Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6113.1
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: 13892
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.27
Warning! 1639 characters in sequence are not A, C, G, or T
Found at i:251 original size:40 final size:40
Alignment explanation
Indices: 172--348 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
162 CAGATGATAA
* * * * *
172 CCGGACTAAGATCCGAAGGCATTCGTGCGACTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
212 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
252 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
292 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
332 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
349 ATGCTTGGGT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 101 0.85
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:6742 original size:62 final size:62
Alignment explanation
Indices: 6676--6798 Score: 228
Period size: 62 Copynumber: 2.0 Consensus size: 62
6666 TAAATAGGAC
*
6676 TTATGTGATAAAATTTAGAAATGTGCTAGGCAAATGTAAAGTGGCCTAATAATGCATGTTAT
1 TTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATGTAAAGTGGCCTAATAATGCATGTTAT
*
6738 TTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATGTAAAGTGGCCTATTAATGCATGTTA
1 TTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATGTAAAGTGGCCTAATAATGCATGTTA
6799 AAAAAATGAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (62 bp):
TTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATGTAAAGTGGCCTAATAATGCATGTTAT
Found at i:9389 original size:27 final size:27
Alignment explanation
Indices: 9348--9439 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
9338 GGGCAAAATA
* *
9348 GTCATTTTACCCTACAGGGGTATGTCG
1 GTCATTTTACACTACAAGGGTATGTCG
* *
9375 GTCATTTCACACTACAAGGGTATTTCG
1 GTCATTTTACACTACAAGGGTATGTCG
* * *
9402 GTAATTTTACACTATAAGGGTATTTCG
1 GTCATTTTACACTACAAGGGTATGTCG
* *
9429 ATAATTTTACA
1 GTCATTTTACA
9440 AATCGAGGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACACTACAAGGGTATGTCG
Found at i:9423 original size:54 final size:54
Alignment explanation
Indices: 9351--9466 Score: 126
Period size: 54 Copynumber: 2.1 Consensus size: 54
9341 CAAAATAGTC
* * * * *
9351 ATTTTACCCTACAGGGGTATGTCGGTCATTTCAC-ACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATGTCGATAATTTCACAAAT-CAAGGGTATTTCGGTA
* * * * *
9405 ATTTTACACTATAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCGGTA
1 ATTTTACACTACAAGGGTATGTCGATAATTTCACAAATCAAGGGTATTTCGGTA
9459 ATTTTACA
1 ATTTTACA
9467 AATCGAGGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 49 0.96
55 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (54 bp):
ATTTTACACTACAAGGGTATGTCGATAATTTCACAAATCAAGGGTATTTCGGTA
Found at i:9476 original size:54 final size:53
Alignment explanation
Indices: 9391--9556 Score: 210
Period size: 54 Copynumber: 3.1 Consensus size: 53
9381 TCACACTACA
* * * *
9391 AGGGTATTTCGGTAATTTTACACTAT-AAGGGTATTTCGA-TAATTTTACAAATCG
1 AGGGTGTTTCGGTAATTTTACA-AATCGAGGGT-TTTC-ACTAATTTTACAAATTG
* * *
9445 AGGGTGTTTCGGTAATTTTACAAATCGAGGGTGTTTTAGTAATTTCACAAATTG
1 AGGGTGTTTCGGTAATTTTACAAATCGAGGGT-TTTCACTAATTTTACAAATTG
*
9499 GGGGTGTTTCGGTAATTTTACAAATCGAGGGTTTTCACTAATTTTACAAATTG
1 AGGGTGTTTCGGTAATTTTACAAATCGAGGGTTTTCACTAATTTTACAAATTG
9552 AGGGT
1 AGGGT
9557 ATTTTAGTAA
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
53 25 0.26
54 73 0.74
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (53 bp):
AGGGTGTTTCGGTAATTTTACAAATCGAGGGTTTTCACTAATTTTACAAATTG
Found at i:9541 original size:26 final size:27
Alignment explanation
Indices: 9391--9569 Score: 184
Period size: 27 Copynumber: 6.7 Consensus size: 27
9381 TCACACTACA
* * * *
9391 AGGGTATTTCGGTAATTTTACACTAT-A
1 AGGGTGTTTCAGTAATTTTACA-AATCG
*
9418 AGGGTATTTC-GATAATTTTACAAATCG
1 AGGGTGTTTCAG-TAATTTTACAAATCG
*
9445 AGGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTGTTTCAGTAATTTTACAAATCG
* * *
9472 AGGGTGTTTTAGTAATTTCACAAATTG
1 AGGGTGTTTCAGTAATTTTACAAATCG
* *
9499 GGGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTGTTTCAGTAATTTTACAAATCG
* *
9526 AGGGT-TTTCACTAATTTTACAAATTG
1 AGGGTGTTTCAGTAATTTTACAAATCG
* *
9552 AGGGTATTTTAGTAATTT
1 AGGGTGTTTCAGTAATTT
9570 CTTTTTATTA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 26 0.20
27 103 0.79
28 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
AGGGTGTTTCAGTAATTTTACAAATCG
Found at i:9570 original size:80 final size:81
Alignment explanation
Indices: 9419--9570 Score: 243
Period size: 80 Copynumber: 1.9 Consensus size: 81
9409 TACACTATAA
** *
9419 GGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAATCGAGGGTGTTTTAG
1 GGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCACTAATTTTACAAATCGAGGGTATTTTAG
9484 TAATTTCACAAATTGG
66 TAATTTCACAAATTGG
* * *
9500 GGGTGTTTCGGTAATTTTACAAATCGAGGGT-TTTCACTAATTTTACAAATTGAGGGTATTTTAG
1 GGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCACTAATTTTACAAATCGAGGGTATTTTAG
9564 TAATTTC
66 TAATTTC
9571 TTTTTATTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
80 36 0.55
81 29 0.45
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (81 bp):
GGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCACTAATTTTACAAATCGAGGGTATTTTAG
TAATTTCACAAATTGG
Found at i:9930 original size:28 final size:28
Alignment explanation
Indices: 9889--9977 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
9879 CCCTTTTAGG
* * *
9889 CCCAATCTCGTTCACATGGCCCATCAGA
1 CCCAATCACATTCATATGGCCCATCAGA
9917 CCCAATCACATTCATATGGCCCATCA-A
1 CCCAATCACATTCATATGGCCCATCAGA
* * * *
9944 GCCCTATCATATTCATATTGCCCATCAGG
1 -CCCAATCACATTCATATGGCCCATCAGA
9973 CCCAA
1 CCCAA
9978 GTACTTCCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 1 0.02
28 50 0.98
ACGTcount: A:0.28, C:0.37, G:0.11, T:0.24
Consensus pattern (28 bp):
CCCAATCACATTCATATGGCCCATCAGA
Found at i:11752 original size:20 final size:19
Alignment explanation
Indices: 11720--11785 Score: 54
Period size: 20 Copynumber: 3.7 Consensus size: 19
11710 AAATGAGATA
*
11720 TTTTGAAATCCATTTGTTG
1 TTTTGAAAACCATTTGTTG
11739 TTTTGGAAAACCA-----TG
1 TTTT-GAAAACCATTTGTTG
*
11754 -TTTGAAATCCATTTGTTG
1 TTTTGAAAACCATTTGTTG
11772 TTTTGGAAAACCAT
1 TTTT-GAAAACCAT
11786 GCCTTACTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 15
0.67 0.06 0.28
Matches are distributed among these distances:
13 7 0.19
14 3 0.08
15 2 0.06
18 2 0.06
19 7 0.19
20 15 0.42
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (19 bp):
TTTTGAAAACCATTTGTTG
Found at i:11763 original size:33 final size:33
Alignment explanation
Indices: 11721--11786 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
11711 AATGAGATAT
11721 TTTGAAATCCATTTGTTGTTTTGGAAAACCATG
1 TTTGAAATCCATTTGTTGTTTTGGAAAACCATG
11754 TTTGAAATCCATTTGTTGTTTTGGAAAACCATG
1 TTTGAAATCCATTTGTTGTTTTGGAAAACCATG
11787 CCTTACTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (33 bp):
TTTGAAATCCATTTGTTGTTTTGGAAAACCATG
Found at i:12746 original size:27 final size:27
Alignment explanation
Indices: 12703--12777 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
12693 AAGGGCAAAA
* *
12703 TAGTCATTTTACCCTACAGGGGTATGT
1 TAGTCATTTTACACTACAAGGGTATGT
* *
12730 TGGTCATTTTACACTACAAGGGTATTT
1 TAGTCATTTTACACTACAAGGGTATGT
** *
12757 TAGAAATTTTACACTATAAGG
1 TAGTCATTTTACACTACAAGG
12778 TTATTTCGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (27 bp):
TAGTCATTTTACACTACAAGGGTATGT
Found at i:12819 original size:54 final size:55
Alignment explanation
Indices: 12751--13235 Score: 267
Period size: 54 Copynumber: 9.0 Consensus size: 55
12741 CACTACAAGG
* * *
12751 GTATTTTAGA-AATTTTACACTAT-AAGGTTATTTC-GATAAATTTT-TAAATCGGGG
1 GTATTTT-GATAATTTTACACAATCAAGGGTATTTCAG-T-AATTTTATAAATCGGGA
* * *
12805 GTGTTTTGGTAATTTTAC-CAATCGAGGGTATTTCAGTAATTTTATAAATCGGGA
1 GTATTTTGATAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCGGGA
* * * * * *
12859 GTATTTTGATAATTTTACA-AGTCGAGGGTGTTTCAGTAATTTCACAAATCGGGG
1 GTATTTTGATAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCGGGA
** * * * *
12913 GTATTTCAATAATTTTACA-AATCGAGCGTATTTCAGTAATTTCA-CAATCGAGG-
1 GTATTTTGATAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCG-GGA
* * * * * * *
12966 GTATTTCGATAATTTTACA-ATTCGAGGGTATTTCAATAATTTCA-CAATTGAGG-
1 GTATTTTGATAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCG-GGA
* * * * * *
13019 GTATTTT-AGTAATTTTACA-AATCGAGGTTGTTTCAATAATTTTAAAAATCAAGG-
1 GTATTTTGA-TAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATC-GGGA
* * ***
13073 GTATTTT-AGTAA-TTT-CACAATCAAGGGTATTTCGGTAATTTTACAAATTAATG-
1 GTATTTTGA-TAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAA-TCGGGA
* * * ** * * * * * *
13126 GTGTTTCGGTAATTTTACA-AATTGAGGGTGTTTTAGTAATTTCACAAATTGGGG
1 GTATTTTGATAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCGGGA
* * * *
13180 GTA-TTTCAGTAATTTTACA-AATCGAGGGTATTTCAGTAATTTTACAAATCGAGA
1 GTATTTTGA-TAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCGGGA
13234 GT
1 GT
13236 GTTTCAGTAA
Statistics
Matches: 352, Mismatches: 63, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
52 3 0.01
53 140 0.40
54 206 0.59
55 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (55 bp):
GTATTTTGATAATTTTACACAATCAAGGGTATTTCAGTAATTTTATAAATCGGGA
Found at i:12833 original size:27 final size:27
Alignment explanation
Indices: 12813--13248 Score: 470
Period size: 27 Copynumber: 16.3 Consensus size: 27
12803 GGGTGTTTTG
*
12813 GTAATTTTACCAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* *
12840 GTAATTTTATAAATCG-GGAGTATTT-T
1 GTAATTTTACAAATCGAGG-GTATTTCA
* *
12866 GATAATTTTACAAGTCGAGGGTGTTTCA
1 G-TAATTTTACAAATCGAGGGTATTTCA
* *
12894 GTAATTTCACAAATCGGGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* *
12921 ATAATTTTACAAATCGAGCGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
*
12948 GTAATTTCAC-AATCGAGGGTATTTC-
1 GTAATTTTACAAATCGAGGGTATTTCA
*
12973 GATAATTTTACAATTCGAGGGTATTTCA
1 G-TAATTTTACAAATCGAGGGTATTTCA
* * * *
13001 ATAATTTCAC-AATTGAGGGTATTTTA
1 GTAATTTTACAAATCGAGGGTATTTCA
* *
13027 GTAATTTTACAAATCGAGGTTGTTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* * * *
13054 ATAATTTTAAAAATCAAGGGTATTTTA
1 GTAATTTTACAAATCGAGGGTATTTCA
* * *
13081 GTAATTTCAC-AATCAAGGGTATTTCG
1 GTAATTTTACAAATCGAGGGTATTTCA
** * * *
13107 GTAATTTTACAAATTAATGGTGTTTCG
1 GTAATTTTACAAATCGAGGGTATTTCA
* * *
13134 GTAATTTTACAAATTGAGGGTGTTTTA
1 GTAATTTTACAAATCGAGGGTATTTCA
* * *
13161 GTAATTTCACAAATTGGGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
13188 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* *
13215 GTAATTTTACAAATCGAGAGTGTTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
13242 GTAATTT
1 GTAATTT
13249 ATCTTTATTA
Statistics
Matches: 341, Mismatches: 59, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
25 1 0.00
26 69 0.20
27 268 0.79
28 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAATCGAGGGTATTTCA
Found at i:13002 original size:80 final size:80
Alignment explanation
Indices: 12796--13248 Score: 466
Period size: 80 Copynumber: 5.6 Consensus size: 80
12786 ATAAATTTTT
* ** * * *
12796 AAATCGGGGGTGTTTTGGTAATTTTACCAATCGAGGGTATTTCAGTAATTTTATAAATCG-GGAG
1 AAATCGAGGGTG-TTTCATAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGAGG-G
*
12860 TATTT-TGATAATTTTAC
64 TATTTCAG-TAATTTTAC
* * * * * *
12877 AAGTCGAGGGTGTTTCAGTAATTTCACAAATCGGGGGTATTTCAATAATTTTACAAATCGAGCGT
1 AAATCGAGGGTGTTTCA-TAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGAGGGT
*
12942 ATTTCAGTAATTTCAC
65 ATTTCAGTAATTTTAC
* * * *
12958 -AATCGAGGGTATTTCGATAATTTTACAATTCGAGGGTATTTCAATAATTTCAC-AATTGAGGGT
1 AAATCGAGGGTGTTTC-ATAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGAGGGT
*
13021 ATTTTAGTAATTTTAC
65 ATTTCAGTAATTTTAC
* * * * *
13037 AAATCGAGGTTGTTTCAATAATTTTAAAAATCAAGGGTATTTTAGTAATTTCAC-AATCAAGGGT
1 AAATCGAGGGTGTTTC-ATAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGAGGGT
*
13101 ATTTCGGTAATTTTAC
65 ATTTCAGTAATTTTAC
** * * * * * * *
13117 AAATTAATGGTGTTTCGGTAATTTTACAAATTGAGGGTGTTTTAGTAATTTCACAAATTGGGGGT
1 AAATCGAGGGTGTTTC-ATAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGAGGGT
13182 ATTTCAGTAATTTTAC
65 ATTTCAGTAATTTTAC
* * *
13198 AAATCGAGGGTATTTCAGTAATTTTACAAATCGAGAGTGTTTCAGTAATTT
1 AAATCGAGGGTGTTTCA-TAATTTTACAAATCGAGGGTATTTCAGTAATTT
13249 ATCTTTATTA
Statistics
Matches: 309, Mismatches: 56, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
79 22 0.07
80 159 0.51
81 126 0.41
82 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (80 bp):
AAATCGAGGGTGTTTCATAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGAGGGTA
TTTCAGTAATTTTAC
Found at i:13608 original size:28 final size:28
Alignment explanation
Indices: 13547--13656 Score: 123
Period size: 28 Copynumber: 3.9 Consensus size: 28
13537 GATGCACACT
* * *
13547 TATTCATTTGGCCCCTTTAGGCCCAATC-
1 TATTCATATGG-CCCATCAGGCCCAATCA
* * *
13575 TCATTCACATGGCCTATCAAGCCCAATCA
1 T-ATTCATATGGCCCATCAGGCCCAATCA
*
13604 TATTCATATGGCCCATCAGGCCCTATCA
1 TATTCATATGGCCCATCAGGCCCAATCA
*
13632 CATTCATATGGCCCATCAGGCCCAA
1 TATTCATATGGCCCATCAGGCCCAA
13657 CTACTTCCCA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 59 0.87
29 9 0.13
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (28 bp):
TATTCATATGGCCCATCAGGCCCAATCA
Found at i:13643 original size:56 final size:57
Alignment explanation
Indices: 13547--13656 Score: 141
Period size: 56 Copynumber: 1.9 Consensus size: 57
13537 GATGCACACT
* * * * *
13547 TATTCATTTGGCCCCTTTAGGCCCAATCTCATTCACATGGCCTATCAAGCCCAATCA
1 TATTCATATGGCCCCATCAGGCCCAATCACATTCACATGGCCCATCAAGCCCAATCA
* * *
13604 TATTCATATGG-CCCATCAGGCCCTATCACATTCATATGGCCCATCAGGCCCAA
1 TATTCATATGGCCCCATCAGGCCCAATCACATTCACATGGCCCATCAAGCCCAA
13657 CTACTTCCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
56 35 0.78
57 10 0.22
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (57 bp):
TATTCATATGGCCCCATCAGGCCCAATCACATTCACATGGCCCATCAAGCCCAATCA
Done.