Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold528
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: 91176
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.30
Warning! 6513 characters in sequence are not A, C, G, or T
Found at i:1314 original size:5 final size:5
Alignment explanation
Indices: 1304--1347 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
1294 GATTATGTTT
1304 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -TATA T
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T
1348 ACATAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 22 0.63
6 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:1329 original size:19 final size:19
Alignment explanation
Indices: 1305--1347 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1295 ATTATGTTTT
1305 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
1324 TATATTATATTATATTATA
1 TATATTATATTATATTATA
1343 TATAT
1 TATAT
1348 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:1377 original size:15 final size:15
Alignment explanation
Indices: 1357--1398 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1347 TACATAAAAC
*
1357 AAAAGAAAGAATAGA
1 AAAAGAAAGAAAAGA
1372 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
1387 AACAGAATAGAA
1 AAAAGAA-AGAA
1399 GAGACGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:1455 original size:4 final size:4
Alignment explanation
Indices: 1448--1475 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1438 GAGAAGGAAG
1448 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1476 AAGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:8331 original size:24 final size:24
Alignment explanation
Indices: 8304--8355 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
8294 TTAGTAAGTC
*
8304 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
8328 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
8352 AAAT
1 AAAT
8356 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13593 original size:29 final size:30
Alignment explanation
Indices: 13534--13591 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
13524 TCCGAGCCTT
*
13534 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
13564 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
13592 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:13821 original size:13 final size:13
Alignment explanation
Indices: 13803--13834 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13793 TTTCCAGCAA
13803 TTATGAATTTATT
1 TTATGAATTTATT
13816 TTATGAATTTATT
1 TTATGAATTTATT
*
13829 TGATGA
1 TTATGA
13835 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:16335 original size:8 final size:7
Alignment explanation
Indices: 16287--16333 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
16277 TACATTAATA
16287 CATTTCC
1 CATTTCC
16294 CATTTCC
1 CATTTCC
16301 C--TTCC
1 CATTTCC
* *
16306 C-CTCCC
1 CATTTCC
16312 CATTTCC
1 CATTTCC
16319 CATTTCC
1 CATTTCC
16326 CATTTCC
1 CATTTCC
16333 C
1 C
16334 CAACCCCGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.14
6 4 0.11
7 26 0.74
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.38
Consensus pattern (7 bp):
CATTTCC
Found at i:17169 original size:28 final size:29
Alignment explanation
Indices: 17138--17194 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
17128 TTAATAATTT
* **
17138 TTAATAAAAATGTGTATT-AAGGACTAAA
1 TTAAGAAAAATGTAAATTGAAGGACTAAA
*
17166 TTAAGAAAAGTGTAAATTGAAGGACTAAA
1 TTAAGAAAAATGTAAATTGAAGGACTAAA
17195 ATGTGAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.28
Consensus pattern (29 bp):
TTAAGAAAAATGTAAATTGAAGGACTAAA
Found at i:17473 original size:8 final size:8
Alignment explanation
Indices: 17460--17484 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17450 GGAAGTCAAA
17460 AGTAGTCG
1 AGTAGTCG
17468 AGTAGTCG
1 AGTAGTCG
17476 AGTAGTCG
1 AGTAGTCG
17484 A
1 A
17485 CTGTGTCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24
Consensus pattern (8 bp):
AGTAGTCG
Found at i:19547 original size:23 final size:23
Alignment explanation
Indices: 19521--19650 Score: 98
Period size: 24 Copynumber: 5.5 Consensus size: 23
19511 TGATGCTTAA
19521 ATGCTGCCCAATTTGTTACATAT
1 ATGCTGCCCAATTTGTTACATAT
** * * * *
19544 ATGCTGTTCAATTTTGATGCCTAA
1 ATGCTGCCCAA-TTTGTTACATAT
19568 ATGCTGCCCAATTTGTTACATAT
1 ATGCTGCCCAATTTGTTACATAT
* * * * *
19591 ATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGCCCAA-TTTGTTACATAT
* * *
19615 ATGCTACCCAAATTGTTGTATATAT
1 ATGCTGCCCAATTTG-T-TACATAT
19640 ATGCTGCCCAA
1 ATGCTGCCCAA
19651 ATTGATGAAT
Statistics
Matches: 77, Mismatches: 26, Indels: 6
0.71 0.24 0.06
Matches are distributed among these distances:
23 30 0.39
24 34 0.44
25 13 0.17
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTACATAT
Found at i:19571 original size:24 final size:24
Alignment explanation
Indices: 19504--19663 Score: 114
Period size: 23 Copynumber: 6.8 Consensus size: 24
19494 NNNNNNNNNN
*
19504 CCAATTTTGATGCTTAAATGCTGC
1 CCAATTTTGATGCATAAATGCTGC
* * * *
19528 CCAA-TTTGTTACATATATGCTGT
1 CCAATTTTGATGCATAAATGCTGC
* *
19551 TCAATTTTGATGCCTAAATGCTGC
1 CCAATTTTGATGCATAAATGCTGC
* * * *
19575 CCAA-TTTGTTACATATATGCTGT
1 CCAATTTTGATGCATAAATGCTGC
* *
19598 CCAATTTTGATGCTTAAATGCTAC
1 CCAATTTTGATGCATAAATGCTGC
*
19622 CCAAATTGTTGTAT--ATATATGCTGC
1 CC-AATT-TTG-ATGCATAAATGCTGC
* *
19647 CCAA-ATTGATGAATAAA
1 CCAATTTTGATGCATAAA
19664 AGTTGTTCAA
Statistics
Matches: 101, Mismatches: 28, Indels: 15
0.70 0.19 0.10
Matches are distributed among these distances:
21 2 0.02
22 3 0.03
23 39 0.39
24 38 0.38
25 14 0.14
26 3 0.03
27 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (24 bp):
CCAATTTTGATGCATAAATGCTGC
Found at i:19574 original size:47 final size:47
Alignment explanation
Indices: 19504--19650 Score: 222
Period size: 47 Copynumber: 3.1 Consensus size: 47
19494 NNNNNNNNNN
19504 CCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGT
1 CCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGT
* *
19551 TCAATTTTGATGCCTAAATGCTGCCCAATTTGTTACATATATGCTGT
1 CCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGT
* * * *
19598 CCAATTTTGATGCTTAAATGCTACCCAAATTGTTGTATATATATGCTGC
1 CCAATTTTGATGCTTAAATGCTGCCCAATTTG-T-TACATATATGCTGT
19647 CCAA
1 CCAA
19651 ATTGATGAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 73 0.81
48 1 0.01
49 16 0.18
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (47 bp):
CCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGT
Found at i:25314 original size:3 final size:3
Alignment explanation
Indices: 25306--25364 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
25296 GTATGAATGA
** * * *
25306 AAT AAT AAT AAT AAT AAT GTT AAT AAT GAT AAC AAT AAAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
25352 AA- AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT
25365 GTAGCATAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:26604 original size:22 final size:21
Alignment explanation
Indices: 26583--26630 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
26573 AAGTGCAATA
* *
26583 ATTAAATATTATTAAATTAAT
1 ATTAAATACTATTAAAATAAT
26604 A--AAATACTATTAAAATAATT
1 ATTAAATACTATTAAAATAA-T
26624 ATTAAAT
1 ATTAAAT
26631 TAAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 15 0.68
20 2 0.09
21 1 0.05
22 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAAATACTATTAAAATAAT
Found at i:26608 original size:19 final size:19
Alignment explanation
Indices: 26579--26622 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
26569 ACACAAGTGC
* *
26579 AATAATTAAATATTATTAA
1 AATAATAAAATACTATTAA
*
26598 ATTAATAAAATACTATTAA
1 AATAATAAAATACTATTAA
26617 AATAAT
1 AATAAT
26623 TATTAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAATAAAATACTATTAA
Found at i:27463 original size:74 final size:73
Alignment explanation
Indices: 27318--27461 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
27308 TATCTACTTG
* * *
27318 GTACTTAAGCTTTTTTTGGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGTGGTACT
1 GTACTTAAACTTTTTTTAGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGAGGTACT
27383 TTTTTTAA
66 TTTTTTAA
* * * * *
27391 GTACTTAAACTTTCTTTTAGACCTAATTGGTACTTGAACTTGAAAACC-TAAATCAAAGAGGTAT
1 GTACTTAAACTTT-TTTTAGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGAGGTAC
27455 TTTTTTT
65 TTTTTTT
27462 TAGATCCAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 32 0.52
74 30 0.48
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (73 bp):
GTACTTAAACTTTTTTTAGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGAGGTACT
TTTTTTAA
Found at i:28201 original size:31 final size:31
Alignment explanation
Indices: 28164--28240 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
28154 TATTTTTATT
* *
28164 TTTTTGTCTAAATTCCTTTTTCGGATCTATA
1 TTTTTGTCTAAACTCATTTTTCGGATCTATA
28195 TTTTTGTCTAAACTCATTTTTCGGATCTATA
1 TTTTTGTCTAAACTCATTTTTCGGATCTATA
28226 TTTTTGT-TCAAACTC
1 TTTTTGTCT-AAACTC
28241 TCTCACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (31 bp):
TTTTTGTCTAAACTCATTTTTCGGATCTATA
Found at i:47246 original size:23 final size:23
Alignment explanation
Indices: 47216--47262 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
47206 TCATAGTACT
47216 GTAAAATATAATGTACATTTATC
1 GTAAAATATAATGTACATTTATC
47239 GTAAAATATAATGTACATTTATC
1 GTAAAATATAATGTACATTTATC
47262 G
1 G
47263 ATACGTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (23 bp):
GTAAAATATAATGTACATTTATC
Found at i:58266 original size:3 final size:3
Alignment explanation
Indices: 58258--58301 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
58248 ATTCTTTATA
58258 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58302 AAGAAACTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:71954 original size:19 final size:20
Alignment explanation
Indices: 71930--71975 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
71920 ATAATGATCG
71930 AAAATTAAAT-AAAAGCTAT
1 AAAATTAAATCAAAAGCTAT
* **
71949 AAAATTATATCAATTGCTAT
1 AAAATTAAATCAAAAGCTAT
71969 AAAATTA
1 AAAATTA
71976 CACAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTAAATCAAAAGCTAT
Found at i:75352 original size:29 final size:30
Alignment explanation
Indices: 75308--75366 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
75298 AAATTGAATC
* *
75308 AAATCAAATTATCATATGTGAA-ATTGCACA
1 AAATCAAAGTATCATATAT-AACATTGCACA
75338 AAATCAAAGT-TCATATATAACATTGCACA
1 AAATCAAAGTATCATATATAACATTGCACA
75367 TAGACTCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.58
30 9 0.35
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATCAAAGTATCATATATAACATTGCACA
Found at i:77180 original size:23 final size:23
Alignment explanation
Indices: 77154--77197 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
77144 TAAATATTAT
77154 TTTATTAACATTTTATTTAGATA
1 TTTATTAACATTTTATTTAGATA
**
77177 TTTATTATTATTTTATTTAGA
1 TTTATTAACATTTTATTTAGA
77198 AAATGGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAACATTTTATTTAGATA
Found at i:79742 original size:16 final size:16
Alignment explanation
Indices: 79696--79744 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
79686 AAAACATGGA
79696 TTTTATTTTATTAGTAT
1 TTTTATTTTATTA-TAT
*
79713 TTTT-TATGTATTATAT
1 TTTTAT-TTTATTATAT
*
79729 TTTTATTTTTTTATAT
1 TTTTATTTTATTATAT
79745 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTATTTTATTATAT
Found at i:80441 original size:29 final size:29
Alignment explanation
Indices: 80385--80441 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
80375 ACACAAAAAA
****
80385 TATTTTAAAAATAAAAAATATTTTTAAAT
1 TATTTTAAAAATAAAAAATAAAAATAAAT
*
80414 TATTTTAAAATTAAAAAATAAAAATAAA
1 TATTTTAAAAATAAAAAATAAAAATAAA
80442 AAATATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TATTTTAAAAATAAAAAATAAAAATAAAT
Done.