Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1247
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: 2274
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Found at i:1096 original size:44 final size:44
Alignment explanation
Indices: 1046--1800 Score: 552
Period size: 44 Copynumber: 17.0 Consensus size: 44
1036 TGAAAAGCAG
*
1046 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
** * * * *
1090 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGATAA
1135 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGA-AA
1 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
* ** * * *
1178 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAAAA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGATAA
* * *
1223 CAAATCTTGTCTTCATGTACTGGC--GAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
* * * * * * * *
1265 TAGGTCCTGTCTTCCTATA-TCGGTAGCGAAGTGGATCAAATA-AA
1 CAGATCTTGTCTTCATATACT-GG-CGTGAAGTAGATCAAAGATAA
* * * * ** * *
1309 CATATTTTATATTCCCATACTGGTGGTGAAGTAGATCGAAGA-AA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGATAA
*
1353 GCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA
1 -CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
** * * * *
1398 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTTGATCGAAAGAAGAAA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATC-AAAG-A-TAA
* * * * *
1446 GCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCAAAAATAG
1 -CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
* * * * * *
1491 CAGATTTTATCTTCATGTACTGGCATAAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
** * * ** *
1535 CAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGA-AA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGATAA
* *
1579 CCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAA
1 -CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
* ** * * * * *
1624 CAGATATTGTCTTCCCATACCGGTGGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGATAA
** * * * * *
1669 TGGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATACAA
1 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
* * ** * * * * *
1713 CAGATATTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAAA
1 CAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGATAA
* * *
1758 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAGGATA
1 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATA
1801 GTAGGTCTTG
Statistics
Matches: 536, Mismatches: 155, Indels: 40
0.73 0.21 0.05
Matches are distributed among these distances:
41 1 0.00
42 30 0.06
43 22 0.04
44 246 0.46
45 197 0.37
46 5 0.01
47 4 0.01
48 12 0.02
49 19 0.04
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGATAA
Found at i:1578 original size:226 final size:223
Alignment explanation
Indices: 1044--1707 Score: 871
Period size: 226 Copynumber: 3.0 Consensus size: 223
1034 GTTGAAAAGC
*
1044 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATC-AAGATAACAGATCTTGTCTTCCCATA
*
1109 CTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAA
65 CTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA
* * * *
1174 GA-AACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-AAAG-AAAA-CAAATCTTGTCT
130 GATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAGAAAAAGCAGATCTTGTCT
* * *
1235 TCATGTACT-GGCGAAGTAGATCAAAGAT
195 TCATGTATTGGGTGAAGTAGATCAAAAAT
* * * * * * * * * * * *
1263 AGTAGGTCCTGTCTTCCTATA-TCGGTAGCGAAGTGGATCAA-ATAAACATATTTTATATTCCCA
1 AGCAGATCTTGTCTTCATGTACT-GGCA-TGAAGTAGATCAAGAT-AACAGATCTTGTCTTCCCA
* *
1326 TACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
63 TACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
*
1391 AAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTTGATCGAAAGAAGAAAGCAGATCTTG
128 AAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAGAA-AAAGCAGATCTTG
1456 TCTTCATGTATTGGTGTGAAGTAGATCAAAAAT
192 TCTTCATGTATTGG-GTGAAGTAGATCAAAAAT
* * *
1489 AGCAGATTTTATCTTCATGTACTGGCATAAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATC-AAGATAACAGATCTTGTCTTCCCATA
** * *
1554 CTGGTGGCGAAACAGATCGAAGAAACCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAA
65 CTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA
* * * *
1619 GATAACAGATATTGTCTTCCCATACCGGTGGCGAAGTAGATCG-AAGAAAATG--GATCTTATCT
130 GATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAGAAAAAGCAGATCTTGTCT
1681 TCATGTATTGGCGTGAAGTAGATCAAA
195 TCATGTATTGG-GTGAAGTAGATCAAA
1708 TACAACAGAT
Statistics
Matches: 382, Mismatches: 50, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
218 3 0.01
219 101 0.26
220 44 0.12
221 4 0.01
222 36 0.09
223 3 0.01
224 22 0.06
225 14 0.04
226 152 0.40
227 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (223 bp):
AGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAGATAACAGATCTTGTCTTCCCATAC
TGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAG
ATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAGAAAAAGCAGATCTTGTCTT
CATGTATTGGGTGAAGTAGATCAAAAAT
Found at i:1812 original size:89 final size:89
Alignment explanation
Indices: 1046--1800 Score: 749
Period size: 89 Copynumber: 8.5 Consensus size: 89
1036 TGAAAAGCAG
1046 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
1111 GGTGGCGAAGTAGATCGAAGAAAA
66 GGTGGCGAAGTAGATCGAAGAAAA
* *
1135 CAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
* * *
1199 GGTGGTGGAGTAGATCAAAGAAAA
66 GGTGGCGAAGTAGATCGAAGAAAA
* ** * * *
1223 CAAATCTTGTCTTCATGTACTGGC--GAAGTAGATCAAAGATAGTAGGTCCTGTCTTCCTATA-T
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
* *
1285 CGGTAGCGAAGTGGATC-AA-ATAAA
66 -GGTGGCGAAGTAGATCGAAGA-AAA
* * * * *** * * ***
1309 CATATTTTATATTCCCATACTGGTGGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATGTA
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCATA
* * * *
1373 CTGG-CGTGAAGTAGATCAAAGATAA
64 CTGGTGGCGAAGTAGATCGAAGAAAA
*** * * * * **
1398 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTTGATCGAAAGAAGAAAGCAGATCTTGTCTTCAT
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAG-A-TAA-CAGATCTTGTCTTCCC
* * *
1463 GTATTGGT-GTGAAGTAGATC-AA-AAATA
61 ATACTGGTGGCGAAGTAGATCGAAGAAA-A
* * * * *
1490 GCAGATTTTATCTTCATGTACTGGCATAAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATAC
1 -CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATAC
** *
1555 TGGTGGCGAAACAGATCGAAGAAAC
65 TGGTGGCGAAGTAGATCGAAGAAAA
* * *
1580 CAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATATTGTCTTCCCATACC
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
1645 GGTGGCGAAGTAGATCGAAGAAAA
66 GGTGGCGAAGTAGATCGAAGAAAA
** * * * * * *
1669 TGGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATACAACAGATATTGTCTCCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
* * *
1734 GGTGGTGGAGTAGGTCGAAGAAAA
66 GGTGGCGAAGTAGATCGAAGAAAA
* *
1758 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAGGATA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
1801 GTAGGTCTTG
Statistics
Matches: 554, Mismatches: 92, Indels: 40
0.81 0.13 0.06
Matches are distributed among these distances:
85 1 0.00
86 37 0.07
87 27 0.05
88 96 0.17
89 310 0.56
90 8 0.01
91 9 0.02
92 11 0.02
93 55 0.10
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
GGTGGCGAAGTAGATCGAAGAAAA
Found at i:1822 original size:133 final size:132
Alignment explanation
Indices: 1046--1817 Score: 592
Period size: 133 Copynumber: 5.8 Consensus size: 132
1036 TGAAAAGCAG
*** * * ***
1046 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATAC
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTAC
* * * * * *
1110 TGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAA
66 TGG-CGTGAAGTAGATC-AAGATAATAGGTCTTGTCTTCATATACTGGTCGCGAAGTAGATCAAA
*
1174 GAAA
129 TAAA
* * *
1178 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAAAACAAATCTTGTCTTCATGTAC
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTAC
* * * * *
1243 TGGC--GAAGTAGATCAAAGATAGTAGGTCCTGTCTTCCTATA-TCGGTAGCGAAGTGGATCAAA
66 TGGCGTGAAGTAGATC-AAGATAATAGGTCTTGTCTTCATATACT-GGTCGCGAAGTAGATCAAA
1305 TAAA
129 TAAA
* * * * * *
1309 CATATTTTATATTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTAC
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTAC
* * ** * *
1374 TGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTTGATCGAAA
66 TGGCGTGAAGTAGATC-AAGATAATAGGTCTTGTCTTCATATACTGGTCGCGAAGTAGATC---A
*
1439 GAAGAAA
127 -AATAAA
*** * * * *
1446 GCAGATCTTGTCTTCATGTATTGGT-GTGAAGTAGATCAAA-AATAGCAGATTTTATCTTCATGT
1 -CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAA-AACAGATCTTGTCTTCATGT
* * * * ** * ** *
1509 ACTGGCATAAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGA
64 ACTGGCGTGAAGTAGATC-AAGATAATAGGTCTTGTCTTCATATACTGGTCGCGAAGTAGATCAA
*
1574 AGAAA
128 ATAAA
*** ** * * ***
1579 CCAGATCTTGTCTTCATGTACTGG-CATGAAGTAGATCAAAGATAACAGATATTGTCTTCCCATA
1 -CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTA
* * * * * * * *
1643 CCGGTGGCGAAGTAGATCGAAGAAAAT-GGATCTTATCTTCATGTATTGG-CGTGAAGTAGATCA
65 CTGG-CGTGAAGTAGATC-AAGATAATAGG-TCTTGTCTTCATATACTGGTCGCGAAGTAGATCA
1706 AATACAA
127 AATA-AA
* * * * * *
1713 CAGATATTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAAACAGATCTTGTCTTCATGTAT
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTAC
* *
1778 TGGCGTGAAGTAGATCAAGGATAGTAGGTCTTGTCCTCAT
66 TGGCGTGAAGTAGATCAA-GATAATAGGTCTTGTCTTCAT
1818 GTATTAGCAC
Statistics
Matches: 510, Mismatches: 110, Indels: 39
0.77 0.17 0.06
Matches are distributed among these distances:
129 1 0.00
130 32 0.06
131 76 0.15
132 21 0.04
133 199 0.39
134 68 0.13
136 3 0.01
137 94 0.18
138 16 0.03
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (132 bp):
CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTAC
TGGCGTGAAGTAGATCAAGATAATAGGTCTTGTCTTCATATACTGGTCGCGAAGTAGATCAAATA
AA
Done.