Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2428
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: 42742
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:7269 original size:30 final size:30
Alignment explanation
Indices: 7198--7280 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
7188 CTTTTGTTTC
* *
7198 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
7229 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
7258 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
7281 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:7280 original size:18 final size:18
Alignment explanation
Indices: 7231--7286 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
7221 CACTCTCAAA
* *
7231 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
7248 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
7266 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
7285 TT
1 TT
7287 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:7287 original size:12 final size:12
Alignment explanation
Indices: 7256--7280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7246 TTTTTCAATC
7256 TCATTTTCTTTT
1 TCATTTTCTTTT
7268 TCATTTTCTTTT
1 TCATTTTCTTTT
7280 T
1 T
7281 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:7359 original size:5 final size:5
Alignment explanation
Indices: 7349--7405 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
7339 CTCTTGCCTC
*
7349 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
7396 TCTTT TCTTT
1 TCTTT TCTTT
7406 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:7389 original size:15 final size:14
Alignment explanation
Indices: 7349--7405 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
7339 CTCTTGCCTC
*
7349 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
7364 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
7379 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
7396 TCTTTTCTTT
1 TCTTTTCTTT
7406 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:7415 original size:21 final size:20
Alignment explanation
Indices: 7347--7416 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
7337 GCCTCTTGCC
7347 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
7370 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
7390 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
7410 TCTCTTT
1 TCTCTTT
7417 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:10830 original size:22 final size:22
Alignment explanation
Indices: 10802--10845 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10792 TTTTGAACCA
10802 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
10824 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
10846 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:11563 original size:30 final size:30
Alignment explanation
Indices: 11529--11625 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
11519 TAAACTAAAA
*
11529 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * *
11559 TGAGCTGAGGTTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
11589 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
11618 ATGAGCTA
1 -TGAGCTA
11626 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:12371 original size:9 final size:10
Alignment explanation
Indices: 12364--12420 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
12354 AAGAGAAAAT
12364 AAAGAAAAGA
1 AAAGAAAAGA
12374 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
12386 AAAGAAGA-A
1 AAAGAAAAGA
12395 AAAGAAAATGA
1 AAAGAAAA-GA
12406 AATA-AAAAGA
1 AA-AGAAAAGA
12416 AAAGA
1 AAAGA
12421 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:12388 original size:6 final size:5
Alignment explanation
Indices: 12364--12420 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
12354 AAGAGAAAAT
*
12364 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
12411 AAAGA AAAGA
1 AAAGA AAAGA
12421 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:12395 original size:15 final size:14
Alignment explanation
Indices: 12364--12420 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
12354 AAGAGAAAAT
12364 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
12380 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
12395 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
12411 AAAGAAAAGA
1 AAAGAAAAGA
12421 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:16275 original size:20 final size:20
Alignment explanation
Indices: 16229--16275 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16219 AGCTCGTTTC
*
16229 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
16249 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
16269 CAGCTCA
1 CAGCTCA
16276 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25109 original size:40 final size:40
Alignment explanation
Indices: 25065--25289 Score: 205
Period size: 40 Copynumber: 5.6 Consensus size: 40
25055 GCTCCTCGTT
*
25065 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
* * *
25105 CAAATGCCTTCGGGACTTAACCTGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCA
*
25145 CAAATGCCTTCGGGACTTAGCCCGG-AATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAAT-TCGCA
* *
25185 CAAATGCCTTC-GAATCTTAGTCCGGATT-TAGT-ATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTATAGTAAT-TCGCA
* * * * * *
25225 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AATTCGCA
25266 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
25290 ACATCATTCA
Statistics
Matches: 155, Mismatches: 19, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
39 4 0.03
40 137 0.88
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCA
Found at i:25244 original size:80 final size:80
Alignment explanation
Indices: 25065--25283 Score: 243
Period size: 80 Copynumber: 2.7 Consensus size: 80
25055 GCTCCTCGTT
* * *
25065 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGAACTTAACCTGG
25130 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
*
25145 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGT-ATCTCGCACAAATGCCTTC-GAATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAAT-TCGCACAAATGCCTTCGGAA-CTTA-AC
*
25207 C-GGATTTAGTATCTCGCA
62 CTGGATTTAGTAACTCGCA
* * * * * *
25225 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-AATTCGCACAAATGCCTTCGGAACTTA
25284 GCCCGGACAT
Statistics
Matches: 119, Mismatches: 11, Indels: 18
0.80 0.07 0.12
Matches are distributed among these distances:
79 8 0.07
80 97 0.82
81 13 0.11
82 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGAACTTAACCTGG
ATTTAGTAACTCGCA
Found at i:28522 original size:22 final size:22
Alignment explanation
Indices: 28494--28537 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28484 TTTGGTATTT
28494 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
28516 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
28538 TGGTTCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:29962 original size:30 final size:31
Alignment explanation
Indices: 29928--30024 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
29918 AGCTCACTCC
*
29928 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
29958 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
29988 CAGCTCAACTTT-AGCTCACGAGCTAAATCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
30018 TAGCTCA
1 TAGCTCA
30025 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:33837 original size:20 final size:20
Alignment explanation
Indices: 33791--33837 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33781 AGCTCGTTTC
*
33791 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33811 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33831 CAGCTCA
1 CAGCTCA
33838 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:37679 original size:20 final size:21
Alignment explanation
Indices: 37649--37697 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
37639 TTAGCTCGTT
*
37649 TCAAGCTCACTCGAGCTCAAG
1 TCAAGCTCACTCAAGCTCAAG
*
37670 TCAA-CTCACTCAAGCTCAAT
1 TCAAGCTCACTCAAGCTCAAG
37690 TC-AGCTCA
1 TCAAGCTCA
37698 ATTTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (21 bp):
TCAAGCTCACTCAAGCTCAAG
Found at i:41196 original size:17 final size:18
Alignment explanation
Indices: 41176--41213 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
41166 TTTCTTCAAC
* *
41176 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
41193 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
41211 TTC
1 TTC
41214 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Done.