Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1565
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: 127326
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:258 original size:20 final size:19
Alignment explanation
Indices: 216--259 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
206 AAGCTGCAAT
* * *
216 AAATTAGAGAATTGGGCAT
1 AAATTAGAGAATTAGCCAA
235 AAATTAGAGAAATTAGCCAA
1 AAATTAGAG-AATTAGCCAA
255 AAATT
1 AAATT
260 TCTCTTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (19 bp):
AAATTAGAGAATTAGCCAA
Found at i:2758 original size:27 final size:26
Alignment explanation
Indices: 2689--2758 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
2679 ATAAAAGTTA
*
2689 TTTTTTATTTATT-AAAATTAGTAAT
1 TTTTTTATTTATTAAAAAATAGTAAT
* *
2714 TATTTTATGTT-TGTAAAAAATAGTATT
1 TTTTTTAT-TTAT-TAAAAAATAGTAAT
2741 TTTTTTATTTATTAAAAA
1 TTTTTTATTTATTAAAAA
2759 TGATGATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 8 0.22
26 11 0.30
27 18 0.49
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (26 bp):
TTTTTTATTTATTAAAAAATAGTAAT
Found at i:9735 original size:62 final size:62
Alignment explanation
Indices: 9628--9748 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 62
9618 CAAAGTGTAC
*
9628 TACTTAACAATGAAACCAAATCATATGATTTCAGTCGTCTAATTGAAAGCCTTTCACGTTAT
1 TACTTAACAATGAAACCAAATAATATGATTTCAGTCGTCTAATTGAAAGCCTTTCACGTTAT
* * * *
9690 TACTTAACAATGAAACCAAGTAATATGATTTGAG-CTGTCTGATTGAAAGTCTTTCACGT
1 TACTTAACAATGAAACCAAATAATATGATTTCAGTC-GTCTAATTGAAAGCCTTTCACGT
9749 CAGTAGTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 1 0.02
62 52 0.98
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (62 bp):
TACTTAACAATGAAACCAAATAATATGATTTCAGTCGTCTAATTGAAAGCCTTTCACGTTAT
Found at i:12394 original size:3 final size:3
Alignment explanation
Indices: 12388--12424 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12378 GTACTCCAAA
12388 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12425 TTACAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13518 original size:13 final size:14
Alignment explanation
Indices: 13500--13528 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13490 TATTAATGTA
13500 TAAAATATA-AATT
1 TAAAATATATAATT
13513 TAAAATATATAATT
1 TAAAATATATAATT
13527 TA
1 TA
13529 TATTTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATATAATT
Found at i:14401 original size:41 final size:41
Alignment explanation
Indices: 14354--14483 Score: 129
Period size: 41 Copynumber: 3.2 Consensus size: 41
14344 TAATCAGTCA
* *
14354 TATTAACGACGTTTTTACTGTGAATGTCGCTAAATTTTTCT
1 TATTAACGACGTTTTTAATGTGAATGTCACTAAATTTTTCT
** * ***
14395 TATTAACGGTGTTTTTAAGGTGAACACCACTAAATTTTTCT
1 TATTAACGACGTTTTTAATGTGAATGTCACTAAATTTTTCT
* * *
14436 TATTAGCGACGTTTATAAATG-AAATGTCACTAAATTTTT-T
1 TATTAACGACGTTT-TTAATGTGAATGTCACTAAATTTTTCT
14476 CTATTAAC
1 -TATTAAC
14484 AGTGTTTTTA
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
40 1 0.01
41 64 0.93
42 4 0.06
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (41 bp):
TATTAACGACGTTTTTAATGTGAATGTCACTAAATTTTTCT
Found at i:14901 original size:18 final size:19
Alignment explanation
Indices: 14878--14913 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
14868 TTGTTAGGTA
14878 AATTTTATTTTTT-TTTTT
1 AATTTTATTTTTTCTTTTT
14896 AATTTTATTTTTTCTTTT
1 AATTTTATTTTTTCTTTT
14914 GTCAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
AATTTTATTTTTTCTTTTT
Found at i:15953 original size:2 final size:2
Alignment explanation
Indices: 15946--15972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15936 TTTTATATTA
15946 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15973 AACTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17026 original size:8 final size:7
Alignment explanation
Indices: 17009--17105 Score: 51
Period size: 7 Copynumber: 13.6 Consensus size: 7
16999 ATATAGATAC
17009 ATTATCAT
1 ATTAT-AT
17017 ATTATAAT
1 ATTAT-AT
17025 ATTATA-
1 ATTATAT
17031 ATTATAAT
1 ATTAT-AT
17039 ATTATAT
1 ATTATAT
17046 ATT-TATT
1 ATTATA-T
17053 ACTT-TAT
1 A-TTATAT
*
17060 GA-TATAA
1 -ATTATAT
17067 ATTATAT
1 ATTATAT
*
17074 AATATAT
1 ATTATAT
*
17081 A-TAAAT
1 ATTATAT
*
17087 ATATAAAT
1 AT-TATAT
*
17095 AATATAT
1 ATTATAT
17102 ATTA
1 ATTA
17106 CATGATTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
6 14 0.19
7 30 0.42
8 28 0.39
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (7 bp):
ATTATAT
Found at i:17119 original size:21 final size:21
Alignment explanation
Indices: 17061--17103 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
17051 TTACTTTATG
17061 ATATAAAT-TAT--ATAATAT
1 ATATAAATATATAAATAATAT
17079 ATATAAATATATAAATAATAT
1 ATATAAATATATAAATAATAT
17100 ATAT
1 ATAT
17104 TACATGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
21 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAAATATATAAATAATAT
Found at i:17236 original size:17 final size:16
Alignment explanation
Indices: 17203--17255 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 16
17193 CATTAAATCT
17203 AATATTTTT--ATTTA
1 AATATTTTTAAATTTA
17217 AATATTTTTAAATATTA
1 AATATTTTTAAAT-TTA
*
17234 AATAAATTTTTAAATTAA
1 AAT--ATTTTTAAATTTA
17252 AATA
1 AATA
17256 AATAACTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 9 0.27
16 3 0.09
17 6 0.18
18 5 0.15
19 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATTTTTAAATTTA
Found at i:17244 original size:19 final size:18
Alignment explanation
Indices: 17220--17258 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
17210 TTATTTAAAT
*
17220 ATTTTTAAATATTAAATAA
1 ATTTTTAAAT-TAAAATAA
17239 ATTTTTAAATTAAAATAA
1 ATTTTTAAATTAAAATAA
17257 AT
1 AT
17259 AACTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTAAATTAAAATAA
Found at i:17564 original size:13 final size:13
Alignment explanation
Indices: 17546--17572 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17536 GATATTTGAA
17546 TAAAAGTCAAATG
1 TAAAAGTCAAATG
17559 TAAAAGTCAAATG
1 TAAAAGTCAAATG
17572 T
1 T
17573 TGTTGGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (13 bp):
TAAAAGTCAAATG
Found at i:19707 original size:14 final size:16
Alignment explanation
Indices: 19683--19744 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 16
19673 TCATATAAAT
*
19683 TTTTATATTTTT-ATA
1 TTTTATTTTTTTCATA
*
19698 -TTTATTTTTTTCGTA
1 TTTTATTTTTTTCATA
19713 TTTTATTTTTTGTCATA
1 TTTTATTTTTT-TCATA
19730 TGTCTTATTTATTTT
1 T-T-TTATTT-TTTT
19745 TTGATAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.26
15 2 0.05
16 10 0.26
17 5 0.13
18 1 0.03
19 7 0.18
20 3 0.08
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (16 bp):
TTTTATTTTTTTCATA
Found at i:21975 original size:2 final size:2
Alignment explanation
Indices: 21968--22011 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
21958 GAGTTAAGAG
21968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22010 AT
1 AT
22012 GATTATTAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22595 original size:14 final size:15
Alignment explanation
Indices: 22576--22605 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
22566 CCAAACATAA
22576 TGTAAAAA-TTGTCT
1 TGTAAAAACTTGTCT
22590 TGTAAAAACTTGTCT
1 TGTAAAAACTTGTCT
22605 T
1 T
22606 ATTATTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (15 bp):
TGTAAAAACTTGTCT
Found at i:23014 original size:16 final size:17
Alignment explanation
Indices: 22993--23035 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
22983 AAATAATATT
22993 ATTTTATATTAGTTA-A
1 ATTTTATATTAGTTATA
* *
23009 ATTTTAAATTATTTATA
1 ATTTTATATTAGTTATA
23026 ATTTTATATT
1 ATTTTATATT
23036 TAAATTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTATATTAGTTATA
Found at i:24829 original size:2 final size:2
Alignment explanation
Indices: 24822--24878 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
24812 ATCATCAATA
24822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24864 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
24879 GGGTATGCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26529 original size:2 final size:2
Alignment explanation
Indices: 26524--26575 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
26514 GTGTACATAC
* *
26524 AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26566 AT AT AT AT AT
1 AT AT AT AT AT
26576 TTGAAAACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:26538 original size:18 final size:18
Alignment explanation
Indices: 26517--26572 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
26507 TATGTGTGTG
26517 TACATACATATATATATA
1 TACATACATATATATATA
26535 TACATACATATATATATA
1 TACATACATATATATATA
* *
26553 TATATATATATATATATA
1 TACATACATATATATATA
26571 TA
1 TA
26573 TATTTGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
TACATACATATATATATA
Found at i:27082 original size:2 final size:2
Alignment explanation
Indices: 27077--27101 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27067 ATACACATGC
27077 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27102 CACACACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28228 original size:2 final size:2
Alignment explanation
Indices: 28221--28248 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28211 AAATGGATAG
28221 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28249 AGGCATATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28806 original size:42 final size:42
Alignment explanation
Indices: 28757--28837 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
28747 ATTTATTTAT
* *
28757 TTTAAAAATTTATTTAAATATGAATTAAAAATTAAAAATATA
1 TTTAAAAATATATTTAAATATGAATTAAAAATAAAAAATATA
* *
28799 TTTAAAAATATATTTTAATATTAATTAAAAATAAAAAAT
1 TTTAAAAATATATTTAAATATGAATTAAAAATAAAAAAT
28838 TATAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (42 bp):
TTTAAAAATATATTTAAATATGAATTAAAAATAAAAAATATA
Found at i:28815 original size:13 final size:12
Alignment explanation
Indices: 28788--28831 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
28778 GAATTAAAAA
28788 TTAAAAATATAT
1 TTAAAAATATAT
28800 TTAAAAATATAT
1 TTAAAAATATAT
* * *
28812 TTTAATAT-TAA
1 TTAAAAATATAT
28823 TTAAAAATA
1 TTAAAAATA
28832 AAAAATTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAAAATATAT
Found at i:28848 original size:41 final size:42
Alignment explanation
Indices: 28759--28851 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
28749 TTATTTATTT
* * *
28759 TAAAAATTTATTTAAATATGAATTAAAAATTAAAAATATATT
1 TAAAAATATATTTAAATATGAATTAAAAATAAAAAATATATA
* *
28801 TAAAAATATATTTTAATATTAATTAAAAATAAAAAAT-TATA
1 TAAAAATATATTTAAATATGAATTAAAAATAAAAAATATATA
28842 -ATAAAATATA
1 TA-AAAATATA
28852 AAAATTTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 1 0.02
41 11 0.24
42 33 0.73
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (42 bp):
TAAAAATATATTTAAATATGAATTAAAAATAAAAAATATATA
Found at i:34588 original size:25 final size:25
Alignment explanation
Indices: 34526--34595 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
34516 AATAAAAATT
*
34526 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
*
34550 AGCCACCAATTTTGATAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
34575 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
34596 CAAAGGAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:34651 original size:25 final size:25
Alignment explanation
Indices: 34528--34652 Score: 90
Period size: 27 Copynumber: 4.8 Consensus size: 25
34518 TAAAAATTAG
* * *
34528 CCACCAATTTTGACAAAC-AACAAG
1 CCACCATTTTTGACAAACAAAGAAA
* * * * *
34552 CCACCAATTTTGATAAATAAACAAG
1 CCACCATTTTTGACAAACAAAGAAA
* *
34577 CCTCCATATTTGACAAATACAAAGGAAA
1 CCACCATTTTTGAC-AA-ACAAA-GAAA
* *
34605 CCACCATTTTTTACAAACACAAAATAA
1 CCACCATTTTTGACAAACA-AAGA-AA
34632 CCACCATTTTTGACAAACAAA
1 CCACCATTTTTGACAAACAAA
34653 TGGGTGGCTT
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
24 16 0.20
25 16 0.20
26 8 0.10
27 28 0.35
28 13 0.16
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.22
Consensus pattern (25 bp):
CCACCATTTTTGACAAACAAAGAAA
Found at i:34653 original size:24 final size:24
Alignment explanation
Indices: 34528--34653 Score: 74
Period size: 24 Copynumber: 4.9 Consensus size: 24
34518 TAAAAATTAG
* *
34528 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * * *
34552 CCACCAATTTTGATAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
34576 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
*
34605 CCACCATTTTTTACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
34632 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
34654 GGGTGGCTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
23 1 0.01
24 23 0.29
25 12 0.15
26 4 0.05
27 19 0.24
28 16 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:36162 original size:21 final size:21
Alignment explanation
Indices: 36137--36191 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
36127 TTGTAGCGAA
36137 CATCTTTTTTGCTAGAAGATC
1 CATCTTTTTTGCTAGAAGATC
*
36158 CATCTTTCTTGCTAGAAGATC
1 CATCTTTTTTGCTAGAAGATC
36179 CATCTTTCTTTGC
1 CATCTTT-TTTGC
36192 AAATACCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (21 bp):
CATCTTTTTTGCTAGAAGATC
Found at i:39203 original size:25 final size:25
Alignment explanation
Indices: 39141--39210 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
39131 AATAAAAATT
*
39141 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
*
39165 AGCCACCAATTTTGATAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
39190 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
39211 CAAAGGAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:39231 original size:28 final size:27
Alignment explanation
Indices: 39195--39265 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
39185 AAACAAGCCT
* * *
39195 CCATATTTGACAAATACAAAGGA-AACTA
1 CCATTTTTGACAAACACAAA--ATAACCA
*
39223 CCATTTTTGATAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
*
39250 TCATTTTTGACAAACA
1 CCATTTTTGACAAACA
39266 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:39694 original size:1 final size:1
Alignment explanation
Indices: 39688--39721 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
39678 TGCTATTTAC
39688 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39722 AATATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43782 original size:109 final size:109
Alignment explanation
Indices: 43591--43807 Score: 344
Period size: 109 Copynumber: 2.0 Consensus size: 109
43581 AGAAACACTT
* * *
43591 CAAATTAGGAAAAATTCAAGCAACATTCTCAAAGTTTGTCTTCTTGATTCATTATTATACCACCT
1 CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
* * **
43656 AGATTATACAACAACAACTAAAGGAAACTTAAGTTACAATTCTG
66 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCTG
* * *
43700 CAAATTAGGAAATATTAAAGCAATATTCTCAAAGTTTTTCTCCTTGATTCATTATCATACCACCT
1 CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
43765 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCT
66 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCT
43808 TTTTTCCCCT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (109 bp):
CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCTG
Found at i:45214 original size:2 final size:2
Alignment explanation
Indices: 45207--45235 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45197 ACACAAGGAA
45207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45236 AAATTTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45601 original size:3 final size:3
Alignment explanation
Indices: 45593--45620 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
45583 AGCTTGATGC
45593 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
45621 CTCCTTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:47144 original size:27 final size:27
Alignment explanation
Indices: 47101--47188 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
47091 GGTGGATGTC
*
47101 TAAACAATAA-AAGTTATTTTTTATTTGT
1 TAAA-AATAATAA-TTATTTTTTATTTAT
* *
47129 TAAAAATAGTAATTATTTTATATTTAT
1 TAAAAATAATAATTATTTTTTATTTAT
*
47156 AAAAAATAATAATT-TTTTTTATTTAT
1 TAAAAATAATAATTATTTTTTATTTAT
47182 TAAAAAT
1 TAAAAAT
47189 GATGACATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 17 0.33
27 29 0.56
28 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (27 bp):
TAAAAATAATAATTATTTTTTATTTAT
Found at i:47199 original size:27 final size:25
Alignment explanation
Indices: 47117--47199 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 25
47107 ATAAAAGTTA
*
47117 TTTTTTATTTGTTAAAAATA-GTAAT
1 TTTTTTATTTATTAAAAATATG-AAT
*
47142 TATTTTATATTTATAAAAAATAAT-AATT
1 T-TTTT-TATTTATTAAAAAT-ATGAA-T
47170 TTTTTTATTTATTAAAAATGATGACAT
1 TTTTTTATTTATTAAAAAT-ATGA-AT
47197 TTT
1 TTT
47200 ATTTGTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 1 0.02
26 19 0.40
27 23 0.49
28 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (25 bp):
TTTTTTATTTATTAAAAATATGAAT
Found at i:51672 original size:27 final size:27
Alignment explanation
Indices: 51641--51709 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
51631 AGCCACCATT
51641 TGTTTGTCAAAAATGGTAGTTACTTTG
1 TGTTTGTCAAAAATGGTAGTTACTTTG
* * * *
51668 TGTTTGTCAAAAATTGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTAGTTACTTTG
*
51695 TATTTGTCAAAAATG
1 TGTTTGTCAAAAATG
51710 ATGGCATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTAGTTACTTTG
Found at i:52194 original size:103 final size:103
Alignment explanation
Indices: 52015--52227 Score: 419
Period size: 103 Copynumber: 2.1 Consensus size: 103
52005 CAAGAATCAT
52015 CAAATTTCACTTGTAACAAGTGAATAAACTTAATGAAGCATAGTATTTTAACAAAATCTTGAAAA
1 CAAATTTCACTTGTAACAAGTGAATAAACTTAATGAAGCATAGTATTTTAACAAAATCTTGAAAA
52080 AAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
66 AAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
52118 CAAATTTCACTTGTAACAAGTGAATAAACTTAATGAAGCATAGTATTTTAACAAAATCTTGAAAA
1 CAAATTTCACTTGTAACAAGTGAATAAACTTAATGAAGCATAGTATTTTAACAAAATCTTGAAAA
52183 AAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
66 AAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
52221 C-AATTTC
1 CAAATTTC
52228 TTACAGTAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 6 0.05
103 104 0.95
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (103 bp):
CAAATTTCACTTGTAACAAGTGAATAAACTTAATGAAGCATAGTATTTTAACAAAATCTTGAAAA
AAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
Found at i:54316 original size:12 final size:12
Alignment explanation
Indices: 54299--54324 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54289 GAAAACAAAG
54299 GCTGCCAACTGT
1 GCTGCCAACTGT
54311 GCTGCCAACTGT
1 GCTGCCAACTGT
54323 GC
1 GC
54325 CGTCAATTTT
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:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:54349 original size:12 final size:12
Alignment explanation
Indices: 54327--54377 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
54317 AACTGTGCCG
54327 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
54340 TCAATTTGAAAT
1 TCAATTTGAAAT
*
54352 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
54367 TCAATTTGAAA
1 TCAATTTGAAA
54378 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:54389 original size:27 final size:27
Alignment explanation
Indices: 54333--54389 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
54323 GCCGTCAATT
* *
54333 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
54360 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
54387 TTG
1 TTG
54390 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:59066 original size:12 final size:12
Alignment explanation
Indices: 59049--59074 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59039 GAAAACAAAG
59049 GCTGCCAACTGT
1 GCTGCCAACTGT
59061 GCTGCCAACTGT
1 GCTGCCAACTGT
59073 GC
1 GC
59075 CGTCAATTTT
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:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:59099 original size:12 final size:12
Alignment explanation
Indices: 59077--59127 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
59067 AACTGTGCCG
59077 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
59090 TCAATTTGAAAT
1 TCAATTTGAAAT
*
59102 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
59117 TCAATTTGAAA
1 TCAATTTGAAA
59128 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:59139 original size:27 final size:27
Alignment explanation
Indices: 59083--59139 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
59073 GCCGTCAATT
* *
59083 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
59110 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
59137 TTG
1 TTG
59140 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:60836 original size:16 final size:16
Alignment explanation
Indices: 60811--60849 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
60801 AACTGTATTC
60811 TTTT-TTTTTAACATT
1 TTTTATTTTTAACATT
*
60826 TTTTATTTTTAATATT
1 TTTTATTTTTAACATT
*
60842 TTATATTT
1 TTTTATTT
60850 ACCTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTAACATT
Found at i:62358 original size:22 final size:24
Alignment explanation
Indices: 62333--62394 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
62323 TAATAAAATA
*
62333 TAAATTTAAACTT-AAATCT-ATT
1 TAAATTTAAACTTAAAAGCTCATT
62355 TAAATTTAAA-TTAAAAGCTCATT
1 TAAATTTAAACTTAAAAGCTCATT
* *
62378 TAAACTTAAACTAAAAA
1 TAAATTTAAACTTAAAA
62395 TTTAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.44
23 12 0.35
24 5 0.15
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAATTTAAACTTAAAAGCTCATT
Found at i:62873 original size:22 final size:22
Alignment explanation
Indices: 62829--62874 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
62819 GAAAAAAAAG
*
62829 TCTAATTTTGTTGGCAACTAAA
1 TCTAATTTTGTTGGCAACGAAA
*
62851 TCTAA-TTTGTTGGCTAAGGAAA
1 TCTAATTTTGTTGGC-AACGAAA
62873 TC
1 TC
62875 ACAGCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (22 bp):
TCTAATTTTGTTGGCAACGAAA
Found at i:68766 original size:2 final size:2
Alignment explanation
Indices: 68759--68785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
68749 TTTTCCCCCA
68759 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
68786 TTTTCCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:69976 original size:2 final size:2
Alignment explanation
Indices: 69959--69996 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
69949 ATCATTAATA
*
69959 AT AT -T AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69997 AATAGGGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71631 original size:2 final size:2
Alignment explanation
Indices: 71626--71659 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71616 GTGTACATAC
71626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71660 TTGAAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72158 original size:2 final size:2
Alignment explanation
Indices: 72153--72187 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
72143 ACACACACGC
72153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72188 CACACCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72912 original size:20 final size:20
Alignment explanation
Indices: 72887--72961 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
72877 TGCTTTTTTC
*
72887 AATAAAAATGAAAAGCAAAA
1 AATAAAAATAAAAAGCAAAA
**
72907 AAT-AAAATAAAAAAGCTGAA
1 AATAAAAAT-AAAAAGCAAAA
72927 AATAAAGAA-AAAATAGCAAAA
1 AATAAA-AATAAAA-AGCAAAA
*
72948 TATAAAAATAAAAA
1 AATAAAAATAAAAA
72962 CACCAAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 5 0.11
20 21 0.48
21 16 0.36
22 2 0.05
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (20 bp):
AATAAAAATAAAAAGCAAAA
Found at i:73712 original size:2 final size:2
Alignment explanation
Indices: 73700--73743 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
73690 AAATGGATAG
*
73700 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
73742 GA
1 GA
73744 AGGCATATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:74086 original size:20 final size:19
Alignment explanation
Indices: 74038--74088 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
74028 TTAAAATATT
*
74038 TTTAAATAAAAATAATAAA
1 TTTAAAAAAAAATAATAAA
* *
74057 TTATATAAAAAAATAATCATA
1 TT-TAAAAAAAAATAAT-AAA
74078 TTTAAAAAAAA
1 TTTAAAAAAAA
74089 GAAAGTACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTTAAAAAAAAATAATAAA
Found at i:74290 original size:30 final size:30
Alignment explanation
Indices: 74256--74324 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
74246 TTTATTTATT
74256 TTAAAAATTTATTTAAATATGAATTAAAAA
1 TTAAAAATTTATTTAAATATGAATTAAAAA
* *
74286 TTAAAAATATATTTAAATATTAATTAAAAA
1 TTAAAAATTTATTTAAATATGAATTAAAAA
*
74316 TAAAAAATT
1 TTAAAAATT
74325 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TTAAAAATTTATTTAAATATGAATTAAAAA
Found at i:74329 original size:20 final size:20
Alignment explanation
Indices: 74310--74346 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
74300 AAATATTAAT
74310 TAAAA-ATAAAAAATTATAA
1 TAAAATATAAAAAATTATAA
*
74329 TAAAATATAAAAATTTAT
1 TAAAATATAAAAAATTAT
74347 CTAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATATAAAAAATTATAA
Found at i:75108 original size:45 final size:46
Alignment explanation
Indices: 74990--75108 Score: 118
Period size: 47 Copynumber: 2.5 Consensus size: 46
74980 TATAATTAAT
* * * *
74990 AATTAATAAAAATATATATTTAATTTAATAATATAATCTTTATTATAA
1 AATTAAAAAAAAT-TA-ATTTAATTTTATAATATAATATTTATTAAAA
75038 AATTAAAAAAAATTAATTTTAATTTTATAATA-AA-ATTT-TTAAAA
1 AATTAAAAAAAATTAA-TTTAATTTTATAATATAATATTTATTAAAA
* *
75082 AATATATAACAAATTTAATTTAATTTT
1 AAT-TA-AAAAAAATTAATTTAATTTT
75109 TAACCGATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
44 8 0.13
45 14 0.23
46 12 0.19
47 16 0.26
48 12 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (46 bp):
AATTAAAAAAAATTAATTTAATTTTATAATATAATATTTATTAAAA
Found at i:78104 original size:3 final size:3
Alignment explanation
Indices: 78083--78118 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
78073 AAGTGAGTGG
* *
78083 TTC TTC ATC TTC ATC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
78119 ATCATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:80897 original size:347 final size:348
Alignment explanation
Indices: 80251--80934 Score: 1210
Period size: 347 Copynumber: 2.0 Consensus size: 348
80241 ATATATTCAA
* *
80251 ATCAAATATATATTTTTATTCAATTTTTATCTTTAAATCTAAATAACGTAATAAAATACTTCTCA
1 ATCAAACATATATTTTTATTCAATTTTTATCTTTAAATCTAAATAACATAATAAAATACTTCTCA
* *
80316 CTGTAGTGTCCATGACAGTATTGACCAGTCTTTAATAACTATTCTTTGTTTTGAGCAGGCTCACT
66 C----GTGTCCATGACAATATTGAACAGTCTTTAATAACTATTCTTTGTTTTGAGCAGGCTCACT
80381 TTATTACTAACATCACAGTCCAAAATCATCCAAATTTGTCATCCCAATACTGTAAGGTATGTAAT
127 TTATTACTAACATCACAGTCCAAAATCATCCAAATTTGTCATCCCAATACTGTAAGGTATGTAAT
* *
80446 AAAAAATTGTCTAATGTATTCCCTTTATTTTGTTCATCTATAAATCCTCCATTCTGTAATGGATT
192 AAAAAATTATCTAATGTATTCCCTTTATTTTGTTCATCTATAAATCCTCCATTCTGTAATGAATT
80511 TTGAGTTTTATTTGCATTTATCACTCTGAAAATTTATTCATAAAGAATGAAATTTTCAAGG-AAA
257 TTGAGTTTTATTTGCATTTATCACTCTGAAAATTTATTCATAAAGAATGAAATTTTCAAGGAAAA
80575 AAAAAACACCTAATAAAATACTTCTAT
322 AAAAAACACCTAATAAAATACTTCTAT
*
80602 ATCAAACATATATTTTTATTCAATTTTTATCTTTAAATCTGAATAACATAATAAAATACTTCTCA
1 ATCAAACATATATTTTTATTCAATTTTTATCTTTAAATCTAAATAACATAATAAAATACTTCTCA
*
80667 C-TGTCCATGACAATATTGAACAGTTTTTAATCAACTATTCTTTGTTTTGAGCAGGCTCACTTTA
66 CGTGTCCATGACAATATTGAACAGTCTTTAAT-AACTATTCTTTGTTTTGAGCAGGCTCACTTTA
80731 TTACTAACATCACAGTCCAAAATCATCCAAATTTGTCATCCCAATACTGTAAGGTATGTAATAAA
130 TTACTAACATCACAGTCCAAAATCATCCAAATTTGTCATCCCAATACTGTAAGGTATGTAATAAA
* *
80796 AAATTATCTAATGTATTCCCTTTATTTTGTTCATCTATAAATCCTCCCTTCTGTCATGAATTTTG
195 AAATTATCTAATGTATTCCCTTTATTTTGTTCATCTATAAATCCTCCATTCTGTAATGAATTTTG
*
80861 AGTTTTATTTGCATTTATCACTTTGAAAATTTATTCATAAAGAATGAAATTTTCAAGGAAAAAAA
260 AGTTTTATTTGCATTTATCACTCTGAAAATTTATTCATAAAGAATGAAATTTTCAAGGAAAAAAA
80926 AAACACCTA
325 AAACACCTA
80935 TCATTTTGAG
Statistics
Matches: 320, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
346 27 0.08
347 215 0.67
348 15 0.05
351 63 0.20
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (348 bp):
ATCAAACATATATTTTTATTCAATTTTTATCTTTAAATCTAAATAACATAATAAAATACTTCTCA
CGTGTCCATGACAATATTGAACAGTCTTTAATAACTATTCTTTGTTTTGAGCAGGCTCACTTTAT
TACTAACATCACAGTCCAAAATCATCCAAATTTGTCATCCCAATACTGTAAGGTATGTAATAAAA
AATTATCTAATGTATTCCCTTTATTTTGTTCATCTATAAATCCTCCATTCTGTAATGAATTTTGA
GTTTTATTTGCATTTATCACTCTGAAAATTTATTCATAAAGAATGAAATTTTCAAGGAAAAAAAA
AACACCTAATAAAATACTTCTAT
Found at i:83421 original size:31 final size:31
Alignment explanation
Indices: 83355--83424 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
83345 AGCTTGTGTT
* *
83355 GAAACAAAGACACTTCTCAACAACTTGAGCT
1 GAAACAAAGACACTTCTCAACAACTTGAACC
*
83386 GAAACAAAGACACTTCTCAACAA-TTTATACC
1 GAAACAAAGACACTTCTCAACAACTTGA-ACC
83417 GAAACAAA
1 GAAACAAA
83425 TAGCTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.19
Consensus pattern (31 bp):
GAAACAAAGACACTTCTCAACAACTTGAACC
Found at i:88682 original size:108 final size:109
Alignment explanation
Indices: 88493--88708 Score: 335
Period size: 108 Copynumber: 2.0 Consensus size: 109
88483 AGAAACACTT
* * *
88493 CAAATTAGGAAAAATTCAAGCAACATTCTCAAAGTTTGTCTTCTTGATTCATTATTATACCACCT
1 CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
* * **
88558 AGATTATACAACAACAACTAAAGGAAA-CTTAGTTACAATTCTG
66 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCTG
* * *
88601 CAAATTAGGAAATATTAAAGCAATATTCTCAAAGTTTTTCTCCTTGATTCATTATCATACCACCT
1 CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
88666 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCT
66 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCT
88709 TTTTTCCCCT
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 84 0.87
109 13 0.13
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (109 bp):
CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCTG
Found at i:90540 original size:3 final size:3
Alignment explanation
Indices: 90532--90559 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
90522 AGCTTGATGC
90532 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
90560 CTCCTTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:92326 original size:22 final size:22
Alignment explanation
Indices: 92296--92338 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
92286 AAAAATTATT
*
92296 TTATTTAAAT-TTAATTATAAAA
1 TTATATAAATATTAATT-TAAAA
92318 TTATATAAATATTAATTTAAA
1 TTATATAAATATTAATTTAAA
92339 TATAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATATAAATATTAATTTAAAA
Found at i:92346 original size:23 final size:22
Alignment explanation
Indices: 92301--92346 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
92291 TTATTTTATT
*
92301 TAAATTTAATTATAAAATTATA
1 TAAATTTAATTATAAAATAATA
92323 TAAATATTAATT-TAAATATAATA
1 TAAAT-TTAATTATAAA-ATAATA
92346 T
1 T
92347 TTTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATTTAATTATAAAATAATA
Found at i:92625 original size:9 final size:9
Alignment explanation
Indices: 92611--92636 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
92601 AAACTTTGTT
92611 TTTTTTTTC
1 TTTTTTTTC
92620 TTTTTTTTC
1 TTTTTTTTC
92629 TTTTTTTT
1 TTTTTTTT
92637 TTAAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:93985 original size:27 final size:27
Alignment explanation
Indices: 93938--94070 Score: 123
Period size: 27 Copynumber: 5.0 Consensus size: 27
93928 GTGTGGTGGA
93938 TGTCTAAACAATAA-AAGTTATTTTTTATT
1 TGTC-AAA-AATAATAA-TTATTTTTTATT
* *
93967 TGTTAAAAATAATAATTATTTTATATT
1 TGTCAAAAATAATAATTATTTTTTATT
* *
93994 TATAAAAAATAATAATT-TTTTTTATT
1 TGTCAAAAATAATAATTATTTTTTATT
* *
94020 TGTCAAAAATGATGA-TA--TTTTATT
1 TGTCAAAAATAATAATTATTTTTTATT
* * *
94044 TGTCAAAATTTATAATTAATTTTTATT
1 TGTCAAAAATAATAATTATTTTTTATT
94071 ACAAAATGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
24 19 0.22
25 3 0.03
26 19 0.22
27 38 0.44
28 5 0.06
29 3 0.03
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (27 bp):
TGTCAAAAATAATAATTATTTTTTATT
Found at i:98523 original size:27 final size:26
Alignment explanation
Indices: 98492--98559 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 26
98482 AGCCACCATT
98492 TGTTTGTCAAAAATGGTAGTTACTTTG
1 TGTTTGTCAAAAATGGTAGTT-CTTTG
* * *
98519 TGTTTGTCAAAAATGGTGGTTTTTTT
1 TGTTTGTCAAAAATGGTAGTTCTTTG
*
98545 TATTTGTCAAAAATG
1 TGTTTGTCAAAAATG
98560 ATGGCATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 17 0.46
27 20 0.54
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (26 bp):
TGTTTGTCAAAAATGGTAGTTCTTTG
Found at i:99040 original size:103 final size:104
Alignment explanation
Indices: 98866--99081 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 104
98856 CAAGAATCAT
98866 CAAATTTCACTTGTAACAAGTGAATAAACTTAATAAAGAAGCATAGTATTTTAACAAAATCTTGA
1 CAAATTTCACTTGTAACAAGTGAATAAACTTAAT--AGAAGCATAGTATTTTAACAAAATCTTGA
98931 AAAAAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
64 AAAAAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
*
98972 CAAATTTCACTTGTAACAAGTGAATAAACTTAAT-GAAGCATGGTATTTTAACAAAATCTTGAAA
1 CAAATTTCACTTGTAACAAGTGAATAAACTTAATAGAAGCATAGTATTTTAACAAAATCTTGAAA
99036 AAAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
66 AAAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
99075 C-AATTTC
1 CAAATTTC
99082 TTACAGTAAA
Statistics
Matches: 109, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
102 6 0.06
103 69 0.63
106 34 0.31
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (104 bp):
CAAATTTCACTTGTAACAAGTGAATAAACTTAATAGAAGCATAGTATTTTAACAAAATCTTGAAA
AAAACATTGAAGCCTTGATTGATTTTTTACAAAATTTGG
Found at i:103402 original size:13 final size:13
Alignment explanation
Indices: 103384--103409 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
103374 TGAACCAAAT
103384 TGTATTCACCATA
1 TGTATTCACCATA
103397 TGTATTCACCATA
1 TGTATTCACCATA
103410 GAATCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
TGTATTCACCATA
Found at i:106838 original size:2 final size:2
Alignment explanation
Indices: 106831--106859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
106821 TTTTCCCCCA
106831 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
106860 TTTTCCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:109688 original size:2 final size:2
Alignment explanation
Indices: 109683--109728 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
109673 GTGTACATAC
* *
109683 AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109725 AT AT
1 AT AT
109729 TTGAAAACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:109697 original size:18 final size:18
Alignment explanation
Indices: 109676--109728 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
109666 TATGTGTGTG
109676 TACATACATATATATATA
1 TACATACATATATATATA
109694 TACATACATATATATATA
1 TACATACATATATATATA
* *
109712 TATATATATATATATAT
1 TACATACATATATATAT
109729 TTGAAAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (18 bp):
TACATACATATATATATA
Found at i:110973 original size:20 final size:20
Alignment explanation
Indices: 110948--111022 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
110938 TGCTTTTTTC
*
110948 AATAAAAATGAAAAGCAAAA
1 AATAAAAATAAAAAGCAAAA
**
110968 AAT-AAAATAAAAAAGCTGAA
1 AATAAAAAT-AAAAAGCAAAA
110988 AATAAAGAA-AAAATAGCAAAA
1 AATAAA-AATAAAA-AGCAAAA
*
111009 TATAAAAATAAAAA
1 AATAAAAATAAAAA
111023 CACCAAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 5 0.11
20 21 0.48
21 16 0.36
22 2 0.05
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (20 bp):
AATAAAAATAAAAAGCAAAA
Found at i:111773 original size:2 final size:2
Alignment explanation
Indices: 111761--111804 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
111751 AAATGGATAG
*
111761 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
111803 GA
1 GA
111805 AGGCATATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:112005 original size:14 final size:14
Alignment explanation
Indices: 111982--112021 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
111972 AATCATTGTT
*
111982 AAAATATTAAAATA
1 AAAATTTTAAAATA
111996 AAAATTTTAAAATA
1 AAAATTTTAAAATA
* *
112010 GAAGTTTTAAAA
1 AAAATTTTAAAA
112022 ATTTAGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAATTTTAAAATA
Found at i:112146 original size:20 final size:19
Alignment explanation
Indices: 112098--112148 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
112088 TTAAAATATT
*
112098 TTTAAATAAAAATAATAAA
1 TTTAAAAAAAAATAATAAA
* *
112117 TTATATAAAAAAATAATCATA
1 TT-TAAAAAAAAATAAT-AAA
112138 TTTAAAAAAAA
1 TTTAAAAAAAA
112149 GAAAGTACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTTAAAAAAAAATAATAAA
Found at i:112348 original size:30 final size:30
Alignment explanation
Indices: 112314--112382 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
112304 TTTATTTATT
112314 TTAAAAATTTATTTAAATATGAATTAAAAA
1 TTAAAAATTTATTTAAATATGAATTAAAAA
* *
112344 TTAAAAATATATTTAAATATTAATTAAAAA
1 TTAAAAATTTATTTAAATATGAATTAAAAA
*
112374 TAAAAAATT
1 TTAAAAATT
112383 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TTAAAAATTTATTTAAATATGAATTAAAAA
Found at i:112387 original size:20 final size:20
Alignment explanation
Indices: 112368--112404 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
112358 AAATATTAAT
112368 TAAAA-ATAAAAAATTATAA
1 TAAAATATAAAAAATTATAA
*
112387 TAAAATATAAAAATTTAT
1 TAAAATATAAAAAATTAT
112405 CTAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATATAAAAAATTATAA
Found at i:113169 original size:46 final size:46
Alignment explanation
Indices: 113050--113169 Score: 118
Period size: 47 Copynumber: 2.5 Consensus size: 46
113040 TATAATTAAT
* * ** *
113050 AATTAATAAAAATATATATTTAATTTAATAATATAATCTTTATTATAA
1 AATTAAAAAAAAT-TA-ATTTAATTTTATAATATAAAATTTATTAAAA
113098 AATTAAAAAAAATTAATTTTAATTTTATAATA-AAAATTT-TTAAAA
1 AATTAAAAAAAATTAA-TTTAATTTTATAATATAAAATTTATTAAAA
* *
113143 AATATATAACAAATTTAATTTAATTTT
1 AAT-TA-AAAAAAATTAATTTAATTTT
113170 TAACCGATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
45 8 0.13
46 17 0.27
47 25 0.40
48 12 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (46 bp):
AATTAAAAAAAATTAATTTAATTTTATAATATAAAATTTATTAAAA
Found at i:121116 original size:31 final size:31
Alignment explanation
Indices: 121050--121119 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
121040 AGCTTGTGTT
* *
121050 GAAACAAAGACACTTCTCAACAACTTGAGCT
1 GAAACAAAGACACTTCTCAACAACTTGAACC
*
121081 GAAACAAAGACACTTCTCAACAA-TTTATACC
1 GAAACAAAGACACTTCTCAACAACTTGA-ACC
121112 GAAACAAA
1 GAAACAAA
121120 TAGCTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.19
Consensus pattern (31 bp):
GAAACAAAGACACTTCTCAACAACTTGAACC
Found at i:126374 original size:109 final size:109
Alignment explanation
Indices: 126183--126399 Score: 335
Period size: 109 Copynumber: 2.0 Consensus size: 109
126173 AGAAACACTT
* * *
126183 CAAATTAGGAAAAATTCAAGCAACATTCTCAAAGTTTGTCTTCTTGATTCATTATTATACCACCT
1 CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
* * ** *
126248 AGATTATACAACAACAACTAAAGGAAACTTAGGTTACAATTCTG
66 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCTG
* * *
126292 CAAATTAGGAAATATTAAAGCAATATTCTCAAAGTTTTTCTCCTTGATTCATTATCATACCACCT
1 CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
126357 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCT
66 AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCT
126400 TTTTTCCCCT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 97 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (109 bp):
CAAATTAGGAAAAATTAAAGCAACATTCTCAAAGTTTGTCTCCTTGATTCATTATCATACCACCT
AGATCATACAACAACAACTAAAGAAAACCCAAGTTACAATTCTG
Done.