Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_35492
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, 720
Length: 1200
ACGTcount: A:0.13, C:0.08, G:0.53, T:0.26
Found at i:226 original size:18 final size:18
Alignment explanation
Indices: 204--267 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
194 GTGGTGGTCT
204 AGGTGGTGGTTTTGGTGG
1 AGGTGGTGGTTTTGGTGG
* * *
222 TGGTGGAGGTATTGGTGG
1 AGGTGGTGGTTTTGGTGG
* *
240 AGGAGGTGGTTTAGGTGG
1 AGGTGGTGGTTTTGGTGG
* *
258 GGGTGCTGGT
1 AGGTGGTGGT
268 GGAGGCTTTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.09, C:0.02, G:0.56, T:0.33
Consensus pattern (18 bp):
AGGTGGTGGTTTTGGTGG
Found at i:298 original size:18 final size:18
Alignment explanation
Indices: 259--364 Score: 70
Period size: 18 Copynumber: 5.6 Consensus size: 18
249 TTTAGGTGGG
* *
259 GGTGCTGGTGGA-GGCTTT
1 GGTGGTGGTGGAGGGC-TA
277 GGTGGTGGTGGAGGGCTA
1 GGTGGTGGTGGAGGGCTA
*
295 GGTGGCGGTGGTGGAGGAGGATTA
1 GGT---GGTGGTGGA-G-GG-CTA
* * *
319 GGTGGTGGAGGAGGTCTT
1 GGTGGTGGTGGAGGGCTA
* *
337 GGGGGTGGTGGAGGCCTA
1 GGTGGTGGTGGAGGGCTA
355 GGTGGTGGTG
1 GGTGGTGGTG
365 CGGGAGGAGG
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
18 39 0.57
19 4 0.06
20 1 0.01
21 17 0.25
22 1 0.01
23 2 0.03
24 5 0.07
ACGTcount: A:0.10, C:0.07, G:0.58, T:0.25
Consensus pattern (18 bp):
GGTGGTGGTGGAGGGCTA
Found at i:299 original size:30 final size:30
Alignment explanation
Indices: 192--299 Score: 76
Period size: 30 Copynumber: 3.6 Consensus size: 30
182 GGCATGGCAT
* * * *
192 TGGTGGTGGTCTAGGTGGTGGTTTTGGTGG
1 TGGTGGAGGGCTAGGTGGAGGATTTGGTGG
** * ** *
222 TGGTGGAGGTATTGGTGGAGGAGGTGGT-T
1 TGGTGGAGGGCTAGGTGGAGGATTTGGTGG
* *
251 TAGGTGGGGGTGCT-GGTGGAGGCTTTGGTGG
1 T-GGTGGAGG-GCTAGGTGGAGGATTTGGTGG
282 TGGTGGAGGGCTAGGTGG
1 TGGTGGAGGGCTAGGTGG
300 CGGTGGTGGA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
29 4 0.07
30 52 0.90
31 2 0.03
ACGTcount: A:0.08, C:0.04, G:0.56, T:0.31
Consensus pattern (30 bp):
TGGTGGAGGGCTAGGTGGAGGATTTGGTGG
Found at i:304 original size:24 final size:24
Alignment explanation
Indices: 277--323 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
267 TGGAGGCTTT
* *
277 GGTGGTGGTGGAGGGCTAGGTGGC
1 GGTGGTGGAGGAGGACTAGGTGGC
*
301 GGTGGTGGAGGAGGATTAGGTGG
1 GGTGGTGGAGGAGGACTAGGTGG
324 TGGAGGAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.04, G:0.62, T:0.21
Consensus pattern (24 bp):
GGTGGTGGAGGAGGACTAGGTGGC
Found at i:332 original size:60 final size:60
Alignment explanation
Indices: 275--406 Score: 203
Period size: 60 Copynumber: 2.2 Consensus size: 60
265 GGTGGAGGCT
*
275 TTGGTGGTGGTGGAGGGCTAGGTGGCGGTG-GTGGAGGAGGATTAGGTGGTGGAGGAGGTC
1 TTGGTGGTGGTGGAGGCCTAGGTGGCGGTGCG-GGAGGAGGATTAGGTGGTGGAGGAGGTC
* * *
335 TTGGGGGTGGTGGAGGCCTAGGTGGTGGTGCGGGAGGAGGATTAGGTGGTGGAGGTGGTC
1 TTGGTGGTGGTGGAGGCCTAGGTGGCGGTGCGGGAGGAGGATTAGGTGGTGGAGGAGGTC
*
395 TTGGTGGAGGTG
1 TTGGTGGTGGTG
407 CTGGTGGTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 64 0.98
61 1 0.02
ACGTcount: A:0.12, C:0.05, G:0.58, T:0.24
Consensus pattern (60 bp):
TTGGTGGTGGTGGAGGCCTAGGTGGCGGTGCGGGAGGAGGATTAGGTGGTGGAGGAGGTC
Found at i:347 original size:42 final size:41
Alignment explanation
Indices: 216--347 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 41
206 GTGGTGGTTT
* *
216 TGGTGGTGGTGGAGGTATTGGTGGAGGAGGTGGT-TTAGGTGGG
1 TGGTGGTGGTGGAGG-ATTGGTGGTGGAGGAGGTCTT-GG-GGG
* * * * * *
259 -GGTGCTGGTGGAGGCTTTGGTGGTGGTGGAGGGCTAGGTGG
1 TGGTGGTGGTGGAGG-ATTGGTGGTGGAGGAGGTCTTGGGGG
* *
300 CGGTGGTGGAGGAGGATTAGGTGGTGGAGGAGGTCTTGGGGG
1 TGGTGGTGGTGGAGGATT-GGTGGTGGAGGAGGTCTTGGGGG
342 TGGTGG
1 TGGTGG
348 AGGCCTAGGT
Statistics
Matches: 69, Mismatches: 17, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
41 4 0.06
42 64 0.93
43 1 0.01
ACGTcount: A:0.11, C:0.04, G:0.59, T:0.27
Consensus pattern (41 bp):
TGGTGGTGGTGGAGGATTGGTGGTGGAGGAGGTCTTGGGGG
Found at i:364 original size:21 final size:20
Alignment explanation
Indices: 259--364 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 20
249 TTTAGGTGGG
* *
259 GGTGCTGGTGGAGGCT--TT
1 GGTGGTGGTGGAGGCTAGGT
277 GGTGGTGGTGGAGGGCTAGGT
1 GGTGGTGGTGGA-GGCTAGGT
*
298 GGCGGTGGTGGAGG--AGGATT
1 GGTGGTGGTGGAGGCTAGG--T
*
318 AGGTGGTGGAGGAGGTCT---T
1 -GGTGGTGGTGGAGG-CTAGGT
*
337 GGGGGTGGTGGAGGCCTAGGT
1 GGTGGTGGTGGAGG-CTAGGT
358 GGTGGTG
1 GGTGGTG
365 CGGGAGGAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
18 28 0.42
19 5 0.07
20 3 0.04
21 31 0.46
ACGTcount: A:0.10, C:0.07, G:0.58, T:0.25
Consensus pattern (20 bp):
GGTGGTGGTGGAGGCTAGGT
Found at i:383 original size:78 final size:78
Alignment explanation
Indices: 301--467 Score: 219
Period size: 78 Copynumber: 2.1 Consensus size: 78
291 GCTAGGTGGC
* * * *
301 GGTGGTGGAGGAGGAT-TAGGTGGTGGAGGAGGTCTTGGGGGTGGTGGAGGCCTAGGTGGTGGTG
1 GGTGGTGGAGGAGG-TCTAGGTGGAGGAGCAGGTCGTGGAGGTGGTGGAGGCCTAGGTGGTGGTG
365 CGGGAGGAGGATTA
65 CGGGAGGAGGATTA
* * * * * * *
379 GGTGGTGGAGGTGGTCTTGGTGGAGGTGCTGGTGGTGGAGTTGGTGGAGGCCTGGGTGGTGGTGC
1 GGTGGTGGAGGAGGTCTAGGTGGAGGAGCAGGTCGTGGAGGTGGTGGAGGCCTAGGTGGTGGTGC
444 GGGAGGAGGATTA
66 GGGAGGAGGATTA
457 GGTGGTGGAGG
1 GGTGGTGGAGG
468 TGGTGTTGGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 76 0.99
ACGTcount: A:0.13, C:0.05, G:0.59, T:0.23
Consensus pattern (78 bp):
GGTGGTGGAGGAGGTCTAGGTGGAGGAGCAGGTCGTGGAGGTGGTGGAGGCCTAGGTGGTGGTGC
GGGAGGAGGATTA
Found at i:405 original size:24 final size:24
Alignment explanation
Indices: 378--428 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
368 GAGGAGGATT
* *
378 AGGTGGTGGAGGTGGTCTTGGTGG
1 AGGTGCTGGAGGTGGACTTGGTGG
* *
402 AGGTGCTGGTGGTGGAGTTGGTGG
1 AGGTGCTGGAGGTGGACTTGGTGG
426 AGG
1 AGG
429 CCTGGGTGGT
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:0.10, C:0.04, G:0.59, T:0.27
Consensus pattern (24 bp):
AGGTGCTGGAGGTGGACTTGGTGG
Found at i:414 original size:15 final size:15
Alignment explanation
Indices: 379--418 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
369 AGGAGGATTA
*
379 GGTGGTGGAGGTGGT
1 GGTGGTGGAGGTGCT
**
394 CTTGGTGGAGGTGCT
1 GGTGGTGGAGGTGCT
409 GGTGGTGGAG
1 GGTGGTGGAG
419 TTGGTGGAGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.07, C:0.05, G:0.60, T:0.28
Consensus pattern (15 bp):
GGTGGTGGAGGTGCT
Found at i:436 original size:24 final size:24
Alignment explanation
Indices: 395--440 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
385 GGAGGTGGTC
*
395 TTGGTGGAGGTGCTGGTGGTGGAG
1 TTGGTGGAGGTCCTGGTGGTGGAG
419 TTGGTGGAGG-CCTGGGTGGTGG
1 TTGGTGGAGGTCCT-GGTGGTGG
441 TGCGGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.07, C:0.07, G:0.59, T:0.28
Consensus pattern (24 bp):
TTGGTGGAGGTCCTGGTGGTGGAG
Found at i:586 original size:60 final size:60
Alignment explanation
Indices: 522--877 Score: 522
Period size: 60 Copynumber: 6.0 Consensus size: 60
512 GTCACAAGCT
* * *
522 TGGAGGAGCAGGAGGTGGATTGGGCGGTGGTGGGGGACTTGGCGGTGGCCATGGGCTGGG
1 TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
* *
582 TGGAGGTGCAGAAGGTAGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
1 TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
* *
642 AGGAGGTGCAGGAGGTGGATTGGGTGGTGGT---GGACTTGGCAGTGGCCATGGGCTGGG
1 TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
*
699 TGGAGGTGCAGGAGGTGGAGTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
1 TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
* * * *
759 TGGGGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTCGGTGG-GGCCATGGGCTTGG
1 TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
* * * * * *
818 TGGAGGTGCAGGAGGTGGACTAGGAGGGGGTGGAGGACTAGGTGGTGGCCATGGGCTGGG
1 TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
878 AGGTGGAGGC
Statistics
Matches: 268, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
57 54 0.20
59 52 0.19
60 162 0.60
ACGTcount: A:0.13, C:0.10, G:0.56, T:0.20
Consensus pattern (60 bp):
TGGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGG
Found at i:688 original size:117 final size:117
Alignment explanation
Indices: 523--880 Score: 493
Period size: 117 Copynumber: 3.0 Consensus size: 117
513 TCACAAGCTT
* * *
523 GGAGGAGCAGGAGGTGGATTGGGCGGTGGTGGGGGACTTGGCGGTGGCCATGGGCTGGGTGGAGG
1 GGAGGTGCAGGAGGTGGATT--G-GGTGGTGGTGGACTTGGCAGTGGCCATGGGCTGGGTGGAGG
* * *
588 TGCAGAAGGTAGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGA
63 TGCAGGAGGTGGACTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGA
643 GGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGACTTGGCAGTGGCCATGGGCTGGGTGGAGGTGC
1 GGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGACTTGGCAGTGGCCATGGGCTGGGTGGAGGTGC
* *
708 AGGAGGTGGAGTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGT
66 AGGAGGTGGACTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGA
* * * * *
760 GGGGGTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTCGG-TGGGGCCATGGGCTTGGTGGAGG
1 GGAGGTGCAGGAGGTGGATTGGGTGGTGGT---GGACTTGGCAGTGGCCATGGGCTGGGTGGAGG
* * * * *
824 TGCAGGAGGTGGACTAGGAGGGGGTGGAGGACTAGGTGGTGGCCATGGGCTGGGA
63 TGCAGGAGGTGGACTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGA
879 GG
1 GG
881 TGGAGGCGAA
Statistics
Matches: 216, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
117 119 0.55
118 1 0.00
119 70 0.32
120 26 0.12
ACGTcount: A:0.13, C:0.10, G:0.57, T:0.20
Consensus pattern (117 bp):
GGAGGTGCAGGAGGTGGATTGGGTGGTGGTGGACTTGGCAGTGGCCATGGGCTGGGTGGAGGTGC
AGGAGGTGGACTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGA
Found at i:739 original size:177 final size:179
Alignment explanation
Indices: 522--877 Score: 529
Period size: 177 Copynumber: 2.0 Consensus size: 179
512 GTCACAAGCT
* *
522 TGGAGGAGCAGGAGGTGGATTGGGCGGTGGTGGGGGACTTGGCGGTGGCCATGGGCTGGGTGGAG
1 TGGAGGAGCAGGAGGTGGAGTGGGCGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGTGGAG
*
587 GTGCAGAAGGTAGATTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGAGGAGGTGCA
66 GTGCAGAAGGTAGATTGGGTGGTGGTGGAGGACTCGGCGG-GGCCATGGGCTGGGAGGAGGTGCA
* * * *
652 GGAGGTGGA-T-TG-GGTGGTGGTGGACTTGGCAGTGGCCATGGGCTGGG
130 GGAGGTGGACTAGGAGGGGGTGGAGGACTAGGCAGTGGCCATGGGCTGGG
* * *
699 TGGAGGTGCAGGAGGTGGAGTGGGTGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGTGGGG
1 TGGAGGAGCAGGAGGTGGAGTGGGCGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGTGGAG
* * * * *
764 GTGCAGGAGGTGGATTGGGTGGTGGTGGAGGACTCGGTGGGGCCATGGGCTTGGTGGAGGTGCAG
66 GTGCAGAAGGTAGATTGGGTGGTGGTGGAGGACTCGGCGGGGCCATGGGCTGGGAGGAGGTGCAG
**
829 GAGGTGGACTAGGAGGGGGTGGAGGACTAGGTGGTGGCCATGGGCTGGG
131 GAGGTGGACTAGGAGGGGGTGGAGGACTAGGCAGTGGCCATGGGCTGGG
878 AGGTGGAGGC
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
176 31 0.19
177 97 0.61
178 1 0.01
179 30 0.19
ACGTcount: A:0.13, C:0.10, G:0.56, T:0.20
Consensus pattern (179 bp):
TGGAGGAGCAGGAGGTGGAGTGGGCGGTGGTGGAGGACTTGGCGGTGGCCATGGGCTGGGTGGAG
GTGCAGAAGGTAGATTGGGTGGTGGTGGAGGACTCGGCGGGGCCATGGGCTGGGAGGAGGTGCAG
GAGGTGGACTAGGAGGGGGTGGAGGACTAGGCAGTGGCCATGGGCTGGG
Found at i:942 original size:42 final size:42
Alignment explanation
Indices: 893--997 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
883 GAGGCGAATT
* * * *
893 AGGTGGTGGTGCAGGTGGTGGAGGTGGAGTAGGGCTCGGTGG
1 AGGTGGTGGTGCTGGTGGAGGAGCTGGAGGAGGGCTCGGTGG
* *
935 AGGTGGTGGTGCTGGAGGAGGAGCTGGAGGAGGGCTTGGTGG
1 AGGTGGTGGTGCTGGTGGAGGAGCTGGAGGAGGGCTCGGTGG
*
977 AGTTGGTGGTGCTGGTGGAGG
1 AGGTGGTGGTGCTGGTGGAGG
998 TTTTGGAGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.12, C:0.07, G:0.59, T:0.22
Consensus pattern (42 bp):
AGGTGGTGGTGCTGGTGGAGGAGCTGGAGGAGGGCTCGGTGG
Found at i:994 original size:18 final size:18
Alignment explanation
Indices: 971--1063 Score: 71
Period size: 18 Copynumber: 5.0 Consensus size: 18
961 GAGGAGGGCT
*
971 TGGTGGAGTTGGTGGTGC
1 TGGTGGAGTTGGTGGTGG
*
989 TGGTGGAGGTTTTGGAGGTGG
1 TGGTGGA-G--TTGGTGGTGG
* * *
1010 AGGAGGATTTGGTGGTGG
1 TGGTGGAGTTGGTGGTGG
* *
1028 TGGTGGAGTTGGGGGAGG
1 TGGTGGAGTTGGTGGTGG
*
1046 AT-TTGGAGTTGGTGGTGG
1 -TGGTGGAGTTGGTGGTGG
1064 ATTTGGCAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
18 42 0.74
19 2 0.04
21 13 0.23
ACGTcount: A:0.11, C:0.01, G:0.57, T:0.31
Consensus pattern (18 bp):
TGGTGGAGTTGGTGGTGG
Found at i:1011 original size:48 final size:47
Alignment explanation
Indices: 911--1053 Score: 134
Period size: 48 Copynumber: 3.1 Consensus size: 47
901 GTGCAGGTGG
* *
911 TGGAGGTGGAGTAGGGCTCGGTGGAGGTGGTGGTGC---TGGAGG--
1 TGGAGGTGGAGGAGGGCTTGGTGGAGGTGGTGGTGCTGGTGGAGGTT
* * *
953 AGGAGCTGGAGGAGGGCTTGGTGGAGTTGGTGGTGCTGGTGGAGGTTT
1 TGGAGGTGGAGGAGGGCTTGGTGGAGGTGGTGGTGCTGGTGGAGG-TT
** * * * *
1001 TGGAGGTGGAGGAGGATTTGGTGGTGGTGGTGGAGTTGGGGGAGGATT
1 TGGAGGTGGAGGAGGGCTTGGTGGAGGTGGTGGTGCTGGTGGAGG-TT
1049 TGGAG
1 TGGAG
1054 TTGGTGGTGG
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 31 0.39
45 6 0.08
48 43 0.54
ACGTcount: A:0.13, C:0.04, G:0.57, T:0.25
Consensus pattern (47 bp):
TGGAGGTGGAGGAGGGCTTGGTGGAGGTGGTGGTGCTGGTGGAGGTT
Found at i:1023 original size:30 final size:30
Alignment explanation
Indices: 899--1051 Score: 87
Period size: 30 Copynumber: 5.1 Consensus size: 30
889 AATTAGGTGG
* * **
899 TGGTGCAGGTGGTGGAGGTGGAGTAGGGCT
1 TGGTGGAGGTGGTGGAGGTGGAGGAGGATT
* * * **
929 CGGTGGAGGTGGTGGTGCTGGAGGAGGAGC
1 TGGTGGAGGTGGTGGAGGTGGAGGAGGATT
* * * * *
959 TGGAGGAGGGCTTGGTGGAGTTGGTGG-TG--C
1 TGGTGGA-GG--TGGTGGAGGTGGAGGAGGATT
**
989 TGGTGGAGGTTTTGGAGGTGGAGGAGGATT
1 TGGTGGAGGTGGTGGAGGTGGAGGAGGATT
* * *
1019 TGGTGGTGGTGGTGGAGTTGGGGGAGGATT
1 TGGTGGAGGTGGTGGAGGTGGAGGAGGATT
1049 TGG
1 TGG
1052 AGTTGGTGGT
Statistics
Matches: 91, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
27 11 0.12
28 1 0.01
29 2 0.02
30 62 0.68
31 2 0.02
32 1 0.01
33 12 0.13
ACGTcount: A:0.12, C:0.05, G:0.58, T:0.25
Consensus pattern (30 bp):
TGGTGGAGGTGGTGGAGGTGGAGGAGGATT
Found at i:1059 original size:30 final size:30
Alignment explanation
Indices: 1001--1069 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
991 GTGGAGGTTT
* *
1001 TGGAGGTGGAGGAGGATTTGGTGGTGGTGG
1 TGGAGTTGGAGGAGGATTTGGAGGTGGTGG
* *
1031 TGGAGTTGGGGGAGGATTTGGAGTTGGTGG
1 TGGAGTTGGAGGAGGATTTGGAGGTGGTGG
*
1061 TGGATTTGG
1 TGGAGTTGG
1070 CAAAGGTGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.13, C:0.00, G:0.57, T:0.30
Consensus pattern (30 bp):
TGGAGTTGGAGGAGGATTTGGAGGTGGTGG
Found at i:1065 original size:18 final size:18
Alignment explanation
Indices: 1018--1069 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1008 GGAGGAGGAT
*
1018 TTGGTGGTGG-TGGTGGAG
1 TTGGTGGTGGAT-TTGGAG
* *
1036 TTGGGGGAGGATTTGGAG
1 TTGGTGGTGGATTTGGAG
1054 TTGGTGGTGGATTTGG
1 TTGGTGGTGGATTTGG
1070 CAAAGGTGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.10, C:0.00, G:0.56, T:0.35
Consensus pattern (18 bp):
TTGGTGGTGGATTTGGAG
Done.