Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 124 of 132
Found at i:38092333 original size:18 final size:18
Alignment explanation
Indices: 38092312--38092348 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38092302 TCAAATTTAG
38092312 AATTTAATCCATATTTTT
1 AATTTAATCCATATTTTT
* *
38092330 AATTTGATCTATATTTTT
1 AATTTAATCCATATTTTT
38092348 A
1 A
38092349 TAATATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTTAATCCATATTTTT
Found at i:38092932 original size:33 final size:31
Alignment explanation
Indices: 38092864--38092942 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
38092854 AATATAATAT
* *
38092864 TTGGTACTTGAACTTGACACTTTTTACTAAT
1 TTGGTACTTAAACTTGACACTTTTTACTAAG
* **
38092895 TTGGTACCTAAACTTGACACTTTTTTTTTAAAG
1 TTGGTACTTAAACTTGACAC-TTTTTACT-AAG
*
38092928 TTGGTGCTTAAACTT
1 TTGGTACTTAAACTT
38092943 TTTGGGATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 18 0.46
32 6 0.15
33 15 0.38
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTACTAAG
Found at i:38093217 original size:28 final size:27
Alignment explanation
Indices: 38093141--38093231 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 27
38093131 AATTGAATCT
38093141 AAAAAAAAG-TTAGGTATCAAATTAGG
1 AAAAAAAAGTTTAGGTATCAAATTAGG
* * *
38093167 AAAAAATGCCAAGTTCAGATATCAAATTGGG
1 AAAAAA----AAGTTTAGGTATCAAATTAGG
*
38093198 TCAAAAAAAGTTTAGGTATCAAATTAGG
1 -AAAAAAAAGTTTAGGTATCAAATTAGG
38093226 AAAAAA
1 AAAAAA
38093232 TATTAGGTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
26 6 0.12
27 5 0.10
28 18 0.35
30 3 0.06
31 14 0.27
32 5 0.10
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.23
Consensus pattern (27 bp):
AAAAAAAAGTTTAGGTATCAAATTAGG
Found at i:38093242 original size:59 final size:58
Alignment explanation
Indices: 38093142--38093252 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 58
38093132 ATTGAATCTA
*
38093142 AAAAAAAGTTAGGTATCAAATTAGGAAAAAATGCCAAGTTC-AGATATCAAATTGGGTC
1 AAAAAAAGTTAGGTATCAAATTAGGAAAAAATACCAAGTTCAAG-TATCAAATTGGGTC
** *
38093200 AAAAAAAGTTTAGGTATCAAATTAGGAAAAAATATTAGGTTCAAGTATCAAAT
1 AAAAAAAG-TTAGGTATCAAATTAGGAAAAAATACCAAGTTCAAGTATCAAAT
38093253 GTTATATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
58 8 0.17
59 37 0.79
60 2 0.04
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (58 bp):
AAAAAAAGTTAGGTATCAAATTAGGAAAAAATACCAAGTTCAAGTATCAAATTGGGTC
Found at i:38096653 original size:13 final size:13
Alignment explanation
Indices: 38096635--38096660 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38096625 TCTAGTGGAC
38096635 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
38096648 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
38096661 CAGGAATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:38106830 original size:3 final size:3
Alignment explanation
Indices: 38106822--38106848 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38106812 ATATAATGCC
38106822 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
38106849 TGTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:38119474 original size:24 final size:25
Alignment explanation
Indices: 38119435--38119483 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
38119425 TTATATTTTT
* * *
38119435 AATTTTTAATATTTTATAATTATAA
1 AATTTTGAATATTTTAGAATAATAA
38119460 AATTTTGAATA-TTTAGAATAATAA
1 AATTTTGAATATTTTAGAATAATAA
38119484 TTGAGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
AATTTTGAATATTTTAGAATAATAA
Found at i:38126745 original size:24 final size:24
Alignment explanation
Indices: 38126700--38126745 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38126690 TTTTATATTA
*
38126700 ATATTAATGTAAATTAATATAATT
1 ATATTAATGTAAATTAAAATAATT
*
38126724 ATATTAATATTAAA-TAAAATAA
1 ATATTAAT-GTAAATTAAAATAA
38126746 ACCCTTACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATTAATGTAAATTAAAATAATT
Found at i:38126766 original size:6 final size:6
Alignment explanation
Indices: 38126757--38126784 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38126747 CCCTTACCCG
38126757 TCCCTC TCCCTC TCCCTC TCCCTC TCCC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCC
38126785 CCACTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
TCCCTC
Found at i:38126802 original size:18 final size:19
Alignment explanation
Indices: 38126757--38126816 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
38126747 CCCTTACCCG
* * *
38126757 TCCCTCTCCCTCTCCCTC-
1 TCCCTCTCCCCCACCATCA
*
38126775 TCCCTCTCCCCCACTATCA
1 TCCCTCTCCCCCACCATCA
*
38126794 TCCCT-TCCCTCACCATCA
1 TCCCTCTCCCCCACCATCA
38126812 -CCCTC
1 TCCCTC
38126817 ACACTCTCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 4 0.12
18 25 0.74
19 5 0.15
ACGTcount: A:0.10, C:0.62, G:0.00, T:0.28
Consensus pattern (19 bp):
TCCCTCTCCCCCACCATCA
Found at i:38127062 original size:7 final size:7
Alignment explanation
Indices: 38127050--38127093 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
38127040 GGACGGGTGT
38127050 GGGGGGA
1 GGGGGGA
38127057 GGGGGGA
1 GGGGGGA
38127064 GGGGGGA
1 GGGGGGA
38127071 GGGGGGA
1 GGGGGGA
38127078 GGGGGGA
1 GGGGGGA
38127085 -GGGGGA
1 GGGGGGA
38127091 GGG
1 GGG
38127094 ATGTTGGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (7 bp):
GGGGGGA
Found at i:38130662 original size:28 final size:27
Alignment explanation
Indices: 38130618--38130672 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
38130608 CGAGTTAAAC
38130618 TAAAAATTTTGATTTTTTTATTCAAGT
1 TAAAAATTTTGATTTTTTTATTCAAGT
38130645 TAAAAATTTTGATTTTTTTATTCAAGT
1 TAAAAATTTTGATTTTTTTATTCAAGT
38130672 T
1 T
38130673 GATCCGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (27 bp):
TAAAAATTTTGATTTTTTTATTCAAGT
Found at i:38132470 original size:15 final size:15
Alignment explanation
Indices: 38132450--38132479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38132440 AATAATAATA
38132450 TAATTTACTCTATAG
1 TAATTTACTCTATAG
*
38132465 TAATTTACTTTATAG
1 TAATTTACTCTATAG
38132480 AAAATGGATT
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:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
TAATTTACTCTATAG
Found at i:38164841 original size:21 final size:21
Alignment explanation
Indices: 38164806--38164859 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
38164796 ACAAATTAGT
* * *
38164806 AAATATGTATAAAAACATAATA
1 AAATATTTTTAAAAATA-AATA
*
38164828 AAATATTTTTAAAATTAAATA
1 AAATATTTTTAAAAATAAATA
*
38164849 TAATATTTTTA
1 AAATATTTTTA
38164860 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATATTTTTAAAAATAAATA
Found at i:38165579 original size:34 final size:34
Alignment explanation
Indices: 38165540--38165604 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
38165530 GCAACAGCAG
38165540 TGAGTTGATTGAAGTTTGACTGCTGCAGCAACAA
1 TGAGTTGATTGAAGTTTGACTGCTGCAGCAACAA
*
38165574 TGAGTTGATTGAAGTTTGATTGCTGCAGCAA
1 TGAGTTGATTGAAGTTTGACTGCTGCAGCAA
38165605 ACACTTCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (34 bp):
TGAGTTGATTGAAGTTTGACTGCTGCAGCAACAA
Found at i:38166318 original size:25 final size:23
Alignment explanation
Indices: 38166282--38166327 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
38166272 TTATTATATA
38166282 TGTTTAAATTGTTGTGAGATTATCG
1 TGTTTAAATTGTT-TG-GATTATCG
*
38166307 TGTTTAATTTGTTTGGATTAT
1 TGTTTAAATTGTTTGGATTAT
38166328 TATTTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (23 bp):
TGTTTAAATTGTTTGGATTATCG
Found at i:38166403 original size:21 final size:21
Alignment explanation
Indices: 38166379--38166418 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38166369 TTATAAATGA
*
38166379 ATTTTATTTAAAATTATTTTT
1 ATTTGATTTAAAATTATTTTT
* *
38166400 ATTTGATTTTATATTATTT
1 ATTTGATTTAAAATTATTT
38166419 CTCAAATTTG
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:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTGATTTAAAATTATTTTT
Found at i:38169442 original size:19 final size:18
Alignment explanation
Indices: 38169409--38169444 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38169399 GTTCACAAGC
38169409 TGTTAATATCAGTTAGTT
1 TGTTAATATCAGTTAGTT
*
38169427 TGTTATTATACAGTTAGT
1 TGTTAATAT-CAGTTAGT
38169445 AGTTGCTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (18 bp):
TGTTAATATCAGTTAGTT
Found at i:38170730 original size:15 final size:16
Alignment explanation
Indices: 38170676--38170731 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 16
38170666 TATATTTACC
38170676 TCATATTACATTTTAG
1 TCATATTACATTTTAG
*
38170692 TCAT-TTATA-TTT-G
1 TCATATTACATTTTAG
**
38170705 AAATATTACATTTTAG
1 TCATATTACATTTTAG
38170721 TCAT-TTACATT
1 TCATATTACATT
38170732 ATCATTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 14 0.45
16 7 0.23
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (16 bp):
TCATATTACATTTTAG
Found at i:38174265 original size:13 final size:14
Alignment explanation
Indices: 38174240--38174269 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
38174230 TTACACCTTA
38174240 AAACTCAAAATATT
1 AAACTCAAAATATT
38174254 AAACTC-AAATATT
1 AAACTCAAAATATT
38174267 AAA
1 AAA
38174270 AATTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACTCAAAATATT
Found at i:38177828 original size:26 final size:26
Alignment explanation
Indices: 38177797--38177850 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
38177787 CAGCTTGTTA
38177797 CATGGTCTAAATCATTCCCTATACAC
1 CATGGTCTAAATCATTCCCTATACAC
*
38177823 CATGGTCTAGATCATTCCCTATACAC
1 CATGGTCTAAATCATTCCCTATACAC
38177849 CA
1 CA
38177851 GTAAATGTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (26 bp):
CATGGTCTAAATCATTCCCTATACAC
Found at i:38180514 original size:31 final size:31
Alignment explanation
Indices: 38180450--38180520 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
38180440 TAAGTTAGTC
* *
38180450 CTTGAACTTGACAATTGTTCTCATATTAGGA
1 CTTGAACTTGACAATTGTTCTAACATTAGGA
*
38180481 CTTGAACTTGGCAATTGTTCTAACATT-GAGA
1 CTTGAACTTGACAATTGTTCTAACATTAG-GA
*
38180512 CTTAAACTT
1 CTTGAACTT
38180521 TAGGGTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (31 bp):
CTTGAACTTGACAATTGTTCTAACATTAGGA
Found at i:38185000 original size:16 final size:16
Alignment explanation
Indices: 38184981--38185011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38184971 TTTAAATTAT
38184981 ATAATATAAAAATAAC
1 ATAATATAAAAATAAC
*
38184997 ATAATATAAATATAA
1 ATAATATAAAAATAA
38185012 AGTATTATAA
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATATAAAAATAAC
Found at i:38193656 original size:2 final size:2
Alignment explanation
Indices: 38193649--38193673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38193639 TACTTAATTA
38193649 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
38193674 AAAACAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:38194255 original size:55 final size:56
Alignment explanation
Indices: 38194186--38194330 Score: 186
Period size: 55 Copynumber: 2.6 Consensus size: 56
38194176 CCCTATTAAA
* * **
38194186 AATCGATTGTTTATATATTTAAATTGATTGTTATG-GTAGAATACTGTTTCTTTTG
1 AATCGATTGTTTATATGTTTAAATCGATTGTTATGAGTAGAATACTACTTCTTTTG
* * * * *
38194241 AATCAATTGTTTATATGTTTAAATCAATTGTTA-GATTGGAATATTACTTCTTTTG
1 AATCGATTGTTTATATGTTTAAATCGATTGTTATGAGTAGAATACTACTTCTTTTG
*
38194296 AATCGTTTGTTTATATGTTTAAATCGATTGTTATG
1 AATCGATTGTTTATATGTTTAAATCGATTGTTATG
38194331 TAGCACGATT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 1 0.01
55 74 0.97
56 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.50
Consensus pattern (56 bp):
AATCGATTGTTTATATGTTTAAATCGATTGTTATGAGTAGAATACTACTTCTTTTG
Found at i:38198300 original size:34 final size:33
Alignment explanation
Indices: 38198226--38198321 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 33
38198216 AATAATAGTC
* *
38198226 TTAATATTTT-ATAAAAAATAT-TAATATTAATA
1 TTAATATTTTAATAATAAATATATATTA-TAATA
*
38198258 TTAATATTTTAATAATAAATATATATTATAATT
1 TTAATATTTTAATAATAAATATATATTATAATA
38198291 TATAATATTTTAATAATACAA-ATATGATTAT
1 T-TAATATTTTAATAATA-AATATAT-ATTAT
38198322 TTATTTAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
32 10 0.18
33 15 0.27
34 24 0.43
35 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
TTAATATTTTAATAATAAATATATATTATAATA
Found at i:38198314 original size:17 final size:16
Alignment explanation
Indices: 38198228--38198315 Score: 56
Period size: 17 Copynumber: 5.3 Consensus size: 16
38198218 TAATAGTCTT
38198228 AATATTTT-ATAA-AA
1 AATATTTTAATAATAA
* * *
38198242 AATATTAATATTAATATT
1 AATATT-TTAATAATA-A
38198260 AATATTTTAATAATAA
1 AATATTTTAATAATAA
* *
38198276 ATATATATTATAAT-TTAT
1 A-ATAT-TT-TAATAATAA
38198294 AATATTTTAATAATACA
1 AATATTTTAATAATA-A
38198311 AATAT
1 AATAT
38198316 GATTATTTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
14 6 0.11
15 5 0.09
16 8 0.15
17 21 0.38
18 11 0.20
19 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTTTAATAATAA
Found at i:38199196 original size:12 final size:12
Alignment explanation
Indices: 38199179--38199206 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38199169 GACATATTTT
38199179 AACTATAAGTAG
1 AACTATAAGTAG
38199191 AACTATAAGTAG
1 AACTATAAGTAG
38199203 AACT
1 AACT
38199207 GGTTAGCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (12 bp):
AACTATAAGTAG
Found at i:38206997 original size:15 final size:16
Alignment explanation
Indices: 38206977--38207012 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
38206967 ACAAATTTAC
38206977 AAAAAATTAAA-TTAA
1 AAAAAATTAAACTTAA
38206992 AAAAAATTAAACTTTAA
1 AAAAAATTAAAC-TTAA
38207009 AAAA
1 AAAA
38207013 TCATGATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAATTAAACTTAA
Found at i:38207408 original size:31 final size:31
Alignment explanation
Indices: 38207340--38207405 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
38207330 ATAATTTATG
* *
38207340 TTTTTA-TATTTTTTAAAATATTAAATTAAA
1 TTTTTATTATTTTTTAAAAAATTAAAATAAA
38207370 TTTTTATTA-TTTTTAGAAAAATTAAAATATAA
1 TTTTTATTATTTTTTA-AAAAATTAAAATA-AA
38207402 TTTT
1 TTTT
38207406 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 12 0.39
31 13 0.42
32 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTTTATTATTTTTTAAAAAATTAAAATAAA
Found at i:38208341 original size:3 final size:3
Alignment explanation
Indices: 38208333--38208361 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38208323 TGATTTCTAA
38208333 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38208362 GTTGTGTTTG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:38211010 original size:57 final size:57
Alignment explanation
Indices: 38210934--38211246 Score: 301
Period size: 57 Copynumber: 5.4 Consensus size: 57
38210924 AAAAATTGGG
*** * * *
38210934 GGTGTTGGCCATTGCATGGCCGACAACCACTGTT-TCA-AAAAAAATTTAAAATTTTTT
1 GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCAGAAAAAAA-TT-AAATTTTTT
* * *
38210991 GGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTC-GAAAAAAATTACATTTTTG
1 GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCAGAAAAAAATTAAATTTTTT
* * ** *
38211047 GGTATTGGCCATCAAATGGCCGACACTCCCTTTTCTCGAGAAAAAAATTGCATTTTTG
1 GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTC-AGAAAAAAATTAAATTTTTT
*** * *
38211105 GGTGTTGGCCATTGCATGGCCGACACCCCCTGTT-TCAGAAAAAAATTCAATTTTTTT
1 GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCAGAAAAAAATT-AAATTTTTT
* * *
38211162 TGTGTTGGCCATCAAATGGTCGACACCCCCTTTTCTCGAATAAAAAAATTTCAAATTTTTTT
1 GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTC--AGAAAAAAA-TT-AAA-TTTTTT
**
38211224 TATGTTGGCCATCAAATGGCCGA
1 GGTGTTGGCCATCAAATGGCCGA
38211247 TACCAACTTC
Statistics
Matches: 214, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
56 52 0.24
57 65 0.30
58 57 0.27
60 8 0.04
61 5 0.02
62 27 0.13
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (57 bp):
GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCAGAAAAAAATTAAATTTTTT
Found at i:38212147 original size:30 final size:30
Alignment explanation
Indices: 38212074--38212165 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
38212064 AAATAATTAG
* * ** *
38212074 AATATACATGAAATTAGAAAGAAAAATTAA
1 AATATAAAAGAAATTAGAAATTAAATTTAA
* *
38212104 AATATACAAGAAATTCGAAATTAAATTTAA
1 AATATAAAAGAAATTAGAAATTAAATTTAA
*
38212134 AATA-AAAACGAAATTATAAATTAAATTTAA
1 AATATAAAA-GAAATTAGAAATTAAATTTAA
38212164 AA
1 AA
38212166 AGCAAAGGGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 3 0.06
30 50 0.94
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (30 bp):
AATATAAAAGAAATTAGAAATTAAATTTAA
Found at i:38215425 original size:23 final size:23
Alignment explanation
Indices: 38215397--38215520 Score: 126
Period size: 23 Copynumber: 5.3 Consensus size: 23
38215387 ACACTAGCGC
38215397 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
38215420 GTTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
38215443 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* * *
38215468 GCTCTCTGATTAGTACTTTATGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
38215491 ACTCTCT-ATTTAGCACTTTGTGT
1 GCTCTCTGA-TTAGCACTGTGTGT
38215514 GCTCTCT
1 GCTCTCT
38215521 ATTCAATACT
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
22 4 0.05
23 59 0.71
25 17 0.20
26 3 0.04
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:38215496 original size:48 final size:47
Alignment explanation
Indices: 38215398--38215545 Score: 137
Period size: 48 Copynumber: 3.2 Consensus size: 47
38215388 CACTAGCGCG
* * * * *
38215398 CTCTCTG--ATTAGCACTGTGTGTGTTCTCTGTTTAGCACGTCTCGTG
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTAC-TTTCGTA
*
38215444 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTATGTA
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTT-CGTA
* * *
38215492 CTCTCT-AT-TTAGCACTTTGTGTGCTCTCT-ATTCAATAC-TTCGGTA
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT-AGTACTTTC-GTA
38215537 CTCTCTGTT
1 CTCTCTGTT
38215546 TGTTCCGTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
45 14 0.16
46 32 0.38
47 3 0.04
48 36 0.42
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (47 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTCGTA
Found at i:38218772 original size:61 final size:59
Alignment explanation
Indices: 38218704--38219166 Score: 390
Period size: 61 Copynumber: 7.8 Consensus size: 59
38218694 AGGAGAAGTT
* * *
38218704 GGTGTCGGCCATTTGATAGCCAACACCAAAAAAATTTAGAATTTTTTTATTCGAGAAAAAG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTA-AATTTTTTT-TTCGAGAAAAGG
* * *
38218765 GGTGTCGGCCATTTGATGGCCAACACGAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTTTCGAGAAAA-GG
* *
38218825 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTGAAATTTTTTTTCTCGAGAAAAGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTT-TCGAGAAAAGG
* * * *
38218885 TTGGTGTCGGCCATTTGATGGCCAATACAAAAAAAATTTGAATTTTTTTTCCGA-AATAGGG
1 --GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTTTCGAGAA-AAGG
* * *** ** ** * * * *
38218946 GGTGTCGACTATGCAATGGCCAACAC-CCAAAAA-TGCAATTTTTTTCTCAAAAAAAAG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTTTCGAGAAAAGG
** * * * * * *
38219003 GGTGTTAGCCATTTGATGGCTAACACCAAAAGAATTTGAATTTTTTTCT-GA-AACAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTTTCGAGAA-AAGG
* ** *
38219061 GGTGTCGACCATTTGA-GGACCAA-A-ATCCAAAAATAT-AA--TTTTTTTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGG-CCAACACA-AAAAAAATTTAAATTTTTTTTTCGAGAAAA-GG
* *
38219117 GGTGTCGGCCATTTGATGGCCAACACTAAAAAATTTTGAAATTTTTTTTT
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTT-AAATTTTTTTTT
38219167 GAAACAGTGA
Statistics
Matches: 317, Mismatches: 64, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
54 6 0.02
55 3 0.01
56 25 0.08
57 52 0.16
58 30 0.09
59 43 0.14
60 56 0.18
61 58 0.18
62 44 0.14
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTTTCGAGAAAAGG
Found at i:38218855 original size:59 final size:60
Alignment explanation
Indices: 38218704--38219163 Score: 365
Period size: 60 Copynumber: 7.8 Consensus size: 60
38218694 AGGAGAAGTT
* * * * * *
38218704 GGTGTCGGCCATTTGATAGCCAACACCAAAAAAATTTAGAATTTTTTTATTCGAGAAAA-AG
1 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTA-AAATTTTTT-CTCGAGAAAAGGG
* *
38218765 GGTGTCGGCCATTTGATGGCCAACACGAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
1 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
* * *
38218825 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTGAAATTTTTTTTCTCGAGAAAAGGTT
1 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTAAA-ATTTTTTCTCGAGAAAAGG-G
* * * * *
38218887 GGTGTCGGCCATTTGATGGCCAATACAAAAAAAATTT-GAATTTTTTTTCCGA-AATAGGG
1 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTTCT-CGAGAAAAGGG
* *** ** ** * * **
38218946 GGTGTCGACTATGCAATGGCCAACAC-CCAAAAA-TGCAATTTTTTTCTC-AAAAAAAAG
1 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
* * * * * * *
38219003 GGTGT-TAGCCATTTGATGGCTAACACCAAAAGAATTTGAATTTTTTTCT-GA-AACAGGG
1 GGTGTCGA-CCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
** *
38219061 GGTGTCGACCATTTGA-GGACCAA-A-ATCCAAAAA--TATAATTTTTT-TCGAGAAAAGGG
1 GGTGTCGACCATTTGATGG-CCAACACA-AAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
* * * *
38219117 GGTGTCGGCCATTTGATGGCCAACACTAAAAAATTTTGAAATTTTTT
1 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTT
38219164 TTTGAAACAG
Statistics
Matches: 315, Mismatches: 64, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
54 1 0.00
55 10 0.03
56 27 0.09
57 38 0.12
58 37 0.12
59 52 0.17
60 58 0.18
61 58 0.18
62 34 0.11
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (60 bp):
GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
Found at i:38219104 original size:115 final size:114
Alignment explanation
Indices: 38218704--38219182 Score: 431
Period size: 115 Copynumber: 4.1 Consensus size: 114
38218694 AGGAGAAGTT
* * * * * *
38218704 GGTGTCGGCCATTTGATAGCCAACACCAAAAAAATTTAGAATTTTTTTATTCGAGAAAAAGGGTG
1 GGTGTCGACCATTTGATGGCCAACACC--AAAAA--TATAATTTTTTT-CTCAAAAAAAAGGGTG
* * * *
38218769 TCGGCCATTTGATGGCCAACACGAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
61 TCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTCT-GA-AACAGGG
* * * * *
38218825 GGTGTCGACCATTTGATGGCCAACACAAAAAAAATTGAAATTTTTTTTCTCGAGAAAAGGTTGGT
1 GGTGTCGACCATTTGATGGCCAACACCAAAAATA-T--AA-TTTTTTTCTCAAAAAAAAG--GGT
* * *
38218890 GTCGGCCATTTGATGGCCAATACAAAAAAAATTTGAATTTTTTTTCCGAAATAGGG
60 GTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAA-TTTTTTTCTGAAACAGGG
* *** ** **
38218946 GGTGTCGACTATGCAATGGCCAACACCCAAAAATGCAATTTTTTTCTCAAAAAAAAGGGTGTTAG
1 GGTGTCGACCATTTGATGGCCAACA-CCAAAAATATAATTTTTTTCTCAAAAAAAAGGGTGTCGG
* * *
38219011 CCATTTGATGGCTAACACCAAAAGAATTTGAATTTTTTTCTGAAACAGGG
65 CCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTCTGAAACAGGG
* * * **
38219061 GGTGTCGACCATTTGA-GGACCAAAATCCAAAAATATAATTTTTTTC-GAGAAAAGGGGGTGTCG
1 GGTGTCGACCATTTGATGG-CCAACA-CCAAAAATATAATTTTTTTCTCAAAAAAAAGGGTGTCG
* * * *
38219124 GCCATTTGATGGCCAACACTAAAAAATTTTGAAATTTTTTTTTGAAACAGTG
64 GCCATTTGATGGCCAACACAAAAAAAATTTG-AATTTTTTTCTGAAACAGGG
*
38219176 AGTGTCG
1 GGTGTCG
38219183 GCTATGCAAT
Statistics
Matches: 295, Mismatches: 53, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
114 40 0.14
115 75 0.25
116 34 0.12
117 1 0.00
118 16 0.05
119 7 0.02
120 12 0.04
121 58 0.20
122 45 0.15
123 7 0.02
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
GGTGTCGACCATTTGATGGCCAACACCAAAAATATAATTTTTTTCTCAAAAAAAAGGGTGTCGGC
CATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTCTGAAACAGGG
Found at i:38219181 original size:59 final size:59
Alignment explanation
Indices: 38218704--38219184 Score: 414
Period size: 59 Copynumber: 8.2 Consensus size: 59
38218694 AGGAGAAGTT
* * *
38218704 GGTGTCGGCCATTTGATAGCCAACACCAAAAAAATTTAGAATTTTTTTATTCGAGAAAA-AG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT-GAAATTTTTT-TTCGA-AAAAGGG
* * *
38218765 GGTGTCGGCCATTTGATGGCCAACACGAAAAAAATTTAAAATTTTTTCTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTTCGA-AAAAGGG
* * *
38218825 GGTGTCGACCATTTGATGGCCAACA-CAAAAAAAATTGAAATTTTTTTTCTCGAGAAAAGGTT
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAA-TTTTTTT-TCGA-AAAAGG-G
* * *
38218887 GGTGTCGGCCATTTGATGGCCAATACAAAAAAAATTTG-AATTTTTTTTCCGAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTT-CGAAAAAGGG
* * *** * * * **
38218946 GGTGTCGACTATGCAATGGCCAACACC-CAAAAA--TGCAATTTTTTTCTCAAAAAAAAG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTT-TCGAAAAAGGG
** * * *
38219003 GGTGTTAGCCATTTGATGGCTAACACCAAAAGAATTTG-AA-TTTTTTTCTGAAACAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTTC-GAAAAAGGG
* * *
38219061 GGTGTCGACCATTTGA-GGACCAAAATCC--AAAAATAT--AA-TTTTTTTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGG-CCAACA-CCAAAAAAATTTGAAATTTTTTTTCGA-AAAAGGG
* * * * *
38219117 GGTGTCGGCCATTTGATGGCCAACACTAAAAAATTTTGAAATTTTTTTTTGAAACAGTG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTTCGAAAAAGGG
*
38219176 AGTGTCGGC
1 GGTGTCGGC
38219185 TATGCAATGG
Statistics
Matches: 338, Mismatches: 61, Indels: 44
0.76 0.14 0.10
Matches are distributed among these distances:
55 3 0.01
56 38 0.11
57 52 0.15
58 38 0.11
59 60 0.18
60 56 0.17
61 56 0.17
62 25 0.07
63 10 0.03
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTTCGAAAAAGGG
Found at i:38234064 original size:24 final size:24
Alignment explanation
Indices: 38234036--38234098 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
38234026 AGAAATAATC
* *
38234036 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTA
*
38234060 TTTCAATTAAACTCTATTTATTTA
1 TTTCAGTTAAACTCTATTTATTTA
* *
38234084 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
38234099 TATTACTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTA
Found at i:38236630 original size:23 final size:23
Alignment explanation
Indices: 38236600--38236751 Score: 105
Period size: 23 Copynumber: 6.5 Consensus size: 23
38236590 ACGCTAGCGC
38236600 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* *
38236623 GCTTACTGTTTCTCACCTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * * *
38236646 GCCTACTGATTT-GCGCTATGTGC
1 GCTTACTG-TTTCGCACTTTGTGT
* * *
38236669 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * * *
38236691 GCCTACTGGATT-GTACTGTGTGT
1 GCTTACT-GTTTCGCACTTTGTGT
38236714 GCTTACTGTTTCCCCAGCAC-TTGTGT
1 GCTTACTGTTT---C-GCACTTTGTGT
38236740 GCTTACTGTTTC
1 GCTTACTGTTTC
38236752 CCCAGCACTT
Statistics
Matches: 105, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
22 20 0.19
23 63 0.60
24 3 0.03
26 16 0.15
27 3 0.03
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:38236721 original size:45 final size:46
Alignment explanation
Indices: 38236603--38236721 Score: 111
Period size: 45 Copynumber: 2.6 Consensus size: 46
38236593 CTAGCGCGCT
* * *
38236603 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCTCACCTTGTGTGCC
1 TACTGATTT-GCACTATGTGTGCTTACTGATTCGCACCTTGTGTGCC
* * *
38236649 TACTGATTTGCGCTATGTGCGCCTACTGATT-GCA-CTGTGTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACCT-TGTGTGCC
* *
38236694 TACTGGA-TTGTACTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
38236722 TTTCCCCAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.03
45 30 0.51
46 24 0.41
47 3 0.05
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACCTTGTGTGCC
Found at i:38236739 original size:26 final size:26
Alignment explanation
Indices: 38236709--38236775 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
38236699 GATTGTACTG
38236709 TGTGTGCTTACTGTTTCCCCAGCACT
1 TGTGTGCTTACTGTTTCCCCAGCACT
38236735 TGTGTGCTTACTGTTTCCCCAGCACT
1 TGTGTGCTTACTGTTTCCCCAGCACT
*
38236761 TGTGTGCTTATTGTT
1 TGTGTGCTTACTGTT
38236776 AAGTACTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.43
Consensus pattern (26 bp):
TGTGTGCTTACTGTTTCCCCAGCACT
Found at i:38238536 original size:24 final size:24
Alignment explanation
Indices: 38238503--38238549 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38238493 AGAAATAATC
* *
38238503 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
38238527 TTTCAATTAAACTCTATTTATTT
1 TTTCAATTAAACTCTATTTATTT
38238550 ATTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:38238562 original size:24 final size:24
Alignment explanation
Indices: 38238511--38238565 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
38238501 TCTTTCAGTT
* * *
38238511 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTATTTCAATC
* *
38238535 AAACTCTATTTATTTATTTGAGTC
1 AAACTCTATTTATTTATTTCAATC
38238559 AAACTCT
1 AAACTCT
38238566 TATTACTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTATTTCAATC
Found at i:38245207 original size:21 final size:24
Alignment explanation
Indices: 38245152--38245215 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
38245142 GGTGATCAAC
*
38245152 AACAGCAGGAGCTGCAACATGAGG
1 AACAGCAGCAGCTGCAACATGAGG
38245176 AACAGCAGCAGCTGCAACATGAGG
1 AACAGCAGCAGCTGCAACATGAGG
38245200 AACAGCAGCAGCTGCA
1 AACAGCAGCAGCTGCA
38245216 TCAGCAACAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.38, C:0.25, G:0.30, T:0.08
Consensus pattern (24 bp):
AACAGCAGCAGCTGCAACATGAGG
Found at i:38245224 original size:21 final size:22
Alignment explanation
Indices: 38245146--38245225 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 22
38245136 TGGCAAGGTG
* *
38245146 ATCAACAACAGCAGGAGCTGCAAC
1 ATCAGCAACAGCAGCAGCTG--AC
* *
38245170 ATGAGGAACAGCAGCAGCTGCAAC
1 ATCAGCAACAGCAGCAGCTG--AC
* *
38245194 ATGAGGAACAGCAGCAGCTG-C
1 ATCAGCAACAGCAGCAGCTGAC
38245215 ATCAGCAACAG
1 ATCAGCAACAG
38245226 AATGATTCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.20
24 40 0.80
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.09
Consensus pattern (22 bp):
ATCAGCAACAGCAGCAGCTGAC
Found at i:38269933 original size:4 final size:4
Alignment explanation
Indices: 38269924--38269953 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
38269914 CCATGGAATG
38269924 CATT CATT CATT CATT CAATT CATT CATT C
1 CATT CATT CATT CATT C-ATT CATT CATT C
38269954 TGTAGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (4 bp):
CATT
Found at i:38283874 original size:31 final size:31
Alignment explanation
Indices: 38283798--38283877 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
38283788 TTATTGTAAG
* *
38283798 GCATGGAAATTGAAACAATAAGGAGGTATAA
1 GCATGGAAATTGAAGCAATAAGGAGGCATAA
*
38283829 TCATGGAAATTGAAGCAATAACGG-GGCATAA
1 GCATGGAAATTGAAGCAATAA-GGAGGCATAA
*
38283860 GCATAGAAATTGAAGCAA
1 GCATGGAAATTGAAGCAA
38283878 ATGAAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 41 0.95
32 2 0.05
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (31 bp):
GCATGGAAATTGAAGCAATAAGGAGGCATAA
Found at i:38286119 original size:6 final size:6
Alignment explanation
Indices: 38286110--38286148 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
38286100 CTTTCTCATT
38286110 GTCGGC GTCGGC GTCGGC GTCGGC GTCGGC GTCGGC GTC
1 GTCGGC GTCGGC GTCGGC GTCGGC GTCGGC GTCGGC GTC
38286149 ATCTTCGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.49, T:0.18
Consensus pattern (6 bp):
GTCGGC
Found at i:38286255 original size:6 final size:6
Alignment explanation
Indices: 38286147--38286254 Score: 108
Period size: 6 Copynumber: 17.5 Consensus size: 6
38286137 GGCGTCGGCG
* * * * *
38286147 TCATCT TCGTCT TCGTCT TCTTCT TCATCAT CCTCATCT TCATCC CCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT
* * *
38286198 CCATCT TCATCC TCATTT TCATCT TCATCT TCATCT TCATCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
38286246 TCAGCT TCA
1 TCATCT TCA
38286255 GGCTCAGTCT
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
6 80 0.92
7 1 0.01
8 1 0.01
9 5 0.06
ACGTcount: A:0.15, C:0.37, G:0.03, T:0.45
Consensus pattern (6 bp):
TCATCT
Found at i:38297664 original size:16 final size:16
Alignment explanation
Indices: 38297640--38297678 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38297630 CACAGACGCG
*
38297640 AAGACAAAAAAAAGAA
1 AAGAAAAAAAAAAGAA
*
38297656 AAGAAAAAAGAAAGAA
1 AAGAAAAAAAAAAGAA
38297672 AGAGAAA
1 A-AGAAA
38297679 GCATTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAGAA
Found at i:38304988 original size:18 final size:18
Alignment explanation
Indices: 38304965--38305001 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38304955 AAAAGAACGC
*
38304965 AAATAAAGAAACGAAAGA
1 AAATAAACAAACGAAAGA
*
38304983 AAATAAACAAATGAAAGA
1 AAATAAACAAACGAAAGA
38305001 A
1 A
38305002 GGGGGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (18 bp):
AAATAAACAAACGAAAGA
Found at i:38312054 original size:17 final size:18
Alignment explanation
Indices: 38312032--38312065 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38312022 AAATTGCTTC
*
38312032 AAATTGATA-AAAATAAA
1 AAATTGAGACAAAATAAA
38312049 AAATTGAGACAAAATAA
1 AAATTGAGACAAAATAA
38312066 TCAACAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATTGAGACAAAATAAA
Found at i:38316199 original size:59 final size:60
Alignment explanation
Indices: 38316117--38316229 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
38316107 ACGCTTTAAA
* *
38316117 TAAATGGAATAATAGAATCTATTG-AAATTTGACCTTTGGAGCTCGTTTTAATGTTGAAG
1 TAAATGAAATAATAGAATCTATTGAAAATTTGACCTTTGGAACTCGTTTTAATGTTGAAG
* * *
38316176 TAAATGAAATATTAGAATGTATTGAAAATTTGACTTTTGGAACTCGTTTTAATG
1 TAAATGAAATAATAGAATCTATTGAAAATTTGACCTTTGGAACTCGTTTTAATG
38316230 CTTAAGTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 21 0.44
60 27 0.56
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (60 bp):
TAAATGAAATAATAGAATCTATTGAAAATTTGACCTTTGGAACTCGTTTTAATGTTGAAG
Found at i:38316550 original size:16 final size:16
Alignment explanation
Indices: 38316521--38316555 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38316511 ATAAGTTTCA
*
38316521 TATTTGTTATATATTT
1 TATTTGTTAAATATTT
*
38316537 TATTTTTTAAATATTT
1 TATTTGTTAAATATTT
38316553 TAT
1 TAT
38316556 AATATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTGTTAAATATTT
Found at i:38324133 original size:27 final size:27
Alignment explanation
Indices: 38324095--38324149 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
38324085 TGCTAAAATA
38324095 CCTCTTTTAATTTTATAACTATTTTTT
1 CCTCTTTTAATTTTATAACTATTTTTT
38324122 CCTCTTTTAATTTTATAACTATTTTTT
1 CCTCTTTTAATTTTATAACTATTTTTT
38324149 C
1 C
38324150 TATAATACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (27 bp):
CCTCTTTTAATTTTATAACTATTTTTT
Found at i:38324161 original size:35 final size:35
Alignment explanation
Indices: 38324122--38324188 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
38324112 ACTATTTTTT
38324122 CCTCTTTTAATTTTATAACTATTTTTTCTATAATA
1 CCTCTTTTAATTTTATAACTATTTTTTCTATAATA
*
38324157 CCTCTTTTAATTTTATGACTATTTTTTCTATA
1 CCTCTTTTAATTTTATAACTATTTTTTCTATA
38324189 TACTAATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.01, T:0.58
Consensus pattern (35 bp):
CCTCTTTTAATTTTATAACTATTTTTTCTATAATA
Found at i:38324203 original size:34 final size:35
Alignment explanation
Indices: 38324130--38324203 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
38324120 TTCCTCTTTT
* **
38324130 AATTTTATAACTATTTTTTCTATAATACCTCTTTT
1 AATTTTATAACTATTTTTTCTATAATACCTATTAG
*
38324165 AATTTTATGACTATTTTTTCTAT-ATA-CTAATTAG
1 AATTTTATAACTATTTTTTCTATAATACCT-ATTAG
38324199 AATTT
1 AATTT
38324204 CTCAAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 2 0.06
34 10 0.29
35 22 0.65
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.55
Consensus pattern (35 bp):
AATTTTATAACTATTTTTTCTATAATACCTATTAG
Found at i:38330737 original size:20 final size:20
Alignment explanation
Indices: 38330714--38330763 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
38330704 TAGAGAATGT
38330714 TATCGATACTTGATTAAAGG
1 TATCGATACTTGATTAAAGG
* ** **
38330734 TATCAATACTTTTTTATGGG
1 TATCGATACTTGATTAAAGG
38330754 TATCGATACT
1 TATCGATACT
38330764 CAGGCAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (20 bp):
TATCGATACTTGATTAAAGG
Found at i:38334511 original size:19 final size:18
Alignment explanation
Indices: 38334487--38334527 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
38334477 ATTAATACTT
* *
38334487 TAAACTAAATATTATAAAA
1 TAAACTAAA-ATAACAAAA
38334506 TAAACTAAAATAACAAAA
1 TAAACTAAAATAACAAAA
38334524 TAAA
1 TAAA
38334528 ATATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAACTAAAATAACAAAA
Found at i:38344582 original size:18 final size:18
Alignment explanation
Indices: 38344559--38344593 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38344549 TTGTCTTCTT
*
38344559 CATTTTCCCTTTTCTCTA
1 CATTTTCCATTTTCTCTA
*
38344577 CATTTTTCATTTTCTCT
1 CATTTTCCATTTTCTCT
38344594 TCTCTCTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
CATTTTCCATTTTCTCTA
Found at i:38345373 original size:21 final size:21
Alignment explanation
Indices: 38345349--38345404 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
38345339 TGATAGTCAA
38345349 GTCTTGAGACATAGACTAAAT
1 GTCTTGAGACATAGACTAAAT
* * *
38345370 GTCTCGAGACATTA-TCTATAT
1 GTCTTGAGACA-TAGACTAAAT
*
38345391 GTCTTGAAACATAG
1 GTCTTGAGACATAG
38345405 CCTTCCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (21 bp):
GTCTTGAGACATAGACTAAAT
Found at i:38346100 original size:6 final size:6
Alignment explanation
Indices: 38346089--38346114 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38346079 TTCCCAAACA
38346089 AAGAAT AAGAAT AAGAAT AAGAAT AA
1 AAGAAT AAGAAT AAGAAT AAGAAT AA
38346115 TGAGCTCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAGAAT
Found at i:38360582 original size:31 final size:30
Alignment explanation
Indices: 38360528--38360585 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38360518 TTCACTTCCA
* *
38360528 TAAAAATAATATAAATTTAATTTAATTATT
1 TAAAAATAATAAAAATATAATTTAATTATT
*
38360558 TAAAAATTATAAAAATGATAATTTAATT
1 TAAAAATAATAAAAAT-ATAATTTAATT
38360586 TCGATCTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TAAAAATAATAAAAATATAATTTAATTATT
Found at i:38372444 original size:29 final size:28
Alignment explanation
Indices: 38372402--38372458 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
38372392 CTTGAAAATA
*
38372402 GAAATACTTATAATTAAATATCTAACAT
1 GAAATACATATAATTAAATATCTAACAT
* *
38372430 GAAATAGCATATAATTAGATATGTAACAT
1 GAAATA-CATATAATTAAATATCTAACAT
38372459 CAATTTCCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (28 bp):
GAAATACATATAATTAAATATCTAACAT
Found at i:38374208 original size:14 final size:13
Alignment explanation
Indices: 38374181--38374206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38374171 TATCGTTTAC
38374181 ATGATCTGTTTTT
1 ATGATCTGTTTTT
38374194 ATGATCTGTTTTT
1 ATGATCTGTTTTT
38374207 TACTTATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
ATGATCTGTTTTT
Found at i:38376645 original size:13 final size:13
Alignment explanation
Indices: 38376627--38376654 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38376617 TTCTACTGGG
38376627 TTTTTAAATCCTC
1 TTTTTAAATCCTC
38376640 TTTTTAAATCCTC
1 TTTTTAAATCCTC
38376653 TT
1 TT
38376655 ATTATGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAATCCTC
Found at i:38379259 original size:3 final size:3
Alignment explanation
Indices: 38379253--38379290 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
38379243 TATTATTATT
38379253 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
38379291 CACCTTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:38380113 original size:52 final size:54
Alignment explanation
Indices: 38380003--38380118 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 54
38379993 GACAGTTAAA
* ** *
38380003 GGTTTCTTCCATGTATCAATGAACCAAGAAGAAAGAATACCAAGGGTCACACTTAG
1 GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATACC-A-GGTCACACCTAG
* *
38380059 GGTTCCTTCCGTGTATCAAACAACCAAGAAGAAAGAATA-C-TGTCACACCTAG
1 GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATACCAGGTCACACCTAG
38380111 GGTTCCTT
1 GGTTCCTT
38380119 AGGAGTCTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
52 18 0.33
55 1 0.02
56 35 0.65
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (54 bp):
GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATACCAGGTCACACCTAG
Found at i:38384735 original size:20 final size:20
Alignment explanation
Indices: 38384710--38384750 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38384700 AAATGATTTT
*
38384710 TTTTATAAAAAATTCTAAAA
1 TTTTATAAAAAATTCAAAAA
*
38384730 TTTTATAAAAATTTCAAAAA
1 TTTTATAAAAAATTCAAAAA
38384750 T
1 T
38384751 CATATTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTATAAAAAATTCAAAAA
Found at i:38387549 original size:149 final size:151
Alignment explanation
Indices: 38387309--38387589 Score: 381
Period size: 149 Copynumber: 1.9 Consensus size: 151
38387299 TCACAATTTG
* * * *
38387309 ATTTTTTTATTCATTTTAACATTATTTCATTTGTTACTATTAATTAGTTTCAAACTATACTTTTT
1 ATTTTTTTATTCATTGTAACATTATTTCATATGTTACTATTAATTAGTTTCAAACAATACTATTT
* *
38387374 TATTATTTATTGTATGTTATTTTTAAACACACCTTTGTGTTATAAATAAGT-GATTTCCACATGC
66 CATTATTTATTGTATGTTATTTTTAAACACACATTTGTGTTATAAATAAGTAG-TTTCCACATGC
38387438 ATACGTTTATGATAAGATTTTA
130 ATACGTTTATGATAAGATTTTA
* ** *
38387460 ATTTTTTTATTTTATTGTAA-A-TATTTCATATGTTGTTATTAGTTAGTTTCAAACAATA-TATT
1 ATTTTTTTA-TTCATTGTAACATTATTTCATATGTTACTATTAATTAGTTTCAAACAATACTATT
* * * **
38387522 TCATTATTTATTGTATGTTATTTTTAAATACGCATTTGTGTTGTAAATTTGTAGTTTCCACATGC
65 TCATTATTTATTGTATGTTATTTTTAAACACACATTTGTGTTATAAATAAGTAGTTTCCACATGC
38387587 ATA
130 ATA
38387590 TATGTGTAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
149 62 0.55
150 33 0.29
151 10 0.09
152 8 0.07
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.52
Consensus pattern (151 bp):
ATTTTTTTATTCATTGTAACATTATTTCATATGTTACTATTAATTAGTTTCAAACAATACTATTT
CATTATTTATTGTATGTTATTTTTAAACACACATTTGTGTTATAAATAAGTAGTTTCCACATGCA
TACGTTTATGATAAGATTTTA
Found at i:38395571 original size:14 final size:13
Alignment explanation
Indices: 38395551--38395579 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38395541 ATTAAGCACA
38395551 AAATTTTTTAATC
1 AAATTTTTTAATC
38395564 AAATTTTTTAATC
1 AAATTTTTTAATC
38395577 AAA
1 AAA
38395580 ACTTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTTTTTAATC
Found at i:38405067 original size:31 final size:30
Alignment explanation
Indices: 38404996--38405075 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
38404986 TTTAATAGTT
* * *
38404996 TATAATTTTA-TAATTTTAAATAATTAAAT
1 TATAATTTTATTATTTTTAAAGAATTAAAA
*
38405025 TA-AATTATTATTATTTTTAGAAGGATTAAAA
1 TATAATT-TTATTATTTTTA-AAGAATTAAAA
*
38405056 TATAATTTTATTATTATTAA
1 TATAATTTTATTATTTTTAA
38405076 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.10
29 5 0.12
30 8 0.19
31 21 0.50
32 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
TATAATTTTATTATTTTTAAAGAATTAAAA
Found at i:38405074 original size:22 final size:23
Alignment explanation
Indices: 38405049--38405098 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
38405039 TTTTAGAAGG
* *
38405049 ATTAAAATATAATTTTAT-TATT
1 ATTAAAATAAAATTTTATAAATT
**
38405071 ATTAATTTAAAATTTTATAAATT
1 ATTAAAATAAAATTTTATAAATT
38405094 ATTAA
1 ATTAA
38405099 GTATTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTAAAATAAAATTTTATAAATT
Found at i:38405240 original size:28 final size:28
Alignment explanation
Indices: 38405179--38405243 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
38405169 TTAACAAGTC
*
38405179 AATTAATCGAATTAATTAATTTTTTTAAT
1 AATTAATCGAATTAATT-ATTTTTTTAAA
* *
38405208 CATTAATTGAATTGAATT-TTTTTTTAAA
1 AATTAATCGAATT-AATTATTTTTTTAAA
38405236 AATTAATC
1 AATTAATC
38405244 AAATCGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 15 0.50
29 11 0.37
30 4 0.13
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (28 bp):
AATTAATCGAATTAATTATTTTTTTAAA
Found at i:38405375 original size:20 final size:21
Alignment explanation
Indices: 38405337--38405378 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
38405327 AAATAAAAAT
38405337 AAATTAATAATATTTATTTAATC
1 AAATTAATAATA--TATTTAATC
38405360 AAATTAATAATA-ATTTAAT
1 AAATTAATAATATATTTAAT
38405379 ACATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
23 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAATAATATATTTAATC
Found at i:38405428 original size:23 final size:23
Alignment explanation
Indices: 38405402--38405455 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
38405392 TATTAAATTT
38405402 AATTAATTAAAT-TATTAATCAAA
1 AATTAATTAAATCT-TTAATCAAA
* *
38405425 AATTTAA-AAAATCTTTAATCAAT
1 AA-TTAATTAAATCTTTAATCAAA
38405448 AATTAATT
1 AATTAATT
38405456 TTATTGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTAATTAAATCTTTAATCAAA
Found at i:38409196 original size:53 final size:53
Alignment explanation
Indices: 38409116--38409222 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
38409106 CACATCAAAA
38409116 CGGTCAAAACACACACAAATCTTGGTCATAACGAAACCTAGATTACTTTGTAT
1 CGGTCAAAACACACACAAATCTTGGTCATAACGAAACCTAGATTACTTTGTAT
*
38409169 CGGTCAAAACACACATAAATCTTGGTCATAACGAAACCTAGATTACTTTGTAT
1 CGGTCAAAACACACACAAATCTTGGTCATAACGAAACCTAGATTACTTTGTAT
38409222 C
1 C
38409223 AATTAAGGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (53 bp):
CGGTCAAAACACACACAAATCTTGGTCATAACGAAACCTAGATTACTTTGTAT
Found at i:38410252 original size:6 final size:6
Alignment explanation
Indices: 38410241--38410276 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
38410231 AAGTTATTCT
38410241 TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA
1 TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA
38410277 CAAGCATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TTCCCA
Found at i:38422227 original size:21 final size:21
Alignment explanation
Indices: 38422201--38422244 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
38422191 CGGCGGCGGC
*
38422201 GGCGGCGGAGCAGACAGAGGA
1 GGCGGCGGAGCAGAAAGAGGA
* *
38422222 GGCGGCGGCGGAGAAAGAGGA
1 GGCGGCGGAGCAGAAAGAGGA
38422243 GG
1 GG
38422245 AAACGATGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.57, T:0.00
Consensus pattern (21 bp):
GGCGGCGGAGCAGAAAGAGGA
Found at i:38424758 original size:151 final size:150
Alignment explanation
Indices: 38424529--38424830 Score: 419
Period size: 151 Copynumber: 2.0 Consensus size: 150
38424519 CTCTTGCTAA
* *
38424529 TTGGAGTGTGAACAAGTAAACATCACAATCTTGAAATTGAGTTGTTGCCATTTTCAAAGAAAGAA
1 TTGGAGTGTGAACAAGTAAACACCACAATCTTGAAATTGAGTTGCTGCCATTTTCAAAGAAAGAA
*** * **
38424594 CAAGAATTGAATCTTATAAAAATTCTC-AGAGTAAATTACAAAGCAAAGTATCCCATGTATAGAC
66 CAAGAACCAAATCTTATAAAAACTCTCAAGAGTAAATTACAAAGCAAAGTATCCCATACAT-GAC
*
38424658 TTAAGTTACTTGAAAAATAAG
130 TTAAGTTACATGAAAAATAAG
* * *
38424679 TTGGAGTGTGAAGAAGTAAACACCACTATCTTGAAGATTGAGTTGCTGCCGCTTTT-AAAGAAAG
1 TTGGAGTGTGAACAAGTAAACACCACAATCTTGAA-ATTGAGTTGCTGCC-ATTTTCAAAGAAAG
* *
38424743 AACAAGAACCAAATCTTGTAAAAACTCTCAAAGAGTAAATTACAAAGCATAGTATCCCATACATG
64 AACAAGAACCAAATCTTATAAAAACTCTC-AAGAGTAAATTACAAAGCAAAGTATCCCATACATG
*
38424808 ACTTAGGTTACATGAAAAATAAG
128 ACTTAAGTTACATGAAAAATAAG
38424831 GAAACAACCC
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
150 32 0.24
151 45 0.34
152 26 0.20
153 30 0.23
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (150 bp):
TTGGAGTGTGAACAAGTAAACACCACAATCTTGAAATTGAGTTGCTGCCATTTTCAAAGAAAGAA
CAAGAACCAAATCTTATAAAAACTCTCAAGAGTAAATTACAAAGCAAAGTATCCCATACATGACT
TAAGTTACATGAAAAATAAG
Found at i:38433781 original size:13 final size:13
Alignment explanation
Indices: 38433763--38433789 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38433753 AAGTAATTTG
38433763 CTTCAAGGAAAAT
1 CTTCAAGGAAAAT
38433776 CTTCAAGGAAAAT
1 CTTCAAGGAAAAT
38433789 C
1 C
38433790 ATGTGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (13 bp):
CTTCAAGGAAAAT
Found at i:38436452 original size:19 final size:17
Alignment explanation
Indices: 38436423--38436495 Score: 76
Period size: 17 Copynumber: 4.1 Consensus size: 17
38436413 TAAATTTTAA
38436423 TTTAGTTTAAGTTTAAACT
1 TTTA-TTTAAGTTTAAA-T
*
38436442 TTTCTTTTAAGTTTAAAT
1 TTT-ATTTAAGTTTAAAT
*
38436460 TTTAATTAAGTTTAAAT
1 TTTATTTAAGTTTAAAT
*
38436477 TTAATTTGAA-TTTAAAT
1 TTTATTT-AAGTTTAAAT
38436494 TT
1 TT
38436496 AAAATTAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
17 26 0.55
18 6 0.13
19 15 0.32
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTATTTAAGTTTAAAT
Found at i:38436479 original size:23 final size:24
Alignment explanation
Indices: 38436447--38436503 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
38436437 AAACTTTTCT
* * *
38436447 TTTAAGTTTAAATTTTAA-TTAAG
1 TTTAAATTTAAATTTGAATTTAAA
38436470 TTTAAATTT-AATTTGAATTTAAA
1 TTTAAATTTAAATTTGAATTTAAA
*
38436493 TTTAAAATTAA
1 TTTAAATTTAA
38436504 TTAAAAAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 7 0.25
23 20 0.71
24 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (24 bp):
TTTAAATTTAAATTTGAATTTAAA
Found at i:38436498 original size:6 final size:6
Alignment explanation
Indices: 38436447--38436503 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
38436437 AAACTTTTCT
* * * *
38436447 TTTAAG TTTAAA TTTTAA -TTAAG TTTAAA TTT-AA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
38436493 TTTAAA ATTAA
1 TTTAAA TTTAA
38436504 TTAAAAAGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 8 0.19
6 34 0.81
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:38436505 original size:17 final size:17
Alignment explanation
Indices: 38436448--38436503 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
38436438 AACTTTTCTT
*
38436448 TTAAGTTTAAATTTTAA
1 TTAAGTTTAAATTTAAA
*
38436465 TTAAGTTTAAATTTAAT
1 TTAAGTTTAAATTTAAA
38436482 TTGAA-TTTAAATTTAAAA
1 TT-AAGTTTAAATTT-AAA
38436500 TTAA
1 TTAA
38436504 TTAAAAAGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 28 0.82
18 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:38437206 original size:21 final size:20
Alignment explanation
Indices: 38437176--38437216 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
38437166 TAATGGTAGT
* *
38437176 TAATAATATTGTTTATAATA
1 TAATAATATTATTAATAATA
38437196 TAATAAATATTATTAATAATA
1 TAAT-AATATTATTAATAATA
38437217 ATGTTAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATAATATTATTAATAATA
Found at i:38438394 original size:30 final size:29
Alignment explanation
Indices: 38438350--38438547 Score: 218
Period size: 30 Copynumber: 6.6 Consensus size: 29
38438340 AAAGCCCCTG
* **
38438350 AACTGTTC-AAAAATTATATTTTGACCTTGA
1 AACT-TTCTAAAAATTATATTTTAACC-CAA
*
38438380 AACTTCCTAAAAATTATATTTTAACCCCAA
1 AACTTTCTAAAAATTATATTTTAA-CCCAA
*
38438410 AACTTTTTAAAAATTATATTTTAATCCCAA
1 AACTTTCTAAAAATTATATTTTAA-CCCAA
* * *
38438440 AACTTTTTAAAAATTACATTTTGACCCCAA
1 AACTTTCTAAAAATTATATTTT-AACCCAA
* *
38438470 AACTTTCTAAAAATTACATTCTAAACCCAA
1 AACTTTCTAAAAATTATATT-TTAACCCAA
*
38438500 AACTTTCTAAAAATTATATTTTGACCTCAA
1 AACTTTCTAAAAATTATATTTTAACC-CAA
*
38438530 AATTTTCTAAAAATTATA
1 AACTTTCTAAAAATTATA
38438548 AAACTTTCAA
Statistics
Matches: 147, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.04
30 137 0.93
31 4 0.03
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTTCTAAAAATTATATTTTAACCCAA
Found at i:38438451 original size:60 final size:60
Alignment explanation
Indices: 38438379--38438547 Score: 241
Period size: 60 Copynumber: 2.8 Consensus size: 60
38438369 TTTGACCTTG
* * * *
38438379 AAACTTCCTAAAAATTATATTTTAACCCCAAAACTTTTTAAAAATTATATTTTAATCCCA
1 AAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTATATTCTAAACCCA
* * * *
38438439 AAACTTTTTAAAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTCTAAACCCA
1 AAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTATATTCTAAACCCA
*
38438499 AAACTTTCTAAAAATTATATTTTGACCTCAAAA-TTTTCTAAAAATTATA
1 AAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTT-TAAAAATTATA
38438548 AAACTTTCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 3 0.03
60 92 0.97
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (60 bp):
AAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTATATTCTAAACCCA
Found at i:38438464 original size:90 final size:90
Alignment explanation
Indices: 38438358--38438545 Score: 254
Period size: 90 Copynumber: 2.1 Consensus size: 90
38438348 TGAACTGTTC
* *** * * * *
38438358 AAAAATTATATTTTGACCTTGAAACTTCCTAAAAATTATATTTTAACCCCAAAACTTTTTAAAAA
1 AAAAATTACATTTTGACCCCAAAACTTCCTAAAAATTACATTCTAAACCCAAAACTTTCTAAAAA
38438423 TTATATTTTAATCC-CAAAACTTTT-T
66 TTATATTTTAA-CCTCAAAA-TTTTCT
*
38438448 AAAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTCTAAACCCAAAACTTTCTAAAAA
1 AAAAATTACATTTTGACCCCAAAACTTCCTAAAAATTACATTCTAAACCCAAAACTTTCTAAAAA
*
38438513 TTATATTTTGACCTCAAAATTTTCT
66 TTATATTTTAACCTCAAAATTTTCT
38438538 AAAAATTA
1 AAAAATTA
38438546 TAAAACTTTC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 6 0.07
90 80 0.93
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (90 bp):
AAAAATTACATTTTGACCCCAAAACTTCCTAAAAATTACATTCTAAACCCAAAACTTTCTAAAAA
TTATATTTTAACCTCAAAATTTTCT
Found at i:38438550 original size:19 final size:19
Alignment explanation
Indices: 38438528--38438564 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38438518 TTTTGACCTC
* *
38438528 AAAATTTTCTAAAAATTAT
1 AAAACTTTCAAAAAATTAT
38438547 AAAACTTTCAAAAAATTA
1 AAAACTTTCAAAAAATTA
38438565 CATTTTGACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAACTTTCAAAAAATTAT
Found at i:38438551 original size:49 final size:49
Alignment explanation
Indices: 38438498--38438594 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
38438488 TTCTAAACCC
* * * * *
38438498 AAAACTTTCTAAAAATTATATTTTGACCTCAAAATTTTCTAAAAATTAT
1 AAAACTTTCAAAAAATTACATTTTGACCCCAAAACTTTCCAAAAATTAT
*
38438547 AAAACTTTCAAAAAATTACATTTTGACCCCCAAACTTTCCAAAAATTA
1 AAAACTTTCAAAAAATTACATTTTGACCCCAAAACTTTCCAAAAATTA
38438595 GATTTTATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (49 bp):
AAAACTTTCAAAAAATTACATTTTGACCCCAAAACTTTCCAAAAATTAT
Found at i:38448278 original size:14 final size:16
Alignment explanation
Indices: 38448253--38448285 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
38448243 GAAATTCAAA
38448253 TCAGGTCAAAATTT-C
1 TCAGGTCAAAATTTGC
38448268 TCAGG-CAAAATTTGC
1 TCAGGTCAAAATTTGC
38448283 TCA
1 TCA
38448286 TGATAGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (16 bp):
TCAGGTCAAAATTTGC
Found at i:38448969 original size:18 final size:18
Alignment explanation
Indices: 38448948--38448988 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38448938 ATGAAGGATT
* *
38448948 ACAATGAATTGAAATTAA
1 ACAATGAAATAAAATTAA
*
38448966 ACAATTAAATAAAATTAA
1 ACAATGAAATAAAATTAA
38448984 ACAAT
1 ACAAT
38448989 AAGAAGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (18 bp):
ACAATGAAATAAAATTAA
Found at i:38449161 original size:21 final size:21
Alignment explanation
Indices: 38449137--38449185 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38449127 AAGATAAGAC
*
38449137 TGAAGAAAAGAAGGGCGTGCG
1 TGAAGAAAAGAAGGGCGTGCA
** *
38449158 TGAAGAATGGAAGGGTGTGCA
1 TGAAGAAAAGAAGGGCGTGCA
38449179 TGAAGAA
1 TGAAGAA
38449186 GAAGGCAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.41, T:0.14
Consensus pattern (21 bp):
TGAAGAAAAGAAGGGCGTGCA
Found at i:38449575 original size:30 final size:30
Alignment explanation
Indices: 38449556--38449668 Score: 51
Period size: 29 Copynumber: 3.7 Consensus size: 30
38449546 TATATTATTT
* * *
38449556 ATTATTAA-TATTAAGTAATTAATAATCTTT
1 ATTATTAAGTATTAA-TAATTTATATTATTT
38449586 A-TATTAAGTAATTAATAATATTTATATTAATATT
1 ATTATTAAGT-ATTAAT-A-ATTTATATT-AT-TT
*
38449620 A-TATTTA-TATTAATAATTAGTATATT-TTT
1 ATTATTAAGTATTAATAATT--TATATTATTT
*
38449649 A-TATTTA-TATTAATATATTT
1 ATTATTAAGTATTAATA-ATTT
38449669 CGATTTAGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 20
0.74 0.04 0.21
Matches are distributed among these distances:
28 1 0.01
29 23 0.33
30 10 0.14
31 7 0.10
32 19 0.27
33 2 0.03
34 8 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
ATTATTAAGTATTAATAATTTATATTATTT
Found at i:38449591 original size:23 final size:21
Alignment explanation
Indices: 38449563--38449668 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 21
38449553 TTTATTATTA
38449563 ATATTAAGTAATTAATAATCTTT
1 ATATTAA-TAATTAATAAT-TTT
38449586 ATATTAAGTAATTAATAATATTT
1 ATATTAA-TAATTAATAAT-TTT
38449609 ATATTAAT-ATT-AT-A-TTT
1 ATATTAATAATTAATAATTTT
*
38449626 ATATTAATAATTAGTATATTTTT
1 ATATTAATAATTA--ATAATTTT
*
38449649 ATATTTAT-ATTAATATATTT
1 ATATTAATAATTAATA-ATTT
38449669 CGATTTAGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
17 11 0.15
18 3 0.04
19 1 0.01
20 5 0.07
21 8 0.11
22 5 0.07
23 39 0.54
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
ATATTAATAATTAATAATTTT
Found at i:38449605 original size:40 final size:38
Alignment explanation
Indices: 38449543--38449638 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 38
38449533 ATTATTATTA
* * *
38449543 ATTTATATTATTTATTATTAATATTAAGTAATTAATA-AT
1 ATTTATATTAATAATTAATAATATTAA-T-ATTAATATAT
* *
38449582 CTTTATATTAAGTAATTAATAATATTTATATTAATATTAT
1 ATTTATATTAA-TAATTAATAATATTAATATTAATA-TAT
38449622 ATTTATATTAATAATTA
1 ATTTATATTAATAATTA
38449639 GTATATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 7 0.15
39 16 0.33
40 25 0.52
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (38 bp):
ATTTATATTAATAATTAATAATATTAATATTAATATAT
Found at i:38449623 original size:17 final size:17
Alignment explanation
Indices: 38449603--38449664 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
38449593 GTAATTAATA
38449603 ATATTTATATTAATATT
1 ATATTTATATTAATATT
*
38449620 ATATTTATATTAATAAT
1 ATATTTATATTAATATT
*
38449637 -TA-GTATATT--T-TT
1 ATATTTATATTAATATT
38449649 ATATTTATATTAATAT
1 ATATTTATATTAATAT
38449665 ATTTCGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
12 1 0.03
13 3 0.08
14 6 0.17
15 6 0.17
16 3 0.08
17 17 0.47
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATTTATATTAATATT
Found at i:38449633 original size:29 final size:29
Alignment explanation
Indices: 38449601--38449664 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
38449591 AAGTAATTAA
38449601 TAATATTTA-TATTAATATTATATTTATAT
1 TAATATTTAGTA-TAATATTATATTTATAT
* * *
38449630 TAATAATTAGTATATTTTTATATTTATAT
1 TAATATTTAGTATAATATTATATTTATAT
38449659 TAATAT
1 TAATAT
38449665 ATTTCGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TAATATTTAGTATAATATTATATTTATAT
Found at i:38449709 original size:8 final size:8
Alignment explanation
Indices: 38449698--38449742 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
38449688 TCTATATTAT
38449698 TTATTTTA
1 TTATTTTA
*
38449706 TTATTCTA
1 TTATTTTA
38449714 TCTATTATTA
1 T-TATT-TTA
38449724 TATATTTTA
1 T-TATTTTA
38449733 TTATTTTA
1 TTATTTTA
38449741 TT
1 TT
38449743 TAAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 17 0.53
9 8 0.25
10 7 0.22
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:38449709 original size:12 final size:12
Alignment explanation
Indices: 38449692--38449803 Score: 70
Period size: 12 Copynumber: 8.8 Consensus size: 12
38449682 TATATTTCTA
38449692 TATTATTTATTT
1 TATTATTTATTT
38449704 TATTATTCTATCTAT
1 TATTATT-TAT-T-T
*
38449719 TATTATATATTT
1 TATTATTTATTT
38449731 TATTATTTTATTT
1 TATTA-TTTATTT
38449744 AAATATTATTTAAATTAT
1 ---TATTATTT--ATT-T
38449762 TATT-TTTATTT
1 TATTATTTATTT
*
38449773 TGTTA-TTA-TT
1 TATTATTTATTT
38449783 TA-TATTTAGTTT
1 TATTATTTA-TTT
*
38449795 TTTTATTTA
1 TATTATTTA
38449804 AATATTATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 29
0.70 0.04 0.25
Matches are distributed among these distances:
9 2 0.03
10 6 0.08
11 7 0.09
12 19 0.24
13 16 0.20
14 7 0.09
15 14 0.17
16 5 0.06
17 3 0.04
18 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:38449750 original size:55 final size:59
Alignment explanation
Indices: 38449691--38449813 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 59
38449681 CTATATTTCT
**
38449691 ATATTATTTATTTTATTA-TTCTA-TCTATTATTATATAT-TTTA-TTATTTTATTTAA
1 ATATTATTTAAATTATTATTTCTATTCTATTATTATATATATTTAGTTATTTTATTTAA
* * * * *
38449746 ATATTATTTAAATTATTATTTTTATTTTGTTATTATTTATATTTAGTTTTTTTATTTAA
1 ATATTATTTAAATTATTATTTCTATTCTATTATTATATATATTTAGTTATTTTATTTAA
38449805 ATATTATTT
1 ATATTATTT
38449814 TGATTTCTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
55 16 0.28
56 4 0.07
57 12 0.21
58 4 0.07
59 21 0.37
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (59 bp):
ATATTATTTAAATTATTATTTCTATTCTATTATTATATATATTTAGTTATTTTATTTAA
Found at i:38449754 original size:11 final size:12
Alignment explanation
Indices: 38449738--38449766 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
38449728 TTTTATTATT
38449738 TTATTTAAA-TA
1 TTATTTAAATTA
38449749 TTATTTAAATTA
1 TTATTTAAATTA
38449761 TTATTT
1 TTATTT
38449767 TTATTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTAAATTA
Found at i:38449779 original size:29 final size:30
Alignment explanation
Indices: 38449716--38449813 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
38449706 TTATTCTATC
*
38449716 TATTATTATATATTTTATTA-TTTTATTTAAA
1 TATTATT-TATA-ATTATTATTTTTATTTAAA
***
38449747 TATTATTTA-AATTATTATTTTTATTTTGT
1 TATTATTTATAATTATTATTTTTATTTAAA
*
38449776 TATTATTTATATTTAGTT-TTTTTATTTAAA
1 TATTATTTATAATTA-TTATTTTTATTTAAA
38449806 TATTATTT
1 TATTATTT
38449814 TGATTTCTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 6 0.11
29 18 0.32
30 23 0.41
31 9 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (30 bp):
TATTATTTATAATTATTATTTTTATTTAAA
Found at i:38451642 original size:58 final size:58
Alignment explanation
Indices: 38451573--38451830 Score: 358
Period size: 58 Copynumber: 4.4 Consensus size: 58
38451563 TTTGGATGTC
* * *
38451573 CGGGGGCAAAATGGTAATTTTTGGTTAGATCGGGGTAAAAATGGAATTTTGGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTGGGAAGTT
* *
38451631 CGGGGGTAAAATGGTAATTTTTGGTGAGATCGGGGTAATAATGGAATTTTGGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTGGGAAGTT
* * *
38451689 TGGGGGTAAAATAGTAATTTTTGGTGAAATAAATCGGGGTTAAAAATGGAATTTTGAGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTG----AAATCGGGG-TAAAAATGGAATTTTGGGAAGTT
* * *
38451752 TGGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTGGGAAGTT
38451809 C-GGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
38451831 AACAGTTCAG
Statistics
Matches: 181, Mismatches: 13, Indels: 13
0.87 0.06 0.06
Matches are distributed among these distances:
56 15 0.08
57 26 0.14
58 87 0.48
62 16 0.09
63 37 0.20
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTGGGAAGTT
Found at i:38451838 original size:29 final size:28
Alignment explanation
Indices: 38451575--38451830 Score: 182
Period size: 29 Copynumber: 8.8 Consensus size: 28
38451565 TGGATGTCCG
* * *
38451575 GGGGCAAAATGGTAATTTTTGGTTAGATC
1 GGGGTAAAATGGTAATTTTTGG-AAGTTC
*
38451604 GGGGTAAAAATGG-AATTTTGGGAAGTTC
1 GGGGT-AAAATGGTAATTTTTGGAAGTTC
* *
38451632 GGGGGTAAAATGGTAATTTTTGGTGAGATC
1 -GGGGTAAAATGGTAATTTTTGG-AAGTTC
* *
38451662 GGGGTAATAATGG-AATTTTGGGAAGTTTG
1 GGGGTAA-AATGGTAATTTTTGGAAG-TTC
* *
38451691 GGGGTAAAATAGTAATTTTTGGTGAAATAAATC
1 GGGGTAAAATGGTAATTTTT-G-GAAGT---TC
*
38451724 GGGGTTAAAAATGG-AA-TTTTGAGAAGTTTG
1 GGGG-T-AAAATGGTAATTTTTG-GAAG-TTC
* *
38451754 GGGGTAAAATGGTAATTTTGGTGAA-ATC
1 GGGGTAAAATGGTAATTTTTG-GAAGTTC
* *
38451782 GAGGTTAAAATGG-AATTTTGGGAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGTTC
38451810 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
38451831 AACAGTTCAG
Statistics
Matches: 180, Mismatches: 27, Indels: 41
0.73 0.11 0.17
Matches are distributed among these distances:
27 13 0.07
28 44 0.24
29 67 0.37
30 30 0.17
31 3 0.02
32 4 0.02
33 10 0.06
34 3 0.02
35 6 0.03
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTC
Found at i:38452530 original size:17 final size:18
Alignment explanation
Indices: 38452510--38452549 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38452500 CTTTTTCATC
38452510 TTTTATTC-TTTATTTCT
1 TTTTATTCATTTATTTCT
* *
38452527 TTTTCTTCATTTTTTTCT
1 TTTTATTCATTTATTTCT
38452545 TTTTA
1 TTTTA
38452550 AAACAAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTCATTTATTTCT
Found at i:38452578 original size:16 final size:16
Alignment explanation
Indices: 38452554--38452584 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38452544 TTTTTAAAAC
38452554 AAAACCCAGATCTGGG
1 AAAACCCAGATCTGGG
*
38452570 AAAATCCAGATCTGG
1 AAAACCCAGATCTGG
38452585 AAATATTTTA
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:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (16 bp):
AAAACCCAGATCTGGG
Found at i:38454057 original size:129 final size:129
Alignment explanation
Indices: 38453827--38454085 Score: 500
Period size: 129 Copynumber: 2.0 Consensus size: 129
38453817 TTGACCCATA
*
38453827 GCTTGGGCCCGGATAAATTGGGCTTCAACATTGCTAACATCTATATATTAGCTTAAGCAAACATC
1 GCTTGGGCCCGGATAAATTGGGCTTCAACATTGCTAACATCTATATATGAGCTTAAGCAAACATC
38453892 TCACTCATGAAACTTAAAGTTTGATCGAGCGATCCAAACATATGATTTTAAGCAAAGCATTCAT
66 TCACTCATGAAACTTAAAGTTTGATCGAGCGATCCAAACATATGATTTTAAGCAAAGCATTCAT
*
38453956 GCTTGGGCCTGGATAAATTGGGCTTCAACATTGCTAACATCTATATATGAGCTTAAGCAAACATC
1 GCTTGGGCCCGGATAAATTGGGCTTCAACATTGCTAACATCTATATATGAGCTTAAGCAAACATC
38454021 TCACTCATGAAACTTAAAGTTTGATCGAGCGATCCAAACATATGATTTTAAGCAAAGCATTCAT
66 TCACTCATGAAACTTAAAGTTTGATCGAGCGATCCAAACATATGATTTTAAGCAAAGCATTCAT
38454085 G
1 G
38454086 ATTCTTGTGT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (129 bp):
GCTTGGGCCCGGATAAATTGGGCTTCAACATTGCTAACATCTATATATGAGCTTAAGCAAACATC
TCACTCATGAAACTTAAAGTTTGATCGAGCGATCCAAACATATGATTTTAAGCAAAGCATTCAT
Found at i:38454955 original size:40 final size:41
Alignment explanation
Indices: 38454820--38454971 Score: 171
Period size: 41 Copynumber: 3.7 Consensus size: 41
38454810 GGCGCTTGAC
**
38454820 CATAAGCACCGCTATTGCTCTGACCTTTAGCGGCGTTTTCA
1 CATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCA
* ** ** **
38454861 CATAAGCGTCGCTGTTATTCTGACCTTTAGCGGCACTTTGT
1 CATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCA
* * * *
38454902 CATAAGCGTCGCTATTGCTTTGACATTTAGCGACGTTTTCC
1 CATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCA
*
38454943 CA-AAGCGTCGCTATTGCTCTGACTTTTAG
1 CATAAGCGTCGCTATTGCTCTGACCTTTAG
38454972 TGGTGCTATT
Statistics
Matches: 90, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
40 25 0.28
41 65 0.72
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (41 bp):
CATAAGCGTCGCTATTGCTCTGACCTTTAGCGGCGTTTTCA
Found at i:38455062 original size:41 final size:39
Alignment explanation
Indices: 38455010--38455197 Score: 189
Period size: 41 Copynumber: 4.6 Consensus size: 39
38455000 GCTCTCTCAA
*
38455010 AAGCGCTGCTATTGCTCTGACCTTTAGAGGCTCTTACCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGAGGCT-TT-CCCAT
* * * *
38455051 AAGTGCCGCTATTTCTCTGACCTTTAGCAGTGCTTTTCCAA
1 AAGCGCCGCTATTGCTCTGACCTTTAG-AG-GCTTTCCCAT
* * * *
38455092 AAGCGTCGCTATTGCTCTGACCTTCAGCGGCGATTGCCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGAGGC--TTTCCCAT
* *
38455133 AAGCGTCGCTATTGCTCTGACCTTTAGCGATGCTTTCCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTA--GAGGCTTTCCCAT
*
38455174 AAGCGCCGCTATTACTCT-ACCTTT
1 AAGCGCCGCTATTGCTCTGACCTTT
38455198 TGCGACGTTT
Statistics
Matches: 122, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
39 2 0.02
40 7 0.06
41 103 0.84
42 4 0.03
43 6 0.05
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (39 bp):
AAGCGCCGCTATTGCTCTGACCTTTAGAGGCTTTCCCAT
Found at i:38455113 original size:82 final size:80
Alignment explanation
Indices: 38454976--38455197 Score: 232
Period size: 82 Copynumber: 2.7 Consensus size: 80
38454966 TTTTAGTGGT
* * *
38454976 GCTATTACTCTGACATTTAGCCGCGC-TCTCTCAAAAGCGCTGCTATTGCTCTGACCTTTAGAGG
1 GCTATTACTCTGACCTTTAG-CGTGCTTTTC-CAAAAGCGC-GCTATTGCTCTGACCTTTAGAGG
** *
38455040 CTCTTACCCATAAGTGCC
63 CGATTACCCATAAGCGCC
* * *
38455058 GCTATTTCTCTGACCTTTAGCAGTGCTTTTCCAAAAGCGTCGCTATTGCTCTGACCTTCAGCGGC
1 GCTATTACTCTGACCTTTAGC-GTGCTTTTCCAAAAGCG-CGCTATTGCTCTGACCTTTAGAGGC
* *
38455123 GATTGCCCATAAGCGTC
64 GATTACCCATAAGCGCC
* * * *
38455140 GCTATTGCTCTGACCTTTAGCGATGCTTTCCCATAAGCGCCGCTATTACTCT-ACCTTT
1 GCTATTACTCTGACCTTTAGCG-TGCTTTTCCAAAAGCG-CGCTATTGCTCTGACCTTT
38455198 TGCGACGTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
81 7 0.06
82 108 0.91
83 4 0.03
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.32
Consensus pattern (80 bp):
GCTATTACTCTGACCTTTAGCGTGCTTTTCCAAAAGCGCGCTATTGCTCTGACCTTTAGAGGCGA
TTACCCATAAGCGCC
Found at i:38458061 original size:2 final size:2
Alignment explanation
Indices: 38458054--38458082 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38458044 ATTAAAATGA
38458054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38458083 ATTACGACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38460653 original size:16 final size:18
Alignment explanation
Indices: 38460620--38460660 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
38460610 TTTTATCTTT
*
38460620 TTAAAATATTTATTAAAA
1 TTAAAATATTTATAAAAA
38460638 TTAAAAT-TTTA-AAAAA
1 TTAAAATATTTATAAAAA
*
38460654 TTTAAAT
1 TTAAAAT
38460661 GAAAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATATTTATAAAAA
Found at i:38460658 original size:17 final size:19
Alignment explanation
Indices: 38460619--38460659 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
38460609 ATTTTATCTT
*
38460619 TTTAAAATATTTATTAAAA
1 TTTAAAATATTTATAAAAA
38460638 -TTAAAAT-TTTA-AAAAA
1 TTTAAAATATTTATAAAAA
38460654 TTTAAA
1 TTTAAA
38460660 TGAAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAAATATTTATAAAAA
Found at i:38460929 original size:24 final size:23
Alignment explanation
Indices: 38460882--38460930 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
38460872 TCCCAGATTT
* *
38460882 AATGGAAAATAAAAAGAAAGAAG
1 AATGGAAAAGAAAAAGAAAAAAG
*
38460905 AATGGAAAAGAAAAGTGAAAAAAG
1 AATGGAAAAGAAAA-AGAAAAAAG
38460929 AA
1 AA
38460931 AGAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (23 bp):
AATGGAAAAGAAAAAGAAAAAAG
Found at i:38462420 original size:17 final size:16
Alignment explanation
Indices: 38462380--38462427 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
38462370 ATATGATTAA
*
38462380 AATAAATAATAAAATT
1 AATAAATAATAAAATC
*
38462396 AATAAAATACTAACAATC
1 AAT-AAATAATAA-AATC
38462414 AATAAATAATAAAA
1 AATAAATAATAAAA
38462428 GCTTAATGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 16 0.59
18 6 0.22
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAATAATAAAATC
Found at i:38462900 original size:60 final size:62
Alignment explanation
Indices: 38462766--38462901 Score: 154
Period size: 61 Copynumber: 2.2 Consensus size: 62
38462756 AACTTTAAAA
* *
38462766 TGGTGAAGTTTAAAAACGTCACAAAAAGATGTGAAAAAAAATCACAAAAAAATGTTTTAATT
1 TGGTGAGGTTTCAAAACGTCACAAAAAGATGTGAAAAAAAATCACAAAAAAATGTTTTAATT
* * * ** **
38462828 T-TTGAGGCTTCAAAAGGTCATGAAAAGATGTG-AAAACCATCAC-AAAAAATAG-TTTAATT
1 TGGTGAGGTTTCAAAACGTCACAAAAAGATGTGAAAAAAAATCACAAAAAAAT-GTTTTAATT
38462887 TGGTGAGGTTTCAAA
1 TGGTGAGGTTTCAAA
38462902 GTGTTGCGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 15 0.25
60 21 0.34
61 24 0.39
62 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (62 bp):
TGGTGAGGTTTCAAAACGTCACAAAAAGATGTGAAAAAAAATCACAAAAAAATGTTTTAATT
Done.