Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2048
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: 12029
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:986 original size:473 final size:473
Alignment explanation
Indices: 1--1236 Score: 1723
Period size: 473 Copynumber: 2.6 Consensus size: 473
* * *
1 CAAAGGAAACATTTCCATGCAAAATAAAATCATCAATATCATTTATCGTAATGAAAAGAATGTGC
1 CAAAGGAAACATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATG-AGAGAATGTGT
*
66 TTATTGTGTCTAATCATGAAATGAATGAAGATCGTTACTAGAATCCATGTTTGACTCATTTGAGG
65 TTATTGTGTCTAATCATGAAATGAATGAAGATCATTACTAGAATCCATGTTTGACTCATTTGAGG
* *
131 CA-GAAACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTCTTGTAAAACCAAAGTGTCAA
130 CACG-AACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTCTTGTGAAACCAAAGCGTCAA
* *
195 TATCGTGTATCCTTATGAGAAGACTATGTTTGTGGTACCTAATCTTGAAAAGAATGGGGATTAAT
194 TATCATGTATCCTTATGAGAAGACTATGTTTGTGGTACCTAATCTTGAAAAGAATGGGGATTAGT
* * *
260 ATGACTATTTATGTTTGTCTTATTGAAGAGACAAATTTTGATTCTAACAAAAACGGTTAAAAGAA
259 ATGACTATTCATGTTTGTCTTATTGAAGAGACAAATCTTGATTCTAACAAAAACGGTGAAAAGAA
** *
325 AAGCTTTTCTTACGACACCAAAGCATCAATGTCTTCTATCCTAATGAAGGAATATGTTTTTAGTT
324 AAGCTTTTCTTACGACACCAAAGCATCAATGTCAACTATCCTAATAAAGGAATATGTTTTTAGTT
* * * * * **
390 CCCAATCTGGGAAGAATGGGGACTATTACGAGAATCAATGCTTGCCTTATTTAATTGATGAACTT
389 CCCAATCTGAGAAGAATCGAGACTATTACGAAAATCAATGCTTCCCTTATTTAAGGGATGAACTT
*
455 TGATTTTATGGAAAATAAGG
454 TGATTTTAAGGAAAATAAGG
* * * *
475 CAAAGGAAACATTTCCCTACAAAAGAAAATCATCAATATCATTTA-CACTAATGAGATAATGTGT
1 CAAAGGAAACATTTCCATGCAAAATAAAATCATCAATATCATTTATC-CTAATGAGAGAATGTGT
** * * ** * * ** *
539 TTATAATGCCTAATGACAAAATGAATGATGATCATTACTAGAATCCATGTATGTTTTATTTGAGG
65 TTATTGTGTCTAATCATGAAATGAATGAAGATCATTACTAGAATCCATGTTTGACTCATTTGAGG
* * *
604 CACGAACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTGTTGCGAAACCAAAGCATCAAT
130 CACGAACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTCTTGTGAAACCAAAGCGTCAAT
** * * *
669 ATCACCTAT-CTTAATGAGTAGACTATGTTTATGGTACCTAATCCTGAAAAGAATGGGGATTAGT
195 ATCATGTATCCTT-ATGAGAAGACTATGTTTGTGGTACCTAATCTTGAAAAGAATGGGGATTAGT
* * *
733 ATGACTATTCATGTTTGTCTTATTTAAGAGACAAA-CTTGATTCT-ACCAAAACGGTGGAAAGAA
259 ATGACTATTCATGTTTGTCTTATTGAAGAGACAAATCTTGATTCTAACAAAAACGGTGAAAAGAA
* * * * *
796 TAGCTTTTCTTGCGATC-CCAAAGCATCAGTGTCAAGTATCCTAATAAAGGGAATATGTTTTTGG
324 AAGCTTTTCTTACGA-CACCAAAGCATCAATGTCAACTATCCTAATAAA-GGAATATGTTTTTAG
* *
860 TTCCCAATCTTGAGAAGAATCGAGACTGTTACGAAAATCAATGCTTCCCTTTTTTAAGGGATGAA
387 TTCCCAATC-TGAGAAGAATCGAGACTATTACGAAAATCAATGCTTCCCTTATTTAAGGGATGAA
925 CTTTGATTTTAAGGAAAATAAGG
451 CTTTGATTTTAAGGAAAATAAGG
* * * * *
948 CAGAGGAAACATTTCCTTGCAAAATAAAATCGTCAATATCATTTATCCTAATGAGGAGAAAGTAT
1 CAAAGGAAACATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGA-GAGAATGTGT
*
1013 TTATTGTGTCTAATCATGAAATGAATGAAGATCATTACTAGAATCCACGTTTGACTCATTTGAGG
65 TTATTGTGTCTAATCATGAAATGAATGAAGATCATTACTAGAATCCATGTTTGACTCATTTGAGG
*
1078 CACAAACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTCTTGTGAAACCAAAGCGTCAAT
130 CACGAACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTCTTGTGAAACCAAAGCGTCAAT
* * * * *
1143 ATCATGTATCCTTATGTGAAGACTGTGTTTGTGGTGCCTAATCTTGAAAAGAATCGGGA-T-GTC
195 ATCATGTATCCTTATGAGAAGACTATGTTTGTGGTACCTAATCTTGAAAAGAATGGGGATTAGTA
* *
1206 TAACTATTCATTTTTGTCTTATTGAAGAGAC
260 TGACTATTCATGTTTGTCTTATTGAAGAGAC
1237 TTGTTAGGAT
Statistics
Matches: 661, Mismatches: 92, Indels: 20
0.86 0.12 0.03
Matches are distributed among these distances:
471 55 0.08
472 65 0.10
473 322 0.49
474 216 0.33
475 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (473 bp):
CAAAGGAAACATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGAGAATGTGTT
TATTGTGTCTAATCATGAAATGAATGAAGATCATTACTAGAATCCATGTTTGACTCATTTGAGGC
ACGAACTTAGACTTTACAAAAATTGGAGGGAAGAAAGCCTTTCTTGTGAAACCAAAGCGTCAATA
TCATGTATCCTTATGAGAAGACTATGTTTGTGGTACCTAATCTTGAAAAGAATGGGGATTAGTAT
GACTATTCATGTTTGTCTTATTGAAGAGACAAATCTTGATTCTAACAAAAACGGTGAAAAGAAAA
GCTTTTCTTACGACACCAAAGCATCAATGTCAACTATCCTAATAAAGGAATATGTTTTTAGTTCC
CAATCTGAGAAGAATCGAGACTATTACGAAAATCAATGCTTCCCTTATTTAAGGGATGAACTTTG
ATTTTAAGGAAAATAAGG
Found at i:1561 original size:20 final size:19
Alignment explanation
Indices: 1506--1561 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1496 AAAACCCTTA
*
1506 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
1526 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
1546 AATGTATCGATACATG
1 AAAGTATCGATACATG
1562 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1638 original size:13 final size:13
Alignment explanation
Indices: 1620--1645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1610 TACACCAAAT
1620 ATGTATCGATACA
1 ATGTATCGATACA
1633 ATGTATCGATACA
1 ATGTATCGATACA
1646 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1643 original size:32 final size:34
Alignment explanation
Indices: 1602--1666 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1592 TAGCCAAACT
*
1602 TGTATCGATACACC-AAATA-TGTATCGATACAA
1 TGTATCGATACACCAAAAAATTGTATCGATACAA
1634 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAAATTGTATCGATACA
1667 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
33 4 0.13
34 12 0.40
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAATTGTATCGATACAA
Found at i:3886 original size:22 final size:22
Alignment explanation
Indices: 3859--3914 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3849 TTGCAAGTTG
3859 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
3881 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
3902 AAATAAA-AACTTG
1 AAATAAAGAACTTG
3915 CATGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:7785 original size:20 final size:20
Alignment explanation
Indices: 7759--7836 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
7749 AATGTCCAAA
7759 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
7779 GTGTATCGATACATCTGGATATTCA
1 ATGTATCGATACA--T-G-T-TTCT
*
7804 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
7824 TTGTATCGATACA
1 ATGTATCGATACA
7837 CTGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 27 0.57
21 1 0.02
22 1 0.02
23 2 0.04
24 1 0.02
25 15 0.32
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:7843 original size:13 final size:13
Alignment explanation
Indices: 7825--7849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7815 CATTTTTCTT
7825 TGTATCGATACAC
1 TGTATCGATACAC
7838 TGTATCGATACA
1 TGTATCGATACA
7850 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:10411 original size:13 final size:13
Alignment explanation
Indices: 10393--10417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10383 TAGCCAAACT
10393 TGTATCGATACAA
1 TGTATCGATACAA
10406 TGTATCGATACA
1 TGTATCGATACA
10418 CCAAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.