Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3704
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: 35191
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:6002 original size:40 final size:40
Alignment explanation
Indices: 5958--6138 Score: 164
Period size: 40 Copynumber: 4.6 Consensus size: 40
5948 GCTCCTCGTT
*
5958 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
* *
5998 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCA
* *
6038 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGT-ATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAAT-TCGCA
* * * * *
6077 CAAATGCCTTC-GGATCTTAG--TGGATATTGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AATTCGCA
6116 C-AA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
6139 ACATCATTCA
Statistics
Matches: 115, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
37 11 0.10
38 13 0.11
39 35 0.30
40 54 0.47
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
Found at i:6079 original size:39 final size:40
Alignment explanation
Indices: 5958--6089 Score: 180
Period size: 40 Copynumber: 3.3 Consensus size: 40
5948 GCTCCTCGTT
*
5958 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
5998 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* *
6038 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
6077 CAAATGCCTTCGG
1 CAAATGCCTTCGG
6090 ATCTTAGTGG
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
39 35 0.42
40 46 0.55
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:11241 original size:45 final size:45
Alignment explanation
Indices: 11177--11262 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
11167 CCAAAACATG
*
11177 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTTGGA
1 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTTGGA
* *
11222 TGTCACATATATCATGAACTCAAACCACGACTCAATGAGTT
1 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTT
11263 CAGATCACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTTGGA
Found at i:18090 original size:43 final size:43
Alignment explanation
Indices: 17887--18106 Score: 230
Period size: 45 Copynumber: 5.1 Consensus size: 43
17877 CATGCTATAT
* * * * *
17887 CATATCGATGCCACTATCCCAGACAAGGTTTTACACG-AATCA
1 CATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAAACA
* *
17929 AATA-CGATGCCGATGTCCCAGACATGGTCTTACAC-ATAACCACA
1 CATATCGATGCCAATGTCCCAGACATGGTCTTACACGA-AA--ACA
* * *
17973 TATATCGATGCCAATGTCCCAGACGTGGTCTTACATGAAAACA
1 CATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAAACA
* * * *
18016 CATATATCGATGCCAACGTCCTAGACGTGGTCTTACACGAGAACA
1 C--ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAAACA
* *
18061 CATATCGATGCCAATGACCCAAACATGGTCTTACACGAAAACA
1 CATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAAACA
18104 CAT
1 CAT
18107 TTTGAAATCT
Statistics
Matches: 148, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
41 26 0.18
42 5 0.03
43 42 0.28
44 5 0.03
45 69 0.47
46 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
CATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAAACA
Found at i:18095 original size:88 final size:89
Alignment explanation
Indices: 17888--18106 Score: 236
Period size: 88 Copynumber: 2.5 Consensus size: 89
17878 ATGCTATATC
* * * * * * *
17888 ATATCGATGCCACT-ATCCCAGACAAGGTTTTACACG-AATCA-A-ATA-CGATGCCGATGTCCC
1 ATATCGATGCCAATGA-CCCAAACATGGTCTTACACGAAAACACATATATCGATGCCAACGTCCC
*
17948 AGACATGGTCTTACACATAACCACA
65 AGACATGGTCTTACACAGAACCACA
* * * * *
17973 TATATCGATGCCAATGTCCCAGACGTGGTCTTACATGAAAACACATATATCGATGCCAACGTCCT
1 -ATATCGATGCCAATGACCCAAACATGGTCTTACACGAAAACACATATATCGATGCCAACGTCCC
*
18038 AGACGTGGTCTTACACGAGAA-CAC-
65 AGACATGGTCTTACAC-AGAACCACA
18062 ATATCGATGCCAATGACCCAAACATGGTCTTACACGAAAACACAT
1 ATATCGATGCCAATGACCCAAACATGGTCTTACACGAAAACACAT
18107 TTTGAAATCT
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
86 29 0.26
87 4 0.04
88 42 0.38
89 3 0.03
90 30 0.27
91 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (89 bp):
ATATCGATGCCAATGACCCAAACATGGTCTTACACGAAAACACATATATCGATGCCAACGTCCCA
GACATGGTCTTACACAGAACCACA
Found at i:19203 original size:14 final size:15
Alignment explanation
Indices: 19186--19214 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19176 TCACGAAAAT
19186 TTCACACAT-ATAAA
1 TTCACACATAATAAA
19200 TTCACACATAATAAA
1 TTCACACATAATAAA
19215 CACAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:25179 original size:39 final size:41
Alignment explanation
Indices: 25084--25267 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
25074 TTGAATGATG
*
25084 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
25123 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
25163 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
25202 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
25242 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25268 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:25219 original size:79 final size:81
Alignment explanation
Indices: 25084--25267 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
25074 TTGAATGATG
25084 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
25147 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
25162 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
25223 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
25242 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25268 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:25289 original size:79 final size:79
Alignment explanation
Indices: 25136--25300 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
25126 GGACTAAGAT
* ** *
25136 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
25201 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
25215 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
25277 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
25294 CCGAAGG
1 CCGAAGG
25301 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:32323 original size:1 final size:1
Alignment explanation
Indices: 32317--32434 Score: 182
Period size: 1 Copynumber: 118.0 Consensus size: 1
32307 ATTTTCGTGA
* * * *
32317 TTTTTTTTATTTTTTGTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
32382 TTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32435 CCCCCTGAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 105 1.00
ACGTcount: A:0.03, C:0.01, G:0.01, T:0.95
Consensus pattern (1 bp):
T
Found at i:33642 original size:38 final size:39
Alignment explanation
Indices: 33594--33682 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
33584 CTCCTCCGTT
* *
33594 CAAATG-CTTCGGACATAGCCC-G-TTATAGTAATTCGCA
1 CAAATGCCTTCGGACATAACCCGGATT-TAGTAACTCGCA
*
33631 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACATAACCCGGATTTAGTAACTCGCA
33670 CAAATGCCTTCGG
1 CAAATGCCTTCGG
33683 CTTAGCGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
37 6 0.13
38 13 0.28
39 25 0.54
40 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGACATAACCCGGATTTAGTAACTCGCA
Found at i:33669 original size:39 final size:38
Alignment explanation
Indices: 33619--33781 Score: 156
Period size: 39 Copynumber: 4.6 Consensus size: 38
33609 TAGCCCGTTA
* *
33619 TAGTAATTCGCACAAATGCCTTCGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGG-CTTAACCCGGAAT
*
33658 TAGTAACTCGCACAAATGCCTTCGGCTT-A-GCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGCTTAACCCGGAAT
* *
33694 TAGT-A-TCTCACAAATG-CTT---CTT-AGCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGCTTAACCCGGAAT
*
33725 TAGT-ACT-GCAC-AATGCCTTCGG--TAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGCTTAACCCGGAAT
*
33758 TAGTATCTCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCG
33782 ATCTTAGTAC
Statistics
Matches: 105, Mismatches: 9, Indels: 23
0.77 0.07 0.17
Matches are distributed among these distances:
30 8 0.08
31 17 0.16
32 2 0.02
33 14 0.13
34 12 0.11
35 5 0.05
36 19 0.18
37 1 0.01
38 3 0.03
39 24 0.23
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (38 bp):
TAGTAACTCGCACAAATGCCTTCGGCTTAACCCGGAAT
Found at i:33726 original size:31 final size:32
Alignment explanation
Indices: 33651--33776 Score: 116
Period size: 31 Copynumber: 3.8 Consensus size: 32
33641 CGGACTTAAC
* *
33651 CCGGATTTAGTAACTCGCACAAATGCCTTCGGCTTAG
1 CCGGAATTAGTATCT-GCACAAATG-CTT---CTTAG
33688 -CGGAATTAGTATCT-CACAAATGCTTCTTAG
1 CCGGAATTAGTATCTGCACAAATGCTTCTTAG
*
33718 CCGGAATTAGTA-CTGCAC-AATGCCTTCGGTAG
1 CCGGAATTAGTATCTGCACAAATG-CTTC-TTAG
33750 CCCGGAATTAGTATCTCGCACAAATGC
1 -CCGGAATTAGTATCT-GCACAAATGC
33777 CTTCGATCTT
Statistics
Matches: 78, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
30 11 0.14
31 18 0.23
32 3 0.04
33 15 0.19
34 10 0.13
35 5 0.06
36 16 0.21
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (32 bp):
CCGGAATTAGTATCTGCACAAATGCTTCTTAG
Found at i:33756 original size:64 final size:67
Alignment explanation
Indices: 33651--33776 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 67
33641 CGGACTTAAC
*
33651 CCGGATTTAGTAACTCGCACAAATGCCTTCGGCTTAGCGGAATTAGTATCT-CACAAATGCTTCT
1 CCGGAATTAGTAACTCGCACAAATGCCTTCGGC-TAGCGGAATTAGTATCTCCACAAATGCTTCT
33715 TAG
65 TAG
33718 CCGGAATTAGT-ACT-GCAC-AATGCCTTCGG-TAGCCCGGAATTAGTATCTCGCACAAATGC
1 CCGGAATTAGTAACTCGCACAAATGCCTTCGGCTAG--CGGAATTAGTATCTC-CACAAATGC
33777 CTTCGATCTT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
62 3 0.06
64 25 0.46
65 4 0.07
66 12 0.22
67 10 0.19
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (67 bp):
CCGGAATTAGTAACTCGCACAAATGCCTTCGGCTAGCGGAATTAGTATCTCCACAAATGCTTCTT
AG
Done.