Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold209
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: 944012
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 59703 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:918581 original size:16 final size:15
Alignment explanation
Indices: 918548--918577 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
918538 TATAAAATGC
*
918548 AATACTTAATTTTTT
1 AATAATTAATTTTTT
918563 AATAATTAATTTTTT
1 AATAATTAATTTTTT
918578 TAATTTATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
AATAATTAATTTTTT
Found at i:926468 original size:16 final size:16
Alignment explanation
Indices: 926443--926474 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
926433 CAAAGAAATA
*
926443 AAACATCACACCCAGT
1 AAACACCACACCCAGT
926459 AAACACCACACCCAGT
1 AAACACCACACCCAGT
926475 GAGTTAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.41, G:0.06, T:0.09
Consensus pattern (16 bp):
AAACACCACACCCAGT
Found at i:927040 original size:3 final size:3
Alignment explanation
Indices: 927025--927058 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
927015 TATACATGAA
927025 AAT AAT GAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
927059 TAAAATAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:928756 original size:122 final size:126
Alignment explanation
Indices: 928537--928902 Score: 429
Period size: 122 Copynumber: 2.9 Consensus size: 126
928527 CACTGCAATA
** * * * * *
928537 TCAGGGAAATAGGGTAACTGGCTTCAATGTACTCCACTGTAACCACATGGAGGTAAAATCCACTA
1 TCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTGTAACTACAGGGAGGTAAAATTCACCA
* *
928602 TCTTTGATCTACTCCACCACTGCTTAGAGAGACAAGATCTGAAATCTC-C-A-CA-GCTGC
66 TCTTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTCACTATCACGCTGC
*
928659 TCAGGGAAATAGAATTACTGGCTTCAATATACTCCACTGTAACTACAGGGAGGTAAAATTCACCA
1 TCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTGTAACTACAGGGAGGTAAAATTCACCA
* *
928724 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAATATCTGAAATCTTCAATCTATTCCACTGCT
66 TCTTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATC-TC-A-CTA-T-CAC-GCT
928789 GC
125 GC
* * * * *
928791 CCAGGGAGATAGAATTATTGGCCTCAATGTACTCCACTGTAACCT-CAGGGAGGTAAAA-TCTGC
1 TCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTGTAA-CTACAGGGAGGTAAAATTC-AC
* * * *
928854 CATCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCT
64 CATCTTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCT
928903 TCAATTTGTT
Statistics
Matches: 208, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
122 99 0.48
123 2 0.01
126 1 0.00
127 1 0.00
130 2 0.01
131 3 0.01
132 98 0.47
133 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (126 bp):
TCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTGTAACTACAGGGAGGTAAAATTCACCA
TCTTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTCACTATCACGCTGC
Found at i:928885 original size:132 final size:132
Alignment explanation
Indices: 928648--928907 Score: 371
Period size: 132 Copynumber: 2.0 Consensus size: 132
928638 ATCTGAAATC
* *
928648 TCCACAGCTGCTCAGGGAAATAGAATTACTGGCTTCAATATACTCCACTGTAACTACAGGGAGGT
1 TCCACAGCTGCCCAGGGAAATAGAATTACTGGCCTCAATATACTCCACTGTAACTACAGGGAGGT
* * * *
928713 AAAATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAATATCTGAAATCTTCAATCT
66 AAAATTCACCATCTTCGATCTACTCCACTACTGCCTAGGGAGACAAGATCTGAAATCTTCAATCT
928778 AT
131 AT
* * * *
928780 TCCACTGCTGCCCAGGGAGATAGAATTATTGGCCTCAATGTACTCCACTGTAACCT-CAGGGAGG
1 TCCACAGCTGCCCAGGGAAATAGAATTACTGGCCTCAATATACTCCACTGTAA-CTACAGGGAGG
* * *
928844 TAAAA-TCTGCCATCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAAT
65 TAAAATTC-ACCATCTTCGATCTACTCCACTACTGCCTAGGGAGACAAGATCTGAAATCTTCAAT
928908 TTGTTCAACT
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
131 2 0.02
132 109 0.96
133 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (132 bp):
TCCACAGCTGCCCAGGGAAATAGAATTACTGGCCTCAATATACTCCACTGTAACTACAGGGAGGT
AAAATTCACCATCTTCGATCTACTCCACTACTGCCTAGGGAGACAAGATCTGAAATCTTCAATCT
AT
Found at i:928903 original size:44 final size:44
Alignment explanation
Indices: 928730--928907 Score: 121
Period size: 44 Copynumber: 4.0 Consensus size: 44
928720 ACCATCTTTG
* * * * *
928730 ATCTGCTCCACTACTGCTTAGGGAGACAATATCTGAAATCTTCA
1 ATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCA
* * * * * *
928774 ATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TATTGGCCTCA
1 ATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * * ** *
928817 ATGTACTCCACT-GTAACCTCAGGGAGGTAAAATCTGCCATCTTCG
1 ATCTACTCCACTACT-GCCT-AGGGAGATAAGATCTGTAATCTTCA
928862 ATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCA
928906 AT
1 AT
928908 TTGTTCAACT
Statistics
Matches: 94, Mismatches: 32, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 18 0.19
44 50 0.53
45 19 0.20
46 2 0.02
47 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCA
Found at i:929049 original size:100 final size:100
Alignment explanation
Indices: 928929--929389 Score: 737
Period size: 100 Copynumber: 4.6 Consensus size: 100
928919 CAATGTCGGA
*
928929 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA-TCGCACCG-TCAGGGAAGTAAGATCCG
1 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACT-GCACCGCT-AAGGAAGTAAGATCCG
*
928992 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGG
64 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
* * * * * *
929029 AAAACTAGATCCGCCGTCGTAGTTTCAATCTATTCCATTGCACTGCTAAGGAAGTAAGATCCGCC
1 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAGATCCGCC
929094 GTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
66 GTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
* * * * * *
929129 GAAACTAGATCTGCTGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCACT
1 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAGATCCGCC
929194 GTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
66 GTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
929229 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAGATCCGCC
1 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAGATCCGCC
* *
929294 ATTGTGGCTTCAATCTTTTTAATTGTAATATCAGG
66 GTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
*
929329 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATC
1 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAGATC
929390 TATGGTTCCG
Statistics
Matches: 335, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
100 333 0.99
101 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (100 bp):
GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAGATCCGCC
GTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
Found at i:929389 original size:50 final size:50
Alignment explanation
Indices: 928935--929389 Score: 312
Period size: 50 Copynumber: 9.1 Consensus size: 50
928925 CGGAGAAACC
* * *
928935 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATCGCACCG-TCAGGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCT-AAGGAAGTA
* * * ** * * *
928985 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATG-TCAGGAA-AA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCTAAGGAAGTA
* *
929033 CTAGATCCGCCGTCGTAGTTTCAATCTATTCCATTGCACTGCTAAGGAAGTA
1 --AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCTAAGGAAGTA
* * * ** * * * *
929085 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACT-
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCT-AAGG-AAGTA
* * *
929135 AGATCTGCTGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCTAAGGAAGTA
* * * * * ** * * * ***
929185 AGATCCACTGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCT-AAGGAAGTA
* *
929235 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCTAAGGAAGTA
* * * * ** * * * * ***
929285 AGATCCGCCATTGTGGCTTCAATCTTTTTAATTGTAAT-ATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCT-AAGGAAGTA
*
929335 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCTAAGGAAGTA
929385 AGATC
1 AGATC
929390 TATGGTTCCG
Statistics
Matches: 293, Mismatches: 100, Indels: 24
0.70 0.24 0.06
Matches are distributed among these distances:
48 1 0.00
49 10 0.03
50 269 0.92
51 12 0.04
52 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
AGATCCGCCGTCGTAGCTTCAATCTGTTCCATTGCACTGCTAAGGAAGTA
Found at i:930683 original size:6 final size:7
Alignment explanation
Indices: 930651--930682 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
930641 TCCATTTTAC
930651 TTTTTCT
1 TTTTTCT
930658 TTTTTCT
1 TTTTTCT
930665 TTTTTCT
1 TTTTTCT
930672 TTTTTCT
1 TTTTTCT
930679 TTTT
1 TTTT
930683 CGGACTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:936342 original size:3 final size:3
Alignment explanation
Indices: 936327--936387 Score: 86
Period size: 3 Copynumber: 19.7 Consensus size: 3
936317 TGTACATGAA
*
936327 AAT AAT GAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGAC AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
936374 AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AA
936388 CAAGTAATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:936972 original size:32 final size:32
Alignment explanation
Indices: 936936--936998 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
936926 CGATTTCGCC
936936 GGAGAAGACACCGGCCTGACTACTCCAGCGAT
1 GGAGAAGACACCGGCCTGACTACTCCAGCGAT
*
936968 GGAGAAGACACCGGCCTGACTACTCCGGCGA
1 GGAGAAGACACCGGCCTGACTACTCCAGCGA
936999 CCAGGTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.32, G:0.30, T:0.11
Consensus pattern (32 bp):
GGAGAAGACACCGGCCTGACTACTCCAGCGAT
Found at i:943088 original size:39 final size:40
Alignment explanation
Indices: 942987--943092 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 40
942977 TTAGAGGTGT
*
942987 AATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTG
1 AATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
* * ***
943027 AATGTAAGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTG
1 AA--T--GGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
943070 AATGGAATAGAGGTGTAATAGCA
1 AATGGAATAGAGGTGTAATAGCA
943093 TAATGGAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
39 17 0.32
40 2 0.04
41 1 0.02
42 1 0.02
43 16 0.30
44 16 0.30
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (40 bp):
AATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
Found at i:943891 original size:12 final size:12
Alignment explanation
Indices: 943874--943907 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
943864 CTGACCAGTT
943874 TCCCCCACCACC
1 TCCCCCACCACC
*
943886 TCCCCCGCCACC
1 TCCCCCACCACC
*
943898 TCCACCACCA
1 TCCCCCACCA
943908 TCATCATCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.71, G:0.03, T:0.09
Consensus pattern (12 bp):
TCCCCCACCACC
Done.