Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2252
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: 43818
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:1225 original size:20 final size:19
Alignment explanation
Indices: 1202--1262 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
1192 AAATATTTTT
1202 TATTTATATAAATTTTAATA
1 TATTTA-ATAAATTTTAATA
*
1222 TA-TTAAT-AATTTATATTA
1 TATTTAATAAATTT-TAATA
1240 TATATTAA-AAA-TTT-ATA
1 TAT-TTAATAAATTTTAATA
1257 TATTTA
1 TATTTA
1263 TATTATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 9 0.26
19 5 0.14
20 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTAATAAATTTTAATA
Found at i:1238 original size:13 final size:13
Alignment explanation
Indices: 1220--1310 Score: 68
Period size: 12 Copynumber: 7.2 Consensus size: 13
1210 TAAATTTTAA
1220 TATATTA-ATAATT
1 TATATTATAT-ATT
1233 TATATTATATATT
1 TATATTATATATT
* *
1246 AAAAATTTATATATT
1 -TATA-TTATATATT
1261 TATA-T-TATATT
1 TATATTATATATT
*
1272 TATATT-TTTATAT
1 TATATTATATAT-T
1285 TATATTATAT-TT
1 TATATTATATATT
*
1297 GATATTATAT-TT
1 TATATTATATATT
1309 TA
1 TA
1311 ATAATTTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
11 10 0.16
12 19 0.30
13 18 0.28
14 8 0.12
15 9 0.14
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (13 bp):
TATATTATATATT
Found at i:1270 original size:5 final size:5
Alignment explanation
Indices: 1252--1307 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
1242 TATTAAAAAT
1252 TTATA -TAT- TTATA TTATA TTTATA TT-T- TTATA TTATA TTATA TTTGATA
1 TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA TTATA -TT-ATA
1301 TTATA TT
1 TTATA TT
1308 TTAATAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
3 2 0.05
4 8 0.18
5 22 0.50
6 9 0.20
7 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:1274 original size:19 final size:18
Alignment explanation
Indices: 1220--1342 Score: 95
Period size: 19 Copynumber: 6.2 Consensus size: 18
1210 TAAATTTTAA
*
1220 TATATTAATAATTTATATTA
1 TATATT-AT-ATTTATATTT
*
1240 TATATTAAAAATTTATATATT
1 TATATT--ATATTTATAT-TT
1261 TATATTATATTTATATTTT
1 TATATTATATTTATA-TTT
1280 TATATTATA-TTATATTT
1 TATATTATATTTATATTT
*
1297 GATATTATATTTTAATAATTTTTT
1 TATATTATA-TTT-AT-A---TTT
*
1321 TATGTTATATTTATATTT
1 TATATTATATTTATATTT
1339 TATA
1 TATA
1343 ATCAATTGTA
Statistics
Matches: 86, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
17 11 0.13
18 11 0.13
19 21 0.24
20 17 0.20
21 11 0.13
22 2 0.02
23 3 0.03
24 10 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATATTATATTTATATTT
Found at i:1305 original size:41 final size:42
Alignment explanation
Indices: 1260--1338 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 42
1250 ATTTATATAT
* *
1260 TTATATTATATTTATATTTTTATATTATA-TTATATTTGATA
1 TTATATTATAATAATATTTTTATATTATATTTATATTTGATA
* * *
1301 TTATATTTTAATAATTTTTTTATGTTATATTTATATTT
1 TTATATTATAATAATATTTTTATATTATATTTATATTT
1339 TATAATCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 24 0.75
42 8 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (42 bp):
TTATATTATAATAATATTTTTATATTATATTTATATTTGATA
Found at i:1329 original size:36 final size:35
Alignment explanation
Indices: 1255--1337 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 35
1245 TAAAAATTTA
*
1255 TATATTTATATTATATTTATATTTTTATATTATAT
1 TATATTTATATTATATTTATAATTTTATATTATAT
*
1290 TATATTTGATATTATATTTTAATAATTTT-T-TTATGT
1 TATATTT-ATATTATA-TTT-ATAATTTTATATTATAT
1326 TATATTTATATT
1 TATATTTATATT
1338 TTATAATCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 12 0.28
36 20 0.47
37 4 0.09
38 7 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (35 bp):
TATATTTATATTATATTTATAATTTTATATTATAT
Found at i:5567 original size:20 final size:20
Alignment explanation
Indices: 5535--5572 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5525 TTATTTCATA
*
5535 ATTTTTTACTTAATAAATAT
1 ATTTTTTACTTAAAAAATAT
5555 ATTTTATTA-TTAAAAAAT
1 ATTTT-TTACTTAAAAAAT
5573 CTAAAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTTACTTAAAAAATAT
Found at i:5717 original size:175 final size:171
Alignment explanation
Indices: 5522--6064 Score: 536
Period size: 175 Copynumber: 3.1 Consensus size: 171
5512 TTTTTTCAAT
*
5522 TTATTATTTCATAATTTTTTACTTAATAAATATATTTTATTATTAAAAAATCTAAAATTACTTAG
1 TTATTATTTCATAATTTTTTACTTAATAAATATATTTTATTATTAAAATATCTAAAATTACTTAG
* * * *
5587 TAATATTTTTAAAAATATTAAAATCTAAAATTATATAAAATAAATTTTTTATGCTTAAGAAACTA
66 TAA-ATATTTAAAAATTTTAAAATCTAAAATTATGTAAAATAAATTTTTT-TGCTTGAGAAACTA
* * *
5652 TTGTAGTTTAATACGAAAGTGCCAATATATATTTTTCTTTGAGAC
129 TTGTATTTTAATACAAAAGTGTCAAT-TAT-TTTTTCTTTGAGAC
* * * * * * *
5697 TTATTATTTCGTAATTTTTTAATTAAGTAAATACATTTTATTATTAAAGTTTTTAAAATTATCTG
1 TTATTATTTCATAATTTTTTACTTAA-TAAATATATTTTATTATTAAAATATCTAAAATTA-CTT
* * * * *** * *
5762 A-TAAATATTTAAAACTTTTAAGATATAAAATTTTGTTTCACAAAATTTTTTGACTTGAGAAACT
64 AGTAAATATTTAAAAATTTTAAAATCTAAAATTATGTAAAATAAATTTTTTTG-CTTGAGAAACT
* * *
5826 ATTGTATTTTAATA-AAAAATATTAATTTATTTTTTCTTTGAGAC
128 ATTGTATTTTAATACAAAAGTGTCAA-TTATTTTTTCTTTGAGAC
* * *** * *
5870 TTAATATTTCATAATTTCTTAACTCGGTAAATATATTTTATTATCAAAATA-CATAAAATTATTT
1 TTATTATTTCATAATTT-TTTACTTAATAAATATATTTTATTATTAAAATATC-TAAAATTACTT
** *
5934 AGTAAATATTTAAAAATTTTAAAATCTAAAATTATGTAAAATGATTTTTTGTTTGTTTGAGAAAC
64 AGTAAATATTTAAAAATTTTAAAATCTAAAATTATGTAAAAT-AAATTTT-TTTGCTTGAGAAAC
* ** * * * *
5999 TGTCCTATTTTACTACAAAAGAGTCAATTATGTTTTTCTTTAAAAC
127 TATTGTATTTTAATACAAAAGTGTCAATTAT-TTTTTCTTTGAGAC
*
6045 TTATTATTT-GTAATTTTTTA
1 TTATTATTTCATAATTTTTTA
6065 ATCTGACAAT
Statistics
Matches: 291, Mismatches: 66, Indels: 24
0.76 0.17 0.06
Matches are distributed among these distances:
172 2 0.01
173 92 0.32
174 49 0.17
175 113 0.39
176 32 0.11
177 3 0.01
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (171 bp):
TTATTATTTCATAATTTTTTACTTAATAAATATATTTTATTATTAAAATATCTAAAATTACTTAG
TAAATATTTAAAAATTTTAAAATCTAAAATTATGTAAAATAAATTTTTTTGCTTGAGAAACTATT
GTATTTTAATACAAAAGTGTCAATTATTTTTTCTTTGAGAC
Found at i:6405 original size:14 final size:13
Alignment explanation
Indices: 6385--6425 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
6375 AGCATAAAAA
6385 TTTATTTTAATAT
1 TTTATTTTAATAT
6398 TTTAATTTTAAT-T
1 TTT-ATTTTAATAT
6411 TATT-TTTTAATAT
1 T-TTATTTTAATAT
6424 TT
1 TT
6426 ATAAGATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.32
13 7 0.28
14 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTTAATAT
Found at i:12059 original size:16 final size:17
Alignment explanation
Indices: 12040--12076 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12030 AAAATATATT
12040 TTTAAAATA-ATAAAAA
1 TTTAAAATACATAAAAA
12056 TTT-AAATACATAAAAA
1 TTTAAAATACATAAAAA
*
12072 ATTAA
1 TTTAA
12077 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 12 0.67
17 1 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTAAAATACATAAAAA
Found at i:12090 original size:20 final size:19
Alignment explanation
Indices: 12065--12137 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
12055 ATTTAAATAC
12065 ATAAAAAATTAATTTTTTAA
1 ATAAAAAATT-ATTTTTTAA
12085 ATAAAAATACTT-TTTATTTAA
1 ATAAAAA-A-TTATTT-TTTAA
** *
12106 ATTATTAAATTATAATTTTAA
1 A-TAAAAAATTAT-TTTTTAA
12127 ATAAAAAATTA
1 ATAAAAAATTA
12138 AATATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 20 0.48
21 15 0.36
22 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAAAATTATTTTTTAA
Found at i:14267 original size:2 final size:2
Alignment explanation
Indices: 14260--14288 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14250 CCAAAAAGAG
14260 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 A
14289 AAATGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14894 original size:16 final size:16
Alignment explanation
Indices: 14867--14906 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
14857 AAATATCAAA
*
14867 AAAAATATTTAAAATAAT
1 AAAAAT-TTAAAAAT-AT
14885 AAAAATTTAAAAATAT
1 AAAAATTTAAAAATAT
14901 AAAAAT
1 AAAAAT
14907 AATTAAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATTTAAAAATAT
Found at i:19412 original size:2 final size:2
Alignment explanation
Indices: 19400--19436 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19390 ATGGCTGGAA
*
19400 AT AT AT CT 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 AT AT AT A
19437 CACACACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22576 original size:16 final size:16
Alignment explanation
Indices: 22555--22590 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
22545 AAATTTTCTT
22555 TAAATT-TTTTTTAGAA
1 TAAATTATTTTTTA-AA
22571 TAAATTATTTTTTAAA
1 TAAATTATTTTTTAAA
22587 TAAA
1 TAAA
22591 AATGGGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TAAATTATTTTTTAAA
Found at i:22719 original size:23 final size:23
Alignment explanation
Indices: 22693--22741 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
22683 TCAAATTTGT
*
22693 ATTTTTT-TAATAATTTTATTTAA
1 ATTTTTTATAA-AATTTTAATTAA
22716 ATTTTTTATAAAATTTTAATTAA
1 ATTTTTTATAAAATTTTAATTAA
22739 ATT
1 ATT
22742 AACGTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTATAAAATTTTAATTAA
Found at i:23696 original size:2 final size:2
Alignment explanation
Indices: 23689--23740 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
23679 CTCCCTCCCC
23689 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23731 CT CT CT CT CT
1 CT CT CT CT CT
23741 TTGGAATCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:26390 original size:4 final size:4
Alignment explanation
Indices: 26381--26429 Score: 80
Period size: 4 Copynumber: 11.8 Consensus size: 4
26371 TTATAGAACT
26381 TTTA TTTA TTTA TTTA TTTA TTTA TTTCCA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTT
26430 GAATTTATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 39 0.91
6 4 0.09
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:26437 original size:22 final size:20
Alignment explanation
Indices: 26381--26429 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 20
26371 TTATAGAACT
26381 TTTATTTATTTATTTATTTA
1 TTTATTTATTTATTTATTTA
26401 TTTATTTCCATTTATTTATTTA
1 TTTATTT--ATTTATTTATTTA
26423 TTTATTT
1 TTTATTT
26430 GAATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.26
22 20 0.74
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTATTTATTTATTTA
Found at i:27198 original size:19 final size:19
Alignment explanation
Indices: 27162--27200 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
27152 TATAAGTGAG
* **
27162 TAATTTTTTAAATTTTTAT
1 TAATTATTTAAAAGTTTAT
27181 TAATTATTTAAAAGTTTAT
1 TAATTATTTAAAAGTTTAT
27200 T
1 T
27201 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TAATTATTTAAAAGTTTAT
Found at i:27768 original size:27 final size:27
Alignment explanation
Indices: 27738--27797 Score: 97
Period size: 25 Copynumber: 2.3 Consensus size: 27
27728 ACCAATTCTC
27738 GGATTGCTTGGCTTTCTCTGCTGATGT
1 GGATTGCTTGGCTTTCTCTGCTGATGT
27765 GGATTG--TGGCTTTCTCTGCTGATGT
1 GGATTGCTTGGCTTTCTCTGCTGATGT
*
27790 GGAGTGCT
1 GGATTGCT
27798 GTTGGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 24 0.80
27 6 0.20
ACGTcount: A:0.08, C:0.17, G:0.33, T:0.42
Consensus pattern (27 bp):
GGATTGCTTGGCTTTCTCTGCTGATGT
Found at i:37563 original size:16 final size:17
Alignment explanation
Indices: 37527--37564 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
37517 AAGCTTAAAT
*
37527 TTTATTATTTAAATTTA
1 TTTATTATTTAAATATA
*
37544 TTTATT-TTTTAATATA
1 TTTATTATTTAAATATA
37560 TTTAT
1 TTTAT
37565 ATTCAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTATTTAAATATA
Found at i:39490 original size:2 final size:2
Alignment explanation
Indices: 39473--39507 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39463 CAACTTTAAA
* *
39473 AT AT AT AC AT AC 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 AT AT A
39508 AAGTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Done.