Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1882
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: 18137
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:2385 original size:24 final size:24
Alignment explanation
Indices: 2358--2431 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
2348 TTTATGATAT
2358 AAATATAATATAAAAAAATAATTA
1 AAATATAATATAAAAAAATAATTA
*
2382 AAATAT-ATGGT-AAAAAATAA-TA
1 AAATATAAT-ATAAAAAAATAATTA
* *
2404 TGAATATAATATATAAAAATAATTA
1 -AAATATAATATAAAAAAATAATTA
2429 AAA
1 AAA
2432 CATCATACAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 2 0.05
23 17 0.43
24 19 0.47
25 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATATAATATAAAAAAATAATTA
Found at i:2457 original size:47 final size:47
Alignment explanation
Indices: 2359--2465 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 47
2349 TTATGATATA
* * ** *
2359 AATATAATATAAAAAAATAATTAAAATATATGGTAAAAAATAATATG
1 AATATAATATATAAAAATAATTAAAACATATGACAAAAAATAAAATG
*
2406 AATATAATATATAAAAATAATTAAAACATCAT-ACAAAACATAAAAAT-
1 AATATAATATATAAAAATAATTAAAACAT-ATGACAAAAAAT-AAAATG
2453 AATATAA-ATATAA
1 AATATAATATATAA
2466 TATAAATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
46 6 0.12
47 40 0.77
48 6 0.12
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (47 bp):
AATATAATATATAAAAATAATTAAAACATATGACAAAAAATAAAATG
Found at i:2465 original size:11 final size:11
Alignment explanation
Indices: 2445--2475 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2435 CATACAAAAC
*
2445 ATAAAAATAAT
1 ATAAATATAAT
2456 ATAAATATAAT
1 ATAAATATAAT
2467 ATAAATATA
1 ATAAATATA
2476 CGAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2546 original size:27 final size:27
Alignment explanation
Indices: 2494--2547 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2484 AAAAAATTTA
* *
2494 TTTTATACATTATTAATACATCAAAAT
1 TTTTATAAATTATTAATACATAAAAAT
*
2521 TTTTATAAA-TATATAATACTTAAAAAT
1 TTTTATAAATTAT-TAATACATAAAAAT
2548 AATTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTTATAAATTATTAATACATAAAAAT
Found at i:4248 original size:18 final size:19
Alignment explanation
Indices: 4227--4276 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
4217 AATTAAATTA
4227 TTTATTTAATTTAAT-AAG
1 TTTATTTAATTTAATAAAG
4245 TTTATGTTAA-TTAATAAAG
1 TTTAT-TTAATTTAATAAAG
4264 TTCTATTTGAATT
1 TT-TATTT-AATT
4277 ATTGTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 5 0.19
21 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTATTTAATTTAATAAAG
Found at i:5326 original size:23 final size:22
Alignment explanation
Indices: 5300--5343 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
5290 AATTATAAAT
5300 ATATAAAACACCAAATAAAATAA
1 ATATAAAACACCAAA-AAAATAA
* * *
5323 ATATGAAGCACTAAAAAAATA
1 ATATAAAACACCAAAAAAATA
5344 TAGTAAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (22 bp):
ATATAAAACACCAAAAAAATAA
Found at i:5716 original size:2 final size:2
Alignment explanation
Indices: 5709--5750 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5699 ATTTTTATGA
5709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5751 CAAGGAAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7461 original size:24 final size:25
Alignment explanation
Indices: 7433--7502 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
7423 AATAAAAATT
*
7433 AGCCACAAATTTTGACAAA-CAACA
1 AGCCACAAATTTTGACAAATAAACA
*
7457 AGCCACCAATTTTGACAAATAAACA
1 AGCCACAAATTTTGACAAATAAACA
* *
7482 AGCCTC-CATATTTGACAAATA
1 AGCCACAAAT-TTTGACAAATA
7503 CAAAGGAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACAAATTTTGACAAATAAACA
Found at i:7495 original size:25 final size:25
Alignment explanation
Indices: 7433--7502 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
7423 AATAAAAATT
* *
7433 AGCCACAAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
7457 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
7482 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
7503 CAAAGGAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:7548 original size:27 final size:27
Alignment explanation
Indices: 7487--7557 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
7477 AAACAAGCCT
* *
7487 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
7515 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
7542 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
7558 AATGGGTGAC
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:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:13208 original size:2 final size:2
Alignment explanation
Indices: 13201--13228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13191 AAGCATACCA
13201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13229 TATGATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13434 original size:21 final size:20
Alignment explanation
Indices: 13401--13442 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
13391 TATTTTAAAA
*
13401 ATATTTTTTTA-TTAATATTT
1 ATATTTTTATATTTAA-ATTT
13421 ATATATTTTATATTTAAATTT
1 ATAT-TTTTATATTTAAATTT
13442 A
1 A
13443 AATAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTTTTATATTTAAATTT
Found at i:14350 original size:16 final size:17
Alignment explanation
Indices: 14314--14355 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
14304 ATATTAAATT
14314 TAAAAAATAAATTTAGA
1 TAAAAAATAAATTTAGA
14331 TAAAAAATAATATTT-G-
1 TAAAAAATAA-ATTTAGA
14347 TAAAAAATA
1 TAAAAAATA
14356 GAATAGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.38
17 11 0.46
18 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
TAAAAAATAAATTTAGA
Found at i:14360 original size:18 final size:18
Alignment explanation
Indices: 14314--14360 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
14304 ATATTAAATT
14314 TAAAAAATAAAT-TTAGA
1 TAAAAAATAAATATTAGA
*
14331 TAAAAAAT-AATATTTG-
1 TAAAAAATAAATATTAGA
14347 TAAAAAATAGAATA
1 TAAAAAATA-AATA
14361 GGGCTTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.42
17 11 0.42
18 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
TAAAAAATAAATATTAGA
Found at i:14450 original size:24 final size:24
Alignment explanation
Indices: 14397--14461 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
14387 ATACTCGACC
14397 TAATTTTTAATTATATAATGTATA
1 TAATTTTTAATTATATAATGTATA
* *
14421 TTATTTTTATATCTATAT-AT-TATG
1 TAATTTTTA-AT-TATATAATGTATA
*
14445 TAATTTAT-ATTATATAA
1 TAATTTTTAATTATATAA
14462 AAATAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
24 17 0.50
25 4 0.12
26 5 0.15
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (24 bp):
TAATTTTTAATTATATAATGTATA
Found at i:14777 original size:4 final size:4
Alignment explanation
Indices: 14762--14791 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
14752 TTTGCTTAAA
*
14762 AGGG AAGG AGGG AGGG AGGG AGGG AGGG AG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AG
14792 TTGATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:15150 original size:14 final size:14
Alignment explanation
Indices: 15131--15176 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
15121 GCCGTTAACA
15131 TATATATATATGTG
1 TATATATATATGTG
*
15145 TATATATATATATTG
1 TATATATATAT-GTG
15160 T-TATCATATATGT-
1 TATAT-ATATATGTG
15173 TATA
1 TATA
15177 GTTTTCATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 17 0.63
15 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (14 bp):
TATATATATATGTG
Found at i:15151 original size:16 final size:15
Alignment explanation
Indices: 15130--15170 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
15120 CGCCGTTAAC
15130 ATATATATATATGTGT
1 ATATATATATAT-TGT
15146 ATATATATATATTGT
1 ATATATATATATTGT
15161 -TATCATATAT
1 ATAT-ATATAT
15171 GTTATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 12 0.50
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (15 bp):
ATATATATATATTGT
Found at i:16077 original size:27 final size:27
Alignment explanation
Indices: 16046--16097 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
16036 AAACTTAATC
16046 AATATTAGT-TTTTTATAATAATTATTT
1 AATATTA-TCTTTTTATAATAATTATTT
*
16073 AATATTATCTTTTTATGATAATTAT
1 AATATTATCTTTTTATAATAATTAT
16098 ATGAGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (27 bp):
AATATTATCTTTTTATAATAATTATTT
Done.