Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 67 of 199
Found at i:19848975 original size:31 final size:31
Alignment explanation
Indices: 19848925--19849008 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
19848915 GAATATATTA
** * *
19848925 TTGGGTGATTAAAACGAAAGTGACCTAG-GAT
1 TTGGGTGACCAAAACGAAAGTGA-CTAGCAAG
* * *
19848956 TTGGGTGACCAAAATGAAAGTCACTTGCAAG
1 TTGGGTGACCAAAACGAAAGTGACTAGCAAG
19848987 TTGGGTGACCAAAACGAAAGTG
1 TTGGGTGACCAAAACGAAAGTG
19849009 CAAGCATGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.23
Consensus pattern (31 bp):
TTGGGTGACCAAAACGAAAGTGACTAGCAAG
Found at i:19853737 original size:21 final size:21
Alignment explanation
Indices: 19853708--19853757 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
19853698 AACAAAATAT
*
19853708 ATAAAATTATCATAAAGATAA
1 ATAATATTATCATAAAGATAA
*
19853729 ATAATATTATCATAAATATAA
1 ATAATATTATCATAAAGATAA
*
19853750 ATATTATT
1 ATAATATT
19853758 CAATTAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAATATTATCATAAAGATAA
Found at i:19857476 original size:25 final size:25
Alignment explanation
Indices: 19857432--19857575 Score: 177
Period size: 25 Copynumber: 5.8 Consensus size: 25
19857422 CGGACACACA
*
19857432 ATAGCTCGT-ATGAGCTTACCAATTT
1 ATAGCTCGTGA-GAGCATACCAATTT
*
19857457 ATAGCTTGTGA-ATGCATACCAATTT
1 ATAGCTCGTGAGA-GCATACCAATTT
19857482 ATAGCTCGTGAGAGCATACCAATTT
1 ATAGCTCGTGAGAGCATACCAATTT
*
19857507 ATAGCTCGTGAGAGCATACCGATTT
1 ATAGCTCGTGAGAGCATACCAATTT
* * *
19857532 ATAGCTCGAGAGAGCATACCGATTC
1 ATAGCTCGTGAGAGCATACCAATTT
*
19857557 ACAGCTCGT-ATGAGCATAC
1 ATAGCTCGTGA-GAGCATAC
19857576 ATGTACAGGA
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.02
25 103 0.96
26 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATACCAATTT
Found at i:19864279 original size:25 final size:24
Alignment explanation
Indices: 19864211--19864291 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
19864201 TATGCTCATA
* *
19864211 CGAGCTATGAATCGGTATGGT-TACT
1 CGAGCTATGAAT-TGTATGCTCT-CT
19864236 CGAGCTAT-AGATTGATATGCTCTCT
1 CGAGCTATGA-ATTG-TATGCTCTCT
* *
19864261 CGAGCTATGAATTAGTATGCTCACA
1 CGAGCTATGAATT-GTATGCTCTCT
19864286 CGAGCT
1 CGAGCT
19864292 GTGGGTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
24 2 0.04
25 42 0.89
26 3 0.06
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (24 bp):
CGAGCTATGAATTGTATGCTCTCT
Found at i:19871938 original size:25 final size:25
Alignment explanation
Indices: 19871871--19871965 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 25
19871861 TCCATGTACA
* * * *
19871871 TGTATGCTCAAACGAGCTGTGAACC
1 TGTATACTCACACGAGCTGTAAATC
* * * * * *
19871896 GGTATGCTCACTCAAGCTGTAGATT
1 TGTATACTCACACGAGCTGTAAATC
* *
19871921 TGTATACTCTCACGAGCTATAAATC
1 TGTATACTCACACGAGCTGTAAATC
*
19871946 TGTATGCTCACACGAGCTGT
1 TGTATACTCACACGAGCTGT
19871966 GGGTCAGAAC
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
TGTATACTCACACGAGCTGTAAATC
Found at i:19873606 original size:27 final size:27
Alignment explanation
Indices: 19873576--19873644 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
19873566 CCATACAAAA
19873576 TACGCCACAAAGGCTATAT-ATAAAGAG
1 TACGCCACAAAGGCTAT-TCATAAAGAG
** ** **
19873603 TACGCCGTAAAGATTATTCATTTAGAG
1 TACGCCACAAAGGCTATTCATAAAGAG
19873630 TACGCCACAAAGGCT
1 TACGCCACAAAGGCT
19873645 GACAGGATGC
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
TACGCCACAAAGGCTATTCATAAAGAG
Found at i:19874515 original size:72 final size:72
Alignment explanation
Indices: 19874408--19874552 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
19874398 CTATACACCT
* * *
19874408 ACACGTATACGCCAAAATAATAGTTTTGGAGGATAACACCACACCAAATAGACTGTTTACTGCTA
1 ACACGTATACGCCAAAATAATAGTTTAGGAGGATAACACCACACCAAACAGACTGTTTACTACTA
19874473 TACGTCC
66 TACGTCC
* * ** *
19874480 ACACTTATACGCCAAAATAATCA-TTTAGGTGGATAACACCACGTCAGACAGACTGTTTACTACT
1 ACACGTATACGCCAAAATAAT-AGTTTAGGAGGATAACACCACACCAAACAGACTGTTTACTACT
*
19874544 ATACTTCC
65 ATACGTCC
19874552 A
1 A
19874553 AAACCTTAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (72 bp):
ACACGTATACGCCAAAATAATAGTTTAGGAGGATAACACCACACCAAACAGACTGTTTACTACTA
TACGTCC
Found at i:19880635 original size:15 final size:15
Alignment explanation
Indices: 19880615--19880646 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19880605 GAGATTGGCC
19880615 GTGGTAGAGGTGATG
1 GTGGTAGAGGTGATG
*
19880630 GTGGTAGAGGTGCTG
1 GTGGTAGAGGTGATG
19880645 GT
1 GT
19880647 TAGAGTGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.53, T:0.28
Consensus pattern (15 bp):
GTGGTAGAGGTGATG
Found at i:19882630 original size:25 final size:25
Alignment explanation
Indices: 19882602--19882653 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19882592 TTTTATGTCG
19882602 CTTGTGTATTCCAGAGGACAAGGAT
1 CTTGTGTATTCCAGAGGACAAGGAT
19882627 CTTGTGTATTCCAGAGGACAAGGAT
1 CTTGTGTATTCCAGAGGACAAGGAT
19882652 CT
1 CT
19882654 GAGGCGCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (25 bp):
CTTGTGTATTCCAGAGGACAAGGAT
Found at i:19885335 original size:13 final size:13
Alignment explanation
Indices: 19885317--19885341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19885307 TTAGAAGCTT
19885317 AATTAATTATTAC
1 AATTAATTATTAC
19885330 AATTAATTATTA
1 AATTAATTATTA
19885342 TGGTTGAATG
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTATTAC
Found at i:19889284 original size:18 final size:19
Alignment explanation
Indices: 19889250--19889287 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19889240 TATACTTTAT
*
19889250 ATTTTATATATACATATAC
1 ATTTTATATACACATATAC
19889269 ATTTTATA-ACACATATAC
1 ATTTTATATACACATATAC
19889287 A
1 A
19889288 CTTTCCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTATATACACATATAC
Found at i:19893718 original size:155 final size:155
Alignment explanation
Indices: 19893425--19893740 Score: 578
Period size: 155 Copynumber: 2.0 Consensus size: 155
19893415 TCGTGGAGCC
19893425 TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
1 TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
* *
19893490 CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTGAACTTCTGT
66 CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
* *
19893555 AGTGCCTGGTTTAGGATTAAGTATG
131 AGTACCTGGTTTAGGATTAAGGATG
*
19893580 TGTATCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
1 TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
*
19893645 CCTGTCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
66 CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
19893710 AGTACCTGGTTTAGGATTAAGGATG
131 AGTACCTGGTTTAGGATTAAGGATG
19893735 TGTAGC
1 TGTAGC
19893741 GGATAGTTAA
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
155 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (155 bp):
TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
AGTACCTGGTTTAGGATTAAGGATG
Found at i:19897323 original size:104 final size:104
Alignment explanation
Indices: 19897143--19897354 Score: 397
Period size: 104 Copynumber: 2.0 Consensus size: 104
19897133 TTTAAGAATT
*
19897143 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGGT
1 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
*
19897208 CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
66 CGTCAATTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
*
19897247 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCCTTAGGGAT
1 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
19897312 CGTCAATTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
66 CGTCAATTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
19897351 AAAT
1 AAAT
19897355 GTGCATAGAC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (104 bp):
AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
CGTCAATTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
Found at i:19908080 original size:26 final size:27
Alignment explanation
Indices: 19908051--19908107 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
19908041 TAAAACGATA
**
19908051 ATTTTACCCTTGGA-GGTATTTTGGTC
1 ATTTTACCCTTGGAGGGTATTTCAGTC
* *
19908077 ATTTTACCTTTTGAGGGTATTTCAGTC
1 ATTTTACCCTTGGAGGGTATTTCAGTC
19908104 ATTT
1 ATTT
19908108 AACCACCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (27 bp):
ATTTTACCCTTGGAGGGTATTTCAGTC
Found at i:19912550 original size:39 final size:39
Alignment explanation
Indices: 19912496--19912575 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
19912486 ACACGAATGC
19912496 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
19912535 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
19912574 GT
1 GT
19912576 TTCCAAACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (39 bp):
GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
Found at i:19920893 original size:19 final size:20
Alignment explanation
Indices: 19920851--19920902 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
19920841 TTAAAGGATG
19920851 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
19920872 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
19920891 TGCAATCTTAGA
1 TGCAATCTTAGA
19920903 ACATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:19921386 original size:3 final size:3
Alignment explanation
Indices: 19921378--19921415 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
19921368 ATCTTGTATC
*
19921378 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19921416 ATTCATGTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:19928220 original size:14 final size:14
Alignment explanation
Indices: 19928198--19928235 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19928188 TTCAAAATAT
19928198 AAAAAAAAAGAG-C
1 AAAAAAAAAGAGCC
*
19928211 AAAAATAAAATAGCC
1 AAAAA-AAAAGAGCC
19928226 AAAAAAAAAG
1 AAAAAAAAAG
19928236 GAAAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 5 0.24
14 10 0.48
15 6 0.29
ACGTcount: A:0.76, C:0.08, G:0.11, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAGAGCC
Found at i:19929611 original size:88 final size:88
Alignment explanation
Indices: 19929462--19930226 Score: 899
Period size: 88 Copynumber: 8.7 Consensus size: 88
19929452 AACAGATCAT
* *
19929462 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACA-CTGGAGCAGATCGAAGACACCAGTCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC-GAAGCAGATCGAAGACACCAGTCTTGCC
*
19929526 TCCCTAGGTTGTAGTGGAGCAGAC
65 TCCCTAGGTTGCAGTGGAGCAGAC
* *
19929550 TGAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
19929615 CCCTAGGTTGTACTGGAACAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * * * *
19929638 TGTAGATAGTAGATCTTGCCTTCATATACTGACAGCGAAGCAGATCAAAGACAGCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
19929703 CCCTAGGTTGTAGTGGAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * *
19929726 TGAAGACAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATC-AAGGACACCAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACACCAGTCTTGCC
* * **
19929790 TCCCTGGGTTGCAGCGGAGCAGGT
65 TCCCTAGGTTGCAGTGGAGCAGAC
* * ** *
19929814 TGAAAATAGCAGATCTTGCCTTCCTATACTGACAGCGAATTAGATCGAAGACACCAGTCTTGCGT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
19929879 CCCTAGGTTGCAGTGGAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * *
19929902 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCAAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
** **
19929967 CCCT-GGATTGCAGCAGAGCAGGT
66 CCCTAGG-TTGCAGTGGAGCAGAC
* * * * *
19929990 TGAAAATAGTAGATCTTGCCTTACTGTACTGACAGCGAAGCAGATTGAAGACAACAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
19930055 TCCTAGGTTGCAGTGGAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * * * * * * * * * *
19930078 TTAAGATAGCAGATCTTACCTTCTTGTTCCGGCAGTGAAGCAGATCAAAAACTCCAGCCTTGTCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
** * **
19930143 CCCT-GAGCAGCAGTGGAGTAGGT
66 CCCTAG-GTTGCAGTGGAGCAGAC
* * * * *
19930166 TGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACATCAGTCTT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTT
19930227 ATTGCCTTGA
Statistics
Matches: 569, Mismatches: 102, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
87 5 0.01
88 559 0.98
89 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTAGGTTGCAGTGGAGCAGAC
Found at i:19930443 original size:117 final size:116
Alignment explanation
Indices: 19930253--19930604 Score: 578
Period size: 117 Copynumber: 3.0 Consensus size: 116
19930243 AATGAAAAAT
* *
19930253 ATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAATGGAGCG
1 ATTGAAGCCACGACG-CGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
*
19930318 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAACAG
65 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
*
19930370 ATTGAAGCCACAACAGCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
1 ATTGAAGCCACGAC-GCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
* *
19930435 GATTAAAGCCGAGGGTAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
65 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
* * *
19930487 ATTGAAGCTACGACGGCAAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTAAAGTGGAGCG
1 ATTGAAGCCACGAC-GCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
* *
19930552 GATTAAAGCTGAGGGCAACGAATCCTATCTCTTTGGCATTGTAGTGGAGCAG
65 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
19930604 A
1 A
19930605 CTGAGTAAAA
Statistics
Matches: 219, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
117 218 1.00
118 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (116 bp):
ATTGAAGCCACGACGCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCGG
ATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
Found at i:19931171 original size:19 final size:20
Alignment explanation
Indices: 19931129--19931180 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
19931119 TTCAAGGATG
19931129 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
19931150 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
19931169 TGCAATCTTAGA
1 TGCAATCTTAGA
19931181 AGATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:19931431 original size:23 final size:23
Alignment explanation
Indices: 19931387--19931431 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
19931377 TCTTATTTTG
* *
19931387 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
19931410 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
19931432 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:19936983 original size:15 final size:15
Alignment explanation
Indices: 19936965--19936995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19936955 CACCACGCTA
19936965 ACCAGCACCTCTACC
1 ACCAGCACCTCTACC
*
19936980 ACCATCACCTCTACC
1 ACCAGCACCTCTACC
19936995 A
1 A
19936996 TGGCCTCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.52, G:0.03, T:0.16
Consensus pattern (15 bp):
ACCAGCACCTCTACC
Found at i:19975403 original size:58 final size:58
Alignment explanation
Indices: 19975333--19975448 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
19975323 AGTAATTTTA
*
19975333 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATGTTGAAAGATCCGT
1 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
19975391 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
1 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
19975449 TCCAGTTTGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.31
Consensus pattern (58 bp):
AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
Found at i:19975886 original size:17 final size:17
Alignment explanation
Indices: 19975864--19975896 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19975854 GTATTGATTT
19975864 TGACAAC-CTTATGTCAA
1 TGACAACACTT-TGTCAA
19975881 TGACAACACTTTGTCA
1 TGACAACACTTTGTCA
19975897 TCAATCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (17 bp):
TGACAACACTTTGTCAA
Found at i:19981110 original size:41 final size:41
Alignment explanation
Indices: 19980999--19981115 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 41
19980989 AAGAATATTG
19980999 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * *
19981040 ATAAATTG--C-TACGTGCCCCTGTTTGTACTTCGTTACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
19981078 CTGAATTGCACATACGTGCCCCTATTTCTACTTCGGTA
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
19981116 ATTCTAAACT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
38 34 0.52
39 1 0.02
40 1 0.02
41 29 0.45
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (41 bp):
CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
Found at i:19988298 original size:41 final size:41
Alignment explanation
Indices: 19987942--19988309 Score: 335
Period size: 41 Copynumber: 9.0 Consensus size: 41
19987932 AAGAATATTG
* * * *
19987942 CTGAATTGCACATGCGTGCCCC-AGTTTGTACTCCGGTACTC
1 CTGAATTGCACATACGTGCCCCTA-TTTGTACTTCGATACCC
* * * * * *
19987983 CTAAATTGCACATACGTGCCTCGATTTATTCTTCGGTACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* *
19988024 TTAAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * * * * *
19988065 CTAAATTGCACATACATGCCCGTGTCTATGCTTCGATACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * ** *
19988106 TTAAATTGCACATATGTGCCCCTGCTTGTAGTTCGATA-CC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* *
19988146 CTGAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
1 CTG-AATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * *
19988188 CTGAATTACACATACGTGTCCCTATTTGTACTTTGATACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * * * *
19988229 CTGAAATGCATATATGCGCCCCTATTTGTACTTCAATACTC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * * *
19988270 CTGAATTGCACATATGTGCACCTTTTTGTACATCGGTACC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACC
19988310 TCTGGATGTA
Statistics
Matches: 266, Mismatches: 58, Indels: 6
0.81 0.18 0.02
Matches are distributed among these distances:
40 3 0.01
41 257 0.97
42 6 0.02
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (41 bp):
CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
Found at i:19991355 original size:41 final size:41
Alignment explanation
Indices: 19991289--19991385 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
19991279 TATGGGTCTG
* * * **
19991289 CTCATACAAGTTGTCAGTCGGAACATAGCTACATTGTACTA
1 CTCACACAAGCTGTCAGTCGAAACATAGCTACACGGTACTA
19991330 CTCACACAAGCTGTCAGTCGAAACATAGCTACACGGTACTA
1 CTCACACAAGCTGTCAGTCGAAACATAGCTACACGGTACTA
19991371 CTCACACAAGCTGTC
1 CTCACACAAGCTGTC
19991386 GAGTATCCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (41 bp):
CTCACACAAGCTGTCAGTCGAAACATAGCTACACGGTACTA
Found at i:20011159 original size:30 final size:30
Alignment explanation
Indices: 20011124--20011192 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
20011114 ATGCAGGGGT
* *
20011124 CACACGGCCGTGTGACTCACACGGTTGAGA
1 CACACGCCCGTATGACTCACACGGTTGAGA
*
20011154 CACACGCCCGTATGACTCACATGGTTGAGA
1 CACACGCCCGTATGACTCACACGGTTGAGA
20011184 CACACGCCC
1 CACACGCCC
20011193 ATGTCTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.16
Consensus pattern (30 bp):
CACACGCCCGTATGACTCACACGGTTGAGA
Found at i:20012124 original size:35 final size:35
Alignment explanation
Indices: 20012078--20012158 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
20012068 ACTAAACTAT
20012078 ATTTTGACCATGTTGAGATCAACTTATCACATACC
1 ATTTTGACCATGTTGAGATCAACTTATCACATACC
*
20012113 ATTTTGACCATGTTTAGATCAACTTATCACATACC
1 ATTTTGACCATGTTGAGATCAACTTATCACATACC
20012148 ATTTTGACCAT
1 ATTTTGACCAT
20012159 TTAAAGATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (35 bp):
ATTTTGACCATGTTGAGATCAACTTATCACATACC
Found at i:20012455 original size:17 final size:17
Alignment explanation
Indices: 20012433--20012489 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
20012423 ATTTCCGACA
20012433 AGCTTCCAACCCGATCG
1 AGCTTCCAACCCGATCG
20012450 AGCTTCCAACCCGATCG
1 AGCTTCCAACCCGATCG
**
20012467 AGCTTCCAACATGATCG
1 AGCTTCCAACCCGATCG
20012484 AGCTTC
1 AGCTTC
20012490 TAACAATCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.21
Consensus pattern (17 bp):
AGCTTCCAACCCGATCG
Found at i:20014707 original size:3 final size:3
Alignment explanation
Indices: 20014699--20014735 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20014689 TTATGTTTTC
20014699 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20014736 ATTTTAACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20026693 original size:22 final size:23
Alignment explanation
Indices: 20026663--20026707 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
20026653 TAAGAAAAAT
* *
20026663 AAGAAAAATTTTTAAAA-AATAA
1 AAGAAAAATATTCAAAATAATAA
*
20026685 AAGATAAATATTCAAAATAATAA
1 AAGAAAAATATTCAAAATAATAA
20026708 CTAAATCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (23 bp):
AAGAAAAATATTCAAAATAATAA
Found at i:20043213 original size:21 final size:21
Alignment explanation
Indices: 20043188--20043230 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20043178 TGTAATTAAA
*
20043188 TAATTATGAGT-GAAAAATAAT
1 TAATT-TGAGTCGAAAAAGAAT
*
20043209 TAATTTGGGTCGAAAAAGAAT
1 TAATTTGAGTCGAAAAAGAAT
20043230 T
1 T
20043231 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (21 bp):
TAATTTGAGTCGAAAAAGAAT
Found at i:20045400 original size:15 final size:15
Alignment explanation
Indices: 20045380--20045408 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20045370 GTATTGTTGC
20045380 TTGATAACACGGTGA
1 TTGATAACACGGTGA
20045395 TTGATAACACGGTG
1 TTGATAACACGGTG
20045409 TGTGAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:20053522 original size:55 final size:56
Alignment explanation
Indices: 20053463--20053604 Score: 175
Period size: 55 Copynumber: 2.6 Consensus size: 56
20053453 TAATAAGATT
20053463 ATTATTAAATATAATTTAATAAAAATAATAAAAAATTTAATCA-TATT-TTAACATA
1 ATTATTAAATATAATTTAATAAAAATAATAAAAAATTTAAT-AGTATTCTTAACATA
* * * * *
20053518 ATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAGTATTCTTAATATT
1 ATTATTAAATATAATTTAATAAAAATAATAAAAAATTTAATAGTATTCTTAACATA
*
20053573 ATTATTAAAATATGAA-TTAATAAAAATCATAA
1 ATTATT-AAATAT-AATTTAATAAAAATAATAA
20053605 TATATAATAT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
53 1 0.01
54 22 0.30
55 31 0.42
56 10 0.14
57 10 0.14
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (56 bp):
ATTATTAAATATAATTTAATAAAAATAATAAAAAATTTAATAGTATTCTTAACATA
Found at i:20053609 original size:24 final size:23
Alignment explanation
Indices: 20053582--20053631 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
20053572 TATTATTAAA
*
20053582 ATATGAAT-TAATAAAAATCATAAT
1 ATAT-AATATAATAAAAATAAT-AT
*
20053606 ATATAATATTATAAAAATAATAT
1 ATATAATATAATAAAAATAATAT
20053629 ATA
1 ATA
20053632 ACCTACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAAAAATAATAT
Found at i:20055763 original size:3 final size:3
Alignment explanation
Indices: 20055755--20055779 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20055745 TTTCAACATG
20055755 GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT G
20055780 GTATTCATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:20062388 original size:21 final size:21
Alignment explanation
Indices: 20062364--20062412 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
20062354 CCACACTGGT
20062364 TGGCCCATCTTCCATCTCGGC
1 TGGCCCATCTTCCATCTCGGC
20062385 TGGCCCATCTTCCATCTCGGC
1 TGGCCCATCTTCCATCTCGGC
*
20062406 TAGCCCA
1 TGGCCCA
20062413 CAGCAACTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.43, G:0.18, T:0.27
Consensus pattern (21 bp):
TGGCCCATCTTCCATCTCGGC
Found at i:20062819 original size:26 final size:26
Alignment explanation
Indices: 20062743--20062819 Score: 61
Period size: 26 Copynumber: 3.1 Consensus size: 26
20062733 GAGCGGGCCG
20062743 AAGTAGAACTTGTGAGATCTGACTTT
1 AAGTAGAACTTGTGAGATCTGACTTT
** ** * * * *
20062769 AAG-A-AAAATCAG-GTTATGCCATT
1 AAGTAGAACTTGTGAGATCTGACTTT
20062792 AAGTAGAACTTGTGAGATCTGACTTT
1 AAGTAGAACTTGTGAGATCTGACTTT
20062818 AA
1 AA
20062820 TTCCCAAAAA
Statistics
Matches: 32, Mismatches: 16, Indels: 6
0.59 0.30 0.11
Matches are distributed among these distances:
23 10 0.31
24 5 0.16
25 5 0.16
26 12 0.38
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (26 bp):
AAGTAGAACTTGTGAGATCTGACTTT
Found at i:20065164 original size:48 final size:48
Alignment explanation
Indices: 20065112--20065210 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
20065102 ATGGTTTTGC
20065112 TGTGTTGAATAAGATAGGAATGGATATGCCATTCATGTGAAACAAACA
1 TGTGTTGAATAAGATAGGAATGGATATGCCATTCATGTGAAACAAACA
* *
20065160 TGTGTTGAATAAGATAGGAATGGCTATGCCATTCATGTGAAATAAACA
1 TGTGTTGAATAAGATAGGAATGGATATGCCATTCATGTGAAACAAACA
20065208 TGT
1 TGT
20065211 TGTTATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (48 bp):
TGTGTTGAATAAGATAGGAATGGATATGCCATTCATGTGAAACAAACA
Found at i:20065583 original size:21 final size:22
Alignment explanation
Indices: 20065550--20065590 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20065540 GTGCTTTGAT
*
20065550 TTTTTTTAATTATTTTGGATGA
1 TTTTTTTAATTATTCTGGATGA
*
20065572 TTTTTTT-CTTATTCTGGAT
1 TTTTTTTAATTATTCTGGAT
20065591 TGGTTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (22 bp):
TTTTTTTAATTATTCTGGATGA
Found at i:20069051 original size:30 final size:30
Alignment explanation
Indices: 20069015--20069085 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
20069005 TAAATTGAAT
*
20069015 AAAAGTAAAATATTAGGGGCAATTTTGTAA
1 AAAAGTAAAATATTAGGGGAAATTTTGTAA
*
20069045 AAAAGTAAAATGTTAGGGGAAATTTTGTAA
1 AAAAGTAAAATATTAGGGGAAATTTTGTAA
20069075 AAAAGTCAAAA
1 AAAAGT-AAAA
20069086 ATGACTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.27
Consensus pattern (30 bp):
AAAAGTAAAATATTAGGGGAAATTTTGTAA
Found at i:20069842 original size:101 final size:101
Alignment explanation
Indices: 20069662--20069873 Score: 284
Period size: 101 Copynumber: 2.1 Consensus size: 101
20069652 ACTCGACAAC
* * * * *
20069662 TTGTGTGAGCAGCATTGTGTAGCTTCCATTCTGACTATCAGCTTTTGTTAGCAGGCCCATTTTAC
1 TTGTGTGAGCAACATTGTGTAGCTTCCATTCTGACCATCAGCCTATGTGAGCAGGCCCATTTTAC
* * *
20069727 TGTTCATATGAGCTACGACTATATGTTTACCACACT
66 AGCTCATATAAGCTACGACTATATGTTTACCACACT
* * *
20069763 TTGTGTGAGCAATATTGTGTAGCTTCCATT-TCGACCGTCAGCCTATGTGAGCGGGCCCATTTTA
1 TTGTGTGAGCAACATTGTGTAGCTTCCATTCT-GACCATCAGCCTATGTGAGCAGGCCCATTTTA
*
20069827 CAGCTCGA-ATAAGCTATGACTATATGTTTACCACACT
65 CAGCTC-ATATAAGCTACGACTATATGTTTACCACACT
20069864 TTGTGTGAGC
1 TTGTGTGAGC
20069874 TTTACCGAGT
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
100 1 0.01
101 95 0.98
102 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (101 bp):
TTGTGTGAGCAACATTGTGTAGCTTCCATTCTGACCATCAGCCTATGTGAGCAGGCCCATTTTAC
AGCTCATATAAGCTACGACTATATGTTTACCACACT
Found at i:20077137 original size:6 final size:6
Alignment explanation
Indices: 20077096--20077136 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
20077086 AGGTTTCTAA
*
20077096 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGA AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
20077137 ATCCATTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:20077321 original size:26 final size:26
Alignment explanation
Indices: 20077282--20077343 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
20077272 ACATATTTTT
*
20077282 TCAAAATTTGACTAGGGGCAAAATCA
1 TCAAAATTTTACTAGGGGCAAAATCA
* *
20077308 TCAAAATTTTACTAGGGGTAAAATCG
1 TCAAAATTTTACTAGGGGCAAAATCA
20077334 TCAAAATTTT
1 TCAAAATTTT
20077344 GTAAGAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGCAAAATCA
Found at i:20077353 original size:26 final size:26
Alignment explanation
Indices: 20077282--20077356 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
20077272 ACATATTTTT
* * *
20077282 TCAAAATTTGACTAGGGGCAAAATCA
1 TCAAAATTTTACTAGAGGTAAAATCA
* *
20077308 TCAAAATTTTACTAGGGGTAAAATCG
1 TCAAAATTTTACTAGAGGTAAAATCA
*
20077334 TCAAAATTTT-GTAAGAGGTAAAA
1 TCAAAATTTTACT-AGAGGTAAAA
20077357 AAAGGATGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 1 0.02
26 42 0.98
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (26 bp):
TCAAAATTTTACTAGAGGTAAAATCA
Found at i:20079809 original size:32 final size:32
Alignment explanation
Indices: 20079773--20079833 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
20079763 CTTATTTGGA
20079773 TATTGCTTTCTCATAGCTTCCTCGGGTTCGGG
1 TATTGCTTTCTCATAGCTTCCTCGGGTTCGGG
* *
20079805 TATTGCTTTCTCATAGCTTTCTTGGGTTC
1 TATTGCTTTCTCATAGCTTCCTCGGGTTC
20079834 CCGAGTGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (32 bp):
TATTGCTTTCTCATAGCTTCCTCGGGTTCGGG
Found at i:20084602 original size:27 final size:27
Alignment explanation
Indices: 20084513--20084613 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
20084503 ATAATGGGCC
*
20084513 TAAAATGACCGAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* *
20084540 TAAAATGAAC-GAAATACTCTCGAAGGG
1 TAAAATG-ACTGAAATACCCTCAAAGGG
*
20084567 TAAAATGACTGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
**
20084594 TAAAATGACTGTTATACCCT
1 TAAAATGACTGAAATACCCT
20084614 TAAGAGTTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.03
27 60 0.94
28 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCAAAGGG
Found at i:20084806 original size:26 final size:26
Alignment explanation
Indices: 20084777--20084853 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
20084767 TTGCCACATA
* *
20084777 TACTGTTACTCGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
*
20084803 TACTATTACTGGCAGCGTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
*
20084829 TACTATTATTGGCAGCTTTGCTGCG
1 TACTATTACTGGCAGCTTTGCTGCG
20084854 ATATTGGTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:20085252 original size:32 final size:32
Alignment explanation
Indices: 20085213--20085290 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
20085203 ATTTTTCCTT
20085213 GAATATTTTAAACTGCTAGATTAGGAGATGAA
1 GAATATTTTAAACTGCTAGATTAGGAGATGAA
20085245 GAATATTTTAAACTGCTAGATTAGGAGATGAA
1 GAATATTTTAAACTGCTAGATTAGGAGATGAA
20085277 GAATATTTTAAACT
1 GAATATTTTAAACT
20085291 AATTACCGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (32 bp):
GAATATTTTAAACTGCTAGATTAGGAGATGAA
Found at i:20088184 original size:24 final size:22
Alignment explanation
Indices: 20088143--20088186 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
20088133 AATTTATCAA
*
20088143 ATTTCATATACATGTATCATCC
1 ATTTCATATACATATATCATCC
20088165 ATTTCATATATCTATATATCAT
1 ATTTCATATA-C-ATATATCAT
20088187 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCATATACATATATCATCC
Found at i:20093812 original size:42 final size:42
Alignment explanation
Indices: 20093752--20093850 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 42
20093742 ACGGCCTAGC
* * *
20093752 ACACGGCCTGGCACATGGGCGTGTGAGGCCATATCGAGTGTT
1 ACACGGCCTGGCACATGGGAGTGTAAGGCCATATCAAGTGTT
* * * *
20093794 ACACGGCCTGGCATATGGGATTTTAAGGCCATTTCAAGTGTT
1 ACACGGCCTGGCACATGGGAGTGTAAGGCCATATCAAGTGTT
* *
20093836 ACACAGCCTAGCACA
1 ACACGGCCTGGCACA
20093851 CGGGCATGTG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (42 bp):
ACACGGCCTGGCACATGGGAGTGTAAGGCCATATCAAGTGTT
Found at i:20101540 original size:17 final size:17
Alignment explanation
Indices: 20101496--20101555 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
20101486 CTACCTATCA
*
20101496 TTTTCACAGTCTATAG-
1 TTTTCACAGTCTTTAGT
* *
20101512 TTGTCCCAGTCTTTAGT
1 TTTTCACAGTCTTTAGT
*
20101529 TTTTCACAGTCTTTAAT
1 TTTTCACAGTCTTTAGT
20101546 TTTTCACAGT
1 TTTTCACAGT
20101556 GTATAGTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 13 0.35
17 24 0.65
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTTCACAGTCTTTAGT
Found at i:20102628 original size:22 final size:22
Alignment explanation
Indices: 20102602--20102646 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
20102592 AGATCAACAC
20102602 AAATAT-AATCGCATACATATCA
1 AAATATCAATCGCA-ACATATCA
*
20102624 AAATATCAATCTCAACATATCA
1 AAATATCAATCGCAACATATCA
20102646 A
1 A
20102647 TCATCACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATATCAATCGCAACATATCA
Found at i:20107561 original size:47 final size:47
Alignment explanation
Indices: 20107492--20107583 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
20107482 ATTTAATAAT
*
20107492 ATCAAAATATCATCTAAAATAAATGAATAATAAATAAATAAAATTAA
1 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATTAA
*
20107539 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAATTAAAATT
1 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATT
20107584 CGGGCGACCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (47 bp):
ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATTAA
Found at i:20117074 original size:13 final size:13
Alignment explanation
Indices: 20117037--20117067 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20117027 TTCTTGGCTT
20117037 TATA-CACCCTAG
1 TATATCACCCTAG
20117049 TATATCACCCTAG
1 TATATCACCCTAG
20117062 TATATC
1 TATATC
20117068 CTCCTAGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (13 bp):
TATATCACCCTAG
Found at i:20134866 original size:17 final size:17
Alignment explanation
Indices: 20134844--20134878 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20134834 TTTAAGCGTC
*
20134844 CATCTCACATTGTCTTA
1 CATCTCACACTGTCTTA
20134861 CATCTCACACTGTCTTA
1 CATCTCACACTGTCTTA
20134878 C
1 C
20134879 CATAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.37
Consensus pattern (17 bp):
CATCTCACACTGTCTTA
Found at i:20136207 original size:25 final size:25
Alignment explanation
Indices: 20136168--20136236 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
20136158 CTATGAATTG
* *
20136168 GTATGCTCACTCGAGCTGTAGATCA
1 GTATGCTCACACGAGCTGTAAATCA
* * **
20136193 GTATGCTCTCACGAGCTATAAATTG
1 GTATGCTCACACGAGCTGTAAATCA
*
20136218 GTATGCTCACACAAGCTGT
1 GTATGCTCACACGAGCTGT
20136237 GGGTCGTAAC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCA
Found at i:20136928 original size:145 final size:145
Alignment explanation
Indices: 20136661--20136964 Score: 592
Period size: 145 Copynumber: 2.1 Consensus size: 145
20136651 CCCGAATCAT
*
20136661 ATTT-TTTCAAAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
1 ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
20136725 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAGTCCTTAG
66 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAGTCCTTAG
20136790 CAAGCCCTATATTTC
131 CAAGCCCTATATTTC
20136805 ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
1 ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
20136870 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAGTCCTTAG
66 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAGTCCTTAG
20136935 CAAGCCCTATATTTC
131 CAAGCCCTATATTTC
20136950 ATTTATTTCACAATT
1 ATTTATTTCACAATT
20136965 TCACCATATA
Statistics
Matches: 158, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
144 4 0.03
145 154 0.97
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (145 bp):
ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAGTCCTTAG
CAAGCCCTATATTTC
Found at i:20139937 original size:43 final size:43
Alignment explanation
Indices: 20139859--20139957 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
20139849 TGTCCCAGAC
** ** *
20139859 ATGGTCTTACATGGAAATCTCGCATCGATGTCAATAGCCCAGCT
1 ATGGTCTTACA-CAAAATCTCAAATCGATGCCAATAGCCCAGCT
20139903 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
20139946 ATGGTCTTACAC
1 ATGGTCTTACAC
20139958 GAAACCACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 39 0.78
44 11 0.22
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:20140122 original size:31 final size:31
Alignment explanation
Indices: 20140081--20140164 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
20140071 ATCCAATGCT
*
20140081 CAAATC-AATTCGACAATGTATATCCATAAA
1 CAAATCAAATTCGGCAATGTATATCCATAAA
* * * *
20140111 CAATTCGAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATAAA
20140142 CAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
20140165 AACATATACA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.11
31 42 0.89
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATAAA
Found at i:20140172 original size:31 final size:30
Alignment explanation
Indices: 20140081--20140174 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 30
20140071 ATCCAATGCT
* ** *
20140081 CAAATCAATTCGACAATGTATATCCATAAA
1 CAAATCAATTCGGCAATGTATAAACATATA
* *
20140111 CAATTCGAATTCGGCAATGTAT-ATCTATATA
1 CAAATC-AATTCGGCAATGTATAAAC-ATATA
20140142 CAAATCAAATTCGGCAATGTATAAACATATA
1 CAAATC-AATTCGGCAATGTATAAACATATA
20140173 CA
1 CA
20140175 TTTAAATTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 6 0.11
31 45 0.85
32 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATAAACATATA
Found at i:20148271 original size:22 final size:23
Alignment explanation
Indices: 20148228--20148271 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
20148218 TTCTAGAACT
*
20148228 TATTTTAAATAAATAATTTAATA
1 TATTTTAAATAAATAATATAATA
20148251 TATTTT-AAT-AATATATATAAT
1 TATTTTAAATAAATA-ATATAAT
20148272 TCACTTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTTAAATAAATAATATAATA
Found at i:20149445 original size:62 final size:59
Alignment explanation
Indices: 20149330--20149446 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 59
20149320 ATCAATTTAA
* * * * *
20149330 TATTAAATTAATATAATATTTATCAAGATAATTACTAGATTAAATTTAGTATTAATTCT
1 TATTAAATTAATAGAATATTTATCAAGATAAATACTACAATAAATTTAATATTAATTCT
* *
20149389 TATTTAATTAATAGAATATTTATCTACAAGATAAATATTACAATAAATTTAATATTAA
1 TATTAAATTAATAGAATATTTA--T-CAAGATAAATACTACAATAAATTTAATATTAA
20149447 GATAATCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 20 0.42
61 1 0.02
62 27 0.56
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (59 bp):
TATTAAATTAATAGAATATTTATCAAGATAAATACTACAATAAATTTAATATTAATTCT
Found at i:20149451 original size:17 final size:18
Alignment explanation
Indices: 20149422--20149468 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
20149412 CTACAAGATA
20149422 AATATTACAATAA-A-TTT
1 AATATTA-AATAACACTTT
20149439 AATATTAAGATAATCACTTT
1 AATATTAA-ATAA-CACTTT
20149459 AATATTAAAT
1 AATATTAAAT
20149469 TAGTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
19 3 0.12
20 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATAACACTTT
Found at i:20151298 original size:50 final size:49
Alignment explanation
Indices: 20151164--20151308 Score: 143
Period size: 50 Copynumber: 2.9 Consensus size: 49
20151154 GATAATAACA
* * * *
20151164 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTT-TCCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAC
* * *
20151213 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAC
* **
20151261 GGTGCCCATGCCATGTCCCAGACATGGTCTT-CTATGGGACCTCTCATA
1 --TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGAGTTCTCATA
20151309 ACCTCAATAA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
48 4 0.05
49 37 0.47
50 38 0.48
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.30
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAC
Found at i:20161567 original size:41 final size:40
Alignment explanation
Indices: 20161517--20161712 Score: 248
Period size: 41 Copynumber: 4.7 Consensus size: 40
20161507 TAATCGTTAC
*
20161517 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAAT
1 ACGG-GGAATCAGCACTTAGCAACC-CCTTATAATCAATGAT
* * *
20161559 ACGGGGAATCAACACATAGCAACCCCTTTCACAATCAATGAT
1 ACGGGGAATCAGCACTTAGCAACCCC-TT-ATAATCAATGAT
20161601 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGG-GGAATCAGCACTTAGCAACC-CCTTATAATCAATGAT
* * *
20161643 ACGGGGAATCAGCACATAGCAACCCCTATTTGATCAATGAT
1 ACGGGGAATCAGCACTTAGCAACCCCT-TATAATCAATGAT
* *
20161684 TCGGGGAATCTGCACTTAGCAACCCCTTA
1 ACGGGGAATCAGCACTTAGCAACCCCTTA
20161713 CATCCAAAGA
Statistics
Matches: 135, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
40 6 0.04
41 74 0.55
42 33 0.24
43 20 0.15
44 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (40 bp):
ACGGGGAATCAGCACTTAGCAACCCCTTATAATCAATGAT
Found at i:20161659 original size:84 final size:83
Alignment explanation
Indices: 20161517--20161712 Score: 299
Period size: 84 Copynumber: 2.4 Consensus size: 83
20161507 TAATCGTTAC
20161517 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAAC
20161582 CCCT-TTCACAATCAATGAT
66 CCCTATT--CAATCAATGAT
* *
20161601 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAAC
**
20161666 CCCTATTTGATCAATGAT
66 CCCTATTCAATCAATGAT
* *
20161684 TCGG-GGAATCTGCACTTAGCAACC-CCTTA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTA
20161713 CATCCAAAGA
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
81 5 0.05
82 19 0.18
83 12 0.11
84 67 0.64
85 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (83 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAAC
CCCTATTCAATCAATGAT
Found at i:20164176 original size:20 final size:20
Alignment explanation
Indices: 20164151--20164189 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
20164141 TATTTTCTTC
20164151 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
20164171 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
20164190 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:20164534 original size:50 final size:49
Alignment explanation
Indices: 20164448--20164586 Score: 134
Period size: 50 Copynumber: 2.8 Consensus size: 49
20164438 TACTACAAAT
* * ** * *
20164448 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCAGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTAC-TGGGACCTCTCATATCAGTGCCAAC
** * * *
20164498 GCGTTGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTAC-TGGGACCTCTCATATCAGTGCCAAC
* *
20164548 GCCATGTCCTAGACAAGGTCTTAACTGGGACCTCTCATA
1 GCCATGTCCCAGACATGGTCTT-ACTGGGACCTCTCATA
20164587 ACCTCAATAA
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
50 68 0.97
51 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACATGGTCTTACTGGGACCTCTCATATCAGTGCCAAC
Found at i:20165215 original size:13 final size:13
Alignment explanation
Indices: 20165199--20165224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20165189 AATCGCCTAG
20165199 CAAAAGTTATTTA
1 CAAAAGTTATTTA
20165212 CAAAAGTTATTTA
1 CAAAAGTTATTTA
20165225 ACTTAATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
CAAAAGTTATTTA
Found at i:20170350 original size:36 final size:36
Alignment explanation
Indices: 20170301--20170369 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
20170291 GGCCTAACAC
* *
20170301 ACGGGCACGGACTGGGACACAAGCATAGATTGGAAA
1 ACGGGCACAGACTGGGACACAAGCACAGATTGGAAA
*
20170337 ACGGGCACAGACTGGGACACAGGCACAGATTGG
1 ACGGGCACAGACTGGGACACAAGCACAGATTGG
20170370 CACACAGCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.35, T:0.10
Consensus pattern (36 bp):
ACGGGCACAGACTGGGACACAAGCACAGATTGGAAA
Found at i:20170363 original size:18 final size:18
Alignment explanation
Indices: 20170299--20170376 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 18
20170289 ATGGCCTAAC
* *
20170299 ACACGGGCACGGACTGGG
1 ACACAGGCACAGACTGGG
* * * *
20170317 ACACAAGCATAGATTGGA
1 ACACAGGCACAGACTGGG
* *
20170335 AAACGGGCACAGACTGGG
1 ACACAGGCACAGACTGGG
* *
20170353 ACACAGGCACAGATTGGC
1 ACACAGGCACAGACTGGG
20170371 ACACAG
1 ACACAG
20170377 CCTGGCAAGT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.09
Consensus pattern (18 bp):
ACACAGGCACAGACTGGG
Found at i:20173563 original size:20 final size:20
Alignment explanation
Indices: 20173535--20173572 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20173525 TACATATTGG
20173535 ATCCACTTAACCCTCAATGT
1 ATCCACTTAACCCTCAATGT
*
20173555 ATCCGCTTAACCCTCAAT
1 ATCCACTTAACCCTCAAT
20173573 ACATATGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.29
Consensus pattern (20 bp):
ATCCACTTAACCCTCAATGT
Found at i:20182818 original size:14 final size:14
Alignment explanation
Indices: 20182799--20182827 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20182789 ATTCAATATG
20182799 AACTAAGACATGTA
1 AACTAAGACATGTA
20182813 AACTAAGACATGTA
1 AACTAAGACATGTA
20182827 A
1 A
20182828 GCATGAAATT
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:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
AACTAAGACATGTA
Found at i:20189087 original size:41 final size:40
Alignment explanation
Indices: 20189030--20189220 Score: 177
Period size: 41 Copynumber: 4.6 Consensus size: 40
20189020 GGATCCCTAT
*
20189030 GGAATCAACACTTAGCAACCACCTTATAATCAATGATACGG
1 GGAATCAACACATAGCAACC-CCTTATAATCAATGATACGG
* * *
20189071 GGAATCAACAAATAGCAACCCCTT-TCCCAATAAAGGATACGG
1 GGAATCAACACATAGCAACCCCTTAT---AATCAATGATACGG
* * *
20189113 TGGAATCAGCACTTAGCAAGCACCTTATAATCAATGATACGG
1 -GGAATCAACACATAGCAA-CCCCTTATAATCAATGATACGG
* * * *
20189155 GGAATCAGCACATAGCAACCCCTTTTTGATCAATGATTCGG
1 GGAATCAACACATAGCAACCCC-TTATAATCAATGATACGG
** * *
20189196 GGAATCTGCACTTAGCAACCACTTA
1 GGAATCAACACATAGCAACCCCTTA
20189221 CATTCAAAGA
Statistics
Matches: 124, Mismatches: 19, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
39 1 0.01
40 9 0.07
41 69 0.56
42 24 0.19
43 15 0.12
44 5 0.04
45 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (40 bp):
GGAATCAACACATAGCAACCCCTTATAATCAATGATACGG
Found at i:20190462 original size:51 final size:51
Alignment explanation
Indices: 20190386--20190622 Score: 237
Period size: 51 Copynumber: 4.7 Consensus size: 51
20190376 ATATAAATAA
*
20190386 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTGTGTGTACCGAGAAGCTT
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTT
* ** * * * * * * *
20190437 TGGTCATATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAA-ATGA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCT-T
* *
20190488 TGGTCAAATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTT
* * * * *
20190539 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-T
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AGAAGCTT
* * * *
20190589 TGATCACGTGTGTAGAACTATGTGAAGGCTACTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTA
20190623 CATGTATCAA
Statistics
Matches: 152, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
50 34 0.22
51 116 0.76
52 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (51 bp):
TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTT
Found at i:20190554 original size:102 final size:102
Alignment explanation
Indices: 20190378--20190578 Score: 339
Period size: 102 Copynumber: 2.0 Consensus size: 102
20190368 TGTTACATAT
* **
20190378 ATAAATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACTGTGTGTACCGAGAAGCTTTGGTCA
1 ATAAATAATGGTCAAATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCA
* *
20190443 TATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCA
66 CATGTGTAGTACTATGTGAAGGCTACTACGTGAATCA
*
20190480 ATAAATGATGGTCAAATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCA
1 ATAAATAATGGTCAAATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCA
*
20190545 CGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
66 CATGTGTAGTACTATGTGAAGGCTACTACGTGAA
20190579 CCGTAAAACT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (102 bp):
ATAAATAATGGTCAAATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCA
CATGTGTAGTACTATGTGAAGGCTACTACGTGAATCA
Found at i:20197753 original size:21 final size:22
Alignment explanation
Indices: 20197723--20197764 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20197713 GAACCAGTTG
20197723 GTGCTAGTAGTACAT-GTGCAT
1 GTGCTAGTAGTACATCGTGCAT
* *
20197744 GTGCTTGTAGTTCATCGTGCA
1 GTGCTAGTAGTACATCGTGCA
20197765 CCAATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.36
Consensus pattern (22 bp):
GTGCTAGTAGTACATCGTGCAT
Found at i:20203479 original size:21 final size:21
Alignment explanation
Indices: 20203439--20203479 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20203429 GATTCTAGTA
*
20203439 TGGATGCATCTGGCTTTGCTC
1 TGGATGCATCTGGCTGTGCTC
20203460 TGGATGCATCTGAG-TGTGCT
1 TGGATGCATCTG-GCTGTGCT
20203480 GATTGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.37
Consensus pattern (21 bp):
TGGATGCATCTGGCTGTGCTC
Found at i:20210570 original size:16 final size:16
Alignment explanation
Indices: 20210544--20210592 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
20210534 TAGAATTGGG
20210544 TTGAGAAAATTATTTAA
1 TTGA-AAAATTATTTAA
*
20210561 TTGAAAAATTAATTAA
1 TTGAAAAATTATTTAA
20210577 TT--AAAATTAATTTAA
1 TTGAAAAATT-ATTTAA
20210592 T
1 T
20210593 AAATAATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 13 0.45
17 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTGAAAAATTATTTAA
Found at i:20239910 original size:33 final size:32
Alignment explanation
Indices: 20239873--20239950 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
20239863 CAGCCTTGCC
* * *
20239873 ATGGTCTTACACTTATACTGCCATAACCCAGTT
1 ATGGTCTTACA-TTAGAATGCCATAACCCAGCT
* *
20239906 ATGGTCTTATCATTAGAATGTCATAGCCCAGCT
1 ATGGTCTTA-CATTAGAATGCCATAACCCAGCT
20239939 ATGGTCTTACAT
1 ATGGTCTTACAT
20239951 ATATATATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.08
33 34 0.87
34 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (32 bp):
ATGGTCTTACATTAGAATGCCATAACCCAGCT
Found at i:20242822 original size:159 final size:159
Alignment explanation
Indices: 20242531--20242855 Score: 569
Period size: 159 Copynumber: 2.0 Consensus size: 159
20242521 TTGCTAGGAA
* *
20242531 AGGTCTCCCAAGTATGATTGGTACCTTTTTATCAACCTCACATTCCAAAATAATAAAAGCTTCTA
1 AGGTCTCCCAAGTATGATTGGTACCTCTTTATCAACCTCACATTCCAAAATAATAAAAGCTGCTA
* * *
20242596 GAAAAATAAATTTGTCAACTCTTACCAACACATCTTCTATTTTACCTTCTGGATGTGCATACGAA
66 GAAAAATAAATTTGTCAACCCTTACCAACACATCTTCTATTTTACCTTCTGGAGGTGCATACAAA
20242661 TGATTAGCTAATTGCAATGTGATAGTTGT
131 TGATTAGCTAATTGCAATGTGATAGTTGT
* *
20242690 AGGTCTCCCAAGTATGATTGGTACCTCTTTATCAACCTCACATTCCAAAATCATAAAAGCTGCTG
1 AGGTCTCCCAAGTATGATTGGTACCTCTTTATCAACCTCACATTCCAAAATAATAAAAGCTGCTA
*
20242755 GAAAAATAAATTTGTCAACCCTTACCAACACATCTTCTATTTTACCTTCTGGAGGTGCATATAAA
66 GAAAAATAAATTTGTCAACCCTTACCAACACATCTTCTATTTTACCTTCTGGAGGTGCATACAAA
*
20242820 TGATTAGGTAATTGCAATGTGATAGTTGT
131 TGATTAGCTAATTGCAATGTGATAGTTGT
20242849 AGGTCTC
1 AGGTCTC
20242856 GCCTTCCCTA
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 157 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (159 bp):
AGGTCTCCCAAGTATGATTGGTACCTCTTTATCAACCTCACATTCCAAAATAATAAAAGCTGCTA
GAAAAATAAATTTGTCAACCCTTACCAACACATCTTCTATTTTACCTTCTGGAGGTGCATACAAA
TGATTAGCTAATTGCAATGTGATAGTTGT
Found at i:20247745 original size:28 final size:28
Alignment explanation
Indices: 20247705--20247764 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
20247695 TATTAACAGA
20247705 AGAAACAAAATGTATTAGAATGAGTAAT
1 AGAAACAAAATGTATTAGAATGAGTAAT
20247733 AGAAACAAAATGTATTAGAATGAGTAAT
1 AGAAACAAAATGTATTAGAATGAGTAAT
20247761 AGAA
1 AGAA
20247765 TAAGAAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.23
Consensus pattern (28 bp):
AGAAACAAAATGTATTAGAATGAGTAAT
Found at i:20247986 original size:17 final size:16
Alignment explanation
Indices: 20247957--20248003 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
20247947 AAACCACATA
*
20247957 ATTTTTTTA-TTTTTT
1 ATTTTTTCATTTTTTT
*
20247972 ATTTTTTCAATTTTTAT
1 ATTTTTTC-ATTTTTTT
*
20247989 GTTTTTTCATTTTTT
1 ATTTTTTCATTTTTT
20248004 CGATCACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (16 bp):
ATTTTTTCATTTTTTT
Found at i:20271245 original size:32 final size:32
Alignment explanation
Indices: 20271209--20271272 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20271199 GATTAATAGA
*
20271209 CACAATAATTGAAAGGTGCATGCTTAATTTAG
1 CACAATAACTGAAAGGTGCATGCTTAATTTAG
20271241 CACAATAACTGAAAGGTGCATGCTTAATTTAG
1 CACAATAACTGAAAGGTGCATGCTTAATTTAG
20271273 TTCCTAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (32 bp):
CACAATAACTGAAAGGTGCATGCTTAATTTAG
Found at i:20273392 original size:18 final size:19
Alignment explanation
Indices: 20273360--20273395 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20273350 ATCTTTGCAG
*
20273360 AACCTTCTTCTTCTATAGA
1 AACCTTCTTCATCTATAGA
20273379 AACCTT-TTCATCTATAG
1 AACCTTCTTCATCTATAG
20273396 GAATTTCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (19 bp):
AACCTTCTTCATCTATAGA
Found at i:20277485 original size:41 final size:41
Alignment explanation
Indices: 20277440--20277557 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 41
20277430 GATTATTGTG
*
20277440 AATTGCACATAGGTGCCCCTGGTTT-TACTTCAGTACCCCTA
1 AATTGCACATAAGTGCCCCT-GTTTGTACTTCAGTACCCCTA
* *
20277481 AATTGCACATAAGTGCCCCTATTTGTACTT-TGATACCCCTA
1 AATTGCACATAAGTGCCCCTGTTTGTACTTCAG-TACCCCTA
*
20277522 AATTGCACATACA-TGCCCCTGTTTGTACTTCGGTAC
1 AATTGCACATA-AGTGCCCCTGTTTGTACTTCAGTAC
20277558 TCCTGAACGC
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
40 4 0.06
41 62 0.91
42 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (41 bp):
AATTGCACATAAGTGCCCCTGTTTGTACTTCAGTACCCCTA
Found at i:20278032 original size:24 final size:24
Alignment explanation
Indices: 20278005--20278059 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
20277995 CTCGTGTCGT
* *
20278005 ATGTTTTGAATTGGCTCAAATGGC
1 ATGTTTTGAAATGACTCAAATGGC
20278029 ATGTTTTGAAATGACTCAAATGGC
1 ATGTTTTGAAATGACTCAAATGGC
20278053 ATGTTTT
1 ATGTTTT
20278060 AGTGATGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (24 bp):
ATGTTTTGAAATGACTCAAATGGC
Found at i:20278510 original size:25 final size:24
Alignment explanation
Indices: 20278476--20278555 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
20278466 TAAGAGTTGA
*
20278476 CCTGGCACACAAGAGTGTGACACGG
1 CCTGGCACAC-AGCGTGTGACACGG
* * *
20278501 CCTGGGACACGGGCGTGTGACACAG
1 CCTGGCACAC-AGCGTGTGACACGG
* *
20278526 CCTAGTACATCAGCGTGTGACACGG
1 CCTGGCACA-CAGCGTGTGACACGG
20278551 CCTGG
1 CCTGG
20278556 AACAGGGGCA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
25 43 0.98
26 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.34, T:0.15
Consensus pattern (24 bp):
CCTGGCACACAGCGTGTGACACGG
Found at i:20278569 original size:25 final size:25
Alignment explanation
Indices: 20278490--20278572 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
20278480 GCACACAAGA
*
20278490 GTGTGACACGGCCTGGGACACGGGC
1 GTGTGACACGGCCTGGAACACGGGC
* * * *
20278515 GTGTGACACAGCCTAGTACATC-AGC
1 GTGTGACACGGCCTGGAACA-CGGGC
*
20278540 GTGTGACACGGCCTGGAACAGGGGC
1 GTGTGACACGGCCTGGAACACGGGC
*
20278565 ATGTGACA
1 GTGTGACA
20278573 TGGCTGTGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
25 45 0.98
26 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.36, T:0.16
Consensus pattern (25 bp):
GTGTGACACGGCCTGGAACACGGGC
Found at i:20280005 original size:21 final size:21
Alignment explanation
Indices: 20279981--20280044 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
20279971 TGGGAGCTAA
20279981 TTAATATCACATGGACACAAG
1 TTAATATCACATGGACACAAG
** *
20280002 TTAAT-T--TTTGGAGC-TAA-
1 TTAATATCACATGGA-CACAAG
20280019 TTAATATCACATGGACACAAG
1 TTAATATCACATGGACACAAG
20280040 TTAAT
1 TTAAT
20280045 TTTTACTCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
17 5 0.16
18 7 0.23
19 2 0.06
20 7 0.23
21 10 0.32
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
TTAATATCACATGGACACAAG
Found at i:20280015 original size:38 final size:38
Alignment explanation
Indices: 20279973--20280048 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
20279963 AACGAGTATG
20279973 GGAGCTAATTAATATCACATGGACACAAGTTAATTTTT
1 GGAGCTAATTAATATCACATGGACACAAGTTAATTTTT
20280011 GGAGCTAATTAATATCACATGGACACAAGTTAATTTTT
1 GGAGCTAATTAATATCACATGGACACAAGTTAATTTTT
20280049 ACTCCATGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (38 bp):
GGAGCTAATTAATATCACATGGACACAAGTTAATTTTT
Found at i:20291754 original size:30 final size:30
Alignment explanation
Indices: 20291713--20291769 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
20291703 TAGGCATTTA
* * *
20291713 CACATGGGCTGGGCACACGCCCGTGTGAGC
1 CACACGGGCTGGCCACACGCCCATGTGAGC
*
20291743 CACACGGGCTGGCCACATGCCCATGTG
1 CACACGGGCTGGCCACACGCCCATGTG
20291770 CCAGCCCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.35, G:0.33, T:0.14
Consensus pattern (30 bp):
CACACGGGCTGGCCACACGCCCATGTGAGC
Found at i:20296051 original size:19 final size:18
Alignment explanation
Indices: 20296004--20296051 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
20295994 ATTGATTTTA
*
20296004 TTTGTTTTTCTTTTTAGT
1 TTTGTTTTTATTTTTAGT
*
20296022 TTTATTTTTTATTTTTATGT
1 TTT-GTTTTTATTTTTA-GT
20296042 TTTGTTTTTA
1 TTTGTTTTTA
20296052 GTTGTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTGTTTTTATTTTTAGT
Found at i:20296059 original size:35 final size:34
Alignment explanation
Indices: 20296002--20296086 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 34
20295992 TCATTGATTT
* *
20296002 TATTTGTTTTTCTT-TTTAGTTTTATTTTTTATTTT-
1 TATTT-TTTTTCTTAGTT-GTTTTA-TCTTTATTTTC
20296037 TATGTTTTGTTT-TTAGTTGTTTTATCTTTATTTTC
1 TAT-TTTT-TTTCTTAGTTGTTTTATCTTTATTTTC
20296072 TATTTTTTTTCTTAG
1 TATTTTTTTTCTTAG
20296087 ACTTATTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
33 3 0.07
34 17 0.40
35 16 0.37
36 7 0.16
ACGTcount: A:0.12, C:0.05, G:0.08, T:0.75
Consensus pattern (34 bp):
TATTTTTTTTCTTAGTTGTTTTATCTTTATTTTC
Found at i:20303411 original size:43 final size:42
Alignment explanation
Indices: 20303230--20303431 Score: 205
Period size: 43 Copynumber: 4.7 Consensus size: 42
20303220 AAAGCTCGTA
* * *
20303230 CGATGCCAACGTCCTAGACATGGTCTTACATGTAA-TCAACTAT
1 CGATGCCAACGTCCCAGACGTGGTCTTACACGTAACTCAA--AT
* * * * *
20303273 CGATGCC-ACTGTCCTAGATGGGGTCTTACACG-AAATCATAT
1 CGATGCCAAC-GTCCCAGACGTGGTCTTACACGTAACTCAAAT
* *
20303314 ACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAAT
1 -CGATGCCAACGTCCCAGACGTGGTCTTACACGT-AA-CTCAAAT
*
20303359 CAATGCCAACGTCCCAGACGTGGTCTTACACG-ACATCTCAAAT
1 CGATGCCAACGTCCCAGACGTGGTCTTACACGTA-A-CTCAAAT
20303402 CGATGCCAACGTCCCAGACGTGGTCTTACA
1 CGATGCCAACGTCCCAGACGTGGTCTTACA
20303432 TGAAATCACA
Statistics
Matches: 135, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
41 2 0.01
42 30 0.22
43 67 0.50
44 31 0.23
45 5 0.04
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
CGATGCCAACGTCCCAGACGTGGTCTTACACGTAACTCAAAT
Found at i:20308546 original size:6 final size:6
Alignment explanation
Indices: 20308535--20308569 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
20308525 TAATTCCATA
* *
20308535 AATTTT AATTTT AATTTT AGTTTT AATTTT TATTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
20308570 ATAGTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (6 bp):
AATTTT
Found at i:20308558 original size:18 final size:19
Alignment explanation
Indices: 20308537--20308576 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
20308527 ATTCCATAAA
20308537 TTTTAATTTTAATTT-TAG
1 TTTTAATTTTAATTTATAG
*
20308555 TTTTAATTTTTATTTATAG
1 TTTTAATTTTAATTTATAG
20308574 TTT
1 TTT
20308577 ATATGTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTAATTTTAATTTATAG
Found at i:20317512 original size:154 final size:154
Alignment explanation
Indices: 20317232--20317543 Score: 516
Period size: 154 Copynumber: 2.0 Consensus size: 154
20317222 ATCATGAAAC
* *
20317232 TCTTAATACTAATAGCCTTAATAGGTATATGTTATTTGTAAATTTATATTTCTTAGTAAAGTTAG
1 TCTTAATACTAATAGCCTTAACAAGTATATGTTATTTGTAAATTTATATTTCTTAGTAAAGTTAG
* *
20317297 TGAAATAATTAGAATACAATTAACATGTCAATAGAAATTAGATGTAAAATTCTATATGATTTGGA
66 TGAAATAATTAGAATAAAATTAACATGTCAATAGAAATTAGATGTAAAATTCTATATGATTTGAA
* *
20317362 CTTATATTGTCTTTGAATTTTGCA
131 CTTATATTATCTTCGAATTTTGCA
20317386 TCTTAATACTAATAGCCTTAACAAGTATATGTTATTTGTAAATTTATATTTCTTAGTAAAGTTAG
1 TCTTAATACTAATAGCCTTAACAAGTATATGTTATTTGTAAATTTATATTTCTTAGTAAAGTTAG
* * **
20317451 TGAAATAGTTAGGATAAAATTAACATGTCAATAGAAATTAGATGTGGAATTCTATATGATTTGAA
66 TGAAATAATTAGAATAAAATTAACATGTCAATAGAAATTAGATGTAAAATTCTATATGATTTGAA
* *
20317516 GTTATATTATCTTCGTATTTTGCA
131 CTTATATTATCTTCGAATTTTGCA
20317540 TCTT
1 TCTT
20317544 TTGTGTGTAC
Statistics
Matches: 146, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
154 146 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (154 bp):
TCTTAATACTAATAGCCTTAACAAGTATATGTTATTTGTAAATTTATATTTCTTAGTAAAGTTAG
TGAAATAATTAGAATAAAATTAACATGTCAATAGAAATTAGATGTAAAATTCTATATGATTTGAA
CTTATATTATCTTCGAATTTTGCA
Found at i:20318709 original size:2 final size:2
Alignment explanation
Indices: 20318697--20318749 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
20318687 AGAAATTTTA
*
20318697 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20318739 AT AT AT A- AT AT
1 AT AT AT AT AT AT
20318750 GTAGCTCGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20319120 original size:24 final size:24
Alignment explanation
Indices: 20319085--20319130 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20319075 CGGGGAGGAA
*
20319085 GGATATATTGAATTTCATTTTTGT
1 GGATATATTGAATTCCATTTTTGT
20319109 GGATGATA-TGAATTCCATTTTT
1 GGAT-ATATTGAATTCCATTTTT
20319131 TCTTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (24 bp):
GGATATATTGAATTCCATTTTTGT
Found at i:20326424 original size:40 final size:38
Alignment explanation
Indices: 20326349--20326449 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 38
20326339 CGAATATTAT
* * * *
20326349 AATTATAATTACCATAACTATAATAATGTTTGATCGAAAA
1 AATTATAATTACAATAATTATAATAATATTCGATCG--AA
* * *
20326389 AATTACAATTACAATAATTATAATTATATTCGATCGTA
1 AATTATAATTACAATAATTATAATAATATTCGATCGAA
20326427 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
20326450 CAAGGATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 23 0.43
40 30 0.57
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCGATCGAA
Found at i:20328609 original size:12 final size:12
Alignment explanation
Indices: 20328584--20328622 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20328574 ACTCGCTTCT
* *
20328584 TTACTTACTCAC
1 TTACTTGCTTAC
*
20328596 TTACTTGTTTAC
1 TTACTTGCTTAC
20328608 TTACTTGCTTAC
1 TTACTTGCTTAC
20328620 TTA
1 TTA
20328623 AATAATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:20328945 original size:50 final size:50
Alignment explanation
Indices: 20328883--20329006 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 50
20328873 CAATGTCATA
* * ** * **
20328883 TCCCAAATATGGTATTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACACCATG
** *
20328933 TCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACACCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACACCATG
*
20328983 TCCCAGACATGGTCTTACATGGGA
1 TCCCAAACATGGTCTTACATGGGA
20329007 TCTCATTCCC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACACCATG
Found at i:20329382 original size:30 final size:30
Alignment explanation
Indices: 20329348--20329405 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20329338 CCTTGATTCT
20329348 AACTTTGGAAAAATTACAATTTTGCCCCTA
1 AACTTTGGAAAAATTACAATTTTGCCCCTA
* * * *
20329378 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGAAAAATTACAATTTTGCCCC
20329406 AATGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACAATTTTGCCCCTA
Found at i:20333844 original size:48 final size:48
Alignment explanation
Indices: 20333762--20333952 Score: 224
Period size: 48 Copynumber: 4.0 Consensus size: 48
20333752 TATGCGTACT
20333762 GATAATCTGTTATGACACAAGGGTGGCA-AGGACTGTGTGCAGGCCACC
1 GATAATCTGTTATGACACAAGGGTGGCACA-GACTGTGTGCAGGCCACC
* * *
20333810 GATATTCTGTTGTGACACAAGGGTGGCACAGACTGTGTACAGGCCACC
1 GATAATCTGTTATGACACAAGGGTGGCACAGACTGTGTGCAGGCCACC
* * * * * *
20333858 AATAA-CTTATTAAGATACAAGGGTGGCATAGACTATGTGCAGGCCACC
1 GATAATC-TGTTATGACACAAGGGTGGCACAGACTGTGTGCAGGCCACC
* * * * *
20333906 GAGAATCTGTTATTACACAAAGGTGGTACGGACTGTGTGCAGGCCAC
1 GATAATCTGTTATGACACAAGGGTGGCACAGACTGTGTGCAGGCCAC
20333953 TTAGAAATCT
Statistics
Matches: 117, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
47 1 0.01
48 114 0.97
49 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
GATAATCTGTTATGACACAAGGGTGGCACAGACTGTGTGCAGGCCACC
Found at i:20333942 original size:96 final size:96
Alignment explanation
Indices: 20333778--20333952 Score: 253
Period size: 96 Copynumber: 1.8 Consensus size: 96
20333768 CTGTTATGAC
* * * * *
20333778 ACAAGGGTGGCAAGGACTGTGTGCAGGCCACCGATATTCTGTTGTGACACAAGGGTGGCACAGAC
1 ACAAGGGTGGCAAGGACTATGTGCAGGCCACCGAGAATCTGTTATGACACAAAGGTGGCACAGAC
20333843 TGTGTACAGGCCACCAATAACTTATTAAGAT
66 TGTGTACAGGCCACCAATAACTTATTAAGAT
* * *
20333874 ACAAGGGTGGCATA-GACTATGTGCAGGCCACCGAGAATCTGTTATTACACAAAGGTGGTACGGA
1 ACAAGGGTGGCA-AGGACTATGTGCAGGCCACCGAGAATCTGTTATGACACAAAGGTGGCACAGA
*
20333938 CTGTGTGCAGGCCAC
65 CTGTGTACAGGCCAC
20333953 TTAGAAATCT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
96 68 0.99
97 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (96 bp):
ACAAGGGTGGCAAGGACTATGTGCAGGCCACCGAGAATCTGTTATGACACAAAGGTGGCACAGAC
TGTGTACAGGCCACCAATAACTTATTAAGAT
Found at i:20334111 original size:38 final size:38
Alignment explanation
Indices: 20334060--20334139 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
20334050 TATGTGGAAC
* * *
20334060 TGAATTGAATAGTGACTTGAAAATGGAAAA-GTG-AATTT
1 TGAATGGAATAGTGA-TTAAAAAT-AAAAAGGTGAAATTT
20334098 TGAATGGAATAGTGATTAAAAATAAAAAGGTGAAATTT
1 TGAATGGAATAGTGATTAAAAATAAAAAGGTGAAATTT
20334136 TGAA
1 TGAA
20334140 AAAGTAGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 4 0.11
37 10 0.27
38 23 0.62
ACGTcount: A:0.46, C:0.01, G:0.23, T:0.30
Consensus pattern (38 bp):
TGAATGGAATAGTGATTAAAAATAAAAAGGTGAAATTT
Found at i:20338731 original size:28 final size:29
Alignment explanation
Indices: 20338699--20338761 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
20338689 TAATCCACCA
20338699 CCCAACTTTTTG-AAAATTACAATTTTG-C
1 CCCAAC-TTTTGCAAAATTACAATTTTGTC
* *
20338727 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGTC
20338757 CCCAA
1 CCCAA
20338762 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.27
29 18 0.60
30 4 0.13
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGTC
Found at i:20338735 original size:29 final size:30
Alignment explanation
Indices: 20338706--20338761 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
20338696 CCACCCAACT
20338706 TTTTG-AAAATTACAATTTTG-CCCCAAAC
1 TTTTGCAAAATTACAATTTTGTCCCCAAAC
* *
20338734 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGTCCCCAA
20338762 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGTCCCCAAAC
Found at i:20345318 original size:10 final size:10
Alignment explanation
Indices: 20345303--20345327 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20345293 CTAGTATTTA
20345303 TCCTCCTACG
1 TCCTCCTACG
20345313 TCCTCCTACG
1 TCCTCCTACG
20345323 TCCTC
1 TCCTC
20345328 TTCTTCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.52, G:0.08, T:0.32
Consensus pattern (10 bp):
TCCTCCTACG
Found at i:20353192 original size:41 final size:41
Alignment explanation
Indices: 20353146--20353232 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
20353136 AGAATATTTT
20353146 TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCC
* * *
20353187 TGAATTGCACATATGTGCCCCTCTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCC
20353228 TGAAT
1 TGAAT
20353233 ATACTTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCC
Found at i:20365076 original size:30 final size:30
Alignment explanation
Indices: 20365040--20365356 Score: 241
Period size: 30 Copynumber: 10.6 Consensus size: 30
20365030 GTATCAATGA
*
20365040 CCATCGAATTATGAAAAGGGATAGCTTCGT
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
*
20365070 CCATCGAATTATGAAAAGGGATAACTTCGG
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
* * * * * *
20365100 CTATTGAATTGTGAAAAGAGATAACTTTGG
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
* * * * * * *
20365130 CTATTGAACTATGAAAAAGGAT-GGTAACGA
1 CCATCGAATTATGAAAAGGGATAGCT-TCGG
*
20365160 CCATCGAATTATGAAAAGGGATAGCTTTGG
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
* * * *
20365190 CTATCAAACTATGCAAAGGGATAGCTTCGG
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
* * *
20365220 TCATCGAATTATGAAAAGGGAT-G-GT-GA
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
* * * * **
20365247 CCATCATCAACTATGAAAAGGGAT-GGTGACTA
1 CCATC--GAATTATGAAAAGGGATAGCT-TCGG
*
20365279 CCATCGAATTATGAAAAGGGATAGCTTTGG
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
* * **
20365309 CTATTGAATTATGAAAAGGGATAGCTTCAA
1 CCATCGAATTATGAAAAGGGATAGCTTCGG
*
20365339 CTATCG-ATTATGAAAAGG
1 CCATCGAATTATGAAAAGG
20365357 AATGGTGATA
Statistics
Matches: 224, Mismatches: 55, Indels: 17
0.76 0.19 0.06
Matches are distributed among these distances:
27 5 0.02
28 1 0.00
29 30 0.13
30 178 0.79
31 4 0.02
32 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (30 bp):
CCATCGAATTATGAAAAGGGATAGCTTCGG
Found at i:20365270 original size:29 final size:30
Alignment explanation
Indices: 20365220--20365300 Score: 128
Period size: 29 Copynumber: 2.7 Consensus size: 30
20365210 ATAGCTTCGG
20365220 TCATCGAATTATGAAAAGGGATGGTGACCA
1 TCATCGAATTATGAAAAGGGATGGTGACCA
* *
20365250 TCATC-AACTATGAAAAGGGATGGTGACTA
1 TCATCGAATTATGAAAAGGGATGGTGACCA
*
20365279 CCATCGAATTATGAAAAGGGAT
1 TCATCGAATTATGAAAAGGGAT
20365301 AGCTTTGGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 26 0.57
30 20 0.43
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (30 bp):
TCATCGAATTATGAAAAGGGATGGTGACCA
Found at i:20371246 original size:8 final size:8
Alignment explanation
Indices: 20371233--20371278 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
20371223 ATCCAATTCA
20371233 CTCTCATT
1 CTCTCATT
20371241 CTCTCATT
1 CTCTCATT
**
20371249 CTCTCCCT
1 CTCTCATT
20371257 CTCTCACGTT
1 CTCTCA--TT
20371267 CTCTCATT
1 CTCTCATT
20371275 CTCT
1 CTCT
20371279 TTTTAAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 25 0.78
10 7 0.22
ACGTcount: A:0.09, C:0.43, G:0.02, T:0.46
Consensus pattern (8 bp):
CTCTCATT
Found at i:20382027 original size:25 final size:25
Alignment explanation
Indices: 20381999--20382047 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20381989 TGAGCTTTCC
*
20381999 AATTTATAACTCGTGA-GAGCATACT
1 AATTCATAACTCGT-ATGAGCATACT
*
20382024 AATTCATAGCTCGTATGAGCATAC
1 AATTCATAACTCGTATGAGCATAC
20382048 ATGTACAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (25 bp):
AATTCATAACTCGTATGAGCATACT
Found at i:20393764 original size:71 final size:71
Alignment explanation
Indices: 20393646--20393788 Score: 268
Period size: 71 Copynumber: 2.0 Consensus size: 71
20393636 CATTTTAGCG
20393646 ATAGGAAACATAATTGCTTGATTAAAAGAAGTGGGAATATCAATACCTAAGCGATGCTTCCGCTC
1 ATAGGAAACATAATTGCTTGATTAAAAGAAGTGGGAATATCAATACCTAAGCGATGCTTCCGCTC
20393711 ACCCCT
66 ACCCCT
* *
20393717 ATAGGAAACATAATTGCTTGATTAAAAGAATTGGGAATATCAGTACCTAAGCGATGCTTCCGCTC
1 ATAGGAAACATAATTGCTTGATTAAAAGAAGTGGGAATATCAATACCTAAGCGATGCTTCCGCTC
20393782 ACCCCT
66 ACCCCT
20393788 A
1 A
20393789 CCTTATGTTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (71 bp):
ATAGGAAACATAATTGCTTGATTAAAAGAAGTGGGAATATCAATACCTAAGCGATGCTTCCGCTC
ACCCCT
Found at i:20395533 original size:21 final size:20
Alignment explanation
Indices: 20395507--20395546 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20395497 AAAACACAAG
20395507 TTGAAATAAACAGATTTAATT
1 TTGAAA-AAACAGATTTAATT
* *
20395528 TTGAAAACACATATTTAAT
1 TTGAAAAAACAGATTTAAT
20395547 ATTTCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (20 bp):
TTGAAAAAACAGATTTAATT
Done.