Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_10639
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, 685
Length: 1142
ACGTcount: A:0.19, C:0.07, G:0.49, T:0.25
Found at i:157 original size:6 final size:6
Alignment explanation
Indices: 148--259 Score: 62
Period size: 6 Copynumber: 18.2 Consensus size: 6
138 GGGTGGTTTT
* ** * * *
148 GGTGGA GGTGGA GGTGGA GGTCTTGGA GGTGGT TTTGGT GGTGGT GCTGGA
1 GGTGGA GGTGGA GGTGGA GG---TGGA GGTGGA GGTGGA GGTGGA GGTGGA
* * ** * * * **
199 GGTGGA GCTGGT TTTGGA GGTGGA GCTGGG GGTGGT GGTGGA CTTGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
247 GGTGGA GGTGGA G
1 GGTGGA GGTGGA G
260 CTGGTGGAGG
Statistics
Matches: 79, Mismatches: 24, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
6 73 0.92
9 6 0.08
ACGTcount: A:0.11, C:0.04, G:0.58, T:0.27
Consensus pattern (6 bp):
GGTGGA
Found at i:238 original size:18 final size:18
Alignment explanation
Indices: 195--263 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
185 GTGGTGGTGC
***
195 TGGAGGTGGAGCTGGTTT
1 TGGAGGTGGAGCTGGAGG
*
213 TGGAGGTGGAGCTGGGGG
1 TGGAGGTGGAGCTGGAGG
*
231 TGGTGGTGGA-CTTGGAGG
1 TGGAGGTGGAGC-TGGAGG
249 TGGAGGTGGAGCTGG
1 TGGAGGTGGAGCTGG
264 TGGAGGGCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
17 1 0.02
18 41 0.95
19 1 0.02
ACGTcount: A:0.12, C:0.06, G:0.58, T:0.25
Consensus pattern (18 bp):
TGGAGGTGGAGCTGGAGG
Found at i:246 original size:30 final size:30
Alignment explanation
Indices: 212--299 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
202 GGAGCTGGTT
* * *
212 TTGGAGGTGGAGCTGGGGGTGGTGGTGGAC
1 TTGGAGGTGGAGCTGGAGCTGGTGGAGGAC
* *
242 TTGGAGGTGGAGGTGGAGCTGGTGGAGGGC
1 TTGGAGGTGGAGCTGGAGCTGGTGGAGGAC
* * * *
272 TTGGTGGTGGAGGTGGAGCAGGGGGAGG
1 TTGGAGGTGGAGCTGGAGCTGGTGGAGG
300 GTTTGGTGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.12, C:0.06, G:0.61, T:0.20
Consensus pattern (30 bp):
TTGGAGGTGGAGCTGGAGCTGGTGGAGGAC
Found at i:300 original size:30 final size:30
Alignment explanation
Indices: 241--312 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
231 TGGTGGTGGA
* * *
241 CTTGGAGGTGGAGGTGGAGCTGGTGGAGGG
1 CTTGGTGGTGGAGGTGGAGCAGGGGGAGGG
271 CTTGGTGGTGGAGGTGGAGCAGGGGGAGGG
1 CTTGGTGGTGGAGGTGGAGCAGGGGGAGGG
*
301 TTTGGTGGTGGA
1 CTTGGTGGTGGA
313 ATTGGTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.12, C:0.06, G:0.60, T:0.22
Consensus pattern (30 bp):
CTTGGTGGTGGAGGTGGAGCAGGGGGAGGG
Found at i:336 original size:30 final size:30
Alignment explanation
Indices: 302--484 Score: 199
Period size: 30 Copynumber: 6.1 Consensus size: 30
292 GGGGGAGGGT
* *
302 TTGGTGGTGGAATTGGTAAAGGTGGTGGAC
1 TTGGTGGTGGGATTGGCAAAGGTGGTGGAC
*
332 TTGGTGGTGGCATTGG-AAAGGGTGGTGGAC
1 TTGGTGGTGGGATTGGCAAA-GGTGGTGGAC
* * *
362 TTGGTGGTGGCATTGGCAAGGGTGG-GGTC
1 TTGGTGGTGGGATTGGCAAAGGTGGTGGAC
* * *
391 TTGGTGGTGGGATTGGCAAGGGTGGAGGCC
1 TTGGTGGTGGGATTGGCAAAGGTGGTGGAC
* * * *
421 TTGGCGGTGGGATTGGAAAAGGTGGAGGCC
1 TTGGTGGTGGGATTGGCAAAGGTGGTGGAC
* * *
451 TTGGTGGTGGGATTGGCCAGGGAGGTGGAC
1 TTGGTGGTGGGATTGGCAAAGGTGGTGGAC
481 TTGG
1 TTGG
485 AGGAGGACAT
Statistics
Matches: 135, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
29 30 0.22
30 103 0.76
31 2 0.01
ACGTcount: A:0.15, C:0.08, G:0.51, T:0.26
Consensus pattern (30 bp):
TTGGTGGTGGGATTGGCAAAGGTGGTGGAC
Found at i:430 original size:89 final size:88
Alignment explanation
Indices: 298--472 Score: 233
Period size: 89 Copynumber: 2.0 Consensus size: 88
288 AGCAGGGGGA
* * * * *
298 GGGTTTGGTGGTGGAATTGGTAAAGGTGGTGGACTTGGTGGTGGCATTGGAAAGGGTGGTGGACT
1 GGGTTTGGTGGTGGAATTGGCAAAGGTGGAGGACTTGGCGGTGGCATTGGAAAAGGTGGAGGACT
363 TGGTGGTGGCATTGGCAAGGGTG
66 TGGTGGTGGCATTGGCAAGGGTG
* * * * *
386 GGGTCTTGGTGGTGGGATTGGCAAGGGTGGAGGCCTTGGCGGTGGGATTGGAAAAGGTGGAGGCC
1 GGGT-TTGGTGGTGGAATTGGCAAAGGTGGAGGACTTGGCGGTGGCATTGGAAAAGGTGGAGGAC
* *
451 TTGGTGGTGGGATTGGCCAGGG
65 TTGGTGGTGGCATTGGCAAGGG
473 AGGTGGACTT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
88 4 0.05
89 70 0.95
ACGTcount: A:0.15, C:0.08, G:0.51, T:0.26
Consensus pattern (88 bp):
GGGTTTGGTGGTGGAATTGGCAAAGGTGGAGGACTTGGCGGTGGCATTGGAAAAGGTGGAGGACT
TGGTGGTGGCATTGGCAAGGGTG
Found at i:484 original size:60 final size:60
Alignment explanation
Indices: 262--937 Score: 297
Period size: 60 Copynumber: 11.1 Consensus size: 60
252 AGGTGGAGCT
* ** * * ** * * *
262 GGTGGAGGGCTTGGTGGTGGAGGTGGAGCAGGG-GGAGGGTTTGGTGGTGGAATTGGTAAA
1 GGTGGAGGACTTGGTGGTGGAATTGGA-AAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * * * * *
322 GGTGGTGGACTTGGTGGTGGCATTGGAAAGGGTGGTGGACTTGGTGGTGGCATTGGCAAG
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * * * *
382 GGTGG-GGTCTTGGTGGTGGGATTGGCAAGGGTGGAGGCCTTGGCGGTGGGATTGGAAAA
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * ** *
441 GGTGGAGGCCTTGGTGGTGGGATTGGCCAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAAT
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTT------GG-C--GGT-G-GG-AT
*
506 AGGAAAA
54 TGGAAAA
* * * * * *
513 GGAGGTGGACTTGGAGGCGGAATTGGAAAGGGTGGTGGACTTGGAGGTGGTATTGGAAAA
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * * *
573 GGAGGAGGCCTTGGTGGTGGAATAGGAAAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAAT
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTT------GG-C--GGT-G-GG-AT
*
638 AGGAAAA
54 TGGAAAA
* * * * * * * * * *
645 GGAGGTGGACTTGGAGGTGGAATTGGCAAA-GGAGGAGGCCTCGGAGGTGGAATTGGAAAG
1 GGTGGAGGACTTGGTGGTGGAATTGG-AAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * * * * *
705 GGTGGTGGAC-T--TGGAGG-A--GGACATGGTGGTGGACTTGGAGGTGGTG-TTGGCAAA
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGG-GATTGGAAAA
* * * * * *
759 GGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGGTGGACTT---GG-AGGA--GGACAT
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * * * * * * * *
813 GGTGGTGGACTTGGAGGTGGTATTGGCAAA-GGAGGAGGCCTTGGAGGTGGTATTGGCAAA
1 GGTGGAGGACTTGGTGGTGGAATTGG-AAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
* * * * * * *
873 GGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGGTGGACTTGGTGGAGGAATTGGAAAG
1 GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
933 GGTGG
1 GGTGG
938 TGGCATTGGA
Statistics
Matches: 466, Mismatches: 106, Indels: 88
0.71 0.16 0.13
Matches are distributed among these distances:
53 2 0.00
54 65 0.14
55 5 0.01
56 2 0.00
57 12 0.03
58 3 0.01
59 58 0.12
60 206 0.44
61 2 0.00
62 2 0.00
63 6 0.01
66 8 0.02
67 1 0.00
69 6 0.01
70 2 0.00
71 3 0.01
72 80 0.17
73 3 0.01
ACGTcount: A:0.22, C:0.07, G:0.50, T:0.21
Consensus pattern (60 bp):
GGTGGAGGACTTGGTGGTGGAATTGGAAAGGGTGGTGGACTTGGCGGTGGGATTGGAAAA
Found at i:490 original size:42 final size:42
Alignment explanation
Indices: 471--661 Score: 186
Period size: 42 Copynumber: 4.4 Consensus size: 42
461 GATTGGCCAG
471 GGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAA
1 GGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAA
* * * * ***
513 GGAGGTGGACTTGGAGGCGGAATTGGAAAGGGTGGTGGACTTGGAGGT
1 GGAGGTGGACTTGGA---GG-A--GGACATGGTGGTGGAATAGGAAAA
* *** * * *
561 GGTA-TTGGAAAAGGAGGAGGCCTTGGTGGTGGAATAGGAAAG
1 GG-AGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAA
603 GGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAA
1 GGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAA
645 GGAGGTGGACTTGGAGG
1 GGAGGTGGACTTGGAGG
662 TGGAATTGGC
Statistics
Matches: 114, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
41 1 0.01
42 80 0.70
44 1 0.01
45 4 0.04
46 1 0.01
48 26 0.23
49 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.49, T:0.18
Consensus pattern (42 bp):
GGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAA
Found at i:535 original size:30 final size:30
Alignment explanation
Indices: 483--619 Score: 157
Period size: 30 Copynumber: 4.6 Consensus size: 30
473 AGGTGGACTT
* * *
483 GGAGGAGGACATGGTGGTGGAATAGGAAAA
1 GGAGGTGGACTTGGAGGTGGAATAGGAAAA
* * *
513 GGAGGTGGACTTGGAGGCGGAATTGGAAAG
1 GGAGGTGGACTTGGAGGTGGAATAGGAAAA
* * *
543 GGTGGTGGACTTGGAGGTGGTATTGGAAAA
1 GGAGGTGGACTTGGAGGTGGAATAGGAAAA
* * * *
573 GGAGGAGGCCTTGGTGGTGGAATAGGAAAG
1 GGAGGTGGACTTGGAGGTGGAATAGGAAAA
603 GGAGGTGGACTTGGAGG
1 GGAGGTGGACTTGGAGG
620 AGGACATGGT
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.27, C:0.05, G:0.50, T:0.18
Consensus pattern (30 bp):
GGAGGTGGACTTGGAGGTGGAATAGGAAAA
Found at i:619 original size:102 final size:102
Alignment explanation
Indices: 513--730 Score: 319
Period size: 102 Copynumber: 2.1 Consensus size: 102
503 AATAGGAAAA
* * * * * *
513 GGAGGTGGACTTGGAGGCGGAATTGGAAAGGGTGGTGGACTTGGAGGTGGTATTGGAAAAGGAGG
1 GGAGGAGGACATGGAGGCGGAATAGGAAAAGGAGGTGGACTTGGAGGTGGAATTGGAAAAGGAGG
* *
578 AGGCCTTGGTGGTGGAATAGGAAAGGGAGGTGGACTT
66 AGGCCTCGGAGGTGGAATAGGAAAGGGAGGTGGACTT
* * *
615 GGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGTGGACTTGGAGGTGGAATTGGCAAAGGAGG
1 GGAGGAGGACATGGAGGCGGAATAGGAAAAGGAGGTGGACTTGGAGGTGGAATTGGAAAAGGAGG
* *
680 AGGCCTCGGAGGTGGAATTGGAAAGGGTGGTGGACTT
66 AGGCCTCGGAGGTGGAATAGGAAAGGGAGGTGGACTT
717 GGAGGAGGACATGG
1 GGAGGAGGACATGG
731 TGGTGGACTT
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.26, C:0.06, G:0.49, T:0.18
Consensus pattern (102 bp):
GGAGGAGGACATGGAGGCGGAATAGGAAAAGGAGGTGGACTTGGAGGTGGAATTGGAAAAGGAGG
AGGCCTCGGAGGTGGAATAGGAAAGGGAGGTGGACTT
Found at i:664 original size:30 final size:30
Alignment explanation
Indices: 615--952 Score: 243
Period size: 30 Copynumber: 11.7 Consensus size: 30
605 AGGTGGACTT
* * * *
615 GGAGGAGGACATGGTGGTGGAATAGGAAAA
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
*
645 GGAGGTGGACTTGGAGGTGGAATTGGCAAA
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * * *
675 GGAGGAGGCCTCGGAGGTGGAATTGGAAAG
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * *
705 GGTGGTGGACTTGGA---GG-A--GGACAT
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* ** *
729 GGTGGTGGACTTGGAGGTGGTGTTGGCAAA
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * *
759 GGAGGAGGCCTTGGAGGTGGAATTGGAAAG
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * *
789 GGTGGTGGACTTGGA---GG-A--GGACAT
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * *
813 GGTGGTGGACTTGGAGGTGGTATTGGCAAA
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * * *
843 GGAGGAGGCCTTGGAGGTGGTATTGGCAAA
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * *
873 GGAGGAGGCCTTGGAGGTGGAATTGGAAAG
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
* * * *
903 GGTGGTGGACTTGGTGGAGGAATTGGAAAG
1 GGAGGTGGACTTGGAGGTGGAATTGGAAAA
*
933 GGTGGTGG-CATTGGAGGTGG
1 GGAGGTGGAC-TTGGAGGTGG
953 CGGCGGCTTT
Statistics
Matches: 247, Mismatches: 48, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
24 38 0.15
26 2 0.01
27 8 0.03
28 1 0.00
29 1 0.00
30 197 0.80
ACGTcount: A:0.24, C:0.07, G:0.49, T:0.20
Consensus pattern (30 bp):
GGAGGTGGACTTGGAGGTGGAATTGGAAAA
Found at i:691 original size:42 final size:39
Alignment explanation
Indices: 645--862 Score: 147
Period size: 42 Copynumber: 5.2 Consensus size: 39
635 AATAGGAAAA
645 GGAGGTGGACTTGGAGGTGGAATTGGCAAAGGAGGAGGCCT
1 GGAGGTGGACTTGGAGGTGG--TTGGCAAAGGAGGAGGCCT
* ** *
686 CGGAGGTGGAATTGGAAAGGGTGG-TGG-ACTTGGAGGAGGACAT
1 -GGAGGTGGACTTGG--A-GGTGGTTGGCA-AAGGAGGAGG-CCT
*
729 GGTGGTGGACTTGGAGGTGGTGTTGGCAAAGGAGGAGGCCTT
1 GGAGGTGGACTTGGAGGT-G-GTTGGCAAAGGAGGAGGCC-T
* ** *
771 GGAGGTGGAATTGGAAAGGGTGG-TGG-ACTTGGAGGAGGACAT
1 GGAGGTGGACTTGG--A-GGTGGTTGGCA-AAGGAGGAGG-CCT
*
813 GGTGGTGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTT
1 GGAGGTGGACTTGGAGGTGG--TTGGCAAAGGAGGAGGCC-T
855 GGAGGTGG
1 GGAGGTGG
863 TATTGGCAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 40
0.69 0.10 0.20
Matches are distributed among these distances:
39 8 0.06
40 3 0.02
41 5 0.04
42 103 0.76
43 6 0.04
44 3 0.02
45 8 0.06
ACGTcount: A:0.22, C:0.08, G:0.50, T:0.20
Consensus pattern (39 bp):
GGAGGTGGACTTGGAGGTGGTTGGCAAAGGAGGAGGCCT
Found at i:718 original size:132 final size:132
Alignment explanation
Indices: 390--718 Score: 471
Period size: 132 Copynumber: 2.5 Consensus size: 132
380 AGGGTGGGGT
* * * * *
390 CTTGGTGGTGGGATTGGCAAGGGTGGAGGCCTTGGCGGTGGGATTGGAAAAGGTGGAGGCCTTGG
1 CTTGGAGGTGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGGAAAAGGTGGAGGCCTTGG
* * **
455 TGGTGGGATTGGCCAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGTG
66 TGGTGGAATAGGAAAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGTG
520 GA
131 GA
* * * * *
522 CTTGGAGGCGGAATTGG-AAAGGGTGGTGGACTTGGAGGTGGTATTGGAAAAGGAGGAGGCCTTG
1 CTTGGAGGTGGAATTGGCAAA-GGTGGAGGCCTTGGAGGTGGAATTGGAAAAGGTGGAGGCCTTG
586 GTGGTGGAATAGGAAAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGT
65 GTGGTGGAATAGGAAAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGT
651 GGA
130 GGA
* * * * *
654 CTTGGAGGTGGAATTGGCAAAGGAGGAGGCCTCGGAGGTGGAATTGGAAAGGGTGGTGGACTTGG
1 CTTGGAGGTGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGGAAAAGGTGGAGGCCTTGG
719 AGGAGGACAT
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
131 2 0.01
132 167 0.97
133 3 0.02
ACGTcount: A:0.24, C:0.07, G:0.49, T:0.20
Consensus pattern (132 bp):
CTTGGAGGTGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGGAAAAGGTGGAGGCCTTGG
TGGTGGAATAGGAAAGGGAGGTGGACTTGGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGTG
GA
Found at i:747 original size:12 final size:12
Alignment explanation
Indices: 708--748 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
698 TGGAAAGGGT
708 GGTGGACTTGGA
1 GGTGGACTTGGA
* * *
720 GGAGGACATGGT
1 GGTGGACTTGGA
732 GGTGGACTTGGA
1 GGTGGACTTGGA
744 GGTGG
1 GGTGG
749 TGTTGGCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.07, G:0.54, T:0.22
Consensus pattern (12 bp):
GGTGGACTTGGA
Found at i:805 original size:114 final size:116
Alignment explanation
Indices: 615--949 Score: 357
Period size: 114 Copynumber: 2.9 Consensus size: 116
605 AGGTGGACTT
* * * * * * * *
615 GGAGGAGGACATGGTGGTGGAATAGGAAAAGGAGGTGGACTTGGAGGTGGAATTGGCAAA-GGAG
1 GGAGGAGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGG-AAAGGGTG
* * * *
679 GAGGCCTCGGAGGTGGAATTGGAAAGGGTGGTGGACTTGGAGGAGG-A-C-AT
65 GTGGACTTGGAGG-GGAATTGGAAAGGGTGGTGGACTTGGAGGAGGTAGCAAA
* * *
729 GGTGGTGGACTTGGAGGTGGTGTTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGG
1 GGAGGAGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGG
* * *
794 TGGACTTGGA--GG-A--GGACATGGTGGTGGACTTGGAGGTGGTATTGGCAAA
66 TGGACTTGGAGGGGAATTGGAAAGGGTGGTGGACTTGGAGGAGGTA---GCAAA
*
843 GGAGGAGGCCTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGG
1 GGAGGAGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGG
*
908 TGGACTTGGTGGAGGAATTGGAAAGGGTGGTGG-CATTGGAGG
66 TGGACTTGGAGG-GGAATTGGAAAGGGTGGTGGAC-TTGGAGG
950 TGGCGGCGGC
Statistics
Matches: 182, Mismatches: 25, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
108 23 0.13
109 1 0.01
110 1 0.01
111 2 0.01
113 4 0.02
114 128 0.70
117 2 0.01
118 1 0.01
119 1 0.01
120 19 0.10
ACGTcount: A:0.24, C:0.07, G:0.49, T:0.20
Consensus pattern (116 bp):
GGAGGAGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGG
TGGACTTGGAGGGGAATTGGAAAGGGTGGTGGACTTGGAGGAGGTAGCAAA
Found at i:831 original size:12 final size:12
Alignment explanation
Indices: 792--832 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
782 TGGAAAGGGT
792 GGTGGACTTGGA
1 GGTGGACTTGGA
* * *
804 GGAGGACATGGT
1 GGTGGACTTGGA
816 GGTGGACTTGGA
1 GGTGGACTTGGA
828 GGTGG
1 GGTGG
833 TATTGGCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.07, G:0.54, T:0.22
Consensus pattern (12 bp):
GGTGGACTTGGA
Found at i:889 original size:84 final size:84
Alignment explanation
Indices: 648--874 Score: 409
Period size: 84 Copynumber: 2.7 Consensus size: 84
638 AGGAAAAGGA
* *
648 GGTGGACTTGGAGGTGGAATTGGCAAAGGAGGAGGCCTCGGAGGTGGAATTGGAAAGGGTGGTGG
1 GGTGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGGTGG
713 ACTTGGAGGAGGACATGGT
66 ACTTGGAGGAGGACATGGT
*
732 GGTGGACTTGGAGGTGGTGTTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGGTGG
1 GGTGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGGTGG
797 ACTTGGAGGAGGACATGGT
66 ACTTGGAGGAGGACATGGT
*
816 GGTGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGTATTGGCAAAGG
1 GGTGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGG-AAAGG
875 AGGAGGCCTT
Statistics
Matches: 137, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
84 132 0.96
85 5 0.04
ACGTcount: A:0.22, C:0.08, G:0.49, T:0.21
Consensus pattern (84 bp):
GGTGGACTTGGAGGTGGTATTGGCAAAGGAGGAGGCCTTGGAGGTGGAATTGGAAAGGGTGGTGG
ACTTGGAGGAGGACATGGT
Found at i:911 original size:18 final size:18
Alignment explanation
Indices: 888--947 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 18
878 AGGCCTTGGA
888 GGTGGAATTGGAAAGGGT
1 GGTGGAATTGGAAAGGGT
*
906 GGTGGACTT------GGT
1 GGTGGAATTGGAAAGGGT
*
918 GGAGGAATTGGAAAGGGT
1 GGTGGAATTGGAAAGGGT
*
936 GGTGGCATTGGA
1 GGTGGAATTGGA
948 GGTGGCGGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
12 10 0.32
18 21 0.68
ACGTcount: A:0.23, C:0.03, G:0.50, T:0.23
Consensus pattern (18 bp):
GGTGGAATTGGAAAGGGT
Found at i:1008 original size:24 final size:24
Alignment explanation
Indices: 980--1038 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
970 GTGGTGGTTT
*
980 CGGTGGCGGTGCTGGAGGTGGTGC
1 CGGTGGAGGTGCTGGAGGTGGTGC
* *
1004 TGGTGGAGGAT-TTGGAGGTGGTGC
1 CGGTGGAGG-TGCTGGAGGTGGTGC
*
1028 CGGTGGTGGTG
1 CGGTGGAGGTG
1039 GAGGATTCGG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.07, C:0.10, G:0.58, T:0.25
Consensus pattern (24 bp):
CGGTGGAGGTGCTGGAGGTGGTGC
Found at i:1040 original size:30 final size:30
Alignment explanation
Indices: 999--1066 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
989 TGCTGGAGGT
* * *
999 GGTGCTGGTGGAGGATTTGGAGGTGGTGCC
1 GGTGGTGGTGGAGGATTCGGAGGTGGAGCC
*
1029 GGTGGTGGTGGAGGATTCGGAGGTGGAGCT
1 GGTGGTGGTGGAGGATTCGGAGGTGGAGCC
1059 GGTGGTGG
1 GGTGGTGG
1067 ATTTGGAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.10, C:0.07, G:0.57, T:0.25
Consensus pattern (30 bp):
GGTGGTGGTGGAGGATTCGGAGGTGGAGCC
Found at i:1056 original size:6 final size:6
Alignment explanation
Indices: 1047--1096 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
1037 TGGAGGATTC
* * ** *
1047 GGAGGT GGAGCT GGTGGT GGATTT GGAGGT GGAGGT GGAGCT GGAGGT
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
1095 GG
1 GG
1097 TTTTGGCGGA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.14, C:0.04, G:0.60, T:0.22
Consensus pattern (6 bp):
GGAGGT
Found at i:1068 original size:24 final size:24
Alignment explanation
Indices: 992--1080 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 24
982 GTGGCGGTGC
* *
992 TGGAGGTGGTGCTGGTGGAGGATT
1 TGGAGGTGGAGCTGGTGGTGGATT
*
1016 TGGAGGTGGTGCCGGTGGTGGTGGAGGATT
1 TGGAGGTGGAG-C--TGGTGGT---GGATT
*
1046 CGGAGGTGGAGCTGGTGGTGGATT
1 TGGAGGTGGAGCTGGTGGTGGATT
1070 TGGAGGTGGAG
1 TGGAGGTGGAG
1081 GTGGAGCTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 26 0.47
25 1 0.02
27 13 0.24
29 1 0.02
30 14 0.25
ACGTcount: A:0.12, C:0.06, G:0.56, T:0.26
Consensus pattern (24 bp):
TGGAGGTGGAGCTGGTGGTGGATT
Found at i:1091 original size:24 final size:24
Alignment explanation
Indices: 1041--1091 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1031 TGGTGGTGGA
* *
1041 GGATTCGGAGGTGGAGCTGGTGGT
1 GGATTCGGAGGTGGAGCTGGAGCT
* *
1065 GGATTTGGAGGTGGAGGTGGAGCT
1 GGATTCGGAGGTGGAGCTGGAGCT
1089 GGA
1 GGA
1092 GGTGGTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.06, G:0.55, T:0.24
Consensus pattern (24 bp):
GGATTCGGAGGTGGAGCTGGAGCT
Done.