Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 82 of 313
Found at i:27544241 original size:27 final size:27
Alignment explanation
Indices: 27544211--27544265 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
27544201 AATATATAAT
*
27544211 AATTA-TAAAATAATTAAATTTTACTTA
1 AATTATTAAAAT-ATTAAATTTTAATTA
* *
27544238 AATTATTAACATGTTAAATTTTAATTA
1 AATTATTAAAATATTAAATTTTAATTA
27544265 A
1 A
27544266 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTATTAAAATATTAAATTTTAATTA
Found at i:27544446 original size:16 final size:16
Alignment explanation
Indices: 27544425--27544467 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
27544415 AAATTATGAA
27544425 TATTAATTTATAGTAT
1 TATTAATTTATAGTAT
*
27544441 TATTAATTT-TAGTTT
1 TATTAATTTATAGTAT
27544456 TAATCTAATTTA
1 T-AT-TAATTTA
27544468 ATTTGGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (16 bp):
TATTAATTTATAGTAT
Found at i:27556515 original size:924 final size:924
Alignment explanation
Indices: 27554728--27556576 Score: 3664
Period size: 924 Copynumber: 2.0 Consensus size: 924
27554718 AGAAGAGGGG
27554728 TCCTTTCATAAATGCAAAGCAAATTAAGCTAAATATGTCCATAAGCTGCTGTAAGTCTTTGGATG
1 TCCTTTCATAAATGCAAAGCAAATTAAGCTAAATATGTCCATAAGCTGCTGTAAGTCTTTGGATG
27554793 TCCTTCGCACACATATCGGAATTTTGTAAAGCTGCTTCTTGTTGCTGTTGCTGCTGCTGCTGTTG
66 TCCTTCGCACACATATCGGAATTTTGTAAAGCTGCTTCTTGTTGCTGTTGCTGCTGCTGCTGTTG
27554858 GTTAAGAGACCACACGGTGTTTGATGAAGTATTAGTGAAGAAATCTGTTTCTGATTTTATCTCGA
131 GTTAAGAGACCACACGGTGTTTGATGAAGTATTAGTGAAGAAATCTGTTTCTGATTTTATCTCGA
27554923 TATTGCAGAAGGACTGTGGGGTTTGATTTTGCAAAGCAGCCGCCATTAACAATGGGTTATTGAGA
196 TATTGCAGAAGGACTGTGGGGTTTGATTTTGCAAAGCAGCCGCCATTAACAATGGGTTATTGAGA
27554988 TACTCTGGCCACTTAATTTCATCTGCTTGGGTTTCCATTAAATGGATTGGATTTGGAGCCTCTTT
261 TACTCTGGCCACTTAATTTCATCTGCTTGGGTTTCCATTAAATGGATTGGATTTGGAGCCTCTTT
27555053 CTCTGATGTACTACAGTCGGTCAATCCCCATGAGTAACTGTTGTTCTCAAAGAAGGAATTGTTGC
326 CTCTGATGTACTACAGTCGGTCAATCCCCATGAGTAACTGTTGTTCTCAAAGAAGGAATTGTTGC
27555118 TTTGTAGCTCAGTGCTGCTGCTGCTGTTACTGTTATTAGCGGAGGCACCCGTTTCCCAATATCGG
391 TTTGTAGCTCAGTGCTGCTGCTGCTGTTACTGTTATTAGCGGAGGCACCCGTTTCCCAATATCGG
*
27555183 GACCCATTGATATGTGTGAAGGAGGGGATTGAAGGGGTATCAGAGGGCTTGAACACCACAGGAGC
456 GACCCATTGATATGAGTGAAGGAGGGGATTGAAGGGGTATCAGAGGGCTTGAACACCACAGGAGC
27555248 AGAGAGAAAAGAAGAGGTCAATGGTGGGAGAAGGGCAGACATGGAAGTTGAAGGGAATTCAGAAT
521 AGAGAGAAAAGAAGAGGTCAATGGTGGGAGAAGGGCAGACATGGAAGTTGAAGGGAATTCAGAAT
27555313 TGATATCGAAAGATTTACTGGTTTGGGTGAACCAGAGAGTGGGGTTTGAGGTTGTGGAGGAGAGC
586 TGATATCGAAAGATTTACTGGTTTGGGTGAACCAGAGAGTGGGGTTTGAGGTTGTGGAGGAGAGC
27555378 CTAGCATTGGATGCATAATTCAATTGCTGAATTGGAAAATGCCCCACCAAATCAGATGGCTGGCT
651 CTAGCATTGGATGCATAATTCAATTGCTGAATTGGAAAATGCCCCACCAAATCAGATGGCTGGCT
27555443 GTCCATGAACAAGTCTTTGCTACTGTTATTGCTGCTGTTGATTGTGTTGGAGCAAGGGGAGCCTT
716 GTCCATGAACAAGTCTTTGCTACTGTTATTGCTGCTGTTGATTGTGTTGGAGCAAGGGGAGCCTT
27555508 CTATTTCCAATTGGAAATGGTGTGCAGTGACCGACGGTGGTCCTGCTTTAGGATTGTCGGTGTTG
781 CTATTTCCAATTGGAAATGGTGTGCAGTGACCGACGGTGGTCCTGCTTTAGGATTGTCGGTGTTG
27555573 AGGTTCAGTTCAGCAGATGCACCTGAAGTTGCCATATCCAGGCTATTTGTGGGTTGACTCTTGCT
846 AGGTTCAGTTCAGCAGATGCACCTGAAGTTGCCATATCCAGGCTATTTGTGGGTTGACTCTTGCT
27555638 GTCTTCACCACCAT
911 GTCTTCACCACCAT
27555652 TCCTTTCATAAATGCAAAGCAAATTAAGCTAAATATGTCCATAAGCTGCTGTAAGTCTTTGGATG
1 TCCTTTCATAAATGCAAAGCAAATTAAGCTAAATATGTCCATAAGCTGCTGTAAGTCTTTGGATG
*
27555717 TCCTTCGCACACATATCGGAATTTTGTAAAGCTGCTTGTTGTTGCTGTTGCTGCTGCTGCTGTTG
66 TCCTTCGCACACATATCGGAATTTTGTAAAGCTGCTTCTTGTTGCTGTTGCTGCTGCTGCTGTTG
27555782 GTTAAGAGACCACACGGTGTTTGATGAAGTATTAGTGAAGAAATCTGTTTCTGATTTTATCTCGA
131 GTTAAGAGACCACACGGTGTTTGATGAAGTATTAGTGAAGAAATCTGTTTCTGATTTTATCTCGA
27555847 TATTGCAGAAGGACTGTGGGGTTTGATTTTGCAAAGCAGCCGCCATTAACAATGGGTTATTGAGA
196 TATTGCAGAAGGACTGTGGGGTTTGATTTTGCAAAGCAGCCGCCATTAACAATGGGTTATTGAGA
27555912 TACTCTGGCCACTTAATTTCATCTGCTTGGGTTTCCATTAAATGGATTGGATTTGGAGCCTCTTT
261 TACTCTGGCCACTTAATTTCATCTGCTTGGGTTTCCATTAAATGGATTGGATTTGGAGCCTCTTT
27555977 CTCTGATGTACTACAGTCGGTCAATCCCCATGAGTAACTGTTGTTCTCAAAGAAGGAATTGTTGC
326 CTCTGATGTACTACAGTCGGTCAATCCCCATGAGTAACTGTTGTTCTCAAAGAAGGAATTGTTGC
27556042 TTTGTAGCTCAGTGCTGCTGCTGCTGTTACTGTTATTAGCGGAGGCACCCGTTTCCCAATATCGG
391 TTTGTAGCTCAGTGCTGCTGCTGCTGTTACTGTTATTAGCGGAGGCACCCGTTTCCCAATATCGG
27556107 GACCCATTGATATGAGTGAAGGAGGGGATTGAAGGGGTATCAGAGGGCTTGAACACCACAGGAGC
456 GACCCATTGATATGAGTGAAGGAGGGGATTGAAGGGGTATCAGAGGGCTTGAACACCACAGGAGC
27556172 AGAGAGAAAAGAAGAGGTCAATGGTGGGAGAAGGGCAGACATGGAAGTTGAAGGGAATTCAGAAT
521 AGAGAGAAAAGAAGAGGTCAATGGTGGGAGAAGGGCAGACATGGAAGTTGAAGGGAATTCAGAAT
27556237 TGATATCGAAACG-TTTACTGGTTTGGGTGAACCAGAGAGTGGGGTTTGAGGTTGTGGAGGAGAG
586 TGATATCGAAA-GATTTACTGGTTTGGGTGAACCAGAGAGTGGGGTTTGAGGTTGTGGAGGAGAG
27556301 CCTAGCATTGGATGCATAATTCAATTGCTGAATTGGAAAATGCCCCACCAAATCAGATGGCTGGC
650 CCTAGCATTGGATGCATAATTCAATTGCTGAATTGGAAAATGCCCCACCAAATCAGATGGCTGGC
27556366 TGTCCATGAACAAGTCTTTGCTACTGTTATTGCTGCTGTTGATTGTGTTGGAGCAAGGGGAGCCT
715 TGTCCATGAACAAGTCTTTGCTACTGTTATTGCTGCTGTTGATTGTGTTGGAGCAAGGGGAGCCT
27556431 TCTATTTCCAATTGGAAATGGTGTGCAGTGACCGACGGTGGTCCTGCTTTAGGATTGTCGGTGTT
780 TCTATTTCCAATTGGAAATGGTGTGCAGTGACCGACGGTGGTCCTGCTTTAGGATTGTCGGTGTT
27556496 GAGGTTCAGTTCAGCAGATGCACCTGAAGTTGCCATATCCAGGCTATTTGTGGGTTGACTCTTGC
845 GAGGTTCAGTTCAGCAGATGCACCTGAAGTTGCCATATCCAGGCTATTTGTGGGTTGACTCTTGC
27556561 TGTCTTCACCACCAT
910 TGTCTTCACCACCAT
27556576 T
1 T
27556577 TTCAACCTCT
Statistics
Matches: 922, Mismatches: 2, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
924 921 1.00
925 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (924 bp):
TCCTTTCATAAATGCAAAGCAAATTAAGCTAAATATGTCCATAAGCTGCTGTAAGTCTTTGGATG
TCCTTCGCACACATATCGGAATTTTGTAAAGCTGCTTCTTGTTGCTGTTGCTGCTGCTGCTGTTG
GTTAAGAGACCACACGGTGTTTGATGAAGTATTAGTGAAGAAATCTGTTTCTGATTTTATCTCGA
TATTGCAGAAGGACTGTGGGGTTTGATTTTGCAAAGCAGCCGCCATTAACAATGGGTTATTGAGA
TACTCTGGCCACTTAATTTCATCTGCTTGGGTTTCCATTAAATGGATTGGATTTGGAGCCTCTTT
CTCTGATGTACTACAGTCGGTCAATCCCCATGAGTAACTGTTGTTCTCAAAGAAGGAATTGTTGC
TTTGTAGCTCAGTGCTGCTGCTGCTGTTACTGTTATTAGCGGAGGCACCCGTTTCCCAATATCGG
GACCCATTGATATGAGTGAAGGAGGGGATTGAAGGGGTATCAGAGGGCTTGAACACCACAGGAGC
AGAGAGAAAAGAAGAGGTCAATGGTGGGAGAAGGGCAGACATGGAAGTTGAAGGGAATTCAGAAT
TGATATCGAAAGATTTACTGGTTTGGGTGAACCAGAGAGTGGGGTTTGAGGTTGTGGAGGAGAGC
CTAGCATTGGATGCATAATTCAATTGCTGAATTGGAAAATGCCCCACCAAATCAGATGGCTGGCT
GTCCATGAACAAGTCTTTGCTACTGTTATTGCTGCTGTTGATTGTGTTGGAGCAAGGGGAGCCTT
CTATTTCCAATTGGAAATGGTGTGCAGTGACCGACGGTGGTCCTGCTTTAGGATTGTCGGTGTTG
AGGTTCAGTTCAGCAGATGCACCTGAAGTTGCCATATCCAGGCTATTTGTGGGTTGACTCTTGCT
GTCTTCACCACCAT
Found at i:27561222 original size:16 final size:18
Alignment explanation
Indices: 27561201--27561239 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27561191 TTAGGACTGC
27561201 TATTTTCA-GTG-TTTGT
1 TATTTTCAGGTGTTTTGT
*
27561217 TATTTTTAGGTGTTTTGT
1 TATTTTCAGGTGTTTTGT
27561235 TATTT
1 TATTT
27561240 GAATTTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 10 0.50
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.67
Consensus pattern (18 bp):
TATTTTCAGGTGTTTTGT
Found at i:27569986 original size:9 final size:9
Alignment explanation
Indices: 27569972--27570014 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
27569962 ATTATTATTT
27569972 TATTATTAC
1 TATTATTAC
*
27569981 TATTATTTC
1 TATTATTAC
*
27569990 TATTATTAT
1 TATTATTAC
**
27569999 TATTATGGC
1 TATTATTAC
27570008 TATTATT
1 TATTATT
27570015 TTATTGTGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (9 bp):
TATTATTAC
Found at i:27569995 original size:18 final size:18
Alignment explanation
Indices: 27569964--27570014 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
27569954 CTAATACCAT
27569964 TATTATTT-TATTATTAC
1 TATTATTTCTATTATTAC
*
27569981 TATTATTTCTATTATTAT
1 TATTATTTCTATTATTAC
**
27569999 TATTATGGCTATTATT
1 TATTATTTCTATTATT
27570015 TTATTGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (18 bp):
TATTATTTCTATTATTAC
Found at i:27570014 original size:3 final size:3
Alignment explanation
Indices: 27569962--27570004 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
27569952 TTCTAATACC
*
27569962 ATT ATT ATT -TT ATT ATT ACT ATT ATT -TCT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT
27570005 GGCTATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 31 0.89
4 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27570123 original size:5 final size:5
Alignment explanation
Indices: 27570115--27570149 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
27570105 TATATGCGTA
*
27570115 TTATT TTATT TTATA TTATT TTATT TTA-T TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
27570150 GTCCTTGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:27570133 original size:15 final size:15
Alignment explanation
Indices: 27570113--27570149 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
27570103 TTTATATGCG
27570113 TATTATTTTATTTTA
1 TATTATTTTATTTTA
27570128 TATTATTTTATTTTA
1 TATTATTTTATTTTA
27570143 T-TTATTT
1 TATTATTT
27570150 GTCCTTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTATTTTATTTTA
Found at i:27570282 original size:26 final size:26
Alignment explanation
Indices: 27570248--27570307 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
27570238 AACTATTTTT
*
27570248 TATTTTTTATTTCAAATTATTTTAGA
1 TATTATTTATTTCAAATTATTTTAGA
* * **
27570274 TATTATTTATTTTAAATTGTTTTCTA
1 TATTATTTATTTCAAATTATTTTAGA
27570300 TATTATTT
1 TATTATTT
27570308 GATTAAACTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (26 bp):
TATTATTTATTTCAAATTATTTTAGA
Found at i:27578979 original size:19 final size:20
Alignment explanation
Indices: 27578943--27578980 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
27578933 TTTATTTCAA
*
27578943 TTTTATATTTTAACAATAAG
1 TTTTATATTTCAACAATAAG
*
27578963 TTTTA-ATTTCAATAATAA
1 TTTTATATTTCAACAATAA
27578981 AGATATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTATATTTCAACAATAAG
Found at i:27582413 original size:96 final size:97
Alignment explanation
Indices: 27582237--27582429 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 97
27582227 ACAGGTTCTT
* *
27582237 TTGGTTTATGACTAGAGGCAACTCGTTAGAACCATTAGTTTTTTTACAGTGAGATTGAAAAGACA
1 TTGGTTTATGACTAGAGGCAACCCGTTAAAACCATTAGTTTTTTTACAGTGAGATTGAAAAGACA
27582302 ACTCGCAGAAATCGTAGAGAGGTTAGAGAAGC
66 ACTCGCAGAAATCGTAGAGAGGTTAGAGAAGC
27582334 TTGGTTTATGACTAGAGGCAACCCGTTAAAACCATTAG-TTTTTTACAGTGAGATTGAAAAGACA
1 TTGGTTTATGACTAGAGGCAACCCGTTAAAACCATTAGTTTTTTTACAGTGAGATTGAAAAGACA
27582398 ACTCGCAGAAATCGTAGAGAGGTTAGAGAAGC
66 ACTCGCAGAAATCGTAGAGAGGTTAGAGAAGC
27582430 AAGGCAAGGT
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 58 0.62
97 36 0.38
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (97 bp):
TTGGTTTATGACTAGAGGCAACCCGTTAAAACCATTAGTTTTTTTACAGTGAGATTGAAAAGACA
ACTCGCAGAAATCGTAGAGAGGTTAGAGAAGC
Found at i:27590847 original size:12 final size:12
Alignment explanation
Indices: 27590832--27590868 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
27590822 ATTATTTTTA
27590832 TTATTATACATT
1 TTATTATACATT
*
27590844 TTATTTATAAATT
1 TTA-TTATACATT
27590857 TTATTATACATT
1 TTATTATACATT
27590869 ATATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTATACATT
Found at i:27590870 original size:19 final size:19
Alignment explanation
Indices: 27590848--27590889 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27590838 TACATTTTAT
*
27590848 TTATAAATTTTATTATACA
1 TTATAAATTTTACTATACA
* *
27590867 TTATATATTTTACTATATA
1 TTATAAATTTTACTATACA
27590886 TTAT
1 TTAT
27590890 TCCTTGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAAATTTTACTATACA
Found at i:27592724 original size:31 final size:31
Alignment explanation
Indices: 27592689--27592758 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
27592679 TCTTTAAATG
*
27592689 TATATAATTAAATCAAAATAAAAAGTTTTAT-
1 TATATAATTAAAGCAAAAT-AAAAGTTTTATA
* *
27592720 TATAT-ATTTAAGCACAATAAAAGTTTTATA
1 TATATAATTAAAGCAAAATAAAAGTTTTATA
27592750 TATATAATT
1 TATATAATT
27592759 GCATCAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.32
30 15 0.44
31 8 0.24
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (31 bp):
TATATAATTAAAGCAAAATAAAAGTTTTATA
Found at i:27594259 original size:8 final size:8
Alignment explanation
Indices: 27594237--27594271 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
27594227 ATTGATTATT
27594237 AAAATAGA
1 AAAATAGA
27594245 GAAAATAGA
1 -AAAATAGA
27594254 AAAATAGA
1 AAAATAGA
27594262 AAAATAGA
1 AAAATAGA
27594270 AA
1 AA
27594272 TCATGGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAATAGA
Found at i:27594688 original size:25 final size:25
Alignment explanation
Indices: 27594654--27594701 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
27594644 CTAAGTCCTT
27594654 ATTAAAGTCCCTAATAATTTCACTG
1 ATTAAAGTCCCTAATAATTTCACTG
*
27594679 ATTAAAGTCCTTAATAATTTCAC
1 ATTAAAGTCCCTAATAATTTCAC
27594702 AAACAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (25 bp):
ATTAAAGTCCCTAATAATTTCACTG
Found at i:27609633 original size:34 final size:34
Alignment explanation
Indices: 27609589--27609656 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
27609579 GCACAATTGA
* *
27609589 ATAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ATAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
27609624 ATAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ATAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
27609657 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (34 bp):
ATAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:27633333 original size:13 final size:13
Alignment explanation
Indices: 27633315--27633339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27633305 AAACAAACTC
27633315 TGCTAGCAACAAT
1 TGCTAGCAACAAT
27633328 TGCTAGCAACAA
1 TGCTAGCAACAA
27633340 AAATTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (13 bp):
TGCTAGCAACAAT
Found at i:27634456 original size:9 final size:9
Alignment explanation
Indices: 27634442--27634471 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
27634432 ATCATCACTT
*
27634442 AAAAATATA
1 AAAAATTTA
27634451 AAAAATTTA
1 AAAAATTTA
27634460 AAAAATTTA
1 AAAAATTTA
27634469 AAA
1 AAA
27634472 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTTA
Found at i:27634938 original size:37 final size:37
Alignment explanation
Indices: 27634888--27634961 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
27634878 AAAAAACCGG
27634888 GTCGTAACTTGATAACATGATTATACTCGATTAAATT
1 GTCGTAACTTGATAACATGATTATACTCGATTAAATT
27634925 GTCGTAACTTGATAACATGATTATACTCGATTAAATT
1 GTCGTAACTTGATAACATGATTATACTCGATTAAATT
27634962 AAGATAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (37 bp):
GTCGTAACTTGATAACATGATTATACTCGATTAAATT
Found at i:27640754 original size:297 final size:295
Alignment explanation
Indices: 27640212--27640805 Score: 1134
Period size: 297 Copynumber: 2.0 Consensus size: 295
27640202 TACTGGTACA
27640212 AATACATTTACTATTTGGCACGACAAGTTAGACCATCATAGATCATATATGATGCAAAAATTAAT
1 AATACATTTACTATTTGGCACGACAAGTTAGACCATCATAGATCATATATGATGCAAAAATTAAT
27640277 TGAGAATTCGTATAGATTCATTAAAGAACCACAAGTTCTTTAATTTAAATAATTCTCATGTGTTG
66 TGAGAATTCGTATAGATTCATTAAAGAACCACAAGTTCTTTAATTTAAATAATTCTCATGTGTTG
*
27640342 CTTATTCTCAATGATAATTGATTATTAAAAACTCACTGACTAAATTTGAGGTTTAATGTGTTGCA
131 CTTATTCTCAATGATAATTGATTATTAAAAACTCACTGACTAAAGTTGAGGTTTAATGTGTTGCA
* * *
27640407 TTTCTAAAATGAATATGGGCCTCATTCGTCCACCATGTGGATGGTTTTGATATTATATAATTTTA
196 TTTCTAAAATGAATATGGGCCCCATTCGTCCACCATGTAGATGCTTTTGATATTATATAATTTTA
27640472 GTAGATGCATCTATAAAATAATCACATGAGTTATC
261 GTAGATGCATCTATAAAATAATCACATGAGTTATC
27640507 AATACATTTACTATTTGGCACGACAAGTTAGACCATCATAGATCATATATGATGCAAAAATTAAT
1 AATACATTTACTATTTGGCACGACAAGTTAGACCATCATAGATCATATATGATGCAAAAATTAAT
27640572 TGAGAATTCGTATAGACATTCATTAAAGAACCACAAGTTCTTTAATTTAAATAATTCTCATGTGT
66 TGAGAATTCGTATAG--ATTCATTAAAGAACCACAAGTTCTTTAATTTAAATAATTCTCATGTGT
27640637 TGCTTATTCTCAATGATAATTGATTATTAAAAACTCACTGACTAAAGTTGAGGTTTAATGTGTTG
129 TGCTTATTCTCAATGATAATTGATTATTAAAAACTCACTGACTAAAGTTGAGGTTTAATGTGTTG
27640702 CATTTCTAAAATGAATATGGGCCCCATTCGTCCACCATGTAGATGCTTTTGATATTATATAATTT
194 CATTTCTAAAATGAATATGGGCCCCATTCGTCCACCATGTAGATGCTTTTGATATTATATAATTT
27640767 TAGTAGATGCATCTATAAAATAATCACATGAGTTATC
259 TAGTAGATGCATCTATAAAATAATCACATGAGTTATC
27640804 AA
1 AA
27640806 CTTGCAACTA
Statistics
Matches: 293, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
295 80 0.27
297 213 0.73
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (295 bp):
AATACATTTACTATTTGGCACGACAAGTTAGACCATCATAGATCATATATGATGCAAAAATTAAT
TGAGAATTCGTATAGATTCATTAAAGAACCACAAGTTCTTTAATTTAAATAATTCTCATGTGTTG
CTTATTCTCAATGATAATTGATTATTAAAAACTCACTGACTAAAGTTGAGGTTTAATGTGTTGCA
TTTCTAAAATGAATATGGGCCCCATTCGTCCACCATGTAGATGCTTTTGATATTATATAATTTTA
GTAGATGCATCTATAAAATAATCACATGAGTTATC
Found at i:27642619 original size:25 final size:25
Alignment explanation
Indices: 27642573--27642621 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27642563 AGTAAAGACT
* *
27642573 AATGAAATAAGAAATCTATTTAAAC
1 AATGAAATAAAAAAACTATTTAAAC
27642598 AATGAAATAAAAAAAACT-TTTAAA
1 AATGAAAT-AAAAAAACTATTTAAA
27642622 TGGTAATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (25 bp):
AATGAAATAAAAAAACTATTTAAAC
Found at i:27655668 original size:21 final size:20
Alignment explanation
Indices: 27655630--27655668 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27655620 TTTGATTTTT
*
27655630 TTCAAGATAAAATCCTGAAA
1 TTCAAGATAAAATACTGAAA
*
27655650 TTCAGGATAAAAATACTGA
1 TTCAAGAT-AAAATACTGA
27655669 TGTGGTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCAAGATAAAATACTGAAA
Found at i:27664674 original size:14 final size:14
Alignment explanation
Indices: 27664657--27664684 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27664647 ATATTATGTT
27664657 ATGTATAAATTATG
1 ATGTATAAATTATG
27664671 ATGTATAAATTATG
1 ATGTATAAATTATG
27664685 TTTAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
ATGTATAAATTATG
Found at i:27668012 original size:19 final size:17
Alignment explanation
Indices: 27667968--27668025 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
27667958 GGCATGATGA
* *
27667968 CTTTATTTTTCTATTTCA
1 CTTTTTTTTTCT-TTTCC
27667986 CTTTTTTTTTCTTTTCC
1 CTTTTTTTTTCTTTTCC
27668003 CTCTTCTTTTATTC-TTTCC
1 CT-TT-TTTT-TTCTTTTCC
27668022 CTTT
1 CTTT
27668026 CATTTCCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.17
18 15 0.43
19 11 0.31
20 3 0.09
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTTTTTTTCTTTTCC
Found at i:27668068 original size:17 final size:18
Alignment explanation
Indices: 27668046--27668090 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
27668036 TCCAGTTTCC
27668046 ATTTTCTTTTATTATT-T
1 ATTTTCTTTTATTATTCT
*
27668063 ATTTTCTTCTTATTCTTCT
1 ATTTTCTT-TTATTATTCT
*
27668082 ATTCTCTTT
1 ATTTTCTTT
27668091 CCAAACCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTCTTTTATTATTCT
Found at i:27668659 original size:30 final size:31
Alignment explanation
Indices: 27668617--27668674 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
27668607 TTATAGATTG
* *
27668617 ATGGATTTTTGTTTGTTATGTTAATTTTTTA
1 ATGGATTTTTGTTTCTGATGTTAATTTTTTA
27668648 ATGGA-TTTTGTTTCTGATGTTAATTTT
1 ATGGATTTTTGTTTCTGATGTTAATTTT
27668675 CTTGATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (31 bp):
ATGGATTTTTGTTTCTGATGTTAATTTTTTA
Found at i:27670518 original size:3 final size:3
Alignment explanation
Indices: 27670510--27670536 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27670500 GGAAATTTGC
27670510 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
27670537 GTGCTCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27672103 original size:3 final size:3
Alignment explanation
Indices: 27672095--27672119 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27672085 CAATCACATG
27672095 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
27672120 AGAGGGCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:27672905 original size:3 final size:3
Alignment explanation
Indices: 27672897--27672921 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27672887 GTTTGTACTT
27672897 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
27672922 CACGCAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27676089 original size:14 final size:14
Alignment explanation
Indices: 27676070--27676120 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
27676060 AAAAGAGATA
27676070 ATTTTAATTTTAAT
1 ATTTTAATTTTAAT
**
27676084 ATTTTAAAATTATAT
1 ATTTTAATTTTA-AT
27676099 AATTTTAATTTTAAT
1 -ATTTTAATTTTAAT
27676114 ATTTTAA
1 ATTTTAA
27676121 AATTATAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 17 0.55
15 4 0.13
16 10 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTAATTTTAAT
Found at i:27676101 original size:30 final size:30
Alignment explanation
Indices: 27676067--27676127 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
27676057 TATAAAAGAG
27676067 ATAATTTTAATTTTAATATTTTAAAATTAT
1 ATAATTTTAATTTTAATATTTTAAAATTAT
27676097 ATAATTTTAATTTTAATATTTTAAAATTAT
1 ATAATTTTAATTTTAATATTTTAAAATTAT
27676127 A
1 A
27676128 ACAAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATAATTTTAATTTTAATATTTTAAAATTAT
Found at i:27676656 original size:22 final size:22
Alignment explanation
Indices: 27676562--27676675 Score: 76
Period size: 22 Copynumber: 5.2 Consensus size: 22
27676552 TAAACACCAG
*
27676562 ACCC-TAAATCTCAAATCATAA
1 ACCCTTAAATCTCAAACCATAA
* * *
27676583 CCCCTTAAGA-CTAAAAACGATAA
1 ACCCTTAA-ATCT-CAAACCATAA
* *
27676606 A-CCTT-AATCCCAACACCTTAA
1 ACCCTTAAATCTCAA-ACCATAA
*
27676627 ACCC-TAAATCTCAAATCATAA
1 ACCCTTAAATCTCAAACCATAA
* *
27676648 ACCCTTAAAACTCCAACCTATAA
1 ACCCTTAAATCTCAAACC-ATAA
27676671 ACCCT
1 ACCCT
27676676 AACGCCCAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
20 3 0.04
21 21 0.30
22 28 0.41
23 17 0.25
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (22 bp):
ACCCTTAAATCTCAAACCATAA
Found at i:27676671 original size:65 final size:64
Alignment explanation
Indices: 27676492--27676673 Score: 181
Period size: 65 Copynumber: 2.8 Consensus size: 64
27676482 ACTTTAACCC
* * * *
27676492 CCAAACCCTAAATCTCTAATCATAAACCCTTAAAACTACAAACACTAATTAA--TTACTCTTTAA
1 CCAAACCCTAAATCTCAAATCATAAACCCTTAAAACT-CAAAC-CT-ATAAACCTTAATC-TCAA
27676555 ACA
62 ACA
* * * * * * *
27676558 CCAGACCCTAAATCTCAAATCATAACCCCTTAAGACTAAAAACGATAAACCTTAATC-CCAACA
1 CCAAACCCTAAATCTCAAATCATAAACCCTTAAAACTCAAACCTATAAACCTTAATCTCAAACA
*
27676621 CCTTAAACCCTAAATCTCAAATCATAAACCCTTAAAACTCCAACCTATAAACC
1 CC--AAACCCTAAATCTCAAATCATAAACCCTTAAAACTCAAACCTATAAACC
27676674 CTAACGCCCA
Statistics
Matches: 94, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
63 10 0.11
64 1 0.01
65 50 0.53
66 33 0.35
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.23
Consensus pattern (64 bp):
CCAAACCCTAAATCTCAAATCATAAACCCTTAAAACTCAAACCTATAAACCTTAATCTCAAACA
Found at i:27676767 original size:28 final size:28
Alignment explanation
Indices: 27676724--27676796 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
27676714 ACTAACTTTT
*
27676724 AAACCCATAAAATATAGA-TCATAAATCAC
1 AAACCC-TAAAATATA-ACCCATAAATCAC
* *
27676753 AAACCCTAAACTATAACCCATAAATCAT
1 AAACCCTAAAATATAACCCATAAATCAC
27676781 AAACCCTAAAATATAA
1 AAACCCTAAAATATAA
27676797 AAATAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 1 0.03
28 32 0.82
29 6 0.15
ACGTcount: A:0.55, C:0.23, G:0.01, T:0.21
Consensus pattern (28 bp):
AAACCCTAAAATATAACCCATAAATCAC
Found at i:27676978 original size:7 final size:7
Alignment explanation
Indices: 27676966--27677014 Score: 89
Period size: 7 Copynumber: 7.0 Consensus size: 7
27676956 AGATCTTTAA
27676966 AAAAATT
1 AAAAATT
27676973 AAAAATT
1 AAAAATT
27676980 AAAAATT
1 AAAAATT
27676987 AAAAATT
1 AAAAATT
*
27676994 AAGAATT
1 AAAAATT
27677001 AAAAATT
1 AAAAATT
27677008 AAAAATT
1 AAAAATT
27677015 TAATATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:27677050 original size:7 final size:7
Alignment explanation
Indices: 27677012--27677036 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27677002 AAAATTAAAA
27677012 ATTTAAT
1 ATTTAAT
27677019 ATTTAAT
1 ATTTAAT
27677026 ATTTAAT
1 ATTTAAT
27677033 ATTT
1 ATTT
27677037 TAGTTCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:27681271 original size:43 final size:43
Alignment explanation
Indices: 27681088--27681271 Score: 178
Period size: 43 Copynumber: 4.3 Consensus size: 43
27681078 GTTTATATTT
* * * *
27681088 TTTAGCGGCGTTTTT-AAAAAAACGTCGCTAAAGGTC-TGTTA
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
* * ** ** *
27681129 TATAGTGGCG-TCCTGAAAAAAGCGCCATTAAATGTCATGGTC
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
* *
27681171 TTTAGCGGCG-TTTTCAAGAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTTTGAA-AAAAGCGCCGCTAAAGGTCATGGTC
* * * *
27681214 TTTAGCTGCATTTTTGAGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
27681257 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
27681272 TTCTAAAAAA
Statistics
Matches: 111, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
40 2 0.02
41 24 0.22
42 15 0.14
43 65 0.59
44 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:27681623 original size:16 final size:17
Alignment explanation
Indices: 27681604--27681641 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
27681594 AAAAATATTT
27681604 AAAATTGAAAA-ATAAA
1 AAAATTGAAAAGATAAA
*
27681620 AAAA-TGAAAAGGTAAA
1 AAAATTGAAAAGATAAA
27681636 AAAATT
1 AAAATT
27681642 ATTTTACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 12 0.63
17 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAATTGAAAAGATAAA
Found at i:27691024 original size:204 final size:204
Alignment explanation
Indices: 27690674--27691081 Score: 816
Period size: 204 Copynumber: 2.0 Consensus size: 204
27690664 CAGAACATGG
27690674 CAATTGTGGAGAACCTTTCCCGGTGGAGTTTTTAGTTCCTATGCGATGATGAGCTTTGGAGCTCT
1 CAATTGTGGAGAACCTTTCCCGGTGGAGTTTTTAGTTCCTATGCGATGATGAGCTTTGGAGCTCT
27690739 TTTATAACTATGATAGAATCAGGAACCTTTTAGGAAATATAAGGAAGCATAATTACTCGTAATGA
66 TTTATAACTATGATAGAATCAGGAACCTTTTAGGAAATATAAGGAAGCATAATTACTCGTAATGA
27690804 AATAGCCGAAATTGAAAATTGTAAAATAATAATTATAAAACCTAATAAAAATAAGCTTAAAGAAA
131 AATAGCCGAAATTGAAAATTGTAAAATAATAATTATAAAACCTAATAAAAATAAGCTTAAAGAAA
27690869 AATAAAAAA
196 AATAAAAAA
27690878 CAATTGTGGAGAACCTTTCCCGGTGGAGTTTTTAGTTCCTATGCGATGATGAGCTTTGGAGCTCT
1 CAATTGTGGAGAACCTTTCCCGGTGGAGTTTTTAGTTCCTATGCGATGATGAGCTTTGGAGCTCT
27690943 TTTATAACTATGATAGAATCAGGAACCTTTTAGGAAATATAAGGAAGCATAATTACTCGTAATGA
66 TTTATAACTATGATAGAATCAGGAACCTTTTAGGAAATATAAGGAAGCATAATTACTCGTAATGA
27691008 AATAGCCGAAATTGAAAATTGTAAAATAATAATTATAAAACCTAATAAAAATAAGCTTAAAGAAA
131 AATAGCCGAAATTGAAAATTGTAAAATAATAATTATAAAACCTAATAAAAATAAGCTTAAAGAAA
27691073 AATAAAAAA
196 AATAAAAAA
27691082 TAGTCTTAAA
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 204 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (204 bp):
CAATTGTGGAGAACCTTTCCCGGTGGAGTTTTTAGTTCCTATGCGATGATGAGCTTTGGAGCTCT
TTTATAACTATGATAGAATCAGGAACCTTTTAGGAAATATAAGGAAGCATAATTACTCGTAATGA
AATAGCCGAAATTGAAAATTGTAAAATAATAATTATAAAACCTAATAAAAATAAGCTTAAAGAAA
AATAAAAAA
Found at i:27698355 original size:33 final size:33
Alignment explanation
Indices: 27698313--27698378 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
27698303 TAAATCATTC
* *
27698313 ATTAAAATTT-GAAAGGTTACAATTTAGTCACTA
1 ATTAAAATTTAGAAA-GTGACAAATTAGTCACTA
27698346 ATTAAAATTTACGAAAGTGACAAATTAGTCACT
1 ATTAAAATTTA-GAAAGTGACAAATTAGTCACT
27698379 CGAAAACGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.34
34 15 0.52
35 4 0.14
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTAAAATTTAGAAAGTGACAAATTAGTCACTA
Found at i:27698864 original size:41 final size:41
Alignment explanation
Indices: 27698809--27698986 Score: 185
Period size: 41 Copynumber: 4.3 Consensus size: 41
27698799 CACTAAACGG
* ** * * *
27698809 AAAATGCCGCAAAAGGTTTAGCATTAACGGCGTTTATGATA
1 AAAACGCCGCAAAAGGTCCAGAATTAGCGGCGTTTATGAGA
* * ***
27698850 AAAACGCTGCAAAAGGTCCAGCATTAGCAATGTTTATGAGA
1 AAAACGCCGCAAAAGGTCCAGAATTAGCGGCGTTTATGAGA
* *
27698891 AAAACGCCACAAAAGGTCCATAATTAGCGGCGTTTATGAGA
1 AAAACGCCGCAAAAGGTCCAGAATTAGCGGCGTTTATGAGA
* ** * **
27698932 AAAACGCAGCAAAAGGTTTAGAATTAGTGGCGTTTATGCTA
1 AAAACGCCGCAAAAGGTCCAGAATTAGCGGCGTTTATGAGA
27698973 AAAACGCCGCAAAA
1 AAAACGCCGCAAAA
27698987 AACATTTTAT
Statistics
Matches: 112, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCAAAAGGTCCAGAATTAGCGGCGTTTATGAGA
Found at i:27699555 original size:14 final size:15
Alignment explanation
Indices: 27699536--27699568 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27699526 ATGGGATAGG
27699536 GGTTTTAAG-TTTAA
1 GGTTTTAAGATTTAA
*
27699550 GGTTTTGAGATTTAA
1 GGTTTTAAGATTTAA
27699565 GGTT
1 GGTT
27699569 CAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
GGTTTTAAGATTTAA
Found at i:27699589 original size:7 final size:7
Alignment explanation
Indices: 27699574--27699647 Score: 55
Period size: 7 Copynumber: 11.0 Consensus size: 7
27699564 AGGTTCAAAT
*
27699574 TTTATGG
1 TTTAGGG
27699581 TTTAGGG
1 TTTAGGG
*
27699588 -TTAGTG
1 TTTAGGG
* *
27699594 -TTAAGA
1 TTTAGGG
27699600 TTTAGGG
1 TTTAGGG
27699607 TTTAGGG
1 TTTAGGG
*
27699614 TTTAGTG
1 TTTAGGG
**
27699621 TTTATAG
1 TTTAGGG
*
27699628 CTT-GGG
1 TTTAGGG
27699634 TTTAGGG
1 TTTAGGG
27699641 TTTAGGG
1 TTTAGGG
27699648 AAGATCAAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
6 11 0.22
7 40 0.78
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:27699618 original size:27 final size:28
Alignment explanation
Indices: 27699574--27699645 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
27699564 AGGTTCAAAT
*
27699574 TTTATGGTTTAGGG-TTAGTG-TTA-AG
1 TTTAGGGTTTAGGGTTTAGTGTTTATAG
27699599 ATTTAGGGTTTAGGGTTTAGTGTTTATAG
1 -TTTAGGGTTTAGGGTTTAGTGTTTATAG
*
27699628 CTT-GGGTTTAGGGTTTAG
1 TTTAGGGTTTAGGGTTTAG
27699646 GGAAGATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 13 0.32
27 21 0.51
28 5 0.12
29 2 0.05
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.47
Consensus pattern (28 bp):
TTTAGGGTTTAGGGTTTAGTGTTTATAG
Found at i:27700887 original size:27 final size:28
Alignment explanation
Indices: 27700835--27700892 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
27700825 AAAATTGTAG
* *
27700835 CCCAACCTTTTTTTCTCTACTTTTTTTC
1 CCCAACCTTTTCTCCTCTACTTTTTTTC
27700863 CCCAACCTTTTCTCCT-TA-TTCTTTTTC
1 CCCAACCTTTTCTCCTCTACTT-TTTTTC
27700890 CCC
1 CCC
27700893 CGAAATCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 11 0.41
28 14 0.52
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (28 bp):
CCCAACCTTTTCTCCTCTACTTTTTTTC
Found at i:27703201 original size:9 final size:9
Alignment explanation
Indices: 27703187--27703417 Score: 159
Period size: 9 Copynumber: 25.9 Consensus size: 9
27703177 TTCTTTAAAA
27703187 TTACATAAC
1 TTACATAAC
*
27703196 TTACATACC
1 TTACATAAC
27703205 TTACATAA-
1 TTACATAAC
* * *
27703213 ATATATATC
1 TTACATAAC
*
27703222 ATATCATAAC
1 TTA-CATAAC
*
27703232 TTACATACC
1 TTACATAAC
*
27703241 TCACATAAC
1 TTACATAAC
*
27703250 ATACATAAC
1 TTACATAAC
27703259 TTACATAAC
1 TTACATAAC
*
27703268 TTATATAA-
1 TTACATAAC
* * *
27703276 ATATATATC
1 TTACATAAC
*
27703285 ATATCATAAC
1 TTA-CATAAC
27703295 TTACATAAC
1 TTACATAAC
27703304 TTACATAA-
1 TTACATAAC
*
27703312 -TGCATAA-
1 TTACATAAC
* * *
27703319 ATATATATC
1 TTACATAAC
* *
27703328 ATACCATAAA
1 TTA-CATAAC
27703338 TGT-CATAAC
1 T-TACATAAC
27703347 TTACATAAC
1 TTACATAAC
*
27703356 TTACATAAG
1 TTACATAAC
*
27703365 TTACATAAT
1 TTACATAAC
*
27703374 TTACATAAT
1 TTACATAAC
27703383 TTACATAAC
1 TTACATAAC
* *
27703392 TTACACAAT
1 TTACATAAC
27703401 TTACATAAC
1 TTACATAAC
*
27703410 TGACATAA
1 TTACATAA
27703418 ATGAATATCA
Statistics
Matches: 176, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
7 6 0.03
8 16 0.09
9 138 0.78
10 15 0.09
11 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
TTACATAAC
Found at i:27703287 original size:63 final size:63
Alignment explanation
Indices: 27703188--27703396 Score: 219
Period size: 63 Copynumber: 3.3 Consensus size: 63
27703178 TCTTTAAAAT
* *
27703188 TACATAACTTACATACCTTACATAAATATATATCATATCATAACTTACATACCTCACATAACA
1 TACATAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTCACATAACA
* *
27703251 TACATAACTTACATAACTTATATAAATATATATCATATCATAACTTACATAACTTACAT-A-A
1 TACATAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTCACATAACA
* * * * * * * * * * **
27703312 TGCATAA-ATATATATCATACCATAAATGTCATAACTTA-CATAACTTACATAAGTTACATAATT
1 TACATAACTTACATAACTTA-CATAAATAT-ATATCATATCATAACTTACATAACTCACATAACA
*
27703375 TACATAATTTACATAACTTACA
1 TACATAACTTACATAACTTACA
27703397 CAATTTACAT
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
60 8 0.07
61 34 0.28
62 8 0.07
63 63 0.52
64 8 0.07
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.34
Consensus pattern (63 bp):
TACATAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTCACATAACA
Found at i:27703293 original size:45 final size:45
Alignment explanation
Indices: 27703244--27703363 Score: 165
Period size: 43 Copynumber: 2.7 Consensus size: 45
27703234 ACATACCTCA
* *
27703244 CATAACATACATAACTTACATAACTTATATAAATATATATCATAT
1 CATAACATACATAACTTACATAACTTACATAAATATATATCATAC
* *
27703289 CATAACTTACATAACTTACATAA--TGCATAAATATATATCATAC
1 CATAACATACATAACTTACATAACTTACATAAATATATATCATAC
*
27703332 CATAA-ATGTCATAACTTACATAACTTACATAA
1 CATAACAT-ACATAACTTACATAACTTACATAA
27703364 GTTACATAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
42 1 0.02
43 36 0.55
45 28 0.43
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.33
Consensus pattern (45 bp):
CATAACATACATAACTTACATAACTTACATAAATATATATCATAC
Found at i:27703417 original size:27 final size:27
Alignment explanation
Indices: 27703332--27703450 Score: 123
Period size: 27 Copynumber: 4.3 Consensus size: 27
27703322 TATATCATAC
* *
27703332 CATAAATGT-CATAACTTACATAACTTA
1 CATAAAT-TACATAATTTACATAACTGA
* * *
27703359 CATAAGTTACATAATTTACATAATTTA
1 CATAAATTACATAATTTACATAACTGA
* *
27703386 CATAACTTACACAATTTACATAACTGA
1 CATAAATTACATAATTTACATAACTGA
27703413 CATAAATGAATATCATAATTTACATAACTGA
1 CATAAAT---TA-CATAATTTACATAACTGA
27703444 CATAAAT
1 CATAAAT
27703451 AAATATCATA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 51 0.65
30 2 0.03
31 24 0.31
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (27 bp):
CATAAATTACATAATTTACATAACTGA
Found at i:27708482 original size:13 final size:14
Alignment explanation
Indices: 27708466--27708494 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27708456 TTTTAAATAT
27708466 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
27708479 TTATAATGGTTTAA
1 TTATAATGGTTTAA
27708493 TT
1 TT
27708495 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:27709459 original size:43 final size:43
Alignment explanation
Indices: 27709311--27709515 Score: 196
Period size: 43 Copynumber: 4.8 Consensus size: 43
27709301 TTTTGTAAAA
* ** * *
27709311 GCGCCGCTAAAAGTCATATTCTTTAGCAGCATTTGTATGAGAG
1 GCGCCGCTAAAGGTCACGTTCTTTAGCGGCATTTGTATGAAAG
* * * * * *
27709354 GCGCCGCTAAAGGTCACGTCCCTTAACGGCGTTTGTATGGAAT
1 GCGCCGCTAAAGGTCACGTTCTTTAGCGGCATTTGTATGAAAG
* * *
27709397 GCGCCGTTAAAGGTCACGTTCTTTAGCGGTATTTGTGTGAAAG
1 GCGCCGCTAAAGGTCACGTTCTTTAGCGGCATTTGTATGAAAG
* ** * *
27709440 GCGCCGTTAAAGGTCACGTTCTTTAGCGGCGCTT-TATCAAAA
1 GCGCCGCTAAAGGTCACGTTCTTTAGCGGCATTTGTATGAAAG
** * *
27709482 ATGCCACTAAAGGTCATGTTCTTTAGCGGCATTT
1 GCGCCGCTAAAGGTCACGTTCTTTAGCGGCATTT
27709516 TTTTACATAA
Statistics
Matches: 129, Mismatches: 33, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 32 0.25
43 97 0.75
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (43 bp):
GCGCCGCTAAAGGTCACGTTCTTTAGCGGCATTTGTATGAAAG
Found at i:27709964 original size:24 final size:25
Alignment explanation
Indices: 27709920--27709966 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
27709910 TCATTTTGCA
*
27709920 TTTTTTGTGTTGTTGGTGGTGTGAC
1 TTTTTTGTGTTGTTAGTGGTGTGAC
27709945 TTTTTTG-GTTGTTAAG-GGTGTG
1 TTTTTTGTGTTGTT-AGTGGTGTG
27709967 GTGAGGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.06, C:0.02, G:0.36, T:0.55
Consensus pattern (25 bp):
TTTTTTGTGTTGTTAGTGGTGTGAC
Found at i:27712589 original size:2 final size:2
Alignment explanation
Indices: 27712582--27712627 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
27712572 ATCTCTTCTA
27712582 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
27712624 AC AC
1 AC AC
27712628 GCACGCAGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27713048 original size:12 final size:12
Alignment explanation
Indices: 27713028--27713068 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
27713018 CTTATTTGTT
27713028 TTATT-ATATTG
1 TTATTCATATTG
27713039 TTATTCATATTG
1 TTATTCATATTG
*
27713051 TTATTTC-TATTT
1 TTA-TTCATATTG
27713063 TTATTC
1 TTATTC
27713069 TGCTAAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 8 0.30
12 16 0.59
13 3 0.11
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (12 bp):
TTATTCATATTG
Found at i:27715140 original size:27 final size:27
Alignment explanation
Indices: 27715102--27715197 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 27
27715092 TAGAATCTTT
* *
27715102 AGCTATTTACTTATGTATTCATATCAA
1 AGCTATCTACTTATGTGTTCATATCAA
27715129 AGCTATCTACTTAAT-TGTTCATAT-AA
1 AGCTATCTACTT-ATGTGTTCATATCAA
*
27715155 TTCCA-CTATTTACTTATGTGTTCATATCAA
1 ----AGCTATCTACTTATGTGTTCATATCAA
*
27715185 AGCTGTCTACTTA
1 AGCTATCTACTTA
27715198 AGTCATAGTC
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
26 3 0.05
27 28 0.50
28 4 0.07
29 18 0.32
30 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (27 bp):
AGCTATCTACTTATGTGTTCATATCAA
Found at i:27716251 original size:11 final size:11
Alignment explanation
Indices: 27716235--27716281 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
27716225 CTATTTTTAA
27716235 TAAAATATTAT
1 TAAAATATTAT
27716246 TAAAATATCTTAT
1 TAAAATA--TTAT
*
27716259 TAAAATATTAA
1 TAAAATATTAT
*
27716270 TAAATTATTAT
1 TAAAATATTAT
27716281 T
1 T
27716282 TATCTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 20 0.65
13 11 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAAATATTAT
Found at i:27716260 original size:13 final size:13
Alignment explanation
Indices: 27716242--27716266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27716232 TAATAAAATA
27716242 TTATTAAAATATC
1 TTATTAAAATATC
27716255 TTATTAAAATAT
1 TTATTAAAATAT
27716267 TAATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATTAAAATATC
Found at i:27734431 original size:41 final size:39
Alignment explanation
Indices: 27734382--27734495 Score: 101
Period size: 41 Copynumber: 2.9 Consensus size: 39
27734372 TTCGACTTCG
27734382 AGTCGATGAGACACTGGGTGTCACATTATTACTTCGG-AT
1 AGTCGATGAGACACTGGGTGTCACATT-TTACTTCGGCAT
* ** * *
27734421 AAATTCGATGAGGTACTGGGT-AC-CAATTTACTTCGGCAT
1 --AGTCGATGAGACACTGGGTGTCACATTTTACTTCGGCAT
*
27734460 AGCCGATGAGACACTGGGTGTCA-ACTTGTTACTTCG
1 AGTCGATGAGACACTGGGTGTCACA-TT-TTACTTCG
27734496 AACTATCCGA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
37 15 0.26
38 11 0.19
39 6 0.11
40 9 0.16
41 16 0.28
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (39 bp):
AGTCGATGAGACACTGGGTGTCACATTTTACTTCGGCAT
Found at i:27739571 original size:47 final size:49
Alignment explanation
Indices: 27739514--27739672 Score: 146
Period size: 49 Copynumber: 3.3 Consensus size: 49
27739504 CATGGTCTTA
* * *
27739514 ATGGTCTTACACTGGCTCATC-CATCAAGTC-GATGACATGTCCCAAAT
1 ATGGTCTTACACTGGCTCATCAAATCAAGGCTGATGACATGTCCCAAAC
* * * *
27739561 ATTGTCTTACACTGACT-ATCGAAATCGAGGCTGATGCCATGTCCCAAAC
1 ATGGTCTTACACTGGCTCATC-AAATCAAGGCTGATGACATGTCCCAAAC
* ** * * *
27739610 ATGGTCTTACACTGGCTC-TCACATCTTTGTGTTGATGCCATGTCCCAGAC
1 ATGGTCTTACACTGGCTCATCAAATC-AAG-GCTGATGACATGTCCCAAAC
27739660 ATGGTCTTACACT
1 ATGGTCTTACACT
27739673 AACACATCTC
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
46 3 0.03
47 15 0.16
48 10 0.11
49 33 0.36
50 31 0.34
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
ATGGTCTTACACTGGCTCATCAAATCAAGGCTGATGACATGTCCCAAAC
Found at i:27739736 original size:46 final size:48
Alignment explanation
Indices: 27739593--27739812 Score: 176
Period size: 46 Copynumber: 4.7 Consensus size: 48
27739583 AATCGAGGCT
* * ** * **
27739593 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA-CATCTTTGTGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCT-TCATC-TCAAT-AGCC
* * *
27739643 GATGCCATGTCCCAGACATGGTCTTACACTAAC-ACATCTC-GTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTCATCTCAATAGCC
27739689 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTTTCATCTCAAT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC-TTCATCTCAATAGCC
* *
27739735 GATGCCATGTCTCAGACATGGTCTTACACTAGC-TC-TCAT-AATGTGGTCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTCATC-TCAA--TAG-CC
27739784 -ATG-CATGTCCCAGACAT-GTCTTACACTAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAG
27739813 TGCACAAATG
Statistics
Matches: 146, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
44 12 0.08
45 18 0.12
46 33 0.23
47 29 0.20
48 21 0.14
49 3 0.02
50 30 0.21
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.30
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTTCATCTCAATAGCC
Found at i:27739758 original size:92 final size:93
Alignment explanation
Indices: 27739643--27739812 Score: 247
Period size: 92 Copynumber: 1.8 Consensus size: 93
27739633 TCTTTGTGTT
27739643 GATGCCATGTCCCAGACATGGTCTTACACTAACACATC-T-CGTAG-CCGATGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACAC-TCATACGTAGTCC-ATGCATGTCCCAGAC
27739705 ATGTCTTACACTAGCTTTCATCTCAATGCC
64 ATGTCTTACACTAGCTTTCATCTCAATGCC
* * * * *
27739735 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAATGTGGTCCATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTAACACTCAT-ACGTAGTCCATGCATGTCCCAGACA
27739800 TGTCTTACACTAG
65 TGTCTTACACTAG
27739813 TGCACAAATG
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
91 2 0.03
92 33 0.48
94 32 0.46
95 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAACACTCATACGTAGTCCATGCATGTCCCAGACAT
GTCTTACACTAGCTTTCATCTCAATGCC
Found at i:27745631 original size:46 final size:48
Alignment explanation
Indices: 27745503--27745764 Score: 280
Period size: 46 Copynumber: 5.6 Consensus size: 48
27745493 AGGCCAACGC
*
27745503 CATGTCCCAGACATGGTCTTACACTGGCTCTCACATCTCCGT-GTCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCT-ACATCT-CGTAGTCGATG
* *
27745552 CCATGTCCCAGAAATGGTCTTACACT-G-AC-ACATCTCGTAGTCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGTAGTCGATG
27745598 CATGTCCCAGACAT-GTCTTACACTAGCT-TACATCTCG-AGGTCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGTA-GTCGATG
* * *
27745644 CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATACT-GATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTACATCTC-GTAGTCGATG
* * * *
27745690 CCATGTCCCAAACATGGTCTTACACTGGCTCT-CATAAT-GTGGTCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCTCTACAT-CTCGTAGTCGATG
27745738 CATGTCCCAGACAT-GTCTTACACTAGC
1 CATGTCCCAGACATGGTCTTACACTAGC
27745765 ACACAAATGA
Statistics
Matches: 184, Mismatches: 16, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
44 10 0.05
45 18 0.10
46 77 0.42
47 30 0.16
48 23 0.12
49 2 0.01
50 24 0.13
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGTAGTCGATG
Found at i:27745734 original size:94 final size:93
Alignment explanation
Indices: 27745501--27745769 Score: 307
Period size: 94 Copynumber: 2.9 Consensus size: 93
27745491 CGAGGCCAAC
* * *
27745501 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCACATCTCCGTGTCGATGCCATGTCCCAGAAA
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGT--G-GTCGATG-CATGTCCCAGACA
* *
27745566 TGGTCTTACACT-G-ACACATCTCGTAGTCGAT
62 T-GTCTTACACTAGCACACATCTCATACTCGAT
* * *
27745597 G-CATGTCCCAGACAT-GTCTTACACTAGCT-TACATCTCGAGGTCGATGCATGTCCCAGACATG
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAT-GTGGTCGATGCATGTCCCAGACATG
* * *
27745659 TCTTACACTAGCTCTCGTCTCAATACT-GAT
64 TCTTACACTAGCACACATCTC-ATACTCGAT
*
27745689 GCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGCATGTCCCAGACATGT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATGTGGTCGATGCATGTCCCAGACATGT
27745754 CTTACACTAGCACACA
65 CTTACACTAGCACACA
27745770 AATGACCCAA
Statistics
Matches: 146, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
90 10 0.07
91 14 0.10
92 17 0.12
93 18 0.12
94 70 0.48
95 16 0.11
96 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (93 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGGTCGATGCATGTCCCAGACATGTC
TTACACTAGCACACATCTCATACTCGAT
Found at i:27745742 original size:140 final size:140
Alignment explanation
Indices: 27745503--27745764 Score: 354
Period size: 140 Copynumber: 1.9 Consensus size: 140
27745493 AGGCCAACGC
* ** *
27745503 CATGTCCCAGACATGGTCTTACACTGGCTCTCACATCTCCGTGTCGATGCCATGTCCCAGAAATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCT-ACATCTCAATCTCGATGCCATGTCCCAGAAATG
27745568 GTCTTACACTGACACATCTCGTAGTCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCT
65 GTCTTACACTGACACATCTCGTAGTCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCT
27745633 CGAGGTCGATG
130 CGAGGTCGATG
*
27745644 CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATACT-GATGCCATGTCCCA-AACAT
1 CATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCAAT-CTCGATGCCATGTCCCAGAA-AT
* * * *
27745705 GGTCTTACACTGGCTC-TCATAATGTGGTCGATGCATGTCCCAGACATGTCTTACACTAGC
64 GGTCTTACACTGACACATC-T--CGTAGTCGATGCATGTCCCAGACATGTCTTACACTAGC
27745765 ACACAAATGA
Statistics
Matches: 107, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
137 4 0.04
138 37 0.35
139 1 0.01
140 51 0.48
141 14 0.13
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCAATCTCGATGCCATGTCCCAGAAATGG
TCTTACACTGACACATCTCGTAGTCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTC
GAGGTCGATG
Found at i:27757313 original size:20 final size:19
Alignment explanation
Indices: 27757269--27757314 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
27757259 TATCCAAACA
27757269 CCAGAAAAATAAATCATTT
1 CCAGAAAAATAAATCATTT
* *
27757288 CTAGAAAAGTAAATCATTTT
1 CCAGAAAAATAAATCA-TTT
27757308 CCAGAAA
1 CCAGAAA
27757315 TCATTTTCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (19 bp):
CCAGAAAAATAAATCATTT
Found at i:27757334 original size:14 final size:14
Alignment explanation
Indices: 27757298--27757335 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
27757288 CTAGAAAAGT
*
27757298 AAATCATTTTCCAG
1 AAATCATTTTCCAA
27757312 AAATCATTTTCCGAA
1 AAATCATTTTCC-AA
27757327 AAAT-ATTTT
1 AAATCATTTT
27757336 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:27762933 original size:21 final size:20
Alignment explanation
Indices: 27762907--27762946 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
27762897 AAGATTCAAA
27762907 AGTATAAAAATTATTAAAAAG
1 AGTATAAAAATTA-TAAAAAG
27762928 AGTATAAAAATTATAAAAA
1 AGTATAAAAATTATAAAAA
27762947 TATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AGTATAAAAATTATAAAAAG
Found at i:27764330 original size:27 final size:27
Alignment explanation
Indices: 27764299--27764357 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
27764289 AAGAAAAACA
27764299 TATTTTTAAAAAAAAAATTAAGGAACT
1 TATTTTTAAAAAAAAAATTAAGGAACT
*** * *
27764326 TATTTTTTTTAACAAAATTAAGGACCT
1 TATTTTTAAAAAAAAAATTAAGGAACT
27764353 TATTT
1 TATTT
27764358 ATATTAAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (27 bp):
TATTTTTAAAAAAAAAATTAAGGAACT
Found at i:27764364 original size:27 final size:27
Alignment explanation
Indices: 27764312--27764364 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
27764302 TTTTAAAAAA
* *
27764312 AAAATTAAGGAACTTATTTTTTTTAAC
1 AAAATTAAGGAACTTATTTATATTAAC
*
27764339 AAAATTAAGGACCTTATTTATATTAA
1 AAAATTAAGGAACTTATTTATATTAA
27764365 ACAATTGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (27 bp):
AAAATTAAGGAACTTATTTATATTAAC
Found at i:27764477 original size:42 final size:41
Alignment explanation
Indices: 27764399--27764482 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
27764389 AGTGGCTGAA
* *
27764399 ATTTTAGGGTACTTTAGTCTTTTTAAAAAAATAAAAAATTT
1 ATTTAAGGGTACTTTAATCTTTTTAAAAAAATAAAAAATTT
*
27764440 ATTTAAGGGTACTTTAATCTTTTTTAAAAAATAAAAAATTT
1 ATTTAAGGGTACTTTAATCTTTTTAAAAAAATAAAAAATTT
27764481 AT
1 AT
27764483 ATGTGGTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (41 bp):
ATTTAAGGGTACTTTAATCTTTTTAAAAAAATAAAAAATTT
Found at i:27764823 original size:33 final size:33
Alignment explanation
Indices: 27764781--27764848 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
27764771 CTCTAAATAG
*
27764781 ATAGTTTCCATATATATTATATATTTACCTCAT
1 ATAGTTTCCACATATATTATATATTTACCTCAT
27764814 ATAGTTTCCACATATATTATATATTTACCTCAT
1 ATAGTTTCCACATATATTATATATTTACCTCAT
27764847 AT
1 AT
27764849 TTATAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (33 bp):
ATAGTTTCCACATATATTATATATTTACCTCAT
Found at i:27764835 original size:20 final size:19
Alignment explanation
Indices: 27764812--27764858 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
27764802 TATTTACCTC
27764812 ATATAGTTT-CCACATATATT
1 ATATA-TTTACCACATAT-TT
*
27764832 ATATATTTACCTCATATTT
1 ATATATTTACCACATATTT
*
27764851 ATAAATTT
1 ATATATTT
27764859 CAATTTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTACCACATATTT
Found at i:27765189 original size:24 final size:22
Alignment explanation
Indices: 27765137--27765204 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
27765127 ATTACACAAG
*
27765137 TAAAAAATTAGTTTAATTACTTCT
1 TAAAAAATTAGTTTAATT--TTAT
27765161 T-AAAAATTAGTTTAATTTTAT
1 TAAAAAATTAGTTTAATTTTAT
**
27765182 GATAAAAAATTAGTGAAATTTTA
1 --TAAAAAATTAGTTTAATTTTA
27765205 ATTTTGTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.08
23 17 0.45
24 18 0.47
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (22 bp):
TAAAAAATTAGTTTAATTTTAT
Found at i:27769166 original size:30 final size:31
Alignment explanation
Indices: 27769111--27769176 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
27769101 TATAGTTTAT
* * *
27769111 ATTTTTATAATTTTTAAATGATTAAATTA-A
1 ATTTTTATAATTTTAAAAAGATTAAAGTACA
27769141 ATTTTTATAATTTTAAGAAAG-TTAAAGTACA
1 ATTTTTATAATTTTAA-AAAGATTAAAGTACA
27769172 ATTTT
1 ATTTT
27769177 ATCTTTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (31 bp):
ATTTTTATAATTTTAAAAAGATTAAAGTACA
Found at i:27769420 original size:18 final size:18
Alignment explanation
Indices: 27769399--27769445 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27769389 TATAATTAGT
*
27769399 ATAAAAATAACGATTATA
1 ATAAAAATAAAGATTATA
* *
27769417 ATAAAATTAAATATTATA
1 ATAAAAATAAAGATTATA
*
27769435 ATATAAATAAA
1 ATAAAAATAAA
27769446 AAAATAAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAAAATAAAGATTATA
Found at i:27771113 original size:9 final size:8
Alignment explanation
Indices: 27771077--27771110 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
27771067 TATACATAGA
27771077 TTTAAA-T
1 TTTAAATT
27771084 TTTAAATT
1 TTTAAATT
27771092 TTTAAATT
1 TTTAAATT
27771100 TTTAAATT
1 TTTAAATT
27771108 TTT
1 TTT
27771111 TAAGTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAAATT
Found at i:27774445 original size:27 final size:27
Alignment explanation
Indices: 27774415--27774498 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
27774405 GTGACGAAGT
27774415 CACTAGATACAGATATTGTGGCAAAGC
1 CACTAGATACAGATATTGTGGCAAAGC
*
27774442 CACTAGA-ACAGATATATGTGGCAGAGC
1 CACTAGATACAGATAT-TGTGGCAAAGC
* *
27774469 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACTAGATACAGAT-ATTGTGGCAAAGC
27774496 CAC
1 CAC
27774499 CAGGACAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
26 8 0.16
27 41 0.80
28 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
CACTAGATACAGATATTGTGGCAAAGC
Found at i:27774499 original size:27 final size:26
Alignment explanation
Indices: 27774419--27774510 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 26
27774409 CGAAGTCACT
*
27774419 AGATACAGATATTGTGGCAAAGCCACT
1 AGAT-CAGATATTGTGGCAAAGCCACC
* *
27774446 AGAACAGATATATGTGGCAGAGCCACC
1 AGATCAGATAT-TGTGGCAAAGCCACC
*
27774473 AGATCAGATAATTGTGGCATAGCCACC
1 AGATCAGAT-ATTGTGGCAAAGCCACC
27774500 AGGA-CAGATAT
1 A-GATCAGATAT
27774511 ATGTNNNNNN
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.16
27 44 0.77
28 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
AGATCAGATATTGTGGCAAAGCCACC
Found at i:27775649 original size:26 final size:26
Alignment explanation
Indices: 27775619--27775674 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
27775609 TGAAATTCCC
27775619 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27775645 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27775671 ATCA
1 ATCA
27775675 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:27779419 original size:40 final size:40
Alignment explanation
Indices: 27779309--27779434 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
27779299 GCGTTATACT
*
27779309 TTCTGTTTGGCGTGA-TTCAGGTGGATCAGCTCTTATGAGC
1 TTCTGTTTGGCGT-ATTTTAGGTGGATCAGCTCTTATGAGC
* * *
27779349 TTCTG-TTGGCATGTTTTGGGTGGA-CTAGCTCTTATGAGC
1 TTCTGTTTGGCGTATTTTAGGTGGATC-AGCTCTTATGAGC
* *
27779388 TTCTGTTTGGCGTATTTTAGTTGGATCAGCTCTTATGAGT
1 TTCTGTTTGGCGTATTTTAGGTGGATCAGCTCTTATGAGC
27779428 TTCTGTT
1 TTCTGTT
27779435 GTTGTGTTCG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 32 0.44
40 39 0.53
41 1 0.01
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (40 bp):
TTCTGTTTGGCGTATTTTAGGTGGATCAGCTCTTATGAGC
Found at i:27784198 original size:38 final size:38
Alignment explanation
Indices: 27784156--27784232 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
27784146 TTTTCATATA
27784156 CTAAGCTTAATTTCTAACAATTTAACACCTAAATCATT
1 CTAAGCTTAATTTCTAACAATTTAACACCTAAATCATT
27784194 CTAAGCTTAATTTCTAACAATTTAACACCTAAATCATT
1 CTAAGCTTAATTTCTAACAATTTAACACCTAAATCATT
27784232 C
1 C
27784233 AATTCTCAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (38 bp):
CTAAGCTTAATTTCTAACAATTTAACACCTAAATCATT
Found at i:27788241 original size:26 final size:26
Alignment explanation
Indices: 27788208--27788315 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
27788198 TGATACAAAT
27788208 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
27788234 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27788260 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
27788286 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27788312 TGAT
1 TGAT
27788316 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27790423 original size:8 final size:8
Alignment explanation
Indices: 27790410--27790438 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
27790400 AGAGGAAGAT
27790410 GAAAAAAA
1 GAAAAAAA
27790418 G-AAAAAA
1 GAAAAAAA
27790425 GAAAAAAA
1 GAAAAAAA
27790433 GAAAAA
1 GAAAAA
27790439 GAGAGGATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:27790430 original size:15 final size:15
Alignment explanation
Indices: 27790410--27790438 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27790400 AGAGGAAGAT
27790410 GAAAAAAAGAAAAAA
1 GAAAAAAAGAAAAAA
27790425 GAAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
27790439 GAGAGGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
GAAAAAAAGAAAAAA
Found at i:27794630 original size:20 final size:20
Alignment explanation
Indices: 27794605--27794643 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27794595 TACTAAAGTG
27794605 GGCTAAGGCCCACACTGATT
1 GGCTAAGGCCCACACTGATT
27794625 GGCTAAGGCCCACACTGAT
1 GGCTAAGGCCCACACTGAT
27794644 ATTGCGACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (20 bp):
GGCTAAGGCCCACACTGATT
Found at i:27803801 original size:53 final size:53
Alignment explanation
Indices: 27803721--27803825 Score: 210
Period size: 53 Copynumber: 2.0 Consensus size: 53
27803711 GCTATGAATT
27803721 GGTATATATGTATGGTTTTCTTTTGATAGCTAATATATGGTGCATATATTTTC
1 GGTATATATGTATGGTTTTCTTTTGATAGCTAATATATGGTGCATATATTTTC
27803774 GGTATATATGTATGGTTTTCTTTTGATAGCTAATATATGGTGCATATATTTT
1 GGTATATATGTATGGTTTTCTTTTGATAGCTAATATATGGTGCATATATTTT
27803826 GAAAATGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.50
Consensus pattern (53 bp):
GGTATATATGTATGGTTTTCTTTTGATAGCTAATATATGGTGCATATATTTTC
Found at i:27803811 original size:29 final size:29
Alignment explanation
Indices: 27803724--27803812 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
27803714 ATGAATTGGT
27803724 ATATATGTATGGTTTTCTTTTGATAGCTA
1 ATATATGTATGGTTTTCTTTTGATAGCTA
* ** * *
27803753 ATATATG-GTGCATATATTTTCG---G-T-
1 ATATATGTATGGTTTTCTTTT-GATAGCTA
27803777 ATATATGTATGGTTTTCTTTTGATAGCTA
1 ATATATGTATGGTTTTCTTTTGATAGCTA
27803806 ATATATG
1 ATATATG
27803813 GTGCATATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
24 8 0.19
25 9 0.21
26 1 0.02
27 1 0.02
28 9 0.21
29 15 0.35
ACGTcount: A:0.26, C:0.07, G:0.18, T:0.49
Consensus pattern (29 bp):
ATATATGTATGGTTTTCTTTTGATAGCTA
Found at i:27803812 original size:25 final size:25
Alignment explanation
Indices: 27803731--27803814 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
27803721 GGTATATATG
27803731 TATGGTTTTCTTTTGATAGCTAATA
1 TATGGTTTTCTTTTGATAGCTAATA
* * * *
27803756 TATGGTGCATATATTTTCGGTA--TATATG
1 TATGGT---TTTCTTTT-GATAGCTA-ATA
27803784 TATGGTTTTCTTTTGATAGCTAATA
1 TATGGTTTTCTTTTGATAGCTAATA
27803809 TATGGT
1 TATGGT
27803815 GCATATATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
24 3 0.07
25 20 0.45
26 2 0.05
27 2 0.05
28 14 0.32
29 3 0.07
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (25 bp):
TATGGTTTTCTTTTGATAGCTAATA
Found at i:27804249 original size:21 final size:20
Alignment explanation
Indices: 27804225--27804263 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27804215 ACAAAACAAT
27804225 TATAAAAATTAAATGCTAACA
1 TATAAAAATTAAAT-CTAACA
* *
27804246 TATAATAATTTAATCTAA
1 TATAAAAATTAAATCTAA
27804264 TCATGACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TATAAAAATTAAATCTAACA
Found at i:27806090 original size:3 final size:3
Alignment explanation
Indices: 27806082--27806106 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27806072 AGAGATTCAA
27806082 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
27806107 TCACTTAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27807066 original size:21 final size:21
Alignment explanation
Indices: 27807042--27807084 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27807032 CATGCCATAA
27807042 TTCGAGTTTAACTTATAAAGG
1 TTCGAGTTTAACTTATAAAGG
27807063 TTCGAGTTTAACTTATAAAGG
1 TTCGAGTTTAACTTATAAAGG
27807084 T
1 T
27807085 AAAATAGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (21 bp):
TTCGAGTTTAACTTATAAAGG
Found at i:27807873 original size:43 final size:43
Alignment explanation
Indices: 27807792--27807875 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
27807782 AAGTCGTACA
* *
27807792 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATATAAACACATATCG
*
27807835 ATGCCACTGTCCCAGACAG-GGTCTTAC-TCATAAACACATAT
1 ATGCCAATGTCCCAGAC-GTGGTCTTACAT-ATAAACACATAT
27807876 TAGAATCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 34 0.94
44 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATATAAACACATATCG
Found at i:27808993 original size:26 final size:26
Alignment explanation
Indices: 27808963--27809013 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
27808953 GATACATAGT
*
27808963 ACCTGCTAAATAAACACCGGCTCAAA
1 ACCTGCTAAATAAACACCAGCTCAAA
27808989 ACCTGCTAAATAAACACCAGCTCAA
1 ACCTGCTAAATAAACACCAGCTCAA
27809014 GGCCTACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.31, G:0.10, T:0.16
Consensus pattern (26 bp):
ACCTGCTAAATAAACACCAGCTCAAA
Found at i:27818177 original size:14 final size:14
Alignment explanation
Indices: 27818158--27818187 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27818148 TTTGTGTTAA
27818158 TTATGTGTGAATTT
1 TTATGTGTGAATTT
*
27818172 TTATGTGTTAATTT
1 TTATGTGTGAATTT
27818186 TT
1 TT
27818188 CGTGTTTTAA
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:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (14 bp):
TTATGTGTGAATTT
Found at i:27818721 original size:15 final size:15
Alignment explanation
Indices: 27818701--27818730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27818691 ATTATGAAAG
27818701 ATATGTTTTGGATTA
1 ATATGTTTTGGATTA
*
27818716 ATATGTTTTGTATTA
1 ATATGTTTTGGATTA
27818731 GAATTTTTGA
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:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTA
Found at i:27819404 original size:56 final size:56
Alignment explanation
Indices: 27819341--27819451 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
27819331 ACCATGGCAT
*
27819341 CGATATATGTGTGCGAGTAAGTCCACGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
*
27819397 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATTGATATGTGATT
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATT
27819452 TCAATTTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
Found at i:27819476 original size:56 final size:56
Alignment explanation
Indices: 27819343--27819464 Score: 199
Period size: 56 Copynumber: 2.2 Consensus size: 56
27819333 CATGGCATCG
* *
27819343 ATATATGTGTGCGAGTAAGTCCACGTTTAATACGTTGGCATCGATATGTGATTCCG
1 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCA
* *
27819399 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATTGATATGTGATTTCA
1 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCA
*
27819455 ATTTATGTGT
1 ATATATGTGT
27819465 CTTAGTAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (56 bp):
ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCA
Found at i:27820951 original size:5 final size:5
Alignment explanation
Indices: 27820941--27820972 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
27820931 TATATTGTGA
27820941 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
27820973 GAACACAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:27820966 original size:9 final size:9
Alignment explanation
Indices: 27820942--27820972 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
27820932 ATATTGTGAA
27820942 AAATAAAAT
1 AAATAAAAT
27820951 AAAATAAAAT
1 -AAATAAAAT
27820961 AAATAAAAT
1 AAATAAAAT
27820970 AAA
1 AAA
27820973 GAACACAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:27825091 original size:5 final size:5
Alignment explanation
Indices: 27825081--27825112 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
27825071 CAATTTGTGA
27825081 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
27825113 GAACACAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:27825106 original size:9 final size:9
Alignment explanation
Indices: 27825082--27825112 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
27825072 AATTTGTGAA
27825082 AAATAAAAT
1 AAATAAAAT
27825091 AAAATAAAAT
1 -AAATAAAAT
27825101 AAATAAAAT
1 AAATAAAAT
27825110 AAA
1 AAA
27825113 GAACACAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:27835487 original size:648 final size:649
Alignment explanation
Indices: 27833331--27835929 Score: 4620
Period size: 648 Copynumber: 4.0 Consensus size: 649
27833321 ATAATATATG
27833331 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
1 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
* *
27833396 TGTATGCTAGTTTAAATTATTCTGTTGCTAAATGGTAAGCGTTGCATGTATTGCATGATCATTTT
66 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
* *
27833461 GGTCGGTTGTTTTTACTATGTAATTAATGCTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGTAT
131 GGTCGGTTGTTTTTAATATGTAATTAATGCTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
*
27833526 TATATACATGAGCATTGCTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
196 TATATACATGAGCATTGTTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
* *
27833591 CAGGTCACGTGGTTGATGAATAGAAATCAAAGCGTATGCATGGCTATATAGATTGTTAGTTAATT
261 TAGGTCACGTGGTTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
*
27833656 GTAAGTTATAAAATATGTATAAATGGGTTACTTATAACCGAATG-ATTGTTTTAAATTATG---T
326 GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCA-TGTTTTAAATTATGTTAT
* * * *
27833717 --TGCAAACATATGAATTTCATACAGACAAACGCATTAATGCCGCATACATGGATAAAAGGGTTA
390 GATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACATACATGGATAAAAGGGTTA
*
27833780 GTAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATATGTATGACT-TATATATATATCT
455 GTAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATACGTATGACTATATATATATATCT
27833844 ATATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTT
520 ATATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTT
* *
27833909 GTAATTTTGATCTGTAAAATGAAATGCATATTTGTCTGAATTGTAATATGATCGGTAGCACCGTA
585 GTAATTTCGATCTGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGCACCGTA
27833974 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
1 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
27834039 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
66 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
* *
27834104 GGTCGGTTGTTTTTAATATTTAATTAATGGTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
131 GGTCGGTTGTTTTTAATATGTAATTAATGCTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
*
27834169 TATATACATGAGCATTGTTAGTATGTTTTAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
196 TATATACATGAGCATTGTTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
* * *
27834234 TAGGTCACGTGGTTGATGAACATAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATC
261 TAGGTCACGTGGTTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
*
27834299 GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCATGTTTTGAATTATGTTATG
326 GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCATGTTTTAAATTATGTTATG
*
27834364 ATGCAAACATGTGAATTTCACATAGACAAATGCATTAATGCCACATACATGGATAAAAGGGTTAG
391 ATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACATACATGGATAAAAGGGTTAG
*
27834429 TAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATACGTGTGACTTATATATATATATCT
456 TAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATACGTATGAC-TATATATATATATCT
*
27834494 ATATAGGTCTAATATTCGATCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTT
520 ATATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTT
* * * *
27834559 GTAATTTTGACCTGTAAAATGAAATGCATATTTGTTTGAACTATAATATGATCGGTAGCACCGTA
585 GTAATTTCGATCTGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGCACCGTA
*
27834624 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATTTGTAATGTGATAATTAAAGTGATGGATGAA
1 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
27834689 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
66 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
* * * *
27834754 GGTCGATTGTTTTTAGTATGTAATTAATGCTAAATATAGTCTTTATTTTGGAGTAAGTTGCGCAT
131 GGTCGGTTGTTTTTAATATGTAATTAATGCTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
* * *
27834819 TATATACATGAGCATTGTTAGTATATTTTAGCCATATGTTTATATGGATGTTAATTGAACTAAGG
196 TATATACATGAGCATTGTTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
*
27834884 TAGGTCACGTGATTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
261 TAGGTCACGTGGTTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
27834949 GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCATGTTTTAAATTATGTTATG
326 GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCATGTTTTAAATTATGTTATG
*
27835014 ATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACGTACATGGATAAAAGGGTTAG
391 ATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACATACATGGATAAAAGGGTTAG
*
27835079 TAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATATGTATGACT-TATATATATATCTA
456 TAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATACGTATGACTATATATATATATCTA
27835143 TATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTTG
521 TATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTTG
27835208 TAATTTCGATCTGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGCACCGTA
586 TAATTTCGATCTGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGCACCGTA
27835272 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
1 TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
27835337 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
66 TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
*
27835402 GGTCGGTTGTTTTTAATATGTAATTAATGGTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
131 GGTCGGTTGTTTTTAATATGTAATTAATGCTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
27835467 TATATACATGAGCATTGTTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
196 TATATACATGAGCATTGTTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
27835532 TAGGTCACGTGGTTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
261 TAGGTCACGTGGTTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
*
27835597 GTAAGTTATAAAATATGTATAAATGGGTTACTTATAACCGAATGCATGTTTTAAATTATGTTATG
326 GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCATGTTTTAAATTATGTTATG
27835662 ATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACATACATGGATAAAAGGGTTAG
391 ATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACATACATGGATAAAAGGGTTAG
* *
27835727 TAATGAAAATTTATTCCAATTGATGTATGATTTGGTCTATACGTATGAATTATATATATAAATAT
456 TAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATACGTATG----A-CTATAT--ATAT
* * **
27835792 ATATCTATATAGGTCTAATATTTGGTCAATGAAGTTAATGATGTGACATATGTTTTGCGTATGCA
514 ATATCTATATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCA
*
27835857 TAAGTTGTAATTTCGATCCGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGC
579 TAAGTTGTAATTTCGATCTGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGC
27835922 ACCGTA
644 ACCGTA
27835928 TA
1 TA
27835930 ACCCCAATCC
Statistics
Matches: 1870, Mismatches: 70, Indels: 19
0.95 0.04 0.01
Matches are distributed among these distances:
643 368 0.20
644 1 0.00
646 1 0.00
648 732 0.39
649 2 0.00
650 624 0.33
652 1 0.00
653 1 0.00
654 3 0.00
656 137 0.07
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (649 bp):
TACTTGGTATATTAGTTAGTTTTTGATGGAAAATGTGTAATGTGATAATTAAAGTGATGGATGAA
TGTATGCTAGTTTAAATTATTCGGTTGCTAAATGGTAAGTGTTGCATGTATTGCATGATCATTTT
GGTCGGTTGTTTTTAATATGTAATTAATGCTAAGTGTAGTCTTTATTTTGGAGTAAGTTGCGCAT
TATATACATGAGCATTGTTAGTATGTTTCAGCCATATGTTTATTTGGATGTTAATTGAACTAAGG
TAGGTCACGTGGTTGATGAATAGAAATCAAAGCATATGCATGGCTATATAGATTGTTAGTTAATT
GTAAGTTATAAAATATGTATAAATGGATTACTTATAACCGAATGCATGTTTTAAATTATGTTATG
ATGCAAACATGTGAATTTCACATAGACAAACGCATTAATGCCACATACATGGATAAAAGGGTTAG
TAATGAAAATTTATTCCAATTGATGTATGATTTGGTGTATACGTATGACTATATATATATATCTA
TATAGGTCTAATATTCGGTCAATAAAGTTAATGATGTGACATATGTTTTGTATATGCATAAGTTG
TAATTTCGATCTGTAAAATGAAATGCATATTTGTCTGAACTGTAATATGATCGGTAGCACCGTA
Found at i:27838770 original size:33 final size:33
Alignment explanation
Indices: 27838675--27838834 Score: 121
Period size: 33 Copynumber: 4.8 Consensus size: 33
27838665 TCTTTGGGTT
* *
27838675 GTATCCA-CTGCAGTATAGCACTCCTCCCGACCC
1 GTATCCACCT-CAGTACAGCACTCCTCCCGGCCC
* * *
27838708 ATATCCATCCT-AGTACAGTACTTCTCCCGGCCC
1 GTATCCA-CCTCAGTACAGCACTCCTCCCGGCCC
* *
27838741 GTATCCACCTCAGTACAGCACTCCCCCCGGCCT
1 GTATCCACCTCAGTACAGCACTCCTCCCGGCCC
* * **
27838774 GTATCCACCGT-AGTAC-TCTACTCCTCCTGGGTC
1 GTATCCACC-TCAGTACAGC-ACTCCTCCCGGCCC
* * **
27838807 GTATCCGCCGCAGTATGGCACTCCTCCC
1 GTATCCACCTCAGTACAGCACTCCTCCC
27838835 AGCTCAAGTT
Statistics
Matches: 99, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
32 4 0.04
33 91 0.92
34 2 0.02
35 2 0.02
ACGTcount: A:0.18, C:0.42, G:0.16, T:0.24
Consensus pattern (33 bp):
GTATCCACCTCAGTACAGCACTCCTCCCGGCCC
Found at i:27838810 original size:66 final size:66
Alignment explanation
Indices: 27838669--27838830 Score: 157
Period size: 66 Copynumber: 2.5 Consensus size: 66
27838659 TTGATATCTT
* * * *
27838669 TGGGTTGTATCCA-CTGCAGTATAGCACTCCTCCCGACCCATATCCATCCTAGTACAGTACTTCT
1 TGGGTCGTATCCACCT-CAGTATAGCACTCCCCCCGACCCATATCCATCCTAGTACACTACTCCT
27838733 CC
65 CC
* ** * * ** *
27838735 CGGCCCGTATCCACCTCAGTACAGCACTCCCCCCGGCCTGTATCCA-CCGTAGTACTCTACTCCT
1 TGGGTCGTATCCACCTCAGTATAGCACTCCCCCCGACCCATATCCATCC-TAGTACACTACTCCT
27838799 CC
65 CC
* * *
27838801 TGGGTCGTATCCGCCGCAGTATGGCACTCC
1 TGGGTCGTATCCACCTCAGTATAGCACTCC
27838831 TCCCAGCTCA
Statistics
Matches: 75, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
65 2 0.03
66 71 0.95
67 2 0.03
ACGTcount: A:0.18, C:0.40, G:0.18, T:0.25
Consensus pattern (66 bp):
TGGGTCGTATCCACCTCAGTATAGCACTCCCCCCGACCCATATCCATCCTAGTACACTACTCCTC
C
Found at i:27845105 original size:18 final size:19
Alignment explanation
Indices: 27845076--27845111 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
27845066 AAAAATTACC
27845076 TTTTCTTTTCTTTCTTCTA
1 TTTTCTTTTCTTTCTTCTA
27845095 TTTTC-TTTCTTTCTTCT
1 TTTTCTTTTCTTTCTTCT
27845112 CATCTCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTCTTTCTTCTA
Found at i:27852367 original size:21 final size:23
Alignment explanation
Indices: 27852341--27852386 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
27852331 TAAAAGGTAT
*
27852341 TTAC-AAATTAAATC-TCTAAGA
1 TTACAAAATCAAATCTTCTAAGA
*
27852362 TTACAAAATCATATCTTCTAAGA
1 TTACAAAATCAAATCTTCTAAGA
27852385 TT
1 TT
27852387 GCATATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 9 0.43
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (23 bp):
TTACAAAATCAAATCTTCTAAGA
Found at i:27852385 original size:23 final size:22
Alignment explanation
Indices: 27852341--27852399 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
27852331 TAAAAGGTAT
* *
27852341 TTACAAATTAAATC-TCTAAGA
1 TTACAAATCATATCTTCTAAGA
27852362 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATCTTCTAAGA
* *
27852385 TTGCATATCATATCT
1 TTACAAATCATATCT
27852400 AAGATTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.56
23 10 0.31
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (22 bp):
TTACAAATCATATCTTCTAAGA
Found at i:27852402 original size:19 final size:19
Alignment explanation
Indices: 27852378--27852428 Score: 88
Period size: 17 Copynumber: 2.8 Consensus size: 19
27852368 AATCATATCT
27852378 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
27852397 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
27852414 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
27852429 TGAAGATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 17 0.57
19 13 0.43
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:27852413 original size:22 final size:19
Alignment explanation
Indices: 27852369--27852416 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
27852359 AGATTACAAA
27852369 ATCATATCTTCTAAGATTG
1 ATCATATCTTCTAAGATTG
27852388 --CATATCATATCTAAGATTG
1 ATCATATC-T-TCTAAGATTG
27852407 TATCATATCT
1 -ATCATATCT
27852417 AAGATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.25
18 1 0.04
19 10 0.42
21 1 0.04
22 6 0.25
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
ATCATATCTTCTAAGATTG
Found at i:27866422 original size:13 final size:13
Alignment explanation
Indices: 27866404--27866430 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27866394 ACACATTGAA
27866404 CTGAAAAAAAAAT
1 CTGAAAAAAAAAT
27866417 CTGAAAAAAAAAT
1 CTGAAAAAAAAAT
27866430 C
1 C
27866431 ATTCGTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.11, G:0.07, T:0.15
Consensus pattern (13 bp):
CTGAAAAAAAAAT
Found at i:27866892 original size:7 final size:7
Alignment explanation
Indices: 27866880--27866907 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
27866870 GTTGTGTTGC
27866880 ATCAAAT
1 ATCAAAT
27866887 ATCAAAT
1 ATCAAAT
27866894 ATCAAAT
1 ATCAAAT
27866901 ATCAAAT
1 ATCAAAT
27866908 TGACTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCAAAT
Found at i:27869645 original size:25 final size:25
Alignment explanation
Indices: 27869612--27869662 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
27869602 CCTCAAGTTT
27869612 TTTGGTTTT-CTTCTCTCAATTAAAC
1 TTTGGTTTTACTT-TCTCAATTAAAC
* * *
27869637 TTTGTTTTTAGTTTCTCACTTAAAC
1 TTTGGTTTTACTTTCTCAATTAAAC
27869662 T
1 T
27869663 CTGATTAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.55
Consensus pattern (25 bp):
TTTGGTTTTACTTTCTCAATTAAAC
Found at i:27870376 original size:31 final size:31
Alignment explanation
Indices: 27870338--27870401 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
27870328 GTTAGTGTTA
27870338 AAACAACATCTCTACACGTTTAAAATAACCG
1 AAACAACATCTCTACACGTTTAAAATAACCG
*
27870369 AAACAACATCTCTACACGTTTAGAATAACCG
1 AAACAACATCTCTACACGTTTAAAATAACCG
27870400 AA
1 AA
27870402 GGTGAGTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (31 bp):
AAACAACATCTCTACACGTTTAAAATAACCG
Found at i:27870777 original size:27 final size:27
Alignment explanation
Indices: 27870746--27870827 Score: 146
Period size: 27 Copynumber: 3.0 Consensus size: 27
27870736 TAAGGCAAAG
*
27870746 AATGTGGCTACTGCAAAAAGAAGGGCC
1 AATGTGGCTACTGCAAGAAGAAGGGCC
27870773 AATGTGGCTACTGCAAGAAGAAGGGCC
1 AATGTGGCTACTGCAAGAAGAAGGGCC
*
27870800 AATGTGGCTACTACAAGAAGAAGGGCC
1 AATGTGGCTACTGCAAGAAGAAGGGCC
27870827 A
1 A
27870828 TATCAAGTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (27 bp):
AATGTGGCTACTGCAAGAAGAAGGGCC
Found at i:27879321 original size:13 final size:13
Alignment explanation
Indices: 27879296--27879330 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
27879286 TGAAAATTAA
*
27879296 ATAAATTAAAATT
1 ATAAATAAAAATT
*
27879309 ATATATAAAAATT
1 ATAAATAAAAATT
27879322 ATAAATAAA
1 ATAAATAAA
27879331 TAAAGTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:27885451 original size:23 final size:22
Alignment explanation
Indices: 27885399--27885451 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27885389 TCCACGTCTT
*
27885399 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
27885421 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
27885444 TTTCTTTT
1 TTTCTTTT
27885452 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:27887804 original size:4 final size:4
Alignment explanation
Indices: 27887795--27887822 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
27887785 TTAAACTAAG
27887795 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
27887823 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:27888458 original size:12 final size:11
Alignment explanation
Indices: 27888412--27888454 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
27888402 AGTTAAATAT
27888412 TATTTTATTAA
1 TATTTTATTAA
*
27888423 TATTTTAATTGGA
1 TATTTT-ATT-AA
27888436 TA-TTTATTAA
1 TATTTTATTAA
27888446 TATTTTATT
1 TATTTTATT
27888455 TAATTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.11
11 15 0.56
12 6 0.22
13 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Done.