Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold696
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: 65812
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7732 original size:10 final size:11
Alignment explanation
Indices: 7705--7753 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
7695 CATAAATAAA
7705 TGAGCTGAAAT
1 TGAGCTGAAAT
7716 TGTAGCT-AAAT
1 TG-AGCTGAAAT
*
7727 TGAGCTCG-ATT
1 TGAGCT-GAAAT
7738 TGAGCTGAAA-
1 TGAGCTGAAAT
7748 TGAGCT
1 TGAGCT
7754 CAATTGAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 11 0.34
11 17 0.53
12 4 0.12
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (11 bp):
TGAGCTGAAAT
Found at i:15437 original size:21 final size:21
Alignment explanation
Indices: 15411--15473 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
15401 TTGGTATTTG
15411 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
15432 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
15453 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
15474 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:20512 original size:20 final size:20
Alignment explanation
Indices: 20489--20542 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
20479 AGTTTTTCCC
*
20489 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
20509 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
20529 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
20543 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:20524 original size:30 final size:30
Alignment explanation
Indices: 20489--20562 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20479 AGTTTTTCCC
20489 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
20519 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
20549 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
20563 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:20552 original size:20 final size:20
Alignment explanation
Indices: 20489--20553 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
20479 AGTTTTTCCC
* * * *
20489 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
20509 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
20528 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
20549 AGCTC
1 AGCTC
20554 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:23252 original size:24 final size:24
Alignment explanation
Indices: 23225--23310 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
23215 CCATTGAGCG
*
23225 AGAAAAGGAGAAAGAGATTGAAAA
1 AGAAATGGAGAAAGAGATTGAAAA
* * * **
23249 AGAAATCGAAAAAGTGAGAGAAAA
1 AGAAATGGAGAAAGAGATTGAAAA
* *
23273 AGAAATGAAGAAAAGAAAATTGAAAA
1 AGAAATGGAG-AAAG-AGATTGAAAA
*
23299 AGAAATTGAGAA
1 AGAAATGGAGAA
23311 TGAAAAAAAA
Statistics
Matches: 45, Mismatches: 15, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
24 25 0.56
25 6 0.13
26 14 0.31
ACGTcount: A:0.64, C:0.01, G:0.24, T:0.10
Consensus pattern (24 bp):
AGAAATGGAGAAAGAGATTGAAAA
Found at i:23297 original size:26 final size:28
Alignment explanation
Indices: 23268--23332 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
23258 AAAAGTGAGA
23268 GAAAAAGAAA-T-GAA-GAAAAGAAAATT
1 GAAAAAGAAATTAGAATGAAAA-AAAATT
23294 GAAAAAGAAATTGAGAATGAAAAAAAATT
1 GAAAAAGAAATT-AGAATGAAAAAAAATT
23323 GAAAAAGAAA
1 GAAAAAGAAA
23333 AAGCGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.29
27 1 0.03
29 19 0.54
30 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.12
Consensus pattern (28 bp):
GAAAAAGAAATTAGAATGAAAAAAAATT
Found at i:23305 original size:12 final size:12
Alignment explanation
Indices: 23235--23332 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
23225 AGAAAAGGAG
*
23235 AAAGAGATTGAA
1 AAAGAAATTGAA
*
23247 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
23259 AAAGTGAGAGAA
1 AAAGAAATTGAA
23271 AAAGAAA-TGAAGA
1 AAAGAAATTG-A-A
23284 AAAGAAAATTGAA
1 AAAG-AAATTGAA
23297 AAAGAAATTG--
1 AAAGAAATTGAA
23307 --AG-AA-TGAA
1 AAAGAAATTGAA
23315 AAA-AAATTGAA
1 AAAGAAATTGAA
23326 AAAGAAA
1 AAAGAAA
23333 AAGCGAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 2 0.03
10 3 0.05
11 8 0.12
12 33 0.50
13 10 0.15
14 4 0.06
15 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.20, T:0.12
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:23321 original size:17 final size:18
Alignment explanation
Indices: 23287--23335 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
23277 ATGAAGAAAA
23287 GAAAATTGAAAAAGAAATT
1 GAAAA-TGAAAAAGAAATT
*
23306 GAGAATGAAAAA-AAATT
1 GAAAATGAAAAAGAAATT
*
23323 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
23336 CGAAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 15 0.58
18 7 0.27
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:23353 original size:13 final size:13
Alignment explanation
Indices: 23269--23353 Score: 57
Period size: 13 Copynumber: 6.2 Consensus size: 13
23259 AAAGTGAGAG
23269 AAAAAGAAA-TGA
1 AAAAAGAAATTGA
23281 AGAAAAGAAAATTG-
1 A-AAAAG-AAATTGA
23295 AAAAAGAAATTGAGA
1 AAAAAGAAATT--GA
*
23310 ATGAAAAAAAATTGA
1 A--AAAAGAAATTGA
* **
23325 AAAAGAAAAAGCGA
1 AAAA-AGAAATTGA
23339 AAAAAGAAATTGA
1 AAAAAGAAATTGA
23352 AA
1 AA
23354 GAGAGCTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
12 6 0.10
13 21 0.36
14 16 0.28
15 6 0.10
17 9 0.16
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.12
Consensus pattern (13 bp):
AAAAAGAAATTGA
Found at i:23387 original size:33 final size:33
Alignment explanation
Indices: 23350--23412 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
23340 AAAAGAAATT
23350 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
23383 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
23413 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:25206 original size:20 final size:20
Alignment explanation
Indices: 25183--25236 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25173 AGTTTTTCCC
*
25183 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25203 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25223 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25237 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:25218 original size:30 final size:30
Alignment explanation
Indices: 25183--25256 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25173 AGTTTTTCCC
25183 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25213 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25243 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25257 TCGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:25246 original size:20 final size:20
Alignment explanation
Indices: 25183--25247 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25173 AGTTTTTCCC
* * * *
25183 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25203 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25222 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25243 AGCTC
1 AGCTC
25248 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:29803 original size:23 final size:23
Alignment explanation
Indices: 29770--29835 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
29760 TCGGTTTAGG
* *
29770 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
29793 TTTGGTTCGAAATGGTATTACGA
1 TTTGGTACGAAATGGTAATGCGA
29816 TTTGGTACGAAATGGTAATG
1 TTTGGTACGAAATGGTAATG
29836 GTTTAAAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:35673 original size:20 final size:19
Alignment explanation
Indices: 35649--35710 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
35639 CAACTCCGAC
*
35649 TAGCTCAATTGAACTCATT
1 TAGCTCAATTGAGCTCATT
* *
35668 TCAGCTTAATCGAGCTCAATT
1 T-AGCTCAATTGAGCTC-ATT
*
35689 TAGCTACAATTCAGCTCATT
1 TAGCT-CAATTGAGCTCATT
35709 TA
1 TA
35711 TTTTATTGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.03
20 21 0.62
21 12 0.35
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (19 bp):
TAGCTCAATTGAGCTCATT
Found at i:36744 original size:12 final size:12
Alignment explanation
Indices: 36708--36745 Score: 60
Period size: 13 Copynumber: 3.2 Consensus size: 12
36698 TTTTTTTTCC
36708 TTTTTTTTG-AT
1 TTTTTTTTGAAT
36719 TTTTTTTTGAAAT
1 TTTTTTTTG-AAT
36732 TTTTTTTTGAAT
1 TTTTTTTTGAAT
36744 TT
1 TT
36746 CTTCTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.36
12 5 0.20
13 11 0.44
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:43507 original size:11 final size:10
Alignment explanation
Indices: 43485--43545 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
43475 ACCAATAAAA
43485 TAAA-TGAGC
1 TAAATTGAGC
43494 TAAATTGTAGC
1 TAAATTG-AGC
43505 TAAATTGAGC
1 TAAATTGAGC
**
43515 TCGATTGAGC
1 TAAATTGAGC
43525 TGAAA-TGAGC
1 T-AAATTGAGC
*
43535 TCAATTGAGC
1 TAAATTGAGC
43545 T
1 T
43546 GGTCGGAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 6 0.14
10 26 0.60
11 11 0.26
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:43525 original size:20 final size:20
Alignment explanation
Indices: 43486--43546 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
43476 CCAATAAAAT
*
43486 AAATGAGCTAAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
43506 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
43527 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
43547 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:44827 original size:12 final size:12
Alignment explanation
Indices: 44810--44836 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
44800 TTACCTTTTC
44810 GAAATGAAAAAT
1 GAAATGAAAAAT
44822 GAAATGAAAAAT
1 GAAATGAAAAAT
44834 GAA
1 GAA
44837 TTTCATGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (12 bp):
GAAATGAAAAAT
Found at i:45663 original size:6 final size:6
Alignment explanation
Indices: 45654--45759 Score: 54
Period size: 6 Copynumber: 17.3 Consensus size: 6
45644 TCAATCTCAA
* * * ** **
45654 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
45706 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
45752 TTTCTT TT
1 TTTCTT TT
45760 AATTTCTTTT
Statistics
Matches: 70, Mismatches: 25, Indels: 10
0.67 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 50 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:45665 original size:12 final size:12
Alignment explanation
Indices: 45618--45690 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
45608 TCAACATCTT
45618 TTTCTTTTTCAA
1 TTTCTTTTTCAA
45630 TTT-TTTTCTCAA
1 TTTCTTTT-TCAA
* ** *
45642 TCTCAATCTCAA
1 TTTCTTTTTCAA
45654 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
45666 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
45681 TTTCTTTTTC
1 TTTCTTTTTC
45691 TCTCACTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 4 0.09
12 24 0.51
13 8 0.17
14 7 0.15
15 4 0.09
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:45675 original size:18 final size:17
Alignment explanation
Indices: 45654--45783 Score: 59
Period size: 18 Copynumber: 7.2 Consensus size: 17
45644 TCAATCTCAA
45654 TTTCTTTTTCAATTTTCT
1 TTTCTTTTTC-ATTTTCT
*
45672 TTTCTTCATTTTCTTTTTCT
1 TTTC-T--TTTTCATTTTCT
** *
45692 CTCACTATTTTGA-TTTCTT
1 -TTTCT-TTTTCATTTTC-T
* *
45711 TTTCTTTTGCAATTTCTT
1 TTTCTTTTTCATTTTC-T
*
45729 TTTCTTTTTCGTTTTCT
1 TTTCTTTTTCATTTTCT
**
45746 TTT-TGTTTTC-TTTTAA
1 TTTCT-TTTTCATTTTCT
*
45762 TTTCTTTTTCAATTTTAT
1 TTTCTTTTTC-ATTTTCT
45780 TTTC
1 TTTC
45784 GACCTCACTC
Statistics
Matches: 87, Mismatches: 15, Indels: 20
0.71 0.12 0.16
Matches are distributed among these distances:
16 13 0.15
17 14 0.16
18 39 0.45
19 7 0.08
20 7 0.08
21 7 0.08
ACGTcount: A:0.10, C:0.16, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTCTTTTTCATTTTCT
Found at i:45771 original size:6 final size:6
Alignment explanation
Indices: 45705--45759 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
45695 ACTATTTTGA
* ** * *
45705 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
45752 TTTCTT TT
1 TTTCTT TT
45760 AATTTCTTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.04, C:0.15, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:46138 original size:21 final size:20
Alignment explanation
Indices: 46114--46171 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
46104 TTGTCACTTC
*
46114 TTTTTTTCCTTTTTTTTCAA
1 TTTTTTTTCTTTTTTTTCAA
** *
46134 TTTTTTTGAATTTTTTTTGAA
1 TTTTTTT-TCTTTTTTTTCAA
* *
46155 TTTCTTCTCTTTTTTTT
1 TTTTTTTTCTTTTTTTT
46172 AAATCCAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTTTCAA
Found at i:46249 original size:10 final size:11
Alignment explanation
Indices: 46234--46262 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
46224 CAACTCAAAT
46234 TTTTTTTTGA-
1 TTTTTTTTGAC
46244 TTTTTTTTGAC
1 TTTTTTTTGAC
46255 TTTTTTTT
1 TTTTTTTT
46263 ACATTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:48729 original size:12 final size:12
Alignment explanation
Indices: 48692--48764 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
48682 AATAGTGAGA
*
48692 GAAAAAGAAAAT
1 GAAAAAGAAATT
48704 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATT
48719 GAAAAAGAAATT
1 GAAAAAGAAATT
* ** *
48731 GAGATTGAGATT
1 GAAAAAGAAATT
48743 GAGAAAA-AAATT
1 GA-AAAAGAAATT
48755 GAAAAAGAAA
1 GAAAAAGAAA
48765 AAGATATTGA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 4 0.09
12 25 0.53
13 7 0.15
14 6 0.13
15 5 0.11
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:48765 original size:16 final size:18
Alignment explanation
Indices: 48744--48782 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
48734 ATTGAGATTG
48744 AGAAAAA-A-ATTGAAAA
1 AGAAAAAGATATTGAAAA
*
48760 AGAAAAAGATATTGAAGA
1 AGAAAAAGATATTGAAAA
48778 AGAAA
1 AGAAA
48783 CGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (18 bp):
AGAAAAAGATATTGAAAA
Found at i:51834 original size:10 final size:10
Alignment explanation
Indices: 51818--51875 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
51808 CAACTTCGAC
51818 CAGCTCAATT
1 CAGCTCAATT
* *
51828 GAGCTCATTT
1 CAGCTCAATT
51838 CAGCTCAA-T
1 CAGCTCAATT
51847 CGAGCTCAATT
1 C-AGCTCAATT
*
51858 TAGCTACAATT
1 CAGCT-CAATT
51869 CAGCTCA
1 CAGCTCA
51876 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:51841 original size:20 final size:20
Alignment explanation
Indices: 51818--51878 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
51808 CAACTTCGAC
51818 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
51838 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
51859 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
51879 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:52602 original size:13 final size:13
Alignment explanation
Indices: 52584--52626 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
52574 ACGAGATTGT
52584 AAAAAAAATTCGA
1 AAAAAAAATTCGA
52597 AAAAAAAATTCGA
1 AAAAAAAATTCGA
52610 AAAAAAAATTC-A
1 AAAAAAAATTCGA
52622 AAAAA
1 AAAAA
52627 TAGTTTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 6 0.20
13 24 0.80
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:55386 original size:22 final size:22
Alignment explanation
Indices: 55356--55399 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55346 TTTGGTATTT
55356 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
55378 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
55400 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
Done.