Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2553
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: 52705
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:17537 original size:41 final size:39
Alignment explanation
Indices: 17491--17670 Score: 161
Period size: 41 Copynumber: 4.5 Consensus size: 39
17481 TCGTTCAAAG
*
17491 GCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCAACAATT
1 GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCAA-AA-T
*
17532 GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAAAAT
1 GCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAAAAT
* * *
17571 GCCTTCAGG-CTTAGCCCGGAATTAGTATCTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA-AAAT
* * * * * * *
17610 GCATTC-GGATCTTAGTCCAGATATGGTCACTTAGCACAAA-
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA-AAAT
17650 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAGCCCGGA
17671 CATCATTATC
Statistics
Matches: 115, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
38 24 0.21
39 18 0.16
40 29 0.25
41 42 0.37
42 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAAAAT
Found at i:17610 original size:39 final size:40
Alignment explanation
Indices: 17514--17611 Score: 128
Period size: 38 Copynumber: 2.5 Consensus size: 40
17504 AGCCCGGTTA
* * *
17514 TAGTAACTCGCAACAATTGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGC-ACAAATGCCTTCAGGACTTAACCCGGAAT
*
17555 TAGTAACTCGCA-AAATGCCTTCAGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAAT
*
17593 TAGTATCTCGCACAAATGC
1 TAGTAACTCGCACAAATGC
17612 ATTCGGATCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 22 0.43
39 17 0.33
40 1 0.02
41 11 0.22
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAAT
Found at i:23273 original size:79 final size:79
Alignment explanation
Indices: 23141--23357 Score: 319
Period size: 79 Copynumber: 2.7 Consensus size: 79
23131 AACCCAAGTA
* * * * * * *
23141 CCTTCGGAATTTAG-CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCCTGGACATAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC-GGACTTAGCCCGGACATAA
23205 TCACTAGCACAAATG
65 TCACTAGCACAAATG
*
23220 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAAT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGACATAAT
23285 CACTAGCACAAATG
66 CACTAGCACAAATG
* *
23299 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGATCTTAGTCCGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGA-CTTAGCCCGG
23358 TTATCATTCG
Statistics
Matches: 126, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
79 90 0.71
80 36 0.29
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGACATAAT
CACTAGCACAAATG
Found at i:23352 original size:40 final size:40
Alignment explanation
Indices: 23141--23345 Score: 315
Period size: 40 Copynumber: 5.2 Consensus size: 40
23131 AACCCAAGTA
* * * * *
23141 CCTTCGGAATTTAG-CCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
23180 CCTTCGGGACTTAGCCTGGACATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
23220 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
23260 CCTTC-GGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
23299 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
23339 CCTTCGG
1 CCTTCGG
23346 ATCTTAGTCC
Statistics
Matches: 154, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 50 0.32
40 104 0.68
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:31200 original size:79 final size:79
Alignment explanation
Indices: 31069--31285 Score: 278
Period size: 79 Copynumber: 2.7 Consensus size: 79
31059 AACCCAAGTA
* * * * *
31069 CCTTCGGAATTTAG-CCAGATATAG-CAACTCGCACGAATGCCTTCGGGACTTAGCCCGGACATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC-GGACTTAGCCCGGACATA
*
31132 GTCACTAGCACAAATG
64 ATCACTAGCACAAATG
* *
31148 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-AATGCCTTCGAGACTTAGCCAGGATATAA
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCG-GACTTAGCCCGGACATAA
31212 TCACTAGCACAAATG
65 TCACTAGCACAAATG
* * *
31227 CCTTCGGGACTTAGCCTGGATATAATCACTAGCACAAATGCCTTCGGATCTTAGTCCGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGA-CTTAGCCCGG
31286 TTATCATTTG
Statistics
Matches: 122, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 86 0.70
80 34 0.28
81 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGACATAAT
CACTAGCACAAATG
Found at i:31280 original size:40 final size:40
Alignment explanation
Indices: 31099--31273 Score: 280
Period size: 40 Copynumber: 4.4 Consensus size: 40
31089 ATAGCAACTC
* * *
31099 GCACGAATGCCTTCGGGACTTAGCCCGGACATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
*
31139 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
* *
31179 GCAC-AATGCCTTCGAGACTTAGCCAGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
*
31218 GCACAAATGCCTTCGGGACTTAGCCTGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
31258 GCACAAATGCCTTCGG
1 GCACAAATGCCTTCGG
31274 ATCTTAGTCC
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
39 36 0.28
40 91 0.72
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
Found at i:37493 original size:26 final size:27
Alignment explanation
Indices: 37463--37514 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
37453 GTTTTAATTC
* *
37463 AAGATATA-TAAAAAAATCAAAAATCA
1 AAGATATACAAAAAAAATAAAAAATCA
37489 AAGATATACCAAAAAAAATAAAAAAT
1 AAGATATA-CAAAAAAAATAAAAAAT
37515 TAATCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.17
Consensus pattern (27 bp):
AAGATATACAAAAAAAATAAAAAATCA
Found at i:46719 original size:43 final size:43
Alignment explanation
Indices: 46649--46761 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 43
46639 CAATGTCTAC
*
46649 GTCCCAGACGA-GGTCTTACA--TATAATCA-ACTATCGATGCCACT
1 GTCCCAGAC-ATGGTCTTACACGTA-AATCATA-TAT-GATGCCAAT
*
46692 GTCCCAGATA-GGTTCTTACACG-AAATCATATATGATGCCAAT
1 GTCCCAGACATGG-TCTTACACGTAAATCATATATGATGCCAAT
*
46734 GTCCTAGACATGGTCTTACACGTAAATC
1 GTCCCAGACATGGTCTTACACGTAAATC
46762 TCAAATCGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
42 28 0.47
43 30 0.50
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAATCATATATGATGCCAAT
Found at i:48641 original size:40 final size:40
Alignment explanation
Indices: 48536--48752 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
48526 CGGATGATAA
* *
48536 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
48576 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
48615 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
48655 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
48695 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
48735 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
48753 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 51 0.31
40 115 0.69
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:48750 original size:119 final size:119
Alignment explanation
Indices: 48532--48752 Score: 331
Period size: 119 Copynumber: 1.9 Consensus size: 119
48522 TATTCGGATG
* *
48532 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* * *
48597 TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGAGCAAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
*
48651 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
48715 ATTTGAGCAAG-TAGCTATATCC-GGCTAAATTCCGAAGG
64 ATTTGAGCAAGTTA-CTATATCCGGGCTAAATCCCGAAGG
48753 TACTTGGTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
118 2 0.02
119 64 0.70
120 26 0.28
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGAGCAAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52291 original size:35 final size:35
Alignment explanation
Indices: 52245--52315 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
52235 GGTCTGTGAA
52245 AAAGAAGGACGGAACCATGAGGTTGTGCATCGACT
1 AAAGAAGGACGGAACCATGAGGTTGTGCATCGACT
52280 AAAGAAGGACGGAACCATGAGGTTGTGCATCGACT
1 AAAGAAGGACGGAACCATGAGGTTGTGCATCGACT
52315 A
1 A
52316 TCGTCAGCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (35 bp):
AAAGAAGGACGGAACCATGAGGTTGTGCATCGACT
Done.