Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 73 of 328
Found at i:20045846 original size:22 final size:22
Alignment explanation
Indices: 20045816--20045859 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20045806 CAAGAAGTAA
20045816 TTTT-AAAAATATTAAAATTATT
1 TTTTAAAAAATA-TAAAATTATT
*
20045838 TTTTTAAAAATATAAAATTATT
1 TTTTAAAAAATATAAAATTATT
20045860 AAGTGCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAAAATATAAAATTATT
Found at i:20047217 original size:16 final size:16
Alignment explanation
Indices: 20047196--20047266 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
20047186 GTTTGGTTCA
*
20047196 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
20047212 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
20047228 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
**
20047244 CTGTAACAGAATAGAG
1 CTGTAATGGAATAGAG
20047260 CTGTAAT
1 CTGTAAT
20047267 CAGTAATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:20047332 original size:44 final size:46
Alignment explanation
Indices: 20047252--20047341 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 46
20047242 AGCTGTAACA
20047252 GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
*
20047298 GAATAGAGCTGTAAT-AG-AATTCTTA-TGTTTGGTTGAATGGAATG
1 GAATAGAGCTGTAATCAGTAATTC-AACTGTTTGGTTGAATGGAATG
20047342 ATGTTGTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 24 0.57
45 3 0.07
46 15 0.36
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (46 bp):
GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:20047505 original size:61 final size:55
Alignment explanation
Indices: 20047423--20047571 Score: 140
Period size: 61 Copynumber: 2.5 Consensus size: 55
20047413 GATTATTGTT
*
20047423 ATTAAATTTTAATA-AGATTATTGATACATATATTTTAATAAAAATAAAAATAAATAATTTA
1 ATTAAATTTTAATATA-ATTATT-ATA-ATATAATTTAAT-AAAAT---AATAAATAATTTA
* * *
20047484 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATATTTTA
1 ATTAAATTTTAATATAATTATTA-T-AATATAATTTAATAAAATAATAAATAATTTA
20047541 A-TAACATTATTAATATAATTATTAATAATAT
1 ATTAA-ATT-TTAATATAATTATT-ATAATAT
20047572 TTAATAATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
56 2 0.03
57 20 0.26
58 15 0.19
59 1 0.01
60 6 0.08
61 31 0.40
62 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (55 bp):
ATTAAATTTTAATATAATTATTATAATATAATTTAATAAAATAATAAATAATTTA
Found at i:20047553 original size:12 final size:11
Alignment explanation
Indices: 20047492--20047589 Score: 51
Period size: 12 Copynumber: 8.5 Consensus size: 11
20047482 TAATTATATT
20047492 TTAATATAATTA
1 TTAATA-AATTA
*
20047504 TTATTAAATATAA
1 TTAATAAAT-T-A
*
20047517 TTTAATAAAATA
1 -TTAATAAATTA
* *
20047529 AT-ATATATT-
1 TTAATAAATTA
20047538 TTAATAACATTA
1 TTAATAA-ATTA
20047550 TTAATATAATTA
1 TTAATA-AATTA
20047562 TTAATAATATTTA
1 TTAATAA-A-TTA
*
20047575 ATAAT-AATT-
1 TTAATAAATTA
20047584 TTAATA
1 TTAATA
20047590 TAAAATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
9 5 0.08
10 10 0.15
11 9 0.14
12 25 0.38
13 10 0.15
14 7 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATAAATTA
Found at i:20047577 original size:46 final size:47
Alignment explanation
Indices: 20047478--20047592 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 47
20047468 AAAAATAAAT
*
20047478 AATTTAAT-TATATTTTAATATAATTATTATTAAATATAATTTAATA
1 AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA
*
20047524 AA-ATAATATATATTTTAATA-ACATTATTAATATAAT-T-A-TTAATA
1 AATTTAATATATATTTTAATATA-ATTATTAATA-AATATAATTTAATA
20047568 ATATTTAATA-ATAATTTTAATATAA
1 A-ATTTAATATAT-ATTTTAATATAA
20047593 AATTATTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
44 7 0.12
45 9 0.15
46 39 0.66
47 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (47 bp):
AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA
Found at i:20049149 original size:2 final size:2
Alignment explanation
Indices: 20049142--20049166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20049132 CAGGGTAAAA
20049142 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20049167 ATTTATTATT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20050393 original size:44 final size:45
Alignment explanation
Indices: 20050303--20050431 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
20050293 GACAGAACGA
*
20050303 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
20050349 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
20050393 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20050432 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:20056450 original size:44 final size:45
Alignment explanation
Indices: 20056360--20056488 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
20056350 GACAGAACGA
*
20056360 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
20056406 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
20056450 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20056489 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:20066581 original size:83 final size:83
Alignment explanation
Indices: 20066479--20066983 Score: 784
Period size: 83 Copynumber: 6.2 Consensus size: 83
20066469 GAAGCAGATC
* * *
20066479 CAAGATGATTTGGCATCCTTGTGCTTCCAAGGAACAAATCGAGGACATAGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
20066544 AACGTTCTCAAACAGACT
66 AACGTTCTCAAACAGACT
20066562 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATC---GACGTTGCAGATATG-------
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
20066617 -AC--TCTCAAACAGACT
66 AACGTTCTCAAACAGACT
*
20066632 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATTGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
20066697 AACGTTCTCAAACAGACT
66 AACGTTCTCAAACAGACT
20066715 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
* *
20066780 AATGTTCTTAAACAGACT
66 AACGTTCTCAAACAGACT
*
20066798 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
* *
20066863 AATGTCCTCAAACAGACT
66 AACGTTCTCAAACAGACT
* *
20066881 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
* *
20066946 AATGTTCTCAAGCAGACT
66 AACGTTCTCAAACAGACT
* *
20066964 CAAGATAATTTGACATCCTT
1 CAAGATGATTTGGCATCCTT
20066984 ACAAATCGAA
Statistics
Matches: 393, Mismatches: 16, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
70 52 0.13
72 2 0.01
73 15 0.04
80 13 0.03
81 2 0.01
83 309 0.79
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (83 bp):
CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTTGCAGATATGACTCTCA
AACGTTCTCAAACAGACT
Found at i:20067390 original size:17 final size:20
Alignment explanation
Indices: 20067354--20067390 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
20067344 TAATCAGGCC
20067354 CAAACTACCCAGTAGACCCA
1 CAAACTACCCAGTAGACCCA
20067374 CAAAC-ACCC-GT-GACCCA
1 CAAACTACCCAGTAGACCCA
20067391 ATTAAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 4 0.24
20 5 0.29
ACGTcount: A:0.38, C:0.43, G:0.11, T:0.08
Consensus pattern (20 bp):
CAAACTACCCAGTAGACCCA
Found at i:20068521 original size:19 final size:19
Alignment explanation
Indices: 20068497--20068534 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20068487 AAATTTAGTC
*
20068497 CTATATTTATTATAT-TATT
1 CTATATATA-TATATGTATT
20068516 CTATATATATATATGTATT
1 CTATATATATATATGTATT
20068535 ATTTGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (19 bp):
CTATATATATATATGTATT
Found at i:20068846 original size:20 final size:19
Alignment explanation
Indices: 20068799--20068846 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
20068789 ATATAATCTT
20068799 TATTATGTT-TTATTTTCA
1 TATTATGTTATTATTTTCA
* *
20068817 TATTAT-TTATTGTTTTTA
1 TATTATGTTATTATTTTCA
20068835 TATATATGTTAT
1 TAT-TATGTTAT
20068847 GTATATCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
TATTATGTTATTATTTTCA
Found at i:20078977 original size:19 final size:19
Alignment explanation
Indices: 20078953--20079001 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
20078943 CATGGTTTTT
20078953 TAAAAAAATTATAAAAATA
1 TAAAAAAATTATAAAAATA
*
20078972 TAAAAAAAATT-TAAAATTA
1 T-AAAAAAATTATAAAAATA
*
20078991 TAAAAATATTA
1 TAAAAAAATTA
20079002 GAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.31
19 9 0.35
20 9 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAAATTATAAAAATA
Found at i:20078995 original size:17 final size:17
Alignment explanation
Indices: 20078955--20079014 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
20078945 TGGTTTTTTA
*
20078955 AAAAAATTATAAAAATATAA
1 AAAAAATT-T-AAAAT-TAT
20078975 AAAAAATTTAAAATTAT
1 AAAAAATTTAAAATTAT
*
20078992 -AAAAATATTAGAATTATT
1 AAAAAAT-TTAAAATTA-T
20079010 AAAAA
1 AAAAA
20079015 CAAAGTCTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 6 0.17
17 10 0.29
18 6 0.17
19 5 0.14
20 8 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAAATTTAAAATTAT
Found at i:20080590 original size:20 final size:20
Alignment explanation
Indices: 20080561--20080611 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
20080551 ATTAATAATA
* *
20080561 TTTTTAAATTTTTTTATC-T
1 TTTTTAAATTATTTAATCAT
20080580 TTTTTATAATTATTTAATCATT
1 TTTTTA-AATTATTTAATCA-T
20080602 TTTTTAAATT
1 TTTTTAAATT
20080612 CATTCCAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.22
20 10 0.37
21 4 0.15
22 7 0.26
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAAATTATTTAATCAT
Found at i:20080641 original size:10 final size:10
Alignment explanation
Indices: 20080626--20080671 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
20080616 CCAGAAGTTG
*
20080626 TTTTTAATTA
1 TTTTTAATAA
20080636 TTTTT-ATAA
1 TTTTTAATAA
20080645 TTTATT-ATAA
1 TTT-TTAATAA
*
20080655 TTATTAATAA
1 TTTTTAATAA
20080665 TTTTTAA
1 TTTTTAA
20080672 ATATATATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:20090970 original size:41 final size:41
Alignment explanation
Indices: 20090899--20090980 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
20090889 GTTTACTGAT
**** * *
20090899 TAATGCATATCTGATACTGTTACTGTAATAGGCTTAGGCCC
1 TAATGCATATCTGATACCAAAACTGAAATAGGCTAAGGCCC
20090940 TAATGCATATCTGATACCAAAACTGAAATAGGCTAAGGCCC
1 TAATGCATATCTGATACCAAAACTGAAATAGGCTAAGGCCC
20090981 GAACTGCTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
TAATGCATATCTGATACCAAAACTGAAATAGGCTAAGGCCC
Found at i:20092437 original size:12 final size:12
Alignment explanation
Indices: 20092420--20092453 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20092410 CGGCCCGCCC
20092420 ATATTAATTTTT
1 ATATTAATTTTT
*
20092432 ATATTATTTTTT
1 ATATTAATTTTT
20092444 ATA-TAATTTT
1 ATATTAATTTT
20092454 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:20092689 original size:14 final size:14
Alignment explanation
Indices: 20092670--20092700 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20092660 ATCCAAACAA
20092670 TAACAACAAAATAG
1 TAACAACAAAATAG
*
20092684 TAACAACATAATAG
1 TAACAACAAAATAG
20092698 TAA
1 TAA
20092701 AATAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:20103260 original size:12 final size:13
Alignment explanation
Indices: 20103243--20103271 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20103233 AGATACACAA
20103243 ATATATAA-AAAT
1 ATATATAACAAAT
20103255 ATATATAACAAAT
1 ATATATAACAAAT
20103268 ATAT
1 ATAT
20103272 TTGTTATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATATAACAAAT
Found at i:20103776 original size:2 final size:2
Alignment explanation
Indices: 20103769--20103817 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
20103759 AAATACATTA
20103769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20103811 AT AT AT A
1 AT AT AT A
20103818 ATGGAGGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20105097 original size:18 final size:20
Alignment explanation
Indices: 20105074--20105117 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
20105064 CCAAAATTAT
*
20105074 TATTTTAGAATAT-TTTA-A
1 TATTTTAAAATATCTTTACA
*
20105092 TATTTTAAAATTTCTTTACA
1 TATTTTAAAATATCTTTACA
20105112 TATTTT
1 TATTTT
20105118 TTAGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 4 0.18
20 7 0.32
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTTTAAAATATCTTTACA
Found at i:20110406 original size:15 final size:15
Alignment explanation
Indices: 20110386--20110456 Score: 71
Period size: 15 Copynumber: 5.1 Consensus size: 15
20110376 ATTTAAAACA
* *
20110386 TAATTTTTATTATAT
1 TAATTTATAATATAT
20110401 TAATTTATAATATA-
1 TAATTTATAATATAT
20110415 T--TTTAT--TATAT
1 TAATTTATAATATAT
*
20110426 GAATTTATAATATAT
1 TAATTTATAATATAT
*
20110441 GAATTTATAATATAT
1 TAATTTATAATATAT
20110456 T
1 T
20110457 TTATTAATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
10 4 0.09
12 5 0.11
13 5 0.11
14 1 0.02
15 32 0.68
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TAATTTATAATATAT
Found at i:20110424 original size:25 final size:25
Alignment explanation
Indices: 20110390--20110440 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20110380 AAAACATAAT
*
20110390 TTTTATTATATTAATTTATAATATA
1 TTTTATTATATGAATTTATAATATA
20110415 TTTTATTATATGAATTTATAATATA
1 TTTTATTATATGAATTTATAATATA
20110440 T
1 T
20110441 GAATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTTATTATATGAATTTATAATATA
Found at i:20110446 original size:40 final size:40
Alignment explanation
Indices: 20110387--20110462 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
20110377 TTTAAAACAT
* * *
20110387 AATTTTTATTATATTAATTTATAATATATTTTATTATATG
1 AATTTATAATATATGAATTTATAATATATTTTATTATATG
20110427 AATTTATAATATATGAATTTATAATATATTTTATTA
1 AATTTATAATATATGAATTTATAATATATTTTATTA
20110463 ATACATACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (40 bp):
AATTTATAATATATGAATTTATAATATATTTTATTATATG
Found at i:20110448 original size:25 final size:25
Alignment explanation
Indices: 20110393--20110449 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
20110383 ACATAATTTT
* **
20110393 TATTATATTAATTTATAATATATTT
1 TATTATATGAATTTATAATATATAA
20110418 TATTATATGAATTTATAATATATGAA
1 TATTATATGAATTTATAATATAT-AA
20110444 T-TTATA
1 TATTATA
20110450 ATATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
TATTATATGAATTTATAATATATAA
Found at i:20114188 original size:20 final size:19
Alignment explanation
Indices: 20114160--20114198 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
20114150 CAAAAACACG
20114160 ATAAAAATGAAATAAATAAA
1 ATAAAAATGAAAT-AATAAA
* *
20114180 ATAATAATGGAATAATAAA
1 ATAAAAATGAAATAATAAA
20114199 TGAAATAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (19 bp):
ATAAAAATGAAATAATAAA
Found at i:20114346 original size:3 final size:3
Alignment explanation
Indices: 20114332--20114594 Score: 128
Period size: 3 Copynumber: 86.7 Consensus size: 3
20114322 GGATCGCAAA
* *
20114332 AAT AAT AGT AAT AAT AAT AAT ACT -AT AAT GAA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* * * **
20114376 AAT AAT AAT AA- AGAT AAA AAT AAT AAT TAT AGAA AAT AAT TGT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * * *
20114422 AGT AAA AAT AAT AAT GAT AGT AAT AAT AAT AGT AAC AAT AAT GAA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * *
20114467 CAT AAAT AAT AGT AAAT AA- AA- AGAT AAA AAT AAT AAT AGT AAT AAT
1 AAT -AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * ** * * *
20114513 AAC AAT -GT CAAT AAAT AAT AAT GGT AAT AGT AAT AAC AAT AGT AAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
20114559 AAT ACT AAAT AAT CAT AAT AA- ATGT AAT AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
20114595 ATATAAAACC
Statistics
Matches: 188, Mismatches: 55, Indels: 34
0.68 0.20 0.12
Matches are distributed among these distances:
2 10 0.05
3 159 0.85
4 19 0.10
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20114569 original size:28 final size:28
Alignment explanation
Indices: 20114538--20114597 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20114528 TAATAATGGT
* *
20114538 AATAGTAATAAC-AATAGTAATAATACTA
1 AATAATAATAACAAAT-GTAATAATAATA
* *
20114566 AATAATCATAATAAATGTAATAATAATA
1 AATAATAATAACAAATGTAATAATAATA
20114594 AATA
1 AATA
20114598 TAAAACCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (28 bp):
AATAATAATAACAAATGTAATAATAATA
Found at i:20114578 original size:37 final size:35
Alignment explanation
Indices: 20114494--20114579 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 35
20114484 AAAAAGATAA
*
20114494 AAATAATAATAGTAATAATAACAATGTCAATAAAT
1 AAATAATAATAATAATAATAACAATGTCAATAAAT
** *
20114529 -AATAATGGTAATAGTAATAACAATAGT-AATAATACT
1 AAATAATAATAATAATAATAACAAT-GTCAATAA-A-T
*
20114565 AAATAATCATAATAA
1 AAATAATAATAATAA
20114580 ATGTAATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
34 25 0.62
35 3 0.08
36 1 0.03
37 11 0.28
ACGTcount: A:0.58, C:0.06, G:0.07, T:0.29
Consensus pattern (35 bp):
AAATAATAATAATAATAATAACAATGTCAATAAAT
Found at i:20115937 original size:44 final size:43
Alignment explanation
Indices: 20115886--20116301 Score: 174
Period size: 44 Copynumber: 9.5 Consensus size: 43
20115876 ATTTGCTCTG
* *
20115886 CTACTGCTTAGGGAGATATGATTTGTAATATTCAGCCTGCTCCA
1 CTACTGCTTAGGGAGATAAGATCT-TAATATTCAGCCTGCTCCA
* * * * * *
20115930 CTGCTGCTCAGGGAGATAAG-GCTTACTGTCCTC-GATCTGCTCCA
1 CTACTGCTTAGGGAGATAAGATCTTAATAT--TCAG-CCTGCTCCA
* * *
20115974 CTACTGCTTAGGGAGATAAGATCTACAATTTTCAGCCTACTCCA
1 CTACTGCTTAGGGAGATAAGATCT-TAATATTCAGCCTGCTCCA
** *
20116018 CTACTGCTTAGGGAGAT-AGGGCTTACCAT-TTGC-GATCTGCTCCA
1 CTACTGCTTAGGGAGATAAGATCTTA--ATATT-CAG-CCTGCTCCA
* * * * * *
20116062 CTACTGTTTAAGGAGATAAGATATGTAATTTTTAGCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGATCT-TAATATTCAGCCTG-CTCCA
* * * **
20116106 CTACTGCTTAGGGAGATAAGA-CTCACCGTCTTC-GATTTGCTCCA
1 CTACTGCTTAGGGAGATAAGATCTTA--ATATTCAG-CCTGCTCCA
* * *
20116150 CTACTGCTTAGGGAGATAAGATTTGTAACT-TTCAACCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGATCT-TAA-TATTCAGCCTG-CTCCA
* * * * * * * *
20116194 CTACTGCTTAAGGAGATAAG-GCTCACCGTCTTC-GATCTACTCTA
1 CTACTGCTTAGGGAGATAAGATCTTA--ATATTCAG-CCTGCTCCA
* * * *
20116238 CTACTACTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGATCT-TAATATTCAGCCTG-CTCCA
*
20116282 CTACTGCTTAGGGGGATAAG
1 CTACTGCTTAGGGAGATAAG
20116302 GCTAGTGGCT
Statistics
Matches: 270, Mismatches: 69, Indels: 66
0.67 0.17 0.16
Matches are distributed among these distances:
42 7 0.03
43 18 0.07
44 216 0.80
45 22 0.08
46 7 0.03
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (43 bp):
CTACTGCTTAGGGAGATAAGATCTTAATATTCAGCCTGCTCCA
Found at i:20115971 original size:88 final size:88
Alignment explanation
Indices: 20115886--20116304 Score: 511
Period size: 88 Copynumber: 4.8 Consensus size: 88
20115876 ATTTGCTCTG
* * * * * *
20115886 CTACTGCTTAGGGAGATATGATTTGTAATATTCAGCCTG-CTCCACTGCTGCTCAGGGAGATAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCC-CTACTGCTTAGGGAGATAAG
* * *
20115950 GCTTACTGTCCTCGATCTGCTCCA
65 GCTCACCGTCTTCGATCTGCTCCA
** ** *
20115974 CTACTGCTTAGGGAGATAAGATCTACAATTTTCAGCCT-ACTCCACTACTGCTTAGGGAGATAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCC-CTACTGCTTAGGGAGATAAG
* *
20116038 GCTTACCAT-TTGCGATCTGCTCCA
65 GCTCACCGTCTT-CGATCTGCTCCA
* * * * *
20116062 CTACTGTTTAAGGAGATAAGATATGTAATTTTTAGCCTGTTTCCCTACTGCTTAGGGAGATAAGA
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGAGATAAGG
*
20116127 CTCACCGTCTTCGATTTGCTCCA
66 CTCACCGTCTTCGATCTGCTCCA
* * * *
20116150 CTACTGCTTAGGGAGATAAGATTTGTAACTTTCAACCTGTTTCCCTACTGCTTAAGGAGATAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGAGATAAGG
* *
20116215 CTCACCGTCTTCGATCTACTCTA
66 CTCACCGTCTTCGATCTGCTCCA
* * *
20116238 CTACTACTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTTCCCTACTGCTTAGGGGGATAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGAGATAAGG
20116303 CT
66 CT
20116305 AGTGGCTTAA
Statistics
Matches: 285, Mismatches: 42, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
87 1 0.00
88 279 0.98
89 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (88 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGAGATAAGG
CTCACCGTCTTCGATCTGCTCCA
Found at i:20116531 original size:43 final size:43
Alignment explanation
Indices: 20116484--20116692 Score: 138
Period size: 43 Copynumber: 4.8 Consensus size: 43
20116474 AAGCTCCCCG
* *
20116484 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGTCTGCAA
1 TCTTCAATCTGTTCCACTACTGCTTAGGGAGATAAGTCTGCAA
* * * * *
20116527 TCTTCAACCTGTTCC-CTATTGCTTAGGGGGATAAGGCT--AG
1 TCTTCAATCTGTTCCACTACTGCTTAGGGAGATAAGTCTGCAA
* * * * * ** * * * *
20116567 TGGCTTAAATCCGCTCCATTGCCACTACATGGAGATAAGGTTTGCTA
1 T--CTTCAATCTGTTCCACTACTGCT-TAGGGAGATAA-GTCTGCAA
* **
20116614 TCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTATAA
1 TCTTCAATCTGTTCCACTACTGCTTAGGGAGATAAG-TCTGCAA
* *
20116658 TTTTCAACCTGTTCC-CTACTGCTTAGGGAGATAAG
1 TCTTCAATCTGTTCCACTACTGCTTAGGGAGATAAG
20116693 GCTAGTGGCT
Statistics
Matches: 118, Mismatches: 40, Indels: 16
0.68 0.23 0.09
Matches are distributed among these distances:
40 2 0.02
42 30 0.25
43 36 0.31
44 32 0.27
45 17 0.14
47 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (43 bp):
TCTTCAATCTGTTCCACTACTGCTTAGGGAGATAAGTCTGCAA
Found at i:20116565 original size:260 final size:260
Alignment explanation
Indices: 20116205--20116826 Score: 888
Period size: 260 Copynumber: 2.4 Consensus size: 260
20116195 TACTGCTTAA
* * *
20116205 GGAGATAAGGCTCACCGTCTTCGATCTACTCTACTACTACTTAGGGAGATAAGATCTGTAATTTT
1 GGAGATAA-GCTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTT
* *
20116270 TAGCCTGTTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGTTCCATTGCCAGTAC
65 TAGCCTG-TTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTAC
*
20116335 ATGGAGATAAGATTCGCCGTCCTCGATCTGCTACACTACAACTTAGGGAGATAAGATCTATAATT
129 ATGGAGATAAGATTCGCCATCCTCGATCTGCTACACTACAACTTAGGGAGATAAGATCTATAATT
* * * *
20116400 TTCAACCCGTTCCCTACTGCTTAAGGG-GATAAGGCTAGTGGATTGAATCTGCTCCATTTTCGCT
194 TTCAACCCGTTCCCTACTGCTT-AGGGAGATAAGGCTAGTGGATTAAATCCGCTCCA-TTGCACT
20116464 ACAT
257 ACAT
* * * *
20116468 GGAGATAAGCTCCCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG-TCTGCAATCTTC
1 GGAGATAAGCTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTT
* *
20116532 AACCTGTTCCCTATTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACAT
66 AGCCTGTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACAT
* * * * * * **
20116597 GGAGATAAGGTTTGCTATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTATAATTTT
131 GGAGATAAGATTCGCCATCCTCGATCTGCTACACTACAACTTAGGGAGATAAGATCTATAATTTT
* * *
20116662 CAACCTGTTCCCTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCCGCTCTATTGCACTACAT
196 CAACCCGTTCCCTACTGCTTAGGGAGATAAGGCTAGTGGATTAAATCCGCTCCATTGCACTACAT
* * * * * *
20116727 AGAGATACGATTAATCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTT
1 GGAGATAAG-CTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTT
20116792 TAGCCTGTTCCCTACTGCTTAGGGGGATAAGGCTA
65 TAGCCTGTTCCCTACTGCTTAGGGGGATAAGGCTA
20116827 ATCTAAACTT
Statistics
Matches: 317, Mismatches: 39, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
259 20 0.06
260 193 0.61
261 56 0.18
262 40 0.13
263 8 0.03
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (260 bp):
GGAGATAAGCTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTT
AGCCTGTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACAT
GGAGATAAGATTCGCCATCCTCGATCTGCTACACTACAACTTAGGGAGATAAGATCTATAATTTT
CAACCCGTTCCCTACTGCTTAGGGAGATAAGGCTAGTGGATTAAATCCGCTCCATTGCACTACAT
Found at i:20116698 original size:131 final size:131
Alignment explanation
Indices: 20116205--20116826 Score: 800
Period size: 130 Copynumber: 4.8 Consensus size: 131
20116195 TACTGCTTAA
** * * * *
20116205 GGAGATAAGGCTCACCGTCTTCGATCTACTCTACTACTACTTAGGGAGATAAGATCTGTAATTTT
1 GGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
* * * *
20116270 TAGCCTGTTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGTTCCATTGCCAGTAC
66 CAACCTG-TTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTAC
20116335 AT
130 AT
* * ** *
20116337 GGAGATAAGATTCGCCGTCCTCGATCTGCTACACTACAACTTAGGGAGATAAGATCTATAATTTT
1 GGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
* * * * * ** *
20116402 CAACCCGTTCCCTACTGCTTAAGGGGATAAGGCTAGTGGATTGAATCTGCTCCATTTTCGCTACA
66 CAACCTGTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACA
20116467 T
131 T
* * * *
20116468 GGAGATAAG-CTCCCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG-TCTGCAATCTT
1 GGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
*
20116531 CAACCTGTTCCCTATTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACA
66 CAACCTGTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACA
20116596 T
131 T
* * ** * *
20116597 GGAGATAAGGTTTGCTATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTATAATTTT
1 GGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
* *
20116662 CAACCTGTTCCCTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCCGCTCTATTG-CACTACA
66 CAACCTGTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACA
20116726 T
131 T
* * *** * * *
20116727 AGAGATACGATTAATCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTT
1 GGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
* *
20116792 TAGCCTGTTCCCTACTGCTTAGGGGGATAAGGCTA
66 CAACCTGTTCCCTACTGCTTAGGGGGATAAGGCTA
20116827 ATCTAAACTT
Statistics
Matches: 421, Mismatches: 67, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
129 74 0.18
130 166 0.39
131 121 0.29
132 60 0.14
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (131 bp):
GGAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
CAACCTGTTCCCTACTGCTTAGGGGGATAAGGCTAGTGGCTTAAATCCGCTCCATTGCCACTACA
T
Found at i:20128499 original size:39 final size:39
Alignment explanation
Indices: 20128456--20128711 Score: 361
Period size: 39 Copynumber: 6.5 Consensus size: 39
20128446 TAACGGAGAA
*
20128456 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGAG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
** *
20128495 TTATATCCGGGCTAAGTCTTGAAGGCATTCGTACTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
20128534 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
20128573 TCATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
20128612 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
20128651 TTATATCCGAGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
20128690 TTATATTCGGGCTTAAAGTCCC
1 TTATATCCGGGC-T-AAGTCCC
20128712 ACATGCTTTG
Statistics
Matches: 196, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
39 176 0.90
40 20 0.10
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:20132102 original size:127 final size:128
Alignment explanation
Indices: 20131928--20132162 Score: 337
Period size: 127 Copynumber: 1.8 Consensus size: 128
20131918 CATGATTTCC
* * * *
20131928 AAAACATGCAAAGAAATTTTGAAAGGGTATTCGGTTATTTGGTCAAACGGTAAATCGAAACCCAA
1 AAAACATGCAAAGAAATTTCGAAAGGATATTCAGTTATTTGGTCAAACGGAAAATCGAAACCCAA
* *
20131993 CACGTTAGGGCACGATTTATCTAATTTCCAAACACGAAATATTGCCTTGTTTTTTAATTTAAG
66 CACGTTAGGGCACGATTTATCGAATTTCCAAACACAAAATATTGCCTTGTTTTTTAATTTAAG
* * * * *
20132056 AAAACATGGATAG-AATTTCGAAAGGATATTTAGTTATTTGGTCAAACGGAAAATCGAAACTCAG
1 AAAACATGCAAAGAAATTTCGAAAGGATATTCAGTTATTTGGTCAAACGGAAAATCGAAACCCAA
* * *
20132120 CACGTTAGGGCACGATTTCTCGAATTTTCAAATACAAAATATT
66 CACGTTAGGGCACGATTTATCGAATTTCCAAACACAAAATATT
20132163 ACCTCTATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
127 82 0.88
128 11 0.12
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (128 bp):
AAAACATGCAAAGAAATTTCGAAAGGATATTCAGTTATTTGGTCAAACGGAAAATCGAAACCCAA
CACGTTAGGGCACGATTTATCGAATTTCCAAACACAAAATATTGCCTTGTTTTTTAATTTAAG
Found at i:20132580 original size:3 final size:3
Alignment explanation
Indices: 20132566--20132856 Score: 272
Period size: 3 Copynumber: 96.7 Consensus size: 3
20132556 GGATAGTAAA
* *
20132566 AAT AAT AGT AAT AAT AAT ACT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * * *
20132613 AAT AAT AAT AAT AAT AAT AGAA AAT AAT TGT AAT AGT AAA AAT AAA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
20132659 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
20132707 AAT AAT AAT AAT AAT AAT AA- ACAT AAAT AAT AGT AA- AAT AA- AA-
1 AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT
* * * *
20132750 AGAT AAA AAT AAT AAT AGT AAT AAT AAC AAT -GT CAAT AAAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT
** * * * * *
20132797 GGT AAT AGT AAT AAC AAT AGT AAT AAT ACT AAAT AAT CAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
20132842 ATGT AAT AAT AAT AA
1 A-AT AAT AAT AAT AA
20132857 ATATAAAACC
Statistics
Matches: 232, Mismatches: 43, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
2 9 0.04
3 210 0.91
4 12 0.05
5 1 0.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20132831 original size:28 final size:28
Alignment explanation
Indices: 20132800--20132859 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20132790 TAATAATGGT
* *
20132800 AATAGTAATAAC-AATAGTAATAATACTA
1 AATAATAATAACAAAT-GTAATAATAATA
* *
20132828 AATAATCATAATAAATGTAATAATAATA
1 AATAATAATAACAAATGTAATAATAATA
20132856 AATA
1 AATA
20132860 TAAAACCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (28 bp):
AATAATAATAACAAATGTAATAATAATA
Found at i:20133409 original size:12 final size:12
Alignment explanation
Indices: 20133392--20133416 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20133382 TCGCTGTTGC
20133392 ACGCGCCACCGT
1 ACGCGCCACCGT
20133404 ACGCGCCACCGT
1 ACGCGCCACCGT
20133416 A
1 A
20133417 TACGGTGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.48, G:0.24, T:0.08
Consensus pattern (12 bp):
ACGCGCCACCGT
Found at i:20133908 original size:19 final size:19
Alignment explanation
Indices: 20133884--20133922 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20133874 TTGTGTTGGG
20133884 TATTTACTTTGGGCTGTAA
1 TATTTACTTTGGGCTGTAA
20133903 TATTTACTTTGGGCTGTAA
1 TATTTACTTTGGGCTGTAA
20133922 T
1 T
20133923 TTGGACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (19 bp):
TATTTACTTTGGGCTGTAA
Found at i:20133930 original size:19 final size:19
Alignment explanation
Indices: 20133884--20133932 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
20133874 TTGTGTTGGG
*
20133884 TATTTACTTTGGGCTGTAA
1 TATTGACTTTGGGCTGTAA
*
20133903 TATTTACTTTGGGCTGTAA
1 TATTGACTTTGGGCTGTAA
20133922 T-TTGGACTTTG
1 TATT-GACTTTG
20133933 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.18, C:0.10, G:0.22, T:0.49
Consensus pattern (19 bp):
TATTGACTTTGGGCTGTAA
Found at i:20138484 original size:25 final size:24
Alignment explanation
Indices: 20138428--20138477 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
20138418 AATTTGTGCA
* * *
20138428 TTTAAATAGGTTTTTTTCTTTAAT
1 TTTAAATTGATTTTTTTCTATAAT
20138452 TTTAAATTGATTTTTTTC-ATAAT
1 TTTAAATTGATTTTTTTCTATAAT
20138475 TTT
1 TTT
20138478 TGAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTAAATTGATTTTTTTCTATAAT
Found at i:20139246 original size:3 final size:3
Alignment explanation
Indices: 20139238--20139354 Score: 234
Period size: 3 Copynumber: 39.0 Consensus size: 3
20139228 AATCCCTAAT
20139238 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20139286 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20139334 TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC
20139355 CCTTAACCCA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 114 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:20141369 original size:27 final size:30
Alignment explanation
Indices: 20141323--20141396 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 30
20141313 AATAATATAT
* * *
20141323 TAATAAGAATAATTATAGT-ATAA-AACAA
1 TAATAAAAAGAATAATAGTAATAATAACAA
* * *
20141351 TAGTAAAAA-AATAATAGTAATAATAATAT
1 TAATAAAAAGAATAATAGTAATAATAACAA
20141380 TAATAAAAAGAATAATA
1 TAATAAAAAGAATAATA
20141397 AAAATAACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 8 0.22
28 11 0.30
29 11 0.30
30 7 0.19
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (30 bp):
TAATAAAAAGAATAATAGTAATAATAACAA
Found at i:20141460 original size:3 final size:3
Alignment explanation
Indices: 20141310--20141441 Score: 62
Period size: 3 Copynumber: 46.0 Consensus size: 3
20141300 GAAAAAAGAA
* * * * * *
20141310 AAT AAT AAT -AT ATT AAT AAG AAT AAT TAT AGT -AT AA- AAC AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
20141355 AA- AAA AAT AAT AGT AAT AAT AAT ATT AAT AAA AAG AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
20141402 AACG AAT -GT AAT AGT -AT CAT -AT AAT AAT AAT AAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20141442 GAAATCACGC
Statistics
Matches: 94, Mismatches: 27, Indels: 16
0.69 0.20 0.12
Matches are distributed among these distances:
2 11 0.12
3 81 0.86
4 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20141621 original size:16 final size:16
Alignment explanation
Indices: 20141588--20141646 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
20141578 ATAATATATT
*
20141588 AATAATAATAGTAGAA
1 AATAATAATAATAGAA
*
20141604 AATAATAATAAATAAAA
1 AATAATAAT-AATAGAA
* *
20141621 AATCAGTTATAAT-GAA
1 AAT-AATAATAATAGAA
20141637 AATAATAATA
1 AATAATAATA
20141647 CTAATAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 5 0.15
16 14 0.41
17 11 0.32
18 4 0.12
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (16 bp):
AATAATAATAATAGAA
Found at i:20142316 original size:6 final size:7
Alignment explanation
Indices: 20142300--20142325 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20142290 ATATGTAAAC
20142300 AAAAATA
1 AAAAATA
20142307 AAAAATA
1 AAAAATA
20142314 AAAAATA
1 AAAAATA
20142321 AAAAA
1 AAAAA
20142326 AATAATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:20143695 original size:5 final size:5
Alignment explanation
Indices: 20143685--20143714 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
20143675 AAATCAACCT
20143685 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
20143715 AACGTGGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:20148181 original size:1 final size:1
Alignment explanation
Indices: 20148175--20148205 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
20148165 TCCCTCTTCC
20148175 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20148206 GAAGAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20150451 original size:30 final size:30
Alignment explanation
Indices: 20150393--20150451 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
20150383 TTTGACTTAT
* *
20150393 CTCACACGGCCAAGTCACACGCCCGTGTGC
1 CTCACACAGCCAAGACACACGCCCGTGTGC
* * *
20150423 CTCACACAGCTAAGACACATGCCTGTGTG
1 CTCACACAGCCAAGACACACGCCCGTGTG
20150452 GAGATTTCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.17
Consensus pattern (30 bp):
CTCACACAGCCAAGACACACGCCCGTGTGC
Found at i:20152411 original size:14 final size:14
Alignment explanation
Indices: 20152378--20152422 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
20152368 CATCCTTATC
*
20152378 TTTCTTTCTTTTTCTA
1 TTTCTTT-TATTT-TA
*
20152394 TTTCTTTTGTTTTA
1 TTTCTTTTATTTTA
20152408 TTTCTTTTATTTTA
1 TTTCTTTTATTTTA
20152422 T
1 T
20152423 GTTATTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 16 0.59
15 4 0.15
16 7 0.26
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTCTTTTATTTTA
Found at i:20153246 original size:14 final size:14
Alignment explanation
Indices: 20153227--20153254 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20153217 GGGTGATATA
20153227 GGTAGAGCTTTACG
1 GGTAGAGCTTTACG
20153241 GGTAGAGCTTTACG
1 GGTAGAGCTTTACG
20153255 ATAAGGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
GGTAGAGCTTTACG
Found at i:20155485 original size:33 final size:33
Alignment explanation
Indices: 20155443--20155510 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
20155433 GTTTTTCACA
20155443 ATCAAACATCATGATCTCATAATCAAATCGTGT
1 ATCAAACATCATGATCTCATAATCAAATCGTGT
20155476 ATCAAACATCATGATCTCATAATCAAATCGTGT
1 ATCAAACATCATGATCTCATAATCAAATCGTGT
20155509 AT
1 AT
20155511 ACTAAACTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (33 bp):
ATCAAACATCATGATCTCATAATCAAATCGTGT
Found at i:20157229 original size:13 final size:13
Alignment explanation
Indices: 20157211--20157236 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20157201 TTAGGCCACC
20157211 TCACATGGGCGTG
1 TCACATGGGCGTG
20157224 TCACATGGGCGTG
1 TCACATGGGCGTG
20157237 CCCCTGTCGA
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:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
TCACATGGGCGTG
Found at i:20157322 original size:12 final size:12
Alignment explanation
Indices: 20157305--20157329 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20157295 AAGCCTACAT
20157305 AAACACCCTAGG
1 AAACACCCTAGG
20157317 AAACACCCTAGG
1 AAACACCCTAGG
20157329 A
1 A
20157330 GGCAGAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (12 bp):
AAACACCCTAGG
Found at i:20164358 original size:6 final size:6
Alignment explanation
Indices: 20164347--20164384 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
20164337 TTTAGACTCG
* *
20164347 TTTTAT TTTTAT TTTTAT TTTTAC TTTTAT TTCTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
20164385 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:20172617 original size:20 final size:21
Alignment explanation
Indices: 20172592--20172631 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20172582 CACTTGGAAC
*
20172592 AGGGC-ACGCGCCCATGTGGA
1 AGGGCAACACGCCCATGTGGA
*
20172612 AGGGCAACACGCCCTTGTGG
1 AGGGCAACACGCCCATGTGG
20172632 CCCTGTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:20173976 original size:49 final size:49
Alignment explanation
Indices: 20173916--20174041 Score: 164
Period size: 49 Copynumber: 2.6 Consensus size: 49
20173906 ATTAAAGTCA
* *
20173916 ATGCCGTGTCCCAGACAGGTCTTATACTGACTTTCATATATCGAG-ACCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCG-GTACCG
* * * **
20173965 ATGCCATGTCCCACACAGGTCTTACACTGGCTTTCATCTATCGGTGTCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGGTACCG
*
20174014 ATGCCATGTCCTAGACAGGTCTTACACT
1 ATGCCATGTCCCAGACAGGTCTTACACT
20174042 AACACTCAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
48 1 0.01
49 66 0.99
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGGTACCG
Found at i:20177402 original size:29 final size:28
Alignment explanation
Indices: 20177367--20177445 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 28
20177357 TAATAAATAA
20177367 TATTAAAATAATAAAATAATAAAATATCT
1 TATTAAAATAATAAAATAAT-AAATATCT
**
20177396 TATTAAAATATTAATAAAATAATATTTATCT
1 TATT-AAA-A-TAATAAAATAATAAATATCT
* *
20177427 AATTAATAATTATAAAATA
1 TATTAA-AATAATAAAATA
20177446 TCATCAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 13 0.31
30 6 0.14
31 11 0.26
32 12 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (28 bp):
TATTAAAATAATAAAATAATAAATATCT
Found at i:20180701 original size:21 final size:20
Alignment explanation
Indices: 20180667--20180709 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20180657 ATTGTCGAGG
20180667 AAGGAACAAGATGACTCAAGC
1 AAGGAACAAGATGA-TCAAGC
*
20180688 AAGG-ACAAGAATGATGAAGC
1 AAGGAACAAG-ATGATCAAGC
20180708 AA
1 AA
20180710 AAGCTGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.51, C:0.14, G:0.26, T:0.09
Consensus pattern (20 bp):
AAGGAACAAGATGATCAAGC
Found at i:20192759 original size:47 final size:49
Alignment explanation
Indices: 20192708--20192818 Score: 156
Period size: 47 Copynumber: 2.3 Consensus size: 49
20192698 GTTTTGTAGT
*
20192708 AAAATGTCAAGGGGAGTTTACTTGACGTGGTGATCA--TTTTGTGT-TGC
1 AAAATGTCAAGGGGAGATTACTTGACGTGGTGATCAGTTTTTGT-TCTGC
* * *
20192755 AAAATGTCAAAGGGAGATTACTTGACGTGGTGATGAGTTTTTGTTCTGT
1 AAAATGTCAAGGGGAGATTACTTGACGTGGTGATCAGTTTTTGTTCTGC
20192804 AAAATGTCAAGGGGA
1 AAAATGTCAAGGGGA
20192819 TCAGAATTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 33 0.59
48 1 0.02
49 22 0.39
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (49 bp):
AAAATGTCAAGGGGAGATTACTTGACGTGGTGATCAGTTTTTGTTCTGC
Found at i:20203890 original size:16 final size:16
Alignment explanation
Indices: 20203869--20203914 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
20203859 AATTGAGTTG
20203869 AGAAAATTATTTAATT
1 AGAAAATTATTTAATT
*
20203885 AGAAAATTAATTAATT
1 AGAAAATTATTTAATT
20203901 --AAAATTAATTTAAT
1 AGAAAATT-ATTTAAT
20203915 AAATAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 6 0.22
16 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
AGAAAATTATTTAATT
Found at i:20205734 original size:2 final size:2
Alignment explanation
Indices: 20205727--20205755 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20205717 ACACTGAGCA
20205727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20205756 AGATAATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20211480 original size:55 final size:55
Alignment explanation
Indices: 20211414--20211523 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
20211404 TTGACAATCC
20211414 GATATGTTAGTTTTCTTGTCTAAATCTTTACATTTGAATTATGTATAGTGAAGAT
1 GATATGTTAGTTTTCTTGTCTAAATCTTTACATTTGAATTATGTATAGTGAAGAT
*
20211469 GATATGTTAGTTTTCTTGTCTAAATTTTTACATTTGAATTATGTATAGTGAAGAT
1 GATATGTTAGTTTTCTTGTCTAAATCTTTACATTTGAATTATGTATAGTGAAGAT
20211524 TTCAAAGGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (55 bp):
GATATGTTAGTTTTCTTGTCTAAATCTTTACATTTGAATTATGTATAGTGAAGAT
Found at i:20216526 original size:2 final size:2
Alignment explanation
Indices: 20216519--20216551 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20216509 GAATTTGGGT
20216519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20216552 TGCCCTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20217337 original size:31 final size:31
Alignment explanation
Indices: 20217290--20217366 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
20217280 TCAACTTTAA
* * * *
20217290 AAAAGTAACAACTCAGTCACTAGCGTTATTG
1 AAAAGTGACAAATCAGTCACTAACGTTATCG
20217321 AAAAGTGACAAATCAGTCACTAACGTTATCG
1 AAAAGTGACAAATCAGTCACTAACGTTATCG
20217352 AAAAGTGACAAATCA
1 AAAAGTGACAAATCA
20217367 ATCATCCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (31 bp):
AAAAGTGACAAATCAGTCACTAACGTTATCG
Found at i:20223943 original size:30 final size:32
Alignment explanation
Indices: 20223909--20223968 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
20223899 AAATTATTAT
20223909 TTTAATATAAT-A-AT-TAATAATATTTAAAAA
1 TTTAATATAATGATATGTAA-AATATTTAAAAA
20223939 TTTAATATAATGATATGTAAAATATTTAAA
1 TTTAATATAATGATATGTAAAATATTTAAA
20223969 TAATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 11 0.41
31 1 0.04
32 12 0.44
33 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTAATATAATGATATGTAAAATATTTAAAAA
Found at i:20223949 original size:23 final size:24
Alignment explanation
Indices: 20223919--20223976 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
20223909 TTTAATATAA
*
20223919 TAAT-TAATAATATTTAAAA-ATT
1 TAATATAATAATATGTAAAATATT
*
20223941 TAATATAATGATATGTAAAATATT
1 TAATATAATAATATGTAAAATATT
20223965 TAA-ATAATAATA
1 TAATATAATAATA
20223977 AATGTTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 21 0.68
24 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
TAATATAATAATATGTAAAATATT
Found at i:20227247 original size:20 final size:20
Alignment explanation
Indices: 20227222--20227304 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
20227212 ATTATAAAAA
20227222 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
20227242 AAAAATTCAAAATAATTCTT
1 AAAAATTCAAAATAATTTTT
*
20227262 AAAAATTTAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
20227282 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTTT
20227300 AAAAA
1 AAAAA
20227305 CTCCAAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
18 5 0.09
19 15 0.26
20 37 0.65
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:20227338 original size:10 final size:10
Alignment explanation
Indices: 20227323--20227361 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
20227313 TTCATATTTC
20227323 TTAAAAAATT
1 TTAAAAAATT
20227333 TT-AAAAATT
1 TTAAAAAATT
20227342 TTAAAAAAATT
1 TT-AAAAAATT
*
20227353 CTAAAAAAT
1 TTAAAAAAT
20227362 ATATAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 9 0.35
10 9 0.35
11 8 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:20227709 original size:20 final size:21
Alignment explanation
Indices: 20227669--20227709 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20227659 AAAAAGAAAT
* *
20227669 ACACCAAAAAATGGCTGAAAG
1 ACACCAAAAAATGACTAAAAG
20227690 ACACCAAAAAAT-ACTAAAAG
1 ACACCAAAAAATGACTAAAAG
20227710 TACAAACTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (21 bp):
ACACCAAAAAATGACTAAAAG
Found at i:20228168 original size:12 final size:12
Alignment explanation
Indices: 20228151--20228184 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20228141 CGATCTGACC
20228151 ATATTAATTTTT
1 ATATTAATTTTT
*
20228163 ATATTATTTTTT
1 ATATTAATTTTT
20228175 ATA-TAATTTT
1 ATATTAATTTT
20228185 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:20228329 original size:30 final size:30
Alignment explanation
Indices: 20228293--20228355 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
20228283 ACTTAACAAG
20228293 CAAATGTCTCCAAAATAATAACAAAATTAA
1 CAAATGTCTCCAAAATAATAACAAAATTAA
** *
20228323 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATGTCTCCAAAATAATAACAAAATTAA
20228353 CAA
1 CAA
20228356 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCCAAAATAATAACAAAATTAA
Found at i:20228410 original size:22 final size:22
Alignment explanation
Indices: 20228385--20228427 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20228375 TATCCAAACA
20228385 ATAATAACAAAATAGTAGCAAT
1 ATAATAACAAAATAGTAGCAAT
** *
20228407 ATAATAGTAAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
20228428 AATAGGGCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAT
Found at i:20232226 original size:33 final size:33
Alignment explanation
Indices: 20232177--20232421 Score: 131
Period size: 33 Copynumber: 7.5 Consensus size: 33
20232167 ATGGACTTTT
* * *
20232177 CCTTTTCTAGTTGTACACTCGAGGTGTACATTC
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* *
20232210 CCTTTTCAAGTGGTACACACGAAGTGTACATAC
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* * * * *
20232243 CCTTTTCAATTTGTACACTCAAAGTGCATATAA
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* * **
20232276 CATTTTCAAG-TGTACACAT--ATAGTGTACCTTT
1 CCTTTTCAAGTTGTACAC-TCGA-AGTGTACATAC
* * * * * * **
20232308 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* * * * * * **
20232341 CCTTTTCATA-TGGTATACACAAAGTATACCTTT
1 CCTTTTCA-AGTTGTACACTCGAAGTGTACATAC
* * *
20232374 CCTTTTCAAG-TGTACACACAAAGTGTACATAA
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
20232406 CCTTTTCAAGTTGTAC
1 CCTTTTCAAGTTGTAC
20232422 CATTTGGGTA
Statistics
Matches: 174, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
31 1 0.01
32 49 0.28
33 122 0.70
34 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (33 bp):
CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
Found at i:20232314 original size:32 final size:32
Alignment explanation
Indices: 20232278--20232421 Score: 164
Period size: 33 Copynumber: 4.4 Consensus size: 32
20232268 GCATATAACA
* * *
20232278 TTTTCAAGTGTACACATATAGTGTACCTTTCC
1 TTTTCAAGTGTACACACAAAGTATACCTTTCC
*
20232310 TTTTCAAGTGGTATACACAAAGTATACCTTTCC
1 TTTTCAAGT-GTACACACAAAGTATACCTTTCC
*
20232343 TTTTCATA-TGGTATACACAAAGTATACCTTTCC
1 TTTTCA-AGT-GTACACACAAAGTATACCTTTCC
* * **
20232376 TTTTCAAGTGTACACACAAAGTGTACATAACC
1 TTTTCAAGTGTACACACAAAGTATACCTTTCC
20232408 TTTTCAAGTTGTAC
1 TTTTCAAG-TGTAC
20232422 CATTTGGGTA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
32 36 0.36
33 62 0.63
34 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (32 bp):
TTTTCAAGTGTACACACAAAGTATACCTTTCC
Found at i:20232331 original size:65 final size:61
Alignment explanation
Indices: 20232210--20232421 Score: 174
Period size: 65 Copynumber: 3.2 Consensus size: 61
20232200 GTGTACATTC
* ** * *
20232210 CCTTTTCAAGTGGTACACACGAAGTGTACATACCCTTTTCAATTTGTACACTCAAAGTGCATATA
1 CCTTTTCAAGT-GTACACA--AAGTGTACCTTTCCTTTTCAA-GTGTACACACAAAGTG-ATATA
20232275 A
61 A
* * *
20232276 CATTTTCAAGTGTACACATATAGTGTACCTTTCCTTTTCAAGTGGTATACACAAAGT-ATACCTT
1 CCTTTTCAAGTGTACACA-A-AGTGTACCTTTCCTTTTCAAGT-GTACACACAAAGTGATA--TA
*
20232340 T
61 A
* * *
20232341 CCTTTTCATATGGTATACACAAAGTATACCTTTCCTTTTCAAGTGTACACACAAAGTGTACATAA
1 CCTTTTCA-A--GTGTACACAAAGTGTACCTTTCCTTTTCAAGTGTACACACAAAGTG-ATATAA
20232406 CCTTTTCAAGTTGTAC
1 CCTTTTCAAG-TGTAC
20232422 CATTTGGGTA
Statistics
Matches: 118, Mismatches: 18, Indels: 23
0.74 0.11 0.14
Matches are distributed among these distances:
62 1 0.01
63 7 0.06
64 3 0.03
65 64 0.54
66 32 0.27
67 3 0.03
68 8 0.07
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (61 bp):
CCTTTTCAAGTGTACACAAAGTGTACCTTTCCTTTTCAAGTGTACACACAAAGTGATATAA
Found at i:20233147 original size:20 final size:22
Alignment explanation
Indices: 20233105--20233152 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
20233095 TGTAAAAGTG
*
20233105 ATTTATCTATCAACAATCTTTC
1 ATTTATCTATCAACAAACTTTC
20233127 ATTT-TCTATCAA-AAACTTTC
1 ATTTATCTATCAACAAACTTTC
20233147 AATTTA
1 -ATTTA
20233153 CAGCATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTATCTATCAACAAACTTTC
Found at i:20239904 original size:34 final size:32
Alignment explanation
Indices: 20239860--20239951 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 32
20239850 ACTCGAGGTA
*
20239860 CACATTCCCTTTTTCAAGTGGTACACACAAAGTG
1 CACATACCC-TTTTCAAGT-GTACACACAAAGTG
* *
20239894 TACATACCCTTTTC-AGTTTGTACACTCAAAGTG
1 CACATACCCTTTTCAAG--TGTACACACAAAGTG
*
20239927 CATATAACCC-TTTCAAGTGTACACA
1 CACAT-ACCCTTTTCAAGTGTACACA
20239952 TATTGTAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
32 9 0.19
33 25 0.52
34 14 0.29
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (32 bp):
CACATACCCTTTTCAAGTGTACACACAAAGTG
Found at i:20241473 original size:24 final size:24
Alignment explanation
Indices: 20241435--20241515 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
20241425 CTGGAGGCCT
20241435 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCAAA
*
20241460 AGCCCTTTTGATAACTGGGGCATAA
1 AGCCCTTTTAATAACTGGGGCA-AA
* *
20241485 A-CCC-TTTAATAACTAGGGCATA
1 AGCCCTTTTAATAACTGGGGCAAA
20241507 AGCCCTTTT
1 AGCCCTTTT
20241516 GCACTTCCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
22 2 0.04
23 17 0.35
24 23 0.47
25 7 0.14
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCAAA
Found at i:20241503 original size:23 final size:23
Alignment explanation
Indices: 20241442--20241514 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
20241432 CCTAGCCTCT
20241442 TTTAATAACTGGGGCA-AAAGCCC
1 TTTAATAACTGGGGCATAAA-CCC
*
20241465 TTTTGATAACTGGGGCATAAACCC
1 -TTTAATAACTGGGGCATAAACCC
* *
20241489 TTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAACCC
20241512 TTT
1 TTT
20241515 TGCACTTCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 23 0.52
24 18 0.41
25 3 0.07
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAACCC
Found at i:20241589 original size:20 final size:20
Alignment explanation
Indices: 20241561--20241631 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
20241551 GCATTTATGA
*
20241561 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
20241581 ACATATCATGTGTATATCAT
1 ACATATCATGTGCATATCAT
*
20241601 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
20241621 ACATATCATGT
1 ACATATCATGT
20241632 TTATCAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:20243441 original size:33 final size:33
Alignment explanation
Indices: 20243403--20243518 Score: 146
Period size: 33 Copynumber: 3.5 Consensus size: 33
20243393 ACATATAGTG
20243403 TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
1 TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
*
20243436 TACCTTTCATTTTCATA-TGGTATACACAAAGTA
1 TACCTTTCCTTTTCA-AGTGGTATACACAAAGTA
* * *
20243469 TACCTTTCTTTTTCAAGT-GTACACACAAAGTG
1 TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
* **
20243501 TACATAACCTTTTCAAGT
1 TACCTTTCCTTTTCAAGT
20243519 TGTACCATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.37
33 45 0.62
34 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (33 bp):
TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
Found at i:20244910 original size:33 final size:33
Alignment explanation
Indices: 20244868--20244935 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
20244858 CATAAGAAAG
20244868 AAAGGATTTGATTTCATGATAATCTGTTATATT
1 AAAGGATTTGATTTCATGATAATCTGTTATATT
20244901 AAAGGATTTGATTTCATGATAATCTGTTATATT
1 AAAGGATTTGATTTCATGATAATCTGTTATATT
20244934 AA
1 AA
20244936 GGAAAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (33 bp):
AAAGGATTTGATTTCATGATAATCTGTTATATT
Found at i:20244953 original size:30 final size:32
Alignment explanation
Indices: 20244878--20244953 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
20244868 AAAGGATTTG
**
20244878 ATTTCATGATAATCTGTTATATTAAAGGATTTG
1 ATTTCATGATAATCTGTTATATTAAAGGA-TAA
20244911 ATTTCATGATAATCTGTTATATT-AAGGA-AA
1 ATTTCATGATAATCTGTTATATTAAAGGATAA
**
20244941 ATTTTGTGATAAT
1 ATTTCATGATAAT
20244954 TGATAAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 11 0.28
32 5 0.13
33 23 0.59
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (32 bp):
ATTTCATGATAATCTGTTATATTAAAGGATAA
Found at i:20246303 original size:27 final size:27
Alignment explanation
Indices: 20246273--20246327 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
20246263 GTAAGATATG
20246273 AATAAGTCTTTTAGTTCTATAATAAGT
1 AATAAGTCTTTTAGTTCTATAATAAGT
20246300 AATAAGTCTTTTAGTTCTATAATAAGT
1 AATAAGTCTTTTAGTTCTATAATAAGT
20246327 A
1 A
20246328 TGGTTAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (27 bp):
AATAAGTCTTTTAGTTCTATAATAAGT
Found at i:20251006 original size:53 final size:54
Alignment explanation
Indices: 20250875--20251128 Score: 258
Period size: 55 Copynumber: 4.8 Consensus size: 54
20250865 ACACGGGTAC
* * * * *
20250875 CTTACCATTGCCATGACTTGTCATAGTCTTACATCGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
20250924 CTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * * *
20250977 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
*
20251032 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
20251085 CATTACCAATTGTCATG-CTTGGCATTGG-CTTACATGGTATCCTT
1 C-TTACCAA-TGCCATGTCTTGACA-TGGTCTTACATGGTATCCTT
20251129 AAACCCTAAT
Statistics
Matches: 173, Mismatches: 20, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
49 36 0.21
50 1 0.01
52 2 0.01
53 49 0.28
54 31 0.18
55 52 0.30
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:20251066 original size:108 final size:109
Alignment explanation
Indices: 20250922--20251121 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 109
20250912 ATCCTTTTGA
*
20250922 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AAC-TCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTA-GAAACATCACCAA
20250985 -TGCCATGCCTTGGCA-TGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATG-CTTGGCATTGG-CTTACATGGGACCTTTGCCTTATAGT
* * *
20251030 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACATTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAGAAACATCACCAAT
*
20251095 TGTCATGCTTGGCATTGGCTTACATGG
66 TGCCATGCTTGGCATTGGCTTACATGG
20251122 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
107 1 0.01
108 51 0.61
109 22 0.27
110 9 0.11
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (109 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAGAAACATCACCAAT
TGCCATGCTTGGCATTGGCTTACATGGGACCTTTGCCTTATAGT
Found at i:20257980 original size:58 final size:58
Alignment explanation
Indices: 20257896--20258039 Score: 182
Period size: 58 Copynumber: 2.5 Consensus size: 58
20257886 ACATCCCTCT
*
20257896 AACACACTAGAGAGCACTAAAATGCTAAACTTCAAAATAATAGATCAAATCCCTCCAA
1 AACACACTAGAGAGCACTAAAATGCTAAACTTCAAAACAATAGATCAAATCCCTCCAA
* * * * *
20257954 AACACACT-GAAGAGCACTAAAGTGCTAAACTTGAAGACAATAGATCACATCCCTCTAA
1 AACACACTAG-AGAGCACTAAAATGCTAAACTTCAAAACAATAGATCAAATCCCTCCAA
* * * *
20258012 AACACACCAAAAAGCACTAAGATGCTAA
1 AACACACTAGAGAGCACTAAAATGCTAA
20258040 GCCCAAAGAC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 1 0.01
58 72 0.99
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.17
Consensus pattern (58 bp):
AACACACTAGAGAGCACTAAAATGCTAAACTTCAAAACAATAGATCAAATCCCTCCAA
Found at i:20258049 original size:58 final size:57
Alignment explanation
Indices: 20257886--20258062 Score: 180
Period size: 58 Copynumber: 3.1 Consensus size: 57
20257876 GCAACAAATT
* *
20257886 ACATCCCTCT--AACACACTAGAGAGCACTAAAATGCTAAACTTCAAA-ATAATAGATC
1 ACATCCCTCTAAAACACACTAAAGAGCACT-AAATGCTAAAC-TCAAAGACAATAGATC
* * * **
20257942 AAATCCCTCCAAAACACACTGAAGAGCACTAAAGTGCTAAACTTGAAGACAATAGATC
1 ACATCCCTCTAAAACACACTAAAGAGCACTAAA-TGCTAAACTCAAAGACAATAGATC
* * * * * *
20258000 ACATCCCTCTAAAACACACCAAAAAGCACTAAGATGCTAAGCCCAAAGACAACAAATC
1 ACATCCCTCTAAAACACACTAAAGAGCACTAA-ATGCTAAACTCAAAGACAATAGATC
20258058 ACATC
1 ACATC
20258063 TCACATCATT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
56 8 0.08
57 6 0.06
58 83 0.85
59 1 0.01
ACGTcount: A:0.46, C:0.27, G:0.10, T:0.17
Consensus pattern (57 bp):
ACATCCCTCTAAAACACACTAAAGAGCACTAAATGCTAAACTCAAAGACAATAGATC
Found at i:20258914 original size:40 final size:40
Alignment explanation
Indices: 20258870--20258947 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
20258860 ACATACCATG
* * **
20258870 TGGGGATAAAATCGACCCATCCATCCCTGTACACCATATA
1 TGGGGATAAAATCAACCCATCCAACCCTACACACCATATA
20258910 TGGGGATAAAATCAACCCATCCAACCCTACACACCATA
1 TGGGGATAAAATCAACCCATCCAACCCTACACACCATA
20258948 AAGTACCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.19
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCATCCAACCCTACACACCATATA
Found at i:20269261 original size:40 final size:40
Alignment explanation
Indices: 20269217--20269409 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
20269207 GCGTATTGAG
20269217 ATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGA
1 ATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGA
* * ** *
20269257 ATAGCTTCGACTATATAAAGCACTTACTGTGTGAATCAGA
1 ATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGA
** * * * **
20269297 ATAGCTTTAGTTATATATAGAACTTAGTGTGTGAATCGGA
1 ATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGA
** * *
20269337 ATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA-CTGA
1 ATAGCTTCGGCTATATAAAGCACTTAGTGTGC-AAATCGGA
*
20269377 GATAGCTTCGGCTATGA-AAGGCACTTAGTGTGC
1 -ATAGCTTCGGCTAT-ATAAAGCACTTAGTGTGC
20269410 GAGATTATAA
Statistics
Matches: 127, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
40 96 0.76
41 30 0.24
42 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
ATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGA
Found at i:20269303 original size:80 final size:81
Alignment explanation
Indices: 20269214--20269409 Score: 227
Period size: 80 Copynumber: 2.4 Consensus size: 81
20269204 TGTGCGTATT
20269214 GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
1 GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
*
20269279 CTTACTGTGTGA-ATCA
66 CTTACTGTGCGAGA-CA
** * * * ** * **
20269295 GA-ATAGCTTTAGTTATATATAGAACTTAGTGTGTGAATCGGAATAGCTTCGGCTATATATGGCA
1 GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
* *
20269359 CTTAGTGTGCGAGACT
66 CTTACTGTGCGAGACA
*
20269375 GAGATAGCTTCGGCTATGA-AAGGCACTTAGTGTGC
1 GAGATAGCTTCGGCTAT-ATAAAGCACTTAGTGTGC
20269410 GAGATTATAA
Statistics
Matches: 92, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
80 65 0.71
81 26 0.28
82 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (81 bp):
GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
CTTACTGTGCGAGACA
Found at i:20269433 original size:41 final size:41
Alignment explanation
Indices: 20269355--20269456 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 41
20269345 GGCTATATAT
* **
20269355 GGCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATG-AAA
1 GGCACTTAGTGTGCGAGA-TGAAATAGCTTCAACTATGCAAA
* * **
20269396 GGCACTTAGTGTGCGAGATTATAATAGCTTTAACTATGCTTTA
1 GGCACTTAGTGTGCGAGATGA-AATAGCTTCAACTATGC-AAA
20269439 -GCACTTAGTGTGCGAGAT
1 GGCACTTAGTGTGCGAGAT
20269457 ATCGAGTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.04
41 30 0.59
42 18 0.35
43 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (41 bp):
GGCACTTAGTGTGCGAGATGAAATAGCTTCAACTATGCAAA
Found at i:20272610 original size:39 final size:39
Alignment explanation
Indices: 20272556--20272654 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
20272546 CAGTGATATA
*
20272556 TCCGCAGGCTATGTGCTGGAATTATATCCGAACTTAGGG
1 TCCGCAGGCTATGTGCTGGAATTATATCCGAACTTAAGG
* *
20272595 TCCGCAGGCTATGTGCTTGAATTATATCCGGACTTAAGG
1 TCCGCAGGCTATGTGCTGGAATTATATCCGAACTTAAGG
*
20272634 TCCGCAGGCTACGTGCTGGAA
1 TCCGCAGGCTATGTGCTGGAA
20272655 ATATGTTCGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGCAGGCTATGTGCTGGAATTATATCCGAACTTAAGG
Found at i:20276840 original size:23 final size:24
Alignment explanation
Indices: 20276796--20276842 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
20276786 AGACTGTACC
* * *
20276796 TAGATCGATTTTTTGTTGTATTCA
1 TAGATCGATATTTTGATATATTCA
20276820 TAGAT-GATATTTTGATATATTCA
1 TAGATCGATATTTTGATATATTCA
20276843 CGAGATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (24 bp):
TAGATCGATATTTTGATATATTCA
Found at i:20282549 original size:40 final size:40
Alignment explanation
Indices: 20282505--20282635 Score: 169
Period size: 40 Copynumber: 3.2 Consensus size: 40
20282495 ATCGAGATAA
**
20282505 CTTCGGCTATATAAAGCACTTAGTGTCTGAATCGGAATAG
1 CTTCGGCTATATATGGCACTTAGTGTCTGAATCGGAATAG
*
20282545 CTTCGGCTATATATGGAACTTAGTG-CGTGAATCGGAATAG
1 CTTCGGCTATATATGGCACTTAGTGTC-TGAATCGGAATAG
*
20282585 CTTCGGCTATATATGGCACTTAGTGTGC-GAGA-CTGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGT-CTGA-ATCGGA-ATAG
20282626 CTTCGGCTAT
1 CTTCGGCTAT
20282636 GAAAGGCATT
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
39 1 0.01
40 64 0.79
41 15 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (40 bp):
CTTCGGCTATATATGGCACTTAGTGTCTGAATCGGAATAG
Found at i:20282667 original size:41 final size:41
Alignment explanation
Indices: 20282505--20282670 Score: 130
Period size: 40 Copynumber: 4.1 Consensus size: 41
20282495 ATCGAGATAA
* *
20282505 CTTCGGCTATATAAAGCACTTAGTGT-CTGA-A-TCGGAATAG
1 CTTCGGCTATATAAGGCACTTAGTGTGC-GAGACT-GAAATAG
* * * * *
20282545 CTTCGGCTATATATGGAACTTA--GTGCGTGAATCGGAATAG
1 CTTCGGCTATATAAGGCACTTAGTGTGCGAGACT-GAAATAG
* *
20282585 CTTCGGCTATATATGGCACTTAGTGTGCGAGACTGAGATAG
1 CTTCGGCTATATAAGGCACTTAGTGTGCGAGACTGAAATAG
* * *
20282626 CTTCGGCTATGA-AAGGCATTTAGTGTGTGAGA-TTATAATAG
1 CTTCGGCTAT-ATAAGGCACTTAGTGTGCGAGACTGA-AATAG
20282667 CTTC
1 CTTC
20282671 AACTATGCTT
Statistics
Matches: 105, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 51 0.49
41 40 0.38
42 9 0.09
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (41 bp):
CTTCGGCTATATAAGGCACTTAGTGTGCGAGACTGAAATAG
Found at i:20291098 original size:2 final size:2
Alignment explanation
Indices: 20291091--20291117 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20291081 AATTATCTAC
20291091 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20291118 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20293728 original size:16 final size:16
Alignment explanation
Indices: 20293707--20293738 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20293697 TAAAGGAGGA
20293707 GAATAAATTTTTTCTT
1 GAATAAATTTTTTCTT
20293723 GAATAAATTTTTTCTT
1 GAATAAATTTTTTCTT
20293739 TATTTTTCCA
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:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
GAATAAATTTTTTCTT
Found at i:20295378 original size:6 final size:6
Alignment explanation
Indices: 20295367--20295406 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
20295357 GACCAAGGCG
* *
20295367 GCTGTT GCTGTT GCTGTT GCTGTT GTTGTT GCGGTT GCTG
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTG
20295407 AGCAGCAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.15, G:0.38, T:0.47
Consensus pattern (6 bp):
GCTGTT
Found at i:20296287 original size:2 final size:2
Alignment explanation
Indices: 20296280--20296319 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20296270 TAATGTAGCC
20296280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20296320 CGCCAATCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20301805 original size:44 final size:45
Alignment explanation
Indices: 20301715--20301843 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
20301705 GACAGAACAA
*
20301715 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
20301761 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
20301805 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20301844 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:20306058 original size:30 final size:30
Alignment explanation
Indices: 20306024--20306085 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
20306014 ATCCCCGTGG
20306024 AAGAAAGTTCTCAGATTTGGCAAGAAAGGC
1 AAGAAAGTTCTCAGATTTGGCAAGAAAGGC
20306054 AAGAAAGTTCTCAGATTTGGCAAGAAAGGC
1 AAGAAAGTTCTCAGATTTGGCAAGAAAGGC
20306084 AA
1 AA
20306086 ACTAAGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (30 bp):
AAGAAAGTTCTCAGATTTGGCAAGAAAGGC
Found at i:20307783 original size:44 final size:45
Alignment explanation
Indices: 20307693--20307821 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
20307683 GACAGAACAA
*
20307693 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
20307739 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
20307783 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20307822 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:20324411 original size:105 final size:101
Alignment explanation
Indices: 20324219--20324411 Score: 226
Period size: 105 Copynumber: 1.9 Consensus size: 101
20324209 AATTGACGGA
* * * *
20324219 TAAGACCATGGTTGGAGCATGACAAAATTTAAATGTAAGACCATAGCTGGGCTATGGCATTTCAG
1 TAAGACCATGGTTGGACCATGACAAAATTTAAATGTAAGACCATAGCTAGGCTATAGCATCTCAG
**
20324284 TGACAAGACCATAACTGGGTTATGGCACCATGAACG
66 TGACAAGACCATAACAAGGTTATGGCACCATGAACG
* * *
20324320 TAAGACCATGGTTGGACCATGTCAGTATATGTATAAGTGTAAGACCATAGCTAGGCTATAGCATC
1 TAAGACCATGGTTGGACCATGACA--AAAT-T-TAAATGTAAGACCATAGCTAGGCTATAGCATC
* * *
20324385 -CTGATGATAAGACCATAACAATGTTAT
62 TCAG-TGACAAGACCATAACAAGGTTAT
20324412 TATATTACGA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
101 22 0.29
103 3 0.04
104 3 0.04
105 47 0.63
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAAAATTTAAATGTAAGACCATAGCTAGGCTATAGCATCTCAG
TGACAAGACCATAACAAGGTTATGGCACCATGAACG
Found at i:20325550 original size:22 final size:23
Alignment explanation
Indices: 20325525--20325584 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
20325515 AGCTCAACAC
* *
20325525 CGTAGATAGGACT-ACTCAATGT
1 CGTAGACAGGACTGACTCAACGT
20325547 CGTAGACAGGA-TGACTCAACGT
1 CGTAGACAGGACTGACTCAACGT
20325569 CGTAGACAGGAC-GACT
1 CGTAGACAGGACTGACT
20325585 AAAGGCCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGACAGGACTGACTCAACGT
Found at i:20325594 original size:22 final size:22
Alignment explanation
Indices: 20325517--20325594 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
20325507 AACAGAATAG
* * *
20325517 CTCAACACCGTAGATAGGACTA
1 CTCAACGCCGTAGACAGGACGA
* * *
20325539 CTCAATGTCGTAGACAGGATGA
1 CTCAACGCCGTAGACAGGACGA
*
20325561 CTCAACGTCGTAGACAGGACGA
1 CTCAACGCCGTAGACAGGACGA
* *
20325583 CTAAAGGCCGTA
1 CTCAACGCCGTA
20325595 ATTATCGCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (22 bp):
CTCAACGCCGTAGACAGGACGA
Found at i:20325858 original size:27 final size:27
Alignment explanation
Indices: 20325828--20325893 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
20325818 GGGCATAATC
20325828 GTCATTCTACCA-TACAAGGGTATTACG
1 GTCATT-TACCACTACAAGGGTATTACG
** *
20325855 GTCATTTTGCACTACAAGGGTATTTCG
1 GTCATTTACCACTACAAGGGTATTACG
*
20325882 GTGATTTTACCA
1 GTCA-TTTACCA
20325894 ATATTGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.74
28 5 0.16
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTACCACTACAAGGGTATTACG
Found at i:20331916 original size:17 final size:18
Alignment explanation
Indices: 20331883--20331916 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20331873 TTTAAAGAAG
20331883 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
20331901 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
20331917 TTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:20332756 original size:22 final size:22
Alignment explanation
Indices: 20332692--20332746 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
20332682 CACCAAGTCA
*
20332692 ACAAGACGACTCAACGCCGTAG
1 ACAAGACGACTCAACACCGTAG
* *
20332714 ACAGGACGACTCAACAACGTAG
1 ACAAGACGACTCAACACCGTAG
20332736 ACAAGACGACT
1 ACAAGACGACT
20332747 AAAGCCCGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.29, G:0.22, T:0.09
Consensus pattern (22 bp):
ACAAGACGACTCAACACCGTAG
Found at i:20345594 original size:2 final size:2
Alignment explanation
Indices: 20345587--20345613 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20345577 TTTTAAATCC
20345587 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20345614 ATTTATGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20347069 original size:14 final size:14
Alignment explanation
Indices: 20347050--20347087 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20347040 GTTTGCTAAT
*
20347050 AAAATGTTTTCCAG
1 AAAATGATTTCCAG
*
20347064 AAAATGATTTCTAG
1 AAAATGATTTCCAG
20347078 AAAATGATTT
1 AAAATGATTT
20347088 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCAG
Found at i:20347100 original size:20 final size:19
Alignment explanation
Indices: 20347071--20347116 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
20347061 CAGAAAATGA
*
20347071 TTTCTAGAAAATGATTTACT
1 TTTCTAG-AAATAATTTACT
*
20347091 TTTCTGGAAATAATTTACT
1 TTTCTAGAAATAATTTACT
20347110 TTTCTAG
1 TTTCTAG
20347117 TGTTTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (19 bp):
TTTCTAGAAATAATTTACT
Found at i:20347220 original size:20 final size:20
Alignment explanation
Indices: 20347197--20347236 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20347187 TTATTTTTAC
20347197 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
20347217 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
20347237 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:20347241 original size:16 final size:18
Alignment explanation
Indices: 20347192--20347236 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
20347182 AAAAGTTATT
* *
20347192 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
20347210 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
20347230 TTTATAT
1 TTTATAT
20347237 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:20348757 original size:94 final size:93
Alignment explanation
Indices: 20348635--20348821 Score: 322
Period size: 94 Copynumber: 2.0 Consensus size: 93
20348625 GAGTTGCCAG
20348635 GAAATAATAGAAAAAAGATGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGTTCAAT
1 GAAATAATAGAAAAAAGATGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGTTCAAT
*
20348700 CCTAA-TAAAGTAAATAAAGGCGAAGAA
66 CCTAACAAAAGTAAATAAAGGCGAAGAA
*
20348727 GAAATAATAGAAAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGTTCA
1 GAAATAATAG--AAAAAAGATGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGTTCA
*
20348792 ATCCTAACAAAAGTAAATAAAGGCTAAGAA
64 ATCCTAACAAAAGTAAATAAAGGCGAAGAA
20348822 AAGGATTGCT
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
92 10 0.11
94 59 0.66
95 20 0.22
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.18
Consensus pattern (93 bp):
GAAATAATAGAAAAAAGATGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGTTCAAT
CCTAACAAAAGTAAATAAAGGCGAAGAA
Found at i:20351210 original size:14 final size:14
Alignment explanation
Indices: 20351191--20351218 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20351181 TAAAATCAGG
20351191 AAAATATTTTCCAA
1 AAAATATTTTCCAA
20351205 AAAATATTTTCCAA
1 AAAATATTTTCCAA
20351219 GCTTCCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATTTTCCAA
Done.