
5827 ACTATAGACTTGAA
1 ACTATAGACTTGAA
5841 ACTATAGACTTGAA
1 ACTATAGACTTGAA
5855 AC
1 AC
5857 ATTTCAAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (14 bp):
ACTATAGACTTGAA
Found at i:8903 original size:27 final size:27
Alignment explanation
Indices: 8873--8964 Score: 184
Period size: 27 Copynumber: 3.4 Consensus size: 27
8863 GAACGACGAG
8873 TTCCCTTTTCTCTCTCTCGAATCTCCC
1 TTCCCTTTTCTCTCTCTCGAATCTCCC
8900 TTCCCTTTTCTCTCTCTCGAATCTCCC
1 TTCCCTTTTCTCTCTCTCGAATCTCCC
8927 TTCCCTTTTCTCTCTCTCGAATCTCCC
1 TTCCCTTTTCTCTCTCTCGAATCTCCC
8954 TTCCCTTTTCT
1 TTCCCTTTTCT
8965 TGTTATTGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.07, C:0.43, G:0.03, T:0.47
Consensus pattern (27 bp):
TTCCCTTTTCTCTCTCTCGAATCTCCC
Found at i:9080 original size:18 final size:18
Alignment explanation
Indices: 9035--9069 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9025 ATGTGTTATG
*
9035 ATTTGTTTTTGGATTTTT
1 ATTTGATTTTGGATTTTT
9053 ATTTGATTTTGGATTTT
1 ATTTGATTTTGGATTTT
9070 GTTTTGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (18 bp):
ATTTGATTTTGGATTTTT
Found at i:14478 original size:3 final size:3
Alignment explanation
Indices: 14470--14516 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
14460 TATGGGTTTG
*
14470 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14517 AGGGATCAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:14826 original size:44 final size:45
Alignment explanation
Indices: 14716--14830 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 45
14706 TTGGAAATGT
* * * *
14716 TGATCCACCTCATTCTATGATGAAATCAAGCAAAAAAAGTGATGC
1 TGATCCAACTCCTTATATGATGGAATCAAGCAAAAAAAGTGATGC
* * * ** * *
14761 TAATCCAACTTCTTTTATGATGGAATCAAGC-AAAGTATTGGTGC
1 TGATCCAACTCCTTATATGATGGAATCAAGCAAAAAAAGTGATGC
14805 TGATCCAACTCCTTATATGAT-GAATC
1 TGATCCAACTCCTTATATGATGGAATC
14831 GAGCTAAGGT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 5 0.09
44 27 0.47
45 25 0.44
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (45 bp):
TGATCCAACTCCTTATATGATGGAATCAAGCAAAAAAAGTGATGC
Found at i:14995 original size:118 final size:119
Alignment explanation
Indices: 14847--15063 Score: 330
Period size: 118 Copynumber: 1.8 Consensus size: 119
14837 AGGTTGAACA
* *
14847 AGTTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACATCCTTCTGTGATGGAATCAA
1 AGTTCTTCTCATTACGAACTCCTTCATTGGAAATGTTGATCCACATCCTTCTGTGATGGAATCAA
*
14912 AT-CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGTATG
66 ATGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGTATG
* *
14965 AGTTCTTCTCATTACGAAC-CCTTCCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCG
1 AGTTCTTCTCATTACGAACTCCTT-CATTGGAAATGTTGATCCACATCCTTCTGTGATGGAATCA
* * * *
15029 AGTGAAATGTTGAACAATTTTTTCTCATTATGAAC
65 AATGAAAGGTTGAACAAGTTCTTCTCATTATGAAC
15064 CCTTCCACCA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 3 0.03
118 58 0.66
119 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (119 bp):
AGTTCTTCTCATTACGAACTCCTTCATTGGAAATGTTGATCCACATCCTTCTGTGATGGAATCAA
ATGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGTATG
Found at i:15637 original size:37 final size:37
Alignment explanation
Indices: 15572--15659 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
15562 TAGGGAGACA
* * *
15572 ATCCTAAGAATGACTCAAATAACATTCTAGAGAAACG
1 ATCCTAAGAAGGACTCAAACAACATTCTACAGAAACG
* ** **
15609 GTCCTAAGAAGGACTCAAACAATTTTCTACAGAATTG
1 ATCCTAAGAAGGACTCAAACAACATTCTACAGAAACG
15646 ATCCTAAGAAGGAC
1 ATCCTAAGAAGGAC
15660 AAAATAGTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (37 bp):
ATCCTAAGAAGGACTCAAACAACATTCTACAGAAACG
Found at i:16583 original size:60 final size:57
Alignment explanation
Indices: 16529--16642 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
16519 GCTTCTTCAA
* * *
16529 AAAAAATTCATTTATAGTTATCATCAAG-AAACCCTTGAAA-ATCAGGCTTAGCTTCTT
1 AAAAAATACATTTACAATTATCATCAAGAAAACCC-T-AAACATCAGGCTTAGCTTCTT
* *
16586 TAAAAATACATTTACAATTATCATCAAGAAAACCCTAAACATTAGGCTTAGCTTCTT
1 AAAAAATACATTTACAATTATCATCAAGAAAACCCTAAACATCAGGCTTAGCTTCTT
16643 TTCAAATCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
56 3 0.06
57 41 0.82
58 6 0.12
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (57 bp):
AAAAAATACATTTACAATTATCATCAAGAAAACCCTAAACATCAGGCTTAGCTTCTT
Found at i:16829 original size:109 final size:107
Alignment explanation
Indices: 16550--16919 Score: 375
Period size: 109 Copynumber: 3.3 Consensus size: 107
16540 TTATAGTTAT
* ** * **
16550 CATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTAAAAATACATTTACAATTATCATCAAGA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCCAAATCCATTTGTAA--A-CATCAAGA
* * ** * *
16615 AAACCCT-AAACATTAGGCTTAGCTTCTTTTCAAATCTATTTGTAAA
63 AACCCCTGAAA-ATCAGGCTTAGC-TCTTTAAAAATTTATTTGAAAA
** * * * *
16661 CATCATTAAACCCTTGAAAATCAGGCTTAGCTCCTTTCCCAAATCCATTTGTAAACATCAACAAG
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-CCAAATCCATTTGTAAACATCAAGAAA
16726 CCCCTGAAAATCAGGCTTAGCTCATTTAAAAAATTTATTTGAAAA
65 CCCCTGAAAATCAGGCTTAGCTC-TTT-AAAAATTTATTTGAAAA
* *
16771 CATCAAGAAACCCCTGAAAATCAGGCATAACTTCTTTCCAAATCCATTTGTAAACATCAAGAAAC
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCCAAATCCATTTGTAAACATCAAGAAAC
** *
16836 CCCTGAAAATCATTCTTATTGCTCCTTTAAAAATTCATTTGAAGTAA
66 CCCTGAAAATCAGGCTTA--GCT-CTTTAAAAATTTATTTGAA--AA
*
16883 TCATCAAGAAACCCCT-AAACATTAGGCTTAGCTTCTT
1 -CATCAAGAAACCCCTGAAA-ATCAGGCTTAGCTTCTT
16920 AAAAAATCAT
Statistics
Matches: 218, Mismatches: 30, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
108 2 0.01
109 68 0.31
110 62 0.28
111 40 0.18
112 17 0.08
113 29 0.13
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (107 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCCAAATCCATTTGTAAACATCAAGAAAC
CCCTGAAAATCAGGCTTAGCTCTTTAAAAATTTATTTGAAAA
Found at i:16832 original size:54 final size:54
Alignment explanation
Indices: 16550--16932 Score: 333
Period size: 55 Copynumber: 6.9 Consensus size: 54
16540 TTATAGTTAT
* * * **
16550 CATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTAAAAATACATTTACAATTA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTACAAATCCATTTGTAA--A
* * * *
16606 TCATCAAGAAAACCCT-AAACATTAGGCTTAGCTTCTTTTCAAATCTATTTGTAAA
1 -CATCAAGAAACCCCTGAAA-ATCAGGCTTAGCTTCTTTACAAATCCATTTGTAAA
** * * *
16661 CATCATTAAACCCTTGAAAATCAGGCTTAGCTCCTTTCCCAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-ACAAATCCATTTGTAAA
* * * ** *
16716 CATCAACAAGCCCCTGAAAATCAGGCTTAGC-TCATTTAAAAAATTTATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTC-TTT-ACAAATCCATTTGTAAA
* * *
16771 CATCAAGAAACCCCTGAAAATCAGGCATAACTTCTTTCCAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTACAAATCCATTTGTAAA
** * * * *
16825 CATCAAGAAACCCCTGAAAATCATTCTTATTGCTCCTTTAAAAATTCATTTGAAGTAAT
1 CATCAAGAAACCCCTGAAAATCAGGCTTA--GCTTCTTTACAAATCCATTT---GTAAA
* * *
16884 CATCAAGAAACCCCT-AAACATTAGGCTTAGCTTCTTAAAAAAT-CATTTG
1 CATCAAGAAACCCCTGAAA-ATCAGGCTTAGCTTCTTTACAAATCCATTTG
16933 AAGATATCTT
Statistics
Matches: 264, Mismatches: 51, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
53 1 0.00
54 66 0.25
55 91 0.34
56 25 0.09
57 52 0.20
58 3 0.01
59 26 0.10
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.30
Consensus pattern (54 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTACAAATCCATTTGTAAA
Found at i:20691 original size:28 final size:28
Alignment explanation
Indices: 20643--20697 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
20633 ATATTCTTGA
20643 GTCCAACTTGTTGCCTCAGTAGGTAGAT
1 GTCCAACTTGTTGCCTCAGTAGGTAGAT
* *
20671 GTCCTACTTGTCT-CCTTAGTAGGTAGA
1 GTCCAACTTGT-TGCCTCAGTAGGTAGA
20698 CTATCTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (28 bp):
GTCCAACTTGTTGCCTCAGTAGGTAGAT
Found at i:23752 original size:21 final size:21
Alignment explanation
Indices: 23727--23769 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
23717 CGAAACATCG
23727 TCGTTCGGTTGATCTATATAA
1 TCGTTCGGTTGATCTATATAA
23748 TCGTTCGGTTGATCTATATAA
1 TCGTTCGGTTGATCTATATAA
23769 T
1 T
23770 TCCTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (21 bp):
TCGTTCGGTTGATCTATATAA
Found at i:25847 original size:20 final size:17
Alignment explanation
Indices: 25801--25837 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25791 TTAAATATTA
*
25801 TTTTA-AATAATTACAT
1 TTTTACAATAATAACAT
25817 TTTTACAATAATAACAT
1 TTTTACAATAATAACAT
25834 TTTT
1 TTTT
25838 TACATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTACAATAATAACAT
Found at i:28823 original size:27 final size:27
Alignment explanation
Indices: 28785--28839 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28775 CAAAGTAAAC
28785 AGCATCGAAGGAACAATCATATTTAAT
1 AGCATCGAAGGAACAATCATATTTAAT
28812 AGCATCGAAGGAACAATCATATTTAAT
1 AGCATCGAAGGAACAATCATATTTAAT
28839 A
1 A
28840 TGTATGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (27 bp):
AGCATCGAAGGAACAATCATATTTAAT
Found at i:33548 original size:21 final size:21
Alignment explanation
Indices: 33522--33623 Score: 100
Period size: 21 Copynumber: 4.9 Consensus size: 21
33512 TCTATTACAA
33522 ATTTAGAGTTTAGGGTTTAAG
1 ATTTAGAGTTTAGGGTTTAAG
33543 ATTTAGAGTTTAGGGTTTAAG
1 ATTTAGAGTTTAGGGTTTAAG
* * * *
33564 -TTTATAGTTTATGATTTAGG
1 ATTTAGAGTTTAGGGTTTAAG
* * * *
33584 ATTTAG-GATTCAAGGTATAAT
1 ATTTAGAG-TTTAGGGTTTAAG
*
33605 ATTTATAGTTTAGGGTTTA
1 ATTTAGAGTTTAGGGTTTA
33624 GGTTTTTTGA
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
20 17 0.27
21 45 0.71
22 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (21 bp):
ATTTAGAGTTTAGGGTTTAAG
Found at i:33574 original size:27 final size:27
Alignment explanation
Indices: 33536--33588 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
33526 AGAGTTTAGG
*
33536 GTTTAAGATTTA-GAGTTTAGGGTTTAA
1 GTTTAAGATTTATGA-TTTAGGATTTAA
33563 GTTTATAG-TTTATGATTTAGGATTTA
1 GTTTA-AGATTTATGATTTAGGATTTA
33589 GGATTCAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (27 bp):
GTTTAAGATTTATGATTTAGGATTTAA
Found at i:34554 original size:18 final size:19
Alignment explanation
Indices: 34519--34555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
34509 TTATTCATGA
34519 TATCGATACCTAAAGGGTAG
1 TATCGATACC-AAAGGGTAG
34539 TATCGATACC-AAGGGTA
1 TATCGATACCAAAGGGTA
34556 CGATATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (19 bp):
TATCGATACCAAAGGGTAG
Found at i:36043 original size:23 final size:23
Alignment explanation
Indices: 36016--36062 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
36006 TTATAATATA
36016 CTTCTAAAGTTTAGGGTTTAATG
1 CTTCTAAAGTTTAGGGTTTAATG
36039 CTTCTAAAGTTTAGGGTTTAATG
1 CTTCTAAAGTTTAGGGTTTAATG
36062 C
1 C
36063 CTAGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (23 bp):
CTTCTAAAGTTTAGGGTTTAATG
Found at i:36194 original size:19 final size:21
Alignment explanation
Indices: 36155--36205 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
36145 GTGTATTGGT
*
36155 TTTAGGGTTCAATGTTTAGGA
1 TTTAAGGTTCAATGTTTAGGA
36176 TTTAAGGTTCAA-G-TTAGGA
1 TTTAAGGTTCAATGTTTAGGA
*
36195 TTTAATGTTCA
1 TTTAAGGTTCA
36206 TGGTTTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.57
20 1 0.04
21 11 0.39
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (21 bp):
TTTAAGGTTCAATGTTTAGGA
Found at i:36227 original size:13 final size:13
Alignment explanation
Indices: 36209--36238 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36199 ATGTTCATGG
36209 TTTAAGATTAGGA
1 TTTAAGATTAGGA
*
36222 TTTAAGGTTAGGA
1 TTTAAGATTAGGA
36235 TTTA
1 TTTA
36239 TAATTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (13 bp):
TTTAAGATTAGGA
Found at i:36275 original size:14 final size:14
Alignment explanation
Indices: 36256--36341 Score: 70
Period size: 14 Copynumber: 6.2 Consensus size: 14
36246 ACTTTATGGT
*
36256 TTTATGGTTTGGGG
1 TTTATGGTTTAGGG
* *
36270 TTTATGATTTAAGG
1 TTTATGGTTTAGGG
*
36284 TTTATGATTT--GG
1 TTTATGGTTTAGGG
* *
36296 TTTA-GGGTTAGGA
1 TTTATGGTTTAGGG
36309 TTTATGGTTTAGGG
1 TTTATGGTTTAGGG
*
36323 TTTTAGGGTTTTAGGG
1 -TTTATGG-TTTAGGG
36339 TTT
1 TTT
36342 TAGGGTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.05
12 6 0.10
13 5 0.09
14 28 0.48
15 9 0.16
16 7 0.12
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (14 bp):
TTTATGGTTTAGGG
Found at i:36304 original size:7 final size:7
Alignment explanation
Indices: 36294--36349 Score: 60
Period size: 8 Copynumber: 7.7 Consensus size: 7
36284 TTTATGATTT
36294 GGTTTAG
1 GGTTTAG
36301 GG-TTAG
1 GGTTTAG
* *
36307 GATTTAT
1 GGTTTAG
36314 GGTTTAG
1 GGTTTAG
36321 GGTTTTAG
1 GG-TTTAG
36329 GGTTTTAG
1 GG-TTTAG
36337 GGTTTTAG
1 GG-TTTAG
36345 GGTTT
1 GGTTT
36350 TAGTCTATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.12
7 15 0.35
8 23 0.53
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:36329 original size:8 final size:8
Alignment explanation
Indices: 36316--36352 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
36306 GGATTTATGG
36316 TTTAGGGT
1 TTTAGGGT
36324 TTTAGGGT
1 TTTAGGGT
36332 TTTAGGGT
1 TTTAGGGT
36340 TTTAGGGT
1 TTTAGGGT
36348 TTTAG
1 TTTAG
36353 TCTATGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (8 bp):
TTTAGGGT
Found at i:36523 original size:35 final size:35
Alignment explanation
Indices: 36484--36557 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
36474 AGATTTATTA
*
36484 TTTATTATTTAAGATTTAGGGTTTAAGGTTCAAAG
1 TTTATGATTTAAGATTTAGGGTTTAAGGTTCAAAG
* * * * *
36519 TTTATGATTTATGGTTTAGTGTTTAAGGTTTAGAG
1 TTTATGATTTAAGATTTAGGGTTTAAGGTTCAAAG
36554 TTTA
1 TTTA
36558 CCTTCTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.01, G:0.22, T:0.50
Consensus pattern (35 bp):
TTTATGATTTAAGATTTAGGGTTTAAGGTTCAAAG
Done.