Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2457
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: 23294
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:2229 original size:21 final size:22
Alignment explanation
Indices: 2185--2236 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2175 ATACTAAAAT
* *
2185 AAATATAAATAAAATAAAGGAA
1 AAATAAAAATAAAAAAAAGGAA
**
2207 AAA-AAAAATAAAAAAAATTAA
1 AAATAAAAATAAAAAAAAGGAA
2228 AAATAAAAA
1 AAATAAAAA
2237 AATATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (22 bp):
AAATAAAAATAAAAAAAAGGAA
Found at i:2243 original size:26 final size:26
Alignment explanation
Indices: 2179--2264 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
2169 AAAATTATAC
*
2179 TAAAATAAATATAAATAAAA-TAAAGGAA
1 TAAAA-AAATATAAAAAAAATTAAA--AA
2207 -AAAAAAA-ATAAAAAAAATTAAAAA
1 TAAAAAAATATAAAAAAAATTAAAAA
* *
2231 TAAAAAAATATAATAATAATTATAAAA
1 TAAAAAAATATAAAAAAAATTA-AAAA
2258 TAAAAAA
1 TAAAAAA
2265 TAATATAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.04
25 16 0.31
26 18 0.35
27 15 0.29
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (26 bp):
TAAAAAAATATAAAAAAAATTAAAAA
Found at i:2248 original size:16 final size:15
Alignment explanation
Indices: 2210--2249 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2200 AAAGGAAAAA
2210 AAAAATAAAAAAAATT
1 AAAAAT-AAAAAAATT
2226 AAAAATAAAAAAATAT
1 AAAAATAAAAAAAT-T
*
2242 AATAATAA
1 AAAAATAA
2250 TTATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAATAAAAAAATT
Found at i:2264 original size:29 final size:28
Alignment explanation
Indices: 2205--2273 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
2195 AAAATAAAGG
*
2205 AAAAAAAAA-ATAAAAAAAATTAAAAAT
1 AAAAAAAAATATAATAAAAATTAAAAAT
*
2232 --AAAAAAATATAATAATAATTATAAAAT
1 AAAAAAAAATATAATAAAAATTA-AAAAT
*
2259 AAAAAATAATATAAT
1 AAAAAAAAATATAAT
2274 TTAAAAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 7 0.20
26 11 0.31
27 5 0.14
29 12 0.34
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (28 bp):
AAAAAAAAATATAATAAAAATTAAAAAT
Found at i:2278 original size:50 final size:48
Alignment explanation
Indices: 2205--2309 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 48
2195 AAAATAAAGG
*
2205 AAAA-AAAAAATAAAAAAAATTAAAAATA-AAAAAATATAATAATAATTAT
1 AAAATAAAAAATAAAAAAAATTAAAAA-AGAAAAAATAT-A-AATAATCAT
* * * *
2254 AAAATAAAAAATAATATAATTTAAAAAAGGAAAAATATAAATAATCAT
1 AAAATAAAAAATAAAAAAAATTAAAAAAGAAAAAATATAAATAATCAT
2302 -AAATAAAA
1 AAAATAAAA
2310 TGCCAAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
47 8 0.16
48 8 0.16
49 6 0.12
50 27 0.55
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (48 bp):
AAAATAAAAAATAAAAAAAATTAAAAAAGAAAAAATATAAATAATCAT
Found at i:2287 original size:23 final size:24
Alignment explanation
Indices: 2205--2309 Score: 78
Period size: 25 Copynumber: 4.4 Consensus size: 24
2195 AAAATAAAGG
* *
2205 AAAA-AAAAAATAAAAAAAATTA-
1 AAAATAAAAAATAATAATAATTAT
2227 AAAATAAAAAAATATAATAATAATTAT
1 AAAAT--AAAAA-ATAATAATAATTAT
2254 AAAATAAAAAATAAT-ATAATT-T
1 AAAATAAAAAATAATAATAATTAT
* *
2276 AAAAAAGGAAAAAT-ATAAATAATCAT
1 AAAATA--AAAAATAAT-AATAATTAT
2302 -AAATAAAA
1 AAAATAAAA
2310 TGCCAAATGA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
22 10 0.15
23 11 0.16
24 11 0.16
25 19 0.28
26 12 0.18
27 5 0.07
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAATAAAAAATAATAATAATTAT
Found at i:3328 original size:3 final size:3
Alignment explanation
Indices: 3320--3354 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3310 TATGGTTTTA
* *
3320 TAT TAT TAT TAT TAT TAG TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3355 AATGAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4656 original size:23 final size:23
Alignment explanation
Indices: 4602--4662 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
4592 ACACATAAAA
4602 GTGCCT-AAA-ACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
*
4623 GTGTCTG--ATACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
4644 GTGCCTGAAATACGACACA
1 GTGCCTGAAATACGACACA
4663 TAAAGTGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 23 0.68
23 10 0.29
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (23 bp):
GTGCCTGAAATACGACACACGAG
Found at i:4670 original size:23 final size:23
Alignment explanation
Indices: 4586--4674 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 23
4576 ACCTGATCAG
*
4586 AATACGACACATAAAAGTGCCT-A
1 AATACGACACA-CAAAGTGCCTGA
* * *
4609 AA-ACGACACACGAGGTGTCTG-
1 AATACGACACACAAAGTGCCTGA
* *
4630 -ATACGACACACGAGGTGCCTGA
1 AATACGACACACAAAGTGCCTGA
*
4652 AATACGACACATAAAGTGCCTGA
1 AATACGACACACAAAGTGCCTGA
4675 TCAGTAAAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 24 0.44
22 8 0.15
23 21 0.39
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (23 bp):
AATACGACACACAAAGTGCCTGA
Found at i:6549 original size:3 final size:3
Alignment explanation
Indices: 6541--6578 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
6531 TTACTTCATT
* *
6541 TAA TAA TAA TAA TAA CAA TAC TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6579 TAAACCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:6618 original size:13 final size:12
Alignment explanation
Indices: 6601--6634 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
6591 ATGGTTTATA
6601 ATTATATATAAT
1 ATTATATATAAT
6613 ATT-TATATAAT
1 ATTATATATAAT
6624 ATTTATATATA
1 A-TTATATATA
6635 TAACCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 5 0.25
13 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTATATATAAT
Found at i:6621 original size:11 final size:11
Alignment explanation
Indices: 6605--6632 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
6595 TTTATAATTA
6605 TATATAATATT
1 TATATAATATT
6616 TATATAATATT
1 TATATAATATT
6627 TATATA
1 TATATA
6633 TATAACCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATAATATT
Found at i:15303 original size:21 final size:21
Alignment explanation
Indices: 15273--15323 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
15263 AAGAGTTATT
*
15273 TTTTTTAAATTT-TTAATATA
1 TTTTTAAAATTTATTAATATA
**
15293 TATTTTAAAATTTATTGTTATA
1 T-TTTTAAAATTTATTAATATA
15315 TTTTTAAAA
1 TTTTTAAAA
15324 ATATTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTAAAATTTATTAATATA
Found at i:15328 original size:20 final size:22
Alignment explanation
Indices: 15289--15328 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15279 AAATTTTTAA
*
15289 TATATATTTTAAAATTTATTGT
1 TATATATTTTAAAATATATTGT
15311 TATAT-TTTTAAAA-ATATT
1 TATATATTTTAAAATATATT
15329 TATGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
TATATATTTTAAAATATATTGT
Found at i:15719 original size:6 final size:6
Alignment explanation
Indices: 15708--15734 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15698 AAGTATAGGC
15708 CCCCCT CCCCCT CCCCCT CCCCCT CCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCC
15735 AGTCCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:15984 original size:37 final size:37
Alignment explanation
Indices: 15934--16007 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
15924 TTGGAGTGTA
*
15934 CCACTTTTGCAAGTAACATCTATCTACCAAAATCATC
1 CCACTTTTGCAAGTAACATCTATCTAACAAAATCATC
15971 CCACTTTTGCAAGTAACATCTATCTAACAAAATCATC
1 CCACTTTTGCAAGTAACATCTATCTAACAAAATCATC
16008 AACATGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (37 bp):
CCACTTTTGCAAGTAACATCTATCTAACAAAATCATC
Found at i:18888 original size:46 final size:46
Alignment explanation
Indices: 18821--18940 Score: 222
Period size: 46 Copynumber: 2.6 Consensus size: 46
18811 TGTAACCCAC
*
18821 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGTGTGCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTGCGCAT
*
18867 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGTGTGCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTGCGCAT
18913 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
18941 AAGTTCGGAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTGCGCAT
Found at i:21062 original size:30 final size:30
Alignment explanation
Indices: 21026--21085 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
21016 CAGTTTGGAA
21026 ACAACCTGGGATCAAATCGAATACTAAAAT
1 ACAACCTGGGATCAAATCGAATACTAAAAT
21056 ACAACCTGGGATCAAATCGAATACTAAAAT
1 ACAACCTGGGATCAAATCGAATACTAAAAT
21086 CATTCAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (30 bp):
ACAACCTGGGATCAAATCGAATACTAAAAT
Found at i:21898 original size:71 final size:71
Alignment explanation
Indices: 21775--21906 Score: 194
Period size: 72 Copynumber: 1.9 Consensus size: 71
21765 CATGATTCCC
* * * *
21775 TTTTCAACACATCATTTTCATTTGTCATCCTTTTCGAATAACATCCTTTTCAACCTTTTCATTTG
1 TTTTCAACACATCATTTCCATGTGTCATCCCTTGCGAATAACATCCTTTTCAACCTTTTCATTTG
21840 ATATCT
66 ATATCT
* *
21846 TTTTCAAATACATCATTTCCATGTGTTATCCCTTGCGAATAAC-TCCTTTTCAACCTTTTCA
1 TTTTC-AACACATCATTTCCATGTGTCATCCCTTGCGAATAACATCCTTTTCAACCTTTTCA
21907 AGGATTCGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 23 0.43
72 31 0.57
ACGTcount: A:0.24, C:0.25, G:0.05, T:0.45
Consensus pattern (71 bp):
TTTTCAACACATCATTTCCATGTGTCATCCCTTGCGAATAACATCCTTTTCAACCTTTTCATTTG
ATATCT
Found at i:22839 original size:19 final size:19
Alignment explanation
Indices: 22815--22863 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
22805 AGTACTAAAA
*
22815 AGTACCAAAATTATAAGGG
1 AGTACCAAAACTATAAGGG
*
22834 AGTACCTAAAAACTATTAGGG
1 AGTACC--AAAACTATAAGGG
22855 AGTA-CAAAA
1 AGTACCAAAA
22864 GAAAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 6 0.23
20 1 0.04
21 15 0.58
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (19 bp):
AGTACCAAAACTATAAGGG
Found at i:22931 original size:20 final size:20
Alignment explanation
Indices: 22906--22972 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
22896 AATACCCCAA
22906 AAAAAAATATGAAGAAGTAT
1 AAAAAAATATGAAGAAGTAT
* *
22926 AAAAAATTAT-AAGAAAGTAC
1 AAAAAAATATGAAG-AAGTAT
* * *
22946 CAAAAAATACGAGGGAA-TAT
1 AAAAAAATATGA-AGAAGTAT
22966 AAAAAAA
1 AAAAAAA
22973 ATCAGATGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.08
20 29 0.81
21 3 0.08
22 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.13, T:0.16
Consensus pattern (20 bp):
AAAAAAATATGAAGAAGTAT
Done.