Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2409
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: 154369
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:110414 original size:33 final size:30
Alignment explanation
Indices: 110353--110416 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 30
110343 TATGAAATTA
* * *
110353 AAATTTTTTTATTATTAATATATCAAATAT
1 AAATATTTTAATTATTAATATATAAAATAT
110383 AAATATTTTAATTATTAATAATTATAAAAATAT
1 AAATATTTTAATTATTAAT-A-TAT-AAAATAT
110416 A
1 A
110417 TAAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 17 0.61
31 1 0.04
32 3 0.11
33 7 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATATTTTAATTATTAATATATAAAATAT
Found at i:111337 original size:6 final size:5
Alignment explanation
Indices: 111315--111347 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
111305 ATCTCTTAGA
*
111315 ATTTT ATTTT ATTTT ATTTT -TATT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
111348 GATATGCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:120859 original size:14 final size:14
Alignment explanation
Indices: 120842--120876 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
120832 AAAATCTTCT
120842 ATGAAAAACAAAAA
1 ATGAAAAACAAAAA
*
120856 ATGAAAAAGAAAAA
1 ATGAAAAACAAAAA
120870 A-GAAAAA
1 ATGAAAAA
120877 AGCACAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (14 bp):
ATGAAAAACAAAAA
Found at i:125151 original size:20 final size:20
Alignment explanation
Indices: 125104--125178 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
125094 AAAAAGACAT
*
125104 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
125123 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
125144 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
125164 AATGTATCGATACAT
1 AATGTATCGATACAT
125179 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:125172 original size:40 final size:39
Alignment explanation
Indices: 125101--125178 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
125091 GGTAAAAAGA
* *
125101 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
125140 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
125179 CAGGGTATGA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:125755 original size:32 final size:30
Alignment explanation
Indices: 125706--126500 Score: 786
Period size: 32 Copynumber: 26.2 Consensus size: 30
125696 AATATGGTGA
*
125706 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACTGACTTG--TGGGC
* *
125738 TTTTAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
* *
125770 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
* * *
125802 TTTGGAATGGGTTGCCACCGACTTTTGTGGGT
1 TTTGAAATGGGTTGCCACTGAC--TTGTGGGC
*
125834 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
*
125866 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
*
125898 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
*
125930 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
* *
125962 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
* *
125994 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
* * *
126026 TTTGGAATGGGTTGCCGCCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
* *
126058 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGAC-T-TGTGGGC
*
126090 TTTGAAATGGGTTGCCACCGACTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
* * * *
126120 TCTGAAAAGAG-TGCCACTGGCTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
126149 TTTGAAA-GGAG-TGCCACTGACTTGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGGGC
* * *
126178 TTTGAAA--GGATGCCAATGAGTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
126206 TTTGAAA-GGG-TGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
* * *
126234 TTTGAAAAGAG-TGCCACTGATTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
126263 TTTGAAA-GGAG-TGCCACTGACTTGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGGGC
126292 TTTGAAA-GGAG-TGCCACTGACTTGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGGGC
* * * *
126321 TTTAAAAAGAG-TGCCACTGATTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
* * * * *
126350 TTTGAAAAGAG-TACCACTAACTTGTAGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
126379 TTTGAAA-GGAG-TGCCACTGACTTGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGGGC
126408 TTTGAAA-GGG-TGCCACTGACTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
* * *
126436 TTTGAAAAGAG-TGCCACTGATTTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGGGC
126465 TTTGAAA-GGAG-TGCCACTGACTTGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGGGC
126494 TTTGAAA
1 TTTGAAA
126501 GGGATGAACA
Statistics
Matches: 703, Mismatches: 47, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.00
28 77 0.11
29 253 0.36
30 16 0.02
31 3 0.00
32 348 0.50
33 3 0.00
34 2 0.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (30 bp):
TTTGAAATGGGTTGCCACTGACTTGTGGGC
Found at i:127734 original size:10 final size:9
Alignment explanation
Indices: 127719--127787 Score: 65
Period size: 8 Copynumber: 8.0 Consensus size: 9
127709 ATCTAGACCC
127719 TTCTATTTT
1 TTCTATTTT
127728 TTGCTATTTT
1 TT-CTATTTT
127738 TTCT-TTTT
1 TTCTATTTT
* *
127746 TTTTGTTTT
1 TTCTATTTT
127755 TT-TATTTT
1 TTCTATTTT
* *
127763 TTTTGTTTT
1 TTCTATTTT
127772 TT-TATTTT
1 TTCTATTTT
127780 TT-TATTTT
1 TTCTATTTT
127788 CTTGTTTTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
8 27 0.51
9 17 0.32
10 9 0.17
ACGTcount: A:0.07, C:0.04, G:0.04, T:0.84
Consensus pattern (9 bp):
TTCTATTTT
Found at i:127746 original size:9 final size:9
Alignment explanation
Indices: 127719--127774 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
127709 ATCTAGACCC
127719 TTCTATTTTT
1 TTCT-TTTTT
* *
127729 TGCTATTTT
1 TTCTTTTTT
127738 TTCTTTTTT
1 TTCTTTTTT
127747 TT-TGTTTTT
1 TTCT-TTTTT
*
127756 TTATTTTTT
1 TTCTTTTTT
*
127765 TTGTTTTTT
1 TTCTTTTTT
127774 T
1 T
127775 ATTTTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 34 0.87
10 4 0.10
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.84
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:127755 original size:18 final size:17
Alignment explanation
Indices: 127724--127782 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 17
127714 GACCCTTCTA
127724 TTTTTTGCTATTTTTTCTTT
1 TTTTTTG-T-TTTTTT-TTT
*
127744 TTTTTTGTTTTTTTATT
1 TTTTTTGTTTTTTTTTT
127761 TTTTTTGTTTTTTTATTT
1 TTTTTTGTTTTTTT-TTT
127779 TTTT
1 TTTT
127783 ATTTTCTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 16 0.44
18 12 0.33
19 1 0.03
20 7 0.19
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.86
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTTT
Found at i:127780 original size:25 final size:25
Alignment explanation
Indices: 127722--127796 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
127712 TAGACCCTTC
127722 TATTTTTTGCTATTTTTTCTT-TTTTTT
1 TATTTTTT--TATTTTTT-TTGTTTTTT
*
127749 TGTTTTTTTATTTTTTTTGTTTTTT
1 TATTTTTTTATTTTTTTTGTTTTTT
*
127774 TATTTTTTTA-TTTTCTTGTTTTT
1 TATTTTTTTATTTTTTTTGTTTTT
127797 GGGTGTAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
24 14 0.32
25 23 0.52
27 7 0.16
ACGTcount: A:0.07, C:0.04, G:0.05, T:0.84
Consensus pattern (25 bp):
TATTTTTTTATTTTTTTTGTTTTTT
Found at i:127795 original size:8 final size:8
Alignment explanation
Indices: 127743--127796 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
127733 ATTTTTTCTT
127743 TTTTTTTG
1 TTTTTTTG
*
127751 TTTTTTTAT
1 TTTTTTT-G
127760 TTTTTTTG
1 TTTTTTTG
*
127768 TTTTTTTA
1 TTTTTTTG
*
127776 TTTTTTTA
1 TTTTTTTG
*
127784 TTTTCTTG
1 TTTTTTTG
127792 TTTTT
1 TTTTT
127797 GGGTGTAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
8 32 0.82
9 7 0.18
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:127796 original size:1 final size:1
Alignment explanation
Indices: 127734--127787 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
127724 TTTTTTGCTA
* * * * * *
127734 TTTTTTCTTTTTTTTTGTTTTTTTATTTTTTTTGTTTTTTTATTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
127788 CTTGTTTTTG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.06, C:0.02, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:141854 original size:20 final size:20
Alignment explanation
Indices: 141807--141881 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
141797 TAAAAGACAT
*
141807 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
141826 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
141847 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
141867 AATGTATCGATACAT
1 AATGTATCGATACAT
141882 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:141875 original size:40 final size:39
Alignment explanation
Indices: 141804--141881 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
141794 GGGTAAAAGA
* *
141804 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
141843 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
141882 CAGGGTATGA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:149635 original size:19 final size:19
Alignment explanation
Indices: 149611--149673 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
149601 ACACGTGGAG
*
149611 AGTATCCATATATGTGAAC
1 AGTATCCATATACGTGAAC
** *
149630 AGTATCTGTGTACGTGAAC
1 AGTATCCATATACGTGAAC
149649 AGTA-CCTATATACGTGAAC
1 AGTATCC-ATATACGTGAAC
149668 AGTATC
1 AGTATC
149674 TTGACAACCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 1 0.03
19 33 0.94
20 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (19 bp):
AGTATCCATATACGTGAAC
Found at i:152562 original size:39 final size:39
Alignment explanation
Indices: 152516--152595 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
152506 AATCATGTGT
152516 TTGAACTCACTTAACCACAAATCCAGACCTGAAAATTAA
1 TTGAACTCACTTAACCACAAATCCAGACCTGAAAATTAA
152555 TTGAACTCACTTAACCACAAATCCAGACCTGAAAATTAA
1 TTGAACTCACTTAACCACAAATCCAGACCTGAAAATTAA
152594 TT
1 TT
152596 TTACCCCAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (39 bp):
TTGAACTCACTTAACCACAAATCCAGACCTGAAAATTAA
Found at i:153753 original size:19 final size:19
Alignment explanation
Indices: 153725--153797 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
153715 AAAAAGACAT
*
153725 AATGTATCGATACATTGAG
1 AATGTATCGATACATTGAA
* *
153744 AATATATCGATACATTCATA
1 AATGTATCGATACATTGA-A
* *
153764 CATGTATCGATATATTGAA
1 AATGTATCGATACATTGAA
153783 AATGTATCGATACAT
1 AATGTATCGATACAT
153798 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 30 0.68
20 14 0.32
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:153781 original size:39 final size:38
Alignment explanation
Indices: 153722--153797 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
153712 GGTAAAAAGA
*
153722 CATAATGTATCGATACATTGAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAATATATCGATACATT
* *
153760 CATACATGTATCGATATATTGAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAATATATCGATACAT
153798 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (38 bp):
CATAATGTATCGATACATTGAAAATATATCGATACATT
Done.