Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 91 of 125
Found at i:27665742 original size:15 final size:15
Alignment explanation
Indices: 27665714--27665744 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
27665704 TTTATCTTAA
27665714 ATAATAAATATTTTT
1 ATAATAAATATTTTT
27665729 ATAA-AAATATTTTT
1 ATAATAAATATTTTT
27665743 AT
1 AT
27665745 CTTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATAAATATTTTT
Found at i:27674249 original size:27 final size:27
Alignment explanation
Indices: 27674213--27674269 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
27674203 AAATACCTGA
*
27674213 CACCAGTGGAGGAACACCAAGTGACGG
1 CACCAATGGAGGAACACCAAGTGACGG
* * *
27674240 CACCAATGGAGGAATATCAAGTGGCGG
1 CACCAATGGAGGAACACCAAGTGACGG
27674267 CAC
1 CAC
27674270 TAAGGGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.32, T:0.11
Consensus pattern (27 bp):
CACCAATGGAGGAACACCAAGTGACGG
Found at i:27674447 original size:4 final size:4
Alignment explanation
Indices: 27674438--27674475 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
27674428 AAATAAACGG
*
27674438 GAAA GAAA GAGAG GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
27674476 GTAATGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:27677687 original size:21 final size:20
Alignment explanation
Indices: 27677659--27677698 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
27677649 GTCTAATTGC
*
27677659 CCCGGAGGAGTAGAGTATTA
1 CCCGGAGGAGTAAAGTATTA
27677679 CCCGAGAGGAGTAAAGTATT
1 CCCG-GAGGAGTAAAGTATT
27677699 GCGGTGGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.20
Consensus pattern (20 bp):
CCCGGAGGAGTAAAGTATTA
Found at i:27679651 original size:30 final size:30
Alignment explanation
Indices: 27679551--27679652 Score: 73
Period size: 30 Copynumber: 3.4 Consensus size: 30
27679541 TAAATACAAA
*
27679551 AAATATGTTATTTACTAAAATTGTACAAAAT
1 AAATAT-TTATTTACTAAAATAGTACAAAAT
* * * * * *
27679582 ATATTTTTATATACCAAAATAGTATCCACA-
1 AAATATTTATTTACTAAAATAGTA-CAAAAT
* ** *
27679612 CACCA-TTATTTACTAAAATGGTACAAAAT
1 AAATATTTATTTACTAAAATAGTACAAAAT
27679641 AAATATTTATTT
1 AAATATTTATTT
27679653 TGTACCATTT
Statistics
Matches: 48, Mismatches: 20, Indels: 7
0.64 0.27 0.09
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 21 0.44
31 7 0.15
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (30 bp):
AAATATTTATTTACTAAAATAGTACAAAAT
Found at i:27680087 original size:20 final size:21
Alignment explanation
Indices: 27680062--27680104 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
27680052 TTACTACTAC
27680062 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
27680082 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
27680103 TA
1 TA
27680105 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:27680113 original size:94 final size:95
Alignment explanation
Indices: 27679923--27680101 Score: 279
Period size: 95 Copynumber: 1.9 Consensus size: 95
27679913 TACATTATTT
*
27679923 TTTTAAATTAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
***** *
27679988 TACTAACTAATTTTTTTAAACATTATTAAA
66 TACTAACTAACAAAATTAAACATTAGTAAA
27680018 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTAC-TACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
*
27680082 TACTAACTAGCAAAATTAAA
66 TACTAACTAACAAAATTAAA
27680102 TTAAAGTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 34 0.44
95 43 0.56
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (95 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
TACTAACTAACAAAATTAAACATTAGTAAA
Found at i:27680489 original size:4 final size:4
Alignment explanation
Indices: 27680461--27680529 Score: 67
Period size: 4 Copynumber: 18.2 Consensus size: 4
27680451 TCCTTCTTCC
* *
27680461 CTTT CTTCT CCTT C-TT CCTT C-TT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTT-T CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
*
27680508 CTCT C-TT -TTT CTTT CTTT -TTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
27680530 CCTCAATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
3 12 0.21
4 41 0.73
5 3 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:27680539 original size:22 final size:22
Alignment explanation
Indices: 27680493--27680540 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
27680483 TCTTTCTTTC
* *
27680493 TTTCTTTCTTTCTTTCTCTCTT
1 TTTCTTTCTTTCTTTCCCTCAT
27680515 TTTCTTTCTTT-TTTCCCTCAAT
1 TTTCTTTCTTTCTTTCCCTC-AT
27680537 TTTC
1 TTTC
27680541 GTTGGTCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTCTTTCTTTCCCTCAT
Found at i:27680736 original size:27 final size:27
Alignment explanation
Indices: 27680706--27680765 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
27680696 AAAACACCCC
27680706 TTAGTGCCG-CAACTTGATATTCCTCCA
1 TTAGTGCCGTC-ACTTGATATTCCTCCA
* *
27680733 TTAGTGCCGTCACTTGATGTTTCTCCA
1 TTAGTGCCGTCACTTGATATTCCTCCA
*
27680760 CTAGTG
1 TTAGTG
27680766 TCAGATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (27 bp):
TTAGTGCCGTCACTTGATATTCCTCCA
Found at i:27680887 original size:11 final size:10
Alignment explanation
Indices: 27680867--27680892 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
27680857 TTAAATATAT
27680867 AAAAATAAAA
1 AAAAATAAAA
27680877 AAAAATAAAA
1 AAAAATAAAA
27680887 AAAAAT
1 AAAAAT
27680893 GTCAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:27683021 original size:26 final size:26
Alignment explanation
Indices: 27682992--27683047 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
27682982 TCTTCTGACC
*
27682992 AAAA-TAGAA-AATATATCAAAAAACTA
1 AAAAGTAGAATAATAAAT-AAAAAA-TA
*
27683018 AAAAGTATAATAATAAATAAAAAATA
1 AAAAGTAGAATAATAAATAAAAAATA
27683044 AAAA
1 AAAA
27683048 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 10 0.38
28 6 0.23
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAAGTAGAATAATAAATAAAAAATA
Found at i:27683036 original size:7 final size:7
Alignment explanation
Indices: 27683026--27683055 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
27683016 TAAAAAGTAT
*
27683026 AATAATA
1 AATAAAA
27683033 AATAAAA
1 AATAAAA
27683040 AATAAAA
1 AATAAAA
27683047 AATAAAA
1 AATAAAA
27683054 AA
1 AA
27683056 ATTACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AATAAAA
Found at i:27688030 original size:24 final size:25
Alignment explanation
Indices: 27688003--27688049 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27687993 TTTAATATGA
*
27688003 TTTT-AATAATACCCACTTAGATAC
1 TTTTAAATAAAACCCACTTAGATAC
27688027 TTTTAAATAAAACCCACTTAGAT
1 TTTTAAATAAAACCCACTTAGAT
27688050 CTCCACATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (25 bp):
TTTTAAATAAAACCCACTTAGATAC
Found at i:27688200 original size:51 final size:50
Alignment explanation
Indices: 27688135--27688239 Score: 140
Period size: 51 Copynumber: 2.1 Consensus size: 50
27688125 TATCTCTACC
* *
27688135 ATTATTTATTTATGTAATTTTGT-TTTTAGGTTATTCAGTTATCTATTTTTA
1 ATTATTTATCTATGTAATTTTGTATTTT-GGTTACTCAGTTATCTA-TTTTA
* * *
27688186 ATTATTTATCTATGTATTTTTGTATTTTGTTTACTCATTTATCTATTTTA
1 ATTATTTATCTATGTAATTTTGTATTTTGGTTACTCAGTTATCTATTTTA
27688236 ATTA
1 ATTA
27688240 CAAAATAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 9 0.19
51 35 0.73
52 4 0.08
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.63
Consensus pattern (50 bp):
ATTATTTATCTATGTAATTTTGTATTTTGGTTACTCAGTTATCTATTTTA
Found at i:27688448 original size:25 final size:25
Alignment explanation
Indices: 27688397--27688447 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
27688387 ACATATTATG
* *
27688397 AATTTATTAAATTATTTTTATGTAA
1 AATTAATTAAATTATTATTATGTAA
*
27688422 AATTAATT-AATTATTATTATTTAA
1 AATTAATTAAATTATTATTATGTAA
27688446 AA
1 AA
27688448 AGTTGCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTAATTAAATTATTATTATGTAA
Found at i:27693662 original size:62 final size:59
Alignment explanation
Indices: 27693555--27693673 Score: 166
Period size: 62 Copynumber: 2.0 Consensus size: 59
27693545 ATCATTTTAA
* * *
27693555 TATTAAATTAATATAATAATTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAAAATAATTATCAAAATAAATATTAAATTAAATTTAATATTAAATCT
* *
27693614 TATTAAATTAATAAAATATTTATCTATAAAATAAATATTAAATTAAATTTACTATTAAAT
1 TATTAAATTAATAAAATAATTATC---AAAATAAATATTAAATTAAATTTAATATTAAAT
27693674 TAATAAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 22 0.42
62 30 0.58
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (59 bp):
TATTAAATTAATAAAATAATTATCAAAATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:27693687 original size:19 final size:18
Alignment explanation
Indices: 27693614--27693690 Score: 56
Period size: 17 Copynumber: 4.3 Consensus size: 18
27693604 TATTAAATCT
27693614 TATTAAATTAATAAAATA-
1 TATTAAATT-ATAAAATAC
*
27693632 T-TT--ATCTATAAAATAAA
1 TATTAAAT-TATAAAAT-AC
**
27693649 TATTAAATTA-AATTTAC
1 TATTAAATTATAAAATAC
27693666 TATTAAATTAATAAAATAC
1 TATTAAATT-ATAAAATAC
27693685 TATTAA
1 TATTAA
27693691 GATAATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
15 9 0.20
16 2 0.04
17 13 0.28
18 7 0.15
19 13 0.28
20 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTAAATTATAAAATAC
Found at i:27693721 original size:48 final size:51
Alignment explanation
Indices: 27693614--27693711 Score: 139
Period size: 48 Copynumber: 2.0 Consensus size: 51
27693604 TATTAAATCT
*
27693614 TATTAAATTAATAAAATATTTATCTATAAAATAAATATTAAATTAAATTTAC
1 TATTAAATTAATAAAATATCTA-CTATAAAATAAATATTAAATTAAATTTAC
* *
27693666 TATTAAATTAATAAAATA-CTA-T-TAAGATAATTATTAAATTAAATTT
1 TATTAAATTAATAAAATATCTACTATAAAATAAATATTAAATTAAATTT
27693712 TTTTATAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 22 0.51
49 1 0.02
51 2 0.05
52 18 0.42
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (51 bp):
TATTAAATTAATAAAATATCTACTATAAAATAAATATTAAATTAAATTTAC
Found at i:27695729 original size:12 final size:12
Alignment explanation
Indices: 27695706--27695740 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
27695696 AAAACAATTA
27695706 TAAAATTATTTT
1 TAAAATTATTTT
* *
27695718 TTAAATTTTTTT
1 TAAAATTATTTT
27695730 TAAAATTATTT
1 TAAAATTATTT
27695741 AAAAAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAAAATTATTTT
Found at i:27695747 original size:24 final size:24
Alignment explanation
Indices: 27695706--27695757 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
27695696 AAAACAATTA
*** * *
27695706 TAAAATTATTTTTTAAATTTTTTT
1 TAAAATTATTTAAAAAATATTTCT
27695730 TAAAATTATTTAAAAAATATTTCT
1 TAAAATTATTTAAAAAATATTTCT
27695754 TAAA
1 TAAA
27695758 TCTTTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAAATTATTTAAAAAATATTTCT
Found at i:27697682 original size:2 final size:2
Alignment explanation
Indices: 27697670--27697715 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
27697660 GTCCCCCTAC
*
27697670 AT AT AT GT 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
27697712 AT AT
1 AT AT
27697716 GAATAGAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27702925 original size:22 final size:23
Alignment explanation
Indices: 27702876--27702927 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27702866 TGGGGACCAA
* *
27702876 AATTAAAATGTAATTTTTACGAT
1 AATTAAAATATAATTTTTACAAT
27702899 AATTAAAATATAATTTTTA-AAT
1 AATTAAAATATAATTTTTACAAT
*
27702921 GATTAAA
1 AATTAAA
27702928 TCAACATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (23 bp):
AATTAAAATATAATTTTTACAAT
Found at i:27705116 original size:28 final size:29
Alignment explanation
Indices: 27705085--27705144 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
27705075 AAATGGGACC
27705085 TTTGGATACC-CGAGGGTAAAATGGT-AAT
1 TTTGGA-ACCTCGAGGGTAAAATGGTAAAT
*
27705113 TTTGGACCCTCGAGGGTAAAATGGTAAAT
1 TTTGGAACCTCGAGGGTAAAATGGTAAAT
27705142 TTT
1 TTT
27705145 AGTGAAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 2 0.07
28 21 0.72
29 6 0.21
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.32
Consensus pattern (29 bp):
TTTGGAACCTCGAGGGTAAAATGGTAAAT
Found at i:27705205 original size:29 final size:27
Alignment explanation
Indices: 27705163--27705378 Score: 105
Period size: 29 Copynumber: 7.5 Consensus size: 27
27705153 CAGGGTTAAA
* * *
27705163 AAAATGGAATTTTGTAGAGTTTGGGGT
1 AAAATGGAATTTTGTAAAGATCGGGGT
*
27705190 AAAATGGTAATTTTTGGTAAA-ATCGAGGTT
1 AAAATGG-AA-TTTT-GTAAAGATCG-GGGT
* *
27705220 AAAAATGGAATTTTGGAAAGCTCGGGGGT
1 -AAAATGGAATTTTGTAAAGATC-GGGGT
* *
27705249 AAAATGGTAATTTTTGGTGAA-ATTGGGGTT
1 AAAATGG-AA-TTTT-GTAAAGATCGGGG-T
* * *
27705279 AAAATGGAATTTTGGAAAGCTCGGGAT
1 AAAATGGAATTTTGTAAAGATCGGGGT
* *
27705306 AAAATGGTAATTTTTGGTGAA-ATCGAGGTT
1 AAAATGG-AA-TTTT-GTAAAGATCG-GGGT
* * * *
27705336 AAAAATGGAATCTTGGAAAGTTCGGGGGC
1 -AAAATGGAATTTTGTAAAGATC-GGGGT
27705365 AAAATGGTAATTTT
1 AAAATGG-AATTTT
27705379 TGGTGAAATC
Statistics
Matches: 142, Mismatches: 27, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
27 18 0.13
28 33 0.23
29 42 0.30
30 32 0.23
31 17 0.12
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (27 bp):
AAAATGGAATTTTGTAAAGATCGGGGT
Found at i:27705283 original size:58 final size:59
Alignment explanation
Indices: 27705102--27705407 Score: 372
Period size: 58 Copynumber: 5.2 Consensus size: 59
27705092 ACCCGAGGGT
** * * *
27705102 AAAATGGTAATTTTGG-ACCCTCGAGGGTAAAATGGTAAATTTTAGTGAAATC-AGGGTTAAA
1 AAAATGG-AATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTT--A
* * ** *
27705163 AAAATGGAATTTTGTAGAG-TTTGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTA
1 AAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTA
* *
27705221 AAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT-
1 AAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTA
*
27705279 AAAATGGAATTTTGGAAAGCTC-GGGATAAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTA
* * * *
27705337 AAAATGGAATCTTGGAAAGTTCGGGGGCAAAATGGTAATTTTTGGTGAAATCGAGATT-
1 AAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTA
*
27705395 AAAATGTAATTTT
1 AAAATGGAATTTT
27705408 CTAAAATTTT
Statistics
Matches: 213, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
57 32 0.15
58 71 0.33
59 65 0.31
60 37 0.17
61 8 0.04
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTA
Found at i:27705440 original size:59 final size:59
Alignment explanation
Indices: 27705162--27705398 Score: 228
Period size: 59 Copynumber: 4.1 Consensus size: 59
27705152 TCAGGGTTAA
* * * * * * * *
27705162 AAAAATGGAATTTTGTAGAGTT-TGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTT
1 AAAAATGGAATCTTGAAAAGTTCGGGGGCAAAATGGCAATTTTTGGTGAAATCGAGATT
* * * * * * * *
27705220 AAAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
1 AAAAATGGAATCTTGAAAAGTTCGGGGGCAAAATGGCAATTTTTGGTGAAATCGAGATT
* * * ** * *
27705279 -AAAATGGAATTTTGGAAAGCTC-GGGATAAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAAATGGAATCTTGAAAAGTTCGGGGGCAAAATGGCAATTTTTGGTGAAATCGAGATT
* *
27705336 AAAAATGGAATCTTGGAAAGTTCGGGGGCAAAATGGTAATTTTTGGTGAAATCGAGATT
1 AAAAATGGAATCTTGAAAAGTTCGGGGGCAAAATGGCAATTTTTGGTGAAATCGAGATT
27705395 AAAA
1 AAAA
27705399 TGTAATTTTC
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
57 32 0.20
58 61 0.38
59 68 0.42
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAAATGGAATCTTGAAAAGTTCGGGGGCAAAATGGCAATTTTTGGTGAAATCGAGATT
Found at i:27706532 original size:21 final size:20
Alignment explanation
Indices: 27706483--27706533 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
27706473 TTTTTATAAC
27706483 ATTATTATTATAAAACATTT
1 ATTATTATTATAAAACATTT
* * *
27706503 AATACTATTATCAGAACATTT
1 ATTATTATTAT-AAAACATTT
27706524 ATTATTATTA
1 ATTATTATTA
27706534 ATGTTTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTATTATTATAAAACATTT
Found at i:27707276 original size:31 final size:30
Alignment explanation
Indices: 27707256--27707330 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
27707246 TTAGTATGTT
*
27707256 AATTTTAAT-TTAAATTTAAATTTAAGGTA
1 AATTTAAATATTAAATTTAAATTTAAGGTA
*
27707285 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAAT-ATTAAATTTAAATTTAAGGTA
27707316 AATTTAAAT-TTAAAT
1 AATTTAAATATTAAAT
27707331 CAATTTAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 14 0.33
31 28 0.67
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (30 bp):
AATTTAAATATTAAATTTAAATTTAAGGTA
Found at i:27707279 original size:6 final size:6
Alignment explanation
Indices: 27707256--27707330 Score: 75
Period size: 6 Copynumber: 12.5 Consensus size: 6
27707246 TTAGTATGTT
* **
27707256 AATTTT AATTTA AATTTA AATTT- AAGGTA AATTTA AATAATTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT--TTA AATTTA
27707305 AATTTA AGA--TA AATTTA AATTTA AAT
1 AATTTA A-ATTTA AATTTA AATTTA AAT
27707331 CAATTTAACT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
4 1 0.02
5 6 0.10
6 44 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:27707279 original size:17 final size:17
Alignment explanation
Indices: 27707254--27707328 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
27707244 ATTTAGTATG
* *
27707254 TTAATTTTAATTTAAAT
1 TTAAATTTAAGTTAAAT
*
27707271 TTAAATTTAAGGTAAAT
1 TTAAATTTAAGTTAAAT
27707288 TTAAA--TAA-TTAAAT
1 TTAAATTTAAGTTAAAT
*
27707302 TTAAATTTAAGATAAAT
1 TTAAATTTAAGTTAAAT
27707319 TTAAATTTAA
1 TTAAATTTAA
27707329 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 3 0.06
17 34 0.68
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAGTTAAAT
Found at i:27707345 original size:16 final size:16
Alignment explanation
Indices: 27707299--27707346 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
27707289 TAAATAATTA
* *
27707299 AATTTAAATTTAAGATA
1 AATTTAAATCTAA-ATC
*
27707316 AATTTAAATTTAAATC
1 AATTTAAATCTAAATC
*
27707332 AATTTAACTCTAAAT
1 AATTTAAATCTAAAT
27707347 TAAAACAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTAAATCTAAATC
Found at i:27707668 original size:38 final size:37
Alignment explanation
Indices: 27707617--27708503 Score: 308
Period size: 38 Copynumber: 23.5 Consensus size: 37
27707607 GCTTCCTCTT
* *
27707617 GCTCTTATTTCAATTTCAGAGATAAAGGCTTGATCCCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGAT--CCA
** **
27707656 GCT-TTACTTCAATTTCAAGAGATAAAGAAATGATCTT
1 GCTCTTACTTCAATTTC-AGAGATAAAGACTTGATCCA
27707693 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTG--ATCCA
* ** * **
27707732 ACTC-TACTTCAATTTCAAGAGGATAGGGA-ATGATCTT
1 GCTCTTACTTCAATTTC-AGA-GATAAAGACTTGATCCA
27707769 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTG--ATCCA
* * *
27707808 ACTC-TACTTCGATTTCAAGAGATAGGAATGATCTT-ACTCTTA
1 GCTCTTACTTCAATTTC-AGAGATA--AA-GA-CTTGA-TC-CA
*
27707850 -CTCTTACTT-ATTCATTTTAGAGATAAAGACTTGATATCCA
1 GCTCTTACTTCA---ATTTCAGAGATAAAGACTTG--ATCCA
* * * **
27707890 ACTCTT-CTTCAATTTCAAGAGGAT-AGGTA-ATGATCTT
1 GCTCTTACTTCAATTTC-AGA-GATAAAG-ACTTGATCCA
27707927 GCTCTTACTTCTTTCAATTTCAGAGATAAAGACTTGATATCCA
1 GCTCTTA---C-TTCAATTTCAGAGATAAAGACTTG--ATCCA
* * ** **
27707970 ACTC-TACTTCAATTTCAAGAGGAT-AGGAAATGATCTT
1 GCTCTTACTTCAATTTC-AGA-GATAAAGACTTGATCCA
27708007 GCTCTT--TTCAATTCATCAGAGATAAAGACTTGATATCCA
1 GCTCTTACTTCAATT--TCAGAGATAAAGACTTG--ATCCA
* *** * *
27708046 GCTC-AACTTCAATTTCA-AGCGGATGAC--G-T-TA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATCCA
* *
27708077 -CTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGAC-T-TGATCCA
* * * *** **
27708115 ACTC-TACTTCAATTTCAAGCGGAT-AGGAAAAGATCTT
1 GCTCTTACTTCAATTTC-AG-AGATAAAGACTTGATCCA
27708152 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTG--ATCCA
* * * **
27708191 ACTCTT-CTTCAATTTCAAGAGGAT-AGGTA-ATGATCTT
1 GCTCTTACTTCAATTTC-AGA-GATAAAG-ACTTGATCCA
27708228 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTG--ATCCA
*** * *
27708267 GCTC-TACTTCAATTTCA-AGCGGATGAC--G-T--T
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATCCA
*
27708297 GCTCTTACTTCAATTTCAAAGATAAAGA-TGTGTTATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACT-TG--ATCCA
* * * *** **
27708336 ACTC-TACTTCAATTTCAAGCGGAT-AGGAAAAGATCTT
1 GCTCTTACTTCAATTTC-AG-AGATAAAGACTTGATCCA
*
27708373 GCTCTTACTTCAGTTT-AGAGATAAAGACTTGATATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTG--ATCCA
* * ** * *
27708411 ACTC-TACTTCAATTTCAAGAGGACAGGGA-ATGA-CCTT
1 GCTCTTACTTCAATTTC-AGA-GATAAAGACTTGATCC-A
*
27708448 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
1 GCTCTTACTTCAATTTCAGAGATAAAGAC-T-TGATCCA
* *
27708487 ACTC-TACTTCAGTTTCA
1 GCTCTTACTTCAATTTCA
27708504 AGAGGATAGG
Statistics
Matches: 617, Mismatches: 134, Indels: 195
0.65 0.14 0.21
Matches are distributed among these distances:
30 7 0.01
31 25 0.04
32 13 0.02
34 1 0.00
35 5 0.01
36 36 0.06
37 114 0.18
38 188 0.30
39 115 0.19
40 48 0.08
41 25 0.04
42 20 0.03
43 16 0.03
44 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (37 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACTTGATCCA
Found at i:27707740 original size:76 final size:76
Alignment explanation
Indices: 27707613--27708526 Score: 1159
Period size: 76 Copynumber: 12.1 Consensus size: 76
27707603 CGAGGCTTCC
* * ** * *
27707613 TCTTGCTCTTATTTCAATTTCAGAGATAAAGGCTTGATCCCCAGCTTTACTTCAATTTCAAGA-G
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
27707677 ATAAAGAAATGA
66 AT-AGGAAATGA
*
27707689 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
27707754 ATAGGGAATGA
66 ATAGGAAATGA
* *
27707765 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCGATTTCAAGA-G
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
27707829 ATAGG-AATGA
66 ATAGGAAATGA
* * *
27707839 TCTTACTCTTACTCTTACTTATTCATTTTAGAGATAAAGACTTGATATCCAACTCTTCTTCAATT
1 TCTTGCTCTTA--CTT-C--A---ATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATT
*
27707904 TCAAGAGGATAGGTAATGA
58 TCAAGAGGATAGGAAATGA
27707923 TCTTGCTCTTACTTCTTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
1 TCTTGCTCTTA---C-TTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
27707988 GAGGATAGGAAATGA
62 GAGGATAGGAAATGA
* * *
27708003 TCTTGCTCTT--TTCAATTCATCAGAGATAAAGACTTGATATCCAGCTCAACTTCAATTTCAAGC
1 TCTTGCTCTTACTTCAATT--TCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGA
*
27708066 GGAT--G--ACG-
64 GGATAGGAAATGA
* * * * *
27708074 --TTACTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
27708137 ATAGGAAAAGA
66 ATAGGAAATGA
*
27708148 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTTCTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
27708213 ATAGGTAATGA
66 ATAGGAAATGA
* *
27708224 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTCTACTTCAATTTCAAGCGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
27708289 AT--G--ACG-
66 ATAGGAAATGA
* * *
27708295 --TTGCTCTTACTTCAATTTCAAAGATAAAGA-TGTGTTATCCAACTCTACTTCAATTTCAAGCG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACT-TGATATCCAACTCTACTTCAATTTCAAGAG
*
27708357 GATAGGAAAAGA
65 GATAGGAAATGA
*
27708369 TCTTGCTCTTACTTCAGTTT-AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
* *
27708433 ACAGGGAATGA
66 ATAGGAAATGA
* * * *
27708444 CCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
*
27708509 ATAGGGAATGA
66 ATAGGAAATGA
27708520 TCTTGCT
1 TCTTGCT
27708527 GCGGTTTGAT
Statistics
Matches: 743, Mismatches: 61, Indels: 68
0.85 0.07 0.08
Matches are distributed among these distances:
68 1 0.00
69 110 0.15
71 9 0.01
72 4 0.01
73 4 0.01
74 24 0.03
75 71 0.10
76 378 0.51
77 4 0.01
79 1 0.00
80 67 0.09
82 43 0.06
83 7 0.01
84 15 0.02
85 3 0.00
86 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (76 bp):
TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
ATAGGAAATGA
Found at i:27708202 original size:145 final size:147
Alignment explanation
Indices: 27707615--27708520 Score: 1023
Period size: 145 Copynumber: 6.0 Consensus size: 147
27707605 AGGCTTCCTC
* * ** * * *
27707615 TTGCTCTTATTTCAATTTCAGAGATAAAGGCTTGATCCCCAGCTTTACTTCAATTTCAAGAGATA
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGAT-
* *
27707680 AAGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAAT
65 AGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAAT
27707745 TTCAAGAGGATAGGGAATGA
130 TTCAAGAGGAT--GGAATGA
* * *
27707765 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCGATTTCAAGAGA
1 --TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGA
* *
27707830 TAGG-AATGATCTTACTCTTACTCTTACTTATTCATTTTAGAGATAAAGACTTGATATCCAACTC
64 TAGGAAATGATCTTGCTCTTA--CTT-C--A---ATTTCAGAGATAAAGACTTGATATCCAACTC
*
27707894 TTCTTCAATTTCAAGAGGATAGGTAATGA
121 TACTTCAATTTCAAGAGGAT-GG-AATGA
27707923 TCTTGCTCTTACTTCTTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
1 --TTGCTCTTA---C-TTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
* *
27707988 GAGGATAGGAAATGATCTTGCTCTT--TTCAATTCATCAGAGATAAAGACTTGATATCCAGCTCA
60 G-GGATAGGAAATGATCTTGCTCTTACTTCAATT--TCAGAGATAAAGACTTGATATCCAACTCT
* *
27708051 ACTTCAATTTCAAGCGGAT-G-ACG-
122 ACTTCAATTTCAAGAGGATGGAATGA
* * * *
27708074 TTACTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAG-GGAT
* *
27708139 AGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTTCTTCAAT
65 AGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAAT
27708204 TTCAAGAGGATAGGTAATGA
130 TTCAAGAGGAT-GG-AATGA
*
27708224 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTCTACTTCAATTTCAA--G-
1 --TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGA
* * *
27708286 -CGG--ATGA-CGTTGCTCTTACTTCAATTTCAAAGATAAAGA-TGTGTTATCCAACTCTACTTC
64 TAGGAAATGATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACT-TGATATCCAACTCTACTTC
* *
27708346 AATTTCAAGCGGATAGGAAAAGA
127 AATTTCAAGAGGAT-GG-AATGA
*
27708369 TCTTGCTCTTACTTCAGTTT-AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
1 --TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAG-GG
* * * * *
27708433 ACAGGGAATGACCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCA
63 ATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCA
*
27708498 GTTTCAAGAGGATAGGGAATGA
128 ATTTCAAGAGGAT--GGAATGA
27708520 T
1 T
27708521 CTTGCTGCGG
Statistics
Matches: 659, Mismatches: 57, Indels: 79
0.83 0.07 0.10
Matches are distributed among these distances:
144 41 0.06
145 201 0.31
146 1 0.00
147 11 0.02
149 14 0.02
150 15 0.02
151 70 0.11
152 118 0.18
153 1 0.00
154 4 0.01
155 1 0.00
156 43 0.07
157 3 0.00
158 64 0.10
159 1 0.00
160 2 0.00
161 1 0.00
162 48 0.07
163 6 0.01
164 14 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (147 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGATA
GGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATT
TCAAGAGGATGGAATGA
Found at i:27708250 original size:221 final size:221
Alignment explanation
Indices: 27707856--27708510 Score: 1023
Period size: 221 Copynumber: 3.0 Consensus size: 221
27707846 CTTACTCTTA
* * * * *
27707856 CTTA-TTC-ATTTTAGAGATAAAGACTTGATATCCAACTCTTCTTCAATTTCAAGAGGATAGGTA
1 CTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAA
*
27707919 ATGATCTTGCTCTTACTTCTTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATT
66 AAGATCTTGCTCTTA---C-TTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATT
27707984 TCAAGAGGATAGGAAATGATCTTGCTCTT--TTCAATTCATCAGAGATAAAGACTTGATATCCAG
127 TCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATT--TCAGAGATAAAGACTTGATATCCAG
*
27708047 CTCAACTTCAATTTCAAGCGGATGACGTTACT
190 CTCTACTTCAATTTCAAGCGGATGACGTTACT
27708079 CTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAA
1 CTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAA
*
27708144 AAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTTCTTCAATTTCAA
66 AAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
*
27708209 GAGGATAGGTAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTCTAC
131 GAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTCTAC
*
27708274 TTCAATTTCAAGCGGATGACGTTGCT
196 TTCAATTTCAAGCGGATGACGTTACT
* * *
27708300 CTTACTTCAATTTCAAAGATAAAGATGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAA
1 CTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAA
*
27708365 AAGATCTTGCTCTTACTTCAGTTT-AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
66 AAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
* * * * * *
27708429 GAGGACAGGGAATGACCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTAC
131 GAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTCTAC
* *
27708494 TTCAGTTTCAAGAGGAT
196 TTCAATTTCAAGCGGAT
27708511 AGGGAATGAT
Statistics
Matches: 405, Mismatches: 23, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
220 113 0.28
221 212 0.52
222 1 0.00
223 11 0.03
224 3 0.01
225 65 0.16
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (221 bp):
CTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAA
AAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA
GAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTCTAC
TTCAATTTCAAGCGGATGACGTTACT
Found at i:27720825 original size:29 final size:28
Alignment explanation
Indices: 27720792--27720895 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
27720782 TAAATTGGTT
*
27720792 TAAAATTGAAATTTTGGAAAGCTCGGGGG
1 TAAAATGGAAATTTTGGAAAG-TCGGGGG
* * *
27720821 TAAAATGGTAATTTTTGGTGAAA-TCGAGGT
1 TAAAATGG-AAATTTT-G-GAAAGTCGGGGG
*
27720851 TAAAAATGG-AATCTTGGAAAGTTC-GGGG
1 T-AAAATGGAAATTTTGGAAAG-TCGGGGG
*
27720879 TAAAATGGTAATTTTGG
1 TAAAATGGAAATTTTGG
27720896 TGAAATCGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
27 11 0.19
28 11 0.19
29 13 0.22
30 12 0.20
31 8 0.14
32 4 0.07
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (28 bp):
TAAAATGGAAATTTTGGAAAGTCGGGGG
Found at i:27720909 original size:57 final size:58
Alignment explanation
Indices: 27720760--27720912 Score: 197
Period size: 57 Copynumber: 2.7 Consensus size: 58
27720750 AATTTTTGTG
* * * * *
27720760 GGGGGTAAAATGGT-TTGTTTGGT-AAATTG-GTTTAAAATTGAAATTTTGGAAAGCTC
1 GGGGGTAAAATGGTAAT-TTTGGTGAAATCGAGGTTAAAAATGAAATCTTGGAAAGCTC
* *
27720816 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATCTTGGAAAGTTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGAAATCTTGGAAAGCTC
27720875 -GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAA
1 GGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAA
27720913 TGTAATTTTC
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
56 14 0.16
57 29 0.34
58 21 0.24
59 22 0.26
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGAAATCTTGGAAAGCTC
Found at i:27720917 original size:28 final size:29
Alignment explanation
Indices: 27720821--27720921 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 29
27720811 AGCTCGGGGG
27720821 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGGTAA-TTTTGGTGAAATCGAGGT
* *
27720851 TAAAAATGG-AATCTT-G-GAAAGTTCG-GGG
1 T-AAAATGGTAATTTTGGTGAAA--TCGAGGT
27720879 TAAAATGGTAATTTTGGTGAAATCGAGGT
1 TAAAATGGTAATTTTGGTGAAATCGAGGT
27720908 TAAAAT-GTAATTTT
1 TAAAATGGTAATTTT
27720922 CTAAAAATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
27 11 0.18
28 20 0.33
29 15 0.25
30 7 0.12
31 7 0.12
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
TAAAATGGTAATTTTGGTGAAATCGAGGT
Found at i:27720937 original size:58 final size:57
Alignment explanation
Indices: 27720817--27720951 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 57
27720807 GGAAAGCTCG
**
27720817 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATCTTGGAAAGTTC
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATCTTAAAAAGTTC
* * * *
27720875 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTT-AAAATGTAATTTTCTAAAAATTTT
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAA-TCT-TAAAAAGTTC
27720933 GGGGTCAAAAT-GTAATTTT
1 GGGGT-AAAATGGTAATTTT
27720952 TGGACTGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
56 8 0.12
57 21 0.31
58 34 0.50
59 5 0.07
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATCTTAAAAAGTTC
Found at i:27722044 original size:21 final size:21
Alignment explanation
Indices: 27722018--27722064 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
27722008 TTAACATTAT
27722018 TATTATAAAAACATTTAATAC
1 TATTATAAAAACATTTAATAC
* * * *
27722039 TATTATTAGAACATTTATTAT
1 TATTATAAAAACATTTAATAC
27722060 TATTA
1 TATTA
27722065 ATGTTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTATAAAAACATTTAATAC
Found at i:27722813 original size:6 final size:6
Alignment explanation
Indices: 27722790--27722864 Score: 66
Period size: 6 Copynumber: 12.5 Consensus size: 6
27722780 TTAGTATGTT
* * **
27722790 AATTTT AATTTT AATTTA AATTT- AAGGTA AATTTA AATAATTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT--TTA AATTTA
27722839 AATTTA AGA--TA AATTTA AATTTA AAT
1 AATTTA A-ATTTA AATTTA AATTTA AAT
27722865 CAATTTAACT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
4 1 0.02
5 6 0.10
6 44 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:27722813 original size:11 final size:11
Alignment explanation
Indices: 27722788--27722864 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
27722778 ATTTAGTATG
*
27722788 TTAATTTTAATT
1 TTAA-TTTAAAT
27722800 TTAATTTAAAT
1 TTAATTTAAAT
**
27722811 TTAAGGTAAAT
1 TTAATTTAAAT
*
27722822 TTAA-AT-AAT
1 TTAATTTAAAT
*
27722831 TAAATTTAAAT
1 TTAATTTAAAT
**
27722842 TTAAGATAAAT
1 TTAATTTAAAT
27722853 TTAAATTTAAAT
1 TT-AATTTAAAT
27722865 CAATTTAACT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 32 0.63
12 11 0.22
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:27722813 original size:17 final size:17
Alignment explanation
Indices: 27722788--27722862 Score: 84
Period size: 17 Copynumber: 4.6 Consensus size: 17
27722778 ATTTAGTATG
* * *
27722788 TTAATTTTAATTTTAAT
1 TTAAATTTAAGTTAAAT
*
27722805 TTAAATTTAAGGTAAAT
1 TTAAATTTAAGTTAAAT
27722822 TTAAA--TAA-TTAAAT
1 TTAAATTTAAGTTAAAT
*
27722836 TTAAATTTAAGATAAAT
1 TTAAATTTAAGTTAAAT
27722853 TTAAATTTAA
1 TTAAATTTAA
27722863 ATCAATTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 3 0.06
17 33 0.67
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
TTAAATTTAAGTTAAAT
Found at i:27722879 original size:16 final size:16
Alignment explanation
Indices: 27722833--27722880 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
27722823 TAAATAATTA
* *
27722833 AATTTAAATTTAAGATA
1 AATTTAAATCTAA-ATC
*
27722850 AATTTAAATTTAAATC
1 AATTTAAATCTAAATC
*
27722866 AATTTAACTCTAAAT
1 AATTTAAATCTAAAT
27722881 TAAAACAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTAAATCTAAATC
Found at i:27727698 original size:17 final size:17
Alignment explanation
Indices: 27727676--27727720 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
27727666 TGTATTTTGG
27727676 TTAGGGTTTTTTATGGT
1 TTAGGGTTTTTTATGGT
27727693 TTAGGGTTTTTTATGGT
1 TTAGGGTTTTTTATGGT
27727710 TTAGGGTTTTT
1 TTAGGGTTTTT
27727721 AGGATAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.11, C:0.00, G:0.29, T:0.60
Consensus pattern (17 bp):
TTAGGGTTTTTTATGGT
Found at i:27730982 original size:42 final size:42
Alignment explanation
Indices: 27730904--27730988 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
27730894 TTTTTAAATG
* *
27730904 TTTTTTACAACTTTTAATATTTTTAGAATATTTTAAATTTTT
1 TTTTTTACAACTTTTAATATTTTTACAATATCTTAAATTTTT
*
27730946 TTTTTTAC-ATTTTTATATAATTTTTACAAT-TCTTAAATTTTT
1 TTTTTTACAACTTTTA-AT-ATTTTTACAATATCTTAAATTTTT
27730988 T
1 T
27730989 ATAATACCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 6 0.16
42 22 0.58
43 10 0.26
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (42 bp):
TTTTTTACAACTTTTAATATTTTTACAATATCTTAAATTTTT
Found at i:27731000 original size:43 final size:41
Alignment explanation
Indices: 27730915--27731001 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
27730905 TTTTTACAAC
* * * **
27730915 TTTTAATATTTTTAGAATATTTTAAATTTTTTTTTTTACAT
1 TTTTAATATTTTTACAATATCTTAAATTTTTTATAATACAT
27730956 TTTTATATAATTTTTACAAT-TCTTAAATTTTTTATAATACCAT
1 TTTTA-AT-ATTTTTACAATATCTTAAATTTTTTATAATA-CAT
27730999 TTT
1 TTT
27731002 AATTTAAGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 5 0.13
42 17 0.45
43 16 0.42
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (41 bp):
TTTTAATATTTTTACAATATCTTAAATTTTTTATAATACAT
Found at i:27732113 original size:21 final size:21
Alignment explanation
Indices: 27732089--27732128 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27732079 GTAAAAAAAT
**
27732089 ATTATCAAAATTTATAATTAA
1 ATTATCAAAAAATATAATTAA
*
27732110 ATTATTAAAAAATATAATT
1 ATTATCAAAAAATATAATT
27732129 TTTAATGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTATCAAAAAATATAATTAA
Found at i:27737023 original size:25 final size:25
Alignment explanation
Indices: 27736991--27737041 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
27736981 AAATACTTTT
27736991 AAAATAATAGTAAAATTAATAATTA
1 AAAATAATAGTAAAATTAATAATTA
27737016 AAAATAATAGTAAAATTAATAATTA
1 AAAATAATAGTAAAATTAATAATTA
27737041 A
1 A
27737042 GTGTAACACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
AAAATAATAGTAAAATTAATAATTA
Found at i:27737029 original size:12 final size:12
Alignment explanation
Indices: 27736991--27737036 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
27736981 AAATACTTTT
27736991 AAAATAATAGTA
1 AAAATAATAGTA
* *
27737003 AAATTAATAATTA
1 AAAATAAT-AGTA
27737016 AAAATAATAGTA
1 AAAATAATAGTA
*
27737028 AAATTAATA
1 AAAATAATA
27737037 ATTAAGTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (12 bp):
AAAATAATAGTA
Found at i:27737675 original size:29 final size:29
Alignment explanation
Indices: 27737570--27737700 Score: 156
Period size: 29 Copynumber: 4.5 Consensus size: 29
27737560 TAGAAATAAT
27737570 ACAGATACAGTTACAGATACAGTCATGTC
1 ACAGATACAGTTACAGATACAGTCATGTC
* * *
27737599 AGAGATATAGTTACAGATACAATCATGTC
1 ACAGATACAGTTACAGATACAGTCATGTC
* *
27737628 AGAGATACAGTTACAGATGCAGTCATGTC
1 ACAGATACAGTTACAGATACAGTCATGTC
* * * *
27737657 ACAGATATAGTTACGGATGCAGACATGAT-
1 ACAGATACAGTTACAGATACAGTCATG-TC
*
27737686 ACAGATACAATTACA
1 ACAGATACAGTTACA
27737701 AATGCAGACG
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 87 0.99
30 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (29 bp):
ACAGATACAGTTACAGATACAGTCATGTC
Found at i:27737692 original size:58 final size:58
Alignment explanation
Indices: 27737568--27737707 Score: 185
Period size: 58 Copynumber: 2.4 Consensus size: 58
27737558 TATAGAAATA
* *
27737568 ATACAGATACAGTTACAGATACAGTCATGTCAGAGATATAGTTACAGATACAATCATG
1 ATACAGATACAGTTACAGATGCAGTCATGTCACAGATATAGTTACAGATACAATCATG
* * *
27737626 -TCAGAGATACAGTTACAGATGCAGTCATGTCACAGATATAGTTACGGATGCAGA-CATG
1 AT-ACAGATACAGTTACAGATGCAGTCATGTCACAGATATAGTTACAGATACA-ATCATG
* *
27737684 ATACAGATACAATTACAAATGCAG
1 ATACAGATACAGTTACAGATGCAG
27737708 ACGTGATACC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.01
58 68 0.96
59 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (58 bp):
ATACAGATACAGTTACAGATGCAGTCATGTCACAGATATAGTTACAGATACAATCATG
Found at i:27737705 original size:29 final size:29
Alignment explanation
Indices: 27737568--27737716 Score: 126
Period size: 29 Copynumber: 5.1 Consensus size: 29
27737558 TATAGAAATA
* *
27737568 ATACAGATACAGTTACAGATACAGTCATG
1 ATACAGATACAGTTACAGATGCAGACATG
* * *
27737597 -TCAGAGATATAGTTACAGATACA-ATCATG
1 AT-ACAGATACAGTTACAGATGCAGA-CATG
* *
27737626 -TCAGAGATACAGTTACAGATGCAGTCATG
1 AT-ACAGATACAGTTACAGATGCAGACATG
* *
27737655 -TCACAGATATAGTTACGGATGCAGACATG
1 AT-ACAGATACAGTTACAGATGCAGACATG
* * *
27737684 ATACAGATACAATTACAAATGCAGACGTG
1 ATACAGATACAGTTACAGATGCAGACATG
27737713 ATAC
1 ATAC
27737717 CCCTATCCGT
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 99 0.98
30 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (29 bp):
ATACAGATACAGTTACAGATGCAGACATG
Found at i:27738469 original size:57 final size:57
Alignment explanation
Indices: 27738404--27738511 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
27738394 CAAAACAGTT
* * * * *
27738404 AGTATACACATACACACCCTGACACACGCC-CGTGTGCTAACCCATGTGCCATCAAAC
1 AGTATACACACACAAACCCTAACACAC-CCTCGTGTCCCAACCCATGTGCCATCAAAC
* *
27738461 AGTATACACACACAAACTCTAACACACCCTCGTGTCCCAGCCCATGTGCCA
1 AGTATACACACACAAACCCTAACACACCCTCGTGTCCCAACCCATGTGCCA
27738512 CGCACACCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 2 0.05
57 41 0.95
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (57 bp):
AGTATACACACACAAACCCTAACACACCCTCGTGTCCCAACCCATGTGCCATCAAAC
Found at i:27744289 original size:13 final size:13
Alignment explanation
Indices: 27744268--27744298 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27744258 GAAAAATCAT
27744268 AAAAA-TTATAAA
1 AAAAATTTATAAA
27744280 AAAAATTTATAAA
1 AAAAATTTATAAA
27744293 AAAAAT
1 AAAAAT
27744299 AAAGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATTTATAAA
Found at i:27744467 original size:17 final size:17
Alignment explanation
Indices: 27744436--27744469 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27744426 TATAATTTTT
**
27744436 TAATTTTTATGTTTTAA
1 TAATTTTTAAATTTTAA
27744453 TAATTTTTAAATTTTAA
1 TAATTTTTAAATTTTAA
27744470 AATAGCTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TAATTTTTAAATTTTAA
Found at i:27745470 original size:154 final size:154
Alignment explanation
Indices: 27745235--27745542 Score: 616
Period size: 154 Copynumber: 2.0 Consensus size: 154
27745225 GTGCTTATGT
27745235 GTGCAAGGTGTGTGCGCGTTGTCAAAGGGTTAAGAAAGTATGAACAGATACTACCATGTAATCAC
1 GTGCAAGGTGTGTGCGCGTTGTCAAAGGGTTAAGAAAGTATGAACAGATACTACCATGTAATCAC
27745300 ACCATTGTATTTTAGTCAGAGAGCTTTGGGACTTTCTATTTTATGAGGAGAAAAAGTTGAAAATC
66 ACCATTGTATTTTAGTCAGAGAGCTTTGGGACTTTCTATTTTATGAGGAGAAAAAGTTGAAAATC
27745365 AAATTAGAGACAATTACAAAGGTA
131 AAATTAGAGACAATTACAAAGGTA
27745389 GTGCAAGGTGTGTGCGCGTTGTCAAAGGGTTAAGAAAGTATGAACAGATACTACCATGTAATCAC
1 GTGCAAGGTGTGTGCGCGTTGTCAAAGGGTTAAGAAAGTATGAACAGATACTACCATGTAATCAC
27745454 ACCATTGTATTTTAGTCAGAGAGCTTTGGGACTTTCTATTTTATGAGGAGAAAAAGTTGAAAATC
66 ACCATTGTATTTTAGTCAGAGAGCTTTGGGACTTTCTATTTTATGAGGAGAAAAAGTTGAAAATC
27745519 AAATTAGAGACAATTACAAAGGTA
131 AAATTAGAGACAATTACAAAGGTA
27745543 TTATTCTATA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (154 bp):
GTGCAAGGTGTGTGCGCGTTGTCAAAGGGTTAAGAAAGTATGAACAGATACTACCATGTAATCAC
ACCATTGTATTTTAGTCAGAGAGCTTTGGGACTTTCTATTTTATGAGGAGAAAAAGTTGAAAATC
AAATTAGAGACAATTACAAAGGTA
Found at i:27747234 original size:15 final size:16
Alignment explanation
Indices: 27747206--27747238 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
27747196 TAAAACAAAT
27747206 AAAATCTAAGTTTTCA
1 AAAATCTAAGTTTTCA
*
27747222 AAAATTTAA-TTTTCA
1 AAAATCTAAGTTTTCA
27747237 AA
1 AA
27747239 TTATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATCTAAGTTTTCA
Found at i:27751671 original size:18 final size:17
Alignment explanation
Indices: 27751648--27751687 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
27751638 AAAAATCCAT
*
27751648 AAAATATAAAATAATCTA
1 AAAATATAAAACAAT-TA
*
27751666 AAAATATATAACAATTA
1 AAAATATAAAACAATTA
27751683 AAAAT
1 AAAAT
27751688 CATATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATATAAAACAATTA
Found at i:27751741 original size:42 final size:44
Alignment explanation
Indices: 27751638--27751741 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 44
27751628 AGAATTATAC
27751638 AAAAATCCATAAAATATAAAATAATCTAAAAATATATAACAATT
1 AAAAATCCATAAAATATAAAATAATCTAAAAATATATAACAATT
** **
27751682 AAAAAT-CATATTTATATAATTTTAA-C-AAAAAT-TATAA-AATAT
1 AAAAATCCATA-AAATATAA-AATAATCTAAAAATATATAACAAT-T
27751724 AAAAATCCATAAAATATA
1 AAAAATCCATAAAATATA
27751742 TTAAAAATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
41 3 0.06
42 17 0.34
43 14 0.28
44 13 0.26
45 3 0.06
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (44 bp):
AAAAATCCATAAAATATAAAATAATCTAAAAATATATAACAATT
Found at i:27752051 original size:15 final size:15
Alignment explanation
Indices: 27752031--27752059 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27752021 TATGAAAATA
27752031 ATATATATATATATT
1 ATATATATATATATT
27752046 ATATATATATATAT
1 ATATATATATATAT
27752060 ATAATTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:27752079 original size:2 final size:2
Alignment explanation
Indices: 27752031--27752062 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27752021 TATGAAAATA
27752031 AT AT AT AT AT AT AT -T 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 A
27752063 ATTCCATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27752133 original size:8 final size:8
Alignment explanation
Indices: 27752120--27752144 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27752110 AAAAGTGAAC
27752120 AAAATATA
1 AAAATATA
27752128 AAAATATA
1 AAAATATA
27752136 AAAATATA
1 AAAATATA
27752144 A
1 A
27752145 CTTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:27755712 original size:14 final size:14
Alignment explanation
Indices: 27755690--27755721 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27755680 CGTTTGTTTA
*
27755690 TATGTAAAATATTT
1 TATGGAAAATATTT
27755704 TATGGAAAATATTT
1 TATGGAAAATATTT
27755718 TATG
1 TATG
27755722 TATTTTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (14 bp):
TATGGAAAATATTT
Found at i:27756121 original size:17 final size:15
Alignment explanation
Indices: 27756101--27756130 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27756091 TTTTATTTTA
27756101 ATAA-AATTTTAAAT
1 ATAATAATTTTAAAT
27756115 ATAATAATTTTAAAT
1 ATAATAATTTTAAAT
27756130 A
1 A
27756131 ATATTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAATTTTAAAT
Found at i:27756186 original size:21 final size:20
Alignment explanation
Indices: 27756160--27756211 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
27756150 GAAATTATTC
*
27756160 AATATTAATAT-TTTAATAATA
1 AATATTAATATACTT-ATAA-A
*
27756181 AATATTTATTATACTTATAAA
1 AATA-TTAATATACTTATAAA
27756202 AATATTAATA
1 AATATTAATA
27756212 ATAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 10 0.38
23 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTAATATACTTATAAA
Found at i:27756629 original size:32 final size:33
Alignment explanation
Indices: 27756593--27756664 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
27756583 AGCTTTTATG
*
27756593 AAATATTTT-CAAGAAATCTAT-CAAACAAC-AGA
1 AAATATTTTAC-ACAAATCTATCCAAAC-ACTAGA
*
27756625 AAATATTTTACACAAATTTATCCAAACACTAGA
1 AAATATTTTACACAAATCTATCCAAACACTAGA
27756658 AAATATT
1 AAATATT
27756665 AACATTTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 19 0.54
33 16 0.46
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.29
Consensus pattern (33 bp):
AAATATTTTACACAAATCTATCCAAACACTAGA
Found at i:27761259 original size:58 final size:59
Alignment explanation
Indices: 27761180--27761311 Score: 212
Period size: 58 Copynumber: 2.2 Consensus size: 59
27761170 ACCCGGGGGC
* *
27761180 AAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGT-
1 AAAATGGT-AATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTA
* *
27761239 AAAATGGTAATTTTAGTGAAATCGAGGTTTAAAATGGGATTTAGGGAAGTTTGGGGGTA
1 AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTA
27761298 AAAATGGTAATTTT
1 AAAATGGTAATTTT
27761312 TGAAAGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 46 0.68
59 22 0.32
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTA
Found at i:27761272 original size:30 final size:30
Alignment explanation
Indices: 27761180--27761275 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
27761170 ACCCGGGGGC
* * *
27761180 AAAATGGTAAATTTTGGTGAAATCGGGGTTA
1 AAAATGGT-AATTTTAGTGAAATCGAGGTTT
* * * * *
27761211 AAAATGG-GA-TTTAGGGAAGTTTGAGG-GT
1 AAAATGGTAATTTTAGTGAA-ATCGAGGTTT
27761239 AAAATGGTAATTTTAGTGAAATCGAGGTTT
1 AAAATGGTAATTTTAGTGAAATCGAGGTTT
27761269 AAAATGG
1 AAAATGG
27761276 GATTTAGGGA
Statistics
Matches: 48, Mismatches: 13, Indels: 9
0.69 0.19 0.13
Matches are distributed among these distances:
28 14 0.29
29 11 0.23
30 16 0.33
31 7 0.15
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTAGTGAAATCGAGGTTT
Found at i:27761299 original size:28 final size:28
Alignment explanation
Indices: 27761211--27761300 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
27761201 ATCGGGGTTA
*
27761211 AAAATGGGATTTAGGGAAGTTTGAGGGT
1 AAAATGGGATTTAGGGAAGTTTGGGGGT
* * * * **
27761239 AAAATGGTAATTTTAGTGAA-ATCGAGGTTT
1 AAAATGG-GA-TTTAGGGAAGTTTG-GGGGT
27761269 AAAATGGGATTTAGGGAAGTTTGGGGGT
1 AAAATGGGATTTAGGGAAGTTTGGGGGT
27761297 AAAA
1 AAAA
27761301 ATGGTAATTT
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
28 22 0.49
29 6 0.13
30 17 0.38
ACGTcount: A:0.36, C:0.01, G:0.33, T:0.30
Consensus pattern (28 bp):
AAAATGGGATTTAGGGAAGTTTGGGGGT
Found at i:27761326 original size:30 final size:29
Alignment explanation
Indices: 27761285--27761611 Score: 314
Period size: 30 Copynumber: 10.9 Consensus size: 29
27761275 GGATTTAGGG
* * *
27761285 AAGTTTGGGGGTAAAAATGGTAATTTTTGA
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGA
* * *
27761315 AAGTTTCGGGGTAAAAATGCAATTTTTTTGGA
1 AAGTTTTGGGGTCAAAATGTAA---TTTTGGA
* * *
27761347 AA-TTTTAGGGTCAAAATATGATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGG-A
* * *
27761376 AAGTTTTGCGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGG-A
* *
27761406 AAGTTTTGGGGTTAAAATGTAATTTTTAGA
1 AAGTTTTGGGGTCAAAATGTAA-TTTTGGA
*
27761436 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGG-A
* *
27761466 AAGTTTTAGGGTCAAAATGTAATTTTCAGA
1 AAGTTTTGGGGTCAAAATGTAATTTT-GGA
* *
27761496 AAGTTTTGGGGTTAAAATGTAATTTCTAGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
*
27761526 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGG-A
* * * **
27761556 AAGTTTTGGGATCGAAATATAATTTCCAGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
27761586 AAGTTTTGGGGTCAAAATGTAATTTT
1 AAGTTTTGGGGTCAAAATGTAATTTT
27761612 TGGACCAAGG
Statistics
Matches: 251, Mismatches: 35, Indels: 23
0.81 0.11 0.07
Matches are distributed among these distances:
28 6 0.02
29 13 0.05
30 203 0.81
31 21 0.08
32 8 0.03
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:27761330 original size:58 final size:55
Alignment explanation
Indices: 27761180--27761330 Score: 169
Period size: 58 Copynumber: 2.6 Consensus size: 55
27761170 ACCCGGGGGC
*
27761180 AAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGT
1 AAAATGGT-AATTTT-ATGAAATCGGGG-T-AAAATGGGATTTAGGGAAGTTTGAGGGT
* *
27761239 AAAATGGTAATTTTAGTGAAATCGAGGTTTAAAATGGGATTTAGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTA-TGAAATCG-GG-GTAAAATGGGATTTAGGGAAGTTTGAGGGT
27761297 AAAAATGGTAATTTT-TGAAAGTTTCGGGGTAAAA
1 -AAAATGGTAATTTTATGAAA---TCGGGGTAAAA
27761331 ATGCAATTTT
Statistics
Matches: 81, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
57 5 0.06
58 46 0.57
59 27 0.33
60 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.32
Consensus pattern (55 bp):
AAAATGGTAATTTTATGAAATCGGGGTAAAATGGGATTTAGGGAAGTTTGAGGGT
Found at i:27761466 original size:90 final size:89
Alignment explanation
Indices: 27761305--27761612 Score: 415
Period size: 90 Copynumber: 3.4 Consensus size: 89
27761295 GTAAAAATGG
* * * * * * *
27761305 TAATTTT-TGAAAGTTTCGGGGTAAAAATGCAATTTTTTTGGAAA-TTTTAGGGTCAAAATATGA
1 TAATTTTCAGAAAGTTTTGGGGTTAAAATGTAA--TTTTTAGAAAGTTTTGGGGTCAAAATATAA
*
27761368 TTTTGGAAAAGTTTTGCGGTTAAAATA
64 TTTTGGAAAAGTTTTG-GGTCAAAATA
*
27761395 TAATTTT-GGAAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAAT
1 TAATTTTCAG-AAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAAT
*
27761459 TTTGGAAAAGTTTTAGGGTCAAAATG
65 TTTGGAAAAGTTTT-GGGTCAAAATA
*
27761485 TAATTTTCAGAAAGTTTTGGGGTTAAAATGTAATTTCTAGAAAGTTTTGGGGTCAAAATATAATT
1 TAATTTTCAGAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATT
*
27761550 TTGGAAAAGTTTTGGGATCGAAATA
66 TTGGAAAAGTTTTGGG-TCAAAATA
* *
27761575 TAATTTCCAGAAAGTTTTGGGGTCAAAATGTAATTTTT
1 TAATTTTCAGAAAGTTTTGGGGTTAAAATGTAATTTTT
27761613 GGACCAAGGT
Statistics
Matches: 197, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
89 12 0.06
90 163 0.83
91 22 0.11
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (89 bp):
TAATTTTCAGAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATT
TTGGAAAAGTTTTGGGTCAAAATA
Found at i:27761992 original size:6 final size:6
Alignment explanation
Indices: 27761967--27762008 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
27761957 TAATTTGACT
27761967 TTTTAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
27762009 AAAGTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 23 0.70
7 4 0.12
8 4 0.12
9 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:27761997 original size:28 final size:26
Alignment explanation
Indices: 27761952--27762004 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
27761942 GTTGGGCTTT
*
27761952 TATTGTAATTTGACTTTTTAATGTTTAG
1 TATTGTAATTTGA-ATTTTAAT-TTTAG
* *
27761980 TATTTTAATTTTAATTTTAATTTTA
1 TATTGTAATTTGAATTTTAATTTTA
27762005 ATTTAAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 7 0.32
28 11 0.50
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (26 bp):
TATTGTAATTTGAATTTTAATTTTAG
Found at i:27762018 original size:11 final size:10
Alignment explanation
Indices: 27762004--27762063 Score: 61
Period size: 11 Copynumber: 5.8 Consensus size: 10
27761994 TTTTAATTTT
27762004 AATTTAAAGTA
1 AATTTAAA-TA
27762015 AATTTAAAT-
1 AATTTAAATA
27762024 AA-TTAAATTTA
1 AATTTAAA--TA
27762035 AATTTAAATA
1 AATTTAAATA
*
27762045 AATTTAAAATC
1 AATTT-AAATA
27762056 AATTTAAA
1 AATTTAAA
27762064 ACAAAAAGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 12 0.28
11 19 0.44
12 5 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
AATTTAAATA
Found at i:27762022 original size:6 final size:6
Alignment explanation
Indices: 27761981--27762052 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
27761971 AATGTTTAGT
* * * * *
27761981 ATTTTA ATTTTA ATTTTA ATTTTA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
27762030 ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
27762053 ATCAATTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 44 0.76
8 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:27762533 original size:68 final size:68
Alignment explanation
Indices: 27762329--27763464 Score: 1827
Period size: 68 Copynumber: 16.7 Consensus size: 68
27762319 TGCTCTTCAG
** *
27762329 AGAGATAAAGATTTGCTATCCCACT-TCACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCA
1 AGAGATAAAGACGTGTTAT-CCACTCT-ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCA
27762393 ATTTC
64 ATTTC
*
27762398 AGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCA-GATGACGTTGCTCTTACTTCA
1 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAG-AGGATGACGTTGCTCTTACTTCA
27762462 ATTTC
64 ATTTC
* *
27762467 AGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTTAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27762532 TTC
66 TTC
* *
27762535 AGAGAAAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCGAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27762600 TTC
66 TTC
* *
27762603 AGAGA-AAAGACGTGTTATCCACTCAACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27762667 TTC
66 TTC
*
27762670 AGAGATAAAGACGTGTAATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27762735 TTC
66 TTC
* * *
27762738 AGATATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAA
1 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAA
27762803 TTTC
65 TTTC
*
27762807 AGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCA-GATGACGTTGCTCTTACTTCA
1 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAG-AGGATGACGTTGCTCTTACTTCA
27762871 ATTTC
64 ATTTC
* *
27762876 AGAGATAAAGACGTGTTATCTAACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAA
1 AGAGATAAAGACGTGTTATC-CACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAA
27762941 TTTC
65 TTTC
*
27762945 AGAGAAAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCA-GATGACGTTGCTCTTACTTCAA
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG-AGGATGACGTTGCTCTTACTTCAA
27763009 TTTC
65 TTTC
*
27763013 AGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27763078 TTC
66 TTC
27763081 AGAGA-AAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27763145 TTC
66 TTC
* * * *
27763148 AGAGATGAAGACTTGTTATCCACTCAACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27763213 TTC
66 TTC
27763216 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG-GGATGACGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27763280 TTC
66 TTC
* * *
27763283 AGAGATAAAAACGTATTATCCACTCTACTTCAACTTCAAGAGGATGACGTTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27763348 TTC
66 TTC
* * * * *
27763351 AGAGATGATGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAAT
1 AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
27763416 TTC
66 TTC
* * *
27763419 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGAT
1 AGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT
27763465 AGAAAATAAT
Statistics
Matches: 997, Mismatches: 56, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
67 196 0.20
68 506 0.51
69 293 0.29
70 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (68 bp):
AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
TTC
Found at i:27762707 original size:203 final size:204
Alignment explanation
Indices: 27762356--27763464 Score: 1834
Period size: 203 Copynumber: 5.4 Consensus size: 204
27762346 ATCCCACTTC
*
27762356 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAA
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-A
*
27762421 CTCTACTTCAATTTCAAGCA-GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTA
65 CTCTACTTCAATTTCAAG-AGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTA
* **
27762485 TCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTTAATTTCAGAGAAAAAGACGTG
129 TCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTG
27762550 TTATCCACTCT
194 TTATCCACTCT
*
27762561 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCGATTTCAGAGA-AAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
* * *
27762625 TCAACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTAATC
66 TCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATC
*
27762690 CACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGATATGAAGACGTGTT
131 CACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTT
27762755 ATCCAACTCT
196 ATCC-ACTCT
* *
27762765 ACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAA
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-A
27762830 CTCTACTTCAATTTCAAGCA-GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTA
65 CTCTACTTCAATTTCAAG-AGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTA
* * **
27762894 TCTAACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAAAAAGACGT
129 TC-CACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGT
27762959 GTTATCCACTCT
193 GTTATCCACTCT
*
27762971 ACTTCAATTTCAAGCA-GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCA
1 ACTTCAATTTCAAG-AGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
27763035 CTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGA-AAAGACGTGTTAT
65 CTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTAT
*
27763099 CCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGT
130 CCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGT
*
27763164 TATCCACTCA
195 TATCCACTCT
*
27763174 ACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
* *
27763239 TCTACTTCAATTTCAAG-GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAAACGTATTATC
66 TCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATC
* * *
27763303 CACTCTACTTCAACTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGATGACATGTT
131 CACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTT
27763368 ATCCACTCT
196 ATCCACTCT
* * * *
27763377 ACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAG
1 ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-
*
27763442 CTTTACTTCAATTTCAAGAGGAT
65 CTCTACTTCAATTTCAAGAGGAT
27763465 AGAAAATAAT
Statistics
Matches: 849, Mismatches: 43, Indels: 24
0.93 0.05 0.03
Matches are distributed among these distances:
202 33 0.04
203 415 0.49
204 96 0.11
205 114 0.13
206 126 0.15
207 65 0.08
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (204 bp):
ACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
TCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATC
CACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTT
ATCCACTCT
Found at i:27764328 original size:8 final size:8
Alignment explanation
Indices: 27764315--27764346 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
27764305 CTCTCCGTTT
27764315 TTTTTTTA
1 TTTTTTTA
27764323 TTTTTTTA
1 TTTTTTTA
27764331 TTTTTTTTA
1 -TTTTTTTA
27764340 TTTTTTT
1 TTTTTTT
27764347 TATGTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTTA
Found at i:27764328 original size:9 final size:9
Alignment explanation
Indices: 27764314--27764349 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
27764304 CCTCTCCGTT
27764314 TTTTTTTTA
1 TTTTTTTTA
27764323 -TTTTTTTA
1 TTTTTTTTA
27764331 TTTTTTTTA
1 TTTTTTTTA
27764340 TTTTTTTTA
1 TTTTTTTTA
27764349 T
1 T
27764350 GTGTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:27764349 original size:18 final size:17
Alignment explanation
Indices: 27764314--27764346 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27764304 CCTCTCCGTT
27764314 TTTTTTTTATTTTTTTA
1 TTTTTTTTATTTTTTTA
27764331 TTTTTTTTATTTTTTT
1 TTTTTTTTATTTTTTT
27764347 TATGTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTA
Found at i:27775218 original size:59 final size:60
Alignment explanation
Indices: 27775155--27775281 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 60
27775145 ACCCGGGGGC
* *
27775155 AAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATAGGATTTAGGGAAGCTT-GAGGGT-
1 AAAATGGTAAATTTTAGTAAAATCGGGGTTAAAAATAGGATTTAGGGAAGCTTCG-GGGTA
* * * *
27775214 AAAATGGT-AATTTTAGTAAAATCGGGGTTTATAATGGGATTTAGGGAAGTTTCGGGGTA
1 AAAATGGTAAATTTTAGTAAAATCGGGGTTAAAAATAGGATTTAGGGAAGCTTCGGGGTA
27775273 AAAATGGTA
1 AAAATGGTA
27775282 CTTTTGAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 42 0.71
59 17 0.29
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.31
Consensus pattern (60 bp):
AAAATGGTAAATTTTAGTAAAATCGGGGTTAAAAATAGGATTTAGGGAAGCTTCGGGGTA
Found at i:27775279 original size:29 final size:29
Alignment explanation
Indices: 27775246--27775304 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
27775236 CGGGGTTTAT
*
27775246 AATGGGA-TTTAGGGAAGTTTCGGGGTAAA
1 AATGGGACTTT-GGAAAGTTTCGGGGTAAA
* *
27775275 AATGGTACTTTTGAAAGTTTCGGGGTAAA
1 AATGGGACTTTGGAAAGTTTCGGGGTAAA
27775304 A
1 A
27775305 TGTAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.31
Consensus pattern (29 bp):
AATGGGACTTTGGAAAGTTTCGGGGTAAA
Found at i:27775375 original size:30 final size:30
Alignment explanation
Indices: 27775313--27775586 Score: 286
Period size: 30 Copynumber: 9.1 Consensus size: 30
27775303 AATGTAATTT
* * *
27775313 TTTTGG-AAA-TTTTAGGGTCAAAATATGA
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
* **
27775341 TTTTGGAAAAGTTTTGGGGTTAAAATGTTT
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
27775371 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
*** * *
27775401 TTTCCAAAAAGTTTTGGGGTTAAAATATAA
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
*
27775431 TTTTGGAAAAGTTTTAGGGTCAAAATGTAA
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
* * *
27775461 TTTTTAGAAAGAAGTTTTAAGGTCAAAATGTAA
1 -TTTT-GGAA-AAGTTTTAGGGTTAAAATGTAA
* * * *
27775494 TTTCTAG-AAAGGTTTAGGGTCAAAATATAA
1 TTT-TGGAAAAGTTTTAGGGTTAAAATGTAA
*
27775524 TTTTGGAAAAGTTTTGGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
* *
27775554 TTTTAG-AAAGTTTTGGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
27775583 TTTT
1 TTTT
27775587 TAAACAATTT
Statistics
Matches: 207, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
28 6 0.03
29 32 0.15
30 136 0.66
31 5 0.02
32 6 0.03
33 22 0.11
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.40
Consensus pattern (30 bp):
TTTTGGAAAAGTTTTAGGGTTAAAATGTAA
Found at i:27775519 original size:93 final size:93
Alignment explanation
Indices: 27775323--27775563 Score: 346
Period size: 93 Copynumber: 2.6 Consensus size: 93
27775313 TTTTGGAAAT
* * *
27775323 TTTAGGGTCAAAATATGATTTTGGAAAAGTTTTGGGGTTAAAATGT--TTTTTTGGAA-AAGTTT
1 TTTAGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGAAGTTT
* * *
27775385 TAGGGTTAAAATGTAATTTCCAAAAAGT
66 TAAGGTCAAAATGTAATTTCCAAAAAGG
* * * *
27775413 TTTGGGGTTAAAATATAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTTAGAAAGAAGTTT
1 TTTAGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGAAGTTT
* *
27775478 TAAGGTCAAAATGTAATTTCTAGAAAGG
66 TAAGGTCAAAATGTAATTTCCAAAAAGG
27775506 TTTAGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATGTAA-TTTTAGAAAG
1 TTTAGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAG
27775564 TTTTGGGGTT
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
90 41 0.31
92 18 0.14
93 73 0.55
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (93 bp):
TTTAGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGAAGTTT
TAAGGTCAAAATGTAATTTCCAAAAAGG
Found at i:27777337 original size:6 final size:6
Alignment explanation
Indices: 27777312--27777353 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
27777302 TAATTTGACT
27777312 TTTTAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
27777354 AAAGTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 23 0.70
7 4 0.12
8 4 0.12
9 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:27777342 original size:28 final size:26
Alignment explanation
Indices: 27777297--27777349 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
27777287 GTTGGGCTTT
*
27777297 TATTGTAATTTGACTTTTTAATGTTTAG
1 TATTGTAATTTGA-ATTTTAAT-TTTAG
* *
27777325 TATTTTAATTTTAATTTTAATTTTA
1 TATTGTAATTTGAATTTTAATTTTA
27777350 ATTTAAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 7 0.32
28 11 0.50
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (26 bp):
TATTGTAATTTGAATTTTAATTTTAG
Found at i:27777367 original size:6 final size:6
Alignment explanation
Indices: 27777326--27777414 Score: 71
Period size: 6 Copynumber: 15.2 Consensus size: 6
27777316 AATGTTTAGT
* * * * *
27777326 ATTTTA ATTTTA ATTTTA ATTTTA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
27777375 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
27777415 ATCAATTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.07
5 7 0.10
6 53 0.74
7 1 0.01
8 6 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:27777384 original size:37 final size:37
Alignment explanation
Indices: 27777335--27777407 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
27777325 TATTTTAATT
* * **
27777335 TTAATTTTAATTTTAATTTAAA-GTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
*
27777371 TTAAATTTAAATTTAAGATAAATTTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
27777408 ATTTAAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 18 0.58
37 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (37 bp):
TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
Found at i:27777416 original size:11 final size:11
Alignment explanation
Indices: 27777349--27777426 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
27777339 TTTTAATTTT
*
27777349 AATTTAAAGTA
1 AATTTAAAATA
27777360 AATTTAAATAATTA
1 AATTT-AA-AA-TA
* *
27777374 AATTTAAATTT
1 AATTTAAAATA
** *
27777385 AAGATAAATTTA
1 AATTTAAA-ATA
27777397 AATTT-AAATA
1 AATTTAAAATA
*
27777407 AATTTAAAATC
1 AATTTAAAATA
27777418 AATTTAAAA
1 AATTTAAAA
27777427 CAAAAAGTCC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
10 7 0.13
11 27 0.52
12 8 0.15
13 3 0.06
14 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:27777425 original size:17 final size:16
Alignment explanation
Indices: 27777343--27777414 Score: 94
Period size: 17 Copynumber: 4.5 Consensus size: 16
27777333 TTTTAATTTT
*
27777343 AATTTTAATTTAAAGTA
1 AATTTAAATTTAAA-TA
*
27777360 AATTTAAA--TAATTA
1 AATTTAAATTTAAATA
27777374 AATTTAAATTTAAGATA
1 AATTTAAATTTAA-ATA
27777391 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
27777407 AATTTAAA
1 AATTTAAA
27777415 ATCAATTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 14 0.29
17 22 0.45
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:27778441 original size:29 final size:31
Alignment explanation
Indices: 27778399--27778460 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
27778389 ATTCAAGTAT
*
27778399 CACATTGGATATTTT-T-AAAGTAGAGGTAC
1 CACATTGGATATTTTATGAAAGTACAGGTAC
27778428 CACATTGGATATTTTATGAAAGTACAGGTAC
1 CACATTGGATATTTTATGAAAGTACAGGTAC
27778459 CA
1 CA
27778461 TAATAGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 15 0.50
30 1 0.03
31 14 0.47
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (31 bp):
CACATTGGATATTTTATGAAAGTACAGGTAC
Found at i:27780295 original size:113 final size:114
Alignment explanation
Indices: 27780076--27780308 Score: 371
Period size: 113 Copynumber: 2.1 Consensus size: 114
27780066 TTGTGTCCGG
*
27780076 TTAATAGGGATTATGGAACATGTAGTTTGCTTATTGACATGGGATATTGAATGTTAAAAGTGAAT
1 TTAATAGCGATTATGGAACATGTAGTTTGCTTATTGACATGGGATATTGAATGTTAAAAGTGAAT
27780141 TGTGAAATTGCATATTAATGTTAAAGCAATAAAAGATCATGCAATTCGA
66 TGTGAAATTGCATATTAATGTTAAAGCAATAAAAGATCATGCAATTCGA
** * * *
27780190 TTAATAGCGATTATGGGCCATGTATTTTGCTTATTGGCATGGGTTATTGAATG-TAAAAGTGAAT
1 TTAATAGCGATTATGGAACATGTAGTTTGCTTATTGACATGGGATATTGAATGTTAAAAGTGAAT
* *
27780254 TGTGAAATTGCATATTAATGTTAAAGCAATGAAAA-ATCATGCAGTTCGT
66 TGTGAAATTGCATATTAATGTTAAAGCAAT-AAAAGATCATGCAATTCGA
27780303 TTAATA
1 TTAATA
27780309 CGAGCCTTAG
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
113 59 0.54
114 51 0.46
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (114 bp):
TTAATAGCGATTATGGAACATGTAGTTTGCTTATTGACATGGGATATTGAATGTTAAAAGTGAAT
TGTGAAATTGCATATTAATGTTAAAGCAATAAAAGATCATGCAATTCGA
Found at i:27786869 original size:10 final size:10
Alignment explanation
Indices: 27786856--27786910 Score: 65
Period size: 10 Copynumber: 5.2 Consensus size: 10
27786846 GAATTTTTTG
27786856 GAATCGAGTC
1 GAATCGAGTC
27786866 GAATCGAGTC
1 GAATCGAGTC
27786876 GAATCGAGTC
1 GAATCGAGTC
*
27786886 AAAATTTCGAGTC
1 -GAA--TCGAGTC
*
27786899 GAGTCGAGTC
1 GAATCGAGTC
27786909 GA
1 GA
27786911 CTTACCGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
10 29 0.74
11 2 0.05
12 1 0.03
13 7 0.18
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (10 bp):
GAATCGAGTC
Found at i:27787448 original size:27 final size:27
Alignment explanation
Indices: 27787398--27787470 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
27787388 TTTAGATTCC
* *
27787398 AAAATTAT-TATTTTATAAAATTTTTAA
1 AAAATTATATATTTT-TTAATTTTTTAA
***
27787425 ATTTTTATATATTTTTTAATTTTTTAA
1 AAAATTATATATTTTTTAATTTTTTAA
27787452 AAAATTATATATTTTTTAA
1 AAAATTATATATTTTTTAA
27787471 AAAATACAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
AAAATTATATATTTTTTAATTTTTTAA
Found at i:27787511 original size:19 final size:19
Alignment explanation
Indices: 27787408--27787531 Score: 65
Period size: 19 Copynumber: 6.2 Consensus size: 19
27787398 AAAATTATTA
27787408 TTTTATAAA-ATTTTTAAAT
1 TTTTATAAATA-TTTTAAAT
* * *
27787427 TTTTATATATTTTTTAATT
1 TTTTATAAATATTTTAAAT
* * *
27787446 TTTTA-AAAAATTATATATT
1 TTTTATAAATATTTTA-AAT
*
27787465 TTTTAAAAAATACAAATTTTAGAAT
1 TTTT-ATAAAT----ATTTTA-AAT
27787490 TTTTATAAATATTTTAAA-
1 TTTTATAAATATTTTAAAT
* *
27787508 TTTTAAAAATTATTTTCAAT
1 TTTTATAAA-TATTTTAAAT
27787528 TTTT
1 TTTT
27787532 GAAAATTATT
Statistics
Matches: 81, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
18 14 0.17
19 37 0.46
20 11 0.14
21 3 0.04
24 5 0.06
25 11 0.14
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (19 bp):
TTTTATAAATATTTTAAAT
Found at i:27787536 original size:20 final size:18
Alignment explanation
Indices: 27787487--27787543 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
27787477 CAAATTTTAG
27787487 AATTTTTATAAA-TATTTT
1 AATTTTTA-AAATTATTTT
*
27787505 AAATTTTAAAAATTATTTT
1 -AATTTTTAAAATTATTTT
27787524 CAATTTTTGAAAATTATTTT
1 -AATTTTT-AAAATTATTTT
27787544 GATTAGTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.09
19 19 0.58
20 11 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTTTAAAATTATTTT
Found at i:27788059 original size:19 final size:19
Alignment explanation
Indices: 27788003--27788059 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
27787993 CGCTGTCACC
*
27788003 CATCGTAATCAAATTTGTC
1 CATCGTAATCAAATTTGTT
27788022 CATCGTAATCAAATTTGTT
1 CATCGTAATCAAATTTGTT
* * *
27788041 TATTGTAATCAAAATTGTT
1 CATCGTAATCAAATTTGTT
27788060 ACTAACTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (19 bp):
CATCGTAATCAAATTTGTT
Found at i:27788825 original size:22 final size:23
Alignment explanation
Indices: 27788786--27788832 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
27788776 TGAAAGGAGT
*
27788786 AAAAGTTTTGGGGGAAAA-GTAA
1 AAAAGTTTTGGGGAAAAATGTAA
*
27788808 AAAAGTTTTGGGTAAAAATGTAA
1 AAAAGTTTTGGGGAAAAATGTAA
27788831 AA
1 AA
27788833 TATTATAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (23 bp):
AAAAGTTTTGGGGAAAAATGTAA
Found at i:27794680 original size:13 final size:13
Alignment explanation
Indices: 27794664--27794697 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27794654 TTCTCATTTC
27794664 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
*
27794677 TTTTTCCTTCTTT
1 TTTTTCTTTCTTT
*
27794690 CTTTTCTT
1 TTTTTCTT
27794698 CAAACTTCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:27795230 original size:15 final size:15
Alignment explanation
Indices: 27795206--27795235 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27795196 AACCCACATT
27795206 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
27795221 CATTTGAACCAAACC
1 CATTTAAACCAAACC
27795236 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:27795285 original size:10 final size:10
Alignment explanation
Indices: 27795272--27795339 Score: 64
Period size: 10 Copynumber: 6.7 Consensus size: 10
27795262 AGTCAAACCA
27795272 TTGACCGACG
1 TTGACCGACG
* *
27795282 TTGACTGGCG
1 TTGACCGACG
27795292 TTGACCGACG
1 TTGACCGACG
** *
27795302 TTGATTGGCG
1 TTGACCGACG
*
27795312 TTGACCGATG
1 TTGACCGACG
*
27795322 TTGATCGACCG
1 TTGACCGA-CG
27795333 TTGACCG
1 TTGACCG
27795340 GTGTTGATTG
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (10 bp):
TTGACCGACG
Found at i:27795336 original size:21 final size:21
Alignment explanation
Indices: 27795272--27795380 Score: 102
Period size: 20 Copynumber: 5.3 Consensus size: 21
27795262 AGTCAAACCA
* * *
27795272 TTGACCGACGTTGACTG-GCG
1 TTGACCGATGTTGATTGACCG
* *
27795292 TTGACCGACGTTGATTG-GCG
1 TTGACCGATGTTGATTGACCG
*
27795312 TTGACCGATGTTGATCGACCG
1 TTGACCGATGTTGATTGACCG
*
27795333 TTGACCGGTGTTGATTGACCG
1 TTGACCGATGTTGATTGACCG
27795354 TTGACC---GTTGACTTTGACCG
1 TTGACCGATGTTGA--TTGACCG
27795374 TTGACCG
1 TTGACCG
27795381 TTGACCGTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
18 5 0.06
20 47 0.59
21 27 0.34
ACGTcount: A:0.16, C:0.23, G:0.31, T:0.30
Consensus pattern (21 bp):
TTGACCGATGTTGATTGACCG
Found at i:27795357 original size:7 final size:7
Alignment explanation
Indices: 27795347--27795392 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
27795337 CCGGTGTTGA
27795347 TTGACCG
1 TTGACCG
27795354 TTGACCG
1 TTGACCG
*
27795361 TTGA-CT
1 TTGACCG
27795367 TTGACCG
1 TTGACCG
27795374 TTGACCG
1 TTGACCG
27795381 TTGACCG
1 TTGACCG
27795388 TTGAC
1 TTGAC
27795393 TTTTTCGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (7 bp):
TTGACCG
Found at i:27795381 original size:20 final size:20
Alignment explanation
Indices: 27795347--27795385 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27795337 CCGGTGTTGA
27795347 TTGACCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGACT
27795367 TTGACCGTTGACCGTTGAC
1 TTGACCGTTGACCGTTGAC
27795386 CGTTGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:27796447 original size:3 final size:3
Alignment explanation
Indices: 27796439--27796467 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27796429 AATATTCTAT
27796439 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27796468 TTGAGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27809376 original size:133 final size:134
Alignment explanation
Indices: 27809111--27809382 Score: 411
Period size: 133 Copynumber: 2.0 Consensus size: 134
27809101 TTTAATAAAA
* * ** *
27809111 TAATGGGTGAACTATATAAATGGCTACCCAACTGTTAGCATATTTCTATTTTTGTTATTCAAGTT
1 TAATGGGTGAACAATATAAATGGCCACCCAACCATTAGCATATTTCTATTTTGGTTATTCAAGTT
* * *
27809176 TAAAAATGTCTATTTTAGTCACTAACATTATTGAAATTTAATATTTTAGTCACTCATCTATCAAA
66 TAAAAATATATATTTTAGTCACTAACATTATTGAAATTTAATATTTTAGTCACTCATCCATCAAA
27809241 TCAC
131 TCAC
* *
27809245 TAATGGGTGAACAATATAAATGGCCACTCAACCATTAGCATGTTTCTATTTTGGTTATTCAAGTT
1 TAATGGGTGAACAATATAAATGGCCACCCAACCATTAGCATATTTCTATTTTGGTTATTCAAGTT
* * * *
27809310 T-AAAATATATATTTTAGTCACTAACGTTATTGAAATTTAATATTTTGGTCAGTCATCCATTAAA
66 TAAAAATATATATTTTAGTCACTAACATTATTGAAATTTAATATTTTAGTCACTCATCCATCAAA
27809374 TCAC
131 TCAC
27809378 TAATG
1 TAATG
27809383 AAAAGTTGAC
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
133 65 0.52
134 59 0.48
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (134 bp):
TAATGGGTGAACAATATAAATGGCCACCCAACCATTAGCATATTTCTATTTTGGTTATTCAAGTT
TAAAAATATATATTTTAGTCACTAACATTATTGAAATTTAATATTTTAGTCACTCATCCATCAAA
TCAC
Found at i:27809526 original size:8 final size:7
Alignment explanation
Indices: 27809498--27809525 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
27809488 ATCTTGATTC
27809498 TTAAAAA
1 TTAAAAA
27809505 TTAAAAA
1 TTAAAAA
27809512 TTAAAAA
1 TTAAAAA
27809519 TTAAAAA
1 TTAAAAA
27809526 AATAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:27809659 original size:17 final size:17
Alignment explanation
Indices: 27809630--27809673 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
27809620 ATCAAATTTA
*
27809630 TTTATTAAAATAATAAT
1 TTTATTAAAATAACAAT
27809647 TTTA-TAAATATAACAAT
1 TTTATTAAA-ATAACAAT
*
27809664 TTTCTTAAAA
1 TTTATTAAAA
27809674 AATTCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATTAAAATAACAAT
Found at i:27809850 original size:17 final size:17
Alignment explanation
Indices: 27809806--27809851 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
27809796 AATTAAAGTG
* *
27809806 ATTTCATTTAGTTTTAT
1 ATTTTATTTATTTTTAT
27809823 ATTTTATTTATTTTTAT
1 ATTTTATTTATTTTTAT
27809840 -TTTTATCTTATT
1 ATTTTAT-TTATT
27809852 ATATACTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (17 bp):
ATTTTATTTATTTTTAT
Found at i:27809906 original size:16 final size:16
Alignment explanation
Indices: 27809885--27809915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27809875 GTCGGTTGTT
*
27809885 TTTTTATTTTGTTATC
1 TTTTTATTTTCTTATC
27809901 TTTTTATTTTCTTAT
1 TTTTTATTTTCTTAT
27809916 TTATTTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTCTTATC
Found at i:27809990 original size:22 final size:22
Alignment explanation
Indices: 27809965--27810007 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27809955 TGTACTTCAT
*
27809965 TTAGAATCGCCTACGATTCCAA
1 TTAGAATCGCCCACGATTCCAA
*
27809987 TTAGAATCGCCCATGATTCCA
1 TTAGAATCGCCCACGATTCCA
27810008 GTTTTCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (22 bp):
TTAGAATCGCCCACGATTCCAA
Found at i:27810729 original size:22 final size:22
Alignment explanation
Indices: 27810685--27810730 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
27810675 TTAACCCATA
*
27810685 TTTATGTTGTAAAATTATCTTT
1 TTTATGTTGTAAAATTATATTT
27810707 TTTATGTTGTAAAAGTT-TATTT
1 TTTATGTTGTAAAA-TTATATTT
27810729 TT
1 TT
27810731 GATAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (22 bp):
TTTATGTTGTAAAATTATATTT
Found at i:27810867 original size:19 final size:20
Alignment explanation
Indices: 27810841--27810888 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
27810831 ATTTATTTAT
*
27810841 TAAAATAATAATGTAATAAA
1 TAAAATAATAATATAATAAA
**
27810861 T-AAATAACGATATAATAAA
1 TAAAATAATAATATAATAAA
27810880 TAAAATAAT
1 TAAAATAAT
27810889 TTAAGGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAAATAATAATATAATAAA
Found at i:27814338 original size:35 final size:35
Alignment explanation
Indices: 27814292--27814362 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
27814282 ACTCCGTCAC
27814292 TGCTTTTATTCAAAATACATTAATCTATTCTATTA
1 TGCTTTTATTCAAAATACATTAATCTATTCTATTA
27814327 TGCTTTTATTCAAAATACATTAATCTATTCTATTA
1 TGCTTTTATTCAAAATACATTAATCTATTCTATTA
27814362 T
1 T
27814363 TAAGTTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (35 bp):
TGCTTTTATTCAAAATACATTAATCTATTCTATTA
Found at i:27815338 original size:17 final size:18
Alignment explanation
Indices: 27815316--27815350 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27815306 AAAATCGAAA
*
27815316 TGAATTTT-TATTTTTAT
1 TGAATTTTAAATTTTTAT
27815333 TGAATTTTAAATTTTTAT
1 TGAATTTTAAATTTTTAT
27815351 GATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TGAATTTTAAATTTTTAT
Found at i:27817000 original size:12 final size:13
Alignment explanation
Indices: 27816981--27817014 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
27816971 AGCTCTTTTC
27816981 TCCTTTTTCTT-T
1 TCCTTTTTCTTCT
*
27816993 TTCTTTTTCTTCT
1 TCCTTTTTCTTCT
27817006 TCCTTTTTC
1 TCCTTTTTC
27817015 CCTTTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TCCTTTTTCTTCT
Found at i:27819459 original size:9 final size:9
Alignment explanation
Indices: 27819445--27819536 Score: 51
Period size: 9 Copynumber: 9.3 Consensus size: 9
27819435 ATTATATTTT
27819445 AAATTATAA
1 AAATTATAA
27819454 AAATTAT-A
1 AAATTATAA
27819462 AAATTAATAA
1 AAATT-ATAA
*
27819472 AACTTATTTAA
1 AAATTA--TAA
**
27819483 ATTTTAATAA
1 AAATT-ATAA
*
27819493 AAATGATAA
1 AAATTATAA
*
27819502 AAGTTGATAA
1 AAATT-ATAA
27819512 AAACTTATTGAAA
1 AAA-TTA-T--AA
27819525 AAATTATAA
1 AAATTATAA
27819534 AAA
1 AAA
27819537 ATAGTCGTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
8 6 0.09
9 22 0.34
10 17 0.27
11 10 0.16
12 4 0.06
13 5 0.08
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Done.