Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_31358
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, 973
Length: 1622
ACGTcount: A:0.54, C:0.05, G:0.31, T:0.09
Found at i:305 original size:18 final size:18
Alignment explanation
Indices: 282--330 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
272 AAGAGGTGGT
*
282 AGAAGATGATGAAG-AGAA
1 AGAAGA-GAAGAAGAAGAA
300 AGAAGAGAAGAAGAAGAA
1 AGAAGAGAAGAAGAAGAA
* *
318 AAAAGAAAAGAAG
1 AGAAGAGAAGAAG
331 CAAAAGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (18 bp):
AGAAGAGAAGAAGAAGAA
Found at i:726 original size:99 final size:99
Alignment explanation
Indices: 549--1207 Score: 948
Period size: 99 Copynumber: 6.7 Consensus size: 99
539 AGAGACAGAG
* * * * *
549 AAGAAGAAAGACAAAGAGGCAAAGGAGGAGAAG-AAGAAAGAAAAGAATAAGGATAAAGTAGAAG
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAA-AGAAGAAGAAGGAT-GAG--GTAG
*
613 GAGATGAAGATGAAGAAATAGAAGAGGGAAAGAAAGAA
62 GAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * * *
651 AAGAAGAAAGACAAAGAAGCAAAGGAAAAGAAGAAAGAGAAGAAGAAGAAGGATGATGTAGGAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
716 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* *
750 AAGGAGAAAGACAAAGAGGCAAA--AG-AGAAG-AAG-AAAGAA-AAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
* * * *
809 AGATGAAGAAGAATTAGAAGAGGGAAAAAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * *
843 AAGAAGAAAGACAAAGAAGCAAAGGAGAAGAAGAAAGAAAAGAAGAACAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
908 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
942 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAG--G-
*
1007 AGATGAAGATGAAGAATCAGAAGAGGGAAAGAAAGAA
63 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
1044 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTA-GA-A
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
*
1107 -GAAGCTGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * *
1140 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAG--AA-ATGAAGAAGGATGAGGTAGAAGG
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
1202 TGAAGA
66 TGAAGA
1208 GAAAGAAGAG
Statistics
Matches: 507, Mismatches: 37, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
93 86 0.17
94 8 0.02
95 5 0.01
96 82 0.16
97 5 0.01
98 7 0.01
99 170 0.34
101 1 0.00
102 138 0.27
103 5 0.01
ACGTcount: A:0.59, C:0.03, G:0.33, T:0.06
Consensus pattern (99 bp):
AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
Found at i:876 original size:192 final size:197
Alignment explanation
Indices: 549--1200 Score: 1016
Period size: 192 Copynumber: 3.3 Consensus size: 197
539 AGAGACAGAG
* * * *
549 AAGAAGAAAGACAAAGAGGCAAAGGAGGAGAAGAAGAAAGAAAAGAATAAGGATAAAGTAGAAGG
1 AAGAAGAAAGACAAAGAGGCAAA-GA-GAGAAGAAGAAAG--AAGAAGAAGGATGAGGTAGAAGA
* *
614 AGATGAAGATGAAGAAATAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAAA
62 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGA
* *
679 AGAAGAAAGAGAAGAAGAAGAAGGATGATGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
127 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
744 AAAGAA
192 AAAGAA
*
750 AAGGAGAAAGACAAAGAGGCAAA-AGAGAAGAAGAAAGAA-AAGAAGGATGAGGTAGAAGAAGAT
1 AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAGAAGAAGAAGGATGAGGTAGAAGAAGAT
*
813 G-A-A-GAAGAATTAGAAGAGGGAAAAAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
66 GAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
* *
875 GAAAGAAAAGAAGAACAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
131 GAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
940 AA
196 AA
942 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAA-GAG-AGAAG-AAG-AAAGAAGAAGAAGGATGAGGTAGAAGA
* *
1007 AGATGAAGATGAAGAATCAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAGGCAAAGGAGA
62 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGA
*
1072 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTA-GA-A-GAAGCTGAAGAATTAGAAGAGGGAAAG
127 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
1134 AAAGAA
192 AAAGAA
1140 AAGAAGAAAGACAAAGAGGCAAAG-GAGAAGAAGAAAGAAATGAAGAAGGATGAGGTAGAAG
1 AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAG-AA-GAAGAAGGATGAGGTAGAAG
1201 GTGAAGAGAA
Statistics
Matches: 421, Mismatches: 19, Indels: 28
0.90 0.04 0.06
Matches are distributed among these distances:
192 141 0.33
193 5 0.01
194 8 0.02
195 51 0.12
196 6 0.01
197 7 0.02
198 93 0.22
199 3 0.01
200 2 0.00
201 105 0.25
ACGTcount: A:0.59, C:0.03, G:0.33, T:0.06
Consensus pattern (197 bp):
AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAGAAGAAGAAGGATGAGGTAGAAGAAGAT
GAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
GAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
AA
Found at i:894 original size:27 final size:27
Alignment explanation
Indices: 843--895 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
833 AAAAAAAGAA
*
843 AAGAAGAAAGACAAAGAAGCAAAGGAG
1 AAGAAGAAAGACAAAGAAGAAAAGGAG
870 AAGAAGAAAGA-AAAGAAGAACAAGGA
1 AAGAAGAAAGACAAAGAAGAA-AAGGA
896 TGAGGTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.66, C:0.06, G:0.28, T:0.00
Consensus pattern (27 bp):
AAGAAGAAAGACAAAGAAGAAAAGGAG
Found at i:993 original size:27 final size:28
Alignment explanation
Indices: 933--994 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
923 AGAAGAGGGA
* *
933 AAGAAAGAAAAGAAGAAAGACAAAGAGG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
* *
961 CA-AAGGAGAAGAAGAAAGA-AAAGAAG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
987 AAGAAGGA
1 AAGAAGGA
995 TGAGGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.25
27 20 0.71
28 1 0.04
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAAGAAGAAAGACAAAGAAG
Found at i:1095 original size:27 final size:28
Alignment explanation
Indices: 1035--1096 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
1025 AGAAGAGGGA
* *
1035 AAGAAAGAAAAGAAGAAAGACAAAGAGG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
* *
1063 CA-AAGGAGAAGAAGAAAGA-AAAGAAG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
1089 AAGAAGGA
1 AAGAAGGA
1097 TGAGGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.25
27 20 0.71
28 1 0.04
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAAGAAGAAAGACAAAGAAG
Found at i:1146 original size:12 final size:12
Alignment explanation
Indices: 1131--1186 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
1121 AGAAGAGGGA
1131 AAGAAAGAAAAG
1 AAGAAAGAAAAG
1143 AAGAAAGACAAAG
1 AAGAAAGA-AAAG
* *
1156 AGGCAAAGGAGAAG
1 AAG-AAA-GAAAAG
*
1170 AAGAAAGAAATG
1 AAGAAAGAAAAG
1182 AAGAA
1 AAGAA
1187 GGATGAGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 17 0.47
13 9 0.25
14 8 0.22
15 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.29, T:0.02
Consensus pattern (12 bp):
AAGAAAGAAAAG
Done.