Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004215.1 Kokia drynarioides strain JFW-HI SEQ_117464, 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: 159228
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:7932 original size:18 final size:18
Alignment explanation
Indices: 7909--7945 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
7899 GTATCTAATA
*
7909 TTGCTCCTTGTAATTATT
1 TTGCTCCTTGTAAATATT
7927 TTGCTCCTTGTAAATATT
1 TTGCTCCTTGTAAATATT
7945 T
1 T
7946 GGCAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.54
Consensus pattern (18 bp):
TTGCTCCTTGTAAATATT
Found at i:8463 original size:49 final size:48
Alignment explanation
Indices: 8410--8738 Score: 174
Period size: 49 Copynumber: 6.7 Consensus size: 48
8400 AGAAAATGCA
* *
8410 GTACCATGAAGATAATAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
1 GTACC-TGAAGATAAGAAGGGAAAGATTTAAGTCGCAACGACGAACCTT
* * * * *
8459 GTACCTCAGAAGCAT--GAAGGGAAAGATTTAAGCCACAACGGCAAATCC-A
1 GTACCT--GAAG-ATAAGAAGGGAAAGATTTAAGTCGCAACGACGAA-CCTT
* * *
8508 GTAACAC-GAAGATAATG-GGGGAAAGGTTTAAGTCGCAACGATGAACCTT
1 GT-AC-CTGAAGATAA-GAAGGGAAAGATTTAAGTCGCAACGACGAACCTT
**
8557 GTACCTCAGAAGCAT--GAAGGGAAAGATTTAAG-CTGCAACGAC-AAATTT
1 GTACCT--GAAG-ATAAGAAGGGAAAGATTTAAGTC-GCAACGACGAACCTT
* * * * *
8605 AGTACCACGAAGATACGAAAGGAAATG-TTTAAGTCGCAACGGCGAACCCT
1 -GTACC-TGAAGATAAGAAGGGAAA-GATTTAAGTCGCAACGACGAACCTT
* * * * * * * *
8655 GTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGATGAATCTA
1 GTACCTGAAGA-TAAGAAGGGAAAGATTTAAGTCGCAACGACGAACCTT
* * * *
8704 GTACCGCGAAGACATGAAGGGAAAGATTGAAGTCG
1 GTACC-TGAAGATAAGAAGGGAAAGATTTAAGTCG
8739 TAACAGTAAA
Statistics
Matches: 211, Mismatches: 43, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
47 5 0.02
48 23 0.11
49 157 0.74
50 21 0.10
51 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (48 bp):
GTACCTGAAGATAAGAAGGGAAAGATTTAAGTCGCAACGACGAACCTT
Found at i:8542 original size:98 final size:98
Alignment explanation
Indices: 8368--8738 Score: 440
Period size: 98 Copynumber: 3.8 Consensus size: 98
8358 TCATTACCAT
* * * * * * *
8368 GAAGACATGAAGGAAAAGATTTAAGCCGTAACAGAAAATGCAGTACCATGAAGATAATAAGGGAA
1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATAATGAGGGAA
8433 AGGTTTAAGTCGCAACGACGAACCTTGTACCTCA
65 AGGTTTAAGTCGCAACGACGAACCTTGTACCTCA
* * *
8467 GAAGCATGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTAACACGAAGATAATGGGGGAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATAATGAGGGAAA
*
8532 GGTTTAAGTCGCAACGATGAACCTTGTACCTCA
66 GGTTTAAGTCGCAACGACGAACCTTGTACCTCA
* * ** * *
8565 GAAGCATGAAGGGAAAGATTTAAGCTGCAACGACAAATTTAGTACCACGAAGAT-ACGAAAGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATAATG-AGGGAA
* * *
8629 ATGTTTAAGTCGCAACGGCGAACCCTGTACCTCA
65 AGGTTTAAGTCGCAACGACGAACCTTGTACCTCA
* *** * * *
8663 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGATGAATCTAGTACCGCGAAGA-CATGAAGGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATAATG-AGGGAA
* *
8727 AGATTGAAGTCG
65 AGGTTTAAGTCG
8739 TAACAGTAAA
Statistics
Matches: 235, Mismatches: 35, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
97 2 0.01
98 229 0.97
99 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (98 bp):
GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGATAATGAGGGAAA
GGTTTAAGTCGCAACGACGAACCTTGTACCTCA
Found at i:8728 original size:196 final size:197
Alignment explanation
Indices: 8368--8738 Score: 487
Period size: 196 Copynumber: 1.9 Consensus size: 197
8358 TCATTACCAT
* * * *
8368 GAAGACATGAAGGAAAAGATTTAAGCCGTAACAGAAAATGCAGTACCATGAAGATAATAAGGGAA
1 GAAGACATGAAGGAAAAGATTTAAGCCGCAACAGAAAATGCAGTACCACGAAGATAAGAAAGGAA
* *
8433 AGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCACAAC
66 AGGTTTAAGTCGCAACGACGAACCCTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCACAAC
* * * *
8498 GGCAAATCCAGTAACACGAAGATAATGGGGGAAAGGTTTAAGTCGCAACGATGAACCTTGTACCT
131 GACAAATCCAGTAACACGAAGATAATGAGGGAAAGATTGAAGTCGCAACGATGAACCTTGTACCT
8563 CA
196 CA
* * ** *
8565 GAAG-CATGAAGGGAAAGATTTAAGCTGCAAC-GACAAATTTAGTACCACGAAGATACGAAAGGA
1 GAAGACATGAAGGAAAAGATTTAAGCCGCAACAGA-AAATGCAGTACCACGAAGATAAGAAAGGA
* * *
8628 AATGTTTAAGTCGCAACGGCGAACCCTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAA
65 AAGGTTTAAGTCGCAACGACGAACCCTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCACAA
** * * * *
8693 CGATGAATCTAGTACCGCGAAGA-CATGAAGGGAAAGATTGAAGTCG
130 CGACAAATCCAGTAACACGAAGATAATG-AGGGAAAGATTGAAGTCG
8739 TAACAGTAAA
Statistics
Matches: 148, Mismatches: 24, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
195 5 0.03
196 139 0.94
197 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (197 bp):
GAAGACATGAAGGAAAAGATTTAAGCCGCAACAGAAAATGCAGTACCACGAAGATAAGAAAGGAA
AGGTTTAAGTCGCAACGACGAACCCTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCACAAC
GACAAATCCAGTAACACGAAGATAATGAGGGAAAGATTGAAGTCGCAACGATGAACCTTGTACCT
CA
Found at i:10826 original size:13 final size:13
Alignment explanation
Indices: 10808--10835 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10798 CAAAAGAATG
10808 ATTCATTTACTTT
1 ATTCATTTACTTT
10821 ATTCATTTACTTT
1 ATTCATTTACTTT
10834 AT
1 AT
10836 ATATATATAT
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:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTCATTTACTTT
Found at i:25654 original size:93 final size:93
Alignment explanation
Indices: 25495--25680 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
25485 AGAATAGAGG
25495 AGGATGAAACTTGCAACTTTTAAAGGCTATAAATAGAGGAAAGAAGAGGAGGAAAAATCATCAAG
1 AGGATGAAACTTGCAACTTTTAAAGGCTATAAATAGAGGAAAGAAGAGGAGGAAAAATCATCAAG
25560 AGGTAGAAGAATTAAATTCTACAATTAC
66 AGGTAGAAGAATTAAATTCTACAATTAC
25588 AGGATGAAACTTGCAACTTTTAAAGGCTATAAATAGAGGAAAGAAGAGGAGGAAAAATCATCAAG
1 AGGATGAAACTTGCAACTTTTAAAGGCTATAAATAGAGGAAAGAAGAGGAGGAAAAATCATCAAG
25653 AGGTAGAAGAATTAAATTCTACAATTAC
66 AGGTAGAAGAATTAAATTCTACAATTAC
25681 TTTGTGTTTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (93 bp):
AGGATGAAACTTGCAACTTTTAAAGGCTATAAATAGAGGAAAGAAGAGGAGGAAAAATCATCAAG
AGGTAGAAGAATTAAATTCTACAATTAC
Found at i:30566 original size:18 final size:20
Alignment explanation
Indices: 30529--30568 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
30519 TTATAACTCT
30529 AATAAAATAAAAATCCTAAA
1 AATAAAATAAAAATCCTAAA
30549 AATAAAAT-AAAA-CCTAAA
1 AATAAAATAAAAATCCTAAA
30567 AA
1 AA
30569 CCCTAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
AATAAAATAAAAATCCTAAA
Found at i:35984 original size:18 final size:18
Alignment explanation
Indices: 35961--35995 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35951 TCGGCGTAGA
35961 AAAAGAAAACAAAGAAAC
1 AAAAGAAAACAAAGAAAC
*
35979 AAAAGAAAATAAAGAAA
1 AAAAGAAAACAAAGAAA
35996 ACGACATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAGAAAACAAAGAAAC
Found at i:37797 original size:47 final size:47
Alignment explanation
Indices: 37743--37839 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
37733 TAAAAATGGA
*
37743 ACTGATATATGCTTCTGCTACATGCCATATTCCTATAAGAATAGATC
1 ACTGATATATACTTCTGCTACATGCCATATTCCTATAAGAATAGATC
*
37790 ACTGATATATACTTCTGCTGCATGCCATATTCCTATAAGAATAGATC
1 ACTGATATATACTTCTGCTACATGCCATATTCCTATAAGAATAGATC
37837 ACT
1 ACT
37840 TACGATATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (47 bp):
ACTGATATATACTTCTGCTACATGCCATATTCCTATAAGAATAGATC
Found at i:40626 original size:20 final size:19
Alignment explanation
Indices: 40601--40652 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
40591 GATCAATAAC
40601 TATACCAAAATTTCTAATG
1 TATACCAAAATTTCTAATG
* *
40620 TTATACCAATATATCTAATG
1 -TATACCAAAATTTCTAATG
*
40640 TGTACCAAAATTT
1 TATACCAAAATTT
40653 TTAAGAGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (19 bp):
TATACCAAAATTTCTAATG
Found at i:40724 original size:20 final size:19
Alignment explanation
Indices: 40680--40741 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
40670 ATATTTTAAC
40680 ATATCAAAATTTATAATGA
1 ATATCAAAATTTATAATGA
*
40699 ATATCAAAATTTCTAACGTG-
1 ATATCAAAATTTATAA--TGA
* *
40719 ATATCAATATTTTTAATGA
1 ATATCAAAATTTATAATGA
40738 ATAT
1 ATAT
40742 AGTTGTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.05
19 19 0.51
20 14 0.38
21 2 0.05
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (19 bp):
ATATCAAAATTTATAATGA
Found at i:42883 original size:21 final size:22
Alignment explanation
Indices: 42857--42904 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42847 GATAATATTG
* *
42857 ATTTTAGAAT-ATTTTGTTTAT
1 ATTTTAAAATCATTTTATTTAT
*
42878 ATTTTAAAATCATTTTATTTTT
1 ATTTTAAAATCATTTTATTTAT
42900 ATTTT
1 ATTTT
42905 TTGAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
ATTTTAAAATCATTTTATTTAT
Found at i:44565 original size:22 final size:22
Alignment explanation
Indices: 44540--44589 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
44530 ACGTGTCTGA
*
44540 AGACATTTGCTC-ATATGTCTTG
1 AGACATTTACTCTA-ATGTCTTG
*
44562 AGACAATTACTCTAATGTCTTG
1 AGACATTTACTCTAATGTCTTG
44584 AGACAT
1 AGACAT
44590 GACTCCTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (22 bp):
AGACATTTACTCTAATGTCTTG
Found at i:47457 original size:20 final size:21
Alignment explanation
Indices: 47432--47484 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
47422 ATTTTTACTT
47432 TTATATACTTTTTA-A-ATTTA
1 TTATATA-TTTTTATATATTTA
47452 TTATATATTTTTATATATTTA
1 TTATATATTTTTATATATTTA
*
47473 TTTTAT-TTTTTA
1 TTATATATTTTTA
47485 GAATTAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 6 0.20
20 14 0.47
21 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATATATTTTTATATATTTA
Found at i:51154 original size:14 final size:15
Alignment explanation
Indices: 51128--51164 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
51118 ATAATTATTA
*
51128 CTCTTTTTCTTTTGT
1 CTCTTTTTATTTTGT
51143 CT-TTTTTATTTTGT
1 CTCTTTTTATTTTGT
51157 CTCTTTTT
1 CTCTTTTT
51165 GATTGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
CTCTTTTTATTTTGT
Found at i:53053 original size:11 final size:11
Alignment explanation
Indices: 53020--53062 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
53010 GGGTGAAAAT
53020 AATTATATAATA
1 AATTATATAA-A
53032 AATT-TATTAAA
1 AATTATA-TAAA
53043 AATTATATAAA
1 AATTATATAAA
*
53054 AGTTATATA
1 AATTATATA
53063 TGTTTTTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
AATTATATAAA
Found at i:55873 original size:27 final size:27
Alignment explanation
Indices: 55818--55867 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
55808 AATAGAAGTT
*
55818 TTAAAATATTTTATTTTTATAAAATTA
1 TTAAAATATTTTATTTTAATAAAATTA
55845 TTAAAAT-TTTTA-TTTAATAAAAT
1 TTAAAATATTTTATTTTAATAAAAT
55868 CATATTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 5 0.23
27 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAAATATTTTATTTTAATAAAATTA
Found at i:82061 original size:21 final size:21
Alignment explanation
Indices: 82036--82099 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
82026 AGCTCTCTGG
82036 AGTAAGACTTGTTTCGGTAGA
1 AGTAAGACTTGTTTCGGTAGA
*
82057 AGTAAGACTTGTTTCAGTAGA
1 AGTAAGACTTGTTTCGGTAGA
* * * *
82078 AGTTACACTTATATCGGTAGA
1 AGTAAGACTTGTTTCGGTAGA
82099 A
1 A
82100 CTTTCTCAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (21 bp):
AGTAAGACTTGTTTCGGTAGA
Found at i:83923 original size:99 final size:99
Alignment explanation
Indices: 83752--83949 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
83742 GCTATGCGAA
*
83752 ATTTGTGCCATGTCAGATCATCCGATGGATTTGTGTCCTATTTTACATGATGGCACGACAGAACA
1 ATTTGTGCCATGTCAGATCATCCGACGGATTTGTGTCCTATTTTACATGATGGCACGACAGAACA
83817 AGCTAATGTAGTCGGGAACTTTCCAAGGCCACCC
66 AGCTAATGTAGTCGGGAACTTTCCAAGGCCACCC
83851 ATTTGTGCCATGTCAGATCATCCGACGGATTTGTGTCCTATTTTACATGATGGCACGACAGAACA
1 ATTTGTGCCATGTCAGATCATCCGACGGATTTGTGTCCTATTTTACATGATGGCACGACAGAACA
*
83916 AGCTAATGTAGTCGGGAACTTTCCAGGGCCACCC
66 AGCTAATGTAGTCGGGAACTTTCCAAGGCCACCC
83950 CAAAGGAGAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (99 bp):
ATTTGTGCCATGTCAGATCATCCGACGGATTTGTGTCCTATTTTACATGATGGCACGACAGAACA
AGCTAATGTAGTCGGGAACTTTCCAAGGCCACCC
Found at i:85824 original size:140 final size:139
Alignment explanation
Indices: 85647--85927 Score: 517
Period size: 140 Copynumber: 2.0 Consensus size: 139
85637 GTAATATGGG
*
85647 ATTAAGTAGGGGGATTCATTATACATGTCATGATCTTTCTCTTTGCATATTGCTTATGATATTAA
1 ATTAAGTAGGGGAATTCATTATACATGTCATGATCTTTCTCTTTGCATATTGCTTATGATATTAA
85712 TATTATTTGATAATTATTGTCACGATTGAATTCTTTCTTATGCTTAGTTCATTTGGATAATAAAG
66 TATTATTTGATAATTATTGTCACGATTGAATTCTTTCTTATGCTTAGTTCATTTGGATAATAAAG
85777 AACTCAAGA
131 AACTCAAGA
* *
85786 ATTAAGTAAGGGGAATTCATTATACATGTCATGATCTTTCTTTTTTCATATTGCTTATGATATTA
1 ATTAAGT-AGGGGAATTCATTATACATGTCATGATCTTTCTCTTTGCATATTGCTTATGATATTA
85851 ATATTATTTGATAATTATTGTCACGATTGAATTCTTTCTTATGCTTAGTTCATTTGGATAATAAA
65 ATATTATTTGATAATTATTGTCACGATTGAATTCTTTCTTATGCTTAGTTCATTTGGATAATAAA
*
85916 GAACTCATGA
130 GAACTCAAGA
85926 AT
1 AT
85928 AATAATTGCT
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
139 7 0.05
140 130 0.95
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (139 bp):
ATTAAGTAGGGGAATTCATTATACATGTCATGATCTTTCTCTTTGCATATTGCTTATGATATTAA
TATTATTTGATAATTATTGTCACGATTGAATTCTTTCTTATGCTTAGTTCATTTGGATAATAAAG
AACTCAAGA
Found at i:95739 original size:23 final size:24
Alignment explanation
Indices: 95713--95759 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
95703 GAATTTTTTA
95713 AAATATTTAATTTTTT-TAAATAT
1 AAATATTTAATTTTTTATAAATAT
*
95736 AAATTTTTAATTTTTTATAAATAT
1 AAATATTTAATTTTTTATAAATAT
95760 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATATTTAATTTTTTATAAATAT
Found at i:95742 original size:15 final size:16
Alignment explanation
Indices: 95699--95743 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
95689 TTTATGTTTT
95699 TATAGAATTTTTTAAAA
1 TATA-AATTTTTTAAAA
* *
95716 TATTTAATTTTTTTAAA
1 TA-TAAATTTTTTAAAA
95733 TATAAATTTTT
1 TATAAATTTTT
95744 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.33
17 15 0.62
18 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATAAATTTTTTAAAA
Found at i:95761 original size:20 final size:19
Alignment explanation
Indices: 95704--95788 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 19
95694 GTTTTTATAG
95704 AATTTTTTAAAATA--TTT
1 AATTTTTTAAAATATTTTT
95721 AATTTTTTTAAATATAAATTTTT
1 AA-TTTTTTAAA-AT--ATTTTT
*
95744 AATTTTTTATAAATATTTTA
1 AATTTTTTA-AAATATTTTT
*
95764 AATTTTTTAAAATTATTTTG
1 AATTTTTTAAAA-TATTTTT
95784 AATTT
1 AATTT
95789 CTTTTTGTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.03
18 9 0.16
19 5 0.09
20 25 0.43
21 1 0.02
22 9 0.16
23 7 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
AATTTTTTAAAATATTTTT
Found at i:97385 original size:18 final size:18
Alignment explanation
Indices: 97362--97398 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
97352 AAACTGAATT
*
97362 AATTCGATTAATCGATCG
1 AATTCGATTAATCAATCG
97380 AATTCGATTAATCAATCG
1 AATTCGATTAATCAATCG
97398 A
1 A
97399 TTAATCGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (18 bp):
AATTCGATTAATCAATCG
Found at i:97447 original size:15 final size:15
Alignment explanation
Indices: 97419--97468 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
97409 TAACTAAACT
* *
97419 TAATAAATAGTATTA
1 TAATATATAATATTA
97434 TAATATATAATATTA
1 TAATATATAATATTA
*
97449 TAATATAAAAGTATTA
1 TAATATATAA-TATTA
97465 TAAT
1 TAAT
97469 TGATCGGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
TAATATATAATATTA
Found at i:101286 original size:30 final size:31
Alignment explanation
Indices: 101217--101287 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
101207 ATTTGAAAAA
*
101217 ATTTGAA-TTTCGAGTTGATTAAATTAAATT
1 ATTTGAATTTTCGAGTTAATTAAATTAAATT
**
101247 ATTCAAATTTTC-AGTTAATTTAAA-TAAATT
1 ATTTGAATTTTCGAGTTAA-TTAAATTAAATT
101277 ATTTGAATTTT
1 ATTTGAATTTT
101288 GAATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (31 bp):
ATTTGAATTTTCGAGTTAATTAAATTAAATT
Found at i:101328 original size:23 final size:22
Alignment explanation
Indices: 101271--101339 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
101261 TTAATTTAAA
*
101271 TAAATTATTTGAATTTTGAATT
1 TAAATAATTTGAATTTTGAATT
* *
101293 TAAATTGAGTTGAATTATAT-AATT
1 TAAA-TAATTTGAATT-T-TGAATT
101317 TAAATAATTTGAATAATTTGAAT
1 TAAATAATTTGAAT--TTTGAAT
101340 AACTCAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
22 4 0.11
23 18 0.49
24 13 0.35
25 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TAAATAATTTGAATTTTGAATT
Found at i:101466 original size:20 final size:20
Alignment explanation
Indices: 101441--101479 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
101431 TAAAATAAAA
101441 TAAAATAACTTTTAAAATTT
1 TAAAATAACTTTTAAAATTT
*
101461 TAAAATAATTTTTAAAATT
1 TAAAATAACTTTTAAAATT
101480 CAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATAACTTTTAAAATTT
Found at i:101484 original size:19 final size:20
Alignment explanation
Indices: 101442--101495 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
101432 AAAATAAAAT
* *
101442 AAAATAACTTTTAAAATTTT
1 AAAATAATTTTTAAAATTTC
101462 AAAATAATTTTTAAAA-TTC
1 AAAATAATTTTTAAAATTTC
*
101481 AAAAT-ATTTATAAAA
1 AAAATAATTTTTAAAA
101496 ATTTTAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 15 0.48
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTTC
Found at i:101539 original size:9 final size:9
Alignment explanation
Indices: 101522--101587 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
101512 TTTTAAAGAA
*
101522 ATTATAAAT
1 ATTAAAAAT
101531 ATTAAAAAT
1 ATTAAAAAT
101540 ATT-AAAAT
1 ATTAAAAAT
* *
101548 TTCTAAAAAA
1 AT-TAAAAAT
101558 ATCTAAAGAAT
1 AT-TAAA-AAT
101569 ATATAAAAAT
1 AT-TAAAAAT
*
101579 TTTAAAAAT
1 ATTAAAAAT
101588 TTGAAAACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 6 0.13
9 19 0.40
10 14 0.30
11 8 0.17
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:102472 original size:27 final size:26
Alignment explanation
Indices: 102414--102472 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
102404 TAAAAAAAAT
102414 AAATAAAAACTATAAAAAAAACTTAG
1 AAATAAAAACTATAAAAAAAACTTAG
* *
102440 ATAATAAAAA-TGTAATAAAAAATTATAG
1 A-AATAAAAACTATAA-AAAAAACT-TAG
102468 AAATA
1 AAATA
102473 TACCATGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 5 0.18
27 19 0.68
28 4 0.14
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (26 bp):
AAATAAAAACTATAAAAAAAACTTAG
Found at i:104392 original size:173 final size:174
Alignment explanation
Indices: 104203--104554 Score: 679
Period size: 173 Copynumber: 2.0 Consensus size: 174
104193 TCGTTTCTGA
104203 AATTAAGGGCCGTAAATATTTTTATTAAATATTTATAGAGTCTTATTATATGTGAATTGAAGTTC
1 AATTAAGGGCCGTAAATATTTTTATTAAATATTTATAGAGTCTTATTATATGTGAATTGAAGTTC
*
104268 GGTTGGGTAATTTTGATGATTAATTGCTTAATTAAGGAAAAATGAGTAAA-TTGTAAAAGGGATA
66 GGTTGGGTAATTTTGATGATTAATTGCTTAATTAAGGAAAAAGGAGTAAATTTGTAAAAGGGATA
104332 AAAGTTAATTGCTATTGATTAAAAATAAAAGGGACCAAAGTGGT
131 AAAGTTAATTGCTATTGATTAAAAATAAAAGGGACCAAAGTGGT
*
104376 AATTAAGGGCCGTAAATATTTTTATTAAATATTTATAGAGTCTTATTGTATGTGAATTGAAGTTC
1 AATTAAGGGCCGTAAATATTTTTATTAAATATTTATAGAGTCTTATTATATGTGAATTGAAGTTC
104441 GGTTGGGTAATTTTGATGATTAATTGCTTAATTAAGGAAAAAGGAGTAAATTTGTAAAAGGGATA
66 GGTTGGGTAATTTTGATGATTAATTGCTTAATTAAGGAAAAAGGAGTAAATTTGTAAAAGGGATA
104506 AAAGTTAATTGCTATTGATTAAAAATAAAAGGGACCAAAGTGGT
131 AAAGTTAATTGCTATTGATTAAAAATAAAAGGGACCAAAGTGGT
104550 AATTA
1 AATTA
104555 GACCATGGTA
Statistics
Matches: 176, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
173 113 0.64
174 63 0.36
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (174 bp):
AATTAAGGGCCGTAAATATTTTTATTAAATATTTATAGAGTCTTATTATATGTGAATTGAAGTTC
GGTTGGGTAATTTTGATGATTAATTGCTTAATTAAGGAAAAAGGAGTAAATTTGTAAAAGGGATA
AAAGTTAATTGCTATTGATTAAAAATAAAAGGGACCAAAGTGGT
Found at i:106075 original size:52 final size:52
Alignment explanation
Indices: 105946--106185 Score: 340
Period size: 52 Copynumber: 4.6 Consensus size: 52
105936 TGTAAAAAAA
*
105946 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC-CTTTACGGATTATG
*
105999 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACAGG-TTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC-GGATTATG
* * *
106051 AGGTCCGATGACCATGTGTAATCGTGATTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * ** *
106103 AGGTCCGATGACTATGTGTCATCATGAGTATATAAATCCTATTATAGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATG
*
106155 AGGTCCGATGACTTTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
106186 TAAATGGGAA
Statistics
Matches: 168, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.01
52 120 0.71
53 46 0.27
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:120301 original size:20 final size:21
Alignment explanation
Indices: 120265--120314 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
120255 TCATTAAGCT
*
120265 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
120285 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
120305 TTAATATAAA
1 TTAAT-TAAA
120315 CCATGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:125334 original size:52 final size:52
Alignment explanation
Indices: 125250--125487 Score: 336
Period size: 52 Copynumber: 4.6 Consensus size: 52
125240 GAAAAAAAAG
* *
125250 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC-GTATTATGA
1 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACAG-ATTATGA
** *
125302 GGTCCGATGACTATACGTCATCATGAGGATATGAATCCTTTACAGATTATGA
1 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACAGATTATGA
** *
125354 GGTCCGATGACTATGTGTCATTGTGATTATATGAATCCTTTACAGATTATGA
1 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACAGATTATGA
*
125406 GGTCCGATGACTATGTGTCATCATGAGTATATGGATCCTATTACAGATT-TGA
1 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCCT-TTACAGATTATGA
* * *
125458 GGTCCGGTGACTTTGTGTCATCGTGAGTAT
1 GGTCCGATGACTATGTGTCATCATGAGTAT
125488 TAAATGGGAA
Statistics
Matches: 166, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
52 156 0.94
53 10 0.06
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACAGATTATGA
Found at i:126315 original size:21 final size:19
Alignment explanation
Indices: 126264--126316 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
126254 TTGGCTTGAG
126264 TTGTATCGGTAGTTGTATC
1 TTGTATCGGTAGTTGTATC
126283 TTAGGTATCGGTAGTTCGTATAC
1 TT--GTATCGGTAGTT-GTAT-C
*
126306 TTGTACCGGTA
1 TTGTATCGGTA
126317 TAGTTGCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 2 0.07
21 20 0.69
22 4 0.14
23 3 0.10
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (19 bp):
TTGTATCGGTAGTTGTATC
Found at i:127886 original size:42 final size:42
Alignment explanation
Indices: 127840--127922 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
127830 TATCAGAATA
* *
127840 TAAGATTACTTAGCATATTAGTGAGTATTATTATATTATTTG
1 TAAGATTACTTAGCATATTAGTAAGTATTATTACATTATTTG
* *
127882 TAAGATTACTTAGTATATTATTAAGTATTATTACATTATTT
1 TAAGATTACTTAGCATATTAGTAAGTATTATTACATTATTT
127923 TGTTTGATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (42 bp):
TAAGATTACTTAGCATATTAGTAAGTATTATTACATTATTTG
Found at i:127906 original size:21 final size:22
Alignment explanation
Indices: 127840--127911 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
127830 TATCAGAATA
* *
127840 TAAG-ATTACTTAGCATATTAG
1 TAAGTATTACTTAGTATATTAT
*
127861 TGAGTATTA-TTA-TATTATT-T
1 TAAGTATTACTTAGTA-TATTAT
127881 GTAAG-ATTACTTAGTATATTAT
1 -TAAGTATTACTTAGTATATTAT
127903 TAAGTATTA
1 TAAGTATTA
127912 TTACATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
20 5 0.12
21 24 0.60
22 11 0.28
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.47
Consensus pattern (22 bp):
TAAGTATTACTTAGTATATTAT
Found at i:127921 original size:21 final size:20
Alignment explanation
Indices: 127863--127922 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
127853 CATATTAGTG
127863 AGTATTATTATATTATTTGTA
1 AGTATTATTA-ATTATTTGTA
*
127884 AG-ATTACTTAGTATATTAT-TA
1 AGTATTA-TTAAT-TATT-TGTA
127905 AGTATTATTACATTATTT
1 AGTATTATTA-ATTATTT
127923 TGTTTGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (20 bp):
AGTATTATTAATTATTTGTA
Found at i:133084 original size:23 final size:21
Alignment explanation
Indices: 133025--133090 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
133015 TTCAAATATT
*
133025 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
* * *
133046 TTAATTATTTGAAATATCATTATG
1 TTTA-TATGTGAAATAT-ATTA-A
*
133070 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
133091 ATATACTTAC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 3 0.09
22 14 0.41
23 14 0.41
24 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTATATGTGAAATATATTAA
Found at i:133360 original size:20 final size:21
Alignment explanation
Indices: 133335--133375 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
133325 TAAAGAAATT
133335 AATTAT-A-TTAAAAAATAAAA
1 AATTATAACTTAAAAAA-AAAA
133355 AATTATAACTTAAAAAAAAAA
1 AATTATAACTTAAAAAAAAAA
133376 CACGTCCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTATAACTTAAAAAAAAAA
Found at i:144546 original size:98 final size:98
Alignment explanation
Indices: 144372--144774 Score: 439
Period size: 98 Copynumber: 4.1 Consensus size: 98
144362 GGTTTTAAGA
* * * * *
144372 GAAAGATTGAAG-TCGCAACGATAAATCTTATACCCTAAAGATGTGGAGGGAAAGATTGAAGCCG
1 GAAAGATTGAAGCT-GCAACGACAAATCTTATACCATAAAGATGTGAAGGGAAAGGTTAAAGCCG
*
144436 CAACGGCAAACCTTGTACCTTAGAGACGTGATGG
65 CAACGGCGAACCTTGTACCTTAGAGACGTGATGG
* * * * * * *
144470 GAAAGATTGAAGCTGCAACGACGATTCTTATACCATAGAGATTTGAAGGGAAAGGTTGAAGCTGT
1 GAAAGATTGAAGCTGCAACGACAAATCTTATACCATAAAGATGTGAAGGGAAAGGTTAAAGCCGC
* *
144535 AACGACGAACCTTGTACCTTAGAGACGTGATAG
66 AACGGCGAACCTTGTACCTTAGAGACGTGATGG
* * ** * ** * * *
144568 GAAAGATTAAAGCTGTAACGGTAAATCTTGTACCATGGAGATATGGAGGGAAAAGTTAAAGCCGC
1 GAAAGATTGAAGCTGCAACGACAAATCTTATACCATAAAGATGTGAAGGGAAAGGTTAAAGCCGC
*
144633 AACGGTGAACCTTGTACCTTAGAGACGTGATGG
66 AACGGCGAACCTTGTACCTTAGAGACGTGATGG
* * * * * * *
144666 AAAATATTAAAGCCGCAACGACGAATCTTATACCCCTAAAGATGTGAAGGGAAAGGTTAAAGACG
1 GAAAGATTGAAGCTGCAACGACAAATCTTATA-CCATAAAGATGTGAAGGGAAAGGTTAAAGCCG
* * * * *
144731 CAATGGCGAACTTTATACCTTAGAGATGTGAAGG
65 CAACGGCGAACCTTGTACCTTAGAGACGTGATGG
144765 GAAAGATTGA
1 GAAAGATTGA
144775 GGCCGTAATG
Statistics
Matches: 249, Mismatches: 54, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
98 188 0.76
99 61 0.24
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.22
Consensus pattern (98 bp):
GAAAGATTGAAGCTGCAACGACAAATCTTATACCATAAAGATGTGAAGGGAAAGGTTAAAGCCGC
AACGGCGAACCTTGTACCTTAGAGACGTGATGG
Found at i:144798 original size:49 final size:49
Alignment explanation
Indices: 144372--144798 Score: 302
Period size: 49 Copynumber: 8.7 Consensus size: 49
144362 GGTTTTAAGA
* * *** * * *
144372 GAAAGATTGAAGTCGCAACGATAAATCTTATACCCTAAAGATGTGGAGG
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGAAGG
* * * * * *
144421 GAAAGATTGAAGCCGCAACGGCAAACCTTGTACCTTAGAGACGTGATGG
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGAAGG
* * * * * *
144470 GAAAGATTGAAGCTGCAACGACGATTCTTATACCATAGAGATTTGAAGG
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGAAGG
* * * * * * * *
144519 GAAAGGTTGAAGCTGTAACGACGAACCTTGTACCTTAGAGACGTGATA-G
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGA-AGG
* * ** * * * * *
144568 GAAAGATTAAAGCTGTAACGGTAAATCTTGTACCATGGAGATATGGAGG
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGAAGG
* * * * *
144617 GAAA-AGTTAAAGCCGCAACGGTGAACCTTGTACCTTAGAGACGTGATGG
1 GAAAGA-TTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGAAGG
* * * * *
144666 AAAATATTAAAGCCGCAACGACGAATCTTATACCCCTAAAGATGTGAAGG
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATA-CCTTAGAGATGTGAAGG
* * *
144716 GAAAGGTTAAAGACGCAATGGCGAA-CTTTATACCTTAGAGATGTGAAGG
1 GAAAGATTAAAGCCGCAACGGCGAATC-TTATACCTTAGAGATGTGAAGG
* * * * *
144765 GAAAGATTGAGGCCGTAATGGCGAATCTCATACC
1 GAAAGATTAAAGCCGCAACGGCGAATCTTATACC
144799 CTGAAGATGA
Statistics
Matches: 299, Mismatches: 72, Indels: 14
0.78 0.19 0.04
Matches are distributed among these distances:
48 2 0.01
49 257 0.86
50 40 0.13
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (49 bp):
GAAAGATTAAAGCCGCAACGGCGAATCTTATACCTTAGAGATGTGAAGG
Found at i:145121 original size:40 final size:39
Alignment explanation
Indices: 145016--145333 Score: 215
Period size: 38 Copynumber: 8.2 Consensus size: 39
145006 AAGCTACCAT
* * * *
145016 CCAATCTCATACCCTAATCATGCGGCAGATT-AAAGTA-T
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAA-CACA
* * * *
145054 CCAATCT-TTTCCCTAATCA-GAGGGTAGATTGAATACACA
1 CCAATCTCATACCCCAATCATG-GGGCAGATTGAA-ACACA
** * * *
145093 CCAATCTCATACCCCGTTCATGGGGTAGATTGAAGCA-T
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAACACA
** * **
145131 CCAATCTTTTACCCTAATCAAAGGGCAGATTGAGAACACA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGA-AACACA
* *
145171 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCA-T
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAACACA
** * * *
145209 CCAATCTTTTA-CCTAATTA-GAAGGCAGATTGAAGACACA
1 CCAATCTCATACCCCAATCATG-GGGCAGATTGAA-ACACA
* * *
145248 CCAATCTCATACCCCAATCATGGGGCAAATTGAAGCA-T
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAACACA
** *
145286 CCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACACA
1 CCAATCTCATACCCCAATCATG-GGGCAGATTGAA-ACACA
145326 CCAATCTC
1 CCAATCTC
145334 TTAACCTCAA
Statistics
Matches: 212, Mismatches: 52, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
36 2 0.01
37 35 0.17
38 74 0.35
39 29 0.14
40 70 0.33
41 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
CCAATCTCATACCCCAATCATGGGGCAGATTGAAACACA
Found at i:145263 original size:77 final size:78
Alignment explanation
Indices: 145016--145333 Score: 473
Period size: 77 Copynumber: 4.1 Consensus size: 78
145006 AAGCTACCAT
* * * * * *
145016 CCAATCTCATACCCTAATCATGCGGCAGATTAAAGTATCCAATCTTTT-CCCTAATCAGAGGGTA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCA
*
145080 GATTGAATACACA
66 GATTGAAGACACA
** *
145093 CCAATCTCATACCCCGTTCATGGGGTAGATTGAAGCATCCAATCTTTTACCCTAATCA-AAGGGC
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAA-GGC
145157 AGATTG-AGAACACA
65 AGATTGAAG-ACACA
*
145171 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTA-CCTAATTAGAAGGCA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCA
145235 GATTGAAGACACA
66 GATTGAAGACACA
* *
145248 CCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCA
145313 GATTGAAGACACA
66 GATTGAAGACACA
145326 CCAATCTC
1 CCAATCTC
145334 TTAACCTCAA
Statistics
Matches: 218, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
77 112 0.51
78 106 0.49
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (78 bp):
CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCA
GATTGAAGACACA
Found at i:145298 original size:155 final size:155
Alignment explanation
Indices: 145016--145333 Score: 494
Period size: 155 Copynumber: 2.1 Consensus size: 155
145006 AAGCTACCAT
* * * * *
145016 CCAATCTCATACCCTAATCATGCGGCAGATTAAAGTATCCAATCTTTTCCCTAATCAGAGGGTAG
1 CCAATCTCATACCCCAATCATGCGGCAGATTAAAGCATCCAATCTTTTACCTAATCAGAAGGCAG
* ** * *
145081 ATTGAATACACACCAATCTCATACCCCGTTCATGGGGTAGATTGAAGCATCCAATCTTTTACCCT
66 ATTGAAGACACACCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCT
145146 AATCAAAGGGCAGATTG-AGAACACA
131 AATCAAAGGGCAGATTGAAG-ACACA
* * *
145171 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTAATTAGAAGGCAG
1 CCAATCTCATACCCCAATCATGCGGCAGATTAAAGCATCCAATCTTTTACCTAATCAGAAGGCAG
145236 ATTGAAGACACACCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCT
66 ATTGAAGACACACCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCT
*
145301 AATCAGAGGGCAGATTGAAGACACA
131 AATCAAAGGGCAGATTGAAGACACA
145326 CCAATCTC
1 CCAATCTC
145334 TTAACCTCAA
Statistics
Matches: 148, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
155 146 0.99
156 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (155 bp):
CCAATCTCATACCCCAATCATGCGGCAGATTAAAGCATCCAATCTTTTACCTAATCAGAAGGCAG
ATTGAAGACACACCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCT
AATCAAAGGGCAGATTGAAGACACA
Found at i:145378 original size:46 final size:45
Alignment explanation
Indices: 145270--145493 Score: 171
Period size: 46 Copynumber: 5.1 Consensus size: 45
145260 CCCAATCATG
*
145270 GGGCAAATTGAAG---CATCCAATCTTTTA-CCCTAA-TC-AG-A
1 GGGCAAATTGAAGCCACATCCAATCTTTAACCCCTAAGTCAAGAA
* * * *
145308 GGGCAGATTGAAGACACA-CCAATCTCTTAACCTC-AAGTCAAGAG
1 GGGCAAATTGAAGCCACATCCAATCT-TTAACCCCTAAGTCAAGAA
* *
145352 GGGTAAATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAA
1 GGGCAAATTGAAGCCA-CATCCAATCTTTAACCCCTAAGTCAAGAA
* * * * * *
145398 GGGCATATTAAAGCCACCATTCAATCTTTTACCCCTAACTTAA-AA
1 GGGCAAATTGAAGCCA-CATCCAATCTTTAACCCCTAAGTCAAGAA
* * * *
145443 GGGGCAGATTGAAGCTACTATCCAATCTTTTACCCCTAAAATCAAGAA
1 -GGGCAAATTGAAGCCAC-ATCCAATCTTTAACCCCT-AAGTCAAGAA
145491 GGG
1 GGG
145494 TAGATTAAAG
Statistics
Matches: 148, Mismatches: 23, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
38 12 0.08
40 7 0.05
41 7 0.05
42 4 0.03
43 2 0.01
44 13 0.09
45 11 0.07
46 82 0.55
47 8 0.05
48 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (45 bp):
GGGCAAATTGAAGCCACATCCAATCTTTAACCCCTAAGTCAAGAA
Found at i:147260 original size:29 final size:31
Alignment explanation
Indices: 147199--147284 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 31
147189 AAATTTAATT
*
147199 CCCAAACTTTTTAAAAATTTCATTTT-AGCC
1 CCCAAACTTTCTAAAAATTTCATTTTGAGCC
* *
147229 CCCTAAC-TTCTAAAAATTTCATTTTGA-TC
1 CCCAAACTTTCTAAAAATTTCATTTTGAGCC
* * *
147258 CCCAAACTTTCCAAAATTTTGATTTTG
1 CCCAAACTTTCTAAAAATTTCATTTTG
147285 GCCTCGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 24 0.51
30 23 0.49
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (31 bp):
CCCAAACTTTCTAAAAATTTCATTTTGAGCC
Found at i:153664 original size:24 final size:26
Alignment explanation
Indices: 153637--153691 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
153627 TTTTTTAAAA
153637 TTTTTTAA-AAATTCT-TT-TTTTAT
1 TTTTTTAATAAATTCTATTATTTTAT
* *
153660 TTTTTAAATAAATTCTATTATTTTCT
1 TTTTTTAATAAATTCTATTATTTTAT
153686 TTTTTT
1 TTTTTT
153692 TTTCATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 2 0.08
26 10 0.38
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTTTAATAAATTCTATTATTTTAT
Done.