Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008708.1 Hibiscus syriacus cultivar Beakdansim tig00111754_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: 1112311
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:610030 original size:103 final size:103
Alignment explanation
Indices: 609859--610171 Score: 502
Period size: 103 Copynumber: 3.0 Consensus size: 103
609849 TAATGTCCAT
*
609859 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGGCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
609924 GACTTCACACATGTTGCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
609962 AAGGACCGCATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
610027 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * **
610065 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-GTCAAGGATCAAGTATGTGTCTCAAA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACT-AGGGATCAAGTATGTGTCTCACC
* * *
610129 AGACCTCACACCTATTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
610168 AAGG
1 AAGG
610172 GCCGCGTAGA
Statistics
Matches: 194, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
102 1 0.01
103 193 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:615635 original size:103 final size:103
Alignment explanation
Indices: 615467--615770 Score: 491
Period size: 103 Copynumber: 3.0 Consensus size: 103
615457 TGTCCATAAG
615467 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
615532 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
* *
615570 GACCACATATCATTTCTTAAGAATCATATACATATACTAGGGATCAAGTATGAGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
* *
615635 TTCACACATGTTCCAAAGAATACATATATGTTCTGAAT
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
* * ** * **
615673 GACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTCTCTCAAAAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
* *
615738 CTCACACCTGTTCCAAAGAATACATATATGTCC
66 TTCACACATGTTCCAAAGAATACATATATGTCC
615771 AGAAGAACCG
Statistics
Matches: 185, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 185 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.29
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
Found at i:616721 original size:64 final size:65
Alignment explanation
Indices: 616576--616723 Score: 153
Period size: 64 Copynumber: 2.3 Consensus size: 65
616566 CCGATGAATC
* **
616576 GATGCACTACTTGTGCATCGGTGCACAAAATATATTCGATGTTTGTTTATTACTAGGATGCATAT
1 GATGCACTACTTGTGCATCGGTGCACAAAATACATTCGATGTTTGTTTATTAAAAGGATGCATAT
** * * * *
616641 -ATGCA-TACCTAATGCATCGGTGCACTAATTGCATTCGATGTTT-TTATTTTAAAA-GAGTGCA
1 GATGCACTA-CTTGTGCATCGGTGCACAAAATACATTCGATGTTTGTT-TATTAAAAGGA-TGCA
616702 T-T
63 TAT
616704 GATGCACTACTTGTGCATCG
1 GATGCACTACTTGTGCATCG
616724 ATACACCTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
63 7 0.10
64 58 0.87
65 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (65 bp):
GATGCACTACTTGTGCATCGGTGCACAAAATACATTCGATGTTTGTTTATTAAAAGGATGCATAT
Found at i:617328 original size:2 final size:2
Alignment explanation
Indices: 617321--617352 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
617311 CCACGTGTAA
617321 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
617353 CCCCACTATC
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:626131 original size:26 final size:26
Alignment explanation
Indices: 626083--626135 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
626073 AAAAATTATA
**
626083 TATTTTTAAAATATATGAATATAATT
1 TATTTTTAAAATATAAAAATATAATT
626109 TATTTTTAAAAT-TAAAAATTATAATT
1 TATTTTTAAAATATAAAAA-TATAATT
626135 T
1 T
626136 TTTGAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTTTTAAAATATAAAAATATAATT
Found at i:628478 original size:2 final size:2
Alignment explanation
Indices: 628471--628508 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
628461 GTCCATTCGA
628471 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
628509 GGAAAAAGAG
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:631304 original size:19 final size:18
Alignment explanation
Indices: 631280--631329 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
631270 GAAAAGTTAT
* *
631280 TTTTAAACTAAGTAATTAA
1 TTTTAAAATAA-TAATAAA
*
631299 TTTTAAAATTATAATAAA
1 TTTTAAAATAATAATAAA
631317 TTTTAAAA-AATAA
1 TTTTAAAATAATAA
631330 AACTCGTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 4 0.15
18 14 0.52
19 9 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTTAAAATAATAATAAA
Found at i:632360 original size:18 final size:19
Alignment explanation
Indices: 632333--632379 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
632323 TAATCCAACA
*
632333 AAATTGTAAACAG-TAAT-T
1 AAATTATAAA-AGTTAATAT
*
632351 AAATTATAAAAGTTACTAT
1 AAATTATAAAAGTTAATAT
632370 AAATTATAAA
1 AAATTATAAA
632380 TAAATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 12 0.48
19 11 0.44
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (19 bp):
AAATTATAAAAGTTAATAT
Found at i:644043 original size:16 final size:16
Alignment explanation
Indices: 644022--644053 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
644012 ACGGCACTAC
644022 AGACGCATACATTCAT
1 AGACGCATACATTCAT
644038 AGACGCATACATTCAT
1 AGACGCATACATTCAT
644054 GACATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
AGACGCATACATTCAT
Found at i:653651 original size:18 final size:18
Alignment explanation
Indices: 653625--653660 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
653615 TAATTGCCCC
*
653625 TAAAGTGTAAAATGACCT
1 TAAACTGTAAAATGACCT
653643 TAAACTGTAAAATGACCT
1 TAAACTGTAAAATGACCT
653661 AAAATATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (18 bp):
TAAACTGTAAAATGACCT
Found at i:654704 original size:31 final size:31
Alignment explanation
Indices: 654669--654771 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 31
654659 AAGACTACGG
654669 TAGGTTCAGTCGATGCTGGTAATTCCTTGTA
1 TAGGTTCAGTCGATGCTGGTAATTCCTTGTA
* * *
654700 TAGGTTTA-AC-ACTGACTGGTAATTCCTATATCTA
1 TAGGTTCAGTCGA-TG-CTGGTAATTCC--T-TGTA
* * *
654734 GCAGGTTCAGTCGCTGCCGGTAATTCCTTGTA
1 -TAGGTTCAGTCGATGCTGGTAATTCCTTGTA
654766 TAGGTT
1 TAGGTT
654772 TAGCACCGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
29 1 0.02
30 3 0.06
31 23 0.43
32 3 0.06
33 2 0.04
34 3 0.06
35 16 0.30
36 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
TAGGTTCAGTCGATGCTGGTAATTCCTTGTA
Found at i:654787 original size:31 final size:31
Alignment explanation
Indices: 654684--654793 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 31
654674 TCAGTCGATG
*
654684 CTGGTAATTCCTTGTATAGGTTTAACACTGA
1 CTGGTAATTCCTTGTATAGGTTTAGCACTGA
* * * *
654715 CTGGTAATTCCTATATCTAGCAGGTTCAGTCGCTG-
1 CTGGTAATTCC--T-TGTA-TAGGTTTAG-CACTGA
* *
654750 CCGGTAATTCCTTGTATAGGTTTAGCACCGA
1 CTGGTAATTCCTTGTATAGGTTTAGCACTGA
654781 CTGGTAATTCCTT
1 CTGGTAATTCCTT
654794 ATGGACTTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
30 3 0.05
31 30 0.49
32 3 0.05
33 2 0.03
34 3 0.05
35 16 0.26
36 4 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (31 bp):
CTGGTAATTCCTTGTATAGGTTTAGCACTGA
Found at i:655962 original size:15 final size:16
Alignment explanation
Indices: 655935--655966 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
655925 TTCACATTAA
655935 ATTTTATAAATAAATT
1 ATTTTATAAATAAATT
655951 ATTTTA-AAATAAATT
1 ATTTTATAAATAAATT
655966 A
1 A
655967 CACCAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTATAAATAAATT
Found at i:661295 original size:22 final size:22
Alignment explanation
Indices: 661267--661310 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
661257 GCTCGGTTCA
*
661267 CAATTTT-GAACGTCGAAGAACT
1 CAATTTTGGAACATCGAA-AACT
661289 CAATTTTGGAACATCGAAAACT
1 CAATTTTGGAACATCGAAAACT
661311 TTGATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (22 bp):
CAATTTTGGAACATCGAAAACT
Found at i:665388 original size:22 final size:22
Alignment explanation
Indices: 665347--665391 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
665337 CATTGCATAA
665347 AAATTAAACAGTTATAACTCCTG
1 AAATTAAACAG-TATAACTCCTG
665370 AAATTAAATCAG-ATAACTCCTG
1 AAATTAAA-CAGTATAACTCCTG
665392 TAACTCCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
AAATTAAACAGTATAACTCCTG
Found at i:667751 original size:14 final size:14
Alignment explanation
Indices: 667734--667763 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
667724 TACCATTGTT
667734 CTCATATAGATCTC
1 CTCATATAGATCTC
*
667748 CTCATCTAGATCTC
1 CTCATATAGATCTC
667762 CT
1 CT
667764 TTCAAAAATG
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:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:669950 original size:22 final size:22
Alignment explanation
Indices: 669922--669975 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
669912 ACATCATTAT
669922 TATGCATTATTATAATAAAACG
1 TATGCATTATTATAATAAAACG
669944 TATGCATTATTATAATAAAACG
1 TATGCATTATTATAATAAAACG
669966 TATGCATTAT
1 TATGCATTAT
669976 GGAAATGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGCATTATTATAATAAAACG
Found at i:671707 original size:18 final size:18
Alignment explanation
Indices: 671671--671707 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
671661 AACAACACTG
* *
671671 TCTAAGAAACATGAGACC
1 TCTAAGAAACATCAAACC
671689 TCTAAGAAACATCAAACC
1 TCTAAGAAACATCAAACC
671707 T
1 T
671708 GCTGTAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (18 bp):
TCTAAGAAACATCAAACC
Found at i:674259 original size:31 final size:32
Alignment explanation
Indices: 674206--674275 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
674196 AGTTATAATA
*
674206 GGTCATTAACATTTATCAATTTGTAACAAATT
1 GGTCACTAACATTTATCAATTTGTAACAAATT
* *
674238 GGTCACTAACA-TTATCGATTTGTAATAAATT
1 GGTCACTAACATTTATCAATTTGTAACAAATT
674269 GGTCACT
1 GGTCACT
674276 CGATGTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (32 bp):
GGTCACTAACATTTATCAATTTGTAACAAATT
Found at i:675317 original size:12 final size:13
Alignment explanation
Indices: 675300--675332 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
675290 AGTAAAAAAG
675300 TATATTTT-TAAA
1 TATATTTTATAAA
675312 TATATTTTATAAA
1 TATATTTTATAAA
675325 TATTATTT
1 TA-TATTT
675333 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 6 0.32
14 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATATTTTATAAA
Found at i:679512 original size:27 final size:27
Alignment explanation
Indices: 679482--679549 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
679472 TTGAGAAAAA
679482 AAGTATTGATGAGAGTATGAAGGAATC
1 AAGTATTGATGAGAGTATGAAGGAATC
*
679509 AAGTATCGATGAGAGTATGAAGGAATC
1 AAGTATTGATGAGAGTATGAAGGAATC
* *
679536 AAGGAATGATGAGA
1 AAGTATTGATGAGA
679550 AGAGAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.43, C:0.04, G:0.31, T:0.22
Consensus pattern (27 bp):
AAGTATTGATGAGAGTATGAAGGAATC
Found at i:680418 original size:28 final size:28
Alignment explanation
Indices: 680351--680435 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
680341 ATTGTTAAAA
* *
680351 ATATGAATTGAAGTTACCTATATTTTCT
1 ATATGAATTGAAGTTACATATATATTCT
*
680379 ATA-GAAACTGAAGTTACATATATATTCT
1 ATATG-AATTGAAGTTACATATATATTCT
* * *
680407 GTATGAATTGAAATTACATAGATATTCT
1 ATATGAATTGAAGTTACATATATATTCT
680435 A
1 A
680436 GTGTTAGAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
27 1 0.02
28 45 0.96
29 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (28 bp):
ATATGAATTGAAGTTACATATATATTCT
Found at i:681503 original size:42 final size:42
Alignment explanation
Indices: 681457--681651 Score: 133
Period size: 42 Copynumber: 4.5 Consensus size: 42
681447 TATTTTTCTC
* *
681457 TTTATTATTGAAGCCTCTAATTTTTAAATCACACTTTTTACA
1 TTTATAATTGAAGCCTCTAATTTTTCAATCACACTTTTTACA
* * *
681499 TTTATAATCAAGATTCGAGACCTTTAATTTTTTCAAT-ATCACTTCTTACA
1 TTTATAAT--TGA----AG-CCTCTAA-TTTTTCAATCA-CACTTTTTACA
* * * * *
681549 TTTATAATTGAGGCCCCTAATTATTTTAATCTCACTTTCTAC-
1 TTTATAATTGAAGCCTCTAATT-TTTCAATCACACTTTTTACA
* * * * *
681591 CTTATAATTGAAGCCCCTAATTTTTCATTCCCACTTTTTACT
1 TTTATAATTGAAGCCTCTAATTTTTCAATCACACTTTTTACA
* *
681633 TTTATAATTTAGGCCTCTA
1 TTTATAATTGAAGCCTCTA
681652 GTTTAATCAT
Statistics
Matches: 118, Mismatches: 23, Indels: 24
0.72 0.14 0.15
Matches are distributed among these distances:
41 15 0.13
42 44 0.37
43 19 0.16
44 3 0.03
48 4 0.03
49 7 0.06
50 26 0.22
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (42 bp):
TTTATAATTGAAGCCTCTAATTTTTCAATCACACTTTTTACA
Found at i:687770 original size:3 final size:3
Alignment explanation
Indices: 687762--687798 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
687752 GACGATGATT
*
687762 ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
687799 CAGTCTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:690132 original size:21 final size:23
Alignment explanation
Indices: 690106--690150 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
690096 AGCAAGAGAC
690106 AGACTA-G-TTGGTATTATGATG
1 AGACTATGTTTGGTATTATGATG
690127 AGACTATGTTTGGTATTATGATG
1 AGACTATGTTTGGTATTATGATG
690150 A
1 A
690151 TGCAGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 15 0.68
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (23 bp):
AGACTATGTTTGGTATTATGATG
Found at i:690763 original size:21 final size:19
Alignment explanation
Indices: 690734--690788 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
690724 AATGTTAGAG
*
690734 ACATCATTAAAAATATTTA
1 ACATTATTAAAAATATTTA
690753 TTACATTATTAAATAAT-TTTA
1 --ACATTATTAAA-AATATTTA
*
690774 AAATTA-TAAAAATAT
1 ACATTATTAAAAATAT
690789 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 5 0.17
21 14 0.47
22 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ACATTATTAAAAATATTTA
Found at i:690799 original size:14 final size:13
Alignment explanation
Indices: 690777--690820 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
690767 AATTTTAAAA
*
690777 TTATAAAAATATAT
1 TTATTAAAATA-AT
*
690791 TTTTTAAAATAAT
1 TTATTAAAATAAT
690804 TTATTATAAATAAT
1 TTATTA-AAATAAT
690818 TTA
1 TTA
690821 ACGATAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATTAAAATAAT
Found at i:702162 original size:22 final size:21
Alignment explanation
Indices: 702120--702159 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
702110 GAGTTTATTT
*
702120 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
702141 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
702160 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:711645 original size:15 final size:15
Alignment explanation
Indices: 711622--711651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
711612 ATGTAGGTTC
711622 TAATATTAATCTAAT
1 TAATATTAATCTAAT
*
711637 TAATTTTAATCTAAT
1 TAATATTAATCTAAT
711652 ATTAAACCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATTAATCTAAT
Found at i:718691 original size:24 final size:24
Alignment explanation
Indices: 718664--718717 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
718654 CGTTCATTTA
718664 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCAGT-AACGTTCGGTTATGTT
* * *
718688 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTAACGTTCGGTTATGTT
718712 CGTTCA
1 CGTTCA
718718 TTTATGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (24 bp):
CGTTCAGTAACGTTCGGTTATGTT
Found at i:718697 original size:14 final size:14
Alignment explanation
Indices: 718674--718725 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
718664 CGTTCGTGAA
*
718674 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
718688 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
718702 CG-T---TTATGTT
1 CGTTCAGTTATGTT
*
718712 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
718726 TAACCCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.12, C:0.13, G:0.21, T:0.54
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:718722 original size:24 final size:24
Alignment explanation
Indices: 718675--718725 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
718665 GTTCGTGAAC
718675 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* *
718699 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
718723 GTT
1 GTT
718726 TAACCCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:719826 original size:16 final size:15
Alignment explanation
Indices: 719805--719866 Score: 81
Period size: 16 Copynumber: 4.0 Consensus size: 15
719795 GGTCTCCAAC
719805 GTTCGTGTTCATTTAT
1 GTTCGTGTT-ATTTAT
*
719821 GTTCGTGTTCGTTTAT
1 GTTCGTGTT-ATTTAT
719837 GTTCGTGTTAGTTTAT
1 GTTCGTGTTA-TTTAT
719853 GTTCGT-TTATTTAT
1 GTTCGTGTTATTTAT
719867 TAAATGAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.12
15 3 0.07
16 35 0.81
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.58
Consensus pattern (15 bp):
GTTCGTGTTATTTAT
Found at i:719840 original size:26 final size:26
Alignment explanation
Indices: 719810--719862 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
719800 CCAACGTTCG
*
719810 TGTTCAT-TTATGTTCGTGTTCGTTTA
1 TGTTCATGTTA-GTTCATGTTCGTTTA
* *
719836 TGTTCGTGTTAGTTTATGTTCGTTTA
1 TGTTCATGTTAGTTCATGTTCGTTTA
719862 T
1 T
719863 TTATTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.11, C:0.09, G:0.21, T:0.58
Consensus pattern (26 bp):
TGTTCATGTTAGTTCATGTTCGTTTA
Found at i:725988 original size:3 final size:3
Alignment explanation
Indices: 725982--726038 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
725972 ATAATAATGT
725982 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
726030 TTA TT- TTA T
1 TTA TTA TTA T
726039 CTCGGATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:728525 original size:16 final size:15
Alignment explanation
Indices: 728486--728532 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
728476 TAATTTTAAA
728486 ATTAGAAAAATATATTT
1 ATTA-AAAAATA-ATTT
728503 -TTAAAAAATAATTT
1 ATTAAAAAATAATTT
*
728517 ATTATAAAATAATTT
1 ATTAAAAAATAATTT
728532 A
1 A
728533 ACGATGGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 21 0.75
16 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTAAAAAATAATTT
Found at i:747193 original size:14 final size:14
Alignment explanation
Indices: 747170--747221 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
747160 AGTTCGTGAA
*
747170 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
747184 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
747198 CG-T---TTATGTT
1 CGTTCAGTTATGTT
*
747208 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
747222 TAACCCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.12, C:0.13, G:0.21, T:0.54
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:747198 original size:24 final size:24
Alignment explanation
Indices: 747171--747221 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
747161 GTTCGTGAAC
747171 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* *
747195 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
747219 GTT
1 GTT
747222 TAACCCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:748295 original size:16 final size:15
Alignment explanation
Indices: 748274--748335 Score: 81
Period size: 16 Copynumber: 4.0 Consensus size: 15
748264 GGTCTCCAAC
748274 GTTCGTGTTCATTTAT
1 GTTCGTGTT-ATTTAT
*
748290 GTTCGTGTTCGTTTAT
1 GTTCGTGTT-ATTTAT
748306 GTTCGTGTTAGTTTAT
1 GTTCGTGTTA-TTTAT
748322 GTTCGT-TTATTTAT
1 GTTCGTGTTATTTAT
748336 TAATGAACGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.12
15 3 0.07
16 35 0.81
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.58
Consensus pattern (15 bp):
GTTCGTGTTATTTAT
Found at i:748309 original size:26 final size:26
Alignment explanation
Indices: 748279--748331 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
748269 CCAACGTTCG
*
748279 TGTTCAT-TTATGTTCGTGTTCGTTTA
1 TGTTCATGTTA-GTTCATGTTCGTTTA
* *
748305 TGTTCGTGTTAGTTTATGTTCGTTTA
1 TGTTCATGTTAGTTCATGTTCGTTTA
748331 T
1 T
748332 TTATTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.11, C:0.09, G:0.21, T:0.58
Consensus pattern (26 bp):
TGTTCATGTTAGTTCATGTTCGTTTA
Found at i:753521 original size:52 final size:51
Alignment explanation
Indices: 753443--753548 Score: 203
Period size: 52 Copynumber: 2.1 Consensus size: 51
753433 AAAGATTTAA
753443 AATACAATGAATGAAATTGGAGAAAGAGTAAAGGTTCAGTTACCAAATTTGT
1 AATACAATGAATGAAATTGGAGAAAGAGTAAA-GTTCAGTTACCAAATTTGT
753495 AATACAATGAATGAAATTGGAGAAAGAGTAAAGTTCAGTTACCAAATTTGT
1 AATACAATGAATGAAATTGGAGAAAGAGTAAAGTTCAGTTACCAAATTTGT
753546 AAT
1 AAT
753549 TTAACCTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 22 0.41
52 32 0.59
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (51 bp):
AATACAATGAATGAAATTGGAGAAAGAGTAAAGTTCAGTTACCAAATTTGT
Found at i:760898 original size:14 final size:14
Alignment explanation
Indices: 760879--760926 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
760869 TATATGTTTG
760879 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
760893 TTTA---T-GTTCA
1 TTTATGTTCGTTCA
760903 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
760917 TTTATATTCG
1 TTTATGTTCG
760927 AACAGAGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:761203 original size:10 final size:10
Alignment explanation
Indices: 761188--761252 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
761178 GTGTTTGTGT
761188 TGTTCGTTTA
1 TGTTCGTTTA
**
761198 TGTTCGTTCG
1 TGTTCGTTTA
*
761208 TATTCGTTTA
1 TGTTCGTTTA
*
761218 TGTTCGTTCGTTCT
1 TGTTCG-T--TT-A
761232 TGTTCGTTTA
1 TGTTCGTTTA
761242 TGTTCGTTTA
1 TGTTCGTTTA
761252 T
1 T
761253 TTATTAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
10 31 0.72
11 3 0.07
13 3 0.07
14 6 0.14
ACGTcount: A:0.08, C:0.14, G:0.20, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:761237 original size:24 final size:21
Alignment explanation
Indices: 761186--761249 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 21
761176 TTGTGTTTGT
761186 GTTGTTCGTTTATGTTCGTTC
1 GTTGTTCGTTTATGTTCGTTC
*
761207 G-TATTCGTTTATGTTCGTTC
1 GTTGTTCGTTTATGTTCGTTC
761227 GTTCTTGTTCGTTTATGTTCGTT
1 G---TTGTTCGTTTATGTTCGTT
761250 TATTTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 19 0.51
21 1 0.03
24 17 0.46
ACGTcount: A:0.06, C:0.14, G:0.22, T:0.58
Consensus pattern (21 bp):
GTTGTTCGTTTATGTTCGTTC
Found at i:761246 original size:20 final size:20
Alignment explanation
Indices: 761187--761249 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 20
761177 TGTGTTTGTG
761187 TTGTTCGTTTATGTTCGTTC
1 TTGTTCGTTTATGTTCGTTC
* *
761207 GTATTCGTTTATGTTCGTTCGTTC
1 TTGTTCGTTTA---T-GTTCGTTC
761231 TTGTTCGTTTATGTTCGTT
1 TTGTTCGTTTATGTTCGTT
761250 TATTTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 16 0.46
21 1 0.03
23 1 0.03
24 17 0.49
ACGTcount: A:0.06, C:0.14, G:0.21, T:0.59
Consensus pattern (20 bp):
TTGTTCGTTTATGTTCGTTC
Found at i:763699 original size:35 final size:35
Alignment explanation
Indices: 763659--763795 Score: 132
Period size: 35 Copynumber: 3.9 Consensus size: 35
763649 AGTTTATGCG
**
763659 GGTTCAGTTCAATCAAACTGGTAATTCCTTATATA
1 GGTTCAGACCAATCAAACTGGTAATTCCTTATATA
* * **
763694 GGTTCAGACCGATCGAACTGGTAATTCCTTACGGTA
1 GGTTCAGACCAATCAAACTGGTAATTCCTTA-TATA
*** *
763730 GGTTCAG-CTTGGTCAAATTGGTAATTCCTTATATA
1 GGTTCAGAC-CAATCAAACTGGTAATTCCTTATATA
* * *
763765 GGTTTAGACCAATCGAGCTGGTAATTCCTTA
1 GGTTCAGACCAATCAAACTGGTAATTCCTTA
763796 CGGATCTAAG
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
35 52 0.65
36 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (35 bp):
GGTTCAGACCAATCAAACTGGTAATTCCTTATATA
Found at i:767542 original size:20 final size:20
Alignment explanation
Indices: 767513--767550 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
767503 TAGTACCCTA
*
767513 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
767533 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
767551 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:767585 original size:20 final size:21
Alignment explanation
Indices: 767532--767593 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
767522 GATTCCCCTG
767532 TGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGAATCGGTT-CCC-TCAA
*
767555 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGAATCGGTTCCCTCAA
* *
767575 TGGGGGGATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
767594 TGTACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCTCAA
Found at i:774044 original size:30 final size:29
Alignment explanation
Indices: 773990--774050 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
773980 ACCGGTAAAG
* *
773990 AACCGGAAGAACCGACTGAGAACCGACAA
1 AACCGGAAGAACCGACTAAAAACCGACAA
* *
774019 AACCGGAATGAACCGGCTAAAAACCGGCAA
1 AACCGGAA-GAACCGACTAAAAACCGACAA
774049 AA
1 AA
774051 TCAGTGTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.46, C:0.26, G:0.23, T:0.05
Consensus pattern (29 bp):
AACCGGAAGAACCGACTAAAAACCGACAA
Found at i:774760 original size:2 final size:2
Alignment explanation
Indices: 774755--774789 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
774745 AAAAAAATGT
774755 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 T
774790 TAATATTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:781328 original size:10 final size:11
Alignment explanation
Indices: 781307--781331 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
781297 TGTTTATATG
781307 AATACAAAAAA
1 AATACAAAAAA
781318 AATACAAAAAA
1 AATACAAAAAA
781329 AAT
1 AAT
781332 TCTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (11 bp):
AATACAAAAAA
Found at i:782157 original size:32 final size:32
Alignment explanation
Indices: 782121--782189 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
782111 TAGTTTCTGA
782121 TTTAGTTATCTTTTTGTTTTTGAACAGTAGAG
1 TTTAGTTATCTTTTTGTTTTTGAACAGTAGAG
782153 TTTAGTTATCTTTTTGTTTTTGAACAGTAGAG
1 TTTAGTTATCTTTTTGTTTTTGAACAGTAGAG
782185 TTTAG
1 TTTAG
782190 ATAGGGATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.54
Consensus pattern (32 bp):
TTTAGTTATCTTTTTGTTTTTGAACAGTAGAG
Found at i:783853 original size:19 final size:20
Alignment explanation
Indices: 783829--783873 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
783819 GAGCGTTCGG
*
783829 TTGAGTCGAGTAAAAATA-T
1 TTGAGTCGAGTAAAAAAATT
783848 TTGAGTCGAGTAAAAAAATT
1 TTGAGTCGAGTAAAAAAATT
783868 TTGAGT
1 TTGAGT
783874 TATTTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGAGTCGAGTAAAAAAATT
Found at i:784699 original size:2 final size:2
Alignment explanation
Indices: 784692--784729 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
784682 TAAAAATTAG
784692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
784730 ACATCTACTT
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):
TA
Found at i:785337 original size:17 final size:16
Alignment explanation
Indices: 785311--785343 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
785301 TTTATACATA
785311 TTTAAAAATTATTAAT
1 TTTAAAAATTATTAAT
785327 TTTAAATAATTATTAAT
1 TTTAAA-AATTATTAAT
785344 CCAATAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAAATTATTAAT
Found at i:795677 original size:123 final size:122
Alignment explanation
Indices: 795524--795760 Score: 341
Period size: 123 Copynumber: 1.9 Consensus size: 122
795514 GGGGCACGAT
* **
795524 TGAACCCCCATCATTTTGAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAAT
1 TGAACCCACATCATGATGAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAAT
* * * * *
795589 TTGAGGTGA-TGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATGTTGGGGCGAC
66 TTGAGAT-ATTGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATGTTGGGGCGAC
* ** *
795646 TGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAATGAGCCTTATAA
1 TGAACCCACATCATGATG-AATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAA
795711 TTTGAGATATTGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATGTT
65 TTTGAGATATTGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATGTT
795761 ACGACATTAG
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
122 16 0.16
123 85 0.84
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (122 bp):
TGAACCCACATCATGATGAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAAT
TTGAGATATTGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATGTTGGGGCGAC
Found at i:796999 original size:36 final size:36
Alignment explanation
Indices: 796959--797193 Score: 223
Period size: 36 Copynumber: 6.5 Consensus size: 36
796949 AAGTCAATCT
796959 TAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCAT-C
*
796995 TAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCATC
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
* * *
797030 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAATC
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
* *
797066 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACAATC
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
*
797102 ATAAGTCTTCACC--AGAGAGTAGTGAAGCAAACCATC
1 -TAAGCCTTCACCGAAGAGA-TAGTGAAGCAAACCATC
* * * * *
797138 TGAAGTCTTCACCAAAAAG-TAGTGAAGCAGATCCATTT
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCA-AACCA-TC
* *
797176 TAAGCCTTCTCAGAAGAG
1 TAAGCCTTCACCGAAGAG
797194 TGTTGGAACA
Statistics
Matches: 175, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
34 3 0.02
35 5 0.03
36 145 0.83
37 17 0.10
38 5 0.03
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (36 bp):
TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATC
Found at i:797161 original size:108 final size:108
Alignment explanation
Indices: 796946--797193 Score: 320
Period size: 108 Copynumber: 2.3 Consensus size: 108
796936 ATGAGATTGG
* * *
796946 AGCAAGTCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAG
1 AGCAA-TCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCATAAGCCTTCACCAGAG
* *
797011 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGA
65 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGA
* * *
797055 AGCAATCAATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACAATCATAAGTCTTCACCAGAG
1 AGCAATCAATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACAATCATAAGCCTTCACCAGAG
* *
797119 AGTAGTGAAGCAAACCATCTGAAGTCTTCACC-AAAAAGTAGTGA
65 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAA-TAGTGA
* * * *
797163 AGCAGATCCATTTTAAGCCTTCTCAGAAGAG
1 AGCA-ATCAATCTTAAGCCTTCACCGAAGAG
797194 TGTTGGAACA
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
107 4 0.03
108 91 0.76
109 24 0.20
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (108 bp):
AGCAATCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCATAAGCCTTCACCAGAGA
ATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGA
Found at i:797166 original size:72 final size:70
Alignment explanation
Indices: 796953--797150 Score: 263
Period size: 72 Copynumber: 2.7 Consensus size: 70
796943 TGGAGCAAGT
*
796953 CAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCT-AAGCCTTCACCGGAGAATAGT
1 CAATC-TAAGCCTTCACCG-AGAGTAGTGAAGCAAACCAT-CTGAAGCCTTCACCGGAGAATAGT
797017 GAAGCAAA
63 GAAGCAAA
* * * *
797025 CCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTG
1 CAATCT-AAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTG
797090 AAGCAAA
64 AAGCAAA
* *
797097 CAATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTGAAGTCTTCACC
1 CAATC-TAAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTGAAGCCTTCACC
797151 AAAAAGTAGT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
71 3 0.03
72 105 0.95
73 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (70 bp):
CAATCTAAGCCTTCACCGAGAGTAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAA
GCAAA
Found at i:797694 original size:54 final size:55
Alignment explanation
Indices: 797566--798466 Score: 1029
Period size: 54 Copynumber: 16.6 Consensus size: 55
797556 AAGATTACTT
* * *
797566 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCG--T-ATGAAGA-TATCC
1 GAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* * *
797617 GAGTTCTATACT-CCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGAAAATT-TCC
1 GAGTTCTATACTCCCTGAA-GAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* * * *
797671 AAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCTGTTTGCAGAAGATTATTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* * ** * *
797726 GAGTTCTATACTTCCTGAAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATTCT-T
1 GAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAGATTATCC
* *
797781 GAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTAT-C
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* ** *
797835 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTATTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* *
797890 GAGTTCTATACT-CCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGAA-ATT-TCC
1 GAGTTCTATACTCCCTGAA-GAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* * *
797943 AAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTAT-C
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* ** * *
797997 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGAATTGTTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG-ATTATCC
* *
798053 GAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGTTTGAAGAAGATGT-T-T
1 GAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAGAT-TATCC
* * *
798108 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGAGAACTCGTTTGAAGAA-ATT-TCC
1 GAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* * *
798161 AAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTAT-C
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* ** * *
798215 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGAATTGTTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG-ATTATCC
* * *
798271 GAGTTCTATACTCCCTGAAGAAAGAGCGAAGCAAACCCGTTTGAAGAAGATGT-T-T
1 GAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAGAT-TATCC
* * * * *
798326 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGAGAACTCGTTTGAAGAATA-TGTCC
1 GAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
* * *
798380 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCTGTTTGCAGAAGATTATTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
798435 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCG
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCG
798467 GACCAGATTA
Statistics
Matches: 734, Mismatches: 84, Indels: 60
0.84 0.10 0.07
Matches are distributed among these distances:
50 4 0.01
51 29 0.04
52 3 0.00
53 82 0.11
54 310 0.42
55 188 0.26
56 79 0.11
57 39 0.05
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (55 bp):
GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATCC
Found at i:797822 original size:164 final size:161
Alignment explanation
Indices: 797555--798466 Score: 1085
Period size: 164 Copynumber: 5.6 Consensus size: 161
797545 TGAAGCAAAT
* * * * *
797555 GAAGATTACTT-GAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCGTATGAAG-ATA-TC
1 GAAGATTA-TTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTT
* * * *
797616 CGAGTTCTATACT-CCTTAATGAAAGAAGG-AGCGAACCCGTTTGAAGAAAATTTCCAAGTTCTA
64 TGAGTTCTATACTCCCTGAA-GAAAG-AGGAAGCGAACCCGTTTGAAGAAGATTT-CGAGTTCTA
* *
797679 TACTCCCTGAAGAAAGAGGGAGCGAACCTGTTTGCA
126 TACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGCA
* * **
797715 GAAGATTATTCGAGTTCTATACTTCCTGAAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATTCT
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAGATT-T
*
797780 TGAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTATCGAGTTCTATA
64 TGAGTTCTATACTCCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATT-TCGAGTTCTATA
*
797845 CTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCA
128 CTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGCA
* *
797879 GAAGATTATTCGAGTTCTATACT-CCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGAA-ATTTC
1 GAAGATTATTCGAGTTCTATACTCCCTGAA-GAAAGAGGGAGCGAACCCGTTTGAAGAAGATTT-
** *
797942 CAAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTATCGAGTTCTATA
64 TGAGTTCTATACTCCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATT-TCGAGTTCTATA
*
798007 CTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCA
128 CTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGCA
* *
798041 GAAGAATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGTTTGAAGAAGATGT
1 GAAG-ATTATTCGAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAGAT-T
* * * * *
798106 TTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGAGAACTCGTTTGAAGAA-ATTTCCAAGTTCTA
63 TTGAGTTCTATACTCCCTGA-AGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTT-CGAGTTCTA
* *
798169 TACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAA
126 TACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGCA
* **
798205 GAAGATTA-TCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGAATTGT
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG-ATT-T
* * *
798269 TCGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCAAACCCGTTTGAAGAAGATGTTTGAGTTCCA
64 T-GAGTTCTATACTCCCTGAAGAAAGAG-GAAGCGAACCCGTTTGAAGAAGAT-TTCGAGTTCTA
* * * *
798334 TACTCCCT-AGAGAAAGAGGGAGAGAACTCGTTTGAA
126 TACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGCA
* * * * *
798370 GAATA-TGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCTGTTTGCAGAAGATTATT
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATT-TT
*
798434 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCG
65 -GAGTTCTATACTCCCTGAAGAAAGAGGAAGCG
798467 GACCAGATTA
Statistics
Matches: 663, Mismatches: 62, Indels: 51
0.85 0.08 0.07
Matches are distributed among these distances:
159 2 0.00
160 30 0.05
161 38 0.06
162 137 0.21
163 82 0.12
164 235 0.35
165 135 0.20
166 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (161 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTTG
AGTTCTATACTCCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTTCGAGTTCTATACTT
CCTGAAGAAAGAGGGAGCGAACCCGTTTGCA
Found at i:798172 original size:218 final size:216
Alignment explanation
Indices: 797555--798512 Score: 1192
Period size: 218 Copynumber: 4.4 Consensus size: 216
797545 TGAAGCAAAT
* * * * * *
797555 GAAGATTACTTGAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCG-TAT--GAAGA-TAT
1 GAAGATTA-TCGAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGT
* * * ** *
797615 CCGAGTTCTATACT-CCTTAATGAAAGAAGG-AGCGAACCCGTTTGAAGAAAATTTCCAAGTTCT
64 TCGAGTTCTATACTCCCTGAA-GAAAG-AGGAAGCGAACCCGTTTGAAGAAGATTT-TGAGTTCC
* * * *
797678 ATACTCCCT-GAAGAAAGAGGGAGCGAAC-CTGTTTGCAGAAGATTATTCGAGTTCTATACTTCC
126 ATACTCCCTAG-AGAAAGAGGGAGAGAACTC-GTTTGAAGAAGATT-TCCAAGTTCTATACTTCC
**
797741 TGAAGAAAGAGCGAAGCGAACCCGTAAGAA
188 TGAAGAAAGAG-GAAGCGAACCCGTTTGAA
* * * ** *
797771 GAAGATTCTTGAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATT-ATC
1 GAAGATTATCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGTTC
* * ** *
797835 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTATTCGAGTTCTATA
66 GAGTTCTATACTCCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATT-TT-GAGTTCCATA
* * * *
797900 CTCCTTA-ATGAAAGAAGGAGCGAACCCGTTTGAAGAA-ATTTCCAAGTTCTATACTTCCTGAAG
129 CTCCCTAGA-GAAAGAGGGAGAGAACTCGTTTGAAGAAGATTTCCAAGTTCTATACTTCCTGAAG
797963 AAAGAGGAAGCGAACCCGTTTGAA
193 AAAGAGGAAGCGAACCCGTTTGAA
797987 GAAGATTATCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGAATTGTT
1 GAAGATTATCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAG-ATTGTT
798052 CGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGTTTGAAGAAGATGTTTGAGTTCCAT
65 CGAGTTCTATACTCCCTGAAGAAAGAG-GAAGCGAACCCGTTTGAAGAAGAT-TTTGAGTTCCAT
798117 ACTCCCTAGAGAAAGAGGGAGAGAACTCGTTTGAAGAA-ATTTCCAAGTTCTATACTTCCTGAAG
128 ACTCCCTAGAGAAAGAGGGAGAGAACTCGTTTGAAGAAGATTTCCAAGTTCTATACTTCCTGAAG
798181 AAAGAGGAAGCGAACCCGTTTGAA
193 AAAGAGGAAGCGAACCCGTTTGAA
798205 GAAGATTATCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGAATTGTT
1 GAAGATTATCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAG-ATTGTT
*
798270 CGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCAAACCCGTTTGAAGAAGATGTTTGAGTTCCAT
65 CGAGTTCTATACTCCCTGAAGAAAGAG-GAAGCGAACCCGTTTGAAGAAGAT-TTTGAGTTCCAT
* * * *
798335 ACTCCCTAGAGAAAGAGGGAGAGAACTCGTTTGAAGAATATGTCCGAGTTCTATACTCCCTGAAG
128 ACTCCCTAGAGAAAGAGGGAGAGAACTCGTTTGAAGAAGATTTCCAAGTTCTATACTTCCTGAAG
* * *
798400 AAAGAGGGAGCGAACCTGTTTGCA
193 AAAGAGGAAGCGAACCCGTTTGAA
* * *
798424 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCAGATTATT--GAAGATTG
1 GAAGATTA-TCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCG-TT-TTCAGAAGATTG
**
798487 TTCGAG-TCTTATACTCTTTGAAGAAA
63 TTCGAGTTC-TATACTCCCTGAAGAAA
798513 TAAGGAATAA
Statistics
Matches: 671, Mismatches: 49, Indels: 41
0.88 0.06 0.05
Matches are distributed among these distances:
215 34 0.05
216 78 0.12
217 33 0.05
218 333 0.50
219 146 0.22
220 43 0.06
221 2 0.00
222 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (216 bp):
GAAGATTATCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATTGTTC
GAGTTCTATACTCCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTTTGAGTTCCATACT
CCCTAGAGAAAGAGGGAGAGAACTCGTTTGAAGAAGATTTCCAAGTTCTATACTTCCTGAAGAAA
GAGGAAGCGAACCCGTTTGAA
Found at i:808623 original size:24 final size:24
Alignment explanation
Indices: 808596--808645 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
808586 TATATCAAAA
*
808596 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * *
808620 ATCAGATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
808644 AT
1 AT
808646 TCGATAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:808657 original size:24 final size:24
Alignment explanation
Indices: 808606--808663 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
808596 ATCAAAACAT
808606 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
808630 AATCTAGGTCAAGTATTC-GAT-AA
1 AATCCAGGTCAAGTA-TCAGATCAA
808653 GAATCCAGGTC
1 -AATCCAGGTC
808664 GGGTATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 26 0.87
25 2 0.07
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:811798 original size:17 final size:17
Alignment explanation
Indices: 811776--811810 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
811766 GCACTTCTCC
811776 CTTTAAAAACATTGTAA
1 CTTTAAAAACATTGTAA
811793 CTTTAAAAACATTGTAA
1 CTTTAAAAACATTGTAA
811810 C
1 C
811811 ACTTAACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (17 bp):
CTTTAAAAACATTGTAA
Found at i:811816 original size:18 final size:17
Alignment explanation
Indices: 811778--811816 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
811768 ACTTCTCCCT
*
811778 TTAAAAACATTGTAACT
1 TTAAAAACATTGTAACC
811795 TTAAAAACATTGTAACAC
1 TTAAAAACATTGTAAC-C
811813 TTAA
1 TTAA
811817 CACTGCTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (17 bp):
TTAAAAACATTGTAACC
Found at i:814070 original size:23 final size:22
Alignment explanation
Indices: 814041--814120 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
814031 GCATGACCCC
814041 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
814063 CGTGCATCGGTGTACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
**
814085 GTATATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
814107 ATGCATCGATGCAC
1 GTGCATCGATGCAC
814121 TGTTAGGTGT
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
21 13 0.30
22 15 0.35
23 15 0.35
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:823432 original size:141 final size:142
Alignment explanation
Indices: 823230--823779 Score: 682
Period size: 141 Copynumber: 3.9 Consensus size: 142
823220 TAAGGAATGC
* ** *
823230 GGAAGACTCTTAATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTAT-CATCGAAGA
1 GGAAGACTCTTGATAGGATTTCAGGAAAGATCAAGAATCTTGAGTTCATTCATATGC-TCGAAGA
**
823294 AGCTTTCTGGAATACTTTCTATA-CGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTT
65 AGCTTTCTGGAATACTCGCTATATCGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTT
823358 CGACAAGGAAATT
130 CGACAAGGAAATT
* *
823371 GGAAGACTCTTGATAGGATTCCAGGAAAGATCAAGAATCTTGAGTTCATTCGTAT-CATCGAAGA
1 GGAAGACTCTTGATAGGATTTCAGGAAAGATCAAGAATCTTGAGTTCATTCATATGC-TCGAAGA
** * * * *
823435 AGCTTTCTGGAATACTTTCTATA-AGACAATGACAAAACAACAATGTTGTGAGCCCGGGACACTT
65 AGCTTTCTGGAATACTCGCTATATCGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTT
823499 CGACAAGGAAATT
130 CGACAAGGAAATT
* * * * * *
823512 GGAAGACTCTTGGTAGGATTTCTGGAAAGATCAAGAACCTTGAGTGCATCCATATGCTTGAA-AA
1 GGAAGACTCTTGATAGGATTTCAGGAAAGATCAAGAATCTTGAGTTCATTCATATGCTCGAAGAA
* * * * *
823576 TCGTTCTGGAATACTCGCTATATTG-CATTGAGACAACAACAATGTTGTGAGCCCGGGACACTTC
66 GCTTTCTGGAATACTCGCTATATCGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTTC
*
823640 GACAAAGAAATT
131 GACAAGGAAATT
* * * ** * *
823652 GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAATCCTAAGCCCATGCATATGCTTGAAGAA
1 GGAAGACTCTTGATAGGATTTCAGGAAAGATCAAGAATCTTGAGTTCATTCATATGCTCGAAGAA
* * * * * *
823717 CCCTTCCGGAATACTCGCTATATC-ACAATCAGACAACAGCAATGTTGTGAGCCTGGGGCACTT
66 GCTTTCTGGAATACTCGCTATATCGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTT
823780 TGGGGGTGAC
Statistics
Matches: 365, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
140 122 0.33
141 242 0.66
142 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (142 bp):
GGAAGACTCTTGATAGGATTTCAGGAAAGATCAAGAATCTTGAGTTCATTCATATGCTCGAAGAA
GCTTTCTGGAATACTCGCTATATCGACAATCAGACAACAACAATGTTGTGAGCCCGGGACACTTC
GACAAGGAAATT
Found at i:824584 original size:36 final size:36
Alignment explanation
Indices: 824535--824606 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
824525 CCATTTGACG
*
824535 GCTCAGGATTTCCTATTCTCTCAAGTGAAACCTTCT
1 GCTCAGGAATTCCTATTCTCTCAAGTGAAACCTTCT
*
824571 GCTCAGGAATTCCTATTTTCTCAAGTGAAACCTTCT
1 GCTCAGGAATTCCTATTCTCTCAAGTGAAACCTTCT
824607 CCCATAGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (36 bp):
GCTCAGGAATTCCTATTCTCTCAAGTGAAACCTTCT
Found at i:829870 original size:105 final size:105
Alignment explanation
Indices: 829760--830344 Score: 1008
Period size: 105 Copynumber: 5.6 Consensus size: 105
829750 GTCGGATGAT
* * * *
829760 TTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
829825 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
829865 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
**
829930 ACATACTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
* *
829970 TTCTTCTCATTATGAACTCTTCTAGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
* * *
830035 ACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAT
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
* *
830075 TTCTTCTCATTATGAACTCTTTTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
*
830140 ACAGGCTCTTCTCATTACAAACCTTCTCCTTTAAGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
830180 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
* *
830245 ACAGTCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
* *
830285 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
830345 TTGTTGTTGA
Statistics
Matches: 456, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 456 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (105 bp):
TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGACGAG
Found at i:831278 original size:8 final size:8
Alignment explanation
Indices: 831267--831367 Score: 95
Period size: 8 Copynumber: 13.0 Consensus size: 8
831257 TTCTTTTTTC
831267 TTTTCATT
1 TTTTCATT
831275 TTTTCATT
1 TTTTCATT
*
831283 TTTTCCTTT
1 TTTT-CATT
831292 TTTTCATT
1 TTTTCATT
831300 TTTT--TT
1 TTTTCATT
*
831306 TCTT--TT
1 TTTTCATT
*
831312 TTTTAATT
1 TTTTCATT
831320 TTTT-ATT
1 TTTTCATT
831327 TTTTCATT
1 TTTTCATT
**
831335 TTTTTTTCT
1 TTTTCAT-T
*
831344 TTTTCACT
1 TTTTCATT
831352 TTTTCATT
1 TTTTCATT
831360 TTTTCATT
1 TTTTCATT
831368 CATTCTCTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
6 10 0.13
7 7 0.09
8 49 0.63
9 12 0.15
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:831295 original size:17 final size:16
Alignment explanation
Indices: 831267--831381 Score: 88
Period size: 17 Copynumber: 6.8 Consensus size: 16
831257 TTCTTTTTTC
*
831267 TTTTCATTTTTTCATT
1 TTTTCTTTTTTTCATT
831283 TTTTCCTTTTTTTCATTTTT
1 TTTT-CTTTTTTTCA---TT
*
831303 TTTTCTTTTTTTTAATT
1 TTTTC-TTTTTTTCATT
*
831320 TTTT-ATTTTTTCATT
1 TTTTCTTTTTTTCATT
* *
831335 TTTTTTTCTTTTTCACT
1 TTTTCTT-TTTTTCATT
*
831352 TTTTCATTTTTTCATT
1 TTTTCTTTTTTTCATT
*
831368 CATTCTCTTTTTTT
1 --TTTTCTTTTTTT
831382 TTCAAGCATA
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
15 13 0.16
16 13 0.16
17 28 0.35
18 10 0.13
19 1 0.01
20 14 0.18
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTTCATT
Found at i:831301 original size:25 final size:24
Alignment explanation
Indices: 831267--831339 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 24
831257 TTCTTTTTTC
831267 TTTTCATTTTTTCATTTTTTCCTTT
1 TTTTCATTTTTT-ATTTTTTCCTTT
*
831292 TTTTCA---TTT-TTTTTTCTTTT
1 TTTTCATTTTTTATTTTTTCCTTT
* *
831312 TTTTAATTTTTTATTTTTTCATTT
1 TTTTCATTTTTTATTTTTTCCTTT
831336 TTTT
1 TTTT
831340 TTCTTTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 15 0.37
22 3 0.07
23 3 0.07
24 14 0.34
25 6 0.15
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTCATTTTTTATTTTTTCCTTT
Found at i:831301 original size:44 final size:44
Alignment explanation
Indices: 831251--831339 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
831241 TCTCGAACCC
* *
831251 TCATTTTTCTTT-TTTCTTTTCATTTTTTCATTTTTTCCTTTTTT
1 TCATTTTTCTTTCTTTCTTTTAATTTTTT-ATTTTTTCATTTTTT
* *
831295 TCATTTTTTTTTCTTTTTTTTAATTTTTTATTTTTTCATTTTTT
1 TCATTTTTCTTTCTTTCTTTTAATTTTTTATTTTTTCATTTTTT
831339 T
1 T
831340 TTCTTTTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 26 0.65
45 14 0.35
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (44 bp):
TCATTTTTCTTTCTTTCTTTTAATTTTTTATTTTTTCATTTTTT
Found at i:831340 original size:25 final size:25
Alignment explanation
Indices: 831267--831363 Score: 92
Period size: 25 Copynumber: 3.8 Consensus size: 25
831257 TTCTTTTTTC
831267 TTTTCATTTTTTCATTTTTTCCTT--T
1 TTTTCATTTTTTCATTTTTT--TTAAT
831292 TTTTCATTTTTTTTTC-TTTTTTTTAAT
1 TTTTCA---TTTTTTCATTTTTTTTAAT
* **
831319 TTTTTATTTTTTCATTTTTTTTTCT
1 TTTTCATTTTTTCATTTTTTTTAAT
*
831344 TTTTCACTTTTTCATTTTTT
1 TTTTCATTTTTTCATTTTTT
831364 CATTCATTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
24 7 0.11
25 35 0.57
27 12 0.20
28 7 0.11
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTCATTTTTTCATTTTTTTTAAT
Found at i:831361 original size:7 final size:7
Alignment explanation
Indices: 831251--831367 Score: 52
Period size: 8 Copynumber: 16.7 Consensus size: 7
831241 TCTCGAACCC
831251 TCATTTT
1 TCATTTT
*
831258 TCTTTTT
1 TCATTTT
831265 TC--TTT
1 TCATTTT
831270 TCATTTTT
1 TCA-TTTT
831278 TCATTTTT
1 TCA-TTTT
*
831286 TCCTTTTTT
1 T-C-ATTTT
831295 TCATTTT
1 TCATTTT
831302 T--TTTT
1 TCATTTT
**
831307 CTTTTTTT
1 -TCATTTT
*
831315 TAATTTT
1 TCATTTT
*
831322 TTATTTTT
1 TCA-TTTT
831330 TCA-TTT
1 TCATTTT
831336 T--TTTT
1 TCATTTT
831341 TC-TTTT
1 TCATTTT
831347 TCACTTTT
1 TCA-TTTT
831355 TCATTTTT
1 TCA-TTTT
831363 TCATT
1 TCATT
831368 CATTCTCTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
5 13 0.15
6 11 0.12
7 22 0.25
8 37 0.42
9 6 0.07
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (7 bp):
TCATTTT
Found at i:831379 original size:25 final size:25
Alignment explanation
Indices: 831324--831381 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
831314 TTAATTTTTT
* * *
831324 ATTTTTTCATTTTTTTTTCTTTTTC
1 ATTTTTTCATTTTTTATTCATTCTC
*
831349 ACTTTTTCATTTTTTCATTCATTCTC
1 ATTTTTTCATTTTTT-ATTCATTCTC
*
831375 TTTTTTT
1 ATTTTTT
831382 TTCAAGCATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (25 bp):
ATTTTTTCATTTTTTATTCATTCTC
Found at i:831385 original size:16 final size:16
Alignment explanation
Indices: 831255--831385 Score: 67
Period size: 16 Copynumber: 8.0 Consensus size: 16
831245 GAACCCTCAT
831255 TTTTCTTTTTTCTTTTCA
1 TTTTC-TTTTT-TTTTCA
* *
831273 TTTT-TTCATTTTTTCC
1 TTTTCTT-TTTTTTTCA
*
831289 TTTT-TTTCATTTTT--
1 TTTTCTTT-TTTTTTCA
*
831303 TTTTC-TTTTTTTTAA
1 TTTTCTTTTTTTTTCA
*
831318 TTTT-TTATTTTTTCA
1 TTTTCTTTTTTTTTCA
*
831333 TTTTTTTTTCTTTTTCA
1 TTTTCTTTT-TTTTTCA
*
831350 CTTTTTCATTTTTTCATTCA
1 --TTTTC-TTTTTT-TTTCA
*
831370 TTCTCTTTTTTTTTCA
1 TTTTCTTTTTTTTTCA
831386 AGCATAGTAC
Statistics
Matches: 89, Mismatches: 12, Indels: 26
0.70 0.09 0.20
Matches are distributed among these distances:
13 5 0.06
14 6 0.07
15 16 0.18
16 25 0.28
17 15 0.17
18 8 0.09
19 6 0.07
20 8 0.09
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTTTTCA
Found at i:834923 original size:14 final size:14
Alignment explanation
Indices: 834904--834930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
834894 AAATTAATGT
834904 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
834918 AAAGAATGAAGAA
1 AAAGAATGAAGAA
834931 TGAAAACGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:846258 original size:24 final size:24
Alignment explanation
Indices: 846226--846281 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
846216 CTATTCTTTC
*
846226 GCTTCAATTGAGCTAAAATTTTTG
1 GCTTCAATTGAGCTAAAATTTTAG
*
846250 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTAAAATTTTAG
846274 GCTTCAAT
1 GCTTCAAT
846282 CGAACTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTAAAATTTTAG
Found at i:846529 original size:11 final size:10
Alignment explanation
Indices: 846505--846550 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
846495 GCGGTTCAAA
846505 CCGGTTTT-G
1 CCGGTTTTCG
846514 CCGGTTTTCAG
1 CCGGTTTTC-G
846525 CCGGTTTTC-
1 CCGGTTTTCG
*
846534 TCGGTTTTCAG
1 CCGGTTTTC-G
846545 CCGGTT
1 CCGGTT
846551 CTTTCGATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 16 0.52
11 15 0.48
ACGTcount: A:0.04, C:0.26, G:0.28, T:0.41
Consensus pattern (10 bp):
CCGGTTTTCG
Found at i:846530 original size:20 final size:20
Alignment explanation
Indices: 846505--846550 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
846495 GCGGTTCAAA
846505 CCGGTTTTGC-CGGTTTTCAG
1 CCGGTTTT-CTCGGTTTTCAG
846525 CCGGTTTTCTCGGTTTTCAG
1 CCGGTTTTCTCGGTTTTCAG
846545 CCGGTT
1 CCGGTT
846551 CTTTCGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.04, C:0.26, G:0.28, T:0.41
Consensus pattern (20 bp):
CCGGTTTTCTCGGTTTTCAG
Found at i:847818 original size:22 final size:22
Alignment explanation
Indices: 847774--847821 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
847764 GTTCAATTCA
*
847774 TTTATGTTCATAAACAAGTTCG
1 TTTATGTTCATAAACAAGCTCG
*
847796 TTTATGTTCATGAACCAA-CTCG
1 TTTATGTTCAT-AAACAAGCTCG
847818 TTTA
1 TTTA
847822 GAATATCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTATGTTCATAAACAAGCTCG
Found at i:854159 original size:13 final size:13
Alignment explanation
Indices: 854138--854168 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
854128 TATTGAGTGA
854138 TGTTGAACATACT
1 TGTTGAACATACT
*
854151 TGTTTAACATACT
1 TGTTGAACATACT
854164 TGTTG
1 TGTTG
854169 CATCCCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (13 bp):
TGTTGAACATACT
Found at i:863133 original size:22 final size:22
Alignment explanation
Indices: 863089--863136 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
863079 GTTCAATTCA
*
863089 TTTATGTTCATAAACAAGTTCG
1 TTTATGTTCATAAACAAGCTCG
*
863111 TTTATGTTCATGAACCAA-CTCG
1 TTTATGTTCAT-AAACAAGCTCG
863133 TTTA
1 TTTA
863137 GAATATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTATGTTCATAAACAAGCTCG
Found at i:865567 original size:18 final size:18
Alignment explanation
Indices: 865544--865584 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
865534 GTTTTGCTCG
865544 CCCCGTCCCCGAACCC-AT
1 CCCCGTCCCCG-ACCCGAT
865562 CCCCGTCCCCGACCCGAT
1 CCCCGTCCCCGACCCGAT
865580 CCCCG
1 CCCCG
865585 ATAGGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.12, C:0.63, G:0.15, T:0.10
Consensus pattern (18 bp):
CCCCGTCCCCGACCCGAT
Found at i:866354 original size:16 final size:16
Alignment explanation
Indices: 866333--866376 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
866323 GGAAACAGTC
866333 TTGAATAAGACCAAAG
1 TTGAATAAGACCAAAG
866349 TTGAATAAGACCAAAG
1 TTGAATAAGACCAAAG
866365 TTGAATAAGACC
1 TTGAATAAGACC
866377 TTCCTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (16 bp):
TTGAATAAGACCAAAG
Found at i:878062 original size:2 final size:2
Alignment explanation
Indices: 878057--878084 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
878047 TGTGTGTGTG
878057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
878085 CAGTGATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:895325 original size:18 final size:19
Alignment explanation
Indices: 895291--895326 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
895281 TTTAAAATTG
*
895291 AAAAAGAAAACTCAAGAAA
1 AAAAAGAAAACTAAAGAAA
895310 AAAAAGAAAAC-AAAGAA
1 AAAAAGAAAACTAAAGAA
895327 CACAATATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.08, G:0.11, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAACTAAAGAAA
Found at i:895427 original size:12 final size:12
Alignment explanation
Indices: 895402--895437 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
895392 TGGTATCGAC
895402 AATTAAACAAAAA
1 AATTAAA-AAAAA
895415 AATTAAAAAAAA
1 AATTAAAAAAAA
895427 AATTAAAAAAA
1 AATTAAAAAAA
895438 TAGTAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
AATTAAAAAAAA
Found at i:895743 original size:8 final size:8
Alignment explanation
Indices: 895730--895755 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
895720 TGAACATCAA
895730 ATATGAAT
1 ATATGAAT
895738 ATATGAAT
1 ATATGAAT
895746 ATATGAAT
1 ATATGAAT
895754 AT
1 AT
895756 GCATTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (8 bp):
ATATGAAT
Found at i:903189 original size:143 final size:145
Alignment explanation
Indices: 902827--903198 Score: 407
Period size: 143 Copynumber: 2.6 Consensus size: 145
902817 CCGAAATACA
* * * * * *
902827 TTTTATTTAATATAACTATAATTATTATTTATATATATTTCTGTTGTATTATTTAAAAATTTGTT
1 TTTTATTTAATATAATTAAAATTATTATTTATATATATTTCTGTTTTAATCTTTAAAAATTTATT
** * * *
902892 ACCAATA-ATTTTTTCTTGACGTGAAAGATACAATACAAGTTATTTTAATTTTATATAAAGAAGT
66 AGTAATATTTTTTTTCTTGACGAGAAAGATACAATACAAGTTATTTTAATTTGATATAAAGAAGT
*
902956 ATTAAGATAAAAACC
131 ATTAAAATAAAAACC
* * * * * *
902971 TTTTATTTAATATAATTAAAATTACTGTTTTTATATGTTTCTGTTTT-ATCATTT-AACATTTAA
1 TTTTATTTAATATAATTAAAATTATTATTTATATATATTTCTGTTTTAATC-TTTAAAAATTTAT
* * *
903034 TAGTAATAATTTTTTTTCTTGACGAGGAAGATACAATATAAGTTATTTTAATTTGATATATA-AA
65 TAGTAAT-ATTTTTTTTCTTGACGAGAAAGATACAATACAAGTTATTTTAATTTGATATAAAGAA
* *
903098 -TATTAAAAT-AAATCAT
129 GTATTAAAATAAAAAC-C
* * * *
903114 TTTTATTTAACATAATTAAAATTATTATTTCTATATATTTATATTTTAATCTTTAAAAATCTT-T
1 TTTTATTTAATATAATTAAAATTATTATTTATATATATTTCTGTTTTAATCTTTAAAAAT-TTAT
*
903178 TAGTAATATTTTTTTCCTTGA
65 TAGTAATATTTTTTTTCTTGA
903199 GTTTATTTTA
Statistics
Matches: 188, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
142 4 0.02
143 76 0.40
144 60 0.32
145 48 0.26
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (145 bp):
TTTTATTTAATATAATTAAAATTATTATTTATATATATTTCTGTTTTAATCTTTAAAAATTTATT
AGTAATATTTTTTTTCTTGACGAGAAAGATACAATACAAGTTATTTTAATTTGATATAAAGAAGT
ATTAAAATAAAAACC
Found at i:918853 original size:14 final size:14
Alignment explanation
Indices: 918834--918862 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
918824 TTTTCTTATT
918834 AATGTGATACTATA
1 AATGTGATACTATA
918848 AATGTGATACTATA
1 AATGTGATACTATA
918862 A
1 A
918863 TTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
AATGTGATACTATA
Found at i:922291 original size:21 final size:20
Alignment explanation
Indices: 922265--922540 Score: 94
Period size: 20 Copynumber: 13.5 Consensus size: 20
922255 CAGTTTCAAG
922265 AATCGCAACGCGAATTTGGAA
1 AATCGCAACGCGAATTT-GAA
* *
922286 AATCGCAATGCGAATTTGTAC
1 AATCGCAACGCGAATTTG-AA
* ** * * *
922307 TATCGCATTGCGATTTTCCAG
1 AATCGCAACGCGAATTT-GAA
922328 AATCGCAACGCGAATATT-AA
1 AATCGCAACGCGAAT-TTGAA
**
922348 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATTTGA-A
*
922368 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATT-TGAA
* * *** *
922388 TATCGCAACGAGTACCCGTAAA
1 AATCGCAACGCG-A-ATTTGAA
* ** *
922410 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATTTGAA
**
922430 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATTTG-AA
* ** *
922451 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATTTGAA
* ** *
922471 AATCGCAACGAGAATAAGTA
1 AATCGCAACGCGAATTTGAA
*
922491 AATCGCAACACG-ATTCTGAA
1 AATCGCAACGCGAATT-TGAA
* * * *
922511 TATCGCAACGCGTATTCGTA
1 AATCGCAACGCGAATTTGAA
922531 AATCGCAACG
1 AATCGCAACG
922541 ACAATACGAA
Statistics
Matches: 188, Mismatches: 53, Indels: 29
0.70 0.20 0.11
Matches are distributed among these distances:
19 5 0.03
20 106 0.56
21 63 0.34
22 14 0.07
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATTTGAA
Found at i:922434 original size:20 final size:20
Alignment explanation
Indices: 922389--922581 Score: 151
Period size: 20 Copynumber: 9.4 Consensus size: 20
922379 GATTCTGACT
* *
922389 ATCGCAACGAGTACCCGTAAAA
1 ATCGCAACGCGTATCCGT--AA
922411 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
922431 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
922452 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * **
922472 ATCGCAACGAGAATAAGTAA
1 ATCGCAACGCGTATCCGTAA
* *
922492 ATCGCAACACG-ATTC-TGAA
1 ATCGCAACGCGTATCCGT-AA
*
922511 TATCGCAACGCGTATTCGTAA
1 -ATCGCAACGCGTATCCGTAA
* * *
922532 ATCGCAACGAC-AATACGAAAA
1 ATCGCAACG-CGTATCCG-TAA
*
922553 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
922573 ATCGCAACG
1 ATCGCAACG
922582 TGATTTTTAA
Statistics
Matches: 138, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 78 0.57
21 38 0.28
22 17 0.12
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:922465 original size:41 final size:41
Alignment explanation
Indices: 922408--922499 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
922398 AGTACCCGTA
*
922408 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAAGT
*
922449 AAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATAAGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAAGT
922490 -AAATCGCAAC
1 AAAATCGCAAC
922500 ACGATTCTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 10 0.20
41 39 0.80
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.16
Consensus pattern (41 bp):
AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAAGT
Found at i:923197 original size:21 final size:20
Alignment explanation
Indices: 923159--923214 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
923149 GCAACGAGAG
* * *
923159 AATCTCAACGCGAAAATGAC
1 AATCGCAACGAGAAAATGAA
*
923179 TATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGA-AAATGAA
*
923200 AATCGCAACGCGAAA
1 AATCGCAACGAGAAA
923215 CCAAAATCGC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (20 bp):
AATCGCAACGAGAAAATGAA
Found at i:923266 original size:20 final size:20
Alignment explanation
Indices: 923226--923320 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
923216 CAAAATCGCA
923226 TTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCCGCG
923245 TTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
*
923265 TTGCAATTTTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
** *
923285 TTGCGATAGTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CGCG
923305 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
923321 AACCAAAAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
19 18 0.27
20 45 0.68
21 3 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCG
Found at i:925203 original size:93 final size:93
Alignment explanation
Indices: 925014--925204 Score: 321
Period size: 93 Copynumber: 2.1 Consensus size: 93
925004 TAGATTGCTT
925014 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
925079 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTCTGTCTTTTGGTTGAA
* * * *
925107 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTTTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA-ATAGT
925172 ATTTGTCTTTGTTCTGTCTTTTGGTTG-A
65 ATTTGTCTTTGTTCTGTCTTTTGGTTGAA
925200 AGTAA
1 AGTAA
925205 TGTAATCCAT
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 62 0.67
94 30 0.33
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTCTGTCTTTTGGTTGAA
Found at i:925349 original size:19 final size:19
Alignment explanation
Indices: 925252--925351 Score: 112
Period size: 19 Copynumber: 5.2 Consensus size: 19
925242 TAGTTTACTT
*
925252 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
925272 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
* *
925291 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
* * *
925310 TCGCAATGCAAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
925329 TCGCAACGCGAAACTATAA
1 TCGCAACGCGAAACTAAAA
925348 TCGC
1 TCGC
925352 GTTGCGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.01
19 57 0.81
20 12 0.17
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:925370 original size:19 final size:19
Alignment explanation
Indices: 925348--925482 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
925338 GAAACTATAA
**
925348 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
925367 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
925386 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
925405 TCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
925419 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
925438 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
925452 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
925471 TCGTGTTGCGAT
1 TCGCGTTGCGAT
925483 AGTCATTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
14 20 0.21
16 6 0.06
17 6 0.06
19 65 0.67
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:925424 original size:14 final size:14
Alignment explanation
Indices: 925405--925464 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
925395 GATTTTCATT
925405 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
925419 TCTCGTTGCGATTTTC
1 TCTCGTTGCGA--TTC
* *
925435 ATTTCGCGTTACGATTC
1 ---TCTCGTTGCGATTC
925452 TCTCGTTGCGATT
1 TCTCGTTGCGATT
925465 TTCATTTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 22 0.59
16 3 0.08
17 3 0.08
19 9 0.24
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:925431 original size:33 final size:33
Alignment explanation
Indices: 925389--925482 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
925379 TTTCATTTCG
925389 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
* *
925422 CGTTGCGATTTTCATTTCGCGTTACGATTCTCT
1 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
925455 CGTTGCGATTTTCATTTCGT-GTTGCGAT
1 CGTTGCGATTTTCATTTC-TCGTTGCGAT
925483 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
Found at i:925490 original size:52 final size:52
Alignment explanation
Indices: 925351--925482 Score: 139
Period size: 52 Copynumber: 2.5 Consensus size: 52
925341 ACTATAATCG
* *
925351 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCT
1 CGTTGCGATTTT-CTTTCG-GTTGCGATTTTCATTTCGCGTTACGA-TTTC--TTCT
*
925408 CGTTGCGA--TTCTCTC-GTTGCGATTTTCATTTCGCGTTACGA-TTC-TCT
1 CGTTGCGATTTTCTTTCGGTTGCGATTTTCATTTCGCGTTACGATTTCTTCT
925455 CGTTGCGATTTTCATTTCGTGTTGCGAT
1 CGTTGCGATTTTC-TTTCG-GTTGCGAT
925483 AGTCATTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
47 11 0.17
49 3 0.05
50 6 0.09
52 33 0.50
54 3 0.05
55 2 0.03
57 8 0.12
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (52 bp):
CGTTGCGATTTTCTTTCGGTTGCGATTTTCATTTCGCGTTACGATTTCTTCT
Found at i:927407 original size:14 final size:14
Alignment explanation
Indices: 927388--927423 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
927378 ATTGTTTAAT
927388 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
927402 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
927416 TGATTTGT
1 TGATTTGT
927424 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:927586 original size:19 final size:18
Alignment explanation
Indices: 927530--927588 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
927520 AAAAATGACT
*
927530 ATCGCAATGCTAAATAAAA
1 ATCGCAATGC-AAATGAAA
*
927549 ATCGCAA--C-AA-GAGA
1 ATCGCAATGCAAATGAAA
927563 ATCGCAATGCGAAATGAAA
1 ATCGCAATGC-AAATGAAA
927582 ATCGCAA
1 ATCGCAA
927589 CGACATTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 17 0.53
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCAAATGAAA
Found at i:927656 original size:20 final size:19
Alignment explanation
Indices: 927594--927795 Score: 119
Period size: 20 Copynumber: 11.2 Consensus size: 19
927584 CGCAACGACA
* *
927594 TTCATTTCGCATTGCGATA
1 TTCATTTCGCGTTGCGATT
* * *
927613 GTAATTTCCGCGTTGCGATA
1 TTCATTT-CGCGTTGCGATT
927633 TTCATATTCGCGTTGCGATT
1 TTCAT-TTCGCGTTGCGATT
*
927653 TTCA-----CATTGCGATT
1 TTCATTTCGCGTTGCGATT
*
927667 TTCATTTCGCATTGCGA--
1 TTCATTTCGCGTTGCGATT
*
927684 TTC---TCTCGTTGCGATT
1 TTCATTTCGCGTTGCGATT
*
927700 TTCATTTCGCATTGCGA--
1 TTCATTTCGCGTTGCGATT
*
927717 TTC-TAT--CGTTGCGATT
1 TTCATTTCGCGTTGCGATT
* *
927733 TTCATTTCGCATTGCGATA
1 TTCATTTCGCGTTGCGATT
* * *
927752 GTAATTTCCGCGTTGCGATA
1 TTCATTT-CGCGTTGCGATT
*
927772 TTCATATTTGCGTTGCGATT
1 TTCAT-TTCGCGTTGCGATT
927792 TTCA
1 TTCA
927796 CGTTGCAATT
Statistics
Matches: 141, Mismatches: 23, Indels: 37
0.70 0.11 0.18
Matches are distributed among these distances:
14 29 0.21
16 8 0.06
17 8 0.06
19 35 0.25
20 57 0.40
21 4 0.03
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCATTTCGCGTTGCGATT
Found at i:927682 original size:33 final size:33
Alignment explanation
Indices: 927623--927838 Score: 218
Period size: 33 Copynumber: 6.3 Consensus size: 33
927613 GTAATTTCCG
* * *
927623 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCA
* *
927657 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
927690 CGTTGCGATTTTCATTTCGCATTGCGATTCT-A
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
* *
927722 TCGTTGCGATTTTCATTTCGCATTGCGATAGTAATTTCCG
1 -CGTTGCGATTTTCATTTCGCATTGCG--A-T--TCT-CA
* * * *
927762 CGTTGCGATATTCATATTTGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCA
* * *
927796 CGTTGCAATTTTAATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
927829 CGTTGCGATT
1 CGTTGCGATT
927839 GTAATTTCCG
Statistics
Matches: 152, Mismatches: 21, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
33 94 0.62
34 26 0.17
35 4 0.03
36 1 0.01
37 1 0.01
38 3 0.02
39 14 0.09
40 9 0.06
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
Found at i:927846 original size:139 final size:140
Alignment explanation
Indices: 927594--927855 Score: 454
Period size: 139 Copynumber: 1.9 Consensus size: 140
927584 CGCAACGACA
927594 TTCATTTCGCATTGCGATAGTAATTTCCGCGTTGCGATATTCATATTCGCGTTGCGATTTTCACA
1 TTCATTTCGCATTGCGATAGTAATTTCCGCGTTGCGATATTCATATTCGCGTTGCGATTTTCACA
* * * *
927659 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTCTAT
66 TTGCAATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGCATTGCGATTCTAT
927723 CGTTGCGATT
131 CGTTGCGATT
* *
927733 TTCATTTCGCATTGCGATAGTAATTTCCGCGTTGCGATATTCATATTTGCGTTGCGATTTTCACG
1 TTCATTTCGCATTGCGATAGTAATTTCCGCGTTGCGATATTCATATTCGCGTTGCGATTTTCACA
*
927798 TTGCAATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGCGTTGCG
66 TTGCAATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGCATTGCG
927856 GTAGTCATTA
Statistics
Matches: 115, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
139 107 0.93
140 8 0.07
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (140 bp):
TTCATTTCGCATTGCGATAGTAATTTCCGCGTTGCGATATTCATATTCGCGTTGCGATTTTCACA
TTGCAATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGCATTGCGATTCTAT
CGTTGCGATT
Found at i:930394 original size:24 final size:24
Alignment explanation
Indices: 930360--930413 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
930350 CTGAAACATC
930360 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
930384 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
930408 ATCAAA
1 ATCAAA
930414 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:930427 original size:24 final size:24
Alignment explanation
Indices: 930360--930427 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
930350 CTGAAACATC
* * *
930360 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
930384 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
930408 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
930428 TAATACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:931250 original size:20 final size:20
Alignment explanation
Indices: 931223--931532 Score: 204
Period size: 20 Copynumber: 15.4 Consensus size: 20
931213 AATTTCAGTT
931223 TTGCGATTTACAGATTCTCG
1 TTGCGATTTACAGATTCTCG
* * *
931243 TCGCGATTTACGGATTATCG
1 TTGCGATTTACAGATTCTCG
931263 TTGCGATTTACAGATTCTCG
1 TTGCGATTTACAGATTCTCG
* *
931283 TTGCGATTTACAGATACGCG
1 TTGCGATTTACAGATTCTCG
931303 TTGCGATTTTAC-GTATTCTCG
1 TTGCGA-TTTACAG-ATTCTCG
* * * *
931324 TTGCGATTTACGGATACGCA
1 TTGCGATTTACAGATTCTCG
* *
931344 TTGCGATTAAC-GTATTCTCA
1 TTGCGATTTACAG-ATTCTCG
* * *
931364 TTGCGA-TAATCAGAATCGCG
1 TTGCGATTTA-CAGATTCTCG
*
931384 TTGCGATTTAC-GTATTCTCA
1 TTGCGATTTACAG-ATTCTCG
* * * *
931404 TTGTGATTTACGGATACGCG
1 TTGCGATTTACAGATTCTCG
*
931424 TTGCGATTTTAC-GTATTGTCG
1 TTGCGA-TTTACAG-ATTCTCG
* * *
931445 TTGCGATTTACGGGTACTCG
1 TTGCGATTTACAGATTCTCG
* * *
931465 TTGCGATAGT-CAGAATCGCG
1 TTGCGAT-TTACAGATTCTCG
* *
931485 TTGCGATTTATATG-TTCGCG
1 TTGCGATTTACA-GATTCTCG
* *
931505 TTGCGATTTTA-ATATTCGCG
1 TTGCGA-TTTACAGATTCTCG
931525 TTGCGATT
1 TTGCGATT
931533 CTGGAAAATC
Statistics
Matches: 229, Mismatches: 44, Indels: 35
0.74 0.14 0.11
Matches are distributed among these distances:
19 8 0.03
20 178 0.78
21 43 0.19
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAGATTCTCG
Found at i:931278 original size:40 final size:41
Alignment explanation
Indices: 931223--931532 Score: 236
Period size: 40 Copynumber: 7.7 Consensus size: 41
931213 AATTTCAGTT
* *
931223 TTGCGATTTACAGATTCTCGTCGCGATTTACGGATTA-TCG
1 TTGCGATTTACAGATTCTCGTTGCGATTTACGGATTACGCG
*
931263 TTGCGATTTACAGATTCTCGTTGCGATTTACAGA-TACGCG
1 TTGCGATTTACAGATTCTCGTTGCGATTTACGGATTACGCG
*
931303 TTGCGATTTTAC-GTATTCTCGTTGCGATTTACGGA-TACGCA
1 TTGCGA-TTTACAG-ATTCTCGTTGCGATTTACGGATTACGCG
* * * * *
931344 TTGCGATTAAC-GTATTCTCATTGCGA-TAATCAGAAT-CGCG
1 TTGCGATTTACAG-ATTCTCGTTGCGATTTA-CGGATTACGCG
* *
931384 TTGCGATTTAC-GTATTCTCATTGTGATTTACGGA-TACGCG
1 TTGCGATTTACAG-ATTCTCGTTGCGATTTACGGATTACGCG
* * *
931424 TTGCGATTTTAC-GTATTGTCGTTGCGATTTACGG-GTACTCG
1 TTGCGA-TTTACAG-ATTCTCGTTGCGATTTACGGATTACGCG
* * * * *
931465 TTGCGATAGT-CAGAATCGCGTTGCGATTTA--TATGTTCGCG
1 TTGCGAT-TTACAGATTCTCGTTGCGATTTACGGAT-TACGCG
* *
931505 TTGCGATTTTA-ATATTCGCGTTGCGATT
1 TTGCGA-TTTACAGATTCTCGTTGCGATT
931533 CTGGAAAATC
Statistics
Matches: 226, Mismatches: 29, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
39 5 0.02
40 144 0.64
41 77 0.34
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TTGCGATTTACAGATTCTCGTTGCGATTTACGGATTACGCG
Found at i:931412 original size:101 final size:101
Alignment explanation
Indices: 931281--931494 Score: 236
Period size: 101 Copynumber: 2.1 Consensus size: 101
931271 TACAGATTCT
* * * *
931281 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGA-TTTACGGATACG-CA
1 CGTTGCGATTTACAGATACGCATTGCGA-TTTACGGATACGCGTTGCGATTTTACGGAT-CGTCA
* *
931344 TTGCGATTAACGTATTCTCATTGCGATAATCAGAATCG
64 TTGCGATTAACGGATACTCATTGCGATAATCAGAATCG
* * * * * *
931382 CGTTGCGATTTAC-GTATTCTCATTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
1 CGTTGCGATTTACAG-ATACGCATTGCGATTTACGGATACGCGTTGCGATTTTACGGATCGTCAT
* * * *
931446 TGCGATTTACGGGTACTCGTTGCGATAGTCAGAATCG
65 TGCGATTAACGGATACTCATTGCGATAATCAGAATCG
931483 CGTTGCGATTTA
1 CGTTGCGATTTA
931495 TATGTTCGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
100 19 0.20
101 75 0.80
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (101 bp):
CGTTGCGATTTACAGATACGCATTGCGATTTACGGATACGCGTTGCGATTTTACGGATCGTCATT
GCGATTAACGGATACTCATTGCGATAATCAGAATCG
Found at i:942726 original size:60 final size:60
Alignment explanation
Indices: 942657--942782 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
942647 GATAATGGAG
* * * *
942657 TTGGAACAAGACAAGGGTAAACAATGTGCTGATGATACAGTTGATGATAAGAAAAAGGAC
1 TTGGGACAAGACAAGCGTAAACAATGTGCCGATCATACAGTTGATGATAAGAAAAAGGAC
*
942717 TTGGGACAAGACAAGCGTAAACAATGTGCCGATCATACAGTTGATGATAAGAAAAAGGAG
1 TTGGGACAAGACAAGCGTAAACAATGTGCCGATCATACAGTTGATGATAAGAAAAAGGAC
942777 TTGGGA
1 TTGGGA
942783 AAAGTAATGG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (60 bp):
TTGGGACAAGACAAGCGTAAACAATGTGCCGATCATACAGTTGATGATAAGAAAAAGGAC
Found at i:947664 original size:60 final size:59
Alignment explanation
Indices: 947543--947666 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 59
947533 CTCGAATGAT
* * **
947543 CATTTTATAACTTTTAATAATTGAGGGACTTAACAAAACAACATCCTACAATTGGGAAAC
1 CATTTTATAACTTTTAAT-ATTGAAGGAATTAACAAAACAACATCCTACAATCAGGAAAC
* * * *
947603 CATTTTATAACTTTTAAT-TGTGAAAGGAATTAATAAAACAACATCTTATAATCAGGTAAC
1 CATTTTATAACTTTTAATAT-TG-AAGGAATTAACAAAACAACATCCTACAATCAGGAAAC
947663 CATT
1 CATT
947667 CCTGTAGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 1 0.02
59 2 0.04
60 51 0.94
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (59 bp):
CATTTTATAACTTTTAATATTGAAGGAATTAACAAAACAACATCCTACAATCAGGAAAC
Found at i:949497 original size:29 final size:29
Alignment explanation
Indices: 949454--949579 Score: 200
Period size: 29 Copynumber: 4.4 Consensus size: 29
949444 ACCGTTGATC
949454 GGGTGCTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTATTTTAGTAATTAATTCGAAAT
*
949483 AGGTGCTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTATTTTAGTAATTAATTCGAAAT
949512 GGGTGCTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTATTTTAGTAATTAATTCGAAAT
* ** *
949541 GGGTGTTATTTTAGTAATT-ATTTTAAAA
1 GGGTGCTATTTTAGTAATTAATTCGAAAT
949569 GGGTGCTATTT
1 GGGTGCTATTT
949580 CTGAAGAATG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
28 16 0.18
29 74 0.82
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.44
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTAATTCGAAAT
Found at i:949627 original size:12 final size:12
Alignment explanation
Indices: 949610--949673 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
949600 TGTTGACCTC
949610 CTTTGACCAAAA
1 CTTTGACCAAAA
**
949622 CTTTGACC--TC
1 CTTTGACCAAAA
949632 CTTTGACCAAAA
1 CTTTGACCAAAA
**
949644 CTTTGACC--GG
1 CTTTGACCAAAA
949654 CTTTGACCAAAA
1 CTTTGACCAAAA
949666 CTTTGACC
1 CTTTGACC
949674 GGCTTTGACC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
10 16 0.40
12 24 0.60
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (12 bp):
CTTTGACCAAAA
Found at i:949628 original size:22 final size:22
Alignment explanation
Indices: 949602--949684 Score: 130
Period size: 22 Copynumber: 3.8 Consensus size: 22
949592 TGACAGTTTG
*
949602 TTGACCTCCTTTGACCAAAACT
1 TTGACCGCCTTTGACCAAAACT
*
949624 TTGACCTCCTTTGACCAAAACT
1 TTGACCGCCTTTGACCAAAACT
*
949646 TTGACCGGCTTTGACCAAAACT
1 TTGACCGCCTTTGACCAAAACT
*
949668 TTGACCGGCTTTGACCA
1 TTGACCGCCTTTGACCA
949685 GTTATTAAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (22 bp):
TTGACCGCCTTTGACCAAAACT
Found at i:950662 original size:117 final size:117
Alignment explanation
Indices: 950455--950742 Score: 418
Period size: 117 Copynumber: 2.5 Consensus size: 117
950445 GTATTTCATG
*
950455 CTCCTTTATTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGAGAA
1 CTCCTTTGTTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGAGAA
* *
950520 CATACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTGCAGA
66 CATACACATTGCAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTGCAGA
* *
950572 CTCCTTTGTTGTGTGCTCAGGGTAAGTCATTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGTTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGAGAA
* * * *
950637 CCTACACATTGCAGTGA-TGGAAGTGACTGGCTGGAGACGTTATTACTGCAGG
66 CATACACATTGCAGTGATTGG-AGTGACTGGATGGAGAAGTTATTACTGCAGA
* ** * *
950689 CTCATCGGCTT-CGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 CTCCTTTG-TTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
950743 TTTCGGGAAA
Statistics
Matches: 154, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.02
117 149 0.97
118 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.32
Consensus pattern (117 bp):
CTCCTTTGTTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGAGAA
CATACACATTGCAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTGCAGA
Done.