Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1331
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: 39252
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:364 original size:28 final size:28
Alignment explanation
Indices: 332--456 Score: 162
Period size: 28 Copynumber: 4.4 Consensus size: 28
322 AGTAAGTCCA
*
332 CACACTTAGTGTTATATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
*
360 CACACTTAGT-CTTACATAATCAAACTCG
1 CACACTTAGTGC-TATATAATCAAACTCG
*
388 CACACTTAGTGCTATATAATCAAACTTG
1 CACACTTAGTGCTATATAATCAAACTCG
** * *
416 CACACTTAGTGCTATGCAATTTAAACCCG
1 CACACTTAGTGCTATATAA-TCAAACTCG
445 CACACTTAGTGC
1 CACACTTAGTGC
457 CAATCTCATG
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
28 66 0.78
29 19 0.22
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (28 bp):
CACACTTAGTGCTATATAATCAAACTCG
Found at i:5261 original size:24 final size:24
Alignment explanation
Indices: 5211--5264 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
5201 AATCGAATTT
*
5211 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
5235 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
5259 GCACAC
1 GCACAC
5265 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:15722 original size:403 final size:404
Alignment explanation
Indices: 14970--15780 Score: 1229
Period size: 403 Copynumber: 2.0 Consensus size: 404
14960 CACACTTTTT
* *
14970 ACTCTCCTATGCTCACCTAAGTATAAAACATGAAATTAAAGGATTAGGAGCATCGAATTCACCAA
1 ACTCTCCTATGCTCACCTAAGTATAAAACATGAAATTAAAGCATTAGAAGCATCGAATTCACCAA
* *
15035 TTCTAAGGAGAAACCATCCATAAATGTGCTAAGCATGGGATAAAAATATGTATAAATTATGGCTT
66 TTCTAAGGAGAAACCATCCATAAATGTACTAAACATGGGATAAAAATATGTATAAATTATGGCTT
15100 ATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAAATCCTCAACTCATAATCAAA
131 ATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAAATCCTCAACTCATAATCAAA
* * * *
15165 ATAAATTTTTCTCAATTTATAATCCCTATCAATAATATCTCAAAATAATCCATAAGTATTCATAC
196 ATAAATTCTCCTCAACTTATAATCCCTATCAATAATATCTCAAAATAATCCATAAGTAATCATAC
* *
15230 ATTGAAAATTCAACTAAAAGTAAATCAAAGTTTCAAACATTCCAAGTTGAGCATTTTATCAAGAA
261 ATTGAAAATTCAACTAAAAGTAAATAAAAGTTTCAAACATTCCAAGTTGAGCATTTAATCAAGAA
* *
15295 AACATAGGTGTCTCCCCTCATCTAAGTGATTACCTTTGA-TCAAAATATCACAAAGTTT-ATCAT
326 AACATAGGTGTCTCCCCGCATCTAAGTAATTACCTTTGATTCAAAATATCACAAAGTTTCA-CAT
15358 CCTCACTAAAGATTC
390 CCTCACTAAAGATTC
* *
15373 ACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATTAAAGCATTAGAAGCATTGAATTCACCAA
1 ACTCTCCTATGCTCACCTAAGTATAAAACATGAAATTAAAGCATTAGAAGCATCGAATTCACCAA
* * * * *
15438 TTCTAATGGA-CAATCATCCATAAAATGTATTAAACATGGGGTAAAAATATGTATAATTTACT-G
66 TTCTAA-GGAGAAACCATCCAT-AAATGTACTAAACATGGGATAAAAATATGTATAAATTA-TGG
* * *
15501 TTTATCAAATACCCCCACATTTAAGCATTTGCTTGTCCTTAAGC-AAAATCCTCAACTCATAATC
128 CTTATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAAATCCTCAACTCATAATC
* * * *
15565 AAAATAAATTCTCCTCAACTTATAATTCTTATCGATAATATCTCAAAATAATCCATAGGTAATCA
193 AAAATAAATTCTCCTCAACTTATAATCCCTATCAATAATATCTCAAAATAATCCATAAGTAATCA
* * *
15630 TACATTGAGAATTCAACTAAAAG-ATCATAAAAGTTTCAAACATTCCAAGTTGAGTATTTAATCA
258 TACATTGAAAATTCAACTAAAAGTA-AATAAAAGTTTCAAACATTCCAAGTTGAGCATTTAATCA
* * * * *
15694 TGCAAACATAGGTGTCTCTCCGCATCTAAGTAATTACCTTTGATTCAGAATATCACAGAGTTTCA
322 AGAAAACATAGGTGTCTCCCCGCATCTAAGTAATTACCTTTGATTCAAAATATCACAAAGTTTCA
15759 CATCCTCACTAAAGATTC
387 CATCCTCACTAAAGATTC
15777 ACTC
1 ACTC
15781 AAATCACTCG
Statistics
Matches: 368, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
402 1 0.00
403 248 0.67
404 117 0.32
405 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (404 bp):
ACTCTCCTATGCTCACCTAAGTATAAAACATGAAATTAAAGCATTAGAAGCATCGAATTCACCAA
TTCTAAGGAGAAACCATCCATAAATGTACTAAACATGGGATAAAAATATGTATAAATTATGGCTT
ATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAAATCCTCAACTCATAATCAAA
ATAAATTCTCCTCAACTTATAATCCCTATCAATAATATCTCAAAATAATCCATAAGTAATCATAC
ATTGAAAATTCAACTAAAAGTAAATAAAAGTTTCAAACATTCCAAGTTGAGCATTTAATCAAGAA
AACATAGGTGTCTCCCCGCATCTAAGTAATTACCTTTGATTCAAAATATCACAAAGTTTCACATC
CTCACTAAAGATTC
Found at i:15933 original size:38 final size:38
Alignment explanation
Indices: 15891--15966 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
15881 ATAATTTAAG
15891 ATGATACATCAAGCAAAAGGCCTTTAGAGGGTTGTAGT
1 ATGATACATCAAGCAAAAGGCCTTTAGAGGGTTGTAGT
15929 ATGATACATCAAGCAAAAGGCCTTTAGAGGGTTGTAGT
1 ATGATACATCAAGCAAAAGGCCTTTAGAGGGTTGTAGT
15967 GATGCTTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (38 bp):
ATGATACATCAAGCAAAAGGCCTTTAGAGGGTTGTAGT
Found at i:22038 original size:48 final size:48
Alignment explanation
Indices: 21982--22077 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
21972 GACCTCCACC
21982 CCCACCTATTCCTCAACAAACCCCTATAGTTCCTCAAGGTATTGATCT
1 CCCACCTATTCCTCAACAAACCCCTATAGTTCCTCAAGGTATTGATCT
22030 CCCACCTATTCCTCAACAAACCCCTATAGTTCCTCAAGGTATTGATCT
1 CCCACCTATTCCTCAACAAACCCCTATAGTTCCTCAAGGTATTGATCT
22078 TCTGTGATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.29
Consensus pattern (48 bp):
CCCACCTATTCCTCAACAAACCCCTATAGTTCCTCAAGGTATTGATCT
Found at i:27783 original size:43 final size:43
Alignment explanation
Indices: 27689--27808 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
27679 CCGAGATGTG
* **
27689 ATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTG
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGCA
*
27732 ATTACGTGTAAGACCATGTCTGGGACATTGG-TTTCGTTATT-CA
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCATT-G-TATTGCA
* * * *
27775 ATTCCGTGTAAGACCCTGTATGGGACAGTGGCAT
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCAT
27809 CGATATGAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 58 0.89
44 5 0.08
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
ATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGCA
Found at i:31212 original size:76 final size:79
Alignment explanation
Indices: 31033--31248 Score: 266
Period size: 76 Copynumber: 2.8 Consensus size: 79
31023 AATGATGTCC
* * *
31033 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGACTAAGATCCGAAGGCATTTGTG
*
31097 CGAGTTACTAATTCG
65 CGAGTTACTAATCCG
* *
31112 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-ATCCGG-TTAAG-TCCGAAGGCA-TTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGACTAAGATCCGAAGGCATTTGTGC
31172 GAGTTACTAAATCCG
66 GAGTTACT-AATCCG
* * * *
31187 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGACTAAGAT-CCGAAGGCATTTG
31249 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
74 14 0.12
75 21 0.18
76 29 0.24
77 11 0.09
78 19 0.16
79 22 0.18
80 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGACTAAGATCCGAAGGCATTTGTGC
GAGTTACTAATCCG
Found at i:31217 original size:40 final size:40
Alignment explanation
Indices: 31033--31248 Score: 252
Period size: 40 Copynumber: 5.5 Consensus size: 40
31023 AATGATGTCC
* * * *
31033 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* *
31073 GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT-AATTCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
31112 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT-AATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
31149 GGTTAAGT-CCGAAGGCA-TTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
31187 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
31227 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
31249 AACGAGTAGC
Statistics
Matches: 154, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.08
37 20 0.13
38 35 0.23
39 19 0.12
40 57 0.37
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:35969 original size:22 final size:22
Alignment explanation
Indices: 35941--35992 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
35931 CCTTGTTAAG
35941 CATATCCACACCTCTCAATAAC
1 CATATCCACACCTCTCAATAAC
35963 CATATCCACACCTCTCAATAAC
1 CATATCCACACCTCTCAATAAC
35985 CATATCCA
1 CATATCCA
35993 TATCAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (22 bp):
CATATCCACACCTCTCAATAAC
Found at i:36610 original size:39 final size:38
Alignment explanation
Indices: 36565--36781 Score: 255
Period size: 39 Copynumber: 5.7 Consensus size: 38
36555 GCTACTCGTT
* *
36565 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGAT-TAGTAACTCGCA
*
36605 C-AATGCCTTC-GACTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
*
36641 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGA-TTAGTAACTCGCA
*
36681 CAAATGCCTTCGG-CTTAGTCCGGATTAGT-ACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
* * * *
36717 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGAT-TAGTAACTCGCA
36757 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
36782 CATCATTCGA
Statistics
Matches: 160, Mismatches: 8, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
36 33 0.21
37 25 0.16
38 21 0.13
39 43 0.27
40 38 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:36742 original size:76 final size:76
Alignment explanation
Indices: 36542--36768 Score: 266
Period size: 76 Copynumber: 3.0 Consensus size: 76
36532 CCTTCGGAAT
** *
36542 TTAA-CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 TTAACCCGGAT-TAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
36605 C-AATGCCTTCGAC
63 CAAATGCCTTCGGC
*
36618 TTAACCCGGATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 TTAACCCGGATTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
36683 AATGCCTTCGGC
65 AATGCCTTCGGC
** * * * * *
36695 TTAGTCCGGATTAGTACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTAGCACA
1 TTAACCCGGATTAGTACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACA
36759 AA-GCCTTCGG
65 AATGCCTTCGG
36769 GACTTAGCCC
Statistics
Matches: 133, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
75 12 0.09
76 89 0.67
77 32 0.24
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (76 bp):
TTAACCCGGATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAA
ATGCCTTCGGC
Done.