Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1049
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: 22440
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:2205 original size:12 final size:12
Alignment explanation
Indices: 2167--2198 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2157 CACTCTCAAA
2167 TTTC-TTTTCAT
1 TTTCTTTTTCAT
2178 TTTCTTTTTCAT
1 TTTCTTTTTCAT
2190 TTTCTTTTT
1 TTTCTTTTT
2199 GCTTTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTCAT
Found at i:2216 original size:12 final size:12
Alignment explanation
Indices: 2201--2231 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2191 TTCTTTTTGC
2201 TTTTCAAAGGCT
1 TTTTCAAAGGCT
2213 TTTTCAAAGGCT
1 TTTTCAAAGGCT
2225 TTTTCAA
1 TTTTCAA
2232 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:2301 original size:6 final size:5
Alignment explanation
Indices: 2279--2339 Score: 56
Period size: 5 Copynumber: 12.2 Consensus size: 5
2269 CTCTTGCCTC
* *
2279 TCTTT TCTTT T-TATT TCATTT TCTTT TCTCTT GC-TT T-TTC TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCT-TT TCTTT TCTTT TCTTT
2324 TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT T
2340 TCTCTTTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
4 5 0.11
5 33 0.72
6 7 0.15
7 1 0.02
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:2319 original size:12 final size:11
Alignment explanation
Indices: 2302--2345 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
2292 TTTCATTTTC
2302 TTTTCTCTTGCT
1 TTTTCTCTT-CT
*
2314 TTTTCTCTTTT
1 TTTTCTCTTCT
*
2325 CTTTTCTTTTCT
1 -TTTTCTCTTCT
2337 TTTTCTCTT
1 TTTTCTCTT
2346 TACAAGAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTCTCTTCT
Found at i:2319 original size:17 final size:17
Alignment explanation
Indices: 2277--2345 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
2267 GCCTCTTGCC
*
2277 TCTCTTTTCTTTT-TAT
1 TCTCTTTTCTTTTCTCT
2293 T-TCATTTTCTTTTCTCT
1 TCTC-TTTTCTTTTCTCT
2310 TGCT-TTTTCTCTTT-TCT
1 T-CTCTTTTCT-TTTCTCT
*
2327 TTTCTTTTCTTTTTCTCT
1 TCTCTTTTC-TTTTCTCT
2345 T
1 T
2346 TACAAGAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
15 2 0.05
16 11 0.26
17 21 0.49
18 8 0.19
19 1 0.02
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (17 bp):
TCTCTTTTCTTTTCTCT
Found at i:2342 original size:23 final size:23
Alignment explanation
Indices: 2279--2346 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
2269 CTCTTGCCTC
* *
2279 TCTTTTCTTTT-TATTTC-ATTT
1 TCTTTTCTTTTCTTTTTCTCTTT
*
2300 TCTTTTCTCTTGCTTTTTCTCTTT
1 TCTTTTCT-TTTCTTTTTCTCTTT
2324 TCTTTTCTTTTCTTTTTCTCTTT
1 TCTTTTCTTTTCTTTTTCTCTTT
2347 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.20
22 2 0.05
23 19 0.47
24 11 0.28
ACGTcount: A:0.03, C:0.21, G:0.01, T:0.75
Consensus pattern (23 bp):
TCTTTTCTTTTCTTTTTCTCTTT
Found at i:3220 original size:12 final size:12
Alignment explanation
Indices: 3202--3251 Score: 59
Period size: 11 Copynumber: 4.3 Consensus size: 12
3192 ATATACTTCG
3202 ATTTTTTTTT-A
1 ATTTTTTTTTAA
**
3213 ATTTTTTTTTCG
1 ATTTTTTTTTAA
3225 A-TTTTTTTTAA
1 ATTTTTTTTTAA
*
3236 ATTTTTTTTCAA
1 ATTTTTTTTTAA
3248 ATTT
1 ATTT
3252 CCTCTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 19 0.58
12 14 0.42
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTAA
Found at i:3224 original size:23 final size:23
Alignment explanation
Indices: 3198--3244 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3188 TTTTATATAC
*
3198 TTCGATTTTTTTTTAATTTTTTT
1 TTCGATTTTTTTTAAATTTTTTT
3221 TTCGATTTTTTTTAAATTTTTTT
1 TTCGATTTTTTTTAAATTTTTTT
3244 T
1 T
3245 CAAATTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (23 bp):
TTCGATTTTTTTTAAATTTTTTT
Found at i:3229 original size:22 final size:23
Alignment explanation
Indices: 3198--3245 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
3188 TTTTATATAC
*
3198 TTCGATTTTTTTTTAATTTTTTT
1 TTCGATTTTTTTTTAAATTTTTT
3221 TTCGA-TTTTTTTTAAATTTTTT
1 TTCGATTTTTTTTTAAATTTTTT
3243 TTC
1 TTC
3246 AAATTTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (23 bp):
TTCGATTTTTTTTTAAATTTTTT
Found at i:5042 original size:30 final size:30
Alignment explanation
Indices: 5008--5095 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
4998 TAAACTAAAA
5008 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
5038 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
5068 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAA
5096 TATGATCTAG
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:8083 original size:13 final size:13
Alignment explanation
Indices: 8029--8086 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
8019 ACGGTATTGT
8029 AAAAAAATA-T-A
1 AAAAAAATATTCA
8040 TAAAAAAA-ATTCA
1 -AAAAAAATATTCA
* **
8053 AAAAAAAAATTTTG
1 AAAAAAATA-TTCA
8067 AAAAAAATATTCA
1 AAAAAAATATTCA
8080 AAAAAAA
1 AAAAAAA
8087 GTTTGTATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 1 0.03
12 15 0.41
13 11 0.30
14 10 0.27
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (13 bp):
AAAAAAATATTCA
Found at i:8171 original size:27 final size:29
Alignment explanation
Indices: 8131--8196 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 29
8121 AGTATTGAAG
*
8131 AAAAAAAGAAGAAGAAAAAATTCGGAATT-A
1 AAAAAAAGAAGAA-AAAAAA-TCGAAATTGA
8161 AAAAAAAGAAGAAAAAAAATCGAAATTGA
1 AAAAAAAGAAGAAAAAAAATCGAAATTGA
8190 AAAAAAA
1 AAAAAAA
8197 AGAGTGATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.21
29 14 0.41
30 13 0.38
ACGTcount: A:0.73, C:0.03, G:0.14, T:0.11
Consensus pattern (29 bp):
AAAAAAAGAAGAAAAAAAATCGAAATTGA
Found at i:8199 original size:27 final size:30
Alignment explanation
Indices: 8130--8199 Score: 101
Period size: 28 Copynumber: 2.4 Consensus size: 30
8120 TAGTATTGAA
*
8130 GAAAAAAAGAAGAAGAAAAAATTCGGAATT
1 GAAAAAAAGAAGAAGAAAAAATTCGAAATT
*
8160 AAAAAAAAGAAGAA-AAAAAA-TCGAAATT
1 GAAAAAAAGAAGAAGAAAAAATTCGAAATT
8188 GAAAAAAA-AAGA
1 GAAAAAAAGAAGA
8200 GTGATTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.11
28 14 0.38
29 6 0.16
30 13 0.35
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.10
Consensus pattern (30 bp):
GAAAAAAAGAAGAAGAAAAAATTCGAAATT
Found at i:9061 original size:6 final size:6
Alignment explanation
Indices: 9052--9087 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
9042 AAAAAAGAAT
* *
9052 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
9088 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:9062 original size:27 final size:28
Alignment explanation
Indices: 8997--9063 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
8987 ACGAATCTTG
*
8997 AATGAAATTGAG-AAAAGAAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAAGAA
*
9024 AATGAGAGTGAGAAAAAG-AAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAAGAA
**
9051 TTTGAGATTGAGA
1 AATGAGATTGAGA
9064 TTGAGATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (28 bp):
AATGAGATTGAGAAAAAGAAAAAAAGAA
Found at i:12361 original size:12 final size:12
Alignment explanation
Indices: 12346--12388 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
12336 TAAAAAATAT
12346 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
12358 AAAAAATTTTGAA
1 AAAAAA-ATTCAA
*
12371 AAAAATATTCAA
1 AAAAAAATTCAA
12383 AAAAAA
1 AAAAAA
12389 GTTTGTATTC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:12380 original size:25 final size:24
Alignment explanation
Indices: 12346--12393 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
12336 TAAAAAATAT
*
12346 AAAAAAATTCAAAAAAAATTTTGA
1 AAAAAAATTCAAAAAAAAGTTTGA
12370 AAAAAATATTCAAAAAAAAGTTTG
1 AAAAAA-ATTCAAAAAAAAGTTTG
12394 TATTCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (24 bp):
AAAAAAATTCAAAAAAAAGTTTGA
Found at i:12471 original size:31 final size:30
Alignment explanation
Indices: 12433--12503 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 30
12423 AGTATTGAAG
*
12433 AAAAAAAAGAAGAAAAAAAATTCGGAATTAA
1 AAAAAAAAGAAGAAAAAAAA-TCGAAATTAA
*
12464 AAAAAAAAGAAGAAAAAAAATCGAAATTGA
1 AAAAAAAAGAAGAAAAAAAATCGAAATTAA
12494 AAAAAAAAGA
1 AAAAAAAAGA
12504 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 18 0.47
31 20 0.53
ACGTcount: A:0.75, C:0.03, G:0.13, T:0.10
Consensus pattern (30 bp):
AAAAAAAAGAAGAAAAAAAATCGAAATTAA
Found at i:13367 original size:6 final size:6
Alignment explanation
Indices: 13358--13393 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
13348 AAAAAAGAAT
* *
13358 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
13394 AAAAATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:13368 original size:27 final size:28
Alignment explanation
Indices: 13303--13369 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
13293 ACGAATCTTG
*
13303 AATGAAATTGAG-AAAAGAAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAAGAA
*
13330 AATGAGAGTGAGAAAAAG-AAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAAGAA
**
13357 TTTGAGATTGAGA
1 AATGAGATTGAGA
13370 TTGAGATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (28 bp):
AATGAGATTGAGAAAAAGAAAAAAAGAA
Found at i:16919 original size:10 final size:10
Alignment explanation
Indices: 16904--16948 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
16894 AACTTATTTG
16904 AGCTCGTTTC
1 AGCTCGTTTC
*
16914 AGCTCGTTTG
1 AGCTCGTTTC
* *
16924 AGTTCATTTC
1 AGCTCGTTTC
*
16934 AGCTCGTTTG
1 AGCTCGTTTC
16944 AGCTC
1 AGCTC
16949 AACCAAGCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.40
Consensus pattern (10 bp):
AGCTCGTTTC
Found at i:16923 original size:20 final size:20
Alignment explanation
Indices: 16900--16949 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
16890 ATTCAACTTA
*
16900 TTTGAGCTCGTTTCAGCTCG
1 TTTGAGCTCATTTCAGCTCG
*
16920 TTTGAGTTCATTTCAGCTCG
1 TTTGAGCTCATTTCAGCTCG
16940 TTTGAGCTCA
1 TTTGAGCTCA
16950 ACCAAGCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
TTTGAGCTCATTTCAGCTCG
Found at i:18164 original size:12 final size:12
Alignment explanation
Indices: 18147--18172 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18137 ATAAACTAAG
18147 TTTTAATTTAGT
1 TTTTAATTTAGT
18159 TTTTAATTTAGT
1 TTTTAATTTAGT
18171 TT
1 TT
18173 GCTACAGCTT
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:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTAATTTAGT
Found at i:20487 original size:15 final size:14
Alignment explanation
Indices: 20459--20513 Score: 67
Period size: 15 Copynumber: 3.8 Consensus size: 14
20449 ACGAGAAAAC
20459 AAAGAAAAGAAAGAA
1 AAAGAAAAG-AAGAA
20474 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
20489 AGAGAAAATGAA-AA
1 AAAGAAAA-GAAGAA
20503 AAAGAAAAGAA
1 AAAGAAAAGAA
20514 AGGCAAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
13 3 0.08
14 13 0.36
15 15 0.42
16 5 0.14
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:20494 original size:9 final size:9
Alignment explanation
Indices: 20452--20515 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
20442 TCTTGTAACG
*
20452 AGAAAACAA
1 AGAAAAGAA
20461 AGAAAAGAA
1 AGAAAAGAA
20470 AGAAAAAGCAA
1 AG-AAAAG-AA
*
20481 A-AGAAGAA
1 AGAAAAGAA
*
20489 AGAGAA-AA
1 AGAAAAGAA
*
20497 TGAAAA-AA
1 AGAAAAGAA
20505 AGAAAAGAA
1 AGAAAAGAA
20514 AG
1 AG
20516 GCAAAAGGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
8 16 0.35
9 22 0.48
10 5 0.11
11 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:20506 original size:39 final size:42
Alignment explanation
Indices: 20463--20541 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 42
20453 GAAAACAAAG
20463 AAAAG-AAAGAAAAAGCAAAA-G-AAGAAAGAGA-AAATGAAA
1 AAAAGAAAAG-AAAAGCAAAAGGCAAGAAAGAGAGAAATGAAA
* *
20502 AAAAGAAAAGAAAGGCAAAAGGCAAGTAAGAGAGAAATGA
1 AAAAGAAAAGAAAAGCAAAAGGCAAGAAAGAGAGAAATGA
20542 GCGAATATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 14 0.41
40 5 0.15
41 9 0.26
42 6 0.18
ACGTcount: A:0.68, C:0.04, G:0.24, T:0.04
Consensus pattern (42 bp):
AAAAGAAAAGAAAAGCAAAAGGCAAGAAAGAGAGAAATGAAA
Found at i:20521 original size:19 final size:20
Alignment explanation
Indices: 20454--20514 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
20444 TTGTAACGAG
20454 AAAA-CAAAGAAAAG-AAAGA
1 AAAAGCAAA-AAAAGAAAAGA
*
20473 AAAAGCAAAAGAAGAAAGAGA
1 AAAAGCAAAAAAAGAAA-AGA
*
20494 AAATG-AAAAAAAGAAAAGA
1 AAAAGCAAAAAAAGAAAAGA
20513 AA
1 AA
20515 GGCAAAAGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 13 0.36
20 16 0.44
21 7 0.19
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAGCAAAAAAAGAAAAGA
Done.