Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1405
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: 15986
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Found at i:7183 original size:16 final size:16
Alignment explanation
Indices: 7158--7209 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
7148 CTTTACACCC
7158 AAAA-AAAAAAAAAAA
1 AAAACAAAAAAAAAAA
*
7173 AAAACAAAAAAAAAAC
1 AAAACAAAAAAAAAAA
7189 AAAACAAAAAAAAAGAA
1 AAAACAAAAAAAAA-AA
7206 AAAA
1 AAAA
7210 ATAGCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.12
16 24 0.73
17 5 0.15
ACGTcount: A:0.92, C:0.06, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAAAAAA
Found at i:7220 original size:1 final size:1
Alignment explanation
Indices: 7158--7210 Score: 70
Period size: 1 Copynumber: 53.0 Consensus size: 1
7148 CTTTACACCC
* * * *
7158 AAAAAAAAAAAAAAAAAAACAAAAAAAAAACAAAACAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7211 TAGCAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.92, C:0.06, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:8488 original size:28 final size:28
Alignment explanation
Indices: 8429--9482 Score: 1575
Period size: 28 Copynumber: 37.9 Consensus size: 28
8419 ATGTTCATCC
8429 CTTTCAAAG-CCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
8456 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
8485 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
8512 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8540 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8568 CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
8595 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8623 CTTTCAAAGCCCACAA-TCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8650 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8678 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
8707 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
8735 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8763 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8791 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
8820 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8848 CTTTCAAAGCCCACAAGTCAGTGGC-C-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8874 CTTTCAAAGCCCACAAGT-AGTGGCA--
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8899 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
8927 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
8956 CTTTTCAAAGCCCACAA-TCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
8984 CTTTTCAAAGCCCA-AA-TCAGTGGCAC-
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
9010 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
9039 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
9067 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
9095 CCTTTCAAAGCCCACAA-TCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
9123 -TTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
9150 CTTTCAAAGCCCACAAGT-AGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
9177 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
9205 CTTTCAAAGCCCACAAGT-AGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
9231 CATTC-AAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
9258 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
9286 CTTTTAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
9314 CCTTT-AAAGCTCACGCAAGT-AGTGGTAC-
1 -CTTTCAAAGC-C-CACAAGTCAGTGGCACT
9342 CTTCTCAAAGCCCACAAGTCAGTGGCACT
1 CTT-TCAAAGCCCACAAGTCAGTGGCACT
9371 CTTTC-AAGCCCACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
9397 CCTTTCAAAGCCCACGAGTTAGTGGCATT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
9426 CTTTC-AAGCCCATGCAAGTCAGTGGTACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
9455 CTTTTAAAGCCCATGCAAGTCAATGGCA
1 CTTTCAAAGCCCA--CAAGTCAGTGGCA
9483 ACCCTTTTAA
Statistics
Matches: 961, Mismatches: 28, Indels: 72
0.91 0.03 0.07
Matches are distributed among these distances:
25 35 0.04
26 67 0.07
27 211 0.22
28 428 0.45
29 194 0.20
30 26 0.03
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:8527 original size:55 final size:55
Alignment explanation
Indices: 8429--9482 Score: 1559
Period size: 55 Copynumber: 19.0 Consensus size: 55
8419 ATGTTCATCC
*
8429 CTTTCAAAG-CCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
8485 CTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACT
8540 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCACT
8595 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-TCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACT
8650 CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
8707 CTTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACT
8763 CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTCAAAGCCCACAAGTCAGTGGCACT
8820 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGC-C-
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCACT
8874 CTTTCAAAGCCCACAAGT-AGTGGCA-CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACT
8927 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA-TCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCAC-C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
8984 CTTTTCAAAGCCCA-AA-TCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCACT
9039 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
9095 CCTTTCAAAGCCCACAA-TCAGTGGCACTTTTCAAAGCCCACAAGTCAGTGGCACC
1 -CTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACT
*
9150 CTTTCAAAGCCCACAAGT-AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
9205 CTTTCAAAGCCCACAAGT-AGTGGCACCATTC-AAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACT
*
9258 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
9314 CCTTT-AAAGCTCACGCAAGT-AGTGGTACCTTCTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGC-C-CACAAGTCAGTGGCACCTT-TCAAAGCCCACAAGTCAGTGGCACT
* * *
9371 CTTTC-AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTTAGTGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
9426 CTTTC-AAGCCCATGCAAGTCAGTGGTACCCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CTTTCAAAGCCCA--CAAGTCAGTGGCA-CCTTTCAAAGCCCA--CAAGTCAGTGGCA
9483 ACCCTTTTAA
Statistics
Matches: 929, Mismatches: 30, Indels: 75
0.90 0.03 0.07
Matches are distributed among these distances:
51 25 0.03
52 1 0.00
53 45 0.05
54 116 0.12
55 304 0.33
56 199 0.21
57 183 0.20
58 46 0.05
59 10 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (55 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:8567 original size:83 final size:84
Alignment explanation
Indices: 8427--9482 Score: 1595
Period size: 83 Copynumber: 12.7 Consensus size: 84
8417 GAATGTTCAT
*
8427 CCCTTTCAAAG-CCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
8491 AAGCCCACAAGTCAGTGGCA
65 AAGCCCACAAGTCAGTGGCA
8511 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
8575 AGCCCACAAGTCAGTGGCA
66 AGCCCACAAGTCAGTGGCA
8594 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-TCAGTGGCACTCTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
8657 AGCCCACAAGTCAGTGGCA
66 AGCCCACAAGTCAGTGGCA
*
8676 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTC
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTC
8740 AAAGCCCACAAGTCAGTGGCA
64 AAAGCCCACAAGTCAGTGGCA
8761 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
8826 AAGCCCACAAGTCAGTGGCA
65 AAGCCCACAAGTCAGTGGCA
*
8846 CTCTTTCAAAGCCCACAAGTCAGTGG--CCCTTTCAAAGCCCACAAGT-AGTGGCA--CTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
8906 AGCCCACAAGTCAGTGGCA
66 AGCCCACAAGTCAGTGGCA
*
8925 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA-TCAGTGGCACTCTTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTT
8989 CAAAGCCCA-AA-TCAGTGGCA
63 CAAAGCCCACAAGTCAGTGGCA
*
9009 CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
9074 AGCCCACAAGTCAGTGGCA
66 AGCCCACAAGTCAGTGGCA
* *
9093 CTCCTTTCAAAGCCCACAA-TCAGTGGCA-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
9156 AAGCCCACAAGT-AGTGGCA
65 AAGCCCACAAGTCAGTGGCA
*
9175 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT-AGTGGCAC-CATTC-A
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
*
9237 AGCCCACAATTCAGTGGCA
66 AGCCCACAAGTCAGTGGCA
* *
9256 CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTCCTTT-A
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCA
* *
9320 AAGCTCACGCAAGT-AGTGGTA
65 AAGC-C-CACAAGTCAGTGGCA
*
9341 -CCTTCTCAAAGCCCACAAGTCAGTGGCACTCTTTC-AAGCCCACAAGTCAGTGGCA-TCCTTTC
1 CCCTT-TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTC
* *
9403 AAAGCCCACGAGTTAGTGGCA
64 AAAGCCCACAAGTCAGTGGCA
** * * *
9424 TTCTTTC-AAGCCCATGCAAGTCAGTGGTACCCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCA
9483 ACCCTTTTAA
Statistics
Matches: 905, Mismatches: 31, Indels: 69
0.90 0.03 0.07
Matches are distributed among these distances:
79 27 0.03
80 35 0.04
81 81 0.09
82 131 0.14
83 252 0.28
84 185 0.20
85 155 0.17
86 27 0.03
87 12 0.01
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.21
Consensus pattern (84 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
AGCCCACAAGTCAGTGGCA
Found at i:10032 original size:20 final size:20
Alignment explanation
Indices: 10004--10077 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
9994 TCATACCCTG
10004 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
10024 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
10044 A-GTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
10063 ATGTATCGATACATT
1 ATGTATCGATACATT
10078 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:10070 original size:39 final size:38
Alignment explanation
Indices: 10006--10080 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
9996 ATACCCTGAT
* *
10006 GTATCGATACATTTTTCAATATATCGATACATGTATGAA
1 GTATCGATACATTCTACAATATATCGATACAT-TATGAA
* *
10045 GTATCGATATATTCTACAATGTATCGATACATTATG
1 GTATCGATACATTCTACAATATATCGATACATTATG
10081 TCTTTTTACC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (38 bp):
GTATCGATACATTCTACAATATATCGATACATTATGAA
Done.