Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007110.1 Hibiscus syriacus cultivar Beakdansim tig00018583_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: 75353
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2612 original size:23 final size:23
Alignment explanation
Indices: 2553--2615 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
2543 CAGCTCATAT
2553 AATTGCACC-TAAGTGCCACGTAG
1 AATTGCACCGT-AGTGCCACGTAG
* * *
2576 AA-TGCACTGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCACGTAG
2598 AATTGCACCGTAGTGCCA
1 AATTGCACCGTAGTGCCA
2616 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCACGTAG
Found at i:2746 original size:103 final size:103
Alignment explanation
Indices: 2631--2947 Score: 552
Period size: 103 Copynumber: 3.1 Consensus size: 103
2621 TAATGTCCAT
2631 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTATGTGTCTCACCA
* * * *
2696 GACCTCTCACATGTTCCAAACAATATATATATATCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
2734 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTATGTGTCTCACCA
2799 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2837 AAGGACCACATATCATTCCTTAAGAATCATATACATATA-CAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTATGTGTCTCACCA
2901 GACCTCACACA--TTCCAAAGAATACATATATGT-CCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2936 AAGGACAACATA
1 AAGGACCACATA
2948 GACCCTCTAC
Statistics
Matches: 208, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
99 14 0.07
100 21 0.10
102 35 0.17
103 138 0.66
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAATGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3444 original size:18 final size:18
Alignment explanation
Indices: 3421--3457 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3411 TTTTTCATTA
*
3421 TGGGGGAATCGGTTCCCC
1 TGGGGGAATCGATTCCCC
*
3439 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
3457 T
1 T
3458 CTAGCATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.27, G:0.35, T:0.27
Consensus pattern (18 bp):
TGGGGGAATCGATTCCCC
Found at i:9805 original size:103 final size:103
Alignment explanation
Indices: 9626--9946 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
9616 TAATGTCCAT
*
9626 AAGGACCACATATCATTTCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
9691 GACCTCACACATGTTCCAAAGAATAAATATATATCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
9729 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
9794 GACCTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
9832 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCACGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
9897 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
9935 AAGGACCACATA
1 AAGGACCACATA
9947 GACCCTCTAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:10513 original size:21 final size:21
Alignment explanation
Indices: 10489--10531 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
10479 TCATATTCGT
*
10489 TTGAGTGGGTATCGATTCCCC
1 TTGAATGGGTATCGATTCCCC
10510 TTGAATGGGTATCGATTCCCC
1 TTGAATGGGTATCGATTCCCC
10531 T
1 T
10532 AGCCCAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGAATGGGTATCGATTCCCC
Found at i:15656 original size:41 final size:41
Alignment explanation
Indices: 15611--15851 Score: 365
Period size: 41 Copynumber: 5.8 Consensus size: 41
15601 ACGCGATAGT
* * *
15611 CGAAGTTTGCGTTGCGATTCATTCCAATTTGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
15652 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
15693 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTACGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
15734 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
* * *
15775 CGAAGTTCGCGTTGCGATTCATTCCAAATTCATTGCGATAGG
1 CGAAGTTCGCATTGCGATTCATTCC-AATTCGTTGCGACAGG
* * * *
15817 CAAAGTTCGCGTTACAATTCATTCCAAATTCGTTG
1 CGAAGTTCGCATTGCGATTCATTCC-AATTCGTTG
15852 TGATAGTCCA
Statistics
Matches: 187, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
41 142 0.76
42 45 0.24
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (41 bp):
CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:15946 original size:6 final size:6
Alignment explanation
Indices: 15935--15966 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
15925 GACACGTATT
15935 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
15967 CTACCTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:16831 original size:20 final size:20
Alignment explanation
Indices: 16806--16916 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
16796 AACTTCACCT
16806 ATCGCAACGAATTGGAATGA
1 ATCGCAACGAATTGGAATGA
* **
16826 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAA-TTGGAATGA
*
16847 ATCGCAACGATTTGGAATGA
1 ATCGCAACGAATTGGAATGA
* *
16867 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAA-TTGGAATGA
*
16888 ATCGCAACGATTTGGAATGA
1 ATCGCAACGAATTGGAATGA
16908 ATCGCAACG
1 ATCGCAACG
16917 CGAATTTCGC
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
18 9 0.13
19 6 0.09
20 23 0.34
21 14 0.21
22 7 0.10
23 9 0.13
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAATTGGAATGA
Found at i:16831 original size:41 final size:41
Alignment explanation
Indices: 16762--16975 Score: 315
Period size: 41 Copynumber: 5.2 Consensus size: 41
16752 AATATTTGGA
16762 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCAC
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCAC
*
16804 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCAC
*
16845 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGA-
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTC-AC
* * *
16886 CTATCGCAACGATTTGGAATGAATCGCAACGCGAATTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCAC
* *
16927 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA-
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTC-AC
16969 CTATCGC
1 CTATCGC
16976 GTTGCGAATC
Statistics
Matches: 158, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
41 115 0.73
42 43 0.27
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (41 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCAC
Found at i:16867 original size:82 final size:83
Alignment explanation
Indices: 16762--16975 Score: 369
Period size: 82 Copynumber: 2.6 Consensus size: 83
16752 AATATTTGGA
16762 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC-ACCTATCGCAACGAATTGGAATGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGA-CTATCGCAACGAATTGGAATGA
16826 ATCGCAACGCGAACTTCGC
65 ATCGCAACGCGAACTTCGC
*
16845 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATGAA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTGGAATGAA
*
16909 TCGCAACGCGAATTTCGC
66 TCGCAACGCGAACTTCGC
* *
16927 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGC
16976 GTTGCGAATC
Statistics
Matches: 125, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
82 78 0.62
83 47 0.38
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (83 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTGGAATGAA
TCGCAACGCGAACTTCGC
Found at i:20913 original size:2 final size:2
Alignment explanation
Indices: 20906--20938 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20896 TTTTGGGTTT
*
20906 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20939 TTAATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29256 original size:29 final size:29
Alignment explanation
Indices: 29213--29280 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
29203 TTGCAATGGC
* *
29213 TCCCTTAATGTTTAACAAA-TTATATTTTGG
1 TCCC-TAAAGTTTAA-AAAGTTATAATTTGG
*
29243 TCCCTAAAGTTTAAAAAGTTGTAATTTGG
1 TCCCTAAAGTTTAAAAAGTTATAATTTGG
29272 TCCCTAAAG
1 TCCCTAAAG
29281 ATGGATTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 3 0.09
29 27 0.79
30 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
TCCCTAAAGTTTAAAAAGTTATAATTTGG
Found at i:30470 original size:23 final size:24
Alignment explanation
Indices: 30417--30470 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
30407 TGATATAAAA
*
30417 AATTATTTTTTATTAAATATTTTT
1 AATTAATTTTTATTAAATATTTTT
* *
30441 GA-T-ATTTTTATTTAAT-TTTTT
1 AATTAATTTTTATTAAATATTTTT
30462 AATTAATTT
1 AATTAATTT
30471 GAATATGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.25
22 12 0.50
23 5 0.21
24 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
AATTAATTTTTATTAAATATTTTT
Found at i:31506 original size:29 final size:29
Alignment explanation
Indices: 31464--31552 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
31454 CTACAGTGGT
31464 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
31493 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
31522 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
31551 CT
1 CT
31553 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:31597 original size:18 final size:18
Alignment explanation
Indices: 31574--31610 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31564 AGAATAGGGC
31574 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
31592 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
31610 C
1 C
31611 GTGGGAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:31640 original size:44 final size:43
Alignment explanation
Indices: 31592--31682 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 43
31582 CAACATGGGA
31592 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGA-GGGATG
31636 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGATG
31679 CATG
1 CATG
31683 GGGTGGGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 10 0.21
44 37 0.79
ACGTcount: A:0.27, C:0.14, G:0.42, T:0.16
Consensus pattern (43 bp):
CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGATG
Found at i:31716 original size:64 final size:66
Alignment explanation
Indices: 31642--31767 Score: 220
Period size: 64 Copynumber: 1.9 Consensus size: 66
31632 GATGCATGCA
31642 ATCAACATGGGACGTGGGAATGCATGGGGGA-GGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
31705 G
66 G
*
31706 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
31768 TGGGAATGCA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
64 30 0.52
65 12 0.21
67 16 0.28
ACGTcount: A:0.24, C:0.10, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:31768 original size:82 final size:83
Alignment explanation
Indices: 31657--31832 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 83
31647 CATGGGACGT
* *
31657 GGGAATGCATGGG-GGAGGG-ATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
31718 TGTGGGAATGCATGGGGGA
66 CGTGGGAATGCAT-GGGGA
* *** *
31737 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
31802 CGTGGGAATGCATGGGGT
66 CGTGGGAATGCATGGGGA
31820 GGGAATGCATGGG
1 GGGAATGCATGGG
31833 GGAGGGGATG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 12 0.15
81 4 0.05
82 27 0.33
83 21 0.26
84 18 0.22
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.18
Consensus pattern (83 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
CGTGGGAATGCATGGGGA
Found at i:31818 original size:51 final size:51
Alignment explanation
Indices: 31719--31860 Score: 254
Period size: 51 Copynumber: 2.8 Consensus size: 51
31709 AACATGGGAT
*
31719 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
31767 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
31818 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
31861 CTGTGCATGG
Statistics
Matches: 90, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
48 23 0.26
51 67 0.74
ACGTcount: A:0.20, C:0.08, G:0.54, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:31823 original size:15 final size:15
Alignment explanation
Indices: 31655--31833 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
31645 AACATGGGAC
31655 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
*
31670 G-GAGGGATGCATGGG
1 GTG-GGAATGCATGGG
31685 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
31700 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
31717 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
31735 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
31750 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
31767 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
31783 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
31803 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
31818 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
31833 G
1 G
31834 GAGGGGATGG
Statistics
Matches: 131, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.02
15 60 0.46
16 18 0.14
17 30 0.23
18 3 0.02
19 15 0.11
20 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:31974 original size:32 final size:32
Alignment explanation
Indices: 31933--31996 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31923 AAGGTCCTGC
31933 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
31965 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
31997 CAGAGATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:32334 original size:21 final size:21
Alignment explanation
Indices: 32309--32353 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32299 AATCTAGTTA
*
32309 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTAAGTATAAATT
* *
32330 ATTAGTTTGTAAGTTTAAGTT
1 ATTAGTTTGTAAGTATAAATT
32351 ATT
1 ATT
32354 TATATTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (21 bp):
ATTAGTTTGTAAGTATAAATT
Found at i:32391 original size:25 final size:26
Alignment explanation
Indices: 32329--32431 Score: 81
Period size: 27 Copynumber: 4.0 Consensus size: 26
32319 TAGTATAAAT
* *
32329 TATTAGTTTGTAAGTTTAAGTTATTTA
1 TATTAGTTTATTAGTTTAAGTTA-TTA
32356 TATTAGTTTATTAGTTTAAGTTA-TA
1 TATTAGTTTATTAGTTTAAGTTATTA
** *
32381 TATTA-TATTA-TA-TAAAAAATTAGTTA
1 TATTAGT-TTATTAGT-TTAAGTTA-TTA
*
32407 -ATTAGTTTCTTAGTTTAAGTTATTA
1 TATTAGTTTATTAGTTTAAGTTATTA
32432 AATATAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
23 1 0.02
24 8 0.13
25 19 0.32
26 10 0.17
27 22 0.37
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (26 bp):
TATTAGTTTATTAGTTTAAGTTATTA
Found at i:32896 original size:16 final size:16
Alignment explanation
Indices: 32875--32930 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
32865 TAATTTCCGT
32875 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
32891 TTTAAAAATATTAGTGTTG
1 TTTAAAAA-A-TATTG-TG
* *
32910 TTTTAAAAATATTTTG
1 TTTAAAAAATATTGTG
32926 TTTAA
1 TTTAA
32931 TTTACATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 14 0.44
17 4 0.12
18 5 0.16
19 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:32899 original size:15 final size:16
Alignment explanation
Indices: 32879--32908 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32869 TTCCGTTTTA
32879 AAAAATATT-GTGTTT
1 AAAAATATTAGTGTTT
32894 AAAAATATTAGTGTT
1 AAAAATATTAGTGTT
32909 GTTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
AAAAATATTAGTGTTT
Found at i:33212 original size:26 final size:25
Alignment explanation
Indices: 33183--33241 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
33173 AAATCATATT
*
33183 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
33209 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
33235 ATTATTA
1 ATTATTA
33242 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:36140 original size:26 final size:26
Alignment explanation
Indices: 36111--36464 Score: 301
Period size: 26 Copynumber: 14.3 Consensus size: 26
36101 TTTGATGATT
36111 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
36137 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
36163 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* *
36185 TA--AAT-ATTTAATGAACAAAT-ATT-
1 TAGTAATGATTTGAT-AA-TAATCATTA
36208 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
36234 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
36260 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
36286 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
36308 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
36332 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
36358 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
36384 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
36406 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
36430 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
36456 TAGTAATGA
1 TAGTAATGA
36465 ATACTAACAA
Statistics
Matches: 277, Mismatches: 22, Indels: 58
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.01
20 15 0.05
22 9 0.03
23 39 0.14
24 24 0.09
25 27 0.10
26 148 0.53
27 12 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:36245 original size:123 final size:123
Alignment explanation
Indices: 36111--36401 Score: 494
Period size: 123 Copynumber: 2.3 Consensus size: 123
36101 TTTGATGATT
* *
36111 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGATTTA
36176 ATAATGATTTAAATATTTAATGAACAAAT-ATTTAGTAATGATTTGATAATAATCATTA
65 ATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGATTTGATAATAATCATTA
36234 TAGTAATGATTTGATAATAATCATTATAATAATGATTTATTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
****
36299 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
65 ATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGATTTGATAATAATCATTA
36358 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAAT
36402 GATTTAAATA
Statistics
Matches: 159, Mismatches: 6, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
122 1 0.01
123 86 0.54
124 71 0.45
125 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (123 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGATTTGATAATAATCATTA
Found at i:36248 original size:97 final size:98
Alignment explanation
Indices: 36056--36375 Score: 384
Period size: 98 Copynumber: 3.3 Consensus size: 98
36046 ATGTATTTAT
* ****
36056 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
36121 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
36154 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAAT-ATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
36218 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
* * * * * *
36251 TAATCATTATAATAATGATTTATTAATAATCATTATAAA-AATGATTTAA-TAATGATTTA--AA
1 TAATCATTATAATAATGA--T-TTAATAATGATT-TAAATATTTAATGAACAAATGATTTAGTAA
* * * *
36312 T-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAA
62 TGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAA
* *
36349 TAATCATTATAGTAATGATTTGATAAT
1 TAATCATTATAATAATGATTTAATAAT
36376 AATCATTATA
Statistics
Matches: 198, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
95 7 0.04
96 1 0.01
97 70 0.35
98 84 0.42
99 10 0.05
100 22 0.11
101 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (98 bp):
TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAA
Found at i:36369 original size:98 final size:98
Alignment explanation
Indices: 36234--36464 Score: 428
Period size: 98 Copynumber: 2.4 Consensus size: 98
36224 ATAATCATTA
*
36234 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAAAAATGATTT
36298 AATAATGATTTAAATATTTAATGATTTGATGATT
65 AATAATGATTTAAATATTTAATGATTTGATGATT
*
36332 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTA
36397 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
36430 TAGTAATGATTTGATAATAATCATTATAGTAATGA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGA
36465 ATACTAACAA
Statistics
Matches: 130, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
98 129 0.99
99 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:36678 original size:17 final size:17
Alignment explanation
Indices: 36653--36685 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36643 ACTAAATATC
*
36653 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
36670 TAATGATTTGATACTA
1 TAATGATTTGATACTA
36686 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:38987 original size:34 final size:32
Alignment explanation
Indices: 38923--39004 Score: 89
Period size: 34 Copynumber: 2.6 Consensus size: 32
38913 GCTAAACCCT
*
38923 TAAAC-AACTAATAAAATATTCTTCTATATAA
1 TAAACTAACTAATAAACTATTCTTCTATATAA
*
38954 CTAAAACTAACTAATAAACTATTTTTC-ATTATAA
1 -T-AAACTAACTAATAAACTATTCTTCTA-TATAA
*
38988 TATACT-ACTAATAAACT
1 TAAACTAACTAATAAACT
39005 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 11 0.25
32 5 0.11
33 6 0.14
34 22 0.50
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAACTAACTAATAAACTATTCTTCTATATAA
Found at i:39148 original size:47 final size:47
Alignment explanation
Indices: 39045--39135 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
39035 CAACAAACAA
39045 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
* *
39093 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
39136 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
Found at i:39368 original size:21 final size:20
Alignment explanation
Indices: 39338--39389 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
39328 TTTCGAATTC
*
39338 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTT-CTTTCTCCCT
* *
39359 TTCTTTCTTTCTTTTTCCTT
1 TTCTTTCTTTCTTTCTCCCT
39379 TCTCTTTCTTT
1 T-TCTTTCTTT
39390 TTCTCGGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTTCTTTCTTTCTCCCT
Found at i:39372 original size:25 final size:24
Alignment explanation
Indices: 39338--39389 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
39328 TTTCGAATTC
39338 TTCTTAC-TTTCCTTTCTCCCTTTCT
1 TTCTTACTTTTCCTTTCT--CTTTCT
*
39363 TTCTTTCTTTTTCCTTTCTCTTTCT
1 TTCTTAC-TTTTCCTTTCTCTTTCT
39388 TT
1 TT
39390 TTCTCGGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 14 0.58
27 10 0.42
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (24 bp):
TTCTTACTTTTCCTTTCTCTTTCT
Found at i:39483 original size:25 final size:25
Alignment explanation
Indices: 39455--39506 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
39445 TTTCTTTTAT
*
39455 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
39480 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
39505 AA
1 AA
39507 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:39654 original size:23 final size:23
Alignment explanation
Indices: 39627--39673 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39617 GAATCTATAT
39627 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
39650 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
39673 G
1 G
39674 AATGGACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.26
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:39678 original size:13 final size:13
Alignment explanation
Indices: 39660--39691 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39650 GGCTGCATGT
*
39660 GAATGGATGATGG
1 GAATGGACGATGG
39673 GAATGGACGATGG
1 GAATGGACGATGG
39686 GAATGG
1 GAATGG
39692 TGCCGGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (13 bp):
GAATGGACGATGG
Found at i:39726 original size:29 final size:29
Alignment explanation
Indices: 39693--39829 Score: 222
Period size: 29 Copynumber: 4.7 Consensus size: 29
39683 TGGGAATGGT
*
39693 GCCGGGACTACATGGCGACCTATAAGGTC
1 GCCGGGACTACATGGCGACCTACAAGGTC
*
39722 GCCGGGAGTACATGGCGACCTACAAGGTC
1 GCCGGGACTACATGGCGACCTACAAGGTC
39751 GCCGGGACTACATGGCGACCTACAAGGTC
1 GCCGGGACTACATGGCGACCTACAAGGTC
39780 GCCGGGACTACATGGCGACCTACAAGGTC
1 GCCGGGACTACATGGCGACCTACAAGGTC
* *
39809 GCCTAGG-CTGCATGGCGACCT
1 GCC-GGGACTACATGGCGACCT
39830 CTCTATTCCA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
29 100 0.98
30 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.15
Consensus pattern (29 bp):
GCCGGGACTACATGGCGACCTACAAGGTC
Found at i:39888 original size:41 final size:41
Alignment explanation
Indices: 39841--40056 Score: 142
Period size: 41 Copynumber: 5.2 Consensus size: 41
39831 TCTATTCCAC
39841 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
39882 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
39924 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
39966 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
40008 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
40050 TGCATGG
1 TGCATGG
40057 GGAGAACCAT
Statistics
Matches: 127, Mismatches: 28, Indels: 40
0.65 0.14 0.21
Matches are distributed among these distances:
38 6 0.05
39 6 0.05
40 2 0.02
41 51 0.40
42 4 0.03
43 44 0.35
44 2 0.02
45 6 0.05
46 6 0.05
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:39921 original size:84 final size:84
Alignment explanation
Indices: 39824--40059 Score: 472
Period size: 84 Copynumber: 2.8 Consensus size: 84
39814 GGCTGCATGG
39824 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
39889 GGACCTCGCATGGGGAGAA
66 GGACCTCGCATGGGGAGAA
39908 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
39973 GGACCTCGCATGGGGAGAA
66 GGACCTCGCATGGGGAGAA
39992 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
40057 GGA
66 GGA
40060 GAACCATTGG
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 152 1.00
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (84 bp):
CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGG
GGACCTCGCATGGGGAGAA
Found at i:39938 original size:43 final size:43
Alignment explanation
Indices: 39882--40028 Score: 135
Period size: 43 Copynumber: 3.5 Consensus size: 43
39872 ATGGCTCGTA
**
39882 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCAC
1 TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTATTCCAC
*** * *
39925 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA-
1 TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CAC
**
39966 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCAC
1 TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTATTCCAC
40009 TGCATGGCCACCTCGCATGG
1 TGCATGGCCACCTCGCATGG
40029 CTCGCACTCG
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 22 0.28
42 2 0.03
43 40 0.51
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (43 bp):
TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTATTCCAC
Found at i:40081 original size:35 final size:35
Alignment explanation
Indices: 40035--40147 Score: 226
Period size: 35 Copynumber: 3.2 Consensus size: 35
40025 ATGGCTCGCA
40035 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
40070 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
40105 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
40140 CTCGTATG
1 CTCGTATG
40148 TTCCCGTATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
Found at i:42752 original size:16 final size:16
Alignment explanation
Indices: 42731--42772 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
42721 AGTGAAATAG
42731 TAGGAGCTATCCGTAA
1 TAGGAGCTATCCGTAA
42747 TAGGAGCTATCCGTAA
1 TAGGAGCTATCCGTAA
*
42763 TAGAAGCTAT
1 TAGGAGCTAT
42773 GTCAACGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (16 bp):
TAGGAGCTATCCGTAA
Found at i:48600 original size:31 final size:31
Alignment explanation
Indices: 48565--48626 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
48555 TTTTGACCAT
48565 GCACCATTCGGTGACAAACTTTGATTTTCAA
1 GCACCATTCGGTGACAAACTTTGATTTTCAA
* * * *
48596 GCACCATTTGGTGCCAACCTTTTATTTTCAA
1 GCACCATTCGGTGACAAACTTTGATTTTCAA
48627 CAATATCTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (31 bp):
GCACCATTCGGTGACAAACTTTGATTTTCAA
Found at i:51065 original size:31 final size:31
Alignment explanation
Indices: 51030--51093 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
51020 TGCTTTTGAC
* *
51030 CATGCATCATTCAGTGCCAAACTTTGATTTT
1 CATGCACCACTCAGTGCCAAACTTTGATTTT
* *
51061 CATGCACCACTCGGTGCCAACCTTTGATTTT
1 CATGCACCACTCAGTGCCAAACTTTGATTTT
51092 CA
1 CA
51094 ACAAATGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.34
Consensus pattern (31 bp):
CATGCACCACTCAGTGCCAAACTTTGATTTT
Found at i:52192 original size:3 final size:3
Alignment explanation
Indices: 52184--52228 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
52174 CACTTTCATA
*
52184 TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA
52229 AATAAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
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:53539 original size:11 final size:11
Alignment explanation
Indices: 53525--53576 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
53515 CTTTTTAATC
53525 ATTA-TTTATTT
1 ATTATTTTA-TT
*
53536 ATTATTTTGTT
1 ATTATTTTATT
53547 ATTACTTTTA-T
1 ATTA-TTTTATT
53558 ATTATTTTATT
1 ATTATTTTATT
53569 ATTATTTT
1 ATTATTTT
53577 CATATTAGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 24 0.67
12 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:53560 original size:22 final size:22
Alignment explanation
Indices: 53535--53583 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
53525 ATTATTTATT
*
53535 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
53557 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
53579 TATTA
1 TATTA
53584 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:53582 original size:11 final size:10
Alignment explanation
Indices: 53525--53583 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
53515 CTTTTTAATC
*
53525 ATTATTTATTT
1 ATTATTT-TAT
*
53536 ATTATTTTGTT
1 ATTATTTT-AT
53547 ATTACTTTTAT
1 ATTA-TTTTAT
53558 ATTATTTTATT
1 ATTATTTTA-T
53569 ATTATTTTCAT
1 ATTATTTT-AT
53580 ATTA
1 ATTA
53584 GTCACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 6 0.14
11 32 0.74
12 5 0.12
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:54495 original size:26 final size:27
Alignment explanation
Indices: 54443--54510 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
54433 TAATTCTTTC
* *
54443 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATAC-TATTA
*
54471 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCATAATATTTATATATACTATTA
54497 TTTT-ATTAATATTT
1 TTTTCA-TAATATTT
54511 CATTTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 17 0.47
28 18 0.50
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTTCATAATATTTATATATACTATTA
Found at i:56061 original size:8 final size:7
Alignment explanation
Indices: 56037--56078 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
56027 TTTTCATACA
56037 TGCA-TT
1 TGCATTT
56043 TGCATTT
1 TGCATTT
56050 TGCATCTT
1 TGCAT-TT
56058 TGCATTT
1 TGCATTT
* *
56065 TTCATTG
1 TGCATTT
56072 TGCATTT
1 TGCATTT
56079 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:56061 original size:15 final size:14
Alignment explanation
Indices: 56037--56078 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
56027 TTTTCATACA
56037 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
56050 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
56065 TTCATTGTGCATTT
1 TGCATTTTGCATTT
56079 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:56154 original size:12 final size:12
Alignment explanation
Indices: 56137--56164 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
56127 ACATTCACAT
56137 ATTTACATTTGC
1 ATTTACATTTGC
56149 ATTTACATTTGC
1 ATTTACATTTGC
56161 ATTT
1 ATTT
56165 TTTTATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:58953 original size:11 final size:10
Alignment explanation
Indices: 58936--59003 Score: 73
Period size: 11 Copynumber: 6.3 Consensus size: 10
58926 CTCATCCAGC
58936 AAAAAAAGAA
1 AAAAAAAGAA
*
58946 AGAAAAAAAAA
1 A-AAAAAAGAA
58957 AGAAAAAAGAA
1 A-AAAAAAGAA
58968 AAGAAAAAGAA
1 AA-AAAAAGAA
*
58979 AAGAAAAGAA
1 AAAAAAAGAA
58989 AAAATGAAAGAA
1 AAAA--AAAGAA
59001 AAA
1 AAA
59004 GAAGGAGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 12 0.24
11 29 0.58
12 9 0.18
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:58953 original size:12 final size:12
Alignment explanation
Indices: 58936--59003 Score: 68
Period size: 12 Copynumber: 5.4 Consensus size: 12
58926 CTCATCCAGC
58936 AAAAAAAGAAAG
1 AAAAAAAGAAAG
58948 AAAAAAA-AAAG
1 AAAAAAAGAAAG
58959 -AAAAAAGAAAAG
1 AAAAAAAG-AAAG
58971 AAAAAGAAAAGAAAAG
1 --AAA-AAAAG-AAAG
*
58987 AAAAAATGAAAG
1 AAAAAAAGAAAG
58999 AAAAA
1 AAAAA
59004 GAAGGAGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 20 0.41
13 4 0.08
14 3 0.06
15 2 0.04
16 10 0.20
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:58962 original size:5 final size:5
Alignment explanation
Indices: 58939--58990 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
58929 ATCCAGCAAA
58939 AAAAG -AAAG AAAA- AAAA- AAGAA- AAAAG AAAAG AAAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG -AAAAG AAAAG AAAAG
58987 AAAA
1 AAAA
58991 AATGAAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.28
5 26 0.60
6 5 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:58985 original size:28 final size:28
Alignment explanation
Indices: 58939--59006 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
58929 ATCCAGCAAA
58939 AAAAGAAAGAA-AAAAAAAAGAAAAAA-G
1 AAAAGAAA-AAGAAAAAAAAGAAAAAATG
58966 AAAAGAAAAAGAAAAGAAAAGAAAAAATG
1 AAAAGAAAAAGAAAA-AAAAGAAAAAATG
58995 -AAAGAAAAAGAA
1 AAAAGAAAAAGAA
59007 GGAGAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 2 0.05
27 12 0.32
28 23 0.61
29 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (28 bp):
AAAAGAAAAAGAAAAAAAAGAAAAAATG
Found at i:61361 original size:114 final size:114
Alignment explanation
Indices: 61161--61380 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
61151 CACGTTCTCG
* *
61161 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTT
* * *
61226 GGTATGAACCCTAAAACCAATCATTTGATTTAAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
61275 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTT
* *
61340 GGTATGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTATGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
61381 CTGCATGATT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTT
GGTATGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
Found at i:63950 original size:22 final size:22
Alignment explanation
Indices: 63924--64000 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
63914 ATCTACACTC
63924 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
63946 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
63968 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
63990 TTCAAAGATGA
1 TTCAAAGATGA
64001 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:65652 original size:17 final size:16
Alignment explanation
Indices: 65621--65654 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
65611 CACGTGAGGA
65621 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
65637 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
65654 T
1 T
65655 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Done.