Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 73 of 120
Found at i:21505903 original size:45 final size:44
Alignment explanation
Indices: 21505853--21505937 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
21505843 TTAAAACAGC
* * *
21505853 AAAAAATAACAACCAAAATAGTAAAAACAACAACATCAAAATAGT
1 AAAAAACAACAACCAAAACAGTAAAAA-AACAACACCAAAATAGT
* *
21505898 AAAAAACAACATCCAAAACAGTGAAAAAACAACACCAAAA
1 AAAAAACAACAACCAAAACAGTAAAAAAACAACACCAAAA
21505938 CAACAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 12 0.34
45 23 0.66
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.09
Consensus pattern (44 bp):
AAAAAACAACAACCAAAACAGTAAAAAAACAACACCAAAATAGT
Found at i:21505935 original size:22 final size:21
Alignment explanation
Indices: 21505845--21505939 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 21
21505835 AAAAAAAATT
* *
21505845 AAAACAGCAAAAAATAACAACC
1 AAAACAGTAAAAAACAAC-ACC
* *
21505867 AAAATAGTAAAAACAACAACATC
1 AAAACAGT-AAAA-AACAACACC
*
21505890 AAAATAGTAAAAAACAACATCC
1 AAAACAGTAAAAAACAACA-CC
21505912 AAAACAGTGAAAAAACAACACC
1 AAAACAGT-AAAAAACAACACC
21505934 AAAACA
1 AAAACA
21505940 ACAATATAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
21 7 0.11
22 26 0.41
23 25 0.40
24 5 0.08
ACGTcount: A:0.66, C:0.20, G:0.05, T:0.08
Consensus pattern (21 bp):
AAAACAGTAAAAAACAACACC
Found at i:21507840 original size:120 final size:119
Alignment explanation
Indices: 21507688--21507927 Score: 426
Period size: 120 Copynumber: 2.0 Consensus size: 119
21507678 ATAAGCTTGA
*
21507688 ATAAATAAAAACCAACAAGCAGGTCCACAGATGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
1 ATAAATAAAAACCAACAAGCAGGTCCAAAGATGGAAGAAATTCAATAAAGAGATTAGATTT-AAA
21507753 AAAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
65 AAAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
* ***
21507808 ATAAATAAAAATCAACAAGCAGGTCCAAAGATGGAAGAAATTCAATAAAGAGATTAGATTTTTTA
1 ATAAATAAAAACCAACAAGCAGGTCCAAAGATGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
21507873 AAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
66 AAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
21507927 A
1 A
21507928 CCATATTAGT
Statistics
Matches: 115, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 56 0.49
120 59 0.51
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (119 bp):
ATAAATAAAAACCAACAAGCAGGTCCAAAGATGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
AAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
Found at i:21508988 original size:19 final size:19
Alignment explanation
Indices: 21508952--21508991 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21508942 TTTTATTCTA
*
21508952 AAAAAAATTAAATCCAAAT
1 AAAAAAATTAAATACAAAT
* *
21508971 AAAAATATTGAATACAAAT
1 AAAAAAATTAAATACAAAT
21508990 AA
1 AA
21508992 TTAGTAATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAAAAATTAAATACAAAT
Found at i:21510607 original size:43 final size:44
Alignment explanation
Indices: 21510560--21510649 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 44
21510550 ATTGACGTAA
* * *
21510560 AATAGAAACTATGATAATTATA-ATTTAACAATAATAATTATTT
1 AATAGAAACTATGATAATTACATATTTAAAAATAATAATAATTT
* * *
21510603 AATAGAAATTATGATAATTACATGTTTAAAAATAATTATAATTT
1 AATAGAAACTATGATAATTACATATTTAAAAATAATAATAATTT
21510647 AAT
1 AAT
21510650 TTACTGGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 20 0.50
44 20 0.50
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (44 bp):
AATAGAAACTATGATAATTACATATTTAAAAATAATAATAATTT
Found at i:21511258 original size:23 final size:23
Alignment explanation
Indices: 21511207--21511259 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
21511197 TTTTATCTAC
* * *
21511207 CTTTGTGGTACACTTTTCTTTTG
1 CTTTGTGATACACTTTTCCTCTG
*
21511230 CATTGTGATACACTTTTCCTCTG
1 CTTTGTGATACACTTTTCCTCTG
*
21511253 TTTTGTG
1 CTTTGTG
21511260 GCATGTTTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.53
Consensus pattern (23 bp):
CTTTGTGATACACTTTTCCTCTG
Found at i:21523247 original size:30 final size:29
Alignment explanation
Indices: 21523213--21523276 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
21523203 AATTTACAAG
*
21523213 AATTGAATC-AAATCAAAATTTCATGTACAC
1 AATTGAA-CAAAATC-AAAGTTCATGTACAC
* *
21523243 AATTGCACAAAATCAAAGTTCATGTATAC
1 AATTGAACAAAATCAAAGTTCATGTACAC
21523272 AATTG
1 AATTG
21523277 CACATTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (29 bp):
AATTGAACAAAATCAAAGTTCATGTACAC
Found at i:21523265 original size:29 final size:30
Alignment explanation
Indices: 21523222--21523280 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
21523212 GAATTGAATC
*
21523222 AAATCAAAATTTCATGTACACAATTGCACA
1 AAATCAAAAGTTCATGTACACAATTGCACA
*
21523252 AAATC-AAAGTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTACACAATTGCACA
21523281 TTACAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTACACAATTGCACA
Found at i:21529342 original size:18 final size:21
Alignment explanation
Indices: 21529287--21529330 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
21529277 TTCAAACGTG
*
21529287 GAAAGAATTGGAGGAGTGGAT
1 GAAAGAATTAGAGGAGTGGAT
21529308 GAAAGAATTAGAGGAGTGGAT
1 GAAAGAATTAGAGGAGTGGAT
21529329 GA
1 GA
21529331 CAAATGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.18
Consensus pattern (21 bp):
GAAAGAATTAGAGGAGTGGAT
Found at i:21533340 original size:3 final size:3
Alignment explanation
Indices: 21533332--21533363 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21533322 AGTAAAAATA
21533332 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21533364 GAGAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21537265 original size:2 final size:2
Alignment explanation
Indices: 21537258--21537284 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21537248 AATGTGTAAT
21537258 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21537285 TGTCGAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21539179 original size:55 final size:55
Alignment explanation
Indices: 21539076--21539187 Score: 176
Period size: 55 Copynumber: 2.1 Consensus size: 55
21539066 TTATTTATTT
* *
21539076 TATATTTAGTTAATATTTATTTTGAAATAGGTAGGAAGAAAATAATATATATATA
1 TATATTTACTTAATATTTATTTCGAAATAGGTAGGAAGAAAATAATATATATATA
21539131 TATATTTACTTAATATTTACTTTCGAAATAGGTAGG-A-AAAAT-ATATATATATA
1 TATATTTACTTAATATTTA-TTTCGAAATAGGTAGGAAGAAAATAATATATATATA
21539184 TATA
1 TATA
21539188 ATACAACAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
53 15 0.28
54 5 0.09
55 19 0.35
56 15 0.28
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (55 bp):
TATATTTACTTAATATTTATTTCGAAATAGGTAGGAAGAAAATAATATATATATA
Found at i:21540063 original size:45 final size:45
Alignment explanation
Indices: 21540014--21540235 Score: 251
Period size: 45 Copynumber: 5.1 Consensus size: 45
21540004 AGTTGTGTGT
* *
21540014 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAAATAGGATG
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGATG
* * *
21540059 GTGACTTCAATCTGCCCCTCTAGATTAAGGGTAAAAGACTGAAT-
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGATG
* * * *
21540103 G-G-CTTCAATTTGCTCCTCCAGATTAAGGGTAAAAGATTGGATG
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGATG
* * * *
21540146 ATGGCTTCAATCTGCCCCTCTGGATTGGGGGTAAAAGATTGGAT-
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGATG
* * *
21540190 G-G-CTTCAAT-TTCCCCACTGGATTAGGGGTAAAAGATTGGATG
1 GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGATG
21540232 GTGA
1 GTGA
21540236 TGTAACTTCA
Statistics
Matches: 150, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
41 29 0.19
42 43 0.29
43 3 0.02
44 2 0.01
45 73 0.49
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (45 bp):
GTGACTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGATG
Found at i:21540145 original size:87 final size:87
Alignment explanation
Indices: 21540018--21540235 Score: 294
Period size: 87 Copynumber: 2.5 Consensus size: 87
21540008 GTGTGTGTGA
* * *
21540018 CTTCAATCTGCCCCTCTAGATTAGGGGTAAAAAATAGGATGGTGACTTCAATCTGCCCCTCTAGA
1 CTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCCCTCTAGA
21540083 TTAAGGGTAAAAGACTGAATGG
66 TTAAGGGTAAAAGACTGAATGG
* * * * * *
21540105 CTTCAATTTGCTCCTCCAGATTAAGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCCTCTGGA
1 CTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCCCTCTAGA
** * *
21540170 TTGGGGGTAAAAGATTGGATGG
66 TTAAGGGTAAAAGACTGAATGG
* *
21540192 CTTCAATTT-CCCCACTGGATTAGGGGTAAAAGATTGGATGGTGA
1 CTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGA
21540236 TGTAACTTCA
Statistics
Matches: 111, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 28 0.25
87 83 0.75
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (87 bp):
CTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCCCTCTAGA
TTAAGGGTAAAAGACTGAATGG
Found at i:21540616 original size:99 final size:99
Alignment explanation
Indices: 21540426--21540668 Score: 252
Period size: 99 Copynumber: 2.5 Consensus size: 99
21540416 AGGAAGATAG
* * * * * *
21540426 GATTTGGTGTTG-AAGCTTCTCTCCATCCCTCTGTAACCTTAGGGACATTGAGACCTGTTTCGTT
1 GATTTGATGTTGTAA-CTTCTCTCCATTCCACTGTAACCTCAGGGACATTGAGACCTGTTACGTC
* * ** * * *
21540490 ATTTTTATTTGACCTACAGCAATTTAGGGGTATAA
65 ATGTTGATCCGACCCACAGCAACTTAGGGATATAA
21540525 GATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTCAGGGACATTGAGATCC-GTTAC-TC
1 GATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTCAGGGACATTGAGA-CCTGTTACGTC
*
21540588 ATGTTGATCCGACCCACTGCAACCTTAGGGATATAA
65 ATGTTGATCCGACCCACAGCAA-CTTAGGGATATAA
* *
21540624 GA--T-ATGGTGT---TTCACTCCATTCCACTGTAACCTCAGGGACATTGA
1 GATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTCAGGGACATTGA
21540669 AATCTGCCTT
Statistics
Matches: 125, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
93 34 0.27
96 6 0.05
97 1 0.01
98 17 0.14
99 63 0.50
100 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (99 bp):
GATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTCAGGGACATTGAGACCTGTTACGTCA
TGTTGATCCGACCCACAGCAACTTAGGGATATAA
Found at i:21540728 original size:93 final size:93
Alignment explanation
Indices: 21540545--21540728 Score: 219
Period size: 93 Copynumber: 2.0 Consensus size: 93
21540535 TGTAACTTCT
* * *
21540545 CTCCATTCCACTGTAACCTCAGGGACATTGAGATCCGTTACTCATGTTGATCCGACCCACTGCAA
1 CTCCATTCCACTGTAACCTCAGGGACATTGAAATCCCTTACTCATGTTAATCCGACCCACTGCAA
* *
21540610 CCTTAGGGATATAAGATATGGTGTTTCA
66 CCTCAGGGATATAAGATATGATGTTTCA
* ** *
21540638 CTCCATTCCACTGTAACCTCAGGGACATTGAAATCTGCCTT-GTTGTTTTAATCCGACCCACTGC
1 CTCCATTCCACTGTAACCTCAGGGACATTGAAATC--CCTTACTCATGTTAATCCGACCCACTGC
* ** *
21540702 AA-CTCAGGGGTATGGGATTTGATGTTT
64 AACCTCAGGGATATAAGATATGATGTTT
21540729 ATTCGATCCA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
93 53 0.70
94 20 0.26
95 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (93 bp):
CTCCATTCCACTGTAACCTCAGGGACATTGAAATCCCTTACTCATGTTAATCCGACCCACTGCAA
CCTCAGGGATATAAGATATGATGTTTCA
Found at i:21553197 original size:52 final size:51
Alignment explanation
Indices: 21553131--21553240 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
21553121 TCCTTTTTTA
* * * * * *
21553131 TTTTCTTTCTTTGGGTTTCAAGATGCCTCTTTGCTAGTTTTTATCTCGACCT
1 TTTTTTTTCTTTGGGTTTCAAGATACC-CTTTACGAGTTTTCATCTCGACCC
21553183 TTTTTTTTCTTTGGGTTTCAAGATACCCTTTACGAGTTTTCATCTCGACCC
1 TTTTTTTTCTTTGGGTTTCAAGATACCCTTTACGAGTTTTCATCTCGACCC
21553234 TTTTTTT
1 TTTTTTT
21553241 ATTTTCTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 27 0.52
52 25 0.48
ACGTcount: A:0.13, C:0.21, G:0.14, T:0.53
Consensus pattern (51 bp):
TTTTTTTTCTTTGGGTTTCAAGATACCCTTTACGAGTTTTCATCTCGACCC
Found at i:21559875 original size:29 final size:30
Alignment explanation
Indices: 21559836--21559893 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
21559826 ATACTTATAG
21559836 TTTTTTTGTCCTA-TA-TTGGTACCTGAACT
1 TTTTTTTGTCC-ACTAGTTGGTACCTGAACT
21559865 TTTTTTTGTCCACTAGTTTGGTACCTGAA
1 TTTTTTTGTCCACTAG-TTGGTACCTGAA
21559894 TTTAACACCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 1 0.04
29 13 0.50
31 12 0.46
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (30 bp):
TTTTTTTGTCCACTAGTTGGTACCTGAACT
Found at i:21560363 original size:6 final size:6
Alignment explanation
Indices: 21560354--21560391 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
21560344 TTGCTAAATC
**
21560354 TGGGTT TGGGTT TGGGTT TGATTT TGGGTT TGGGTT TG
1 TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT TG
21560392 TGATTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.53
Consensus pattern (6 bp):
TGGGTT
Found at i:21567295 original size:15 final size:15
Alignment explanation
Indices: 21567277--21567316 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
21567267 TAACCAAAAA
*
21567277 AAATATAAAATTATT
1 AAATATAAAATAATT
21567292 AAATATTAAAATAATT
1 AAATA-TAAAATAATT
*
21567308 TAATATAAA
1 AAATATAAA
21567317 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATAAAATAATT
Found at i:21568548 original size:16 final size:16
Alignment explanation
Indices: 21568529--21568589 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
21568519 ATTAATAATA
* *
21568529 AACAGTAGTAATTATT
1 AACAGTAATAAATATT
*
21568545 AACATTAATAAATATT
1 AACAGTAATAAATATT
* *
21568561 AACAATAAT-AATAAT
1 AACAGTAATAAATATT
*
21568576 ACCAGTAATAAATA
1 AACAGTAATAAATA
21568590 CAATAATAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
15 12 0.32
16 25 0.68
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (16 bp):
AACAGTAATAAATATT
Found at i:21568614 original size:17 final size:18
Alignment explanation
Indices: 21568581--21568618 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
21568571 ATAATACCAG
21568581 TAATAAATACAATAATAA
1 TAATAAATACAATAATAA
21568599 TAAT-AATA-AATGAATAA
1 TAATAAATACAAT-AATAA
21568616 TAA
1 TAA
21568619 AAAAGGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 12 0.63
18 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TAATAAATACAATAATAA
Found at i:21569827 original size:30 final size:30
Alignment explanation
Indices: 21569754--21569832 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
21569744 AAACTATCCA
* * **
21569754 AAAATTATATTTTGACCCTCAATCTTCTCC
1 AAAATTATATTTTAACCCCCAAAATTCTCC
* * *
21569784 AAATTTATGTTTTAACCCCCAAAATTCTCT
1 AAAATTATATTTTAACCCCCAAAATTCTCC
21569814 AAAATTATATTTTAACCCC
1 AAAATTATATTTTAACCCC
21569833 TAATCTTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAACCCCCAAAATTCTCC
Found at i:21569905 original size:29 final size:29
Alignment explanation
Indices: 21569880--21570124 Score: 126
Period size: 29 Copynumber: 8.4 Consensus size: 29
21569870 TTCAAAATCC
*
21569880 CATTTTTACCCTGATTTTTCCAAAAAATA
1 CATTTTTACCCTGATTTTTCCAAAAATTA
* * ** *
21569909 CATTCTTACCCCTAAACTTTCC-AAAATTC
1 CATTTTTA-CCCTGATTTTTCCAAAAATTA
**
21569938 CATTTTTAATCTCGATTTTTCCAAAAATTA
1 CATTTTTACCCT-GATTTTTCCAAAAATTA
***
21569968 CATTTTTACCCCT-AAACTTCCAAAAATTA
1 CATTTTTA-CCCTGATTTTTCCAAAAATTA
* ** *** ** *
21569997 C-CTTTTACCCCCAAACTTCCTGAAATTC
1 CATTTTTACCCTGATTTTTCCAAAAATTA
* *
21570025 CATTTTTGACCTTGATTTTTCCCAAAATTA
1 CATTTTT-ACCCTGATTTTTCCAAAAATTA
** * *
21570055 CCA-TTTTACCCTCGA-ACTTCCTAAAATTC
1 -CATTTTTACCCT-GATTTTTCCAAAAATTA
21570084 CATTTTCTATCCC-GATTTTTCCAAAAATTA
1 CATTTT-TA-CCCTGATTTTTCCAAAAATTA
21570114 CCA-TTTTACCC
1 -CATTTTTACCC
21570125 CCGTATGTCA
Statistics
Matches: 160, Mismatches: 42, Indels: 29
0.69 0.18 0.13
Matches are distributed among these distances:
27 3 0.02
28 26 0.16
29 64 0.40
30 58 0.36
31 9 0.06
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.39
Consensus pattern (29 bp):
CATTTTTACCCTGATTTTTCCAAAAATTA
Found at i:21569918 original size:58 final size:59
Alignment explanation
Indices: 21569849--21569992 Score: 202
Period size: 58 Copynumber: 2.5 Consensus size: 59
21569839 TTTTGAAATT
* * * *
21569849 TACATTTTTACCCTTTAACTTTTCAAAATCCCATTTTTACCCT-GATTTTTCCAAAAAA
1 TACATTTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTTTCCAAAAAA
* * * *
21569907 TACATTCTTACCCCTAAACTTTCCAAAATTCCATTTTTAATCTCGATTTTTCCAAAAAT
1 TACATTTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTTTCCAAAAAA
21569966 TACATTTTTACCCCTAAAC-TTCCAAAA
1 TACATTTTTACCCCTAAACTTTCCAAAA
21569993 ATTACCTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
58 44 0.58
59 32 0.42
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.40
Consensus pattern (59 bp):
TACATTTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTTTCCAAAAAA
Found at i:21569963 original size:87 final size:85
Alignment explanation
Indices: 21569868--21570089 Score: 200
Period size: 87 Copynumber: 2.6 Consensus size: 85
21569858 ACCCTTTAAC
* *** *
21569868 TTTT-CAAAATCCCATTTTTACCCTGATTTTTCCAAAAAATACATTCTTACCCCTAAACTTTCC-
1 TTTTCCAAAATACCATTTTTACCCT-AAACTTCCAAAAAATACATT-TTACCCCCAAAC-TTCCT
*
21569931 AAAATTCCATTTTTAATCTCGAT
63 AAAATTCCATTTTTAACCTCGAT
* *
21569954 TTTTCCAAAAATTA-CATTTTTACCCCTAAACTTCCAAAAATTACCTTTTACCCCCAAACTTCCT
1 TTTTCC-AAAA-TACCATTTTTA-CCCTAAACTTCCAAAAAATACATTTTACCCCCAAACTTCCT
* * *
21570018 GAAATTCCATTTTTGACCTTGAT
63 AAAATTCCATTTTTAACCTCGAT
* * * *
21570041 TTTTCCCAAAATTACCA-TTTTACCCTCGAACTTCCTAAAATTCCATTTT
1 TTTT-CCAAAA-TACCATTTTTACCCT-AAACTTCCAAAAAATACATTTT
21570090 CTATCCCGAT
Statistics
Matches: 113, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
86 12 0.11
87 65 0.58
88 31 0.27
89 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.40
Consensus pattern (85 bp):
TTTTCCAAAATACCATTTTTACCCTAAACTTCCAAAAAATACATTTTACCCCCAAACTTCCTAAA
ATTCCATTTTTAACCTCGAT
Found at i:21570023 original size:28 final size:29
Alignment explanation
Indices: 21569956--21570016 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
21569946 ATCTCGATTT
* *
21569956 TTCCAAAAATTACATTTTTACCCCTAAAC
1 TTCCAAAAATTACACTTTTACCCCCAAAC
21569985 TTCCAAAAATTAC-CTTTTACCCCCAAAC
1 TTCCAAAAATTACACTTTTACCCCCAAAC
21570013 TTCC
1 TTCC
21570017 TGAAATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33
Consensus pattern (29 bp):
TTCCAAAAATTACACTTTTACCCCCAAAC
Found at i:21570147 original size:58 final size:59
Alignment explanation
Indices: 21569985--21570180 Score: 204
Period size: 59 Copynumber: 3.4 Consensus size: 59
21569975 ACCCCTAAAC
* * ** * *
21569985 TTCCAAAAATTACC-TTTTACCCCCAAACTTCCTGAAATTCCATTTTTGA-CCTTGATTT
1 TTCCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTCATCC-CGATTT
* *
21570043 TTCCCAAAATTACCATTTTACCCTCGAACTTCCTAAAATTCCA-TTTTCTATCCCGATTT
1 TTCCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTC-ATCCCGATTT
* * * **
21570102 TTCCAAAAATTACCATTTTACCCCCGTA-TGT-CAAAAATTTCATTTTTCATCCCGAACT
1 TTCCCAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTTCATCCCGATTT
*
21570160 TTCCCAAAATTATCATTTTAC
1 TTCCCAAAATTACCATTTTAC
21570181 TCCTGGGTAT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
58 54 0.46
59 62 0.53
60 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.04, T:0.39
Consensus pattern (59 bp):
TTCCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTCATCCCGATTT
Found at i:21570522 original size:97 final size:97
Alignment explanation
Indices: 21570416--21570606 Score: 244
Period size: 97 Copynumber: 2.0 Consensus size: 97
21570406 ACTTTAAAAT
* * * *
21570416 TCGAGGCAATA-TTCTTTTAT-TTTGATATTTGAAAATTTGTGCCTTAACTTACTAAGTGTAATT
1 TCGAGGCAATATTTC-TTTATCTCTGAT-TCTGAAAATTTGTGCCTTAACTTACTAAGTGCAACT
*
21570479 TTTCTTCGAATCG-GAACAATCGAATACCCTTAAA
64 TTTCTTCAAATCGAG-ACAATCGAATACCCTTAAA
* * *
21570513 TCGAGGCAATGTTTCTTTATCTCTGATTCTGAAAATTTGTGCCTTAACTTACTAGGTGCGACTTT
1 TCGAGGCAATATTTCTTTATCTCTGATTCTGAAAATTTGTGCCTTAACTTACTAAGTGCAACTTT
* *
21570578 TCTTCAAATCGAGATAATCGAATATCCTT
66 TCTTCAAATCGAGACAATCGAATACCCTT
21570607 TTCCAAGGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
97 72 0.89
98 9 0.11
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (97 bp):
TCGAGGCAATATTTCTTTATCTCTGATTCTGAAAATTTGTGCCTTAACTTACTAAGTGCAACTTT
TCTTCAAATCGAGACAATCGAATACCCTTAAA
Found at i:21575054 original size:20 final size:18
Alignment explanation
Indices: 21575016--21575056 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
21575006 AAAACCTAAT
21575016 AAAAAAAGAAAAAAAGGA
1 AAAAAAAGAAAAAAAGGA
*
21575034 AAAAGAAAGAGAAAGAAGGA
1 AAAA-AAAGA-AAAAAAGGA
21575054 AAA
1 AAA
21575057 GTCAAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 11 0.55
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAGGA
Found at i:21577213 original size:50 final size:50
Alignment explanation
Indices: 21577116--21577290 Score: 164
Period size: 49 Copynumber: 3.6 Consensus size: 50
21577106 TAGCACCATG
* *
21577116 AAACACGAAGGGAAAGATCTAAGACCGCAACGGAGGATCCAGTACCACAA
1 AAACACGAAGGGAAAGATCTAAGACCGCAACGGAGAATCCAATACCACAA
** * * *
21577166 AGATACAC-AAGGGAAAGATCTAAG-TTGGAACGGTGAATCCAATACCACGA
1 A-A-ACACGAAGGGAAAGATCTAAGACCGCAACGGAGAATCCAATACCACAA
* * *
21577216 AAACACGAAGGGAAAGATCTAAG-CCGCAAC-GACGGATCCAGTACCGCAA
1 AAACACGAAGGGAAAGATCTAAGACCGCAACGGA-GAATCCAATACCACAA
** *
21577265 CGACA-AAAGGGAAAGATCTAAG-CCGC
1 AAACACGAAGGGAAAGATCTAAGACCGC
21577291 GATGGTGGAT
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
48 25 0.24
49 36 0.35
50 21 0.20
51 17 0.17
52 4 0.04
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (50 bp):
AAACACGAAGGGAAAGATCTAAGACCGCAACGGAGAATCCAATACCACAA
Found at i:21577287 original size:48 final size:47
Alignment explanation
Indices: 21577123--21577317 Score: 176
Period size: 48 Copynumber: 4.0 Consensus size: 47
21577113 ATGAAACACG
*
21577123 AAGGGAAAGATCTAAGACCGCAACGGA-GGATCCAGTACCACAAAGATACAC
1 AAGGGAAAGATCTAAG-CCGCAAC-GATGGATCCAGTACCAC-AAG--ACAA
** * * * * * *
21577174 AAGGGAAAGATCTAAGTTGGAACGGTGAATCCAATACCACGAAAACACG
1 AAGGGAAAGATCTAAGCCGCAACGATGGATCCAGTACCAC-AAGACA-A
* *
21577223 AAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCGCAACGACAA
1 AAGGGAAAGATCTAAGCCGCAACGATGGATCCAGTACCACAA-GACAA
* * *
21577271 AAGGGAAAGATCTAAGCCGCGATGGTGGATCCAGTACCACGAAGACA
1 AAGGGAAAGATCTAAGCCGCAACGATGGATCCAGTACCAC-AAGACA
21577318 CAAGCGGTGG
Statistics
Matches: 116, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
48 44 0.38
49 38 0.33
50 18 0.16
51 16 0.14
ACGTcount: A:0.41, C:0.23, G:0.26, T:0.11
Consensus pattern (47 bp):
AAGGGAAAGATCTAAGCCGCAACGATGGATCCAGTACCACAAGACAA
Found at i:21577309 original size:97 final size:99
Alignment explanation
Indices: 21577116--21577318 Score: 270
Period size: 97 Copynumber: 2.1 Consensus size: 99
21577106 TAGCACCATG
*
21577116 AAACACGAAGGGAAAGATCTAAGACCGCAACGGAGGATCCAGTACCACAAAGATACACAAGGGAA
1 AAACACGAAGGGAAAGATCTAAGACCGCAACGGAGGATCCAGTACCACAAAGA-ACAAAAGGGAA
**
21577181 AGATCTAAGTTGGAACGGTGAATCCAATACCACGA
65 AGATCTAAGCCGGAACGGTGAATCCAATACCACGA
* *
21577216 AAACACGAAGGGAAAGATCTAAG-CCGCAAC-GACGGATCCAGTACCGCAACG-ACAAAAGGGAA
1 AAACACGAAGGGAAAGATCTAAGACCGCAACGGA-GGATCCAGTACCACAAAGAACAAAAGGGAA
* * *
21577278 AGATCTAAGCCGCG-ATGGTGGATCCAGTACCACGA
65 AGATCTAAGCCG-GAACGGTGAATCCAATACCACGA
*
21577313 AGACAC
1 AAACAC
21577319 AAGCGGTGGA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
97 43 0.47
98 3 0.03
99 23 0.25
100 23 0.25
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (99 bp):
AAACACGAAGGGAAAGATCTAAGACCGCAACGGAGGATCCAGTACCACAAAGAACAAAAGGGAAA
GATCTAAGCCGGAACGGTGAATCCAATACCACGA
Found at i:21577369 original size:125 final size:126
Alignment explanation
Indices: 21577208--21577435 Score: 350
Period size: 125 Copynumber: 1.8 Consensus size: 126
21577198 GTGAATCCAA
* *
21577208 TACCACGAAAACACGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCGCAACGACAAAA
1 TACCACGAAAACACGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACAAAGACAAAA
* * *
21577273 GGGAAAGATCTAAGCCGCGATGGTGGATCCAGTACCACGAAGACACAAGCGGTGGATCTAG
66 GGGAAAGATCTAAGCCACAATGGCGGATCCAGTACCACGAAGACACAAGCGGTGGATCTAG
* * * * *
21577334 TACCACGAAGACA-TAAGGGAAAGATTTAAGCCGCAACGGCGGATCCAGTACCACAAAGACACAA
1 TACCACGAAAACACGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACAAAGACAAAA
*
21577398 GGGAAATATCTAAGCCACAATGGCGGATCCAGTACCAC
66 GGGAAAGATCTAAGCCACAATGGCGGATCCAGTACCAC
21577436 AAAAACATGA
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
125 79 0.87
126 12 0.13
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (126 bp):
TACCACGAAAACACGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACAAAGACAAAA
GGGAAAGATCTAAGCCACAATGGCGGATCCAGTACCACGAAGACACAAGCGGTGGATCTAG
Found at i:21577378 original size:77 final size:77
Alignment explanation
Indices: 21577249--21577398 Score: 212
Period size: 77 Copynumber: 1.9 Consensus size: 77
21577239 CCGCAACGAC
* * * * *
21577249 GGATCCAGTACCGCAACGACAAAAGGGAAAGATCTAAGCCGCGATGGTGGATCCAGTACCACGAA
1 GGATCCAGTACCACAACGACAAAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAA
21577314 GACACAAGCGGT
66 GACACAAGCGGT
* * *
21577326 GGATCTAGTACCACGAA-GACATAAGGGAAAGATTTAAGCCGCAACGGCGGATCCAGTACCACAA
1 GGATCCAGTACCAC-AACGACAAAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAA
21577390 AGACACAAG
65 AGACACAAG
21577399 GGAAATATCT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 62 0.97
78 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (77 bp):
GGATCCAGTACCACAACGACAAAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAA
GACACAAGCGGT
Found at i:21577538 original size:48 final size:48
Alignment explanation
Indices: 21577326--21577538 Score: 273
Period size: 48 Copynumber: 4.4 Consensus size: 48
21577316 CACAAGCGGT
* * *
21577326 GGATCTAGTACCACGAAGACATAAGGGAAAGATTTAAGCCGCAACGGC
1 GGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCCGCAACGGC
* * * *
21577374 GGATCCAGTACCACAAAGACACAAGGGAAATATCTAAGCCACAATGGC
1 GGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCCGCAACGGC
* * * *
21577422 GGATCCAGTACCACAAAAACATGACGGGAAAGATCTAAGACCGCAACGGC
1 GGATCCAGTACCACGAAGACA-CAAGGGAAAGATCTAAG-CCGCAACGGC
* * *
21577472 GGATCCAGTATCGCGAAGACACAAGGGAAAGATTTAAGCCGCAACGGC
1 GGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCCGCAACGGC
*
21577520 GGATCCAGTACCATGAAGA
1 GGATCCAGTACCACGAAGA
21577539 TTTGAAGGGA
Statistics
Matches: 140, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
48 87 0.62
49 28 0.20
50 25 0.18
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.13
Consensus pattern (48 bp):
GGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCCGCAACGGC
Found at i:21577549 original size:98 final size:97
Alignment explanation
Indices: 21577316--21577569 Score: 303
Period size: 98 Copynumber: 2.6 Consensus size: 97
21577306 ACCACGAAGA
* * *
21577316 CACAAGCGGTGGATCTAGTACCACGAAGACAT-AAGGGAAAGATTTAAGCCGCAACGGCGGATCC
1 CACAA-CGGCGGATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCC
*
21577380 AGTACCACAAAGACACAAGGGAAATATCTAAGC
65 AGTACCACAAAGACACAAGGGAAAGATCTAAGC
* * * *
21577413 CACAATGGCGGATCCAGTACCACAAAAACATGACGGGAAAGATCTAAGACCGCAACGGCGGATCC
1 CACAACGGCGGATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCC
* * * *
21577478 AGTATCGCGAAGACACAAGGGAAAGATTTAAGC
65 AGTACCACAAAGACACAAGGGAAAGATCTAAGC
* * ** * * * *
21577511 CGCAACGGCGGATCCAGTACCATGAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGGCG
1 CACAACGGCGGATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCG
21577570 AACTCGGTAC
Statistics
Matches: 131, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
96 21 0.16
97 28 0.21
98 82 0.63
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (97 bp):
CACAACGGCGGATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCA
GTACCACAAAGACACAAGGGAAAGATCTAAGC
Found at i:21577861 original size:102 final size:101
Alignment explanation
Indices: 21577669--21578266 Score: 908
Period size: 101 Copynumber: 5.9 Consensus size: 101
21577659 ACAATGACAT
21577669 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAATTCCTATCCTCTT
1 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAATTCCTATCCTCTT
* *
21577734 GAAGTTGTAGTAAAGTTGGATTAAAAATAATAGCAA
66 GAAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAA
* *
21577770 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTTCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTC-AACATCAATTCCTATCCTCT
* *
21577835 TGAAGTTGTAGTAAAGTTGGGTTAAAAACAATAGCAA
65 TGAAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAA
* * *
21577872 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAACTTCAGACATCAATTCCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCA-ACATCAATTCCTATCCTCT
* *
21577937 TGAAGTTGCAATAAAGTTGGATTAAAAACAATGGCAA
65 TGAAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAA
* * * * *
21577974 GTCTTTATCTCTCTAAAGTTACAGTAAGAGAAAGATGAAGCTTTAACGTCAATTCCTATCCTCTT
1 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAATTCCTATCCTCTT
*
21578039 GAAGTTGCAGTAAAGTTGGATTAAAAACAATGGCAA
66 GAAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAA
* * **
21578075 GTCTTTATCTCTCCGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACGCCAATTCCTATCCTCTT
1 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAATTCCTATCCTCTT
*
21578140 GAAGTTGCAGTAAAGTTGGATTAAAAATAATAGCAA
66 GAAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAA
* * * * * *
21578176 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCATCAACATCAAATCCTATCTTCCT
1 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAATTCCTATCCTCTT
**
21578241 GAAGTTGCAGCGAAGTTGGATTAAAA
66 GAAGTTGCAGTAAAGTTGGATTAAAA
21578267 CTACTGCAGC
Statistics
Matches: 456, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
101 271 0.59
102 185 0.41
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (101 bp):
GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAATTCCTATCCTCTT
GAAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAA
Found at i:21578373 original size:39 final size:40
Alignment explanation
Indices: 21578321--21578399 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 40
21578311 AGTGAAGTTA
* *
21578321 CATCATCAACCAATCTCTTACCCCGAGCCT-GGGGCAGAT
1 CATCATCAACCAATCTCCTACCCCAAGCCTAGGGGCAGAT
21578360 CATCATCAACCAATCTCCTACCCCAAGCCTAGGGGCAGAT
1 CATCATCAACCAATCTCCTACCCCAAGCCTAGGGGCAGAT
21578400 TGTAGTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 28 0.76
40 9 0.24
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (40 bp):
CATCATCAACCAATCTCCTACCCCAAGCCTAGGGGCAGAT
Found at i:21578827 original size:17 final size:17
Alignment explanation
Indices: 21578802--21578905 Score: 109
Period size: 17 Copynumber: 6.1 Consensus size: 17
21578792 ACTTTTAATT
*
21578802 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
* *
21578819 TTTTGAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
21578836 TTTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
* * *
21578853 TGTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
21578870 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
* * *
21578887 TTTTGAATTAAAAATTA
1 TTTTAAATTTAAATTTA
21578904 TT
1 TT
21578906 AATATTAAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 70 1.00
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:21578840 original size:34 final size:34
Alignment explanation
Indices: 21578802--21578905 Score: 136
Period size: 34 Copynumber: 3.1 Consensus size: 34
21578792 ACTTTTAATT
* *
21578802 TTTTAAATTTTAATTTATTTTGAATTTGAATTTA
1 TTTTAAATTTAAATTTATTTTGAATTTAAATTTA
* * *
21578836 TTTTAAATTTAAATTCATGTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTATTTTGAATTTAAATTTA
* * *
21578870 TTTTAAATTTGAATTTATTTTGAATTAAAAATTA
1 TTTTAAATTTAAATTTATTTTGAATTTAAATTTA
21578904 TT
1 TT
21578906 AATATTAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.57
Consensus pattern (34 bp):
TTTTAAATTTAAATTTATTTTGAATTTAAATTTA
Found at i:21579575 original size:16 final size:16
Alignment explanation
Indices: 21579556--21579613 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
21579546 ATTAATAATA
* *
21579556 AACAGTAGTAATTATT
1 AACAGTAATAAATATT
*
21579572 AACATTAATAAATATT
1 AACAGTAATAAATATT
*
21579588 AAC---AAT-AATAAT
1 AACAGTAATAAATATT
21579600 AACAGTAATAAATA
1 AACAGTAATAAATA
21579614 CAATAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
15 3 0.09
16 20 0.59
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (16 bp):
AACAGTAATAAATATT
Found at i:21579599 original size:3 final size:3
Alignment explanation
Indices: 21579577--21579651 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
21579567 TTATTAACAT
* * * * *
21579577 TAA TAAA TAT TAA CAA TAA TAA TAA CAG TAA TAA -ATA CAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
21579623 TAA TAA TAA TAA TAA TAAA TGAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
21579652 AAAAGGAAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
2 1 0.02
3 47 0.81
4 10 0.17
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:21579602 original size:12 final size:12
Alignment explanation
Indices: 21579582--21579651 Score: 70
Period size: 12 Copynumber: 5.7 Consensus size: 12
21579572 AACATTAATA
*
21579582 AATATTAACAAT
1 AATAATAACAAT
*
21579594 AATAATAACAGT
1 AATAATAACAAT
21579606 AATAA-ATACAAT
1 AATAATA-ACAAT
*
21579618 AATAATAATAAT
1 AATAATAACAAT
*
21579630 AATAATAATAAAT
1 AATAATAA-CAAT
21579643 GAATAATAA
1 -AATAATAA
21579652 AAAAGGAAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
11 1 0.02
12 36 0.73
13 4 0.08
14 8 0.16
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (12 bp):
AATAATAACAAT
Found at i:21580875 original size:30 final size:30
Alignment explanation
Indices: 21580773--21580867 Score: 147
Period size: 30 Copynumber: 3.2 Consensus size: 30
21580763 AAACTATCCA
21580773 AAAATTATATTTTGACCCTCAAACTTCTCT
1 AAAATTATATTTTGACCCTCAAACTTCTCT
* *
21580803 AAAATTATGTTTTGACCCCCAAACTTCTCT
1 AAAATTATATTTTGACCCTCAAACTTCTCT
* *
21580833 AAAATTATATTTTGACCCTCGAA-TTTTCT
1 AAAATTATATTTTGACCCTCAAACTTCTCT
21580862 AAAATT
1 AAAATT
21580868 TACATTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 11 0.19
30 48 0.81
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAATTATATTTTGACCCTCAAACTTCTCT
Found at i:21580904 original size:59 final size:59
Alignment explanation
Indices: 21580842--21580955 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
21580832 TAAAATTATA
* ** * *
21580842 TTTTGACCCTCGAATTTTCTAAAATTTACATTTTTACTCCTAACCTTTCCAAAATCCCAT
1 TTTTGA-CCTCGAATTTTCCAAAAAATACATTTTTACCCCTAAACTTTCCAAAATCCCAT
* * *
21580902 TTTTGACCTTGATTTTTCCAAAAAATACTTTTTTACCCCTAAACTTTCCAAAAT
1 TTTTGACCTCGAATTTTCCAAAAAATACATTTTTACCCCTAAACTTTCCAAAAT
21580956 TCCTGATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 40 0.87
60 6 0.13
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (59 bp):
TTTTGACCTCGAATTTTCCAAAAAATACATTTTTACCCCTAAACTTTCCAAAATCCCAT
Found at i:21580983 original size:48 final size:48
Alignment explanation
Indices: 21580911--21581006 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
21580901 TTTTTGACCT
*
21580911 TGATTTTTCCAAAAAATACTTTTTTACC-CCTAAACTTTCCAAAATTCC
1 TGATTTTTCCAAAAAATACATTTTTACCTCC-AAACTTTCCAAAATTCC
*
21580959 TGATTTTTCCAAAAATTACATTTTTACCTCCAAACTTTCCAAAATTCC
1 TGATTTTTCCAAAAAATACATTTTTACCTCCAAACTTTCCAAAATTCC
21581007 ATTTTAACCC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (48 bp):
TGATTTTTCCAAAAAATACATTTTTACCTCCAAACTTTCCAAAATTCC
Found at i:21581009 original size:29 final size:28
Alignment explanation
Indices: 21580964--21581159 Score: 137
Period size: 29 Copynumber: 6.7 Consensus size: 28
21580954 ATTCCTGATT
*
21580964 TTTCCAAAAATTACATTTTTACCTCCAAAC
1 TTTCC-AAAATTCCATTTTTACC-CCAAAC
* **
21580994 TTTCCAAAATTCCATTTTAACCCCAATTT
1 TTTCCAAAATTCCATTTTTACCCCAA-AC
* * *
21581023 TTTCAAAAATTGCATTTTTACCCCTGAAC
1 TTTCCAAAATTCCATTTTTACCCC-AAAC
* *
21581052 -TTCTAAAAATTACATTTTTACCCCCAAAC
1 TTTC-CAAAATTCCATTTTTA-CCCCAAAC
* * * * **
21581081 TTTCTAAAATTTCATTTTTGATCCCGATT
1 TTTCCAAAATTCCATTTTT-ACCCCAAAC
21581110 TTTCCCAAAATTACCA-TTTTACCCCAGAAC
1 TTT-CCAAAATT-CCATTTTTACCCCA-AAC
21581140 -TTCCTAAAATTCCATTTTTA
1 TTTCC-AAAATTCCATTTTTA
21581160 ATCCTGTTTT
Statistics
Matches: 131, Mismatches: 24, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
28 12 0.09
29 91 0.69
30 26 0.20
31 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTCCAAAATTCCATTTTTACCCCAAAC
Found at i:21581041 original size:107 final size:106
Alignment explanation
Indices: 21580856--21581053 Score: 247
Period size: 106 Copynumber: 1.9 Consensus size: 106
21580846 GACCCTCGAA
* * * * ***
21580856 TTTTCTAAAATTTACATTTTTACTCCTAACCTTTCCAAAATCCCATTTTTGACCTTGATTTTTCC
1 TTTTCCAAAAATTACATTTTTACTCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTTTCC
21580921 AAAAAATACTTTTTTACCCCTAAACTTTCCAAAATTCCTGAT
66 AAAAAATAC-TTTTTACCCCTAAACTTTCCAAAATTCCTGAT
* *
21580963 TTTTCCAAAAATTACATTTTTACCTCC-AAACTTTCCAAAATTCCA-TTTTAACCCCAATTTTTT
1 TTTTCCAAAAATTACATTTTTA-CTCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTTTC
* * *
21581026 CAAAAATTGCATTTTTACCCCTGAACTT
65 CAAAAAATAC-TTTTTACCCCTAAACTT
21581054 CTAAAAATTA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 37 0.48
107 36 0.47
108 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (106 bp):
TTTTCCAAAAATTACATTTTTACTCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTTTCC
AAAAAATACTTTTTACCCCTAAACTTTCCAAAATTCCTGAT
Found at i:21581183 original size:60 final size:58
Alignment explanation
Indices: 21581056--21581246 Score: 187
Period size: 59 Copynumber: 3.2 Consensus size: 58
21581046 CTGAACTTCT
*
21581056 AAAAATTA-CATTTTTACCCCCA-AACTTTCTAAAATTTCATTTTTGATCCCGATTTTTCC
1 AAAAATTACCA-TTTTA-CCCCAGAAC-TTCTAAAATTTCATTTTTAATCCCGATTTTTCC
* * * * *
21581115 CAAAATTACCATTTTACCCCAGAACTTCCTAAAATTCCATTTTTAATCCTGTTTTTTTTC
1 AAAAATTACCATTTTACCCCAGAACTT-CTAAAATTTCATTTTTAATCCCG-ATTTTTCC
* *
21581175 AAAAATTACAATTTTACCCTC-GAA-TGTCTAAAATTTCATTTTTAA-CCTCGAACTTTTCC
1 AAAAATTACCATTTTACCC-CAGAACT-TCTAAAATTTCATTTTTAATCC-CG-ATTTTTCC
21581234 -AAAATTACCATTT
1 AAAAATTACCATTT
21581247 GCTCCCGGGT
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
58 21 0.19
59 59 0.54
60 29 0.26
61 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCAGAACTTCTAAAATTTCATTTTTAATCCCGATTTTTCC
Found at i:21587300 original size:98 final size:98
Alignment explanation
Indices: 21587124--21587301 Score: 297
Period size: 98 Copynumber: 1.8 Consensus size: 98
21587114 AACCTTGGAA
* * *
21587124 AAGGGTATTCGATTATCCCGATTTGAAGAAAAGTTGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCAGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
21587189 AAACCAAAGATAAAAAAAACATTGCCTCTTTTT
66 AAACCAAAGATAAAAAAAACATTGCCTCTTTTT
21587222 AAGGGTATTCGATTATCACAG-TTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGGTATTCGATTATC-CAGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
21587286 AAAACCCAAA-ATAAAA
65 AAAA-CCAAAGATAAAA
21587302 GAATATTGCC
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
98 68 0.91
99 7 0.09
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (98 bp):
AAGGGTATTCGATTATCCAGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAAAGATAAAAAAAACATTGCCTCTTTTT
Found at i:21587320 original size:98 final size:98
Alignment explanation
Indices: 21587124--21587321 Score: 294
Period size: 98 Copynumber: 2.0 Consensus size: 98
21587114 AACCTTGGAA
* * *
21587124 AAGGGTATTCGATTATCCCGATTTGAAGAAAAGTTGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCAGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
*
21587189 AAACCAAAGATAAAAAAAACATTGCCTCTTTTT
66 AAACCAAAGATAAAAAAAACATTGCCTCATTTT
21587222 AAGGGTATTCGATTATCACAG-TTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGGTATTCGATTATC-CAGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
* *
21587286 AAAACCCAAA-AT-AAAAGAATATTGCCTCGATTTT
65 AAAA-CCAAAGATAAAAAAAACATTGCCTC-ATTTT
21587320 AA
1 AA
21587322 ATATTTTGGA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
97 14 0.15
98 70 0.77
99 7 0.08
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (98 bp):
AAGGGTATTCGATTATCCAGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAAAGATAAAAAAAACATTGCCTCATTTT
Found at i:21587640 original size:29 final size:28
Alignment explanation
Indices: 21587608--21587919 Score: 123
Period size: 29 Copynumber: 10.7 Consensus size: 28
21587598 GAAAGTTTTA
* *
21587608 AGGGTAAAAATGTCATTTTGGGAAAATTC
1 AGGGTAAAAATGTGATTTTTGG-AAATTC
* **
21587637 AGGGT-AAAACGTGATTTTTGGAGGTTC
1 AGGGTAAAAATGTGATTTTTGGAAATTC
* *
21587664 GGGGTAAAATATGTGATTTTTGGAAGATTA
1 AGGGTAAAA-ATGTGATTTTTGGAA-ATTC
* *
21587694 AGGGGCAAAAATGT-ACTTTTTGGAAGTTC
1 A-GGGTAAAAATGTGA-TTTTTGGAAATTC
*
21587723 AAGGGTAAAAATGTAATTTTT-GAAAGTTC
1 -AGGGTAAAAATGTGATTTTTGGAAA-TTC
* * * *
21587752 GGGGGCAAAAATGTAATTTTTGAGAAGCTT-
1 -AGGGTAAAAATGTGATTTTTG-GAA-ATTC
* * *
21587782 GGGGT-AAAATGTAATTTTTGAGAAGTT-
1 AGGGTAAAAATGTGATTTTTG-GAAATTC
* * * * * *
21587809 TGGAGCCAAAAAAGTAATTTTTGAGAAGTTT
1 AGG-G-TAAAAATGTGATTTTTG-GAAATTC
* * * * * *
21587840 GGGGCAAAAATGTAATTTTTAAGAAGTTTA
1 AGGGTAAAAATGTGATTTTT-GGAA-ATTC
* * *
21587870 AGGGTAAAAATGTAATTTTTGAGAAGTTT
1 AGGGTAAAAATGTGATTTTTG-GAAATTC
*
21587899 AGGGGTAAAAATGTAATTTTT
1 A-GGGTAAAAATGTGATTTTT
21587920 AGAAGTTTAA
Statistics
Matches: 229, Mismatches: 35, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
27 12 0.05
28 39 0.17
29 83 0.36
30 81 0.35
31 14 0.06
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (28 bp):
AGGGTAAAAATGTGATTTTTGGAAATTC
Found at i:21587923 original size:29 final size:30
Alignment explanation
Indices: 21587664--21588049 Score: 395
Period size: 29 Copynumber: 13.1 Consensus size: 30
21587654 TTGGAGGTTC
* * *
21587664 GGGGTAAAATATGTGATTTTTG-GAAGATTAA
1 GGGGCAAAA-ATGTAATTTTTGAGAAG-TTTA
* *
21587695 GGGGCAAAAATGTACTTTTTG-GAAGTTCA
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
* * **
21587724 AGGGTAAAAATGTAATTTTTGA-AAGTTCG
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
*
21587753 GGGGCAAAAATGTAATTTTTGAGAAGCTT-
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
*
21587782 GGGG-TAAAATGTAATTTTTGAGAAGTTT-
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
* *
21587810 GGAGCCAAAAAAGTAATTTTTGAGAAGTTT-
1 GG-GGCAAAAATGTAATTTTTGAGAAGTTTA
*
21587840 GGGGCAAAAATGTAATTTTTAAGAAGTTTA
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
* *
21587870 AGGGTAAAAATGTAATTTTTGAGAAGTTTA
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
*
21587900 GGGGTAAAAATGTAATTTTT-AGAAGTTTA
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
* *
21587929 AGAGCAAAAATGTAATTTTTGAGAAGTTT-
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
*
21587958 GACGGC-AAAATGTAATTTTTGAGAAGTTTA
1 G-GGGCAAAAATGTAATTTTTGAGAAGTTTA
* * *
21587988 GGGACAAAAATGTAA-TTTTGAAAAGTATA
1 GGGGCAAAAATGTAATTTTTGAGAAGTTTA
*
21588017 GGGATCAAAATATG--ATTTTTG-GATAGTTTA
1 GGG-GCAAAA-ATGTAATTTTTGAGA-AGTTTA
21588047 GGG
1 GGG
21588050 ACCTCTTGGG
Statistics
Matches: 305, Mismatches: 37, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.08
29 144 0.47
30 126 0.41
31 11 0.04
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTTTTGAGAAGTTTA
Found at i:21588026 original size:59 final size:58
Alignment explanation
Indices: 21587665--21588051 Score: 355
Period size: 59 Copynumber: 6.6 Consensus size: 58
21587655 TGGAGGTTCG
* * * * *
21587665 GGGTAAAATATGTGATTTTTG-GAAGATTAAGGGGCAAAAATGTACTTTTTG-GAAGTTCAA
1 GGGTCAAA-ATGTAATTTTTGAGAAG-TTTAGGGACAAAAATGTAATTTTTGAGAAGTT--A
* ** * *
21587725 GGGTAAAAATGTAATTTTTGA-AAGTTCGGGGGCAAAAATGTAATTTTTGAGAAGCTTG
1 GGGTCAAAATGTAATTTTTGAGAAGTTTAGGGACAAAAATGTAATTTTTGAGAAG-TTA
* * *
21587783 GGGT-AAAATGTAATTTTTGAGAAGTTT-GGAGCCAAAAAAGTAATTTTTGAGAAGTTT
1 GGGTCAAAATGTAATTTTTGAGAAGTTTAGG-GACAAAAATGTAATTTTTGAGAAGTTA
* * *
21587840 GGGGCAAAAATGTAATTTTTAAGAAGTTTAAGGG-TAAAAATGTAATTTTTGAGAAGTTTA
1 GGGTC-AAAATGTAATTTTTGAGAAGTTT-AGGGACAAAAATGTAATTTTTGAGAAG-TTA
* *
21587900 GGGGTAAAAATGTAATTTTT-AGAAGTTTA-AGAGCAAAAATGTAATTTTTGAGAAGTTTGA
1 -GGGTCAAAATGTAATTTTTGAGAAGTTTAGGGA-CAAAAATGTAATTTTTGAGAAG-TT-A
* *
21587960 CGG-CAAAATGTAATTTTTGAGAAGTTTAGGGACAAAAATGTAA-TTTTGAAAAGTATA
1 GGGTCAAAATGTAATTTTTGAGAAGTTTAGGGACAAAAATGTAATTTTTGAGAAGT-TA
* *
21588017 GGGATCAAAATATGATTTTTG-GATAGTTTAGGGAC
1 GGG-TCAAAATGTAATTTTTGAGA-AGTTTAGGGAC
21588052 CTCTTGGGCA
Statistics
Matches: 282, Mismatches: 25, Indels: 41
0.81 0.07 0.12
Matches are distributed among these distances:
57 28 0.10
58 80 0.28
59 139 0.49
60 30 0.11
61 5 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (58 bp):
GGGTCAAAATGTAATTTTTGAGAAGTTTAGGGACAAAAATGTAATTTTTGAGAAGTTA
Found at i:21589757 original size:26 final size:27
Alignment explanation
Indices: 21589709--21589759 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
21589699 AATTTAGAAT
21589709 AATTTAAATTTAAAAATAAATTTAACA
1 AATTTAAATTTAAAAATAAATTTAACA
21589736 AATTTAAATTT-AAAATAAATTTAA
1 AATTTAAATTTAAAAATAAATTTAA
21589760 AAAAGTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTTAAATTTAAAAATAAATTTAACA
Found at i:21595461 original size:27 final size:28
Alignment explanation
Indices: 21595431--21595487 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
21595421 ACCCTAAAGA
*
21595431 ACAAAG-CAAAACGTGCTAAACTAGCAG
1 ACAAAGACAAAACGAGCTAAACTAGCAG
* * *
21595458 ACAAAGAGAAAATGAGCTAAACTAGTAG
1 ACAAAGACAAAACGAGCTAAACTAGCAG
21595486 AC
1 AC
21595488 CAATTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.51, C:0.18, G:0.19, T:0.12
Consensus pattern (28 bp):
ACAAAGACAAAACGAGCTAAACTAGCAG
Found at i:21596662 original size:4 final size:4
Alignment explanation
Indices: 21596653--21596712 Score: 77
Period size: 4 Copynumber: 15.0 Consensus size: 4
21596643 AAATAAACAG
* * *
21596653 GAAA GAAA GAAA GAAA GAAA GAAA GAAG GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
21596701 GAAA GAAA GAAA
1 GAAA GAAA GAAA
21596713 TGTAATGTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 3 0.06
4 45 0.87
5 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21601022 original size:14 final size:13
Alignment explanation
Indices: 21601013--21601095 Score: 60
Period size: 14 Copynumber: 6.0 Consensus size: 13
21601003 AGGGTTTAGG
21601013 GTTTAAGGTTTTAA
1 GTTTAAGG-TTTAA
* * *
21601027 GTCTAAGATTTATG
1 GTTTAAGGTTTA-A
21601041 GTTTAAGGTTTCAA
1 GTTTAAGGTTT-AA
21601055 GTTT-AGTGTTTATA
1 GTTTAAG-GTTTA-A
*
21601069 GTTTAAGGTTTAG
1 GTTTAAGGTTTAA
*
21601082 GTTTTAGGGTTTAA
1 G-TTTAAGGTTTAA
21601096 TGTTATGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
13 8 0.15
14 43 0.80
15 3 0.06
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.48
Consensus pattern (13 bp):
GTTTAAGGTTTAA
Found at i:21601028 original size:28 final size:28
Alignment explanation
Indices: 21600992--21601079 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
21600982 TTTTAAAAAT
*
21600992 GTTTCAAGTCTAGGGTTTAGGGTTTAAG
1 GTTTCAAGTCTAGGGTTTATGGTTTAAG
* * *
21601020 GTTTTAAGTCTAAGATTTATGGTTTAAG
1 GTTTCAAGTCTAGGGTTTATGGTTTAAG
* * *
21601048 GTTTCAAGTTTAGTGTTTATAGTTTAAG
1 GTTTCAAGTCTAGGGTTTATGGTTTAAG
21601076 GTTT
1 GTTT
21601080 AGGTTTTAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.24, C:0.05, G:0.25, T:0.47
Consensus pattern (28 bp):
GTTTCAAGTCTAGGGTTTATGGTTTAAG
Found at i:21601087 original size:28 final size:28
Alignment explanation
Indices: 21600992--21601094 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 28
21600982 TTTTAAAAAT
* **
21600992 GTTTCAAGTCTAGGGTTTAGGGTTTAAG
1 GTTTCAAGTTTAGGGTTTATAGTTTAAG
* * * * *
21601020 GTTTTAAGTCTAAGATTTATGGTTTAAG
1 GTTTCAAGTTTAGGGTTTATAGTTTAAG
*
21601048 GTTTCAAGTTTAGTGTTTATAGTTTAAG
1 GTTTCAAGTTTAGGGTTTATAGTTTAAG
*
21601076 GTTT-AGGTTTTAGGGTTTA
1 GTTTCAAG-TTTAGGGTTTA
21601095 ATGTTATGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
27 2 0.03
28 60 0.97
ACGTcount: A:0.23, C:0.04, G:0.26, T:0.47
Consensus pattern (28 bp):
GTTTCAAGTTTAGGGTTTATAGTTTAAG
Found at i:21601349 original size:21 final size:21
Alignment explanation
Indices: 21601320--21601380 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
21601310 GTCCATTTGC
21601320 CCCGA-AGGAGTAGAGTATTG
1 CCCGAGAGGAGTAGAGTATTG
* *
21601340 CTCGGGAGGAGTAGAGTATTG
1 CCCGAGAGGAGTAGAGTATTG
21601361 CCCGAGAGGAGTAGAGTATT
1 CCCGAGAGGAGTAGAGTATT
21601381 TCGATGGCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 3 0.08
21 33 0.92
ACGTcount: A:0.28, C:0.13, G:0.38, T:0.21
Consensus pattern (21 bp):
CCCGAGAGGAGTAGAGTATTG
Found at i:21601423 original size:45 final size:45
Alignment explanation
Indices: 21601374--21601465 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
21601364 GAGAGGAGTA
* * *
21601374 GAGTATTTCGATGGCTCGTCAAACTGAGGCTGATATGCTTTGCTT
1 GAGTATTGCGATGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
* *
21601419 GAGTATTGCGGTGGCTCGTCAAACTGAGGTTGATATCCTTGGCTT
1 GAGTATTGCGATGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
21601464 GA
1 GA
21601466 TAAGCTATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (45 bp):
GAGTATTGCGATGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Found at i:21603432 original size:16 final size:16
Alignment explanation
Indices: 21603411--21603460 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
21603401 TGATGGAGAT
21603411 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
21603427 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
21603442 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
21603457 ATTA
1 ATTA
21603461 GCAAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:21603648 original size:13 final size:13
Alignment explanation
Indices: 21603630--21603655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21603620 TAAAAAATAT
21603630 TTAATATTTTATA
1 TTAATATTTTATA
21603643 TTAATATTTTATA
1 TTAATATTTTATA
21603656 ATTTTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATATTTTATA
Found at i:21603663 original size:13 final size:14
Alignment explanation
Indices: 21603630--21603658 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21603620 TAAAAAATAT
21603630 TTAATATTTTAT-A
1 TTAATATTTTATAA
21603643 TTAATATTTTATAA
1 TTAATATTTTATAA
21603657 TT
1 TT
21603659 TTATTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.80
14 3 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATATTTTATAA
Found at i:21604027 original size:20 final size:21
Alignment explanation
Indices: 21604002--21604044 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21603992 TCTTACTTAC
21604002 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
21604022 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
21604043 TA
1 TA
21604045 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:21604145 original size:23 final size:22
Alignment explanation
Indices: 21604119--21604196 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
21604109 CTATAACAAC
21604119 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAA-TAAAA
*
21604142 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAA-T-AACAAATCAATAAAA
* *
21604165 CTTAAAATAATCAAATTAACTAACAA
1 ATT-AAATAA-CAAATCAA-TAA-AA
21604191 ATTAAA
1 ATTAAA
21604197 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 4 0.09
25 14 0.33
26 4 0.09
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
ATTAAATAACAAATCAATAAAA
Found at i:21604414 original size:15 final size:16
Alignment explanation
Indices: 21604394--21604427 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21604384 CATTACATTT
21604394 TTCTCTTTC-CCCTTC
1 TTCTCTTTCTCCCTTC
*
21604409 TTCTCTTTCTTCCTTC
1 TTCTCTTTCTCCCTTC
21604425 TTC
1 TTC
21604428 CTTCTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCTCTTTCTCCCTTC
Found at i:21604436 original size:4 final size:4
Alignment explanation
Indices: 21604406--21604471 Score: 66
Period size: 4 Copynumber: 16.8 Consensus size: 4
21604396 CTCTTTCCCC
* *
21604406 TTCT TCTCT TTC- TTCC TTC- TTCC TTCT TTCT TTCT TTCT TTCT TTCT
1 TTCT T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
21604453 CTTAT TTCT TTCT TT-T TTC
1 -TTCT TTCT TTCT TTCT TTC
21604472 CTTCAAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
3 9 0.17
4 38 0.70
5 7 0.13
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:21604940 original size:33 final size:33
Alignment explanation
Indices: 21604902--21604968 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
21604892 AAGCAATTAC
*
21604902 TTTCTTGTGAAGTTGAAATCTTAACATTTATAA
1 TTTCTTATGAAGTTGAAATCTTAACATTTATAA
*
21604935 TTTCTTATGAAGTTGAAATCTTAACCTTTATAA
1 TTTCTTATGAAGTTGAAATCTTAACATTTATAA
21604968 T
1 T
21604969 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (33 bp):
TTTCTTATGAAGTTGAAATCTTAACATTTATAA
Found at i:21608261 original size:14 final size:15
Alignment explanation
Indices: 21608223--21608256 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21608213 AGGGTTAAAG
*
21608223 TTAAAAA-ATTTGTA
1 TTAAAAATATTTATA
21608237 TTAAAAATATTTATA
1 TTAAAAATATTTATA
21608252 TTAAA
1 TTAAA
21608257 TTATTAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAAAAATATTTATA
Found at i:21608360 original size:13 final size:13
Alignment explanation
Indices: 21608344--21608371 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21608334 TTAATTTTGG
21608344 AGAAAAATTATAA
1 AGAAAAATTATAA
21608357 AGAAAAATTATAA
1 AGAAAAATTATAA
21608370 AG
1 AG
21608372 CAATTTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (13 bp):
AGAAAAATTATAA
Found at i:21612203 original size:24 final size:24
Alignment explanation
Indices: 21612176--21612230 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
21612166 ACAATCCATT
21612176 CATTTTATATTACAGTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
* * *
21612200 CATTTTGTATTACATTTGCAGTGA
1 CATTTTATATTACAGTTGCACTGA
21612224 CAGTTTT
1 CA-TTTT
21612231 TACTCTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (24 bp):
CATTTTATATTACAGTTGCACTGA
Found at i:21622473 original size:24 final size:24
Alignment explanation
Indices: 21622446--21622500 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
21622436 ACAATCCATT
21622446 CATTTTATATTACAGTCGCACTGA
1 CATTTTATATTACAGTCGCACTGA
* * *
21622470 CATTTTGTATTACATTTGCACTGA
1 CATTTTATATTACAGTCGCACTGA
21622494 CAATTTT
1 C-ATTTT
21622501 TACTCTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (24 bp):
CATTTTATATTACAGTCGCACTGA
Found at i:21624493 original size:24 final size:24
Alignment explanation
Indices: 21624442--21624489 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21624432 AAAGTGGGCC
*
21624442 ATTAAATTAATTTAATAAAGCATG
1 ATTAAAATAATTTAATAAAGCATG
* *
21624466 ATTAAAATCATTTCATAAA-CATG
1 ATTAAAATAATTTAATAAAGCATG
21624489 A
1 A
21624490 ATTATTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (24 bp):
ATTAAAATAATTTAATAAAGCATG
Found at i:21624943 original size:7 final size:7
Alignment explanation
Indices: 21624931--21624959 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21624921 ACTTCTCAAT
21624931 TCATCCC
1 TCATCCC
21624938 TCATCCC
1 TCATCCC
21624945 TCATCCC
1 TCATCCC
21624952 TCATCCC
1 TCATCCC
21624959 T
1 T
21624960 TCATTGATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.55, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:21627779 original size:120 final size:120
Alignment explanation
Indices: 21627561--21627798 Score: 323
Period size: 120 Copynumber: 2.0 Consensus size: 120
21627551 ATATGCACAA
* * * *
21627561 ATACTGTATCGATGGCTGCGGTACCGCTTATGTTGCAAGTCCTTGATAGCTCGTGTAAGCAGCAT
1 ATACCGTATCGATGGCTGCGGTACCGCATATGTTGCAAGTCCTCGACAGCTCGTGTAAGCAGCAT
* * **
21627626 CGTATACTGGTAACAGAGTTGATACAGATATAAGAATGAAATTCGGGATTATACC
66 CGTATACTGGTAACAAAGTTGATACAGACATAAGAATGAAATTCAAGATTATACC
* * * * *
21627681 ATACCGTATCGATGGCTGGGGTACTGCATATGTTGCTAGTTCTCGACAGCTCGTGTGAGCAGCAT
1 ATACCGTATCGATGGCTGCGGTACCGCATATGTTGCAAGTCCTCGACAGCTCGTGTAAGCAGCAT
** * *
21627746 CGTATACTTTTAACAAAGTTGATATAGACATAAGGATGAAATTCAAGATTATA
66 CGTATACTGGTAACAAAGTTGATACAGACATAAGAATGAAATTCAAGATTATA
21627799 GCTTGTGGAA
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (120 bp):
ATACCGTATCGATGGCTGCGGTACCGCATATGTTGCAAGTCCTCGACAGCTCGTGTAAGCAGCAT
CGTATACTGGTAACAAAGTTGATACAGACATAAGAATGAAATTCAAGATTATACC
Found at i:21635269 original size:19 final size:20
Alignment explanation
Indices: 21635240--21635287 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
21635230 AATTTTCTAG
*
21635240 TTAATTTTTAAATTTTTATGT
1 TTAA-TTTTAAATTGTTATGT
*
21635261 TT-ATTTT-AATTGTTATTT
1 TTAATTTTAAATTGTTATGT
21635279 TTAATTTTA
1 TTAATTTTA
21635288 GTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 11 0.48
19 9 0.39
20 1 0.04
21 2 0.09
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTAATTTTAAATTGTTATGT
Found at i:21635298 original size:6 final size:6
Alignment explanation
Indices: 21635251--21635298 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
21635241 TAATTTTTAA
* * * * *
21635251 ATTTTT ATGTTT ATTTTA ATTGTT ATTTTT AATTTT AGTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
21635299 TTAATAAGAG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:21636720 original size:9 final size:9
Alignment explanation
Indices: 21636696--21636731 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
21636686 GTTCATGAGC
21636696 TGAACCAAA
1 TGAACCAAA
*
21636705 TTGAACCAAG
1 -TGAACCAAA
21636715 TGAACCAAA
1 TGAACCAAA
21636724 TGAACCAA
1 TGAACCAA
21636732 CAATCGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (9 bp):
TGAACCAAA
Found at i:21636729 original size:18 final size:19
Alignment explanation
Indices: 21636696--21636731 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21636686 GTTCATGAGC
21636696 TGAACCAAATTGAACCAAG
1 TGAACCAAATTGAACCAAG
21636715 TGAACCAAA-TGAACCAA
1 TGAACCAAATTGAACCAA
21636732 CAATCGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (19 bp):
TGAACCAAATTGAACCAAG
Found at i:21649069 original size:21 final size:22
Alignment explanation
Indices: 21649045--21649091 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
21649035 AGAAAAGATA
21649045 AAAAATGTATT-AAAAGCAGAG
1 AAAAATGTATTAAAAAGCAGAG
* * *
21649066 AAAACTGTGTTAAAAAGGAGAG
1 AAAAATGTATTAAAAAGCAGAG
21649088 AAAA
1 AAAA
21649092 CCGTGCTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.57, C:0.04, G:0.21, T:0.17
Consensus pattern (22 bp):
AAAAATGTATTAAAAAGCAGAG
Found at i:21649081 original size:22 final size:22
Alignment explanation
Indices: 21649056--21649110 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
21649046 AAAATGTATT
* *
21649056 AAAAGCAGAGAAAACTGTGTTA
1 AAAAGCAGAGAAAACCGTGCTA
*
21649078 AAAAGGAGAGAAAACCGTGCTA
1 AAAAGCAGAGAAAACCGTGCTA
*
21649100 AGAAGCAGAGA
1 AAAAGCAGAGA
21649111 TACCTAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.27, T:0.11
Consensus pattern (22 bp):
AAAAGCAGAGAAAACCGTGCTA
Found at i:21653783 original size:93 final size:93
Alignment explanation
Indices: 21653624--21653809 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
21653614 TTACCACTCG
*
21653624 ACGTTTCTATTCTCACACCAACAAGTGATTAAACCCCATGAATGGCTACTACCCGGTATATTTAT
1 ACGTTTCTATTCTCACACCAACAAGTGATTAAACCCCATGAATGGCTACCACCCGGTATATTTAT
*
21653689 TTATACATGCATATCTTTGTGAGCCTGA
66 TTATACATGCATATCTATGTGAGCCTGA
* **
21653717 ACGTTTCTATTCTCACACCAACAAGTGATTACACTTCATGAATGGCTACCACCCGGTATATTTAT
1 ACGTTTCTATTCTCACACCAACAAGTGATTAAACCCCATGAATGGCTACCACCCGGTATATTTAT
21653782 TTATACATGCATATCTATGTGAGCCTGA
66 TTATACATGCATATCTATGTGAGCCTGA
21653810 GAAAAAGAAC
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (93 bp):
ACGTTTCTATTCTCACACCAACAAGTGATTAAACCCCATGAATGGCTACCACCCGGTATATTTAT
TTATACATGCATATCTATGTGAGCCTGA
Found at i:21653871 original size:14 final size:15
Alignment explanation
Indices: 21653854--21653883 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
21653844 TATATGCCTT
21653854 TTCATATA-TGTATA
1 TTCATATAGTGTATA
21653868 TTCATATAGTGTATA
1 TTCATATAGTGTATA
21653883 T
1 T
21653884 CTGTAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (15 bp):
TTCATATAGTGTATA
Found at i:21665346 original size:14 final size:14
Alignment explanation
Indices: 21665327--21665356 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21665317 CTGAATATGA
21665327 GTACGTCTAATTCT
1 GTACGTCTAATTCT
*
21665341 GTACGTCTGATTCT
1 GTACGTCTAATTCT
21665355 GT
1 GT
21665357 GTATTCGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (14 bp):
GTACGTCTAATTCT
Found at i:21666235 original size:83 final size:83
Alignment explanation
Indices: 21666095--21666261 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
21666085 AGACATTTCA
*
21666095 TACATCTCATAAAGTATGTATATCAAATTGAACTAGCATACAAGATTATGTTCAACATTTAACTA
1 TACATCTCATAAAGTATGTATATCAAATTAAACTAGCATACAAGATTATGTTCAACATTTAACTA
21666160 AAATTCACAACAAGGAAT
66 AAATTCACAACAAGGAAT
* *
21666178 TACATCTCATAAAGTATGTATATCACATTAAACTAGCATACAAGATTATGTTTAACATTTAACTA
1 TACATCTCATAAAGTATGTATATCAAATTAAACTAGCATACAAGATTATGTTCAACATTTAACTA
21666243 AAATTCACAACAAGGAAT
66 AAATTCACAACAAGGAAT
21666261 T
1 T
21666262 CAATAATCCC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (83 bp):
TACATCTCATAAAGTATGTATATCAAATTAAACTAGCATACAAGATTATGTTCAACATTTAACTA
AAATTCACAACAAGGAAT
Found at i:21674037 original size:5 final size:5
Alignment explanation
Indices: 21674027--21674071 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
21674017 GACTAAATTG
*
21674027 AAAAT AAAAT AAAATT AACAAG AAAA- AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA-T AA-AAT AAAAT AAAAT AAAAT AAAAT AAAA
21674072 GGAATAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
4 4 0.11
5 25 0.69
6 5 0.14
7 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:21675087 original size:16 final size:14
Alignment explanation
Indices: 21675054--21675091 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
21675044 TTGGTTTTGG
21675054 TTTGGGT-TTGGTA
1 TTTGGGTATTGGTA
21675067 TTTGGGTATTGGGTAA
1 TTTGGGTATT-GGT-A
21675083 TTTGGGTAT
1 TTTGGGTAT
21675092 ATTTTGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 3 0.14
16 10 0.45
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (14 bp):
TTTGGGTATTGGTA
Found at i:21675654 original size:50 final size:50
Alignment explanation
Indices: 21675518--21675655 Score: 136
Period size: 50 Copynumber: 2.8 Consensus size: 50
21675508 AGGATTTTAC
* * *
21675518 ATTGTAACTTTATCTTGCTCCACTGCATCTTCAAGGAGATAGGACTTGCT
1 ATTGTAAATTTATCTTGCTCCACTGCATCTTCAGGGAGATAGGACTTGAT
* * * * * * * *
21675568 AATGT-AGTTTCAATC-CGATCCATTGCAGCTTCAGGGATATAGGATTTGAT
1 ATTGTAAATTT--ATCTTGCTCCACTGCATCTTCAGGGAGATAGGACTTGAT
*
21675618 GTTGTAAATTTATCTTGCTCCACTGCATCTTCAGGGAG
1 ATTGTAAATTTATCTTGCTCCACTGCATCTTCAGGGAG
21675656 GTAATATTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 8
0.72 0.20 0.09
Matches are distributed among these distances:
49 7 0.11
50 52 0.79
51 7 0.11
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (50 bp):
ATTGTAAATTTATCTTGCTCCACTGCATCTTCAGGGAGATAGGACTTGAT
Found at i:21675667 original size:100 final size:99
Alignment explanation
Indices: 21675519--21675853 Score: 341
Period size: 100 Copynumber: 3.4 Consensus size: 99
21675509 GGATTTTACA
* * * * * *
21675519 TTGTAACTTTATCTTGCTCCACTGCATCTTCAAGGAGATAGGACTTGCTAATGTAGTTTCAATCC
1 TTGTAACTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTACTGTAGTTTCAATCC
* *
21675584 GATCCATTGCAGCTTCAGGGATATAGGATTTGATG
66 GATCCA-TGCAACTTCAGGGATATAAGATTTGATG
* * * * * * * *
21675619 TTGTAAATTTATCTTGCTCCACTGCATCTTCAGGGAGGTAATATTTGCTTCTATAGCTTCAATCC
1 TTGTAACTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTACTGTAGTTTCAATCC
* *
21675684 GACCCACTACAACTTCAAGGG-TATAAGATTTGATG
66 GATCCA-TGCAACTTC-AGGGATATAAGATTTGATG
* * * * * *
21675719 TGGTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATAAAGATTTGCTACTGTAGCTTT-AAT
1 TTGTAACTTCATCTTGCTCCACTGCAACTTCAGGGAGAT-AAGATTTGCTACTGTAG-TTTCAAT
* * *
21675783 CCTATCTATGCAACTCCAGGGATATAAGATTTGATG
64 CCGATCCATGCAACTTCAGGGATATAAGATTTGATG
** *
21675819 TCATAACTTCATCTTGCTCCACTGTAACTTCAGGG
1 TTGTAACTTCATCTTGCTCCACTGCAACTTCAGGG
21675854 GTATAGGATT
Statistics
Matches: 189, Mismatches: 42, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
99 4 0.02
100 157 0.83
101 26 0.14
102 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (99 bp):
TTGTAACTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTACTGTAGTTTCAATCC
GATCCATGCAACTTCAGGGATATAAGATTTGATG
Found at i:21675912 original size:151 final size:151
Alignment explanation
Indices: 21675694--21675989 Score: 407
Period size: 151 Copynumber: 2.0 Consensus size: 151
21675684 GACCCACTAC
21675694 AACTTCAAGGGTATAAGATTTGATGTGGTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATA
1 AACTTCAAGGGTATAAGATTTGATGTGGTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATA
* * * * * *
21675759 AAGATTTGCTACTGTAGCTTTAATCCTATCTA-TGCAACTCCAGGGATATAAGATTTGATGTCAT
66 AAGAATTGCTACTGTAGCTTCAATCCAATCCACTACAACTCCAGGGATATAAGATTTGATATCAT
21675823 AACTTCATCTTGCTCCACTGT
131 AACTTCATCTTGCTCCACTGT
* * * * * *
21675844 AACTTCAGGGGTATAGGATTTGATTTTTGTAGCTTCATCTTGCTCTACTGCAACTTC-GAAGAGA
1 AACTTCAAGGGTATAAGATTTGA-TGTGGTAGCTTCATCTTACTCTACTACAACTTCAG-AGAGA
* * *
21675908 TAAAGAATTGCTTCTGTAGCTTCAATCCAATCCACTACAACTTCAGGGATATAAGATTTGATATT
64 TAAAGAATTGCTACTGTAGCTTCAATCCAATCCACTACAACTCCAGGGATATAAGATTTGATATC
**
21675973 ATTGCTTCATCTTGCTC
129 ATAACTTCATCTTGCTC
21675990 TATTGGATCT
Statistics
Matches: 126, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
150 22 0.17
151 63 0.50
152 41 0.33
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (151 bp):
AACTTCAAGGGTATAAGATTTGATGTGGTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATA
AAGAATTGCTACTGTAGCTTCAATCCAATCCACTACAACTCCAGGGATATAAGATTTGATATCAT
AACTTCATCTTGCTCCACTGT
Found at i:21676026 original size:151 final size:151
Alignment explanation
Indices: 21675721--21676031 Score: 365
Period size: 151 Copynumber: 2.1 Consensus size: 151
21675711 ATTTGATGTG
* * *
21675721 GTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATAAAGATTTGCTACTGTAGCTTTAATCCT
1 GTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATAAAGAATTGCTACTGTAGCTTCAATCCA
* * * *
21675786 ATCTATGCAACTCCAGGGATATAAGATTTGATGTCATAACTTCATCTTGCTCCACTGTAACTTCA
66 ATCCATACAACTCCAGGGATATAAGATTTGATATCATAACTTCATCTTGCTCCACTGGAACTTCA
** * * **
21675851 GGGGTATAGGATTTGATTTTT
131 GGGAAATAAGATTTGACTAAT
* * *
21675872 GTAGCTTCATCTTGCTCTACTGCAACTTC-GAAGAGATAAAGAATTGCTTCTGTAGCTTCAATCC
1 GTAGCTTCATCTTACTCTACTACAACTTCAG-AGAGATAAAGAATTGCTACTGTAGCTTCAATCC
* * ** * * *
21675936 AATCCACTACAACTTCAGGGATATAAGATTTGATATTATTGCTTCATCTTGCTCTATTGGATCTT
65 AATCCA-TACAACTCCAGGGATATAAGATTTGATATCATAACTTCATCTTGCTCCACTGGAACTT
*
21676001 TAGGGAAATAAGATTTG-CTAAT
129 CAGGGAAATAAGATTTGACTAAT
*
21676023 GTAGTTTCA
1 GTAGCTTCA
21676032 ATTTGATCCA
Statistics
Matches: 133, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
150 1 0.01
151 71 0.53
152 61 0.46
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (151 bp):
GTAGCTTCATCTTACTCTACTACAACTTCAGAGAGATAAAGAATTGCTACTGTAGCTTCAATCCA
ATCCATACAACTCCAGGGATATAAGATTTGATATCATAACTTCATCTTGCTCCACTGGAACTTCA
GGGAAATAAGATTTGACTAAT
Found at i:21676047 original size:100 final size:100
Alignment explanation
Indices: 21675922--21676169 Score: 309
Period size: 100 Copynumber: 2.5 Consensus size: 100
21675912 GAATTGCTTC
* * * *
21675922 TGTAGCTTCAATCCAATCCACTACAACTTCAGGGATATAAGATTTGATATTATTGCTTCATCTTG
1 TGTAGTTTCAATCTAATCCATTACAACTTCAGGGATATAAGATTTGATACTATTGCTTCATCTTG
* * ** * *
21675987 CTCTATTGGATCTTTAGGGAAATAAGATTTGCTAA
66 CTCCACTACATCTTCAGGGAAATAAGATTTGATAA
* * * * *
21676022 TGTAGTTTCAATTTGATCCATTACAACTTAAGGGATATAATATTTGATACTGTTGCTTCATCTTG
1 TGTAGTTTCAATCTAATCCATTACAACTTCAGGGATATAAGATTTGATACTATTGCTTCATCTTG
*
21676087 CTCCACTACATCTTCAGGGAAATAAGATTTGATAT
66 CTCCACTACATCTTCAGGGAAATAAGATTTGATAA
* * *
21676122 TGTGGTTTCAATCTAATTCATTGCAACTTCAGGGATAT-AGAATTTGAT
1 TGTAGTTTCAATCTAATCCATTACAACTTCAGGGATATAAG-ATTTGAT
21676170 GTTCCACTAA
Statistics
Matches: 124, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
99 1 0.01
100 123 0.99
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (100 bp):
TGTAGTTTCAATCTAATCCATTACAACTTCAGGGATATAAGATTTGATACTATTGCTTCATCTTG
CTCCACTACATCTTCAGGGAAATAAGATTTGATAA
Found at i:21676118 original size:252 final size:252
Alignment explanation
Indices: 21675663--21676119 Score: 546
Period size: 252 Copynumber: 1.8 Consensus size: 252
21675653 GAGGTAATAT
* * *
21675663 TTGCTTCTATAGCTTCAATCCGACCCACTACAACTTCAAGGGTATAAGATTTGATGTGGTAGCTT
1 TTGCTTCTATAGCTTCAATCCAACCCACTACAACTTCAAGGGTATAAGATTTGATATGATAGCTT
* * * *
21675728 CATCTTACTCTACTACAACTTCAGAGAGATAAAGATTTGCTACTGTAGCTTTAATCCTATCTATG
66 CATCTTACTCTACTACAACTTCAGAGAAATAAAGATTTGCTAATGTAGCTTTAATCCTATCCATA
* * ** **
21675793 CAACTCCAGGGATATAAGATTTGATGTCATAACTTCATCTTGCTCCACTGTAACTTCAGGGGTAT
131 CAACTCAAGGGATATAAGATTTGATCTCATAACTTCATCTTGCTCCACTACAACTTCAGGGAAAT
*
21675858 AGGATTTGATTTTTGTAGCTTCATCTTGCTCTACTGCAACTTCGAAGAGATAAAGAA
196 AAGATTTGATTTTTGTAGCTTCATCTTGCTCTACTGCAACTTCGAAGAGATAAAGAA
* * * *
21675915 TTGCTTCTGTAGCTTCAATCCAATCCACTACAACTTC-AGGGATATAAGATTTGATATTATTGCT
1 TTGCTTCTATAGCTTCAATCCAACCCACTACAACTTCAAGGG-TATAAGATTTGATATGATAGCT
* * ** * * * *
21675979 TCATCTTGCTCTATTGGATCTTTAGGGAAAT-AAGATTTGCTAATGTAG-TTTCAAT-TTGATCC
65 TCATCTTACTCTACTACAACTTCAGAGAAATAAAGATTTGCTAATGTAGCTTT-AATCCT-ATCC
* * * ** *
21676041 ATTACAACTTAAGGGATATAATATTTGATACT-GTTGCTTCATCTTGCTCCACTACATCTTCAGG
128 A-TACAACTCAAGGGATATAAGATTTGAT-CTCATAACTTCATCTTGCTCCACTACAACTTCAGG
21676105 GAAATAAGATTTGAT
191 GAAATAAGATTTGAT
21676120 ATTGTGGTTT
Statistics
Matches: 168, Mismatches: 32, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
250 4 0.02
251 27 0.16
252 136 0.81
253 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (252 bp):
TTGCTTCTATAGCTTCAATCCAACCCACTACAACTTCAAGGGTATAAGATTTGATATGATAGCTT
CATCTTACTCTACTACAACTTCAGAGAAATAAAGATTTGCTAATGTAGCTTTAATCCTATCCATA
CAACTCAAGGGATATAAGATTTGATCTCATAACTTCATCTTGCTCCACTACAACTTCAGGGAAAT
AAGATTTGATTTTTGTAGCTTCATCTTGCTCTACTGCAACTTCGAAGAGATAAAGAA
Found at i:21676152 original size:50 final size:49
Alignment explanation
Indices: 21675691--21676169 Score: 189
Period size: 50 Copynumber: 9.6 Consensus size: 49
21675681 TCCGACCCAC
* * * * * *
21675691 TACAACTTCAAGGG-TATAAGATTTGATGTGGTAGCTTCATCTTACTCTAC
1 TACAACTTC-AGGGATATAAGATTTGATATTGTTGCTTCATCTGA-TCCAT
* * * * *
21675741 TACAACTTCAGAGAGATA-AAGATTTGCTACTGTAGCTTTAATCCT-ATCTA-
1 TACAACTTCAG-G-GATATAAGATTTGATATTGTTGC-TTCAT-CTGATCCAT
* * * ** ** * *
21675791 TGCAACTCCAGGGATATAAGATTTGATGTCATAACTTCATCTTGCTCCAC
1 TACAACTTCAGGGATATAAGATTTGATATTGTTGCTTCATC-TGATCCAT
** * * * * * * *
21675841 TGTAACTTCAGGGGTATAGGATTTGATTTTTGTAGCTTCATCTTGCTCTAC
1 TACAACTTCAGGGATATAAGATTTGA-TATTGTTGCTTCATC-TGATCCAT
* * * * * ** *
21675892 TGCAACTTCGAAGAGATA-AAGAATTGCT-TCTGTAGCTTCAATCCAATCCAC
1 TACAACTTC--AGGGATATAAGATTTGATAT-TGTTGCTTC-ATCTGATCCAT
* * *
21675943 TACAACTTCAGGGATATAAGATTTGATATTATTGCTTCATCTTGCTCTAT
1 TACAACTTCAGGGATATAAGATTTGATATTGTTGCTTCATC-TGATCCAT
** * * * * * * * *
21675993 TGGATCTTTAGGGAAATAAGATTTGCTAATGTAGTTTCAATTTGATCCAT
1 TACAACTTCAGGGATATAAGATTTGATATTGTTGCTTC-ATCTGATCCAT
* * * * *
21676043 TACAACTTAAGGGATATAATATTTGATACTGTTGCTTCATCTTGCTCCAC
1 TACAACTTCAGGGATATAAGATTTGATATTGTTGCTTCATC-TGATCCAT
* * * * * *
21676093 TACATCTTCAGGGAAATAAGATTTGATATTGTGGTTTCAATCTAATTCAT
1 TACAACTTCAGGGATATAAGATTTGATATTGTTGCTTC-ATCTGATCCAT
*
21676143 TGCAACTTCAGGGATAT-AGAATTTGAT
1 TACAACTTCAGGGATATAAG-ATTTGAT
21676170 GTTCCACTAA
Statistics
Matches: 322, Mismatches: 86, Indels: 42
0.72 0.19 0.09
Matches are distributed among these distances:
47 1 0.00
48 9 0.03
49 31 0.10
50 184 0.57
51 74 0.23
52 16 0.05
53 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (49 bp):
TACAACTTCAGGGATATAAGATTTGATATTGTTGCTTCATCTGATCCAT
Found at i:21689029 original size:17 final size:17
Alignment explanation
Indices: 21688998--21689044 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
21688988 TAGCTATCAT
21688998 TGCATTTCTATTTGTCAC
1 TGCATTTC-ATTTGTCAC
* *
21689016 TGCATTTCATTTGTTAG
1 TGCATTTCATTTGTCAC
21689033 TGCATTTGCATT
1 TGCATTT-CATT
21689045 GTAGTTGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTCATTTGTCAC
Found at i:21689046 original size:17 final size:17
Alignment explanation
Indices: 21688997--21689057 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
21688987 TTAGCTATCA
21688997 TTGCATTTCTATTTGTCA-
1 TTGCATTTC-ATTTGT-AG
*
21689015 CTGCATTTCATTTGTTAG
1 TTGCATTTCATTTG-TAG
21689033 -TGCATTTGCA-TTGTAG
1 TTGCATTT-CATTTGTAG
21689049 TTGCATTTC
1 TTGCATTTC
21689058 CGTTCTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
16 4 0.11
17 23 0.61
18 11 0.29
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (17 bp):
TTGCATTTCATTTGTAG
Found at i:21689635 original size:10 final size:10
Alignment explanation
Indices: 21689622--21689662 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
21689612 AAAAAATCAC
21689622 AAAAAGAAAG
1 AAAAAGAAAG
21689632 AAAAAGAAAG
1 AAAAAGAAAG
*
21689642 AAGAAGAAAAG
1 AAAAAG-AAAG
21689653 AGAAAAGAAA
1 A-AAAAGAAA
21689663 TACATTACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 15 0.56
11 8 0.30
12 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:21689854 original size:25 final size:26
Alignment explanation
Indices: 21689826--21689882 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
21689816 CAATTTAAGT
*
21689826 TGTTAG-AATAATGATTGCGGTGACA
1 TGTTAGTAATAATGATTACGGTGACA
* *
21689851 TGTTTGCTTGATAATGATTACGGTGACA
1 TGTTAG--TAATAATGATTACGGTGACA
21689879 TGTT
1 TGTT
21689883 TGCTTGTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
28 21 0.81
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (26 bp):
TGTTAGTAATAATGATTACGGTGACA
Found at i:21689865 original size:28 final size:28
Alignment explanation
Indices: 21689833--21689888 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
21689823 AGTTGTTAGA
*
21689833 ATAATGATTGCGGTGACATGTTTGCTTG
1 ATAATGATTACGGTGACATGTTTGCTTG
21689861 ATAATGATTACGGTGACATGTTTGCTTG
1 ATAATGATTACGGTGACATGTTTGCTTG
21689889 TGAGGTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (28 bp):
ATAATGATTACGGTGACATGTTTGCTTG
Found at i:21692339 original size:905 final size:905
Alignment explanation
Indices: 21690576--21692363 Score: 3119
Period size: 906 Copynumber: 2.0 Consensus size: 905
21690566 CTTTATGTTG
* * *
21690576 GAGACTGGTGAGCTGATCGATTAGGCGAGCAACAACTTCTAACGAGAAGAGCTTGGTGTTGTACA
1 GAGACCGGTGAGCTGATCGATCAGGCGAGAAACAACTTCTAACGAGAAGAGCTTGGTGTTGTACA
21690641 AGAGGAGCAGTTAAGAGATAATCCTAGTAGCCTAGGGATAGTATGCTTCGATTATTTGTTAATTC
66 AGAGGAGCAGTTAAGAGATAATCCTAGTAGCCTAGGGATAGTATGCTTCGATTATTTGTTAATTC
21690706 CTCTTTGAATGATGATGAATTCTAATGACATTTGATTGTATATGAGAATATCTTTCAATGTTAGA
131 CTCTTTGAATGATGATGAATTCTAATGACATTTGATTGTATATGAGAATATCTTTCAATGTTAGA
*
21690771 TTACTTTGATTCAAACTTAATTCTTCTCATCTGTTTATTGTTGGATTTAACTGCTTAACCACGAG
196 TTACTTTGATTCAAACTTAATTCTTCTCATCTGTTTATTCTTGGATTTAACTGCTTAACCACGAG
* *
21690836 AGTGTAATTACAGTTTATAGACATTGAGAGGTGCGGTGACAAGTTGATTTAACAAGCAAGTCAGC
261 AGTGTAATTACAGTCTACAGACATTGAGAGGTGCGGTGACAAGTTGATTTAACAAGCAAGTCAGC
* *
21690901 GAGAGTTACTTGAGACTAGAAGAGATTCTGTCACTTGTTCTTAGGTGTGAAGCAATGCCAGCACT
326 AAGAGTTACTTGAGACTAGAAGAGATTCTGTCACTTGTTCTTAGGTGTGAAGCAATACCAGCACT
* * *
21690966 AAGAGGTGTGGTACTTGTGAGCACTGAGTCTTGATTAAATGAAGAGTTGTTATTGGTATGATTTC
391 AAGAGGTGTGGTACTTGTGAGCACTAAGTCTTGATTAAACGAAGAGTTATTATTGGTATGATTTC
* * * *
21691031 ATTGGATCCTTATTGCGGTGAAAATTCATCTACACTATATCTTGTCGACACATCTAGCGTTGCTA
456 ATTGGAACCTTATTGCGGTAAAAATTCATCTACACTATACCTTGTCGACACATCTAGCATTGCTA
*
21691096 CTTAGTGAAATCAGTGATCCACTCCAATCCTTTACACTTGATCACACTTTTACTTTTATGCATTT
521 CTTAGTGAAATCAGTGATCCACTCCAATCCTTTACACTTGATCACACTTTTACTTTTATACATTT
* * *
21691161 AAATTCTTCAAACTTCAACAACTATTTGATTTACTTTCATTTTCTCTAACAATTAACTTTTATAA
586 AAATTCTCCAAACTTCAACAACTATTTGATTTACTTTCATTTTCTCTAACAATTAAATCTTATAA
21691226 TTACATTGACAACTTTGATTAATTTAATGGTATAGATCTAATTTAATTGCGCTGACATCCTTACT
651 TTACATTGACAACTTTGATTAATTTAATGGTATAGATCTAATTTAATTGCGCTGACATCCTTACT
*
21691291 AGAATTTTCCCTAATCTTAGTTTTAGTCACTTTGACAATTGAACATCAAGAACTCCTTCCTCATG
716 AGAATTTTCCCTAATCTTAGTTTTAGTCACTTCGACAATTGAACATCAAGAACTCCTTCCTCATG
*
21691356 GGATCGATATACGATAGAGCAATCTATCAACTATACTTACATCGACGTGTGTCTGCTTGCACTTA
781 GGATCGATATACGATAGAGCAATCTATCAACTATACTTACATCGACGTATGTCTGCTTGCACTTA
*
21691421 AATGCTCTGATGATTACAGGCTGATCATCCAGCCAGTATCAACTATACTTACATCGACGT
846 AATGCTCTGATGATTACAGGCCGATCATCCAGCCAGTATCAACTATACTTACATCGACGT
* * *
21691481 GAGACCGGTGAGCTGATCGATCAGGCGAGAAACAACTTCTGACTAGAAGTGCTTGGTGTTGTACA
1 GAGACCGGTGAGCTGATCGATCAGGCGAGAAACAACTTCTAACGAGAAGAGCTTGGTGTTGTACA
*
21691546 ATAGGAGCAGTTAAGAGATAATCCTAGTAGCCTAGGGATAGTATGCTTCGATTATTTGTTAATTC
66 AGAGGAGCAGTTAAGAGATAATCCTAGTAGCCTAGGGATAGTATGCTTCGATTATTTGTTAATTC
21691611 CTCTTTGAATGATGATGAATTCTAATGACATTTGATTGTATATGAGAATATCTTTCAATGTTAGA
131 CTCTTTGAATGATGATGAATTCTAATGACATTTGATTGTATATGAGAATATCTTTCAATGTTAGA
* *
21691676 TTACTTTGAATTCAAACTTAATTCTTCTCATCTGTTTTTTCTTGGATTTAACTGCTTGACCACGA
196 TTACTTTG-ATTCAAACTTAATTCTTCTCATCTGTTTATTCTTGGATTTAACTGCTTAACCACGA
*
21691741 GAGTGTAATTGCAGTCTACAGACATTGAGAGGTGCGGTGACAAGTTGATTTAACAAGCAAGTCAG
260 GAGTGTAATTACAGTCTACAGACATTGAGAGGTGCGGTGACAAGTTGATTTAACAAGCAAGTCAG
* *
21691806 CAAGAGTTGCTTGAGACTAGAAGAGATTTTGTCACTTGTTCTTAGGTGTGAAGCAATACCAGCAC
325 CAAGAGTTACTTGAGACTAGAAGAGATTCTGTCACTTGTTCTTAGGTGTGAAGCAATACCAGCAC
* ** *
21691871 TGAGAGGTGTGGTACTTGTGAGTGCTAAGTCTTGATTAAACGGAGAGTTATTATTGGTATGATTT
390 TAAGAGGTGTGGTACTTGTGAGCACTAAGTCTTGATTAAACGAAGAGTTATTATTGGTATGATTT
* *
21691936 CATTGGAACCTTATTGCGGTAAAAATTCATCTACACTATACCTTGTCGGCATATCTAGCATTGCT
455 CATTGGAACCTTATTGCGGTAAAAATTCATCTACACTATACCTTGTCGACACATCTAGCATTGCT
*
21692001 ACTTAGTGAAATCAGTGATTCACTCCAATCCTTTACACTTGATCACACTTTTACTTTTATACATT
520 ACTTAGTGAAATCAGTGATCCACTCCAATCCTTTACACTTGATCACACTTTTACTTTTATACATT
*
21692066 TAAATTCTCCAAACTTCAACAACTGTTTGATTTACTTTCATTTTCTCTAACAATTAAATCTTATA
585 TAAATTCTCCAAACTTCAACAACTATTTGATTTACTTTCATTTTCTCTAACAATTAAATCTTATA
*
21692131 ATTACATTGACAACTTTGATTAATTT-GTGGTATAGATCTAATTTAATTGCGCTGACATCCTTAC
650 ATTACATTGACAACTTTGATTAATTTAATGGTATAGATCTAATTTAATTGCGCTGACATCCTTAC
* ** * *
21692195 TAGTATTTTCCCTAATCTTAGTTTTAGTTGCTTCGATAATTGAACATCAAGAACTCCTTCCTTAT
715 TAGAATTTTCCCTAATCTTAGTTTTAGTCACTTCGACAATTGAACATCAAGAACTCCTTCCTCAT
*
21692260 GGGATCGATATCCGATAGAGCAATCTATCAACTATACTTACATCGACGTATGTCTGCTTGCACTT
780 GGGATCGATATACGATAGAGCAATCTATCAACTATACTTACATCGACGTATGTCTGCTTGCACTT
* * *
21692325 AAATGTTGTGATGATTACAGGCCGATCATCTAGCCAGTA
845 AAATGCTCTGATGATTACAGGCCGATCATCCAGCCAGTA
21692364 GTTGGGTCAG
Statistics
Matches: 833, Mismatches: 49, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
905 390 0.47
906 443 0.53
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (905 bp):
GAGACCGGTGAGCTGATCGATCAGGCGAGAAACAACTTCTAACGAGAAGAGCTTGGTGTTGTACA
AGAGGAGCAGTTAAGAGATAATCCTAGTAGCCTAGGGATAGTATGCTTCGATTATTTGTTAATTC
CTCTTTGAATGATGATGAATTCTAATGACATTTGATTGTATATGAGAATATCTTTCAATGTTAGA
TTACTTTGATTCAAACTTAATTCTTCTCATCTGTTTATTCTTGGATTTAACTGCTTAACCACGAG
AGTGTAATTACAGTCTACAGACATTGAGAGGTGCGGTGACAAGTTGATTTAACAAGCAAGTCAGC
AAGAGTTACTTGAGACTAGAAGAGATTCTGTCACTTGTTCTTAGGTGTGAAGCAATACCAGCACT
AAGAGGTGTGGTACTTGTGAGCACTAAGTCTTGATTAAACGAAGAGTTATTATTGGTATGATTTC
ATTGGAACCTTATTGCGGTAAAAATTCATCTACACTATACCTTGTCGACACATCTAGCATTGCTA
CTTAGTGAAATCAGTGATCCACTCCAATCCTTTACACTTGATCACACTTTTACTTTTATACATTT
AAATTCTCCAAACTTCAACAACTATTTGATTTACTTTCATTTTCTCTAACAATTAAATCTTATAA
TTACATTGACAACTTTGATTAATTTAATGGTATAGATCTAATTTAATTGCGCTGACATCCTTACT
AGAATTTTCCCTAATCTTAGTTTTAGTCACTTCGACAATTGAACATCAAGAACTCCTTCCTCATG
GGATCGATATACGATAGAGCAATCTATCAACTATACTTACATCGACGTATGTCTGCTTGCACTTA
AATGCTCTGATGATTACAGGCCGATCATCCAGCCAGTATCAACTATACTTACATCGACGT
Found at i:21694696 original size:32 final size:32
Alignment explanation
Indices: 21694660--21694720 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
21694650 ACTAAAGATA
21694660 AATAAAAAATAAAAGT-AAAATAAAATAAAAGC
1 AATAAAAAA-AAAAGTAAAAATAAAATAAAAGC
* * *
21694692 AATAAAACAAATAGTAAAAATAAGATAAA
1 AATAAAAAAAAAAGTAAAAATAAAATAAA
21694721 GGACTGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (32 bp):
AATAAAAAAAAAAGTAAAAATAAAATAAAAGC
Found at i:21695023 original size:25 final size:26
Alignment explanation
Indices: 21694968--21695023 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
21694958 TAAATTGAAA
21694968 AGAAAATAAAATTAACAAGGAAAAAT
1 AGAAAATAAAATTAACAAGGAAAAAT
* *
21694994 -TAAAATAAAA-TAA-AAGGACTAAAT
1 AGAAAATAAAATTAACAAGGA-AAAAT
21695018 AGAAAA
1 AGAAAA
21695024 CAAGGCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 5 0.20
24 7 0.28
25 13 0.52
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.16
Consensus pattern (26 bp):
AGAAAATAAAATTAACAAGGAAAAAT
Found at i:21699643 original size:22 final size:23
Alignment explanation
Indices: 21699618--21699660 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
21699608 AGGGTTTTAG
*
21699618 AATTTTATA-TAAAAAATAGTTT
1 AATTTTAGAGTAAAAAATAGTTT
*
21699640 AATTTTAGAGTTAAAAATAGT
1 AATTTTAGAGTAAAAAATAGT
21699661 AATAAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (23 bp):
AATTTTAGAGTAAAAAATAGTTT
Found at i:21702230 original size:24 final size:25
Alignment explanation
Indices: 21702202--21702264 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
21702192 GGACACCAGT
21702202 GCCAACACCACCACCAG-CTCCACC
1 GCCAACACCACCACCAGACTCCACC
* *
21702226 GCCAACAGCACC-CCCGACTCCACC
1 GCCAACACCACCACCAGACTCCACC
21702250 GCCAACACCACCACC
1 GCCAACACCACCACC
21702265 CCCACCCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.09
24 29 0.85
25 2 0.06
ACGTcount: A:0.29, C:0.59, G:0.10, T:0.03
Consensus pattern (25 bp):
GCCAACACCACCACCAGACTCCACC
Found at i:21702237 original size:12 final size:12
Alignment explanation
Indices: 21702202--21702261 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
21702192 GGACACCAGT
21702202 GCCAACACCACC
1 GCCAACACCACC
* * *
21702214 ACCAGCTCCACC
1 GCCAACACCACC
*
21702226 GCCAACAGCACC
1 GCCAACACCACC
* * *
21702238 CCCGACTCCACC
1 GCCAACACCACC
21702250 GCCAACACCACC
1 GCCAACACCACC
21702262 ACCCCCACCC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.28, C:0.58, G:0.10, T:0.03
Consensus pattern (12 bp):
GCCAACACCACC
Found at i:21702330 original size:18 final size:18
Alignment explanation
Indices: 21702293--21702335 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21702283 TCCTCCGAGC
*
21702293 CCACCGAGTCCACTACCT
1 CCACCAAGTCCACTACCT
*
21702311 CCTCCAAGTCCACCTA-CT
1 CCACCAAGTCCA-CTACCT
21702329 CCACCAA
1 CCACCAA
21702336 TGCCCCCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.26, C:0.51, G:0.07, T:0.16
Consensus pattern (18 bp):
CCACCAAGTCCACTACCT
Found at i:21703022 original size:21 final size:20
Alignment explanation
Indices: 21702996--21703050 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
21702986 TTAGGATCAT
21702996 AAATAATTAATTAAAGTATTA
1 AAATAATTAATTAAA-TATTA
*
21703017 AAATAATATAATCAAATATTA
1 AAATAAT-TAATTAAATATTA
**
21703038 TTAT-ATTAATTAA
1 AAATAATTAATTAA
21703051 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 2 0.07
21 14 0.48
22 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATAATTAATTAAATATTA
Found at i:21703357 original size:184 final size:186
Alignment explanation
Indices: 21703042--21703427 Score: 695
Period size: 184 Copynumber: 2.1 Consensus size: 186
21703032 ATATTATTAT
*
21703042 ATTAATTAATAAAAAATTAACCTTTATTAAGAAGTTTAATTTGAAAATAGTGTGTTTTAATTAAG
1 ATTAA-TAATAAAAAATTAACCTTTATTAAGAAATTTAATTTGAAAATAG-GTGTTTTAATTAAG
21703107 TTAGGATCAAATTAAAAAATGAGTAAAATAAATTAAAATATTAATAATGAGACTTGACTACAAGT
64 TTAGGATCAAATTAAAAAATGAGTAAAATAAATTAAAATATTAATAATGAGACTTGACTACAAGT
21703172 ATTAATTATTGTATATAAACTAAAATAGGAATTTGTTAAAAAATATAAAGTTAAATAA
129 ATTAATTATTGTATATAAACTAAAATAGGAATTTGTTAAAAAATATAAAGTTAAATAA
21703230 ATTAATAATAAAAAATTAACCTTTATTAAGAAATTTAATTTGAAAATA-GTGTTTTAATTAAGTT
1 ATTAATAATAAAAAATTAACCTTTATTAAGAAATTTAATTTGAAAATAGGTGTTTTAATTAAGTT
* * * *
21703294 AGGATCTAATTGAAAAATGAG-CAAATAAATTAAAATATTAATAATGAGACTTGACTGCAAGTAT
66 AGGATCAAATTAAAAAATGAGTAAAATAAATTAAAATATTAATAATGAGACTTGACTACAAGTAT
21703358 TAATTATTGTATATAAACTAAAATAGGAATTTGTTAAAAAATATAAAGTTAAATAA
131 TAATTATTGTATATAAACTAAAATAGGAATTTGTTAAAAAATATAAAGTTAAATAA
21703414 ATTAATAATAAAAA
1 ATTAATAATAAAAA
21703428 TTACGTAAAT
Statistics
Matches: 193, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
184 111 0.58
185 35 0.18
187 42 0.22
188 5 0.03
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (186 bp):
ATTAATAATAAAAAATTAACCTTTATTAAGAAATTTAATTTGAAAATAGGTGTTTTAATTAAGTT
AGGATCAAATTAAAAAATGAGTAAAATAAATTAAAATATTAATAATGAGACTTGACTACAAGTAT
TAATTATTGTATATAAACTAAAATAGGAATTTGTTAAAAAATATAAAGTTAAATAA
Found at i:21703412 original size:92 final size:92
Alignment explanation
Indices: 21703132--21703423 Score: 255
Period size: 92 Copynumber: 3.2 Consensus size: 92
21703122 AAAATGAGTA
21703132 AAATAAATTAA-AATATTAATAATGAGACTTGACTACAAGTATTAATTATTGTATATAAACTAAA
1 AAATAAATTAATAATATTAATAATGAGACTTGACT-CAAGTATTAATTATTGTATATAAACTAAA
21703196 ATAGGAATTTGTTAAAAAATATAAAGTT
65 ATAGGAATTTGTTAAAAAATATAAAGTT
* * * * * * * * *
21703224 AAATAAATTAATAATA--AAAAATTA-ACCTTTA-TTAAGAAATTTAATTTGAAAATAGTGTTTT
1 AAATAAATTAATAATATTAATAATGAGA-CTTGACTCAAG-TA-TTAA-TT----ATTGTATATA
* ** ** * * *
21703285 AATTAAGTTAGG-ATCTAATT-GAAAA-AT-GAG-C
58 AACTAAAATAGGAAT-TTGTTAAAAAATATAAAGTT
21703316 AAATAAATTAA-AATATTAATAATGAGACTTGACTGCAAGTATTAATTATTGTATATAAACTAAA
1 AAATAAATTAATAATATTAATAATGAGACTTGACT-CAAGTATTAATTATTGTATATAAACTAAA
21703380 ATAGGAATTTGTTAAAAAATATAAAGTT
65 ATAGGAATTTGTTAAAAAATATAAAGTT
21703408 AAATAAATTAATAATA
1 AAATAAATTAATAATA
21703424 AAAATTACGT
Statistics
Matches: 145, Mismatches: 34, Indels: 41
0.66 0.15 0.19
Matches are distributed among these distances:
88 18 0.12
89 9 0.06
90 5 0.03
91 20 0.14
92 37 0.26
93 24 0.17
94 5 0.03
95 9 0.06
96 18 0.12
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (92 bp):
AAATAAATTAATAATATTAATAATGAGACTTGACTCAAGTATTAATTATTGTATATAAACTAAAA
TAGGAATTTGTTAAAAAATATAAAGTT
Found at i:21704620 original size:30 final size:27
Alignment explanation
Indices: 21704571--21704707 Score: 109
Period size: 27 Copynumber: 5.0 Consensus size: 27
21704561 CAGTCGTGTG
* * *
21704571 TCCCCTGTTTTTCAAATTTTATAATTT
1 TCCCCTATTTTTTAGATTTTATAATTT
* * *
21704598 TGCCCTTTGTTTTTTTAGATTTTACAATTT
1 T-CCC-CT-ATTTTTTAGATTTTATAATTT
*
21704628 TCCCCTATTTTTTAGATTTAATAATTT
1 TCCCCTATTTTTTAGATTTTATAATTT
* * *
21704655 T--CCT-TTTTTTATATTTTACAGTTT
1 TCCCCTATTTTTTAGATTTTATAATTT
* *
21704679 TGCCCCTAGTTTTTAGATTTTACAATTT
1 T-CCCCTATTTTTTAGATTTTATAATTT
21704707 T
1 T
21704708 ATCTTTATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
24 17 0.20
25 3 0.03
27 23 0.26
28 22 0.25
29 4 0.05
30 18 0.21
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (27 bp):
TCCCCTATTTTTTAGATTTTATAATTT
Found at i:21704671 original size:51 final size:52
Alignment explanation
Indices: 21704607--21704707 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 52
21704597 TTGCCCTTTG
* *
21704607 TTTTTTTAGATTTTACAATTTT-CCCCTATTTTTTAGATTTAATAATTTTCC
1 TTTTTTTAGATTTTACAATTTTGCCCCTAGTTTTTAGATTTAACAATTTTCC
* * *
21704658 TTTTTTTATATTTTACAGTTTTGCCCCTAGTTTTTAGATTTTACAATTTT
1 TTTTTTTAGATTTTACAATTTTGCCCCTAGTTTTTAGATTTAACAATTTT
21704708 ATCTTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 20 0.45
52 24 0.55
ACGTcount: A:0.22, C:0.13, G:0.06, T:0.59
Consensus pattern (52 bp):
TTTTTTTAGATTTTACAATTTTGCCCCTAGTTTTTAGATTTAACAATTTTCC
Found at i:21704692 original size:28 final size:28
Alignment explanation
Indices: 21704572--21704796 Score: 120
Period size: 28 Copynumber: 8.1 Consensus size: 28
21704562 AGTCGTGTGT
* * * *
21704572 CCCCTGTTTTTCAAATTTTATAATTTTG
1 CCCCTATTTTTCAGATTTTACAGTTTTG
* * * *
21704600 CCCTTTGTTTTTTTAGATTTTACAATTTT-
1 CCC-CT-ATTTTTCAGATTTTACAGTTTTG
* * * *
21704629 CCCCTATTTTTTAGATTTAATAATTTT-
1 CCCCTATTTTTCAGATTTTACAGTTTTG
* *
21704656 --CCT-TTTTTTATATTTTACAGTTTTG
1 CCCCTATTTTTCAGATTTTACAGTTTTG
* *
21704681 CCCCTAGTTTTT-AGATTTTACAATTTTA
1 CCCCTA-TTTTTCAGATTTTACAGTTTTG
* ** * * *
21704709 TCTTTATTTTTCAAATTTTATAGTTATG
1 CCCCTATTTTTCAGATTTTACAGTTTTG
*
21704737 CCCTTATTTTTCAGATTTTACAGTTTTG
1 CCCCTATTTTTCAGATTTTACAGTTTTG
* * * *
21704765 TCCCCCTATTTCTCAGTTTTTAAAGTGTTG
1 --CCCCTATTTTTCAGATTTTACAGTTTTG
21704795 CC
1 CC
21704797 TAGAATTTTA
Statistics
Matches: 153, Mismatches: 34, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
24 17 0.11
25 3 0.02
27 27 0.18
28 56 0.37
29 9 0.06
30 41 0.27
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.55
Consensus pattern (28 bp):
CCCCTATTTTTCAGATTTTACAGTTTTG
Found at i:21706578 original size:16 final size:16
Alignment explanation
Indices: 21706557--21706590 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21706547 CGAAAAAAAT
21706557 GCCGCAAAAGGTAAGA
1 GCCGCAAAAGGTAAGA
21706573 GCCGCAAAAGGTAAGA
1 GCCGCAAAAGGTAAGA
21706589 GC
1 GC
21706591 AATAGTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.21, G:0.32, T:0.06
Consensus pattern (16 bp):
GCCGCAAAAGGTAAGA
Found at i:21706613 original size:57 final size:57
Alignment explanation
Indices: 21706520--21706630 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
21706510 ATAAACGTCC
*
21706520 CAAAAGGTAAAGCAATAGCGGCATTTACGAAAAAAATGCCGCAAAAGGTAAGAGCCG
1 CAAAAGGTAAAGCAATAGCGGCATTTACGAAAAAAATGCCACAAAAGGTAAGAGCCG
* ** * * *
21706577 CAAAAGGTAAGAGCAATAGTGGTGTTTATG-ACAAAATGCTACAAAAGGTAAGAG
1 CAAAAGGTAA-AGCAATAGCGGCATTTACGAAAAAAATGCCACAAAAGGTAAGAG
21706631 AATTAGTGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 31 0.67
58 15 0.33
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.16
Consensus pattern (57 bp):
CAAAAGGTAAAGCAATAGCGGCATTTACGAAAAAAATGCCACAAAAGGTAAGAGCCG
Found at i:21706695 original size:82 final size:83
Alignment explanation
Indices: 21706573--21706769 Score: 226
Period size: 82 Copynumber: 2.4 Consensus size: 83
21706563 AAAGGTAAGA
* * *
21706573 GCCGCAAAAGGTAAGAGCAATAGTGG-TGTTTATGACAAAATG-C-TACAAAAGGTAAGAGAATT
1 GCCGCAAAAGGTAAGAGCATTAGCGGCTGTTTATCACAAAATGCCGTA-AAAA-GTAAGAGAATT
* * *
21706635 AGTGGTGTTTATGACAAAAT
64 AGCGGCGTTTATGACAAAAC
* *
21706655 GCCGCAAAAGGTAAGAGCATTAGCGGCAT-TTTCTCA-AAAATGCCGTAAAAAGTAAGAGCATTA
1 GCCGCAAAAGGTAAGAGCATTAGCGGC-TGTTTATCACAAAATGCCGTAAAAAGTAAGAGAATTA
*
21706718 GCGGCGTTTATGAGAAAAC
65 GCGGCGTTTATGACAAAAC
* *
21706737 GCCGTAAAAGATAAGAGCATTAGCGGC-GTTTAT
1 GCCGCAAAAGGTAAGAGCATTAGCGGCTGTTTAT
21706770 GGGAAAAACG
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
81 4 0.04
82 81 0.83
83 10 0.10
84 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (83 bp):
GCCGCAAAAGGTAAGAGCATTAGCGGCTGTTTATCACAAAATGCCGTAAAAAGTAAGAGAATTAG
CGGCGTTTATGACAAAAC
Found at i:21706776 original size:41 final size:41
Alignment explanation
Indices: 21706573--21706781 Score: 170
Period size: 41 Copynumber: 5.1 Consensus size: 41
21706563 AAAGGTAAGA
* * * * * * *
21706573 GCCGCAAAAGGTAAGAGCAATAGTGGTGTTTATGACAAAAT
1 GCCGTAAAAGATAAGAGCATTAGCGGCGTTTATGAGAAAAC
*** * * * * * *
21706614 GCTACAAAAGGTAAGAGAATTAGTGGTGTTTATGACAAAAT
1 GCCGTAAAAGATAAGAGCATTAGCGGCGTTTATGAGAAAAC
* * * * * *
21706655 GCCGCAAAAGGTAAGAGCATTAGCGGCATTTTCTCA-AAAAT
1 GCCGTAAAAGATAAGAGCATTAGCGGC-GTTTATGAGAAAAC
21706696 GCCGTAAAA-AGTAAGAGCATTAGCGGCGTTTATGAGAAAAC
1 GCCGTAAAAGA-TAAGAGCATTAGCGGCGTTTATGAGAAAAC
*
21706737 GCCGTAAAAGATAAGAGCATTAGCGGCGTTTATGGGAAAAAC
1 GCCGTAAAAGATAAGAGCATTAGCGGCGTTTATGAG-AAAAC
21706779 GCC
1 GCC
21706782 ACTAAAGGTT
Statistics
Matches: 144, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.03
41 125 0.87
42 14 0.10
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (41 bp):
GCCGTAAAAGATAAGAGCATTAGCGGCGTTTATGAGAAAAC
Found at i:21709582 original size:19 final size:19
Alignment explanation
Indices: 21709558--21709595 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21709548 ACAAATATGA
21709558 ATCAAATTAAATATGGCAT
1 ATCAAATTAAATATGGCAT
21709577 ATCAAATTAAATATGGCAT
1 ATCAAATTAAATATGGCAT
21709596 TTTAAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
ATCAAATTAAATATGGCAT
Done.