Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold696
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: 18872
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:692 original size:19 final size:19
Alignment explanation
Indices: 650--699 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
640 ACACTCAGAT
*
650 GTATCAATACATATTGCTTA
1 GTATCGATACATATT-CTTA
670 GTATCGATACATATT-TATA
1 GTATCGATACATATTCT-TA
*
689 GTATTGATACA
1 GTATCGATACA
700 CCTTGAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 12 0.44
20 14 0.52
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
GTATCGATACATATTCTTA
Found at i:2567 original size:24 final size:24
Alignment explanation
Indices: 2531--2581 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2521 CATTTGGTTC
* *
2531 ATAAACAAGTCCAATAATTAGGTG
1 ATAAACAAATCCAATAATTAAGTG
2555 ATAAACAAATCCAATAATTAAGTG
1 ATAAACAAATCCAATAATTAAGTG
2579 ATA
1 ATA
2582 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
ATAAACAAATCCAATAATTAAGTG
Found at i:2874 original size:26 final size:27
Alignment explanation
Indices: 2836--2898 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
2826 ATGAACAACT
*
2836 TAATA-TATTTTTAATATTA-A-CACTA
1 TAATATTATATTTAATATTATACCA-TA
*
2861 TAATATTATATTTAATTTTATACCATA
1 TAATATTATATTTAATATTATACCATA
2888 TAA-ATTATATT
1 TAATATTATATT
2899 ATATAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 5 0.15
26 20 0.61
27 6 0.18
28 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTATATTTAATATTATACCATA
Found at i:2947 original size:31 final size:32
Alignment explanation
Indices: 2886--2953 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
2876 TTTTATACCA
* *
2886 TATAAATTATATTATATAATAAAAAGATATAT
1 TATAAATAATATTATATAAGAAAAAGATATAT
2918 TATAAATAATA-TATATAAGAAAATA-ATATAT
1 TATAAATAATATTATATAAGAAAA-AGATATAT
2949 TATAA
1 TATAA
2954 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (32 bp):
TATAAATAATATTATATAAGAAAAAGATATAT
Found at i:2963 original size:18 final size:16
Alignment explanation
Indices: 2898--2963 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
2888 TAAATTATAT
2898 TATATAATAAAAAGATA
1 TATATAATAAAAA-ATA
*
2915 TAT-T-ATAAATAATA
1 TATATAATAAAAAATA
*
2929 TATATAAGAAAATAATA
1 TATATAATAAAA-AATA
2946 TATTATAATTAAAAAATA
1 TA-TATAA-TAAAAAATA
2964 AGCTGAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.15
15 7 0.17
16 5 0.12
17 9 0.22
18 9 0.22
19 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TATATAATAAAAAATA
Found at i:5767 original size:11 final size:11
Alignment explanation
Indices: 5753--5777 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5743 TTTTTTATAT
5753 TATTTTAAAGC
1 TATTTTAAAGC
5764 TATTTTAAAGC
1 TATTTTAAAGC
5775 TAT
1 TAT
5778 GATGCTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
TATTTTAAAGC
Found at i:13738 original size:174 final size:174
Alignment explanation
Indices: 13429--13742 Score: 425
Period size: 174 Copynumber: 1.8 Consensus size: 174
13419 AAGAACCTAT
* * *
13429 AACCCGAAAAACTCGCTCCATTCAATTGGTGGAAAGCACAAAATGTAGAATTAAACAAATGATGA
1 AACCCAAAAAACTCGCTCCATTCAATTGGTGGAAAACACAAAATGTACAATTAAACAAATGATGA
* ** * * * * ** *
13494 TTACAAGTTAGCAGTTCAGAAAAGGTAATACTTTCCATTTTGGAGACAGAAAACCTGGCAACATG
66 TTACAAGTTAGCACTTCAGAAAAGAAAACACTTTACATTTTGGAAACAGAAAACCCGAAAACACG
13559 AACAAAACTTTTATAGATCAAATACTTGAAAGCAATGAAAAAGA
131 AACAAAACTTTTATAGATCAAATACTTGAAAGCAATGAAAAAGA
* * **
13603 AACCCAAAAAACTTGCTTCATTTC-ATTGGTGGAAAATGCAAAATGTACAATTAAACAAATGATG
1 AACCCAAAAAACTCGCTCCA-TTCAATTGGTGGAAAACACAAAATGTACAATTAAACAAATGATG
**
13667 ATTACAAGTTAGCACTTCATG-AAAGAAAACACTTTACATTTTGGAAATGGAAAACCCGAAAACA
65 ATTACAAGTTAGCACTTCA-GAAAAGAAAACACTTTACATTTTGGAAACAGAAAACCCGAAAACA
13731 CGAACAAAACTT
129 CGAACAAAACTT
13743 AGATAAAGCA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
174 115 0.97
175 4 0.03
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.24
Consensus pattern (174 bp):
AACCCAAAAAACTCGCTCCATTCAATTGGTGGAAAACACAAAATGTACAATTAAACAAATGATGA
TTACAAGTTAGCACTTCAGAAAAGAAAACACTTTACATTTTGGAAACAGAAAACCCGAAAACACG
AACAAAACTTTTATAGATCAAATACTTGAAAGCAATGAAAAAGA
Found at i:13952 original size:149 final size:149
Alignment explanation
Indices: 13629--14074 Score: 840
Period size: 149 Copynumber: 3.0 Consensus size: 149
13619 TTCATTTCAT
*
13629 TGGTGGAAAATGCAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
1 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
13694 AACACTTTACATTTTGGAAATGGAAAA-CCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
66 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
13758 TTCAAAGCAATAAAATGGA
131 TTCAAAGCAATAAAATGGA
*
13777 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATTATTACAAGTTAGCACTTCATGAAAGAA
1 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
*
13842 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGACAC
66 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
*
13907 TTCAAAGCAATGAAATGGA
131 TTCAAAGCAATAAAATGGA
13926 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
1 TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
13991 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
66 AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
*
14056 TTGAAAGCAATAAAATGGA
131 TTCAAAGCAATAAAATGGA
14075 AAAATTTGTT
Statistics
Matches: 289, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
148 90 0.31
149 199 0.69
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (149 bp):
TGGTGGAAAATGAAAAATGTACAATTAAACAAATGATGATTACAAGTTAGCACTTCATGAAAGAA
AACACTTTACATTTTGGAAATGGAAAACCCCGAAAACACGAACAAAACTTAGATAAAGCAGATAC
TTCAAAGCAATAAAATGGA
Found at i:14954 original size:26 final size:25
Alignment explanation
Indices: 14908--14962 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
14898 TAAATGAAAT
*
14908 ATAAAATAAAACAAAACAAACCCAA
1 ATAAAATAAAACAAAACAAACACAA
* *
14933 CATAAAATAAAGCCTAAA-AAACACAA
1 -ATAAAATAAA-ACAAAACAAACACAA
14959 ATAA
1 ATAA
14963 GAAGGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 17 0.68
27 4 0.16
ACGTcount: A:0.69, C:0.18, G:0.02, T:0.11
Consensus pattern (25 bp):
ATAAAATAAAACAAAACAAACACAA
Found at i:15880 original size:21 final size:22
Alignment explanation
Indices: 15854--15907 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
15844 AATATAATAA
*
15854 AATATTAAAATATTTTA-AATT
1 AATATTTAAATATTTTATAATT
*
15875 AATATTTATATATTTTATAATT
1 AATATTTAAATATTTTATAATT
15897 AA-ATTTAAATA
1 AATATTTAAATA
15908 AAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTAAATATTTTATAATT
Done.