Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2233
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, 615
Length: 1026
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Found at i:339 original size:100 final size:100
Alignment explanation
Indices: 1--1018 Score: 1063
Period size: 100 Copynumber: 10.2 Consensus size: 100
* *** * * *
1 TTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCATTATTGTGGTTTAAATCATTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
*
66 TACAATGT-GGGAGAAACAAGATTCACCGTTGTAGC
66 TGCAATGTCGGG-GAAACAAGATTCACCGTTGTAGC
* * * * *
101 TTCAATCTGCTCCACTGCACCGCCAGGGATGTAAGATTTACCATTGTGGTTTCAATCTTTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
* * * * *
166 TGGAATGTCGTGG-AGCAA-AGTTCGCTGTTGTAGC
66 TGCAATGTCGGGGAAACAAGA-TTCACCGTTGTAGC
* * * * *
200 TTCAATATGTTCCACTGCACCGCCAGAGAAGTAAAATTCACCATTATGGCTTCAATCTTTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
* * *
265 AGCAATGTCAGGGAAATAAGATTCACCGTTGTAGC
66 TGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* * *
300 TTTAATCTGTTCCACTCCACCACCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
*
365 TGCAATGTCGGGGAAACAAGATTCACCGTTATAGC
66 TGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* ** * *
400 TTCAATCTGTTCCACTCCACCTTCAGGAAAGTAAGATT----G--GCT-GCTCTCAAGCTTTTTA
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG-TGGCT-TCAATCTTTTTA
* ***
458 ATTGCAATGTCGGGGAAGCAAGATTTGTCGTTGTAGC
64 ATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* * ** * ** *
495 TTCACTCTGCTCCACTATACCGCCAGGAAAGTAAGATTCATTGTTGTGGCTTCAATATTTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
* *
560 TGCAATGTCGTGG-AGCAAGATTCACCGTTGTAGC
66 TGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* * * * **** *
594 TTCAATTTTTTCCACTACACTGCCAGGGAAGTAAGATTCGTTATTGTGGCTTGAATCTTTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
* * *
659 TACAATCTCGGGGAAACAAGATTCACCGTTCTAGC
66 TGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* **
694 TTCAATCTGTTCCACTGTACCGCCAGGGAAGTAAGATTTGCCGTTGTGGCTTCAATCTTTTTAAT
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
* ** *
759 TGCAATATC-GGGAGTGCCAGATTCACCGTTGTAGC
66 TGCAATGTCGGGGA-AACAAGATTCACCGTTGTAGC
* * *
794 TTCAATCTGTTCCACTGCACCGCTAGGGAAGTAAGATTCCCCGTGTTGTGGCTTCAAACTTTTTA
1 TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACC--GTTGTGGCTTCAATCTTTTTA
* * * *
859 ATTGCAATGTCGGGGGAGCCAGATTAACCGTTGTAGC
64 ATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* * * * *
896 TTCAATCTGCTCTATTGCACAC-CCAGGGAAGTAAGATTCACGGTTGTGGCTTCAATCTTGTTAA
1 TTCAATCTGTTCCACTGCAC-CGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAA
* * *** **
960 TTGTAATGTCGGGGGAGTGAGATTCACCGAGGTAGC
65 TTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
* **
996 TTCGATCTACTCCACTGCACCGC
1 TTCAATCTGTTCCACTGCACCGC
1019 TAGAGAAG
Statistics
Matches: 775, Mismatches: 123, Indels: 40
0.83 0.13 0.04
Matches are distributed among these distances:
94 4 0.01
95 76 0.10
96 1 0.00
98 1 0.00
99 170 0.22
100 429 0.55
101 7 0.01
102 83 0.11
103 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (100 bp):
TTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
TGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC
Found at i:787 original size:394 final size:397
Alignment explanation
Indices: 1--1026 Score: 1145
Period size: 394 Copynumber: 2.6 Consensus size: 397
* * * * * ** * * *
1 TTCAATTTGTTCCACTGCACCGCCAGGGAAGTAAGATTCATTATTGTGGTTTAAATCATTTTAAT
1 TTCAATCTGTTCCACTCCACCGCTAGGAAAGTAAGATTC-GTGCTGTGCTTCAAA-CTTTTTAAT
* * *
66 TACAATGT-GGGAGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGA
64 TGCAATGTCGGG-GAAGCAAGATTAACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGA
* * * * * * *
130 TGTAAGATTTACCATTGTGGTTTCAATCTTTTTAATTGGAATGTCGTGGAGCAA-AGTTCGCTGT
128 AGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGTGGAGCAAGA-TTCACCGT
*
194 TGTAGCTTCAATATGTTCCACTGCACCGCCAGAGAAGTAAAATTCACCATTATGGCTTCAATCTT
192 TGTAGCTTCAATATGTTCCACTACACCGCCAGAGAAGTAAAATTCACCATTATGGCTTCAATCTT
* * * *
259 TTTAATAGCAATGTCAGGGAAATAAGATTCACCGTTGTAGCTTTAATCTGTTCCACTCCACCACC
257 TTTAATAGCAATCTCAGGGAAACAAGATTCACCGTTCTAGCTTCAATCTGTTCCACTCCACCACC
*
324 AGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTC
322 AGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAACAAGATTC
389 ACCGTTATAGC
387 ACCGTTATAGC
* *
400 TTCAATCTGTTCCACTCCACC-TTCAGGAAAGTAAGATT-G-GC--TGCTCTCAAGCTTTTTAAT
1 TTCAATCTGTTCCACTCCACCGCT-AGGAAAGTAAGATTCGTGCTGTGCT-TCAAACTTTTTAAT
*** * ** *
460 TGCAATGTCGGGGAAGCAAGATTTGTCGTTGTAGCTTCACTCTGCTCCACTATACCGCCAGGAAA
64 TGCAATGTCGGGGAAGCAAGATTAACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
** *
525 GTAAGATTCATTGTTGTGGCTTCAATATTTTTAATTGCAATGTCGTGGAGCAAGATTCACCGTTG
129 GTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGTGGAGCAAGATTCACCGTTG
* * * * * *** * *
590 TAGCTTCAATTTTTTCCACTACACTGCCAGGGAAGTAAGATTCGTTATTGTGGCTTGAATCTTTT
194 TAGCTTCAATATGTTCCACTACACCGCCAGAGAAGTAAAATTCACCATTATGGCTTCAATCTTTT
* ** *
655 TAATTA-CAATCTCGGGGAAACAAGATTCACCGTTCTAGCTTCAATCTGTTCCACTGTACCGCCA
259 TAA-TAGCAATCTCAGGGAAACAAGATTCACCGTTCTAGCTTCAATCTGTTCCACTCCACCACCA
** ** *
719 GGGAAGTAAGATTTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATC-GGGAGTGCCAGATTC
323 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATATCGGGGA-AACAAGATTC
*
783 ACCGTTGTAGC
387 ACCGTTATAGC
* * *
794 TTCAATCTGTTCCACTGCACCGCTAGGGAAGTAAGATTCCCCGTGTTGTGGCTTCAAACTTTTTA
1 TTCAATCTGTTCCACTCCACCGCTAGGAAAGTAAGATT---CGTGCTGT-GCTTCAAACTTTTTA
* * * *
859 ATTGCAATGTCGGGGGAGCCAGATTAACCGTTGTAGCTTCAATCTGCTCTATTGCACAC-CCAGG
62 ATTGCAATGTCGGGGAAGCAAGATTAACCGTTGTAGCTTCAATCTGCTCCACTGCAC-CGCCAGG
* * * * **
923 GAAGTAAGATTCACGGTTGTGGCTTCAATCTTGTTAATTGTAATGTCGGGGGAGTGAGATTCACC
126 GAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GTGGAGCAAGATTCACC
** * * ** * *
988 GAGGTAGCTTCGATCTACTCCACTGCACCGCTAGAGAAG
190 GTTGTAGCTTCAATATGTTCCACTACACCGCCAGAGAAG
Statistics
Matches: 519, Mismatches: 91, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
393 4 0.01
394 319 0.61
395 10 0.02
398 1 0.00
399 33 0.06
401 105 0.20
402 47 0.09
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (397 bp):
TTCAATCTGTTCCACTCCACCGCTAGGAAAGTAAGATTCGTGCTGTGCTTCAAACTTTTTAATTG
CAATGTCGGGGAAGCAAGATTAACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGT
AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGTGGAGCAAGATTCACCGTTGTA
GCTTCAATATGTTCCACTACACCGCCAGAGAAGTAAAATTCACCATTATGGCTTCAATCTTTTTA
ATAGCAATCTCAGGGAAACAAGATTCACCGTTCTAGCTTCAATCTGTTCCACTCCACCACCAGGG
AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAACAAGATTCACCG
TTATAGC
Found at i:831 original size:50 final size:50
Alignment explanation
Indices: 83--953 Score: 220
Period size: 50 Copynumber: 17.5 Consensus size: 50
73 TGGGAGAAAC
* * *
83 AAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGATGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
* * * * * ** * * ** * *
133 AAGATTTACCATTGTGGTTTCAATCTTTTTAATTGGAATG-TCGTGG-AGC
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAG-GGAAGT
* * * * *
182 AA-AGTTCGCTGTTGTAGCTTCAATATGTTCCACTGCACCGCCAGAGAAGT
1 AAGA-TTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
* * * * ** * ** *
232 AAAATTCACCATTATGGCTTCAATCT-TTTTAATAGCAATG-TCAGGGAAAT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACT-GCACCGCT-AGGGAAGT
* * * *
282 AAGATTCACCGTTGTAGCTTTAATCTGTTCCACTCCACCACCAGGGAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
* * ** * ** * **
332 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATG-TCGGGGAAAC
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCT-AGGGAAGT
* * * *
382 AAGATTCACCGTTATAGCTTCAATCTGTTCCACTCCACC-TTCAGGAAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCT-AGGGAAGT
* * ** * ** * *
432 AAGATT----G--GCT-GCTCTCAAGCTTTTTAATTGCAATG-TCGGGGAAGC
1 AAGATTCACCGTTG-TAGCT-TCAATCTGTTCCACTGCACCGCT-AGGGAAGT
*** * * ** * *
477 AAGATTTGTCGTTGTAGCTTCACTCTGCTCCACTATACCGCCAGGAAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
** * * * ** * ** * *
527 AAGATTCATTGTTGTGGCTTCAATATTTTTAATTGCAATG-TCGTGG-AGC
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAG-GGAAGT
* * * * *
576 AAGATTCACCGTTGTAGCTTCAATTTTTTCCACTACACTGCCAGGGAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
**** * * * ** * * ** * **
626 AAGATTCGTTATTGTGGCTTGAATCTTTTTAATTACA-ATCTCGGGGAAAC
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCT-AGGGAAGT
* * *
676 AAGATTCACCGTTCTAGCTTCAATCTGTTCCACTGTACCGCCAGGGAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
** * * ** * *** *
726 AAGATTTGCCGTTGTGGCTTCAATCTTTTTAATTGCA-ATATCGGG-AGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
*
774 GCCAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
1 --AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
* * * * ** * ** * * *
826 AAGATTCCCCGTGTTGTGGCTTCAAACTTTTTAATTGCAATG-TCGGGGGAGC
1 AAGATTCACC--GTTGTAGCTTCAATCTGTTCCACTGCACCGCT-AGGGAAGT
* * * * * *
878 CAGATTAACCGTTGTAGCTTCAATCTGCTCTATTGCACAC-CCAGGGAAGT
1 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC-CGCTAGGGAAGT
* *
928 AAGATTCACGGTTGTGGCTTCAATCT
1 AAGATTCACCGTTGTAGCTTCAATCT
954 TGTTAATTGT
Statistics
Matches: 545, Mismatches: 240, Indels: 72
0.64 0.28 0.08
Matches are distributed among these distances:
44 3 0.01
45 26 0.05
46 1 0.00
48 4 0.01
49 72 0.13
50 387 0.71
51 15 0.03
52 37 0.07
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (50 bp):
AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCTAGGGAAGT
Done.