Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006942.1 Hibiscus syriacus cultivar Beakdansim tig00017836_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: 63627
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:30 original size:2 final size:2
Alignment explanation
Indices: 25--68 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
15 TTCTTAAATA
*
25 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67 AT
1 AT
69 TATTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:7169 original size:21 final size:21
Alignment explanation
Indices: 7145--7194 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
7135 GGCTATTTAT
7145 AGCCGAGAGAAGATGCCTTAA
1 AGCCGAGAGAAGATGCCTTAA
7166 AGCCGAGAGAAGATGCCTTAA
1 AGCCGAGAGAAGATGCCTTAA
7187 AGCCGAGA
1 AGCCGAGA
7195 AGTTTGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (21 bp):
AGCCGAGAGAAGATGCCTTAA
Found at i:8806 original size:39 final size:39
Alignment explanation
Indices: 8763--8848 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
8753 GAAGAGACAC
* * *
8763 CTCAGTTGCCAACTCCAAAAGAGTGCGTTGAGGAAAAAT
1 CTCAGTTGCCAACACCAAAAGAGTCCGTTGAAGAAAAAT
**** *
8802 CTCAGTTGGTGGCACCGAAAGAGTCCGTTGAAGAAAAAT
1 CTCAGTTGCCAACACCAAAAGAGTCCGTTGAAGAAAAAT
8841 CTCAGTTG
1 CTCAGTTG
8849 TTGACCGCAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (39 bp):
CTCAGTTGCCAACACCAAAAGAGTCCGTTGAAGAAAAAT
Found at i:12604 original size:21 final size:23
Alignment explanation
Indices: 12560--12605 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
12550 TAAATATATT
12560 ATTATACAAATTTTAATGATTTA
1 ATTATACAAATTTTAATGATTTA
*
12583 ATTA-ACAAATTTT-ATTATTTA
1 ATTATACAAATTTTAATGATTTA
12604 AT
1 AT
12606 AGTAAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 9 0.41
23 4 0.18
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTATACAAATTTTAATGATTTA
Found at i:13744 original size:16 final size:17
Alignment explanation
Indices: 13713--13756 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
13703 ATTTGAGTAG
*
13713 TTTAATTATTTTATATT
1 TTTAATTATTTAATATT
13730 TTTAA-TATTTAATA-T
1 TTTAATTATTTAATATT
*
13745 ATTAATTATTTA
1 TTTAATTATTTA
13757 TAATTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATTATTTAATATT
Found at i:16571 original size:7 final size:7
Alignment explanation
Indices: 16559--16584 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16549 TAAATCAATA
16559 AAACAGT
1 AAACAGT
16566 AAACAGT
1 AAACAGT
16573 AAACAGT
1 AAACAGT
16580 AAACA
1 AAACA
16585 TGCGAAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (7 bp):
AAACAGT
Found at i:16695 original size:95 final size:95
Alignment explanation
Indices: 16570--16748 Score: 295
Period size: 95 Copynumber: 1.9 Consensus size: 95
16560 AACAGTAAAC
* * * *
16570 AGTAAACAGTAAACATGCGAAGACAATAAACCAATATCAAAATCAGTAAACAATATAATCATCTC
1 AGTAAACAGTAAACATACCAAGACAATAAACCAATATCAAAATCAGTAAACAATAAAATCAGCTC
16635 CAATAAAATAGTAAAACAAATCAATACAAT
66 CAATAAAATAGTAAAACAAATCAATACAAT
* * *
16665 AGTAAATAGTAAACATACCAAGACAGTAAACCAATATCAAAATCAGTAAATAATAAAATCAGCTC
1 AGTAAACAGTAAACATACCAAGACAATAAACCAATATCAAAATCAGTAAACAATAAAATCAGCTC
16730 CAATAAAATAGTAAAACAA
66 CAATAAAATAGTAAAACAA
16749 TAAAATAGTA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (95 bp):
AGTAAACAGTAAACATACCAAGACAATAAACCAATATCAAAATCAGTAAACAATAAAATCAGCTC
CAATAAAATAGTAAAACAAATCAATACAAT
Found at i:16714 original size:44 final size:44
Alignment explanation
Indices: 16569--16721 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 44
16559 AAACAGTAAA
* * * *
16569 CAGTAAACAGTAAACATGCGAAGACAATAAACCAATATCAAAAT
1 CAGTAAACAATAAACATACCAAGACAGTAAACCAATATCAAAAT
* * * *
16613 CAGTAAACAATATAATCATCTCCAATAAAATAGTAAAACAA-ATCAATACAAT
1 CAGTAAACAATA-AA-CAT-ACC---AAGACAGTAAACCAATATC-A-A-AAT
* *
16665 -AGTAAATAGTAAACATACCAAGACAGTAAACCAATATCAAAAT
1 CAGTAAACAATAAACATACCAAGACAGTAAACCAATATCAAAAT
*
16708 CAGTAAATAATAAA
1 CAGTAAACAATAAA
16722 ATCAGCTCCA
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
43 3 0.04
44 24 0.29
45 15 0.18
46 6 0.07
47 1 0.01
48 2 0.02
49 6 0.07
50 14 0.17
51 10 0.12
52 3 0.04
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (44 bp):
CAGTAAACAATAAACATACCAAGACAGTAAACCAATATCAAAAT
Found at i:16751 original size:16 final size:16
Alignment explanation
Indices: 16730--16770 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
16720 AAATCAGCTC
16730 CAATAAAATAGTAAAA
1 CAATAAAATAGTAAAA
16746 CAATAAAATAGTAAAA
1 CAATAAAATAGTAAAA
16762 CAATAAAAT
1 CAATAAAAT
16771 GAATCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (16 bp):
CAATAAAATAGTAAAA
Found at i:20271 original size:31 final size:29
Alignment explanation
Indices: 20215--20273 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
20205 GAAATACTAG
*
20215 AAAACCCTAAATTTTTTGTTTTAAAAATT
1 AAAACCCTAAATTTTTTGTTATAAAAATT
20244 AAAACCCT-AATTATTTTCGTGTATAAAAAT
1 AAAACCCTAAATT-TTTT-GT-TATAAAAAT
20274 CGCAACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 12 0.46
30 2 0.08
31 8 0.31
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAACCCTAAATTTTTTGTTATAAAAATT
Found at i:21616 original size:14 final size:14
Alignment explanation
Indices: 21599--21633 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
21589 ATATAACTAT
21599 TAAATTATAATTAA
1 TAAATTATAATTAA
21613 TAAA-TATAATTAA
1 TAAATTATAATTAA
*
21626 AAAATTAT
1 TAAATTAT
21634 TTCTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATTATAATTAA
Found at i:21679 original size:21 final size:20
Alignment explanation
Indices: 21640--21679 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21630 TTATTTCTTT
*
21640 TATTAAAAACATTAAAAATA
1 TATTAAAAACAGTAAAAATA
*
21660 TATTAAAAAACAGTATAAAT
1 TATT-AAAAACAGTAAAAAT
21680 TACAGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (20 bp):
TATTAAAAACAGTAAAAATA
Found at i:23771 original size:20 final size:21
Alignment explanation
Indices: 23748--23796 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
23738 GACAAAACTT
*
23748 GTTGGAATTTGAC-AAACCCG
1 GTTGAAATTTGACTAAACCCG
23768 GTTGAAATTTGACTAAA-CCG
1 GTTGAAATTTGACTAAACCCG
*
23788 ATTGAAATT
1 GTTGAAATT
23797 GGACAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (21 bp):
GTTGAAATTTGACTAAACCCG
Found at i:23854 original size:20 final size:20
Alignment explanation
Indices: 23821--23860 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23811 CTAGCACAAT
*
23821 TAGTTTGAAATTGACAAAAC
1 TAGTTGGAAATTGACAAAAC
* *
23841 TAGTTGGAATTTGATAAAAC
1 TAGTTGGAAATTGACAAAAC
23861 CGATTTAGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (20 bp):
TAGTTGGAAATTGACAAAAC
Found at i:23896 original size:20 final size:20
Alignment explanation
Indices: 23873--23919 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
23863 ATTTAGCGCG
* *
23873 ACCGGTTGGAATTTGACAAA
1 ACCGGTTGCAATTTAACAAA
*
23893 ACCGGTTTCAATTTAACAAA
1 ACCGGTTGCAATTTAACAAA
*
23913 ACTGGTT
1 ACCGGTT
23920 AAGCGCGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
ACCGGTTGCAATTTAACAAA
Found at i:27479 original size:31 final size:30
Alignment explanation
Indices: 27414--27473 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
27404 TATGTGAATG
*
27414 AAATTATGTATGTGATTACCAAAGTTACAAC
1 AAATTATGTATGTGATTACCAAAGCTA-AAC
*
27445 AAATTATGTATGTTCGGTTACCAAAGCTA
1 AAATTATGTATG-T-GATTACCAAAGCTA
27474 GCAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 12 0.48
32 1 0.04
33 12 0.48
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (30 bp):
AAATTATGTATGTGATTACCAAAGCTAAAC
Found at i:35044 original size:18 final size:18
Alignment explanation
Indices: 35021--35091 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
35011 AGGGATTATA
* *
35021 AGTGGTCATTTTGGACAT
1 AGTGGTCCTTTGGGACAT
*
35039 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTTGGGACAT
35057 AGTGG-CCTTTCGGGACAT
1 AGTGGTCCTTT-GGGACAT
* *
35075 AGTGGCCCTTCGGGACA
1 AGTGGTCCTTTGGGACA
35092 AATTTTTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 4 0.09
18 38 0.83
19 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Found at i:39674 original size:21 final size:20
Alignment explanation
Indices: 39656--39692 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39646 ATATAAGTGA
*
39656 TATAT-ATATTTACATAAGT
1 TATATGATATTGACATAAGT
39675 TATATGATATTGACATAA
1 TATATGATATTGACATAA
39693 TGAATGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (20 bp):
TATATGATATTGACATAAGT
Found at i:40510 original size:18 final size:18
Alignment explanation
Indices: 40487--40557 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
40477 AGGGATTATA
* *
40487 AGTGGTCATTCTAGACAT
1 AGTGGTCCTTCTGGACAT
40505 AGTGGTCCTTCTGGACAT
1 AGTGGTCCTTCTGGACAT
*
40523 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCTGGACAT
*
40541 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCTGGACA
40558 AATTTTTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCTGGACAT
Found at i:46753 original size:22 final size:21
Alignment explanation
Indices: 46699--46762 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
46689 ATTCAAGGGT
46699 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTCATTCGGGACAA
*
46720 CTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTCGGGACA-A
*
46742 TTCACAGGTCATTCGGGACAA
1 TTCATAGGTCATTCGGGACAA
46763 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCATTCGGGACAA
Found at i:52935 original size:16 final size:16
Alignment explanation
Indices: 52914--52961 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
52904 TAGAATGTCA
52914 TAAGGGTACCGATACC
1 TAAGGGTACCGATACC
52930 TAAGGGTACCGATACC
1 TAAGGGTACCGATACC
52946 TAAGGGTACCGATACC
1 TAAGGGTACCGATACC
52962 CGCAGTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (16 bp):
TAAGGGTACCGATACC
Found at i:58435 original size:145 final size:143
Alignment explanation
Indices: 58136--58589 Score: 511
Period size: 145 Copynumber: 3.2 Consensus size: 143
58126 GTATTCATCT
* * * *
58136 TGCTTATTTCAAAACAAAATATGCAATATCTTCAATGTTAAAGTATCAATAATTGTTATAAAAGT
1 TGCTTATTTCGAAACAAAATATACAATATCTTCAATGTCAAAGTATCAATAATTGTTATGAAAGT
* * * * *
58201 ATCGATACATTTAGGACATTATGCTCTATCAAACAATTTTCAT-AACAAAGTATCGATACACATA
66 ATCGATACTTTTA-TACAATATGCTCTCTCAAACAATTTGCATGAA-AAAGTATCGATACACATA
* * *
58265 TATAAAGTATCAATC
129 GATCAAGTATCGATC
* * * *
58280 T-TTATAATTTCGAAACAAAATATACGATATCTTCAATGTCAAAGCATCAATACTTGTTATGAAA
1 TGCT-T-ATTTCGAAACAAAATATACAATATCTTCAATGTCAAAGTATCAATAATTGTTATGAAA
* * * * *
58344 GTACCGATACTTTTTTTTTCAGTATGCTCTCTCAAACAATTTGCATGAAAACGTATCGATACACA
64 GTATCGATAC--TTTTATACAATATGCTCTCTCAAACAATTTGCATGAAAAAGTATCGATACACA
58409 TAGATCAAGTATCGATC
127 TAGATCAAGTATCGATC
* * * * * *
58426 TGCTTATTTCGAAACAAAATATGCAATATCTTCAATGTCATAGTATCTATATTTGTCATGACAGT
1 TGCTTATTTCGAAACAAAATATACAATATCTTCAATGTCAAAGTATCAATAATTGTTATGAAAGT
* * * * *
58491 ATCGATACTTTTATCCAATATGCTATCTCAAACAATTTGCATGAAAATGTATTGACACACATAGA
66 ATCGATACTTTTATACAATATGCTCTCTCAAACAATTTGCATGAAAAAGTATCGATACACATAGA
* *
58556 TC-ATTATCGGTC
131 TCAAGTATCGATC
*
58568 TACTTATTTCGAAAC-AAATATA
1 TGCTTATTTCGAAACAAAATATA
58590 ATGTCAAATA
Statistics
Matches: 263, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
141 6 0.02
142 22 0.08
143 53 0.20
144 2 0.01
145 119 0.45
146 55 0.21
147 6 0.02
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (143 bp):
TGCTTATTTCGAAACAAAATATACAATATCTTCAATGTCAAAGTATCAATAATTGTTATGAAAGT
ATCGATACTTTTATACAATATGCTCTCTCAAACAATTTGCATGAAAAAGTATCGATACACATAGA
TCAAGTATCGATC
Found at i:58624 original size:21 final size:21
Alignment explanation
Indices: 58599--58669 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
58589 AATGTCAAAT
58599 ATACTTGTTATGACAGTACCA
1 ATACTTGTTATGACAGTACCA
** *
58620 ATACTT-TT-TTCCAGTATGCTCT
1 ATACTTGTTATGACAGTA--C-CA
*
58642 CTCACTTGTTATGACAGTACCA
1 AT-ACTTGTTATGACAGTACCA
58664 ATACTT
1 ATACTT
58670 TTTTCCAGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 11 0.31
22 4 0.11
23 5 0.14
24 2 0.06
25 6 0.17
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (21 bp):
ATACTTGTTATGACAGTACCA
Found at i:58664 original size:44 final size:44
Alignment explanation
Indices: 58601--58689 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
58591 TGTCAAATAT
58601 ACTTGTTATGACAGTACCAATACTTTTTTCCAGTATGCTCTCTC
1 ACTTGTTATGACAGTACCAATACTTTTTTCCAGTATGCTCTCTC
58645 ACTTGTTATGACAGTACCAATACTTTTTTCCAGTATGCTCTCTC
1 ACTTGTTATGACAGTACCAATACTTTTTTCCAGTATGCTCTCTC
58689 A
1 A
58690 AACAATTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (44 bp):
ACTTGTTATGACAGTACCAATACTTTTTTCCAGTATGCTCTCTC
Found at i:58902 original size:143 final size:142
Alignment explanation
Indices: 58645--59275 Score: 705
Period size: 145 Copynumber: 4.5 Consensus size: 142
58635 ATGCTCTCTC
*
58645 ACTTGTTATGACAGTACCAATACTTTTTTCCAGTATGCTCTCTCAAACAATTTGCATGAAAAC--
1 ACTTGTTATGACAGTATCAATA-TTTTTTCCAGTATGCTCTCTCAAACAATTT-CATGAAAACGT
* * *
58708 ATCGATACACATAGATCAAGTATCAATCTTGCTTATTTCGAAACAAAATATGAAATATCTTCAAT
64 ATCGATACATATAGATCAAGTATCAATCTTGCTTATTTCGAAACAAAATATGCAATATATTCAAT
58773 ATCAAAGTATTGAT
129 ATCAAAGTATTGAT
* *
58787 ACTTGTTATGACATTATCAATATTTTTTCCAGTATGCTCTCTTAAACAATTTCCATGAAAACGTA
1 ACTTGTTATGACAGTATCAATATTTTTTCCAGTATGCTCTCTCAAACAATTT-CATGAAAACGTA
* * * * * * * *
58852 TCGATACAAATAGATCAAGAATCGATCTTGCTTATTTTGAAACAAAATATGCAATATCTTTATTG
65 TCGATACATATAGATCAAGTATCAATCTTGCTTATTTCGAAACAAAATATGCAATATATTCAATA
58917 TCAAAGTATTGAT
130 TCAAAGTATTGAT
*
58930 ACTTG-TATTGACAGTATCAAAATGTTTTTTCCAGTATGCTCTCTCAAACAATTTGCATGAAAAC
1 ACTTGTTA-TGACAGTATC--AATATTTTTTCCAGTATGCTCTCTCAAACAATTT-CATGAAAAC
* * * * * ** * * *
58994 GTATTGATACTTATATATAAAGTATCGATCTTTATAATTTTGACACAAAATATGCAATATATTCA
62 GTATCGATACATATAGATCAAGTATCAATCTTGCTTATTTCGAAACAAAATATGCAATATATTCA
*
59059 ATGTCAAAGTATTGAT
127 ATATCAAAGTATTGAT
* ** ** *
59075 ACTTGTTTTGACAGTATTGATACTTTTTTATAGTATGCTCTCTCAAACAA-TT--TGAAAACATA
1 ACTTGTTATGACAGTATCAATA-TTTTTTCCAGTATGCTCTCTCAAACAATTTCATGAAAACGTA
* * *
59137 TCGAT--ATATAGATCAAGTATCAATATTGCATA-TTCGAAACAAAATATCCAATATATTCAATG
65 TCGATACATATAGATCAAGTATCAATCTTGCTTATTTCGAAACAAAATATGCAATATATTCAAT-
* *
59199 A--ATATGTATCGAT
129 ATCA-AAGTATTGAT
* * *
59212 ACTTTTTATGATAGTATCAATACTTTTT--AGTATGCTCTCTCAAACAATTGTCATGAAAA-GTA
1 ACTTGTTATGACAGTATCAATATTTTTTCCAGTATGCTCTCTCAAACAATT-TCATGAAAACGTA
59274 TC
65 TC
59276 AATCTGAATA
Statistics
Matches: 417, Mismatches: 59, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
134 19 0.05
135 1 0.00
136 7 0.02
137 55 0.13
138 24 0.06
140 13 0.03
141 38 0.09
142 22 0.05
143 89 0.21
144 25 0.06
145 123 0.29
146 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (142 bp):
ACTTGTTATGACAGTATCAATATTTTTTCCAGTATGCTCTCTCAAACAATTTCATGAAAACGTAT
CGATACATATAGATCAAGTATCAATCTTGCTTATTTCGAAACAAAATATGCAATATATTCAATAT
CAAAGTATTGAT
Found at i:59524 original size:21 final size:21
Alignment explanation
Indices: 59490--59542 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
59480 CAATGTATAT
59490 GTATCAATA-TTGTTATGACA
1 GTATCAATACTTGTTATGACA
*
59510 GTATCTATACTTGTTATGACA
1 GTATCAATACTTGTTATGACA
* *
59531 TTATCGATACTT
1 GTATCAATACTT
59543 TTTCGATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (21 bp):
GTATCAATACTTGTTATGACA
Found at i:60746 original size:43 final size:43
Alignment explanation
Indices: 60685--60807 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 43
60675 TTTTAACTGA
* *
60685 TTAGGTTATCAATATTTTACCGTTTACATTATTATTATACCGG
1 TTAGGTTATAAATATTTTATCGTTTACATTATTATTATACCGG
* *
60728 TTAGGTTATAAATATTTTATCATTTAAATTATTA-T-TACCGG
1 TTAGGTTATAAATATTTTATCGTTTACATTATTATTATACCGG
* * *
60769 TTATGTTGTAAATATTCTATCGTTTACATTA-TATTATAC
1 TTAGGTTATAAATATTTTATCGTTTACATTATTATTATAC
60808 TGGGTAACTT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.03
41 33 0.48
42 4 0.06
43 30 0.43
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.49
Consensus pattern (43 bp):
TTAGGTTATAAATATTTTATCGTTTACATTATTATTATACCGG
Found at i:60955 original size:101 final size:98
Alignment explanation
Indices: 60839--61087 Score: 313
Period size: 101 Copynumber: 2.5 Consensus size: 98
60829 GTTGTGCATG
* * * * *
60839 TTTTTTTAACTGGTTAAGTTGTAATTATTTTACCGTTTACACTATTATTAAACCTA-CAACAAAC
1 TTTTTTTAACCGGTTAGGTTGTAA-TATTTTACTGTTTACATTATTATTAAACCTATAAACAAAC
*
60903 TGGTAGCAAGTTTAAAGTAATAGGTTGAGCCTATTAC
65 TGGTAGCAAGTTT-AAGTAATAGGTTGAGCCTA--AA
*
60940 TTTTTTTAACCGGTTAGGTTGTACATATTTTACTGTTTACATTATTTTTAAACCTATAAACAAAC
1 TTTTTTTAACCGGTTAGGTTGTA-ATATTTTACTGTTTACATTATTATTAAACCTATAAACAAAC
* *
61005 TGGTAGTAAGTTTAAGTAATAGGTTGTGCCTAAA
65 TGGTAGCAAGTTTAAGTAATAGGTTGAGCCTAAA
* *
61039 TTGTTTTAACTC-GTTAGGTTGTAAATATTTTTAATGTTTACATTATTAT
1 TTTTTTTAAC-CGGTTAGGTTGT-AATA-TTTTACTGTTTACATTATTAT
61088 ATTTGTACCA
Statistics
Matches: 131, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
99 23 0.18
100 21 0.16
101 67 0.51
102 20 0.15
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (98 bp):
TTTTTTTAACCGGTTAGGTTGTAATATTTTACTGTTTACATTATTATTAAACCTATAAACAAACT
GGTAGCAAGTTTAAGTAATAGGTTGAGCCTAAA
Found at i:61678 original size:23 final size:25
Alignment explanation
Indices: 61650--61700 Score: 88
Period size: 23 Copynumber: 2.1 Consensus size: 25
61640 TTGCAGGTAA
61650 AGTTAAACAGA-TTTTTCGT-AATT
1 AGTTAAACAGATTTTTTCGTAAATT
61673 AGTTAAACAGATTTTTTCGTAAATT
1 AGTTAAACAGATTTTTTCGTAAATT
61698 AGT
1 AGT
61701 GTTTTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 11 0.42
24 8 0.31
25 7 0.27
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (25 bp):
AGTTAAACAGATTTTTTCGTAAATT
Found at i:62408 original size:6 final size:6
Alignment explanation
Indices: 62394--62434 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
62384 CCAATACTTA
* *
62394 AATTTC AATTCC AATTTC AATTTC AATTTC AATTTT AATTT
1 AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC AATTT
62435 GATCGTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTC
Found at i:62570 original size:31 final size:32
Alignment explanation
Indices: 62535--62611 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
62525 TGATATGGAG
62535 TAATCAACCAACAA-CATC-GAAAAATCTCGAC
1 TAATCAACCAACAACCATCGGAAAAA-CTCGAC
* *
62566 TAATCAATCAACAACTCATCGGAAAAACTCGAG
1 TAATCAACCAACAAC-CATCGGAAAAACTCGAC
*
62599 TAATCAACTAACA
1 TAATCAACCAACA
62612 GTATTCATCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 13 0.33
33 20 0.51
34 6 0.15
ACGTcount: A:0.48, C:0.26, G:0.08, T:0.18
Consensus pattern (32 bp):
TAATCAACCAACAACCATCGGAAAAACTCGAC
Done.