Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3689
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: 17569
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:925 original size:47 final size:48
Alignment explanation
Indices: 766--1021 Score: 222
Period size: 46 Copynumber: 5.6 Consensus size: 48
756 CTAAGTCAAT
* *
766 CATGTCCCAGACAGGTCTTACACT-GATTTCATATTTACAAGGCCGATGC
1 CATGTCCCAGACAGGTCTTACACTAG-CTTCATATCT-CAAGGCCGATGC
* * *
815 CATGTCCCAGACAGGTCTTACACT-G--ACACATGTCAA-GCCGATGC
1 CATGTCCCAGACAGGTCTTACACTAGCTTCATATCTCAAGGCCGATGC
*
859 CATGTCCCAGA-AGGT-TTACACTAGCTTGCATATCTCGAGGCCGATG-
1 CATGTCCCAGACAGGTCTTACACTAGCTT-CATATCTCAAGGCCGATGC
* * * *
905 CATGT-CCAGACATGTCTTACACTA-C-T--TATCTTAATGCTGATGC
1 CATGTCCCAGACAGGTCTTACACTAGCTTCATATCTCAAGGCCGATGC
* *
948 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT---GGCCGATG-
1 CATGTCCCAGACA-GGTCTTACACTAGCT-TCAT-ATCTCAAGGCCGATGC
*
995 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACAGGTCTTACACTAGC
1022 ACACATCCAT
Statistics
Matches: 172, Mismatches: 19, Indels: 35
0.76 0.08 0.15
Matches are distributed among these distances:
42 19 0.11
43 10 0.06
44 26 0.15
45 19 0.11
46 34 0.20
47 28 0.16
48 7 0.04
49 25 0.15
50 1 0.01
51 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (48 bp):
CATGTCCCAGACAGGTCTTACACTAGCTTCATATCTCAAGGCCGATGC
Found at i:927 original size:89 final size:91
Alignment explanation
Indices: 766--1028 Score: 288
Period size: 91 Copynumber: 2.9 Consensus size: 91
756 CTAAGTCAAT
* * * *
766 CATGTCCCAGACAGGTCTTACACTGATTTCATATTTACAAGGCCGATGCCATGTCCCAGACAGGT
1 CATGTCCCAGACAGGTCTTACACTG-CTTCATATAT-CGAGGCCGATG-CATGTCCCAGACATGT
*
831 CTTACACTGACACATGTCAA-GCCGATGC
63 CTTACACTGACACATCTCAATGCCGATGC
*
859 CATGTCCCAGA-AGGT-TTACACTAGCTTGCATATCTCGAGGCCGATGCATGT-CCAGACATGTC
1 CATGTCCCAGACAGGTCTTACACT-GCTT-CATATATCGAGGCCGATGCATGTCCCAGACATGTC
** * *
921 TTACACT-ACTTATCTTAATGCTGATGC
64 TTACACTGACACATCTCAATGCCGATGC
*
948 CATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT-GTGGCCGATGCATGTCCCAGACATGT
1 CATGTCCCAGACA-GGTCTTACACT-GCT-TCATATATCGAGGCCGATGCATGTCCCAGACATGT
1011 CTTACACTAGCACACATC
63 CTTACACT-G-ACACATC
1029 CATAACACCC
Statistics
Matches: 145, Mismatches: 14, Indels: 21
0.81 0.08 0.12
Matches are distributed among these distances:
88 7 0.05
89 35 0.24
90 20 0.14
91 41 0.28
92 25 0.17
93 12 0.08
94 5 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (91 bp):
CATGTCCCAGACAGGTCTTACACTGCTTCATATATCGAGGCCGATGCATGTCCCAGACATGTCTT
ACACTGACACATCTCAATGCCGATGC
Found at i:7536 original size:47 final size:47
Alignment explanation
Indices: 7277--7635 Score: 254
Period size: 46 Copynumber: 7.7 Consensus size: 47
7267 AGGGTACGAT
* * * * *
7277 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGC-TCAACATCT-AA
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTTC-ATATCTGAG
* * *
7324 GTCGATGCCATGTCCCAGACAGGTCTTACACT-GACTTTCATATATCGAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAG-C-TTCATATCT-GAG
*
7373 GCCGATGCCATGTCCCAGACA-GTCTT--ACTGGCTCTCATCTATC-G-G
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCT-TCA--TATCTGAG
* * * * * *
7418 TGTCGATGCCATGTCCCAGATAGGTCTTACACT-GAC-ACATGTC--AA
1 -GCCGATGCCATGTCCCAGACATGTCTTACACTAG-CTTCATATCTGAG
*
7463 GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGCATATCTCGAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTT-CATATCT-GAG
* *
7512 GCCGATG-CATGT-CCAGACATGTCTTACACTAGC-TC-TATCTTAAT
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTCATATC-TGAG
* * *
7556 G-CGATGCCATGTCCCAAACATGGTCTTACACT-GCTCTCATA-ATGTG
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCT-TCATATCTGAG
7602 GCCGATG-CATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGC
7636 AACATCCATA
Statistics
Matches: 254, Mismatches: 28, Indels: 61
0.74 0.08 0.18
Matches are distributed among these distances:
43 5 0.02
44 42 0.17
45 28 0.11
46 71 0.28
47 57 0.22
48 18 0.07
49 33 0.13
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTCATATCTGAG
Found at i:7541 original size:91 final size:92
Alignment explanation
Indices: 7275--7636 Score: 293
Period size: 91 Copynumber: 3.9 Consensus size: 92
7265 ATAGGGTACG
* * * * ** *
7275 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTG-GCTCA-ACATCTAAGTCGATGCCATGTC
1 ATGCCGATGCCATGTCCCAGACA-GGTCTTACACTGCTCTCATATATC-GGGCCGATG-CATGTC
* * * *
7338 CCAGACAGGTCTTACACT-GACTTTCATATATCG
63 CCAGACATGTCTTACACTAG-C--AC-TATCTCA
* * *
7371 AGGCCGATGCCATGTCCCAGACA-GTCTT--ACTGGCTCTCATCTATCGGTGTCGATGCCATGTC
1 ATGCCGATGCCATGTCCCAGACAGGTCTTACACT-GCTCTCATATATCGG-GCCGATG-CATGTC
* * *
7433 CCAGATAGGTCTTACACT-GACAC-ATGTCA
63 CCAGACATGTCTTACACTAG-CACTATCTCA
*
7462 A-GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCT-TGCATATCTCGAGGCCGATGCATGT-
1 ATGCCGATGCCATGTCCCAGACAGGTCTTACACT-GCTCT-CATATATCG-GGCCGATGCATGTC
* *
7524 CCAGACATGTCTTACACTAGCTCTATCTTA
63 CCAGACATGTCTTACACTAGCACTATCTCA
*
7554 ATG-CGATGCCATGTCCCAAACATGGTCTTACACTGCTCTCATA-AT-GTGGCCGATGCATGTCC
1 ATGCCGATGCCATGTCCCAGACA-GGTCTTACACTGCTCTCATATATCG-GGCCGATGCATGTCC
7616 CAGACATGTCTTACACTAGCA
64 CAGACATGTCTTACACTAGCA
7637 ACATCCATAA
Statistics
Matches: 226, Mismatches: 25, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
90 35 0.15
91 50 0.22
92 40 0.18
93 34 0.15
94 10 0.04
95 37 0.16
96 20 0.09
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (92 bp):
ATGCCGATGCCATGTCCCAGACAGGTCTTACACTGCTCTCATATATCGGGCCGATGCATGTCCCA
GACATGTCTTACACTAGCACTATCTCA
Found at i:7606 original size:139 final size:141
Alignment explanation
Indices: 7279--7635 Score: 421
Period size: 139 Copynumber: 2.6 Consensus size: 141
7269 GGTACGATGC
* * *
7279 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCA-ACATCTAAGTCGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAAACATGGTCTTACACTGACTCATA-ATCT-AGCCGATGCCATGTCCCAGA
* *
7343 CAGGTCTTACACT-GACTTTCATATATCGAGGCCGATGCCATGTCCCAGACAGTCTTACTGGCTC
64 CAGGTCTTACACTAG-CTTGCATATATCGAGGCCGATGCCATGTCCCAGACAGTCTTACTAGCTC
**
7407 TCATCTATCGGTGT
128 TCATCTATCAATGT
* * * * *
7421 CGATGCCATGTCCCAGATA-GGTCTTACACTGACACAT-GTCAAGCCGATGCCATGTCCCAGACA
1 CGATGCCATGTCCCAAACATGGTCTTACACTGACTCATAATCTAGCCGATGCCATGTCCCAGACA
*
7484 GGTCTTACACTAGCTTGCATATCTCGAGGCCGATG-CATGT-CCAGACATGTCTTACACTAGCTC
66 GGTCTTACACTAGCTTGCATATATCGAGGCCGATGCCATGTCCCAGACA-GTCTT--ACTAGCTC
7547 T-ATCT-T-AATG-
128 TCATCTATCAATGT
* * *
7557 CGATGCCATGTCCCAAACATGGTCTTACACTGCTCTCATAATGTGGCCGATG-CATGTCCCAGAC
1 CGATGCCATGTCCCAAACATGGTCTTACACTG-ACTCATAATCTAGCCGATGCCATGTCCCAGAC
*
7621 ATGTCTTACACTAGC
65 AGGTCTTACACTAGC
7636 AACATCCATA
Statistics
Matches: 185, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
136 17 0.09
137 21 0.11
138 41 0.22
139 64 0.35
140 11 0.06
141 15 0.08
142 16 0.09
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (141 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGACTCATAATCTAGCCGATGCCATGTCCCAGACA
GGTCTTACACTAGCTTGCATATATCGAGGCCGATGCCATGTCCCAGACAGTCTTACTAGCTCTCA
TCTATCAATGT
Found at i:16394 original size:14 final size:16
Alignment explanation
Indices: 16374--16413 Score: 66
Period size: 14 Copynumber: 2.6 Consensus size: 16
16364 AGTCTAAAGG
16374 AAGAAATTTTATTC-T
1 AAGAAATTTTATTCAT
16389 -AGAAATTTTATTCAT
1 AAGAAATTTTATTCAT
16404 AAGAAATTTT
1 AAGAAATTTT
16414 GTGCACACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.57
15 1 0.04
16 9 0.39
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (16 bp):
AAGAAATTTTATTCAT
Done.