Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3450
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: 18578
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:10854 original size:72 final size:72
Alignment explanation
Indices: 10737--10882 Score: 213
Period size: 72 Copynumber: 2.0 Consensus size: 72
10727 TTCAATTTAA
* *
10737 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTC-AGGTAATTTCAATTTA
1 AAAATCAACTCATATTGAGAGAGGTGAGCTGAGCCTCAGGACACGC-CGAGGTAATTTCAATTTA
10801 TGCTTTTC
65 TGCTTTTC
* * * *
10809 AAAATCAACTCATATTGAGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTTTTAATTTAT
1 AAAATCAACTCATATTGAGAGAGGTGAGCTGAGCCTCAGGACACGCCGAGGTAATTTCAATTTAT
*
10874 GTTTTTC
66 GCTTTTC
10881 AA
1 AA
10883 TTTCTGCTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.02
72 65 0.98
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (72 bp):
AAAATCAACTCATATTGAGAGAGGTGAGCTGAGCCTCAGGACACGCCGAGGTAATTTCAATTTAT
GCTTTTC
Found at i:10906 original size:13 final size:13
Alignment explanation
Indices: 10862--10906 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
10852 CGCCGAGGTA
*
10862 TTTTTAATTTATG
1 TTTTTAATTTCTG
10875 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
* *
10889 CTTTTAATTTCCG
1 TTTTTAATTTCTG
10902 TTTTT
1 TTTTT
10907 CAAAATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.16, C:0.11, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:10930 original size:99 final size:100
Alignment explanation
Indices: 10802--11077 Score: 403
Period size: 99 Copynumber: 2.8 Consensus size: 100
10792 TTCAATTTAT
* * * *
10802 GCTTTTCAAAATCAACTCATATTGAGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTTTT
1 GCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC
** *
10867 AATTTATGTTTTTCAATTTCTG-CTTTTAATTTCC
66 AATTTATGTTTTTCAATTTCTGCCTTACAAATTCC
*
10901 GTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC
1 GCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC
* * *
10966 AATTTCTGTTTTTCAATTTTTGCCTTACAAATTCT
66 AATTTATGTTTTTCAATTTCTGCCTTACAAATTCC
** *
11001 GCTTTTC-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTC
1 GCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC
*
11065 AATTTTTGTTTTT
66 AATTTATGTTTTT
11078 TTAATTTATG
Statistics
Matches: 160, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
99 146 0.91
100 14 0.09
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (100 bp):
GCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC
AATTTATGTTTTTCAATTTCTGCCTTACAAATTCC
Found at i:11260 original size:77 final size:71
Alignment explanation
Indices: 11095--11804 Score: 408
Period size: 77 Copynumber: 9.6 Consensus size: 71
11085 ATGTTTCAAA
* * * * *
11095 CAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCA--AGACGCTGAGATAATTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-TT
11158 TTGTTTGT
65 TTGTTT-T
* *
11166 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGATATTTTCAAATT
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC-AATT
*
11231 CTATTTTTAT
65 -T-TGTTT-T
* *
11241 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTAAGGTATTTTCAAT
1 C--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
*
11306 TAATGTTTTT
64 T-TTG-TTTT
** *** * ** * * * * * * * * * *
11316 CAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG-TTGA-GCCTCG-GGACACGC
1 CAA-AAAT-CAACTC--ATAT-TGC-GAGA--G-GTGAGTTGAGCCTCAGGACACGCTG--A-GG
** **
11378 TGAGGTAATTTCAATTTCTGTTTT
54 T-A--TTTTCA--ATTT-TGTTTT
* ** * *
11402 CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GA-AC-TTGA-GTATTTTTAATTT
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
11463 TGTTTT
66 TGTTTT
* * * *
11469 C----AT-AACTTATATTGCGAAAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTTAA
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAA
11528 TTTCTGTCTTT
63 TTT-TGT-TTT
* * *
11539 CAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAAT
1 C--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
11604 TTCTGTTTT
64 TT-TGTTTT
* ** * *
11613 CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
11678 CTGTTTT
66 -TGTTTT
* *
11685 CAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTC
1 C--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTC
11749 AATTTTCGTCTTT
61 AATTTT-GT-TTT
* *
11762 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 --CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
11805 ATCACACACT
Statistics
Matches: 491, Mismatches: 93, Indels: 103
0.71 0.14 0.15
Matches are distributed among these distances:
62 28 0.06
63 1 0.00
65 1 0.00
66 1 0.00
67 10 0.02
68 17 0.03
69 3 0.01
70 7 0.01
71 37 0.08
72 65 0.13
73 22 0.04
74 43 0.09
75 38 0.08
76 32 0.07
77 135 0.27
78 7 0.01
79 2 0.00
80 6 0.01
81 4 0.01
82 13 0.03
83 1 0.00
84 3 0.01
85 3 0.01
86 7 0.01
87 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (71 bp):
CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
TGTTTT
Found at i:11317 original size:14 final size:14
Alignment explanation
Indices: 11298--11332 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11288 CGCTAAGGTA
*
11298 TTTTCAATTAATGT
1 TTTTCAATTAATGC
*
11312 TTTTCAATTTATGC
1 TTTTCAATTAATGC
11326 TTTTCAA
1 TTTTCAA
11333 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTAATGC
Found at i:11432 original size:72 final size:72
Alignment explanation
Indices: 11312--11799 Score: 548
Period size: 72 Copynumber: 6.7 Consensus size: 72
11302 CAATTAATGT
*
11312 TTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
1 TTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
11377 CTGAGGTA
65 CTGAGGTA
* * ** * *
11385 ATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGA-AC-T
1 TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
11447 TGA-GTA
66 TGAGGTA
* * * * *
11453 TTTTTAATTT-TGTTTTC----AT-AACTTATATTGCGAAAGGTGAGTTGAGCCTCGGTTCACAT
1 TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACAC
11512 GCTGAGGTA
64 GCTGAGGTA
* *
11521 TTTTTAATTTCTGTCTTTCAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
1 TTTTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
11586 CGCTGAGGTA
63 CGCTGAGGTA
* * ** ** *
11596 ATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
11661 TGAGGTA
66 TGAGGTA
* *
11668 TTTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
1 TTTTCAATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GAC
*
11733 ATGCTGAGGTA
62 ACGCTGAGGTA
*
11744 TTTTCAATTT-TCGTCTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTTCAATTTCT-GT-TTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
11800 TTCAGATCAC
Statistics
Matches: 349, Mismatches: 43, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
62 27 0.08
63 1 0.00
65 1 0.00
66 1 0.00
67 10 0.03
68 24 0.07
69 6 0.02
70 6 0.02
71 2 0.01
72 104 0.30
73 11 0.03
74 38 0.11
75 25 0.07
76 25 0.07
77 68 0.19
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (72 bp):
TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
TGAGGTA
Found at i:11630 original size:211 final size:218
Alignment explanation
Indices: 11331--11799 Score: 783
Period size: 211 Copynumber: 2.2 Consensus size: 218
11321 TATGCTTTTC
11331 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
11396 TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGA-AC-TTGA-GTATTTT
66 TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
*
11457 TAATTT-TGTTTTC-AT-AACTTATATTGCGAAAGGTGAGTTGAGCCTCGGTTCACATGCTGAGG
131 CAATTTCTGTTTTCAATCAACTTATATTGCGAAAGGTGAGTTGAGCCTCGGTTCACATGCTGAGG
* *
11519 TATTTTTAA-TTTCTGTCTTTCAA
196 TATTTTCAATTTTC-GTCTTTAAA
*
11542 AAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
11607 TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
66 TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
*
11672 CAATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGC
131 CAATTTCTGTTTTC-----AATCAACTTATATTGCGAAAGGTGAGTTGAGCCTCGGTTCACATGC
11737 TGAGGTATTTTCAATTTTCGTCTTTAAA
191 TGAGGTATTTTCAATTTTCGTCTTTAAA
11765 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
11800 TTCAGATCAC
Statistics
Matches: 239, Mismatches: 6, Indels: 14
0.92 0.02 0.05
Matches are distributed among these distances:
211 109 0.46
212 3 0.01
213 2 0.01
214 4 0.02
215 12 0.05
216 7 0.03
222 2 0.01
223 96 0.40
224 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (218 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
CAATTTCTGTTTTCAATCAACTTATATTGCGAAAGGTGAGTTGAGCCTCGGTTCACATGCTGAGG
TATTTTCAATTTTCGTCTTTAAA
Found at i:11810 original size:77 final size:75
Alignment explanation
Indices: 11472--11824 Score: 423
Period size: 77 Copynumber: 4.7 Consensus size: 75
11462 TTGTTTTCAT
* * * *
11472 AACTTATATTGCGAAAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTTAATTTCTGTCT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA-GCTGAGGTATTTTCAATTTCTGT-T
*
11537 TTCAAAAAAATA
64 TTCAAAAAAATC
*
11549 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA-CAC-GCTGAGGTAATTTCAATTTCTGTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCACAGCTGAGGTATTTTCAATTTCTGTTT
*
11612 TC--AAAATTC
65 TCAAAAAAATC
** * *
11621 AACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA-CAC-GTTGAGGTATTTTCAATTTCTGTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCACAGCTGAGGTATTTTCAATTTCTGTTT
11684 TCAAAAAAATC
65 TCAAAAAAATC
* *
11695 AACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTT-TCGTC
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA-GCTGAGGTATTTTCAATTTCT-GT-
*
11759 TTTAAAAAAAATC
63 TTTCAAAAAAATC
* * * *
11772 AACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGTGGTATTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACA-GCTGAGGTATTTT
11825 TTCAATTTAT
Statistics
Matches: 240, Mismatches: 28, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
72 64 0.27
73 1 0.00
74 41 0.17
75 22 0.09
76 20 0.08
77 90 0.38
78 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (75 bp):
AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACAGCTGAGGTATTTTCAATTTCTGTTTT
CAAAAAAATC
Found at i:12987 original size:17 final size:17
Alignment explanation
Indices: 12965--13003 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12955 CCTAAAGGTG
*
12965 ATTTTA-TCTTCTTTATT
1 ATTTTACTCTTATTT-TT
12982 ATTTTACTCTTATTTTT
1 ATTTTACTCTTATTTTT
12999 ATTTT
1 ATTTT
13004 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTACTCTTATTTTT
Found at i:13073 original size:14 final size:14
Alignment explanation
Indices: 13054--13105 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
13044 TATATACATC
13054 ATAATAAAAAATAT
1 ATAATAAAAAATAT
*
13068 ATAATAAAATATAT
1 ATAATAAAAAATAT
*
13082 A-AATACAAAACAAAT
1 ATAATA-AAAA-ATAT
13097 ATAA-AAAAA
1 ATAATAAAAA
13106 TACCTTTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 4 0.12
14 21 0.66
15 5 0.16
16 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAATAAAAAATAT
Found at i:13220 original size:11 final size:11
Alignment explanation
Indices: 13204--13238 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
13194 CCCTTCCCCC
13204 CTCCCTTCTCT
1 CTCCCTTCTCT
13215 CTCCCTTCTCT
1 CTCCCTTCTCT
13226 CTTCCC-TCTCT
1 C-TCCCTTCTCT
13237 CT
1 CT
13239 TTTTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:13788 original size:11 final size:11
Alignment explanation
Indices: 13764--13806 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
13754 TTCTAATACG
*
13764 TATATATATTA
1 TATATATTTTA
*
13775 TATGTATTTTA
1 TATATATTTTA
* *
13786 TATATATTATG
1 TATATATTTTA
13797 TATATATTTT
1 TATATATTTT
13807 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Done.