Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1349
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: 26328
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1989 original size:13 final size:13
Alignment explanation
Indices: 1971--2000 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1961 AGCCCAAACT
1971 CAATTACCCAACC
1 CAATTACCCAACC
*
1984 CAATTATCCAACC
1 CAATTACCCAACC
1997 CAAT
1 CAAT
2001 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:2152 original size:9 final size:9
Alignment explanation
Indices: 2140--2198 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
2130 AAAATAAAAA
2140 AATTCGGGT
1 AATTCGGGT
*
2149 AATTCAGGT
1 AATTCGGGT
*
2158 ATTTTTC-GGT
1 A--ATTCGGGT
*
2168 AATTCGGTT
1 AATTCGGGT
*
2177 AATTCGGTT
1 AATTCGGGT
2186 AATTCGGGT
1 AATTCGGGT
2195 AATT
1 AATT
2199 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 3 0.07
9 32 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:5541 original size:26 final size:26
Alignment explanation
Indices: 5512--5561 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5502 AAGTTTAATT
* *
5512 AATTTTATATTTAAATAAGTTAATAA
1 AATTATATATTTAAATAAGATAATAA
5538 AATTATATATTTAAATAAGATAAT
1 AATTATATATTTAAATAAGATAAT
5562 TTATTAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AATTATATATTTAAATAAGATAATAA
Found at i:22157 original size:44 final size:45
Alignment explanation
Indices: 22097--22687 Score: 177
Period size: 44 Copynumber: 13.5 Consensus size: 45
22087 CATCTAGTCA
* * *
22097 TATCTCCCTGAGGTTGCAGTGGAGCAGACT-ATG-TAAGCAAGTAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT-AGCAAATAT
* * * *
22141 TATCCCCCTGAAGTTGCAGT-GAGGTAGACTAAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGA-GCAGACTAAAGATAGCAAATAT
* * ** **
22186 TATCTCCCTGAACTTGCAGTGGAGCAGATTAAAG-CCG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCA-AATAT
* * * *** *
22230 TATCTCTCTGAAGTTGCAGTGAAGCAGATTAAA-ACCTCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATAT
* * * **
22274 TACCTCTCTGAAGTTGCA---GAG-AG-C--AA-ATCGCATTTAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATA-T
* * * * *
22312 CATATCTCCTTGAGGTTGCAGTGGAGCAGACT-ACG-TAAGCAAGTCT
1 --TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT-AGCAAATAT
* * *
22358 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGATAGCAAATAT
* * * ** **
22403 TATCTCCCTGAAGTTACAGTGAAGCAGATTAAAG-CCG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCA-AATAT
* * *** **
22447 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA-ACCTCAAATCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATAT
* * * * * * * *
22491 TACCTCTCTGAAATTGCAG-AGAGCAGA-T-CACAT--CTAGTCA-
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAAT-AT
* * * ***
22531 TATCTCCTTGAGGTTGCAGTGGAGCAGACT-ACG-TAAGCAAGCCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT-AGCAAATAT
* * * *
22575 TATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGATAGCAAATAT
* * * **
22620 TATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGCT-G-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCA-AATAT
*
22664 TATCTCCCTGAAGTTACAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
22688 TGGATTAAAA
Statistics
Matches: 416, Mismatches: 89, Indels: 84
0.71 0.15 0.14
Matches are distributed among these distances:
37 7 0.02
38 1 0.00
40 33 0.08
41 11 0.03
42 3 0.01
43 20 0.05
44 217 0.52
45 107 0.26
46 13 0.03
47 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATAT
Found at i:22448 original size:217 final size:217
Alignment explanation
Indices: 22068--22778 Score: 1145
Period size: 217 Copynumber: 3.3 Consensus size: 217
22058 AGTCACATCT
* *
22068 AGTTACAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTATGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
* * * *
22133 GCAAGTATTATCCCCCTGAAGTTGCAGTGAGGTAGACTAAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
* * * *
22198 CTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCTCTGAAGTTGCAGTGAAGCAGATTAAA
131 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
22263 ACCTCAAATCTTACCTCTCTGA
196 ACCTCAAATCTTACCTCTCTGA
* * *
22285 AGTTGCAGAGAGCAAATCGCATTTAGTCATATCTCCTTGAGGTTGCAGTGGAGCAGACTACGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
22350 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
* *
22415 GTTACAGTGAAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
131 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
*
22480 ACCTCAAATCGTACCTCTCTGA
196 ACCTCAAATCTTACCTCTCTGA
* * *
22502 AATTGCAGAGAGCAGATCACATCTAGTCATATCTCCTTGAGGTTGCAGTGGAGCAGACTACGTAA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
* *
22567 GCAAGCCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
66 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
* * * *
22632 GTTGCAGTGGAGCATATTAAAGCTGATAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAA
131 GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
* *
22697 ACCTTAGATCTTATCCT-TCTGA
196 ACCTCAAATCTTA-CCTCTCTGA
* *
22719 AGTTGCAGAGAACAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGTAGACTA
1 AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTA
22779 AGATAGCAAA
Statistics
Matches: 457, Mismatches: 36, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
217 454 0.99
218 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (217 bp):
AGTTGCAGAGAGCAGATCGCATCTAGTCATATCTCCCTGAGGTTGCAGTGGAGCAGACTACGTAA
GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
GTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
ACCTCAAATCTTACCTCTCTGA
Found at i:24818 original size:19 final size:20
Alignment explanation
Indices: 24777--24818 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
24767 GTTTCTATGC
* *
24777 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
24797 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
24816 CAT
1 CAT
24819 CGCATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Done.