Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3410
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: 9271
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Found at i:8310 original size:72 final size:73
Alignment explanation
Indices: 8108--8357 Score: 334
Period size: 72 Copynumber: 3.5 Consensus size: 73
8098 GCTTTTCAGG
* * * * *
8108 AAAAT-AACTCATATTGCGAGAGATTGAGTTGAGTCTCAAGACACGTTGAGATACTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAG-GTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
*
8171 TGTTTTTC-
65 TGTTTGTCA
* *
8179 AAAATCAACTCATA-TGCTA-AGGTGAGTTGAGCCTCAGGACAC-TTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCT
8241 GTTTGTCA
66 GTTTGTCA
* *
8249 AAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCT
8313 GTTTGTCA
66 GTTTGTCA
* *
8321 AAAATCAACTCATATTGCTAGAGGTGAGTGGAGCCTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
8358 GGCTCACAGC
Statistics
Matches: 159, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
68 15 0.09
69 25 0.16
70 20 0.13
71 30 0.19
72 49 0.31
73 20 0.13
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCT
GTTTGTCA
Found at i:8393 original size:12 final size:12
Alignment explanation
Indices: 8376--8401 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8366 GCTGAGGTCT
8376 TTTCAATTTATG
1 TTTCAATTTATG
8388 TTTCAATTTATG
1 TTTCAATTTATG
8400 TT
1 TT
8402 CGTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTCAATTTATG
Found at i:8587 original size:72 final size:75
Alignment explanation
Indices: 8410--8835 Score: 284
Period size: 74 Copynumber: 5.5 Consensus size: 75
8400 TTCGTTAAAA
*
8410 AAAAATCAACTCATATTGCGAGAGGTGAGTT-AGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAAATTT
*
8474 CTGTTTTTTTC
66 CTG-TTTTGTC
* * *
8485 AAAAATCAACTCATATTGCGAGAGGGGAGTTGAG-CTCGGGACACGCTGAGGTAATTTTCAA-TT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAAATTT
8548 CTG-TTTGTC
66 CTGTTTTGTC
* *
8557 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGGCCTC-GGCTCACTGCTGAGGTCTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGA-GCCTCAGG-ACAC-GCTGAGG----T-AATT
*** **
8621 TCTGTTCTTTCAATTTCTGTTC
58 T-T-AAATTTCTGTTT-TG-TC
* ** * * * * * *
8643 GTAAAAAAAAATCA-ACT-C-ATATTGCGAGAGGTGAGTTGAGCGCTCAAGACACGCTGAGGT-A
1 -AAAAATCAACTCATATTGCGAGA--G-GTGAGTT-----GAGC-CTCAGGACACGCTGAGGTAA
**
8704 TTTTAAATGCCTG-TTT-TC
56 TTTTAAATTTCTGTTTTGTC
* * * *
8722 AAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGTCTCGGGAACACGCTGAGGTAA-TTTCAAT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTTAAAT
8786 TTCTG-TTTGTC
64 TTCTGTTTTGTC
*
8797 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
8836 CTCACATGCT
Statistics
Matches: 269, Mismatches: 49, Indels: 67
0.70 0.13 0.17
Matches are distributed among these distances:
72 36 0.13
73 7 0.03
74 73 0.27
75 64 0.24
76 2 0.01
79 17 0.06
80 8 0.03
81 3 0.01
82 4 0.01
83 5 0.02
84 5 0.02
85 7 0.03
86 5 0.02
87 15 0.06
91 9 0.03
92 8 0.03
93 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAAATTT
CTGTTTTGTC
Found at i:8631 original size:15 final size:15
Alignment explanation
Indices: 8611--8642 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8601 ACTGCTGAGG
8611 TCTTTCAATTTCTGT
1 TCTTTCAATTTCTGT
8626 TCTTTCAATTTCTGT
1 TCTTTCAATTTCTGT
8641 TC
1 TC
8643 GTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.22, G:0.06, T:0.59
Consensus pattern (15 bp):
TCTTTCAATTTCTGT
Found at i:8785 original size:166 final size:164
Alignment explanation
Indices: 8485--8792 Score: 435
Period size: 166 Copynumber: 1.9 Consensus size: 164
8475 TGTTTTTTTC
** * *
8485 AAAAATCAACTCATATTGCGAGAGGGGAGTTGAGCTCGGGACACGCTGAGGTAATTTTCAATTCT
1 AAAAATCAACTCATATTGCGAGAGGGGAGTTGAGCTCAAGACACGCTGAGGTAATTTTAAATCCT
* * ** *
8550 GTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGGCCTCGGCTCACTGCTGAGGTCTT
66 GTTTGTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGGCCTCGGAACACTGCTGAGGTATT
8615 TCAATTTCTGTTCTTTCAATTTCTGTTCGTAAAA
131 TCAATTTCTGTTCTTTCAATTTCTGTTCGTAAAA
*
8649 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGCTCAAGACACGCTGAGGT-ATTTTAAATG
1 AAAAATCAACTCATATTGCGAGAGGGGAGTTGA--GCTCAAGACACGCTGAGGTAATTTTAAAT-
*
8713 CCTGTTT-TCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGA-GTCTCGGGAACAC-GCTGAG
63 CCTGTTTGTC-AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGGCCTC-GGAACACTGCTGAG
8775 GTAATTTCAATTTCTGTT
126 GT-ATTTCAATTTCTGTT
8793 TGTCAAAAAT
Statistics
Matches: 127, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
164 32 0.25
165 22 0.17
166 73 0.57
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (164 bp):
AAAAATCAACTCATATTGCGAGAGGGGAGTTGAGCTCAAGACACGCTGAGGTAATTTTAAATCCT
GTTTGTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGGCCTCGGAACACTGCTGAGGTATT
TCAATTTCTGTTCTTTCAATTTCTGTTCGTAAAA
Found at i:8794 original size:240 final size:235
Alignment explanation
Indices: 8179--8877 Score: 1006
Period size: 238 Copynumber: 3.0 Consensus size: 235
8169 TTTGTTTTTC
* * * *
8179 AAAATCAACTCATA-TGCTA-AGGTGAGTTGAGCCTCAGGACAC-TTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCT
**
8241 GTTTGTCAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTC-AAAACACGCTGAGGTAATT
66 GTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTCGGGAACACGCTGAGGTAATT
* * * *
8304 TCAATTTCTGTTTGTCAAAAATCAACTCATATTGCTAGAGGTGAGTGGAGCCTCGGCTCACAGCT
129 TCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACTGCT
* *
8369 GAGGTCTTTTCAATTTATG-TTTCAATTTATGTTCGTTAAAAA
194 GAGGTC-TTTCAATTTCTGTTTTCAATTTCTGTTCGTTAAAAA
8411 AAAATCAACTCATATTGCGAGAGGTGAGTT-AGCCTCAGGACACGCTGAGGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTTAAATTTC
*
8475 TGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGGGAGTTGAGCTCGGG-ACACGCTGAGGTAA
65 TG---TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTCGGGAACACGCTGAGGTAA
8539 TTTTCAA-TTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGGCCTCGGCTCAC
127 -TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGA-GCCTCGGCTCAC
8603 TGCTGAGGTCTTTCAATTTCTGTTCTTTCAATTTCTGTTCG-TAAAAA
190 TGCTGAGGTCTTTCAATTTCTG-T-TTTCAATTTCTGTTCGTTAAAAA
* **
8650 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGCTCAAGACACGCTGAGGTATTTTAAATGCC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGC-CTCAGGACACGCTGAGGTATTTTAAATTTC
*
8715 TGTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGTCTCGGGAACACGCTGAGGTAAT
65 TGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTCGGGAACACGCTGAGGTAAT
*
8780 TTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTC-ACTCACATG
128 TTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC-TG
*
8844 CTGAGGTCTTTTAATTTCTGCTTTTCAATTTCTG
192 CTGAGGTCTTTCAATTTCTG-TTTTCAATTTCTG
8878 ATTTTTTCAA
Statistics
Matches: 425, Mismatches: 21, Indels: 36
0.88 0.04 0.07
Matches are distributed among these distances:
232 14 0.03
233 17 0.04
234 16 0.04
235 11 0.03
237 91 0.21
238 96 0.23
239 75 0.18
240 87 0.20
241 18 0.04
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (235 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCT
GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTCGGGAACACGCTGAGGTAATTTC
AATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACTGCTGA
GGTCTTTCAATTTCTGTTTTCAATTTCTGTTCGTTAAAAA
Found at i:8847 original size:74 final size:72
Alignment explanation
Indices: 8649--8871 Score: 250
Period size: 74 Copynumber: 3.0 Consensus size: 72
8639 GTTCGTAAAA
* * **
8649 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGCTCAAGACACGCTGAGGTATTTTAAATGC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC-CTCAAAACACGCTGAGGTAATTTAAATTT
8714 CTGTTTTC
65 CTGTTTTC
* * ** *
8722 AAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGTCTCGGGAACACGCTGAGGTAATTTCAATT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AAAACACGCTGAGGTAATTTAAATT
8787 TCTGTTTGTC
64 TCTGTTT-TC
* ** * * *
8797 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCACTCACATGCTGAGGT-CTTTTAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-AAACACGCTGAGGTAATTTAAATTT
8861 CTGCTTTTC
65 CTG-TTTTC
8870 AA
1 AA
8872 TTTCTGATTT
Statistics
Matches: 127, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
73 18 0.14
74 107 0.84
75 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGCTGAGGTAATTTAAATTTC
TGTTTTC
Done.