Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2101
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: 51132
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1055 original size:23 final size:23
Alignment explanation
Indices: 1028--1071 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1018 CTGTTATCGA
1028 TTTTCATAATTATTTTTTTAAAT
1 TTTTCATAATTATTTTTTTAAAT
* *
1051 TTTTCATACTTGTTTTTTTAA
1 TTTTCATAATTATTTTTTTAA
1072 CACAATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTCATAATTATTTTTTTAAAT
Found at i:3283 original size:27 final size:29
Alignment explanation
Indices: 3234--3288 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
3224 AGTAGCTATA
*
3234 TAATCAACATCGGACACTTAGTG-CTACG
1 TAATCAACATCGCACACTTAGTGTCTACG
3262 TAATCAA-ATCGCA-ACTTCAGTGTCTAC
1 TAATCAACATCGCACACTT-AGTGTCTAC
3289 TAGGTCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (29 bp):
TAATCAACATCGCACACTTAGTGTCTACG
Found at i:11556 original size:27 final size:27
Alignment explanation
Indices: 11526--11703 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
11516 ATATTGAGTC
* * * *
11526 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
11553 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11580 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
11608 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
11635 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
11662 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11689 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11704 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:11665 original size:82 final size:81
Alignment explanation
Indices: 11547--11702 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
11537 TGCTATATAA
* *
11547 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
11612 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
11629 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
11693 CACTTAGTGC
65 CACTTAGTGC
11703 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19860 original size:18 final size:18
Alignment explanation
Indices: 19821--19857 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19811 CAATCATCCC
*
19821 TCATCCCTCATCCTTCAT
1 TCATCCCTCATCATTCAT
19839 TCATCCCTCACTCATTCAT
1 TCATCCCTCA-TCATTCAT
19858 CATTCTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (18 bp):
TCATCCCTCATCATTCAT
Found at i:22540 original size:27 final size:28
Alignment explanation
Indices: 22466--22542 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
22456 TATCAAGGCA
*
22466 GTGGCATAGCCACTAATATCA--AAATAC
1 GTGGCAAAGCCACTAATA-CAGTAAATAC
* * *
22493 GTGGAAAAGCCACCAAAACAGTAAA-AC
1 GTGGCAAAGCCACTAATACAGTAAATAC
*
22520 GTGGCAAAGCCACTAGTACAGTA
1 GTGGCAAAGCCACTAATACAGTA
22543 CTTCCTCCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.05
27 35 0.88
28 3 0.08
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (28 bp):
GTGGCAAAGCCACTAATACAGTAAATAC
Found at i:28125 original size:40 final size:40
Alignment explanation
Indices: 28070--28162 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
28060 ATTTGATGTG
*
28070 TATCCAGGCTTAAAGACCCGCAGGCTAT-ATGCTAGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCT-TCATGCTAGAATTA
* * *
28110 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTAGAATTA
*
28150 TATCCGGACTTAA
1 TATCCGGGCTTAA
28163 GGTCCGCAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTAGAATTA
Found at i:28181 original size:39 final size:39
Alignment explanation
Indices: 28099--28234 Score: 137
Period size: 39 Copynumber: 3.5 Consensus size: 39
28089 GCAGGCTATA
* * **
28099 TGCTAGAATTATATCCGGGCTTAAAGACCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGACTT-AAGGTCCGCAGGCTTCG
* *
28139 TGCTGGAATTGTATCCGGACTTAAGGTCCGCAAGCTTCG
1 TGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTTCG
* * ** *
28178 TGCTGGTACTATATCCAAACTTAAGGTCCGTAGGCTTCG
1 TGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTTCG
* * *
28217 TACTGGTACTATATCCGG
1 TGCTGGAATTATATCCGG
28235 GCCTAAAGTC
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
39 61 0.76
40 19 0.24
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.29
Consensus pattern (39 bp):
TGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTTCG
Found at i:36339 original size:21 final size:21
Alignment explanation
Indices: 36315--36363 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
36305 GGACAACAAT
**
36315 ACACGGGAGTGGTAACCTAAC
1 ACACGGGAGCAGTAACCTAAC
*
36336 ACACGGGTGCAGTAACCTAAC
1 ACACGGGAGCAGTAACCTAAC
36357 ACACGGG
1 ACACGGG
36364 CGTGAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.29, T:0.12
Consensus pattern (21 bp):
ACACGGGAGCAGTAACCTAAC
Found at i:43250 original size:27 final size:27
Alignment explanation
Indices: 43146--43250 Score: 76
Period size: 27 Copynumber: 4.0 Consensus size: 27
43136 TGCTAATAGT
*
43146 AACGTAGCAAAGCTACTAATAACAGT-A
1 AACGTAGCAAAGCCACT-ATAACAGTAA
* *
43173 AACGT-G-ATAGCCACTAATATCA--AA
1 AACGTAGCAAAGCCACT-ATAACAGTAA
* * * *
43197 ATACGTGGCAAAGCCACCAGAATAGTAA
1 A-ACGTAGCAAAGCCACTATAACAGTAA
*
43225 AACGTAGCAAAGCCACTATTACAGTA
1 AACGTAGCAAAGCCACTATAACAGTA
43251 CTTCCTCCGA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
24 2 0.03
25 17 0.29
26 5 0.08
27 32 0.54
28 3 0.05
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (27 bp):
AACGTAGCAAAGCCACTATAACAGTAA
Found at i:46228 original size:113 final size:113
Alignment explanation
Indices: 46066--46291 Score: 416
Period size: 113 Copynumber: 2.0 Consensus size: 113
46056 TACACTTAAT
*
46066 CAAACAAGTTAGTTACATAAATGTTCATATAAGCATCAAGCAAGTATAGATGAGCTCATCATACT
1 CAAACAAGTTAGTTACATAAATGTTCATATAAGCATCAAGCAAGCATAGATGAGCTCATCATACT
*
46131 ATATTTTTTCTAGACATCATTCATTTCATCTCATATCATGTCAAGTAA
66 ATATTTTTTCAAGACATCATTCATTTCATCTCATATCATGTCAAGTAA
* *
46179 CAAACAAGTTAGTTACATAAATGTTCATATAAGCATCAAGTAAGCATAGATGAGCTTATCATACT
1 CAAACAAGTTAGTTACATAAATGTTCATATAAGCATCAAGCAAGCATAGATGAGCTCATCATACT
46244 ATATTTTTTCAAGACATCATTCATTTCATCTCATATCATGTCAAGTAA
66 ATATTTTTTCAAGACATCATTCATTTCATCTCATATCATGTCAAGTAA
46292 TTTATCTGTT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (113 bp):
CAAACAAGTTAGTTACATAAATGTTCATATAAGCATCAAGCAAGCATAGATGAGCTCATCATACT
ATATTTTTTCAAGACATCATTCATTTCATCTCATATCATGTCAAGTAA
Found at i:48467 original size:46 final size:46
Alignment explanation
Indices: 48414--48678 Score: 267
Period size: 46 Copynumber: 5.7 Consensus size: 46
48404 TGGTTGAGCA
48414 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
48460 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
48505 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * ** *
48553 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAAACGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-TG
*
48597 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
48645 CCCGAGCAT-GTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAAC-TCGTTGAGTTGAGTCCGAGTTCACTTA
48679 GTGGCGGGTT
Statistics
Matches: 179, Mismatches: 24, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.01
43 9 0.05
44 1 0.01
45 5 0.03
46 116 0.65
47 31 0.17
48 4 0.02
49 5 0.03
50 4 0.02
51 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:48570 original size:93 final size:92
Alignment explanation
Indices: 48411--48673 Score: 449
Period size: 93 Copynumber: 2.8 Consensus size: 92
48401 GGATGGTTGA
*
48411 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
48476 TGAGTCCGAGTTCGTGAAATGT-AACTAG
66 TGAGTCCGAGTTCGTGAAATGTAAAC--G
48504 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
48569 TGAGTCCGAGTTCGTGAAATGTAAACG
66 TGAGTCCGAGTTCGTGAAATGTAAACG
* * *
48596 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCAT-GTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAAC-TCGTTGAG
48660 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
48674 ACTTAGTGGC
Statistics
Matches: 164, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
92 74 0.45
93 87 0.53
94 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAAACG
Done.