Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006564.1 Hibiscus syriacus cultivar Beakdansim tig00016065_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: 1886890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1529299 original size:40 final size:40
Alignment explanation
Indices: 1529255--1529336 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1529245 ACCGTAGTGC
1529255 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1529295 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1529335 TA
1 TA
1529337 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1536123 original size:47 final size:45
Alignment explanation
Indices: 1536053--1536178 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
1536043 TATAAAATCT
*
1536053 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1536098 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * **
1536145 CTTGCCA-TTATTCCGTAAGCTTATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1536179 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1536327 original size:40 final size:40
Alignment explanation
Indices: 1536283--1536364 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1536273 ACCGTAGTGC
1536283 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1536323 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1536363 TA
1 TA
1536365 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1542198 original size:30 final size:30
Alignment explanation
Indices: 1542142--1542199 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1542132 TATTTATTTA
* *
1542142 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
*
1542172 GTGAGCAAAGTATAAACTTT-GAAAAGTT
1 GTGACCAAAGTATAAA-TTTGGAAAAGTT
1542200 AAAGGACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:1547108 original size:62 final size:62
Alignment explanation
Indices: 1547027--1547155 Score: 233
Period size: 62 Copynumber: 2.1 Consensus size: 62
1547017 TGATGAAAAT
*
1547027 GAGGGTGTAACTGAAGATATTTCCATTGAACATGGGAACATAAATTTATAATGCAATGAACC
1 GAGGGTGTAACTGAAGATATTTCCATTGAACATGGGAACATAAATTCATAATGCAATGAACC
*
1547089 GAGGGTGTAACTGAAGATATTTCCATTGAACATGGGAACGTAAATTCATAATGCAATGAACC
1 GAGGGTGTAACTGAAGATATTTCCATTGAACATGGGAACATAAATTCATAATGCAATGAACC
1547151 -AGGGT
1 GAGGGT
1547156 AGCGAATAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 5 0.08
62 60 0.92
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.26
Consensus pattern (62 bp):
GAGGGTGTAACTGAAGATATTTCCATTGAACATGGGAACATAAATTCATAATGCAATGAACC
Found at i:1547441 original size:18 final size:19
Alignment explanation
Indices: 1547406--1547442 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1547396 CACGGAATGT
1547406 AAGATTACCAGCGGGAATAA
1 AAGATTACCA-CGGGAATAA
1547426 AAGATTACCA-GGGAATA
1 AAGATTACCACGGGAATA
1547443 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (19 bp):
AAGATTACCACGGGAATAA
Found at i:1553468 original size:23 final size:23
Alignment explanation
Indices: 1553416--1553469 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1553406 ATGAGGCGAA
* * *
1553416 CAACGAACATCGAGCTTAATGAG
1 CAACGAGCATCGAACTTAACGAG
1553439 CAACGAGCATCGAACTTAACGAG
1 CAACGAGCATCGAACTTAACGAG
1553462 CAACGAGC
1 CAACGAGC
1553470 TTAACGAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (23 bp):
CAACGAGCATCGAACTTAACGAG
Found at i:1553484 original size:16 final size:16
Alignment explanation
Indices: 1553440--1553484 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1553430 CTTAATGAGC
* *
1553440 AACGAGCATCGAACTT
1 AACGAGCAACGAGCTT
1553456 AACGAGCAACGAGCTT
1 AACGAGCAACGAGCTT
*
1553472 AACGAGTAACGAG
1 AACGAGCAACGAG
1553485 ACAAACAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (16 bp):
AACGAGCAACGAGCTT
Found at i:1564670 original size:35 final size:36
Alignment explanation
Indices: 1564625--1564770 Score: 171
Period size: 35 Copynumber: 4.2 Consensus size: 36
1564615 TTAATATGTG
* *
1564625 TCTTATAACTGTAAAA-CATCTGATATTTGTAAATA
1 TCTTATAACTGTAAAATCATATGATAATTGTAAATA
*
1564660 TCTTATAACTGT--AATC-TATGATATTTGTAAATA
1 TCTTATAACTGTAAAATCATATGATAATTGTAAATA
* *
1564693 TCTAATAACTG-AAAATCATCTGATAATTGTAAATA
1 TCTTATAACTGTAAAATCATATGATAATTGTAAATA
*
1564728 T-TTGATAACT-AAAAATCATATGATAATTGTAAATA
1 TCTT-ATAACTGTAAAATCATATGATAATTGTAAATA
*
1564763 TCTGATAA
1 TCTTATAA
1564771 AGGTGAAATG
Statistics
Matches: 97, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
33 28 0.29
34 6 0.06
35 62 0.64
36 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (36 bp):
TCTTATAACTGTAAAATCATATGATAATTGTAAATA
Found at i:1564718 original size:18 final size:17
Alignment explanation
Indices: 1564629--1564770 Score: 79
Period size: 17 Copynumber: 8.2 Consensus size: 17
1564619 TATGTGTCTT
*
1564629 ATAACTGTAAAACATCTG
1 ATAACTG-AAAATATCTG
** * *
1564647 ATATTTGTAAATATCTT
1 ATAACTGAAAATATCTG
* * *
1564664 ATAACTG-TAATCTATG
1 ATAACTGAAAATATCTG
** * *
1564680 ATATTTGTAAATATCTA
1 ATAACTGAAAATATCTG
1564697 ATAACTGAAAATCATCTG
1 ATAACTGAAAAT-ATCTG
* * *
1564715 ATAATTGTAAATATTTG
1 ATAACTGAAAATATCTG
* *
1564732 ATAACTAAAAATCATATG
1 ATAACTGAAAAT-ATCTG
* *
1564750 ATAATTGTAAATATCTG
1 ATAACTGAAAATATCTG
1564767 ATAA
1 ATAA
1564771 AGGTGAAATG
Statistics
Matches: 89, Mismatches: 32, Indels: 7
0.70 0.25 0.05
Matches are distributed among these distances:
16 10 0.11
17 47 0.53
18 32 0.36
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
ATAACTGAAAATATCTG
Found at i:1564723 original size:68 final size:70
Alignment explanation
Indices: 1564629--1564770 Score: 193
Period size: 68 Copynumber: 2.1 Consensus size: 70
1564619 TATGTGTCTT
* ** *
1564629 ATAACTGTAAAACATCTGATATTTGTAAATATCTT-ATAACT-GTAATC-TATGATATTTGTAAA
1 ATAACTGTAAAACATCTGATAATTGTAAATAT-TTGATAACTAAAAATCATATGATAATTGTAAA
1564691 TATCTA
65 TATCTA
1564697 ATAACTG-AAAATCATCTGATAATTGTAAATATTTGATAACTAAAAATCATATGATAATTGTAAA
1 ATAACTGTAAAA-CATCTGATAATTGTAAATATTTGATAACTAAAAATCATATGATAATTGTAAA
*
1564761 TATCTG
65 TATCTA
1564767 ATAA
1 ATAA
1564771 AGGTGAAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
67 6 0.09
68 32 0.49
69 4 0.06
70 23 0.35
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (70 bp):
ATAACTGTAAAACATCTGATAATTGTAAATATTTGATAACTAAAAATCATATGATAATTGTAAAT
ATCTA
Found at i:1565123 original size:2 final size:2
Alignment explanation
Indices: 1565116--1565141 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1565106 TTTCGTATTA
1565116 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
1565142 TGAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1570512 original size:51 final size:51
Alignment explanation
Indices: 1570445--1570559 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
1570435 GCAATTAATG
* * * * *
1570445 AATAAAATAACAATAAACTAAAGATAATGTTTTGACTCTATCTTAATTTCA
1 AATAAAATAATAATAAACTAAAGATAATATGTTGAATCTATCTTAATTCCA
* *
1570496 AATAATATAATAATAAACTAAAGATAATATGTTGAATCTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATGTTGAATCTATCTTAATTCCA
1570547 AATAAAATAATAA
1 AATAAAATAATAA
1570560 ATCAAATCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATATGTTGAATCTATCTTAATTCCA
Found at i:1577440 original size:20 final size:19
Alignment explanation
Indices: 1577412--1577450 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1577402 TAGTGAATAA
*
1577412 ATTTAATGAATTTAATTATT
1 ATTTAATG-ATTTAAATATT
*
1577432 ATTTGATGATTTAAATATT
1 ATTTAATGATTTAAATATT
1577451 TTATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
ATTTAATGATTTAAATATT
Found at i:1578586 original size:124 final size:125
Alignment explanation
Indices: 1578432--1578680 Score: 491
Period size: 124 Copynumber: 2.0 Consensus size: 125
1578422 ATAAAATCAC
1578432 TTATACATTGTCGTAATAGTGAAATTTGAAAATTCGAATCAATATTTAAAATTTTATCCTTTTAT
1 TTATACATTGTCGTAATAGTGAAATTTGAAAATTCGAATCAATATTTAAAATTTTATCCTTTTAT
1578497 TTTGAACATTGATAAATTTATTTCGAAATA-TTATTAAGGAACGTTCTCTATTTTGAGAA
66 TTTGAACATTGATAAATTTATTTCGAAATATTTATTAAGGAACGTTCTCTATTTTGAGAA
1578556 TTATACATTGTCGTAATAGTGAAATTTGAAAATTCGAATCAATATTTAAAATTTTATCCTTTTAT
1 TTATACATTGTCGTAATAGTGAAATTTGAAAATTCGAATCAATATTTAAAATTTTATCCTTTTAT
1578621 TTTGAACATTGATAAATTTATTTCGAAATATTTATTAAGGAACGTTCTCTATTTTGAGAA
66 TTTGAACATTGATAAATTTATTTCGAAATATTTATTAAGGAACGTTCTCTATTTTGAGAA
1578681 GAAACCATGG
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
124 95 0.77
125 29 0.23
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (125 bp):
TTATACATTGTCGTAATAGTGAAATTTGAAAATTCGAATCAATATTTAAAATTTTATCCTTTTAT
TTTGAACATTGATAAATTTATTTCGAAATATTTATTAAGGAACGTTCTCTATTTTGAGAA
Found at i:1581713 original size:60 final size:60
Alignment explanation
Indices: 1581643--1581768 Score: 234
Period size: 60 Copynumber: 2.1 Consensus size: 60
1581633 ATAATAAATG
*
1581643 ATTTGATTTTAAGAATCCGTGAATTTTGATAAAATTTCTTAAAGTTTAAATACTGGGATT
1 ATTTGGTTTTAAGAATCCGTGAATTTTGATAAAATTTCTTAAAGTTTAAATACTGGGATT
*
1581703 ATTTGGTTTTAAGAATCCGTGAATTTTGATAAATTTTCTTAAAGTTTAAATACTGGGATT
1 ATTTGGTTTTAAGAATCCGTGAATTTTGATAAAATTTCTTAAAGTTTAAATACTGGGATT
1581763 ATTTGG
1 ATTTGG
1581769 ATATGAAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (60 bp):
ATTTGGTTTTAAGAATCCGTGAATTTTGATAAAATTTCTTAAAGTTTAAATACTGGGATT
Found at i:1583439 original size:15 final size:15
Alignment explanation
Indices: 1583419--1583448 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1583409 AGCTTTCCAA
1583419 ATCTCACTCTGTTAC
1 ATCTCACTCTGTTAC
1583434 ATCTCACTCTGTTAC
1 ATCTCACTCTGTTAC
1583449 TCATTTTCAG
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:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
ATCTCACTCTGTTAC
Found at i:1583582 original size:17 final size:18
Alignment explanation
Indices: 1583547--1583586 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1583537 TAAATTTTAC
1583547 TTTTATATTTATAAATTG
1 TTTTATATTTATAAATTG
1583565 TTTTATGATTT-T-AATTG
1 TTTTAT-ATTTATAAATTG
1583582 TTTTA
1 TTTTA
1583587 ATAAAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 7 0.33
19 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTATATTTATAAATTG
Found at i:1590034 original size:18 final size:18
Alignment explanation
Indices: 1590011--1590047 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1590001 GCACAAGGTT
1590011 GCACCACAAGCCTTCCTA
1 GCACCACAAGCCTTCCTA
1590029 GCACCACAAGCCTTCCTA
1 GCACCACAAGCCTTCCTA
1590047 G
1 G
1590048 AACCCCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (18 bp):
GCACCACAAGCCTTCCTA
Found at i:1598512 original size:25 final size:25
Alignment explanation
Indices: 1598484--1598534 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1598474 ACATTCTGTT
*
1598484 TGCATTTTGGTTAAAAGA-TCGTAGC
1 TGCATTTTGCTTAAAA-ATTCGTAGC
1598509 TGCATTTTGCTTAAAAATTCGTAGC
1 TGCATTTTGCTTAAAAATTCGTAGC
1598534 T
1 T
1598535 CTTCAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (25 bp):
TGCATTTTGCTTAAAAATTCGTAGC
Found at i:1598843 original size:17 final size:19
Alignment explanation
Indices: 1598821--1598858 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1598811 AAAAGCTATG
1598821 AATGC-AAG-GAAAGAATT
1 AATGCAAAGAGAAAGAATT
*
1598838 AATGCAAAGATAAAGAATT
1 AATGCAAAGAGAAAGAATT
1598857 AA
1 AA
1598859 AAGAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.18
Consensus pattern (19 bp):
AATGCAAAGAGAAAGAATT
Found at i:1602970 original size:13 final size:13
Alignment explanation
Indices: 1602952--1602991 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1602942 CATAGGTGAA
1602952 CAGTCTTCATATG
1 CAGTCTTCATATG
* *
1602965 CAGTCTTCCTATA
1 CAGTCTTCATATG
1602978 CAGTCTTCATATG
1 CAGTCTTCATATG
1602991 C
1 C
1602992 GCGTCTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1610298 original size:18 final size:18
Alignment explanation
Indices: 1610275--1610311 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1610265 TACAGTGGAC
1610275 TACTCGAAGACCTTTGTT
1 TACTCGAAGACCTTTGTT
1610293 TACTCGAAGACCTTTGTT
1 TACTCGAAGACCTTTGTT
1610311 T
1 T
1610312 CAGGTGGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (18 bp):
TACTCGAAGACCTTTGTT
Found at i:1616262 original size:29 final size:29
Alignment explanation
Indices: 1616230--1616320 Score: 166
Period size: 29 Copynumber: 3.2 Consensus size: 29
1616220 TAATTAATGT
1616230 ATGTAGCAATACTTAAATAAACCAATGCA
1 ATGTAGCAATACTTAAATAAACCAATGCA
*
1616259 ATGTAGCAATACTTAAATAAACCAATGTA
1 ATGTAGCAATACTTAAATAAACCAATGCA
1616288 ATGTAGCAATACTT-AATAAACCAATGCA
1 ATGTAGCAATACTTAAATAAACCAATGCA
1616316 ATGTA
1 ATGTA
1616321 AATGCATGTA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
28 18 0.30
29 42 0.70
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.26
Consensus pattern (29 bp):
ATGTAGCAATACTTAAATAAACCAATGCA
Found at i:1620733 original size:3 final size:3
Alignment explanation
Indices: 1620725--1620768 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1620715 TGGGTTTTCT
*
1620725 ATA ATA AT- ATA AT- ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1620769 ATAGCACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1621555 original size:12 final size:12
Alignment explanation
Indices: 1621524--1621555 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1621514 ACAAAAGAGG
1621524 CTCTAAAA-TCC
1 CTCTAAAACTCC
1621535 CTC-AAAACTCC
1 CTCTAAAACTCC
1621546 CTCTAAAACT
1 CTCTAAAACT
1621556 TTCGGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.21
11 9 0.47
12 6 0.32
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (12 bp):
CTCTAAAACTCC
Found at i:1622849 original size:42 final size:41
Alignment explanation
Indices: 1622756--1622869 Score: 113
Period size: 42 Copynumber: 2.8 Consensus size: 41
1622746 ACATCCTACC
* * ** * *
1622756 CGAAGGACTTATGGATGGCCCGAAGGACTTATCATCTTGCT
1 CGAAAGACTTATAGATGAACCGAAGGACTTAGCATCATGCT
*
1622797 CGAAAGACTTATAGATGAACCGAAGGATTTAAGCATCATGCT
1 CGAAAGACTTATAGATGAACCGAAGGACTT-AGCATCATGCT
* **
1622839 TGAAAGACTTACT-GATGGCCCGAAGGACTTA
1 CGAAAGACTTA-TAGATGAACCGAAGGACTTA
1622870 CTTAGTAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 26 0.43
42 33 0.55
43 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (41 bp):
CGAAAGACTTATAGATGAACCGAAGGACTTAGCATCATGCT
Found at i:1623326 original size:239 final size:239
Alignment explanation
Indices: 1622734--1623350 Score: 817
Period size: 240 Copynumber: 2.6 Consensus size: 239
1622724 ACTCTTCGAC
* * * *
1622734 AATCATGTGGAAACATCCTACCCGAAGGACTTATGGATGGCCCGAAGGACTTATCATCTTGCTCG
1 AATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTACTCG
* *
1622799 AAAGACTTATAGATGAACCGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAG
66 AAAGACTTATAGATG-ACCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAG
* * * * **
1622864 GACTTACTTAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAGAAGTCAATTTTCAGAA
130 GACTTACTCAGTAAGAAACTTTAGAAATCGATTTCTTACTTTTCAAGAAAAAACAATTTTCAGAA
*
1622929 AATATTTAAAAGAGAAACTTTGGAAATCACATTCTCATTTTTGAA
195 AAGATTTAAAAGAGAAACTTTGGAAATCACATTCTCATTTTTGAA
* * * * *
1622974 AATCATGTGAAAACATCCTGCCCGAAGGTCTTAGGGATGTCCCAAAGTACTTATCATCTTACTTG
1 AATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTACTCG
* ** * * * *
1623039 AAAGACTTATAGATGACCCAAACAATATAAGCATCATGCTCAAAAGACTTATTGATAGCCCGAGG
66 AAAGACTTATAGATGA-CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAG
*
1623104 GACTTACTCAGTAAGAAATTTTAGAAATCGATTTCTTACTTTTCAAGAAAAAACAATTTTCAGAA
130 GACTTACTCAGTAAGAAACTTTAGAAATCGATTTCTTACTTTTCAAGAAAAAACAATTTTCAGAA
* *
1623169 AAGATTTAAATA-AG-AACTTTGGAAATCGCTTTCTCATTTTTGAA
195 AAGATTTAAA-AGAGAAACTTTGGAAATCACATTCTCATTTTTGAA
* * * * *
1623213 AATTATGTGAAAAAATCCCACCCGAAAGTCTTATGGATGGCCCAAAGGACTTATCATCTTTCTCG
1 AATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTACTCG
* * * * *
1623278 AAAAACTTATAAAAGACCGGAAGGATTTAAGCATCATACTCGAAAGACTTACTCAT-GACCCGAA
66 AAAGACTTATAGATGACC-GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAG-CCCGAA
*
1623342 GGACATACT
129 GGACTTACT
1623351 AATCAAGAAA
Statistics
Matches: 322, Mismatches: 51, Indels: 9
0.84 0.13 0.02
Matches are distributed among these distances:
238 3 0.01
239 139 0.43
240 179 0.56
241 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (239 bp):
AATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTACTCG
AAAGACTTATAGATGACCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAGG
ACTTACTCAGTAAGAAACTTTAGAAATCGATTTCTTACTTTTCAAGAAAAAACAATTTTCAGAAA
AGATTTAAAAGAGAAACTTTGGAAATCACATTCTCATTTTTGAA
Found at i:1623479 original size:57 final size:57
Alignment explanation
Indices: 1623352--1623632 Score: 282
Period size: 56 Copynumber: 4.9 Consensus size: 57
1623342 GGACATACTA
* * * * * * * * *
1623352 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAAACTTTCGTTTA-CAGTTATC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAA--TTCATTTAGAAATAATC
* * *
1623410 ATCAAGAAACCCCTAAAAATTAGGCTTAGATTCTTTAAAAATT-ATTTAGAAGTAATC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT-AAAATTCATTTAGAAATAATC
*
1623467 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCA-TTGGAAATAATC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTTAGAAATAATC
* * * **
1623523 ATTAAGAAACCCCAAAAAATCACGCTTAGCTTCTTTAAAATTCATCGA-AAATAATC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTTAGAAATAATC
* * * ** *
1623579 ATCAAGAAACCCATGAAATTCAGGCTTAGCTTCTTTGAAAGCTCATTTAAAAAT
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT-AAAATTCATTTAGAAAT
1623633 CGTCAAGAAC
Statistics
Matches: 188, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
56 99 0.53
57 51 0.27
58 34 0.18
59 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (57 bp):
ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTTAGAAATAATC
Found at i:1623533 original size:56 final size:56
Alignment explanation
Indices: 1623407--1623614 Score: 283
Period size: 56 Copynumber: 3.7 Consensus size: 56
1623397 GTTTACAGTT
* * * *
1623407 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGATTCTTTAAAAATT-ATTTAGAAGTA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT-AAAATTCA-TTGGAAATA
1623464 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTGGAAATA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTGGAAATA
* * * * *
1623520 ATCATTAAGAAACCCCAAAAAATCACGCTTAGCTTCTTTAAAATTCATCGAAAATA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTGGAAATA
* * *
1623576 ATCATCAAGAAACCCATGAAATTCAGGCTTAGCTTCTTT
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT
1623615 GAAAGCTCAT
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
56 97 0.72
57 38 0.28
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.29
Consensus pattern (56 bp):
ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAATTCATTGGAAATA
Found at i:1623668 original size:55 final size:55
Alignment explanation
Indices: 1623352--1623775 Score: 209
Period size: 56 Copynumber: 7.6 Consensus size: 55
1623342 GGACATACTA
** * **
1623352 ATCAAGAAACCCTTGAAAATCA-AGCTTAGTTTC-TTAAAAACTTTCGTTTACAGTTATC
1 ATCAAGAAACTTTTGAAAATCAGA-CTTAGTTTCTTTAAAAAC--TCATTTA-A-AAATC
*** * * * * *
1623410 ATCAAGAAACCCCTAAAAATTAGGCTTAGATTCTTTAAAAA-TTATTTAGAAGTAATC
1 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTA-AA--AATC
*** * * * * *
1623467 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT-AAAATTCATTGGAAATAATC
1 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCATT-TAAA-AATC
* ***** * * **
1623523 ATTAAGAAACCCCAAAAAATCACG-CTTAGCTTCTTT-AAAATTCATCGAAAATAATC
1 ATCAAGAAACTTTTGAAAATCA-GACTTAGTTTCTTTAAAAACTCAT-TTAAA-AATC
*** * * * * *
1623579 ATCAAGAAACCCATGAAATTCAGGCTTAGCTTCTTTGAAAGCTCATTTAAAAATC
1 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATC
* * * * *
1623634 GTCAAGAACCTTTTGATTATTCA-ACTTAGTTTCTTTAAAAACTCATTTGAAAATC
1 ATCAAGAAACTTTTGA-AAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATC
1623689 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTT-AAAAT-
1 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATC
* *** * *
1623742 ATAAAGAAACCCCTGAAAACCAGGCTTAGTTTCT
1 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCT
1623776 AAAAAATCGT
Statistics
Matches: 306, Mismatches: 48, Indels: 29
0.80 0.13 0.08
Matches are distributed among these distances:
53 28 0.09
54 9 0.03
55 82 0.27
56 101 0.33
57 51 0.17
58 28 0.09
59 7 0.02
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (55 bp):
ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATC
Found at i:1628121 original size:23 final size:23
Alignment explanation
Indices: 1628095--1628164 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1628085 CAGTCGAGGG
*
1628095 TTCTATGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* *
1628118 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAA
* *
1628141 TTCTACGCGGTACTTCAGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
1628164 T
1 T
1628165 ACTATGTAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:1629512 original size:24 final size:24
Alignment explanation
Indices: 1629479--1629524 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1629469 TTCGAGACAT
*
1629479 TTCTATGTGGCACTTCGATGCATA
1 TTCTACGTGGCACTTCGATGCATA
*
1629503 TTCTACGTGGCACTTCGGTGCA
1 TTCTACGTGGCACTTCGATGCA
1629525 ATTTATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (24 bp):
TTCTACGTGGCACTTCGATGCATA
Found at i:1629662 original size:18 final size:18
Alignment explanation
Indices: 1629641--1629675 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1629631 GAGCAGTGCA
1629641 TGATAATGATGATGATGT
1 TGATAATGATGATGATGT
1629659 TGATAATGATGATGATG
1 TGATAATGATGATGATG
1629676 ATATGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (18 bp):
TGATAATGATGATGATGT
Found at i:1629669 original size:15 final size:15
Alignment explanation
Indices: 1629649--1629678 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1629639 CATGATAATG
*
1629649 ATGATGATGTTGATA
1 ATGATGATGATGATA
1629664 ATGATGATGATGATA
1 ATGATGATGATGATA
1629679 TGTACATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (15 bp):
ATGATGATGATGATA
Found at i:1633276 original size:19 final size:18
Alignment explanation
Indices: 1633248--1633288 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1633238 AAAACCAGAA
*
1633248 CCCCAGGGGGTATCGATT
1 CCCCAGGGGGAATCGATT
*
1633266 CCCCAAGGGGGAATCGGTT
1 CCCC-AGGGGGAATCGATT
1633285 CCCC
1 CCCC
1633289 TTCAAAGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (18 bp):
CCCCAGGGGGAATCGATT
Found at i:1638791 original size:76 final size:75
Alignment explanation
Indices: 1638661--1638803 Score: 250
Period size: 76 Copynumber: 1.9 Consensus size: 75
1638651 CCGTTAAACA
* *
1638661 GGGGGGAATCGGTTCCCTCCGAGCATTCTGTTTTTCTTGGAGCCAAACCATTCAGGGGGGAATCG
1 GGGGGGAATCAGTTCCCTCCGAGCAATCTGTTTTTCTTGGAGCCAAACCATTCAGGGGGGAATCG
1638726 GTACCCCCTT
66 GTACCCCCTT
*
1638736 GGGGTGGAATCAGTTCCCTCTGAGCAATCTGTTTTTCTTGGAGCCAAACCATTCAGGGGGGAATC
1 GGGG-GGAATCAGTTCCCTCCGAGCAATCTGTTTTTCTTGGAGCCAAACCATTCAGGGGGGAATC
1638801 GGT
65 GGT
1638804 TCCCTCTGAG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
75 4 0.06
76 60 0.94
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (75 bp):
GGGGGGAATCAGTTCCCTCCGAGCAATCTGTTTTTCTTGGAGCCAAACCATTCAGGGGGGAATCG
GTACCCCCTT
Found at i:1642035 original size:2 final size:2
Alignment explanation
Indices: 1642028--1642106 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1642018 ATTTTAACAA
1642028 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
1642070 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
1642107 ACGTGCAAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1646785 original size:42 final size:42
Alignment explanation
Indices: 1646730--1646813 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
1646720 TTTCCTTTGG
*
1646730 CCAGCACAACTATTCTATCCATCATTTTGGTCATTTTCTCCC
1 CCAGCACAACTATTCTATCCATCATCTTGGTCATTTTCTCCC
*
1646772 CCAGCACAGCTATTCTATCCATCATCTTGGTCATTTTCTCCC
1 CCAGCACAACTATTCTATCCATCATCTTGGTCATTTTCTCCC
1646814 TTATTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (42 bp):
CCAGCACAACTATTCTATCCATCATCTTGGTCATTTTCTCCC
Found at i:1648300 original size:16 final size:16
Alignment explanation
Indices: 1648253--1648302 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
1648243 TGTATTGTTC
1648253 TACATGATCTATGTGT
1 TACATGATCTATGTGT
* *
1648269 TATATTTCATTCTATGTGT
1 TACA--TGA-TCTATGTGT
1648288 TACATGATCTATGTG
1 TACATGATCTATGTG
1648303 ATTATAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 2 0.07
19 12 0.44
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (16 bp):
TACATGATCTATGTGT
Found at i:1648329 original size:30 final size:30
Alignment explanation
Indices: 1648293--1648368 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
1648283 TGTGTTACAT
1648293 GATCTATGTGATTATAAGTTATATGAAAAC
1 GATCTATGTGATTATAAGTTATATGAAAAC
*
1648323 GATCTATGTGATTATAAGTTATATGAAAAT
1 GATCTATGTGATTATAAGTTATATGAAAAC
*
1648353 GATCTATGTGAATATA
1 GATCTATGTGATTATA
1648369 TGTCTATGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.38
Consensus pattern (30 bp):
GATCTATGTGATTATAAGTTATATGAAAAC
Found at i:1648503 original size:23 final size:23
Alignment explanation
Indices: 1648469--1648513 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1648459 GAGTCGAGTG
1648469 TTCTACGCGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
*
1648492 TTCTACGTGGTCCTTCGGGACA
1 TTCTACGCGGTCCTTCGGGACA
1648514 ATACTATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.27, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:1648528 original size:23 final size:23
Alignment explanation
Indices: 1648479--1648529 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1648469 TTCTACGCGG
* * *
1648479 TCCTTCGGGACATTTCTACGTGG
1 TCCTTCGGGACAATACTACGTGA
*
1648502 TCCTTCGGGACAATACTATGTGA
1 TCCTTCGGGACAATACTACGTGA
1648525 TCCTT
1 TCCTT
1648530 GTTGGAGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (23 bp):
TCCTTCGGGACAATACTACGTGA
Found at i:1650740 original size:15 final size:15
Alignment explanation
Indices: 1650717--1650761 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
1650707 GTGTAAAGGT
1650717 AAATGCAAATGCAAA
1 AAATGCAAATGCAAA
*
1650732 AATTGCAAATGCAAA
1 AAATGCAAATGCAAA
*
1650747 AAATACAAATGCAAA
1 AAATGCAAATGCAAA
1650762 TGCAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (15 bp):
AAATGCAAATGCAAA
Found at i:1670555 original size:16 final size:17
Alignment explanation
Indices: 1670530--1670563 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1670520 TATTAAGATC
*
1670530 AAAATAAAGTAATTAAA
1 AAAATAAAGTAAATAAA
1670547 AAAAT-AAGTAAATAAA
1 AAAATAAAGTAAATAAA
1670563 A
1 A
1670564 GGAATGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATAAAGTAAATAAA
Found at i:1671641 original size:14 final size:14
Alignment explanation
Indices: 1671606--1671647 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1671596 AATAAATCGA
*
1671606 AAAATAATTAATAAT
1 AAAATAATAAAT-AT
*
1671621 AATATAATAAATAT
1 AAAATAATAAATAT
1671635 AAAATAATAAATA
1 AAAATAATAAATA
1671648 ATACTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATAATAAATAT
Found at i:1671641 original size:29 final size:31
Alignment explanation
Indices: 1671606--1671674 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
1671596 AATAAATCGA
*
1671606 AAAATAATTAATAATAATAT-AATAA-ATAT
1 AAAATAATAAATAATAATATAAATAACATAT
*
1671635 AAAATAATAAATAATACTATAAATAACATAT
1 AAAATAATAAATAATAATATAAATAACATAT
*
1671666 AATATAATA
1 AAAATAATA
1671675 TGTACAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 18 0.51
30 5 0.14
31 12 0.34
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAATAATAAATAATAATATAAATAACATAT
Found at i:1671642 original size:19 final size:20
Alignment explanation
Indices: 1671618--1671675 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
1671608 AATAATTAAT
1671618 AATAATATAATAAATATA-A
1 AATAATATAATAAATATATA
1671637 AATAATA-AAT-AATACTATA
1 AATAATATAATAAATA-TATA
1671656 AATAACATATAATATAATAT
1 AAT-A-ATATAATA-AATAT
1671676 GTACAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.12
18 5 0.16
19 11 0.34
20 1 0.03
21 3 0.09
22 3 0.09
23 1 0.03
24 4 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATATAATAAATATATA
Found at i:1671656 original size:12 final size:11
Alignment explanation
Indices: 1671615--1671675 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
1671605 AAAAATAATT
1671615 AATAATA-ATA
1 AATAATATATA
1671625 TAATAA-ATAT-
1 -AATAATATATA
1671635 AA-AATA-ATA
1 AATAATATATA
1671644 AATAATACTATA
1 AATAATA-TATA
*
1671656 AATAACATATA
1 AATAATATATA
1671667 ATATAATAT
1 A-ATAATAT
1671676 GTACAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
8 4 0.10
9 5 0.12
10 5 0.12
11 12 0.29
12 15 0.37
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATATATA
Found at i:1671706 original size:20 final size:20
Alignment explanation
Indices: 1671681--1671749 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 20
1671671 AATATGTACA
1671681 ATATATTTATTTTAAAAACT
1 ATATATTTATTTTAAAAACT
1671701 ATATATTATATTTTCAAAAACT
1 ATATATT-TATTTT-AAAAACT
* *
1671723 ATATTATATACTTTCAAAAAACT
1 ATA-TATTTA-TTT-TAAAAACT
1671746 ATAT
1 ATAT
1671750 TATATACGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.17
21 6 0.14
22 13 0.31
23 16 0.38
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATTTATTTTAAAAACT
Found at i:1671719 original size:22 final size:22
Alignment explanation
Indices: 1671681--1671749 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
1671671 AATATGTACA
1671681 ATATATT-TATTTT-AAAAACT
1 ATATATTATATTTTCAAAAACT
1671701 ATATATTATATTTTCAAAAACT
1 ATATATTATATTTTCAAAAACT
*
1671723 ATAT-TATATACTTTCAAAAAACT
1 ATATAT-TATATTTTC-AAAAACT
1671746 ATAT
1 ATAT
1671750 TATATACGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
20 7 0.16
21 7 0.16
22 19 0.43
23 11 0.25
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATTATATTTTCAAAAACT
Found at i:1671767 original size:25 final size:23
Alignment explanation
Indices: 1671690--1671769 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 23
1671680 AATATATTTA
1671690 TTTT-AAAAACTATA-TATTATA-
1 TTTTCAAAAACTATATTA-TATAC
1671711 TTTTCAAAAACTATATTATATAC
1 TTTTCAAAAACTATATTATATAC
1671734 -TTTCAAAAAACTATATTATATAC
1 TTTTC-AAAAACTATATTATATAC
1671757 GTTTTTCAAAAAC
1 --TTTTCAAAAAC
1671770 CCTTTTTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.08
22 18 0.35
23 20 0.38
25 6 0.12
26 4 0.08
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.42
Consensus pattern (23 bp):
TTTTCAAAAACTATATTATATAC
Found at i:1671781 original size:38 final size:38
Alignment explanation
Indices: 1671738--1671917 Score: 176
Period size: 36 Copynumber: 4.8 Consensus size: 38
1671728 ATATACTTTC
*
1671738 AAAAAACTATAT-TATATACGTTTTTCAAAAACCCTTTTTA
1 AAAAAACTATATAT-TATACG-TTTTCAAAAA-CCATTTTA
*
1671778 AAAAAACTATATATTATACATTTTC-AAAACCATTTT-
1 AAAAAACTATATATTATACGTTTTCAAAAACCATTTTA
* *
1671814 AAAAAACTAAATATTATACGTTTTCAAAAA-TATTTTAAA
1 AAAAAACTATATATTATACGTTTTCAAAAACCATTTT--A
* * **
1671853 AAAAAACTATATTTTATATGTTTTC-AAAACTGTTTT-
1 AAAAAACTATATATTATACGTTTTCAAAAACCATTTTA
* *
1671889 -AAAAACTATATATTATACATTTTAAAAAA
1 AAAAAACTATATATTATACGTTTTCAAAAA
1671918 AAAAATATGT
Statistics
Matches: 120, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
35 20 0.17
36 32 0.27
37 10 0.08
38 8 0.07
39 32 0.27
40 17 0.14
41 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (38 bp):
AAAAAACTATATATTATACGTTTTCAAAAACCATTTTA
Found at i:1671856 original size:75 final size:75
Alignment explanation
Indices: 1671738--1671917 Score: 213
Period size: 75 Copynumber: 2.4 Consensus size: 75
1671728 ATATACTTTC
* *
1671738 AAAAAACTATAT-TATATACGTTTTTCAAAAACCCTTTTTAAAAAAACTATATATTATACATTTT
1 AAAAAACTATATAT-TATACG-TTTTCAAAAACCATTTTAAAAAAAACTATATATTATACATTTT
1671802 CAAAACCATTTT
64 CAAAACCATTTT
* * * **
1671814 AAAAAACTAAATATTATACGTTTTCAAAAA-TATTTTAAAAAAAAACTATATTTTATATGTTTTC
1 AAAAAACTATATATTATACGTTTTCAAAAACCATTTT-AAAAAAAACTATATATTATACATTTTC
**
1671878 AAAACTGTTTT
65 AAAACCATTTT
* *
1671889 -AAAAACTATATATTATACATTTTAAAAAA
1 AAAAAACTATATATTATACGTTTTCAAAAA
1671918 AAAAATATGT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
74 30 0.33
75 42 0.47
76 17 0.19
77 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (75 bp):
AAAAAACTATATATTATACGTTTTCAAAAACCATTTTAAAAAAAACTATATATTATACATTTTCA
AAACCATTTT
Found at i:1673220 original size:24 final size:24
Alignment explanation
Indices: 1673166--1673220 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1673156 GCAATTATTC
* *
1673166 ATTCAAAAGATGTGACCTTATGAG
1 ATTCAAAAGACGTGACCTCATGAG
**
1673190 AACCAAAAGACGTGA-CTCATGAAG
1 ATTCAAAAGACGTGACCTCATG-AG
1673214 ATTCAAA
1 ATTCAAA
1673221 GGGTGTGCCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (24 bp):
ATTCAAAAGACGTGACCTCATGAG
Found at i:1673347 original size:14 final size:14
Alignment explanation
Indices: 1673328--1673378 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1673318 AACATATTCA
1673328 TTCAAAACAATGTC
1 TTCAAAACAATGTC
* *
1673342 TTCAAAAGACATGAC
1 TTCAAAACA-ATGTC
*
1673357 TTGTAAAACAATGTC
1 TT-CAAAACAATGTC
1673372 TTCAAAA
1 TTCAAAA
1673379 GACATGACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 12 0.41
15 12 0.41
16 5 0.17
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (14 bp):
TTCAAAACAATGTC
Found at i:1673367 original size:30 final size:30
Alignment explanation
Indices: 1673331--1673390 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1673321 ATATTCATTC
1673331 AAAACAATGTCTTCAAAAGACATGACTTGT
1 AAAACAATGTCTTCAAAAGACATGACTTGT
1673361 AAAACAATGTCTTCAAAAGACATGACTTGT
1 AAAACAATGTCTTCAAAAGACATGACTTGT
1673391 GACCATCCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (30 bp):
AAAACAATGTCTTCAAAAGACATGACTTGT
Found at i:1678951 original size:57 final size:57
Alignment explanation
Indices: 1678863--1679030 Score: 300
Period size: 57 Copynumber: 2.9 Consensus size: 57
1678853 GGCAATTCTT
* *
1678863 GATTTTGTCGCGAAATTAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
*
1678920 GATTTTCTTGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
*
1678977 GATTTTCTCGCGAAATCAGTTTGGTGTATCGAACCAGACTGACGTTCTGCTGCA
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCA
1679031 ACCATGAATT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 106 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (57 bp):
GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
Found at i:1682053 original size:168 final size:167
Alignment explanation
Indices: 1681760--1682096 Score: 620
Period size: 168 Copynumber: 2.0 Consensus size: 167
1681750 CAAATTGAGG
* * *
1681760 GACTGATAGCAAATGTTTTCGTATGTCTAGAGCATGTAGCATATTTTGTAGATACAAAGGCTTAG
1 GACTGATAACAAATATTTTCGTATGCCTAGAGCATGTAGCATATTTTGTAGATACAAAGGCTTAG
*
1681825 ACAACGTGTGCAAACTATCTTGACCAACATGAGTAATAAGAACACTAACACCGTTACCCATAAGC
66 ACAACGTGTGCAAACTACCTTGACCAACATGAGTAATAAGAACACTAACACCGTTACCCATAAGC
1681890 AAAAAATTATTACCTGTGTAAACTTGATCTGTTTTGA
131 AAAAAATTATTACCTGTGTAAACTTGATCTGTTTTGA
1681927 GACTGATAACAAAATATTTTCGTATGCCTAGAGCATGTAGCATATTTTGTAGATACAAAGGCTTA
1 GACTGATAAC-AAATATTTTCGTATGCCTAGAGCATGTAGCATATTTTGTAGATACAAAGGCTTA
*
1681992 GACAACGTGTGCAAACTACCTTTACCAACATGAGTAATAAGAACACTAACACCGTTACCCATAAG
65 GACAACGTGTGCAAACTACCTTGACCAACATGAGTAATAAGAACACTAACACCGTTACCCATAAG
1682057 CAAAAAATTATTACCTGTGTAAACTTGATCTGTTTTGA
130 CAAAAAATTATTACCTGTGTAAACTTGATCTGTTTTGA
1682095 GA
1 GA
1682097 TTTGAACGGT
Statistics
Matches: 164, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
167 9 0.05
168 155 0.95
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (167 bp):
GACTGATAACAAATATTTTCGTATGCCTAGAGCATGTAGCATATTTTGTAGATACAAAGGCTTAG
ACAACGTGTGCAAACTACCTTGACCAACATGAGTAATAAGAACACTAACACCGTTACCCATAAGC
AAAAAATTATTACCTGTGTAAACTTGATCTGTTTTGA
Found at i:1684448 original size:314 final size:313
Alignment explanation
Indices: 1683875--1684515 Score: 1088
Period size: 314 Copynumber: 2.0 Consensus size: 313
1683865 CTAACCTTTG
*
1683875 AGAATTTTTTTCTAAATCCCTAAATTAATTTTAGTGTCCAATTTGAAAATACTCCAAAACTTGTT
1 AGAAATTTTTTCTAAATCCCTAAATTAATTTTAGTGTCCAATTTGAAAATACTCCAAAACTTGTT
* *
1683940 ATCAGATTCGAAAGCCCTAGAAAGATCAGTGATCAACTGATAATTATACCAAAAATTTCTTTAAA
66 ATCAGATTCGAAAGCCCTAGAAAGATCAGTGATCAACAGATAATTATACCAAAAAATTCTTTAAA
** *
1684005 TCCTATTCTAACCCTTCTTTCTTCTTCGCAGCCGCTTCTTCTTCCTTTTATTTCTTTTCTTCATG
131 TCCTATTCTAACCCTTCTTTCTTCCCCGCAACCGCTTCTTCTTCCTTTTATTTCTTTTCTTCATG
*
1684070 AACAAAAGTTCGAATGAAACCCAGAAAATAGAACTGAAAGACGGAACCGAAGAGACAAGTAGTAT
196 AACAAAAGTTCGAATGAAACCCAGAAAATAGAACTGAAAGACGAAACCGAAGAGACAAGTAGTAT
* * * *
1684135 TACCATGGAGATGAGAAGCAACGGACCCACGGGAAGATAACTGAAATACGTCA
261 TACCATGGAGACGAGAAGCAAAGGACCCACGAGAAGAGAACTGAAATACGTCA
1684188 AGAAATTTTTTCTAAATCCCTAAATTAATTTTAGTGTCCAATTTGAAAATACTCCAAAACTTTGT
1 AGAAATTTTTTCTAAATCCCTAAATTAATTTTAGTGTCCAATTTGAAAATACTCCAAAAC-TTGT
*
1684253 TA-CTAGATTCGAAAGCCCTAGAAAGATCAG-GTATCAACAGGTAATTATACCAAAAAATTCTTT
65 TATC-AGATTCGAAAGCCCTAGAAAGATCAGTG-ATCAACAGATAATTATACCAAAAAATTCTTT
*
1684316 AAATCCTATTCTAACCCTTCTTTCTTCCCCGCAACCGCTTCTTCTTCCTTTTATTTCTTTTCTTT
128 AAATCCTATTCTAACCCTTCTTTCTTCCCCGCAACCGCTTCTTCTTCCTTTTATTTCTTTTCTTC
* **
1684381 ATGAACAAAAGTTCGAATGAAACCCAGAAAATAGAACTGAAAGACGAAACCGAGGAGACTGGTAG
193 ATGAACAAAAGTTCGAATGAAACCCAGAAAATAGAACTGAAAGACGAAACCGAAGAGACAAGTAG
1684446 TATTACCATGGAGACGAGAAGCAAAGGACCCACGAGAAGAGAACTGAAATACGTCA
258 TATTACCATGGAGACGAGAAGCAAAGGACCCACGAGAAGAGAACTGAAATACGTCA
1684502 AGAAATCTTTTTCT
1 AGAAAT-TTTTTCT
1684516 TTCCTTTGGT
Statistics
Matches: 308, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
313 61 0.20
314 240 0.78
315 7 0.02
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (313 bp):
AGAAATTTTTTCTAAATCCCTAAATTAATTTTAGTGTCCAATTTGAAAATACTCCAAAACTTGTT
ATCAGATTCGAAAGCCCTAGAAAGATCAGTGATCAACAGATAATTATACCAAAAAATTCTTTAAA
TCCTATTCTAACCCTTCTTTCTTCCCCGCAACCGCTTCTTCTTCCTTTTATTTCTTTTCTTCATG
AACAAAAGTTCGAATGAAACCCAGAAAATAGAACTGAAAGACGAAACCGAAGAGACAAGTAGTAT
TACCATGGAGACGAGAAGCAAAGGACCCACGAGAAGAGAACTGAAATACGTCA
Found at i:1685511 original size:5 final size:5
Alignment explanation
Indices: 1685118--1685493 Score: 262
Period size: 5 Copynumber: 73.6 Consensus size: 5
1685108 TTTTTTAGTA
* *
1685118 TATAA TATAT TATA- TAGTAT ATATATT GTATAT TATA- TAT-T AATAT
1 TATAT TATAT TATAT TA-TAT -TATA-T -TATAT TATAT TATAT TATAT
* *
1685164 CATAT TATA- TA-GT TATAT TAT-T TAGTAT ATATAT TATAT AGTATAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT -TATAT TATAT --TATAT
* * * *
1685210 TATAA TATAT ATATAT ATATAT ATAGAT TATAT TTTA- TATAC TATTAT
1 TATAT TATAT -TATAT -TATAT -TATAT TATAT TATAT TATAT TA-TAT
* *
1685258 TATA- TAT-T ATATAT TATA- TAT-T ATATAT TATA- TGTAT TATAT AATAT
1 TATAT TATAT -TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT
* * * * * *
1685305 ACATAGT T-TATT ATATAT TATAT T-TGTT TGTAG TATATT TATTT TAAAT
1 -TATA-T TATA-T -TATAT TATAT TAT-AT TATAT TATA-T TATAT TATAT
* *
1685354 TATA- TATGT TATAG TATA- TATAT ATATAT ATATAT ATATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT -TATAT -TATAT -TATAT -TATAT
1685401 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1685451 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1685494 TTCATGTCCA
Statistics
Matches: 306, Mismatches: 32, Indels: 66
0.76 0.08 0.16
Matches are distributed among these distances:
4 34 0.11
5 194 0.63
6 61 0.20
7 17 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:1686764 original size:21 final size:20
Alignment explanation
Indices: 1686729--1686774 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1686719 TTTTATTTCT
* *
1686729 ATTTTTATTATTTCTTTTAG
1 ATTTTTATTAATTCTTTTAA
1686749 ATTTTATATTAATTCTTTTAA
1 ATTTT-TATTAATTCTTTTAA
1686770 ATTTT
1 ATTTT
1686775 CTTTTATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTATTAATTCTTTTAA
Found at i:1687834 original size:29 final size:29
Alignment explanation
Indices: 1687795--1687924 Score: 117
Period size: 31 Copynumber: 4.5 Consensus size: 29
1687785 AAATGTACGT
*
1687795 ATAATAT--TATTAATAATTAAATATAGA
1 ATAATATAATATTAATAATTAAATATATA
* * *
1687822 ATAATATAATATTATTAA-CAATTA-ATA
1 ATAATATAATATTAATAATTAAATATATA
* *
1687849 AT-ATAATAATATTTTATATATGAAATATATA
1 ATAAT-ATAATA-TTAATA-ATTAAATATATA
*
1687880 ATAATATATTATTAATAATTAAATATATATA
1 ATAATATAATATTAATAATT-AA-ATATATA
1687911 ATAATATAATATTA
1 ATAATATAATATTA
1687925 TTTTATATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.02
27 17 0.21
28 8 0.10
29 11 0.14
30 11 0.14
31 30 0.37
32 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (29 bp):
ATAATATAATATTAATAATTAAATATATA
Found at i:1687882 original size:34 final size:34
Alignment explanation
Indices: 1687844--1687937 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 34
1687834 TATTAACAAT
*
1687844 TAATAATATAATAATATTTTATATATGAA-ATATA
1 TAATAATATAAT-ATATTTTATATATAAATATATA
*
1687878 TAATAATAT-AT-TA-TTAATA-ATTAAATATATA
1 TAATAATATAATATATTTTATATA-TAAATATATA
1687909 TAATAATATAATATTATTTTATATATAAA
1 TAATAATATAATA-TATTTTATATATAAA
1687938 AAATCCCTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
29 1 0.02
30 8 0.16
31 16 0.32
32 2 0.04
33 2 0.04
34 11 0.22
35 9 0.18
36 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
TAATAATATAATATATTTTATATATAAATATATA
Found at i:1688647 original size:50 final size:50
Alignment explanation
Indices: 1688569--1688698 Score: 219
Period size: 50 Copynumber: 2.6 Consensus size: 50
1688559 AACGACCGGT
*
1688569 TTTTTTA-CCGGATTAAAAACCGGTTTTTTTCAAACCGGATAAAAAACTGG
1 TTTTTTATCCGGATAAAAAACCGG-TTTTTTCAAACCGGATAAAAAACTGG
1688619 TTTTTTATCCGGATAAAAAACCGGTTTTTTCAAACCGGATAAAAAACTGG
1 TTTTTTATCCGGATAAAAAACCGGTTTTTTCAAACCGGATAAAAAACTGG
1688669 TTTTTTATCCGGA-AAAAAATCCGGTTTTTT
1 TTTTTTATCCGGATAAAAAA-CCGGTTTTTT
1688699 AAAAAAAAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
49 6 0.08
50 56 0.73
51 15 0.19
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (50 bp):
TTTTTTATCCGGATAAAAAACCGGTTTTTTCAAACCGGATAAAAAACTGG
Found at i:1688699 original size:24 final size:24
Alignment explanation
Indices: 1688563--1688699 Score: 152
Period size: 24 Copynumber: 5.5 Consensus size: 24
1688553 AAATTGAACG
*
1688563 ACCGGTTTTTT-TACCGGATTAAAA
1 ACCGGTTTTTTAT-CCGGATAAAAA
*
1688587 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGG-TTTTTT--ATCCGGATAAAAA
*
1688614 ACTGGTTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTATCCGGATAAAAA
*
1688638 ACCGGTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTT--ATCCGGATAAAAA
*
1688664 ACTGGTTTTTTATCCGGA-AAAAA
1 ACCGGTTTTTTATCCGGATAAAAA
1688687 ATCCGGTTTTTTA
1 A-CCGGTTTTTTA
1688700 AAAAAAAAAC
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
23 6 0.06
24 43 0.44
25 6 0.06
26 28 0.29
27 14 0.14
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (24 bp):
ACCGGTTTTTTATCCGGATAAAAA
Found at i:1688706 original size:20 final size:20
Alignment explanation
Indices: 1688681--1688718 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1688671 TTTTATCCGG
*
1688681 AAAAAAATCCGGTTTTTTAA
1 AAAAAAAACCGGTTTTTTAA
1688701 AAAAAAAACCGGTTTTTT
1 AAAAAAAACCGGTTTTTT
1688719 GCAAACCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
AAAAAAAACCGGTTTTTTAA
Found at i:1696161 original size:21 final size:21
Alignment explanation
Indices: 1696110--1696162 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1696100 ATTATGACTA
1696110 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1696131 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1696152 TCGCAATGCGA
1 TCGCAATGCGA
1696163 ATATGGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1696176 original size:21 final size:21
Alignment explanation
Indices: 1696152--1696196 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1696142 TTTTCCCAAT
*
1696152 TCGCAATGCGAATATGGTAAA
1 TCGCAATGCGAATATGGAAAA
*
1696173 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATATGGAAAA
1696194 TCG
1 TCG
1696197 TAACGCGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATATGGAAAA
Found at i:1696217 original size:41 final size:41
Alignment explanation
Indices: 1696190--1696327 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
1696180 GCGAATTTGG
* *
1696190 AAAATCGTAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
1696231 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
1696271 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1696312 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1696328 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1696221 original size:20 final size:20
Alignment explanation
Indices: 1696193--1696307 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1696183 AATTTGGAAA
* *
1696193 ATCGTAACGCGGTACTGACT
1 ATCGCAACGCGATACTGACT
* *
1696213 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1696234 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
1696254 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
1696274 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1696294 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1696308 ATACATAATC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.03
20 57 0.75
21 15 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1696528 original size:22 final size:22
Alignment explanation
Indices: 1696500--1696543 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1696490 CACTCTCTCA
1696500 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
1696522 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1696544 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1697055 original size:25 final size:24
Alignment explanation
Indices: 1697001--1697055 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1696991 TGTTTATTAT
* *
1697001 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1697025 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1697051 TGTTT
1 TGTTT
1697056 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1698206 original size:18 final size:18
Alignment explanation
Indices: 1698185--1698232 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1698175 TCCACTTCGG
1698185 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1698203 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1698221 GAGCCATCACCT
1 GAGCCATCACCT
1698233 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1698827 original size:19 final size:20
Alignment explanation
Indices: 1698773--1698839 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1698763 TAGTTTACTT
* *
1698773 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1698793 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1698813 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1698832 TCGCAACG
1 TCGCAACG
1698840 ACAAAATTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1698870 original size:19 final size:19
Alignment explanation
Indices: 1698773--1698896 Score: 105
Period size: 19 Copynumber: 6.7 Consensus size: 19
1698763 TAGTTTACTT
* **
1698773 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1698793 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1698813 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1698832 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* *
1698846 TTGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1698865 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1698884 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1698897 AGCGATTTTC
Statistics
Matches: 87, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.54
20 24 0.28
21 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1698922 original size:19 final size:19
Alignment explanation
Indices: 1698898--1698954 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
1698888 AACGCGAAAA
1698898 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
*
1698917 GCGA-TTT--TGTCG--TT
1 GCGATTTTCATTTCGCATT
1698931 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
1698950 GCGAT
1 GCGAT
1698955 AGCCATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 4 0.13
17 4 0.13
18 3 0.10
19 11 0.35
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATT
Found at i:1698966 original size:20 final size:20
Alignment explanation
Indices: 1698941--1698993 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1698931 GCGATTTTCA
*
1698941 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
1698961 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
1698981 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
1698994 AAGTAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1699004 original size:20 final size:20
Alignment explanation
Indices: 1698961--1699019 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1698951 CGATAGCCAT
* * *
1698961 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTAAG
1698981 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
**
1699001 TTTCATGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
1699020 ACTATTCTTC
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:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:1699446 original size:41 final size:42
Alignment explanation
Indices: 1699356--1699446 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
1699346 CCCGATTCAC
* * *
1699356 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* * *
1699398 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTTAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
1699439 CTGTCATC
1 CTGTCATC
1699447 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 22 0.52
42 20 0.48
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:1700890 original size:14 final size:14
Alignment explanation
Indices: 1700856--1700894 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1700846 TTGATTGTTT
1700856 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1700870 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1700884 TGTTGATTTGT
1 AATTGATTTGT
1700895 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1701053 original size:19 final size:19
Alignment explanation
Indices: 1701031--1701117 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
1701021 ATCGCAACGA
*
1701031 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCGAAAT
1701050 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1701069 AAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1701088 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1701102 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1701118 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
16 2 0.03
17 2 0.03
19 46 0.74
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1701116 original size:33 final size:33
Alignment explanation
Indices: 1701021--1701117 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 33
1701011 GAAACTGACT
*
1701021 ATCGCAACGAGAAAATCGCAATGCAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
*
1701054 ATCGCAATGCGAAATAAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
1701092 ATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGAGAAAATCGCAATGCGA
1701118 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
33 22 0.39
34 1 0.02
35 2 0.04
36 2 0.04
37 1 0.02
38 28 0.50
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1701161 original size:20 final size:20
Alignment explanation
Indices: 1701144--1701251 Score: 121
Period size: 20 Copynumber: 5.4 Consensus size: 20
1701134 CGATTTTCTA
1701144 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
** *
1701164 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGTCATTTTCGC
* *
1701184 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
* *
1701204 GTTGCGATAGCCATTTTTGC
1 GTTGCGATAGTCATTTTCGC
1701224 GTTGCGATA-TCCATTTTCGC
1 GTTGCGATAGT-CATTTTCGC
1701244 GTTGCGAT
1 GTTGCGAT
1701252 TTCCCCGTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 66 0.90
21 4 0.05
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:1701568 original size:20 final size:21
Alignment explanation
Indices: 1701521--1701572 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1701511 ATAGTCAGTA
*
1701521 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
1701542 TCACATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1701562 TCGCATTGCGA
1 TCGCATTGCGA
1701573 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1701788 original size:12 final size:12
Alignment explanation
Indices: 1701769--1701802 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1701759 CTCTCCGGCG
1701769 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1701781 ATATCCGTTCCT
1 ACATCCGTTCCT
1701793 ACATCC-TTCC
1 ACATCCGTTCC
1701803 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1702384 original size:24 final size:24
Alignment explanation
Indices: 1702357--1702410 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1702347 GTATTCGAAA
*
1702357 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1702381 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1702405 TTTGAT
1 TTTGAT
1702411 GATGTTTCAG
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:1702602 original size:12 final size:12
Alignment explanation
Indices: 1702585--1702609 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1702575 ATATAATCCT
1702585 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1702597 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1702609 G
1 G
1702610 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1704919 original size:39 final size:33
Alignment explanation
Indices: 1704896--1704958 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1704886 GGAAATTACT
*
1704896 ATCGCAATGCAAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCAAAATGAAAATCGCAACGCGGGA
*
1704929 ATCGCAATGCGAAATGAAAATCGCAACGCG
1 ATCGCAATGCAAAATGAAAATCGCAACGCG
1704959 AATTTAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCAAAATGAAAATCGCAACGCGGGA
Found at i:1704952 original size:19 final size:19
Alignment explanation
Indices: 1704896--1704960 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
1704886 GGAAATTACT
*
1704896 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1704915 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1704929 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1704948 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1704961 TTTAGTTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 21 0.60
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1704998 original size:19 final size:19
Alignment explanation
Indices: 1704956--1705032 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
1704946 AAATCGCAAC
* *
1704956 GCGAATTTAGTTTCACGTT
1 GCGATTTTAGTTTCGCGTT
1704975 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1704994 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
1705008 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
1705027 GCGATT
1 GCGATT
1705033 CTCTCGTTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1705013 original size:33 final size:33
Alignment explanation
Indices: 1704971--1705097 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1704961 TTTAGTTTCA
* *
1704971 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTGCGATTCTCT
1705004 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1705037 CGTTACGATTTTCATTTCGCGTTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1705070 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
1705098 AGTACTTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
33 84 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1705094 original size:19 final size:19
Alignment explanation
Indices: 1705006--1705097 Score: 60
Period size: 19 Copynumber: 5.4 Consensus size: 19
1704996 GATTTTGTCG
*
1705006 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
1705025 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
* *
1705039 TTACGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
* *
1705058 TTGTGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
1705072 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1705091 TTGCGAT
1 TTGCGAT
1705098 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
14 13 0.24
16 10 0.19
17 10 0.19
19 21 0.39
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1707075 original size:91 final size:90
Alignment explanation
Indices: 1706906--1707090 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1706896 ATTTCAAACT
* * *
1706906 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATT--A-AATAAACAGTTTAGC
1706971 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1706999 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTATT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTATTAAATAAACAGTTTAGCA
*
1707063 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1707090 T
1 T
1707091 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.49
93 19 0.22
95 25 0.29
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1708805 original size:20 final size:20
Alignment explanation
Indices: 1708775--1708834 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1708765 CTTTTGGTTG
1708775 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* * *
1708795 TAATGAGAATCGCAACGCGA
1 AAATGAAAATCGCAACGAGA
** *
1708815 AAATGACTATCACAACGAGA
1 AAATGAAAATCGCAACGAGA
1708835 GAATCGCAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:1708856 original size:33 final size:33
Alignment explanation
Indices: 1708799--1708961 Score: 245
Period size: 33 Copynumber: 4.9 Consensus size: 33
1708789 ACGAGATAAT
** *
1708799 GAGAATCGCAACGCGAAAATGACTATCACAACGA
1 GAGAATCGCAACGCG-AAATGAAAATCGCAACGA
* * **
1708833 GAGAATCGCAACACAAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
1708866 GAGAATCGCAACGCGAAATGAAAATCGCAATGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1708899 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1708932 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1708962 TGCGATTTTG
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 107 0.89
34 13 0.11
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1708875 original size:14 final size:14
Alignment explanation
Indices: 1708856--1708944 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
1708846 CAAAATGACT
1708856 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1708870 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
1708889 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
*
1708903 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1708922 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1708936 ATCGCAACG
1 ATCGCAACG
1708945 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 29 0.49
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1708893 original size:19 final size:19
Alignment explanation
Indices: 1708869--1708966 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1708859 GCAACGAGAG
1708869 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1708888 AATCGCAA--TG--A-GAG
1 AATCGCAACGCGAAATGAA
1708902 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1708921 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1708935 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1708954 AATCGCAATGCGA
1 AATCGCAACGCGA
1708967 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1708995 original size:19 final size:19
Alignment explanation
Indices: 1708962--1709006 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1708952 AAAATCGCAA
**
1708962 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1708981 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1709000 TGCGATT
1 TGCGATT
1709007 CTCTCGTTGC
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:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1709386 original size:22 final size:22
Alignment explanation
Indices: 1709358--1709413 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
1709348 TTTCGCCGGC
1709358 GATGGGGACGGAAATCTTCGGA
1 GATGGGGACGGAAATCTTCGGA
1709380 GATGGGGACGGAAATCTTCGGA
1 GATGGGGACGGAAATCTTCGGA
1709402 GATGGGGACGGA
1 GATGGGGACGGA
1709414 TTTCGTCGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.45, T:0.16
Consensus pattern (22 bp):
GATGGGGACGGAAATCTTCGGA
Found at i:1709608 original size:20 final size:20
Alignment explanation
Indices: 1709583--1709694 Score: 64
Period size: 20 Copynumber: 5.5 Consensus size: 20
1709573 GCTATGTAAA
1709583 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* * *
1709603 TCGCATTACGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
1709623 TCGCATTGCGATTTTCCTACT
1 TCGCATTGCGATGTAAGTA-T
* ** *
1709644 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
1709664 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
*
1709684 TCGCGTTGCGA
1 TCGCATTGCGA
1709695 ATTATGAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.73
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:1709648 original size:21 final size:20
Alignment explanation
Indices: 1709601--1709694 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
1709591 CGATAGTAAG
* *
1709601 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
1709621 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
*
1709641 ACTTCGCATTGCGATTTACTT
1 A-TTCGCATTGCGATTTACCT
* * *
1709662 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
1709682 ATTCGCGTTGCGA
1 ATTCGCATTGCGA
1709695 ATTATGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:1709656 original size:41 final size:40
Alignment explanation
Indices: 1709601--1709694 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
1709591 CGATAGTAAG
* * *
1709601 ATTCGCATTACGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
1709641 ACTTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 A-TTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
*
1709682 ATTCGCGTTGCGA
1 ATTCGCATTGCGA
1709695 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
40 12 0.26
41 34 0.74
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:1709715 original size:21 final size:21
Alignment explanation
Indices: 1709691--1709746 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1709681 TATTCGCGTT
*
1709691 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
1709712 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
1709732 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
1709747 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:1709755 original size:21 final size:21
Alignment explanation
Indices: 1709690--1709756 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1709680 GTATTCGCGT
*
1709690 TGCGAATTATGAAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* *
1709711 CGCGAA-TACGTAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* * *
1709731 TGCGAATTAGGAAAATTGCAT
1 TGCGAATTACGAAAATCGCAA
1709752 TGCGA
1 TGCGA
1709757 TAGTCAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCGAATTACGAAAATCGCAA
Found at i:1715728 original size:3 final size:3
Alignment explanation
Indices: 1715720--1715758 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1715710 ATACTACGTA
1715720 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1715759 GTGATTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1716169 original size:140 final size:140
Alignment explanation
Indices: 1716004--1716306 Score: 412
Period size: 140 Copynumber: 2.2 Consensus size: 140
1715994 ATTAGATGGG
* * * *
1716004 TTTTTAATTTGGTCATCGCTTTTGCTTGTTATTTTATTTTAATTATTCGATTCAATAAA-TGAGT
1 TTTTTAATTTGGTCCTCGCTTTTGCTCGATATTTCATTTTAATTATTCGATTCAATAAATTG-GT
* *** * *
1716068 TTAAATTGACTAGGTTAATAATTAGAGCCTCTACTTTAGGCTTAATTTTATACTTAGTCCTTTAA
65 TAAAACCAACTAAGTTAATAATTAGAGCCTCTACTTTAGGCTTAATTTTAAACTTAGTCCTTTAA
* *
1716133 TTT-AGGGGAA
130 TTTAAGAGAAA
*
1716143 TTTTTAAATTTGGTCCTCGCTTTTGCTCGATATTTCATTTTAATTATTTGATTCAATAAATTGGT
1 TTTTT-AATTTGGTCCTCGCTTTTGCTCGATATTTCATTTTAATTATTCGATTCAATAAATTGGT
* * *
1716208 TAAAACCAATTAAGTTAATAATTAGAGCCTTTACTTTAGGTTTAATTTTAAACTTAGTCCTTTAA
65 TAAAACCAACTAAGTTAATAATTAGAGCCTCTACTTTAGGCTTAATTTTAAACTTAGTCCTTTAA
1716273 TTTAAGAGAAA
130 TTTAAGAGAAA
* *
1716284 TTTTTTATTTGGTCCTCACTTTT
1 TTTTTAATTTGGTCCTCGCTTTT
1716307 ATGCTTGAGG
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
139 5 0.03
140 126 0.88
141 12 0.08
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (140 bp):
TTTTTAATTTGGTCCTCGCTTTTGCTCGATATTTCATTTTAATTATTCGATTCAATAAATTGGTT
AAAACCAACTAAGTTAATAATTAGAGCCTCTACTTTAGGCTTAATTTTAAACTTAGTCCTTTAAT
TTAAGAGAAA
Found at i:1717385 original size:2 final size:2
Alignment explanation
Indices: 1717378--1717427 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1717368 TCTAATCATA
1717378 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
1717420 AT AT AT AT
1 AT AT AT AT
1717428 CTTTTTTTAC
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:1718385 original size:20 final size:20
Alignment explanation
Indices: 1718360--1718403 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1718350 TAAAAATATT
*
1718360 TTATACTCTATCAATAAATC
1 TTATACTCTAGCAATAAATC
*
1718380 TTATACTCTAGCAATAAATT
1 TTATACTCTAGCAATAAATC
1718400 TTAT
1 TTAT
1718404 GTTAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (20 bp):
TTATACTCTAGCAATAAATC
Found at i:1746088 original size:22 final size:22
Alignment explanation
Indices: 1746050--1746097 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1746040 TTGTACATCT
*
1746050 TTCTAGAAGTGTAGATTAGACC
1 TTCTAGAAGTCTAGATTAGACC
*
1746072 TTCTAGAAGTACT-GATTGGACC
1 TTCTAGAAGT-CTAGATTAGACC
1746094 TTCT
1 TTCT
1746098 GAAAGCTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (22 bp):
TTCTAGAAGTCTAGATTAGACC
Found at i:1746114 original size:23 final size:22
Alignment explanation
Indices: 1746068--1746114 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1746058 GTGTAGATTA
*
1746068 GACCTTCTAGAAGTACTGATTG
1 GACCTTCTAGAAGTACTGACTG
1746090 GACCTTCT-GAAAGCTACTGACTG
1 GACCTTCTAG-AAG-TACTGACTG
1746113 GA
1 GA
1746115 TGCCATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 11 0.50
23 10 0.45
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
GACCTTCTAGAAGTACTGACTG
Found at i:1750841 original size:35 final size:35
Alignment explanation
Indices: 1750795--1750865 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1750785 TAAGCGATCT
1750795 AAATTAGGGGTGGCGATAGAGATGGAGCAAATTCG
1 AAATTAGGGGTGGCGATAGAGATGGAGCAAATTCG
1750830 AAATTAGGGGTGGCGATAGAGATGGAGCAAATTCG
1 AAATTAGGGGTGGCGATAGAGATGGAGCAAATTCG
1750865 A
1 A
1750866 TTTTGGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.08, G:0.37, T:0.20
Consensus pattern (35 bp):
AAATTAGGGGTGGCGATAGAGATGGAGCAAATTCG
Found at i:1751048 original size:26 final size:26
Alignment explanation
Indices: 1751015--1751073 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
1751005 ACCTAATTAG
1751015 ATAAAATTTAGAAAAAATAAAATAAA
1 ATAAAATTTAGAAAAAATAAAATAAA
* *
1751041 ATAAAATTTAGTAAAAATTAAATAAA
1 ATAAAATTTAGAAAAAATAAAATAAA
*
1751067 ATGAAAT
1 ATAAAAT
1751074 GGGTTGCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (26 bp):
ATAAAATTTAGAAAAAATAAAATAAA
Found at i:1756210 original size:12 final size:12
Alignment explanation
Indices: 1756170--1756212 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1756160 TTGTAAAATA
*
1756170 TAAATTAAGAAG
1 TAAATTAAAAAG
* *
1756182 GAAATTAAGAAAA
1 TAAATTAA-AAAG
1756195 TAAATTAAAAAG
1 TAAATTAAAAAG
1756207 TAAATT
1 TAAATT
1756213 CAATTATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.26
Consensus pattern (12 bp):
TAAATTAAAAAG
Found at i:1756826 original size:29 final size:29
Alignment explanation
Indices: 1756760--1756826 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1756750 ATACTTAACA
*
1756760 TTTTAAAAATAAATAAAAATAAAGAAAAC
1 TTTTAAAAATAAAGAAAAATAAAGAAAAC
* *
1756789 TTTGAAAAATAAAGAAAGA-AAAGAAAAC
1 TTTTAAAAATAAAGAAAAATAAAGAAAAC
1756817 TTTTATAAAA
1 TTTTA-AAAA
1756827 ACCAAAAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (29 bp):
TTTTAAAAATAAAGAAAAATAAAGAAAAC
Found at i:1761521 original size:20 final size:20
Alignment explanation
Indices: 1761496--1761548 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1761486 GAGGGTTCAT
1761496 AGGTCCTTCGGGATATACAG
1 AGGTCCTTCGGGATATACAG
*
1761516 AGGTCCTTCGGGATATACAT
1 AGGTCCTTCGGGATATACAG
*
1761536 AGGTCCTTTGGGA
1 AGGTCCTTCGGGA
1761549 CAAATTTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (20 bp):
AGGTCCTTCGGGATATACAG
Found at i:1768332 original size:44 final size:44
Alignment explanation
Indices: 1768282--1768647 Score: 174
Period size: 44 Copynumber: 8.3 Consensus size: 44
1768272 TCGATCCAGA
* * *
1768282 TCCTTCTATGATGGAATCGAACGAGATGTTGGTGCTGATCTACC
1 TCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCTGATCCACC
* * * * ** * *
1768326 TCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTTATCCAAC
1 TCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCTGATCCACC
* * * ** **
1768370 TTCTTCT-TCGATGGATTTGAGTGAAATAAAT-GT-C-GATCCACC
1 TCCTTCTGT-GATGGAATCGAACGAAAT-GTTGGTGCTGATCCACC
* * *
1768412 TCATTCTGTGATGGAATCGAAC-AAGATGTTGGTGCTAATCTACC
1 TCCTTCTGTGATGGAATCGAACGAA-ATGTTGGTGCTGATCCACC
* * * * * * *
1768456 TCCTTCTGTGATAGAATCGAGCTAAAAGTTGATGTTGATCCAAC
1 TCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCTGATCCACC
* * * * **
1768500 TCCTTCTGCGATGGATTTGAGA-AAAATAAAT-GT-C-GATCCACC
1 TCCTTCTGTGATGGAATCGA-ACGAAAT-GTTGGTGCTGATCCACC
** * * * * *
1768542 TATTTCTGTGATGGAATCGAACGAGATGTCGATGTTGATCTACCTCC
1 TCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCTGA--T-CCACC
* * *
1768589 TTCTCATTCTGTGATGGAATCGAACGAGATGTCGGTGCTGATCTACC
1 -TC-C-TTCTGTGATGGAATCGAACGAAATGTTGGTGCTGATCCACC
1768636 TCCTTCTGTGAT
1 TCCTTCTGTGAT
1768648 ATAATATAGC
Statistics
Matches: 228, Mismatches: 74, Indels: 40
0.67 0.22 0.12
Matches are distributed among these distances:
41 4 0.02
42 50 0.22
43 4 0.02
44 120 0.53
45 5 0.02
46 3 0.01
47 7 0.03
48 2 0.01
50 33 0.14
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (44 bp):
TCCTTCTGTGATGGAATCGAACGAAATGTTGGTGCTGATCCACC
Found at i:1768425 original size:130 final size:130
Alignment explanation
Indices: 1768228--1768592 Score: 502
Period size: 130 Copynumber: 2.8 Consensus size: 130
1768218 TTGACGATGC
* * * ** * *
1768228 TGATCCAACT-CTGTATGCAATGGATTTGAGCGAAAATAGAAATGTCGATCCAGATCCTTCTATG
1 TGATCCAACTCCT-TCTGCGATGGATTTGAGAG-AAAT--AAATGTCGATCCACCTCATTCTGTG
1768292 ATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTG
62 ATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTG
1768357 ACGCT
127 ACG-T
* * *
1768362 T-ATCCAACTTCTTCTTCGATGGATTTGAGTGAAATAAATGTCGATCCACCTCATTCTGTGATGG
1 TGATCCAACTCCTTCTGCGATGGATTTGAGAGAAATAAATGTCGATCCACCTCATTCTGTGATGG
* * *
1768426 AATCGAACAAGATGTTGGTGCTAATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGATGT
66 AATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGT
*
1768491 TGATCCAACTCCTTCTGCGATGGATTTGAGAAAAATAAATGTCGATCCACCT-ATTTCTGTGATG
1 TGATCCAACTCCTTCTGCGATGGATTTGAGAGAAATAAATGTCGATCCACCTCA-TTCTGTGATG
* * *
1768555 GAATCGAACGAGATGTCGATGTTGATCTACCTCCTTCT
65 GAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCT
1768593 CATTCTGTGA
Statistics
Matches: 208, Mismatches: 20, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
129 3 0.01
130 175 0.84
132 4 0.02
133 23 0.11
134 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (130 bp):
TGATCCAACTCCTTCTGCGATGGATTTGAGAGAAATAAATGTCGATCCACCTCATTCTGTGATGG
AATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGT
Found at i:1768620 original size:50 final size:50
Alignment explanation
Indices: 1768545--1768642 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
1768535 ATCCACCTAT
*
1768545 TTCTGTGATGGAATCGAACGAGATGTCGATGTTGATCTACCTCCTTCTCA
1 TTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTCA
*
1768595 TTCTGTGATGGAATCGAACGAGATGTCGGTGCTGATCTACCTCCTTCT
1 TTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCT
1768643 GTGATATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (50 bp):
TTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTCA
Found at i:1769197 original size:33 final size:33
Alignment explanation
Indices: 1769104--1769194 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
1769094 TTGTCTCAAG
*
1769104 AGAGACAAAATTTGTTTCAAGAGAAACTGTCTT
1 AGAGACAAACTTTGTTTCAAGAGAAACTGTCTT
1769137 AGAGACAAACTTTGTTTCAAGAGAAACTGTCTT
1 AGAGACAAACTTTGTTTCAAGAGAAACTGTCTT
1769170 AGAGACAAACTTTGTTTCAAG-GAAA
1 AGAGACAAACTTTGTTTCAAGAGAAA
1769195 ACTATCTCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 4 0.07
33 53 0.93
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (33 bp):
AGAGACAAACTTTGTTTCAAGAGAAACTGTCTT
Done.