Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2419
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: 34787
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:279 original size:38 final size:39
Alignment explanation
Indices: 241--393 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 39
231 CATTTCAATG
* * *
241 CTTCGGGACTTAACCCGGATTTAAAACTCGCACGAATGC
1 CTTCGGGACTTAACCCGGAATTAAAACTCGCACAAAGGC
* ***
280 CTTCGGGATTTAAACCCGGAATTAGTCTCTCGCACAAAGGC
1 CTTCGGGACTT-AACCCGGAATTA-AAACTCGCACAAAGGC
*
321 CTTCGGGAC-T-ACCCGGAATT-ATACTCGCACAAAGGC
1 CTTCGGGACTTAACCCGGAATTAAAACTCGCACAAAGGC
357 CTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
1 CTTCGGGACTTAACCCGGAATTAA-AACTCGCACAAA
394 ATACCTTTCC
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
36 22 0.23
37 1 0.01
38 20 0.21
39 11 0.11
40 23 0.24
41 19 0.20
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (39 bp):
CTTCGGGACTTAACCCGGAATTAAAACTCGCACAAAGGC
Found at i:364 original size:77 final size:79
Alignment explanation
Indices: 241--393 Score: 204
Period size: 76 Copynumber: 2.0 Consensus size: 79
231 CATTTCAATG
* * * * *
241 CTTCGGGACTTAACCCGGATTTAAAACTCGCACGAATGCCTTCGGGATTTAAACCCGGAATTAGT
1 CTTCGGGACTTAACCCGGAATTAAAACTCGCACAAAGGCCTTCGGGACTT-AACCCGGAATTAAT
**
306 CTCTCGCACAAAGGC
65 AACTCGCACAAAGGC
*
321 CTTCGGGAC-T-ACCCGGAATT-ATACTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTAATA
1 CTTCGGGACTTAACCCGGAATTAAAACTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTAATA
383 ACTCGCACAAA
66 ACTCGCACAAA
394 ATACCTTTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
76 23 0.35
77 23 0.35
78 9 0.14
79 1 0.02
80 9 0.14
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (79 bp):
CTTCGGGACTTAACCCGGAATTAAAACTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTAATA
ACTCGCACAAAGGC
Found at i:8273 original size:38 final size:38
Alignment explanation
Indices: 8143--8347 Score: 137
Period size: 38 Copynumber: 5.5 Consensus size: 38
8133 CTCATTCAAT
* *
8143 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAAT
1 GCCTTC-GGACTTAACCCGGA-ATTAATAACTCGCAC-AAA
*
8183 GCC-TCGG--TTAACCCGG-A-T-AT--TTCGCACAAA
1 GCCTTCGGACTTAACCCGGAATTAATAACTCGCACAAA
* *
8213 GCCTTCGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 GCCTTCGGACTTAACCCGGAATTAATAACTCGCACAAA
8251 GGCCTTCGGACTTAACCC-GAATTAATAACTCGC-CAAA
1 -GCCTTCGGACTTAACCCGGAATTAATAACTCGCACAAA
* ** * * *
8288 TACCTTCGGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA
1 -GCCTTCGGA-CTTAACCCGGAAT-TAATAAC-TCGCACAAA
*
8329 GCCTTCGGGACTTAGCCCG
1 GCCTTC-GGACTTAACCCG
8348 ACAGCATTCA
Statistics
Matches: 133, Mismatches: 16, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
30 5 0.04
31 10 0.08
32 1 0.01
33 10 0.08
34 1 0.01
35 1 0.01
36 10 0.08
37 12 0.09
38 32 0.24
39 25 0.19
40 19 0.14
41 7 0.05
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (38 bp):
GCCTTCGGACTTAACCCGGAATTAATAACTCGCACAAA
Found at i:13982 original size:136 final size:132
Alignment explanation
Indices: 13723--13972 Score: 366
Period size: 136 Copynumber: 1.9 Consensus size: 132
13713 TTTTTGTCTT
13723 TTATATTTGACCGAAATTAATTAATATAACTATATGATTAATAAATTCGGTACAATATATCAATT
1 TTATATTTGACCGAAATTAATTAATATAACTATATGATTAATAAATTCGGTACAATATATCAATT
*
13788 AAATTTTGTAATGAATCAAATTCATATATTTAATTATATTCTTCCAAAAAATCATAATTTCGTGT
66 AAATTTTGTAACGAATCAAATTCATATATTTAATTATATTCTTCCAAAAAATCATAATTTCGTGT
13853 TC
131 TC
*
13855 TTATATTTTGACCGAAATTATTTAATATAACTATTTAT-ATT-ATAAAATTCGGTTA-AACTATA
1 TTATA-TTTGACCGAAATTAATTAATATAACTA--TATGATTAAT-AAATTCGG-TACAA-TATA
13917 TACAATTAATATTTTGT-ACGAATCAAATTCAT-TATATTAATTATATTCTTCCAAAA
60 T-CAATTAA-ATTTTGTAACGAATCAAATTCATATAT-TTAATTATATTCTTCCAAAA
13973 GAATTTAATT
Statistics
Matches: 107, Mismatches: 2, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
132 5 0.05
133 28 0.26
134 13 0.12
135 13 0.12
136 41 0.38
137 7 0.07
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (132 bp):
TTATATTTGACCGAAATTAATTAATATAACTATATGATTAATAAATTCGGTACAATATATCAATT
AAATTTTGTAACGAATCAAATTCATATATTTAATTATATTCTTCCAAAAAATCATAATTTCGTGT
TC
Found at i:14053 original size:136 final size:135
Alignment explanation
Indices: 13723--14098 Score: 347
Period size: 136 Copynumber: 2.8 Consensus size: 135
13713 TTTTTGTCTT
* * *
13723 TTATA-TTTGACCGAAATTAATTAATATAACTA--TATGATTA-ATAAATTC-GGTACAA-TATA
1 TTATATTTTGACAGAAATTAATTAATATAACTAGTTAT-ATTATA-AAATACAGTTA-AACTATA
13782 T-CAATTAA-ATTTTGTAATGAATCAAATTCATATATTTAATTATATTCTTCCAAAAAATCATAA
63 TACAATTAATATTTTGT-ATGAATCAAATTCATATA-TTAATTATATTCTTCCAAAAAATCATAA
13845 TTTCGTGTTC
126 TTTCGTGTTC
* * * * *
13855 TTATATTTTGACCGAAATTATTTAATATAACTATTTATATTATAAAATTCGGTTAAACTATATAC
1 TTATATTTTGACAGAAATTAATTAATATAACTAGTTATATTATAAAATACAGTTAAACTATATAC
* *
13920 AATTAATATTTTGTACGAATCAAATTCATTATATTAATTATATTCTTCCAAAAGAAT-TTAATTA
66 AATTAATATTTTGTATGAATCAAATTCA-TATATTAATTATATTCTTCCAAAA-AATCATAATT-
13984 TCATGTCGTT-
128 TC--GT-GTTC
** *
13994 TTATATTTTTGTTAGAAATTTAAATTAATATAA-T-GTTATA-TA-AAAA-ACAG-TAAATTATA
1 TTATA-TTTTGACAGAAA-TT-AATTAATATAACTAGTTATATTATAAAATACAGTTAAACTATA
* *
14053 TTACAA-TAATATTTTTTATGAAGCAAATTTCATATATT-ATTATATT
63 -TACAATTAATATTTTGTATGAATCAAA-TTCATATATTAATTATATT
14099 TTGTTCTCTA
Statistics
Matches: 210, Mismatches: 15, Indels: 35
0.81 0.06 0.13
Matches are distributed among these distances:
132 5 0.02
133 26 0.12
134 12 0.06
135 20 0.10
136 77 0.37
137 27 0.13
138 4 0.02
139 9 0.04
140 17 0.08
141 3 0.01
142 10 0.05
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (135 bp):
TTATATTTTGACAGAAATTAATTAATATAACTAGTTATATTATAAAATACAGTTAAACTATATAC
AATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTCCAAAAAATCATAATTTCG
TGTTC
Found at i:21174 original size:326 final size:327
Alignment explanation
Indices: 20560--21215 Score: 1126
Period size: 326 Copynumber: 2.0 Consensus size: 327
20550 ATACCCAAAT
20560 TCTCTTTTCTCATTCTGGTAGTTTCTAGGTTCCTTTTCCTAAAGGACTTCTACTCATTTCCATAG
1 TCTCTTTTCTCATTCTGGTAGTTTCTAGGTTCCTTTTCCTAAAGGACTTCTACTCATTTCCATAG
20625 CCAAACTTTAACTTAATACACCCCAATCCCATATTAACATCCTAGCGATGACCCCGTCTTTAATG
66 CCAAACTTTAACTTAATACACCCCAATCCCATATTAACATCCTAGCGATGACCCCGTCTTTAATG
* *
20690 TCCCATCGGACTTCCCCATTTTATCGTCTTGAAAGGCTATCTATTTTAAACATCCCATCAGGCTA
131 TCCCATCGGACTTCCCCATTTTATCATCTTGAAAGGCTATCTATTTTAAACATCCCATCAGACTA
* * *
20755 CTTGAGTTGCCATATTCCTAAATATGGTTTTACACCTTATATTTCCCATGTTTACTATTACGGAT
196 CTTGAGTTGCCATATTCCCAAATATGGTTTTACACATTATATTTCCCATGTTTACTATCACGGAT
20820 AAGACACTAGGAAGCCATATCTTCTTTCAACTATGGTCTTAGTCCCA-TTACCTTTGATGTCATG
261 AAGACACTAGGAAGCCATATCTTCTTTCAACTATGGTCTTAGTCCCATTTACC-TTGATGTCATG
20884 ACG
325 ACG
20887 TCTC-TTTCTCATTCTGGTAGTTTCTAGGTTCCTTTTCCTAAAGGACTTCTACTCATTTCCATAG
1 TCTCTTTTCTCATTCTGGTAGTTTCTAGGTTCCTTTTCCTAAAGGACTTCTACTCATTTCCATAG
* * *
20951 CCAAACTTTAACTTAATACACCCTAGTCCCCATGTTAACATCCTAGCAGATGACCCCGTCTTTAA
66 CCAAACTTTAACTTAATACACCCCAAT-CCCATATTAACATCCTAGC-GATGACCCCGTCTTTAA
* * *
21016 TGTCCCATCGGACTT-TCCATTTTATCATCTTGAAAGGCTATCTATTTTTAACATCCCATTAGAC
129 TGTCCCATCGGACTTCCCCATTTTATCATCTTGAAAGGCTATCTATTTTAAACATCCCATCAGAC
21080 TACTTGAGGTTGCCATA-TCCCAAATATGGTTTTACACATTATATTTCCCATGTTTACTATCACG
194 TACTTGA-GTTGCCATATTCCCAAATATGGTTTTACACATTATATTTCCCATGTTTACTATCACG
21144 G-T-AGACTACTAGGAAGCCATATCTTCTTTCAACTATGGTCTTAGTCCCATTTACCTTGATGTC
258 GATAAGAC-ACTAGGAAGCCATATCTTCTTTCAACTATGGTCTTAGTCCCATTTACCTTGATGTC
21207 ATGACG
322 ATGACG
21213 TCT
1 TCT
21216 TTCAGCTATG
Statistics
Matches: 313, Mismatches: 11, Indels: 11
0.93 0.03 0.03
Matches are distributed among these distances:
325 4 0.01
326 145 0.46
327 123 0.39
328 41 0.13
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (327 bp):
TCTCTTTTCTCATTCTGGTAGTTTCTAGGTTCCTTTTCCTAAAGGACTTCTACTCATTTCCATAG
CCAAACTTTAACTTAATACACCCCAATCCCATATTAACATCCTAGCGATGACCCCGTCTTTAATG
TCCCATCGGACTTCCCCATTTTATCATCTTGAAAGGCTATCTATTTTAAACATCCCATCAGACTA
CTTGAGTTGCCATATTCCCAAATATGGTTTTACACATTATATTTCCCATGTTTACTATCACGGAT
AAGACACTAGGAAGCCATATCTTCTTTCAACTATGGTCTTAGTCCCATTTACCTTGATGTCATGA
CG
Found at i:21318 original size:47 final size:46
Alignment explanation
Indices: 21168--21328 Score: 134
Period size: 45 Copynumber: 3.5 Consensus size: 46
21158 AGCCATATCT
* * * *
21168 TCTTTCAACTATGGTCTTAGTCCCATTT--ACCTTGATGTCAT-GACG
1 TCTTTCAACTATGGTCTTACT-CAATTTAGAGCATGATGTCATAG-CG
* * * * ** *
21213 TCTTTCAGCTATGGT-TTACTC-ATTTATATCATGACGTTGTAGCA
1 TCTTTCAACTATGGTCTTACTCAATTTAGAGCATGATGTCATAGCG
*
21257 TCTTTTCAACTATGGTCTTACTCAATTATAGAGCGTGATGTCATAGCG
1 TC-TTTCAACTATGGTCTTACTCAATT-TAGAGCATGATGTCATAGCG
21305 TCTTTCAACTATGGTCTTTACTCA
1 TCTTTCAACTATGGTC-TTACTCA
21329 TCTGTAGGCA
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
42 4 0.04
43 1 0.01
44 15 0.16
45 27 0.29
46 6 0.07
47 17 0.18
48 22 0.24
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (46 bp):
TCTTTCAACTATGGTCTTACTCAATTTAGAGCATGATGTCATAGCG
Done.