Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 222 of 222
Found at i:70698302 original size:3 final size:3
Alignment explanation
Indices: 70698294--70698318 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
70698284 ATGACCTGAC
70698294 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
70698319 CATCATCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:70700555 original size:21 final size:22
Alignment explanation
Indices: 70700514--70700565 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
70700504 TTTCTTTTTG
* *
70700514 TTTATATTTCTTTTTTATTTCTT
1 TTTAT-TTTCTTTTATATTTCAT
70700537 TTTATTTTCTTTTAT-TTTCAT
1 TTTATTTTCTTTTATATTTCAT
*
70700558 TTTGTTTT
1 TTTATTTT
70700566 ACCTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTATTTTCTTTTATATTTCAT
Found at i:70700560 original size:11 final size:10
Alignment explanation
Indices: 70700514--70700565 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
70700504 TTTCTTTTTG
70700514 TTTATATTTCT
1 TTTAT-TTTCT
*
70700525 TTTTTATTTCTT
1 TTTAT-TTTC-T
70700537 TTTATTTTCT
1 TTTATTTTCT
70700547 TTTATTTTCAT
1 TTTATTTTC-T
*
70700558 TTTGTTTT
1 TTTATTTT
70700566 ACCTAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.28
11 21 0.58
12 5 0.14
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTATTTTCT
Found at i:70701171 original size:3 final size:3
Alignment explanation
Indices: 70701165--70701197 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
70701155 TTTGACATTG
70701165 TAT TAT TAT TA- TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
70701198 ATTTTCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:70701176 original size:21 final size:17
Alignment explanation
Indices: 70701165--70701201 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
70701155 TTTGACATTG
70701165 TATTATTATTATATTATT
1 TATTATTATTAT-TTATT
70701183 TATTATTATTATTATATT
1 TATTATTATTATT-TATT
70701201 T
1 T
70701202 TCTATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTATTATTTATT
Found at i:70701248 original size:24 final size:23
Alignment explanation
Indices: 70701196--70701248 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
70701186 TATTATTATT
*
70701196 ATATTTTCTATACATATATTCGC
1 ATATTTTATATACATATATTCGC
*
70701219 ATATTTTATATATCATGTATAT-GC
1 ATATTTTATATA-CATATAT-TCGC
70701243 ATATTT
1 ATATTT
70701249 AACGTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 14 0.54
25 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (23 bp):
ATATTTTATATACATATATTCGC
Found at i:70701391 original size:29 final size:29
Alignment explanation
Indices: 70701358--70701425 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
70701348 TTTCACATGC
* **
70701358 TTTATATTTTATACATACT-TATACATTTT
1 TTTATATTTTAAACATA-TATATACATAAT
*
70701387 TTTAT-TTTGTAAATATATATATACATAAT
1 TTTATATTT-TAAACATATATATACATAAT
70701416 TTTATATTTT
1 TTTATATTTT
70701426 TATTTTATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.12
29 25 0.78
30 3 0.09
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTATATTTTAAACATATATATACATAAT
Found at i:70704773 original size:92 final size:91
Alignment explanation
Indices: 70704616--70704800 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 91
70704606 ATCTAATTTT
70704616 CAGTCCTAAATAGATTAACCAAAGTTAAAGTGGTTTAAATCTAATTTTCAGTCGGTTTCGATAAT
1 CAGTCCTAAATAGATTAACCAAAGTTAAAGTGGTTTAAATCTAATTTTCAGTCGGTTTCGATAAT
70704681 TTCCCTAAATAGTCCACAAACTTTAGG
66 TTCCCTAAATAGTCCACAAACTTT-GG
70704708 CAGTCCTAAATAGATTAACCAAAGTTAAAGTGGTTTAAATCTAATTTTCAGTCGGTTTCGATAAT
1 CAGTCCTAAATAGATTAACCAAAGTTAAAGTGGTTTAAATCTAATTTTCAGTCGGTTTCGATAAT
70704773 TTCCCTAAATAGTCCACAAACTTTGG
66 TTCCCTAAATAGTCCACAAACTTTGG
70704799 CA
1 CA
70704801 ACTTAGAACA
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 4 0.04
92 89 0.96
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (91 bp):
CAGTCCTAAATAGATTAACCAAAGTTAAAGTGGTTTAAATCTAATTTTCAGTCGGTTTCGATAAT
TTCCCTAAATAGTCCACAAACTTTGG
Found at i:70706027 original size:19 final size:20
Alignment explanation
Indices: 70705995--70706033 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
70705985 CGAAGTGTTT
*
70705995 AAAAAGTTATTAATATTTAA
1 AAAAAATTATTAATATTTAA
70706015 AAAAAATTA-TAATATTTAA
1 AAAAAATTATTAATATTTAA
70706034 TATTCCAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAAAATTATTAATATTTAA
Found at i:70706651 original size:2 final size:2
Alignment explanation
Indices: 70706644--70706676 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
70706634 TCTTAACCAG
*
70706644 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
70706677 TTACCATACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:70712462 original size:15 final size:15
Alignment explanation
Indices: 70712442--70712471 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
70712432 TGTTAATTTC
*
70712442 ATAATTACTTTTTTT
1 ATAATTAATTTTTTT
70712457 ATAATTAATTTTTTT
1 ATAATTAATTTTTTT
70712472 TTCCCTATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATAATTAATTTTTTT
Found at i:70720188 original size:359 final size:355
Alignment explanation
Indices: 70719528--70720193 Score: 1099
Period size: 359 Copynumber: 1.9 Consensus size: 355
70719518 TTTTATTGTC
*
70719528 TCCTGGTTTTCCCTTTTTCAACTAGTAAAAACATTATATTTGTTGAGGGAATAAGAAAACACTAA
1 TCCTGGTTTTCCCTTTTTCAACTAGTAAAAACATTATATTTGTTGAGGGAATAAGAAAAAACTAA
**
70719593 TTAAATCATACTGAGTTTTTTTTTAAAAAAAAGCCCAAGTGGTAATATCAAAGAAAAAAAAATTC
66 TTAAATCATACTGAGTTTTTTTGAAAAAAAAAGCCCAAGTGGTAATATCAAAGAAAAAAAAATTC
* *
70719658 TGGAATGAAATGGAAATGAAATGAAAGATCGGAGAGGGTATCGTATCGTCAAAGAGAAGCTCGGG
131 TGGAATGAAAAGGAAATGAAATGAAAGATCGGAGACGGTATCGTATCGTCAAAGAGAAGCTCGGG
*
70719723 GCATTAGGAAAATTACTGGGACTGAAAGACTATTGAGGAAATTAATTAAAAAATCTATTTTTTTT
196 GCATTAGGAAAATTACTGGGACTGAAAGACTATTGAGGAAAATAATTAAAAAATCTATTTTTTTT
* *
70719788 TCTTGTTCTAGTTAATTTTCGTTCTTTTTCTGCGTCAGGGATATCCCTGTTTTAACCTGCTTCGG
261 TCTTGTTCCAGTTAATTTTCGTTCTTTTTC-GCGCCAGGGATATCCCTGTTTTAACCTGCTTCGG
70719853 AATAAGCTATTTTTTGAATATTCACATCGTA
325 AATAAGCTATTTTTTGAATATTCACATCGTA
70719884 TCCTGGTTTTCCCTTTTTCAACTAGTAAAAACATTATATTTGTTGAGGGAATAAGAAAAAAACTA
1 TCCTGGTTTTCCCTTTTTCAACTAGTAAAAACATTATATTTGTTGAGGGAATAAG-AAAAAACTA
* * *
70719949 ATTGAATCATACTGAGTTTTTTTAAGAAAAAAAAAGGCCTAAGTGGTAATTTCAAAGAAAAAAAA
65 ATTAAATCATACTGAGTTTTTTT--GAAAAAAAAA-GCCCAAGTGGTAATATCAAAGAAAAAAAA
*
70720014 ATTCTGGAATGAAAAGGAAATGAAATG-AAGATCGGAGACGGTATCGTATTGTCAAAGAGAAGCT
127 ATTCTGGAATGAAAAGGAAATGAAATGAAAGATCGGAGACGGTATCGTATCGTCAAAGAGAAGCT
70720078 CGGGGCATTAGGAAAATTACTGGGACTGAATA-ACTATT-ACGGAAAATAATTAAAAAAATCTA-
192 CGGGGCATTAGGAAAATTACTGGGACTGAA-AGACTATTGA-GGAAAATAATT-AAAAAATCTAT
70720140 TTTTTTTTCTTGTTCCAGTTAATTTTCGTTCTTATTTC-CAGCCAGGGATATCCC
254 TTTTTTTTCTTGTTCCAGTTAATTTTCGTTCTT-TTTCGC-GCCAGGGATATCCC
70720194 GCTGATATCC
Statistics
Matches: 289, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
356 55 0.19
357 30 0.10
358 2 0.01
359 134 0.46
360 68 0.24
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (355 bp):
TCCTGGTTTTCCCTTTTTCAACTAGTAAAAACATTATATTTGTTGAGGGAATAAGAAAAAACTAA
TTAAATCATACTGAGTTTTTTTGAAAAAAAAAGCCCAAGTGGTAATATCAAAGAAAAAAAAATTC
TGGAATGAAAAGGAAATGAAATGAAAGATCGGAGACGGTATCGTATCGTCAAAGAGAAGCTCGGG
GCATTAGGAAAATTACTGGGACTGAAAGACTATTGAGGAAAATAATTAAAAAATCTATTTTTTTT
TCTTGTTCCAGTTAATTTTCGTTCTTTTTCGCGCCAGGGATATCCCTGTTTTAACCTGCTTCGGA
ATAAGCTATTTTTTGAATATTCACATCGTA
Found at i:70720386 original size:16 final size:15
Alignment explanation
Indices: 70720366--70720413 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
70720356 CCTATTCTAT
*
70720366 GGATATCCCGGCTTT
1 GGATATCCCGGCTTA
* *
70720381 GTGATATCCCGCCTAA
1 G-GATATCCCGGCTTA
70720397 GGATATCCCGGCTTA
1 GGATATCCCGGCTTA
70720412 GG
1 GG
70720414 TTTATCTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (15 bp):
GGATATCCCGGCTTA
Found at i:70723714 original size:78 final size:78
Alignment explanation
Indices: 70723585--70723735 Score: 221
Period size: 78 Copynumber: 1.9 Consensus size: 78
70723575 CTCATATTCT
* * * *
70723585 ACCATTAAACCGTGATCCCTTGATCTCACCAACTGGGAGAGTCGGTGATCATGTTGATAATGATC
1 ACCATTAAACCCTGATCCCTTGATCGCACCAACTAGGAGAGTCGGTGATCATGTTGATAACGATC
*
70723650 ACTATGGAGTTCG
66 ACCATGGAGTTCG
* * * *
70723663 ACCATTAAACCCTGATCCCTTGATCGCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCCTGATCCCTTGATCGCACCAACTAGGAGAGTCGGTGATCATGTTGATAACGATC
70723728 ACCATGGA
66 ACCATGGA
70723736 CTTTGTGTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (78 bp):
ACCATTAAACCCTGATCCCTTGATCGCACCAACTAGGAGAGTCGGTGATCATGTTGATAACGATC
ACCATGGAGTTCG
Found at i:70727897 original size:16 final size:16
Alignment explanation
Indices: 70727876--70727907 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
70727866 ATTTGGCTTA
70727876 CTGTTTTCCTCTTTTT
1 CTGTTTTCCTCTTTTT
70727892 CTGTTTTCCTCTTTTT
1 CTGTTTTCCTCTTTTT
70727908 TATATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (16 bp):
CTGTTTTCCTCTTTTT
Done.