Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1155
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: 18835
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Found at i:1834 original size:93 final size:93
Alignment explanation
Indices: 1719--1889 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
1709 GCCCATAAGT
* *
1719 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1784 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
1812 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1877 CGAGTTCGGATGC
66 CGAGTTCGGATGC
1890 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:1886 original size:46 final size:46
Alignment explanation
Indices: 1711--1886 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
1701 TGTAACCCGC
* * *
1711 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
1757 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
1807 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1850 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1887 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 63 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:6955 original size:37 final size:37
Alignment explanation
Indices: 6905--6983 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
6895 TTATTACGAA
* * *
6905 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
6942 GTCTTACCCGGACAAAATCCCCACATGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
6979 GTCTT
1 GTCTT
6984 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:7231 original size:47 final size:47
Alignment explanation
Indices: 7102--7481 Score: 597
Period size: 47 Copynumber: 8.1 Consensus size: 47
7092 CCCTTCGGGA
* * * * * * *
7102 CTTATCACATTTATACACTTTCACATCCGTCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7149 CCTCTCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7197 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7244 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7291 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7338 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7386 C-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7432 C-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7478 CTTA
1 CTTA
7482 CTATCATTTC
Statistics
Matches: 312, Mismatches: 15, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
46 102 0.33
47 127 0.41
48 74 0.24
49 9 0.03
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11283 original size:39 final size:40
Alignment explanation
Indices: 11204--11379 Score: 227
Period size: 39 Copynumber: 4.5 Consensus size: 40
11194 CCAGCATGAT
* *
11204 TGCTCTTCGGGACCTAG-CCGGAATA-A-CACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGG-ATACATCACTAGCACGAA
* * *
11242 TGCTCTTCGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
11281 TGCTCTTC-GAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
11320 TGCTCTTCGGGACTTAGCCCGGACACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
11360 TGCTCTTCGGGACTTAGCCC
1 TGCTCTTCGGGACTTAGCCC
11380 AGACATCATT
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
37 6 0.05
38 16 0.13
39 51 0.42
40 49 0.40
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:11348 original size:40 final size:40
Alignment explanation
Indices: 11186--11384 Score: 226
Period size: 39 Copynumber: 5.1 Consensus size: 40
11176 AGGCCCGAAT
* * * *
11186 ACACGTCACCAGCATGATTGCTCTTCGGGACCTAG-CCGG
1 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
* * * * * *
11225 A-ATAACACCAGCACGAATGCTCTTCGGG-TTTAGCACGG
1 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
* * * *
11263 ATATATCACTAGCACGAATGCTCTTC-GAACTTAGCCCGG
1 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
*
11302 ATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
1 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
*
11342 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCAG
1 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
11382 ACA
1 ACA
11385 TCATTCGAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
37 3 0.02
38 27 0.20
39 55 0.40
40 53 0.38
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
Found at i:11354 original size:79 final size:79
Alignment explanation
Indices: 11186--11379 Score: 216
Period size: 79 Copynumber: 2.5 Consensus size: 79
11176 AGGCCCGAAT
* * * * * * *
11186 ACACGTCACCAGCATGATTGCTCTTCGGGACCTAG-CCGGAATA-A-CACCAGCACGAATGCTCT
1 ACACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGG-ATACATCACTAGCACGAATGCTCT
*
11248 TCGGGTTTAGCACGG
65 TCGGGCTTAGCACGG
* * *
11263 ATATATCACTAGCACGAATGCTCTTC-GAACTTAGCCCGGATACATCACTAGCATGAATGCTCTT
1 ACACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTT
*
11327 CGGGACTTAGCCCGG
66 CGGG-CTTAGCACGG
* *
11342 ACACATCACTAGCATGAATGCTCTTCGGGACTTAGCCC
1 ACACATCACTAGCACGAATGCTCTTCGGAACTTAGCCC
11380 AGACATCATT
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
76 9 0.09
77 25 0.26
78 21 0.22
79 31 0.32
80 10 0.10
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (79 bp):
ACACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTT
CGGGCTTAGCACGG
Found at i:11757 original size:26 final size:29
Alignment explanation
Indices: 11688--11758 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
11678 TAATCAACCA
* *
11688 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACG
*
11717 CGCACACTTAGTGCCATGCA-TTTCAA-G
1 CGCACACTTAGTGCCATGCACTTTAAACG
11744 CGC-CACTTAGTGCCA
1 CGCACACTTAGTGCCA
11759 ATCTCACAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 12 0.31
27 3 0.08
28 5 0.13
29 19 0.49
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACG
Found at i:13687 original size:35 final size:37
Alignment explanation
Indices: 13616--13692 Score: 113
Period size: 35 Copynumber: 2.1 Consensus size: 37
13606 CTATTACGAA
* *
13616 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
*
13653 GTCTTA-CCGGACAAAATC-CCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
13688 GTCTT
1 GTCTT
13693 TAGAGATCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 20 0.54
36 11 0.30
37 6 0.16
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:13971 original size:45 final size:47
Alignment explanation
Indices: 13808--14081 Score: 388
Period size: 45 Copynumber: 6.0 Consensus size: 47
13798 GCCCTTCGGA
* * * *
13808 CTTATCACATTTATACACTTTCACA-TC-TCACGTTGGCCA--CGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
13851 CCTCTCACATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13898 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13945 C-T-TCACGTATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13989 CTTATCACATATATA-ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14035 C-TATCACATATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14082 TACTATCATT
Statistics
Matches: 209, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
43 21 0.10
44 13 0.06
45 68 0.33
46 22 0.11
47 63 0.30
48 22 0.11
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.