Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 23 of 144
Found at i:5683546 original size:204 final size:198
Alignment explanation
Indices: 5683189--5683624 Score: 719
Period size: 204 Copynumber: 2.2 Consensus size: 198
5683179 GATGGTAATA
* *
5683189 AAGGTGGTGAGGGTGATGGTGGTGGTGAGGGTTCAGGTGAGGGTAAGGGTGTTGAGGGTGAGGGT
1 AAGGTGTTGAGGGTGATGGTGGTGGTGAGGGTTCAAGTGAGGGTAAGGGTGTTGAGGGTGAGGGT
* * * * *
5683254 TTGGATGATGGCAGTAAGGGTGGTGAGGGTTTGAGAGGTGGTGAGGGTTCGAGTCAGGGTGCTGT
66 TTGGATGATGACAGTAAGGGTAGTGAGGGTTTGAAAGGTGGTGAGGGTTCGAGTAAGGGTGATGT
5683319 TAGTGAAGGTGTTGAGGGTGAGGGAGGTGGTGAGGATGAGGGTGAGGGAAGGGGTGCTGTTAGTG
131 TAGTGAAGGTGTTGAGGGTGAGGGA---GGT--GG-TGAGGGTGAGGGAAGGGGTGCTGTTAGTG
5683384 AAGGTGTTG
190 AAGGTGTTG
*
5683393 AAGGTGTTGAGGGTGATGGTGGTGGTGAGGGTTTAAGTGAGGGTAAGGGTGTTGAGGGTGAGGGT
1 AAGGTGTTGAGGGTGATGGTGGTGGTGAGGGTTCAAGTGAGGGTAAGGGTGTTGAGGGTGAGGGT
*
5683458 TTGGATTATGACAGTAAGGGTAGTGAGGGTTTGAAAGGTGGTGAGGGTTCGAGTAAGGGTGATGT
66 TTGGATGATGACAGTAAGGGTAGTGAGGGTTTGAAAGGTGGTGAGGGTTCGAGTAAGGGTGATGT
5683523 TAGTGAAGGTGTTGAGGGTGAGGGAGGTGGTGAGGGTGAGGGAAGGGGTGCTGTTAGTGAAGGTG
131 TAGTGAAGGTGTTGAGGGTGAGGGAGGTGGTGAGGGTGAGGGAAGGGGTGCTGTTAGTGAAGGTG
5683588 TTG
196 TTG
* *
5683591 AAGGTGTTGAGGGTGAAGGAGGTGGTGAGGGTTC
1 AAGGTGTTGAGGGTGATGGTGGTGGTGAGGGTTC
5683625 GGGTAAAGGT
Statistics
Matches: 220, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
198 69 0.31
199 2 0.01
201 3 0.01
204 146 0.66
ACGTcount: A:0.19, C:0.02, G:0.52, T:0.26
Consensus pattern (198 bp):
AAGGTGTTGAGGGTGATGGTGGTGGTGAGGGTTCAAGTGAGGGTAAGGGTGTTGAGGGTGAGGGT
TTGGATGATGACAGTAAGGGTAGTGAGGGTTTGAAAGGTGGTGAGGGTTCGAGTAAGGGTGATGT
TAGTGAAGGTGTTGAGGGTGAGGGAGGTGGTGAGGGTGAGGGAAGGGGTGCTGTTAGTGAAGGTG
TTG
Found at i:5683572 original size:18 final size:18
Alignment explanation
Indices: 5683529--5683565 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5683519 ATGTTAGTGA
*
5683529 AGGTGTTGAGGGTGAGGG
1 AGGTGGTGAGGGTGAGGG
5683547 AGGTGGTGAGGGTGAGGG
1 AGGTGGTGAGGGTGAGGG
5683565 A
1 A
5683566 AGGGGTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.62, T:0.19
Consensus pattern (18 bp):
AGGTGGTGAGGGTGAGGG
Found at i:5688359 original size:87 final size:87
Alignment explanation
Indices: 5688256--5688430 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
5688246 CTAAAATCAA
* * *
5688256 TCCCTGACAAGACAAACACTGCTGACTTATGCAGCATACCAATCAAACATTAGACAAAAACATAA
1 TCCCTGACAAGACAAACACTGCCGACTTATACAGCATACCAATCAAACATAAGACAAAAACATAA
5688321 CTCCTAAGCCTAGAGGCAAAAG
66 CTCCTAAGCCTAGAGGCAAAAG
5688343 TCCCTGACAAGACAAACACTGCCGACTTATACAGCATACCAATCAAACATAAGACAAAAACATAA
1 TCCCTGACAAGACAAACACTGCCGACTTATACAGCATACCAATCAAACATAAGACAAAAACATAA
5688408 CTCCTAAGCCTAGAGGCAAAAG
66 CTCCTAAGCCTAGAGGCAAAAG
5688430 T
1 T
5688431 AAGTCTCAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.43, C:0.27, G:0.13, T:0.17
Consensus pattern (87 bp):
TCCCTGACAAGACAAACACTGCCGACTTATACAGCATACCAATCAAACATAAGACAAAAACATAA
CTCCTAAGCCTAGAGGCAAAAG
Found at i:5689228 original size:44 final size:43
Alignment explanation
Indices: 5689155--5689243 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 43
5689145 CTAAGTCCCG
* * *
5689155 AAAATCTCCAAATTTTTAAACTTAAACCAAAATCTCCAAACCC
1 AAAATCCCCAAATTTTTAAACCTAAACCAAAATCCCCAAACCC
*
5689198 AAAATCCCCAAATTTCTTAAACCTAAACCAAATTCCCCAAACCC
1 AAAATCCCCAAATTT-TTAAACCTAAACCAAAATCCCCAAACCC
5689242 AA
1 AA
5689244 CAACCCTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 14 0.34
44 27 0.66
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (43 bp):
AAAATCCCCAAATTTTTAAACCTAAACCAAAATCCCCAAACCC
Found at i:5689291 original size:32 final size:30
Alignment explanation
Indices: 5689253--5689349 Score: 104
Period size: 32 Copynumber: 3.1 Consensus size: 30
5689243 ACAACCCTAA
5689253 AAATCCCGAAAATCCCTAAATTTTTAAAACCT
1 AAATCCCGAAAATCCC-AAATTTTT-AAACCT
* * * *
5689285 AAATCCCCAAATTCCCAAAAATTTTGAAATCT
1 AAATCCCGAAAATCCC--AAATTTTTAAACCT
* *
5689317 AAAACCCGAAAATCCCACATTTTTAAACCT
1 AAATCCCGAAAATCCCAAATTTTTAAACCT
5689347 AAA
1 AAA
5689350 CCAAAATCCC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 14 0.26
32 32 0.60
33 7 0.13
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATCCCGAAAATCCCAAATTTTTAAACCT
Found at i:5689605 original size:17 final size:18
Alignment explanation
Indices: 5689580--5689616 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5689570 AAAAATTATA
*
5689580 TTATTTTTTAA-TTTAAT
1 TTATATTTTAATTTTAAT
5689597 TTATATTTTAATTTTAAT
1 TTATATTTTAATTTTAAT
5689615 TT
1 TT
5689617 TTTTGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATTTTAATTTTAAT
Found at i:5693117 original size:26 final size:26
Alignment explanation
Indices: 5693088--5693138 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
5693078 AGTTAAAAGG
5693088 CAAAACTACGTCGTTTTGATAAATGA
1 CAAAACTACGTCGTTTTGATAAATGA
5693114 CAAAACTACGTCGTTTTGATAAATG
1 CAAAACTACGTCGTTTTGATAAATG
5693139 TTTACCCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (26 bp):
CAAAACTACGTCGTTTTGATAAATGA
Found at i:5699277 original size:2 final size:2
Alignment explanation
Indices: 5699270--5699300 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5699260 AAATTTCCCG
5699270 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5699301 CTTCCTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5704987 original size:34 final size:34
Alignment explanation
Indices: 5704949--5705016 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
5704939 TGTAAAAACA
*
5704949 GCAATGGTGGTGAGATTAGATGCTGTAACGATAC
1 GCAATGGTGATGAGATTAGATGCTGTAACGATAC
* *
5704983 GCAATGGTGATGAGATTAGATGCTTTAGCGATAC
1 GCAATGGTGATGAGATTAGATGCTGTAACGATAC
5705017 TGTAACATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (34 bp):
GCAATGGTGATGAGATTAGATGCTGTAACGATAC
Found at i:5705252 original size:154 final size:154
Alignment explanation
Indices: 5704972--5705281 Score: 611
Period size: 154 Copynumber: 2.0 Consensus size: 154
5704962 GATTAGATGC
5704972 TGTAACGATACGCAATGGTGATGAGATTAGATGCTTTAGCGATACTGTAACATGAGATAAAAAGT
1 TGTAACGATACGCAATGGTGATGAGATTAGATGCTTTAGCGATACTGTAACATGAGATAAAAAGT
5705037 AAGTTAAACACACTACACCGCATCGCTCATCCAAACCCATCCTAAGCCTAACACATTTCAAAATG
66 AAGTTAAACACACTACACCGCATCGCTCATCCAAACCCATCCTAAGCCTAACACATTTCAAAATG
5705102 GATAAGGAGATTAGCATTTGAAAA
131 GATAAGGAGATTAGCATTTGAAAA
5705126 TGTAACGATACGCAATGGTGATGAGATTAGATGCTTTAGCGATACTGTAACATGAGATAAAAAGT
1 TGTAACGATACGCAATGGTGATGAGATTAGATGCTTTAGCGATACTGTAACATGAGATAAAAAGT
*
5705191 AAGTTAAACGCACTACACCGCATCGCTCATCCAAACCCATCCTAAGCCTAACACATTTCAAAATG
66 AAGTTAAACACACTACACCGCATCGCTCATCCAAACCCATCCTAAGCCTAACACATTTCAAAATG
5705256 GATAAGGAGATTAGCATTTGAAAA
131 GATAAGGAGATTAGCATTTGAAAA
5705280 TG
1 TG
5705282 AAATTGACCA
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (154 bp):
TGTAACGATACGCAATGGTGATGAGATTAGATGCTTTAGCGATACTGTAACATGAGATAAAAAGT
AAGTTAAACACACTACACCGCATCGCTCATCCAAACCCATCCTAAGCCTAACACATTTCAAAATG
GATAAGGAGATTAGCATTTGAAAA
Found at i:5708639 original size:60 final size:61
Alignment explanation
Indices: 5708562--5708862 Score: 195
Period size: 61 Copynumber: 5.0 Consensus size: 61
5708552 AAAATTTAGG
* * *
5708562 GTGTTGGCCATGC-AATGGTCGACACCCCTTTTTTGTC-AGAAAAAAATTCAAAATTTTTAA
1 GTGTTAGCCAT-CAAATGGCCGACACCCCTTTTTTCTCGAGAAAAAAATTCAAAATTTTTAA
* * * **
5708622 TTGTTAGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAAATT-TAAATTTTTTG
1 GTGTTAGCCATCAAATGGCCGACACCCCTTTTTTCTCGAG-AAAAAAATTCAAAATTTTTAA
* **** **
5708683 GTGTTAGTCATTGCGTGGCCGACA-CCCTTTTTTCTCGAGAAAAAAATTC-AAATTTTTTG
1 GTGTTAGCCATCAAATGGCCGACACCCCTTTTTTCTCGAGAAAAAAATTCAAAATTTTTAA
*** * * * * * **
5708742 GTGTT-GACCATTGCATGGTCGATAACCCC-CTTTTCTCGAGAAAAAAATTTAAATTTTTTTG
1 GTGTTAG-CCATCAAATGGCCGA-CACCCCTTTTTTCTCGAGAAAAAAATTCAAAATTTTTAA
* * *** * * **
5708803 GTGTTGGTCATTGCATAGTCGACACCCCCCTTTTCTCGAGAAAAAAAATTC-AAATTTTTA
1 GTGTTAGCCATCAAATGGCCGACACCCCTTTTTTCTCGAG-AAAAAAATTCAAAATTTTTA
5708863 CACCTTTTTT
Statistics
Matches: 202, Mismatches: 28, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
58 1 0.00
59 37 0.18
60 69 0.34
61 76 0.38
62 19 0.09
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (61 bp):
GTGTTAGCCATCAAATGGCCGACACCCCTTTTTTCTCGAGAAAAAAATTCAAAATTTTTAA
Found at i:5708688 original size:61 final size:60
Alignment explanation
Indices: 5708561--5708861 Score: 315
Period size: 60 Copynumber: 5.0 Consensus size: 60
5708551 AAAAATTTAG
* * * *
5708561 GGTGTTGGCCA-TGCAATGGTCGACACCCCTTTTTTGTC-AGAAAAAAATTCAAAATTTTTA
1 GGTGTTAGCCATTGC-ATGGTCGACACCCCCTTTTTCTCGAGAAAAAAATTC-AAATTTTTT
** *** * *
5708621 ATTGTTAGCCATCAAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAAATTTAAATTTTTT
1 GGTGTTAGCCATTGCATGGTCGACACCCCCTTTTTCTCGAG-AAAAAAATTCAAATTTTTT
* * * *
5708682 GGTGTTAGTCATTGCGTGGCCGACA-CCCTTTTTTCTCGAGAAAAAAATTCAAATTTTTT
1 GGTGTTAGCCATTGCATGGTCGACACCCCCTTTTTCTCGAGAAAAAAATTCAAATTTTTT
* *
5708741 GGTGTT-GACCATTGCATGGTCGATAACCCCC-TTTTCTCGAGAAAAAAATTTAAATTTTTTT
1 GGTGTTAG-CCATTGCATGGTCGA-CACCCCCTTTTTCTCGAGAAAAAAATTCAAA-TTTTTT
* * * *
5708802 GGTGTTGGTCATTGCATAGTCGACACCCCCCTTTTCTCGAGAAAAAAAATTCAAATTTTT
1 GGTGTTAGCCATTGCATGGTCGACACCCCCTTTTTCTCGAG-AAAAAAATTCAAATTTTT
5708862 ACACCTTTTT
Statistics
Matches: 201, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.00
59 36 0.18
60 71 0.35
61 71 0.35
62 22 0.11
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (60 bp):
GGTGTTAGCCATTGCATGGTCGACACCCCCTTTTTCTCGAGAAAAAAATTCAAATTTTTT
Found at i:5709262 original size:45 final size:45
Alignment explanation
Indices: 5709211--5709297 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
5709201 CTGTCATGCA
5709211 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGC
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGC
*
5709256 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAA
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAA
5709298 AAGGAGGGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (45 bp):
ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGC
Found at i:5709378 original size:50 final size:52
Alignment explanation
Indices: 5709279--5709383 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 52
5709269 AAAAAATTTG
***
5709279 AATTTTTTTCTCGAGAAAAAAGGAGGGTGTCGACCATTTGATGGCCAACACCA
1 AATTTTTTTCTCGAG-AAAAAGGAGGGTGTCGACCATGCAATGGCCAACACCA
*
5709332 AATTTTTTTCTCGAG-AAAAGG-GGGTGTCGGCCATGCAATGGCCAACACCA
1 AATTTTTTTCTCGAGAAAAAGGAGGGTGTCGACCATGCAATGGCCAACACCA
5709382 AA
1 AA
5709384 AAAATTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
50 27 0.56
51 6 0.12
53 15 0.31
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (52 bp):
AATTTTTTTCTCGAGAAAAAGGAGGGTGTCGACCATGCAATGGCCAACACCA
Found at i:5709875 original size:16 final size:16
Alignment explanation
Indices: 5709835--5709875 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5709825 TCTTAAAATG
5709835 ATAAAATTT-TAATTT
1 ATAAAATTTATAATTT
*
5709850 A-AATATTTTATAATTT
1 ATAA-AATTTATAATTT
5709866 ATAAAATTTA
1 ATAAAATTTA
5709876 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 2 0.10
15 5 0.24
16 12 0.57
17 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAAAATTTATAATTT
Found at i:5709884 original size:25 final size:25
Alignment explanation
Indices: 5709845--5709894 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5709835 ATAAAATTTT
* * * *
5709845 AATTTAAATATTTTATAATTTATAA
1 AATTTAAAAAATTTAAAATTAATAA
5709870 AATTTAAAAAATTTAAAATTAATAA
1 AATTTAAAAAATTTAAAATTAATAA
5709895 TGGTAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTTAAAAAATTTAAAATTAATAA
Found at i:5711784 original size:22 final size:22
Alignment explanation
Indices: 5711759--5711831 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
5711749 ATTATATTGT
5711759 TGTTTTGGTGCTATTTTTTTAC
1 TGTTTTGGTGCTATTTTTTTAC
*
5711781 TGTTTTGGTTGCTA-TTTTTTGC
1 TGTTTTGG-TGCTATTTTTTTAC
* * * * *
5711803 TGTTTTAGTGTTGTGTTTTTAT
1 TGTTTTGGTGCTATTTTTTTAC
5711825 TGTTTTG
1 TGTTTTG
5711832 ATTGCTGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.07
22 33 0.80
23 5 0.12
ACGTcount: A:0.07, C:0.05, G:0.22, T:0.66
Consensus pattern (22 bp):
TGTTTTGGTGCTATTTTTTTAC
Found at i:5711854 original size:12 final size:12
Alignment explanation
Indices: 5711839--5711913 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 12
5711829 TTGATTGCTG
*
5711839 TTTTGGTACTAT
1 TTTTGTTACTAT
*
5711851 TTTTTTTACTAT
1 TTTTGTTACTAT
*
5711863 TTTGGTGT--TAT
1 TTTTGT-TACTAT
* **
5711874 TTTTATTGTTAT
1 TTTTGTTACTAT
5711886 TTTTGTTACTAT
1 TTTTGTTACTAT
*
5711898 TTTT-TTATTAT
1 TTTTGTTACTAT
5711909 TTTTG
1 TTTTG
5711914 CTGCTGTTGG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.02
11 17 0.35
12 30 0.61
13 1 0.02
ACGTcount: A:0.15, C:0.04, G:0.11, T:0.71
Consensus pattern (12 bp):
TTTTGTTACTAT
Found at i:5711865 original size:23 final size:23
Alignment explanation
Indices: 5711839--5711911 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
5711829 TTGATTGCTG
*
5711839 TTTTGGTACTATTTTTTTTACTA
1 TTTTGGTACTATTTTTTTTATTA
** * *
5711862 TTTTGGTGTTATTTTTATTGTTA
1 TTTTGGTACTATTTTTTTTATTA
*
5711885 TTTTTGTTACTA-TTTTTTTATTA
1 -TTTTGGTACTATTTTTTTTATTA
5711908 TTTT
1 TTTT
5711912 TGCTGCTGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
22 4 0.10
23 27 0.69
24 8 0.21
ACGTcount: A:0.15, C:0.04, G:0.10, T:0.71
Consensus pattern (23 bp):
TTTTGGTACTATTTTTTTTATTA
Found at i:5712099 original size:13 final size:13
Alignment explanation
Indices: 5712060--5712103 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
5712050 AATATAAAGA
5712060 ATTTTTAATG--T
1 ATTTTTAATGTTT
5712071 ATTTTTAATTTGTTT
1 ATTTTTAA--TGTTT
5712086 ATTTTTAATGTTT
1 ATTTTTAATGTTT
5712099 ATTTT
1 ATTTT
5712104 AAAGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.28
13 12 0.41
15 9 0.31
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
ATTTTTAATGTTT
Found at i:5714217 original size:20 final size:20
Alignment explanation
Indices: 5714173--5714220 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
5714163 CTCCCAAAAC
* *
5714173 CCCTTCCCCCTTTCTCTTTT
1 CCCTTCCCCCTTCCCCTTTT
5714193 CCCTTCCCCCTTCCGCCTTTT
1 CCCTTCCCCCTTCC-CCTTTT
5714214 -CCTTCCC
1 CCCTTCCC
5714221 TTTTGCCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.00, C:0.56, G:0.02, T:0.42
Consensus pattern (20 bp):
CCCTTCCCCCTTCCCCTTTT
Found at i:5715488 original size:24 final size:24
Alignment explanation
Indices: 5715460--5715510 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5715450 AGAAATAATC
* *
5715460 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
5715484 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
5715508 TTT
1 TTT
5715511 GAGTCGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:5720316 original size:26 final size:26
Alignment explanation
Indices: 5720286--5720385 Score: 67
Period size: 29 Copynumber: 3.6 Consensus size: 26
5720276 GTTATTTTGG
5720286 TATAACATACCATAAATACAAATTGA
1 TATAACATACCATAAATACAAATTGA
* * * **
5720312 TATAAAATACAAAAAATAAAACAAA-AAA
1 TATAACATACCATAAAT---ACAAATTGA
*
5720340 TATGATCATACCATAAATACAGAAAATTGA
1 TAT-AACATACCATAAATAC---AAATTGA
*
5720370 TATAAGATACCATAAA
1 TATAACATACCATAAA
5720386 ACATTAATAA
Statistics
Matches: 53, Mismatches: 13, Indels: 13
0.67 0.16 0.16
Matches are distributed among these distances:
26 16 0.30
28 4 0.08
29 29 0.55
30 4 0.08
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (26 bp):
TATAACATACCATAAATACAAATTGA
Found at i:5723071 original size:14 final size:14
Alignment explanation
Indices: 5723054--5723105 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
5723044 TTCTCATATA
5723054 GGGCTCGCACATTG
1 GGGCTCGCACATTG
5723068 GGGCTCGCACATTG
1 GGGCTCGCACATTG
* * **
5723082 AGGCTCACAC-TAA
1 GGGCTCGCACATTG
5723095 GGGCTCGCACA
1 GGGCTCGCACA
5723106 CACGGGTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (14 bp):
GGGCTCGCACATTG
Found at i:5723181 original size:28 final size:28
Alignment explanation
Indices: 5723128--5723183 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5723118 CATACTAACC
* **
5723128 TAGGGGTTCGCACACAGGTTTGCACATA
1 TAGGGGTTCACACACAGGTTCACACATA
*
5723156 TAGGGGTTCACACACGGGTTCACACATA
1 TAGGGGTTCACACACAGGTTCACACATA
5723184 CTAGCATAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (28 bp):
TAGGGGTTCACACACAGGTTCACACATA
Found at i:5723227 original size:28 final size:28
Alignment explanation
Indices: 5723191--5723261 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
5723181 ATACTAGCAT
5723191 AGGGATTCGTACAT-GA-GCTCGTACATATA
1 AGGG-TTCGTACATAGAGGCTCGTAC-TA-A
5723220 AGGGTTCGTACATAGAGGCTCGTACTAA
1 AGGGTTCGTACATAGAGGCTCGTACTAA
* *
5723248 GGGGCTCGTACATA
1 AGGGTTCGTACATA
5723262 AGGGTTTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 22 0.58
29 8 0.21
30 8 0.21
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (28 bp):
AGGGTTCGTACATAGAGGCTCGTACTAA
Found at i:5723244 original size:14 final size:14
Alignment explanation
Indices: 5723197--5723261 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
5723187 GCATAGGGAT
5723197 TCGTACAT-GA-GC
1 TCGTACATAGAGGC
* *
5723209 TCGTACATATAAGGGT
1 TCGTACATA-GA-GGC
5723225 TCGTACATAGAGGC
1 TCGTACATAGAGGC
*
5723239 TCGTAC-TAAGGGGC
1 TCGTACAT-AGAGGC
5723253 TCGTACATA
1 TCGTACATA
5723262 AGGGTTTGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 8 0.19
13 1 0.02
14 21 0.50
15 2 0.05
16 10 0.24
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (14 bp):
TCGTACATAGAGGC
Found at i:5723274 original size:28 final size:28
Alignment explanation
Indices: 5723243--5723300 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
5723233 AGAGGCTCGT
* *
5723243 ACTAAGGGGCTCGTACATAAGGGTTTGC
1 ACTAAGAGGCTCGCACATAAGGGTTTGC
* *
5723271 ACTAAGAGGCTCGCACCTAGGGGTTTGC
1 ACTAAGAGGCTCGCACATAAGGGTTTGC
5723299 AC
1 AC
5723301 ATTAGGATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (28 bp):
ACTAAGAGGCTCGCACATAAGGGTTTGC
Found at i:5724842 original size:28 final size:28
Alignment explanation
Indices: 5724783--5724842 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5724773 CAATTATGGT
* ***
5724783 TTATTTACCTATAATTGATTAAATTGGT
1 TTATTTACCTATAATTGATTAAACTCAA
**
5724811 TTATTTACCTATAATTTTTTAAACTCAA
1 TTATTTACCTATAATTGATTAAACTCAA
5724839 TTAT
1 TTAT
5724843 GGTTTTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (28 bp):
TTATTTACCTATAATTGATTAAACTCAA
Found at i:5728014 original size:2 final size:2
Alignment explanation
Indices: 5728007--5728048 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5727997 TCTATTTTTA
5728007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5728049 TATTTTTCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5729128 original size:31 final size:31
Alignment explanation
Indices: 5729085--5729143 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5729075 TGTAGAACAT
*
5729085 TCGACAAGTACCAAATCGAACAAAAAAAAGA
1 TCGACAAGTACCAAATCAAACAAAAAAAAGA
*
5729116 TCGATAAGTACCAAATCAAACAAAAAAA
1 TCGACAAGTACCAAATCAAACAAAAAAA
5729144 TTAAGTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.12
Consensus pattern (31 bp):
TCGACAAGTACCAAATCAAACAAAAAAAAGA
Found at i:5729169 original size:24 final size:25
Alignment explanation
Indices: 5729120--5729173 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
5729110 AAAAGATCGA
5729120 TAAGTACCAAATCAAACAAAAAAAT
1 TAAGTACCAAATCAAACAAAAAAAT
* *
5729145 TAAGTACCAAAT-TAAGAAAAAAAT
1 TAAGTACCAAATCAAACAAAAAAAT
5729169 TAAGT
1 TAAGT
5729174 TTAAGTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.20
Consensus pattern (25 bp):
TAAGTACCAAATCAAACAAAAAAAT
Found at i:5729221 original size:56 final size:57
Alignment explanation
Indices: 5729120--5729271 Score: 141
Period size: 56 Copynumber: 2.7 Consensus size: 57
5729110 AAAAGATCGA
* * * * *
5729120 TAAGTACCAAA-TCAAACAAAAAAATTAAGTACCAAATTAAGAAAAAA-ATTAAGTT
1 TAAGTACCAAACTGAACCCAAAAAATTAAGTACCAAATTAAGAAAAAACATCAAATT
* ** *
5729175 TAAGTACTAAACTGAACCCAAAAAATTAAGTATTAACTTGAA-AAAAAACATCAAATT
1 TAAGTACCAAACTGAACCCAAAAAATTAAGTACCAAATT-AAGAAAAAACATCAAATT
* * *
5729232 TAAGTACCAAATTGAA-CAAAAATAATTTAAATACCAAATT
1 TAAGTACCAAACTGAACCCAAAA-AA-TTAAGTACCAAATT
5729272 TAAATACTAA
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
55 10 0.13
56 32 0.42
57 24 0.32
58 10 0.13
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (57 bp):
TAAGTACCAAACTGAACCCAAAAAATTAAGTACCAAATTAAGAAAAAACATCAAATT
Found at i:5731496 original size:25 final size:24
Alignment explanation
Indices: 5731463--5731517 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
5731453 TTTGAAATAT
*
5731463 TTTAATTTAAAATAAAATATTATTA
1 TTTAATTTAAAATAAAA-ATAATTA
*
5731488 TTTAATTTAATATAAAAATAATTA
1 TTTAATTTAAAATAAAAATAATTA
5731512 TATTAA
1 T-TTAA
5731518 AAATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAATTTAAAATAAAAATAATTA
Found at i:5731525 original size:29 final size:28
Alignment explanation
Indices: 5731436--5731525 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 28
5731426 AGACTCAAAA
*
5731436 AATATAAAAATAATATATTTGAAATATTTT
1 AATATAAAAATAATATA-TT-AAAAATTTT
* * **
5731466 AATTTAAAATAAAATATTATTATTTAA-TTT
1 AATATAAAA-ATAATA-TATTA-AAAATTTT
5731496 AATATAAAAATAATTATATTAAAAATTTT
1 AATATAAAAATAA-TATATTAAAAATTTT
5731525 A
1 A
5731526 TTAAATTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
28 2 0.04
29 12 0.26
30 22 0.48
31 8 0.17
32 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
AATATAAAAATAATATATTAAAAATTTT
Found at i:5734561 original size:70 final size:67
Alignment explanation
Indices: 5734468--5734600 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
5734458 TCCAAATAAA
* * * *
5734468 AAAAAGTAAAACTACGTCGTTTTGATAAATGTTTACCCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAAGTAAAACTACGTCATTTTGATAAATGTTTACAC-AT-T-AAGTTAAAAGGCAAAACCATT
5734533 AAGTT
63 AAGTT
* * * *
5734538 AAAAGGTAAAATTATGTCATTTTGATGAATGTTTACACATTAAGTTAAAAGGCAAAACCATTA
1 AAAAAGTAAAACTACGTCATTTTGATAAATGTTTACACATTAAGTTAAAAGGCAAAACCATTA
5734601 TATTATTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 1 0.02
70 32 0.58
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (67 bp):
AAAAAGTAAAACTACGTCATTTTGATAAATGTTTACACATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:5740516 original size:17 final size:17
Alignment explanation
Indices: 5740494--5740527 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5740484 ATATTTGATT
*
5740494 TTTAAAACTAATTTTTA
1 TTTAAAAATAATTTTTA
5740511 TTTAAAAATAATTTTTA
1 TTTAAAAATAATTTTTA
5740528 AAAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAAATAATTTTTA
Found at i:5740813 original size:18 final size:19
Alignment explanation
Indices: 5740779--5740815 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5740769 GAATATAAAT
5740779 ATATATAATTATTATTTAAC
1 ATATATAATTA-TATTTAAC
5740799 ATATATAATTA-ATTTAA
1 ATATATAATTATATTTAA
5740816 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATAATTATATTTAAC
Found at i:5745900 original size:26 final size:27
Alignment explanation
Indices: 5745839--5745908 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
5745829 AATAAAATTG
* * *
5745839 AAATATTAAATAATTTATTATTTTTATT
1 AAATATT-AATAATTTATTATTATGACT
5745867 AATTATATTAATAATTTATTA-TATGACT
1 AA--ATATTAATAATTTATTATTATGACT
*
5745895 AAATATAAATAATT
1 AAATATTAATAATT
5745909 AAATATGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 11 0.31
28 8 0.22
29 12 0.33
30 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
AAATATTAATAATTTATTATTATGACT
Found at i:5746102 original size:21 final size:22
Alignment explanation
Indices: 5746078--5746118 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5746068 CATAAGTTTT
*
5746078 TTTTTAAAA-AATAACTTATGC
1 TTTTCAAAAGAATAACTTATGC
*
5746099 TTTTCAAAAGAATAAGTTAT
1 TTTTCAAAAGAATAACTTAT
5746119 TTTACAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTTCAAAAGAATAACTTATGC
Found at i:5746740 original size:30 final size:30
Alignment explanation
Indices: 5746717--5746779 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
5746707 AGTTGGTGGC
*
5746717 TTAAAATGATAAAATCAAATAGTTGAGTGA
1 TTAAAAAGATAAAATCAAATAGTTGAGTGA
* * *
5746747 TTAAAAAGATAAAATTAAATAATTGAGAGA
1 TTAAAAAGATAAAATCAAATAGTTGAGTGA
5746777 TTA
1 TTA
5746780 TTTTATAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (30 bp):
TTAAAAAGATAAAATCAAATAGTTGAGTGA
Found at i:5748480 original size:30 final size:30
Alignment explanation
Indices: 5748444--5748520 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
5748434 TACCTCCCCG
5748444 CAGTATTATCCACCTTCACAACCGGAGCCA
1 CAGTATTATCCACCTTCACAACCGGAGCCA
*
5748474 CAGTATTATCCACCTTCACAACCGGAGCCG
1 CAGTATTATCCACCTTCACAACCGGAGCCA
5748504 CAGTATTATCCACCTTC
1 CAGTATTATCCACCTTC
5748521 GCAAAACCGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.27, C:0.36, G:0.13, T:0.23
Consensus pattern (30 bp):
CAGTATTATCCACCTTCACAACCGGAGCCA
Found at i:5758495 original size:39 final size:39
Alignment explanation
Indices: 5758441--5758525 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
5758431 AATCTTGGAC
5758441 TCTGAGCGGGTGCACTCTCAAACAACCTTCAGGATCGGG
1 TCTGAGCGGGTGCACTCTCAAACAACCTTCAGGATCGGG
5758480 TCTGAGCGGGTGCACTCTCAAACAACCTTCAGGATCGGG
1 TCTGAGCGGGTGCACTCTCAAACAACCTTCAGGATCGGG
5758519 TCTGAGC
1 TCTGAGC
5758526 AAAGTTAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.21
Consensus pattern (39 bp):
TCTGAGCGGGTGCACTCTCAAACAACCTTCAGGATCGGG
Found at i:5768262 original size:53 final size:53
Alignment explanation
Indices: 5768199--5768310 Score: 190
Period size: 53 Copynumber: 2.1 Consensus size: 53
5768189 ATTGACTAAA
* *
5768199 AATGT-ATGTTCGTGCATATGTATGATAAGCATGCCGTATAGGTTAGGAAAAG
1 AATGTCATGTTCATGCATATGTATGATAAGCATGCCATATAGGTTAGGAAAAG
*
5768251 AATGTCATGTTCATGCATATGTATGATAAGCATGCCATATAGTTTAGGAAAAG
1 AATGTCATGTTCATGCATATGTATGATAAGCATGCCATATAGGTTAGGAAAAG
5768304 AATGTCA
1 AATGTCA
5768311 CATGTACTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 5 0.09
53 51 0.91
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (53 bp):
AATGTCATGTTCATGCATATGTATGATAAGCATGCCATATAGGTTAGGAAAAG
Found at i:5777654 original size:12 final size:11
Alignment explanation
Indices: 5777638--5777683 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
5777628 CTTTAACATA
5777638 ATTTTTAATAT
1 ATTTTTAATAT
5777649 ATTTTTAATA-
1 ATTTTTAATAT
* *
5777659 ATTTAT-ATTT
1 ATTTTTAATAT
5777669 ATTTTTAATAT
1 ATTTTTAATAT
5777680 -TTTT
1 ATTTT
5777684 AGAATTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 2 0.07
10 14 0.48
11 13 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:5777691 original size:21 final size:20
Alignment explanation
Indices: 5777648--5777697 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
5777638 ATTTTTAATA
* *
5777648 TATTTTTAATAATTTATATT
1 TATTTTTAATAATTTAGAAT
*
5777668 TATTTTTAATATTTTTAGAAT
1 TATTTTTAATA-ATTTAGAAT
*
5777689 TATTGTTAA
1 TATTTTTAA
5777698 GAAAAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TATTTTTAATAATTTAGAAT
Found at i:5782893 original size:12 final size:12
Alignment explanation
Indices: 5782876--5782901 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5782866 ATAAGCAACG
5782876 TTGCATTGGTTC
1 TTGCATTGGTTC
5782888 TTGCATTGGTTC
1 TTGCATTGGTTC
5782900 TT
1 TT
5782902 TGTTCCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.54
Consensus pattern (12 bp):
TTGCATTGGTTC
Found at i:5787849 original size:13 final size:13
Alignment explanation
Indices: 5787827--5787857 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5787817 AAAAGTTTCA
*
5787827 TTTTATATTAATG
1 TTTTAAATTAATG
5787840 TTTTAAATTAATG
1 TTTTAAATTAATG
5787853 TTTTA
1 TTTTA
5787858 GTGGTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (13 bp):
TTTTAAATTAATG
Found at i:5792733 original size:19 final size:19
Alignment explanation
Indices: 5792711--5792755 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5792701 TTATATTAGG
5792711 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATAT
* *
5792730 ATTTATTATTTAAATTTAT
1 ATTTAATATTTAAATATAT
5792749 ATTTAAT
1 ATTTAAT
5792756 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATAT
Found at i:5792758 original size:11 final size:11
Alignment explanation
Indices: 5792730--5792764 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
5792720 TTAAGATATT
5792730 ATTTATTATTTAA
1 ATTTA-TATTT-A
5792743 ATTTATATTTA
1 ATTTATATTTA
5792754 ATTTATATTTA
1 ATTTATATTTA
5792765 TCTTTTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 5 0.23
13 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:5793604 original size:22 final size:22
Alignment explanation
Indices: 5793557--5793602 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
5793547 TTTCTATTTC
*
5793557 TTTCAATTCTGTTTTCTTTTAT
1 TTTCAATTCTGTTTTCGTTTAT
5793579 TTTCAATTCTG-TTTCGTTTAT
1 TTTCAATTCTGTTTTCGTTTAT
5793600 TTT
1 TTT
5793603 TCCTCAGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTCAATTCTGTTTTCGTTTAT
Found at i:5797609 original size:20 final size:20
Alignment explanation
Indices: 5797579--5797619 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5797569 TATTGCTTTA
5797579 AAAAATAAATTATATTATTTT
1 AAAAATAAATTATATT-TTTT
*
5797600 AAAAAT-AATTTTATTTTTT
1 AAAAATAAATTATATTTTTT
5797619 A
1 A
5797620 TATCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAAATAAATTATATTTTTT
Found at i:5801367 original size:56 final size:56
Alignment explanation
Indices: 5801284--5801445 Score: 229
Period size: 56 Copynumber: 2.9 Consensus size: 56
5801274 TTCATCTTCT
5801284 TCCATATGATGCCATAGCCACC-TGACTAGGTCTTACACTATATGGTCTTCATTTCC
1 TCCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTC-TTTCC
* * * * * *
5801340 T-CATATGTTTCCATTGTCACCATGACTAGGTCTTACACTATATTGTCTTCTTTTC
1 TCCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCTTTCC
* *
5801395 TCCATATGATGCCATAGCCACCATGACTAGGACTTACACTACATGGTCTTC
1 TCCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTC
5801446 GATTGCCATG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
55 21 0.23
56 70 0.77
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (56 bp):
TCCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCTTTCC
Found at i:5802335 original size:21 final size:21
Alignment explanation
Indices: 5802307--5802362 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
5802297 CAGTAGCAGA
* *
5802307 CTTCTACCGATACTTGTGATAG
1 CTTCTACCGATACTAGTG-TAC
*
5802329 C-TCTACCGATACAAGTGTAC
1 CTTCTACCGATACTAGTGTAC
5802349 CTTCTACCGATACT
1 CTTCTACCGATACT
5802363 CAATATGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 25 0.86
22 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (21 bp):
CTTCTACCGATACTAGTGTAC
Found at i:5803105 original size:18 final size:18
Alignment explanation
Indices: 5803084--5803167 Score: 114
Period size: 18 Copynumber: 4.7 Consensus size: 18
5803074 TGCTCTTACA
*
5803084 AGCTAGTATGCTTTAACG
1 AGCTAGTATGCTTAAACG
* *
5803102 AGCTAATATGCTTTAACG
1 AGCTAGTATGCTTAAACG
*
5803120 AGCTAGTATGCTCAAACG
1 AGCTAGTATGCTTAAACG
*
5803138 AGCCAGTATGCTTAAACG
1 AGCTAGTATGCTTAAACG
*
5803156 AGCCAGTATGCT
1 AGCTAGTATGCT
5803168 CATTCTTCTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (18 bp):
AGCTAGTATGCTTAAACG
Found at i:5806178 original size:46 final size:46
Alignment explanation
Indices: 5806118--5806211 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
5806108 AATCAAATGA
*
5806118 CCACTACATGTACTGTTATTGCAAAAAAGGCAGTCACACCATCAAT
1 CCACCACATGTACTGTTATTGCAAAAAAGGCAGTCACACCATCAAT
*
5806164 CCACCACATGTACTGTTATTGCAAAAACGGCAGTCACACCATCAAT
1 CCACCACATGTACTGTTATTGCAAAAAAGGCAGTCACACCATCAAT
5806210 CC
1 CC
5806212 GATGATATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (46 bp):
CCACCACATGTACTGTTATTGCAAAAAAGGCAGTCACACCATCAAT
Found at i:5820280 original size:75 final size:75
Alignment explanation
Indices: 5820199--5820420 Score: 322
Period size: 75 Copynumber: 3.0 Consensus size: 75
5820189 GAAAACTAGA
* * *
5820199 ATTATTCCCTTATTAATACAGAAGGTAAATGAAAAGTTAGAAAAATAAATTATATTCTTTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATAAATTATATTCTTTCCAAA
*
5820264 AAAATATA-G
66 AGAATATATG
* * *
5820273 CGTTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAATGAATTATATTCTTTCCAA
1 -ATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATAAATTATATTCTTTCCAA
5820338 AAGAATATATG
65 AAGAATATATG
* * *
5820349 ATTATTCGCTTATTAATAGAGAAGGCAAATGGAAAGCTAGAAAAA-AGAATTATATTCTTTCTAA
1 ATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATA-AATTATATTCTTTCCAA
5820413 AAGAATAT
65 AAGAATAT
5820421 TAATTTTCAT
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
75 131 0.99
76 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (75 bp):
ATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATAAATTATATTCTTTCCAAA
AGAATATATG
Found at i:5820838 original size:137 final size:138
Alignment explanation
Indices: 5820396--5820954 Score: 863
Period size: 138 Copynumber: 4.1 Consensus size: 138
5820386 TAGAAAAAAG
* * *
5820396 AATTATATTCTTTCTAAAAGAATATTAATTTTCATGTATTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATTTATTTTATATTTTGACCGAAATTAATTAA
* * *
5820461 TATAATTATTTATATTAATAATTTCAGTAAAATATATATAATT-ATATTTTGTATGAATCAAATT
66 TATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
5820525 CATTTATT
131 CATATATT
* *
5820533 AATTTTTATTCTTTCCAAAAGAATATTAATTTTCATTTATTTTATATTTTGATCGAAATTAATTA
1 AA-TTATATTCTTTCCAAAAGAATATTAATTTTCATTTATTTTATATTTTGACCGAAATTAATTA
* *
5820598 ATATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCTAAT
65 ATATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
5820663 TCATATATT
130 TCATATATT
* * * * * *
5820672 AATTATATTCTTTCCTAAAGAATACTAATTTTCATATCTTTTATATTTTGATCGAAAGTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATTTATTTTATATTTTGACCGAAATTAATTAA
*
5820737 TATAACTATTTATATTAAT-AATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
5820801 CATATATT
131 CATATATT
* * * * *
5820809 AATTATATTCTTTTCAAAATAATATTAATTTCCATTTCTTTTATATTTTGACCGAAATTAATTTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATTTATTTTATATTTTGACCGAAATTAATTAA
*
5820874 TATAATTGTTTATATTAATAAATTCGGTAAAATATATA-AATTAATATTTTGTATGAATCAAATT
66 TATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
5820938 CATATATT
131 CATATATT
*
5820946 AATTTTATT
1 AATTATATT
5820955 TATGTTCTCT
Statistics
Matches: 387, Mismatches: 32, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
137 168 0.43
138 191 0.49
139 28 0.07
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATTTATTTTATATTTTGACCGAAATTAATTAA
TATAATTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:5840436 original size:20 final size:20
Alignment explanation
Indices: 5840407--5840452 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5840397 AAACACAAAA
*
5840407 TTCTATAAAAATGCTATGAG
1 TTCTACAAAAATGCTATGAG
* *
5840427 TTCTACAAAAGTGTTATGAG
1 TTCTACAAAAATGCTATGAG
5840447 TTCTAC
1 TTCTAC
5840453 TCTTTAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
TTCTACAAAAATGCTATGAG
Found at i:5843453 original size:25 final size:24
Alignment explanation
Indices: 5843404--5843452 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
5843394 GATATTTAAT
5843404 CCATTTTCTTTGAGAGTATCAAAAG
1 CCATTTTCTTTGAGAGTAT-AAAAG
*
5843429 CCATTTTGTTTGTAGAGTTATAAA
1 CCATTTTCTTTG-AGAG-TATAAA
5843453 GAGCAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 7 0.33
27 3 0.14
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (24 bp):
CCATTTTCTTTGAGAGTATAAAAG
Found at i:5859413 original size:50 final size:50
Alignment explanation
Indices: 5859345--5859741 Score: 391
Period size: 50 Copynumber: 7.9 Consensus size: 50
5859335 TATGTATGTA
* * * *
5859345 TTTACGCTCGCCAACTTGCACACGTTTACGCTCGTCAACTTATATATGCA
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* * * * * * *
5859395 TTTACACTTGCTAGCTTGCATACGTTTATGCTCATTAGCATATATATGCG
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* ** * * * **
5859445 TTTACGCTCGCCAGCTTGTTCAAGTTTACACTCGTCAGCTAATATATGTA
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* * *
5859495 TTTACGCTCGCTAGCTTACACACGTTTAAGCTCGTCAGCTTATATATGTG
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* * * *
5859545 TTTACGCTCGCCAGCTTGCGCACGTTTACACTCGTCAGCTTATATATTCG
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* * ** * * *
5859595 TTTATGCTCTCCGGCTTACACATGTTTACGCTCATCAGCTTATATATGCG
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* * * * * *
5859645 TTTAGGCTCGCTAGCTTGTACATGTTTATGCTCGTTAGTTTATATATGCG
1 TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
* * * *
5859695 TTTACGCTCG-TCAACTTGCACATGTTTACGCTTGTCAACTTATATAT
1 TTTACGCTCGCT-AGCTTGCACACGTTTACGCTCGTCAGCTTATATAT
5859742 ATATATATAT
Statistics
Matches: 277, Mismatches: 69, Indels: 2
0.80 0.20 0.01
Matches are distributed among these distances:
49 1 0.00
50 276 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (50 bp):
TTTACGCTCGCTAGCTTGCACACGTTTACGCTCGTCAGCTTATATATGCG
Found at i:5859504 original size:26 final size:25
Alignment explanation
Indices: 5859369--5859741 Score: 115
Period size: 24 Copynumber: 14.9 Consensus size: 25
5859359 CTTGCACACG
* *
5859369 TTTACGCTCGTCAACTTATATATGCA
1 TTTACGCTCGTCAGCTTATATATG-T
* * ** *
5859395 TTTACACTTG-CTAGCTTGCATACG-
1 TTTACGCTCGTC-AGCTTATATATGT
* * * * *
5859419 TTTATGCTCATTAGCATATATATGCG
1 TTTACGCTCGTCAGCTTATATATG-T
* * *
5859445 TTTACGCTCGCCAGCTTGT-TCAAG-
1 TTTACGCTCGTCAGCTTATAT-ATGT
* *
5859469 TTTACACTCGTCAGCTAATATATGT
1 TTTACGCTCGTCAGCTTATATATGT
* * *
5859494 ATTTACGCTCG-CTAGCTTACACACG-
1 -TTTACGCTCGTC-AGCTTATATATGT
*
5859519 TTTAAGCTCGTCAGCTTATATATGT
1 TTTACGCTCGTCAGCTTATATATGT
* **** *
5859544 GTTTACGCTCGCCAGCTTGCGCACG-
1 -TTTACGCTCGTCAGCTTATATATGT
*
5859569 TTTACACTCGTCAGCTTATATAT-T
1 TTTACGCTCGTCAGCTTATATATGT
* * * *
5859593 CGTTTATGCTC-TCCGGCTTACACATG-
1 --TTTACGCTCGT-CAGCTTATATATGT
* *
5859619 TTTACGCTCATCAGCTTATATATGCG
1 TTTACGCTCGTCAGCTTATATATG-T
* * *
5859645 TTTAGGCTCG-CTAGCTTGTACATG-
1 TTTACGCTCGTC-AGCTTATATATGT
* * * *
5859669 TTTATGCTCGTTAGTTTATATATGCG
1 TTTACGCTCGTCAGCTTATATATG-T
* ** *
5859695 TTTACGCTCGTCAACTTGCACATG-
1 TTTACGCTCGTCAGCTTATATATGT
* *
5859719 TTTACGCTTGTCAACTTATATAT
1 TTTACGCTCGTCAGCTTATATAT
5859742 ATATATATAT
Statistics
Matches: 244, Mismatches: 79, Indels: 50
0.65 0.21 0.13
Matches are distributed among these distances:
24 120 0.49
25 8 0.03
26 116 0.48
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
TTTACGCTCGTCAGCTTATATATGT
Found at i:5860894 original size:138 final size:139
Alignment explanation
Indices: 5860731--5861004 Score: 327
Period size: 138 Copynumber: 2.0 Consensus size: 139
5860721 TAAATCTTTA
* ** * * * * **
5860731 AAACTTTAACGATTTTACAAATAAATCCCCGGGTTAGCTAGATTAAGGTACCAGGA-TTCTAAAA
1 AAACTTTAACAATTTTACAAATAAATCCCCGAATTAACTAAATTAAGATACAAAAATTTC-AAAA
* * *
5860795 ATATAAAAATTAT-AAGATAATGGCTTGATTAAACTTACCAATTTAAAGATTGAACCTATTAAAA
65 ATATAAAAATTATAAAAAAAATGGCTTAATTAAACTTACCAATTTAAAGATTGAACCTATTAAAA
5860859 ACCCTAAATT
130 ACCCTAAATT
* * *
5860869 AAACTTTAACAATTTTATAAATAAATCCTCGAATTAATTAAATTAAGATACAAAAATTTCAAAAA
1 AAACTTTAACAATTTTACAAATAAATCCCCGAATTAACTAAATTAAGATACAAAAATTTCAAAAA
* * * * * * *
5860934 TATAAAAATTATAAAAAAAATGGCTTAATTAAGCTTATCAATTTGACGCTTGAATCTATTAAAAG
66 TATAAAAATTATAAAAAAAATGGCTTAATTAAACTTACCAATTTAAAGATTGAACCTATTAAAAA
5860999 CCCTAA
131 CCCTAA
5861005 CTTTTCTCTT
Statistics
Matches: 112, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
138 61 0.54
139 51 0.46
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (139 bp):
AAACTTTAACAATTTTACAAATAAATCCCCGAATTAACTAAATTAAGATACAAAAATTTCAAAAA
TATAAAAATTATAAAAAAAATGGCTTAATTAAACTTACCAATTTAAAGATTGAACCTATTAAAAA
CCCTAAATT
Found at i:5861501 original size:36 final size:36
Alignment explanation
Indices: 5861461--5861536 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
5861451 CGTGAGCTTT
5861461 TGAAAAACTAATTGGTGTAAGCGCAACATGTGTTGA
1 TGAAAAACTAATTGGTGTAAGCGCAACATGTGTTGA
* *
5861497 TGAAAAACTGATTGGTGTGAGCGCAACATGTGTTGA
1 TGAAAAACTAATTGGTGTAAGCGCAACATGTGTTGA
5861533 TGAA
1 TGAA
5861537 GTAATTATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (36 bp):
TGAAAAACTAATTGGTGTAAGCGCAACATGTGTTGA
Found at i:5865040 original size:21 final size:22
Alignment explanation
Indices: 5865016--5865066 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
5865006 AGTCAATTGA
* *
5865016 TTACCAAATAAGTT-TATTATT
1 TTACAAAATAAATTATATTATT
5865037 TTACAAAATAAATTATATTATT
1 TTACAAAATAAATTATATTATT
5865059 TTA-AAAAT
1 TTACAAAAT
5865067 GATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (22 bp):
TTACAAAATAAATTATATTATT
Found at i:5865058 original size:22 final size:21
Alignment explanation
Indices: 5865016--5865075 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
5865006 AGTCAATTGA
* *
5865016 TTACCAAATAAGTTTATTATT
1 TTACAAAATAAATTTATTATT
5865037 TTACAAAATAAATTATATTATT
1 TTACAAAATAAATT-TATTATT
* *
5865059 TTA-AAAATGATTTTATT
1 TTACAAAATAAATTTATT
5865076 TTCTTTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.12
21 20 0.59
22 10 0.29
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (21 bp):
TTACAAAATAAATTTATTATT
Found at i:5865075 original size:20 final size:22
Alignment explanation
Indices: 5865028--5865075 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5865018 ACCAAATAAG
5865028 TTTATTATTTTACAAAATAAAT
1 TTTATTATTTTACAAAATAAAT
* *
5865050 TATATTATTTTA-AAAAT-GAT
1 TTTATTATTTTACAAAATAAAT
5865070 TTTATT
1 TTTATT
5865076 TTCTTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 11 0.48
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTATTATTTTACAAAATAAAT
Found at i:5865308 original size:29 final size:31
Alignment explanation
Indices: 5865266--5865330 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
5865256 CTCTAATTCT
*
5865266 CTCT-TTGTTTATATGGTAGAAGG-AAAAAA
1 CTCTGTTGTTTATATAGTAGAAGGAAAAAAA
5865295 CTCTGTTG-TTATATAGTAGAAGGAAAAAAA
1 CTCTGTTGTTTATATAGTAGAAGGAAAAAAA
5865325 CTCTGT
1 CTCTGT
5865331 CGGTTGACAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (31 bp):
CTCTGTTGTTTATATAGTAGAAGGAAAAAAA
Found at i:5868034 original size:17 final size:18
Alignment explanation
Indices: 5868012--5868045 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5868002 TGGATGCACC
*
5868012 TGAAGATTTTGG-ATATG
1 TGAAGATCTTGGCATATG
5868029 TGAAGATCTTGGCATAT
1 TGAAGATCTTGGCATAT
5868046 TTCCTGAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.38
Consensus pattern (18 bp):
TGAAGATCTTGGCATATG
Found at i:5871798 original size:41 final size:41
Alignment explanation
Indices: 5871747--5871830 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
5871737 AGCAATTTTG
* *
5871747 AGAAGGTGGCTCTCTCTTTTCCAATTATGGGATATTAGAAA
1 AGAAAGTGGCTCTCTCTTTTCCAATGATGGGATATTAGAAA
5871788 AGAAAGTGGCTCTCTCTTTTCCAATGATGGGATATTAGAAA
1 AGAAAGTGGCTCTCTCTTTTCCAATGATGGGATATTAGAAA
5871829 AG
1 AG
5871831 CTTTCTTGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (41 bp):
AGAAAGTGGCTCTCTCTTTTCCAATGATGGGATATTAGAAA
Found at i:5872662 original size:158 final size:158
Alignment explanation
Indices: 5872374--5872670 Score: 432
Period size: 158 Copynumber: 1.9 Consensus size: 158
5872364 TATTTTTATA
* * ***
5872374 TATTTCAATTTTATTGTACAAAAGGTTTCACCCGCATTGTTTTCATATTTGTAATTACTATTACT
1 TATTTCAATTTTATTGCACAAAAGGTTTCACCCACATTGTTTTCATATCCATAATTACTATTACT
* * * * * * * *
5872439 TAAGTGTGTTGAGTTGGTTTCATAAATCAACTTGATACCAACTTAGTCAAGGAAATTACTAAAAT
66 TAAGTGTATTGAATTGGTGTCATAAACCAACTCGATAACAAATCAGTCAAGGAAATTACTAAAAT
5872504 AATCTTACAATTTTTAAATAAGTTATGT
131 AATCTTACAATTTTTAAATAAGTTATGT
* * *
5872532 TATTTCAATTTTATTGCACAGAAGGTTTCACCCACATTGTTTTTATATCCATAATTACTATTATT
1 TATTTCAATTTTATTGCACAAAAGGTTTCACCCACATTGTTTTCATATCCATAATTACTATTACT
* *
5872597 TAAGTGTATTGAATTGGTGTCATAAGCCAACTCGATAACAAATCAGTTAAGGAAATTACTAAAAT
66 TAAGTGTATTGAATTGGTGTCATAAACCAACTCGATAACAAATCAGTCAAGGAAATTACTAAAAT
5872662 AATCTTACA
131 AATCTTACA
5872671 TATCTTAATT
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 121 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (158 bp):
TATTTCAATTTTATTGCACAAAAGGTTTCACCCACATTGTTTTCATATCCATAATTACTATTACT
TAAGTGTATTGAATTGGTGTCATAAACCAACTCGATAACAAATCAGTCAAGGAAATTACTAAAAT
AATCTTACAATTTTTAAATAAGTTATGT
Found at i:5873919 original size:30 final size:30
Alignment explanation
Indices: 5873885--5874046 Score: 111
Period size: 29 Copynumber: 5.5 Consensus size: 30
5873875 GTTTCCTTTG
*
5873885 CAGAGATTGCCACAAAAGCTATCCTTTTTA
1 CAGAGTTTGCCACAAAAGCTATCCTTTTTA
* * *
5873915 CAGAGTTTGCCACAAAGGCTATTCTATTT-
1 CAGAGTTTGCCACAAAAGCTATCCTTTTTA
* *
5873944 -AGAGTTTTTCCACAAAGGCTATCC-TTTTA
1 CAGAG-TTTGCCACAAAAGCTATCCTTTTTA
* * * * * *
5873973 CAGAGTTCGCCATAAAAACTATTCTATCT-
1 CAGAGTTTGCCACAAAAGCTATCCTTTTTA
* * **
5874002 -AGAGTTTTTCCATAAAATTTATCC-TTTTA
1 CAGAG-TTTGCCACAAAAGCTATCCTTTTTA
*
5874031 TAGAGTTTGCCACAAA
1 CAGAGTTTGCCACAAA
5874047 GGCCATCTTA
Statistics
Matches: 101, Mismatches: 24, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
28 13 0.13
29 53 0.52
30 35 0.35
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (30 bp):
CAGAGTTTGCCACAAAAGCTATCCTTTTTA
Found at i:5873996 original size:58 final size:58
Alignment explanation
Indices: 5873894--5874046 Score: 207
Period size: 58 Copynumber: 2.6 Consensus size: 58
5873884 GCAGAGATTG
** *
5873894 CCACAAAAGCTATCCTTTTTACAGAGTTTGCCACAAAGGCTATTCTATTTAGAGTTTTT
1 CCACAAAAGCTATCC-TTTTACAGAGTTTGCCACAAAAACTATTCTATCTAGAGTTTTT
* * *
5873953 CCACAAAGGCTATCCTTTTACAGAGTTCGCCATAAAAACTATTCTATCTAGAGTTTTT
1 CCACAAAAGCTATCCTTTTACAGAGTTTGCCACAAAAACTATTCTATCTAGAGTTTTT
* ** *
5874011 CCATAAAATTTATCCTTTTATAGAGTTTGCCACAAA
1 CCACAAAAGCTATCCTTTTACAGAGTTTGCCACAAA
5874047 GGCCATCTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
58 67 0.83
59 14 0.17
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (58 bp):
CCACAAAAGCTATCCTTTTACAGAGTTTGCCACAAAAACTATTCTATCTAGAGTTTTT
Found at i:5884830 original size:17 final size:18
Alignment explanation
Indices: 5884808--5884848 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5884798 TAGTTTTTCA
5884808 TGCATTTT-TATTGTTAC
1 TGCATTTTCTATTGTTAC
*
5884825 TGCATTTTCTATTGTTAT
1 TGCATTTTCTATTGTTAC
5884843 TGCATT
1 TGCATT
5884849 CATTTTGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.59
Consensus pattern (18 bp):
TGCATTTTCTATTGTTAC
Found at i:5890507 original size:88 final size:88
Alignment explanation
Indices: 5890407--5890596 Score: 197
Period size: 88 Copynumber: 2.1 Consensus size: 88
5890397 TTCGGAGGCT
* * * * *
5890407 AAATGGTAAATTTTG-GATACTCGAGGGCAAAAAT-GTAATTTTTG-GAATTTTGGATGTCAAAA
1 AAATGGT-AATTTTGAAAT-CTCGAGGGCAAAAATGGTAATTTTTGAAAAGTTT-AAGGTC-AAA
*
5890469 AATGTAATTTTTGGACATCCGAGGGTA
62 AATGTAATTTTTGGACATCCAAGGGTA
* * ** **
5890496 AAATGGTAATTTTTAAATGTTTAGGGGTAAAATGGTAATTTTTGAAAAGTTTAAGGTCAAAAATG
1 AAATGGTAATTTTGAAATCTCGAGGGCAAAAATGGTAATTTTTGAAAAGTTTAAGGTCAAAAATG
**
5890561 TAATTTTTGGACATTTAAGGGTA
66 TAATTTTTGGACATCCAAGGGTA
5890584 AAATGGTAATTTT
1 AAATGGTAATTTT
5890597 TAGATTTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
88 56 0.67
89 23 0.27
90 5 0.06
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (88 bp):
AAATGGTAATTTTGAAATCTCGAGGGCAAAAATGGTAATTTTTGAAAAGTTTAAGGTCAAAAATG
TAATTTTTGGACATCCAAGGGTA
Found at i:5890523 original size:29 final size:30
Alignment explanation
Indices: 5890491--5890774 Score: 145
Period size: 29 Copynumber: 9.7 Consensus size: 30
5890481 GGACATCCGA
5890491 GGGT-AAAATGGTAATTTTTAAATGTTTAG
1 GGGTAAAAATGGTAATTTTTAAATGTTTAG
*
5890520 GGGT-AAAATGGTAATTTTTGAAAAGTTTA-
1 GGGTAAAAATGGTAATTTTT-AAATGTTTAG
* ** ** *
5890549 AGGTCAAAAAT-GTAATTTTTGGACATTTAA
1 GGGT-AAAAATGGTAATTTTTAAATGTTTAG
* * *
5890579 GGGT-AAAATGGTAATTTTTAGATTTTTTG
1 GGGTAAAAATGGTAATTTTTAAATGTTTAG
*
5890608 GGGTTAAAAATGG-AATTTTGGAAA-GTTTAG
1 GGG-TAAAAATGGTAATTTT-TAAATGTTTAG
5890638 GGGTAAAAAT-GTAATTTTTGGAAAT-TTT-G
1 GGGTAAAAATGGTAATTTTT--AAATGTTTAG
*** *
5890667 GAACAAAAAATGG-AATTTTGGAAA-GTTT-G
1 G-GGTAAAAATGGTAATTTT-TAAATGTTTAG
**
5890696 GGAGTAAAAAT-GTAATTTTTTGAAA-AATTAG
1 GG-GTAAAAATGGTAA-TTTTT-AAATGTTTAG
* * * *
5890727 GGTTAAAAAT-G-AAATTTTAGAAAGTTTTG
1 GGGTAAAAATGGTAATTTTTA-AATGTTTAG
5890756 GGGT-AAAATGGTAATTTTT
1 GGGTAAAAATGGTAATTTTT
5890775 GGATAGTTTA
Statistics
Matches: 196, Mismatches: 34, Indels: 49
0.70 0.12 0.18
Matches are distributed among these distances:
27 1 0.01
28 18 0.09
29 84 0.43
30 75 0.38
31 18 0.09
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (30 bp):
GGGTAAAAATGGTAATTTTTAAATGTTTAG
Found at i:5890597 original size:88 final size:88
Alignment explanation
Indices: 5890466--5890664 Score: 269
Period size: 88 Copynumber: 2.3 Consensus size: 88
5890456 TTGGATGTCA
***
5890466 AAAAATGTAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTAAATGTTTAGGGG-T-AAAAT
1 AAAAATGTAATTTTTGGACATTTAAGGGTAAAATGGTAATTTTTAAATGTTTAGGGGTTAAAAAT
5890529 GGTAATTTTTGAAAAGTTTA-AGGT
66 GG-AA-TTTTGAAAAGTTTAGAGGT
* * *
5890553 CAAAAATGTAATTTTTGGACATTTAAGGGTAAAATGGTAATTTTTAGATTTTTTGGGGTTAAAAA
1 -AAAAATGTAATTTTTGGACATTTAAGGGTAAAATGGTAATTTTTAAATGTTTAGGGGTTAAAAA
* *
5890618 TGGAATTTTGGAAAGTTTAGGGGT
65 TGGAATTTTGAAAAGTTTAGAGGT
*
5890642 AAAAATGTAATTTTTGGAAATTT
1 AAAAATGTAATTTTTGGACATTT
5890665 TGGAACAAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
88 86 0.87
89 6 0.06
90 7 0.07
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.39
Consensus pattern (88 bp):
AAAAATGTAATTTTTGGACATTTAAGGGTAAAATGGTAATTTTTAAATGTTTAGGGGTTAAAAAT
GGAATTTTGAAAAGTTTAGAGGT
Found at i:5890666 original size:59 final size:59
Alignment explanation
Indices: 5890495--5890777 Score: 270
Period size: 59 Copynumber: 4.8 Consensus size: 59
5890485 ATCCGAGGGT
* * * ** *
5890495 AAAATGGTAATTTT-TAAATGTTTAGGGGTAAAATGGTAATTTTTGAAAAGTTTAAGGTCA
1 AAAATGG-AATTTTGGAAA-GTTTAGGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTTA
* * * * **
5890555 AAAATGTAATTTTTGGACA-TTTAAGGGTAAAATGGTAATTTTTAGATTTTTTGGGGTTA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTTA
****
5890614 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAAT-GTAATTTTTGGAAATTTTGGAACAA
1 AAAATGGAATTTTGGAAAGTTTAGGGGT-AAAATGGTAATTTTTGGAAATTTTGGGGTTA
* ** *
5890673 AAAATGGAATTTTGGAAAGTTT-GGGAGTAAAAAT-GTAATTTTTTGAAAAATTAGGGTTA
1 AAAATGGAATTTTGGAAAGTTTAGGG-GT-AAAATGGTAATTTTTGGAAATTTTGGGGTTA
* * *
5890732 AAAATGAAATTTTAGAAAGTTTTGGGGTAAAATGGTAATTTTTGGA
1 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGA
5890778 TAGTTTAGGG
Statistics
Matches: 183, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
58 16 0.09
59 147 0.80
60 18 0.10
61 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTTA
Found at i:5890676 original size:118 final size:117
Alignment explanation
Indices: 5890495--5890789 Score: 305
Period size: 118 Copynumber: 2.5 Consensus size: 117
5890485 ATCCGAGGGT
* * *
5890495 AAAATGGTAATTTTTAAATGTTTAGGGGTAAAATGGTAATTTTTGAAAAGTTTAAGGTCAAAAAT
1 AAAATGG-AATTTTGAAA-GTTTAGGGGTAAAATGGTAATTTTTGGAAAGTTTAAGGACAAAAAT
* * **** *
5890560 GTAATTTTTGGACA-TTTAAGG-GT-AAAATGGTAATTTTTAGATTTTTTGGGGTTA
64 GGAA-TTTTGGAAAGTTT-AGGAGTAAAAAT-GTAATTTTTAGAAAAATTAGGGTTA
*
5890614 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAAT-GTAATTTTTGGAAA-TTT-TGGAACAAAAA
1 AAAATGGAATTTT-GAAAGTTTAGGGGT-AAAATGGTAATTTTTGGAAAGTTTAAGG-AC-AAAA
* *
5890676 ATGGAATTTTGGAAAGTTTGGGAGTAAAAATGTAATTTTTTGAAAAATTAGGGTTA
62 ATGGAATTTTGGAAAGTTTAGGAGTAAAAATGTAATTTTTAGAAAAATTAGGGTTA
* * * *
5890732 AAAATGAAATTTTAGAAAGTTTTGGGGTAAAATGGTAATTTTTGGATAGTTTAGGGAC
1 AAAATGGAATTTT-GAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAGTTTAAGGAC
5890790 CTTTAAGCAA
Statistics
Matches: 148, Mismatches: 18, Indels: 20
0.80 0.10 0.11
Matches are distributed among these distances:
116 2 0.01
117 19 0.13
118 100 0.68
119 25 0.17
120 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (117 bp):
AAAATGGAATTTTGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAGTTTAAGGACAAAAATGG
AATTTTGGAAAGTTTAGGAGTAAAAATGTAATTTTTAGAAAAATTAGGGTTA
Found at i:5891761 original size:3 final size:3
Alignment explanation
Indices: 5891753--5891821 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
5891743 AATTTCTTTT
* * *
5891753 TTA TTA TTA TTA ATA TTA TTTA TTA CTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5891799 TTA TTA ATA TTAA TAA TTA TTA T
1 TTA TTA TTA TT-A TTA TTA TTA T
5891822 AAAGAACTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 49 0.91
4 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5892578 original size:6 final size:6
Alignment explanation
Indices: 5892522--5892621 Score: 64
Period size: 6 Copynumber: 17.0 Consensus size: 6
5892512 ATGGACTTTG
* * * * *
5892522 AATTTA ATTTTA AAGTTTA AGTTTA AAATT- -ATTTCA GATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
** * * *
5892569 AATTTA AATTTA AAAATG AATTTA AATATA AATTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
5892616 AATTTA
1 AATTTA
5892622 GAAATAAATC
Statistics
Matches: 69, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
4 3 0.04
5 8 0.12
6 49 0.71
7 9 0.13
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:5892617 original size:17 final size:18
Alignment explanation
Indices: 5892591--5892635 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
5892581 AAAATGAATT
5892591 TAAATATAAATTTA-AAA
1 TAAATATAAATTTAGAAA
*
5892608 TAAATTTAAATTTAGAAA
1 TAAATATAAATTTAGAAA
*
5892626 TAAATCTAAA
1 TAAATATAAA
5892636 ACTAATCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAATATAAATTTAGAAA
Found at i:5892629 original size:23 final size:23
Alignment explanation
Indices: 5892567--5892618 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5892557 AGATTTAAAC
* * *
5892567 TAAATTTAAATTTAAAAATGAATT
1 TAAATATAAATAT-AAAATAAATT
*
5892591 TAAATATAAATTTAAAATAAATT
1 TAAATATAAATATAAAATAAATT
5892614 TAAAT
1 TAAAT
5892619 TTAGAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAATATAAATATAAAATAAATT
Found at i:5892646 original size:29 final size:29
Alignment explanation
Indices: 5892587--5892646 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
5892577 TTTAAAAATG
* *
5892587 AATTTAAATATAAATTTAAAATAAATTTA
1 AATTTAAATATAAATCTAAAATAAATCTA
5892616 AATTTAGAA-ATAAATCTAAAACT-AATCTA
1 AATTTA-AATATAAATCTAAAA-TAAATCTA
5892645 AA
1 AA
5892647 CTCAAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (29 bp):
AATTTAAATATAAATCTAAAATAAATCTA
Found at i:5893399 original size:29 final size:29
Alignment explanation
Indices: 5893357--5893414 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5893347 AAGAAAACCA
*
5893357 TCCTACAACTACTTCG-AAATGTGGGGGTG
1 TCCTACAACCACTT-GAAAATGTGGGGGTG
5893386 TCCTACAACCACTTGAAAATGTGGGGGTG
1 TCCTACAACCACTTGAAAATGTGGGGGTG
5893415 ACTTGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (29 bp):
TCCTACAACCACTTGAAAATGTGGGGGTG
Found at i:5897681 original size:217 final size:217
Alignment explanation
Indices: 5897294--5897725 Score: 783
Period size: 217 Copynumber: 2.0 Consensus size: 217
5897284 CAAATAACAT
*
5897294 CTTAATTAAAGCTCTCCCAATGATTCAACTATTAAATAAATATTTTATAACTATATTTTTAATGT
1 CTTAATTAAAGCTCTCCCAATGATTCAACTATTAAATAAATATTTTATAACTAAATTTTTAATGT
5897359 TGAATTTTTCTTTCAGCGACATGATAACATTTTGACATTTTGATGATATGTTAAATTATGCTACC
66 TGAATTTTTCTTTCAGCGACATGATAACATTTTGACATTTTGATGATATGTTAAATTATGCTACC
*
5897424 TAAGGGAGAAGCTAGGAATTTTGATTAGCAAGTCTAAGATAAAATTATAAAATTTGAAGGGCAAA
131 TAAGGGAGAAGCTAGGAATTTTGATTAGCAAGTCTAAGATAAAATTATAAAATTTGAAGGACAAA
5897489 ACTAAAAATATTATGTTTTAAC
196 ACTAAAAATATTATGTTTTAAC
* *
5897511 CTTAATTAAAGCTGTCTCAATGATTCAACTATTAAATAAATATTTTATAACTAAATTTTTAATGT
1 CTTAATTAAAGCTCTCCCAATGATTCAACTATTAAATAAATATTTTATAACTAAATTTTTAATGT
*
5897576 TGAATTTTTCTTTCAGCGACATGATAACATTTTGACGTTTTGATGATATGTTAAATTATGCTACC
66 TGAATTTTTCTTTCAGCGACATGATAACATTTTGACATTTTGATGATATGTTAAATTATGCTACC
* * *
5897641 TAAGGGAGAAGTTAGGAATTTTGATTAGGAAGTTTAAGATAAAATTATAAAATTTGAAGGACAAA
131 TAAGGGAGAAGCTAGGAATTTTGATTAGCAAGTCTAAGATAAAATTATAAAATTTGAAGGACAAA
*
5897706 GCTAAAAATATTATGTTTTA
196 ACTAAAAATATTATGTTTTA
5897726 CATTTCAGAG
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 206 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (217 bp):
CTTAATTAAAGCTCTCCCAATGATTCAACTATTAAATAAATATTTTATAACTAAATTTTTAATGT
TGAATTTTTCTTTCAGCGACATGATAACATTTTGACATTTTGATGATATGTTAAATTATGCTACC
TAAGGGAGAAGCTAGGAATTTTGATTAGCAAGTCTAAGATAAAATTATAAAATTTGAAGGACAAA
ACTAAAAATATTATGTTTTAAC
Found at i:5909279 original size:24 final size:24
Alignment explanation
Indices: 5909241--5909414 Score: 147
Period size: 24 Copynumber: 7.2 Consensus size: 24
5909231 AATAATGTAC
* * *
5909241 GTTTAAGCTCATCAGCCATTTTAA
1 GTTTATGCTCGTCAGCCACTTTAA
*
5909265 GTTTATGC-CTGTCAGCCATTTTACA
1 GTTTATGCTC-GTCAGCCACTTTA-A
* *
5909290 -TTTATGCTCGTCAGTCACTTTAC
1 GTTTATGCTCGTCAGCCACTTTAA
* *
5909313 GTTTATGCTCGTCAACCACTTTAC
1 GTTTATGCTCGTCAGCCACTTTAA
* **
5909337 GTTTATTCTAATCAGCCACTTTACA
1 GTTTATGCTCGTCAGCCACTTTA-A
* * * * *
5909362 -TTTTTGCTCATTAGCTACTTTAC
1 GTTTATGCTCGTCAGCCACTTTAA
*
5909385 GTTTATGCTCGTCAGCCACTTTAC
1 GTTTATGCTCGTCAGCCACTTTAA
5909409 GTTTAT
1 GTTTAT
5909415 CCTTACAAAT
Statistics
Matches: 122, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.01
24 119 0.98
25 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (24 bp):
GTTTATGCTCGTCAGCCACTTTAA
Found at i:5909317 original size:72 final size:72
Alignment explanation
Indices: 5909238--5909417 Score: 229
Period size: 72 Copynumber: 2.5 Consensus size: 72
5909228 TCAAATAATG
* * * * * * *
5909238 TACGTTTAAGCTCATCAGCCATTTTAAGTTTATGCCT-GTCAGCCATTTTACATTTATGCTCGTC
1 TACGTTTATGCTCGTCAGCCACTTTACGTTTAT-CCTAATCAGCCACTTTACATTTATGCTCATC
5909302 AG-TCACTT
65 AGCT-ACTT
* * * *
5909310 TACGTTTATGCTCGTCAACCACTTTACGTTTATTCTAATCAGCCACTTTACATTTTTGCTCATTA
1 TACGTTTATGCTCGTCAGCCACTTTACGTTTATCCTAATCAGCCACTTTACATTTATGCTCATCA
5909375 GCTACTT
66 GCTACTT
5909382 TACGTTTATGCTCGTCAGCCACTTTACGTTTATCCT
1 TACGTTTATGCTCGTCAGCCACTTTACGTTTATCCT
5909418 TACAAATTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
71 2 0.02
72 90 0.97
73 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (72 bp):
TACGTTTATGCTCGTCAGCCACTTTACGTTTATCCTAATCAGCCACTTTACATTTATGCTCATCA
GCTACTT
Found at i:5909342 original size:48 final size:48
Alignment explanation
Indices: 5909238--5909414 Score: 194
Period size: 48 Copynumber: 3.7 Consensus size: 48
5909228 TCAAATAATG
* * * *
5909238 TACGTTTAAGCTCATCAGCCATTTTAAGTTTATGC-CTGTCAGCCATTT
1 TACGTTTATGCTCATCAGCCACTTTACGTTTATGCTC-GTCAGCCACTT
* * * *
5909286 TACATTTATGCTCGTCAGTCACTTTACGTTTATGCTCGTCAACCACTT
1 TACGTTTATGCTCATCAGCCACTTTACGTTTATGCTCGTCAGCCACTT
* * * * * * *
5909334 TACGTTTATTCTAATCAGCCACTTTACATTTTTGCTCATTAGCTACTT
1 TACGTTTATGCTCATCAGCCACTTTACGTTTATGCTCGTCAGCCACTT
*
5909382 TACGTTTATGCTCGTCAGCCACTTTACGTTTAT
1 TACGTTTATGCTCATCAGCCACTTTACGTTTAT
5909415 CCTTACAAAT
Statistics
Matches: 104, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
48 103 0.99
49 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (48 bp):
TACGTTTATGCTCATCAGCCACTTTACGTTTATGCTCGTCAGCCACTT
Found at i:5909522 original size:27 final size:27
Alignment explanation
Indices: 5909491--5909545 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5909481 CTCCAATACA
5909491 TAATTTTTCACTCATTTATTTACAAGG
1 TAATTTTTCACTCATTTATTTACAAGG
*
5909518 TAATTTTTCACTTATTTATTTACAAGG
1 TAATTTTTCACTCATTTATTTACAAGG
5909545 T
1 T
5909546 CAAATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (27 bp):
TAATTTTTCACTCATTTATTTACAAGG
Found at i:5910294 original size:3 final size:3
Alignment explanation
Indices: 5910286--5910314 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5910276 ATATAATTCT
5910286 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5910315 TAATCATTTC
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:5927946 original size:24 final size:24
Alignment explanation
Indices: 5927890--5928023 Score: 144
Period size: 24 Copynumber: 5.6 Consensus size: 24
5927880 TAAGTCTTAA
** * *
5927890 TTACGTTTCCGCTCGTCAGCTAAT
1 TTACGTTTATGCTCGTCAGCCATT
* * * *
5927914 GTACATTTAAGCTCGTCAACCATT
1 TTACGTTTATGCTCGTCAGCCATT
*
5927938 TTACGTTTATGTTCGTCAGCCATT
1 TTACGTTTATGCTCGTCAGCCATT
* *
5927962 TTACGTTTATGCTTGTCAGCCACT
1 TTACGTTTATGCTCGTCAGCCATT
*
5927986 TTACGTTTATGCTCGTCAGTCACTT
1 TTACGTTTATGCTCGTCAGCCA-TT
5928011 TT-CGTTTATGCTC
1 TTACGTTTATGCTC
5928024 ATTAACCACT
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
24 88 0.97
25 3 0.03
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (24 bp):
TTACGTTTATGCTCGTCAGCCATT
Found at i:5927989 original size:48 final size:48
Alignment explanation
Indices: 5927919--5928043 Score: 153
Period size: 48 Copynumber: 2.6 Consensus size: 48
5927909 CTAATGTACA
* * *
5927919 TTTAAGCTCGTCAACCATTTTACGTTTATGTTCGTCAGCCA-TTTTACG
1 TTTATGCTCGTCAACCACTTTACGTTTATGCTCGTCAGCCACTTTT-CG
* * *
5927967 TTTATGCTTGTCAGCCACTTTACGTTTATGCTCGTCAGTCACTTTTCG
1 TTTATGCTCGTCAACCACTTTACGTTTATGCTCGTCAGCCACTTTTCG
* * *
5928015 TTTATGCTCATTAACCACTTTACATTTAT
1 TTTATGCTCGTCAACCACTTTACGTTTAT
5928044 CCTTACGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 61 0.94
49 4 0.06
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (48 bp):
TTTATGCTCGTCAACCACTTTACGTTTATGCTCGTCAGCCACTTTTCG
Found at i:5928033 original size:24 final size:24
Alignment explanation
Indices: 5927919--5928043 Score: 106
Period size: 24 Copynumber: 5.2 Consensus size: 24
5927909 CTAATGTACA
* * *
5927919 TTTAAGCTCGTCAACCATTTTACG
1 TTTATGCTCATCAACCACTTTACG
* * * *
5927943 TTTATGTTCGTCAGCCATTTTACG
1 TTTATGCTCATCAACCACTTTACG
** *
5927967 TTTATGCTTGTCAGCCACTTTACG
1 TTTATGCTCATCAACCACTTTACG
* ** *
5927991 TTTATGCTCGTCAGTCACTTTTCG
1 TTTATGCTCATCAACCACTTTACG
* *
5928015 TTTATGCTCATTAACCACTTTACA
1 TTTATGCTCATCAACCACTTTACG
5928039 TTTAT
1 TTTAT
5928044 CCTTACGAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (24 bp):
TTTATGCTCATCAACCACTTTACG
Found at i:5928878 original size:3 final size:3
Alignment explanation
Indices: 5928870--5929023 Score: 146
Period size: 3 Copynumber: 51.3 Consensus size: 3
5928860 CATATAATTC
* * * *
5928870 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAC TAT TAT TAC TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
5928918 TAT TAT TTT TAC TAT TAT TAT TAC TAC CAT TAT TAT TAC TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
5928966 TAC TAT TAC TAC TAT TAT TAC TAC TAT TAT TAT TAT TAC TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5929014 TAT TAT TAT T
1 TAT TAT TAT T
5929024 GTTGGAGCCC
Statistics
Matches: 123, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 123 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:5928894 original size:15 final size:15
Alignment explanation
Indices: 5928869--5929023 Score: 166
Period size: 15 Copynumber: 10.3 Consensus size: 15
5928859 TCATATAATT
5928869 CTATTATTATTATTA
1 CTATTATTATTATTA
* *
5928884 TTATTACTATTATTA
1 CTATTATTATTATTA
* * *
5928899 TTACTATTATTACTA
1 CTATTATTATTATTA
*
5928914 CTATTATTATTTTTA
1 CTATTATTATTATTA
*
5928929 CTATTATTATTACTA
1 CTATTATTATTATTA
* *
5928944 CCATTATTATTACTA
1 CTATTATTATTATTA
* * *
5928959 TTAATATTACTATTA
1 CTATTATTATTATTA
* *
5928974 CTACTATTATTACTA
1 CTATTATTATTATTA
5928989 CTATTATTATTATTA
1 CTATTATTATTATTA
*
5929004 CTATTATTACTATTA
1 CTATTATTATTATTA
*
5929019 TTATT
1 CTATT
5929024 GTTGGAGCCC
Statistics
Matches: 115, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 115 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (15 bp):
CTATTATTATTATTA
Found at i:5930451 original size:5 final size:5
Alignment explanation
Indices: 5930443--5930476 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
5930433 AGATTAGTTA
5930443 TTTAT TTTAT TTTAT TTTAT TTTATT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTT
5930477 TTTGCCCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:5936146 original size:30 final size:30
Alignment explanation
Indices: 5936110--5936170 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5936100 GCTTCTAAGG
5936110 AAGGGGCACTAGGAAAGACTTATGAGGCCA
1 AAGGGGCACTAGGAAAGACTTATGAGGCCA
5936140 AAGGGGCACTAGGAAAGACTTATGAGGCCA
1 AAGGGGCACTAGGAAAGACTTATGAGGCCA
5936170 A
1 A
5936171 CTTACCAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.33, T:0.13
Consensus pattern (30 bp):
AAGGGGCACTAGGAAAGACTTATGAGGCCA
Found at i:5942417 original size:50 final size:50
Alignment explanation
Indices: 5942290--5942417 Score: 186
Period size: 50 Copynumber: 2.6 Consensus size: 50
5942280 ATCTTTTACC
*
5942290 CCTAAAGCTATAG-AGGTGCAGATTGAAACCGCAATAGCAAATCTCATACA
1 CCTAAAGCTATAGAAGG-GCAGATTGAAGCCGCAATAGCAAATCTCATACA
* * * *
5942340 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTATAGAAGGGCAGATTGAAGCCGCAATAGCAAATCTCATACA
*
5942390 CCTAAAGCTGTAGAAGGGCAGATTGAAG
1 CCTAAAGCTATAGAAGGGCAGATTGAAG
5942418 TCACAAGGAC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 67 0.97
51 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (50 bp):
CCTAAAGCTATAGAAGGGCAGATTGAAGCCGCAATAGCAAATCTCATACA
Found at i:5942433 original size:50 final size:50
Alignment explanation
Indices: 5942290--5942449 Score: 162
Period size: 50 Copynumber: 3.2 Consensus size: 50
5942280 ATCTTTTACC
* * * *
5942290 CCTAAAGCTATAG-AGGTGCAGATTGAAACCGCAATAGCAAATCTCATACA
1 CCTAAAGCTATAGAAGG-GCAGAATGAAGCCACAATGGCAAATCTCATACA
* * *
5942340 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTATAGAAGGGCAGAATGAAGCCACAATGGCAAATCTCATACA
* * * * * *
5942390 CCTAAAGCTGTAGAAGGGCAGATTGAAGTCACAA-GGACGAATCTTATACT
1 CCTAAAGCTATAGAAGGGCAGAATGAAGCCACAATGG-CAAATCTCATACA
*
5942440 CCTGAAGCTA
1 CCTAAAGCTA
5942450 AAATGAAGTG
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 88 0.96
51 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTATAGAAGGGCAGAATGAAGCCACAATGGCAAATCTCATACA
Found at i:5942526 original size:40 final size:40
Alignment explanation
Indices: 5942467--5942803 Score: 267
Period size: 40 Copynumber: 8.5 Consensus size: 40
5942457 GTGAAGTTAC
* *
5942467 AACC-TCCAATCTTTTACCCTAGTTAGAGGGCAGATTGAA
1 AACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAA
*
5942506 AACCATCCAATCTTTTACCCTAATCAGAGGGTAGATTGAA
1 AACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAA
* * *
5942546 GACCATCCAATCTTTTACCCTAATCAGAGGGTAGA-TCAA
1 AACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAA
* * * * * * *
5942585 AGACAATCCAATCTCTTACCCCAACCATG-GGGAAAATTTAA
1 A-ACCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAA
* * * * *
5942626 GACAATCCAATCTCTTACCCTAACCAAAGGGCAGATTGAA
1 AACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAA
* * * * **
5942666 GATCATTCGATCTTTTACCCCGATCATG-GGGCAGATTGAA
1 AACCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAA
* * *
5942706 AACTATTCAATCTTTTACCCTAAGT-AGAGGGCAAATTGAA
1 AACCATCCAATCTTTTACCCTAA-TCAGAGGGCAGATTGAA
* * * ** *
5942746 TACCATCAAATCTCTTACCCGGACCATG-GGGCAGATTG--
1 AACCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAA
*
5942784 AACAATCCAATCTTTTACCC
1 AACCATCCAATCTTTTACCC
5942804 CTAAAGTTAT
Statistics
Matches: 240, Mismatches: 48, Indels: 21
0.78 0.16 0.07
Matches are distributed among these distances:
38 16 0.07
39 8 0.03
40 210 0.88
41 6 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (40 bp):
AACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAA
Found at i:5943395 original size:17 final size:17
Alignment explanation
Indices: 5943368--5943435 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
5943358 ATAATTTAAT
5943368 TTTTAAA-TTAAATTTA
1 TTTTAAATTTAAATTTA
5943384 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
5943401 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
* *
5943418 TTATAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
5943435 T
1 T
5943436 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:5944421 original size:3 final size:3
Alignment explanation
Indices: 5944413--5944438 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5944403 TTTCGTTTAA
5944413 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5944439 AACCCAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5945299 original size:162 final size:162
Alignment explanation
Indices: 5945122--5945621 Score: 820
Period size: 162 Copynumber: 3.1 Consensus size: 162
5945112 GGTTTTCAAT
* * * ** * *
5945122 TTAATCCTTTGACTGTTGGACTGCATCGGAGGCTACCACGTGTCACTTTTTGGTTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGTCACTTTTTGGTTTGTTTATGTA
* * *
5945187 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGTTTAATTACAA
66 TCTAGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGTTTAATTACAA
5945252 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
5945284 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGTCACTTTTTGGTTTGTTTATGTA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGTCACTTTTTGGTTTGTTTATGTA
*
5945349 TCTAGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTACTGTTTAATTACAA
66 TCTAGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGTTTAATTACAA
5945414 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
* *
5945446 TTAATCCTTTGACTATTTGACTGCACCAGAGGCCGCCACGTGCCACTTTTTGGTTTGTTTATGTA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGTCACTTTTTGGTTTGTTTATGTA
* * *
5945511 TCTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCTTCAAATCAACTTCTGCTTAATTACAA
66 TCTAGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGTTTAATTACAA
* *
5945576 AATTGGCCCGATAATTTTTCAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
**
5945608 TTCGTCCTTTGACT
1 TTAATCCTTTGACT
5945622 TCTGGATGCC
Statistics
Matches: 317, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 317 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGTCACTTTTTGGTTTGTTTATGTA
TCTAGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGTTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTATAAA
Found at i:5945741 original size:29 final size:26
Alignment explanation
Indices: 5945695--5945851 Score: 107
Period size: 29 Copynumber: 5.5 Consensus size: 26
5945685 GGATTGTCCA
5945695 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATT-CCATTTTACCCCC-AA-TTTCC
* *
5945724 AAAATTCCATTTTAACCCCGATTTCACC
1 AAAATTCCATTTTACCCCCAATTT--CC
*
5945752 AAAATTACCAATTTACCCCCGAACTTTCC
1 AAAATT-CCATTTTACCCCC-AA-TTTCC
* * *
5945781 AAAATTCTATTTTTAACCCCGATTTCACC
1 AAAATTCCA-TTTTACCCCCAATTT--CC
* * *
5945810 AAAATCACCATTTTTCCCCTAAATTTTCC
1 AAAAT-TCCATTTTACCCC-CAA-TTTCC
5945839 AAAATTCCATTTT
1 AAAATTCCATTTT
5945852 CGACCCCGAT
Statistics
Matches: 101, Mismatches: 16, Indels: 23
0.72 0.11 0.16
Matches are distributed among these distances:
26 3 0.03
27 4 0.04
28 30 0.30
29 54 0.53
30 4 0.04
31 6 0.06
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAATTCCATTTTACCCCCAATTTCC
Found at i:5945802 original size:58 final size:58
Alignment explanation
Indices: 5945695--5945888 Score: 282
Period size: 58 Copynumber: 3.3 Consensus size: 58
5945685 GGATTGTCCA
5945695 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
5945752 AAAATTACCAATTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * * * **
5945810 AAAATCACCATTTTTCCCCTAAATTTTCCAAAATTCCATTTTCGACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
5945868 AAAAATTACCATTTTGCCCCC
1 -AAAATTACCATTTTACCCCC
5945889 GCAAGTCCCA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
57 35 0.29
58 68 0.57
59 17 0.14
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:5945869 original size:29 final size:27
Alignment explanation
Indices: 5945722--5945887 Score: 122
Period size: 29 Copynumber: 5.7 Consensus size: 27
5945712 CCCAAACTTT
5945722 CCAAAATTCCATTTTAACCCCGATTTCA
1 CCAAAATTCCATTTT-ACCCCGATTTCA
*
5945750 CCAAAATTACCAATTTACCCCCGAACTTT--
1 CCAAAATT-CCATTTTA-CCCCG-A-TTTCA
*
5945779 CCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAATTCCA-TTTT-ACCCCGATTTCA
* * * *
5945808 CCAAAATCACCATTTTTCCCCTAAATTT-T
1 CCAAAAT-TCCATTTTACCCC--GATTTCA
5945837 CCAAAATTCCATTTTCGACCCCGATTTCA
1 CCAAAATTCCATTTT--ACCCCGATTTCA
*
5945866 CCAAAAATTACCATTTTGCCCC
1 CC-AAAATT-CCATTTTACCCC
5945888 CGCAAGTCCC
Statistics
Matches: 109, Mismatches: 13, Indels: 31
0.71 0.08 0.20
Matches are distributed among these distances:
27 3 0.03
28 27 0.25
29 51 0.47
30 18 0.17
31 10 0.09
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.33
Consensus pattern (27 bp):
CCAAAATTCCATTTTACCCCGATTTCA
Found at i:5947894 original size:11 final size:11
Alignment explanation
Indices: 5947880--5947938 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
5947870 AAATTAGGTT
5947880 TAAATTTAAAA
1 TAAATTTAAAA
5947891 TAAATTT-AAA
1 TAAATTTAAAA
* *
5947901 T-AA-GTAAATT
1 TAAATTTAAA-A
*
5947911 TAAATTTAAGA
1 TAAATTTAAAA
5947922 TAAATTTAAAA
1 TAAATTTAAAA
*
5947933 TTAATT
1 TAAATT
5947939 CAAACATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
8 1 0.03
9 4 0.11
10 5 0.14
11 24 0.65
12 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:5948340 original size:68 final size:68
Alignment explanation
Indices: 5948230--5948884 Score: 1049
Period size: 68 Copynumber: 9.6 Consensus size: 68
5948220 CCTCAGAGAA
* * *
5948230 ATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
1 ATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
*
5948295 AAAG
65 AGAG
*
5948299 ATAAAGACATGTTATCCACTCTACTTCAACTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948364 GAG
66 GAG
* * *
5948367 ATAAAGACATGTTATCCACTTTACTTCAACTTCAAGAGGATGACGTTGTTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948432 GAG
66 GAG
5948435 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948500 GAG
66 GAG
* * *
5948503 ATAAAGACATGTTATCCACTTTACTTCAACTTCAAGAGGATGGCGTTGCTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948568 GAG
66 GAG
** * *
5948571 ATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATGGCGTTGTTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948636 GAG
66 GAG
5948639 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948704 GAG
66 GAG
* * *
5948707 ATAAAGACATGTTATCCACTTTACTTCAACTTCAAGAGGATGGCGTTGCTCTTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948772 GAG
66 GAG
** * *
5948775 ATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATGGCGTTGCTCCTACTTCAATTTCA
1 ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
5948840 GAG
66 GAG
* * * * *
5948843 ATAAAGACGTGATATCCAGCTTTATTTTAATTTCAAGAGGAT
1 ATAAAGACATGTTATCCA-CTCTACTTCAATTTCAAGAGGAT
5948885 AGGAAATGAT
Statistics
Matches: 550, Mismatches: 35, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
68 515 0.94
69 35 0.06
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (68 bp):
ATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
GAG
Found at i:5960978 original size:28 final size:28
Alignment explanation
Indices: 5960945--5961162 Score: 119
Period size: 29 Copynumber: 7.5 Consensus size: 28
5960935 TTTGGTGTCA
* *
5960945 TCGAGGTTAAAATGGAATTTTAAAAGAT
1 TCGAGGGTAAAATGGAATTTTAGAAGAT
* * * * ** *
5960973 TTGAGGGGCAAAATGGTGATTTTTGGTGAAA
1 TCGA-GGGTAAAATGG-AATTTTAGAAG-AT
*
5961004 TCG-GGGTTAAAAATGGAATTTTAAAAGAT
1 TCGAGGG-T-AAAATGGAATTTTAGAAGAT
* *
5961033 TCAAGGGTAAAATGGTAATTTTCGGTGAAG-T
1 TCGAGGGTAAAATGG-AATTTT---AGAAGAT
5961064 T-G-GGGTTAAAAATGGAATTTTAGAAGAT
1 TCGAGGG-T-AAAATGGAATTTTAGAAGAT
*
5961092 TCGAGGGTAAAATGGTAATTTTGGTGAA-A-
1 TCGAGGGTAAAATGG-AATTTT--AGAAGAT
*
5961121 TCG-GGGTTAAAATGGAATTTTAAAAGAT
1 TCGAGGG-TAAAATGGAATTTTAGAAGAT
5961149 TC-AGGGTAAAATGG
1 TCGAGGGTAAAATGG
5961163 TAAATTTTGA
Statistics
Matches: 143, Mismatches: 25, Indels: 45
0.67 0.12 0.21
Matches are distributed among these distances:
26 2 0.01
27 13 0.09
28 33 0.23
29 44 0.31
30 26 0.18
31 22 0.15
32 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (28 bp):
TCGAGGGTAAAATGGAATTTTAGAAGAT
Found at i:5961025 original size:29 final size:27
Alignment explanation
Indices: 5960993--5961198 Score: 100
Period size: 29 Copynumber: 7.1 Consensus size: 27
5960983 AAATGGTGAT
5960993 TTTTGGTGAAATCGGGGTTAAAAATGGAA
1 TTTT-GTGAAATCGGGGTT-AAAATGGAA
** *
5961022 TTTT-AAAAGATTCAAGGG-TAAAATGGTAA
1 TTTTGTGAA-A-TC-GGGGTTAAAATGG-AA
* *
5961051 TTTTCGGTGAAGTTGGGGTTAAAAATGGAA
1 TTTT--GTGAAATCGGGGTT-AAAATGGAA
*
5961081 TTTT-AGAAGATTCGAGGG-TAAAATGGTAA
1 TTTTGTGAA-A-TCG-GGGTTAAAATGG-AA
5961110 TTTTGGTGAAATCGGGGTTAAAATGGAA
1 TTTT-GTGAAATCGGGGTTAAAATGGAA
** *
5961138 TTTT-AAAAGATTCAGGG-TAAAATGGTAAA
1 TTTTGTGAA-A-TCGGGGTTAAAATGG--AA
*
5961167 TTTTGATGAAATCGGGGTTAAAAATGGGA
1 TTTTG-TGAAATCGGGGTT-AAAATGGAA
5961196 TTT
1 TTT
5961199 ATGGAAGTTT
Statistics
Matches: 134, Mismatches: 19, Indels: 48
0.67 0.09 0.24
Matches are distributed among these distances:
26 2 0.01
27 14 0.10
28 29 0.22
29 51 0.38
30 17 0.13
31 19 0.14
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (27 bp):
TTTTGTGAAATCGGGGTTAAAATGGAA
Found at i:5961045 original size:59 final size:58
Alignment explanation
Indices: 5960919--5961198 Score: 377
Period size: 59 Copynumber: 4.8 Consensus size: 58
5960909 TGGATACCCG
* ** * *
5960919 AGGGCAAAATGGTAATTTTGGTGTCATCGAGGTT-AAAATGGAATTTTAAAAGATTTGA
1 AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGA-TTCA
* * *
5960977 GGGGCAAAATGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
1 AGGGTAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
* * * *
5961036 AGGGTAAAATGGTAATTTTCGGTGAAGTTGGGGTTAAAAATGGAATTTTAGAAGATTCG
1 AGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
5961095 AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAAAAGATTC-
1 AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
* *
5961151 AGGGTAAAATGGTAAATTTTGATGAAATCGGGGTTAAAAATGGGATTT
1 AGGGTAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTT
5961199 ATGGAAGTTT
Statistics
Matches: 199, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
56 13 0.07
57 41 0.21
58 41 0.21
59 85 0.43
60 19 0.10
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
Found at i:5961433 original size:31 final size:30
Alignment explanation
Indices: 5961203--5961445 Score: 310
Period size: 30 Copynumber: 8.0 Consensus size: 30
5961193 GGATTTATGG
* **
5961203 AAGTTTAGGGGT-AAAATGATAATTTT-TTA
1 AAGTTTTGGGGTCAAAAT-ATAATTTTGGAA
* *
5961232 AAGTTTTGGGGTCAAAATGTGATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
*
5961262 AAGTTTTGGGGTCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
*
5961292 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
*
5961322 AAGTTTTGGGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* * *
5961352 AAGTTTTGGGGTTAAAAATGTAATTTTAGAA
1 AAGTTTTGGGG-TCAAAATATAATTTTGGAA
5961383 AAGTTTTTGGGGTCAAAATATAATTTTGGAA
1 AAG-TTTTGGGGTCAAAATATAATTTTGGAA
*
5961414 AAGTTTTTGGGGTTAAAATATGAATTTCTGGA
1 AAG-TTTTGGGGTCAAAATAT-AATTT-TGGA
5961446 TAATTTAGGG
Statistics
Matches: 189, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
29 17 0.09
30 100 0.53
31 55 0.29
32 13 0.07
33 4 0.02
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATATAATTTTGGAA
Found at i:5963199 original size:17 final size:17
Alignment explanation
Indices: 5963179--5963212 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5963169 CCCAATTGGG
5963179 CTTTCTGTAATCGGGCC
1 CTTTCTGTAATCGGGCC
*
5963196 CTTTTTGTAATCGGGCC
1 CTTTCTGTAATCGGGCC
5963213 TTTAATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (17 bp):
CTTTCTGTAATCGGGCC
Found at i:5963265 original size:31 final size:30
Alignment explanation
Indices: 5963191--5963266 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
5963181 TTCTGTAATC
5963191 GGGCCCTTTTTGTAATCGGGCCTTTAATTT
1 GGGCCCTTTTTGTAATCGGGCCTTTAATTT
*
5963221 GAGCCCTTTTTGTAATCGGGCCTTTAATTT
1 GGGCCCTTTTTGTAATCGGGCCTTTAATTT
5963251 GGGCCCTTTTTTGTAA
1 GGGCCC-TTTTTGTAA
5963267 ATGGACATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 34 0.79
31 9 0.21
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (30 bp):
GGGCCCTTTTTGTAATCGGGCCTTTAATTT
Found at i:5963332 original size:11 final size:11
Alignment explanation
Indices: 5963318--5963388 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
5963308 AAATTAGGTT
5963318 TAAATTTAAAA
1 TAAATTTAAAA
5963329 TAAATTT-AAA
1 TAAATTTAAAA
* *
5963339 T-AA-GTAAATT
1 TAAATTTAAA-A
*
5963349 TAAATTTAAGA
1 TAAATTTAAAA
5963360 TAAATTTAAAAA
1 TAAATTT-AAAA
*
5963372 TGAATTTAAAA
1 TAAATTTAAAA
*
5963383 TTAATT
1 TAAATT
5963389 CAAACATTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 25 0.53
12 12 0.26
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:5963354 original size:31 final size:29
Alignment explanation
Indices: 5963316--5963386 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
5963306 TTAAATTAGG
5963316 TTTAAATTTAAAATAAATTTAAATAAGTAAA
1 TTTAAATTTAAAATAAATTTAAA-AA-TAAA
* *
5963347 TTTAAATTTAAGATAAATTTAAAAATGAA
1 TTTAAATTTAAAATAAATTTAAAAATAAA
*
5963376 TTTAAAATTAA
1 TTTAAATTTAA
5963387 TTCAAACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTAAATTTAAAATAAATTTAAAAATAAA
Found at i:5966143 original size:27 final size:27
Alignment explanation
Indices: 5966113--5966170 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
5966103 AAACGGGACT
5966113 TTTGGATACTT-GGGGGCAAAATGGTAA
1 TTTGGA-ACTTAGGGGGCAAAATGGTAA
5966140 TTTGGAACTTACGGGGGCAAAATGGTAA
1 TTTGGAACTTA-GGGGGCAAAATGGTAA
5966168 TTT
1 TTT
5966171 TTGGTGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 19 0.66
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (27 bp):
TTTGGAACTTAGGGGGCAAAATGGTAA
Found at i:5966220 original size:58 final size:57
Alignment explanation
Indices: 5966153--5966461 Score: 404
Period size: 58 Copynumber: 5.3 Consensus size: 57
5966143 GGAACTTACG
* *
5966153 GGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAATTTA
1 GGGG-AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
5966212 GGGGAAAATGGTGATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
1 GGGGAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * *
5966269 GGGGTAAAATGGTAATTTTGGTGAAATTGGGGTTAAAAATAGAATTTTGGAAAGTTCAA
1 GGGG-AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT-TA
* ** *
5966328 GGGTAAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAG-TTC
1 GGGGAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * *
5966384 GAGGGTAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGAAAGTTCGA
1 G-GGGAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT-TA
*
5966444 GGGTAAAATGGTAATTTT
1 GGGGAAAATGGTAATTTT
5966462 TGGACAGTCT
Statistics
Matches: 220, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
56 1 0.00
57 55 0.25
58 144 0.65
59 19 0.09
60 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (57 bp):
GGGGAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:5966345 original size:116 final size:115
Alignment explanation
Indices: 5966153--5966461 Score: 453
Period size: 116 Copynumber: 2.7 Consensus size: 115
5966143 GGAACTTACG
* * * * *
5966153 GGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAATT-TAGGGGA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAATTTTGGAAAGTTCAAGGGTA
* *
5966217 AAATGGTGATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
65 AAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTC
*
5966268 AGGGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATAGAATTTTGGAAAGTTCAAGGGT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAATTTTGGAAAGTTCAAGGGT
*
5966332 AAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTC
64 AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTC
* *
5966384 GAGGGT-AAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGAAAGTTCGAGGGT
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATG-AATTTTGGAAAGTTCAAGGGT
5966448 AAAATGGTAATTTT
64 AAAATGGTAATTTT
5966462 TGGACAGTCT
Statistics
Matches: 176, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
115 47 0.27
116 129 0.73
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (115 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAATTTTGGAAAGTTCAAGGGTAA
AATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTC
Done.