Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1883
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: 30232
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:1264 original size:23 final size:23
Alignment explanation
Indices: 1238--1282 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1228 GAGATAAAGT
*
1238 TTTTTCTAGTTCAATTTTAACAA
1 TTTTTCTAATTCAATTTTAACAA
*
1261 TTTTTCTAATTCAGTTTTAACA
1 TTTTTCTAATTCAATTTTAACA
1283 TTATGTACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTTCTAATTCAATTTTAACAA
Found at i:7891 original size:30 final size:31
Alignment explanation
Indices: 7845--7908 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
7835 AATTTGATTA
* *
7845 TAAGATTATTATAATTGATGTAACAT-TTAT
1 TAAGATTATCATAATTGATATAACATCTTAT
*
7875 TAAGGTTATCATAATTGATATAACATCTTAT
1 TAAGATTATCATAATTGATATAACATCTTAT
7906 TAA
1 TAA
7909 TTTATTTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (31 bp):
TAAGATTATCATAATTGATATAACATCTTAT
Found at i:8150 original size:21 final size:21
Alignment explanation
Indices: 8115--8154 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
8105 GTATTCACCA
*
8115 ATTATTTTTATTAATATAAAGG
1 ATTATTTTTACTAAT-TAAAGG
8137 ATTATTTTT-CTAATTAAA
1 ATTATTTTTACTAATTAAA
8155 AATCATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTATTTTTACTAATTAAAGG
Found at i:8972 original size:15 final size:15
Alignment explanation
Indices: 8935--8976 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
8925 CTTTATTCTG
*
8935 ATAT-TTATTGATAT
1 ATATATTATTTATAT
8949 ATCACTATTATTTATAT
1 AT-A-TATTATTTATAT
8966 ATATATTATTT
1 ATATATTATTT
8977 TTAGGGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 2 0.08
17 11 0.46
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (15 bp):
ATATATTATTTATAT
Found at i:13846 original size:30 final size:30
Alignment explanation
Indices: 13812--13874 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
13802 TAAAATAAGA
13812 TTTATTTATTATTATGTTTAATTTTATTCC
1 TTTATTTATTATTATGTTTAATTTTATTCC
* *
13842 TTTATTTATTGTTTTGTTTAATTTTATTCC
1 TTTATTTATTATTATGTTTAATTTTATTCC
13872 TTT
1 TTT
13875 CTCTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (30 bp):
TTTATTTATTATTATGTTTAATTTTATTCC
Found at i:15223 original size:17 final size:16
Alignment explanation
Indices: 15201--15232 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
15191 AATGGCCCAT
15201 TTATTTTTTCATTTTTA
1 TTATTTTTTC-TTTTTA
15218 TTATTTTTTCTTTTT
1 TTATTTTTTCTTTTT
15233 CCATTTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTATTTTTTCTTTTTA
Found at i:16062 original size:162 final size:164
Alignment explanation
Indices: 15740--16150 Score: 578
Period size: 163 Copynumber: 2.5 Consensus size: 164
15730 AAAAATAAGA
* * * * *
15740 AAATTTCAAGAAAAAAATGAAAAACTCAAGAAAATGAGTGAATTTTTGAAAAATAATTTAATATG
1 AAATTTCAAGAAAAAAATGAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATATA
* *
15805 AAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAAAAAAATCTCCCCGAAAAAAT
66 AAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAAAAAAATCTCCCCAAAAAAAA
* *
15870 TTACGGAGTAAAAAACTCTGTATTTCGAAAG-GG
131 TTACGAAATAAAAAACTCTGTATTTCGAAAGAGG
*
15903 -AATTTCAAGAAAAAAATGAAAAAACTCATGAAAATGAATTAATTTTTGAAAACTAATTTAATAT
1 AAATTTCAAGAAAAAAATG-AAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATAT
* *
15967 AAAATAAATAATAATATTTGTTAAATTTTAAAAATTAAAAACCAAGAAAAATC-CCCCAAAAAAA
65 AAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAAAAAAATCTCCCCAAAAAAA
*
16031 ATTACGAAATAGAAAACTCTGTATTTCGAAAGTAGG
130 ATTACGAAATAAAAAACTCTGTATTTCGAAAG-AGG
* * * *
16067 AAAATTTCAAGAAAAAAATGAAAAA-TGAATGAAAATGAATAAATTTTTAAAAACTAATTAAATG
1 -AAATTTCAAGAAAAAAATGAAAAACT-CATGAAAATGAATAAATTTTTGAAAACTAATTTAATA
* * *
16131 GAAATTAAATGATAATATTT
64 TAAAATAAATAATAATATTT
16151 AAAGAATTTT
Statistics
Matches: 222, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
162 56 0.25
163 91 0.41
164 3 0.01
165 54 0.24
166 18 0.08
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.28
Consensus pattern (164 bp):
AAATTTCAAGAAAAAAATGAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATATA
AAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAAAAAAATCTCCCCAAAAAAAA
TTACGAAATAAAAAACTCTGTATTTCGAAAGAGG
Found at i:19174 original size:15 final size:16
Alignment explanation
Indices: 19152--19188 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
19142 TCCTTTTGAC
19152 CTCATTTATGCTACTT
1 CTCATTTATGCTACTT
19168 C-CATTTATGCTACTT
1 CTCATTTATGCTACTT
19183 CTCATT
1 CTCATT
19189 AGACTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.19, C:0.27, G:0.05, T:0.49
Consensus pattern (16 bp):
CTCATTTATGCTACTT
Found at i:22879 original size:17 final size:18
Alignment explanation
Indices: 22841--22891 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
22831 TCCAAGTTTT
* *
22841 TTTTCATTTTTTTATTAA
1 TTTTCATTTATTTATAAA
22859 -TTTCA-TTATTTATAAA
1 TTTTCATTTATTTATAAA
* *
22875 TTTTCTTTTAATTATAA
1 TTTTCATTTATTTATAA
22892 GCCAATAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 9 0.33
17 9 0.33
18 9 0.33
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTCATTTATTTATAAA
Found at i:23209 original size:26 final size:26
Alignment explanation
Indices: 23179--23231 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
23169 AAAGAAAGGT
*
23179 TAGAATTTGTAATAACAATTAAGAAC
1 TAGAATTTGTAACAACAATTAAGAAC
23205 TAGAATTTGTAACAACAATTAAGAAC
1 TAGAATTTGTAACAACAATTAAGAAC
23231 T
1 T
23232 GGCTATTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (26 bp):
TAGAATTTGTAACAACAATTAAGAAC
Found at i:28337 original size:167 final size:164
Alignment explanation
Indices: 27972--28343 Score: 389
Period size: 167 Copynumber: 2.2 Consensus size: 164
27962 AGACTTTGAA
* * *
27972 TATGTAAGTTTTATATATTTGATGTTTAATTTCGT-GTTTCAATTATGTAAGGACCAATTTGTAA
1 TATGTTAGTTTTATATATTTGATG-TTAATTTTGTATTTTCAATTATGTAAGGACCAATTTGTAA
* ** * *
28036 TGTTAGAAAGTTTAAGGGTTTATTTGTAAATATGTAAAATTTTTGTTCCAAGCCAAAGGTATTTA
65 TGTTAGAAAGTTTAAGGGTTTATTTGTAAATATGTAAAAATTTTACTCCAAGCCAAAGATATTGA
* * **
28101 GCCGAATCTTTCTTGTAATTTTTGAATCTGATTTT
130 GCCAAATCTTTCTTGTAATTTTGGAATCAAATTTT
* * * *
28136 TATGTT-GATTTAACTGTATTTGTTGCTTAATTTTGTATTTTTAATTATGTAAAGG-CCAATTTT
1 TATGTTAG-TTTTA-TATATTTGATG-TTAATTTTGTATTTTCAATTATGT-AAGGACCAA-TTT
* * * *
28199 TTATTTTTAGAAAGTTTAGGGGTTTATTTGTAAATAT-TAAAAAATTTTACTCCAAGGCCAAAGA
61 GTAATGTTAGAAAGTTTAAGGGTTTATTTGTAAATATGT-AAAAATTTTACTCCAA-GCCAAAGA
*
28263 TGA-TGAGCCAAAT-TTTCTTGTAGCTTTTGGAA-CAAATTTT
124 T-ATTGAGCCAAATCTTTCTTGTA-ATTTTGGAATCAAATTTT
*
28303 TGTGTTAGTTTTGATATATTTGATGTTAAATTTTGTATTTT
1 TATGTTAGTTTT-ATATATTTGATGTT-AATTTTGTATTTT
28344 AATCATATAG
Statistics
Matches: 170, Mismatches: 26, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
163 1 0.01
164 9 0.05
165 18 0.11
166 18 0.11
167 98 0.58
168 25 0.15
169 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (164 bp):
TATGTTAGTTTTATATATTTGATGTTAATTTTGTATTTTCAATTATGTAAGGACCAATTTGTAAT
GTTAGAAAGTTTAAGGGTTTATTTGTAAATATGTAAAAATTTTACTCCAAGCCAAAGATATTGAG
CCAAATCTTTCTTGTAATTTTGGAATCAAATTTT
Done.