Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 96 of 128
Found at i:31662124 original size:12 final size:12
Alignment explanation
Indices: 31662107--31662138 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
31662097 AATATTAACA
31662107 TGTTGTGATGAC
1 TGTTGTGATGAC
31662119 TGTTGTGATGAC
1 TGTTGTGATGAC
31662131 TGTTGTGA
1 TGTTGTGA
31662139 CGATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.34, T:0.44
Consensus pattern (12 bp):
TGTTGTGATGAC
Found at i:31664017 original size:17 final size:17
Alignment explanation
Indices: 31663996--31664038 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
31663986 ACGGAATTAG
31663996 AATTTAGTTGAGAAAATT
1 AATTTAGTTGAG-AAATT
*
31664014 -ATTTAATTGAGAAATT
1 AATTTAGTTGAGAAATT
31664030 AATTTAGTT
1 AATTTAGTT
31664039 AATTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (17 bp):
AATTTAGTTGAGAAATT
Found at i:31664959 original size:25 final size:25
Alignment explanation
Indices: 31664902--31664959 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
31664892 AAAAGCATTC
*
31664902 ATTCATTAGGTCATATATACTTAGG
1 ATTCATTTGGTCATATATACTTAGG
31664927 ATTCATTTGGTCATATATACTTAGG
1 ATTCATTTGGTCATATATACTTAGG
31664952 ATTCATTT
1 ATTCATTT
31664960 TATTTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (25 bp):
ATTCATTTGGTCATATATACTTAGG
Found at i:31684921 original size:4 final size:4
Alignment explanation
Indices: 31684914--31684943 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
31684904 ATGATTTTTC
31684914 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
31684944 AGTTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:31688747 original size:137 final size:137
Alignment explanation
Indices: 31688399--31688912 Score: 773
Period size: 137 Copynumber: 3.8 Consensus size: 137
31688389 ACTGGTCCTA
* * *
31688399 AATGTCCTAT-CGGTGGCTGAGTT-CTGACATTTGTTGCGGATACTCGACAACTTGTGTGAGCAG
1 AATGTCCT-TCCGGTGGCTGAGTTCCAG-CATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAG
* *
31688462 CACTGTGTAGCTACGTTCCAACCGACAGCTTGTGTGAGCAGACCTAGGTTATCATGTTTCAGGTG
64 CACTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTG
*
31688527 TTGGTGTTG
129 TTGGTGATG
* *
31688536 -ATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGGAGATACTCGATAGCTTGTGTGAGCAGCA
1 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
* * *
31688600 CTGTGTAGCTACATTCCAACCGATAGCTTGTGTGAGCAAACCCAGGTTATCATGTTTTAGGTGTT
66 CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTGTT
31688665 GGTGATG
131 GGTGATG
* **
31688672 AATGTCCTTCCGGTGGCTGAGTTCTAGCATTTGTTGCAGATACTCGACAGCTTACGTGAGCAGCA
1 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
* * * *
31688737 CTGTGTAGCTACATTCCAATCAACAGCTTGTGTGAGCAGACCCAGGTTATCATCTTTCAAGTGTT
66 CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTGTT
*
31688802 GGTGCTG
131 GGTGATG
* *
31688809 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGTAGATACTCGACAGCTTGTGTGACCAGCA
1 AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
** *
31688874 CTGTGTAGCTACATTCCAATTGACAGCTTGTGTAAGCAG
66 CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAG
31688913 GCTCATTTAT
Statistics
Matches: 342, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
135 1 0.00
136 120 0.35
137 221 0.65
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (137 bp):
AATGTCCTTCCGGTGGCTGAGTTCCAGCATTTGTTGCAGATACTCGACAGCTTGTGTGAGCAGCA
CTGTGTAGCTACATTCCAACCGACAGCTTGTGTGAGCAGACCCAGGTTATCATGTTTCAGGTGTT
GGTGATG
Found at i:31695469 original size:25 final size:25
Alignment explanation
Indices: 31695437--31695534 Score: 60
Period size: 25 Copynumber: 4.0 Consensus size: 25
31695427 AGCTCTCCCT
31695437 TGAGCCATATAATC-GGAAGCTCATA
1 TGAGCCATATAA-CAGGAAGCTCATA
* * * * *
31695462 TGAGCCATGTAACGGGAAACTTATC
1 TGAGCCATATAACAGGAAGCTCATA
* **
31695487 TGGGCTGTATAAC-GGAAAGCTCATA
1 TGAGCCATATAACAGG-AAGCTCATA
*
31695512 AGAG-C-TATAATCAGGAAGCTCAT
1 TGAGCCATATAA-CAGGAAGCTCAT
31695535 GCAAGCCTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
23 5 0.09
24 12 0.22
25 38 0.69
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATA
Found at i:31695662 original size:26 final size:26
Alignment explanation
Indices: 31695632--31695691 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
31695622 GTAGCTCTGG
31695632 AGAGCCATTAATTAG-GAAGCTCATAA
1 AGAGCCATTAA-TAGAGAAGCTCATAA
* * *
31695658 AGAGCCTTTAATCGAGAAGCTCATGA
1 AGAGCCATTAATAGAGAAGCTCATAA
31695684 AGAGCCAT
1 AGAGCCAT
31695692 ACATCGGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (26 bp):
AGAGCCATTAATAGAGAAGCTCATAA
Found at i:31695697 original size:26 final size:25
Alignment explanation
Indices: 31695647--31695713 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
31695637 CATTAATTAG
*
31695647 GAAGCTCATAAAGAGCCTTTAATCGA
1 GAAGCTCAT-AAGAGCCTATAATCGA
*
31695673 GAAGCTCATGAAGAGCC-ATACATCGG
1 GAAGCTCAT-AAGAGCCTATA-ATCGA
*
31695699 GACGCTCATAAGAGC
1 GAAGCTCATAAGAGC
31695714 TGTGGTGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 8 0.22
26 28 0.78
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCTATAATCGA
Found at i:31696360 original size:19 final size:18
Alignment explanation
Indices: 31696314--31696361 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
31696304 GATAGAATTT
*
31696314 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
31696333 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
31696351 TTGTATTAAAA
1 TTGTA-TAAAA
31696362 ATTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:31697370 original size:110 final size:111
Alignment explanation
Indices: 31697164--31697385 Score: 410
Period size: 110 Copynumber: 2.0 Consensus size: 111
31697154 CATGAAGTAT
* *
31697164 TTCCCGCCGAGCAAGAATGCCAAGTTGTGGAATGAGATCACTGCCTTCCAAAAAATGGATGATGA
1 TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAAAAAATAGATGATGA
31697229 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
66 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
*
31697275 TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCC-TCCAACAAATAGATGATGA
1 TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAAAAAATAGATGATGA
31697339 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
66 GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
31697385 T
1 T
31697386 GCCCTCATCA
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 64 0.59
111 44 0.41
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (111 bp):
TTCCCGCCGAGCAAGAATGCCAAGTTGAGGAATGAGATCACTGCCTTCCAAAAAATAGATGATGA
GTCCCTGTATGAAGCATGGGAAAGGTACAAAGAGTTATTACGAAAG
Found at i:31706096 original size:19 final size:18
Alignment explanation
Indices: 31706055--31706092 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31706045 AATTTTTGTC
*
31706055 ATAAAATAATTAATTTTT
1 ATAAAATAATTAAATTTT
31706073 ATAAAATAATTAAATTTT
1 ATAAAATAATTAAATTTT
31706091 AT
1 AT
31706093 TAAAGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAAATAATTAAATTTT
Found at i:31706732 original size:14 final size:14
Alignment explanation
Indices: 31706709--31706738 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31706699 CGTCCCTCAT
*
31706709 TCACATCTCTTCTC
1 TCACAACTCTTCTC
31706723 TCACAACTCTTCTC
1 TCACAACTCTTCTC
31706737 TC
1 TC
31706739 CTCTCTTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:31708766 original size:14 final size:14
Alignment explanation
Indices: 31708749--31708779 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31708739 ATTAATTTTC
31708749 CATGGATGGATCAT
1 CATGGATGGATCAT
31708763 CATGGATGGATCAT
1 CATGGATGGATCAT
31708777 CAT
1 CAT
31708780 ACTTATCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (14 bp):
CATGGATGGATCAT
Found at i:31723416 original size:18 final size:18
Alignment explanation
Indices: 31723393--31723431 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
31723383 AGGAAGATAG
31723393 TGACCCACTCACATATGA
1 TGACCCACTCACATATGA
*
31723411 TGACCCACTTACATATGA
1 TGACCCACTCACATATGA
31723429 TGA
1 TGA
31723432 AGAGATGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (18 bp):
TGACCCACTCACATATGA
Found at i:31734459 original size:44 final size:45
Alignment explanation
Indices: 31734380--31734602 Score: 148
Period size: 44 Copynumber: 4.8 Consensus size: 45
31734370 CATGGCAGAT
* *
31734380 CTTATCTTCCTGAAGTTGGAGTGGAGCAGATTGAAGCCACT-AGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
* * * * * **
31734424 CTTATCTCCCTGAAGTTGCAGCGGAACAGACTGAAGACAGTGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
* * *
31734469 CTTATCTCCCT-ATCA-TTGCAGTGGAACAGATTAAAGCTACAAATCATGGCAGAT
1 CTTATCTCCCTGA--AGTTGCAGTGGAGCAGATTGAAGC--C--A-C-T-G-AG-C
* * *
31734523 CTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCAC-CAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
* ** *
31734567 CTTATCTCCATGAAGTTGCAGCAGAGCAGACTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
31734603 ACAGCAGATC
Statistics
Matches: 139, Mismatches: 26, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
44 66 0.47
45 32 0.23
46 1 0.01
47 1 0.01
49 2 0.01
50 1 0.01
51 1 0.01
52 2 0.01
53 2 0.01
54 30 0.22
55 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTGAGC
Found at i:31735317 original size:143 final size:143
Alignment explanation
Indices: 31734225--31735309 Score: 1405
Period size: 143 Copynumber: 7.6 Consensus size: 143
31734215 GATTGAAGTC
* * * * * * * *
31734225 ATTACGGCAAATCTCATCTTCTTAAAGTTGCAGTGCAGCATATTGAAGTCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * * * * * * *
31734290 CTAAAGTTACAGCAGAGCAGACTAAAGATAGTGGATCTGATCTCCCTGGAGTTACAGTGGAATAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
**
31734355 ATTAACTCTACAA
131 ATTAAAGCTACAA
* * *
31734368 ATCATGGCAGATCTTATCTTCCTGAAGTTGGAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
31734433 CTGAAGTTGCAGCGGAACAGACTGAAGACAGTGAATCTTATCTCCCTATCATTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
31734498 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* *
31734511 ATCATGGCAGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * ** *
31734576 ATGAAGTTGCAGCAGAGCAGACTGAAGACAGCAGATCTTATTTATCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
31734641 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * *
31734654 ATTATGGCAAATTTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * * *
31734719 CTGAAGTTGTAGCAGAGCAGACTAAAGATAGCGAATCTTATTTCCCTAGTGTTGTAGTGGAACAA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
31734784 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
31734797 ATTTTGGCGGATATTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAAGACACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* *
31734862 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGTGGATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
31734927 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
31734940 ATTATGGCAGATCTTATCTTTCTAAAGTTGCAGTAGAGCAGATTGAAACCACCAGCCTTGTCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
31735005 CTGAAGTTGCAGCGTAGCAGACTGAAGATAGCGGATCTTATTTCCCTGGCGTTGCAGTGGAATAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
*
31735070 ATTAAAGCTAAAA
131 ATTAAAGCTACAA
** * *
31735083 ATTATGGTGGATATTATTTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
31735148 CTAAATTTACAGCGGAGTAGACTGAAGACAGCGGATTTTATTTCCCTAGCGCTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
31735213 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
31735226 ACTATGACAGATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTTAAGCTACCAGCCTTATCTCC
1 ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* *
31735291 TTGAAGTTGCAGTGGAGCA
66 CTGAAGTTGCAGCGGAGCA
31735310 AATTGAAGTT
Statistics
Matches: 814, Mismatches: 128, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
143 814 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (143 bp):
ATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAGCGTTGCAGTGGAACAG
ATTAAAGCTACAA
Found at i:31740729 original size:9 final size:10
Alignment explanation
Indices: 31740703--31740730 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
31740693 TCGGTAGAAA
31740703 AAGAAAAAAT
1 AAGAAAAAAT
31740713 AAGAAAAAAT
1 AAGAAAAAAT
31740723 AAGAAAAA
1 AAGAAAAA
31740731 GAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAGAAAAAAT
Found at i:31754394 original size:44 final size:43
Alignment explanation
Indices: 31754346--31754794 Score: 138
Period size: 44 Copynumber: 10.2 Consensus size: 43
31754336 AAGATTGTAG
*
31754346 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCA-TAGTGGAGCAGATTAAAGACGGCAA
* * * * ** *
31754390 ATCTTATCTTTCC-AAG-ATAGTGGGAAGCGGATTTAAGCCACCGA
1 ATCTTATC-TCCCTAAGCATAGT-GG-AGCAGATTAAAGACGGCAA
* * * * * * * * * ** * *
31754434 ACCTTGTCTCCCTGAGTTACAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAG-CATAGTGGAGCAGATTAAAGACGGCAA
* *
31754478 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACGGCAA
1 ATCTTATCTCCCTAAGCA-TAGTGGAGCAGATTAAAGACGGCAA
* * * * ** *
31754522 ATCTTATCTTTCC-AAG-ATAGTGGGAAGCGGATTTAAGCCACCGA
1 ATCTTATC-TCCCTAAGCATAGT-GG-AGCAGATTAAAGACGGCAA
* * * * * * * * ** *
31754566 ACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATTGCAG
1 ATCTTATCTCCCTAAGC-ATAGTGGAGCAGATTAAAGACGGCAA
* *
31754610 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCA-TAGTGGAGCAGATTAAAGACGGCAA
* * ***
31754654 ATCTTATCTTTCC-AAG-ATAGTGGGAAGCAGATTTAAG-CCATAA
1 ATCTTATC-TCCCTAAGCATAGT-GG-AGCAGATTAAAGACGGCAA
* * * * * * * * ** * *
31754697 AGCCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATTGTAG
1 A-TCTTATCTCCCTAAGC-ATAGTGGAGCAGATTAAAGACGGCAA
* *
31754742 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCA-TAGTGGAGCAGATTAAAGACGGCAA
31754786 ATCTTATCT
1 ATCTTATCT
31754795 TTCCAAGATA
Statistics
Matches: 272, Mismatches: 110, Indels: 46
0.64 0.26 0.11
Matches are distributed among these distances:
42 12 0.04
43 26 0.10
44 207 0.76
45 18 0.07
46 9 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (43 bp):
ATCTTATCTCCCTAAGCATAGTGGAGCAGATTAAAGACGGCAA
Found at i:31754449 original size:132 final size:132
Alignment explanation
Indices: 31754212--31754883 Score: 1121
Period size: 132 Copynumber: 5.1 Consensus size: 132
31754202 TAAGGATAGC
* * * * *
31754212 AGATCTTATCTCACTAGGCAGTAGTGGAGCAGATCGAAGACGCCAAATCTTATCTTTCCAATATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
31754277 GTGGGAAGCAGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
31754342 GT
131 GT
*
31754344 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
* **
31754409 GTGGGAAGCGGATTTAAGCCACCGAACCTTGTCTCCCTGAGTTACAGCGGAGTAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
31754474 GT
131 GT
* *
31754476 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACGGCAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
*
31754541 GTGGGAAGCGGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
*
31754606 GC
131 GT
31754608 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
**
31754673 GTGGGAAGCAGATTTAAGCCA-TAAAGCCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGAT
66 GTGGGAAGCAGATTTAAGCCACCGAA-CCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGAT
31754737 TGT
130 TGT
31754740 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
* * ** *
31754805 GTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGTAGAGTAGGTTGAAAATT
66 GTGGGAAGCAGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
**
31754870 AC
131 GT
*
31754872 AGGTCTTATCTC
1 AGATCTTATCTC
31754884 TCTGAAGTTG
Statistics
Matches: 510, Mismatches: 28, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.00
132 507 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (132 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATA
GTGGGAAGCAGATTTAAGCCACCGAACCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATT
GT
Found at i:31770528 original size:11 final size:10
Alignment explanation
Indices: 31770514--31770565 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
31770504 ATTCTCTTTC
*
31770514 TTTTCTTTTGA
1 TTTTATTTT-A
31770525 TTTTATTTTA
1 TTTTATTTTA
31770535 TTTTATTTTTA
1 TTTTA-TTTTA
31770546 TTATTATTATTA
1 TT-TTATT-TTA
31770558 TTATTATT
1 TT-TTATT
31770566 GTTGTTGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 6 0.16
11 17 0.46
12 14 0.38
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:31770551 original size:3 final size:3
Alignment explanation
Indices: 31770527--31770565 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
31770517 TCTTTTGATT
*
31770527 TTA TT- TTA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31770566 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:31770570 original size:3 final size:3
Alignment explanation
Indices: 31770564--31770598 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31770554 ATTATTATTA
31770564 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
31770599 ATTATTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:31772095 original size:36 final size:36
Alignment explanation
Indices: 31772041--31772158 Score: 130
Period size: 36 Copynumber: 3.3 Consensus size: 36
31772031 CTCTCTATTT
* * *
31772041 TGGTGTGTTTCTGTTGGATTAAATCTTCGGAGC-TAC
1 TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCAT-C
** ** *
31772077 TGGTGTGTTTCAGATGGATTAGCTCTAATGAGCATT
1 TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCATC
* *
31772113 TGGTGTGTTTCAGATGGACTAATTCTTCTGAGCATC
1 TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCATC
31772149 TGGTGTGTTT
1 TGGTGTGTTT
31772159 TGTTGGTATT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
36 66 0.99
37 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.42
Consensus pattern (36 bp):
TGGTGTGTTTCAGATGGATTAAATCTTCTGAGCATC
Found at i:31780721 original size:19 final size:20
Alignment explanation
Indices: 31780684--31780723 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
31780674 AAACAAATTT
*
31780684 AGAAAATAACAAAAGAAATA
1 AGAAAATAACAAAAAAAATA
*
31780704 AGAAAA-AATAAAAAAAATA
1 AGAAAATAACAAAAAAAATA
31780723 A
1 A
31780724 AGGATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (20 bp):
AGAAAATAACAAAAAAAATA
Found at i:31784481 original size:16 final size:16
Alignment explanation
Indices: 31784460--31784498 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
31784450 ATTTAATAAA
31784460 ATTCTTAATAATCAAT
1 ATTCTTAATAATCAAT
31784476 ATTCTTAATAATCAAT
1 ATTCTTAATAATCAAT
31784492 ATTCTTA
1 ATTCTTA
31784499 TAACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTCTTAATAATCAAT
Found at i:31790019 original size:13 final size:13
Alignment explanation
Indices: 31789993--31790029 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
31789983 AAACATCAAC
31789993 TAATTTTT-TATA
1 TAATTTTTATATA
31790005 T-ATTTTTCATATA
1 TAATTTTT-ATATA
31790018 TAATTTTTATAT
1 TAATTTTTATAT
31790030 GTGAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 1 0.05
13 9 0.41
14 6 0.27
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TAATTTTTATATA
Found at i:31790203 original size:46 final size:46
Alignment explanation
Indices: 31790154--31790279 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 46
31790144 ATGCAGGTGA
*
31790154 AAAAAT-ATTGATATTTGAATTAATTATTTGAAATATTTCACATAT
1 AAAAATAATTGATATTTGAAATAATTATTTGAAATATTTCACATAT
*** * *
31790199 AAAAATAAAAAATATTTGAAATAATTTTTTTGAAATATTTCACATGT
1 AAAAATAATTGATATTTGAAATAA-TTATTTGAAATATTTCACATAT
31790246 AAAAATAATTGTGATATTTGAAATAATTATTTGA
1 AAAAATAA-T-TGATATTTGAAATAATTATTTGA
31790280 TTTTATAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 6 0.09
46 13 0.19
47 28 0.42
48 7 0.10
49 13 0.19
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (46 bp):
AAAAATAATTGATATTTGAAATAATTATTTGAAATATTTCACATAT
Found at i:31791257 original size:19 final size:19
Alignment explanation
Indices: 31791233--31791273 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
31791223 TGATTTATTC
31791233 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
31791252 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
31791271 TAA
1 TAA
31791274 CTTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:31796743 original size:41 final size:41
Alignment explanation
Indices: 31796659--31796746 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 41
31796649 ACCGGCTTTT
* * *
31796659 AGCCTGCTAGACTTATTGTCTGAAATGTATCACCGACATTA
1 AGCCTGCTAGACGTATAGTCTGAAATGTATCACCGACAATA
*
31796700 AGCCTGCTAGACGTATAGTCTGAATAAT-T-TCACTGACAATA
1 AGCCTGCTAGACGTATAGTCTG-A-AATGTATCACCGACAATA
31796741 AGCCTG
1 AGCCTG
31796747 ATAGGCACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 36 0.88
42 2 0.05
43 3 0.07
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACGTATAGTCTGAAATGTATCACCGACAATA
Found at i:31800267 original size:49 final size:49
Alignment explanation
Indices: 31800153--31800330 Score: 180
Period size: 49 Copynumber: 3.6 Consensus size: 49
31800143 TCATGAGAGG
* * * **
31800153 TCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGATATGAGAAC
** *
31800203 TCCCCCGTAAGACCATGTCGGGGACATGGCATGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGATATGAGAAC
* * * * * **
31800252 TCCCATGTAAAACCATATCTGGGATATGGCATTG-ACAG-TACAAGAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGATATGAG-AAC
31800300 ATCCCATGTAAGACCATGTCTGGGACATGGC
1 -TCCCATGTAAGACCATGTCTGGGACATGGC
31800331 TTTGGCATGT
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
47 4 0.04
48 6 0.06
49 69 0.66
50 26 0.25
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGATATGAGAAC
Found at i:31800337 original size:99 final size:102
Alignment explanation
Indices: 31800096--31800338 Score: 244
Period size: 99 Copynumber: 2.4 Consensus size: 102
31800086 GGGTAAAGAG
* **
31800096 ATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATCATGAGAGGTCCCATGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGC-TTGGCATC--T-AGATCATGAGAACTCCCATGT
* * * * * * * *
31800161 AAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAG
62 AAAACCATATCTGGGATATGGCATTGGCACAGACAAGAAAC
* ** * * *
31800202 GTCCCCCGTAAGACCATGTCGGGGACATGGCATGGCA-C-CGAT-ATGAGAACTCCCATGTAAAA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCTTGGCATCTAGATCATGAGAACTCCCATGTAAAA
31800264 CCATATCTGGGATATGGCATT-G-ACAGTACAAGAAAC
66 CCATATCTGGGATATGGCATTGGCACAG-ACAAGAAAC
31800300 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGC-TTGGCAT
31800339 GTTATTATCA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
97 3 0.03
98 33 0.29
99 41 0.37
100 3 0.03
104 1 0.01
105 5 0.04
106 26 0.23
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (102 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCTTGGCATCTAGATCATGAGAACTCCCATGTAAAA
CCATATCTGGGATATGGCATTGGCACAGACAAGAAAC
Found at i:31805860 original size:50 final size:50
Alignment explanation
Indices: 31805755--31805921 Score: 178
Period size: 50 Copynumber: 3.4 Consensus size: 50
31805745 GGGGTGTTAC
* *
31805755 ACATGGTCTTACATGGGATGTT-TCTTGTAC--TGCCAATGCCATATCCCAG
1 ACATGGTCTTACATGGGA-GTTCTCATAT-CGGTGCCAATGCCATATCCCAG
* * * *
31805804 ATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAA
1 ACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATGCCATATCCCAG
** ** * **
31805854 ACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACACCATATCCCAG
1 ACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATGCCATATCCCAG
31805904 ACATGGTCTTACATGGGA
1 ACATGGTCTTACATGGGA
31805922 CCTCTCATGA
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
48 4 0.04
49 21 0.22
50 71 0.74
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
ACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATGCCATATCCCAG
Found at i:31807768 original size:21 final size:21
Alignment explanation
Indices: 31807744--31807844 Score: 78
Period size: 21 Copynumber: 4.8 Consensus size: 21
31807734 CAGAAGCTCT
* *
31807744 TAAGAGCTGAACGGAAACCCA
1 TAAGAGCTAAACGGAAACTCA
* * *
31807765 TAAGGGTTAAACAGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
*
31807786 AAAGAGCTAAACGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * * *
31807807 TATGAGTTAAAC-AAAAGCTCG
1 TAAGAGCTAAACGGAAA-CTCA
* *
31807828 TGAGAGCTAAATGGAAA
1 TAAGAGCTAAACGGAAA
31807845 GTAAACACGA
Statistics
Matches: 59, Mismatches: 19, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (21 bp):
TAAGAGCTAAACGGAAACTCA
Found at i:31807772 original size:42 final size:42
Alignment explanation
Indices: 31807690--31807844 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 42
31807680 CCGAAGGCTG
* ** ** * *
31807690 AACAGAAGCTCATAAGAGCCAAACAAAAACGTATACGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* *
31807732 AACAGAAGCTCTTAAGAGCTGAACGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * * *
31807774 AACAGAAACTCAAAAGAGCTAAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * *
31807816 AACAAAAGCTCGTGAGAGCTAAATGGAAA
1 AACAGAAGCTCATAAGAGCTAAACGGAAA
31807845 GTAAACACGA
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
Found at i:31808190 original size:20 final size:20
Alignment explanation
Indices: 31808165--31808205 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
31808155 AGTATCTACG
31808165 AGCTCTTAATCTAAAATATA
1 AGCTCTTAATCTAAAATATA
31808185 AGCTCTTAATCTAAAATATA
1 AGCTCTTAATCTAAAATATA
31808205 A
1 A
31808206 AATTACTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (20 bp):
AGCTCTTAATCTAAAATATA
Found at i:31808291 original size:26 final size:26
Alignment explanation
Indices: 31808262--31808314 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31808252 ATTAATACCC
31808262 CTTAATTTTTCAAATTTACACAATTA
1 CTTAATTTTTCAAATTTACACAATTA
31808288 CTTAATTTTTCAAATTTACACAATTA
1 CTTAATTTTTCAAATTTACACAATTA
31808314 C
1 C
31808315 CCCAACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (26 bp):
CTTAATTTTTCAAATTTACACAATTA
Found at i:31812124 original size:12 final size:12
Alignment explanation
Indices: 31812107--31812132 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31812097 TATAAAATTT
31812107 ATATATAAAAAA
1 ATATATAAAAAA
31812119 ATATATAAAAAA
1 ATATATAAAAAA
31812131 AT
1 AT
31812133 TAGTTGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATATATAAAAAA
Found at i:31813351 original size:7 final size:7
Alignment explanation
Indices: 31813339--31813370 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31813329 CGGGCAATTG
31813339 TCTCCAC
1 TCTCCAC
31813346 TCTCCAC
1 TCTCCAC
31813353 TCTCCAC
1 TCTCCAC
*
31813360 TCTTCAC
1 TCTCCAC
31813367 TCTC
1 TCTC
31813371 ATCCAATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.34
Consensus pattern (7 bp):
TCTCCAC
Found at i:31822248 original size:92 final size:92
Alignment explanation
Indices: 31822091--31822277 Score: 374
Period size: 92 Copynumber: 2.0 Consensus size: 92
31822081 GCACCACGTG
31822091 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
1 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
31822156 AAGACCTTGTTTTTCATATAGTGGGCA
66 AAGACCTTGTTTTTCATATAGTGGGCA
31822183 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
1 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
31822248 AAGACCTTGTTTTTCATATAGTGGGCA
66 AAGACCTTGTTTTTCATATAGTGGGCA
31822275 GCT
1 GCT
31822278 TGCTTATTTC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 95 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (92 bp):
GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
AAGACCTTGTTTTTCATATAGTGGGCA
Found at i:31823995 original size:12 final size:12
Alignment explanation
Indices: 31823978--31824002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31823968 CCAAGTTTCT
31823978 TTTATTTATTTG
1 TTTATTTATTTG
31823990 TTTATTTATTTG
1 TTTATTTATTTG
31824002 T
1 T
31824003 CACTTCAGGA
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:31839150 original size:50 final size:50
Alignment explanation
Indices: 31839048--31839337 Score: 287
Period size: 50 Copynumber: 5.7 Consensus size: 50
31839038 TAAAGAGATT
* *
31839048 CCATGTAATACCATGTCTGGGACATGGCATTGGCATCAATGAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTC
* *
31839104 CCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* *
31839154 TCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
** * * **
31839204 CCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAATTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * * * * * * **
31839254 CCATATAATACCATATTTGGGATATGACATTGGCA--GTATAGGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTC
*
31839303 CCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31839338 TGTTATTATC
Statistics
Matches: 197, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 36 0.18
50 123 0.62
53 3 0.02
55 1 0.01
56 33 0.17
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:31840100 original size:24 final size:25
Alignment explanation
Indices: 31840073--31840124 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
31840063 AATGAAAGCT
31840073 TATTGA-TCTACTTTCATAGAAAAA
1 TATTGAGTCTACTTTCATAGAAAAA
31840097 TATTGAGTCTACTTTCATAGAAAAA
1 TATTGAGTCTACTTTCATAGAAAAA
31840122 TAT
1 TAT
31840125 CGGTCCAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (25 bp):
TATTGAGTCTACTTTCATAGAAAAA
Found at i:31845861 original size:32 final size:32
Alignment explanation
Indices: 31845817--31845882 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
31845807 AAAGAGATCC
*
31845817 CATGTAATACCATGTCTGGGACATGGCATTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
*
31845849 CATGTAAGACCATGTTTGGGACATGGCATTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
31845881 CA
1 CA
31845883 CCGAGAGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (32 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGG
Found at i:31845924 original size:50 final size:50
Alignment explanation
Indices: 31845849--31846081 Score: 202
Period size: 50 Copynumber: 4.7 Consensus size: 50
31845839 ATGGCATTGG
*
31845849 CATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
* * *
31845899 CATGTAAGACCATGTCTGGGACATGGCGTTGGCAACGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
*** * * * * ** **
31845949 CCCATAAGACTATGTCTGAGACATGACA-TGGACACCGATATAAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGAGGAGAGGTCC
* * * * ** * **
31845999 CATGTAAGAACATATCTGGGATATGACATTGGCA--GTACTGGAAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGAGGAGAGGTCC
*
31846048 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
31846082 TGTTATTATC
Statistics
Matches: 144, Mismatches: 36, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
48 1 0.01
49 38 0.26
50 102 0.71
51 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
Found at i:31849731 original size:34 final size:36
Alignment explanation
Indices: 31849693--31849777 Score: 115
Period size: 34 Copynumber: 2.5 Consensus size: 36
31849683 TTGACAAAGC
31849693 TAGCTCGCATATAAACACAAC-T-CATATATAAACA
1 TAGCTCGCATATAAACACAACTTGCATATATAAACA
* **
31849727 TAGCTCGCATGTAAACACAACTTGCATATATGCACA
1 TAGCTCGCATATAAACACAACTTGCATATATAAACA
31849763 -A-CTCGCATATAAACA
1 TAGCTCGCATATAAACA
31849778 TAGCTAACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 33 0.73
35 2 0.04
36 10 0.22
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (36 bp):
TAGCTCGCATATAAACACAACTTGCATATATAAACA
Found at i:31849741 original size:17 final size:17
Alignment explanation
Indices: 31849693--31849782 Score: 72
Period size: 17 Copynumber: 5.3 Consensus size: 17
31849683 TTGACAAAGC
31849693 TAGCTCGCATATAAACA
1 TAGCTCGCATATAAACA
* * **
31849710 CAACTCATATATAAACA
1 TAGCTCGCATATAAACA
*
31849727 TAGCTCGCATGTAAACA
1 TAGCTCGCATATAAACA
* * * **
31849744 CAACTTGCATATATGCA
1 TAGCTCGCATATAAACA
* *
31849761 CAACTCGCATATAAACA
1 TAGCTCGCATATAAACA
31849778 TAGCT
1 TAGCT
31849783 AACATAGAAA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (17 bp):
TAGCTCGCATATAAACA
Found at i:31849775 original size:51 final size:51
Alignment explanation
Indices: 31849699--31849799 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
31849689 AAGCTAGCTC
* **
31849699 GCATATAAACACAACTCATATATAAACATAGCTCGCAT-GTAAACACAACTT
1 GCATATAAACACAACTCACATATAAACATAGCTAACATAG-AAACACAACTT
** *
31849750 GCATATATGCACAACTCGCATATAAACATAGCTAACATAGAAACACAACT
1 GCATATAAACACAACTCACATATAAACATAGCTAACATAGAAACACAACT
31849800 CGCACATTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.22
Consensus pattern (51 bp):
GCATATAAACACAACTCACATATAAACATAGCTAACATAGAAACACAACTT
Found at i:31852572 original size:20 final size:21
Alignment explanation
Indices: 31852535--31852592 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
31852525 TAGGACATTA
31852535 TATGATTATGATAAGATATGC
1 TATGATTATGATAAGATATGC
** *
31852556 TATG-TTATGATTTGATATGA
1 TATGATTATGATAAGATATGC
* *
31852576 AATGATT-CGATAAGATA
1 TATGATTATGATAAGATA
31852593 CGTTAAGATA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (21 bp):
TATGATTATGATAAGATATGC
Found at i:31858672 original size:31 final size:31
Alignment explanation
Indices: 31858637--31858699 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
31858627 AATGAAGATA
31858637 ATTCCCACCTCAATCTCGTATAAGATGACTG
1 ATTCCCACCTCAATCTCGTATAAGATGACTG
*
31858668 ATTCCCACCTCAATCTCGTATAGGATGACTG
1 ATTCCCACCTCAATCTCGTATAAGATGACTG
31858699 A
1 A
31858700 AAAAGATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (31 bp):
ATTCCCACCTCAATCTCGTATAAGATGACTG
Found at i:31859282 original size:24 final size:25
Alignment explanation
Indices: 31859250--31859301 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
31859240 TCTAAAAGAG
* *
31859250 TTAGTATTTATTAATATAATATA-T
1 TTAGCATTTATTAACATAATATAGT
*
31859274 TTAGCATTTATTAGCATAATATAGT
1 TTAGCATTTATTAACATAATATAGT
31859299 TTA
1 TTA
31859302 CATAAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (25 bp):
TTAGCATTTATTAACATAATATAGT
Found at i:31859310 original size:24 final size:24
Alignment explanation
Indices: 31859265--31859311 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31859255 ATTTATTAAT
**
31859265 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATAAATTAGC
31859289 ATAATATAGTTTA-CATAAATTAG
1 ATAATATA-TTTAGCATAAATTAG
31859312 AATTAGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (24 bp):
ATAATATATTTAGCATAAATTAGC
Found at i:31861551 original size:21 final size:22
Alignment explanation
Indices: 31861521--31861561 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31861511 TTCGTGTAAC
* *
31861521 TTGAATTATAT-TCTTAGATGA
1 TTGAAATATATATATTAGATGA
31861542 TTGAAATATATATATTAGAT
1 TTGAAATATATATATTAGAT
31861562 TGAGAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (22 bp):
TTGAAATATATATATTAGATGA
Found at i:31863052 original size:7 final size:7
Alignment explanation
Indices: 31863040--31863073 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
31863030 TGGAAGAATC
31863040 AAATGAG
1 AAATGAG
31863047 AAATGAG
1 AAATGAG
31863054 AAATGAG
1 AAATGAG
31863061 AAATGAG
1 AAATGAG
31863068 AAATGA
1 AAATGA
31863074 TTATGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (7 bp):
AAATGAG
Found at i:31876870 original size:42 final size:42
Alignment explanation
Indices: 31876824--31876908 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
31876814 ATAGAAGCAT
** *
31876824 ATAAGTGCTAAACAGAAACCCATGAGGGTTGAACGGAAGCTC
1 ATAAGTGCTAAACAGAAACCCACAAGGGTTAAACGGAAGCTC
* ** *
31876866 ATAAGTGCTGAATGGAAACCCACAAGGGTTAAACTGAAGCTC
1 ATAAGTGCTAAACAGAAACCCACAAGGGTTAAACGGAAGCTC
31876908 A
1 A
31876909 AAAGACTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.18
Consensus pattern (42 bp):
ATAAGTGCTAAACAGAAACCCACAAGGGTTAAACGGAAGCTC
Found at i:31876925 original size:42 final size:42
Alignment explanation
Indices: 31876838--31876945 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 42
31876828 GTGCTAAACA
** * * * *
31876838 GAAACCCATGAGGGTTGAACGGAAGCTCATAAGTGCTGAATG
1 GAAACCCACAAGGGTTAAACGGAAGCTCAAAAGTACTGAACG
*
31876880 GAAACCCACAAGGGTTAAACTGAAGCTCAAAAG-ACTTGAACG
1 GAAACCCACAAGGGTTAAACGGAAGCTCAAAAGTAC-TGAACG
** *
31876922 GAAACCCATTACGGTTAAACGGAA
1 GAAACCCACAAGGGTTAAACGGAA
31876946 AACGGAAACT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 53 0.98
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (42 bp):
GAAACCCACAAGGGTTAAACGGAAGCTCAAAAGTACTGAACG
Found at i:31889623 original size:111 final size:111
Alignment explanation
Indices: 31889429--31889759 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
31889419 CAATACCATG
31889429 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
31889494 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
31889540 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
31889605 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
* *
31889651 CATGTAGTTGTATTGCTGTATTAAAGTTTGTTTATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
31889716 GTTTATATGGTATACATATATCACTA--CTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
31889760 TACTTCATCA
Statistics
Matches: 218, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
109 18 0.08
111 200 0.92
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (111 bp):
CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
Found at i:31894351 original size:29 final size:29
Alignment explanation
Indices: 31894304--31894372 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
31894294 GAAGATGTGG
* *
31894304 AGAACTTGTTTATTGAGAGTTCGTGATGA
1 AGAACTTGTTCATTAAGAGTTCGTGATGA
31894333 AGAACTTGTTCATTAAGAGTTCGTGATGA
1 AGAACTTGTTCATTAAGAGTTCGTGATGA
31894362 AGAACTTGTTC
1 AGAACTTGTTC
31894373 GTTGAGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (29 bp):
AGAACTTGTTCATTAAGAGTTCGTGATGA
Found at i:31894504 original size:24 final size:24
Alignment explanation
Indices: 31894484--31894548 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
31894474 AAGATTTAGT
**
31894484 ACTTATTAGTGTAATATATTTAAC
1 ACTTATTAGCATAATATATTTAAC
* *
31894508 ATTTATTAGCATAATATATTTGAC
1 ACTTATTAGCATAATATATTTAAC
*
31894532 A-TTGATTAGAATAATAT
1 ACTT-ATTAGCATAATAT
31894549 TTTTCTACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (24 bp):
ACTTATTAGCATAATATATTTAAC
Found at i:31911044 original size:15 final size:15
Alignment explanation
Indices: 31911024--31911057 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
31911014 TTTATTGATT
31911024 ATTAATATTTTTTAG
1 ATTAATATTTTTTAG
31911039 ATTAATATTTTTTAG
1 ATTAATATTTTTTAG
31911054 ATTA
1 ATTA
31911058 TGACATCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTAATATTTTTTAG
Found at i:31924760 original size:26 final size:25
Alignment explanation
Indices: 31924730--31924795 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
31924720 GCAACTCTTA
* *
31924730 TGAGCGTCCCGTTATATGGCTCTTCG
1 TGAGCTTCCCGTTA-AAGGCTCTTCG
*
31924756 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCG-TTAAAGGCTCTTCG
31924782 TGAGCTTCCCGTTA
1 TGAGCTTCCCGTTA
31924796 GTGCTCGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.08
26 30 0.83
27 3 0.08
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGTTAAAGGCTCTTCG
Found at i:31924867 original size:24 final size:24
Alignment explanation
Indices: 31924840--31924891 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
31924830 GGTGTTGCGT
*
31924840 GTTAATTGCTCTTCGGAGCTACCC
1 GTTAATTGCTCTTCGAAGCTACCC
*
31924864 GTTAATTGCTCTTTGAAGCTACCC
1 GTTAATTGCTCTTCGAAGCTACCC
31924888 GTTA
1 GTTA
31924892 TAGGCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (24 bp):
GTTAATTGCTCTTCGAAGCTACCC
Found at i:31924898 original size:24 final size:24
Alignment explanation
Indices: 31924840--31924902 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
31924830 GGTGTTGCGT
* * *
31924840 GTTAATTGCTCTTCGGAGCTACCC
1 GTTAATGGCTCTTTGAAGCTACCC
*
31924864 GTTAATTGCTCTTTGAAGCTACCC
1 GTTAATGGCTCTTTGAAGCTACCC
31924888 GTT-ATAGGCTCTTTG
1 GTTAAT-GGCTCTTTG
31924903 TGAGCTTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (24 bp):
GTTAATGGCTCTTTGAAGCTACCC
Found at i:31929569 original size:26 final size:26
Alignment explanation
Indices: 31929450--31929575 Score: 121
Period size: 26 Copynumber: 4.8 Consensus size: 26
31929440 AAGGCCTTAG
31929450 GAGTTTGAGTTGGTC-AGAGGACCCTT
1 GAGTTTGAGTTGGTCGA-AGGACCCTT
* ** *
31929476 GAATTTGAGTTGGTC-AGAGGATACTC
1 GAGTTTGAGTTGGTCGA-AGGACCCTT
* * * * * *
31929502 GAGTTTTAGTGGGTCGGAGAAGCCTA
1 GAGTTTGAGTTGGTCGAAGGACCCTT
*
31929528 AAGTTTGAGTTGGTCGAAGGACCCTT
1 GAGTTTGAGTTGGTCGAAGGACCCTT
31929554 GAGTTTGAGTTGGTCGAAGGAC
1 GAGTTTGAGTTGGTCGAAGGAC
31929576 TATGAACGGA
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.29
Consensus pattern (26 bp):
GAGTTTGAGTTGGTCGAAGGACCCTT
Found at i:31931129 original size:86 final size:86
Alignment explanation
Indices: 31930976--31931137 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 86
31930966 TACATGCATA
* * * * *
31930976 AGGTTGAGTTCTCACTCTTAGTGAATTTATATCCCAGGATTTGGGTGGTCCTATTGCGACAATCT
1 AGGTTGAGTTCTCACTCTTAATGAATTCATATCCCAGGATTTAGCTGGTCCTATTGAGACAATCT
31931041 TGATGAATTCACTAACATATG
66 TGATGAATTCACTAACATATG
* *
31931062 AGGTTGAGTTCATTACTCTTAATGAGTTCATAT-CCA-GAGTTTAGCTGGTCCTATTGAGACCAA
1 AGGTTGAGTTC-TCACTCTTAATGAATTCATATCCCAGGA-TTTAGCTGGTCCTATTGAGA-CAA
31931125 -CTTGATGAATTCA
63 TCTTGATGAATTCA
31931138 TCAAATTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
85 2 0.03
86 44 0.67
87 20 0.30
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (86 bp):
AGGTTGAGTTCTCACTCTTAATGAATTCATATCCCAGGATTTAGCTGGTCCTATTGAGACAATCT
TGATGAATTCACTAACATATG
Found at i:31931644 original size:38 final size:38
Alignment explanation
Indices: 31931602--31931676 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
31931592 AAAAATATAT
* *
31931602 TTTTAAACGGTTACGATTTGAAAAAATTAGAATCTAGC
1 TTTTAAACGGTTACAATTTGAAAAAATCAGAATCTAGC
* *
31931640 TTTTAAACGGTTACAATTTGACAGAATCAGAATCTAG
1 TTTTAAACGGTTACAATTTGAAAAAATCAGAATCTAG
31931677 TGGTTGAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (38 bp):
TTTTAAACGGTTACAATTTGAAAAAATCAGAATCTAGC
Found at i:31933044 original size:21 final size:21
Alignment explanation
Indices: 31933005--31933044 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31932995 GGCTTCTTTA
*
31933005 TTATTCATTAAAGACATTTCT
1 TTATTCATTAAAGAAATTTCT
31933026 TTATTCATTAATA-AAATTT
1 TTATTCATTAA-AGAAATTT
31933045 TCAACTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
TTATTCATTAAAGAAATTTCT
Found at i:31943516 original size:14 final size:14
Alignment explanation
Indices: 31943497--31943536 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31943487 TTGATTACCA
31943497 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
31943511 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
31943525 GAAAAATGTTTT
1 GTAAAATGTTTT
31943537 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:31943549 original size:34 final size:35
Alignment explanation
Indices: 31943505--31943571 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
31943495 CAGTAAAATG
* *
31943505 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
* *
31943539 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
31943572 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:31943557 original size:20 final size:20
Alignment explanation
Indices: 31943520--31943559 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
31943510 CGTAAAATGA
**
31943520 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATAATTTACT
*
31943540 TTTCTGTAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
31943560 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:31945642 original size:20 final size:17
Alignment explanation
Indices: 31945627--31945661 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31945617 TTATTATTAC
31945627 AAATATTTTATAATTATT
1 AAATATTTTA-AATTATT
*
31945645 AAGTATTTTAAATTATT
1 AAATATTTTAAATTATT
31945662 TAGGAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AAATATTTTAAATTATT
Found at i:31945671 original size:18 final size:18
Alignment explanation
Indices: 31945631--31945673 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31945621 TATTACAAAT
*
31945631 ATTTTATAATTATTAAGT
1 ATTTTATAATTATTAAGG
*
31945649 ATTTTA-AATTATTTAGG
1 ATTTTATAATTATTAAGG
31945666 AGTTTTAT
1 A-TTTTAT
31945674 GTTAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
ATTTTATAATTATTAAGG
Found at i:31945989 original size:41 final size:44
Alignment explanation
Indices: 31945899--31945989 Score: 107
Period size: 47 Copynumber: 2.1 Consensus size: 44
31945889 AATATTGTTG
* *
31945899 TTGTTGTTTAAATGAAAAACCAACTTATGTGATAGCTGATATTGTTA
1 TTGTTGTTGAAATGAAAAACCAACTTATGTGA-AGCTG--ATTGGTA
*
31945946 TTGTTGTTGAAATGGAAAACCAACTTATGTG-A-CTG-TTGGTA
1 TTGTTGTTGAAATGAAAAACCAACTTATGTGAAGCTGATTGGTA
31945987 TTG
1 TTG
31945990 GGAGATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 8 0.20
44 3 0.07
45 1 0.02
47 29 0.71
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (44 bp):
TTGTTGTTGAAATGAAAAACCAACTTATGTGAAGCTGATTGGTA
Found at i:31951330 original size:206 final size:206
Alignment explanation
Indices: 31950976--31951470 Score: 698
Period size: 206 Copynumber: 2.4 Consensus size: 206
31950966 TGATACTGTT
* * *
31950976 AGTCATAAAGATAGGAATTGATTTGTCTTTTTCCTAAGGCTATTAGTAGGCACATGGCAAACAAT
1 AGTCATAAAAATAGGAATTGATTTGTCTATTTCCTAAGGCTATTAGTATGCACATGGCAAACAAT
* *
31951041 AACTTTATAAAAATCCAAACCTGCAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
66 AACTTTAGAAAAATCCAAACCTACAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
* *
31951106 TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACATACACA-TATTCGAATAATTCAA
131 TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGT-TTCAAATAATTCAA
*
31951170 TAAAGACTGATA
195 TAAAAACTGATA
* * * *
31951182 AGTCATAAAAATAAGAATTGATTTGTCTCTTTCCTAAGGATATTAGTATGCACATGGCAGACAAT
1 AGTCATAAAAATAGGAATTGATTTGTCTATTTCCTAAGGCTATTAGTATGCACATGGCAAACAAT
* * *
31951247 ACCTTTAGAAAAATCCAAACCTACAATTCACTTTGATACAAACAATGATCATATTTGGATCAACA
66 AACTTTAGAAAAATCCAAACCTACAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
* *
31951312 TTTGAAAAATGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGTTTCAAATAATTCAAT
131 TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGTTTCAAATAATTCAAT
* *
31951377 AAAAATTGATT
196 AAAAACTGATA
* * * *
31951388 TGTC----AAATAGGAACTT-ATTTGTCTATTTCCTAAGGCTA-TATGTATGCATATGACAAACC
1 AGTCATAAAAATAGGAA-TTGATTTGTCTATTTCCTAAGGCTATTA-GTATGCACATGGCAAACA
*
31951447 ATAACTTTGGAAAAATCCAAACCT
64 ATAACTTTAGAAAAATCCAAACCT
31951471 GCCATACACT
Statistics
Matches: 258, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
201 2 0.01
202 64 0.25
203 2 0.01
206 189 0.73
207 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (206 bp):
AGTCATAAAAATAGGAATTGATTTGTCTATTTCCTAAGGCTATTAGTATGCACATGGCAAACAAT
AACTTTAGAAAAATCCAAACCTACAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGTTTCAAATAATTCAAT
AAAAACTGATA
Found at i:31954638 original size:27 final size:27
Alignment explanation
Indices: 31954603--31954675 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
31954593 CTTTCCACAT
* *
31954603 GATATTCTTGATGGACTTTTCACGTTA
1 GATACTCTTGATGGACTTCTCACGTTA
* *
31954630 GATACTCTTGACGGACTTCTCATGTTA
1 GATACTCTTGATGGACTTCTCACGTTA
*
31954657 GATAGTCTTGATGGACTTC
1 GATACTCTTGATGGACTTC
31954676 CTACATATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (27 bp):
GATACTCTTGATGGACTTCTCACGTTA
Found at i:31955163 original size:50 final size:50
Alignment explanation
Indices: 31955088--31955189 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
31955078 TCAACATAAC
31955088 TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
1 TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
*
31955138 TAGTTTACAACCATCTATATATTTAGGTACCATATTGCTTGCAACCACTA
1 TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
31955188 TA
1 TA
31955190 CACCGTTACT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (50 bp):
TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
Found at i:31957195 original size:84 final size:84
Alignment explanation
Indices: 31957091--31957289 Score: 226
Period size: 84 Copynumber: 2.3 Consensus size: 84
31957081 GATTCTTTGA
* *
31957091 ATGAAAGGGGTTGTTATGTGCTGATTCCCCGTATCA-TTGATTAT-AAGGTGGTTGCTAAGTGCT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTTGATTATAAAGG-GGTTGCTAAGTGCT
* *
31957154 GATTCCACCGTATCCTTGATT
65 GATTCC-CCGTATCATTAATT
* * * *
31957175 CTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTCCTTGTTTGTGAAAGGGGTTGCTATGT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCATATCA---CTTGATTAT-AAAGGGGTTGCTAAGT
31957240 GCTGATTCCCCGTATCATTAATT
62 GCTGATTCCCCGTATCATTAATT
*
31957263 AT--AAGGTGGTTGCTAAGTGCTGATTCC
1 ATGAAAGG-GGTTGCTATGTGCTGATTCC
31957290 ATCGTGTAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
84 33 0.34
86 4 0.04
87 19 0.19
88 19 0.19
89 19 0.19
90 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (84 bp):
ATGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTTGATTATAAAGGGGTTGCTAAGTGCTG
ATTCCCCGTATCATTAATT
Found at i:31957233 original size:46 final size:45
Alignment explanation
Indices: 31957091--31957289 Score: 199
Period size: 46 Copynumber: 4.6 Consensus size: 45
31957081 GATTCTTTGA
*
31957091 ATGAAAGGGGTTGTTATGTGCTGATTCCCCGTATCA---TTGATT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATCCTTGATT
*
31957133 AT--AAGGTGGTTGCTAAGTGCTGATTCCACCG--T-ATCCTTGATT
1 ATGAAAGG-GGTTGCTATGTGCTGATTCC-CCGTATCATCCTTGATT
* * *
31957175 CTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTCCTTGTTT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCA-TCCTTGATT
* *
31957221 GTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCA---TTAATT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATCCTTGATT
*
31957263 AT--AAGGTGGTTGCTAAGTGCTGATTCC
1 ATGAAAGG-GGTTGCTATGTGCTGATTCC
31957290 ATCGTGTAAC
Statistics
Matches: 133, Mismatches: 12, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
39 1 0.01
40 9 0.07
41 37 0.28
42 19 0.14
43 19 0.14
44 5 0.04
45 1 0.01
46 42 0.32
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (45 bp):
ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATCCTTGATT
Found at i:31961981 original size:382 final size:382
Alignment explanation
Indices: 31961275--31962038 Score: 1528
Period size: 382 Copynumber: 2.0 Consensus size: 382
31961265 GGATAGTCTT
31961275 GATTTCTTTAGGATAATATTTATTCTCTCAATATGATCCTATTTCATCTCATTGTAACCATTACA
1 GATTTCTTTAGGATAATATTTATTCTCTCAATATGATCCTATTTCATCTCATTGTAACCATTACA
31961340 TCTTCCTTCATGAAAAGTCAATCACTATCAAATATTGATCAAGTCATTCATCAAAAAGATGAACG
66 TCTTCCTTCATGAAAAGTCAATCACTATCAAATATTGATCAAGTCATTCATCAAAAAGATGAACG
31961405 GCCAATGACCATGTTTACTTTTCATCAGCCATGTAATGCCAATGAGAGGATATCATTTACTCATG
131 GCCAATGACCATGTTTACTTTTCATCAGCCATGTAATGCCAATGAGAGGATATCATTTACTCATG
31961470 TATCGAGCTATAAATTTCACTATTGTGAATGACGCTATATAATACAAAAGTTGTACACCTAATGC
196 TATCGAGCTATAAATTTCACTATTGTGAATGACGCTATATAATACAAAAGTTGTACACCTAATGC
31961535 ACCAGCTTTTGGTTCCTTATCTATTCGAACTCAAGCTTTTACTTGCATCAAAGTGTACGAGTCAA
261 ACCAGCTTTTGGTTCCTTATCTATTCGAACTCAAGCTTTTACTTGCATCAAAGTGTACGAGTCAA
31961600 ACATACATAGTTCTCCATCCACTCATGATTTAGGTATGCCACACTATGAATGTCACA
326 ACATACATAGTTCTCCATCCACTCATGATTTAGGTATGCCACACTATGAATGTCACA
31961657 GATTTCTTTAGGATAATATTTATTCTCTCAATATGATCCTATTTCATCTCATTGTAACCATTACA
1 GATTTCTTTAGGATAATATTTATTCTCTCAATATGATCCTATTTCATCTCATTGTAACCATTACA
31961722 TCTTCCTTCATGAAAAGTCAATCACTATCAAATATTGATCAAGTCATTCATCAAAAAGATGAACG
66 TCTTCCTTCATGAAAAGTCAATCACTATCAAATATTGATCAAGTCATTCATCAAAAAGATGAACG
31961787 GCCAATGACCATGTTTACTTTTCATCAGCCATGTAATGCCAATGAGAGGATATCATTTACTCATG
131 GCCAATGACCATGTTTACTTTTCATCAGCCATGTAATGCCAATGAGAGGATATCATTTACTCATG
31961852 TATCGAGCTATAAATTTCACTATTGTGAATGACGCTATATAATACAAAAGTTGTACACCTAATGC
196 TATCGAGCTATAAATTTCACTATTGTGAATGACGCTATATAATACAAAAGTTGTACACCTAATGC
31961917 ACCAGCTTTTGGTTCCTTATCTATTCGAACTCAAGCTTTTACTTGCATCAAAGTGTACGAGTCAA
261 ACCAGCTTTTGGTTCCTTATCTATTCGAACTCAAGCTTTTACTTGCATCAAAGTGTACGAGTCAA
31961982 ACATACATAGTTCTCCATCCACTCATGATTTAGGTATGCCACACTATGAATGTCACA
326 ACATACATAGTTCTCCATCCACTCATGATTTAGGTATGCCACACTATGAATGTCACA
31962039 AGTGAATAAA
Statistics
Matches: 382, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
382 382 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (382 bp):
GATTTCTTTAGGATAATATTTATTCTCTCAATATGATCCTATTTCATCTCATTGTAACCATTACA
TCTTCCTTCATGAAAAGTCAATCACTATCAAATATTGATCAAGTCATTCATCAAAAAGATGAACG
GCCAATGACCATGTTTACTTTTCATCAGCCATGTAATGCCAATGAGAGGATATCATTTACTCATG
TATCGAGCTATAAATTTCACTATTGTGAATGACGCTATATAATACAAAAGTTGTACACCTAATGC
ACCAGCTTTTGGTTCCTTATCTATTCGAACTCAAGCTTTTACTTGCATCAAAGTGTACGAGTCAA
ACATACATAGTTCTCCATCCACTCATGATTTAGGTATGCCACACTATGAATGTCACA
Found at i:31963613 original size:22 final size:21
Alignment explanation
Indices: 31963588--31963636 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
31963578 GTTGGTTTAA
*
31963588 TAATAAAAATAATGTTATATAT
1 TAATAAAAATAATATTAT-TAT
*
31963610 TAATAACAATAATATTATTAT
1 TAATAAAAATAATATTATTAT
31963631 TAATAA
1 TAATAA
31963637 TAAAACCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAATAAAAATAATATTATTAT
Found at i:31963630 original size:25 final size:24
Alignment explanation
Indices: 31963584--31963641 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
31963574 CTATGTTGGT
* *
31963584 TTAATAATAAAAATAATGTTATATA
1 TTAATAACAAAAATAATATTAT-TA
31963609 TTAATAAC---AATAATATTATTA
1 TTAATAACAAAAATAATATTATTA
*
31963630 TTAATAATAAAA
1 TTAATAACAAAA
31963642 CCCACTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 9 0.33
22 10 0.37
24 1 0.04
25 7 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
TTAATAACAAAAATAATATTATTA
Found at i:31977863 original size:10 final size:10
Alignment explanation
Indices: 31977848--31977877 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
31977838 ATAAATGTTT
31977848 ATTTATTTTA
1 ATTTATTTTA
31977858 ATTTATTTTA
1 ATTTATTTTA
31977868 ATTTAGTTTT
1 ATTTA-TTTT
31977878 TTTTATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (10 bp):
ATTTATTTTA
Found at i:31980691 original size:39 final size:39
Alignment explanation
Indices: 31980648--31980725 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
31980638 TTATAATTAA
31980648 AAAAATAAATTTGAAATTTCT-ATAAA-TATTTTGAATCTT
1 AAAAATAAATTTG-AATTTCTGA-AAATTATTTTGAATCTT
* * *
31980687 AAAAATTATTTTGAATTTTTGAAAATTATTTTGAATCTT
1 AAAAATAAATTTGAATTTCTGAAAATTATTTTGAATCTT
31980726 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (39 bp):
AAAAATAAATTTGAATTTCTGAAAATTATTTTGAATCTT
Found at i:31980696 original size:19 final size:19
Alignment explanation
Indices: 31980674--31980725 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
31980664 TTTCTATAAA
31980674 TATTTTGAATCTTAAAAAT
1 TATTTTGAATCTTAAAAAT
* *
31980693 TATTTTGAATTTTTGAAAAT
1 TATTTTGAA-TCTTAAAAAT
31980713 TATTTTGAATCTT
1 TATTTTGAATCTT
31980726 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (19 bp):
TATTTTGAATCTTAAAAAT
Found at i:31980826 original size:9 final size:9
Alignment explanation
Indices: 31980812--31980840 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
31980802 GACCAATCTG
31980812 TTATTCGAA
1 TTATTCGAA
31980821 TTATTCGAA
1 TTATTCGAA
31980830 TTATTCGAA
1 TTATTCGAA
31980839 TT
1 TT
31980841 GTAAAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:31983197 original size:42 final size:43
Alignment explanation
Indices: 31983141--31983250 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 43
31983131 GATGCCACTA
* * *
31983141 TCCCAAACAGGGTCTTACAAG-AAATCAT-ATAA-GACGCCAATG
1 TCCCAGACATGGTCTTACAAGTAAATC-TCA-AACGACGCCAACG
* *
31983183 TCCCAGACATGGTCTTACACGTAAATCTCAAATCGATGCCAACG
1 TCCCAGACATGGTCTTACAAGTAAATCTCAAA-CGACGCCAACG
*
31983227 TCCCAGACATGGTCTTACACGTAA
1 TCCCAGACATGGTCTTACAAGTAA
31983251 TCACATACCG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 21 0.36
43 6 0.10
44 32 0.54
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACAAGTAAATCTCAAACGACGCCAACG
Found at i:31994149 original size:26 final size:22
Alignment explanation
Indices: 31994121--31994166 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
31994111 AGTGTAACAA
31994121 GAAAGAAAAATTGATTTAATAT
1 GAAAGAAAAATTGATTTAATAT
31994143 GAAAGAAAAATTGATTTAATAT
1 GAAAGAAAAATTGATTTAATAT
31994165 GA
1 GA
31994167 TTAATTAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.30
Consensus pattern (22 bp):
GAAAGAAAAATTGATTTAATAT
Found at i:31999464 original size:13 final size:13
Alignment explanation
Indices: 31999446--31999475 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31999436 TCCGTAGGCT
31999446 AACATCCCTCCAA
1 AACATCCCTCCAA
31999459 AACATCCCTCCAA
1 AACATCCCTCCAA
31999472 AACA
1 AACA
31999476 CACCTTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.13
Consensus pattern (13 bp):
AACATCCCTCCAA
Found at i:32025301 original size:16 final size:17
Alignment explanation
Indices: 32025276--32025310 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
32025266 ACTTTTTCAA
32025276 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
32025292 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
32025309 TC
1 TC
32025311 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:32027039 original size:25 final size:25
Alignment explanation
Indices: 32027010--32027061 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
32027000 AAACAAACAG
*
32027010 AAAAAAAATGGAATT-AAAATTTAAC
1 AAAAAAAATAGAATTCAAAA-TTAAC
32027035 AAAAAAAATAGAATTCAAAATTAAC
1 AAAAAAAATAGAATTCAAAATTAAC
32027060 AA
1 AA
32027062 TTTCACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAAAAAATAGAATTCAAAATTAAC
Found at i:32035953 original size:27 final size:27
Alignment explanation
Indices: 32035923--32036039 Score: 182
Period size: 27 Copynumber: 4.3 Consensus size: 27
32035913 TTAAACTATT
32035923 GAAATACCCTCGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATC
32035950 GAAATACCCTCGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATC
*
32035977 GAAATACCCACGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATC
* * *
32036004 AAAATACCCCCGAAAGGG-AAAATGATC
1 GAAATACCCTCG-AAGGGTAAAATTATC
32036031 GAAATACCC
1 GAAATACCC
32036040 CATGGGGTAA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
27 79 0.94
28 5 0.06
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (27 bp):
GAAATACCCTCGAAGGGTAAAATTATC
Found at i:32036718 original size:259 final size:259
Alignment explanation
Indices: 32036252--32036769 Score: 991
Period size: 259 Copynumber: 2.0 Consensus size: 259
32036242 GTTCAAGGCT
32036252 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
1 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
*
32036317 GTGCTACAACTGGTGCTAAGCTTGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
66 GTGCTACAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
32036382 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
131 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
32036447 ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
196 ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
32036511 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
1 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
* *
32036576 GTGCTGCAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATTCCCACATGGTGT
66 GTGCTACAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
32036641 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
131 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
* *
32036706 ATACTTATTCTGTAATGGGTTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
196 ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
32036770 CTATGCCTGG
Statistics
Matches: 254, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 254 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (259 bp):
TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
GTGCTACAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
Found at i:32052995 original size:40 final size:41
Alignment explanation
Indices: 32052951--32053098 Score: 144
Period size: 40 Copynumber: 3.7 Consensus size: 41
32052941 TTGCACAAAT
* * *
32052951 GTGCCCCTGTTTGTACTTCGGTACCCCTT-ATAGCACATGC
1 GTGCCCCTATTTGTACTTCGATACCCCTTGATAGCACATAC
* * *
32052991 GTGCCCTTATTTG-ACTTCGATA-CCCTTGGTTGCACATAC
1 GTGCCCCTATTTGTACTTCGATACCCCTTGATAGCACATAC
* *
32053030 GTGACCCTACTTGTACTTCGATACCCC-TGATTA-CACATAC
1 GTGCCCCTATTTGTACTTCGATACCCCTTGA-TAGCACATAC
* * * *
32053070 ATCCCCCTATTTGCACTTTGATACCCCTT
1 GTGCCCCTATTTGTACTTCGATACCCCTT
32053099 ATTGCAAATG
Statistics
Matches: 86, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
38 5 0.06
39 26 0.30
40 50 0.58
41 5 0.06
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.34
Consensus pattern (41 bp):
GTGCCCCTATTTGTACTTCGATACCCCTTGATAGCACATAC
Found at i:32074363 original size:78 final size:77
Alignment explanation
Indices: 32074258--32074409 Score: 277
Period size: 78 Copynumber: 2.0 Consensus size: 77
32074248 GTAATTAGGC
32074258 CTTAGGATAGAAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATAG
1 CTTAGGATAGAAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATAG
32074323 GCTAACACGGGA
66 GCTAACACGGGA
* *
32074335 CTTAGGATAGAAAATTAATAAAAATAAGTGTTTTTAACACATTTCGTAGGTGTTATGACCCAATA
1 CTTAGGATAG-AAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATA
32074400 GGCTAACACG
65 GGCTAACACG
32074410 AGCCTTATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 10 0.14
78 62 0.86
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (77 bp):
CTTAGGATAGAAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATAG
GCTAACACGGGA
Found at i:32075452 original size:8 final size:8
Alignment explanation
Indices: 32075407--32075437 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
32075397 ATTGATTTAT
32075407 TTTATTTG
1 TTTATTTG
32075415 TTTATTTG
1 TTTATTTG
32075423 TTTATTTG
1 TTTATTTG
32075431 TTTATTT
1 TTTATTT
32075438 TCATTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (8 bp):
TTTATTTG
Found at i:32078265 original size:11 final size:10
Alignment explanation
Indices: 32078245--32078282 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
32078235 GGGGGTTACA
32078245 TAAATTTTTT
1 TAAATTTTTT
*
32078255 TAAGTTTTTT
1 TAAATTTTTT
32078265 TAAA-TTTTT
1 TAAATTTTTT
32078274 TAAATTTTT
1 TAAATTTTT
32078283 AATTACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:32081203 original size:10 final size:10
Alignment explanation
Indices: 32081188--32081218 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
32081178 GTTATGCATA
32081188 AAATGGATTG
1 AAATGGATTG
32081198 AAATGGATTG
1 AAATGGATTG
*
32081208 AAATGGTTTG
1 AAATGGATTG
32081218 A
1 A
32081219 TTTTAGGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
AAATGGATTG
Found at i:32082658 original size:19 final size:19
Alignment explanation
Indices: 32082612--32082658 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
32082602 ATTTGTCTTA
*
32082612 GTTAATTTTATTAATTTAT
1 GTTAATTTGATTAATTTAT
*
32082631 GTTATTTTGATTAATTTAAT
1 GTTAATTTGATTAATTT-AT
32082651 -TTAATTTG
1 GTTAATTTG
32082659 GTTTTTCGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.62
Consensus pattern (19 bp):
GTTAATTTGATTAATTTAT
Found at i:32094230 original size:41 final size:41
Alignment explanation
Indices: 32094163--32094244 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
32094153 ATGCAATAAC
* * *
32094163 AAAAATTAAAAATGAAAGCAAGAAATATTTTTGGATTTTTT
1 AAAAATTAAAAATAAAAACAAGAAATATTTTTGGAATTTTT
32094204 AAAAATTAAAAATAAAAACGAA-AAATATTTTTGGAATTTTT
1 AAAAATTAAAAATAAAAAC-AAGAAATATTTTTGGAATTTTT
32094245 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.35
Consensus pattern (41 bp):
AAAAATTAAAAATAAAAACAAGAAATATTTTTGGAATTTTT
Found at i:32094302 original size:18 final size:18
Alignment explanation
Indices: 32094271--32094307 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32094261 TGTATAAAAA
* *
32094271 ATAAACACACAAATAAAC
1 ATAAAAACAAAAATAAAC
32094289 ATAAAAACAAAAATAAAC
1 ATAAAAACAAAAATAAAC
32094307 A
1 A
32094308 CACATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.16, G:0.00, T:0.11
Consensus pattern (18 bp):
ATAAAAACAAAAATAAAC
Found at i:32096220 original size:32 final size:32
Alignment explanation
Indices: 32096179--32096243 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
32096169 TATAGGGACT
32096179 AGAAATGTAAATAAACCTTAGCTACAATATTA
1 AGAAATGTAAATAAACCTTAGCTACAATATTA
*
32096211 AGAAATGTAAATACACCTTAGCTACAATATTA
1 AGAAATGTAAATAAACCTTAGCTACAATATTA
32096243 A
1 A
32096244 CTAACTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (32 bp):
AGAAATGTAAATAAACCTTAGCTACAATATTA
Found at i:32098478 original size:18 final size:18
Alignment explanation
Indices: 32098457--32098514 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
32098447 ACAAAAAATT
*
32098457 ATAAAATAGACTAA-TAAA
1 ATAAAATA-AATAACTAAA
*
32098475 ATAAATTAAATAACTAAA
1 ATAAAATAAATAACTAAA
**
32098493 AT-AAATAAATAAGAAAA
1 ATAAAATAAATAACTAAA
32098510 ATAAA
1 ATAAA
32098515 CAACCGACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
ATAAAATAAATAACTAAA
Found at i:32098485 original size:22 final size:22
Alignment explanation
Indices: 32098460--32098502 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32098450 AAAAATTATA
*
32098460 AAATAGACTAATA-AAATAAATT
1 AAATA-ACTAAAATAAATAAATT
32098482 AAATAACTAAAATAAATAAAT
1 AAATAACTAAAATAAATAAAT
32098503 AAGAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAACTAAAATAAATAAATT
Found at i:32098503 original size:17 final size:18
Alignment explanation
Indices: 32098471--32098514 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
32098461 AATAGACTAA
32098471 TAAAATAAATTAAATAAC
1 TAAAATAAATTAAATAAC
*
32098489 TAAAATAAA-TAAATAAG
1 TAAAATAAATTAAATAAC
*
32098506 AAAAATAAA
1 TAAAATAAA
32098515 CAACCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAATAAATTAAATAAC
Found at i:32098514 original size:13 final size:13
Alignment explanation
Indices: 32098473--32098514 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
32098463 TAGACTAATA
*
32098473 AAATAAATTAAAT
1 AAATAAAATAAAT
*
32098486 AACTAAAATAAAT
1 AAATAAAATAAAT
32098499 AAATAAGAA-AAAT
1 AAATAA-AATAAAT
32098512 AAA
1 AAA
32098515 CAACCGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 23 0.92
14 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:32103675 original size:243 final size:240
Alignment explanation
Indices: 32103247--32103734 Score: 859
Period size: 243 Copynumber: 2.0 Consensus size: 240
32103237 TGTAGGGTAC
*
32103247 AACAAGTATGTAAGTGGTAAAAGTACTAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
1 AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
* *
32103312 CCCCTCTACTGAAAAAATGGGCAAATTAGCCGTTATACATTTCAAAACGTGCAAATTAGCATCTC
66 CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGCATATC
* *
32103377 TGTTAAATTTTATTTGTTAAATGATGGCGTGGAAGGTTAATTTAAATGATTAATTACTAATTTAG
131 TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAG
32103442 TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTTTTAAATTATT
196 TCCCTGAACTATAATTAAAATATCATTTTGA---TTTTTTAAATTATT
* * *
32103490 AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGCGGATTGCATTTTGG
1 AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
*
32103555 CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGTATATC
66 CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGCATATC
*
32103620 TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAT
131 TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAG
32103685 TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTAAATTATT
196 TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTAAATTATT
32103730 AACAA
1 AACAA
32103735 TAATTCTAAA
Statistics
Matches: 235, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
240 19 0.08
243 216 0.92
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (240 bp):
AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGCATATC
TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAG
TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTAAATTATT
Found at i:32103791 original size:9 final size:9
Alignment explanation
Indices: 32103743--32103832 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
32103733 AATAATTCTA
*
32103743 AAAAATTTT
1 AAAAATATT
*
32103752 AAAAATCTT
1 AAAAATATT
*
32103761 AAAAATAAAT
1 AAAAAT-ATT
*
32103771 ATAAATTATT
1 A-AAAATATT
32103781 AAAAATATT
1 AAAAATATT
*
32103790 AAGAATATT
1 AAAAATATT
*
32103799 AGAAATTATGTT
1 A-AAA--ATATT
32103811 AAAATATATT
1 AAAA-ATATT
*
32103821 TAAAA-ATT
1 AAAAATATT
32103829 AAAA
1 AAAA
32103833 TTATAAATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
8 6 0.09
9 31 0.48
10 15 0.23
11 7 0.11
12 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAAATATT
Found at i:32103791 original size:29 final size:28
Alignment explanation
Indices: 32103745--32103827 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
32103735 TAATTCTAAA
* *
32103745 AAATT-TTAAAAATCTTAAAAATAAATAT
1 AAATTATTAAAAATATTAAAAAT-AATAG
* *
32103773 AAATTATTAAAAATATTAAGAATATTAG
1 AAATTATTAAAAATATTAAAAATAATAG
32103801 AAATTATGTTAAAATATATTTAAAAAT
1 AAATTA--TTAAAA-ATA-TTAAAAAT
32103828 TAAAATTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 14 0.31
29 15 0.33
30 6 0.13
31 3 0.07
32 7 0.16
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (28 bp):
AAATTATTAAAAATATTAAAAATAATAG
Found at i:32103833 original size:29 final size:30
Alignment explanation
Indices: 32103779--32103836 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
32103769 ATATAAATTA
32103779 TTAAAAATATTAAGAATATTAGAAATTATG
1 TTAAAAATATTAAGAATATTAGAAATTATG
32103809 TTAAAATATATTTAA-AA-ATTA-AAATTAT
1 TTAAAA-ATA-TTAAGAATATTAGAAATTAT
32103837 AAATGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.27
30 10 0.38
31 5 0.19
32 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (30 bp):
TTAAAAATATTAAGAATATTAGAAATTATG
Found at i:32112869 original size:11 final size:11
Alignment explanation
Indices: 32112855--32112880 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32112845 AATTTTTTAA
32112855 TTTTAAAATAT
1 TTTTAAAATAT
32112866 TTTTAAAATAT
1 TTTTAAAATAT
32112877 TTTT
1 TTTT
32112881 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:32112902 original size:22 final size:21
Alignment explanation
Indices: 32112863--32112903 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
32112853 AATTTTAAAA
*
32112863 TATTTTTAAAATATTTTTTTT
1 TATTTTTAAAATAATTTTTTT
*
32112884 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAATAATTTTTT
32112904 CGTGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTTT
Found at i:32126505 original size:14 final size:15
Alignment explanation
Indices: 32126466--32126508 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
32126456 TATTTAACAC
32126466 ATATATATATA-TAT
1 ATATATATATATTAT
*
32126480 ATAAATAT-TATTAT
1 ATATATATATATTAT
32126494 ATAT-TATATATTAT
1 ATATATATATATTAT
32126508 A
1 A
32126509 CCAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATATATTAT
Found at i:32126569 original size:7 final size:7
Alignment explanation
Indices: 32126559--32126583 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32126549 TAACATCTAA
32126559 TATATAT
1 TATATAT
32126566 TATATAT
1 TATATAT
32126573 TATATAT
1 TATATAT
32126580 TATA
1 TATA
32126584 AGCTCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:32130767 original size:17 final size:17
Alignment explanation
Indices: 32130727--32130769 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
32130717 ATGGAATTAG
*
32130727 AATTGAATTGAAAAAATG
1 AATT-AATTGAAAAAATA
* *
32130745 ATTTAATTGAATAAATA
1 AATTAATTGAAAAAATA
32130762 AATTAATT
1 AATTAATT
32130770 TAAATAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AATTAATTGAAAAAATA
Found at i:32139309 original size:36 final size:37
Alignment explanation
Indices: 32139262--32139339 Score: 140
Period size: 36 Copynumber: 2.1 Consensus size: 37
32139252 CTTTATTTTT
*
32139262 AAAATTAAAAAATATTTATTTGAAAATTATGTAAATA
1 AAAATTAAAAAATATTTATTTGAAAATTATATAAATA
32139299 AAAATT-AAAAATATTTATTTGAAAATTATATAAATA
1 AAAATTAAAAAATATTTATTTGAAAATTATATAAATA
32139335 AAAAT
1 AAAAT
32139340 GAATTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 34 0.85
37 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (37 bp):
AAAATTAAAAAATATTTATTTGAAAATTATATAAATA
Found at i:32145237 original size:29 final size:29
Alignment explanation
Indices: 32145187--32145248 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
32145177 TTTTTTAAAG
* *
32145187 TTTTTTTAATATTGATCTTTTTATTATTC
1 TTTTTTTAATATTGATCTTTTTAGTATTA
32145216 TTTTTTTAAATATTG-T-TGTTTTAGTATTA
1 TTTTTTT-AATATTGATCT-TTTTAGTATTA
32145245 TTTT
1 TTTT
32145249 CTTGAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.72
30 7 0.24
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.69
Consensus pattern (29 bp):
TTTTTTTAATATTGATCTTTTTAGTATTA
Found at i:32148684 original size:13 final size:11
Alignment explanation
Indices: 32148652--32148694 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
32148642 CTATTTTCTA
*
32148652 AATAAAATAAT
1 AATAAAATATT
32148663 AAT-AAATATTT
1 AATAAAATA-TT
32148674 AAGTAAAATATT
1 AA-TAAAATATT
32148686 AATAAAATA
1 AATAAAATA
32148695 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:32161054 original size:28 final size:28
Alignment explanation
Indices: 32161018--32161084 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
32161008 TTTCGTCTTC
* *
32161018 AAGATAGTCCTTGGCAAACTTTCCTCAT
1 AAGACAGTCCTTGGCAAACTTTCCACAT
*
32161046 AAGACAGTCCTTGGCAGACTTTCCACAT
1 AAGACAGTCCTTGGCAAACTTTCCACAT
32161074 AAGACAGTCCT
1 AAGACAGTCCT
32161085 CAGCGGACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (28 bp):
AAGACAGTCCTTGGCAAACTTTCCACAT
Found at i:32161093 original size:28 final size:28
Alignment explanation
Indices: 32161035--32161097 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
32161025 TCCTTGGCAA
* **
32161035 ACTTTCCTCATAAGACAGTCCTTGGCAG
1 ACTTTCCACATAAGACAGTCCTCAGCAG
*
32161063 ACTTTCCACATAAGACAGTCCTCAGCGG
1 ACTTTCCACATAAGACAGTCCTCAGCAG
32161091 ACTTTCC
1 ACTTTCC
32161098 CTGATTCTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ACTTTCCACATAAGACAGTCCTCAGCAG
Found at i:32169753 original size:54 final size:54
Alignment explanation
Indices: 32169642--32169833 Score: 277
Period size: 57 Copynumber: 3.6 Consensus size: 54
32169632 AGAAAATATG
* *
32169642 CTGCAAGAAAAGACAAGTGAACAGGAAATATTCGCTG---AC-G-AAATATTCC
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGAAAACAGTAAATATTCC
*
32169691 CTGCAAGAAAAGACGAGTGAACAAGAAATATTCTCTGAAAACAGTAAATATTCC
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGAAAACAGTAAATATTCC
* *
32169745 CTGGAAGAAAAGACGAGTGAACAGGAAATATTCTCTGATTAAAACAGTAAAAATTCC
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTG---AAAACAGTAAATATTCC
32169802 CTGCAAGAAAAGACGAGTGAACAGGAAATATT
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATT
32169834 TTGTGTAATT
Statistics
Matches: 128, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
49 34 0.27
52 2 0.02
53 1 0.01
54 44 0.34
57 47 0.37
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (54 bp):
CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGAAAACAGTAAATATTCC
Found at i:32172425 original size:13 final size:13
Alignment explanation
Indices: 32172407--32172447 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
32172397 AATACAACTT
32172407 AGAAAGAAAAGAA
1 AGAAAGAAAAGAA
*
32172420 AGAAAGAAAAATAA
1 AGAAAG-AAAAGAA
32172434 AG-AAGAAAAGAA
1 AGAAAGAAAAGAA
32172446 AG
1 AG
32172448 TCACGCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
14 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
AGAAAGAAAAGAA
Done.