Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold503
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: 995855
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 7 of 7
Found at i:964072 original size:22 final size:21
Alignment explanation
Indices: 964038--964078 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
964028 TTAATTTATT
964038 ATATATTTTATTAT-ATTTTG
1 ATATATTTTATTATCATTTTG
964058 ATATATTTATAATTATCATTT
1 ATATATTT-T-ATTATCATTT
964079 ATAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 5 0.28
23 4 0.22
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATATTTTATTATCATTTTG
Found at i:964901 original size:22 final size:20
Alignment explanation
Indices: 964876--964915 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
964866 TTTTGAAATA
964876 TTTTTAAATTTAATTAATATAT
1 TTTTTAAA-TTAA-TAATATAT
*
964898 TTTTTATATTAATAATAT
1 TTTTTAAATTAATAATAT
964916 TATATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAAATTAATAATATAT
Found at i:964910 original size:17 final size:17
Alignment explanation
Indices: 964884--964916 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
964874 TATTTTTAAA
964884 TTTAATTAAT-ATATTT
1 TTTAATTAATAATATTT
964900 TTTATATTAATAATATT
1 TTTA-ATTAATAATATT
964917 ATATTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATTAATAATATTT
Found at i:965876 original size:13 final size:13
Alignment explanation
Indices: 965858--965883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
965848 ATTTTTTTGG
965858 TGTATCGATACAT
1 TGTATCGATACAT
965871 TGTATCGATACAT
1 TGTATCGATACAT
965884 ACTTTGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:968273 original size:21 final size:20
Alignment explanation
Indices: 968227--968273 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
968217 TTTGAAGGTG
*
968227 ATTTTGATGAAAAACGATGT
1 ATTTTGATGAAAAACGAAGT
*
968247 AATTTGAAGTGAAAAAC-AAGT
1 ATTTTG-A-TGAAAAACGAAGT
968268 ATTTTG
1 ATTTTG
968274 CAAAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:968416 original size:13 final size:13
Alignment explanation
Indices: 968398--968433 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
968388 ATCCACCTGC
*
968398 ATCGATACAGTGT
1 ATCGATACAATGT
968411 ATCGATACAATGT
1 ATCGATACAATGT
968424 ATCGATACAA
1 ATCGATACAA
968434 AGAATGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (13 bp):
ATCGATACAATGT
Found at i:973358 original size:33 final size:33
Alignment explanation
Indices: 973321--973387 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
973311 TTCAACGATT
973321 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
973354 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
973387 T
1 T
973388 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:973359 original size:13 final size:13
Alignment explanation
Indices: 973341--973365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
973331 CATAAAATGT
973341 TGTATCGATACAA
1 TGTATCGATACAA
973354 TGTATCGATACA
1 TGTATCGATACA
973366 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:973446 original size:13 final size:13
Alignment explanation
Indices: 973428--973452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
973418 ATTACTCAAA
973428 TGTATCGATACAT
1 TGTATCGATACAT
973441 TGTATCGATACA
1 TGTATCGATACA
973453 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:973554 original size:52 final size:52
Alignment explanation
Indices: 973461--973588 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 52
973451 CACTGATCTT
*
973461 TGTATCGATACATGCAGGC-AATTTACCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATT-AAA
* *
973512 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATTAAA
*
973564 TGTATTGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
973589 TCATATTTCG
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 18 0.26
52 49 0.70
53 3 0.04
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATTAAA
Found at i:978194 original size:34 final size:32
Alignment explanation
Indices: 978150--978214 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
978140 TACAAGCTAA
**
978150 TGTATCGATACATTTTTTTGGTGTATCGATACAT
1 TGTATCGATACA-TACTTT-GTGTATCGATACAT
*
978184 TGTATGGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
978215 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 4 0.14
34 11 0.39
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:978802 original size:7 final size:7
Alignment explanation
Indices: 978792--978823 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
978782 TCGTTTAAAA
978792 AAATTTT
1 AAATTTT
978799 AAATTTT
1 AAATTTT
978806 AAATTTT
1 AAATTTT
978813 AAA-TTT
1 AAATTTT
978819 AAATT
1 AAATT
978824 AAATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:978811 original size:14 final size:13
Alignment explanation
Indices: 978792--978851 Score: 59
Period size: 13 Copynumber: 4.4 Consensus size: 13
978782 TCGTTTAAAA
978792 AAATTTTAAATTTT
1 AAATTTTAAA-TTT
978806 AAATTTTAAATTT
1 AAATTTTAAATTT
978819 AAATTAAATTAAATTT
1 AAATT---TTAAATTT
* *
978835 -ATTTTTTAATTT
1 AAATTTTAAATTT
978847 AAATT
1 AAATT
978852 ATTATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 7 0.18
13 11 0.28
14 10 0.26
15 3 0.08
16 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AAATTTTAAATTT
Found at i:978821 original size:6 final size:6
Alignment explanation
Indices: 978796--978851 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
978786 TTAAAAAAAT
** *
978796 TTTAAA TTTTAAA TTTTAAA TTTAAA -TTAAA -TTAAA TTTATT TTTTAA
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
978844 TTTAAA TT
1 TTTAAA TT
978852 ATTATTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 10 0.24
6 19 0.45
7 13 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:978853 original size:17 final size:18
Alignment explanation
Indices: 978822--978861 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
978812 TAAATTTAAA
*
978822 TTAAATTAAATTTATTTT
1 TTAAATTAAATTTATTAT
*
978840 TTAATTTAAA-TTATTAT
1 TTAAATTAAATTTATTAT
978857 TTAAA
1 TTAAA
978862 ATATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTAAATTTATTAT
Found at i:979192 original size:10 final size:10
Alignment explanation
Indices: 979187--979220 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
979177 TTTAAAATAT
979187 TATAAATTTA
1 TATAAATTTA
979197 TATAAATTTA
1 TATAAATTTA
979207 TATAAATTTA
1 TATAAATTTA
979217 TATA
1 TATA
979221 TATTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TATAAATTTA
Found at i:979314 original size:11 final size:12
Alignment explanation
Indices: 979268--979324 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 12
979258 GATACATTTG
*
979268 TATATTTTATGT
1 TATATTTTATAT
979280 TATA-TTTATGA-
1 TATATTTTAT-AT
979291 TAT-TTTTATAT
1 TATATTTTATAT
979302 TATATTTTA-AT
1 TATATTTTATAT
*
979313 TATTTTTTATAT
1 TATATTTTATAT
979325 ATCGTATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.03
11 26 0.68
12 11 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:979316 original size:22 final size:23
Alignment explanation
Indices: 979272--979324 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
979262 CATTTGTATA
* *
979272 TTTTATGTTATATTTATGATA-T
1 TTTTATATTATATTTATAATATT
979294 TTTTATATTATATTT-TAATTATT
1 TTTTATATTATATTTATAA-TATT
979317 TTTTATAT
1 TTTTATAT
979325 ATCGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 16 0.59
23 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTATATTATATTTATAATATT
Found at i:979453 original size:24 final size:24
Alignment explanation
Indices: 979403--979493 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
979393 ACTAATTATT
* * *
979403 TATTTATTTATTTATGTT-TTGACA
1 TATTTATGTATTTATATTATTTA-A
979427 TATTTATGTATTTATATTATTTAA
1 TATTTATGTATTTATATTATTTAA
979451 TA-TTAT-T-TTTATATTATAATTAAA
1 TATTTATGTATTTATATTAT--TT-AA
*
979475 TTTTTATGTATGTTATATT
1 TATTTATGTAT-TTATATT
979494 CGTATTGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
21 10 0.18
22 1 0.02
23 6 0.11
24 22 0.40
25 7 0.13
26 1 0.02
27 1 0.02
28 7 0.13
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (24 bp):
TATTTATGTATTTATATTATTTAA
Found at i:979779 original size:10 final size:12
Alignment explanation
Indices: 979750--979790 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
979740 AGCGTTCATG
979750 TTATTTTTTATA
1 TTATTTTTTATA
979762 TTATTTTTTA-A
1 TTATTTTTTATA
979773 TTATTTTTCTTATA
1 TTA-TTTT-TTATA
979787 TTAT
1 TTAT
979791 ATTTATGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.15
12 14 0.54
13 4 0.15
14 4 0.15
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:980273 original size:26 final size:25
Alignment explanation
Indices: 980244--980296 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
980234 ATTTAATATG
*
980244 ATTTAACTTAA-ATTTTGTAATTATTA
1 ATTT-ACTTAATA-TTTGTAAATATTA
*
980270 ATTTAGTTAATATTTGTAAATATTA
1 ATTTACTTAATATTTGTAAATATTA
980295 AT
1 AT
980297 AGCAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
ATTTACTTAATATTTGTAAATATTA
Found at i:980322 original size:17 final size:18
Alignment explanation
Indices: 980300--980333 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
980290 TATTAATAGC
980300 AAAAATAT-TAAAAAATT
1 AAAAATATATAAAAAATT
980317 AAAAATATATAAAAAAT
1 AAAAATATATAAAAAAT
980334 AGGTGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATATATAAAAAATT
Found at i:980889 original size:20 final size:19
Alignment explanation
Indices: 980851--980890 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
980841 TTAAAATATA
*
980851 AAAAAATTATAATAGAAAT
1 AAAAAATTAAAATAGAAAT
*
980870 AAAAAATTAAAGATATAAAT
1 AAAAAATTAAA-ATAGAAAT
980890 A
1 A
980891 TATTTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAAATTAAAATAGAAAT
Found at i:984971 original size:28 final size:27
Alignment explanation
Indices: 984916--984986 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
984906 GCCACCCATT
* *
984916 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTG
984943 TGTTTGTCAAAAATGGTGGTT-TCCCTTG
1 TGTTTGTCAAAAATGGTGGTTAT--CTTG
* *
984971 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
984987 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATCTTG
Found at i:987603 original size:21 final size:22
Alignment explanation
Indices: 987561--987606 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
987551 TGTTCAGACA
* * *
987561 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAAGTGG
987583 AGTA-TACTCCAAAACAAGTGG
1 AGTAGTACTCCAAAACAAGTGG
987604 AGT
1 AGT
987607 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAAGTGG
Found at i:989544 original size:28 final size:27
Alignment explanation
Indices: 989489--989559 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
989479 GCCACCCATT
989489 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
989516 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
989544 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
989560 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:992459 original size:26 final size:26
Alignment explanation
Indices: 992410--992464 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
992400 TTTTTCTTTC
*
992410 TTTATAAAATTAATTTAATTTATT-T
1 TTTATAAAATTAATTTAATGTATTAT
* *
992435 TTTATTAAATTTATTTACATGTATTAT
1 TTTATAAAATTAATTTA-ATGTATTAT
992462 TTT
1 TTT
992465 TCGGTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATAAAATTAATTTAATGTATTAT
Found at i:992983 original size:13 final size:13
Alignment explanation
Indices: 992965--992990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
992955 ACACCAAAGT
992965 ATGTATCGATACA
1 ATGTATCGATACA
992978 ATGTATCGATACA
1 ATGTATCGATACA
992991 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:992988 original size:33 final size:33
Alignment explanation
Indices: 992946--993010 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
992936 GTAGCCAACT
* *
992946 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
992979 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
993011 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.