Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold9296.1
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: 4495
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.29
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:505 original size:75 final size:75
Alignment explanation
Indices: 374--1049 Score: 1041
Period size: 75 Copynumber: 8.9 Consensus size: 75
364 CGAAAACTAA
* *
374 AAGAAAATTAAATGTGGTTAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGG
1 AAGAAAA-TAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGG
439 AGTAAAAATGG
65 AGTAAAAATGG
450 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
1 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
515 GTAAAAATGG
66 GTAAAAATGG
525 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
1 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
590 GTAAAAATGG
66 GTAAAAATGG
600 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
1 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
665 GTAAAAATGG
66 GTAAAAATGG
675 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
1 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
740 GTAAAAATGG
66 GTAAAAATGG
* **
750 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGATGAGAGAGTTAGGA
1 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
**
815 G-AAAAATAA
66 GTAAAAATGG
* * *
824 ATGAGAAAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACT
1 A--AG-AAAAT-AAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACT
889 AGGAGTAAAAATGG
62 AGGAGTAAAAATGG
* **
903 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGATGAGAGAGTTAGGA
1 AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
**
968 G-AAAAATAA
66 GTAAAAATGG
* * *** *
977 ATGAGAAAAATAAAATGTGGTGAGTGTCATTTATTGAATCCACAACCTCTTGAATAGAGGAGAGA
1 A--AG-AAAAT-AAATGAGGTAAGTG---GGGATTGAACCCACAACCTCTTGAATAGAGGAGAGA
1042 ACTAGGAG
59 ACTAGGAG
1050 AATTATAAAA
Statistics
Matches: 556, Mismatches: 32, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
74 14 0.03
75 406 0.73
76 16 0.03
77 12 0.02
78 64 0.12
79 7 0.01
81 37 0.07
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.19
Consensus pattern (75 bp):
AAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGA
GTAAAAATGG
Found at i:840 original size:14 final size:13
Alignment explanation
Indices: 813--837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
803 AGAGAGTTAG
813 GAGAAAAATAAAT
1 GAGAAAAATAAAT
826 GAGAAAAATAAA
1 GAGAAAAATAAA
838 ATGTGGTGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
GAGAAAAATAAAT
Found at i:993 original size:14 final size:13
Alignment explanation
Indices: 966--990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
956 AGAGAGTTAG
966 GAGAAAAATAAAT
1 GAGAAAAATAAAT
979 GAGAAAAATAAA
1 GAGAAAAATAAA
991 ATGTGGTGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
GAGAAAAATAAAT
Found at i:1149 original size:153 final size:150
Alignment explanation
Indices: 377--1135 Score: 949
Period size: 150 Copynumber: 5.0 Consensus size: 150
367 AAACTAAAAG
* * *
377 AAAATTAAATGTGGTTAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
1 AAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
442 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGA-ATAGAGGAGA
66 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAGAT-GA-GAGA
* **
506 GAACTAGGAGTAAAAATGGA--AG-
129 G--TTAGGAG-AAAAATAAATGAGA
* * *
528 AAAAT-AAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
1 AAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
592 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGA-ATAGAGGAGA
66 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAGAT-GA-GAGA
* **
656 GAACTAGGAGTAAAAATGGA--AG-
129 G--TTAGGAG-AAAAATAAATGAGA
* * *
678 AAAAT-AAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
1 AAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
742 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGATGAGAG
66 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTG---AGATGAGAG
807 AGTTAGGAGAAAAATAAATGAGA
128 AGTTAGGAGAAAAATAAATGAGA
830 AAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
1 AAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
895 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAATAGATGAGAG
66 AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTG---AGATGAGAG
960 AGTTAGGAGAAAAATAAATGAGA
128 AGTTAGGAGAAAAATAAATGAGA
***
983 AAAATAAAATGTGGTGAGTGTCATTTATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGG
1 AAAATAAAATGTGGTGAGTG---GGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGG
** ** * * * *
1048 AG-AATTATAAAAGCGAAATAAAATGAGGTGAGAT-GGGATGGAACCCACAACCTGTTG-GAT-A
63 AGTAAAAATGGAAG-AAAAT-AAATGAGGTAAG-TGGGGATTGAACCCACAACCTCTTGAGATGA
* *
1109 -A-AGTTAGGAGAAAAGTTAA-GAGA
125 GAGAGTTAGGAGAAAAATAAATGAGA
1132 AAAA
1 AAAA
1136 GAATAAGTCT
Statistics
Matches: 573, Mismatches: 21, Indels: 30
0.92 0.03 0.05
Matches are distributed among these distances:
149 15 0.03
150 282 0.49
151 8 0.01
152 11 0.02
153 170 0.30
154 2 0.00
155 7 0.01
156 45 0.08
157 32 0.06
158 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (150 bp):
AAAATAAAATGTGGTGAGTGGGGATTGAATCCACAACCTCTTGAATAGAGGAGAGAACTAGGAGT
AAAAATGGAAGAAAATAAATGAGGTAAGTGGGGATTGAACCCACAACCTCTTGAGATGAGAGAGT
TAGGAGAAAAATAAATGAGA
Found at i:4003 original size:265 final size:265
Alignment explanation
Indices: 3530--4040 Score: 1022
Period size: 265 Copynumber: 1.9 Consensus size: 265
3520 TGACTCCAAA
3530 AATATAGAAGCAGTTGACAGTTGGCTGACCTATATCTCCAACAGAGATAAGGGGTTTCTTAGGTT
1 AATATAGAAGCAGTTGACAGTTGGCTGACCTATATCTCCAACAGAGATAAGGGGTTTCTTAGGTT
3595 AAGTTGACTATTATAGGAGATTTGTTCAACGGTTTTCATCTATCTTTTTTCCTTTGACAAAGATA
66 AAGTTGACTATTATAGGAGATTTGTTCAACGGTTTTCATCTATCTTTTTTCCTTTGACAAAGATA
3660 ACTTAGAAGACTGTCAAGTTTCAATGTTTTGAAGCTTTTGAGAAAAGCTCTTAGGAGTTGAAAAA
131 ACTTAGAAGACTGTCAAGTTTCAATGTTTTGAAGCTTTTGAGAAAAGCTCTTAGGAGTTGAAAAA
3725 GAGATTGACTACTAATTCTGTTTTGAAATTTCCAAAAAGTACTCAATGTTTCCGATCTCCGAACT
196 GAGATTGACTACTAATTCTGTTTTGAAATTTCCAAAAAGTACTCAATGTTTCCGATCTCCGAACT
3790 CATTT
261 CATTT
3795 AATATAGAAGCAGTTGACAGTTGGCTGACCTATATCTCCAACAGAGATAAGGGGTTTCTTAGGTT
1 AATATAGAAGCAGTTGACAGTTGGCTGACCTATATCTCCAACAGAGATAAGGGGTTTCTTAGGTT
3860 AAGTTGACTATTATAGGAGATTTGTTCAACGGTTTTCATCTATCTTTTTTCCTTTGACAAAGATA
66 AAGTTGACTATTATAGGAGATTTGTTCAACGGTTTTCATCTATCTTTTTTCCTTTGACAAAGATA
3925 ACTTAGAAGACTGTCAAGTTTCAATGTTTTGAAGCTTTTGAGAAAAGCTCTTAGGAGTTGAAAAA
131 ACTTAGAAGACTGTCAAGTTTCAATGTTTTGAAGCTTTTGAGAAAAGCTCTTAGGAGTTGAAAAA
3990 GAGATTGACTACTAATTCTGTTTTGAAATTTCCAAAAAGTACTCAATGTTT
196 GAGATTGACTACTAATTCTGTTTTGAAATTTCCAAAAAGTACTCAATGTTT
4041 TTGTGTTATA
Statistics
Matches: 246, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
265 246 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (265 bp):
AATATAGAAGCAGTTGACAGTTGGCTGACCTATATCTCCAACAGAGATAAGGGGTTTCTTAGGTT
AAGTTGACTATTATAGGAGATTTGTTCAACGGTTTTCATCTATCTTTTTTCCTTTGACAAAGATA
ACTTAGAAGACTGTCAAGTTTCAATGTTTTGAAGCTTTTGAGAAAAGCTCTTAGGAGTTGAAAAA
GAGATTGACTACTAATTCTGTTTTGAAATTTCCAAAAAGTACTCAATGTTTCCGATCTCCGAACT
CATTT
Done.