Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold216
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: 33906
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Found at i:1045 original size:40 final size:40
Alignment explanation
Indices: 1000--1344 Score: 548
Period size: 40 Copynumber: 8.6 Consensus size: 40
990 CAAGCTCAAT
* * * * *
1000 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
1040 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
1080 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
1120 CGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
1160 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
1200 TGCCTTTGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
1240 TGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
1280 TGCCTTCGGGTCTTAACCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1320 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
1345 CATTCAAATG
Statistics
Matches: 281, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
39 2 0.01
40 278 0.99
41 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:2967 original size:15 final size:15
Alignment explanation
Indices: 2947--2976 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2937 ATGAAAAAGG
2947 ATGAACACATTTTTT
1 ATGAACACATTTTTT
2962 ATGAACACATTTTTT
1 ATGAACACATTTTTT
2977 TCTCCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
ATGAACACATTTTTT
Found at i:8661 original size:40 final size:40
Alignment explanation
Indices: 8578--8921 Score: 566
Period size: 40 Copynumber: 8.6 Consensus size: 40
8568 CAAGCTCAAT
* * * *
8578 TGCCTTCGGGTCTTAACCCGG-TATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
8617 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
8657 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
8697 CGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
8737 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
8777 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
8817 TGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
8857 TGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
8897 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
8922 CATTCAAATG
Statistics
Matches: 284, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
39 22 0.08
40 261 0.92
41 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:16190 original size:40 final size:40
Alignment explanation
Indices: 16145--16488 Score: 550
Period size: 40 Copynumber: 8.6 Consensus size: 40
16135 CAAGCTCAAT
* * * * *
16145 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
16185 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
16225 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
16265 CG-CTGTCGGGTCTTAGCCCGGATA-ATCAGTTCGCACAAA
1 TGCCT-TCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
16304 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
16344 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
16384 TGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
16424 TGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
16464 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
16489 CATTCAAATG
Statistics
Matches: 282, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
39 37 0.13
40 244 0.87
41 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:16324 original size:119 final size:120
Alignment explanation
Indices: 16146--16488 Score: 539
Period size: 119 Copynumber: 2.9 Consensus size: 120
16136 AAGCTCAATT
* * * * * * *
16146 GCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATA
1 GCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATATA
*
16211 TCAACTT-GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAAC
66 TCAA-TTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAAC
* * *
16266 G-CTGTCGGGTCTTAGCCCGGATA-ATCAGTTCGCACAAATGCCTTCGGGTCTTATCCCGGATAT
1 GCCT-TCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATAT
*
16329 ATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAAT
65 ATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAAC
16385 GCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATATA
1 GCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATATA
16450 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
66 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
16489 CATTCAAATG
Statistics
Matches: 207, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
118 2 0.01
119 107 0.52
120 98 0.47
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (120 bp):
GCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATATA
TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAAC
Found at i:16407 original size:159 final size:160
Alignment explanation
Indices: 16145--16488 Score: 550
Period size: 159 Copynumber: 2.2 Consensus size: 160
16135 CAAGCTCAAT
* *
16145 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
* *
16210 ATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAACG-CTGTCGG
66 ATCAACTTGCACAAATGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAACGCCT-TCGG
* *
16274 GTCTTAGCCCGGATA-ATCAGTTCGCACAAA
130 GTCTTAACCCGGATATATCAATTCGCACAAA
* * *
16304 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
*
16369 ATCAA-TTCGCACAAATGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGG
66 ATCAACTT-GCACAAATGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAACGCCTTCGG
16433 GTCTTAACCCGGATATATCAATTCGCACAAA
130 GTCTTAACCCGGATATATCAATTCGCACAAA
*
16464 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAACCCGGATAT
16489 CATTCAAATG
Statistics
Matches: 171, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
158 2 0.01
159 129 0.75
160 40 0.23
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (160 bp):
TGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
ATCAACTTGCACAAATGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAACGCCTTCGGG
TCTTAACCCGGATATATCAATTCGCACAAA
Found at i:24836 original size:16 final size:16
Alignment explanation
Indices: 24817--24847 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24807 CTTCTTCAGT
24817 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
24833 TACTTACTTACTTAA
1 TACTCACTTACTTAA
24848 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:25229 original size:55 final size:53
Alignment explanation
Indices: 25099--25283 Score: 185
Period size: 55 Copynumber: 3.4 Consensus size: 53
25089 TTACCATTGG
*
25099 CATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATGAACTCACCAATGC
1 CATGTCTTGACATGGTCTTACATGGGAGCCTTGCCTTATGAACTCACCAATGC
* * * * *
25152 CATGCCTTGGCATGATCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATGC
1 CATGTCTTGACATGGTCTTACATGGGAGCC-TTGCCTTAT-G-AACTCACCAATGC
**** * *
25207 CATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAACCTTACCAATTTC
1 CATGTCTTGACATGGTCTTACATGGGAGCCTTGCCTTATG-AA-CTCACCAA-TGC
*
25262 CATGTCTTGGCATGGTCTTACA
1 CATGTCTTGACATGGTCTTACA
25284 CGGTATTCTT
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 35 0.32
54 8 0.07
55 63 0.57
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (53 bp):
CATGTCTTGACATGGTCTTACATGGGAGCCTTGCCTTATGAACTCACCAATGC
Found at i:25405 original size:15 final size:15
Alignment explanation
Indices: 25385--25413 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25375 CATGCTTAAG
25385 GGATGTTATATTTCA
1 GGATGTTATATTTCA
25400 GGATGTTATATTTC
1 GGATGTTATATTTC
25414 TCCCCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
GGATGTTATATTTCA
Found at i:31416 original size:23 final size:24
Alignment explanation
Indices: 31378--31422 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
31368 TTTGCTCTTC
*
31378 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGTCTTACCTTTT
31402 TAGCAT-AACTCGTCTTACCTT
1 TAGCATGAACTCGTCTTACCTT
31423 ATCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (24 bp):
TAGCATGAACTCGTCTTACCTTTT
Found at i:31620 original size:53 final size:54
Alignment explanation
Indices: 31491--31743 Score: 256
Period size: 53 Copynumber: 4.8 Consensus size: 54
31481 ACCCGGGTAC
* * * * *
31491 CTTACCATTACCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
31540 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
31593 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAATAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATGA-AA
* * * *
31648 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCC-TA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
*
31700 CCTTACCAATTGCCATGCCTTGGCAT-GTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
31744 AAACCTTAAT
Statistics
Matches: 170, Mismatches: 23, Indels: 18
0.81 0.11 0.09
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 4 0.02
53 70 0.41
54 18 0.11
55 38 0.22
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:31690 original size:108 final size:108
Alignment explanation
Indices: 31538--31736 Score: 305
Period size: 108 Copynumber: 1.8 Consensus size: 108
31528 ATCCTTTTGA
* *
31538 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCC-TA-GAAACCTCACCAA
31601 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAAT
64 TTGCCATGCCTTGGCAT-GTCTTACATGGGACCTTTGCCTTATAAT
* * *
31646 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTAGAAACCTTACCAATT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTAGAAACCTCACCAATT
31711 GCCATGCCTTGGCATGTCTTACATGG
66 GCCATGCCTTGGCATGTCTTACATGG
31737 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
106 1 0.01
107 4 0.05
108 62 0.75
109 16 0.19
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (108 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTAGAAACCTCACCAATT
GCCATGCCTTGGCATGTCTTACATGGGACCTTTGCCTTATAAT
Done.