Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 4 of 8
Found at i:775261 original size:26 final size:27
Alignment explanation
Indices: 775213--775263 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
775203 TCTTATACAA
* *
775213 ACTAATTTAATTTCTTTTGTTTTGTAC
1 ACTAATTTAATTTCTTCTCTTTTGTAC
775240 ACTAATTT-ATTTCTTCTCTTTTGT
1 ACTAATTTAATTTCTTCTCTTTTGT
775264 TTGTGTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.61
Consensus pattern (27 bp):
ACTAATTTAATTTCTTCTCTTTTGTAC
Found at i:777222 original size:16 final size:16
Alignment explanation
Indices: 777198--777237 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
777188 ATTGATAAAA
*
777198 ACATACATCAATACAT
1 ACATACATCAACACAT
*
777214 ACATGCATCAACACAT
1 ACATACATCAACACAT
777230 ACATACAT
1 ACATACAT
777238 GTTACACGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.23
Consensus pattern (16 bp):
ACATACATCAACACAT
Found at i:777753 original size:105 final size:104
Alignment explanation
Indices: 777625--777938 Score: 373
Period size: 105 Copynumber: 3.0 Consensus size: 104
777615 GCTTGAAATA
* ** *
777625 ATTTCTTTCAAAAACAAACTTCGTCTCGCTCCAGACATATTTTCTTTGAGATACAAATTTCGAAT
1 ATTTCTTTC-AAAACAAATTTCGTCTCGCTTGAGACATATTTTCTTTGAGAT-CAAATTTCAAAT
777690 TTGATTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
64 TTGATTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
* * *
777731 ATTTCTTTCAAAACATATTTCGTCTCGTTTGAGACAT-TTTTCCTTTGATATCTAAATTTCAAAT
1 ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATATTTT-CTTTGAGATC-AAATTTCAAAT
* * *
777795 CTGGTTCACTTTAAACAAAATTAATCTCACTTGAGATTGTT
64 TTGATTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
* * * ** * *
777836 GTTTATTTCAAAACAAATTTCGTCTCACTTGAGAC--ATTTTCCCTCAGAATGCAAATTTCAAAG
1 ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATATTTTCTTTGAG-AT-CAAATTTCAAAT
* * *
777899 TTGTTTTACTTGAAACAAAATTAATTTCACTTGAGATTGT
64 TTGATTCACTTGAAACAAAATTAATCTCACTTGAGATTGT
777939 CAAAATCGAT
Statistics
Matches: 178, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
103 3 0.02
104 56 0.31
105 110 0.62
106 9 0.05
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (104 bp):
ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATATTTTCTTTGAGATCAAATTTCAAATTT
GATTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
Found at i:778175 original size:30 final size:29
Alignment explanation
Indices: 778096--778196 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 29
778086 CTTGAGACAA
* *
778096 TTTCTCTT-TAAACAAATCTTTGAGTCTG
1 TTTCTCTTGAAAAAAAATCTTTGAGTCTG
*
778124 -TTCTTTTGAAAAAAAATCTTTGAGTCTG
1 TTTCTCTTGAAAAAAAATCTTTGAGTCTG
* * *
778152 TTTCTCTT-AACAAAATCATCTTTGAGCCTA
1 TTTCTCTTGAA-AAAA-AATCTTTGAGTCTG
778182 TTTCT-TTGAAAAAAA
1 TTTCTCTTGAAAAAAA
778197 TTTTTGTCTC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 6 0.10
28 20 0.33
29 16 0.27
30 18 0.30
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.43
Consensus pattern (29 bp):
TTTCTCTTGAAAAAAAATCTTTGAGTCTG
Found at i:778197 original size:30 final size:28
Alignment explanation
Indices: 778111--778197 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 28
778101 CTTTAAACAA
*
778111 ATCTTTGAGTCTGTTCTTTTGAAAAAAA-
1 ATCTTTGAGTCTTTTC-TTTGAAAAAAAT
*
778139 ATCTTTGAGTCTGTTTCTCTT-AACAAAAT
1 ATCTTTGAGTCT-TTTCT-TTGAAAAAAAT
*
778168 CATCTTTGAGCCTATTTCTTTGAAAAAAAT
1 -ATCTTTGAGTCT-TTTCTTTGAAAAAAAT
778198 TTTTGTCTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
28 19 0.39
29 7 0.14
30 23 0.47
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (28 bp):
ATCTTTGAGTCTTTTCTTTGAAAAAAAT
Found at i:778484 original size:30 final size:30
Alignment explanation
Indices: 778444--778507 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
778434 TTTTTTTGAA
*
778444 AAAAATCTTTGAGTCTGTTTCTCTTCAAAC
1 AAAAATCTTTGAGTCTGTTTCCCTTCAAAC
* *
778474 AAAAGTCTTTGAGTCTGTTTCCCTTGAAAC
1 AAAAATCTTTGAGTCTGTTTCCCTTCAAAC
778504 AAAA
1 AAAA
778508 CAAACAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (30 bp):
AAAAATCTTTGAGTCTGTTTCCCTTCAAAC
Found at i:778548 original size:39 final size:39
Alignment explanation
Indices: 778469--778545 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
778459 TGTTTCTCTT
* *
778469 CAAACAAAAGTCTTTGAGTCTGTTTCCCTTGAAACAAAA
1 CAAACAAAAGTCTTTGAGTATGCTTCCCTTGAAACAAAA
**
778508 CAAACAAAA-TCTTTGAGTATGCTTGTCTTGAAACAAAA
1 CAAACAAAAGTCTTTGAGTATGCTTCCCTTGAAACAAAA
778546 ACATCTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (39 bp):
CAAACAAAAGTCTTTGAGTATGCTTCCCTTGAAACAAAA
Found at i:778735 original size:31 final size:30
Alignment explanation
Indices: 778694--778775 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 30
778684 GAGACAGTTG
778694 CTTTTGAAACAAATCATCTTTGAGTTTGTTT
1 CTTTTGAAAC-AATCATCTTTGAGTTTGTTT
778725 -TTCTTGAAACAA--ATCTTTGAGTTTGTTT
1 CTT-TTGAAACAATCATCTTTGAGTTTGTTT
*
778753 CTTTTGAAAC-ATCACCTTTGAGT
1 CTTTTGAAACAATCATCTTTGAGT
778776 CAGTTTCCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
27 1 0.02
28 23 0.50
29 11 0.24
30 4 0.09
31 7 0.15
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (30 bp):
CTTTTGAAACAATCATCTTTGAGTTTGTTT
Found at i:778781 original size:29 final size:29
Alignment explanation
Indices: 778678--778782 Score: 88
Period size: 28 Copynumber: 3.6 Consensus size: 29
778668 GAGTTTCGTC
* *
778678 TCTTTCGAGACAGTTGCTTTTGAAACAAATCA
1 TCTTT-GAGTCAGTTTCTTTTGAAAC--ATCA
** *
778710 TCTTTGAGTTTGTTT-TTCTTGAAACA-AA
1 TCTTTGAGTCAGTTTCTT-TTGAAACATCA
**
778738 TCTTTGAGTTTGTTTCTTTTGAAACATCA
1 TCTTTGAGTCAGTTTCTTTTGAAACATCA
*
778767 CCTTTGAGTCAGTTTC
1 TCTTTGAGTCAGTTTC
778783 CCTTGATCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
28 24 0.39
29 17 0.28
30 2 0.03
31 13 0.21
32 5 0.08
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (29 bp):
TCTTTGAGTCAGTTTCTTTTGAAACATCA
Found at i:778808 original size:224 final size:224
Alignment explanation
Indices: 778565--779012 Score: 869
Period size: 224 Copynumber: 2.0 Consensus size: 224
778555 AGTTTGTTTC
778565 TCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTT
1 TCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTT
778630 TCCTTTAAAAGTCATCTTTGAGTTGTTTCCCTTGAAACGAGTTTCGTCTCTTTCGAGACAGTTGC
66 TCCTTTAAAAGTCATCTTTGAGTTGTTTCCCTTGAAACGAGTTTCGTCTCTTTCGAGACAGTTGC
778695 TTTTGAAACAAATCATCTTTGAGTTTGTTTTTCTTGAAACAAATCTTTGAGTTTGTTTCTTTTGA
131 TTTTGAAACAAATCATCTTTGAGTTTGTTTTTCTTGAAACAAATCTTTGAGTTTGTTTCTTTTGA
778760 AACATCACCTTTGAGTCAGTTTCCCTTGA
196 AACATCACCTTTGAGTCAGTTTCCCTTGA
*
778789 TCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTTTCGCTTGAGACAGTT
1 TCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTT
*
778854 TCTTTTAAAAGTCATCTTTGAGTTGTTTCCCTTGAAACGAGTTTCGTCTCTTTCGAGACAGTTGC
66 TCCTTTAAAAGTCATCTTTGAGTTGTTTCCCTTGAAACGAGTTTCGTCTCTTTCGAGACAGTTGC
*
778919 TTTTGAAACACATCATCTTTGAGTTTGTTTTTCTTGAAACAAATCTTTGAGTTTGTTTCTTTTGA
131 TTTTGAAACAAATCATCTTTGAGTTTGTTTTTCTTGAAACAAATCTTTGAGTTTGTTTCTTTTGA
778984 AACATCACCTTTGAGTCAGTTTCCCTTGA
196 AACATCACCTTTGAGTCAGTTTCCCTTGA
779013 AACCATTATC
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
224 221 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (224 bp):
TCTCGAAACACCGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTT
TCCTTTAAAAGTCATCTTTGAGTTGTTTCCCTTGAAACGAGTTTCGTCTCTTTCGAGACAGTTGC
TTTTGAAACAAATCATCTTTGAGTTTGTTTTTCTTGAAACAAATCTTTGAGTTTGTTTCTTTTGA
AACATCACCTTTGAGTCAGTTTCCCTTGA
Found at i:778959 original size:31 final size:31
Alignment explanation
Indices: 778918--778999 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 31
778908 GAGACAGTTG
778918 CTTTTGAAACACATCATCTTTGAGTTTGTTT
1 CTTTTGAAACACATCATCTTTGAGTTTGTTT
778949 -TTCTTGAAACA-A--ATCTTTGAGTTTGTTT
1 CTT-TTGAAACACATCATCTTTGAGTTTGTTT
*
778977 CTTTTG-AA-ACATCACCTTTGAGT
1 CTTTTGAAACACATCATCTTTGAGT
779000 CAGTTTCCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 19 0.42
29 11 0.24
30 3 0.07
31 8 0.18
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.46
Consensus pattern (31 bp):
CTTTTGAAACACATCATCTTTGAGTTTGTTT
Found at i:779005 original size:29 final size:29
Alignment explanation
Indices: 778902--779015 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
778892 GAGTTTCGTC
* *
778902 TCTTTCGAGACAGTTGCTTTTGAAACACATCA
1 TCTTT-GAGTCAGTTTCTTTTG-AA-ACATCA
** *
778934 TCTTTGAGTTTGTTT-TTCTTGAAACA-AA
1 TCTTTGAGTCAGTTTCTT-TTGAAACATCA
**
778962 TCTTTGAGTTTGTTTCTTTTGAAACATCA
1 TCTTTGAGTCAGTTTCTTTTGAAACATCA
* **
778991 CCTTTGAGTCAGTTTCCCTTGAAAC
1 TCTTTGAGTCAGTTTCTTTTGAAAC
779016 CATTATCCCT
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
28 24 0.35
29 26 0.38
30 4 0.06
31 9 0.13
32 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (29 bp):
TCTTTGAGTCAGTTTCTTTTGAAACATCA
Found at i:779242 original size:94 final size:93
Alignment explanation
Indices: 779073--779252 Score: 227
Period size: 94 Copynumber: 1.9 Consensus size: 93
779063 TCATCCCCTA
** * * *
779073 ACCAGACCTCCTCATTGCGTAGGAGTCGTGTCAACCTTGATAACCATATATCCTCATCACGAAGG
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTAGATAACCATACATCCTCATCACGAAGG
** *
779138 AATTGAGTTATCACCTTTCCTTTAGGCG
66 AACCGAGTTATCACCCTTCCTTTAGGCG
* * * *
779166 ACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCCCTAGATAACCAGT-CATCCTCATCGCGTA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCA-ACCTAGATAACCA-TACATCCTCATCACGAA
779230 GGAACCGAGTTATCACCCTTCCT
64 GGAACCGAGTTATCACCCTTCCT
779253 AAAGATGGGC
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
93 29 0.40
94 43 0.59
95 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (93 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTAGATAACCATACATCCTCATCACGAAGG
AACCGAGTTATCACCCTTCCTTTAGGCG
Found at i:781754 original size:12 final size:10
Alignment explanation
Indices: 781722--781752 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
781712 TTCATCACAC
781722 CAAATTCTCT
1 CAAATTCTCT
781732 CAAATTCTCT
1 CAAATTCTCT
781742 CAAATTCTCT
1 CAAATTCTCT
781752 C
1 C
781753 TCTGTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:781829 original size:17 final size:18
Alignment explanation
Indices: 781801--781834 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
781791 GTATTTAATT
781801 TATTTAAGTATTTTACTC
1 TATTTAAGTATTTTACTC
781819 TATTTAA-TATTTTACT
1 TATTTAAGTATTTTACT
781835 AATATAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (18 bp):
TATTTAAGTATTTTACTC
Found at i:783901 original size:3 final size:3
Alignment explanation
Indices: 783893--783942 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
783883 ACCTTCTCAG
* * * * *
783893 GAC GAC GAC GAC GAC GGC AAC GAT GAT GAC GAC GAC GAC GAC AAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
783941 GA
1 GA
783943 TGACAGCGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.28, G:0.32, T:0.04
Consensus pattern (3 bp):
GAC
Found at i:783928 original size:24 final size:24
Alignment explanation
Indices: 783896--783946 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
783886 TTCTCAGGAC
* *
783896 GACGACGACGACGGCAACGATGAT
1 GACGACGACGACGACAACGACGAT
783920 GACGACGACGACGACAACGACGAT
1 GACGACGACGACGACAACGACGAT
783944 GAC
1 GAC
783947 AGCGAGGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.31, T:0.06
Consensus pattern (24 bp):
GACGACGACGACGACAACGACGAT
Found at i:790225 original size:17 final size:17
Alignment explanation
Indices: 790181--790224 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
790171 AGGATTTGGA
790181 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
790198 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
*
790215 -TTTGAGTTTT
1 ATTAGAGTTTT
790225 TTTTATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:791182 original size:2 final size:2
Alignment explanation
Indices: 791177--791207 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
791167 ATATGTTTAT
791177 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
791208 CACCATGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:794577 original size:3 final size:3
Alignment explanation
Indices: 794543--794643 Score: 68
Period size: 3 Copynumber: 34.0 Consensus size: 3
794533 GATAAAAAAG
* * * *
794543 TAA TAA AAA TAT TAAA TAA TAA -AA TAA AAA TAA TAA T-A GAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
794587 TAA -AA TAA TAAA TCAA -AA CAAA TAA TAA -AA AAA TAA AAA TAA TAA
1 TAA TAA TAA T-AA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
794632 TAA TAA TAA TAA
1 TAA TAA TAA TAA
794644 ATATAAATCA
Statistics
Matches: 77, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
2 9 0.12
3 59 0.77
4 9 0.12
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:794577 original size:9 final size:9
Alignment explanation
Indices: 794537--794781 Score: 108
Period size: 9 Copynumber: 26.6 Consensus size: 9
794527 ATGTTAGATA
794537 AAAAAGTAAT
1 AAAAA-TAAT
*
794547 AAAAATATT
1 AAAAATAAT
794556 AAATAATAAAAT
1 AAA-AAT--AAT
794568 AAAAATAAT
1 AAAAATAAT
794577 AATAGAATAAT
1 AA-A-AATAAT
794588 -AAAATAAT
1 AAAAATAAT
794596 --AAATCAA-
1 AAAAAT-AAT
794603 AACAAATAAT
1 AA-AAATAAT
794613 AAAAA-AAT
1 AAAAATAAT
794621 AAAAATAAT
1 AAAAATAAT
*
794630 AATAATAAT
1 AAAAATAAT
794639 AATAAAT-AT
1 AA-AAATAAT
*
794648 AAATCAGAGAA-
1 AAA--A-ATAAT
794659 AAAAATTAA-
1 AAAAA-TAAT
*
794668 ATAAATGAATT
1 AAAAAT-AA-T
794679 GAAAAA-AAT
1 -AAAAATAAT
794688 AAATAA-AA-
1 AAA-AATAAT
*
794696 AAGAATAAGT
1 AAAAATAA-T
794706 CAAAAATAAT
1 -AAAAATAAT
794716 ---AATAAT
1 AAAAATAAT
794722 AAAAATAAT
1 AAAAATAAT
794731 -AAAATAAT
1 AAAAATAAT
*
794739 AAAAAATAAA
1 -AAAAATAAT
*
794749 AAAAATAAAA
1 AAAAAT-AAT
*
794759 AAAAAGAAT
1 AAAAATAAT
794768 ATAAAA-AAT
1 A-AAAATAAT
794777 AAAAA
1 AAAAA
794782 GGTAAAATTT
Statistics
Matches: 189, Mismatches: 13, Indels: 68
0.70 0.05 0.25
Matches are distributed among these distances:
6 6 0.03
7 6 0.03
8 38 0.20
9 67 0.35
10 42 0.22
11 20 0.11
12 10 0.05
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:794585 original size:25 final size:25
Alignment explanation
Indices: 794557--794756 Score: 107
Period size: 25 Copynumber: 7.9 Consensus size: 25
794547 AAAAATATTA
*
794557 AATAATAAAATAAAAATAATAATAG
1 AATAATAAAATAAAAATAATAATAT
* *
794582 AATAATAAAATAATAAATCAAAACAAAT
1 AATAATAAAATAA-AAAT-AATA-ATAT
*
794610 AATAAAAAAATAAAAATAATAATAAT
1 AATAATAAAATAAAAATAATAAT-AT
* *
794636 AATAAT-AAATATAAATCAGAGAA-A-
1 AATAATAAAATAAAAAT-A-ATAATAT
*
794660 AA-AATTAAATAAATGAATTGAA-AA-A-
1 AATAATAAAATAAA--AA-T-AATAATAT
*
794685 AATAAATAAAA-AAGAATAAGTCAA-A-
1 AAT-AATAAAATAAAAATAA-T-AATAT
*
794710 AATAATAATAATAAAAATAATAAAAT
1 AATAATAA-AATAAAAATAATAATAT
*
794736 AATAA-AAAATAAAAAAAATAA
1 AATAATAAAATAAAAATAATAA
794757 AAAAAAAGAA
Statistics
Matches: 141, Mismatches: 15, Indels: 39
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.01
23 4 0.03
24 30 0.21
25 41 0.29
26 32 0.23
27 18 0.13
28 14 0.10
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (25 bp):
AATAATAAAATAAAAATAATAATAT
Found at i:794593 original size:33 final size:34
Alignment explanation
Indices: 794534--794781 Score: 119
Period size: 33 Copynumber: 7.2 Consensus size: 34
794524 AAAATGTTAG
* * *
794534 ATAAAAA-AGTAATAAAAATAT-TAAATAATAAA
1 ATAAAAATAATAATAAAAAAATAAAAATAATAAA
* *
794566 ATAAAAATAATAATAGAATAAT-AAAATAAT-AA
1 ATAAAAATAATAATAAAAAAATAAAAATAATAAA
794598 ATCAAAACA-AATAATAAAAAAATAAAAATAATAATA
1 AT-AAAA-ATAATAATAAAAAAATAAAAATAATAA-A
* * * * *
794634 ATAATAATAA-ATATAAATCAGAGAAAAA-AATTAA
1 ATAAAAATAATA-ATAAA-AAAATAAAAATAATAAA
* *
794668 ATAAATGAATTGAA-AA-AAATAAATAAAAAAGAAT-AA
1 ATAAA--AA-T-AATAATAAAAAAAT-AAAAATAATAAA
*
794704 GTCAAAAATAATAATAATAAAAATAATAAAATAATAAA
1 AT-AAAAATAATAATAA-AAAAAT-A-AAAATAATAAA
*
794742 A-AATAAA-AAAAATAAAAAAA-AAGAATATAA-AAA
1 ATAA-AAATAATAATAAAAAAATAA-AA-ATAATAAA
794775 ATAAAAA
1 ATAAAAA
794782 GGTAAAATTT
Statistics
Matches: 170, Mismatches: 21, Indels: 49
0.71 0.09 0.20
Matches are distributed among these distances:
32 12 0.07
33 45 0.26
34 25 0.15
35 26 0.15
36 39 0.23
37 18 0.11
38 5 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (34 bp):
ATAAAAATAATAATAAAAAAATAAAAATAATAAA
Found at i:794640 original size:92 final size:88
Alignment explanation
Indices: 794537--794779 Score: 217
Period size: 92 Copynumber: 2.6 Consensus size: 88
794527 ATGTTAGATA
794537 AAAAAGTAATAAAAATATTAAATAATAAAATAAAAATAATAATAGAATAATAAAATAATAAATCA
1 AAAAA-TAATAAAAATA-TAAATAATAAAA-AAAAATAA-AATAGAATAATAAAA-AATAAAT-A
*
794602 AAACA-AATAA-TAAAAAAATAAAAATAAT
60 AAAAAGAATAAGT-AAAAAATAAAAATAAT
* * * * *
794630 AATAATAATAATAAATATAAATCAGAGAAAAAAATTAAATA-AATGAATTGAAAAAAATAAATAA
1 AAAAATAATAA-AAATATAAATAATAAAAAAAAATAAAATAGAAT-AA-T--AAAAAATAAATAA
* *
794694 AAAAGAATAAGTCAAAAATAATAATAAT
61 AAAAGAATAAGTAAAAAATAAAAATAAT
* * *
794722 AAAAATAAT-AAAATAATAAAAAATAAAAAAAATAAAAAAAAAGAAT-ATAAAAAATAAA
1 AAAAATAATAAAAAT-ATAAATAAT-AAAAAAA-AATAAAATAGAATAATAAAAAATAAA
794780 AAGGTAAAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 26
0.75 0.10 0.16
Matches are distributed among these distances:
89 13 0.11
90 10 0.08
91 21 0.17
92 56 0.46
93 20 0.16
94 3 0.02
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (88 bp):
AAAAATAATAAAAATATAAATAATAAAAAAAAATAAAATAGAATAATAAAAAATAAATAAAAAAG
AATAAGTAAAAAATAAAAATAAT
Found at i:794673 original size:22 final size:21
Alignment explanation
Indices: 794646--794694 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
794636 AATAATAAAT
794646 ATAAATCAGA-GAAAAAAATTAA
1 ATAAATCA-ATGAAAAAAA-TAA
*
794668 ATAAATGAATTGAAAAAAATAA
1 ATAAATCAA-TGAAAAAAATAA
794690 ATAAA
1 ATAAA
794695 AAAGAATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.20
Consensus pattern (21 bp):
ATAAATCAATGAAAAAAATAA
Found at i:796732 original size:84 final size:84
Alignment explanation
Indices: 796357--798140 Score: 1908
Period size: 84 Copynumber: 21.5 Consensus size: 84
796347 AACTCGACAA
* ** * *
796357 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTATAAATTATGGTGCCTTTGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAG
* * **
796422 TGGAACCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * * * *
796442 ---T-TTGGAAGATAGCCCTTCTTGCCTTAAGCTATACTACAAATGATGGTGTCTTTGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAG
* *
796503 CGGAATCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * * **
796523 ---T-TTGGCAGATAGCTCTTCTTGCCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGCTAAAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
796584 GGAATCGAACTTGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
796603 ---T-TTGGCAGATAACCCTTCTATCCTTGAGTTATGTTGCAAATGATGTGCCTCT-GAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCT-TGGAGCTGAG
796663 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * *
796683 TTTTGTTGGCATATAGA-CCTTCTTGCCTTGAGCTATGTTGTAAACGATGTGCCTTGGAGCTGAG
1 TTTTGTTGGCAGATA-ACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
796747 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
796767 TTTTGTTGGCAGATAACCCTTCTAGGCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
796832 GTAGTCGAACTCGAAAGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * *
796851 ATTTGTTGGCAAATAGCCCATCTTGCCTTGAGCTATGCTGCAAATGATGTGTCTTTGAGCTGAAC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* **
796916 GAAACCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
796935 ---T-TTGGCAGACAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTCT-GAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCT-TGGAGCTGAG
*
796995 CATAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * *
797015 TTTTGTTGGCAAATAGCCATTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGCAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
797080 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
797099 TTTTGTTGGTAAATAACCCTTCTAGCCTAGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
797164 GTAGTCAAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
797183 ATTTGTTGGCAAATAACTCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCC-T-----TG-G-
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
797240 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * *
797259 TTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTACAAATGATATGCCTTAGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
797324 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* *
797343 TTTTGATGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
797408 GTAGTCGAACTCGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* * * * * * *
797427 TTTGGTTGGAAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGTCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
797492 ATAGTAGAACTCGAAGATC
66 GTAGTCGAACTCGAAGGTC
* * * *
797511 TTTT-TTAGGCAGATAACCCTTCTAGCTTTGAGTTGTGCTACAAATGATGTGCCTTGGAGCTGAG
1 TTTTGTT-GGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
797575 CGTAGTCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * *
797595 TTTTGATGGCAGATAGCCCTTCTAGCCTTAAGCTATG-TCACAAATGATGTGCCTTGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCT-GCAAATGATGTGCCTTGGAGCTGAG
* *
797659 CGGAGTCAAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * * *
797679 TTTGGTTGGTAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
797744 GTAGTTGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * * *
797763 TTTGGTTGACATATAACCCTTATAGCCTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAAC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
797828 GTAGTCGAAGTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
** * * * *
797847 TTTTGGCGGCAGATAACCCTTCTAGTCTTAAGCTATACTACAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
797912 ATAGTCGAACTCGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* * * * * * *
797931 TTTTATTGGCAAATAGCGCTCCTTA-CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGGG
1 TTTTGTTGGCAGATAACCCTTC-TAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* *
797995 CGAAGTCAAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * **
798015 TTTTGTTAGCAGATAA-CCTTCTAG-CTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
798078 GTAATCGAGCTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
798097 -TTGGTTGGCAGATAACCCTTCTCA-CCTTGAGCTATACCGCAAAT
1 TTTTGTTGGCAGATAACCCTTCT-AGCCTTGAGCTATGCTGCAAAT
798141 AAAAAATGGC
Statistics
Matches: 1433, Mismatches: 235, Indels: 64
0.83 0.14 0.04
Matches are distributed among these distances:
76 63 0.04
77 2 0.00
78 2 0.00
80 159 0.11
81 126 0.09
82 59 0.04
83 30 0.02
84 987 0.69
85 5 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:799441 original size:88 final size:88
Alignment explanation
Indices: 799326--799505 Score: 252
Period size: 88 Copynumber: 2.0 Consensus size: 88
799316 ATTGTATAGA
* * *
799326 TATTATAACCACCTTTATCAGGCTAGCTGAATATTATTCATAAAGCCGGGGAGTTTAACCAATTG
1 TATTATAACCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGAGTTTAAACAATTA
*
799391 CTCTAGAGGGATAACTCAAGCTT
66 CTCTAGAGGGACAACTCAAGCTT
* * * * * * *
799414 TATTATAATCATCTTTATCTGTCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAAACAATTA
1 TATTATAACCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGAGTTTAAACAATTA
*
799479 CTTTAGAGGGACAACTCAAGCTT
66 CTCTAGAGGGACAACTCAAGCTT
799502 TATT
1 TATT
799506 GTATATATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (88 bp):
TATTATAACCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGAGTTTAAACAATTA
CTCTAGAGGGACAACTCAAGCTT
Found at i:801944 original size:19 final size:19
Alignment explanation
Indices: 801922--801958 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
801912 TGAAAATGAT
801922 GAAAATAAAAT-AAAAGAGA
1 GAAAA-AAAATGAAAAGAGA
801941 GAAAAAAAATGAAAAGAG
1 GAAAAAAAATGAAAAGAG
801959 TTAGTGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (19 bp):
GAAAAAAAATGAAAAGAGA
Found at i:803027 original size:31 final size:30
Alignment explanation
Indices: 802986--803082 Score: 79
Period size: 34 Copynumber: 3.0 Consensus size: 30
802976 TGTTAGATAG
802986 AAAAGTAATAAATAAATATTAAATAAAATAAT
1 AAAA-TAATAAATAAATATTAAA-AAAATAAT
* *
803018 AAAATAATAAAAATAATAAATCAAAAAAAATAAT
1 AAAATAAT--AAATAA-ATAT-TAAAAAAATAAT
*
803052 TAAATAA-AAATAAAATAATTAAAAAACATAA
1 AAAATAATAAAT-AAAT-ATTAAAAAA-ATAA
803083 ATCAGAGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
31 15 0.28
32 12 0.23
33 6 0.11
34 17 0.32
35 3 0.06
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.24
Consensus pattern (30 bp):
AAAATAATAAATAAATATTAAAAAAATAAT
Found at i:803032 original size:9 final size:9
Alignment explanation
Indices: 803010--803186 Score: 61
Period size: 9 Copynumber: 19.4 Consensus size: 9
803000 AATATTAAAT
803010 AAAATAAT-
1 AAAATAATA
803018 AAAATAATA
1 AAAATAATA
803027 AAAATAAT-
1 AAAATAATA
*
803035 -AAATCAAAA
1 AAAAT-AATA
803044 AAAATAATTA
1 AAAATAA-TA
*
803054 AATAAAAAT-
1 AA-AATAATA
*
803063 AAAATAATT
1 AAAATAATA
*
803072 AAAA-AACA
1 AAAATAATA
* *
803080 TAAATCAGAGA
1 AAAAT-A-ATA
*
803091 AAAA-ATTA
1 AAAATAATA
803099 AATAACTGAATTGAA
1 AA-AA-T-AA-T--A
*
803114 AAAAAAATA
1 AAAATAATA
*
803123 AAAAAAATA
1 AAAATAATA
*
803132 ATAATAATA
1 AAAATAATA
803141 AAAATAAT-
1 AAAATAATA
803149 --AATAATA
1 AAAATAATA
*
803156 AAAATAAGA
1 AAAATAATA
803165 GAATAATAA-A
1 -AA-AATAATA
803175 AAAAT-ATA
1 AAAATAATA
803183 AAAA
1 AAAA
803187 AGAAAAAGAA
Statistics
Matches: 129, Mismatches: 17, Indels: 46
0.67 0.09 0.24
Matches are distributed among these distances:
6 6 0.05
7 5 0.04
8 31 0.24
9 51 0.40
10 12 0.09
11 15 0.12
12 3 0.02
13 1 0.01
14 2 0.02
15 3 0.02
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAATAATA
Found at i:803032 original size:17 final size:16
Alignment explanation
Indices: 803006--803227 Score: 100
Period size: 17 Copynumber: 13.1 Consensus size: 16
802996 AATAAATATT
803006 AAATAAAATAATAAAA
1 AAATAAAATAATAAAA
*
803022 TAATAAAAATAATAAATCA
1 AAAT-AAAATAATAAA--A
803041 AAA-AAAATAATTAAATAA
1 AAATAAAATAA-T-AA-AA
803059 AAATAAAATAATTAAAA
1 AAATAAAATAA-TAAAA
* *
803076 AACAT-AAATCAGAGAAA
1 AA-ATAAAATAATA-AAA
* **
803093 AAATTAAATAACTGAATTG
1 AAATAAAATAA-T-AA-AA
803112 AAA-AAAA-AATAAAA
1 AAATAAAATAATAAAA
*
803126 AAA-ATAATAATAATAA
1 AAATAAAATAATAA-AA
803142 AAATAATAATAATAAAA
1 AAATAA-AATAATAAAA
* *
803159 ATAAGAGAATAATAAAA
1 A-AATAAAATAATAAAA
* *
803176 AAATATAAAAAAGAAAA
1 AAATA-AAATAATAAAA
803193 AGAA-AAAA-AATGAAATA
1 A-AATAAAATAAT-AAA-A
*
803210 GAATATAAA-AATAAAA
1 AAATA-AAATAATAAAA
803226 AA
1 AA
803228 GTTTAAATTT
Statistics
Matches: 160, Mismatches: 22, Indels: 48
0.70 0.10 0.21
Matches are distributed among these distances:
14 6 0.04
15 9 0.06
16 25 0.16
17 69 0.43
18 32 0.20
19 18 0.11
20 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (16 bp):
AAATAAAATAATAAAA
Found at i:803143 original size:15 final size:15
Alignment explanation
Indices: 803119--803180 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
803109 TTGAAAAAAA
*
803119 AATAAAAAAAATAAT
1 AATAATAAAAATAAT
803134 AATAATAAAAATAAT
1 AATAATAAAAATAAT
*
803149 AATAATAAAAATAAGAG
1 AATAATAAAAAT-A-AT
803166 AATAATAAAAA-AAT
1 AATAATAAAAATAAT
803180 A
1 A
803181 TAAAAAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
14 2 0.05
15 27 0.64
16 1 0.02
17 12 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAATAAAAATAAT
Found at i:803173 original size:3 final size:3
Alignment explanation
Indices: 803128--803162 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
803118 AAATAAAAAA
* *
803128 AAT AAT AAT AAT AAA AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
803163 GAGAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:803225 original size:6 final size:6
Alignment explanation
Indices: 803112--803226 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
803102 AACTGAATTG
*
803112 AAAA-A AAAATA AAAA-A AATAATA ATAATA AAAATAA TAATAATA AAAATA
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AAAAT-A -AA-AATA AAAATA
* * *
803162 AGAGAATA ATAAA-A AAATATAA AAAAGA AAAAGA AAAAAA ATGAAATA
1 A-A-AATA A-AAATA AAA-AT-A AAAATA AAAATA AAAATA A--AAATA
*
803210 GAATATA AAAATA AAAA
1 -AAAATA AAAATA AAAA
803227 AGTTTAAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 27
0.72 0.07 0.22
Matches are distributed among these distances:
5 9 0.10
6 45 0.51
7 13 0.15
8 17 0.19
9 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:807952 original size:3 final size:3
Alignment explanation
Indices: 807944--807972 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
807934 AATTTAATCC
807944 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
807973 ATATACAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:808735 original size:19 final size:20
Alignment explanation
Indices: 808711--808761 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
808701 CTGCCCATAT
*
808711 TATTTTATTTTTAATATAA-
1 TATTTTATTTTTAATAAAAG
808730 TATTTT-TATTTTAATAAAAG
1 TATTTTAT-TTTTAATAAAAG
808750 TATTTTTATTTT
1 TA-TTTTATTTT
808762 GTTATATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
19 16 0.59
20 2 0.07
21 7 0.26
22 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTTATTTTTAATAAAAG
Found at i:808738 original size:20 final size:21
Alignment explanation
Indices: 808713--808761 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
808703 GCCCATATTA
*
808713 TTTTATTTTTAATATAA-TAT
1 TTTTATTTTTAATAAAAGTAT
808733 TTTTA-TTTTAATAAAAGTAT
1 TTTTATTTTTAATAAAAGTAT
808753 TTTTATTTT
1 TTTTATTTT
808762 GTTATATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.38
20 13 0.50
21 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTATTTTTAATAAAAGTAT
Found at i:810483 original size:3 final size:3
Alignment explanation
Indices: 810475--810559 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
810465 TTAACATGGT
810475 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
810523 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
810560 GGTAAACTAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:811313 original size:2 final size:2
Alignment explanation
Indices: 811306--811351 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
811296 ACGTATTGAT
811306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
811348 TA TA
1 TA TA
811352 AATGTATGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:816065 original size:27 final size:27
Alignment explanation
Indices: 816032--816084 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
816022 AATTTCTACA
816032 TATTTTATATTTAGGTCACTGATTTAG
1 TATTTTATATTTAGGTCACTGATTTAG
* *
816059 TATTTTATGTTTAGGTCATTGATTTA
1 TATTTTATATTTAGGTCACTGATTTA
816085 TTTATGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.55
Consensus pattern (27 bp):
TATTTTATATTTAGGTCACTGATTTAG
Found at i:817872 original size:45 final size:48
Alignment explanation
Indices: 817805--817917 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 48
817795 TTTATTTTTG
817805 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* * *
817852 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
817898 TTTTT-GAATAACAATGCATG
1 TTTTTCGAAT-A-AATGCATG
817918 GGGTAGATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
45 31 0.54
46 10 0.18
47 9 0.16
48 2 0.04
49 5 0.09
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:826023 original size:200 final size:202
Alignment explanation
Indices: 825673--826075 Score: 792
Period size: 200 Copynumber: 2.0 Consensus size: 202
825663 TAATTCTTTG
825673 CAAGCAGGGCTTCGAAAGAATATGAGTCCTTGAGCTTTGATTTCCCAGATGAGGATTTAATGGCT
1 CAAGCAGGGCTTCGAAAGAATATGAGTCCTTGAGCTTTGATTTCCCAGATGAGGATTTAATGGCT
825738 ATTTCGGTGGAAGAAACGTTATGTCCACTAGTAAATATTGGAAGTTGAACTTCGATGGTGCTTCA
66 ATTTCGGTGGAAGAAACGTTATGTCCACTAGTAAATATTGGAAGTTGAACTTCGATGGTGCTTCA
825803 AATGCCATGGGACATAGAATCGAGGCAATTTTGGTCTCACCAGAGGGATAACATTATCCTTTCAC
131 AATGCCATGGGACATAGAATCGAGGCAATTTTGGTCTCACCAGAGGGATAACATTATCCTTTCAC
825868 CA-TCGA
196 CAGTCGA
825874 CAAGCA-GGCTTCGAAAGAATATGAGTCCTTGAGCTTTGATTTCCCAGATGAGGATTTAATGGCT
1 CAAGCAGGGCTTCGAAAGAATATGAGTCCTTGAGCTTTGATTTCCCAGATGAGGATTTAATGGCT
825938 ATTTCGGTGGAAGAAACGTTATGTCCACTAGTAAATATTGGAAGTTGAACTTCGATGGTGCTTCA
66 ATTTCGGTGGAAGAAACGTTATGTCCACTAGTAAATATTGGAAGTTGAACTTCGATGGTGCTTCA
826003 AATGCCATGGGACATAGAATCGAGGCAATTTTGGTCTCACCAGAGGGATAACATTATCCTTTCAC
131 AATGCCATGGGACATAGAATCGAGGCAATTTTGGTCTCACCAGAGGGATAACATTATCCTTTCAC
826068 CAGTCGA
196 CAGTCGA
826075 C
1 C
826076 TTAATTTTGA
Statistics
Matches: 201, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 190 0.95
201 11 0.05
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (202 bp):
CAAGCAGGGCTTCGAAAGAATATGAGTCCTTGAGCTTTGATTTCCCAGATGAGGATTTAATGGCT
ATTTCGGTGGAAGAAACGTTATGTCCACTAGTAAATATTGGAAGTTGAACTTCGATGGTGCTTCA
AATGCCATGGGACATAGAATCGAGGCAATTTTGGTCTCACCAGAGGGATAACATTATCCTTTCAC
CAGTCGA
Found at i:827343 original size:24 final size:24
Alignment explanation
Indices: 827298--827343 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
827288 CTCTGGTATA
* * *
827298 TGAGATGGAAGTTGTCTTACTTAT
1 TGAGATGGAAATTCTCTCACTTAT
*
827322 TGAGGTGGAAATTCTCTCACTT
1 TGAGATGGAAATTCTCTCACTT
827344 CAGATTTTGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (24 bp):
TGAGATGGAAATTCTCTCACTTAT
Found at i:827633 original size:50 final size:50
Alignment explanation
Indices: 827578--827678 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
827568 GTGGATGCCC
827578 AACTGGGAAGGACCTTATGTTGTCAAGAAAGCCTTTTCTGGGGAAGCTCT
1 AACTGGGAAGGACCTTATGTTGTCAAGAAAGCCTTTTCTGGGGAAGCTCT
827628 AACTGGGAAGGACCTTATGTTGTCAAGAAAGCCTTTTCTGGGGAAGCTCT
1 AACTGGGAAGGACCTTATGTTGTCAAGAAAGCCTTTTCTGGGGAAGCTCT
827678 A
1 A
827679 TTCTTAACTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (50 bp):
AACTGGGAAGGACCTTATGTTGTCAAGAAAGCCTTTTCTGGGGAAGCTCT
Found at i:827796 original size:7 final size:7
Alignment explanation
Indices: 827786--827934 Score: 59
Period size: 8 Copynumber: 19.4 Consensus size: 7
827776 AAAAATGATG
827786 AAAAAGA
1 AAAAAGA
827793 AAAAA-A
1 AAAAAGA
* *
827799 TAGAAG-
1 AAAAAGA
*
827805 AAATAGA
1 AAAAAGA
827812 AGAAAAGA
1 A-AAAAGA
827820 AAAATGAGA
1 AAAA--AGA
827829 ACAAAATGA
1 A-AAAA-GA
*
827838 AAAATGA
1 AAAAAGA
*
827845 AAAGAAAA
1 AAA-AAGA
827853 AAAAAGA
1 AAAAAGA
**
827860 AAATGGAA
1 AAAAAG-A
827868 AAATGGAAGA
1 AAA---AAGA
*
827878 AAAAATA
1 AAAAAGA
827885 AAAAATGA
1 AAAAA-GA
827893 AAAAAGA
1 AAAAAGA
827900 AGAAAGAGA
1 A-AAA-AGA
*
827909 AAAATGAA
1 AAAAAG-A
827917 AAAAAGA
1 AAAAAGA
*
827924 GAAAAATA
1 -AAAAAGA
827932 AAA
1 AAA
827935 GGGGTTCAAG
Statistics
Matches: 106, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
6 7 0.07
7 37 0.35
8 43 0.41
9 11 0.10
10 7 0.07
11 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.07
Consensus pattern (7 bp):
AAAAAGA
Found at i:827807 original size:19 final size:18
Alignment explanation
Indices: 827775--827934 Score: 67
Period size: 17 Copynumber: 9.2 Consensus size: 18
827765 AAAGAGAAAT
*
827775 AAAAAATGATGAAAAAGA
1 AAAAAATGAAGAAAAAGA
*
827793 AAAAAATAGAAGAAATAGA
1 AAAAAAT-GAAGAAAAAGA
* *
827812 AGAAAA-GAA-AAATGAGA
1 AAAAAATGAAGAAA-AAGA
* *
827829 ACAAAATGAAAAATGAAAAGA
1 AAAAAATG-AAGA--AAAAGA
*
827850 AAAAAA--AAGAAAATG-
1 AAAAAATGAAGAAAAAGA
*
827865 GAAAAATGGAAGAAAAA-A
1 AAAAAAT-GAAGAAAAAGA
827883 TAAAAAATG-A-AAAAAG-
1 -AAAAAATGAAGAAAAAGA
*
827899 AAGAAA-G-AGAAAAATGA
1 AAAAAATGAAGAAAAA-GA
*
827916 AAAAAA-G-AGAAAAATA
1 AAAAAATGAAGAAAAAGA
827932 AAA
1 AAA
827935 GGGGTTCAAG
Statistics
Matches: 111, Mismatches: 15, Indels: 34
0.69 0.09 0.21
Matches are distributed among these distances:
14 2 0.02
15 15 0.14
16 17 0.15
17 25 0.23
18 19 0.17
19 22 0.20
20 1 0.01
21 8 0.07
22 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAAATGAAGAAAAAGA
Found at i:827829 original size:17 final size:17
Alignment explanation
Indices: 827800--827857 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
827790 AGAAAAAAAT
827800 AGAAGAAAT-AGAAGAAA
1 AGAA-AAATGAGAAGAAA
*
827817 AGAAAAATGAGAACAAA
1 AGAAAAATGAGAAGAAA
*
827834 ATGAAAAATGAAAAGAAA
1 A-GAAAAATGAGAAGAAA
827852 A-AAAAA
1 AGAAAAA
827858 GAAAATGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.25
17 12 0.33
18 15 0.42
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (17 bp):
AGAAAAATGAGAAGAAA
Found at i:827852 original size:18 final size:18
Alignment explanation
Indices: 827783--827852 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
827773 ATAAAAAATG
827783 ATGAAAAA-G-AAA-AAA
1 ATGAAAAATGAAAAGAAA
*
827798 ATAGAAGAAAT-AGAAGAAA
1 AT-GAA-AAATGAAAAGAAA
* *
827817 A-GAAAAATGAGAACAAA
1 ATGAAAAATGAAAAGAAA
827834 ATGAAAAATGAAAAGAAA
1 ATGAAAAATGAAAAGAAA
827852 A
1 A
827853 AAAAAGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 2 0.05
16 7 0.16
17 14 0.32
18 17 0.39
19 4 0.09
ACGTcount: A:0.73, C:0.01, G:0.17, T:0.09
Consensus pattern (18 bp):
ATGAAAAATGAAAAGAAA
Found at i:827927 original size:48 final size:48
Alignment explanation
Indices: 827794--827934 Score: 130
Period size: 48 Copynumber: 2.9 Consensus size: 48
827784 TGAAAAAGAA
* * * *
827794 AAAAATAGAAGAAATAGAAGAAAAG-AAAAATGAGAACAAAATGAAAAATG
1 AAAAA-AGAAGAAAAAGAA-AAATGAAAAAAAGAGAA-AAAATAAAAAATG
**
827844 AAAAGAA-AA-AAAAAG-AAAATGGAAAAATGGAAGAAAAAATAAAAAATG
1 AAAA-AAGAAGAAAAAGAAAAAT-GAAAAAAAG-AGAAAAAATAAAAAATG
*
827892 AAAAAAGAAGAAAGAGAAAAATGAAAAAAAGAG-AAAAATAAAA
1 AAAAAAGAAGAAAAAGAAAAATGAAAAAAAGAGAAAAAATAAAA
827935 GGGGTTCAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
46 3 0.04
47 14 0.18
48 30 0.39
49 18 0.24
50 10 0.13
51 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (48 bp):
AAAAAAGAAGAAAAAGAAAAATGAAAAAAAGAGAAAAAATAAAAAATG
Found at i:827929 original size:40 final size:39
Alignment explanation
Indices: 827776--827934 Score: 107
Period size: 40 Copynumber: 3.9 Consensus size: 39
827766 AAGAGAAATA
*
827776 AAAAATGATGAAAAA-GAAAAAAATAGAAGAAATAGAAGAAAAG
1 AAAAA-GA-GAAAAATGAAAAAAAGAGAA-AAAT-GAA-AAAAG
* *
827819 AAAAATGAGAACAAAATG-AAAAATGA-AAAGAA-AAAAAAAG
1 AAAAA-GAG-A-AAAATGAAAAAAAGAGAAA-AATGAAAAAAG
* *
827859 AAAATG-GAAAAATGGAAGAAAAA-ATAAAAAATGAAAAAAG
1 AAAAAGAGAAAAAT-GAA-AAAAAGA-GAAAAATGAAAAAAG
827899 AAGAAAGAGAAAAATGAAAAAAAGAGAAAAAT-AAAA
1 AA-AAAGAGAAAAATGAAAAAAAGAGAAAAATGAAAA
827935 GGGGTTCAAG
Statistics
Matches: 95, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
36 5 0.05
37 2 0.02
38 3 0.03
39 11 0.12
40 32 0.34
41 9 0.09
42 9 0.09
43 13 0.14
44 10 0.11
45 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (39 bp):
AAAAAGAGAAAAATGAAAAAAAGAGAAAAATGAAAAAAG
Found at i:829180 original size:37 final size:37
Alignment explanation
Indices: 829128--829225 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
829118 TCGAAATAAG
* * * *
829128 TCAATCTTAAACCTTCACGAAAGAACAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGGAAGAACAGAGAAGCAAA
**
829165 TCAATCTTAAGCCTTCACGGAAGAGTAGAGAAGCAAA
1 TCAATCTTAAGCCTTCACGGAAGAACAGAGAAGCAAA
*
829202 TC-ATTTATAAGCCTTCACGGAAGA
1 TCAATCT-TAAGCCTTCACGGAAGA
829226 GTAGTGAAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 3 0.06
37 50 0.94
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGAAGAACAGAGAAGCAAA
Found at i:829226 original size:37 final size:38
Alignment explanation
Indices: 829172--829245 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
829162 AATTCAATCT
*
829172 TAAGCCTTCACGGAAGAGTAGAGAAGCAAA-TCATTTA
1 TAAGCCTTCACGGAAGAGTAGAGAAACAAACTCATTTA
*
829209 TAAGCCTTCACGGAAGAGTAGTGAAACAAACTCATTT
1 TAAGCCTTCACGGAAGAGTAGAGAAACAAACTCATTT
829246 TATGAAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 28 0.82
38 6 0.18
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (38 bp):
TAAGCCTTCACGGAAGAGTAGAGAAACAAACTCATTTA
Found at i:829312 original size:51 final size:51
Alignment explanation
Indices: 829248--829353 Score: 167
Period size: 51 Copynumber: 2.1 Consensus size: 51
829238 ACTCATTTTA
*
829248 TGAAGATAAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTGT
1 TGAAGATAAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
** * *
829299 TGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT
1 TGAAGATAAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
829350 TGAA
1 TGAA
829354 TATTGTTTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (51 bp):
TGAAGATAAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
Found at i:829489 original size:56 final size:55
Alignment explanation
Indices: 829321--829557 Score: 223
Period size: 56 Copynumber: 4.3 Consensus size: 55
829311 CTTATACTCT
* * * * *
829321 CTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAATATTGTTTGAGTTCTACT-C-C
1 CTGAAGGAATAAGGAGCGGACCCATTTTTATGAAGATTGTTCGAGTTCTA-TACAC
* * * * * * *
829374 CT-AGAGGAAGAGGGAGCGGACCCGTTTGT-TGAATATTGTTCGAGTTATATACTC
1 CTGA-AGGAATAAGGAGCGGACCCATTTTTATGAAGATTGTTCGAGTTCTATACAC
* *
829428 TCTGAAGGAATAAAGAGCGGACTCATTTTTATGAAGATTGTTCGAGTTCTATACGAC
1 -CTGAAGGAATAAGGAGCGGACCCATTTTTATGAAGATTGTTCGAGTTCTATAC-AC
* * * * *
829485 CTGAACGAATAGGGAACGGACCCGTTTTTATGAAGATTGTTCGAGTTCTATACTCC
1 CTGAAGGAATAAGGAGCGGACCCATTTTTATGAAGATTGTTCGAGTTCTATAC-AC
829541 CTGAAGGAATAAGGAGC
1 CTGAAGGAATAAGGAGC
829558 AGAAACATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.01
53 45 0.29
54 1 0.01
55 21 0.14
56 84 0.55
57 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (55 bp):
CTGAAGGAATAAGGAGCGGACCCATTTTTATGAAGATTGTTCGAGTTCTATACAC
Found at i:829593 original size:55 final size:54
Alignment explanation
Indices: 829261--829671 Score: 307
Period size: 55 Copynumber: 7.6 Consensus size: 54
829251 AGATAAAGTC
* * * *
829261 TTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTGTTGAAGA----TCGAGT
1 TTATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTAAAGATTGTTCGAGT
* * * * * *
829311 CTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAATATTGTTTGAG-
1 -TTATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTAAAGATTGTTCGAGT
* * * * * *
829365 TTCTACTCCCT-AGAGGAAGAGGGAGCGGACCCGTTTGTTGAATATTGTTCGAGT
1 TTATACTCCCTGA-AGGAATAGGGAGCGGACACATTTGTTAAAGATTGTTCGAGT
* ** *
829419 TATATACTCTCTGAAGGAATAAAGAGCGGACTCATTT-TTATGAAGATTGTTCGAGT
1 T-TATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTA--AAGATTGTTCGAGT
** * * * *
829475 TCTATACGACCTGAACGAATAGGGAACGGACCCGTTT-TTATGAAGATTGTTCGAGT
1 T-TATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTA--AAGATTGTTCGAGT
* * * * *
829531 TCTATACTCCCTGAAGGAATAAGGAGCAGAAACATTTGTTAAATATTGTTTGAGT
1 T-TATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTAAAGATTGTTCGAGT
* * ** ** *
829586 CTTATACTCCCTAAACGAATAGGGAGTAGACACATTTACTGAAGATTGTTCGAGT
1 -TTATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTAAAGATTGTTCGAGT
* *
829641 CTTACACTCCCTGAAGGAATAGAGAGCGGAC
1 -TTATACTCCCTGAAGGAATAGGGAGCGGAC
829672 TTATCATTTG
Statistics
Matches: 293, Mismatches: 55, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
51 40 0.14
52 1 0.00
53 47 0.16
54 3 0.01
55 110 0.38
56 89 0.30
57 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (54 bp):
TTATACTCCCTGAAGGAATAGGGAGCGGACACATTTGTTAAAGATTGTTCGAGT
Found at i:831257 original size:27 final size:27
Alignment explanation
Indices: 831217--831270 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
831207 TAATTTATGT
831217 GTATTTTATATTTAGGTCACTGATTTA
1 GTATTTTATATTTAGGTCACTGATTTA
*
831244 GTATTTTATGTTTAGGTCACTGATTTA
1 GTATTTTATATTTAGGTCACTGATTTA
831271 TTTCTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (27 bp):
GTATTTTATATTTAGGTCACTGATTTA
Found at i:833994 original size:32 final size:32
Alignment explanation
Indices: 833950--834011 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
833940 TCTTACTTGT
*
833950 ACTAACTAATTTCTTTTCTTTCGTTTGTGTAC
1 ACTAACTAATTTCTTCTCTTTCGTTTGTGTAC
* *
833982 ACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 ACTAACTAATTTCTTCTCTTTCGTTTGTGT
834012 CATTTTGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTCTTCTCTTTCGTTTGTGTAC
Found at i:835878 original size:14 final size:12
Alignment explanation
Indices: 835848--835931 Score: 66
Period size: 12 Copynumber: 6.8 Consensus size: 12
835838 AAATCAAAGT
835848 AAAGAGAAAAAC
1 AAAGAGAAAAAC
835860 AAAGAGAAAGAATC
1 AAAGAGAAA-AA-C
835874 AAAGAG-AAAAC
1 AAAGAGAAAAAC
*
835885 AATTAAAGAAAAAC
1 AA--AGAGAAAAAC
*
835899 AAAGA-AAAACTC
1 AAAGAGAAAA-AC
*
835911 AAAGAAAAATAAC
1 AAAGAGAAA-AAC
835924 AAA-AGAAA
1 AAAGAGAAA
835932 GAAAACAAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
11 7 0.12
12 23 0.39
13 14 0.24
14 15 0.25
ACGTcount: A:0.73, C:0.08, G:0.13, T:0.06
Consensus pattern (12 bp):
AAAGAGAAAAAC
Found at i:837015 original size:32 final size:32
Alignment explanation
Indices: 836970--837033 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
836960 AAGAAACGAT
836970 GAATGATGAGGCATCTTTGGAGATTCAACATC
1 GAATGATGAGGCATCTTTGGAGATTCAACATC
* * * *
837002 GAATGTTGGGGCATTTTTGGGGATTCAACATC
1 GAATGATGAGGCATCTTTGGAGATTCAACATC
837034 CTGATGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (32 bp):
GAATGATGAGGCATCTTTGGAGATTCAACATC
Found at i:837656 original size:131 final size:131
Alignment explanation
Indices: 837439--837680 Score: 308
Period size: 131 Copynumber: 1.8 Consensus size: 131
837429 TGGTATGCCA
* * * *
837439 TCCTCATCGCGTAAGAACCGTGTCATCCCCCGATCAGACCTCCTCATCATGTAGGAGCCGTGTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCAGTGTCA
* * *
837504 ACCTTAGATAACATGTTGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATTTCTTGTA
66 ACCTTAAATAACATGTCGTCCTCATCACATAGGAACCGTGTTATCATTCCTAAAGATTTCTTGTA
837569 G
131 G
* * * * * *
837570 TCCTCATCACGTAGGAACCGTTTCATCCACCGACCATATCTCTTCATCATGTAGGAGCAGTGT-T
1 TCCTCATCACGTAAGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCAGTGTCA
** *
837634 ACCTCTAAATAAC-TAGTCGTCCTCATTGCATAGGAACTGTGTTATCA
66 ACCT-TAAATAACAT-GTCGTCCTCATCACATAGGAACCGTGTTATCA
837681 CCCTCCCTAA
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
130 5 0.05
131 88 0.95
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (131 bp):
TCCTCATCACGTAAGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCAGTGTCA
ACCTTAAATAACATGTCGTCCTCATCACATAGGAACCGTGTTATCATTCCTAAAGATTTCTTGTA
G
Found at i:837963 original size:3 final size:3
Alignment explanation
Indices: 837957--838003 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
837947 CTCAAAAAAA
* *
837957 TAT TAT TA- TAT TAT AAA TAT TAAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
838002 TA
1 TA
838004 CAAATGTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:851019 original size:10 final size:10
Alignment explanation
Indices: 851004--851030 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
850994 TTTAAGAGCC
851004 CTCTCTCACT
1 CTCTCTCACT
851014 CTCTCTCACT
1 CTCTCTCACT
851024 CTCTCTC
1 CTCTCTC
851031 TCCCTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (10 bp):
CTCTCTCACT
Found at i:851826 original size:30 final size:30
Alignment explanation
Indices: 851790--851906 Score: 87
Period size: 30 Copynumber: 3.9 Consensus size: 30
851780 ACTTAGTACC
*
851790 TTAAGTTTCTATTTTTGCTATTTTAATCCT
1 TTAAGTTTCTATTTTTACTATTTTAATCCT
* * **
851820 TTAAGTTTTTATTTTTATTATTTTGGTCCT
1 TTAAGTTTCTATTTTTACTATTTTAATCCT
* * * *
851850 TTAACTTTTTGTATTTACTA-TTTAA-CCAT
1 TTAAGTTTCTATTTTTACTATTTTAATCC-T
* * *
851879 TTAAATTTCTGTTAATTA-TATTTTAATC
1 TTAAGTTTCTATT-TTTACTATTTTAATC
851907 TCTTAGATGA
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
28 2 0.03
29 16 0.24
30 49 0.72
31 1 0.01
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (30 bp):
TTAAGTTTCTATTTTTACTATTTTAATCCT
Found at i:852786 original size:24 final size:24
Alignment explanation
Indices: 852759--852820 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
852749 AAACATCAAA
852759 TTTTCAAAATAAAGTCATAATCGT
1 TTTTCAAAATAAAGTCATAATCGT
* ** *
852783 TTTTTAAAATAACA-TTTTAATTGT
1 TTTTCAAAATAA-AGTCATAATCGT
*
852807 TTTTCAAAAAAAAG
1 TTTTCAAAATAAAG
852821 GTTATGACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (24 bp):
TTTTCAAAATAAAGTCATAATCGT
Found at i:854816 original size:24 final size:24
Alignment explanation
Indices: 854778--854847 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
854768 CAAAACAGAG
* *
854778 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
854802 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
854826 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
854848 CTATTTGTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:855577 original size:29 final size:29
Alignment explanation
Indices: 855541--855722 Score: 163
Period size: 29 Copynumber: 6.4 Consensus size: 29
855531 CATTTTACAC
* * *
855541 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
855570 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
***
855599 AAATAGCACAAATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* * * *
855628 GAATATCA--CTTTTTGAA-AAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* *
855654 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* *****
855683 GAATAGCACCAAAACTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
855712 GAATAGCACCC
1 AAATAGCACCC
855723 GGTCAACGGT
Statistics
Matches: 123, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
26 13 0.11
27 7 0.06
28 7 0.06
29 96 0.78
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAATTAATTCCCA
Found at i:855703 original size:84 final size:85
Alignment explanation
Indices: 855551--855716 Score: 264
Period size: 84 Copynumber: 2.0 Consensus size: 85
855541 AAATAGCACC
* **
855551 CTTTTTAAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACAAATTTTG
1 CTTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACAAATACTG
855616 AATTAATTCCCAGAATATCA
66 AATTAATTCCCAGAATATCA
* *
855636 CTTTTTGAAA-AATTACCAAAATAGCACCCATTTCGAATTAATTCCCAGAATAGCACCAAA-ACT
1 CTTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCA-CAAATACT
855699 GAATTAATTCCCAGAATA
65 GAATTAATTCCCAGAATA
855717 GCACCCGGTC
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
84 62 0.83
85 13 0.17
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (85 bp):
CTTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACAAATACTG
AATTAATTCCCAGAATATCA
Found at i:855753 original size:18 final size:18
Alignment explanation
Indices: 855730--855781 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
855720 CCCGGTCAAC
855730 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
855748 GGTCAACGAGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
855766 GGTCAACGGATCGGGT
1 GGTCAACGGGTCGGGT
855782 TATGATCGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:862062 original size:23 final size:23
Alignment explanation
Indices: 862036--862080 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
862026 ATCAAAAATT
* *
862036 AAAACATAATTCATGTCAAGTAC
1 AAAACAGAATCCATGTCAAGTAC
*
862059 AAAACAGAGTCCATGTCAAGTA
1 AAAACAGAATCCATGTCAAGTA
862081 TCATATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (23 bp):
AAAACAGAATCCATGTCAAGTAC
Found at i:862106 original size:24 final size:24
Alignment explanation
Indices: 862079--862124 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
862069 CCATGTCAAG
*
862079 TATCATATAAAAATTCAGGTCATA
1 TATCATATAAAAATCCAGGTCATA
* *
862103 TATCATATCAGAATCCAGGTCA
1 TATCATATAAAAATCCAGGTCA
862125 AAAATCAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (24 bp):
TATCATATAAAAATCCAGGTCATA
Found at i:862131 original size:24 final size:24
Alignment explanation
Indices: 862080--862137 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
862070 CATGTCAAGT
* * *
862080 ATCATATAAAAATTCAGGTCATAT
1 ATCATATAAAAATCCAGGTCAAAA
* *
862104 ATCATATCAGAATCCAGGTCAAAA
1 ATCATATAAAAATCCAGGTCAAAA
*
862128 ATCAGATAAA
1 ATCATATAAA
862138 CTATTTGTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (24 bp):
ATCATATAAAAATCCAGGTCAAAA
Found at i:862861 original size:29 final size:29
Alignment explanation
Indices: 862825--862891 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
862815 CATTTTACAC
*
862825 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* * *
862854 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
862883 AAATAGCAC
1 AAATAGCAC
862892 AAATTTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTACCA
Found at i:862902 original size:29 final size:28
Alignment explanation
Indices: 862825--862979 Score: 94
Period size: 29 Copynumber: 5.4 Consensus size: 28
862815 CATTTTACAC
* * * *
862825 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCA-CCATTTTGAATTAATTCCCA
*
862854 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCATTTT-GAATTAATTCCCA
* * *
862883 AAATAGCACAAATTTTGAATGAATTCCCC
1 AAATAGCAC-CATTTTGAATTAATTCCCA
* * ** * ** * *
862912 GAATATCACTTTTTTTCAAAAAATTACTA
1 AAATAGCAC-CATTTTGAATTAATTCCCA
*
862941 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTGAATTAATTCCCA
*
862970 GAATAGCACC
1 AAATAGCACC
862980 GGTCAACGGT
Statistics
Matches: 93, Mismatches: 30, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
28 8 0.09
29 80 0.86
30 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (28 bp):
AAATAGCACCATTTTGAATTAATTCCCA
Found at i:863010 original size:18 final size:18
Alignment explanation
Indices: 862987--863021 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
862977 ACCGGTCAAC
*
862987 GGTCAACGGGTCGGGTCG
1 GGTCAACGGATCGGGTCG
863005 GGTCAACGGATCGGGTC
1 GGTCAACGGATCGGGTC
863022 ATGACCGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGATCGGGTCG
Found at i:863045 original size:10 final size:10
Alignment explanation
Indices: 863025--863060 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
863015 TCGGGTCATG
863025 ACCGGTC-AA
1 ACCGGTCAAA
863034 ACCGGTCAAA
1 ACCGGTCAAA
863044 ACCGGTTCAAA
1 ACCGG-TCAAA
863055 ACCGGT
1 ACCGGT
863061 TTCTAGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:864119 original size:16 final size:16
Alignment explanation
Indices: 864098--864128 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
864088 GATCGATATG
*
864098 AACTCAAACTGAAAAT
1 AACTCAAACCGAAAAT
864114 AACTCAAACCGAAAA
1 AACTCAAACCGAAAA
864129 CAATCAAAAT
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:0.58, C:0.23, G:0.06, T:0.13
Consensus pattern (16 bp):
AACTCAAACCGAAAAT
Found at i:865095 original size:16 final size:16
Alignment explanation
Indices: 865062--865097 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
865052 TCGTCGTCTC
* *
865062 AAATCCCTAAATTTTT
1 AAATCCCTAAAATCTT
865078 AAATCCCTAAAATCTT
1 AAATCCCTAAAATCTT
865094 AAAT
1 AAAT
865098 ATTCAATCCC
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:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATCCCTAAAATCTT
Found at i:865316 original size:96 final size:97
Alignment explanation
Indices: 865195--865389 Score: 279
Period size: 96 Copynumber: 2.0 Consensus size: 97
865185 TAAATTATCA
* *
865195 AATAAAAAGTATTAGAAAAATTTTAATTACATAAAAATTTAAAAATTTT-AAGAGA-GTTG-TTT
1 AATAAAAAGTACTAGAAAAATTTTAATTACATAAAAATTT--AAATTTTCAAGAGATATTGTTTT
*
865257 CTATCAACCTCGTGAGTCGATCCCGGAGCATACC
64 CTATCAACCTCGTGAGCCGATCCCGGAGCATACC
*
865291 AATAAAAAGTACTAGAAAAATTTTAATTACATAAAAATTTAAATTTTCAAGAGATTATTGTTTTT
1 AATAAAAAGTACTAGAAAAATTTTAATTACATAAAAATTTAAATTTTCAAGAGA-TATTGTTTTC
* * *
865356 TATCAACCTTGTGAGCCGATCCTGGAGCTTACC
65 TATCAACCTCGTGAGCCGATCCCGGAGCATACC
865389 A
1 A
865390 GCAATGATCA
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
94 7 0.08
95 6 0.07
96 39 0.44
97 3 0.03
98 33 0.38
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (97 bp):
AATAAAAAGTACTAGAAAAATTTTAATTACATAAAAATTTAAATTTTCAAGAGATATTGTTTTCT
ATCAACCTCGTGAGCCGATCCCGGAGCATACC
Found at i:867765 original size:29 final size:30
Alignment explanation
Indices: 867694--867766 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
867684 AAAACCGAAT
*
867694 TAAACGGGGACGGGAAAAAACTGTTTATGC
1 TAAACGGGGACGGGAAAAAACCGTTTATGC
* *
867724 TAAACGAGAACGGG-AAAAACCGTTTATGC
1 TAAACGGGGACGGGAAAAAACCGTTTATGC
867753 TAAACGGGGACGGG
1 TAAACGGGGACGGG
867767 GATGGGTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.37, C:0.15, G:0.32, T:0.16
Consensus pattern (30 bp):
TAAACGGGGACGGGAAAAAACCGTTTATGC
Found at i:867811 original size:12 final size:12
Alignment explanation
Indices: 867788--867819 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
867778 TAATCTCCGC
867788 CCCGATTACCCGG
1 CCCGA-TACCCGG
867801 CCCGATACCCGG
1 CCCGATACCCGG
867813 CCCGATA
1 CCCGATA
867820 AATATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (12 bp):
CCCGATACCCGG
Found at i:867907 original size:15 final size:15
Alignment explanation
Indices: 867843--867926 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 15
867833 ATTATTTTAT
867843 ATATATATAATATTA
1 ATATATATAATATTA
* *
867858 ATAAATTTAAT-TTA
1 ATATATATAATATTA
* * *
867872 ATTTAAATTAA-AATA
1 ATATATA-TAATATTA
*
867887 TATATATATAATATTT
1 -ATATATATAATATTA
*
867903 ATATATTTAAT-TTAA
1 ATATATATAATATT-A
867918 ATATATATA
1 ATATATATA
867927 CCTGGCCCAA
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
14 8 0.16
15 35 0.70
16 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATAATATTA
Found at i:869703 original size:26 final size:26
Alignment explanation
Indices: 869657--869707 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
869647 ACTAATTTAA
**
869657 AACCTAATTTTTTATCTAAATTATTT
1 AACCTAATTTTTTATAGAAATTATTT
869683 AACCTAAATTTTTT-TAGAAATTATT
1 AACCT-AATTTTTTATAGAAATTATT
869708 AATTATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (26 bp):
AACCTAATTTTTTATAGAAATTATTT
Found at i:869928 original size:18 final size:20
Alignment explanation
Indices: 869901--869937 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
869891 AAAATTAAAA
869901 AAAAACAACATAAA-ATAAT
1 AAAAACAACATAAATATAAT
869920 AAAAA-AACATAAATATAA
1 AAAAACAACATAAATATAA
869938 GGACCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAACAACATAAATATAAT
Found at i:872362 original size:24 final size:25
Alignment explanation
Indices: 872326--872373 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
872316 TAGATATATT
*
872326 ATTATTATTAAATA-TATTATTTTA
1 ATTATTATTAAATACTAATATTTTA
872350 ATTATT-TTAAAATACTAATATTTT
1 ATTATTATT-AAATACTAATATTTT
872374 GTATATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 11 0.52
25 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTATTATTAAATACTAATATTTTA
Found at i:874778 original size:15 final size:15
Alignment explanation
Indices: 874758--874788 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
874748 ACATTACTAC
874758 ATAGAAATTAAAAGT
1 ATAGAAATTAAAAGT
874773 ATAGAAATTAAAAGT
1 ATAGAAATTAAAAGT
874788 A
1 A
874789 GCAATTCAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (15 bp):
ATAGAAATTAAAAGT
Found at i:877997 original size:16 final size:17
Alignment explanation
Indices: 877976--878009 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
877966 AGGTGTCACA
877976 TTAACTT-TTCAAAACT
1 TTAACTTGTTCAAAACT
*
877992 TTAACTTGTTGAAAACT
1 TTAACTTGTTCAAAACT
878009 T
1 T
878010 ATTAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (17 bp):
TTAACTTGTTCAAAACT
Found at i:878578 original size:23 final size:23
Alignment explanation
Indices: 878549--878634 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
878539 ATAGTTTTCG
*
878549 CCGAAGGACCACATAGGTTTATC
1 CCGAAGGACCACATAGGTTTGTC
*
878572 CCCAAGGACCACATAGGTTTGTC
1 CCGAAGGACCACATAGGTTTGTC
* *
878595 CCGAAGGACTACATAGTTTTGTC
1 CCGAAGGACCACATAGGTTTGTC
*
878618 CTGAAGGACCACATAGG
1 CCGAAGGACCACATAGG
878635 ACCCTCAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (23 bp):
CCGAAGGACCACATAGGTTTGTC
Found at i:882829 original size:3 final size:3
Alignment explanation
Indices: 882821--883014 Score: 93
Period size: 3 Copynumber: 60.7 Consensus size: 3
882811 TAGCATTTTA
* * * * *
882821 AAT AAT AAT AAT AAT AAT AAGC ACT ACT AAC AATT AAT AAT AGT AAGT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AA-T
* * * *
882869 AAT AAT AAT AATT AAT AAT AAT TAT AAAT ATT GAT AAT AATT AAT GAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT
* * * * *
882917 AAT AATT AAT ATTT ATT AAT ATTT ATT AAT -AT TAT CAAT AAAT AAT
1 AAT AA-T AAT A-AT AAT AAT A-AT AAT AAT AAT AAT -AAT -AAT AAT
* * * * *
882963 AAT AAT AAT AAT AAT AGT AAC AAC AAC AACT AAT AAT AACC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT
883010 AAT AA
1 AAT AA
883015 CAAGTTTCAG
Statistics
Matches: 150, Mismatches: 28, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
2 2 0.01
3 118 0.79
4 30 0.20
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:882858 original size:26 final size:26
Alignment explanation
Indices: 882821--882890 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
882811 TAGCATTTTA
* *
882821 AATAATAA-TAATAATAATAAGCACT
1 AATAACAATTAATAATAATAAGCAAT
* * *
882846 ACTAACAATTAATAATAGTAAGTAAT
1 AATAACAATTAATAATAATAAGCAAT
*
882872 AATAATAATTAATAATAAT
1 AATAACAATTAATAATAAT
882891 TATAAATATT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 6 0.17
26 30 0.83
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (26 bp):
AATAACAATTAATAATAATAAGCAAT
Found at i:882884 original size:10 final size:10
Alignment explanation
Indices: 882871--882977 Score: 82
Period size: 10 Copynumber: 11.0 Consensus size: 10
882861 TAGTAAGTAA
882871 TAATAATAAT
1 TAATAATAAT
882881 TAATAATAAT
1 TAATAATAAT
882891 T-ATAA-ATAT
1 TAATAATA-AT
*
882900 TGATAATAAT
1 TAATAATAAT
*
882910 TAATGATAA-
1 TAATAATAAT
*
882919 TAATTAATATT
1 TAA-TAATAAT
* *
882930 TATTAATATT
1 TAATAATAAT
*
882940 TATTAAT-AT
1 TAATAATAAT
*
882949 T-ATCAATAAA
1 TAAT-AATAAT
882959 TAATAATAA-
1 TAATAATAAT
882968 TAATAATAAT
1 TAATAATAAT
882978 AGTAACAACA
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.03
9 24 0.30
10 49 0.61
11 5 0.06
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (10 bp):
TAATAATAAT
Found at i:882898 original size:13 final size:13
Alignment explanation
Indices: 882821--883014 Score: 70
Period size: 13 Copynumber: 14.6 Consensus size: 13
882811 TAGCATTTTA
882821 AATAATAAT-AAT
1 AATAATAATAAAT
** *
882833 AATAATAAGCACT
1 AATAATAATAAAT
* * *
882846 ACTAACAATTAAT
1 AATAATAATAAAT
*
882859 AATAGTAAGT-AAT
1 AATAATAA-TAAAT
*
882872 AATAATAATTAAT
1 AATAATAATAAAT
*
882885 AATAATTATAAAT
1 AATAATAATAAAT
* * *
882898 ATTGATAATAATT
1 AATAATAATAAAT
* *
882911 AATGATAATAATT
1 AATAATAATAAAT
* * *
882924 AATATTTATTAAT
1 AATAATAATAAAT
* * *
882937 ATTTATTAATATTAT
1 A-ATAATAATA-AAT
882952 CAATAAATAAT-AAT
1 -AAT-AATAATAAAT
882966 AATAATAATAATAGT
1 AATAATAATAA-A-T
* * * *
882981 AACAACAACAACT
1 AATAATAATAAAT
**
882994 AATAATAACCAAT
1 AATAATAATAAAT
883007 AATAATAA
1 AATAATAA
883015 CAAGTTTCAG
Statistics
Matches: 134, Mismatches: 38, Indels: 19
0.70 0.20 0.10
Matches are distributed among these distances:
12 15 0.11
13 91 0.68
14 10 0.07
15 12 0.09
16 6 0.04
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.35
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:886208 original size:22 final size:22
Alignment explanation
Indices: 886180--886232 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
886170 ATGAACAGTG
*
886180 GGGGAATCGATTCCCTGTAGCA
1 GGGGAATCGATTCCCTATAGCA
886202 GGGGAATCGATTCCCTATAGCA
1 GGGGAATCGATTCCCTATAGCA
886224 GGGGAATCG
1 GGGGAATCG
886233 GTACCCCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.21
Consensus pattern (22 bp):
GGGGAATCGATTCCCTATAGCA
Found at i:886898 original size:33 final size:33
Alignment explanation
Indices: 886861--886927 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
886851 ACCGTAGTGC
886861 TAATCCGTATGACACATAAGGTCCTGTCCACCA
1 TAATCCGTATGACACATAAGGTCCTGTCCACCA
*
886894 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCCTGTCCACCA
886927 T
1 T
886928 CTGTACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCCTGTCCACCA
Found at i:892466 original size:13 final size:13
Alignment explanation
Indices: 892448--892473 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
892438 CATCTCATCA
892448 ACTTTTTTTATTT
1 ACTTTTTTTATTT
892461 ACTTTTTTTATTT
1 ACTTTTTTTATTT
892474 GTAATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
ACTTTTTTTATTT
Found at i:895348 original size:12 final size:11
Alignment explanation
Indices: 895327--895401 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
895317 AAAATATAAC
895327 AAAT-TATTAT
1 AAATATATTAT
895337 AAAATATATTATTT
1 -AAATATATTA--T
*
895351 TAAT-TATT-T
1 AAATATATTAT
*
895360 AAA-ATATAAT
1 AAATATATTAT
895370 AAATA-ATTAT
1 AAATATATTAT
*
895380 AGATATATTATT
1 AAATATATTA-T
895392 AAATATATTA
1 AAATATATTA
895402 CATTAATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
9 6 0.12
10 12 0.24
11 9 0.18
12 19 0.38
13 3 0.06
14 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
AAATATATTAT
Found at i:899642 original size:17 final size:18
Alignment explanation
Indices: 899609--899642 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
899599 TATTTTGATA
899609 TTTAATCTCCAAGGAATC
1 TTTAATCTCCAAGGAATC
*
899627 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAAGGAAT
899643 ATACTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTAATCTCCAAGGAATC
Found at i:899873 original size:59 final size:58
Alignment explanation
Indices: 899803--899974 Score: 224
Period size: 59 Copynumber: 3.0 Consensus size: 58
899793 ATACTTCCCC
* * *
899803 TTTCATTTTAGCACACGAAGTACCCTAT-TCAAAAATCCATACCATTAGTATGATTTTG
1 TTTCATTTTAGCACATGAAATACCCTATGT-GAAAATCCATACCATTAGTATGATTTTG
* * *
899861 TTTCTATTTTAGCACATGAAATGCCCTATGTGAATATTCATACCATTAGTATGATTTTG
1 TTTC-ATTTTAGCACATGAAATACCCTATGTGAAAATCCATACCATTAGTATGATTTTG
* *
899920 TTACCATTTTAGCACATGAAATTCCCTATGTGAAAATCC--ACCATTAGTATGATTT
1 TT-TCATTTTAGCACATGAAATACCCTATGTGAAAATCCATACCATTAGTATGATTT
899975 CCTTATCCTT
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
57 16 0.16
58 4 0.04
59 79 0.78
60 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (58 bp):
TTTCATTTTAGCACATGAAATACCCTATGTGAAAATCCATACCATTAGTATGATTTTG
Found at i:907058 original size:59 final size:59
Alignment explanation
Indices: 906928--907058 Score: 219
Period size: 59 Copynumber: 2.2 Consensus size: 59
906918 CTGCCCCTTT
* *
906928 CATTTTAGCACACGAAGTGCCCTATTCGAAAATCCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACATGAAATGCCCTATTCGAAAATCCATACCATTAGTATGATTTTGTTAC
*
906987 CATTTTAGCACATGAAATGCCCTATGT-GAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACATGAAATGCCCTAT-TCGAAAATCCATACCATTAGTATGATTTTGTTAC
907046 CATTTTAGCACAT
1 CATTTTAGCACAT
907059 TAGCACCCTT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 67 0.99
60 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (59 bp):
CATTTTAGCACATGAAATGCCCTATTCGAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:907162 original size:126 final size:125
Alignment explanation
Indices: 906957--907182 Score: 276
Period size: 126 Copynumber: 1.8 Consensus size: 125
906947 CCCTATTCGA
* *** * * * *
906957 AAATCCATACCATTAGTATGATTTTGTTACCATTTTAGCACATGAAATGCCCTATGTGAAAATTC
1 AAATCCATACCATCAGTATGATTCCCTTACCATTTTAGAACATAAAATGCCCTATCTGAAAATCC
* **
907022 ATACCATTAGTATGATTTTGTTACCATTTTAGCACATTAGCACCCTTAGTGCTTTATCTGG
66 ATACCATTAATATGATTTCCTTACCA-TTTAGCACATTAGCACCCTTAGTGCTTTATCTGG
*
907083 AAATCCATA-CACTCAGTATGATTCCCTTACCATTTTAGAACATAAAATGCCCTATCTGGAAATC
1 AAATCCATACCA-TCAGTATGATTCCCTTACCATTTTAGAACATAAAATGCCCTATCTGAAAATC
** *
907147 CATA-TTTTCAATATGATTTCCTTATCATTTAGCACA
65 CATACCATT-AATATGATTTCCTTACCATTTAGCACA
907183 CTCAGGGATC
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
125 13 0.16
126 70 0.84
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (125 bp):
AAATCCATACCATCAGTATGATTCCCTTACCATTTTAGAACATAAAATGCCCTATCTGAAAATCC
ATACCATTAATATGATTTCCTTACCATTTAGCACATTAGCACCCTTAGTGCTTTATCTGG
Found at i:917256 original size:13 final size:13
Alignment explanation
Indices: 917238--917266 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
917228 GGTACCAATA
917238 TTGCATGGTAATC
1 TTGCATGGTAATC
917251 TTGCATGGTAATC
1 TTGCATGGTAATC
917264 TTG
1 TTG
917267 TTATATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (13 bp):
TTGCATGGTAATC
Found at i:920200 original size:29 final size:29
Alignment explanation
Indices: 920164--920222 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
920154 TGAGCATATG
920164 TCTTGGATTATTATGTGACAGTCATAACA
1 TCTTGGATTATTATGTGACAGTCATAACA
920193 TCTTGGATTATTATGTGACAGTCATAACA
1 TCTTGGATTATTATGTGACAGTCATAACA
920222 T
1 T
920223 TGGTCATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (29 bp):
TCTTGGATTATTATGTGACAGTCATAACA
Found at i:924694 original size:3 final size:3
Alignment explanation
Indices: 924681--924744 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
924671 GTACACTAAA
*
924681 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* * *
924726 GAT CAT -AT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
924745 ATTATAACCC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:925248 original size:133 final size:133
Alignment explanation
Indices: 924929--925363 Score: 427
Period size: 134 Copynumber: 3.2 Consensus size: 133
924919 ACGTTGACTG
* * * *
924929 ATTCTACTGTTCCTCATGGAAGATTGAATCGAGGTAGACTTGTTCTACTGTCACTCAGGGAATAT
1 ATTCTACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCAACTGTTACTCAGGGAATAT
* * * * *
924994 CAAATCTTGAAAGAGAGGGATCTGTTAT-GCTTCTTAC-TGAGGAAAAATTAGATATGGGGACTT
66 CAAATCTTGAAA-AGAGGGATATGTT-TCGCTTCTT-CTTAAGGGAAAATCAGATATAGGGACTT
925057 TTATTC
128 TTATTC
* * * *
925063 ACTCTATTTTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCAATTGTTACTCAGGGAATAT
1 ATTCTACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCAACTGTTACTCAGGGAATAT
* * * * *
925128 CAAACCTTGAAAAGAGGGATTTGTTTCACTTCTTCTTAAGGGAAAATCAGATCTAGTGA-TTTTG
66 CAAATCTTGAAAAGAGGGATATGTTTCGCTTCTTCTTAAGGGAAAATCAGATATAGGGACTTTT-
925192 ATTC
130 ATTC
* * * *
925196 ATTCCACTGTTCTTCAGGGAAGATTAAATCAAGGCAGACTTGTTTC-ACTGTTACTCTA-GGAAT
1 ATTCTACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTG-TTCAACTGTTACTC-AGGGAAT
* * * * *
925259 ATCAAATCTTAAAAAAGAGGGATATATTCCGTTTCTTCTTAAGGGAAAAATTCAAATAT-GGG-C
64 ATCAAATCTT-GAAAAGAGGGATATGTTTCGCTTCTTCTTAAGGG-AAAA-TCAGATATAGGGAC
*
925322 ATGTTGATTC
126 -T-TTTATTC
* ** *
925332 ATTCCACTACTCTTCA-GGAAAATTGAATCGAG
1 ATTCTACTGTTCTTCAGGGAAGATTGAATCGAG
925364 TTTGATTCAC
Statistics
Matches: 249, Mismatches: 41, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
132 6 0.02
133 97 0.39
134 100 0.40
135 19 0.08
136 25 0.10
137 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (133 bp):
ATTCTACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCAACTGTTACTCAGGGAATAT
CAAATCTTGAAAAGAGGGATATGTTTCGCTTCTTCTTAAGGGAAAATCAGATATAGGGACTTTTA
TTC
Found at i:930559 original size:6 final size:6
Alignment explanation
Indices: 930548--930576 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
930538 GATGAATTTT
930548 GGGTAA GGGTAA GGGTAA GGGTAA GGGTA
1 GGGTAA GGGTAA GGGTAA GGGTAA GGGTA
930577 TTGGTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.52, T:0.17
Consensus pattern (6 bp):
GGGTAA
Found at i:930671 original size:21 final size:19
Alignment explanation
Indices: 930647--930697 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
930637 CGATGAATAA
930647 TATCGATACTAATTGAAGTAG
1 TATCGATACTAATTGAAG--G
* *
930668 TATCGATAGTGATGTGAAGG
1 TATCGATACTAAT-TGAAGG
930688 TATCGATACT
1 TATCGATACT
930698 GTAATTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 11 0.42
22 5 0.19
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (19 bp):
TATCGATACTAATTGAAGG
Found at i:931356 original size:15 final size:15
Alignment explanation
Indices: 931336--931372 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
931326 TATGTTTATA
931336 TGAAAATGTTCAAAG
1 TGAAAATGTTCAAAG
*
931351 TGAAAATGTTCAACG
1 TGAAAATGTTCAAAG
931366 TGAAAAT
1 TGAAAAT
931373 ACCTATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (15 bp):
TGAAAATGTTCAAAG
Found at i:931554 original size:22 final size:22
Alignment explanation
Indices: 931512--931582 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 22
931502 GTTCAACGCA
*
931512 GTCCTTTGGGACATATCTATGTG
1 GTCCTTCGGGACA-ATCTATGTG
931535 GTCCTTCGGGACAATCTATGTG
1 GTCCTTCGGGACAATCTATGTG
* *
931557 ATCCTTCAAGG-CAAATCTATGTG
1 GTCCTTC-GGGAC-AATCTATGTG
931580 GTC
1 GTC
931583 ATTTGAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.38
23 26 0.62
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (22 bp):
GTCCTTCGGGACAATCTATGTG
Found at i:934568 original size:16 final size:17
Alignment explanation
Indices: 934547--934580 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
934537 ATGTGTCACA
934547 TTGACTT-TTCAAAACT
1 TTGACTTGTTCAAAACT
*
934563 TTGACTTGTTGAAAACT
1 TTGACTTGTTCAAAACT
934580 T
1 T
934581 ATTGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (17 bp):
TTGACTTGTTCAAAACT
Found at i:935190 original size:23 final size:23
Alignment explanation
Indices: 935164--935287 Score: 162
Period size: 23 Copynumber: 5.4 Consensus size: 23
935154 GTCCTGAATA
935164 ACCACATAGTTTTGTCTCGAAGG
1 ACCACATAGTTTTGTCTCGAAGG
* *
935187 ACCACATAGGTTTGTCCCGAAGG
1 ACCACATAGTTTTGTCTCGAAGG
* *
935210 ACCACATA-TGCTTGTCACGAAGG
1 ACCACATAGT-TTTGTCTCGAAGG
*
935233 ACCACATAGCTTTGTCTCGAAGG
1 ACCACATAGTTTTGTCTCGAAGG
*
935256 ACCACATAGTTTTAG-CTCGAAGA
1 ACCACATAGTTTT-GTCTCGAAGG
935279 ACCACATAG
1 ACCACATAG
935288 GACCCGACTC
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
23 87 0.99
24 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
ACCACATAGTTTTGTCTCGAAGG
Found at i:935203 original size:46 final size:46
Alignment explanation
Indices: 935144--935288 Score: 165
Period size: 46 Copynumber: 3.2 Consensus size: 46
935134 CACCAAAGTG
**
935144 CCACATA--TTTGTCCTGAATAACCACATAGTTTTGTCTCGAAGGA
1 CCACATAGGTTTGTCCTGAAGGACCACATAGTTTTGTCTCGAAGGA
* * *
935188 CCACATAGGTTTGTCCCGAAGGACCACATA-TGCTTGTCACGAAGGA
1 CCACATAGGTTTGTCCTGAAGGACCACATAGT-TTTGTCTCGAAGGA
* *
935234 CCACATAGCTTTGT-CTCGAAGGACCACATAGTTTTAG-CTCGAAGAA
1 CCACATAGGTTTGTCCT-GAAGGACCACATAGTTTT-GTCTCGAAGGA
935280 CCACATAGG
1 CCACATAGG
935289 ACCCGACTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
44 7 0.08
45 2 0.02
46 73 0.87
47 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (46 bp):
CCACATAGGTTTGTCCTGAAGGACCACATAGTTTTGTCTCGAAGGA
Found at i:935976 original size:17 final size:18
Alignment explanation
Indices: 935933--935978 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
935923 AATTTCAATT
935933 CTACTTACAATATCGATAC
1 CTACTT-CAATATCGATAC
* *
935952 CCACTTCAGTATCGATA-
1 CTACTTCAATATCGATAC
935969 CTACTTCAAT
1 CTACTTCAAT
935979 TAGTATCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (18 bp):
CTACTTCAATATCGATAC
Found at i:937634 original size:29 final size:28
Alignment explanation
Indices: 937580--937636 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
937570 CAAGTCTTAG
* *
937580 AAAAATTGGGGACCATTTTGTAATTTTT
1 AAAAATTAGGGACCATTTTGGAATTTTT
* *
937608 AAAAAGTTAGGGATCATTTTGGCATTTTT
1 AAAAA-TTAGGGACCATTTTGGAATTTTT
937637 GGAAAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (28 bp):
AAAAATTAGGGACCATTTTGGAATTTTT
Found at i:938446 original size:59 final size:59
Alignment explanation
Indices: 938347--938474 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
938337 CAGCAGGCTG
** *
938347 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGACACGACCTTATGTGC
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGC
* ** * * * *
938406 CATATTCGGGACTGTACTTAAGGATATCTAGTACAGATGGTGGACATGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGC
*
938465 CATACTCGGG
1 CATATTCGGG
938475 TTAACACTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGC
Found at i:944691 original size:23 final size:23
Alignment explanation
Indices: 944640--944760 Score: 122
Period size: 23 Copynumber: 5.3 Consensus size: 23
944630 CACTGAAGTG
944640 CCACATA--TTTGTCCCGAAGGA
1 CCACATAGTTTTGTCCCGAAGGA
* *
944661 CTATATAGTTTTCG-CCCGAAGGA
1 CCACATAGTTTT-GTCCCGAAGGA
* * * *
944684 CCACATAGGTTTATCCCCAAGGG
1 CCACATAGTTTTGTCCCGAAGGA
* **
944707 CCACATAGGTTTGTCCCGAATAA
1 CCACATAGTTTTGTCCCGAAGGA
*
944730 CTACATAGTTTTGTCCCGAAGGA
1 CCACATAGTTTTGTCCCGAAGGA
944753 CCACATAG
1 CCACATAG
944761 GACCCTGAAC
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
21 5 0.06
23 72 0.92
24 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (23 bp):
CCACATAGTTTTGTCCCGAAGGA
Found at i:949195 original size:20 final size:20
Alignment explanation
Indices: 949150--949196 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
949140 TAATAAAAGC
*
949150 AAATAAAATAAAAACAAATG
1 AAATAAAATAAAAACAAATA
* *
949170 AGATAAAATAAAAAGGAAA-A
1 AAATAAAATAAAAA-CAAATA
949190 AAATAAA
1 AAATAAA
949197 GATGGCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (20 bp):
AAATAAAATAAAAACAAATA
Found at i:949265 original size:13 final size:12
Alignment explanation
Indices: 949240--949274 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
949230 GAAAAAACTG
949240 AAATAAA-AAAT
1 AAATAAACAAAT
949251 AAATAAACAAGAT
1 AAATAAACAA-AT
949264 AAATAAACAAA
1 AAATAAACAAA
949275 ATGGACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 3 0.14
13 12 0.55
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATAAACAAAT
Found at i:962430 original size:13 final size:12
Alignment explanation
Indices: 962403--962437 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
962393 GAAGAAACTG
962403 AAATAAA-AAAT
1 AAATAAACAAAT
962414 AAATAAACAAGAT
1 AAATAAACAA-AT
962427 AAATAAACAAA
1 AAATAAACAAA
962438 ATGGACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 3 0.14
13 12 0.55
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATAAACAAAT
Found at i:962593 original size:2 final size:2
Alignment explanation
Indices: 962588--962613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
962578 AATAGAACTA
962588 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
962614 TAATATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:963980 original size:29 final size:29
Alignment explanation
Indices: 963916--963981 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
963906 GTGAAAATGA
* * *
963916 TATGTGAATATGTTTAAATGAAAATATTC
1 TATGTGAAAATGTTCAAATGAAAATATCC
* *
963945 TAAGTGAAAATGTTCCACATGAAAATA-CC
1 TATGTGAAAATGTT-CAAATGAAAATATCC
963974 TATGTGAA
1 TATGTGAA
963982 CGTGCTTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (29 bp):
TATGTGAAAATGTTCAAATGAAAATATCC
Found at i:964131 original size:23 final size:24
Alignment explanation
Indices: 964098--964201 Score: 142
Period size: 23 Copynumber: 4.5 Consensus size: 24
964088 AGAGCCGAGG
* * *
964098 ATTCTACGTGGTTCTTCGGGACAT
1 ATTCTATGTGGTCCTTCGGGACAA
964122 A-TCTATGTGGTCCTTCGGGAC-A
1 ATTCTATGTGGTCCTTCGGGACAA
*
964144 ATTCTACGTGGTCCTTCGGGA-AA
1 ATTCTATGTGGTCCTTCGGGACAA
*
964167 AATCTATGTGGTCCTTCGGGACAA
1 ATTCTATGTGGTCCTTCGGGACAA
964191 ATTCTATGTGG
1 ATTCTATGTGG
964202 CACTTTGGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
22 1 0.01
23 56 0.80
24 13 0.19
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (24 bp):
ATTCTATGTGGTCCTTCGGGACAA
Done.