Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 91 of 193
Found at i:29685633 original size:14 final size:14
Alignment explanation
Indices: 29685614--29685640 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29685604 TTTATTTTAA
29685614 ATTTAAATTTACTC
1 ATTTAAATTTACTC
29685628 ATTTAAATTTACT
1 ATTTAAATTTACT
29685641 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATTTACTC
Found at i:29685733 original size:24 final size:26
Alignment explanation
Indices: 29685713--29685770 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
29685703 TTACAAATGT
29685713 CCAATTACAAACAAACCCAAATTGAGGC
1 CCAATTACAAACAAACCCAAATT--GGC
29685741 CCAATTACAAACAAACCC--ATTGGC
1 CCAATTACAAACAAACCCAAATTGGC
29685765 CCAATT
1 CCAATT
29685771 GGCCCAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.30
26 3 0.10
28 18 0.60
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (26 bp):
CCAATTACAAACAAACCCAAATTGGC
Found at i:29686342 original size:59 final size:59
Alignment explanation
Indices: 29686278--29686654 Score: 519
Period size: 59 Copynumber: 6.4 Consensus size: 59
29686268 CCTGGACTGT
*
29686278 CCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
** * *
29686337 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATT-CATTTTTGATCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
29686395 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACC-CTAATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTC-GATTTCA
* *
29686454 CCACCAAAATTACCATTTTACCCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
1 CCA--AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* **
29686516 CCAAAAGTTACCATTTTACCCC-AGAACTTTCCAAAATTCCATTTTCGACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTA-AACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * * *
29686575 CCAAAAATTACTATTTTACCCTTGAATTTTCCAAAATTCCATTTTTAACC-CGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
29686633 CCGAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
29686655 CACGAGTCCA
Statistics
Matches: 281, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
58 80 0.28
59 129 0.46
60 18 0.06
61 19 0.07
62 34 0.12
63 1 0.00
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:29686633 original size:179 final size:176
Alignment explanation
Indices: 29686281--29686654 Score: 588
Period size: 179 Copynumber: 2.1 Consensus size: 176
29686271 GGACTGTCCA
*
29686281 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATT
* * *
29686346 ACCATTTTACCCCCGAACTTTCCAAAATTCATTTTTGATCTCGATTTCACCAAAAATTACCATTT
66 ACCATTTTACCCCAGAACTTTCCAAAATTCATTTTCGACCTCGATTTCACCAAAAATTACCATTT
29686411 TACCCTTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCACC
131 TACCCTTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA-C-CC
* * *
29686459 AAAATTACCATTTTACCCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAAGT
1 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAAT
*
29686524 TACCATTTTACCCCAGAACTTTCCAAAATTCCATTTTCGACCTCGATTTCACCAAAAATTACTAT
65 TACCATTTTACCCCAGAACTTTCCAAAATT-CATTTTCGACCTCGATTTCACCAAAAATTACCAT
* * * *
29686589 TTTACCCTTGAATTTTCCAAAATTCCATTTTTAACCC-GATTTCACCG
129 TTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCC
*
29686636 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
29686655 CACGAGTCCA
Statistics
Matches: 181, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
177 19 0.10
178 21 0.12
179 75 0.41
180 66 0.36
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (176 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATT
ACCATTTTACCCCAGAACTTTCCAAAATTCATTTTCGACCTCGATTTCACCAAAAATTACCATTT
TACCCTTAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCC
Found at i:29686785 original size:15 final size:16
Alignment explanation
Indices: 29686758--29686803 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
29686748 ATTTATTTGC
*
29686758 ATCTGCATTTTATATT
1 ATCTGCATATTATATT
*
29686774 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
29686788 ATCTGCTTATTATATT
1 ATCTGCATATTATATT
29686804 GCTTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.57
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:29691156 original size:22 final size:22
Alignment explanation
Indices: 29691112--29691156 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29691102 ACATTCAAAC
*
29691112 AATAACAACAAAATGGAAGCAA
1 AATAACAACAAAATGGAAACAA
*
29691134 AATAACATCAAAAT-GACAACAA
1 AATAACAACAAAATGGA-AACAA
29691156 A
1 A
29691157 CAACAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.64, C:0.16, G:0.09, T:0.11
Consensus pattern (22 bp):
AATAACAACAAAATGGAAACAA
Found at i:29692430 original size:26 final size:26
Alignment explanation
Indices: 29692382--29692446 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
29692372 GACCCTTGGC
29692382 CTTTCACCTACT-AAAAACTCTTGAT
1 CTTTCACCTACTAAAAAACTCTTGAT
*
29692407 CTTTCATCTACTAAAAAACTCTTGAT
1 CTTTCACCTACTAAAAAACTCTTGAT
29692433 CTTTCACCTACTAA
1 CTTTCACCTACTAA
29692447 CTACTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
25 11 0.30
26 26 0.70
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (26 bp):
CTTTCACCTACTAAAAAACTCTTGAT
Found at i:29696784 original size:26 final size:26
Alignment explanation
Indices: 29696730--29696800 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
29696720 AGATTTGACC
* *
29696730 CTTGACCTTTCACCTACT-AAAAACT
1 CTTGATCTTTCAACTACTAAAAAACT
*
29696755 CTTGATCTTTCATCTACTAAAAAACT
1 CTTGATCTTTCAACTACTAAAAAACT
29696781 CTTGATCTTTCAACTACTAA
1 CTTGATCTTTCAACTACTAA
29696801 CTACTAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 16 0.38
26 26 0.62
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (26 bp):
CTTGATCTTTCAACTACTAAAAAACT
Found at i:29701669 original size:21 final size:21
Alignment explanation
Indices: 29701643--29701682 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29701633 TTACTACTAT
29701643 TTACTACTTTCCATAATATAA
1 TTACTACTTTCCATAATATAA
* *
29701664 TTACTATTTTTCATAATAT
1 TTACTACTTTCCATAATAT
29701683 TTTTTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACTACTTTCCATAATATAA
Found at i:29707259 original size:25 final size:23
Alignment explanation
Indices: 29707218--29707263 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
29707208 TCAATTAGGG
29707218 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
29707241 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
29707264 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:29715611 original size:51 final size:51
Alignment explanation
Indices: 29715485--29715876 Score: 504
Period size: 51 Copynumber: 7.6 Consensus size: 51
29715475 CTATAAACAA
* * * *
29715485 AAAGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCTTTTAAGGATTT
1 AAAGGTCCGATGACTAAGTGTCATCGAGAGTAAATGAATCCTTTACGGA-TT
* *
29715537 AAAGGTCCAATGACTAAGTGTCATCGAGAGTAAATAAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGAGAGTAAATGAATCCTTTACGGATT
*
29715588 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGAGAGTAAATGAATCCTTTACGGATT
29715639 AAAGGTCCGATGACTAAGTGTCATCGTA-AGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCG-AGAGTAAATGAATCCTTTACGGATT
* *
29715690 AAAGGTCCGATAACTAAGTGTCATC-ATGAGTAAATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGA-GAGTAAATGAATCCTTTACGGATT
* * * *
29715741 AAAGGTCTGATAACTAAGTGTCATCGTA-AGTAAACGAATCTTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCG-AGAGTAAATGAATCCTTTACGGATT
* * * * * **
29715792 AAAGGTCCGATGACTAAGAGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGAGAGTAAATGAA-TCCTTTACGGATT
*
29715844 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGAGAGTA
29715877 TTAAATGAAA
Statistics
Matches: 305, Mismatches: 26, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
49 1 0.00
51 220 0.72
52 55 0.18
53 28 0.09
54 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGAGAGTAAATGAATCCTTTACGGATT
Found at i:29722920 original size:51 final size:51
Alignment explanation
Indices: 29722860--29723070 Score: 208
Period size: 52 Copynumber: 4.2 Consensus size: 51
29722850 GTCCGATGAC
*
29722860 TCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATGACTAAGTG
1 TCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTG
*
29722911 TCATCGTGAGTAAATAAAATCCTTTACGGATTAAAGGTCC---G-----GTG
1 TCATCGTGAGTAAAT-GAATCCTTTACGGATTAAAGGTCCGATGACTAAGTG
*
29722955 TCATCGT-ACGTAAATGAATCCTTTACGGATTAAAGGTCCGATGATTAAGTG
1 TCATCGTGA-GTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTG
* * * * ** * *
29723006 TCATCATGAGTATATGAATTCCTATATGGAACAAGAAGTTCGATGACTACA-TG
1 TCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTCCGATGACTA-AGTG
29723059 TCATCGTGAGTA
1 TCATCGTGAGTA
29723071 TTAAATGAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
43 24 0.18
44 16 0.12
46 1 0.01
49 1 0.01
51 32 0.24
52 34 0.26
53 24 0.18
54 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (51 bp):
TCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTG
Found at i:29722986 original size:43 final size:44
Alignment explanation
Indices: 29722908--29722994 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 44
29722898 CGATGACTAA
29722908 GTGTCATCGTGAGTAAATAAAATCCTTTACGGATTAAAGGTCCG
1 GTGTCATCGTGAGTAAATAAAATCCTTTACGGATTAAAGGTCCG
*
29722952 GTGTCATCGT-ACGTAAAT-GAATCCTTTACGGATTAAAGGTCCG
1 GTGTCATCGTGA-GTAAATAAAATCCTTTACGGATTAAAGGTCCG
29722995 ATGATTAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 25 0.61
44 16 0.39
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (44 bp):
GTGTCATCGTGAGTAAATAAAATCCTTTACGGATTAAAGGTCCG
Found at i:29723576 original size:19 final size:19
Alignment explanation
Indices: 29723552--29723608 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
29723542 AAATGAACTT
29723552 GATTTGGTATAATTCTTGA
1 GATTTGGTATAATTCTTGA
*
29723571 GATTT-G-A-ACTT-TT--
1 GATTTGGTATAATTCTTGA
29723584 -ATTTGGTATAATTCTTGA
1 GATTTGGTATAATTCTTGA
29723602 GATTTGG
1 GATTTGG
29723609 CATACTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 4 0.14
13 1 0.03
14 1 0.03
15 5 0.17
16 5 0.17
17 1 0.03
18 1 0.03
19 11 0.38
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49
Consensus pattern (19 bp):
GATTTGGTATAATTCTTGA
Found at i:29723590 original size:31 final size:30
Alignment explanation
Indices: 29723545--29723607 Score: 108
Period size: 31 Copynumber: 2.1 Consensus size: 30
29723535 ATGAAATAAA
29723545 TGAACTTGATTTGGTATAATTCTTGAGATT
1 TGAACTTGATTTGGTATAATTCTTGAGATT
*
29723575 TGAACTTTTATTTGGTATAATTCTTGAGATT
1 TGAAC-TTGATTTGGTATAATTCTTGAGATT
29723606 TG
1 TG
29723608 GCATACTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.49
Consensus pattern (30 bp):
TGAACTTGATTTGGTATAATTCTTGAGATT
Found at i:29726563 original size:21 final size:22
Alignment explanation
Indices: 29726539--29726580 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
29726529 AATTACACTT
* *
29726539 GTATTGGTAGAACT-TGCACAA
1 GTATCGGTAGAAATCTGCACAA
29726560 GTATCGGTAGAAATCTGCACA
1 GTATCGGTAGAAATCTGCACA
29726581 GTTTTTGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (22 bp):
GTATCGGTAGAAATCTGCACAA
Found at i:29731066 original size:57 final size:57
Alignment explanation
Indices: 29730931--29731146 Score: 204
Period size: 57 Copynumber: 3.7 Consensus size: 57
29730921 TTCAGGGTCT
* ** **
29730931 AAAATGAAATTTTTGGAAGTTTAAGGTCAAAAATAGAATTTTTGTAAGTTT-GGGGGC
1 AAAATGTAATTTTTGGAAGTTTTGGGT-AAAAATAGAATTTTTGTAAGTTTAGGGGTA
*** * * *
29730988 AAAATGTAATTTTCAAAAGTTTTGGGTTAAAATGGAAATTTTGTAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTTTGGGTAAAAATAGAATTTTTGTAAGTTTAGGGGTA
* * * *
29731045 AAAATGTAATTTTTGGTAGTTTCGAGGCAAAAATTGAATTTTTAG-AAGTTTTA-GGGTA
1 AAAATGTAATTTTTGGAAGTTTTG-GGTAAAAATAGAATTTTT-GTAAG-TTTAGGGGTA
* *
29731103 AAAATATAATTTTTGGAAGTTTTGGGGTCAAAAATATAATTTTT
1 AAAATGTAATTTTTGGAAGTTTT-GGGT-AAAAATAGAATTTTT
29731147 TGGAAGTTCG
Statistics
Matches: 127, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
56 20 0.16
57 44 0.35
58 44 0.35
59 19 0.15
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.39
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTTTGGGTAAAAATAGAATTTTTGTAAGTTTAGGGGTA
Found at i:29731106 original size:58 final size:60
Alignment explanation
Indices: 29730938--29731214 Score: 191
Period size: 60 Copynumber: 4.7 Consensus size: 60
29730928 TCTAAAATGA
* * ** *
29730938 AATTTTTGGAAGTTT-AAGGTCAAAAATAGAATTTTT-GTAAG-TTT-GGGGGCAAAATGT
1 AATTTTTGGAAGTTTCGAGGTCAAAAATATAATTTTTAG-AAGTTTTAGGGGTAAAAATAT
*** * * ** * *
29730995 AATTTTCAAAAGTTTTG-GGT-TAAAATGGAAATTTT-GTAAG-TTTAGGGGTAAAAATGT
1 AATTTTTGGAAGTTTCGAGGTCAAAAATATAATTTTTAG-AAGTTTTAGGGGTAAAAATAT
*
29731052 AATTTTTGGTAGTTTCGAGG-CAAAAAT-TGAATTTTTAGAAGTTTTA-GGGTAAAAATAT
1 AATTTTTGGAAGTTTCGAGGTCAAAAATAT-AATTTTTAGAAGTTTTAGGGGTAAAAATAT
* * * ** ** *
29731110 AATTTTTGGAAGTTTTGGGGTCAAAAATATAATTTTTTGGAAGTTCGA-GGACAAAATTAT
1 AATTTTTGGAAGTTTCGAGGTCAAAAATATAA-TTTTTAGAAGTTTTAGGGGTAAAAATAT
* * *
29731170 AATTTTTGGAAGTTACGGGGTCAAAAATATAATTTTAGAGAAGTT
1 AATTTTTGGAAGTTTCGAGGTCAAAAATATAATTTT-TAGAAGTT
29731215 CAAGGGTCAA
Statistics
Matches: 178, Mismatches: 31, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
56 20 0.11
57 38 0.21
58 44 0.25
59 18 0.10
60 58 0.33
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (60 bp):
AATTTTTGGAAGTTTCGAGGTCAAAAATATAATTTTTAGAAGTTTTAGGGGTAAAAATAT
Found at i:29731195 original size:30 final size:29
Alignment explanation
Indices: 29730907--29731234 Score: 179
Period size: 29 Copynumber: 11.2 Consensus size: 29
29730897 GGTAAAATGG
* *
29730907 TAATTTTT-GAGAGTTTCAGGGTCTAAAATGA
1 TAATTTTTGGA-AG-TTCGGGGTCAAAAAT-A
***
29730938 -AATTTTTGGAAGTTTAAGGTCAAAAATA
1 TAATTTTTGGAAGTTCGGGGTCAAAAATA
* * * * *
29730966 GAATTTTTGTAAGTTTGGGGGC-AAAATG
1 TAATTTTTGGAAGTTCGGGGTCAAAAATA
*** ** * *
29730994 TAATTTTCAAAAGTTTTGGGT-TAAAATG
1 TAATTTTTGGAAGTTCGGGGTCAAAAATA
* * * * *
29731022 GAAATTTTGTAAGTTTAGGGGT-AAAAATG
1 TAATTTTTGGAAG-TTCGGGGTCAAAAATA
* *
29731051 TAATTTTTGGTAGTTTCGAGG-CAAAAAT-
1 TAATTTTTGGAAG-TTCGGGGTCAAAAATA
* **
29731079 TGAATTTTTAGAAGTTTTAGGGT-AAAAATA
1 T-AATTTTTGGAAG-TTCGGGGTCAAAAATA
*
29731109 TAATTTTTGGAAGTTTTGGGGTCAAAAATA
1 TAATTTTTGGAAG-TTCGGGGTCAAAAATA
* * *
29731139 TAATTTTTTGGAAGTTCGAGGACAAAATTA
1 TAA-TTTTTGGAAGTTCGGGGTCAAAAATA
29731169 TAATTTTTGGAAGTTACGGGGTCAAAAATA
1 TAATTTTTGGAAGTT-CGGGGTCAAAAATA
* *
29731199 TAATTTTAGAGAAGTTCAAGGGTC-AAAATA
1 TAATTTTTG-GAAGTTC-GGGGTCAAAAATA
*
29731229 CAATTT
1 TAATTT
29731235 CTAAATAGTT
Statistics
Matches: 239, Mismatches: 45, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
28 36 0.15
29 114 0.48
30 66 0.28
31 23 0.10
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (29 bp):
TAATTTTTGGAAGTTCGGGGTCAAAAATA
Found at i:29731234 original size:60 final size:59
Alignment explanation
Indices: 29731040--29731234 Score: 200
Period size: 60 Copynumber: 3.3 Consensus size: 59
29731030 GTAAGTTTAG
* * * * * **
29731040 GGGTAAAAATGTAATTTTTGGTAGTTTCGAGG-CAAAAAT-TGAATTTTTAGAAGTTTTA
1 GGGTCAAAATATAATTTTTGGAAGTTTCGGGGTCAAAAATAT-AATTTTGAGAAGTTCAA
* * *
29731098 GGGTAAAAATATAATTTTTGGAAGTTTTGGGGTCAAAAATATAATTTTTTG-GAAGTTCGA
1 GGGTCAAAATATAATTTTTGGAAGTTTCGGGGTCAAAAATATAA--TTTTGAGAAGTTCAA
* *
29731158 -GGACAAAATTATAATTTTTGGAAGTTACGGGGTCAAAAATATAATTTTAGAGAAGTTCAA
1 GGGTCAAAA-TATAATTTTTGGAAGTTTCGGGGTCAAAAATATAATTTT-GAGAAGTTCAA
*
29731218 GGGTCAAAATACAATTT
1 GGGTCAAAATATAATTT
29731235 CTAAATAGTT
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
58 32 0.28
59 16 0.14
60 56 0.49
61 11 0.10
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (59 bp):
GGGTCAAAATATAATTTTTGGAAGTTTCGGGGTCAAAAATATAATTTTGAGAAGTTCAA
Found at i:29732332 original size:14 final size:15
Alignment explanation
Indices: 29732313--29732343 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
29732303 TTATTATTAT
29732313 TTATTATT-AAAACA
1 TTATTATTAAAAACA
29732327 TTATTATTAAAAACA
1 TTATTATTAAAAACA
29732342 TT
1 TT
29732344 TATTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATTATTAAAAACA
Found at i:29733160 original size:6 final size:6
Alignment explanation
Indices: 29733140--29733204 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
29733130 TTAATACTAT
* *
29733140 TTTAAA TTT-AA -TTAAA TTTAAA CTTAAA -GTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29733184 TTAGATAAA TTTAAA TTTAAA
1 TT---TAAA TTTAAA TTTAAA
29733205 ATCAATTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
4 2 0.04
5 12 0.24
6 30 0.61
8 1 0.02
9 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:29733213 original size:17 final size:17
Alignment explanation
Indices: 29733140--29733215 Score: 82
Period size: 17 Copynumber: 4.4 Consensus size: 17
29733130 TTAATACTAT
*
29733140 TTTAAATTT-AATTAAA
1 TTTAAATTTAAAATAAA
* *
29733156 TTTAAACTTAAAGTAAA
1 TTTAAATTTAAAATAAA
29733173 TTTAAATTTAATTAGATAAA
1 TTTAAATTTAA--A-ATAAA
*
29733193 TTTAAATTTAAAATCAA
1 TTTAAATTTAAAATAAA
29733210 TTTAAA
1 TTTAAA
29733216 ACCAATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.16
17 26 0.51
18 1 0.02
19 1 0.02
20 15 0.29
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:29733216 original size:11 final size:11
Alignment explanation
Indices: 29733197--29733226 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29733187 GATAAATTTA
*
29733197 AATTTAAAATC
1 AATTTAAAACC
29733208 AATTTAAAACC
1 AATTTAAAACC
29733219 AATTTAAA
1 AATTTAAA
29733227 CCTCAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTTAAAACC
Found at i:29734062 original size:205 final size:199
Alignment explanation
Indices: 29733596--29734155 Score: 744
Period size: 205 Copynumber: 2.8 Consensus size: 199
29733586 ATCTGCTCAA
** * * * * * * * *
29733596 GAAGATGACCGCATCACTTGTTTCGATCCACTTTTCTGGGTTTCCACAGGAAGATGGATTTGGT-
1 GAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTC
* * *
29733660 TCACTTCTCCGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
66 T-ACTTCTCAGTGTCTCATCAGGAAGCTAACCA-TTTATTGCTTCGACCTGCTTCTCAGTGTCTC
* * * ** * *
29733725 CTCAGGAAGCTGGGGTTCGAAGATTTGCTCATATTGAGTCTGGGTTGGTATACTTCTTTGTATCT
129 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTAAACCTGGGTTGGTATACTTCTTAGTACCT
29733790 CATCAG
194 CATCAG
* * * *
29733796 GAAGATGACCGCCTTACTTGTTTTAATTAGCTTCTCTAGATCTCCTCAGGAAGACGAATTTGGTC
1 GAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTC
* *
29733861 TACTTCTTAGTGTCTCATCAGGAAGCTAACCATTTATTACTTCGACCTGCTTCTCAGTGTCTCAT
66 TACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
* * * *
29733926 CAGGAAGCTGGGGTTTGAAGATTTGCTCGCATTAAACCTGGGTTTAATTTGGTCTTCTTCTTAGT
131 CAGGAAGCTGGGGTTCGAAGATTTGCTCACATTAAACCTGGG------TTGGTATACTTCTTAGT
* *
29733991 GCCTCATTAG
190 ACCTCATCAG
29734001 GAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTC
1 GAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTC
*
29734066 CACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
66 TACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
29734131 CAGGAAGCTGGGGTTCGAAGATTTG
131 CAGGAAGCTGGGGTTCGAAGATTTG
29734156 AGTTGGTATA
Statistics
Matches: 313, Mismatches: 40, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
199 67 0.21
200 77 0.25
201 1 0.00
205 168 0.54
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (199 bp):
GAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTC
TACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
CAGGAAGCTGGGGTTCGAAGATTTGCTCACATTAAACCTGGGTTGGTATACTTCTTAGTACCTCA
TCAG
Found at i:29736149 original size:9 final size:9
Alignment explanation
Indices: 29736135--29736160 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29736125 TCCATATATT
29736135 TGGCACTTG
1 TGGCACTTG
29736144 TGGCACTTG
1 TGGCACTTG
29736153 TGGCACTT
1 TGGCACTT
29736161 CCTTGCATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.31, T:0.35
Consensus pattern (9 bp):
TGGCACTTG
Found at i:29746394 original size:30 final size:29
Alignment explanation
Indices: 29746353--29746513 Score: 157
Period size: 29 Copynumber: 5.4 Consensus size: 29
29746343 GAGGGAAAAT
29746353 AAATGGTAATTTTTGTGAGTTTCGAGGTCAA
1 AAATGG-AATTTTTG-GAGTTTCGAGGTCAA
* *
29746384 AAATGGAATTTTTAGAAGTTT-GAGGTTAA
1 AAATGGAATTTTT-GGAGTTTCGAGGTCAA
* * * *
29746413 AAATAGAAGTTTTAGAAGTTTTG-GGATCAA
1 AAATGGAA-TTTTTGGAGTTTCGAGG-TCAA
*
29746443 AAATGGAATTTTTGGAAGTTTC-AGGACAA
1 AAATGGAATTTTTGG-AGTTTCGAGGTCAA
*
29746472 AAATGTAATTTTTGGAAGTTTCGAGGTCAA
1 AAATGGAATTTTTGG-AGTTTCGAGGTCAA
*
29746502 AAATGTAATTTT
1 AAATGGAATTTT
29746514 GGAAAAGTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
29 52 0.47
30 52 0.47
31 7 0.06
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
AAATGGAATTTTTGGAGTTTCGAGGTCAA
Found at i:29746409 original size:29 final size:29
Alignment explanation
Indices: 29746353--29746553 Score: 190
Period size: 30 Copynumber: 6.7 Consensus size: 29
29746343 GAGGGAAAAT
*
29746353 AAATGGTAATTTTT-GTGAGTTTCGAGGTCAA
1 AAATGG-AATTTTTAG-AAGTTT-GAGGTCAA
*
29746384 AAATGGAATTTTTAGAAGTTTGAGGTTAA
1 AAATGGAATTTTTAGAAGTTTGAGGTCAA
* *
29746413 AAATAGAAGTTTTAGAAGTTTTG-GGATCAA
1 AAATGGAATTTTTAGAAG-TTTGAGG-TCAA
* * *
29746443 AAATGGAATTTTTGGAAGTTTCAGGACAA
1 AAATGGAATTTTTAGAAGTTTGAGGTCAA
* *
29746472 AAATGTAATTTTTGGAAGTTTCGAGGTCAA
1 AAATGGAATTTTTAGAAGTTT-GAGGTCAA
* * *
29746502 AAATGTAATTTTGGAAAAGTTTGAGGGTCAA
1 AAATGGAATTTT-TAGAAGTTTGA-GGTCAA
* *
29746533 GAATGTAATTTTTAGAAGTTT
1 AAATGGAATTTTTAGAAGTTT
29746554 AACGGAACCA
Statistics
Matches: 144, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
29 51 0.35
30 63 0.44
31 30 0.21
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AAATGGAATTTTTAGAAGTTTGAGGTCAA
Found at i:29746443 original size:59 final size:59
Alignment explanation
Indices: 29746353--29746553 Score: 219
Period size: 59 Copynumber: 3.4 Consensus size: 59
29746343 GAGGGAAAAT
* *
29746353 AAATGGTAATTTTT-GTGAGTTTCGAGGTCAAAAATGGAATTTTTAGAAGTTTGAGGTTAA
1 AAAT-GTAATTTTTAG-AAGTTTCGAGGTCAAAAATGGAATTTTTAGAAGTTTGAGGTCAA
* * * * *
29746413 AAATAG-AAGTTTTAGAAGTTTTG-GGATCAAAAATGGAATTTTTGGAAGTTTCAGGACAA
1 AAAT-GTAATTTTTAGAAGTTTCGAGG-TCAAAAATGGAATTTTTAGAAGTTTGAGGTCAA
* * * *
29746472 AAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATGTAATTTTGGAAAAGTTTGAGGGTCAA
1 AAATGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTT-TAGAAGTTTGA-GGTCAA
*
29746533 GAATGTAATTTTTAGAAGTTT
1 AAATGTAATTTTTAGAAGTTT
29746554 AACGGAACCA
Statistics
Matches: 116, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
58 3 0.03
59 74 0.64
60 15 0.13
61 24 0.21
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (59 bp):
AAATGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTTTAGAAGTTTGAGGTCAA
Found at i:29746531 original size:31 final size:31
Alignment explanation
Indices: 29746370--29746621 Score: 133
Period size: 29 Copynumber: 8.3 Consensus size: 31
29746360 AATTTTTGTG
* *
29746370 AGTTTCGA-GGTCAAAAATGGAATTTT-TAGA
1 AGTTTCGAGGGTCAAAAATGTAATTTTGGA-A
* *
29746400 AGTTT-GA-GGTTAAAAATAG-AAGTTTTAG-A
1 AGTTTCGAGGGTCAAAAAT-GTAA-TTTTGGAA
* * *
29746429 AGTTTTG-GGATCAAAAATGGAATTTTTGG-A
1 AGTTTCGAGGGTCAAAAATGTAA-TTTTGGAA
*
29746459 AGTTTC-A-GGACAAAAATGTAATTTTTGG-A
1 AGTTTCGAGGGTCAAAAATGTAA-TTTTGGAA
29746488 AGTTTCGA-GGTCAAAAATGTAATTTTGGAAA
1 AGTTTCGAGGGTCAAAAATGTAATTTTGG-AA
* *
29746519 AGTTT-GAGGGTCAAGAATGTAATTTT-TAGA
1 AGTTTCGAGGGTCAAAAATGTAATTTTGGA-A
*** *
29746549 AGTTTAACG-GAACCAAAAAATGTAATTTT-AAA
1 AGTTT--CGAGGGTC-AAAAATGTAATTTTGGAA
* *
29746581 AGTTTCG-GTGTCAAAAATATAATTTTGGAGA
1 AGTTTCGAGGGTCAAAAATGTAATTTTGGA-A
*
29746612 AGTTTAGAGG
1 AGTTTCGAGG
29746622 TTAAAATATA
Statistics
Matches: 178, Mismatches: 25, Indels: 36
0.74 0.10 0.15
Matches are distributed among these distances:
29 65 0.37
30 59 0.33
31 30 0.17
32 9 0.05
33 15 0.08
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (31 bp):
AGTTTCGAGGGTCAAAAATGTAATTTTGGAA
Found at i:29746595 original size:93 final size:94
Alignment explanation
Indices: 29746470--29746647 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 94
29746460 GTTTCAGGAC
** *
29746470 AAAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATGTAATTTTGGAAAAGTTT-GAGGGTCAAG
1 AAAAATGTAATTTTTAAAAGTTTCGAGGTCAAAAATATAATTTTGGAAAAGTTTAGA-GGTCAA-
*
29746534 AATGTAATTTTTAGA-AGTTTAACGGAACCA
64 AATATAATTTTTAGATAGTTTAACGGAACCA
* *
29746564 AAAAATGTAA-TTTTAAAAGTTTCG-GTGTCAAAAATATAATTTTGGAGAAGTTTAGAGGTTAAA
1 AAAAATGTAATTTTTAAAAGTTTCGAG-GTCAAAAATATAATTTTGGAAAAGTTTAGAGGTCAAA
29746627 ATATAATTTTTAGATAGTTTA
65 ATATAATTTTTAGATAGTTTA
29746648 GGGACTTTCA
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
92 15 0.20
93 48 0.64
94 12 0.16
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (94 bp):
AAAAATGTAATTTTTAAAAGTTTCGAGGTCAAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAA
TATAATTTTTAGATAGTTTAACGGAACCA
Found at i:29746980 original size:17 final size:16
Alignment explanation
Indices: 29746950--29746983 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29746940 AAAAAGGACT
*
29746950 AAATTGAAATAACTAA
1 AAATTGAAAGAACTAA
29746966 AAATGTGAAAGAACTAA
1 AAAT-TGAAAGAACTAA
29746983 A
1 A
29746984 TGAGAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (16 bp):
AAATTGAAAGAACTAA
Found at i:29747777 original size:14 final size:15
Alignment explanation
Indices: 29747760--29747790 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
29747750 TATTATTATT
29747760 TTATTATT-AAAACA
1 TTATTATTAAAAACA
29747774 TTATTATTAAAAACA
1 TTATTATTAAAAACA
29747789 TT
1 TT
29747791 TATTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATTATTAAAAACA
Found at i:29747778 original size:19 final size:18
Alignment explanation
Indices: 29747754--29747802 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
29747744 TTTTTTTATT
29747754 ATTATTTTATTATTAAAAC
1 ATTATTTTATTA-TAAAAC
29747773 ATTA--TTATTA-AAAAC
1 ATTATTTTATTATAAAAC
29747788 ATTTATTGTTATTAT
1 A-TTATT-TTATTAT
29747803 CATTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 6 0.24
16 3 0.12
17 6 0.24
19 10 0.40
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTATTTTATTATAAAAC
Found at i:29748630 original size:5 final size:6
Alignment explanation
Indices: 29748595--29748649 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
29748585 TTAATACTAT
* *
29748595 TTTAAA TTTAAA CTTAAA -GTAAA TTTAAA TTT-AA TTAGATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT---TAAA TTTAAA
29748644 TTTAAA
1 TTTAAA
29748650 CCAATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
5 8 0.20
6 28 0.68
8 1 0.02
9 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:29748639 original size:20 final size:17
Alignment explanation
Indices: 29748597--29748649 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 17
29748587 AATACTATTT
*
29748597 TAAATTTAAACTTAAAG
1 TAAATTTAAATTTAAAG
29748614 TAAATTTAAATTTAATTAG
1 TAAATTTAAATTTAA--AG
29748633 ATAAATTTAAATTTAAA
1 -TAAATTTAAATTTAAA
29748650 CCAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 14 0.44
18 1 0.03
19 2 0.06
20 15 0.47
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:29750398 original size:71 final size:71
Alignment explanation
Indices: 29750304--29750440 Score: 256
Period size: 71 Copynumber: 1.9 Consensus size: 71
29750294 TAATTTTTTG
*
29750304 AAATTTAATCCCCATACATTATTAAAACTAATCCAATTGTTGATAAAAACATATAAATTTAAACC
1 AAATTTAATCCCCATACAATATTAAAACTAATCCAATTGTTGATAAAAACATATAAATTTAAACC
29750369 AAAATT
66 AAAATT
*
29750375 AAATTTAATCCCCATACAATATTAAAACTAATCCAATTGTTGATAAAAACATATAAATTTAGACC
1 AAATTTAATCCCCATACAATATTAAAACTAATCCAATTGTTGATAAAAACATATAAATTTAAACC
29750440 A
66 A
29750441 TTGATTCTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (71 bp):
AAATTTAATCCCCATACAATATTAAAACTAATCCAATTGTTGATAAAAACATATAAATTTAAACC
AAAATT
Found at i:29751471 original size:12 final size:12
Alignment explanation
Indices: 29751454--29751478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29751444 AATACTACTC
29751454 AAATTCTCTTCT
1 AAATTCTCTTCT
29751466 AAATTCTCTTCT
1 AAATTCTCTTCT
29751478 A
1 A
29751479 TATTTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTCTCTTCT
Found at i:29752033 original size:23 final size:23
Alignment explanation
Indices: 29752007--29752078 Score: 135
Period size: 23 Copynumber: 3.1 Consensus size: 23
29751997 AACATATCGC
29752007 CATTATGTAATTACAAACAATTA
1 CATTATGTAATTACAAACAATTA
29752030 CATTATGTAATTACAAACAATTA
1 CATTATGTAATTACAAACAATTA
*
29752053 CATTATGTAATTATAAACAATTA
1 CATTATGTAATTACAAACAATTA
29752076 CAT
1 CAT
29752079 CCAAATTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.36
Consensus pattern (23 bp):
CATTATGTAATTACAAACAATTA
Found at i:29757111 original size:29 final size:30
Alignment explanation
Indices: 29757047--29757120 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
29757037 ACTACAAAAA
*
29757047 TAGTCACTTTTGTTTGTCACAAATTACGTTT
1 TAGTCACTTATGTTTG-CACAAATTACGTTT
29757078 TAGTCACTTATGTTTG-A-AATATTACGTTT
1 TAGTCACTTATGTTTGCACAA-ATTACGTTT
29757107 TAGTCACTTATGTT
1 TAGTCACTTATGTT
29757121 ATTGTTTTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.59
31 15 0.37
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (30 bp):
TAGTCACTTATGTTTGCACAAATTACGTTT
Found at i:29757265 original size:14 final size:14
Alignment explanation
Indices: 29757246--29757288 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
29757236 GAGAATAAGT
29757246 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
29757260 TTTAATTAATTAAAA
1 TTTAATTAAAT-AAA
29757275 TTT--TTAAATAAA
1 TTTAATTAAATAAA
29757287 TT
1 TT
29757289 ACCCCTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 10 0.38
15 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:29764326 original size:30 final size:31
Alignment explanation
Indices: 29764290--29764353 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
29764280 TTGTGAGAGC
29764290 TTTTTTTAGTTTTA-TTTTCTTCTTTCTCAT
1 TTTTTTTAGTTTTATTTTTCTTCTTTCTCAT
29764320 TTTTTTTAGTTTTATTTTTCTTCTTTCTCAT
1 TTTTTTTAGTTTTATTTTTCTTCTTTCTCAT
29764351 TTT
1 TTT
29764354 ACAATACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTTTTTAGTTTTATTTTTCTTCTTTCTCAT
Found at i:29766187 original size:18 final size:17
Alignment explanation
Indices: 29766164--29766197 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
29766154 GTTCTAAATT
29766164 ACATAATATAGAAATATA
1 ACATAATATA-AAATATA
29766182 ACATAATATAAAATAT
1 ACATAATATAAAATAT
29766198 TATAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
ACATAATATAAAATATA
Found at i:29767552 original size:22 final size:23
Alignment explanation
Indices: 29767511--29767554 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
29767501 ATTATTTGAT
*
29767511 AAATGATAATATAATCTTAAATG
1 AAATGATAATAAAATCTTAAATG
*
29767534 AAATGA-AATAAAATTTTAAAT
1 AAATGATAATAAAATCTTAAAT
29767555 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (23 bp):
AAATGATAATAAAATCTTAAATG
Found at i:29769519 original size:22 final size:23
Alignment explanation
Indices: 29769474--29769527 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
29769464 AATATCTATT
* *
29769474 ATTATTTAATAAATTATACCTAAA
1 ATTATTT-ATAAATTACACATAAA
29769498 ATTATTTAT-AATTACACATAAA
1 ATTATTTATAAATTACACATAAA
*
29769520 ATAATTTA
1 ATTATTTA
29769528 CTTTTGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 18 0.67
23 2 0.07
24 7 0.26
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTATTTATAAATTACACATAAA
Found at i:29770780 original size:21 final size:21
Alignment explanation
Indices: 29770754--29770814 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
29770744 AACCTCAAAT
*
29770754 TTGAATCTTGAACTCTAAACC
1 TTGAATCTTAAACTCTAAACC
* *
29770775 TTGAATTTTAAACTTTAAACC
1 TTGAATCTTAAACTCTAAACC
* * *
29770796 CTAAATCATAAACTCTAAA
1 TTGAATCTTAAACTCTAAA
29770815 TCTCAAACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
TTGAATCTTAAACTCTAAACC
Found at i:29772736 original size:20 final size:20
Alignment explanation
Indices: 29772701--29772741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
29772691 TTTTAAGTAA
*
29772701 TTTAATTTTTTCTTTATGTTT
1 TTTAACTTTTTCTTTAT-TTT
29772722 TTTAACTTTTT-TTTATTTT
1 TTTAACTTTTTCTTTATTTT
29772741 T
1 T
29772742 CAGTCTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTAACTTTTTCTTTATTTT
Found at i:29788771 original size:87 final size:86
Alignment explanation
Indices: 29788622--29788784 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 86
29788612 TTAAGTTCGG
* * * *
29788622 TGAATTCATCAAGTCTGTCTCAATATGACCACCCAAACTCTAGGATATGAATTCATTTAGAGTAA
1 TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAACTCTAGGATATGAACTCATTAAGAGTAA
29788687 TAAACTCAACCTCTCATGTCGA
66 -AAACTCAACCTCTCATGTCGA
*
29788709 TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAA-TCTTAGGATATGAACTCATTAAGAGTG
1 TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAACTC-TAGGATATGAACTCATTAAGAGTA
*
29788773 AGAACTCAACCT
65 AAAACTCAACCT
29788785 TATGCATGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
86 12 0.17
87 57 0.83
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (86 bp):
TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAACTCTAGGATATGAACTCATTAAGAGTAA
AAACTCAACCTCTCATGTCGA
Found at i:29796973 original size:87 final size:86
Alignment explanation
Indices: 29796825--29796992 Score: 230
Period size: 87 Copynumber: 1.9 Consensus size: 86
29796815 CAAATTTAAG
* * *
29796825 TTCGGTTAATTCATCAAGTCCGTTTCAATAGGACCACCCAAACTCTAGGATATGAATTCATTAAG
1 TTCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTAGGATATGAACTCATTAAG
29796890 AGTAATAAACTCAACCTCGCAT
66 AGTAA-AAACTCAACCTCGCAT
* ** * *
29796912 TTCGGTGAATTTATCAAGTTTGTCTCAGTAGGACCACCTAAA-TCTTAGGATATGAACTCATTAA
1 TTCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTC-TAGGATATGAACTCATTAA
*
29796976 GAGTGAAAACTCAACCT
65 GAGTAAAAACTCAACCT
29796993 TATGCATGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
86 13 0.18
87 58 0.82
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (86 bp):
TTCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTAGGATATGAACTCATTAAG
AGTAAAAACTCAACCTCGCAT
Found at i:29797446 original size:21 final size:22
Alignment explanation
Indices: 29797398--29797447 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
29797388 TATGTAAATT
*
29797398 ACCCTTTTTTATTGATATTTAAA
1 ACCC-TTTTTATTGATATTCAAA
* *
29797421 CCCCTTTTTATTTA-ATTCAAA
1 ACCCTTTTTATTGATATTCAAA
29797442 ACCCTT
1 ACCCTT
29797448 AGCCTCCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.48
22 9 0.39
23 3 0.13
ACGTcount: A:0.28, C:0.22, G:0.02, T:0.48
Consensus pattern (22 bp):
ACCCTTTTTATTGATATTCAAA
Found at i:29798146 original size:18 final size:19
Alignment explanation
Indices: 29798111--29798152 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
29798101 TGACTTGACT
* *
29798111 GTTGACCCAATGTTGACCC
1 GTTGACCCAATGTCGACCA
*
29798130 GTTGACCTAAT-TCGACCA
1 GTTGACCCAATGTCGACCA
29798148 GTTGA
1 GTTGA
29798153 TTGACCTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (19 bp):
GTTGACCCAATGTCGACCA
Found at i:29805967 original size:104 final size:105
Alignment explanation
Indices: 29805815--29806015 Score: 257
Period size: 104 Copynumber: 1.9 Consensus size: 105
29805805 GAAAATAAAA
* * *
29805815 AATAAATTAGGAGTGTGTTGGGCTGAGTAACTGGGATGGAGTGTTTGGGTTGTCATT-TCATTTC
1 AATAAATTAGGAGTCTATTGGGCTGAGTAACTGGGATGGAGTGCTTGGGTTGTCATTCT-ATTTC
*
29805879 ACGTCAAAAGAGCCAATACATTCTTAAGTAAAAAAAATGAT
65 ACGTCAAAAGAGCCAATACATTCTTAAGCAAAAAAAATGAT
* * *
29805920 AATAAATTGGGAGTCTATT-GGCTTAGTAA-TCGGGATAGG-GTGCTTGGGTTGTCATTCTGTTT
1 AATAAATTAGGAGTCTATTGGGCTGAGTAACT-GGGAT-GGAGTGCTTGGGTTGTCATTCTATTT
* * *
29805982 CGCGTCAAAAGGGCCAATATATTCTTAAGCAAAA
64 CACGTCAAAAGAGCCAATACATTCTTAAGCAAAA
29806016 GAAACAAGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
103 1 0.01
104 63 0.76
105 19 0.23
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (105 bp):
AATAAATTAGGAGTCTATTGGGCTGAGTAACTGGGATGGAGTGCTTGGGTTGTCATTCTATTTCA
CGTCAAAAGAGCCAATACATTCTTAAGCAAAAAAAATGAT
Found at i:29806605 original size:13 final size:13
Alignment explanation
Indices: 29806583--29806613 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
29806573 ATTGAAATTC
29806583 TATT-TTTAGGAT
1 TATTATTTAGGAT
29806595 TATTATTTAGGAT
1 TATTATTTAGGAT
29806608 TATTAT
1 TATTAT
29806614 GATATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (13 bp):
TATTATTTAGGAT
Found at i:29813009 original size:115 final size:115
Alignment explanation
Indices: 29812789--29813040 Score: 351
Period size: 117 Copynumber: 2.2 Consensus size: 115
29812779 CTACCCTGCA
* ** * *
29812789 ACTTCTACCGATACAAGTATTTAAGTTACCGATATCTTAATGTACAAAACTACCGATACCTGTTA
1 ACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTACAAAACTACCGATACCTGTTA
* * *
29812854 TACAACTACGGAAACAACTCAAGTTAAAAACAACCTCTCTCCTACCCTAT
66 AACAACTACCGAAACAACTCAAGTCAAAAACAACCTCTCTCCTACCCTAT
* **
29812904 ACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTATATAAACTATTGATACCTGTT
1 ACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTACA-AAACTACCGATACCTGTT
* * * *
29812969 AAACAACTACCGAAATAACTTAAGTCAGAGAACAACCTCTCTCCTACCCTGT
65 AAACAACTACCGAAACAACTCAAGTCA-AAAACAACCTCTCTCCTACCCTAT
29813021 ACTTCTACCGATACAAGCAT
1 ACTTCTACCGATACAAGCAT
29813041 GAGTTCTACT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
115 40 0.33
116 38 0.32
117 42 0.35
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.27
Consensus pattern (115 bp):
ACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTACAAAACTACCGATACCTGTTA
AACAACTACCGAAACAACTCAAGTCAAAAACAACCTCTCTCCTACCCTAT
Found at i:29813035 original size:117 final size:115
Alignment explanation
Indices: 29812777--29813040 Score: 357
Period size: 116 Copynumber: 2.3 Consensus size: 115
29812767 AGCTGAGAAG
* * ** * *
29812777 TCCTACCCTGCAACTTCTACCGATACAAGTATTTAAGTTACCGATATCTTAATGTACAAAACTAC
1 TCCTACCCTG-TACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTACAAAACTAC
* * *
29812842 CGATACCTGTTATACAACTACGGAAACAACTCAAGTTAAAAACAACCTCTC
65 CGATACCTGTTAAACAACTACCGAAACAACTCAAGTCAAAAACAACCTCTC
* * *
29812893 TCCTACCCTATACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTATATAAACTAT
1 TCCTACCCTGTACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTACA-AAACTAC
* * * *
29812958 TGATACCTGTTAAACAACTACCGAAATAACTTAAGTCAGAGAACAACCTCTC
65 CGATACCTGTTAAACAACTACCGAAACAACTCAAGTCA-AAAACAACCTCTC
29813010 TCCTACCCTGTACTTCTACCGATACAAGCAT
1 TCCTACCCTGTACTTCTACCGATACAAGCAT
29813041 GAGTTCTACT
Statistics
Matches: 129, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
115 40 0.31
116 47 0.36
117 42 0.33
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.27
Consensus pattern (115 bp):
TCCTACCCTGTACTTCTACCGATACAAGCATTTAAACTACCGATACCTCAATGTACAAAACTACC
GATACCTGTTAAACAACTACCGAAACAACTCAAGTCAAAAACAACCTCTC
Found at i:29813578 original size:37 final size:35
Alignment explanation
Indices: 29813527--29813625 Score: 126
Period size: 36 Copynumber: 2.7 Consensus size: 35
29813517 TGATCGTTAT
*
29813527 TTTTACTCCCTGTTGACCCTAAAAGTCACGATGCTCA
1 TTTTACT-CCTGTTGACCC-AAAGGTCACGATGCTCA
**
29813564 TTTTACTCCTTGTTGACCCAAAGGTCATTATGCTCA
1 TTTTACTCC-TGTTGACCCAAAGGTCACGATGCTCA
* *
29813600 TTTTTCTCCTGTTTACCCAAAGGTCA
1 TTTTACTCCTGTTGACCCAAAGGTCA
29813626 TGCCTGTTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 16 0.29
36 24 0.43
37 16 0.29
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.37
Consensus pattern (35 bp):
TTTTACTCCTGTTGACCCAAAGGTCACGATGCTCA
Found at i:29815397 original size:21 final size:21
Alignment explanation
Indices: 29815373--29815414 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29815363 TGTTTTCTTA
29815373 CTCATGATTCTTTTATTTTTG
1 CTCATGATTCTTTTATTTTTG
** *
29815394 CTCATTTTTCTTTTCTTTTTG
1 CTCATGATTCTTTTATTTTTG
29815415 ATTTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.67
Consensus pattern (21 bp):
CTCATGATTCTTTTATTTTTG
Found at i:29819218 original size:18 final size:19
Alignment explanation
Indices: 29819180--29819218 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
29819170 GAATTTTAAT
29819180 GAATTTTAGTGACTAATTTG
1 GAATTTTAGTGAC-AATTTG
29819200 GAATTTTAGTGAC-ATTTG
1 GAATTTTAGTGACAATTTG
29819218 G
1 G
29819219 GGACTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (19 bp):
GAATTTTAGTGACAATTTG
Found at i:29821963 original size:6 final size:6
Alignment explanation
Indices: 29821952--29821990 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
29821942 GTGATCAAAA
* * *
29821952 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
29821991 TATGAATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:29824646 original size:16 final size:16
Alignment explanation
Indices: 29824621--29824657 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
29824611 TCTCAAGTAT
*
29824621 GTGAAGGGCACAACAA
1 GTGAAAGGCACAACAA
29824637 GTGAAAGGCACAACAA
1 GTGAAAGGCACAACAA
29824653 GTGAA
1 GTGAA
29824658 GGGATGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.16, G:0.30, T:0.08
Consensus pattern (16 bp):
GTGAAAGGCACAACAA
Found at i:29825321 original size:62 final size:62
Alignment explanation
Indices: 29825224--29825344 Score: 233
Period size: 62 Copynumber: 2.0 Consensus size: 62
29825214 CAGTTGCTTT
*
29825224 AGGCTATCAATAATAGGCTGCTGTAATTTCTGCTGACAGTTTCTTTTACTTATGTTTTATTC
1 AGGCTATCAATAATAGGCTGCTGTAATTTCTGCTGAAAGTTTCTTTTACTTATGTTTTATTC
29825286 AGGCTATCAATAATAGGCTGCTGTAATTTCTGCTGAAAGTTTCTTTTACTTATGTTTTA
1 AGGCTATCAATAATAGGCTGCTGTAATTTCTGCTGAAAGTTTCTTTTACTTATGTTTTA
29825345 CGTTTTTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.45
Consensus pattern (62 bp):
AGGCTATCAATAATAGGCTGCTGTAATTTCTGCTGAAAGTTTCTTTTACTTATGTTTTATTC
Found at i:29844893 original size:9 final size:9
Alignment explanation
Indices: 29844879--29844926 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
29844869 TTAATAATTA
29844879 TTTAAAAAT
1 TTTAAAAAT
29844888 TTTAAAAAT
1 TTTAAAAAT
*
29844897 TTGAAAAAT
1 TTTAAAAAT
*
29844906 TGTCAATAAAT
1 T-TTAA-AAAT
29844917 TTATAAAAAT
1 TT-TAAAAAT
29844927 AATTTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 18 0.55
10 8 0.24
11 7 0.21
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:29844924 original size:20 final size:19
Alignment explanation
Indices: 29844863--29844924 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
29844853 TTAAAAATAT
29844863 AAAA-TGTTAATAATTATTTA
1 AAAATTGTTAATAA--ATTTA
29844883 AAAATT-TTAA-AAATTTGA
1 AAAATTGTTAATAAATTT-A
*
29844901 AAAATTGTCAATAAATTTA
1 AAAATTGTTAATAAATTTA
29844920 TAAAA
1 -AAAA
29844925 ATAATTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.11
18 7 0.19
19 6 0.17
20 18 0.50
21 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATTGTTAATAAATTTA
Found at i:29846323 original size:15 final size:15
Alignment explanation
Indices: 29846303--29846331 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29846293 CCTGTAAATT
29846303 CAAATCCAACCAATG
1 CAAATCCAACCAATG
29846318 CAAATCCAACCAAT
1 CAAATCCAACCAAT
29846332 AACTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:29846567 original size:21 final size:21
Alignment explanation
Indices: 29846532--29846584 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
29846522 CTTGTAGCCT
* *
29846532 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
*
29846553 CTGTTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
29846574 CTGCTGCCTCC
1 CTGCTGCCTCC
29846585 ACTTTAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.45, G:0.21, T:0.34
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCG
Found at i:29846685 original size:66 final size:66
Alignment explanation
Indices: 29846574--29846727 Score: 227
Period size: 66 Copynumber: 2.3 Consensus size: 66
29846564 GCTTGCCTCG
* * * * *
29846574 CTGCTGCCTCCACTTTAAGTTGTAGGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGATCATCATATTTTTTTTGAGACTCTGCTTCTCTC
29846639 A
66 A
* * *
29846640 CTGCAGCCTCCTCTTTCAGTTTTAGATGGAGATCATCATATTTTTTTTGAGCCTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGATCATCATATTTTTTTTGAGACTCTGCTTCTCTC
*
29846705 G
66 A
29846706 CTGCAGCCTCCTCTTTAAGTTG
1 CTGCAGCCTCCTCTTTAAGTTG
29846728 AGCAATTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (66 bp):
CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGATCATCATATTTTTTTTGAGACTCTGCTTCTCTC
A
Found at i:29851797 original size:26 final size:26
Alignment explanation
Indices: 29851760--29851840 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
29851750 TAACTGAAGG
29851760 TAAATCTTTTAACTTAAATATTTAAT
1 TAAATCTTTTAACTTAAATATTTAAT
** * **
29851786 TATTTAC-TTTAA-TATAATTAAATAAT
1 TAAAT-CTTTTAACT-TAAATATTTAAT
29851812 TAAATCTTTTAACTTAAATATTTAAT
1 TAAATCTTTTAACTTAAATATTTAAT
29851838 TAA
1 TAA
29851841 TCGATACTGT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
25 2 0.05
26 37 0.90
27 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAATCTTTTAACTTAAATATTTAAT
Found at i:29854446 original size:21 final size:21
Alignment explanation
Indices: 29854422--29854487 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
29854412 TTCTGGGGGT
29854422 GAAGAGGGAACGGAGTGAGGG
1 GAAGAGGGAACGGAGTGAGGG
**
29854443 GAAGA--GAAGCGGTTTTG-GGG
1 GAAGAGGGAA-CGG-AGTGAGGG
*
29854463 TGAAGAGGGAACGGGGTGAGGG
1 -GAAGAGGGAACGGAGTGAGGG
29854485 GAA
1 GAA
29854488 CAGAAGCGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 6 0.17
21 17 0.49
22 6 0.17
23 3 0.09
ACGTcount: A:0.30, C:0.05, G:0.55, T:0.11
Consensus pattern (21 bp):
GAAGAGGGAACGGAGTGAGGG
Found at i:29854527 original size:44 final size:42
Alignment explanation
Indices: 29854403--29854534 Score: 165
Period size: 42 Copynumber: 3.0 Consensus size: 42
29854393 GATCGGCTCA
*
29854403 AGAAGCGGGTTCTGGGGGTGAAGAGGGAACGGAGTGAGGGGAAG
1 AGAAGC-GGTTCT-GGGGTGAAGAGGGAACGGAGTGAGGGGAAC
* *
29854447 AGAAGCGGTTTTGGGGTGAAGAGGGAACGGGGTGAGGGGAAC
1 AGAAGCGGTTCTGGGGTGAAGAGGGAACGGAGTGAGGGGAAC
* * * *
29854489 AGAAGCGAGTTCTGCAGGTGAAGAGGCAACGGAATGAGGGAAAC
1 AGAAGCG-GTTCTG-GGGTGAAGAGGGAACGGAGTGAGGGGAAC
29854533 AG
1 AG
29854535 CAGAGGGTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 35 0.45
43 10 0.13
44 32 0.42
ACGTcount: A:0.30, C:0.09, G:0.48, T:0.12
Consensus pattern (42 bp):
AGAAGCGGTTCTGGGGTGAAGAGGGAACGGAGTGAGGGGAAC
Found at i:29854545 original size:44 final size:43
Alignment explanation
Indices: 29854409--29854549 Score: 153
Period size: 42 Copynumber: 3.3 Consensus size: 43
29854399 CTCAAGAAGC
* *
29854409 GGGTTCTGGGGGTGAAGAGGGAACGGAGTGAGGGGAAGAGA-A
1 GGGTTCTGCGGGTGAAGAGGGAACGGAGTGAGGGGAACAGAGA
* *
29854451 GCGGTTTTG-GGGTGAAGAGGGAACGGGGTGAGGGGAACAGA-A
1 G-GGTTCTGCGGGTGAAGAGGGAACGGAGTGAGGGGAACAGAGA
* * * *
29854493 GCGAGTTCTGCAGGTGAAGAGGCAACGGAATGAGGGAAACAGCAGA
1 G-G-GTTCTGCGGGTGAAGAGGGAACGGAGTGAGGGGAACAG-AGA
29854539 GGGTTCTGCGG
1 GGGTTCTGCGG
29854550 TCTGGAGGTG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
42 35 0.42
43 11 0.13
44 34 0.40
45 2 0.02
46 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.49, T:0.13
Consensus pattern (43 bp):
GGGTTCTGCGGGTGAAGAGGGAACGGAGTGAGGGGAACAGAGA
Found at i:29854825 original size:41 final size:41
Alignment explanation
Indices: 29854689--29855133 Score: 427
Period size: 41 Copynumber: 10.9 Consensus size: 41
29854679 GCTTATAGAA
* * * **
29854689 AAGCGCCGCTAATG-CAC-ACCTTTAGCGGCGCTTATTAGAA
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTT-GTGGCT
* * * ***
29854729 AAGCGCCGCTAATAACCTGACCTTTA-CTGGCGCTTTATATAT
1 AAGCGCCGCTAATGACCCGACCTTTAGC-GGCGC-TTGTGGCT
* * * *
29854771 AAGCGCCGCTAATGACACGACCTTCAGCGGCGTTTGTGGGT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
* *
29854812 AAGCGCCGCTAATGACTCC-ACTTTTAGCGGCGCTTGCGG-T
1 AAGCGCCGCTAATGAC-CCGACCTTTAGCGGCGCTTGTGGCT
* * * * * *
29854852 GAAGCACCACTAATGACTCGACCATTAGCGGTGCTTGTAGCT
1 -AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
* * *
29854894 AAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
* * *
29854935 AAGCGCCGCTAATAACCCGACTTTTAGCGGCGCTT-TTG-T
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
* * *
29854974 AAAGCGCCGCTAATGACTCGACCTTTAGCGGCGCATGTGTCT
1 -AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
* * *
29855016 AAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
** *
29855057 AAGCGCCGCTAATGAGTCGACCTTTAGCGGCGCTTGTGGGT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
*
29855098 AAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTT
1 -AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTT
29855134 ACACAAAGCG
Statistics
Matches: 332, Mismatches: 60, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.00
40 47 0.14
41 205 0.62
42 76 0.23
43 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (41 bp):
AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT
Found at i:29854897 original size:82 final size:82
Alignment explanation
Indices: 29854689--29855192 Score: 404
Period size: 82 Copynumber: 6.2 Consensus size: 82
29854679 GCTTATAGAA
* * ** * *
29854689 AAGCGCCGCTAATG-CAC-ACCTTTAGCGGCGCTTATTAGAAAAGCGCCGCTAATAAC-CTGACC
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTT-GTAGCTAAGCGCCGCTAATGACTC-CACC
*** *
29854751 TTTA-CTGGCGCTTTATATAT
64 TTTAGC-GGCGC-TTGGGTCT
* * * * * *
29854771 AAGCGCCGCTAATGACACGACCTTCAGCGGCGTTTGTGGGTAAGCGCCGCTAATGACTCCACTTT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTAGCTAAGCGCCGCTAATGACTCCACCTT
*
29854836 TAGCGGCGCTTGCGGT-G
66 TAGCGGCGCTTG-GGTCT
* * * * * *
29854853 AAGCACCACTAATGACTCGACCATTAGCGGTGCTTGTAGCTAAGCGCCGCTAATGAC-CCGACTT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTAGCTAAGCGCCGCTAATGACTCC-ACCT
* *
29854917 TTAGTGGCGCTTGTGTCT
65 TTAGCGGCGCTTGGGTCT
* * * *
29854935 AAGCGCCGCTAATAACCCGACTTTTAGCGGCGCTT-TTG-TAAAGCGCCGCTAATGACTCGACCT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTAGCT-AAGCGCCGCTAATGACTCCACCT
* *
29854998 TTAGCGGCGCATGTGTCT
65 TTAGCGGCGCTTGGGTCT
* * * *
29855016 AAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGT-GTCTAAGCGCCGCTAATGAGTCGACCT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTAG-CTAAGCGCCGCTAATGACTCCACCT
*
29855080 TTAGCGGCGCTTGTGGGT-A
65 TTAGCGGCGC-T-TGGGTCT
* ** * **
29855099 AAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTACA-CAAAGCGCCGCTAATGA-TTTACCTT
1 AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTAGCTAAGCGCCGCTAATGACTCCACCTT
* * **
29855162 TTGCGGCGCATTAGG-AA
66 TAGCGGCGC-TTGGGTCT
29855179 AAGCGCCGCTAATG
1 AAGCGCCGCTAATG
29855193 CTTCACCTTT
Statistics
Matches: 351, Mismatches: 55, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
80 18 0.05
81 90 0.26
82 158 0.45
83 65 0.19
84 20 0.06
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (82 bp):
AAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTAGCTAAGCGCCGCTAATGACTCCACCTT
TAGCGGCGCTTGGGTCT
Found at i:29855032 original size:122 final size:123
Alignment explanation
Indices: 29854689--29855133 Score: 508
Period size: 122 Copynumber: 3.6 Consensus size: 123
29854679 GCTTATAGAA
* * * * * *
29854689 AAGCGCCGCTAATG-CAC-ACCTTTAGCGGCGCTTATTAGAAAAGCGCCGCTAATAAC-CTGACC
1 AAGCGCCGCTAATGACCCGACTTTTAGCGGCGCTT-GTGGTAAAGCGCCGCTAATGACTC-GACC
* * * * * * * * **
29854751 TTTA-CTGGCGCTTTATATATAAGCGCCGCTAATGACACGACCTTCAGCGGCGTTTGTGGGT
64 TTTAGC-GGCGC-TTGTGTCTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
* * * * *
29854812 AAGCGCCGCTAATGACTCC-ACTTTTAGCGGCGCTTGCGGTGAAGCACCACTAATGACTCGACCA
1 AAGCGCCGCTAATGAC-CCGACTTTTAGCGGCGCTTGTGGTAAAGCGCCGCTAATGACTCGACCT
*
29854876 TTAGCGGTGCTTGTAG-CTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
65 TTAGCGGCGCTTGT-GTCTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
* *
29854935 AAGCGCCGCTAATAACCCGACTTTTAGCGGCGCTT-TTGTAAAGCGCCGCTAATGACTCGACCTT
1 AAGCGCCGCTAATGACCCGACTTTTAGCGGCGCTTGTGGTAAAGCGCCGCTAATGACTCGACCTT
*
29854999 TAGCGGCGCATGTGTCTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
66 TAGCGGCGCTTGTGTCTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
** * * *
29855057 AAGCGCCGCTAATGAGTCGACCTTTAGCGGCGCTTGTGGGTAAAGCGCCGCTAAAGACCCGACCT
1 AAGCGCCGCTAATGACCCGACTTTTAGCGGCGCTTGT-GGTAAAGCGCCGCTAATGACTCGACCT
29855122 TTAGCGGCGCTT
65 TTAGCGGCGCTT
29855134 ACACAAAGCG
Statistics
Matches: 274, Mismatches: 39, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
121 1 0.00
122 110 0.40
123 84 0.31
124 61 0.22
125 18 0.07
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (123 bp):
AAGCGCCGCTAATGACCCGACTTTTAGCGGCGCTTGTGGTAAAGCGCCGCTAATGACTCGACCTT
TAGCGGCGCTTGTGTCTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCT
Found at i:29855145 original size:204 final size:206
Alignment explanation
Indices: 29854670--29855151 Score: 559
Period size: 204 Copynumber: 2.4 Consensus size: 206
29854660 ATTTAAATAA
* * * * * *
29854670 ATTAGTGGCGCTTATAG-AAAAGCGCCGCTAATG-CAC-ACCTTTAGCGGCGCTTATTAGAAAAG
1 ATTAGCGGCGCTTGTAGCTAAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTA-CA-CAAAG
*
29854732 CGCCGCTAATAACCTGACCTTTACTGGCGCTTTATATATAAGCGCCGCTAATGACACGACCTTCA
64 CGCCGCTAATAACCCGACCTTTACTGGCGCTTTATATATAAGCGCCGCTAATGACACGACCTTCA
** *
29854797 GCGGCGTTTGTGGGTAAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTGCGGTGAAGCACCAC
129 GCGGCGCATGTGGCTAAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTGCGGTGAAGCACCAC
29854862 TAATGACTCGACC
194 TAATGACTCGACC
* * * *** *
29854875 ATTAGCGGTGCTTGTAGCT-AAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCTAAGC
1 ATTAGCGGCGCTTGTAGCTAAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTT-ACACAAAGC
* * * *
29854939 GCCGCTAATAACCCGACTTTTAGC-GGCGCTTT-TGTA-AAGCGCCGCTAATGACTCGACCTTTA
65 GCCGCTAATAACCCGACCTTTA-CTGGCGCTTTATATATAAGCGCCGCTAATGACACGACCTTCA
* * * * *
29855001 GCGGCGCATGTGTCTAAGCGCCGCTAATGAC-CCGACTTTTAGTGGCGCTTG-TGTCTAAGCGCC
129 GCGGCGCATGTGGCTAAGCGCCGCTAATGACTCC-ACTTTTAGCGGCGCTTGCGGT-GAAGCACC
* *
29855064 GCTAATGAGTCGACC
192 ACTAATGACTCGACC
* * * *
29855079 TTTAGCGGCGCTTGTGGGTAAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTACACAAAGCG
1 ATTAGCGGCGCTTGTAGCTAAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTACACAAAGCG
29855144 CCGCTAAT
66 CCGCTAAT
29855152 GATTTACCTT
Statistics
Matches: 231, Mismatches: 38, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
203 4 0.02
204 115 0.50
205 63 0.27
206 34 0.15
207 15 0.06
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (206 bp):
ATTAGCGGCGCTTGTAGCTAAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTACACAAAGCG
CCGCTAATAACCCGACCTTTACTGGCGCTTTATATATAAGCGCCGCTAATGACACGACCTTCAGC
GGCGCATGTGGCTAAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTGCGGTGAAGCACCACTA
ATGACTCGACC
Found at i:29855172 original size:163 final size:163
Alignment explanation
Indices: 29854812--29855231 Score: 433
Period size: 163 Copynumber: 2.6 Consensus size: 163
29854802 GTTTGTGGGT
* * * ** * * **
29854812 AAGCGCCGCTAATGACTCCACTTTTAGCGGCGC-TTGCGGTGAAGCACCACTAATGACTCGACCA
1 AAGCGCCGCTAATGACTCGACCTTTAGCGGCGCATT-AGGAAAAGCGCCGCTAATGACTCGACTT
* * * * *
29854876 TTAGCGGTGCTTGTAG-CTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCTAAGCG
65 TTAGTGGCGCTTGT-GTCTAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCTAAGCG
* ****
29854940 CCGCTAATAACCCGACTTTTAGCGGCGCTTTTGTA
129 CCGCTAATAACCCGACCTTTAGCGGCGCTTACACA
*** *
29854975 AAGCGCCGCTAATGACTCGACCTTTAGCGGCGCATGT-GTCTAAGCGCCGCTAATGACCCGACTT
1 AAGCGCCGCTAATGACTCGACCTTTAGCGGCGCAT-TAGGAAAAGCGCCGCTAATGACTCGACTT
** *
29855039 TTAGTGGCGCTTGTGTCTAAGCGCCGCTAATGAGTCGACCTTTAGCGGCGCTTGTGGGTAAAGCG
65 TTAGTGGCGCTTGTGTCTAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCT-AAGCG
29855104 CCGCTAA-AGACCCGACCTTTAGCGGCGCTTACACA
129 CCGCTAATA-ACCCGACCTTTAGCGGCGCTTACACA
** *
29855139 AAGCGCCGCTAATGA-TTTACCTTTTGCGGCGCATTAGGAAAAGCGCCGCTAATG-CTTC-ACCT
1 AAGCGCCGCTAATGACTCGACCTTTAGCGGCGCATTAGGAAAAGCGCCGCTAATGAC-TCGA-CT
* *
29855201 TTT-GTGGCGCTTTGTGTCCAAACGCCGCTAA
64 TTTAGTGGCGC-TTGTGTCTAAGCGCCGCTAA
29855232 AAGTGCCGCT
Statistics
Matches: 216, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
162 11 0.05
163 155 0.72
164 49 0.23
165 1 0.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (163 bp):
AAGCGCCGCTAATGACTCGACCTTTAGCGGCGCATTAGGAAAAGCGCCGCTAATGACTCGACTTT
TAGTGGCGCTTGTGTCTAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTGTGGCTAAGCGCC
GCTAATAACCCGACCTTTAGCGGCGCTTACACA
Found at i:29855184 original size:204 final size:204
Alignment explanation
Indices: 29854670--29855231 Score: 518
Period size: 204 Copynumber: 2.8 Consensus size: 204
29854660 ATTTAAATAA
* * ** * * * *
29854670 ATTAGTGGCGCTTATAGAAAAGCGCCGCTAATG-CAC-ACCTTTAGCGGCGCTT-ATTAGAAAAG
1 ATTAGCGGCGCTTGTAGCTAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTGA-CA-CAAAG
* * * *
29854732 CGCCGCTAATAACCTGACCTTTA-CTGGCGCTTTA-TATATAAGCGCCGCTAATGACACGACCTT
64 CGCCGCTAATAACCCGACTTTTAGC-GGCGC-TTAGGA-A-AAGCGCCGCTAATGACTCGACCTT
* * **
29854795 CAGCGGCGTTTGTGGGTAAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTGCGGTGAAGCACC
125 TAGCGGCGCTTGTGTCTAAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTGCGGTGAAGCACC
29854860 ACTAATGACTCGACC
190 ACTAATGACTCGACC
* * * * *** *
29854875 ATTAGCGGTGCTTGTAGCTAAGCGCCGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCTAAGCG
1 ATTAGCGGCGCTTGTAGCTAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTGACACAAAGCG
** *
29854940 CCGCTAATAACCCGACTTTTAGCGGCGCTTTTGTAAAGCGCCGCTAATGACTCGACCTTTAGCGG
66 CCGCTAATAACCCGACTTTTAGCGGCGCTTAGGAAAAGCGCCGCTAATGACTCGACCTTTAGCGG
* * * * * *
29855005 CGCATGTGTCTAAGCGCCGCTAATGAC-CCGACTTTTAGTGGCGCTTG-TGTCTAAGCGCCGCTA
131 CGCTTGTGTCTAAGCGCCGCTAATGACTCC-ACTTTTAGCGGCGCTTGCGGT-GAAGCACCACTA
*
29855068 ATGAGTCGACC
194 ATGACTCGACC
* * *
29855079 TTTAGCGGCGCTTGTGGGTAAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTT-ACACAAAGC
1 ATTAGCGGCGCTTGTAGCT-AAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTGACACAAAGC
* *** *
29855143 GCCGCTAATGA-TTTACCTTTT-GCGGCGCATTAGGAAAAGCGCCGCTAATG-CTTC-ACCTTTT
65 GCCGCTAATAACCCGA-CTTTTAGCGGCGC-TTAGGAAAAGCGCCGCTAATGAC-TCGACCTTTA
* * *
29855204 GTGGCGCTTTGTGTCCAAACGCCGCTAA
127 GCGGCGC-TTGTGTCTAAGCGCCGCTAA
29855232 AAGTGCCGCT
Statistics
Matches: 292, Mismatches: 53, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
203 25 0.09
204 158 0.54
205 63 0.22
206 31 0.11
207 15 0.05
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (204 bp):
ATTAGCGGCGCTTGTAGCTAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTGACACAAAGCG
CCGCTAATAACCCGACTTTTAGCGGCGCTTAGGAAAAGCGCCGCTAATGACTCGACCTTTAGCGG
CGCTTGTGTCTAAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTGCGGTGAAGCACCACTAAT
GACTCGACC
Found at i:29861084 original size:17 final size:16
Alignment explanation
Indices: 29861048--29861104 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
29861038 AAATAATCAA
*
29861048 AATAATAGTAACA-AAT
1 AATAATAG-AACATGAT
29861064 AATAATACG-ACTATGAT
1 AATAATA-GAAC-ATGAT
29861081 AATAATAGTAACATGAT
1 AATAATAG-AACATGAT
29861098 AATAATA
1 AATAATA
29861105 ATAACACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
17 22 0.63
18 2 0.06
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.28
Consensus pattern (16 bp):
AATAATAGAACATGAT
Found at i:29861138 original size:17 final size:17
Alignment explanation
Indices: 29861061--29861136 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
29861051 AATAGTAACA
29861061 AATAATAATACGACTATGAT
1 AATAATAATA--AC-ATGAT
*
29861081 AATAATAGTAACATGAT
1 AATAATAATAACATGAT
*
29861098 AATAATAATAACA-CAT
1 AATAATAATAACATGAT
*
29861114 AATAATTACTAACATGAT
1 AATAA-TAATAACATGAT
29861132 -ATAAT
1 AATAAT
29861137 TAACACAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.16
17 28 0.57
18 4 0.08
20 9 0.18
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (17 bp):
AATAATAATAACATGAT
Found at i:29870205 original size:18 final size:19
Alignment explanation
Indices: 29870164--29870207 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
29870154 GGGGTAAAAA
* *
29870164 TCATTTTTCGCTTCAATTC
1 TCATTTTTCACATCAATTC
29870183 T-ATTTTTCACATC-ATTC
1 TCATTTTTCACATCAATTC
29870200 TCATTTTT
1 TCATTTTT
29870208 GTCCCATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (19 bp):
TCATTTTTCACATCAATTC
Found at i:29871225 original size:3 final size:3
Alignment explanation
Indices: 29871217--29871255 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
29871207 TCATTTATAT
29871217 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29871256 TTATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29871261 original size:18 final size:18
Alignment explanation
Indices: 29871222--29871284 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
29871212 TATATTAATA
*
29871222 ATAATAATAATAATAATAAT
1 ATAATAATAA-AAT-ATTAT
29871242 ATAATAATAAAATATTAT
1 ATAATAATAAAATATTAT
** * * *
29871260 ATTTTAATTAATTATTAA
1 ATAATAATAAAATATTAT
29871278 ATAATAA
1 ATAATAA
29871285 CTTTAATATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 22 0.63
19 3 0.09
20 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATAATAAAATATTAT
Found at i:29871387 original size:13 final size:13
Alignment explanation
Indices: 29871370--29871402 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
29871360 GTCTTTCCAT
29871370 TAAAATAAAAATAA
1 TAAAATAAAAA-AA
29871384 -AAAATAAAAAAA
1 TAAAATAAAAAAA
29871396 TAAAATA
1 TAAAATA
29871403 TTTGCACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 16 0.89
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:29872888 original size:23 final size:23
Alignment explanation
Indices: 29872845--29872888 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29872835 ACTACCATTT
*
29872845 TCTAAATAAAATAATAGTAAATA
1 TCTAAATAAAATAATAATAAATA
* *
29872868 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
29872889 ATAATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:29873696 original size:102 final size:102
Alignment explanation
Indices: 29873400--29873996 Score: 715
Period size: 102 Copynumber: 5.9 Consensus size: 102
29873390 ATGTTACAGT
* *
29873400 TTCACTCCATTCCACTGCAACTTCAAGGAGACTGAGATCTGCTACTGTTAGTTTTAATTCGATCC
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTACTACTGTTAGTTTTAATTCGATCC
* *
29873465 ACTGCAACTTCAAGGATATAGGATTTGGTGATGTAAC
66 ACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAAC
* * * * * * *
29873502 TTCACTCCATTTCACTTCAACTTCAGGGAGATTGAGATCCATTACTG-TAGTTTTAATCCGATCT
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTACTACTGTTAGTTTTAATTCGATCC
* *
29873566 ACTACAACTTCAGGGATAT-AGAATTTGGTGTTGTAAC
66 ACTGCAACTTCAAGGATATAAG-ATTTGGTGTTGTAAC
* *
29873603 TTCACTCCATTCCACTGCAACTTCAAGGAGATTAAGATCTACTATTGTTAGTTTTAATTCGATCC
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTACTACTGTTAGTTTTAATTCGATCC
29873668 ACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAAC
66 ACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAAC
* * * ** * *
29873705 TTCACTCAATTCTACTGTAACTTC-AGAGAGATTGAGATCTGTTATTGTTAGTTTTAA-TCTAAT
1 TTCACTCCATTCCACTGCAACTTCAAG-GAGATTGAGATCTACTACTGTTAGTTTTAATTC-GAT
* * * *
29873768 CCACTGGAACTTCAGGGATATAGGATTTGGTGTTCTAAC
64 CCACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAAC
** * *
29873807 TTCACTCCATTTGACTGCAACTTCAACGAGATTGAGATC-AGCTACTGTTAGTTTTAATTTGATC
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTA-CTACTGTTAGTTTTAATTCGATC
29873871 CACTGCAACTTC-AGAGATATAAGATTTGGTGTTGTAAC
65 CACTGCAACTTCAAG-GATATAAGATTTGGTGTTGTAAC
* * * ** * * * *
29873909 TTCACTCCATTCCACTGTAACTT-TAGGCAGATTAAGATCCGCTATTGTTAATTTTACTGC-ATT
1 TTCACTCCATTCCACTGCAACTTCAAGG-AGATTGAGATCTACTACTGTTAGTTTTAATTCGA-T
*
29873972 CCACTGCAACTTCAGGGATATAAGA
64 CCACTGCAACTTCAAGGATATAAGA
29873997 GTTGTCGTTT
Statistics
Matches: 420, Mismatches: 62, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
100 1 0.00
101 94 0.22
102 320 0.76
103 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (102 bp):
TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTACTACTGTTAGTTTTAATTCGATCC
ACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAAC
Found at i:29873873 original size:204 final size:202
Alignment explanation
Indices: 29873400--29873993 Score: 820
Period size: 204 Copynumber: 2.9 Consensus size: 202
29873390 ATGTTACAGT
* *
29873400 TTCACTCCATTCCACTGCAACTTCAAGGAGACTGAGATCTGCTACTGTTAGTTTTAATTCGATCC
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCAGCTACTGTTAGTTTTAATTCGATCC
* *
29873465 ACTGCAACTTCAAGGATATAGGATTTGGTGATGTAACTTCACTCCATT-TCACT-TCAACTTCAG
66 ACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAACTTCACTCCATTCT-ACTGT-AACTTCA-
* * * * *
29873528 GGAGATTGAGATCCATTACTG-TAGTTTTAATCCGATCTACTACAACTTCAGGGATATAGAATTT
128 GGAGATTGAGATCCGTTATTGTTAGTTTTAAT-CAATCCACTGCAACTTCAGGGATATAGAATTT
*
29873592 GGTGTTGTAAC
192 GGTGTTCTAAC
* *
29873603 TTCACTCCATTCCACTGCAACTTCAAGGAGATTAAGATCTA-CTATTGTTAGTTTTAATTCGATC
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATC-AGCTACTGTTAGTTTTAATTCGATC
*
29873667 CACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAACTTCACTCAATTCTACTGTAACTTCAGA
65 CACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAACTTCACTCCATTCTACTGTAACTTCAG-
* * *
29873732 GAGATTGAGATCTGTTATTGTTAGTTTTAATCTAATCCACTGGAACTTCAGGGATATAGGATTTG
129 GAGATTGAGATCCGTTATTGTTAGTTTTAATC-AATCCACTGCAACTTCAGGGATATAGAATTTG
29873797 GTGTTCTAAC
193 GTGTTCTAAC
** * *
29873807 TTCACTCCATTTGACTGCAACTTCAACGAGATTGAGATCAGCTACTGTTAGTTTTAATTTGATCC
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCAGCTACTGTTAGTTTTAATTCGATCC
* *
29873872 ACTGCAACTTC-AGAGATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTGTAACTTTAGG
66 ACTGCAACTTCAAG-GATATAAGATTTGGTGTTGTAACTTCACTCCATTCTACTGTAACTTCAGG
* * * * *
29873936 CAGATTAAGATCCGCTATTGTTAATTTTACTGCATTCCACTGCAACTTCAGGGATATA
130 -AGATTGAGATCCGTTATTGTTAGTTTTAAT-CAATCCACTGCAACTTCAGGGATATA
29873994 AGAGTTGTCG
Statistics
Matches: 349, Mismatches: 32, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
202 1 0.00
203 137 0.39
204 210 0.60
205 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (202 bp):
TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCAGCTACTGTTAGTTTTAATTCGATCC
ACTGCAACTTCAAGGATATAAGATTTGGTGTTGTAACTTCACTCCATTCTACTGTAACTTCAGGA
GATTGAGATCCGTTATTGTTAGTTTTAATCAATCCACTGCAACTTCAGGGATATAGAATTTGGTG
TTCTAAC
Found at i:29874848 original size:17 final size:16
Alignment explanation
Indices: 29874828--29874882 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
29874818 TCGACACCTC
29874828 TTTTTTCTTTTATCTTT
1 TTTTTTCTTTT-TCTTT
29874845 TTTTTTCTCTTTTCTTT
1 TTTTTTCT-TTTTCTTT
*
29874862 TCTTTTC-TTTTCTTT
1 TTTTTTCTTTTTCTTT
29874877 TCTTTT
1 T-TTTT
29874883 GGTGAAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
17 19 0.56
18 3 0.09
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTT
Found at i:29874850 original size:5 final size:5
Alignment explanation
Indices: 29874830--29874882 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
29874820 GACACCTCTT
* *
29874830 TTTTC TTTTA TCTTT- TTTT- TTCTC TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
29874879 TTTT
1 TTTT
29874883 GGTGAAATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
4 6 0.14
5 34 0.79
6 3 0.07
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:29881293 original size:17 final size:17
Alignment explanation
Indices: 29881273--29881349 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 17
29881263 AAAATAATAA
*
29881273 AAATAATAGTAACAAAT
1 AAATAATAATAACAAAT
29881290 AAATAATAAT-ACAACTAT
1 AAATAATAATAACAA--AT
* *
29881308 GATAATAATAGTAACATGAT
1 -A-AATAATAATAACA-AAT
*
29881328 -AATAATAATAACATAT
1 AAATAATAATAACAAAT
29881344 -AATAAT
1 AAATAAT
29881350 TACTAGCATG
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
16 12 0.24
17 21 0.43
18 2 0.04
19 1 0.02
20 10 0.20
21 3 0.06
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (17 bp):
AAATAATAATAACAAAT
Found at i:29881500 original size:17 final size:17
Alignment explanation
Indices: 29881470--29881512 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
29881460 TGCTAGAAGT
29881470 AAATAAAT--AAATAAA
1 AAATAAATAAAAATAAA
*
29881485 AGATAAATAAAAATAAA
1 AAATAAATAAAAATAAA
*
29881502 AAATTAATAAA
1 AAATAAATAAA
29881513 GTTAAATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
17 16 0.70
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAATAAATAAAAATAAA
Found at i:29887650 original size:3 final size:3
Alignment explanation
Indices: 29887644--29887719 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
29887634 AGTTGTAGTA
* * * * *
29887644 GTT GTT GTT TTT ATT GTT TTT GTT GTT GTT TTT GTT TTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
* * *
29887692 GTT -TT -TT GTT TTT GTT TTT ATT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
29887720 TTCAAATTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.03, C:0.00, G:0.21, T:0.76
Consensus pattern (3 bp):
GTT
Found at i:29887660 original size:9 final size:9
Alignment explanation
Indices: 29887645--29887721 Score: 78
Period size: 9 Copynumber: 9.1 Consensus size: 9
29887635 GTTGTAGTAG
29887645 TTGTTGTTT
1 TTGTTGTTT
*
29887654 TTATTGTTT
1 TTGTTGTTT
29887663 TTGTTGTTGT
1 TTGTTGTT-T
29887673 TT-TTGTTT
1 TTGTTGTTT
29887681 TTGTTG---
1 TTGTTGTTT
29887687 TTGTTG-TT
1 TTGTTGTTT
29887695 TT-TTGTTT
1 TTGTTGTTT
29887703 TTGTT-TTT
1 TTGTTGTTT
29887711 ATTGTTGTTT
1 -TTGTTGTTT
29887721 T
1 T
29887722 CAAATTAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
6 6 0.10
7 3 0.05
8 12 0.21
9 31 0.53
10 6 0.10
ACGTcount: A:0.03, C:0.00, G:0.19, T:0.78
Consensus pattern (9 bp):
TTGTTGTTT
Found at i:29887660 original size:12 final size:12
Alignment explanation
Indices: 29887644--29887721 Score: 81
Period size: 12 Copynumber: 6.7 Consensus size: 12
29887634 AGTTGTAGTA
29887644 GTTGTTGTTT-TT
1 GTTGTT-TTTGTT
*
29887656 ATTGTTTTTGTT
1 GTTGTTTTTGTT
29887668 GTTGTTTTTGTT
1 GTTGTTTTTGTT
* *
29887680 TTTGTTGTTGTT
1 GTTGTTTTTGTT
29887692 G-T-TTTTTGTT
1 GTTGTTTTTGTT
* *
29887702 TTTGTTTTTATT
1 GTTGTTTTTGTT
29887714 GTTGTTTT
1 GTTGTTTT
29887722 CAAATTAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
10 7 0.13
11 5 0.09
12 42 0.78
ACGTcount: A:0.03, C:0.00, G:0.21, T:0.77
Consensus pattern (12 bp):
GTTGTTTTTGTT
Found at i:29887668 original size:21 final size:20
Alignment explanation
Indices: 29887644--29887707 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 20
29887634 AGTTGTAGTA
29887644 GTTGTTGTTTTTATTGTTTTT
1 GTTGTTGTTTTT-TTGTTTTT
29887665 GTTGTTG--TTTTTGTTTTT
1 GTTGTTGTTTTTTTGTTTTT
29887683 GTTGTTGTTGTTTTTTGTTTTT
1 GTTGTTG-T-TTTTTTGTTTTT
29887705 GTT
1 GTT
29887708 TTTATTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.38
19 3 0.08
21 7 0.18
22 14 0.36
ACGTcount: A:0.02, C:0.00, G:0.22, T:0.77
Consensus pattern (20 bp):
GTTGTTGTTTTTTTGTTTTT
Found at i:29889588 original size:19 final size:19
Alignment explanation
Indices: 29889550--29889589 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29889540 TAGATCCACT
*
29889550 ATTGTGGTGTGTAGGATGG
1 ATTGTGGTGTGAAGGATGG
29889569 ATTGTGGTGTGCAAGG-TGG
1 ATTGTGGTGTG-AAGGATGG
29889588 AT
1 AT
29889590 GGGCCTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.17, C:0.03, G:0.45, T:0.35
Consensus pattern (19 bp):
ATTGTGGTGTGAAGGATGG
Found at i:29892998 original size:37 final size:38
Alignment explanation
Indices: 29892945--29893033 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 38
29892935 TCCACTATCG
*
29892945 TGGTGTGTAGGATGGATGGGCCTACCATAGCCC-ATTA
1 TGGTGTGTAGGGTGGATGGGCCTACCATAGCCCAATTA
*
29892982 TGGTGTGTAGGGTGGATGGGCCTACTATAGCCCAATTA
1 TGGTGTGTAGGGTGGATGGGCCTACCATAGCCCAATTA
*
29893020 TAGTGTGTAGGGTG
1 TGGTGTGTAGGGTG
29893034 ATCAAAGTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 31 0.65
38 17 0.35
ACGTcount: A:0.20, C:0.15, G:0.36, T:0.29
Consensus pattern (38 bp):
TGGTGTGTAGGGTGGATGGGCCTACCATAGCCCAATTA
Found at i:29894003 original size:30 final size:26
Alignment explanation
Indices: 29893936--29893999 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
29893926 AGTGATAGTA
*
29893936 AATTAGATCCTTCCAAAGAATAAAATT
1 AATTAG-TACTTCCAAAGAATAAAATT
29893963 AATTAGTACTTCCAAAGAATAAAATT
1 AATTAGTACTTCCAAAGAATAAAATT
29893989 AATTAGTACTT
1 AATTAGTACTT
29894000 ACTTTAGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 30 0.83
27 6 0.17
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (26 bp):
AATTAGTACTTCCAAAGAATAAAATT
Found at i:29906897 original size:28 final size:28
Alignment explanation
Indices: 29906816--29906926 Score: 111
Period size: 28 Copynumber: 4.0 Consensus size: 28
29906806 TCTTCAAGAT
* *
29906816 GAATTTAGAATATTACTTTTTCGAGCCA
1 GAATTTAGAATATTGCTCTTTCGAGCCA
** * * *
29906844 G-ATACAGAGTAATGCTCTATT-AAGCCA
1 GAATTTAGAATATTGCTCT-TTCGAGCCA
29906871 GAATTTAGAATATTGCTCTTTCGAGCCA
1 GAATTTAGAATATTGCTCTTTCGAGCCA
*
29906899 -AAGTCTAGAATATTGCTCTTTCGAGCCA
1 GAA-TTTAGAATATTGCTCTTTCGAGCCA
29906927 AAATACACAA
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
27 21 0.32
28 45 0.68
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (28 bp):
GAATTTAGAATATTGCTCTTTCGAGCCA
Found at i:29906938 original size:28 final size:28
Alignment explanation
Indices: 29906879--29906938 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
29906869 CAGAATTTAG
* *
29906879 AATATTGCTCTTTCGAGCCAAAGTCTAG
1 AATATTGCTCTTTCGAGCCAAAATCTAC
29906907 AATATTGCTCTTTCGAGCCAAAATAC-AC
1 AATATTGCTCTTTCGAGCCAAAAT-CTAC
29906935 AATA
1 AATA
29906939 ACATTCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (28 bp):
AATATTGCTCTTTCGAGCCAAAATCTAC
Found at i:29909305 original size:22 final size:23
Alignment explanation
Indices: 29909280--29909327 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
29909270 CTCAAGATTC
29909280 TTTCTTTTTCG-TTTTT-ACTCAT
1 TTTCTTTTTCGCTTTTTCACT-AT
*
29909302 TTTCTTTTTTGCTTTTTCACTAT
1 TTTCTTTTTCGCTTTTTCACTAT
29909325 TTT
1 TTT
29909328 TCTCTTCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
23 10 0.43
24 3 0.13
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTCTTTTTCGCTTTTTCACTAT
Found at i:29909310 original size:23 final size:22
Alignment explanation
Indices: 29909280--29909327 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
29909270 CTCAAGATTC
29909280 TTTCTTTTT-CGTTTTT-ACTCAT
1 TTTCTTTTTGC-TTTTTCACT-AT
29909302 TTTCTTTTTTGCTTTTTCACTAT
1 TTTC-TTTTTGCTTTTTCACTAT
29909325 TTT
1 TTT
29909328 TCTCTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTCTTTTTGCTTTTTCACTAT
Found at i:29918871 original size:22 final size:21
Alignment explanation
Indices: 29918842--29918885 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
29918832 AATATTTTTC
*
29918842 TAATTTTTACATTTTTTAAAA
1 TAATTTTTACAATTTTTAAAA
**
29918863 TAATATTTTTGAATTTTTAAAA
1 TAAT-TTTTACAATTTTTAAAA
29918885 T
1 T
29918886 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATTTTTACAATTTTTAAAA
Found at i:29918895 original size:32 final size:32
Alignment explanation
Indices: 29918832--29918895 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
29918822 AAATATTTAA
* * **
29918832 AATATTTTTCTAATTTTTACATTTTTTAAAAT
1 AATATTTTTCGAATTTTTAAATTTTAAAAAAT
29918864 AATATTTTT-GAATTTTTAAAATTTTAAAAAAT
1 AATATTTTTCGAATTTTT-AAATTTTAAAAAAT
29918896 TAATTAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (32 bp):
AATATTTTTCGAATTTTTAAATTTTAAAAAAT
Found at i:29919238 original size:5 final size:5
Alignment explanation
Indices: 29919228--29919264 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
29919218 TAAGTTTATA
29919228 ATATT ATATT ATATT ATATT ATATT -TA-T ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
29919265 AATTTAGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.03
4 4 0.13
5 25 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:29919258 original size:13 final size:13
Alignment explanation
Indices: 29919222--29919264 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 13
29919212 CCGTTTTAAG
29919222 TTTATAATATTATA
1 TTTAT-ATATTATA
29919236 TTATATTATATTATA
1 TT-TA-TATATTATA
29919251 TTTATATATTATA
1 TTTATATATTATA
29919264 T
1 T
29919265 AATTTAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.37
14 4 0.15
15 12 0.44
16 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATATATTATA
Found at i:29926292 original size:29 final size:29
Alignment explanation
Indices: 29926224--29926576 Score: 270
Period size: 28 Copynumber: 12.6 Consensus size: 29
29926214 GGTTAGGGGT
* *
29926224 TAGGTCGATTTT-AAAATAATTGGGGGAA
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
* * *
29926252 TAGGTTGATTTTAAAAGTGATTAGGGAAA
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
**
29926281 TAGGTCGATTTTAAAAATAATTA-AAAAA
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
* *
29926309 TAAG-CGGATTCTAAAAATAATTAGGG-AA
1 TAGGTC-GATTTTAAAAATAATTAGGGAAA
* * **
29926337 TAGATTG-TTTCTAAAAATAATTA-AAAAA
1 TAGGTCGATTT-TAAAAATAATTAGGGAAA
*
29926365 TAAGTCGATTTTAAAAATAATTA-GGAAA
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
* * *
29926393 TAGGCCCATTTTAAAAATAATTA--G-AG
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
** *
29926419 TAGGTCGGGTTT-AAAATAATTAGTGG-TA
1 TAGGTCGATTTTAAAAATAATTAG-GGAAA
* * *
29926447 TAGGTTGATTTTAAAATTAATTAGTGG-TA
1 TAGGTCGATTTTAAAAATAATTAG-GGAAA
* *
29926476 TAGGTCAATTTTAAAACTAATTAGGGAAA
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
* * * *
29926505 TAGGTTGGTTTTATAAATAATTAAGG-AA
1 TAGGTCGATTTTAAAAATAATTAGGGAAA
* *
29926533 TAGGAT-GATTTTAAAACTAATTA-AGAAA
1 TAGG-TCGATTTTAAAAATAATTAGGGAAA
29926561 TAGGTCGATTTTAAAA
1 TAGGTCGATTTTAAAA
29926577 TTATTTATAT
Statistics
Matches: 257, Mismatches: 53, Indels: 30
0.76 0.16 0.09
Matches are distributed among these distances:
25 10 0.04
26 9 0.04
27 6 0.02
28 139 0.54
29 93 0.36
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (29 bp):
TAGGTCGATTTTAAAAATAATTAGGGAAA
Found at i:29926517 original size:58 final size:57
Alignment explanation
Indices: 29926224--29926579 Score: 198
Period size: 57 Copynumber: 6.3 Consensus size: 57
29926214 GGTTAGGGGT
* ** * * * *
29926224 TAGGTCGATTTTAAAA-TAATTGGGGGAATAGGTTGATTTTAAAAGTGATTAGGGAAA
1 TAGGTTGATTTTAAAATTAATT-AAGGAATAGGATAATTTTAAAACTAATTAGGGAAA
* * ** * *** * *
29926281 TAGGTCGATTTTAAAAATAATTAAAAAATAAGCGGATTCTAAAAATAATTAGGG-AA
1 TAGGTTGATTTTAAAATTAATTAAGGAATAGGATAATTTTAAAACTAATTAGGGAAA
* * ** * * *
29926337 TAGATTG-TTTCTAAAAATAATTAAAAAATAAG-TCGATTTTAAAAATAATTA-GGAAA
1 TAGGTTGATTT-TAAAATTAATTAAGGAATAGGAT-AATTTTAAAACTAATTAGGGAAA
*** * * *** *
29926393 TAGGCCCATTTTAAAAATAATT-A-GAGTAGG-TCGGGTTTAAAA-TAATTAGTGG-TA
1 TAGGTTGATTTTAAAATTAATTAAGGAATAGGAT-AATTTTAAAACTAATTAG-GGAAA
* *
29926447 TAGGTTGATTTTAAAATTAATTAGTGGTATAGG-TCAATTTTAAAACTAATTAGGGAAA
1 TAGGTTGATTTTAAAATTAATTA-AGGAATAGGAT-AATTTTAAAACTAATTAGGGAAA
* * *
29926505 TAGGTTGGTTTTATAAA-TAATTAAGGAATAGGATGATTTTAAAACTAATTA-AGAAA
1 TAGGTTGATTTTA-AAATTAATTAAGGAATAGGATAATTTTAAAACTAATTAGGGAAA
*
29926561 TAGGTCGATTTTAAAATTA
1 TAGGTTGATTTTAAAATTA
29926580 TTTATATGTT
Statistics
Matches: 242, Mismatches: 42, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
53 6 0.02
54 33 0.14
55 11 0.05
56 77 0.32
57 80 0.33
58 32 0.13
59 3 0.01
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (57 bp):
TAGGTTGATTTTAAAATTAATTAAGGAATAGGATAATTTTAAAACTAATTAGGGAAA
Found at i:29927561 original size:37 final size:37
Alignment explanation
Indices: 29927480--29927671 Score: 197
Period size: 37 Copynumber: 5.2 Consensus size: 37
29927470 TTAGTCTTTT
* * *
29927480 AAACACCAGCACAAAGGCCTACTAAGCACATAGCCC-A
1 AAACACCGGCACAAA-GCCTGCTAGGCACATAGCCCGA
* *
29927517 AATACACCGGTACAAAGCCTGCTAGGCACATAGCTCGA
1 AA-ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGA
* * **
29927555 AAACACCGACACAAAGCCTGTTAGGCACATAGCTTGA
1 AAACACCGGCACAAAGCCTGCTAGGCACATAGCCCGA
* * * *
29927592 ATACACTGGCACAAAGCCTACTAGGCACATAACCCGA
1 AAACACCGGCACAAAGCCTGCTAGGCACATAGCCCGA
* * * *
29927629 ATACATCGACACGAAGCCTGCTAGGCACATAGCCCGA
1 AAACACCGGCACAAAGCCTGCTAGGCACATAGCCCGA
*
29927666 ATACAC
1 AAACAC
29927672 TTAGATGCAA
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
37 115 0.89
38 14 0.11
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.14
Consensus pattern (37 bp):
AAACACCGGCACAAAGCCTGCTAGGCACATAGCCCGA
Found at i:29927606 original size:74 final size:74
Alignment explanation
Indices: 29927480--29927672 Score: 235
Period size: 74 Copynumber: 2.6 Consensus size: 74
29927470 TTAGTCTTTT
* * * * * *
29927480 AAACACC-AGCACAAAGGCCTACTAAGCACATAGCCCAAATACACCGGTACAAAGCCTGCTAGGC
1 AAACACCGA-CACAAA-GCCTGCTAGGCACATAGCCCGAATACACTGGCACAAAGCCTACTAGGC
* *
29927544 ACATAGCTCGA
64 ACATAACCCGA
* **
29927555 AAACACCGACACAAAGCCTGTTAGGCACATAGCTTGAATACACTGGCACAAAGCCTACTAGGCAC
1 AAACACCGACACAAAGCCTGCTAGGCACATAGCCCGAATACACTGGCACAAAGCCTACTAGGCAC
29927620 ATAACCCGA
66 ATAACCCGA
* * *
29927629 ATACATCGACACGAAGCCTGCTAGGCACATAGCCCGAATACACT
1 AAACACCGACACAAAGCCTGCTAGGCACATAGCCCGAATACACT
29927673 TAGATGCAAC
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
74 86 0.86
75 13 0.13
76 1 0.01
ACGTcount: A:0.37, C:0.31, G:0.18, T:0.14
Consensus pattern (74 bp):
AAACACCGACACAAAGCCTGCTAGGCACATAGCCCGAATACACTGGCACAAAGCCTACTAGGCAC
ATAACCCGA
Found at i:29928644 original size:2 final size:2
Alignment explanation
Indices: 29928637--29928672 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
29928627 CTTTAATCTT
29928637 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29928673 TGACAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29928657 original size:17 final size:17
Alignment explanation
Indices: 29928637--29928669 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29928627 CTTTAATCTT
29928637 TATATATATATATATAA
1 TATATATATATATATAA
29928654 TATATATATATATATA
1 TATATATATATATATA
29928670 TATTGACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:29945177 original size:23 final size:22
Alignment explanation
Indices: 29945143--29945266 Score: 83
Period size: 23 Copynumber: 5.3 Consensus size: 22
29945133 CATTTAGTCG
29945143 CATTTAATCACATGAATATTTCAA
1 CATTT-ATCACATGAATATTTC-A
*
29945167 CATTTATCACATCACATATTAATCA
1 CATTTATCACATGA-ATATT--TCA
* *
29945192 CATTTAGTCACAT--TTA-ATCA
1 CATTTA-TCACATGAATATTTCA
*
29945212 TATTTAATCACATGAATATTTCAA
1 CATTT-ATCACATGAATATTTC-A
*
29945236 CATTTATCACATCACATATTAATCA
1 CATTTATCACATGA-ATATT--TCA
29945261 CATTTA
1 CATTTA
29945267 GTTACATTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
20 13 0.16
21 1 0.01
22 2 0.03
23 20 0.25
24 20 0.25
25 14 0.17
26 10 0.12
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (22 bp):
CATTTATCACATGAATATTTCA
Found at i:29945181 original size:59 final size:59
Alignment explanation
Indices: 29945089--29945390 Score: 392
Period size: 59 Copynumber: 5.1 Consensus size: 59
29945079 CACTAAAAAA
*
29945089 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCGCATTT
1 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATTT
29945148 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATTTAATCAT
1 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGT--C-----A-C--
29945213 ATTT
56 ATTT
*
29945217 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTTACA-TT
1 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATTT
*
29945275 AATCACATGAATATTTCATCATTTATCACATCACATA-T--T---A---A-TCACATTT
1 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATTT
* *
29945324 AATCATATGAATATTTCAACATTTATCACATTACATATTAATCACATTTAGTCACATTT
1 AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATTT
29945383 AATCACAT
1 AATCACAT
29945391 TTAATGATAG
Statistics
Matches: 214, Mismatches: 8, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
48 4 0.02
49 37 0.17
50 1 0.00
52 2 0.01
55 2 0.01
57 1 0.00
58 39 0.18
59 68 0.32
61 2 0.01
62 1 0.00
67 1 0.00
69 56 0.26
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.38
Consensus pattern (59 bp):
AATCACATGAATATTTCAACATTTATCACATCACATATTAATCACATTTAGTCACATTT
Found at i:29945204 original size:10 final size:10
Alignment explanation
Indices: 29945177--29945395 Score: 73
Period size: 10 Copynumber: 21.2 Consensus size: 10
29945167 CATTTATCAC
29945177 ATCACATATTA
1 ATCACAT-TTA
29945188 ATCACATTTA
1 ATCACATTTA
*
29945198 GTCACATTTA
1 ATCACATTTA
*
29945208 ATCATATTTA
1 ATCACATTTA
*
29945218 ATCACATGAATA
1 ATCACAT--TTA
*
29945230 TTTCAACATTTATCA
1 -ATC-ACA-TT-T-A
29945245 CATCACATATTA
1 -ATCACAT-TTA
29945257 ATCACATTTA
1 ATCACATTTA
* *
29945267 GTTACA-TTA
1 ATCACATTTA
*
29945276 ATCACA-TGA
1 ATCACATTTA
*
29945285 AT---ATTTC
1 ATCACATTTA
*
29945292 ATCA-TTTATCA
1 ATCACATT-T-A
29945303 CATCACATATTA
1 -ATCACAT-TTA
29945315 ATCACATTTA
1 ATCACATTTA
* *
29945325 ATCATATGAATA
1 ATCACAT--TTA
*
29945337 TTTCAACATTT-
1 -ATC-ACATTTA
29945348 ATCACA-TT-
1 ATCACATTTA
*
29945356 A-CATA-TTA
1 ATCACATTTA
29945364 ATCACATTTA
1 ATCACATTTA
*
29945374 GTCACATTTA
1 ATCACATTTA
29945384 ATCACATTTA
1 ATCACATTTA
29945394 AT
1 AT
29945396 GATAGTTTGG
Statistics
Matches: 156, Mismatches: 29, Indels: 47
0.67 0.12 0.20
Matches are distributed among these distances:
6 1 0.01
7 8 0.05
8 4 0.03
9 19 0.12
10 68 0.44
11 21 0.13
12 11 0.07
13 8 0.05
14 12 0.08
15 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (10 bp):
ATCACATTTA
Found at i:29945219 original size:69 final size:67
Alignment explanation
Indices: 29945118--29945324 Score: 279
Period size: 69 Copynumber: 3.1 Consensus size: 67
29945108 CATTTATCAC
* *
29945118 ATCACATATTAATCACATTTAGTCGCATTTAATCACATGAATATTTCAACATTTATCACATCACA
1 ATCACAT-TTAGTCACATTTAAT--CATTTAATCACATGAATATTTCAACATTTATCACATCACA
29945183 TATTA
63 TATTA
29945188 ATCACATTTAGTCACATTTAATCATATTTAATCACATGAATATTTCAACATTTATCACATCACAT
1 ATCACATTTAGTCACATTTAATC--ATTTAATCACATGAATATTTCAACATTTATCACATCACAT
29945253 ATTA
64 ATTA
*
29945257 ATCACATTTAG------TT-A-CA-TTAATCACATGAATATTTCATCATTTATCACATCACATAT
1 ATCACATTTAGTCACATTTAATCATTTAATCACATGAATATTTCAACATTTATCACATCACATAT
29945313 TA
66 TA
29945315 ATCACATTTA
1 ATCACATTTA
29945325 ATCATATGAA
Statistics
Matches: 132, Mismatches: 3, Indels: 16
0.87 0.02 0.11
Matches are distributed among these distances:
58 51 0.39
59 1 0.01
61 1 0.01
62 1 0.01
63 2 0.02
67 1 0.01
69 68 0.52
70 7 0.05
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (67 bp):
ATCACATTTAGTCACATTTAATCATTTAATCACATGAATATTTCAACATTTATCACATCACATAT
TA
Found at i:29945277 original size:58 final size:59
Alignment explanation
Indices: 29945188--29945390 Score: 259
Period size: 58 Copynumber: 3.6 Consensus size: 59
29945178 TCACATATTA
* * *
29945188 ATCACAT-TTAGTCACATTTAATCATATTTAATCACATGAATATTTCAACATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
* *
29945246 ATCACATATTAATCACATTTAGTTACA-TTAATCACATGAATATTTCATCATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
*
29945304 ATCACATA-T--T---A---A-TCACATTTAATCATATGAATATTTCAACATTTATCAC
1 ATCACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
*
29945353 ATTACATATTAATCACATTTAGTCACATTTAATCACAT
1 ATCACATATTAATCACATTTAGTCACATTTAATCACAT
29945391 TTAATGATAG
Statistics
Matches: 123, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
48 4 0.03
49 37 0.30
50 1 0.01
52 2 0.02
55 2 0.02
57 1 0.01
58 46 0.37
59 30 0.24
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (59 bp):
ATCACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
Found at i:29945281 original size:35 final size:35
Alignment explanation
Indices: 29945166--29945282 Score: 118
Period size: 35 Copynumber: 3.4 Consensus size: 35
29945156 GAATATTTCA
*
29945166 ACATTTATCACATCACATATTAATCACATTTAGTC
1 ACATTTATCACATCACATATTAATCACATTTAGTT
* * *
29945201 ACA-TT-T-A-ATCATAT-TTAATCACATGAATATTT
1 ACATTTATCACATCACATATTAATCACAT--TTAGTT
29945233 CAACATTTATCACATCACATATTAATCACATTTAGTT
1 --ACATTTATCACATCACATATTAATCACATTTAGTT
*
29945270 ACATTAATCACAT
1 ACATTTATCACAT
29945283 GAATATTTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
30 10 0.15
31 6 0.09
32 4 0.06
33 1 0.02
34 5 0.08
35 17 0.26
36 1 0.02
37 5 0.08
38 6 0.09
39 10 0.15
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (35 bp):
ACATTTATCACATCACATATTAATCACATTTAGTT
Found at i:29945297 original size:23 final size:22
Alignment explanation
Indices: 29945270--29945354 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 22
29945260 ACATTTAGTT
29945270 ACATTAATCACATGAATATTTC
1 ACATTAATCACATGAATATTTC
* *
29945292 ATCATTTATCACATCACATATTAATC
1 A-CATTAATCACATGA-ATATT--TC
*
29945318 ACATTTAATCATATGAATATTTC
1 ACA-TTAATCACATGAATATTTC
*
29945341 AACATTTATCACAT
1 -ACATTAATCACAT
29945355 TACATATTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.02
23 22 0.44
24 8 0.16
25 7 0.14
26 12 0.24
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (22 bp):
ACATTAATCACATGAATATTTC
Found at i:29945328 original size:49 final size:49
Alignment explanation
Indices: 29945257--29945380 Score: 180
Period size: 49 Copynumber: 2.6 Consensus size: 49
29945247 TCACATATTA
* * *
29945257 ATCACAT-TTAGTTACA-TTAATCACATGAATATTTCATCATTTATCAC
1 ATCACATATTAATCACATTTAATCACATGAATATTTCAACATTTATCAC
*
29945304 ATCACATATTAATCACATTTAATCATATGAATATTTCAACATTTATCAC
1 ATCACATATTAATCACATTTAATCACATGAATATTTCAACATTTATCAC
* *
29945353 ATTACATATTAATCACATTTAGTCACAT
1 ATCACATATTAATCACATTTAATCACAT
29945381 TTAATCACAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 7 0.10
48 7 0.10
49 54 0.79
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.40
Consensus pattern (49 bp):
ATCACATATTAATCACATTTAATCACATGAATATTTCAACATTTATCAC
Found at i:29945836 original size:35 final size:36
Alignment explanation
Indices: 29945787--29945891 Score: 158
Period size: 35 Copynumber: 2.9 Consensus size: 36
29945777 CTATATTCAG
* *
29945787 TGTCACATGACATGAATAACATACCCACATATTTT-
1 TGTCTCATGGCATGAATAACATACCCACATATTTTC
*
29945822 TGTCTCATGGCATGAATAACATACCCATATATTTTC
1 TGTCTCATGGCATGAATAACATACCCACATATTTTC
* *
29945858 TGTCTCATGGCATGAATAGCATACCTACATATTT
1 TGTCTCATGGCATGAATAACATACCCACATATTT
29945892 ACTTTCACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 32 0.51
36 31 0.49
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.34
Consensus pattern (36 bp):
TGTCTCATGGCATGAATAACATACCCACATATTTTC
Found at i:29952202 original size:5 final size:5
Alignment explanation
Indices: 29952192--29952216 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29952182 CTGAGTGTGT
29952192 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
29952217 ATATGTTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Done.