Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2855
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: 70927
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:3339 original size:29 final size:28
Alignment explanation
Indices: 3293--3348 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
3283 ACTTAATTGT
* *
3293 GAACCCTACTTGTTTGAAATCCTAGGTGC
1 GAACCCTACTTGTATG-AACCCTAGGTGC
*
3322 GAACCCTGCTTGTATGAACCCTAGGTG
1 GAACCCTACTTGTATGAACCCTAGGTG
3349 TGTGCACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (28 bp):
GAACCCTACTTGTATGAACCCTAGGTGC
Found at i:10268 original size:40 final size:40
Alignment explanation
Indices: 10224--10447 Score: 226
Period size: 40 Copynumber: 5.6 Consensus size: 40
10214 GCTCCTCGTT
*
10224 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
10264 CAAATGCCTTCGGGACTTAACCCGGATT-TTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
10304 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * * *
10344 CAAATGCCTTC-GGATCTTAGTCCGGATAT-CTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAACTCGCA
* * * * *
10383 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
*
10424 CAAA-GACTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
10448 ACATCATTCA
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
39 42 0.26
40 108 0.66
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:10328 original size:80 final size:79
Alignment explanation
Indices: 10224--10448 Score: 251
Period size: 80 Copynumber: 2.8 Consensus size: 79
10214 GCTCCTCGTT
* *
10224 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
10289 ATTTTGTAACTCGCA
66 A-TATCTAACTCGCA
* * *
10304 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
*
10367 GGATATCTATCTCGCA
64 GGATATCTAACTCGCA
* * * * * *
10383 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GACTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
10446 GGA
64 GGA
10449 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
78 4 0.03
79 51 0.42
80 65 0.53
81 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATCTAACTCGCA
Found at i:13908 original size:94 final size:92
Alignment explanation
Indices: 13705--13926 Score: 243
Period size: 94 Copynumber: 2.4 Consensus size: 92
13695 GGTAAGGTGT
*
13705 CGATGCCATGTCCCAGACATGGTCTTACACTGACCA-TCATCTCGTAGCCAATGCATATCCCAAA
1 CGATG-CATGTCCCAGACAT-GTCTTACACT-AGCACTCATCTCGTAGCCAATGCATATCCCAAA
* *
13769 CATGTCTTACACTGGCTTACATCTCGAGGC
63 CATGTCTTACACTAGCTTACATATCGAGGC
* * * ** * *
13799 TGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAGT-GTCGGTGCCATGTCCCAGAC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTC-GTAGCCAATG-CATATCCCAAAC
* *
13863 ATGGTCTTACACTAGCTTCCATAAT-GTGGC
64 AT-GTCTTACACTAGCTTACAT-ATCGAGGC
*
13893 CGATGCATGTCCCAGAAATGTCTTACACTAGCAC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCAC
13927 ATACAAGTGA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
91 3 0.03
92 20 0.18
93 28 0.26
94 57 0.52
95 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (92 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCGTAGCCAATGCATATCCCAAACAT
GTCTTACACTAGCTTACATATCGAGGC
Found at i:13924 original size:46 final size:45
Alignment explanation
Indices: 13705--13924 Score: 135
Period size: 46 Copynumber: 4.7 Consensus size: 45
13695 GGTAAGGTGT
* * * * *
13705 CGATGCCATGTCCCAGACATGGTCTTACACTGACCAT-CATCTCGTAGC
1 CGATG-CATGTCCCAGAAAT-GTCTTACACT-AGCTTCCATAT-GTGGC
* * * * * *
13753 CAATGCATATCCCA-AACATGTCTTACACTGGCTTACATCTCGAGGC
1 CGATGCATGTCCCAGAA-ATGTCTTACACTAGCTTCCATAT-GTGGC
* * * *
13799 TGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTC-TCA-GT-GT
1 CGATGCATGTCCCAGAAATGTCTTACACTAGC-TTC--CAT-ATGTGGC
* *
13845 CGGTGCCATGTCCCAGACATGGTCTTACACTAGCTTCCATAATGTGGC
1 CGATG-CATGTCCCAGAAAT-GTCTTACACTAGCTTCCAT-ATGTGGC
13893 CGATGCATGTCCCAGAAATGTCTTACACTAGC
1 CGATGCATGTCCCAGAAATGTCTTACACTAGC
13925 ACATACAAGT
Statistics
Matches: 135, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
45 3 0.02
46 64 0.47
47 44 0.33
48 23 0.17
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGAAATGTCTTACACTAGCTTCCATATGTGGC
Found at i:14603 original size:12 final size:12
Alignment explanation
Indices: 14586--14610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14576 CAAAAATGTA
14586 AAAATCATCAAG
1 AAAATCATCAAG
14598 AAAATCATCAAG
1 AAAATCATCAAG
14610 A
1 A
14611 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:31349 original size:47 final size:47
Alignment explanation
Indices: 31297--31389 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
31287 CCGTGACTAA
31297 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATT
1 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATT
31344 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAAT
1 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAAT
31390 CATTTGAGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (47 bp):
ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATT
Found at i:32698 original size:18 final size:18
Alignment explanation
Indices: 32675--32711 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
32665 GTCCAACAGG
32675 CCTATGTGTAAATTTCGA
1 CCTATGTGTAAATTTCGA
32693 CCTATGTGTAAATTTCGA
1 CCTATGTGTAAATTTCGA
32711 C
1 C
32712 GCTTCAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (18 bp):
CCTATGTGTAAATTTCGA
Found at i:46921 original size:42 final size:42
Alignment explanation
Indices: 46808--46925 Score: 110
Period size: 43 Copynumber: 2.8 Consensus size: 42
46798 CGGAAAGCTC
* ** ** *
46808 ATACAATGCCAACATCCTAGATGTGGTCTTACATGTAATAAA
1 ATACGATGCCAATGTCCTAGACATGGTCTTACATGAAATAAA
* * * * * *
46850 AAATCGATGCCACTGTCCCAGGCAGGGTCTTACATGAAATCAA
1 ATA-CGATGCCAATGTCCTAGACATGGTCTTACATGAAATAAA
*
46893 ATACGATGCCAATGTCCTAGACCTGGTCTTACA
1 ATACGATGCCAATGTCCTAGACATGGTCTTACA
46926 CATAAATTGT
Statistics
Matches: 57, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
42 27 0.47
43 30 0.53
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCTAGACATGGTCTTACATGAAATAAA
Found at i:49312 original size:21 final size:21
Alignment explanation
Indices: 49287--49329 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
49277 GATAGAATAC
49287 ATAAAATACAAATAATTTAAT
1 ATAAAATACAAATAATTTAAT
* *
49308 ATAAAATACAAGTAGTTTAAT
1 ATAAAATACAAATAATTTAAT
49329 A
1 A
49330 GTGATATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAAAATACAAATAATTTAAT
Found at i:56726 original size:48 final size:47
Alignment explanation
Indices: 56650--56818 Score: 232
Period size: 48 Copynumber: 3.6 Consensus size: 47
56640 GTTATATGTG
*
56650 TAACATGGTGCTAAGTGGATATACCACGATTACACTTATTGATACAT
1 TAACGTGGTGCTAAGTGGATATACCACGATTACACTTATTGATACAT
* *
56697 ATAACGTGGTGCTTAGTGGATATACCACGATTACACATATTGATACAT
1 -TAACGTGGTGCTAAGTGGATATACCACGATTACACTTATTGATACAT
* * * *
56745 GTAACGTGGTGCTAAGTGGATATGCCACGGTTACA-TATGTTGATTCAT
1 -TAACGTGGTGCTAAGTGGATATACCACGATTACACT-TATTGATACAT
*
56793 TAACGTGGTGCTATGTGGATATACCA
1 TAACGTGGTGCTAAGTGGATATACCA
56819 TGGTTAAACA
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
47 24 0.22
48 84 0.78
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (47 bp):
TAACGTGGTGCTAAGTGGATATACCACGATTACACTTATTGATACAT
Found at i:56851 original size:37 final size:37
Alignment explanation
Indices: 56795--56868 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
56785 TGATTCATTA
* * *
56795 ACGTGGTGCTATGTGGATATACCATGGTTAAACATGT
1 ACGTGGTGCTAAGTAGATATACCACGGTTAAACATGT
* *
56832 ACGTGGTGCTAAGTAGATATGCCACGGTTATACATGT
1 ACGTGGTGCTAAGTAGATATACCACGGTTAAACATGT
56869 TAATTTGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (37 bp):
ACGTGGTGCTAAGTAGATATACCACGGTTAAACATGT
Found at i:64490 original size:25 final size:25
Alignment explanation
Indices: 64461--64508 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
64451 TTATAACATG
* * *
64461 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
64486 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
64509 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:64559 original size:9 final size:9
Alignment explanation
Indices: 64547--64603 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
64537 TTTGATAAAC
64547 ATGATATGT
1 ATGATATGT
*
64556 ATGATATGCAC
1 ATGATATG--T
*
64567 ATGACATGT
1 ATGATATGT
*
64576 ATGATATGCAC
1 ATGATATG--T
64587 ATGATATGT
1 ATGATATGT
64596 ATGATATG
1 ATGATATG
64604 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:64570 original size:20 final size:20
Alignment explanation
Indices: 64545--64615 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
64535 ATTTTGATAA
64545 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
64565 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
64585 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
64605 ACATGAGATGT
1 ACATGATATGT
64616 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:64592 original size:11 final size:11
Alignment explanation
Indices: 64556--64610 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
64546 CATGATATGT
64556 ATGATATGCAC
1 ATGATATGCAC
* *
64567 ATGACATG--T
1 ATGATATGCAC
64576 ATGATATGCAC
1 ATGATATGCAC
*
64587 ATGATATG--T
1 ATGATATGCAC
64596 ATGATATGCAC
1 ATGATATGCAC
64607 ATGA
1 ATGA
64611 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:64750 original size:23 final size:24
Alignment explanation
Indices: 64661--64779 Score: 188
Period size: 24 Copynumber: 5.0 Consensus size: 24
64651 GAGGAAGTGC
*
64661 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
64685 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
64709 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
64733 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
64756 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
64780 ATGATAAAGC
Statistics
Matches: 90, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
23 19 0.21
24 63 0.70
25 8 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:65007 original size:31 final size:31
Alignment explanation
Indices: 64969--65032 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
64959 CGTTTACAGT
64969 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
65000 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
65031 AA
1 AA
65033 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Done.