Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3179
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: 40343
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:2631 original size:32 final size:31
Alignment explanation
Indices: 2562--2632 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
2552 TACATGGCTT
* *
2562 ACAGCTATCAGTAGTGGTAATTTGATCGCAC
1 ACAGCCATCAGTAGTGGTAATATGATCGCAC
*
2593 AAAGCCATCAGTAGCT-GTAATATGATCGGCAC
1 ACAGCCATCAGTAG-TGGTAATATGATC-GCAC
2625 ACAGCCAT
1 ACAGCCAT
2633 GGGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (31 bp):
ACAGCCATCAGTAGTGGTAATATGATCGCAC
Found at i:3152 original size:24 final size:24
Alignment explanation
Indices: 3120--3166 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3110 TTTACCTTAC
3120 AGGGTATTTCAATAATTTTACACA
1 AGGGTATTTCAATAATTTTACACA
**
3144 AGGGTATTTCGGTAATTTTACAC
1 AGGGTATTTCAATAATTTTACAC
3167 TTCAAGGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (24 bp):
AGGGTATTTCAATAATTTTACACA
Found at i:3179 original size:27 final size:26
Alignment explanation
Indices: 3108--3246 Score: 124
Period size: 27 Copynumber: 5.3 Consensus size: 26
3098 CAAAACAATC
*
3108 ATTTTAC-CTTACAGGGTATTTCAATA
1 ATTTTACACTTA-AGGGTATTTCGATA
*
3134 ATTTTACAC--AAGGGTATTTCGGTA
1 ATTTTACACTTAAGGGTATTTCGATA
* * *
3158 ATTTTACACTTCAAGGGTATTTTGGTG
1 ATTTTACACTT-AAGGGTATTTCGATA
*
3185 ATTTTACCCTATAAGGGTATTTCGATA
1 ATTTTACACT-TAAGGGTATTTCGATA
* * *
3212 ATTATACAAATTGAGGGTA-TTCTGATA
1 ATTTTAC-ACTTAAGGGTATTTC-GATA
3239 ATTTTACA
1 ATTTTACA
3247 TACTAGGATA
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
24 21 0.23
25 1 0.01
26 11 0.12
27 58 0.62
28 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (26 bp):
ATTTTACACTTAAGGGTATTTCGATA
Found at i:3266 original size:26 final size:26
Alignment explanation
Indices: 3132--3272 Score: 99
Period size: 27 Copynumber: 5.4 Consensus size: 26
3122 GGTATTTCAA
* *
3132 TAATTTTAC--ACAAGGGTATTTCGG
1 TAATTTTACATACTAGGGTATTTTGG
* *
3156 TAATTTTACACTTCAAGGGTATTTTGG
1 TAATTTTACA-TACTAGGGTATTTTGG
* * * *
3183 TGATTTTACCCTA-TAAGGGTATTTCGA
1 TAATTTTA-CATACT-AGGGTATTTTGG
* * * * *
3210 TAATTATACAAATTGAGGGTATTCTGA
1 TAATTTTACATACT-AGGGTATTTTGG
*
3237 TAATTTTACATACTAGGATATTTTGG
1 TAATTTTACATACTAGGGTATTTTGG
3263 TAATTTTACA
1 TAATTTTACA
3273 AATCGAGGTC
Statistics
Matches: 90, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
24 9 0.10
26 21 0.23
27 59 0.66
28 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (26 bp):
TAATTTTACATACTAGGGTATTTTGG
Found at i:6314 original size:39 final size:38
Alignment explanation
Indices: 6254--6458 Score: 274
Period size: 39 Copynumber: 5.3 Consensus size: 38
6244 CGGATTGATA
6254 ACCGGGCTAAG-CCCGAAGGCATTCGTGCGAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTAT
6292 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 ACCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTAC--TAT
*
6333 ACC-GGCCAAGTCCCGAAGGCATTGTGCGAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAT
*
6370 AATCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAT
1 -ACCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAT
*
6409 AACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTAT
1 -ACCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTA-CTAT
6449 ATCC-GGCTAA
1 A-CCGGGCTAA
6459 ACTCGAAGGT
Statistics
Matches: 153, Mismatches: 5, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
37 3 0.02
38 13 0.08
39 98 0.64
40 33 0.22
41 6 0.04
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
ACCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAT
Found at i:13283 original size:14 final size:14
Alignment explanation
Indices: 13260--13295 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
13250 TGCCTCTTGG
*
13260 ATTCTCTTTTTAGC
1 ATTCTTTTTTTAGC
13274 ATTCTTTTTTTAGC
1 ATTCTTTTTTTAGC
13288 ATTCTTTT
1 ATTCTTTT
13296 GAGATAGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.17, G:0.06, T:0.64
Consensus pattern (14 bp):
ATTCTTTTTTTAGC
Found at i:14291 original size:39 final size:40
Alignment explanation
Indices: 14183--14399 Score: 306
Period size: 39 Copynumber: 5.6 Consensus size: 40
14173 TATTCGATTG
*
14183 ATAACCGGGCTAAG-CCCGAAGGC-ATTCGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATT-GTGCGAGTTACT
*
14222 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
14262 ATAACCGGGC-AAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
14301 ATAA-CGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
14340 ATAACCGGGCTAAGT-CCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA-CT
* *
14379 ATATCC-GGCTAA-ACCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
14400 TACTTGGTTT
Statistics
Matches: 165, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
38 20 0.12
39 103 0.62
40 40 0.24
41 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
Found at i:21304 original size:39 final size:40
Alignment explanation
Indices: 21240--21385 Score: 262
Period size: 40 Copynumber: 3.7 Consensus size: 40
21230 ATTCGGATTG
21240 ATAACC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
21278 ATAACC-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
21317 ATAACCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
21357 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
21386 ACGATACTAT
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
38 13 0.12
39 31 0.30
40 60 0.58
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:29354 original size:44 final size:41
Alignment explanation
Indices: 29298--29450 Score: 167
Period size: 39 Copynumber: 3.8 Consensus size: 41
29288 TATAAAGGTA
*
29298 TCGCTCAAATGCCTTCGGGACTTTGGCGCCGGTTATAGTGTAAC
1 TCGCACAAATGCCTTC-GGAC-TTGGCGCCGGTTATA-TGTAAC
29342 TCGCACAAATGCCTTCGGACTTGG-GCCGGTTATA-GTAAC
1 TCGCACAAATGCCTTCGGACTTGGCGCCGGTTATATGTAAC
* *
29381 TCGCACGAATGCCTTCGG-CTTAGC-CCGGTTAT-TAGT-AC
1 TCGCACAAATGCCTTCGGACTTGGCGCCGGTTATAT-GTAAC
* *
29419 TCGCACGAAATGCCTTCGGGCTTAGC-CCGGTT
1 TCGCAC-AAATGCCTTCGGACTTGGCGCCGGTT
29451 TATCAAATCC
Statistics
Matches: 100, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
38 20 0.20
39 35 0.35
40 12 0.12
41 10 0.10
42 4 0.04
43 4 0.04
44 15 0.15
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (41 bp):
TCGCACAAATGCCTTCGGACTTGGCGCCGGTTATATGTAAC
Found at i:36820 original size:41 final size:40
Alignment explanation
Indices: 36745--36915 Score: 179
Period size: 41 Copynumber: 4.2 Consensus size: 40
36735 CGCTTCAAAA
* * *
36745 TGCCTTCTGGGACGTAGCCCAGTTTATTGTAACTCGCACAAT
1 TGCCTTCTGGGAC-TTGCCC-GGTTATAGTAACTCGCACAAT
36787 TGCCTTCGTGGGACTTGCCCGGTTATAGTAACTCGCCACAAT
1 TGCCTTC-TGGGACTTGCCCGGTTATAGTAACTCG-CACAAT
*
36829 TGCCTTC-GGGACTTGGCCCGGTTATAGTAACTCGCACAAA
1 TGCCTTCTGGGACTT-GCCCGGTTATAGTAACTCGCACAAT
* *
36869 TGCCTTC--GGACTTGGCCCAGTGTATAGTTAACTCACACGAA-
1 TGCCTTCTGGGACTT-GCCCGGT-TATAG-TAACTCGCAC-AAT
36910 TGCCTT
1 TGCCTT
36916 TCGGGCGTAG
Statistics
Matches: 117, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
39 13 0.11
40 24 0.21
41 47 0.40
42 27 0.23
43 6 0.05
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (40 bp):
TGCCTTCTGGGACTTGCCCGGTTATAGTAACTCGCACAAT
Found at i:36919 original size:82 final size:79
Alignment explanation
Indices: 36745--36934 Score: 197
Period size: 82 Copynumber: 2.3 Consensus size: 79
36735 CGCTTCAAAA
* * * *
36745 TGCCTTCTGGGACGTAGCCCAGTTTATTGTAACTCGCACAATTGCCTTCGTGGGACTTGCCCGGT
1 TGCCTTC-GGG-CGTAGCCC-GGTTATAGTAACTCGCACAAATGCCTTC--GGGACTTGCCCAGT
*
36810 TATAGTAACTCGCCACAAT
61 TATAGTAACTCGACACAAT
* *
36829 TGCCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATGCCTTC-GGACTTGGCCCAGTGTA
1 TGCCTTCGGG-CGTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT-GCCCAGT-TA
36893 TAGTTAACTC-ACACGAA-
63 TAG-TAACTCGACAC-AAT
36910 TGCCTTTCGGGCGTAGCCCGGTTAT
1 TGCC-TTCGGGCGTAGCCCGGTTAT
36935 CAAATCCGAA
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
79 6 0.07
80 6 0.07
81 24 0.26
82 39 0.42
83 10 0.11
84 7 0.08
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.28
Consensus pattern (79 bp):
TGCCTTCGGGCGTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTGCCCAGTTATAG
TAACTCGACACAAT
Found at i:37862 original size:12 final size:12
Alignment explanation
Indices: 37845--37873 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
37835 GTCGTATCTC
37845 AAAGAATGCTAA
1 AAAGAATGCTAA
37857 AAAGAATGCTAA
1 AAAGAATGCTAA
37869 AAAGA
1 AAAGA
37874 GATCCAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (12 bp):
AAAGAATGCTAA
Found at i:38274 original size:13 final size:12
Alignment explanation
Indices: 38246--38284 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
38236 ATGAGAATTT
* *
38246 TTTTTCTTTTCT
1 TTTTTCTTATCA
38258 TTTTTCTTCATCA
1 TTTTTCTT-ATCA
38271 TTTTTCTTATCA
1 TTTTTCTTATCA
38283 TT
1 TT
38285 ATTTTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTCTTATCA
Done.