Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006600.1 Hibiscus syriacus cultivar Beakdansim tig00016189_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: 50904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:920 original size:6 final size:6
Alignment explanation
Indices: 895--985 Score: 79
Period size: 6 Copynumber: 15.5 Consensus size: 6
885 TAGACACATA
895 AAAAAT AAATAA- ACAAAAT AAAAAT AAAAAT --AAAT AAAAAT AAAAAT
1 AAAAAT AAA-AAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
942 AAAGAT AAGAAA- ATAAAAT -AAAA- AAAAAT AAATAA- AAAAAT AAA
1 AAAAAT AA-AAAT A-AAAAT AAAAAT AAAAAT AAA-AAT AAAAAT AAA
986 TAAAATAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
4 4 0.06
5 10 0.14
6 47 0.66
7 10 0.14
ACGTcount: A:0.81, C:0.01, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:922 original size:26 final size:25
Alignment explanation
Indices: 892--1004 Score: 96
Period size: 25 Copynumber: 4.5 Consensus size: 25
882 AAATAGACAC
892 ATAAAAAATAAATAAACAAAATAAAA
1 ATAAAAAATAAATAAA-AAAATAAAA
918 AT-AAAAATAAAT--AAAAATAAAA
1 ATAAAAAATAAATAAAAAAATAAAA
*
940 AT-AAAGATAAGA-AAATAAAATAAAA
1 ATAAAAAATAA-ATAAA-AAAATAAAA
*
965 AAAAATAAATAAA-AAAATAAAT-AAA
1 ATAAA-AAATAAATAAAA-AAATAAAA
990 ATAAAACAAGTAAAT
1 ATAAAA-AA-TAAAT
1005 GAGTAAACAA
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
22 18 0.25
23 2 0.03
24 2 0.03
25 30 0.41
26 16 0.22
27 5 0.07
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.17
Consensus pattern (25 bp):
ATAAAAAATAAATAAAAAAATAAAA
Found at i:923 original size:5 final size:5
Alignment explanation
Indices: 896--995 Score: 65
Period size: 5 Copynumber: 20.8 Consensus size: 5
886 AGACACATAA
*
896 AAAAT -AAAT -AAAC AAAAT AAAAAT AAAA- ATAAAT AAAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT A-AAAT -AAAAT -AAAAT
* *
942 AAAGAT --AAG AAAAT AAAAT AAAAA AAAAT -AAAT -AAA- AAAAT -AAAT
1 AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
987 AAAAT AAAA
1 AAAAT AAAA
996 CAAGTAAATG
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
3 1 0.01
4 23 0.29
5 36 0.46
6 17 0.22
7 1 0.01
ACGTcount: A:0.81, C:0.01, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:931 original size:16 final size:15
Alignment explanation
Indices: 910--1041 Score: 88
Period size: 16 Copynumber: 8.1 Consensus size: 15
900 TAAATAAACA
910 AAATAAAAATAAAAAT
1 AAATAAAAA-AAAAAT
926 AAATAAAAATAAAAAT
1 AAATAAAAA-AAAAAT
* * *
942 AAA-GATAAGAAAAT
1 AAATAAAAAAAAAAT
956 AAA-ATAAAAAAAAAT
1 AAATA-AAAAAAAAAT
971 AAATAAAAAAATAAAT
1 AAATAAAAAAA-AAAT
*
987 AAAATAAAACAAGTAAAT
1 -AAATAAAA-AA-AAAAT
* *
1005 GAGTAAACAAAATAGAAT
1 AAATAAA-AAAA-A-AAT
1023 GAAATAAAAATAAAAAT
1 -AAATAAAAA-AAAAAT
1040 AA
1 AA
1042 GGAAGGACAT
Statistics
Matches: 93, Mismatches: 12, Indels: 22
0.73 0.09 0.17
Matches are distributed among these distances:
14 8 0.09
15 20 0.22
16 26 0.28
17 19 0.20
18 13 0.14
19 7 0.08
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (15 bp):
AAATAAAAAAAAAAT
Found at i:934 original size:56 final size:57
Alignment explanation
Indices: 868--990 Score: 146
Period size: 57 Copynumber: 2.2 Consensus size: 57
858 TAGTTCAAAC
* * *
868 ATAAAGAAAAAGACAAATAGACACATAA-AAAAT-AAAT-AAACAAAATAAA-AATAAAA
1 ATAAATAAAAAGAAAAATA-A-ACATAAGAAAATAAAATAAAAAAAAATAAATAA-AAAA
* *
924 ATAAATAAAAATAAAAATAAAGATAAGAAAATAAAATAAAAAAAAATAAATAAAAAA
1 ATAAATAAAAAGAAAAATAAACATAAGAAAATAAAATAAAAAAAAATAAATAAAAAA
981 ATAAATAAAA
1 ATAAATAAAA
991 TAAAACAAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
54 5 0.09
55 6 0.10
56 20 0.34
57 25 0.43
58 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (57 bp):
ATAAATAAAAAGAAAAATAAACATAAGAAAATAAAATAAAAAAAAATAAATAAAAAA
Found at i:940 original size:41 final size:40
Alignment explanation
Indices: 894--989 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 40
884 ATAGACACAT
*
894 AAAAAATAAATAAACAAAATAAAAATAAAAATAAATAAA-A
1 AAAAAATAAATAAACAAAAT-AAAATAAAAAAAAATAAATA
* *
934 ATAAAAATAAAGATAAGAAAATAAAATAAAAAAAAATAAATA
1 A-AAAAATAAATA-AACAAAATAAAATAAAAAAAAATAAATA
976 AAAAAATAAATAAA
1 AAAAAATAAATAAA
990 ATAAAACAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 3 0.06
41 37 0.76
42 9 0.18
ACGTcount: A:0.81, C:0.01, G:0.02, T:0.16
Consensus pattern (40 bp):
AAAAAATAAATAAACAAAATAAAATAAAAAAAAATAAATA
Found at i:990 original size:57 final size:53
Alignment explanation
Indices: 892--1041 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 53
882 AAATAGACAC
*
892 ATAAAAAATAAATAAACAAAATAAAAATAAAAATAAATAAAAATAAAAATAAAG
1 ATAAAAAATAAATAAAAAAAATAAAAATAAAAATAAAT-AAAATAAAAATAAAG
946 ATAAGAAAATAAAATAAAAAAAAATAAATAA-AAAAATAAATAAAATAAAACAAGTAAATG
1 ATAA-AAAAT-AAAT-AAAAAAAATAAA-AATAAAAATAAATAAAAT-AAA-AA-TAAA-G
1006 AGTAAACAAAATAGAATGAAATAAAAATAAAAATAA
1 A-T-AA-AAAATA-AAT-AAA-AAAAATAAAAATAA
1042 GGAAGGACAT
Statistics
Matches: 80, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
54 4 0.05
55 5 0.06
56 9 0.11
57 24 0.30
58 4 0.05
59 4 0.05
60 2 0.03
61 2 0.03
62 15 0.19
63 11 0.14
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (53 bp):
ATAAAAAATAAATAAAAAAAATAAAAATAAAAATAAATAAAATAAAAATAAAG
Found at i:1284 original size:22 final size:21
Alignment explanation
Indices: 1242--1285 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1232 ATATAAACGT
**
1242 ATAAATAAAAAATTAGAATAA
1 ATAAATAAAAAAAAAGAATAA
1263 ATAAATAAAATAAAAAGAATAA
1 ATAAATAAAA-AAAAAGAATAA
1285 A
1 A
1286 GAAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
ATAAATAAAAAAAAAGAATAA
Found at i:1497 original size:30 final size:30
Alignment explanation
Indices: 1413--1498 Score: 77
Period size: 32 Copynumber: 2.8 Consensus size: 30
1403 ATAAATTATA
* *
1413 AAAAAAATATACATATATAAATAAAAACTAAC
1 AAAAATATATA-AAATATAAATAAAAAC-AAC
* *
1445 AAAACTA-ATAATAGTAATAAATAAAAA-AACC
1 AAAAATATATAA-AAT-ATAAATAAAAACAA-C
1476 AAAAATATATAAAATATAAATAA
1 AAAAATATATAAAATATAAATAA
1499 TTAAATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
30 11 0.25
31 13 0.30
32 20 0.45
ACGTcount: A:0.70, C:0.07, G:0.01, T:0.22
Consensus pattern (30 bp):
AAAAATATATAAAATATAAATAAAAACAAC
Found at i:1506 original size:14 final size:14
Alignment explanation
Indices: 1487--1513 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1477 AAAATATATA
1487 AAATATAAATAATT
1 AAATATAAATAATT
1501 AAATATAAATAAT
1 AAATATAAATAAT
1514 AATAAGGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAATAATT
Found at i:3054 original size:17 final size:17
Alignment explanation
Indices: 3032--3064 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3022 ATAGAATTTT
3032 TGTGTTATTAAGATATG
1 TGTGTTATTAAGATATG
3049 TGTGTTATTAAGATAT
1 TGTGTTATTAAGATAT
3065 TTTTGGATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (17 bp):
TGTGTTATTAAGATATG
Found at i:12234 original size:66 final size:63
Alignment explanation
Indices: 12103--12254 Score: 182
Period size: 66 Copynumber: 2.3 Consensus size: 63
12093 GAATAAATTG
* *
12103 AACATCGAATGCATTATATGCATCGATGCACATACCATGCATCAATGCACTCAAGTTTTTATGAA
1 AACATCGAATGCATT-TATGCATCGATGCACATAACATGCATCAATGCACTCAAGTTGTTATG--
12168 A
63 A
* **
12169 AACATCGAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCTGGCTTGTT-TG
1 AACATCGAATGCATTT-ATGCATCGATGCACATA-ACATGCATCAATGCACTCAAG-TTGTTATG
12232 A
63 A
12233 AACATCGAATGCATTTCATGCA
1 AACATCGAATGCATTT-ATGCA
12255 CTCTTAGTGC
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
64 22 0.29
65 2 0.03
66 49 0.64
67 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACATAACATGCATCAATGCACTCAAGTTGTTATGA
Found at i:13886 original size:21 final size:23
Alignment explanation
Indices: 13860--13902 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
13850 CTAAAATTTA
*
13860 TTTATTTGAATTA-T-TTTAAAT
1 TTTATTTAAATTACTATTTAAAT
13881 TTTATTTAAATTACTATTTAAA
1 TTTATTTAAATTACTATTTAAA
13903 AAATAGCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTATTTAAATTACTATTTAAAT
Found at i:15265 original size:2 final size:2
Alignment explanation
Indices: 15258--15311 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
15248 GCTCAATCTA
15258 AT AT AT 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
*
15300 AT AT AT GT AT AT
1 AT AT AT AT AT AT
15312 GTATGTTTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16629 original size:18 final size:18
Alignment explanation
Indices: 16605--16659 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
16595 GTCATAACCC
16605 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
16623 TACCCGA-CC-A---GTT
1 GACCCGACCCGACCCGTT
16636 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
16654 GACCCG
1 GACCCG
16660 TTGACCCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 15 0.50
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:16657 original size:8 final size:8
Alignment explanation
Indices: 16646--16688 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
16636 GACCCGACCC
16646 GACCCGTT
1 GACCCGTT
16654 GACCCGTT
1 GACCCGTT
16662 GACCCGTT
1 GACCCGTT
16670 GACCCGTT
1 GACCCGTT
*
16678 GA-TCGTT
1 GACCCGTT
16685 GACC
1 GACC
16689 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.14, C:0.35, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:16657 original size:26 final size:28
Alignment explanation
Indices: 16605--16667 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
16595 GTCATAACCC
16605 GACCCGACCCGACCCGTTTACCCGACCAGTT
1 GACCCGACCCGACCCGTTT---CGACCAGTT
*
16636 GACCCGACCCGACCCG-TT-GACCCGTT
1 GACCCGACCCGACCCGTTTCGACCAGTT
16662 GACCCG
1 GACCCG
16668 TTGACCCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 13 0.42
30 2 0.06
31 16 0.52
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.14
Consensus pattern (28 bp):
GACCCGACCCGACCCGTTTCGACCAGTT
Found at i:16659 original size:13 final size:13
Alignment explanation
Indices: 16610--16646 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
16600 AACCCGACCC
16610 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
16623 TACCCGACCAGTT
1 GACCCGACCCGTT
16636 GACCCGACCCG
1 GACCCGACCCG
16647 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:19246 original size:24 final size:24
Alignment explanation
Indices: 19150--19258 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
19140 GAATATTTTA
* *
19150 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
19174 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
19198 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
19222 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
19246 TTTGATTTCTGAT
1 TCTGATATCTGAT
19259 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:24691 original size:13 final size:12
Alignment explanation
Indices: 24668--24737 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 12
24658 CACATCAAAG
24668 CAAAGAAAAAAA
1 CAAAGAAAAAAA
24680 CAAAG-AAAAAA
1 CAAAGAAAAAAA
*
24691 -AAAGAAAAAGA
1 CAAAGAAAAAAA
*
24702 -AAAG-AAAAGA
1 CAAAGAAAAAAA
24712 -AAAGAAAAGAAGA
1 CAAAGAAAA-AA-A
24725 GCAAAGAAAAAAA
1 -CAAAGAAAAAAA
24738 TATGATAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
10 14 0.28
11 18 0.36
12 6 0.12
13 2 0.04
14 2 0.04
15 8 0.16
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAAAA
Found at i:24693 original size:15 final size:15
Alignment explanation
Indices: 24663--24737 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 15
24653 AATATCACAT
24663 CAAAGCAAAGAAAAAAA
1 CAAAG-AAA-AAAAAAA
24680 CAAAGAAAAAAAAAGA
1 CAAAGAAAAAAAAA-A
* *
24696 AAAAGAAAAGAAAAGA
1 CAAAGAAAA-AAAAAA
* * *
24712 -AAAGAAAAGAAGAG
1 CAAAGAAAAAAAAAA
24726 CAAAGAAAAAAA
1 CAAAGAAAAAAA
24738 TATGATAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
14 2 0.04
15 24 0.50
16 13 0.27
17 9 0.19
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (15 bp):
CAAAGAAAAAAAAAA
Found at i:24694 original size:10 final size:10
Alignment explanation
Indices: 24669--24719 Score: 66
Period size: 10 Copynumber: 4.8 Consensus size: 10
24659 ACATCAAAGC
24669 AAAGAAAAAAA
1 AAAG-AAAAAA
24680 CAAAGAAAAAA
1 -AAAGAAAAAA
24691 AAAGAAAAAGA
1 AAAGAAAAA-A
*
24702 AAAGAAAAGA
1 AAAGAAAAAA
24712 AAAGAAAA
1 AAAGAAAA
24720 GAAGAGCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 18 0.49
11 15 0.41
12 4 0.11
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:24698 original size:5 final size:5
Alignment explanation
Indices: 24681--24734 Score: 72
Period size: 5 Copynumber: 10.6 Consensus size: 5
24671 AGAAAAAAAC
* * *
24681 AAAGA AAAAA AAAGAA AAAGA AAAGA AAAGA AAAGA AAAGA AGAGC AAAGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
24732 AAA
1 AAA
24735 AAATATGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:24749 original size:26 final size:22
Alignment explanation
Indices: 24669--24737 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
24659 ACATCAAAGC
*
24669 AAAGAAA-AAAACAAAGAAAAAA
1 AAAGAAAGAAGACAAAG-AAAAA
24691 AAAGAAA-AAGA-AAAGAAAAGA
1 AAAGAAAGAAGACAAAGAAAA-A
24712 AAAGAAAAGAAGAGCAAAGAAAAA
1 AAAG-AAAGAAGA-CAAAGAAAAA
24736 AA
1 AA
24738 TATGATAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 4 0.10
21 9 0.22
22 13 0.32
23 4 0.10
24 3 0.07
25 8 0.20
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGACAAAGAAAAA
Found at i:26025 original size:36 final size:37
Alignment explanation
Indices: 25939--26039 Score: 93
Period size: 36 Copynumber: 2.7 Consensus size: 37
25929 ATAAATTTTA
*
25939 TCTCACTTAAGACAATTTTCTCTAAAATCAAATCTTG
1 TCTCACTGAAGACAATTTTCTCTAAAATCAAATCTTG
**
25976 TCTTGCTTG-AGACAA-TTTCTCTCAAAA-CAAAT-TTCG
1 TCTCAC-TGAAGACAATTTTCTCT-AAAATCAAATCTT-G
* *
26012 TCTCACTGAAGACAGTTTTTCTTTAAAA
1 TCTCACTGAAGACA-ATTTTCTCTAAAA
26040 CACAAATTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
35 4 0.08
36 22 0.43
37 18 0.35
38 7 0.14
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (37 bp):
TCTCACTGAAGACAATTTTCTCTAAAATCAAATCTTG
Found at i:26177 original size:55 final size:56
Alignment explanation
Indices: 26118--26249 Score: 158
Period size: 65 Copynumber: 2.2 Consensus size: 56
26108 GTTTTATATT
26118 TCTTGAGACAGTTT-ATCATCTTTGAGATCATTTCCCTTAAAACGAATTTTGTCTC
1 TCTTGAGACAGTTTAATCATCTTTGAGATCATTTCCCTTAAAACGAATTTTGTCTC
* *
26173 TCTTGAGACAGTTTCTCTTTAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTC
1 TCTTGAGACAG------TTT--A-ATCATCTTTGAGATCATTTCCCTTAAAACGAATTTTGTCTC
26238 TCTTGAGACAGT
1 TCTTGAGACAGT
26250 CTTGAAACAA
Statistics
Matches: 65, Mismatches: 2, Indels: 16
0.78 0.02 0.19
Matches are distributed among these distances:
55 11 0.17
59 1 0.02
61 3 0.05
65 50 0.77
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (56 bp):
TCTTGAGACAGTTTAATCATCTTTGAGATCATTTCCCTTAAAACGAATTTTGTCTC
Found at i:26179 original size:36 final size:36
Alignment explanation
Indices: 26139--26245 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 36
26129 TTTATCATCT
26139 TTGAGATCATTTCCCTTAAAACGAATTTTGTCTCTC
1 TTGAGATCATTTCCCTTAAAACGAATTTTGTCTCTC
* *
26175 TTGAGA-CAGTTTCTCTTTAAAC--A-----TCATCT-
1 TTGAGATCA-TTTCCCTTAAAACGAATTTTGTC-TCTC
* *
26204 TTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTC
1 TTGAGATCATTTCCCTTAAAACGAATTTTGTCTCTC
26240 TTGAGA
1 TTGAGA
26246 CAGTCTTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
29 19 0.35
30 4 0.07
31 1 0.02
34 1 0.02
35 5 0.09
36 25 0.45
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTGAGATCATTTCCCTTAAAACGAATTTTGTCTCTC
Found at i:26455 original size:131 final size:134
Alignment explanation
Indices: 26260--26595 Score: 378
Period size: 131 Copynumber: 2.5 Consensus size: 134
26250 CTTGAAACAA
* ** * * *
26260 ATCCCTAAAGATGGCTAGCCATCCTCATCGTGTAGGAACCGTGTCA-CCCACCGACCAAATCTCC
1 ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACCGTGTCATCCC-CCAATCAGATCTCC
* * * * * * *
26324 TCCTTAGGTAAG-AGCTGCGTCATCCCTAGATAACCAGTCGTCCTCATCATGTAGGAA-C-TG-T
65 TCATCACGT-AGTAGCCGCGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATCGTGTT
*
26385 GTTATC
129 ATTATC
* *
26391 ATCCCTAAAGATGGCTAACCGTCCTCATCACATAGGAACCGTGTCATCCCCCAATCAGATCTCCT
1 ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCCAATCAGATCTCCT
*
26456 CATCACGTAGTAGCCGCGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAAGAATCGTGTTAT
66 CATCACGTAGTAGCCGCGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATCGTGTTAT
26521 TATC
131 TATC
* * * * ** **
26525 ATCCCAAAATATGGCCAGTCGTCCTCATCACGTAGGAATTGTGTCATCCACTGAAT-AGATCTCC
1 ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACCGTGTCATCC-CCCAATCAGATCTCC
26589 TCATCAC
65 TCATCAC
26596 ATATGATTCG
Statistics
Matches: 172, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
130 2 0.01
131 98 0.57
132 4 0.02
133 2 0.01
134 62 0.36
135 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (134 bp):
ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCCAATCAGATCTCCT
CATCACGTAGTAGCCGCGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATCGTGTTAT
TATC
Found at i:26613 original size:134 final size:131
Alignment explanation
Indices: 26340--26598 Score: 331
Period size: 134 Copynumber: 2.0 Consensus size: 131
26330 GGTAAGAGCT
* * * * *
26340 GCGTCATCCCTAGATAACCAGTCGTCCTCATCATGTAGGAACTGTGTTATCATCCCTAAAGATGG
1 GCGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAACTGTATTATCATCCCAAAAGATGG
* *
26405 CTAACCGTCCTCATCACATAGGAACCGTGTCATCCCCCAATCAGATCTCCTCATCACGTAGTAGC
66 CCAACCGTCCTCATCACATAGGAACCGTGTCATCCCCCAATCAGATCTCCTCATCACATAGTAGC
26470 C
131 C
* *
26471 GCGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAAGAATCGTGTTATTATCATCCCAAAATA
1 GCGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAA-C-TG-TATTATCATCCCAAAAGA
** * ** **
26536 TGGCCAGTCGTCCTCATCACGTAGGAATTGTGTCATCCACTGAAT-AGATCTCCTCATCACATA
63 TGGCCAACCGTCCTCATCACATAGGAACCGTGTCATCC-CCCAATCAGATCTCCTCATCACATA
26599 TGATTCGTGT
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
131 37 0.34
132 1 0.01
133 2 0.02
134 64 0.59
135 4 0.04
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (131 bp):
GCGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAACTGTATTATCATCCCAAAAGATGG
CCAACCGTCCTCATCACATAGGAACCGTGTCATCCCCCAATCAGATCTCCTCATCACATAGTAGC
C
Found at i:26817 original size:3 final size:3
Alignment explanation
Indices: 26809--26869 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
26799 TAAAAATATA
* *
26809 TAT TAT TAT TTT TAAT TGT TAT TAT TAT TAT TAT TACT T-T TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
26855 TAT TAAT TAT TAT TA
1 TAT T-AT TAT TAT TA
26870 CATTTTGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 41 0.82
4 7 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:26849 original size:28 final size:28
Alignment explanation
Indices: 26809--26869 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
26799 TAAAAATATA
* * *
26809 TATTATTATTTTTAATTGTTA-TTATTAT
1 TATTATTACTTTT-ATTATTATTAATTAT
26837 TATTATTACTTTTATTATTATTAATTAT
1 TATTATTACTTTTATTATTATTAATTAT
26865 TATTA
1 TATTA
26870 CATTTTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
TATTATTACTTTTATTATTATTAATTAT
Found at i:27293 original size:30 final size:30
Alignment explanation
Indices: 27259--27324 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
27249 AAAACATCAA
*
27259 ACCAAATCGTCAGCAACAGTAAACCAAATC
1 ACCAAATCATCAGCAACAGTAAACCAAATC
27289 ACCAAATCATCAGCAACAGTAAACCAAATC
1 ACCAAATCATCAGCAACAGTAAACCAAATC
27319 ACCAAA
1 ACCAAA
27325 CCCATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.50, C:0.30, G:0.08, T:0.12
Consensus pattern (30 bp):
ACCAAATCATCAGCAACAGTAAACCAAATC
Found at i:27658 original size:65 final size:65
Alignment explanation
Indices: 27554--27680 Score: 200
Period size: 65 Copynumber: 2.0 Consensus size: 65
27544 GGTACGGTGG
* *
27554 TCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAATT
1 TCTCTTGAAACATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTCTCTCTCTTGAGACAATT
* * * *
27619 TCTCTTTATACATCATCTTTGAGATTATTTCCTTTGAAACGAATTTTCTCTCTCTTGAGACA
1 TCTCTTGAAACATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTCTCTCTCTTGAGACA
27681 GTCTTAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (65 bp):
TCTCTTGAAACATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTCTCTCTCTTGAGACAATT
Found at i:27932 original size:131 final size:131
Alignment explanation
Indices: 27693--28044 Score: 384
Period size: 131 Copynumber: 2.7 Consensus size: 131
27683 CTTAAAATAA
* ** * ** *
27693 ATCCCTAAAGATGGCTAGCCATCCTCATCGTGTAGGAACCGTGTCA-CCCACCGACCAAATCTCC
1 ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACTGTGTCATCCC-CC-AATAGATCTCC
* * * *
27757 TCCTCAGGTAGGAGTCGCGTCACCCCTAGATAACCAGCCATCCTCATCATGTAGGAATTGTG-TT
64 TCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAATTGTGTTT
27821 ATC
129 ATC
* *
27824 ATCCCTAAAGATGGCTAACCGTCCTCATCACATAGGAACTGTGTCATCCCCCAATTAGATCTCCT
1 ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACTGTGTCATCCCCCAA-TAGATCTCCT
* *** *
27889 CATCACGTAGTAGTCGTGTCACCCCTAGATAACCAGTTGTCCTCATCGCGTAGGAATTGTGTTAT
65 CATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAATTGTG-T-T
27954 TATC
128 TATC
* * * ** * * * *
27958 ATCCCAAAATATGGCCAGTTGTCCTCATCACGTAAGAATTGTGTCATCCATCGAATAGATCTCCT
1 ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACTGTGTCATCC-CCCAATAGATCTCCT
*
28023 CATCACATAGGAGTCGTGTCAC
65 CATCACGTAGGAGTCGTGTCAC
28045 TCTTAGACGA
Statistics
Matches: 184, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 102 0.55
132 3 0.02
134 75 0.41
135 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (131 bp):
ATCCCTAAAGATGGCTAGCCGTCCTCATCACGTAGGAACTGTGTCATCCCCCAATAGATCTCCTC
ATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAATTGTGTTTAT
C
Found at i:28024 original size:134 final size:131
Alignment explanation
Indices: 27751--28044 Score: 356
Period size: 134 Copynumber: 2.2 Consensus size: 131
27741 CACCGACCAA
* * * *
27751 ATCTCCTCCTCAGGTAGGAGTCGCGTCACCCCTAGATAACCAGCCATCCTCATCATGTAGGAATT
1 ATCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAATT
* * *
27816 GTGTTATCATCCCTAAAGATGGCTAACCGTCCTCATCACATAGGAACTGTGTCATCCCCCAATTA
66 GTGTTATCATCCCAAAAGATGGCCAACCGTCCTCATCACATAAGAACTGTGTCATCCCCCAATTA
27881 G
131 G
* *** *
27882 ATCTCCTCATCACGTAGTAGTCGTGTCACCCCTAGATAACCAGTTGTCCTCATCGCGTAGGAATT
1 ATCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAATT
* *** * * * *
27947 GTGTTATTATCATCCCAAAATATGGCCAGTTGTCCTCATCACGTAAGAATTGTGTCATCCATCGA
66 GTG---TTATCATCCCAAAAGATGGCCAACCGTCCTCATCACATAAGAACTGTGTCATCC-CCCA
28012 A-TAG
127 ATTAG
*
28016 ATCTCCTCATCACATAGGAGTCGTGTCAC
1 ATCTCCTCATCACGTAGGAGTCGTGTCAC
28045 TCTTAGACGA
Statistics
Matches: 137, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
131 59 0.43
134 75 0.55
135 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (131 bp):
ATCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAATT
GTGTTATCATCCCAAAAGATGGCCAACCGTCCTCATCACATAAGAACTGTGTCATCCCCCAATTA
G
Found at i:28251 original size:3 final size:3
Alignment explanation
Indices: 28243--28315 Score: 76
Period size: 3 Copynumber: 23.7 Consensus size: 3
28233 TAAAAATATA
* * *
28243 TAT TAT TAT TAT TTT TAAT TAT TAT TAG TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
28289 TCCT T-T TAT TAT TAT TAAT TAT TAT TA
1 T-AT TAT TAT TAT TAT T-AT TAT TAT TA
28316 CATTTTATGT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.03
3 51 0.85
4 7 0.12
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28260 original size:25 final size:28
Alignment explanation
Indices: 28232--28283 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
28222 TGTCCGGGTC
28232 TTAA-AAATA-TA-TATTATTATTATTT
1 TTAATAAATATTAGTATTATTATTATTT
* *
28257 TTAATTATTATTAGTATTATTATTATT
1 TTAATAAATATTAGTATTATTATTATT
28284 ATTGTTCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 2 0.09
28 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAATAAATATTAGTATTATTATTATTT
Found at i:28281 original size:31 final size:30
Alignment explanation
Indices: 28243--28315 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
28233 TAAAAATATA
*
28243 TATTATTATTATTTTTAATTATTATTAGTAT
1 TATTATTATTATTGTTAATT-TTATTAGTAT
** *
28274 TATTATTATTATTGTTCCTTTTATTATTAT
1 TATTATTATTATTGTTAATTTTATTAGTAT
28304 TAATTATTATTA
1 T-ATTATTATTA
28316 CATTTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 10 0.27
31 27 0.73
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (30 bp):
TATTATTATTATTGTTAATTTTATTAGTAT
Found at i:33280 original size:22 final size:22
Alignment explanation
Indices: 33252--33311 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
33242 TAGCTAACAG
* *
33252 TCAAGCCTTACTGCTAACAAAC
1 TCAAGCCTAACTACTAACAAAC
*
33274 TCAAGCCTAATTACTAACAAAC
1 TCAAGCCTAACTACTAACAAAC
33296 TCAAGCCTAACTACTA
1 TCAAGCCTAACTACTA
33312 CTAACAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (22 bp):
TCAAGCCTAACTACTAACAAAC
Found at i:38406 original size:21 final size:21
Alignment explanation
Indices: 38382--38422 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38372 CAACGATGCA
*
38382 TGCTCCAATAATGTGTGCAAG
1 TGCTCCAATAATGCGTGCAAG
*
38403 TGCTCCGATAATGCGTGCAA
1 TGCTCCAATAATGCGTGCAA
38423 CGCCTGCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCTCCAATAATGCGTGCAAG
Found at i:41965 original size:22 final size:22
Alignment explanation
Indices: 41937--41982 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41927 AATAGGTTTG
41937 TCATGTCTTAAAATGATATTAT
1 TCATGTCTTAAAATGATATTAT
41959 TCATGTCTTAAAATGATATTAT
1 TCATGTCTTAAAATGATATTAT
41981 TC
1 TC
41983 TTACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (22 bp):
TCATGTCTTAAAATGATATTAT
Found at i:43116 original size:16 final size:16
Alignment explanation
Indices: 43095--43125 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43085 TAATATTGAA
43095 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
43111 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
43126 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:44022 original size:15 final size:16
Alignment explanation
Indices: 44002--44046 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
43992 TTATTTTATG
44002 TATAATAT-ATATTTT
1 TATAATATGATATTTT
44017 TATAATATGATATATTT
1 TATAATATGATAT-TTT
44034 T-T-ATATGATATTT
1 TATAATATGATATTT
44047 ATTAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 17 0.61
16 5 0.18
17 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TATAATATGATATTTT
Found at i:47302 original size:21 final size:21
Alignment explanation
Indices: 47278--47318 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47268 AGTAAAATAT
* *
47278 TACCTAAAATATTATTATTTC
1 TACCTAAAACATTAATATTTC
47299 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
47319 TTTTAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Done.