Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014311.1 Kokia drynarioides strain JFW-HI SEQ_129348, 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: 102887
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:1083 original size:19 final size:19
Alignment explanation
Indices: 1059--1111 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1049 TTTTTTTCTT
*
1059 AACTTCAGCAAAAA-CCAC
1 AACTTCAACAAAAACCCAC
*
1077 AAACTTCAACACAAACCCAC
1 -AACTTCAACAAAAACCCAC
1097 AACTTCAACAAAAAC
1 AACTTCAACAAAAAC
1112 AAATTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.53, C:0.34, G:0.02, T:0.11
Consensus pattern (19 bp):
AACTTCAACAAAAACCCAC
Found at i:5941 original size:31 final size:31
Alignment explanation
Indices: 5906--5968 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5896 GTATGGAGAG
5906 ATTGAGACATCTTATTGAGGATATAGTAGTC
1 ATTGAGACATCTTATTGAGGATATAGTAGTC
5937 ATTGAGACATCTTATTGAGGATATAGTAGTC
1 ATTGAGACATCTTATTGAGGATATAGTAGTC
5968 A
1 A
5969 ATGGACAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (31 bp):
ATTGAGACATCTTATTGAGGATATAGTAGTC
Found at i:9090 original size:16 final size:16
Alignment explanation
Indices: 9071--9102 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9061 CACAAGAGTT
9071 GGTTTAGAGTAGAGGA
1 GGTTTAGAGTAGAGGA
9087 GGTTTAGAGTAGAGGA
1 GGTTTAGAGTAGAGGA
9103 TAGTGGGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (16 bp):
GGTTTAGAGTAGAGGA
Found at i:14135 original size:26 final size:26
Alignment explanation
Indices: 14106--14158 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
14096 TCAGTCCTTC
14106 TAAGAATACATCTAGTTGCTGTAAGA
1 TAAGAATACATCTAGTTGCTGTAAGA
14132 TAAGAATACATCTAGTTGCTGTAAGA
1 TAAGAATACATCTAGTTGCTGTAAGA
14158 T
1 T
14159 GAAATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (26 bp):
TAAGAATACATCTAGTTGCTGTAAGA
Found at i:20545 original size:20 final size:20
Alignment explanation
Indices: 20520--20593 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
20510 AGGTGCATGG
20520 GATGGAAAAGGTAAATGGGT
1 GATGGAAAAGGTAAATGGGT
* ** *
20540 GATGGAAAAATGCCAATGAGTGA
1 GATGG-AAAAGGTAAATG-G-GT
20563 GACATGGAAAAGGTAAATGGGT
1 G--ATGGAAAAGGTAAATGGGT
20585 GATGGAAAA
1 GATGGAAAA
20594 ATGCCAATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 13 0.32
21 9 0.22
22 3 0.07
23 3 0.07
24 9 0.22
25 4 0.10
ACGTcount: A:0.43, C:0.04, G:0.35, T:0.18
Consensus pattern (20 bp):
GATGGAAAAGGTAAATGGGT
Found at i:20557 original size:21 final size:21
Alignment explanation
Indices: 20533--20607 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
20523 GGAAAAGGTA
20533 AATGGGTGATGGAAAAATGCC
1 AATGGGTGATGGAAAAATGCC
* * **
20554 AATGAGTGAGACATGG-AAAAGGTA
1 AATG-G-GTG--ATGGAAAAATGCC
20578 AATGGGTGATGGAAAAATGCC
1 AATGGGTGATGGAAAAATGCC
*
20599 AATGAGTGA
1 AATGGGTGA
20608 GACATGGAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
20 4 0.10
21 17 0.43
22 3 0.08
23 3 0.08
24 9 0.22
25 4 0.10
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.19
Consensus pattern (21 bp):
AATGGGTGATGGAAAAATGCC
Found at i:20585 original size:45 final size:45
Alignment explanation
Indices: 20521--20619 Score: 198
Period size: 45 Copynumber: 2.2 Consensus size: 45
20511 GGTGCATGGG
20521 ATGGAAAAGGTAAATGGGTGATGGAAAAATGCCAATGAGTGAGAC
1 ATGGAAAAGGTAAATGGGTGATGGAAAAATGCCAATGAGTGAGAC
20566 ATGGAAAAGGTAAATGGGTGATGGAAAAATGCCAATGAGTGAGAC
1 ATGGAAAAGGTAAATGGGTGATGGAAAAATGCCAATGAGTGAGAC
20611 ATGGAAAAG
1 ATGGAAAAG
20620 AAAAGGAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.43, C:0.06, G:0.33, T:0.17
Consensus pattern (45 bp):
ATGGAAAAGGTAAATGGGTGATGGAAAAATGCCAATGAGTGAGAC
Found at i:22153 original size:27 final size:27
Alignment explanation
Indices: 22095--22158 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
22085 TTAGGATAGG
**
22095 AAAGCCTTTATGGCAAACCTCTAAAAGG
1 AAAGCCTTTATGG-AAACCTCTAAAACA
22123 AAAGCCTTTATGTG-AACCTCTAAAACA
1 AAAGCCTTTATG-GAAACCTCTAAAACA
22150 AAAGCCTTT
1 AAAGCCTTT
22159 GTGGTGAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 20 0.61
28 12 0.36
29 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (27 bp):
AAAGCCTTTATGGAAACCTCTAAAACA
Found at i:22250 original size:28 final size:28
Alignment explanation
Indices: 22092--22332 Score: 188
Period size: 28 Copynumber: 8.7 Consensus size: 28
22082 ACATTAGGAT
* ** *
22092 AGGAAAGCCTTTATGGCAAACCTCTAAA
1 AGGAAAGCCTTTGTGGTGAACCTCTGAA
* *
22120 AGGAAAGCCTTTAT-GTGAACCTCTAAA
1 AGGAAAGCCTTTGTGGTGAACCTCTGAA
** *
22147 ACAAAAGCCTTTGTGGTGAGCCTCTG-A
1 AGGAAAGCCTTTGTGGTGAACCTCTGAA
* * *
22174 AGGAAAAGTCTTTGTGGCGAACCTTTGAA
1 AGG-AAAGCCTTTGTGGTGAACCTCTGAA
22203 AGGAAAGCCTTTGTGGTGAACCTCTGAA
1 AGGAAAGCCTTTGTGGTGAACCTCTGAA
** * *
22231 AGGAAAGCCTTTGTTATGAACATTTGAA
1 AGGAAAGCCTTTGTGGTGAACCTCTGAA
* * * * *
22259 AGAAAAACATTTATGGT-AACCTATGAAAA
1 AGGAAAGCCTTTGTGGTGAACCTCTG--AA
* * *
22288 AGG-AAGCCTTCGTGGT-AATCTCTAAA
1 AGGAAAGCCTTTGTGGTGAACCTCTGAA
22314 ATGG-AAGCCTTTGTGGTGA
1 A-GGAAAGCCTTTGTGGTGA
22333 CTTATGAAAA
Statistics
Matches: 169, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
26 3 0.02
27 44 0.26
28 114 0.67
29 8 0.05
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (28 bp):
AGGAAAGCCTTTGTGGTGAACCTCTGAA
Found at i:22351 original size:28 final size:28
Alignment explanation
Indices: 22272--22379 Score: 96
Period size: 27 Copynumber: 3.9 Consensus size: 28
22262 AAAACATTTA
*
22272 TGGTAACCTATGAAAAAGGAAGCCTTCG
1 TGGTAATCTATGAAAAAGGAAGCCTTCG
* * *
22300 TGGTAATCTCT-AAAATGGAAGCCTTTG
1 TGGTAATCTATGAAAAAGGAAGCCTTCG
* *
22327 TGGTGA-CTTATGAAAAAGGAAGCCTTCA
1 TGGTAATC-TATGAAAAAGGAAGCCTTCG
* * * *
22355 TGATAATATCTG-AAAATGAAGCCTT
1 TGGTAATCTATGAAAAAGGAAGCCTT
22380 TGCGACAACC
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.02
27 33 0.52
28 29 0.46
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (28 bp):
TGGTAATCTATGAAAAAGGAAGCCTTCG
Found at i:22394 original size:55 final size:55
Alignment explanation
Indices: 22276--22401 Score: 157
Period size: 55 Copynumber: 2.3 Consensus size: 55
22266 CATTTATGGT
* * * * **
22276 AACCTATGAAAAAGGAAGCCTTCGTGGTAATCTCTAAAATGGAAGCCTTTGTGGT
1 AACCTATGAAAAAGGAAGCCTTCATGATAATATCTAAAATGGAAGCCTTTGCGAC
* *
22331 GACTTATGAAAAAGGAAGCCTTCATGATAATATCTGAAAAT-GAAGCCTTTGCGAC
1 AACCTATGAAAAAGGAAGCCTTCATGATAATATCT-AAAATGGAAGCCTTTGCGAC
22386 AACCTATG-AAAAGGAA
1 AACCTATGAAAAAGGAA
22402 ACCTCGTGGC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
54 8 0.13
55 47 0.78
56 5 0.08
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (55 bp):
AACCTATGAAAAAGGAAGCCTTCATGATAATATCTAAAATGGAAGCCTTTGCGAC
Found at i:30300 original size:71 final size:71
Alignment explanation
Indices: 30184--30317 Score: 223
Period size: 71 Copynumber: 1.9 Consensus size: 71
30174 TAGTATAAGA
* * *
30184 GAAAGTGAAAGTGTTAGAGTTTGTTACTATTGCTGGTGGATGGAATTAGGGGATGTTGAGATGTT
1 GAAAGTCAAAGTGTCAGAGCTTGTTACTATTGCTGGTGGATGGAATTAGGGGATGTTGAGATGTT
30249 ATAGGG
66 ATAGGG
* *
30255 GAAAGTCAAAGTGTCAGAGCTTGTTACTGTTGTTGGTGGATGGAATTAGGGGATGTTGAGATG
1 GAAAGTCAAAGTGTCAGAGCTTGTTACTATTGCTGGTGGATGGAATTAGGGGATGTTGAGATG
30318 GTATTTTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.26, C:0.04, G:0.37, T:0.33
Consensus pattern (71 bp):
GAAAGTCAAAGTGTCAGAGCTTGTTACTATTGCTGGTGGATGGAATTAGGGGATGTTGAGATGTT
ATAGGG
Found at i:33473 original size:16 final size:16
Alignment explanation
Indices: 33454--33496 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
33444 AATTAAATAC
33454 TAATATATAATATAAA
1 TAATATATAATATAAA
*
33470 TAATATATGAT-TAAA
1 TAATATATAATATAAA
*
33485 TAA-ATAAAATAT
1 TAATATATAATAT
33497 TTAAGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAATATATAATATAAA
Found at i:33781 original size:41 final size:41
Alignment explanation
Indices: 33702--33782 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
33692 AATAAATAAA
* * *
33702 AATTTATTTAAGTTAAATTAATGGATTAATTAACTATAATC
1 AATTTATTTAACTTAAATTAATGGATTAATAAAATATAATC
*
33743 AATTTAATTTAACTTAAA-TAATGGCTTTAA-AAAATATAAT
1 AATTT-ATTTAACTTAAATTAATGG-ATTAATAAAATATAAT
33783 TTCTATAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 19 0.56
42 15 0.44
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (41 bp):
AATTTATTTAACTTAAATTAATGGATTAATAAAATATAATC
Found at i:35181 original size:18 final size:18
Alignment explanation
Indices: 35158--35197 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
35148 ATTCGAATAA
35158 CAAATTTAGATTATCTAT
1 CAAATTTAGATTATCTAT
35176 CAAATTTAGATTATCTAT
1 CAAATTTAGATTATCTAT
35194 -AAAT
1 CAAAT
35198 AAATAATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (18 bp):
CAAATTTAGATTATCTAT
Found at i:47859 original size:25 final size:25
Alignment explanation
Indices: 47831--47881 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
47821 CAGACATACC
*
47831 ATCCATTTTGTTCCCAGAAGGGCCA
1 ATCCATTTTGTTCCCAGAAAGGCCA
*
47856 ATCCATTTTGTTCCTAGAAAGGCCA
1 ATCCATTTTGTTCCCAGAAAGGCCA
47881 A
1 A
47882 CAAAGCGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (25 bp):
ATCCATTTTGTTCCCAGAAAGGCCA
Found at i:49994 original size:11 final size:11
Alignment explanation
Indices: 49978--50007 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
49968 AGATTCAGTT
49978 GTAGCAGAGCA
1 GTAGCAGAGCA
49989 GTAGCAGAGCA
1 GTAGCAGAGCA
50000 GTAGCAGA
1 GTAGCAGA
50008 AAACATGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.37, T:0.10
Consensus pattern (11 bp):
GTAGCAGAGCA
Found at i:53513 original size:30 final size:29
Alignment explanation
Indices: 53454--53772 Score: 226
Period size: 30 Copynumber: 10.8 Consensus size: 29
53444 TATTTTATTT
* * * **
53454 CAAAACTATATTTTGACCCCAAACCTTTC
1 CAAAATTACATTTTAACCCCAAAATTTTC
* *
53483 CAAAATCACATTTTCACTCCCAAAATTTTC
1 CAAAATTACATTTTAAC-CCCAAAATTTTC
* * * *
53513 CAAAATTGCATTTTAACCCTAAACTTATC
1 CAAAATTACATTTTAACCCCAAAATTTTC
** *
53542 CAAAATTACATTTTAACTCTTAAATTTTTC
1 CAAAATTACATTTTAAC-CCCAAAATTTTC
* *
53572 CAAAATTACTTTTTGACCCCAAAACTTTTC
1 CAAAATTACATTTTAACCCCAAAA-TTTTC
* * *
53602 CAAAATTACATTTTAACCCTTAAACTTCTC
1 CAAAATTACATTTTAACCC-CAAAATTTTC
** * *
53632 TGAAATTACACTTTAACCCTCAAATTTTTC
1 CAAAATTACATTTTAACCC-CAAAATTTTC
* * ** ** *
53662 TAAAATCACATTTTAACCTTAAACCTTCC
1 CAAAATTACATTTTAACCCCAAAATTTTC
* * * *
53691 CAAAATCAAAATTTAACCCC-AAACTTTC
1 CAAAATTACATTTTAACCCCAAAATTTTC
* * * *
53719 ATAAAATTACCTTATAACCCCTAAATTCTTC
1 -CAAAATTACATTTTAACCCCAAAATT-TTC
53750 CAAAATTACATTTTAACCCCAAA
1 CAAAATTACATTTTAACCCCAAA
53773 TTCTTTAAAA
Statistics
Matches: 225, Mismatches: 58, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
28 6 0.03
29 77 0.34
30 136 0.60
31 6 0.03
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.35
Consensus pattern (29 bp):
CAAAATTACATTTTAACCCCAAAATTTTC
Found at i:53612 original size:60 final size:59
Alignment explanation
Indices: 53454--53772 Score: 286
Period size: 59 Copynumber: 5.4 Consensus size: 59
53444 TATTTTATTT
* * * * * * * *
53454 CAAAACTATATTTTGACCCCAAACCTTTCCAAAATCACATTTTCACTCC-CAAAATTTTC
1 CAAAATTACATTTTAACCCCAAACTTTTCCAAAATTACATTTTAAC-CCTTAAACTTTTC
* * * * *
53513 CAAAATTGCATTTTAACCCTAAACTTATCCAAAATTACATTTTAACTCTTAAATTTTTC
1 CAAAATTACATTTTAACCCCAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTC
* * *
53572 CAAAATTACTTTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTCTC
1 CAAAATTACATTTTAACCCC-AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTC
** * * * * * *
53632 TGAAATTACACTTTAACCCTCAAATTTTTCTAAAATCACATTTTAA-CCTTAAACCTTCC
1 CAAAATTACATTTTAACCC-CAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTC
* * * * * * *
53691 CAAAATCAAAATTTAACCCCAAAC-TTTCATAAAATTACCTTATAACCCCTAAA-TTCTTC
1 CAAAATTACATTTTAACCCCAAACTTTTC-CAAAATTACATTTTAACCCTTAAACTT-TTC
53750 CAAAATTACATTTTAACCCCAAA
1 CAAAATTACATTTTAACCCCAAA
53773 TTCTTTAAAA
Statistics
Matches: 208, Mismatches: 46, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
57 4 0.02
58 19 0.09
59 113 0.54
60 71 0.34
61 1 0.00
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.35
Consensus pattern (59 bp):
CAAAATTACATTTTAACCCCAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTC
Found at i:57639 original size:91 final size:91
Alignment explanation
Indices: 57479--57660 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
57469 TAAAAAATAG
57479 ATATTAGAAATTACTAATAATCTCCTGACCTAATGGTAAGAGTATTTTATTGTAGGTATGAAAAC
1 ATATTAGAAATTACTAATAATCTCCTGACCTAATGGTAAGAGTATTTTATTGTAGGTATGAAAAC
57544 TTAGATTCGATCCCAACCAATCACAT
66 TTAGATTCGATCCCAACCAATCACAT
* *
57570 ATATTAGAAATTACTAATAATCTCCTGACCTAATGGTAAGAGTATTTTGTTGTAGGTATGAAAAT
1 ATATTAGAAATTACTAATAATCTCCTGACCTAATGGTAAGAGTATTTTATTGTAGGTATGAAAAC
57635 TTAGATTCGATCCCAACCAATCACAT
66 TTAGATTCGATCCCAACCAATCACAT
57661 TCCTCTCCCC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (91 bp):
ATATTAGAAATTACTAATAATCTCCTGACCTAATGGTAAGAGTATTTTATTGTAGGTATGAAAAC
TTAGATTCGATCCCAACCAATCACAT
Found at i:58097 original size:31 final size:30
Alignment explanation
Indices: 58059--58117 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
58049 TCATATATTT
58059 TTTAA-TTTTAAAAATATTTATATTATTTTAA
1 TTTAATTTTTAAAAAT-TTTATA-TATTTTAA
*
58090 TTTAATTTTTAATAATTTTATATATTTT
1 TTTAATTTTTAAAAATTTTATATATTTT
58118 CCTATGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.23
31 11 0.42
32 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTAATTTTTAAAAATTTTATATATTTTAA
Found at i:58758 original size:28 final size:28
Alignment explanation
Indices: 58726--58783 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
58716 TCAATTTGAT
*
58726 TAAAT-AAATTATTAAAA-ATTCATAAAAA
1 TAAATGAAAATATTAAAATATT-A-AAAAA
58754 TAAATGAAAATATTAAAATATTAAAAAA
1 TAAATGAAAATATTAAAATATTAAAAAA
58782 TA
1 TA
58784 GAAAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 12 0.44
29 12 0.44
30 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (28 bp):
TAAATGAAAATATTAAAATATTAAAAAA
Found at i:59427 original size:18 final size:18
Alignment explanation
Indices: 59406--59443 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
59396 AGTGGTAGAT
59406 TATAATATATAATTA-ATG
1 TATAATAT-TAATTATATG
*
59424 TATATTATTAATTATATG
1 TATAATATTAATTATATG
59442 TA
1 TA
59444 ACCCTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATAATATTAATTATATG
Found at i:60423 original size:21 final size:21
Alignment explanation
Indices: 60363--60423 Score: 52
Period size: 25 Copynumber: 2.7 Consensus size: 21
60353 TAATGCATTA
*
60363 AAAATATTAAAAACATTAAAAT
1 AAAATTTTAAAAA-ATTAAAAT
*
60385 AAATATTTTCTAACAAATTGAAAAT
1 AAA-A-TTT-TAAAAAATT-AAAAT
60410 -AAATTTTAAAAAAT
1 AAAATTTTAAAAAAT
60424 ATATACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 7 0.22
22 6 0.19
23 2 0.06
24 7 0.22
25 10 0.31
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTTTAAAAAATTAAAAT
Found at i:60501 original size:30 final size:30
Alignment explanation
Indices: 60465--60526 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
60455 CTTAATAAAT
*
60465 AAATGCCTCTAAAATAGTAACAAAACTAAC
1 AAATGCCTCTAAAATAATAACAAAACTAAC
* *
60495 AAATGCCTCTAAAATAATAACAGAATTAAC
1 AAATGCCTCTAAAATAATAACAAAACTAAC
60525 AA
1 AA
60527 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAACTAAC
Found at i:71539 original size:18 final size:18
Alignment explanation
Indices: 71516--71580 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
71506 ATAAAAATAA
71516 TGAGCTCGCCACTTTATG
1 TGAGCTCGCCACTTTATG
* * **
71534 TGAGCTCGTCAATTGCTG
1 TGAGCTCGCCACTTTATG
* * *
71552 TGAACTCACCCCTTTATG
1 TGAGCTCGCCACTTTATG
71570 TGAGCTCGCCA
1 TGAGCTCGCCA
71581 AATATGTTCG
Statistics
Matches: 33, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (18 bp):
TGAGCTCGCCACTTTATG
Found at i:75752 original size:13 final size:13
Alignment explanation
Indices: 75734--75781 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
75724 TTTAAAATTA
75734 TTAAAATTATTTT
1 TTAAAATTATTTT
*
75747 TTAAAATATAAAATTT
1 TTAAAAT-T--ATTTT
75763 TTAAAATTATTTT
1 TTAAAATTATTTT
75776 TTAAAA
1 TTAAAA
75782 ATAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 17 0.57
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:75768 original size:29 final size:28
Alignment explanation
Indices: 75726--75785 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 28
75716 CAAATGATTT
75726 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAA-A
*
75755 TAAAATTTTTAAAATTATTTTTTAAAAA
1 TAAAATTATTAAAATTATTTTTTAAAAA
75783 TAA
1 TAA
75786 TAAAAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTAAAAA
Found at i:75782 original size:14 final size:14
Alignment explanation
Indices: 75736--75783 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
75726 TAAAATTATT
75736 AAAATTATTTTTTA
1 AAAATTATTTTTTA
* *
75750 AAATATAAAATTTTT-
1 AAA-AT-TATTTTTTA
75765 AAAATTATTTTTTA
1 AAAATTATTTTTTA
75779 AAAAT
1 AAAAT
75784 AATAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 6 0.22
14 10 0.37
15 5 0.19
16 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAATTATTTTTTA
Found at i:76907 original size:31 final size:30
Alignment explanation
Indices: 76869--76938 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 30
76859 ATTAAAATTA
76869 TTTAATAATTTTAT-TATTTTAAAAAAGTAAT
1 TTTAATAATTTTATAT-TTTTAAAAAA-TAAT
76900 TTTAATAATTTTATATTTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTTAAAAAATAAT
76930 TTTAA-AATT
1 TTTAATAATT
76939 ATTTGCTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 4 0.11
30 9 0.24
31 24 0.63
32 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTAATAATTTTATATTTTTAAAAAATAAT
Found at i:76924 original size:30 final size:31
Alignment explanation
Indices: 76869--76938 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
76859 ATTAAAATTA
*
76869 TTTAATAATTTTATTATTTTAAAAAAGTAAT
1 TTTAATAATTTTATTATTTTAAAAAAATAAT
*
76900 TTTAATAATTTTA-TATTTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAAATAAT
76930 TTTAA-AATT
1 TTTAATAATT
76939 ATTTGCTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 4 0.11
30 20 0.54
31 13 0.35
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTTAAAAAAATAAT
Found at i:79935 original size:24 final size:24
Alignment explanation
Indices: 79881--80104 Score: 187
Period size: 24 Copynumber: 9.3 Consensus size: 24
79871 TAAACTCATC
* * * *
79881 ACGTTTTCACTCGTCAGCATATAT
1 ACGTTTACGCTCGTCAACTTATAT
* ** *
79905 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAACTTATAT
* * ** * *
79929 ACATTTACGTTTATCAACATATTT
1 ACGTTTACGCTCGTCAACTTATAT
* **
79953 ACATTTACGCTCGTCCGCTTATAT
1 ACGTTTACGCTCGTCAACTTATAT
** *
79977 ACGTTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAACTTATAT
*
80001 ACATTTACGCTCGTCAACTTATAT
1 ACGTTTACGCTCGTCAACTTATAT
* * *
80025 ATGTTTATGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAACTTATAT
* ** *
80049 ACGTTTATGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAACTTATAT
*
80073 ACGTTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAACTTATAT
80097 ACGTTTAC
1 ACGTTTAC
80105 TCATACATGA
Statistics
Matches: 153, Mismatches: 47, Indels: 0
0.76 0.23 0.00
Matches are distributed among these distances:
24 153 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAACTTATAT
Found at i:80007 original size:72 final size:72
Alignment explanation
Indices: 79890--80104 Score: 277
Period size: 72 Copynumber: 3.0 Consensus size: 72
79880 CACGTTTTCA
* * * * *
79890 CTCGTCAGCATATATACGTTTACGCTCGTCAGCTTGCACACATTTACGTTTATCAACATATTTAC
1 CTCGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACATTTACGCTCATCAACATATATAC
79955 ATTTACG
66 ATTTACG
* * * *
79962 CTCGTCCGCTTATATACGTTTACGCTCGTCAACTTGCACACATTTACGCTCGTCAACTTATATAT
1 CTCGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACATTTACGCTCATCAACATATATAC
* *
80027 GTTTATG
66 ATTTACG
* * * * *
80034 CTCGTCAGCTTATATACGTTTATGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATAC
1 CTCGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACATTTACGCTCATCAACATATATAC
*
80099 GTTTAC
66 ATTTAC
80105 TCATACATGA
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 126 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (72 bp):
CTCGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACATTTACGCTCATCAACATATATAC
ATTTACG
Found at i:83518 original size:30 final size:29
Alignment explanation
Indices: 83475--83811 Score: 227
Period size: 30 Copynumber: 11.4 Consensus size: 29
83465 GAAGGTCCTT
* * * *
83475 AAACTTCCCAAAATTCTATTTTTGACCTCG
1 AAACTTTCAAAAATTCCATTTTT-ACCCCG
* **
83505 AAACTTTCAAAAA-TCACAATTTTACCCTT
1 AAACTTTCAAAAATTC-CATTTTTACCCCG
* *
83534 AAACTTCCTAAAAATTCTATTTTTGACCCCG
1 AAACTTTC-AAAAATTCCATTTTT-ACCCCG
** * *
83565 AAACTTTCAAAAATAACAATTTTACCCCT
1 AAACTTTCAAAAATTCCATTTTTACCCCG
* * *
83594 AAACTTCCAAAAATTCTATTTTTGACCTCG
1 AAACTTTCAAAAATTCCATTTTT-ACCCCG
** *
83624 AAACTTTTTTAAAATTACATTTTTACCCTCG
1 AAAC-TTTCAAAAATTCCATTTTTACCC-CG
* * **
83655 -AAC-TTCCAAAATTCCAATTTTAACCCTA
1 AAACTTTCAAAAATTCC-ATTTTTACCCCG
*
83683 AAAC-TTCTAAAAATTACCA-TTTTACCCCT
1 AAACTTTC-AAAAATT-CCATTTTTACCCCG
* * * *
83712 AAACTTCCAAAAATTCAATTTTTGACCTCA
1 AAACTTTCAAAAATTCCATTTTT-ACCCCG
* *
83742 AAACTTTGAAAAATTACCA-TTTTACCCCC
1 AAACTTTCAAAAATT-CCATTTTTACCCCG
* *
83771 AAACTTCCAAAAAATCCATTTTTAACCCCG
1 AAACTTTCAAAAATTCCATTTTT-ACCCCG
83801 AAACTTTCAAA
1 AAACTTTCAAA
83812 GATTACCCTT
Statistics
Matches: 235, Mismatches: 55, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
28 14 0.06
29 92 0.39
30 96 0.41
31 33 0.14
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTTCAAAAATTCCATTTTTACCCCG
Found at i:83567 original size:60 final size:59
Alignment explanation
Indices: 83474--83827 Score: 399
Period size: 59 Copynumber: 6.0 Consensus size: 59
83464 TGAAGGTCCT
* * * *
83474 TAAACTTCCCAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATCACAATTTTACCCT
1 TAAACTTCCAAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATTACAATTTTACCCC
*
83533 TAAACTTCCTAAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATAACAATTTTACCCC
1 TAAACTTCC-AAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATTACAATTTTACCCC
* ** *
83593 TAAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTTTTTAAAATTACATTTTTA-CCC
1 TAAACTTCCAAAAATTCTATTTTTGACCCCGAAAC-TTTCAAAAATTACAATTTTACCCC
* * * * ** *
83652 TCGAACTTCC-AAAATTCCAATTTTAACCCTAAAAC-TTCTAAAAATTACCATTTTACCCC
1 T-AAACTTCCAAAAATTCTATTTTTGACCCCGAAACTTTC-AAAAATTACAATTTTACCCC
* * * * *
83711 TAAACTTCCAAAAATTCAATTTTTGACCTCAAAACTTTGAAAAATTACCATTTTACCCC
1 TAAACTTCCAAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATTACAATTTTACCCC
* * * * * **
83770 CAAACTTCCAAAAAATCCATTTTTAACCCCGAAACTTTCAAAGATTACCCTTTTACCC
1 TAAACTTCCAAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATTACAATTTTACCC
83828 TCGGATGTCT
Statistics
Matches: 252, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.01
58 20 0.08
59 150 0.60
60 80 0.32
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
TAAACTTCCAAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATTACAATTTTACCCC
Found at i:83844 original size:118 final size:118
Alignment explanation
Indices: 83474--83827 Score: 462
Period size: 118 Copynumber: 3.0 Consensus size: 118
83464 TGAAGGTCCT
* * * *
83474 TAAACTTCCCAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATCACAATTTTACCCTTAAACT
1 TAAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCTCAAACT
* * * *
83539 TCCTAAAAATTCTATTTTTGACCCCGAAACTTTCAAAAATAACAATTTTACCCC
66 TCC-AAAAATTCCATTTTTAACCCCGAAACTTTCAAAAATTACCATTTTACCCC
** *
83593 TAAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTTTTTAAAATTA-CATTTTTACCCTCGAA
1 TAAACTTCCAAAAATTCTATTTTTGACCTCGAAAC-TTTCAAAAATTACCA-TTTTACCCTCAAA
* **
83657 CTTCC-AAAATTCCAATTTTAACCCTAAAAC-TTCTAAAAATTACCATTTTACCCC
64 CTTCCAAAAATTCCATTTTTAACCCCGAAACTTTC-AAAAATTACCATTTTACCCC
* * * *
83711 TAAACTTCCAAAAATTCAATTTTTGACCTCAAAACTTTGAAAAATTACCATTTTACCCCCAAACT
1 TAAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCTCAAACT
* * *
83776 TCCAAAAAATCCATTTTTAACCCCGAAACTTTCAAAGATTACCCTTTTACCC
66 TCCAAAAATTCCATTTTTAACCCCGAAACTTTCAAAAATTACCATTTTACCC
83828 TCGGATGTCT
Statistics
Matches: 203, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
117 29 0.14
118 111 0.55
119 38 0.19
120 25 0.12
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (118 bp):
TAAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCTCAAACT
TCCAAAAATTCCATTTTTAACCCCGAAACTTTCAAAAATTACCATTTTACCCC
Found at i:89385 original size:1 final size:1
Alignment explanation
Indices: 89369--89456 Score: 50
Period size: 1 Copynumber: 88.0 Consensus size: 1
89359 TTCAATGAAT
* * * * * * * * * *
89369 AAAAGAAAAGAAAAAAAGAAGAAGAAAAAGAAAAAAGAAAAAGAAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
89434 AAAAGAGAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
89457 GGAGAGGTCG
Statistics
Matches: 59, Mismatches: 28, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (1 bp):
A
Found at i:89393 original size:6 final size:5
Alignment explanation
Indices: 89369--89457 Score: 57
Period size: 4 Copynumber: 18.0 Consensus size: 5
89359 TTCAATGAAT
*
89369 AAAAG AAAAG -AAA- AAAAG AAGAAG AAAA- AGAA- AAAAG AAAAAG AAAA-
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG -AAAAG AAAAG
*
89416 AAAAG AAAAAAG AAAA- AAAA- AAGAG AAAAAG AAAAAG AAAAG
1 AAAAG --AAAAG AAAAG AAAAG AAAAG -AAAAG -AAAAG AAAAG
89458 GAGAGGTCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 20
0.74 0.04 0.21
Matches are distributed among these distances:
4 23 0.33
5 22 0.31
6 20 0.29
7 5 0.07
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:89395 original size:19 final size:18
Alignment explanation
Indices: 89369--89456 Score: 108
Period size: 19 Copynumber: 4.8 Consensus size: 18
89359 TTCAATGAAT
89369 AAAAGAAAAGAAAAAAAGA
1 AAAAGAAAA-AAAAAAAGA
*
89388 AGAAGAAAAAGAAAAAAGA
1 AAAAGAAAAA-AAAAAAGA
*
89407 AAAAG-AAAAAAAAGA-A
1 AAAAGAAAAAAAAAAAGA
89423 AAAAGAAAAAAAAAAGAGA
1 AAAAGAAAAAAAAAA-AGA
89442 AAAAGAAAAAGAAAA
1 AAAAGAAAAA-AAAA
89457 GGAGAGGTCG
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
16 6 0.10
17 13 0.22
18 6 0.10
19 31 0.52
20 4 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAAGA
Found at i:90725 original size:50 final size:47
Alignment explanation
Indices: 90662--90854 Score: 167
Period size: 48 Copynumber: 4.0 Consensus size: 47
90652 TACAGGTTTG
* *
90662 ACAA-GGAAAGATCTAAGACCGCAACAGCAGATCCAGTACTACAAAAAC
1 ACAAGGGAAAGATCTAAG-CCGCAAC-GCAGATCCAGTACTACGAAGAC
* * * *
90710 ACGACGGGAAAGATCTAAGACCACAACG-ATGGATCCAATACCACGAAGAC
1 AC-AAGGGAAAGATCTAAG-CCGCAACGCA--GATCCAGTACTACGAAGAC
** *
90760 ACAAGGGAAAGATCTAAGCCGTGACGACGGATCCAGTA-TCACGAAGAC
1 ACAAGGGAAAGATCTAAGCCGCAACG-CAGATCCAGTACT-ACGAAGAC
* * * *
90808 ACATGAGAAAGATCTAAGCTGCAACAGCAGATCCAGTACCACGAAGA
1 ACAAGGGAAAGATCTAAGCCGCAAC-GCAGATCCAGTACTACGAAGA
90855 TTTGAAGGGA
Statistics
Matches: 116, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
48 61 0.53
49 18 0.16
50 37 0.32
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.11
Consensus pattern (47 bp):
ACAAGGGAAAGATCTAAGCCGCAACGCAGATCCAGTACTACGAAGAC
Found at i:91126 original size:50 final size:50
Alignment explanation
Indices: 90970--91126 Score: 142
Period size: 50 Copynumber: 3.1 Consensus size: 50
90960 ATCAGATAAA
* *
90970 AAAAACAATAGCAAGTCTTTATTTCTCTGAAGTTGTAGTAAGAGCAAGAT
1 AAAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAAAGCAAGAT
* * * ***
91020 AAAGCTTCAA-AACATCAATTC-TTATC-CTCTTGAAGTTGTAGT-AAAGTTGGATT
1 AAA-----AACAATAGCAAGTCTTTATCTCTC-TGAAGTTGTAGTAAAAGCAAGA-T
*
91073 AAAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAAAGCAAGAT
1 AAAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAAAGCAAGAT
91123 AAAA
1 AAAA
91127 TTTCAAACAT
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
48 2 0.02
49 8 0.10
50 24 0.30
51 9 0.11
52 8 0.10
53 20 0.25
54 8 0.10
55 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (50 bp):
AAAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAAAGCAAGAT
Found at i:91775 original size:205 final size:206
Alignment explanation
Indices: 91418--92104 Score: 1085
Period size: 206 Copynumber: 3.3 Consensus size: 206
91408 TCAATGCGAA
* * *
91418 CAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTA
* *
91483 GCTTCTTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTGATGAGATACAGAGAAGCGGA
66 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGA
*
91548 TTGAAACAAACGATGTGGTCATCTTCCTGATGAGATACTGCGAAGAAGACCAAATCAAACTCACG
131 TTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGCGAAGAAGACCAAATCAAACTCACG
*
91613 CTCGTTATGAG
196 CTCGATATGAG
*
91624 CAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCA-GTCGAAGTAATAAAATGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTA
* * *
91688 GCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGACTTGC-TAATGAGATACAGAGAAGCGG
66 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTT-CTTGATGAGATACAGAGAAGCGG
91752 ATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAC-AAGAAGACCAAATCAAACTCA
130 ATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTG-CGAAGAAGACCAAATCAAACTCA
91816 CGCTCGATATGAG
194 CGCTCGATATGAG
* * *
91829 CAAATCTTCGAATCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCAAAGTAATAAAATGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTA
*
91894 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAAATACAGAGAAGCGGA
66 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGA
*** * *
91959 TTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACAAAGAAGAAGACCAAATCAAATTTACG
131 TTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGCGAAGAAGACCAAATCAAACTCACG
92024 CTCGATATGAG
196 CTCGATATGAG
* * * * * *
92035 AAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGTAGGT-GAAAGTAGTAGAATGGCT
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCG-AAGTAATAAAATGGTT
92099 AGCTTC
65 AGCTTC
92105 GGTGAAAGTA
Statistics
Matches: 442, Mismatches: 33, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
205 190 0.43
206 252 0.57
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (206 bp):
CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTA
GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGA
TTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGCGAAGAAGACCAAATCAAACTCACG
CTCGATATGAG
Found at i:92116 original size:27 final size:27
Alignment explanation
Indices: 92078--92131 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
92068 CTGAGAAGTA
92078 GGTGAAAGTAGTAGAATGGCTAGCTTC
1 GGTGAAAGTAGTAGAATGGCTAGCTTC
92105 GGTGAAAGTAGTAGAATGGCTAGCTTC
1 GGTGAAAGTAGTAGAATGGCTAGCTTC
92132 CTGATGAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (27 bp):
GGTGAAAGTAGTAGAATGGCTAGCTTC
Found at i:93467 original size:40 final size:41
Alignment explanation
Indices: 93400--93533 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
93390 TTTAAATAAA
* * *
93400 TTAGTGGCGCTTATGAGAAAACGCCGCTACTGCT-T-AACCT
1 TTAGCGGCGCTTATGAGAAAACACCGCTAATGCTCTGAA-CT
* *
93440 TTAGCGGCGTTTATGAGGAAACACCGCTAATGCTCTGAACT
1 TTAGCGGCGCTTATGAGAAAACACCGCTAATGCTCTGAACT
* * * * *
93481 TTAGCGGCGCTTTCTTA-TAAACGCCGCTAATGCTCTGACCT
1 TTAGCGGCGC-TTATGAGAAAACACCGCTAATGCTCTGAACT
*
93522 TTAGTGGCGCTT
1 TTAGCGGCGCTT
93534 TCTCATAAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 31 0.39
41 42 0.53
42 6 0.08
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGCTTATGAGAAAACACCGCTAATGCTCTGAACT
Found at i:93508 original size:41 final size:41
Alignment explanation
Indices: 93458--93713 Score: 270
Period size: 41 Copynumber: 6.3 Consensus size: 41
93448 GTTTATGAGG
* * *
93458 AAACACCGCTAATGCTCTGAACTTTAGCGGCGCTTTCTTAT
1 AAACGCCGCTAATGCTCCGAACTTTAGCGGCGCTTTCTCAT
* * *
93499 AAACGCCGCTAATGCTCTGACCTTTAGTGGCGCTTTCTCAT
1 AAACGCCGCTAATGCTCCGAACTTTAGCGGCGCTTTCTCAT
* * **
93540 AAACGCCACTAATGCTCCGACCTTTAGCGATGCTTTCTCAT
1 AAACGCCGCTAATGCTCCGAACTTTAGCGGCGCTTTCTCAT
* ** *
93581 AAATGCCGCTAATGCTCCG-ACTTTTAGCGATGTTTTCTCAT
1 AAACGCCGCTAATGCTCCGAAC-TTTAGCGGCGCTTTCTCAT
* * * *
93622 AAATGCTGCTAATGCTCCGACCTTTA---GCGCTTTCCCAT
1 AAACGCCGCTAATGCTCCGAACTTTAGCGGCGCTTTCTCAT
* *
93660 AAACGTCGCTAATGCTCC-AACCTTTAGCGGCGCTTTATCAT
1 AAACGCCGCTAATGCTCCGAA-CTTTAGCGGCGCTTTCTCAT
*
93701 AAACGTCGCTAAT
1 AAACGCCGCTAAT
93714 AGGGGTGAGT
Statistics
Matches: 184, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
37 1 0.01
38 28 0.15
40 1 0.01
41 153 0.83
42 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCCGAACTTTAGCGGCGCTTTCTCAT
Found at i:93565 original size:82 final size:82
Alignment explanation
Indices: 93418--93713 Score: 305
Period size: 82 Copynumber: 3.7 Consensus size: 82
93408 GCTTATGAGA
* * * * * * *
93418 AAACGCCGCTACTGCT-TAACCTTTAGCGGCG-TTTATGAGGAAACACCGCTAATGCTCTGAACT
1 AAACGCCGCTAATGCTCCAACCTTTAGCGGCGCTTTATCA-TAAACGCCGCTAATGCTCCGACCT
*
93481 TTAGCGGCGCTTTCTTAT
65 TTAGCGGCGCTTTCTCAT
** * * *
93499 AAACGCCGCTAATGCTCTGACCTTTAGTGGCGCTTTCTCATAAACGCCACTAATGCTCCGACCTT
1 AAACGCCGCTAATGCTCCAACCTTTAGCGGCGCTTTATCATAAACGCCGCTAATGCTCCGACCTT
**
93564 TAGCGATGCTTTCTCAT
66 TAGCGGCGCTTTCTCAT
* * * ** * * * *
93581 AAATGCCGCTAATGCTCCGACTTTTAGCGATGTTTTCTCATAAATGCTGCTAATGCTCCGACCTT
1 AAACGCCGCTAATGCTCCAACCTTTAGCGGCGCTTTATCATAAACGCCGCTAATGCTCCGACCTT
*
93646 TA---GCGCTTTCCCAT
66 TAGCGGCGCTTTCTCAT
* *
93660 AAACGTCGCTAATGCTCCAACCTTTAGCGGCGCTTTATCATAAACGTCGCTAAT
1 AAACGCCGCTAATGCTCCAACCTTTAGCGGCGCTTTATCATAAACGCCGCTAAT
93714 AGGGGTGAGT
Statistics
Matches: 176, Mismatches: 37, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
79 52 0.30
81 15 0.09
82 104 0.59
83 5 0.03
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (82 bp):
AAACGCCGCTAATGCTCCAACCTTTAGCGGCGCTTTATCATAAACGCCGCTAATGCTCCGACCTT
TAGCGGCGCTTTCTCAT
Found at i:95889 original size:54 final size:54
Alignment explanation
Indices: 95807--95913 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
95797 CATTGTAGGT
95807 GATCCGGGTTCAAGCATTTATGTGTGCAAGGTGTGTGTGCGCGTTATCAAAGGA
1 GATCCGGGTTCAAGCATTTATGTGTGCAAGGTGTGTGTGCGCGTTATCAAAGGA
95861 GATCCGGGTTCAAGCATTTATGTGTGCAAGGTGTGTGTGCGCGTTATCAAAGG
1 GATCCGGGTTCAAGCATTTATGTGTGCAAGGTGTGTGTGCGCGTTATCAAAGG
95914 GTTAAGAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (54 bp):
GATCCGGGTTCAAGCATTTATGTGTGCAAGGTGTGTGTGCGCGTTATCAAAGGA
Found at i:101384 original size:49 final size:48
Alignment explanation
Indices: 101283--101606 Score: 249
Period size: 49 Copynumber: 6.6 Consensus size: 48
101273 CAGGTTTCAT
* * * * ** * *
101283 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGTAACAACGAATCTAG
1 TACCACAAAGACATGAAGGGAAAGA-TTAAGTCGCAACGGCGAACCTTG
* * * *
101332 TACCACAAAGATATGGAGGGAAACGATTAAGTCGCAATGGCTAACCTTG
1 TACCACAAAGACATGAAGGGAAA-GATTAAGTCGCAACGGCGAACCTTG
* * * * *
101381 TACCTCAGAA-ACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCTAG
1 TACCACA-AAGACATGAAGGGAAAGA-TTAAGTCGCAACGGCGAACCTTG
* * * *
101430 TACCACGAAGATAT-AGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTG
1 TACCACAAAGACATGA-AGGGAAA-GATTAAGTCGCAACGGCGAACCTTG
* * * * * *
101479 TACCTCAAAAACATGAAGAGAAAGATTTAATTCGCAACGGCGAATCTAG
1 TACCACAAAGACATGAAGGGAAAGA-TTAAGTCGCAACGGCGAACCTTG
* * * *
101528 TACCA-ATAAGATATGAAGGGAAAGGTTTAAGTTGCAACGGTGAACCTTG
1 TACCACA-AAGACATGAAGGGAAA-GATTAAGTCGCAACGGCGAACCTTG
* *
101577 TACCTCAAAAACATGAAGGGAAAGATTAAG
1 TACCACAAAGACATGAAGGGAAAGATTAAG
101607 GCTACAGCGA
Statistics
Matches: 210, Mismatches: 54, Indels: 23
0.73 0.19 0.08
Matches are distributed among these distances:
48 13 0.06
49 189 0.90
50 8 0.04
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (48 bp):
TACCACAAAGACATGAAGGGAAAGATTAAGTCGCAACGGCGAACCTTG
Found at i:101452 original size:98 final size:97
Alignment explanation
Indices: 101283--101603 Score: 432
Period size: 98 Copynumber: 3.3 Consensus size: 97
101273 CAGGTTTCAT
* * **
101283 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGTAACAACGAATCTAGTACCACAAAGATATGG
1 TACCTCAAAAACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAAAGATAT-G
* * *
101348 AGGGAAACGATTAAGTCGCAATGGCTAACCTTG
65 AGGGAAAGGTTTAAGTCGCAACGGCTAACCTTG
* *
101381 TACCTCAGAAACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAG
1 TACCTCAAAAACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAAAGATAT-G
* *
101446 AGGGAAAGGTTTAAGTCGCAACGACGAACCTTG
65 AGGGAAAGGTTTAAGTCGCAACGGCTAACCTTG
**
101479 TACCTCAAAAACATG-AAGAGAAAGATTTAATTCGCAACGGCGAATCTAGTACCA-ATAAGATAT
1 TACCTCAAAAACATGAAAG-GAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACA-AAGATAT
*
101542 GAAGGGAAAGGTTTAAGTTGCAACGG-TGAACCTTG
64 G-AGGGAAAGGTTTAAGTCGCAACGGCT-AACCTTG
*
101577 TACCTCAAAAACATGAAGGGAAAGATT
1 TACCTCAAAAACATGAAAGGAAAGATT
101604 AAGGCTACAG
Statistics
Matches: 198, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
97 4 0.02
98 192 0.97
99 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.20
Consensus pattern (97 bp):
TACCTCAAAAACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAAAGATATGA
GGGAAAGGTTTAAGTCGCAACGGCTAACCTTG
Found at i:101649 original size:196 final size:196
Alignment explanation
Indices: 101283--101637 Score: 482
Period size: 196 Copynumber: 1.8 Consensus size: 196
101273 CAGGTTTCAT
* * *
101283 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGTAACAACGAATCTAGTACCACAAAGATATGG
1 TACCTCAAAAACATGAAGAGAAAGATTTAAGCCGCAACAACGAATCTAGTACCACAAAGATATGA
* *
101348 AGGGAAACGATTAAGTCGCAATGGCTAACCTTGTACCTCAGAAACATGAAAGGAAAGATTTAAGC
66 AGGGAAACGATTAAGTCGCAACGGCTAACCTTGTACCTCAAAAACATGAAAGGAAAGATTTAAGC
* * * *
101413 CGCAACGGCGAATCTAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
131 CACAACGACGAACCTACTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
101478 G
196 G
** **
101479 TACCTCAAAAACATGAAGAGAAAGATTTAATTCGCAACGGCGAATCTAGTACCA-ATAAGATATG
1 TACCTCAAAAACATGAAGAGAAAGATTTAAGCCGCAACAACGAATCTAGTACCACA-AAGATATG
* * * *
101543 AAGGGAAAGGTTTAAGTTGCAACGG-TGAACCTTGTACCTCAAAAACATGAAGGGAAAGA-TTAA
65 AAGGGAAACGATTAAGTCGCAACGGCT-AACCTTGTACCTCAAAAACATGAAAGGAAAGATTTAA
* * *
101606 GGCTACAGCGACGAACCTACTACCATGAAGAT
129 -GCCACAACGACGAACCTACTACCACGAAGAT
101638 TTGAAGGGAA
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
195 6 0.04
196 130 0.96
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (196 bp):
TACCTCAAAAACATGAAGAGAAAGATTTAAGCCGCAACAACGAATCTAGTACCACAAAGATATGA
AGGGAAACGATTAAGTCGCAACGGCTAACCTTGTACCTCAAAAACATGAAAGGAAAGATTTAAGC
CACAACGACGAACCTACTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
G
Found at i:101680 original size:98 final size:99
Alignment explanation
Indices: 101283--101657 Score: 406
Period size: 98 Copynumber: 3.8 Consensus size: 99
101273 CAGGTTTCAT
* * *
101283 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGT--AACAACGAATCTAGTACCACAAAGATAT
1 TACCTCAAAAACATGAAGGGAAAGATTTAAGGC-TACAACGACGAATCTAGTACCACGAAGATAT
* *
101346 GGAGGGAAACGA-TTAAGTCGCAATGGCT-AACCTTG
65 GAAGGGAAA-GATTTAAGTCGCAACGG-TGAACCTTG
* * ** *
101381 TACCTCAGAAACATGAAAGGAAAGATTTAA-GCCGCAACGGCGAATCTAGTACCACGAAGATAT-
1 TACCTCAAAAACATGAAGGGAAAGATTTAAGGCTACAACGACGAATCTAGTACCACGAAGATATG
* **
101444 AGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTG
66 A-AGGGAAAGATTTAAGTCGCAACGGTGAACCTTG
* ** * * **
101479 TACCTCAAAAACATGAAGAGAAAGATTTAATTC-GCAACGGCGAATCTAGTACCAATAAGATATG
1 TACCTCAAAAACATGAAGGGAAAGATTTAAGGCTACAACGACGAATCTAGTACCACGAAGATATG
* *
101543 AAGGGAAAGGTTTAAGTTGCAACGGTGAACCTTG
66 AAGGGAAAGATTTAAGTCGCAACGGTGAACCTTG
* * * * *
101577 TACCTCAAAAACATGAAGGGAAAGA-TTAAGGCTACAGCGACGAACCTACTACCATGAAGATTTG
1 TACCTCAAAAACATGAAGGGAAAGATTTAAGGCTACAACGACGAATCTAGTACCACGAAGATATG
*
101641 AAGGGAAAGATTGAAGT
66 AAGGGAAAGATTTAAGT
101658 AGTAATGGTA
Statistics
Matches: 235, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
97 7 0.03
98 226 0.96
99 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (99 bp):
TACCTCAAAAACATGAAGGGAAAGATTTAAGGCTACAACGACGAATCTAGTACCACGAAGATATG
AAGGGAAAGATTTAAGTCGCAACGGTGAACCTTG
Done.