Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1252
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: 29727
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:6316 original size:33 final size:32
Alignment explanation
Indices: 6270--6337 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
6260 CGTTATAAGC
**
6270 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTAT-GTGTATCGATA
* *
6303 CAATGTATTGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
6335 CAA
1 CAA
6338 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:6416 original size:20 final size:21
Alignment explanation
Indices: 6369--6421 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
6359 GCCAATGACC
**
6369 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
6390 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
6410 TGTATCGATACA
1 TGTATCGATACA
6422 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:12846 original size:67 final size:67
Alignment explanation
Indices: 12738--12870 Score: 266
Period size: 67 Copynumber: 2.0 Consensus size: 67
12728 ATTAGGAAGA
12738 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
1 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
12803 TT
66 TT
12805 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
1 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
12870 T
66 T
12871 CTTCTGATGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (67 bp):
GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
TT
Found at i:13817 original size:2 final size:2
Alignment explanation
Indices: 13810--13862 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
13800 TTCTGATGTG
*
13810 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13852 TA TA TA TA TA T
1 TA TA TA TA TA T
13863 TCGAATACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16770 original size:28 final size:30
Alignment explanation
Indices: 16711--16770 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
16701 CTTGTAATAT
* *
16711 TTATATGTAAATGGTAATACTTTTTTGTAA
1 TTATATGTAAATGCTAATACTTTTATGTAA
*
16741 TTATATGTAAA-GCTAAT-GTTTTATGTAA
1 TTATATGTAAATGCTAATACTTTTATGTAA
16769 TT
1 TT
16771 GTAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 5 0.19
30 11 0.41
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (30 bp):
TTATATGTAAATGCTAATACTTTTATGTAA
Found at i:16866 original size:58 final size:57
Alignment explanation
Indices: 16754--16885 Score: 192
Period size: 58 Copynumber: 2.3 Consensus size: 57
16744 TATGTAAAGC
* * * * * *
16754 TAATGTTTTATGTAATTGTAATATTTTTTATAATTGATAATGTTTGTATGTAATTAG
1 TAATGTTTTATGTAATTGCAATATTTTTTATAACTAATAACGTTTATATATAATTAG
*
16811 TAATATTTTATGTAACTTGCAATATTTTTTATAACTAATAACGTTTATATATAATTAG
1 TAATGTTTTATGTAA-TTGCAATATTTTTTATAACTAATAACGTTTATATATAATTAG
16869 TAATGTTTTATGTAATT
1 TAATGTTTTATGTAATT
16886 ACATGTAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
57 16 0.24
58 50 0.76
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (57 bp):
TAATGTTTTATGTAATTGCAATATTTTTTATAACTAATAACGTTTATATATAATTAG
Found at i:16886 original size:19 final size:19
Alignment explanation
Indices: 16754--16886 Score: 101
Period size: 19 Copynumber: 6.9 Consensus size: 19
16744 TATGTAAAGC
16754 TAATGTTTTATGTAATT-G
1 TAATGTTTTATGTAATTAG
* * *
16772 TAATATTTTTTATAATT-G
1 TAATGTTTTATGTAATTAG
16790 ATAATGTTTGTATGTAATTAG
1 -TAATGTTT-TATGTAATTAG
*
16811 TAATATTTTATGTAACTT-G
1 TAATGTTTTATGTAA-TTAG
* * * * * *
16830 CAATATTTTTTATAACTAA
1 TAATGTTTTATGTAATTAG
* *
16849 TAACGTTTATATATAATTAG
1 TAATGTTT-TATGTAATTAG
16869 TAATGTTTTATGTAATTA
1 TAATGTTTTATGTAATTA
16887 CATGTAAATA
Statistics
Matches: 89, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
18 16 0.18
19 41 0.46
20 31 0.35
21 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.52
Consensus pattern (19 bp):
TAATGTTTTATGTAATTAG
Found at i:18359 original size:96 final size:94
Alignment explanation
Indices: 18190--18378 Score: 274
Period size: 96 Copynumber: 2.0 Consensus size: 94
18180 AGGTCTTTTG
* * *
18190 ACATCAACATTTGGATATTTCTTAATAGTACTTAGCTTTTTTGATAAATAAATATTTAACAAAAT
1 ACATCAACATTTGGATATTTCTTAATAATACTTAGCTTTTTTGATAAATAAAAAATTAACAAAAT
* *
18255 AAGTAATTAAAAAAAATAAATTTATGTATTC
66 AAATAATT-AAAAAAAT-AATTTATATATTC
*
18286 ACATCAACATTTGGATATTTCTTAATAATACTTAGC-TTTTTGATAAATAAAAAAATTGACAAAA
1 ACATCAACATTTGGATATTTCTTAATAATACTTAGCTTTTTTGATAAAT-AAAAAATTAACAAAA
18350 -AAATAAATTAAAAAAATAATTTATATATT
65 TAAAT-AATTAAAAAAATAATTTATATATT
18379 TATATCATGT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
94 11 0.13
95 23 0.27
96 51 0.60
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (94 bp):
ACATCAACATTTGGATATTTCTTAATAATACTTAGCTTTTTTGATAAATAAAAAATTAACAAAAT
AAATAATTAAAAAAATAATTTATATATTC
Found at i:18762 original size:19 final size:20
Alignment explanation
Indices: 18711--18764 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
18701 ATTGTAGATC
18711 TATTTAAATTTAAAATTATT
1 TATTTAAATTTAAAATTATT
18731 TATTTAAATTTAAAA-T-TT
1 TATTTAAATTTAAAATTATT
18749 TATTTAATATTTAAAA
1 TATTTAA-ATTTAAAA
18765 AAATAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.27
19 9 0.27
20 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTAAATTTAAAATTATT
Found at i:18923 original size:21 final size:23
Alignment explanation
Indices: 18886--18937 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
18876 ATATTTTTAT
18886 TAATTA-TTAATTATATATGATA
1 TAATTATTTAATTATATATGATA
*
18908 TAA-TATTTAATT-TATATTATA
1 TAATTATTTAATTATATATGATA
18929 TAATTATTT
1 TAATTATTT
18938 CTTTTATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TAATTATTTAATTATATATGATA
Found at i:18937 original size:22 final size:22
Alignment explanation
Indices: 18882--18953 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 22
18872 CATAATATTT
18882 TTAT-TAATTA-TTAATTATATA
1 TTATATAATTATTTAATT-TATA
*
18903 TGATATAA-TATTTAATTTATA
1 TTATATAATTATTTAATTTATA
*
18924 TTATATAATTATTT-CTTT-TA
1 TTATATAATTATTTAATTTATA
*
18944 TTCTATAATT
1 TTATATAATT
18954 TAACAAAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 11 0.25
21 19 0.43
22 14 0.32
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (22 bp):
TTATATAATTATTTAATTTATA
Found at i:20571 original size:39 final size:39
Alignment explanation
Indices: 20493--20659 Score: 121
Period size: 39 Copynumber: 4.3 Consensus size: 39
20483 AACTAACTTT
* * *
20493 AAAGACTTAGTTTTGATG--AAAAT-GTAAAATAAATCTTA
1 AAAG-CTTAATTTTGATGTAAAAATATTAAAAT-AATTTTA
* *
20531 AAAGTTTTATTTTGATGTAAAAATATTAAAATAATTTTA
1 AAAGCTTAATTTTGATGTAAAAATATTAAAATAATTTTA
* * * * *
20570 AAAGCTTGATTTTGATGTGAAAGTGTAAAAATAATCTTTA
1 AAAGCTTAATTTTGATGTAAAAATATTAAAATAAT-TTTA
* * * *
20610 AAA-CTTAATTTTTA-ATATAAAATATTAAAATGACTTTA
1 AAAGCTTAATTTTGATGTA-AAAATATTAAAATAATTTTA
*
20648 AAAG-TTCATTTT
1 AAAGCTTAATTTT
20660 CGTCATAAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
37 10 0.10
38 19 0.19
39 60 0.59
40 13 0.13
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (39 bp):
AAAGCTTAATTTTGATGTAAAAATATTAAAATAATTTTA
Found at i:20597 original size:78 final size:77
Alignment explanation
Indices: 20509--20659 Score: 173
Period size: 78 Copynumber: 1.9 Consensus size: 77
20499 TTAGTTTTGA
* * * *
20509 TGAAAATGT-AAAATAAATC-TTAAAAGTTTTATTTTG-ATGTAAAAATATTAAAATAATTTTAA
1 TGAAAATGTAAAAAT-AATCTTTAAAA-CTTAATTTTGAATAT-AAAATATTAAAATAACTTTAA
*
20571 AAGCTTGATTTTGATG
63 AAG-TTCATTTTGATG
* * *
20587 TGAAAGTGTAAAAATAATCTTTAAAACTTAATTTTTAATATAAAATATTAAAATGACTTTAAAAG
1 TGAAAATGTAAAAATAATCTTTAAAACTTAATTTTGAATATAAAATATTAAAATAACTTTAAAAG
20652 TTCATTTT
66 TTCATTTT
20660 CGTCATAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
77 7 0.11
78 41 0.66
79 14 0.23
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (77 bp):
TGAAAATGTAAAAATAATCTTTAAAACTTAATTTTGAATATAAAATATTAAAATAACTTTAAAAG
TTCATTTTGATG
Found at i:21091 original size:26 final size:25
Alignment explanation
Indices: 21041--21092 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
21031 TTAACTTAAA
*
21041 TTAAATAATAATATTTAAATGATAAT
1 TTAAATAATAATATATAAA-GATAAT
21067 TTAAATAATAATAATATATAA-ATAAT
1 TTAAATAATAAT-ATATA-AAGATAAT
21093 AAATAAGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 17 0.74
27 4 0.17
28 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAATAATAATATATAAAGATAAT
Found at i:25291 original size:2 final size:2
Alignment explanation
Indices: 25284--25308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25274 TGAATTAATT
25284 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25309 TTGATTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26797 original size:11 final size:12
Alignment explanation
Indices: 26760--26830 Score: 54
Period size: 13 Copynumber: 5.7 Consensus size: 12
26750 GATAATATTA
*
26760 AATATAAATAAT
1 AATATAAAAAAT
*
26772 TATATAAAAAAAT
1 AATAT-AAAAAAT
*
26785 AAT-TAAAATAT
1 AATATAAAAAAT
26796 AATATAAATAAAAT
1 AATAT-AA-AAAAT
* *
26810 GATAATACAAAAT
1 AAT-ATAAAAAAT
26823 AATATAAA
1 AATATAAA
26831 TATATAAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 9 0.20
12 10 0.22
13 17 0.38
14 7 0.16
15 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:26808 original size:27 final size:27
Alignment explanation
Indices: 26765--26832 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
26755 TATTAAATAT
* *
26765 AAATAAT-TATATAAAAAAATAATTA-A
1 AAATAATATAAATAAAATAATAA-TACA
*
26791 AATATAATATAAATAAAATGATAATACA
1 AA-ATAATATAAATAAAATAATAATACA
26819 AAATAATATAAATA
1 AAATAATATAAATA
26833 TATAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.06
27 19 0.53
28 15 0.42
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (27 bp):
AAATAATATAAATAAAATAATAATACA
Found at i:26816 original size:17 final size:16
Alignment explanation
Indices: 26783--26919 Score: 59
Period size: 16 Copynumber: 8.3 Consensus size: 16
26773 ATATAAAAAA
*
26783 ATAATTAAAATATAAT
1 ATAAATAAAATATAAT
26799 ATAAATAAAATGATAAT
1 ATAAATAAAAT-ATAAT
* *
26816 ACAAA-ATAATATAA-
1 ATAAATAAAATATAAT
* * **
26830 ATATATAAATTATTTT
1 ATAAATAAAATATAAT
* **
26846 AAAAAT-TTATATAAT
1 ATAAATAAAATATAAT
26861 ATAAATTATTTAAATATCATAT
1 ATAAA-TA---AAATAT-A-AT
26883 ATAAATATAAA-AT-AT
1 ATAAATA-AAATATAAT
*
26898 ATTAAATAAATTATAAT
1 A-TAAATAAAATATAAT
26915 ATAAA
1 ATAAA
26920 AATACACAAT
Statistics
Matches: 88, Mismatches: 20, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
14 3 0.03
15 22 0.25
16 31 0.35
17 12 0.14
18 2 0.02
19 4 0.05
20 4 0.05
21 3 0.03
22 7 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
ATAAATAAAATATAAT
Found at i:26869 original size:27 final size:27
Alignment explanation
Indices: 26823--26919 Score: 94
Period size: 26 Copynumber: 3.6 Consensus size: 27
26813 AATACAAAAT
*
26823 AATATAAAT-ATATAAATTATTTTAAA
1 AATATATATAATATAAATTATTTTAAA
*
26849 AATTTATATAATATAAATTA-TTTAAA
1 AATATATATAATATAAATTATTTTAAA
* * *
26875 TATCATATATAAATATAAAATATATTAAA
1 AAT-ATATAT-AATATAAATTATTTTAAA
26904 TAA-AT-TATAATATAAA
1 -AATATATATAATATAAA
26920 AATACACAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 23 0.39
27 18 0.31
28 12 0.20
29 5 0.08
30 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATATATAATATAAATTATTTTAAA
Found at i:26923 original size:34 final size:35
Alignment explanation
Indices: 26871--26946 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
26861 ATAAATTATT
* * *
26871 TAAA-TATCATATATAAATATAAAATAT-ATTAAA
1 TAAATTATAATATAAAAATACAAAATATGATTAAA
* *
26904 TAAATTATAATATAAAAATACACAATATGATTACA
1 TAAATTATAATATAAAAATACAAAATATGATTAAA
26939 TAAATTAT
1 TAAATTAT
26947 TAGATCTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 4 0.11
34 19 0.53
35 13 0.36
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (35 bp):
TAAATTATAATATAAAAATACAAAATATGATTAAA
Done.