Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006437.1 Hibiscus syriacus cultivar Beakdansim tig00015544_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: 85069
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:12485 original size:22 final size:22
Alignment explanation
Indices: 12457--12510 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12447 GAGACGAAAC
*
12457 AAAAAAAAGGTTACTCCAAAAA
1 AAAAAAAAGATTACTCCAAAAA
*
12479 AAAAAAAAAATTACTCCAAAAA
1 AAAAAAAAGATTACTCCAAAAA
12501 AAAAAAAAGA
1 AAAAAAAAGA
12511 GATGGAGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.72, C:0.11, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAAAAAAGATTACTCCAAAAA
Found at i:12791 original size:23 final size:25
Alignment explanation
Indices: 12756--12802 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
12746 CGGAAATGTT
*
12756 AAAAAATATTAATGTTTTAGGTAAC
1 AAAAAATATTAATATTTTAGGTAAC
12781 AAAAAA-A-TAATATTTTAGGTAA
1 AAAAAATATTAATATTTTAGGTAA
12803 TATTTTACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (25 bp):
AAAAAATATTAATATTTTAGGTAAC
Found at i:17922 original size:31 final size:31
Alignment explanation
Indices: 17849--17922 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
17839 TTTTACAAGC
* * *
17849 TTTGGAAAAA-TTCAGGGATCATTTTGTAAT
1 TTTGGAAAAAGTTGAGGGACCAATTTGTAAT
*
17879 TTTTG-AAAAGTTGAGGGACCAATTTGTAAT
1 TTTGGAAAAAGTTGAGGGACCAATTTGTAAT
17909 TTTGGAAAAAGTTG
1 TTTGGAAAAAGTTG
17923 GGAATGGTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.11
30 25 0.68
31 8 0.22
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (31 bp):
TTTGGAAAAAGTTGAGGGACCAATTTGTAAT
Found at i:19404 original size:35 final size:38
Alignment explanation
Indices: 19247--19409 Score: 174
Period size: 38 Copynumber: 4.4 Consensus size: 38
19237 CTTAAGGAGT
* * *
19247 GGTCCTAT-GGGACACATATGACATCCTTCGAGATAATA
1 GGTCCT-TCGGGACACATATCACATCCTTCGGGATGATA
* * * *
19285 AGT-CTTACGGGACACAGATGACATCCTGCGGGATGATA
1 GGTCCTT-CGGGACACATATCACATCCTTCGGGATGATA
*
19323 GGTCCTTCGGGACACATATCACATCCTTCAGGATGATA
1 GGTCCTTCGGGACACATATCACATCCTTCGGGATGATA
* *
19361 GGTCCTTCGGGACACATA-CA-A-CCTTTGGGATTATA
1 GGTCCTTCGGGACACATATCACATCCTTCGGGATGATA
*
19396 GGTTCTTCGGGACA
1 GGTCCTTCGGGACA
19410 TTTATACGAG
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
35 24 0.22
36 2 0.02
37 4 0.04
38 75 0.69
39 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (38 bp):
GGTCCTTCGGGACACATATCACATCCTTCGGGATGATA
Found at i:19501 original size:12 final size:12
Alignment explanation
Indices: 19484--19515 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19474 CTCAGTACTG
19484 TACATGGGCTAA
1 TACATGGGCTAA
*
19496 TACATGGACTAA
1 TACATGGGCTAA
19508 TACATGGG
1 TACATGGG
19516 ATTATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (12 bp):
TACATGGGCTAA
Found at i:19776 original size:18 final size:18
Alignment explanation
Indices: 19753--19818 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
19743 AAATGTATTA
*
19753 CATGATAATAATAGAGAT
1 CATGATAATGATAGAGAT
**
19771 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
** *
19789 GTTGATAATGATAGATAT
1 CATGATAATGATAGAGAT
19807 CATGATAATGAT
1 CATGATAATGAT
19819 GTTGATAATG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:19783 original size:6 final size:6
Alignment explanation
Indices: 19754--19830 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
19744 AATGTATTAC
* * * * *
19754 ATGATA ATAATA GA-GATC ATGATA ATGATA TTGATG TTGATA ATGATA
1 ATGATA ATGATA -ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
* * *
19802 GAT-ATC ATGATA ATGATG TTGATA ATGAT
1 -ATGATA ATGATA ATGATA ATGATA ATGAT
19831 GGCATATATA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
5 3 0.06
6 47 0.89
7 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (6 bp):
ATGATA
Found at i:19803 original size:36 final size:36
Alignment explanation
Indices: 19755--19824 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
19745 ATGTATTACA
19755 TGATAATAATAGAGATCATGATAATGATATTGATGT
1 TGATAATAATAGAGATCATGATAATGATATTGATGT
* * *
19791 TGATAATGATAGATATCATGATAATGATGTTGAT
1 TGATAATAATAGAGATCATGATAATGATATTGAT
19825 AATGATGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (36 bp):
TGATAATAATAGAGATCATGATAATGATATTGATGT
Found at i:19829 original size:18 final size:18
Alignment explanation
Indices: 19772--19830 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
19762 AATAGAGATC
* *
19772 ATGATAATGATATTGATG
1 ATGATAATGATGTTGATA
* * *
19790 TTGATAATGATAGAT-ATC
1 ATGATAATGAT-GTTGATA
19808 ATGATAATGATGTTGATA
1 ATGATAATGATGTTGATA
19826 ATGAT
1 ATGAT
19831 GGCATATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 2 0.06
18 29 0.91
19 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (18 bp):
ATGATAATGATGTTGATA
Found at i:22766 original size:14 final size:13
Alignment explanation
Indices: 22734--22758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22724 TTATTTCACT
22734 GAAAATATTTTTA
1 GAAAATATTTTTA
22747 GAAAATATTTTT
1 GAAAATATTTTT
22759 TGTAAAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
GAAAATATTTTTA
Found at i:22930 original size:14 final size:14
Alignment explanation
Indices: 22913--22959 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
22903 TATTAAAATA
22913 ATTTATTTAATATT
1 ATTTATTTAATATT
22927 ATTTATGCTT-ATATT
1 ATTTAT--TTAATATT
22942 A-TTATTTAAATATT
1 ATTTATTT-AATATT
22956 ATTT
1 ATTT
22960 CTATAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.07
14 16 0.57
15 8 0.29
16 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:23070 original size:21 final size:23
Alignment explanation
Indices: 23045--23091 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23035 TCTTTAAAAA
*
23045 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
23066 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
23089 TAA
1 TAA
23092 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:23106 original size:23 final size:22
Alignment explanation
Indices: 23045--23107 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
23035 TCTTTAAAAA
* *
23045 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
23066 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
23089 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
23108 TATAATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:36895 original size:20 final size:21
Alignment explanation
Indices: 36774--36961 Score: 114
Period size: 20 Copynumber: 9.4 Consensus size: 21
36764 GACCAACAAT
*
36774 TTCGCAACCCAG--TTTCCAAA
1 TTCGCAACACAGAATTT-CAAA
* * *
36794 TTCACAACGCA-AATTTGTAAA
1 TTCGCAACACAGAATTT-CAAA
* *
36815 -TCGCAACACATAA-GTCAAA
1 TTCGCAACACAGAATTTCAAA
* *
36834 TTCGCAACACATAA-GTCAAA
1 TTCGCAACACAGAATTTCAAA
** *
36854 TTCGCAAC-GTGAATTTGTAAA
1 TTCGCAACACAGAATTT-CAAA
36875 -TCGCAACACAGAATTTCAAA
1 TTCGCAACACAGAATTTCAAA
*
36895 TTCGC-A-ACTGAATTTCAAA
1 TTCGCAACACAGAATTTCAAA
* * *
36914 TTCGCAAC-TAGATTTTCGAA
1 TTCGCAACACAGAATTTCAAA
*
36934 TTCGCAACAC-GAATTT-AAT
1 TTCGCAACACAGAATTTCAAA
36953 TTCGCAACA
1 TTCGCAACA
36962 GGTTTTAGTT
Statistics
Matches: 132, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
19 32 0.24
20 79 0.60
21 21 0.16
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCGCAACACAGAATTTCAAA
Found at i:36909 original size:19 final size:19
Alignment explanation
Indices: 36849--36960 Score: 102
Period size: 19 Copynumber: 5.7 Consensus size: 19
36839 AACACATAAG
36849 TCAAATTCGCAACGTGAATT
1 TCAAATTCGCAAC-TGAATT
* *
36869 TGTAAA-TCGCAACACAGAATT
1 T-CAAATTCGC-A-ACTGAATT
36890 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
36909 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
36929 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
36949 T-AATTTCGCAAC
1 TCAAATTCGCAAC
36961 AGGTTTTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
19 30 0.39
20 30 0.39
21 14 0.18
22 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:36913 original size:60 final size:61
Alignment explanation
Indices: 36790--36961 Score: 176
Period size: 60 Copynumber: 2.9 Consensus size: 61
36780 ACCCAGTTTC
* ** * *
36790 CAAATTCACAACGCAAATTTGTAAATCGCAACACATAA-GTCAAATTCGCAACACATAAGT
1 CAAATTCGCAACGTGAATTTGTAAATCGCAACACAGAATTTCAAATTCGCAACACATAAGT
** **
36850 CAAATTCGCAACGTGAATTTGTAAATCGCAACACAGAATTTCAAATTCGCAACTGA-ATTT
1 CAAATTCGCAACGTGAATTTGTAAATCGCAACACAGAATTTCAAATTCGCAACACATAAGT
* * *
36910 CAAATTCGCAAC-TAGATTTTCG-AATTCGCAACAC-GAATTT-AATTTCGCAACA
1 CAAATTCGCAACGT-GAATTT-GTAAATCGCAACACAGAATTTCAAATTCGCAACA
36962 GGTTTTAGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
58 10 0.10
59 7 0.07
60 64 0.67
61 15 0.16
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (61 bp):
CAAATTCGCAACGTGAATTTGTAAATCGCAACACAGAATTTCAAATTCGCAACACATAAGT
Found at i:36919 original size:40 final size:41
Alignment explanation
Indices: 36829--36961 Score: 141
Period size: 40 Copynumber: 3.3 Consensus size: 41
36819 AACACATAAG
* * *
36829 TCAAATTCGCAACACATAA-GTCAAATTCGCAACGTGAATT
1 TCAAATTCGCAACACAGAATTTCAAATTCGCAACATGAATT
*
36869 TGTAAA-TCGCAACACAGAATTTCAAATTCGCAAC-TGAATT
1 T-CAAATTCGCAACACAGAATTTCAAATTCGCAACATGAATT
* * * *
36909 TCAAATTCGCAAC-TAGATTTTCGAATTCGCAACACGAATT
1 TCAAATTCGCAACACAGAATTTCAAATTCGCAACATGAATT
*
36949 T-AATTTCGCAACA
1 TCAAATTCGCAACA
36962 GGTTTTAGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
39 30 0.38
40 33 0.42
41 16 0.20
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (41 bp):
TCAAATTCGCAACACAGAATTTCAAATTCGCAACATGAATT
Found at i:37138 original size:16 final size:16
Alignment explanation
Indices: 37117--37156 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
37107 TCCTCATCTC
*
37117 TAATTTTTTTTTTACA
1 TAATTTTTTTTCTACA
* *
37133 TAATTTTATTTCTATA
1 TAATTTTTTTTCTACA
37149 TAATTTTT
1 TAATTTTT
37157 CAATGATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATTTTTTTTCTACA
Found at i:37771 original size:12 final size:12
Alignment explanation
Indices: 37750--37783 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37740 ACCACATTTC
*
37750 CAATACCAAACA
1 CAATATCAAACA
37762 CAATATCAAACA
1 CAATATCAAACA
*
37774 CAATCTCAAA
1 CAATATCAAA
37784 ACCCACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:37960 original size:24 final size:24
Alignment explanation
Indices: 37909--37962 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37899 GTATTCAAAA
*
37909 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
37933 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
37957 TTTGAT
1 TTTGAT
37963 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:38752 original size:20 final size:20
Alignment explanation
Indices: 38729--38811 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
38719 AAACTTAAAT
*
38729 TCGCAACGCGAAAATGAAAA
1 TCGCAACGAGAAAATGAAAA
38749 TCGCAACGAGAAAATGAAAA
1 TCGCAACGAGAAAATGAAAA
38769 TCGCAACGAGAAAATGAAAA
1 TCGCAACGAGAAAATGAAAA
* *
38789 TCGCAACGCGAAACT-AAAA
1 TCGCAACGAGAAAATGAAAA
38808 TCGC
1 TCGC
38812 GTTGCGATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
19 8 0.13
20 52 0.87
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:39487 original size:20 final size:20
Alignment explanation
Indices: 39363--39493 Score: 133
Period size: 20 Copynumber: 6.5 Consensus size: 20
39353 TGTATTTCGC
* *
39363 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTCTGT
**
39384 GTTGCGAATTTGACTATC-AC
1 GTTGCGAATTTGACT-TCTGT
*
39404 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
39424 GTTGCGAAATTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
39444 GTTGCGGATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
39464 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
39484 GTTGC-AATTT
1 GTTGCGAATTT
39494 ACAAATTCGC
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
19 8 0.09
20 70 0.75
21 15 0.16
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:39515 original size:60 final size:59
Alignment explanation
Indices: 39387--39516 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 59
39377 ATTCAGTGTT
* * * ****
39387 GCGAATTTGACTATCACGTTGCGAATTTGACTTTTGTGTTGCGAAATTGACTTTTGTGTT
1 GCGAATTTGACTATCACGTTGCGAATTTGACTTCTGTGTTGC-AAATTGACATTCGCAAC
* * *
39447 GCGGATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGC-AATTTACAAATTCGCAAC
1 GCGAATTTGACTATCACGTTGCGAATTTGACTTCTGTGTTGCAAATTGAC--ATTCGCAAC
39507 GCGAATTTGA
1 GCGAATTTGA
39517 AAAATTGCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
58 6 0.11
60 51 0.89
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (59 bp):
GCGAATTTGACTATCACGTTGCGAATTTGACTTCTGTGTTGCAAATTGACATTCGCAAC
Found at i:41088 original size:64 final size:64
Alignment explanation
Indices: 41003--41163 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
40993 TTGTTTAAGG
* * * * *
41003 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAACAAAACATCGAATAGGATTTA
* * *
41067 TGCATCGATGCATAAGGAGTGCATTGATGCATCCCATTAAATACAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAACAAAACATCGAATAGGATTTA
* *
41131 TGCATTGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
41164 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 67 0.81
65 15 0.18
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAACAAAACATCGAATAGGATTTA
Found at i:42307 original size:30 final size:30
Alignment explanation
Indices: 42265--42350 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
42255 TATGGACAAT
* * *
42265 TTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTACCGAGGTTCTTTGTGACCTCTGGACAG
* * *
42295 TTGCCGAGGTTCTTTATGACCTCTGGATAG
1 TTACCGAGGTTCTTTGTGACCTCTGGACAG
*
42325 TTACCG-GGGTCTTTGTGACCTCTGGA
1 TTACCGAGGTTCTTTGTGACCTCTGGA
42351 TAGGTCCTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 18 0.38
30 29 0.62
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (30 bp):
TTACCGAGGTTCTTTGTGACCTCTGGACAG
Found at i:43737 original size:36 final size:37
Alignment explanation
Indices: 43688--43763 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
43678 ATAATATTAC
43688 AAATTGTAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTT-TTTAAAAAATT
* *
43725 AAATT-TATAATATTTATATAATTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTTTTAAAAAATT
43761 AAA
1 AAA
43764 AATATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
AAATTGTAAAATATTTATATAATTTTTTTAAAAAATT
Found at i:44712 original size:21 final size:21
Alignment explanation
Indices: 44683--44738 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
44673 AATTAGTTTG
*
44683 ATTAATTCGGTCGGCCACCGA
1 ATTAGTTCGGTCGGCCACCGA
44704 ATTAGTTCGGTCGGCCACCGA
1 ATTAGTTCGGTCGGCCACCGA
44725 ATTAGTTCGGTCGG
1 ATTAGTTCGGTCGG
44739 AGAACGGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.27
Consensus pattern (21 bp):
ATTAGTTCGGTCGGCCACCGA
Found at i:46999 original size:3 final size:3
Alignment explanation
Indices: 46991--47060 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
46981 TTTTACTTAA
** * *
46991 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47038 ATT A-T ATAT ATT A-T ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT
47061 TAATAAATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:47012 original size:18 final size:18
Alignment explanation
Indices: 46991--47059 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
46981 TTTTACTTAA
46991 ATTATTATTATTA-AAATT
1 ATTATTATTATTATAAA-T
47009 ATTATTATTATTATAAAT
1 ATTATTATTATTATAAAT
*
47027 ATTATTATTATATTATATAT
1 ATTATTA-T-TATTATAAAT
47047 ATTA-TATTATTAT
1 ATTATTATTATTAT
47060 TTAATAAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
17 6 0.13
18 22 0.47
19 6 0.13
20 13 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTATTATTATAAAT
Found at i:47029 original size:15 final size:15
Alignment explanation
Indices: 46988--47072 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 15
46978 TCATTTTACT
46988 TAAATTATTATTATTA
1 TAAA-TATTATTATTA
*
47004 AAATTATTATTATTATTA
1 TAA--A-TATTATTATTA
47022 TAAATATTATTATTA
1 TAAATATTATTATTA
*
47037 T-ATTA-TATATATTA
1 TAAATATTAT-TATTA
* *
47051 T-ATTATTATT-TAA
1 TAAATATTATTATTA
47064 TAAATATTA
1 TAAATATTA
47073 CAAACCCAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
13 6 0.10
14 20 0.34
15 15 0.25
16 3 0.05
18 15 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTATTATTA
Found at i:47054 original size:22 final size:22
Alignment explanation
Indices: 47008--47072 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
46998 TTATTAAAAT
47008 TATTATTATTATTATAAATA-T-
1 TATTATTA-TATTATAAATATTA
*
47029 TATTATTATATTATATATATTA
1 TATTATTATATTATAAATATTA
47051 TATTATTAT-TTAATAAATATTA
1 TATTATTATATT-ATAAATATTA
47073 CAAACCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.26
21 11 0.28
22 18 0.46
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATTATATTATAAATATTA
Found at i:47755 original size:13 final size:13
Alignment explanation
Indices: 47739--47766 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47729 GGTTGGCGGT
47739 GGCTATCGGCGCC
1 GGCTATCGGCGCC
47752 GGCTATCGGCGCC
1 GGCTATCGGCGCC
47765 GG
1 GG
47767 AATTCCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.36, G:0.43, T:0.14
Consensus pattern (13 bp):
GGCTATCGGCGCC
Found at i:48337 original size:27 final size:27
Alignment explanation
Indices: 48307--48388 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
48297 TTAAATGTGT
48307 TCATTTATTTTACTGCTTTTAAATATA
1 TCATTTATTTTACTGCTTTTAAATATA
* *
48334 TCATTCTAATTGTA-T--TTTT--ATCGT-
1 TCATT-T-ATTTTACTGCTTTTAAAT-ATA
48358 T-ATTTATTTTACTGCTTTTAAATATA
1 TCATTTATTTTACTGCTTTTAAATATA
48384 TCATT
1 TCATT
48389 CTAATTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 20
0.63 0.06 0.31
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 3 0.07
24 7 0.17
25 2 0.05
26 7 0.17
27 8 0.20
28 2 0.05
29 5 0.12
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (27 bp):
TCATTTATTTTACTGCTTTTAAATATA
Found at i:48371 original size:50 final size:50
Alignment explanation
Indices: 48309--48404 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
48299 AAATGTGTTC
48309 ATTTATTTTACTGCTTTTAAATATATCATTCTAATTGTATTTTTATCGTT
1 ATTTATTTTACTGCTTTTAAATATATCATTCTAATTGTATTTTTATCGTT
48359 ATTTATTTTACTGCTTTTAAATATATCATTCTAATTGTATTTTTAT
1 ATTTATTTTACTGCTTTTAAATATATCATTCTAATTGTATTTTTAT
48405 TGTTTTATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.58
Consensus pattern (50 bp):
ATTTATTTTACTGCTTTTAAATATATCATTCTAATTGTATTTTTATCGTT
Found at i:48476 original size:24 final size:23
Alignment explanation
Indices: 48448--48498 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
48438 AAATATATAT
48448 AATAAATAATAATTT-ATATTTTTC
1 AATAAAT--TAATTTAATATTTTTC
*
48472 AATAAATTATTTTAATATTTTTC
1 AATAAATTAATTTAATATTTTTC
48495 AATA
1 AATA
48499 TCGAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 13 0.52
24 7 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAAATTAATTTAATATTTTTC
Found at i:55972 original size:83 final size:83
Alignment explanation
Indices: 55764--56188 Score: 742
Period size: 83 Copynumber: 5.1 Consensus size: 83
55754 AAATGCCATA
* * * *
55764 TGCTCATAGCATATTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
55829 GAATTTGGAAAGATGAATG
66 GAATTT-GAAAGATGAATG
55848 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
*
55913 GAATTTGAGAGATGAATG
66 GAATTTGAAAGATGAATG
*
55931 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
55996 GAATTTGAAAGATGAATG
66 GAATTTGAAAGATGAATG
56014 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
*
56079 GAATTTGAGAGATGAATG
66 GAATTTGAAAGATGAATG
* *
56097 TTCTCATAGCGTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
* *
56162 GAATTTAAAAGATGAATT
66 GAATTTGAAAGATGAATG
56180 TGCTCATAG
1 TGCTCATAG
56189 TAAAAATAAG
Statistics
Matches: 326, Mismatches: 15, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
83 259 0.79
84 67 0.21
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
GAATTTGAAAGATGAATG
Found at i:57482 original size:74 final size:75
Alignment explanation
Indices: 57390--57561 Score: 222
Period size: 74 Copynumber: 2.3 Consensus size: 75
57380 ATTAACAAGA
* * *
57390 AGCAAATATTGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
*
57455 TA-TT-TATC
66 CACTTGTATC
* * ** *
57463 AGCAAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGA
*
57528 ACACTTGTATT
65 ACACTTGTATC
*
57539 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
57562 GGCCCACAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 3 0.04
74 55 0.65
75 21 0.25
76 6 0.07
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:58530 original size:54 final size:54
Alignment explanation
Indices: 58445--58601 Score: 206
Period size: 54 Copynumber: 2.9 Consensus size: 54
58435 CATCAATCCC
* * * *
58445 AGCAGAAGCCACATGAGAGGATGAATATGTTGTCAAATGTTTTACGAACATCTG
1 AGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTG
* * *
58499 AGCAGAAACTACAGGAAATGATGAATGTGTTGTCAAAAGTTTTACGAACATCTG
1 AGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTG
* * ***
58553 AGCAGAAGCCACATGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 AGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
58602 CTGCTATTCT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (54 bp):
AGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTG
Found at i:58981 original size:22 final size:22
Alignment explanation
Indices: 58952--59006 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
58942 ATCTACACTC
*
58952 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
58974 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
58996 TTCAAAGATGA
1 TTCAAAGATGA
59007 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:59817 original size:77 final size:76
Alignment explanation
Indices: 59672--60083 Score: 752
Period size: 76 Copynumber: 5.4 Consensus size: 76
59662 CTATTTCCCA
*
59672 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
59737 AGCCTTAGGGT
66 AGCCTTCGGGT
*
59748 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
59813 AAGCCTTAGGGT
65 AAGCCTTCGGGT
59825 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
59890 AAGCCTTCGGGT
65 AAGCCTTCGGGT
59902 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
59967 AGCCTTCGGGT
66 AGCCTTCGGGT
59978 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60043 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
60054 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTT
60084 TTTAAGACCT
Statistics
Matches: 331, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
76 180 0.54
77 151 0.46
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:59846 original size:153 final size:152
Alignment explanation
Indices: 59672--60083 Score: 761
Period size: 153 Copynumber: 2.7 Consensus size: 152
59662 CTATTTCCCA
*
59672 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
59737 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTT
59802 TGATGTTTTCAAAGCCTTAGGGT
130 TGATGTTTTCAAAGCCTTAGGGT
59825 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
59890 AAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
59955 TGATGTTTTCAAAGCCTTCGGGT
130 TGATGTTTTCAAAGCCTTAGGGT
59978 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
60043 AGCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
60084 TTTAAGACCT
Statistics
Matches: 252, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
152 72 0.29
153 106 0.42
154 74 0.29
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGT
Found at i:60246 original size:3 final size:3
Alignment explanation
Indices: 60238--60310 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
60228 TTTTACTTAA
** * *
60238 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
60286 ATA ATAT ATAT ATT A-T ATT ATT ATT
1 ATT AT-T AT-T ATT ATT ATT ATT ATT
60311 TAATAAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:61007 original size:13 final size:13
Alignment explanation
Indices: 60991--61018 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60981 GGTTGGCGGT
60991 GGCTATCGGCGCC
1 GGCTATCGGCGCC
61004 GGCTATCGGCGCC
1 GGCTATCGGCGCC
61017 GG
1 GG
61019 AATTCCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.36, G:0.43, T:0.14
Consensus pattern (13 bp):
GGCTATCGGCGCC
Found at i:61627 original size:50 final size:50
Alignment explanation
Indices: 61559--61654 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
61549 AAATGTGTTC
61559 ATTTATTTTAATGCTTTTAAATATATCATTCTAATTGTATTTTTATCGTT
1 ATTTATTTTAATGCTTTTAAATATATCATTCTAATTGTATTTTTATCGTT
* *
61609 ATTTATTTTACTGTTTTTAAATATATCATTCTAATTGTATTTTTAT
1 ATTTATTTTAATGCTTTTAAATATATCATTCTAATTGTATTTTTAT
61655 TGCTTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.59
Consensus pattern (50 bp):
ATTTATTTTAATGCTTTTAAATATATCATTCTAATTGTATTTTTATCGTT
Found at i:61726 original size:21 final size:23
Alignment explanation
Indices: 61702--61750 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
61692 ATATATAATA
61702 AATA-ATAA-TTT-ATATTTTTTC
1 AATATATAATTTTAATA-TTTTTC
*
61723 AATATATTATTTTAATATTTTTC
1 AATATATAATTTTAATATTTTTC
61746 AATAT
1 AATAT
61751 CGAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 3 0.12
23 14 0.58
24 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATATAATTTTAATATTTTTC
Found at i:62331 original size:2 final size:2
Alignment explanation
Indices: 62324--62365 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
62314 ATTTGAGATT
62324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62366 GCAGATAGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67185 original size:45 final size:46
Alignment explanation
Indices: 67121--67224 Score: 151
Period size: 45 Copynumber: 2.3 Consensus size: 46
67111 AAGGAACAGG
* *
67121 GGGTGGCGG-GGGTGGTGAGGGTGTTGTTGATGAACCAGTTGT-TGT
1 GGGTGGAGGTGGG-GGTGAGGGTGTTGTTGATGAACCAGTTGTGGGT
67166 GGGTGGAGGTGGGGGTGAGGGTGTTGTTGATGAACCAGTTGTGGGT
1 GGGTGGAGGTGGGGGTGAGGGTGTTGTTGATGAACCAGTTGTGGGT
*
67212 GGG-GGTGGTGGGG
1 GGGTGGAGGTGGGG
67225 CTGGTGCTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
45 46 0.85
46 8 0.15
ACGTcount: A:0.11, C:0.05, G:0.57, T:0.28
Consensus pattern (46 bp):
GGGTGGAGGTGGGGGTGAGGGTGTTGTTGATGAACCAGTTGTGGGT
Found at i:67290 original size:36 final size:36
Alignment explanation
Indices: 67250--67370 Score: 134
Period size: 36 Copynumber: 3.3 Consensus size: 36
67240 TAGTTGGTGA
* *
67250 TGGTGGTGGGAATGCAGATGATGTAACAATTGGGGGTGG
1 TGGTGGTGGGAGTGCAGATGATGAAACAATT--GGG-GG
* ** *
67289 TGGTGGTGGGGGTGCAGACAATGAAACAATTGAGGG
1 TGGTGGTGGGAGTGCAGATGATGAAACAATTGGGGG
* *
67325 TGGTGGTGGGAGTGCTGATGATGAAACAATTGGGGT
1 TGGTGGTGGGAGTGCAGATGATGAAACAATTGGGGG
*
67361 TGGTAGTGGG
1 TGGTGGTGGG
67371 GATGGTGCAG
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
36 41 0.59
37 2 0.03
39 26 0.38
ACGTcount: A:0.23, C:0.06, G:0.46, T:0.25
Consensus pattern (36 bp):
TGGTGGTGGGAGTGCAGATGATGAAACAATTGGGGG
Found at i:67293 original size:39 final size:39
Alignment explanation
Indices: 67245--67369 Score: 139
Period size: 39 Copynumber: 3.3 Consensus size: 39
67235 TGATATAGTT
* * *
67245 GGTGATGGTGGTGGGAATGCAGATGATGTAACAATTGGG
1 GGTGGTGGTGGTGGGAGTGCAGATGATGAAACAATTGGG
* **
67284 GGTGGTGGTGGTGGGGGTGCAGACAATGAAACAATT--G
1 GGTGGTGGTGGTGGGAGTGCAGATGATGAAACAATTGGG
* *
67321 AG-GGTGGTGGTGGGAGTGCTGATGATGAAACAATTGGG
1 GGTGGTGGTGGTGGGAGTGCAGATGATGAAACAATTGGG
* *
67359 GTTGGTAGTGG
1 GGTGGTGGTGG
67370 GGATGGTGCA
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
36 29 0.42
37 2 0.03
38 1 0.01
39 37 0.54
ACGTcount: A:0.23, C:0.06, G:0.46, T:0.25
Consensus pattern (39 bp):
GGTGGTGGTGGTGGGAGTGCAGATGATGAAACAATTGGG
Found at i:67456 original size:39 final size:37
Alignment explanation
Indices: 67401--67476 Score: 75
Period size: 39 Copynumber: 2.0 Consensus size: 37
67391 TGATACAGTT
* *
67401 GGAGGT-GGTAGGGGTGCAGATGATGAAACAGTTGGG
1 GGAGGTGGGTGGGGGTGCAGATGATGAAACAATTGGG
* *
67437 GGAGGTGGTGTGGGTGGTGCTA-ATGATGATACAGTTGGG
1 GGAGGTGG-GTGGG-GGTGC-AGATGATGAAACAATTGGG
67476 G
1 G
67477 CTTGTGGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 6 0.18
37 1 0.03
38 4 0.12
39 22 0.65
40 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.50, T:0.24
Consensus pattern (37 bp):
GGAGGTGGGTGGGGGTGCAGATGATGAAACAATTGGG
Found at i:67465 original size:117 final size:114
Alignment explanation
Indices: 67290--67512 Score: 288
Period size: 117 Copynumber: 1.9 Consensus size: 114
67280 TGGGGGTGGT
* * *
67290 GGTGGTGGGGGTGCAGACAATGAAACAATTGAGGGTGGTGGTGGGAGTGCTGATGATGAAACAAT
1 GGTGGTAGGGGTGCAGACAATGAAACAATTGAGGGAGGTGGTGGGAGTGCTAATGATGAAACAAT
67355 TGGGG-TTGGTAGTGGG-GATGGTGCAGGTGCTGATGATGATACAGTTGGA
66 TGGGGCTT-GTAGTGGGCG-TGGTGCAGGTGCTGATGATGATACAGTTGGA
** * * * *
67404 GGTGGTAGGGGTGCAGATGATGAAACAGTTGGGGGAGGTGGTGTGGGTGGTGCTAATGATGATAC
1 GGTGGTAGGGGTGCAGACAATGAAACAATTGAGGGAGGT-G-GTGGG-AGTGCTAATGATGAAAC
* *
67469 AGTTGGGGCTTGTGGTGGGCGTGGTGCAGGTGCTGATGATGATA
63 AATTGGGGCTTGTAGTGGGCGTGGTGCAGGTGCTGATGATGATA
67513 TAATTGGGGC
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
114 33 0.35
115 1 0.01
116 5 0.05
117 51 0.55
118 3 0.03
ACGTcount: A:0.21, C:0.07, G:0.46, T:0.26
Consensus pattern (114 bp):
GGTGGTAGGGGTGCAGACAATGAAACAATTGAGGGAGGTGGTGGGAGTGCTAATGATGAAACAAT
TGGGGCTTGTAGTGGGCGTGGTGCAGGTGCTGATGATGATACAGTTGGA
Found at i:67484 original size:39 final size:40
Alignment explanation
Indices: 67413--67595 Score: 127
Period size: 45 Copynumber: 4.4 Consensus size: 40
67403 AGGTGGTAGG
* * ***
67413 GGTGCAGATGATGAAACAGTTGGGGGAGGTGGTGTGG-GT
1 GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGTGGTGT
* *
67452 GGTGCTAATGATGATACAGTTGGGGCTTGTGGTGGGCGTGGTGCA
1 GGTGCTGATGATGATACAGTTGGGGCTTGTGGT----GTGGTG-T
* * *
67497 GGTGCTGATGATGATATAATTGGGGCTTGTTGTGGGGGTGGTGT
1 GGTGCTGATGATGATACAGTTGGGGC---TTGT-GGTGTGGTGT
* * *
67541 GGGTGCTGATGATGATACAGTTGGGGCTCGAGGTG-GGGGT
1 -GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGTGGTGT
* *
67581 GGTGCGGATGCTGAT
1 GGTGCTGATGATGAT
67596 GAGGAAATAA
Statistics
Matches: 113, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
39 40 0.35
40 4 0.04
41 3 0.03
42 2 0.02
43 4 0.04
44 1 0.01
45 53 0.47
48 4 0.04
49 2 0.02
ACGTcount: A:0.16, C:0.08, G:0.48, T:0.28
Consensus pattern (40 bp):
GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGTGGTGT
Found at i:67625 original size:90 final size:90
Alignment explanation
Indices: 67452--67654 Score: 255
Period size: 90 Copynumber: 2.3 Consensus size: 90
67442 TGGTGTGGGT
* * * * *
67452 GGTGCTAATGATGATACAGTTGGGGCTTGTGGTGGGCGTGGTGCAGGTGCTGATGATGATATAAT
1 GGTGCTGATGATGATACAGTTGGGGCTCGAGGTGGGCGTGGTGCAGGTGCTGATGAGGAAATAAT
* * * *
67517 TGGGGCTTGTTGTGGGGGTGGTGTG
66 TGGGGCTTCTGGTGGGGGTGATGCG
*
67542 GGTGCTGATGATGATACAGTTGGGGCTCGAGGTGGGGGTGGTGC-GGATGCTGATGAGGAAATAA
1 GGTGCTGATGATGATACAGTTGGGGCTCGAGGTGGGCGTGGTGCAGG-TGCTGATGAGGAAATAA
*
67606 TTGGGGCTTCTGGTTGGGGTGATGCG
65 TTGGGGCTTCTGGTGGGGGTGATGCG
* * * *
67632 GGTGATGATAATGAAACAATTGG
1 GGTGCTGATGATGATACAGTTGG
67655 ACCAGTTATA
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 2 0.02
90 95 0.98
ACGTcount: A:0.18, C:0.08, G:0.44, T:0.29
Consensus pattern (90 bp):
GGTGCTGATGATGATACAGTTGGGGCTCGAGGTGGGCGTGGTGCAGGTGCTGATGAGGAAATAAT
TGGGGCTTCTGGTGGGGGTGATGCG
Found at i:67653 original size:45 final size:45
Alignment explanation
Indices: 67452--67654 Score: 210
Period size: 45 Copynumber: 4.5 Consensus size: 45
67442 TGGTGTGGGT
* * * * *
67452 GGTGCTAATGATGATACAGTTGGGGCTTGTGGTGGGCGTGGTGCA
1 GGTGCTGATGATGATACAATTGGGGCTTCTGGTGGGGGTGGTGCG
* * * *
67497 GGTGCTGATGATGATATAATTGGGGCTTGTTGTGGGGGTGGTGTG
1 GGTGCTGATGATGATACAATTGGGGCTTCTGGTGGGGGTGGTGCG
* *
67542 GGTGCTGATGATGATACAGTTGGGGC-TCGAGGTGGGGGTGGTGCG
1 GGTGCTGATGATGATACAATTGGGGCTTC-TGGTGGGGGTGGTGCG
* * * * * *
67587 GATGCTGATGAGGAAATAATTGGGGCTTCTGGTTGGGGTGATGCG
1 GGTGCTGATGATGATACAATTGGGGCTTCTGGTGGGGGTGGTGCG
* * *
67632 GGTGATGATAATGAAACAATTGG
1 GGTGCTGATGATGATACAATTGG
67655 ACCAGTTATA
Statistics
Matches: 130, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.01
45 127 0.98
46 2 0.02
ACGTcount: A:0.18, C:0.08, G:0.44, T:0.29
Consensus pattern (45 bp):
GGTGCTGATGATGATACAATTGGGGCTTCTGGTGGGGGTGGTGCG
Found at i:79988 original size:22 final size:23
Alignment explanation
Indices: 79963--80008 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
79953 AACTTAAAGG
79963 ATTAAAATGGC-AAAA-ACAGAAA
1 ATTAAAA-GGCTAAAATACAGAAA
*
79985 ATTAAAAGGCTAAAATAGAGAAA
1 ATTAAAAGGCTAAAATACAGAAA
80008 A
1 A
80009 CAGAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.52
23 7 0.33
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (23 bp):
ATTAAAAGGCTAAAATACAGAAA
Found at i:79990 original size:30 final size:30
Alignment explanation
Indices: 79956--80061 Score: 117
Period size: 30 Copynumber: 3.5 Consensus size: 30
79946 AAACATGAAC
* *
79956 TTAAAGGATTAAAATGGCAAAAACAGAAAA
1 TTAAAGGACTAAAATAGCAAAAACAGAAAA
*
79986 TTAAAAGG-CTAAAATAG-AGAAAACAGAAAT
1 TT-AAAGGACTAAAATAGCA-AAAACAGAAAA
* *
80016 TTAAAGGACAAAAATAGCAAAAACAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAA
* *
80046 TTAGATGACTAAAATA
1 TTAAAGGACTAAAATA
80062 AAATATTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.09
30 52 0.81
31 6 0.09
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACAGAAAA
Done.