Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2326
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: 43530
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8197 original size:28 final size:28
Alignment explanation
Indices: 8134--8231 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
8124 ATATTAAGTC
*
8134 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
8161 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
8189 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
8218 CGCACACTTAGTGC
1 CGCACACTTAGTGC
8232 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:18430 original size:47 final size:47
Alignment explanation
Indices: 18367--18474 Score: 180
Period size: 47 Copynumber: 2.3 Consensus size: 47
18357 CCCTTCGGGA
*
18367 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTCCACATCCATCACATTGGCCATTCGGC
* *
18414 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTCCACATCCATCACATTGGCCATTCGGC
*
18461 CTTATCTCATATAT
1 CTTATCACATATAT
18475 GTGACACCCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.27, C:0.31, G:0.07, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTCCACATCCATCACATTGGCCATTCGGC
Found at i:20833 original size:47 final size:47
Alignment explanation
Indices: 20779--21037 Score: 428
Period size: 47 Copynumber: 5.5 Consensus size: 47
20769 TATTTGAATA
*
20779 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
20826 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
20873 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
20920 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
20967 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21014 GATGTGAAAGTGTATAAATGTGAT
1 AATGTGAAAGTGTATATATGTGAT
21038 GAGTCCCGAA
Statistics
Matches: 200, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 200 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:22957 original size:47 final size:46
Alignment explanation
Indices: 22888--23227 Score: 464
Period size: 47 Copynumber: 7.1 Consensus size: 46
22878 GGGTGTTACA
* *
22888 ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTC
1 ATATATACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC
*
22935 ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 ATATATACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC
* * *
22982 ACATACACATGTTCACATTCATCACATTGGCCATTCAGCCTTATCAC
1 ATATATACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC
23029 ATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 --ATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
23078 ATATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 ATATAT--ACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
* * *
23127 ATATATACGCTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATAC-ATTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
* *
23174 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 --ATATATACA-TTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
23223 ATATA
1 ATATA
23228 CTATCATGTA
Statistics
Matches: 272, Mismatches: 12, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
47 137 0.50
49 134 0.49
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (46 bp):
ATATATACATTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
Found at i:23064 original size:49 final size:49
Alignment explanation
Indices: 22899--23227 Score: 485
Period size: 49 Copynumber: 6.8 Consensus size: 49
22889 TATATGCATG
* *
22899 TTCACATTCATCACATTGGCCATTCGGCCTTATCTC--ATATATGCA-T
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
* *
22945 GTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ACATACACA-T
1 -TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
*
22992 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACATATATATACACT
1 -TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
*
23042 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACACT
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
*
23091 TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACGCT
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
* *
23138 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACT
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
* *
23187 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
23228 CTATCATGTA
Statistics
Matches: 263, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
47 121 0.46
49 141 0.54
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT
Found at i:23131 original size:96 final size:96
Alignment explanation
Indices: 22899--23227 Score: 504
Period size: 96 Copynumber: 3.4 Consensus size: 96
22889 TATATGCATG
* *
22899 TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCA-TGTTCACATTCATCACATT
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACATT
*
22963 GGCCATTCGGCCTTATCAC--ACATACACA-T
65 GGCCATTCGGCCTTATCACATATATACACACT
*
22992 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACATATATATACACTTTCACATTCATCACA
1 -TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
23057 TTGGCCATTCGGCCTTATCACATATATACACACT
63 TTGGCCATTCGGCCTTATCACATATATACACACT
* *
23091 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACGCTTTCACATTCATCACATCG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
* *
23156 GCCATTAGGCCTTATCACATATATATACACT
66 GCCATTCGGCCTTATCACATATATACACACT
* *
23187 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
23228 CTATCATGTA
Statistics
Matches: 218, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
94 34 0.16
96 139 0.64
97 1 0.00
98 43 0.20
99 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (96 bp):
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTG
GCCATTCGGCCTTATCACATATATACACACT
Found at i:23271 original size:145 final size:144
Alignment explanation
Indices: 22899--23227 Score: 387
Period size: 145 Copynumber: 2.3 Consensus size: 144
22889 TATATGCATG
* * * * ** *
22899 TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCA-TGTT-CACATTCATCACAT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTACAAATTCAT-ACAT
* * * * * * * *
22962 TGGCCATTCGGCCTTATCACACATACAC-ATGTTCACATTCATCACATTGGCCATTCAGCCTTAT
65 TGGCCAATCGACATCATCACATATATACGCT-TTCACATTCATCACATCGGCCATTCAGCCTTAT
23026 CACATATATATACACT
129 CACATATATATACACT
* * * *
23042 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACACTTTCACATTCATCACAT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTACAAATTCAT-ACAT
* * * *
23107 TGGCCATTCGGCCTTATCACATATATACGCTTTCACATTCATCACATCGGCCATT-AGGCCTTAT
65 TGGCCAATCGACATCATCACATATATACGCTTTCACATTCATCACATCGGCCATTCA-GCCTTAT
23171 CACATATATATACACT
129 CACATATATATACACT
23187 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
23228 CTATCATGTA
Statistics
Matches: 172, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
143 43 0.25
144 3 0.02
145 125 0.73
146 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (144 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTACAAATTCATACATT
GGCCAATCGACATCATCACATATATACGCTTTCACATTCATCACATCGGCCATTCAGCCTTATCA
CATATATATACACT
Found at i:24711 original size:56 final size:56
Alignment explanation
Indices: 24644--24763 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
24634 TATTAGTTTA
24644 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
24700 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
24756 TTGCCCAT
1 TTGCCCAT
24764 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:35631 original size:28 final size:28
Alignment explanation
Indices: 35566--35716 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
35556 GAGATTGGCG
* * * *
35566 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
35595 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
35623 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
35651 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
35679 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
35706 CTGAGTGTGCG
1 CTAAGTGTGCG
35717 GACTTAATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.21
28 76 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:38921 original size:16 final size:16
Alignment explanation
Indices: 38877--38922 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38867 ATCCTGTTTT
* *
38877 CTTTGGCCGATTGATG
1 CTTTTGCCGTTTGATG
38893 CTTTTG-CGATTTGATG
1 CTTTTGCCG-TTTGATG
38909 CTTTTGCCGTTTGA
1 CTTTTGCCGTTTGA
38923 CGAATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.46
Consensus pattern (16 bp):
CTTTTGCCGTTTGATG
Done.