Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 16 of 318
Found at i:4186652 original size:2 final size:2
Alignment explanation
Indices: 4186647--4186694 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4186637 TCTCTCTCTC
*
4186647 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4186689 TA TA TA
1 TA TA TA
4186695 AATTGATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4187574 original size:14 final size:14
Alignment explanation
Indices: 4187539--4187580 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4187529 ATACACATAC
*
4187539 ATATTTAATA-TAA
1 ATATTAAATATTAA
4187552 AT-TTAAAATATTAA
1 ATATT-AAATATTAA
4187566 ATATTAAATATTAA
1 ATATTAAATATTAA
4187580 A
1 A
4187581 CATTTGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 2 0.08
13 6 0.24
14 15 0.60
15 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAAATATTAA
Found at i:4195646 original size:11 final size:13
Alignment explanation
Indices: 4195613--4195651 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
4195603 AACATCAAAA
4195613 TAATTATATTTTT
1 TAATTATATTTTT
4195626 TAATTATATTTTT
1 TAATTATATTTTT
4195639 TAATTATTATTTT
1 TAATTA-TATTTT
4195652 AAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTATATTTTT
Found at i:4198515 original size:20 final size:20
Alignment explanation
Indices: 4198490--4198527 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4198480 CATTCAGTTT
4198490 TTTTTTTCCTTAATTCCCCC
1 TTTTTTTCCTTAATTCCCCC
*
4198510 TTTTTTTCTTTAATTCCC
1 TTTTTTTCCTTAATTCCC
4198528 AGCTTCTCTG
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:0.11, C:0.29, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTTCCTTAATTCCCCC
Found at i:4198867 original size:3 final size:3
Alignment explanation
Indices: 4198859--4198899 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4198849 ATGAAAAGTG
4198859 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
4198900 CCCTCACAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:4203921 original size:20 final size:20
Alignment explanation
Indices: 4203896--4203938 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4203886 TCATTGTCTA
4203896 GAATTCGAGTATACGCTGTT
1 GAATTCGAGTATACGCTGTT
4203916 GAATTCGAGTATACGCTGTT
1 GAATTCGAGTATACGCTGTT
4203936 GAA
1 GAA
4203939 CTTCTGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (20 bp):
GAATTCGAGTATACGCTGTT
Found at i:4204984 original size:361 final size:361
Alignment explanation
Indices: 4204320--4205399 Score: 1989
Period size: 361 Copynumber: 3.0 Consensus size: 361
4204310 AGGTGAAGTT
4204320 GTCACACGTGTTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
1 GTCACACGTGTTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
*
4204385 GCATATACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTACGTGAGCGTG
66 GCATATACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTATGTGAGCGTG
* *
4204450 TGCCCAAGCCGTGTGACTCATTGACTTGATGAATATGGGCAAACAAGTAACCATACGACTGTATA
131 TGCCCAAGCCGTGTGACTCATTGACTTGATGAATATGGGCACACAAGTAACCATACGACCGTATA
* * *
4204515 GAGTCACATGAGCAGCCACTTGGGCATGTAAGCCTGAGTCGCCAATTTCTGTTAACTCCATAATT
196 GAGTCACATGAGCAGCCACATGGGCATGTGAGCCTGAGTCGCCAATTTCTGTTAACGCCATAATT
*
4204580 GTTGTATGAGGCGAGTGTAAACTATCAGTAAGTTAGGTATCACCAAATTGAGCTGTATGATTTAC
261 GTTGTATGAGGCGAGTGTAAACTATCAGTAAGTTAGGTATCACCAAATTGAGCTGTATGATTTGC
4204645 TTTACTGAGATTATAAATTGGCTTTAATTACCCGTC
326 TTTACTGAGATTATAAATTGGCTTTAATTACCCGTC
*
4204681 GTCACACGTATTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
1 GTCACACGTGTTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
*
4204746 GCATACACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTATGTGAGCGTG
66 GCATATACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTATGTGAGCGTG
* *
4204811 TGCCCAAGTCGTGTGACTCATTGACTTGATGAATATGGGCACACAAGTAACTATACGACCGTATA
131 TGCCCAAGCCGTGTGACTCATTGACTTGATGAATATGGGCACACAAGTAACCATACGACCGTATA
*
4204876 GAGTCACATGAGCAGCCACATGGGCATGTGAGCCTGAGTCGCCAATTTTTGTTAACGCCATAATT
196 GAGTCACATGAGCAGCCACATGGGCATGTGAGCCTGAGTCGCCAATTTCTGTTAACGCCATAATT
*
4204941 GTTGTATGAGGCGAGTGTAAACTATCAGTAAGCTAGGTATCACCAAATTGAGCTGTATGATTTGC
261 GTTGTATGAGGCGAGTGTAAACTATCAGTAAGTTAGGTATCACCAAATTGAGCTGTATGATTTGC
4205006 TTTACTGAGATTATAAATTGGCTTTAATTACCCGTC
326 TTTACTGAGATTATAAATTGGCTTTAATTACCCGTC
4205042 GTCACACGTGTTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
1 GTCACACGTGTTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
*
4205107 GCATATACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTATGTGAGTGTG
66 GCATATACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTATGTGAGCGTG
*
4205172 TGTCCAAGCCGTGTGACTCATTGACTTGATGAATATGGGCACACAAGTAACCATACGACCGTATA
131 TGCCCAAGCCGTGTGACTCATTGACTTGATGAATATGGGCACACAAGTAACCATACGACCGTATA
* *
4205237 GAGTCACATGAGCAGCTACATGGGCATGTGAGCCTAAGTCGCCAATTTCTGTTAACGCCATAATT
196 GAGTCACATGAGCAGCCACATGGGCATGTGAGCCTGAGTCGCCAATTTCTGTTAACGCCATAATT
*
4205302 GTTGTATGAGGCGAGTGTAAACTATCAGTAAGTTAGGTATCACCAAATTGAGCTGTATGCTTTGC
261 GTTGTATGAGGCGAGTGTAAACTATCAGTAAGTTAGGTATCACCAAATTGAGCTGTATGATTTGC
*
4205367 TTTACTGATATTATAAATTGGCTTTAATTACCC
326 TTTACTGAGATTATAAATTGGCTTTAATTACCC
4205400 TCTGTTATAC
Statistics
Matches: 694, Mismatches: 25, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
361 694 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (361 bp):
GTCACACGTGTTGACACACGAGCGTGTGCTTAGACTGTGTAACTCACTGATTGATAAATAGGGAG
GCATATACAGGAGAAACTGGCATGTGCTGGACAATGTGAGGGACACGGGCTAGTATGTGAGCGTG
TGCCCAAGCCGTGTGACTCATTGACTTGATGAATATGGGCACACAAGTAACCATACGACCGTATA
GAGTCACATGAGCAGCCACATGGGCATGTGAGCCTGAGTCGCCAATTTCTGTTAACGCCATAATT
GTTGTATGAGGCGAGTGTAAACTATCAGTAAGTTAGGTATCACCAAATTGAGCTGTATGATTTGC
TTTACTGAGATTATAAATTGGCTTTAATTACCCGTC
Found at i:4209141 original size:2 final size:2
Alignment explanation
Indices: 4209134--4209186 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4209124 TCTTAATAGG
4209134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4209176 TA TA TA TA TA T
1 TA TA TA TA TA T
4209187 TTCTATTGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4216012 original size:2 final size:2
Alignment explanation
Indices: 4216007--4216032 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4215997 TGAAAAAAAA
4216007 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
4216033 TTCAGAGTTG
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:4219091 original size:2 final size:2
Alignment explanation
Indices: 4219080--4219117 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4219070 CAATTTCAGT
4219080 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4219118 GTTGTCTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4224888 original size:15 final size:15
Alignment explanation
Indices: 4224864--4224893 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4224854 GTTCAAAAAA
4224864 AATAGAAATAATAAT
1 AATAGAAATAATAAT
*
4224879 AATAGTAATAATAAT
1 AATAGAAATAATAAT
4224894 GTAAATAAAT
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:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AATAGAAATAATAAT
Found at i:4224983 original size:3 final size:3
Alignment explanation
Indices: 4224972--4225078 Score: 62
Period size: 3 Copynumber: 35.7 Consensus size: 3
4224962 TGATGATAGC
* * *
4224972 AAT AGT AAT AAT -AT AAT AAT AAT AAGGT -AG AAT -AT AAG AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT AAT
* * * *
4225016 AAT AAT ACATT AGT AAG AAT AAT AAT AGT AAT AA- AAG AAT AA- AAGT
1 AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
*
4225062 AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AA
4225079 CGTATACATA
Statistics
Matches: 79, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
2 8 0.10
3 64 0.81
4 4 0.05
5 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:4224992 original size:17 final size:17
Alignment explanation
Indices: 4224972--4225068 Score: 51
Period size: 17 Copynumber: 5.8 Consensus size: 17
4224962 TGATGATAGC
4224972 AATAGTAATAATATAAT
1 AATAGTAATAATATAAT
* ** *
4224989 AATAATAA-GGTAGAAT
1 AATAGTAATAATATAAT
4225005 -ATAAG-AATAATAATAAT
1 AAT-AGTAATAAT-ATAAT
*
4225022 ACATTAGTAA-GA-ATAAT
1 A-A-TAGTAATAATATAAT
* *
4225039 AATAGTAATAAAAGAAT
1 AATAGTAATAATATAAT
*
4225056 AAAAGTAATAATA
1 AATAGTAATAATA
4225069 ATAAAAATAA
Statistics
Matches: 58, Mismatches: 13, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
15 10 0.17
16 9 0.16
17 32 0.55
19 4 0.07
20 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.10, T:0.28
Consensus pattern (17 bp):
AATAGTAATAATATAAT
Found at i:4226423 original size:18 final size:17
Alignment explanation
Indices: 4226392--4226432 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
4226382 CTATTGTTTC
4226392 CTTTTCTTTGCTGCCAT
1 CTTTTCTTTGCTGCCAT
* *
4226409 CTTTTACTTTTCTGCCTT
1 CTTTT-CTTTGCTGCCAT
4226427 CTTTTC
1 CTTTTC
4226433 ACTGTTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.05, C:0.29, G:0.07, T:0.59
Consensus pattern (17 bp):
CTTTTCTTTGCTGCCAT
Found at i:4227756 original size:28 final size:28
Alignment explanation
Indices: 4227725--4227787 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
4227715 CACTGATTTA
4227725 TGTAACATTAGAATCATTCTAGTATTAC
1 TGTAACATTAGAATCATTCTAGTATTAC
4227753 TGTAACATTAGAATCATTCTAGTATTAC
1 TGTAACATTAGAATCATTCTAGTATTAC
4227781 TGCTAAC
1 TG-TAAC
4227788 GTTACAAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (28 bp):
TGTAACATTAGAATCATTCTAGTATTAC
Found at i:4233783 original size:43 final size:43
Alignment explanation
Indices: 4233746--4233883 Score: 231
Period size: 43 Copynumber: 3.2 Consensus size: 43
4233736 TGATTATGTA
4233746 TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTG
4233789 TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTG
* * ** *
4233832 TAAGACCATGTCTGGGACATTGGTATCGATATATGATAACATG
1 TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTG
4233875 TAAGACCAT
1 TAAGACCAT
4233884 ATCTAGGATA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTG
Found at i:4240845 original size:43 final size:43
Alignment explanation
Indices: 4240784--4240879 Score: 140
Period size: 43 Copynumber: 2.2 Consensus size: 43
4240774 ACGTGATTAT
* *
4240784 GTGTAAGACCATGTCTGGGACATTG-GCATCGTTATATGATATC
1 GTGTAAGACCATGTCTGGGACA-TGAGCATCGATATATGATAAC
*
4240827 GTGTAAGACCATGTCTGGGACATGAGCATCGATATGTGATAAC
1 GTGTAAGACCATGTCTGGGACATGAGCATCGATATATGATAAC
*
4240870 ATGTAAGACC
1 GTGTAAGACC
4240880 GTATCTAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 2 0.04
43 46 0.96
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATGAGCATCGATATATGATAAC
Found at i:4243614 original size:23 final size:23
Alignment explanation
Indices: 4243587--4243669 Score: 91
Period size: 22 Copynumber: 3.7 Consensus size: 23
4243577 AAATTGGGAA
4243587 TAAGGTTTTTAGGG-TTTAAGGTT
1 TAAGG-TTTTAGGGTTTTAAGGTT
*
4243610 TAAGGTTTTAGGGTTTTAGGGTT
1 TAAGGTTTTAGGGTTTTAAGGTT
*
4243633 T-AGAG-TTTAGGGTTTTAGGGTT
1 TAAG-GTTTTAGGGTTTTAAGGTT
* *
4243655 TTAGGGTTTAGGGTT
1 TAAGGTTTTAGGGTT
4243670 CAAGGATGCT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
22 29 0.53
23 26 0.47
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (23 bp):
TAAGGTTTTAGGGTTTTAAGGTT
Found at i:4243624 original size:8 final size:8
Alignment explanation
Indices: 4243593--4243669 Score: 92
Period size: 7 Copynumber: 10.2 Consensus size: 8
4243583 GGAATAAGGT
4243593 TTTTAGGG
1 TTTTAGGG
*
4243601 -TTTAAGG
1 TTTTAGGG
*
4243608 -TTTAAGG
1 TTTTAGGG
4243615 TTTTAGGG
1 TTTTAGGG
4243623 TTTTAGGG
1 TTTTAGGG
*
4243631 -TTTAGAG
1 TTTTAGGG
4243638 -TTTAGGG
1 TTTTAGGG
4243645 TTTTAGGG
1 TTTTAGGG
4243653 TTTTAGGG
1 TTTTAGGG
4243661 -TTTAGGG
1 TTTTAGGG
4243668 TT
1 TT
4243670 CAAGGATGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
7 32 0.52
8 30 0.48
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (8 bp):
TTTTAGGG
Found at i:4243628 original size:30 final size:30
Alignment explanation
Indices: 4243593--4243674 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 30
4243583 GGAATAAGGT
4243593 TTTTAGGGTTTAAGGTTTAAGGTTTTAGGG
1 TTTTAGGGTTTAAGGTTTAAGGTTTTAGGG
*
4243623 TTTTAGGGTTT-AGAGTTTAGGGTTTTAGGG
1 TTTTAGGGTTTAAG-GTTTAAGGTTTTAGGG
* *
4243653 TTTTAGGGTTTAGGGTTCAAGG
1 TTTTAGGGTTTAAGGTTTAAGG
4243675 ATGCTTCGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 2 0.04
30 43 0.93
31 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.45
Consensus pattern (30 bp):
TTTTAGGGTTTAAGGTTTAAGGTTTTAGGG
Found at i:4248441 original size:15 final size:15
Alignment explanation
Indices: 4248421--4248451 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4248411 TAGATCCCTC
4248421 CCCATATCTAAATTA
1 CCCATATCTAAATTA
4248436 CCCATATCTAAATTA
1 CCCATATCTAAATTA
4248451 C
1 C
4248452 TATAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (15 bp):
CCCATATCTAAATTA
Found at i:4252590 original size:18 final size:17
Alignment explanation
Indices: 4252558--4252591 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4252548 GAAGTAATTT
*
4252558 TGAATTAATGAATTTTG
1 TGAATTAAAGAATTTTG
4252575 TGAATTAAAAGAATTTT
1 TGAATT-AAAGAATTTT
4252592 TAGGTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (17 bp):
TGAATTAAAGAATTTTG
Found at i:4254996 original size:87 final size:87
Alignment explanation
Indices: 4254879--4255054 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 87
4254869 AACTTTCCAA
*
4254879 AATAACTCCATTCATTGATTTACTAGTATCTACTACTAAATACTTGCAAACAAACATATATATAT
1 AATAACTCCATTCATTGATTTACTAATATCTACTACTAAATACTTGCAAACAAACATATATATAT
*
4254944 GCATCATTCACATTCATAATTC
66 ACATCATTCACATTCATAATTC
*
4254966 AATAACTCCATTCATTGGTTTACTAATATCTACTACTAAATACTTGCAAACAAACATATATATAT
1 AATAACTCCATTCATTGATTTACTAATATCTACTACTAAATACTTGCAAACAAACATATATATAT
4255031 ACATCATTCACATTCATAATTC
66 ACATCATTCACATTCATAATTC
4255053 AA
1 AA
4255055 GTTTAACTCT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.35
Consensus pattern (87 bp):
AATAACTCCATTCATTGATTTACTAATATCTACTACTAAATACTTGCAAACAAACATATATATAT
ACATCATTCACATTCATAATTC
Found at i:4256942 original size:22 final size:23
Alignment explanation
Indices: 4256883--4256968 Score: 99
Period size: 22 Copynumber: 3.9 Consensus size: 23
4256873 CTGATCAGTT
*
4256883 TACGACACAT-AAGTGCTTG-AA
1 TACGACACATAAAGTGCCTGAAA
** *
4256904 -ACGACACACGAGGTGCCTGAAA
1 TACGACACATAAAGTGCCTGAAA
*
4256926 TACGAC-CATAAAGTGCCTGATA
1 TACGACACATAAAGTGCCTGAAA
4256948 TACGACACATAAAGTGCCTGA
1 TACGACACATAAAGTGCCTGA
4256969 TCGGCAAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 8 0.15
21 7 0.13
22 20 0.37
23 19 0.35
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
TACGACACATAAAGTGCCTGAAA
Found at i:4256962 original size:23 final size:23
Alignment explanation
Indices: 4256883--4256969 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 23
4256873 CTGATCAGTT
*
4256883 TACGACACAT-AAGTGCTTGA-A
1 TACGACACATAAAGTGCCTGATA
** * *
4256904 -ACGACACACGAGGTGCCTGAAA
1 TACGACACATAAAGTGCCTGATA
4256926 TACGAC-CATAAAGTGCCTGATA
1 TACGACACATAAAGTGCCTGATA
4256948 TACGACACATAAAGTGCCTGAT
1 TACGACACATAAAGTGCCTGAT
4256970 CGGCAAAACC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 8 0.15
21 8 0.15
22 19 0.35
23 20 0.36
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (23 bp):
TACGACACATAAAGTGCCTGATA
Found at i:4259247 original size:95 final size:97
Alignment explanation
Indices: 4259093--4259283 Score: 262
Period size: 95 Copynumber: 2.0 Consensus size: 97
4259083 AAACAATTAT
* * * * **
4259093 TCATCCATTGATCTCTAATTCGATCCCTAAAATTATTTTTCACTATTTTTATTGTAAAAAGTACT
1 TCATCCACTGATCTCCAATTCAATCCCTAAAATTATTTTTCACTATTTTCATTACAAAAAGTACT
*
4259158 CTTTCCACATTTGCTGTAACAACTAG-AAAAG
66 CTTTCCACATTGGCTGTAACAACTAGCAAAAG
* *
4259189 TCATCCACTGATCTCCAATTCAATTCCT-CAATTATTTTTCA-TGATTTTCATTACAAAAAGTAC
1 TCATCCACTGATCTCCAATTCAATCCCTAAAATTATTTTTCACT-ATTTTCATTACAAAAAGTAC
*
4259252 TCTTTCCACATTGGTTGTAACAACTAGCAAAA
65 TCTTTCCACATTGGCTGTAACAACTAGCAAAA
4259284 TCAATGCAAG
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
94 1 0.01
95 54 0.65
96 28 0.34
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.38
Consensus pattern (97 bp):
TCATCCACTGATCTCCAATTCAATCCCTAAAATTATTTTTCACTATTTTCATTACAAAAAGTACT
CTTTCCACATTGGCTGTAACAACTAGCAAAAG
Found at i:4262348 original size:102 final size:102
Alignment explanation
Indices: 4262119--4262348 Score: 327
Period size: 102 Copynumber: 2.3 Consensus size: 102
4262109 TAGCGTAGCA
* *
4262119 TAAGACCATGGATGAAAGACACCATGGCAGCATGGTACAAGGTATAAGATATACAGTATAAGACC
1 TAAGACCATAGATGAAAGACACTATGGCAGCATGGTACAAGGTATAAGATATACAGTATAAGACC
*
4262184 ATAGATGAAAGATGCTATGACAACTAAGAATAGTGAG
66 ATAGATGAAAGATGCTATGACAACCAAGAATAGTGAG
* * * * *
4262221 TAAAACCATAAATGAAAGAAACTATGGCAGCATGGTATAAGGTATAAGATATACGGTATAAGACC
1 TAAGACCATAGATGAAAGACACTATGGCAGCATGGTACAAGGTATAAGATATACAGTATAAGACC
* * * *
4262286 ATA-AGTGAAAGATGTTATGGCAGCCAAGTATAGTGAG
66 ATAGA-TGAAAGATGCTATGACAACCAAGAATAGTGAG
*
4262323 TAAGACCATAGATGAAAGACTCTATG
1 TAAGACCATAGATGAAAGACACTATG
4262349 ACATCATATG
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 1 0.01
102 110 0.99
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (102 bp):
TAAGACCATAGATGAAAGACACTATGGCAGCATGGTACAAGGTATAAGATATACAGTATAAGACC
ATAGATGAAAGATGCTATGACAACCAAGAATAGTGAG
Found at i:4262989 original size:4 final size:4
Alignment explanation
Indices: 4262980--4263004 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4262970 TTTAGGCTTT
4262980 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
4263005 GTTTTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4270938 original size:22 final size:21
Alignment explanation
Indices: 4270906--4270976 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
4270896 AGGCCTACTA
*
4270906 GGCACATAGCCCGAATAACACC
1 GGCACAAAGCCC-AATAACACC
*
4270928 GGCACAAAG-CC--TATCA--
1 GGCACAAAGCCCAATAACACC
*
4270944 GGCACATAGCCCAAATAACACC
1 GGCACAAAGCCC-AATAACACC
4270966 GGCACAAAGCC
1 GGCACAAAGCC
4270977 TGCCATGCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
16 8 0.21
17 2 0.05
18 4 0.11
20 4 0.11
21 2 0.05
22 18 0.47
ACGTcount: A:0.38, C:0.35, G:0.18, T:0.08
Consensus pattern (21 bp):
GGCACAAAGCCCAATAACACC
Found at i:4271039 original size:38 final size:38
Alignment explanation
Indices: 4270816--4271036 Score: 264
Period size: 38 Copynumber: 5.8 Consensus size: 38
4270806 AATCCACCAT
* * * **
4270816 CACAAAGTCTGCTAGGCACAGAGCCTGAATAACATGGG
1 CACAAAGCCTGCTAGGCACATAGCCCGAATAACACCGG
* **
4270854 CACAAAGCCTGCTAGGCACATAACCCGAATAACACCAA
1 CACAAAGCCTGCTAGGCACATAGCCCGAATAACACCGG
* *
4270892 CACAAGGCCTACTAGGCACATAGCCCGAATAACACCGG
1 CACAAAGCCTGCTAGGCACATAGCCCGAATAACACCGG
* *
4270930 CACAAAGCCT-ATCAGGCACATAGCCCAAATAACACCGG
1 CACAAAGCCTGCT-AGGCACATAGCCCGAATAACACCGG
* * *
4270968 CACAAAGCCTGCCATGCACATAGCCCGAATATCACCGG
1 CACAAAGCCTGCTAGGCACATAGCCCGAATAACACCGG
* * *
4271006 CACAAAGCTTGTTAGGTACATAGCCCGAATA
1 CACAAAGCCTGCTAGGCACATAGCCCGAATA
4271037 TCATTATGCT
Statistics
Matches: 155, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
37 1 0.01
38 154 0.99
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (38 bp):
CACAAAGCCTGCTAGGCACATAGCCCGAATAACACCGG
Found at i:4276110 original size:3 final size:3
Alignment explanation
Indices: 4276102--4276137 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4276092 TTTTTTCAAG
4276102 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4276138 TTTACGCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4287085 original size:21 final size:21
Alignment explanation
Indices: 4287059--4287103 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4287049 TATTTTGTAA
*
4287059 TTTTTTTATTACTTTT-ATGAT
1 TTTTTTTA-TAATTTTCATGAT
4287080 TTTTTTTATAATTTTCATGAT
1 TTTTTTTATAATTTTCATGAT
4287101 TTT
1 TTT
4287104 AAATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTTTATAATTTTCATGAT
Found at i:4287885 original size:27 final size:27
Alignment explanation
Indices: 4287847--4287900 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
4287837 TTTCATAAGG
4287847 TATGATGACAT-GACACTTTAAGATTGT
1 TATGATGACATGGA-ACTTTAAGATTGT
4287874 TATGATGACATGGAACTTTAAGATTGT
1 TATGATGACATGGAACTTTAAGATTGT
4287901 GCCATGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (27 bp):
TATGATGACATGGAACTTTAAGATTGT
Found at i:4289976 original size:27 final size:27
Alignment explanation
Indices: 4289935--4289991 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
4289925 TTGTGCAAGA
* * *
4289935 TATATATATATAATATGATGTTAAAAG
1 TATACATATAAAATATAATGTTAAAAG
4289962 TATACATATAAAATATAATGTTAAAAG
1 TATACATATAAAATATAATGTTAAAAG
4289989 TAT
1 TAT
4289992 GTATGCATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.39
Consensus pattern (27 bp):
TATACATATAAAATATAATGTTAAAAG
Found at i:4290538 original size:18 final size:17
Alignment explanation
Indices: 4290517--4290550 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
4290507 ATACATTTAA
4290517 TATAACAAATATAAATAT
1 TATAACAAATA-AAATAT
4290535 TATAACAAATAAAATA
1 TATAACAAATAAAATA
4290551 CAGAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAACAAATAAAATAT
Found at i:4292705 original size:60 final size:59
Alignment explanation
Indices: 4292559--4292731 Score: 248
Period size: 60 Copynumber: 3.0 Consensus size: 59
4292549 TAAAAGCAAA
*
4292559 TTTTGAAAAACAGAAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGA-----T
1 TTTTGAAAAACATAAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
4292613 TTTTGAAAAACATGAATTTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 TTTTGAAAAACAT-AAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
4292673 TTTTAAAAAACATAAATTGAAAGGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTT
1 TTTTGAAAAACATAAATT-AAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
4292732 GGAAGGTAGA
Statistics
Matches: 105, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
54 12 0.11
55 38 0.36
59 4 0.04
60 51 0.49
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (59 bp):
TTTTGAAAAACATAAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
Found at i:4292866 original size:54 final size:54
Alignment explanation
Indices: 4292784--4292894 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
4292774 CGTGTGAGCC
4292784 AAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
4292838 AAAGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTGAAAAACATAAATTAA
1 AAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
4292892 AAA
1 AAA
4292895 CAGAAATTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (54 bp):
AAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:4292963 original size:140 final size:142
Alignment explanation
Indices: 4292637--4292965 Score: 414
Period size: 144 Copynumber: 2.3 Consensus size: 142
4292627 AATTTAAAAG
* * **
4292637 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAAACATAAATTGAAAGGGCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTGAAAAACAGAAATTGAAAAAGCTCA
* * ***
4292702 ACTCACCTTTCGCAATATGAGTTGATTTTTGGAAGGTAGAAATTGAAAAAACAAAAATTGAAATT
61 ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAAAACAAAAATTGAAATT
4292767 ACCTCAGCGTGTGAGCCAAA
125 ACCTCAGCGTGT--GCCAAA
4292787 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAAAGCTCAACTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAAGCTCAACTCA
* * * *
4292851 CCTCTCGCAGTATGAGTTGATTTTTGAAAAACATAAATT-AAAAACAGAAATTGAAGA-TGCCTC
66 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAACAAAAATTGAA-ATTACCTC
4292914 AGCGTGT-CCTAAA
130 AGCGTGTGCC-AAA
*
4292927 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
4292966 TCATGAATTA
Statistics
Matches: 163, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
139 2 0.01
140 41 0.25
142 27 0.17
143 1 0.01
144 45 0.28
145 17 0.10
150 30 0.18
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (142 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAAGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAACAAAAATTGAAATTACCTCA
GCGTGTGCCAAA
Found at i:4293128 original size:79 final size:78
Alignment explanation
Indices: 4292992--4293310 Score: 324
Period size: 79 Copynumber: 4.0 Consensus size: 78
4292982 AAATTAGAAG
* * *
4292992 AACATAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
4293057 TTTTGAAAAGCAGA
66 TTTTGAAAAG-AGA
4293071 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
4293136 TTTTTTGAAACATAAATTGAAA
65 -TTTTTG----A-AAA--GAGA
* * * * *
4293158 GAACAGAAATTGGAAA-TACCTCAGTATGTGAACC-GAGGTTCAACTCATCTCTCGCAATGTGAG
1 -AACAGAAATT-GAAATTACCTCAG--CGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAG
** *
4293221 TTGATTTTT---TTGAAA
61 TTGATTTTTGAAAAGAGA
* * * *
4293236 AACAGAAATTAAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTATCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
4293301 TTTTGAAAAG
66 TTTTGAAAAG
4293311 TATAAATTAA
Statistics
Matches: 201, Mismatches: 20, Indels: 39
0.77 0.08 0.15
Matches are distributed among these distances:
74 2 0.01
75 37 0.18
76 3 0.01
77 18 0.09
78 5 0.02
79 61 0.30
81 6 0.03
85 1 0.00
86 3 0.01
87 2 0.01
88 24 0.12
89 4 0.02
90 33 0.16
91 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (78 bp):
AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAAGAGA
Found at i:4293273 original size:165 final size:165
Alignment explanation
Indices: 4292976--4293304 Score: 434
Period size: 165 Copynumber: 2.0 Consensus size: 165
4292966 TCATGAATTA
* *
4292976 AAACAGAAATTAGAAGAACATAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACTTCT
1 AAACAGAAATTAGAAGAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACTTCT
* * * *
4293041 CGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGG
66 CGCAATATGAGTTGATTTTT--AAAGCAAAAACAGAAATTAAAATTACCTCAGCGTGCCCCGAGG
*
4293106 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
129 CTCAACTCACCTATCGCAATATGAGTTGATTTTTTTG
* * * *
4293143 AAACATAAATT-GAAAGAACAGAAATTGGAAATACCTCAGTATGTGAACC-GAGGTTCAACTCA-
1 AAACAGAAATTAG-AAGAACAGAAATTGAAAATACCTCAG--CGTG-ACCTGAGGCTCAACTCAC
* **
4293205 TCTCTCGCAATGTGAGTTGATTTTT-TTG-AAAAACAGAAATTAAAATTACCTCAGCGTGCCCCG
62 T-TCTCGCAATATGAGTTGATTTTTAAAGCAAAAACAGAAATTAAAATTACCTCAGCGTGCCCCG
4293268 AGGCTCAACTCACCTATCGCAATATGAGTTGATTTTT
126 AGGCTCAACTCACCTATCGCAATATGAGTTGATTTTT
4293305 GAAAAGTATA
Statistics
Matches: 143, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
165 67 0.47
166 2 0.01
167 34 0.24
168 1 0.01
169 37 0.26
170 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (165 bp):
AAACAGAAATTAGAAGAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACTTCT
CGCAATATGAGTTGATTTTTAAAGCAAAAACAGAAATTAAAATTACCTCAGCGTGCCCCGAGGCT
CAACTCACCTATCGCAATATGAGTTGATTTTTTTG
Found at i:4305932 original size:27 final size:27
Alignment explanation
Indices: 4305895--4305946 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4305885 TGCAAGATAT
* * *
4305895 ATATATAATATGATGTTAAGAGTATAC
1 ATATAAAATATAATGTTAAAAGTATAC
4305922 ATATAAAATATAATGTTAAAAGTAT
1 ATATAAAATATAATGTTAAAAGTAT
4305947 GTATGCATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (27 bp):
ATATAAAATATAATGTTAAAAGTATAC
Found at i:4306427 original size:8 final size:8
Alignment explanation
Indices: 4306414--4306453 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
4306404 AATATTGAAA
4306414 ATACATAT
1 ATACATAT
4306422 ATACATAT
1 ATACATAT
*
4306430 ATATATAT
1 ATACATAT
*
4306438 ATATATAT
1 ATACATAT
4306446 ATAACATA
1 AT-ACATA
4306454 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 25 0.86
9 4 0.14
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (8 bp):
ATACATAT
Found at i:4306431 original size:2 final size:2
Alignment explanation
Indices: 4306418--4306448 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4306408 TTGAAAATAC
*
4306418 AT AT AT AC 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 A
4306449 ACATAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4306507 original size:18 final size:17
Alignment explanation
Indices: 4306486--4306519 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
4306476 ATACATTTAA
4306486 TATAACAAATATAAATAT
1 TATAACAAATA-AAATAT
4306504 TATAACAAATAAAATA
1 TATAACAAATAAAATA
4306520 CAGAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAACAAATAAAATAT
Found at i:4310321 original size:31 final size:31
Alignment explanation
Indices: 4310232--4310311 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
4310222 ATCAAATTAA
* * *
4310232 AAAACTTAAATACTAAAGTGAACATTAAAACT
1 AAAA-TTAAATACCAAATTAAACATTAAAACT
* *
4310264 AAAATTACATACCAAATTAAACATTAAAATT
1 AAAATTAAATACCAAATTAAACATTAAAACT
* *
4310295 AAATTTAAATATCAAAT
1 AAAATTAAATACCAAAT
4310312 AATATATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAATTAAATACCAAATTAAACATTAAAACT
Found at i:4310582 original size:26 final size:27
Alignment explanation
Indices: 4310547--4310598 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
4310537 CTGACCTTAG
4310547 TTTTATTGT-CCAATTTGGTACTTGAT
1 TTTTATTGTCCCAATTTGGTACTTGAT
*
4310573 TTTTCTTGTCCCAATTTGGTACTTGA
1 TTTTATTGTCCCAATTTGGTACTTGA
4310599 ATTTGGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.52
Consensus pattern (27 bp):
TTTTATTGTCCCAATTTGGTACTTGAT
Found at i:4310724 original size:25 final size:25
Alignment explanation
Indices: 4310696--4310748 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4310686 ATGTAATTAG
* *
4310696 GAAAAAAAAACTCAAGTATCAAATT
1 GAAAAAAAAACTCAAGTACCAAAGT
* *
4310721 GAAAAAAAAATTCAGGTACCAAAGT
1 GAAAAAAAAACTCAAGTACCAAAGT
4310746 GAA
1 GAA
4310749 CATTGAAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.17
Consensus pattern (25 bp):
GAAAAAAAAACTCAAGTACCAAAGT
Found at i:4311496 original size:17 final size:17
Alignment explanation
Indices: 4311474--4311522 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
4311464 AATATATAAT
*
4311474 ATAAATTTTAAAAATTA
1 ATAAATATTAAAAATTA
4311491 ATAAATATTAAAAATTA
1 ATAAATATTAAAAATTA
4311508 ATAAATATTAAAAAT
1 ATAAATATTAAAAAT
4311523 AATGCCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATATTAAAAATTA
Found at i:4318906 original size:25 final size:25
Alignment explanation
Indices: 4318878--4318929 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4318868 AAAAAAGTTC
4318878 AAATGATAATTACAGCAAAAACCCA
1 AAATGATAATTACAGCAAAAACCCA
4318903 AAATGATAATTACAGCAAAAACCCA
1 AAATGATAATTACAGCAAAAACCCA
4318928 AA
1 AA
4318930 TCACCATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (25 bp):
AAATGATAATTACAGCAAAAACCCA
Found at i:4320080 original size:24 final size:24
Alignment explanation
Indices: 4320053--4320112 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
4320043 GTTCGTCTAG
* **
4320053 TTCAATTAAATAAATTATTAAATT
1 TTCAATTAAATAAAATATTAAAAA
*
4320077 TTC-ATAAAATAAAAATATTAAAAA
1 TTCAATTAAAT-AAAATATTAAAAA
*
4320101 TTCAATTCAATA
1 TTCAATTAAATA
4320113 TATTCATACC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
23 6 0.21
24 17 0.61
25 5 0.18
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (24 bp):
TTCAATTAAATAAAATATTAAAAA
Found at i:4321186 original size:14 final size:14
Alignment explanation
Indices: 4321167--4321204 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
4321157 GTTTGTCAGT
*
4321167 AAAATGTTTTCTGG
1 AAAATGATTTCTGG
4321181 AAAATGATTTCTGG
1 AAAATGATTTCTGG
4321195 AAAATGATTT
1 AAAATGATTT
4321205 ACTTTTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:4321220 original size:19 final size:20
Alignment explanation
Indices: 4321188--4321233 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
4321178 TGGAAAATGA
4321188 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
*
4321208 TTTCTGG-AAATGATTTATT
1 TTTCTGGAAAATGATTTACT
4321227 TTTCTGG
1 TTTCTGG
4321234 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:4321335 original size:16 final size:18
Alignment explanation
Indices: 4321314--4321356 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
4321304 CTATTTTTAC
*
4321314 ATATATTAATAAATTTAT
1 ATATATTAATAAATATAT
4321332 ATATATTAATAAA-AT-T
1 ATATATTAATAAATATAT
*
4321348 ATATTTTAA
1 ATATATTAA
4321357 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
18 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATTAATAAATATAT
Found at i:4321335 original size:18 final size:18
Alignment explanation
Indices: 4321309--4321351 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4321299 AAAAACTATT
*
4321309 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
4321327 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
*
4321345 ATTATAT
1 TTTATAT
4321352 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:4327536 original size:43 final size:43
Alignment explanation
Indices: 4327472--4327557 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
4327462 TATGTGATTG
* * *
4327472 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTCAAATAGCAAAGATGAGAAATGAATATGAAATGAGAAA
* *
4327515 ATATTCAAATAGCAAATATGAGAAATGATTATGAAATGAGAAA
1 ATATTCAAATAGCAAAGATGAGAAATGAATATGAAATGAGAAA
4327558 TGAAATATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.23
Consensus pattern (43 bp):
ATATTCAAATAGCAAAGATGAGAAATGAATATGAAATGAGAAA
Found at i:4327555 original size:18 final size:19
Alignment explanation
Indices: 4327532--4327572 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
4327522 AATAGCAAAT
*
4327532 ATGAGAAATG-ATTATGAA
1 ATGAGAAATGAAATATGAA
4327550 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
4327569 ATGA
1 ATGA
4327573 TGAATTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:4333264 original size:43 final size:43
Alignment explanation
Indices: 4333200--4333285 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
4333190 TATGTGATTG
* * *
4333200 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTCAAATAGCAAAGATGAGAAATGAATATGAAATGAGAAA
* *
4333243 ATATTCAAATAGCAAATATGAGAAATGATTATGAAATGAGAAA
1 ATATTCAAATAGCAAAGATGAGAAATGAATATGAAATGAGAAA
4333286 TGAAATATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.23
Consensus pattern (43 bp):
ATATTCAAATAGCAAAGATGAGAAATGAATATGAAATGAGAAA
Found at i:4333283 original size:18 final size:19
Alignment explanation
Indices: 4333260--4333300 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
4333250 AATAGCAAAT
*
4333260 ATGAGAAATG-ATTATGAA
1 ATGAGAAATGAAATATGAA
4333278 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
4333297 ATGA
1 ATGA
4333301 TGAATTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:4344364 original size:2 final size:2
Alignment explanation
Indices: 4344348--4344381 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
4344338 AAGCTAATTG
4344348 TA TA -A TA TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
4344382 CTCGTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4349489 original size:46 final size:45
Alignment explanation
Indices: 4349422--4349596 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
4349412 TGTAACCCGC
*
4349422 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * *
4349468 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** * **
4349514 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
4349561 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
4349597 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 69 0.66
47 33 0.31
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:4349541 original size:93 final size:93
Alignment explanation
Indices: 4349429--4349601 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
4349419 CGCCCATAAG
** *
4349429 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
4349494 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
4349522 CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
4349587 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
4349602 CAAATATCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:4351573 original size:15 final size:15
Alignment explanation
Indices: 4351504--4351580 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
4351494 AACAAAGATA
*
4351504 AAAGAAAACC-GAAT
1 AAAGAAATCCAGAAT
4351518 AAAGAAATCCA-AGAT
1 AAAGAAATCCAGA-AT
* * *
4351533 AGAGAAACCCGGAAT
1 AAAGAAATCCAGAAT
4351548 AAAGAAATCCAGAAT
1 AAAGAAATCCAGAAT
* *
4351563 AAAGAGATCCAGGAT
1 AAAGAAATCCAGAAT
4351578 AAA
1 AAA
4351581 AAACCCAAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
14 10 0.20
15 40 0.78
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAGAAATCCAGAAT
Found at i:4351580 original size:30 final size:30
Alignment explanation
Indices: 4351498--4351592 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
4351488 TTATGGAACA
4351498 AAGATAAAAGAAAACC--GAATAAAGAAATCC
1 AAGAT-AAAG-AAACCAGGAATAAAGAAATCC
* *
4351528 AAGATAGAGAAACCCGGAATAAAGAAATCC
1 AAGATAAAGAAACCAGGAATAAAGAAATCC
* *
4351558 -AGAATAAAGAGATCCAGG-ATAAA-AAACCC
1 AAG-ATAAAGA-AACCAGGAATAAAGAAATCC
4351587 AAGATA
1 AAGATA
4351593 CAATACTATG
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
28 5 0.09
29 13 0.24
30 32 0.58
31 5 0.09
ACGTcount: A:0.58, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGATAAAGAAACCAGGAATAAAGAAATCC
Found at i:4354482 original size:46 final size:45
Alignment explanation
Indices: 4354415--4354589 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
4354405 TGTAACCCGC
4354415 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * *
4354461 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** * ** *
4354507 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
4354554 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
4354590 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 69 0.66
47 33 0.31
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:4354535 original size:93 final size:93
Alignment explanation
Indices: 4354423--4354594 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
4354413 GCCCATAAGT
** * *
4354423 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
4354488 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
4354516 GAACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
4354581 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
4354595 CAAATATCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:4357326 original size:5 final size:5
Alignment explanation
Indices: 4357316--4357357 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
4357306 TAAGTAAATA
*
4357316 ATATT ATATT ATATT ATATT ATATT AATATT ATAAT ATATT A
1 ATATT ATATT ATATT ATATT ATATT -ATATT ATATT ATATT A
4357358 AGTAAACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:4359737 original size:30 final size:30
Alignment explanation
Indices: 4359703--4359765 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4359693 ACTTAACAAG
4359703 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
4359733 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
4359763 CAA
1 CAA
4359766 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:4361061 original size:18 final size:19
Alignment explanation
Indices: 4361038--4361078 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
4361028 CTAATATATT
*
4361038 TAATTTCAAAAAA-TTAAA
1 TAATTTAAAAAAAGTTAAA
4361056 TAATTTAAAAAAAGGTTAAA
1 TAATTTAAAAAAA-GTTAAA
4361076 TAA
1 TAA
4361079 CCAAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
TAATTTAAAAAAAGTTAAA
Found at i:4362654 original size:27 final size:30
Alignment explanation
Indices: 4362608--4362667 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 30
4362598 TTAAATTAAT
4362608 AATAATAAAATTACACTTTAACCTTAAAAA
1 AATAATAAAATTACACTTTAACCTTAAAAA
* *
4362638 AATAA-AAAATTA-A-TTTAATCTTTAAAA
1 AATAATAAAATTACACTTTAACCTTAAAAA
4362665 AAT
1 AAT
4362668 TATTCCCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.54
28 1 0.04
29 7 0.25
30 5 0.18
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (30 bp):
AATAATAAAATTACACTTTAACCTTAAAAA
Found at i:4369258 original size:21 final size:22
Alignment explanation
Indices: 4369232--4369273 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
4369222 CACGTTAGCG
4369232 AACAAATATTTA-ATATAAATA
1 AACAAATATTTATATATAAATA
4369253 AACAAATATTTATATATAAAT
1 AACAAATATTTATATATAAAT
4369274 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AACAAATATTTATATATAAATA
Found at i:4370683 original size:38 final size:38
Alignment explanation
Indices: 4370632--4370721 Score: 91
Period size: 38 Copynumber: 2.4 Consensus size: 38
4370622 GGCATAAGGT
4370632 GTAAAT-T-TATTATATATAT-TATTA-ATAA-ATTAAA
1 GTAAATATATATTATA-ATATGTATTACATAATATTAAA
* * *
4370666 GTTAAAATATATATTATAATATGTTTTACTTAATATTTAA
1 G-T-AAATATATATTATAATATGTATTACATAATATTAAA
4370706 GTAAATATATATTATA
1 GTAAATATATATTATA
4370722 GTAATAAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
34 1 0.02
35 1 0.02
36 4 0.09
37 5 0.11
38 25 0.54
39 4 0.09
40 6 0.13
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (38 bp):
GTAAATATATATTATAATATGTATTACATAATATTAAA
Found at i:4372693 original size:2 final size:2
Alignment explanation
Indices: 4372686--4372725 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4372676 TTTAAATGTC
4372686 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
4372726 TAAATTGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4378394 original size:38 final size:38
Alignment explanation
Indices: 4378344--4378433 Score: 91
Period size: 38 Copynumber: 2.4 Consensus size: 38
4378334 GGCATAAGGT
4378344 GTAAA-AT-TATTATATATAT-TATTA-ATAA-ATTAAA
1 GTAAATATATATTATA-ATATGTATTACATAATATTAAA
* * *
4378378 GTTAAAATATATATTATAATATGTTTTACTTAATATTTAA
1 G-T-AAATATATATTATAATATGTATTACATAATATTAAA
4378418 GTAAATATATATTATA
1 GTAAATATATATTATA
4378434 GTAATAAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
34 1 0.02
35 1 0.02
36 3 0.07
37 6 0.13
38 25 0.54
39 4 0.09
40 6 0.13
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (38 bp):
GTAAATATATATTATAATATGTATTACATAATATTAAA
Found at i:4381721 original size:3 final size:3
Alignment explanation
Indices: 4381713--4381738 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4381703 ATATTTAGGT
4381713 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4381739 CTTTTCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4381951 original size:30 final size:30
Alignment explanation
Indices: 4381912--4381980 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
4381902 TTAAATTAGT
* * *
4381912 AATAGTAAAATTATATTTTATTTTTTTAAA
1 AATAATAAAATTATAATTTAATTTTTTAAA
*
4381942 AATAATAAAATTTTAATTTAATTTTTTAAA
1 AATAATAAAATTATAATTTAATTTTTTAAA
*
4381972 AATTATAAA
1 AATAATAAA
4381981 GATATAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
AATAATAAAATTATAATTTAATTTTTTAAA
Found at i:4383239 original size:15 final size:16
Alignment explanation
Indices: 4383219--4383251 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4383209 AACACTCTTA
4383219 TTTTATTT-TTTTCTC
1 TTTTATTTATTTTCTC
*
4383234 TTTTATTTATTTTTTC
1 TTTTATTTATTTTCTC
4383250 TT
1 TT
4383252 AGTGCAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTATTTTCTC
Found at i:4383636 original size:42 final size:41
Alignment explanation
Indices: 4383578--4383705 Score: 175
Period size: 42 Copynumber: 3.0 Consensus size: 41
4383568 TTCCAACAAG
* * *
4383578 AAGAACCAAACCAAGCTTGTTAAACCATCAAATGTATCCACC
1 AAGAACCAAACCAAGCTCGTTAAATCAT-GAATGTATCCACC
* *
4383620 AAGAACCAAACCAAGCTGGTTGAATCAGTGAATGTATCCACC
1 AAGAACCAAACCAAGCTCGTTAAATCA-TGAATGTATCCACC
*
4383662 AAGAACCAAACCAAGCTCGTTAAATCATTGAATGTATCAACC
1 AAGAACCAAACCAAGCTCGTTAAATCA-TGAATGTATCCACC
4383704 AA
1 AA
4383706 AACGTCGAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 76 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.20
Consensus pattern (41 bp):
AAGAACCAAACCAAGCTCGTTAAATCATGAATGTATCCACC
Found at i:4401925 original size:22 final size:23
Alignment explanation
Indices: 4401876--4401927 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
4401866 TATTTTCTTG
*
4401876 TTATTTT-CTCATTATTTTGCTA
1 TTATTTTACTCATTATGTTGCTA
**
4401898 CCATTTTACT-ATTATGTTGCTA
1 TTATTTTACTCATTATGTTGCTA
4401920 TTATTTTA
1 TTATTTTA
4401928 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (23 bp):
TTATTTTACTCATTATGTTGCTA
Found at i:4402001 original size:30 final size:30
Alignment explanation
Indices: 4401967--4402026 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4401957 TATTTTATTA
*
4401967 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTAATTATTTTAAAGACATTTG
* *
4401997 TTAATTTTGTAATTATTTTAGAGGCATTTG
1 TTAATTTTGTAATTATTTTAAAGACATTTG
4402027 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.55
Consensus pattern (30 bp):
TTAATTTTGTAATTATTTTAAAGACATTTG
Found at i:4402753 original size:17 final size:18
Alignment explanation
Indices: 4402721--4402754 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4402711 ATATACTAAC
*
4402721 TTAAAAATTTATAAATTT
1 TTAAAAATTTAAAAATTT
4402739 TTAAAAA-TTAAAAATT
1 TTAAAAATTTAAAAATT
4402755 GAAAATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAAATTTAAAAATTT
Found at i:4404533 original size:22 final size:23
Alignment explanation
Indices: 4404508--4404550 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4404498 CGCTGACTTT
* *
4404508 TTTTTTTAATTTTA-ATTTTAAA
1 TTTTTTAAATGTTATATTTTAAA
4404530 TTTTTTAAATGTTATATTTTA
1 TTTTTTAAATGTTATATTTTA
4404551 TGTGATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTTAAATGTTATATTTTAAA
Found at i:4418786 original size:14 final size:12
Alignment explanation
Indices: 4418753--4418799 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
4418743 AAAGTACCGA
*
4418753 AAATAATAAAAT
1 AAATAAAAAAAT
4418765 AAATAAAAAAAT
1 AAATAAAAAAAT
4418777 AACGATAAAAAAAT
1 AA--ATAAAAAAAT
4418791 --ATAAAAAAA
1 AAATAAAAAAA
4418800 GTAGGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.28
12 13 0.41
14 10 0.31
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:4419370 original size:42 final size:42
Alignment explanation
Indices: 4419307--4419392 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
4419297 CACGGAGCCA
* * * *
4419307 GCGAGTCTGCGCCCTGGCCACCGGTCATCAGTGACGGCGACC
1 GCGAGTCTGCACCCTGACCACCGATCATCAGTGACGGCAACC
*
4419349 GCGAGTCTGCACCCTGACCACCGATCATCGGTGACGGCAACC
1 GCGAGTCTGCACCCTGACCACCGATCATCAGTGACGGCAACC
4419391 GC
1 GC
4419393 CGCCTCCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.17, C:0.38, G:0.30, T:0.14
Consensus pattern (42 bp):
GCGAGTCTGCACCCTGACCACCGATCATCAGTGACGGCAACC
Found at i:4425068 original size:16 final size:16
Alignment explanation
Indices: 4425028--4425069 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
4425018 CAAACGAGTT
4425028 TAAATTTTTTTTTATC
1 TAAATTTTTTTTTATC
4425044 TAAACTTTTTTTTT-TC
1 TAAA-TTTTTTTTTATC
4425060 TAATATTTTT
1 TAA-ATTTTT
4425070 ACTCAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (16 bp):
TAAATTTTTTTTTATC
Found at i:4425320 original size:2 final size:2
Alignment explanation
Indices: 4425313--4425339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4425303 AAATTTAATT
4425313 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4425340 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4426016 original size:20 final size:20
Alignment explanation
Indices: 4425991--4426042 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4425981 TCTATGAATG
4425991 ATCCGATGCCTTGTTAAGAA
1 ATCCGATGCCTTGTTAAGAA
4426011 ATCCGATGCCTTGTTAAGAA
1 ATCCGATGCCTTGTTAAGAA
*
4426031 ATCCAATGCCTT
1 ATCCGATGCCTT
4426043 TATGTATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (20 bp):
ATCCGATGCCTTGTTAAGAA
Found at i:4430288 original size:21 final size:20
Alignment explanation
Indices: 4430249--4430288 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4430239 TCGATGTTTT
*
4430249 TAAATGTTTTTACATATATA
1 TAAATGTTATTACATATATA
*
4430269 TAAATGATTATTATATATAT
1 TAAATG-TTATTACATATAT
4430289 TTTTATTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TAAATGTTATTACATATATA
Found at i:4433609 original size:9 final size:8
Alignment explanation
Indices: 4433586--4433620 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
4433576 TTTTAAAAAC
4433586 AATT-AAA
1 AATTCAAA
4433593 AA-TCAAA
1 AATTCAAA
4433600 AATTCAAA
1 AATTCAAA
4433608 AATTCAAA
1 AATTCAAA
4433616 AATTC
1 AATTC
4433621 TGAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 1 0.04
7 7 0.27
8 18 0.69
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (8 bp):
AATTCAAA
Found at i:4434566 original size:19 final size:20
Alignment explanation
Indices: 4434534--4434572 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4434524 CTCTTGCATT
4434534 TGAAACAATCTTTCTTATTTC
1 TGAAACAATCTTTCTT-TTTC
4434555 TGAAAC-AT-TTTCTTTTTC
1 TGAAACAATCTTTCTTTTTC
4434573 CATGAGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 2 0.11
21 6 0.33
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (20 bp):
TGAAACAATCTTTCTTTTTC
Found at i:4436014 original size:14 final size:16
Alignment explanation
Indices: 4435995--4436033 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4435985 ATCTACATAG
4435995 TATTTT-TTTTAA-AT
1 TATTTTATTTTAATAT
4436009 TATTTTATTTTAATAT
1 TATTTTATTTTAATAT
*
4436025 TATTATATT
1 TATTTTATT
4436034 ATGTTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 6 0.27
16 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTATTTTAATAT
Found at i:4436029 original size:19 final size:19
Alignment explanation
Indices: 4436007--4436094 Score: 63
Period size: 22 Copynumber: 4.3 Consensus size: 19
4435997 TTTTTTTTAA
*
4436007 ATTATTTTATTTTAATATT
1 ATTATTTTATTTTATTATT
*
4436026 ATTATATTATGTTTACTT-TT
1 ATTATTTTAT-TTTA-TTATT
*
4436046 -TTGAATTTCTATATTATTATT
1 ATT--ATTT-TATTTTATTATT
4436067 ATTATTATTATTGTTACTTATT
1 ATTATT-TTATT-TTA-TTATT
4436089 ATTATT
1 ATTATT
4436095 ACTGTTGTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
19 11 0.20
20 14 0.26
21 13 0.24
22 16 0.30
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTATTTTATTTTATTATT
Found at i:4436065 original size:3 final size:3
Alignment explanation
Indices: 4436057--4436165 Score: 71
Period size: 3 Copynumber: 35.3 Consensus size: 3
4436047 TGAATTTCTA
* * * *
4436057 TAT TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * *
4436103 GTACA TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TAT TAT TA-
1 -TA-T TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
*
4436149 TATT TAC TAT TAT TAT T
1 TA-T TAT TAT TAT TAT T
4436166 TATAAATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
2 5 0.06
3 69 0.82
4 10 0.12
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:4436120 original size:23 final size:22
Alignment explanation
Indices: 4436063--4436139 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
4436053 TCTATATTAT
* * *
4436063 TATTATTATTATTATTGTTACT
1 TATTATTATTACTGTTGTTACA
4436085 TATTATTATTACTGTTGTGTACA
1 TATTATTATTACTGTTGT-TACA
* **
4436108 TATTATT-TATACTATACTTA-A
1 TATTATTAT-TACTGTTGTTACA
4436129 TATTATTATTA
1 TATTATTATTA
4436140 TTATTATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 10 0.22
22 20 0.43
23 16 0.35
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTATTATTACTGTTGTTACA
Found at i:4436839 original size:11 final size:11
Alignment explanation
Indices: 4436817--4436847 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
4436807 ATATTTATTT
4436817 TATATATATATG
1 TATATAT-TATG
4436829 TATATATTATG
1 TATATATTATG
4436840 TATATATT
1 TATATATT
4436848 TTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:4438052 original size:136 final size:137
Alignment explanation
Indices: 4437834--4438119 Score: 493
Period size: 136 Copynumber: 2.1 Consensus size: 137
4437824 CATTGGGCCT
** *
4437834 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCTTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
4437899 AGACCCTTATTCAGATAACAGTATGGCCCATAGACCCATTTCAAAATACATGCAACATCAGTAAA
66 AGACCCTTATTCAGATAACAGTATGGCCCATAGACCCATTTCAAAATACATACAACATCAGTAAA
4437964 CATATGC
131 CATATGC
4437971 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAG-GCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
* * *
4438035 AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATACAACATCAGTAAA
66 AGACCCTTATTCAGATAACAGTATGGCCCATAGACCCATTTCAAAATACATACAACATCAGTAAA
4438100 CATATGC
131 CATATGC
*
4438107 AAGGCCATTTGGG
1 AAGCCCATTTGGG
4438120 GAGACTACTC
Statistics
Matches: 141, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
136 110 0.78
137 31 0.22
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGACCCTTATTCAGATAACAGTATGGCCCATAGACCCATTTCAAAATACATACAACATCAGTAAA
CATATGC
Found at i:4439065 original size:30 final size:30
Alignment explanation
Indices: 4439029--4439203 Score: 228
Period size: 30 Copynumber: 5.8 Consensus size: 30
4439019 ACTTTTCTCA
*
4439029 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
* *
4439059 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
* *
4439089 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
*
4439119 ACTAGCCACACCTTCTCCACCACCAAATCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
** *
4439149 ACTAGCCACA-CTTGCTCCATTACCTACTCC
1 ACTAGCCACACCTT-CTCCACCACCAACTCC
*
4439179 ACTAACCACA-CTTGCTCCACCACCA
1 ACTAGCCACACCTT-CTCCACCACCA
4439204 CTTGTACCTA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
29 3 0.02
30 129 0.98
ACGTcount: A:0.26, C:0.49, G:0.04, T:0.21
Consensus pattern (30 bp):
ACTAGCCACACCTTCTCCACCACCAACTCC
Found at i:4439781 original size:29 final size:27
Alignment explanation
Indices: 4439749--4439826 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 27
4439739 ATTTTAAATT
4439749 CTATATTACGTATATATATATATTTTATA
1 CTATATTA--TATATATATATATTTTATA
* * *
4439778 CTAT-TT-TATTTATATATCTTTAATA
1 CTATATTATATATATATATATTTTATA
* *
4439803 TTATATTATTTATATATATATTTT
1 CTATATTATATATATATATATTTT
4439827 TTTTCTACAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
25 19 0.49
26 2 0.05
27 12 0.31
28 2 0.05
29 4 0.10
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (27 bp):
CTATATTATATATATATATATTTTATA
Found at i:4439893 original size:25 final size:24
Alignment explanation
Indices: 4439843--4439907 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 24
4439833 ACATGTTATC
4439843 TTATGTATATA-TCTT-AACTATA
1 TTATGTATATATTCTTAAACTATA
*
4439865 TTATGTATATATTTTTAACACTATA
1 TTATGTATATATTCTTAA-ACTATA
*
4439890 TTATGTACATATTCTTAA
1 TTATGTATATATTCTTAA
4439908 TATTATCACG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.30
23 3 0.08
24 1 0.03
25 22 0.59
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (24 bp):
TTATGTATATATTCTTAAACTATA
Found at i:4440084 original size:16 final size:15
Alignment explanation
Indices: 4440060--4440107 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
4440050 TAATTATTAT
*
4440060 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
4440076 TATTTTAATATTTTA
1 TATTTTAATATTTTA
4440091 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
4440107 T
1 T
4440108 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:4440095 original size:7 final size:8
Alignment explanation
Indices: 4440060--4440111 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
4440050 TAATTATTAT
*
4440060 TATTCTAA
1 TATTTTAA
*
4440068 TATTTTGA
1 TATTTTAA
4440076 TATTTTAA
1 TATTTTAA
4440084 TATTTT-A
1 TATTTTAA
4440091 TATTTTATA
1 TATTTTA-A
*
4440100 TATTTTAT
1 TATTTTAA
4440108 TATT
1 TATT
4440112 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:4441777 original size:26 final size:26
Alignment explanation
Indices: 4441746--4441853 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
4441736 TGAAATTCCC
*
4441746 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
4441772 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
4441798 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
4441824 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
4441850 ATCA
1 ATCA
4441854 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:4445486 original size:13 final size:13
Alignment explanation
Indices: 4445468--4445502 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
4445458 TGCCTAGCTT
4445468 GCCACCGCCATTG
1 GCCACCGCCATTG
4445481 GCCACCGCCATTG
1 GCCACCGCCATTG
4445494 GCCACCGCC
1 GCCACCGCC
4445503 TCTGCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.51, G:0.23, T:0.11
Consensus pattern (13 bp):
GCCACCGCCATTG
Found at i:4448964 original size:19 final size:19
Alignment explanation
Indices: 4448922--4448982 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
4448912 CATATCATAT
4448922 CATATCATATCTAAGATT-
1 CATATCATATCTAAGATTG
4448940 -ATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
4448958 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
4448977 CATATC
1 CATATC
4448983 CTTAAAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.41
19 24 0.59
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
CATATCATATCTAAGATTG
Found at i:4449771 original size:259 final size:259
Alignment explanation
Indices: 4449299--4449785 Score: 710
Period size: 259 Copynumber: 1.9 Consensus size: 259
4449289 AAACTCGGAT
* *
4449299 TGTCATGTTGATATCTTCGATCTGTTCTCCGTCGAACACAGAGACGCCAAATCTGCTTTTTCGAT
1 TGTCATGTTGATATCTTCGATCTGCTCTCCGCCGAACACAGAGACGCCAAATCTGCTTTTTCGAT
* * * * *
4449364 TTGTTTTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAG
66 TTGTTCTCTAACAATACAGAGATGCCAAATAATCTTAGATCTGCTTCAGCGTAAACACGCGAAAA
* * * * *
4449429 CCAAATCTGTTGTGTCTTCAATTTGCTCCTTGTGAACACAAGGATACCAAATCATCTTGGATCTA
131 CCAAATCAGCTATGTCTTCAATTTGCTCCTTGTAAACACAAGGATACCAAACCATCTTGGATCTA
4449494 CTTCAGTAAAATCATCTGAAGGTCAGATCTGCTGTCTTTAATCTGCTTCTTGTAAACTTATGAC
196 CTTCAGTAAAATCATCTGAAGGTCAGATCTGCTGTCTTTAATCTGCTTCTTGTAAACTTATGAC
* *
4449558 TGTCCTGTTGATATCTTCGATCTGCTCTCCGCCGAATACAGAGACGCCAAATCTG-TTTCTTCGA
1 TGTCATGTTGATATCTTCGATCTGCTCTCCGCCGAACACAGAGACGCCAAATCTGCTTT-TTCGA
* * * *
4449622 TTTGTTCTCTAACAATACAGATATGCCAAATAATCTTAGATTTGCTTTAGCGTAAGCACGCGAAA
65 TTTGTTCTCTAACAATACAGAGATGCCAAATAATCTTAGATCTGCTTCAGCGTAAACACGCGAAA
** * *
4449687 ACCAAATCAGCTATGTCTTTGATTTGTTCCTTG-AAAGCACAAGGATGCCAAACCATCTTGGATC
130 ACCAAATCAGCTATGTCTTCAATTTGCTCCTTGTAAA-CACAAGGATACCAAACCATCTTGGATC
* *
4449751 TGCTTCAGTATAAA-CATCTGAAGGTTAGATCTGCT
194 TACTTCAGTA-AAATCATCTGAAGGTCAGATCTGCT
4449786 ATGTATCTGC
Statistics
Matches: 201, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
258 5 0.02
259 193 0.96
260 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (259 bp):
TGTCATGTTGATATCTTCGATCTGCTCTCCGCCGAACACAGAGACGCCAAATCTGCTTTTTCGAT
TTGTTCTCTAACAATACAGAGATGCCAAATAATCTTAGATCTGCTTCAGCGTAAACACGCGAAAA
CCAAATCAGCTATGTCTTCAATTTGCTCCTTGTAAACACAAGGATACCAAACCATCTTGGATCTA
CTTCAGTAAAATCATCTGAAGGTCAGATCTGCTGTCTTTAATCTGCTTCTTGTAAACTTATGAC
Found at i:4449865 original size:205 final size:205
Alignment explanation
Indices: 4449620--4450371 Score: 1287
Period size: 205 Copynumber: 3.7 Consensus size: 205
4449610 CTGTTTCTTC
* * * * *
4449620 GATTTGTTCTCT-AACAATACAGATATGCCAAATAATCTTAGATTTGCTTTAGCGTAAGCACGCG
1 GATTTGTTCTCTGAA-AATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
* * *
4449684 AAAACCAAATCAGCTATGTCTTTGATTTGTTCCTTGAAAGCACAAGGATGCCAAACCATCTTGGA
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGA
4449749 TCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGA
130 TCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGA
4449814 TGCCAGACTTT
195 TGCCAGACTTT
*
4449825 GATTTTTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
*
4449890 AATCCAAATCA-CTATGTCTTCGATTTGTTCCTTGTAAGCAC-AGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
*
4449953 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGT-TCTGCTCTCCGTCGAAATAGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
4450017 GCCAGACTTT
196 GCCAGACTTT
* *
4450027 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTACTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
4450092 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
4450157 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
* *
4450222 GCTAGACTTC
196 GCCAGACTTT
* *
4450232 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACATGA
1 GATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
**
4450297 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGTTAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
4450362 CTTGCTTCAG
131 C-TGCTTCAG
4450372 CCAGATCTGC
Statistics
Matches: 521, Mismatches: 21, Indels: 9
0.95 0.04 0.02
Matches are distributed among these distances:
202 105 0.20
203 92 0.18
204 90 0.17
205 224 0.43
206 10 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (205 bp):
GATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
CTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
GCCAGACTTT
Found at i:4450436 original size:407 final size:403
Alignment explanation
Indices: 4449615--4450371 Score: 1226
Period size: 407 Copynumber: 1.9 Consensus size: 403
4449605 CAAATCTGTT
* * * *
4449615 TCTTCGATTTGTTCTCTAACAATACAGATATGCCAAATAATCTTAGATTTGCTTTAGCGTAAGCA
1 TCTTTGATTTGTTCTCTAACAATACAGAGATGCCAAATAATCTTAGATTTACTTCAGCGTAAGCA
*
4449680 CGCGAAAACCAAATCAGCTATGTCTTTGATTTGTTCCTTGAAAGCACAAGGATGCCAAACCATCT
66 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGAAAGCACAAGGATGCCAAACCATCT
4449745 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATG
131 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATG
* *
4449810 GAGATGCCAGACTTTGATTTTTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
196 GAGATGCCAGACTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
* *
4449875 ATCGTAAGCACGTGAAATCCAAATCACTATGTCTTCGATTTGTTCCTTGTAAGCACAGGATGCCA
261 ATCGTAAGCACATGAAAGCCAAATCACTATGTCTTCGATTTGTTCCTTGTAAGCACAGGATGCCA
* * *
4449940 AACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTTCTGCTCTCCGT
326 AACCATCTTGGATCTGCTTCAG--TAAACATCTGAAGGCTAGA-CGGCTATGTAC-GCTCTCCGT
* *
4450005 CGAAATAGAGATGCCAG
387 AGAAATAGAGACGCCAG
* * * *
4450022 ACTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTACTTCATCGTAAGCA
1 TCTTTGATTTGTTCTCTAACAATACAGAGATGCCAAATAATCTTAGATTTACTTCAGCGTAAGCA
* * *
4450087 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
66 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGAAAGCACAAGGATGCCAAACCATCT
4450152 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATG
131 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATG
* *
4450217 GAGATGCTAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
196 GAGATGCCAGACTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
*
4450282 ATCGTAAGCACATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGT
261 ATCGTAAGCACATGAAAGCCAAATCA-CTATGTCTTCGATTTGTTCCTTGTAAGCAC-AGGATGC
*
4450347 TAAACCATCTTGGATCTTGCTTCAG
324 CAAACCATCTTGGATC-TGCTTCAG
4450372 CCAGATCTGC
Statistics
Matches: 327, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
407 268 0.82
408 30 0.09
409 21 0.06
410 8 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (403 bp):
TCTTTGATTTGTTCTCTAACAATACAGAGATGCCAAATAATCTTAGATTTACTTCAGCGTAAGCA
CGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGAAAGCACAAGGATGCCAAACCATCT
TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATG
GAGATGCCAGACTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
ATCGTAAGCACATGAAAGCCAAATCACTATGTCTTCGATTTGTTCCTTGTAAGCACAGGATGCCA
AACCATCTTGGATCTGCTTCAGTAAACATCTGAAGGCTAGACGGCTATGTACGCTCTCCGTAGAA
ATAGAGACGCCAG
Found at i:4451324 original size:1 final size:1
Alignment explanation
Indices: 4451314--4451353 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
4451304 GGCCTCTCCA
* * *
4451314 TTTTTCTTTTTTTTTTTTTTTTTCTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4451354 GAAATAGAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:4451337 original size:18 final size:19
Alignment explanation
Indices: 4451314--4451353 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
4451304 GGCCTCTCCA
4451314 TTTTTCTTTT-TTTTTTTT
1 TTTTTCTTTTCTTTTTTTT
4451332 TTTTTCTTTTCTTTTTTTT
1 TTTTTCTTTTCTTTTTTTT
4451351 TTT
1 TTT
4451354 GAAATAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTTTT
Found at i:4458160 original size:17 final size:17
Alignment explanation
Indices: 4458138--4458171 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4458128 ATATCATATC
4458138 ATATCATATCTAAGATT
1 ATATCATATCTAAGATT
4458155 ATATCATATCTAAGATT
1 ATATCATATCTAAGATT
4458172 GCATATCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATCATATCTAAGATT
Found at i:4460406 original size:15 final size:16
Alignment explanation
Indices: 4460375--4460407 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4460365 TGCCACCATT
*
4460375 TTTATTCATCTTTCCA
1 TTTATTCATCATTCCA
4460391 TTTATTCAT-ATTCCA
1 TTTATTCATCATTCCA
4460406 TT
1 TT
4460408 CCTTCTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTCATCATTCCA
Found at i:4469439 original size:37 final size:37
Alignment explanation
Indices: 4469366--4469441 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
4469356 CAAATTCATT
*
4469366 AATAGTAATTATTTAGATAATTATTAAAATTATAAAA
1 AATAGTAATTATTTAGATAATTATAAAAATTATAAAA
* * *
4469403 AATAGTAGTTA-TTA-ATAATTATAAGAAATTGTTAAA
1 AATAGTAATTATTTAGATAATTATAA-AAATTATAAAA
4469439 AAT
1 AAT
4469442 TATAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 9 0.26
36 15 0.44
37 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (37 bp):
AATAGTAATTATTTAGATAATTATAAAAATTATAAAA
Found at i:4469454 original size:13 final size:13
Alignment explanation
Indices: 4469436--4469462 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4469426 AGAAATTGTT
4469436 AAAAATTATAAAA
1 AAAAATTATAAAA
4469449 AAAAATTATAAAA
1 AAAAATTATAAAA
4469462 A
1 A
4469463 TTATTAAAAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAATTATAAAA
Found at i:4470275 original size:30 final size:31
Alignment explanation
Indices: 4470241--4470304 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
4470231 ATTTATTTTA
4470241 TTGTT-AATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAAATTTTCTTATTATTTTAAAGGCAT
* * * *
4470271 TTGTTAAATTTTTTTGTTATTTTAGAGGTAT
1 TTGTTAAATTTTCTTATTATTTTAAAGGCAT
4470302 TTG
1 TTG
4470305 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.59
Consensus pattern (31 bp):
TTGTTAAATTTTCTTATTATTTTAAAGGCAT
Found at i:4470740 original size:21 final size:20
Alignment explanation
Indices: 4470690--4470760 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
4470680 TATTTTACTA
* *
4470690 TTTTTATAATTCTTAATAAAT
1 TTTTTATAATT-TTTATAATT
**
4470711 TTTAAATAATTTTCTATAATT
1 TTTTTATAATTTT-TATAATT
*
4470732 TTTTTATAATGTTTAT-ATT
1 TTTTTATAATTTTTATAATT
4470751 TTTTTATAAT
1 TTTTTATAAT
4470761 CATCTAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.31
20 5 0.12
21 24 0.57
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTTATAATTTTTATAATT
Found at i:4471077 original size:19 final size:19
Alignment explanation
Indices: 4471042--4471079 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4471032 TTTAAAATCC
*
4471042 TAATTAACTCAATTAAATT
1 TAATTAAATCAATTAAATT
4471061 TAATTAAATCTAA-TAAATT
1 TAATTAAATC-AATTAAATT
4471080 ATTAGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTAAATCAATTAAATT
Found at i:4480285 original size:39 final size:39
Alignment explanation
Indices: 4480215--4480391 Score: 255
Period size: 39 Copynumber: 4.5 Consensus size: 39
4480205 ATCGTGATTT
* * * *
4480215 GAAGCCCGAAGTCTAGCTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* * * *
4480254 GAAACCTGAAGGCTAACTGAAGTACACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* *
4480293 GCAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
4480332 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
4480371 GAAGCCTGAAGGCTAACTGAA
1 GAAGCCCGAAGGCTAACTGAA
4480392 ACTCATCAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 121 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:4480336 original size:21 final size:21
Alignment explanation
Indices: 4480311--4480375 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 21
4480301 AAGGCTAACT
4480311 GAAGCACACAAGTGCTAAATG
1 GAAGCACACAAGTGCTAAATG
*
4480332 GAAGC-C-CGAAG-GCTAACT-
1 GAAGCACAC-AAGTGCTAAATG
*
4480350 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAATG
4480371 GAAGC
1 GAAGC
4480376 CTGAAGGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 10 0.28
21 10 0.28
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAATG
Found at i:4512551 original size:43 final size:43
Alignment explanation
Indices: 4512490--4512577 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
4512480 TCACAAAGTG
4512490 TTGAAATATGTATATATTTTAAATTTATTTAGGTAGATAAATC
1 TTGAAATATGTATATATTTTAAATTTATTTAGGTAGATAAATC
4512533 TTGAAATATGTATATATTTTAAATTTATTTAGGTAGATAAATC
1 TTGAAATATGTATATATTTTAAATTTATTTAGGTAGATAAATC
4512576 TT
1 TT
4512578 ATTTAGGTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (43 bp):
TTGAAATATGTATATATTTTAAATTTATTTAGGTAGATAAATC
Found at i:4512598 original size:19 final size:19
Alignment explanation
Indices: 4512552--4512599 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4512542 GTATATATTT
4512552 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
4512570 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
4512589 TAAATTTTATT
1 TAAATTTTATT
4512600 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:4516477 original size:2 final size:2
Alignment explanation
Indices: 4516470--4516497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4516460 GGGTGTTGAA
4516470 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
4516498 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.