Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold895
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: 25321
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:331 original size:40 final size:39
Alignment explanation
Indices: 248--429 Score: 185
Period size: 39 Copynumber: 4.6 Consensus size: 39
238 TTGAATGATG
* * *
248 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
286 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
* *
327 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
*
366 TCC-GGTTATAGTCCCGAAGGCA-TTGTGCGAGTTACT-AT
1 TCCGGGCTA-AGT-CCGAAGGCATTTGTGCGAGTTACTAAT
* *
404 AACCGGGCTATGTCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCGAAGGCATTTG
430 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
38 14 0.12
39 61 0.51
40 36 0.30
41 9 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:421 original size:78 final size:80
Alignment explanation
Indices: 249--429 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 80
239 TGAATGATGT
*
249 CCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
*
313 TGCGAGATACTAATT
66 TGCGAGATACTAATA
* * * * *
328 CCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGG-TTATAG-TCCCGAAGGCA-T
1 CCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTA-AGAT-CCGAAGGCATT
*
389 TGTGCGAGTTACT-ATAA
64 TGTGCGAGATACTAAT-A
*
406 CCGGGCTATGTCCGAAGGCATTTG
1 CCGGGCTAAGTCCGAAGGCATTTG
430 AACGAGGAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 38 0.43
79 41 0.47
80 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAATA
Found at i:447 original size:78 final size:79
Alignment explanation
Indices: 300--451 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 79
290 GGACTAAGAT
* ** *
300 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
365 ATCCGGTTATAGTC
66 ATCCGGTTATAGTC
* * *
379 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAG-GAGCT
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGA-CT
*
441 ATATCCGGTTA
64 AAATCCGGTTA
452 AATTCCGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
77 3 0.05
78 51 0.81
79 9 0.14
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGTTATAGTC
Found at i:8207 original size:79 final size:81
Alignment explanation
Indices: 8071--8255 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
8061 TTGAATGATG
* *
8071 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGAATT
8135 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
8150 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGAA
*
8212 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
8230 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
8256 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGAATT
TGTGCGAGATACTATA
Found at i:8269 original size:40 final size:40
Alignment explanation
Indices: 8072--8255 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
8062 TGAATGATGT
* * * *
8072 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
8112 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
8152 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
8190 TCCGGGTTAAGTCCCGAAGGAATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
8231 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
8256 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:8277 original size:79 final size:79
Alignment explanation
Indices: 8072--8288 Score: 192
Period size: 79 Copynumber: 2.7 Consensus size: 79
8062 TGAATGATGT
** * * * ** *
8072 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGAATT
*
8135 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
8152 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGAATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGAATTTGT
*
8217 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
8231 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
8289 TACGTGATTT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.03
79 70 0.61
80 42 0.37
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGAATTTGT
GCGAGATACTAATA
Found at i:10065 original size:18 final size:18
Alignment explanation
Indices: 10044--10101 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
10034 TATATACTTA
10044 CTTACTAAGCTATATAAG
1 CTTACTAAGCTATATAAG
* *
10062 CTTACTTA--TATACTTA-
1 CTTACTAAGCTATA-TAAG
10078 CTTACTAAGCTATATAAG
1 CTTACTAAGCTATATAAG
10096 CTTACT
1 CTTACT
10102 TTCTTTTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.34
17 4 0.12
18 17 0.53
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (18 bp):
CTTACTAAGCTATATAAG
Found at i:10076 original size:34 final size:34
Alignment explanation
Indices: 10033--10102 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
10023 TTGTTATTAT
10033 TTATATACTTACTTACTAAGCTATATAAGCTTAC
1 TTATATACTTACTTACTAAGCTATATAAGCTTAC
10067 TTATATACTTACTTACTAAGCTATATAAGCTTAC
1 TTATATACTTACTTACTAAGCTATATAAGCTTAC
10101 TT
1 TT
10103 TCTTTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (34 bp):
TTATATACTTACTTACTAAGCTATATAAGCTTAC
Found at i:14234 original size:40 final size:40
Alignment explanation
Indices: 14151--14367 Score: 205
Period size: 40 Copynumber: 5.5 Consensus size: 40
14141 AAGCCAAGTA
* * * *
14151 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATA-ATAACTCGCACAAATG
* * *
14189 CCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATG
* ***
14229 CCTTCGAGACTTAGCATAGATATAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATG
* *
14269 CCTTCGGGACTTAGCCCTGAATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GGATATAATAACTCGCACAAATG
* *
14310 CCTTCGGGACTTAGCCC-GA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAATAACT--CGCACAAATG
14350 CCTTC-GGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
14368 TTATCATCCA
Statistics
Matches: 148, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 12 0.08
39 33 0.22
40 62 0.42
41 41 0.28
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATG
Found at i:14315 original size:81 final size:79
Alignment explanation
Indices: 14177--14324 Score: 215
Period size: 81 Copynumber: 1.8 Consensus size: 79
14167 GGATATAGCT
* * *
14177 ACTCGCTCAATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGAGACTTA
1 ACTCGCACAATGCCTTCGGGACATAGCCCGAATATAATAACTCACACAAATGCCTTCGAGACTTA
14242 GCATAGATATAATA
66 GCATAGATATAATA
* * * *
14256 ACTCGCACAAATGCCTTCGGGACTTAGCCCTGAATGTAATAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCAC-AATGCCTTCGGGACATAGCCC-GAATATAATAACTCACACAAATGCCTTCGAGACT
14321 TAGC
64 TAGC
14325 CCGAACTAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 7 0.12
80 20 0.33
81 33 0.55
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (79 bp):
ACTCGCACAATGCCTTCGGGACATAGCCCGAATATAATAACTCACACAAATGCCTTCGAGACTTA
GCATAGATATAATA
Found at i:14349 original size:81 final size:80
Alignment explanation
Indices: 14177--14366 Score: 210
Period size: 81 Copynumber: 2.4 Consensus size: 80
14167 GGATATAGCT
* * * *
14177 ACTCGCTC-AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGAGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAATAACTCACACAAATGCCTTCGAGACTT
*
14241 AGCATAGATATAATA
66 AGCACAGATATAATA
* * *
14256 ACTCGCACAAATGCCTTCGGGACTTAGCCCTGAATGTAATAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC-GAATATAATAACTCACACAAATGCCTTCGAGACT
* * *
14321 TAGC-CCGA-ACTAGTC
65 TAGCACAGATA-TAATA
14336 ACTAGCGCA-AAATGCCTTC-GGACTTAGCCCG
1 ACT--CGCACAAATGCCTTCGGGACTTAGCCCG
14367 GTTATCATCC
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
79 9 0.09
80 39 0.41
81 43 0.45
82 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAATAACTCACACAAATGCCTTCGAGACTT
AGCACAGATATAATA
Found at i:22592 original size:41 final size:40
Alignment explanation
Indices: 22505--22684 Score: 160
Period size: 41 Copynumber: 4.5 Consensus size: 40
22495 GCTACTCCTC
* * * *
22505 AATGCCTTCGGGACATAGCCC--ATATATAGAACTCACACA
1 AATGCCTTCGGGACTTAGCCCGAATGTA-ATAACTCGCACA
* *
22544 AATGCCTTCGAGACTTAGCCGGATATG-AATAACTCGCCACA
1 AATGCCTTCGGGACTTAGCCCGA-ATGTAATAACTCG-CACA
*
22585 AATGCCTTCGGGACTTAGCCCGAATGTAATAACTCGCACT
1 AATGCCTTCGGGACTTAGCCCGAATGTAATAACTCGCACA
* * *
22625 AA--CCTTCGGGACTTAGCCCAGAA-CTAGTCACTAGCGCA-A
1 AATGCCTTCGGGACTTAGCCC-GAATGTAATAACT--CGCACA
22664 AATGCCTTC-GGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
22685 CCGTTATCAT
Statistics
Matches: 118, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
38 23 0.19
39 24 0.20
40 29 0.25
41 40 0.34
42 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGAATGTAATAACTCGCACA
Found at i:23856 original size:9 final size:9
Alignment explanation
Indices: 23842--23866 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23832 TCAAGCTAAC
23842 AAATAAATA
1 AAATAAATA
23851 AAATAAATA
1 AAATAAATA
23860 AAATAAA
1 AAATAAA
23867 AACATGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Done.