Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 33
Found at i:1771734 original size:32 final size:32
Alignment explanation
Indices: 1771698--1771779 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
1771688 CGAGAGAGGC
* * * *
1771698 AGAGAGTGAGAGAGAGTGTGGGCGAGAATGAG
1 AGAGAGAGAGAGAGAGAGTGGGAGAGAATGAA
* *
1771730 AGAGAGAAAGGGAGAGAGTGGGAGAGAATGAA
1 AGAGAGAGAGAGAGAGAGTGGGAGAGAATGAA
*
1771762 AGAGAGAGAGAGCGAGAG
1 AGAGAGAGAGAGAGAGAG
1771780 AGAGAAAGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.41, C:0.02, G:0.49, T:0.07
Consensus pattern (32 bp):
AGAGAGAGAGAGAGAGAGTGGGAGAGAATGAA
Found at i:1771754 original size:24 final size:24
Alignment explanation
Indices: 1771727--1771801 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
1771717 GGGCGAGAAT
1771727 GAGAGAGAGAAAGGGAGAGAGTGG
1 GAGAGAGAGAAAGGGAGAGAGTGG
* * *
1771751 GAGAGA-ATGAAAGAGAGAGAGAGC
1 GAGAGAGA-GAAAGGGAGAGAGTGG
*
1771775 GAGAGAGAGAAAGTGTGAGGGAGTGG
1 GAGAGAGAGAAAG-G-GAGAGAGTGG
1771801 G
1 G
1771802 TGATAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 1 0.03
24 30 0.75
25 1 0.03
26 8 0.20
ACGTcount: A:0.41, C:0.01, G:0.51, T:0.07
Consensus pattern (24 bp):
GAGAGAGAGAAAGGGAGAGAGTGG
Found at i:1771926 original size:7 final size:7
Alignment explanation
Indices: 1771914--1771940 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1771904 GATCCAGGTA
1771914 CGGAAAT
1 CGGAAAT
1771921 CGGAAAT
1 CGGAAAT
1771928 CGGAAAT
1 CGGAAAT
1771935 CGGAAA
1 CGGAAA
1771941 GAATAGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.30, T:0.11
Consensus pattern (7 bp):
CGGAAAT
Found at i:1772110 original size:25 final size:25
Alignment explanation
Indices: 1772080--1772135 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
1772070 TTTCTTTTCT
1772080 CAAAACTATTTTGAGAAATTTCATC
1 CAAAACTATTTTGAGAAATTTCATC
1772105 CAAAACTATTTTGAGAAATTTCATC
1 CAAAACTATTTTGAGAAATTTCATC
1772130 CAAAAC
1 CAAAAC
1772136 GACTAAGCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (25 bp):
CAAAACTATTTTGAGAAATTTCATC
Found at i:1772881 original size:18 final size:19
Alignment explanation
Indices: 1772858--1772895 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1772848 TTGAAATAAT
*
1772858 ATTATATA-TTATTTTTAA
1 ATTATATATTTAATTTTAA
1772876 ATTATATATTTAATTTTAA
1 ATTATATATTTAATTTTAA
1772895 A
1 A
1772896 CAGTATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATATATTTAATTTTAA
Found at i:1775461 original size:29 final size:29
Alignment explanation
Indices: 1775428--1775509 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
1775418 AAATTAAATT
1775428 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
1775457 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
1775486 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1775510 GTTAGGTGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 47 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1776068 original size:22 final size:22
Alignment explanation
Indices: 1776040--1776092 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1776030 CATACCAAGT
1776040 TCCGACAATCAACAACAACAAC
1 TCCGACAATCAACAACAACAAC
1776062 TCCGACAATCAACAACAACAAC
1 TCCGACAATCAACAACAACAAC
*
1776084 TACGACAAT
1 TCCGACAAT
1776093 TGGAGTATCA
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:0.49, C:0.34, G:0.06, T:0.11
Consensus pattern (22 bp):
TCCGACAATCAACAACAACAAC
Found at i:1780225 original size:29 final size:29
Alignment explanation
Indices: 1780188--1780268 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1780178 AACTAAATTG
1780188 ATGTCATTGCTTACATCATTTAAGTAA-A
1 ATGTCATTGCTTACATCATTTAAGTAATA
*
1780216 TATGTCATTGCTTACATCATTTAAGTGATA
1 -ATGTCATTGCTTACATCATTTAAGTAATA
*
1780246 ATGCCATTGCTTACATCAATTTA
1 ATGTCATTGCTTACATC-ATTTA
1780269 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
29 42 0.88
30 6 0.12
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAAGTAATA
Found at i:1780873 original size:26 final size:26
Alignment explanation
Indices: 1780817--1780875 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
1780807 ACAACCCTGA
*
1780817 AAATCGTTATAAAGATCTGGAATATC
1 AAATTGTTATAAAGATCTGGAATATC
1780843 AAATTGTTATAAAGATCTGGAATATC
1 AAATTGTTATAAAGATCTGGAATATC
1780869 AAATTGT
1 AAATTGT
1780876 GAGTGCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (26 bp):
AAATTGTTATAAAGATCTGGAATATC
Found at i:1789019 original size:57 final size:57
Alignment explanation
Indices: 1788935--1789109 Score: 194
Period size: 57 Copynumber: 3.1 Consensus size: 57
1788925 AAGATAAATT
* * *
1788935 GATGGTAGATGGAATATG-AGTGAAAGAATGTTTTATGGTAGGTGATATAACAGCGAGA
1 GATGG-AGATGGTATA-GCAGTGAAAGAATGATTTATGGTAGGTGATATAGCAGCGAGA
* * * *
1788993 GATGGAGATGGTATAGCAG-GAGAAGAAGGATTAATGGTAGGTGATATAGCAGTGGGA
1 GATGGAGATGGTATAGCAGTGA-AAGAATGATTTATGGTAGGTGATATAGCAGCGAGA
* * * *
1789050 GATGGAGATGGTGTAGTAGTGAAAG-ATAAATTTATGGTAGGTGTTATAGCAGCGAGA
1 GATGGAGATGGTATAGCAGTGAAAGAAT-GATTTATGGTAGGTGATATAGCAGCGAGA
1789107 GAT
1 GAT
1789110 TAAGACAGTG
Statistics
Matches: 98, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
56 4 0.04
57 87 0.89
58 7 0.07
ACGTcount: A:0.35, C:0.03, G:0.36, T:0.26
Consensus pattern (57 bp):
GATGGAGATGGTATAGCAGTGAAAGAATGATTTATGGTAGGTGATATAGCAGCGAGA
Found at i:1789121 original size:57 final size:57
Alignment explanation
Indices: 1788966--1789149 Score: 165
Period size: 57 Copynumber: 3.2 Consensus size: 57
1788956 GAAAGAATGT
* * ** * * *
1788966 TTTATGGTAGGTGATATAACAGCGAGAGATGGAGATGGTATAGCAG-GAGAAGA-AGGA
1 TTTATGGTAGGTGATATAGCAGCGAGAGATGAAGACAGTGTAGTAGTGA-AAGATA-AA
* * * * **
1789023 TTAATGGTAGGTGATATAGCAGTGGGAGATGGAGATGGTGTAGTAGTGAAAGATAAA
1 TTTATGGTAGGTGATATAGCAGCGAGAGATGAAGACAGTGTAGTAGTGAAAGATAAA
* * * * *
1789080 TTTATGGTAGGTGTTATAGCAGCGAGAGATTAAGACAGTGTAGTAGTGAGAGGTGAA
1 TTTATGGTAGGTGATATAGCAGCGAGAGATGAAGACAGTGTAGTAGTGAAAGATAAA
*
1789137 TTTATGATAGGTG
1 TTTATGGTAGGTG
1789150 GTGTAACAGC
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
57 103 0.97
58 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.36, T:0.27
Consensus pattern (57 bp):
TTTATGGTAGGTGATATAGCAGCGAGAGATGAAGACAGTGTAGTAGTGAAAGATAAA
Found at i:1793453 original size:32 final size:31
Alignment explanation
Indices: 1793398--1793491 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
1793388 ACCCTAAGGG
1793398 AACATCTTAGGGCCTG-AGAGCCTACCTAAGA
1 AACATCTTAGGGCC-GCAGAGCCTACCTAAGA
* **
1793429 ACACATCTTAGGGCCGCAGGGCCTACCCGAGA
1 A-ACATCTTAGGGCCGCAGAGCCTACCTAAGA
** *
1793461 ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 AACATCTTAGGGCCGCAGAGCCTACCTAAGA
1793492 GTCACATTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 26 0.50
32 26 0.50
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
AACATCTTAGGGCCGCAGAGCCTACCTAAGA
Found at i:1794470 original size:29 final size:29
Alignment explanation
Indices: 1794382--1794598 Score: 287
Period size: 29 Copynumber: 7.6 Consensus size: 29
1794372 AATTCGAAAA
* * *
1794382 TTCCCAAAATGTCA-CTTTTTCAAAATAA
1 TTCCCAGAATGTCACCTATTTCAAAATAT
* *
1794410 TTCCCAGAATGTCATCT-TTTCAAAATAA
1 TTCCCAGAATGTCACCTATTTCAAAATAT
1794438 TTCCCAGAATGTCACCTATTTCAAAATAT
1 TTCCCAGAATGTCACCTATTTCAAAATAT
* * *
1794467 TTCCCATAATGTCACTTTTTTTCAAAATAT
1 TTCCCAGAATGTCAC-CTATTTCAAAATAT
*
1794497 TTCCCAGAATGTTACCT-TTTCAAAATAT
1 TTCCCAGAATGTCACCTATTTCAAAATAT
* *
1794525 TTCTCAGAATGTCACATATTTCAAAATAT
1 TTCCCAGAATGTCACCTATTTCAAAATAT
*
1794554 TTCTCAGAATGTCACCTATTTCAAAATAT
1 TTCCCAGAATGTCACCTATTTCAAAATAT
*
1794583 TTCCCAGAATATCACC
1 TTCCCAGAATGTCACC
1794599 GGGTCGGGTC
Statistics
Matches: 170, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
28 65 0.38
29 80 0.47
30 25 0.15
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (29 bp):
TTCCCAGAATGTCACCTATTTCAAAATAT
Found at i:1794641 original size:19 final size:19
Alignment explanation
Indices: 1794617--1794654 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1794607 TCGGGTCGGG
*
1794617 TCAGACCAGTCAACCCGGT
1 TCAGACCAGTCAAACCGGT
*
1794636 TCAGACCGGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
1794655 CACAACATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.24, T:0.16
Consensus pattern (19 bp):
TCAGACCAGTCAAACCGGT
Found at i:1801861 original size:29 final size:29
Alignment explanation
Indices: 1801801--1801958 Score: 185
Period size: 29 Copynumber: 5.5 Consensus size: 29
1801791 AATTAGAAAA
* * *
1801801 TTCCCAAAATGTCA-CTTTTTAAAAATAA
1 TTCCCAGAATGTCACCTTTTTCAAAATAT
*
1801829 TTCCCATAATGTCACCTTTTTCAAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAT
** * *
1801858 TTCCTTGAATGTCACATTTTTTAAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAT
* *
1801887 TTCCCAGAATGTTACCTATTTCAAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAT
*
1801916 TTCTCAGAATGTCACCTATTTT-AAAATAT
1 TTCCCAGAATGTCACCT-TTTTCAAAATAT
*
1801945 TTCACAGAATGTCA
1 TTCCCAGAATGTCA
1801959 ACGGGTCGGG
Statistics
Matches: 110, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
28 13 0.12
29 94 0.85
30 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (29 bp):
TTCCCAGAATGTCACCTTTTTCAAAATAT
Found at i:1803193 original size:36 final size:36
Alignment explanation
Indices: 1803134--1803373 Score: 322
Period size: 36 Copynumber: 6.7 Consensus size: 36
1803124 ACACAAATCT
* * *
1803134 TTCCGTTCAACTTGAATCAGAAGTGTCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* *
1803170 TTCCATTCGATTTGAATCGGAAGTGCCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
*
1803206 TTCCTTTC-ATCTTGAATCGGAAGTGCCGATGCTTCC
1 TTCCGTTCGA-CTTGAATCGGAAGTGCCGATGCTTCC
* **
1803242 TTTCGTTCTTCTTGAATCGGAAGTGCCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* * *
1803278 CTCCGTTCGACTTGAATTGGAAGTGCAGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
* **
1803314 TTCCGTTTGACTTGAATCGGAAGTATCG-TGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
1803349 TTCCGTTCGACTTGAATCGGAAGTG
1 TTCCGTTCGACTTGAATCGGAAGTG
1803374 AACTTTTGAT
Statistics
Matches: 178, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
35 31 0.17
36 147 0.83
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (36 bp):
TTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC
Found at i:1806604 original size:29 final size:28
Alignment explanation
Indices: 1806518--1806607 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
1806508 ATCCTCATTT
*
1806518 TAAATTGATCTTTAAATTTTTGAATATTC
1 TAAATT-ATCTTTAAACTTTTGAATATTC
* * * *
1806547 TAAATTATCCTTAGAC-TATGATCTCATTC
1 TAAATTATCTTTAAACTTTTGA-AT-ATTC
*
1806576 TAAATTAATTTTTAAACTTTTGAATATTC
1 TAAATT-ATCTTTAAACTTTTGAATATTC
1806605 TAA
1 TAA
1806608 TTTCATTCCT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
27 4 0.09
28 8 0.17
29 23 0.49
30 8 0.17
31 4 0.09
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.48
Consensus pattern (28 bp):
TAAATTATCTTTAAACTTTTGAATATTC
Found at i:1808116 original size:2 final size:2
Alignment explanation
Indices: 1808111--1808146 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1808101 TCGCTCAAAT
1808111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1808147 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1809405 original size:2 final size:2
Alignment explanation
Indices: 1809398--1809429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1809388 CATCCAAGAA
1809398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1809430 TATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1810028 original size:15 final size:15
Alignment explanation
Indices: 1810008--1810036 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1809998 CCGGATGTTA
1810008 CGGGTACCCGATACT
1 CGGGTACCCGATACT
1810023 CGGGTACCCGATAC
1 CGGGTACCCGATAC
1810037 CCGGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.17
Consensus pattern (15 bp):
CGGGTACCCGATACT
Found at i:1810834 original size:84 final size:85
Alignment explanation
Indices: 1810725--1810895 Score: 317
Period size: 85 Copynumber: 2.0 Consensus size: 85
1810715 TATTGCTATA
*
1810725 TCCTTCTTGTAATGGAAATCATTTAATATTTTAA-TTTTTTTGGGTAAAAAAATACATTATACAC
1 TCCTTCTTGTAATGGAAATCATTTAATATTTTAATTTTTTTTGGGTAAAAAAATACATTATACAA
1810789 ATTAAGCATTAGATTGTTTG
66 ATTAAGCATTAGATTGTTTG
1810809 TCCTTCTTGTAATGGAAATCATTTAATATTTTAATTTTTTTTGGGTAAAAAAATACATTATACAA
1 TCCTTCTTGTAATGGAAATCATTTAATATTTTAATTTTTTTTGGGTAAAAAAATACATTATACAA
*
1810874 ATTAAGCATTGGATTGTTTG
66 ATTAAGCATTAGATTGTTTG
1810894 TC
1 TC
1810896 TCTAAAGGTT
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 34 0.40
85 50 0.60
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (85 bp):
TCCTTCTTGTAATGGAAATCATTTAATATTTTAATTTTTTTTGGGTAAAAAAATACATTATACAA
ATTAAGCATTAGATTGTTTG
Found at i:1815046 original size:28 final size:28
Alignment explanation
Indices: 1815006--1815067 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
1814996 AAATAACAAG
1815006 ATGAGTAAATTAGAAAGGGATTTGTAAA
1 ATGAGTAAATTAGAAAGGGATTTGTAAA
1815034 ATGAGTAAATTAGAAAGGGATTTGTAAA
1 ATGAGTAAATTAGAAAGGGATTTGTAAA
1815062 ATGAGT
1 ATGAGT
1815068 TTTGAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (28 bp):
ATGAGTAAATTAGAAAGGGATTTGTAAA
Found at i:1821297 original size:31 final size:31
Alignment explanation
Indices: 1821234--1821297 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
1821224 CAGTTGTCAT
* ** * *
1821234 ATATTAATTAAATAAGAATGAAAGTGACCAA
1 ATATTAATTAAATAAAAACAAAAATAACCAA
*
1821265 ATATTAATTAAATAAAAACAAAAATAATCAA
1 ATATTAATTAAATAAAAACAAAAATAACCAA
1821296 AT
1 AT
1821298 GTTATGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (31 bp):
ATATTAATTAAATAAAAACAAAAATAACCAA
Found at i:1827779 original size:64 final size:64
Alignment explanation
Indices: 1827674--1827836 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
1827664 CTTGTTCAAG
* * * **
1827674 GTGTATCGATGCACATGAAGTGCATCGATGCACTATTTTAAAATAAAAACATCGAAT-GACATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCACCTT-AAATAAAAACATCGAATAGACATCA
* * * ** *
1827738 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAATATCGAATAGGATTTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATA-GACATCA
* *
1827803 -TGTATCGATGCATAAATAGTGCATCGATGCACCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCA
1827837 GTCAAGGGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 15 0.18
64 64 0.77
65 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATAGACATCA
Found at i:1828510 original size:23 final size:23
Alignment explanation
Indices: 1828476--1828557 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
1828466 CAATCTTATA
*
1828476 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGTAATTCTACG
* *
1828499 CGGCACTTCGGTGTAATTCTATG
1 TGGCACTTCGGTGTAATTCTACG
* **
1828522 TGGTACTTCGGTACAATTCTACG
1 TGGCACTTCGGTGTAATTCTACG
1828545 TGGCACTTCGGTG
1 TGGCACTTCGGTG
1828558 CATTTATACG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGTAATTCTACG
Found at i:1833195 original size:29 final size:29
Alignment explanation
Indices: 1833162--1833241 Score: 160
Period size: 29 Copynumber: 2.8 Consensus size: 29
1833152 AAACTAAATT
1833162 GATGTCATTGCTTACATCAATTAGGTGAA
1 GATGTCATTGCTTACATCAATTAGGTGAA
1833191 GATGTCATTGCTTACATCAATTAGGTGAA
1 GATGTCATTGCTTACATCAATTAGGTGAA
1833220 GATGTCATTGCTTACATCAATT
1 GATGTCATTGCTTACATCAATT
1833242 TAGTTAGGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (29 bp):
GATGTCATTGCTTACATCAATTAGGTGAA
Found at i:1840748 original size:127 final size:127
Alignment explanation
Indices: 1840523--1841148 Score: 979
Period size: 127 Copynumber: 5.0 Consensus size: 127
1840513 ACTATTCACA
* * *
1840523 TGAAGGCGCGTTCCTGGGGG-GCGCCTTCCATTATTTTATCATAGAATATGTTATCATTACCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
*
1840587 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACTG
66 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
* *
1840649 TGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
* *
1840714 TTATGTCAATTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAAGGGACCG
66 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
* ** * * * *
1840776 TGAAGGCGCATTCTTGGAGGCGCGTCTTCCATTATTTTTTAAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
* *
1840841 TTATGTCACTTATGTCCCACGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACAG
66 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
* * * * * *
1840903 TGAATGCGTGTTCCCGGGAGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
*
1840968 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAAGGGACCG
66 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
*
1841030 TGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
* * *
1841095 TTATGTCACTTATGTCCCCCGGG-A-TATTTATGTCAATACCTACTATTTCTTAGG
66 TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGG
1841149 TATTTAACCC
Statistics
Matches: 453, Mismatches: 46, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
125 26 0.06
126 20 0.04
127 407 0.90
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (127 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
Found at i:1841229 original size:42 final size:42
Alignment explanation
Indices: 1841156--1841240 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
1841146 AGGTATTTAA
* * * *
1841156 CCCTGCGGAGATGGCATATGAACTGGTGGGCTTGGCATATAC
1 CCCTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
* * *
1841198 CCCTGAGGAGATGACATCTGAAGTGGAGGGCTGGGCATGTAC
1 CCCTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
1841240 C
1 C
1841241 ACTGTGGCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.21
Consensus pattern (42 bp):
CCCTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
Found at i:1842964 original size:20 final size:18
Alignment explanation
Indices: 1842931--1842967 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1842921 ATAAATGTAG
1842931 ACAAAAAAAATAATTAAC
1 ACAAAAAAAATAATTAAC
1842949 ACAAAAAATAATTAATTAA
1 ACAAAAAA-AA-TAATTAA
1842968 GAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (18 bp):
ACAAAAAAAATAATTAAC
Found at i:1843018 original size:31 final size:33
Alignment explanation
Indices: 1842973--1843051 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 33
1842963 ATTAAGAAAT
* *
1842973 TTAA-ATAAATAATAATTATATAAAT-ATTATT
1 TTAATATAAAAAATAATTATATAAATAATTATA
* *
1843004 TTAATA-AAAAAATAA-TATTTATATAATTATA
1 TTAATATAAAAAATAATTATATAAATAATTATA
*
1843035 TTAATATAAAATATAAT
1 TTAATATAAAAAATAAT
1843052 AACTATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 7 0.18
31 23 0.59
32 9 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TTAATATAAAAAATAATTATATAAATAATTATA
Found at i:1843062 original size:24 final size:23
Alignment explanation
Indices: 1843026--1843070 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1843016 TAATATTTAT
* *
1843026 ATAATTATATTAATATAAAATATA
1 ATAACTATATTAA-AAAAAATATA
*
1843050 ATAACTATTTTAAAAAAAATA
1 ATAACTATATTAAAAAAAATA
1843071 CTAACTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAACTATATTAAAAAAAATATA
Found at i:1845069 original size:20 final size:19
Alignment explanation
Indices: 1845042--1845100 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1845032 CTTTTAAATA
1845042 AATTTTAACATAAAATATAT
1 AATTTTAA-ATAAAATATAT
* *
1845062 ATTTTTAAATGAAAATAAAAAT
1 AATTTTAAAT-AAAAT--ATAT
1845084 AATTTTAAATAAAATAT
1 AATTTTAAATAAAATAT
1845101 TCTCCCAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 5 0.16
22 12 0.38
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AATTTTAAATAAAATATAT
Found at i:1848059 original size:20 final size:21
Alignment explanation
Indices: 1848029--1848145 Score: 149
Period size: 20 Copynumber: 5.9 Consensus size: 21
1848019 AAATGACTAA
1848029 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAATA-GT
1848051 -AAA-TCGCAACGC-AATAGT
1 CAAATTCGCAACGCGAATAGT
1848069 CAAATTCGCAACGCGAA-AGT
1 CAAATTCGCAACGCGAATAGT
*
1848089 CAAATTCGCAACGCGAA-ATT
1 CAAATTCGCAACGCGAATAGT
* *
1848109 CAAATTCGCAAC-TGAAT-TT
1 CAAATTCGCAACGCGAATAGT
1848128 CAAATTCGCAACGCGAAT
1 CAAATTCGCAACGCGAAT
1848146 TTAATTTCGC
Statistics
Matches: 87, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.02
19 24 0.28
20 56 0.64
21 5 0.06
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATAGT
Found at i:1848097 original size:60 final size:59
Alignment explanation
Indices: 1848029--1848144 Score: 166
Period size: 60 Copynumber: 1.9 Consensus size: 59
1848019 AAATGACTAA
1848029 CAAATTCGCAACGCGAATATGT-AAA-TCGCAAC-GCAATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAA-AT-TCAAATTCGCAACTG-AAT-GTCAAATTCGCAACGCGAAAGT
*
1848089 CAAATTCGCAACGCGAAATTCAAATTCGCAACTGAATTTCAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAAATTCAAATTCGCAACTGAATGTCAAATTCGCAACGCGAA
1848145 TTTAATTTCG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
58 1 0.02
59 23 0.44
60 27 0.52
61 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (59 bp):
CAAATTCGCAACGCGAAATTCAAATTCGCAACTGAATGTCAAATTCGCAACGCGAAAGT
Found at i:1848926 original size:12 final size:12
Alignment explanation
Indices: 1848905--1848938 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1848895 ACCACATTTC
*
1848905 CAATACCAAACA
1 CAATATCAAACA
1848917 CAATATCAAACA
1 CAATATCAAACA
*
1848929 CAATCTCAAA
1 CAATATCAAA
1848939 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1849092 original size:24 final size:24
Alignment explanation
Indices: 1849065--1849118 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1849055 GTATTCGAAA
1849065 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
1849089 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1849113 TTTGAT
1 TTTGAT
1849119 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1851752 original size:20 final size:20
Alignment explanation
Indices: 1851729--1851772 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1851719 AATAAGAGTT
1851729 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
1851749 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
1851769 GCGA
1 GCGA
1851773 AATCACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:1851807 original size:20 final size:20
Alignment explanation
Indices: 1851783--1851859 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
1851773 AATCACAAAC
* *
1851783 CGAATTTGACTTTCACGTTG
1 CGAATTTGACTTTCGCATTG
* * *
1851803 TGAATTTGACTATCGCATAG
1 CGAATTTGACTTTCGCATTG
1851823 CGAATTTGACTTTCGCATTG
1 CGAATTTGACTTTCGCATTG
*
1851843 CGAATTTGACTATCGCA
1 CGAATTTGACTTTCGCA
1851860 AAGCTTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (20 bp):
CGAATTTGACTTTCGCATTG
Found at i:1851848 original size:40 final size:40
Alignment explanation
Indices: 1851783--1851859 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
1851773 AATCACAAAC
* *
1851783 CGAATTTGACTTTCACGTTGTGAATTTGACTATCGCATAG
1 CGAATTTGACTTTCACATTGCGAATTTGACTATCGCATAG
*
1851823 CGAATTTGACTTTCGCATTGCGAATTTGACTATCGCA
1 CGAATTTGACTTTCACATTGCGAATTTGACTATCGCA
1851860 AAGCTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (40 bp):
CGAATTTGACTTTCACATTGCGAATTTGACTATCGCATAG
Found at i:1851987 original size:25 final size:25
Alignment explanation
Indices: 1851949--1851998 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1851939 AAATCAATTA
*
1851949 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1851974 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1851999 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1852392 original size:12 final size:12
Alignment explanation
Indices: 1852377--1852417 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1852367 TTTCATATGT
1852377 AATTTGAGTTTG
1 AATTTGAGTTTG
* * *
1852389 AATTTAAATTTC
1 AATTTGAGTTTG
1852401 AATTTGAGTTTG
1 AATTTGAGTTTG
1852413 AATTT
1 AATTT
1852418 CAATATAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (12 bp):
AATTTGAGTTTG
Found at i:1852393 original size:24 final size:25
Alignment explanation
Indices: 1852366--1852420 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
1852356 TTTCAAATTC
*
1852366 ATTTCATATGT-AATTTGAGTTTGA
1 ATTTCAAATGTCAATTTGAGTTTGA
*
1852390 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTTGAGTTTGA
1852414 ATTTCAA
1 ATTTCAA
1852421 TATAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 21 0.78
25 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (25 bp):
ATTTCAAATGTCAATTTGAGTTTGA
Found at i:1852406 original size:18 final size:18
Alignment explanation
Indices: 1852385--1852421 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1852375 GTAATTTGAG
1852385 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1852403 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1852421 T
1 T
1852422 ATAAATTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1852428 original size:24 final size:24
Alignment explanation
Indices: 1852377--1852429 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1852367 TTTCATATGT
* *
1852377 AATTTGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1852401 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1852425 AATTT
1 AATTT
1852430 CTGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1852775 original size:39 final size:39
Alignment explanation
Indices: 1852732--1852818 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1852722 TCCGATGCTC
*
1852732 ATCAAAATCCAAAGCTTATATGGTACCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
* *
1852771 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
1852810 ATCAAAATC
1 ATCAAAATC
1852819 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTACCAAGCAAAAGGAA
Found at i:1853043 original size:20 final size:20
Alignment explanation
Indices: 1852994--1853036 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1852984 ATGTTGTGAT
*
1852994 CAACGCGAAAGTTAAATTCG
1 CAACGCGAAAGTCAAATTCG
1853014 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1853034 CAA
1 CAA
1853037 ACCGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:1853070 original size:20 final size:20
Alignment explanation
Indices: 1853044--1853088 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1853034 CAAACCGAAA
1853044 ATCGCGTTGCGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
*
1853064 TTCGCGTTGCGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
1853084 ATCGC
1 ATCGC
1853089 AATGCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCGAATTTGACT
Found at i:1853273 original size:66 final size:60
Alignment explanation
Indices: 1853193--1853332 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
1853183 TTTTAGAAAC
*
1853193 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACAAATC-AATT
1853258 A
60 A
* * **
1853259 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
1853319 AACAAATCAACTTT
1 AACAAATCAACTTT
1853333 CAATATAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 19 0.28
61 21 0.30
62 3 0.04
66 26 0.38
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:1854735 original size:21 final size:21
Alignment explanation
Indices: 1854711--1854806 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 21
1854701 GGCGGGACCA
*
1854711 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * **
1854732 CTTGAACGGTGGGAGGGGATT
1 CTTGAACGATGAGAGGGGCCT
* *
1854753 CTTCG-ATGATGAGAAGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
* *
1854774 CTTGAACGATAAGAGGCGCCT
1 CTTGAACGATGAGAGGGGCCT
* *
1854795 TTTGAATGATGA
1 CTTGAACGATGA
1854807 TAGGTGCATC
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 53 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:1857010 original size:14 final size:14
Alignment explanation
Indices: 1856991--1857034 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1856981 ACGATTTTAG
1856991 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
* *
1857005 TTTCGCGTTTCGAA
1 TTTCGCGTTGCGAT
* *
1857019 TTTGGTGTTGCGAT
1 TTTCGCGTTGCGAT
1857033 TT
1 TT
1857035 AGGGTTTCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:1857064 original size:13 final size:13
Alignment explanation
Indices: 1857046--1857083 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1857036 GGGTTTCTTC
1857046 AACAAAAAGACAA
1 AACAAAAAGACAA
1857059 AACAAAAAGAC-A
1 AACAAAAAGACAA
1857071 AA-AAAAAGACAA
1 AACAAAAAGACAA
1857083 A
1 A
1857084 TACTAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 5 0.21
13 11 0.46
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:1857078 original size:11 final size:12
Alignment explanation
Indices: 1857046--1857083 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
1857036 GGGTTTCTTC
1857046 AACAAAAAGACAA
1 AACAAAAAGAC-A
1857059 AACAAAAAGACA
1 AACAAAAAGACA
1857071 AA-AAAAAGACA
1 AACAAAAAGACA
1857082 AA
1 AA
1857084 TACTAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 3 0.12
13 11 0.44
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (12 bp):
AACAAAAAGACA
Found at i:1857591 original size:21 final size:21
Alignment explanation
Indices: 1857525--1857581 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1857515 AATTCAAGTT
1857525 GCGAATTTGGAAAATCACAAC
1 GCGAATTTGGAAAATCACAAC
1857546 GCGAATTTGGAAAATCACAAC
1 GCGAATTTGGAAAATCACAAC
1857567 GCGAATTTGGAAAAT
1 GCGAATTTGGAAAAT
1857582 TGCAATGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
GCGAATTTGGAAAATCACAAC
Found at i:1858874 original size:33 final size:34
Alignment explanation
Indices: 1858837--1858901 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1858827 AGTAACACAC
*
1858837 GAGAGTTTCAAACCCTAAAAGGAAA-AAAATACA
1 GAGAGTTTCAAACCCAAAAAGGAAAGAAAATACA
*
1858870 GAGAGTTTCGAACCCAAAAAGGAAAGAAAATA
1 GAGAGTTTCAAACCCAAAAAGGAAAGAAAATA
1858902 AAAAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (34 bp):
GAGAGTTTCAAACCCAAAAAGGAAAGAAAATACA
Found at i:1859765 original size:30 final size:30
Alignment explanation
Indices: 1859653--1859764 Score: 127
Period size: 30 Copynumber: 3.7 Consensus size: 30
1859643 ATCATTGTTC
*
1859653 AGTCC-TTAAACTATCTATTTTTATTGTTTT
1 AGTCCTTTAAA-TTTCTATTTTTATTGTTTT
* * * *
1859683 AGTCCTTTAACTTTATGTTTTTACTGTTTT
1 AGTCCTTTAAATTTCTATTTTTATTGTTTT
* * *
1859713 AATCCTTTAAGTTTCTATTTTTGTTGTTTT
1 AGTCCTTTAAATTTCTATTTTTATTGTTTT
*
1859743 AGTCCTATAAATTTCTATTTTT
1 AGTCCTTTAAATTTCTATTTTT
1859765 GCTATTTAGT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
30 63 0.94
31 4 0.06
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.59
Consensus pattern (30 bp):
AGTCCTTTAAATTTCTATTTTTATTGTTTT
Found at i:1859773 original size:29 final size:30
Alignment explanation
Indices: 1859653--1859777 Score: 92
Period size: 30 Copynumber: 4.2 Consensus size: 30
1859643 ATCATTGTTC
* ** *
1859653 AGTCCT-TAAACTATCTATTTTTATTGTTTT
1 AGTCCTATAAA-TTTCTATTTTTGCTGATTT
* * * * * *
1859683 AGTCCTTTAACTTTATGTTTTTACTGTTTT
1 AGTCCTATAAATTTCTATTTTTGCTGATTT
* * * * *
1859713 AATCCTTTAAGTTTCTATTTTTGTTGTTTT
1 AGTCCTATAAATTTCTATTTTTGCTGATTT
1859743 AGTCCTATAAATTTCTATTTTTGCT-ATTT
1 AGTCCTATAAATTTCTATTTTTGCTGATTT
1859772 AGTCCT
1 AGTCCT
1859778 TTATTTGATT
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
29 9 0.12
30 66 0.85
31 3 0.04
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.58
Consensus pattern (30 bp):
AGTCCTATAAATTTCTATTTTTGCTGATTT
Found at i:1861710 original size:21 final size:21
Alignment explanation
Indices: 1861683--1861741 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1861673 AAATGTGTAT
1861683 CGATGCACTGCTACAGTGCTC
1 CGATGCACTGCTACAGTGCTC
* *
1861704 TGATGCACTGCTACAGTGTTC
1 CGATGCACTGCTACAGTGCTC
1861725 CGATGCACTGCTACAGT
1 CGATGCACTGCTACAGT
1861742 AATTTCAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (21 bp):
CGATGCACTGCTACAGTGCTC
Found at i:1862201 original size:45 final size:45
Alignment explanation
Indices: 1862137--1862377 Score: 378
Period size: 45 Copynumber: 5.4 Consensus size: 45
1862127 AATTTCTTAT
*
1862137 CAATATATTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
* * *
1862182 CAATATACTTACTATTTATCCCATAAGCTCGTAAGCTTATTTTAA
1 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
* *
1862227 CAATACACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
1862272 CAATATACTTACCATTTAT-TCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCT-CATAAGCTCGTAAGCTTATTTTAC
*
1862317 CAATATACTTATCATTTAT-TCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCT-CATAAGCTCGTAAGCTTATTTTAC
*
1862362 CAATATACTTGCCATT
1 CAATATACTTACCATT
1862378 ATTCCATAAC
Statistics
Matches: 183, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 183 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAC
Found at i:1862268 original size:25 final size:25
Alignment explanation
Indices: 1862150--1862223 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1862140 TATATTTACC
*
1862150 ATTTATCTCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
*
1862175 ATTT-TACCAATATA-CT--T-A-C-T
1 ATTTAT-CCCATA-AGCTCGTAAGCTT
1862195 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
1862220 ATTT
1 ATTT
1862224 TAACAATACA
Statistics
Matches: 37, Mismatches: 3, Indels: 18
0.64 0.05 0.31
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 15 0.41
26 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTATCCCATAAGCTCGTAAGCTT
Found at i:1862963 original size:24 final size:24
Alignment explanation
Indices: 1862920--1862965 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1862910 CTTTCTGATG
* *
1862920 ATGTATAAAACATCTATGTACATC
1 ATGTATAAAAAAGCTATGTACATC
*
1862944 ATGTATAAAAAAGCTTTGTACA
1 ATGTATAAAAAAGCTATGTACA
1862966 ATGTCATGCA
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:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (24 bp):
ATGTATAAAAAAGCTATGTACATC
Found at i:1864978 original size:4 final size:4
Alignment explanation
Indices: 1864969--1865774 Score: 1603
Period size: 4 Copynumber: 201.5 Consensus size: 4
1864959 TTATAATTCC
*
1864969 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865017 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865065 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865113 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865161 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865209 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865257 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865305 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865353 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865401 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865449 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865497 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865545 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865593 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865641 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865689 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1865737 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1865775 AAAAAATGGA
Statistics
Matches: 800, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 800 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1867297 original size:39 final size:40
Alignment explanation
Indices: 1867254--1867355 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 40
1867244 CTATTCATAA
* *
1867254 TTGTGATGAAAATATTTTT-CACTAGTCTTAGTTGGTGAT
1 TTGTGACGAAAATATTTTTACACTAGTCTTAATTGGTGAT
*
1867293 TTGTGACGATAAT-TGTTTATGACACTAGTCTTAATTGGTGAT
1 TTGTGACGAAAATAT-TTT-T-ACACTAGTCTTAATTGGTGAT
*
1867335 TTGTGACGACAATAATTTTTA
1 TTGTGACGAAAAT-ATTTTTA
1867356 TCATTGTTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
38 1 0.02
39 14 0.26
40 1 0.02
41 1 0.02
42 32 0.60
43 3 0.06
44 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (40 bp):
TTGTGACGAAAATATTTTTACACTAGTCTTAATTGGTGAT
Found at i:1869181 original size:106 final size:105
Alignment explanation
Indices: 1869053--1869252 Score: 276
Period size: 106 Copynumber: 1.9 Consensus size: 105
1869043 ATTAAATTCT
* *
1869053 TCACTAAAAAACACTTATTGTGACAACATTGGTGGCCACAAAATATACTTTCAGTGTCAAATAAA
1 TCACTAAAAAACACTTAGTGTGACAACATTGATGGCCACAAAATATACTTTCAGTGTCAAA-AAA
* * *
1869118 -TTTATCACAATTTCTATTGATAATAGTATCGAACATTTGA
65 GATCATCACAATTTATATTGATAATAGTATCGAACATTTGA
* * * * *
1869158 TCACTAAAAAAATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTTTAGTGTCAAAAAA
1 TCACT-AAAAAACACTTAGTGTGACAACATTGATGGCCACAAAATATACTTTCAGTGTCAAAAAA
*
1869223 GATCATCACAATTTATATTGATAATTGTAT
65 GATCATCACAATTTATATTGATAATAGTAT
1869253 TGAATAGATG
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
105 8 0.10
106 74 0.90
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (105 bp):
TCACTAAAAAACACTTAGTGTGACAACATTGATGGCCACAAAATATACTTTCAGTGTCAAAAAAG
ATCATCACAATTTATATTGATAATAGTATCGAACATTTGA
Found at i:1869634 original size:15 final size:15
Alignment explanation
Indices: 1869614--1869645 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1869604 GCATTCAATT
*
1869614 ATTGAGAGTATGAAC
1 ATTGAGAATATGAAC
1869629 ATTGAGAATATGAAC
1 ATTGAGAATATGAAC
1869644 AT
1 AT
1869646 GTGATCTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (15 bp):
ATTGAGAATATGAAC
Found at i:1870753 original size:15 final size:16
Alignment explanation
Indices: 1870735--1870792 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 16
1870725 TCATTATTTT
1870735 TATTA-TATTATAAAA
1 TATTATTATTATAAAA
* *
1870750 TATTATTATTAT-TAT
1 TATTATTATTATAAAA
*
1870765 TATTATTATTACAAAA
1 TATTATTATTATAAAA
*
1870781 TATTTTTATTAT
1 TATTATTATTAT
1870793 TTATTACAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 17 0.50
16 17 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTATTATAAAA
Found at i:1870784 original size:22 final size:23
Alignment explanation
Indices: 1870759--1870802 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1870749 ATATTATTAT
1870759 TATTATTATTA-TTATTACAAAA
1 TATTATTATTATTTATTACAAAA
*
1870781 TATTTTTATTATTTATTACAAA
1 TATTATTATTATTTATTACAAA
1870803 CCCATTACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATTATTATTTATTACAAAA
Found at i:1870793 original size:3 final size:3
Alignment explanation
Indices: 1870714--1870775 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
1870704 TCAACCATCC
* * * * *
1870714 TAT TAT TAT CAT CAT TAT TTT TAT TA- TAT TAT AAAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
1870759 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1870776 CAAAATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.94
4 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1872746 original size:13 final size:13
Alignment explanation
Indices: 1872728--1872753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1872718 TCAGGACGTC
1872728 GAAAAACATAAAA
1 GAAAAACATAAAA
1872741 GAAAAACATAAAA
1 GAAAAACATAAAA
1872754 CATGACTTTT
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:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
GAAAAACATAAAA
Found at i:1872840 original size:18 final size:19
Alignment explanation
Indices: 1872795--1872851 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
1872785 TCAACTCTAG
*
1872795 TCAAAGTCAATGGGTCAGA
1 TCAAAGTCAACGGGTCAGA
* *
1872814 TCAAAGTCAACGGGTCGGG
1 TCAAAGTCAACGGGTCAGA
*
1872833 TC-AAGTCAACGGGTTAGA
1 TCAAAGTCAACGGGTCAGA
1872851 T
1 T
1872852 TGGTTCAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.21
Consensus pattern (19 bp):
TCAAAGTCAACGGGTCAGA
Found at i:1875226 original size:14 final size:14
Alignment explanation
Indices: 1875206--1875242 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1875196 AATCGGACAG
1875206 CAGATTCTGCAAAA
1 CAGATTCTGCAAAA
*
1875220 TAGATTCTGCAAAA
1 CAGATTCTGCAAAA
1875234 CAGATTCTG
1 CAGATTCTG
1875243 TTGGTCAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (14 bp):
CAGATTCTGCAAAA
Found at i:1876081 original size:40 final size:40
Alignment explanation
Indices: 1876026--1876187 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
1876016 TTTAGGTTTA
1876026 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1876066 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1876106 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1876146 TAATATACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1876186 TA
1 TA
1876188 GCACTACGGT
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1876387 original size:47 final size:45
Alignment explanation
Indices: 1876292--1876417 Score: 146
Period size: 47 Copynumber: 2.8 Consensus size: 45
1876282 GTAACCATGC
* * * **
1876292 AAATAAGCTTATGAGCTTACGGAAT-AATGACAAGTATATTGGAA
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
1876336 AAATAAACTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAACTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
* *
1876383 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAG
1876418 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:1876957 original size:30 final size:30
Alignment explanation
Indices: 1876921--1876982 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1876911 ATTGTTCACG
1876921 GTTCACGGTACTGTAGCGAATCGATACACT
1 GTTCACGGTACTGTAGCGAATCGATACACT
*
1876951 GTTCACGTTACTGTAGCGAATCGATACACT
1 GTTCACGGTACTGTAGCGAATCGATACACT
1876981 GT
1 GT
1876983 AGCGAATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (30 bp):
GTTCACGGTACTGTAGCGAATCGATACACT
Found at i:1876983 original size:18 final size:18
Alignment explanation
Indices: 1876960--1876997 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1876950 TGTTCACGTT
1876960 ACTGTAGCGAATCGATAC
1 ACTGTAGCGAATCGATAC
1876978 ACTGTAGCGAATCGATAC
1 ACTGTAGCGAATCGATAC
1876996 AC
1 AC
1876998 GGTTCACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (18 bp):
ACTGTAGCGAATCGATAC
Found at i:1883181 original size:24 final size:24
Alignment explanation
Indices: 1883154--1883257 Score: 122
Period size: 24 Copynumber: 4.4 Consensus size: 24
1883144 CGAAACTGTG
*
1883154 CGTAGAATTTGCACTGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
*
1883178 CGTAGAATATGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
*
1883202 CGTAGAATATGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
* * * *
1883226 CATAGATTTTTC-CTGAAG-GACCA
1 CGTAGAATTTGCACCGAAGTG-CCA
1883249 CGTAGAATT
1 CGTAGAATT
1883258 GTCTCGAAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.01
23 15 0.21
24 54 0.77
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGCACCGAAGTGCCA
Found at i:1883506 original size:57 final size:57
Alignment explanation
Indices: 1883368--1883570 Score: 205
Period size: 57 Copynumber: 3.5 Consensus size: 57
1883358 ATAGTTTCAT
* * * * *
1883368 TCAAATTATCATTTGTCCACATAAAACATATACTCATAGTC-TTTCACATGGCATTAC
1 TCAAATTATCATTTATTCACATAGAACATATACTCATAG-CATTTCATATAGCATTAC
* * * * *
1883425 CCAAATTTATTATTTATTCTCATAGAACA-ATTATTCATAGCATTTCCTATAGCATTAC
1 TCAAA-TTATCATTTATTCACATAGAACATA-TACTCATAGCATTTCATATAGCATTAC
* * ** *
1883483 TCAACTTATCATTTATTCACATAGAACATATACTCATTGTGTTTCATATAGCATTAT
1 TCAAATTATCATTTATTCACATAGAACATATACTCATAGCATTTCATATAGCATTAC
*
1883540 TCAAATTATCATTTATTCCCATCA-AACATAT
1 TCAAATTATCATTTATTCACAT-AGAACATAT
1883571 TCACATAAAT
Statistics
Matches: 119, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
57 75 0.63
58 44 0.37
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.39
Consensus pattern (57 bp):
TCAAATTATCATTTATTCACATAGAACATATACTCATAGCATTTCATATAGCATTAC
Found at i:1884068 original size:20 final size:20
Alignment explanation
Indices: 1884040--1884088 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1884030 TCAATTACAA
*
1884040 TATCGATAC-CTCCACATCAG
1 TATCAATACACTCCA-ATCAG
*
1884060 TATCAATACTACTTCAATCAG
1 TATCAATAC-ACTCCAATCAG
1884081 TATCAATA
1 TATCAATA
1884089 TTATTTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 13 0.52
22 4 0.16
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31
Consensus pattern (20 bp):
TATCAATACACTCCAATCAG
Found at i:1884901 original size:18 final size:19
Alignment explanation
Indices: 1884870--1884916 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
1884860 GTAATGAGAT
1884870 ATTTAAAT-AATAAAATCA
1 ATTTAAATAAATAAAATCA
1884888 A-TTAAATAAATAAAATCA
1 ATTTAAATAAATAAAATCA
1884906 ATTTAAATAAA
1 ATTTAAATAAA
1884917 AATAAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.22
18 12 0.44
19 9 0.33
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTTAAATAAATAAAATCA
Found at i:1889668 original size:5 final size:6
Alignment explanation
Indices: 1889653--1889677 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1889643 TTGATGAAAC
1889653 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
1889678 TAACAGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1896151 original size:64 final size:62
Alignment explanation
Indices: 1896083--1896290 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 62
1896073 TGCACTAAGA
1896083 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGG-TG
* * *
1896147 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAC-CAGAGTGCATCGATGCATGGT-
*
1896211 T
62 G
* * * *
1896212 GTGCATCGATCCATGAAATGCATTTGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG--
1896275 TG
61 TG
*
1896277 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1896291 CACTTTGAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 19
0.78 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.39
65 64 0.53
66 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGTG
Found at i:1896758 original size:2 final size:2
Alignment explanation
Indices: 1896751--1896805 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1896741 TAGCCAATTA
1896751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1896793 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1896806 GCTTAAGCTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1896949 original size:2 final size:2
Alignment explanation
Indices: 1896942--1896991 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1896932 CAACCAAACC
1896942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1896984 AT AT AT AT
1 AT AT AT AT
1896992 CAAGTTCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1898996 original size:23 final size:22
Alignment explanation
Indices: 1898968--1899049 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
1898958 GCATGGCCTT
*
1898968 GTGCATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1898990 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1899012 GTGTATCGATGCACATTCAAATGG
1 GTGCATCGATGCACATTC-AA-GG
* *
1899036 ATGCATCAATGCAC
1 GTGCATCGATGCAC
1899050 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 16 0.36
24 12 0.27
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1904946 original size:46 final size:45
Alignment explanation
Indices: 1904847--1904954 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
1904837 CGGTGCACTA
* *
1904847 AGAGTGCAACGATGCATGAAATGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCC
*
1904892 AGAGTGCATCTATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGC-C
*
1904938 TGAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
1904955 AGTATGTGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
45 30 0.55
46 22 0.40
47 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (45 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCC
Found at i:1907933 original size:31 final size:29
Alignment explanation
Indices: 1907907--1907967 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1907897 GTCTAATCTA
1907907 TTATCGTT-TTTCTAATTTAGTGTCTAACGT
1 TTAT-GTTATTTC-AATTTAGTGTCTAACGT
*
1907937 TTATTTTATTTCAATTTAGTGTCTAACGT
1 TTATGTTATTTCAATTTAGTGTCTAACGT
1907966 TT
1 TT
1907968 CATTCCGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.56
Consensus pattern (29 bp):
TTATGTTATTTCAATTTAGTGTCTAACGT
Found at i:1909600 original size:20 final size:20
Alignment explanation
Indices: 1909579--1909684 Score: 106
Period size: 20 Copynumber: 5.2 Consensus size: 20
1909569 AAATCACAAT
*
1909579 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
1909599 GCGATACTTACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
1909619 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
1909640 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
1909660 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
1909680 GCGAT
1 GCGAT
1909685 TTACATAGCG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:1909615 original size:61 final size:61
Alignment explanation
Indices: 1909568--1909684 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1909558 GCGAATTGGG
* * * * *
1909568 AAAATCACAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
1909629 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1909685 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1910263 original size:19 final size:19
Alignment explanation
Indices: 1910239--1910283 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1910229 GCAACGAGAG
*
1910239 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
1910258 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
1910277 AATCGCA
1 AATCGCA
1910284 TTGCGATTTT
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:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:1910301 original size:19 final size:19
Alignment explanation
Indices: 1910279--1910424 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
1910269 GAAACCAAAA
*
1910279 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1910298 TCGCGTTGCGA--TTCA--
1 TCGCGTTGCGATTTTCATT
*
1910313 -CTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1910331 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1910350 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1910364 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1910383 TCTGCGTTGCGATTCTCATT
1 TC-GCGTTGCGATTTTCATT
* **
1910403 ATCTCGTTGATATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1910423 TC
1 TC
1910425 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.19
16 6 0.06
17 6 0.06
19 40 0.40
20 27 0.27
21 2 0.02
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1910362 original size:52 final size:52
Alignment explanation
Indices: 1910279--1910395 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
1910269 GAAACCAAAA
* ** **
1910279 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCACTCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCACTCGTTGCGATAGTCATT
*
1910331 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCACTCGTTGCGATAGTCATT
1910383 TCTGCGTTGCGAT
1 TC-GCGTTGCGAT
1910396 TCTCATTATC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 48 0.83
53 10 0.17
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (52 bp):
TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCACTCGTTGCGATAGTCATT
Found at i:1910371 original size:33 final size:34
Alignment explanation
Indices: 1910334--1910399 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
1910324 TTTCATTTCG
1910334 CGTTGCGATAGTCATTTC-GCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCTGCGTTGCGATTCTCT
1910367 CGTTGCGATAGTCATTTCTGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCTGCGTTGCGATTCTC
1910400 ATTATCTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 18 0.56
34 14 0.44
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCTGCGTTGCGATTCTCT
Found at i:1912280 original size:91 final size:88
Alignment explanation
Indices: 1912111--1912280 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 88
1912101 TAGATTGCTT
* *
1912111 AGTAAATTTATTCGGTTGCTGTCAATACTGCTAAACTGTTTATTAACATTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
*
1912176 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC---TTCTTTTGTCTTTTGGTTGA
* *
1912202 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1912267 ATTTGTC-TCTTTTG
62 ATTTGTCTTCTTTTG
1912281 GTTGAAAGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
91 40 0.57
93 3 0.04
94 2 0.03
95 25 0.36
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (88 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTCTTTTGTCTTTTGGTTGA
Found at i:1912606 original size:42 final size:42
Alignment explanation
Indices: 1912505--1912710 Score: 200
Period size: 42 Copynumber: 4.9 Consensus size: 42
1912495 CCCGACTCAC
* * * * *
1912505 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCC-
1 CTGTCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
* * *
1912546 CATATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 C-TGTCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
* * * * *
1912589 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
* * *
1912631 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
** * *
1912673 CTGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAG
1912711 CCCGATTCAC
Statistics
Matches: 131, Mismatches: 31, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
41 1 0.01
42 127 0.97
43 3 0.02
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1912668 original size:21 final size:21
Alignment explanation
Indices: 1912560--1912710 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
1912550 TCATTCCTCG
1912560 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
1912581 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
1912602 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
1912623 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
1912644 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1912665 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1912686 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1912707 AGAG
1 AGAG
1912711 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1912689 original size:84 final size:84
Alignment explanation
Indices: 1912505--1912680 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
1912495 CCCGACTCAC
*
1912505 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCCCATATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCT
1912570 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
1912589 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCT
1912654 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1912673 CTGTCATC
1 CTGTCATC
1912681 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1912710 original size:84 final size:84
Alignment explanation
Indices: 1912505--1912710 Score: 279
Period size: 84 Copynumber: 2.5 Consensus size: 84
1912495 CCCGACTCAC
* * * * *
1912505 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCCCATATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCT
1912570 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * * *
1912589 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCT
1912654 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
1912673 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1912711 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1914227 original size:14 final size:14
Alignment explanation
Indices: 1914208--1914264 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1914198 GCGAAATGAA
1914208 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1914222 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1914241 AATCGCAACGAGGG
1 AATCGCAACGAGAG
1914255 AATCGCAACG
1 AATCGCAACG
1914265 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1914235 original size:33 final size:33
Alignment explanation
Indices: 1914190--1914279 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1914180 AAAAAGTACT
*
1914190 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
1914223 ATCGCAACGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1914256 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1914280 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1914249 original size:19 final size:19
Alignment explanation
Indices: 1914190--1914250 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1914180 AAAAAGTACT
*
1914190 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1914209 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1914223 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1914242 ATCGCAACG
1 ATCGCAACG
1914251 AGGGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1914297 original size:19 final size:19
Alignment explanation
Indices: 1914275--1914392 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
1914265 CGAAATTAAA
1914275 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1914294 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1914309 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1914327 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1914342 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1914360 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1914379 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1914393 AGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1914321 original size:33 final size:33
Alignment explanation
Indices: 1914279--1914372 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1914269 ATTAAATTCG
1914279 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1914312 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1914345 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1914373 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1916675 original size:3 final size:3
Alignment explanation
Indices: 1916667--1916711 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1916657 TGGGGACTTT
* * *
1916667 TTC TTC TTC TTT TTC TTC TTC TTT TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1916712 AGGATTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:1916680 original size:12 final size:12
Alignment explanation
Indices: 1916663--1916711 Score: 98
Period size: 12 Copynumber: 4.1 Consensus size: 12
1916653 TCTTTGGGGA
1916663 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1916675 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1916687 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1916699 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1916711 C
1 C
1916712 AGGATTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1916920 original size:24 final size:24
Alignment explanation
Indices: 1916886--1916939 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1916876 CTGAAACATC
*
1916886 ATCAAAATCCGAGTATTAACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* * *
1916910 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
1916934 ATCAAA
1 ATCAAA
1916940 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1917716 original size:20 final size:21
Alignment explanation
Indices: 1917691--1917742 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1917681 TTTTCCTAAT
*
1917691 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1917711 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1917732 TCGCAATGCGA
1 TCGCAATGCGA
1917743 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1917816 original size:20 final size:20
Alignment explanation
Indices: 1917727--1917818 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1917717 TGCGAATTTG
* *
1917727 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
1917747 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
1917767 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
1917788 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
1917808 GAAAATCGCAA
1 GAAAATCGCAA
1917819 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:1918127 original size:20 final size:20
Alignment explanation
Indices: 1918032--1918119 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
1918022 CAACGGGGAA
1918032 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1918052 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ****
1918072 ATCACAATTCG-AAATAAAAA
1 ATCGCAACGCGAAAAT-GGCT
1918092 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1918112 ATCGCAAC
1 ATCGCAAC
1918120 TAGAAAATCG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 4 0.08
20 44 0.85
21 4 0.08
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1918170 original size:14 final size:14
Alignment explanation
Indices: 1918151--1918204 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1918141 GAAAATCGCA
1918151 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1918165 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1918182 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1918198 TTGCGAT
1 TTGCGAT
1918205 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1920244 original size:20 final size:19
Alignment explanation
Indices: 1920221--1920288 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1920211 GAAACTTAAA
1920221 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
1920241 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1920261 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1920280 ATCGCAACG
1 ATCGCAACG
1920289 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1920296 original size:14 final size:14
Alignment explanation
Indices: 1920277--1920367 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1920267 ATGCGAAATG
*
1920277 AAAATCGCAACGAC
1 AAAATCGCAACGAA
1920291 AAAATCGCAATGCGAAA
1 AAAATCGCAA--CG-AA
*
1920308 TGAAAATCGCAACGAC
1 --AAAATCGCAACGAA
*
1920324 AAAATCGTAATGCGAA
1 AAAATCGCAA--CGAA
1920340 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
1920356 AAAATCGCAACG
1 AAAATCGCAACG
1920368 CGAAACACAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 30 0.48
16 12 0.19
17 3 0.05
18 8 0.13
19 10 0.16
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:1920303 original size:33 final size:33
Alignment explanation
Indices: 1920261--1920372 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
1920251 GGAAATGGCT
1920261 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1920294 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1920327 ATCGTAATGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1920359 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1920373 CACAAATCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 27 0.36
33 48 0.64
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1920380 original size:65 final size:66
Alignment explanation
Indices: 1920261--1920383 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
1920251 GGAAATGGCT
* * *
1920261 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
1920326 A
66 A
*
1920327 ATCGTAATGCGAAATG-AAATCGCAACGAAAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAACGCGAAATCA-AAATCGCA
1920384 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.69
66 15 0.29
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:1920401 original size:19 final size:19
Alignment explanation
Indices: 1920379--1920460 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
1920369 GAAACACAAA
1920379 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1920398 TCGCTTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1920416 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1920432 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1920449 TCGCATTGCGAT
1 TCGCATTGCGAT
1920461 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1920497 original size:20 final size:20
Alignment explanation
Indices: 1920445--1920488 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1920435 TTGCGATTTT
*
1920445 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1920464 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
1920484 CATTT
1 CATTT
1920489 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1921007 original size:18 final size:18
Alignment explanation
Indices: 1920981--1921025 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1920971 GTCGATCAGA
*
1920981 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1920999 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1921017 TGATGGCTC
1 TGATGGCTC
1921026 CCGAAGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1922394 original size:20 final size:20
Alignment explanation
Indices: 1922346--1922404 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1922336 AATAGTTTCT
** *
1922346 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1922366 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1922386 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1922405 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1922891 original size:20 final size:20
Alignment explanation
Indices: 1922866--1922917 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1922856 ATTATGTATT
1922866 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
1922886 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
1922906 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1922918 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1922978 original size:41 final size:40
Alignment explanation
Indices: 1922888--1922979 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 40
1922878 AAGTCAGAAT
* * * **
1922888 CGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTA
1 CGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCAATTA
*
1922928 TCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTCCCAATTA
1 -CGCGTTGCGAAAGTAAGTATCGCATTGCGATTTT--CAATTA
1922971 -GCGTTGCGA
1 CGCGTTGCGA
1922980 TTTACTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
41 38 0.90
43 4 0.10
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (40 bp):
CGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCAATTA
Found at i:1930989 original size:30 final size:30
Alignment explanation
Indices: 1930953--1931012 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1930943 TTGCAGAGCC
*
1930953 GATATAGAATAGATATCTAGATGTGCTCTT
1 GATATAGAATAGATATCCAGATGTGCTCTT
1930983 GATATAGAATAGATATCCAGATGTGCTCTT
1 GATATAGAATAGATATCCAGATGTGCTCTT
1931013 TTGATCATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (30 bp):
GATATAGAATAGATATCCAGATGTGCTCTT
Found at i:1938602 original size:11 final size:11
Alignment explanation
Indices: 1938588--1938613 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1938578 TTTTTGTTCT
1938588 TTTTATTTTTA
1 TTTTATTTTTA
1938599 TTTTATTTTTA
1 TTTTATTTTTA
1938610 TTTT
1 TTTT
1938614 TTCCTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Done.