Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005652.1 Hibiscus syriacus cultivar Beakdansim tig00013210_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: 92031
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:16303 original size:36 final size:36
Alignment explanation
Indices: 16239--16307 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
16229 ATTAAAATGG
*
16239 TTTTCAAGTTTGGTAAATGTTTCTTTGAAAAATAGT
1 TTTTCAAGTTTGGTAAATGTTTCGTTGAAAAATAGT
*
16275 TTTTCAAAGTTTGGTAGATGTTT-GTTGAAAAAT
1 TTTTC-AAGTTTGGTAAATGTTTCGTTGAAAAAT
16308 GATAATGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (36 bp):
TTTTCAAGTTTGGTAAATGTTTCGTTGAAAAATAGT
Found at i:16738 original size:16 final size:16
Alignment explanation
Indices: 16717--16749 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16707 TACTATTCAT
*
16717 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
16733 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
16749 G
1 G
16750 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:20828 original size:36 final size:36
Alignment explanation
Indices: 20788--20856 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
20778 ATTAAAATGG
*
20788 TTTTC-AAGTTTGGTAAATGTTTCTTTGAAAAATAGT
1 TTTTCAAAGTTTGGTAAATGTTT-GTTGAAAAATAGT
*
20824 TTTTCAAAGTTTGGTAGATGTTTGTTGAAAAAT
1 TTTTCAAAGTTTGGTAAATGTTTGTTGAAAAAT
20857 GATAATGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (36 bp):
TTTTCAAAGTTTGGTAAATGTTTGTTGAAAAATAGT
Found at i:26810 original size:23 final size:23
Alignment explanation
Indices: 26776--26889 Score: 156
Period size: 23 Copynumber: 5.0 Consensus size: 23
26766 CACCACAGCT
* * *
26776 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
* * *
26799 CGTAGAATTGCACCTAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCG
*
26822 CGTAGAAATGAACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
26845 CGTAGAAATGCACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
26868 CGTAGAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
26890 ATATAAGATT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:27174 original size:30 final size:29
Alignment explanation
Indices: 27121--27179 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
27111 TGTAAACATA
* *
27121 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
27151 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
27180 ATAAATTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:28394 original size:20 final size:20
Alignment explanation
Indices: 28369--28422 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
28359 GAAATATTGA
28369 TGCATCGATGCACCCCTTAC
1 TGCATCGATGCACCCCTTAC
28389 TGCATCGATGCACCCCTTAC
1 TGCATCGATGCACCCCTTAC
28409 TGCATCGATGCACC
1 TGCATCGATGCACC
28423 TTCAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACCCCTTAC
Found at i:31121 original size:2 final size:2
Alignment explanation
Indices: 31114--31138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31104 CCAAACATAA
31114 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 A
31139 CCATTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31595 original size:23 final size:23
Alignment explanation
Indices: 31569--31637 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
31559 CACCACAGCT
*
31569 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
31592 CGTAGAATTGCACCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
31615 CGTAGAAATGCACCGAATTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
31638 TATAAGATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:31654 original size:46 final size:46
Alignment explanation
Indices: 31569--31668 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 46
31559 CACCACAGCT
* * *
31569 CGTATAAATGCACCGAAGTGCCACGTAGAATTGCACCTAAGTG-CCG
1 CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACCTAAG-GACCA
* *
31615 CGTAGAAATGCACCGAATTGCCATATA-AGATTGTC-CCTAAGGACCA
1 CGTAGAAATGCACCGAAGTGCCACATAGA-ATTG-CACCTAAGGACCA
31661 CGTAGAAA
1 CGTAGAAA
31669 ATTCCTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
45 2 0.04
46 43 0.93
47 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (46 bp):
CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACCTAAGGACCA
Found at i:38025 original size:28 final size:27
Alignment explanation
Indices: 37945--38025 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
37935 GGATTAAGTA
37945 TTTAGGGTTTAAGGTTTAAGGTTTATGT
1 TTTAGGGTTTAA-GTTTAAGGTTTATGT
* *
37973 TTTAGGGTTTAGGATTTAAGATTTATAG-
1 TTTAGGGTTTAAG-TTTAAGGTTTAT-GT
*
38001 TTTAGGGTTTATAGTTTAGGGTTTA
1 TTTAGGGTTTA-AGTTTAAGGTTTA
38026 GGGTGTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 42 0.93
29 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.49
Consensus pattern (27 bp):
TTTAGGGTTTAAGTTTAAGGTTTATGT
Found at i:38026 original size:7 final size:7
Alignment explanation
Indices: 37945--38029 Score: 71
Period size: 7 Copynumber: 12.1 Consensus size: 7
37935 GGATTAAGTA
37945 TTTAGGG
1 TTTAGGG
*
37952 TTTAAGG
1 TTTAGGG
*
37959 TTTAAGG
1 TTTAGGG
* *
37966 TTTATGT
1 TTTAGGG
37973 TTTAGGG
1 TTTAGGG
*
37980 TTTAGGA
1 TTTAGGG
* *
37987 TTTAAGA
1 TTTAGGG
**
37994 TTTATAG
1 TTTAGGG
38001 TTTAGGG
1 TTTAGGG
**
38008 TTTATAG
1 TTTAGGG
38015 TTTAGGG
1 TTTAGGG
38022 TTTAGGG
1 TTTAGGG
38029 T
1 T
38030 GTAATCTAAC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:38026 original size:21 final size:22
Alignment explanation
Indices: 37952--38029 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 22
37942 GTATTTAGGG
* * *
37952 TTTAAGGTTTAAGGTTTAT-GT
1 TTTAGGGTTTAGGGTTTATAGA
*
37973 TTTAGGGTTTAGGATTTA-AGA
1 TTTAGGGTTTAGGGTTTATAGA
**
37994 TTTATAGTTTAGGGTTTATAG-
1 TTTAGGGTTTAGGGTTTATAGA
38015 TTTAGGGTTTAGGGT
1 TTTAGGGTTTAGGGT
38030 GTAATCTAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 44 0.96
22 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
TTTAGGGTTTAGGGTTTATAGA
Found at i:41988 original size:21 final size:21
Alignment explanation
Indices: 41962--42015 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
41952 GACAAATATT
41962 TTCATTTGCTAGGGCCTAGAA
1 TTCATTTGCTAGGGCCTAGAA
*
41983 TTCATTTGCTAGGTCCTAGAA
1 TTCATTTGCTAGGGCCTAGAA
*
42004 TTCATTTTCTAG
1 TTCATTTGCTAG
42016 CATGTCCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (21 bp):
TTCATTTGCTAGGGCCTAGAA
Found at i:44780 original size:2 final size:2
Alignment explanation
Indices: 44773--44800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44763 GTCATAAATA
44773 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
44801 TAAATAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48675 original size:22 final size:22
Alignment explanation
Indices: 48640--48681 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
48630 TTAATTTATA
48640 AAATGTTAAGTTATAAATTACT
1 AAATGTTAAGTTATAAATTACT
48662 AAATGTGTAA-TTATAAATTA
1 AAATGT-TAAGTTATAAATTA
48682 GTTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATGTTAAGTTATAAATTACT
Found at i:49246 original size:2 final size:2
Alignment explanation
Indices: 49234--49276 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
49224 TAATACAATA
*
49234 AT AT GAT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT -T AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49276 A
1 A
49277 ATTGATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:50656 original size:15 final size:15
Alignment explanation
Indices: 50636--50671 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
50626 TAATTATACG
50636 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
50651 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
50666 ATTAAT
1 TTTAAT
50672 TTAATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATACTTTATAA
Found at i:51883 original size:22 final size:23
Alignment explanation
Indices: 51838--51884 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
51828 GTTTAAAATA
*
51838 TAAAATTTTAGATAATAATGTTT
1 TAAAATTTTAGATAATAATATTT
51861 TAAAA-TTTAGATAGA-AATATTT
1 TAAAATTTTAGATA-ATAATATTT
51883 TA
1 TA
51885 CAAACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (23 bp):
TAAAATTTTAGATAATAATATTT
Found at i:55412 original size:42 final size:42
Alignment explanation
Indices: 55365--55472 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
55355 AAATTTTGTG
* * * *
55365 TTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCCCGTA
1 TTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCCGTA
* *
55407 TTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCTGTG
1 TTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCCGTA
55449 TTTGTTTCACGTAATTCGTTTTCC
1 TTTGTTTCACGTAATTCGTTTTCC
55473 AGAATGTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.50
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCCGTA
Found at i:55677 original size:12 final size:12
Alignment explanation
Indices: 55641--55678 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
55631 ATCAAAATAT
55641 TATATTTATTAA
1 TATATTTATTAA
* *
55653 AATATTTA-AAA
1 TATATTTATTAA
55664 TATATTTATTAA
1 TATATTTATTAA
55676 TAT
1 TAT
55679 TTATAATAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATTTATTAA
Found at i:55677 original size:21 final size:22
Alignment explanation
Indices: 55641--55686 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
55631 ATCAAAATAT
55641 TATATTTATTAAAATATTTAAAA
1 TATATTTATT-AAATATTTAAAA
*
55664 TATATTTATT-AATATTTATAA
1 TATATTTATTAAATATTTAAAA
55685 TA
1 TA
55687 ACATAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
23 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATTTATTAAATATTTAAAA
Found at i:55698 original size:55 final size:52
Alignment explanation
Indices: 55639--55744 Score: 124
Period size: 55 Copynumber: 2.0 Consensus size: 52
55629 CCATCAAAAT
* **
55639 ATTATATTTATTAA-AATATTTAAAATATATTTATTAATATTTATAATAACATAAC
1 ATTATATTT-TTAATAATATATAAAATA-ATCAATT-ATA-TTATAATAACATAAC
* *
55694 ATTATATTTTTAATATTATATAAAATAATCAATTATATTATAATAATATAA
1 ATTATATTTTTAATAATATATAAAATAATCAATTATATTATAATAACATAA
55745 TATAAGATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
52 13 0.29
53 3 0.07
54 9 0.20
55 20 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (52 bp):
ATTATATTTTTAATAATATATAAAATAATCAATTATATTATAATAACATAAC
Found at i:55710 original size:31 final size:32
Alignment explanation
Indices: 55664--55749 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 32
55654 ATATTTAAAA
*
55664 TATATTTATTAATATTTATAATAACATAA-C-AT
1 TATATTTATTAATA-TTAT-ATAAAATAATCAAT
55696 TATATTT-TTAATATTATATAAAATAATCAAT
1 TATATTTATTAATATTATATAAAATAATCAAT
* *
55727 TATATTATAATAATATAATATAA
1 TATATT-TATTAATATTATATAA
55750 GATATTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
29 8 0.17
30 5 0.11
31 14 0.30
32 8 0.17
33 12 0.26
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
TATATTTATTAATATTATATAAAATAATCAAT
Found at i:55779 original size:31 final size:31
Alignment explanation
Indices: 55744--55805 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
55734 TAATAATATA
*
55744 ATATAAGATATTATATTTT-TAT-TTTAATAAT
1 ATATAAGAAATT-T-TTTTATATATTTAATAAT
*
55775 ATATAATAAATTTTTTTATATATTTAATAAT
1 ATATAAGAAATTTTTTTATATATTTAATAAT
55806 GAATAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 4 0.15
31 19 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
ATATAAGAAATTTTTTTATATATTTAATAAT
Found at i:56010 original size:19 final size:20
Alignment explanation
Indices: 55978--56016 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
55968 TAATAAAATT
55978 ATAAAAAAAATA-TTTAATA
1 ATAAAAAAAATATTTTAATA
* *
55997 ATAAATAAATTATTTTAATA
1 ATAAAAAAAATATTTTAATA
56017 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAAAAATATTTTAATA
Found at i:56235 original size:15 final size:15
Alignment explanation
Indices: 56217--56256 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
56207 ATTCATTTTC
56217 CAGTAATTCAAATTG
1 CAGTAATTCAAATTG
56232 CAGTAATTCAAATTG
1 CAGTAATTCAAATTG
56247 CAGTAATTCA
1 CAGTAATTCA
56257 TTTTCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (15 bp):
CAGTAATTCAAATTG
Found at i:56239 original size:30 final size:30
Alignment explanation
Indices: 56175--56256 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
56165 TTCCAGAAAT
*
56175 GTAATTCATTTTCCAG-AATTTAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
56204 CTAATTCATTTTCCAGTAATTCAAATTGCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
** *
56234 GTAATTCAAATTGCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
56257 TTTTCCGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 15 0.33
30 30 0.67
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:56647 original size:2 final size:2
Alignment explanation
Indices: 56636--56678 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
56626 CATATTTTAA
56636 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56677 AT
1 AT
56679 TAAAAATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:72992 original size:43 final size:43
Alignment explanation
Indices: 72931--73016 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
72921 GTGTAACATC
72931 CTAAATCAGGGCCAGTTACTAAATTGCAAATTTTAAAAACTAT
1 CTAAATCAGGGCCAGTTACTAAATTGCAAATTTTAAAAACTAT
72974 CTAAATCAGGGCCAGTTACTAAATTGCAAATTTTAAAAACTAT
1 CTAAATCAGGGCCAGTTACTAAATTGCAAATTTTAAAAACTAT
73017 GTGCCCAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (43 bp):
CTAAATCAGGGCCAGTTACTAAATTGCAAATTTTAAAAACTAT
Found at i:73968 original size:20 final size:20
Alignment explanation
Indices: 73924--73968 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
73914 AATAGTGTTA
73924 TATTATATTTTAAAAATATT
1 TATTATATTTTAAAAATATT
* * *
73944 AATTATATTTTAAATATCTT
1 TATTATATTTTAAAAATATT
73964 TATTA
1 TATTA
73969 AATATATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATATTTTAAAAATATT
Found at i:74042 original size:19 final size:20
Alignment explanation
Indices: 73989--74042 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
73979 ATTATTAGAT
*
73989 TAATATT-A-AATATATAAA
1 TAATATTAATAATATATTAA
* *
74007 TAATATTATTCAT-TATTAA
1 TAATATTAATAATATATTAA
74026 TAAT-TTAATAATATATT
1 TAATATTAATAATATATT
74043 TCTATGGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 13 0.46
19 13 0.46
20 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTAATAATATATTAA
Found at i:74172 original size:22 final size:23
Alignment explanation
Indices: 74144--74190 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
74134 TTGATTGTTT
74144 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
74166 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
74189 TA
1 TA
74191 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:74195 original size:22 final size:22
Alignment explanation
Indices: 74152--74206 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
74142 TTTATTATAA
*
74152 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
74174 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
*
74196 ATTTTAAAAAT
1 -TATTAAAAAT
74207 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:74206 original size:23 final size:23
Alignment explanation
Indices: 74154--74250 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 23
74144 TATTATAATA
*
74154 TTAAAAATA-TAAT-ATTATATT
1 TTAAAAATATTAATAAATATATT
*
74175 ATTAGAAATATTAATAAATATATT
1 -TTAAAAATATTAATAAATATATT
*
74199 TTAAAAATTTTAA-AAATTAATATT
1 TTAAAAATATTAATAAA-T-ATATT
* *
74223 TTGATTAAAATGTTATTAAA-ATATT
1 TT-A--AAAATATTAATAAATATATT
74248 TTA
1 TTA
74251 TTAATAGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
22 11 0.18
23 16 0.26
24 15 0.25
25 8 0.13
27 8 0.13
28 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
TTAAAAATATTAATAAATATATT
Found at i:75683 original size:17 final size:16
Alignment explanation
Indices: 75661--75694 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
75651 AGCGATATAA
*
75661 ATTATATGTTATGGTAT
1 ATTATATGATAT-GTAT
75678 ATTATATGATATGTAT
1 ATTATATGATATGTAT
75694 A
1 A
75695 AATTCAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTATATGATATGTAT
Found at i:84987 original size:20 final size:19
Alignment explanation
Indices: 84958--85124 Score: 99
Period size: 20 Copynumber: 8.6 Consensus size: 19
84948 AAATGACCAA
84958 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
* * **
84977 CCAATTTCGCAAC-AGTTTT
1 -CAAATTCGCAACGCGAATT
*
84996 CAATTTCGCAACGCGAATAT
1 CAAATTCGCAACGCGAAT-T
*** *
85016 -AAATTCGCGTTGCGATTTT
1 CAAATTCGCAACGCGA-ATT
* * *
85035 CCAAATTCGCAACACAAAAGT
1 -CAAATTCGCAACGC-GAATT
*
85056 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AATT
*
85076 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAA-TT
85095 C-AATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
* *
85113 TAATTTCGCAAC
1 CAAATTCGCAAC
85125 AGGTTTTAGT
Statistics
Matches: 111, Mismatches: 26, Indels: 21
0.70 0.16 0.13
Matches are distributed among these distances:
18 26 0.23
19 32 0.29
20 42 0.38
21 10 0.09
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (19 bp):
CAAATTCGCAACGCGAATT
Found at i:85101 original size:18 final size:18
Alignment explanation
Indices: 85058--85124 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
85048 ACAAAAGTCA
**
85058 AATTCGCAACGCGAAAGTCA
1 AATTCGCAACGCG-AA-TTT
*
85078 AATTCGCAAC-TGAATTT
1 AATTCGCAACGCGAATTT
85095 CAATTCGCAACGCGAATTT
1 -AATTCGCAACGCGAATTT
85114 AATTTCGCAAC
1 AA-TTCGCAAC
85125 AGGTTTTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.03
18 14 0.35
19 15 0.38
20 10 0.25
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (18 bp):
AATTCGCAACGCGAATTT
Found at i:86075 original size:24 final size:24
Alignment explanation
Indices: 86024--86077 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
86014 GTATTCGAAA
*
86024 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* * *
86048 TTTGATCTTGGTTAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
86072 TTTGAT
1 TTTGAT
86078 GATGTGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:88348 original size:18 final size:18
Alignment explanation
Indices: 88325--88360 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
88315 AAGCAAAAGG
88325 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
88343 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
88361 CAACAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:88714 original size:20 final size:20
Alignment explanation
Indices: 88688--88762 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
88678 GCGTTACGAT
88688 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
* * *
88708 AGACAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAA
*
88728 AGTCAAATTCGCAATGC--A
1 AGTCAAATTCGCAACGCGAA
88746 AGTCAAATTCGCAACGC
1 AGTCAAATTCGCAACGC
88763 AAAATCGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
18 16 0.33
20 33 0.67
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAA
Found at i:88739 original size:40 final size:38
Alignment explanation
Indices: 88684--88759 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 38
88674 ATAAGCGTTA
88684 CGATAGTCAAATTCGCAACGCGAAAGACAAATTCGCAATG
1 CGATAGTCAAATTCGCAACGC--AAGACAAATTCGCAATG
* *
88724 CGATAGTCAAATTCGCAATGCAAGTCAAATTCGCAA
1 CGATAGTCAAATTCGCAACGCAAGACAAATTCGCAA
88760 CGCAAAATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 14 0.41
40 20 0.59
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (38 bp):
CGATAGTCAAATTCGCAACGCAAGACAAATTCGCAATG
Found at i:88918 original size:25 final size:25
Alignment explanation
Indices: 88880--88929 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
88870 AAATCAATTA
*
88880 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
88905 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
88930 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:89391 original size:39 final size:39
Alignment explanation
Indices: 89304--89392 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
89294 TCCGATGCTC
* *
89304 ATCAAAATCCAAAGCTCATTTGGTGCCAAGAAAAAGAAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGAAAAAGAAA
* * * *
89343 ATCCAAATCTAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGAAAAAGAAA
89382 ATCAAAATCTA
1 ATCAAAATCTA
89393 CAACTTGAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.20
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGAAAAAGAAA
Found at i:89654 original size:20 final size:20
Alignment explanation
Indices: 89629--89672 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
89619 AAACCAAAAA
* *
89629 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCAAATTTGACTG
89649 TCGCGTTGCAAATTTGACTG
1 TCGCGTTGCAAATTTGACTG
89669 TCGC
1 TCGC
89673 AACGCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCAAATTTGACTG
Found at i:89830 original size:63 final size:60
Alignment explanation
Indices: 89757--89893 Score: 193
Period size: 63 Copynumber: 2.2 Consensus size: 60
89747 TTTTAGGAAC
*
89757 AACAAATCAACTTTTACAAATCAATTAAACAAAAAAAATAATTCTTATTTACAAATCAAAGTA
1 AACAAATCAACTTTTACAAATCAATTAAAC--AAAAAATAAATCTTATTTACAAATC-AAGTA
* * ** *
89820 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAAAAATAAATCTTATTTACAAATCAAGTA
89880 AACAAATCAACTTT
1 AACAAATCAACTTT
89894 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 18 0.26
61 21 0.31
63 29 0.43
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAAAAATAAATCTTATTTACAAATCAAGTA
Done.