Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 98 of 185
Found at i:31183341 original size:44 final size:44
Alignment explanation
Indices: 31183231--31183840 Score: 478
Period size: 44 Copynumber: 13.7 Consensus size: 44
31183221 TAAATTACAG
* * **** *
31183231 ATCTTATCTCTCTGAAGTTGCAGTAGAGCACACCGAAGATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CCA
*
31183276 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
* * * **
31183320 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
* * * **
31183364 ATCCTATCTCCTTGAAGTTGCAGTGGAGC-GGATT-AAAATGATGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTGAAGAT-ACCA
* * * * * *
31183408 ATCCTATAC-CTCTAAAGTTACAGTAGG-TC-GGATTAAATCGACCATGA-CA
1 ATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGG-TTGAA--G---AT-ACCA
* * * ** *
31183457 AGTCTTATCTCCCTGAAGTTGTAGTGAAACAGACTGAAGATAACAA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT-ACCA
* * *
31183503 ACCTTATCTTCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
* * ** *
31183547 GTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CCA
* **
31183592 ACCTTATCTTGCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
*
31183635 AGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
** * * * **
31183680 ATCTTATCTTACTAAAGCTGCAGTGGAGCAGATTGAAGATATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
* *
31183724 ATCCTATCACCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
** * * * * **
31183768 ATCTTATCTTACTAAAGCTGCAGTGGAGCAGATTGAAGCTATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
* *
31183812 ATCCTATCACCCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
31183841 GGATTAAAAC
Statistics
Matches: 449, Mismatches: 98, Indels: 37
0.77 0.17 0.06
Matches are distributed among these distances:
43 6 0.01
44 298 0.66
45 113 0.25
46 2 0.00
48 1 0.00
49 4 0.01
50 24 0.05
51 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
Found at i:31183729 original size:316 final size:318
Alignment explanation
Indices: 31183134--31183747 Score: 776
Period size: 316 Copynumber: 1.9 Consensus size: 318
31183124 CGAAGCCCCT
* ** * * *
31183134 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGAAACAGACTGAAGATAACAAACCTTATTTCCCTAAAGTT
* *
31183199 GCAGTGGAATAGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCACAC
66 GCAGTGGAACAGATTGAAG-----AATTACAGATCTTATCTCCCTGAAGTTGCAGTAGAGCACAC
*
31183264 CGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCT
126 CGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAACCTTATCT
* ** * * * *
31183329 CCCTAAAGTTGCAGTGGAGCAGATTGAAGCTATTAATCCTATCTCCTTGAAGTTGCAGTGGAGCG
191 CCCTAAAGTTGCAGTGGAGCAGATTGAAGATACCAATCCTATCTACTTAAAGCTGCAGTGGAGCA
31183394 GATTAAAATGATGAATCCTAT-ACCTCTAAAGTTACAGTAGGTCGGATTAAATCGACCATGACA
256 GATTAAAATGATGAATCCTATCACC-CTAAAGTTACAGTAGGTCGGATTAAATCGACCATGACA
* *
31183457 AGTCTTATCTCCCTGAAGTTGTAGTGAAACAGACTGAAGATAACAAACCTTATCTT-CCTGAAGT
1 AGTCTTATCTCCCTGAAGTTGCAGTGAAACAGACTGAAGATAACAAACCTTAT-TTCCCTAAAGT
* * * * * *
31183521 TGCAGTGGAGCAGGTTGAAG-A-TAC-GAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGA
65 TGCAGTGGAACAGATTGAAGAATTACAGA-TCTTATCTCCCTGAAGTTGCAGTAGAGCACACCGA
**
31183583 AGATAGCAAACCTTATCTTGCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAAGCCTTATCTCC
129 AGATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAA-CCTTATCTCC
* * *
31183647 CTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTTAC-TAAAGCTGCAGTGGAGCAG
193 CTAAAGTTGCAGTGGAGCAGATTGAAGATACCAATCCTATC-TACTTAAAGCTGCAGTGGAGCAG
* * * *
31183711 ATTGAAGAT-ATTAATCCTATCACCCTGAAGTTGCAGT
257 ATT-AAAATGATGAATCCTATCACCCTAAAGTTACAGT
31183748 GGAGCAGGTT
Statistics
Matches: 252, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
315 5 0.02
316 165 0.65
317 10 0.04
323 70 0.28
324 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (318 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGAAACAGACTGAAGATAACAAACCTTATTTCCCTAAAGTT
GCAGTGGAACAGATTGAAGAATTACAGATCTTATCTCCCTGAAGTTGCAGTAGAGCACACCGAAG
ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAACCTTATCTCCCTA
AAGTTGCAGTGGAGCAGATTGAAGATACCAATCCTATCTACTTAAAGCTGCAGTGGAGCAGATTA
AAATGATGAATCCTATCACCCTAAAGTTACAGTAGGTCGGATTAAATCGACCATGACA
Found at i:31184705 original size:4 final size:4
Alignment explanation
Indices: 31184696--31184723 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31184686 ATTCTCTACG
31184696 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
31184724 AAAAAAAACC
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:31185772 original size:20 final size:23
Alignment explanation
Indices: 31185747--31185793 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
31185737 GATACATTAG
*
31185747 TATTATTTTG-TTGTT-G-TTGT
1 TATTATTGTGATTGTTAGATTGT
31185767 TATTATTGTGATTGTTAGATTGT
1 TATTATTGTGATTGTTAGATTGT
31185790 TATT
1 TATT
31185794 TGCATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 1 0.04
23 8 0.35
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (23 bp):
TATTATTGTGATTGTTAGATTGT
Found at i:31187992 original size:26 final size:27
Alignment explanation
Indices: 31187938--31187994 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
31187928 CCAGTTCTTC
31187938 ACCAAATCACAACCACAAAACCACTAAA
1 ACCAAATCACAACCAC-AAACCACTAAA
31187966 ACCAAATCACAACCAC-AACCACTAAA
1 ACCAAATCACAACCACAAACCACTAAA
31187992 ACC
1 ACC
31187995 TTCTCTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 13 0.45
28 16 0.55
ACGTcount: A:0.54, C:0.39, G:0.00, T:0.07
Consensus pattern (27 bp):
ACCAAATCACAACCACAAACCACTAAA
Found at i:31188569 original size:6 final size:6
Alignment explanation
Indices: 31188558--31188594 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
31188548 ATTTCTTCCC
*
31188558 TTGGAA TTGGAA TTGAAA TTGGAA TTGGAA TTGGAA T
1 TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA T
31188595 CGAGTTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (6 bp):
TTGGAA
Found at i:31190538 original size:47 final size:46
Alignment explanation
Indices: 31190474--31190566 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 46
31190464 ATAAAATATC
*
31190474 ATTTAAAAATTAAATTAAAATATTAATAAACTAATATTTATTTATT
1 ATTTAAAAATGAAATTAAAATATTAATAAACTAATATTTATTTATT
31190520 NATTTAAAAATGAAATTAAAATATTAATAAACTAATATTTATTTATT
1 -ATTTAAAAATGAAATTAAAATATTAATAAACTAATATTTATTTATT
31190567 TAATTAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (46 bp):
ATTTAAAAATGAAATTAAAATATTAATAAACTAATATTTATTTATT
Found at i:31191085 original size:12 final size:12
Alignment explanation
Indices: 31191068--31191112 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
31191058 TTAAGATCTA
31191068 TTTTTAATATCC
1 TTTTTAATATCC
*
31191080 TTTTTACTATCC
1 TTTTTAATATCC
31191092 TTTTTACTAATATCC
1 -TTTT--TAATATCC
31191107 TTTTTA
1 TTTTTA
31191113 CTAATCCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 13 0.46
13 4 0.14
14 4 0.14
15 7 0.25
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTAATATCC
Found at i:31191102 original size:27 final size:29
Alignment explanation
Indices: 31191072--31191125 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
31191062 GATCTATTTT
31191072 TAATATCCTTTTTACT-ATCC-TTTTTAC
1 TAATATCCTTTTTACTAATCCATTTTTAC
31191099 TAATATCCTTTTTACTAATCCATTTTT
1 TAATATCCTTTTTACTAATCCATTTTT
31191126 TTTAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.64
28 4 0.16
29 5 0.20
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (29 bp):
TAATATCCTTTTTACTAATCCATTTTTAC
Found at i:31191107 original size:15 final size:15
Alignment explanation
Indices: 31191072--31191117 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
31191062 GATCTATTTT
31191072 TAATATCCTTTTTAC
1 TAATATCCTTTTTAC
31191087 ---TATCCTTTTTAC
1 TAATATCCTTTTTAC
31191099 TAATATCCTTTTTAC
1 TAATATCCTTTTTAC
31191114 TAAT
1 TAAT
31191118 CCATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.43
15 16 0.57
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATCCTTTTTAC
Found at i:31191718 original size:14 final size:14
Alignment explanation
Indices: 31191683--31191719 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31191673 AACACAAGTA
*
31191683 ACTATTTCGAATTG
1 ACTATTTTGAATTG
31191697 ACTATTTTGAATTG
1 ACTATTTTGAATTG
31191711 ACTATTTTG
1 ACTATTTTG
31191720 GTGAATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (14 bp):
ACTATTTTGAATTG
Found at i:31191919 original size:42 final size:42
Alignment explanation
Indices: 31191860--31191972 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 42
31191850 TTTTATTAAG
* * *
31191860 TGAGATTTGATTTGCATGCTATGCATGCCGACTATGATAAAC
1 TGAGATTTGAGTTGCATGTTAAGCATGCCGACTATGATAAAC
* * *
31191902 TGAGATTTGAGTTGCATGTTAAGCATGCCGACTATGTTGACC
1 TGAGATTTGAGTTGCATGTTAAGCATGCCGACTATGATAAAC
*
31191944 TTAGATTTG-GTTCGCATGTTAAGCATGCC
1 TGAGATTTGAGTT-GCATGTTAAGCATGCC
31191973 TACTGAAGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 3 0.05
42 60 0.95
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (42 bp):
TGAGATTTGAGTTGCATGTTAAGCATGCCGACTATGATAAAC
Found at i:31196493 original size:6 final size:6
Alignment explanation
Indices: 31196484--31196523 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
31196474 AGAACAACTA
* *
31196484 AAAAAG AAAAAG AAAAAG AAAAAG AAAATG GAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
31196524 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:31200937 original size:29 final size:29
Alignment explanation
Indices: 31200903--31201162 Score: 367
Period size: 29 Copynumber: 9.0 Consensus size: 29
31200893 GATAGTTGAA
* *
31200903 ACCATCCCTTTTCATATTCAATGATCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
31200932 ACCATCCCTTTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
****
31200961 ACCATCCCTTTTCATATTCGATGGTTAAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
*
31200990 ACCATCCCTTTTCATATTCGATGGTCTTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * * * *
31201019 GCCATCCCTCTTAATATTCGATGTTCATC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
*
31201048 ACCATCCCTTTTCATATTCGATGGCCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
**
31201077 ACCATCCCTTTTCATATTCGATGGTCGAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
*
31201106 ACCATCCCTTTTCATATTCGATGGTCCTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
*
31201135 ACCATCTCTTTTCATATTCGATGGTCGT
1 ACCATCCCTTTTCATATTCGATGGTCGT
31201163 TTGTAACGCC
Statistics
Matches: 202, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 202 1.00
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATGGTCGTC
Found at i:31206919 original size:16 final size:17
Alignment explanation
Indices: 31206889--31206922 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31206879 ACCATTTTTG
31206889 AGAAAAAAAAGAAAAGA
1 AGAAAAAAAAGAAAAGA
*
31206906 AGAAAAACAA-AAAAGA
1 AGAAAAAAAAGAAAAGA
31206922 A
1 A
31206923 AACAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAGAAAAGA
Found at i:31207313 original size:29 final size:29
Alignment explanation
Indices: 31207226--31207343 Score: 137
Period size: 29 Copynumber: 4.1 Consensus size: 29
31207216 GGGTGTTATA
31207226 TCGTCACCATTCCTTTTCATATTCGATGG
1 TCGTCACCATTCCTTTTCATATTCGATGG
* * *
31207255 CCATCACCATCCCTTTTCATATTCGATGG
1 TCGTCACCATTCCTTTTCATATTCGATGG
* *
31207284 TCGTCATCATTCTTTTTCATATTCGATGG
1 TCGTCACCATTCCTTTTCATATTCGATGG
** * * * *
31207313 TCGTTGCCATCCCCTTTCATACTCTATGG
1 TCGTCACCATTCCTTTTCATATTCGATGG
31207342 TC
1 TC
31207344 ATCATTCAAT
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.41
Consensus pattern (29 bp):
TCGTCACCATTCCTTTTCATATTCGATGG
Found at i:31207323 original size:58 final size:58
Alignment explanation
Indices: 31207226--31207348 Score: 156
Period size: 58 Copynumber: 2.1 Consensus size: 58
31207216 GGGTGTTATA
* * *
31207226 TCGTCACCATTCCTTTTCATATTCGATGGCCATCACCATCCCTTTTCATATTCGATGG
1 TCGTCATCATTCCTTTTCATATTCGATGGCCATCACCATCCCCTTTCATACTCGATGG
* * * ** *
31207284 TCGTCATCATTCTTTTTCATATTCGATGGTCGTTGCCATCCCCTTTCATACTCTATGG
1 TCGTCATCATTCCTTTTCATATTCGATGGCCATCACCATCCCCTTTCATACTCGATGG
*
31207342 TCATCAT
1 TCGTCAT
31207349 TCAATGGTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (58 bp):
TCGTCATCATTCCTTTTCATATTCGATGGCCATCACCATCCCCTTTCATACTCGATGG
Found at i:31207385 original size:29 final size:29
Alignment explanation
Indices: 31207342--31207500 Score: 165
Period size: 29 Copynumber: 5.4 Consensus size: 29
31207332 TACTCTATGG
* **
31207342 TCATCATTCAATGGTCAAAACCATCCCTTT
1 TCAT-ATTCGATGGTCATCACCATCCCTTT
**
31207372 TCATATTCGATGGTTGTCACCATCCCTTT
1 TCATATTCGATGGTCATCACCATCCCTTT
* * *
31207401 TCATATTTGATGGTCGTCACCGTCCCTTT
1 TCATATTCGATGGTCATCACCATCCCTTT
*
31207430 TCATATTCGATGGTCCTCACCATCCCTTT
1 TCATATTCGATGGTCATCACCATCCCTTT
* * * ** *
31207459 TCATATTCAATAGTTAAAATCATCCCTTT
1 TCATATTCGATGGTCATCACCATCCCTTT
*
31207488 TCATATTTGATGG
1 TCATATTCGATGG
31207501 GCGTCAATAC
Statistics
Matches: 108, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 104 0.96
30 4 0.04
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (29 bp):
TCATATTCGATGGTCATCACCATCCCTTT
Found at i:31207443 original size:101 final size:101
Alignment explanation
Indices: 31207260--31207444 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
31207250 GATGGCCATC
* * * **
31207260 ACCATCCCTTTTCATATTCGATGGTCGTCATCATTCTTTTTCATATTCGATGGTCGTTGCCATCC
1 ACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCC
*
31207325 CCTTTCATACTCTATGGTCATCATTCAATGGTCAAA
66 CCTTTCATACTCGATGGTCATCATTCAATGGTCAAA
* * *
31207361 ACCATCCCTTTTCATATTCGATGGTTGTCACCATCCCTTTTCATATTTGATGGTCGTCACCGTCC
1 ACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCC
* *
31207426 CTTTTCATATTCGATGGTC
66 CCTTTCATACTCGATGGTC
31207445 CTCACCATCC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 73 1.00
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.40
Consensus pattern (101 bp):
ACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCC
CCTTTCATACTCGATGGTCATCATTCAATGGTCAAA
Found at i:31207485 original size:58 final size:58
Alignment explanation
Indices: 31207342--31207500 Score: 201
Period size: 58 Copynumber: 2.7 Consensus size: 58
31207332 TACTCTATGG
**
31207342 TCATCATTCAATGGTCAAAACCATCCCTTTTCATATTCGATGGTTGTCACCATCCCTTT
1 TCAT-ATTCAATGGTCAAAACCATCCCTTTTCATATTCGATGGTCCTCACCATCCCTTT
** *** *
31207401 TCATATTTGATGGTCGTCACCGTCCCTTTTCATATTCGATGGTCCTCACCATCCCTTT
1 TCATATTCAATGGTCAAAACCATCCCTTTTCATATTCGATGGTCCTCACCATCCCTTT
* * * *
31207459 TCATATTCAATAGTTAAAATCATCCCTTTTCATATTTGATGG
1 TCATATTCAATGGTCAAAACCATCCCTTTTCATATTCGATGG
31207501 GCGTCAATAC
Statistics
Matches: 82, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
58 78 0.95
59 4 0.05
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (58 bp):
TCATATTCAATGGTCAAAACCATCCCTTTTCATATTCGATGGTCCTCACCATCCCTTT
Found at i:31213849 original size:38 final size:38
Alignment explanation
Indices: 31213798--31213876 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
31213788 ACTCTTTAGC
31213798 TTCCTACTAATTGTTTTTGTTCTTTTAAAAAGAATAAA
1 TTCCTACTAATTGTTTTTGTTCTTTTAAAAAGAATAAA
* * *
31213836 TTCCTGCTGATTGTTTTTGTTCTTTTGAAAAGAATAAA
1 TTCCTACTAATTGTTTTTGTTCTTTTAAAAAGAATAAA
31213874 TTC
1 TTC
31213877 AGTATTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.48
Consensus pattern (38 bp):
TTCCTACTAATTGTTTTTGTTCTTTTAAAAAGAATAAA
Found at i:31215545 original size:20 final size:20
Alignment explanation
Indices: 31215500--31215567 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
31215490 CACATTAGTG
* *
31215500 CCCCTGTTTGTACTTTGCTA
1 CCCCTGTTTGTACTTCGGTA
**
31215520 GTCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* *
31215540 CCCCTGTTTGCACTTCGGTG
1 CCCCTGTTTGTACTTCGGTA
31215560 CCCCTGTT
1 CCCCTGTT
31215568 CGCACATATG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.07, C:0.31, G:0.21, T:0.41
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:31215572 original size:20 final size:20
Alignment explanation
Indices: 31215522--31215605 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
31215512 CTTTGCTAGT
* *
31215522 CCTGTTTGTACTTCGGTACC
1 CCTGTTTGCACTTCGGTGCC
31215542 CCTGTTTGCACTTCGGTGCC
1 CCTGTTTGCACTTCGGTGCC
* * **
31215562 CCTGTTCGCACATATGTGCC
1 CCTGTTTGCACTTCGGTGCC
* * *
31215582 CCTATTTGCAGTTCAGTGCC
1 CCTGTTTGCACTTCGGTGCC
31215602 CCTG
1 CCTG
31215606 ACTGCACGTA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.11, C:0.33, G:0.21, T:0.35
Consensus pattern (20 bp):
CCTGTTTGCACTTCGGTGCC
Found at i:31215584 original size:40 final size:40
Alignment explanation
Indices: 31215540--31215628 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
31215530 TACTTCGGTA
* * *
31215540 CCCCTGTTTGCACTTCGGTGCCCCTG-TTCGCACATATGTG
1 CCCCTATTTGCACTTCAGTGCCCCTGACT-GCACATATGTG
* *
31215580 CCCCTATTTGCAGTTCAGTGCCCCTGACTGCACGTATGTG
1 CCCCTATTTGCACTTCAGTGCCCCTGACTGCACATATGTG
31215620 CCCCTATTT
1 CCCCTATTT
31215629 TGCATTTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 42 0.98
41 1 0.02
ACGTcount: A:0.12, C:0.35, G:0.20, T:0.33
Consensus pattern (40 bp):
CCCCTATTTGCACTTCAGTGCCCCTGACTGCACATATGTG
Found at i:31217939 original size:21 final size:18
Alignment explanation
Indices: 31217887--31217946 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
31217877 TGTTTCCATC
*
31217887 CAAACCTATGTTATTATG
1 CAAACCCATGTTATTATG
31217905 CAAACCCATGTTATTATG
1 CAAACCCATGTTATTATG
* *
31217923 CCAACCCATGATATTATG
1 CAAACCCATGTTATTATG
*
31217941 TAAACC
1 CAAACC
31217947 TATGATTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (18 bp):
CAAACCCATGTTATTATG
Found at i:31218673 original size:19 final size:17
Alignment explanation
Indices: 31218649--31218701 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
31218639 TGGATTATTT
31218649 TTATTTAATATTAATATCA
1 TTATTTAATATTAA-AT-A
*
31218668 TTATTT-TTATTAAATA
1 TTATTTAATATTAAATA
31218684 TTAATATTAATATTAAAT
1 TT-AT-TTAATATTAAAT
31218702 TTAAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 3 0.10
17 4 0.14
18 8 0.28
19 14 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTAATATTAAATA
Found at i:31218676 original size:25 final size:25
Alignment explanation
Indices: 31218642--31218690 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
31218632 AGGGAGATGG
*
31218642 ATTATTTTTATTTAATATTAATATC
1 ATTATTTTTATTAAATATTAATATC
31218667 ATTATTTTTATTAAATATTAATAT
1 ATTATTTTTATTAAATATTAATAT
31218691 TAATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTTTATTAAATATTAATATC
Found at i:31218697 original size:25 final size:25
Alignment explanation
Indices: 31218644--31218697 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
31218634 GGAGATGGAT
* *
31218644 TATTTTTATTTAATATTAATATCAT
1 TATTTTTATTAAATATTAATATCAA
*
31218669 TATTTTTATTAAATATTAATATTAA
1 TATTTTTATTAAATATTAATATCAA
31218694 TATT
1 TATT
31218698 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTTTATTAAATATTAATATCAA
Found at i:31218730 original size:18 final size:18
Alignment explanation
Indices: 31218686--31218742 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
31218676 ATTAAATATT
**
31218686 AATATTAATATTAAATTTA
1 AATATTAATA-TATTTTTA
31218705 AATTTATTAATATATTTTTA
1 AA--TATTAATATATTTTTA
* *
31218725 AATATTTATGTATTTTTA
1 AATATTAATATATTTTTA
31218743 TATCTTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
20 8 0.25
21 8 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATATTAATATATTTTTA
Found at i:31223661 original size:20 final size:21
Alignment explanation
Indices: 31223636--31223693 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
31223626 AAGTACACCC
*
31223636 CAAAGGCT-TTTAGAATGCCA
1 CAAAGGCTAATTAGAATGCCA
31223656 CAAAGGCTAGATTAGAATGCCA
1 CAAAGGCTA-ATTAGAATGCCA
* *
31223678 TAAAGGCCAAATTAGA
1 CAAAGG-CTAATTAGA
31223694 TTACGCCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 8 0.25
22 22 0.69
23 2 0.06
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
CAAAGGCTAATTAGAATGCCA
Found at i:31223673 original size:22 final size:22
Alignment explanation
Indices: 31223645--31223693 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
31223635 CCAAAGGCTT
* *
31223645 TTAGAATGCCACAAAGGCTAGA
1 TTAGAATGCCACAAAGGCCAAA
*
31223667 TTAGAATGCCATAAAGGCCAAA
1 TTAGAATGCCACAAAGGCCAAA
31223689 TTAGA
1 TTAGA
31223694 TTACGCCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (22 bp):
TTAGAATGCCACAAAGGCCAAA
Found at i:31225718 original size:43 final size:43
Alignment explanation
Indices: 31225670--31225761 Score: 157
Period size: 43 Copynumber: 2.1 Consensus size: 43
31225660 GCAATCTTGT
*
31225670 ATCGATGCCAATAGCCTAGCTATGGTCTTACACAAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACAAAATCTCAA
**
31225713 ATCGATGCCAATAGCCCAGCTATGGTCTTACATGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACAAAATCTCAA
31225756 ATCGAT
1 ATCGAT
31225762 ATTGGAACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
ATCGATGCCAATAGCCCAGCTATGGTCTTACACAAAATCTCAA
Found at i:31227725 original size:32 final size:32
Alignment explanation
Indices: 31227689--31227753 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
31227679 TATAATGCTT
*
31227689 AGTAAGTTCGTAAATCATGAACATAGCTTACC
1 AGTAAGTTCGTAAATAATGAACATAGCTTACC
31227721 AGTAAGTTCGTAAATAATGAACATAGCTTACC
1 AGTAAGTTCGTAAATAATGAACATAGCTTACC
31227753 A
1 A
31227754 TTTCAAATGC
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:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (32 bp):
AGTAAGTTCGTAAATAATGAACATAGCTTACC
Found at i:31245150 original size:12 final size:12
Alignment explanation
Indices: 31245133--31245159 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31245123 CACACCCGTG
31245133 TTTTATAATTAA
1 TTTTATAATTAA
31245145 TTTTATAATTAA
1 TTTTATAATTAA
31245157 TTT
1 TTT
31245160 AATTCAAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTATAATTAA
Found at i:31252568 original size:29 final size:30
Alignment explanation
Indices: 31252512--31252568 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
31252502 CAACTTTTAT
**
31252512 TTTAGAAAAAAACAAAAATTAGTTGTCGAC
1 TTTAGAAAAAAACAAAAATTAGGAGTCGAC
* *
31252542 TTTA-AAAAAAATAAAAATTGGGAGTCG
1 TTTAGAAAAAAACAAAAATTAGGAGTCG
31252569 CCACCAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (30 bp):
TTTAGAAAAAAACAAAAATTAGGAGTCGAC
Found at i:31253868 original size:3 final size:3
Alignment explanation
Indices: 31253849--31253887 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
31253839 GCGCATGAAT
* *
31253849 ATA AAA ATA AAA ATA ATA ATAA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT
31253888 GATACAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:31253874 original size:16 final size:16
Alignment explanation
Indices: 31253849--31253886 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
31253839 GCGCATGAAT
31253849 ATAA-AAATAAAAATA
1 ATAATAAATAAAAATA
*
31253864 ATAATAAATAATAATA
1 ATAATAAATAAAAATA
31253880 ATAATAA
1 ATAATAA
31253887 TGATACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAATAAATAAAAATA
Found at i:31254388 original size:19 final size:19
Alignment explanation
Indices: 31254364--31254455 Score: 150
Period size: 19 Copynumber: 4.8 Consensus size: 19
31254354 AATCATATCT
31254364 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
31254383 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
31254402 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
31254421 TCTAAGA-TGACATATCATA
1 TCTAAGATTG-CATATCATA
31254440 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
31254456 CTTGAGAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
18 2 0.03
19 63 0.94
20 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:31254417 original size:38 final size:38
Alignment explanation
Indices: 31254341--31254455 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 38
31254331 AAATTAAATC
*
31254341 TCTAAGATTACAGAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACA-TATCATA---TCTAAGATTGCATATCATA
*
31254383 TCTAAGATTACATATCATATCTAAGATTGTATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
31254421 TCTAAGATGACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
31254456 CTTGAGAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
38 51 0.74
41 6 0.09
42 12 0.17
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:31254420 original size:24 final size:19
Alignment explanation
Indices: 31254341--31254455 Score: 140
Period size: 19 Copynumber: 5.8 Consensus size: 19
31254331 AAATTAAATC
*
31254341 TCTAAGATTACAGAATCATA
1 TCTAAGATTACA-TATCATA
*
31254361 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
31254383 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
**
31254402 TCTAAGATTGTATATCATA
1 TCTAAGATTACATATCATA
*
31254421 TCTAAGATGACATATCATA
1 TCTAAGATTACATATCATA
*
31254440 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
31254456 CTTGAGAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
22 6 0.07
23 11 0.13
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:31257364 original size:37 final size:38
Alignment explanation
Indices: 31257323--31257407 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
31257313 TAACATAAAG
* * *
31257323 AAATTGAAAAAATA-TTTTTAAACGGTTACGATTTGAC
1 AAATTCAAAAAATAGCTTCTAAACGGTTACGATTTGAC
* **
31257360 AAATTCAGAATGTAGCTTCTAAACGGTTACGATTTGAC
1 AAATTCAAAAAATAGCTTCTAAACGGTTACGATTTGAC
*
31257398 AAAATCAAAA
1 AAATTCAAAA
31257408 TCTAGCTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 10 0.26
38 29 0.74
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (38 bp):
AAATTCAAAAAATAGCTTCTAAACGGTTACGATTTGAC
Found at i:31257383 original size:38 final size:38
Alignment explanation
Indices: 31257341--31257414 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
31257331 AAAATATTTT
* * *
31257341 TAAACGGTTACGATTTGACAAATTCAGAATGTAGCTTC
1 TAAACGGTTACGATTTGACAAAATCAAAATCTAGCTTC
31257379 TAAACGGTTACGATTTGACAAAATCAAAATCTAGCT
1 TAAACGGTTACGATTTGACAAAATCAAAATCTAGCT
31257415 ATTGAGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (38 bp):
TAAACGGTTACGATTTGACAAAATCAAAATCTAGCTTC
Found at i:31260425 original size:24 final size:23
Alignment explanation
Indices: 31260398--31260475 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 23
31260388 TAGAACTTAA
31260398 TATAATCAGCACACACATACTTTG
1 TATAAT-AGCACACACATACTTTG
*
31260422 TATAGATAGCTCACACATAGAACTTT-
1 TATA-ATAGCACACACAT---ACTTTG
* * *
31260448 TATAATTAGTACACATATGCTTTG
1 TATAA-TAGCACACACATACTTTG
31260472 TATA
1 TATA
31260476 GACAGTTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
23 4 0.09
24 18 0.42
25 3 0.07
26 13 0.30
27 5 0.12
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (23 bp):
TATAATAGCACACACATACTTTG
Found at i:31260451 original size:26 final size:26
Alignment explanation
Indices: 31260416--31260496 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 26
31260406 GCACACACAT
31260416 ACTTTGTATAGATAGCTCACACATAGA
1 ACTTTGTATAGATAG-TCACACATAGA
31260443 ACTTT-TATA-ATTAGT-ACACATATG-
1 ACTTTGTATAGA-TAGTCACACATA-GA
* *
31260467 -CTTTGTATAGACAGTTCATACATAGA
1 ACTTTGTATAGATAG-TCACACATAGA
31260493 ACTT
1 ACTT
31260497 ATATAATCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
23 4 0.09
24 13 0.30
25 6 0.14
26 13 0.30
27 8 0.18
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (26 bp):
ACTTTGTATAGATAGTCACACATAGA
Found at i:31260471 original size:50 final size:50
Alignment explanation
Indices: 31260378--31260634 Score: 300
Period size: 50 Copynumber: 5.1 Consensus size: 50
31260368 CTACAATGCT
* * *
31260378 AGTTCGCATATAGAACTTAATATAATCAGCACACACATACTTTGTATAGAT
1 AGTTCACACATAGAACTT-ATATAATCAGCACACACATACTTTGTATAGAC
* * * * * *
31260429 AGCTCACACATAGAACTTTTATAATTAGTACACATATGCTTTGTATAGAC
1 AGTTCACACATAGAACTTATATAATCAGCACACACATACTTTGTATAGAC
* * *
31260479 AGTTCATACATAGAACTTATATAATCCA-CACACACATACTTCGTATAAAC
1 AGTTCACACATAGAACTTATATAAT-CAGCACACACATACTTTGTATAGAC
* ** * * *
31260529 AATTTGCACATAGAACTTATATAATAAGCACGCACATGCTTTGTATAGAC
1 AGTTCACACATAGAACTTATATAATCAGCACACACATACTTTGTATAGAC
* * *
31260579 AGTTCACACATAGAACTTATATAATTAGCTCACACATACTTTGTATAGAT
1 AGTTCACACATAGAACTTATATAATCAGCACACACATACTTTGTATAGAC
31260629 AGTTCA
1 AGTTCA
31260635 TAGACCCTTT
Statistics
Matches: 169, Mismatches: 35, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
49 1 0.01
50 152 0.90
51 16 0.09
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (50 bp):
AGTTCACACATAGAACTTATATAATCAGCACACACATACTTTGTATAGAC
Found at i:31261233 original size:22 final size:20
Alignment explanation
Indices: 31261208--31261250 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
31261198 AAAATTCTTC
31261208 CACGGTACTTCTAGTTATTCAA
1 CACGGTACTTCTA-TT-TTCAA
* *
31261230 CACGTTCCTTCTATTTTCAA
1 CACGGTACTTCTATTTTCAA
31261250 C
1 C
31261251 CATGACCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (20 bp):
CACGGTACTTCTATTTTCAA
Found at i:31273321 original size:18 final size:17
Alignment explanation
Indices: 31273262--31273322 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
31273252 GTACTCTTTC
*
31273262 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
31273281 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
31273298 TGTTTCTTTTTCAGTTTCT
1 T-TTTCTTTTTCAATTT-T
31273317 TTTTCT
1 TTTTCT
31273323 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:31274265 original size:11 final size:12
Alignment explanation
Indices: 31274248--31274295 Score: 62
Period size: 11 Copynumber: 3.8 Consensus size: 12
31274238 CTAGCTCTCT
31274248 TTTTTTTTCAAA
1 TTTTTTTTCAAA
31274260 TTTTTTTTTTCACAA
1 --TTTTTTTTCA-AA
31274275 TTTTTTTTC-AA
1 TTTTTTTTCAAA
31274286 TTTTTTTTCA
1 TTTTTTTTCA
31274296 CAACTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.34
13 9 0.28
14 10 0.31
15 2 0.06
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:31274265 original size:13 final size:13
Alignment explanation
Indices: 31274247--31274293 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
31274237 ACTAGCTCTC
31274247 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
31274260 TTTTTTTTTTCACAA
1 -TTTTTTTTTCA-AA
31274275 -TTTTTTTTC-AA
1 TTTTTTTTTCAAA
31274286 TTTTTTTT
1 TTTTTTTT
31274294 CACAACTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.06
12 7 0.23
13 9 0.29
14 11 0.35
15 2 0.06
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:31274266 original size:14 final size:14
Alignment explanation
Indices: 31274247--31274293 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 14
31274237 ACTAGCTCTC
31274247 TTTTTTTTTCAAAT
1 TTTTTTTTTCAAAT
31274261 TTTTTTTTTCACAA-
1 TTTTTTTTTCA-AAT
31274275 -TTTTTTTTC-AAT
1 TTTTTTTTTCAAAT
31274287 TTTTTTT
1 TTTTTTT
31274294 CACAACTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
13 15 0.50
14 11 0.37
15 2 0.07
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTCAAAT
Found at i:31274267 original size:15 final size:15
Alignment explanation
Indices: 31274247--31274282 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
31274237 ACTAGCTCTC
31274247 TTTTTTTTTCA-AAT
1 TTTTTTTTTCACAAT
31274261 TTTTTTTTTCACAAT
1 TTTTTTTTTCACAAT
31274276 TTTTTTT
1 TTTTTTT
31274283 CAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTCACAAT
Found at i:31274293 original size:15 final size:16
Alignment explanation
Indices: 31274247--31274282 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
31274237 ACTAGCTCTC
31274247 TTTTTTTTT--CAAAT
1 TTTTTTTTTCACAAAT
31274261 TTTTTTTTTCAC-AAT
1 TTTTTTTTTCACAAAT
31274276 TTTTTTT
1 TTTTTTT
31274283 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 10 0.50
16 1 0.05
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTTTCACAAAT
Found at i:31276805 original size:18 final size:17
Alignment explanation
Indices: 31276770--31276804 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
31276760 TTCTTTGTGT
*
31276770 ATTCAGTATTAAAAAAA
1 ATTCAGAATTAAAAAAA
31276787 ATTCAGAATTAAAAAAA
1 ATTCAGAATTAAAAAAA
31276804 A
1 A
31276805 AAGAGAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (17 bp):
ATTCAGAATTAAAAAAA
Found at i:31278852 original size:14 final size:15
Alignment explanation
Indices: 31278828--31278870 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
31278818 TATTGATCAA
31278828 TAAAAAGAAAAAGAG
1 TAAAAAGAAAAAGAG
*
31278843 -AAAAACAAAAAGAG
1 TAAAAAGAAAAAGAG
*
31278857 TGAAAAGAAAAAGA
1 TAAAAAGAAAAAGA
31278871 AAGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
TAAAAAGAAAAAGAG
Found at i:31278862 original size:15 final size:14
Alignment explanation
Indices: 31278829--31278880 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
31278819 ATTGATCAAT
31278829 AAAAAGAAAAAGAG
1 AAAAAGAAAAAGAG
*
31278843 AAAAACAAAAAGAG
1 AAAAAGAAAAAGAG
* *
31278857 TGAAAAGAAAAAGAA
1 -AAAAAGAAAAAGAG
31278872 AGAAAAGAA
1 A-AAAAGAA
31278881 TGAGGAGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAAGAG
Found at i:31282260 original size:14 final size:15
Alignment explanation
Indices: 31282236--31282278 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
31282226 TATTGATCAA
31282236 TAAAAAGAAAAAGAG
1 TAAAAAGAAAAAGAG
*
31282251 -AAAAACAAAAAGAG
1 TAAAAAGAAAAAGAG
*
31282265 TGAAAAGAAAAAGA
1 TAAAAAGAAAAAGA
31282279 AAGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
TAAAAAGAAAAAGAG
Found at i:31282270 original size:15 final size:14
Alignment explanation
Indices: 31282237--31282288 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
31282227 ATTGATCAAT
31282237 AAAAAGAAAAAGAG
1 AAAAAGAAAAAGAG
*
31282251 AAAAACAAAAAGAG
1 AAAAAGAAAAAGAG
* *
31282265 TGAAAAGAAAAAGAA
1 -AAAAAGAAAAAGAG
31282280 AGAAAAGAA
1 A-AAAAGAA
31282289 TGAGGAGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAAGAG
Found at i:31284220 original size:51 final size:51
Alignment explanation
Indices: 31284143--31284258 Score: 214
Period size: 51 Copynumber: 2.3 Consensus size: 51
31284133 AGGCTCATCG
31284143 TGTTTGCAAGCTCTACGTAGCTCAATTTTATTTTGTGGAGCTTCAATTAGCT
1 TGTTT-CAAGCTCTACGTAGCTCAATTTTATTTTGTGGAGCTTCAATTAGCT
31284195 TGTTTCAAGCTCTACGTAGCTCAATTTTATTTTGTGGAGCTTCAATTAGCT
1 TGTTTCAAGCTCTACGTAGCTCAATTTTATTTTGTGGAGCTTCAATTAGCT
*
31284246 TGTTTCCAGCTCT
1 TGTTTCAAGCTCT
31284259 TTACAACCTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
51 58 0.92
52 5 0.08
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (51 bp):
TGTTTCAAGCTCTACGTAGCTCAATTTTATTTTGTGGAGCTTCAATTAGCT
Found at i:31286996 original size:100 final size:100
Alignment explanation
Indices: 31286823--31287024 Score: 404
Period size: 100 Copynumber: 2.0 Consensus size: 100
31286813 AAATGGGTTC
31286823 AAAAGATGGTTTGGATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTATTTATAATTTAA
1 AAAAGATGGTTTGGATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTATTTATAATTTAA
31286888 TAGTTAAAATGGAATTGAAAAATAGAAATCAAGCG
66 TAGTTAAAATGGAATTGAAAAATAGAAATCAAGCG
31286923 AAAAGATGGTTTGGATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTATTTATAATTTAA
1 AAAAGATGGTTTGGATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTATTTATAATTTAA
31286988 TAGTTAAAATGGAATTGAAAAATAGAAATCAAGCG
66 TAGTTAAAATGGAATTGAAAAATAGAAATCAAGCG
31287023 AA
1 AA
31287025 GAACGATTCA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.31
Consensus pattern (100 bp):
AAAAGATGGTTTGGATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTATTTATAATTTAA
TAGTTAAAATGGAATTGAAAAATAGAAATCAAGCG
Found at i:31287874 original size:48 final size:48
Alignment explanation
Indices: 31287819--31287924 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31287809 TTGTCTTTTC
*
31287819 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31287867 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31287915 TTTCTTTTTC
1 TTTCTTTTTC
31287925 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31287921 original size:18 final size:17
Alignment explanation
Indices: 31287900--31287984 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
31287890 TTTTCACATC
31287900 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
* *
31287918 CTTTTTCCATGACACTCGTTT
1 CTTTTT-CA--A-TCTCATTT
* *
31287939 CTTTTACACTCTCATTT
1 CTTTTTCAATCTCATTT
*
31287956 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCA-TTT
31287975 CTTTTTCAAT
1 CTTTTTCAAT
31287985 TTCTTGTTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
17 10 0.19
18 20 0.38
19 8 0.15
20 2 0.04
21 9 0.17
22 3 0.06
ACGTcount: A:0.18, C:0.28, G:0.02, T:0.52
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:31294063 original size:21 final size:21
Alignment explanation
Indices: 31294020--31294065 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31294010 AAGAAAAAAA
**
31294020 GAAATGAAAGAAAAAGAGTGT
1 GAAATGAAAGAAAAAGAAAGT
31294041 GAAA-GAAAGCAAAAAGAAAGT
1 GAAATGAAAG-AAAAAGAAAGT
31294062 GAAA
1 GAAA
31294066 AAGAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.63, C:0.02, G:0.26, T:0.09
Consensus pattern (21 bp):
GAAATGAAAGAAAAAGAAAGT
Found at i:31294071 original size:6 final size:6
Alignment explanation
Indices: 31294046--31294093 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
31294036 AGTGTGAAAG
** * *
31294046 AAAGCAA AAAGAA AGTGAA AAAGAA AAAGAG AAGGAA AAAGAA AAAGA
1 AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
31294094 GATCGAGAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:31294074 original size:18 final size:18
Alignment explanation
Indices: 31294015--31294143 Score: 81
Period size: 18 Copynumber: 7.2 Consensus size: 18
31294005 TTTAAAAGAA
31294015 AAAAAGAAA-TG--AAAG
1 AAAAAGAAAGTGAAAAAG
**
31294030 AAAAAGAGTGTGAAAGAAAG
1 AAAAAGAAAGTG-AA-AAAG
31294050 CAAAAAGAAAGTGAAAAAG
1 -AAAAAGAAAGTGAAAAAG
31294069 AAAAAGAGAAG-GAAAAAG
1 AAAAAGA-AAGTGAAAAAG
* * **
31294087 AAAAAGAGA-TCGAGAGTG
1 AAAAAGAAAGT-GAAAAAG
* *
31294105 AAAAAGAATGTG-AGAAG
1 AAAAAGAAAGTGAAAAAG
*
31294122 AAAAAGAAAATTGAAAAAG
1 AAAAAG-AAAGTGAAAAAG
31294141 AAA
1 AAA
31294144 TTGAGTCTGA
Statistics
Matches: 85, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
15 7 0.08
16 2 0.02
17 8 0.09
18 37 0.44
19 15 0.18
20 6 0.07
21 10 0.12
ACGTcount: A:0.66, C:0.02, G:0.25, T:0.08
Consensus pattern (18 bp):
AAAAAGAAAGTGAAAAAG
Found at i:31295919 original size:21 final size:20
Alignment explanation
Indices: 31295875--31295923 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
31295865 TCAGCTCCCA
* *
31295875 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
31295895 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
31295916 TCAGCTCG
1 TCAGCTCG
31295924 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:31299678 original size:20 final size:20
Alignment explanation
Indices: 31299632--31299678 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31299622 AGCTCGTTTC
**
31299632 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31299652 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31299672 CAGCTCA
1 CAGCTCA
31299679 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31301456 original size:30 final size:30
Alignment explanation
Indices: 31301375--31301457 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
31301365 TCATATTCAA
31301375 CTCACGAGCTAAACCTTAGCTCAACTTTAG
1 CTCACGAGCTAAACCTTAGCTCAACTTTAG
* * * * * *
31301405 CTTAGGAGTTTAATCTCAGCTCAACTTTAG
1 CTCACGAGCTAAACCTTAGCTCAACTTTAG
*
31301435 CTCACGAGCTAAAGCTTAGCTCA
1 CTCACGAGCTAAACCTTAGCTCA
31301458 TTTTAGTTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCACGAGCTAAACCTTAGCTCAACTTTAG
Found at i:31303553 original size:22 final size:22
Alignment explanation
Indices: 31303523--31303566 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31303513 TTTGGTATTT
31303523 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31303545 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31303567 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31305373 original size:38 final size:38
Alignment explanation
Indices: 31305331--31305412 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
31305321 AATTGTGCTG
31305331 GCTTAGTTCAGCTGAATGTTAATGGGAGTTTATGAGCT
1 GCTTAGTTCAGCTGAATGTTAATGGGAGTTTATGAGCT
31305369 GCTTAGTTCAGCTGAATGTTAATGGGAGTTTATGAGCT
1 GCTTAGTTCAGCTGAATGTTAATGGGAGTTTATGAGCT
*
31305407 ACTTAG
1 GCTTAG
31305413 GGCACATTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (38 bp):
GCTTAGTTCAGCTGAATGTTAATGGGAGTTTATGAGCT
Found at i:31305487 original size:32 final size:33
Alignment explanation
Indices: 31305427--31305488 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
31305417 CATTACGGCT
* ***
31305427 CTTGAAGTGTGAACAAGCTAAGTTGAATGGTCA
1 CTTGAAGTGTGAACAAGCAAAACCGAATGGTCA
31305460 CTTG-AGTGTGAACAAGCAAAACCGAATGG
1 CTTGAAGTGTGAACAAGCAAAACCGAATGG
31305489 CCTTTGGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (33 bp):
CTTGAAGTGTGAACAAGCAAAACCGAATGGTCA
Found at i:31306577 original size:14 final size:14
Alignment explanation
Indices: 31306543--31306577 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
31306533 GTACGAATGG
*
31306543 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
31306557 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
31306571 AATGGTA
1 AATGGTA
31306578 TAAACAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.34, T:0.14
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:31309339 original size:236 final size:236
Alignment explanation
Indices: 31308926--31309394 Score: 884
Period size: 236 Copynumber: 2.0 Consensus size: 236
31308916 ATTCGGCTAT
31308926 TAGGCATTAGGCTATAAATAGTTACTCATTTTCTTGTAAAAGGACTTTTGACAAATTTCTGAATG
1 TAGGCATTAGGCTATAAATAGTTACTCATTTTCTTGTAAAAGGACTTTTGACAAATTTCTGAATG
31308991 AAATATCATTTTAGTGAGGCAATTCACTCTCTTTATTCTCCAAAGCTCAAATTGACTTATCTTCA
66 AAATATCATTTTAGTGAGGCAATTCACTCTCTTTATTCTCCAAAGCTCAAATTGACTTATCTTCA
* *
31309056 ACAAGTGGCATCAATCTGACTTTGTTTCGCACTTATCACTATTGGTGTGGCGTTCTTCATACCGT
131 ACAAGTGGCATCAATCTGACTTTGTTTCGAACTTATCACCATTGGTGTGGCGTTCTTCATACCGT
* *
31309121 AGGTTCCTATTTTGCTAAATAGAGGGTCTCGGTTTTATCCC
196 AGGTTCCTATTTTACTAAATAGAGGGTCTCAGTTTTATCCC
31309162 TAGGCATTAGGCTATAAATAGTTACTCATTTTCTTGTAAAAGGACTTTTGACAAATTTCTGAATG
1 TAGGCATTAGGCTATAAATAGTTACTCATTTTCTTGTAAAAGGACTTTTGACAAATTTCTGAATG
31309227 AAATATCATTTTAGTGAGGCAATTCACTCTCTTTATTCTCCAAAGCTCAAATTGACTTATCTTCA
66 AAATATCATTTTAGTGAGGCAATTCACTCTCTTTATTCTCCAAAGCTCAAATTGACTTATCTTCA
* *
31309292 ACAAGTGGCGTCAATCTGACTTTGTTTCGAACTTATCACCATTGGTGTGGCGTTCTTCATACCTT
131 ACAAGTGGCATCAATCTGACTTTGTTTCGAACTTATCACCATTGGTGTGGCGTTCTTCATACCGT
31309357 AGGTTCCTATTTTACTAAATAGAGGGTCTCAGTTTTAT
196 AGGTTCCTATTTTACTAAATAGAGGGTCTCAGTTTTAT
31309395 ATCACCATTG
Statistics
Matches: 227, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
236 227 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (236 bp):
TAGGCATTAGGCTATAAATAGTTACTCATTTTCTTGTAAAAGGACTTTTGACAAATTTCTGAATG
AAATATCATTTTAGTGAGGCAATTCACTCTCTTTATTCTCCAAAGCTCAAATTGACTTATCTTCA
ACAAGTGGCATCAATCTGACTTTGTTTCGAACTTATCACCATTGGTGTGGCGTTCTTCATACCGT
AGGTTCCTATTTTACTAAATAGAGGGTCTCAGTTTTATCCC
Found at i:31309436 original size:69 final size:69
Alignment explanation
Indices: 31309325--31309463 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
31309315 GTTTCGAACT
*
31309325 TATCACCATTGGTGTGGCGTTCTTCATACCTTAGGTTCCTATTTTACTAAATAGAGGGTCTCAGT
1 TATCACCATTGGTGTGGCGTTCTTCATACCGTAGGTTCCTATTTTACTAAATAGAGGGTCTCAGT
31309390 TTTA
66 TTTA
* *
31309394 TATCACCATTGTTGTGGCGTTCTTCATACCGTAGGTTCCTATTTTGCTAAATAGAGGGTCTCAGT
1 TATCACCATTGGTGTGGCGTTCTTCATACCGTAGGTTCCTATTTTACTAAATAGAGGGTCTCAGT
31309459 TTTA
66 TTTA
31309463 T
1 T
31309464 CCCAAATCCT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (69 bp):
TATCACCATTGGTGTGGCGTTCTTCATACCGTAGGTTCCTATTTTACTAAATAGAGGGTCTCAGT
TTTA
Found at i:31309755 original size:12 final size:12
Alignment explanation
Indices: 31309740--31309781 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
31309730 ATTGTAGATT
31309740 AAAAAAATTGAA
1 AAAAAAATTGAA
*
31309752 AAAAAAATCGAA
1 AAAAAAATTGAA
*
31309764 AAAAAAATTTAA
1 AAAAAAATTGAA
31309776 AAAAAA
1 AAAAAA
31309782 CAAATTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:31312652 original size:23 final size:22
Alignment explanation
Indices: 31312622--31312666 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
31312612 AAAAATCGAC
31312622 CTTAAGAGCGGATATCACCAAA
1 CTTAAGAGCGGATATCACCAAA
*
31312644 NCTTAAGAGCGGTTATCACCAAA
1 -CTTAAGAGCGGATATCACCAAA
31312667 TACGGATGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.20
Consensus pattern (22 bp):
CTTAAGAGCGGATATCACCAAA
Found at i:31316036 original size:20 final size:20
Alignment explanation
Indices: 31316013--31316059 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31316003 GGGTTAAGAT
*
31316013 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31316033 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31316053 TGAGCTG
1 TGAGCTG
31316060 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31318791 original size:38 final size:38
Alignment explanation
Indices: 31318737--31318818 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
31318727 GATCTCCGTT
* *
31318737 ACGAGCATCAATGACCCAATTTCGGTAGGAGATGGATC
1 ACGAGCATCAACGACCCAATTTCAGTAGGAGATGGATC
* *
31318775 ATGAGCATCAACGACCCAATTTCAGTGGGAGATGGATC
1 ACGAGCATCAACGACCCAATTTCAGTAGGAGATGGATC
31318813 ACGAGC
1 ACGAGC
31318819 CCAAATTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (38 bp):
ACGAGCATCAACGACCCAATTTCAGTAGGAGATGGATC
Found at i:31323600 original size:13 final size:12
Alignment explanation
Indices: 31323584--31323657 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 12
31323574 TTTTTTGCAA
31323584 TTTTTTTCCTTCT
1 TTTTTTTCCTT-T
31323597 TTTTTTT-CTTT
1 TTTTTTTCCTTT
*
31323608 TTTTTTTCGGATTT
1 TTTTTTTC--CTTT
31323622 TTTTTTTCGAAACTTT
1 TTTTTTTC----CTTT
**
31323638 TTTTTTAACTTT
1 TTTTTTTCCTTT
31323650 TTTTTTTC
1 TTTTTTTC
31323658 GAAGCTACGA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
11 8 0.17
12 13 0.27
13 7 0.15
14 11 0.23
16 9 0.19
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTCCTTT
Found at i:31325509 original size:20 final size:19
Alignment explanation
Indices: 31325486--31325550 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
31325476 AAGCTCAAAC
31325486 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
31325506 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
31325526 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
31325546 GAGCT
1 GAGCT
31325551 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:31326838 original size:17 final size:18
Alignment explanation
Indices: 31326816--31326849 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31326806 ACAACACTCC
*
31326816 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
31326833 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
31326850 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:31327913 original size:16 final size:14
Alignment explanation
Indices: 31327894--31327960 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 14
31327884 TTAACTTGAT
31327894 TTTTTTTTTGGTCACC
1 TTTTTTTTT-GTCA-C
31327910 TTTTTTTTTGCTCGA-
1 TTTTTTTTTG-TC-AC
31327925 TTTTTTTTT-TCAC
1 TTTTTTTTTGTCAC
* * *
31327938 TTTTTTTTTTTGAA
1 TTTTTTTTTGTCAC
31327952 TTTTTTTTT
1 TTTTTTTTT
31327961 CAATCAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 1 0.02
13 11 0.24
14 11 0.24
15 10 0.22
16 11 0.24
17 1 0.02
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTGTCAC
Found at i:31327955 original size:13 final size:14
Alignment explanation
Indices: 31327894--31327978 Score: 57
Period size: 14 Copynumber: 5.8 Consensus size: 14
31327884 TTAACTTGAT
*
31327894 TTTTTTTTTGGTCACC
1 TTTTTTTTT--TCACA
* *
31327910 TTTTTTTTTGCTCGA
1 TTTTTTTTTTCAC-A
*
31327925 TTTTTTTTTTCACT
1 TTTTTTTTTTCACA
*
31327939 TTTTTTTTTTGA-A
1 TTTTTTTTTTCACA
31327952 -TTTTTTTTTCAATCAA
1 TTTTTTTTTTC-A-C-A
31327968 TTTTTTTTTTC
1 TTTTTTTTTTC
31327979 GAAATTTTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
12 9 0.17
13 1 0.02
14 13 0.24
15 11 0.20
16 10 0.19
17 10 0.19
ACGTcount: A:0.11, C:0.12, G:0.06, T:0.72
Consensus pattern (14 bp):
TTTTTTTTTTCACA
Found at i:31327984 original size:15 final size:14
Alignment explanation
Indices: 31327910--31327986 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 14
31327900 TTTGGTCACC
31327910 TTTTTTTTTGCTCG-A
1 TTTTTTTTT--TCGAA
*
31327925 TTTTTTTTTTC-AC
1 TTTTTTTTTTCGAA
*
31327938 TTTTTTTTTTTGAA
1 TTTTTTTTTTCGAA
31327952 TTTTTTTTTCAATC-AA
1 TTTTTTTTT---TCGAA
31327968 TTTTTTTTTTCGAAA
1 TTTTTTTTTTCG-AA
31327983 TTTT
1 TTTT
31327987 CTTATTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
13 14 0.27
14 10 0.20
15 15 0.29
16 11 0.22
17 1 0.02
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:31329615 original size:20 final size:19
Alignment explanation
Indices: 31329592--31329656 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
31329582 AAGCTCAAAC
31329592 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
31329612 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
31329632 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
31329652 GAGCT
1 GAGCT
31329657 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:31332289 original size:79 final size:79
Alignment explanation
Indices: 31332178--31332401 Score: 231
Period size: 79 Copynumber: 2.8 Consensus size: 79
31332168 GCTACTCGTT
* * *
31332178 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGG
*
31332243 ATTTAATAACTCGCA
65 AATTAATAACTCGCA
* * *
31332258 CAAATGCCTTCAGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCAGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGG
* *
31332321 AATTAGTATCTCGCA
65 AATTAATAACTCGCA
* * * * * * *
31332336 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCAGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGG-CTTAACCC
31332399 GGA
63 GGA
31332402 CATCATTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
77 2 0.02
78 32 0.26
79 56 0.46
80 33 0.27
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGA
ATTAATAACTCGCA
Found at i:31332295 original size:39 final size:40
Alignment explanation
Indices: 31332178--31332401 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
31332168 GCTACTCGTT
* *
31332178 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * * *
31332218 CAATTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
31332258 CAAATGCCTTCAGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
31332297 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * * *
31332336 CAAATGCCTT-TGGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
31332377 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31332402 CATCATTCAA
Statistics
Matches: 158, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 71 0.45
40 72 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:31336769 original size:101 final size:102
Alignment explanation
Indices: 31336654--31336838 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
31336644 AAAGTGATGG
* *
31336654 TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTATGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
31336717 ACTATGTGCAGGCTACTATGCGTACGGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACGGGATAGCTTCGA
* * * *
31336755 TCACGTGTGTAGTACTATATTCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTATGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
31336820 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
31336839 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.49
102 35 0.46
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTATGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACGGGATAGCTTCGA
Found at i:31336784 original size:51 final size:50
Alignment explanation
Indices: 31336661--31336838 Score: 166
Period size: 51 Copynumber: 3.5 Consensus size: 50
31336651 TGGTCACGTA
* * * * * *
31336661 TGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-AT-GATCACATG
*
31336711 TGTAGTACTATGTGCAGGCTACTATGCGTA-CGGGATAGCT-TCGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTATGCGTATC-GGATAG-TAT-GATCACATG
* * * * *
31336762 TGTAGTACTATATTCAGGCTACTACGTGTATCGGATAGTGATGGTCACATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-ATGATCACATG
31336813 TGTAGTACTATGTGCAGGCTACTATG
1 TGTAGTACTATGTGCAGGCTACTATG
31336839 TGAACCGGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
49 1 0.01
50 31 0.30
51 70 0.67
52 2 0.02
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
TGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTATGATCACATG
Found at i:31343738 original size:209 final size:209
Alignment explanation
Indices: 31343378--31343797 Score: 840
Period size: 209 Copynumber: 2.0 Consensus size: 209
31343368 TTTCTCAACA
31343378 AGGGAAGAACTTACCACATTGGTGCAACTTCCACTATCGATGATCAATGAACTAGGTTGTCCACT
1 AGGGAAGAACTTACCACATTGGTGCAACTTCCACTATCGATGATCAATGAACTAGGTTGTCCACT
31343443 AATCAAACATCTCATGTGGAAAATGTTATCTCTTTGTTCGTACCCTTCCTCTTTAAACTGGACAT
66 AATCAAACATCTCATGTGGAAAATGTTATCTCTTTGTTCGTACCCTTCCTCTTTAAACTGGACAT
31343508 TTAAACCCCTTCGAGCAACAAGTGCTTTCTCACCATACTCCAAGTATTCTTCATACTCATCATGA
131 TTAAACCCCTTCGAGCAACAAGTGCTTTCTCACCATACTCCAAGTATTCTTCATACTCATCATGA
31343573 GTACGCACATCATC
196 GTACGCACATCATC
31343587 AGGGAAGAACTTACCACATTGGTGCAACTTCCACTATCGATGATCAATGAACTAGGTTGTCCACT
1 AGGGAAGAACTTACCACATTGGTGCAACTTCCACTATCGATGATCAATGAACTAGGTTGTCCACT
31343652 AATCAAACATCTCATGTGGAAAATGTTATCTCTTTGTTCGTACCCTTCCTCTTTAAACTGGACAT
66 AATCAAACATCTCATGTGGAAAATGTTATCTCTTTGTTCGTACCCTTCCTCTTTAAACTGGACAT
31343717 TTAAACCCCTTCGAGCAACAAGTGCTTTCTCACCATACTCCAAGTATTCTTCATACTCATCATGA
131 TTAAACCCCTTCGAGCAACAAGTGCTTTCTCACCATACTCCAAGTATTCTTCATACTCATCATGA
31343782 GTACGCACATCATC
196 GTACGCACATCATC
31343796 AG
1 AG
31343798 CATCTTCCAA
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 211 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (209 bp):
AGGGAAGAACTTACCACATTGGTGCAACTTCCACTATCGATGATCAATGAACTAGGTTGTCCACT
AATCAAACATCTCATGTGGAAAATGTTATCTCTTTGTTCGTACCCTTCCTCTTTAAACTGGACAT
TTAAACCCCTTCGAGCAACAAGTGCTTTCTCACCATACTCCAAGTATTCTTCATACTCATCATGA
GTACGCACATCATC
Found at i:31346229 original size:18 final size:18
Alignment explanation
Indices: 31346208--31346254 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
31346198 TTCCTTTTAC
* *
31346208 TATTTTATTTTCTTTATT
1 TATTGTATTTACTTTATT
*
31346226 TATTGTATTTAGTTTATT
1 TATTGTATTTACTTTATT
31346244 TAATTGT-TTTA
1 T-ATTGTATTTA
31346255 TTATTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (18 bp):
TATTGTATTTACTTTATT
Found at i:31355506 original size:29 final size:29
Alignment explanation
Indices: 31355462--31355675 Score: 266
Period size: 29 Copynumber: 7.4 Consensus size: 29
31355452 ATGACGTATC
* * *
31355462 GACGCCCATCCAATATGAAAAGTGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
* *
31355491 GACGACCTTCGAATATGAAAAGGCATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
*
31355520 GACGACCATCGAATATGAAAAGGGACGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** *
31355549 TTCAACCATCGAATATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
* * *
31355578 GACAACCATGGAATATTAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** *
31355607 TTCGACCATTGAATATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
*
31355636 GACGACCATTGAATATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
**
31355665 TTCGACCATCG
1 GACGACCATCG
31355676 TTTAGCACAC
Statistics
Matches: 159, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 159 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (29 bp):
GACGACCATCGAATATGAAAAGGGATGGT
Found at i:31355561 original size:58 final size:58
Alignment explanation
Indices: 31355462--31355675 Score: 302
Period size: 58 Copynumber: 3.7 Consensus size: 58
31355452 ATGACGTATC
* * * ** * *
31355462 GACGCCCATCCAATATGAAAAGTGATGGTGACGACCTTCGAATATGAAAAGGCATGGT
1 GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGT
* *
31355520 GACGACCATCGAATATGAAAAGGGACGGTTTCAACCATCGAATATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGT
* * * *
31355578 GACAACCATGGAATATTAAAAGGGATGGTTTCGACCATTGAATATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGT
*
31355636 GACGACCATTGAATATGAAAAGGGATGGTTTCGACCATCG
1 GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCG
31355676 TTTAGCACAC
Statistics
Matches: 137, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 137 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (58 bp):
GACGACCATCGAATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGT
Found at i:31370772 original size:41 final size:41
Alignment explanation
Indices: 31370690--31370772 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
31370680 TAAAGAGTGA
**
31370690 ATCGTGAAATCAAAGGTATCCTTGAAAAGGTAGTATGCCCT
1 ATCGTGAAATCAAAGGTATCCTTGAAAAGGTAGTACACCCT
*
31370731 ATCGTGAAATCAAATGTATCCTTGAAAAGGTAGTACACCCT
1 ATCGTGAAATCAAAGGTATCCTTGAAAAGGTAGTACACCCT
31370772 A
1 A
31370773 GTAGAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (41 bp):
ATCGTGAAATCAAAGGTATCCTTGAAAAGGTAGTACACCCT
Found at i:31372643 original size:3 final size:3
Alignment explanation
Indices: 31372631--31372722 Score: 80
Period size: 3 Copynumber: 30.3 Consensus size: 3
31372621 ACATTATTAG
* * * *
31372631 TAA TAG TAA TAA TAA TAA TAC TAA TAA TAA TGAA -AG TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * *
31372676 TAA TAAA TAA TAG TACA -AA TAA TAA TAA TAG TAT TAA TAA TAA TAA
1 TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31372722 T
1 T
31372723 GATAGCGATA
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
2 2 0.03
3 66 0.90
4 5 0.07
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31372660 original size:18 final size:18
Alignment explanation
Indices: 31372637--31372722 Score: 104
Period size: 18 Copynumber: 4.7 Consensus size: 18
31372627 TTAGTAATAG
*
31372637 TAATAATAATAATACTAA
1 TAATAATAATAATAGTAA
*
31372655 TAATAATGAA-AGTAGTAA
1 TAATAAT-AATAATAGTAA
31372673 TAATAATAAATAATAGTACA
1 TAATAAT-AATAATAGTA-A
*
31372693 -AATAATAATAATAGTAT
1 TAATAATAATAATAGTAA
31372710 TAATAATAATAAT
1 TAATAATAATAAT
31372723 GATAGCGATA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
18 44 0.75
19 14 0.24
20 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
TAATAATAATAATAGTAA
Found at i:31374475 original size:172 final size:171
Alignment explanation
Indices: 31374254--31374705 Score: 652
Period size: 172 Copynumber: 2.6 Consensus size: 171
31374244 TTGTTCTACC
* * *
31374254 ACAACTTTAGAGAGGTAAGATCCATCATTTTAATCTGCTCCGCTGCAACTTCAGAGAGATAGGAT
1 ACAACTTCAGAGAGATAAGAT-CATCATTTTAATCTGCTCC-ATGCAACTTCAGAGAGATAGGAT
** ** ** * * *
31374319 TTATAACTTCAATCTGCTCTATTGCAACTTCAAGGAGATAAGATTAGTTTATTCAGTCTGCTCCG
64 TGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTATTCAGTCTGCTCCG
*
31374384 CTGCATATTCAGGGAGATAAGACCTGATGCGATCTACTCTATT
129 CTGCATATTCAAGGAGATAAGACCTGATGCGATCTACTCTATT
* *
31374427 GCAACTTCAGAGAGATAAGATCAATCATTTTAATCTGCTCCATGCAACTTCAAAGAGATAGGATT
1 ACAACTTCAGAGAGATAAGATC-ATCATTTTAATCTGCTCCATGCAACTTCAGAGAGATAGGATT
* *
31374492 GGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTTCGC
65 GGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTATTCAGTCTGCTCCGC
* * *
31374557 TGCCTGTTCAAGGAGATAAGGCCTGATGCGATCTACTCTATT
130 TGCATATTCAAGGAGATAAGACCTGATGCGATCTACTCTATT
* * *
31374599 ACAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCCACTTCAGGGAAATAGGAT
1 ACAACTTCAGAGAGATAAGA-TCATCATTTTAATCTGCTCCA-TGCAACTTCAGAGAGATAGGAT
31374664 TGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAG
64 TGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAG
31374706 TCTTGTAACT
Statistics
Matches: 251, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
172 153 0.61
173 98 0.39
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (171 bp):
ACAACTTCAGAGAGATAAGATCATCATTTTAATCTGCTCCATGCAACTTCAGAGAGATAGGATTG
GTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTATTCAGTCTGCTCCGCT
GCATATTCAAGGAGATAAGACCTGATGCGATCTACTCTATT
Found at i:31374526 original size:128 final size:129
Alignment explanation
Indices: 31374297--31374533 Score: 334
Period size: 128 Copynumber: 1.8 Consensus size: 129
31374287 TCTGCTCCGC
* ** * *
31374297 TGCAACTTCAGAGAGATAGGATTTATAACTTCAATCTGCTCTATTGCAACTTCAAGGAGATAAGA
1 TGCAACTTCAGAGAGATAAGATCAATAACTTCAATCTGCTCCATTGCAACTTCAAAGAGATAAGA
*
31374362 TTAGTTTATTCAGTCTGCTCCGCTGCATATTCAGGGAGATAAGACCTGATGCGATCTACTCTAT
66 TTAGTTTATTCAGTCTGCTCCACTGCATATTCAGGGAGATAAGACCTGATGCGATCTACTCTAT
* * * *
31374426 TGCAACTTCAGAGAGATAAGATCAATCATTTTAATCTGCTCCA-TGCAACTTCAAAGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCAATAACTTCAATCTGCTCCATTGCAACTTCAAAGAGATAAGA
* * *
31374490 TTGGTTTCTTCTGTCTGCTCCACTGCA-ACTTCAGGGAGATAAGA
66 TTAGTTTATTCAGTCTGCTCCACTGCATA-TTCAGGGAGATAAGA
31374534 TTGGTTTATT
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
127 1 0.01
128 57 0.61
129 36 0.38
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (129 bp):
TGCAACTTCAGAGAGATAAGATCAATAACTTCAATCTGCTCCATTGCAACTTCAAAGAGATAAGA
TTAGTTTATTCAGTCTGCTCCACTGCATATTCAGGGAGATAAGACCTGATGCGATCTACTCTAT
Found at i:31374572 original size:44 final size:44
Alignment explanation
Indices: 31374287--31374705 Score: 167
Period size: 44 Copynumber: 9.7 Consensus size: 44
31374277 ATCATTTTAA
* * * *
31374287 TCTGCTCCGCTGCAACTTC-AGAGAGATAGGATT--TATAACTTCAA
1 TCTGCTCCACTGCAACTTCAAG-GAGATAAGATTGGT-TTA-TTCAG
* * *
31374331 TCTGCTCTATTGCAACTTCAAGGAGATAAGATTAGTTTATTCAG
1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCAG
* * * *
31374375 TCTGCTCCGCTGCATA-TTCAGGGAGATAAGACCT-G---ATGC-G
1 TCTGCTCCACTGCA-ACTTCAAGGAGATAAGA-TTGGTTTATTCAG
* * * *** *
31374415 ATCTACTCTATTGCAACTTC-AGAGAGATAAGATCAATCATT-TT-AA
1 -TCTGCTCCACTGCAACTTCAAG-GAGATAAGATTGGT--TTATTCAG
* * * *
31374460 TCTGCTCCA-TGCAACTTCAAAGAGATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCAG
*
31374503 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAG
1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCAG
* * *** ** * *
31374547 TCTGCTTCGCTGCCTGTTCAAGGAGATAAG---GCCTGATGC-G
1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCAG
* * * * ** *
31374587 ATCTACTCTATTACAACTTC-AGAGAGATAAGATTCATCATT-TT-AA
1 -TCTGCTCCACTGCAACTTCAAG-GAGATAAGATTGGT--TTATTCAG
* * * * * *
31374632 TCTGCTCCACTGCCACTTCAGGGAAATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCAG
*
31374676 TCTGCTCCACTGCAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTCAAGGAGATAAG
31374706 TCTTGTAACT
Statistics
Matches: 269, Mismatches: 76, Indels: 60
0.66 0.19 0.15
Matches are distributed among these distances:
40 6 0.02
41 50 0.19
42 4 0.01
43 30 0.11
44 168 0.62
45 9 0.03
46 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCAG
Found at i:31374645 original size:85 final size:85
Alignment explanation
Indices: 31374330--31374644 Score: 238
Period size: 85 Copynumber: 3.7 Consensus size: 85
31374320 TATAACTTCA
* * *
31374330 ATCTGCTCTATTGCAACTTCA-AGGAGATAAGATT-AGT--TTATTCAGTCTGCTCCGCTGCATA
1 ATCTACTCTATTGCAACTTCAGA-GAGATAAGATTCA-TCATT-TT-AATCTGCTCCACTGCATA
* *
31374391 TTCAGGGAGATAAGACCTGATGCG
62 TTCAAGGAGATAAGGCCTGATGCG
31374415 ATCTACTCTATTGCAACTTCAGAGAGATAAGA-TCAATCATTTTAATCTGCTCCA-TGCA-ACTT
1 ATCTACTCTATTGCAACTTCAGAGAGATAAGATTC-ATCATTTTAATCTGCTCCACTGCATA-TT
* * ** *
31374477 CAAAGAGATAGGATTGG-TTTCTTCTG
64 CAAGGAGATA--A--GGCCTGATGC-G
* * * * ** * * * * *
31374503 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT--TTATTCAGTCTGCTTCGCTGCCTGTT
1 ATCTACTCTATTGCAACTTCAGAGAGATAAGATTCATCATT-TT-AATCTGCTCCACTGCATATT
31374565 CAAGGAGATAAGGCCTGATGCG
64 CAAGGAGATAAGGCCTGATGCG
*
31374587 ATCTACTCTATTACAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGC
1 ATCTACTCTATTGCAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGC
31374645 CACTTCAGGG
Statistics
Matches: 174, Mismatches: 36, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
83 1 0.01
84 18 0.10
85 85 0.49
86 10 0.06
87 43 0.25
88 17 0.10
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (85 bp):
ATCTACTCTATTGCAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCATATTCA
AGGAGATAAGGCCTGATGCG
Found at i:31384881 original size:40 final size:40
Alignment explanation
Indices: 31384837--31384984 Score: 269
Period size: 40 Copynumber: 3.7 Consensus size: 40
31384827 GCAAACACAT
* *
31384837 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
31384877 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
31384917 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
31384957 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
31384985 TCCAATGCTC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:31407128 original size:18 final size:18
Alignment explanation
Indices: 31407105--31407148 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
31407095 AATTATAAAG
31407105 ATTCAATATGATTAAACA
1 ATTCAATATGATTAAACA
*
31407123 ATTCAATATTATTAAACA
1 ATTCAATATGATTAAACA
31407141 ATTCAATA
1 ATTCAATA
31407149 ATATAATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTCAATATGATTAAACA
Found at i:31407157 original size:21 final size:20
Alignment explanation
Indices: 31407109--31407153 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
31407099 ATAAAGATTC
31407109 AATATGATTAAACAATTCAAT
1 AATAT-ATTAAACAATTCAAT
31407130 -AT-TATTAAACAATTCAAT
1 AATATATTAAACAATTCAAT
31407148 AATATA
1 AATATA
31407154 ATTAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 15 0.68
19 3 0.14
20 4 0.18
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (20 bp):
AATATATTAAACAATTCAAT
Found at i:31407503 original size:18 final size:18
Alignment explanation
Indices: 31407480--31407516 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31407470 TATAGTTTGG
*
31407480 TATTTGATTTATTCGAAT
1 TATTTGAGTTATTCGAAT
31407498 TATTTGAGTTATTCGAAT
1 TATTTGAGTTATTCGAAT
31407516 T
1 T
31407517 TGAAAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TATTTGAGTTATTCGAAT
Found at i:31407740 original size:15 final size:15
Alignment explanation
Indices: 31407722--31407760 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
31407712 AGAAAGAAAA
* *
31407722 AATGAATGAATGAGT
1 AATGAATGAAGGAAT
31407737 AATGAATGAAGGAAT
1 AATGAATGAAGGAAT
*
31407752 AATGGATGA
1 AATGAATGA
31407761 TTTTTAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (15 bp):
AATGAATGAAGGAAT
Found at i:31408396 original size:31 final size:31
Alignment explanation
Indices: 31408361--31408453 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
31408351 AGGAAAATTA
31408361 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
*
31408392 CAAGAGTAATTGAATCCTAATAAAATTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
31408423 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
31408454 AAAATTATCT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:31410055 original size:39 final size:39
Alignment explanation
Indices: 31410012--31410089 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
31410002 TTAAACGTTG
*
31410012 AGGTTAGCATTTGGGTTGTTGAATATGCCGAACTTGGAT
1 AGGTTAGCATTTGGGTTGTTCAATATGCCGAACTTGGAT
*
31410051 AGGTTAGCATTTGGGTTGTTCAATATGCCGAATTTGGAT
1 AGGTTAGCATTTGGGTTGTTCAATATGCCGAACTTGGAT
31410090 TTAGGGAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.37
Consensus pattern (39 bp):
AGGTTAGCATTTGGGTTGTTCAATATGCCGAACTTGGAT
Found at i:31411776 original size:49 final size:49
Alignment explanation
Indices: 31411721--31412847 Score: 1977
Period size: 49 Copynumber: 23.2 Consensus size: 49
31411711 AATTCTAAAT
*
31411721 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31411770 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31411819 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31411868 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31411917 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31411966 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31412015 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31412064 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31412113 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31412162 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31412211 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412260 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
* *
31412307 TGTGAATAGGGCTTAATGGCCGATGTGATGAATGTGAAAGTG--TATATG
1 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
* *
31412355 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412404 TGTGATAAGGCTTAATGGCCGATGGGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412453 TGTGATAAGGCTTAATGGCCGATGGGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412502 TGTGATAAGGCTTAATGGCCGATGGGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412551 TGTGATAAGGCTTAATGGCCGATGGGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412600 TGTGATAAGGCTTAATGGCCGATGGGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412649 TGTGATAAGGCTTAATGGCCGATGGGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412698 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG--TATATG
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
31412745 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
* * ** * * * *
31412792 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATA-A-A
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
31412839 TGTGATAAG
1 TGTGATAAG
31412848 TCCTGAAGGG
Statistics
Matches: 1047, Mismatches: 26, Indels: 12
0.96 0.02 0.01
Matches are distributed among these distances:
47 135 0.13
48 45 0.04
49 867 0.83
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (49 bp):
TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
Found at i:31413022 original size:37 final size:37
Alignment explanation
Indices: 31412968--31413043 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
31412958 GAGTTCTAAG
* * *
31412968 GACCCGATGACTACGTGTGGGGATTTTGTCCGGGTAA
1 GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
*
31413005 GACCCGATAACTTCGTGTGGAGATTATGTCCGGGTAA
1 GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
31413042 GA
1 GA
31413044 TTTCGTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.26
Consensus pattern (37 bp):
GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAA
Found at i:31418694 original size:12 final size:12
Alignment explanation
Indices: 31418677--31418702 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31418667 CAAAAATTTA
31418677 AAAATACTAAAT
1 AAAATACTAAAT
31418689 AAAATACTAAAT
1 AAAATACTAAAT
31418701 AA
1 AA
31418703 GAATTTAAAA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATACTAAAT
Found at i:31419279 original size:21 final size:21
Alignment explanation
Indices: 31419253--31419307 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
31419243 CACGCAAAAG
*
31419253 CTTGTGTCGCGACACAAGGGT
1 CTTGTGTCGCGACACAAAGGT
* * *
31419274 CTTGTGTTGCAACACAAAGTT
1 CTTGTGTCGCGACACAAAGGT
*
31419295 C-TGTGTCACGACA
1 CTTGTGTCGCGACA
31419308 TGCACACCCT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (21 bp):
CTTGTGTCGCGACACAAAGGT
Found at i:31426065 original size:30 final size:31
Alignment explanation
Indices: 31426024--31426094 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
31426014 TTAATAGCCT
* *
31426024 AAATGTTTATAATTTTTAAAGGA-TTAAATTA
1 AAAT-TTTATAATTTTTAAAGGAGTCAAAGTA
**
31426055 AAATTTTATAATTTTTTGAGGAGTCAAAGTA
1 AAATTTTATAATTTTTAAAGGAGTCAAAGTA
31426086 AAATTTTAT
1 AAATTTTAT
31426095 CTTTACGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (31 bp):
AAATTTTATAATTTTTAAAGGAGTCAAAGTA
Found at i:31427116 original size:21 final size:19
Alignment explanation
Indices: 31427087--31427125 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
31427077 TAAAAAATAT
*
31427087 AATATTTTAAATATATTAAAA
1 AATAATTTAAA-A-ATTAAAA
31427108 AATAATTTAAAAATTAAA
1 AATAATTTAAAAATTAAA
31427126 TATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATTTAAAAATTAAAA
Found at i:31430601 original size:55 final size:56
Alignment explanation
Indices: 31430490--31430604 Score: 178
Period size: 55 Copynumber: 2.0 Consensus size: 56
31430480 TTAACCCTTC
*
31430490 TTACTTTTACAAACAAATAGAACATTTAAAAAAAAAAATGGTACATGATAGTAAACCT
1 TTACTTTTACAAACAAATAAAACATTT--AAAAAAAAATGGTACATGATAGTAAACCT
* *
31430548 TTACTTTTACAAGCCAATAAAACATTT-AAAAAAAATGGTACATGATAGTAAACCT
1 TTACTTTTACAAACAAATAAAACATTTAAAAAAAAATGGTACATGATAGTAAACCT
31430603 TT
1 TT
31430605 TTTTTTTTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
55 30 0.56
58 24 0.44
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (56 bp):
TTACTTTTACAAACAAATAAAACATTTAAAAAAAAATGGTACATGATAGTAAACCT
Found at i:31432826 original size:43 final size:44
Alignment explanation
Indices: 31432744--31432890 Score: 117
Period size: 43 Copynumber: 3.4 Consensus size: 44
31432734 TTGGCATCGC
* * * **
31432744 AGTGCATCAT-TGGATATACCAAAAGAAAGATAC-AGGCACACAT
1 AGTGCATCATCTGGATAAATCAAAACAATTATACTA-GCACACAT
*
31432787 AGTGCATCATCTGGA-AAATCAAAGCAATTATACTAGCACACGA-
1 AGTGCATCATCTGGATAAATCAAAACAATTATACTAGCACAC-AT
* * * * *
31432830 GGTACATCA-CTGGATGAATCAAAACAATTATATTGGCACACAT
1 AGTGCATCATCTGGATAAATCAAAACAATTATACTAGCACACAT
* *
31432873 AATGCAACATC-GGATAAA
1 AGTGCATCATCTGGATAAA
31432891 CTGAGGCAAT
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
42 6 0.07
43 68 0.84
44 7 0.09
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (44 bp):
AGTGCATCATCTGGATAAATCAAAACAATTATACTAGCACACAT
Found at i:31435928 original size:13 final size:13
Alignment explanation
Indices: 31435910--31435934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31435900 TGGAAAACAA
31435910 ATTAATTAGTAAG
1 ATTAATTAGTAAG
31435923 ATTAATTAGTAA
1 ATTAATTAGTAA
31435935 ATCCTCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
ATTAATTAGTAAG
Found at i:31437619 original size:18 final size:16
Alignment explanation
Indices: 31437596--31437635 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
31437586 GAATCCTTGT
31437596 TAAAATAAAATACAAAGG
1 TAAAATAAAATA-AAA-G
31437614 TAAAATAAAATAAAAG
1 TAAAATAAAATAAAAG
31437630 TAAAAT
1 TAAAAT
31437636 GCATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 12 0.55
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (16 bp):
TAAAATAAAATAAAAG
Found at i:31444408 original size:51 final size:51
Alignment explanation
Indices: 31444309--31444471 Score: 256
Period size: 51 Copynumber: 3.2 Consensus size: 51
31444299 ACTTATGATC
* * *
31444309 AGTGACAAATGATAAGTGGTAGC-TTAGCTACACTTATCTGATCGGTGACA
1 AGTGACAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
31444359 AGTGACAAGTAATAAGTGGTAGCTTTAGCTATACTTATCTGATCAGTGACA
1 AGTGACAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
31444410 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
31444461 AATGACAAGTA
1 AGTGACAAGTA
31444472 GGGGTGAGCA
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 21 0.20
51 82 0.80
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:31444551 original size:9 final size:9
Alignment explanation
Indices: 31444537--31444567 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31444527 GTTAAACGAA
31444537 TCGAGTTAT
1 TCGAGTTAT
*
31444546 TCGAGTTAA
1 TCGAGTTAT
31444555 TCGAGTTAT
1 TCGAGTTAT
31444564 TCGA
1 TCGA
31444568 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:31444725 original size:21 final size:21
Alignment explanation
Indices: 31444684--31444726 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31444674 ACCCCAAACT
* *
31444684 CCCAAACCTTTTTACTTTTCC
1 CCCAAAACTTTTTACTCTTCC
31444705 CCCAAAAC-TTTTACTCCTTCC
1 CCCAAAACTTTTTACT-CTTCC
31444726 C
1 C
31444727 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (21 bp):
CCCAAAACTTTTTACTCTTCC
Found at i:31445711 original size:7 final size:7
Alignment explanation
Indices: 31445699--31445724 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31445689 GCTCACCCCT
31445699 AGTGACA
1 AGTGACA
31445706 AGTGACA
1 AGTGACA
31445713 AGTGACA
1 AGTGACA
31445720 AGTGA
1 AGTGA
31445725 TAAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (7 bp):
AGTGACA
Done.