Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2018
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: 21300
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:5494 original size:56 final size:56
Alignment explanation
Indices: 5427--5546 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
5417 TATTAGTTTA
5427 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
5483 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
5539 TTGCCCAT
1 TTGCCCAT
5547 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:8033 original size:21 final size:21
Alignment explanation
Indices: 7995--8035 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7985 TATGATATTT
*
7995 TTATAAAGTATTACATTTTGG
1 TTATAAAGTAATACATTTTGG
* *
8016 TTATAAATTAATATATTTTG
1 TTATAAAGTAATACATTTTG
8036 TTTAATGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTATAAAGTAATACATTTTGG
Found at i:8531 original size:15 final size:15
Alignment explanation
Indices: 8511--8541 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8501 ATTCTTTCTT
*
8511 CATCTATTTTACATA
1 CATCTAATTTACATA
8526 CATCTAATTTACATA
1 CATCTAATTTACATA
8541 C
1 C
8542 CTTTCTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (15 bp):
CATCTAATTTACATA
Found at i:9499 original size:15 final size:17
Alignment explanation
Indices: 9465--9500 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
9455 TTTGATATTT
9465 AATAAAGGTCTTATAAA
1 AATAAAGGTCTTATAAA
9482 AATAAA-GTCTTA-AAA
1 AATAAAGGTCTTATAAA
9497 AATA
1 AATA
9501 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (17 bp):
AATAAAGGTCTTATAAA
Found at i:12464 original size:47 final size:47
Alignment explanation
Indices: 12390--12679 Score: 489
Period size: 47 Copynumber: 6.2 Consensus size: 47
12380 TATGCGTGAT
12390 GAAT-GCCAATGTGAT-AA-GTGAACATGTGTATGTGTGATAAGGCC
1 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
12434 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
1 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
12481 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
1 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
12528 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
1 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
** * *
12575 GAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCC
1 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
* *
12622 GAATGGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCC
1 GAATGGCCAATGTGATGAATGTGAACA-TGTGTATGTGTGATAAGGCC
12669 GAATGGCCAAT
1 GAATGGCCAAT
12680 TGGCCAATGT
Statistics
Matches: 236, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
44 4 0.02
45 11 0.05
46 3 0.01
47 218 0.92
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCC
Found at i:12582 original size:141 final size:139
Alignment explanation
Indices: 12331--12679 Score: 496
Period size: 141 Copynumber: 2.5 Consensus size: 139
12321 ATGTACAAGT
* * * * * * **
12331 ATATATGTGATAGGGCCGAGTGGCCAATGTGATG-ATATGAAAGTATATATATGCG-T---GATG
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCG
12391 AAT-GCCAATGTGATAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
66 AATGGCCAATGTGATAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
*
12455 TGAACATGT
131 TGAACATGC
* * * * *
12464 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGTGTATGTGTGATAAGGCC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCC
12528 GAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGA
65 GAATGGCCAATGTGAT-AA-GTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGA
12593 ATGTGAACATGC
128 ATGTGAACATGC
12605 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCG
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCG
12670 AATGGCCAAT
66 AATGGCCAAT
12680 TGGCCAATGT
Statistics
Matches: 189, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
133 30 0.16
134 14 0.07
135 2 0.01
138 5 0.03
139 11 0.06
140 3 0.02
141 124 0.66
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (139 bp):
ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCG
AATGGCCAATGTGATAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
TGAACATGC
Found at i:12735 original size:55 final size:55
Alignment explanation
Indices: 12625--12736 Score: 154
Period size: 55 Copynumber: 2.0 Consensus size: 55
12615 TAAGGCCGAA
* * *
12625 TGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAAT
1 TGGCCAATGTGACGAATGTGAAAGTGTATAAATGTGATAAGCCCGAATGGCCAAT
* * *
12680 TGGCCAATGTGACGGATGTGGAAGTGTATAAATGTGATAAGTCCCGAA-GGGCAAT
1 TGGCCAATGTGACGAATGTGAAAGTGTATAAATGTGATAAG-CCCGAATGGCCAAT
12735 TG
1 TG
12737 TGTCAGTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 45 0.90
56 5 0.10
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (55 bp):
TGGCCAATGTGACGAATGTGAAAGTGTATAAATGTGATAAGCCCGAATGGCCAAT
Found at i:15211 original size:38 final size:38
Alignment explanation
Indices: 15147--15221 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
15137 AATCCGAGTT
*
15147 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
15185 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
15222 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:15334 original size:40 final size:40
Alignment explanation
Indices: 15275--15594 Score: 484
Period size: 40 Copynumber: 8.1 Consensus size: 40
15265 AGGTCTCGAC
15275 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
15314 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
15354 GATGTATCCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTAT-CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
15395 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
15435 GATGTATCC-GGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
15474 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * *
15514 GATATATCCGTGCTAA-ACCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
15553 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
15593 GA
1 GA
15595 CGTGTATTCG
Statistics
Matches: 257, Mismatches: 20, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
39 75 0.29
40 142 0.55
41 40 0.16
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:15497 original size:79 final size:80
Alignment explanation
Indices: 15275--15594 Score: 484
Period size: 79 Copynumber: 4.0 Consensus size: 80
15265 AGGTCTCGAC
15275 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
15339 AGCATTCATGCTAGT
66 AGCATTCATGCTAGT
*
15354 GATGTATCCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAA
1 GATGTAT-CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAA
*
15419 GAGCATTCGTGCTAGT
65 GAGCATTCATGCTAGT
* * *
15435 GATGTATCC-GGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
15499 AGCATTCGTGCTAGT
66 AGCATTCATGCTAGT
* * * * * * *
15514 GATATATCCGTGCTAA-ACCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
15578 AGCAATCATGCTAGT
66 AGCATTCATGCTAGT
15593 GA
1 GA
15595 CGTGTATTCG
Statistics
Matches: 220, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
79 133 0.60
80 9 0.04
81 78 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
AGCATTCATGCTAGT
Found at i:19107 original size:47 final size:47
Alignment explanation
Indices: 18967--19152 Score: 286
Period size: 48 Copynumber: 3.9 Consensus size: 47
18957 ATATCACTGC
* *
18967 GTGATAAGGCCGAATGGCC-ATGGTGATAAAGGTGAACAATGTGTATGT
1 GTGATAAGGCCGAATGGCCAAT-GTGATGAATGTGAAC-ATGTGTATGT
19015 GTGATAAGGGCCGAATGGACCAATGTGATGAATGTGAACATGTGTATGT
1 GTGATAA-GGCCGAATGG-CCAATGTGATGAATGTGAACATGTGTATGT
19064 GTGATAAGGCCGAATGGCCAATGTGAATGAATGTGAACA-GTGTATGT
1 GTGATAAGGCCGAATGGCCAATGTG-ATGAATGTGAACATGTGTATGT
19111 GTGATAAGGCCGAAATGGCCAATGTGATGAATGTGAACATGT
1 GTGATAAGGCCG-AATGGCCAATGTGATGAATGTGAACATGT
19153 TCCATATATG
Statistics
Matches: 130, Mismatches: 2, Indels: 12
0.90 0.01 0.08
Matches are distributed among these distances:
47 41 0.32
48 45 0.35
49 27 0.21
50 15 0.12
51 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.25
Consensus pattern (47 bp):
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGT
Found at i:19143 original size:95 final size:97
Alignment explanation
Indices: 18967--19152 Score: 292
Period size: 95 Copynumber: 1.9 Consensus size: 97
18957 ATATCACTGC
18967 GTGATAAGGCCGAATGGCCATGGTGATAAAGGTGAACAATGTGTATGTGTGATAAGGGCCGAATG
1 GTGATAAGGCCGAATGGCCATGGTGATAAAGGTGAACAATGTGTATGTGTGATAAGGGCCGAATG
19032 GACCAATGTGATGAATGTGAACATGTGTATGT
66 GACCAATGTGATGAATGTGAACATGTGTATGT
* *
19064 GTGATAAGGCCGAATGGCCAAT-GTGAATGAATGTGAAC-A-GTGTATGTGTGATAA-GGCCGAA
1 GTGATAAGGCCGAATGGCC-ATGGTG-ATAAAGGTGAACAATGTGTATGTGTGATAAGGGCCG-A
19125 ATGG-CCAATGTGATGAATGTGAACATGT
63 ATGGACCAATGTGATGAATGTGAACATGT
19153 TCCATATATG
Statistics
Matches: 84, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
95 29 0.35
96 20 0.24
97 23 0.27
98 12 0.14
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.25
Consensus pattern (97 bp):
GTGATAAGGCCGAATGGCCATGGTGATAAAGGTGAACAATGTGTATGTGTGATAAGGGCCGAATG
GACCAATGTGATGAATGTGAACATGTGTATGT
Found at i:19217 original size:47 final size:47
Alignment explanation
Indices: 18967--19215 Score: 176
Period size: 47 Copynumber: 5.1 Consensus size: 47
18957 ATATCACTGC
* * * *
18967 GTGATAAGGCCG-AATGGCC-ATGGTGATAAAGGTGAACAATGTGTAT-GT
1 GTGATAAGGCCGAAATGGCCAAT-GTGATGAATGTG--GAA-GTGTATAAT
* *
19015 GTGATAAGGGCCG-AATGGACCAATGTGATGAATGTGAACATGTGTAT-GT
1 GTGATAA-GGCCGAAATGG-CCAATGTGATGAATGTGGA-A-GTGTATAAT
* *
19064 GTGATAAGGCCG-AATGGCCAATGTGAATGAATGTGAACAGTGTAT-GT
1 GTGATAAGGCCGAAATGGCCAATGTG-ATGAATGTGGA-AGTGTATAAT
*
19111 GTGATAAGGCCGAAATGGCCAATGTGATGAATGT-GAACATGTTCCATATAT
1 GTGATAAGGCCGAAATGGCCAATGTGATGAATGTGGAA-GTG-T--ATA-AT
* *
19162 GAGATAAAGGCCGAAATGGCCAAT-TGA-GGATGTGGAAGTGTATAAAT
1 GTGAT-AAGGCCGAAATGGCCAATGTGATGAATGTGGAAGTGTAT-AAT
19209 GTGATAA
1 GTGATAA
19216 AGTTCGCTGA
Statistics
Matches: 176, Mismatches: 10, Indels: 32
0.81 0.05 0.15
Matches are distributed among these distances:
45 1 0.01
46 5 0.03
47 45 0.26
48 45 0.26
49 30 0.17
50 19 0.11
51 13 0.07
52 18 0.10
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.25
Consensus pattern (47 bp):
GTGATAAGGCCGAAATGGCCAATGTGATGAATGTGGAAGTGTATAAT
Done.