Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold654
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: 44394
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:2743 original size:43 final size:43
Alignment explanation
Indices: 2589--2760 Score: 184
Period size: 43 Copynumber: 3.8 Consensus size: 43
2579 ATTTGGGCAT
*
2589 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT--GAACG
*** * * *
2634 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACT-AGGCAT
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGA-AC-G
*
2682 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAACG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAACG
*
2725 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2761 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
43 36 0.34
44 2 0.02
45 2 0.02
46 33 0.31
47 31 0.29
48 1 0.01
49 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (43 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAACG
Found at i:5684 original size:15 final size:15
Alignment explanation
Indices: 5645--5724 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
5635 GTATCTTGGG
*
5645 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
5660 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
5675 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
5690 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
5705 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
5719 TTTCTT
1 TTTCTT
5725 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:5714 original size:30 final size:30
Alignment explanation
Indices: 5636--5723 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
5626 CATAGTATCG
* * *
5636 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
5666 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
5696 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
5724 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:8203 original size:92 final size:93
Alignment explanation
Indices: 8081--8251 Score: 281
Period size: 92 Copynumber: 1.8 Consensus size: 93
8071 AGGATATTTG
* * *
8081 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-TCGAACTCGTTGAG
1 GGCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
8145 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
8173 GGCATCCGAGCACGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
8238 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
8252 TTATGGGCGG
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 46 0.64
93 26 0.36
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:13712 original size:16 final size:16
Alignment explanation
Indices: 13687--13721 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13677 GTAGCCAAAC
13687 TTTTGACTTTTCGGCA
1 TTTTGACTTTTCGGCA
* *
13703 TTTTGGCTTTTCGGGA
1 TTTTGACTTTTCGGCA
13719 TTT
1 TTT
13722 GTTGATCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTTGACTTTTCGGCA
Found at i:19871 original size:20 final size:19
Alignment explanation
Indices: 19848--19912 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
19838 AAGCTCAAAC
19848 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
19868 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
19888 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
19908 GAGCT
1 GAGCT
19913 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21725 original size:33 final size:33
Alignment explanation
Indices: 21687--21749 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21677 GATTACTCAC
21687 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21720 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21750 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21776 original size:21 final size:21
Alignment explanation
Indices: 21747--21802 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
21737 CAAGCTCTCT
*
21747 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
21768 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
21789 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
21803 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:21776 original size:27 final size:26
Alignment explanation
Indices: 21746--21871 Score: 78
Period size: 28 Copynumber: 4.6 Consensus size: 26
21736 TCAAGCTCTC
21746 TTTCAATTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTCTTTTTTC-CTTTTTCTT
* *
21773 TTTCAATTTTCTTTTCTTCATTTTCTTTT
1 TTTCAA-TTTCTTTT-TTCCTTTT-TCTT
* *
21802 TCTCTCACTTT-TTCGATTT-CTTTTTCTT
1 T-T-TCAATTTCTT--TTTTCCTTTTTCTT
* * *
21830 TTGCAATTTC-TTTTTCTTTTTGTTTT
1 TTTCAATTTCTTTTTTCCTTTT-TCTT
21856 CTTTCAATTTCTTTTT
1 -TTTCAATTTCTTTTT
21872 CAATCTCTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
24 3 0.04
25 4 0.05
26 9 0.12
27 16 0.21
28 20 0.27
29 13 0.17
30 6 0.08
31 4 0.05
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCCTTTTTCTT
Found at i:21795 original size:14 final size:14
Alignment explanation
Indices: 21746--21802 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21736 TCAAGCTCTC
21746 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21759 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21773 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21787 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21801 TT
1 TT
21803 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21830 original size:18 final size:18
Alignment explanation
Indices: 21809--21859 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
21799 TTTTCTCTCA
21809 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21827 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
21845 CTTTTT-GTTTTCTTT
1 CTTTTTCGATTTCTTT
21860 CAATTTCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:21872 original size:6 final size:6
Alignment explanation
Indices: 21764--21859 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
21754 TCTTTTTTCG
* * * **
21764 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
21815 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
21860 CAATTTCTTT
Statistics
Matches: 64, Mismatches: 23, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 48 0.75
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:22925 original size:11 final size:12
Alignment explanation
Indices: 22909--22950 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
22899 TTGTCACTTC
*
22909 TTTTTTTTT-AA
1 TTTTTTTTTCGA
22920 TTTTTTTTTCGA
1 TTTTTTTTTCGA
*
22932 TTTTTTTTTGGA
1 TTTTTTTTTCGA
22944 TTTTTTT
1 TTTTTTT
22951 GTTACGCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTCGA
Found at i:24502 original size:20 final size:20
Alignment explanation
Indices: 24455--24502 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
24445 AGTAAGCTCG
24455 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
24475 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
24495 GTTGAGCT
1 GTTGAGCT
24503 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:29580 original size:42 final size:41
Alignment explanation
Indices: 29421--29583 Score: 130
Period size: 42 Copynumber: 3.9 Consensus size: 41
29411 ATAGCAATGT
* * * * *
29421 CATATCCCAGAAATGGTCTTACATGGGATCTCATATCGATGC
1 CATATCCCAGATATGGTCTTACA-CGAAACTCATAACGATGC
* * * ** *
29463 CAATAGCCCAGCTATGGTCTTGCACGATTCTCATACCGATGC
1 C-ATATCCCAGATATGGTCTTACACGAAACTCATAACGATGC
* * * *
29505 CATGTCCTATACT-TGGTCTTACATGAAATCTCATAACGATGC
1 CATATCCCAGA-TATGGTCTTACACGAAA-CTCATAACGATGC
*
29547 CATATCCTAGATATGGTCTTACACGTAAACTCATAAC
1 CATATCCCAGATATGGTCTTACACG-AAACTCATAAC
29584 CCTAATGTCA
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 17 0.18
42 57 0.60
43 21 0.22
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (41 bp):
CATATCCCAGATATGGTCTTACACGAAACTCATAACGATGC
Found at i:30499 original size:26 final size:26
Alignment explanation
Indices: 30470--30519 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
30460 ACCGAATTCG
* *
30470 CAGCAAAGCTGCCAGTAATAATAACA
1 CAGCAAAGCTGCCAGGAACAATAACA
*
30496 CAGCATAGCTGCCAGGAACAATAA
1 CAGCAAAGCTGCCAGGAACAATAA
30520 ATGTGGCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGGAACAATAACA
Found at i:30578 original size:27 final size:27
Alignment explanation
Indices: 30517--30598 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
30507 CCAGGAACAA
*
30517 TAAATGTGGCAAAGCCACCAGTATCAG
1 TAAATGTGGCATAGCCACCAGTATCAG
** *
30544 TATTTGTGGCATAGCCACTAGTAAT-AG
1 TAAATGTGGCATAGCCACCAGT-ATCAG
* * *
30571 TAAATGTGACATAGTCACCAATA-CAG
1 TAAATGTGGCATAGCCACCAGTATCAG
30597 TA
1 TA
30599 CTTCCTCCAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
26 5 0.12
27 36 0.84
28 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
TAAATGTGGCATAGCCACCAGTATCAG
Found at i:30779 original size:27 final size:27
Alignment explanation
Indices: 30724--30795 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
30714 CGGAACATAA
* * * *
30724 GGGCATAATCGTCATTTTTCCATATAG
1 GGGCATTATGGTCATTTTACCATACAG
*
30751 GGGCATTATGGTCATTTTACCCTACAG
1 GGGCATTATGGTCATTTTACCATACAG
* *
30778 GGGTATTTTGGTCATTTT
1 GGGCATTATGGTCATTTT
30796 TTCTATTTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGCATTATGGTCATTTTACCATACAG
Found at i:33077 original size:46 final size:45
Alignment explanation
Indices: 33025--33199 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 45
33015 TGGTTGAGCA
33025 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* ** * *
33071 TTCGAACTCGTTGAGTTGAGTCCGAGTT-TGTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
* *
33116 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* *
33164 -CCTGAGCTCGTTTAGTTGAGTCCGAGTTCACTTAGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
33200 GGGGTTACAT
Statistics
Matches: 104, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 7 0.07
46 55 0.53
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:33181 original size:93 final size:93
Alignment explanation
Indices: 33022--33191 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
33012 GGATGGTTGA
* *
33022 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCTCGAACTCGTTGAGT
33087 TGAGTCCGAGTTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTTGTGAGATGTAACTAG
* * * *
33115 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGC-CTGAGCTCGTTTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCTC-GAACTCGTTGAG
33179 TTGAGTCCGAGTT
65 TTGAGTCCGAGTT
33192 CACTTAGGGG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 69 0.99
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCTCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAGATGTAACTAG
Found at i:41189 original size:46 final size:46
Alignment explanation
Indices: 41139--41311 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
41129 TGGTTGAGCA
41139 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAATG
* * * *
41185 TCCGAACTCGTTGAGTTTGAGTCCGAG-TC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAG-TTGAGTCCGAGTTCACTTATGGATGGAA--ATG
*
41230 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCG-AATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAAATG
* *
41278 -CCGAGCTCGTTGAGTTGAGT-CG-GTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41312 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
43 16 0.15
44 2 0.02
45 23 0.22
46 28 0.26
47 28 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAATG
Found at i:44247 original size:14 final size:15
Alignment explanation
Indices: 44225--44262 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
44215 TATCTGGGTT
44225 TCTTTATTCTGGATC
1 TCTTTATTCTGGATC
*
44240 TC-TTATTCTGGATT
1 TCTTTATTCTGGATC
44254 TCTTTATTC
1 TCTTTATTC
44263 GGTTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.13, C:0.18, G:0.11, T:0.58
Consensus pattern (15 bp):
TCTTTATTCTGGATC
Done.