Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1103
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: 12957
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:2165 original size:470 final size:473
Alignment explanation
Indices: 1--2546 Score: 3107
Period size: 472 Copynumber: 5.4 Consensus size: 473
* * *
1 CATTACTAGAATCCATGTTTGACTCATTT-ATGACACAAACTTAGACTTTACAAAAATTGGTGGG
1 CATTACTAGAATCCATGTTTGACTCATTTGA-GGCACGAACTTAGACTTTACAAAAATTGGAGGG
* * * * * *
65 AAGAAAGCTTTTCTTGGGAAACCAAAGCATCAACATCATGTATCCTTATGTGAAAACTATGTTTG
65 AAGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTTATGAGAAGACTATGTTTA
* * *
130 GGGTGCCTAATCCTG-AAAGAATGGGGATTAGTATGACTATTCATGTTCGTCTTATTAAAGAGAC
130 TGGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGAC
* *
194 AAACTTTGATTCTAACAAAAACGGTTGAAAGAAAAGCTTTTCTTACGACACC-AAGCATCAAAGT
195 AAAC-TTGATTCTAACAAAAACGGTTGAAAGAAAAGCTTTTCTTGCGACACCAAAGCATCAATGT
* * * * * * * *
258 C-ATTACCCTAATGAAA-GGACA-GTGTTTTTGGTTCCCAGTCATGAGAAGAATAGAGATTGTTA
259 CAAGTATCCTAAT-AAAGGGA-ATATGTTTTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTA
* * * *
320 TGAGAATCAATGCTTGCCTTATTTAAGAGATGAACTTTGATATTAAGGAAAATAGGGCAAAGTAA
322 CGAGAATCAATGCTTGCCTTATTTAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGGAA
* *
385 TCATTTCAATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGGAGAATGTGTTTATTGTG
387 ACATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGGAGAATGTGTTTATTGTG
450 TCTAATCATGAAATGAATAAGAT
452 TCTAATCATGAAATGAAT-AGAT
* * * * * *
473 CGTTACTAGAATCTATGTTTGACTCATTTGAGGCCCAAACTTAGACTTTAGAAAAATTAGAGGGA
1 CATTACTAGAATCCATGTTTGACTCATTTGAGGCACGAACTTAGACTTTACAAAAATTGGAGGGA
* * * * *
538 A-AATGCCTTTCTTACGAAACAAAAGCGTAAATATCATGTATCCTTATGAGAAGACTATGTTTAT
66 AGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTTATGAGAAGACTATGTTTAT
* * * *
602 GGTGCCTAATCCTAAAAAGAATGGGGATTAGTATGACTATTCATATTTGTCTTATTAAAGAGATA
131 GGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGA-C
* * *
667 AAATTTGATTCTAACAAAAACAGTTAAAAGAAAAGCTTTTCTTGCGACACCAAAGCATCAATGTC
195 AAACTTGATTCTAACAAAAACGGTTGAAAGAAAAGCTTTTCTTGCGACACCAAAGCATCAATGTC
* *** * * * * *
732 ATGTATCCTAA-AGAAGGGAATATGTTACAAGATT----GTGTT-ACAAGAAT-AGGACTGTTAC
260 AAGTATCCTAATA-AAGGGAATATGTT-TTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTAC
* * * *
790 AAGAATCAATGCTTGCCTTATTTAATGGATGAACTTTGATTTTAAGAAAAATAGGGTAAAGGAAA
323 GAGAATCAATGCTTGCCTTATTTAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGGAAA
* * * * *
855 CATTTCC-TGTAAAAGAAAATCATCAATATCATTTACCCTAATGAAGAGAATGTGTTTTATAGTG
388 CATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGGAGAATGTG-TTTATTGTG
* ** *
919 CCTAATCACAAAAAGAATGATGAT
452 TCTAATCATGAAATGAAT-A-GAT
*
943 CATTACTAGAATCCATG-TT---T-ATTTGAGGCACGAACTTAGACTTTACAAAAATTAGAGGGA
1 CATTACTAGAATCCATGTTTGACTCATTTGAGGCACGAACTTAGACTTTACAAAAATTGGAGGGA
* * * * *
1003 AGAAAGCCTTTATTGCGAAACCAAAGCATCGATATCGTTTAT-CTTAATGAGTAGACTATGTTTA
66 AGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTT-ATGAGAAGACTATGTTTA
* * * * *
1067 TGGTATCTAATCCTAAAAACAATGGGGATTAGTATGACTATTAATGTTTGTCTTATTTAAGAGAC
130 TGGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGAC
* * * * *
1132 AAACTTTGATTCT-ACAAAAAAGAGTGGAACGAATAGCTTTTCTTGCGATC-CTAAAGCATCAAT
195 AAAC-TTGATTCTAACAAAAACG-GTTGAAAGAAAAGCTTTTCTTGCGA-CACCAAAGCATCAAT
*
1195 GTCAAGTATCCTACTAAAGGGAATATGTTTTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTA
257 GTCAAGTATCCTAATAAAGGGAATATGTTTTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTA
* * * *
1260 CGAAAATTAATGCTTGCCTT-CTTAAGGGATAAACTTTGATTTTAAGGAAAATAGGGCAAAGGAA
322 CGAGAATCAATGCTTGCCTTATTTAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGGAA
* ** *
1324 ACATTTCCATGCAAAATAAAATCATCAATATCATTTATCGTAATGAAAAGAATGTGCTTATTGTG
387 ACATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGGAGAATGTGTTTATTGTG
1389 TCTAATCATGAAATGAATGAAGAT
452 TCTAATCATGAAATGAAT--AGAT
*
1413 CGTTACTAGAATCCATGTTTGACTCATTTGAGGCA-GAAACTTAGACTTTAC-AAAATTGGAGGG
1 CATTACTAGAATCCATGTTTGACTCATTTGAGGCACG-AACTTAGACTTTACAAAAATTGGAGGG
** ** * *
1476 AAGAAAGCCTTTCTTGTAAAACCAAAGTGTCAATATCGTGTATCCTTATGAGAAGAC-ATGTTTG
65 AAGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTTATGAGAAGACTATGTTTA
* * * *
1540 TGGTACCTAATCTTGAAAAGAATGGGGATTAATATGACTATTTATGTTTGTC-TATTGAAGAGAC
130 TGGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGAC
* * *
1604 AAATTTTGATTCTAACAAAAACGGTTAAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATGT
195 AAA-CTTGATTCTAACAAAAACGGTTGAAAGAAAAGCTTTTCTTGCGACACCAAAGCATCAATGT
*** * * * *
1669 CTTCTATCCTAATGAA-GGAATATGTTTTTAGTTCCCAATCTTGGGAAGAATGGGGACTATTACG
259 CAAGTATCCTAATAAAGGGAATATGTTTTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTACG
** * *
1733 AGAATCAATGCTTGCCTTATTTAATTGATGAACTTTGATTTTATGG-AAATAAGGCAAAGGAAAC
324 AGAATCAATGCTTGCCTTATTTAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGGAAAC
* * * * ** *
1797 ATTTCCCTACAAAAGAAAATCATC-ATATCATTTA-CACTAATGAGGATAATGTGTTTATAATGC
389 ATTTCCATGCAAAATAAAATCATCAATATCATTTATC-CTAATGAGGAGAATGTGTTTATTGTGT
* **
1860 CTAATGACAAAATGAAT-GAT
453 CTAATCATGAAATGAATAGAT
* ** *
1880 CATTACTAGAATCCATGTATGTTTTTATTTGAGGCACGAACTTAGACTTTACAAAAATTGGAGGG
1 CATTACTAGAATCCATGTTTG-ACTCATTTGAGGCACGAACTTAGACTTTACAAAAATTGGAGGG
* ** *
1945 AAGAAAGCCTTTGTTGCGAAACCAAAGCATCAATATCACCTAT-CTTAATGAGTAGACTATGTTT
65 AAGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTT-ATGAGAAGACTATGTTT
*
2009 ATGGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTTAAGAGA
129 ATGGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGA
* * * *
2074 CAAACTTGATTCT-ACCAAAACGGTGGAAAGAATAGCTTTTCTTGCGATC-CCAAAGCATCAGTG
194 CAAACTTGATTCTAACAAAAACGGTTGAAAGAAAAGCTTTTCTTGCGA-CACCAAAGCATCAATG
* *
2137 TCAAGTATCCTAATAAAGGGAATATGTTTTTGGTTCCCAATCTTGAGAAGAATCGAGACTGTTAC
258 TCAAGTATCCTAATAAAGGGAATATGTTTTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTAC
* * * * *
2202 GAAAATCAATGCTTCCCTTTTTTAAGGGATGAACTTTGATTTTAAGGAAAATAAGGCAGAGGAAA
323 GAGAATCAATGCTTGCCTTATTTAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGGAAA
* * * *
2267 CATTTCCTTGCAAAATAAAATCGTCAATATCATTTATCCTAATGAGGAGAAAGTATTTATTGTGT
388 CATTTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGGAGAATGTGTTTATTGTGT
2332 CTAATCATGAAATGAATGAAGAT
453 CTAATCATGAAATGAAT--AGAT
* *
2355 CATTACTAGAATCCACGTTTGACTCATTTGAGGCACAAACTTAGACTTTACAAAAATTGGAGGGA
1 CATTACTAGAATCCATGTTTGACTCATTTGAGGCACGAACTTAGACTTTACAAAAATTGGAGGGA
* * * * *
2420 AGAAAGCCTTTCTTGTGAAACCAAAGCGTCAATATCATGTATCCTTATGTGAAGACTGTGTTTGT
66 AGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTTATGAGAAGACTATGTTTAT
* * * * * * *
2485 GGTGCCTAATCTTGAAAAGAATCGGGA-T-GTCTAACTATTCATTTTTGTCTTATTGAAGAGAC
131 GGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGAC
2547 TTGTTAGGAT
Statistics
Matches: 1767, Mismatches: 255, Indels: 104
0.83 0.12 0.05
Matches are distributed among these distances:
465 54 0.03
466 173 0.10
467 24 0.01
468 71 0.04
469 211 0.12
470 309 0.17
471 289 0.16
472 312 0.18
473 81 0.05
474 188 0.11
475 55 0.03
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (473 bp):
CATTACTAGAATCCATGTTTGACTCATTTGAGGCACGAACTTAGACTTTACAAAAATTGGAGGGA
AGAAAGCCTTTCTTGCGAAACCAAAGCATCAATATCATGTATCCTTATGAGAAGACTATGTTTAT
GGTACCTAATCCTGAAAAGAATGGGGATTAGTATGACTATTCATGTTTGTCTTATTAAAGAGACA
AACTTGATTCTAACAAAAACGGTTGAAAGAAAAGCTTTTCTTGCGACACCAAAGCATCAATGTCA
AGTATCCTAATAAAGGGAATATGTTTTTGGTTCCCAATCTTGAGAAGAATGGGGACTGTTACGAG
AATCAATGCTTGCCTTATTTAAGGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGGAAACAT
TTCCATGCAAAATAAAATCATCAATATCATTTATCCTAATGAGGAGAATGTGTTTATTGTGTCTA
ATCATGAAATGAATAGAT
Found at i:2928 original size:17 final size:17
Alignment explanation
Indices: 2906--2952 Score: 66
Period size: 13 Copynumber: 3.0 Consensus size: 17
2896 TAGCCAAACT
2906 TGTATCGATACACCAAA
1 TGTATCGATACACCAAA
2923 TGTATCGAT--A-C-AA
1 TGTATCGATACACCAAA
2936 TGTATCGATACACCAAA
1 TGTATCGATACACCAAA
2953 AAATTGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 2 0.08
16 1 0.04
17 11 0.42
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (17 bp):
TGTATCGATACACCAAA
Found at i:5175 original size:22 final size:22
Alignment explanation
Indices: 5148--5203 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
5138 TTGCAAGTTG
5148 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
5170 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
5191 AAATAAA-AACTTG
1 AAATAAAGAACTTG
5204 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:9052 original size:20 final size:20
Alignment explanation
Indices: 9026--9106 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 20
9016 AATGTCCAAA
9026 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* * *
9046 GTGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACA--T-G--TTTCT
*
9071 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
9091 TTGTATCGATACATGT
1 ATGTATCGATACATGT
9107 ATCGATACAC
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
20 29 0.62
22 1 0.02
23 2 0.04
25 15 0.32
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:9109 original size:12 final size:13
Alignment explanation
Indices: 9092--9128 Score: 67
Period size: 12 Copynumber: 2.9 Consensus size: 13
9082 CATTTTTCTT
9092 TGTATCGATACA-
1 TGTATCGATACAC
9104 TGTATCGATACAC
1 TGTATCGATACAC
9117 TGTATCGATACA
1 TGTATCGATACA
9129 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:9121 original size:45 final size:45
Alignment explanation
Indices: 9025--9128 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
9015 AAATGTCCAA
* *
9025 AATGTATCGATACATGTTTCTGTGTATCGATACATCTGGAAATTC
1 AATGTATCGATACATGTTTCTGTGTATCGATACATCTAGAAATAC
* * * ***
9070 AATGTATCGATACATTTTTCTTTGTATCGATACATGTATCGATAC
1 AATGTATCGATACATGTTTCTGTGTATCGATACATCTAGAAATAC
*
9115 ACTGTATCGATACA
1 AATGTATCGATACA
9129 GGGGGATTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (45 bp):
AATGTATCGATACATGTTTCTGTGTATCGATACATCTAGAAATAC
Found at i:9292 original size:20 final size:20
Alignment explanation
Indices: 9249--9294 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
9239 AAATCTTTTG
9249 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
9270 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
9290 CAAAA
1 CAAAA
9295 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:11686 original size:13 final size:13
Alignment explanation
Indices: 11668--11693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11658 TACACCAAGT
11668 ATGTATCGATACA
1 ATGTATCGATACA
11681 ATGTATCGATACA
1 ATGTATCGATACA
11694 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:11712 original size:34 final size:32
Alignment explanation
Indices: 11650--11714 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
11640 TAGCCAAACT
**
11650 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
11682 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
11715 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Done.