Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2554
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: 28016
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Found at i:2166 original size:28 final size:27
Alignment explanation
Indices: 2083--2170 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 27
2073 GTGACAGAGT
*
2083 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
*
2112 CACCAGAACAGAT-A--TGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
2137 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
2165 CACCAG
1 CACCAG
2171 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
25 23 0.44
26 1 0.02
28 21 0.40
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:2322 original size:27 final size:27
Alignment explanation
Indices: 2279--2335 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
2269 TTAACCCTAG
*
2279 GGGTATAAAGGTCATTTTGCATACATA
1 GGGTATAAAGGTAATTTTGCATACATA
*
2306 GGGTATAATGGTAATTTTGCATACATA
1 GGGTATAAAGGTAATTTTGCATACATA
2333 GGG
1 GGG
2336 GTATTCTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (27 bp):
GGGTATAAAGGTAATTTTGCATACATA
Found at i:11428 original size:39 final size:40
Alignment explanation
Indices: 11284--11505 Score: 246
Period size: 40 Copynumber: 5.7 Consensus size: 40
11274 TTGAATGATG
* *
11284 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
11323 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA-
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
11363 TCCGGACTAAG--CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
11401 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
11440 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
11479 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
11506 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
37 26 0.16
38 10 0.06
39 47 0.29
40 68 0.42
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:11527 original size:79 final size:79
Alignment explanation
Indices: 11374--11538 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
11364 CCGGACTAAG
* ** *
11374 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
11439 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
11453 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-C
* *
11516 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
11532 CCGAAGG
1 CCGAAGG
11539 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:19367 original size:40 final size:40
Alignment explanation
Indices: 19184--19405 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
19174 TTGAATGATG
* * * *
19184 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
19224 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
19263 TCCGGGCTAAG--CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
19301 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
19340 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
19381 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19406 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
37 24 0.15
38 12 0.07
39 46 0.28
40 71 0.44
41 10 0.06
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:19427 original size:79 final size:79
Alignment explanation
Indices: 19237--19438 Score: 202
Period size: 79 Copynumber: 2.6 Consensus size: 79
19227 GGACTAAGAT
** * *
19237 CCGAAGGCATTTGTGCGAGAT-ACT-AATCCGGGCT-AA-GCCGAAGGCATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACT
*
19298 AATTCCGGGCTAAGC
65 AATACCGGGCTAAGC
** * * *
19313 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTA
*
19377 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* *
19393 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
19439 TACGTGATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
75 1 0.01
76 22 0.21
77 9 0.08
78 3 0.03
79 47 0.44
80 25 0.23
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:27135 original size:39 final size:39
Alignment explanation
Indices: 26994--27210 Score: 222
Period size: 38 Copynumber: 5.7 Consensus size: 39
26984 TTGAATGATG
* *
26994 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTA-A
*
27034 TCCGGACTAAGAT----AAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAA
*
27070 TCCGGACTAAG--CCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
*
27107 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AA
* *
27147 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGAATA-TAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-ATACTAA
*
27186 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27211 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 10, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
36 12 0.08
37 31 0.20
38 42 0.27
39 36 0.23
40 32 0.21
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
Found at i:27199 original size:38 final size:38
Alignment explanation
Indices: 27047--27210 Score: 217
Period size: 39 Copynumber: 4.3 Consensus size: 38
27037 GGACTAAGAT
*
27047 AAGGCATTTGTGCGAGATACTAATCCGGACTAAG-CCG
1 AAGGCATTTGTGCGAGATACTAATCCGGGCTAAGCCCG
27084 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAA-TCCGGGCTAAGCCCG
* *
27123 AAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCG
1 AAGGCATTTGTGCGAGATACT-AATCCGGGCTAAG-CCCG
* *
27163 AAGGCATTTGTGTGAGAATA-TAA-CCGGGCTATGTCCCG
1 AAGGCATTTGTGCGAG-ATACTAATCCGGGCTAAG-CCCG
27201 AAGGCATTTG
1 AAGGCATTTG
27211 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
37 23 0.20
38 33 0.29
39 35 0.30
40 22 0.19
41 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (38 bp):
AAGGCATTTGTGCGAGATACTAATCCGGGCTAAGCCCG
Found at i:27228 original size:78 final size:77
Alignment explanation
Indices: 27081--27243 Score: 188
Period size: 78 Copynumber: 2.1 Consensus size: 77
27071 CCGGACTAAG
** *
27081 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAA-TCCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
27146 ATCCGGGTTAAGTC
65 ATCC-GGTTAAATC
* *
27160 CCGAAGGCATTTGTGTGAGAATA-TAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCT
1 CCGAAGGCATTTGTGCGAG-ATACTAATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CT
* *
27222 ATATCCGGTTAAATT
63 AAATCCGGTTAAATC
27237 CCGAAGG
1 CCGAAGG
27244 TACGTGATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
77 24 0.33
78 25 0.34
79 21 0.29
80 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
TCCGGTTAAATC
Done.