Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold645
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: 29797
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Found at i:1370 original size:49 final size:49
Alignment explanation
Indices: 1311--1487 Score: 230
Period size: 49 Copynumber: 3.6 Consensus size: 49
1301 CTGGAACGCA
*
1311 TAGTAGCCTGCACATAGTACTACACATGTCACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTCACCAATTATCCGGTACACG
* * *
1360 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTCACCAATTATCCGGTACACG
* * * ** *
1409 TAGTAGCCTGCACTTAGTACTACACACGTGATCA-CAGTTTTCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACA--TG-TCACCAATTATCCGGTACACG
1460 TAGTAGCCTGCACTTAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
1488 CGACCTCACA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
49 73 0.65
51 37 0.33
52 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTCACCAATTATCCGGTACACG
Found at i:13914 original size:40 final size:40
Alignment explanation
Indices: 13851--14033 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
13841 CCAGCATGAT
* *
13851 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * **
13891 TGCTCTTCGGAACTTTGCCCGGATACATCACTAGCTTGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
13931 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
13972 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
14012 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
14034 CATCATTCAA
Statistics
Matches: 115, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
39 3 0.03
40 93 0.81
41 19 0.17
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:14380 original size:29 final size:29
Alignment explanation
Indices: 14339--14417 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
14329 CTTAATAATC
*
14339 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
* *
14369 AACTCTCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
14398 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
14418 ATCTCACAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.07
29 36 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:14448 original size:43 final size:43
Alignment explanation
Indices: 14399--14501 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
14389 TGCATTTCAA
14399 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
14442 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
14485 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
14502 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:16414 original size:37 final size:37
Alignment explanation
Indices: 16364--16442 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
16354 TTATTACGAA
* * *
16364 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
16401 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
16438 GTCTT
1 GTCTT
16443 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:16686 original size:47 final size:47
Alignment explanation
Indices: 16561--16848 Score: 468
Period size: 47 Copynumber: 6.1 Consensus size: 47
16551 CCCTTCGGGA
* * * * * *
16561 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
16608 CCTGTCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16657 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
16704 CTTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16751 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
16798 CTTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16845 CTTA
1 CTTA
16849 CTATCATTTC
Statistics
Matches: 226, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
47 187 0.83
49 39 0.17
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20707 original size:40 final size:39
Alignment explanation
Indices: 20644--20745 Score: 150
Period size: 40 Copynumber: 2.6 Consensus size: 39
20634 CCAGCATGAT
* * *
20644 TGCTCTTCGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
*
20683 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
20723 TGCTCTTCGGGACTTAGCCCGGA
1 TGCTCTTC-GGACTTAGCCCGGA
20746 CATCATTCGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 10 0.18
40 45 0.79
41 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:21090 original size:29 final size:29
Alignment explanation
Indices: 21051--21129 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
21041 CTTAATAATC
*
21051 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
21081 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
21110 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
21130 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:21172 original size:43 final size:43
Alignment explanation
Indices: 21111--21213 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
21101 TGCATTTCAA
21111 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
21154 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
21197 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
21214 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:23119 original size:37 final size:37
Alignment explanation
Indices: 23069--23147 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
23059 TTATTACGAA
* * *
23069 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
23106 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
23143 GTCTT
1 GTCTT
23148 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:23397 original size:47 final size:47
Alignment explanation
Indices: 23265--23546 Score: 455
Period size: 47 Copynumber: 6.1 Consensus size: 47
23255 CCCTTCGGGA
* * * * * *
23265 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23312 CCTGTCACATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23358 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23405 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23452 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23499 CTTAT---ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23543 CTTA
1 CTTA
23547 CTATCATTTC
Statistics
Matches: 222, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
44 43 0.19
46 39 0.18
47 140 0.63
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:26461 original size:16 final size:16
Alignment explanation
Indices: 26440--26470 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26430 ATAAAATTGA
26440 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
26456 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
26471 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Done.