Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_pilon, whole genome shotgun sequence
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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1674133 original size:20 final size:20
Alignment explanation
Indices: 1674105--1674414 Score: 343
Period size: 20 Copynumber: 15.5 Consensus size: 20
1674095 AAATTTCAGT
* *
1674105 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1674125 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1674145 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1674165 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1674185 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1674205 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1674225 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1674245 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* * *
1674265 GTTGCTATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1674285 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1674305 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1674325 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
1674345 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
1674365 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
1674385 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
1674405 GTTGCGATTT
1 GTTGCGATTT
1674415 TGGAAAATCG
Statistics
Matches: 254, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
20 253 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1674431 original size:21 final size:21
Alignment explanation
Indices: 1674401--1674483 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1674391 ATTTTCATAT
*
1674401 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1674422 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1674443 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1674464 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1674484 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1674474 original size:42 final size:43
Alignment explanation
Indices: 1674381--1674479 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1674371 ATTTATGTGT
* *
1674381 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1674422 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1674464 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1674480 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1676775 original size:217 final size:215
Alignment explanation
Indices: 1676400--1676847 Score: 668
Period size: 217 Copynumber: 2.1 Consensus size: 215
1676390 CCCTCGTGTA
* *
1676400 TTATTAAGATGTAACTCCTCTTCCCTTGATGCATAATTACCTCTTTATACAATTAAGACATAGTT
1 TTATTAAGATGTAACTCCTCTTCCCTTGATGCATAATTACCTCTTTATACAATTAAAACATAGGT
** ** *
1676465 GTAAATATCTGCTAGGATGACTATTGAGTATTGAGTCGTATGTAATACAAGCTATCTAATGCGTC
66 GTAAATATCTGCTAGGATGACTATTGAGTATTGAAACG-ACATAATACAAGCTATCTAACGCGTC
* *
1676530 ATAAAAAGCTAGGGAATGAAAACTATTACCATACAGTTTTCACAAAAGAGAACAATCCATAAACC
130 ATAAAAAACTAGGGAATGAAAACTATTACCATACA-TTTTCACAAAAGAGAACAAACCATAAACC
*
1676595 TTACAAGGTTAATCCCCCTTGG
194 TTACAAGGCTAATCCCCCTTGG
1676617 TTATTAAGATG-AAGCTCCTCTTCCCTTGATGCATAATTACCTCTTTATACAATTAAAACATAGG
1 TTATTAAGATGTAA-CTCCTCTTCCCTTGATGCATAATTACCTCTTTATACAATTAAAACATAGG
* * *
1676681 TGTAAATATCTGCTAGGTTGACTATTGAGTCGTATGTAAAC-ACAT-ATACAAGCTATCTACCGC
65 TGTAAATATCTGCTAGGATGACTATTGAGT-AT-TG-AAACGACATAATACAAGCTATCTAACGC
* * *
1676744 GTCATAAAAAACTAGGGAGTGAAAACTATTACCATACATTTTCACAAACGAGAACAAAGCATAAA
127 GTCATAAAAAACTAGGGAATGAAAACTATTACCATACATTTTCACAAAAGAGAACAAACCATAAA
*
1676809 CCTTACAAGGCTAATCCCTCTTGG
192 CCTTACAAGGCTAATCCCCCTTGG
1676833 TTATTAAGATGTAAC
1 TTATTAAGATGTAAC
1676848 AGCTAAGAAC
Statistics
Matches: 209, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
216 60 0.29
217 142 0.68
218 3 0.01
219 2 0.01
220 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (215 bp):
TTATTAAGATGTAACTCCTCTTCCCTTGATGCATAATTACCTCTTTATACAATTAAAACATAGGT
GTAAATATCTGCTAGGATGACTATTGAGTATTGAAACGACATAATACAAGCTATCTAACGCGTCA
TAAAAAACTAGGGAATGAAAACTATTACCATACATTTTCACAAAAGAGAACAAACCATAAACCTT
ACAAGGCTAATCCCCCTTGG
Found at i:1680013 original size:7 final size:7
Alignment explanation
Indices: 1680001--1680028 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1679991 CTCTGTGTAG
1680001 TTGAAAT
1 TTGAAAT
1680008 TTGAAAT
1 TTGAAAT
1680015 TTGAAAT
1 TTGAAAT
1680022 TTGAAAT
1 TTGAAAT
1680029 AGATTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TTGAAAT
Found at i:1701780 original size:2 final size:2
Alignment explanation
Indices: 1701773--1701812 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1701763 ACTGCACTGT
1701773 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1701813 GGATGAGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1703311 original size:21 final size:21
Alignment explanation
Indices: 1703278--1703317 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1703268 GATTTTGATT
** *
1703278 ATTTAATTTTTTATTATTACA
1 ATTTAATCATTTATGATTACA
1703299 ATTTAATCATTTATGATTA
1 ATTTAATCATTTATGATTA
1703318 TAATCAAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTTAATCATTTATGATTACA
Found at i:1705501 original size:64 final size:63
Alignment explanation
Indices: 1705416--1705575 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
1705406 TTGTTTAAGG
* * *
1705416 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTT
1705479 A
63 A
* * *
1705480 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTA
* *
1705544 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
1705576 ACATTCATTG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTA
Found at i:1706325 original size:31 final size:31
Alignment explanation
Indices: 1706231--1706325 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
1706221 AGTCGAGGGT
*
1706231 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTATGTTCTTT-GGGACATATGGACAG
* ** * *
1706262 TATACCTATGTTCTAAGGAATATATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
* *
1706293 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
1706324 TT
1 TT
1706326 GCCGAGGTTC
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 47 0.94
32 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (31 bp):
TTTACCTATGTTCTTTGGGACATATGGACAG
Found at i:1706345 original size:30 final size:30
Alignment explanation
Indices: 1706253--1706359 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 30
1706243 TTTCGAGACA
* * **
1706253 TATGGACAGTATACCTATGTTCTA-AGGAATA
1 TATGGACAGT-TACCGAGGTTCTATAGG-ACC
* * *
1706284 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTATAGGACC
* *
1706315 TATGGACAGTTGCCGAGGTTCTATATGACC
1 TATGGACAGTTACCGAGGTTCTATAGGACC
* *
1706345 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
1706360 GGGTCTGTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
30 28 0.46
31 30 0.49
32 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTATAGGACC
Found at i:1709740 original size:64 final size:63
Alignment explanation
Indices: 1709655--1709814 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
1709645 TTGTTTAAGG
* * *
1709655 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTT
1709718 A
63 A
* * *
1709719 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTA
* *
1709783 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
1709815 ACATTCATTG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTA
Found at i:1710525 original size:19 final size:19
Alignment explanation
Indices: 1710498--1710563 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
1710488 AATGTTTTTA
* *
1710498 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1710517 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1710536 TGAACAATAAATCACTATT
1 TGAACAGTAAATTACTATT
1710555 TGAACAGTA
1 TGAACAGTA
1710564 TCGAGGCTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1710694 original size:21 final size:21
Alignment explanation
Indices: 1710668--1710709 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1710658 ATTTGAATAT
*
1710668 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1710689 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1710710 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1710771 original size:21 final size:21
Alignment explanation
Indices: 1710738--1710777 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1710728 TTTGAGTAGA
*
1710738 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1710760 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1710778 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1711031 original size:34 final size:32
Alignment explanation
Indices: 1710992--1711061 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1710982 TTTTGTAAAG
*
1710992 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1711026 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1711058 GGGA
1 GGGA
1711062 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1711945 original size:19 final size:20
Alignment explanation
Indices: 1711921--1711968 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1711911 AATGATTTTC
*
1711921 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1711940 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1711960 TTTTGAAAA
1 TTTTGAAAA
1711969 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1713361 original size:19 final size:19
Alignment explanation
Indices: 1713334--1713399 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
1713324 AATGTTTTTA
* *
1713334 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1713353 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1713372 TGAACAATAAATCACTATT
1 TGAACAGTAAATTACTATT
1713391 TGAACAGTA
1 TGAACAGTA
1713400 CCGATGCTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1713530 original size:21 final size:21
Alignment explanation
Indices: 1713504--1713545 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1713494 ATTTGAATAT
*
1713504 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1713525 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1713546 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1713607 original size:21 final size:21
Alignment explanation
Indices: 1713574--1713613 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1713564 TTTGAGTAGA
*
1713574 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1713596 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1713614 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1713867 original size:34 final size:32
Alignment explanation
Indices: 1713828--1713897 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1713818 TTTTGTAAAG
*
1713828 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1713862 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1713894 GGGA
1 GGGA
1713898 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1714367 original size:31 final size:31
Alignment explanation
Indices: 1714273--1714367 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
1714263 AGTCGAGGGT
*
1714273 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTATGTTCTTT-GGGACATATGGACAG
* ** *
1714304 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
* *
1714335 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
1714366 TT
1 TT
1714368 GCCGATGTTC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTCTTTGGGACATATGGACAG
Found at i:1715819 original size:31 final size:31
Alignment explanation
Indices: 1715762--1715839 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1715752 AATTTTTAAA
** *
1715762 ACTTGCAATATAATCCCCCAATATTTAATCC
1 ACTTGCAATATGGTCCCCCAACATTTAATCC
* * * *
1715793 ATTTTCAATATGGTCCCTCAACATTTAGTCC
1 ACTTGCAATATGGTCCCCCAACATTTAATCC
*
1715824 GCTTGCAATATGGTCC
1 ACTTGCAATATGGTCC
1715840 TCGACGTAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (31 bp):
ACTTGCAATATGGTCCCCCAACATTTAATCC
Found at i:1719080 original size:2 final size:2
Alignment explanation
Indices: 1719073--1719113 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1719063 TTGTCCTTAT
1719073 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
1719114 TTAACAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1719706 original size:19 final size:20
Alignment explanation
Indices: 1719682--1719732 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1719672 AATGACCAAT
1719682 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1719701 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1719721 AAAATCGCAACG
1 AAAATCGCAACG
1719733 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1719726 original size:20 final size:20
Alignment explanation
Indices: 1719682--1719939 Score: 117
Period size: 20 Copynumber: 12.6 Consensus size: 20
1719672 AATGACCAAT
* *
1719682 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1719701 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1719721 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1719741 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1719761 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1719782 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1719805 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
1719825 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1719845 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1719865 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1719885 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1719908 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
1719928 AGAATCGCAACG
1 AAAATCGCAACG
1719940 GTCAAAAGAA
Statistics
Matches: 187, Mismatches: 40, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.09
20 127 0.68
21 14 0.07
23 29 0.16
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1719858 original size:40 final size:40
Alignment explanation
Indices: 1719807--1719937 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
1719797 TTTAGAAGAA
*
1719807 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* *
1719847 AATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* * *
1719887 AGTCGCAACGCGATTTAGA-AGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-GATAG--AATCGCAATGCGATTGAGAG
1719930 AATCGCAA
1 AATCGCAA
1719938 CGGTCAAAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 48 0.62
41 3 0.04
42 1 0.01
43 26 0.33
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (40 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
Found at i:1720066 original size:5 final size:6
Alignment explanation
Indices: 1720027--1720063 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1720017 GACACGTATT
1720027 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1720064 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1720762 original size:6 final size:6
Alignment explanation
Indices: 1720746--1720849 Score: 201
Period size: 6 Copynumber: 17.5 Consensus size: 6
1720736 TCTCGTCTCG
1720746 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1720793 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1720841 GGTCGT GGT
1 GGTCGT GGT
1720850 AATACGTGTC
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 93 0.95
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1720952 original size:20 final size:20
Alignment explanation
Indices: 1720927--1720966 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1720917 TTTTTAACTA
*
1720927 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
1720947 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
1720967 CTCTCAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.53
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:1720980 original size:20 final size:20
Alignment explanation
Indices: 1720957--1721116 Score: 131
Period size: 20 Copynumber: 7.4 Consensus size: 20
1720947 TTCTTTTTAA
*
1720957 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
*
1720977 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* *
1720997 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTAAATCG
1721017 CATTCGCATTGCGATTTTCTTCTAAATCG
1 ----CG--TTGCGA--TTC-TCTAAATCG
* *
1721046 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* *
1721066 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTAAATCG
*
1721086 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTAAATCG
1721109 CGTTGCGA
1 CGTTGCGA
1721117 ACTTGGAAGC
Statistics
Matches: 115, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
20 69 0.60
21 2 0.02
22 3 0.03
23 21 0.18
24 1 0.01
25 2 0.02
26 6 0.05
28 3 0.03
29 8 0.07
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTCTCTAAATCG
Found at i:1721090 original size:63 final size:66
Alignment explanation
Indices: 1720972--1721116 Score: 233
Period size: 69 Copynumber: 2.2 Consensus size: 66
1720962 CGATTCTCTC
*
1720972 AATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTCGCATTGCGATTTTCT
1 AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAA---CATTCGCATTGCGATTTTCT
1721037 TCTA
63 TCTA
1721041 AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAT-AA-A-TCGCATTGCGATTTTCTTCT
1 AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAACATTCGCATTGCGATTTTCTTCT
1721103 A
66 A
1721104 AATCGCGTTGCGA
1 AATCGCGTTGCGA
1721117 ACTTGGAAGC
Statistics
Matches: 75, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
63 34 0.45
64 1 0.01
68 2 0.03
69 38 0.51
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (66 bp):
AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAACATTCGCATTGCGATTTTCTTCT
A
Found at i:1721193 original size:20 final size:20
Alignment explanation
Indices: 1720957--1721220 Score: 120
Period size: 20 Copynumber: 12.6 Consensus size: 20
1720947 TTCTTTTTAA
* *
1720957 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1720977 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1720997 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
1721017 CATTCGCATTGCGATTTTCTTCTAAATCG
1 ----CG--TTGCGA--TT-TTCTAAATCG
* * *
1721046 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1721066 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
*
1721086 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1721109 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1721130 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
1721148 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1721170 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1721190 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1721209 CGTTGCGATTTT
1 CGTTGCGATTTT
1721221 ATTGGTCATT
Statistics
Matches: 191, Mismatches: 36, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
18 2 0.01
19 17 0.09
20 114 0.60
21 14 0.07
22 4 0.02
23 21 0.11
24 1 0.01
25 2 0.01
26 6 0.03
28 2 0.01
29 8 0.04
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1721210 original size:19 final size:20
Alignment explanation
Indices: 1721170--1721220 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1721160 TTCTTTTTAA
*
1721170 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1721190 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1721209 CGTTGCGATTTT
1 CGTTGCGATTTT
1721221 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1722843 original size:14 final size:15
Alignment explanation
Indices: 1722819--1722849 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1722809 AAAAGGAAAA
1722819 AAATGAATAATAAAT
1 AAATGAATAATAAAT
1722834 AAAT-AATAATAAAT
1 AAATGAATAATAAAT
1722848 AA
1 AA
1722850 TGTATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATGAATAATAAAT
Found at i:1723356 original size:33 final size:31
Alignment explanation
Indices: 1723319--1723394 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 31
1723309 AGTCCTACTT
*
1723319 GGACTCAAATGCTTCAGTTTTAGTGTTTCAATA
1 GGACTCAAATG-TT-AGTTTTAGTATTTCAATA
*
1723352 GGACTCAAACATGTTGGTTTTAGTATTTCAATA
1 GGACTC-AA-ATGTTAGTTTTAGTATTTCAATA
*
1723385 AGACTCAAAT
1 GGACTCAAAT
1723395 ACGTTGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 27 0.71
34 4 0.11
35 3 0.08
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (31 bp):
GGACTCAAATGTTAGTTTTAGTATTTCAATA
Found at i:1723474 original size:13 final size:13
Alignment explanation
Indices: 1723455--1723504 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1723445 GCTTGCAAAA
1723455 ATAATAAAA-AAT
1 ATAATAAAATAAT
1723467 ATTAATAACAATAAT
1 A-TAATAA-AATAAT
1723482 A-AATAAATATAAT
1 ATAATAAA-ATAAT
1723495 ATAATAAAAT
1 ATAATAAAAT
1723505 GTTTTTGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 19 0.58
14 8 0.24
15 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAAAATAAT
Found at i:1723482 original size:22 final size:22
Alignment explanation
Indices: 1723454--1723495 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1723444 GGCTTGCAAA
1723454 AATAATAAA-AAATATTAATAAC
1 AATAATAAATAAATA-TAATAAC
1723476 AATAATAAATAAATATAATA
1 AATAATAAATAAATATAATA
1723496 TAATAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAATAAATAAATATAATAAC
Found at i:1724147 original size:35 final size:34
Alignment explanation
Indices: 1723996--1724152 Score: 139
Period size: 32 Copynumber: 4.7 Consensus size: 34
1723986 AAATGAACAC
* *
1723996 GATATTCTTCGTCGTGAAGTTGAAATCATGG-A-T-
1 GATATCCTTCGTCGTGAAGTTG-AA-CCTGGAATTG
* *
1724029 GA-ACCCTTCGTCGTGAAGTTGAGCCTGGAATTG
1 GATATCCTTCGTCGTGAAGTTGAACCTGGAATTG
* **
1724062 GATATCCTTCGTCGTGAAGTTGAA-ATCCAATATG
1 GATATCCTTCGTCGTGAAGTTGAACCTGGAAT-TG
* *
1724096 G-T-CCCTTCGTCGTGAAGTTGAACCTTGGAGTTG
1 GATATCCTTCGTCGTGAAGTTGAACC-TGGAATTG
*
1724129 GATATCATTCGTCGTGAAGTTGAA
1 GATATCCTTCGTCGTGAAGTTGAA
1724153 ATCCAATGTA
Statistics
Matches: 99, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.04
31 2 0.02
32 37 0.37
33 12 0.12
34 26 0.26
35 18 0.18
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (34 bp):
GATATCCTTCGTCGTGAAGTTGAACCTGGAATTG
Found at i:1724154 original size:67 final size:67
Alignment explanation
Indices: 1724003--1724160 Score: 232
Period size: 66 Copynumber: 2.4 Consensus size: 67
1723993 CACGATATTC
*
1724003 TTCGTCGTGAAGTTGAAAT-C-ATGGATGAACCCTTCGTCGTGAAGTTGAGCCTGGAATTGGATA
1 TTCGTCGTGAAGTTGAAATCCAAT-GATGAACCCTTCGTCGTGAAGTTGAACCTGGAATTGGATA
*
1724066 TCC
65 TCA
** *
1724069 TTCGTCGTGAAGTTGAAATCCAAT-ATGGTCCCTTCGTCGTGAAGTTGAACCTTGGAGTTGGATA
1 TTCGTCGTGAAGTTGAAATCCAATGATGAACCCTTCGTCGTGAAGTTGAACC-TGGAATTGGATA
1724133 TCA
65 TCA
1724136 TTCGTCGTGAAGTTGAAATCCAATG
1 TTCGTCGTGAAGTTGAAATCCAATG
1724161 TAAGTTGTGA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
66 43 0.52
67 38 0.46
68 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (67 bp):
TTCGTCGTGAAGTTGAAATCCAATGATGAACCCTTCGTCGTGAAGTTGAACCTGGAATTGGATAT
CA
Found at i:1724650 original size:109 final size:106
Alignment explanation
Indices: 1724429--1724677 Score: 347
Period size: 109 Copynumber: 2.3 Consensus size: 106
1724419 GTATTGCTTC
* * * * *
1724429 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTAGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAAATAGAAAATTGTTTGTTGACAA
* *
1724494 TCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
66 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTGTCTT
*
1724535 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG---GAAATAGAAAA-TTGTTTGTTG
1724600 ACAATCA-CCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTGTCTT
62 ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
1724644 GGGTCCAATATCTTTCGCTGTGAAGTTAAAATTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1724678 GCTATGAAAT
Statistics
Matches: 127, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
106 37 0.29
109 73 0.57
110 17 0.13
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAAATAGAAAATTGTTTGTTGACAA
TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:1727612 original size:15 final size:16
Alignment explanation
Indices: 1727592--1727622 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1727582 TAGTGAGGTA
1727592 AATAAAAAT-AAAAAT
1 AATAAAAATGAAAAAT
1727607 AATAAAAATGAAAAAT
1 AATAAAAATGAAAAAT
1727623 CCTACCCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AATAAAAATGAAAAAT
Found at i:1728674 original size:7 final size:7
Alignment explanation
Indices: 1728664--1728713 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
1728654 AGAAAAAATG
1728664 AATAATA
1 AATAATA
1728671 AATAATAA
1 AATAAT-A
1728679 AATAAATA
1 AAT-AATA
1728687 AATAATA
1 AATAATA
1728694 AATAA-A
1 AATAATA
1728700 TAATAATA
1 -AATAATA
1728708 AATAAT
1 AATAAT
1728714 GTATTATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 26 0.67
8 9 0.23
9 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:1728685 original size:4 final size:4
Alignment explanation
Indices: 1728667--1728712 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
1728657 AAAAATGAAT
1728667 AATA AAT- AATAA AATA AATA AAT- AATA AATA AAT- AAT- AATA AATA
1 AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA
1728712 A
1 A
1728713 TGTATTATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.32
4 23 0.61
5 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1729221 original size:33 final size:33
Alignment explanation
Indices: 1729184--1729267 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
1729174 TCCTATATGA
* *
1729184 ACTCAAATGC-TTCGATTTTAGTGTTTCAATAGG
1 ACTCAAATACGTT-GATTTTAGTGTTTCAATAAG
*
1729217 ACTCAAATACGTTGATTTTTGTGTTTCAATAAG
1 ACTCAAATACGTTGATTTTAGTGTTTCAATAAG
1729250 ACTCAAATACGTTGATTT
1 ACTCAAATACGTTGATTT
1729268 ATTTTTTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 45 0.96
34 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (33 bp):
ACTCAAATACGTTGATTTTAGTGTTTCAATAAG
Found at i:1729325 original size:3 final size:3
Alignment explanation
Indices: 1729317--1729370 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
1729307 GGCTTGCAAA
*
1729317 AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AAAT AA- ATAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A-AT AAT AAT
1729362 AAT AA- AAT A
1 AAT AAT AAT A
1729371 TTTTTGTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 5 0.11
3 35 0.80
4 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1735988 original size:25 final size:25
Alignment explanation
Indices: 1735955--1736023 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
1735945 ATGTTAGGAG
* *
1735955 GGGT-GAACTTGTAAACTTTAAGTA
1 GGGTAGAACTTATAAAATTTAAGTA
*
1735979 GGGTATAACTTATAAAATTTAAGTA
1 GGGTAGAACTTATAAAATTTAAGTA
1736004 GGGTAGAACTTATAAAATTT
1 GGGTAGAACTTATAAAATTT
1736024 TAGGGAGTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 4 0.10
25 36 0.90
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
GGGTAGAACTTATAAAATTTAAGTA
Found at i:1737136 original size:2 final size:2
Alignment explanation
Indices: 1737131--1737178 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1737121 ATTTTTTGTG
*
1737131 TA TA TA TA TA TA TA TA TA TA TA TA TA -A CA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1737170 TA TA TA TA T
1 TA TA TA TA T
1737179 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1738111 original size:15 final size:16
Alignment explanation
Indices: 1738088--1738117 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1738078 ACATGTCATA
1738088 TTTAGATTTTTAAAAT
1 TTTAGATTTTTAAAAT
1738104 TTTA-ATTTTTAAAA
1 TTTAGATTTTTAAAA
1738118 ATAAAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTAGATTTTTAAAAT
Found at i:1743262 original size:21 final size:21
Alignment explanation
Indices: 1743236--1743306 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
1743226 AACAAATGCA
* * *
1743236 TTGCGATTTTGGAGTATCGCG
1 TTGCGAATTTCGACTATCGCG
*
1743257 TTGCGAATTTCGACTTTCGCG
1 TTGCGAATTTCGACTATCGCG
* * *
1743278 TTGCGAAATT-GAAT-TTGCG
1 TTGCGAATTTCGACTATCGCG
1743297 TTGCGAATTT
1 TTGCGAATTT
1743307 GTTGGTCATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.31
20 3 0.07
21 26 0.62
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (21 bp):
TTGCGAATTTCGACTATCGCG
Found at i:1743299 original size:19 final size:21
Alignment explanation
Indices: 1743252--1743303 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1743242 TTTTGGAGTA
* *
1743252 TCGCGTTGCGAATTTCGACTT
1 TCGCGTTGCGAAATTCGAATT
1743273 TCGCGTTGCGAAATT-GAATT
1 TCGCGTTGCGAAATTCGAATT
1743293 T-GCGTTGCGAA
1 TCGCGTTGCGAA
1743304 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.34
20 5 0.17
21 14 0.48
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGAAATTCGAATT
Found at i:1759719 original size:12 final size:12
Alignment explanation
Indices: 1759702--1759742 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1759692 ACCGTATTTA
1759702 TGAACAATACCG
1 TGAACAATACCG
* *
1759714 TGAACAATATCA
1 TGAACAATACCG
*
1759726 TGAACAGTACCG
1 TGAACAATACCG
1759738 TGAAC
1 TGAAC
1759743 TAAAATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (12 bp):
TGAACAATACCG
Found at i:1760365 original size:18 final size:18
Alignment explanation
Indices: 1760342--1760422 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 18
1760332 ACTGAATATT
1760342 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
1760360 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAAGACCAC----TA
* *
1760382 TGTCACGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
1760400 TGTCCC-AAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
1760417 TATCCC
1 TGTCCC
1760423 TCGACTCTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 15 0.28
18 22 0.41
22 17 0.31
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:1768439 original size:26 final size:26
Alignment explanation
Indices: 1768408--1768477 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
1768398 TTCTCTTATA
*
1768408 GCTTTGTTAAGCTATTTCTCATCCTT
1 GCTTTGCTAAGCTATTTCTCATCCTT
* * *
1768434 GCTTTGCTAAGTTTTTTCTCGTCCTT
1 GCTTTGCTAAGCTATTTCTCATCCTT
*
1768460 GCTTTGCTAAGCTTTTTC
1 GCTTTGCTAAGCTATTTC
1768478 ATTCTCTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.11, C:0.23, G:0.14, T:0.51
Consensus pattern (26 bp):
GCTTTGCTAAGCTATTTCTCATCCTT
Found at i:1772635 original size:17 final size:18
Alignment explanation
Indices: 1772599--1772638 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1772589 AATAAAAAAT
1772599 ATAAAGAAAATATCTAAA
1 ATAAAGAAAATATCTAAA
1772617 ATAAAGAATAAT-T-TAAA
1 ATAAAGAA-AATATCTAAA
1772634 ATAAA
1 ATAAA
1772639 AAATGGCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 9 0.43
19 3 0.14
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (18 bp):
ATAAAGAAAATATCTAAA
Found at i:1774314 original size:13 final size:13
Alignment explanation
Indices: 1774296--1774331 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1774286 AACTGCAAAA
*
1774296 AAATAAAATATTT
1 AAATAAAATAATT
1774309 AAATAAAATAATT
1 AAATAAAATAATT
1774322 AAATAAAATA
1 AAATAAAATA
1774332 CTAACAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1774416 original size:10 final size:10
Alignment explanation
Indices: 1774398--1774427 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1774388 TTGGTTTTTA
1774398 AGAGGATTTG
1 AGAGGATTTG
*
1774408 AGAGAATTTG
1 AGAGGATTTG
1774418 AGAGGATTTG
1 AGAGGATTTG
1774428 GTGTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (10 bp):
AGAGGATTTG
Found at i:1774946 original size:16 final size:16
Alignment explanation
Indices: 1774925--1774976 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1774915 ATATTTTATA
1774925 AAATTATTTATATTTT
1 AAATTATTTATATTTT
* * *
1774941 AAATTA-CT-TACTCT
1 AAATTATTTATATTTT
*
1774955 CAATTATTTATATTTT
1 AAATTATTTATATTTT
1774971 AAATTA
1 AAATTA
1774977 CTTACTCTCA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 15 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTATTTATATTTT
Found at i:1774962 original size:30 final size:30
Alignment explanation
Indices: 1774926--1774987 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1774916 TATTTTATAA
1774926 AATTATTTATATTTTAAATTACTTACTCTC
1 AATTATTTATATTTTAAATTACTTACTCTC
1774956 AATTATTTATATTTTAAATTACTTACTCTC
1 AATTATTTATATTTTAAATTACTTACTCTC
1774986 AA
1 AA
1774988 AGTTTTCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTATTTATATTTTAAATTACTTACTCTC
Found at i:1775273 original size:28 final size:28
Alignment explanation
Indices: 1775231--1775285 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1775221 GGATTTCAAT
* *
1775231 TGAAGACGCCTAGAGATCCCAACACCAC
1 TGAAGACGCCGAGAGATCCCAAAACCAC
1775259 TGAAGACGCCGAGAGATCCCAAAACCA
1 TGAAGACGCCGAGAGATCCCAAAACCA
1775286 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.33, G:0.20, T:0.09
Consensus pattern (28 bp):
TGAAGACGCCGAGAGATCCCAAAACCAC
Found at i:1775733 original size:21 final size:20
Alignment explanation
Indices: 1775647--1775804 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1775637 AAATGACCAA
**
1775647 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1775666 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1775686 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1775706 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1775727 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1775748 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1775768 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1775789 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1775805 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1776149 original size:20 final size:20
Alignment explanation
Indices: 1775772--1776162 Score: 450
Period size: 20 Copynumber: 19.4 Consensus size: 20
1775762 GATTTTCAAT
* ** *
1775772 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1775792 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1775812 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1775832 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A
**
1775853 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1775873 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1775893 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
1775913 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
1775934 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1775954 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1775974 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1775994 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1776014 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1776034 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1776054 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1776074 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1776094 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1776114 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1776134 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1776154 AATCACAAC
1 AATCGCAAC
1776163 ACTGAAATTT
Statistics
Matches: 319, Mismatches: 40, Indels: 24
0.83 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 279 0.87
21 35 0.11
22 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1776488 original size:14 final size:14
Alignment explanation
Indices: 1776469--1776558 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1776459 TTGAAATGAA
1776469 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1776483 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1776500 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1776516 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1776535 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1776549 AATCGCAACG
1 AATCGCAACG
1776559 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1776506 original size:33 final size:33
Alignment explanation
Indices: 1776461--1776575 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1776451 TCTTTTGGTT
1776461 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
1776494 GAGATGACAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1776527 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1776560 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1776576 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1776507 original size:19 final size:17
Alignment explanation
Indices: 1776468--1776580 Score: 82
Period size: 19 Copynumber: 6.8 Consensus size: 17
1776458 GTTGAAATGA
1776468 AAATCGCAA-CGAGA-G
1 AAATCGCAAGCGAGATG
1776483 -AATCGCAACGCGAGATG
1 AAATCGCAA-GCGAGATG
1776500 ACAATCGCAA-CGAGA-G
1 A-AATCGCAAGCGAGATG
*
1776516 -AATCGCAATGCGAAATG
1 AAATCGCAA-GCGAGATG
1776533 AAAATCGCAA-CGAGA-G
1 -AAATCGCAAGCGAGATG
*
1776549 -AATCGCAACGCGAAATG
1 AAATCGCAA-GCGAGATG
1776566 AAAATCGCAATGCGA
1 -AAATCGCAA-GCGA
1776581 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (17 bp):
AAATCGCAAGCGAGATG
Found at i:1776611 original size:14 final size:14
Alignment explanation
Indices: 1776592--1776646 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1776582 TTTGGTTTCG
1776592 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1776606 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1776625 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1776639 CGTTGCGA
1 CGTTGCGA
1776647 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1776624 original size:33 final size:33
Alignment explanation
Indices: 1776576--1776646 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1776566 AAAATCGCAA
**
1776576 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1776609 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1776642 TGCGA
1 TGCGA
1776647 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1776654 original size:33 final size:33
Alignment explanation
Indices: 1776587--1776668 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1776577 GCGATTTTGG
***
1776587 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1776620 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1776653 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1776669 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1776673 original size:20 final size:20
Alignment explanation
Indices: 1776599--1776687 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1776589 TCGCGTTGCG
1776599 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1776619 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1776632 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1776652 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1776672 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1776688 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1776809 original size:33 final size:33
Alignment explanation
Indices: 1776767--1776837 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1776757 AATACTAACT
1776767 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
***
1776800 TGAAAATCGCAACGAGAGAATCTTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1776833 TGAAA
1 TGAAA
1776838 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1777071 original size:22 final size:22
Alignment explanation
Indices: 1777019--1777073 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1777009 TGGTTGTGAG
**
1777019 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1777041 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1777063 GGATTTCTTCG
1 GGATTTCTTCG
1777074 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1777244 original size:20 final size:20
Alignment explanation
Indices: 1777219--1777412 Score: 212
Period size: 20 Copynumber: 9.6 Consensus size: 20
1777209 CTTTAAATAT
1777219 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1777239 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1777261 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1777280 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1777300 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1777320 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1777341 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1777361 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1777381 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1777401 CGCGTTGCGATT
1 CGCGTTGCGATT
1777413 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 110 0.75
21 32 0.22
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1777296 original size:61 final size:60
Alignment explanation
Indices: 1777219--1777412 Score: 237
Period size: 61 Copynumber: 3.2 Consensus size: 60
1777209 CTTTAAATAT
*
1777219 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTAGCGTTGCGATTTACGGATA
* * ***
1777280 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTA-GCGTTGCGA-TTTACGGATA
* * * * ** *
1777341 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
1777401 CGCGTTGCGATT
1 CGCGTTGCGATT
1777413 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.02
60 30 0.27
61 78 0.70
62 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
Found at i:1777389 original size:81 final size:81
Alignment explanation
Indices: 1777218--1777412 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 81
1777208 GCTTTAAATA
** * * *
1777218 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
1777283 GTTGCGATATACGGAT
66 GTTGCGATATACGGAT
* * *
1777299 ACGCATTGCGATTTACCCATACGCGTTGCGATTTTACGGA-TACACGTTGCGATTTACGGATACG
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTA-ACGTTGCGATTTACGGATACG
* *
1777363 CGTTGCGATTTATGTG-T
65 CGTTGCGATATACG-GAT
* * *
1777380 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACACATACGCGTTGCGATT
1777413 ATTGAAAATC
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 94 0.97
82 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (81 bp):
TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
GTTGCGATATACGGAT
Found at i:1782521 original size:33 final size:33
Alignment explanation
Indices: 1782479--1782545 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1782469 CATTAAAAAG
*
1782479 TATTAAAATAAAGTTTTAATTATTACTGAGAAA
1 TATTAAAATAAAATTTTAATTATTACTGAGAAA
*
1782512 TATTAAAATAAAATTTTAATTATTATTGAGAAA
1 TATTAAAATAAAATTTTAATTATTACTGAGAAA
1782545 T
1 T
1782546 CGAATTCAAT
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:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (33 bp):
TATTAAAATAAAATTTTAATTATTACTGAGAAA
Found at i:1787762 original size:75 final size:75
Alignment explanation
Indices: 1787605--1787744 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
1787595 TCATATTTTA
* * * * * *
1787605 AATTTTAAGTTAAAATAAATCATGTTGGATGAAAATCGTTAGTTAACTAATGATCAACACATGTT
1 AATTTTTAGTCAAAATAAATCATGTTGGATAAAAATCGTTAATTAACTAACGATCAAAACATGTT
**
1787670 ACAACGTTTC
66 ACAACGTGAC
* *
1787680 AATTTTTAGTCAAAATAAATCATGTTGGATAAAAA-CTGTTAATTGACTAACGATCAAAACTTGT
1 AATTTTTAGTCAAAATAAATCATGTTGGATAAAAATC-GTTAATTAACTAACGATCAAAACATGT
1787744 T
65 T
1787745 GTTAATGTGA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 1 0.02
75 55 0.98
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (75 bp):
AATTTTTAGTCAAAATAAATCATGTTGGATAAAAATCGTTAATTAACTAACGATCAAAACATGTT
ACAACGTGAC
Found at i:1787896 original size:104 final size:104
Alignment explanation
Indices: 1787716--1787921 Score: 376
Period size: 104 Copynumber: 2.0 Consensus size: 104
1787706 GGATAAAAAC
*
1787716 TGTTAATTGACTAACGATCAAAACTTGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
1 TGTTAATTGACTAACGATCAAAACATGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
1787781 CATAGTATGTACCACATAACTCAAAATAATGACATGAAA
66 CATAGTATGTACCACATAACTCAAAATAATGACATGAAA
* *
1787820 TGTTAATTGACTAACGATCAACACATGTTGTTAATGTGATATTTTTACATATGTTAAATTATTGA
1 TGTTAATTGACTAACGATCAAAACATGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
*
1787885 CATAGTATGTACCACATAATTCAAAATAATGACATGA
66 CATAGTATGTACCACATAACTCAAAATAATGACATGA
1787922 CATATGTCAT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (104 bp):
TGTTAATTGACTAACGATCAAAACATGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
CATAGTATGTACCACATAACTCAAAATAATGACATGAAA
Found at i:1790196 original size:21 final size:22
Alignment explanation
Indices: 1790172--1790212 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1790162 CAGATTGCTC
1790172 AGAGGGAACCGATTC-CCCCGA
1 AGAGGGAACCGATTCTCCCCGA
*
1790193 AGAGGGTACCGATTCTCCCC
1 AGAGGGAACCGATTCTCCCC
1790213 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.34, G:0.27, T:0.15
Consensus pattern (22 bp):
AGAGGGAACCGATTCTCCCCGA
Found at i:1796097 original size:23 final size:22
Alignment explanation
Indices: 1796055--1796138 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
1796045 TTAGTACAGA
*
1796055 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
1796077 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
1796100 GGGAACCGATTCCCTCC-TGTAG
1 GGGAACCGATACCC-CCTTGAAG
*
1796122 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
1796139 GAGGTTCTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 2 0.04
22 30 0.56
23 20 0.37
24 2 0.04
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1797716 original size:18 final size:18
Alignment explanation
Indices: 1797681--1797719 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1797671 AGAGCAGTAC
*
1797681 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
1797699 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
1797717 GAG
1 GAG
1797720 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:1803398 original size:63 final size:62
Alignment explanation
Indices: 1803292--1803415 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 62
1803282 AACCTCGACA
* **
1803292 ACTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCTTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
1803354 ACTGTCCATATGTCTCGAAAG-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTC-CCAAAGAACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTA
1803416 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
62 22 0.41
63 32 0.59
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:1803411 original size:32 final size:32
Alignment explanation
Indices: 1803292--1803416 Score: 123
Period size: 31 Copynumber: 4.0 Consensus size: 32
1803282 AACCTCGACA
* * ** *
1803292 ACTGTCCATAGGTCCCAAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
**
1803323 ACTGTCCATATGTTCTTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
1803354 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
1803386 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
1803417 ACCCTCGACT
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 5 0.06
31 43 0.56
32 25 0.32
33 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:1803823 original size:25 final size:24
Alignment explanation
Indices: 1803769--1803823 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1803759 AGTCACATTT
*
1803769 CATATAACACTTATATTACATATT
1 CATATAACACTTATATTACATATA
* *
1803793 CTTATAATTACTTATATTA-ATATCA
1 CATATAA-CACTTATATTACATAT-A
1803818 CATATA
1 CATATA
1803824 TCAAAGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (24 bp):
CATATAACACTTATATTACATATA
Found at i:1805300 original size:2 final size:2
Alignment explanation
Indices: 1805293--1805318 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1805283 TTCTCTTCCA
1805293 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1805319 GATAAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1805556 original size:72 final size:72
Alignment explanation
Indices: 1805469--1805603 Score: 207
Period size: 72 Copynumber: 1.9 Consensus size: 72
1805459 AAAATATGAT
* * * *
1805469 ATATGCACATGCATATGAACAATCCTTATTCTTAGAATTTGCACCCTAATGATTTTATATATATA
1 ATATGCACATGCATATCAACAATCCTTACTCTCAGAATTTGCACCCTAATGATTTTACATATATA
1805534 ACGTGAC
66 ACGTGAC
* * *
1805541 ATATGCACCTGCATATCAACAATCCTTACTCTCATAATTTGCTCCCTAATGATTTTACATATA
1 ATATGCACATGCATATCAACAATCCTTACTCTCAGAATTTGCACCCTAATGATTTTACATATA
1805604 GAAGATGGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (72 bp):
ATATGCACATGCATATCAACAATCCTTACTCTCAGAATTTGCACCCTAATGATTTTACATATATA
ACGTGAC
Found at i:1806003 original size:30 final size:31
Alignment explanation
Indices: 1805969--1806028 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1805959 TTATTTTGAT
*
1805969 TTTACCCCTTATT-TTCTATGG-TAATTATAC
1 TTTACCCCTCATTATT-TATGGTTAATTATAC
*
1805999 TTTACCCGTCATTATTTATGGTTAATTATA
1 TTTACCCCTCATTATTTATGGTTAATTATA
1806029 TTTTGCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (31 bp):
TTTACCCCTCATTATTTATGGTTAATTATAC
Found at i:1811241 original size:23 final size:23
Alignment explanation
Indices: 1811204--1811247 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1811194 TCTGAATGAT
*
1811204 ACAGTGCTGACTGATTCAACAAA
1 ACAGTGCTGAATGATTCAACAAA
*
1811227 ACAGTGTTGAATGATTCAACA
1 ACAGTGCTGAATGATTCAACA
1811248 CAGAAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (23 bp):
ACAGTGCTGAATGATTCAACAAA
Found at i:1812180 original size:21 final size:22
Alignment explanation
Indices: 1812146--1812191 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
1812136 AATATATTTA
1812146 TTATATTTTAATAATATA-ATAT
1 TTATATTTTAATAAT-TACATAT
1812168 TTATATTTT-ATAATTACATAT
1 TTATATTTTAATAATTACATAT
1812189 TTA
1 TTA
1812192 ATAAAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 12 0.52
22 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATTTTAATAATTACATAT
Found at i:1813597 original size:175 final size:170
Alignment explanation
Indices: 1813288--1813627 Score: 626
Period size: 175 Copynumber: 2.0 Consensus size: 170
1813278 CATTTCCCTC
1813288 TCATACGAAGAGTGAGAACCCTCAGTCACTTCAGGGTCTTGAATAGTCGGAGTCTGATGAGTCAC
1 TCATACGAAGAGTGAGAACCCTCAGTCACTTCAGGGTCTTGAATAGTCGGAGTCTGATGAGTCAC
1813353 TGTTCAGTGCTGACACATATCATTGTATTCTTGTTGAACTATCATCTCCTTCCAACAATGTACTC
66 TGTTCAGTGCTGACACATATCATTGTATTCTTGTTGAACTATCATCTCCTTCCAACAATGTACTC
1813418 GATGGTTCATCAGAGAACTCAGCAACCGGGTTCCTCTCTA
131 GATGGTTCATCAGAGAACTCAGCAACCGGGTTCCTCTCTA
*
1813458 TCATCCGAAGAGTGAGAACCCTCAGTCACTTCAGGGTCTTCTGAATAGTCGGAGTCTGATGAGTC
1 TCATACGAAGAGTGAGAACCCTCAGTCACTTCAGGGTC-T-TGAATAGTCGGAGTCTGATGAGTC
1813523 ACTGTTCAGTGCTGACACATTATCATTTGTCATTCTTGTTGAACTATCATCTCCTTCCAACAATG
64 ACTGTTCAGTGCTGACACA-TATCA-TTGT-ATTCTTGTTGAACTATCATCTCCTTCCAACAATG
1813588 TACTCGATGGTTCATCAGAGAACTCAGCAACCGGGTTCCT
126 TACTCGATGGTTCATCAGAGAACTCAGCAACCGGGTTCCT
1813628 TTCCCCACTA
Statistics
Matches: 164, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
170 37 0.23
171 1 0.01
172 43 0.26
173 5 0.03
174 4 0.02
175 74 0.45
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (170 bp):
TCATACGAAGAGTGAGAACCCTCAGTCACTTCAGGGTCTTGAATAGTCGGAGTCTGATGAGTCAC
TGTTCAGTGCTGACACATATCATTGTATTCTTGTTGAACTATCATCTCCTTCCAACAATGTACTC
GATGGTTCATCAGAGAACTCAGCAACCGGGTTCCTCTCTA
Found at i:1817321 original size:15 final size:15
Alignment explanation
Indices: 1817289--1817329 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1817279 TTTAATAAAT
1817289 ACACGAACA-AACGA
1 ACACGAACATAACGA
*
1817303 ACACGAACATAATGA
1 ACACGAACATAACGA
1817318 ACACGAACATAA
1 ACACGAACATAA
1817330 ACGTTAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.07
Consensus pattern (15 bp):
ACACGAACATAACGA
Found at i:1821204 original size:23 final size:24
Alignment explanation
Indices: 1821170--1821230 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
1821160 TATTATGTTA
*
1821170 AACATAAATGAACGCACAT-AACG
1 AACATAACTGAACGCACATAAACG
*
1821193 AACATAACTGAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
1821217 AACATAACCGAACG
1 AACATAACTGAACG
1821231 TTCACGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.51, C:0.23, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:1827229 original size:21 final size:21
Alignment explanation
Indices: 1827203--1827251 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1827193 ACCTAATATT
1827203 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
1827224 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
*
1827245 ATAATGT
1 ACAATGT
1827252 TTGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (21 bp):
ACAATGTCAAAATTAGGTGCA
Found at i:1835596 original size:20 final size:22
Alignment explanation
Indices: 1835556--1835598 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1835546 TTTCATTACA
1835556 TTTTTATAATTAAATTTTTAAAT
1 TTTTTATAATT-AATTTTTAAAT
1835579 TTTTTATAATT-A-TTTTAAAT
1 TTTTTATAATTAATTTTTAAAT
1835599 ATAAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
23 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATAATTAATTTTTAAAT
Found at i:1838856 original size:3 final size:3
Alignment explanation
Indices: 1838848--1838874 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1838838 AATGACATCA
1838848 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1838875 TTTTATTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1839697 original size:2 final size:2
Alignment explanation
Indices: 1839655--1839680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1839645 ACATACATAC
1839655 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1839681 CAAAGTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1841363 original size:2 final size:2
Alignment explanation
Indices: 1841356--1841393 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1841346 ATTCAATTTA
1841356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1841394 GAAGTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1843360 original size:21 final size:22
Alignment explanation
Indices: 1843314--1843360 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1843304 ATAACATTAC
*
1843314 AAATCTTACGTACAAATGATAA
1 AAATATTACGTACAAATGATAA
*
1843336 AAATATTACGTACACATGA-AA
1 AAATATTACGTACAAATGATAA
1843357 AAAT
1 AAAT
1843361 TATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.26
Consensus pattern (22 bp):
AAATATTACGTACAAATGATAA
Found at i:1845420 original size:21 final size:21
Alignment explanation
Indices: 1845378--1845420 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1845368 TTTCTGGGCT
* *
1845378 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1845399 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1845420 A
1 A
1845421 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1845971 original size:2 final size:2
Alignment explanation
Indices: 1845964--1846037 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1845954 ACATGTTACA
1845964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1846006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1846038 GAGTTGTGTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1846203 original size:4 final size:4
Alignment explanation
Indices: 1846194--1846218 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1846184 GAGGGATGAC
1846194 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
1846219 ATGGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1846504 original size:30 final size:30
Alignment explanation
Indices: 1846470--1846782 Score: 599
Period size: 30 Copynumber: 10.4 Consensus size: 30
1846460 GGTTCTTCGG
*
1846470 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846500 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846530 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1846560 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1846590 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846620 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846650 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846680 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846710 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846740 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1846770 GACCTCTGGATAG
1 GACCTCTGGATAG
1846783 GTCCTTCGGA
Statistics
Matches: 280, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 280 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1849521 original size:2 final size:2
Alignment explanation
Indices: 1849514--1849555 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1849504 TAATTAAATG
1849514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1849556 GGATAAGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1850115 original size:21 final size:21
Alignment explanation
Indices: 1850073--1850115 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1850063 TTTCTGGGCT
* *
1850073 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1850094 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1850115 A
1 A
1850116 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1850664 original size:2 final size:2
Alignment explanation
Indices: 1850657--1850688 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1850647 ACATGTTACA
1850657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1850689 GAGTTGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1851124 original size:31 final size:31
Alignment explanation
Indices: 1851038--1851130 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
1851028 GTCAAAGAAC
* * * *
1851038 TACCTATGTTTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTTCGGGACATATGGATAGTT
** *
1851069 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTTCGGGACATATGGATAGTT
* *
1851100 TACCTAGGTTCTTCGGGACCTATGGATAGTT
1 TACCTATGTTCTTCGGGACATATGGATAGTT
1851131 ACCGAGGATC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGGATAGTT
Found at i:1851150 original size:30 final size:30
Alignment explanation
Indices: 1851116--1851398 Score: 512
Period size: 30 Copynumber: 9.4 Consensus size: 30
1851106 GGTTCTTCGG
*
1851116 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1851146 GACCTCCGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1851176 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1851206 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* * *
1851236 GACCTATGGATAATTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1851266 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1851296 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1851326 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1851356 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1851386 GACCTCTGGATAG
1 GACCTCTGGATAG
1851399 GTCCTTCGGA
Statistics
Matches: 244, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 244 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1854391 original size:18 final size:19
Alignment explanation
Indices: 1854351--1854392 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1854341 AAATTCCCCC
* *
1854351 CTTTTGTATTGGTTTATTG
1 CTTTTGGATTGGTTTATCG
1854370 -TTTTGGATTGGTTT-TCG
1 CTTTTGGATTGGTTTATCG
1854387 CTTTTG
1 CTTTTG
1854393 AATGTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.07, C:0.07, G:0.24, T:0.62
Consensus pattern (19 bp):
CTTTTGGATTGGTTTATCG
Found at i:1860330 original size:29 final size:30
Alignment explanation
Indices: 1860284--1860344 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
1860274 ATATGTCTTT
* * *
1860284 TTTCAGTTTAATGTCTAATGTTT-ATTTCG
1 TTTCAGTTTAATGCCTAACGTTTCATTCCG
**
1860313 TTTCAGTTTGGTGCCTAACGTTTCATTCCG
1 TTTCAGTTTAATGCCTAACGTTTCATTCCG
1860343 TT
1 TT
1860345 ACTTAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (30 bp):
TTTCAGTTTAATGCCTAACGTTTCATTCCG
Found at i:1862371 original size:21 final size:22
Alignment explanation
Indices: 1862346--1862389 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1862336 ATTGCATTAG
*
1862346 GGGTAATGATACCC-TGCTACA
1 GGGTAACGATACCCTTGCTACA
*
1862367 GGGTACCGATACCCTTGCTACA
1 GGGTAACGATACCCTTGCTACA
1862389 G
1 G
1862390 TACTGCTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (22 bp):
GGGTAACGATACCCTTGCTACA
Found at i:1862398 original size:11 final size:11
Alignment explanation
Indices: 1862382--1862413 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1862372 CCGATACCCT
1862382 TGCTACAGTAC
1 TGCTACAGTAC
1862393 TGCTACAGTAC
1 TGCTACAGTAC
1862404 TGCTACAGTA
1 TGCTACAGTA
1862414 ATTTCGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (11 bp):
TGCTACAGTAC
Found at i:1863679 original size:13 final size:13
Alignment explanation
Indices: 1863661--1863707 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
1863651 GAGGAGAGGA
1863661 AGAAGAAAGAAGG
1 AGAAGAAAGAAGG
*
1863674 AGAAGAGAAGAGGG
1 AGAAGA-AAGAAGG
1863688 AGAAGAAAGAAGG
1 AGAAGAAAGAAGG
1863701 AGAAGAA
1 AGAAGAA
1863708 GAGAGTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGAAGAAAGAAGG
Found at i:1863691 original size:27 final size:27
Alignment explanation
Indices: 1863655--1863706 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1863645 ATACGGGAGG
1863655 AGAGGAAGAAGAAAGAAGGAGAAGAGA
1 AGAGGAAGAAGAAAGAAGGAGAAGAGA
*
1863682 AGAGGGAGAAGAAAGAAGGAGAAGA
1 AGAGGAAGAAGAAAGAAGGAGAAGA
1863707 AGAGAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (27 bp):
AGAGGAAGAAGAAAGAAGGAGAAGAGA
Found at i:1863712 original size:27 final size:26
Alignment explanation
Indices: 1863654--1863712 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
1863644 TATACGGGAG
1863654 GAGAGGAAGAAGAAAGAAGGAGAAGA
1 GAGAGGAAGAAGAAAGAAGGAGAAGA
*
1863680 GAAGAGGGAGAAGAAAGAAGGAGAAGAA
1 G-AGAGGAAGAAGAAAGAAGGAGAAG-A
1863708 GAGAG
1 GAGAG
1863713 TTTTCTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 27 0.90
28 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (26 bp):
GAGAGGAAGAAGAAAGAAGGAGAAGA
Found at i:1866498 original size:2 final size:2
Alignment explanation
Indices: 1866491--1866527 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1866481 TTACGGAAGC
1866491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1866528 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1866532 original size:2 final size:2
Alignment explanation
Indices: 1866527--1866559 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1866517 ATATATATAT
1866527 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1866560 AGAATGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1868712 original size:2 final size:2
Alignment explanation
Indices: 1868700--1868732 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1868690 AAACTCAAAA
1868700 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1868733 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1871724 original size:174 final size:174
Alignment explanation
Indices: 1871429--1871776 Score: 538
Period size: 174 Copynumber: 2.0 Consensus size: 174
1871419 TGCTGTTCCC
1871429 GATTTCTTAAATCTGCTTTGTTTCTTGAGATTTCATGATATCTGATTCTTTCACTGCTTTAGAGC
1 GATTTCTTAAATCTGCTTTGTTTCTTGAGATTTCATGATATCTGATTCTTTCACTGCTTTAGAGC
* * * * *
1871494 GAATGTGTTGGATCTTATTTTGTTTGATGATTTCTTTACTCGTAAATTGGTGAATGCTTTGATCT
66 GAATGTGTTGGATCCTATTTTGTTTGATGATTTCCTTACTCGTAAATCGATGAATGCTTTGACCT
** *
1871559 GATTTTGCTTCTACGGATTCTAGTGATGCATTACATCGTCGAAT
131 GATTTAACTTCTACGGATTCTAGTGAGGCATTACATCGTCGAAT
** * *
1871603 GATTTCTTAAATCTGCTTTGTTTCTTTTGATTTCTTGATATCTGGTTCTTTCACTG-TTTCAGAG
1 GATTTCTTAAATCTGCTTTGTTTCTTGAGATTTCATGATATCTGATTCTTTCACTGCTTT-AGAG
*
1871667 -GAAATGTGTTGGATCCTATTTTGTTTGATGATTTCCTTACTTGTAAATCGATGAATGCTTTGAC
65 CG-AATGTGTTGGATCCTATTTTGTTTGATGATTTCCTTACTCGTAAATCGATGAATGCTTTGAC
*
1871731 CTGATTTAACTTCTACGGATTCTAGTGAGGCATTGCATCGTCGAAT
129 CTGATTTAACTTCTACGGATTCTAGTGAGGCATTACATCGTCGAAT
1871777 TAGAGCTTCA
Statistics
Matches: 158, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
173 4 0.03
174 154 0.97
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (174 bp):
GATTTCTTAAATCTGCTTTGTTTCTTGAGATTTCATGATATCTGATTCTTTCACTGCTTTAGAGC
GAATGTGTTGGATCCTATTTTGTTTGATGATTTCCTTACTCGTAAATCGATGAATGCTTTGACCT
GATTTAACTTCTACGGATTCTAGTGAGGCATTACATCGTCGAAT
Found at i:1882276 original size:32 final size:31
Alignment explanation
Indices: 1882231--1882293 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 31
1882221 TTGTATCAGT
1882231 CAATAACTAATCATCATCCATAAGAGCAAAA
1 CAATAACTAATCATCATCCATAAGAGCAAAA
1882262 CAATCAACTAATCATCATCCATAAGAGCAAAA
1 CAAT-AACTAATCATCATCCATAAGAGCAAAA
1882294 AAGGTTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.51, C:0.24, G:0.06, T:0.19
Consensus pattern (31 bp):
CAATAACTAATCATCATCCATAAGAGCAAAA
Found at i:1886433 original size:67 final size:67
Alignment explanation
Indices: 1886325--1886458 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
1886315 AAGGGCTCCC
1886325 GTGATTTAAAATTTCAGAGATAATCAATAAAAAATAGAAAGAAAATATCTAAATTATAAGAAAAT
1 GTGATTTAAAATTTCAGAGATAATCAATAAAAAATAGAAAGAAAATATCTAAATTATAAGAAAAT
1886390 TT
66 TT
1886392 GTGATTTAAAATTTCAGAGATAATCAATAAAAAATAGAAAGAAAATATCTAAATTATAAGAAAAT
1 GTGATTTAAAATTTCAGAGATAATCAATAAAAAATAGAAAGAAAATATCTAAATTATAAGAAAAT
1886457 TT
66 TT
1886459 AAAATTTTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.30
Consensus pattern (67 bp):
GTGATTTAAAATTTCAGAGATAATCAATAAAAAATAGAAAGAAAATATCTAAATTATAAGAAAAT
TT
Found at i:1888747 original size:2 final size:2
Alignment explanation
Indices: 1888740--1888780 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1888730 TCGTAACTGC
*
1888740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1888781 AAAGAAAGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1892484 original size:2 final size:2
Alignment explanation
Indices: 1892477--1892518 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1892467 CCCCACCTCC
1892477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1892519 TAGTTCTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.