Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6072.1
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: 14227
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:67 original size:14 final size:14
Alignment explanation
Indices: 26--68 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16 TAGCTAAGTA
*
26 AATTAATTGATTTTT
1 AATTAATTGA-ATTT
* *
41 AATTAAATAAATTT
1 AATTAATTGAATTT
55 AATTAATTGAATTT
1 AATTAATTGAATTT
69 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AATTAATTGAATTT
Found at i:844 original size:43 final size:43
Alignment explanation
Indices: 796--1037 Score: 312
Period size: 43 Copynumber: 5.7 Consensus size: 43
786 AAAACAGGCT
*** *
796 TTTAGCGGCGCTTTTTTTACAAACGCCACTATAGATCAAGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
* * *
839 TTTAGCGGCGC-TTTCCCAAAAACGACGCTATAGATCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
* *
881 TTTAGCGGCGC-TTTCCCAAAAACACCGCTATAGATC--GACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
*
921 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAAACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
* * * *
964 TTTAGCTGCGCTTTTCCTACAAACGCCACTATAGATCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
**
1007 TTTAGCGGCGCTTTTTTCACAAACGCCGCTA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTA
1038 AAAGTGCCAT
Statistics
Matches: 174, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 15 0.09
41 23 0.13
42 58 0.33
43 78 0.45
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
Found at i:874 original size:42 final size:42
Alignment explanation
Indices: 824--1020 Score: 256
Period size: 42 Copynumber: 4.7 Consensus size: 42
814 ACAAACGCCA
824 CTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAACGACG
1 CTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAACGACG
*
866 CTATAGATCAGGACCTTTAGCGGCGCTTTCCCAAAAAC-ACCG
1 CTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAACGA-CG
* *
908 CTATAGATC--GACCTTTAGCGGCGCTTTTCCCACAAACGCCG
1 CTATAGATCAAGACCTTTAGCGGCGC-TTTCCCAAAAACGACG
* * * * * *
949 CTATAGATCAAAACCTTTAGCTGCGCTTTTCCTACAAACGCCA
1 CTATAGATCAAGACCTTTAGCGGCGC-TTTCCCAAAAACGACG
*
992 CTATAGATCAGGACCTTTAGCGGCGCTTT
1 CTATAGATCAAGACCTTTAGCGGCGCTTT
1021 TTTCACAAAC
Statistics
Matches: 140, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
40 15 0.11
41 23 0.16
42 51 0.36
43 51 0.36
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (42 bp):
CTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAACGACG
Found at i:952 original size:83 final size:85
Alignment explanation
Indices: 796--1037 Score: 301
Period size: 84 Copynumber: 2.9 Consensus size: 85
786 AAAACAGGCT
*** * * *
796 TTTAGCGGCGCTTTTTTTACAAACGCCACTATAGATCAAGACCTTTAGCGGCGC-TTTCCCAAAA
1 TTTAGCGGCGCTTTTCCCAAAAACACCACTATAGATC-AGACCTTTAGCGGCGCTTTTCCCACAA
* **
860 ACGACGCTATAGATCAGGACC
65 ACGCCGCTATAGATCAAAACC
*
881 TTTAGCGGCGC-TTTCCCAAAAACACCGCTATAGATC-GACCTTTAGCGGCGCTTTTCCCACAAA
1 TTTAGCGGCGCTTTTCCCAAAAACACCACTATAGATCAGACCTTTAGCGGCGCTTTTCCCACAAA
944 CGCCGCTATAGATCAAAACC
66 CGCCGCTATAGATCAAAACC
* * * * **
964 TTTAGCTGCGCTTTTCCTACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTTTTCACAA
1 TTTAGCGGCGCTTTTCCCAAAAACACCACTATAGATCA-GACCTTTAGCGGCGCTTTTCCCACAA
1029 ACGCCGCTA
65 ACGCCGCTA
1038 AAAGTGCCAT
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
82 15 0.11
83 37 0.27
84 40 0.29
85 11 0.08
86 33 0.24
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (85 bp):
TTTAGCGGCGCTTTTCCCAAAAACACCACTATAGATCAGACCTTTAGCGGCGCTTTTCCCACAAA
CGCCGCTATAGATCAAAACC
Found at i:1157 original size:13 final size:13
Alignment explanation
Indices: 1139--1185 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1129 ATAAAAGTAA
1139 AATAAATTATAGT
1 AATAAATTATAGT
**
1152 AATAAATT-TCAAC
1 AATAAATTAT-AGT
*
1165 ATTAAATTATAGT
1 AATAAATTATAGT
1178 AATAAATT
1 AATAAATT
1186 TCAACATTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
AATAAATTATAGT
Found at i:1172 original size:26 final size:26
Alignment explanation
Indices: 1141--1193 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1131 AAAAGTAAAA
1141 TAAATTATAGTAATAAATTTCAACAT
1 TAAATTATAGTAATAAATTTCAACAT
1167 TAAATTATAGTAATAAATTTCAACAT
1 TAAATTATAGTAATAAATTTCAACAT
1193 T
1 T
1194 CACCTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAATTATAGTAATAAATTTCAACAT
Found at i:1201 original size:26 final size:26
Alignment explanation
Indices: 1141--1212 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
1131 AAAAGTAAAA
*
1141 TAAATTATAGTAATAAATTTCAACAT
1 TAAACTATAGTAATAAATTTCAACAT
*
1167 TAAATTATAGTAATAAATTTCAACAT
1 TAAACTATAGTAATAAATTTCAACAT
* * *
1193 TCACCTATAATAAATAAATT
1 TAAACTATAGT-AATAAATT
1213 AACATAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 33 0.80
27 8 0.20
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (26 bp):
TAAACTATAGTAATAAATTTCAACAT
Found at i:1630 original size:21 final size:21
Alignment explanation
Indices: 1567--1621 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1557 TCTGCCTTCT
1567 TTGAGTAACTACATGGCAATC
1 TTGAGTAACTACATGGCAATC
1588 TTGAGTAACTACATGGCAATC
1 TTGAGTAACTACATGGCAATC
1609 TTGAGTAACTACA
1 TTGAGTAACTACA
1622 GTAGCATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (21 bp):
TTGAGTAACTACATGGCAATC
Found at i:4158 original size:57 final size:57
Alignment explanation
Indices: 4045--4158 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
4035 CTCCACTCCA
* **
4045 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
4102 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
4159 TCTTCAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 48 0.94
58 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Found at i:5646 original size:110 final size:111
Alignment explanation
Indices: 5469--5735 Score: 310
Period size: 110 Copynumber: 2.4 Consensus size: 111
5459 TATATAAGAA
* *
5469 CTTATTTAGTATATAAATTAAAAAATATTAATTAATCTAAACCTTAAACCCTAACCCGACCCCGA
1 CTTATTTAATATATAAATT-AAAAATACTAATTAATCTAAACCTTAAACCCTAACCCGACCCCGA
*
5534 ATCTCTAAACCCTAAATCAC-TAA-CTA-TT-AACCCCAAACCCCTAAAC
65 ATCTCT-AACCCTAAA-C-CTTAACCAACTTGAACCCCAAACCCCTAAAC
* **
5580 CTTATTTAATATATAAATTAAAAATACTAATTAATCTAAATCC-TAAACCCTAACCTGACCTTGA
1 CTTATTTAATATATAAATTAAAAATACTAATTAATCTAAA-CCTTAAACCCTAACCCGACCCCGA
* * * * *
5644 ATCTCTAACCCTAAACCTTAACCCAACCTTGAATCTCTAACCCTTAAAT
65 ATCTCTAACCCTAAACCTTAA-CCAA-CTTGAACCCCAAACCCCTAAAC
* *
5693 ATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACC
1 CTTATTTAATATATAAATTAAAA-ATACTAATTAATCTAAACC
5736 ATAACCTGAC
Statistics
Matches: 135, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
107 1 0.01
108 4 0.03
109 9 0.07
110 46 0.34
111 20 0.15
112 2 0.01
113 37 0.27
114 16 0.12
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (111 bp):
CTTATTTAATATATAAATTAAAAATACTAATTAATCTAAACCTTAAACCCTAACCCGACCCCGAA
TCTCTAACCCTAAACCTTAACCAACTTGAACCCCAAACCCCTAAAC
Found at i:5657 original size:32 final size:32
Alignment explanation
Indices: 5621--5687 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
5611 TAATCTAAAT
**
5621 CCTAAACCCTAACCTGACCTTGAATCTCTAAC
1 CCTAAACCCTAACCCAACCTTGAATCTCTAAC
*
5653 CCTAAACCTTAACCCAACCTTGAATCTCTAAC
1 CCTAAACCCTAACCCAACCTTGAATCTCTAAC
5685 CCT
1 CCT
5688 TAAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.39, G:0.04, T:0.25
Consensus pattern (32 bp):
CCTAAACCCTAACCCAACCTTGAATCTCTAAC
Found at i:6214 original size:21 final size:21
Alignment explanation
Indices: 6188--6230 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
6178 ATATTTATTT
6188 TTATT-TTTAATAT-TATA-A
1 TTATTATTTAATATATATATA
6206 TTATTATTTAATATATATATA
1 TTATTATTTAATATATATATA
6227 TTAT
1 TTAT
6231 GTACATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 4 0.18
21 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATTTAATATATATATA
Found at i:6727 original size:16 final size:16
Alignment explanation
Indices: 6706--6736 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6696 CTTTTTACTC
6706 AATTTTAAAAATAGAA
1 AATTTTAAAAATAGAA
*
6722 AATTTTCAAAATAGA
1 AATTTTAAAAATAGA
6737 GATAATACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
AATTTTAAAAATAGAA
Found at i:8127 original size:22 final size:22
Alignment explanation
Indices: 8097--8139 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
8087 ACAGCAGAAC
* *
8097 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
8119 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
8140 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:8285 original size:42 final size:42
Alignment explanation
Indices: 8211--8478 Score: 285
Period size: 42 Copynumber: 6.4 Consensus size: 42
8201 ACGTCACTAA
* *
8211 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
*
8255 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * *
8297 CTTTAGCGACGCTT--AAAAAAACGCCCCTAAAGATCATATT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * *
8337 CTTTAGCGGCGCTTAGAAACAACCGCCGCTAAAGAACATGAT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * *
8379 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* ***
8422 CTATAGCGGCGCTTATTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGA-TCA-TGTT
8464 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
8479 TTTCACAAAC
Statistics
Matches: 189, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
40 36 0.19
41 1 0.01
42 108 0.57
43 31 0.16
44 13 0.07
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:8365 original size:82 final size:83
Alignment explanation
Indices: 8228--8454 Score: 287
Period size: 82 Copynumber: 2.7 Consensus size: 83
8218 GGCGCTTACA
* *
8228 TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCA
1 TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACA
*
8293 TGCTCTTTAGCGACGC-T
66 TGATCTTTAGCGACGCTT
* * *
8310 TAAAAAAACGCCCCTAAAGATCATATTCTTTAGCGGCGCTTAGAAACAACCGCCGCTAAAGAACA
1 TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACA
*
8375 TGATCTTTAGCGGCGCTT
66 TGATCTTTAGCGACGCTT
* * * * ***
8393 TGGAAGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTATTCAAAAACGCCGCTAAA
1 T--AAAAAAACGCCCCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAA
8455 AGTAGTGTTC
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
82 74 0.60
83 2 0.02
84 1 0.01
85 47 0.38
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (83 bp):
TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACA
TGATCTTTAGCGACGCTT
Found at i:8917 original size:12 final size:12
Alignment explanation
Indices: 8900--8939 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
8890 TTTTGAACCT
*
8900 CTGCTTCTATTG
1 CTGCTTCTATCG
*
8912 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
8924 CTGCTTCTCTCG
1 CTGCTTCTATCG
8936 CTGC
1 CTGC
8940 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:8950 original size:21 final size:21
Alignment explanation
Indices: 8924--8992 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
8914 GCTTCTCTCG
*
8924 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
8945 CTGCTTCTCTCGTTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
8966 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
8987 CTGCTT
1 CTGCTT
8993 TAGGTTGCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.01, C:0.42, G:0.20, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Done.