Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006140.1 Hibiscus syriacus cultivar Beakdansim tig00014570_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: 56960
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9092 original size:31 final size:31
Alignment explanation
Indices: 9019--9092 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
9009 TAAAACTTAT
* * *
9019 AATATAGTCCCCTAACATTTAGTCTGTTTAC
1 AATATAGTCCCCCAACATTTAGTCTATTCAC
9050 AATAT-GATCCCCCAACATTTAGTCTATTCAC
1 AATATAG-TCCCCCAACATTTAGTCTATTCAC
9081 AATATAGTCCCC
1 AATATAGTCCCC
9093 AACCGTTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (31 bp):
AATATAGTCCCCCAACATTTAGTCTATTCAC
Found at i:14970 original size:46 final size:46
Alignment explanation
Indices: 14905--14998 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
14895 TTCAGAAGGA
* * * *
14905 ATTCGAGGCACTCATCGGATGTTCTTCTTCATCATGGTAGTAATCC
1 ATTCGAGACACTCACCGGATCTTCTTCTTCATCACGGTAGTAATCC
* *
14951 ATTCGAGACATTCACCGGATCTTCTTCTTCATCCCGGTAGTAATCC
1 ATTCGAGACACTCACCGGATCTTCTTCTTCATCACGGTAGTAATCC
14997 AT
1 AT
14999 GTGGGAACCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (46 bp):
ATTCGAGACACTCACCGGATCTTCTTCTTCATCACGGTAGTAATCC
Found at i:15536 original size:18 final size:18
Alignment explanation
Indices: 15480--15523 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
15470 TGATGTATGC
15480 GTTAATTCGATTTTTTTT
1 GTTAATTCGATTTTTTTT
15498 GTTAATTCGATTTTTTTT
1 GTTAATTCGATTTTTTTT
15516 GTTAATTC
1 GTTAATTC
15524 AAATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (18 bp):
GTTAATTCGATTTTTTTT
Found at i:16511 original size:16 final size:16
Alignment explanation
Indices: 16490--16520 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16480 CATATAAACA
16490 AACATGTTCACGAACG
1 AACATGTTCACGAACG
*
16506 AACATGTTCATGAAC
1 AACATGTTCACGAAC
16521 ATATAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (16 bp):
AACATGTTCACGAACG
Found at i:16567 original size:23 final size:23
Alignment explanation
Indices: 16505--16579 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
16495 GTTCACGAAC
*
16505 GAACATGTTCATGAACATATAAAT
1 GAACATGTTCGTGAACAT-TAAAT
* * * *
16529 GAGCACGTTTGCGAACATTAAAT
1 GAACATGTTCGTGAACATTAAAT
*
16552 GAACATGTTCGTGAACAATAAAT
1 GAACATGTTCGTGAACATTAAAT
*
16575 AAACA
1 GAACA
16580 AATATGAACA
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 27 0.68
24 13 0.32
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (23 bp):
GAACATGTTCGTGAACATTAAAT
Found at i:17539 original size:2 final size:2
Alignment explanation
Indices: 17534--17584 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17524 TTTTTTTTTG
17534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17576 TA TA TA TA T
1 TA TA TA TA T
17585 GAACTCCTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17645 original size:35 final size:35
Alignment explanation
Indices: 17599--17668 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
17589 TCCTAGAAAT
17599 AATAAGGAAGCTTTATCTGGGATCGAAAATAAGGG
1 AATAAGGAAGCTTTATCTGGGATCGAAAATAAGGG
17634 AATAAGGAAGCTTTATCTGGGATCGAAAATAAGGG
1 AATAAGGAAGCTTTATCTGGGATCGAAAATAAGGG
17669 GTATTTGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.23
Consensus pattern (35 bp):
AATAAGGAAGCTTTATCTGGGATCGAAAATAAGGG
Found at i:23894 original size:21 final size:20
Alignment explanation
Indices: 23870--23909 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
23860 TCTGGGCAAG
*
23870 AGTATCAATATTGGGATGAAT
1 AGTATCAATACT-GGATGAAT
*
23891 AGTATCGATACTGGATGAA
1 AGTATCAATACTGGATGAA
23910 ATGGGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (20 bp):
AGTATCAATACTGGATGAAT
Found at i:23983 original size:20 final size:19
Alignment explanation
Indices: 23941--24012 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
23931 TCAAGCCAAT
23941 AGTATCGATACTTTTCAAG
1 AGTATCGATACTTTTCAAG
23960 AGTATCGATACTTTACTC-AG
1 AGTATCGATACTTT--TCAAG
23980 AGTATCGATAC-TTTCAAAG
1 AGTATCGATACTTTTC-AAG
* *
23999 AGGATCGGTACTTT
1 AGTATCGATACTTT
24013 CCGTAACAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
17 2 0.04
19 27 0.59
20 15 0.33
21 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (19 bp):
AGTATCGATACTTTTCAAG
Found at i:25120 original size:32 final size:32
Alignment explanation
Indices: 25078--25180 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
25068 CTAGTGATGC
*
25078 ATTCAAATAATACATACCAGAGTTACTCTTGT
1 ATTCAGATAATACATACCAGAGTTACTCTTGT
* * * **
25110 ATTCAGATAATGCAAACCAGAGTTAATCTTAC
1 ATTCAGATAATACATACCAGAGTTACTCTTGT
*
25142 ATTCAGATAATACATACCAGAGTTACTCATGT
1 ATTCAGATAATACATACCAGAGTTACTCTTGT
25174 ATTCAGA
1 ATTCAGA
25181 CAATGCACAG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (32 bp):
ATTCAGATAATACATACCAGAGTTACTCTTGT
Found at i:25208 original size:64 final size:63
Alignment explanation
Indices: 25077--25216 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 63
25067 ACTAGTGATG
* * * *
25077 CATTCAAATAATACATACCAGAGTTACTCTTGTATTCAGATAATGCAAACCAGAGTTAATCTTA
1 CATTCAAATAATACATACCAGAGTTACTCATGTATTCAGACAATGC-AACCAGAGTTAATATCA
*
25141 CATTCAGATAATACATACCAGAGTTACTCATGTATTCAGACAATGC-A-CAGTAGTTTCAATATC
1 CATTCAAATAATACATACCAGAGTTACTCATGTATTCAGACAATGCAACCAG-AG-TT-AATATC
25204 A
63 A
*
25205 CATTCAACTAAT
1 CATTCAAATAAT
25217 GCACAACAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
61 3 0.05
62 3 0.05
63 2 0.03
64 58 0.88
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (63 bp):
CATTCAAATAATACATACCAGAGTTACTCATGTATTCAGACAATGCAACCAGAGTTAATATCA
Found at i:26827 original size:27 final size:27
Alignment explanation
Indices: 26797--26904 Score: 71
Period size: 31 Copynumber: 3.9 Consensus size: 27
26787 AAATAAATAC
*
26797 AATAGATAATAAAGATAAATAAAAGTT
1 AATAGATAATAAAGATAAATAAAAATT
* * *
26824 AATA-A-AA-AAGGAAAAATAATAAAAT
1 AATAGATAATAAAGATAAATAA-AAATT
* *
26849 AATAAAGCAATAAA-ATAAAATTAAAAAAATAT
1 AATAGA-TAATAAAGAT-AAA-T--AAAAAT-T
26881 AATAGATAATAAAGATAAATAAAA
1 AATAGATAATAAAGATAAATAAAA
26905 GTTAGTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 21
0.67 0.10 0.23
Matches are distributed among these distances:
24 10 0.16
25 9 0.15
26 2 0.03
27 4 0.07
28 7 0.11
29 5 0.08
30 2 0.03
31 12 0.20
32 10 0.16
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.21
Consensus pattern (27 bp):
AATAGATAATAAAGATAAATAAAAATT
Found at i:26839 original size:75 final size:81
Alignment explanation
Indices: 26777--26960 Score: 255
Period size: 84 Copynumber: 2.2 Consensus size: 81
26767 TTTATATAAT
26777 AATAACAACAAAA-T-AAATACAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGGAAAAA
1 AATAA-AACAAAATTAAAATACAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGGAAAAA
26840 TAATAAAATAATAAAGC
65 TAATAAAATAATAAAGC
* * *
26857 AATAAAATAAAATTAAAAAAATATAATAGATAATAAAGATAAATAAAAGTTAGTAAAAAAGGAAA
1 AATAAAACAAAATT---AAAATACAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGG--A
*
26922 AAAATAATAACATAATAAAGC
61 AAAATAATAAAATAATAAAGC
*
26943 AATAAAATAAAATTAAAA
1 AATAAAACAAAATTAAAA
26961 AAACATAAAT
Statistics
Matches: 93, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
79 6 0.06
80 6 0.06
83 4 0.04
84 42 0.45
86 35 0.38
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (81 bp):
AATAAAACAAAATTAAAATACAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGGAAAAAT
AATAAAATAATAAAGC
Found at i:26890 original size:84 final size:85
Alignment explanation
Indices: 26786--26968 Score: 305
Period size: 86 Copynumber: 2.1 Consensus size: 85
26776 TAATAACAAC
*
26786 AAAATAAATACAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGG-AAAAATAATAAAATA
1 AAAA-AAATATAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGGAAAAAATAATAAAATA
26850 ATAAAGCAATAAAATAAAATT
65 ATAAAGCAATAAAATAAAATT
* *
26871 AAAAAAATATAATAGATAATAAAGATAAATAAAAGTTAGTAAAAAAGGAAAAAAATAATAACATA
1 AAAAAAATATAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGG-AAAAAATAATAAAATA
26936 ATAAAGCAATAAAATAAAATT
65 ATAAAGCAATAAAATAAAATT
*
26957 AAAAAAACATAA
1 AAAAAAATATAA
26969 ATGCAAGTGG
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
84 42 0.46
85 4 0.04
86 46 0.50
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (85 bp):
AAAAAAATATAATAGATAATAAAGATAAATAAAAGTTAATAAAAAAGGAAAAAATAATAAAATAA
TAAAGCAATAAAATAAAATT
Found at i:26900 original size:22 final size:21
Alignment explanation
Indices: 26775--26901 Score: 72
Period size: 22 Copynumber: 6.0 Consensus size: 21
26765 TATTTATATA
* *
26775 ATAATAACAACAAA-ATAAAT
1 ATAATAATAATAAAGATAAAT
*
26795 ACAATAGATAATAAAGATAAAT
1 ATAATA-ATAATAAAGATAAAT
* * *
26817 AAAAGTTAATAAAAAAGGAAAAAT
1 ATAA--TAATAATAAA-GATAAAT
26841 AATAA-AATAATAAAGCAATAAA-
1 -ATAATAATAATAAAG--ATAAAT
26863 ATAA-AAT--TAAA-A-AAAT
1 ATAATAATAATAAAGATAAAT
26879 ATAATAGATAATAAAGATAAAT
1 ATAATA-ATAATAAAGATAAAT
26901 A
1 A
26902 AAAGTTAGTA
Statistics
Matches: 83, Mismatches: 9, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
15 3 0.04
16 5 0.06
17 1 0.01
18 2 0.02
19 4 0.05
20 9 0.11
21 15 0.18
22 22 0.27
23 11 0.13
24 8 0.10
25 3 0.04
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.21
Consensus pattern (21 bp):
ATAATAATAATAAAGATAAAT
Found at i:26962 original size:47 final size:46
Alignment explanation
Indices: 26872--26963 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 46
26862 AATAAAATTA
*
26872 AAAAAATATAATAGATAATAAAGATAAATAAAAGTTAGTAAAAAAGG
1 AAAAAATATAATACATAATAAAGATAAATAAAAGTTAG-AAAAAAGG
26919 AAAAAA-ATAATAACATAATAAAGCAATAAAATAAAA-TTA-AAAAAA
1 AAAAAATATAAT-ACATAATAAAG--AT-AAATAAAAGTTAGAAAAAA
26964 CATAAATGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
46 5 0.12
47 22 0.55
49 5 0.12
50 8 0.20
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (46 bp):
AAAAAATATAATACATAATAAAGATAAATAAAAGTTAGAAAAAAGG
Found at i:29357 original size:16 final size:15
Alignment explanation
Indices: 29333--29362 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29323 AATATAAAAA
29333 AAATAAACAATAAAC
1 AAATAAACAATAAAC
29348 AAATAGAACAATAAA
1 AAATA-AACAATAAA
29363 TCGTGTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.10, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATAAACAATAAAC
Found at i:31688 original size:23 final size:23
Alignment explanation
Indices: 31632--31688 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
31622 CAGAGAGAAT
* *
31632 CGATACCCCCCTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
31655 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
31678 CGATTCCCCCT
1 CGATTCCCCCT
31689 AGGGGAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGGAAC
Found at i:31711 original size:18 final size:19
Alignment explanation
Indices: 31647--31706 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 19
31637 CCCCCCTTGA
*
31647 AGGGGAACCGATTCCCCCTTT
1 AGGGGAACCGATACCCCC--T
*
31668 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATACCCCCT
*
31689 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
31707 CGGGGTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.46
21 1 0.03
23 18 0.51
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:39538 original size:21 final size:23
Alignment explanation
Indices: 39514--39555 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
39504 TGAAGTGCCA
39514 CATAGA-AA-TGTCCCGAAGGAC
1 CATAGAGAATTGTCCCGAAGGAC
*
39535 CATAGAGAATTGTCTCGAAGG
1 CATAGAGAATTGTCCCGAAGG
39556 GTCGCGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (23 bp):
CATAGAGAATTGTCCCGAAGGAC
Found at i:43030 original size:31 final size:31
Alignment explanation
Indices: 42966--43039 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
42956 ATGACGGTGG
* * *
42966 AGTAACCATTTTGTTACAAACCGATAACATT
1 AGTAACCATTTTGCTACAAACCAAGAACATT
* **
42997 AGTAACCATTTTGCTACAAATCAAGAATGTT
1 AGTAACCATTTTGCTACAAACCAAGAACATT
*
43028 AGTTACCATTTT
1 AGTAACCATTTT
43040 ATTACTTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (31 bp):
AGTAACCATTTTGCTACAAACCAAGAACATT
Found at i:45973 original size:19 final size:19
Alignment explanation
Indices: 45951--46000 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
45941 AAGCAACTCA
45951 AAAGTGTCCTACGTGCGGG
1 AAAGTGTCCTACGTGCGGG
*
45970 AAAGTATCCTACGTGCGGG
1 AAAGTGTCCTACGTGCGGG
45989 AAAGTGTCCTAC
1 AAAGTGTCCTAC
46001 AAGCATGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (19 bp):
AAAGTGTCCTACGTGCGGG
Found at i:46973 original size:5 final size:5
Alignment explanation
Indices: 46958--46991 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
46948 CCAAAAATTT
46958 AAAAG -AAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
46992 TGCATTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:48888 original size:42 final size:42
Alignment explanation
Indices: 48825--48935 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 42
48815 TATTATAAAG
* *
48825 CTTTAATTGTTAAAGTCCATGGCTTTGTCTTATTCCATAGTA
1 CTTTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTA
* * *
48867 CTTTAATTATTAAATTTCATGGCTTTTTCTTATTCCATAGTG
1 CTTTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTA
48909 CTTTAATTATTAAATTCCATGGCTTTG
1 CTTTAATTATTAAATTCCATGGCTTTG
48936 CCTTCTCCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (42 bp):
CTTTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTA
Found at i:53462 original size:14 final size:14
Alignment explanation
Indices: 53435--53500 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 14
53425 ATTCAATCAG
*
53435 AACAAAAAGGGAAAA
1 AACAAAAA-AGAAAA
53450 AACAAAAAAGAAAA
1 AACAAAAAAGAAAA
53464 GAAGCAAAAAAGAAGAA
1 -AA-CAAAAAAGAA-AA
*
53481 AAC--AAAAGAAAG
1 AACAAAAAAGAAAA
53493 AACAAAAA
1 AACAAAAA
53501 TCAAAAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 8 0.18
15 11 0.25
16 12 0.27
17 2 0.05
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (14 bp):
AACAAAAAAGAAAA
Found at i:53482 original size:24 final size:23
Alignment explanation
Indices: 53446--53490 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
53436 ACAAAAAGGG
*
53446 AAAAAACAAAAAAGAAAAGAAGC
1 AAAAAACAAAAAACAAAAGAAGC
*
53469 AAAAAAGAAGAAAACAAAAGAA
1 AAAAAACAA-AAAACAAAAGAA
53491 AGAACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAACAAAAAACAAAAGAAGC
Found at i:54143 original size:22 final size:22
Alignment explanation
Indices: 54115--54167 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
54105 GCTACCCCAT
*
54115 CAAACCTTTGAGTATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
54137 CAAACCTTTGAGCATCAAATTC
1 CAAACCTTTGAGCATCAAATGC
54159 CAAACCTTT
1 CAAACCTTT
54168 ACCAAACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.28
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:55297 original size:106 final size:106
Alignment explanation
Indices: 55081--55926 Score: 1262
Period size: 106 Copynumber: 8.0 Consensus size: 106
55071 GTGCCACTTG
* * * *
55081 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
55145 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
55186 AGACAACACAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
55251 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
55292 TGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * * *
55357 CAGAGCCAATTTAAACTTTACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
55398 AGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
55463 TAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
55504 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
55569 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
55610 AGACAACGTAAGTTCAACTTCACGATGAAGGGACAGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * * * * *
55675 TAGAGCCAATTTTAACTTCACAGCAAAGTATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
55716 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
55781 CGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * * * *
55822 AGACAACACAAGTTCAGCTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
55887 CAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
55927 GGAACAATGC
Statistics
Matches: 677, Mismatches: 63, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
105 45 0.07
106 632 0.93
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Done.