Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold884
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: 4687
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.32
Warning! 157 characters in sequence are not A, C, G, or T
Found at i:137 original size:45 final size:44
Alignment explanation
Indices: 76--313 Score: 130
Period size: 44 Copynumber: 5.4 Consensus size: 44
66 AGAATTACGA
* * *
76 CTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAACC-CAGAGAGATAAAATCTGACAT
* * * * * *
121 CTTCGATCTGCTCCAC--TAATGCCTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTGTAA--CCCAGAGAGATAAAATCTGACAT
* * * * * **
165 CTTCAATCTATTCCATTGCCAA-CCAGGGAGATAGAAT-T-ACGG
1 CTTCAATCTACTCCACTG-TAACCCAGAGAGATAAAATCTGACAT
* * *
207 CTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAACC-CAGAGAGATAAAATCTGACAT
* * * * * *
252 CTTCGATCTGCTCCAC--TAATGCCTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTGTAA--CCCAGAGAGATAAAATCTGACAT
*
296 CTTCAATCTATTCCACTG
1 CTTCAATCTACTCCACTG
314 CTGCCCAGGG
Statistics
Matches: 138, Mismatches: 42, Indels: 25
0.67 0.20 0.12
Matches are distributed among these distances:
41 2 0.01
42 17 0.12
43 18 0.13
44 68 0.49
45 31 0.22
47 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTAACCCAGAGAGATAAAATCTGACAT
Found at i:235 original size:131 final size:132
Alignment explanation
Indices: 1--567 Score: 874
Period size: 131 Copynumber: 4.3 Consensus size: 132
* *
1 TCCACTACTGCCTAGGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCCAACCAGGG-AGT
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAAG-
*
65 TAGAATTAC-GACTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATC
65 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATC
129 TGC
130 TGC
* *
132 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCATTGCCAACCAGGG-AGA
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAAG-
196 TAGAATTAC-GGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATC
65 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATC
260 TGC
130 TGC
* ***
263 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGT
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAAGT
* * *
328 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTGATCT
66 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCT
393 GC
131 GC
* * * ***
395 TCCACTACTGCTTAGGGAGACAAGATCTGAAATC-TCAATCTATTCCGCTGCTTCCCAGGGAAGT
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAAGT
* * *
459 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTGATCT
66 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCT
524 GC
131 GC
* *
526 TCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCT
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCT
568 GCTTCTCTGT
Statistics
Matches: 415, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
131 320 0.77
132 95 0.23
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (132 bp):
TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAAGT
AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCT
GC
Found at i:478 original size:263 final size:262
Alignment explanation
Indices: 1--567 Score: 870
Period size: 263 Copynumber: 2.2 Consensus size: 262
* *
1 TCCACTACTGCCTAGGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCCAACCAGGGAGTT
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGTT
66 AGAATTACGACTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTG
66 AGAATTACGACTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTG
* *
131 CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCATTGCCAACCAGGGAGA
131 CTCCACTAATGCCTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
196 TAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCT
196 TAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCT
261 GC
261 GC
* ***
263 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGG-AGT
* * * *
327 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTGATC
65 TAGAATTAC-GACTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATC
* * * ***
392 TGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATC-TCAATCTATTCCGCTGCTTCCCAGGGA
129 TGCTCCACTAATGCCTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGA
* * *
456 -AGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTG
194 GA-TAGAATTAC-GGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCG
520 ATCTGC
257 ATCTGC
* *
526 TCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCT
1 TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCT
568 GCTTCTCTGT
Statistics
Matches: 277, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
261 1 0.00
262 95 0.34
263 181 0.65
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (262 bp):
TCCACTACTGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGTT
AGAATTACGACTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTG
CTCCACTAATGCCTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
TAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCT
GC
Found at i:2560 original size:17 final size:17
Alignment explanation
Indices: 2532--2603 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
2522 AGCGGGGTTC
2532 TTTTCT-TTTTTTTTCT
1 TTTTCTCTTTTTTTTCT
*
2548 TTTTCCCTTTTTTTTCT
1 TTTTCTCTTTTTTTTCT
* *
2565 TTTTCTTTTTTTTTTGT
1 TTTTCTCTTTTTTTTCT
2582 TTTCTCTCTTCTTTTTT-T
1 TTT-TCTCTT-TTTTTTCT
2600 TTTT
1 TTTT
2604 TGGATTGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.10
17 28 0.58
18 9 0.19
19 6 0.12
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.83
Consensus pattern (17 bp):
TTTTCTCTTTTTTTTCT
Found at i:2571 original size:33 final size:36
Alignment explanation
Indices: 2532--2604 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 36
2522 AGCGGGGTTC
2532 TTTTCTTTTTTTTTCT-TTTTC-C-CTT-TTTTTTCT
1 TTTTCTTTTTTTTT-TGTTTTCTCTCTTCTTTTTTCT
*
2565 TTTTCTTTTTTTTTTGTTTTCTCTCTTCTTTTTTTT
1 TTTTCTTTTTTTTTTGTTTTCTCTCTTCTTTTTTCT
2601 TTTT
1 TTTT
2605 GGATTGAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 1 0.03
33 19 0.54
34 1 0.03
35 3 0.09
36 11 0.31
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (36 bp):
TTTTCTTTTTTTTTTGTTTTCTCTCTTCTTTTTTCT
Found at i:2584 original size:16 final size:15
Alignment explanation
Indices: 2532--2602 Score: 70
Period size: 18 Copynumber: 4.3 Consensus size: 15
2522 AGCGGGGTTC
2532 TTTTCTTTTTTTTTCT
1 TTTTCTTTTTTTTT-T
*
2548 TTTTCCCTTTTTTTTCT
1 TTTT--CTTTTTTTTTT
2565 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
2580 GTTTTCTCTCTTCTTTTTT
1 -TTTTCT-T-TT-TTTTTT
2599 TTTT
1 TTTT
2603 TTGGATTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
15 10 0.21
16 10 0.21
17 6 0.13
18 15 0.32
19 6 0.13
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:2584 original size:23 final size:21
Alignment explanation
Indices: 2532--2604 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
2522 AGCGGGGTTC
*
2532 TTTTCTTTT-TTTTTCTTTTT
1 TTTTTTTTTCTTTTTCTTTTT
*
2552 CCCTTTTTTTTCTTTTTCTTTTT
1 --TTTTTTTTTCTTTTTCTTTTT
*
2575 TTTTTGTTTTCTCTCTTCTTTTT
1 TTTTT-TTTTCT-TTTTCTTTTT
2598 TTTTTTT
1 TTTTTTT
2605 GGATTGAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.09
22 15 0.34
23 25 0.57
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTCTTTTT
Done.