Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 131 of 433
Found at i:40410828 original size:19 final size:19
Alignment explanation
Indices: 40410806--40410842 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40410796 CATAATTTAT
* *
40410806 TAATTTTTATAATTTTTTG
1 TAATATTTACAATTTTTTG
40410825 TAATATTTACAATTTTTT
1 TAATATTTACAATTTTTT
40410843 TCTTTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TAATATTTACAATTTTTTG
Found at i:40410917 original size:21 final size:20
Alignment explanation
Indices: 40410883--40410923 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40410873 TTTATTTTTT
*
40410883 TATTTTTAACATTTTTATGA
1 TATTTTTAACATTTCTATGA
*
40410903 TATTTTTAATGATTTCTATGA
1 TATTTTTAA-CATTTCTATGA
40410924 GAAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TATTTTTAACATTTCTATGA
Found at i:40411442 original size:7 final size:7
Alignment explanation
Indices: 40411430--40411468 Score: 55
Period size: 6 Copynumber: 5.7 Consensus size: 7
40411420 CTACCTTTGC
40411430 TTTTTCT
1 TTTTTCT
40411437 TTTTTCT
1 TTTTTCT
40411444 TTCTTTCT
1 TT-TTTCT
40411452 TTTTT-T
1 TTTTTCT
40411458 TTTTT-T
1 TTTTTCT
40411464 TTTTT
1 TTTTT
40411469 TTGAGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTCT
Found at i:40411452 original size:15 final size:13
Alignment explanation
Indices: 40411430--40411470 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 13
40411420 CTACCTTTGC
40411430 TTTTTCTTTTTTCT
1 TTTTTCTTTTTT-T
40411444 TTCTTTCTTTTTTT
1 TT-TTTCTTTTTTT
40411458 TTTTT-TTTTTTT
1 TTTTTCTTTTTTT
40411470 T
1 T
40411471 GAGTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.31
13 3 0.12
14 5 0.19
15 10 0.38
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:40415961 original size:14 final size:14
Alignment explanation
Indices: 40415942--40415976 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40415932 AAATGGTTTT
*
40415942 TGCAAATGGATGTA
1 TGCAAATGGATGAA
*
40415956 TGCAAATGTATGAA
1 TGCAAATGGATGAA
40415970 TGCAAAT
1 TGCAAAT
40415977 ACACTAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (14 bp):
TGCAAATGGATGAA
Found at i:40418491 original size:20 final size:20
Alignment explanation
Indices: 40418466--40418506 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40418456 GTGACCACAC
40418466 TCCCTACCCACACGGGCGTG
1 TCCCTACCCACACGGGCGTG
* *
40418486 TCCCTATCCACACGGGTGTG
1 TCCCTACCCACACGGGCGTG
40418506 T
1 T
40418507 AGCCCTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (20 bp):
TCCCTACCCACACGGGCGTG
Found at i:40426883 original size:60 final size:59
Alignment explanation
Indices: 40426750--40426942 Score: 203
Period size: 59 Copynumber: 3.3 Consensus size: 59
40426740 GGCCATCAGT
* * * ****
40426750 CACGGTCGTGTGTCCCGTAACACACGCCCGTGTGGAATCCCTAGGCCCCAAATCAGTCA
1 CACGGCCGTGTGTCCCATAACACACGCCCGTGTGGAAGCCCTAATTGCCAAATCAGTCA
* * * * *
40426809 CACGGCCGTCTGTCCCGA-AGCACATGCCCGTGTGGGAA-CCCTAATTTTCCAAATCAGTTA
1 CACGGCCGTGTGTCCC-ATAACACACGCCCGTGT-GGAAGCCCTAA-TTGCCAAATCAGTCA
* *
40426869 CACGGCCTTGTGTCCCATAACACACGCCCGTGTGGAAGCCTTAATTGCCGAAA-CAGTCA
1 CACGGCCGTGTGTCCCATAACACACGCCCGTGTGGAAGCCCTAATTGCC-AAATCAGTCA
40426928 CACGGCCGTGTGTCC
1 CACGGCCGTGTGTCC
40426943 AATGGACATG
Statistics
Matches: 110, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
59 60 0.55
60 50 0.45
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (59 bp):
CACGGCCGTGTGTCCCATAACACACGCCCGTGTGGAAGCCCTAATTGCCAAATCAGTCA
Found at i:40429893 original size:34 final size:34
Alignment explanation
Indices: 40429854--40429928 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
40429844 CAACATTCAA
40429854 GCATACAAAACCTTACTAG-GACAACTATCAACAT
1 GCATACAAAACCTTACTAGTG-CAACTATCAACAT
40429888 GCATACAAAACCTTACTAGTGCAACTATCAACAT
1 GCATACAAAACCTTACTAGTGCAACTATCAACAT
40429922 GCATACA
1 GCATACA
40429929 CAAATAATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 39 0.98
35 1 0.03
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (34 bp):
GCATACAAAACCTTACTAGTGCAACTATCAACAT
Found at i:40434149 original size:2 final size:2
Alignment explanation
Indices: 40434142--40434177 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40434132 ATAATTGAAC
40434142 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
40434178 GATAAGGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40442160 original size:12 final size:12
Alignment explanation
Indices: 40442145--40442169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40442135 AAATAAAAAC
40442145 TAAAATCATAAA
1 TAAAATCATAAA
40442157 TAAAATCATAAA
1 TAAAATCATAAA
40442169 T
1 T
40442170 TGCTAAATTT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAATCATAAA
Found at i:40447679 original size:41 final size:41
Alignment explanation
Indices: 40447622--40447703 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
40447612 TGTTACTGAT
* ** *
40447622 TAATGTATATCTGATACTGTTACT-ATAATGGGCTTAGGCCC
1 TAATGCATATCTGATACTGAAACTGA-AATGGGCTCAGGCCC
40447663 TAATGCATATCTGATACTGAAACTGAAATGGGCTCAGGCCC
1 TAATGCATATCTGATACTGAAACTGAAATGGGCTCAGGCCC
40447704 GAACTTTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (41 bp):
TAATGCATATCTGATACTGAAACTGAAATGGGCTCAGGCCC
Found at i:40450845 original size:48 final size:49
Alignment explanation
Indices: 40450774--40451104 Score: 304
Period size: 48 Copynumber: 6.9 Consensus size: 49
40450764 GTAAATTGTT
* *
40450774 GATGCCATGTCCCAAACATGGTCTTACACTGGCT-TACATGTCAAGGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACATATCAATGCC
* * * * * *
40450822 GATGCTATGTCCCAGACATGGTCTTACACTAGCTCT-CGTCTCAATACC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACATATCAATGCC
**
40450870 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCT-CATAATGTA-GCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACAT-ATCAATGCC
* * ** * * * * *
40450918 AATACCATGTCCCAGGCATCGTGTTACACTAGCAC-ACATATCAATGCT
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACATATCAATGCC
* * *
40450966 GATGCTATGTCCCAAACATGGTCTCACACTGGCTCTCACA-A-CATTGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCT-ACATATCAATGCC
* *
40451014 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCT-CATATC-ATGACC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACATATCAATG-CC
* * * * *
40451062 GACGCCATGTCCCAGACATAGTCTTACACTAGCGC-ACATATCA
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACATATCA
40451105 CCCAAATGTC
Statistics
Matches: 222, Mismatches: 50, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
46 2 0.01
47 6 0.03
48 207 0.93
49 4 0.02
50 3 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (49 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTACATATCAATGCC
Found at i:40451038 original size:144 final size:143
Alignment explanation
Indices: 40450778--40451104 Score: 388
Period size: 144 Copynumber: 2.3 Consensus size: 143
40450768 ATTGTTGATG
* * * ** * * * *
40450778 CCATGTCCCAAACATGGTCTTACACTGGCTTACATGTCAAGGCCGATGCTATGTCCCAGACATGG
1 CCATGTCCCAGACATAGTCTTACACTAGCACACATATCAATGCTGATGCTATGTCCCAAACATGG
* * *
40450843 TCTTACACTAGCTCTCGTCTCAATACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA
66 TCTCACACTAGCTCTCGACACAATACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA
*
40450908 TA-ATGTAGCCAATA
131 TACATG-A-CCAACA
* * *
40450922 CCATGTCCCAGGCATCGTGTTACACTAGCACACATATCAATGCTGATGCTATGTCCCAAACATGG
1 CCATGTCCCAGACATAGTCTTACACTAGCACACATATCAATGCTGATGCTATGTCCCAAACATGG
* * * * *
40450987 TCTCACACTGGCTCTC-ACAACATTGCCGATGCCATGTTCCAAACATGGTCTTACATTGGCTCTC
66 TCTCACACTAGCTCTCGAC-ACAATACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTC
* *
40451051 ATATCATGACCGACG
130 ATA-CATGACCAACA
*
40451066 CCATGTCCCAGACATAGTCTTACACTAGCGCACATATCA
1 CCATGTCCCAGACATAGTCTTACACTAGCACACATATCA
40451105 CCCAAATGTC
Statistics
Matches: 154, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
143 1 0.01
144 149 0.97
145 1 0.01
146 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (143 bp):
CCATGTCCCAGACATAGTCTTACACTAGCACACATATCAATGCTGATGCTATGTCCCAAACATGG
TCTCACACTAGCTCTCGACACAATACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA
TACATGACCAACA
Found at i:40458234 original size:48 final size:47
Alignment explanation
Indices: 40458074--40458390 Score: 264
Period size: 48 Copynumber: 6.6 Consensus size: 47
40458064 GTAAATTACT
* * * *
40458074 GATGCCATGTCCCAGACATGGTCTTACACAGGCTCACATGTCGAAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC-ATGCC
* * * * * *
40458122 GGTGCCATATCTCAGACATGGTCTTACACTAG-TCTCGTCA-CAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATC-ATGCC
* *
40458169 GATGCCATGTCCTAGACATGATCTTACACTGGCTCTCATAAT-ATGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCAT-GCC
* * * * **
40458217 GATGCCATGTCCCAGACATGGTCCTACACTAGCACACATATCAATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC-ATGCC
* *
40458265 GATGCCATGTCCCAGATATAGTCTTACACTGGCTCTCATCA-CATTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCA-TGCC
* * * * * *
40458313 GATGCCATGTTCGAAACATGGTCTTACATTAGCTCTCATATCGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAT-GCC
* * *
40458361 GACGTCATGTCCCAGGCATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
40458391 AGCGCACATA
Statistics
Matches: 208, Mismatches: 51, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
47 41 0.20
48 164 0.79
49 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGCC
Found at i:40458297 original size:96 final size:94
Alignment explanation
Indices: 40458073--40458354 Score: 291
Period size: 96 Copynumber: 2.9 Consensus size: 94
40458063 GGTAAATTAC
* * * * * *
40458073 TGATGCCATGTCCCAGACATGGTCTTACACAGGCTCACATGTCGA-AGCCGGTGCCATATCTCAG
1 TGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAT--ATAGCCGATGCCATGTCCCAG
*
40458137 ACATGGTCTTACACTAG-TCTCGTCA-CAATGT
63 ACATGGTCTTACACTAGCTCTCAT-ATCAATGT
* * *
40458168 CGATGCCATGTCCTAGACATGATCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCCAGA
1 TGATGCCATGTCCCAGACATG-TCTTACACTGGCTCTCAT-ATATAGCCGATGCCATGTCCCAGA
* * *
40458233 CATGGTCCTACACTAGCACACATATCAATGT
64 CATGGTCTTACACTAGCTCTCATATCAATGT
* * * * * *
40458264 TGATGCCATGTCCCAGATATAGTCTTACACTGGCTCTCATCACATTGCCGATGCCATGTTCGAAA
1 TGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-ATATAGCCGATGCCATGTCCCAGA
*
40458329 CATGGTCTTACATTAGCTCTCATATC
64 CATGGTCTTACACTAGCTCTCATATC
40458355 GTGGCCGACG
Statistics
Matches: 155, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
94 2 0.01
95 66 0.43
96 86 0.55
97 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (94 bp):
TGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATATATAGCCGATGCCATGTCCCAGACA
TGGTCTTACACTAGCTCTCATATCAATGT
Found at i:40458370 original size:144 final size:142
Alignment explanation
Indices: 40458077--40458403 Score: 370
Period size: 144 Copynumber: 2.3 Consensus size: 142
40458067 AATTACTGAT
* * * *
40458077 GCCATGTCCCAGACATGGTCTTACAC-AGGCTCACATGTCGAAGCCGGTGCCATATCTCAGACAT
1 GCCATGTCCCAGACATGGTCTTACACTA-GCACACATATC-AAGCCGATGCCATATCCCAGACAT
* * * * * *
40458141 GGTCTTACACTAGTCTCGTCACAATGTCGATGCCATGTCCTAGACATGATCTTACACTGGCTCTC
64 AGTCTTACACTAGTCTCATCACAATGCCGATGCCATGTCCGAAACATGATCTTACACTAGCTCTC
*
40458206 ATAATATGGCCGAT
129 ATAATATGGCCGAC
* ** * *
40458220 GCCATGTCCCAGACATGGTCCTACACTAGCACACATATCAATGTTGATGCCATGTCCCAGATATA
1 GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAA-GCCGATGCCATATCCCAGACATA
* * * * *
40458285 GTCTTACACTGGCTCTCATCACATTGCCGATGCCATGTTCGAAACATGGTCTTACATTAGCTCTC
65 GTCTTACACTAG-TCTCATCACAATGCCGATGCCATGTCCGAAACATGATCTTACACTAGCTCTC
*
40458350 AT-ATCGTGGCCGAC
129 ATAAT-ATGGCCGAC
* * *
40458364 GTCATGTCCCAGGCATGGTCTTACACTAGCGCACATATCA
1 GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA
40458404 CCCAAATGTC
Statistics
Matches: 154, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
142 2 0.01
143 63 0.41
144 89 0.58
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (142 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAGCCGATGCCATATCCCAGACATAG
TCTTACACTAGTCTCATCACAATGCCGATGCCATGTCCGAAACATGATCTTACACTAGCTCTCAT
AATATGGCCGAC
Found at i:40462720 original size:17 final size:17
Alignment explanation
Indices: 40462700--40462734 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40462690 AAAATACATG
*
40462700 TTTTTATAATTTATAAT
1 TTTTTATAATTTAAAAT
*
40462717 TTTTTATATTTTAAAAT
1 TTTTTATAATTTAAAAT
40462734 T
1 T
40462735 ATATATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTATAATTTAAAAT
Found at i:40463660 original size:17 final size:17
Alignment explanation
Indices: 40463640--40463672 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40463630 TTATTTTATT
40463640 ATTATATTA-AATTTAAA
1 ATTA-ATTATAATTTAAA
40463657 ATTAATTATAATTTAA
1 ATTAATTATAATTTAA
40463673 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAATTATAATTTAAA
Found at i:40463676 original size:22 final size:21
Alignment explanation
Indices: 40463640--40463682 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
40463630 TTATTTTATT
40463640 ATTATATTAAATTTAAAATTA
1 ATTATATTAAATTTAAAATTA
*
40463661 ATTATAATTTAATTTAAAATTA
1 ATTAT-ATTAAATTTAAAATTA
40463683 TTAGTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATATTAAATTTAAAATTA
Found at i:40465128 original size:40 final size:40
Alignment explanation
Indices: 40465073--40465205 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
40465063 CTAGTTTGGT
40465073 ACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGAC
1 ACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGAC
* *
40465113 ACCCAGTGTCTCATCGG-----TCAAACCGAAGTAAATTGAC
1 ACCCAGTGCCTCATCGGATAATTCAAA--GTAGTAAATTGAC
* * * *
40465150 A-CCAGTGCCTCATCGAATAAATCCGAAGTAATAAATTGAC
1 ACCCAGTGCCTCATCGGAT-AATTCAAAGTAGTAAATTGAC
* *
40465190 ACCAAGTGTCTCATCG
1 ACCCAGTGCCTCATCG
40465206 ACTCGAAGTC
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
35 5 0.07
36 13 0.18
37 13 0.18
40 28 0.38
41 12 0.16
42 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (40 bp):
ACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGAC
Found at i:40465152 original size:37 final size:38
Alignment explanation
Indices: 40465102--40465206 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 38
40465092 AATTCAAAGT
*
40465102 AGTAAATTGACACCCAGTGTCTCATCG-GTCAAA-CCGA
1 AGTAAATTGACACCCAGTGTCTCATCGAAT-AAATCCGA
*
40465139 AGTAAATTGACA-CCAGTGCCTCATCGAATAAATCCGA
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAATCCGA
*
40465176 AGTAATAAATTGACACCAAGTGTCTCATCGA
1 AG---TAAATTGACACCCAGTGTCTCATCGA
40465207 CTCGAAGTCG
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
36 16 0.28
37 19 0.33
40 10 0.17
41 13 0.22
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (38 bp):
AGTAAATTGACACCCAGTGTCTCATCGAATAAATCCGA
Found at i:40465385 original size:2 final size:2
Alignment explanation
Indices: 40465378--40465409 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40465368 TACATTCAGA
40465378 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
40465410 CAATTCAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40466112 original size:4 final size:4
Alignment explanation
Indices: 40466103--40466130 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40466093 TGTCTTTCTC
40466103 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
40466131 TTATTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:40466198 original size:20 final size:20
Alignment explanation
Indices: 40466175--40466234 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
40466165 ATATAATATA
40466175 TATACTTAATAATTGAGATT
1 TATACTTAATAATTGAGATT
* * *
40466195 TATA--TAAT-A-TAATATA
1 TATACTTAATAATTGAGATT
40466211 TATACTTAATAATTGAGATT
1 TATACTTAATAATTGAGATT
40466231 TATA
1 TATA
40466235 TATATTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 8 0.27
17 1 0.03
18 8 0.27
19 1 0.03
20 12 0.40
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (20 bp):
TATACTTAATAATTGAGATT
Found at i:40466205 original size:36 final size:36
Alignment explanation
Indices: 40466165--40466236 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
40466155 TTATTATAAT
40466165 ATATAATATATATACTTAATAATTGAGATTTATATA
1 ATATAATATATATACTTAATAATTGAGATTTATATA
40466201 ATATAATATATATACTTAATAATTGAGATTTATATA
1 ATATAATATATATACTTAATAATTGAGATTTATATA
40466237 TATTTTAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATAATATATATACTTAATAATTGAGATTTATATA
Found at i:40466237 original size:38 final size:37
Alignment explanation
Indices: 40466157--40466238 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 37
40466147 TCATTTACTT
40466157 ATTATA-AT-ATATAATATATATACTTAATAATTGAG
1 ATTATATATAATATAATATATATACTTAATAATTGAG
40466192 ATT-TATATAATATAATATATATACTTAATAATTGAG
1 ATTATATATAATATAATATATATACTTAATAATTGAG
40466228 ATTTATATATA
1 A-TTATATATA
40466239 TTTTAACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
34 2 0.05
35 5 0.12
36 28 0.65
37 2 0.05
38 6 0.14
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (37 bp):
ATTATATATAATATAATATATATACTTAATAATTGAG
Found at i:40468437 original size:19 final size:20
Alignment explanation
Indices: 40468413--40468462 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
40468403 ATTCGGGACT
* *
40468413 AATTTGAAACAAA-TCAGAA
1 AATTTGAAAAAAAGTCACAA
*
40468432 AATTTGAGAAAAAAGTTACAA
1 AATTTGA-AAAAAAGTCACAA
40468453 AATTTGAAAA
1 AATTTGAAAA
40468463 CAGAGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 11 0.42
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (20 bp):
AATTTGAAAAAAAGTCACAA
Found at i:40471335 original size:29 final size:29
Alignment explanation
Indices: 40471293--40471352 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
40471283 TTAAGTAAGG
*
40471293 TTTTAAGTCATTCAATTTCGGATGGATTC
1 TTTTAAGCCATTCAATTTCGGATGGATTC
40471322 TTTTAAGCCATTCAATTTCGGATGGATTC
1 TTTTAAGCCATTCAATTTCGGATGGATTC
40471351 TT
1 TT
40471353 AGTCGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (29 bp):
TTTTAAGCCATTCAATTTCGGATGGATTC
Found at i:40472972 original size:27 final size:26
Alignment explanation
Indices: 40472928--40472978 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
40472918 TCCCAAAAAG
* *
40472928 TAAATAAAAAGAATGGAAATAATGTC
1 TAAATAAAAAGAAAGGAAAAAATGTC
*
40472954 TAAATATAAGAGAAAGGAAAAAATG
1 TAAATA-AAAAGAAAGGAAAAAATG
40472979 AAGACAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.61, C:0.02, G:0.18, T:0.20
Consensus pattern (26 bp):
TAAATAAAAAGAAAGGAAAAAATGTC
Found at i:40476205 original size:2 final size:2
Alignment explanation
Indices: 40476198--40476232 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40476188 ATTTATTCAT
40476198 TA 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 T
40476233 CTTTTCCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40476275 original size:3 final size:3
Alignment explanation
Indices: 40476260--40476315 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
40476250 AAAAGCTTAG
*
40476260 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40476308 ATT ATT AT
1 ATT ATT AT
40476316 CCTTTTAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:40476385 original size:8 final size:7
Alignment explanation
Indices: 40476373--40476420 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
40476363 TATTTTAAAC
40476373 TTTTATT
1 TTTTATT
40476380 TGTTTATT
1 T-TTTATT
40476388 TATTTACTT
1 T-TTTA-TT
*
40476397 TTTTAGT
1 TTTTATT
40476404 TTTTATT
1 TTTTATT
*
40476411 TATTATT
1 TTTTATT
40476418 TTT
1 TTT
40476421 CTTTTTACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 16 0.47
8 15 0.44
9 3 0.09
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (7 bp):
TTTTATT
Found at i:40481838 original size:48 final size:48
Alignment explanation
Indices: 40481785--40481920 Score: 191
Period size: 48 Copynumber: 2.8 Consensus size: 48
40481775 TATGGTAGGG
* ** * *
40481785 TGCCAATGCCATATCCTGGATATGGTCTTACATGGGATCACATATCGA
1 TGCCAATGCCATGTCCCAGAAATGGTCTTACATGAGATCACATATCGA
*
40481833 TGCCAATGCCATGTCCCAGAAAAGGTCTTACATGAGATCACATATCGA
1 TGCCAATGCCATGTCCCAGAAATGGTCTTACATGAGATCACATATCGA
* * *
40481881 TGCTAATGCCATGTCCCAGACATGGTCATACATGAGATCA
1 TGCCAATGCCATGTCCCAGAAATGGTCTTACATGAGATCA
40481921 TAAATAACCC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGAAATGGTCTTACATGAGATCACATATCGA
Found at i:40485127 original size:40 final size:40
Alignment explanation
Indices: 40485053--40485234 Score: 296
Period size: 40 Copynumber: 4.6 Consensus size: 40
40485043 AACCCAAGTA
* *
40485053 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
40485092 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40485132 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
40485172 CCTTCGGGACTTAGCCTGGATATAGTCATTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40485212 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
40485235 CATTCGAATA
Statistics
Matches: 134, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 12 0.09
40 121 0.90
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40493276 original size:40 final size:40
Alignment explanation
Indices: 40493198--40493339 Score: 198
Period size: 40 Copynumber: 3.6 Consensus size: 40
40493188 AACCCAAGTA
* * * *
40493198 CCTTCGGGATTTAG-CCGGATATAG-CAATTCGCAAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
40493237 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40493277 CCTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40493317 CCTTCAGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
40493340 CATTCGAATA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 12 0.13
40 79 0.86
41 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40493860 original size:2 final size:2
Alignment explanation
Indices: 40493853--40493881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40493843 CACCATACGC
40493853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40493882 CTCTAGTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40500413 original size:31 final size:31
Alignment explanation
Indices: 40500372--40500435 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
40500362 CCTTTTCATA
*
40500372 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
** *
40500403 TTTCAAATTTCATATTACTGGGCCGAAGTCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40500434 TT
1 TT
40500436 ACGGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40500732 original size:24 final size:24
Alignment explanation
Indices: 40500629--40500817 Score: 278
Period size: 24 Copynumber: 8.0 Consensus size: 24
40500619 GCTTTATCAT
*
40500629 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
40500654 ATAACTGGGGCAAAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
40500677 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40500700 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40500724 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40500748 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
40500772 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40500795 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40500818 TCACTTCCTC
Statistics
Matches: 153, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
22 3 0.02
23 58 0.38
24 80 0.52
25 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40500763 original size:71 final size:71
Alignment explanation
Indices: 40500629--40500817 Score: 285
Period size: 71 Copynumber: 2.7 Consensus size: 71
40500619 GCTTTATCAT
* *
40500629 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTATAACTGGGGCATAAG
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAG
40500693 CCC-TTTA
64 CCCTTTTA
* *
40500700 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGC
*
40500765 CCTTTTG
65 CCTTTTA
40500772 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
40500818 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
70 31 0.28
71 57 0.52
72 21 0.19
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCC
CTTTTA
Found at i:40500817 original size:47 final size:47
Alignment explanation
Indices: 40500650--40500817 Score: 293
Period size: 47 Copynumber: 3.6 Consensus size: 47
40500640 CCTAGCCTCT
*
40500650 TTTAATAACTGGGGCAAAAGCCCTTTT-ATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
*
40500696 TTTAATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
*
40500743 TTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
40500791 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
40500818 TCACTTCCTC
Statistics
Matches: 115, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
46 25 0.22
47 45 0.39
48 45 0.39
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
Found at i:40500889 original size:9 final size:9
Alignment explanation
Indices: 40500875--40500951 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
40500865 ATCTCGTGTG
40500875 CATATCATA
1 CATATCATA
*
40500884 CATATCATGTG
1 CATATCA--TA
40500895 CATATCATA
1 CATATCATA
* *
40500904 CATGTCATGTG
1 CATATCA--TA
*
40500915 TATATCATA
1 CATATCATA
*
40500924 CATATCATGTG
1 CATATCA--TA
40500935 CATATCATA
1 CATATCATA
40500944 CATATCAT
1 CATATCAT
40500952 GTTTATCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 30 0.58
11 22 0.42
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (9 bp):
CATATCATA
Found at i:40500894 original size:20 final size:20
Alignment explanation
Indices: 40500871--40500953 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
40500861 GAACATCTCG
40500871 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
40500891 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
40500911 TGTGTATATCATACATATCA
1 TGTGCATATCATACATATCA
40500931 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
40500951 TGT
1 TGT
40500954 TTATCAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:40500900 original size:11 final size:11
Alignment explanation
Indices: 40500871--40500942 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
40500861 GAACATCTCG
40500871 TGTGCATATCA
1 TGTGCATATCA
*
40500882 --TACATATCA
1 TGTGCATATCA
40500891 TGTGCATATCA
1 TGTGCATATCA
* *
40500902 --TACATGTCA
1 TGTGCATATCA
*
40500911 TGTGTATATCA
1 TGTGCATATCA
*
40500922 --TACATATCA
1 TGTGCATATCA
40500931 TGTGCATATCA
1 TGTGCATATCA
40500942 T
1 T
40500943 ACATATCATG
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
9 22 0.49
11 23 0.51
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:40502301 original size:27 final size:27
Alignment explanation
Indices: 40502271--40502635 Score: 438
Period size: 27 Copynumber: 13.6 Consensus size: 27
40502261 AGGGTATTTT
* *
40502271 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
40502298 AGTAATTCTATAAATC-AAGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
40502324 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
40502351 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
40502378 GGTAATTCTATAAATCGAGGGTAAAA-
1 AGTAATTCTATAAATCGAGGGTAAAAC
* * *
40502404 TGATAATTATGTAAATCG-GGGTAAAAC
1 AG-TAATTCTATAAATCGAGGGTAAAAC
* * * *
40502431 GGTAATTATGTAAATTG-GGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
40502457 -GATAATTCTATAAATCGAGGGTAAAAC
1 AG-TAATTCTATAAATCGAGGGTAAAAC
* * *
40502484 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
40502511 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTATAAATC-GAGGGTAAAAC
*
40502538 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
40502565 AGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
40502592 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTATAAATC-GAGGGTAAAAC
* *
40502619 GGTAATTCTGTAAATCG
1 AGTAATTCTATAAATCG
40502636 GGAGTACTTT
Statistics
Matches: 297, Mismatches: 31, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.00
26 71 0.24
27 222 0.75
28 3 0.01
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:40502561 original size:81 final size:80
Alignment explanation
Indices: 40502270--40502635 Score: 488
Period size: 81 Copynumber: 4.5 Consensus size: 80
40502260 AAGGGTATTT
* * *
40502270 TAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATC-AAGGTAAAACAGTAATTCTA
1 TAGTAATTCTGTAAAT-GAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
40502334 TAAATCGAGGGTAAAA
65 TAAATCGAGGGTAAAA
* * *
40502350 TGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA-TGATAATTAT
1 TAGTAATTCTGTAAAT-GAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAG-TAATTCT
*
40502414 GTAAATCG-GGGTAAAA
64 ATAAATCGAGGGTAAAA
** * * *
40502430 CGGTAATTATGTAAATTG-GGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTG
1 TAGTAATTCTGTAAA-TGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
*
40502494 TAAATCAAGGGTAAAA
65 TAAATCGAGGGTAAAA
*
40502510 TAGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTA
1 TAGTAATTCTGTAAA-TGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
*
40502575 CAAATCGAGGGTAAAA
65 TAAATCGAGGGTAAAA
* * *
40502591 CAGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATCG
1 TAGTAATTCTGTAAA-TGAGGGTAAAACGGTAATTCTATAAATCG
40502636 GGAGTACTTT
Statistics
Matches: 255, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
79 47 0.18
80 87 0.34
81 121 0.47
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (80 bp):
TAGTAATTCTGTAAATGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTAT
AAATCGAGGGTAAAA
Found at i:40509059 original size:30 final size:30
Alignment explanation
Indices: 40509004--40509134 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
40508994 ATAGTGAATC
*
40509004 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
40509033 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
40509063 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
40509091 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
40509121 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40509135 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:40509114 original size:58 final size:58
Alignment explanation
Indices: 40509003--40509134 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
40508993 TATAGTGAAT
* * * * *
40509003 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
40509062 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
40509120 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
40509135 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:40516829 original size:30 final size:30
Alignment explanation
Indices: 40516774--40516902 Score: 178
Period size: 30 Copynumber: 4.5 Consensus size: 30
40516764 ATAGTGAATC
40516774 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40516803 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40516833 CGCACACTTAGTGCTATATAA---TCA-CT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* * * * *
40516859 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40516889 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40516903 AATTTCACGT
Statistics
Matches: 91, Mismatches: 4, Indels: 9
0.88 0.04 0.09
Matches are distributed among these distances:
26 21 0.23
27 3 0.03
29 21 0.23
30 46 0.51
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:40516868 original size:56 final size:58
Alignment explanation
Indices: 40516773--40516902 Score: 183
Period size: 56 Copynumber: 2.3 Consensus size: 58
40516763 TATAGTGAAT
* * * *
40516773 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAGCTCGCACACTTAGTGCTATACAATTTTAAAC
* *
40516832 TCGCACACTTAGTGCTATATA-ATCA-CTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATCAGCTCGCACACTTAGTGCTATACAATTTTAAAC
40516888 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
40516903 AATTTCACGT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
56 41 0.64
57 3 0.05
59 20 0.31
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAGCTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:40517995 original size:124 final size:125
Alignment explanation
Indices: 40517833--40518059 Score: 341
Period size: 124 Copynumber: 1.8 Consensus size: 125
40517823 AGCTTTAAGA
* * *
40517833 GGATATTTGAATATTCAAAACAAACAAAGAAAGTGAAACCCAGTACGTAAGGGTACGATCCTCTG
1 GGATATTTGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACATAAGGGCACGATCCTCTG
* * * *
40517898 AATTCTTTAAATATCGAATATTGCCTTTATTTTGAAAATTTTGAGAGTGAACCAGTAAAG
66 AATTCTTTAAATACCGAACATTGCCATTATTTTAAAAATTTTGAGAGTGAACCAGTAAAG
* * *
40517958 GGATATTCTG-ATATTCAAGAC-AACAAAGAAAGCGAAACCCAGTACATTAGGGCACGATCCTTT
1 GGATATT-TGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACATAAGGGCACGATCCTCT
40518021 GAATTCTTTAAATACCGAACATTGCCATTATTTTAAAAA
65 GAATTCTTTAAATACCGAACATTGCCATTATTTTAAAAA
40518060 CAATTGAGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
124 72 0.79
125 17 0.19
126 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (125 bp):
GGATATTTGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACATAAGGGCACGATCCTCTG
AATTCTTTAAATACCGAACATTGCCATTATTTTAAAAATTTTGAGAGTGAACCAGTAAAG
Found at i:40524141 original size:28 final size:28
Alignment explanation
Indices: 40524088--40524171 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
40524078 CACTTTGTGC
40524088 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
40524117 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
40524145 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
40524172 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:40524183 original size:23 final size:24
Alignment explanation
Indices: 40524092--40524185 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
40524082 TTGTGCTATT
40524092 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
40524119 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
40524149 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
40524172 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
40524186 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:40524413 original size:22 final size:23
Alignment explanation
Indices: 40524376--40524420 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
40524366 GCTTTACTGA
40524376 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
40524399 TCAGGCAC-TTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
40524421 CTGATCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:40528532 original size:390 final size:390
Alignment explanation
Indices: 40527657--40529209 Score: 2958
Period size: 390 Copynumber: 4.0 Consensus size: 390
40527647 TAGTCTAACT
40527657 TTGAAAAATCTCAAAA-ATTTTAGA-ATCTAATTAGAG-ATGAATAAAATATGAAATTAAAGCTT
1 TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
40527719 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
66 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
40527784 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTT-CCCTGTTCTGACTTTGGAAAATCAT-AA
131 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
* *
40527847 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAATCCTTAAAGAGTCTATTTTC
196 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAAGAGTCTATTTTT
*
40527912 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAGTGAAGAA
261 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
*
40527977 GGGTCGGAACTGTCAAACAGCA-AACA-GGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
326 GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
* *
40528040 TTGAAAAATCTCAAAAAAATTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
1 TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
40528105 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
66 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
40528170 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
131 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
*
40528235 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAGGAGTCTATTTTT
196 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAAGAGTCTATTTTT
40528300 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
261 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
40528365 GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
326 GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
40528430 TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
1 TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
40528495 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
66 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
40528560 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
131 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
*
40528625 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAGGAGTCTATTTTT
196 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAAGAGTCTATTTTT
40528690 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
261 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
40528755 GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
326 GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
40528820 TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
1 TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
40528885 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
66 ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
40528950 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
131 AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
* *
40529015 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAATCCTTAAATAGTCTATTTTT
196 AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAAGAGTCTATTTTT
40529080 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
261 AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
*
40529145 GGGTCGGAACTGTCAGACAGCAGAATAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
326 GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
40529210 ACAAAAAATT
Statistics
Matches: 1151, Mismatches: 12, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
383 16 0.01
384 7 0.01
385 12 0.01
386 127 0.11
387 25 0.02
388 149 0.13
389 4 0.00
390 811 0.70
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (390 bp):
TTGAAAAATCTCAAAACATTTTAGATATCTAATTAGAGAATGAATAAAATATGAAATTAAAGCTT
ATTGAGTCTAGTTTCTTATAGAAGAAACGGTGTAAGCAATGGAATTGTAAATCATGAGATATAAT
AAGTTTTGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTGGAAAATCATAAA
AAATTGGAGAAAAATAATTAAGGGATTAAATTTATATGTTTAAAACCCTTAAAGAGTCTATTTTT
AATAGAAATAAGCGGGAACATCATCTGAATCTCGTACGATGAGATAATTAATTCTTAATGAAGAA
GGGTCGGAACTGTCAGACAGCAGAACAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGCTAA
Found at i:40530764 original size:18 final size:18
Alignment explanation
Indices: 40530741--40530775 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40530731 TAATAGATAT
40530741 ACTTAAAATCAAGTTGGC
1 ACTTAAAATCAAGTTGGC
*
40530759 ACTTAAAATCTAGTTGG
1 ACTTAAAATCAAGTTGG
40530776 ATTGCCACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (18 bp):
ACTTAAAATCAAGTTGGC
Found at i:40531538 original size:33 final size:33
Alignment explanation
Indices: 40531461--40531609 Score: 108
Period size: 33 Copynumber: 4.5 Consensus size: 33
40531451 TAGGAGTGCC
* ** * *
40531461 ATACTGCGGTGGATACGACCCAGGAAGAGTG-A
1 ATACTGCGATGGATACGGGCCAGGAAGAATGCT
** *
40531493 AGTACTATGATGGATACGGGCCAGGAAGACTGCT
1 A-TACTGCGATGGATACGGGCCAGGAAGAATGCT
40531527 ATACTGCGATGGATACGGGCTCTAGG--GAATGCT
1 ATACTGCGATGGATACGGGC-C-AGGAAGAATGCT
* ** *
40531560 GTACTATGATGGATACGGGCC-CGAAGGAATGCT
1 ATACTGCGATGGATACGGGCCAGGAA-GAATGCT
* *
40531593 GTACTGCGGTGGATACG
1 ATACTGCGATGGATACG
40531610 ACCCAAAGAT
Statistics
Matches: 93, Mismatches: 17, Indels: 13
0.76 0.14 0.11
Matches are distributed among these distances:
30 1 0.01
32 2 0.02
33 85 0.91
34 2 0.02
35 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (33 bp):
ATACTGCGATGGATACGGGCCAGGAAGAATGCT
Found at i:40532409 original size:14 final size:14
Alignment explanation
Indices: 40532390--40532424 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40532380 CAAATTACAT
40532390 GTTAGAATAGTATC
1 GTTAGAATAGTATC
40532404 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
40532418 ATTAGAA
1 GTTAGAA
40532425 ATAAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:40534667 original size:27 final size:27
Alignment explanation
Indices: 40534612--40534668 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
40534602 ATCCATAGTG
*
40534612 GTGCCGCCTCTGCCATCCTCACCACCA
1 GTGCCGCCTCTGCCATCCTCACCAACA
*
40534639 GTGCCGCCTGC-GCCAGTCC-CTCCAACA
1 GTGCCGCCT-CTGCCA-TCCTCACCAACA
40534666 GTG
1 GTG
40534669 TCACCTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.14, C:0.47, G:0.21, T:0.18
Consensus pattern (27 bp):
GTGCCGCCTCTGCCATCCTCACCAACA
Found at i:40535085 original size:21 final size:21
Alignment explanation
Indices: 40535060--40535103 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40535050 TATTAGAATA
*
40535060 TTACATAATT-TATAATTTAAT
1 TTACATAATTAT-TAATATAAT
40535081 TTACATAATTATTAATATAAT
1 TTACATAATTATTAATATAAT
40535102 TT
1 TT
40535104 TATAACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTACATAATTATTAATATAAT
Found at i:40541735 original size:24 final size:24
Alignment explanation
Indices: 40541706--40541751 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
40541696 TTTCTATATT
*
40541706 AATTTTAATAATATTTTTTATTCA
1 AATTTTAATAATATTATTTATTCA
40541730 AATTTTAATAATATTATTTATT
1 AATTTTAATAATATTATTTATT
40541752 AATTCAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTTTAATAATATTATTTATTCA
Found at i:40541792 original size:23 final size:24
Alignment explanation
Indices: 40541741--40541793 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
40541731 ATTTTAATAA
* *
40541741 TATTATTTATTAATTCAATGTTAT
1 TATTATTTATTAACTCAATATTAT
40541765 T-TTATTTAATT-ACTCAATATT-T
1 TATTATTT-ATTAACTCAATATTAT
40541787 TATTATT
1 TATTATT
40541794 GCTTTATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 19 0.76
24 4 0.16
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TATTATTTATTAACTCAATATTAT
Found at i:40544532 original size:5 final size:5
Alignment explanation
Indices: 40544522--40544547 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40544512 CTGTAATTAC
40544522 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
40544548 GATGCTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:40545010 original size:16 final size:16
Alignment explanation
Indices: 40544989--40545021 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40544979 CTATTCAAAT
*
40544989 AATTATAAATCTTTTA
1 AATTATAAATATTTTA
40545005 AATTATAAATATTTTA
1 AATTATAAATATTTTA
40545021 A
1 A
40545022 TTTTAAAGAT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATAAATATTTTA
Found at i:40545028 original size:15 final size:15
Alignment explanation
Indices: 40544988--40545028 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
40544978 TCTATTCAAA
*
40544988 TAATTATAAATCTTT
1 TAATTATAAATATTT
40545003 TAAATTATAAATATTT
1 T-AATTATAAATATTT
*
40545019 TAATTTTAAA
1 TAATTATAAA
40545029 GATAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATTATAAATATTT
Found at i:40545784 original size:21 final size:21
Alignment explanation
Indices: 40545759--40545799 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40545749 TCACAAAACT
40545759 TATTTATA-TTTTAATTAATCA
1 TATTT-TAGTTTTAATTAATCA
*
40545780 TATTTTAGTTTTAGTTAATC
1 TATTTTAGTTTTAATTAATC
40545800 TTAATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTTAGTTTTAATTAATCA
Found at i:40545807 original size:21 final size:20
Alignment explanation
Indices: 40545765--40545824 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
40545755 AACTTATTTA
* *
40545765 TATTTTAATTAATCATATTT
1 TATTTTAATTAATCTTAATT
*
40545785 TAGTTTTAGTTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
*
40545806 TA-CTTAATTAATCTTAATT
1 TATTTTAATTAATCTTAATT
40545825 GTTAATTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:40548676 original size:20 final size:19
Alignment explanation
Indices: 40548653--40548691 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
40548643 TAAAGAAATA
40548653 TAAAAA-AATACATAATATTT
1 TAAAAATAATA-ATAA-ATTT
40548673 TAAAAATAATAATAAATTT
1 TAAAAATAATAATAAATTT
40548692 AAATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATAATAATAAATTT
Found at i:40548692 original size:18 final size:18
Alignment explanation
Indices: 40548656--40548694 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40548646 AGAAATATAA
*
40548656 AAAAATACATAATATTTT
1 AAAAATACATAATAATTT
40548674 AAAAATA-ATAATAAATTT
1 AAAAATACATAAT-AATTT
40548692 AAA
1 AAA
40548695 TTTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATACATAATAATTT
Found at i:40548732 original size:30 final size:29
Alignment explanation
Indices: 40548698--40548754 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
40548688 ATTTAAATTT
* * *
40548698 TATATTAATATTAATATTAAATACATATAA
1 TATATCAATATTAA-ATAAAATAAATATAA
40548728 TATATCAATATTAAATAAAATAAATAT
1 TATATCAATATTAAATAAAATAAATAT
40548755 CTTCCATCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (29 bp):
TATATCAATATTAAATAAAATAAATATAA
Found at i:40548753 original size:24 final size:24
Alignment explanation
Indices: 40548705--40548755 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
40548695 TTTTATATTA
* *
40548705 ATATTAATATTAAATACATATAAT
1 ATATCAATATTAAATAAATATAAT
40548729 ATATCAATATTAAATAAA-ATAA-
1 ATATCAATATTAAATAAATATAAT
40548751 ATATC
1 ATATC
40548756 TTCCATCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 4 0.16
24 16 0.64
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATCAATATTAAATAAATATAAT
Found at i:40550780 original size:573 final size:578
Alignment explanation
Indices: 40549406--40550785 Score: 1758
Period size: 585 Copynumber: 2.4 Consensus size: 578
40549396 ATTTATTCCA
* * * * * * *
40549406 TTTTCTCTTCTGAATAGATCGTGTTCTTCACCTAAGTTATTCAATCGAGAAAGAGATCATGAATA
1 TTTTCTCTTTTGAATCGATCAT-TTTTTCACCTGATTTATTCAATCGAGAAAGAGATTATGAATA
* * * * *
40549471 ACATTAATGGCTAAATCGCTTA-AGAGAGATTAACAAGTGGATGGGGATGTTATTAATGAAGGAT
65 ACATGAGTGGCTAAATCACTTAGAG-GAGATTAACGAGTGGATGGGGATGTGATTAATGAAGGAT
*
40549535 TTAGGGTTTCTTGA-ATGGGAATAGTTAGTATA-AATTACGTATGCTTAAACCACTAAGCTTGAC
129 TTAGGGTTTCTTGAGA-GGGATTAGTTAGTA-AGAATTACGTATGCTTAAACCACTAAGCTTGAC
* * *
40549598 AAAGC-TAGAAAGTTATCATAGGCAATACGACCACAAAAACAACAACGATCCACTCAAGCACTGA
192 -AACCTTAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGA
* ** ** ** *
40549662 GTAATCTTGATGCCAATCGTTTCCATAATACGAAAGTCAAACTTTTTTTTCAACAAATGAGTGGA
256 GTAATATCAATGCCAATCACTTCCATAATACGAAAGTCAAACGGTTTTTTCAACAAATGAGTAGA
** * * * *
40549727 CAATCGTTTATACAAGAATGTGTGTTCGATCCTATCATGACTGTTTACCATGAAATATGAGAGTT
321 CAATCGTTTATACAAGAACATGGGTTCGATCCCAACATGACTGCTTACCATGAAATATGAGAGTT
**
40549792 GGTACAGTTCCATCATTGGAACAAATTTTGCGCAACCTCGACTGAACTGGCGGTTAACGTAGTAG
386 GGTACAGTTCCATCATTGGAACAAATTTT------CCTCGACTGAACTGGCGGTTAACCCAGTAG
* * ** *
40549857 TTTATGAATCCTACGCCTCTCTGAAAGATAAGGAGAATTTCTAGCAACGTGGCGAGATGATCTCT
445 TTTATGAAACCTACGCCTCTCTAAAAGATAAGGAGAATCACTAGCAACGTGGCGAGACGATCTCT
* * * ** **
40549922 CTTGTGGTTGTTAGGGGAAAAGAGGTGTCGATTGCATCTTGTGATCAAATCCATTATTATTCCAT
510 ATAGTGGTTGTTAAGGGAAAAGAGGTGTCGATTGCATCTTGCAATCAAATCCACAATTATTCCAT
40549987 TCTC
575 TCTC
*
40549991 TTTTCTCTTTTGAATCGATTATTTTCTTCACCTGATTTATTCAATCGAGAAAGAGATTATGAATA
1 TTTTCTCTTTTGAATCGATCATTTT-TTCACCTGATTTATTCAATCGAGAAAGAGATTATGAATA
* * * * *
40550056 ACATGAGTGGCTAAAACACTTAGAGGAGATTAATGAGTGGATGAGAATGTGATTAATGGAGGATT
65 ACATGAGTGGCTAAATCACTTAGAGGAGATTAACGAGTGGATGGGGATGTGATTAATGAAGGATT
* * *
40550121 TAGGGTTT-TCGAAGAGGGATTAGTTAGTATGAATTACGTATGCCTAAACCACTAAGCTTGACAA
130 TAGGGTTTCTTG-AGAGGGATTAGTTAGTAAGAATTACGTATGCTTAAACCACTAAGCTTGACAA
* * * *
40550185 CTTTAGGAATTTATCATAGGCAAGATGACCACGAAAACAACAACGATCCACTCAAGCA-TCGAGT
194 CCTTAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACT-GAGT
* * * **** *
40550249 AATATCAATGCCAATCACTTCTATAATACGGAAGTCGAACGGTTTTTTGTTTAAATGAGTAGACG
258 AATATCAATGCCAATCACTTCCATAATACGAAAGTCAAACGGTTTTTTCAACAAATGAGTAGACA
* * * *
40550314 ATCTTTTATACAAGAACATGGGTTCGATCCCAACATGACTGCTTGCGATGAAATATGGGAGTTGG
323 ATCGTTTATACAAGAACATGGGTTCGATCCCAACATGACTGCTTACCATGAAATATGAGAGTTGG
* * *
40550379 TACAGTTCCATCATTGGAACAAA-TTT-CTCGACTGAACTTGTGGTTGACCCAGTAGTTTATGAA
388 TACAGTTCCATCATTGGAACAAATTTTCCTCGACTGAACTGGCGGTTAACCCAGTAGTTTATGAA
* * * *
40550442 ACC-ATGCC-CTCTAAAAGTTAGGGAGAATCACTAGCAGCGTGGCGAGACGATCTCTATAGTGGT
453 ACCTACGCCTCTCTAAAAGATAAGGAGAATCACTAGCAACGTGGCGAGACGATCTCTATAGTGGT
40550505 TGTTAAGGGAAAAGAGGTGTCGATTGCA-CTTCGCAATCAAATCCACAATTATT-CATTCTC
518 TGTTAAGGGAAAAGAGGTGTCGATTGCATCTT-GCAATCAAATCCACAATTATTCCATTCTC
*
40550565 TTTTCTCTTTTGAATCGATCATTTTTTCACCTGATTTATTCAATCGAGAAAGCGATTATGAATAA
1 TTTTCTCTTTTGAATCGATCATTTTTTCACCTGATTTATTCAATCGAGAAAGAGATTATGAATAA
* * * ** *
40550630 TATGAGTGGCTAAATCCCTTAGAGGAGATGAACGAGTGGATGGGGATGTGATTAACAAAAGATTT
66 CATGAGTGGCTAAATCACTTAGAGGAGATTAACGAGTGGATGGGGATGTGATTAATGAAGGATTT
* * * *
40550695 AGGGTTTCTTGAGAGGGATTAGTTAGTAAGCATTATGTATGCTTAAACTACTAGGCTTGACAACC
131 AGGGTTTCTTGAGAGGGATTAGTTAGTAAGAATTACGTATGCTTAAACCACTAAGCTTGACAACC
40550760 TTAGGAAGTTATCATAGGCAAGACGA
196 TTAGGAAGTTATCATAGGCAAGACGA
40550786 GGTCAAGAGA
Statistics
Matches: 687, Mismatches: 99, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
573 171 0.25
574 36 0.05
575 90 0.13
576 4 0.01
577 34 0.05
584 10 0.01
585 339 0.49
586 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (578 bp):
TTTTCTCTTTTGAATCGATCATTTTTTCACCTGATTTATTCAATCGAGAAAGAGATTATGAATAA
CATGAGTGGCTAAATCACTTAGAGGAGATTAACGAGTGGATGGGGATGTGATTAATGAAGGATTT
AGGGTTTCTTGAGAGGGATTAGTTAGTAAGAATTACGTATGCTTAAACCACTAAGCTTGACAACC
TTAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGAGTAAT
ATCAATGCCAATCACTTCCATAATACGAAAGTCAAACGGTTTTTTCAACAAATGAGTAGACAATC
GTTTATACAAGAACATGGGTTCGATCCCAACATGACTGCTTACCATGAAATATGAGAGTTGGTAC
AGTTCCATCATTGGAACAAATTTTCCTCGACTGAACTGGCGGTTAACCCAGTAGTTTATGAAACC
TACGCCTCTCTAAAAGATAAGGAGAATCACTAGCAACGTGGCGAGACGATCTCTATAGTGGTTGT
TAAGGGAAAAGAGGTGTCGATTGCATCTTGCAATCAAATCCACAATTATTCCATTCTC
Found at i:40552383 original size:6 final size:7
Alignment explanation
Indices: 40552370--40552415 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
40552360 ACCTAAGTCC
40552370 ATAACAG
1 ATAACAG
40552377 A-AACAG
1 ATAACAG
*
40552383 ATATCAG
1 ATAACAG
*
40552390 A-ATCAG
1 ATAACAG
*
40552396 ATAACAT
1 ATAACAG
40552403 ATAACAG
1 ATAACAG
40552410 ATAACA
1 ATAACA
40552416 TATCAGATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (7 bp):
ATAACAG
Found at i:40553116 original size:8 final size:8
Alignment explanation
Indices: 40553103--40553132 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
40553093 TTTAGCAACC
40553103 AATTTACG
1 AATTTACG
40553111 AATTTACG
1 AATTTACG
40553119 AATTTACG
1 AATTTACG
40553127 AATTTA
1 AATTTA
40553133 TCAAACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (8 bp):
AATTTACG
Found at i:40553514 original size:5 final size:5
Alignment explanation
Indices: 40553506--40553534 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40553496 ATTTTGGAAA
40553506 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
40553535 ATAATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:40553547 original size:16 final size:16
Alignment explanation
Indices: 40553506--40553538 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
40553496 ATTTTGGAAA
40553506 AAAATAAAAT-AAAAT
1 AAAATAAAATAAAAAT
40553521 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
40553537 AA
1 AA
40553539 TATCAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:40558835 original size:40 final size:39
Alignment explanation
Indices: 40558790--40558997 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 39
40558780 CGGAATACAA
*
40558790 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
40558830 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
40558870 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
40558910 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
40558950 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
40558990 CCGGATAT
1 CCGGATAT
40558998 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40558930 original size:80 final size:80
Alignment explanation
Indices: 40558790--40558996 Score: 254
Period size: 80 Copynumber: 2.6 Consensus size: 80
40558780 CGGAATACAA
* * * *
40558790 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTAGCACAAATG
*
40558855 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * *
40558870 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGCCACTAGCACAATT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAG-AACCACTAGCACAAAT
*
40558934 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
40558950 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
40558997 TCATTCAATT
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
79 1 0.01
80 107 0.99
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:40560953 original size:40 final size:39
Alignment explanation
Indices: 40560788--40560971 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40560778 AAATTGAATG
* * *
40560788 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40560828 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40560868 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40560908 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40560947 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40560972 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40560996 original size:80 final size:81
Alignment explanation
Indices: 40560828--40561016 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40560818 GCTGGAAATT
* * * *
40560828 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40560893 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40560909 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40560972 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40560988 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40561017 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:40569071 original size:40 final size:39
Alignment explanation
Indices: 40568906--40569089 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40568896 AAATTGAATG
* * *
40568906 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40568946 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40568986 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40569026 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40569065 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40569090 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40569114 original size:80 final size:81
Alignment explanation
Indices: 40568946--40569134 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40568936 GCTGGAAATT
* * * *
40568946 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40569011 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40569027 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40569090 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40569106 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40569135 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:40579153 original size:45 final size:45
Alignment explanation
Indices: 40579071--40579199 Score: 199
Period size: 45 Copynumber: 2.9 Consensus size: 45
40579061 CTGAATTCAT
* *
40579071 TCACCGGCATT-TCGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTACTAGGCTC-AAAGGCCCGAATAGTATC
* *
40579115 TCATCGGTATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATC
40579160 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATA
1 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATA
40579200 ATACTGTACG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 12 0.16
45 65 0.84
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATC
Found at i:40580078 original size:47 final size:47
Alignment explanation
Indices: 40580022--40580164 Score: 259
Period size: 47 Copynumber: 3.0 Consensus size: 47
40580012 AAATTTTTCT
* *
40580022 TTAACTAAGTAACTTATCCAGAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
40580069 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
*
40580116 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
40580163 TT
1 TT
40580165 TAAATTCAAC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
Found at i:40589272 original size:41 final size:40
Alignment explanation
Indices: 40589130--40589292 Score: 156
Period size: 41 Copynumber: 4.0 Consensus size: 40
40589120 TCGGGGTTTA
* *
40589130 AATCTGAGCTTGGTTTCGAAGGGCCTTTGAGCCAGTG-CT
1 AATCCGAGCTTAGTTTCGAAGGGCCTTTGAGCCAGTGTCT
* * *
40589169 AATAACCGAACTTAGTTTTGAAGGG-CTTTAGAGCTAGTGTCAT
1 AAT--CCGAGCTTAGTTTCGAAGGGCCTTT-GAGCCAGTGTC-T
* *
40589212 AA-CCG-GACTTAGTTCCGAAGGGCCTTCGAGCCAGTGGTCT
1 AATCCGAG-CTTAGTTTCGAAGGGCCTTTGAGCCAGT-GTCT
* *
40589252 AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGTG-CT
1 AATCCGAGCTTAGTTTCGAAGGGCCTTTGAGCCAGTGTCT
40589291 AA
1 AA
40589293 GAATCGGGCT
Statistics
Matches: 100, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
39 7 0.07
40 31 0.31
41 57 0.57
42 2 0.02
43 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
AATCCGAGCTTAGTTTCGAAGGGCCTTTGAGCCAGTGTCT
Found at i:40597677 original size:41 final size:40
Alignment explanation
Indices: 40597607--40597766 Score: 173
Period size: 41 Copynumber: 3.9 Consensus size: 40
40597597 GGGTTTAAAT
* *
40597607 CCGAGCTTGGTTTCGAAGGGCCTTTGAGCCAGTGCTAATAA
1 CCGAACTTAGTTTCGAAGGG-CTTTGAGCCAGTGCTAATAA
*
40597648 CCGAACTTAGTTTCGAAGGGCTTTAGAGCCAGTG-TCATAA
1 CCGAACTTAGTTTCGAAGGGCTTT-GAGCCAGTGCTAATAA
* * *
40597688 CCGGACTTAGTTCCGAAGGGCCTTCGAGCCAGTGGTCTAAT--
1 CCGAACTTAGTTTCGAAGGG-CTTTGAGCCAGT-G-CTAATAA
* *
40597729 CCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
1 CCGAACTTAGTTTCGAAGGGC-TTTGAGCCAGTGCTAA
40597767 GAATCGGGCT
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
39 4 0.04
40 37 0.37
41 57 0.56
43 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAACTTAGTTTCGAAGGGCTTTGAGCCAGTGCTAATAA
Found at i:40597786 original size:81 final size:79
Alignment explanation
Indices: 40597618--40597787 Score: 200
Period size: 81 Copynumber: 2.1 Consensus size: 79
40597608 CGAGCTTGGT
* *
40597618 TTCGAAGGGCCTTTGAGCCAGTGCTAATAACCGAACTTAGTTTCGAAGGGCTTTAGAGCCAGTGT
1 TTCGAAGGGCCTTCGAGCCAGTGCTAAT-ACCGAACTTAGTCTCGAAGGGCTTTAGAGCCAGTGT
* *
40597683 CATAACCGGACTTAG
65 AAGAACCGGACTTAG
* *
40597698 TTCCGAAGGGCCTTCGAGCCAGTGGTCTAAT-CCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
1 TT-CGAAGGGCCTTCGAGCCAGT-G-CTAATACCGAACTTAGTCTCGAAGGGCTTTAGAGCCAGT
* *
40597762 GCTAAGAATCGGGCTT-G
63 G-TAAGAACCGGACTTAG
40597779 ATTCGAAGG
1 -TTCGAAGG
40597788 ATGTTTGTGC
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
80 2 0.03
81 57 0.74
82 13 0.17
83 5 0.06
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (79 bp):
TTCGAAGGGCCTTCGAGCCAGTGCTAATACCGAACTTAGTCTCGAAGGGCTTTAGAGCCAGTGTA
AGAACCGGACTTAG
Found at i:40602675 original size:20 final size:20
Alignment explanation
Indices: 40602650--40602689 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40602640 CCGATAATGT
40602650 GTTAGTAGCAGAATTAAGGG
1 GTTAGTAGCAGAATTAAGGG
*
40602670 GTTAGTAGCAGACTTAAGGG
1 GTTAGTAGCAGAATTAAGGG
40602690 CTAAACCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.35, T:0.25
Consensus pattern (20 bp):
GTTAGTAGCAGAATTAAGGG
Found at i:40606297 original size:41 final size:41
Alignment explanation
Indices: 40606131--40606275 Score: 165
Period size: 41 Copynumber: 3.6 Consensus size: 41
40606121 CTTGGTTTCA
*
40606131 AAGGGCCTTTGAGCCAGTGCTAATAACCGAACTTAGTTTCG
1 AAGGGCCTTTGAGCCAGTGCTAATAACCGAACTTAGTTCCG
* *
40606172 AAGGG-CTTTAGAGCCAGTG-TCATAACCGGACTTAGTTCCG
1 AAGGGCCTTT-GAGCCAGTGCTAATAACCGAACTTAGTTCCG
* *
40606212 AAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTAG-TCTCG
1 AAGGGCCTTTGAGCCAGT-G-CTAATAACCGAACTTAGTTC-CG
*
40606253 AAGGGCTTTTGAGCCAGTGCTAA
1 AAGGGCCTTTGAGCCAGTGCTAA
40606276 GAATCGGGCT
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
39 4 0.04
40 38 0.43
41 44 0.49
43 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
AAGGGCCTTTGAGCCAGTGCTAATAACCGAACTTAGTTCCG
Found at i:40608738 original size:25 final size:25
Alignment explanation
Indices: 40608693--40608832 Score: 131
Period size: 25 Copynumber: 5.6 Consensus size: 25
40608683 GAATCGATAT
*
40608693 GCTCTTACGAGCT--ATAAATGGTAA
1 GCTCCTACGAGCTGAAT-AATGGTAA
* * *
40608717 GTTCCTATGAGCTGCATAATGGTAA
1 GCTCCTACGAGCTGAATAATGGTAA
*
40608742 GCTCCTCCGAGCTGAATAATGGTAA
1 GCTCCTACGAGCTGAATAATGGTAA
* ** * *
40608767 GCTCATGTGAGCTGAGTAACGGTAA
1 GCTCCTACGAGCTGAATAATGGTAA
* * *
40608792 GCTCATACGAGCTGAGTAACGGTAA
1 GCTCCTACGAGCTGAATAATGGTAA
*
40608817 GCTCATACGAGCTGAA
1 GCTCCTACGAGCTGAA
40608833 ATCGGTAACG
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
24 10 0.10
25 87 0.88
26 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (25 bp):
GCTCCTACGAGCTGAATAATGGTAA
Found at i:40608778 original size:50 final size:50
Alignment explanation
Indices: 40608693--40608831 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 50
40608683 GAATCGATAT
* * * *
40608693 GCTCTTACGAGCT--ATAAATGGTAAGTTCCTATGAGCTGCA-TAATGGTAA
1 GCTCATACGAGCTGAAT-AATGGTAAGCTCATATGAGCTG-AGTAACGGTAA
* * *
40608742 GCTCCTCCGAGCTGAATAATGGTAAGCTCATGTGAGCTGAGTAACGGTAA
1 GCTCATACGAGCTGAATAATGGTAAGCTCATATGAGCTGAGTAACGGTAA
* * *
40608792 GCTCATACGAGCTGAGTAACGGTAAGCTCATACGAGCTGA
1 GCTCATACGAGCTGAATAATGGTAAGCTCATATGAGCTGA
40608832 AATCGGTAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
49 12 0.16
50 61 0.81
51 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (50 bp):
GCTCATACGAGCTGAATAATGGTAAGCTCATATGAGCTGAGTAACGGTAA
Found at i:40609717 original size:20 final size:19
Alignment explanation
Indices: 40609688--40609727 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40609678 TAAAAGATGA
40609688 TATCTTTAATATATTTTAT
1 TATCTTTAATATATTTTAT
*
40609707 TATCATTTAATATGTTTTAT
1 TATC-TTTAATATATTTTAT
40609727 T
1 T
40609728 TTAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TATCTTTAATATATTTTAT
Found at i:40615889 original size:15 final size:14
Alignment explanation
Indices: 40615862--40615888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40615852 CTCTAAAAAT
40615862 AAAAAATTATTTTA
1 AAAAAATTATTTTA
40615876 AAAAAATTATTTT
1 AAAAAATTATTTT
40615889 TTGTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAAATTATTTTA
Found at i:40621897 original size:28 final size:28
Alignment explanation
Indices: 40621857--40621914 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40621847 TGAAAAAAAA
40621857 GTCAATTCATTTAGTTATGGACACCATG
1 GTCAATTCATTTAGTTATGGACACCATG
40621885 GTCAATTCATTTAGTTATGGACACCATG
1 GTCAATTCATTTAGTTATGGACACCATG
40621913 GT
1 GT
40621915 TTTTGTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (28 bp):
GTCAATTCATTTAGTTATGGACACCATG
Found at i:40622735 original size:23 final size:24
Alignment explanation
Indices: 40622681--40622735 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
40622671 AACTAATTTA
* *
40622681 AAAGTAAATAGAAATAAGTAATGC
1 AAAGTAAATACAAATAAATAATGC
*
40622705 AAATTAAAT-CAAATAAATAAT-C
1 AAAGTAAATACAAATAAATAATGC
40622727 AATAGTAAA
1 AA-AGTAAA
40622736 ACCTTAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 8 0.31
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.24
Consensus pattern (24 bp):
AAAGTAAATACAAATAAATAATGC
Found at i:40622999 original size:14 final size:14
Alignment explanation
Indices: 40622980--40623031 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
40622970 AATTGATAGC
40622980 TAATTAAAGTACAA
1 TAATTAAAGTACAA
* *
40622994 TAATTAAATTGATAA
1 TAATTAAAGT-ACAA
40623009 CTAATTAAAGTACAA
1 -TAATTAAAGTACAA
40623024 TAATTAAA
1 TAATTAAA
40623032 TTGTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 17 0.53
15 6 0.19
16 9 0.28
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (14 bp):
TAATTAAAGTACAA
Found at i:40623002 original size:30 final size:30
Alignment explanation
Indices: 40622968--40623034 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
40622958 ATATTAAATA
*
40622968 TAAATTGATAGCTAATTAAAGTACAATAAT
1 TAAATTGATAACTAATTAAAGTACAATAAT
40622998 TAAATTGATAACTAATTAAAGTACAATAAT
1 TAAATTGATAACTAATTAAAGTACAATAAT
40623028 TAAATTG
1 TAAATTG
40623035 TAAAAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (30 bp):
TAAATTGATAACTAATTAAAGTACAATAAT
Found at i:40624200 original size:42 final size:42
Alignment explanation
Indices: 40624154--40624371 Score: 215
Period size: 42 Copynumber: 5.2 Consensus size: 42
40624144 CAGTTTATTT
*
40624154 GATGATGCACTTATGTGTCAGTATATTTTCTTCAGTATATCC
1 GATGATGCACTTATGTGTCAGTATATTTTCTTCGGTATATCC
* * *
40624196 GATGATACTCTTACGTGTCAGTATATTTTCTTCGGTATATCC
1 GATGATGCACTTATGTGTCAGTATATTTTCTTCGGTATATCC
* * * * *
40624238 AATGATGCACTTATGTGCCAGTATATTTTCTTTGGTACATCT
1 GATGATGCACTTATGTGTCAGTATATTTTCTTCGGTATATCC
* * * * * * * *
40624280 GATAATGCACTTACGTGCCAGCATAATTGCTTCGGTTTATCT
1 GATGATGCACTTATGTGTCAGTATATTTTCTTCGGTATATCC
* * *
40624322 GATGATGCAC-TATGTTTTCCAGTATATTTCCTTCGGTTTA-CTC
1 GATGATGCACTTATG-TGT-CAGTATATTTTCTTCGGTATATC-C
40624365 GATGATG
1 GATGATG
40624372 TACTGTGGTT
Statistics
Matches: 144, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
41 3 0.02
42 116 0.81
43 25 0.17
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (42 bp):
GATGATGCACTTATGTGTCAGTATATTTTCTTCGGTATATCC
Found at i:40626159 original size:21 final size:21
Alignment explanation
Indices: 40626124--40626163 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40626114 TATATAGTTG
40626124 AATAAAAACTCTATTATTTAAA
1 AATAAAAACTCTATT-TTTAAA
*
40626146 AATAAAAA-TTTATTTTTA
1 AATAAAAACTCTATTTTTA
40626164 TATAATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
AATAAAAACTCTATTTTTAAA
Found at i:40639011 original size:10 final size:9
Alignment explanation
Indices: 40638989--40639084 Score: 51
Period size: 9 Copynumber: 10.6 Consensus size: 9
40638979 TGAATCCTCC
40638989 TATTT-TTT
1 TATTTATTT
40638997 TATTTATTCT
1 TATTTATT-T
*
40639007 TATTT-TTA
1 TATTTATTT
40639015 T-TTTATTT
1 TATTTATTT
40639023 TATTTATTT
1 TATTTATTT
*
40639032 TCTTT-TTCT
1 TATTTATT-T
*
40639041 T-TTTCTTTT
1 TATTT-ATTT
*
40639050 GTTTTTATTT
1 -TATTTATTT
40639060 TCATTTCAATTT
1 T-ATTT--ATTT
40639072 TA-TTATTT
1 TATTTATTT
40639080 TATTT
1 TATTT
40639085 TGAAAAAGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
7 3 0.04
8 20 0.29
9 21 0.30
10 17 0.24
11 4 0.06
12 5 0.07
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (9 bp):
TATTTATTT
Found at i:40639014 original size:12 final size:11
Alignment explanation
Indices: 40638989--40639085 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 11
40638979 TGAATCCTCC
*
40638989 TATTTTTTTATT
1 TATTTTATT-TT
40639001 TATTCTTATTTT
1 TATT-TTATTTT
40639013 TATTTTA-TTT
1 TATTTTATTTT
40639023 TA-TTTATTTT
1 TATTTTATTTT
*
40639033 CT-TTTTCTTTT
1 -TATTTTATTTT
* *
40639044 TCTTTTGTTTT
1 TATTTTATTTT
*
40639055 TATTTTCATTTC
1 TATTTT-ATTTT
*
40639067 AATTTTATTATTT
1 TATTTTA-T-TTT
40639080 TATTTT
1 TATTTT
40639086 GAAAAAGATA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
9 4 0.06
10 9 0.13
11 25 0.37
12 19 0.28
13 11 0.16
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.77
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:40639014 original size:16 final size:16
Alignment explanation
Indices: 40638994--40639085 Score: 59
Period size: 17 Copynumber: 5.9 Consensus size: 16
40638984 CCTCCTATTT
*
40638994 TTTTA-TTTATTCTTA
1 TTTTATTTTATTTTTA
40639009 TTTTTATTTTA-TTTTA
1 -TTTTATTTTATTTTTA
* *
40639025 -TTTATTTTCTTTTTCT
1 TTTTATTTTATTTTT-A
* *
40639041 TTTTCTTTTGTTTTTA
1 TTTTATTTTATTTTTA
* *
40639057 TTTTCATTTCAATTTTA
1 TTTT-ATTTTATTTTTA
40639074 --TTATTTTATTTT
1 TTTTATTTTATTTT
40639086 GAAAAAGATA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 16 0.27
15 6 0.10
16 13 0.22
17 24 0.41
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATTTTTA
Found at i:40639025 original size:26 final size:25
Alignment explanation
Indices: 40638994--40639085 Score: 84
Period size: 25 Copynumber: 3.7 Consensus size: 25
40638984 CCTCCTATTT
40638994 TTTTATTTATTCTTATTTTTATTTTA
1 TTTTATTTATT-TTATTTTTATTTTA
* *
40639020 TTTTATTTATTTTCTTTTTCTTTT-
1 TTTTATTTATTTTATTTTTATTTTA
* * *
40639044 TCTTT-TGT-TTTTATTTTCATTTCAA
1 T-TTTATTTATTTTATTTTTATTT-TA
40639069 TTTTA-TTATTTTATTTT
1 TTTTATTTATTTTATTTT
40639086 GAAAAAGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
23 11 0.21
24 7 0.13
25 24 0.45
26 11 0.21
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTATTTATTTTATTTTTATTTTA
Found at i:40641548 original size:27 final size:27
Alignment explanation
Indices: 40641510--40641566 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
40641500 TACTGATTCA
40641510 AGATAAGCTTTTATTCAGAGGAGGAAT
1 AGATAAGCTTTTATTCAGAGGAGGAAT
40641537 AGATAAGCTTTTATTCAGAGGAGGAAT
1 AGATAAGCTTTTATTCAGAGGAGGAAT
40641564 AGA
1 AGA
40641567 CCCTGTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (27 bp):
AGATAAGCTTTTATTCAGAGGAGGAAT
Found at i:40645225 original size:64 final size:64
Alignment explanation
Indices: 40645120--40645248 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
40645110 GCTATTTGAT
*
40645120 AGGCCCATAATGCATCATCGAGCCTCCGAGACCAATCTTTTCTGCTAGGGCGTGCTACCTTTTC
1 AGGCCCATAATGCATCATCGAGCCTCCGAGACCAATCTTTTCTGCTAGGGCATGCTACCTTTTC
* *
40645184 AGGCCCATAATGCATCATTGAGCCTCCGAGACCAATTTTTTCTGCTAGGGCATGCTACCTTTTC
1 AGGCCCATAATGCATCATCGAGCCTCCGAGACCAATCTTTTCTGCTAGGGCATGCTACCTTTTC
40645248 A
1 A
40645249 AGGATACGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (64 bp):
AGGCCCATAATGCATCATCGAGCCTCCGAGACCAATCTTTTCTGCTAGGGCATGCTACCTTTTC
Found at i:40649004 original size:40 final size:40
Alignment explanation
Indices: 40648960--40649072 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
40648950 TGCTGGAAAT
* * *
40648960 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* * *
40649000 TATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* *
40649040 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC
40649073 ACGTGATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.05
40 57 0.92
41 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:40656986 original size:40 final size:40
Alignment explanation
Indices: 40656942--40657054 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
40656932 TGCTGGAAAT
* * *
40656942 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* * *
40656982 TATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* *
40657022 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC
40657055 ACGTGATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.05
40 57 0.92
41 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:40658676 original size:13 final size:13
Alignment explanation
Indices: 40658629--40658699 Score: 79
Period size: 13 Copynumber: 5.5 Consensus size: 13
40658619 AAATTTTTCC
40658629 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
40658642 AAAGTACTTCTCA
1 AAAGCACTTCTCA
*
40658655 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* * *
40658668 AAAACACTTTTCC
1 AAAGCACTTCTCA
* *
40658681 ACAGCACTTTTCA
1 AAAGCACTTCTCA
40658694 AAAGCA
1 AAAGCA
40658700 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:40663360 original size:29 final size:29
Alignment explanation
Indices: 40663318--40663375 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40663308 TAAATAAATT
40663318 CTTTTTTGGAACTACATAGATCTATGGAA
1 CTTTTTTGGAACTACATAGATCTATGGAA
40663347 CTTTTTTGGAACTACATAGATCTATGGAA
1 CTTTTTTGGAACTACATAGATCTATGGAA
40663376 TCGGTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (29 bp):
CTTTTTTGGAACTACATAGATCTATGGAA
Found at i:40664553 original size:14 final size:14
Alignment explanation
Indices: 40664534--40664561 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40664524 TATTTACCTT
40664534 CGATCAATATTATC
1 CGATCAATATTATC
40664548 CGATCAATATTATC
1 CGATCAATATTATC
40664562 TTTATCTTGA
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:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CGATCAATATTATC
Found at i:40665128 original size:23 final size:23
Alignment explanation
Indices: 40665102--40665147 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40665092 GGGATATTAG
40665102 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
40665125 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
40665148 TCAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
ATATTGACTAGTTATATACGAAC
Found at i:40676520 original size:2 final size:2
Alignment explanation
Indices: 40676513--40676554 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
40676503 AGGATAAAAA
40676513 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
40676555 AATGAATGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:40678676 original size:14 final size:12
Alignment explanation
Indices: 40678648--40678690 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
40678638 TAAAATTATT
40678648 TATTATTTATAA
1 TATTATTTATAA
40678660 TATTATTTGAGTAA
1 TATTATTT-A-TAA
*
40678674 TATTATCTATAA
1 TATTATTTATAA
40678686 -ATTAT
1 TATTAT
40678691 CTATCAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.18
12 11 0.39
13 2 0.07
14 10 0.36
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (12 bp):
TATTATTTATAA
Found at i:40679054 original size:91 final size:90
Alignment explanation
Indices: 40678864--40679083 Score: 266
Period size: 90 Copynumber: 2.4 Consensus size: 90
40678854 TGTAAAAACT
* *
40678864 CCTCAAATTTTTTCAAAAAATGCAATTAAGTCTCTTTCTCTCTCTTTTGCATCAATTAAACACTT
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAG-CTCTTGCTCTCTCTTTTGCATCAATTAAACACTT
* *
40678929 AAACTTTCAAAATGCATCAAACAGGC
65 AAACTTTCAAAATACATCAAACAGAC
* * * ***
40678955 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCTCTTGCT-TTTTTTTTTCACTCAATTAGGTACTT
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCTCTTGCTCTCTCTTTTGCA-TCAATTAAACACTT
*
40679019 GAACTTTCAAAATACATCAAGA-AGAC
65 AAACTTTCAAAATACATCAA-ACAGAC
* * *
40679045 CCTCAAAATTTTTC-AAAAAAGCAATTAAGCCCATGCTCT
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCTCTTGCTCT
40679084 TATTAAAAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
89 29 0.26
90 53 0.47
91 30 0.27
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.35
Consensus pattern (90 bp):
CCTCAAATTTTTTCAAAAAAAGCAATTAAGCTCTTGCTCTCTCTTTTGCATCAATTAAACACTTA
AACTTTCAAAATACATCAAACAGAC
Found at i:40679134 original size:15 final size:15
Alignment explanation
Indices: 40679116--40679167 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
40679106 ATAAAAAATA
40679116 AAAAATTTAAATTTT
1 AAAAATTTAAATTTT
* * *
40679131 AAAAATATAAAATAT
1 AAAAATTTAAATTTT
*
40679146 AAAAATATAAAATTTT
1 AAAAAT-TTAAATTTT
40679162 ATAAAA
1 A-AAAA
40679168 ATCATAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 18 0.64
16 6 0.21
17 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATTTAAATTTT
Found at i:40679148 original size:31 final size:33
Alignment explanation
Indices: 40679099--40679178 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 33
40679089 AAAATTAGAA
*
40679099 AAAAATTATAAAAAATAAAAA-ATTTAAA-TTT-T
1 AAAAA-TATAAAAAATAAAAATA-TAAAATTTTAT
*
40679131 AAAAATATAAAATATAAAAATATAAAATTTTAT
1 AAAAATATAAAAAATAAAAATATAAAATTTTAT
40679164 AAAAATCATAAAAAA
1 AAAAAT-ATAAAAAA
40679179 AAACTAGGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 18 0.44
32 9 0.22
33 7 0.17
34 7 0.17
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (33 bp):
AAAAATATAAAAAATAAAAATATAAAATTTTAT
Found at i:40681263 original size:241 final size:241
Alignment explanation
Indices: 40680800--40681359 Score: 656
Period size: 241 Copynumber: 2.3 Consensus size: 241
40680790 ATTTAGGGGG
*
40680800 AAAA-ATAGGATCGTAGAATTCTAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATA
1 AAAATATAGGATCGTAGAA-TCTAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATT
* * * * * *
40680864 ATTGTTTTTAATAAAGTTTCGTAGCTAATAAATTTATTAATCTGAATTATTATTTATTTTTCGAA
65 ATTG--TTTAAT--A-TTCCGTACCTAACAAATTGAATAATCTGAATAATTATTTATTTTT--AA
* * *
40680929 ATTTGATAAAAAAGTTATGTTGTTTTTTCTTTGTCTTCATTTTTGTTTCTCAATTGTTAATTCCA
123 ATTTGATAAAAAAGTTAGGTTGTTTTTTCTTTGTCATCATTTTTGTTTCTCAATTATTAATTCCA
*
40680994 ATGCGCTAGTTTGTGGAAGTAGGTTTTTCATTTC-GAGTTGTATATAGGGG-AAA
188 ATGCGCCAGTTTGTGGAAGTAGGTTTTTCATTTCGGA-TTGTATATAGGGGAAAA
* * *
40681047 AGAA-A-A-GATCGTAGAATCTAAATTTATAGTCAATTATATCAGCCTAACATTTTTGTTAATTA
1 AAAATATAGGATCGTAGAATCTAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATTA
* *
40681109 TTGTTTCAT-TTCCGTACCTAACAAATTGAATAATCTGAATAAGTTATTTATTATTT-ATTTTGC
66 TTGTTTAATATTCCGTACCTAACAAATTGAATAATCTGAATAA-TTATTTATT-TTTAAATTTG-
* *
40681172 ACTGATAAAAGATTAGGTTGTTTTTTCTTTGTCATCATTTTT-TCTTCTCAATTATTAATTTCAA
128 A-T-AAAAAAG-TTAGGTTGTTTTTTCTTTGTCATCATTTTTGT-TTCTCAATTATTAATTCCAA
* * * *
40681236 TGCGCCATTTTGTGGAATTTA-GTTTTTCATTTTGGATTGTATTTAGGGGAAAA
189 TGCGCCAGTTTGTGGAA-GTAGGTTTTTCATTTCGGATTGTATATAGGGGAAAA
* * *
40681289 AAAATATAGGATCTTGGAAT-TGAAATTTATATTCAATTAAATCAGCCTAATATTTTTGTTAATT
1 AAAATATAGGATCGTAGAATCT-AAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATT
40681353 ATTGTTT
65 ATTGTTT
40681360 GTTTCTAATC
Statistics
Matches: 271, Mismatches: 28, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
237 5 0.02
238 28 0.10
239 10 0.04
240 10 0.04
241 84 0.31
242 15 0.06
243 1 0.00
244 48 0.18
245 65 0.24
246 1 0.00
247 4 0.01
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (241 bp):
AAAATATAGGATCGTAGAATCTAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATTA
TTGTTTAATATTCCGTACCTAACAAATTGAATAATCTGAATAATTATTTATTTTTAAATTTGATA
AAAAAGTTAGGTTGTTTTTTCTTTGTCATCATTTTTGTTTCTCAATTATTAATTCCAATGCGCCA
GTTTGTGGAAGTAGGTTTTTCATTTCGGATTGTATATAGGGGAAAA
Found at i:40685488 original size:22 final size:22
Alignment explanation
Indices: 40685463--40685532 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 22
40685453 CTGAATTATA
40685463 TATTAATATATTATTTTTATTT
1 TATTAATATATTATTTTTATTT
** * *
40685485 TATTTTTA-ATTATTTTAAATT
1 TATTAATATATTATTTTTATTT
* *
40685506 T-TTAATATAACTATTTTTTATTA
1 TATTAATAT-ATTA-TTTTTATTT
40685529 TATT
1 TATT
40685533 GTTAATTTGT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
20 4 0.12
21 12 0.35
22 9 0.26
23 7 0.21
24 2 0.06
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTAATATATTATTTTTATTT
Found at i:40685499 original size:15 final size:16
Alignment explanation
Indices: 40685479--40685511 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40685469 TATATTATTT
40685479 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
40685494 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
40685511 T
1 T
40685512 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:40685597 original size:22 final size:22
Alignment explanation
Indices: 40685558--40685616 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
40685548 GTTTTAAGAA
*
40685558 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
40685579 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
40685601 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
40685617 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:40685633 original size:26 final size:24
Alignment explanation
Indices: 40685587--40685646 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
40685577 ATTTGTTTTA
*
40685587 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
40685611 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
40685637 TTTTTTATTT
1 ATATTTATTT
40685647 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Done.