Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_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: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:753453 original size:42 final size:42
Alignment explanation
Indices: 753381--753498 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
753371 GATTCACCTG
* * ** *
753381 TCATCGTTCAAGAGGCCTCTCCTATTGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGACCCTA
*
753423 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGACCCTA
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGACCCTA
* ** *
753465 TCATCGTTCAAAAGATCCCTCCCACCATTCAAGA
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGA
753499 TCCCGATTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGACCCTA
Found at i:755136 original size:16 final size:16
Alignment explanation
Indices: 755107--755142 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
755097 TGTAAATAAG
* *
755107 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
755123 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
755139 AATT
1 AATT
755143 TCACTTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:755299 original size:20 final size:20
Alignment explanation
Indices: 755208--755296 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
755198 GAAAGTCAAA
*
755208 TTCGCGTTGCGA-TTTACCT
1 TTCGCGTTGCGATTTTAACT
755227 ATTCGCGTTGCGATTTTAACT
1 -TTCGCGTTGCGATTTTAACT
755248 TTCGCGTTGCGATTTTAACT
1 TTCGCGTTGCGATTTTAACT
* *
755268 TTCGCGTTGTGATTTTGACT
1 TTCGCGTTGCGATTTTAACT
755288 TTCGCGTTG
1 TTCGCGTTG
755297 TGAAAGTGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 59 0.91
21 6 0.09
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAACT
Found at i:758831 original size:40 final size:40
Alignment explanation
Indices: 758772--758847 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
758762 ATAAAAGCTG
* *
758772 TTGCAAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAA
1 TTGCAAAATCAAAATTCGTGTTGCGAATTAGAAAATCGAA
* *
758812 TTGCGAAATCAAAATTCGTGTTGCGATTTAGAAAAT
1 TTGCAAAATCAAAATTCGTGTTGCGAATTAGAAAAT
758848 ATTGTTGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (40 bp):
TTGCAAAATCAAAATTCGTGTTGCGAATTAGAAAATCGAA
Found at i:758836 original size:20 final size:20
Alignment explanation
Indices: 758770--758837 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
758760 AAATAAAAGC
* *
758770 TGTTGCAAAATTAAAATTCG
1 TGTTGCGAAATCAAAATTCG
*
758790 TGTTGCGAATTCGAAAA-TCG
1 TGTTGCGAAATC-AAAATTCG
**
758810 AATTGCGAAATCAAAATTCG
1 TGTTGCGAAATCAAAATTCG
758830 TGTTGCGA
1 TGTTGCGA
758838 TTTAGAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.11
20 30 0.79
21 4 0.11
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATCAAAATTCG
Found at i:758856 original size:40 final size:40
Alignment explanation
Indices: 758770--758859 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
758760 AAATAAAAGC
* * * *
758770 TGTTGCAAAATTAAAATTCGTGTTGCGAATTCGAAAATCG
1 TGTTGCGAAATCAAAATTCGTGTTGCGAATTAGAAAATAG
** * *
758810 AATTGCGAAATCAAAATTCGTGTTGCGATTTAGAAAATAT
1 TGTTGCGAAATCAAAATTCGTGTTGCGAATTAGAAAATAG
758850 TGTTGCGAAA
1 TGTTGCGAAA
758860 AGGAAACTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (40 bp):
TGTTGCGAAATCAAAATTCGTGTTGCGAATTAGAAAATAG
Found at i:758935 original size:20 final size:21
Alignment explanation
Indices: 758891--758983 Score: 77
Period size: 20 Copynumber: 4.6 Consensus size: 21
758881 ATAAATTTGC
* *
758891 GTTGTGAATTTGAAATTCCGT
1 GTTGTGAATTTGAACTTCTGT
*
758912 GTTGCGAATTTG-ACTTCTGT
1 GTTGTGAATTTGAACTTCTGT
*
758932 GTTGTGATTTTGGAAC--CTGT
1 GTTGTGAATTT-GAACTTCTGT
* * * *
758952 GTTGCGAAATTGGAGTTC-GT
1 GTTGTGAATTTGAACTTCTGT
758972 GTTGTGAATTTG
1 GTTGTGAATTTG
758984 TTGGTCATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
19 2 0.04
20 39 0.70
21 13 0.23
22 2 0.04
ACGTcount: A:0.18, C:0.10, G:0.29, T:0.43
Consensus pattern (21 bp):
GTTGTGAATTTGAACTTCTGT
Found at i:758936 original size:41 final size:40
Alignment explanation
Indices: 758891--758983 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
758881 ATAAATTTGC
*
758891 GTTGTGAATTTGAAATTCC-GTGTTGCG-AATTTGACTTCTGT
1 GTTGTGAATTTGAAA--CCTGTGTTGCGAAATTGGACTTC-GT
* * *
758932 GTTGTGATTTTGGAACCTGTGTTGCGAAATTGGAGTTCGT
1 GTTGTGAATTTGAAACCTGTGTTGCGAAATTGGACTTCGT
758972 GTTGTGAATTTG
1 GTTGTGAATTTG
758984 TTGGTCATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.04
40 21 0.47
41 22 0.49
ACGTcount: A:0.18, C:0.10, G:0.29, T:0.43
Consensus pattern (40 bp):
GTTGTGAATTTGAAACCTGTGTTGCGAAATTGGACTTCGT
Found at i:768778 original size:72 final size:72
Alignment explanation
Indices: 768695--768838 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
768685 GACTAAAAAC
*
768695 TTAAAATACCATAATTGTTTACCCTATTATTTATTTCAAATTTAAGAGGGTTGATGTCTGTTAGT
1 TTAAAATACCATAATTGTTTACCCTATTATTTATTTCAAATTTAAGAGGGTTGATGTCTGTTAAT
768760 CGTTTAA
66 CGTTTAA
*
768767 TTAAAATACCATCATTGTTTACCCTATTATTTATTTCAAATTTAAGAGGGTTGATGTCTGTTAAT
1 TTAAAATACCATAATTGTTTACCCTATTATTTATTTCAAATTTAAGAGGGTTGATGTCTGTTAAT
768832 CGTTTAA
66 CGTTTAA
768839 GGATCGAAGG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (72 bp):
TTAAAATACCATAATTGTTTACCCTATTATTTATTTCAAATTTAAGAGGGTTGATGTCTGTTAAT
CGTTTAA
Found at i:774161 original size:2 final size:2
Alignment explanation
Indices: 774154--774206 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
774144 CGATGCTTTC
774154 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
774196 CT CT CT CT CT C
1 CT CT CT CT CT C
774207 CTCAAAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:777624 original size:25 final size:25
Alignment explanation
Indices: 777590--777639 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
777580 ACTTGAGCAA
777590 ATTAAACAATAAAGCTCACAAGTGT
1 ATTAAACAATAAAGCTCACAAGTGT
777615 ATTAAACAATAAAGCTCACAAGTGT
1 ATTAAACAATAAAGCTCACAAGTGT
777640 GTTACAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (25 bp):
ATTAAACAATAAAGCTCACAAGTGT
Found at i:777653 original size:25 final size:24
Alignment explanation
Indices: 777594--777647 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
777584 GAGCAAATTA
777594 AACAATAAAGCTCACAAGTGTATT
1 AACAATAAAGCTCACAAGTGTATT
*
777618 AAACAATAAAGCTCACAAGTGTGTT
1 -AACAATAAAGCTCACAAGTGTATT
777643 -ACAAT
1 AACAAT
777648 GAAAAGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 5 0.18
25 23 0.82
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (24 bp):
AACAATAAAGCTCACAAGTGTATT
Found at i:777829 original size:22 final size:23
Alignment explanation
Indices: 777804--777847 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
777794 TAGTCATTAC
777804 ATACAACAAAAAAT-AA-CATTTA
1 ATAC-ACAAAAAATCAATCATTTA
*
777826 ATACACAACAAATCAATCATTT
1 ATACACAAAAAATCAATCATTT
777848 TGTGAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (23 bp):
ATACACAAAAAATCAATCATTTA
Found at i:777918 original size:21 final size:21
Alignment explanation
Indices: 777894--777951 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
777884 CGTTGCAAGA
777894 AAGGGATCTATCCTTTAGGGG
1 AAGGGATCTATCCTTTAGGGG
777915 AAGGGATCTATCCTTTAGGGG
1 AAGGGATCTATCCTTTAGGGG
*
777936 AAGGGATCAATCCTTT
1 AAGGGATCTATCCTTT
777952 TCATCGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (21 bp):
AAGGGATCTATCCTTTAGGGG
Found at i:782547 original size:60 final size:58
Alignment explanation
Indices: 782330--782530 Score: 202
Period size: 60 Copynumber: 3.5 Consensus size: 58
782320 CATCAAAGAA
* * * *
782330 CCCTAAAAATTAGGCTTAGATTCATTTTAAAAACTCTTTGGAGATAATCATCAAGAAAG
1 CCCTAAAAATTAGGCTTAGTTTC-TTTTAAAAACTCTTTGAAAATAATCATCAAGAAAC
* * * * * *
782389 CCCTGAAAATCAGGCTTAGTTTC---AAAAAACTCATTTG---AGAA-CATAAAAAAAC
1 CCCTAAAAATTAGGCTTAGTTTCTTTTAAAAACTC-TTTGAAAATAATCATCAAGAAAC
*
782441 CCCTAAAAATTAGGCTTAGTTTCTTTTTAAAAAATTCTTTGAAAATAATCATCAAGAAAC
1 CCCTAAAAATTAGGCTTAGTTTC-TTTT-AAAAACTCTTTGAAAATAATCATCAAGAAAC
*
782501 CCCTGAAAATTAGGCTTAGTTTC-TTTAAAA
1 CCCTAAAAATTAGGCTTAGTTTCTTTTAAAA
782531 TCTTTCTTTT
Statistics
Matches: 116, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
52 29 0.25
53 3 0.03
55 8 0.07
56 8 0.07
57 11 0.09
58 3 0.03
59 23 0.20
60 31 0.27
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (58 bp):
CCCTAAAAATTAGGCTTAGTTTCTTTTAAAAACTCTTTGAAAATAATCATCAAGAAAC
Found at i:784892 original size:59 final size:56
Alignment explanation
Indices: 784709--784901 Score: 164
Period size: 59 Copynumber: 3.4 Consensus size: 56
784699 TTATTAGTTG
* ** * *
784709 TCATCAAGGAACCCCTAAAAAATTAGATTTAGCATCCTTTTAAAAACTCTTTGGAGATAA
1 TCATCAAGAAACCCCT-AAAAATTAGGCTTAAC-TCTTTTTAAAAACTCTTT-GA-ATAA
* * * *
784769 TCATCAAGAAACCCCTGAAAATTAGGCTT-A--GTTTCTAAAAACTCATTTG-AGAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAACTCTTTTTAAAAACTC-TTTGAATAA
*
784822 -CATCAAGAAACCCCT-AAAATTAGGCTTAACTTCTTTTTAAAATATTCTTTGAAAATAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAAC-TCTTTTTAAAA-ACTCTTTG--AATAA
*
784880 TCATCAAGAAACCCCTGAAAAT
1 TCATCAAGAAACCCCTAAAAAT
784902 CAAGCTTAGT
Statistics
Matches: 109, Mismatches: 13, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
51 12 0.11
52 16 0.15
53 3 0.03
55 24 0.22
56 6 0.06
58 3 0.03
59 25 0.23
60 20 0.18
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (56 bp):
TCATCAAGAAACCCCTAAAAATTAGGCTTAACTCTTTTTAAAAACTCTTTGAATAA
Found at i:784909 original size:111 final size:111
Alignment explanation
Indices: 784710--784913 Score: 284
Period size: 111 Copynumber: 1.8 Consensus size: 111
784700 TATTAGTTGT
* * * * *
784710 CATCAAGGAACCCCTAAAAAATTAGATTTAGCATCCTTTTAAAAACTCTTTGGAGATAATCATCA
1 CATCAAGAAACCCCT-AAAAATTAGACTTAACATCCTTTTAAAAACTCTTTGAAAATAATCATCA
* *
784775 AGAAACCCCTGAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAGAA
65 AGAAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAGAA
* * * *
784822 CATCAAGAAACCCCT-AAAATTAGGCTTAACTTCTTTTTAAAATATTCTTTGAAAATAATCATCA
1 CATCAAGAAACCCCTAAAAATTAGACTTAACATCCTTTTAAAA-ACTCTTTGAAAATAATCATCA
784886 AGAAACCCCTGAAAATCAAGCTTAGTTT
65 AGAAACCCCTGAAAATCAAGCTTAGTTT
784914 ATTTAAAATC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 22 0.28
111 44 0.55
112 14 0.17
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (111 bp):
CATCAAGAAACCCCTAAAAATTAGACTTAACATCCTTTTAAAAACTCTTTGAAAATAATCATCAA
GAAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAGAA
Found at i:784942 original size:59 final size:59
Alignment explanation
Indices: 784822--784942 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 59
784812 CATTTGAGAA
* * * *
784822 CATCAAGAAACCCCTAAAATTAGGCTTAACTTCTTTTTAAAATATTCTTTGAAAATAAT
1 CATCAAGAAACCCCTAAAATCAAGCTTAACTTCTATTTAAAATATTCTTTAAAAATAAT
* *
784881 CATCAAGAAACCCCTGAAAATCAAGCTT-AGTT-TATTTAAAATCCTTCTTTTAAAAAT-AT
1 CATCAAGAAACCCCT-AAAATCAAGCTTAACTTCTATTTAAAAT-ATTC-TTTAAAAATAAT
784940 CAT
1 CAT
784943 GTTGTTTGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 9 0.17
59 26 0.49
60 18 0.34
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (59 bp):
CATCAAGAAACCCCTAAAATCAAGCTTAACTTCTATTTAAAATATTCTTTAAAAATAAT
Found at i:786964 original size:26 final size:24
Alignment explanation
Indices: 786913--786967 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
786903 TTCTTTTTTC
*
786913 TTTTTTTCTTTTTTTCATTTCATT
1 TTTTTTTCTTTTTATCATTTCATT
786937 TTTTATTTCTTTTCTATCATTTC-TT
1 TTTT-TTTCTTTT-TATCATTTCATT
786962 TTTTTT
1 TTTTTT
786968 GCTATATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 14 0.50
26 8 0.29
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTTCTTTTTATCATTTCATT
Found at i:786977 original size:25 final size:26
Alignment explanation
Indices: 786927--786978 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
786917 TTTCTTTTTT
* *
786927 TCATTTCATTTTTTATTTCTTTTCTA
1 TCATTTCATTTTTTATTGCTTATCTA
786953 TCATTTC-TTTTTT-TTGCTATATCTA
1 TCATTTCATTTTTTATTGCT-TATCTA
786978 T
1 T
786979 TCTTTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.67
Consensus pattern (26 bp):
TCATTTCATTTTTTATTGCTTATCTA
Found at i:794116 original size:41 final size:41
Alignment explanation
Indices: 794041--794145 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 41
794031 AAATGTTGAA
* * * * * *
794041 AACATCCTGCCCAAAGGTCTTATGGATGGCTTGAAGGACTT
1 AACATCATGCTCAAAAGACTTATAGATGACTTGAAGGACTT
* * *
794082 ATA-ATCTTGCTTAAAAGACTTATAGATGACTTGAAGGATTT
1 A-ACATCATGCTCAAAAGACTTATAGATGACTTGAAGGACTT
794123 AAGCATCATGCTCAAAAGACTTA
1 AA-CATCATGCTCAAAAGACTTA
794146 CTGATGGCCC
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.02
41 32 0.63
42 18 0.35
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (41 bp):
AACATCATGCTCAAAAGACTTATAGATGACTTGAAGGACTT
Found at i:794393 original size:20 final size:21
Alignment explanation
Indices: 794367--794422 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
794357 TTATCATGTT
794367 GCTCGAAAGACTTATAG-ATGA
1 GCTCGAAAGACTTA-AGCATGA
* *
794388 -CTCGAAGGATTTAAGCATGA
1 GCTCGAAAGACTTAAGCATGA
794408 TGCTCGAAAGACTTA
1 -GCTCGAAAGACTTA
794423 CTGATGGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
22 11 0.39
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (21 bp):
GCTCGAAAGACTTAAGCATGA
Found at i:794419 original size:42 final size:41
Alignment explanation
Indices: 794329--794422 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
794319 ACATCCTGCC
* * * * *
794329 CGAAAGTCTTATGGATGGCCCGAAGGACTTATCATGTTGCT
1 CGAAAGACTTATAGATGACCCGAAGGACTTAGCATGATGCT
* *
794370 CGAAAGACTTATAGATGACTCGAAGGATTTAAGCATGATGCT
1 CGAAAGACTTATAGATGACCCGAAGGACTT-AGCATGATGCT
794412 CGAAAGACTTA
1 CGAAAGACTTA
794423 CTGATGGCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 25 0.56
42 20 0.44
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (41 bp):
CGAAAGACTTATAGATGACCCGAAGGACTTAGCATGATGCT
Found at i:794714 original size:60 final size:59
Alignment explanation
Indices: 794489--794719 Score: 135
Period size: 60 Copynumber: 4.0 Consensus size: 59
794479 TTAGTTGTCG
* * * * * ** *
794489 TCAAGGAACCCCTAAAAAT-TAGATTTAGCATC-CTTTTAAAAATTCTTTGGAGATAATCA
1 TCAAGAAACCCCTAAAAATCAAG-CTTAGCTTCTCTTTAAAAAATTCTTTAAAAAT-ATCA
* * * * *
794548 TCAAGAAACCCCTGAAAATCAGGCTTAG-TT-TC--T-AAAAACTCATTT-GAGA-A-CA
1 TCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTCTTTAAAAAATTC-TTTAAAAATATCA
* * * * *
794600 TTAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAAATTCTTTGAAAATAATCA
1 TCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTCTTTAAAAAATTCTTTAAAAAT-ATCA
* **
794660 TCAAGAAACCCCTGAAAATCAAGCTTAG-TT-TCTTTAAAATCTTTCTTTTAAAAATATCA
1 TCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTCTTTAAAA-AATTC-TTTAAAAATATCA
794719 T
1 T
794720 GTTGTTTGAG
Statistics
Matches: 136, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
52 27 0.20
53 3 0.02
54 1 0.01
55 11 0.08
56 8 0.06
57 9 0.07
58 10 0.07
59 32 0.24
60 35 0.26
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (59 bp):
TCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTCTTTAAAAAATTCTTTAAAAATATCA
Found at i:796667 original size:10 final size:9
Alignment explanation
Indices: 796654--796737 Score: 80
Period size: 10 Copynumber: 9.0 Consensus size: 9
796644 TTTGATCGGA
796654 TTTCTTTTT
1 TTTCTTTTT
*
796663 CTTTCTTTCT
1 -TTTCTTTTT
796673 TTTCTTTTTT
1 TTTC-TTTTT
796683 TTTCATTTTT
1 TTTC-TTTTT
*
796693 TTTCATTTT
1 TTTCTTTTT
796702 TTTCATTTTT
1 TTTC-TTTTT
*
796712 TCTCTTTTT
1 TTTCTTTTT
* *
796721 GTT-TTTTC
1 TTTCTTTTT
796729 TTTCTTTTT
1 TTTCTTTTT
796738 ATCATTTCTT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
8 6 0.10
9 22 0.37
10 32 0.53
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:796678 original size:9 final size:8
Alignment explanation
Indices: 796658--796756 Score: 67
Period size: 9 Copynumber: 11.6 Consensus size: 8
796648 ATCGGATTTC
796658 TTTTTCTT
1 TTTTTCTT
*
796666 TCTTTCTT
1 TTTTTCTT
*
796674 TTCTT-TT
1 TTTTTCTT
796681 TTTTTCATTT
1 TTTTTC--TT
796691 TTTTTCATT
1 TTTTTC-TT
796700 TTTTTCATT
1 TTTTTC-TT
796709 TTTTCTCTT
1 TTTT-TCTT
796718 TTTGTT-TT
1 TTT-TTCTT
796726 TTCTTTCTT
1 TT-TTTCTT
*
796735 TTTATCATT
1 TTTTTC-TT
* *
796744 TCTTTGTT
1 TTTTTCTT
796752 TTTTT
1 TTTTT
796757 GCTACATCTA
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
7 6 0.08
8 25 0.34
9 31 0.42
10 11 0.15
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:796678 original size:19 final size:19
Alignment explanation
Indices: 796654--796748 Score: 85
Period size: 19 Copynumber: 5.1 Consensus size: 19
796644 TTTGATCGGA
796654 TTTCTTTTTCTTTC-TTTCT
1 TTTCTTTTT-TTTCATTTCT
*
796673 TTTCTTTTTTTTTCATTTTT
1 TTTC-TTTTTTTTCATTTCT
*
796693 TTTCATTTTTTTCATTT-T
1 TTTCTTTTTTTTCATTTCT
796711 TTCTCTTTTTGTTT--TTTC-
1 TT-TCTTTTT-TTTCATTTCT
*
796729 TTTC-TTTTTATCATTTCT
1 TTTCTTTTTTTTCATTTCT
796747 TT
1 TT
796749 GTTTTTTTGC
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
15 2 0.03
16 4 0.06
17 6 0.09
18 10 0.16
19 26 0.41
20 16 0.25
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTCTTTTTTTTCATTTCT
Found at i:796745 original size:17 final size:16
Alignment explanation
Indices: 796660--796755 Score: 68
Period size: 17 Copynumber: 5.6 Consensus size: 16
796650 CGGATTTCTT
*
796660 TTTCTTTCTTTCTTTTC
1 TTTCTTT-TTTCATTTC
*
796677 TTT-TTTTTTCATTTTT
1 TTTCTTTTTTCA-TTTC
*
796693 TTTCATTTTTTTCATTTT
1 TTTC--TTTTTTCATTTC
**
796711 TTCTCTTTTTGTTTTTTC
1 TT-TCTTTTT-TCATTTC
796729 TTTCTTTTTATCATTTC
1 TTTCTTTTT-TCATTTC
*
796746 TTTGTTTTTT
1 TTTCTTTTTT
796756 TGCTACATCT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
15 4 0.06
16 10 0.16
17 28 0.44
18 12 0.19
19 10 0.16
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTTCATTTC
Found at i:796755 original size:44 final size:42
Alignment explanation
Indices: 796660--796756 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
796650 CGGATTTCTT
* * *
796660 TTTCTTTCTTTCTTTTCTTTTTTTTTCATTTTTTTTCATTTT
1 TTTCTTTTTTTCTTTTCTTGTTTTTTCATTTTTTTTCATTTC
* *
796702 TTTCATTTTTTCTCTTT-TTGTTTTTTCTTTCTTTTTATCATTTC
1 TTTCTTTTTTTCT-TTTCTTGTTTTTTCATT-TTTTT-TCATTTC
*
796746 TTTGTTTTTTT
1 TTTCTTTTTTT
796757 GCTACATCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
42 22 0.49
43 8 0.18
44 15 0.33
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.79
Consensus pattern (42 bp):
TTTCTTTTTTTCTTTTCTTGTTTTTTCATTTTTTTTCATTTC
Found at i:803142 original size:42 final size:41
Alignment explanation
Indices: 803042--803148 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
803032 GACTGAAGGT
* * * *
803042 CTTATGGATGGTCCGAAGGACTTATCATCTTGCTCGAAATA
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAATA
* * *
803083 CTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAATA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAATA
* *
803125 CTTTTTGATGGCCCGAAGGACTTA
1 CTTATAGATGGCCCGAAGGACTTA
803149 CTCATAAAGA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 19 0.36
42 34 0.64
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAATA
Found at i:805428 original size:17 final size:19
Alignment explanation
Indices: 805386--805449 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
805376 TTGATCGATT
* * *
805386 TTCTTTCTTCTTTCTTTTCA
1 TTCTTTTTTCATT-TTTTCC
805406 TT-TTTTTTCATTTTTT-C
1 TTCTTTTTTCATTTTTTCC
*
805423 -TCTTTTTT-GTTTTTTCC
1 TTCTTTTTTCATTTTTTCC
805440 TTCTTTTTTC
1 TTCTTTTTTC
805450 TTACTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 12 0.33
19 8 0.22
20 2 0.06
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.77
Consensus pattern (19 bp):
TTCTTTTTTCATTTTTTCC
Found at i:807758 original size:22 final size:22
Alignment explanation
Indices: 807733--807780 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
807723 AGGCCCAATG
807733 CTCCTCATGAGGTGTGACGTTT
1 CTCCTCATGAGGTGTGACGTTT
807755 CTCCTCATGAGGTGTGACGTTT
1 CTCCTCATGAGGTGTGACGTTT
807777 CTCC
1 CTCC
807781 ATACTTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.27, G:0.25, T:0.35
Consensus pattern (22 bp):
CTCCTCATGAGGTGTGACGTTT
Found at i:808950 original size:26 final size:26
Alignment explanation
Indices: 808914--808964 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
808904 CACTTTTTAT
* * *
808914 AAATTGTTACTGCTAAACAAGCTAAA
1 AAATTGCTACTACTAAACAACCTAAA
808940 AAATTGCTACTACTAAACAACCTAA
1 AAATTGCTACTACTAAACAACCTAA
808965 CTCATATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATTGCTACTACTAAACAACCTAAA
Found at i:813442 original size:16 final size:17
Alignment explanation
Indices: 813413--813449 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
813403 TTATGAGGTG
813413 AAAAAATGATATTATTGT
1 AAAAAATGATATTATT-T
813431 AAAAAAT-A-ATTATTT
1 AAAAAATGATATTATTT
813446 AAAA
1 AAAA
813450 TACTATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 1 0.05
18 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
AAAAAATGATATTATTT
Found at i:815947 original size:2 final size:2
Alignment explanation
Indices: 815940--815967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
815930 TATTTTAAAC
815940 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
815968 TCATGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:816665 original size:19 final size:20
Alignment explanation
Indices: 816641--816684 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
816631 TAAATAATTA
816641 TAAATTATAAATTT-ATAAT
1 TAAATTATAAATTTAATAAT
* *
816660 TAAATTTTAATTTTAATAAT
1 TAAATTATAAATTTAATAAT
816680 TAAAT
1 TAAAT
816685 AAATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATTATAAATTTAATAAT
Found at i:823157 original size:23 final size:24
Alignment explanation
Indices: 823124--823186 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
823114 TAATTTAAAA
* *
823124 TATTTATTATTTTCATAAA-ATAT
1 TATTTAATATTTTAATAAACATAT
823147 TATTTAATA-TTTAATAAACATAT
1 TATTTAATATTTTAATAAACATAT
823170 T-TTTCAATATTTTAATA
1 TATTT-AATATTTTAATA
823187 CTTAAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 11 0.31
23 17 0.49
24 7 0.20
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTAATATTTTAATAAACATAT
Found at i:823308 original size:19 final size:20
Alignment explanation
Indices: 823284--823339 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
823274 TTTTATTTTT
823284 AAAATATTA-TAAAATTAAA
1 AAAATATTATTAAAATTAAA
*
823303 AAAATAATATTAATAA-TAAA
1 AAAATATTATTAA-AATTAAA
823323 AAAAT-TTATTAAAATTA
1 AAAATATTATTAAAATTA
823340 TTGATACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 16 0.50
20 12 0.38
21 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATATTATTAAAATTAAA
Found at i:823311 original size:22 final size:20
Alignment explanation
Indices: 823286--823336 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
823276 TTATTTTTAA
823286 AATATTATAAAATTAAAAAAAT
1 AATATTA-AAAA-TAAAAAAAT
*
823308 AATATTAATAATAAAAAAAT
1 AATATTAAAAATAAAAAAAT
*
823328 -TTATTAAAA
1 AATATTAAAA
823337 TTATTGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 7 0.27
20 9 0.35
21 3 0.12
22 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATTAAAAATAAAAAAAT
Found at i:824933 original size:12 final size:12
Alignment explanation
Indices: 824918--824942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
824908 AAAAACATAG
824918 AACAAAAAAAAA
1 AACAAAAAAAAA
824930 AACAAAAAAAAA
1 AACAAAAAAAAA
824942 A
1 A
824943 CACCCAGAAG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAAAAAAAA
Found at i:838645 original size:55 final size:55
Alignment explanation
Indices: 838571--838977 Score: 599
Period size: 55 Copynumber: 7.5 Consensus size: 55
838561 GAGATTATGG
*
838571 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* * *
838626 GTCTTATACTCTCTAAAGAAATAGGGGACATACGCGATTGTTGAAGATTGTTCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* *
838681 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGCTCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* * *
838736 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGATGAAGATTG-T-GG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* *
838789 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGCTCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* *
838844 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* * * *
838897 GTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTCCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
* *
838952 GT-TCTATACTCTCTAAAGAAAGAGGG
1 GTCT-TATACTCTCTGAAGAAATAGGG
838978 ATCGAACCCG
Statistics
Matches: 319, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
53 95 0.30
54 4 0.01
55 220 0.69
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
Found at i:838839 original size:108 final size:108
Alignment explanation
Indices: 838555--838977 Score: 661
Period size: 108 Copynumber: 3.9 Consensus size: 108
838545 TTCCCCACGT
* * * *
838555 TTGATGGAGATTATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATT
1 TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
* * *
838620 GTTCGAGTCTTATACTCTCTAAAGAAATAGGGGACATACGCGA
66 GCTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGA
* *
838663 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGA
1 TTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGA
* *
838728 TTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA
64 TTGCTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGA
838773 TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
1 TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
*
838838 GCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
66 GCTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGA
* *
838881 TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATT
1 TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
*
838946 G-TCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
66 GCT-CGAGTCT-TATACTCTCTAAAGAAATAGGG
838978 ATCGAACCCG
Statistics
Matches: 293, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
107 2 0.01
108 191 0.65
109 2 0.01
110 98 0.33
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATT
GCTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGA
Found at i:838962 original size:163 final size:162
Alignment explanation
Indices: 838550--838977 Score: 619
Period size: 163 Copynumber: 2.6 Consensus size: 162
838540 ACAGGTTCCC
* * * **
838550 CACGTTTGATGGAGATTATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 CACGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGA
* * *
838615 AGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGACATACGCGATTGTTGAAGATTGTTCG
66 AGATTG-TCGAGTCTTATACTCTCTAAAGAAATAGGGGACAGACACGATTGTTGAAGATTGCTCG
838680 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGA
130 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGA
* * *
838713 CACGATTGTTGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGA-
1 CACGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-AT
* * *
838777 TGAAGATTGT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGCT
63 TGAAGATTGTCGAGTCTTATACTCTCTAAAGAAATAGGGGACAGACACGATTGTTGAAGATTGCT
838841 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGA
128 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGA
* * *
838876 CGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
1 CACGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGA
*
838941 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
66 AGATTGT-CGAGTCT-TATACTCTCTAAAGAAATAGGG
838978 ATCGAACCCG
Statistics
Matches: 235, Mismatches: 23, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
160 1 0.00
161 47 0.20
162 2 0.01
163 136 0.58
164 2 0.01
165 47 0.20
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (162 bp):
CACGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGA
AGATTGTCGAGTCTTATACTCTCTAAAGAAATAGGGGACAGACACGATTGTTGAAGATTGCTCGA
GTCTTATACTCTCTGAAGAAATAGGGGGCAGA
Found at i:843965 original size:14 final size:14
Alignment explanation
Indices: 843946--843977 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
843936 TGAAGACTTG
843946 ACGACAAAGCTTCA
1 ACGACAAAGCTTCA
843960 ACGACAAAGCTTCA
1 ACGACAAAGCTTCA
843974 ACGA
1 ACGA
843978 ATAGTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.16, T:0.12
Consensus pattern (14 bp):
ACGACAAAGCTTCA
Found at i:849339 original size:2 final size:2
Alignment explanation
Indices: 849332--849366 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
849322 ATAAAATGAT
849332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
849367 TACTTATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:850258 original size:12 final size:12
Alignment explanation
Indices: 850243--850279 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
850233 TTTTCGTCCA
850243 ATTTTTTCTCTG
1 ATTTTTTCTCTG
850255 A-TTTTTCT-TG
1 ATTTTTTCTCTG
850265 ATTATTTTCTCTG
1 ATT-TTTTCTCTG
850278 AT
1 AT
850280 GTTTCTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.14
11 8 0.36
12 7 0.32
13 4 0.18
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.65
Consensus pattern (12 bp):
ATTTTTTCTCTG
Found at i:850266 original size:10 final size:11
Alignment explanation
Indices: 850245--850286 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
850235 TTCGTCCAAT
850245 TTTTTCTCTGA
1 TTTTTCTCTGA
850256 TTTTTCT-TGA
1 TTTTTCTCTGA
850266 TTATTTTCTCTGA
1 -T-TTTTCTCTGA
*
850279 TGTTTCTC
1 TTTTTCTC
850287 CAAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 3 0.11
11 14 0.52
12 7 0.26
13 3 0.11
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.64
Consensus pattern (11 bp):
TTTTTCTCTGA
Found at i:850295 original size:23 final size:23
Alignment explanation
Indices: 850214--850296 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
850204 TTCATCTTTT
* *
850214 TTTCTTCAATTTTCT-TCT-AT-
1 TTTCTCCAATTTTTTCTCTGATG
*
850234 TTTCGTCCAATTTTTTCTCTGATT
1 TTTC-TCCAATTTTTTCTCTGATG
**
850258 TTTCT-TGATTATTTTCTCTGATG
1 TTTCTCCAATT-TTTTCTCTGATG
850281 TTTCTCCAAATTTTTT
1 TTTCTCC-AATTTTTT
850297 TATTTATTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.08
21 9 0.18
22 6 0.12
23 19 0.39
24 8 0.16
25 3 0.06
ACGTcount: A:0.14, C:0.18, G:0.06, T:0.61
Consensus pattern (23 bp):
TTTCTCCAATTTTTTCTCTGATG
Found at i:854988 original size:19 final size:20
Alignment explanation
Indices: 854964--855010 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
854954 CAAAAAAATT
*
854964 TATGAATAATATT-GTACTG
1 TATGAATAATATTACTACTG
* *
854983 TATGAATAGTATTACTATTG
1 TATGAATAATATTACTACTG
855003 TATGAATA
1 TATGAATA
855011 GTACCAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (20 bp):
TATGAATAATATTACTACTG
Found at i:855133 original size:21 final size:21
Alignment explanation
Indices: 855104--855161 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
855094 CGATACTGCT
*
855104 ATAGGAGTATCGATACCGTGA
1 ATAGTAGTATCGATACCGTGA
855125 ATAGTAGTATCGATACCGTGA
1 ATAGTAGTATCGATACCGTGA
* *
855146 ATACTAGTGTCGATAC
1 ATAGTAGTATCGATAC
855162 TATCAAGCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (21 bp):
ATAGTAGTATCGATACCGTGA
Found at i:867193 original size:20 final size:20
Alignment explanation
Indices: 867170--867214 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
867160 ATTCTTAGTA
*
867170 ACTTCAGTGTCACTAGGGTG
1 ACTTCAGTGTCACTAGGGAG
867190 ACTTCAGTGTCACTAGGGAG
1 ACTTCAGTGTCACTAGGGAG
867210 ACTTC
1 ACTTC
867215 TATGTGGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (20 bp):
ACTTCAGTGTCACTAGGGAG
Found at i:870505 original size:21 final size:21
Alignment explanation
Indices: 870479--870526 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
870469 CGATACTGTG
870479 TGAACAGTAGTATCAATACCA
1 TGAACAGTAGTATCAATACCA
* *
870500 TGAACAGTGGTATCGATACCA
1 TGAACAGTAGTATCAATACCA
*
870521 TAAACA
1 TGAACA
870527 ATACCGATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (21 bp):
TGAACAGTAGTATCAATACCA
Found at i:870602 original size:21 final size:21
Alignment explanation
Indices: 870576--870633 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
870566 CGATACTGCT
870576 ATAGTAGTATCGATACCATGA
1 ATAGTAGTATCGATACCATGA
* * *
870597 ATAGTAGTATTGATATCGTGA
1 ATAGTAGTATCGATACCATGA
* *
870618 ACAGTATTATCGATAC
1 ATAGTAGTATCGATAC
870634 TATCAAGCCC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
ATAGTAGTATCGATACCATGA
Found at i:874689 original size:24 final size:24
Alignment explanation
Indices: 874640--874689 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
874630 TAGTAATAAT
* *
874640 AATAAAAATAAAATGAAAAACCAA
1 AATAAAAATAAAATAAAAAACAAA
* *
874664 AATAAGAATAAAATAAAAAAGAAA
1 AATAAAAATAAAATAAAAAACAAA
874688 AA
1 AA
874690 AAGGTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (24 bp):
AATAAAAATAAAATAAAAAACAAA
Found at i:874766 original size:4 final size:4
Alignment explanation
Indices: 874757--874790 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
874747 AGAAACCAAA
*
874757 AAAT AAAT AAAT AAAT AAAT AAAT AAAC AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
874791 GGGACCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:875997 original size:84 final size:84
Alignment explanation
Indices: 875880--876048 Score: 214
Period size: 84 Copynumber: 2.0 Consensus size: 84
875870 AACTCGACAA
* * *
875880 TTTTGTTGACAGATAGCCCTTCTTGCCTCGAGCTATACTGTAAATGATGTTCCCTT-GAGCTAAG
1 TTTTGGTGACAGATAGCCCTTCTAGCCTCGAGCTATACTGCAAATGATG-TCCCTTGGAGCTAAG
*
875944 TGTAATCGAACTCAAAGGTT
65 CGTAATCGAACTCAAAGGTT
* * * * *
875964 TTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGGTGACAGATAGCCCTTCTAGCCTCGAGCTATACTGCAAATGATGTCCCTTGGAGCTAAGC
* **
876029 GTAGTCGAACTTGAAGGTT
66 GTAATCGAACTCAAAGGTT
876048 T
1 T
876049 GGTGTTTCAA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 5 0.07
84 67 0.93
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (84 bp):
TTTTGGTGACAGATAGCCCTTCTAGCCTCGAGCTATACTGCAAATGATGTCCCTTGGAGCTAAGC
GTAATCGAACTCAAAGGTT
Found at i:876122 original size:34 final size:36
Alignment explanation
Indices: 876050--876135 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 36
876040 TGAAGGTTTG
* *
876050 GTGTTTCAAGAAAAACATTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACATTTTCAAAGGTATTTTTTT
876086 GTGTTTCAAGAGAAACGA-TTTCAAA-G-ATTTTTTT
1 GTGTTTCAAGAGAAAC-ATTTTCAAAGGTATTTTTTT
876120 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
876136 TGTCTCCAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
34 23 0.49
35 1 0.02
36 22 0.47
37 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACATTTTCAAAGGTATTTTTTT
Found at i:876168 original size:71 final size:67
Alignment explanation
Indices: 876087--876237 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
876077 TTTTTTTTTG
* * * *
876087 TGTTTCAAGAGAAACGAT-TTCAAAGATTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGGC
1 TGTTTCAAGAGAAAC-ATATTCAAAGA----TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
*
876151 AAAATTT
61 AAAACTT
* * *
876158 TGTTTCAAGAGAAACATATTCAGAGATTGGTTTTTCAAGAGAAACTGTCTCAAGAGAGATAAAAC
1 TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
876223 TT
66 TT
876225 TGTTTCAAG-GAAA
1 TGTTTCAAGAGAAA
876238 AATGTCTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
66 4 0.06
67 43 0.61
70 2 0.03
71 22 0.31
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (67 bp):
TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
TT
Found at i:876271 original size:19 final size:18
Alignment explanation
Indices: 876212--876274 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
876202 CTGTCTCAAG
876212 AGAGATAAAACTTTGTTTCA
1 AGAGA-AAAA-TTTGTTTCA
*
876232 AG-GAAAAA--TGTCTCAA
1 AGAGAAAAATTTGTTTC-A
876248 CAGAGACAAAATTTGTTTCA
1 -AGAGA-AAAATTTGTTTCA
876268 AGAGAAA
1 AGAGAAA
876275 CTATCTCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 5 0.14
16 1 0.03
17 2 0.06
18 8 0.23
19 11 0.31
20 3 0.09
21 5 0.14
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.25
Consensus pattern (18 bp):
AGAGAAAAATTTGTTTCA
Found at i:876282 original size:36 final size:37
Alignment explanation
Indices: 876190--876321 Score: 162
Period size: 37 Copynumber: 3.6 Consensus size: 37
876180 GAGATTGGTT
*
876190 TTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
* *
876227 TTTCAAG-GAAAAATGTCTCAACAGAGACAAAA-TTTG
1 TTTCAAGAG-AAACTGTCTCAAGAGAGACAAAACTTTG
* *
876263 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
* *
876300 -TTCTAAAAGAAATTGTCTCAAG
1 TTTC-AAGAGAAACTGTCTCAAG
876322 CGAAACGAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
36 35 0.43
37 46 0.57
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (37 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
Found at i:876317 original size:73 final size:73
Alignment explanation
Indices: 876190--876337 Score: 192
Period size: 73 Copynumber: 2.0 Consensus size: 73
876180 GAGATTGGTT
* * * * * *
876190 TTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGAAAAATGTCTCAA-CAGAGA
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTAAAAGAAAAATGTCTCAAGC-GAAA
876254 CAAAATTTG
65 CAAAATTTG
*
876263 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAG-AAATTGTCTCAAGCGAAA
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTT-TAAAAGAAAAATGTCTCAAGCGAAA
*
876327 CGAAATTTG
65 CAAAATTTG
876336 TT
1 TT
876338 CAAATATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
73 60 0.92
74 5 0.08
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (73 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTAAAAGAAAAATGTCTCAAGCGAAAC
AAAATTTG
Found at i:876366 original size:122 final size:121
Alignment explanation
Indices: 876223--876442 Score: 325
Period size: 122 Copynumber: 1.8 Consensus size: 121
876213 GAGATAAAAC
876223 TTTGTTTCAAGGAAAAATGTCTCAACAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
1 TTTGTTTCAAGGAAAAATGTCTCAACAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
*
876288 GACAAAACTTAG-TTCTAAAAGAAATTGTCTCAAGCGAAACGAAATTTGTTCAAATAT
66 GACAAAA-TTAGTTTC-AAAAGAAACTGTCTCAAGCGAAACGAAATTTGTTCAAATAT
* * * * * * *
876345 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACATAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
1 TTTGTTTCAAGGAAAAATGTCTCAACAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
* *
876410 GACAAAATTTGTTTCAAGAGAAACTGTCTCAAG
66 GACAAAATTAGTTTCAAAAGAAACTGTCTCAAG
876443 AGAGACAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
121 19 0.22
122 68 0.78
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (121 bp):
TTTGTTTCAAGGAAAAATGTCTCAACAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
GACAAAATTAGTTTCAAAAGAAACTGTCTCAAGCGAAACGAAATTTGTTCAAATAT
Found at i:876385 original size:21 final size:20
Alignment explanation
Indices: 876361--876430 Score: 51
Period size: 21 Copynumber: 3.6 Consensus size: 20
876351 TCAAGGGAAA
876361 TTGTCTCAAGAGAGACATAAT
1 TTGTCTCAAGAGAGACA-AAT
*
876382 TTGTTTCAAG-G-G--AAA-
1 TTGTCTCAAGAGAGACAAAT
* *
876397 CTGTCTCAAGGGAGACAAAAT
1 TTGTCTCAAGAGAGAC-AAAT
*
876418 TTGTTTCAAGAGA
1 TTGTCTCAAGAGA
876431 AACTGTCTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 8 0.22
16 3 0.08
17 2 0.05
19 1 0.03
20 4 0.11
21 19 0.51
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (20 bp):
TTGTCTCAAGAGAGACAAAT
Found at i:876385 original size:36 final size:36
Alignment explanation
Indices: 876345--876452 Score: 180
Period size: 36 Copynumber: 3.0 Consensus size: 36
876335 GTTCAAATAT
* *
876345 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACATAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
876381 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
876417 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
876453 CTTTATTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:876426 original size:86 final size:86
Alignment explanation
Indices: 876259--876422 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 86
876249 AGAGACAAAA
*
876259 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAATTGTCTCAAGCG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGCG
*
876324 AAACGAAATTTGTTCAAATAT
66 AAACAAAATTTGTTCAAATAT
* * * * * ** *
876345 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACATAA-TTTGTT-TCAAGGGAAACTGTCTCAAGG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAGC
*
876408 GAGACAAAATTTGTT
65 GAAACAAAATTTGTT
876423 TCAAGAGAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.02
85 33 0.50
86 32 0.48
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (86 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGCG
AAACAAAATTTGTTCAAATAT
Found at i:880768 original size:32 final size:31
Alignment explanation
Indices: 880709--880768 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
880699 TAAAGAAATG
**
880709 AAAAAAAATAAAAATAAAAAATGAATAACTC
1 AAAAAAAATAAAAATAAAAAAAAAATAACTC
880740 AAAAAGAAA-AAAAAGTAAAAAAAAAATAA
1 AAAAA-AAATAAAAA-TAAAAAAAAAATAA
880769 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (31 bp):
AAAAAAAATAAAAATAAAAAAAAAATAACTC
Found at i:880867 original size:24 final size:26
Alignment explanation
Indices: 880800--880867 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 26
880790 CATAAAATTT
880800 AATAAAAATAGTAATAATAATGAAAATAA
1 AATAAAAA-AGTAA-AATAATG-AAATAA
* **
880829 AATGAAAAACCAAAATAA-G-AATAA
1 AATAAAAAAGTAAAATAATGAAATAA
880853 AATAAAAAAGTAAAA
1 AATAAAAAAGTAAAA
880868 AAAGGTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 17 0.52
26 1 0.03
27 5 0.15
28 3 0.09
29 7 0.21
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (26 bp):
AATAAAAAAGTAAAATAATGAAATAA
Found at i:883603 original size:24 final size:24
Alignment explanation
Indices: 883571--883619 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
883561 AGTCTTCCTG
*
883571 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATATATGTAC
*
883595 ATGATGTATAAAACATATGTGTAC
1 ATGATGTATAAAACATATATGTAC
883619 A
1 A
883620 ATGCCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATATATGTAC
Found at i:891387 original size:24 final size:24
Alignment explanation
Indices: 891355--891403 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
891345 AGTCTTCTTG
891355 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
891379 ATGATGTATAAAACATCTGTGTAC
1 ATGATGTATAAAACATCTATGTAC
891403 A
1 A
891404 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:892877 original size:31 final size:31
Alignment explanation
Indices: 892836--892946 Score: 213
Period size: 31 Copynumber: 3.6 Consensus size: 31
892826 AAATGCTAAA
*
892836 TTACCAATTTACCCTTAAAATTAAAATATCT
1 TTACTAATTTACCCTTAAAATTAAAATATCT
892867 TTACTAATTTACCCTTAAAATTAAAATATCT
1 TTACTAATTTACCCTTAAAATTAAAATATCT
892898 TTACTAATTTACCCTTAAAATTAAAATATCT
1 TTACTAATTTACCCTTAAAATTAAAATATCT
892929 TTACTAATTTACCCTTAA
1 TTACTAATTTACCCTTAA
892947 TGAACTTAAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (31 bp):
TTACTAATTTACCCTTAAAATTAAAATATCT
Found at i:895359 original size:33 final size:34
Alignment explanation
Indices: 895322--895393 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
895312 CCTTCATAAC
*
895322 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * *
895355 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
895389 TCCCT
1 TCCCT
895394 TTTACAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:895757 original size:19 final size:19
Alignment explanation
Indices: 895733--895769 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
895723 TGTGTGAACA
*
895733 GTAGCAGTATCGGTACCCT
1 GTAGCAGTATCGATACCCT
895752 GTAGCAGTATCGATACCC
1 GTAGCAGTATCGATACCC
895770 CTTTTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (19 bp):
GTAGCAGTATCGATACCCT
Found at i:896080 original size:21 final size:20
Alignment explanation
Indices: 896052--896113 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 20
896042 ATGTTTATGA
*
896052 AAAAGATACCAATTGTTAAC
1 AAAAGATATCAATTGTTAAC
896072 AAAAGGATATCAATTGTT-A-
1 AAAA-GATATCAATTGTTAAC
*
896091 AAAAGATATCAATTGTTACC
1 AAAAGATATCAATTGTTAAC
896111 AAA
1 AAA
896114 TGTTGGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 13 0.35
19 4 0.11
20 8 0.22
21 12 0.32
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.27
Consensus pattern (20 bp):
AAAAGATATCAATTGTTAAC
Found at i:900731 original size:18 final size:19
Alignment explanation
Indices: 900708--900744 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
900698 ATATATACCA
900708 CATGCA-ACAACACGTATT
1 CATGCATACAACACGTATT
900726 CATGCATACAACACGTATT
1 CATGCATACAACACGTATT
900745 TACATACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (19 bp):
CATGCATACAACACGTATT
Found at i:900752 original size:17 final size:18
Alignment explanation
Indices: 900714--900752 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
900704 ACCACATGCA
*
900714 ACAACACGTATTCATGCAT
1 ACAACACGTATT-ATACAT
900733 ACAACACGTATT-TACAT
1 ACAACACGTATTATACAT
900750 ACA
1 ACA
900753 CATGTGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (18 bp):
ACAACACGTATTATACAT
Found at i:902453 original size:50 final size:50
Alignment explanation
Indices: 902343--902483 Score: 165
Period size: 50 Copynumber: 2.7 Consensus size: 50
902333 ATGATGGGTT
* *
902343 CGCTCCCTATTTCTTCAGAGAGTATAGGACTCAAAAAATCTTCAACAAATGTGTC
1 CGCTCCCTATTT-TTCAGAGAGTATAGGACT----AGATCTTCAACAAACGTGTC
* *
902398 TGCTCCCTATTTTTCAGAGAGTATAGGACTTGATCTTCAACAAACGTGTC
1 CGCTCCCTATTTTTCAGAGAGTATAGGACTAGATCTTCAACAAACGTGTC
* * *
902448 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATC
1 CGCTCCCTATT-TTTCAGAGAGTATAGGACTAGATC
902484 AATCTTCAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
50 27 0.35
51 21 0.27
54 18 0.23
55 11 0.14
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (50 bp):
CGCTCCCTATTTTTCAGAGAGTATAGGACTAGATCTTCAACAAACGTGTC
Found at i:902515 original size:44 final size:44
Alignment explanation
Indices: 902451--902536 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
902441 ACGTGTCCGC
*
902451 TCCCTATTCCTTCAGAGAGTATA-AGACTCGATCAATCTTCAATA
1 TCCCTATTCCTTCAGAGAGTATATA-ACTCGAACAATCTTCAATA
* *
902495 TCCCTATTCGTTCAGGGAGTATATAACTCGAACAATCTTCAA
1 TCCCTATTCCTTCAGAGAGTATATAACTCGAACAATCTTCAA
902537 CAAACGGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (44 bp):
TCCCTATTCCTTCAGAGAGTATATAACTCGAACAATCTTCAATA
Found at i:902579 original size:55 final size:55
Alignment explanation
Indices: 902505--902855 Score: 409
Period size: 55 Copynumber: 6.4 Consensus size: 55
902495 TCCCTATTCG
* ** * * *
902505 TTCAGGGAGTATATAACTCGAACAATCTTCAACAAACGGGTTTGCTCCCTATT-C
1 TTCAGGGAGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
* * *
902559 TTTCAGGGAGTATAGAACTCGAATAATCTTCTTCCAACGGGTTCACTCACTCTTGC
1 -TTCAGGGAGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
* * * *
902615 TAC-GGGAAGTATATAACTTGATCAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
1 TTCAGGG-AGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
* * * *
902670 TTCAAGGAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTCGCTCCCTCTTGC
1 TTCAGGGAGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
* * * *
902725 TTCAGGAAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTCGCTCCCTCTTGC
1 TTCAGGGAGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
* * * * *
902780 TTTAGGAAGTATAGAACTCAAACAATCTTCTTCCAACGAGTTCACTCCCTCTTGC
1 TTCAGGGAGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
* * *
902835 TACAAGGAGTATATAACTCGA
1 TTCAGGGAGTATAGAACTCGA
902856 TCTTCATAAA
Statistics
Matches: 256, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
54 3 0.01
55 250 0.98
56 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (55 bp):
TTCAGGGAGTATAGAACTCGAACAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
Found at i:902719 original size:165 final size:165
Alignment explanation
Indices: 902505--902855 Score: 452
Period size: 165 Copynumber: 2.1 Consensus size: 165
902495 TCCCTATTCG
* * * *
902505 TTCAGGGAGTATATAACTCGAACAATCTTCAACAAACGGGTTTGCTCCCTATT-CTTTCAGGGAG
1 TTCAAGGAGTATATAACTCGAACAATCTTCAACAAACGAGTTCGCTCCCTATTGC-TTCAGGAAG
* * * * *
902569 TATAGAACTCGAATAATCTTCTTCCAACGGGTTCACTCACTCTTGCTACGGGAAGTATATAACTT
65 TATAGAACTCGAACAATCTTCTTCCAACGAGTTCACTCACTCTTGCTACAGGAAGTATAGAACTC
* * * *
902634 GATCAATCTTCTTCCAACGGGTTCGCTCCCTCTTGC
130 AAACAATCTTCTTCCAACGAGTTCACTCCCTCTTGC
* ** * * *
902670 TTCAAGGAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTCGCTCCCTCTTGCTTCAGGAAGT
1 TTCAAGGAGTATATAACTCGAACAATCTTCAACAAACGAGTTCGCTCCCTATTGCTTCAGGAAGT
* * * * **
902735 ATAGAACTCGAACAATCTTCTTCGAATGAGTTCGCTCCCTCTTGCTTTAGGAAGTATAGAACTCA
66 ATAGAACTCGAACAATCTTCTTCCAACGAGTTCACTCACTCTTGCTACAGGAAGTATAGAACTCA
902800 AACAATCTTCTTCCAACGAGTTCACTCCCTCTTGC
131 AACAATCTTCTTCCAACGAGTTCACTCCCTCTTGC
*
902835 TACAAGGAGTATATAACTCGA
1 TTCAAGGAGTATATAACTCGA
902856 TCTTCATAAA
Statistics
Matches: 158, Mismatches: 27, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
165 157 0.99
166 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (165 bp):
TTCAAGGAGTATATAACTCGAACAATCTTCAACAAACGAGTTCGCTCCCTATTGCTTCAGGAAGT
ATAGAACTCGAACAATCTTCTTCCAACGAGTTCACTCACTCTTGCTACAGGAAGTATAGAACTCA
AACAATCTTCTTCCAACGAGTTCACTCCCTCTTGC
Found at i:902976 original size:37 final size:37
Alignment explanation
Indices: 902867--902989 Score: 149
Period size: 37 Copynumber: 3.3 Consensus size: 37
902857 CTTCATAAAA
* *
902867 TGAATTTGCTTCACTACTCTTCCGTGAAGGCTTATA-AA
1 TGAA-TTGCTTCAATACTCTTCCGTGAAGGCTTA-AGAT
* * *
902905 TGATTTGCTTCACTACTCTTCCGTGAAGGTTTAAGAT
1 TGAATTGCTTCAATACTCTTCCGTGAAGGCTTAAGAT
* *
902942 TGAATTGCTTCAATGCTCTTTCGTGAAGGCTTAAGAT
1 TGAATTGCTTCAATACTCTTCCGTGAAGGCTTAAGAT
*
902979 TGAATTTCTTC
1 TGAATTGCTTC
902990 GAATGTCAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
36 1 0.01
37 71 0.95
38 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (37 bp):
TGAATTGCTTCAATACTCTTCCGTGAAGGCTTAAGAT
Found at i:904290 original size:13 final size:13
Alignment explanation
Indices: 904261--904312 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
904251 CTTAAACCCC
904261 CTTTTATTTCTTTTT
1 CTTTT-TTTC-TTTT
904276 CTTTTTTTCTTTT
1 CTTTTTTTCTTTT
904289 C-TTTTTTC-TTT
1 CTTTTTTTCTTTT
* *
904300 CATTTTTTGTTTT
1 CTTTTTTTCTTTT
904313 TCATCTCTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 4 0.12
12 13 0.38
13 8 0.24
14 4 0.12
15 5 0.15
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (13 bp):
CTTTTTTTCTTTT
Found at i:904295 original size:12 final size:13
Alignment explanation
Indices: 904267--904402 Score: 72
Period size: 13 Copynumber: 10.2 Consensus size: 13
904257 CCCCCTTTTA
*
904267 TTTCTTTTTCTTTT
1 TTTC-TTTTCATTT
904281 TTTCTTTTC-TTT
1 TTTCTTTTCATTT
904293 TTTC-TTTCATTT
1 TTTCTTTTCATTT
*
904305 TTTGTTTTTCATCTCT
1 TTT-CTTTTCAT-T-T
*
904321 CTTT-TTTTCATTCA
1 -TTTCTTTTCATT-T
904335 TTT-TTTTCATTT
1 TTTCTTTTCATTT
*
904347 TTTCATTT--TTT
1 TTTCTTTTCATTT
*
904358 TATCATTTTTCA--T
1 TTTC--TTTTCATTT
904371 TTTCTTTTCATTTT
1 TTTCTTTTCA-TTT
904385 TTTCTTTTTTCATTT
1 TTTC--TTTTCATTT
904400 TTT
1 TTT
904403 TCATTTCTTT
Statistics
Matches: 99, Mismatches: 7, Indels: 31
0.72 0.05 0.23
Matches are distributed among these distances:
11 16 0.16
12 16 0.16
13 26 0.26
14 17 0.17
15 14 0.14
16 7 0.07
17 3 0.03
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTCTTTTCATTT
Found at i:915422 original size:45 final size:45
Alignment explanation
Indices: 915356--915481 Score: 198
Period size: 45 Copynumber: 2.8 Consensus size: 45
915346 TGTTATTCAC
* * *
915356 AAAAAGAAATCCTAACTGCATGATATCTAATTCGCATGCTTGTTCG
1 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTGTTCG
*
915402 AAAAATAAACCTAACCGCATGATATCTAGTTCACATGCTTGTTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTCG
*
915447 AAAAATAAACTTAACCGCATGATATCTAGTTCGCA
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCA
915482 AGCATTTATT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 66 0.89
46 8 0.11
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (45 bp):
AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTCG
Found at i:925189 original size:19 final size:19
Alignment explanation
Indices: 925162--925206 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
925152 AGGTCTCTAG
* *
925162 CTTCTATAATGGCGGTCTT
1 CTTCGATAATGGCAGTCTT
925181 CTTCGATAATGGCAGTCTT
1 CTTCGATAATGGCAGTCTT
925200 CTTCGAT
1 CTTCGAT
925207 TGTCACGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (19 bp):
CTTCGATAATGGCAGTCTT
Found at i:925817 original size:12 final size:12
Alignment explanation
Indices: 925800--925824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
925790 TATCAATATT
925800 ATTATTTTTATA
1 ATTATTTTTATA
925812 ATTATTTTTATA
1 ATTATTTTTATA
925824 A
1 A
925825 AAATACTGTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTTTTATA
Found at i:926257 original size:16 final size:17
Alignment explanation
Indices: 926236--926269 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
926226 ATTTTTTATT
*
926236 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
926252 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
926269 A
1 A
926270 AAAACATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:927508 original size:47 final size:47
Alignment explanation
Indices: 927449--927538 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
927439 GATAAAACAG
*
927449 CATATATATTATCATAAGATTATATTAAAATATTAATAACAATACAA
1 CATATATATTATCATAAGATTATATTAAAATATCAATAACAATACAA
927496 CATATATATTATCATAAGATTATATTAAAATATCAATAACAAT
1 CATATATATTATCATAAGATTATATTAAAATATCAATAACAAT
927539 TTTTGAAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (47 bp):
CATATATATTATCATAAGATTATATTAAAATATCAATAACAATACAA
Found at i:929765 original size:18 final size:18
Alignment explanation
Indices: 929742--929784 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
929732 AAACTACAAC
929742 AAAACCCCAAAAACTTTT
1 AAAACCCCAAAAACTTTT
*
929760 AAAACCTCAAAAACTTTT
1 AAAACCCCAAAAACTTTT
929778 AAAACCC
1 AAAACCC
929785 TAATTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAACCCCAAAAACTTTT
Found at i:930928 original size:19 final size:19
Alignment explanation
Indices: 930879--930927 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
930869 TGCCAAGCAA
930879 TGAAAATAAAATACATAAT
1 TGAAAATAAAATACATAAT
930898 TGGAAAATAAAATACATAAT
1 T-GAAAATAAAATACATAAT
930918 TGAAAA-AAAA
1 TGAAAATAAAA
930928 AACGAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 19 0.66
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.22
Consensus pattern (19 bp):
TGAAAATAAAATACATAAT
Found at i:931652 original size:12 final size:12
Alignment explanation
Indices: 931631--931707 Score: 55
Period size: 12 Copynumber: 5.8 Consensus size: 12
931621 TAATTTATTA
*
931631 TTAAATCATATG
1 TTAAAACATATG
931643 TTAAAACATATG
1 TTAAAACATATG
*
931655 TAAAAAAAATCATATG
1 T---TAAAA-CATATG
931671 TTAAAACATATG
1 TTAAAACATATG
*
931683 TAAAAAAAATCATATG
1 T---TAAAA-CATATG
931699 TTAAAACAT
1 TTAAAACAT
931708 GAGAATGGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
12 22 0.42
13 8 0.15
15 8 0.15
16 14 0.27
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (12 bp):
TTAAAACATATG
Found at i:931670 original size:16 final size:15
Alignment explanation
Indices: 931645--931704 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
931635 ATCATATGTT
931645 AAAACATATGTAAAA
1 AAAACATATGTAAAA
*
931660 AAAATCATATGT---T
1 AAAA-CATATGTAAAA
931673 AAAACATATGTAAAA
1 AAAACATATGTAAAA
931688 AAAATCATATGTTAAAA
1 AAAA-CATATG-TAAAA
931705 CATGAGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 7 0.19
13 4 0.11
15 8 0.22
16 13 0.35
17 5 0.14
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
AAAACATATGTAAAA
Found at i:931673 original size:28 final size:28
Alignment explanation
Indices: 931633--931707 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
931623 ATTTATTATT
931633 AAATCATATGTTAAAACATATGTAAAAA
1 AAATCATATGTTAAAACATATGTAAAAA
931661 AAATCATATGTTAAAACATATGTAAAAA
1 AAATCATATGTTAAAACATATGTAAAAA
931689 AAATCATATGTTAAAACAT
1 AAATCATATGTTAAAACAT
931708 GAGAATGGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (28 bp):
AAATCATATGTTAAAACATATGTAAAAA
Found at i:942214 original size:20 final size:20
Alignment explanation
Indices: 942189--942239 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
942179 GATTCAATCG
*
942189 GTATCGATACCGAAGAGGGA-
1 GTATCGATACCGAAG-GGAAT
*
942209 GTATCGATACTGAAGGGAAT
1 GTATCGATACCGAAGGGAAT
942229 GTATCGATACC
1 GTATCGATACC
942240 ATTCAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (20 bp):
GTATCGATACCGAAGGGAAT
Found at i:942847 original size:47 final size:47
Alignment explanation
Indices: 942732--942962 Score: 269
Period size: 47 Copynumber: 5.0 Consensus size: 47
942722 AACGAATGAA
* * * *
942732 CAAATAATAATAATACATATGGTTGCATTATCGGCATAAAAAGGATGC
1 CAAATAATAATAATGCATATGGGTGCATTATCGACAT-GAAAGGATGC
*
942780 C--A-AATAATAATGCATATGGGTGCATTATCGACATGAAAGGGTGC
1 CAAATAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
*
942824 CAAATAATAATAATGCATATGGGTGCATTAT-TAGCATGAAAGGATGC
1 CAAATAATAATAATGCATATGGGTGCATTATCGA-CATGAAAGGATGC
* *
942871 CAAATAATAATAATGCATATGGATGCATTATCGGCATGAAAGGATGC
1 CAAATAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* * * * *
942918 C--ATAGTTGA-AATGCATATGGGTGCATTATCAACATAAAAGTATGC
1 CAAATA-ATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
942963 TATAATTGAA
Statistics
Matches: 160, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
44 9 0.06
45 63 0.39
46 5 0.03
47 82 0.51
48 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (47 bp):
CAAATAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
Found at i:942988 original size:46 final size:44
Alignment explanation
Indices: 942747--943007 Score: 188
Period size: 47 Copynumber: 5.7 Consensus size: 44
942737 AATAATAATA
** *
942747 CATATGGTTGCATTATCGGCATAAAAAGGATGCCA-AA-TAATAATG
1 CATATGG-TGCATTATCAACAT-AAAAGGATGCCATAATTGA-AATG
* * * *
942792 CATATGGGTGCATTATCGACATGAAAGGGTGCCA-AATAATAATAATG
1 CATAT-GGTGCATTATCAACATAAAAGGATGCCATAAT--TGA-AATG
* * * *
942839 CATATGGGTGCATTATTAGCATGAAAGGATGCCA-AATAATAATAATG
1 CATAT-GGTGCATTATCAACATAAAAGGATGCCATAAT--TGA-AATG
** * *
942886 CATATGGATGCATTATCGGCATGAAAGGATGCCATAGTTGAAATG
1 CATATGG-TGCATTATCAACATAAAAGGATGCCATAATTGAAATG
* *
942931 CATATGGGTGCATTATCAACATAAAAGTATGCTATAATTGAAAATG
1 CATAT-GGTGCATTATCAACATAAAAGGATGCCATAATTG-AAATG
* *
942977 CATAATGGTGCATTATAAACATAAATGGATG
1 CAT-ATGGTGCATTATCAACATAAAAGGATG
943008 TTATTAATGA
Statistics
Matches: 187, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
44 12 0.06
45 53 0.28
46 38 0.20
47 82 0.44
48 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (44 bp):
CATATGGTGCATTATCAACATAAAAGGATGCCATAATTGAAATG
Found at i:943967 original size:38 final size:37
Alignment explanation
Indices: 943890--943967 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
943880 TTTTTATATT
*
943890 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
943927 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAAAAAAATTATATAAATATTAT-CAA
943965 TTT
1 TTT
943968 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 18 0.51
38 17 0.49
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:949109 original size:22 final size:20
Alignment explanation
Indices: 949069--949122 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
949059 ATCATAGCAA
*
949069 AGTATCGGTACCATAGTATG
1 AGTATCGATACCATAGTATG
* *
949089 ATAGTATCGATACCTTGGTATG
1 --AGTATCGATACCATAGTATG
*
949111 GGTATCGATACC
1 AGTATCGATACC
949123 GAGGAGCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (20 bp):
AGTATCGATACCATAGTATG
Found at i:949632 original size:92 final size:94
Alignment explanation
Indices: 949521--949757 Score: 338
Period size: 92 Copynumber: 2.6 Consensus size: 94
949511 GCTCTAAAAT
* **
949521 GAATGAACAAATAATAATAATACATATGGGTGCATTATTGTTATGAAAGGATGCC-AA-AATAAT
1 GAATG-ACAAATAATAATAATGCATATGGGTGCATTATTGCCATGAAAGGATGCCAAATAATAAT
*
949584 AATGTATATGGGTGCAATATCAGCATCAAA
65 AATGCATATGGGTGCAATATCAGCATCAAA
* * *
949614 GGATGTCAAATAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAATAATAATA
1 GAATGACAAATAATAATAATGCATATGGGTGCATTATTGCCATGAAAGGATGCCAAATAATAATA
* *
949679 ATGCATATGGGTGCATTATCAGCATGAAA
66 ATGCATATGGGTGCAATATCAGCATCAAA
* *
949708 GAATGAC-AA-AATATTAATGCATATGGGTGCATTATCGCCATGAAAGGATG
1 GAATGACAAATAATAATAATGCATATGGGTGCATTATTGCCATGAAAGGATG
949758 TCATAGTTGA
Statistics
Matches: 129, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
92 83 0.64
93 8 0.06
94 38 0.29
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (94 bp):
GAATGACAAATAATAATAATGCATATGGGTGCATTATTGCCATGAAAGGATGCCAAATAATAATA
ATGCATATGGGTGCAATATCAGCATCAAA
Found at i:949706 original size:139 final size:137
Alignment explanation
Indices: 949528--949787 Score: 355
Period size: 139 Copynumber: 1.9 Consensus size: 137
949518 AATGAATGAA
* * * * *
949528 CAAATAATAATAATACATATGGGTGCATTATTGTTATGAAAGGATGCCAAAATAATAATGTATAT
1 CAAATAATAATAATACATATGGGTGCATTATAGTCATGAAAGAATGACAAAATAATAATGCATAT
949593 GGGTGCAATATCAG-CATCAAAGGATGTCAAATA-ATAATAATGCATATGGGTGCATTATTGGCA
66 GGGTGCAATATC-GCCATCAAAGGATGTC--ATAGATAA-AATGCATATGGGTGCATTATTGGCA
949656 TGAAAGGATGC
127 TGAAAGGATGC
* *
949667 CAAATAATAATAATGCATATGGGTGCATTATCAG-CATGAAAGAATGACAAAATATTAATGCATA
1 CAAATAATAATAATACATATGGGTGCATTAT-AGTCATGAAAGAATGACAAAATAATAATGCATA
* * * *
949731 TGGGTGCATTATCGCCATGAAAGGATGTCATAGTTGAAATGCATATGGGTGCATTAT
65 TGGGTGCAATATCGCCATCAAAGGATGTCATAGATAAAATGCATATGGGTGCATTAT
949788 CAACCTAAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
137 23 0.21
138 3 0.03
139 80 0.75
140 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (137 bp):
CAAATAATAATAATACATATGGGTGCATTATAGTCATGAAAGAATGACAAAATAATAATGCATAT
GGGTGCAATATCGCCATCAAAGGATGTCATAGATAAAATGCATATGGGTGCATTATTGGCATGAA
AGGATGC
Found at i:949772 original size:45 final size:44
Alignment explanation
Indices: 949531--949788 Score: 275
Period size: 45 Copynumber: 5.7 Consensus size: 44
949521 GAATGAACAA
* * *
949531 ATAATAATAATACATATGGGTGCATTATTGTTATGAAAGGATGCC
1 ATAATAATAATGCATATGGGTGCATTATCG-CATGAAAGGATGCC
* * * * *
949576 AAAATAATAATGTATATGGGTGCAATATCAGCATCAAAGGATGTCAA
1 ATAATAATAATGCATATGGGTGCATTATC-GCATGAAAGGATG-C-C
*
949623 ATAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCC
1 ATAATAATAATGCATATGGGTGCATTA-TCGCATGAAAGGATGCC
* *
949668 AAATAATAATAATGCATATGGGTGCATTATCAGCATGAAAGAATGAC
1 --ATAATAATAATGCATATGGGTGCATTATC-GCATGAAAGGATGCC
* * *
949715 AAAATATTAATGCATATGGGTGCATTATCGCCATGAAAGGATGTC
1 ATAATAATAATGCATATGGGTGCATTATCG-CATGAAAGGATGCC
* *
949760 ATAGTTGA-AATGCATATGGGTGCATTATC
1 ATA-ATAATAATGCATATGGGTGCATTATC
949789 AACCTAAAAG
Statistics
Matches: 179, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
44 1 0.01
45 96 0.54
46 5 0.03
47 76 0.42
48 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (44 bp):
ATAATAATAATGCATATGGGTGCATTATCGCATGAAAGGATGCC
Found at i:949813 original size:45 final size:45
Alignment explanation
Indices: 949631--949821 Score: 149
Period size: 45 Copynumber: 4.2 Consensus size: 45
949621 AAATAATAAT
** * * * *
949631 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AATAATAA
1 AATGCATATGGGTGCATTATCAGCCTGAAAGAATGCTATAAT--TGA
* * *
949677 TAATGCATATGGGTGCATTATCAGCATGAAAGAATGAC-AAAATAT-T
1 -AATGCATATGGGTGCATTATCAGCCTGAAAGAATG-CTATAAT-TGA
* *
949723 AATGCATATGGGTGCATTATC-GCCATGAAAGGATG-TCATAGTTGA
1 AATGCATATGGGTGCATTATCAGCC-TGAAAGAATGCT-ATAATTGA
* * *
949768 AATGCATATGGGTGCATTATCAACCTAAAAGTATGCTATAATTGAA
1 AATGCATATGGGTGCATTATCAGCCTGAAAGAATGCTATAATTG-A
949814 AATGCATA
1 AATGCATA
949822 ATGGTGTATT
Statistics
Matches: 122, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
44 3 0.02
45 68 0.56
46 12 0.10
47 35 0.29
48 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAGCCTGAAAGAATGCTATAATTGA
Found at i:950733 original size:19 final size:21
Alignment explanation
Indices: 950709--950751 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
950699 GGTTTTGGTA
*
950709 AAAATGAT-TAAA-TAATAAT
1 AAAATGATATAAAGTAAAAAT
950728 AAAATGATATAAAGTAAAAAT
1 AAAATGATATAAAGTAAAAAT
950749 AAA
1 AAA
950752 GAAAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
21 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAATGATATAAAGTAAAAAT
Found at i:954345 original size:5 final size:5
Alignment explanation
Indices: 954335--954362 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
954325 TTCTTAACCG
954335 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
954363 ATGCAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:962627 original size:2 final size:2
Alignment explanation
Indices: 962561--962610 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
962551 CTCTCTAATC
* *
962561 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
962602 AT AT AT AT A
1 AT AT AT AT A
962611 CAAATTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:971282 original size:24 final size:24
Alignment explanation
Indices: 971255--971307 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
971245 TTTTGATTTG
*
971255 AAAGTTAAGCTTGAAAGCTTAACA
1 AAAGATAAGCTTGAAAGCTTAACA
971279 AAAGATAAGCTTGAAAGCTTAACA
1 AAAGATAAGCTTGAAAGCTTAACA
971303 AAAGA
1 AAAGA
971308 AAAAGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (24 bp):
AAAGATAAGCTTGAAAGCTTAACA
Found at i:974163 original size:3 final size:3
Alignment explanation
Indices: 974140--974213 Score: 77
Period size: 3 Copynumber: 26.0 Consensus size: 3
974130 CTACAAAAAC
*
974140 ATT A-T ATT A-T ATT ATT GTT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
974185 ATT -TT ATT AAT -TT ATAT ATT ATA ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
974214 TTTTACAGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
2 9 0.15
3 47 0.80
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:974166 original size:17 final size:17
Alignment explanation
Indices: 974140--974213 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
974130 CTACAAAAAC
974140 ATTA-TATTATATTATT
1 ATTATTATTATATTATT
*
974156 GTTATTATTATATTATT
1 ATTATTATTATATTATT
974173 ATTATTATTATTATT-TT
1 ATTATTATTA-TATTATT
*
974190 ATTAAT-TTATA-TATT
1 ATTATTATTATATTATT
*
974205 ATAATTATT
1 ATTATTATT
974214 TTTTACAGGC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 1 0.02
15 8 0.16
16 8 0.16
17 28 0.57
18 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (17 bp):
ATTATTATTATATTATT
Found at i:974174 original size:20 final size:19
Alignment explanation
Indices: 974149--974218 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 19
974139 CATTATATTA
974149 TATTATTGTTATTATTATAT
1 TATTATT-TTATTATTATAT
*
974169 TATTATTATTATTATTATTT
1 TATTATT-TTATTATTATAT
*
974189 TATTAATTTATATATTATAAT
1 TATTATTTTAT-TATTAT-AT
974210 TATT-TTTTA
1 TATTATTTTA
974219 CAGGCCCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 4 0.09
20 34 0.79
21 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (19 bp):
TATTATTTTATTATTATAT
Found at i:975272 original size:13 final size:15
Alignment explanation
Indices: 975243--975274 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
975233 GCAAACAAAC
975243 CCCAAAATCCAAATT
1 CCCAAAATCCAAATT
975258 CCCAAAAT-C-AATT
1 CCCAAAATCCAAATT
975271 CCCA
1 CCCA
975275 GATCCTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (15 bp):
CCCAAAATCCAAATT
Found at i:975836 original size:16 final size:16
Alignment explanation
Indices: 975815--975875 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
975805 TAATAAATAA
**
975815 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
975831 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
975847 ACGAATATAAATGAAC
1 ACGAACATAAACGAAC
975863 ACGAACATAAACG
1 ACGAACATAAACG
975876 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:976141 original size:12 final size:11
Alignment explanation
Indices: 976104--976155 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
976094 TCGAGACTTG
*
976104 AGCTCGATTGA
1 AGCTCGATTCA
976115 AGCTCGATTCA
1 AGCTCGATTCA
*
976126 AGCTCAATTCCA
1 AGCTCGATT-CA
976138 AGCTCGATTCA
1 AGCTCGATTCA
976149 AGCTCGA
1 AGCTCGA
976156 CATTGCCCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:976992 original size:14 final size:14
Alignment explanation
Indices: 976975--977020 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
976965 AATGAACATA
976975 AACGAACATAACCG
1 AACGAACATAACCG
*
976989 AACGAACATAACAG
1 AACGAACATAACCG
977003 AACGAACATAACCG
1 AACGAACATAACCG
977017 AACG
1 AACG
977021 TTCACGAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:977237 original size:8 final size:8
Alignment explanation
Indices: 977226--977262 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
977216 ATTTTATATT
977226 TTATTTAA
1 TTATTTAA
977234 TTATTTAA
1 TTATTTAA
977242 TTATTTAA
1 TTATTTAA
977250 TTATTT-A
1 TTATTTAA
977257 TTATTT
1 TTATTT
977263 TTTAGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTATTTAA
Found at i:977247 original size:16 final size:15
Alignment explanation
Indices: 977226--977311 Score: 68
Period size: 16 Copynumber: 5.3 Consensus size: 15
977216 ATTTTATATT
977226 TTATTTAATTATTTAA
1 TTATTTAATTATTT-A
977242 TTATTTAATTATTTA
1 TTATTTAATTATTTA
*
977257 TTATTT-TTTAGATTT-
1 TTATTTAATT--ATTTA
977272 TTATTTAATCTTATTTA
1 TTATTTAA--TTATTTA
*
977289 TCTATTTTATTTATTTTA
1 T-TA-TTTAATTA-TTTA
977307 TTATT
1 TTATT
977312 ACTATATTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
14 2 0.03
15 13 0.22
16 24 0.41
17 6 0.10
18 9 0.16
19 4 0.07
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (15 bp):
TTATTTAATTATTTA
Found at i:977289 original size:4 final size:4
Alignment explanation
Indices: 977225--977304 Score: 58
Period size: 4 Copynumber: 19.8 Consensus size: 4
977215 TATTTTATAT
* * * *
977225 TTTA TTTA ATTA TTTA ATTA TTTA ATTA TTTA -TTA TTT- TTTA GATT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
*
977271 TTTA TTTAA TCTTA TTTA TCTA TTTTA TTTA TTT
1 TTTA TTT-A T-TTA TTTA TTTA -TTTA TTTA TTT
977305 TATTATTACT
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
3 8 0.14
4 40 0.68
5 9 0.15
6 2 0.03
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:981147 original size:156 final size:156
Alignment explanation
Indices: 980863--981210 Score: 554
Period size: 156 Copynumber: 2.2 Consensus size: 156
980853 AACCAATTTG
* *
980863 GATTTCAACTTCACAACGAATGATATCCAATTCAAAGATCAACTTCACAGCGAAGGGGCAACTAT
1 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGATCAACTTCACAGCGAAGAGGCAACTAT
* * *
980928 CAACAAACAACTTTCCAGTTTCATTCAGATTCAATTTTAACTTCACAGCGAATGATATTGAACTC
66 CAACAAACAACTTTCCAATTTCATTCAGATTCAATTTCAACTTCACAGCGAAGGATATTGAACTC
980993 GAAGTGACACAATTTACTCAAGATTA
131 GAAGTGACACAATTTACTCAAGATTA
* * *
981019 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACAGTGAATAGGCAACTAT
1 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGATCAACTTCACAGCGAAGAGGCAACTAT
*
981084 CAACATACAACTTTCCAATTTCATTCAGAGTT-AATTTCAACTTCACAGCGAAGGATATTGAACT
66 CAACAAACAACTTTCCAATTTCATTCAGA-TTCAATTTCAACTTCACAGCGAAGGATATTGAACT
* *
981148 CGAAGTGACACAATTTACTCAATATTG
130 CGAAGTGACACAATTTACTCAAGATTA
* * *
981175 GATTTTAACTTCACGACGAAGGATATCCAACTCAAA
1 GATTTCAACTTCACGACGAATGATATCCAATTCAAA
981211 CCAATTTGGA
Statistics
Matches: 177, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
156 175 0.99
157 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (156 bp):
GATTTCAACTTCACGACGAATGATATCCAATTCAAAGATCAACTTCACAGCGAAGAGGCAACTAT
CAACAAACAACTTTCCAATTTCATTCAGATTCAATTTCAACTTCACAGCGAAGGATATTGAACTC
GAAGTGACACAATTTACTCAAGATTA
Found at i:981362 original size:200 final size:201
Alignment explanation
Indices: 981019--981411 Score: 601
Period size: 200 Copynumber: 2.0 Consensus size: 201
981009 CTCAAGATTA
* * * * * *
981019 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACAGTGAATAGGCAACTAT
1 GATTTCAACTTCACAAAGAATGATATCCAATACAAAGATCAACTTCACAGCGAAGAGGCAACTAT
* *
981084 CAACATACAACTTTCCAATTTCATTCAGAGTTAATTTCAACTTCACAGCGAAGGATATTGAACTC
66 CAACAAACAACTTTCCAATTTCATTCAGAGTTAATTTCAACTTCACAGCAAAGGATATTGAACTC
* * *
981149 GAAGTGACACAATTTACTC-AATATTGGATTTTAACTTCACGACGAAGGATATCCAACTCAAACC
131 GAAGTGACACAATTTACTCAAAGATTAGATTTCAACTTCACGACGAAGGATATCCAACTCAAACC
981213 AATTTG
196 AATTTG
* * *
981219 GATTTCAACTTCACAAAGAATGATATCCAATACAAATATCAACTTCACAGCGAAGGGGCAACTCT
1 GATTTCAACTTCACAAAGAATGATATCCAATACAAAGATCAACTTCACAGCGAAGAGGCAACTAT
*
981284 CAACAAACAACTTTCCAGTTTCATTCAGA-TTCAATTTCAACTTCACAGCAAAGGATATTGAACT
66 CAACAAACAACTTTCCAATTTCATTCAGAGTT-AATTTCAACTTCACAGCAAAGGATATTGAACT
* * *
981348 CGAAGTGACACAATTTAGTCAAAGATTAGATTTCAACTTCACGACGAATGATATCCAATTCAAA
130 CGAAGTGACACAATTTACTCAAAGATTAGATTTCAACTTCACGACGAAGGATATCCAACTCAAA
981412 GCTCAACTTC
Statistics
Matches: 173, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
199 2 0.01
200 133 0.77
201 38 0.22
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (201 bp):
GATTTCAACTTCACAAAGAATGATATCCAATACAAAGATCAACTTCACAGCGAAGAGGCAACTAT
CAACAAACAACTTTCCAATTTCATTCAGAGTTAATTTCAACTTCACAGCAAAGGATATTGAACTC
GAAGTGACACAATTTACTCAAAGATTAGATTTCAACTTCACGACGAAGGATATCCAACTCAAACC
AATTTG
Found at i:981375 original size:357 final size:356
Alignment explanation
Indices: 980700--981468 Score: 1290
Period size: 357 Copynumber: 2.2 Consensus size: 356
980690 TGGTGGTTGT
* * * * *
980700 TCAACTTCACAGCGAATGAGCATCTATCAAGAAACAAATTTCCAATTTCATTCAGAGTTAATTTC
1 TCAACTTCACAGTGAATG-GCAACTATCAACATACAACTTTCCAATTTCATTCAGAGTTAATTTC
980765 AACTTCACAGCGAAGGATATTAAACTCCAAGTGACACAATTTACTCAAGATTGGATTTCAACTTC
65 AACTTCACAGCGAAGGATATTAAACTCCAAGTGACACAATTTACTCAAGATTGGATTTCAACTTC
* * *
980830 ATGACGAAAAATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAACGAATGATATCCAATT
130 ACGACGAAAAATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAAAGAATGATATCCAATA
980895 CAAAGATCAACTTCACAGCGAAGGGGCAACTATCAACAAACAACTTTCCAGTTTCATTCAGATTC
195 CAAAGATCAACTTCACAGCGAAGGGGCAACTATCAACAAACAACTTTCCAGTTTCATTCAGATTC
* * *
980960 AATTTTAACTTCACAGCGAATGATATTGAACTCGAAGTGACACAATTTACTCAAGATTAGATTTC
260 AATTTCAACTTCACAGCAAAGGATATTGAACTCGAAGTGACACAATTTACTCAAGATTAGATTTC
981025 AACTTCACGACGAATGATATCCAATTCAAAGC
325 AACTTCACGACGAATGATATCCAATTCAAAGC
981057 TCAACTTCACAGTGAATAGGCAACTATCAACATACAACTTTCCAATTTCATTCAGAGTTAATTTC
1 TCAACTTCACAGTGAAT-GGCAACTATCAACATACAACTTTCCAATTTCATTCAGAGTTAATTTC
* * * *
981122 AACTTCACAGCGAAGGATATTGAACTCGAAGTGACACAATTTACTCAATATTGGATTTTAACTTC
65 AACTTCACAGCGAAGGATATTAAACTCCAAGTGACACAATTTACTCAAGATTGGATTTCAACTTC
**
981187 ACGACGAAGGATATCCAACTC-AAACCAATTTGGATTTCAACTTCACAAAGAATGATATCCAATA
130 ACGACGAAAAATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAAAGAATGATATCCAATA
* *
981251 CAAATATCAACTTCACAGCGAAGGGGCAACTCTCAACAAACAACTTTCCAGTTTCATTCAGATTC
195 CAAAGATCAACTTCACAGCGAAGGGGCAACTATCAACAAACAACTTTCCAGTTTCATTCAGATTC
*
981316 AATTTCAACTTCACAGCAAAGGATATTGAACTCGAAGTGACACAATTTAGTCAAAGATTAGATTT
260 AATTTCAACTTCACAGCAAAGGATATTGAACTCGAAGTGACACAATTTACTC-AAGATTAGATTT
981381 CAACTTCACGACGAATGATATCCAATTCAAAGC
324 CAACTTCACGACGAATGATATCCAATTCAAAGC
*
981414 TCAACTTCACA-TCGAATGGGCAACTGTCAACATACAACTTTCCAATTTCATTCAG
1 TCAACTTCACAGT-GAAT-GGCAACTATCAACATACAACTTTCCAATTTCATTCAG
981469 TTAATAGATT
Statistics
Matches: 387, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
356 153 0.40
357 233 0.60
358 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (356 bp):
TCAACTTCACAGTGAATGGCAACTATCAACATACAACTTTCCAATTTCATTCAGAGTTAATTTCA
ACTTCACAGCGAAGGATATTAAACTCCAAGTGACACAATTTACTCAAGATTGGATTTCAACTTCA
CGACGAAAAATATCCAACTCAAAACCAATTTGGATTTCAACTTCACAAAGAATGATATCCAATAC
AAAGATCAACTTCACAGCGAAGGGGCAACTATCAACAAACAACTTTCCAGTTTCATTCAGATTCA
ATTTCAACTTCACAGCAAAGGATATTGAACTCGAAGTGACACAATTTACTCAAGATTAGATTTCA
ACTTCACGACGAATGATATCCAATTCAAAGC
Found at i:981497 original size:104 final size:104
Alignment explanation
Indices: 981370--981572 Score: 406
Period size: 104 Copynumber: 2.0 Consensus size: 104
981360 ATTTAGTCAA
981370 AGATTAGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACATCGAATGGGC
1 AGATTAGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACATCGAATGGGC
981435 AACTGTCAACATACAACTTTCCAATTTCATTCAGTTAAT
66 AACTGTCAACATACAACTTTCCAATTTCATTCAGTTAAT
981474 AGATTAGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACATCGAATGGGC
1 AGATTAGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACATCGAATGGGC
981539 AACTGTCAACATACAACTTTCCAATTTCATTCAG
66 AACTGTCAACATACAACTTTCCAATTTCATTCAG
981573 AGTTAATTTC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (104 bp):
AGATTAGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACATCGAATGGGC
AACTGTCAACATACAACTTTCCAATTTCATTCAGTTAAT
Found at i:981874 original size:112 final size:112
Alignment explanation
Indices: 981637--982008 Score: 437
Period size: 112 Copynumber: 3.2 Consensus size: 112
981627 TCAAGATTGG
* *** * *
981637 ATTTCAACTTCACGACGAAGGATATCCAACTCCA-AACC-AA-TTTGGATTTCAACTTCACAACG
1 ATTTCAACTTCACGACGAATGATATCGTGC-CCACAACCAAAGATTGGATTTCAACTTCACGACG
* *
981699 AAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
65 AAGGATATCCAATTCAAAG-ACAACTTCACAACGAATGAGCCATCCACA
*
981748 ATTTCAACTTCACGACGAATGATATCGTGCCCACAACCAAAGATTGGATTTCAACTTCAGGACGA
1 ATTTCAACTTCACGACGAATGATATCGTGCCCACAACCAAAGATTGGATTTCAACTTCACGACGA
* * *
981813 AGGATATCCAATTCAAAGAAAACTTCACAACAAATGAGCCATCCACT
66 AGGATATCCAATTCAAAGACAACTTCACAACGAATGAGCCATCCACA
* * *
981860 ACTTCAACTTCACGACGAATGATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAACTT
1 ATTTCAACTTCACGACGAATGATATCGTGCCCAC---AACCAAAG--A---TTGGATTTCAACTT
* * *
981925 CACGAAGAAGGATATCCAATTCAAAGATCAACTTCATAACGAAGGAGCCATCCACA
58 CACGACGAAGGATATCCAATTCAAAGA-CAACTTCACAACGAATGAGCCATCCACA
*
981981 ATTTCAACTTTACGACGAA-GAATATCGT
1 ATTTCAACTTCACGACGAATG-ATATCGT
982009 ACCTAACGGA
Statistics
Matches: 225, Mismatches: 23, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
110 3 0.01
111 30 0.13
112 60 0.27
113 38 0.17
115 6 0.03
117 1 0.00
120 40 0.18
121 47 0.21
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (112 bp):
ATTTCAACTTCACGACGAATGATATCGTGCCCACAACCAAAGATTGGATTTCAACTTCACGACGA
AGGATATCCAATTCAAAGACAACTTCACAACGAATGAGCCATCCACA
Done.