Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3562
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: 59609
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8199 original size:13 final size:13
Alignment explanation
Indices: 8183--8228 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
8173 AAAAAAAAGG
8183 AAAAAAAATTCGA
1 AAAAAAAATTCGA
8196 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
8209 AAAATAAATTC-A
1 AAAAAAAATTCGA
8221 AAAAAAAA
1 AAAAAAAA
8229 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:8318 original size:32 final size:31
Alignment explanation
Indices: 8273--8344 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 31
8263 AGTATTGAAG
*
8273 AAAAAAAAG-AAGAAAAAAAATTCGGAATT-A
1 AAAAAAAAGAAAGAAAAAAAA-TCGAAATTGA
8303 AAAAAAAAGAAAAGAAAAAAAATCGAAATTGA
1 AAAAAAAAG-AAAGAAAAAAAATCGAAATTGA
8335 AAAAAAAAGA
1 AAAAAAAAGA
8345 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
30 9 0.24
31 8 0.21
32 21 0.55
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (31 bp):
AAAAAAAAGAAAGAAAAAAAATCGAAATTGA
Found at i:8321 original size:31 final size:31
Alignment explanation
Indices: 8273--8344 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
8263 AGTATTGAAG
* * *
8273 AAAAAAAAGAAGAAAAAAAATTCGGAATT-A
1 AAAAAAAAGAAAAAAAAAAAATCGAAATTGA
8303 AAAAAAAAGAAAAGAAAAAAAATCGAAATTGA
1 AAAAAAAAGAAAA-AAAAAAAATCGAAATTGA
8335 AAAAAAAAGA
1 AAAAAAAAGA
8345 GTGATTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 12 0.32
31 14 0.38
32 11 0.30
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (31 bp):
AAAAAAAAGAAAAAAAAAAAATCGAAATTGA
Found at i:8330 original size:16 final size:16
Alignment explanation
Indices: 8282--8341 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 16
8272 GAAAAAAAAG
*
8282 AAGAAAAAAAATTCGGA
1 AAGAAAAAAAA-TCGAA
** *
8299 ATTAAAAAAAA-AGAA
1 AAGAAAAAAAATCGAA
8314 AAGAAAAAAAATCGAA
1 AAGAAAAAAAATCGAA
*
8330 ATTGAAAAAAAA
1 A-AGAAAAAAAA
8342 AGAGTGATTG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 11 0.33
16 4 0.12
17 18 0.55
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
AAGAAAAAAAATCGAA
Found at i:9250 original size:17 final size:15
Alignment explanation
Indices: 9228--9266 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
9218 GCGAGCGAGA
9228 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
9245 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
9260 AAGATGA
1 AA-ATGA
9267 GTGGGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:12569 original size:14 final size:14
Alignment explanation
Indices: 12552--12599 Score: 82
Period size: 13 Copynumber: 3.6 Consensus size: 14
12542 AAAAAAAAGG
12552 AAAAAAAAATTCG-
1 AAAAAAAAATTCGA
12565 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
12579 AAAAAAAAATTC-A
1 AAAAAAAAATTCGA
12592 AAAAAAAA
1 AAAAAAAA
12600 GTTTGTATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 22 0.65
14 12 0.35
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.12
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:12658 original size:13 final size:13
Alignment explanation
Indices: 12640--12664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12630 ATTTAGTATT
12640 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
12653 GAAGAAAAAAAA
1 GAAGAAAAAAAA
12665 TTTGGAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:12709 original size:31 final size:33
Alignment explanation
Indices: 12637--12714 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 33
12627 TGTATTTAGT
* *
12637 ATTGAAGAAAAAAAAAGAAGAAAAAAAATTTGGA
1 ATTGAA-AAAAAAAAAGAAGAAAAAAAATTCGAA
*
12671 ATT-AAAAAAAAGAA-AAGAAAAAAAA-TCGAA
1 ATTGAAAAAAAAAAAGAAGAAAAAAAATTCGAA
12701 ATTGAAAAAAAAAA
1 ATTGAAAAAAAAAA
12715 GAGTGATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 6 0.15
31 20 0.51
32 8 0.21
33 2 0.05
34 3 0.08
ACGTcount: A:0.73, C:0.01, G:0.13, T:0.13
Consensus pattern (33 bp):
ATTGAAAAAAAAAAAGAAGAAAAAAAATTCGAA
Found at i:13627 original size:17 final size:15
Alignment explanation
Indices: 13605--13643 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
13595 GCGAGTGAGA
13605 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
13622 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
13637 AAGATGA
1 AA-ATGA
13644 GTGGGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:17197 original size:13 final size:13
Alignment explanation
Indices: 17179--17222 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
17169 TAGTTTCTTG
*
17179 AAAAAAACTCGAA
1 AAAAAAATTCGAA
17192 AAAAAAATTC-AA
1 AAAAAAATTCGAA
*
17204 AAAAAAATTTGAA
1 AAAAAAATTCGAA
17217 AAAAAA
1 AAAAAA
17223 CTAGTTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:17284 original size:13 final size:14
Alignment explanation
Indices: 17260--17314 Score: 94
Period size: 14 Copynumber: 3.9 Consensus size: 14
17250 GGATATCAAG
17260 TTGTGAAAAAAAAAA
1 TTGTG-AAAAAAAAA
17275 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
17288 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
17302 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
17315 GAGCTAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
13 11 0.28
14 26 0.67
15 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.22
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:18294 original size:19 final size:21
Alignment explanation
Indices: 18272--18317 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
18262 AAACGAAATT
* *
18272 GAGAAAGAGAA-AAAGATTG-
1 GAGAAAGAAAAGAAAGAGTGC
18291 GAGAAAGAAAAGAAAGAGTGC
1 GAGAAAGAAAAGAAAGAGTGC
18312 GAGAAA
1 GAGAAA
18318 CAAGTGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.33, T:0.07
Consensus pattern (21 bp):
GAGAAAGAAAAGAAAGAGTGC
Found at i:27597 original size:40 final size:41
Alignment explanation
Indices: 27528--27608 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 41
27518 AAATTCAAAG
27528 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAG-TCAAATGTTTGAATTTCAAACGTTTT
27570 GGATAAGAACAAGA-TCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTCAAATGTTTGAATTTCAAACGTTT
27609 CACACATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 25 0.64
42 14 0.36
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (41 bp):
GGATAAGAACAAGAGTCAAATGTTTGAATTTCAAACGTTTT
Found at i:34918 original size:22 final size:22
Alignment explanation
Indices: 34888--34931 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34878 TTTGGTATTT
34888 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
34910 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
34932 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39909 original size:22 final size:22
Alignment explanation
Indices: 39879--39922 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39869 TTTGGTATTT
39879 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39901 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39923 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:45389 original size:18 final size:19
Alignment explanation
Indices: 45358--45399 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
45348 CTTTTTTAAA
*
45358 TTTTTATTGAATTTCGTCTT
1 TTTTTATT-AATTTCGACTT
*
45378 TTTTTATT-ATTTTGACTT
1 TTTTTATTAATTTCGACTT
45396 TTTT
1 TTTT
45400 GACTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTTTATTAATTTCGACTT
Found at i:51083 original size:11 final size:11
Alignment explanation
Indices: 51067--51111 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
51057 TATGTAATAT
51067 ATTTTTTTTCA
1 ATTTTTTTTCA
*
51078 ATTTTTTTTTCG
1 A-TTTTTTTTCA
51090 ATTTTTTTT-A
1 ATTTTTTTTCA
*
51100 TTTTTTTTTCA
1 ATTTTTTTTCA
51111 A
1 A
51112 AAACTACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 10 0.36
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:51085 original size:12 final size:12
Alignment explanation
Indices: 51068--51111 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
51058 ATGTAATATA
51068 TTTTTTTTCAAT
1 TTTTTTTTCAAT
*
51080 TTTTTTTTCGA-
1 TTTTTTTTCAAT
51091 TTTTTTTT--AT
1 TTTTTTTTCAAT
51101 TTTTTTTTCAA
1 TTTTTTTTCAA
51112 AAACTACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 1 0.04
10 8 0.29
11 8 0.29
12 11 0.39
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:51095 original size:21 final size:21
Alignment explanation
Indices: 51070--51109 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51060 GTAATATATT
51070 TTTTTTCAATTTTTTTTTCGA
1 TTTTTTCAATTTTTTTTTCGA
**
51091 TTTTTTTTATTTTTTTTTC
1 TTTTTTCAATTTTTTTTTC
51110 AAAAACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTTTCAATTTTTTTTTCGA
Done.