Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 135 of 211
Found at i:42775941 original size:16 final size:16
Alignment explanation
Indices: 42775917--42775947 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42775907 TTACTCATGA
*
42775917 AAAATAATAAATAAAC
1 AAAAGAATAAATAAAC
42775933 AAAAGAATAAATAAA
1 AAAAGAATAAATAAA
42775948 ATTTAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAGAATAAATAAAC
Found at i:42778367 original size:14 final size:14
Alignment explanation
Indices: 42778348--42778375 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42778338 CCAATTTATT
42778348 AATGAATTATTAAA
1 AATGAATTATTAAA
42778362 AATGAATTATTAAA
1 AATGAATTATTAAA
42778376 TATAACTTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:42786702 original size:28 final size:28
Alignment explanation
Indices: 42786644--42786736 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
42786634 GGCATCCTTG
*
42786644 CACAGTAGATAAATAGCCACAAAGGCATC
1 CACA-TAGATAGATAGCCACAAAGGCATC
* * **
42786673 CATATAGATAGATAGCCACAAATGTGTC
1 CACATAGATAGATAGCCACAAAGGCATC
* *
42786701 CACATAACATTAGATAGCCATAAAGGCATC
1 CACAT-AGA-TAGATAGCCACAAAGGCATC
*
42786731 CTCATA
1 CACATA
42786737 TAACAGGCTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
28 24 0.48
29 6 0.12
30 20 0.40
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (28 bp):
CACATAGATAGATAGCCACAAAGGCATC
Found at i:42786914 original size:30 final size:30
Alignment explanation
Indices: 42786880--42786966 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
42786870 TCACGTTAAT
* * * *
42786880 AGAGAACAGCCATAGAGGCTTCCACTTATC
1 AGAGAATAGCCACAAAGGCTTCCACATATC
*
42786910 AGAGAATAGCCACAAAGGCTTTCACATATC
1 AGAGAATAGCCACAAAGGCTTCCACATATC
*
42786940 TGAGAATAGCCACAAAGGCTTCCACAT
1 AGAGAATAGCCACAAAGGCTTCCACAT
42786967 TTTAGTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (30 bp):
AGAGAATAGCCACAAAGGCTTCCACATATC
Found at i:42791997 original size:27 final size:27
Alignment explanation
Indices: 42791967--42792030 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
42791957 TTAAATAACC
* * *
42791967 GAAATACCCTCGAAGGGTAAAATTATT
1 GAAATACCCCCAAAGGGTAAAATTACT
42791994 GAAATACCCCCAAAGGGTAAAATTACT
1 GAAATACCCCCAAAGGGTAAAATTACT
*
42792021 AAAATACCCC
1 GAAATACCCC
42792031 TGTAAGGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (27 bp):
GAAATACCCCCAAAGGGTAAAATTACT
Found at i:42792154 original size:16 final size:16
Alignment explanation
Indices: 42792133--42792174 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
42792123 CTGAGCATGG
*
42792133 CATACTGCATACACGA
1 CATACTGCATACACAA
42792149 CATACTGCATACACAA
1 CATACTGCATACACAA
42792165 CATACTGCAT
1 CATACTGCAT
42792175 GGGGCTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (16 bp):
CATACTGCATACACAA
Found at i:42793639 original size:28 final size:28
Alignment explanation
Indices: 42793608--42793713 Score: 135
Period size: 28 Copynumber: 3.8 Consensus size: 28
42793598 ATTATGGTTC
42793608 AAAAA-TGTAAAATTTGAAAAATAGTGG
1 AAAAATTGTAAAATTTGAAAAATAGTGG
* * * *
42793635 CAAAATTGTAAAATATGAAAAACAATGG
1 AAAAATTGTAAAATTTGAAAAATAGTGG
42793663 AAAAATTGTAAAATTTGAAAAATAAG-GG
1 AAAAATTGTAAAATTTGAAAAAT-AGTGG
*
42793691 AAAAATTATAAAAATTTGAAAAA
1 AAAAATTGT-AAAATTTGAAAAA
42793714 ATAAAGGCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 4 0.06
28 49 0.73
29 14 0.21
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (28 bp):
AAAAATTGTAAAATTTGAAAAATAGTGG
Found at i:42793674 original size:56 final size:56
Alignment explanation
Indices: 42793608--42793713 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
42793598 ATTATGGTTC
* *
42793608 AAAAATGTAAAATTTGAAAAAT-AGTGGCAAAATTGT-AAAATATGAAAAACAATGG
1 AAAAATGTAAAATTTGAAAAATAAG-GGAAAAATTATAAAAATATGAAAAACAATGG
*
42793663 AAAAATTGTAAAATTTGAAAAATAAGGGAAAAATTATAAAAATTTGAAAAA
1 AAAAA-TGTAAAATTTGAAAAATAAGGGAAAAATTATAAAAATATGAAAAA
42793714 ATAAAGGCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
55 5 0.11
56 26 0.58
57 14 0.31
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (56 bp):
AAAAATGTAAAATTTGAAAAATAAGGGAAAAATTATAAAAATATGAAAAACAATGG
Found at i:42793751 original size:29 final size:28
Alignment explanation
Indices: 42793615--42793748 Score: 99
Period size: 28 Copynumber: 4.7 Consensus size: 28
42793605 TTCAAAAATG
* * *
42793615 TAAAATTTGAAAAAT-AGTGGCAAAATTG
1 TAAAATTTAAAAAATAAG-GGCAAAACTA
* * * * * * *
42793643 TAAAATATGAAAAACAATGGAAAAATTG
1 TAAAATTTAAAAAATAAGGGCAAAACTA
* * *
42793671 TAAAATTTGAAAAATAAGGGAAAAATTA
1 TAAAATTTAAAAAATAAGGGCAAAACTA
*
42793699 TAAAAATTTGAAAAAATAAAGGCAAAACTA
1 T-AAAATTT-AAAAAATAAGGGCAAAACTA
*
42793729 TAAAATATAAAAAATAAGGG
1 TAAAATTTAAAAAATAAGGG
42793749 GCACACAACC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
28 58 0.65
29 14 0.16
30 17 0.19
ACGTcount: A:0.60, C:0.03, G:0.14, T:0.23
Consensus pattern (28 bp):
TAAAATTTAAAAAATAAGGGCAAAACTA
Found at i:42798799 original size:31 final size:30
Alignment explanation
Indices: 42798764--42798842 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
42798754 ATAAACGCCG
42798764 GTACATAGTACCTGATATAATAT-AGTCACT
1 GTACATAGTACCTGATATAATATGA-TCACT
*
42798794 AGTACATAATACCT-ACTATAATATGATCACT
1 -GTACATAGTACCTGA-TATAATATGATCACT
*
42798825 GATACATAGTACTTGATA
1 G-TACATAGTACCTGATA
42798843 CTTTTAAACC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 2 0.05
31 37 0.90
32 2 0.05
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (30 bp):
GTACATAGTACCTGATATAATATGATCACT
Found at i:42803693 original size:75 final size:69
Alignment explanation
Indices: 42803591--42803790 Score: 195
Period size: 69 Copynumber: 2.8 Consensus size: 69
42803581 ATCATTAGAA
42803591 TGCCATAGCC-CAGCTATGGTCTTACATATATGTATACACTGCCATGGTCCAACCATGGTCTTAC
1 TGCCATAGCCTC-GCTATGGTCTTACATA-A-G----CACTGCCATGGTCCAACCATGGTCTTAC
*
42803655 ATTTGAAAAAC
59 ATCTGAAAAAC
* * * ***
42803666 TGCCATAGCCTCGCTATGGTCTTACATAAGCATTGTCATGTTCCAACCATGGTCTTGTGTCTGAA
1 TGCCATAGCCTCGCTATGGTCTTACATAAGCACTGCCATGGTCCAACCATGGTCTTACATCTGAA
42803731 AAAC
66 AAAC
* * * * * * * *
42803735 TACCATAGTCTCGCTACGGTCTTACGTAAACATTGTCATTGTCCAACCATGGTCTT
1 TGCCATAGCCTCGCTATGGTCTTACATAAGCACTGCCATGGTCCAACCATGGTCTT
42803791 GTACATCTTT
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
69 81 0.74
73 1 0.01
74 1 0.01
75 26 0.24
76 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (69 bp):
TGCCATAGCCTCGCTATGGTCTTACATAAGCACTGCCATGGTCCAACCATGGTCTTACATCTGAA
AAAC
Found at i:42803741 original size:69 final size:69
Alignment explanation
Indices: 42803633--42803793 Score: 216
Period size: 69 Copynumber: 2.3 Consensus size: 69
42803623 TATACACTGC
* ** * * * *
42803633 CATGGTCCAACCATGGTCTTACATTTGAAAAACTGCCATAGCCTCGCTATGGTCTTACATAAGCA
1 CATGTTCCAACCATGGTCTTGTATCTGAAAAACTACCATAGCCTCGCTACGGTCTTACATAAACA
42803698 TTGT
66 TTGT
* * *
42803702 CATGTTCCAACCATGGTCTTGTGTCTGAAAAACTACCATAGTCTCGCTACGGTCTTACGTAAACA
1 CATGTTCCAACCATGGTCTTGTATCTGAAAAACTACCATAGCCTCGCTACGGTCTTACATAAACA
42803767 TTGT
66 TTGT
42803771 CAT-TGTCCAACCATGGTCTTGTA
1 CATGT-TCCAACCATGGTCTTGTA
42803794 CATCTTTATG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
68 1 0.01
69 79 0.99
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (69 bp):
CATGTTCCAACCATGGTCTTGTATCTGAAAAACTACCATAGCCTCGCTACGGTCTTACATAAACA
TTGT
Found at i:42806058 original size:16 final size:18
Alignment explanation
Indices: 42806032--42806065 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42806022 TAGAACCGGG
42806032 TTGATAAATTT-ATTTAA
1 TTGATAAATTTGATTTAA
42806049 TTGA-AAATTTGATTTAA
1 TTGATAAATTTGATTTAA
42806066 ATTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTGATAAATTTGATTTAA
Found at i:42811938 original size:39 final size:39
Alignment explanation
Indices: 42811839--42811940 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 39
42811829 CATATTCACT
* * * *
42811839 TTTAATCATATATCACATTACACATATAATCTCATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
42811878 TTTAAGTATATACCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
42811917 TTTAGGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
42811941 AAAACATGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:42813869 original size:14 final size:13
Alignment explanation
Indices: 42813852--42813899 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
42813842 ATTCTAGTAG
42813852 GTTAATTTAAGTTA
1 GTTAATTTAA-TTA
42813866 GTTAATTTAATTA
1 GTTAATTTAATTA
42813879 GTTTAA-TTAATATA
1 G-TTAATTTAAT-TA
42813893 -TTAATTT
1 GTTAATTT
42813900 GGATCAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.13
13 11 0.35
14 16 0.52
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
GTTAATTTAATTA
Found at i:42818062 original size:29 final size:29
Alignment explanation
Indices: 42818029--42818225 Score: 152
Period size: 29 Copynumber: 6.8 Consensus size: 29
42818019 TATGGTTGTA
* * *
42818029 ACCATCCTTTTTTATATTCGATGGTCGAG
1 ACCATCCCTTTTCATATTCGATGGTCGAC
* *
42818058 ACCATCCCTTTTCATTAATCGATGGTCGTC
1 ACCATCCCTTTTCA-TATTCGATGGTCGAC
* *
42818088 ACCATCCCTTTTCATAGTT-GATGGTTGTC
1 ACCATCCCTTTTCATA-TTCGATGGTCGAC
* * * *
42818117 ACCATCCCTTTTCAT-TAACCAGTAGCCGA-
1 ACCATCCCTTTTCATAT-TCGA-TGGTCGAC
* * * *
42818146 AGCCATCCC-TTTCAAATTCGATAGTTGTC
1 A-CCATCCCTTTTCATATTCGATGGTCGAC
*
42818175 ACCATCCCTTTTCATAATT-GATGGTCGTC
1 ACCATCCCTTTTCAT-ATTCGATGGTCGAC
*
42818204 ACCATCCCTTTTCATAATCGAT
1 ACCATCCCTTTTCATATTCGAT
42818226 AACCGAAGCT
Statistics
Matches: 134, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.01
28 13 0.10
29 79 0.59
30 41 0.31
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATGGTCGAC
Found at i:42818112 original size:59 final size:59
Alignment explanation
Indices: 42818020--42818225 Score: 215
Period size: 59 Copynumber: 3.5 Consensus size: 59
42818010 GTGATAAAAT
* * * * **
42818020 ATGGTTGTAACCATCCTTTTTTATATTCGATGGTCGAGACCATCCCTTTTCATTAATCG
1 ATGGTCGTAACCATCCCTTTTCATATTCGATGGTTGTCACCATCCCTTTTCATTAATCG
* *
42818079 ATGGTCGTCACCATCCCTTTTCATAGTT-GATGGTTGTCACCATCCCTTTTCATTAA-CC
1 ATGGTCGTAACCATCCCTTTTCATA-TTCGATGGTTGTCACCATCCCTTTTCATTAATCG
* * * * *
42818137 AGTAGCCG-AAGCCATCCC-TTTCAAATTCGATAGTTGTCACCATCCCTTTTCA-TAATTG
1 A-TGGTCGTAA-CCATCCCTTTTCATATTCGATGGTTGTCACCATCCCTTTTCATTAATCG
* *
42818195 ATGGTCGTCACCATCCCTTTTCATAATCGAT
1 ATGGTCGTAACCATCCCTTTTCATATTCGAT
42818226 AACCGAAGCT
Statistics
Matches: 120, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
57 16 0.13
58 45 0.38
59 57 0.47
60 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (59 bp):
ATGGTCGTAACCATCCCTTTTCATATTCGATGGTTGTCACCATCCCTTTTCATTAATCG
Found at i:42818186 original size:87 final size:86
Alignment explanation
Indices: 42818059--42818243 Score: 248
Period size: 87 Copynumber: 2.1 Consensus size: 86
42818049 ATGGTCGAGA
* * *
42818059 CCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTTGTCACCATCC
1 CCATCCC-TTTCA-TAATCGATAGTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATCC
*
42818124 CTTTTCATTAACC-AGTAGCCGAAG
64 CTTTTCA-TAACCGA-TAACCGAAG
*
42818148 CCATCCCTTTCA-AATTCGATAGTTGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATCCC
1 CCATCCCTTTCATAA-TCGATAGTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATCCC
*
42818212 TTTTCATAATCGATAACCGAAG
65 TTTTCATAACCGATAACCGAAG
*
42818234 CTATCCCTTT
1 CCATCCCTTT
42818244 TGTAACACCC
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
86 23 0.26
87 52 0.60
88 5 0.06
89 7 0.08
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (86 bp):
CCATCCCTTTCATAATCGATAGTCGTCACCATCCCTTTTCATAATTGATGGTCGTCACCATCCCT
TTTCATAACCGATAACCGAAG
Found at i:42818217 original size:58 final size:60
Alignment explanation
Indices: 42818058--42818226 Score: 208
Period size: 58 Copynumber: 2.9 Consensus size: 60
42818048 GATGGTCGAG
* *
42818058 ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAGTT-GATGGTTGTC
1 ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGTTGTC
* * * *
42818117 ACCATCCCTTTTCATTAA-CCAGTAGCCG-AAGCCATCCC-TTTCA-AATTCGATAGTTGTC
1 ACCATCCCTTTTCATTAATCGA-TGGTCGTCA-CCATCCCTTTTCATAATTCGATAGTTGTC
*
42818175 ACCATCCCTTTTCA-TAATTGATGGTCGTCACCATCCCTTTTCATAA-TCGATA
1 ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAATTCGATA
42818227 ACCGAAGCTA
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
57 17 0.18
58 44 0.48
59 31 0.34
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (60 bp):
ACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAATTCGATAGTTGTC
Found at i:42819440 original size:27 final size:27
Alignment explanation
Indices: 42819410--42819468 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
42819400 TCATCTCTTA
42819410 GGGGTATAATAG-TCATTTTACCCTATG
1 GGGGTAT-ATAGATCATTTTACCCTATG
* * *
42819437 GGGGTATTTCGATCATTTTACTCTATG
1 GGGGTATATAGATCATTTTACCCTATG
42819464 GGGGT
1 GGGGT
42819469 CATTTTACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (27 bp):
GGGGTATATAGATCATTTTACCCTATG
Found at i:42819474 original size:46 final size:46
Alignment explanation
Indices: 42819421--42819554 Score: 216
Period size: 46 Copynumber: 2.9 Consensus size: 46
42819411 GGGTATAATA
42819421 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACTCTATGGGG
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACTCTATGGGG
** *
42819467 GTCATTTTACCCTATGATGGTATTTCGGTCATTTTACTCTATGGGG
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACTCTATGGGG
*
42819513 GTCATTTTACCCTATGGGGGTATTTC-AGTCATTTTACCCTAT
1 GTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACTCTAT
42819555 AGAGGTATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.43
Consensus pattern (46 bp):
GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACTCTATGGGG
Found at i:42819537 original size:18 final size:19
Alignment explanation
Indices: 42819449--42819537 Score: 81
Period size: 19 Copynumber: 4.3 Consensus size: 19
42819439 GGTATTTCGA
*
42819449 TCATTTTACTCTATGGGGG
1 TCATTTTACCCTATGGGGG
42819468 TCATTTTACCCTATGATGGTATTTCGG
1 TCATTTTACCCTATG--GG------GG
*
42819495 TCATTTTACTCTATGGGGG
1 TCATTTTACCCTATGGGGG
42819514 TCATTTTACCCTATGGGGG
1 TCATTTTACCCTATGGGGG
42819533 T-ATTT
1 TCATTT
42819538 CAGTCATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
18 4 0.07
19 35 0.59
21 2 0.03
25 2 0.03
27 16 0.27
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (19 bp):
TCATTTTACCCTATGGGGG
Found at i:42819543 original size:27 final size:27
Alignment explanation
Indices: 42819512--42819627 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
42819502 ACTCTATGGG
*
42819512 GGTCATTTTACCCTATGGGGGTATTTC
1 GGTCATTTTACCCTATAGGGGTATTTC
* *
42819539 AGTCATTTTACCCTATAGAGGTATTTC
1 GGTCATTTTACCCTATAGGGGTATTTC
* * *
42819566 GGTTATTTTACCCTATATGGGTATTTT
1 GGTCATTTTACCCTATAGGGGTATTTC
* ** *
42819593 GGTCATTTCAATCTCT-GAGGGTATTTC
1 GGTCATTTTACCCTATAG-GGGTATTTC
42819620 GGTCATTT
1 GGTCATTT
42819628 GTTGACCTCT
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (27 bp):
GGTCATTTTACCCTATAGGGGTATTTC
Found at i:42829470 original size:50 final size:51
Alignment explanation
Indices: 42829346--42829578 Score: 244
Period size: 50 Copynumber: 4.7 Consensus size: 51
42829336 GATAATAACA
* * * *
42829346 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATCT-CGG
* * * * * *
42829395 TGCCAATGCCATATCCCATATATGGTCTTATATGGGA-GTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATCTCGG
* * * * *
42829445 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGAC-CTCTAATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATCTCGG
* * *
42829495 TGCCAACGCCATGTCACAGACATGGTTTTAGATGGGACG-TCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATCTCGG
*
42829545 TGCCAACGCCATGTCCAAGACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
42829579 AGACCTCATC
Statistics
Matches: 152, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
48 4 0.03
49 36 0.24
50 112 0.74
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (51 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATCTCGG
Found at i:42832399 original size:73 final size:73
Alignment explanation
Indices: 42832279--42832443 Score: 240
Period size: 73 Copynumber: 2.3 Consensus size: 73
42832269 CACAGCCTAA
* * *
42832279 CGACATGGTCGTGTGAATACTGGAAGGGGAACAAATGTGGAACCACACGGTTCCCAAAAGGCACA
1 CGACATAGCCGTGTGAATACTGGAAGGGGAACAAATGTGGAACCACACGATTCCCAAAAGGCACA
42832344 TAACCTGG
66 TAACCTGG
* * * * *
42832352 TGACATAGCCGTGTGAATACTGGAAGGGGAATAATTGTGGAACCACACGATTCTCGAAAGGCACA
1 CGACATAGCCGTGTGAATACTGGAAGGGGAACAAATGTGGAACCACACGATTCCCAAAAGGCACA
**
42832417 TAGTCTGG
66 TAACCTGG
42832425 CGACATAGCCGTGTGAATA
1 CGACATAGCCGTGTGAATA
42832444 TCGGAGTGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 81 1.00
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.19
Consensus pattern (73 bp):
CGACATAGCCGTGTGAATACTGGAAGGGGAACAAATGTGGAACCACACGATTCCCAAAAGGCACA
TAACCTGG
Found at i:42832645 original size:7 final size:7
Alignment explanation
Indices: 42832633--42832669 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
42832623 TTCATTTTCA
42832633 TTTTATT
1 TTTTATT
42832640 TTTTATT
1 TTTTATT
42832647 TTTTATT
1 TTTTATT
42832654 TTTTATT
1 TTTTATT
*
42832661 TTTTCTT
1 TTTTATT
42832668 TT
1 TT
42832670 CCTTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:42832834 original size:17 final size:17
Alignment explanation
Indices: 42832800--42832847 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
42832790 ATTATATATT
* *
42832800 TTTCTTTGTTTTTTTTA
1 TTTCTTTCTTTTTCTTA
42832817 TTT-TTTCTATTTTCTTA
1 TTTCTTTCT-TTTTCTTA
42832834 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
42832848 CCTTTCCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 18 0.67
18 5 0.19
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTTA
Found at i:42832934 original size:16 final size:16
Alignment explanation
Indices: 42832913--42832945 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42832903 TTTTCACTAC
42832913 ATTTTTATTTGTTTTT
1 ATTTTTATTTGTTTTT
*
42832929 ATTTTTCTTTGTTTTT
1 ATTTTTATTTGTTTTT
42832945 A
1 A
42832946 GATTTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (16 bp):
ATTTTTATTTGTTTTT
Found at i:42835779 original size:21 final size:21
Alignment explanation
Indices: 42835753--42835798 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
42835743 TAGATATGAT
*
42835753 ATTTTATTTATTTTATTTTTA
1 ATTTTATTTAATTTATTTTTA
*
42835774 ATTTTATTTAATTTCTTTTTA
1 ATTTTATTTAATTTATTTTTA
42835795 ATTT
1 ATTT
42835799 GTAGGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
ATTTTATTTAATTTATTTTTA
Found at i:42845173 original size:15 final size:15
Alignment explanation
Indices: 42845153--42845260 Score: 60
Period size: 15 Copynumber: 7.2 Consensus size: 15
42845143 TTTATGGAAA
42845153 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
42845168 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
*
42845182 AGTCAAAGATATGAGT
1 A-TCAAAGATATGGGT
* **
42845198 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
42845212 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* * **
42845228 ATCAAATAT-TAGAA
1 ATCAAAGATATGGGT
42845242 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
42845258 ATC
1 ATC
42845261 GAGATATTGG
Statistics
Matches: 63, Mismatches: 24, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
14 10 0.16
15 43 0.68
16 10 0.16
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:42845190 original size:30 final size:30
Alignment explanation
Indices: 42845149--42845260 Score: 188
Period size: 30 Copynumber: 3.7 Consensus size: 30
42845139 CATATTTATG
* *
42845149 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATATTA
* *
42845179 GAAAGTCAAAGATATGAGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATATTA
42845209 GAAAGTCAAAGATATGGGTATCAAATATTA
1 GAAAGTCAAAGATATGGGTATCAAATATTA
42845239 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
42845261 GAGATATTGG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATATTA
Found at i:42849865 original size:15 final size:15
Alignment explanation
Indices: 42849845--42849952 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
42849835 TTTATGGAAA
42849845 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
42849860 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
42849874 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
42849890 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
42849904 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
42849920 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
42849934 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
42849950 ATC
1 ATC
42849953 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:42849882 original size:30 final size:30
Alignment explanation
Indices: 42849839--42849962 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
42849829 TCCATATTTA
* *
42849839 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
42849869 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
42849899 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
42849929 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
42849960 TGG
1 TGG
42849963 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:42850592 original size:18 final size:18
Alignment explanation
Indices: 42850545--42850588 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
42850535 TGATAATATA
* *
42850545 AATAAACATATAAGTTTT
1 AATAAATATATAAATTTT
*
42850563 AATTAATATATAAATTTT
1 AATAAATATATAAATTTT
42850581 AA-AAATAT
1 AATAAATAT
42850589 TATAGAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAAATATATAAATTTT
Found at i:42850632 original size:28 final size:28
Alignment explanation
Indices: 42850597--42850653 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
42850587 ATTATAGAAG
42850597 AATATTCAAATTTTATAAGTTAAATATT
1 AATATTCAAATTTTATAAGTTAAATATT
42850625 AATATTCAAATTTTATAAGTTAAATATT
1 AATATTCAAATTTTATAAGTTAAATATT
42850653 A
1 A
42850654 TTAAATTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
AATATTCAAATTTTATAAGTTAAATATT
Found at i:42850649 original size:14 final size:14
Alignment explanation
Indices: 42850604--42850654 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
42850594 AAGAATATTC
*
42850604 AAATTTTATAAGTT
1 AAATATTATAAGTT
42850618 AAATATTA-ATA-TT
1 AAATATTATA-AGTT
*
42850631 CAAATTTTATAAGTT
1 -AAATATTATAAGTT
42850646 AAATATTAT
1 AAATATTAT
42850655 TAAATTACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.10
14 24 0.80
15 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (14 bp):
AAATATTATAAGTT
Found at i:42850650 original size:22 final size:25
Alignment explanation
Indices: 42850597--42850660 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 25
42850587 ATTATAGAAG
42850597 AATATTCAAATTTTATAAGTTAAATATT
1 AATATTCAAATTTTATAAGTT--ATA-T
*
42850625 AATATTCAAATTTTATAAGTTAAAT
1 AATATTCAAATTTTATAAGTTATAT
*
42850650 ATTATT-AAATT
1 AATATTCAAATT
42850661 ACCATTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 5 0.15
25 6 0.18
26 2 0.06
28 21 0.62
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
AATATTCAAATTTTATAAGTTATAT
Found at i:42850877 original size:14 final size:14
Alignment explanation
Indices: 42850855--42850905 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
42850845 TGGTAATTTA
*
42850855 ATAATATTTAACTT
1 ATAAAATTTAACTT
42850869 ATAAAATTTGAA--T
1 ATAAAATTT-AACTT
*
42850882 ATTAATATTTAACTT
1 A-TAAAATTTAACTT
42850897 ATAAAATTT
1 ATAAAATTT
42850906 GAATATTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.13
14 22 0.73
15 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (14 bp):
ATAAAATTTAACTT
Found at i:42850889 original size:28 final size:28
Alignment explanation
Indices: 42850856--42850912 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
42850846 GGTAATTTAA
42850856 TAATATTTAACTTATAAAATTTGAATAT
1 TAATATTTAACTTATAAAATTTGAATAT
42850884 TAATATTTAACTTATAAAATTTGAATAT
1 TAATATTTAACTTATAAAATTTGAATAT
42850912 T
1 T
42850913 CTTCTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (28 bp):
TAATATTTAACTTATAAAATTTGAATAT
Found at i:42860503 original size:3 final size:3
Alignment explanation
Indices: 42860495--42860535 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42860485 ATTTCATTCA
42860495 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42860536 GGGTTAATAG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42869817 original size:34 final size:35
Alignment explanation
Indices: 42869769--42869841 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 35
42869759 TCGTGTCATC
* *
42869769 CAAATTCTAAGAGATTGTTTGTAAGTCAAGTTAAA
1 CAAATTCTAAGAGATTGCTTGCAAGTCAAGTTAAA
*
42869804 CAAA-TCTAAGAGATTGCTTGCAAGTCAAGTTAGA
1 CAAATTCTAAGAGATTGCTTGCAAGTCAAGTTAAA
42869838 CAAA
1 CAAA
42869842 ATATAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 31 0.89
35 4 0.11
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (35 bp):
CAAATTCTAAGAGATTGCTTGCAAGTCAAGTTAAA
Found at i:42870169 original size:42 final size:43
Alignment explanation
Indices: 42870105--42870191 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 43
42870095 TTAACATAAG
* * * *
42870105 TCAAGCTTAAGCCACAGGAAAGCTGA-GTCTATCAATTTTTTC
1 TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
*
42870147 TCAAACTTAAGCCACAGAAAAGCTGACCTTTATCAATTTTGTC
1 TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
42870190 TC
1 TC
42870192 GCTGCTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 24 0.62
43 15 0.38
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (43 bp):
TCAAACTTAAGCCACAGAAAAGCTGACCTCTATCAATTTTGTC
Found at i:42874230 original size:22 final size:22
Alignment explanation
Indices: 42874205--42874246 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42874195 TCCAAAACAC
42874205 GGGAAAATGCCTTACAATTTTT
1 GGGAAAATGCCTTACAATTTTT
* * *
42874227 GGGAAATTGTCTTACCATTT
1 GGGAAAATGCCTTACAATTT
42874247 CAATTTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (22 bp):
GGGAAAATGCCTTACAATTTTT
Found at i:42874305 original size:18 final size:18
Alignment explanation
Indices: 42874282--42874346 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
42874272 AGCTCTCAGG
42874282 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
42874300 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
42874318 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
42874336 CATTCTTCTCC
1 CATTCTTCTCC
42874347 TTTCCTTCAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.14, C:0.43, G:0.03, T:0.40
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:42877439 original size:34 final size:35
Alignment explanation
Indices: 42877381--42877447 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
42877371 CAAACACCAG
42877381 AAAATATTTTCCAGTAAATCATTTTACAAAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAAAAAAGT
*
42877416 AAAATATTTTCCAG-AAATCATTTTACGAAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAAAAAA
42877448 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAAAAAAGT
Found at i:42877608 original size:21 final size:21
Alignment explanation
Indices: 42877584--42877625 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42877574 ATATATAATT
42877584 TTTTATAATATAAAA-TAAATA
1 TTTTAT-ATATAAAATTAAATA
*
42877605 TTTTATATTTAAAATTAAATA
1 TTTTATATATAAAATTAAATA
42877626 AAATGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTATATATAAAATTAAATA
Found at i:42878293 original size:68 final size:68
Alignment explanation
Indices: 42878184--42878317 Score: 268
Period size: 68 Copynumber: 2.0 Consensus size: 68
42878174 TTGTACCATC
42878184 TCTTATACATGTGTCTTTATTAGACAAGTCTCACACCAAGTGGACTTAGTACATCAAGTAGCATC
1 TCTTATACATGTGTCTTTATTAGACAAGTCTCACACCAAGTGGACTTAGTACATCAAGTAGCATC
42878249 AAG
66 AAG
42878252 TCTTATACATGTGTCTTTATTAGACAAGTCTCACACCAAGTGGACTTAGTACATCAAGTAGCATC
1 TCTTATACATGTGTCTTTATTAGACAAGTCTCACACCAAGTGGACTTAGTACATCAAGTAGCATC
42878317 A
66 A
42878318 TGGCGAGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (68 bp):
TCTTATACATGTGTCTTTATTAGACAAGTCTCACACCAAGTGGACTTAGTACATCAAGTAGCATC
AAG
Found at i:42882553 original size:4 final size:4
Alignment explanation
Indices: 42882546--42882586 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
42882536 TGTGTGTGTG
42882546 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
42882587 TTATTGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:42884128 original size:37 final size:37
Alignment explanation
Indices: 42884056--42884128 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
42884046 AAATAATCAC
*
42884056 TTTAATATTAAATTAATAAAATACTACTAAGATAAGT
1 TTTAATATTAAATTAATAAAATACTACTAAAATAAGT
* *
42884093 TTTAA-ATTAAATTTAATATTAAT-CTATTAAAATAAG
1 TTTAATATTAAA-TTAATA-AAATACTACTAAAATAAG
42884129 ATTATTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 6 0.19
37 22 0.71
38 3 0.10
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (37 bp):
TTTAATATTAAATTAATAAAATACTACTAAAATAAGT
Found at i:42885331 original size:15 final size:15
Alignment explanation
Indices: 42885311--42885341 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42885301 GCTATGCATG
*
42885311 AAAAATATAAAAGAC
1 AAAAATACAAAAGAC
42885326 AAAAATACAAAAGAC
1 AAAAATACAAAAGAC
42885341 A
1 A
42885342 TAATATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAATACAAAAGAC
Found at i:42885943 original size:12 final size:12
Alignment explanation
Indices: 42885928--42885952 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42885918 TAGAAGATAT
42885928 GATAGAAGAAGA
1 GATAGAAGAAGA
42885940 GATAGAAGAAGA
1 GATAGAAGAAGA
42885952 G
1 G
42885953 GTGGAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (12 bp):
GATAGAAGAAGA
Found at i:42906377 original size:28 final size:28
Alignment explanation
Indices: 42906337--42906390 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
42906327 TCTACTCTAA
* *
42906337 ACAAATTAGTCCACCTAGAGTCATATCC
1 ACAAATCAGTCCACCTAGAGCCATATCC
42906365 ACAAATCAGTCCACCTAGAGCCATAT
1 ACAAATCAGTCCACCTAGAGCCATAT
42906391 GCTCACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (28 bp):
ACAAATCAGTCCACCTAGAGCCATATCC
Found at i:42921781 original size:9 final size:9
Alignment explanation
Indices: 42921764--42921830 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
42921754 GTAGTGATTC
*
42921764 AATTTGGTT
1 AATTCGGTT
42921773 AATTCGGTT
1 AATTCGGTT
42921782 AATTCGGTT
1 AATTCGGTT
*
42921791 AATTCGGGT
1 AATTCGGTT
42921800 AATTCAGG-T
1 AATTC-GGTT
*
42921809 AATTTGGTT
1 AATTCGGTT
*
42921818 AATTTGGTT
1 AATTCGGTT
42921827 AATT
1 AATT
42921831 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
8 2 0.04
9 49 0.92
10 2 0.04
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.46
Consensus pattern (9 bp):
AATTCGGTT
Found at i:42921893 original size:30 final size:30
Alignment explanation
Indices: 42921859--42921933 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
42921849 AACATAGAAT
42921859 TTTCGGTTCGGTTAATTTTTTTGAAAAAAA
1 TTTCGGTTCGGTTAATTTTTTTGAAAAAAA
42921889 TTTCGGTTCGGTTAATTTTTTTGAAAAAAA
1 TTTCGGTTCGGTTAATTTTTTTGAAAAAAA
42921919 TTTCGGTTCGGTTAA
1 TTTCGGTTCGGTTAA
42921934 CGGTTAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (30 bp):
TTTCGGTTCGGTTAATTTTTTTGAAAAAAA
Found at i:42923560 original size:14 final size:15
Alignment explanation
Indices: 42923518--42923554 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
42923508 TTGAGAAACA
42923518 ATAAA-TTCATAAATT
1 ATAAATTTCA-AAATT
42923533 ATAAATTTCAAAATT
1 ATAAATTTCAAAATT
42923548 -TAAATTT
1 ATAAATTT
42923555 TGAAATCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 10 0.48
16 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATTTCAAAATT
Found at i:42923566 original size:6 final size:6
Alignment explanation
Indices: 42923557--42923590 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
42923547 TTAAATTTTG
*
42923557 AAATCC AAATCC AAATCC AAATCT AAATCC AAAT
1 AAATCC AAATCC AAATCC AAATCC AAATCC AAAT
42923591 TTTGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATCC
Found at i:42929486 original size:10 final size:10
Alignment explanation
Indices: 42929464--42929514 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 10
42929454 TTTTTTGCAC
*
42929464 TTTTAT-ATA
1 TTTTATGATT
42929473 TTTTATGATT
1 TTTTATGATT
*
42929483 TTTTAT-AAT
1 TTTTATGATT
*
42929492 TTTTATGTTTT
1 TTTTATG-ATT
42929503 TTTTATGATT
1 TTTTATGATT
42929513 TT
1 TT
42929515 AATTATAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 14 0.41
10 12 0.35
11 8 0.24
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (10 bp):
TTTTATGATT
Found at i:42929486 original size:19 final size:18
Alignment explanation
Indices: 42929464--42929515 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
42929454 TTTTTTGCAC
42929464 TTTTATATATTTTATGATT
1 TTTTATATATTTTATG-TT
42929483 TTTTATA-ATTTTTATGTT
1 TTTTATATA-TTTTATGTT
*
42929501 TTTTTTATGATTTTA
1 TTTTATAT-ATTTTA
42929516 ATTATAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 9 0.31
19 19 0.66
20 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTATATATTTTATGTT
Found at i:42930512 original size:18 final size:19
Alignment explanation
Indices: 42930472--42930521 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
42930462 AGTTGATATG
*
42930472 ATTAATATTT-TTAATCATC
1 ATTAA-ATTTATTAATCATA
42930491 ATTAAATTTATTAATC-TA
1 ATTAAATTTATTAATCATA
*
42930509 ATTATATTTATTA
1 ATTAAATTTATTA
42930522 TGAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTAAATTTATTAATCATA
Found at i:42940381 original size:51 final size:51
Alignment explanation
Indices: 42940296--42940495 Score: 246
Period size: 51 Copynumber: 3.9 Consensus size: 51
42940286 TCAAAGATAT
* *
42940296 CGATTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATC
* *
42940347 CGATACACTTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATC
* * * *
42940398 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATC
* * *
42940448 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
42940496 TTCACTTTTA
Statistics
Matches: 128, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
49 4 0.03
50 42 0.33
51 79 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (51 bp):
CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATC
Found at i:42940481 original size:101 final size:102
Alignment explanation
Indices: 42940303--42940487 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
42940293 TATCGATTCA
* *
42940303 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACTTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
42940368 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* *
42940405 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
42940468 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
42940488 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 39 0.50
102 35 0.45
103 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:42942879 original size:21 final size:21
Alignment explanation
Indices: 42942853--42942903 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
42942843 GTTATCTTCC
42942853 TCTCTTGATGGATATGGAAAT
1 TCTCTTGATGGATATGGAAAT
42942874 TCTCTTGATGGATATGGAAAT
1 TCTCTTGATGGATATGGAAAT
*
42942895 TCTTTTGAT
1 TCTCTTGAT
42942904 TTTTAGGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (21 bp):
TCTCTTGATGGATATGGAAAT
Found at i:42943072 original size:8 final size:8
Alignment explanation
Indices: 42943059--42943090 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
42943049 ATACTAAACG
42943059 ATAAAATA
1 ATAAAATA
42943067 ATAAAATA
1 ATAAAATA
42943075 ATAAAATA
1 ATAAAATA
42943083 ATAAAATA
1 ATAAAATA
42943091 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
ATAAAATA
Found at i:42956098 original size:25 final size:25
Alignment explanation
Indices: 42956064--42956111 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
42956054 GCCTGAGAAA
42956064 CAACATAAATAGCATACACAAAGAG
1 CAACATAAATAGCATACACAAAGAG
*
42956089 CAACTTAAATAGCATACACAAAG
1 CAACATAAATAGCATACACAAAG
42956112 TGTTTGAGTA
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:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (25 bp):
CAACATAAATAGCATACACAAAGAG
Found at i:42958375 original size:50 final size:52
Alignment explanation
Indices: 42958312--42958426 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 52
42958302 AAAATTATAT
* * * * *
42958312 AAATTACAAAAAATAAAAATGAACAA-TTTATTAAAATATAAAAGT-TATTAA
1 AAATTACATAAAATAAAAATGAAAAAGATTA-TAAAATATAAAAATATATGAA
* *
42958363 AAATTA-ATAAAATAAAATTGAAAAAGATTATAAAATTTAAAAATATATGAA
1 AAATTACATAAAATAAAAATGAAAAAGATTATAAAATATAAAAATATATGAA
*
42958414 AAATTATATAAAA
1 AAATTACATAAAA
42958427 AACCATTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
50 28 0.52
51 20 0.37
52 6 0.11
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (52 bp):
AAATTACATAAAATAAAAATGAAAAAGATTATAAAATATAAAAATATATGAA
Found at i:42960832 original size:51 final size:51
Alignment explanation
Indices: 42960706--42960887 Score: 296
Period size: 50 Copynumber: 3.6 Consensus size: 51
42960696 GAGGTCCCAT
**
42960706 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT-CCCAT
1 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
42960756 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
1 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
* *
42960807 GTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATGAGAGG-CCCCCC
1 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
* *
42960857 GTAAGACCATGTCTAGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCGTTGGCA
42960888 TGTTATTACC
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 79 0.64
51 45 0.36
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (51 bp):
GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
Found at i:42960886 original size:101 final size:101
Alignment explanation
Indices: 42960706--42960887 Score: 301
Period size: 101 Copynumber: 1.8 Consensus size: 101
42960696 GAGGTCCCAT
* * * *
42960706 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTG
1 GTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGCCCCACGTAAGACCATGTCTA
42960771 GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
66 GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
* *
42960807 GTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATGAGAGGCCCCCCGTAAGACCATGTCTA
1 GTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGCCCCACGTAAGACCATGTCTA
*
42960872 GGACATGGCTTTGGCA
66 GGACATGGCGTTGGCA
42960888 TGTTATTACC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (101 bp):
GTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGCCCCACGTAAGACCATGTCTA
GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCC
Found at i:42964836 original size:18 final size:20
Alignment explanation
Indices: 42964798--42964842 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
42964788 TGCCACCGAA
42964798 ATAGAACCAGTGCGTCGGGAT
1 ATAGAACCAGT-CGTCGGGAT
42964819 ATAGAACCAGT-G-CGGGAT
1 ATAGAACCAGTCGTCGGGAT
42964837 ATAGAA
1 ATAGAA
42964843 TCTTTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.50
19 1 0.04
21 11 0.46
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.18
Consensus pattern (20 bp):
ATAGAACCAGTCGTCGGGAT
Found at i:42973808 original size:12 final size:13
Alignment explanation
Indices: 42973791--42973819 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42973781 AAACTGAAAG
42973791 AAAATAAAAAC-T
1 AAAATAAAAACGT
42973803 AAAATAAAAACGT
1 AAAATAAAAACGT
42973816 AAAA
1 AAAA
42973820 CTAACTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAATAAAAACGT
Found at i:42982010 original size:31 final size:31
Alignment explanation
Indices: 42981968--42982027 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
42981958 AAAAAAAGTC
42981968 TAAATATTTC-AAATAAAGTTTTGATTTTCT
1 TAAATATTTCAAAATAAAGTTTTGATTTTCT
*
42981998 TAAACTATTTCAAAATAAGGTTTTGATTTT
1 TAAA-TATTTCAAAATAAAGTTTTGATTTT
42982028 TAAGAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 6 0.22
32 17 0.63
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (31 bp):
TAAATATTTCAAAATAAAGTTTTGATTTTCT
Found at i:42982586 original size:24 final size:25
Alignment explanation
Indices: 42982542--42982588 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
42982532 TCACTTGCAT
42982542 TTATGCATTATATATTTAATGTTAA
1 TTATGCATTATATATTTAATGTTAA
42982567 TTATGCACTT-TAT-TTTAATGTT
1 TTATGCA-TTATATATTTAATGTT
42982589 TATATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 10 0.48
26 2 0.10
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTATGCATTATATATTTAATGTTAA
Found at i:42982772 original size:12 final size:12
Alignment explanation
Indices: 42982753--42982783 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42982743 GAATAAGGTG
42982753 TATTATTGTTAT
1 TATTATTGTTAT
*
42982765 TGTTATTGTTAT
1 TATTATTGTTAT
42982777 TATTATT
1 TATTATT
42982784 ATCATCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (12 bp):
TATTATTGTTAT
Found at i:42993902 original size:16 final size:16
Alignment explanation
Indices: 42993883--42993915 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42993873 TTTCATTGCA
42993883 TTTAGAGACCCAGGTG
1 TTTAGAGACCCAGGTG
42993899 TTTAGAGACCCAGGTG
1 TTTAGAGACCCAGGTG
42993915 T
1 T
42993916 GAAGGTCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (16 bp):
TTTAGAGACCCAGGTG
Found at i:42993931 original size:58 final size:58
Alignment explanation
Indices: 42993841--42993957 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 58
42993831 ATTCATTGCA
* * * *
42993841 TTTAGAGGCCCAGGTGTGGAGGTCCGTTTACTTTTCATTGCATTTAGAGACCCAGGTG
1 TTTAGAGACCCAGGTGTGAAGGTCCGTTTACTTTTCATTACATTTAGAAACCCAGGTG
*
42993899 TTTAGAGACCCAGGTGTGAAGGTCCGTTTACTTTTCATTACATTTAGAAACTCAGGTG
1 TTTAGAGACCCAGGTGTGAAGGTCCGTTTACTTTTCATTACATTTAGAAACCCAGGTG
42993957 T
1 T
42993958 GGAGGTCCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (58 bp):
TTTAGAGACCCAGGTGTGAAGGTCCGTTTACTTTTCATTACATTTAGAAACCCAGGTG
Found at i:42993958 original size:42 final size:42
Alignment explanation
Indices: 42993899--42994310 Score: 513
Period size: 42 Copynumber: 9.9 Consensus size: 42
42993889 GACCCAGGTG
* * *
42993899 TTTAGAGACCCAGGTGTGAAGGTCCGTTTACTTTTCATTACA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* *
42993941 TTTAGAAACTCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* * *
42993983 TTTAGAGGCCCGGGTATGGAGGTCCATTTACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* * * * *
42994025 TTTAGAGGCCTAGGTATGAAGGCCCATTTACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* *
42994067 TTTAGAGACCCAGGTGTGGAGGCCCGTTTACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
*
42994109 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTTATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
** * **
42994151 TTT--AGACTTAAGACTGGAGGTCCATTTACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* * * * *
42994191 TTTAGAGGCTCAGGTGTAGAGGTCAATTCACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* * * *
42994233 TTTAAAGACTCAGGTGTGGAGGTTCATTAACTTTTCATTGCA
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
* * *
42994275 TTTAGAAACCTAGGTGTGGAGGTCCGTTTACTTTTC
1 TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTC
42994311 TAGTTTACTT
Statistics
Matches: 319, Mismatches: 49, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
40 34 0.11
42 285 0.89
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCA
Found at i:42994648 original size:16 final size:16
Alignment explanation
Indices: 42994622--42994661 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
42994612 TATTTGAGAC
*
42994622 CTTTA-TTTCTCTTTT
1 CTTTATTTTCTCTCTT
42994637 CTTTATTTTCTCTCTT
1 CTTTATTTTCTCTCTT
*
42994653 CTTTCTTTT
1 CTTTATTTT
42994662 TTGGGCTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (16 bp):
CTTTATTTTCTCTCTT
Found at i:42995562 original size:151 final size:150
Alignment explanation
Indices: 42995072--42995800 Score: 922
Period size: 152 Copynumber: 4.8 Consensus size: 150
42995062 AGTTTTGACT
* * * * *
42995072 TTTTTTTTAAAGG-GAAAGTTTAGATTTT-AACAAAT-AAAAATCTTTTTTTTTTACTTATTTCA
1 TTTTTTTT-AAGGAGAAAGTTTAGATTTTGAA-AAATAAAAAATCTGTTTTTTTAAGTCATTTTA
* * * *
42995134 AAGGAAAGTTTAAAATTTTAAAACAAATTTTTTATTTTTTTTTTCAACTATTTCAGAGTAAAAGC
64 AAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGA-TTTTTTTTTCAACTATTTCAAAATAAAAGC
42995199 TTTAATCTTTAAGAAAAATAGTG
128 TTTAATCTTTAAGAAAAATAGTG
42995222 TTTTTTTTTTTAAAAGGAGAAAGTTTAGATTTTGAAAAAT-AAAAATCTGTTTTTTT--GTCATT
1 ---TTTTTTTT--AAGGAGAAAGTTTAGATTTTGAAAAATAAAAAATCTGTTTTTTTAAGTCATT
* *
42995284 TTAAAGGAAAGTTTAAAATTTTTAAACAAAGTTTTAATTTTTTTTTCAACTATTTCAAAATAAAA
61 TTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAATAAAA
*
42995349 TCTTTAATCTTTAAGAAAAATAGTG
126 GCTTTAATCTTTAAGAAAAATAGTG
* *
42995374 TTTTTCTTAAAAAGGAAGAAAGTTTAGATTTTGAAAAATAAAAAATCTGTTTTTTTAAATCATTT
1 TTTTT-TT--TAAGG-AGAAAGTTTAGATTTTGAAAAATAAAAAATCTGTTTTTTTAAGTCATTT
* * * *
42995439 TAAAGGAAAGTTTAAATTTTTAAAATAAAGTTTCGATTTTTTTTTCAACTATTTCAAAGTAAAAA
62 TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAAT-AAAA
* *
42995504 ACTTTAATCATTAAGAAAAATAGTG
126 GCTTTAATCTTTAAGAAAAATAGTG
* **
42995529 TTTTTTTTAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTCAT-TTTTGTTTTTGTCATTTTA
1 TTTTTTTTAAGGAGAAAGTTTAGATTTTGAAAAATAAAAAATC-TGTTTT-TTTAAGTCATTTTA
** *
42995593 AAGGAATCTTTAAAATTTTAAAACAAAGTTTTGA-TTTTTTTTCAACTATTTCAAAATAAAAGTT
64 AAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAATAAAAGCT
42995657 TTAATCTTTAAGAAAAATAGTG
129 TTAATCTTTAAGAAAAATAGTG
* * *
42995679 TTTTTTTTAAGGGAGAAAGTTTAGATTTTAAAAAAATAAAAAAT-TGTTTCTTTAAGCCATTTTA
1 TTTTTTTTAA-GGAGAAAGTTTAGATTTT-GAAAAATAAAAAATCTGTTTTTTTAAGTCATTTTA
* * * * *
42995743 AAGAAAAGTTTAAACTTTTAAAATAAAATTTTGA-TTTTTTTT-AACTATTTCGAAATAA
64 AAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAATAA
42995801 GTTTTTGATT
Statistics
Matches: 513, Mismatches: 47, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
149 20 0.04
150 90 0.18
151 100 0.19
152 123 0.24
153 45 0.09
154 67 0.13
155 66 0.13
156 2 0.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (150 bp):
TTTTTTTTAAGGAGAAAGTTTAGATTTTGAAAAATAAAAAATCTGTTTTTTTAAGTCATTTTAAA
GGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAATAAAAGCTTT
AATCTTTAAGAAAAATAGTG
Found at i:42995786 original size:31 final size:32
Alignment explanation
Indices: 42995755--42995813 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
42995745 GAAAAGTTTA
42995755 AACT-TTT-AAAATAAAATTTTGATTTTTTTT
1 AACTATTTCAAAATAAAATTTTGATTTTTTTT
* **
42995785 AACTATTTCGAAATAAGTTTTTGATTTTT
1 AACTATTTCAAAATAAAATTTTGATTTTT
42995814 AAGAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 3 0.12
32 17 0.71
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (32 bp):
AACTATTTCAAAATAAAATTTTGATTTTTTTT
Found at i:42995859 original size:20 final size:20
Alignment explanation
Indices: 42995831--42995869 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42995821 TTAATGATTT
* * *
42995831 TTTTCTAAAGAAAACTTTGA
1 TTTTATAAAAAAAAATTTGA
42995851 TTTTATAAAAAAAAATTTG
1 TTTTATAAAAAAAAATTTG
42995870 CCACCGTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTATAAAAAAAAATTTGA
Found at i:42996422 original size:11 final size:10
Alignment explanation
Indices: 42996392--42996451 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
42996382 CACTTGTATA
42996392 ATTTTTATTT
1 ATTTTTATTT
*
42996402 ATTCTTATTT
1 ATTTTTATTT
*
42996412 CGTTTTTATTT
1 -ATTTTTATTT
*
42996423 ATTTTAATTT
1 ATTTTTATTT
42996433 ATATTTATATTT
1 AT-TTT-TATTT
*
42996445 TTTTTTA
1 ATTTTTA
42996452 CACATTCCCC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 21 0.52
11 14 0.35
12 5 0.12
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:42996534 original size:3 final size:3
Alignment explanation
Indices: 42996528--42996569 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
42996518 GAAGAAGGTA
* * *
42996528 TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42996570 CATCATGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42997911 original size:43 final size:43
Alignment explanation
Indices: 42997864--42997977 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 43
42997854 ATGCCGTGTT
* *
42997864 CTTTAGCGACGCATTTATAACAAACGTCGCTAAAGAACATGAC
1 CTTTAGCAACGCTTTTATAACAAACGTCGCTAAAGAACATGAC
** * * * * * *
42997907 CTTTAATAACACTTTTCTAACAATCGCCGTTAAATAACATGAC
1 CTTTAGCAACGCTTTTATAACAAACGTCGCTAAAGAACATGAC
*
42997950 CTTTAGCAACGCTTTTTATCACAAACGT
1 CTTTAGCAACGC-TTTTATAACAAACGT
42997978 TAACTTTTAG
Statistics
Matches: 53, Mismatches: 17, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
43 42 0.79
44 11 0.21
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (43 bp):
CTTTAGCAACGCTTTTATAACAAACGTCGCTAAAGAACATGAC
Found at i:42998028 original size:23 final size:24
Alignment explanation
Indices: 42998001--42998056 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
42997991 CATTTAAAAA
* *
42998001 TATTAAATAT-TAAAATTAAACAT
1 TATTAAATATCAAAAATTAAACAG
**
42998024 TATT-AATATCAAAAATTAATTAG
1 TATTAAATATCAAAAATTAAACAG
42998047 TATTAAATAT
1 TATTAAATAT
42998057 ATACTTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 17 0.63
24 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
TATTAAATATCAAAAATTAAACAG
Found at i:43000460 original size:14 final size:14
Alignment explanation
Indices: 43000425--43000467 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
43000415 TTCTGATTTG
43000425 ATCAATATGTAT--
1 ATCAATATGTATAA
*
43000437 A-CACTATGTATAA
1 ATCAATATGTATAA
43000450 ATCAATATGTATAA
1 ATCAATATGTATAA
43000464 ATCA
1 ATCA
43000468 TAAACAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
13 1 0.04
14 15 0.58
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (14 bp):
ATCAATATGTATAA
Found at i:43001585 original size:15 final size:15
Alignment explanation
Indices: 43001550--43001587 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
43001540 TCCCGACCCT
*
43001550 TAAATT-ATAATTTC
1 TAAATTCATAATTCC
43001564 T-AATTCATAATTCC
1 TAAATTCATAATTCC
43001578 TAAATTCATA
1 TAAATTCATA
43001588 TATAATCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTCATAATTCC
Found at i:43002200 original size:40 final size:40
Alignment explanation
Indices: 43002105--43002202 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
43002095 ACGGCGCTTT
* *
43002105 CAAAAA-CGCTGCTAATGCTTGATCTATAGCGGCGTTTTC
1 CAAAAAGCGCCGCTAATGCTTGATCTATAGCGGCATTTTC
* *
43002144 CAAAAAGCGCCACTAATGCTTGATCTATAGCGGCATTTTT
1 CAAAAAGCGCCGCTAATGCTTGATCTATAGCGGCATTTTC
* * *
43002184 TAGAAAGCGTCGCTAATGC
1 CAAAAAGCGCCGCTAATGC
43002203 CACCAAAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
39 6 0.12
40 44 0.88
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (40 bp):
CAAAAAGCGCCGCTAATGCTTGATCTATAGCGGCATTTTC
Found at i:43002428 original size:114 final size:114
Alignment explanation
Indices: 43002133--43002431 Score: 374
Period size: 115 Copynumber: 2.6 Consensus size: 114
43002123 TTGATCTATA
* * * * * *
43002133 GCGGCGTTTTCCAAAAAGCGCCACTAATGCTTGATCTATAGCGGCATTTTTTAGAAAGCGTCGCT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGC-ACGCT
* *
43002198 AATGCCACCAAAGCTTAACATAAAACGATGGCGTTGTGCTTAATTTTTTT
65 AATGCCACCAAAGCTCAACATAAAACGATGGCGTTGTACTTAATTTTTTT
* * *
43002248 GCGGCGTTTTTCAAGAAGCGCCGCT-ATAGGTCGAGC-ATTAGCGGCATTTTTCAAAAAGCACTG
1 GCGGCGTTTTTCAAAAAGCGCCGCTAAT-GCTCGATCTA-TAGCGGCATTTTTCAAAAAGCAC-G
*
43002311 CTAATGCCACCGAAGCTCAACATAAAACGATGG-GTTGTACTTAATTTTTTT
63 CTAATGCCACCAAAGCTCAACATAAAACGATGGCGTTGTACTTAATTTTTTT
* *
43002362 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGGGC-TTTTTGAAAAATGC-CG
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGC--GGCATTTTTCAAAAA-GCACG
43002425 CTAATGC
63 CTAATGC
43002432 TCGATCTATA
Statistics
Matches: 159, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
114 62 0.39
115 92 0.58
116 5 0.03
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (114 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCACGCTA
ATGCCACCAAAGCTCAACATAAAACGATGGCGTTGTACTTAATTTTTTT
Found at i:43002430 original size:40 final size:40
Alignment explanation
Indices: 43002362--43002492 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 40
43002352 TAATTTTTTT
*
43002362 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* * *
43002402 GCGGGGCTTTTTGAAAAA-TGCCGCTAATGCTCGATCTATA
1 GCGGCG-TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* * *
43002442 GTGGCGTTTTTCAAAAAGCGCCGCTAATG-TAAGATCTACA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCT-CGATCTATA
*
43002482 GTGGCGTTTTT
1 GCGGCGTTTTT
43002493 ATCCAAACGC
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 11 0.14
40 57 0.73
41 10 0.13
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
Found at i:43004001 original size:22 final size:24
Alignment explanation
Indices: 43003964--43004017 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
43003954 GAAGGGAGGG
43003964 AAAAAAATGAAGAATAAAAAGAA-
1 AAAAAAATGAAGAATAAAAAGAAT
*
43003987 AAATAAAAT-AA-AATAAAGAGAAT
1 AAA-AAAATGAAGAATAAAAAGAAT
43004010 AAAAAAAT
1 AAAAAAAT
43004018 TGTTAGAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 15 0.54
23 8 0.29
24 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAAAATGAAGAATAAAAAGAAT
Found at i:43008922 original size:35 final size:33
Alignment explanation
Indices: 43008883--43008970 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
43008873 GTTTTTGCTA
* *
43008883 CCCTTAGTTTTATCCCCAAATTATTTTCCCGAAAT
1 CCCTTAGTTTT-TCCCCAAA-AATTTTCCCCAAAT
*
43008918 CCCTTATTTTTTCCCCTAAAAATTTTCCCCAAAT
1 CCCTTAGTTTTTCCCC-AAAAATTTTCCCCAAAT
*
43008952 CCCTTAGATTTTCCCCAAA
1 CCCTTAGTTTTTCCCCAAA
43008971 CGTCTGCTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 3 0.06
34 31 0.66
35 13 0.28
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (33 bp):
CCCTTAGTTTTTCCCCAAAAATTTTCCCCAAAT
Found at i:43008955 original size:21 final size:20
Alignment explanation
Indices: 43008931--43008970 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43008921 TTATTTTTTC
43008931 CCCTAAAAATTTTCCCCAAAT
1 CCCT-AAAATTTTCCCCAAAT
* *
43008952 CCCTTAGATTTTCCCCAAA
1 CCCTAAAATTTTCCCCAAA
43008971 CGTCTGCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (20 bp):
CCCTAAAATTTTCCCCAAAT
Found at i:43009034 original size:25 final size:25
Alignment explanation
Indices: 43008973--43009034 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
43008963 TCCCCAAACG
* *
43008973 TCTGCTGCATCACCGTCTACAATCC
1 TCTGCTGCATCGCCGTCGACAATCC
*
43008998 TCTGCTGCATCGCCGTCGACAGTCC
1 TCTGCTGCATCGCCGTCGACAATCC
*
43009023 TCTGCTACATCG
1 TCTGCTGCATCG
43009035 TCGTGTAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.16, C:0.39, G:0.18, T:0.27
Consensus pattern (25 bp):
TCTGCTGCATCGCCGTCGACAATCC
Found at i:43009964 original size:20 final size:20
Alignment explanation
Indices: 43009927--43009965 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43009917 TCACAATTTG
*
43009927 TTTTAAAAATTTTGATTAAT
1 TTTTAAAAATTTTAATTAAT
43009947 TTTTAAAAGA-TTTAATTAA
1 TTTTAAAA-ATTTTAATTAA
43009966 AACCTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTTAAAAATTTTAATTAAT
Found at i:43011239 original size:59 final size:59
Alignment explanation
Indices: 43011167--43011771 Score: 954
Period size: 59 Copynumber: 10.3 Consensus size: 59
43011157 AAACGCTAGG
* * *
43011167 TCATATTTCATAATAATTTAATGAATAATTAATTAATTTCTGATTAATTATATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
* *
43011226 TCATATTTCATAATAATTTTATAAATAATTAATTAATTTTCGATTACA-TAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTA-ATTAAATAAATAA
43011285 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
* * *
43011344 TCATATTTCATAATAATTATACGAATAATTAATTAATTTTTGGTTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
43011403 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTTG-TTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAA-TTTTTGATTAATTAAATAAATAA
* *
43011462 TCATATTTCATAATAATTCTACGAATAATTAATTAATTTTTTG-TTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAA-TTTTTGATTAATTAAATAAATAA
43011521 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
** *
43011580 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAAAAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
* * *
43011639 TCATATTTCATTATAATTCTATGAATAATTAATTAATTTTTTATTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
* * *
43011698 TCATATTTCATAATAATTCTATG---AA-TAATTAATTTTCGATTAAATAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
43011753 TCATATTTCATAATTAATT
1 TCATATTTCATAA-TAATT
43011772 AATTTTCGAT
Statistics
Matches: 513, Mismatches: 28, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
55 40 0.08
56 7 0.01
58 7 0.01
59 452 0.88
60 7 0.01
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (59 bp):
TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
Found at i:43011332 original size:19 final size:20
Alignment explanation
Indices: 43011298--43011619 Score: 71
Period size: 20 Copynumber: 16.4 Consensus size: 20
43011288 TATTTCATAA
43011298 TAATTTTATGAATAATTAAT
1 TAATTTTATGAATAATTAAT
* *
43011318 TAATTTT-TGATTAATTAAA
1 TAATTTTATGAATAATTAAT
* * * * *
43011337 TAA-ATAAT-CATATTTCATAA
1 TAATTTTATGAATAATT-A-AT
* *
43011357 TAATTATACGAATAATTAAT
1 TAATTTTATGAATAATTAAT
** *
43011377 TAATTTT-TGGTTAATTAAA
1 TAATTTTATGAATAATTAAT
* * * * *
43011396 TAA-ATAAT-CATATTTCATAA
1 TAATTTTATGAATAATT-A-AT
43011416 TAATTTTATGAATAATTAAT
1 TAATTTTATGAATAATTAAT
* * *
43011436 TAATTTTTTG-TTAATTAAA
1 TAATTTTATGAATAATTAAT
* * * * *
43011455 TAA-ATAAT-CATATTTCATAA
1 TAATTTTATGAATAATT-A-AT
* *
43011475 TAATTCTACGAATAATTAAT
1 TAATTTTATGAATAATTAAT
* * *
43011495 TAATTTTTTG-TTAATTAAA
1 TAATTTTATGAATAATTAAT
* * * * *
43011514 TAA-ATAAT-CATATTTCATAA
1 TAATTTTATGAATAATT-A-AT
43011534 TAATTTTATGAATAATTAAT
1 TAATTTTATGAATAATTAAT
* *
43011554 TAATTTT-TGATTAATTAAA
1 TAATTTTATGAATAATTAAT
* * * * *
43011573 TAA-ATAAT-CATATTTCATAA
1 TAATTTTATGAATAATT-A-AT
43011593 TAATTTTATGAATAATTAAT
1 TAATTTTATGAATAATTAAT
43011613 TAATTTT
1 TAATTTT
43011620 CAATTAATTA
Statistics
Matches: 206, Mismatches: 71, Indels: 50
0.63 0.22 0.15
Matches are distributed among these distances:
18 27 0.13
19 65 0.32
20 73 0.35
21 16 0.08
22 25 0.12
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (20 bp):
TAATTTTATGAATAATTAAT
Found at i:43011711 original size:44 final size:46
Alignment explanation
Indices: 43011662--43011777 Score: 119
Period size: 55 Copynumber: 2.4 Consensus size: 46
43011652 TAATTCTATG
*
43011662 AATAATTAATTAATTTTTT-ATTAATTAAATAAATAATCATATTTC
1 AATAATTAATTAATTTTTTCATTAAATAAATAAATAATCATATTTC
*
43011707 ATAATAATTCTATGAATAATTAATTTTCGATTAAATAAATAAATAATCATATTTC
1 --AATAA-T-TA--ATTAATT--TTTTC-ATTAAATAAATAAATAATCATATTTC
43011762 -ATAATTAATTAATTTT
1 AATAATTAATTAATTTT
43011778 CGATTAATCA
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
46 2 0.03
47 5 0.09
48 7 0.12
49 2 0.03
50 2 0.03
51 7 0.12
52 4 0.07
53 4 0.07
55 25 0.43
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (46 bp):
AATAATTAATTAATTTTTTCATTAAATAAATAAATAATCATATTTC
Found at i:43012273 original size:7 final size:7
Alignment explanation
Indices: 43012261--43012292 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
43012251 TAAATAATTA
43012261 GATACTT
1 GATACTT
43012268 GATACTT
1 GATACTT
43012275 GATACTT
1 GATACTT
43012282 GATACTT
1 GATACTT
43012289 GATA
1 GATA
43012293 TATATTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (7 bp):
GATACTT
Found at i:43019770 original size:27 final size:27
Alignment explanation
Indices: 43019706--43019776 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
43019696 GGTGGAGGGC
* * *
43019706 CTGCCACAGGTGGCACTAGTGGTGCCA
1 CTGCCACAGGCGGCACCAATGGTGCCA
* * * *
43019733 GTGGCAGAGGCGACACCAATGGTGCCA
1 CTGCCACAGGCGGCACCAATGGTGCCA
43019760 CTGCCACAGGCGGCACC
1 CTGCCACAGGCGGCACC
43019777 GGCCCTTATA
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAATGGTGCCA
Found at i:43020634 original size:8 final size:8
Alignment explanation
Indices: 43020623--43020648 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
43020613 CTAAAAAATT
43020623 TAAAATAA
1 TAAAATAA
43020631 TAAAATAA
1 TAAAATAA
43020639 TAAAATAA
1 TAAAATAA
43020647 TA
1 TA
43020649 TATTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAAATAA
Found at i:43020670 original size:156 final size:158
Alignment explanation
Indices: 43020272--43021333 Score: 1556
Period size: 156 Copynumber: 6.8 Consensus size: 158
43020262 AGGGTTTTTT
** * *
43020272 ACTAAATTAATGTATTTCAAACATAATGTACTAAAATAATGTTAAATAATAAAATACGAAAATAA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAGAAAATAA
* * *** * *
43020337 CATATT-TT-TTGAAA-CAATGAGGCTT-CGGTAAAAAAATACGAACAAATGGCCG-AA-AAGGG
66 TATATTATTATTGAAAGTAAT-AAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
* *
43020396 TT-TTTTTTACTAAATTTATTTAAAAAACAC
130 TTAATTTTT--GAAATTTATTTAAAAAACAC
* *
43020426 ACTAAATTAATACATTTCAAATATAATATACTAAAATAATGTAAAATAATAAAATACA-AAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATA-AGAAAATA
* * * *
43020490 ATATATTTTTATTAAAAGTAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCAGAAATAAGGG
65 ATATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
43020555 TTAATTTTTGAAATTTATTT-AAAAACAC
130 TTAATTTTTGAAATTTATTTAAAAAACAC
* * *
43020583 ACTAAATTAATACATTTAAAACATAATGTACTAAAA-AATTTAAAATAATAAAATAATAAAATAA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAGAAAATAA
*
43020647 TATATTATTATTGAAAGTAATAAAATTCAGGG--AAAAATACGAACAAAGGGCCGAAATAAGGGT
66 TATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
43020710 TAATTTTTGAAATTTATTT-AAAAACAC
131 TAATTTTTGAAATTTATTTAAAAAACAC
* * * *
43020737 ACTAAATTAATACATTTCAAACATAATGTACT-AAA-AATATAAAATAATTAAATTAGAAAATTA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAGAAAATAA
43020800 TATATTATTATTGAAAGTAATAAAA-TCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
66 TATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
43020864 TAATTTTTGAAATTTATTT-AAAAACAC
131 TAATTTTTGAAATTTATTTAAAAAACAC
* * *
43020891 ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAACTAATAAAATTAGAAAATAA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAGAAAATAA
*
43020956 TATATTTTTATTGAAAGTAATAAAA-TCCGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGGT
66 TATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
43021019 TAATTTTTGAAATTTATTTAAAAAACAC
131 TAATTTTTGAAATTTATTTAAAAAACAC
* * *
43021047 ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAACTAATAAAATTAGAAAATAA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAGAAAATAA
* * *
43021112 TATATTTTTATTGAAAGTAATAAAA-TCCGGG-AAAAAATACGAACAAAGAGCCTAAATAAGGGT
66 TATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
43021175 TAATTTTTGAAATTTATTTAAAAAACAC
131 TAATTTTTGAAATTTATTTAAAAAACAC
* *
43021203 ACTAAATTAATACATTTCAAACATAATATACTAAAATAATGTAAAATAATAAAATTAGAAAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAG-AAAATA
* *
43021268 ATATGTTATTATTTAAAGTAATAAAATT-CGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
65 ATATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
43021332 TT
130 TT
43021334 TTTTACTAAA
Statistics
Matches: 842, Mismatches: 49, Indels: 30
0.91 0.05 0.03
Matches are distributed among these distances:
152 5 0.01
153 51 0.06
154 240 0.29
155 57 0.07
156 333 0.40
157 100 0.12
158 44 0.05
159 7 0.01
160 5 0.01
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (158 bp):
ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAGAAAATAA
TATATTATTATTGAAAGTAATAAAATTCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
TAATTTTTGAAATTTATTTAAAAAACAC
Found at i:43021099 original size:465 final size:469
Alignment explanation
Indices: 43020272--43021337 Score: 1597
Period size: 465 Copynumber: 2.3 Consensus size: 469
43020262 AGGGTTTTTT
** * *
43020272 ACTAAATTAATGTATTTCAAACATAATGTACTAAAATAATGTTAAATAA-TAAAATACGAAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATTAAATTA-GAAAATA
* * *** * *
43020336 ACATATT-TT-TTGAAA-CAATGAGGCTTCGGTAAAAAAATACGAACAAATGGCCG-AA-AAGGG
65 ATATATTATTATTGAAAGTAAT-AAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG
* * * *
43020396 TTTTTTTTACTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAAA
129 TTATTTTTA-GAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATATACTAAA
*
43020461 ATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTAAAAGTAATAAAATTCGGGGAAA
193 ATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTAAAAGTAATAAAATTCCGGGAAA
43020526 AAAATACGAACAAAGGGCAGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAACACACTAAATT
258 AAAATACGAACAAAGGGCAGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAACACACTAAATT
* * *
43020591 AATACATTTAAAACATAATGTACTAAAAAATTTAAAATAATAAAATAATAAAATAATATATTATT
323 AATAAATTTAAAACATAATGTACTAAAAAATGTAAAATAATAAAATAAGAAAATAATATATTATT
*
43020656 ATTGAAAGTAATAAAATTCAGGG-AAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGA
388 ATTGAAAGTAATAAAA-TCAGGGAAAAAATACGAACAAAGAGCCGAAATAAGGGTTAATTTTTGA
43020720 AATTTATTT-AAAAACAC
452 AATTTATTTAAAAAACAC
* *
43020737 ACTAAATTAATACATTTCAAACATAATGTACT-AAA-AATATAAAATAATTAAATTAGAAAATTA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATTAAATTAGAAAATAA
*
43020800 TATATTATTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTT
66 TATATTATTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTT
*
43020865 AATTTTT-GAAATTTATTT-AAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAAT
131 -ATTTTTAGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATATACTAAAAT
* * *
43020928 AATGTAAACTAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATAAAA-TCCGGG-AAA
195 AATGTAAAATAATAAAA-TACAAAAATAATATATTTTTATTAAAAGTAATAAAATTCCGGGAAAA
*
43020990 AAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATT
259 AAATACGAACAAAGGGCAGAAATAAGGGTTAATTTTTGAAATTTATTT-AAAAACACACTAAATT
* * * *
43021055 AATAAATTTCAAACATAATGTACTAAAATAATGTAAACTAATAAAATTAGAAAATAATATATTTT
323 AATAAATTTAAAACATAATGTACTAAAA-AATGTAAAATAATAAAATAAGAAAATAATATATTAT
* *
43021120 TATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGAGCCTAAATAAGGGTTAATTTTTGA
387 TATTGAAAGTAATAAAATCAGGGAAAAAATACGAACAAAGAGCCGAAATAAGGGTTAATTTTTGA
43021185 AATTTATTTAAAAAACAC
452 AATTTATTTAAAAAACAC
* *
43021203 ACTAAATTAATACATTTCAAACATAATATACTAAAATAATGTAAAATAATAAAATTAGAAAAATA
1 ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATTAAATTAG-AAAATA
* *
43021268 ATATGTTATTATTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
65 ATATATTATTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGT
43021333 T-TTTT
130 TATTTT
43021338 ACTAAATTTG
Statistics
Matches: 545, Mismatches: 41, Indels: 28
0.89 0.07 0.05
Matches are distributed among these distances:
463 72 0.13
464 63 0.12
465 248 0.46
466 56 0.10
467 14 0.03
468 24 0.04
469 68 0.12
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (469 bp):
ACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATTAAATTAGAAAATAA
TATATTATTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTT
ATTTTTAGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATATACTAAAATA
ATGTAAAATAATAAAATACAAAAATAATATATTTTTATTAAAAGTAATAAAATTCCGGGAAAAAA
ATACGAACAAAGGGCAGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAACACACTAAATTAAT
AAATTTAAAACATAATGTACTAAAAAATGTAAAATAATAAAATAAGAAAATAATATATTATTATT
GAAAGTAATAAAATCAGGGAAAAAATACGAACAAAGAGCCGAAATAAGGGTTAATTTTTGAAATT
TATTTAAAAAACAC
Found at i:43026657 original size:23 final size:23
Alignment explanation
Indices: 43026612--43026658 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43026602 TAAAAATAAT
*
43026612 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
43026635 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
43026658 A
1 A
43026659 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:43026972 original size:3 final size:3
Alignment explanation
Indices: 43026966--43026999 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
43026956 CCAGCACCAC
*
43026966 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTC CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
43027000 AGTTGGGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:43028585 original size:13 final size:13
Alignment explanation
Indices: 43028559--43028591 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
43028549 ATATAAATTG
43028559 TATATTTTTATTA
1 TATATTTTTATTA
43028572 TATTATTTTT-TTA
1 TA-TATTTTTATTA
43028585 TATATTT
1 TATATTT
43028592 AATTTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 7 0.37
14 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATATTTTTATTA
Found at i:43030787 original size:43 final size:43
Alignment explanation
Indices: 43030720--43030990 Score: 276
Period size: 43 Copynumber: 6.3 Consensus size: 43
43030710 TTTTAGAAAT
43030720 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
* * * *
43030763 AAACACCGCTATAGATCATGACCTTTAGCGGCACTTTT-CCAC
1 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
* * **
43030805 AAACGTCGCTATAGACCATTACCTTTAGCAGCGCTTTTATCAC
1 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
* * *** ** *
43030848 AAACGCCGATAAAGACCATTA-CTTTAGCAATGCTTTTATCGC
1 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
43030890 TAACGCCACTAAAAACCATTACCTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
** * *
43030933 AAACGCCGCTATAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
* *
43030976 AATCGCCACTATAGA
1 AAACGCCGCTATAGA
43030991 ACAGATCTTT
Statistics
Matches: 184, Mismatches: 42, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
42 71 0.39
43 113 0.61
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCAC
Found at i:43030957 original size:85 final size:84
Alignment explanation
Indices: 43030720--43030986 Score: 237
Period size: 85 Copynumber: 3.1 Consensus size: 84
43030710 TTTTAGAAAT
* * * *
43030720 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCTTTTCCCACAAACACCGCTATAGATCATGAC
1 AAACGCCACTAAAAACCATTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGA-
**
43030785 CTTTAGCGGCACTTTTCCAC
65 CTTTAGCAACACTTTTCCAC
* * * * * ** * * * *
43030805 AAACGTCGCTATAGACCATTACCTTTAGCAGCGCTTTTATCACAAACGCCGATAAAGACCATTAC
1 AAACGCCACTAAAAACCATTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGAC
** * *
43030870 TTTAGCAATGCTTTTATCGC
66 TTTAGCAACACTTTT-CCAC
* * * *
43030890 TAACGCCACTAAAAACCATTACCTTTAGTGGCGCTTCTCCCACAAACGCCGCTATAGGTCATGAC
1 AAACGCCACTAAAAACCATTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGAC
** *
43030955 TTTTAGCGGCGCTTTTCCCAC
66 -TTTAGCAACACTTTT-CCAC
*
43030976 AATCGCCACTA
1 AAACGCCACTA
43030987 TAGAACAGAT
Statistics
Matches: 142, Mismatches: 38, Indels: 3
0.78 0.21 0.02
Matches are distributed among these distances:
84 12 0.08
85 107 0.75
86 23 0.16
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (84 bp):
AAACGCCACTAAAAACCATTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGAC
TTTAGCAACACTTTTCCAC
Found at i:43031066 original size:15 final size:15
Alignment explanation
Indices: 43031048--43031077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43031038 TCTTTTAAAA
*
43031048 AAATAATTTTTTTTC
1 AAATAAATTTTTTTC
43031063 AAATAAATTTTTTTC
1 AAATAAATTTTTTTC
43031078 TATGATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATAAATTTTTTTC
Found at i:43031354 original size:43 final size:43
Alignment explanation
Indices: 43031306--43031396 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
43031296 ACATATGCAA
** * * *
43031306 GGTAATAAATTATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
43031349 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
43031392 -GTAAT
1 GGTAAT
43031397 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 5 0.12
43 37 0.88
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:43036204 original size:14 final size:14
Alignment explanation
Indices: 43036185--43036212 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43036175 TACACATTAT
43036185 TAATATTATTTAAA
1 TAATATTATTTAAA
43036199 TAATATTATTTAAA
1 TAATATTATTTAAA
43036213 ATTTTGATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:43036695 original size:7 final size:7
Alignment explanation
Indices: 43036685--43036715 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
43036675 CCATAACTAT
43036685 TAACCCC
1 TAACCCC
43036692 TAACCCC
1 TAACCCC
*
43036699 TAACTCC
1 TAACCCC
43036706 TAACCCC
1 TAACCCC
43036713 TAA
1 TAA
43036716 ACCTTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (7 bp):
TAACCCC
Found at i:43036731 original size:21 final size:21
Alignment explanation
Indices: 43036686--43036739 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
43036676 CATAACTATT
* * *
43036686 AACCCCTAACCCCTAACTCCT
1 AACCCCTAAACCCTAAATCCC
*
43036707 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCCTAAATCCC
*
43036728 AACCCTTAAACC
1 AACCCCTAAACC
43036740 ATGATCCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCCTAAACCCTAAATCCC
Found at i:43036767 original size:15 final size:15
Alignment explanation
Indices: 43036734--43036771 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
43036724 TCCCAACCCT
*
43036734 TAAA-CCATGATCCC
1 TAAATCCATAATCCC
43036748 T-AATCCATAATCCC
1 TAAATCCATAATCCC
43036762 TAAATCCATA
1 TAAATCCATA
43036772 TGCAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:43037041 original size:7 final size:7
Alignment explanation
Indices: 43037031--43037125 Score: 50
Period size: 7 Copynumber: 13.4 Consensus size: 7
43037021 TCTAAACCCC
43037031 AAACCAT
1 AAACCAT
*
43037038 AAACCCT
1 AAACCAT
*
43037045 TAACACAT
1 AAAC-CAT
*
43037053 -AACCTCT
1 AAACC-AT
*
43037060 AAACCTT
1 AAACCAT
43037067 AAACC-T
1 AAACCAT
* **
43037073 CAACTTT
1 AAACCAT
43037080 AAACCAT
1 AAACCAT
43037087 AAACCAT
1 AAACCAT
* *
43037094 AACCCCT
1 AAACCAT
43037101 AAACCCAT
1 AAA-CCAT
*
43037109 AATCCAT
1 AAACCAT
*
43037116 AAACCTT
1 AAACCAT
43037123 AAA
1 AAA
43037126 ATGGTAACAA
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
6 5 0.08
7 50 0.76
8 11 0.17
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCAT
Found at i:43037110 original size:15 final size:15
Alignment explanation
Indices: 43037083--43037120 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43037073 CAACTTTAAA
43037083 CCATAAA-CCATAAC
1 CCATAAACCCATAAC
* *
43037097 CCCTAAACCCATAAT
1 CCATAAACCCATAAC
43037112 CCATAAACC
1 CCATAAACC
43037121 TTAAAATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (15 bp):
CCATAAACCCATAAC
Found at i:43037440 original size:41 final size:41
Alignment explanation
Indices: 43037395--43037678 Score: 320
Period size: 41 Copynumber: 7.0 Consensus size: 41
43037385 AAAATAGAGA
* * *
43037395 ATTAGCAGCGCTTAATCAAAAACGCCGCTAAAGCCCTGATC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
* * * * *
43037436 ATTAGCTGTGCTTTCTCAAAAACGCCGCTAAATCACTGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
* *
43037477 ATTAGCGGCGCTTTATTAAAAACGCCGCTAAAACCCTGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
* ** * * *
43037518 ATCAGCGGCGCTTTCCCAAAAACGTCGCTAAATCACTGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
*
43037559 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAATCCCTGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
* ** * *
43037600 --TAGCGGCACTTCCTCAAAAACACCGCTAAAGGCCTGAGC
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
* * *
43037639 ATTAGCGGCACTTTATCAAAAACACCGTTAAAGCCTCTGA
1 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCC-CTGA
43037679 AAACTCAGAA
Statistics
Matches: 205, Mismatches: 35, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
39 33 0.16
41 168 0.82
42 4 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGC
Found at i:43037488 original size:82 final size:82
Alignment explanation
Indices: 43037370--43037678 Score: 367
Period size: 82 Copynumber: 3.8 Consensus size: 82
43037360 AATCCCTGAG
* * * *
43037370 CAAAAAGCGCCGCTAAA--AATAGAGAATTAGCAGCGCTTAATCAAAAACGCCGCTAAAGCCCTG
1 CAAAAA-CGCCGCTAAATCACT-GAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTG
* * *
43037433 ATCATTAGCTGTGCTTTCT
64 AGCATTAGCGGCGCTTTCT
* *
43037452 CAAAAACGCCGCTAAATCACTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAAACCCTGAG
1 CAAAAACGCCGCTAAATCACTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAG
* *
43037517 CATCAGCGGCGCTTTCC
66 CATTAGCGGCGCTTTCT
* *
43037534 CAAAAACGTCGCTAAATCACTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAATCCCTGAG
1 CAAAAACGCCGCTAAATCACTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAG
* *
43037599 C--TAGCGGCACTTCCT
66 CATTAGCGGCGCTTTCT
* * * * *
43037614 CAAAAACACCGCTAAAGGC-CTGAGCATTAGCGGCACTTTATCAAAAACACCGTTAAAGCCTCTG
1 CAAAAACGCCGCTAAA-TCACTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCC-CTG
43037678 A
64 A
43037679 AAACTCAGAA
Statistics
Matches: 198, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
80 61 0.31
81 15 0.08
82 120 0.61
83 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.20
Consensus pattern (82 bp):
CAAAAACGCCGCTAAATCACTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAG
CATTAGCGGCGCTTTCT
Found at i:43042554 original size:32 final size:32
Alignment explanation
Indices: 43042518--43042580 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
43042508 TCATAAACTT
*
43042518 ATAAATTAATTACTTAAATTTAATAACTCATG
1 ATAAATTAATTAATTAAATTTAATAACTCATG
* *
43042550 ATAAATTAATTAATTTAATTTTATAACTCAT
1 ATAAATTAATTAATTAAATTTAATAACTCAT
43042581 ATTGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (32 bp):
ATAAATTAATTAATTAAATTTAATAACTCATG
Found at i:43050148 original size:32 final size:32
Alignment explanation
Indices: 43050112--43050174 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
43050102 CCATAAACTT
*
43050112 ATAAATTAATTACTTGAATTTAATAACTCATG
1 ATAAATTAATTAATTGAATTTAATAACTCATG
* * *
43050144 ATAAATTAATTAATTTAATTTTATAATTCAT
1 ATAAATTAATTAATTGAATTTAATAACTCAT
43050175 ATTGGTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCATG
Found at i:43055281 original size:114 final size:114
Alignment explanation
Indices: 43054863--43055421 Score: 419
Period size: 114 Copynumber: 4.9 Consensus size: 114
43054853 TTTACCACAC
* * * * *
43054863 AGCGCCGCAAAATCTC-AAGACCAACACGCAGCA-TTCTGGTGTTGATGTATATTGGC-ATTAGT
1 AGCGCCGCAAAATATCTTA-ACCAAAACGCAG-AGTT-TGGTCTTGATGTATATT-ACAATTAGT
* * * * * *
43054925 GGCGCTTACGAACAAACGCCGGTAATGTATAG-TATTAGCGGCGCTTAGTG-GA
62 GGCGCTTATGAA-AAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTGGTGTTA
* * *
43054977 A--GCCGCAAAAGATGTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTTCAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTACAATTAGTGGCG
* * ** **
43055040 CTTATAAAGAAAACGCCGCTAATGTATAG-TATTAGCGGCG-CAGAGCCTTA
66 CTTAT-GA-AAAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTG-GTGTTA
* * * * * * * *
43055090 AACGCCGCAAGACATCTTAATCAAAATGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGT-TTGGTCTTGATGTATATTACAATTAGTGGC
* * * * *
43055155 GTTTAAGGAAAACGCCAG-TAAAGGATAGTTA-TAGCAGCGTTTGGTGTTA
65 GCTTATGAAAAACGCC-GCTAAAGTATAGTTATTAGCGGCGTTTGGTGTTA
* * * *
43055204 AGCGCCTCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTGTATTAGAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTACAATTAGTGGCG
* *
43055269 CTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCGTTT-GTG-GA
66 CTT-ATGAAAAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTGGTGTTA
* * ** * * **
43055316 ACGCGCCGCAAAGTATCTTAACCAAAACACATCGTTTAGTTCTTGATGTATACTGGAATTAGTGG
1 A-GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGATGTATATTACAATTAGTGG
** * * *
43055381 CGCAAATGGGAAAACGCCGCTGAAGCATAG-TATTAGCGGCG
64 CGCTTAT-GAAAAACGCCGCTAAAGTATAGTTATTAGCGGCG
43055422 CTTTTACCGA
Statistics
Matches: 355, Mismatches: 70, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
110 1 0.00
111 31 0.09
112 56 0.16
113 71 0.20
114 136 0.38
115 29 0.08
116 31 0.09
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (114 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTACAATTAGTGGCG
CTTATGAAAAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTGGTGTTA
Found at i:43055548 original size:18 final size:18
Alignment explanation
Indices: 43055527--43055562 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
43055517 TCATTTTATA
43055527 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
43055545 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
43055563 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Done.