Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1909
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: 26701
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:288 original size:18 final size:18
Alignment explanation
Indices: 263--348 Score: 100
Period size: 18 Copynumber: 4.8 Consensus size: 18
253 AAAATAAATA
* *
263 GTGCAGTAATAGTAATTG
1 GTGCAGTAACAGTAATCG
* *
281 GTGTAGTAACAGTAATCA
1 GTGCAGTAACAGTAATCG
299 GTGCAGTAACAGTAATCG
1 GTGCAGTAACAGTAATCG
* * **
317 GTGCATTAATAGTAATAA
1 GTGCAGTAACAGTAATCG
335 GTGCAGTAACAGTA
1 GTGCAGTAACAGTA
349 TAGAAGTCCT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (18 bp):
GTGCAGTAACAGTAATCG
Found at i:302 original size:36 final size:36
Alignment explanation
Indices: 262--348 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
252 AAAAATAAAT
* * * *
262 AGTGCAGTAATAGTAATTGGTGTAGTAACAGTAATC
1 AGTGCAGTAACAGTAATCGGTGCAGTAACAGTAATA
* *
298 AGTGCAGTAACAGTAATCGGTGCATTAATAGTAATA
1 AGTGCAGTAACAGTAATCGGTGCAGTAACAGTAATA
334 AGTGCAGTAACAGTA
1 AGTGCAGTAACAGTA
349 TAGAAGTCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (36 bp):
AGTGCAGTAACAGTAATCGGTGCAGTAACAGTAATA
Found at i:7713 original size:18 final size:18
Alignment explanation
Indices: 7692--7772 Score: 74
Period size: 18 Copynumber: 4.5 Consensus size: 18
7682 AAACAGTTTT
*
7692 GTAACAGTAAT-CGATACA
1 GTAACAGTAATAAG-TACA
* *
7710 GTAACAATAATAAGTGCA
1 GTAACAGTAATAAGTACA
* *
7728 GTAACAGTAATTAGTATA
1 GTAACAGTAATAAGTACA
* *
7746 GTAACAGTAATTAGTGCA
1 GTAACAGTAATAAGTACA
*
7764 GTAATAGTA
1 GTAACAGTA
7773 TAGAAGTCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
18 51 0.98
19 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (18 bp):
GTAACAGTAATAAGTACA
Found at i:7732 original size:36 final size:36
Alignment explanation
Indices: 7670--7772 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 36
7660 CTTGGCCCAT
***
7670 TACAGTAACAATAA-ACAGTTTTGTAACAGTAATCGA-
1 TACAGTAACAATAATA-AGTGCAGTAACAGTAAT-GAG
*
7706 TACAGTAACAATAATAAGTGCAGTAACAGTAATTAG
1 TACAGTAACAATAATAAGTGCAGTAACAGTAATGAG
* * * *
7742 TATAGTAACAGTAATTAGTGCAGTAATAGTA
1 TACAGTAACAATAATAAGTGCAGTAACAGTA
7773 TAGAAGTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
35 1 0.02
36 55 0.96
37 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28
Consensus pattern (36 bp):
TACAGTAACAATAATAAGTGCAGTAACAGTAATGAG
Found at i:9089 original size:5 final size:5
Alignment explanation
Indices: 9079--9105 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9069 ATTTGAGAGT
9079 GAGAA GAGAA GAGAA GAGAA GAGAA GA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GA
9106 ATTGAGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:10610 original size:23 final size:23
Alignment explanation
Indices: 10584--10661 Score: 104
Period size: 23 Copynumber: 3.3 Consensus size: 23
10574 AGCTAAAACG
10584 GTAAGCT-CTGACGAGCTGAATTA
1 GTAAGCTCCT-ACGAGCTGAATTA
*
10607 GTAAGCTCCTACGAGCTGAATCA
1 GTAAGCTCCTACGAGCTGAATTA
* *
10630 GTAAGCTCCTATGAGCTGAAAATA
1 GTAAGCTCCTACGAGCTG-AATTA
10654 GTAAGCTC
1 GTAAGCTC
10662 TTATGAGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 36 0.73
24 13 0.27
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (23 bp):
GTAAGCTCCTACGAGCTGAATTA
Found at i:10613 original size:46 final size:46
Alignment explanation
Indices: 10524--10662 Score: 111
Period size: 46 Copynumber: 2.9 Consensus size: 46
10514 TTCTCTTCCA
* * ** * *
10524 AGCTATAAACAGTAAGCTCCTCCTGACCTGACGGACAGTAAGCTCTATTG
1 AGCTA-AAACAGTAAGCTCCTAC-GAGCTGA-AAATAGTAAGCTCTA-CG
* *
10574 AGCTAAAACGGTAAGCT-CTGACGAGCTG-AATTAGTAAGCTCCTACG
1 AGCTAAAACAGTAAGCTCCT-ACGAGCTGAAAATAGTAAGCT-CTACG
* * *
10620 AGCTGAATCAGTAAGCTCCTATGAGCTGAAAATAGTAAGCTCT
1 AGCTAAAACAGTAAGCTCCTACGAGCTGAAAATAGTAAGCTCT
10663 TATGAGTTGA
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
46 32 0.44
47 16 0.22
48 7 0.10
49 12 0.17
50 5 0.07
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (46 bp):
AGCTAAAACAGTAAGCTCCTACGAGCTGAAAATAGTAAGCTCTACG
Found at i:14663 original size:18 final size:18
Alignment explanation
Indices: 14621--14666 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
14611 GCTTTGTGGG
*
14621 CCACATAGGCGTGAGGGC
1 CCACATGGGCGTGAGGGC
14639 CCACATGGGCGTGAGGGC
1 CCACATGGGCGTGAGGGC
14657 CCACATGGGC
1 CCACATGGGC
14667 CGTGTTATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.30, G:0.39, T:0.11
Consensus pattern (18 bp):
CCACATGGGCGTGAGGGC
Found at i:14871 original size:26 final size:27
Alignment explanation
Indices: 14791--14872 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
14781 CTTAAATTGG
* * * * *
14791 TAAAATGACTATTTTGTACTTATGAGG
1 TAAAATGACTGTTTTGTCCCTATGTGA
* * **
14818 TAAAATGATTGTTTTGCCCCTAACTGA
1 TAAAATGACTGTTTTGTCCCTATGTGA
14845 TAAAATGACTGTTTT-TCCCTATGTGA
1 TAAAATGACTGTTTTGTCCCTATGTGA
14871 TA
1 TA
14873 TATGTTTATA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
26 10 0.24
27 32 0.76
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (27 bp):
TAAAATGACTGTTTTGTCCCTATGTGA
Found at i:15253 original size:17 final size:17
Alignment explanation
Indices: 15227--15271 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
15217 ATTGCACAGT
*
15227 TTACTATTACTGCACTG
1 TTACTATTACTACACTG
*
15244 TTACTGTTACTACACTGG
1 TTACTATTACTACACT-G
15262 TTTACTATTA
1 -TTACTATTA
15272 TTCCAATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 1 0.04
19 8 0.35
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (17 bp):
TTACTATTACTACACTG
Found at i:19776 original size:47 final size:47
Alignment explanation
Indices: 19713--20106 Score: 626
Period size: 47 Copynumber: 8.4 Consensus size: 47
19703 CGCTTCGGGA
* * * *
19713 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19760 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19807 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCGTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19854 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19901 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19948 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19995 CATATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20042 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20089 CTTATCACATATACACAC
1 CTTATCACATATATACAC
20107 CTTGTACACC
Statistics
Matches: 326, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 326 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19910 original size:22 final size:22
Alignment explanation
Indices: 19882--19957 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
19872 TTTCACATTC
19882 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
19904 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
19928 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
19951 ATCACAT
1 ATCACAT
19958 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:20051 original size:22 final size:22
Alignment explanation
Indices: 20023--20098 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
20013 TTTCACATTC
20023 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** *** *
20045 ATCACATATACACACTTTCACATT
1 ATCACATCGGC-CA-TTAGGCCTT
20069 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
20092 ATCACAT
1 ATCACAT
20099 ATACACACCT
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 15 0.41
23 7 0.19
24 7 0.19
25 8 0.22
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:23897 original size:40 final size:40
Alignment explanation
Indices: 23865--24176 Score: 480
Period size: 40 Copynumber: 7.8 Consensus size: 40
23855 CCAGCATGAT
* * * *
23865 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
23905 TGCTCTTCGGGACTTAGTCCGGATACGTCACTGGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
23945 TGCTCTTCGGGACTTAGCCCAGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** *
23985 TGCTCTTCTAGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
24025 TGCTCTTCGGGACTTAGCCCGGATAGATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
24065 TGCTCTTCGAGACTTAGCCCGAATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
24105 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
24145 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
24177 CTCAATTCTC
Statistics
Matches: 246, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 246 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:26444 original size:27 final size:27
Alignment explanation
Indices: 26389--26564 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
26379 ATATTGAGCC
* *
26389 CGCACACTCAGTGCT-TATAATCAACT
1 CGCACACTTAGTGCTATATAATCAAAT
*
26415 CGCACACTTAGTGCTATGTAATCAAAT
1 CGCACACTTAGTGCTATATAATCAAAT
* *
26442 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTATATAATCAAA-T
*** * *
26470 CGC-CACTTAGTGCCGCATGATCAATT
1 CGCACACTTAGTGCTATATAATCAAAT
* **
26496 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTAT-ATAATCAAAT
* * * *
26523 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATATAATCAAAT
26550 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
26565 GTACAATTTA
Statistics
Matches: 123, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
26 18 0.15
27 100 0.81
28 5 0.04
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAAAT
Found at i:26543 original size:81 final size:81
Alignment explanation
Indices: 26408--26563 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
26398 AGTGCTTATA
* *
26408 ATCAACTCGCACACTTAGTGCTATGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 ATCAACTCGCACACTTAGTGCTATATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
26473 -CACTTAGTGCCGCATG
65 ACACTTAGTGCCGCATG
* * ** *
26489 ATCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGC
1 ATCAACTCGCACACTTAGTGCTAT-ATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGC
26553 ACACTTAGTGC
65 ACACTTAGTGC
26564 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 6 0.09
81 60 0.91
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
ATCAACTCGCACACTTAGTGCTATATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATG
Done.