Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2924
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: 92899
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:10875 original size:23 final size:22
Alignment explanation
Indices: 10849--10901 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10839 TTGAGAGTGA
*
10849 AAAAGAAATT-GAAGAAAGAAGAT
1 AAAAGAAATTAGAA-AAAGAA-AC
10872 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
10894 AAAAGAAA
1 AAAAGAAA
10902 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:16701 original size:20 final size:19
Alignment explanation
Indices: 16678--16744 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
16668 ATTGAGCTTG
16678 TTGAGCTAAAGTAAGCTAAA
1 TTGAGCTAAAGT-AGCTAAA
16698 TTGAGCTCAAACG-AGCTAAA
1 TTGAGCT-AAA-GTAGCTAAA
* * *
16718 TTAAGCTCATGTGAGCTAAA
1 TTGAGCTAAAGT-AGCTAAA
16738 TTGAGCT
1 TTGAGCT
16745 GGGTAAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 33 0.85
21 3 0.08
22 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (19 bp):
TTGAGCTAAAGTAGCTAAA
Found at i:16704 original size:10 final size:10
Alignment explanation
Indices: 16678--16744 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
16668 ATTGAGCTTG
16678 TTGAGCTAAA
1 TTGAGCTAAA
* *
16688 GTAAGCTAAA
1 TTGAGCTAAA
16698 TTGAGCTCAAA
1 TTGAGCT-AAA
*
16709 -CGAGCTAAA
1 TTGAGCTAAA
* *
16718 TTAAGCT-CA
1 TTGAGCTAAA
16727 TGTGAGCTAAA
1 T-TGAGCTAAA
16738 TTGAGCT
1 TTGAGCT
16745 GGGTAAAACT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
9 5 0.12
10 33 0.77
11 5 0.12
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:16712 original size:90 final size:90
Alignment explanation
Indices: 16611--16774 Score: 319
Period size: 90 Copynumber: 1.8 Consensus size: 90
16601 ACTTAAGCCA
16611 AGCTCAAACGAGCTAAATTAAGCTCATGTGAGCTAAATCGAGCTGGGTAAAACTAAGATTGAGCT
1 AGCTCAAACGAGCTAAATTAAGCTCATGTGAGCTAAATCGAGCTGGGTAAAACTAAGATTGAGCT
16676 TGTTGAGCTAAAGTAAGCTAAATTG
66 TGTTGAGCTAAAGTAAGCTAAATTG
*
16701 AGCTCAAACGAGCTAAATTAAGCTCATGTGAGCTAAATTGAGCTGGGTAAAACTAAGATTGAGCT
1 AGCTCAAACGAGCTAAATTAAGCTCATGTGAGCTAAATCGAGCTGGGTAAAACTAAGATTGAGCT
16766 TGTTGAGCT
66 TGTTGAGCT
16775 GAGATTGAGC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (90 bp):
AGCTCAAACGAGCTAAATTAAGCTCATGTGAGCTAAATCGAGCTGGGTAAAACTAAGATTGAGCT
TGTTGAGCTAAAGTAAGCTAAATTG
Found at i:16744 original size:30 final size:30
Alignment explanation
Indices: 16611--16744 Score: 80
Period size: 30 Copynumber: 4.5 Consensus size: 30
16601 ACTTAAGCCA
16611 AGCTCAAA-CGAGCTAAATTAAGCTCATGTG
1 AGCT-AAATCGAGCTAAATTAAGCTCATGTG
*** * * *
16641 AGCTAAATCGAGCTGGGTAAAACT-AAGATTG
1 AGCTAAATCGAGCTAAATTAAGCTCATG--TG
** * * *
16672 AGCT-TGTTGAGCTAAAGTAAGCTAAAT-TG
1 AGCTAAATCGAGCTAAATTAAGCT-CATGTG
16701 AGCTCAAA-CGAGCTAAATTAAGCTCATGTG
1 AGCT-AAATCGAGCTAAATTAAGCTCATGTG
*
16731 AGCTAAATTGAGCT
1 AGCTAAATCGAGCT
16745 GGGTAAAACT
Statistics
Matches: 73, Mismatches: 22, Indels: 18
0.65 0.19 0.16
Matches are distributed among these distances:
29 16 0.22
30 50 0.68
31 6 0.08
32 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (30 bp):
AGCTAAATCGAGCTAAATTAAGCTCATGTG
Found at i:17775 original size:17 final size:17
Alignment explanation
Indices: 17729--17775 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
17719 AAAGCAAGCG
*
17729 AGAAAAGAAGAAGATGAAA
1 AGAAAAG-AG-AGATCAAA
17748 AGCAAAA-AGAGATCAAA
1 AG-AAAAGAGAGATCAAA
17765 AGAAAAGAGAG
1 AGAAAAGAGAG
17776 GCAAGAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 2 0.08
19 2 0.08
20 4 0.16
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (17 bp):
AGAAAAGAGAGATCAAA
Found at i:20224 original size:13 final size:13
Alignment explanation
Indices: 20206--20230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20196 AATAGTTGTG
20206 TGTTATTTAATTA
1 TGTTATTTAATTA
20219 TGTTATTTAATT
1 TGTTATTTAATT
20231 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:22064 original size:12 final size:12
Alignment explanation
Indices: 22009--22071 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
21999 GTTCCTTTTG
*
22009 TTTCAATTTCTT
1 TTTCATTTTCTT
*
22021 TTTCATCTTCTT
1 TTTCATTTTCTT
* * **
22033 TTTCACTCTCAA
1 TTTCATTTTCTT
*
22045 TCTCATTTTCTT
1 TTTCATTTTCTT
*
22057 TTTCATTTCCTT
1 TTTCATTTTCTT
22069 TTT
1 TTT
22072 TTTCCAAACT
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:22176 original size:15 final size:15
Alignment explanation
Indices: 22152--22189 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
22142 CTTGCCGCTC
22152 TTTT-TTTTATTTCA
1 TTTTCTTTTATTTCA
22166 TTTTCTTTTATTTCA
1 TTTTCTTTTATTTCA
22181 TTTTCTTTT
1 TTTTCTTTT
22190 TCTTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTATTTCA
Found at i:24925 original size:10 final size:10
Alignment explanation
Indices: 24910--24936 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
24900 TAAGTTGAAG
24910 TTGAGCTGAT
1 TTGAGCTGAT
24920 TTGAGCTGAT
1 TTGAGCTGAT
24930 TTGAGCT
1 TTGAGCT
24937 TGAAGAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:26675 original size:26 final size:24
Alignment explanation
Indices: 26635--26693 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
26625 CTTTTTCATC
* *
26635 TTCTTTTTTACTCTCAAATTTCTTT
1 TTCTTTTTCAATCTC-AATTTCTTT
*
26660 TCTCTTTTTCAATCTCATTTTCTTT
1 T-TCTTTTTCAATCTCAATTTCTTT
*
26685 TTCATTTTC
1 TTCTTTTTC
26694 TTTTTGCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 10 0.34
26 12 0.41
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (24 bp):
TTCTTTTTCAATCTCAATTTCTTT
Found at i:26705 original size:12 final size:12
Alignment explanation
Indices: 26674--26698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26664 TTTTTCAATC
26674 TCATTTTCTTTT
1 TCATTTTCTTTT
26686 TCATTTTCTTTT
1 TCATTTTCTTTT
26698 T
1 T
26699 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:26833 original size:21 final size:20
Alignment explanation
Indices: 26765--26834 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
26755 GCCTCTTGCC
26765 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
*
26788 TCT-TTTTCTTCTTTTGATTT
1 TCTCTTTTCTT-TTTTTATTT
26808 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
26828 TCTCTTT
1 TCTCTTT
26835 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 19 0.46
21 9 0.22
22 7 0.17
23 3 0.07
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:27759 original size:11 final size:12
Alignment explanation
Indices: 27743--27796 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
27733 CATTAAACAC
*
27743 TTTTTTTCAGAT
1 TTTTTTTCAAAT
27755 TTTTTTTCAAAT
1 TTTTTTTCAAAT
*
27767 TTTTTTT-GAAT
1 TTTTTTTCAAAT
*
27778 TTTTTTTCGAAT
1 TTTTTTTCAAAT
27790 TTTTTTT
1 TTTTTTT
27797 GACTTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:27779 original size:23 final size:24
Alignment explanation
Indices: 27743--27798 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 24
27733 CATTAAACAC
*
27743 TTTTTTTCAGATTTTTTTTCAAAT
1 TTTTTTTGAGATTTTTTTTCAAAT
*
27767 TTTTTTTGA-ATTTTTTTTCGAAT
1 TTTTTTTGAGATTTTTTTTCAAAT
27790 TTTTTTTGA
1 TTTTTTTGA
27799 CTTATATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (24 bp):
TTTTTTTGAGATTTTTTTTCAAAT
Found at i:29544 original size:30 final size:30
Alignment explanation
Indices: 29510--29606 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
29500 TAAACTAAAA
29510 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
29540 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
29570 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
29600 TGAGCTA
1 TGAGCTA
29607 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:30599 original size:19 final size:19
Alignment explanation
Indices: 30575--30614 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30565 AGCTCCCATG
30575 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
30594 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
30613 TA
1 TA
30615 TTAGCTCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:32241 original size:11 final size:10
Alignment explanation
Indices: 32225--32271 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
32215 TATACAAGTT
32225 AAAAAAATCA
1 AAAAAAATCA
*
32235 AAAAAAATTGA
1 AAAAAAA-TCA
32246 AAAAAAAT-A
1 AAAAAAATCA
*
32255 AAAAAAATCG
1 AAAAAAATCA
32265 AAAAAAA
1 AAAAAAA
32272 GTGATTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 9 0.27
10 15 0.45
11 9 0.27
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:32248 original size:20 final size:20
Alignment explanation
Indices: 32225--32271 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
32215 TATACAAGTT
*
32225 AAAAAAATCAAAAAAAATTGA
1 AAAAAAAT-AAAAAAAATCGA
32246 AAAAAAATAAAAAAAATCGA
1 AAAAAAATAAAAAAAATCGA
32266 AAAAAA
1 AAAAAA
32272 GTGATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAAAAATAAAAAAAATCGA
Found at i:37501 original size:19 final size:19
Alignment explanation
Indices: 37477--37516 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
37467 AGCTCCCATG
37477 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
37496 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
37515 TA
1 TA
37517 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:39646 original size:10 final size:10
Alignment explanation
Indices: 39631--39657 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39621 AAGTTTGAAG
39631 TTGAGCTGAT
1 TTGAGCTGAT
39641 TTGAGCTGAT
1 TTGAGCTGAT
39651 TTGAGCT
1 TTGAGCT
39658 TGAAGAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:46169 original size:30 final size:31
Alignment explanation
Indices: 46113--46175 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
46103 AAGGATTCAA
46113 AGATGGGTTTATCGGATATGACAGTTTATGT
1 AGATGGGTTTATCGGATATGACAGTTTATGT
*
46144 AGATGGGTTTAT-GGATAT-ACAAGTTTTTGT
1 AGATGGGTTTATCGGATATGAC-AGTTTATGT
46174 AG
1 AG
46176 GATTTGGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 16 0.53
31 12 0.40
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.40
Consensus pattern (31 bp):
AGATGGGTTTATCGGATATGACAGTTTATGT
Found at i:48450 original size:13 final size:13
Alignment explanation
Indices: 48401--48451 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
48391 AGGTTGGGTT
* *
48401 AAAAAAAAAGTGT
1 AAAAAAAAATTGA
* *
48414 CAAAAAAAATGGA
1 AAAAAAAAATTGA
48427 AAAAAAAAATTGA
1 AAAAAAAAATTGA
48440 AAAAAAAAATTG
1 AAAAAAAAATTG
48452 CATACGGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:48498 original size:1 final size:1
Alignment explanation
Indices: 48492--48518 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
48482 AAGAATCCGT
48492 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
48519 GATCTGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:48626 original size:21 final size:22
Alignment explanation
Indices: 48587--48627 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
48577 CCCCGTAGTG
48587 AAATTTCCGCAATTAAAAAAAA
1 AAATTTCCGCAATTAAAAAAAA
48609 AAATTT-CG-AATATAAAAAA
1 AAATTTCCGCAAT-TAAAAAA
48628 CAAAGGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 9 0.50
22 6 0.33
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
AAATTTCCGCAATTAAAAAAAA
Found at i:55482 original size:13 final size:13
Alignment explanation
Indices: 55464--55488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55454 TGGTCATCAT
55464 GGTGTGAACACAA
1 GGTGTGAACACAA
55477 GGTGTGAACACA
1 GGTGTGAACACA
55489 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:55991 original size:30 final size:30
Alignment explanation
Indices: 55893--55993 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
55883 AGTTTAAACT
*
55893 AAAATGAGCTAAGCTTTAGCTCGTGAGCT-
1 AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
* * * * * * *
55922 AAAGTTGAGCTGAGGCTAAACTCCTAAGCTG
1 AAA-ATGAGCTAAGGTTTAGCTCGTGAGCTG
** *
55953 AAGTTGAGCTAAGGTTTAGCTCGTGAGTTG
1 AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
55983 AAAATGAGCTA
1 AAAATGAGCTA
55994 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 18, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
29 3 0.06
30 47 0.90
31 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (30 bp):
AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
Found at i:59789 original size:23 final size:22
Alignment explanation
Indices: 59737--59789 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
59727 TCCACGTCTT
*
59737 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
59759 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
59782 TTTCTTTT
1 TTTCTTTT
59790 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:69648 original size:30 final size:30
Alignment explanation
Indices: 69614--69701 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
69604 CTAGCTTATA
* *
69614 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
* * *
69644 TTCAGCTTAGGAG-TATAATCTCAGCTCAAC
1 TTCAGCTTAAGAGCTA-AACCTTAGCTCAAC
* * *
69674 TTTAGCTTAAGGGCTAAAGCTTAGCTCA
1 TTCAGCTTAAGAGCTAAACCTTAGCTCA
69702 TTTTAGCTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 43 0.91
31 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (30 bp):
TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
Found at i:74309 original size:14 final size:14
Alignment explanation
Indices: 74287--74331 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
74277 TTAAAGAAGC
74287 AACTCATTAAATTA
1 AACTCATTAAATTA
*
74301 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
74314 AACTCATTTAATTA
1 AACTCATTAAATTA
74328 AACT
1 AACT
74332 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:74369 original size:22 final size:22
Alignment explanation
Indices: 74343--74412 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
74333 AGATGAGTTG
74343 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
74365 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
74384 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
74407 TATTAA
1 TATTAA
74413 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:74375 original size:42 final size:42
Alignment explanation
Indices: 74314--74419 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
74304 TCATTAAATA
74314 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
74357 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
74399 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
74420 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:83705 original size:14 final size:14
Alignment explanation
Indices: 83683--83727 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
83673 TTAAAGAAGC
83683 AACTCATTAAATTA
1 AACTCATTAAATTA
*
83697 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
83710 AACTCATTTAATTA
1 AACTCATTAAATTA
83724 AACT
1 AACT
83728 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:84966 original size:30 final size:30
Alignment explanation
Indices: 84871--84967 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
84861 AGCTCACTCC
* * *
84871 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGGTAAAGCT
* * * **
84901 TAGCTCAACTTCAGCTTAGGA-GTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGGTAAAG-CT
*
84931 CAGCTCAACTTTAGCTCACGAGGTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGGTAAAGCT
84961 TAGCTCA
1 TAGCTCA
84968 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 39 0.80
31 8 0.16
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGGTAAAGCT
Found at i:86712 original size:13 final size:14
Alignment explanation
Indices: 86685--86743 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 14
86675 TATACAAGTC
86685 AAAAAAATTCG---
1 AAAAAAATTCGAAA
86696 AAAAAAATTC-AAA
1 AAAAAAATTCGAAA
*
86709 AAAATAATTCGAAA
1 AAAAAAATTCGAAA
*
86723 AGAAAAAAATCTGAAA
1 A-AAAAAATTC-GAAA
86739 AAAAA
1 AAAAA
86744 GTGTTTAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 10 0.26
13 9 0.23
14 4 0.10
15 11 0.28
16 5 0.13
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:86713 original size:10 final size:10
Alignment explanation
Indices: 86683--86713 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
86673 GTTATACAAG
86683 TCAAAAAAAT
1 TCAAAAAAAT
86693 TCGAAAAAAAT
1 TC-AAAAAAAT
86704 TCAAAAAAAT
1 TCAAAAAAAT
86714 AATTCGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.19
Consensus pattern (10 bp):
TCAAAAAAAT
Found at i:86723 original size:11 final size:11
Alignment explanation
Indices: 86685--86713 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
86675 TATACAAGTC
86685 AAAAAAATTCG
1 AAAAAAATTCG
86696 AAAAAAATTC-
1 AAAAAAATTCG
86706 AAAAAAAT
1 AAAAAAAT
86714 AATTCGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:87692 original size:30 final size:29
Alignment explanation
Indices: 87656--87713 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
87646 AAGAGAAAAC
87656 AAAGAAAA-GAAAAGAAAAAGCAAAAGAGAA
1 AAAGAAAATG-AAAGAAAAAG-AAAAGAGAA
*
87686 AAAGAAAATGAAATAAAAAGAAAAGAGA
1 AAAGAAAATGAAAGAAAAAGAAAAGAGA
87714 GGCAAGAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 17 0.65
31 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (29 bp):
AAAGAAAATGAAAGAAAAAGAAAAGAGAA
Found at i:87791 original size:11 final size:12
Alignment explanation
Indices: 87759--87789 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
87749 TTGAGAGAAC
87759 TTGAAAAAGCCT
1 TTGAAAAAGCCT
87771 TTGAAAAAGCCT
1 TTGAAAAAGCCT
87783 TTGAAAA
1 TTGAAAA
87790 GCAAAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:87800 original size:12 final size:12
Alignment explanation
Indices: 87792--87816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87782 TTTGAAAAGC
87792 AAAAAGAAAATG
1 AAAAAGAAAATG
87804 AAAAAGAAAATG
1 AAAAAGAAAATG
87816 A
1 A
87817 GATTGAAAAG
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:87826 original size:29 final size:31
Alignment explanation
Indices: 87792--87872 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 31
87782 TTTGAAAAGC
*
87792 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
87822 -AAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
87851 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
87873 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
28 8 0.20
29 16 0.39
30 8 0.20
31 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:87858 original size:28 final size:28
Alignment explanation
Indices: 87805--87858 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
87795 AAGAAAATGA
*
87805 AAAAGAAAATGAGATTGAAAAGAGAACG
1 AAAAGAAAATGAGAGTGAAAAGAGAACG
*
87833 AAAAGAAATTTGAGAGTGAAAA-AGAA
1 AAAAGAAA-ATGAGAGTGAAAAGAGAA
87859 GATGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAAATGAGAGTGAAAAGAGAACG
Done.