Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold891
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: 35210
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:6721 original size:79 final size:79
Alignment explanation
Indices: 6577--6794 Score: 221
Period size: 79 Copynumber: 2.7 Consensus size: 79
6567 AAATCACGTA
* * * * *
6577 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAG-TACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAG
*
6641 TAACTCGCACAAATG
65 TAACTCGCAAAAATG
*
6656 CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATA
* *
6719 GTATCTCGCAAAAATT
64 GTAACTCGCAAAAATG
* * * *
6735 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
6795 CATCATTCAA
Statistics
Matches: 117, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.03
79 66 0.56
80 48 0.41
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCGCAAAAATG
Found at i:6739 original size:39 final size:40
Alignment explanation
Indices: 6610--6794 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
6600 GCTACTCGTT
*
6610 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
6650 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
6690 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * * *
6729 AAAATTCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
6770 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6795 CATCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 77 0.64
41 12 0.10
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12309 original size:56 final size:56
Alignment explanation
Indices: 12159--12348 Score: 283
Period size: 56 Copynumber: 3.4 Consensus size: 56
12149 CCATGGCATT
* * * * * *
12159 GATATATGTGTGTGAGTAAGACCATGTTTAATACGTTGGTATCAATATGTCACACC
1 GATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCC
*
12215 GATATATGTGTGC-AATAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCC
*
12270 GATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCC
* *
12326 GATTTATGTGTGTGAGTAAGACC
1 GATATATGTGTGCGAGTAAGACC
12349 CTGTCTGGGA
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
55 49 0.40
56 73 0.60
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (56 bp):
GATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCC
Found at i:12366 original size:56 final size:56
Alignment explanation
Indices: 12159--12377 Score: 212
Period size: 56 Copynumber: 3.9 Consensus size: 56
12149 CCATGGCATT
* * * * * * * *
12159 GATATATGTGTGTGAGTAAGACCATGTTTAATAC-GTTGGTATCAATATGTCACACC
1 GATATATGTGTGCGAGTAAGACCACGTCTAAGACAG-TGGCATCGATATGTGACTCC
* * *
12215 GATATATGTGTGC-AATAAGACCACGTTTAATAC-GTTGGCATCGATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCACGTCTAAGACAG-TGGCATCGATATGTGACTCC
* * *
12270 GATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCACGTCTAAGACAGTGGCATCGATATGTGACTCC
* * ** *
12326 GATTTATGTGTGTGAGTAAGACC-CTGTCTGGGACAGTGGCATCAATATGTGA
1 GATATATGTGTGCGAGTAAGACCAC-GTCTAAGACAGTGGCATCGATATGTGA
12378 TTACATGTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
55 50 0.35
56 93 0.65
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (56 bp):
GATATATGTGTGCGAGTAAGACCACGTCTAAGACAGTGGCATCGATATGTGACTCC
Found at i:22253 original size:40 final size:40
Alignment explanation
Indices: 22193--22374 Score: 260
Period size: 40 Copynumber: 4.6 Consensus size: 40
22183 TATTCGAATG
22193 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* * *
22233 ATATACGGGCTAAGTGCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
22273 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* * *
22313 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT-TCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
* *
22353 ATATCC-GGCTAAATCCTGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
22375 TACTTGGGTT
Statistics
Matches: 127, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 13 0.10
40 112 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:30419 original size:40 final size:40
Alignment explanation
Indices: 30364--30625 Score: 393
Period size: 40 Copynumber: 6.6 Consensus size: 40
30354 TATTCGAATG
30364 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
30404 ATATCCGGGCTAAGTCCCGAAGACATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
** *
30444 ATATTTGGGCTAAGTCCCGAAGGCATTTGTGCTGTTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
30484 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
30524 ATATCCGGGCTAAGTACCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* * *
30564 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
* *
30604 ATATCC-AGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
30626 TACTTGGATT
Statistics
Matches: 200, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
39 13 0.06
40 184 0.92
41 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:33825 original size:41 final size:42
Alignment explanation
Indices: 33736--33880 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 42
33726 TAAGACCACG
* * * *
33736 TCTGGGACGTTGGCATCGATATATGTGGTTAGATGTAAGACCATA
1 TCTGGGACATTGGCATCGATAT-T-TGATT-CATGTAAGACCCTA
33781 TCTGGGACATTGGCATCG-TATTTGATTCATGTAAGACCCTA
1 TCTGGGACATTGGCATCGATATTTGATTCATGTAAGACCCTA
* * ** * *
33822 TCTGAGACAGTGGCATCGATATGAGATAGCATGTAAGACCAC-G
1 TCTGGGACATTGGCATCGATATTTGAT-TCATGTAAGACC-CTA
*
33865 TCTGGGACGTTGGCAT
1 TCTGGGACATTGGCAT
33881 TGTACAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
41 28 0.33
42 10 0.12
43 25 0.30
44 4 0.05
45 17 0.20
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
TCTGGGACATTGGCATCGATATTTGATTCATGTAAGACCCTA
Done.