Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000417.1 Hibiscus syriacus cultivar Beakdansim tig00000764_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: 2005044
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1787287 original size:22 final size:21
Alignment explanation
Indices: 1787257--1787299 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1787247 TCGCGTTGCG
1787257 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
1787279 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
1787300 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:1789642 original size:12 final size:12
Alignment explanation
Indices: 1789627--1789677 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
1789617 TTTTTCATTT
1789627 TTATTTTAATTA
1 TTATTTTAATTA
*
1789639 TTATTATAATTA
1 TTATTTTAATTA
1789651 TTATTATTATTATTA
1 TTATT-TTA--ATTA
1789666 TTATTTT-ATTA
1 TTATTTTAATTA
1789677 T
1 T
1789678 AAATAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.15
12 16 0.47
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:1789643 original size:3 final size:3
Alignment explanation
Indices: 1789635--1789677 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1789625 TTTTATTTTA
*
1789635 ATT ATT ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1789678 AAATAATTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1789728 original size:23 final size:22
Alignment explanation
Indices: 1789683--1789736 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1789673 ATTATAAATA
*
1789683 ATTACAAATAAACCCGAAACCCG
1 ATTAC-AATAAACACGAAACCCG
* **
1789706 TTTTACAATAAACACGATGCCCG
1 -ATTACAATAAACACGAAACCCG
1789729 ATTACAAT
1 ATTACAAT
1789737 TCTAGGCCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (22 bp):
ATTACAATAAACACGAAACCCG
Found at i:1791104 original size:2 final size:2
Alignment explanation
Indices: 1791097--1791133 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1791087 ATAAAAACAA
1791097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1791134 GTTATTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1791375 original size:2 final size:2
Alignment explanation
Indices: 1791368--1791431 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1791358 AAATATCCTG
1791368 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
1791410 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
1791432 CTTCGTTTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1792772 original size:24 final size:22
Alignment explanation
Indices: 1792733--1792779 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
1792723 GTACTAACCA
*
1792733 TTTTATTTTTCTCATTTTATTT
1 TTTTATTTTTATCATTTTATTT
1792755 TTTTATTTTTTATACATTTTATTT
1 TTTTA-TTTTTAT-CATTTTATTT
1792779 T
1 T
1792780 GCTTTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
24 11 0.50
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATTTTTATCATTTTATTT
Found at i:1794541 original size:21 final size:21
Alignment explanation
Indices: 1794490--1794543 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1794480 TTTTTCATTA
1794490 CATTTGCATTTTTTATGTTTG
1 CATTTGCATTTTTTATGTTTG
* *
1794511 CTTTTGCATTTTTATAT-TTTT
1 CATTTGCATTTTT-TATGTTTG
*
1794532 CATTTACATTTT
1 CATTTGCATTTT
1794544 CATTTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.07, T:0.65
Consensus pattern (21 bp):
CATTTGCATTTTTTATGTTTG
Found at i:1794565 original size:48 final size:47
Alignment explanation
Indices: 1794457--1794568 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 47
1794447 ACCTTTGTTG
*
1794457 TATTTGCATTTTGCATTCGTATTTTTTTCATTACATTTGCATTTTTTA
1 TATTTGCATTTTGCATTCGTATATTTTTCATTACATTTGCA-TTTTTA
* ** *
1794505 TGTTTGC-TTTTGCATTTTTATATTTTTCATTTACATTTTCA-TTTTA
1 TATTTGCATTTTGCATTCGTATATTTTTCA-TTACATTTGCATTTTTA
1794551 TATTTGCATCTTTGCATT
1 TATTTGCAT-TTTGCATT
1794569 GCACAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
46 11 0.20
47 20 0.36
48 24 0.44
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (47 bp):
TATTTGCATTTTGCATTCGTATATTTTTCATTACATTTGCATTTTTA
Found at i:1795518 original size:19 final size:18
Alignment explanation
Indices: 1795494--1795530 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1795484 GAAGGAATTC
*
1795494 GAGAATTTATTGATAAATG
1 GAGAATTAATTGA-AAATG
1795513 GAGAATTAATTGAAAATG
1 GAGAATTAATTGAAAATG
1795531 TGATCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (18 bp):
GAGAATTAATTGAAAATG
Found at i:1797069 original size:9 final size:9
Alignment explanation
Indices: 1797057--1797116 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
1797047 CAGAAAAATG
1797057 AAAAAAAGA
1 AAAAAAAGA
*
1797066 AAAAAGAGA
1 AAAAAAAGA
*
1797075 AAAAAGAGA
1 AAAAAAAGA
**
1797084 TGAAAAAGA
1 AAAAAAAGA
*
1797093 CGAAAAAAG-
1 -AAAAAAAGA
1797102 -AAAAAAGA
1 AAAAAAAGA
1797110 AAAAAAA
1 AAAAAAA
1797117 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 7 0.17
9 29 0.69
10 6 0.14
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:1797089 original size:11 final size:9
Alignment explanation
Indices: 1797056--1797115 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 9
1797046 TCAGAAAAAT
1797056 GAAAAAA-A
1 GAAAAAAGA
1797064 GAAAAAAGA
1 GAAAAAAGA
1797073 GAAAAAAGA
1 GAAAAAAGA
1797082 GATGAAAAAGA
1 GA--AAAAAGA
1797093 CG-AAAAA-A
1 -GAAAAAAGA
1797101 GAAAAAAGA
1 GAAAAAAGA
1797110 -AAAAAA
1 GAAAAAA
1797116 ATTGAATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 19 0.41
9 18 0.39
11 7 0.15
12 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:1797112 original size:6 final size:7
Alignment explanation
Indices: 1797048--1797114 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
1797038 CTCATTCATC
1797048 AGAAAAA
1 AGAAAAA
*
1797055 TGAAAAAA
1 AG-AAAAA
1797063 AGAAAAA
1 AGAAAAA
1797070 AGAGAAAA
1 AGA-AAAA
* *
1797078 A-AGAGA
1 AGAAAAA
*
1797084 TGAAAAA
1 AGAAAAA
1797091 GACGAAAAA
1 -A-GAAAAA
1797100 AGAAAAA
1 AGAAAAA
1797107 AGAAAAA
1 AGAAAAA
1797114 A
1 A
1797115 AATTGAATCA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
6 2 0.04
7 27 0.57
8 12 0.26
9 6 0.13
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (7 bp):
AGAAAAA
Found at i:1798851 original size:43 final size:43
Alignment explanation
Indices: 1798803--1798890 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
1798793 GCTAAATCTA
*
1798803 CTCATCAATTGCTCCAACAGATCACCATTCAGTTCTTGCGCAT
1 CTCATCAATTGCTCCAACAGATCACCATTCAGTTCTTGCACAT
*
1798846 CTCATCAATTGCTCCAACTGATCACCATTCAGTTCTTGCACAT
1 CTCATCAATTGCTCCAACAGATCACCATTCAGTTCTTGCACAT
1798889 CT
1 CT
1798891 GCTTTAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.32
Consensus pattern (43 bp):
CTCATCAATTGCTCCAACAGATCACCATTCAGTTCTTGCACAT
Found at i:1801175 original size:22 final size:22
Alignment explanation
Indices: 1801147--1801201 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1801137 ATCTACATTA
* *
1801147 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAAATTATCTC
* *
1801169 TTCAAAGATAATAAATTATCTT
1 TTCAAAGATGATAAATTATCTC
1801191 TTCAAAGATGA
1 TTCAAAGATGA
1801202 AAACTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAAATTATCTC
Found at i:1802080 original size:116 final size:115
Alignment explanation
Indices: 1801875--1802208 Score: 544
Period size: 116 Copynumber: 2.9 Consensus size: 115
1801865 ACTATTTCTC
* * *
1801875 ACATCCATAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGAAACTTTTTGATATTTAAA
1 ACATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGG-AGCTTTTTGATATTTAAA
*
1801940 GCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
65 GCCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
* * *
1801991 TCATCCATAAGACCTACAGTGCAGGATGTTTTCAGAAAGCCTTCAGGAGCTTTTTGATATTTAAA
1 ACATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTC-GGAGCTTTTTGATATTTAAA
1802056 GCCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
65 GCCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
1802107 ACATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAA
1 ACATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTC-GGAGCTTTTTGATATTTAAA
* *
1802172 GCCTTTGGGTCATCTGTAAGACATACA-TCGCAAGATG
65 GCCTCTGGGTCATCTGTAAGACCTACAGT-GCAAGATG
1802209 TTTTTTAAGT
Statistics
Matches: 204, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
115 1 0.00
116 201 0.99
117 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (115 bp):
ACATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGAGCTTTTTGATATTTAAAG
CCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
Found at i:1802100 original size:22 final size:22
Alignment explanation
Indices: 1802072--1802134 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 22
1802062 GGGTCATCTG
1802072 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGCAAGATGA
* * *
1802094 TAAGACCT-CAG-G-GACATCCA
1 TAAGACCTACAGTGCAAGAT-GA
1802114 TAAGACCTACAGTGCAAGATG
1 TAAGACCTACAGTGCAAGATG
1802135 TTTTCAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 6 0.19
22 9 0.29
23 3 0.10
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (22 bp):
TAAGACCTACAGTGCAAGATGA
Found at i:1802393 original size:3 final size:3
Alignment explanation
Indices: 1802385--1802421 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1802375 TCATTTTAAA
1802385 ATT ATT ATT ATT ATT ATAT ATT ATT ATT -TT -TT ATT AT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT AT
1802422 AAATAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1802408 original size:10 final size:10
Alignment explanation
Indices: 1802385--1802422 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1802375 TCATTTTAAA
1802385 ATTATTAT-T
1 ATTATTATAT
1802394 ATTATTATAT
1 ATTATTATAT
*
1802404 ATTATTATTT
1 ATTATTATAT
*
1802414 TTTATTATA
1 ATTATTATA
1802423 AATAATTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTATTATAT
Found at i:1802480 original size:22 final size:21
Alignment explanation
Indices: 1802427--1802480 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
1802417 ATTATAAATA
1802427 ATTACAAATAAACCCGAAGCCC
1 ATTAC-AATAAACCCGAAGCCC
*
1802449 ATTTTACAATAAACCCGAGGCCC
1 A--TTACAATAAACCCGAAGCCC
1802472 GATTACAAT
1 -ATTACAAT
1802481 TCCAGGCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 8 0.29
23 15 0.54
24 5 0.18
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (21 bp):
ATTACAATAAACCCGAAGCCC
Found at i:1803807 original size:2 final size:2
Alignment explanation
Indices: 1803800--1803836 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1803790 ATAAAAACAA
1803800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1803837 GTTATTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1804859 original size:2 final size:2
Alignment explanation
Indices: 1804852--1804914 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1804842 GCCAAAATAC
*
1804852 AT AT AT AT AC 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
1804894 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1804915 CACGTACACA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1813292 original size:31 final size:31
Alignment explanation
Indices: 1813220--1813285 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1813210 AGTTACGTCG
** *
1813220 GGGACCATATTGCAAATGGACTAAATGTTGA
1 GGGACCATATTGCAAACAGACTAAATATTGA
*
1813251 GGGACCATATTGCAAACAGACTAAATATTGG
1 GGGACCATATTGCAAACAGACTAAATATTGA
1813282 GGGA
1 GGGA
1813286 TTATATTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATATTGA
Found at i:1814829 original size:21 final size:21
Alignment explanation
Indices: 1814803--1814847 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1814793 GATTTCTGGG
* *
1814803 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1814824 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1814845 CAA
1 CAA
1814848 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1815455 original size:18 final size:18
Alignment explanation
Indices: 1815432--1815466 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1815422 CTAGGAGATT
1815432 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1815450 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1815467 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1815713 original size:2 final size:2
Alignment explanation
Indices: 1815706--1815737 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1815696 AATCTTGAGG
*
1815706 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1815738 GAAATGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1816552 original size:149 final size:149
Alignment explanation
Indices: 1816372--1816675 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1816362 GAGTCGAGGG
1816372 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1816437 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1816502 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1816521 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1816586 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1816651 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1816670 TCTACG
1 TCTACG
1816676 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1816698 original size:23 final size:23
Alignment explanation
Indices: 1816654--1816698 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1816644 ATCATTATAT
*
1816654 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1816677 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1816699 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1817539 original size:3 final size:3
Alignment explanation
Indices: 1817531--1817563 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1817521 AATTTTTTAA
1817531 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1817564 TTCTAACCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1818375 original size:32 final size:32
Alignment explanation
Indices: 1818338--1818398 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1818328 AAAGACTAAA
*
1818338 ATAATATAACTGAATTTAGAATAAT-CAAATAT
1 ATAATATAACTGAATTCAGAA-AATACAAATAT
*
1818370 ATAATATAACTTAATTCAGAAAATACAAA
1 ATAATATAACTGAATTCAGAAAATACAAA
1818399 GATTAAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (32 bp):
ATAATATAACTGAATTCAGAAAATACAAATAT
Found at i:1818547 original size:31 final size:31
Alignment explanation
Indices: 1818512--1818572 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1818502 TATAATATCC
* *
1818512 CAACATTTAGTCCGTTTGTAATATGGTCCCT
1 CAACATTTAGTCCGTTTGCAATATGATCCCT
1818543 CAACATTTAGTCCGTTTGCAATATGATCCC
1 CAACATTTAGTCCGTTTGCAATATGATCCC
1818573 CGATGTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (31 bp):
CAACATTTAGTCCGTTTGCAATATGATCCCT
Found at i:1850549 original size:20 final size:20
Alignment explanation
Indices: 1850524--1850564 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1850514 GTTAGTATAA
*
1850524 TTAATGTTTAAATATAGTCT
1 TTAATGTTTAAATACAGTCT
1850544 TTAATGTTTAAATACAGTCT
1 TTAATGTTTAAATACAGTCT
1850564 T
1 T
1850565 ATGCCTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (20 bp):
TTAATGTTTAAATACAGTCT
Found at i:1852836 original size:20 final size:20
Alignment explanation
Indices: 1852811--1852850 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1852801 AGCAACAGAA
*
1852811 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1852831 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1852851 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:1852879 original size:53 final size:52
Alignment explanation
Indices: 1852807--1852936 Score: 244
Period size: 53 Copynumber: 2.5 Consensus size: 52
1852797 AATTAGCAAC
1852807 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1852858 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1852911 AGAATAAAAACTGATTCTATCTAATT
1 AGAATAAAAACTGATTCTATCTAATT
1852937 TAATTTAGAT
Statistics
Matches: 77, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
51 5 0.06
52 26 0.34
53 46 0.60
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:1852893 original size:20 final size:21
Alignment explanation
Indices: 1852864--1852903 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1852854 TAATAGAATA
*
1852864 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1852885 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1852904 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1857527 original size:20 final size:20
Alignment explanation
Indices: 1857502--1857541 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1857492 AGTAACAGAA
*
1857502 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1857522 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1857542 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:1857570 original size:53 final size:52
Alignment explanation
Indices: 1857498--1857627 Score: 235
Period size: 53 Copynumber: 2.5 Consensus size: 52
1857488 AATTAGTAAC
1857498 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1857549 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
1857602 AGAATAAAAACTGGTTCTATCTAATT
1 AGAATAAAAACTGATTCTATCTAATT
1857628 TAATTTAGAT
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 5 0.07
52 25 0.33
53 46 0.61
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:1857584 original size:20 final size:21
Alignment explanation
Indices: 1857555--1857594 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1857545 TAATAGAATA
*
1857555 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1857576 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1857595 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1868726 original size:27 final size:27
Alignment explanation
Indices: 1868695--1868789 Score: 151
Period size: 27 Copynumber: 3.6 Consensus size: 27
1868685 TCTATTTACA
1868695 AAATCATATCTCTATAGGAATTGTAAC
1 AAATCATATCTCTATAGGAATTGTAAC
1868722 AAATCATATCTCTATAGGAA-TGATAAC
1 AAATCATATCTCTATAGGAATTG-TAAC
*
1868749 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATTGTAAC
1868776 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1868790 ATTCCTACAC
Statistics
Matches: 65, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
25 9 0.14
26 2 0.03
27 53 0.82
28 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATTGTAAC
Found at i:1872495 original size:27 final size:27
Alignment explanation
Indices: 1872464--1872531 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1872454 TCTATTTACA
1872464 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1872491 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1872518 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1872532 ATTCCTACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1882839 original size:2 final size:2
Alignment explanation
Indices: 1882832--1882872 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1882822 ATTTTATAAT
1882832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1882873 ATTATATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1891666 original size:2 final size:2
Alignment explanation
Indices: 1891659--1891695 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1891649 CATATAATTA
1891659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1891696 ATCATATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1894819 original size:31 final size:31
Alignment explanation
Indices: 1894783--1894841 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1894773 AAATTAAAAG
* *
1894783 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1894814 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1894842 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1894877 original size:21 final size:22
Alignment explanation
Indices: 1894853--1894903 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1894843 CATACAACTA
1894853 AAAT-AATAAAT-TATTTAAAAT
1 AAATCAATAAATAT-TTTAAAAT
**
1894874 AAATCAATCTATATTTTAAAAT
1 AAATCAATAAATATTTTAAAAT
1894896 AAATCAAT
1 AAATCAAT
1894904 CTATACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATCAATAAATATTTTAAAAT
Found at i:1894891 original size:22 final size:22
Alignment explanation
Indices: 1894866--1894908 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1894856 TAATAAATTA
1894866 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
1894888 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
1894909 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:1894917 original size:22 final size:22
Alignment explanation
Indices: 1894868--1894916 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1894858 ATAAATTATT
**
1894868 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
1894890 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
1894913 TAAA
1 TAAA
1894917 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:1894997 original size:22 final size:22
Alignment explanation
Indices: 1894924--1894997 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
1894914 AAATTATTTA
*
1894924 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
1894949 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
1894971 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
1894994 AAAT
1 AAAT
1894998 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:1895007 original size:32 final size:32
Alignment explanation
Indices: 1894968--1895247 Score: 305
Period size: 32 Copynumber: 9.7 Consensus size: 32
1894958 CAATCCATAT
*
1894968 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1895000 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1895032 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1895064 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1895086 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1895118 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1895140 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1895172 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1895194 TTTAAAGTAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1895226 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
1895248 AGCTACAATA
Statistics
Matches: 213, Mismatches: 5, Indels: 60
0.77 0.02 0.22
Matches are distributed among these distances:
22 47 0.22
23 5 0.02
24 3 0.01
25 1 0.00
26 9 0.04
28 9 0.04
29 1 0.00
30 3 0.01
31 5 0.02
32 130 0.61
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1895090 original size:22 final size:22
Alignment explanation
Indices: 1895064--1895106 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1895054 TAATAAATTA
1895064 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1895086 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1895107 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1895092 original size:54 final size:54
Alignment explanation
Indices: 1894951--1895242 Score: 458
Period size: 54 Copynumber: 5.2 Consensus size: 54
1894941 CAACTACAAT
*
1894951 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1895005 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1895069 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1895123 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
1895177 AATAAATCAATTCATATTTTAAAGTAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1895231 AATAAATCAATC
1 AATAAATCAATC
1895243 TATACAGCTA
Statistics
Matches: 223, Mismatches: 5, Indels: 20
0.90 0.02 0.08
Matches are distributed among these distances:
54 165 0.74
55 1 0.00
56 1 0.00
58 3 0.01
60 3 0.01
62 1 0.00
63 1 0.00
64 48 0.22
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1895115 original size:22 final size:22
Alignment explanation
Indices: 1895066--1895114 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1895056 ATAAATTATT
**
1895066 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1895088 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1895111 TAAA
1 TAAA
1895115 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1895144 original size:22 final size:22
Alignment explanation
Indices: 1895118--1895160 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1895108 TAATAAATTA
1895118 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1895140 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1895161 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1895169 original size:22 final size:22
Alignment explanation
Indices: 1895120--1895168 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1895110 ATAAATTATT
**
1895120 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1895142 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1895165 TAAA
1 TAAA
1895169 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1895303 original size:22 final size:22
Alignment explanation
Indices: 1895257--1895302 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1895247 CAGCTACAAT
**
1895257 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATAATAA
1895279 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TAATAA
1895302 A
1 A
1895303 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATCAATCCATATAATAA
Found at i:1895326 original size:15 final size:15
Alignment explanation
Indices: 1895297--1895429 Score: 151
Period size: 15 Copynumber: 8.5 Consensus size: 15
1895287 AATCCATACT
1895297 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1895311 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1895326 AATAAATCAATCTATATTTTAT
1 AAT--A--AA--T-TATTTTAA
*
1895348 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
1895363 AATAAATTAGTTTAT
1 AATAAATTATTTTAA
*
1895378 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1895393 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1895408 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1895423 AATAAAT
1 AATAAAT
1895430 AACCTTATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
14 9 0.09
15 77 0.75
16 1 0.01
17 1 0.01
18 1 0.01
19 2 0.02
20 1 0.01
21 1 0.01
22 10 0.10
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1895334 original size:47 final size:46
Alignment explanation
Indices: 1895271--1895452 Score: 178
Period size: 45 Copynumber: 3.9 Consensus size: 46
1895261 AATCAATCCA
1895271 TATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAAT
1 TATTTTAAAATAAAT-AATCCATA-TAATAAATTATTTTAAAATAAAT
* *
1895318 TATTTTAAAATAAATCAATCTATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAAT-AATC--CA---TATAATAAATTATTTTAAAATAAAT
* * * **
1895370 TAGTTTATAATAAATTAT-TTTATAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATAATCCATATAATAAATTATTTTAAAATAAAT
*
1895415 TATTTTAAAATAAATAA-CC-T-TATTAAATTA-TTTAAAAT
1 TATTTTAAAATAAATAATCCATATAATAAATTATTTTAAAAT
1895453 TATTTTAATA
Statistics
Matches: 116, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
42 8 0.07
43 9 0.08
44 1 0.01
45 38 0.33
47 20 0.17
48 1 0.01
49 1 0.01
51 11 0.09
52 27 0.23
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (46 bp):
TATTTTAAAATAAATAATCCATATAATAAATTATTTTAAAATAAAT
Found at i:1902334 original size:20 final size:21
Alignment explanation
Indices: 1902299--1902339 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1902289 CAAATGATAA
1902299 TGATGTGGCAAAATGGAATGAC
1 TGATGTGG-AAAATGGAATGAC
1902321 TGATGTGG-AAATGGAATGA
1 TGATGTGGAAAATGGAATGA
1902340 TGGTGGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.24
Consensus pattern (21 bp):
TGATGTGGAAAATGGAATGAC
Found at i:1904424 original size:2 final size:2
Alignment explanation
Indices: 1904417--1904450 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1904407 TCATAACTTC
1904417 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
1904451 TAACATAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1905972 original size:21 final size:21
Alignment explanation
Indices: 1905930--1905972 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1905920 TTTCTGGGCT
* *
1905930 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1905951 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1905972 A
1 A
1905973 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1909162 original size:21 final size:21
Alignment explanation
Indices: 1909120--1909162 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1909110 TTTCTGGGCT
*
1909120 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1909141 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1909162 A
1 A
1909163 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1910081 original size:4 final size:4
Alignment explanation
Indices: 1910072--1910096 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1910062 AAATGATGAC
1910072 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
1910097 ATGGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1910393 original size:30 final size:30
Alignment explanation
Indices: 1910354--1910690 Score: 647
Period size: 30 Copynumber: 11.2 Consensus size: 30
1910344 TCGGGACTTA
*
1910354 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910384 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910414 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910444 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
1910474 TAGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
1910504 TGGATAGTTACCGAGGATCTTTATAACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910534 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910564 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910594 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910624 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910654 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1910684 TGGATAG
1 TGGATAG
1910691 GTCCTTCGGA
Statistics
Matches: 302, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 302 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:1918416 original size:15 final size:15
Alignment explanation
Indices: 1918396--1918425 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1918386 TATCACAATC
1918396 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
1918411 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
1918426 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:1923841 original size:16 final size:16
Alignment explanation
Indices: 1923820--1923851 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1923810 CATCAGACAT
1923820 AATCCATTCGATAAAC
1 AATCCATTCGATAAAC
1923836 AATCCATTCGATAAAC
1 AATCCATTCGATAAAC
1923852 CAGCTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
AATCCATTCGATAAAC
Found at i:1924989 original size:20 final size:18
Alignment explanation
Indices: 1924947--1924981 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1924937 ACAGAAGAAG
* *
1924947 TGAAATTCATTTGTCTTT
1 TGAAAATCATTTGTATTT
1924965 TGAAAATCATTTGTATT
1 TGAAAATCATTTGTATT
1924982 AATTGAAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TGAAAATCATTTGTATTT
Found at i:1928516 original size:17 final size:17
Alignment explanation
Indices: 1928496--1928535 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1928486 ATATAACACG
*
1928496 ATTTTTTAAATATTT-TA
1 ATTTGTTAAA-ATTTGTA
1928513 ATTTGTTAAAATTTGTA
1 ATTTGTTAAAATTTGTA
1928530 ATTTGT
1 ATTTGT
1928536 AATTCTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
ATTTGTTAAAATTTGTA
Found at i:1932927 original size:50 final size:50
Alignment explanation
Indices: 1932842--1932976 Score: 243
Period size: 50 Copynumber: 2.7 Consensus size: 50
1932832 ATGGGTAAGT
*
1932842 GAAAGCAAGTTAGTAAGTTATACATTTTTTTATCATTTTAATTTTTCAAA
1 GAAAGCAAGTTAGTAAGTTATACATTTTTTTATCATTTTAATTTTGCAAA
* *
1932892 GAAATCAAGTTAGTAAGTTATACATTTTTTGATCATTTTAATTTTGCAAA
1 GAAAGCAAGTTAGTAAGTTATACATTTTTTTATCATTTTAATTTTGCAAA
1932942 GAAAGCAAGTTAGTAAGTTATACATTTTTTTATCA
1 GAAAGCAAGTTAGTAAGTTATACATTTTTTTATCA
1932977 GGTTACGAAC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (50 bp):
GAAAGCAAGTTAGTAAGTTATACATTTTTTTATCATTTTAATTTTGCAAA
Found at i:1934047 original size:35 final size:34
Alignment explanation
Indices: 1933962--1934048 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
1933952 ATTTGATATT
*
1933962 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
1933996 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
1934034 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1934049 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:1934666 original size:18 final size:18
Alignment explanation
Indices: 1934638--1934691 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
1934628 ATGGAAAGGC
1934638 GATGACGGCATCATATATA
1 GATG-CGGCATCATATATA
*
1934657 GATGCGGCATCATATATG
1 GATGCGGCATCATATATA
* *
1934675 GTTGCGACATCATATAT
1 GATGCGGCATCATATAT
1934692 GGCTGTGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (18 bp):
GATGCGGCATCATATATA
Found at i:1936343 original size:111 final size:111
Alignment explanation
Indices: 1936206--1936419 Score: 403
Period size: 111 Copynumber: 1.9 Consensus size: 111
1936196 ATTACAAAAA
*
1936206 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1936271 AATTAAAACGTTAAAATGTTACCGTATCAA-CAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTAT-AAGCAAAGTGTCGAGATAT
1936317 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1936382 AATTAAAACGTTAAAATGTTACCGTATAAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATAAGCAAAGTGT
1936420 AGAAATATAT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
110 2 0.02
111 99 0.98
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATAAGCAAAGTGTCGAGATAT
Found at i:1936509 original size:17 final size:18
Alignment explanation
Indices: 1936489--1936529 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1936479 GAATTATATT
*
1936489 AGTAAAATA-TTAAATAA
1 AGTAAAACACTTAAATAA
1936506 AGTAAAACACTTAAATAA
1 AGTAAAACACTTAAATAA
*
1936524 ATTAAA
1 AGTAAA
1936530 TACATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (18 bp):
AGTAAAACACTTAAATAA
Found at i:1936521 original size:18 final size:17
Alignment explanation
Indices: 1936489--1936534 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1936479 GAATTATATT
*
1936489 AGTAAAATATTAAATAA
1 AGTAAAACATTAAATAA
1936506 AGTAAAACACTTAAATAA
1 AGTAAAACA-TTAAATAA
*
1936524 ATTAAATACAT
1 AGTAAA-ACAT
1936535 AATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 14 0.56
19 3 0.12
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (17 bp):
AGTAAAACATTAAATAA
Found at i:1952595 original size:60 final size:59
Alignment explanation
Indices: 1952502--1952619 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 59
1952492 TCCACGATGC
* * * * * *
1952502 CGACATTTAGGTCGAACAAACTGGTAGTTGAATGTCTTTCCCTTGAACTTTAAGGCATCT
1 CGACATTGAGGTCGAACAAACTGGCAGTAGAATGTC-TCCCCTGGAACTTGAAGGCATCT
* * *
1952562 CGACATTGATGTCGAAGAAACTTGCAGTAGAATGTCTCCCCTGGAACTTGAAGGCATC
1 CGACATTGAGGTCGAACAAACTGGCAGTAGAATGTCTCCCCTGGAACTTGAAGGCATC
1952620 ATATCAAATG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 19 0.39
60 30 0.61
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (59 bp):
CGACATTGAGGTCGAACAAACTGGCAGTAGAATGTCTCCCCTGGAACTTGAAGGCATCT
Found at i:1961976 original size:117 final size:117
Alignment explanation
Indices: 1961711--1962351 Score: 600
Period size: 117 Copynumber: 5.5 Consensus size: 117
1961701 TGTTTCTTTT
*
1961711 TTGGTTCTTTTTAAACATGGCTTGGCTT-T-TTTTTCTAATGCTAGAGCTAGCAGAAGATGACAC
1 TTGGTTCTTTTTAAACATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACAC
* ** * * * *
1961774 TAGCCTTCTTACTTGAGCACT-TTAATTTTCTCTGGAAGCTCTGTTCCTTGA
66 CAGCCTTCTTACTTGAGCACTGGGAATTTGCTCTGGAAGATCTCTTTCTTGA
* * * * *
1961825 TTGGTTGTTTTTGAAGATGGCTTGGCTTCTGTTTTTCTAGTGCTAGAGCTAGCAGAAGATGACAC
1 TTGGTTCTTTTTAAACATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACAC
* * * *
1961890 CAGCCGTCTTACGTGAGCGCTGGGAATTTGCTCTGGAAGATCTCTTTCTCGA
66 CAGCCTTCTTACTTGAGCACTGGGAATTTGCTCTGGAAGATCTCTTTCTTGA
* * * * * *
1961942 TTTGTTCTTTTTGAAGATGACCTGGCTTCTGTTTTTCTAATGCTTGAGCTAGAAGAAGATGACAC
1 TTGGTTCTTTTTAAACATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACAC
* * * * * * *
1962007 CAGTCTTGTTACTCGAGTACTGGGAATTTGCACTGGAA-A-CTCCTTTTTTTGC
66 CAGCCTTCTTACTTGAGCACTGGGAATTTGCTCTGGAAGATCT-C-TTTCTTGA
* * * *
1962059 CTGGTTCTTTTTAAACTTGGCTTGGCTTCTGTTGTTCTAATGCTAGAACTAGAAGAAGATGACAC
1 TTGGTTCTTTTTAAACATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACAC
* * * ** ** *
1962124 TAGCCTTGTTACTTGAGCGCTGGGAATTTGAACTGGTAA-CCCTTTTTCTTG-
66 CAGCCTTCTTACTTGAGCACTGGGAATTTGCTCTGG-AAGATCTCTTTCTTGA
* * * * *
1962175 TGTGGTTCTTTTTAAAC-TAGGCTTAGCTTCAGTTTTTTTAAAGCTAGAGATAGAAGAAGATGAC
1 T-TGGTTCTTTTTAAACAT-GGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGAC
* * * * * * * * *
1962239 ACCAGCCTTGTTACTTTAGCCCTAGGAATTTGCACTGGCAA-CTCTGTTTTTTGT
64 ACCAGCCTTCTTACTTGAGCACTGGGAATTTGCTCTGG-AAGATCTCTTTCTTGA
* * * * *
1962293 TTGGTTCTTTTTGAAA-GTGGCTTTGCTTCAGTTTTTATAATGCTAGTGCTAGAAGAAGA
1 TTGGTTCTTTTT-AAACATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGA
1962352 AGAAGACACC
Statistics
Matches: 441, Mismatches: 74, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
114 25 0.06
115 3 0.01
116 53 0.12
117 351 0.80
118 7 0.02
119 2 0.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (117 bp):
TTGGTTCTTTTTAAACATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACAC
CAGCCTTCTTACTTGAGCACTGGGAATTTGCTCTGGAAGATCTCTTTCTTGA
Found at i:1962148 original size:234 final size:230
Alignment explanation
Indices: 1961712--1962351 Score: 669
Period size: 234 Copynumber: 2.7 Consensus size: 230
1961702 GTTTCTTTTT
* *
1961712 TGGTTCTTTTTAAACATGGCTTGGCTT-T-TTTTTCTAATGCTAGAGCTAGCAGAAGATGACACT
1 TGGTTCTTTTT-AA-ATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACC
* ** * * * ** *
1961775 AGCCTTCTTACTTGAGCACTTTAATTTTCTCTGGAAGCTCTGTTCCTTGATTGGTTGTTTTTGAA
64 AGCCTTGTTACTTGAGCACTGGAATTTGCACTGGAAACTCTGTTTTTTGATTGGTTCTTTTT-AA
* * *
1961840 GATGGCTTGGCTTCTGTTTTTCTAGTGCTAGAGCTAGCAGAAGATGACACCAGCCGTCTTACGTG
128 AATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACCAGCCGTCTTACGTG
** *
1961905 AGCGCTGGGAATTTGCTCTGG-AAGATCTCTTTCTCGAT-
193 AGCGCTGGGAATTTGAACTGGTAA-ACCTCTTTCTCG-TG
* * * *
1961943 TTGTTCTTTTTGAAGATGACCTGGCTTCTGTTTTTCTAATGCTTGAGCTAGAAGAAGATGACACC
1 TGGTTCTTTTT-AA-ATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACC
* * * **
1962008 AGTCTTGTTACTCGAGTACTGGGAATTTGCACTGGAAACTCCT-TTTTTTGCCTGGTTCTTTTTA
64 AGCCTTGTTACTTGAGCACT-GGAATTTGCACTGGAAACT-CTGTTTTTTGATTGGTTCTTTTTA
* * * * * * *
1962072 AACTTGGCTTGGCTTCTGTTGTTCTAATGCTAGAACTAGAAGAAGATGACACTAGCCTTGTTACT
127 AA-ATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACCAGCCGTCTTACG
* * *
1962137 TGAGCGCTGGGAATTTGAACTGGTAACCCTTTTTCTTGTG
191 TGAGCGCTGGGAATTTGAACTGGTAAACCTCTTTCTCGTG
* * * * *
1962177 TGGTTCTTTTTAAACTAGGCTTAGCTTCAGTTTTTTTAAAGCTAGAGATAGAAGAAGATGACACC
1 TGGTTCTTTTTAAA-T-GGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACC
* * * *
1962242 AGCCTTGTTACTTTAGCCCTAGGAATTTGCACTGGCAACTCTGTTTTTTGTTTGGTTCTTTTTGA
64 AGCCTTGTTACTTGAGCACT-GGAATTTGCACTGGAAACTCTGTTTTTTGATTGGTTCTTTTT-A
* * * * *
1962307 AAGTGGCTTTGCTTCAGTTTTTATAATGCTAGTGCTAGAAGAAGA
127 AAATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGA
1962352 AGAAGACACC
Statistics
Matches: 335, Mismatches: 63, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
231 22 0.07
232 2 0.01
233 56 0.17
234 248 0.74
235 7 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (230 bp):
TGGTTCTTTTTAAATGGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACCAG
CCTTGTTACTTGAGCACTGGAATTTGCACTGGAAACTCTGTTTTTTGATTGGTTCTTTTTAAAAT
GGCTTGGCTTCTGTTTTTCTAATGCTAGAGCTAGAAGAAGATGACACCAGCCGTCTTACGTGAGC
GCTGGGAATTTGAACTGGTAAACCTCTTTCTCGTG
Found at i:1962730 original size:2 final size:2
Alignment explanation
Indices: 1962723--1962754 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1962713 ATTAAATGCT
1962723 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
1962755 CCTTATCCTT
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):
TA
Found at i:1962776 original size:12 final size:12
Alignment explanation
Indices: 1962759--1962783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1962749 TATATACCTT
1962759 ATCCTTTAAAAC
1 ATCCTTTAAAAC
1962771 ATCCTTTAAAAC
1 ATCCTTTAAAAC
1962783 A
1 A
1962784 GAGCTATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCCTTTAAAAC
Found at i:1965240 original size:87 final size:86
Alignment explanation
Indices: 1965125--1965339 Score: 369
Period size: 87 Copynumber: 2.5 Consensus size: 86
1965115 TAGCAATCAA
* *
1965125 AATTGTAAAAGTCATCCTTTGCTGGGTAAAAGGAATCGACATTGGATCTTGTGAAATTGATTTGG
1 AATTGTAAAAGTCATCCTTTAC-GGGTAAAAGGAATCAACATTGGATCTTGTGAAATTGATTTGG
1965190 GAAATAAGTTGTTTTGAACAAT
65 GAAATAAGTTGTTTTGAACAAT
1965212 AATTGTAAAAGTCATCCTTTACGAGGTAAAAGGAATCAACATTGGATCTTGTGAAATTGATTTGG
1 AATTGTAAAAGTCATCCTTTACG-GGTAAAAGGAATCAACATTGGATCTTGTGAAATTGATTTGG
*
1965277 GAAATAAGTTGTTTTGAATAAT
65 GAAATAAGTTGTTTTGAACAAT
1965299 AATTGTAAAAGTCATCCTTTACGGGGTAAAA-GAATCAACAT
1 AATTGTAAAAGTCATCCTTTAC-GGGTAAAAGGAATCAACAT
1965340 CGGAATTGTT
Statistics
Matches: 123, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
86 11 0.09
87 111 0.90
88 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (86 bp):
AATTGTAAAAGTCATCCTTTACGGGTAAAAGGAATCAACATTGGATCTTGTGAAATTGATTTGGG
AAATAAGTTGTTTTGAACAAT
Found at i:1965950 original size:14 final size:15
Alignment explanation
Indices: 1965914--1965950 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1965904 TAAATTTAGT
1965914 TAAAA-ATTTAAAAG
1 TAAAATATTTAAAAG
*
1965928 TAAATTATTTAAAAG
1 TAAAATATTTAAAAG
1965943 -AAAATATT
1 TAAAATATT
1965951 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:1966459 original size:40 final size:40
Alignment explanation
Indices: 1966360--1966465 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 40
1966350 TAATTAGGCC
* *
1966360 AAATATAGAACCCTAGTTCCCAAATTGAGTACCCTAATTCCT
1 AAAT-TAGAACCATAATTCCCAAATT-AGTACCCTAATTCCT
* * * *
1966402 AAATTAAAACCACAATTCCCAAAATT-GTACCTTAATTTCT
1 AAATTAGAACCATAATTCCC-AAATTAGTACCCTAATTCCT
* * *
1966442 ACATTAGAACCGTAATTCCTAAAT
1 AAATTAGAACCATAATTCCCAAAT
1966466 CCAATATCGA
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
39 4 0.08
40 27 0.52
41 12 0.23
42 9 0.17
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.30
Consensus pattern (40 bp):
AAATTAGAACCATAATTCCCAAATTAGTACCCTAATTCCT
Found at i:1968044 original size:3 final size:3
Alignment explanation
Indices: 1968036--1968095 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1968026 TGCCTTTTAG
1968036 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1968084 AAT AAT AAT AAT
1 AAT AAT AAT AAT
1968096 GGTGATCATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1970367 original size:2 final size:2
Alignment explanation
Indices: 1970360--1970384 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1970350 AGTACGCTTA
1970360 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1970385 ATAATGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1981057 original size:18 final size:18
Alignment explanation
Indices: 1981005--1981058 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1980995 TTGATATTTA
*
1981005 AATTTTAGATAAAATATC
1 AATTTTAGATAAAATATT
*
1981023 AATTTAAG-T---AT-TT
1 AATTTTAGATAAAATATT
1981036 AATTTTAGATAAAATATT
1 AATTTTAGATAAAATATT
1981054 AATTT
1 AATTT
1981059 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
17 3 0.11
18 14 0.50
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
AATTTTAGATAAAATATT
Found at i:1981058 original size:31 final size:31
Alignment explanation
Indices: 1980972--1981071 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 31
1980962 GTTTGATGAC
** *
1980972 TAAATTTTTA-ATAAAATATTGTTTTGATATT
1 TAAA-TTTTAGATAAAATATTAATTTAATATT
*
1981003 TAAATTTTAGATAAAATATCAATTTAAGTATT
1 TAAATTTTAGATAAAATATTAATTTAA-TATT
*
1981035 T-AATTTTAGATAAAATATTAATTTAATTTT
1 TAAATTTTAGATAAAATATTAATTTAATATT
*
1981065 TGAATTT
1 TAAATTT
1981072 GATTTAAGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.15
31 46 0.77
32 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (31 bp):
TAAATTTTAGATAAAATATTAATTTAATATT
Found at i:1981209 original size:2 final size:2
Alignment explanation
Indices: 1981202--1981246 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1981192 ATCTCACGAA
*
1981202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
1981244 AT A
1 AT A
1981247 ATCAATTAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1982048 original size:14 final size:14
Alignment explanation
Indices: 1982031--1982060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1982021 TAGATTAACT
*
1982031 TTTAAATATTAAAA
1 TTTAAATAATAAAA
1982045 TTTAAATAATAAAA
1 TTTAAATAATAAAA
1982059 TT
1 TT
1982061 ATTAGATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAATAATAAAA
Found at i:1982984 original size:3 final size:3
Alignment explanation
Indices: 1982976--1983095 Score: 132
Period size: 3 Copynumber: 40.0 Consensus size: 3
1982966 TGATATTGAT
* * * * * *
1982976 TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TAA TTA CTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1983024 TTA TTA TTA TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1983072 TAA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1983096 AATATATATA
Statistics
Matches: 93, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1983094 original size:30 final size:30
Alignment explanation
Indices: 1982976--1983095 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
1982966 TGATATTGAT
* * *
1982976 TTATTATTATAATTATAATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTATTA
*
1983006 TAATTACTATAAATATTATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTATTA
1983036 TTATTACTATAAATATTATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTATTA
*
1983066 CTA-T--TATAAATATTATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTATTA
1983093 TTA
1 TTA
1983096 AATATATATA
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
27 25 0.30
29 1 0.01
30 57 0.69
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATTACTATAAATATTATTATTATTATTA
Found at i:1983229 original size:16 final size:16
Alignment explanation
Indices: 1983210--1983250 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1983200 CTCTAACCCT
*
1983210 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCCCC
*
1983226 AGCCACCTCTGCCCCC
1 AGCCGCCTCTGCCCCC
*
1983242 AACCGCCTC
1 AGCCGCCTC
1983251 AGCCAATGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.12, C:0.59, G:0.15, T:0.15
Consensus pattern (16 bp):
AGCCGCCTCTGCCCCC
Found at i:1994820 original size:7 final size:7
Alignment explanation
Indices: 1994808--1994863 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
1994798 ATTATGCTTG
1994808 AAGAAAA
1 AAGAAAA
1994815 AAG--AA
1 AAGAAAA
1994820 AAGAAAA
1 AAGAAAA
1994827 AAGAAAA
1 AAGAAAA
1994834 AAGAAAA
1 AAGAAAA
1994841 AA-AAAA
1 AAGAAAA
*
1994847 GAGAAAA
1 AAGAAAA
1994854 AAGAAGAA
1 AAGAA-AA
1994862 AA
1 AA
1994864 AGGGGGGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
5 5 0.12
6 5 0.12
7 29 0.67
8 4 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:1994832 original size:19 final size:19
Alignment explanation
Indices: 1994808--1994864 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1994798 ATTATGCTTG
*
1994808 AAGAAAAAAGAAAAGAAAA
1 AAGAAAAAAGAAAAAAAAA
1994827 AAGAAAAAAGAAAAAAAAA
1 AAGAAAAAAGAAAAAAAAA
1994846 AGAGAAAAAAGAAGAAAAA
1 A-AGAAAAAAGAA-AAAAA
1994865 GGGGGGGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 19 0.54
20 11 0.31
21 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAGAAAAAAAAA
Found at i:1994860 original size:12 final size:12
Alignment explanation
Indices: 1994808--1994858 Score: 66
Period size: 12 Copynumber: 4.0 Consensus size: 12
1994798 ATTATGCTTG
1994808 AAGAAAAAAGAA
1 AAGAAAAAAGAA
1994820 AAGAAAAAAGAAAA
1 AAGAAAAAAG--AA
*
1994834 AAGAAAAAAAAA
1 AAGAAAAAAGAA
1994846 AGAGAAAAAAGAA
1 A-AGAAAAAAGAA
1994859 GAAAAAGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 13 0.38
13 10 0.29
14 11 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:1996133 original size:83 final size:83
Alignment explanation
Indices: 1995994--1996264 Score: 506
Period size: 83 Copynumber: 3.3 Consensus size: 83
1995984 AAACATTAAA
* *
1995994 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1996059 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
1996077 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1996142 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* *
1996160 TGGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1996225 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
1996243 TGGAAGATGAATTTGCTCATAG
1 TGGAAGATGAATTTGCTCATAG
1996265 TATAAATAAG
Statistics
Matches: 182, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 182 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
AGAACCAATCATTGAATT
Found at i:1997264 original size:113 final size:113
Alignment explanation
Indices: 1997080--1997912 Score: 1359
Period size: 113 Copynumber: 7.4 Consensus size: 113
1997070 TAGATTGACA
1997080 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1997145 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
*
1997193 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1997258 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
1997306 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1997371 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
* *
1997419 TTTCCAGAGAAAGTTCATAATTAGAAGAACTCATCTGAAGAAGGAAGATGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
1997484 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
1997532 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
1997597 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
* *
1997645 TTTCCAGAAAAAGTTCATAATGA-AATGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAG
1 TTTCCAGAGAAAGTTCATAATGAGAA-GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * * *
1997709 AAGAATTTGTTCAACCTTTTG-CTCAAATCTATCACTTGATAGATTAGCT
65 AAGAACTTGTTCAACCTTTTGCCTGAATTC-ATCACTTGATGGATCAGCT
**** * * *
1997758 TTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAATGATGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
1997823 AGAATTTGTTCAGA-TTTTTG-CTCAAATACATCACTTGATGGATCAACT
66 AGAACTTGTTCA-ACCTTTTGCCT-GAATTCATCACTTGATGGATCAGCT
*
1997871 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1997913 AGAACTTGTT
Statistics
Matches: 675, Mismatches: 40, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
112 8 0.01
113 661 0.98
114 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
Found at i:1998278 original size:3 final size:3
Alignment explanation
Indices: 1998258--1998368 Score: 114
Period size: 3 Copynumber: 37.0 Consensus size: 3
1998248 CCATATTGAT
* * * * * *
1998258 TTA TTA TAA TTA TAA TTA TTA TTA TTA TAA TTA CTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
1998306 TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA CTA TTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1998354 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1998369 AATATATATA
Statistics
Matches: 84, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1998295 original size:24 final size:24
Alignment explanation
Indices: 1998258--1998397 Score: 157
Period size: 24 Copynumber: 5.9 Consensus size: 24
1998248 CCATATTGAT
* * *
1998258 TTATTATAATTATAATTATTATTA
1 TTATTATTACTATAAATATTATTA
*
1998282 TTATAATTACTATAAATATTATTA
1 TTATTATTACTATAAATATTATTA
1998306 TTATTATTACTATAAATATTATTA
1 TTATTATTACTATAAATATTATTA
1998330 TTATTATTACTATTATAAATATTATTA
1 TTATTATTAC---TATAAATATTATTA
1998357 TTATTATTA-T-TAAATA-TA-TA
1 TTATTATTACTATAAATATTATTA
1998377 -TATATATATAC-ATAAATATTA
1 TTAT-TAT-TACTATAAATATTA
1998398 AAAAATTACA
Statistics
Matches: 103, Mismatches: 5, Indels: 17
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.03
20 5 0.05
21 4 0.04
22 12 0.12
23 3 0.03
24 53 0.51
27 23 0.22
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATTATTACTATAAATATTATTA
Found at i:1998503 original size:16 final size:16
Alignment explanation
Indices: 1998482--1998519 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1998472 CTAACCCTAG
* *
1998482 CGCCTCTGCCTCCAGC
1 CGCCTCTGCCCCCAAC
1998498 CGCCTCTGCCCCCAAC
1 CGCCTCTGCCCCCAAC
1998514 CGCCTC
1 CGCCTC
1998520 AGCCAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.61, G:0.16, T:0.16
Consensus pattern (16 bp):
CGCCTCTGCCCCCAAC
Found at i:1999725 original size:13 final size:13
Alignment explanation
Indices: 1999707--1999746 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
1999697 TAGATATAAA
1999707 TAAATATTTATTT
1 TAAATATTTATTT
*
1999720 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1999734 T-AATATTTATTT
1 TAAATATTTATTT
1999746 T
1 T
1999747 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Done.