Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_D_gene_10000533
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: 2910
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Found at i:1073 original size:21 final size:21
Alignment explanation
Indices: 1021--1089 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1011 AGGACCTTCC
1021 AGTCCACCTCCAAGAGGAGTT
1 AGTCCACCTCCAAGAGGAGTT
* *
1042 -GGCCCCACTCCAAGAGGAGTT
1 AGTCCAC-CTCCAAGAGGAGTT
* *
1063 AGTCTACCTCCAAG-GGAAGTC
1 AGTCCACCTCCAAGAGG-AGTT
1084 AGTCCA
1 AGTCCA
1090 ACTCGGATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 6 0.16
21 29 0.76
22 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (21 bp):
AGTCCACCTCCAAGAGGAGTT
Found at i:1376 original size:84 final size:84
Alignment explanation
Indices: 1271--1476 Score: 229
Period size: 84 Copynumber: 2.4 Consensus size: 84
1261 CCAAGAGGAG
* * * * *
1271 TCAGTCCAACTTCAAGGGTAGTTAGTCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATC
1 TCAGTTCAACTCCAAGGGTAGTAAGTCCAACTCAAATAAGAACATCCA-CATCATCGAGTCAATC
* *
1335 TCATAG-TTCGACTTCAGTTA
65 CCATAGCTT-AACTTCAGTTA
* * ** ** *
1355 TTAGTTCAACTCCAAGGGTAGTCAGTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCC
1 TCAGTTCAACTCCAAGGGTAGTAAGTCCAACTCAAATAAGAACATCCACATCATCGAGTCAATCC
1420 CATAGCTTAACTTCAGTTA
66 CATAGCTTAACTTCAGTTA
1439 TCAGTTCAACTCCAAGAGG-AGTAAGTCCAACTCCAAAT
1 TCAGTTCAACTCCAAG-GGTAGTAAGTCCAACT-CAAAT
1477 GTTATCATTT
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
83 2 0.02
84 92 0.91
85 7 0.07
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (84 bp):
TCAGTTCAACTCCAAGGGTAGTAAGTCCAACTCAAATAAGAACATCCACATCATCGAGTCAATCC
CATAGCTTAACTTCAGTTA
Found at i:1495 original size:42 final size:42
Alignment explanation
Indices: 1435--1516 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
1425 CTTAACTTCA
*
1435 GTTATCAGTTCAACTCCAAGAGGAGT-AAGTCCAACTCCAAAT
1 GTTATCAGTTCAACTCCAAGAGGACTCAA-TCCAACTCCAAAT
* *
1477 GTTATCATTTCAATTCCAAGAGGACTCAATCCAACTCCAA
1 GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAA
1517 TCAGGATATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (42 bp):
GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAAAT
Found at i:1702 original size:21 final size:21
Alignment explanation
Indices: 1676--1723 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1666 GTTATGGATT
1676 CAACTCCAAGAGG-AGCCAGTC
1 CAACTCCAAG-GGTAGCCAGTC
**
1697 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTAGCCAGTC
1718 CAACTC
1 CAACTC
1724 GGATGAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (21 bp):
CAACTCCAAGGGTAGCCAGTC
Found at i:1784 original size:84 final size:84
Alignment explanation
Indices: 1691--1891 Score: 278
Period size: 84 Copynumber: 2.4 Consensus size: 84
1681 CCAAGAGGAG
*
1691 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
1 CCAGTCCAACTCTAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
*
1756 CATAGCTCAACTTCAATTA
66 CATAGCTCAACCTCAATTA
* * * * * *
1775 CCAGTCCAACTCTAATGGTAGTTACTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCT
1 CCAGTCCAACTCTAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
*
1840 CATAGCTCAACCTCAGTTA
66 CATAGCTCAACCTCAATTA
* * *
1859 TCAGTTCAACTCTAAGAGG-AGTCAGTCCAACTC
1 CCAGTCCAACTCTAAG-GGTAGTTAGTCCAACTC
1892 CAAGGGTAGT
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
84 99 0.98
85 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (84 bp):
CCAGTCCAACTCTAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCC
CATAGCTCAACCTCAATTA
Found at i:1785 original size:105 final size:105
Alignment explanation
Indices: 1048--1786 Score: 567
Period size: 105 Copynumber: 7.0 Consensus size: 105
1038 AGTTGGCCCC
* * * * * * *
1048 ACTCCAAGAGGAGTTAGTCTACCTCCAAGGGAAGTCAGTCCAACTCGGATTAGGACATCCATCGC
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
* * * *
1113 ATCAAGTCAATCCCAAAACTCAACTTCAGTTTTCAGTTCA
66 ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* * * * *
1153 ACTCCAAGAGGAGTCATTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTC
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
* * * *
1218 ATCAAGTCAGTCCCATAGCTCAACTTCAGTTCTCATTTCA
66 ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* * * * ** * * *
1258 ACCCCAAGAGGAGTCAGTCCAACTTCAAGGGTAGTTAGTCCAATTCAAATAAGAACATCCAGCAT
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCA-CCT
* * * * *
1323 -ATTGAGTCAATCTCATAGTTCGACTTCAGTTATTAGTTCA
65 CATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* * * * *
1363 ACTCCAAG-GGTAGTCAGTCCAACTCGGATGGG-A-ACA-TCCACCTC--ATCGA-GTCAATCC-
1 ACTCCAAGAGG-AGTCAGTCCAACTC-CAAGGGTAGTCAGTCCAACTCGGAT-GAGGAC-ATCCA
* ** * * * * * ** * *
1420 CAT-AGCTTAACTTCAGT--TATCAGTTCAACTCCAAGAGGAGTAAGTCCA
62 CCTCA--TCGA-GTCAATCCCAT-AGCTCAACTTC-AG-TTA-TCAGTTCA
* * * * * * ** * *
1468 ACTCCAA-ATGTTA-TCATTTCAATTCCAAGAGG-ACTCAATCCAACTCCAATCAGGATATCCAC
1 ACTCCAAGA-G-GAGTCAGTCCAACTCCAAG-GGTAGTCAGTCCAACTCGGATGAGGACATCCAC
*
1530 CTCATCGAGTCAATCCCATAGCTCCACTTCAGTTATCAGTTCA
63 CTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
* *
1573 ACTCCAAGAGG-GTTCAATCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCT
1 ACTCCAAGAGGAG-TCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCT
* *
1637 CATCGAGTCAATGCCATAGCTCAACTTCAGTTAT-GGATTCA
65 CATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAG-TTCA
* *
1678 ACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTC
1 ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
* * *
1743 ATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCA
66 ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
1783 ACTC
1 ACTC
1787 TAATGGTAGT
Statistics
Matches: 498, Mismatches: 104, Indels: 64
0.75 0.16 0.10
Matches are distributed among these distances:
100 4 0.01
101 5 0.01
102 17 0.03
103 12 0.02
104 9 0.02
105 402 0.81
106 13 0.03
107 13 0.03
108 15 0.03
109 7 0.01
110 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (105 bp):
ACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTC
ATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCA
Found at i:1816 original size:189 final size:189
Alignment explanation
Indices: 1590--2137 Score: 589
Period size: 189 Copynumber: 2.9 Consensus size: 189
1580 GAGGGTTCAA
*
1590 TCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATGC-CAT
1 TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAAT-CTCAT
* *
1654 AGCTCAACTTCAGTTAT-GGATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTC
65 AGCTCAACCTCAGTTATCAG-TTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTC
1718 CAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
129 CAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
* * * * *
1779 TCCAACTCTAATGGTAGTTACTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCTCATA
1 TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCTCATA
* *
1844 GCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGTCCA
66 GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCA
* * * **
1909 ACTCGGATGAGGACATCCACCTC-T--AG-CACAACCTCAGTTATCAATTCAACTCCAAGAGGAC
131 ACTCGGATGAGGACATCCACCTCATCGAGTCA-ATCC-CA--TAGC---TCAACTTC-A-ATTAC
*
1970 TTAG
187 -CAG
* *
1974 TCCAACTCCAAGGGTAGTTAGTCCAAATCGGATGAGG--AT--A--TC--C-A--C---CTC-TA
1 TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCTCATA
* ** ** * *
2024 GCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCTTCTCCAAGGGTAGTCAATCCA
66 GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCA
** *
2089 ACTCAAATGAGGACATCCACCTCATCTAGTCAATCCCATAGCTCAACTT
131 ACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTT
2138 TAGATATCAA
Statistics
Matches: 309, Mismatches: 34, Indels: 44
0.80 0.09 0.11
Matches are distributed among these distances:
177 6 0.02
180 84 0.27
181 4 0.01
182 2 0.01
183 5 0.02
184 3 0.01
185 2 0.01
186 6 0.02
187 3 0.01
188 2 0.01
189 144 0.47
190 1 0.00
191 1 0.00
192 7 0.02
193 2 0.01
194 3 0.01
195 34 0.11
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (189 bp):
TCCAACTCCAAGGGTAGTTACTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCTCATA
GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCA
ACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
Found at i:1825 original size:420 final size:420
Alignment explanation
Indices: 1112--1894 Score: 1106
Period size: 420 Copynumber: 1.9 Consensus size: 420
1102 ACATCCATCG
* *
1112 CATCAAGTCAATCCCAAAACTCAACTTCAGTTTTCAGTTCAACTCCAAGAGGAGTCATTCCAACT
1 CATCAAGTCAATCCCAAAACTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAATCCAACT
*
1177 CCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAGTCCCATAGCTCAAC
66 CCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAAC
* * * *
1242 TTCAGTTCTCATTTCAACCCCAAGAGGAGTCAGTCCAACTTCAAGGGTAGTTAGTCCAATTCAAA
131 TTCAGTTATCATTTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAAA
* * * * * ** *
1307 TAAGAACATCCAGCATATTGAGTCAATCTCATAGTTCGACTTCAGTTATTAGTTCAACTCCAAGG
196 TAAGAACATCCAGCATATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCAAGG
* * *
1372 GTAGTCAGTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATAGCTTAACTTCAGT
261 GTAGTCACTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACCTCAGT
1437 TATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCAATTCCAAGAGGAC
326 TATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCAATTCCAAGAGGAC
1502 TCAATCCAACTCCAATCAGGATATCCACCT
391 TCAATCCAACTCCAATCAGGATATCCACCT
* * * *
1532 CATCGAGTCAATCCCATAGCTCCACTTCAGTTATCAGTTCAACTCCAAGAGG-GTTCAATCCAAC
1 CATCAAGTCAATCCCAAAACTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAG-TCAATCCAAC
* * * * * *
1596 TCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATGCCATAGCTCAA
65 TCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAA
* * *
1661 CTTCAGTTATGGA-TTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCG
130 CTTCAGTTAT-CATTTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCA
* * * * *
1725 GATGAGGACATCCA-CCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCTA
194 AATAAGAACATCCAGCAT-ATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCA
* * * * * *
1789 ATGGTAGTTACTCCAACTTGGATGAGG-ACGTCCACCTCATCTAGTCAATCTCATAGCTCAACCT
258 AGGGTAGTCACTCCAACTCGGATG-GGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACCT
* *
1853 CAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAA
322 CAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA
1895 GGGTAGTTAG
Statistics
Matches: 315, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
419 3 0.01
420 309 0.98
421 3 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (420 bp):
CATCAAGTCAATCCCAAAACTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAATCCAACT
CCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAAC
TTCAGTTATCATTTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAAA
TAAGAACATCCAGCATATCGAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCAAGG
GTAGTCACTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACCTCAGT
TATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCAATTCCAAGAGGAC
TCAATCCAACTCCAATCAGGATATCCACCT
Found at i:1906 original size:21 final size:21
Alignment explanation
Indices: 1859--1912 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1849 ACCTCAGTTA
* *
1859 TCAGTTCAACTCTAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
1880 TCAGTCCAACTCCAAG-GGTAG
1 TCAGTCCAACTCCAAGAGG-AG
*
1901 TTAGTCCAACTC
1 TCAGTCCAACTC
1913 GGATGAGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:1945 original size:90 final size:90
Alignment explanation
Indices: 1842--2111 Score: 423
Period size: 90 Copynumber: 3.0 Consensus size: 90
1832 GTCAATCTCA
* * *
1842 TAGCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
1907 CAACTCGGATGAGGACATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
* *
1932 TAGCACAACCTCAGTTATCAATTCAACTCCAAGAGGACTTAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
* *
1997 CAAATCGGATGAGGATATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
** * *
2022 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCTTCTCCAAGGGTAGTCAATC
1 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
**
2087 CAACTCAAATGAGGACATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
2112 ATCTAGTCAA
Statistics
Matches: 163, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 163 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (90 bp):
TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
CAACTCGGATGAGGACATCCACCTC
Found at i:1981 original size:21 final size:21
Alignment explanation
Indices: 1955--1999 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1945 GTTATCAATT
1955 CAACTCCAAGAGG-ACTTAGTC
1 CAACTCCAAG-GGTACTTAGTC
*
1976 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTACTTAGTC
1997 CAA
1 CAA
2000 ATCGGATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
CAACTCCAAGGGTACTTAGTC
Done.