Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CotAD_50283
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: 2193
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Found at i:1122 original size:90 final size:90
Alignment explanation
Indices: 970--1373 Score: 566
Period size: 90 Copynumber: 4.5 Consensus size: 90
960 TAATATCCTT
* * *
970 GATCTGCTTCCCGTCAAATACAGAG-CGCCAAATCTG-CTATCTTCGATCTGCTTTGATGTAAAC
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTC-ATCTTCGATCTGCTTCGATGTAAAC
* *
1033 ATACGAATGTCAGTTCTGCTATCTTC
65 ACACGAATGTCAGATCTGCTATCTTC
* * *
1059 GATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGTCATTTTCGATCTGCTTTGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
1124 CACGAATATCAGA-CTGCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* *
1148 AATCTGC-CCCCTGTCTAATACAGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAAC
1 GATCTGCTCCCC-GTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAAC
*
1212 ACACGAATGTTAGATCTGCTATCTTC
65 ACACGAATGTCAGATCTGCTATCTTC
* * * *
1238 GATCTACTCCCTGTCTAATATAGAGACGCCAAATCTGTCATCTTCGATCTGCTCCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
1303 CACGAATGTCAGATCTTCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* * * *
1328 GATCTGCTCTCTGTCTAATACAGGGACGCC-AATCTATCATCTTCGA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGA
1374 ACGGAGACGC
Statistics
Matches: 285, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
88 4 0.01
89 116 0.41
90 161 0.56
91 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (90 bp):
GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
CACGAATGTCAGATCTGCTATCTTC
Found at i:1239 original size:45 final size:45
Alignment explanation
Indices: 1001--1335 Score: 188
Period size: 45 Copynumber: 7.5 Consensus size: 45
991 AGAGCGCCAA
* *
1001 ATCTGCTATCTTCGATCTGCTTTGATGTAAACATACGAATGTCAG
1 ATCTGCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAG
* * * * * * * *
1046 TTCTGCTATCTTCGATCTGCTCCCCG-TCT-AATATA-GAGACGCCAA
1 ATCTGCTATCTTCGATCTGCT--TCGATGTAAACACACGA-ATGTCAG
* * *
1091 ATCTG-TCATTTTCGATCTGCTTTGATGTAAACACACGAATATCAG
1 ATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAG
* * ** * * * * *
1136 A-CTGCTATCTTCAATCTGC-CCCCTGTCTAATACA-GAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTTCGATGT-AAACACACGA-ATGTCAG
* *
1180 ATCTG-TCATTTTCGATCTGCTTCGATGTAAACACACGAATGTTAG
1 ATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAG
* ** * * * * * *
1225 ATCTGCTATCTTCGATCTAC-TCCCTGTCTAATATA-GAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTTCGATGT-AAACACACGA-ATGTCAG
*
1270 ATCTG-TCATCTTCGATCTGCTCCGATGTAAACACACGAATGTCAG
1 ATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAG
*
1315 ATCTTCTATCTTCGATCTGCT
1 ATCTGCTATCTTCGATCTGCT
1336 CTCTGTCTAA
Statistics
Matches: 205, Mismatches: 64, Indels: 42
0.66 0.21 0.14
Matches are distributed among these distances:
43 6 0.03
44 37 0.18
45 143 0.70
46 18 0.09
47 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAG
Found at i:1299 original size:179 final size:180
Alignment explanation
Indices: 986--1373 Score: 586
Period size: 179 Copynumber: 2.2 Consensus size: 180
976 CTTCCCGTCA
* * *
986 AATACAGAG-CGCCAAATCTG-CTATCTTCGATCTGCTTTGATGTAAACATACGAATGTCAGTTC
1 AATACAGAGACGCCAAATCTGTC-ATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATC
* * **
1049 TGCTATCTTCGATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGTCATTTTCGATCTGCTTT
65 TGCTATCTTCGATCTACTCCCCGTCTAATATAGAGACGCCAAATCTGTCATCTTCGATCTGCTCC
1114 GATGTAAACACACGAATATCAGA-CTGCTATCTTCAATCTGCCCCCTGTCT
130 GATGTAAACACACGAATATCAGATCTGCTATCTTCAATCTGCCCCCTGTCT
* *
1164 AATACAGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTTAGATCT
1 AATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCT
*
1229 GCTATCTTCGATCTACTCCCTGTCTAATATAGAGACGCCAAATCTGTCATCTTCGATCTGCTCCG
66 GCTATCTTCGATCTACTCCCCGTCTAATATAGAGACGCCAAATCTGTCATCTTCGATCTGCTCCG
* * * * *
1294 ATGTAAACACACGAATGTCAGATCTTCTATCTTCGATCTGCTCTCTGTCT
131 ATGTAAACACACGAATATCAGATCTGCTATCTTCAATCTGCCCCCTGTCT
* *
1344 AATACAGGGACGCC-AATCTATCATCTTCGA
1 AATACAGAGACGCCAAATCTGTCATCTTCGA
1374 ACGGAGACGC
Statistics
Matches: 189, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
178 9 0.05
179 143 0.76
180 37 0.20
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (180 bp):
AATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCT
GCTATCTTCGATCTACTCCCCGTCTAATATAGAGACGCCAAATCTGTCATCTTCGATCTGCTCCG
ATGTAAACACACGAATATCAGATCTGCTATCTTCAATCTGCCCCCTGTCT
Found at i:1473 original size:117 final size:118
Alignment explanation
Indices: 1260--1491 Score: 367
Period size: 117 Copynumber: 2.0 Consensus size: 118
1250 GTCTAATATA
*
1260 GAGACGCCAAATCTGTCATCTTCGATCTGCTCCGATGTAAACACACGAATGTCAGATCTTCTATC
1 GAGACGCCAAATCTGTCATCTTCGATCTGCTCCGATGTAAACACACGAATGTCAGATCTACTATC
* * * **
1325 TTCGATCTGCTCTCTGTCTAATACAGGGACGCC-AATCTATCATCTTCGAACG
66 TTCGATCTACTCCCCGTCTAATACAAAGACGCCAAATCTATCATCTTCGAACG
* *
1377 GAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTACTATC
1 GAGACGCCAAATCTGTCATCTTCGATCTGCTCCGATGTAAACACACGAATGTCAGATCTACTATC
* *
1442 TTCGATCTACTCCCCGTCTAATATAAAGACGCCAAATCTGTCATCTTCGA
66 TTCGATCTACTCCCCGTCTAATACAAAGACGCCAAATCTATCATCTTCGA
1492 TCTACTTCAC
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
117 89 0.86
118 15 0.14
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (118 bp):
GAGACGCCAAATCTGTCATCTTCGATCTGCTCCGATGTAAACACACGAATGTCAGATCTACTATC
TTCGATCTACTCCCCGTCTAATACAAAGACGCCAAATCTATCATCTTCGAACG
Found at i:1569 original size:171 final size:171
Alignment explanation
Indices: 1374--2003 Score: 963
Period size: 171 Copynumber: 3.6 Consensus size: 171
1364 TCATCTTCGA
*
1374 ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTACT
1 ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
* * * *
1439 ATCTTCGATCTACTCCCCGTCTAATATAAAGACGCCAAATCTGTCATCTTCGATCTACTTCACAC
66 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCAATCTACTTCACAC
* *
1504 GAATGCCAAATCTACTATCTTCGATCTGCTCCCCGTCTAAT
131 GAATGTCAAATCTGCTATCTTCGATCTGCTCCCCGTCTAAT
1545 ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
1 ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
* *
1610 ATCTTCGATCTGCTCCCCGTCTAATACAGAGGCGCCAAATCTGTCATCTTCAATCTGCTTCACAC
66 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCAATCTACTTCACAC
1675 GAATGTCAAATCTGCTATCTTCGATCTGCTCCCCGTCTAAT
131 GAATGTCAAATCTGCTATCTTCGATCTGCTCCCCGTCTAAT
* *
1716 ACGGAGACGCCAAATCTGTCATTTTCGATCTACTTCGATGTAAACACACGAATGTCAGATTTGCT
1 ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
* * * * * * * *
1781 ATATTTGATCTGCTCCCCATCTAGTACGGAGATGCCAAATCTGTCATTTTCAATCTGCTTCGATG
66 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCAA--T-CTAC--T-
*
1846 TAAACACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAAT
125 T---CACACGAATGTCAAATCTGCTATCTTCGATCTGCTCCCCGTCTAAT
* * *
1896 ACAGAGATGCCAAATCTGTCATTTTCAATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
1 ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
*
1961 ATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTG
66 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTG
2004 CTATCAGTGA
Statistics
Matches: 419, Mismatches: 31, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
171 270 0.64
173 1 0.00
174 3 0.01
176 1 0.00
177 1 0.00
180 143 0.34
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (171 bp):
ACGGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCAATCTACTTCACAC
GAATGTCAAATCTGCTATCTTCGATCTGCTCCCCGTCTAAT
Found at i:1614 original size:90 final size:90
Alignment explanation
Indices: 1499--2003 Score: 767
Period size: 90 Copynumber: 5.7 Consensus size: 90
1489 CGATCTACTT
* * * *
1499 CACACGAATGCCAAATCTACTATCTTCGATCTGCTCCCCGTCTAATACGGAGACGCCAAATCTGT
1 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
*
1564 CATTTTCGATCTGCTTCGATGTAAA
66 CATTTTCAATCTGCTTCGATGTAAA
*
1589 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGGCGCCAAATCTGT
1 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
*
1654 CATCTTCAATCTG---C--T-T---
66 CATTTTCAATCTGCTTCGATGTAAA
* *
1670 CACACGAATGTCAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACGGAGACGCCAAATCTGT
1 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
1735 CATTTTCGATCTACTTCGATGTAAA
66 CATTTTCAATCTGCTTCGATGTAAA
* * * * * * *
1760 CACACGAATGTCAGATTTGCTATATTTGATCTGCTCCCCATCTAGTACGGAGATGCCAAATCTGT
1 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
1825 CATTTTCAATCTGCTTCGATGTAAA
66 CATTTTCAATCTGCTTCGATGTAAA
*
1850 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
1 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
1915 CATTTTCAATCTGCTTCGATGTAAA
66 CATTTTCAATCTGCTTCGATGTAAA
*
1940 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTG
1 CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTG
2004 CTATCAGTGA
Statistics
Matches: 378, Mismatches: 28, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
81 72 0.19
84 2 0.01
85 1 0.00
86 1 0.00
87 2 0.01
90 300 0.79
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (90 bp):
CACACGAATGTCAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
CATTTTCAATCTGCTTCGATGTAAA
Found at i:2016 original size:45 final size:45
Alignment explanation
Indices: 1681--2008 Score: 203
Period size: 45 Copynumber: 7.3 Consensus size: 45
1671 ACACGAATGT
* *
1681 CAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACGGAGACGC
1 CAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
* * * * * *
1726 CAAATCTG-TCATTTTCGATCTACT--TCGATGTAA-ACACACGAATGT
1 CAAATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGC
* * * * * * *
1771 CAGATTTGCTATATTTGATCTGCTCCCCATCTAGTACGGAGATGC
1 CAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
* * * * * *
1816 CAAATCTG-TCATTTTCAATCTGCT--TCGATGTAA-ACACACGAATGT
1 CAAATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGC
*
1861 CAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
1 CAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
* * * * * *
1906 CAAATCTG-TCATTTTCAATCTGCT--TCGATGTAA-ACACACGAATGT
1 CAAATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGC
*
1951 CAGATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
1 CAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
1996 CAAATCTGCTATC
1 CAAATCTGCTATC
2009 AGTGATCTAC
Statistics
Matches: 205, Mismatches: 54, Indels: 48
0.67 0.18 0.16
Matches are distributed among these distances:
43 15 0.07
44 17 0.08
45 140 0.68
46 17 0.08
47 16 0.08
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (45 bp):
CAAATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
Done.