Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1994
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, 698
Length: 1164
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Found at i:516 original size:40 final size:40
Alignment explanation
Indices: 336--598 Score: 324
Period size: 40 Copynumber: 6.7 Consensus size: 40
326 TTGAATGATG
* *
336 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
375 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
415 TTCGGGCTAAG-CCCGAAGGCATTTGTGCTAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
454 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
493 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
533 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
574 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
599 AACGAGGAGC
Statistics
Matches: 200, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
39 88 0.44
40 102 0.51
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:578 original size:80 final size:79
Alignment explanation
Indices: 337--598 Score: 311
Period size: 79 Copynumber: 3.3 Consensus size: 79
327 TGAATGATGT
* *
337 CCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTTACTAA-ATCCGGGCTAAG-TCCCGAAGGCAT
* *
398 TTGTGCGAGATACTAATT
63 TTGTGCGAGTTACTAA-A
* * * * *
416 TCGGGCTAAG-CCCGAAGGCATTTGTGCTAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
479 TGCGAGTTACTAAA
66 TGCGAGTTACTAAA
* * *
493 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
558 GTGCGAGTTACTATAA
65 GTGCGAGTTACTA-AA
*
574 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
599 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
78 41 0.26
79 58 0.37
80 56 0.36
81 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTAAA
Found at i:616 original size:80 final size:77
Alignment explanation
Indices: 337--631 Score: 269
Period size: 79 Copynumber: 3.7 Consensus size: 77
327 TGAATGATGT
* * **
337 CCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAG-GACTA-ATCCGGGTTAAG-TCCCGAAGGCATT
* *
399 TGTGCGAGATACTAATT
62 TGTGCGAGTTACTAA-A
* * * * *
416 TCGGGCTAAG-CCCGAAGGCATTTGTGCTAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACTAA-TCCGGGTTAAGTCCCGAAGGCATTTG
479 TGCGAGTTACTAAA
64 TGCGAGTTACTAAA
* *
493 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACT-AATCCGGGTTAAGTCCCGAAGGCATTT
558 GTGCGAGTTACTATAA
63 GTGCGAGTTACTA-AA
* ** * *
574 CCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGA-CTA-ATCCGGGTTAAGTCCCGAAGG
632 TACGTGATTT
Statistics
Matches: 183, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
78 42 0.23
79 73 0.40
80 66 0.36
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGACTAATCCGGGTTAAGTCCCGAAGGCATTTGTG
CGAGTTACTAAA
Found at i:939 original size:88 final size:88
Alignment explanation
Indices: 789--964 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
779 CCTTTGGCTA
* *
789 AGTTGATCTTTTGTGTATGTACATAAGGGTTGGTAATGTGAAGCAAGTATGATATCGAAAATTTG
1 AGTTGATCTTTTGTGTATGTACATAAGGGTTGATAATGTGAAGCAAGTACGATATCGAAAATTTG
854 TGCATATGAAATTATCCGTTTAG
66 TGCATATGAAATTATCCGTTTAG
*
877 AGTTGATCTTTTGTGTATGTACATAAGGGTTGATAATGTGAAGCAAGTACGATATCGTAAATTTG
1 AGTTGATCTTTTGTGTATGTACATAAGGGTTGATAATGTGAAGCAAGTACGATATCGAAAATTTG
942 TGCATATGAAATTATCCGTTTAG
66 TGCATATGAAATTATCCGTTTAG
965 CTATATGAAT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.38
Consensus pattern (88 bp):
AGTTGATCTTTTGTGTATGTACATAAGGGTTGATAATGTGAAGCAAGTACGATATCGAAAATTTG
TGCATATGAAATTATCCGTTTAG
Done.