Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 92 of 211
Found at i:28728009 original size:55 final size:55
Alignment explanation
Indices: 28727925--28728081 Score: 208
Period size: 55 Copynumber: 3.0 Consensus size: 55
28727915 ATATATACAC
**
28727925 TTTCACATTCATCGCATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
1 TTTCACATTCATCATATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
28727980 TTTCACATTCATCATATCGGCTATTAGGCCTTATCACATATATACACTTTCACA-
1 TTTCACATTCATCATATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
* *
28728034 -TT--CA-TCA-CAT-T-GGCCATTAGGTCTTATCAC--ATATACACTTTCACAT
1 TTTCACATTCATCATATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
28728080 TT
1 TT
28728082 ATTCAAATAT
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
45 15 0.16
47 18 0.19
48 1 0.01
49 3 0.03
50 3 0.03
51 2 0.02
53 2 0.02
55 52 0.54
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (55 bp):
TTTCACATTCATCATATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
Found at i:28728054 original size:102 final size:100
Alignment explanation
Indices: 28727813--28728081 Score: 336
Period size: 102 Copynumber: 2.7 Consensus size: 100
28727803 CCCTTCGGGA
* * * * * *
28727813 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GCCCTATCACATAT--A--
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATATACACT
* *
28727873 -T-ACACTTTCACATTTATCACATCGGCCATTAGGC
65 TTCACATTTTCACATTCATCACATCGGCCATTAGGC
* *
28727907 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATACAC
* *
28727972 TTTCACATTTTCACATTCATCATATCGGCTATTAGGC
64 TTTCACATTTTCACATTCATCACATCGGCCATTAGGC
* *
28728009 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGTCTTATCACATATACACTT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACTT
28728074 TCACATTT
66 TCACATTT
28728082 ATTCAAATAT
Statistics
Matches: 150, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
93 2 0.01
94 44 0.29
96 4 0.03
98 1 0.01
100 18 0.12
101 1 0.01
102 80 0.53
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (100 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACTT
TCACATTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28732003 original size:25 final size:24
Alignment explanation
Indices: 28731966--28732015 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
28731956 AAGGAATTCG
28731966 CACACACACAGTGCCTCTAATCATT
1 CACACACACAGTG-CTCTAATCATT
* *
28731991 CACACACATAGTGCTCTATTCATT
1 CACACACACAGTGCTCTAATCATT
28732015 C
1 C
28732016 GTTATTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (24 bp):
CACACACACAGTGCTCTAATCATT
Found at i:28732230 original size:40 final size:40
Alignment explanation
Indices: 28732174--28732383 Score: 312
Period size: 40 Copynumber: 5.2 Consensus size: 40
28732164 AGGCCCGAGT
* * ** *
28732174 ATACGTCACCAGCACGAATGCTCTTCGGGGTTTAGCACGG
1 ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
* * ** *
28732214 ATATATCACTAGCACGAATGCTTTTCGAAACTTAGTCCGG
1 ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
*
28732254 ATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGG
1 ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
28732294 ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
1 ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
*
28732334 ATACATCACTAGCACGAATGGTCTTCGGGACTTAGCCCGG
1 ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
28732374 ATACATCACT
1 ATACATCACT
28732384 CTCAATTCTC
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 154 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
Found at i:28733875 original size:47 final size:47
Alignment explanation
Indices: 28733804--28734110 Score: 485
Period size: 47 Copynumber: 6.6 Consensus size: 47
28733794 CCCTTCGGGA
* * * * *
28733804 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
*
28733851 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28733898 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28733945 CTTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28733992 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28734039 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28734086 CTTATCAC--ATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28734111 TATTCAAATA
Statistics
Matches: 243, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 17 0.07
46 2 0.01
47 224 0.92
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28740438 original size:34 final size:35
Alignment explanation
Indices: 28740387--28740477 Score: 141
Period size: 34 Copynumber: 2.6 Consensus size: 35
28740377 GTATATGTTT
*
28740387 TATATA-TGGCGAATTGATTTGTATATGTATAC-A
1 TATATATTGCCGAATTGATTTGTATATGTATACAA
28740420 TATATATTGCCGAATTGATTTGTATATGTATACATA
1 TATATATTGCCGAATTGATTTGTATATGTATACA-A
*
28740456 TATATATTGTCGAATTGATTTG
1 TATATATTGCCGAATTGATTTG
28740478 AGCATTGGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
33 6 0.11
34 25 0.47
36 22 0.42
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (35 bp):
TATATATTGCCGAATTGATTTGTATATGTATACAA
Found at i:28756656 original size:23 final size:23
Alignment explanation
Indices: 28756612--28756656 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28756602 TATGAGGAGA
*
28756612 AATGGTTTTTGAAGAAATTTTTC
1 AATGGTTTTTCAAGAAATTTTTC
*
28756635 AATGGTTATTTCAAGCAATTTT
1 AATGGTT-TTTCAAGAAATTTT
28756657 ACTTGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (23 bp):
AATGGTTTTTCAAGAAATTTTTC
Found at i:28759217 original size:41 final size:41
Alignment explanation
Indices: 28759171--28759269 Score: 189
Period size: 41 Copynumber: 2.4 Consensus size: 41
28759161 AGGCTTGTGC
*
28759171 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTAAAATATTTCAGACTATACGT
28759212 CTAGCAGGCTTAATGCCGGTAAAATATTTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTAAAATATTTCAGACTATACGT
28759253 CTAGCAGGCTTAATGCC
1 CTAGCAGGCTTAATGCC
28759270 AGTGTACTGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTAAAATATTTCAGACTATACGT
Found at i:28767475 original size:22 final size:22
Alignment explanation
Indices: 28767448--28767492 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28767438 TTATTAACAC
28767448 AAATTAAATTAGA-TATAAATTA
1 AAATT-AATTAGATTATAAATTA
*
28767470 AAATTAATTATATTATAAATTA
1 AAATTAATTAGATTATAAATTA
28767492 A
1 A
28767493 TACATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTAATTAGATTATAAATTA
Found at i:28767499 original size:17 final size:17
Alignment explanation
Indices: 28767452--28767499 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
28767442 TAACACAAAT
*
28767452 TAAATTAGATATAAATTA
1 TAAATTA-ATATATATTA
28767470 -AAATTAAT-TATATTA
1 TAAATTAATATATATTA
*
28767485 TAAATTAATACATAT
1 TAAATTAATATATAT
28767500 AATTTTGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATTAATATATATTA
Found at i:28782377 original size:47 final size:47
Alignment explanation
Indices: 28782306--28782849 Score: 903
Period size: 47 Copynumber: 11.6 Consensus size: 47
28782296 CCCTTCGGGA
* * * * * *
28782306 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28782353 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28782400 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28782447 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28782494 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28782541 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28782588 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28782635 CTTATCACATATATATACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28782682 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28782729 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28782778 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28782825 CTTATCAC--ATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28782850 TATTCAAATA
Statistics
Matches: 470, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
45 17 0.04
47 409 0.87
49 44 0.09
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28787682 original size:12 final size:10
Alignment explanation
Indices: 28787655--28787695 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
28787645 GAAAATAGTC
*
28787655 AAAATTAATC
1 AAAATTAATT
28787665 AAAATTAACTAT
1 AAAATTAA-T-T
28787677 AAAATTAATT
1 AAAATTAATT
28787687 AAAATTAAT
1 AAAATTAAT
28787696 CATGTTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 18 0.64
11 2 0.07
12 8 0.29
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATT
Found at i:28804757 original size:68 final size:68
Alignment explanation
Indices: 28804648--28804782 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
28804638 GAGTTATAAC
* *
28804648 ACTATCATAGGTTATCTAATGGCATGAATATCTAGACTCACACACGCTACGTTCAGTTCAAGAAT
1 ACTATCACAGGTTATCTAATGGCATGAATATCTAGACTCACACACGCTACGTTCAGTCCAAGAAT
28804713 CAT
66 CAT
* *
28804716 ACTATCACAGGTTATCTAATGGCATGTATATCTAGACTCACACACTCTACGTTCAGTCCAAGAAT
1 ACTATCACAGGTTATCTAATGGCATGAATATCTAGACTCACACACGCTACGTTCAGTCCAAGAAT
28804781 CA
66 CA
28804783 ACAAGCCGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (68 bp):
ACTATCACAGGTTATCTAATGGCATGAATATCTAGACTCACACACGCTACGTTCAGTCCAAGAAT
CAT
Found at i:28806027 original size:17 final size:17
Alignment explanation
Indices: 28805987--28806028 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
28805977 TATAACTCTG
*
28805987 ACAAGCTTCCAACTCGA
1 ACAAGCTTCCAACCCGA
*
28806004 ATAAGCTTCCAACCCGA
1 ACAAGCTTCCAACCCGA
*
28806021 ACGAGCTT
1 ACAAGCTT
28806029 TCAATTCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.19
Consensus pattern (17 bp):
ACAAGCTTCCAACCCGA
Found at i:28818500 original size:41 final size:41
Alignment explanation
Indices: 28818433--28818582 Score: 140
Period size: 41 Copynumber: 3.7 Consensus size: 41
28818423 ATGATATTCG
* * * **
28818433 GGCTTTGTGCCTAGCAGGATTTATGCCGGTGAATTATAGCA
1 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGAACCATAGCA
* * *
28818474 GGCTTTATGCCTCA-CAGGCTTCATGCCAGTGTACCATATCA
1 GGCTTTATGCCT-AGCAGGCTTCATGCCGGTGAACCATAGCA
* * * * *
28818515 GGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTATCATATCT
1 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGAACCATAGCA
* * *
28818556 GGCTTTGTGCCTAGAAGGCTTTATGCC
1 GGCTTTATGCCTAGCAGGCTTCATGCC
28818583 AATGTGGTAT
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.01
41 89 0.98
42 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (41 bp):
GGCTTTATGCCTAGCAGGCTTCATGCCGGTGAACCATAGCA
Found at i:28818575 original size:82 final size:82
Alignment explanation
Indices: 28818433--28818583 Score: 187
Period size: 82 Copynumber: 1.8 Consensus size: 82
28818423 ATGATATTCG
* * * *
28818433 GGCTTTGTGCCTAGCAGGATTTATGCCGGTGAATTATAGCAGGCTTTATGCCTCACAGGCTTCAT
1 GGCTTTATGCCTAGCAGGATTCATGCCGGTGAATCATAGCAGGCTTTATGCCTCAAAGGCTTCAT
28818498 GCCAGTGTACCATATCA
66 GCCAGTGTACCATATCA
* * * * * * *
28818515 GGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTATCATATCTGGCTTTGTGCCT-AGAAGGCTTTA
1 GGCTTTATGCCTAGCAGGATTCATGCCGGTGAATCATAGCAGGCTTTATGCCTCA-AAGGCTTCA
28818579 TGCCA
65 TGCCA
28818584 ATGTGGTATC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 1 0.02
82 56 0.98
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (82 bp):
GGCTTTATGCCTAGCAGGATTCATGCCGGTGAATCATAGCAGGCTTTATGCCTCAAAGGCTTCAT
GCCAGTGTACCATATCA
Found at i:28843874 original size:21 final size:21
Alignment explanation
Indices: 28843850--28843890 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28843840 GCACTTCTCA
*
28843850 TGTTTGTTCGCTT-TCCTTTTT
1 TGTTT-TTCCCTTCTCCTTTTT
28843871 TGTTTTTCCCTTCTCCTTTT
1 TGTTTTTCCCTTCTCCTTTT
28843891 CTCTGCTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.00, C:0.24, G:0.10, T:0.66
Consensus pattern (21 bp):
TGTTTTTCCCTTCTCCTTTTT
Found at i:28845360 original size:28 final size:28
Alignment explanation
Indices: 28845320--28845384 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
28845310 ACGATACTGA
* *
28845320 TACTGTTTTGGGCTAAGGCCCACATTAT
1 TACTGTATTGGGCTAAAGCCCACATTAT
* *
28845348 TACTTTATTGGGCTAAAGCCCACATTGT
1 TACTGTATTGGGCTAAAGCCCACATTAT
28845376 TACTGTATT
1 TACTGTATT
28845385 AGTTTAAGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (28 bp):
TACTGTATTGGGCTAAAGCCCACATTAT
Found at i:28850704 original size:28 final size:29
Alignment explanation
Indices: 28850651--28850705 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
28850641 GCTAGTTTAA
28850651 AATATTTACATAAAAAGACAACTAATTTC
1 AATATTTACATAAAAAGACAACTAATTTC
* *
28850680 AATATTTACA-GAAAGGACAACTAATT
1 AATATTTACATAAAAAGACAACTAATT
28850706 ACAGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (29 bp):
AATATTTACATAAAAAGACAACTAATTTC
Found at i:28862440 original size:7 final size:7
Alignment explanation
Indices: 28862425--28862456 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28862415 CTGGGATTGT
*
28862425 TTTGGAC
1 TTTGCAC
28862432 TTTGCAC
1 TTTGCAC
28862439 TTTGCAC
1 TTTGCAC
28862446 TTTGCAC
1 TTTGCAC
28862453 TTTG
1 TTTG
28862457 GATTGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (7 bp):
TTTGCAC
Found at i:28868821 original size:40 final size:40
Alignment explanation
Indices: 28868733--28868963 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
28868723 ATAACCACAA
* * *
28868733 GCACAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28868772 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
28868812 GCACAAATGCCTTCGGGTCTTATCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * * * *
28868852 GCACAATTGCCTTCGGGTCTTAACGCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28868892 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
28868932 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
28868964 CATTCAAATG
Statistics
Matches: 165, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 30 0.18
40 128 0.78
41 7 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28868940 original size:120 final size:119
Alignment explanation
Indices: 28868704--28868962 Score: 387
Period size: 120 Copynumber: 2.2 Consensus size: 119
28868694 ACCCAAGTTT
* * *
28868704 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGTATAGCA
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGTATAGCA
* *
28868768 ACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGC
66 ACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACTAGCACAAATGC
* * * * *
28868822 CTTCGGGTCTTATCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACGCGGGTATAGC
1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAATTGCCTTCGGGTCTTAAC-CCGGTATAGC
*
28868887 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCATAAATGC
65 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCAACTAGCACAAATGC
28868942 CTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATA
28868963 TCATTCAAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
118 9 0.07
119 37 0.30
120 75 0.60
121 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (119 bp):
CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGTATAGCA
ACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACTAGCACAAATGC
Found at i:28871956 original size:40 final size:40
Alignment explanation
Indices: 28871760--28871942 Score: 207
Period size: 39 Copynumber: 4.6 Consensus size: 40
28871750 TGAATGATGT
* * * *
28871760 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28871800 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28871840 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28871878 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28871918 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28871943 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
38 6 0.05
39 56 0.45
40 54 0.44
41 8 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28871960 original size:79 final size:78
Alignment explanation
Indices: 28871812--28871975 Score: 215
Period size: 79 Copynumber: 2.1 Consensus size: 78
28871802 GGACTAAGAT
* **
28871812 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28871877 ATCCGGTTAAGTC
66 ATCCGGTTAAATC
* *
28871890 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28871953 TATATCCGGTTAAATT
63 TAAATCCGGTTAAATC
28871969 CCGAAGG
1 CCGAAGG
28871976 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
77 2 0.03
78 34 0.45
79 39 0.52
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGTTAAATC
Found at i:28879173 original size:37 final size:37
Alignment explanation
Indices: 28879132--28879248 Score: 122
Period size: 37 Copynumber: 3.3 Consensus size: 37
28879122 AACATAGACA
28879132 TGTATGTTCGGCCACATGAATAAGTACATAAGCTATG
1 TGTATGTTCGGCCACATGAATAAGTACATAAGCTATG
* * * *
28879169 TGTATGTTCGGCCATA-G-GT-AG--CCT-A-TTGATGG
1 TGTATGTTCGGCCACATGAATAAGTACATAAGCT-AT-G
28879201 ATGTATGTTCGGCCACATGAATAAGTACATAAGCTATG
1 -TGTATGTTCGGCCACATGAATAAGTACATAAGCTATG
28879239 TGTATGTTCG
1 TGTATGTTCG
28879249 CCATAGGTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
30 1 0.02
31 3 0.05
32 3 0.05
33 15 0.24
34 3 0.05
35 2 0.03
36 3 0.05
37 25 0.40
38 3 0.05
39 3 0.05
40 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (37 bp):
TGTATGTTCGGCCACATGAATAAGTACATAAGCTATG
Found at i:28879214 original size:70 final size:69
Alignment explanation
Indices: 28879131--28879269 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 69
28879121 CAACATAGAC
28879131 ATGTATGTTCGGCCACATGAATAAGTACATAAGCTATGTGTATGTTCGGCCATAGGTAGCCTATT
1 ATGTATGTTCGGCCACATGAATAAGTACATAAGCTATGTGTATGTTC-GCCATAGGTAGCCTATT
28879196 GATGG
65 GATGG
28879201 ATGTATGTTCGGCCACATGAATAAGTACATAAGCTATGTGTATGTTCGCCATAGGTAGCCTATTG
1 ATGTATGTTCGGCCACATGAATAAGTACATAAGCTATGTGTATGTTCGCCATAGGTAGCCTATTG
28879266 ATGG
66 ATGG
28879270 CTTTAGCTTG
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 22 0.32
70 47 0.68
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (69 bp):
ATGTATGTTCGGCCACATGAATAAGTACATAAGCTATGTGTATGTTCGCCATAGGTAGCCTATTG
ATGG
Found at i:28879950 original size:39 final size:39
Alignment explanation
Indices: 28879820--28879943 Score: 180
Period size: 40 Copynumber: 3.2 Consensus size: 39
28879810 AAATGTGCAT
* *
28879820 GCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCGAAG
1 GCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAG
*
28879858 GCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAG
1 GCATTTGTGCGAGTTACTAAATCCGGGCTAAGT-CCGAAG
*
28879898 GCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCGAAG
1 GCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCGAAG
28879937 GCATTTG
1 GCATTTG
28879944 AACGAGTAGC
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
38 29 0.37
39 13 0.17
40 34 0.44
41 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
GCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAG
Found at i:28879965 original size:78 final size:78
Alignment explanation
Indices: 28879820--28879966 Score: 192
Period size: 78 Copynumber: 1.9 Consensus size: 78
28879810 AAATGTGCAT
* **
28879820 GCATTTGTGCGAGATACTAATTCCGGGCTAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGG
1 GCATTTGTGCGAGATACTAATACCGGGCTAAGCCGAAGGCATTTGAACGAGTTACTAAATCCGGG
28879885 TTAAGTCCCGAAG
66 TTAAGTCCCGAAG
* * *
28879898 GCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAG-TAGCTATATCC
1 GCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCGAAGGCATTTGAACGAGTTA-CTAAATCC
28879961 -GGTTAA
63 GGGTTAA
28879967 ATTCGAAGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
77 2 0.03
78 34 0.57
79 24 0.40
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (78 bp):
GCATTTGTGCGAGATACTAATACCGGGCTAAGCCGAAGGCATTTGAACGAGTTACTAAATCCGGG
TTAAGTCCCGAAG
Found at i:28883295 original size:79 final size:81
Alignment explanation
Indices: 28883159--28883343 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
28883149 TTGAATGATG
*
28883159 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28883223 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28883238 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28883300 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28883318 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28883344 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28883357 original size:40 final size:40
Alignment explanation
Indices: 28883160--28883343 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
28883150 TGAATGATGT
* * * *
28883160 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28883200 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28883240 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28883278 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28883319 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28883344 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28883365 original size:79 final size:79
Alignment explanation
Indices: 28883212--28883376 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28883202 GGACTAAGAT
* **
28883212 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28883277 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28883291 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28883354 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28883370 CCGAAGG
1 CCGAAGG
28883377 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28886119 original size:7 final size:7
Alignment explanation
Indices: 28886107--28886133 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28886097 TTTAATTATT
28886107 TTTTCTC
1 TTTTCTC
28886114 TTTTCTC
1 TTTTCTC
28886121 TTTTCTC
1 TTTTCTC
28886128 TTTTCT
1 TTTTCT
28886134 TTTCATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCTC
Found at i:28887617 original size:21 final size:22
Alignment explanation
Indices: 28887593--28887640 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
28887583 ATCATATTGG
28887593 GAGAGC-GGATATTTTCCTAAA
1 GAGAGCAGGATATTTTCCTAAA
*
28887614 GAGATCAAGGATATTTTCCTAAA
1 GAGAGC-AGGATATTTTCCTAAA
28887637 GAGA
1 GAGA
28887641 TGTAATGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
23 19 0.79
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (22 bp):
GAGAGCAGGATATTTTCCTAAA
Found at i:28889246 original size:20 final size:20
Alignment explanation
Indices: 28889221--28889260 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28889211 CGCTTGTACG
28889221 GGTTTGTACTTCGGTGCCTC
1 GGTTTGTACTTCGGTGCCTC
28889241 GGTTTGTACTTCGGTGCCTC
1 GGTTTGTACTTCGGTGCCTC
28889261 TGTCTACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.25, G:0.30, T:0.40
Consensus pattern (20 bp):
GGTTTGTACTTCGGTGCCTC
Found at i:28889271 original size:20 final size:20
Alignment explanation
Indices: 28889228--28889273 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28889218 ACGGGTTTGT
* **
28889228 ACTTCGGTGCCTCGGTTTGT
1 ACTTCGGTGCCTCGGTCTAC
*
28889248 ACTTCGGTGCCTCTGTCTAC
1 ACTTCGGTGCCTCGGTCTAC
28889268 ACTTCG
1 ACTTCG
28889274 ATGCTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.30, G:0.24, T:0.37
Consensus pattern (20 bp):
ACTTCGGTGCCTCGGTCTAC
Found at i:28894086 original size:11 final size:11
Alignment explanation
Indices: 28894070--28894107 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28894060 TTTTAATCAA
28894070 ATATATATTTT
1 ATATATATTTT
**
28894081 ATATATATTAA
1 ATATATATTTT
28894092 ATATATATTTT
1 ATATATATTTT
28894103 A-ATAT
1 ATATAT
28894108 GAGTCAGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATATTTT
Found at i:28894091 original size:26 final size:24
Alignment explanation
Indices: 28894044--28894107 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
28894034 ATTATATATT
* *
28894044 AAATATATTTTTTTATTTTTAATC
1 AAATATATTTTTATATTATTAATC
28894068 AAATATATATTTTATATATATTAA--
1 AAATATAT-TTTTATAT-TATTAATC
* *
28894092 ATATATATTTTAATAT
1 AAATATATTTTTATAT
28894108 GAGTCAGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.21
24 15 0.44
25 7 0.21
26 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATATATTTTTATATTATTAATC
Found at i:28900856 original size:25 final size:25
Alignment explanation
Indices: 28900826--28900878 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
28900816 TTAGACTAAC
28900826 TTAGTTAAGTTATTAGCTAATATCA
1 TTAGTTAAGTTATTAGCTAATATCA
28900851 TTAGTTAAGTTATTAGCTAATATCA
1 TTAGTTAAGTTATTAGCTAATATCA
28900876 TTA
1 TTA
28900879 TCGGTGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (25 bp):
TTAGTTAAGTTATTAGCTAATATCA
Found at i:28903471 original size:28 final size:28
Alignment explanation
Indices: 28903448--28903510 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
28903438 TTATCTGGTG
28903448 GCTTGACCACAATATTCTGTATCTAGCA
1 GCTTGACCACAATATTCTGTATCTAGCA
* *
28903476 GCTTTACCACAATATTCTGTATCTTGCA
1 GCTTGACCACAATATTCTGTATCTAGCA
28903504 GCTTGAC
1 GCTTGAC
28903511 TACATTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (28 bp):
GCTTGACCACAATATTCTGTATCTAGCA
Found at i:28904660 original size:15 final size:15
Alignment explanation
Indices: 28904642--28904698 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
28904632 TTCTAATATA
28904642 ATGAAACTTTAAACT
1 ATGAAACTTTAAACT
* *
28904657 ATGAAACTTTAGATT
1 ATGAAACTTTAAACT
* *
28904672 GTGAAACATATAAACT
1 ATGAAAC-TTTAAACT
28904688 ATGAAACTTTA
1 ATGAAACTTTA
28904699 GAGTCTAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (15 bp):
ATGAAACTTTAAACT
Found at i:28904687 original size:31 final size:30
Alignment explanation
Indices: 28904643--28904700 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
28904633 TCTAATATAA
*
28904643 TGAAACTTTAAACTATGAAACTTTAGATTG
1 TGAAACTATAAACTATGAAACTTTAGATTG
28904673 TGAAACATATAAACTATGAAACTTTAGA
1 TGAAAC-TATAAACTATGAAACTTTAGA
28904701 GTCTAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (30 bp):
TGAAACTATAAACTATGAAACTTTAGATTG
Found at i:28904710 original size:31 final size:30
Alignment explanation
Indices: 28904651--28904714 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
28904641 AATGAAACTT
* * *
28904651 TAAACTATGAAACTTTAGATTGTGAAACATA
1 TAAACTATGAAACTTTAGAGTCTAAAACA-A
28904682 TAAACTATGAAACTTTAGAGTCTAAAACAA
1 TAAACTATGAAACTTTAGAGTCTAAAACAA
28904712 TAA
1 TAA
28904715 TGAAGCTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (30 bp):
TAAACTATGAAACTTTAGAGTCTAAAACAA
Found at i:28907921 original size:20 final size:20
Alignment explanation
Indices: 28907884--28907922 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28907874 TTACATTTGT
*
28907884 TTTTATTAATTCATTTATTA
1 TTTTATTAATTAATTTATTA
28907904 TTTTATT-ATTAATGTTATT
1 TTTTATTAATTAAT-TTATT
28907923 GGTATGTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTATTAATTAATTTATTA
Found at i:28913060 original size:7 final size:7
Alignment explanation
Indices: 28913048--28913125 Score: 63
Period size: 7 Copynumber: 10.6 Consensus size: 7
28913038 TAGGTCCAAA
28913048 AAAAAAG
1 AAAAAAG
28913055 AAAAAA-
1 AAAAAAG
28913061 AGAAAAAG
1 A-AAAAAG
28913069 AAAAATCA-
1 AAAAA--AG
*
28913077 AAATAAAA
1 AAA-AAAG
28913085 AATAAAAG
1 AA-AAAAG
28913093 AAAAAAG
1 AAAAAAG
28913100 AAGAAAAAG
1 -A-AAAAAG
28913109 AAAAAAG
1 AAAAAAG
28913116 -AAAAAG
1 AAAAAAG
28913122 AAAA
1 AAAA
28913126 GGAGAGGTCA
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
6 7 0.12
7 30 0.50
8 13 0.22
9 10 0.17
ACGTcount: A:0.83, C:0.01, G:0.12, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:28913066 original size:6 final size:6
Alignment explanation
Indices: 28913057--28913125 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
28913047 AAAAAAAGAA
* * * *
28913057 AAAAAG AAAAAG AAAAAT CAAAAT AAAAA- ATAAAAG -AAAA- AAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG
28913103 AAAAAG AAAAAAG AAAAAG AAAA
1 AAAAAG -AAAAAG AAAAAG AAAA
28913126 GGAGAGGTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
7 6 0.11
ACGTcount: A:0.83, C:0.01, G:0.12, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:28913066 original size:13 final size:12
Alignment explanation
Indices: 28913045--28913125 Score: 67
Period size: 13 Copynumber: 6.6 Consensus size: 12
28913035 GTTTAGGTCC
28913045 AAAAAAAAAGAAA
1 AAAAAAAAAG-AA
28913058 AAAAGAAAAAGAA
1 AAAA-AAAAAGAA
** *
28913071 AAATCAAAATAA
1 AAAAAAAAAGAA
*
28913083 AAAATAAAAG--
1 AAAAAAAAAGAA
*
28913093 AAAAAAGAAGAA
1 AAAAAAAAAGAA
28913105 AAAGAAAAAAGAA
1 AAA-AAAAAAGAA
28913118 AAAGAAAA
1 AAA-AAAA
28913126 GGAGAGGTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
10 8 0.15
12 16 0.29
13 25 0.45
14 6 0.11
ACGTcount: A:0.84, C:0.01, G:0.11, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:28915448 original size:128 final size:128
Alignment explanation
Indices: 28915209--28915648 Score: 655
Period size: 128 Copynumber: 3.4 Consensus size: 128
28915199 GTGAATATAG
*
28915209 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTA
* * * * * *
28915274 AGGAAGCAGATTTAAGTCACAAATCCTATCTCCCTAGTCAGTAGTGGAGTAAGTTAGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTAGAAATTA
* * ** * *
28915337 CAGATCTTGCCTCCCTAAGCAGTAGCAGAGTTGATCGAAGACGACGAATCTTATCTTCAAGAGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTA
* *
28915402 AGGAAGTAGATTTAAGCCACAAGTCCTATGTCCCTGGTTAGCAGTGGAGTAGGTTAGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTAGAAATTA
* *
28915465 TAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTA
* *
28915530 AGGAAGCAGATTTAAGCCACAAGTCTTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTAGAAATTA
* * * * * *
28915593 TAGATCTCGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCT
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCT
28915649 CCCTGAGACT
Statistics
Matches: 281, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
128 281 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (128 bp):
CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTA
AGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTAGAAATTA
Found at i:28916093 original size:50 final size:50
Alignment explanation
Indices: 28916039--28916544 Score: 421
Period size: 50 Copynumber: 10.1 Consensus size: 50
28916029 TCCCTGGCGG
*
28916039 TGCAGTGGAACAGATTAACA-CCACAACAGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAA-AGCTACAACAGTGAATCTTGCTTCCCCGACAT
* ** * * * **
28916089 TGCAGTTAGAA-AGATTAAAGCTACAACAGCAAATCTTACTTCCCAGGCGG
1 TGCAG-TGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACAT
* *
28916139 TGCAGTGGAACAAATTAAAGCTACATCAGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACAT
** * ** * * **
28916189 TGCAGTTAAAAAGATTAAAGCTACAACA-TCGAATCTTATTTCCCTGGCGG
1 TGCAGTGGAACAGATTAAAGCTACAACAGT-GAATCTTGCTTCCCCGACAT
* * *
28916239 TGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCTGACAT
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACAT
** * * * ** ** *
28916289 TGCAGTTAAAAAGATCAAAGCTACAACAGCGAATCTTATTTCCTTGGCGA-
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGAC-AT
* * * *
28916339 TGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACAT
* * * * * *
28916389 TGCAGTTGAATAGATTAAAGCTGCAACAGCGAATCTTACCTT-CCCAACAT
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTT-GCTTCCCCGACAT
* ** * * * * *
28916439 TACAGTTAAAAAGAGTAAAGCTACAACAGTGAATCTTACTTCCCTGACAA
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACAT
* ***
28916489 TGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCGGA-AT
1 TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCC-GACAT
28916539 TGCAGT
1 TGCAGT
28916545 TAAAAAAAGG
Statistics
Matches: 349, Mismatches: 97, Indels: 20
0.75 0.21 0.04
Matches are distributed among these distances:
49 10 0.03
50 328 0.94
51 11 0.03
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (50 bp):
TGCAGTGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACAT
Found at i:28916202 original size:100 final size:100
Alignment explanation
Indices: 28916028--28916433 Score: 625
Period size: 100 Copynumber: 4.0 Consensus size: 100
28916018 CAGATATTAT
* *
28916028 TTCCCTGGCGGTGCAGTGGAACAGATTAACA-CCACAACAGTGAATCTTGCTTCCCCGACATTGC
1 TTCCCTGGCGGTGCAGTGGAACAAATTAA-AGCCACATCAGTGAATCTTGCTTCCCCGACATTGC
* *
28916092 AGTTAGAAAGATTAAAGCTACAACAGCAAATCTTAC
65 AGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
* *
28916128 TTCCCAGGCGGTGCAGTGGAACAAATTAAAGCTACATCAGTGAATCTTGCTTCCCCGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
* *
28916193 GTTAAAAAGATTAAAGCTACAACATCGAATCTTAT
66 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
* *
28916228 TTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCTGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
* *
28916293 GTTAAAAAGATCAAAGCTACAACAGCGAATCTTAT
66 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
* * *
28916328 TTCCTTGGCGATGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCA
1 TTCCCTGGCGGTGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
* * *
28916393 GTTGAATAGATTAAAGCTGCAACAGCGAATCTTACC
66 GTTAAAAAGATTAAAGCTACAACAGCGAATCTTA-C
28916429 TTCCC
1 TTCCC
28916434 AACATTACAG
Statistics
Matches: 279, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
99 1 0.00
100 274 0.98
101 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (100 bp):
TTCCCTGGCGGTGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCA
GTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
Found at i:28916458 original size:100 final size:99
Alignment explanation
Indices: 28916038--28916509 Score: 520
Period size: 100 Copynumber: 4.7 Consensus size: 99
28916028 TTCCCTGGCG
* * *
28916038 GTGCAGTGGAACAGATTAACA-CCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTT-AGAAA
1 GTGCAGTGGAAAAAATTAA-AGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTGA-AAA
* *
28916101 GATTAAAGCTACAACAGCAAATCTTACTTCCCAGGCG
64 GATTAAAGCTACAACAGCGAATCTTACTTCCCA-GCA
* * *
28916138 GTGCAGTGGAACAAATTAAAGCTACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
1 GTGCAGTGGAAAAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTGAAAAGA
* * * *
28916203 TTAAAGCTACAACATCGAATCTTATTTCCCTGGCG
66 TTAAAGCTACAACAGCGAATCTTACTTCCC-AGCA
* * * *
28916238 GTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGA
1 GTGCAGTGGAAAAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTGAAAAGA
* * **
28916303 TCAAAGCTACAACAGCGAATCTTATTTCCTTGGC-
66 TTAAAGCTACAACAGCGAATCTTACTTCC-CAGCA
* * *
28916337 GATGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTGAATAG
1 G-TGCAGTGGAAAAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTGAAAAG
* *
28916402 ATTAAAGCTGCAACAGCGAATCTTACCTTCCCAACA
65 ATTAAAGCTACAACAGCGAATCTTA-CTTCCCAGCA
* * * * * * * * * * *
28916438 TTACAGT-TAAAAAGAGTAAAGCTACAACAGTGAATCTTACTTCCCTGACAATGCAGTGGAACAG
1 GTGCAGTGGAAAAA-ATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTGAAAAG
28916502 ATTAAAGC
65 ATTAAAGC
28916510 CACATTGGTG
Statistics
Matches: 327, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
99 6 0.02
100 316 0.97
101 5 0.02
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (99 bp):
GTGCAGTGGAAAAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTGAAAAGA
TTAAAGCTACAACAGCGAATCTTACTTCCCAGCA
Found at i:28916471 original size:200 final size:200
Alignment explanation
Indices: 28916059--28916494 Score: 604
Period size: 200 Copynumber: 2.2 Consensus size: 200
28916049 CAGATTAACA
* * *
28916059 CCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAGAAAGATTAAAGCTACAACAGCAAATC
1 CCACAACAGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATCAAAGCTACAACAGCAAATC
* *
28916124 TTACTTCCCAGGCGGTGCAGTGGAACAAATTAAAGCTACATCAGTGAATCTTGCTTCCCCGACAT
66 TTACTTCCCAGGCGATGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* * ** * * * * *
28916189 TGCAGTTAAAAAGATTAAAGCTACAACATCGAATCTTATTTCCCTGGCGGTGCAGTGGAACAGAT
131 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCTAACAGTACAGTGAAAAAGAG
28916254 TAAAG
196 TAAAG
* *
28916259 CCACATCAGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATCAAAGCTACAACAGCGAATC
1 CCACAACAGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATCAAAGCTACAACAGCAAATC
* ** *
28916324 TTATTTCCTTGGCGATGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
66 TTACTTCCCAGGCGATGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* * * * *
28916389 TGCAGTTGAATAGATTAAAGCTGCAACAGCGAATCTTACCTTCCC-AACATTACAGTTAAAAAGA
131 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTA-CTTCCCTAACAGTACAGTGAAAAAGA
28916453 GTAAAG
195 GTAAAG
* * *
28916459 CTACAACAGTGAATCTTACTTCCCTGACAATGCAGT
1 CCACAACAGTGAATCTTGCTTCCCTGACATTGCAGT
28916495 GGAACAGATT
Statistics
Matches: 206, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
200 201 0.98
201 5 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (200 bp):
CCACAACAGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATCAAAGCTACAACAGCAAATC
TTACTTCCCAGGCGATGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCTAACAGTACAGTGAAAAAGAG
TAAAG
Found at i:28931801 original size:16 final size:15
Alignment explanation
Indices: 28931774--28931807 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
28931764 ATAACTAGTA
*
28931774 TATAATTATATTTAT
1 TATAATTATATTAAT
28931789 TATAATATATATTAAT
1 TATAAT-TATATTAAT
28931805 TAT
1 TAT
28931808 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:28937693 original size:36 final size:35
Alignment explanation
Indices: 28937646--28937733 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 35
28937636 TTTCGGTTGA
* *
28937646 TATTCTGATTCGCATGTTAATCATGCCATTATTACT
1 TATTCTGATTCGCATGTTAAGCATGCCACTA-TACT
*
28937682 TATTCTGATTCGCATGCTAAGCATGCCACTATACT
1 TATTCTGATTCGCATGTTAAGCATGCCACTATACT
* *
28937717 GATTCTGAATCGCATGT
1 TATTCTGATTCGCATGT
28937734 AAAGGATTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 18 0.39
36 28 0.61
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (35 bp):
TATTCTGATTCGCATGTTAAGCATGCCACTATACT
Found at i:28937891 original size:43 final size:42
Alignment explanation
Indices: 28937841--28937932 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 42
28937831 ATGGAGGAAT
** *
28937841 ACATTATCTGGAATTATATCAGCATTATCTGGTGGCTTGACC
1 ACATTATCTGGAATTATATCAGCATTATCTACTAGCTTGACC
* *
28937883 ACAATTATCTGGAATTATATCTGTATTATCTACTAGCTTGACC
1 AC-ATTATCTGGAATTATATCAGCATTATCTACTAGCTTGACC
28937926 ACATTAT
1 ACATTAT
28937933 TGGTGTGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 7 0.16
43 37 0.84
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (42 bp):
ACATTATCTGGAATTATATCAGCATTATCTACTAGCTTGACC
Found at i:28939558 original size:20 final size:20
Alignment explanation
Indices: 28939527--28939625 Score: 81
Period size: 20 Copynumber: 5.0 Consensus size: 20
28939517 ATTTGTGGAA
*
28939527 AAGCCACCAGTAATGCAGAC
1 AAGCTACCAGTAATGCAGAC
* * ** *
28939547 AAGCTGCTAGTAATGTGGTC
1 AAGCTACCAGTAATGCAGAC
* *
28939567 AAGCCACCAGTAATGCAGAT
1 AAGCTACCAGTAATGCAGAC
** * * *
28939587 AAATTGCCAGTAGTGCGGAC
1 AAGCTACCAGTAATGCAGAC
28939607 AAGCTACCAGTAATGCAGA
1 AAGCTACCAGTAATGCAGA
28939626 AAAATTGCTG
Statistics
Matches: 54, Mismatches: 25, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (20 bp):
AAGCTACCAGTAATGCAGAC
Found at i:28939665 original size:80 final size:80
Alignment explanation
Indices: 28939527--28939675 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 80
28939517 ATTTGTGGAA
* * * *
28939527 AAGCCACCAGTAATGCAGACAAGCTGCTAGTAATGTGGTCAAGCCACCAGTAATGCAGATAAATT
1 AAGCCACCAGTAATGCAGAAAAACTGCTAGTAATGTGGACAAGCCACCAATAATGCAGATAAATT
28939592 GCCAGTAGTGCGGAC
66 GCCAGTAGTGCGGAC
* * * *
28939607 AAGCTACCAGTAATGCAGAAAAATTGCTGGTAATGTGGACAAGCCACCAATAATGCAGATTAATT
1 AAGCCACCAGTAATGCAGAAAAACTGCTAGTAATGTGGACAAGCCACCAATAATGCAGATAAATT
28939672 GCCA
66 GCCA
28939676 ATACTTCCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (80 bp):
AAGCCACCAGTAATGCAGAAAAACTGCTAGTAATGTGGACAAGCCACCAATAATGCAGATAAATT
GCCAGTAGTGCGGAC
Found at i:28939672 original size:40 final size:40
Alignment explanation
Indices: 28939520--28939673 Score: 191
Period size: 40 Copynumber: 3.9 Consensus size: 40
28939510 CACTCTAATT
* * **
28939520 TGTGGAAAAGCCACCAGTAATGCAGACAAGCTGCTAGTAA
1 TGTGGACAAGCCACCAGTAATGCAGATAAATTGCTAGTAA
* * *
28939560 TGTGGTCAAGCCACCAGTAATGCAGATAAATTGCCAGTAG
1 TGTGGACAAGCCACCAGTAATGCAGATAAATTGCTAGTAA
* * * *
28939600 TGCGGACAAGCTACCAGTAATGCAGAAAAATTGCTGGTAA
1 TGTGGACAAGCCACCAGTAATGCAGATAAATTGCTAGTAA
* *
28939640 TGTGGACAAGCCACCAATAATGCAGATTAATTGC
1 TGTGGACAAGCCACCAGTAATGCAGATAAATTGC
28939674 CAATACTTCC
Statistics
Matches: 95, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (40 bp):
TGTGGACAAGCCACCAGTAATGCAGATAAATTGCTAGTAA
Found at i:28942763 original size:13 final size:13
Alignment explanation
Indices: 28942736--28942802 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
28942726 ATTATGTGTT
* *
28942736 AAATGTTTAGATG
1 AAATGGTTATATG
*
28942749 AAATGGTTATTTG
1 AAATGGTTATATG
**
28942762 AAAAAGTTATATG
1 AAATGGTTATATG
* *
28942775 AAATGATTGTATG
1 AAATGGTTATATG
*
28942788 AATTGGTTATATG
1 AAATGGTTATATG
28942801 AA
1 AA
28942803 TTTGTTACAC
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.39
Consensus pattern (13 bp):
AAATGGTTATATG
Found at i:28942803 original size:13 final size:13
Alignment explanation
Indices: 28942767--28942809 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
28942757 ATTTGAAAAA
*
28942767 GTTATATGAAATG
1 GTTATATGAATTG
* *
28942780 ATTGTATGAATTG
1 GTTATATGAATTG
*
28942793 GTTATATGAATTT
1 GTTATATGAATTG
28942806 GTTA
1 GTTA
28942810 CACGGAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (13 bp):
GTTATATGAATTG
Found at i:28946143 original size:49 final size:50
Alignment explanation
Indices: 28946029--28946156 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 50
28946019 GAGGTTCCCC
* * *
28946029 GTAAGACCATGTCTGGGACATGGCATGGGTAACGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGTAACGATATGAAAAATCCCAT
* * *
28946079 GTAAGACCATATCTGGGATATGGCATTGGTAGTAC-A-A-GAAAAATCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGTA--ACGATATGAAAAATCCCAT
*
28946128 GTAAGACCATGTCTGGGACATGGCTTTGG
1 GTAAGACCATGTCTGGGACATGGCATTGG
28946157 CATGTTATTA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 35 0.52
50 29 0.43
51 1 0.01
52 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGTAACGATATGAAAAATCCCAT
Found at i:28953212 original size:50 final size:50
Alignment explanation
Indices: 28953102--28953343 Score: 224
Period size: 50 Copynumber: 4.8 Consensus size: 50
28953092 ACATTTGGGT
*
28953102 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
* * *
28953153 GATTATGAGAGGTCCCATGTAAGACCATGTTTGGGATATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
*
28953206 GATGAGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * *
28953256 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A
* * * ** *
28953305 CAAGAAACATCTCATGTAAGACCATGTCTGGGACATGGC
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
28953344 TTTCGCATGT
Statistics
Matches: 159, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
48 1 0.01
49 32 0.20
50 80 0.50
51 2 0.01
53 3 0.02
54 6 0.04
55 1 0.01
56 34 0.21
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:28953272 original size:100 final size:103
Alignment explanation
Indices: 28953115--28953301 Score: 254
Period size: 100 Copynumber: 1.8 Consensus size: 103
28953105 GAGATCCCAT
* **
28953115 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATC--T-AGATTATGAGAACTCCCATGTAAGACCA
* * * *
28953180 TGTTTGGGATATGGCGTTGGCACCGAGATGAGAGGTCCCTC
63 TATCTGGGATATGACATTGGCACCGAGATGAGAGGTCCCTC
*
28953221 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATGTAAGACCATAT
28953283 CTGGGATATGACATTGGCA
66 CTGGGATATGACATTGGCA
28953302 GTACAAGAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 40 0.55
101 2 0.03
105 1 0.01
106 30 0.41
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATGTAAGACCATAT
CTGGGATATGACATTGGCACCGAGATGAGAGGTCCCTC
Found at i:28965228 original size:28 final size:27
Alignment explanation
Indices: 28965091--28965254 Score: 114
Period size: 27 Copynumber: 6.0 Consensus size: 27
28965081 CATGACAACT
* * * *
28965091 AAGAATAGCCTCTATGACAAACTCTTA
1 AAGAATAGCTTTTATGGCAAACTCTGA
* * ** *
28965118 ATGAATAG-TCTTTGTGGCGTACTCTAA
1 AAGAATAGCT-TTTATGGCAAACTCTGA
* *
28965145 AAGAATAGCATTTGTGGCAAACTCTGA
1 AAGAATAGCTTTTATGGCAAACTCTGA
* * * *
28965172 AACAATAGCGTTTATGACGAACTCTGA
1 AAGAATAGCTTTTATGGCAAACTCTGA
* *
28965199 AAGAATAGACTTTTATGGCAAACCCCGA
1 AAGAATAG-CTTTTATGGCAAACTCTGA
* * * *
28965227 AAGAGTAGATTTTACGGCAAACTTTGA
1 AAGAATAGCTTTTATGGCAAACTCTGA
28965254 A
1 A
28965255 TAACCTTTGT
Statistics
Matches: 104, Mismatches: 30, Indels: 6
0.74 0.21 0.04
Matches are distributed among these distances:
27 83 0.80
28 21 0.20
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
AAGAATAGCTTTTATGGCAAACTCTGA
Found at i:28967597 original size:28 final size:27
Alignment explanation
Indices: 28967518--28967611 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 27
28967508 CAGAGATCGT
*
28967518 CACAAAGGCATTTCCTTTCAGAGATTTTC
1 CACAAAGGC-TTTCCTATCAGAG-TTTTC
* * * *
28967547 CACAAAGGCGTTCTTAAACAGAGGTTTC
1 CACAAAGGCTTTCCT-ATCAGAGTTTTC
28967575 CACAAAGGCTTTCCTATCTAGAGTTTTGC
1 CACAAAGGCTTTCCTATC-AGAGTTTT-C
*
28967604 CATAAAGG
1 CACAAAGG
28967612 TTGTCCTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.04
28 28 0.54
29 22 0.42
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (27 bp):
CACAAAGGCTTTCCTATCAGAGTTTTC
Found at i:28967917 original size:53 final size:53
Alignment explanation
Indices: 28967767--28967919 Score: 227
Period size: 53 Copynumber: 2.9 Consensus size: 53
28967757 TTAAATTTCT
* *
28967767 CCATATGATGCCATAACCCACCAGTTATGATCTTACATGATATGATCTTCTTC
1 CCATATGATGCCATAACCCACCAGTTACGATCTTACATGATATGGTCTTCTTC
* * *
28967820 TCATATGATGTCATAACCCACTAGTTAC-AGTCTTACATGATATGGTCTTCTTC
1 CCATATGATGCCATAACCCACCAGTTACGA-TCTTACATGATATGGTCTTCTTC
* *
28967873 CCATATGATGCCATAACCCACCAGTTACGACCTTACAAGATATGGTC
1 CCATATGATGCCATAACCCACCAGTTACGATCTTACATGATATGGTC
28967920 CTTTAGTGCC
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.01
53 86 0.98
54 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
CCATATGATGCCATAACCCACCAGTTACGATCTTACATGATATGGTCTTCTTC
Found at i:28971943 original size:11 final size:11
Alignment explanation
Indices: 28971927--28971951 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28971917 GTGACCACTA
28971927 CTATAAACATT
1 CTATAAACATT
28971938 CTATAAACATT
1 CTATAAACATT
28971949 CTA
1 CTA
28971952 ACCAACATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
CTATAAACATT
Found at i:28981893 original size:16 final size:16
Alignment explanation
Indices: 28981855--28981885 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28981845 CCCAATGCTG
28981855 TAGTCGAATAGATCCA
1 TAGTCGAATAGATCCA
28981871 TAGTCGAATAGATCC
1 TAGTCGAATAGATCC
28981886 TCGATCGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (16 bp):
TAGTCGAATAGATCCA
Found at i:28982508 original size:16 final size:16
Alignment explanation
Indices: 28982487--28982519 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28982477 TCGGTTCAGA
28982487 GCATTTTAACAAATTT
1 GCATTTTAACAAATTT
28982503 GCATTTTAACAAATTT
1 GCATTTTAACAAATTT
28982519 G
1 G
28982520 GGCTTTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (16 bp):
GCATTTTAACAAATTT
Found at i:28982675 original size:17 final size:18
Alignment explanation
Indices: 28982642--28982678 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
28982632 TATACACTTG
28982642 TAAAGTAAATTCAATAAT
1 TAAAGTAAATTCAATAAT
28982660 TAAA-TAAATATC-ATAAT
1 TAAAGTAAAT-TCAATAAT
28982677 TA
1 TA
28982679 TCCACAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAGTAAATTCAATAAT
Found at i:28982826 original size:26 final size:23
Alignment explanation
Indices: 28982797--28982843 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
28982787 CTGGCATTTC
28982797 TTTTAATTAGCTTAATTAATTGATAG
1 TTTTAATTAG-TT-A-TAATTGATAG
28982823 TTTTAATTAGTTATAATTGAT
1 TTTTAATTAGTTATAATTGAT
28982844 TCATTGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 2 0.10
26 10 0.48
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (23 bp):
TTTTAATTAGTTATAATTGATAG
Found at i:28984314 original size:24 final size:24
Alignment explanation
Indices: 28984265--28984314 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
28984255 TAAAATACTC
* *
28984265 TTTGAGTTTTCTTTTCAAGAATCT
1 TTTGAGTTTTCTTTTCAAAAAGCT
*
28984289 TTTGAG-TTTCTTTTAGAAAAAGCT
1 TTTGAGTTTTCTTTT-CAAAAAGCT
28984313 TT
1 TT
28984315 ATCGATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (24 bp):
TTTGAGTTTTCTTTTCAAAAAGCT
Found at i:28994801 original size:36 final size:37
Alignment explanation
Indices: 28994754--28994831 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
28994744 TTATTACGAA
* * *
28994754 GTCTTACCCGGACATAAT-CTCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
28994790 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
28994827 GTCTT
1 GTCTT
28994832 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:28995020 original size:47 final size:47
Alignment explanation
Indices: 28994948--28995195 Score: 383
Period size: 47 Copynumber: 5.3 Consensus size: 47
28994938 GCCCTTCGGG
* * * * **
28994948 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCA-CCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28994994 CCTGTCACATTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-TATATACACTTTCACATTCATCACATCGGCCATTAGGC
28995042 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28995089 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28995136 CTTATCACATATATACACTTTCACATTCATCACATC-GACATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28995182 CTTATCTCATATAT
1 CTTATCACATATAT
28995196 GCATGTTCAC
Statistics
Matches: 188, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 29 0.15
47 149 0.79
48 10 0.05
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28996180 original size:61 final size:61
Alignment explanation
Indices: 28996082--28996284 Score: 264
Period size: 61 Copynumber: 3.3 Consensus size: 61
28996072 TTCTTAAACA
* * * *
28996082 GCCACAAAGGTTGTCATTTATATCTATTACTCCCCACAAAGGCTTTACTATCCAGAGTTTT
1 GCCACAAAGGTTGTCCTTTACATCTAATACTCGCCACAAAGGCTTTACTATCCAGAGTTTT
* * * *
28996143 GCCACAAAAGTTGTCCTTTACATCCAATACTCGCCACAAAGGCATTCCTATCCAGAGTTTT
1 GCCACAAAGGTTGTCCTTTACATCTAATACTCGCCACAAAGGCTTTACTATCCAGAGTTTT
* * * * *
28996204 GCCACAAAGGTTGTCCTTTACATCTAGTACTCGCAACAAAGG-TTTTCATGTCCAAAGTTTT
1 GCCACAAAGGTTGTCCTTTACATCTAATACTCGCCACAAAGGCTTTAC-TATCCAGAGTTTT
*
28996265 TCCACAAAGGTTGTCCTTTA
1 GCCACAAAGGTTGTCCTTTA
28996285 ACTGGTGTTT
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
60 3 0.02
61 121 0.98
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (61 bp):
GCCACAAAGGTTGTCCTTTACATCTAATACTCGCCACAAAGGCTTTACTATCCAGAGTTTT
Found at i:28996220 original size:29 final size:29
Alignment explanation
Indices: 28996115--28996213 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 29
28996105 CTATTACTCC
*
28996115 CCACAAAGGCTTTACTATCCAGAGTTTTG
1 CCACAAAGGCTTTCCTATCCAGAGTTTTG
* * *
28996144 CCACAAAAG-TTGTCCTTTACATCCA-A-TACTCG
1 CCACAAAGGCTT-TCC--T--ATCCAGAGT-TTTG
*
28996176 CCACAAAGGCATTCCTATCCAGAGTTTTG
1 CCACAAAGGCTTTCCTATCCAGAGTTTTG
28996205 CCACAAAGG
1 CCACAAAGG
28996214 TTGTCCTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 18
0.67 0.10 0.23
Matches are distributed among these distances:
28 7 0.13
29 22 0.42
30 2 0.04
31 2 0.04
32 14 0.26
33 6 0.11
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (29 bp):
CCACAAAGGCTTTCCTATCCAGAGTTTTG
Found at i:28996482 original size:16 final size:16
Alignment explanation
Indices: 28996458--28996489 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28996448 TTTTCATATG
28996458 AACCACATTAGGTAAT
1 AACCACATTAGGTAAT
*
28996474 AACCCCATTAGGTAAT
1 AACCACATTAGGTAAT
28996490 GACCTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (16 bp):
AACCACATTAGGTAAT
Found at i:28999755 original size:28 final size:27
Alignment explanation
Indices: 28999715--28999839 Score: 198
Period size: 28 Copynumber: 4.6 Consensus size: 27
28999705 TAAATTGTAC
*
28999715 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATAT
*
28999743 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATAT
28999771 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATAT
28999798 AGCACTAAGTGTGCGAGTTG-TTATAT
1 AGCACTAAGTGTGCGAGTTGATTATAT
*
28999824 AGCACTGAGTGTGCGA
1 AGCACTAAGTGTGCGA
28999840 CTTAATATAT
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
26 21 0.22
27 29 0.31
28 44 0.47
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATAT
Found at i:28999807 original size:55 final size:54
Alignment explanation
Indices: 28999715--28999839 Score: 198
Period size: 55 Copynumber: 2.3 Consensus size: 54
28999705 TAAATTGTAC
* *
28999715 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTG-TTATAT
28999771 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTAAGTGTGCGAGTTGTTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGTTATAT
*
28999824 AGCACTGAGTGTGCGA
1 AGCACTAAGTGTGCGA
28999840 CTTAATATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
53 20 0.30
54 3 0.05
55 26 0.39
56 17 0.26
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGTTATAT
Found at i:29007839 original size:28 final size:28
Alignment explanation
Indices: 29007799--29007924 Score: 200
Period size: 28 Copynumber: 4.5 Consensus size: 28
29007789 TAAATTGTAC
*
29007799 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
* *
29007827 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
29007855 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
*
29007883 AGCACTAAGTGTGCGAG-TTGCTTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
*
29007910 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29007925 GACTTAATGT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 23 0.25
28 70 0.75
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:29010497 original size:27 final size:27
Alignment explanation
Indices: 29010440--29010860 Score: 560
Period size: 27 Copynumber: 15.6 Consensus size: 27
29010430 AGTTGTGGGC
*
29010440 AAATGACCGAAATACCC-CTAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29010466 AAATGACCGAAATAACCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
29010493 AAATGACTGAAATGCCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29010520 AAATAACCGAAATACCCCCG-AGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29010546 AAATGACCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29010573 AAATGACTGAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* * *
29010600 AAATAACCGAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29010627 AAATAACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29010654 AAATGATCGAAATACCCTCAAAGGGTAA
1 AAATGACCGAAATACCCTCGAAGGGT-A
**
29010682 AAATGACTAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29010709 AAATGATCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29010736 AAATGATCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
29010763 AAATGATCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29010790 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
29010817 AAATGATTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
29010844 AAATGACTGAAATACCC
1 AAATGACCGAAATACCC
29010861 CTGACCCTCA
Statistics
Matches: 353, Mismatches: 37, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
26 40 0.11
27 289 0.82
28 24 0.07
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:29010529 original size:54 final size:54
Alignment explanation
Indices: 29010440--29010910 Score: 524
Period size: 54 Copynumber: 8.6 Consensus size: 54
29010430 AGTTGTGGGC
* * *
29010440 AAATGACCGAAATA-CCCCTAAGGGTAAAATGACCGAAATAACCTCGAAGGGTA
1 AAATGACTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
* * *
29010493 AAATGACTGAAATGCCCCCGAAGGGTAAAATAACCGAAATACCCCCG-AGGGTA
1 AAATGACTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
* * * *
29010546 AAATGACCGAAATACCCTCAAAGGGTAAAATGACTGAAATACCC-CTGAAGGGTA
1 AAATGACTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTC-GAAGGGTA
* * * *
29010600 AAATAACCGAAATACCCCCAAAGGGTAAAATAACCGAAATACCCTCGAAGGGTA
1 AAATGACTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
* * **
29010654 AAATGA-TCGAAATACCCTCAAAGGGTAAAAATGACTAAAATACCCTCGAAGGGTA
1 AAATGACT-GAAATACCCCCGAAGGGT-AAAATGACCGAAATACCCTCGAAGGGTA
* *
29010709 AAATGA-TCGAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGTA
1 AAATGACT-GAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
* * *
29010763 AAATGA-TCAAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACT-GAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
* * * * *
29010817 AAATGATTGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCTGACCCTCAAAAGGTA
1 AAATGACTGAAATACCCCCGAAGGGTAAAATGACCG-AA-A----T-ACCCTCGAAGGGTA
29010878 AAATGACTGAAATACCCCC-ATAGGGTAAAATGA
1 AAATGACTGAAATACCCCCGA-AGGGTAAAATGA
29010911 TTTGTATACC
Statistics
Matches: 365, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.00
53 57 0.16
54 210 0.58
55 53 0.15
56 1 0.00
60 2 0.01
61 41 0.11
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (54 bp):
AAATGACTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
Found at i:29010878 original size:34 final size:34
Alignment explanation
Indices: 29010830--29010895 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
29010820 TGATTGAAAT
* *
29010830 ACCCTCGAAGGGTAAAATGACTGAAATACCCCTG
1 ACCCTCAAAAGGTAAAATGACTGAAATACCCCTG
29010864 ACCCTCAAAAGGTAAAATGACTGAAATACCCC
1 ACCCTCAAAAGGTAAAATGACTGAAATACCCC
29010896 CATAGGGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (34 bp):
ACCCTCAAAAGGTAAAATGACTGAAATACCCCTG
Found at i:29011175 original size:28 final size:28
Alignment explanation
Indices: 29011135--29011266 Score: 167
Period size: 28 Copynumber: 4.7 Consensus size: 28
29011125 ACTGTAATGT
* *
29011135 TACTATATTGGGCTAAGGCCAAAACTGA
1 TACTGTATTGGGCTAAGGCCAACACTGA
29011163 TACTGTATTGGGCTAAGGCCAACACTGA
1 TACTGTATTGGGCTAAGGCCAACACTGA
* * *
29011191 TATTGTATTGGGCTAAGGCCCACATTGA
1 TACTGTATTGGGCTAAGGCCAACACTGA
* * *
29011219 TATTGTATTGGGCTAAGTCCCACACT-A
1 TACTGTATTGGGCTAAGGCCAACACTGA
*
29011246 CTACTGAATTGGGCTAAGGCC
1 -TACTGTATTGGGCTAAGGCC
29011267 CTCATTGTAC
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
27 1 0.01
28 92 0.99
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCAACACTGA
Found at i:29021448 original size:20 final size:20
Alignment explanation
Indices: 29021423--29021465 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29021413 AAAAGAAAAG
29021423 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
29021443 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
29021463 AAA
1 AAA
29021466 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:29026284 original size:20 final size:20
Alignment explanation
Indices: 29026259--29026301 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29026249 AAAAGAAAAG
29026259 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
29026279 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
29026299 AAA
1 AAA
29026302 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:29031123 original size:20 final size:20
Alignment explanation
Indices: 29031098--29031140 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29031088 AAAAGAAAAG
29031098 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
29031118 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
29031138 AAA
1 AAA
29031141 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:29034220 original size:22 final size:22
Alignment explanation
Indices: 29034193--29034246 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
29034183 TCAATCAAAG
29034193 ACATTAAGGATGCTTAAAGTCT
1 ACATTAAGGATGCTTAAAGTCT
29034215 ACATTAAGGATGCTTAAAGTCT
1 ACATTAAGGATGCTTAAAGTCT
* *
29034237 TCGTTAAGGA
1 ACATTAAGGA
29034247 GAATTGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (22 bp):
ACATTAAGGATGCTTAAAGTCT
Found at i:29045927 original size:47 final size:47
Alignment explanation
Indices: 29045861--29046481 Score: 972
Period size: 47 Copynumber: 13.1 Consensus size: 47
29045851 GAAATGATAG
*
29045861 TAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29045908 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
29045957 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29046004 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29046051 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
29046100 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29046147 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29046194 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29046241 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
29046290 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29046337 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29046384 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
29046431 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29046478 TAAG
1 TAAG
29046482 TCCCGAAGGG
Statistics
Matches: 538, Mismatches: 30, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
47 400 0.74
49 138 0.26
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:29046119 original size:143 final size:141
Alignment explanation
Indices: 29045861--29046481 Score: 972
Period size: 143 Copynumber: 4.4 Consensus size: 141
29045851 GAAATGATAG
* *
29045861 TAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29045926 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
* *
29045991 CGTATATGTGTGA
129 TGTATATATGTGA
* *
29046004 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29046069 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
*
29046134 TGTATATGTGTGA
129 TGTATATATGTGA
* *
29046147 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29046212 GTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
29046277 TATATATATGTGA
131 --TATATATGTGA
*
29046290 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
*
29046355 GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
29046420 TATATATGTGA
131 TATATATGTGA
*** * * * * * * *
29046431 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29046482 TCCCGAAGGG
Statistics
Matches: 454, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
141 96 0.21
143 358 0.79
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (141 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTGA
Found at i:29046188 original size:190 final size:190
Alignment explanation
Indices: 29045861--29046481 Score: 1061
Period size: 190 Copynumber: 3.3 Consensus size: 190
29045851 GAAATGATAG
*
29045861 TAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
* *
29045924 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
66 ATGTGATGAATGTGAAAGTG--TATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
29045989 AGCGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
129 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29046051 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
29046116 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
*
29046181 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
131 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29046241 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
29046306 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
29046371 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
131 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * *
29046431 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATA-A-ATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
29046482 TCCCGAAGGG
Statistics
Matches: 412, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
188 10 0.02
189 1 0.00
190 354 0.86
192 47 0.11
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (190 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:29046656 original size:37 final size:37
Alignment explanation
Indices: 29046600--29046678 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
29046590 CCGAGCTCTA
* *
29046600 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
29046637 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29046674 AAGAC
1 AAGAC
29046679 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:29048235 original size:19 final size:19
Alignment explanation
Indices: 29048211--29048248 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29048201 ATTTAAACAT
29048211 AAGTTTCCTATACATGCCA
1 AAGTTTCCTATACATGCCA
29048230 AAGTTTCCTATACATGCCA
1 AAGTTTCCTATACATGCCA
29048249 TTATAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
AAGTTTCCTATACATGCCA
Found at i:29055416 original size:50 final size:50
Alignment explanation
Indices: 29055343--29055448 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
29055333 ATTTCGACAA
29055343 AAAGAAAGAAAATGACTGGGGTTTCTTTTGGGATTTGAGGTTGACGGCAC
1 AAAGAAAGAAAATGACTGGGGTTTCTTTTGGGATTTGAGGTTGACGGCAC
29055393 AAAGAAAGAAAATGACTGGGGTTTCTTTTGGGATTTGAGGTTGACGGCAC
1 AAAGAAAGAAAATGACTGGGGTTTCTTTTGGGATTTGAGGTTGACGGCAC
29055443 AAAGAA
1 AAAGAA
29055449 GAGATTTAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.26
Consensus pattern (50 bp):
AAAGAAAGAAAATGACTGGGGTTTCTTTTGGGATTTGAGGTTGACGGCAC
Found at i:29059384 original size:25 final size:25
Alignment explanation
Indices: 29059356--29059407 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29059346 CTTACTTCAC
29059356 CTATCCCTAACATCTTGAAAATAGA
1 CTATCCCTAACATCTTGAAAATAGA
29059381 CTATCCCTAACATCTTGAAAATAGA
1 CTATCCCTAACATCTTGAAAATAGA
29059406 CT
1 CT
29059408 TAGGCATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (25 bp):
CTATCCCTAACATCTTGAAAATAGA
Found at i:29074989 original size:27 final size:26
Alignment explanation
Indices: 29074958--29075011 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
29074948 AAAATTTGAT
* *
29074958 TTTTTTAAATTTATTATTACATAAATTA
1 TTTTATAAATATATT-TTA-ATAAATTA
29074986 TTTTAATAAATATATTTTAATAAATT
1 TTTT-ATAAATATATTTTAATAAATT
29075012 GAGAATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 7 0.30
29 9 0.39
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTATAAATATATTTTAATAAATTA
Found at i:29075003 original size:14 final size:13
Alignment explanation
Indices: 29074963--29075011 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
29074953 TTGATTTTTT
29074963 TAAATTTATTATTACA
1 TAAA-TTATT-TTA-A
29074979 TAAATTATTTTAA
1 TAAATTATTTTAA
29074992 TAAATATATTTTAA
1 TAAAT-TATTTTAA
29075006 TAAATT
1 TAAATT
29075012 GAGAATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.22
14 16 0.50
15 5 0.16
16 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAATTATTTTAA
Found at i:29076032 original size:19 final size:20
Alignment explanation
Indices: 29075990--29076032 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
29075980 TATGTTTAAT
* * *
29075990 TATTTTTTAATTTAGTTTTT
1 TATTTTTTAATTTAATGTTA
29076010 TATTTTTT-ATTTAATGTTA
1 TATTTTTTAATTTAATGTTA
29076029 TATT
1 TATT
29076033 ATTCATGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TATTTTTTAATTTAATGTTA
Found at i:29078185 original size:14 final size:16
Alignment explanation
Indices: 29078161--29078192 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
29078151 TGTTGACATC
29078161 TTTCAAGATTTTC-TT
1 TTTCAAGATTTTCATT
29078176 TTTC-AGATTTTCATT
1 TTTCAAGATTTTCATT
29078191 TT
1 TT
29078193 AAGGCAGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTCAAGATTTTCATT
Found at i:29081573 original size:15 final size:16
Alignment explanation
Indices: 29081553--29081582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29081543 AAAAATGTAG
29081553 AAAAAA-TATATTTAT
1 AAAAAATTATATTTAT
29081568 AAAAAATTATATTTA
1 AAAAAATTATATTTA
29081583 AACCAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAAATTATATTTAT
Found at i:29082201 original size:42 final size:42
Alignment explanation
Indices: 29082154--29082237 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
29082144 AGATGGCGGC
29082154 GGATGATAAAATCCACTAACTTTAGTTAATCATGCTTAAGGT
1 GGATGATAAAATCCACTAACTTTAGTTAATCATGCTTAAGGT
29082196 GGATGATAAAATCCACTAACTTTAGTTAATCATGCTTAAGGT
1 GGATGATAAAATCCACTAACTTTAGTTAATCATGCTTAAGGT
29082238 TTAATTAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (42 bp):
GGATGATAAAATCCACTAACTTTAGTTAATCATGCTTAAGGT
Found at i:29085741 original size:35 final size:35
Alignment explanation
Indices: 29085702--29085773 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
29085692 CTTAATTCCA
*
29085702 CTTCAATGACTATTCAAGAACTTCAATTGTCAAAG
1 CTTCAATGACTATTCAAGAACTCCAATTGTCAAAG
* *
29085737 CTTCAATGACTGTTCGAGAACTCCAATTGTCAAAG
1 CTTCAATGACTATTCAAGAACTCCAATTGTCAAAG
29085772 CT
1 CT
29085774 GATCAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (35 bp):
CTTCAATGACTATTCAAGAACTCCAATTGTCAAAG
Found at i:29113376 original size:26 final size:26
Alignment explanation
Indices: 29113342--29113409 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
29113332 CCTATACATA
29113342 TATGCTCACACGAGCTATGAAATGAG
1 TATGCTCACACGAGCTATGAAATGAG
* *
29113368 TATGTTCACACGAGCTATGAAATGGG
1 TATGCTCACACGAGCTATGAAATGAG
** *
29113394 CCTACTCACACGAGCT
1 TATGCTCACACGAGCT
29113410 GTAGGTCAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (26 bp):
TATGCTCACACGAGCTATGAAATGAG
Found at i:29119545 original size:28 final size:28
Alignment explanation
Indices: 29119503--29119590 Score: 151
Period size: 28 Copynumber: 3.2 Consensus size: 28
29119493 TGCTCTCCCC
*
29119503 AAATCCC-CCTCCAAAATCCTCTTGTAA
1 AAATCCCTCCTCCAAAATCCTCGTGTAA
29119530 AAATCCCTCCTCCAAAATCCTCGTGTAA
1 AAATCCCTCCTCCAAAATCCTCGTGTAA
*
29119558 CAATCCCTCCTCCAAAATCCTCGTGTAA
1 AAATCCCTCCTCCAAAATCCTCGTGTAA
29119586 AAATC
1 AAATC
29119591 TCTCACCTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.12
28 50 0.88
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.25
Consensus pattern (28 bp):
AAATCCCTCCTCCAAAATCCTCGTGTAA
Found at i:29119546 original size:14 final size:14
Alignment explanation
Indices: 29119503--29119577 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
29119493 TGCTCTCCCC
29119503 AAATCCC-CCTCCA
1 AAATCCCTCCTCCA
* **
29119516 AAAT-CCTCTTGTAA
1 AAATCCCTCCT-CCA
29119530 AAATCCCTCCTCCA
1 AAATCCCTCCTCCA
* **
29119544 AAAT-CCTCGTGTA
1 AAATCCCTCCTCCA
29119557 ACAATCCCTCCTCCA
1 A-AATCCCTCCTCCA
29119572 AAATCC
1 AAATCC
29119578 TCGTGTAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
12 2 0.04
13 13 0.29
14 18 0.40
15 12 0.27
ACGTcount: A:0.32, C:0.40, G:0.04, T:0.24
Consensus pattern (14 bp):
AAATCCCTCCTCCA
Found at i:29122127 original size:40 final size:39
Alignment explanation
Indices: 29122083--29122389 Score: 346
Period size: 40 Copynumber: 7.7 Consensus size: 39
29122073 GTTACTAGAG
**
29122083 TACAAACAGGGGCATGTATGTGCAATCAAGGGTATTGAAA
1 TACAAACAGGGGCACATATGTGCAATCAAGGGTA-TGAAA
* ** * *
29122123 TACAAACAAGGGCAGGTATGTGCAATCAGGGGTACTGAAG
1 TACAAACAGGGGCACATATGTGCAATCAAGGGTA-TGAAA
* * *
29122163 TACAAACAGGGGCATATATGTACAATCAAGGGTATCAAA
1 TACAAACAGGGGCACATATGTGCAATCAAGGGTATGAAA
* *
29122202 GTACAAACAGGGGCACATATGTGCAATCAAGGTTATCAAA
1 -TACAAACAGGGGCACATATGTGCAATCAAGGGTATGAAA
* * * *
29122242 GTACAAAAAAGGGCACGTATGTGCAATCAAGGGTACTGGAA
1 -TACAAACAGGGGCACATATGTGCAATCAAGGGTA-TGAAA
**
29122283 TACAAACAGGGGCACATATGTGCAATCAAGGGTACCAAA
1 TACAAACAGGGGCACATATGTGCAATCAAGGGTATGAAA
* * *
29122322 GTACAAATAGGGGCACATATGTGCAATCAGGGGTACCG-AA
1 -TACAAACAGGGGCACATATGTGCAATCAAGGGTA-TGAAA
*
29122362 TACAAACAGGGGCACGTATGTGCAATCA
1 TACAAACAGGGGCACATATGTGCAATCA
29122390 TACAATAGTT
Statistics
Matches: 231, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
39 31 0.13
40 196 0.85
41 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (39 bp):
TACAAACAGGGGCACATATGTGCAATCAAGGGTATGAAA
Found at i:29122185 original size:20 final size:20
Alignment explanation
Indices: 29122162--29122223 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
29122152 GGGTACTGAA
29122162 GTACAAACAGGGGCATATAT
1 GTACAAACAGGGGCATATAT
* * * *
29122182 GTACAATCAAGGGTATCA-AA
1 GTACAAACAGGGGCAT-ATAT
*
29122202 GTACAAACAGGGGCACATAT
1 GTACAAACAGGGGCATATAT
29122222 GT
1 GT
29122224 GCAATCAAGG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19
Consensus pattern (20 bp):
GTACAAACAGGGGCATATAT
Found at i:29122207 original size:80 final size:80
Alignment explanation
Indices: 29122070--29122389 Score: 385
Period size: 80 Copynumber: 4.0 Consensus size: 80
29122060 TATTTGATTC
* ** * * *
29122070 AGGGTTACTAGAGTACAAACAGGGGCATGTATGTGCAATCAAGGGTATTGAAATACAAACAAGGG
1 AGGG-TACTAAAGTACAAACAGGGGCACATATGTGCAATCAAGGGTACTCAAATACAAACAGGGG
**
29122135 CAGGTATGTGCAATCA
65 CACATATGTGCAATCA
* * * *
29122151 GGGGTACTGAAGTACAAACAGGGGCATATATGTACAATCAAGGGTA-TCAAAGTACAAACAGGGG
1 AGGGTACTAAAGTACAAACAGGGGCACATATGTGCAATCAAGGGTACTCAAA-TACAAACAGGGG
29122215 CACATATGTGCAATCA
65 CACATATGTGCAATCA
* * * * **
29122231 AGGTTA-TCAAAGTACAAAAAAGGGCACGTATGTGCAATCAAGGGTACTGGAATACAAACAGGGG
1 AGGGTACT-AAAGTACAAACAGGGGCACATATGTGCAATCAAGGGTACTCAAATACAAACAGGGG
29122295 CACATATGTGCAATCA
65 CACATATGTGCAATCA
* * * *
29122311 AGGGTACCAAAGTACAAATAGGGGCACATATGTGCAATCAGGGGTAC-CGAATACAAACAGGGGC
1 AGGGTACTAAAGTACAAACAGGGGCACATATGTGCAATCAAGGGTACTCAAATACAAACAGGGGC
*
29122375 ACGTATGTGCAATCA
66 ACATATGTGCAATCA
29122390 TACAATAGTT
Statistics
Matches: 208, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.17
80 167 0.80
81 6 0.03
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (80 bp):
AGGGTACTAAAGTACAAACAGGGGCACATATGTGCAATCAAGGGTACTCAAATACAAACAGGGGC
ACATATGTGCAATCA
Found at i:29122294 original size:120 final size:119
Alignment explanation
Indices: 29122081--29122389 Score: 449
Period size: 120 Copynumber: 2.6 Consensus size: 119
29122071 GGGTTACTAG
** * *
29122081 AGTACAAACAGGGGCATGTATGTGCAATCAAGGGTATTGAAATACAAACAAGGGCAGGTATGTGC
1 AGTACAAACAGGGGCACATATGTGCAATCAAGGGTA-TCAAATACAAACAAGGGCACGTATGTGC
* * *
29122146 AATCAGGGGTACTGAAGTACAAACAGGGGCATATATGTACAATCAAGGGTATCAA
65 AATCAAGGGTACTGAAGTACAAACAGGGGCACATATGTACAATCAAGGGTACCAA
* *
29122201 AGTACAAACAGGGGCACATATGTGCAATCAAGGTTATCAAAGTACAAAAAAGGGCACGTATGTGC
1 AGTACAAACAGGGGCACATATGTGCAATCAAGGGTATCAAA-TACAAACAAGGGCACGTATGTGC
*
29122266 AATCAAGGGTACTGGAA-TACAAACAGGGGCACATATGTGCAATCAAGGGTACCAA
65 AATCAAGGGTACT-GAAGTACAAACAGGGGCACATATGTACAATCAAGGGTACCAA
* * * * *
29122321 AGTACAAATAGGGGCACATATGTGCAATCAGGGGTACCGAATACAAACAGGGGCACGTATGTGCA
1 AGTACAAACAGGGGCACATATGTGCAATCAAGGGTATCAAATACAAACAAGGGCACGTATGTGCA
29122386 ATCA
66 ATCA
29122390 TACAATAGTT
Statistics
Matches: 170, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
119 30 0.18
120 137 0.81
121 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.18
Consensus pattern (119 bp):
AGTACAAACAGGGGCACATATGTGCAATCAAGGGTATCAAATACAAACAAGGGCACGTATGTGCA
ATCAAGGGTACTGAAGTACAAACAGGGGCACATATGTACAATCAAGGGTACCAA
Found at i:29131529 original size:26 final size:26
Alignment explanation
Indices: 29131475--29131560 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
29131465 TATAACAGTC
*
29131475 ATTTTACCCTATGGAGGTATTTC-AGTA
1 ATTTTACCCTTTGGA-GTATTTCGA-TA
*
29131502 ATTTTATCCTTTGGAGTATTTCGATA
1 ATTTTACCCTTTGGAGTATTTCGATA
*
29131528 ATTTTACCCTTTGGGGTATTTCGATA
1 ATTTTACCCTTTGGAGTATTTCGATA
29131554 ATTTTAC
1 ATTTTAC
29131561 GGCCCATGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
26 40 0.74
27 14 0.26
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (26 bp):
ATTTTACCCTTTGGAGTATTTCGATA
Found at i:29133816 original size:10 final size:11
Alignment explanation
Indices: 29133793--29133821 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
29133783 ACCACTTTTT
29133793 CGGCCCGAGCC
1 CGGCCCGAGCC
29133804 CGGCCCG-GCC
1 CGGCCCGAGCC
29133814 CGGCCCGA
1 CGGCCCGA
29133822 TATAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.07, C:0.55, G:0.38, T:0.00
Consensus pattern (11 bp):
CGGCCCGAGCC
Found at i:29133902 original size:20 final size:20
Alignment explanation
Indices: 29133837--29133981 Score: 131
Period size: 20 Copynumber: 7.3 Consensus size: 20
29133827 TAAATATATT
29133837 TATTTTTT-TAATTTTAAAA
1 TATTTTTTGTAATTTTAAAA
* ***
29133856 TATTTTTTACGTGATTTTTTTA
1 TATTTTTT--GTAATTTTAAAA
29133878 -ATTTTTT-TAATTTTAAAA
1 TATTTTTTGTAATTTTAAAA
29133896 TATTTTTTGTAATTTTAAAA
1 TATTTTTTGTAATTTTAAAA
** * **
29133916 TATTTTTAAAATACTTTTTTAA
1 TATTTTT--TGTAATTTTAAAA
29133938 -A-TTTTT-TAATTTTAAAA
1 TATTTTTTGTAATTTTAAAA
29133955 TATTTTTTGTAATTTTAAAA
1 TATTTTTTGTAATTTTAAAA
29133975 TATTTTT
1 TATTTTT
29133982 AAAATACTTT
Statistics
Matches: 99, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
17 8 0.08
18 8 0.08
19 20 0.20
20 40 0.40
21 8 0.08
22 15 0.15
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (20 bp):
TATTTTTTGTAATTTTAAAA
Found at i:29133934 original size:60 final size:59
Alignment explanation
Indices: 29133837--29134020 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 59
29133827 TAAATATATT
* ** * *
29133837 TATTTTTT-TAATTTTAAAATATTTTTTACGTGATTTTTTTAATTTTTTTAATTTTAAAA
1 TATTTTTTGTAATTTTAAAATATTTTTAAAAT-ACTTTTTTAAATTTTTTAATTTTAAAA
29133896 TATTTTTTGTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAA
1 TATTTTTTGTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAA
29133955 TATTTTTTGTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAA
1 TATTTTTTGTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAA
29134014 TATTTTT
1 TATTTTT
29134021 AAAATACTTT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
59 99 0.83
60 20 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (59 bp):
TATTTTTTGTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAA
Found at i:29134021 original size:39 final size:39
Alignment explanation
Indices: 29133958--29134044 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
29133948 TTTAAAATAT
29133958 TTTTTGTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
1 TTTTT-TAATTTTAAAATATTTTTAAAATACTTTTTTAAA
*
29133998 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTCAA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
29134037 TTTTTTAA
1 TTTTTTAA
29134045 AAATTTTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 41 0.89
40 5 0.11
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (39 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
Found at i:29134031 original size:28 final size:28
Alignment explanation
Indices: 29133978--29134031 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
29133968 TTTAAAATAT
* *
29133978 TTTTAAAATACTTTTTTAAATTTTTTAA
1 TTTTAAAATACTTTTTAAAATCTTTTAA
29134006 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTTAAAAT-CTTTT
29134032 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAAATCTTTTAA
Found at i:29134645 original size:28 final size:28
Alignment explanation
Indices: 29134613--29134670 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
29134603 TTGCATCATG
* * * *
29134613 TCATCGTAGAATGTACGGTTGCCCGCTA
1 TCATCGTAAAATGCACCGTTGCCCACTA
29134641 TCATCGTAAAATGCACCGTTGCCCACTA
1 TCATCGTAAAATGCACCGTTGCCCACTA
29134669 TC
1 TC
29134671 TTCCAACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (28 bp):
TCATCGTAAAATGCACCGTTGCCCACTA
Found at i:29137469 original size:20 final size:20
Alignment explanation
Indices: 29137428--29137469 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
29137418 CGTTTCAGTC
**
29137428 AAAAACCCTAAACACTTTAA
1 AAAAACCCTAAACACTAAAA
29137448 AAAAACCCTAAA-ATCTAAAA
1 AAAAACCCTAAACA-CTAAAA
29137468 AA
1 AA
29137470 CCCTGAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAACCCTAAACACTAAAA
Found at i:29137504 original size:22 final size:23
Alignment explanation
Indices: 29137479--29137528 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
29137469 ACCCTGAACT
* * *
29137479 TAACCTTAAAAAATTATAA-CCC
1 TAACCCTAAAAAATAAAAAGCCC
29137501 TAACCCTAAAAAATAAAAAGCCC
1 TAACCCTAAAAAATAAAAAGCCC
29137524 TAACC
1 TAACC
29137529 ATGGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (23 bp):
TAACCCTAAAAAATAAAAAGCCC
Found at i:29140863 original size:46 final size:45
Alignment explanation
Indices: 29140796--29140957 Score: 231
Period size: 46 Copynumber: 3.6 Consensus size: 45
29140786 TTTGAGTACT
* *
29140796 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
29140842 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
29140888 CCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
29140933 TCTGATC-AG-G-GACAAGTGATAAGTG
1 TCTGATCAAGTGAGA-AAGTGATAAGTG
29140958 ATCATACGTA
Statistics
Matches: 107, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
42 1 0.01
43 13 0.12
44 2 0.02
45 19 0.18
46 71 0.66
47 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (45 bp):
TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:29143552 original size:24 final size:27
Alignment explanation
Indices: 29143525--29143574 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
29143515 TATAACTTAC
29143525 TTTT-AATATTT-TAA-TAAATAATAA
1 TTTTAAATATTTCTAAGTAAATAATAA
*
29143549 TTTTAAATATTTCTAAGTAATTAATA
1 TTTTAAATATTTCTAAGTAAATAATA
29143575 TTAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 3 0.14
27 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTTAAATATTTCTAAGTAAATAATAA
Found at i:29143642 original size:21 final size:21
Alignment explanation
Indices: 29143590--29143646 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
29143580 TATTTATTAA
*
29143590 ATATAATTAGAATATATAAACT
1 ATATAATTA-AATATTTAAACT
29143612 ATAT--TTAAATATTTAAA-T
1 ATATAATTAAATATTTAAACT
29143630 ATAATAATTAAATATTT
1 AT-ATAATTAAATATTT
29143647 GTAATTAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 11 0.35
20 3 0.10
21 10 0.32
22 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATAATTAAATATTTAAACT
Done.