Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1123
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: 3546
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Found at i:842 original size:28 final size:28
Alignment explanation
Indices: 773--2309 Score: 2539
Period size: 28 Copynumber: 55.3 Consensus size: 28
763 ATGTTCATCC
773 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
801 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
830 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
857 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
885 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
913 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
941 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
968 CTTTTCAAAGCCCACAA-TCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
996 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1024 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
1053 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1081 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1137 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1165 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1193 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1221 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1249 CTTTCAAAGCCCACAA-TCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1276 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1304 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1332 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
1361 -TTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1388 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1416 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1444 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1472 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1500 CTTTCAAAGCCCACAA-TCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1527 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1555 CTTTCAAAGCCCACAA-TCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1581 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1609 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1637 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1665 -TTTCAAAGCCCACAA-TCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1691 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1719 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1747 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1774 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1801 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1829 CTTTCAAAGCCCACAA-TCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1856 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1884 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1912 CCTTTCAAAGCCCACAAGTCAGTGGC-CT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
1940 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1969 C-TTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1996 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
2024 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
2052 CTTTTCAAAGCCCACAAGTCAGTGGC-C-
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
2079 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
2106 CTTTC-AAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
2133 CTTTCAAAGCCCAC-AGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
2160 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
2189 CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
2216 CCTTTCAAAGCCCACGAGT-AGTGGCATT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
2244 CTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
2274 CTTTTAAAGCCCATGCAAGTCAATGGC-C-
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
2302 CTTTCAAA
1 CTTTCAAA
2310 TCACCACTGT
Statistics
Matches: 1447, Mismatches: 29, Indels: 65
0.94 0.02 0.04
Matches are distributed among these distances:
26 71 0.05
27 363 0.25
28 803 0.55
29 179 0.12
30 31 0.02
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.20
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:912 original size:83 final size:83
Alignment explanation
Indices: 772--2309 Score: 2529
Period size: 83 Copynumber: 18.4 Consensus size: 83
762 AATGTTCATC
*
772 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
837 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
856 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
921 GCCCACAAGTCAGTGGCA
66 GCCCACAAGTCAGTGGCA
* *
939 CTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAA-TCAGTGGCACCCTTTCAA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1003 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
*
1022 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
1 --CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
1087 AAGCCCACAAGTCAGTGGCA
64 AAGCCCACAAGTCAGTGGCA
*
1107 CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1172 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
1191 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1256 AGCCCACAA-TCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
1274 CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCA
1339 AAGCCCACAAGTCAGTGGCA
64 AAGCCCACAAGTCAGTGGCA
* *
1359 CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1423 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
1442 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1507 AGCCCACAA-TCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
1525 CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-TCAGTGGCAC-CTTTCAA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1588 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
*
1607 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACT-TTTCAA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1671 AGCCCACAA-TCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
*
1689 CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1754 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
1773 CCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
1837 GCCCACAA-TCAGTGGCA
66 GCCCACAAGTCAGTGGCA
*
1854 CTCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCA
1919 AAGCCCACAAGTCAGTGGC-
64 AAGCCCACAAGTCAGTGGCA
* *
1938 CTCTTTTCAAAGCCCACAAGTCAGTGGCACTC-TTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
2002 AAGCCCACAAGTCAGTGGCA
64 AAGCCCACAAGTCAGTGGCA
2022 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGC-C-CTTTCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
2085 AAGCCCACAAGTCAGTGGCA
64 AAGCCCACAAGTCAGTGGCA
* * *
2105 CCTTTC-AAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCAC-AGTCAGTGGCACCCTTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAA
2168 AGCCCACAAGTCAGTGGCA
65 AGCCCACAAGTCAGTGGCA
* * *
2187 CTCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGT-AGTGGCATTCTTTCAA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
2251 AGCCCACGCAAGTCAGTGGCA
65 AGCCCA--CAAGTCAGTGGCA
* *
2272 CCCTTTTAAAGCCCATGCAAGTCAATGG--CCCTTTCAAA
1 -CCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAA
2310 TCACCACTGT
Statistics
Matches: 1382, Mismatches: 32, Indels: 79
0.93 0.02 0.05
Matches are distributed among these distances:
79 10 0.01
80 14 0.01
81 49 0.04
82 228 0.16
83 454 0.33
84 446 0.32
85 170 0.12
86 1 0.00
87 10 0.01
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (83 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
GCCCACAAGTCAGTGGCA
Found at i:2848 original size:20 final size:20
Alignment explanation
Indices: 2820--2894 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2810 TCATACCCTG
2820 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2840 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
2860 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
2880 ATGTATCGATACATT
1 ATGTATCGATACATT
2895 ATGTTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2887 original size:40 final size:39
Alignment explanation
Indices: 2820--2897 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2810 TCATACCCTG
* *
2820 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
2860 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
2898 TTTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Done.