Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2228
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: 21429
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:101 original size:19 final size:19
Alignment explanation
Indices: 79--120 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
69 ATAATAAAAT
*
79 TAAATGAATAT-AAATTATA
1 TAAA-GAATATGAAAATATA
*
98 TAAAGATTATGAAAATATA
1 TAAAGAATATGAAAATATA
117 TAAA
1 TAAA
121 ATTAAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
TAAAGAATATGAAAATATA
Found at i:220 original size:11 final size:10
Alignment explanation
Indices: 194--235 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
184 CAATCAAATT
*
194 AAATAAATATA
1 AAATATATA-A
*
205 AATTATATAA
1 AAATATATAA
215 AAAT-TATAA
1 AAATATATAA
224 AAATATATAA
1 AAATATATAA
234 AA
1 AA
236 TTAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 9 0.33
10 11 0.41
11 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATATAA
Found at i:2221 original size:74 final size:75
Alignment explanation
Indices: 2099--2266 Score: 268
Period size: 74 Copynumber: 2.3 Consensus size: 75
2089 TGCAATATTT
* * * *
2099 TAGGACTTGCCGTCTCTTTTAAGTCGTTTCCAGTAGCTAATACAAGGAAGCTCCTCATAGGCTGC
1 TAGGACTTGCTGTCTCTTTCAAGTCGTTTCCAGTAGCTAATAAAAGGAAGCTCCTCATAAGCTGC
2164 TTTTGTTCTC
66 TTTTGTTCTC
2174 TAGGACTTGCTGTCT-TTCTCAAGT-GTTTCCAGTAGCTAATAAAAGGAAGCTCCTCATAAGCTG
1 TAGGACTTGCTGTCTCTT-TCAAGTCGTTTCCAGTAGCTAATAAAAGGAAGCTCCTCATAAGCTG
*
2237 CTTTTGTTCTT
65 CTTTTGTTCTC
2248 TAGGACTTGCTGTCTCTTT
1 TAGGACTTGCTGTCTCTTT
2267 TCTCATAAGC
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
74 65 0.76
75 21 0.24
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (75 bp):
TAGGACTTGCTGTCTCTTTCAAGTCGTTTCCAGTAGCTAATAAAAGGAAGCTCCTCATAAGCTGC
TTTTGTTCTC
Found at i:2285 original size:42 final size:42
Alignment explanation
Indices: 2226--2309 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
2216 AAGGAAGCTC
* *
2226 CTCATAAGCTGCTTTTGTTCTTTAGGACTTGCTGTCTCTTTT
1 CTCATAAGCTGCTTTTGTACGTTAGGACTTGCTGTCTCTTTT
2268 CTCATAAGCTGCTTTTGTACGTTAGGACTTGCTGTCTCTTTT
1 CTCATAAGCTGCTTTTGTACGTTAGGACTTGCTGTCTCTTTT
2310 AAGTTGTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (42 bp):
CTCATAAGCTGCTTTTGTACGTTAGGACTTGCTGTCTCTTTT
Found at i:2464 original size:106 final size:106
Alignment explanation
Indices: 2279--2578 Score: 546
Period size: 106 Copynumber: 2.8 Consensus size: 106
2269 TCATAAGCTG
* *
2279 CTTTTGTACGTTAGGACTTGCTGTCTCTTTTAAGTTGTTTCCAGTAGCTAATAAAAGGAAGATCC
1 CTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAGTTGTTTCCAGTAGCTAATAAAAGGAAGATCC
*
2344 TCATGAGCTGCTTTTGTTCTTTAGTTGTTTCCAGTAGCTTC
66 CCATGAGCTGCTTTTGTTCTTTAGTTGTTTCCAGTAGCTTC
2385 CTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAGTTGTTTCCAGTAGCTAATAAAAGGAAGATCC
1 CTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAGTTGTTTCCAGTAGCTAATAAAAGGAAGATCC
2450 CCATGAGCTGCTTTTGTTCTTTAGTTGTTTCCAGTAGCTTC
66 CCATGAGCTGCTTTTGTTCTTTAGTTGTTTCCAGTAGCTTC
*
2491 CTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGTAGCTAATAAAAGGGAGATC
1 CTTTTGTTCTTTAGGACTTGCTGTCTC-TTTTAAGTTGTTTCCAGTAGCTAATAAAAGGAAGATC
*
2556 CCCATGAGCTGCTTTTGTCCTTT
65 CCCATGAGCTGCTTTTGTTCTTT
2579 GGGACTTGCC
Statistics
Matches: 188, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
106 130 0.69
107 58 0.31
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (106 bp):
CTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAGTTGTTTCCAGTAGCTAATAAAAGGAAGATCC
CCATGAGCTGCTTTTGTTCTTTAGTTGTTTCCAGTAGCTTC
Found at i:2642 original size:49 final size:51
Alignment explanation
Indices: 2562--2717 Score: 165
Period size: 52 Copynumber: 3.1 Consensus size: 51
2552 GATCCCCATG
* * * *
2562 AGCTGCTTTTGTCCTTTGGGACTTGCCGTCTCTTTTAAAGCT-CCT-CA-T
1 AGCTCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAAGCTGCCTCCAGT
* * **
2610 AAGCTCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGT
1 -AGCTCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAAGCTGCCTCCAGT
* * **
2662 AGCTTCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGT
1 AGC-TCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAAGCTGCCTCCAGT
2714 AGCT
1 AGCT
2718 AATAAAAGGG
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
49 36 0.38
50 1 0.01
51 6 0.06
52 52 0.55
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (51 bp):
AGCTCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTAAAGCTGCCTCCAGT
Found at i:2682 original size:52 final size:52
Alignment explanation
Indices: 2614--2717 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
2604 CCTCATAAGC
2614 TCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGTAGCT
1 TCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGTAGCT
2666 TCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGTAGCT
1 TCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGTAGCT
2718 AATAAAAGGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.12, C:0.19, G:0.17, T:0.52
Consensus pattern (52 bp):
TCCTTTTGTTCTTTAGGACTTGCTGTCTCTTTTTAAGTTGTTTCCAGTAGCT
Found at i:2697 original size:26 final size:26
Alignment explanation
Indices: 2616--2698 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
2606 TCATAAGCTC
2616 CTTTTGTTCTTTAGGACTTGCTGTCT
1 CTTTTGTTCTTTAGGACTTGCTGTCT
* ** * *
2642 CTTTTTAAGTTGTTT-CCAGTAGCT-TC-
1 C-TTTT--GTTCTTTAGGACTTGCTGTCT
2668 CTTTTGTTCTTTAGGACTTGCTGTCT
1 CTTTTGTTCTTTAGGACTTGCTGTCT
2694 CTTTT
1 CTTTT
2699 TAAGTTGTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 6 0.15
24 5 0.12
25 6 0.15
26 7 0.17
27 6 0.15
28 5 0.12
29 6 0.15
ACGTcount: A:0.10, C:0.19, G:0.17, T:0.54
Consensus pattern (26 bp):
CTTTTGTTCTTTAGGACTTGCTGTCT
Found at i:3467 original size:19 final size:19
Alignment explanation
Indices: 3443--3488 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3433 AAGTACGATG
3443 ATTTATATATTCATATTAT
1 ATTTATATATTCATATTAT
* **
3462 ATTTATATTTTTTTATTAT
1 ATTTATATATTCATATTAT
*
3481 AATTATAT
1 ATTTATAT
3489 TAACCTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTATATATTCATATTAT
Found at i:6030 original size:18 final size:17
Alignment explanation
Indices: 6002--6054 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5992 AATTTAAAAT
6002 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
6019 ATTTTAATATTT-TA-ATA
1 ATTTT-ATATTTATATA-A
6036 A-TTTAT-TTTATATAA
1 ATTTTATATTTATATAA
6051 ATTT
1 ATTT
6055 CAAGATAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 3 0.10
15 6 0.19
16 7 0.23
17 9 0.29
18 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:6765 original size:27 final size:27
Alignment explanation
Indices: 6735--6807 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
6725 AGTCACCTAT
*
6735 TGTTTATCAAAAATTGTGGTTAT-TTTG
1 TGTTTATCAAAAATAGTGGTT-TCTTTG
* *
6762 TGTTTGTCAAAAATAGTGGTTTCTTTT
1 TGTTTATCAAAAATAGTGGTTTCTTTG
*
6789 TATTTATCAAAAATAGTGG
1 TGTTTATCAAAAATAGTGG
6808 CATGTTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (27 bp):
TGTTTATCAAAAATAGTGGTTTCTTTG
Found at i:19029 original size:1 final size:1
Alignment explanation
Indices: 19019--19108 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
19009 TGGCAATTGG
* * * ** * * * **
19019 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAACAAAAAAAAGGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
19084 AAGAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
19109 GTGAAGATTT
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:19067 original size:33 final size:34
Alignment explanation
Indices: 19018--19108 Score: 159
Period size: 33 Copynumber: 2.7 Consensus size: 34
19008 ATGGCAATTG
19018 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAA-AAAAAAACAAAACAAAAAAAAGGAAAAA
19053 G-AAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
19086 GAAAAAAAAAAAACAAAA-AAAAA
1 GAAAAAAAAAAAACAAAACAAAAA
19109 GTGAAGATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
33 34 0.62
34 20 0.36
35 1 0.02
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
Done.