Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1594
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: 47677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:7066 original size:36 final size:38
Alignment explanation
Indices: 7021--7092 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
7011 CCGAAGGCAT
*
7021 TTGTGCGAG-TACTA-AATCCGGGTTAAGTCCCGAAGAA
1 TTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGAA
*
7058 TTGT-CGAGTTACTATAACCGGGCTATGTCCCGAAG
1 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
7093 GCTTTGAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.13
37 25 0.81
38 2 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (38 bp):
TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGAA
Found at i:7079 original size:37 final size:37
Alignment explanation
Indices: 6983--7092 Score: 95
Period size: 37 Copynumber: 2.9 Consensus size: 37
6973 TCCAAGGCAT
* *
6983 TTGTGCGAGAATACTAATTCC-GGC-AAG-CCCGAAGGCAT
1 TTGTGCGAG--TACTAAATCCGGGCTAAGTCCCGAA-G-AA
*
7021 TTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGAA
1 TTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGAA
*
7058 TTGT-CGAGTTACTATAA-CCGGGCTATGTCCCGAAG
1 TTGTGCGAG-TACTA-AATCCGGGCTAAGTCCCGAAG
7093 GCTTTGAACG
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
36 13 0.21
37 28 0.45
38 15 0.24
39 6 0.10
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (37 bp):
TTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGAA
Found at i:14329 original size:38 final size:39
Alignment explanation
Indices: 14269--14396 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
14259 GACATAAGAT
*
14269 CGAAGGCATTTGTGCGAATACTAATTCCGGGCTAAG-CC
1 CGAAGGCATTTGTGCGAGTACTAATTCCGGGCTAAGTCC
* *
14307 CG-AGGCATTTGTGCGAGTTACTAAATCC-GGTTAAGTCC
1 CGAAGGCATTTGTGCGAG-TACTAATTCCGGGCTAAGTCC
* * *
14345 CGAAGGCCAATTGTCGCGAGTACT-ATACCGGGCTATGTCC
1 CGAAGG-CATTTGT-GCGAGTACTAATTCCGGGCTAAGTCC
14385 CGAAGGCATTTG
1 CGAAGGCATTTG
14397 AACGAGTAGC
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 20 0.27
38 15 0.20
39 11 0.15
40 24 0.32
41 5 0.07
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CGAAGGCATTTGTGCGAGTACTAATTCCGGGCTAAGTCC
Found at i:14403 original size:79 final size:76
Alignment explanation
Indices: 14269--14429 Score: 182
Period size: 79 Copynumber: 2.1 Consensus size: 76
14259 GACATAAGAT
* * **
14269 CGAAGGCATTTGTGCGAATACTAATTCCGGGCTAAGCCCGAGGCATTTGTGCGAGTTA-CTAAAT
1 CGAAGGCAATTGTGCGAATACTAATACCGGGCTAAGCCCGAGGCATTTGAACGAG-TAGCTAAAT
*
14333 CCGGTTAAGTCC
65 CCGGTTAAATCC
* *
14345 CGAAGGCCAATTGTCGCGAGTACT-ATACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTA
1 CGAAGG-CAATTGT-GCGAATACTAATACCGGGCTAAG-CCCG-AGGCATTTGAACGAGTAGCTA
* *
14409 TATCCGGTTAAATTC
62 AATCCGGTTAAATCC
14424 CGAAGG
1 CGAAGG
14430 TACGTGATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
76 6 0.08
77 17 0.24
78 14 0.20
79 34 0.48
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (76 bp):
CGAAGGCAATTGTGCGAATACTAATACCGGGCTAAGCCCGAGGCATTTGAACGAGTAGCTAAATC
CGGTTAAATCC
Found at i:20474 original size:19 final size:18
Alignment explanation
Indices: 20450--20488 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
20440 TCTATCAAAC
20450 AATTTTTAGAAATACATAG
1 AATTTTTAGAAAT-CATAG
**
20469 AATTTTTTTAAATCATAG
1 AATTTTTAGAAATCATAG
20487 AA
1 AA
20489 CCCAAGCAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTTTTAGAAATCATAG
Found at i:24347 original size:79 final size:82
Alignment explanation
Indices: 24236--24420 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
24226 GCTACTCGTT
* * *
24236 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
24299 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
24316 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
24379 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
24396 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
24421 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:24420 original size:40 final size:40
Alignment explanation
Indices: 24217--24420 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
24207 CGGAATTTAA
** *
24217 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
24257 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
24297 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
24336 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
24376 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
24416 CCGGA
1 CCGGA
24421 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31835 original size:47 final size:47
Alignment explanation
Indices: 31767--31890 Score: 194
Period size: 47 Copynumber: 2.6 Consensus size: 47
31757 GATGCGAATG
* * *
31767 TCCGAACTCGTTGAGTGGAGTCTGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
*
31814 TCCGCGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* *
31861 TCTGAGCTTGTTGAGTTGAGTCCGAGTTCG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCG
31891 CTTATGGGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (47 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:34897 original size:39 final size:40
Alignment explanation
Indices: 34801--34981 Score: 201
Period size: 40 Copynumber: 4.5 Consensus size: 40
34791 ATGATGTCCA
* * *
34801 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATT-CG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-ATTCCG
* *
34841 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCCG
*
34881 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCG
* * *
34920 GGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-ATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCG
*
34960 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
34982 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 39 0.32
40 73 0.61
41 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCG
Found at i:35003 original size:79 final size:79
Alignment explanation
Indices: 34850--35014 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
34840 GGACTAAGAT
* * **
34850 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
34915 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
34929 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
34992 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
35008 CCGAAGG
1 CCGAAGG
35015 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:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:38447 original size:46 final size:46
Alignment explanation
Indices: 38221--38530 Score: 256
Period size: 46 Copynumber: 6.6 Consensus size: 46
38211 ATGCCGATAC
* * *
38221 CATGTCCCAGACATGGTCTTACACTGGCT-CATCCATC-AAGTCGATTT
1 CATGTCCCAGACATGGTCTTACACTGGCTACAT-C-TCGAGGCCGA-TG
* * ** *
38268 TATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCTGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTA-C-ATCTCGAGGCCGATG
* * * *
38316 CCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTG-TGTCGATG
1 -CATGTCCCAGACATGGTCTTACACT-G-GCT-ACATCTC-GAGGCCGATG
* * *
38366 CCATGTCCGAGACATGGTCTTACACTGAC-ACATCTCGAAGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCTACATCTCGAGGCCGATG
**
38412 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGTTGATG
1 CATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGAGGCCGATG
* * * *
38458 CATGTCTCAGACAT-GTCTTACACTAGCTTACATCTTGAGGCTGATG
1 CATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGAGGCCGATG
*
38504 CATGTCCCAGACAT-GTCTTATACTGGC
1 CATGTCCCAGACATGGTCTTACACTGGC
38531 AACACAAATA
Statistics
Matches: 220, Mismatches: 31, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
44 12 0.05
45 14 0.06
46 92 0.42
47 27 0.12
48 4 0.02
49 30 0.14
50 36 0.16
51 4 0.02
52 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTGGCTACATCTCGAGGCCGATG
Found at i:38504 original size:92 final size:94
Alignment explanation
Indices: 38221--38530 Score: 291
Period size: 92 Copynumber: 3.3 Consensus size: 94
38211 ATGCCGATAC
** *** *
38221 CATGTCCCAGACATGGTCTTACACTGGCTCATC-C--ATC-AAGTCGATTTTATGTCCCAGACAT
1 CATGTCCCAGACAT-GTCTTACACTGGCTC-TCACATATCTGGGTCGATGCCATGTCCGAGACAT
**
38282 GGTCTTACACTGACTATCAAAATCGAGGCTGATG
64 GGTCTTACACTGAC-A-C-ATCTCGAGGCTGATG
* *
38316 CCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTGTGTCGATGCCATGTCCGAGACAT
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCACATATCTGGGTCGATGCCATGTCCGAGACAT
* *
38381 GGTCTTACACTGACACATCTCGAAGCCGATG
64 GGTCTTACACTGACACATCTCGAGGCTGATG
* *
38412 CATGTCCCAGACATGTCTTACACTGGCT-T-ACATCTC-GAGGTTGATG-CATGTCTC-AGACAT
1 CATGTCCCAGACATGTCTTACACTGGCTCTCACATATCTG-GGTCGATGCCATGTC-CGAGACAT
*
38472 -GTCTTACACT-AGCTTACATCTTGAGGCTGATG
64 GGTCTTACACTGA-C--ACATCTCGAGGCTGATG
*
38504 CATGTCCCAGACATGTCTTATACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
38531 AACACAAATA
Statistics
Matches: 186, Mismatches: 19, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
89 1 0.01
90 11 0.06
91 13 0.07
92 53 0.28
93 1 0.01
94 13 0.07
95 16 0.09
96 41 0.22
97 1 0.01
98 4 0.02
99 32 0.17
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCACATATCTGGGTCGATGCCATGTCCGAGACATGG
TCTTACACTGACACATCTCGAGGCTGATG
Found at i:41865 original size:50 final size:50
Alignment explanation
Indices: 41744--41879 Score: 170
Period size: 49 Copynumber: 2.7 Consensus size: 50
41734 TAGGGTATAA
41744 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGACTATCAAAATCAAG
1 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGACTATCAAAATCAAG
* ** * * *
41794 -GCCGACGCCATGTCCCCGACATGGTCTTACACT-AGCTCTCACATATC-CG
1 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGA-CTATCA-AAATCAAG
*
41843 TGCCGATGCCATGTCTTAGACATGGTCTTACACTGAC
1 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGAC
41880 ACATCTCGAG
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
48 1 0.01
49 36 0.50
50 34 0.47
51 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (50 bp):
TGCCGATGCCATGTCCTAGACATGGTCTTACACTGACTATCAAAATCAAG
Found at i:41930 original size:46 final size:44
Alignment explanation
Indices: 41862--41969 Score: 153
Period size: 46 Copynumber: 2.4 Consensus size: 44
41852 CATGTCTTAG
* *
41862 ACATGGTCTTACACTGACACATCTCGAGGCCGATACATGTCCCAA
1 ACAT-GTCTTACACTGGCACATCTCGAGGCCGATACATATCCCAA
* *
41907 ACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATATCCCAG
1 ACATGTCTTACACTGGC--ACATCTCGAGGCCGATACATATCCCAA
41953 ACATGTCTTACACTGGC
1 ACATGTCTTACACTGGC
41970 CACACAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
44 12 0.21
45 4 0.07
46 41 0.72
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (44 bp):
ACATGTCTTACACTGGCACATCTCGAGGCCGATACATATCCCAA
Found at i:45419 original size:27 final size:27
Alignment explanation
Indices: 45349--45421 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
45339 AAAATGATAG
* *
45349 GAAAGAATAGCCTTCGTGGCGAGTTAT
1 GAAAGAATAACCTTTGTGGCGAGTTAT
* *
45376 GAAAGAACAACCATTGTGGC-AGATTAT
1 GAAAGAATAACCTTTGTGGCGAG-TTAT
*
45403 GAAAGAATAATCTTTGTGG
1 GAAAGAATAACCTTTGTGG
45422 TGATTTCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (27 bp):
GAAAGAATAACCTTTGTGGCGAGTTAT
Done.