Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 89
Found at i:2619852 original size:20 final size:20
Alignment explanation
Indices: 2619811--2619852 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2619801 AGACTGAAAG
*
2619811 ATGACCCGAAGGATTAATAA
1 ATGACCCGAAGGATTAACAA
* *
2619831 ATGACCCGAAGGTTTTACAA
1 ATGACCCGAAGGATTAACAA
2619851 AT
1 AT
2619853 TTGTTGGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (20 bp):
ATGACCCGAAGGATTAACAA
Found at i:2622370 original size:174 final size:174
Alignment explanation
Indices: 2622080--2622426 Score: 559
Period size: 174 Copynumber: 2.0 Consensus size: 174
2622070 CCTGGTTCTG
* * * *
2622080 GACACTCATTGCAGCTGTGATTGGCGTAGTATTCACCAGACTCTTTAAATTGTCTCATTCTTCTC
1 GACACTCATTGCAACTGTGATTGGCGTAGTATTCACCAGACTCTTTAAATTGCCCCATTCCTCTC
* **
2622145 TAGTATTCAGAAAATATGATATAGGAGTTTGAGGTGTATTCAAGGTTGTATCTGGCCAATTTATT
66 TAGTATTCAGAAAATATGATATAGGAGTTTGAGGTGCATTCAAGGTTGTATCTACCCAATTTATT
2622210 TTTAAACCTGTAGGCCAATCTCAAATTACATTTCCTTTCAATTC
131 TTTAAACCTGTAGGCCAATCTCAAATTACATTTCCTTTCAATTC
* *
2622254 GACACTCATTGCAACTGTGATTGGCGTAGTATTTACCAGACTCTTTAAATTGCCCCCTTCCTCTC
1 GACACTCATTGCAACTGTGATTGGCGTAGTATTCACCAGACTCTTTAAATTGCCCCATTCCTCTC
* * * *
2622319 TTGTATTCAGAAAATTTGATATAGGAGTTTGAGGTGCCTTCAGGGTTGTATCTACCCAATTTATT
66 TAGTATTCAGAAAATATGATATAGGAGTTTGAGGTGCATTCAAGGTTGTATCTACCCAATTTATT
* *
2622384 TTTAAACCTGTAGGCCAATCTCGAATTACCTTTCCTTTCAATT
131 TTTAAACCTGTAGGCCAATCTCAAATTACATTTCCTTTCAATT
2622427 TTTTATTTCT
Statistics
Matches: 158, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
174 158 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (174 bp):
GACACTCATTGCAACTGTGATTGGCGTAGTATTCACCAGACTCTTTAAATTGCCCCATTCCTCTC
TAGTATTCAGAAAATATGATATAGGAGTTTGAGGTGCATTCAAGGTTGTATCTACCCAATTTATT
TTTAAACCTGTAGGCCAATCTCAAATTACATTTCCTTTCAATTC
Found at i:2625367 original size:21 final size:22
Alignment explanation
Indices: 2625321--2625367 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2625311 CTATATTTAT
*
2625321 TTAAATATTAAAATTACATAGG
1 TTAAATATTAAAATTACATAGA
*
2625343 TTAAAT-TATAAAA-TATATAGA
1 TTAAATAT-TAAAATTACATAGA
2625364 TTAA
1 TTAA
2625368 TAATACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
TTAAATATTAAAATTACATAGA
Found at i:2625632 original size:21 final size:22
Alignment explanation
Indices: 2625586--2625632 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2625576 CTATATTTAT
*
2625586 TTAAATATTAAAATTACATAGG
1 TTAAATATTAAAATTACATAGA
*
2625608 TTAAAT-TATAAAA-TATATAGA
1 TTAAATAT-TAAAATTACATAGA
2625629 TTAA
1 TTAA
2625633 TAATACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
TTAAATATTAAAATTACATAGA
Found at i:2625672 original size:265 final size:265
Alignment explanation
Indices: 2625199--2625725 Score: 1054
Period size: 265 Copynumber: 2.0 Consensus size: 265
2625189 GGTACCGGTG
2625199 TTTATTAATTGATTTGTCTTTGCAATAAATTAACAAAATTTTATTTAATTTAACTTAAATTATAC
1 TTTATTAATTGATTTGTCTTTGCAATAAATTAACAAAATTTTATTTAATTTAACTTAAATTATAC
2625264 AAATAAAATACTACTTAATATATTATTTATTATAAGTATAAATAATCCTATATTTATTTAAATAT
66 AAATAAAATACTACTTAATATATTATTTATTATAAGTATAAATAATCCTATATTTATTTAAATAT
2625329 TAAAATTACATAGGTTAAATTATAAAATATATAGATTAATAATACTAATTCAAAATATTATAAAA
131 TAAAATTACATAGGTTAAATTATAAAATATATAGATTAATAATACTAATTCAAAATATTATAAAA
2625394 TATAAGTACTGATAGTGTAATTAATCCTATAATAATAATATAAAATATTAAAATAATAAGGACTA
196 TATAAGTACTGATAGTGTAATTAATCCTATAATAATAATATAAAATATTAAAATAATAAGGACTA
2625459 AAGGT
261 AAGGT
2625464 TTTATTAATTGATTTGTCTTTGCAATAAATTAACAAAATTTTATTTAATTTAACTTAAATTATAC
1 TTTATTAATTGATTTGTCTTTGCAATAAATTAACAAAATTTTATTTAATTTAACTTAAATTATAC
2625529 AAATAAAATACTACTTAATATATTATTTATTATAAGTATAAATAATCCTATATTTATTTAAATAT
66 AAATAAAATACTACTTAATATATTATTTATTATAAGTATAAATAATCCTATATTTATTTAAATAT
2625594 TAAAATTACATAGGTTAAATTATAAAATATATAGATTAATAATACTAATTCAAAATATTATAAAA
131 TAAAATTACATAGGTTAAATTATAAAATATATAGATTAATAATACTAATTCAAAATATTATAAAA
2625659 TATAAGTACTGATAGTGTAATTAATCCTATAATAATAATATAAAATATTAAAATAATAAGGACTA
196 TATAAGTACTGATAGTGTAATTAATCCTATAATAATAATATAAAATATTAAAATAATAAGGACTA
2625724 AA
261 AA
2625726 TGTGTAATTT
Statistics
Matches: 262, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
265 262 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (265 bp):
TTTATTAATTGATTTGTCTTTGCAATAAATTAACAAAATTTTATTTAATTTAACTTAAATTATAC
AAATAAAATACTACTTAATATATTATTTATTATAAGTATAAATAATCCTATATTTATTTAAATAT
TAAAATTACATAGGTTAAATTATAAAATATATAGATTAATAATACTAATTCAAAATATTATAAAA
TATAAGTACTGATAGTGTAATTAATCCTATAATAATAATATAAAATATTAAAATAATAAGGACTA
AAGGT
Found at i:2627596 original size:33 final size:33
Alignment explanation
Indices: 2627551--2627643 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2627541 TGAAAAGAGG
*
2627551 TCTATGATATCATACAAGAATGTTACACAACGA
1 TCTATGACATCATACAAGAATGTTACACAACGA
2627584 TCTATGACATCATACAAGAATGTTACACAACGA
1 TCTATGACATCATACAAGAATGTTACACAACGA
*
2627617 TCTATGAGATCATACAAGAATGTTACA
1 TCTATGACATCATACAAGAATGTTACA
2627644 TGATAATAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (33 bp):
TCTATGACATCATACAAGAATGTTACACAACGA
Found at i:2627862 original size:21 final size:21
Alignment explanation
Indices: 2627796--2627925 Score: 96
Period size: 21 Copynumber: 6.6 Consensus size: 21
2627786 ATATGATAGG
2627796 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
* * * **
2627817 TCTTTCAGG--A-TGAT-AGG
1 TCCTTCGGGACACAGATGACA
*
2627834 TCATTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
* **
2627855 TCCTTCGGG--A-TGAT-AGG
1 TCCTTCGGGACACAGATGACA
*
2627872 TCCTTCGGGACACAGATGTCA
1 TCCTTCGGGACACAGATGACA
* *
2627893 TCCTTCGGGACACATATGACG
1 TCCTTCGGGACACAGATGACA
2627914 TCCTTCGGGACA
1 TCCTTCGGGACA
2627926 TAAATTTCAC
Statistics
Matches: 80, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
17 18 0.22
18 6 0.08
19 4 0.05
20 6 0.08
21 46 0.57
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:2627899 original size:38 final size:38
Alignment explanation
Indices: 2627788--2627902 Score: 194
Period size: 38 Copynumber: 3.0 Consensus size: 38
2627778 TTCGGGACAT
* *
2627788 ATGATAGGTCCTTCGGGACACAGATGACATCTTTCAGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
2627826 ATGATAGGTCATTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
2627864 ATGATAGGTCCTTCGGGACACAGATGTCATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
2627902 A
1 A
2627903 CACATATGAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:2632909 original size:30 final size:30
Alignment explanation
Indices: 2632865--2632932 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
2632855 AAGCCTTAGA
* ** *
2632865 AAAATTTGGGGACC-ATTTTGTAATTTTTG
1 AAAAGTTGGGGACCAATTCAGTAATTTTGG
2632894 AAAAGTTGGGAGACCAATTCAGTAATTTTGG
1 AAAAGTTGGG-GACCAATTCAGTAATTTTGG
2632925 AAAAGTTG
1 AAAAGTTG
2632933 TGAATGGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 9 0.27
30 4 0.12
31 20 0.61
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAAGTTGGGGACCAATTCAGTAATTTTGG
Found at i:2634079 original size:33 final size:33
Alignment explanation
Indices: 2634031--2634095 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2634021 TATGAAAAGG
*
2634031 GATCTATGAGGTCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
* *
2634064 GATCTGTGAGATCATACAAGAATGTTATACAA
1 GATCTATGAGATCATACAAGAATGTTACACAA
2634096 GCTACATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAT
Found at i:2634361 original size:38 final size:38
Alignment explanation
Indices: 2634246--2634348 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
2634236 TTCGGGACAT
* * * * * **
2634246 ATGATCGGTTCTTCGGGATACAGATGACATCCTTTGAA
1 ATGATAGGTCCTTCGGGACACAAATGACATCCTTCGGG
2634284 ATGATAGGTCCTTCGGGACACAAATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAAATGACATCCTTCGGG
*
2634322 ATGATAGGTCCTTCGGGACACATATGA
1 ATGATAGGTCCTTCGGGACACAAATGA
2634349 TGTTCTTTGG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAAATGACATCCTTCGGG
Found at i:2639513 original size:107 final size:107
Alignment explanation
Indices: 2639396--2639610 Score: 421
Period size: 107 Copynumber: 2.0 Consensus size: 107
2639386 TTCGCGGTTA
2639396 AGTTAACCGAAACCGTTTAACATTAATGATTTAATTAATTAACTTGTTAAATGTAACGATTATAC
1 AGTTAACCGAAACCGTTTAACATTAATGATTTAATTAATTAACTTGTTAAATGTAACGATTATAC
*
2639461 CGATTAACAGTTACATTATGTATTTTTTAACACCCCTAGTTC
66 CAATTAACAGTTACATTATGTATTTTTTAACACCCCTAGTTC
2639503 AGTTAACCGAAACCGTTTAACATTAATGATTTAATTAATTAACTTGTTAAATGTAACGATTATAC
1 AGTTAACCGAAACCGTTTAACATTAATGATTTAATTAATTAACTTGTTAAATGTAACGATTATAC
2639568 CAATTAACAGTTACATTATGTATTTTTTAACACCCCTAGTTC
66 CAATTAACAGTTACATTATGTATTTTTTAACACCCCTAGTTC
2639610 A
1 A
2639611 ATCTATGCTA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (107 bp):
AGTTAACCGAAACCGTTTAACATTAATGATTTAATTAATTAACTTGTTAAATGTAACGATTATAC
CAATTAACAGTTACATTATGTATTTTTTAACACCCCTAGTTC
Found at i:2644521 original size:15 final size:15
Alignment explanation
Indices: 2644478--2644524 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2644468 CTCCCCGCAT
*
2644478 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCGC
*
2644493 CCGCCCCGTATCCGC
1 CCGCCCCGCATCCGC
*
2644508 CCGCCCCACATCCGC
1 CCGCCCCGCATCCGC
2644523 CC
1 CC
2644525 ACCCAGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.11, C:0.66, G:0.15, T:0.09
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:2647676 original size:21 final size:21
Alignment explanation
Indices: 2647652--2647722 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
2647642 GCGTTGTATT
*
2647652 TCGCGTTACGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
2647673 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
2647693 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2647714 TCGCGTTGC
1 TCGCGTTGC
2647723 AATTTTCCAC
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2647711 original size:41 final size:41
Alignment explanation
Indices: 2647649--2647731 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
2647639 TTCGCGTTGT
*
2647649 ATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTACGATAGTTGAAAATCGCGTTGCAATTTTCC
* *
2647690 ATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCC
1 ATTTCGCGTTACGATAGTTGAAAATCGCGTTGCAATTTTCC
2647731 A
1 A
2647732 CAGTTGTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (41 bp):
ATTTCGCGTTACGATAGTTGAAAATCGCGTTGCAATTTTCC
Found at i:2647743 original size:22 final size:22
Alignment explanation
Indices: 2647717--2647772 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2647707 TTGAAAATCG
*
2647717 CGTTGCAATTTTCCACAGTTGT
1 CGTTGCGATTTTCCACAGTTGT
* ** *
2647739 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCACAGTTGT
2647761 CGTTGCGATTTT
1 CGTTGCGATTTT
2647773 TCAAATTCGT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (22 bp):
CGTTGCGATTTTCCACAGTTGT
Found at i:2648395 original size:6 final size:6
Alignment explanation
Indices: 2648386--2648626 Score: 446
Period size: 6 Copynumber: 40.2 Consensus size: 6
2648376 CCGTCTCGTC
*
2648386 TCGTGG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
1 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
2648434 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
1 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
* *
2648482 TCGTGG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTGG TCGTTG
1 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
*
2648530 TCGTTG TCGTTG TCGTGG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
1 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
2648578 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
1 TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG TCGTTG
2648626 T
1 T
2648627 AATACGTGTC
Statistics
Matches: 228, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 228 1.00
ACGTcount: A:0.00, C:0.17, G:0.35, T:0.49
Consensus pattern (6 bp):
TCGTTG
Found at i:2648768 original size:22 final size:22
Alignment explanation
Indices: 2648740--2648855 Score: 107
Period size: 22 Copynumber: 5.4 Consensus size: 22
2648730 AATTTGGAAA
2648740 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
2648762 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
2648784 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC-AACTGTAGACT
* * *
2648804 ATCGCAACG-CGATTATCA-ACT
1 ATCGCAACGACAACTGT-AGACT
*
2648825 ATCGCAACGACAACTGTAGGCT
1 ATCGCAACGACAACTGTAGACT
2648847 ATCGCAACG
1 ATCGCAACG
2648856 CGAAATGGAA
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.03
20 12 0.16
21 12 0.16
22 48 0.65
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:2648809 original size:20 final size:20
Alignment explanation
Indices: 2648784--2648923 Score: 95
Period size: 20 Copynumber: 6.8 Consensus size: 20
2648774 ACTGTAGACT
2648784 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
2648804 ATCGCAACGCGATTAT-CAACT
1 ATCGCAACGCGA-AATGGAA-A
* ***
2648825 ATCGCAACGAC-AACTGTAGGCT
1 ATCGCAACG-CGAAATG--GAAA
2648847 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
2648867 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
2648888 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
2648908 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
2648924 CAACGCGAAT
Statistics
Matches: 90, Mismatches: 22, Indels: 16
0.70 0.17 0.12
Matches are distributed among these distances:
20 47 0.52
21 28 0.31
22 15 0.17
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2648830 original size:21 final size:21
Alignment explanation
Indices: 2648804--2648899 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
2648794 GAAATGGAAA
2648804 ATCGCAACGCGATTATCAACT
1 ATCGCAACGCGATTATCAACT
* * * *
2648825 ATCGCAACGACAACTGT-AGGCT
1 ATCGCAACG-CGATTATCA-ACT
* * *
2648847 ATCGCAACGCGA-AATGGAA-A
1 ATCGCAACGCGATTAT-CAACT
*
2648867 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTATCAACT
2648888 ATCGCAACGCGA
1 ATCGCAACGCGA
2648900 AATGAAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
20 15 0.27
21 25 0.45
22 16 0.29
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATTATCAACT
Found at i:2648896 original size:63 final size:63
Alignment explanation
Indices: 2648759--2648896 Score: 249
Period size: 63 Copynumber: 2.2 Consensus size: 63
2648749 ACAACTGTAG
*
2648759 ACTATCGCAACAACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTATCA
1 ACTATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTATCA
* *
2648822 ACTATCGCAACGACAACTGTAGGCTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTATCA
2648885 ACTATCGCAACG
1 ACTATCGCAACG
2648897 CGAAATGAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (63 bp):
ACTATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTATCA
Found at i:2660273 original size:21 final size:21
Alignment explanation
Indices: 2660247--2660290 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2660237 CCGGACGGCC
2660247 CTTAATCTCCTTAAAACATGG
1 CTTAATCTCCTTAAAACATGG
* *
2660268 CTTAATCTCCTTGAAGCATGG
1 CTTAATCTCCTTAAAACATGG
2660289 CT
1 CT
2660291 GTGATCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (21 bp):
CTTAATCTCCTTAAAACATGG
Found at i:2665656 original size:18 final size:17
Alignment explanation
Indices: 2665634--2665678 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2665624 TTATTTTCTC
2665634 ATTATTTTGTATTTATTAT
1 ATTATTTT-TA-TTATTAT
*
2665653 -TTATTTTTATTATTTT
1 ATTATTTTTATTATTAT
2665669 ATTATTTTTA
1 ATTATTTTTA
2665679 AACCCCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 11 0.46
18 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTATTTTTATTATTAT
Found at i:2667125 original size:29 final size:29
Alignment explanation
Indices: 2667081--2667216 Score: 143
Period size: 29 Copynumber: 4.7 Consensus size: 29
2667071 GACCCGACCC
*
2667081 GGTGATATTCTGGG-AATTTTTGTGAAAAA
1 GGTGACATTCTGGGAAATTTTT-TGAAAAA
* *
2667110 AGTGACATTCTTGGAAATATTTTT-AAAAA
1 GGTGACATTCTGGGAAAT-TTTTTGAAAAA
* *
2667139 GGTGAAATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATTTTTTGAAAAA
** * *
2667168 GGTGACATTCTAAGAAATATTTTGAGAAA
1 GGTGACATTCTGGGAAATTTTTTGAAAAA
*
2667197 GGTGACATT-TTGGAAATTTT
1 GGTGACATTCTGGGAAATTTT
2667217 CGAATGTGGA
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
28 12 0.13
29 70 0.78
30 4 0.04
31 4 0.04
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (29 bp):
GGTGACATTCTGGGAAATTTTTTGAAAAA
Found at i:2667173 original size:58 final size:58
Alignment explanation
Indices: 2667081--2667201 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 58
2667071 GACCCGACCC
* * ** *
2667081 GGTGATATTCTGGGAATTTTTGTGAAAAAAGTGACATTCTTGGAAATATTTTTAAAAA
1 GGTGAAATTCTGGGAATATTTGTGAAAAAAGTGACATTCTAAGAAATATTTTGAAAAA
* *
2667139 GGTGAAATTCTGGGAAATATTT-TGAAAAAGGTGACATTCTAAGAAATATTTTGAGAAA
1 GGTGAAATTCTGGG-AATATTTGTGAAAAAAGTGACATTCTAAGAAATATTTTGAAAAA
2667197 GGTGA
1 GGTGA
2667202 CATTTTGGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 49 0.89
59 6 0.11
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (58 bp):
GGTGAAATTCTGGGAATATTTGTGAAAAAAGTGACATTCTAAGAAATATTTTGAAAAA
Found at i:2674620 original size:29 final size:29
Alignment explanation
Indices: 2674516--2674620 Score: 144
Period size: 29 Copynumber: 3.7 Consensus size: 29
2674506 CGACCCAACC
*
2674516 AGGTGACATTCTGGAAATT-TTTGTGAAAA
1 AGGTGACATTTTGGAAATTATTT-TGAAAA
*
2674545 A-GTGACATTCTGGGAAA-TATTTTGAAAA
1 AGGTGACATT-TTGGAAATTATTTTGAAAA
*
2674573 AGGTGACATTTTGGGAATTATTTTGAAAA
1 AGGTGACATTTTGGAAATTATTTTGAAAA
2674602 AGGTGACATTTTGGAAATT
1 AGGTGACATTTTGGAAATT
2674621 TTCGAATGTG
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
28 21 0.31
29 46 0.69
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (29 bp):
AGGTGACATTTTGGAAATTATTTTGAAAA
Found at i:2676754 original size:6 final size:6
Alignment explanation
Indices: 2676737--2676765 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2676727 TCGTTAAGAA
2676737 CTCGAG -TCGAG CTCGAG CTCGAG CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
2676766 TCAAGACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:2678264 original size:24 final size:24
Alignment explanation
Indices: 2678237--2678282 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2678227 CACCACAGCT
*
2678237 CGTATAAATTACACCGAAGTGCAG
1 CGTAGAAATTACACCGAAGTGCAG
**
2678261 CGTAGAAATTGTACCGAAGTGC
1 CGTAGAAATTACACCGAAGTGC
2678283 CACATAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (24 bp):
CGTAGAAATTACACCGAAGTGCAG
Found at i:2678322 original size:23 final size:23
Alignment explanation
Indices: 2678267--2678374 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
2678257 GCAGCGTAGA
*
2678267 AATTGTACCGAAGTG-CCACATAG
1 AATTGTCCCGAAG-GACCACATAG
2678290 AA-TGTCCCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
* * *
2678312 TATTGTCCCGAATGACCGCATAG
1 AATTGTCCCGAAGGACCACATAG
* * *
2678335 AAATGTCTCGAAGGACCACGTAG
1 AATTGTCCCGAAGGACCACATAG
**
2678358 AATTGTCCTAAAGGACC
1 AATTGTCCCGAAGGACC
2678375 GCGTAAAACC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
21 1 0.01
22 18 0.26
23 50 0.72
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:2678353 original size:46 final size:45
Alignment explanation
Indices: 2678267--2678365 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 45
2678257 GCAGCGTAGA
*
2678267 AATTGTACCGAAGTGCCACATAGAATGTCCCGAAGGACCACATAG
1 AATTGTCCCGAAGTGCCACATAGAATGTCCCGAAGGACCACATAG
* * * *
2678312 TATTGTCCCGAA-TGACCGCATAGAAATGTCTCGAAGGACCACGTAG
1 AATTGTCCCGAAGTG-CCACATAG-AATGTCCCGAAGGACCACATAG
2678358 AATTGTCC
1 AATTGTCC
2678366 TAAAGGACCG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 2 0.04
45 17 0.37
46 27 0.59
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.21
Consensus pattern (45 bp):
AATTGTCCCGAAGTGCCACATAGAATGTCCCGAAGGACCACATAG
Found at i:2686743 original size:2 final size:2
Alignment explanation
Indices: 2686736--2686766 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2686726 ATTTGCAATT
2686736 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 T
2686767 TTTGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2690082 original size:11 final size:12
Alignment explanation
Indices: 2690058--2690087 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2690048 ATTAATATTA
2690058 TTTTATTATAAT
1 TTTTATTATAAT
2690070 TTTTATTAT-AT
1 TTTTATTATAAT
2690081 TTTTATT
1 TTTTATT
2690088 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTATAAT
Found at i:2690832 original size:24 final size:23
Alignment explanation
Indices: 2690786--2690834 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2690776 AACTCTTATG
* * *
2690786 ATATAATATTTAAAATTTGTATA
1 ATATAAAATTTAAAAATTATATA
2690809 ATATAAAATTTTAAAAATTATATA
1 ATATAAAA-TTTAAAAATTATATA
2690833 AT
1 AT
2690835 TAGTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATAAAATTTAAAAATTATATA
Found at i:2693001 original size:2 final size:2
Alignment explanation
Indices: 2692994--2693018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2692984 TGCAGATCTC
2692994 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 A
2693019 TTAGGGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2695328 original size:22 final size:22
Alignment explanation
Indices: 2695277--2695329 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
2695267 ACGCGATTCT
2695277 GACTATCGCATTGTGATTTTCC
1 GACTATCGCATTGTGATTTTCC
* * * *
2695299 AAAT-TCGCGTTGTGATTTTTC
1 GACTATCGCATTGTGATTTTCC
2695320 GACTATCGCA
1 GACTATCGCA
2695330 ATACGAATAT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
GACTATCGCATTGTGATTTTCC
Found at i:2695349 original size:20 final size:20
Alignment explanation
Indices: 2695324--2695435 Score: 172
Period size: 20 Copynumber: 5.6 Consensus size: 20
2695314 TTTTTCGACT
*
2695324 ATCGCAATACGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2695344 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2695364 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2695384 ATCGCAATGCGATTATGTAA
1 ATCGCAATGCGAATATGTAA
* *
2695404 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
2695424 ATCGCAATGCGA
1 ATCGCAATGCGA
2695436 TTTTGATTAT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
19 1 0.01
20 87 0.99
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:2695436 original size:40 final size:40
Alignment explanation
Indices: 2695344--2695470 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
2695334 GAATATGTAA
* * *
2695344 ATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGATTATGTAAATCGCAATGCGATTATG-ACT
2695384 ATCGCAATGCGATTATGTAAATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTATGTAAATCGCAATGCGATTATGACT
* * * *
2695424 ATCGCAATGCGATTTTG-ATTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTATGTA-AATCGCAATGCGATTATGACT
2695464 ATCGCAA
1 ATCGCAA
2695471 CACTGAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.03
40 76 0.97
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (40 bp):
ATCGCAATGCGATTATGTAAATCGCAATGCGATTATGACT
Found at i:2695446 original size:20 final size:20
Alignment explanation
Indices: 2695320--2695470 Score: 130
Period size: 20 Copynumber: 7.5 Consensus size: 20
2695310 GTGATTTTTC
* *
2695320 GACTATCGCAATACGAATAT
1 GACTATCGCAATGCGATTAT
* *
2695340 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
* *
2695360 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
*
2695380 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
2695400 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
2695420 GACTATCGCAATGCGATTTT
1 GACTATCGCAATGCGATTAT
* * *
2695440 GATTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
2695460 GACTATCGCAA
1 GACTATCGCAA
2695471 CACTGAATTT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 118 0.98
21 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:2695448 original size:60 final size:60
Alignment explanation
Indices: 2695323--2695457 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
2695313 ATTTTTCGAC
* *
2695323 TATCGCAATACGAATATGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
1 TATCGCAATGCGATTATGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
* * * * *
2695383 AATCGCAATGCGATTATGTAAATCGCAATGCGATTATG-ACTATCGCAATGCGATTTTG-A
1 TATCGCAATGCGATTATGTAAATCGCAATGCGAATATGTA-AATCGCAATGCGAATATGTA
*
2695442 TTATCGCAACGCGATT
1 -TATCGCAATGCGATT
2695458 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 62 0.97
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (60 bp):
TATCGCAATGCGATTATGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA
Found at i:2696324 original size:24 final size:24
Alignment explanation
Indices: 2696292--2696345 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2696282 GTATTCGAAA
2696292 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2696316 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2696340 TTTGAT
1 TTTGAT
2696346 AATGTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2696564 original size:14 final size:14
Alignment explanation
Indices: 2696535--2696571 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2696525 AGAAAAAGAA
2696535 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
2696550 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
2696564 GAAGAAAA
1 GAAGAAAA
2696572 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:2698631 original size:18 final size:18
Alignment explanation
Indices: 2698608--2698642 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2698598 AGAAAAATGC
*
2698608 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2698626 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2698643 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2698642 original size:12 final size:12
Alignment explanation
Indices: 2698601--2698629 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2698591 GGTGTCAAGA
2698601 AAAAT-GCAATC
1 AAAATCGCAATC
2698612 AAAATCGCAATC
1 AAAATCGCAATC
2698624 AAAATC
1 AAAATC
2698630 AAAATCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (12 bp):
AAAATCGCAATC
Found at i:2698958 original size:140 final size:140
Alignment explanation
Indices: 2698702--2698971 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
2698692 AAACGTTGTA
* *
2698702 TTATGTGTAAACTTTTAGCATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
* *
2698767 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATCACACATTCATTTGAATATCACAACGCGAATTTGACTAT
2698832 TATGTGTATT
131 TATGTGTATT
2698842 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
*
2698907 TGATATGTTCAGTTGTTATCACTTATCACATATTCATTTGAATATCACAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATCACACATTCATTTGAATATCACAACGCGAATTTGACTAT
2698972 CGCAACGCGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATCACACATTCATTTGAATATCACAACGCGAATTTGACTAT
TATGTGTATT
Found at i:2698967 original size:20 final size:20
Alignment explanation
Indices: 2698942--2699166 Score: 179
Period size: 20 Copynumber: 11.8 Consensus size: 20
2698932 TCACATATTC
* *
2698942 ATTTGAATATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
2698962 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2698982 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
2699001 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
2699016 ATTTGACTATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
*
2699036 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2699056 ATTTGTCTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
2699076 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
2699096 A----A--ATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
2699110 ATTTGAGTATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
* * ** *
2699130 ATTTGATTACCGCAACAAGT
1 ATTTGACTATCGCAACGCGA
2699150 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
2699167 AGAAAATCGC
Statistics
Matches: 163, Mismatches: 28, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
14 20 0.12
15 3 0.02
16 1 0.01
18 1 0.01
19 4 0.02
20 133 0.82
21 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2699013 original size:34 final size:38
Alignment explanation
Indices: 2698970--2699071 Score: 124
Period size: 34 Copynumber: 2.7 Consensus size: 38
2698960 GAATTTGACT
2698970 ATCGCAACGCGAATTTGATTATCGCAAC-TCAA-A-A-
1 ATCGCAACGCGAATTTGATTATCGCAACATCAATAGAC
* *
2699004 ATCGCAACGCGAATTTGACTATCGCAACATGAATATGAC
1 ATCGCAACGCGAATTTGATTATCGCAACATCAATA-GAC
2699043 TATCGCAACGCGAATTTG-TCTATCGCAAC
1 -ATCGCAACGCGAATTTGAT-TATCGCAAC
2699072 GGCTATTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
34 27 0.47
35 3 0.05
36 1 0.02
38 1 0.02
40 26 0.45
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (38 bp):
ATCGCAACGCGAATTTGATTATCGCAACATCAATAGAC
Found at i:2699102 original size:74 final size:74
Alignment explanation
Indices: 2699024--2699178 Score: 224
Period size: 74 Copynumber: 2.1 Consensus size: 74
2699014 GAATTTGACT
* * *
2699024 ATCGCAACATGAATATGACTATCGCAACGCGAATTTG-TCTATCGCAAC-GGCTATTTGACTATC
1 ATCGCAACACGAATATGACTATCGCAACGCGAATTTGAT-TACCGCAACAAG-TATTTGACTATC
2699087 GCAACGAGAAA
64 GCAACGAGAAA
* * *
2699098 ATCGCAACACGAATTTGAGTATCGCAACTCGAATTTGATTACCGCAACAAGTATTTGACTATCGC
1 ATCGCAACACGAATATGACTATCGCAACGCGAATTTGATTACCGCAACAAGTATTTGACTATCGC
2699163 AACGAGAAA
66 AACGAGAAA
2699172 ATCGCAA
1 ATCGCAA
2699179 AGCGTATTAG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 71 0.97
75 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (74 bp):
ATCGCAACACGAATATGACTATCGCAACGCGAATTTGATTACCGCAACAAGTATTTGACTATCGC
AACGAGAAA
Found at i:2699115 original size:94 final size:95
Alignment explanation
Indices: 2698949--2699166 Score: 273
Period size: 94 Copynumber: 2.3 Consensus size: 95
2698939 TTCATTTGAA
* * *
2698949 TATCACAACGCGAATTTGACTATCGCAAC-GCGAATTTGATTATCGCAACTCAAAAATCGCAACG
1 TATCGCAACGCGAATTTGACTATCGCAACGGCGAATTTGACTATCGCAACTCAAAAATCGCAACA
2699013 CGAATTTGACTATCGCAACAT-GAATATGAC
66 CGAATTTGACTATCGCAAC-TCGAATATGAC
* * *
2699043 TATCGCAACGCGAATTTGTCTATCGCAACGGC-TATTTGACTATCGCAAC-GAGAAAATCGCAAC
1 TATCGCAACGCGAATTTGACTATCGCAACGGCGAATTTGACTATCGCAACTCA-AAAATCGCAAC
* * *
2699106 ACGAATTTGAGTATCGCAACTCGAATTTGAT
65 ACGAATTTGACTATCGCAACTCGAATATGAC
* ** *
2699137 TACCGCAACAAGTATTTGACTATCGCAACG
1 TATCGCAACGCGAATTTGACTATCGCAACG
2699167 AGAAAATCGC
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.02
94 103 0.96
95 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (95 bp):
TATCGCAACGCGAATTTGACTATCGCAACGGCGAATTTGACTATCGCAACTCAAAAATCGCAACA
CGAATTTGACTATCGCAACTCGAATATGAC
Found at i:2699186 original size:34 final size:34
Alignment explanation
Indices: 2699075--2699199 Score: 108
Period size: 34 Copynumber: 3.5 Consensus size: 34
2699065 TCGCAACGGC
2699075 TATTTGACTATCGCAACGAGAAAATCGCAACACG
1 TATTTGACTATCGCAACGAGAAAATCGCAACACG
* * ** * *
2699109 AATTTGAGTATCGCAACTCGAATTTGATTACCGCAACAAG
1 TATTTGACTATCGCAA--CG-A---GAAAATCGCAACACG
2699149 TATTTGACTATCGCAACGAGAAAATCGCAA-AGCG
1 TATTTGACTATCGCAACGAGAAAATCGCAACA-CG
* *
2699183 TATTAGACTATCACAAC
1 TATTTGACTATCGCAAC
2699200 ATGAATTGAC
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
33 1 0.01
34 38 0.54
36 2 0.03
37 2 0.03
38 2 0.03
40 25 0.36
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (34 bp):
TATTTGACTATCGCAACGAGAAAATCGCAACACG
Found at i:2699234 original size:20 final size:20
Alignment explanation
Indices: 2699205--2699262 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2699195 ACAACATGAA
2699205 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2699225 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2699245 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
2699263 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:2701456 original size:20 final size:20
Alignment explanation
Indices: 2701420--2701504 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
2701410 GAAACTTAAA
2701420 ATCGCAACACG--AATGACT
1 ATCGCAACACGAAAATGACT
2701438 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * *
2701458 ATCGCTACGCAAAAATGACT
1 ATCGCAACACGAAAATGACT
*
2701478 ATCGCAACGCGAAAATGACT
1 ATCGCAACACGAAAATGACT
2701498 ATCGCAA
1 ATCGCAA
2701505 TGCGATTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
18 11 0.18
20 49 0.82
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2701509 original size:20 final size:20
Alignment explanation
Indices: 2701431--2701509 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
2701421 TCGCAACACG
*
2701431 AATGACTATCGCAACACGAA
1 AATGACTATCGCAACGCGAA
* *
2701451 AATGACTATCGCTACGCAAA
1 AATGACTATCGCAACGCGAA
2701471 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
2701491 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
2701510 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:2704199 original size:42 final size:41
Alignment explanation
Indices: 2704134--2704215 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
2704124 TCCAAAATGT
*
2704134 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGAACTCTTCAACGATGACAG-GGCCTCTTGAACGG
* ** *
2704176 TGGGAGGGAACTCTTGAGGGATGATAGGGCCTCTTGAACG
1 TGGGAGGGAACTCTTCAACGATGACAGGGCCTCTTGAACG
2704216 ATAGGGGCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (41 bp):
TGGGAGGGAACTCTTCAACGATGACAGGGCCTCTTGAACGG
Found at i:2704247 original size:21 final size:18
Alignment explanation
Indices: 2704198--2704256 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 18
2704188 CTTGAGGGAT
2704198 GATA-GGGCCTCTTGAAC
1 GATAGGGGCCTCTTGAAC
2704215 GATAGGGGCCTCTTGAAC
1 GATAGGGGCCTCTTGAAC
2704233 GATAGGGGAGGCCTCTTGAAC
1 GATA--GG-GGCCTCTTGAAC
2704254 GAT
1 GAT
2704257 GTCAGGTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.11
18 17 0.45
20 2 0.05
21 15 0.39
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (18 bp):
GATAGGGGCCTCTTGAAC
Found at i:2704784 original size:20 final size:20
Alignment explanation
Indices: 2704748--2704833 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
2704738 GAAACTTAAA
2704748 ATCGCAACACG--AATGACT
1 ATCGCAACACGAAAATGACT
2704766 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* *
2704786 ATCGCAACGCAAAAATGACT
1 ATCGCAACACGAAAATGACT
* *
2704806 ATCACAACGCGAAAATGACT
1 ATCGCAACACGAAAATGACT
2704826 ATCGCAAC
1 ATCGCAAC
2704834 GAGAGAATCG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
18 11 0.18
20 50 0.82
ACGTcount: A:0.43, C:0.27, G:0.15, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2704834 original size:20 final size:20
Alignment explanation
Indices: 2704759--2704834 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
2704749 TCGCAACACG
*
2704759 AATGACTATCGCAACACGAA
1 AATGACTATCGCAACGCGAA
*
2704779 AATGACTATCGCAACGCAAA
1 AATGACTATCGCAACGCGAA
*
2704799 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
2704819 AATGACTATCGCAACG
1 AATGACTATCGCAACG
2704835 AGAGAATCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:2705091 original size:16 final size:17
Alignment explanation
Indices: 2705052--2705099 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
2705042 TTTACTAAGC
*
2705052 AATCTAAGTTAAATGGTT
1 AATCTAAGTGAAATGG-T
2705070 AATCTAAGTGAAATGG-
1 AATCTAAGTGAAATGGT
2705086 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
2705100 TACGAGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 14 0.48
18 15 0.52
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (17 bp):
AATCTAAGTGAAATGGT
Found at i:2706861 original size:20 final size:20
Alignment explanation
Indices: 2706838--2706927 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
2706828 TCTGAAACTT
2706838 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
2706858 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
2706878 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** **
2706898 ACTATCGCAACGTG-AAATG
1 AAAATCGCAACACGAAAATG
2706917 AAAATCGCAAC
1 AAAATCGCAAC
2706928 GTGAAACTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 48 0.80
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2706925 original size:19 final size:19
Alignment explanation
Indices: 2706838--2706944 Score: 90
Period size: 20 Copynumber: 5.5 Consensus size: 19
2706828 TCTGAAACTT
*
2706838 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
*
2706858 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
2706878 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
** *
2706898 ACTATCGCAACGTGAAATG
1 AAAATCGCAACGCGAAATG
*
2706917 AAAATCGCAACGTGAAACT-
1 AAAATCGCAACGCGAAA-TG
2706936 AAAATCGCA
1 AAAATCGCA
2706945 TTGCGATTCT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
19 28 0.36
20 49 0.64
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:2707616 original size:40 final size:40
Alignment explanation
Indices: 2707545--2707645 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
2707535 TGGTGCTTTG
* * *
2707545 AAAACCGCATTGCGATAGTCAGCATCGCGTTGCGACAGTC
1 AAAATCGCGTTGCGATAGTCAGAATCGCGTTGCGACAGTC
* *
2707585 AAAATCGCGTTGCGATAGTTAGAATCTCGTTGCGACAGTC
1 AAAATCGCGTTGCGATAGTCAGAATCGCGTTGCGACAGTC
*
2707625 AGAATCGCGTTGCGATAGTCA
1 AAAATCGCGTTGCGATAGTCA
2707646 TACTCGCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
AAAATCGCGTTGCGATAGTCAGAATCGCGTTGCGACAGTC
Found at i:2707652 original size:20 final size:20
Alignment explanation
Indices: 2707554--2707645 Score: 130
Period size: 20 Copynumber: 4.6 Consensus size: 20
2707544 GAAAACCGCA
*
2707554 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
2707574 TTGCGACAGTCAAAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
2707594 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
2707614 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
2707634 TTGCGATAGTCA
1 TTGCGATAGTCA
2707646 TACTCGCATT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:2707660 original size:20 final size:20
Alignment explanation
Indices: 2707637--2707684 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2707627 AATCGCGTTG
2707637 CGATAGTCATACTCGCATTA
1 CGATAGTCATACTCGCATTA
* * *
2707657 CGAT-TTACATATTCGCATTG
1 CGATAGT-CATACTCGCATTA
2707677 CGATAGTC
1 CGATAGTC
2707685 GGAAAATCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (20 bp):
CGATAGTCATACTCGCATTA
Found at i:2707678 original size:60 final size:61
Alignment explanation
Indices: 2707550--2707684 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 61
2707540 CTTTGAAAAC
* * * *
2707550 CGCATTGCGATAGTCAGCATCGCGTTGCGACAGTCAAAATCGCGTTGCGATAGTTAGAATCT
1 CGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAAAATCGCATTACGATA-TTACAATCT
* * * *
2707612 CG--TTGCGACAGTCAGAATCGCGTTGCGATAGTCATACTCGCATTACGAT-TTACATAT-T
1 CGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAAAATCGCATTACGATATTACA-ATCT
2707670 CGCATTGCGATAGTC
1 CGCATTGCGATAGTC
2707685 GGAAAATCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
58 7 0.11
59 2 0.03
60 50 0.82
62 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (61 bp):
CGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAAAATCGCATTACGATATTACAATCT
Found at i:2707701 original size:15 final size:15
Alignment explanation
Indices: 2707677--2707706 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2707667 ATTCGCATTG
*
2707677 CGATAGTCGGAAAAT
1 CGATAATCGGAAAAT
2707692 CGATAATCGGAAAAT
1 CGATAATCGGAAAAT
2707707 TGTAATGCGA
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:0.13, G:0.23, T:0.20
Consensus pattern (15 bp):
CGATAATCGGAAAAT
Found at i:2708663 original size:6 final size:5
Alignment explanation
Indices: 2708641--2708686 Score: 56
Period size: 6 Copynumber: 8.4 Consensus size: 5
2708631 GGATCGAATG
2708641 GACTC GACTC GATCTC GAGCTC GACTC GATCTC GAGCTC GACTC GA
1 GACTC GACTC GA-CTC GA-CTC GACTC GA-CTC GA-CTC GACTC GA
2708687 GTTCTTAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 17 0.46
6 20 0.54
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (5 bp):
GACTC
Found at i:2708665 original size:17 final size:17
Alignment explanation
Indices: 2708643--2708686 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
2708633 ATCGAATGGA
2708643 CTCGACTCGATCTCGAG
1 CTCGACTCGATCTCGAG
2708660 CTCGACTCGATCTCGAG
1 CTCGACTCGATCTCGAG
2708677 CTCGACTCGA
1 CTCGACTCGA
2708687 GTTCTTAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.36, G:0.23, T:0.23
Consensus pattern (17 bp):
CTCGACTCGATCTCGAG
Found at i:2708668 original size:11 final size:12
Alignment explanation
Indices: 2708643--2708687 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
2708633 ATCGAATGGA
*
2708643 CTCGA-CTCGAT
1 CTCGAGCTCGAG
2708654 CTCGAGCTCGA-
1 CTCGAGCTCGAG
*
2708665 CTCGATCTCGAG
1 CTCGAGCTCGAG
2708677 CTCGA-CTCGAG
1 CTCGAGCTCGAG
2708688 TTCTTAACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.22
Consensus pattern (12 bp):
CTCGAGCTCGAG
Found at i:2711268 original size:19 final size:19
Alignment explanation
Indices: 2711244--2711282 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2711234 GCTAAAATAC
2711244 TTATATGTAACAGTATTTG
1 TTATATGTAACAGTATTTG
*
2711263 TTATATGTAACAGTGTTTG
1 TTATATGTAACAGTATTTG
2711282 T
1 T
2711283 GAAATAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (19 bp):
TTATATGTAACAGTATTTG
Found at i:2713510 original size:23 final size:23
Alignment explanation
Indices: 2713463--2713512 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2713453 AATAACATAT
**
2713463 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
2713486 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
2713509 TAGG
1 TAGG
2713513 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2713572 original size:87 final size:87
Alignment explanation
Indices: 2713426--2713589 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
2713416 TATGTTATAT
*
2713426 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
*
2713491 AGCGCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
* *
2713513 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACTCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
2713578 AACGCTTATATA
66 AACGCTTATATA
2713590 GACCTATTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
AACGCTTATATAATAAAATAGG
Found at i:2714044 original size:199 final size:198
Alignment explanation
Indices: 2713606--2714198 Score: 735
Period size: 204 Copynumber: 2.9 Consensus size: 198
2713596 TTTTCGAAGT
*
2713606 AAACCGATATATTTATACCGGGTACATTGTAAATTTACCTATCACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATCACATTATAATTATCGGTTTCGA
* * * * *
2713671 TGTTTTTTGGATCGATACAATTT--TAAATATATCGACACTTTATGCTTGCACCTCGTTGGGCAT
66 TGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGG---
* * * * *
2713734 TCATATTTCATTTTGGAAAAAAGTATCGACACAAACTAAAAAGCGTCGATACATTAT-TTAGACC
127 -C---TTTCATTATGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTT-GACC
*
2713798 TATTTTCTCATA
187 TATTTTATCATA
* * *
2713810 AAACCGGTATATTTATACCGGGTATATTGTAAATTTACCTATCACATTGTAATTTTC-GTTTCGA
1 AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATCACATTATAATTATCGGTTTCGA
* * *
2713874 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGATACTCTATGCGTGCACCCCGTTTGGCTTT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCTTT
* *
2713939 CATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTCGATACTTTATGCTGACCTATTTTA
131 CATTATGGACAAAA-GTATCGACACAAA-TTAACAAGTGTCGATACATTATGTTGACCTATTTTA
2714004 TCATA
194 TCATA
* * * * * *
2714009 AAATCGGTATATTTATATCTGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATCACATTATAATTATCGGTTTCGA
* * * *
2714074 TGTTTTTGAGATCGATATTTTTAATAAATGTATCGACACTTTATGAGTGCACCTCGTTTGGGCAT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGCTT
* **
2714139 TCATTCTGGACAATAAGTATCGACACAAAATCCACAAGTGTCGATACATTATGTTGACCT
130 TCATTATGGACAA-AAGTATCGACAC-AAATTAACAAGTGTCGATACATTATGTTGACCT
2714199 GTTTGGGCAT
Statistics
Matches: 339, Mismatches: 41, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
197 15 0.04
198 13 0.04
199 81 0.24
200 62 0.18
201 52 0.15
202 8 0.02
203 24 0.07
204 84 0.25
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (198 bp):
AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATCACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCTTT
CATTATGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACCTATTTTATC
ATA
Found at i:2717509 original size:18 final size:17
Alignment explanation
Indices: 2717468--2717505 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2717458 CTTAATCATG
2717468 CATTT-CAAATCAGAAT
1 CATTTCCAAATCAGAAT
2717484 CATTTCCAAATCAGAAT
1 CATTTCCAAATCAGAAT
*
2717501 TATTT
1 CATTT
2717506 TCCATTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (17 bp):
CATTTCCAAATCAGAAT
Found at i:2719848 original size:29 final size:29
Alignment explanation
Indices: 2719766--2719855 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
2719756 CAAAATATAT
* *
2719766 AACTTTTAAAAATTATATTTTTGGTCTCTA
1 AACTTTTAAAAATTACA-TTTTGGTCACTA
* * ** *
2719796 ATCTTTTCAAAATTTACACCTTGGCCACTA
1 AACTTTT-AAAAATTACATTTTGGTCACTA
*
2719826 AACTTTTAAAACTTACATTTTGGTCACTA
1 AACTTTTAAAAATTACATTTTGGTCACTA
2719855 A
1 A
2719856 GAAAAATTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 19 0.40
30 20 0.43
31 8 0.17
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (29 bp):
AACTTTTAAAAATTACATTTTGGTCACTA
Found at i:2722653 original size:8 final size:8
Alignment explanation
Indices: 2722615--2722652 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
2722605 ATAGTAAGAA
2722615 ATACATGC
1 ATACATGC
*
2722623 ATATATGC
1 ATACATGC
2722631 ATACATGC
1 ATACATGC
*
2722639 ATACATAC
1 ATACATGC
2722647 ATACAT
1 ATACAT
2722653 ATATATCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (8 bp):
ATACATGC
Found at i:2722930 original size:23 final size:22
Alignment explanation
Indices: 2722900--2722962 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 22
2722890 TATATATATT
2722900 TGTCCCGAAGGACCACGTAGAAA
1 TGTCCCGAAGGACCAC-TAGAAA
*
2722923 TGTCCCGAATGACCACT----A
1 TGTCCCGAAGGACCACTAGAAA
2722941 TGTCCCGAAGGACCACATAGAA
1 TGTCCCGAAGGACCAC-TAGAA
2722963 CCCTCGACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 16 0.48
19 1 0.03
22 1 0.03
23 15 0.45
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTAGAAA
Found at i:2728287 original size:16 final size:18
Alignment explanation
Indices: 2728268--2728300 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2728258 CAACTTAAAT
2728268 CCTTTA-TA-TCTTAACC
1 CCTTTAGTACTCTTAACC
2728284 CCTTTAGTACTCTTAAC
1 CCTTTAGTACTCTTAAC
2728301 TCAAGTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.24, C:0.30, G:0.03, T:0.42
Consensus pattern (18 bp):
CCTTTAGTACTCTTAACC
Found at i:2734758 original size:13 final size:13
Alignment explanation
Indices: 2734742--2734766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2734732 TAAATACGCC
2734742 TCATAAATGCGTG
1 TCATAAATGCGTG
2734755 TCATAAATGCGT
1 TCATAAATGCGT
2734767 CATAAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:2735302 original size:20 final size:20
Alignment explanation
Indices: 2735266--2735312 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2735256 CAAAATCATT
*
2735266 TTTTCAAAATTTCATTTTGC
1 TTTTCAAAATTCCATTTTGC
*
2735286 TTTTCAAAA-TCCAATTTTTC
1 TTTTCAAAATTCC-ATTTTGC
2735306 -TTTCAAA
1 TTTTCAAA
2735313 CAAAAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGC
Found at i:2736156 original size:18 final size:18
Alignment explanation
Indices: 2736133--2736176 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2736123 CATACACCTA
*
2736133 TATCATTATCAACATTCT
1 TATCATTATCAACATTAT
*
2736151 TATCATTATCAATATTAT
1 TATCATTATCAACATTAT
2736169 TATCATTA
1 TATCATTA
2736177 ACCCCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (18 bp):
TATCATTATCAACATTAT
Found at i:2736422 original size:21 final size:21
Alignment explanation
Indices: 2736394--2736514 Score: 161
Period size: 21 Copynumber: 5.8 Consensus size: 21
2736384 CCATGTAAAT
2736394 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
*
2736415 TATCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
* * *
2736436 TGTTCCAAAGGACCAAATATA
1 TGTCCCGAAGGACCACATATA
* *
2736457 TGTCCCGAAGAATCACATATA
1 TGTCCCGAAGGACCACATATA
* * *
2736478 TGTTCCAAAGGATCACATATA
1 TGTCCCGAAGGACCACATATA
2736499 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
2736515 GTAAAACCCT
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:2736463 original size:42 final size:42
Alignment explanation
Indices: 2736401--2736514 Score: 183
Period size: 42 Copynumber: 2.7 Consensus size: 42
2736391 AATTGTCCCG
*
2736401 AAGGACCACATATATATCCCGAAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTCCCGAAGGACCACATATATGTTCCA
* * *
2736443 AAGGACCAAATATATGTCCCGAAGAATCACATATATGTTCCA
1 AAGGACCACATATATGTCCCGAAGGACCACATATATGTTCCA
*
2736485 AAGGATCACATATATGTCCCGAAGGACCAC
1 AAGGACCACATATATGTCCCGAAGGACCAC
2736515 GTAAAACCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (42 bp):
AAGGACCACATATATGTCCCGAAGGACCACATATATGTTCCA
Found at i:2737166 original size:16 final size:16
Alignment explanation
Indices: 2737141--2737177 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2737131 GTTCACATAT
*
2737141 ACATATATCATGTAGC
1 ACATAGATCATGTAGC
*
2737157 ACATAGATCATGTATC
1 ACATAGATCATGTAGC
2737173 ACATA
1 ACATA
2737178 CAATAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (16 bp):
ACATAGATCATGTAGC
Found at i:2737691 original size:41 final size:39
Alignment explanation
Indices: 2737627--2737705 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 39
2737617 CTTGATAATG
*
2737627 GTATCGATACTAGACCCTTGGTATCGATACCTCCTTAAACA
1 GTATCGATACTA-ACCCTTGGTATCAATA-CTCCTTAAACA
*
2737668 GTATCGATACT-ACTCCTTAGGTATCAATACTTCTTAAA
1 GTATCGATACTAAC-CCTT-GGTATCAATACTCCTTAAA
2737706 GATTTCATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 2 0.06
40 12 0.35
41 20 0.59
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (39 bp):
GTATCGATACTAACCCTTGGTATCAATACTCCTTAAACA
Found at i:2745896 original size:27 final size:27
Alignment explanation
Indices: 2745865--2745918 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2745855 TAATATCAAT
2745865 ATTGAAATAACTTATGTCTTAGGTGTA
1 ATTGAAATAACTTATGTCTTAGGTGTA
* *
2745892 ATTGAAGTAACTTATGTCTTGGGTGTA
1 ATTGAAATAACTTATGTCTTAGGTGTA
2745919 CGATTTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (27 bp):
ATTGAAATAACTTATGTCTTAGGTGTA
Found at i:2749711 original size:36 final size:36
Alignment explanation
Indices: 2749657--2749732 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
2749647 TAGATTACCG
* * * *
2749657 AACATAAACGAGCTGATTACTAAATATAAATGAACA
1 AACATAAACGAACGGATTACCAAACATAAATGAACA
* * *
2749693 AACATAAACTAACGGATTACCAAACGTATATGAACA
1 AACATAAACGAACGGATTACCAAACATAAATGAACA
2749729 AACA
1 AACA
2749733 AACTCTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.20
Consensus pattern (36 bp):
AACATAAACGAACGGATTACCAAACATAAATGAACA
Found at i:2749796 original size:40 final size:40
Alignment explanation
Indices: 2749746--2749830 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
2749736 TCTTTGTTAA
* *
2749746 TGTTCGTTCATTTAATTAAACAAACAAAAGATCTTATTCG
1 TGTTCATTCATTTAATTAAACAAACAAAAAATCTTATTCG
*
2749786 TGTTCATTCATTTAATTAAACAAATAAAAAATCTTATTCG
1 TGTTCATTCATTTAATTAAACAAACAAAAAATCTTATTCG
2749826 TGTTC
1 TGTTC
2749831 GTCAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (40 bp):
TGTTCATTCATTTAATTAAACAAACAAAAAATCTTATTCG
Found at i:2749839 original size:40 final size:39
Alignment explanation
Indices: 2749746--2749849 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 39
2749736 TCTTTGTTAA
*
2749746 TGTTCGTTCATTTAATTAAACAAACAAAAGATCTTATTCG
1 TGTTCG-TCATTTAATTAAACAAACAAAAAATCTTATTCG
* *
2749786 TGTTCATTCATTTAATTAAACAAATAAAAAATCTTATTCG
1 TGTTC-GTCATTTAATTAAACAAACAAAAAATCTTATTCG
*
2749826 TGTTCGTCAATTTAA-TAAATAAAC
1 TGTTCGTC-ATTTAATTAAACAAAC
2749850 TTCCCGCTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 9 0.16
40 47 0.84
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (39 bp):
TGTTCGTCATTTAATTAAACAAACAAAAAATCTTATTCG
Found at i:2751053 original size:9 final size:9
Alignment explanation
Indices: 2751032--2751120 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
2751022 AACTAATCTA
*
2751032 AAAAAAAAG
1 AAAAAAAAT
*
2751041 AAAAATAAT
1 AAAAAAAAT
*
2751050 AAAATAAAT
1 AAAAAAAAT
2751059 AAAATAAAAT
1 AAAA-AAAAT
2751069 AAAATAAAAT
1 AAAA-AAAAT
*
2751079 -AAAAAATT
1 AAAAAAAAT
* * *
2751087 AACATAAAC
1 AAAAAAAAT
2751096 AAAACAAAAT
1 AAAA-AAAAT
2751106 AAAATAGAAAT
1 AAAA-A-AAAT
2751117 AAAA
1 AAAA
2751121 TAAGAAAAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
8 4 0.06
9 28 0.45
10 22 0.35
11 8 0.13
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:2751053 original size:14 final size:13
Alignment explanation
Indices: 2751031--2751129 Score: 71
Period size: 14 Copynumber: 7.4 Consensus size: 13
2751021 AAACTAATCT
*
2751031 AAAAA-AAAAGAA
1 AAAAATAAAATAA
2751043 AAATAATAAAATAA
1 AAA-AATAAAATAA
2751057 ATAAAATAAAAT--
1 A-AAAATAAAATAA
2751069 -AAAATAAAATAA
1 AAAAATAAAATAA
* *
2751081 AAAATTAACATAA
1 AAAAATAAAATAA
*
2751094 ACAAAACAAAATAAA
1 A-AAAATAAAAT-AA
2751109 ATAGAAATAAAATAA
1 A-A-AAATAAAATAA
2751124 GAAAAA
1 -AAAAA
2751130 GAATGTTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
10 10 0.14
12 3 0.04
13 13 0.19
14 25 0.36
15 9 0.13
16 9 0.13
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:2751057 original size:24 final size:23
Alignment explanation
Indices: 2751015--2751084 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
2751005 CTAAATATCC
**
2751015 AAAAAAAAACTAATCTAAAAAAA-
1 AAAAAAAAA-TAAAATAAAAAAAT
2751038 AAGAAAAATAATAAAATAAATAAAAT
1 AA-AAAAA-AATAAAATAAA-AAAAT
*
2751064 AAAATAAAATAAAATAAAAAA
1 AAAAAAAAATAAAATAAAAAA
2751085 TTAACATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 5 0.12
24 23 0.57
25 10 0.25
26 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.16
Consensus pattern (23 bp):
AAAAAAAAATAAAATAAAAAAAT
Found at i:2751105 original size:32 final size:32
Alignment explanation
Indices: 2751042--2751111 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
2751032 AAAAAAAAGA
* *
2751042 AAAATAATAAAATAAATAAAATAAAATAAAAT
1 AAAATAATAAAATAAATAAAACAAAACAAAAT
2751074 AAAATAA-AAAATTAACAT-AAACAAAACAAAAT
1 AAAATAATAAAA-TAA-ATAAAACAAAACAAAAT
2751106 AAAATA
1 AAAATA
2751112 GAAATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 4 0.12
32 28 0.82
33 2 0.06
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (32 bp):
AAAATAATAAAATAAATAAAACAAAACAAAAT
Found at i:2751105 original size:37 final size:38
Alignment explanation
Indices: 2751030--2751128 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 38
2751020 AAAACTAATC
* * * *
2751030 TAAAAAAAAAGAAAAATAATAAAATAAATAAAATAAAA
1 TAAAATAAAATAAAAATAATAAAATAAACAAAACAAAA
* *
2751068 TAAAATAAAATAAAAA-ATTAACATAAACAAAACAAAA
1 TAAAATAAAATAAAAATAATAAAATAAACAAAACAAAA
*
2751105 TAAAATAGAAAT-AAAATAAGAAAA
1 TAAAATA-AAATAAAAATAATAAAA
2751129 AGAATGTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
37 28 0.56
38 22 0.44
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (38 bp):
TAAAATAAAATAAAAATAATAAAATAAACAAAACAAAA
Found at i:2751110 original size:5 final size:5
Alignment explanation
Indices: 2751047--2751123 Score: 81
Period size: 5 Copynumber: 16.0 Consensus size: 5
2751037 AAAGAAAAAT
* *
2751047 AATAA AAT-A AATAA AATAA AATAA AATAA AAT-A AA-AA ATTAA CAT-A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
2751093 AACAA AACAA AATAA AATAGA AATAA AATAA
1 AATAA AATAA AATAA AATA-A AATAA AATAA
2751124 GAAAAAGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
4 11 0.18
5 45 0.74
6 5 0.08
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:2751172 original size:16 final size:15
Alignment explanation
Indices: 2751147--2751189 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
2751137 AAATCAAAAT
2751147 AAAAAAACAAAAACA
1 AAAAAAACAAAAACA
* *
2751162 AAAAAACACAAAGATA
1 AAAAAA-ACAAAAACA
2751178 AAAAAAACAAAA
1 AAAAAAACAAAA
2751190 GATAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (15 bp):
AAAAAAACAAAAACA
Found at i:2751190 original size:16 final size:16
Alignment explanation
Indices: 2751147--2751201 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
2751137 AAATCAAAAT
*
2751147 AAAAAAACAAAA-A-C
1 AAAAAAACAAAAGATA
2751161 AAAAAAACACAAAGATA
1 AAAAAAACA-AAAGATA
2751178 AAAAAAACAAAAGATA
1 AAAAAAACAAAAGATA
2751194 AAATAAAA
1 AAA-AAAA
2751202 AATAAAACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 9 0.25
15 3 0.08
16 11 0.31
17 13 0.36
ACGTcount: A:0.82, C:0.09, G:0.04, T:0.05
Consensus pattern (16 bp):
AAAAAAACAAAAGATA
Found at i:2751392 original size:13 final size:12
Alignment explanation
Indices: 2751368--2751406 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
2751358 TAATAATAAC
*
2751368 AAAAAAGAAATA
1 AAAAAAGTAATA
2751380 AACAAAAGTAAT-
1 AA-AAAAGTAATA
2751392 AAAAAAGTAATA
1 AAAAAAGTAATA
2751404 AAA
1 AAA
2751407 GTATATAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 9 0.38
12 7 0.29
13 8 0.33
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAAAGTAATA
Found at i:2751498 original size:29 final size:29
Alignment explanation
Indices: 2751464--2751521 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2751454 TATAATAATA
2751464 ATAATAAA-GG-ACTAAATTGAAAGATAAAT
1 ATAATAAATGGTAC-AAATTGAAAGA-AAAT
*
2751493 ATAATAAATGGTACAACTTGAAAGAAAAT
1 ATAATAAATGGTACAAATTGAAAGAAAAT
2751522 CGAGGTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 12 0.46
30 12 0.46
31 2 0.08
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (29 bp):
ATAATAAATGGTACAAATTGAAAGAAAAT
Found at i:2765730 original size:51 final size:51
Alignment explanation
Indices: 2765675--2765813 Score: 131
Period size: 51 Copynumber: 2.7 Consensus size: 51
2765665 GAAAAATAAT
* * * * * *
2765675 AAAATAAATAACATAAAATAAAATAAAATAAAATAAAGTA-AAATAAAAAAC
1 AAAATAAATAAAACAAAAT-AAACAAAACAAAACAAAATAGAAATAAAAAAC
2765726 AAAATAAATAAAACAAAATAAACAAAACAAAACAAAATAGAAATAAAATAA-
1 AAAATAAATAAAACAAAATAAACAAAACAAAACAAAATAGAAATAAAA-AAC
*** * *
2765777 AAAA-GGTTAAATCAAAATAAAAAAAACAGAAACAAAA
1 AAAATAAATAAAACAAAATAAACAAAACA-AAACAAAA
2765814 AAACAAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 35 0.47
51 37 0.50
52 2 0.03
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (51 bp):
AAAATAAATAAAACAAAATAAACAAAACAAAACAAAATAGAAATAAAAAAC
Found at i:2765794 original size:6 final size:5
Alignment explanation
Indices: 2765672--2765899 Score: 118
Period size: 5 Copynumber: 45.4 Consensus size: 5
2765662 AAAGAAAAAT
* *
2765672 AATAA AAT-A AATAA CATAA AATAA AATAA AATAA AATAA AGTAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* * * * *
2765721 AA-AA CAAAATA AATAA AACAA AAT-A AACAA AACAA AACAA AATAGA
1 AATAA -AATA-A AATAA AATAA AATAA AATAA AATAA AATAA AATA-A
** * * *
2765767 AATAA AATAA AA-AA GGTTA AATCAA AATAA AA-AA AACAGA AACAA AA-AA
1 AATAA AATAA AATAA AATAA AAT-AA AATAA AATAA AATA-A AATAA AATAA
* *
2765816 ACAAAA AATAGA AGATAA AATAA AA-AA TAA-AA AATAA AACTAC AATATA
1 A-ATAA AATA-A A-ATAA AATAA AATAA -AATAA AATAA AA-TAA AATA-A
* * *
2765865 TATAT AATAGA AA-AA AAT-A AATAA AA-AA GATAA AA
1 AATAA AATA-A AATAA AATAA AATAA AATAA AATAA AA
2765900 AATATATAAA
Statistics
Matches: 177, Mismatches: 24, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
4 32 0.18
5 107 0.60
6 34 0.19
7 4 0.02
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:2765835 original size:19 final size:19
Alignment explanation
Indices: 2765790--2765855 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
2765780 AGGTTAAATC
* *
2765790 AAAATAAAA-AAAACAGAA
1 AAAATAAAACAAAAAATAA
*
2765808 ACAAA-AAAACAAAAAATAG
1 A-AAATAAAACAAAAAATAA
* *
2765827 AAGATAAAATAAAAAATAA
1 AAAATAAAACAAAAAATAA
2765846 AAAATAAAAC
1 AAAATAAAAC
2765856 TACAATATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
18 7 0.19
19 30 0.81
ACGTcount: A:0.80, C:0.06, G:0.05, T:0.09
Consensus pattern (19 bp):
AAAATAAAACAAAAAATAA
Found at i:2765837 original size:12 final size:12
Alignment explanation
Indices: 2765785--2765903 Score: 50
Period size: 12 Copynumber: 9.4 Consensus size: 12
2765775 AAAAAAGGTT
2765785 AAATCAAAATAAA
1 AAAT-AAAATAAA
* *
2765798 AAA-AACAGAAA
1 AAATAAAATAAA
*
2765809 CAAA-AAAACAAA
1 -AAATAAAATAAA
2765821 AAATAGAAGATAAA
1 AAATA-AA-ATAAA
2765835 ATAA-AAAATAAA
1 A-AATAAAATAAA
*
2765847 AAATAAAACTACA
1 AAATAAAA-TAAA
* *
2765860 ATATATATATAATA
1 AAATA-AAATAA-A
2765874 GAAA-AAAATAAA
1 -AAATAAAATAAA
2765886 TAAA-AAAGATAAA
1 -AAATAAA-ATAAA
2765899 AAATA
1 AAATA
2765904 TATAAAGAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 24
0.69 0.10 0.20
Matches are distributed among these distances:
11 11 0.13
12 30 0.37
13 27 0.33
14 10 0.12
15 4 0.05
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:2765932 original size:15 final size:16
Alignment explanation
Indices: 2765890--2765931 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2765880 AATAAATAAA
*
2765890 AAAGATAAAAAATATAT
1 AAAGA-AAAAATTATAT
*
2765907 AAAGAAAAAATTATGT
1 AAAGAAAAAATTATAT
2765923 AAAGAAAAA
1 AAAGAAAAA
2765932 TAATAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAGAAAAAATTATAT
Found at i:2765971 original size:2 final size:2
Alignment explanation
Indices: 2765964--2765997 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2765954 AAAAAGAGAA
2765964 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
2765998 GTGTTAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2768655 original size:75 final size:75
Alignment explanation
Indices: 2768552--2768749 Score: 333
Period size: 75 Copynumber: 2.6 Consensus size: 75
2768542 GTTAAATCCA
* * * *
2768552 CTCTGCAGCAGTCAAAGAATCCAATACCAACTCAAGACTCTACTGATAATATTGCATTGCCAGAG
1 CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAATATTGCACTGCAAGAG
2768617 TTTGAATTGG
66 TTTGAATTGG
*
2768627 CTTTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAATATTGCACTGCAAGAG
1 CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAATATTGCACTGCAAGAG
2768692 TTTGAATTGG
66 TTTGAATTGG
* *
2768702 CTCTGAAGCAGTCAAAGAATCCAGTTCCAACTCAATACTCTACTGATA
1 CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATA
2768750 TCATTAATGA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 115 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (75 bp):
CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAATATTGCACTGCAAGAG
TTTGAATTGG
Found at i:2773518 original size:10 final size:11
Alignment explanation
Indices: 2773505--2773533 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2773495 AAAAAGGGTA
2773505 AAAATAA-CAT
1 AAAATAAGCAT
2773515 AAAATAAGCAT
1 AAAATAAGCAT
2773526 AAAATAAG
1 AAAATAAG
2773534 GACCTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAATAAGCAT
Found at i:2773785 original size:3 final size:3
Alignment explanation
Indices: 2773777--2773823 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2773767 ACTGAAAATG
2773777 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2773824 CTTTTTGTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2775139 original size:22 final size:22
Alignment explanation
Indices: 2775111--2775156 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2775101 GTCAGGGCCG
2775111 GTCCAATGAGTTTTAATATCCC
1 GTCCAATGAGTTTTAATATCCC
2775133 GTCCAATGAGTTTTAATATCCC
1 GTCCAATGAGTTTTAATATCCC
2775155 GT
1 GT
2775157 GCGAGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (22 bp):
GTCCAATGAGTTTTAATATCCC
Found at i:2777188 original size:66 final size:65
Alignment explanation
Indices: 2777081--2777328 Score: 304
Period size: 66 Copynumber: 3.8 Consensus size: 65
2777071 AGGGTTAATG
* * *
2777081 GTTTCAAGAG-AAATCGTCTCAAGAGAGACAAAACAT-GTTTCAAGGGAAATAATCTCAAAGGTT
1 GTTTCAAGAGAAAAT-GTCTCAAGAGAGACAAAA-TTCGTTTCAAGGGAAACAAT-TCAAAGATT
*
2777144 GGA
63 GGT
* * * * *
2777147 ATTTCAAGGGAAAATGTCTCAAGACAGACAAAATTCGTTTCAAGGGAAACGGATTCAAAGATTTG
1 GTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC-AATTCAAAGATTGG
2777212 T
65 T
* * *
2777213 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTGG
1 GTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACA-ATTCAAAGATTGG
2777278 T
65 T
*
2777279 GTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAAC
1 GTTTCAAGAGAAAA-TGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC
2777329 TGTTGGGATT
Statistics
Matches: 156, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
65 5 0.03
66 145 0.93
67 6 0.04
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (65 bp):
GTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATTCAAAGATTGGT
Found at i:2777217 original size:30 final size:30
Alignment explanation
Indices: 2777183--2777292 Score: 80
Period size: 30 Copynumber: 3.5 Consensus size: 30
2777173 GACAAAATTC
*
2777183 GTTTCAAGGGAAACGGATTCAAAGATTTGT
1 GTTTCAAGGGAAACAGATTCAAAGATTTGT
* * *
2777213 GTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT-T
1 GTTTCAAGGGAAACAGAT-TCAA---AG----ATTTGT
*
2777249 GTTTCAAGGGAAACAGATTCAAAGATTGGT
1 GTTTCAAGGGAAACAGATTCAAAGATTTGT
*
2777279 GTTTCAAGGAAAAC
1 GTTTCAAGGGAAAC
2777293 TGTCTCAAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
29 3 0.05
30 32 0.52
33 4 0.06
36 19 0.31
37 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (30 bp):
GTTTCAAGGGAAACAGATTCAAAGATTTGT
Found at i:2777320 original size:132 final size:132
Alignment explanation
Indices: 2777081--2777328 Score: 367
Period size: 132 Copynumber: 1.9 Consensus size: 132
2777071 AGGGTTAATG
* *
2777081 GTTTCAAGAGAAATCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAATAATCTCAAAGGTTGG
1 GTTTCAAGAGAAATCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACAATCTCAAAGATTGG
*
2777146 AATTTCAAGGGAAAATGTCTCAAGACAGACAAAATTCGTTTCAAGGGAAACGGATTCAAAGATTT
66 AATTTCAAGGGAAAATGTCTCAAGACAGACAAAATTCATTTCAAGGGAAACGGATTCAAAGATTT
2777211 GT
131 GT
* **
2777213 GTTTCAAGAGAAA-CTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATT
1 GTTTCAAGAGAAATC-GTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACA-ATCTCAAAGATT
** *
2777276 GGTGTTTCAA-GGAAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAAC
64 GGAATTTCAAGGGAAAA-TGTCTCAAGACAGACAAAATTCATTTCAAGGGAAAC
2777329 TGTTGGGATT
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
131 7 0.07
132 95 0.91
133 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (132 bp):
GTTTCAAGAGAAATCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACAATCTCAAAGATTGG
AATTTCAAGGGAAAATGTCTCAAGACAGACAAAATTCATTTCAAGGGAAACGGATTCAAAGATTT
GT
Found at i:2778085 original size:22 final size:22
Alignment explanation
Indices: 2778052--2778115 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2778042 GTAATTTGAG
2778052 CCTTT-AT-GGGGTATTGATAC
1 CCTTTCATAGGGGTATTGATAC
* *
2778072 CCTTTCATAGGGGTATCGGTAC
1 CCTTTCATAGGGGTATTGATAC
* *
2778094 CCGTTCATAAGAGGTATTGATA
1 CCTTTCAT-AGGGGTATTGATA
2778116 GGGGTATCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 5 0.14
21 2 0.06
22 18 0.51
23 10 0.29
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (22 bp):
CCTTTCATAGGGGTATTGATAC
Found at i:2778141 original size:22 final size:22
Alignment explanation
Indices: 2778113--2778173 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
2778103 AGAGGTATTG
2778113 ATAGGGGTATCGGTACCCATTC
1 ATAGGGGTATCGGTACCCATTC
* * *
2778135 ATAGGGGTATTGATACACATTC
1 ATAGGGGTATCGGTACCCATTC
2778157 ATAGGGGTATCGGTACC
1 ATAGGGGTATCGGTACC
2778174 TCTTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (22 bp):
ATAGGGGTATCGGTACCCATTC
Found at i:2778149 original size:34 final size:35
Alignment explanation
Indices: 2778078--2778149 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
2778068 ATACCCTTTC
*
2778078 ATAGGGGTATCGGTACCCGTTCATAAGAGGTATTG
1 ATAGGGGTATCGGTACCCATTCATAAGAGGTATTG
*
2778113 ATAGGGGTATCGGTACCCATTCAT-AGGGGTATTG
1 ATAGGGGTATCGGTACCCATTCATAAGAGGTATTG
2778147 ATA
1 ATA
2778150 CACATTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 12 0.34
35 23 0.66
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (35 bp):
ATAGGGGTATCGGTACCCATTCATAAGAGGTATTG
Found at i:2778419 original size:22 final size:21
Alignment explanation
Indices: 2778388--2778446 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
2778378 AATGTTTAAT
2778388 TAAAAAGATACCAATTGTTTA
1 TAAAAAGATACCAATTGTTTA
2778409 TAAAAAGGATACCAATTG--T-
1 TAAAAA-GATACCAATTGTTTA
*
2778428 TAAAAATATACCAATTGTT
1 TAAAAAGATACCAATTGTT
2778447 GGAAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 10 0.29
19 6 0.18
20 1 0.03
21 6 0.18
22 11 0.32
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (21 bp):
TAAAAAGATACCAATTGTTTA
Found at i:2778438 original size:18 final size:18
Alignment explanation
Indices: 2778387--2778446 Score: 75
Period size: 18 Copynumber: 3.1 Consensus size: 18
2778377 AAATGTTTAA
2778387 TTAAAAAGATACCAATTG
1 TTAAAAAGATACCAATTG
2778405 TTTATAAAAAGGATACCAATTG
1 --T-TAAAAA-GATACCAATTG
*
2778427 TTAAAAATATACCAATTG
1 TTAAAAAGATACCAATTG
2778445 TT
1 TT
2778447 GGAAAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 12 0.32
19 6 0.16
20 2 0.05
21 6 0.16
22 11 0.30
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (18 bp):
TTAAAAAGATACCAATTG
Found at i:2778452 original size:19 final size:18
Alignment explanation
Indices: 2778387--2778456 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 18
2778377 AAATGTTTAA
*
2778387 TTAAAAAGATACCAATTG
1 TTAAAAATATACCAATTG
*
2778405 TTTATAAAAAGGATACCAATTG
1 --T-TAAAAA-TATACCAATTG
2778427 TTAAAAATATACCAATTG
1 TTAAAAATATACCAATTG
*
2778445 TTGGAAAATATA
1 TT-AAAAATATA
2778457 TGAAAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 12 0.27
19 14 0.31
20 2 0.04
21 6 0.13
22 11 0.24
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (18 bp):
TTAAAAATATACCAATTG
Found at i:2781580 original size:16 final size:16
Alignment explanation
Indices: 2781559--2781590 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2781549 TTTTGCATTT
2781559 TGTAATTTGAGCCTTC
1 TGTAATTTGAGCCTTC
2781575 TGTAATTTGAGCCTTC
1 TGTAATTTGAGCCTTC
2781591 ATGGGGGTAT
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:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
TGTAATTTGAGCCTTC
Found at i:2781613 original size:22 final size:22
Alignment explanation
Indices: 2781588--2781719 Score: 86
Period size: 22 Copynumber: 5.9 Consensus size: 22
2781578 AATTTGAGCC
* * *
2781588 TTCATGGGGGTATTGATACCCT
1 TTCATAGGGGTATCGATACCCG
*
2781610 TTCATAGGGGTATCGGTACCCG
1 TTCATAGGGGTATCGATACCCG
* * ****
2781632 TTCATAAGAGGTATTGATGGGGG
1 TTCAT-AGGGGTATCGATACCCG
* *
2781655 TATTGATAGGGGTATCGATA-CCA
1 --TTCATAGGGGTATCGATACCCG
* * *
2781678 TTCATAGGGGTATTGATACTCA
1 TTCATAGGGGTATCGATACCCG
*
2781700 TTCATAGGGGTATCAATACC
1 TTCATAGGGGTATCGATACC
2781720 TCTTAATATT
Statistics
Matches: 82, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
21 16 0.20
22 42 0.51
23 10 0.12
24 10 0.12
25 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCG
Found at i:2781658 original size:12 final size:12
Alignment explanation
Indices: 2781641--2781674 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2781631 GTTCATAAGA
*
2781641 GGTATTGATGGG
1 GGTATTGATAGG
2781653 GGTATTGATAGG
1 GGTATTGATAGG
*
2781665 GGTATCGATA
1 GGTATTGATA
2781675 CCATTCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.41, T:0.32
Consensus pattern (12 bp):
GGTATTGATAGG
Found at i:2781996 original size:36 final size:36
Alignment explanation
Indices: 2781944--2782062 Score: 103
Period size: 36 Copynumber: 3.5 Consensus size: 36
2781934 CTTAAAGATT
*
2781944 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
*
2781980 TTTGTTTCAAGGGAAACAGAT-TCAA---AG-----A
1 TTTGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAA
* *
2782008 TTGGTGTTTTAAGGGAAACTGTCTCAAGGGAGACAAAC
1 TT--TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
*
2782046 TTTGTTTCAATGGAAAC
1 TTTGTTTCAAGGGAAAC
2782063 ATATTCAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 24
0.67 0.07 0.25
Matches are distributed among these distances:
28 3 0.05
29 1 0.02
30 19 0.30
33 4 0.06
36 34 0.53
37 1 0.02
38 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
Done.