Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1649
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: 31719
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:4563 original size:40 final size:40
Alignment explanation
Indices: 4418--4563 Score: 179
Period size: 40 Copynumber: 3.6 Consensus size: 40
4408 GCTCCTCGTT
* * *
4418 CAAATGACTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
4458 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
4498 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
4539 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4564 CATCATTCAA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.03
40 77 0.85
41 11 0.12
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:9859 original size:42 final size:41
Alignment explanation
Indices: 9750--9871 Score: 122
Period size: 44 Copynumber: 2.9 Consensus size: 41
9740 ATCTGATATG
* *
9750 TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACCTC
1 TGATTTCGTGTAAGA-CATGTCTGGGACATTGGCATCGA-CTC
9793 T-ATTTTACGTGTAAGACAATGTCTGGGACATTGGCATCGTA-TC
1 TGA-TTT-CGTGTAAGAC-ATGTCTGGGACATTGGCATCG-ACTC
* * *
9836 TGATTTCGTGTAAGAGCGTGTCTGCGACAGTGGCAT
1 TGATTTCGTGTAAGA-CATGTCTGGGACATTGGCAT
9872 TAATGTTTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
42 26 0.38
43 12 0.18
44 29 0.43
45 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (41 bp):
TGATTTCGTGTAAGACATGTCTGGGACATTGGCATCGACTC
Found at i:17658 original size:43 final size:41
Alignment explanation
Indices: 17619--17712 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 41
17609 TACTAGGCTT
** *
17619 GAAGCCCGATATCATTTCAATAGCATTATAGCCTGCTAGGACC
1 GAAGCCCGA-ATCACCTCAACAGCATTATAGCCTGCTAGG-CC
* * *
17662 GAAGCCCGAATTACCTCACCGGCATTATAGCCTGCTAGGCCC
1 GAAGCCCGAATCACCTCAACAGCATTATAGCCTGCTAGG-CC
*
17704 AAAGCCCGA
1 GAAGCCCGA
17713 TAATATTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 34 0.79
43 9 0.21
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (41 bp):
GAAGCCCGAATCACCTCAACAGCATTATAGCCTGCTAGGCC
Found at i:23988 original size:27 final size:26
Alignment explanation
Indices: 23944--23995 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
23934 CTCGCTGCAA
23944 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGGCCTCGCCACA-ATATCTGT
* *
23971 TCTGGTGGCTTCGTCACAATATCTG
1 TCTGGTGGCCTCGCCACAATATCTG
23996 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (26 bp):
TCTGGTGGCCTCGCCACAATATCTGT
Found at i:24033 original size:67 final size:68
Alignment explanation
Indices: 23925--24066 Score: 196
Period size: 67 Copynumber: 2.1 Consensus size: 68
23915 GAGGAAGCGT
* * *
23925 TCTGGCACCCTCGCTGCAATCTGGTGGCCTCGCCAC-ATATATCTGTTCTGGTGGCTTCGTCACA
1 TCTGGCACCCTCGCTGCAATCTGGTGGCCTCGCCACAATATATCTGTTCTGGTGGCCTAGCCACA
23989 ATA
66 ATA
* * *
23992 TCTGGCAGCCTCGCTGTAATCTGGTGGCTTCGCCACATATATATATCTGTTCTGGTGGCCTAGCC
1 TCTGGCACCCTCGCTGCAATCTGGTGGCCTCGCCAC--A-ATATATCTGTTCTGGTGGCCTAGCC
24057 ACAATA
63 ACAATA
24063 TCTG
1 TCTG
24067 TATCCGGTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 33 0.51
71 32 0.49
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.31
Consensus pattern (68 bp):
TCTGGCACCCTCGCTGCAATCTGGTGGCCTCGCCACAATATATCTGTTCTGGTGGCCTAGCCACA
ATA
Found at i:31404 original size:27 final size:26
Alignment explanation
Indices: 31360--31411 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
31350 CTCGCTGCAA
*
31360 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
31387 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
31412 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:31476 original size:33 final size:32
Alignment explanation
Indices: 31427--31490 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
31417 CTCGCTGCAA
* *
31427 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
31460 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
31491 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:31504 original size:27 final size:26
Alignment explanation
Indices: 31452--31511 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
31442 ACATATATAT
*
31452 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
31478 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
31505 ATATCTG
1 ATATCTG
31512 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Done.