Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1797
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: 32881
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:1216 original size:11 final size:11
Alignment explanation
Indices: 1187--1217 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1177 GAAAGAACTT
1187 AAAAAAAA-AA
1 AAAAAAAAGAA
1197 AAAAAAAAGAA
1 AAAAAAAAGAA
1208 AAAAAAAAGA
1 AAAAAAAAGA
1218 GAGAAGGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1222 original size:15 final size:15
Alignment explanation
Indices: 1187--1215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1177 GAAAGAACTT
1187 AAAA-AAAAAAAAAA
1 AAAAGAAAAAAAAAA
1201 AAAAGAAAAAAAAAA
1 AAAAGAAAAAAAAAA
1216 GAGAGAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAA
Found at i:2171 original size:21 final size:19
Alignment explanation
Indices: 2125--2194 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 19
2115 TTTTTGTATT
*
2125 ATAAGTAATTTTTTAATTAAA
1 ATAA-TAATTTTTTAA-AAAA
2146 ATAATTAATTTTTTAAAAAA
1 ATAA-TAATTTTTTAAAAAA
2166 ATTAATAAGTTTTTTTATAAAAA
1 A-TAATAA--TTTTTTA-AAAAA
2189 A-AATAA
1 ATAATAA
2195 ATTTAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.16
21 23 0.53
22 7 0.16
23 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAATAATTTTTTAAAAAA
Found at i:2276 original size:11 final size:11
Alignment explanation
Indices: 2250--2286 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2240 TATAAAAATT
*
2250 ATTTAATATTTT
1 ATTTAA-ATTTA
2262 ATTTAAATTTA
1 ATTTAAATTTA
2273 ATTTAAATTTA
1 ATTTAAATTTA
2284 ATT
1 ATT
2287 CGAGTTACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:4564 original size:24 final size:21
Alignment explanation
Indices: 4535--4599 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 21
4525 AAATTGTTTT
4535 TTATTTATTTTAATATTTAAATA
1 TTATTTATTTTAA-ATTT-AATA
*
4558 TATATTTAATTTAAATATTAATA
1 T-TATTTATTTTAAAT-TTAATA
4581 TTATTTGATATTTAAATTT
1 TTATTT-AT-TTTAAATTT
4600 GTTAAATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 5 0.14
23 11 0.31
24 20 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTTATTTTAAATTTAATA
Found at i:4641 original size:29 final size:27
Alignment explanation
Indices: 4595--4649 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
4585 TTGATATTTA
*
4595 AATTTGTTAAATACATAAATTATTAAATT
1 AATTTGTTAAAAACATAAA--ATTAAATT
* *
4624 AATTTTTTAAAAATATAAAATTAAAT
1 AATTTGTTAAAAACATAAAATTAAAT
4650 AATAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
29 16 0.70
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTTGTTAAAAACATAAAATTAAATT
Found at i:4660 original size:13 final size:13
Alignment explanation
Indices: 4634--4693 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
4624 AATTTTTTAA
*
4634 AAAT-ATAAAATT
1 AAATAATAAATTT
4646 AAATAATAAATTT
1 AAATAATAAATTT
4659 AAATATATAAA--T
1 AAATA-ATAAATTT
4671 -AA-AATAAATTT
1 AAATAATAAATTT
4682 AAATAA-AAATTT
1 AAATAATAAATTT
4694 TGATATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
9 5 0.12
10 1 0.02
11 3 0.07
12 13 0.32
13 14 0.34
14 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATAATAAATTT
Found at i:16291 original size:27 final size:27
Alignment explanation
Indices: 16261--16316 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
16251 CATGGGTTCC
*
16261 AGGTTACAAGTTATTATGTATTTGTCT
1 AGGTTACAAGTTAATATGTATTTGTCT
*
16288 AGGTTACAAGTTAATCTGTATTTGTCT
1 AGGTTACAAGTTAATATGTATTTGTCT
16315 AG
1 AG
16317 AAAATATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.45
Consensus pattern (27 bp):
AGGTTACAAGTTAATATGTATTTGTCT
Found at i:18408 original size:2 final size:2
Alignment explanation
Indices: 18401--18431 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18391 AATTTTCTTG
18401 AT AT AT AT 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
18432 ATCCACCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20398 original size:22 final size:22
Alignment explanation
Indices: 20358--20404 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
20348 TAAATTTATA
20358 TATTAAAATAAATAATTATATTT
1 TATTAAAATAAATAATTAT-TTT
20381 TATTAAGAAT-AA-AATTATTTT
1 TATTAA-AATAAATAATTATTTT
20402 TAT
1 TAT
20405 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
22 6 0.26
23 8 0.35
24 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTAAAATAAATAATTATTTT
Found at i:20409 original size:25 final size:25
Alignment explanation
Indices: 20352--20409 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
20342 AATATATAAA
20352 TTTATATATTAAAATAAATAATTAT
1 TTTATATATTAAAATAAATAATTAT
*
20377 ATT-T-TATTAAGAAT-AA-AATTATT
1 TTTATATATTAA-AATAAATAATTA-T
20400 TTTATATATT
1 TTTATATATT
20410 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
22 5 0.19
23 11 0.41
24 5 0.19
25 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTATATATTAAAATAAATAATTAT
Found at i:21033 original size:14 final size:14
Alignment explanation
Indices: 21015--21056 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
21005 TACTTGTTTT
21015 ATTTTTAAATATTA
1 ATTTTTAAATATTA
*
21029 TTTTTTAAATATTA
1 ATTTTTAAATATTA
*
21043 ATATTTAAAT-TTA
1 ATTTTTAAATATTA
21056 A
1 A
21057 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTTAAATATTA
Found at i:21194 original size:2 final size:2
Alignment explanation
Indices: 21187--21234 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
21177 TAATTTCTTC
*
21187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21229 T- TA TA T
1 TA TA TA T
21235 GCAGATTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22089 original size:21 final size:21
Alignment explanation
Indices: 22059--22098 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22049 AGGTACAACC
*
22059 AGAACCAAGAGGAGTTCGAAG
1 AGAACCAAGAAGAGTTCGAAG
*
22080 AGAACGAAGAAGAGTTCGA
1 AGAACCAAGAAGAGTTCGA
22099 GCCCTGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.33, T:0.10
Consensus pattern (21 bp):
AGAACCAAGAAGAGTTCGAAG
Found at i:23865 original size:2 final size:2
Alignment explanation
Indices: 23858--23882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23848 CTTTTTGACT
23858 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 T
23883 GAACTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25033 original size:20 final size:19
Alignment explanation
Indices: 25008--25070 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
24998 ATTACGGATA
25008 TAATAAATATTAATTATAAT
1 TAATAAATA-TAATTATAAT
*
25028 TAATAAA-A-AATTAAAAT
1 TAATAAATATAATTATAAT
25045 T-ATAAAATAATAATTATAA-
1 TAAT-AAAT-ATAATTATAAT
25064 TAATAAA
1 TAATAAA
25071 AGAAAAGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 12 0.33
19 6 0.17
20 16 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATAAATATAATTATAAT
Done.