Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008632.1 Hibiscus syriacus cultivar Beakdansim tig00111602_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: 74520
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4225 original size:14 final size:16
Alignment explanation
Indices: 4203--4244 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4193 TAAATTTCAA
4203 TTTATATTA-TAATAT
1 TTTATATTATTAATAT
4218 TTTA-ATTATTAATAT
1 TTTATATTATTAATAT
*
4233 TTTGTATT-TTAA
1 TTTATATTATTAA
4245 CATAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 17 0.71
16 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTATATTATTAATAT
Found at i:9592 original size:15 final size:15
Alignment explanation
Indices: 9572--9610 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9562 AAATTTTTTG
9572 AATTATTTAAATATA
1 AATTATTTAAATATA
* *
9587 AATTATCTAAATATG
1 AATTATTTAAATATA
9602 AATCTATTT
1 AAT-TATTT
9611 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (15 bp):
AATTATTTAAATATA
Found at i:17048 original size:114 final size:114
Alignment explanation
Indices: 16844--17063 Score: 334
Period size: 114 Copynumber: 1.9 Consensus size: 114
16834 CGTCGATTTG
* * * * *
16844 GAATCAGTCAATAAGATTGATGCTGATTCGGAAAAGGGTACGGAACAGATGGATGAATACAAAGC
1 GAATCAGGCAATAAGATCGATGCTGACTCGGAAAAGGATACAGAACAGATGGATGAATACAAAGC
16909 CGAGAAGAAATTCTTGTCCGAAACAGCAAGCAGTACCATTGTTGATTCT
66 CGAGAAGAAATTCTTGTCCGAAACAGCAAGCAGTACCATTGTTGATTCT
* *
16958 GAATCAGGCAATAAGATCGATGCTGACTCGGGAAAGGATACAGAACAGATGGATGATTACAAAGC
1 GAATCAGGCAATAAGATCGATGCTGACTCGGAAAAGGATACAGAACAGATGGATGAATACAAAGC
* * *
17023 TGAGACGAAA-TCTTTGTCCGGAACAGCAAGCAGTACCATTG
66 CGAGAAGAAATTC-TTGTCCGAAACAGCAAGCAGTACCATTG
17064 ATACCGAGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.02
114 93 0.98
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (114 bp):
GAATCAGGCAATAAGATCGATGCTGACTCGGAAAAGGATACAGAACAGATGGATGAATACAAAGC
CGAGAAGAAATTCTTGTCCGAAACAGCAAGCAGTACCATTGTTGATTCT
Found at i:19623 original size:16 final size:16
Alignment explanation
Indices: 19598--19628 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19588 GACGAATACG
*
19598 GATGAGTATCATTAAT
1 GATGAATATCATTAAT
19614 GATGAATATCATTAA
1 GATGAATATCATTAA
19629 ATTAATTTAT
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:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (16 bp):
GATGAATATCATTAAT
Found at i:19653 original size:15 final size:15
Alignment explanation
Indices: 19629--19671 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
19619 ATATCATTAA
*
19629 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
19644 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
19659 ATTAAATGTATAA
1 ATTAAAT-TATAA
19672 TTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:20843 original size:2 final size:2
Alignment explanation
Indices: 20838--20869 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
20828 TATGTGTGTG
20838 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
20870 TATCGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21523 original size:15 final size:15
Alignment explanation
Indices: 21503--21538 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21493 TAATTATACG
21503 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
21518 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
21533 ATTAAT
1 TTTAAT
21539 TTAATAGTAC
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:22643 original size:221 final size:221
Alignment explanation
Indices: 22406--22829 Score: 581
Period size: 221 Copynumber: 1.9 Consensus size: 221
22396 ATTTAAGTTA
*
22406 TATATATATAGTCTAAAAATTGAT-A-CTTTTTAATTTAATTAATAATTTTACTTTTTATT-AAA
1 TATATATATAGTCT-AAAATTGATAATCATTTTAATTTAATTAATAATTTTACTTTTTATTGAAA
* ** *
22468 AATAAAATAAAT-TG-ATTATTTATATTTCAATTAAATTTTTATTGGATTACATAGTTAAAATGT
65 AATAAAAT--ATGTGAATCATTTATATTTCAATT--ATTTTTATTAAATTACATAATTAAAATGT
** * * * * *
22531 GTAATT-AGAAGTCGAATTTAATCATGTGTAAATCTTAAATATAGTTTTTCTTTTAATTTTGTAT
126 GTAATTAAGAA-TCGAATTTAATCACCTGCAAAACTTAAATATAATTTTTATTTTAATCTTGTAT
22595 AAACTAATGTTTAACATTTATAATTTAATGAT
190 AAACTAATGTTTAACATTTATAATTTAATGAT
* *
22627 TATATATATAGTCTAAAATTTATAATCATTTTAATTTAATTAATAATTTTATTTTTTATTGAAAA
1 TATATATATAGTCTAAAATTGATAATCATTTTAATTTAATTAATAATTTTACTTTTTATTGAAAA
* *
22692 ATAAAATATGTGAATCATTTATATTTTAATTATTTTTATTAAATTGCATAATTAAAATGTGTAAT
66 ATAAAATATGTGAATCATTTATATTTCAATTATTTTTATTAAATTACATAATTAAAATGTGTAAT
* * *
22757 TAAGAATCGATTTTAATCACCTGCAAAACTTAAATTTAATTTTTATTTTAATCTTGTATAAATTA
131 TAAGAATCGAATTTAATCACCTGCAAAACTTAAATATAATTTTTATTTTAATCTTGTATAAACTA
22822 ATGTTTAA
196 ATGTTTAA
22830 AAATACACAA
Statistics
Matches: 178, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
220 8 0.04
221 105 0.59
222 38 0.21
223 27 0.15
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (221 bp):
TATATATATAGTCTAAAATTGATAATCATTTTAATTTAATTAATAATTTTACTTTTTATTGAAAA
ATAAAATATGTGAATCATTTATATTTCAATTATTTTTATTAAATTACATAATTAAAATGTGTAAT
TAAGAATCGAATTTAATCACCTGCAAAACTTAAATATAATTTTTATTTTAATCTTGTATAAACTA
ATGTTTAACATTTATAATTTAATGAT
Found at i:27609 original size:44 final size:45
Alignment explanation
Indices: 27525--27609 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 45
27515 ATAGTGTCTA
* *
27525 AACTTGAATTCATCTTTTTTTATATAGAGGCTAAATGGGTATTTG
1 AACTTGAATTCATCTTTTTTTATATAGAGGCCAAAGGGGTATTTG
*
27570 AACTTGAATTCATC-TTTTTTATATATAGGCCAAAGGGGTA
1 AACTTGAATTCATCTTTTTTTATATAGAGGCCAAAGGGGTA
27610 CTTTTTACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 23 0.62
45 14 0.38
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (45 bp):
AACTTGAATTCATCTTTTTTTATATAGAGGCCAAAGGGGTATTTG
Found at i:27870 original size:30 final size:29
Alignment explanation
Indices: 27830--27930 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
27820 GAATTATGTA
* *
27830 GAGGGATAACATTTGGTCTTTTAAGAAGTTT
1 GAGGG-TAACA-TTGATTTTTTAAGAAGTTT
*
27861 GAGGGTAACATAGATTTTTTAAGAAGTTT
1 GAGGGTAACATTGATTTTTTAAGAAGTTT
*
27890 GAGGGTAATATTGATTTTTTAAGAAGTTT
1 GAGGGTAACATTGATTTTTTAAGAAGTTT
* *
27919 AAGAGTAACATT
1 GAGGGTAACATT
27931 TGTCCTCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 52 0.84
30 5 0.08
31 5 0.08
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.39
Consensus pattern (29 bp):
GAGGGTAACATTGATTTTTTAAGAAGTTT
Found at i:29003 original size:12 final size:13
Alignment explanation
Indices: 28938--29005 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 13
28928 CATAACTTAA
*
28938 AACCTTAAATTGCT
1 AACCTTAAACT-CT
* *
28952 AACCCTAAACTAT
1 AACCTTAAACTCT
* *
28965 AACCCCTAAACCCT
1 AA-CCTTAAACTCT
*
28979 AACCTTAATCTCT
1 AACCTTAAACTCT
28992 AA-CTTAAACTCT
1 AACCTTAAACTCT
29004 AA
1 AA
29006 ATTTAAGGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 11 0.25
13 13 0.30
14 20 0.45
ACGTcount: A:0.40, C:0.31, G:0.01, T:0.28
Consensus pattern (13 bp):
AACCTTAAACTCT
Found at i:29797 original size:3 final size:3
Alignment explanation
Indices: 29786--29854 Score: 83
Period size: 3 Copynumber: 23.7 Consensus size: 3
29776 TACAAAAAAA
29786 TAT TA- TAT TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
29828 TAT TAT TAT TAAT TTT TAT TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TA
29855 ATTTTGCAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
2 8 0.14
3 44 0.76
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29820 original size:16 final size:16
Alignment explanation
Indices: 29785--29836 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 16
29775 CTACAAAAAA
29785 ATATTATATTATTATATT
1 ATATTATATTA-T-TATT
29803 ATATTATATTATTATT
1 ATATTATATTATTATT
29819 ATA-TATTATTATTATT
1 ATATTA-TATTATTATT
29835 AT
1 AT
29837 TAATTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.06
16 19 0.58
17 1 0.03
18 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTATATTATTATT
Found at i:29846 original size:13 final size:13
Alignment explanation
Indices: 29787--29851 Score: 64
Period size: 13 Copynumber: 5.0 Consensus size: 13
29777 ACAAAAAAAT
29787 ATTA-TATTATTA
1 ATTATTATTATTA
*
29799 TATTA-TATTATATT
1 -ATTATTATTAT-TA
29813 ATTATTATATATT-
1 ATTATTAT-TATTA
29826 ATTATTATTATTA
1 ATTATTATTATTA
*
29839 ATTTTTATTATTA
1 ATTATTATTATTA
29852 TTAATTTTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
12 4 0.09
13 34 0.74
14 5 0.11
15 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:29846 original size:16 final size:17
Alignment explanation
Indices: 29793--29859 Score: 79
Period size: 16 Copynumber: 4.1 Consensus size: 17
29783 AAATATTATA
29793 TTATTA-TATTATATTAT
1 TTATTATTATTATATT-T
*
29810 ATTATTATTA-TATATTA
1 -TTATTATTATTATATTT
29827 TTATTATTATTA-ATTT
1 TTATTATTATTATATTT
29843 TTATTATTATTA-ATTT
1 TTATTATTATTATATTT
29859 T
1 T
29860 GCAGGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
16 29 0.64
17 2 0.04
18 12 0.27
19 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTATTATTATATTT
Found at i:30928 original size:12 final size:13
Alignment explanation
Indices: 30911--30942 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
30901 TTAAATCGAA
30911 TAATTTTAA-TTT
1 TAATTTTAATTTT
30923 TAATTTTAATTTT
1 TAATTTTAATTTT
30936 TAATTTT
1 TAATTTT
30943 CGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:30938 original size:7 final size:6
Alignment explanation
Indices: 30911--30942 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
30901 TTAAATCGAA
30911 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
30943 CGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:34994 original size:106 final size:106
Alignment explanation
Indices: 34827--35909 Score: 1609
Period size: 106 Copynumber: 10.3 Consensus size: 106
34817 TCCAATTTCA
* * * * *
34827 TTCAGAGTCTATTTCAACTTCGCAACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
34892 CGACGAAGGGACCGCTGGTTGTTAATAAACAATTTTCCAA-
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * * * *
34932 TACTAGAGCCAATTTCAACTTCACAGCGAATGATAGTGGACTCCAGACAACACAAGTTCAACTTC
1 TTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
34997 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-CCAAT
65 ACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCCCAAT
* * * *
35039 TTCAGAGTCAATTTCAGCTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
35104 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
35145 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
35210 CGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* *
35251 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
35316 CGACGAAGGGACCGCTGGTTATCAACAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * * * * *
35357 TTCATAGCCAATTTCAACTTCACAGCAAATGATATTGGATTCTAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
35422 CGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
35463 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
35528 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
35569 TTCGGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
35634 CGACGAAGGGACCGCTGGTTGTC-A-ATA-AA-----CAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
35667 TTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGATAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
35728 CAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
35769 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
35834 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCGAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
35875 TTCAGAGCCAATTTCAACTTCACGACGAAGGATAT
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
35910 CCAATTCGTG
Statistics
Matches: 895, Mismatches: 67, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
94 77 0.09
95 1 0.00
96 2 0.00
97 2 0.00
98 7 0.01
102 6 0.01
103 2 0.00
104 2 0.00
105 5 0.01
106 786 0.88
107 5 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
Found at i:35739 original size:94 final size:95
Alignment explanation
Indices: 35578--35878 Score: 417
Period size: 94 Copynumber: 3.1 Consensus size: 95
35568 TTTCGGAGCT
35578 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
*
35643 GACCGCTGGTTGTCAATAAACAATTTC-CC
66 GACCGCTGGTTGTCAACAAACAATTTCACC
* * *
35672 AATTTCAACTTCACAACGAAGGATATTGGACTCCGGATAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
*
35737 GACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAAC-A-------ATTTC--A-CC
* *
35778 AATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
35843 GACCGCTGGTTGTCAACAAACAATTTC-CC
66 GACCGCTGGTTGTCAACAAACAATTTCACC
*
35872 GATTTCA
1 AATTTCA
35879 GAGCCAATTT
Statistics
Matches: 185, Mismatches: 10, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
94 91 0.49
95 1 0.01
98 5 0.03
102 5 0.03
105 1 0.01
106 82 0.44
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (95 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAATTTCACC
Found at i:36137 original size:81 final size:80
Alignment explanation
Indices: 35983--36250 Score: 277
Period size: 80 Copynumber: 3.3 Consensus size: 80
35973 AATCGTGCCA
* * ** * *
35983 ACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAGGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAAGT
36048 CGAGAAGGGCTATCT
66 CGAGAAGGGCTATCT
** * * * * * *
36063 ACCAAGGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTATATCATTTACAGCATAACTCAAG
1 ACCAAGGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCAAATCATTTGCAGCATAACTTAAG
* * *
36128 GCTAGAAGGGTTATCTGT
65 TCGAGAAGGGCTATC--T
* * *
36146 GACCAAAGG-CCTTCGAGATCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAA
1 -ACC-AAGGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAA
36210 GTCGAGAAGGGCTATCT
64 GTCGAGAAGGGCTATCT
* * *
36227 GCTAAAGACCTTCGAGTTCGATTA
1 ACCAAGGACCTTCGAGTTCGATTA
36251 TATTCAACTT
Statistics
Matches: 147, Mismatches: 35, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
79 3 0.02
80 41 0.28
81 38 0.26
83 39 0.27
84 22 0.15
85 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (80 bp):
ACCAAGGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAAGT
CGAGAAGGGCTATCT
Found at i:36201 original size:83 final size:82
Alignment explanation
Indices: 35983--36247 Score: 288
Period size: 83 Copynumber: 3.3 Consensus size: 82
35973 AATCGTGCCA
* * * *
35983 ACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAAGT
36048 CGAGAAGGGCTATC--T
66 CGAGAAGGGCTATCTGT
** * * * * * * * *
36063 ACC-AAGGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTATATCATTTACAGCATAACTCAA
1 ACCAAAGG-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCAAATCATTTGCAGCATAACTTAA
* * *
36127 GGCTAGAAGGGTTATCTGT
64 GTCGAGAAGGGCTATCTGT
*
36146 GACCAAAGGCCTTCGAGATCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAAG
1 -ACCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAAG
36211 TCGAGAAGGGCTATCTG-
65 TCGAGAAGGGCTATCTGT
* *
36228 -CTAAAGACCTTCGAGTTCGA
1 ACCAAAGGCCTTCGAGTTCGA
36248 TTATATTCAA
Statistics
Matches: 146, Mismatches: 33, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
79 3 0.02
80 39 0.27
81 37 0.25
83 41 0.28
84 22 0.15
85 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (82 bp):
ACCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTGCAGCATAACTTAAGT
CGAGAAGGGCTATCTGT
Found at i:36875 original size:3 final size:3
Alignment explanation
Indices: 36862--36909 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
36852 CTACAAAAAA
*
36862 TAT TA- TAT TAT TA- TAT TAT TAT TAT TAT TAAT TTT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
36906 TAT T
1 TAT T
36910 TTTGCAGGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36912 original size:16 final size:16
Alignment explanation
Indices: 36867--36912 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
36857 AAAAATATTA
*
36867 TATTATTATATTATTAT
1 TATTATTAT-TTTTTAT
*
36884 TATTATTAATTTTTAT
1 TATTATTATTTTTTAT
36900 TATTATTATTTTT
1 TATTATTATTTTT
36913 GCAGGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTATTTTTTAT
Found at i:37980 original size:12 final size:13
Alignment explanation
Indices: 37963--37994 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
37953 TTAAATCGAA
37963 TAATTTTAA-TTT
1 TAATTTTAATTTT
37975 TAATTTTAATTTT
1 TAATTTTAATTTT
37988 TAATTTT
1 TAATTTT
37995 CGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:37990 original size:7 final size:6
Alignment explanation
Indices: 37963--37994 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
37953 TTAAATCGAA
37963 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
37995 CGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:42941 original size:16 final size:16
Alignment explanation
Indices: 42917--42950 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42907 TATCGCCGAC
*
42917 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
42933 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
42949 CG
1 CG
42951 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:52398 original size:21 final size:21
Alignment explanation
Indices: 52356--52398 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52346 TTTCTGGGCT
*
52356 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
52377 AGGGGAATTGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
52398 A
1 A
52399 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:52451 original size:20 final size:20
Alignment explanation
Indices: 52426--52463 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52416 GAATGCTAGA
*
52426 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
52446 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
52464 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:53269 original size:103 final size:103
Alignment explanation
Indices: 52941--53261 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
52931 GTAGAGGGTC
* *
52941 TATGTGATCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
53006 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
53044 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
53109 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
53147 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
53212 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
53250 TATGTGGTCCTT
1 TATGTGGTCCTT
53262 ATGGACATTA
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:53311 original size:23 final size:23
Alignment explanation
Indices: 53277--53363 Score: 138
Period size: 23 Copynumber: 3.8 Consensus size: 23
53267 CATTATTATA
*
53277 TGGCACTACGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
*
53300 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
53323 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
**
53346 TGGCACTTAGGTGCAATT
1 TGGCACTCCGGTGCAATT
53364 ATATGAGCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:59219 original size:110 final size:110
Alignment explanation
Indices: 59026--59247 Score: 444
Period size: 110 Copynumber: 2.0 Consensus size: 110
59016 TTCATGACCA
59026 TTAGGCAATAGTTAAGCTTAAAGGAAGTTTAAATTATTTTAAAACCTCAAGAGGAGAAGTATATG
1 TTAGGCAATAGTTAAGCTTAAAGGAAGTTTAAATTATTTTAAAACCTCAAGAGGAGAAGTATATG
59091 AAGAATTAAAGAAAGGAAGTAGAAAAGTGAAATCTTAGATTAGAG
66 AAGAATTAAAGAAAGGAAGTAGAAAAGTGAAATCTTAGATTAGAG
59136 TTAGGCAATAGTTAAGCTTAAAGGAAGTTTAAATTATTTTAAAACCTCAAGAGGAGAAGTATATG
1 TTAGGCAATAGTTAAGCTTAAAGGAAGTTTAAATTATTTTAAAACCTCAAGAGGAGAAGTATATG
59201 AAGAATTAAAGAAAGGAAGTAGAAAAGTGAAATCTTAGATTAGAG
66 AAGAATTAAAGAAAGGAAGTAGAAAAGTGAAATCTTAGATTAGAG
59246 TT
1 TT
59248 CATAATAAGA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (110 bp):
TTAGGCAATAGTTAAGCTTAAAGGAAGTTTAAATTATTTTAAAACCTCAAGAGGAGAAGTATATG
AAGAATTAAAGAAAGGAAGTAGAAAAGTGAAATCTTAGATTAGAG
Found at i:59612 original size:20 final size:20
Alignment explanation
Indices: 59587--59624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59577 GAACGCTAGA
*
59587 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
59607 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
59625 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:60433 original size:103 final size:103
Alignment explanation
Indices: 60106--60425 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
60096 GTAGAGGGTC
*
60106 TATGTGATCCTTCGGGACATATA-GTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
60170 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
60208 TATGTGGCCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
60273 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
60311 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
60376 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
60414 TATGTGGTCCTT
1 TATGTGGTCCTT
60426 ATGGACATTA
Statistics
Matches: 210, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
102 21 0.10
103 189 0.90
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:60475 original size:23 final size:23
Alignment explanation
Indices: 60442--60493 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
60432 ATTATTATAT
60442 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTCTACGC
* * *
60465 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTACAATTCTACGC
60488 GGCACT
1 GGCACT
60494 TAGGTTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTACAATTCTACGC
Found at i:60503 original size:23 final size:23
Alignment explanation
Indices: 60441--60504 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
60431 CATTATTATA
60441 TGGCAC-TACGGTACAATTCTACG
1 TGGCACTTA-GGTACAATTCTACG
* ** *
60464 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTTAGGTACAATTCTACG
*
60487 TGGCACTTAGGTTCAATT
1 TGGCACTTAGGTACAATT
60505 ATATGAGCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTTAGGTACAATTCTACG
Found at i:64405 original size:23 final size:23
Alignment explanation
Indices: 64375--64421 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
64365 TATCGATACA
*
64375 TATATATAAGTATCCATACTTAT
1 TATATATAAGTATACATACTTAT
64398 TATATATAAGTATACATACTTAT
1 TATATATAAGTATACATACTTAT
64421 T
1 T
64422 TTACTGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (23 bp):
TATATATAAGTATACATACTTAT
Found at i:64976 original size:75 final size:72
Alignment explanation
Indices: 64897--65033 Score: 166
Period size: 72 Copynumber: 1.9 Consensus size: 72
64887 CTATTTACTG
* * * * * *
64897 GTTTGTTTGAATGCTATTAATAATGTAAATAATAAAATCAAATAGGCGTTACTTATTACGTTAAA
1 GTTTGTTTAAATG-T-TT-ATAATATAAACAATAAAATAAAATAGGCGCTACCTATTACGTTAAA
64962 ATATCTACCA
63 ATATCTACCA
** *
64972 GTTTGTTTAAATGTTTATAATATAAACGGTAAAATAAAATAGGCGCTACCTGTTACGTTAAA
1 GTTTGTTTAAATGTTTATAATATAAACAATAAAATAAAATAGGCGCTACCTATTACGTTAAA
65034 TAAGCATCAC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
72 38 0.72
73 2 0.04
74 1 0.02
75 12 0.23
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (72 bp):
GTTTGTTTAAATGTTTATAATATAAACAATAAAATAAAATAGGCGCTACCTATTACGTTAAAATA
TCTACCA
Found at i:65131 original size:98 final size:95
Alignment explanation
Indices: 64950--65131 Score: 258
Period size: 98 Copynumber: 1.9 Consensus size: 95
64940 AGGCGTTACT
*
64950 TATTACGTTAAAATATCTACCAGTTTGTTTAAATGTTTATAATATAAACGGTAAAATAAAATAGG
1 TATTACGTTAAAATATCTACCAGTTTGTTTAAATGGTTATAATATAAACGGTAAAATAAAATAGG
* *
65015 CGCTACCTGTTACGTTAAATAAGCATCACC
66 CGCTACATATTACGTTAAATAAGCATCACC
* * *
65045 TATTATGTTAAACTATCTACCAGTTTGTTTGAA-GGTTACTAATAAGGTAAACGGTAAAATAAAA
1 TATTACGTTAAAATATCTACCAGTTTGTTTAAATGGTTA-TAAT-A--TAAACGGTAAAATAAAA
*
65109 TAGGCGTTACATATTACGTTAAA
62 TAGGCGCTACATATTACGTTAAA
65132 ATACATACCG
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
94 4 0.05
95 34 0.45
96 1 0.01
98 37 0.49
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (95 bp):
TATTACGTTAAAATATCTACCAGTTTGTTTAAATGGTTATAATATAAACGGTAAAATAAAATAGG
CGCTACATATTACGTTAAATAAGCATCACC
Found at i:65155 original size:75 final size:75
Alignment explanation
Indices: 65068--65206 Score: 233
Period size: 75 Copynumber: 1.9 Consensus size: 75
65058 TATCTACCAG
* *
65068 TTTGTTTGAAGGTTACTAATAAGGTAAACGGTAAAATAAAATAGGCGTTACATATTACGTTAAAA
1 TTTGTTTAAAGGTTACTAATAAGGTAAACGGTAAAATAAAATAGGCGTTACATATTACATTAAAA
65133 TACATACCGA
66 TACATACCGA
* * *
65143 TTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGGTGTTACCTATTACATTAAA
1 TTTGTTTAAAGGTTACTAATAAGGTAAACGGTAAAATAAAATAGGCGTTACATATTACATTAAA
65207 TAAGCGCTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (75 bp):
TTTGTTTAAAGGTTACTAATAAGGTAAACGGTAAAATAAAATAGGCGTTACATATTACATTAAAA
TACATACCGA
Found at i:65282 original size:97 final size:97
Alignment explanation
Indices: 65106--65303 Score: 263
Period size: 97 Copynumber: 2.0 Consensus size: 97
65096 CGGTAAAATA
* *
65106 AAATAGGCGTTACATATTACGTTAAAATACATACCGATTTGTTTAAAGGTTACTAATAATGTAAA
1 AAATAAGCGCTACATATTACGTTAAAATACATACCGATTTGTTTAAA-GTTACTAATAATGTAAA
*
65171 CGGTAAAATAAAATAGGTGTTACCTATTACATT
65 CGGTAAAATAAAATAGGCGTTACCTATTACATT
* * * * *
65204 AAATAAGCGCTACCTATTATGTTAAACTACCTACCGATTTTTTTAATA-TTACTAATAATGTAAA
1 AAATAAGCGCTACATATTACGTTAAAATACATACCGATTTGTTTAA-AGTTACTAATAATGTAAA
* * * *
65268 TGGTAAAATAAAATATGCGTTATCTATTACGTT
65 CGGTAAAATAAAATAGGCGTTACCTATTACATT
65301 AAA
1 AAA
65304 ATACATACTG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
97 47 0.54
98 39 0.45
99 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (97 bp):
AAATAAGCGCTACATATTACGTTAAAATACATACCGATTTGTTTAAAGTTACTAATAATGTAAAC
GGTAAAATAAAATAGGCGTTACCTATTACATT
Found at i:65321 original size:172 final size:173
Alignment explanation
Indices: 64875--65449 Score: 682
Period size: 172 Copynumber: 3.4 Consensus size: 173
64865 AGGTATTATA
** * * * * * * ** *
64875 TATTATGTTAAACTATTTACTGGTTTGTTTGAATGCTATTAATAATGTAAATAATAAAATCAAAT
1 TATTATGTTAAACTAACTACCGATTTATTTAAATGTTACTAATAATGTAAACGATAAAATAAAAT
* * *
64940 AGGCGTTACTTATTACGTTAAAATATC-TACCAGTTTGTTTAAATGTT--T-ATAATATAAACGG
66 AGGCGTTACATATTACGTTAAAATA-CATACCGGTTTGTTTAAAGGTTACTAATAATATAAACGG
* *
65001 TAAAATAAAATAGGCGCTACCTGTTACGTTAAATAAGC-ATCACC
130 TAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCT-ACC
* * * * * *
65045 TATTATGTTAAACTATCTACC-AGTTTGTTTGAAGGTTACTAATAAGGTAAACGGTAAAATAAAA
1 TATTATGTTAAACTAACTACCGA-TTTATTTAAATGTTACTAATAATGTAAACGATAAAATAAAA
* *
65109 TAGGCGTTACATATTACGTTAAAATACATACCGATTTGTTTAAAGGTTACTAATAATGTAAACGG
65 TAGGCGTTACATATTACGTTAAAATACATACCGGTTTGTTTAAAGGTTACTAATAATATAAACGG
* * *
65174 TAAAATAAAATAGGTGTTACCTATTACATTAAATAAGCGCTACC
130 TAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACC
* * * * *
65218 TATTATGTTAAACTACCTACCGATTT-TTTTAATATTACTAATAATGTAAATGGTAAAATAAAAT
1 TATTATGTTAAACTAACTACCGATTTATTTAAATGTTACTAATAATGTAAACGATAAAATAAAAT
* * *
65282 ATGCGTTATC-TATTACGTTAAAATACATACTGGTTTGTTT-AAGGTTACTAATAATATAAACAG
66 AGGCGTTA-CATATTACGTTAAAATACATACCGGTTTGTTTAAAGGTTACTAATAATATAAACGG
* *
65345 TAAAATAAAATAGGCACTACCTATTATGTTAAATAAGCGCTACC
130 TAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACC
* ** *
65389 TATTACGTTAAACTAACTATTGATTTATTTAAATGTTAATAATAATGTAAACGATAAAATA
1 TATTATGTTAAACTAACTACCGATTTATTTAAATGTTACTAATAATGTAAACGATAAAATA
65450 TATAAAATTT
Statistics
Matches: 350, Mismatches: 46, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
169 1 0.00
170 94 0.27
171 82 0.23
172 98 0.28
173 73 0.21
174 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (173 bp):
TATTATGTTAAACTAACTACCGATTTATTTAAATGTTACTAATAATGTAAACGATAAAATAAAAT
AGGCGTTACATATTACGTTAAAATACATACCGGTTTGTTTAAAGGTTACTAATAATATAAACGGT
AAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACC
Found at i:65369 original size:74 final size:74
Alignment explanation
Indices: 65204--65377 Score: 204
Period size: 74 Copynumber: 2.4 Consensus size: 74
65194 CTATTACATT
* * * * * *
65204 AAATAAGCGCTACCTATTATGTTAAACTACCTACCGATTTTTTTAATATTACTAATAATGTAAAT
1 AAATAAGCGCTACCTATTATGTTAAAATACATACCGATTTGTTTAAGATTACTAATAATATAAAC
*
65269 GGTAAAATA
66 AGTAAAATA
* * * * * * *
65278 AAATATGCGTTATCTATTACGTTAAAATACATACTGGTTTGTTTAAGGTTACTAATAATATAAAC
1 AAATAAGCGCTACCTATTATGTTAAAATACATACCGATTTGTTTAAGATTACTAATAATATAAAC
65343 AGTAAAATA
66 AGTAAAATA
* *
65352 AAATAGGCACTACCTATTATGTTAAA
1 AAATAAGCGCTACCTATTATGTTAAA
65378 TAAGCGCTAC
Statistics
Matches: 81, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
74 81 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (74 bp):
AAATAAGCGCTACCTATTATGTTAAAATACATACCGATTTGTTTAAGATTACTAATAATATAAAC
AGTAAAATA
Found at i:65387 original size:23 final size:23
Alignment explanation
Indices: 65352--65400 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
65342 CAGTAAAATA
* *
65352 AAATAGGCACTACCTATTATGTT
1 AAATAAGCACTACCTATTACGTT
*
65375 AAATAAGCGCTACCTATTACGTT
1 AAATAAGCACTACCTATTACGTT
65398 AAA
1 AAA
65401 CTAACTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
AAATAAGCACTACCTATTACGTT
Found at i:68783 original size:34 final size:34
Alignment explanation
Indices: 68703--68787 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 34
68693 TTTTTTTAAT
*
68703 TTCGGGTTCA-GGTCGGGGTTTTTTAAGCTTGATA
1 TTCGGG-TCAGGGTCGGGTTTTTTTAAGCTTGATA
* *
68737 TTCAGGTC-GGGTCGGGTTTTTTTAAGTTTGATA
1 TTCGGGTCAGGGTCGGGTTTTTTTAAGCTTGATA
68770 TTCGGGTCAGGGTCGGGT
1 TTCGGGTCAGGGTCGGGT
68788 CGGGGTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 31 0.69
34 14 0.31
ACGTcount: A:0.13, C:0.12, G:0.35, T:0.40
Consensus pattern (34 bp):
TTCGGGTCAGGGTCGGGTTTTTTTAAGCTTGATA
Found at i:68784 original size:39 final size:40
Alignment explanation
Indices: 68741--68817 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
68731 TTGATATTCA
*
68741 GGTCGGGTC-GGGTTTTTTTAAGTTTGATATTCGGGTCAG
1 GGTCGGGTCGGGGTTTTTTTAAGTATGATATTCGGGTCAG
68780 GGTCGGGTCGGGGTTTTTTTAAGTATGATATTCGGGTC
1 GGTCGGGTCGGGGTTTTTTTAAGTATGATATTCGGGTC
68818 GGATTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 9 0.25
40 27 0.75
ACGTcount: A:0.13, C:0.10, G:0.36, T:0.40
Consensus pattern (40 bp):
GGTCGGGTCGGGGTTTTTTTAAGTATGATATTCGGGTCAG
Found at i:68836 original size:28 final size:28
Alignment explanation
Indices: 68782--68844 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
68772 CGGGTCAGGG
* *
68782 TCGGGTCGGGGTTTTTTTAAGTATGATAT
1 TCGGGTCGGGATTTTTTTAAGCATGAT-T
*
68811 TCGGGTC-GGATTTTTTTAAGCGTGATT
1 TCGGGTCGGGATTTTTTTAAGCATGATT
*
68838 TTGGGTC
1 TCGGGTC
68845 ATGTTCGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.23
28 16 0.53
29 7 0.23
ACGTcount: A:0.14, C:0.10, G:0.32, T:0.44
Consensus pattern (28 bp):
TCGGGTCGGGATTTTTTTAAGCATGATT
Found at i:69042 original size:5 final size:5
Alignment explanation
Indices: 69032--69057 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
69022 ATTCATATAT
69032 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
69058 GAAACTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:69467 original size:17 final size:17
Alignment explanation
Indices: 69445--69478 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
69435 GTTTCAGATT
69445 CAGATTCCAATTCCTTC
1 CAGATTCCAATTCCTTC
**
69462 CAGATTTTAATTCCTTC
1 CAGATTCCAATTCCTTC
69479 AGAAATATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (17 bp):
CAGATTCCAATTCCTTC
Done.