Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004944.1 Hibiscus syriacus cultivar Beakdansim tig00011115_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: 70615
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:3946 original size:2 final size:2
Alignment explanation
Indices: 3939--3991 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
3929 CACAGGTAAG
3939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
3981 TA TA TA -A TA TA
1 TA TA TA TA TA TA
3992 ATAGCTGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 45 0.94
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8175 original size:19 final size:20
Alignment explanation
Indices: 8132--8192 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
8122 AGAAAATATA
* * *
8132 ATAATAAAAATATTTCAAAT
1 ATAATAAAAATGTATAAAAT
*
8152 ATAATATAAAT-TATAAAAT
1 ATAATAAAAATGTATAAAAT
*
8171 GTAATAAAAATGTATAATAAT
1 ATAATAAAAATGTATAA-AAT
8192 A
1 A
8193 ATTAAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.45
20 15 0.45
21 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (20 bp):
ATAATAAAAATGTATAAAAT
Found at i:8194 original size:19 final size:17
Alignment explanation
Indices: 8131--8200 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 17
8121 GAGAAAATAT
*
8131 AATAATAAAAATATTTCAA
1 AATAATAAAAAT-TAT-AA
*
8150 ATATAATATAAATTATAA
1 A-ATAATAAAAATTATAA
8168 AATGTAATAAAAATGTATAA
1 AA--TAATAAAAAT-TATAA
*
8188 TAATAATTAAAAT
1 -AATAATAAAAAT
8201 AAGTTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 21 0.50
20 15 0.36
21 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAATAAAAATTATAA
Found at i:13768 original size:29 final size:29
Alignment explanation
Indices: 13726--13805 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
13716 CAACTAACTA
13726 AATTGATGTAAGCAATGTCATCTTCATCT
1 AATTGATGTAAGCAATGTCATCTTCATCT
13755 AATTGATGTAAGCAATGTCATCTTCATCT
1 AATTGATGTAAGCAATGTCATCTTCATCT
* *
13784 ATTTGATGTAAGCAATGACATC
1 AATTGATGTAAGCAATGTCATC
13806 AATTTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (29 bp):
AATTGATGTAAGCAATGTCATCTTCATCT
Found at i:19903 original size:2 final size:2
Alignment explanation
Indices: 19896--19921 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19886 AAGATTTCCA
19896 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
19922 CATCTATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21511 original size:12 final size:12
Alignment explanation
Indices: 21494--21544 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
21484 TTACCTTTGT
21494 TATTATTATTTA
1 TATTATTATTTA
21506 TATTA-TATTT-
1 TATTATTATTTA
21516 TATTATATATTTCA
1 TATTAT-TATTT-A
* *
21530 TGTCATTATTTA
1 TATTATTATTTA
21542 TAT
1 TAT
21545 ATAGATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 13 0.41
13 5 0.16
14 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:24619 original size:2 final size:2
Alignment explanation
Indices: 24612--24644 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24602 TCAAATTAAA
24612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24645 ATTTTAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25288 original size:42 final size:42
Alignment explanation
Indices: 25242--25424 Score: 246
Period size: 42 Copynumber: 4.4 Consensus size: 42
25232 TTTATTGTAA
* * * * *
25242 AAACGCTGCAATAGAGTTG-ACATATAGCGGCGTTTTTACAAC
1 AAACGCCGCAATAGAGTGGTAAAT-TAGCGGCGTTTATACCAC
25284 AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCAC
25326 AAACGCCGCAATAGA-TCGGTAAATTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAGT-GGTAAATTAGCGGCGTTTATACCAC
* *
25368 AAACGCCGCAATAGA-TCGGTAAATTAGCGGTGATTATACCAC
1 AAACGCCGCAATAGAGT-GGTAAATTAGCGGCGTTTATACCAC
*
25410 AAACGCCGTAATAGA
1 AAACGCCGCAATAGA
25425 TTACACATAT
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
41 1 0.01
42 127 0.97
43 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCAC
Found at i:25425 original size:42 final size:42
Alignment explanation
Indices: 25266--25425 Score: 259
Period size: 42 Copynumber: 3.8 Consensus size: 42
25256 AGTTGACATA
* *
25266 TAGCGGCGTTTTTACAACAAACGCCGCAATAGAGT-GGTAAAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGA-TCGGTAAAT
25308 TAGCGGCGTTTATACCACAAACGCCGCAATAGATCGGTAAAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGATCGGTAAAT
25350 TAGCGGCGTTTATACCACAAACGCCGCAATAGATCGGTAAAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGATCGGTAAAT
* * *
25392 TAGCGGTGATTATACCACAAACGCCGTAATAGAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGAT
25426 TACACATATA
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
41 1 0.01
42 111 0.99
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (42 bp):
TAGCGGCGTTTATACCACAAACGCCGCAATAGATCGGTAAAT
Found at i:25446 original size:84 final size:81
Alignment explanation
Indices: 25282--25463 Score: 206
Period size: 84 Copynumber: 2.2 Consensus size: 81
25272 CGTTTTTACA
*
25282 ACAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATCGGTA
1 ACAAACGCCGCAATAGAGTGGTAAATTAGCGGCGATTATACCACAAACGCCGCAATAGAT--GTA
* *
25347 AATTAGCGGCGTTTATACC
64 AATTAACGGCATTTAT-CC
* *
25366 ACAAACGCCGCAATAGA-TCGGTAAATTAGCGGTGATTATACCACAAACGCCGTAATAGAT-TAC
1 ACAAACGCCGCAATAGAGT-GGTAAATTAGCGGCGATTATACCACAAACGCCGCAATAGATGTA-
* *
25429 ACATATAATGGCATTTATTC
64 A-AT-TAACGGCATTTATCC
**
25449 TTAAACGCCGCAATA
1 ACAAACGCCGCAATA
25464 TTTATAATAA
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
81 2 0.02
82 1 0.01
83 17 0.20
84 65 0.76
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (81 bp):
ACAAACGCCGCAATAGAGTGGTAAATTAGCGGCGATTATACCACAAACGCCGCAATAGATGTAAA
TTAACGGCATTTATCC
Found at i:25496 original size:41 final size:41
Alignment explanation
Indices: 25451--25569 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
25441 ATTTATTCTT
* * * * *
25451 AAACGCCGCAATA-TTTATAATAAATAGTGTCGTTTTTAGAC
1 AAACGCCGCAATAGTTT-TAATCAATAGTGGCATTTTTACAA
* *
25492 AAACGGCGCAATAGTGTTAATCAATAGTGGCATTTTTACAA
1 AAACGCCGCAATAGTTTTAATCAATAGTGGCATTTTTACAA
25533 AAACGCCGCAATAGTTTTAATCAATAGTGGCATTTTT
1 AAACGCCGCAATAGTTTTAATCAATAGTGGCATTTTT
25570 TTAACAAACG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 66 0.97
42 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (41 bp):
AAACGCCGCAATAGTTTTAATCAATAGTGGCATTTTTACAA
Found at i:25596 original size:41 final size:41
Alignment explanation
Indices: 25510--25612 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
25500 CAATAGTGTT
** * * **
25510 AATCAATAGTGGCATTTTTACAAAAACGCCGCAATAGTTTT
1 AATCAATAGTGGCATTTTTTTAAAAACGCCACAATAGATGC
*
25551 AATCAATAGTGGCATTTTTTTAACAAACGCCATAATA-ATGC
1 AATCAATAGTGGCATTTTTTTAA-AAACGCCACAATAGATGC
*
25592 AATCAATAGTGGCGTTTTTTT
1 AATCAATAGTGGCATTTTTTT
25613 GTATAAACGC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 42 0.79
42 11 0.21
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (41 bp):
AATCAATAGTGGCATTTTTTTAAAAACGCCACAATAGATGC
Found at i:25719 original size:41 final size:41
Alignment explanation
Indices: 25674--26017 Score: 359
Period size: 41 Copynumber: 8.3 Consensus size: 41
25664 CCTAAAATCA
* * * *
25674 TTTAGTGGGGTTTTTATACAAACGTCGCTAAAGAATCGTAT
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
25715 TTTAGTGGCATTTTTTGTACAAACGCCGCTAAA-AATGAGTTC
1 TTTAGTGGC-GTTTTTATACAAACGCCGCTAAAGACT-CGTAC
* * * * *
25757 ATTAGTGGCGTTTTTGTACAAACACCGCTAAAAACTAGTTA-
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCG-TAC
*
25798 TTTAGTGGCGTTTTTATACAAACGCCGCTAACGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * ** * *
25839 TTTAGTGGCGTTTGTGTTTACAAATGTTGCTAAAGACTTGTAA
1 TTTAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTAC
* * * *
25882 TTCAGTGGCGTTTTTATATAAACGCCGCTATAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
25923 TTCAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * *
25964 TTCAGTGGCATTTTTATACAAACGCCGCTAAAGACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
26005 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
26018 GTAAACACAA
Statistics
Matches: 252, Mismatches: 44, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.01
41 183 0.73
42 35 0.14
43 32 0.13
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:28796 original size:43 final size:43
Alignment explanation
Indices: 28748--28933 Score: 230
Period size: 43 Copynumber: 4.3 Consensus size: 43
28738 ACTAGATCTT
** * * * *
28748 TTGCGGCGTTTGTGGGGAAAATGACGCAAAATCTCAAGACATA
1 TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTA
* * * *
28791 TTGCGGTGTTTGTGTAAAAAAACG-CTGCTAAATCTCAATACTTA
1 TTGCGGCGTTTGTG-GAAAAAACGAC-GCTAAATCTCAACACCTA
28835 TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTA
* * *
28878 TTGCGGCGTTTGTTGAAAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTA
28921 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
28934 CCAACAAACG
Statistics
Matches: 125, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 91 0.73
44 34 0.27
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTA
Found at i:28867 original size:87 final size:86
Alignment explanation
Indices: 28748--28933 Score: 255
Period size: 87 Copynumber: 2.2 Consensus size: 86
28738 ACTAGATCTT
** * * *
28748 TTGCGGCGTTTGTGGGGAAAATGACGCAAAATCTCAAGACATATTGCGGTGTTTGTGTAAAAAAA
1 TTGCGGCGTTTGTGGAAAAAACGACGCAAAATCTCAACACATATTGCGGCGTTTGT-TAAAAAAA
* * * *
28813 CGCTGCTAAATCTCAATACTTA
65 CGCCGCTAAATATCAACACCTA
* * *
28835 TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTATTGCGGCGTTTGTTGAAAAAAC
1 TTGCGGCGTTTGTGGAAAAAACGACGCAAAATCTCAACACATATTGCGGCGTTTGTTAAAAAAAC
28900 GCCGCTAAATATCAACACCTA
66 GCCGCTAAATATCAACACCTA
28921 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
28934 CCAACAAACG
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 38 0.44
87 49 0.56
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (86 bp):
TTGCGGCGTTTGTGGAAAAAACGACGCAAAATCTCAACACATATTGCGGCGTTTGTTAAAAAAAC
GCCGCTAAATATCAACACCTA
Found at i:28943 original size:43 final size:43
Alignment explanation
Indices: 28748--28974 Score: 204
Period size: 43 Copynumber: 5.3 Consensus size: 43
28738 ACTAGATCTT
* ** * * * * * *
28748 TTGCGGCGTTTGTGGGGAAAATGACGCAAAATCTCAAGACATA
1 TTGCGGCGTTTGTCGAAAAAACGCCGCTAAATATCAACACCTA
* * * * *
28791 TTGCGGTGTTTGT-GTAAAAAAACGCTGCTAAATCTCAATACTTA
1 TTGCGGCGTTTGTCG--AAAAAACGCCGCTAAATATCAACACCTA
* * *
28835 TTGCGGCGTTTGTGGAAAAAACGACGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTCGAAAAAACGCCGCTAAATATCAACACCTA
*
28878 TTGCGGCGTTTGTTGAAAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTCGAAAAAACGCCGCTAAATATCAACACCTA
* * * *** *
28921 TTGCGGCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTG
1 TTGCGGCGTTTGTCGAAAAAACGCCGCTAAATATCAACACCTA
28964 TTGCGGCGTTT
1 TTGCGGCGTTT
28975 TTTGTTACCA
Statistics
Matches: 156, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 122 0.78
44 32 0.21
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (43 bp):
TTGCGGCGTTTGTCGAAAAAACGCCGCTAAATATCAACACCTA
Found at i:29855 original size:32 final size:32
Alignment explanation
Indices: 29799--29859 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
29789 GATTTATATA
*
29799 TATATGTATGTATATATTGTATTTGTTGTTTG
1 TATATGTATGTATATATTGAATTTGTTGTTTG
*
29831 TATATGTATGTATGT-TATGAATTTGTTGT
1 TATATGTATGTATATAT-TGAATTTGTTGT
29860 GACAATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (32 bp):
TATATGTATGTATATATTGAATTTGTTGTTTG
Found at i:30792 original size:16 final size:16
Alignment explanation
Indices: 30757--30802 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
30747 ACTAGGCTAT
*
30757 TATATATATGTTGATTTA
1 TATATATATG-T-ATGTA
30775 TATATATATGTATGTA
1 TATATATATGTATGTA
30791 TATATAT-TGTAT
1 TATATATATGTAT
30803 TTATTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 11 0.41
17 1 0.04
18 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (16 bp):
TATATATATGTATGTA
Found at i:30847 original size:22 final size:22
Alignment explanation
Indices: 30821--30902 Score: 139
Period size: 22 Copynumber: 3.8 Consensus size: 22
30811 TGTATATGTA
30821 TGTATGTTATGAATTTGTTGTT
1 TGTATGTTATGAATTTGTTGTT
30843 TGTATGTTATGAATTTGTTGTT
1 TGTATGTTATGAATTTGTTGTT
*
30865 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGTTGTT
*
30887 TG-ATGTTATGTATTTG
1 TGTATGTTATGAATTTG
30903 ATGTGTATGC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 13 0.22
22 45 0.78
ACGTcount: A:0.18, C:0.01, G:0.23, T:0.57
Consensus pattern (22 bp):
TGTATGTTATGAATTTGTTGTT
Found at i:30847 original size:26 final size:24
Alignment explanation
Indices: 30817--30911 Score: 114
Period size: 22 Copynumber: 4.2 Consensus size: 24
30807 TGTTTGTATA
30817 TGTATGTATGTTATGAATTTGTTG
1 TGTATGTATGTTATGAATTTGTTG
30841 T-T-TGTATGTTATGAATTTGTTG
1 TGTATGTATGTTATGAATTTGTTG
*
30863 T-T-TGTATGTTATGAATTTGCTG
1 TGTATGTATGTTATGAATTTGTTG
* *
30885 T-T-TG-ATGTTATGTATTTGATG
1 TGTATGTATGTTATGAATTTGTTG
30906 TGTATG
1 TGTATG
30912 CTAATTTGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.24
22 46 0.70
23 3 0.05
24 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.24, T:0.56
Consensus pattern (24 bp):
TGTATGTATGTTATGAATTTGTTG
Found at i:30847 original size:32 final size:34
Alignment explanation
Indices: 30779--30847 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
30769 GATTTATATA
*
30779 TATATGTATGTATATATATTGTATTTATTGTTTG
1 TATATGTATGTATATATATTGAATTTATTGTTTG
* *
30813 TATATGTATGTATGT-TA-TGAATTTGTTGTTTG
1 TATATGTATGTATATATATTGAATTTATTGTTTG
30845 TAT
1 TAT
30848 GTTATGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 16 0.50
33 2 0.06
34 14 0.44
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (34 bp):
TATATGTATGTATATATATTGAATTTATTGTTTG
Found at i:32002 original size:30 final size:29
Alignment explanation
Indices: 31968--32136 Score: 168
Period size: 30 Copynumber: 5.9 Consensus size: 29
31958 TCTTTTTGAT
31968 TATG-TAAGAAATATTATATGGTTTGTGGTC
1 TATGTTAA-AAATATTATATGGTTTGT-GTC
*
31998 TATGTTAGAAATATTATATGG-TT-TGTC
1 TATGTTAAAAATATTATATGGTTTGTGTC
* * * * *
32025 GATGTTCAAAACATTATATAGTTTGTGTT
1 TATGTTAAAAATATTATATGGTTTGTGTC
* **
32054 TAAGTTTTAAATATTATATGG-TT-TGTC
1 TATGTTAAAAATATTATATGGTTTGTGTC
* * *
32081 GATGTTCAAAACATTATATGGTTTGTGGTC
1 TATGTTAAAAATATTATATGGTTTGT-GTC
32111 TATGTTAAAAATATTATATGGTTTGT
1 TATGTTAAAAATATTATATGGTTTGT
32137 ATTAAAGTTA
Statistics
Matches: 111, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
27 38 0.34
28 7 0.06
29 21 0.19
30 43 0.39
31 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (29 bp):
TATGTTAAAAATATTATATGGTTTGTGTC
Found at i:32040 original size:27 final size:27
Alignment explanation
Indices: 32010--32136 Score: 121
Period size: 27 Copynumber: 4.5 Consensus size: 27
32000 TGTTAGAAAT
32010 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
* * ** *
32037 ATTATATAGTTTGT-GTTTAAGTTTTAAAT
1 ATTATATGGTTTGTCG---ATGTTCAAAAC
32066 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
* * *
32093 ATTATATGGTTTGTGGTCTATGTTAAAAAT
1 ATTATATGG-TT-T-GTCGATGTTCAAAAC
32123 ATTATATGGTTTGT
1 ATTATATGGTTTGT
32137 ATTAAAGTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
26 1 0.01
27 31 0.39
28 3 0.04
29 23 0.29
30 22 0.28
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (27 bp):
ATTATATGGTTTGTCGATGTTCAAAAC
Found at i:32075 original size:56 final size:57
Alignment explanation
Indices: 31980--32136 Score: 235
Period size: 56 Copynumber: 2.8 Consensus size: 57
31970 TGTAAGAAAT
* * *
31980 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATAGTTTGTGGTCTAAGTTAAAAATATTATATGGTTTGTCGATGTTCAAAAC
* **
32037 ATTATATAGTTTGT-GTTTAAGTTTTAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATAGTTTGTGGTCTAAGTTAAAAATATTATATGGTTTGTCGATGTTCAAAAC
* *
32093 ATTATATGGTTTGTGGTCTATGTTAAAAATATTATATGGTTTGT
1 ATTATATAGTTTGTGGTCTAAGTTAAAAATATTATATGGTTTGT
32137 ATTAAAGTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
56 51 0.57
57 38 0.43
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (57 bp):
ATTATATAGTTTGTGGTCTAAGTTAAAAATATTATATGGTTTGTCGATGTTCAAAAC
Found at i:32127 original size:86 final size:86
Alignment explanation
Indices: 31976--32145 Score: 204
Period size: 86 Copynumber: 2.0 Consensus size: 86
31966 ATTATGTAAG
* * *
31976 AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAACATTA
1 AAATATTATATGGTTTGTGGTCGATGTTAGAAACATTATATGGTTTGTCGATGTTAAAAACATTA
* *
32041 TATAGTTTGTGTTTAAGTTTT
66 TATAGTTTGTATTAAAGTTTT
* *
32062 AAATATTATATGG-TT-T-GTCGATGTTCA-AAACATTATATGGTTTGTGGTCTATGTTAAAAAT
1 AAATATTATATGGTTTGTGGTCGATGTT-AGAAACATTATATGG-TT-T-GTCGATGTTAAAAAC
*
32123 ATTATATGGTTTGTATTAAAGTT
62 ATTATATAGTTTGTATTAAAGTT
32146 ATATTTATCT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
83 20 0.28
84 4 0.06
85 3 0.04
86 45 0.62
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (86 bp):
AAATATTATATGGTTTGTGGTCGATGTTAGAAACATTATATGGTTTGTCGATGTTAAAAACATTA
TATAGTTTGTATTAAAGTTTT
Found at i:33516 original size:31 final size:31
Alignment explanation
Indices: 33459--33517 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
33449 AGTTGTAAGG
*
33459 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTGCAAAACTAAA
* *
33490 ATTATTTAAATTTCAGTGTTGCAAAACT
1 ATTATTTAAATTTCAATATTGCAAAACT
33518 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTGCAAAACTAAA
Found at i:34352 original size:22 final size:21
Alignment explanation
Indices: 34314--34356 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
34304 TTTAAATCTA
*
34314 TTTAATTTTTAATATTAAAAT
1 TTTAATTTTTAAAATTAAAAT
34335 TTTAATTATTTAAAATTAAAAT
1 TTTAATT-TTTAAAATTAAAAT
34357 AATTTAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATTTTTAAAATTAAAAT
Found at i:37244 original size:12 final size:13
Alignment explanation
Indices: 37227--37255 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
37217 CTTAATTGCA
37227 AAAATTAAAA-TT
1 AAAATTAAAATTT
37239 AAAATTAAAATTT
1 AAAATTAAAATTT
37252 AAAA
1 AAAA
37256 ATTTGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:43945 original size:6 final size:6
Alignment explanation
Indices: 43936--43969 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
43926 TCGAATAGAT
43936 AAATTA AAATTA AAATTA AAATTA AAATTTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA-TTA AAA
43970 ATTCAATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:44820 original size:2 final size:2
Alignment explanation
Indices: 44813--44848 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
44803 AAAACCTTCT
44813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44849 TTATTAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:46112 original size:21 final size:20
Alignment explanation
Indices: 46073--46126 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
46063 ATTATTATTG
**
46073 TATTAAATTATTCTATTTTT
1 TATTAAATTATAATATTTTT
46093 TATTAAATATATAATATTTTT
1 TATTAAAT-TATAATATTTTT
* *
46114 AATAAAATTATAA
1 TATTAAATTATAA
46127 AAAATATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAAATTATAATATTTTT
Found at i:54330 original size:26 final size:24
Alignment explanation
Indices: 54266--54330 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
54256 ATCATTTTAA
54266 TCAAAATAT-TAATTATTAAAATAT
1 TCAAAATATAT-ATTATTAAAATAT
*
54290 TCAAAATATAT-TTATTAATAT-T
1 TCAAAATATATATTATTAAAATAT
54312 TCTAATAATATAATATTAT
1 TC-AA-AATAT-ATATTAT
54331 ATTTTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.09
23 11 0.31
24 14 0.40
25 3 0.09
26 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (24 bp):
TCAAAATATATATTATTAAAATAT
Found at i:54332 original size:22 final size:23
Alignment explanation
Indices: 54302--54348 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
54292 AAAATATATT
54302 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
54325 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
54347 TA
1 TA
54349 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:54367 original size:23 final size:23
Alignment explanation
Indices: 54338--54388 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
54328 TATATTTTTA
54338 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
*
54361 ATATTATAATAATATAACATATT
1 ATATTATAATAAAATAACATATT
54384 ATATT
1 ATATT
54389 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:54489 original size:19 final size:18
Alignment explanation
Indices: 54465--54533 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
54455 ATATTATTAA
54465 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
54484 ATTATTTATAA-ATTTAAT
1 ATTATTAATAATA-ATAAT
54502 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
54524 ATT-TTAATAA
1 ATTATTAATAA
54534 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 7 0.17
19 18 0.45
20 6 0.15
22 7 0.17
23 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:54508 original size:27 final size:27
Alignment explanation
Indices: 54428--54513 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
54418 AATAAAATTT
* * *
54428 ATATTATTTATTAATTTCATAGAAATA
1 ATATTATTTATAAATTTAATATAAATA
* *
54455 ATATTA-TTA-AATTATTAATAATGAATA
1 ATATTATTTATAAAT-TTAAT-ATAAATA
54482 ATATTATTTATAAATTTAATATTAATATA
1 ATATTATTTATAAATTTAATA-TAA-ATA
54511 ATA
1 ATA
54514 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.04
26 7 0.15
27 18 0.39
28 10 0.22
29 9 0.20
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTATTTATAAATTTAATATAAATA
Found at i:56829 original size:15 final size:16
Alignment explanation
Indices: 56797--56839 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
56787 ACAAAAACAA
*
56797 ATATAAAGAAATATAC
1 ATATAAATAAATATAC
56813 ATATAAATAAA-ATAC
1 ATATAAATAAATATAC
56828 ATA-AAATAAATA
1 ATATAAATAAATA
56840 AGATAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 10 0.40
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
ATATAAATAAATATAC
Found at i:56838 original size:18 final size:18
Alignment explanation
Indices: 56815--56854 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
56805 AAATATACAT
56815 ATAAATAAAATACATAA-A
1 ATAAATAAAATA-ATAACA
*
56833 ATAAATAAGATAATAACA
1 ATAAATAAAATAATAACA
56851 ATAA
1 ATAA
56855 TAATGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAATAAAATAATAACA
Found at i:56947 original size:33 final size:34
Alignment explanation
Indices: 56896--56967 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
56886 AATGAAATTT
*
56896 ATAAAATAAATATATATAACAT-ATAATAATAGTA
1 ATAAAATAAATATATATAA-ATAATAATAATAATA
* *
56930 ATAAAA-ATATATATATAAATAATCATAATAATA
1 ATAAAATAAATATATATAAATAATAATAATAATA
56963 ATAAA
1 ATAAA
56968 GGTAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 2 0.06
33 26 0.76
34 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (34 bp):
ATAAAATAAATATATATAAATAATAATAATAATA
Found at i:56988 original size:12 final size:12
Alignment explanation
Indices: 56918--57011 Score: 50
Period size: 12 Copynumber: 7.5 Consensus size: 12
56908 TATATAACAT
* *
56918 ATAATAATAGTA
1 ATAAAAATAATA
56930 ATAAAAAT-ATA
1 ATAAAAATAATA
* *
56941 TATATAAATAATC
1 -ATAAAAATAATA
*
56954 ATAATAATAATA
1 ATAAAAATAATA
56966 A-AGGTAAAATAATA
1 ATA---AAAATAATA
56980 ATAAAAATATAGTGA
1 ATAAAAATA-A-T-A
*
56995 A-AAAAATAAAA
1 ATAAAAATAATA
57006 ATAAAA
1 ATAAAA
57012 GATAGTATGA
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
11 5 0.08
12 34 0.54
13 4 0.06
14 17 0.27
15 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:56988 original size:23 final size:21
Alignment explanation
Indices: 56954--57010 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
56944 ATAAATAATC
*
56954 ATAATAATAATAAAGGTAAAATA
1 ATAATAAAAATAAA-GTAAAA-A
* *
56977 ATAATAAAAATATAGTGAAAA
1 ATAATAAAAATAAAGTAAAAA
56998 A-AATAAAAATAAA
1 ATAATAAAAATAAA
57011 AGATAGTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.37
21 2 0.07
22 5 0.17
23 12 0.40
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
ATAATAAAAATAAAGTAAAAA
Found at i:57064 original size:18 final size:18
Alignment explanation
Indices: 57028--57065 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57018 ATGATATAAT
57028 AATAGTAAAAAAAATGAA
1 AATAGTAAAAAAAATGAA
*
57046 AATAG-AAAAATAATAGAA
1 AATAGTAAAAAAAAT-GAA
57064 AA
1 AA
57066 ACTTATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AATAGTAAAAAAAATGAA
Found at i:58281 original size:2 final size:2
Alignment explanation
Indices: 58270--58315 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
58260 AAAATTAAAA
58270 AT AT -T AT AT AT 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
58311 AT AT A
1 AT AT A
58316 ATTATACAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58349 original size:10 final size:10
Alignment explanation
Indices: 58269--58359 Score: 55
Period size: 12 Copynumber: 8.7 Consensus size: 10
58259 TAAAATTAAA
58269 AATATTATAT
1 AATATTATAT
58279 -ATA-TATAT
1 AATATTATAT
58287 ATATATATATAT
1 A-ATAT-TATAT
58299 ATATATATATAT
1 A-ATAT-TATAT
*
58311 ATATAATTATAC
1 A-AT-ATTATAT
* *
58323 AATATAATTTGT
1 AATAT--TATAT
58335 AATATTATAT
1 AATATTATAT
58345 AATA-TA-AT
1 AATATTATAT
58353 AATATTA
1 AATATTA
58360 ATAGTGAAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
8 11 0.16
9 7 0.10
10 12 0.18
11 2 0.03
12 33 0.49
13 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (10 bp):
AATATTATAT
Found at i:60495 original size:8 final size:7
Alignment explanation
Indices: 60477--60518 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
60467 CCCACTTTAT
60477 TTTTTTC
1 TTTTTTC
*
60484 TTTTCTC
1 TTTTTTC
60491 TTTTTTC
1 TTTTTTC
60498 TTTTGTTC
1 TTTT-TTC
60506 TTTTGTTC
1 TTTT-TTC
60514 TTTTT
1 TTTTT
60519 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 17 0.53
8 15 0.47
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:60501 original size:22 final size:23
Alignment explanation
Indices: 60475--60527 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
60465 AACCCACTTT
*
60475 ATTTTTTTCTTTT-CTCTTTTTT
1 ATTTTTTTCTTTTGCTCTTTTTA
* * *
60497 CTTTTGTTCTTTTGTTCTTTTTA
1 ATTTTTTTCTTTTGCTCTTTTTA
60520 ATTTTTTT
1 ATTTTTTT
60528 TTCAATTTAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.79
Consensus pattern (23 bp):
ATTTTTTTCTTTTGCTCTTTTTA
Found at i:60506 original size:17 final size:16
Alignment explanation
Indices: 60476--60517 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
60466 ACCCACTTTA
* *
60476 TTTTTTTCTTTT-CTC
1 TTTTGTTCTTTTGTTC
60491 TTTT-TTCTTTTGTTC
1 TTTTGTTCTTTTGTTC
60506 TTTTGTTCTTTT
1 TTTTGTTCTTTT
60518 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 10 0.42
16 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTTGTTCTTTTGTTC
Done.