Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2457
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: 34650
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:1367 original size:27 final size:27
Alignment explanation
Indices: 1328--1505 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
1318 ATATTGAGTC
* * *
1328 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
**
1355 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* *
1382 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACACAATCAAA-T
** *** *
1410 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
1437 CGCACACTTAGTGC-ATCACATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * *
1464 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
1491 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1506 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:7413 original size:141 final size:138
Alignment explanation
Indices: 7161--7447 Score: 486
Period size: 141 Copynumber: 2.1 Consensus size: 138
7151 GAGAACATAG
7161 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
**
7226 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTT
7291 TGGAAAAAA
131 TGG-AAAAA
7300 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATATTTTA-TAGAATTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTG--TATATATTTTACT-GAATTT
* *
7364 ATTAATATAAACAATTATTTTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTC
63 ATTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTC
*
7429 TTTTGGAAAGA
128 TTTTGGAAAAA
7440 ATATAATT
1 ATATAATT
7448 CCTTTTCTTA
Statistics
Matches: 140, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
139 43 0.31
140 13 0.09
141 84 0.60
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
AATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTT
TGGAAAAA
Found at i:10127 original size:46 final size:46
Alignment explanation
Indices: 10074--10249 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
10064 TGGTTGAGCA
*
10074 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * * * * *
10120 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATACGA-ACG
*
10167 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * * *
10213 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
10250 GCAGGTTACA
Statistics
Matches: 107, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 70 0.65
47 35 0.33
48 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
Found at i:10230 original size:93 final size:93
Alignment explanation
Indices: 10071--10242 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
10061 GGATGGTTGA
* * *
10071 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAGT
10136 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
10164 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAGT
10229 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
10243 CTTATGGGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:13359 original size:12 final size:12
Alignment explanation
Indices: 13342--13387 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
13332 ATTTAATTAC
13342 TTTAATATTAAA
1 TTTAATATTAAA
13354 TTTAATATTAAA
1 TTTAATATTAAA
*
13366 --TATTATTAAA
1 TTTAATATTAAA
*
13376 -TTACTATTAAA
1 TTTAATATTAAA
13387 T
1 T
13388 CTTATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.30
11 9 0.30
12 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:13374 original size:10 final size:10
Alignment explanation
Indices: 13359--13397 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
13349 TTAAATTTAA
13359 TATTAAATAT
1 TATTAAATAT
*
13369 TATTAAATTAC
1 TATTAAA-TAT
*
13380 TATTAAATCT
1 TATTAAATAT
13390 TATTAAAT
1 TATTAAAT
13398 TAATAGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (10 bp):
TATTAAATAT
Found at i:13385 original size:21 final size:21
Alignment explanation
Indices: 13347--13402 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
13337 ATTACTTTAA
13347 TATTAAATTTAATATTAAATAT
1 TATTAAA-TTAATATTAAATAT
* *
13369 TATTAAATTACTATTAAATCT
1 TATTAAATTAATATTAAATAT
13390 TATTAAATTAATA
1 TATTAAATTAATA
13403 GATTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTAAATTAATATTAAATAT
Found at i:14916 original size:24 final size:25
Alignment explanation
Indices: 14876--14948 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 25
14866 CAGACACACG
14876 ACAGCTCGTATGAGCTTCCCGATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
*
14901 ACAGCTCG-ATGAGCTTCCTGATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
** * * *
14925 GTAGCTTGTATCAACTTCCCGATT
1 ACAGCTCGTATGAGCTTCCCGATT
14949 CGTAGCTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCCCGATTT
Found at i:28764 original size:39 final size:40
Alignment explanation
Indices: 28647--28827 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
28637 GCTACTCGTT
*
28647 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
28687 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28727 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28766 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28807 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
28828 GGACATCATT
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 73 0.60
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28830 original size:79 final size:81
Alignment explanation
Indices: 28647--28827 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
28637 GCTACTCGTT
* * *
28647 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
28711 GATTTAGTAACTCGCA
66 GATATAGTAACTAGCA
* **
28727 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
28789 GGATATGGTCACTTAGCA
65 GGATATAGTAAC-TAGCA
28807 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
28828 GGACATCATT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 54 0.62
80 30 0.34
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GATATAGTAACTAGCA
Done.