Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001696.1 Hibiscus syriacus cultivar Beakdansim tig00003386_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: 43560
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3004 original size:2 final size:2
Alignment explanation
Indices: 2997--3025 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2987 CGAAATTTTG
2997 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3026 GAAGGTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9487 original size:2 final size:2
Alignment explanation
Indices: 9480--9516 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9470 AACCCGTTAG
9480 AT AT 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 AT AT A
9517 ACACGATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11032 original size:19 final size:20
Alignment explanation
Indices: 10999--11047 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
10989 AGGATTTATC
10999 TTATTTTTTATTTTTAGGA-A
1 TTATTTTTTATTTTT-GGATA
*
11019 TTATTTTTTA-TTTTGTATA
1 TTATTTTTTATTTTTGGATA
11038 TTATTTTTTA
1 TTATTTTTTA
11048 GGGTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.07
19 15 0.56
20 10 0.37
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (20 bp):
TTATTTTTTATTTTTGGATA
Found at i:13152 original size:24 final size:24
Alignment explanation
Indices: 13107--13152 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
13097 CTCGCTTGGT
**
13107 TAGATCGATTTGGGTCGGTTTGAC
1 TAGATCGATTTGGGTCAATTTGAC
13131 TAGATCGATTT-GGTCCAATTTG
1 TAGATCGATTTGGGT-CAATTTG
13153 GTTGGGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (24 bp):
TAGATCGATTTGGGTCAATTTGAC
Found at i:13982 original size:35 final size:36
Alignment explanation
Indices: 13934--14036 Score: 156
Period size: 37 Copynumber: 2.9 Consensus size: 36
13924 TTTCGTCATA
*
13934 CTAGGATTGAAACTCCTAAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCT-AAAAATAGGATAGAATTTT
*
13970 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
14005 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
14037 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 14 0.23
35 18 0.30
37 29 0.48
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:14060 original size:37 final size:37
Alignment explanation
Indices: 13932--14070 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 37
13922 TTTTTCGTCA
* *
13932 TACTAGGATTGAAACTCCTAAAAAATAGGATAGAATT-
1 TACTAGGATTCAAACTCCT-AAAAATAGGATAAAATTC
*
13969 T--TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
14004 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
14041 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
14071 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 16 0.18
35 16 0.18
37 56 0.64
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:14965 original size:2 final size:2
Alignment explanation
Indices: 14958--14983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14948 TAATACTTTG
14958 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
14984 TTCTTTTTCC
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:16173 original size:5 final size:5
Alignment explanation
Indices: 16163--16190 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16153 TCTTTTCATC
16163 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16191 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:18778 original size:16 final size:16
Alignment explanation
Indices: 18752--18806 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
18742 AGATCCAATC
18752 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
18767 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
*
18784 AA-AA-AAAAAAACAA
1 AAGAACAAAAAAGCAA
*
18798 AAAAACAAA
1 AAGAACAAA
18807 GAAAAAGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 11 0.31
15 7 0.20
16 13 0.37
17 4 0.11
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:18783 original size:8 final size:8
Alignment explanation
Indices: 18757--18806 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
18747 CAATCAAGAA
18757 CAAAAAAG
1 CAAAAAAG
18765 -AAAAGAAG
1 CAAAA-AAG
18773 CAAAAAAG
1 CAAAAAAG
18781 CAAAAAA-
1 CAAAAAAG
*
18788 -AAAAAAA
1 CAAAAAAG
*
18795 CAAAAAAA
1 CAAAAAAG
18803 CAAA
1 CAAA
18807 GAAAAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.16
7 4 0.11
8 24 0.63
9 4 0.11
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (8 bp):
CAAAAAAG
Found at i:18785 original size:22 final size:22
Alignment explanation
Indices: 18760--18812 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
18750 TCAAGAACAA
* * *
18760 AAAAGAAAAGAAGCAAAAAAGC
1 AAAAGAAAAAAAACAAAAAAAC
*
18782 AAAAAAAAAAAAACAAAAAAAC
1 AAAAGAAAAAAAACAAAAAAAC
18804 -AAAGAAAAA
1 AAAAGAAAAA
18813 GAGAAACAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.83, C:0.08, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAACAAAAAAAC
Found at i:19501 original size:22 final size:22
Alignment explanation
Indices: 19474--19522 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
19464 CCATTAATCT
* *
19474 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
19496 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
19518 TTTGA
1 TTTGA
19523 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:19954 original size:18 final size:18
Alignment explanation
Indices: 19931--19966 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19921 TCAACATCAA
* *
19931 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
19949 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
19967 GGATTCATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:20486 original size:36 final size:36
Alignment explanation
Indices: 20443--20724 Score: 285
Period size: 36 Copynumber: 8.0 Consensus size: 36
20433 CACTATAGAG
20443 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
**
20479 TTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
20515 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
20551 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
20587 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
*** * * ** * *
20616 TACCGTCTCCCTTGAGACCGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
20653 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
20688 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
20725 ATCTTTGAAT
Statistics
Matches: 200, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 140 0.70
37 31 0.16
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:20716 original size:138 final size:137
Alignment explanation
Indices: 20469--20787 Score: 372
Period size: 138 Copynumber: 2.3 Consensus size: 137
20459 ACAGTTTCCC
*** *
20469 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTCGTCTATCTTGAGACA
1 TTGAAACAAATACCGTCTCCCTTGAGACAGTTTATCTTGAAACAAATTTCGTCTATCTTGAGACA
*
20534 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
66 GTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
20599 GTTTTCT
131 GTTTTCT
* * * * * * *
20606 TTGAAACAAATACCGTCTCCCTTGAGACCGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATACCGTCTCCCTTGAGACAGTTTATCTTGAAAC-AAATTTCGTCTATCTTGAGAC
* * *
20671 AGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
65 AGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAAT
* * * *
20735 TTATTTCCC
129 ATGTTTTCT
* * ****
20744 CTAAAACAAATTTTATCTCCCTTGAGACAG-TTACTCTTGAAACA
1 TTGAAACAAATACCGTCTCCCTTGAGACAGTTTA-TCTTGAAACA
20788 CAAATCTTCA
Statistics
Matches: 150, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
137 44 0.29
138 106 0.71
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
TTGAAACAAATACCGTCTCCCTTGAGACAGTTTATCTTGAAACAAATTTCGTCTATCTTGAGACA
GTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
GTTTTCT
Found at i:20806 original size:66 final size:66
Alignment explanation
Indices: 20699--20855 Score: 217
Period size: 67 Copynumber: 2.4 Consensus size: 66
20689 TTTCGTCTAT
* **
20699 CTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAACA-AATTTTATCTC
1 CTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTAAAACATAATTTTATCTC
20763 C
66 C
* * * *
20764 CTTGAGACAGTTACTCTTGAAACACAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTTT
1 CTTGAGACAGTTTCTCTTGAAACA-AAATCTTCAAATTTATTTCCCCTAAAACATAATTTTATCT
20829 CC
65 CC
* *
20831 CTTGAGACCGTTTCTCATGAAACAA
1 CTTGAGACAGTTTCTCTTGAAACAA
20856 CAAGTATCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 22 0.28
66 27 0.34
67 31 0.39
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.36
Consensus pattern (66 bp):
CTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTAAAACATAATTTTATCTC
C
Found at i:21679 original size:105 final size:105
Alignment explanation
Indices: 21497--22433 Score: 1470
Period size: 105 Copynumber: 9.0 Consensus size: 105
21487 GCACTCGAGG
* * * *
21497 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
21562 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
21603 CAACGCAAGTTCAACTTCACGATGAAGGGACCCCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
21668 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
21708 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
21773 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
21813 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
21878 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
21918 CAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21983 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
22023 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTACTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
22088 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
22128 CAATGCAAGTTCAACTTCACGAGGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
22193 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
22233 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
22293 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * * ** *
22333 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAAAAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-AACAACAACTTCTCAATTTCAG
* *
22398 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
22434 TGGAACAATG
Statistics
Matches: 778, Mismatches: 47, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
100 79 0.10
101 5 0.01
102 3 0.00
103 4 0.01
104 3 0.00
105 610 0.78
106 74 0.10
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:22844 original size:37 final size:37
Alignment explanation
Indices: 22757--22854 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
22747 GCCACGTGCA
***
22757 GATTCAAATTCCTAAAAATAGGATAAAATTTTGCTAG
1 GATTCAAATTCCTAAAAATAGGATAAAATTCAACTAG
* * * *
22794 GATTCAAACTCCTAAAAATAGGATAGAGTTCAACTAT
1 GATTCAAATTCCTAAAAATAGGATAAAATTCAACTAG
* * *
22831 TATTTAAATTCCTAAAGATAGGAT
1 GATTCAAATTCCTAAAAATAGGAT
22855 CCACAAGCAC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (37 bp):
GATTCAAATTCCTAAAAATAGGATAAAATTCAACTAG
Found at i:23236 original size:17 final size:18
Alignment explanation
Indices: 23210--23252 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
23200 ATTATATGGA
*
23210 TATT-TTATTCAT-TTTT
1 TATTATTATTCATGTTAT
*
23226 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
23244 TATTATTAT
1 TATTATTAT
23253 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:23763 original size:2 final size:2
Alignment explanation
Indices: 23756--23842 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
23746 TAATACTTTG
23756 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
23798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23839 AT AT
1 AT AT
23843 TTCTTTTTCT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 83 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:24832 original size:3 final size:3
Alignment explanation
Indices: 24824--24880 Score: 71
Period size: 3 Copynumber: 18.3 Consensus size: 3
24814 TTTTACTTAA
*
24824 ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT -TAT ATT ATTT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A-TT AT-T ATT
24871 ATT ATT ATT A
1 ATT ATT ATT A
24881 AGTAATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 1 0.02
3 40 0.83
4 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:26466 original size:19 final size:18
Alignment explanation
Indices: 26438--26523 Score: 99
Period size: 18 Copynumber: 4.8 Consensus size: 18
26428 AAATTATTAC
26438 ATTTTTAATATTTATTTT
1 ATTTTTAATATTTATTTT
26456 ATTTATTAATATTTATTTT
1 ATTT-TTAATATTTATTTT
**
26475 A-TTTTAA-ATTATAAATT
1 ATTTTTAATATT-TATTTT
26492 A-TTTT-ATAATTTATTTT
1 ATTTTTAAT-ATTTATTTT
26509 ATTTTTAATATTTAT
1 ATTTTTAATATTTAT
26524 CTTAAAGCAC
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
16 4 0.07
17 18 0.31
18 19 0.33
19 17 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTAATATTTATTTT
Found at i:29343 original size:21 final size:22
Alignment explanation
Indices: 29298--29352 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
29288 CATACATGCA
*
29298 TTTACATTTTGTATCTGTGCAT
1 TTTACATTTTGTATCTGTACAT
*
29320 TTT-CATTTTGTATTCT-TACTT
1 TTTACATTTTGTA-TCTGTACAT
29341 TTTACATCTTTG
1 TTTACAT-TTTG
29353 CATTACACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 15 0.54
22 9 0.32
23 4 0.14
ACGTcount: A:0.16, C:0.15, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTACATTTTGTATCTGTACAT
Found at i:33593 original size:113 final size:112
Alignment explanation
Indices: 33439--33777 Score: 516
Period size: 114 Copynumber: 3.0 Consensus size: 112
33429 AAGTGCCATG
33439 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAG--GACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
**
33504 TGGTTTAATATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
64 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
* * *
33553 TTCTCATAGTAGAAATAAGGATCCCAATAGTATCTTCTGGAAATATTCTTTGAGTTATCTGATCT
1 TGCTCATAGTAGAAATAAGGA-CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCT
*
33618 GGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
65 GGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
* * * *
33666 TGCTTATAGTAGAAATAAAGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAAT-AAG-GACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
* * *
33731 TGGTTTGGTATGAACCCCAGAACCAATCATTGTAATTGAAAGATGAA
64 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
33778 CTGCTGATCG
Statistics
Matches: 205, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
112 2 0.01
113 100 0.49
114 102 0.50
115 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (112 bp):
TGCTCATAGTAGAAATAAGGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
Found at i:35991 original size:49 final size:50
Alignment explanation
Indices: 35894--35994 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 50
35884 GCTTTAACGA
*** *
35894 ACATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTTT
1 ACATCTGAGCAGAAACCACAGAAAAGGATGAATGCACTATCAAATGTTTT
*
35944 ACATCTCGA-CAGAAA-CACAGGAAAA-GATGAATGCACTGTCAAATGTTTT
1 ACATCT-GAGCAGAAACCACA-GAAAAGGATGAATGCACTATCAAATGTTTT
35993 AC
1 AC
35995 GAACCTGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
49 25 0.57
50 17 0.39
51 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (50 bp):
ACATCTGAGCAGAAACCACAGAAAAGGATGAATGCACTATCAAATGTTTT
Found at i:37555 original size:75 final size:76
Alignment explanation
Indices: 37220--37674 Score: 801
Period size: 76 Copynumber: 6.0 Consensus size: 76
37210 CTATTTCCCA
* *
37220 CATCTGTAAGTCCTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37285 AGCCTTAGGGT
66 AGCCTTAGGGT
*
37296 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGGTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37361 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
37372 CATCTGTAAGTCTTGTAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37436 AGCCTTA-GGT
66 AGCCTTAGGGT
*
37446 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37510 AGCCTTAGGGT
66 AGCCTTAGGGT
*
37521 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37585 AGCCTTAGGGT
66 AGCCTTAGGGT
37596 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
37661 ACCCTCAGGGT
66 AGCCTTAGGGT
37672 CAT
1 CAT
37675 TCATAGACCT
Statistics
Matches: 362, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
73 9 0.02
74 61 0.17
75 134 0.37
76 158 0.44
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:37838 original size:3 final size:3
Alignment explanation
Indices: 37830--37875 Score: 65
Period size: 3 Copynumber: 14.3 Consensus size: 3
37820 TTTTACTTAA
37830 ATT ATT ATT ATT ATAT ATT ATT ATT ATTT ATAT ATT ATT ATT ATT A
1 ATT ATT ATT ATT AT-T ATT ATT ATT A-TT AT-T ATT ATT ATT ATT A
37876 AGTAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 31 0.77
4 9 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:37862 original size:17 final size:17
Alignment explanation
Indices: 37830--37874 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
37820 TTTTACTTAA
37830 ATTATTATTA-TTATAT
1 ATTATTATTATTTATAT
37846 ATTATTATTATTTATAT
1 ATTATTATTATTTATAT
37863 ATTATTATTATT
1 ATTATTATTATT
37875 AAGTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATTATTATTTATAT
Done.