Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold531
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: 38107
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:164 original size:17 final size:18
Alignment explanation
Indices: 142--175 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
132 TCCCATGAAA
142 AATATATCT-AATATATG
1 AATATATCTAAATATATG
159 AATATATCTAAATATAT
1 AATATATCTAAATATAT
176 ATAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (18 bp):
AATATATCTAAATATATG
Found at i:516 original size:1 final size:1
Alignment explanation
Indices: 437--509 Score: 101
Period size: 1 Copynumber: 73.0 Consensus size: 1
427 TCCCTTTCTC
* * * * *
437 TTTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
502 TTTTTTTT
1 TTTTTTTT
510 CCTTTTTGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.04, G:0.03, T:0.93
Consensus pattern (1 bp):
T
Found at i:531 original size:8 final size:8
Alignment explanation
Indices: 431--529 Score: 84
Period size: 7 Copynumber: 12.9 Consensus size: 8
421 ACTTTTTCCC
*
431 TTTCTCTT
1 TTTCTTTT
*
439 TTTCTTTC
1 TTTCTTTT
447 TTTCTTTT
1 TTTCTTTT
455 TTT-TTTT
1 TTTCTTTT
462 TTT-TTTT
1 TTTCTTTT
469 TTT-TTTT
1 TTTCTTTT
476 TTT-TTTT
1 TTTCTTTT
483 TTT-TTTT
1 TTTCTTTT
490 TTT-TTTGT
1 TTTCTTT-T
*
498 TTGTTTTTT
1 TT-TCTTTT
*
507 TTTCCTTT
1 TTTCTTTT
* *
515 TTGCTTTC
1 TTTCTTTT
523 TTTCTTT
1 TTTCTTT
530 CTCTATTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
7 38 0.48
8 34 0.43
9 4 0.05
10 3 0.04
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTCTTTT
Found at i:653 original size:20 final size:21
Alignment explanation
Indices: 628--668 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
618 AAATATAGAG
628 ATATAAAAAAT-TAAAATATA
1 ATATAAAAAATATAAAATATA
648 ATATAAAAAATAATAAAATAT
1 ATATAAAAAAT-ATAAAATAT
669 TGTACGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
ATATAAAAAATATAAAATATA
Found at i:892 original size:11 final size:11
Alignment explanation
Indices: 752--894 Score: 51
Period size: 11 Copynumber: 12.3 Consensus size: 11
742 GATATTTATA
*
752 AAAAAT-ATTT
1 AAAAATAATAT
762 AAAACATAATAT
1 AAAA-ATAATAT
*
774 AAAAATGATAT
1 AAAAATAATAT
** *
785 GTACATAATAT
1 AAAAATAATAT
796 AAATATACGTATATAT
1 AAA-A-A--TA-ATAT
812 AAAAATAA-AT
1 AAAAATAATAT
*
822 -AAAATAAAAT
1 AAAAATAATAT
*
832 AAATTATTAATAT
1 AAA--AATAATAT
*
845 ATAAAAAATATAT
1 A-AAAATA-ATAT
858 AAAAATATCATAT
1 AAAAATA--ATAT
***
871 TTTAA-AATAT
1 AAAAATAATAT
881 AAAAATAATAT
1 AAAAATAATAT
892 AAA
1 AAA
895 TACCAAAATA
Statistics
Matches: 97, Mismatches: 21, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
9 7 0.07
10 14 0.14
11 27 0.28
12 17 0.18
13 19 0.20
14 3 0.03
15 3 0.03
16 7 0.07
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:909 original size:36 final size:35
Alignment explanation
Indices: 808--909 Score: 86
Period size: 34 Copynumber: 2.9 Consensus size: 35
798 ATATACGTAT
* *
808 ATATAAAAATAA-ATAAA-ATAAAATAAATTATTAAT
1 ATATAAAAATAATATAAATACAAAAT-AATT-TTAAA
* * **
843 ATATAAAAA-ATATATAAAAATATCAT-ATTTTAAA
1 ATATAAAAATA-ATATAAATACAAAATAATTTTAAA
877 ATATAAAAATAATATAAATACCAAAATAATTTT
1 ATATAAAAATAATATAAATA-CAAAATAATTTT
910 TTTTCTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
34 22 0.41
35 17 0.31
36 10 0.19
37 5 0.09
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (35 bp):
ATATAAAAATAATATAAATACAAAATAATTTTAAA
Found at i:941 original size:21 final size:21
Alignment explanation
Indices: 911--957 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
901 AATAATTTTT
911 TTTC-TTTTTTTTCTCCTTTC
1 TTTCTTTTTTTTTCTCCTTTC
* *
931 TTTCTTTTTTTTTTTTCTTTC
1 TTTCTTTTTTTTTCTCCTTTC
952 TTTCTT
1 TTTCTT
958 GCCTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTCTTTTTTTTTCTCCTTTC
Found at i:954 original size:25 final size:25
Alignment explanation
Indices: 910--957 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
900 AAATAATTTT
910 TTTTCTTTTTTTTCTCCTTTCTTTC
1 TTTTCTTTTTTTTCTCCTTTCTTTC
*
935 TTTT-TTTTTTTTCTTTCTTTCTT
1 TTTTCTTTTTTTTC-TCCTTTCTT
958 GCCTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTCTTTTTTTTCTCCTTTCTTTC
Found at i:967 original size:25 final size:24
Alignment explanation
Indices: 912--967 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
902 ATAATTTTTT
* *
912 TTCTTTTTTTTCTCCTTTCTTTCT
1 TTCTTTTTTTTCTCCTTTCTTGCC
* *
936 TTTTTTTTTTTCTTTCTTTCTTGCC
1 TTCTTTTTTTTC-TCCTTTCTTGCC
961 TTCTTTT
1 TTCTTTT
968 CCCAGCTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (24 bp):
TTCTTTTTTTTCTCCTTTCTTGCC
Found at i:3130 original size:13 final size:13
Alignment explanation
Indices: 3112--3142 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3102 AGTTTTTTAG
3112 TATAATATATATA
1 TATAATATATATA
3125 TATAATATATATA
1 TATAATATATATA
3138 TATAA
1 TATAA
3143 AGAAAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATAATATATATA
Found at i:3572 original size:6 final size:6
Alignment explanation
Indices: 3562--3605 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
3552 CACATGGATT
* * * *
3562 GATGAT GATGAA GATGAA GATGAA GAAGAA GACGAA GAAGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GA
3606 AGGATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.52, C:0.02, G:0.34, T:0.11
Consensus pattern (6 bp):
GATGAA
Found at i:3583 original size:12 final size:12
Alignment explanation
Indices: 3568--3605 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3558 GATTGATGAT
*
3568 GATGAAGATGAA
1 GATGAAGAAGAA
3580 GATGAAGAAGAA
1 GATGAAGAAGAA
*
3592 GACGAAGAAGAA
1 GATGAAGAAGAA
3604 GA
1 GA
3606 AGGATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.03, G:0.34, T:0.08
Consensus pattern (12 bp):
GATGAAGAAGAA
Found at i:4301 original size:2 final size:2
Alignment explanation
Indices: 4294--4340 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4284 GTAGGGAGGG
4294 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4336 G- GA GA
1 GA GA GA
4341 ACAAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5081 original size:4 final size:4
Alignment explanation
Indices: 5072--5096 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5062 GGCTGCGGCT
5072 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
5097 CGAAGGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:9330 original size:2 final size:2
Alignment explanation
Indices: 9323--9357 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9313 TGATCGTGAA
*
9323 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9358 ATCTCCACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11554 original size:2 final size:2
Alignment explanation
Indices: 11547--11589 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
11537 CATTCGAACA
11547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11588 AT
1 AT
11590 GCGCATGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12727 original size:2 final size:2
Alignment explanation
Indices: 12720--12760 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12710 TAAAAGTTTA
12720 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12761 ATAAACATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18887 original size:3 final size:3
Alignment explanation
Indices: 18879--18935 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
18869 AAATTATTCG
* * * *
18879 TAT TAT TAT TAT TAT TAT GAT GAT TCT TAT TAT GAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18926 TAT TAT TAT T
1 TAT TAT TAT T
18936 GGCTTCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:19320 original size:2 final size:2
Alignment explanation
Indices: 19313--19351 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19303 TAACCCATTT
19313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19352 TGCGTTTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19497 original size:2 final size:2
Alignment explanation
Indices: 19492--19522 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19482 CATATATGAC
*
19492 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19523 CATACATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20163 original size:2 final size:2
Alignment explanation
Indices: 20156--20187 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20146 TCTGTTGGCA
20156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20188 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33531 original size:2 final size:2
Alignment explanation
Indices: 33524--33549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33514 CCTGTGTTTA
33524 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
33550 TACGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:36363 original size:2 final size:2
Alignment explanation
Indices: 36356--36393 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
36346 TCCCTCTGCC
36356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36394 TTCAACTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37020 original size:3 final size:3
Alignment explanation
Indices: 37007--37050 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
36997 AAAAAGAAGC
37007 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAAT AAT -AT AAT AAT A
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
37051 GACTTAACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.