Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 112 of 170
Found at i:34427795 original size:79 final size:79
Alignment explanation
Indices: 34427672--34427879 Score: 260
Period size: 79 Copynumber: 2.6 Consensus size: 79
34427662 AATTATTGTA
* * *
34427672 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTG-CCTCTGTT
1 TGAATGCACATACGTGCCCTTG-TTGTACTTCGATACCCCTGAATGCACATGCGTGCCCT-TATT
34427736 TGTACTT-GAGTACCCC
64 TGTACTTCG-GTACCCC
* * * * *
34427752 TGAATGGACATACGTGCCCATGTTGTACTTTGGTATCCCTGAATGCACATGCGTGCCCTTATTTG
1 TGAATGCACATACGTGCCCTTGTTGTACTTCGATACCCCTGAATGCACATGCGTGCCCTTATTTG
34427817 TACTTCGGTACCCC
66 TACTTCGGTACCCC
* *
34427831 TGAATGCACATACGTGCCCTTGTTTATACTTCCG-TACCCTTGAATGCAC
1 TGAATGCACATACGTGCCCTTG-TTGTACTT-CGATACCCCTGAATGCAC
34427880 TTATGTGCCT
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
79 67 0.61
80 42 0.38
81 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (79 bp):
TGAATGCACATACGTGCCCTTGTTGTACTTCGATACCCCTGAATGCACATGCGTGCCCTTATTTG
TACTTCGGTACCCC
Found at i:34427888 original size:119 final size:119
Alignment explanation
Indices: 34427672--34427888 Score: 301
Period size: 119 Copynumber: 1.8 Consensus size: 119
34427662 AATTATTGTA
* * * *
34427672 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
* * *
34427737 GTACTTGAGTACCCCTGAATGGACATACGTGCCCATGTTGTACTTTGGTATCCC
66 ATACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
* *
34427791 TGAATGCACATGCGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCC-CTTGTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTC-TGTT
* * * *
34427855 TATACTTCCGTACCCTTGAATGCACTTATGTGCC
65 TATACTTCAGTACCCCTGAATGCACATACGTGCC
34427889 TTGTTTATAC
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
118 1 0.01
119 83 0.99
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (119 bp):
TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
ATACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
Found at i:34427905 original size:79 final size:76
Alignment explanation
Indices: 34427672--34427914 Score: 254
Period size: 79 Copynumber: 3.1 Consensus size: 76
34427662 AATTATTGTA
* *
34427672 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCG-TA-CCCTGAATGCACATGCGTGCCT-TGTTT
*
34427737 GTACTTGAGTACCCC
63 GTACTCG-GTACCCC
* * * *
34427752 TGAATGGACATACGTGCCCATG-TTGTACTTTGGTATCCCTGAATGCACATGCGTGCCCTTATTT
1 TGAATGCACATACGTGCCCTTGTTTGTAC-TTCGTA-CCCTGAATGCACATGCGTG-CCTTGTTT
34427816 GTACTTCGGTACCCC
63 GTAC-TCGGTACCCC
* * ** *
34427831 TGAATGCACATACGTGCCCTTGTTTATACTTCCGTACCCTTGAATGCACTTATGTGCCTTGTTTA
1 TGAATGCACATACGTGCCCTTGTTTGTACTT-CGTACCC-TGAATGCACATGCGTGCCTTGTTTG
* *
34427896 TACTCCGGTAACTC
64 TACT-CGGTACCCC
34427910 TGAAT
1 TGAAT
34427915 TATGTAGTAT
Statistics
Matches: 137, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
78 1 0.01
79 89 0.65
80 47 0.34
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (76 bp):
TGAATGCACATACGTGCCCTTGTTTGTACTTCGTACCCTGAATGCACATGCGTGCCTTGTTTGTA
CTCGGTACCCC
Found at i:34427913 original size:119 final size:119
Alignment explanation
Indices: 34427672--34427914 Score: 283
Period size: 119 Copynumber: 2.0 Consensus size: 119
34427662 AATTATTGTA
* * * *
34427672 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
* * * * ** *
34427737 GTACTTGAGTACCCCTGAATGGACATACGTGCCCATGTTGTACTTTGGTATCCC
66 ATACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTATACTCCGGTAACCC
* *
34427791 TGAATGCACATGCGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCC-CTTGTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTC-TGTT
* * * * * *
34427855 TATACTTCCGTACCCTTGAATGCACTTATGTG-CCTTGTTTATACTCCGGTAACTC
65 TATACTTCAGTACCCCTGAATGCACATACGTGCCCATG-TTATACTCCGGTAACCC
34427910 TGAAT
1 TGAAT
34427915 TATGTAGTAT
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
118 5 0.05
119 98 0.95
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (119 bp):
TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
ATACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTATACTCCGGTAACCC
Found at i:34429112 original size:39 final size:40
Alignment explanation
Indices: 34428995--34429156 Score: 227
Period size: 40 Copynumber: 4.1 Consensus size: 40
34428985 AATTATTGTA
* *
34428995 TGAATGCACATGCGTACCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
* *
34429035 TAAAGGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
*
34429075 TGAATGCACATACGTGCCCCTG-TTGTACTTCAGTACCCC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
* * * * *
34429114 TGAATGCACATGCATGCCCTTGTTTCTACTTCGGTACCTC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
34429154 TGA
1 TGA
34429157 CTACTCTTAC
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
39 36 0.33
40 72 0.67
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.30
Consensus pattern (40 bp):
TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
Found at i:34429115 original size:19 final size:20
Alignment explanation
Indices: 34429051--34429116 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
34429041 CACATGCGTG
*
34429051 CCCCTGTTTGTACTTCAGTA
1 CCCCTGATTGTACTTCAGTA
* * * *
34429071 CCCCTGAATGCACAT-ACGTG
1 CCCCTGATTGTACTTCA-GTA
34429091 CCCCTG-TTGTACTTCAGTA
1 CCCCTGATTGTACTTCAGTA
34429110 CCCCTGA
1 CCCCTGA
34429117 ATGCACATGC
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.18, C:0.35, G:0.17, T:0.30
Consensus pattern (20 bp):
CCCCTGATTGTACTTCAGTA
Found at i:34429132 original size:79 final size:80
Alignment explanation
Indices: 34428995--34429156 Score: 227
Period size: 79 Copynumber: 2.0 Consensus size: 80
34428985 AATTATTGTA
* * *
34428995 TGAATGCACATGCGTACCCCTGTTTGTACTTCGGTACCCCTAAAGGCACATGCGTGCCCCTGTTT
1 TGAATGCACATACGTACCCCTGTTTGTACTTCAGTACCCCTAAAGGCACATGCATGCCCCTGTTT
*
34429060 GTACTTCAGTACCCC
66 CTACTTCAGTACCCC
* * * *
34429075 TGAATGCACATACGTGCCCCTG-TTGTACTTCAGTACCCCTGAATGCACATGCATGCCCTTGTTT
1 TGAATGCACATACGTACCCCTGTTTGTACTTCAGTACCCCTAAAGGCACATGCATGCCCCTGTTT
* *
34429139 CTACTTCGGTACCTC
66 CTACTTCAGTACCCC
34429154 TGA
1 TGA
34429157 CTACTCTTAC
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 52 0.72
80 20 0.28
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.30
Consensus pattern (80 bp):
TGAATGCACATACGTACCCCTGTTTGTACTTCAGTACCCCTAAAGGCACATGCATGCCCCTGTTT
CTACTTCAGTACCCC
Found at i:34448092 original size:20 final size:20
Alignment explanation
Indices: 34448056--34448093 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34448046 AATCAAAAAT
*
34448056 AAATTAAAATTTAATTACAA
1 AAATTAAAATATAATTACAA
34448076 AAATTAAAA-ATACATTAC
1 AAATTAAAATATA-ATTAC
34448094 TTAAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTAAAATATAATTACAA
Found at i:34450170 original size:13 final size:13
Alignment explanation
Indices: 34450148--34450196 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
34450138 TTAGAAAGCT
34450148 ATTTTGTTATATAA
1 ATTTT-TTATATAA
*
34450162 ATTTTTTATATAT
1 ATTTTTTATATAA
* *
34450175 ATTTTTTCTAGATA
1 ATTTTTTATATA-A
34450189 ATTTTTTA
1 ATTTTTTA
34450197 GAATCATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (13 bp):
ATTTTTTATATAA
Found at i:34450764 original size:20 final size:18
Alignment explanation
Indices: 34450741--34450784 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 18
34450731 TCTTTTTGAA
34450741 TTTTTATGAACTTTTTATATT
1 TTTTTATGAA--TTTTA-ATT
34450762 TTTTT-TGAATTTTAATT
1 TTTTTATGAATTTTAATT
34450779 TTTTTA
1 TTTTTA
34450785 AATTAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 5 0.23
20 4 0.18
21 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTATGAATTTTAATT
Found at i:34454404 original size:14 final size:15
Alignment explanation
Indices: 34454370--34454413 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
34454360 ATATGATAAT
34454370 ATGCGAACCCTATAC
1 ATGCGAACCCTATAC
* *
34454385 ATGCGAACCC-CTAG
1 ATGCGAACCCTATAC
34454399 ATGCGAACCTCTATA
1 ATGCGAACC-CTATA
34454414 TATGTGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.46
15 11 0.46
16 2 0.08
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (15 bp):
ATGCGAACCCTATAC
Found at i:34460441 original size:16 final size:16
Alignment explanation
Indices: 34460402--34460444 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
34460392 CAAGAATCAT
34460402 CAATTGTAAT-GTTTCA
1 CAATT-TAATAGTTTCA
*
34460418 AAACTTTAATAGTTTCA
1 CAA-TTTAATAGTTTCA
34460435 CAATTTAATA
1 CAATTTAATA
34460445 CCCGAGCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (16 bp):
CAATTTAATAGTTTCA
Found at i:34461462 original size:61 final size:61
Alignment explanation
Indices: 34461394--34461556 Score: 168
Period size: 61 Copynumber: 2.7 Consensus size: 61
34461384 TTTTTTAAAA
* * ** *
34461394 TTTTTAGAGTTAGGACTAAATTGACAGATTTTGTAAATGTTTAGGGCCACA-TTTATTGAAT
1 TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTGAGGGCCA-AGTTTATTGAAT
* * * * * *
34461455 TTTTTAGAATTAGAACTAAAATGATAAATTTTGTAAACATTGGGGGCTAAGTTTGTTGAAT
1 TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTGAGGGCCAAGTTTATTGAAT
* * *
34461516 TTTTTATATTTAGGA-TCAAATTGATAGAATTTGTAAACATT
1 TTTTTAGAATTAGGACT-AAATTGATAGATTTTGTAAACATT
34461557 AGAGATATAA
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 2 0.02
61 81 0.98
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (61 bp):
TTTTTAGAATTAGGACTAAATTGATAGATTTTGTAAACATTGAGGGCCAAGTTTATTGAAT
Found at i:34466241 original size:40 final size:41
Alignment explanation
Indices: 34466147--34466243 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 41
34466137 GAAAACGCTT
* *
34466147 CCTCAAGGAAGCG-CTT-AGTCCACGTGGACAGAAAGCGCGC
1 CCTCAAGGAAGCGTTTTCTGTCCACGTGGACA-AAAGCGCGC
* **
34466187 CCTCAAGGACGCGTTTTCTGTCCACGTGGAC-AAAGCGCTT
1 CCTCAAGGAAGCGTTTTCTGTCCACGTGGACAAAAGCGCGC
**
34466227 CCTTGAGGAAGCGTTTT
1 CCTCAAGGAAGCGTTTT
34466244 GCCCGTGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
40 33 0.70
41 2 0.04
42 12 0.26
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.22
Consensus pattern (41 bp):
CCTCAAGGAAGCGTTTTCTGTCCACGTGGACAAAAGCGCGC
Found at i:34466391 original size:11 final size:11
Alignment explanation
Indices: 34466355--34466402 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
34466345 TAAATCCTTT
*
34466355 CTCTC-AATTT
1 CTCTCAAATTC
34466365 CTCTCCAATATT-
1 CTCT-CAA-ATTC
34466377 CTCTCAAATTC
1 CTCTCAAATTC
34466388 CTCTCAAATTC
1 CTCTCAAATTC
34466399 CTCT
1 CTCT
34466403 TAAAAAAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.21
11 19 0.56
12 5 0.15
13 3 0.09
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:34466460 original size:27 final size:29
Alignment explanation
Indices: 34466405--34466463 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
34466395 ATTCCTCTTA
* *
34466405 AAAAAAGCTTTAATTTTTTTAATTATTTTT
1 AAAAAAGCATTAATTTTATT-ATTATTTTT
34466435 AAAAAAGCATTAATTTTATT-TT-TTTTT
1 AAAAAAGCATTAATTTTATTATTATTTTT
34466462 AA
1 AA
34466464 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 2 0.07
30 18 0.67
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
AAAAAAGCATTAATTTTATTATTATTTTT
Found at i:34468226 original size:18 final size:18
Alignment explanation
Indices: 34468203--34468245 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
34468193 TGCCAGGTGC
* *
34468203 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
34468221 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
34468239 GTTTCCT
1 GTATCCT
34468246 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:34472159 original size:126 final size:126
Alignment explanation
Indices: 34471872--34472160 Score: 400
Period size: 126 Copynumber: 2.3 Consensus size: 126
34471862 GGCCAAACAT
* * *
34471872 GAGCTACTGTAGCAAAAGCGCATCCAC-TTAGAAGCTTTTTTCAGTACTTTTGCTGATAAAGCAT
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGAG-AGCTTCTTTCAGTACTTTTGCTGACAAAGCAT
* * * * *
34471936 CCTGTTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTTTACTCGAAATTATTTTTTCAA
65 CCTGCTTAAAGCGTCTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTGCAA
* * * * * *
34471998 GAGCTACTGTAACAAAAACGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTTCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* * *
34472063 CTGCTTAAAGCGTCTTTGACACTATTTGCTCAGGAACATCTATTCGAAATTATTTTTGCAG
66 CTGCTTAAAGCGTCTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTGCAA
*
34472124 GAGCTACTGTAGCAAAAGCACATCCACGTGAGAGCTT
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGAGAGCTT
34472161 TTTTAAATTA
Statistics
Matches: 139, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
126 137 0.99
127 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (126 bp):
GAGCTACTGTAGCAAAAGCGCATCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
CTGCTTAAAGCGTCTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTGCAA
Found at i:34472402 original size:29 final size:27
Alignment explanation
Indices: 34472360--34472424 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
34472350 TTTTCTTTAA
34472360 AACCCTAAACCTAAAAACCCCAAAACCCT
1 AACCCTAAACCT-AAAA-CCCAAAACCCT
* *
34472389 AACCTTAAACCTAAAACCCAAAACCCAA
1 AACCCTAAACCTAAAACCCAAAACCC-T
34472417 AACCCTAA
1 AACCCTAA
34472425 CCATAGTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 11 0.34
29 11 0.34
ACGTcount: A:0.51, C:0.38, G:0.00, T:0.11
Consensus pattern (27 bp):
AACCCTAAACCTAAAACCCAAAACCCT
Found at i:34473874 original size:13 final size:13
Alignment explanation
Indices: 34473856--34473880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34473846 TAAGTTATAT
34473856 GTGTGAAAATTTC
1 GTGTGAAAATTTC
34473869 GTGTGAAAATTT
1 GTGTGAAAATTT
34473881 GATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:34475602 original size:41 final size:41
Alignment explanation
Indices: 34475529--34475637 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 41
34475519 TTCAAGCTTA
* * ** *
34475529 AAGTCTAGCAAGCTTAAGGCCGGTGATGTAATTCGGACTTT
1 AAGTCCAGCAAGCTTAATGCCGGTGAAATAATTCAGACTTT
* *
34475570 ATGTCCAGCATGCTTAATGCCGGTGAAATAATTCAGACTTT
1 AAGTCCAGCAAGCTTAATGCCGGTGAAATAATTCAGACTTT
* * *
34475611 AAGTCTAACAGGC-TAATTGCCGGTGAA
1 AAGTCCAGCAAGCTTAA-TGCCGGTGAA
34475638 CTGAATAAGG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (41 bp):
AAGTCCAGCAAGCTTAATGCCGGTGAAATAATTCAGACTTT
Found at i:34480417 original size:7 final size:8
Alignment explanation
Indices: 34480397--34480430 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
34480387 ATTATTTTCT
34480397 TAAAAATA
1 TAAAAATA
34480405 TAAAAATA
1 TAAAAATA
*
34480413 TAAAAAGA
1 TAAAAATA
*
34480421 TAAATATA
1 TAAAAATA
34480429 TA
1 TA
34480431 TTTTGTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:34488431 original size:6 final size:6
Alignment explanation
Indices: 34488420--34488446 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34488410 GAAAAGCCAT
34488420 GAGCAG GAGCAG GAGCAG GAGCAG GAG
1 GAGCAG GAGCAG GAGCAG GAGCAG GAG
34488447 ATTCCTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.52, T:0.00
Consensus pattern (6 bp):
GAGCAG
Found at i:34509358 original size:31 final size:32
Alignment explanation
Indices: 34509322--34509386 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
34509312 CTTAGATAAT
34509322 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
34509353 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
34509385 TT
1 TT
34509387 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:34517239 original size:21 final size:21
Alignment explanation
Indices: 34517178--34517316 Score: 98
Period size: 21 Copynumber: 6.5 Consensus size: 21
34517168 TAGCTCTCAC
*
34517178 GAGCTTCTGTTTAACTCATAT
1 GAGCTTCTGTTTAACTCTTAT
* ** * * *
34517199 GAGTTTCCATTCAGCTCTCTTTT
1 GAGCTTCTGTTTA--ACTCTTAT
34517222 GAGCTTCTGTTTAACTCTTAT
1 GAGCTTCTGTTTAACTCTTAT
* *
34517243 GAGTTTCTGTTTAGCTCTTAT
1 GAGCTTCTGTTTAACTCTTAT
* * *
34517264 GAGCTTCCGTTCAACCCTTAT
1 GAGCTTCTGTTTAACTCTTAT
* * * *
34517285 GGGTTTCTGTTTAGCACTTAT
1 GAGCTTCTGTTTAACTCTTAT
* *
34517306 GTGCTTTTGTT
1 GAGCTTCTGTT
34517317 CAGCCGTCGG
Statistics
Matches: 87, Mismatches: 29, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
21 73 0.84
23 14 0.16
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (21 bp):
GAGCTTCTGTTTAACTCTTAT
Found at i:34517284 original size:42 final size:42
Alignment explanation
Indices: 34517160--34517316 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 42
34517150 TCGTGTTTAC
* * *
34517160 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * *
34517202 TTTCCATTCAGCTCTCTTTTGAGCTTCTGTTTAACTCTTATGAG
1 TTTCCGTTTAG--CTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * * *
34517246 TTTCTGTTTAGCTCTTATGAGCTTCCGTTCAACCCTTATGGG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
* * * *
34517288 TTTCTGTTTAGCACTTATGTGCTTTTGTT
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTT
34517317 CAGCCGTCGG
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
42 60 0.63
44 35 0.37
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTTATGAGCTTCTGTTTAACTCTTATGAG
Found at i:34519816 original size:26 final size:26
Alignment explanation
Indices: 34519769--34519836 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
34519759 AGTCATATTG
* *
34519769 GGAAGCTC-CAGAGAGCCATTAATTA
1 GGAAGCTCACAAAGAGCCATTAATCA
* * * *
34519794 GGAAGCTTAGAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCATTAATCA
34519820 GGAAGCTCACAAAGAGC
1 GGAAGCTCACAAAGAGC
34519837 TATATAACGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 7 0.21
26 27 0.79
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATTAATCA
Found at i:34520328 original size:5 final size:5
Alignment explanation
Indices: 34520318--34520347 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
34520308 TACAATTTAT
*
34520318 ATTCA ATTCA ATTCA ATTCA AATCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA
34520348 CATCTTAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (5 bp):
ATTCA
Found at i:34520852 original size:13 final size:13
Alignment explanation
Indices: 34520834--34520860 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34520824 TTTTCTTTTA
34520834 TTATTTATCATCT
1 TTATTTATCATCT
34520847 TTATTTATCATCT
1 TTATTTATCATCT
34520860 T
1 T
34520861 GCCAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:34523697 original size:6 final size:6
Alignment explanation
Indices: 34523683--34523712 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
34523673 TCTCTCAATT
*
34523683 TATATA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA
34523713 CACATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (6 bp):
TATACA
Found at i:34534259 original size:13 final size:13
Alignment explanation
Indices: 34534241--34534270 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34534231 TCCAGCAACT
34534241 ATGAATTTATTTC
1 ATGAATTTATTTC
*
34534254 ATGAATTTATTTG
1 ATGAATTTATTTC
34534267 ATGA
1 ATGA
34534271 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:34534440 original size:50 final size:50
Alignment explanation
Indices: 34534365--34534605 Score: 322
Period size: 50 Copynumber: 4.8 Consensus size: 50
34534355 ATTTGGGTAA
* *
34534365 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGAATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATG
* * * *
34534415 AGAGGTCCCACGTAAGACCATGTCTGGGACATGTCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATG
* *
34534465 AGAGGTCCCATGTAAGACCATGCCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATG
** *
34534515 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCA-TGGACACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGA-ACCGAGATG
** * *
34534565 AGAACATCCCATGTAAGACCATGTCTGGGGCATGGCTTTGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
34534606 CATGTTATTA
Statistics
Matches: 167, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
49 3 0.02
50 133 0.80
51 28 0.17
52 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATG
Found at i:34535168 original size:12 final size:12
Alignment explanation
Indices: 34535151--34535187 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34535141 TTTGATGATG
34535151 AATGGTTATTAA
1 AATGGTTATTAA
34535163 AATGGTTA--AA
1 AATGGTTATTAA
*
34535173 TATGGTTATTAA
1 AATGGTTATTAA
34535185 AAT
1 AAT
34535188 TGGCTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (12 bp):
AATGGTTATTAA
Found at i:34544779 original size:30 final size:30
Alignment explanation
Indices: 34544731--34544989 Score: 272
Period size: 30 Copynumber: 8.6 Consensus size: 30
34544721 TTGACAATAT
*
34544731 ATATGTATACAT-TACAAATCAATTCGGCA
1 ATATATATACATATACAAATCAATTCGGCA
34544760 ATATATATACATATACAAATCAATTCGGCA
1 ATATATATACATATACAAATCAATTCGGCA
* *
34544790 ATGTATAT-CTATATATAAATCAATTCGGCA
1 ATATATATAC-ATATACAAATCAATTCGGCA
* * * *
34544820 ATGTATATCCATATATAAATCAATTCGGCT
1 ATATATATACATATACAAATCAATTCGGCA
* * *
34544850 ATGTATATCCATATACAAATCAATTCGGTA
1 ATATATATACATATACAAATCAATTCGGCA
* * * *
34544880 ATGTATATCCATATAAAAATCAATTCGGCT
1 ATATATATACATATACAAATCAATTCGGCA
* *
34544910 ATATATAT-CTATATATAAATCAATTCGACA
1 ATATATATAC-ATATACAAATCAATTCGGCA
* **
34544940 ATATATATATCCATATACAAATTAATTTAGCA
1 ATATATATA--CATATACAAATCAATTCGGCA
*
34544972 ATATATAAAACATATACA
1 ATATAT-ATACATATACA
34544990 TTTGAATTCA
Statistics
Matches: 202, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.06
30 156 0.77
31 9 0.04
32 21 0.10
33 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (30 bp):
ATATATATACATATACAAATCAATTCGGCA
Found at i:34544818 original size:60 final size:60
Alignment explanation
Indices: 34544746--34544966 Score: 307
Period size: 60 Copynumber: 3.6 Consensus size: 60
34544736 TATACATTAC
*
34544746 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCAATGTATATCTATATAT
1 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCTATGTATATCTATATAT
* * * * *
34544806 AAATCAATTCGGCAATGTATATCCATATATAAATCAATTCGGCTATGTATATCCATATAC
1 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCTATGTATATCTATATAT
* * * * *
34544866 AAATCAATTCGGTAATGTATATCCATATAAAAATCAATTCGGCTATATATATCTATATAT
1 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCTATGTATATCTATATAT
* *
34544926 AAATCAATTCGACAATATATATATCCATATACAAATTAATT
1 AAATCAATTCGGCAATATATATA--CATATACAAATCAATT
34544967 TAGCAATATA
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
60 128 0.90
62 14 0.10
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (60 bp):
AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCTATGTATATCTATATAT
Found at i:34544870 original size:90 final size:90
Alignment explanation
Indices: 34544746--34544966 Score: 325
Period size: 90 Copynumber: 2.4 Consensus size: 90
34544736 TATACATTAC
* * * *
34544746 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCAATGTATATCTATATATAAATC
1 AAATCAATTCGGCTATATATATCCATATACAAATCAATTCGGCAATGTATATCCATATAAAAATC
*
34544811 AATTCGGCAATGTATATCCATATAT
66 AATTCGGCAATATATATCCATATAT
* *
34544836 AAATCAATTCGGCTATGTATATCCATATACAAATCAATTCGGTAATGTATATCCATATAAAAATC
1 AAATCAATTCGGCTATATATATCCATATACAAATCAATTCGGCAATGTATATCCATATAAAAATC
* *
34544901 AATTCGGCTATATATATCTATATAT
66 AATTCGGCAATATATATCCATATAT
* *
34544926 AAATCAATTCGACAATATATATATCCATATACAAATTAATT
1 AAATCAATTCGGC--TATATATATCCATATACAAATCAATT
34544967 TAGCAATATA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 93 0.79
92 24 0.21
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (90 bp):
AAATCAATTCGGCTATATATATCCATATACAAATCAATTCGGCAATGTATATCCATATAAAAATC
AATTCGGCAATATATATCCATATAT
Found at i:34546973 original size:41 final size:41
Alignment explanation
Indices: 34546923--34547001 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
34546913 ATATTTTATT
34546923 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTCCC
*
34546964 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTT
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTT
34547002 TCCCAATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTCCC
Found at i:34550716 original size:19 final size:19
Alignment explanation
Indices: 34550692--34550732 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
34550682 TATTTTAAAG
34550692 TTATTTAGGTAGATAAAAC
1 TTATTTAGGTAGATAAAAC
*
34550711 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAAAC
34550730 TTA
1 TTA
34550733 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
TTATTTAGGTAGATAAAAC
Found at i:34550816 original size:41 final size:41
Alignment explanation
Indices: 34550770--34550850 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
34550760 ATATTTTATT
* *
34550770 TTATCTTTTTGTAGTTTATTAGAATAAGGGAACTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTCC
*
34550811 TTATCTTTTAGTAGTTTATTAGAACAAGGGAATTATTTTC
1 TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTC
34550851 TCAATTAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTCC
Found at i:34553482 original size:18 final size:18
Alignment explanation
Indices: 34553459--34553494 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
34553449 TTTGTTGAAA
*
34553459 CAAATCGAATTGGCCAAC
1 CAAATCGAATCGGCCAAC
34553477 CAAATCGAATCGGCCAAC
1 CAAATCGAATCGGCCAAC
34553495 AACCCTCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.31, G:0.17, T:0.14
Consensus pattern (18 bp):
CAAATCGAATCGGCCAAC
Found at i:34556319 original size:10 final size:10
Alignment explanation
Indices: 34556277--34556319 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
34556267 ATTTCTATAA
*
34556277 TTTTAATTAT
1 TTTTAATTTT
34556287 TTTTAATTTT
1 TTTTAATTTT
*
34556297 TTTAAAATATTT
1 TTT-TAAT-TTT
34556309 TTTTAATTTT
1 TTTTAATTTT
34556319 T
1 T
34556320 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 16 0.57
11 6 0.21
12 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:34560877 original size:69 final size:69
Alignment explanation
Indices: 34560773--34560949 Score: 171
Period size: 69 Copynumber: 2.6 Consensus size: 69
34560763 AGTTAGCTTG
* * * * * *
34560773 GCTATGAAAACCAATAGAGTCTATTGGGACAGT-AA-ATACGAATATTTCAAGGTGTAAGACCAT
1 GCTATGACAACCAATAGAGTCTATTAGGACAGTAAACATA-G-AGATTTCAAGATGTAAAAACAT
34560836 AGCTCA
64 AGCTCA
* * * *
34560842 GCTATGACAACCAATAGAGTTTGTTAGGATAGTAAACATAGAGATTTCAATATGTAAAAACATAG
1 GCTATGACAACCAATAGAGTCTATTAGGACAGTAAACATAGAGATTTCAAGATGTAAAAACATAG
*
34560907 CTCG
66 CTCA
* * * *
34560911 GCTTTGGCAACCAATAGAGTCCATCT-GGACATTAAACAT
1 GCTATGACAACCAATAGAGTCTAT-TAGGACAGTAAACAT
34560950 GGGTTTATAC
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
69 80 0.92
70 4 0.05
71 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (69 bp):
GCTATGACAACCAATAGAGTCTATTAGGACAGTAAACATAGAGATTTCAAGATGTAAAAACATAG
CTCA
Found at i:34564017 original size:13 final size:13
Alignment explanation
Indices: 34563999--34564028 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34563989 TCCAGCAACT
34563999 ATGAATTTATTTC
1 ATGAATTTATTTC
*
34564012 ATGAATTTATTTG
1 ATGAATTTATTTC
34564025 ATGA
1 ATGA
34564029 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:34564201 original size:50 final size:50
Alignment explanation
Indices: 34564123--34564265 Score: 162
Period size: 50 Copynumber: 2.8 Consensus size: 50
34564113 ATTTGGGTAA
* * * *
34564123 AGAGGTCCCATGTAAGACCAAGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGACATG
** *
34564173 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGACATG
** * *
34564223 AGAACATCCCATGTAAGACCATGTCTAGGG-CATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGT-TTGGGACATGGCATTGGCA
34564266 TGTTATTATC
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
50 45 0.58
51 28 0.36
52 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGACATG
Found at i:34566566 original size:16 final size:16
Alignment explanation
Indices: 34566545--34566577 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34566535 TTCGCTGTAT
34566545 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
34566561 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
34566577 T
1 T
34566578 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:34566885 original size:120 final size:120
Alignment explanation
Indices: 34566751--34567086 Score: 593
Period size: 120 Copynumber: 2.8 Consensus size: 120
34566741 TTAATCATAT
*
34566751 TTTAACATATTTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
34566816 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
34566871 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
**
34566936 AAATATTCTTATATGAATTTTCCT-TTATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTT-CTAAAATCATAATATATAATACTATAAAATATAA
*
34566991 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* **
34567056 AAATATTCTTATATAAATTTAATAAAATCAT
66 AAATATTCTTATATGAATTTTCTAAAATCAT
34567087 GTAAAAAGAA
Statistics
Matches: 205, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 1 0.00
120 202 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
Found at i:34571718 original size:21 final size:21
Alignment explanation
Indices: 34571684--34571735 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
34571674 CATATCTTCT
34571684 AAGATTGC--ATATCATATCC
1 AAGATTGCATATATCATATCC
*
34571703 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCC
34571724 AAGATTGCATAT
1 AAGATTGCATAT
34571736 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 8 0.27
21 22 0.73
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
AAGATTGCATATATCATATCC
Found at i:34573616 original size:13 final size:13
Alignment explanation
Indices: 34573575--34573625 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
34573565 GTTAATCATA
34573575 TAATATATTA--T
1 TAATATATTATTT
* *
34573586 TAATATGATTAATA
1 TAATAT-ATTATTT
34573600 TAATATATTATTT
1 TAATATATTATTT
*
34573613 TAATAAATTATTT
1 TAATATATTATTT
34573626 AATTTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 17 0.52
14 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TAATATATTATTT
Found at i:34573672 original size:15 final size:16
Alignment explanation
Indices: 34573645--34573674 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34573635 TTTTTATATT
34573645 AATAATAAATTTTAAC
1 AATAATAAATTTTAAC
34573661 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
34573675 AGTTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAC
Found at i:34573785 original size:23 final size:23
Alignment explanation
Indices: 34573759--34573811 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
34573749 TTTAATAATA
34573759 AATATTTTATAGTATA-AAATATG
1 AATATTTTA-AGTATATAAATATG
*
34573782 AATATTTTAATTATATAAATATG
1 AATATTTTAAGTATATAAATATG
*
34573805 AGTATTT
1 AATATTT
34573812 GTTTAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
AATATTTTAAGTATATAAATATG
Found at i:34579715 original size:16 final size:18
Alignment explanation
Indices: 34579678--34579717 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
34579668 GGCTTTTAAC
34579678 GTTGTGATGAGCAATCGAT
1 GTTGTGATGAGCAA-CGAT
34579697 GTTGTGATGA-CAA-GAT
1 GTTGTGATGAGCAACGAT
34579713 GTTGT
1 GTTGT
34579718 AGTCATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
18 3 0.14
19 10 0.48
ACGTcount: A:0.25, C:0.07, G:0.33, T:0.35
Consensus pattern (18 bp):
GTTGTGATGAGCAACGAT
Found at i:34583207 original size:25 final size:25
Alignment explanation
Indices: 34583179--34583404 Score: 94
Period size: 25 Copynumber: 9.1 Consensus size: 25
34583169 TCCTCTCTCA
*
34583179 AGCCATATAATGGGAAGCTCATATG
1 AGCCATATAATGGGAAGCTCATAAG
* * * * *
34583204 AGCCATGTAACGAGAAGCTTATCCAG
1 AGCCATATAATGGGAAGCTCAT-AAG
** * **
34583230 -GCTGTATAACGGGAAGCTCATGCG
1 AGCCATATAATGGGAAGCTCATAAG
* *
34583254 AGCCA-ATAACGGGTAGCTC-TGAAG
1 AGCCATATAATGGGAAGCTCAT-AAG
* * * *
34583278 AGCCAT-TAACGGGAAGCT-TTGGAT
1 AGCCATATAATGGGAAGCTCAT-AAG
* *
34583302 AGCCATAT-ATCGGGAAGTTCA-AGCG
1 AGCCATATAAT-GGGAAGCTCATA-AG
* *
34583327 ATCCATAT--TGGGAAGCTCACAAAG
1 AGCCATATAATGGGAAGCTCA-TAAG
* *
34583351 AGCC-TTTAATCGGGAAGCTCACAAAG
1 AGCCATATAAT-GGGAAGCTCA-TAAG
*
34583377 AGCCATATAATGGGATGCTCATAAG
1 AGCCATATAATGGGAAGCTCATAAG
34583402 AGC
1 AGC
34583405 TGCAGTGTGC
Statistics
Matches: 151, Mismatches: 35, Indels: 30
0.70 0.16 0.14
Matches are distributed among these distances:
23 12 0.08
24 46 0.30
25 59 0.39
26 29 0.19
27 5 0.03
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (25 bp):
AGCCATATAATGGGAAGCTCATAAG
Found at i:34583265 original size:24 final size:24
Alignment explanation
Indices: 34583235--34583318 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
34583225 TCCAGGCTGT
*
34583235 ATAACGGGAAGCTCATG-CGAGCCA
1 ATAACGGGAAGCTC-TGAAGAGCCA
*
34583259 ATAACGGGTAGCTCTGAAGAGCCA
1 ATAACGGGAAGCTCTGAAGAGCCA
* * * *
34583283 TTAACGGGAAGCTTTGGATAGCCA
1 ATAACGGGAAGCTCTGAAGAGCCA
*
34583307 TATATCGGGAAG
1 -ATAACGGGAAG
34583319 TTCAAGCGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 2 0.04
24 38 0.78
25 9 0.18
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (24 bp):
ATAACGGGAAGCTCTGAAGAGCCA
Found at i:34583372 original size:26 final size:26
Alignment explanation
Indices: 34583335--34583397 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
34583325 CGATCCATAT
*
34583335 TGGGAAGCTCACAAAGAGCC-TTTAA
1 TGGGAAGCTCACAAAGAGCCATATAA
34583360 TCGGGAAGCTCACAAAGAGCCATATAA
1 T-GGGAAGCTCACAAAGAGCCATATAA
*
34583387 TGGGATGCTCA
1 TGGGAAGCTCA
34583398 TAAGAGCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 1 0.03
26 28 0.82
27 5 0.15
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
TGGGAAGCTCACAAAGAGCCATATAA
Found at i:34590967 original size:24 final size:24
Alignment explanation
Indices: 34590940--34591018 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
34590930 TGTATAACGT
34590940 GAAGCTCATAAGAGCC-ATAATCAG
1 GAAGCTCATAAGAGCCAATAA-CAG
* **
34590964 GAAGATCATGGGAGCCAATAACAG
1 GAAGCTCATAAGAGCCAATAACAG
* * * *
34590988 GTAGCTC-TGAAGAGTCATTAACGG
1 GAAGCTCAT-AAGAGCCAATAACAG
34591012 GAAGCTC
1 GAAGCTC
34591019 TGGATAGCCA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.02
24 37 0.88
25 4 0.10
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCAATAACAG
Found at i:34591030 original size:24 final size:24
Alignment explanation
Indices: 34590940--34591030 Score: 62
Period size: 24 Copynumber: 3.8 Consensus size: 24
34590930 TGTATAACGT
34590940 GAAGCTCAT-AAGAGCCA-TAATCAG
1 GAAGCTC-TGAAGAGCCATTAA-CAG
* * *
34590964 GAAGATCATG-GGAGCCAATAACAG
1 GAAGCTC-TGAAGAGCCATTAACAG
* * *
34590988 GTAGCTCTGAAGAGTCATTAACGG
1 GAAGCTCTGAAGAGCCATTAACAG
* *
34591012 GAAGCTCTGGATAGCCATT
1 GAAGCTCTGAAGAGCCATT
34591031 TATTGGGAAG
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.04
24 47 0.90
25 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (24 bp):
GAAGCTCTGAAGAGCCATTAACAG
Found at i:34591094 original size:26 final size:26
Alignment explanation
Indices: 34591052--34591119 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
34591042 TCAAGCTAGC
*
34591052 TATATTGGGAAGCTCACAAAGAGCC-
1 TATAATGGGAAGCTCACAAAGAGCCA
* *
34591077 TTTAATCGGGAAGCTCACGAAGAGCCA
1 TATAAT-GGGAAGCTCACAAAGAGCCA
*
34591104 TATAATGGGATGCTCA
1 TATAATGGGAAGCTCA
34591120 TAAGAGCTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.11
26 27 0.75
27 5 0.14
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (26 bp):
TATAATGGGAAGCTCACAAAGAGCCA
Found at i:34591248 original size:25 final size:25
Alignment explanation
Indices: 34591191--34591249 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
34591181 GCTATTAAAA
* *
34591191 GGAAGCTCGCAAGAACCATACAACG
1 GGAAGCTTGCAAGAACCACACAACG
*
34591216 GGAAGCTTGCAAGAACCACATAACG
1 GGAAGCTTGCAAGAACCACACAACG
34591241 GGAAGCTTG
1 GGAAGCTTG
34591250 AGAGGGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (25 bp):
GGAAGCTTGCAAGAACCACACAACG
Found at i:34591562 original size:5 final size:5
Alignment explanation
Indices: 34591552--34591591 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
34591542 ATTCCTATTA
* *
34591552 AATTC AATTC AATTC AATCC TATTC AATTC AATTC AATTC
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC
34591592 TCATCCTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTC
Found at i:34591575 original size:25 final size:25
Alignment explanation
Indices: 34591544--34591591 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
34591534 TTAATACAAT
34591544 TCCTATTAAATTCAATTCAATTCAA
1 TCCTATTAAATTCAATTCAATTCAA
*
34591569 TCCTATTCAATTCAATTCAATTC
1 TCCTATTAAATTCAATTCAATTC
34591592 TCATCCTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (25 bp):
TCCTATTAAATTCAATTCAATTCAA
Found at i:34596560 original size:30 final size:30
Alignment explanation
Indices: 34596526--34596594 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
34596516 AAAAAATATC
* *
34596526 AATTTAACTCTTTTGAAAGGTTGATGGCCA
1 AATTTAACTCTTTTAAAAGGTTGATGGACA
**
34596556 AATTTGATTTCTTTTAAAAGGTTGATGGACA
1 AATTT-AACTCTTTTAAAAGGTTGATGGACA
34596587 AATTTAAC
1 AATTTAAC
34596595 AAAAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.39
Consensus pattern (30 bp):
AATTTAACTCTTTTAAAAGGTTGATGGACA
Found at i:34598059 original size:14 final size:14
Alignment explanation
Indices: 34598040--34598067 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34598030 TAAAAGACAA
34598040 TGATTACTTAATGG
1 TGATTACTTAATGG
34598054 TGATTACTTAATGG
1 TGATTACTTAATGG
34598068 GGTTCTCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
TGATTACTTAATGG
Found at i:34598198 original size:27 final size:27
Alignment explanation
Indices: 34598154--34598467 Score: 326
Period size: 27 Copynumber: 11.6 Consensus size: 27
34598144 CACGACAGAT
* *
34598154 AAGAATAGCCTTTATGGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
** *
34598181 AAGAAAAGTATTTGTGGCGTAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * * *
34598208 AAGAAAATCATTTGTGGCATAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
*
34598235 AAGAAAAGCATTTGTGGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
34598262 AATAATAGCCTTTGTGACGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
34598289 AAGAAAAACCTTTGTGGCATAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
34598316 ATGAAAAGCCTTTGTGACATAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* *
34598343 AATAATAA-CCTTTGTAGCGTAATATGA
1 AAGAA-AAGCCTTTGTGGCGTAATATGA
*
34598370 AAGAAAAGCCTTTGTAGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * **
34598397 AATAATAGCCTTTGTGATGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* ***
34598424 AAGAATAGCCTTTGTGGAAAAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
34598451 AATG-AAAGCCTTTGTGG
1 AA-GAAAAGCCTTTGTGG
34598468 AAAACCATGA
Statistics
Matches: 242, Mismatches: 42, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 237 0.98
28 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (27 bp):
AAGAAAAGCCTTTGTGGCGTAATATGA
Found at i:34598468 original size:27 final size:27
Alignment explanation
Indices: 34598218--34598521 Score: 175
Period size: 27 Copynumber: 11.3 Consensus size: 27
34598208 AAGAAAATCA
* * *
34598218 TTTGTGGCATAATATGTAA-GAAAAGCA
1 TTTGTGGAATAATATGAAATG-AAAGCC
**
34598245 TTTGTGGCGTAATATGAAAT-AATAGCC
1 TTTGTGGAATAATATGAAATGAA-AGCC
* *
34598272 TTTGT-GACGTAATATGAAA-GAAAAACC
1 TTTGTGGA-ATAATATGAAATG-AAAGCC
* *
34598299 TTTGTGGCATAATATG-TATGAAAAGCC
1 TTTGTGGAATAATATGAAATG-AAAGCC
*
34598326 TTTGT-GACATAATATGAAAT-AATAACC
1 TTTGTGGA-ATAATATGAAATGAA-AGCC
* **
34598353 TTTGTAGCGTAATATGAAA-GAAAAGCC
1 TTTGTGGAATAATATGAAATG-AAAGCC
* **
34598380 TTTGTAGCGTAATATGAAAT-AATAGCC
1 TTTGTGGAATAATATGAAATGAA-AGCC
*
34598407 TTTGT-GATGTAATATGAAA-GAATAGCC
1 TTTGTGGA-ATAATATGAAATGAA-AGCC
*
34598434 TTTGTGGAAAAATATGAAATGAAAGCC
1 TTTGTGGAATAATATGAAATGAAAGCC
* * *
34598461 TTTGTGGAA-AACCATGAAAAGAAAGTC
1 TTTGTGGAATAA-TATGAAATGAAAGCC
* * * *
34598488 TTTGTGGCA-AATCACGAAACGGAAGCC
1 TTTGTGGAATAAT-ATGAAATGAAAGCC
34598515 TTTGTGG
1 TTTGTGG
34598522 CGATCTCCCT
Statistics
Matches: 229, Mismatches: 27, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
26 12 0.05
27 204 0.89
28 13 0.06
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.29
Consensus pattern (27 bp):
TTTGTGGAATAATATGAAATGAAAGCC
Found at i:34600482 original size:41 final size:41
Alignment explanation
Indices: 34600425--34600646 Score: 293
Period size: 41 Copynumber: 5.4 Consensus size: 41
34600415 CTTTAATTAT
* *
34600425 TTTGTACTTTGGTACCCCAT-AATTGCACATACGTGCCCCTA
1 TTTGTACTTCGGTACCCC-TGAATTGCACATACGTGCCCCTG
* * * *
34600466 TTTGTACTTCGATACCCATGAATTGCACATACATGCCCTTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
* * *
34600507 TTTGTACTTCAGTACCCCTGGATTGCACATGCGTGCCCCTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
* * *
34600548 TTTGTACTTCGGTACCCTTAAATTGCACATACGTGCCCCCG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
*
34600589 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCTCTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
* *
34600630 TTTATACTTCAGTACCC
1 TTTGTACTTCGGTACCC
34600647 TTTGATGTAC
Statistics
Matches: 155, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 1 0.01
41 154 0.99
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.34
Consensus pattern (41 bp):
TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
Found at i:34600644 original size:123 final size:123
Alignment explanation
Indices: 34600425--34600646 Score: 340
Period size: 123 Copynumber: 1.8 Consensus size: 123
34600415 CTTTAATTAT
* *
34600425 TTTGTACTTTGGTACCCCATAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCATGAATT
1 TTTGTACTTCGGTACCCCATAATTGCACATACGTGCCCCCATTTGTACTTCGATACCCATGAATT
*
34600490 GCACATACATGCCCTTGTTTGTACTTCAGTACCCCTGGATTGCACATGCGTGCCCCTG
66 GCACATACATGCCCTTGTTTATACTTCAGTACCCCTGGATTGCACATGCGTGCCCCTG
* * * *
34600548 TTTGTACTTCGGTA-CCCTTAAATTGCACATACGTGCCCCCGTTTGTACTTCGGTACCCCTGAAT
1 TTTGTACTTCGGTACCCCAT-AATTGCACATACGTGCCCCCATTTGTACTTCGATACCCATGAAT
*
34600612 TGCACATACGTG-CCTCTGTTTATACTTCAGTACCC
65 TGCACATACATGCCCT-TGTTTATACTTCAGTACCC
34600647 TTTGATGTAC
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
122 7 0.08
123 82 0.92
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.34
Consensus pattern (123 bp):
TTTGTACTTCGGTACCCCATAATTGCACATACGTGCCCCCATTTGTACTTCGATACCCATGAATT
GCACATACATGCCCTTGTTTATACTTCAGTACCCCTGGATTGCACATGCGTGCCCCTG
Found at i:34605494 original size:36 final size:36
Alignment explanation
Indices: 34605453--34605521 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
34605443 AGAAGTTATG
*
34605453 ATAATTACACATTTAAAAATAATCACAATTTAATTA
1 ATAATTACACATTTAAAAATAATCAAAATTTAATTA
* * *
34605489 ATAATTATACATTTATAAATAATTAAAATTTAA
1 ATAATTACACATTTAAAAATAATCAAAATTTAA
34605522 ATTACAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (36 bp):
ATAATTACACATTTAAAAATAATCAAAATTTAATTA
Found at i:34605509 original size:18 final size:18
Alignment explanation
Indices: 34605453--34605513 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
34605443 AGAAGTTATG
*
34605453 ATAATTACACATTTAAAA
1 ATAATTACACATTTATAA
* *
34605471 ATAATCACA-ATTTAATTA
1 ATAATTACACATTT-ATAA
*
34605489 ATAATTATACATTTATAA
1 ATAATTACACATTTATAA
34605507 ATAATTA
1 ATAATTA
34605514 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.11
18 27 0.77
19 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTACACATTTATAA
Found at i:34605531 original size:36 final size:36
Alignment explanation
Indices: 34605455--34605532 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
34605445 AAGTTATGAT
* * *
34605455 AATTACACATTTAAAAATAATCACAATTTAATTAAT
1 AATTATACATTTAAAAATAATCAAAATTTAATTAAC
* *
34605491 AATTATACATTTATAAATAATTAAAATTTAAATT-AC
1 AATTATACATTTAAAAATAATCAAAATTT-AATTAAC
34605527 AATTAT
1 AATTAT
34605533 TCCTTAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (36 bp):
AATTATACATTTAAAAATAATCAAAATTTAATTAAC
Found at i:34609368 original size:13 final size:13
Alignment explanation
Indices: 34609350--34609375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34609340 CTGTGGTTGC
34609350 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
34609363 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
34609376 GTATATATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:34616623 original size:28 final size:29
Alignment explanation
Indices: 34616579--34616651 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
34616569 TTTTTAAAAA
* *
34616579 TAATTTTTATATTTTTATAC-CTTTTTTAT
1 TAATTTTTATAATTTTAAACAC-TTTTTAT
34616608 TAATTTTTA-AATTTTAAACACTTTTTAT
1 TAATTTTTATAATTTTAAACACTTTTTAT
*
34616636 AAATTTTT-TGAATTTT
1 TAATTTTTAT-AATTTT
34616652 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (29 bp):
TAATTTTTATAATTTTAAACACTTTTTAT
Found at i:34619238 original size:36 final size:36
Alignment explanation
Indices: 34619191--34619262 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
34619181 TCAAAGGGTA
*
34619191 AAAAAGAAAAGAAAAGATGATTGGTCCTTCTCTGTC
1 AAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTC
34619227 AAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTC
1 AAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTC
34619263 TCTTTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (36 bp):
AAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTC
Found at i:34622319 original size:14 final size:14
Alignment explanation
Indices: 34622300--34622330 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34622290 TTCCATTTTC
34622300 TCTTCTTCTCCTCT
1 TCTTCTTCTCCTCT
*
34622314 TCTTCTTTTCCTCT
1 TCTTCTTCTCCTCT
34622328 TCT
1 TCT
34622331 CCTCTATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTTCTTCTCCTCT
Found at i:34622352 original size:11 final size:11
Alignment explanation
Indices: 34622297--34622355 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
34622287 TCCTTCCATT
34622297 TTCTCTTCTTC
1 TTCTCTTCTTC
*
34622308 TCCTCTTCTTC
1 TTCTCTTCTTC
* *
34622319 TTTTCCTCTTC
1 TTCTCTTCTTC
*
34622330 TCCTCTAT-TTC
1 TTCTCT-TCTTC
*
34622341 TTCTCTTATTC
1 TTCTCTTCTTC
34622352 TTCT
1 TTCT
34622356 TCTACTGCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 1 0.03
11 36 0.95
12 1 0.03
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:34622352 original size:22 final size:22
Alignment explanation
Indices: 34622297--34622352 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
34622287 TCCTTCCATT
34622297 TTCTCTTCTTCTCCTCTTCTTC
1 TTCTCTTCTTCTCCTCTTCTTC
* *
34622319 TTTTCCTCTTCTCCTCTAT-TTC
1 TTCTCTTCTTCTCCTCT-TCTTC
*
34622341 TTCTCTTATTCT
1 TTCTCTTCTTCT
34622353 TCTTCTACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.04, C:0.36, G:0.00, T:0.61
Consensus pattern (22 bp):
TTCTCTTCTTCTCCTCTTCTTC
Found at i:34626091 original size:2 final size:2
Alignment explanation
Indices: 34626084--34626109 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34626074 TTCTTTGTAA
34626084 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
34626110 TACTGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34628301 original size:87 final size:87
Alignment explanation
Indices: 34628148--34628350 Score: 264
Period size: 87 Copynumber: 2.3 Consensus size: 87
34628138 CCGACACTCT
* * * * * *
34628148 AATTTGTGGATGAACCACCAGTGTTTGCAGATGAACTGCCAGTAGGTTATGGATGCACAACATAT
1 AATTTGTGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATAT
* *
34628213 TTGCAAATAAGAGCTGGC-AATA
66 TTGCAAATAAAAGAT-GCTAATA
* *
34628235 AGTTTGTGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACGTAT
1 AATTTGTGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATAT
* * *
34628300 TTGTAGATAAAAGATGCTAGTA
66 TTGCAAATAAAAGATGCTAATA
*
34628322 AATTCGTGGATAAACCATCAGTGTTTGCA
1 AATTTGTGGATAAACCATCAGTGTTTGCA
34628351 GATTATTAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
86 2 0.02
87 98 0.98
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (87 bp):
AATTTGTGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATAT
TTGCAAATAAAAGATGCTAATA
Found at i:34631697 original size:53 final size:53
Alignment explanation
Indices: 34631627--34631759 Score: 178
Period size: 53 Copynumber: 2.5 Consensus size: 53
34631617 TGAAGAATCT
* * * *
34631627 TATCATGTAAGACCGTAATTGGTGGGTTATGACATCATATGGAAAGAAGACCA
1 TATCATGTAAAACCGTAACTGGTAGGTTATGACATCATATGGAAAGAAAACCA
* *
34631680 TATCGTGTAAAACCGTAACTGGTAGGTTATGACATCATATGGAAAGAAAATCA
1 TATCATGTAAAACCGTAACTGGTAGGTTATGACATCATATGGAAAGAAAACCA
* **
34631733 TATCATGTAAGATTGTAACTGGT-GGTT
1 TATCATGTAAAACCGTAACTGGTAGGTT
34631760 TTTGGGAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
52 4 0.06
53 66 0.94
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (53 bp):
TATCATGTAAAACCGTAACTGGTAGGTTATGACATCATATGGAAAGAAAACCA
Found at i:34631975 original size:61 final size:61
Alignment explanation
Indices: 34631883--34632045 Score: 245
Period size: 61 Copynumber: 2.7 Consensus size: 61
34631873 ACCAAGAAAG
* *
34631883 GAAAGCCTTTTTGGCGAGTACTGAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
1 GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
* * * * * *
34631944 GAAAGCCTTTGTGGAGAGTACTAAATGTAAATGAACGCCTTTGTAGCAAAACTCTGGACAT
1 GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
*
34632005 GAAAGCTTTTCTGGCGAGTACTAAATGTAAATGAATGCCTT
1 GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTT
34632046 CGTGGCGCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 91 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (61 bp):
GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
Found at i:34645809 original size:50 final size:52
Alignment explanation
Indices: 34645691--34645814 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 52
34645681 ATGAATTATT
* *
34645691 TAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAAAATGGGAGTTACA
1 TAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAAAATGGAAGTTACA
** * * **
34645743 TAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGAAGTTACA
1 TAATGCATAACTTTATTTAATGATGCAGACTTAAACTAAAATGGAAGTTACA
*
34645793 TAATGCATAACTTTATTAAATG
1 TAATGCATAACTTTATTTAATG
34645815 CAGAACACAC
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
50 30 0.52
51 15 0.26
52 13 0.22
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (52 bp):
TAATGCATAACTTTATTTAATGATGCAGACTTAAACTAAAATGGAAGTTACA
Found at i:34650316 original size:63 final size:62
Alignment explanation
Indices: 34650197--34650394 Score: 204
Period size: 63 Copynumber: 3.1 Consensus size: 62
34650187 CGAAAAACAT
* * *
34650197 GCGTGTGTCT-AGCCCATGTAACTCTCTGATTTCAAATTTGAGTCATACAGGCAAGACACACGG
1 GCGTGTGTCTAAG-CCATGTAACTCTCTGACTTCAGATTGGAGT-ATACAGGCAAGACACACGG
* * *
34650260 GCGTGTGTCTAAGCCTTGTAACTCTCTAACTTCAGATTGGAGT-TACACGAGTAAGACACACGG
1 GCGTGTGTCTAAGCCATGTAACTCTCTGACTTCAGATTGGAGTATACA-G-GCAAGACACACGG
* * * * * *
34650323 GCGTGTGTCCAGGCCATGTAACTCACTGACTTCAGATTTGAG-ACACACGGACAAGGCACACGG
1 GCGTGTGTCTAAGCCATGTAACTCTCTGACTTCAGATTGGAGTATACA-GG-CAAGACACACGG
*
34650386 GCATGTGTC
1 GCGTGTGTC
34650395 AGGCCGTGTA
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
61 4 0.04
62 2 0.02
63 106 0.93
64 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (62 bp):
GCGTGTGTCTAAGCCATGTAACTCTCTGACTTCAGATTGGAGTATACAGGCAAGACACACGG
Found at i:34654501 original size:16 final size:16
Alignment explanation
Indices: 34654480--34654510 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34654470 CAATATCCAA
*
34654480 TTATCATATTTACACG
1 TTATCACATTTACACG
34654496 TTATCACATTTACAC
1 TTATCACATTTACAC
34654511 ATTCATTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATCACATTTACACG
Found at i:34656898 original size:40 final size:39
Alignment explanation
Indices: 34656770--34656905 Score: 105
Period size: 40 Copynumber: 3.4 Consensus size: 39
34656760 CGTTTGGACA
* * * *
34656770 AAAAACGTCGCTAAAAATTGAGCA-TAGCGGTGCTTTACG
1 AAAAACGCCGCTAAAAA-TGAGCATTAGCGGCGTTTTAGG
* * * * **
34656809 TAAAACGCCGCTAAAGATCGAGAATTAGCGGCACTTCCAGG
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGC-GTTTTAGG
* *
34656850 -AAAGCGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCG-TTTTAGG
*
34656889 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
34656906 CCTAAGCCCA
Statistics
Matches: 73, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
38 1 0.01
39 34 0.47
40 35 0.48
41 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTAGG
Found at i:34657296 original size:207 final size:207
Alignment explanation
Indices: 34656928--34657357 Score: 810
Period size: 207 Copynumber: 2.1 Consensus size: 207
34656918 GTCCTTTCGA
34656928 GGCTTTAGCGGCG--TTTTTGAGAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTCAAG
1 GGCTTTAGCGGCGTTTTTTTGAGAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTCAAG
34656991 AAACGCAGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGGGGCTT
66 AAACGCAGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGGGGCTT
34657056 TAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCAACGTTTTTCAAGAAGCGCC
131 TAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCAACGTTTTTCAAGAAGCGCC
34657121 GCTAATGCTCGG
196 GCTAATGCTCGG
34657133 GGCTTTAGCGGCGTTTTTTTGAGAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTCAAG
1 GGCTTTAGCGGCGTTTTTTTGAGAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTCAAG
* *
34657198 AAGCGCAGCTAATGCTTGGGGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGGGGCTT
66 AAACGCAGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGGGGCTT
*
34657263 TAGCGGCTTTTTCCAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCAACGTTTTTCAAGAAGCGCC
131 TAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCAACGTTTTTCAAGAAGCGCC
*
34657328 GCTAATGCTTGG
196 GCTAATGCTCGG
34657340 GGCTTTAGCGGCGTTTTT
1 GGCTTTAGCGGCGTTTTT
34657358 GAAAAAGTGC
Statistics
Matches: 219, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
205 13 0.06
207 206 0.94
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.31
Consensus pattern (207 bp):
GGCTTTAGCGGCGTTTTTTTGAGAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTCAAG
AAACGCAGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGGGGCTT
TAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCAACGTTTTTCAAGAAGCGCC
GCTAATGCTCGG
Found at i:34657370 original size:41 final size:41
Alignment explanation
Indices: 34656928--34657370 Score: 530
Period size: 41 Copynumber: 10.8 Consensus size: 41
34656918 GTCCTTTCGA
* * *
34656928 GGCTTTAGCGGCGTTTTTGAGAAAGCGTCGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
* *
34656969 GGCTTTAGCGGTGTTTTTCAAGAAA-CGCAGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTTCAA-AAAGCGCCGCTAATGCTCGG
* * * *
34657010 GGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
* *
34657051 GGCTTTAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
* ** *
34657092 GGTTTTAGCAACGTTTTTCAAGAAGCGCCGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
* * *
34657133 GGCTTTAGCGGCGTTTTTTTGAGAAAGCGTCGCTAATGCTCGG
1 GGCTTTAGCGGCG--TTTTTCAAAAAGCGCCGCTAATGCTCGG
* * * *
34657176 GGCTTTAGCGGTGTTTTTCAAGAAGCGCAGCTAATGCTTGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
* * * *
34657217 GGTTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTTGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
*
34657258 GGCTTTAGCGGC-TTTTTCCAAGAAGCGCCGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTT-CAAAAAGCGCCGCTAATGCTCGG
* ** * *
34657299 GGTTTTAGCAACGTTTTTCAAGAAGCGCCGCTAATGCTTGG
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
* *
34657340 GGCTTTAGCGGCGTTTTTGAAAAAGTGCCGC
1 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGC
34657371 AAAAACATTT
Statistics
Matches: 340, Mismatches: 56, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
40 8 0.02
41 288 0.85
42 8 0.02
43 36 0.11
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGG
Found at i:34657790 original size:14 final size:15
Alignment explanation
Indices: 34657755--34657794 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
34657745 TAGTGTAAGG
*
34657755 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
34657770 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
34657785 -TTAGGGATTA
1 TTTAGGGATTA
34657795 AGGTTTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:34657805 original size:15 final size:14
Alignment explanation
Indices: 34657750--34657801 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
34657740 GATAATAGTG
*
34657750 TAAGGTTTAGGGAG
1 TAAGGTTTAGGGAT
*
34657764 TATGGATTTAGGGAT
1 TAAGG-TTTAGGGAT
* *
34657779 TATGGATTAGGGAT
1 TAAGGTTTAGGGAT
34657793 TAAGGTTTA
1 TAAGGTTTA
34657802 AGGGTTGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (14 bp):
TAAGGTTTAGGGAT
Found at i:34658374 original size:13 final size:11
Alignment explanation
Indices: 34658345--34658371 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
34658335 AATAAAATAA
34658345 TTTTTACTGCG
1 TTTTTACTGCG
34658356 TTTTTACTGCG
1 TTTTTACTGCG
34658367 TTTTT
1 TTTTT
34658372 TTATAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.63
Consensus pattern (11 bp):
TTTTTACTGCG
Found at i:34661594 original size:42 final size:42
Alignment explanation
Indices: 34661548--34661746 Score: 258
Period size: 43 Copynumber: 4.7 Consensus size: 42
34661538 GAGAAGCGTT
* *
34661548 GCTAAAGGT-TTGTTCTATAGCGGCGTTTGTAGGAAAAGTGCC
1 GCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GGAAAAGCGCC
** * *
34661590 GCTAAAGGTCTTGAGATATAGCGGCATTTGTGAAAAAAGCGCC
1 GCTAAAGGTCTTGATCTATAGCGGCGTTTGTG-GAAAAGCGCC
*
34661633 GCTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAAAGCGCC
1 GCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAGCGCC
* *
34661675 GCTAAAGGTCTCGATCTATAGCGGCATTTGTGGGAAAAGCGCC
1 GCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GGAAAAGCGCC
*
34661718 GCTAAAGGTCAT-AGTCTATAGCGGCGTTT
1 GCTAAAGGTCTTGA-TCTATAGCGGCGTTT
34661747 ATTTTTAAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
42 49 0.36
43 88 0.64
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (42 bp):
GCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAGCGCC
Found at i:34661684 original size:85 final size:86
Alignment explanation
Indices: 34661548--34661746 Score: 287
Period size: 85 Copynumber: 2.3 Consensus size: 86
34661538 GAGAAGCGTT
* * * *
34661548 GCTAAAGGT-TTGTTCTATAGCGGCGTTTGTAGGAAAAGTGCCGCTAAAGGTCTTGAGATATAGC
1 GCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGCAAAAGCGCCGCTAAAGGTCTCGAGATATAGC
34661612 GGCATTTGTGAAAAAAGCGCC
66 GGCATTTGTGAAAAAAGCGCC
**
34661633 GCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GCAAAAGCGCCGCTAAAGGTCTCGATCTATAGC
1 GCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGCAAAAGCGCCGCTAAAGGTCTCGAGATATAGC
**
34661697 GGCATTTGTGGGAAAAGCGCC
66 GGCATTTGTGAAAAAAGCGCC
*
34661718 GCTAAAGGTCAT-AGTCTATAGCGGCGTTT
1 GCTAAAGGTCTTGA-TCTATAGCGGCGTTT
34661747 ATTTTTAAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 1 0.01
85 82 0.80
86 20 0.19
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (86 bp):
GCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGCAAAAGCGCCGCTAAAGGTCTCGAGATATAGC
GGCATTTGTGAAAAAAGCGCC
Found at i:34663190 original size:14 final size:14
Alignment explanation
Indices: 34663171--34663197 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34663161 TTATTTTACT
34663171 GTTTTTGAAAAATG
1 GTTTTTGAAAAATG
34663185 GTTTTTGAAAAAT
1 GTTTTTGAAAAAT
34663198 AGATTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
GTTTTTGAAAAATG
Found at i:34663238 original size:23 final size:23
Alignment explanation
Indices: 34663186--34663231 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
34663176 TGAAAAATGG
*
34663186 TTTTTGAAAAATAGATTAATTTT
1 TTTTTTAAAAATAGATTAATTTT
34663209 TTTTTTAAAAATAGA-T-ATTTT
1 TTTTTTAAAAATAGATTAATTTT
34663230 TT
1 TT
34663232 ATGTTTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTTTTAAAAATAGATTAATTTT
Found at i:34663567 original size:24 final size:23
Alignment explanation
Indices: 34663540--34663586 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
34663530 ACAAATACTC
34663540 ATATTTTATA-TAATTAAAATATTT
1 ATATTTTATACT-A-TAAAATATTT
*
34663564 ATATTTTGTACTATAAAATATTT
1 ATATTTTATACTATAAAATATTT
34663587 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 10 0.48
25 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTTTATACTATAAAATATTT
Found at i:34667361 original size:6 final size:6
Alignment explanation
Indices: 34667350--34667387 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
34667340 AGTTATTGGT
* *
34667350 TTAGGG TTAGGG TTAGGG TTAAGG TTAGAG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
34667388 TTAGTGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:34667608 original size:95 final size:96
Alignment explanation
Indices: 34667455--34667729 Score: 319
Period size: 95 Copynumber: 2.9 Consensus size: 96
34667445 TATAGGGTTT
** * * * **
34667455 TTAATTAT-AATTTTTTCAAAATTGGATT-AGGTTTCGTGTTTATTGTTTTTAAGAAAAAATCAA
1 TTAATTATAAATTTTTAAAAAATTAGATTAAGGTTTAGAGTTTAAGGTTTTTAAGAAAAAATCAA
* *
34667518 TTAAATTAGGGTTTAGGGTTACTTGAGTAAT
66 ATAAATTAGGGTTTAGGGTTACTTGAGTAAA
* *
34667549 TTAA-T-T-AATTTTTAAAAAAAATTAGATTAGGGTTTAGAG-TTAAGGGTTTTTAAGGAAAAAT
1 TTAATTATAAATTTTT--AAAAAATTAGATTAAGGTTTAGAGTTTAA-GGTTTTTAAGAAAAAAT
* *
34667610 CAAATAAATTAGGGTTCAAGGTTACTTGAGTAAA
63 CAAATAAATTAGGGTTTAGGGTTACTTGAGTAAA
* * *
34667644 TTAATTATAAATTTTTATAAAATTAGATTAAGGTTTAGTGTTTAAGGTTTTTAAGTAAAAACTCA
1 TTAATTATAAATTTTTAAAAAATTAGATTAAGGTTTAGAGTTTAAGGTTTTTAAG-AAAAAATCA
*
34667709 AATAAATTAGGGTTTGGGGTT
65 AATAAATTAGGGTTTAGGGTT
34667730 TAGAGTTACT
Statistics
Matches: 151, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
92 8 0.05
93 1 0.01
94 17 0.11
95 56 0.37
96 32 0.21
97 30 0.20
98 7 0.05
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.41
Consensus pattern (96 bp):
TTAATTATAAATTTTTAAAAAATTAGATTAAGGTTTAGAGTTTAAGGTTTTTAAGAAAAAATCAA
ATAAATTAGGGTTTAGGGTTACTTGAGTAAA
Found at i:34667994 original size:126 final size:126
Alignment explanation
Indices: 34667766--34668051 Score: 475
Period size: 126 Copynumber: 2.3 Consensus size: 126
34667756 TAATTTAAAG
* * * * *
34667766 AAGCTCCCACGTGGATGCACTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACTTTT
1 AAGCTCCCACCTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
34667831 CTGAGCAAATAGTGTCAAAAACGCCTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGACCAAATAGTGTCAAAAACGCCTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAA
34667892 AAGCTCCCACCTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACCTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* * * *
34667957 CTGACCAAATAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAG
66 CTGACCAAATAGTGTCAAAAACGCCTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAA
34668018 AAGCTCCCA-CTGGACGCGCTTTTGCTACAGTAGC
1 AAGCTCCCACCTGGACGCGCTTTTGCTACAGTAGC
34668052 GCATGTTTGG
Statistics
Matches: 150, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 25 0.17
126 125 0.83
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACCTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTGACCAAATAGTGTCAAAAACGCCTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:34671063 original size:11 final size:11
Alignment explanation
Indices: 34671047--34671075 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
34671037 AAATAGAAAA
34671047 TTGAGAGGAAT
1 TTGAGAGGAAT
34671058 TTGAGAGGAAT
1 TTGAGAGGAAT
34671069 TTGAGAG
1 TTGAGAG
34671076 AATATTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (11 bp):
TTGAGAGGAAT
Found at i:34673560 original size:31 final size:31
Alignment explanation
Indices: 34673500--34673563 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
34673490 GTTGAATACC
*
34673500 CAATAACTTAAATAAAAACTTCTGAATAGTT
1 CAATAACTTAAATAAAAACTTCTCAATAGTT
* *
34673531 CAATTACTTAAATGAAAACTT-TCATATAGTT
1 CAATAACTTAAATAAAAACTTCTCA-ATAGTT
34673562 CA
1 CA
34673564 GTAATCACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.34
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTCTCAATAGTT
Found at i:34677221 original size:17 final size:18
Alignment explanation
Indices: 34677188--34677228 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34677178 CATATTGTAT
34677188 GCCCATGTGGTCCCACAC
1 GCCCATGTGGTCCCACAC
*
34677206 GCCCGTGTGG-CCCACAC
1 GCCCATGTGGTCCCACAC
34677223 GGCCCA
1 -GCCCA
34677229 ATTCGGCCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.46, G:0.27, T:0.12
Consensus pattern (18 bp):
GCCCATGTGGTCCCACAC
Found at i:34692390 original size:9 final size:9
Alignment explanation
Indices: 34692376--34692406 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34692366 GTTAAACGAA
34692376 TCGAGTTAT
1 TCGAGTTAT
*
34692385 TCGAGTTAA
1 TCGAGTTAT
34692394 TCGAGTTAT
1 TCGAGTTAT
34692403 TCGA
1 TCGA
34692407 ATCAAGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:34692751 original size:30 final size:31
Alignment explanation
Indices: 34692697--34692756 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
34692687 AAACCTTTTA
**
34692697 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACGTTTACTCCCTTCCCAC
* *
34692727 TTTTCCCCTAAAACGTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACGTTTACTCCCTTCCCA
34692757 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.40, G:0.02, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACGTTTACTCCCTTCCCAC
Found at i:34693387 original size:5 final size:5
Alignment explanation
Indices: 34693377--34693423 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
34693367 GAAAAAATAT
* *
34693377 ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG A
34693424 GAAAACTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (5 bp):
ATTCG
Found at i:34701892 original size:45 final size:45
Alignment explanation
Indices: 34701841--34701931 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
34701831 AATTTAATTA
* *
34701841 ACCATTATTAATAGGTTTAGCTTCATTTAAGTCATGCATATGTAT
1 ACCATTATTAACAGGTTTAGCTTCATTTAAGTCATGCATATATAT
* *
34701886 ACCATTATTAGCAGGTTTAGCTTCGTTTAAGTCATGCATATATAT
1 ACCATTATTAACAGGTTTAGCTTCATTTAAGTCATGCATATATAT
34701931 A
1 A
34701932 TATTATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (45 bp):
ACCATTATTAACAGGTTTAGCTTCATTTAAGTCATGCATATATAT
Found at i:34702655 original size:31 final size:31
Alignment explanation
Indices: 34702592--34702655 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
34702582 TGTTGATTTA
* *
34702592 TTTTTATATTATTTATTGTAAACTTTATTTC
1 TTTTTATATTATTTATTGTAAACTATAATTC
*
34702623 TTTTTATTATTATTTA-TGTGAACTATAATTC
1 TTTTTA-TATTATTTATTGTAAACTATAATTC
34702654 TT
1 TT
34702656 CAAATAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTTTATATTATTTATTGTAAACTATAATTC
Found at i:34707039 original size:28 final size:28
Alignment explanation
Indices: 34707007--34707086 Score: 160
Period size: 28 Copynumber: 2.9 Consensus size: 28
34706997 TGTCATAGTT
34707007 TGATGTGTATGATCCGATCTAACCAGTG
1 TGATGTGTATGATCCGATCTAACCAGTG
34707035 TGATGTGTATGATCCGATCTAACCAGTG
1 TGATGTGTATGATCCGATCTAACCAGTG
34707063 TGATGTGTATGATCCGATCTAACC
1 TGATGTGTATGATCCGATCTAACC
34707087 CTTGTTTTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (28 bp):
TGATGTGTATGATCCGATCTAACCAGTG
Found at i:34713226 original size:21 final size:21
Alignment explanation
Indices: 34713200--34713262 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
34713190 TATGATTTTT
*
34713200 AGTTTAACCCTTTTGGGTTTC
1 AGTTTAACCCTTATGGGTTTC
* * * * *
34713221 AGTTTAGCTCTTCTGAGCTTC
1 AGTTTAACCCTTATGGGTTTC
*
34713242 AGATTAACCCTTATGGGTTTC
1 AGTTTAACCCTTATGGGTTTC
34713263 TGTTCAGCTC
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTTTAACCCTTATGGGTTTC
Found at i:34725678 original size:25 final size:25
Alignment explanation
Indices: 34725649--34725698 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
34725639 GTATGTTTGT
34725649 GATGGCTTGTAATTGATCATATGTG
1 GATGGCTTGTAATTGATCATATGTG
34725674 GATGGCTTGTAATTGATCATATGTG
1 GATGGCTTGTAATTGATCATATGTG
34725699 ATATCATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (25 bp):
GATGGCTTGTAATTGATCATATGTG
Found at i:34727831 original size:10 final size:10
Alignment explanation
Indices: 34727816--34727860 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
34727806 TCGAAAATAG
34727816 TCAAAATTAA
1 TCAAAATTAA
34727826 TCAAAATTAA
1 TCAAAATTAA
*
34727836 TTATAAAATTAA
1 -T-CAAAATTAA
*
34727848 TTAAAATTAA
1 TCAAAATTAA
34727858 TCA
1 TCA
34727861 TGTTCATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 21 0.68
11 2 0.06
12 8 0.26
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (10 bp):
TCAAAATTAA
Found at i:34732001 original size:75 final size:75
Alignment explanation
Indices: 34731829--34732038 Score: 318
Period size: 75 Copynumber: 2.8 Consensus size: 75
34731819 TATCCGTTAT
34731829 CGGT-GGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAA-CACTTAGCAACCCC-TTC
1 CGGTGGGA-TCAGCACTTAGCAACCACCAGTGATTCGGGGAAT-AAGCACTTAGCAACCCCTTTC
34731891 ACATTTAAGATA
64 ACATTTAAGATA
* * *
34731903 CGGTGGGATCAGCACTTAACAACCACCAGTAATTCGGGGAATAAGCACTTAGTAACCCCTTTCAC
1 CGGTGGGATCAGCACTTAGCAACCACCAGTGATTCGGGGAATAAGCACTTAGCAACCCCTTTCAC
34731968 ATTTAAGATA
66 ATTTAAGATA
* * * *
34731978 CGGTGGGATCAGCACTTAGCAACCACCAATGAGTCAGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGGATCAGCACTTAGCAACCACCAGTGATTCGGGGAATAAGCACTTAGCAACCCCTT
34732039 GGAGGAATCA
Statistics
Matches: 123, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
73 2 0.02
74 49 0.40
75 72 0.59
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (75 bp):
CGGTGGGATCAGCACTTAGCAACCACCAGTGATTCGGGGAATAAGCACTTAGCAACCCCTTTCAC
ATTTAAGATA
Found at i:34732096 original size:104 final size:102
Alignment explanation
Indices: 34731940--34732172 Score: 351
Period size: 104 Copynumber: 2.3 Consensus size: 102
34731930 AGTAATTCGG
* * *
34731940 GGAAT-AAGCACTTAGTAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAACCAC
1 GGAATCAA-CACTTAGCAACCCCTTTCACATTCAAGATACGGTGGAATCAGCACTTAGCAACCAC
*
34732004 CAATGAGTCAGGGAATCAGCACTTAGCAACCCCTTGGA
65 CAATGAGTCAGGGAATCAACACTTAGCAACCCCTTGGA
* *
34732042 GGAATCAACACTTAGCAACCCCATTTTATATTCAAGGATACGGTGGAATCAGCACTTAGCAACCA
1 GGAATCAACACTTAGCAACCCC-TTTCACATTCAA-GATACGGTGGAATCAGCACTTAGCAACCA
* *
34732107 CCAATGAGTCGGGGAATCAACACTTAGCAACCCCTTGGG
64 CCAATGAGTCAGGGAATCAACACTTAGCAACCCCTTGGA
*
34732146 GGAATCAACACTTAGCAACCCCCTTCA
1 GGAATCAACACTTAGCAACCCCTTTCA
34732173 TCTTCAATGT
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
102 18 0.15
103 14 0.12
104 86 0.73
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (102 bp):
GGAATCAACACTTAGCAACCCCTTTCACATTCAAGATACGGTGGAATCAGCACTTAGCAACCACC
AATGAGTCAGGGAATCAACACTTAGCAACCCCTTGGA
Found at i:34732131 original size:33 final size:27
Alignment explanation
Indices: 34732115--34732167 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
34732105 CACCAATGAG
34732115 TCGGGGAATCAACACTTAGCAACCCCT
1 TCGGGGAATCAACACTTAGCAACCCCT
*
34732142 TGGGGGAATCAACACTTAGCAACCCC
1 TCGGGGAATCAACACTTAGCAACCCC
34732168 CTTCATCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (27 bp):
TCGGGGAATCAACACTTAGCAACCCCT
Found at i:34733259 original size:11 final size:12
Alignment explanation
Indices: 34733231--34733264 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
34733221 GCCCAAACAT
34733231 CGAAATTTTTGAA
1 CGAAATTTTT-AA
34733244 CGAAATTTTT-A
1 CGAAATTTTTAA
34733255 CGAAATTTTT
1 CGAAATTTTT
34733265 CTGTGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:34738988 original size:27 final size:27
Alignment explanation
Indices: 34738954--34739006 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
34738944 TCAATGAGTC
*
34738954 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAACACTTAGCAACCCCTTG
34738981 GGGGAATCAACACTTAGCAACCCCTT
1 GGGGAATCAACACTTAGCAACCCCTT
34739007 TTTATATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (27 bp):
GGGGAATCAACACTTAGCAACCCCTTG
Found at i:34739047 original size:104 final size:102
Alignment explanation
Indices: 34738881--34739108 Score: 375
Period size: 104 Copynumber: 2.2 Consensus size: 102
34738871 AGTAATTCGC
* * *
34738881 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAACCATC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAGATACGGTGGAATCAGCACTTAGCAACCACC
34738946 AATGAGTCGGGGAATCAGCACTTAGCAACCCCTTGGG
66 AATGAGTCGGGGAATCAGCACTTAGCAACCCCTTGGG
* * * *
34738983 GGAATCAACACTTAGCAACCCCTTTTTATATTCAAGGATGCGGTGGAATCAGCACTTAGCAACCA
1 GGAATCAGCACTTAGCAACCCC-TTTCACATTCAA-GATACGGTGGAATCAGCACTTAGCAACCA
34739048 CCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTGGG
64 CCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTGGG
34739087 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
34739109 CTTCGTATTC
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 21 0.18
103 9 0.08
104 86 0.74
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (102 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTCAAGATACGGTGGAATCAGCACTTAGCAACCACC
AATGAGTCGGGGAATCAGCACTTAGCAACCCCTTGGG
Found at i:34739069 original size:33 final size:27
Alignment explanation
Indices: 34739027--34739113 Score: 102
Period size: 27 Copynumber: 3.0 Consensus size: 27
34739017 AGGATGCGGT
34739027 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 GGAATCAGCACTTAGCAACC-CC--T---TCGG
*
34739060 GGAATCAGCACTTAGCAACCCCTTGGG
1 GGAATCAGCACTTAGCAACCCCTTCGG
34739087 GGAATCAGCACTTAGCAACCCCCTTCG
1 GGAATCAGCACTTAGCAA-CCCCTTCG
34739114 TATTCAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
27 21 0.41
28 7 0.14
30 1 0.02
32 2 0.04
33 20 0.39
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (27 bp):
GGAATCAGCACTTAGCAACCCCTTCGG
Found at i:34748553 original size:210 final size:208
Alignment explanation
Indices: 34748186--34748630 Score: 471
Period size: 210 Copynumber: 2.1 Consensus size: 208
34748176 AATAATCAAT
* * * * * ** *
34748186 TGGGAGCTTTTAACTCTCGTTAACTGTTTGGAGGCTATGATGTTAGACCTGTGAGCCTTAAAATG
1 TGGGAGC-TTTAACTCTCGCTAACTGTTTGGAAGATATGATATTAAACCTGCAAACCTTAAAATG
* * * * ***
34748251 ACAGCTGGGAGCTTTGAGCTCTCGCTAATTATTTTGGGGTTATGGTATTAAACATGCGAGTGTTA
65 ACAGCTGGGAGCTTTGAACTCTCGCTAACTATTTTGGGGCTATGGTATTAAACATGCAAACCTTA
* * * * *
34748316 AAATGACAGCTACGAGCTTTGAACTCTCGCTAATTGTTTGGAGTCTGCAGTATTAAAC-CTGCAA
130 AAATGACAACTACGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTACAGTAATAAACTCTG--A
34748380 GCCTTAAAATGACAGC
193 GCCTTAAAATGACAGC
* * *
34748396 TGGGAGCTTTGAACTCTCGCTAATTGTTTGGAAGATGTGGTATTAAACCTGCAAACCTTAAAATG
1 TGGGAGCTTT-AACTCTCGCTAACTGTTTGGAAGATATGATATTAAACCTGCAAACCTTAAAATG
* * * * * * *
34748461 ATAGCTTGGAGCTTTTAACTCTTGCTAACTA-TTTGGAGGCTGTGGTGTTAAACCTGCAAACCTT
65 ACAGCTGGGAGCTTTGAACTCTCGCTAACTATTTTGG-GGCTATGGTATTAAACATGCAAACCTT
** * * * *
34748525 AAAATGACAACTGGGAGCTTTTAACTCTCGCTAATTATTTGGGGGCTACGGTAATGAACTTCTGA
129 AAAATGACAACTACGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTACAGTAATAAAC-TCTGA
* *
34748590 GCCTTAAAATGATAGT
193 GCCTTAAAATGACAGC
34748606 TGGGAGCTTCTAACTCTCGCTAACT
1 TGGGAGCTT-TAACTCTCGCTAACT
34748631 ATTTAGAGTT
Statistics
Matches: 191, Mismatches: 39, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
209 8 0.04
210 179 0.94
211 1 0.01
212 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (208 bp):
TGGGAGCTTTAACTCTCGCTAACTGTTTGGAAGATATGATATTAAACCTGCAAACCTTAAAATGA
CAGCTGGGAGCTTTGAACTCTCGCTAACTATTTTGGGGCTATGGTATTAAACATGCAAACCTTAA
AATGACAACTACGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTACAGTAATAAACTCTGAGCC
TTAAAATGACAGC
Found at i:34748595 original size:70 final size:69
Alignment explanation
Indices: 34748186--34748634 Score: 409
Period size: 70 Copynumber: 6.4 Consensus size: 69
34748176 AATAATCAAT
* * * * * * * * *
34748186 TGGGAGCTTTTAACTCTCGTTAACTGTTTGGAGGCTATGATGTTAGACCTGTGAGCCTTAAAATG
1 TGGGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTGTGGTATTAAACCTG-AAGCCTTAAAATG
34748251 ACAGC
65 ACAGC
* * * * * **
34748256 TGGGAGCTTTGAGCTCTCGCTAATTATTTTGG-GGTTATGGTATTAAACATGCGAGTGTTAAAAT
1 TGGGAGCTTTGAACTCTCGCTAATTA-TTTGGAGGCTGTGGTATTAAACCTG-AAGCCTTAAAAT
34748320 GACAGC
64 GACAGC
** * * **
34748326 TACGAGCTTTGAACTCTCGCTAATTGTTTGGAGTCTGCAGTATTAAACCTGCAAGCCTTAAAATG
1 TGGGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTGTGGTATTAAACCTG-AAGCCTTAAAATG
34748391 ACAGC
65 ACAGC
* * * *
34748396 TGGGAGCTTTGAACTCTCGCTAATTGTTTGGAAGATGTGGTATTAAACCTGCAAACCTTAAAATG
1 TGGGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTGTGGTATTAAACCTG-AAGCCTTAAAATG
*
34748461 ATAGC
65 ACAGC
* * * * * *
34748466 TTGGAGCTTTTAACTCTTGCTAACTATTTGGAGGCTGTGGTGTTAAACCTGCAAACCTTAAAATG
1 TGGGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTGTGGTATTAAACCTG-AAGCCTTAAAATG
*
34748531 ACAAC
65 ACAGC
* * ** * *
34748536 TGGGAGCTTTTAACTCTCGCTAATTATTTGGGGGCTACGGTAATGAACTTCTG-AGCCTTAAAAT
1 TGGGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTGTGGTATTAAAC--CTGAAGCCTTAAAAT
* *
34748600 GATAGT
64 GACAGC
*
34748606 TGGGAGCTTCT-AACTCTCGCTAACTATTT
1 TGGGAGCTT-TGAACTCTCGCTAATTATTT
34748635 AGAGTTTCAA
Statistics
Matches: 315, Mismatches: 59, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
69 5 0.02
70 301 0.96
71 6 0.02
72 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (69 bp):
TGGGAGCTTTGAACTCTCGCTAATTATTTGGAGGCTGTGGTATTAAACCTGAAGCCTTAAAATGA
CAGC
Found at i:34748595 original size:140 final size:139
Alignment explanation
Indices: 34748188--34748634 Score: 495
Period size: 140 Copynumber: 3.2 Consensus size: 139
34748178 TAATCAATTG
* * * * * **
34748188 GGAGCTTTTAACTCTCGTTAACTGTTTGGAGGCTATGATGTTAGACCTGTGAGCCTTAAAATGAC
1 GGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGTGGTGTTAAACCTGCAAGCCTTAAAATGAC
* * * **
34748253 AGCTGGGAGCTTTGAGCTCTCGCTAATTATTTTGGGGTTATGGTATTAAACATGC-GAGTGTTAA
66 AGCTGGGAGCTTTGAACTCTCGCTAATTATTTGGGGGATATGGTATTAAAC-T-CTGAGCCTTAA
* *
34748317 AATGACAGCTA
129 AATGATAGCTT
* * * * * ** *
34748328 CGAGCTTTGAACTCTCGCTAATTGTTTGGAGTCTGCAGTATTAAACCTGCAAGCCTTAAAATGAC
1 GGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGTGGTGTTAAACCTGCAAGCCTTAAAATGAC
* ** * *
34748393 AGCTGGGAGCTTTGAACTCTCGCTAATTGTTTGGAAGATGTGGTATTAAAC-CTGCAAACCTTAA
66 AGCTGGGAGCTTTGAACTCTCGCTAATTATTTGGGGGATATGGTATTAAACTCTG--AGCCTTAA
34748457 AATGATAGCTT
129 AATGATAGCTT
* *
34748468 GGAGCTTTTAACTCTTGCTAACTATTTGGAGGCTGTGGTGTTAAACCTGCAAACCTTAAAATGAC
1 GGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGTGGTGTTAAACCTGCAAGCCTTAAAATGAC
* * * * * *
34748533 AACTGGGAGCTTTTAACTCTCGCTAATTATTTGGGGGCTACGGTAATGAACTTCTGAGCCTTAAA
66 AGCTGGGAGCTTTGAACTCTCGCTAATTATTTGGGGGATATGGTATTAAAC-TCTGAGCCTTAAA
34748598 ATGATAG-TT
130 ATGATAGCTT
*
34748607 GGGAGCTTCTAACTCTCGCTAACTATTT
1 -GGAGCTTTTAACTCTCGCTAACTATTT
34748635 AGAGTTTCAA
Statistics
Matches: 253, Mismatches: 48, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
137 1 0.00
138 1 0.00
139 2 0.01
140 246 0.97
142 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (139 bp):
GGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGTGGTGTTAAACCTGCAAGCCTTAAAATGAC
AGCTGGGAGCTTTGAACTCTCGCTAATTATTTGGGGGATATGGTATTAAACTCTGAGCCTTAAAA
TGATAGCTT
Found at i:34761343 original size:18 final size:18
Alignment explanation
Indices: 34761322--34761356 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34761312 TTGTAAAATT
*
34761322 AAAGCTTAAATTAAATGC
1 AAAGATTAAATTAAATGC
34761340 AAAGATTAAATTAAATG
1 AAAGATTAAATTAAATG
34761357 ATAAAGGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAGATTAAATTAAATGC
Found at i:34762650 original size:70 final size:70
Alignment explanation
Indices: 34762537--34762789 Score: 317
Period size: 70 Copynumber: 3.6 Consensus size: 70
34762527 TCGCGGATGA
*
34762537 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTCGACTAGTGC
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
34762602 TGGGC
66 TGGGC
* * * * * * * *
34762607 ACAACTATCGTCAGTTATCCGACTAGTGCTAGGCGTAATAATTTTTCAACTCATTTGACTAGTGC
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
*
34762672 TAGGC
66 TGGGC
* * *
34762677 ACAACTATCATCGGTTATCCGACTAACGCTGGGCGCAATAATTTGTTGACTCGTTTGACTAGTGT
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
*
34762742 TGGGA
66 TGGGC
* ** * * * *
34762747 AAAACTATCGCCGGTTACCCGACTAGCGTTGGGCACAAAAATT
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATT
34762790 AATTCACGGT
Statistics
Matches: 152, Mismatches: 31, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
70 152 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (70 bp):
ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
TGGGC
Done.