Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006675.1 Kokia drynarioides strain JFW-HI SEQ_121268, 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: 137423
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1595 original size:70 final size:67
Alignment explanation
Indices: 1469--1601 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
1459 ATTAACAATA
* * *
1469 TAATGGTTTTGCCTTTTAACTTAATAGGTAAACATTTATCAAAATGATATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1534 CT
66 CT
* * *
1536 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAATGACGTAGTTTTACTTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAA-GGTAAACATTTATCAAAATGACATAATTTTACCTTT
1601 T
63 T
1602 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 2 0.04
70 33 0.58
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
CT
Found at i:7452 original size:59 final size:60
Alignment explanation
Indices: 7253--7477 Score: 192
Period size: 59 Copynumber: 3.9 Consensus size: 60
7243 AAAATTGATG
* * * *
7253 TTGGCCATTGCATGGTCGACA-CCCTTTTTTATC---T-AACAAATT--TTTTTTT--TG
1 TTGGTCATTGCATGGCCGACACCCCTTTTTTATCTGATAAAAAAATTAATTTTTTTGGTA
* *
7304 TTGGTCA-TGCTATGGCCAACACCTCTTTTTTTATCTGATAAAAAAATTAATTTTTTTGGTA
1 TTGGTCATTGC-ATGGCCGACACC-CCTTTTTTATCTGATAAAAAAATTAATTTTTTTGGTA
** * * *
7365 TTGG-C-TATGCCATGATCGAGACCTCTTTTTTATTTGAT-AAAAAATTAATTTTTTTGGTA
1 TTGGTCAT-TG-CATGGCCGACACCCCTTTTTTATCTGATAAAAAAATTAATTTTTTTGGTA
*
7424 TTGGTCATTGCATGGCCGACACCCC--TTTTATCTGAATAAAAAAATTAAATTTTT
1 TTGGTCATTGCATGGCCGACACCCCTTTTTTATCTG-ATAAAAAAATTAATTTTTT
7478 GGGTGTCGGT
Statistics
Matches: 137, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
50 3 0.02
51 14 0.10
52 1 0.01
53 10 0.07
56 1 0.01
57 15 0.11
58 2 0.01
59 58 0.42
60 16 0.12
61 16 0.12
62 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (60 bp):
TTGGTCATTGCATGGCCGACACCCCTTTTTTATCTGATAAAAAAATTAATTTTTTTGGTA
Found at i:7538 original size:45 final size:46
Alignment explanation
Indices: 7449--7538 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
7439 CCGACACCCC
* * *
7449 TTTTATCTGAATAAAAAAATTAAATTTTTGGGTGTCGGTCATGCCT
1 TTTTATCTGAATAAAAAAATCAAATTTTTGGGTGTAGCTCATGCCT
7495 TTTTATCTGAAT-AAAAAATCAAATTTTTGGGTGTTAGCT-ATGCC
1 TTTTATCTGAATAAAAAAATCAAATTTTTGGGTG-TAGCTCATGCC
7539 ATGACGATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 25 0.62
46 15 0.38
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (46 bp):
TTTTATCTGAATAAAAAAATCAAATTTTTGGGTGTAGCTCATGCCT
Found at i:7587 original size:58 final size:58
Alignment explanation
Indices: 7505--7843 Score: 212
Period size: 58 Copynumber: 5.8 Consensus size: 58
7495 TTTTATCTGA
** * * * *
7505 ATAAAAAATCAAATTTTTGGGTGTTAGCT-ATGCCAT-GACGATACCCTTTTTTGTCAG
1 ATAAAAAATCAAATTTTTTTGTGTT-GCTCATGCAATGGCCGACACCCCTTTTTGTCAG
* * * * *
7562 ATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCCATGGCCGACACCTCTTTTTTTATCTG
1 ATAAAAAA-TCAAATTTTTTTGTGTTGCTCATGCAATGGCCGACACC-C-CTTTTTGTCAG
* * * * *
7623 GTAAAAAA--ACATTTTTTTGTGTTGATCATGTAATGGTCGACACCCCCTTTTTGTCAG
1 ATAAAAAATCAAATTTTTTTGTGTTGCTCATGCAATGGCCGACA-CCCCTTTTTGTCAG
* * *
7680 ATAAAAAATTCTGAA-TTTTTTGTGTTGGC-CATGCAATGGCCGATACCCCTTTTTGTTAG
1 ATAAAAAA-TC-AAATTTTTTTGTGTT-GCTCATGCAATGGCCGACACCCCTTTTTGTCAG
* * * ** * *
7739 ATAAAAATTCTGAA-TTTTTGGTGTTGGC-CATTGC-ATGATCGACACCCCCTTTTTTATCTG
1 ATAAAAAATC-AAATTTTTTTGTGTT-GCTCA-TGCAATGGCCGACA-CCCC-TTTTTGTCAG
* * * * *
7799 GT-AAAAATCAAATTTTTTTATATTGGTCATGCAATGGTCGACACC
1 ATAAAAAATCAAATTTTTTTGTGTTGCTCATGCAATGGCCGACACC
7844 AATTTTCCCT
Statistics
Matches: 225, Mismatches: 40, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
57 25 0.11
58 88 0.39
59 61 0.27
60 33 0.15
61 18 0.08
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (58 bp):
ATAAAAAATCAAATTTTTTTGTGTTGCTCATGCAATGGCCGACACCCCTTTTTGTCAG
Found at i:7757 original size:118 final size:116
Alignment explanation
Indices: 7552--7843 Score: 288
Period size: 118 Copynumber: 2.5 Consensus size: 116
7542 ACGATACCCT
* * *
7552 TTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCCATGGCCGACACCTCTTTTTT
1 TTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTT
* * * * *
7617 TATCTGGTAAAAAAACATTTTTTTGTGTTGATCA-TGTAATGGTCGACACCCCC
66 TA--TGATAAAAAAACAATTTTTGGTGTTGACCATTG-AATGATCGACACCCCC
* *
7670 TTTTTGTCAGATAAAAAATTCTGAA-TTTTTTGTGTTGGCCATGCAATGGCCGATACCCCTTTTT
1 TTTTTGTCAGATAAAAAATTC-AAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTT
** * *
7734 GTTA-GATAAAAATTCTGAATTTTTGGTGTTGGCCATTGCATGATCGACACCCCC
65 -TTATGATAAAAAAAC--AATTTTTGGTGTTGACCATTGAATGATCGACACCCCC
* * * * * * *
7788 TTTTTTATCTGGT-AAAAA-TCAAATTTTTTTATATTGGTCATGCAATGGTCGACACC
1 -TTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACC
7844 AATTTTCCCT
Statistics
Matches: 144, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
116 10 0.07
117 29 0.20
118 89 0.62
119 16 0.11
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (116 bp):
TTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTT
TATGATAAAAAAACAATTTTTGGTGTTGACCATTGAATGATCGACACCCCC
Found at i:7840 original size:59 final size:60
Alignment explanation
Indices: 7548--7843 Score: 254
Period size: 58 Copynumber: 5.0 Consensus size: 60
7538 CATGACGATA
* * *
7548 CCCTTTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGGTCATGCCATGGCCGACACC
1 CCCTTTTTTATCAGAT-AAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACC
* * * * * *
7609 TCTTTTTTTATCTGGTAAAAA---AACATTTTTTTGTGTTGATCATGTAATGGTCGACACC
1 CCCTTTTTTATCAGATAAAAATTCAA-ATTTTTTTGTGTTGGTCATGCAATGGTCGACACC
* * * * *
7667 CCC-TTTTTGTCAGATAAAAAATTCTGAA-TTTTTTGTGTTGGCCATGCAATGGCCGATA-C
1 CCCTTTTTTATCAGAT-AAAAATTC-AAATTTTTTTGTGTTGGTCATGCAATGGTCGACACC
* * * *
7726 CCCTTTTTGT-T-AGATAAAAATTCTGAA-TTTTTGGTGTTGGCCATTGC-ATGATCGACACC
1 CCCTTTTT-TATCAGATAAAAATTC-AAATTTTTTTGTGTTGGTCA-TGCAATGGTCGACACC
* * * *
7785 CCCTTTTTTATCTGGTAAAAA-TCAAATTTTTTTATATTGGTCATGCAATGGTCGACACC
1 CCCTTTTTTATCAGATAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACC
7844 AATTTTCCCT
Statistics
Matches: 189, Mismatches: 32, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
57 11 0.06
58 76 0.40
59 46 0.24
60 42 0.22
61 13 0.07
62 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (60 bp):
CCCTTTTTTATCAGATAAAAATTCAAATTTTTTTGTGTTGGTCATGCAATGGTCGACACC
Found at i:8602 original size:13 final size:13
Alignment explanation
Indices: 8572--8608 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
8562 ATTATCGACA
8572 AATTAAAAAT-AT
1 AATTAAAAATAAT
8584 -ATTAAAAATAAT
1 AATTAAAAATAAT
*
8596 AATTAAAATTAAT
1 AATTAAAAATAAT
8609 TTTAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:10082 original size:6 final size:6
Alignment explanation
Indices: 10013--10094 Score: 58
Period size: 6 Copynumber: 12.7 Consensus size: 6
10003 TCCGTTTACT
* * * *
10013 TTTTAA ATTTAA TTTGTAA TTTT-G TTTTTA TTTTAA ATTTAA TTTCTAA
1 TTTTAA TTTTAA TTT-TAA TTTTAA TTTTAA TTTTAA TTTTAA TTT-TAA
10062 TTCCTGTATA TTTTAA TTTTAA TTTCTAA TTTT
1 TT--T-TA-A TTTTAA TTTTAA TTT-TAA TTTT
10095 CTATATATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.07
6 31 0.51
7 19 0.31
8 1 0.02
9 3 0.05
10 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:10109 original size:30 final size:30
Alignment explanation
Indices: 10013--10107 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 30
10003 TCCGTTTACT
* * * *
10013 TTTTAAATTTAATTTGTAATTTTGTTTTTA
1 TTTTAAATTTAATTTCTAATTTTCTATATA
* *
10043 TTTTAAATTTAATTTCTAA-TTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTTCTATATA
*
10072 TTTTAATTTTAATTTCTAATTTTCTATATA
1 TTTTAAATTTAATTTCTAATTTTCTATATA
10102 TTTTAA
1 TTTTAA
10108 TTATTATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 24 0.43
30 32 0.57
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTTCTATATA
Found at i:10984 original size:59 final size:60
Alignment explanation
Indices: 10894--11167 Score: 274
Period size: 59 Copynumber: 4.6 Consensus size: 60
10884 AGGAAAAGTT
10894 GGTGTCGGCCATTGCATGACCAACACAAAAAAAATT-GATTTTTTACCAGATAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAAATTAGATTTTTTACCAGATAAAAAAGG
* * * * * * *
10953 GGTATCGGCGA-TGCAATGACCAACAC-CAAAAATTTGGATTTTTTATCTA-ATAAAAAGGG
1 GGTGTCGGCCATTGC-ATGACCAACACAAAAAAAATTAGATTTTTTA-CCAGATAAAAAAGG
** * * * *
11012 GGTGTCGATCATTGCATGACCAACACAAAAAAAAATTTAAAATTTTTTATCTGA-CAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACAC-AAAAAAAA-TT-AGATTTTTTACCAGATAAAAAAGG
* * *
11074 AGTGTCAGCCATTGCATGACCAATACAAAAAAAATT-GATTTTTTACCAGATAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAAATTAGATTTTTTACCAGATAAAAAAGG
* *
11133 GGTGTCGACCA-TGTCATGGCCAACACCAAAAAAAA
1 GGTGTCGGCCATTG-CATGACCAACA-CAAAAAAAA
11168 ATTGAAATTT
Statistics
Matches: 170, Mismatches: 33, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
58 23 0.14
59 80 0.47
60 16 0.09
61 13 0.08
62 29 0.17
63 9 0.05
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (60 bp):
GGTGTCGGCCATTGCATGACCAACACAAAAAAAATTAGATTTTTTACCAGATAAAAAAGG
Found at i:11115 original size:121 final size:119
Alignment explanation
Indices: 10894--11262 Score: 319
Period size: 121 Copynumber: 3.1 Consensus size: 119
10884 AGGAAAAGTT
* * * * * * *
10894 GGTGTCGGCCATTGCATGACCAACAC-AAAAAAAATT-GATTTTTTACCAGATAAAAAAGGGGTA
1 GGTGTCGACCATTGCATGACCAACACAAAAAAAAATTAAATTTTTTATCTGA-CAAAAAGGAGTG
* * * * * *
10957 TCGGCGATGCAATGACCAACACCAAAAATTTGGATTTTTTATCTA-ATAAAAAGGG
65 TCAGCCATGCAATGACCAACACAAAAAAATTGGATTTTTTA-CCAGATAAAAAAGG
*
11012 GGTGTCGATCATTGCATGACCAACACAAAAAAAAATTTAAAATTTTTTATCTGACAAAAAGGAGT
1 GGTGTCGACCATTGCATGACCAACACAAAAAAAAA-TT-AAATTTTTTATCTGACAAAAAGGAGT
*
11077 GTCAGCCATTGC-ATGACCAATACAAAAAAAATT-GATTTTTTACCAGATAAAAAAGG
64 GTCAGCCA-TGCAATGACCAACAC-AAAAAAATTGGATTTTTTACCAGATAAAAAAGG
* * *
11133 GGTGTCGACCA-TGTCATGGCCAACACCAAAAAAAAATTGAAA-TTTTTCTCTAACAAAAAGAGA
1 GGTGTCGACCATTG-CATGACCAACA-CAAAAAAAAATT-AAATTTTTTATCTGACAAAAAG-GA
* * * * * *
11196 GTGTC-GACTATGTC-ATGGCCAACATC-CAAAAATTTGATTTTTTATTCAGAT-AAAAAGA
62 GTGTCAG-CCATG-CAATGACCAACA-CAAAAAAATTGGATTTTTTA-CCAGATAAAAAAGG
11254 GGTGTCGAC
1 GGTGTCGAC
11263 TATGTAATGG
Statistics
Matches: 210, Mismatches: 26, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
118 24 0.11
119 8 0.04
120 32 0.15
121 109 0.52
122 37 0.18
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (119 bp):
GGTGTCGACCATTGCATGACCAACACAAAAAAAAATTAAATTTTTTATCTGACAAAAAGGAGTGT
CAGCCATGCAATGACCAACACAAAAAAATTGGATTTTTTACCAGATAAAAAAGG
Found at i:11261 original size:59 final size:57
Alignment explanation
Indices: 10908--11297 Score: 238
Period size: 59 Copynumber: 6.5 Consensus size: 57
10898 TCGGCCATTG
* * * * * * *
10908 CATGACCAACACAAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTATCGGCGATG-
1 CATGGCCAACAC-CAAAAAATTGATTTTTTATCAGAT-AAAAAGAGGTGTCGACTATGT
* * *
10966 CAATGACCAACACCAAAAATTTGGATTTTTTATCTA-ATAAAAAGGGGGTGTCGA-TCAT-T
1 C-ATGGCCAACACCAAAAAATT-GATTTTTTATC-AGATAAAAA-GAGGTGTCGACT-ATGT
* * * * * *
11025 GCATGACCAACACAAAAAAAAATTTAAAATTTTTTATCTGACAAAAAG-GAGTGTC-AGCCAT-T
1 -CATGGCCAACAC--CAAAAAA-TT--GATTTTTTATCAGATAAAAAGAG-GTGTCGA-CTATGT
* * * * * *
11087 GCATGACCAATACAAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCGACCATGT
1 -CATGGCCAACAC-CAAAAAATTGATTTTTTATCAGAT-AAAAAGAGGTGTCGACTATGT
* * *
11147 CATGGCCAACACCAAAAAAAAATTGAAATTTTTCTCTA-ACAAAAAGAGAGTGTCGACTATGT
1 CATGGCCAACACC---AAAAAATTG-ATTTTTTATC-AGATAAAAAGAG-GTGTCGACTATGT
*
11209 CATGGCCAACATCCAAAAATTTGATTTTTTATTCAGATAAAAAGAGGTGTCGACTATGT
1 CATGGCCAACA-CCAAAAAATTGATTTTTTA-TCAGATAAAAAGAGGTGTCGACTATGT
*
11268 AATGGCCAACACCCAAAAAATTGATTTTTT
1 CATGGCCAACA-CCAAAAAATTGATTTTTT
11298 TTTATTAGAT
Statistics
Matches: 270, Mismatches: 34, Indels: 55
0.75 0.09 0.15
Matches are distributed among these distances:
58 24 0.09
59 116 0.43
60 26 0.10
61 31 0.11
62 54 0.20
63 19 0.07
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (57 bp):
CATGGCCAACACCAAAAAATTGATTTTTTATCAGATAAAAAGAGGTGTCGACTATGT
Found at i:11273 original size:121 final size:120
Alignment explanation
Indices: 10968--11347 Score: 350
Period size: 121 Copynumber: 3.1 Consensus size: 120
10958 CGGCGATGCA
10968 ATGACCAACACCAAAAATTTGGATTTTTTATCTA-ATAAAAAGGGGGTGTCGA-TCAT-TGCATG
1 ATGACCAACACCAAAAATTT-GATTTTTTATC-AGATAAAAA-GGGGTGTCGACT-ATGT-CATG
* *
11030 ACCAACA-CAAAAAAAAATTTAAAATTTTTTATCTGACAAAAAGGAGTGTCAGCCATTGC
61 GCCAACACCAAAAAAAAATTTAAAATTTTTTATCTAACAAAAAGGAGTGTCAGCCATTGC
* * * * *
11089 ATGACCAATACAAAAAAAATTGATTTTTTACCAGATAAAAAAGGGGTGTCGACCATGTCATGGCC
1 ATGACCAACAC-CAAAAATTTGATTTTTTATCAGAT-AAAAAGGGGTGTCGACTATGTCATGGCC
* * *
11154 AACACCAAAAAAAAA-TTGAAA-TTTTTCTCTAACAAAAAGAGAGTGTC-GAC-TATGTC
64 AACACCAAAAAAAAATTTAAAATTTTTTATCTAACAAAAAG-GAGTGTCAGCCAT-TG-C
* * *
11210 ATGGCCAACATCCAAAAATTTGATTTTTTATTCAGATAAAAAGAGGTGTCGACTATGTAATGGCC
1 ATGACCAACA-CCAAAAATTTGATTTTTTA-TCAGATAAAAAGGGGTGTCGACTATGTCATGGCC
* * *** * ** *
11275 AACACC--CAAAAAATTGATTTTTTTTTAT-TAGATAAAAAGGAAGTGTCAGTTATGGC
64 AACACCAAAAAAAAATTTAAAATTTTTTATCTA-ACAAAAAGG-AGTGTCAGCCATTGC
*
11331 ATGACCAACACTAAAAA
1 ATGACCAACACCAAAAA
11348 AATCATGGCC
Statistics
Matches: 211, Mismatches: 31, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
119 7 0.03
120 31 0.15
121 141 0.67
122 31 0.15
123 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (120 bp):
ATGACCAACACCAAAAATTTGATTTTTTATCAGATAAAAAGGGGTGTCGACTATGTCATGGCCAA
CACCAAAAAAAAATTTAAAATTTTTTATCTAACAAAAAGGAGTGTCAGCCATTGC
Found at i:11341 original size:62 final size:59
Alignment explanation
Indices: 11102--11321 Score: 214
Period size: 62 Copynumber: 3.6 Consensus size: 59
11092 ACCAATACAA
* ** * *
11102 AAAAAATTGATTTTTTA-CCAGATAAAAAAGGGGTGTCGACCATGTCATGGCCAACACCAAA
1 AAAAAATTGATTTTTTATTCAGAT-AAAAAGAAGTGTCGACTATGTCATGGCCAACACC--C
* * * *
11163 AAAAAATTGAAATTTTT-CTCTA-ACAAAAAGAGAGTGTCGACTATGTCATGGCCAACATCC
1 AAAAAATTG-ATTTTTTATTC-AGATAAAAAGA-AGTGTCGACTATGTCATGGCCAACACCC
* * *
11223 AAAAATTTGATTTTTTATTCAGATAAAAAGAGGTGTCGACTATGTAATGGCCAACACCC
1 AAAAAATTGATTTTTTATTCAGATAAAAAGAAGTGTCGACTATGTCATGGCCAACACCC
11282 AAAAAATTGATTTTTTTTTATT-AGATAAAAAGGAAGTGTC
1 AAAAAATTGA---TTTTTTATTCAGATAAAAA-GAAGTGTC
11322 AGTTATGGCA
Statistics
Matches: 132, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
59 41 0.31
60 18 0.14
61 24 0.18
62 48 0.36
63 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (59 bp):
AAAAAATTGATTTTTTATTCAGATAAAAAGAAGTGTCGACTATGTCATGGCCAACACCC
Found at i:11347 original size:61 final size:62
Alignment explanation
Indices: 11187--11350 Score: 158
Period size: 62 Copynumber: 2.7 Consensus size: 62
11177 TTTCTCTAAC
** * * *
11187 AAAAAGAGAGTGTCGACTATGTCATGGCCAACATCCAAAAATTTGA---TTTTTTATTCAGAT
1 AAAAAGA-AGTGTCGACTATGGAATGACCAACACCCAAAAAATTGATTTTTTTTTATTCAGAT
* * *
11247 AAAAAGAGGTGTCGACTATGTAATGGCCAACACCCAAAAAATTGATTTTTTTTTATT-AGAT
1 AAAAAGAAGTGTCGACTATGGAATGACCAACACCCAAAAAATTGATTTTTTTTTATTCAGAT
* * **
11308 AAAAAGGAAGTGTC-AGTTATGGCATGACCAACACTAAAAAAAT
1 AAAAA-GAAGTGTCGA-CTATGGAATGACCAACACCCAAAAAAT
11351 CATGGCCGAC
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
59 34 0.39
60 7 0.08
61 10 0.11
62 37 0.42
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (62 bp):
AAAAAGAAGTGTCGACTATGGAATGACCAACACCCAAAAAATTGATTTTTTTTTATTCAGAT
Found at i:22308 original size:7 final size:7
Alignment explanation
Indices: 22298--22327 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
22288 TGGGTATTGG
22298 GCTGAAT
1 GCTGAAT
22305 GCTGAAT
1 GCTGAAT
22312 GCTGAAT
1 GCTGAAT
22319 GCTGAAT
1 GCTGAAT
22326 GC
1 GC
22328 CTCGTACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (7 bp):
GCTGAAT
Found at i:23366 original size:18 final size:18
Alignment explanation
Indices: 23322--23401 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
23312 CTGTGCTAGC
23322 TCGCCAATCTTAGA-GGGCT
1 TCGCCAATCTT-GATGGG-T
*
23341 T-GCAAATCTTGATGGG-
1 TCGCCAATCTTGATGGGT
* * *
23357 TCTGTCAATCTTGGTGGAT
1 TC-GCCAATCTTGATGGGT
23376 TCGCCAATCTTGATGGGT
1 TCGCCAATCTTGATGGGT
23394 TCGCCAAT
1 TCGCCAAT
23402 TTTTAAGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.02
17 2 0.04
18 43 0.88
19 3 0.06
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (18 bp):
TCGCCAATCTTGATGGGT
Found at i:23411 original size:18 final size:18
Alignment explanation
Indices: 23322--23418 Score: 56
Period size: 18 Copynumber: 5.4 Consensus size: 18
23312 CTGTGCTAGC
23322 TCGCCAATCTT-AGAGGGCT
1 TCGCCAATCTTGA-AGGG-T
* *
23341 T-GCAAATCTTGATGGG-
1 TCGCCAATCTTGAAGGGT
* ** *
23357 TCTGTCAATCTTGGTGGAT
1 TC-GCCAATCTTGAAGGGT
*
23376 TCGCCAATCTTGATGGGT
1 TCGCCAATCTTGAAGGGT
* *
23394 TCGCCAATTTTTAAGGGT
1 TCGCCAATCTTGAAGGGT
*
23412 TCACCAA
1 TCGCCAA
23419 ATATGAGGAG
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
16 1 0.02
18 56 0.92
19 4 0.07
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (18 bp):
TCGCCAATCTTGAAGGGT
Found at i:42900 original size:24 final size:23
Alignment explanation
Indices: 42843--42901 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
42833 TACAAATTGG
42843 TTAAGGTAAAAATTCTGAAAATT
1 TTAAGGTAAAAATTCTGAAAATT
42866 TTAAGGTAAAAATTCTGAAAATT
1 TTAAGGTAAAAATTCTGAAAATT
42889 TTATA-GTAAAAAT
1 TTA-AGGTAAAAAT
42902 ATGATTGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (23 bp):
TTAAGGTAAAAATTCTGAAAATT
Found at i:43386 original size:24 final size:22
Alignment explanation
Indices: 43311--43387 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
43301 CGTTTCGTAC
*
43311 CCTCTGTTCAGCACTGTGTGTG
1 CCTCTGTTCAGCACTTTGTGTG
*
43333 CTTCTGTTCAGCACTTTGTGTG
1 CCTCTGTTCAGCACTTTGTGTG
43355 CCTACTGTTGCTAGCACTTATGTGT-
1 CCT-CTGTT-C-AGCACTT-TGTGTG
43380 CCTCTGTT
1 CCTCTGTT
43388 AAGTACTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 22 0.46
23 5 0.10
24 6 0.12
25 10 0.21
26 5 0.10
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (22 bp):
CCTCTGTTCAGCACTTTGTGTG
Found at i:46489 original size:47 final size:47
Alignment explanation
Indices: 46411--46500 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
46401 CCATGAGTGG
* * *
46411 CACTCGGGATAACACTACAGACACTCAAGATTGTTTTGACTAGCGGC
1 CACTCAGGATAACACTACAGACACCCAAGATTATTTTGACTAGCGGC
* * *
46458 CACTCAGGATAATACTACAGATACCCGAGATTATTTTGACTAG
1 CACTCAGGATAACACTACAGACACCCAAGATTATTTTGACTAG
46501 AAGTCATGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (47 bp):
CACTCAGGATAACACTACAGACACCCAAGATTATTTTGACTAGCGGC
Found at i:69036 original size:17 final size:18
Alignment explanation
Indices: 69014--69056 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
69004 TTTTTTTTTC
69014 AAAATTAAAAAAATAT-T
1 AAAATTAAAAAAATATAT
*
69031 AAAATTAAAAATATATAT
1 AAAATTAAAAAAATATAT
69049 AGAAATTA
1 A-AAATTA
69057 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.65
18 2 0.09
19 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATTAAAAAAATATAT
Found at i:76351 original size:17 final size:18
Alignment explanation
Indices: 76304--76365 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 18
76294 TAAAATCATA
76304 AAAAATATAGAAAATCATAAAT
1 AAAAATATAGAAAAT--T--AT
76326 AATAAATATAG-AAATTAT
1 AA-AAATATAGAAAATTAT
76344 AAAAATATAGAAAATTAT
1 AAAAATATAGAAAATTAT
76362 AAAA
1 AAAA
76366 TTTATTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.21
18 15 0.39
20 1 0.03
22 6 0.16
23 8 0.21
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAATATAGAAAATTAT
Found at i:76455 original size:9 final size:9
Alignment explanation
Indices: 76441--76575 Score: 60
Period size: 9 Copynumber: 14.0 Consensus size: 9
76431 ATATATTATG
76441 AAAAATATA
1 AAAAATATA
*
76450 AAAAATTTTA
1 AAAAA-TATA
*
76460 AAAAATAGA
1 AAAAATATA
* *
76469 AACATTATA
1 AAAAATATA
76478 TAAAAATATA
1 -AAAAATATA
*
76488 GAAAATTATTTA
1 -AAAA--ATATA
76500 AAAAAT-TA
1 AAAAATATA
76508 ATAAAAT-TA
1 A-AAAATATA
76517 ACAAAATATTA
1 A-AAAATA-TA
*
76528 TAGAAAACATA
1 -A-AAAATATA
**
76539 AAAAGCATA
1 AAAAATATA
*
76548 AAAATTATA
1 AAAAATATA
76557 AAACAA-ATTA
1 AAA-AATA-TA
76567 AAAAATATA
1 AAAAATATA
76576 TGAAAAGGTT
Statistics
Matches: 98, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
8 3 0.03
9 50 0.51
10 27 0.28
11 8 0.08
12 10 0.10
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAAATATA
Found at i:76481 original size:20 final size:19
Alignment explanation
Indices: 76441--76505 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
76431 ATATATTATG
*
76441 AAAAATATAAAAAATT-T-T
1 AAAAA-ATAGAAAATTATAT
76459 AAAAAATAGAAACATTATAT
1 AAAAAATAGAAA-ATTATAT
*
76479 AAAAATATAGAAAATTATTT
1 AAAAA-ATAGAAAATTATAT
76499 AAAAAAT
1 AAAAAAT
76506 TAATAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.15
18 8 0.20
19 3 0.07
20 17 0.41
21 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAAATAGAAAATTATAT
Found at i:76833 original size:20 final size:20
Alignment explanation
Indices: 76808--76856 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
76798 AAATTATAGA
* * *
76808 TATATTTTTTTTTTATATTT
1 TATATTCTTTTTGTAAATTT
76828 TATATTCTTTTTGTAAATTT
1 TATATTCTTTTTGTAAATTT
76848 TATA-TCTTT
1 TATATTCTTT
76857 GAGTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (20 bp):
TATATTCTTTTTGTAAATTT
Found at i:76925 original size:10 final size:10
Alignment explanation
Indices: 76912--76956 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
76902 TTTTTCGCAC
76912 TTTTATATAT
1 TTTTATATAT
76922 TTTTATA-AT
1 TTTTATATAT
* *
76931 ATTTTAAATAA
1 -TTTTATATAT
76942 TTTTATATAT
1 TTTTATATAT
76952 TTTTA
1 TTTTA
76957 AATACTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.90
11 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTATATAT
Found at i:76935 original size:20 final size:19
Alignment explanation
Indices: 76912--76973 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
76902 TTTTTCGCAC
* *
76912 TTTTATATATTTTTATAATA
1 TTTTAAATAATTTTAT-ATA
76932 TTTTAAATAATTTTATATA
1 TTTTAAATAATTTTATATA
* *
76951 TTTTTAAATACTTTCATA-A
1 -TTTTAAATAATTTTATATA
76970 TTTT
1 TTTT
76974 GTTATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 29 0.78
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAATAATTTTATATA
Found at i:76969 original size:28 final size:30
Alignment explanation
Indices: 76912--76982 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
76902 TTTTTCGCAC
*
76912 TTTTATATATTTTTATAATATTTTAAATAA
1 TTTTATATATTTTTATAATACTTTAAATAA
*
76942 TTTTATATATTTTTA-AATACTTT-CATAA
1 TTTTATATATTTTTATAATACTTTAAATAA
*
76970 TTTTGT-TATTTTT
1 TTTTATATATTTTT
76983 TCATAGTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.18
28 9 0.24
29 7 0.18
30 15 0.39
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTTATATATTTTTATAATACTTTAAATAA
Found at i:80049 original size:28 final size:27
Alignment explanation
Indices: 79993--80049 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
79983 GATATACCAA
* * *
79993 TTTTTTCATTTTTTATAATTTATGTAT
1 TTTTTTCATTTATAATAATTTATGAAT
80020 TTTTTGTCATTTATAATAATTTTAT-AAT
1 TTTTT-TCATTTATAATAA-TTTATGAAT
80048 TT
1 TT
80050 CCTATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 5 0.20
28 15 0.60
29 5 0.20
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTTTCATTTATAATAATTTATGAAT
Found at i:80060 original size:18 final size:18
Alignment explanation
Indices: 80002--80122 Score: 83
Period size: 18 Copynumber: 6.8 Consensus size: 18
79992 ATTTTTTCAT
*
80002 TTTTTATAA-TTTATGTA
1 TTTTTATAATTTTATATA
* *
80019 TTTTTTGTCA-TTTATAATA
1 -TTTTTATAATTTTAT-ATA
* **
80038 ATTTTATAATTTCCTATA
1 TTTTTATAATTTTATATA
* *
80056 TTTTTTTATTTTTATATA
1 TTTTTATAATTTTATATA
80074 TTTGTTAT--TTTTATAATA
1 TTT-TTATAATTTTAT-ATA
80092 TTTTTATAATTTT-TATGA
1 TTTTTATAATTTTATAT-A
80110 TTTTTAT-ATTTTA
1 TTTTTATAATTTTA
80123 ATGATTTTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
17 17 0.21
18 52 0.64
19 12 0.15
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTATAATTTTATATA
Found at i:80081 original size:17 final size:16
Alignment explanation
Indices: 80052--80122 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 16
80042 TATAATTTCC
*
80052 TATATTTTTTTATTTT
1 TATATATTTTTATTTT
80068 TATATATTTGTTATTTT
1 TATATATTT-TTATTTT
80085 TATAATATTTTTATAATTT
1 TAT-ATATTTTTAT--TTT
80104 T-TATGATTTTTATATTT
1 TATAT-ATTTTTAT-TTT
80121 TA
1 TA
80123 ATGATTTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
16 8 0.17
17 21 0.44
18 15 0.31
19 4 0.08
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TATATATTTTTATTTT
Found at i:80126 original size:17 final size:16
Alignment explanation
Indices: 80058--80130 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 16
80048 TTCCTATATT
80058 TTTTTAT-TTTTATATA
1 TTTTTATATTTTA-ATA
*
80074 TTTGTTATTTTTATAATA
1 TTT-TTATATTT-TAATA
*
80092 TTTTTATAATTTTTATGA
1 TTTTTAT-ATTTTAAT-A
80110 TTTTTATATTTTAATGA
1 TTTTTATATTTTAAT-A
80127 TTTT
1 TTTT
80131 AAAATTACCA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.06
17 24 0.49
18 20 0.41
19 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
TTTTTATATTTTAATA
Found at i:90918 original size:19 final size:20
Alignment explanation
Indices: 90875--90918 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
90865 TTGAGAAAAT
90875 TATTTAATTAAAAAAATTAA
1 TATTTAATTAAAAAAATTAA
* *
90895 T-TTTAATTTAATAAA-TAA
1 TATTTAATTAAAAAAATTAA
90913 TATTTA
1 TATTTA
90919 TTTTGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 16 0.76
20 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTTAATTAAAAAAATTAA
Found at i:91388 original size:107 final size:107
Alignment explanation
Indices: 91204--91420 Score: 317
Period size: 107 Copynumber: 2.0 Consensus size: 107
91194 GTTGGACTAA
* * *
91204 AAACGCACAACTTTGAGATATTGTTATTCTGCTAGGAAATATGCAGAATTTATTTTTTAAGTATA
1 AAACGCACAACTTTGAGATATTGTTATTCTACTAGAAAATATGCAGAATTTATTTTCTAAGTATA
* * * * * *
91269 AATTCAATTTTCTTGGAATAAATATTCTATTGGTTTCTATTG
66 AACTCAAATTTCTGGGAATAAAGATACTATTGGTTTCTATAG
* * *
91311 AAACGCACAACTTTGAGATATTGTTATTCTACTCGAAAATTTTCAGAATTTATTTTCTAAGTATA
1 AAACGCACAACTTTGAGATATTGTTATTCTACTAGAAAATATGCAGAATTTATTTTCTAAGTATA
*
91376 AACTCAAATTTCTGGGAATAACGATACTATTGGTTTCTATAG
66 AACTCAAATTTCTGGGAATAAAGATACTATTGGTTTCTATAG
91418 AAA
1 AAA
91421 GAGATTTACT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
107 97 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (107 bp):
AAACGCACAACTTTGAGATATTGTTATTCTACTAGAAAATATGCAGAATTTATTTTCTAAGTATA
AACTCAAATTTCTGGGAATAAAGATACTATTGGTTTCTATAG
Found at i:93580 original size:62 final size:61
Alignment explanation
Indices: 93498--93689 Score: 203
Period size: 61 Copynumber: 3.1 Consensus size: 61
93488 ATAAATTTAG
* * * *
93498 GTACCAAATTAAATCTAAAAAAAAGCTTAGGTACCAAATGAGGAAAAAAATGTCAAGTTCAA
1 GTACCAAATTAGATCAAAAAAAAAGTTTAGGTACCAAATTAGG-AAAAAATGTCAAGTTCAA
* * * *
93560 GTACCAAATTTGATC-CAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTTAAGTTC-A
1 GTACCAAATTAGATCAAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
* * * *
93619 GAAACCCAA-TCGAGTCAAAAAAAAAAGTTTAGGTATCAAATTA-GAAAAAATGTCAAGTTCAA
1 G-TACCAAATTAGA-TC-AAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
*
93681 TTACCAAAT
1 GTACCAAAT
93690 GTTATATTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
59 5 0.05
60 21 0.20
61 44 0.41
62 37 0.35
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (61 bp):
GTACCAAATTAGATCAAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:113536 original size:3 final size:3
Alignment explanation
Indices: 113530--113560 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
113520 TATTACTATC
113530 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
113561 TTAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:113985 original size:23 final size:23
Alignment explanation
Indices: 113950--113999 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
113940 TTGTTAGTCA
*
113950 TTTTAAAGGAAAGTGTTTAACTTT
1 TTTTAAAGCAAAGT-TTTAACTTT
* *
113974 TTTTAAA-CAAAGTTTTGATTTT
1 TTTTAAAGCAAAGTTTTAACTTT
113996 TTTT
1 TTTT
114000 TAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 5 0.22
24 7 0.30
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (23 bp):
TTTTAAAGCAAAGTTTTAACTTT
Found at i:114205 original size:18 final size:19
Alignment explanation
Indices: 114167--114206 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
114157 AGAATTTTGA
* *
114167 TTTTTAAGAAATGTAGTTT
1 TTTTTAAAAAATGTAGATT
114186 TTTTTAAAAAAT-TAGATT
1 TTTTTAAAAAATGTAGATT
114204 TTT
1 TTT
114207 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTTTAAAAAATGTAGATT
Found at i:114264 original size:138 final size:138
Alignment explanation
Indices: 113914--114454 Score: 533
Period size: 137 Copynumber: 3.9 Consensus size: 138
113904 AAAACAAAGT
* * ** *
113914 TTAGATTTTTAAAAATAAAAACACG-TTTGTTAGTCATTTTAAAGGAAAGTGTTTAACTTTTTTT
1 TTAGATTTTTAAAAATAAAAA-ATGTTTTTTTAGTCATTTTAAAGGAAAAAGTTTAA--ATTTTT
* * *
113978 AAACAAAGTTTTGATTTTTTTTTAATTATTTTAAAATAAAAATTTTAATTTTTAAGAAAAGTAAT
63 AAACAAAG-TTTGA-TTTTTTTTAACTATTTCAAAATAAAAATTTTAATTTTTAAGAAAAGTAGT
114043 GATTTTTTAAAAAA
126 -ATTTTTTAAAAAA
* ** *** * ** * *
114057 -AAGAAAGTTTAGATTTTTAAAAATAATTTTTTAGTCATTTTAAAGGAAAAAGTCTAAAATTTTA
1 TTAG-ATTTTTA-AAAATAAAAAATGTTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTTTTA
* * * * *
114121 AACAAAGTTTTGATTTTTTTTAATTATTTCAAAATAAGAATTTTGATTTTTAAGAAATGTAGTTT
64 AACAAAG-TTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTAATTTTTAAGAAAAGTAGTAT
114186 TTTTTAAAAAA
128 TTTTTAAAAAA
* * * *
114197 TTAGATTTTTAAAAAT-AAAAATGTTTTTTTATTTATTTTAAAGGAAAATGTTTAAATTTTTAGA
1 TTAGATTTTTAAAAATAAAAAATGTTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTTTTAAA
** * * * *
114261 CAAAGTTTGA-TTTTTTTAACTATTTTGAAATAAAAGTTTTAATTTGTAA-AAAAATAGTAATTT
66 CAAAGTTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTAATTTTTAAGAAAAGTAGTATTTT
**
114324 AAAAAATATA
131 TTAAAA-A-A
* *
114334 TTTGGACTTTTAAAAATAAAAAAT-TGTTTTTTAGTCATTTTAAA--AAAAAGTTTAAATTTTTA
1 -TTAGATTTTTAAAAATAAAAAATGT-TTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTTTTA
* * *
114396 AACAAAGTTT-ATTTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTATGAAAAGTA
64 AACAAAGTTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTAATTTTTAAGAAAAGTA
114455 ATGGTTTTGT
Statistics
Matches: 327, Mismatches: 60, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
135 14 0.04
136 34 0.10
137 66 0.20
138 66 0.20
139 24 0.07
140 17 0.05
141 47 0.14
142 20 0.06
143 6 0.02
144 33 0.10
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (138 bp):
TTAGATTTTTAAAAATAAAAAATGTTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATTTTTAAA
CAAAGTTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTAATTTTTAAGAAAAGTAGTATTTT
TTAAAAAA
Found at i:114402 original size:19 final size:19
Alignment explanation
Indices: 114370--114406 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
114360 TTTTTTAGTC
114370 ATTTTAAAAAAAAGTTTAA
1 ATTTTAAAAAAAAGTTTAA
* *
114389 ATTTTTAAACAAAGTTTA
1 ATTTTAAAAAAAAGTTTA
114407 TTTTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTTAAAAAAAAGTTTAA
Found at i:114412 original size:137 final size:135
Alignment explanation
Indices: 113914--114451 Score: 417
Period size: 138 Copynumber: 3.9 Consensus size: 135
113904 AAAACAAAGT
* * * ** *
113914 TTAGATTTTTAAAAATAAAAACACG-TTTGTTAGTCATTTTAAAGGAAAGTGTTTAACTTTTTTT
1 TTAGACTTTTAAAAAT-AAAA-ATGTTTTTTTAGTCATTTTAAA-GAAAAAGTTTAA--ATTTTT
* ** * * * *
113978 AAACAAAGTTTTGATTTTTTTTTAATTATTTTAAAATAAAAATTTTAATTTTTAAGAAAAGTAAT
61 AAACAAAG-TTTGA-TTTTTTTTAACTATTTCGAAAT-AAAATTTTGATTTGTAAGAAAAATAGT
* *
114043 GATTTTTTAAAAAAA
123 -A-ATTTAAAAAAAA
** *** ** * *
114058 --AGAAAGTTTAGATTTTTAAAAATAATTTTTTAGTCATTTTAAAGGAAAAAGTCTAAAATTTTA
1 TTAG-ACTTTTA-A-AAATAAAAATGTTTTTTTAGTCATTTTAAA-GAAAAAGTTTAAATTTTTA
* * * ** **
114121 AACAAAGTTTTGATTTTTTTTAATTATTTCAAAATAAGAATTTTGATTTTTAAGAAATGTAGTTT
62 AACAAAG-TTTGATTTTTTTTAACTATTTCGAAATAA-AATTTTGATTTGTAAGAAAAATAGTAA
**
114186 TTTTTAAAAAA
125 TTTAAAAAAAA
* * * * *
114197 TTAGATTTTTAAAAATAAAAATGTTTTTTTATTTATTTTAAAGGAAAATGTTTAAATTTTTAGAC
1 TTAGACTTTTAAAAATAAAAATGTTTTTTTAGTCATTTTAAA-GAAAAAGTTTAAATTTTTAAAC
* *
114262 AAAGTTTGA-TTTTTTTAACTATTTTGAAATAAAAGTTTTAATTTGTAA-AAAAATAGTAATTTA
65 AAAGTTTGATTTTTTTTAACTATTTCGAAATAAAA-TTTTGATTTGTAAGAAAAATAGTAATTTA
114325 AAAAATATA
129 AAAAA-A-A
*
114334 TTTGGACTTTTAAAAATAAAAAAT-TGTTTTTTAGTCATTTTAAA-AAAAAGTTTAAATTTTTAA
1 -TTAGACTTTTAAAAAT-AAAAATGT-TTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAA
* *
114397 ACAAAGTTT-ATTTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTATGAAAA
63 ACAAAGTTTGATTTTTTTTAACTATTTCGAAAT-AAAATTTTGATTTGTAAGAAAA
114452 GTAATGGTTT
Statistics
Matches: 325, Mismatches: 53, Indels: 38
0.78 0.13 0.09
Matches are distributed among these distances:
135 16 0.05
136 33 0.10
137 62 0.19
138 69 0.21
139 34 0.10
140 7 0.02
141 45 0.14
142 20 0.06
143 6 0.02
144 32 0.10
145 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (135 bp):
TTAGACTTTTAAAAATAAAAATGTTTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACA
AAGTTTGATTTTTTTTAACTATTTCGAAATAAAATTTTGATTTGTAAGAAAAATAGTAATTTAAA
AAAAA
Found at i:115833 original size:3 final size:3
Alignment explanation
Indices: 115825--115855 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
115815 AAATCTTTTA
115825 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
115856 GATCAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:118212 original size:35 final size:35
Alignment explanation
Indices: 118173--118243 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
118163 AACAGCAACA
118173 TAGAATTGCAAACAAAGTCGATTAATTTCCTTCTT
1 TAGAATTGCAAACAAAGTCGATTAATTTCCTTCTT
118208 TAGAATTGCAAACAAAGTCGATTAATTTCCTTCTT
1 TAGAATTGCAAACAAAGTCGATTAATTTCCTTCTT
118243 T
1 T
118244 CACTGTCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (35 bp):
TAGAATTGCAAACAAAGTCGATTAATTTCCTTCTT
Found at i:120030 original size:23 final size:23
Alignment explanation
Indices: 119980--120031 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
119970 ACAAAGTACT
**
119980 GAGCACACAAAGTGCTAATTAGA
1 GAGCACACAAAGTGCTAAACAGA
* *
120003 TAGCACACAAAGTGCTAAACGGA
1 GAGCACACAAAGTGCTAAACAGA
120026 GAGCAC
1 GAGCAC
120032 GAGATGTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAAACAGA
Found at i:130475 original size:22 final size:22
Alignment explanation
Indices: 130450--130501 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
130440 ATGTGCAAAC
130450 CCTATATGAAGTATTACAG-GAA
1 CCTATATGAAGTATTA-AGTGAA
* *
130472 CCTATATGAATTATTATGTGAA
1 CCTATATGAAGTATTAAGTGAA
130494 CCTATATG
1 CCTATATG
130502 CGAACCCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
CCTATATGAAGTATTAAGTGAA
Found at i:130515 original size:35 final size:35
Alignment explanation
Indices: 130472--130585 Score: 133
Period size: 35 Copynumber: 3.2 Consensus size: 35
130462 ATTACAGGAA
130472 CCTATATGAATTATTATGTGAACCTATATGCGAAC
1 CCTATATGAATTATTATGTGAACCTATATGCGAAC
* * * *
130507 CCTGTATGAAGTATTATGCGAACATATATGC-AGAC
1 CCTATATGAATTATTATGTGAACCTATATGCGA-AC
* *
130542 CCTATATGAATTAGTATGCT-AACCTTATATGTGAAC
1 CCTATATGAATTATTATG-TGAACC-TATATGCGAAC
130578 CCTATATG
1 CCTATATG
130586 CTAACCAGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
34 1 0.02
35 47 0.72
36 16 0.25
37 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (35 bp):
CCTATATGAATTATTATGTGAACCTATATGCGAAC
Found at i:132596 original size:37 final size:38
Alignment explanation
Indices: 132542--132616 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 38
132532 TTGGGACATC
132542 CCCAAACATAAATAACTT-AAGTGCTAAGTAC-TTTCCT
1 CCCAAACATAAATAACTTAAAG-GCTAAGTACATTTCCT
*
132579 CCCAATCATAAGA-AACTTAAAGGCTAAGTACATTTCCT
1 CCCAAACATAA-ATAACTTAAAGGCTAAGTACATTTCCT
132617 ATCCATATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 24 0.71
38 10 0.29
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (38 bp):
CCCAAACATAAATAACTTAAAGGCTAAGTACATTTCCT
Found at i:136316 original size:15 final size:14
Alignment explanation
Indices: 136283--136316 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
136273 ATAAGATTAA
136283 ATTTAAAAAATAAT
1 ATTTAAAAAATAAT
*
136297 TTTTAAAAAATCAAT
1 ATTTAAAAAAT-AAT
136312 ATTTA
1 ATTTA
136317 TTTTTATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTAAAAAATAAT
Done.