Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 78
Found at i:2701903 original size:16 final size:16
Alignment explanation
Indices: 2701882--2701913 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2701872 TAGTAACAAT
2701882 ATTGCATTGTTTCCCA
1 ATTGCATTGTTTCCCA
2701898 ATTGCATTGTTTCCCA
1 ATTGCATTGTTTCCCA
2701914 GAACTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
ATTGCATTGTTTCCCA
Found at i:2709681 original size:15 final size:15
Alignment explanation
Indices: 2709661--2709699 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2709651 CACGATTAGA
2709661 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
2709676 ATAAATAAATGAAAG
1 ATAAATAAACAAAAG
2709691 ATGAAATAA
1 AT-AAATAA
2709700 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Found at i:2720457 original size:2 final size:2
Alignment explanation
Indices: 2720450--2720501 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2720440 CTTCTATCCA
2720450 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
2720492 AT AT AT AT AT
1 AT AT AT AT AT
2720502 GGCAAACTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2723817 original size:74 final size:74
Alignment explanation
Indices: 2723696--2723843 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
2723686 TGCAAATAAG
2723696 AAGAGAAATTATCATTTTGTTAAACAAAAATGAAGCACTGGAGACTGTTTTGCAGGTATCTTGCA
1 AAGAGAAATTATCATTTTGTTAAACAAAAATGAAGCACTGGAGACTGTTTTGCAGGTATCTTGCA
2723761 TATACTGGC
66 TATACTGGC
2723770 AAGAGAAATTATCATTTTGTTAAACAAAAATGAAGCACTGGAGACTGTTTTGCAGGTATCTTGCA
1 AAGAGAAATTATCATTTTGTTAAACAAAAATGAAGCACTGGAGACTGTTTTGCAGGTATCTTGCA
2723835 TATACTGGC
66 TATACTGGC
2723844 TAAAGGTTAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (74 bp):
AAGAGAAATTATCATTTTGTTAAACAAAAATGAAGCACTGGAGACTGTTTTGCAGGTATCTTGCA
TATACTGGC
Found at i:2729604 original size:19 final size:19
Alignment explanation
Indices: 2729580--2729618 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2729570 TCGAATGCAT
2729580 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2729599 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2729618 T
1 T
2729619 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2729635 original size:65 final size:64
Alignment explanation
Indices: 2729536--2729726 Score: 208
Period size: 64 Copynumber: 3.0 Consensus size: 64
2729526 ATGCATCAGT
** * * * **
2729536 CCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCATTCCATGCACCGATGCACTC
1 CCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAA
*
2729599 T
64 G
* * *
2729600 CCATGCATCGATGCACTCTGAATA-TTTTCAAAACATTGAATGCATTTGATGCATCGATGCACAA
1 CCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACAA
2729664 G
64 G
**
2729665 CCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 CCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
2729727 CTTGGTGCAC
Statistics
Matches: 106, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
63 6 0.06
64 51 0.48
65 49 0.46
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:2729720 original size:64 final size:65
Alignment explanation
Indices: 2729566--2729726 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
2729556 GAATTAATTG
* * *** *
2729566 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
2729631 AACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
2729694 A
65 A
2729695 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
2729727 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2729741 original size:64 final size:64
Alignment explanation
Indices: 2729566--2729746 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 64
2729556 GAATTAATTG
* * * *
2729566 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* * ** **
2729631 AACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
2729695 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
2729747 AGTGTTCCAA
Statistics
Matches: 97, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 50 0.52
65 47 0.48
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:2735511 original size:20 final size:21
Alignment explanation
Indices: 2735488--2735536 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2735478 TTCATGCACT
2735488 GATGCAT-TT-AACAATGCATC
1 GATGCATCTTGAA-AATGCATC
*
2735508 GATGCATCCTTGAATATGCATC
1 GATGCAT-CTTGAAAATGCATC
2735530 GATGCAT
1 GATGCAT
2735537 AAGACCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (21 bp):
GATGCATCTTGAAAATGCATC
Found at i:2738144 original size:19 final size:19
Alignment explanation
Indices: 2738120--2738158 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2738110 TCGAATGCAT
2738120 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2738139 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2738158 T
1 T
2738159 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2738258 original size:64 final size:65
Alignment explanation
Indices: 2738106--2738265 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
2738096 GAATTAATTG
* * ** *
2738106 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACTAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
2738171 AACATCGAATGCATTTGATGCATCGATGCA-TAAGCCATGCATCGATGCA-TCAGGCTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACT-AGCCATGCATCGATGCACTCAGAATA-TTTTC
2738234 -A
64 AA
2738235 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
2738266 ACTTGGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACTAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2738281 original size:64 final size:64
Alignment explanation
Indices: 2738106--2738286 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 64
2738096 GAATTAATTG
* * * *
2738106 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* * ** **
2738171 AACATCGAATGCATTTGATGCATCGATGCATAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
2738235 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
2738287 AGTGTTCCAA
Statistics
Matches: 97, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 50 0.52
65 47 0.48
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:2739367 original size:25 final size:25
Alignment explanation
Indices: 2739339--2739388 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2739329 GAGTGATCTC
**
2739339 ATAACAAATGAAGAATCGATTGGAA
1 ATAACAAATGAAGAAAAGATTGGAA
* *
2739364 ATAACAAGTGGAGAAAAGATTGGAA
1 ATAACAAATGAAGAAAAGATTGGAA
2739389 TGGAAAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.24, T:0.18
Consensus pattern (25 bp):
ATAACAAATGAAGAAAAGATTGGAA
Found at i:2741761 original size:17 final size:16
Alignment explanation
Indices: 2741745--2741774 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2741735 ATAATTAATT
2741745 TTAAA-ATATTTTTAA
1 TTAAATATATTTTTAA
2741760 TTAAATATATTTTTA
1 TTAAATATATTTTTA
2741775 TCATCAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATATATTTTTAA
Found at i:2742141 original size:30 final size:30
Alignment explanation
Indices: 2742096--2742164 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
2742086 TTTATTTAAG
*
2742096 TACCTAAA-ATATA-TTTTGATCAAAATAAA
1 TACCTAAAGTTATATTTTTG-TCAAAATAAA
**
2742125 TACCTAAAGTTATATTTTTGTCAAAATAGG
1 TACCTAAAGTTATATTTTTGTCAAAATAAA
2742155 TACCTAAAGT
1 TACCTAAAGT
2742165 AGGGGGCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 22 0.63
31 5 0.14
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (30 bp):
TACCTAAAGTTATATTTTTGTCAAAATAAA
Found at i:2774432 original size:2 final size:2
Alignment explanation
Indices: 2774425--2774454 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2774415 TCTGTCTTTA
2774425 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
2774455 GCGCGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2775909 original size:23 final size:24
Alignment explanation
Indices: 2775883--2775945 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
2775873 TTTGAGTTTG
*
2775883 AGCTTGAATCGAGCTCAA-AATCA
1 AGCTTCAATCGAGCTCAAGAATCA
**
2775906 AGCTTCAATCGAGCTCAAGTCTCA
1 AGCTTCAATCGAGCTCAAGAATCA
2775930 AGCTTCAATCGAGCTC
1 AGCTTCAATCGAGCTC
2775946 CTAAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (24 bp):
AGCTTCAATCGAGCTCAAGAATCA
Found at i:2777195 original size:17 final size:16
Alignment explanation
Indices: 2777166--2777205 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2777156 AAATAATAAG
2777166 AATATTAAATTTAAAT
1 AATATTAAATTTAAAT
* *
2777182 AATATTTAATTTTAA-
1 AATATTAAATTTAAAT
2777197 AATATTAAA
1 AATATTAAA
2777206 ATCCAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTAAATTTAAAT
Found at i:2777684 original size:36 final size:36
Alignment explanation
Indices: 2777621--2777996 Score: 231
Period size: 36 Copynumber: 10.1 Consensus size: 36
2777611 TATATAGTTT
*
2777621 TTTTTAAAACATTTTTTGAAAATATATATATTATATAG
1 TTTTTAAAATA-TTTTTGAAAA-ATATATATTATATAG
*
2777659 TTTTTAAAATATTTTTGAAAAATATATAATATATAG
1 TTTTTAAAATATTTTTGAAAAATATATATTATATAG
* *
2777695 TTTTTAAAACATTTTATTAAAACAATTTTTGAAAATATATATATTATA-
1 TTTTTAAAATA-TTT-TTGAAA-AA----T----ATATAT-TA-TATAG
* * *
2777743 TAGTTTTTAAAATATTTTTGAAAAATATATAATATATAG
1 T-TTTTA--AAATATTTTTGAAAAATATATATTATATAG
* * *
2777782 TTTTTAAAACATTTTTG-AAAAT-TATATAATATAA
1 TTTTTAAAATATTTTTGAAAAATATATATTATATAG
* * * *
2777816 TTTTTAAAATCTTTTAGAAAATTATATAATATATAG
1 TTTTTAAAATATTTTTGAAAAATATATATTATATAG
* *
2777852 TTTTTGAAAACA-TTTTGAAAACATTTATATATTATTTAG
1 TTTTT-AAAATATTTTTGAAAA-A--TATATATTATATAG
*
2777891 GTTTTAAAA-ATCATTTTG-AAAATATATA-TA-ATA-
1 TTTTTAAAATAT--TTTTGAAAAATATATATTATATAG
* *
2777924 ----TAAAATCA-TTTTGAAAATATATATAATATATATT
1 TTTTTAAAAT-ATTTTTGAAAA-ATATATATTATATA-G
*
2777958 TTTTTAAAATATTTTTGAAATATATATATTATATAG
1 TTTTTAAAATATTTTTGAAAAATATATATTATATAG
2777994 TTT
1 TTT
2777997 ATAGCATATT
Statistics
Matches: 265, Mismatches: 34, Indels: 80
0.70 0.09 0.21
Matches are distributed among these distances:
28 5 0.02
29 8 0.03
30 7 0.03
31 3 0.01
32 3 0.01
34 25 0.09
35 11 0.04
36 65 0.25
37 32 0.12
38 41 0.15
39 24 0.09
40 10 0.04
43 1 0.00
44 1 0.00
47 5 0.02
48 5 0.02
49 12 0.05
50 3 0.01
51 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (36 bp):
TTTTTAAAATATTTTTGAAAAATATATATTATATAG
Found at i:2777715 original size:87 final size:87
Alignment explanation
Indices: 2777619--2777796 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 87
2777609 AATATATAGT
* *
2777619 TTTTTTTAAAACATTTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTTTGAAAAATAT
1 TTTTATTAAAACAATTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTTTGAAAAATAT
2777684 ATAATATATAGTTTTTAAAACA
66 ATAATATATAGTTTTTAAAACA
2777706 TTTTATTAAAACAATTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTTTGAAAAATAT
1 TTTTATTAAAACAATTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTTTGAAAAATAT
2777771 ATAATATATAGTTTTTAAAACA
66 ATAATATATAGTTTTTAAAACA
2777793 TTTT
1 TTTT
2777797 TGAAAATTAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (87 bp):
TTTTATTAAAACAATTTTTGAAAATATATATATTATATAGTTTTTAAAATATTTTTGAAAAATAT
ATAATATATAGTTTTTAAAACA
Found at i:2777755 original size:25 final size:26
Alignment explanation
Indices: 2777670--2777757 Score: 85
Period size: 25 Copynumber: 3.5 Consensus size: 26
2777660 TTTTAAAATA
*
2777670 TTTTTGAAAA-ATATATAATATATAG
1 TTTTTGAAAATATATATATTATATAG
* * * * *
2777695 TTTTT-AAAACAT-TTTATTAAAACAA
1 TTTTTGAAAATATATATATT-ATATAG
2777720 TTTTTGAAAATATATATATTATATAG
1 TTTTTGAAAATATATATATTATATAG
2777746 TTTTT-AAAATAT
1 TTTTTGAAAATAT
2777758 TTTTGAAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
24 8 0.16
25 22 0.45
26 14 0.29
27 5 0.10
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
TTTTTGAAAATATATATATTATATAG
Found at i:2777836 original size:70 final size:72
Alignment explanation
Indices: 2777711--2777996 Score: 283
Period size: 70 Copynumber: 4.0 Consensus size: 72
2777701 AAACATTTTA
2777711 TTAAAACAATTTTTGAAAATATATATATTATATAG-TTTTTAAAATATTTTTGAAAAATATATAA
1 TTAAAAC-A-TTTTGAAAATATATATA-TATATAGATTTTTAAAATATTTTTGAAAAATATATAA
2777775 TATATAGTTT
63 TATATAGTTT
* * *
2777785 TTAAAACATTTTTGAAAAT-TATATA-ATATA-ATTTTTAAAATCTTTTAGAAAATTATATAATA
1 TTAAAACA-TTTTGAAAATATATATATATATAGATTTTTAAAATATTTTTGAAAAATATATAATA
2777847 TATAGTTT
65 TATAGTTT
* * * *
2777855 TTGAAAACATTTTGAAAACATTTATATATTATTTAGGTTTTAAAAATCA-TTTTG-AAAATATAT
1 TT-AAAACATTTTG-AAA-ATATATATA-TATATAGATTTTTAAAAT-ATTTTTGAAAAATATAT
2777918 -ATA-ATA----
61 AATATATAGTTT
** * *
2777924 -TAAAATCATTTTGAAAATATATATAATATATATTTTTTTAAAATATTTTTGAAATATATATATT
1 TTAAAA-CATTTTGAAAATATATAT-ATATATAGATTTTTAAAATATTTTTGAAAAATATATAAT
2777988 ATATAGTTT
64 ATATAGTTT
2777997 ATAGCATATT
Statistics
Matches: 177, Mismatches: 16, Indels: 39
0.76 0.07 0.17
Matches are distributed among these distances:
65 1 0.01
66 26 0.15
67 16 0.09
68 10 0.06
69 3 0.02
70 48 0.27
71 9 0.05
72 8 0.05
73 21 0.12
74 10 0.06
75 12 0.07
76 13 0.07
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (72 bp):
TTAAAACATTTTGAAAATATATATATATATAGATTTTTAAAATATTTTTGAAAAATATATAATAT
ATAGTTT
Found at i:2777869 original size:11 final size:11
Alignment explanation
Indices: 2777853--2777877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2777843 AATATATAGT
2777853 TTTTGAAAACA
1 TTTTGAAAACA
2777864 TTTTGAAAACA
1 TTTTGAAAACA
2777875 TTT
1 TTT
2777878 ATATATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:2777969 original size:26 final size:28
Alignment explanation
Indices: 2777897--2777953 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2777887 TTAGGTTTTA
2777897 AAAATCATTTTGAAAATATATATAATAT
1 AAAATCATTTTGAAAATATATATAATAT
2777925 AAAATCATTTTGAAAATATATATAATAT
1 AAAATCATTTTGAAAATATATATAATAT
2777953 A
1 A
2777954 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATCATTTTGAAAATATATATAATAT
Found at i:2779296 original size:15 final size:17
Alignment explanation
Indices: 2779278--2779313 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
2779268 TTTGATTTGA
2779278 TTTTCTTTT-CTT-TTT
1 TTTTCTTTTACTTCTTT
2779293 TTTTCTTTTACTTCTTT
1 TTTTCTTTTACTTCTTT
2779310 TTTT
1 TTTT
2779314 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTTTTACTTCTTT
Found at i:2779327 original size:20 final size:20
Alignment explanation
Indices: 2779288--2779330 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2779278 TTTTCTTTTC
*
2779288 TTTTTTTTTCTTTTACTTCT
1 TTTTTTTTTATTTTACTTCT
2779308 TTTTTTATTTATTTTA-TTCT
1 TTTTTT-TTTATTTTACTTCT
2779328 TTT
1 TTT
2779331 ACTTTGACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTATTTTACTTCT
Found at i:2779408 original size:30 final size:29
Alignment explanation
Indices: 2779372--2779472 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
2779362 ATTTTTTTGC
2779372 TTTATTTAATTTTTTATTTACTATTTTATT
1 TTTATTTAATTTTTTATTTA-TATTTTATT
* *
2779402 TTTATTTTCATTTTTTTATTT-TTTTTTATT
1 TTTA-TTT-AATTTTTTATTTATATTTTATT
* *
2779432 TTCA-TT-ATTTTTT-TATATATTTTATAT
1 TTTATTTAATTTTTTATTTATATTTTAT-T
*
2779459 ATT-TTTAATTTTTT
1 TTTATTTAATTTTTT
2779473 CTCTTGATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
25 2 0.04
26 13 0.23
27 4 0.07
28 9 0.16
30 15 0.26
31 3 0.05
32 11 0.19
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTATTTAATTTTTTATTTATATTTTATT
Found at i:2779416 original size:18 final size:17
Alignment explanation
Indices: 2779372--2779447 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 17
2779362 ATTTTTTTGC
*
2779372 TTTATTTAATTTTTTATT
1 TTTATTTTA-TTTTTATT
*
2779390 TACTATTTTATTTTTATT
1 T-TTATTTTATTTTTATT
* * *
2779408 TTCATTTTTTTATTTTTT
1 TTTATTTTATT-TTTATT
*
2779426 TTTATTTTCATTATT-TT
1 TTTATTTT-ATTTTTATT
2779443 TTTAT
1 TTTAT
2779448 ATATTTTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
17 14 0.30
18 24 0.52
19 8 0.17
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTATTTTTATT
Found at i:2779439 original size:19 final size:18
Alignment explanation
Indices: 2779393--2779464 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 18
2779383 TTTTATTTAC
*
2779393 TATTTTATT-TTTATTTT
1 TATTTTATTATTTTTTTT
* *
2779410 CATTTTTTTATTTTTTTT
1 TATTTTATTATTTTTTTT
2779428 TATTTTCATTATTTTTTTAT
1 TATTTT-ATTATTTTTTT-T
2779448 ATATTTTATATATTTTT
1 -TATTTTAT-TATTTTT
2779465 AATTTTTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.16
18 12 0.27
19 10 0.22
20 3 0.07
21 13 0.29
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTATTATTTTTTTT
Found at i:2779442 original size:24 final size:25
Alignment explanation
Indices: 2779393--2779456 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
2779383 TTTTATTTAC
*
2779393 TATTTTATTTTTATTTTCATTTTTT
1 TATTTTATTTTTATTTTCATTATTT
2779418 TATTTT-TTTTTATTTTCATTATTT
1 TATTTTATTTTTATTTTCATTATTT
2779442 T-TTTATATATTTTAT
1 TATTT-TAT-TTTTAT
2779457 ATATTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 3 0.09
24 19 0.54
25 7 0.20
26 6 0.17
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (25 bp):
TATTTTATTTTTATTTTCATTATTT
Found at i:2779465 original size:19 final size:21
Alignment explanation
Indices: 2779418--2779473 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
2779408 TTCATTTTTT
* *
2779418 TATTTTTTTTTATTTTCATTA
1 TATTTTTATATATTTTCATTA
*
2779439 TTTTTTTATATATTTT-A-TA
1 TATTTTTATATATTTTCATTA
*
2779458 TATTTTTA-ATTTTTTC
1 TATTTTTATATATTTTC
2779474 TCTTGATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.21
19 9 0.31
20 1 0.03
21 13 0.45
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTATATATTTTCATTA
Found at i:2783185 original size:21 final size:20
Alignment explanation
Indices: 2783138--2783214 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
2783128 TATCTTATAT
*
2783138 CACTATAAATAAACTAATAG
1 CACTATAAATAAAATAATAG
2783158 CACTATAAATAAAATAATAAG
1 CACTATAAATAAAATAAT-AG
* **
2783179 CATTATAAATATTATAATAG
1 CACTATAAATAAAATAATAG
*
2783199 CACTATGAATAAAATA
1 CACTATAAATAAAATA
2783215 TAATAAAGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (20 bp):
CACTATAAATAAAATAATAG
Found at i:2783763 original size:29 final size:28
Alignment explanation
Indices: 2783730--2783952 Score: 182
Period size: 29 Copynumber: 7.6 Consensus size: 28
2783720 TTTTGGTTAT
* * *
2783730 GGTGTTATTTTCGTAATTATTTTTAAAA
1 GGTGATATTTTGGTAATTATTGTTAAAA
* * *
2783758 GTGTGTTATTTTCGTATTTATT-TTAAAAAA
1 G-GTGATATTTTGGTAATTATTGTT--AAAA
*
2783788 GG-GTATTATTTTCGTAATTAATT-TTAAAA
1 GGTG-A-TATTTTGGTAATT-ATTGTTAAAA
*
2783817 CGGTGATATTTTGGCAATTATTGTTAAAA
1 -GGTGATATTTTGGTAATTATTGTTAAAA
**
2783846 TAATGATATTTTGGTAATTATTGTTAAAA
1 -GGTGATATTTTGGTAATTATTGTTAAAA
*
2783875 CGGTGCTATTTTGGTAATTATTGTTAAAA
1 -GGTGATATTTTGGTAATTATTGTTAAAA
**
2783904 CAATGATATTTTGGTAATTATTGTTAAAA
1 -GGTGATATTTTGGTAATTATTGTTAAAA
* *
2783933 GCAATGATATTTTGATAATT
1 G--GTGATATTTTGGTAATT
2783953 GTTTAAAAAA
Statistics
Matches: 166, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
28 7 0.04
29 117 0.70
30 36 0.22
31 6 0.04
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.48
Consensus pattern (28 bp):
GGTGATATTTTGGTAATTATTGTTAAAA
Found at i:2783874 original size:58 final size:56
Alignment explanation
Indices: 2783735--2783978 Score: 230
Period size: 58 Copynumber: 4.2 Consensus size: 56
2783725 GTTATGGTGT
* * * * * *
2783735 TATTTTCGTAATTATTTTTAAAA-GTGTGTTATTTTCGTATTTATT-TTAAAAAAGGGTA
1 TATTTTGGTAATTATTGTTAAAACG-GTGATATTTT-GGAATTATTGTTAAAAAA-TG-A
*
2783793 TTATTTTCGTAATTAATT-TTAAAACGGTGATATTTTGGCAATTATTGTTAAAATAATGA
1 -TATTTTGGTAATT-ATTGTTAAAACGGTGATATTTTGG-AATTATTGTTAAAA-AATGA
*
2783852 TATTTTGGTAATTATTGTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAACAATGA
1 TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGG-AATTATTGTTAAAA-AATGA
** *
2783910 TATTTTGGTAATTATTGTTAAAAGCAATGATATTTT-G-ATAATTGTTTAAAAAATGA
1 TATTTTGGTAATTATTGTTAAAA-CGGTGATATTTTGGAATTATTG-TTAAAAAATGA
2783966 TATTTCT-GTAATT
1 TATTT-TGGTAATT
2783979 TTTTACTGTG
Statistics
Matches: 164, Mismatches: 12, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
56 22 0.13
57 10 0.06
58 75 0.46
59 44 0.27
60 11 0.07
61 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (56 bp):
TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGGAATTATTGTTAAAAAATGA
Found at i:2783941 original size:117 final size:113
Alignment explanation
Indices: 2783735--2783978 Score: 257
Period size: 117 Copynumber: 2.1 Consensus size: 113
2783725 GTTATGGTGT
* * *
2783735 TATTTTCGTAATTATTTTTAAAAGTGTGTTATTTTCGTATTTATTTTAAAAAAGGGTATTATTTT
1 TATTTT-GTAATTATTGTTAAAAGTGTGCTATTTTCGTAATTATTTTAAAAAAGGGTATTATTTT
** *
2783800 CGTAATTAATTTTAAAACGGTGATATTTTGGCAATTATTG-TTAAAATAATGA
65 CGTAATTAATTTTAAAACAATGATATTTT-G--ATAATTGTTTAAAA-AATGA
* *
2783852 TATTTTGGTAATTATTGTTAAAACG-GTGCTATTTTGGTAATTATTGTTAAAACAA-TG-A-TAT
1 TATTTT-GTAATTATTGTTAAAA-GTGTGCTATTTTCGTAATTATT-TTAAAA-AAGGGTATTAT
*
2783913 TTTGGTAATT-ATTGTTAAAAGCAATGATATTTTGATAATTGTTTAAAAAATGA
62 TTTCGTAATTAATT-TTAAAA-CAATGATATTTTGATAATTGTTTAAAAAATGA
2783966 TATTTCTGTAATT
1 TATTT-TGTAATT
2783979 TTTTACTGTG
Statistics
Matches: 110, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
114 22 0.20
115 10 0.09
116 19 0.17
117 49 0.45
118 8 0.07
119 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (113 bp):
TATTTTGTAATTATTGTTAAAAGTGTGCTATTTTCGTAATTATTTTAAAAAAGGGTATTATTTTC
GTAATTAATTTTAAAACAATGATATTTTGATAATTGTTTAAAAAATGA
Found at i:2783966 original size:26 final size:26
Alignment explanation
Indices: 2783836--2783983 Score: 102
Period size: 29 Copynumber: 5.3 Consensus size: 26
2783826 TTTGGCAATT
*
2783836 ATTG-TTAAAATAATGATATTTTGGTA
1 ATTGTTTAAAACAATGATATTTT-GTA
* ** *
2783862 ATTATTGTTAAAACGGTGCTATTTTGGTA
1 ATT-GT-TTAAAACAATGATATTTT-GTA
*
2783891 ATTATTGTTAAAACAATGATATTTTGGTA
1 ATT-GT-TTAAAACAATGATATTTT-GTA
*
2783920 ATTATTGTTAAAAGCAATGATATTTTGATA
1 ATT-GT-TTAAAA-CAATGATATTTTG-TA
2783950 ATTGTTTAAAA-AATGATATTTCTGTA
1 ATTGTTTAAAACAATGATATTT-TGTA
*
2783976 ATTTTTTA
1 ATTGTTTA
2783984 CTGTGGACTA
Statistics
Matches: 106, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
26 22 0.21
27 2 0.02
28 6 0.06
29 59 0.56
30 17 0.16
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (26 bp):
ATTGTTTAAAACAATGATATTTTGTA
Found at i:2787071 original size:95 final size:95
Alignment explanation
Indices: 2786949--2787131 Score: 258
Period size: 95 Copynumber: 1.9 Consensus size: 95
2786939 TTATAATATT
* * **
2786949 TATACAATAAAGCTGGAGCTGTTCCTCTAAAACAATTGGTTAAACTCCCCGGGTTTATGGATAAG
1 TATACAATAAAGCTGGAGCTGTCCCTCTAAAACAATTGGTTAAACGCCCCGACTTTATGGATAAG
*
2787014 ATTCAACTAGCCTGATAAAGGTGATTATAA
66 ATTCAACTAACCTGATAAAGGTGATTATAA
* * * * * *
2787044 TATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAT
1 TATACAATAAAGCTGGAGCTGTCCCTCTAAAACAATTGGTTAAACGCCCCGACTTTATGGATAAG
*
2787109 ATTCAGCTAACCTGATAAAGGTG
66 ATTCAACTAACCTGATAAAGGTG
2787132 TTTACATATT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTGGAGCTGTCCCTCTAAAACAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAACTAACCTGATAAAGGTGATTATAA
Found at i:2789179 original size:84 final size:84
Alignment explanation
Indices: 2788329--2789178 Score: 903
Period size: 84 Copynumber: 10.2 Consensus size: 84
2788319 TCTCTCAGCC
* *
2788329 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
* *
2788393 TAAGGGTTATCTGCCAACCA
65 GAAGGGCTATCTGCCAACCA
*
2788413 AAGACCTTCGAGTTCGATTACGCTCAGCTCTAAC-GCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTC-AACGGCACATCATTTGCAGCATAGCTTAAGTCGA
2788477 GAAGGGCTATCTG----CCA
65 GAAGGGCTATCTGCCAACCA
* * * ** * * * * * *
2788493 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAA-TACACATCATTTACAGTATAACTCAAGGCT
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TC-AACGGCACATCATTTGCAGCATAGCTTAAGTCG
* *
2788557 AGAAGGGTTATCTGCCAACAA
64 AGAAGGGCTATCTGCCAACCA
* * * * * * * *
2788578 AAGAACTTTGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
*
2788643 AAGGGCTATCTACC-ACCAA
66 AAGGGCTATCTGCCAACC-A
* * * *
2788662 AAAACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAATCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
*
2788727 AAGGGCTATCTGCTAACCA
66 AAGGGCTATCTGCCAACCA
* * * * * * * * *
2788746 AAGA-CTTCAAGTTCGACTACGCTCAGGTTCGAGGGTACATCATTTGCAGCAAAACTCAAGTCTA
1 AAGACCTTCGAGTTCGACTACGCTCA-GCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * *
2788810 GAAAGGTTATCTGCCAA-CG
65 GAAGGGCTATCTGCCAACCA
* ** * *
2788829 AATACCTTTTAGTTCGACTACGCTCAGCTCAACGACACATTATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
*
2788894 AAGGGTTATCTGCCAACCA
66 AAGGGCTATCTGCCAACCA
* * * * * * *
2788913 AAGACCCTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * *
2788978 GAAGAGTTATCTGTCAA-CA
65 GAAGGGCTATCTGCCAACCA
* * * * * * *
2788997 AAGTCCTTTGAGTTCGACTATGCTCAGCTCAACGACATATCATTTGTAGCATAGCATAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
2789062 AAGGGCTATCTGCCAACCA
66 AAGGGCTATCTGCCAACCA
* * * * * *
2789081 AAAACCTTCAAGTTTGACTACGCTCAGCTCAATGGCATATCATTTGCAGCATAGCTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
2789146 AAGGGCTATCTGCCAACCA
66 AAGGGCTATCTGCCAACCA
2789165 AAGACCTTCGAGTT
1 AAGACCTTCGAGTT
2789179 TAATTACATT
Statistics
Matches: 630, Mismatches: 120, Indels: 32
0.81 0.15 0.04
Matches are distributed among these distances:
80 29 0.05
81 39 0.06
83 112 0.18
84 378 0.60
85 72 0.11
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAACCA
Found at i:2789743 original size:37 final size:35
Alignment explanation
Indices: 2789702--2790050 Score: 349
Period size: 37 Copynumber: 9.5 Consensus size: 35
2789692 TGAAACTACG
2789702 TATATAATATATAGTTTTTAAAAACATTTATAAAAAA
1 TATATAATATATAGTTTTT-AAAACATTT-TAAAAAA
* *
2789739 TATATAATATATAGTTTTGAAATCATTTTAAAAACA
1 TATATAATATATAGTTTTTAAAACATTTTAAAAA-A
* **
2789775 TTTATATATTATATAGTTTTTAAAACATTTTTGAAAA
1 --TATATAATATATAGTTTTTAAAACATTTTAAAAAA
* * * *
2789812 T-TATATTATATAATTTTTAAAACCTTTTAGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTA-AAAAA
*
2789847 TATATAATATATAGTTTTTGAAAACATTTTTAAAATA
1 TATATAATATATAGTTTTT-AAAACA-TTTTAAAAAA
*
2789884 TATATAATATATAGTTTTTAAAACATTTTGAAAATATT
1 TATATAATATATAGTTTTTAAAACATTTT-AAAA-A-A
* *
2789922 TATATATTATATAGTTTTTAAAAATCATTTTGAAAATA
1 TATATAATATATAGTTTTT-AAAA-CATTTT-AAAAAA
* * *
2789960 TATCTAATATATAGTTTTTTAAATCATTTTGAAAATA
1 TATATAATATATAG-TTTTTAAAACATTTT-AAAAAA
* * *
2789997 TATATAATATATAGTTTTTAAAAATATTTTTGAAATA
1 TATATAATATATAGTTTTT-AAAACA-TTTTAAAAAA
*
2790034 TATATATTATATAGTTT
1 TATATAATATATAGTTT
2790051 ATATCATATT
Statistics
Matches: 267, Mismatches: 30, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
34 25 0.09
35 15 0.06
36 39 0.15
37 97 0.36
38 71 0.27
39 9 0.03
40 11 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAACATTTTAAAAAA
Found at i:2789881 original size:11 final size:11
Alignment explanation
Indices: 2789861--2790034 Score: 51
Period size: 11 Copynumber: 14.1 Consensus size: 11
2789851 TAATATATAG
*
2789861 TTTTTGAAAACA
1 TTTTT-AAAATA
2789873 TTTTTAAAATA
1 TTTTTAAAATA
* *
2789884 TATATAATATATA
1 TTTTTAA-A-ATA
*
2789897 GTTTTTAAAACA
1 -TTTTTAAAATA
*
2789909 TTTTGAAAATA
1 TTTTTAAAATA
*
2789920 TTTATATATTATATA
1 TTT-T-TA--AAATA
2789935 GTTTTTAAAAATCA
1 -TTTTT-AAAAT-A
*
2789949 TTTTGAAAATA
1 TTTTTAAAATA
* *
2789960 TATCTAATATATA
1 TTTTTAA-A-ATA
*
2789973 GTTTTTTAAATCA
1 -TTTTTAAAAT-A
*
2789986 TTTTGAAAATA
1 TTTTTAAAATA
* *
2789997 TATATAATATATA
1 TTTTTAA-A-ATA
2790010 GTTTTTAAAAATA
1 -TTTTT-AAAATA
*
2790023 TTTTTGAAATA
1 TTTTTAAAATA
2790034 T
1 T
2790035 ATATATTATA
Statistics
Matches: 118, Mismatches: 26, Indels: 37
0.65 0.14 0.20
Matches are distributed among these distances:
11 38 0.32
12 31 0.26
13 23 0.19
14 15 0.13
15 8 0.07
16 3 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:2790002 original size:145 final size:145
Alignment explanation
Indices: 2789702--2790050 Score: 481
Period size: 145 Copynumber: 2.4 Consensus size: 145
2789692 TGAAACTACG
* * *
2789702 TATATAATATATAGTTTTTAAAAACATTTATAAAAAATATATAATATATAGTTTTGAAATCATTT
1 TATATAATATATAGTTTTTAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATTT
2789767 TAAAAACATTTATATATTATATAGTTTTTAAAACATTTTTGAAAATTATATTATATAATTTTTAA
66 TAAAAACATTTATATATTATATAGTTTTTAAAACATTTTTGAAAATTATATTATATAATTTTTAA
*
2789832 AACCTTTTAGAAA-A
131 AACATTTTAGAAATA
* *
2789846 TTATATAATATATAGTTTTTGAAAACATTTTTAAAATATATATAATATATAGTTTTTAAAACATT
1 -TATATAATATATAGTTTTTAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATT
* *
2789911 TTGAAAATATTTATATATTATATAGTTTTTAAAA-ATCATTTTGAAAA-TATATCTAATATATAG
65 TTAAAAACATTTATATATTATATAGTTTTTAAAACAT--TTTTGAAAATTATAT-T-ATATA-A-
*
2789974 TTTTTTAAATCATTTT-GAAAATA
124 -TTTTTAAAACATTTTAG-AAATA
* * *
2789997 TATATAATATATAGTTTTTAAAAATATTTTTGAAATATATATATTATATAGTTT
1 TATATAATATATAGTTTTTAAAAACATTTTTAAAATATATATAATATATAGTTT
2790051 ATATCATATT
Statistics
Matches: 182, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
144 2 0.01
145 96 0.53
146 10 0.05
147 5 0.03
148 1 0.01
149 1 0.01
150 66 0.36
151 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (145 bp):
TATATAATATATAGTTTTTAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATTT
TAAAAACATTTATATATTATATAGTTTTTAAAACATTTTTGAAAATTATATTATATAATTTTTAA
AACATTTTAGAAATA
Found at i:2790076 original size:25 final size:24
Alignment explanation
Indices: 2790048--2790094 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2790038 TATTATATAG
2790048 TTTATATCATATTATTATTATTTGT
1 TTTATATCATATTATT-TTATTTGT
* *
2790073 TTTATTTCATTTTATTTTATTT
1 TTTATATCATATTATTTTATTT
2790095 TATTTCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTATATCATATTATTTTATTTGT
Found at i:2790087 original size:10 final size:10
Alignment explanation
Indices: 2790072--2790103 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2790062 TTATTATTTG
2790072 TTTTATTTCA
1 TTTTATTTCA
*
2790082 TTTTATTTTA
1 TTTTATTTCA
2790092 TTTTATTTCA
1 TTTTATTTCA
2790102 TT
1 TT
2790104 CATTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATTTCA
Found at i:2791391 original size:24 final size:23
Alignment explanation
Indices: 2791344--2791391 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2791334 TCTGAATTTA
* **
2791344 TTTTTCTTCTTTTTTTCGTTTTC
1 TTTTACTTCTTTTTTTAATTTTC
2791367 TTTTACTTCTTTTTTTAATTATTC
1 TTTTACTTCTTTTTTTAATT-TTC
2791391 T
1 T
2791392 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTACTTCTTTTTTTAATTTTC
Found at i:2791396 original size:16 final size:16
Alignment explanation
Indices: 2791373--2791416 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2791363 TTTCTTTTAC
2791373 TTCT-TTTTTTAATTA
1 TTCTATTTTTTAATTA
*
2791388 TTCTATTTTTTATTTA
1 TTCTATTTTTTAATTA
*
2791404 TTTTATTCTTTTA
1 TTCTATT-TTTTA
2791417 CTTTGACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.16
16 16 0.64
17 5 0.20
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTATTTTTTAATTA
Found at i:2791452 original size:55 final size:53
Alignment explanation
Indices: 2791377--2791505 Score: 138
Period size: 54 Copynumber: 2.4 Consensus size: 53
2791367 TTTTACTTCT
* * *
2791377 TTTTTTAATTATTC-TATTTTTTATTTATTTTATTCTTTTACTTTGACTTTT-TCC
1 TTTTTTCATTTTTCTTATTTTTTATTTATTTAATT-TTTTA-TTT-ACTTTTATCC
* **
2791431 TTTTTTCATTTTTCTTATTTTTTTCTTTATTTAATTTTTTATTTACTTTTATTT
1 TTTTTTCATTTTTCTTA-TTTTTTATTTATTTAATTTTTTATTTACTTTTATCC
2791485 TTATTTTCATTTTT-TTATTTT
1 TT-TTTTCATTTTTCTTATTTT
2791506 CAGTTTTTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
53 10 0.15
54 21 0.32
55 18 0.28
56 16 0.25
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.75
Consensus pattern (53 bp):
TTTTTTCATTTTTCTTATTTTTTATTTATTTAATTTTTTATTTACTTTTATCC
Found at i:2791468 original size:16 final size:17
Alignment explanation
Indices: 2791449--2791490 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2791439 TTTTTCTTAT
*
2791449 TTTTTTCTTTA-TTTAA
1 TTTTTTATTTACTTTAA
*
2791465 TTTTTTATTTACTTTTA
1 TTTTTTATTTACTTTAA
2791482 -TTTTTATTT
1 TTTTTTATTT
2791491 TCATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTACTTTAA
Found at i:2791480 original size:26 final size:26
Alignment explanation
Indices: 2791395--2791480 Score: 61
Period size: 30 Copynumber: 3.2 Consensus size: 26
2791385 TTATTCTATT
* *
2791395 TTTTATTTATTTTATTCTTTTACTTTGAC
1 TTTTCTTTATTTAATT-TTTTA-TTT-AC
*
2791424 TTTTTCCTTT-TTTCATTTTTCTTATTT--
1 -TTTT-CTTTATTT-AATTTT-TTATTTAC
2791451 TTTTCTTTATTTAATTTTTTATTTAC
1 TTTTCTTTATTTAATTTTTTATTTAC
2791477 TTTT
1 TTTT
2791481 ATTTTTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
24 6 0.13
25 9 0.20
26 11 0.24
30 12 0.26
31 8 0.17
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.74
Consensus pattern (26 bp):
TTTTCTTTATTTAATTTTTTATTTAC
Found at i:2791500 original size:72 final size:71
Alignment explanation
Indices: 2791362--2791499 Score: 165
Period size: 72 Copynumber: 1.9 Consensus size: 71
2791352 CTTTTTTTCG
* *
2791362 TTTTCTTTTACTTCTTTTTTTAATTATTCTATTTTTTATTTATTTTATTCTTTTACTTTGACTTT
1 TTTTCTTTTACTTATTTTTTTAATTATTCTATTTTTTATTTATTTTATTCTTTTACTTTCACTTT
2791427 TTCCTT
66 TTCCTT
* ** * *
2791433 TTTTCATTTTTCTTATTTTTTTCTTTATT-TAATTTTTTATTTACTTTTA-T-TTTTATTTTCAT
1 TTTTC-TTTTACTTATTTTTTTAATTATTCT-ATTTTTTATTTA-TTTTATTCTTTTACTTTCAC
2791495 TTTTT
63 TTTTT
2791500 TATTTTCAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
71 20 0.35
72 32 0.56
73 5 0.09
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.75
Consensus pattern (71 bp):
TTTTCTTTTACTTATTTTTTTAATTATTCTATTTTTTATTTATTTTATTCTTTTACTTTCACTTT
TTCCTT
Found at i:2791514 original size:15 final size:14
Alignment explanation
Indices: 2791433--2791516 Score: 68
Period size: 14 Copynumber: 6.1 Consensus size: 14
2791423 CTTTTTCCTT
2791433 TTTTCATTTTTCTTA
1 TTTTCATTTTT-TTA
*
2791448 TTTT--TTTCTTTA
1 TTTTCATTTTTTTA
*
2791460 -TTT-AATTTTTTA
1 TTTTCATTTTTTTA
* *
2791472 TTTACTTTTATTTTTA
1 TTTTC-ATT-TTTTTA
2791488 TTTTCATTTTTTTA
1 TTTTCATTTTTTTA
*
2791502 TTTTCAGTTTTTTA
1 TTTTCATTTTTTTA
2791516 T
1 T
2791517 ATATATTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.05
12 9 0.16
13 6 0.11
14 20 0.36
15 7 0.13
16 10 0.18
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (14 bp):
TTTTCATTTTTTTA
Found at i:2791558 original size:4 final size:4
Alignment explanation
Indices: 2791549--2791595 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
2791539 TTGATTTAAC
* * *
2791549 ATTT ATTT ATTTT ATTT -CTT ATCT ATTT AATT ATTT ATTT ATTT ATT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
2791596 CATTCATTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 2 0.06
4 29 0.83
5 4 0.11
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:2791568 original size:28 final size:27
Alignment explanation
Indices: 2791445--2791592 Score: 73
Period size: 28 Copynumber: 5.4 Consensus size: 27
2791435 TTCATTTTTC
2791445 TTATTTT-TTTCTTTATTTA-ATTTTTTAT
1 TTATTTTATTTCTTTATTTACA---TTTAT
* *
2791473 TTACTTTTA-TT-TTTATTTTCATTTTT
1 TTA-TTTTATTTCTTTATTTACATTTAT
* *
2791499 TTATTTTCAGTTT-TTTATATATATTT-T
1 TTATTTT-A-TTTCTTTATTTACATTTAT
*
2791526 TATATTTT-TTCTCTTGATTTAACATTTAT
1 T-TATTTTATT-TCTTTATTT-ACATTTAT
2791555 TTATTTTATTTCTTATCTATTTA-A-TTAT
1 TTATTTTATTTC-T-T-TATTTACATTTAT
2791583 TTA-TTTATTT
1 TTATTTTATTT
2791593 ATTCATTCAT
Statistics
Matches: 96, Mismatches: 9, Indels: 31
0.71 0.07 0.23
Matches are distributed among these distances:
25 6 0.06
26 9 0.09
27 14 0.15
28 48 0.50
29 13 0.14
30 2 0.02
31 4 0.04
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (27 bp):
TTATTTTATTTCTTTATTTACATTTAT
Found at i:2798233 original size:3 final size:3
Alignment explanation
Indices: 2798225--2799989 Score: 1722
Period size: 3 Copynumber: 593.7 Consensus size: 3
2798215 CCACAAACAC
2798225 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2798273 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * * **
2798321 CTT CCT C-T CCT CCT CTC CTCT CCT CCT CCC CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT
2798366 CTT CTT CTT CTT CTT CTT CTT -TT CTT CTT -TCT CTT CTT CCTT -TT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT -CTT CTT
2798410 C-T CTT CCTT CTT CTT CTT CTTT CTT CTT C-T CTCT CTT CTT -TCT CTT
1 CTT CTT -CTT CTT CTT CTT C-TT CTT CTT CTT CT-T CTT CTT CT-T CTT
*
2798456 CTT CTT CCTT CTTT CTC CTT CTT CTT CTT CTT CTT CTT CTCT CTT CTT
1 CTT CTT -CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT
2798504 C-T CTT -TT CTT C-T CTT CTT CTT -TCT CTT CCTT CTT CTT -TT CCTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT -CTT CTT CTT CTT -CTT
* * *
2798547 CTTT CTT CTT CTT CTT CTT CTTT CTT CTT CTTT CTT CTT -TC CTC CTC
1 C-TT CTT CTT CTT CTT CTT C-TT CTT CTT C-TT CTT CTT CTT CTT CTT
* * * * * * *
2798594 CTC CTT CCT CCT CCT CCT CCT CTT CCTC CTT CTT C-T CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT
*
2798639 CTC CTTT CTT CTT -TT CTT CCTT CTT CTT CTT CTT CTTT CTTT CTTT
1 CTT C-TT CTT CTT CTT CTT -CTT CTT CTT CTT CTT C-TT C-TT C-TT
* * * * * * * *
2798685 CTT CTT CTT CCTT CCT CTC CTC CTCT CTCT CTCT CCT CCT CCT CCT CCT
1 CTT CTT CTT -CTT CTT CTT CTT CT-T CT-T CT-T CTT CTT CTT CTT CTT
* *
2798734 CCT CTT CCT C-T CTT -TT -TT CTT CTT -TT CTT C-T CTT -TT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
2798776 CTT CTCT CTT CTTT CTT CTT CTT C-T CTT CTT -TT CTT CTT CTT -TC
1 CTT CT-T CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
2798820 CTT CTT CTT CTT CTT -TC CTTT CTT CTT CTT CTT CTT CCTC CTT CTT
1 CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT -CTT CTT CTT
* *
2798866 CCTT CTT CTT CTT CTT CTT CCT -TT CTT CCT CATT CTT CTT CTT CTT
1 -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT
* * *
2798912 CTT CCTC CTC CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CCT
1 CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * * * * * * * * *
2798958 C-T CCT CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTCT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T
* * * * * * * * * * * * *
2799003 CCT CTC CTC CTC CTC CTC CTC CTC CTC CTC CTT CTC CTC CTC CTT -TCT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T
* *
2799051 ATT C-T CTT -TCT CTT CTT CTC CTT CTT C-T CTT CTT CTT CTT CTT
1 CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
2799094 CTT CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-T
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
2799141 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT CTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
2799187 CTT C-T CTT CTT CTT CTT CTT CTT -TT CTT C-T CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
2799232 CTT CTC CTT C-T CTT CTT CTT CTT CCT C-T ATT CTT CTT C-T CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
2799277 CTT CTT CTT CTT CCTC CTT CTT CTT CTT CTT CTTT CTT -TT CTT CTC
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT
* * * *
2799323 CTT CTT CTT CTT CTTT CTT CTC CTT CCTT CTC CTT CTC CTT CTT CCTC
1 CTT CTT CTT CTT C-TT CTT CTT CTT -CTT CTT CTT CTT CTT CTT -CTT
* * * * *
2799371 CTT ATT CTT -TT CCT CCT CTT CTT ATT CTT CTT CTC CTT CTT CTT C-T
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
2799417 CTT CTT C-T CTT CTT CTC CTTT CTT CTT CTT -TT CTC CTT CTC CTT
1 CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
2799461 C-T CTT CTC CTT C-T CTT CTC CTT CTC CTT CTC CTT C-T CTT C-T CATT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
* *
2799506 CTC CTT -TC CTT C-T CATT CTT CTT CTT CTT CTT CTT CTT -TCT CTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CT-T CTT
2799550 CTT CTT CTT CTT -TT CTT CTT CTT CTTT CTT CTT CTT CTT C-T CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT
*
2799594 CTT CTT CTT CTT -TT CTT -TT CTT CTT CTT CTT ATT CTT -TT CTT C-T
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
2799638 CTT CTT CTT CTTT CTT CTT CTT TTT C-T CTT CTT CTT CTTT CTT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT
2799684 CTT CTT C-T CTT CTCT CTT CTT CTT CTT C-T CTT CTT CTT CTT CTTT
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
* *
2799729 CTT CTT CTT CGT CTT CTT CTT CTT CTT CTT TTT C-T CTT -TT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2799775 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
2799821 -TT CTT -TT CTT CTT CTT CTT CTT CTT CTT -AT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2799866 CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT CTT C-T CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2799912 CTT CTT CTT CTT CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT -TT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2799958 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
2799990 AACGTAATTT
Statistics
Matches: 1540, Mismatches: 107, Indels: 230
0.82 0.06 0.12
Matches are distributed among these distances:
2 123 0.08
3 1287 0.84
4 130 0.08
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:2798341 original size:13 final size:13
Alignment explanation
Indices: 2798323--2798348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2798313 TTCTTCTTCT
2798323 TCCTCTCCTCCTC
1 TCCTCTCCTCCTC
2798336 TCCTCTCCTCCTC
1 TCCTCTCCTCCTC
2798349 CCCTTCTTCT
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:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (13 bp):
TCCTCTCCTCCTC
Found at i:2800594 original size:32 final size:32
Alignment explanation
Indices: 2800552--2800615 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2800542 AATAATTGAA
* *
2800552 ATTTAGATAAAATATCAA-TTTAATCTTTAAAT
1 ATTTAGATAAAATA-AAATTTTAATCCTTAAAT
*
2800584 ATTTATATAAAATAAAATTTTAATCCTTAAAT
1 ATTTAGATAAAATAAAATTTTAATCCTTAAAT
2800616 CCAATCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
ATTTAGATAAAATAAAATTTTAATCCTTAAAT
Found at i:2805304 original size:20 final size:20
Alignment explanation
Indices: 2805279--2805318 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2805269 AAAACCGATG
*
2805279 ACCGTTGACCGTCGTTGACC
1 ACCGTTGACCGGCGTTGACC
2805299 ACCGTTGACCGGCGTTGACC
1 ACCGTTGACCGGCGTTGACC
2805319 GGGCCTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.28, T:0.23
Consensus pattern (20 bp):
ACCGTTGACCGGCGTTGACC
Found at i:2805320 original size:10 final size:10
Alignment explanation
Indices: 2805281--2805320 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2805271 AACCGATGAC
*
2805281 CGTTGACCGT
1 CGTTGACCGG
**
2805291 CGTTGACCAC
1 CGTTGACCGG
2805301 CGTTGACCGG
1 CGTTGACCGG
2805311 CGTTGACCGG
1 CGTTGACCGG
2805321 GCCTTGAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.23
Consensus pattern (10 bp):
CGTTGACCGG
Found at i:2810448 original size:19 final size:21
Alignment explanation
Indices: 2810426--2810472 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
2810416 GGGGTATCAA
2810426 TTCCCC-T-AGGGGGAATCGG
1 TTCCCCTTAAGGGGGAATCGG
2810445 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTT--AAGGGGGAATCGG
2810468 TTCCC
1 TTCCC
2810473 TCATGGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
23 17 0.71
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (21 bp):
TTCCCCTTAAGGGGGAATCGG
Found at i:2810486 original size:20 final size:21
Alignment explanation
Indices: 2810433--2810493 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
2810423 CAATTCCCCT
2810433 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTT-CCC-TCAA
2810456 AGGGGGAATCGGTTCCCTC-A
1 AGGGGGAATCGGTTCCCTCAA
* * *
2810476 TGGGGGTATCGATTCCCT
1 AGGGGGAATCGGTTCCCT
2810494 TTGCACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 3 0.09
23 14 0.40
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCTCAA
Found at i:2823042 original size:21 final size:21
Alignment explanation
Indices: 2823016--2823069 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 21
2823006 AATTTATCCT
2823016 GAAGGACCACGTAGATGTCCC
1 GAAGGACCACGTAGATGTCCC
2823037 GAAGGACCAC-T--ATGTCCC
1 GAAGGACCACGTAGATGTCCC
2823055 GAAGGACCACGTAGA
1 GAAGGACCACGTAGA
2823070 CCCTCGACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 17 0.57
19 1 0.03
20 1 0.03
21 11 0.37
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.13
Consensus pattern (21 bp):
GAAGGACCACGTAGATGTCCC
Found at i:2832411 original size:30 final size:30
Alignment explanation
Indices: 2832376--2832438 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
2832366 GATCACCATC
2832376 CGCGCCTTCGTGGGGTTTTGACCGAGCTGG
1 CGCGCCTTCGTGGGGTTTTGACCGAGCTGG
2832406 CGCGCCTTCGTGGGGTTTTGACCGAGCTGG
1 CGCGCCTTCGTGGGGTTTTGACCGAGCTGG
2832436 CGC
1 CGC
2832439 CACGTAAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.06, C:0.29, G:0.40, T:0.25
Consensus pattern (30 bp):
CGCGCCTTCGTGGGGTTTTGACCGAGCTGG
Found at i:2833179 original size:29 final size:29
Alignment explanation
Indices: 2833137--2833207 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
2833127 TTGTTAACCT
2833137 TGTAATAATGCATACATACTTCTGCTGAA
1 TGTAATAATGCATACATACTTCTGCTGAA
2833166 TGTAATAATGCATACATACTTCTGCTGAA
1 TGTAATAATGCATACATACTTCTGCTGAA
*
2833195 TGCAATAATGCAT
1 TGTAATAATGCAT
2833208 TATCAACATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (29 bp):
TGTAATAATGCATACATACTTCTGCTGAA
Found at i:2834043 original size:12 final size:12
Alignment explanation
Indices: 2834026--2834050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2834016 CCTAAACAAA
2834026 CACTCTAATATG
1 CACTCTAATATG
2834038 CACTCTAATATG
1 CACTCTAATATG
2834050 C
1 C
2834051 CTATATAAGC
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:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CACTCTAATATG
Found at i:2834457 original size:2 final size:2
Alignment explanation
Indices: 2834450--2834527 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
2834440 TTATAAAGTA
2834450 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
2834492 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
2834528 TTAGAGTCTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2834777 original size:23 final size:23
Alignment explanation
Indices: 2834746--2834792 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2834736 ATATTTTCAT
*
2834746 AAATCATAATTAATATTATTATA
1 AAATCATAATTAATACTATTATA
*
2834769 AAATTATAATTAATACTATTATA
1 AAATCATAATTAATACTATTATA
2834792 A
1 A
2834793 GAGTGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATCATAATTAATACTATTATA
Found at i:2840571 original size:69 final size:69
Alignment explanation
Indices: 2840481--2840626 Score: 247
Period size: 69 Copynumber: 2.1 Consensus size: 69
2840471 CTTTGGCAAC
* *
2840481 CTTCTGATACGACTGTAAGACAAGTTCAGATATGTCAAGTGCACCAAGTTACAAAAGGAATTCGG
1 CTTCTGATACGACTGTAAGACAAGTTCAGATATGTCAAGTGCACCAAGTTAAAAAACGAATTCGG
2840546 AATT
66 AATT
* *
2840550 CTTCTGATTCGACTGTGAGACAAGTTCAGATATGTCAAGTGCACCAAGTTAAAAAACGAATTCGG
1 CTTCTGATACGACTGTAAGACAAGTTCAGATATGTCAAGTGCACCAAGTTAAAAAACGAATTCGG
2840615 AATT
66 AATT
*
2840619 CTTGTGAT
1 CTTCTGAT
2840627 GCATAAGCTC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (69 bp):
CTTCTGATACGACTGTAAGACAAGTTCAGATATGTCAAGTGCACCAAGTTAAAAAACGAATTCGG
AATT
Found at i:2843656 original size:2 final size:2
Alignment explanation
Indices: 2843644--2843695 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
2843634 TAAAATGTAA
* *
2843644 AT AT AT GT AT AT AT AT AT AT AT GT AT AT A- AT -T AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2843683 AT A- AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
2843696 AATAACGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
1 5 0.12
2 36 0.88
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2844306 original size:84 final size:83
Alignment explanation
Indices: 2844100--2845453 Score: 1617
Period size: 84 Copynumber: 16.3 Consensus size: 83
2844090 GAGCAGACAA
* * * * * * * *
2844100 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCCTCGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCT-TGAGCTGAG
* * * **
2844165 TGGAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* * *
2844185 --TT-TT-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
2844246 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * *
2844265 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
2844330 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
*
2844349 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
2844414 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * * *
2844433 TTTTGTTGGCAGACAACCCTTCTAGACTTAAATTGTGCTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
2844498 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
*
2844517 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
2844582 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * **
2844601 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
2844666 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* *
2844685 TCTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
** * **
2844750 TATAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* * * *
2844770 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAGCTGAGC
*
2844831 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * ***
2844850 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGGCATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
2844915 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* *
2844934 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
* * * **
2844999 TGTAATTGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* ** * *
2845019 ---T-TTGGTAGATGGCCCTTTTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
2845080 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * **
2845099 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
2845164 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * *
2845183 TTTGGTTGGCAGATAACCATTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
* * **
2845248 TGTAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* *
2845268 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
2845329 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * **
2845348 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
2845413 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* *
2845432 -TTTGGTGACAGATAACCCTTCT
1 TTTTGTTGGCAGATAACCCTTCT
2845454 AGCCTTGAGT
Statistics
Matches: 1083, Mismatches: 153, Indels: 68
0.83 0.12 0.05
Matches are distributed among these distances:
80 92 0.08
81 173 0.16
82 4 0.00
83 39 0.04
84 694 0.64
85 81 0.07
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (83 bp):
TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCG
TAGTCGAACTCGAAGGTC
Found at i:2844875 original size:249 final size:249
Alignment explanation
Indices: 2844189--2845453 Score: 1964
Period size: 249 Copynumber: 5.1 Consensus size: 249
2844179 GGGGTCTTTT
* * * * * *
2844189 GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
*** * * * * * *
2844253 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCC
66 AACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
* * * *
2844318 -TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
127 GTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGT
* ** * *
2844382 TATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTG
191 TGTGCTGCAAATGACATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* * * * * * * *
2844441 GCAGACAACCCTTCTAGACTTAAATTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
** * *
2844505 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
66 AACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
2844570 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
127 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
*
2844635 GTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTCTGGTTG
192 GTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
*
2844693 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTATAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
* *
2844758 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTTG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
2844823 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
*
2844888 TGCAAATGGCATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
196 TGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* *
2844942 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATTG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
* * *
2845007 AACTCGGGGGTCTTTGGTAGATGGCCCTTTTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
2845072 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
2845137 TGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
196 TGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
* *
2845191 GCAGATAACCATTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
2845256 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
2845321 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
2845386 TGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TG
196 TGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
*
2845439 ACAGATAACCCTTCT
1 GCAGATAACCCTTCT
2845454 AGCCTTGAGT
Statistics
Matches: 951, Mismatches: 57, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
248 15 0.02
249 646 0.68
251 10 0.01
252 251 0.26
253 29 0.03
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (249 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
TGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
Found at i:2848900 original size:18 final size:19
Alignment explanation
Indices: 2848860--2848904 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2848850 AGTTAATGTG
*
2848860 AATGCAAATAAAATAACAA
1 AATGCAAAGAAAATAACAA
2848879 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
2848897 AATGCAAA
1 AATGCAAA
2848905 ATGTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:2851472 original size:2 final size:2
Alignment explanation
Indices: 2851460--2851513 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
2851450 TAAAATGTAA
* *
2851460 AT AT AT GT AT AT AT AT GT AT AT AT AT AT AT A- AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2851499 AT AT A- AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
2851514 AATAACGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2851473 original size:10 final size:10
Alignment explanation
Indices: 2851454--2851490 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2851444 GTGAAATAAA
*
2851454 ATGTAAATAT
1 ATGTATATAT
2851464 ATGTATATAT
1 ATGTATATAT
2851474 ATGTATATAT
1 ATGTATATAT
*
2851484 ATATATA
1 ATGTATA
2851491 ATTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (10 bp):
ATGTATATAT
Found at i:2852815 original size:19 final size:19
Alignment explanation
Indices: 2852787--2852829 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2852777 TAATTCACGT
*
2852787 CTTTTCTCTCTTAAAATTA
1 CTTTTCTCTCCTAAAATTA
*
2852806 CTTTTTTCTCCTAAAATTA
1 CTTTTCTCTCCTAAAATTA
*
2852825 ATTTT
1 CTTTT
2852830 ACTATTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (19 bp):
CTTTTCTCTCCTAAAATTA
Found at i:2858471 original size:45 final size:45
Alignment explanation
Indices: 2858383--2858471 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
2858373 CTCATCTTTG
*
2858383 TCATTTCCAACAGAGTGATCAGATGGAAGGGGTTCCTCGTTTCCC
1 TCATTTCCAACAGAGTGATCAGATGGAAGGGGTTCCTCATTTCCC
* * * *
2858428 TCATTTTCAACAGGGTGATCAGATGG-TGGGGCTTCTTCATTTCC
1 TCATTTCCAACAGAGTGATCAGATGGAAGGGG-TTCCTCATTTCC
2858472 ACCACTCTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 4 0.11
45 34 0.89
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (45 bp):
TCATTTCCAACAGAGTGATCAGATGGAAGGGGTTCCTCATTTCCC
Found at i:2859812 original size:6 final size:7
Alignment explanation
Indices: 2859791--2859815 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2859781 TTAAACAAAC
2859791 GGGAGGG
1 GGGAGGG
2859798 GGGAGGG
1 GGGAGGG
2859805 GGGAGGG
1 GGGAGGG
2859812 GGGA
1 GGGA
2859816 AAACAACCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (7 bp):
GGGAGGG
Found at i:2869211 original size:12 final size:12
Alignment explanation
Indices: 2869196--2869222 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2869186 ATTATACCCG
2869196 TTTTTATTTTAT
1 TTTTTATTTTAT
2869208 TTTTTATTTTAT
1 TTTTTATTTTAT
2869220 TTT
1 TTT
2869223 GGTAGGGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:2877371 original size:21 final size:21
Alignment explanation
Indices: 2877346--2877385 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2877336 AAGAATTTAT
2877346 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
2877367 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
2877386 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:2879605 original size:65 final size:65
Alignment explanation
Indices: 2879457--2879617 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
2879447 TGTACTAAGA
* * *
2879457 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATAGCTAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCTACAGTGCATCGATGCACGGCTG
* * * * *
2879521 GTGTATCGATGCATCAAATGCATTCGATGTTCTTATAAA-ATCTTCAGTGCATCGGTGCACGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCA-AAATAGCTACAGTGCATCGATGCACGGCT
2879584 G
65 G
*
2879585 TGTGCATCGATGCATGAAATGCATTCGATGTTC
1 -GTGCATCGATGCATCAAATGCATTCGATGTTC
2879618 AATTTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 31 0.37
65 50 0.60
66 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCTACAGTGCATCGATGCACGGCTG
Found at i:2890220 original size:19 final size:20
Alignment explanation
Indices: 2890171--2890220 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2890161 TTAACTTTTT
2890171 CTTTTATCTTTCATTATTAA
1 CTTTTATCTTTCATTATTAA
* *
2890191 TTTTTTTCTTTCATT-TTAA
1 CTTTTATCTTTCATTATTAA
*
2890210 CTTTTACCTTT
1 CTTTTATCTTT
2890221 TCTCTTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTTTATCTTTCATTATTAA
Found at i:2900317 original size:65 final size:65
Alignment explanation
Indices: 2900169--2900329 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
2900159 TGCACTAAGA
* * *
2900169 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATAGCCAGAGTGCATCAATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCAATGCACGGCTG
* * * *
2900233 GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAA-ATCCTCAGTGCATCAGTGCACGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCA-AAATAGCCACAGTGCATCAATGCACGGCT
2900296 G
65 G
*
2900297 TGTGCATCGATGCATGAAATGCATTCGATGTTC
1 -GTGCATCGATGCATCAAATGCATTCGATGTTC
2900330 AATTTAATTC
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 32 0.37
65 51 0.59
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCAATGCACGGCTG
Found at i:2904789 original size:20 final size:20
Alignment explanation
Indices: 2904764--2904806 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2904754 GTTTTTAACA
2904764 TTTTGAATGTT-TTGTGGATG
1 TTTTGAAT-TTGTTGTGGATG
*
2904784 TTTTGAATTTGTTTTGGATG
1 TTTTGAATTTGTTGTGGATG
2904804 TTT
1 TTT
2904807 GACTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (20 bp):
TTTTGAATTTGTTGTGGATG
Found at i:2905437 original size:20 final size:20
Alignment explanation
Indices: 2905412--2905450 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2905402 TAGAATGCTC
*
2905412 GGATGGTACCGGTACCCCCT
1 GGATGGTACCGATACCCCCT
2905432 GGATGGTACCGATACCCCC
1 GGATGGTACCGATACCCCC
2905451 CATGGCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.36, G:0.28, T:0.18
Consensus pattern (20 bp):
GGATGGTACCGATACCCCCT
Found at i:2905512 original size:20 final size:20
Alignment explanation
Indices: 2905487--2905545 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
2905477 CAGAATGCTC
2905487 GGATGGTATCGATACCCCCT
1 GGATGGTATCGATACCCCCT
*
2905507 GGATGGTACCGATACCCCCT
1 GGATGGTATCGATACCCCCT
2905527 GGATGGTATCGATACCCCC
1 GGATGGTATCGATACCCCC
2905546 AATCATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.20, C:0.32, G:0.25, T:0.22
Consensus pattern (20 bp):
GGATGGTATCGATACCCCCT
Found at i:2909864 original size:484 final size:485
Alignment explanation
Indices: 2908934--2909902 Score: 1859
Period size: 484 Copynumber: 2.0 Consensus size: 485
2908924 TTTAGGTTGG
2908934 CCAGAATATTATCAGTGATAATGGGTATGAATGAATGTTTTCTGTAGAAAAGGATGCAATATTAC
1 CCAGAATATTATCAGTGATAATGGGTATGAATGAATGTTTTCTGTAGAAAAGGATGCAATATTAC
*
2908999 TTAAAGATGGAAAAACTTTCAATTGCATATGTATGCATCAGTTTTGGACATCAAATGATGCATAT
66 TTAAAGATGGAAAAACTTTCAATTGCATATGTATGCATCAGTTATGGACATCAAATGATGCATAT
2909064 AAATGTGAATCAATATAGATATATAAAGAAGCCATGGTATTGTAACTAGTGTCTGAATATGGAAA
131 AAATGTGAATCAATATAGATATATAAAGAAGCCATGGTATTGTAACTAGTGTCTGAATATGGAAA
*
2909129 TGTAGCCATCCTGGTTTTATTACTTTAAAAATGAACCATTTTAATAGCCAGAGAACATTTTCCCT
196 TGTAGCCATCCTGGCTTTATTACTTTAAAAATGAACCATTTTAATAGCCAGAGAACATTTTCCCT
*
2909194 ATTTATAATTGCTTGCATATCATTAGGTTTAATTGCAACAGAAGTACCCAAGGTATCAGCAAAAT
261 ATTTATAATTGCATGCATATCATTAGGTTTAATTGCAACAGAAGTACCCAAGGTATCAGCAAAAT
*
2909259 TTTAAATTGATCCCAAACCTTCAAAACATTCAAATTGAATCCTGAAACTAAAGTATAGTTCCAAT
326 TTTAAATTGATCCAAAACCTTCAAAACATTCAAATTGAATCCTGAAACTAAAGTATAGTTCCAAT
2909324 CAAGTCATTCTATTAGCTGTTAGTTTGGGTGTTAAATTCCTACTTTAATCTATCTAGTTCTGTTT
391 CAAGTCATTCTATTAGCTGTTAGTTTGGGTGTTAAATTCCTACTTTAATCTATCTAGTTCTGTTT
2909389 CAAAACATGTATAGATTAATAAATATGTTA
456 CAAAACATGTATAGATTAATAAATATGTTA
2909419 CCAGAATATTATCAGTGATAATGGGTATGAATGAATGTTTTCTGTAGAAAAGGATGCAATATTAC
1 CCAGAATATTATCAGTGATAATGGGTATGAATGAATGTTTTCTGTAGAAAAGGATGCAATATTAC
2909484 TTAAAGATGGAAAAACTTTCAATTGCATATGTATGCATCAGTTATGGACATCAAATGATGCATAT
66 TTAAAGATGGAAAAACTTTCAATTGCATATGTATGCATCAGTTATGGACATCAAATGATGCATAT
* *
2909549 AAATGTGAATCAATATAGATGTATAAAGAAGCCATGGTATTGTAACTAGTGTCTGACTATGGAAA
131 AAATGTGAATCAATATAGATATATAAAGAAGCCATGGTATTGTAACTAGTGTCTGAATATGGAAA
2909614 TGTAGCCATCCTGGCTTTATTACTTT-AAAATGAACCATTTTAATAGCCAGAGAACATTTTCCCT
196 TGTAGCCATCCTGGCTTTATTACTTTAAAAATGAACCATTTTAATAGCCAGAGAACATTTTCCCT
*
2909678 ATTTATAATTGCATGCATATCATTGGGTTTAATTGCAACAGAAGTACCCAAGGTATCAGCAAAAT
261 ATTTATAATTGCATGCATATCATTAGGTTTAATTGCAACAGAAGTACCCAAGGTATCAGCAAAAT
2909743 TTTAAATTGATCCAAAACCTTCAAAACATTCAAATTGAATCCTGAAACTAAAGTATAGTTCCAAT
326 TTTAAATTGATCCAAAACCTTCAAAACATTCAAATTGAATCCTGAAACTAAAGTATAGTTCCAAT
*
2909808 CAAGTCATTCTATTAGCTGTTAGTTTGGGTGTTAAATTCGTACTTTAATCTATCTAGTTCTGTTT
391 CAAGTCATTCTATTAGCTGTTAGTTTGGGTGTTAAATTCCTACTTTAATCTATCTAGTTCTGTTT
2909873 CAAAACATGTATAGATTAATAAATATGTTA
456 CAAAACATGTATAGATTAATAAATATGTTA
2909903 AACACTTCAG
Statistics
Matches: 476, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
484 259 0.54
485 217 0.46
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (485 bp):
CCAGAATATTATCAGTGATAATGGGTATGAATGAATGTTTTCTGTAGAAAAGGATGCAATATTAC
TTAAAGATGGAAAAACTTTCAATTGCATATGTATGCATCAGTTATGGACATCAAATGATGCATAT
AAATGTGAATCAATATAGATATATAAAGAAGCCATGGTATTGTAACTAGTGTCTGAATATGGAAA
TGTAGCCATCCTGGCTTTATTACTTTAAAAATGAACCATTTTAATAGCCAGAGAACATTTTCCCT
ATTTATAATTGCATGCATATCATTAGGTTTAATTGCAACAGAAGTACCCAAGGTATCAGCAAAAT
TTTAAATTGATCCAAAACCTTCAAAACATTCAAATTGAATCCTGAAACTAAAGTATAGTTCCAAT
CAAGTCATTCTATTAGCTGTTAGTTTGGGTGTTAAATTCCTACTTTAATCTATCTAGTTCTGTTT
CAAAACATGTATAGATTAATAAATATGTTA
Found at i:2924069 original size:41 final size:41
Alignment explanation
Indices: 2924024--2924118 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
2924014 TTTCTTTGTC
2924024 CTTATTTTTAAAGGAATCAAATGATAAATTTATTATCATGA
1 CTTATTTTTAAAGGAATCAAATGATAAATTTATTATCATGA
*
2924065 CTTATTTTTAAAGGAATCTAATGATAAATTTATTATCATGA
1 CTTATTTTTAAAGGAATCAAATGATAAATTTATTATCATGA
2924106 CTTATTTTTAAAG
1 CTTATTTTTAAAG
2924119 AATTTGAATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (41 bp):
CTTATTTTTAAAGGAATCAAATGATAAATTTATTATCATGA
Found at i:2937636 original size:19 final size:21
Alignment explanation
Indices: 2937601--2937640 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
2937591 CTAATTATCT
2937601 GTCATAAATATTATTTTAATA
1 GTCATAAATATTATTTTAATA
2937622 GTCATAAA-A-TATTTTAATA
1 GTCATAAATATTATTTTAATA
2937641 TTTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
GTCATAAATATTATTTTAATA
Found at i:2938901 original size:31 final size:32
Alignment explanation
Indices: 2938866--2938925 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
2938856 TGGCAATATA
2938866 ACACATG-CTACATATCG-AAAGTGATGATGTG
1 ACACATGTC-ACATATCGAAAAGTGATGATGTG
*
2938897 ACACATGTCACATATTGAAAAGTGATGAT
1 ACACATGTCACATATCGAAAAGTGATGAT
2938926 ATAAAATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (32 bp):
ACACATGTCACATATCGAAAAGTGATGATGTG
Found at i:2938937 original size:32 final size:31
Alignment explanation
Indices: 2938861--2938938 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 31
2938851 GAAAGTGGCA
*
2938861 ATATAACACATG-CTACATATCGAAAGTGATG
1 ATATAAAACATGTC-ACATATCGAAAGTGATG
* * * *
2938892 ATGTGACACATGTCACATATTGAAAAGTGATG
1 ATATAAAACATGTCACATATCG-AAAGTGATG
*
2938924 ATATAAAATATGTCA
1 ATATAAAACATGTCA
2938939 TGTGTTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 17 0.45
32 21 0.55
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (31 bp):
ATATAAAACATGTCACATATCGAAAGTGATG
Found at i:2938970 original size:5 final size:5
Alignment explanation
Indices: 2938960--2938986 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2938950 TAGGGGTGTA
2938960 TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TT
2938987 TTTTACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.37, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:2939637 original size:27 final size:26
Alignment explanation
Indices: 2939599--2939654 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 26
2939589 ACTCTCAAAG
2939599 AAAAAAAAACAAATAACAAACTATGA
1 AAAAAAAAACAAATAACAAACTATGA
2939625 AAAAAAAATACAAATAACAAACTATGA
1 AAAAAAAA-ACAAATAACAAACTATGA
2939652 AAA
1 AAA
2939655 TTCTCACGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.12
Consensus pattern (26 bp):
AAAAAAAAACAAATAACAAACTATGA
Found at i:2943460 original size:65 final size:64
Alignment explanation
Indices: 2943322--2943474 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 64
2943312 CCCCATTTCA
* * * *
2943322 AATGCATTTTATGAACCGATGCACAACCAAGCATCGATGCACTCAGGATTTTATTGAAACATCG
1 AATGCATTTTATGCATCGATGCACAACCAAGCATCGATGCACTCAGGATTGTATTAAAACATCG
* * *
2943386 AATGCATTTTATGCATCGATGCACAGACCATGCATCGATGTACTTCAGGCTTGT-TTAAAACATC
1 AATGCATTTTATGCATCGATGCACA-ACCAAGCATCGATGCAC-TCAGGATTGTATTAAAACATC
2943450 G
64 G
* *
2943451 AATGTATTTTATACATCGATGCAC
1 AATGCATTTTATGCATCGATGCAC
2943475 CCCTAGTGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 23 0.29
65 47 0.60
66 8 0.10
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
AATGCATTTTATGCATCGATGCACAACCAAGCATCGATGCACTCAGGATTGTATTAAAACATCG
Found at i:2945438 original size:21 final size:21
Alignment explanation
Indices: 2945414--2945453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2945404 AAGACTTTAT
2945414 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
2945435 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
2945454 AAATAGTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:2952057 original size:64 final size:65
Alignment explanation
Indices: 2951983--2952138 Score: 203
Period size: 65 Copynumber: 2.4 Consensus size: 65
2951973 ACACCCCATT
* * *
2951983 TCGAATGCATTTTATGCACCGATGCCCA-ACCATGCATCGATGCACT-CAGGAT-TT-TATTGAA
1 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCCA--ATCTTGT-TTAAA
2952044 ACA
63 ACA
*
2952047 TCGAATGCATTTTATGCATCAATGCACAGACCATGCATCGATGCACTCCAATCTTGTTTAAAACA
1 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCCAATCTTGTTTAAAACA
* *
2952112 TCAAATGTATTTTATGCATCGATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
2952139 CCCTAATGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
64 27 0.33
65 51 0.63
66 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (65 bp):
TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCCAATCTTGTTTAAAACA
Found at i:2954843 original size:31 final size:31
Alignment explanation
Indices: 2954793--2954881 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
2954783 TCAGATGCAT
* *
2954793 GGGTTAAATT-ATACTTTATCTAAAGTTTAA
1 GGGTCAAATTAATATTTTATCTAAAGTTTAA
* * *
2954823 TGGTCAAATTAATATTTTATCTAAAATTTAG
1 GGGTCAAATTAATATTTTATCTAAAGTTTAA
2954854 GGGTCAAATTAATATTTTATCTAAAGTT
1 GGGTCAAATTAATATTTTATCTAAAGTT
2954882 CAAAGACCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 8 0.16
31 43 0.84
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (31 bp):
GGGTCAAATTAATATTTTATCTAAAGTTTAA
Found at i:2954893 original size:31 final size:31
Alignment explanation
Indices: 2954798--2954896 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
2954788 TGCATGGGTT
* *
2954798 AAATT-ATACTTTATCTAAAGTTTAATGGTC
1 AAATTAATATTTTATCTAAAGTTTAAAGGTC
* **
2954828 AAATTAATATTTTATCTAAAATTTAGGGGTC
1 AAATTAATATTTTATCTAAAGTTTAAAGGTC
* **
2954859 AAATTAATATTTTATCTAAAGTTCAAAGACC
1 AAATTAATATTTTATCTAAAGTTTAAAGGTC
2954890 AAATTAA
1 AAATTAA
2954897 AAATTAACCA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
30 5 0.09
31 53 0.91
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (31 bp):
AAATTAATATTTTATCTAAAGTTTAAAGGTC
Found at i:2959173 original size:32 final size:31
Alignment explanation
Indices: 2959092--2959188 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 31
2959082 TTTTTATCTC
* *
2959092 TAAAC-TTTTAAAA-ATTATAAAAGGACCAT
1 TAAACTTTTTAAAATATTATAAAATGATCAT
2959121 TAAACTTTTT-AAATATTTATAAAATGATCAT
1 TAAACTTTTTAAAATA-TTATAAAATGATCAT
*
2959152 TCAACTTTATTAAAATATTATAAAACT-ATCAT
1 TAAACTTT-TTAAAATATTATAAAA-TGATCAT
2959184 TAAAC
1 TAAAC
2959189 AAAGGAGTAC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
29 8 0.14
30 5 0.09
31 20 0.34
32 19 0.33
33 6 0.10
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.38
Consensus pattern (31 bp):
TAAACTTTTTAAAATATTATAAAATGATCAT
Found at i:2961023 original size:21 final size:21
Alignment explanation
Indices: 2960999--2961043 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2960989 GGTGTTGATG
* *
2960999 TTAGGGTTTAGGGTTTATAAT
1 TTAGGGATTAGGGTATATAAT
*
2961020 TTAGGGATTAGGGTATATCAT
1 TTAGGGATTAGGGTATATAAT
2961041 TTA
1 TTA
2961044 TAATTTAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (21 bp):
TTAGGGATTAGGGTATATAAT
Found at i:2961070 original size:28 final size:28
Alignment explanation
Indices: 2961012--2961071 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
2961002 GGGTTTAGGG
* *
2961012 TTTATAATTTAGGGATTAGGGTATATCA
1 TTTATAATTTAGGGATTAGGCTATATAA
2961040 TTTATAATTTAGGG-TTCATGGCTA-ATAA
1 TTTATAATTTAGGGATT-A-GGCTATATAA
2961068 TTTA
1 TTTA
2961072 AGGCACATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 22 0.79
29 4 0.14
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (28 bp):
TTTATAATTTAGGGATTAGGCTATATAA
Found at i:2973780 original size:14 final size:15
Alignment explanation
Indices: 2973742--2973781 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2973732 AATTTTTAAC
2973742 TTTTTCTTTT-ATCT
1 TTTTTCTTTTCATCT
*
2973756 TTCTT-TTTTCAT-T
1 TTTTTCTTTTCATCT
2973769 TTTTTCTTTTCAT
1 TTTTTCTTTTCAT
2973782 GTTAACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTCATCT
Found at i:2978290 original size:137 final size:137
Alignment explanation
Indices: 2978044--2978686 Score: 367
Period size: 136 Copynumber: 4.6 Consensus size: 137
2978034 ATTTCACCTG
* * *
2978044 GCCTACTCCACACGTTAGGGCACTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTAGAAG
1 GCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCATGCCTACTCCCCTCTAGAAG
* *
2978109 TGCTCAGCATGAACTATGTCTACCCTGCCTACCCCACACGTTGAAGTGCTCGGAGTTAATCAGGA
66 AGCTCAGCATGAACTATGTCTACCCTGCCTACCCCACACGTTGAAGCGCTCGGAGTTAATCAGGA
2978174 ACACCCT
131 ACACCCT
* * * ** *
2978181 GCCTACTCTACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCATGTCTACTCGTCTCTGGAAG
1 GCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCATGCCTACTCCCCTCTAGAAG
* * * * * *
2978246 AGCTCGGCATGTAC-ATTGTCTCCCCTGCCTACTCTCA-ATGTTGAAGCGCTCGGTGTGATATTA
66 AGCTCAGCATGAACTA-TGTCTACCCTGCCTAC-CCCACACGTTGAAGCGCTC---G-GA-GTT-
* *
2978309 AATCA-CATCTTATTTCACCCG
123 AATCAGGA----A---CACCCT
* * * * * * * * * *
2978330 GCATACTCCACACATTAGAGCTCCCGGCGTAAGATCATGTCATCCTGCCTAATCCCCACTGGAAG
1 GCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCATGCCTACTCCCCTCTAGAAG
* * * * * * * * * *
2978395 TGCTCGGTATGAACTCTGTC-CCCCT-TCTAACTCCTA-ACGGTGAAGCACTCGGTGAG-AAAT-
66 AGCTCAGCATGAACTATGTCTACCCTGCCT-AC-CCCACACGTTGAAGCGCTC-G-GAGTTAATC
*
2978455 AGGAATACCCT
127 AGGAACACCCT
* * * * *
2978466 ACCTACTCCACACGTTAGAGC-GTCCGGCGTAAGATCAGGTCATCCTGCCTACT-CCCTACTGGA
1 GCCTACTCCACACGTTAGAGCACT-CGACGTAAGATCAGGTCATCATGCCTACTCCCCT-CTAGA
* * * * * * ** * * * **
2978529 AGCGCTCAGTATGAACTCTGTC-CCCCTTCCAACTCTTA-ACGGTGTAGCGCTCGGCGAAAAAT-
64 AGAGCTCAGCATGAACTATGTCTACCCTGCCTAC-CCCACACGTTGAAGCGCTCGGAG-TTAATC
* *
2978591 ATGAATACCCT
127 AGGAACACCCT
* * * * *
2978602 GCCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAGGTCATCATGCCTACTCCCCACTAAAAG
1 GCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCATGCCTACTCCCCTCTAGAAG
* * * *
2978667 CGCTCGGCATAAACTCTGTC
66 AGCTCAGCATGAACTATGTC
2978687 CCCTTTCCAA
Statistics
Matches: 406, Mismatches: 75, Indels: 51
0.76 0.14 0.10
Matches are distributed among these distances:
134 2 0.00
135 4 0.01
136 182 0.45
137 98 0.24
138 3 0.01
139 1 0.00
140 1 0.00
141 2 0.00
142 4 0.01
143 9 0.02
146 5 0.01
147 2 0.00
148 21 0.05
149 72 0.18
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (137 bp):
GCCTACTCCACACGTTAGAGCACTCGACGTAAGATCAGGTCATCATGCCTACTCCCCTCTAGAAG
AGCTCAGCATGAACTATGTCTACCCTGCCTACCCCACACGTTGAAGCGCTCGGAGTTAATCAGGA
ACACCCT
Found at i:2978714 original size:136 final size:136
Alignment explanation
Indices: 2978333--2978717 Score: 554
Period size: 136 Copynumber: 2.8 Consensus size: 136
2978323 TCACCCGGCA
* * * * *
2978333 TACTCCACACATTAGAGCTCCCGGCGTAAGATCATGTCATCCTGCCTAATCCCCACTGGAAGTGC
1 TACTCCACACGTTAGAGCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGC
* * * * *
2978398 TCGGTATGAACTCTGTCCCCCTTCTAACTCCTAACGGTGAAGCACTCGGTGAGAAATAGGAATAC
66 TCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAAAAATAGGAATAC
2978463 CCTACC
131 CCTACC
* *
2978469 TACTCCACACGTTAGAGCGTCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCTACTGGAAGCGC
1 TACTCCACACGTTAGAGCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGC
* * *
2978534 TCAGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGTAGCGCTCGGCGAAAAATATGAATAC
66 TCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAAAAATAGGAATAC
*
2978599 CCTGCC
131 CCTACC
* **
2978605 TACTCCACACGTTAGAGCGCCCGGCGTAAGATCAGGTCATCATGCCTACTCCCCACTAAAAGCGC
1 TACTCCACACGTTAGAGCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGC
* * * * *
2978670 TCGGCATAAACTCTGTCCCCTTTCCAACTCTTAACGCTGGAGCGCTCG
66 TCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCG
2978718 TCGTAATTCC
Statistics
Matches: 222, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
136 222 1.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (136 bp):
TACTCCACACGTTAGAGCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGC
TCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAAAAATAGGAATAC
CCTACC
Found at i:2981862 original size:20 final size:21
Alignment explanation
Indices: 2981837--2981876 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2981827 CTTTGTATAG
2981837 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
2981857 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
2981877 CTCAAAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:2983785 original size:19 final size:18
Alignment explanation
Indices: 2983750--2983800 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
2983740 AAAATGATTT
2983750 AATTTTGAAAGAAAAAATTG
1 AATTTTGAAA-AAAAAA-TG
2983770 -ATTTTGAAAAACAAAATG
1 AATTTTGAAAAA-AAAATG
2983788 AATATTTGAAAAA
1 AAT-TTTGAAAAA
2983801 TTATTTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.14
19 15 0.54
20 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (18 bp):
AATTTTGAAAAAAAAATG
Found at i:2985492 original size:20 final size:21
Alignment explanation
Indices: 2985449--2985494 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2985439 TATTTTGTAG
*
2985449 AGAAATCATCCCCAAACAGCT
1 AGAAATCATCACCAAACAGCT
*
2985470 AGAAATCATCACC-AACGGCT
1 AGAAATCATCACCAAACAGCT
2985490 AGAAA
1 AGAAA
2985495 CGTCCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.46, C:0.28, G:0.13, T:0.13
Consensus pattern (21 bp):
AGAAATCATCACCAAACAGCT
Found at i:2989604 original size:2 final size:2
Alignment explanation
Indices: 2989593--2989646 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
2989583 AAATTTATTA
2989593 AT AT -T 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
2989634 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2989647 ATAATTATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2998958 original size:15 final size:14
Alignment explanation
Indices: 2998938--2998992 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 14
2998928 ATTCAATCAG
*
2998938 AACAAAAAGGACAAA
1 AACAAAAAAGA-AAA
2998953 AACAAAAAAGAAAA
1 AACAAAAAAGAAAA
2998967 GAAGCAAAAAAGAAGAA
1 -AA-CAAAAAAGAA-AA
2998984 AACAAAAAA
1 AACAAAAAA
2998993 AAGAACAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 3 0.08
15 19 0.53
16 12 0.33
17 2 0.06
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (14 bp):
AACAAAAAAGAAAA
Found at i:2998962 original size:16 final size:17
Alignment explanation
Indices: 2998941--2999010 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
2998931 CAATCAGAAC
*
2998941 AAAAAGGACAAAAA-CA
1 AAAAAGAACAAAAAGCA
*
2998957 AAAAAGAA-AAGAAGCA
1 AAAAAGAACAAAAAGCA
* *
2998973 AAAAAGAAGAAAACA-AA
1 AAAAAGAACAAAA-AGCA
*
2998990 AAAAAGAACAAAAATCA
1 AAAAAGAACAAAAAGCA
2999007 AAAA
1 AAAA
2999011 GAAAAAGGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 4 0.09
16 18 0.41
17 21 0.48
18 1 0.02
ACGTcount: A:0.79, C:0.09, G:0.11, T:0.01
Consensus pattern (17 bp):
AAAAAGAACAAAAAGCA
Found at i:2999011 original size:16 final size:15
Alignment explanation
Indices: 2998938--2999013 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 15
2998928 ATTCAATCAG
*
2998938 AACAAAAAGGACAAA
1 AACAAAAAGAACAAA
2998953 AACAAAAAAGAA-AAGA
1 AAC-AAAAAGAACAA-A
* *
2998969 AGCAAAAAAGAAGAAAA
1 AAC-AAAAAGAA-CAAA
*
2998986 CAAAAAAAAGAACAAA
1 -AACAAAAAGAACAAA
2999002 AATCAAAAAGAA
1 AA-CAAAAAGAA
2999014 AAAGGGACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.14
16 30 0.61
17 9 0.18
18 3 0.06
ACGTcount: A:0.78, C:0.09, G:0.12, T:0.01
Consensus pattern (15 bp):
AACAAAAAGAACAAA
Found at i:2999673 original size:22 final size:22
Alignment explanation
Indices: 2999620--2999674 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2999610 GCTACCCCAT
*
2999620 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTTAGCATCAAATGC
*
2999642 CAAACCTTTTAGCATCAAATTC
1 CAAACCTTTTAGCATCAAATGC
2999664 CAAACCTTTTA
1 CAAACCTTTTA
2999675 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.29
Consensus pattern (22 bp):
CAAACCTTTTAGCATCAAATGC
Found at i:3000880 original size:106 final size:106
Alignment explanation
Indices: 3000693--3001670 Score: 1535
Period size: 106 Copynumber: 9.2 Consensus size: 106
3000683 TGTCAATAAA
* * *
3000693 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAATTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
3000758 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCTAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
*
3000799 CAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
3000864 CTAGTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
* * * *
3000905 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGAGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
3000970 CTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
** **
3001011 CAACTTCACAGTGAAGGATATTGGACTTGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
*
3001076 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
* *
3001117 CAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
3001182 CTGGTTGTCAACAAACAATTTCCCAATTTTAGATCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
* * *
3001223 CAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
3001288 CTGGTTGTCAACAAACAACTTCTCAATTTCAAAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
3001329 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
3001394 CTGGTTGTCAACAAACAACTTCCTAATTTCAGAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
* * *
3001435 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGATGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
3001500 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
* * * *
3001541 CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
3001605 ACTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTT
66 -CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
* *
3001647 CAACTTCACGACGGAGGATATTGG
1 CAACTTCACAACGAAGGATATTGG
3001671 CCTCGAAACA
Statistics
Matches: 803, Mismatches: 68, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
105 2 0.00
106 801 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTT
Found at i:3015687 original size:3 final size:3
Alignment explanation
Indices: 3015679--3015718 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3015669 TTTTATTCGT
3015679 TTA 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 TTA T
3015719 ATTTGTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3026014 original size:21 final size:21
Alignment explanation
Indices: 3025990--3026029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3025980 AAGACTTTAT
3025990 TTTCAAAATATAAAAATGATA
1 TTTCAAAATATAAAAATGATA
* *
3026011 TTTCAAAATTTAATAATGA
1 TTTCAAAATATAAAAATGA
3026030 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
TTTCAAAATATAAAAATGATA
Found at i:3031573 original size:20 final size:21
Alignment explanation
Indices: 3031519--3031581 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
3031509 GATTCCCCTG
3031519 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
3031543 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
3031563 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
3031582 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:3044453 original size:52 final size:52
Alignment explanation
Indices: 3044392--3044494 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
3044382 AGGATTAAAA
*
3044392 ATGACATTTGAAAGATTTGGAGTAATAATTTGATATTCGAATAATTATATCG
1 ATGACATTTGAAAGATTTAGAGTAATAATTTGATATTCGAATAATTATATCG
3044444 ATGACATTTGAAAGATTTAGAGTAATAATTTGATATTCGAATAATTATATC
1 ATGACATTTGAAAGATTTAGAGTAATAATTTGATATTCGAATAATTATATC
3044495 AAATATACTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.39
Consensus pattern (52 bp):
ATGACATTTGAAAGATTTAGAGTAATAATTTGATATTCGAATAATTATATCG
Found at i:3051367 original size:17 final size:17
Alignment explanation
Indices: 3051345--3051380 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3051335 GAGAAGATTA
3051345 CCTTTCTCGATCATCAT
1 CCTTTCTCGATCATCAT
3051362 CCTTTCTCGATCATCAT
1 CCTTTCTCGATCATCAT
3051379 CC
1 CC
3051381 AAGCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.39, G:0.06, T:0.39
Consensus pattern (17 bp):
CCTTTCTCGATCATCAT
Found at i:3052281 original size:22 final size:22
Alignment explanation
Indices: 3052255--3052310 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
3052245 CCGTTAAACA
3052255 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
3052277 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
3052299 GGGGGAATCGGT
1 GGGGGAATCGGT
3052311 TCCCTCTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:3064725 original size:16 final size:16
Alignment explanation
Indices: 3064704--3064734 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3064694 ATATCAGATA
*
3064704 AGAAATTGAAATAAAT
1 AGAAATGGAAATAAAT
3064720 AGAAATGGAAATAAA
1 AGAAATGGAAATAAA
3064735 AATCCAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (16 bp):
AGAAATGGAAATAAAT
Found at i:3065785 original size:20 final size:20
Alignment explanation
Indices: 3065749--3065786 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3065739 ATCCTATTCC
**
3065749 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3065769 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3065787 GTGAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3068560 original size:2 final size:2
Alignment explanation
Indices: 3068553--3068591 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3068543 TATTTTGGAG
*
3068553 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3068592 ATTTTAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3074002 original size:23 final size:23
Alignment explanation
Indices: 3073971--3074071 Score: 125
Period size: 23 Copynumber: 4.4 Consensus size: 23
3073961 ATTGAATATA
* * *
3073971 TAAACGAACATGTTCTTGAACAC
1 TAAATGAACATGTTCGTGAACAT
*
3073994 TAAATGAACATGTTCGTGAACGT
1 TAAATGAACATGTTCGTGAACAT
*
3074017 TAAATGAAC--GTTCTTGAACAT
1 TAAATGAACATGTTCGTGAACAT
*
3074038 ATAAATGAACACGTTCGTGAACAT
1 -TAAATGAACATGTTCGTGAACAT
3074062 TAAATGAACA
1 TAAATGAACA
3074072 CATTAGCTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
21 10 0.15
22 9 0.13
23 38 0.56
24 11 0.16
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (23 bp):
TAAATGAACATGTTCGTGAACAT
Done.