Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2692
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: 69533
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1611 original size:22 final size:22
Alignment explanation
Indices: 1583--1626 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1573 TTTTGAACCA
1583 TTACCATTCCGTACCAAATCCC
1 TTACCATTCCGTACCAAATCCC
* *
1605 TTACCATTTCGTACCAATTCCC
1 TTACCATTCCGTACCAAATCCC
1627 AAATACCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.05, T:0.32
Consensus pattern (22 bp):
TTACCATTCCGTACCAAATCCC
Found at i:1638 original size:24 final size:22
Alignment explanation
Indices: 1584--1638 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1574 TTTGAACCAT
* *
1584 TACCATTCCGTACCAAATCCCT
1 TACCATTTCGTACCAAATCCCA
*
1606 TACCATTTCGTACCAATTCCCAAA
1 TACCATTTCGTACCAAATCCC--A
1630 TACCATTTC
1 TACCATTTC
1639 TTAATTAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.68
24 9 0.32
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (22 bp):
TACCATTTCGTACCAAATCCCA
Found at i:5668 original size:33 final size:33
Alignment explanation
Indices: 5630--5692 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5620 GATTACTCAC
5630 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
5663 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
5693 AATTTCTTTT
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:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:5719 original size:21 final size:21
Alignment explanation
Indices: 5690--5745 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
5680 CAAGCTCTCT
*
5690 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
5711 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
5732 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
5746 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:5732 original size:18 final size:17
Alignment explanation
Indices: 5709--5844 Score: 64
Period size: 18 Copynumber: 7.6 Consensus size: 17
5699 TTTTTTCGCT
5709 TTTTCTTTTTCAATTTTC
1 TTTTCTTTTTC-ATTTTC
*
5727 TTTTCTTCATTTTCTTTTTC
1 TTTTC-T--TTTTCATTTTC
**
5747 TCTCACTTTTTCGA-TTTC
1 T-TTTCTTTTTC-ATTTTC
* *
5765 TTTTTCTTTTGCAATTTC
1 -TTTTCTTTTTCATTTTC
*
5783 TTTTTCTTTTTCGTTTTC
1 -TTTTCTTTTTCATTTTC
5801 TTTT-TGTTTTC--TTTC
1 TTTTCT-TTTTCATTTTC
* * *
5816 AATTTCTTTTTCAATCTC
1 -TTTTCTTTTTCATTTTC
*
5834 TTTTCCTTTTC
1 TTTTCTTTTTC
5845 TCGCTCAATG
Statistics
Matches: 92, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
15 4 0.04
16 9 0.10
17 20 0.22
18 43 0.47
19 2 0.02
20 7 0.08
21 7 0.08
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCATTTTC
Found at i:5738 original size:14 final size:14
Alignment explanation
Indices: 5689--5745 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
5679 TCAAGCTCTC
5689 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
5702 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
5716 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
5730 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
5744 TT
1 TT
5746 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:5827 original size:6 final size:6
Alignment explanation
Indices: 5707--5814 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
5697 TCTTTTTTCG
* * * **
5707 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
5758 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
5806 -GTTTT CTTT
1 CTTTTT CTTT
5815 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:6919 original size:12 final size:12
Alignment explanation
Indices: 6904--6929 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6894 TTTTTTTCAC
6904 TTTTTTTTGAAT
1 TTTTTTTTGAAT
6916 TTTTTTTTGAAT
1 TTTTTTTTGAAT
6928 TT
1 TT
6930 CGATTTTTTT
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:19170 original size:12 final size:12
Alignment explanation
Indices: 19153--19195 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
19143 AGGAAATTCG
19153 AAAAAAATTTGA
1 AAAAAAATTTGA
* *
19165 AAAAAAAATCGA
1 AAAAAAATTTGA
*
19177 AAAAAAA-TTAA
1 AAAAAAATTTGA
19188 AAAAAAAT
1 AAAAAAAT
19196 CGAAGTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:19179 original size:22 final size:22
Alignment explanation
Indices: 19150--19199 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
19140 AAGAGGAAAT
*
19150 TCGAAAAAAATTTGAAAAAAAAA
1 TCGAAAAAAAATT-AAAAAAAAA
19173 TCGAAAAAAAATTAAAAAAAAA
1 TCGAAAAAAAATTAAAAAAAAA
19195 TCGAA
1 TCGAA
19200 GTATAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.16
Consensus pattern (22 bp):
TCGAAAAAAAATTAAAAAAAAA
Found at i:19189 original size:10 final size:11
Alignment explanation
Indices: 19150--19199 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
19140 AAGAGGAAAT
*
19150 TCGAAAAAAAT
1 TCGAAAAAAAA
*
19161 TTGAAAAAAAAA
1 TCG-AAAAAAAA
19173 TCGAAAAAAAA
1 TCGAAAAAAAA
**
19184 TTAAAAAAAAA
1 TCGAAAAAAAA
19195 TCGAA
1 TCGAA
19200 GTATAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.16
Consensus pattern (11 bp):
TCGAAAAAAAA
Found at i:24898 original size:22 final size:22
Alignment explanation
Indices: 24870--24913 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24860 TTTTGAACCA
24870 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
24892 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
24914 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:25413 original size:15 final size:15
Alignment explanation
Indices: 25383--25435 Score: 88
Period size: 15 Copynumber: 3.4 Consensus size: 15
25373 CTTCTTCTTC
25383 TTTTCACGAAATTTTTT
1 TTTTCACG-AA-TTTTT
25400 TTTTCACGAATTTTT
1 TTTTCACGAATTTTT
25415 TTTTCACGAATTTTT
1 TTTTCACGAATTTTT
25430 TTTTCA
1 TTTTCA
25436 AATTGATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 26 0.72
16 2 0.06
17 8 0.22
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTTCACGAATTTTT
Found at i:25491 original size:10 final size:11
Alignment explanation
Indices: 25473--25507 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
25463 ATGGAAACCA
25473 AATTTTTTTTG
1 AATTTTTTTTG
25484 AATTTTTTTTTG
1 AA-TTTTTTTTG
25496 -ATTTTTTTTG
1 AATTTTTTTTG
25506 AA
1 AA
25508 GAAACTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.41
11 4 0.18
12 9 0.41
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:25492 original size:12 final size:11
Alignment explanation
Indices: 25475--25504 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
25465 GGAAACCAAA
25475 TTTTTTTTGAAT
1 TTTTTTTTG-AT
25487 TTTTTTTTGAT
1 TTTTTTTTGAT
25498 TTTTTTT
1 TTTTTTT
25505 GAAGAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:26542 original size:21 final size:23
Alignment explanation
Indices: 26497--26543 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
26487 TCACCTGCAA
* *
26497 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
26520 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
26541 TAA
1 TAA
26544 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:29756 original size:11 final size:12
Alignment explanation
Indices: 29729--29771 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
29719 TGGAAACTAG
*
29729 TTTTTTTTCAAA
1 TTTTTTTTCGAA
*
29741 TTTTTTTTTGAA
1 TTTTTTTTCGAA
*
29753 TTTTTTTTCGAG
1 TTTTTTTTCGAA
29765 TTTTTTT
1 TTTTTTT
29772 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:32719 original size:20 final size:20
Alignment explanation
Indices: 32696--32742 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32686 GGGTTAAGAT
*
32696 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
32716 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
32736 TGAGCTG
1 TGAGCTG
32743 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:34468 original size:48 final size:48
Alignment explanation
Indices: 34413--34518 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
34403 TTGTCTTTTC
*
34413 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
34461 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
34509 TTTCTTTTTC
1 TTTCTTTTTC
34519 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:35708 original size:11 final size:11
Alignment explanation
Indices: 35694--35722 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
35684 TCCAACTCAA
35694 TTTTTTTTGA-
1 TTTTTTTTGAC
35704 TTTTTTTTGAC
1 TTTTTTTTGAC
35715 TTTTTTTT
1 TTTTTTTT
35723 ACGTTACGAA
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:37158 original size:20 final size:20
Alignment explanation
Indices: 37135--37181 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
37125 GGGTTAAGAT
*
37135 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
37155 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
37175 TGAGCTG
1 TGAGCTG
37182 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:48156 original size:21 final size:19
Alignment explanation
Indices: 48130--48177 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
48120 TCTTTTTGGA
*
48130 TTTCTTTTTCTTTTTCAATCT
1 TTTCTTTTT-TCTTTCAAT-T
48151 TTTCTTCTTTTCTTTCAATT
1 TTTCTT-TTTTCTTTCAATT
*
48171 TCTCTTT
1 TTTCTTT
48178 CTCGCTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 14 0.58
22 3 0.12
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTTTTTCTTTCAATT
Found at i:49160 original size:11 final size:11
Alignment explanation
Indices: 49144--49173 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
49134 TACTTCAAAT
49144 TTTTTTTTCAA
1 TTTTTTTTCAA
*
49155 TTTTTTTTCGA
1 TTTTTTTTCAA
49166 TTTTTTTT
1 TTTTTTTT
49174 TCAAATTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:49181 original size:13 final size:12
Alignment explanation
Indices: 49141--49177 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
49131 TAATACTTCA
49141 AATTTTTTTTTC
1 AATTTTTTTTTC
49153 AA-TTTTTTTTC
1 AATTTTTTTTTC
*
49164 GATTTTTTTTTC
1 AATTTTTTTTTC
49176 AA
1 AA
49178 ATTTCCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:51661 original size:22 final size:21
Alignment explanation
Indices: 51630--51682 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
51620 ACCTCTTTGA
*
51630 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCATACC-AAT
*
51653 ACCATACCATTTCATACCAAT
1 ACCATACCAATTCATACCAAT
*
51674 TCCATACCA
1 ACCATACCA
51683 TTTTGAACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 12 0.44
23 4 0.15
ACGTcount: A:0.38, C:0.34, G:0.02, T:0.26
Consensus pattern (21 bp):
ACCATACCAATTCATACCAAT
Found at i:51680 original size:21 final size:22
Alignment explanation
Indices: 51630--51685 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
51620 ACCTCTTTGA
* *
51630 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCATACCAAAT
51653 ACCATACCATTTCATACC-AAT
1 ACCATACCATTTCATACCAAAT
*
51674 TCCATACCATTT
1 ACCATACCATTT
51686 TGAACCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 14 0.47
22 12 0.40
23 4 0.13
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (22 bp):
ACCATACCATTTCATACCAAAT
Found at i:52870 original size:21 final size:23
Alignment explanation
Indices: 52825--52871 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52815 TCACCTGCAA
* *
52825 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
52848 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
52869 TAA
1 TAA
52872 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:55236 original size:40 final size:40
Alignment explanation
Indices: 55191--55271 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
55181 AAATTTTACA
55191 TACATGTTTTCGGCACTGTGATTGAATATAAAAAAATTAT
1 TACATGTTTTCGGCACTGTGATTGAATATAAAAAAATTAT
55231 TACATGTTTTCGGCACTGTGATTGAATATAAAAAAATTAT
1 TACATGTTTTCGGCACTGTGATTGAATATAAAAAAATTAT
55271 T
1 T
55272 CCCGCAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (40 bp):
TACATGTTTTCGGCACTGTGATTGAATATAAAAAAATTAT
Found at i:56566 original size:11 final size:10
Alignment explanation
Indices: 56541--56601 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
56531 ACCAATAAAA
56541 TAAA-TGAGC
1 TAAATTGAGC
*
56550 TGAATTGTAGC
1 TAAATTG-AGC
56561 TAAATTGAGC
1 TAAATTGAGC
**
56571 TCGATTGAGC
1 TAAATTGAGC
56581 TGAAA-TGAGC
1 T-AAATTGAGC
*
56591 TCAATTGAGC
1 TAAATTGAGC
56601 T
1 T
56602 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:56602 original size:20 final size:20
Alignment explanation
Indices: 56542--56602 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
56532 CCAATAAAAT
*
56542 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
56562 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
56583 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
56603 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:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:58144 original size:23 final size:23
Alignment explanation
Indices: 58112--58155 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
58102 GATTGAGGGT
58112 GAAAAAGAATT-GAAGAAAGAAGA
1 GAAAAAGAATTAGAA-AAAGAAGA
*
58135 GAAAATGAATTAGAAAAAGAA
1 GAAAAAGAATTAGAAAAAGAA
58156 ACAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (23 bp):
GAAAAAGAATTAGAAAAAGAAGA
Found at i:59670 original size:11 final size:10
Alignment explanation
Indices: 59645--59705 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
59635 ACCAATAAAA
59645 TAAA-TGAGC
1 TAAATTGAGC
*
59654 TGAATTGTAGC
1 TAAATTG-AGC
59665 TAAATTGAGC
1 TAAATTGAGC
**
59675 TCGATTGAGC
1 TAAATTGAGC
59685 TGAAA-TGAGC
1 T-AAATTGAGC
*
59695 TCAATTGAGC
1 TAAATTGAGC
59705 T
1 T
59706 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:59706 original size:20 final size:20
Alignment explanation
Indices: 59646--59706 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
59636 CCAATAAAAT
*
59646 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
59666 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
59687 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
59707 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:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:61750 original size:13 final size:13
Alignment explanation
Indices: 61734--61758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61724 AAAGAGTTCG
61734 AAAAAAAAATTGA
1 AAAAAAAAATTGA
61747 AAAAAAAAATTG
1 AAAAAAAAATTG
61759 CATACGGTTT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:64001 original size:19 final size:18
Alignment explanation
Indices: 63955--64020 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
63945 CAAATGAGAG
63955 AAAAAGAAAAGAACGAAAATA
1 AAAAAGAAAAG-A--AAAATA
*
63976 CAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAAT-A
*
63995 AAAAAGAAAAGAAAATTCA
1 AAAAAGAAAAGAAAAAT-A
64014 AAAAAGA
1 AAAAAGA
64021 GAATGAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.12
19 24 0.60
20 1 0.03
21 10 0.25
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATA
Done.