Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold226
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: 24199
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:10537 original size:27 final size:27
Alignment explanation
Indices: 10507--10682 Score: 192
Period size: 27 Copynumber: 6.5 Consensus size: 27
10497 AAATTGTACA
10507 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
10534 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
10561 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
*
10588 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* * *
10616 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGATTTGACTATGTT
* * *
10643 GCACTAAGTGTGCGAGTTGATTAT-AT
1 GCACTAAGTGTGCGATTTGACTATGTT
*
10669 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
10683 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
26 13 0.10
27 92 0.72
28 23 0.18
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:10620 original size:82 final size:81
Alignment explanation
Indices: 10507--10662 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10497 AAATTGTACA
* *
10507 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
10571 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10588 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
10653 TGCGAGTTGA
65 TGCGAATTGA
10663 TTATATGCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20449 original size:96 final size:93
Alignment explanation
Indices: 20253--20475 Score: 242
Period size: 96 Copynumber: 2.3 Consensus size: 93
20243 ATGGTGTAAT
* *
20253 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGTCGATGCCATGTCTTCA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAACTCATCCATCAAGTCGATGCCATGTCTCCA
* *
20318 ACATGGTCTTACACTGACTATAGAAATCGAG
65 ACATGGTATTACACTGAC--TACAAATCGAG
*
20349 GCCGATGTCATGTCCCAGACATGGTCTTACACTAACTC-TCACAT-ATCCGTGCTGATGCCATGT
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAACTCATC-CATCA--AGT-C-GATGCCATGT
**
20412 C-CCAGACATGGTATTACACTGAC-ACATTTCGTA-
60 CTCCA-ACATGGTATTACACTGACTACAAATCG-AG
20445 GCCGATGCATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCATGTCCCAGACATGGTCTTACACT
20476 GGCTTACATC
Statistics
Matches: 112, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
94 10 0.09
95 17 0.15
96 51 0.46
97 3 0.03
98 3 0.03
99 28 0.25
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (93 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTAACTCATCCATCAAGTCGATGCCATGTCTCCAA
CATGGTATTACACTGACTACAAATCGAG
Found at i:20505 original size:46 final size:49
Alignment explanation
Indices: 20253--20615 Score: 278
Period size: 46 Copynumber: 7.7 Consensus size: 49
20243 ATGGTGTAAT
* *
20253 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-ATC-CATCAA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTA-CATATCAAG
* * * * * * *
20300 GTCGATGCCATGTCTTCA-ACATGGTCTTACACTGACTATAGAAATCGAG
1 GCCGATGCCATGTC-CCAGACATGGTCTTACACTGGCTCTACATATCAAG
* ** *
20349 GCCGATGTCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC-CG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-ACATATCAAG
* * * * *
20398 TGCTGATGCCATGTCCCAGACATGGTATTACACT-G-AC-ACATTTCGTA-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATATC-AAG
*
20445 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATATCAAG
* * * *
20491 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATATCAAG
** * * **
20537 GTTGATGCCATGTCTCAAACATGGTCTTACACTGGCTCT-CATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACAT-ATCAAG
20585 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
20616 AGCACACAAA
Statistics
Matches: 254, Mismatches: 45, Indels: 35
0.76 0.13 0.10
Matches are distributed among these distances:
44 9 0.04
45 16 0.06
46 74 0.29
47 55 0.22
48 32 0.13
49 33 0.13
50 35 0.14
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATATCAAG
Found at i:20564 original size:94 final size:92
Alignment explanation
Indices: 20448--20618 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 92
20438 TTTCGTAGCC
* *
20448 GATGCATGTCCCAGACATGTCTTACACTGGCT-TACAT-CTCAAGGCCGATGCATGTCCCAGACA
1 GATGCATGTCCCAAACATGTCTTACACTGGCTCT-CATAAT-AAGGCCGATGCATGTCCCAGACA
20511 TGTCTTACACTAGCTCTCGTCTCAATGTT
64 TGTCTTACACTAGCTCTCGTCTCAATGTT
* **
20540 GATGCCATGTCTCAAACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
1 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTCTCATAATAAGGCCGATGCATGTCCCAGACA
20605 TGTCTTACACTAGC
64 TGTCTTACACTAGC
20619 ACACAAATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
92 4 0.06
93 12 0.17
94 52 0.74
95 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCCAAACATGTCTTACACTGGCTCTCATAATAAGGCCGATGCATGTCCCAGACATG
TCTTACACTAGCTCTCGTCTCAATGTT
Found at i:20595 original size:140 final size:142
Alignment explanation
Indices: 20250--20615 Score: 383
Period size: 140 Copynumber: 2.6 Consensus size: 142
20240 CATATGGTGT
*
20250 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAA-GT--CGATGCCATG
1 AATGCTGATGCCATGTCCCAGACATGGTCTTACACT-GCTC-T-CAT-AATGTGCCGATG-CATG
* * *
20312 TCTTCA-ACATGGTCTTACACTGACTATAGAAATCGAGGCCGATGTCATGTCCCAGACATGGTCT
61 TC-CCAGACAT-GTCTTACACTGACTATACAAATCAAGGCCGATGTCATGTCCCAGACATGGTCT
20376 TACACTAACTCTCACATATC
124 TACACTAACTCT-ACATATC
** * * * *
20396 CGTGCTGATGCCATGTCCCAGACATGGTATTACACTG-ACACAT-TTCGTAGCCGATGCATGTCC
1 AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGCTCTCATAAT-GT-GCCGATGCATGTCC
* **
20459 CAGACATGTCTTACACTGGCT-TACATCTCAAGGCCGATG-CATGTCCCAGACAT-GTCTTACAC
64 CAGACATGTCTTACACTGACTATACAAATCAAGGCCGATGTCATGTCCCAGACATGGTCTTACAC
* * *
20521 TAGCTCT-CGTCTC
129 TAACTCTACATATC
* * *
20534 AATGTTGATGCCATGTCTCAAACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
1 AATGCTGATGCCATGTCCCAGACATGGTCTTACACT-GCTCTCATAATGT-GCCGATGCATGTCC
20599 CAGACATGTCTTACACT
64 CAGACATGTCTTACACT
20616 AGCACACAAA
Statistics
Matches: 185, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
138 34 0.18
139 1 0.01
140 52 0.28
141 15 0.08
142 19 0.10
143 15 0.08
144 11 0.06
145 6 0.03
146 32 0.17
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (142 bp):
AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGCTCTCATAATGTGCCGATGCATGTCCCA
GACATGTCTTACACTGACTATACAAATCAAGGCCGATGTCATGTCCCAGACATGGTCTTACACTA
ACTCTACATATC
Done.