Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 66 of 66
Found at i:26295160 original size:30 final size:30
Alignment explanation
Indices: 26295126--26295193 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
26295116 TTTAAGGCTA
* *
26295126 TTAAAGTTTTTTTAA-GATTTTCAAAAGATT
1 TTAAAGTATTTTAAAGGATTTT-AAAAGATT
* **
26295156 TTAAAGGATTTTAAAGGATTTTAAGGGATT
1 TTAAAGTATTTTAAAGGATTTTAAAAGATT
26295186 TTAAAGTA
1 TTAAAGTA
26295194 AACTTAAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (30 bp):
TTAAAGTATTTTAAAGGATTTTAAAAGATT
Found at i:26295165 original size:10 final size:10
Alignment explanation
Indices: 26295141--26295191 Score: 75
Period size: 10 Copynumber: 5.0 Consensus size: 10
26295131 GTTTTTTTAA
*
26295141 GATTTTCAAAA
1 GATTTT-AAAG
26295152 GATTTTAAAG
1 GATTTTAAAG
26295162 GATTTTAAAG
1 GATTTTAAAG
*
26295172 GATTTTAAGG
1 GATTTTAAAG
26295182 GATTTTAAAG
1 GATTTTAAAG
26295192 TAAACTTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
10 31 0.84
11 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (10 bp):
GATTTTAAAG
Found at i:26295217 original size:30 final size:30
Alignment explanation
Indices: 26295169--26295249 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
26295159 AAGGATTTTA
*
26295169 AAGGAT-TTTAAGGGATTTTAAAGTAAACTT
1 AAGGATATTTAA-GAATTTTAAAGTAAACTT
* *
26295199 AAGGATATTTAAGAATTTT-TAGTAGACTT
1 AAGGATATTTAAGAATTTTAAAGTAAACTT
* *
26295228 ATGGATATTTAAAGATTTTTAA
1 AAGGATATTT-AAGAATTTTAA
26295250 CGATTTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 17 0.40
30 20 0.48
31 5 0.12
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.41
Consensus pattern (30 bp):
AAGGATATTTAAGAATTTTAAAGTAAACTT
Found at i:26295233 original size:29 final size:29
Alignment explanation
Indices: 26295190--26295248 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
26295180 GGGATTTTAA
26295190 AGTAAACTTAAGGATATTT-AAGAATTTTT
1 AGTAAACTTAAGGATATTTAAAG-ATTTTT
* *
26295219 AGTAGACTTATGGATATTTAAAGATTTTT
1 AGTAAACTTAAGGATATTTAAAGATTTTT
26295248 A
1 A
26295249 ACGATTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (29 bp):
AGTAAACTTAAGGATATTTAAAGATTTTT
Found at i:26295254 original size:10 final size:10
Alignment explanation
Indices: 26295230--26295330 Score: 55
Period size: 10 Copynumber: 10.3 Consensus size: 10
26295220 GTAGACTTAT
*
26295230 GGATATTTAA
1 GGATTTTTAA
*
26295240 AGATTTTTAA
1 GGATTTTTAA
* *
26295250 CGATTTTCAA
1 GGATTTTTAA
*
26295260 GGATTATTAA
1 GGATTTTTAA
26295270 GGA--TTTAA
1 GGATTTTTAA
*
26295278 GG-TTTTATAT
1 GGATTTT-TAA
* *
26295288 TGTTTTTTAA
1 GGATTTTTAA
*
26295298 GGATTTTTTA
1 GGATTTTTAA
* *
26295308 GGGTTTATAA
1 GGATTTTTAA
**
26295318 GTTTTTTTAA
1 GGATTTTTAA
26295328 GGA
1 GGA
26295331 ATCTGAGAGA
Statistics
Matches: 65, Mismatches: 22, Indels: 8
0.68 0.23 0.08
Matches are distributed among these distances:
8 6 0.09
9 2 0.03
10 53 0.82
11 4 0.06
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.50
Consensus pattern (10 bp):
GGATTTTTAA
Found at i:26295375 original size:21 final size:21
Alignment explanation
Indices: 26295337--26295376 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
26295327 AGGAATCTGA
* *
26295337 GAGATTGTTAATGGTTTTTAC
1 GAGATTGTTAAAGATTTTTAC
*
26295358 GAGATTTTTAAAGATTTTT
1 GAGATTGTTAAAGATTTTT
26295377 TAATTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.50
Consensus pattern (21 bp):
GAGATTGTTAAAGATTTTTAC
Found at i:26295447 original size:23 final size:22
Alignment explanation
Indices: 26295416--26295483 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
26295406 TTTAAGGATA
*
26295416 TTTAAAGATTTCTATAGATTTTT
1 TTTAAAGATTT-TAAAGATTTTT
* *
26295439 TTTATAGATTTTAAAGGTTTTT
1 TTTAAAGATTTTAAAGATTTTT
*
26295461 TTT-AAGTATTTTTAAAGAGTTTT
1 TTTAAAG-A-TTTTAAAGATTTTT
26295484 AAGGAGACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 2 0.05
22 13 0.35
23 22 0.59
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTAAAGATTTTAAAGATTTTT
Found at i:26295462 original size:22 final size:21
Alignment explanation
Indices: 26295391--26295483 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 21
26295381 TTAAAAAATT
*
26295391 TTTTTTTTAAGGATTTTTAAGG
1 TTTTTTTTAA-GATTTTAAAGG
* * * * *
26295413 -ATATTTAAAGATTTCTATAGA
1 TTTTTTTTAAGATTT-TAAAGG
26295434 TTTTTTTTATAGATTTTAAAGG
1 TTTTTTTTA-AGATTTTAAAGG
26295456 TTTTTTTTAAGTATTTTTAAAGAG
1 TTTTTTTTAAG-A-TTTTAAAG-G
26295480 TTTT
1 TTTT
26295484 AAGGAGACTT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.09
21 11 0.20
22 19 0.35
23 14 0.26
24 5 0.09
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (21 bp):
TTTTTTTTAAGATTTTAAAGG
Found at i:26295538 original size:7 final size:7
Alignment explanation
Indices: 26295528--26295588 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
26295518 CATTTTATGA
26295528 TTTAGGG
1 TTTAGGG
26295535 TTTAGGG
1 TTTAGGG
*
26295542 GTTA-GG
1 TTTAGGG
**
26295548 TTTATAG
1 TTTAGGG
26295555 TTTAGGG
1 TTTAGGG
26295562 TTTAGGG
1 TTTAGGG
*
26295569 TTAAGGG
1 TTTAGGG
*
26295576 TTTGGGG
1 TTTAGGG
26295583 TTTAGG
1 TTTAGG
26295589 TTCGGGGGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 5 0.11
7 39 0.89
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:26295632 original size:21 final size:22
Alignment explanation
Indices: 26295593--26295641 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
26295583 TTTAGGTTCG
26295593 GGGGTTCGGGGATCGAGGGTTT
1 GGGGTTCGGGGATCGAGGGTTT
* *
26295615 GGGGTTGGGGGTTC-AGGGTTT
1 GGGGTTCGGGGATCGAGGGTTT
*
26295636 TGGGTT
1 GGGGTT
26295642 TCGAGTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.06, C:0.06, G:0.55, T:0.33
Consensus pattern (22 bp):
GGGGTTCGGGGATCGAGGGTTT
Found at i:26299251 original size:7 final size:6
Alignment explanation
Indices: 26299220--26299306 Score: 66
Period size: 7 Copynumber: 12.8 Consensus size: 6
26299210 TCGGGGTTGG
*
26299220 GGGTTC GGGTCTA GGGTCTA GGGGTTAA GGGTTA GGGTTTA GGCGTTA
1 GGGTTA GGGT-TA GGGT-TA -GGGTT-A GGGTTA GGG-TTA GG-GTTA
*
26299268 GGGGTCA GGGTTGA GGGATTA GGGTTA GGGGTTA GGGTT
1 -GGGTTA GGGTT-A GGG-TTA GGGTTA -GGGTTA GGGTT
26299307 TGAGGTTTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
6 20 0.29
7 39 0.57
8 10 0.14
ACGTcount: A:0.15, C:0.06, G:0.49, T:0.30
Consensus pattern (6 bp):
GGGTTA
Found at i:26299267 original size:14 final size:13
Alignment explanation
Indices: 26299226--26299306 Score: 90
Period size: 14 Copynumber: 5.8 Consensus size: 13
26299216 TTGGGGGTTC
26299226 GGGTCTAGGGTCTAG
1 GGGT-TAGGGT-TAG
26299241 GGGTTAAGGGTTAG
1 GGGTT-AGGGTTAG
*
26299255 GGTTTAGGCGTTAG
1 GGGTTAGG-GTTAG
*
26299269 GGGTCAGGGTTGAG
1 GGGTTAGGGTT-AG
*
26299283 GGATTAGGGTTAG
1 GGGTTAGGGTTAG
26299296 GGGTTAGGGTT
1 GGGTTAGGGTT
26299307 TGAGGTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
13 18 0.32
14 30 0.53
15 9 0.16
ACGTcount: A:0.16, C:0.05, G:0.49, T:0.30
Consensus pattern (13 bp):
GGGTTAGGGTTAG
Found at i:26302820 original size:7 final size:7
Alignment explanation
Indices: 26302810--26303053 Score: 129
Period size: 7 Copynumber: 34.4 Consensus size: 7
26302800 TAAAGGGTCG
26302810 GGGTTTA
1 GGGTTTA
*
26302817 GGGTTTG
1 GGGTTTA
*
26302824 GGGTTAA
1 GGGTTTA
*
26302831 GGGTTTG
1 GGGTTTA
*
26302838 GGGTTTC
1 GGGTTTA
26302845 GGGTTTTA
1 GGG-TTTA
* *
26302853 GGATTTC
1 GGGTTTA
*
26302860 GGGTTTT
1 GGGTTTA
* *
26302867 GAGTTTG
1 GGGTTTA
**
26302874 GGGTCAGA
1 GGGT-TTA
**
26302882 GGGTCAA
1 GGGTTTA
*
26302889 GGGGTCT-
1 -GGGTTTA
*
26302896 GGG-TTC
1 GGGTTTA
*
26302902 GGGTTTG
1 GGGTTTA
26302909 GGGTTT-
1 GGGTTTA
26302915 GAGGTTTA
1 G-GGTTTA
*
26302923 AGGTTTA
1 GGGTTTA
26302930 TGGGTTTA
1 -GGGTTTA
26302938 GGGTTT-
1 GGGTTTA
26302944 GGGTTTA
1 GGGTTTA
* *
26302951 GGATTGA
1 GGGTTTA
26302958 GGGTTTAA
1 GGGTTT-A
*
26302966 GGTTTTA
1 GGGTTTA
*
26302973 GGGTTCA
1 GGGTTTA
*
26302980 AGGTTTA
1 GGGTTTA
26302987 CTGGGTTTA
1 --GGGTTTA
26302996 GGGTTTA
1 GGGTTTA
**
26303003 GGGTTCG
1 GGGTTTA
*
26303010 GGGTTTG
1 GGGTTTA
26303017 GGGTTT-
1 GGGTTTA
*
26303023 GGGTTGA
1 GGGTTTA
26303030 GGGTTTA
1 GGGTTTA
*
26303037 GGGTTGA
1 GGGTTTA
*
26303044 GGGTTGA
1 GGGTTTA
26303051 GGG
1 GGG
26303054 GTGAGGGGTG
Statistics
Matches: 184, Mismatches: 40, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
5 1 0.01
6 18 0.10
7 133 0.72
8 26 0.14
9 6 0.03
ACGTcount: A:0.12, C:0.04, G:0.45, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:26302928 original size:21 final size:21
Alignment explanation
Indices: 26302903--26302970 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
26302893 TCTGGGTTCG
26302903 GGTTTGGGGTTTGA-GGTTTAA
1 GGTTT-GGGTTTGAGGGTTTAA
*
26302924 GGTTTATGGGTTT-AGGGTTT-G
1 GG-TT-TGGGTTTGAGGGTTTAA
* *
26302945 GGTTTAGGATTGAGGGTTTAA
1 GGTTTGGGTTTGAGGGTTTAA
26302966 GGTTT
1 GGTTT
26302971 TAGGGTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 5 0.13
20 9 0.24
21 10 0.26
22 13 0.34
23 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (21 bp):
GGTTTGGGTTTGAGGGTTTAA
Found at i:26302937 original size:15 final size:15
Alignment explanation
Indices: 26302917--26303007 Score: 77
Period size: 15 Copynumber: 6.3 Consensus size: 15
26302907 TGGGGTTTGA
26302917 GGTTTAAGGTTTATG
1 GGTTTAAGGTTTATG
*
26302932 GGTTT-AGGGTT-TG
1 GGTTTAAGGTTTATG
*
26302945 GGTTT-AGGATTGA-G
1 GGTTTAAGG-TTTATG
26302959 GGTTTAAGGTTT-TAG
1 GGTTTAAGGTTTAT-G
*
26302974 GGTTCAAGGTTTACTG
1 GGTTTAAGGTTTA-TG
*
26302990 GGTTTAGGGTTTA-G
1 GGTTTAAGGTTTATG
26303004 GGTT
1 GGTT
26303008 CGGGGTTTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
13 10 0.16
14 19 0.31
15 20 0.32
16 12 0.19
17 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.38, T:0.43
Consensus pattern (15 bp):
GGTTTAAGGTTTATG
Found at i:26302948 original size:35 final size:36
Alignment explanation
Indices: 26302902--26303048 Score: 97
Period size: 34 Copynumber: 4.1 Consensus size: 36
26302892 GTCTGGGTTC
* *
26302902 GGGTTTGGGGTTTGAGG-TTTAAGGTTTATGGGTTTA
1 GGGTTTGGGGTTT-AGGATTGAAGGTTTAAGGGTTTA
* *
26302938 GGGTTT-GGGTTTAGGATTGAGGGTTTAAGGTTTTA
1 GGGTTTGGGGTTTAGGATTGAAGGTTTAAGGGTTTA
*** * * * **
26302973 GGGTTCAAGGTTTACTGGGTTTAGGGTTT-AGGGTTCG
1 GGGTTTGGGGTTTA--GGATTGAAGGTTTAAGGGTTTA
* * *
26303010 GGGTTTGGGGTTT-GGGTTGAGGGTTT-AGGGTTGA
1 GGGTTTGGGGTTTAGGATTGAAGGTTTAAGGGTTTA
26303044 GGGTT
1 GGGTT
26303049 GAGGGGTGAG
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
34 26 0.29
35 26 0.29
36 12 0.13
37 15 0.17
38 11 0.12
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.41
Consensus pattern (36 bp):
GGGTTTGGGGTTTAGGATTGAAGGTTTAAGGGTTTA
Found at i:26303049 original size:21 final size:21
Alignment explanation
Indices: 26302902--26303077 Score: 99
Period size: 21 Copynumber: 8.2 Consensus size: 21
26302892 GTCTGGGTTC
* *
26302902 GGGTTTGGGGTTTGA-GGTTTA
1 GGGTTTAGGG-TTGAGGGTTGA
* * *
26302923 AGGTTTATGGGTTTAGGGTT-T
1 GGGTTTA-GGGTTGAGGGTTGA
* *
26302944 GGGTTTAGGATTGAGGGTTTAA
1 GGGTTTAGGGTTGAGGG-TTGA
* * * *
26302966 GGTTTTAGGGTTCAAGGTTTA
1 GGGTTTAGGGTTGAGGGTTGA
*
26302987 CTGGGTTTAGGGTTTAGGGTTCG-
1 --GGGTTTAGGGTTGAGGGTT-GA
* *
26303010 GGGTTTGGGGTT-TGGGTTGA
1 GGGTTTAGGGTTGAGGGTTGA
26303030 GGGTTTAGGGTTGAGGGTTGA
1 GGGTTTAGGGTTGAGGGTTGA
* * * *
26303051 GGGGTGAGGGGTGAGGGGTTCA
1 GGGTTTAGGGTTGA-GGGTTGA
26303073 GGGTT
1 GGGTT
26303078 CGGGGGTCGA
Statistics
Matches: 119, Mismatches: 26, Indels: 19
0.73 0.16 0.12
Matches are distributed among these distances:
19 1 0.01
20 24 0.20
21 48 0.40
22 30 0.25
23 16 0.13
ACGTcount: A:0.13, C:0.02, G:0.47, T:0.38
Consensus pattern (21 bp):
GGGTTTAGGGTTGAGGGTTGA
Found at i:26303058 original size:7 final size:7
Alignment explanation
Indices: 26303036--26303069 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
26303026 TTGAGGGTTT
*
26303036 AGGGTTG
1 AGGGGTG
*
26303043 AGGGTTG
1 AGGGGTG
26303050 AGGGGTG
1 AGGGGTG
26303057 AGGGGTG
1 AGGGGTG
26303064 AGGGGT
1 AGGGGT
26303070 TCAGGGTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.65, T:0.21
Consensus pattern (7 bp):
AGGGGTG
Found at i:26303058 original size:14 final size:14
Alignment explanation
Indices: 26303027--26303103 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 14
26303017 GGGTTTGGGT
* *
26303027 TGAGGGTTTAGGGT
1 TGAGGGTTGAGGGG
26303041 TGAGGGTTGAGGGG
1 TGAGGGTTGAGGGG
*
26303055 TGAGGGGTGAGGGG
1 TGAGGGTTGAGGGG
*
26303069 TTCAGGGTTCG-GGGG
1 -TGAGGGTT-GAGGGG
26303084 TCGAGGGTT-AGGGG
1 T-GAGGGTTGAGGGG
26303098 TCGAGG
1 T-GAGG
26303104 TTTAGGCTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
14 36 0.68
15 16 0.30
16 1 0.02
ACGTcount: A:0.13, C:0.05, G:0.58, T:0.23
Consensus pattern (14 bp):
TGAGGGTTGAGGGG
Found at i:26303069 original size:29 final size:29
Alignment explanation
Indices: 26303037--26303103 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
26303027 TGAGGGTTTA
26303037 GGGTTGAGGGTT-GAGGGGT-GAGGGGTGAG
1 GGGTTGAGGGTTCG-GGGGTCGA-GGGTGAG
* *
26303066 GGGTTCAGGGTTCGGGGGTCGAGGGTTAG
1 GGGTTGAGGGTTCGGGGGTCGAGGGTGAG
*
26303095 GGGTCGAGG
1 GGGTTGAGG
26303104 TTTAGGCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.12, C:0.06, G:0.61, T:0.21
Consensus pattern (29 bp):
GGGTTGAGGGTTCGGGGGTCGAGGGTGAG
Found at i:26303108 original size:14 final size:14
Alignment explanation
Indices: 26303023--26303109 Score: 63
Period size: 14 Copynumber: 6.1 Consensus size: 14
26303013 TTTGGGGTTT
*
26303023 GGGTTGAGGGTTTA-
1 GGGTCGAGGG-TTAG
*
26303037 GGGTTGAGGGTTGAG
1 GGGTCGAGGGTT-AG
*
26303052 GGGT-GAGGGGTGAG
1 GGGTCGA-GGGTTAG
*
26303066 GGGTTC-AGGGTTCGG
1 GGG-TCGAGGGTT-AG
26303081 GGGTCGAGGGTTAG
1 GGGTCGAGGGTTAG
*
26303095 GGGTCGAGGTTTAG
1 GGGTCGAGGGTTAG
26303109 G
1 G
26303110 CTTCAGGGGT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
13 2 0.03
14 39 0.64
15 20 0.33
ACGTcount: A:0.13, C:0.05, G:0.57, T:0.25
Consensus pattern (14 bp):
GGGTCGAGGGTTAG
Done.