Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_D_gene_10006814
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, 617
Length: 1029
ACGTcount: A:0.18, C:0.09, G:0.50, T:0.23
Found at i:175 original size:12 final size:12
Alignment explanation
Indices: 160--212 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
150 TTTAGGCTCA
*
160 GGTTCTGGATAT
1 GGTTCAGGATAT
*
172 GGTTCAGGGTAT
1 GGTTCAGGATAT
*
184 GGTTCCGGA-AGT
1 GGTTCAGGATA-T
*
196 GGCTCAGGATAT
1 GGTTCAGGATAT
208 GGTTC
1 GGTTC
213 GGGAGCTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.38, T:0.32
Consensus pattern (12 bp):
GGTTCAGGATAT
Found at i:249 original size:24 final size:24
Alignment explanation
Indices: 222--272 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
212 CGGGAGCTTA
*
222 TGGTAGTGGAGGAGGTGGAGGGGG
1 TGGTAGGGGAGGAGGTGGAGGGGG
* * *
246 TGGTGGGGGCGGAGGTGGAGGTGG
1 TGGTAGGGGAGGAGGTGGAGGGGG
270 TGG
1 TGG
273 CAGCTCTGGA
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:0.12, C:0.02, G:0.69, T:0.18
Consensus pattern (24 bp):
TGGTAGGGGAGGAGGTGGAGGGGG
Found at i:355 original size:3 final size:3
Alignment explanation
Indices: 349--401 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
339 TGGGATAGGA
* * * * * *
349 GGT GGT GGT GGT GGT GGT GGC GGT GGT GGC GGT AGA GGA GGT GGA GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
397 GGT GG
1 GGT GG
402 CAATGGAGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.08, C:0.04, G:0.66, T:0.23
Consensus pattern (3 bp):
GGT
Found at i:410 original size:24 final size:24
Alignment explanation
Indices: 364--413 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
354 TGGTGGTGGT
* **
364 GGTGGCGGTGGTGGCGGTAGAGGA
1 GGTGGAGGTGGTGGCAATAGAGGA
*
388 GGTGGAGGTGGTGGCAATGGAGGA
1 GGTGGAGGTGGTGGCAATAGAGGA
412 GG
1 GG
414 CTCAGGATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.06, G:0.62, T:0.16
Consensus pattern (24 bp):
GGTGGAGGTGGTGGCAATAGAGGA
Found at i:493 original size:21 final size:21
Alignment explanation
Indices: 460--509 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
450 TGGCGGTAGA
460 GGTGGAGGAGGAGGAGGAGGT
1 GGTGGAGGAGGAGGAGGAGGT
* * *
481 GGTGGCGGTGGAGGTGGAGGT
1 GGTGGAGGAGGAGGAGGAGGT
502 GGTGGAGG
1 GGTGGAGG
510 CAATGGTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.68, T:0.14
Consensus pattern (21 bp):
GGTGGAGGAGGAGGAGGAGGT
Found at i:505 original size:15 final size:15
Alignment explanation
Indices: 475--509 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
465 AGGAGGAGGA
*
475 GGAGGTGGTGGCGGT
1 GGAGGTGGAGGCGGT
*
490 GGAGGTGGAGGTGGT
1 GGAGGTGGAGGCGGT
505 GGAGG
1 GGAGG
510 CAATGGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.69, T:0.17
Consensus pattern (15 bp):
GGAGGTGGAGGCGGT
Found at i:536 original size:18 final size:18
Alignment explanation
Indices: 513--558 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
503 GTGGAGGCAA
*
513 TGGTTCAGGTTATGGAAG
1 TGGTTCAGGATATGGAAG
531 TGGTTCAGGATATGGAAG
1 TGGTTCAGGATATGGAAG
*
549 TGGGTCAGGA
1 TGGTTCAGGA
559 GGCGGAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.28
Consensus pattern (18 bp):
TGGTTCAGGATATGGAAG
Found at i:668 original size:15 final size:15
Alignment explanation
Indices: 650--701 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
640 GGGATAGGAA
650 GTGGTGGAGGAGGTG
1 GTGGTGGAGGAGGTG
665 GTGGTGGCAGCGGAGGTG
1 GTGGTGG-A--GGAGGTG
*
683 GTGGTGGTGGAGGTG
1 GTGGTGGAGGAGGTG
698 GTGG
1 GTGG
702 CAACGGAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 18 0.55
16 1 0.03
18 14 0.42
ACGTcount: A:0.10, C:0.04, G:0.65, T:0.21
Consensus pattern (15 bp):
GTGGTGGAGGAGGTG
Found at i:671 original size:18 final size:18
Alignment explanation
Indices: 650--701 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
640 GGGATAGGAA
650 GTGGTGGAGGAGGTGGTG
1 GTGGTGGAGGAGGTGGTG
** *
668 GTGGCAGCGGAGGTGGTG
1 GTGGTGGAGGAGGTGGTG
*
686 GTGGTGGAGGTGGTGG
1 GTGGTGGAGGAGGTGG
702 CAACGGAGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.10, C:0.04, G:0.65, T:0.21
Consensus pattern (18 bp):
GTGGTGGAGGAGGTGGTG
Found at i:684 original size:30 final size:30
Alignment explanation
Indices: 650--713 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
640 GGGATAGGAA
* *
650 GTGGTGGAGGAGGTGGTGGTGGCAGCGGAG
1 GTGGTGGAGGAGGAGGTGGTGGCAACGGAG
* *
680 GTGGTGGTGGTGGAGGTGGTGGCAACGGAG
1 GTGGTGGAGGAGGAGGTGGTGGCAACGGAG
710 GTGG
1 GTGG
714 GTCGGGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.12, C:0.06, G:0.62, T:0.19
Consensus pattern (30 bp):
GTGGTGGAGGAGGAGGTGGTGGCAACGGAG
Found at i:709 original size:15 final size:15
Alignment explanation
Indices: 664--713 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
654 TGGAGGAGGT
664 GGTGGTGGCAGCGGA
1 GGTGGTGGCAGCGGA
** *
679 GGTGGTGGTGGTGGA
1 GGTGGTGGCAGCGGA
*
694 GGTGGTGGCAACGGA
1 GGTGGTGGCAGCGGA
709 GGTGG
1 GGTGG
714 GTCGGGATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.12, C:0.08, G:0.62, T:0.18
Consensus pattern (15 bp):
GGTGGTGGCAGCGGA
Found at i:754 original size:18 final size:18
Alignment explanation
Indices: 710--767 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
700 GGCAACGGAG
* **
710 GTGGGTCGGGATATGGGT
1 GTGGGTCTGGATATGGAA
* *
728 CTGGATCTGGATATGGAA
1 GTGGGTCTGGATATGGAA
746 GTGGGTCTGGATATGGAA
1 GTGGGTCTGGATATGGAA
764 GTGG
1 GTGG
768 AGGTGGTAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.07, G:0.47, T:0.28
Consensus pattern (18 bp):
GTGGGTCTGGATATGGAA
Found at i:788 original size:132 final size:126
Alignment explanation
Indices: 652--956 Score: 378
Period size: 132 Copynumber: 2.4 Consensus size: 126
642 GATAGGAAGT
* * * *
652 GGTGGAGGAGGTGGTGGTGGCAGCGGAGGTGGTGGTGGTGGAGGTGGTGG-CAACGGAGGTGGGT
1 GGTGGAGGAGGAGGTGGTGGCAGTGGAGGTGGTGGTGGCGGAGGTGGTGGTC-ACGGAGGAGGGT
* * * * * * *
716 CGGGATATGGGTCTGGATCTGGATATGGAAGTGGGTCTGGATATGGAAGTGGAGGTGGTAGAGGT
65 CAGGATATGGATCAGGATCCGGATACGGAAGT--G---GGA-ATGGAAGTGGAAGTGGAAGAGGT
781 AGA
124 AGA
*
784 GGTGGAGGAGGAGGTGGTGGCAGTGGAGGTGGTGGTGGCGGAGGTGGTGGTCATGGAGGAGGGTC
1 GGTGGAGGAGGAGGTGGTGGCAGTGGAGGTGGTGGTGGCGGAGGTGGTGGTCACGGAGGAGGGTC
* * * *
849 AGGATATGGATCAGGGTCCGGATACGGAAGTGGGAGTGGGAGTGGAAGTGGAAGCGGTAGA
66 AGGATATGGATCAGGATCCGGATACGGAAGTGGGAATGGAAGTGGAAGTGGAAGAGGTAGA
* *
910 GGTGGAGGAGGAGGTGGTGGCAGTGGAGGTGGAGGAGGCGGAGGTGG
1 GGTGGAGGAGGAGGTGGTGGCAGTGGAGGTGGTGGTGGCGGAGGTGG
957 AGGTGAAGGC
Statistics
Matches: 154, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
126 66 0.43
127 3 0.02
130 1 0.01
132 83 0.54
133 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.56, T:0.19
Consensus pattern (126 bp):
GGTGGAGGAGGAGGTGGTGGCAGTGGAGGTGGTGGTGGCGGAGGTGGTGGTCACGGAGGAGGGTC
AGGATATGGATCAGGATCCGGATACGGAAGTGGGAATGGAAGTGGAAGTGGAAGAGGTAGA
Found at i:802 original size:15 final size:15
Alignment explanation
Indices: 784--833 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
774 TAGAGGTAGA
784 GGTGGAGGAGGAGGT
1 GGTGGAGGAGGAGGT
*
799 GGTGGCA-GTGGAGGT
1 GGTGG-AGGAGGAGGT
* *
814 GGTGGTGGCGGAGGT
1 GGTGGAGGAGGAGGT
829 GGTGG
1 GGTGG
834 TCATGGAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 29 0.97
16 1 0.03
ACGTcount: A:0.12, C:0.04, G:0.66, T:0.18
Consensus pattern (15 bp):
GGTGGAGGAGGAGGT
Found at i:844 original size:18 final size:17
Alignment explanation
Indices: 790--845 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 17
780 TAGAGGTGGA
790 GGAGGAGGTGGTGGCA-
1 GGAGGAGGTGGTGGCAT
*
806 -GTGGAGGTGGTGG--T
1 GGAGGAGGTGGTGGCAT
*
820 GGCGGAGGTGGTGGTCAT
1 GGAGGAGGTGGTGG-CAT
838 GGAGGAGG
1 GGAGGAGG
846 GTCAGGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 24 0.75
18 8 0.25
ACGTcount: A:0.14, C:0.05, G:0.62, T:0.18
Consensus pattern (17 bp):
GGAGGAGGTGGTGGCAT
Found at i:926 original size:27 final size:27
Alignment explanation
Indices: 896--947 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
886 GGGAGTGGAA
*
896 GTGGAAGCGGTAGAGGTGGAGGAGGAG
1 GTGGAAGCAGTAGAGGTGGAGGAGGAG
** *
923 GTGGTGGCAGTGGAGGTGGAGGAGG
1 GTGGAAGCAGTAGAGGTGGAGGAGG
948 CGGAGGTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.04, G:0.62, T:0.13
Consensus pattern (27 bp):
GTGGAAGCAGTAGAGGTGGAGGAGGAG
Found at i:928 original size:15 final size:15
Alignment explanation
Indices: 910--956 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
900 AAGCGGTAGA
910 GGTGGAGGAGGAGGT
1 GGTGGAGGAGGAGGT
*
925 GGTGGCA-GTGGAGGT
1 GGTGG-AGGAGGAGGT
* *
940 GGAGGAGGCGGAGGT
1 GGTGGAGGAGGAGGT
955 GG
1 GG
957 AGGTGAAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.17, C:0.04, G:0.66, T:0.13
Consensus pattern (15 bp):
GGTGGAGGAGGAGGT
Found at i:956 original size:21 final size:21
Alignment explanation
Indices: 908--961 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
898 GGAAGCGGTA
* * *
908 GAGGTGGAGGAGGAGGTGGTG
1 GAGGTGGAGGTGGAGGAGGCG
929 GCA-GTGGAGGTGGAGGAGGCG
1 G-AGGTGGAGGTGGAGGAGGCG
950 GAGGTGGAGGTG
1 GAGGTGGAGGTG
962 AAGGCAATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.19, C:0.04, G:0.65, T:0.13
Consensus pattern (21 bp):
GAGGTGGAGGTGGAGGAGGCG
Done.