Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 182 of 199
Found at i:52898735 original size:23 final size:23
Alignment explanation
Indices: 52898709--52898784 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
52898699 ATAAGTGCAA
*
52898709 CACTGATATGTAGCCGAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
* *
52898732 CACTGTTATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
52898755 CACTGA-AGCGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
52898778 CACTGAT
1 CACTGAT
52898785 CAATAACACT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.02
23 44 0.98
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:52899036 original size:18 final size:17
Alignment explanation
Indices: 52899010--52899048 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52899000 ATTTTCCTTC
52899010 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
52899027 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
52899045 CACA
1 CACA
52899049 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:52919794 original size:15 final size:15
Alignment explanation
Indices: 52919774--52919804 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52919764 GCAATCCATA
52919774 CTTGAAACATTAGGT
1 CTTGAAACATTAGGT
52919789 CTTGAAACATTAGGT
1 CTTGAAACATTAGGT
52919804 C
1 C
52919805 CATCTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (15 bp):
CTTGAAACATTAGGT
Found at i:52921283 original size:15 final size:17
Alignment explanation
Indices: 52921263--52921303 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
52921253 ATAGTCTATT
52921263 TTATTATTTTAA-A-AA
1 TTATTATTTTAATATAA
*
52921278 TTATTAATTTAATTATAA
1 TTATTATTTTAA-TATAA
52921296 TTATTATT
1 TTATTATT
52921304 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
17 1 0.05
18 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTATTTTAATATAA
Found at i:52923902 original size:29 final size:29
Alignment explanation
Indices: 52923841--52923906 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
52923831 ATCAACCACG
* *
52923841 CACACTTAGTGCCATGTACTTTAAACTCG
1 CACACTTAGTGCCATGCACTTTAAACTCA
**
52923870 CACACTTAGTGCCATGCA-TTTCAAGTTCA
1 CACACTTAGTGCCATGCACTTT-AAACTCA
52923899 CACACTTA
1 CACACTTA
52923907 CCTTTTCCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (29 bp):
CACACTTAGTGCCATGCACTTTAAACTCA
Found at i:52924018 original size:174 final size:174
Alignment explanation
Indices: 52923728--52924055 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
52923718 AACTCAAGGT
* * *
52923728 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
52923793 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
*
52923858 ACTTTAAACTCGCACACTTAGTGCCATGCATTTCAAGTTCACAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCACAC
*
52923902 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
52923967 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
52924032 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
52924056 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCACAC
Found at i:52924049 original size:29 final size:30
Alignment explanation
Indices: 52924015--52924086 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
52924005 ATCAACCACG
*
52924015 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
52924044 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
52924073 CACACTTAGTGCCA
1 CACACTTAGTGCCA
52924087 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Found at i:52933283 original size:9 final size:9
Alignment explanation
Indices: 52933269--52933299 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52933259 GTTAAACGAA
52933269 TCGAGTTAT
1 TCGAGTTAT
*
52933278 TCGAGTTAA
1 TCGAGTTAT
52933287 TCGAGTTAT
1 TCGAGTTAT
52933296 TCGA
1 TCGA
52933300 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:52933458 original size:21 final size:21
Alignment explanation
Indices: 52933417--52933459 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
52933407 ACCCCAAATT
* *
52933417 CTCAAACATTTTTACTTTTCC
1 CTCAAACACTTTTACTCTTCC
52933438 CTCAAA-ACTTTTACTCCTTCC
1 CTCAAACACTTTTACT-CTTCC
52933459 C
1 C
52933460 ACTTTGCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAACACTTTTACTCTTCC
Found at i:52935600 original size:17 final size:18
Alignment explanation
Indices: 52935578--52935614 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52935568 ATTGAACCGA
52935578 AATTTT-AATTTGTTTTT
1 AATTTTGAATTTGTTTTT
*
52935595 AATTTTGAATTTTTTTTT
1 AATTTTGAATTTGTTTTT
52935613 AA
1 AA
52935615 ACAAGCTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
AATTTTGAATTTGTTTTT
Found at i:52942174 original size:105 final size:101
Alignment explanation
Indices: 52941995--52942188 Score: 271
Period size: 105 Copynumber: 1.9 Consensus size: 101
52941985 GACGGATAAG
* * *
52941995 ACCATGGTTGGACCATGGCAGTGTTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAATGAA
1 ACCATGGTTGGACCATGGCAGTATTTAAATGTAAGACCATAGCTGGGCTATAGCATTCTAATGAA
*
52942060 AAGATCATAACTAGGTTATGACACCTTGAATGTAAA
66 AAGACCATAACTAGGTTATGACACCTTGAATGTAAA
* * *
52942096 ACCATGGTTGGACCATGGCAGTATATATACATGTGTAATACCATAGCTGGGCTATAGCATTCTGA
1 ACCATGGTTGGACCATGGCAGTAT-T-TA-A-ATGTAAGACCATAGCTGGGCTATAGCATTCTAA
* *
52942161 TGATAAGACCATAACTGGGTTATGACAC
62 TGAAAAGACCATAACTAGGTTATGACAC
52942189 TACAAATGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 23 0.29
102 1 0.01
103 2 0.03
104 1 0.01
105 53 0.66
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (101 bp):
ACCATGGTTGGACCATGGCAGTATTTAAATGTAAGACCATAGCTGGGCTATAGCATTCTAATGAA
AAGACCATAACTAGGTTATGACACCTTGAATGTAAA
Found at i:52942217 original size:105 final size:105
Alignment explanation
Indices: 52942024--52942220 Score: 261
Period size: 105 Copynumber: 1.9 Consensus size: 105
52942014 AGTGTTTAAA
* * * **
52942024 TGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAGATCATAACTAGGTTATGACACCTTGA
1 TGTAAGACCATAGCTGGGCTATAGCATTCTAATGAAAAGACCATAACTAGGTTATGACACCTCAA
**
52942089 ATGTAAAACCATGGTTGGACCATGGCAGTATATATACATG
66 ATGTAAAACCATGGCAGGACCATGGCAGTATATATACATG
* * * *
52942129 TGTAATACCATAGCTGGGCTATAGCATTCTGATGATAAGACCATAACTGGGTTATGACA-CTACA
1 TGTAAGACCATAGCTGGGCTATAGCATTCTAATGAAAAGACCATAACTAGGTTATGACACCT-CA
* *
52942193 AATGTAAGACCATGGCAGGGCCATGGCA
65 AATGTAAAACCATGGCAGGACCATGGCA
52942221 ATGCATGTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 2 0.03
105 76 0.97
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATAGCATTCTAATGAAAAGACCATAACTAGGTTATGACACCTCAA
ATGTAAAACCATGGCAGGACCATGGCAGTATATATACATG
Found at i:52943072 original size:72 final size:72
Alignment explanation
Indices: 52942952--52943138 Score: 268
Period size: 72 Copynumber: 2.6 Consensus size: 72
52942942 CTGCGTGTGA
* * * * *
52942952 CACACGGCCTGGCACATGGGCGTGT-AGTCTGGCCGTGTGACCCTTGCACATTAATTTCATAAAT
1 CACACGGCCTGACACACGAGCGTGTGACT-TGGCCGTGTGACCCCTGCACATTAATTTCATAAAT
52943016 TAGTTACC
65 TAGTTACC
* * *
52943024 CACACGGCCTGACATACGAGCGTGTGACTTGGCCGTGTGACCCCTGCACCTTAATTTTATAAATT
1 CACACGGCCTGACACACGAGCGTGTGACTTGGCCGTGTGACCCCTGCACATTAATTTCATAAATT
52943089 AGTTACC
66 AGTTACC
* *
52943096 CACACGGCCTGGCACACGGGCGTGTGACTTGGCCGTGTGACCC
1 CACACGGCCTGACACACGAGCGTGTGACTTGGCCGTGTGACCC
52943139 AAGTCAGAGA
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 101 0.98
73 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (72 bp):
CACACGGCCTGACACACGAGCGTGTGACTTGGCCGTGTGACCCCTGCACATTAATTTCATAAATT
AGTTACC
Found at i:52943603 original size:24 final size:25
Alignment explanation
Indices: 52943558--52943610 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
52943548 AAATCTTCAT
52943558 TAAATCCTTAAAATATTCAAATCCC
1 TAAATCCTTAAAATATTCAAATCCC
* *
52943583 TAAATCCTT-AAATCTTGAAATCCC
1 TAAATCCTTAAAATATTCAAATCCC
52943607 TAAA
1 TAAA
52943611 ACTTTTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAATCCTTAAAATATTCAAATCCC
Found at i:52947528 original size:51 final size:51
Alignment explanation
Indices: 52947459--52947565 Score: 169
Period size: 51 Copynumber: 2.1 Consensus size: 51
52947449 CATGCAACAT
* *
52947459 CAACATTATCCAATCCATTTGATGTTGCAAAATCACTAGCTTATTCATCAA
1 CAACATTATCCAATCCATTTGATGTTGCAAAATCACCAGCATATTCATCAA
* * *
52947510 CAACGTTATCCACTCCATTTGATGTTGCAAAATCACCAGCATATTCATCAG
1 CAACATTATCCAATCCATTTGATGTTGCAAAATCACCAGCATATTCATCAA
52947561 CAACA
1 CAACA
52947566 ACTTCACTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (51 bp):
CAACATTATCCAATCCATTTGATGTTGCAAAATCACCAGCATATTCATCAA
Found at i:52948627 original size:117 final size:117
Alignment explanation
Indices: 52948418--52948628 Score: 361
Period size: 117 Copynumber: 1.8 Consensus size: 117
52948408 GGTAACAGAA
* * * *
52948418 ATCAACATCATCGGGACCACTGTCGCATTACAAATCGACAAAACAAACCCTACATTGTGGCACTG
1 ATCAACAACATCGGGACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
*
52948483 AAATTGCAATAATAAATCATCATTAACCATCTACAATTTTGACAACAGTTTT
66 AAATTGCAATAATAAATCATCAATAACCATCTACAATTTTGACAACAGTTTT
52948535 ATCAACAACATCGGGACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
1 ATCAACAACATCGGGACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
52948600 AAATTGCAATAATAAATCA-CAAATAACCA
66 AAATTGCAATAATAAATCATC-AATAACCA
52948629 ACAAATCAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
116 1 0.01
117 87 0.99
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (117 bp):
ATCAACAACATCGGGACCACTATCGCATAAAAAATCGACAAAACAAACCCTACATTGTGGCACTG
AAATTGCAATAATAAATCATCAATAACCATCTACAATTTTGACAACAGTTTT
Found at i:52948836 original size:16 final size:16
Alignment explanation
Indices: 52948815--52948859 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
52948805 GAATGGTAAC
*
52948815 GATTTAAGGATTTTAA
1 GATTTAAGGATTTGAA
*
52948831 GATTTAGGGATTTGAA
1 GATTTAAGGATTTGAA
*
52948847 AATTTTAAGGATT
1 GA-TTTAAGGATT
52948860 CAATAAAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (16 bp):
GATTTAAGGATTTGAA
Found at i:52949816 original size:20 final size:20
Alignment explanation
Indices: 52949791--52949853 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
52949781 GTTTTTGGCA
52949791 GAAAAAAAAGAGAAGAAAAT
1 GAAAAAAAAGAGAAGAAAAT
* *
52949811 G-AAAAAATGTAGAAGAAGAT
1 GAAAAAAAAG-AGAAGAAAAT
* * *
52949831 GCAAAAAAAGAAAAAAAAAT
1 GAAAAAAAAGAGAAGAAAAT
52949851 GAA
1 GAA
52949854 GGAAGGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 7 0.21
20 20 0.59
21 7 0.21
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (20 bp):
GAAAAAAAAGAGAAGAAAAT
Found at i:52950107 original size:6 final size:6
Alignment explanation
Indices: 52950092--52950120 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
52950082 TTTAACCCTA
52950092 AATT-T AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT
52950121 TAATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AATTAT
Found at i:52950127 original size:12 final size:13
Alignment explanation
Indices: 52950095--52950128 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
52950085 AACCCTAAAT
52950095 TTAATTATAATTA
1 TTAATTATAATTA
52950108 -TAATTATAATTA
1 TTAATTATAATTA
52950120 TTAA-TATAA
1 TTAATTATAA
52950129 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTATAATTA
Found at i:52950127 original size:18 final size:17
Alignment explanation
Indices: 52950092--52950142 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
52950082 TTTAACCCTA
52950092 AATTTAATTATAATTAT
1 AATTTAATTATAATTAT
*
52950109 AATTATAATTATTAATATAA
1 AATT-TAATTA-TAAT-TAT
*
52950129 AATTTTATT-TAATT
1 AATTTAATTATAATT
52950143 TTTGCACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 8 0.28
18 6 0.21
19 8 0.28
20 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAATTATAATTAT
Found at i:52953057 original size:20 final size:20
Alignment explanation
Indices: 52953032--52953073 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
52953022 TAGTGACAGT
52953032 GATGTTATATCCTAGAATAA
1 GATGTTATATCCTAGAATAA
52953052 GATGTTATATCCTAGAATAA
1 GATGTTATATCCTAGAATAA
52953072 GA
1 GA
52953074 CGTTGTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
GATGTTATATCCTAGAATAA
Found at i:52957364 original size:43 final size:43
Alignment explanation
Indices: 52957317--52957458 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 43
52957307 CATTAAATAA
* ** * *
52957317 CATGTTCTTTAGTGATGTTTGTGGGGAAAGCGTCGTTAAAGGT
1 CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGAT
*
52957360 CATGTTTTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGAT
1 CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGAT
* * * * ** * *
52957403 CATGTTCTTTAGCGGCGTTTGTAGGAAAAGCACCACTAAAGGT
1 CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGAT
*
52957446 CATGTTCTATAGC
1 CATGTTCTTTAGC
52957459 AGCGTTTTTC
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGAT
Found at i:52961423 original size:45 final size:45
Alignment explanation
Indices: 52961359--52961538 Score: 206
Period size: 45 Copynumber: 4.0 Consensus size: 45
52961349 TACGTGTACT
*
52961359 GAGTATCATTGATTATAAAGGTGGTTGTTATGTGTTGATTCCACC
1 GAGTATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACC
* *
52961404 GAGTACCATTGATTATAAAGGTGGTTGTTATGTGCTGACTCCA-C
1 GAGTATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACC
* * ** *
52961448 TAGAAATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACC
1 GAG-TATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACC
* * *
52961494 AAATATAATTGATTATAAAGGGTGG-TGCTT-TGTGCTGA-TCCACC
1 GAGTATCATTGATTATAAA-GGTGGTTG-TTATGTGCTGATTCCACC
52961538 G
1 G
52961539 TGTAACTGTT
Statistics
Matches: 113, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
44 9 0.08
45 96 0.85
46 8 0.07
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (45 bp):
GAGTATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACC
Found at i:52961528 original size:90 final size:89
Alignment explanation
Indices: 52961363--52961536 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 89
52961353 TGTACTGAGT
** * * * * *
52961363 ATCATTGATTATAAAGGTGGTTGTTATGTGTTGATTCCACCGAGTACCATTGATTATAAAGGTGG
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCAAATACAATTGATTATAAAGGTGG
52961428 TTGTTATGTGCTGACTCCACTAGAA
66 TTGTTATGTGCTGA-TCCACTAGAA
*
52961453 ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCAAATATAATTGATTATAAAGGGTG
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCAAATACAATTGATTATAAA-GGTG
52961518 G-TGCTT-TGTGCTGATCCAC
65 GTTG-TTATGTGCTGATCCAC
52961537 CGTGTAACTG
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 5 0.07
90 62 0.84
91 7 0.09
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (89 bp):
ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCAAATACAATTGATTATAAAGGTGG
TTGTTATGTGCTGATCCACTAGAA
Found at i:52967359 original size:15 final size:15
Alignment explanation
Indices: 52967339--52967372 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52967329 CTAAAAGCTC
*
52967339 TTATTGTGACCATTG
1 TTATTGTCACCATTG
52967354 TTATTGTCACCATTG
1 TTATTGTCACCATTG
52967369 TTAT
1 TTAT
52967373 CGACCAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.50
Consensus pattern (15 bp):
TTATTGTCACCATTG
Found at i:52967803 original size:18 final size:17
Alignment explanation
Indices: 52967764--52967806 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
52967754 AAAAACTATT
52967764 TTAAAAATTAAAAATCA
1 TTAAAAATTAAAAATCA
*
52967781 TTAAAAGATTATAAAATTA
1 TTAAAA-ATTA-AAAATCA
52967800 -TAAAAAT
1 TTAAAAAT
52967807 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 6 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAAAAATTAAAAATCA
Found at i:52968372 original size:29 final size:30
Alignment explanation
Indices: 52968340--52968396 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
52968330 AATTAATAAA
*
52968340 AATAAAATTATAATTTAA-CCTTTAAAAGT
1 AATAAAATTATAATTTAATCATTTAAAAGT
*
52968369 AATAAAATTTTAATTTAATCATTTAAAA
1 AATAAAATTATAATTTAATCATTTAAAA
52968397 ATTACATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
AATAAAATTATAATTTAATCATTTAAAAGT
Found at i:52977221 original size:190 final size:190
Alignment explanation
Indices: 52976898--52977278 Score: 699
Period size: 190 Copynumber: 2.0 Consensus size: 190
52976888 ACTTCCAATC
52976898 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
1 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
52976963 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
66 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
52977028 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
131 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
*
52977088 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATTAGATATTCCAACTTTCTTTCTTAACA
1 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
* ** *
52977153 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGTTCTGGCAACGATCCCAGCTTGGAAT
66 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
* *
52977218 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAACCCAAACTCTAAAAGTG
131 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
52977278 A
1 A
52977279 CGGCAAGAAG
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 184 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (190 bp):
AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
Found at i:52978637 original size:21 final size:22
Alignment explanation
Indices: 52978594--52978676 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
52978584 ACCAATTTGG
* *
52978594 ATTAAAAAAATTTAAGTACCAA
1 ATTAAAAAAAATTAAGCACCAA
*
52978616 ATTAAAAAAAATTAA-CATCAA
1 ATTAAAAAAAATTAAGCACCAA
**
52978637 ATTTTTTAAAAAAAACTTAAAAACCAA
1 A----TTAAAAAAAA-TTAAGCACCAA
*
52978664 ATTTAAAAAAATT
1 ATTAAAAAAAATT
52978677 GTGAAGGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 5 0.10
22 16 0.33
23 9 0.18
25 10 0.20
26 4 0.08
27 5 0.10
ACGTcount: A:0.61, C:0.08, G:0.01, T:0.29
Consensus pattern (22 bp):
ATTAAAAAAAATTAAGCACCAA
Found at i:52978664 original size:27 final size:25
Alignment explanation
Indices: 52978617--52978667 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52978607 AAGTACCAAA
* *
52978617 TTAAAAAAAATTAACATCAAATTTT
1 TTAAAAAAAATTAAAACCAAATTTT
52978642 TTAAAAAAAACTTAAAAACCAAATTT
1 TTAAAAAAAA-TT-AAAACCAAATTT
52978668 AAAAAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
27 10 0.45
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (25 bp):
TTAAAAAAAATTAAAACCAAATTTT
Found at i:52985321 original size:21 final size:21
Alignment explanation
Indices: 52985253--52985321 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
52985243 AAGCCCAAAG
* *
52985253 GCTGAATAGAAGCTCATGAGA
1 GCTGAATGGAAGCTCATAAGA
* * * *
52985274 GCTAAATGGAAACCCATAAGG
1 GCTGAATGGAAGCTCATAAGA
* *
52985295 GTTGAATGGAAGCTCGTAAGA
1 GCTGAATGGAAGCTCATAAGA
52985316 GCTGAA
1 GCTGAA
52985322 CGAAAAATCA
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (21 bp):
GCTGAATGGAAGCTCATAAGA
Found at i:52985384 original size:42 final size:42
Alignment explanation
Indices: 52985312--52985397 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
52985302 GGAAGCTCGT
*
52985312 AAGAGCTGAACGAAAAATCATAAGGTTTAAACA-AAAGCTCAA
1 AAGAGCTGAACGAAAAACCATAAGGTTTAAACAGAAA-CTCAA
* * *
52985354 AAGAGCTGAACGGAAACCCAATAAGG-TTAAATAGAAACTCAA
1 AAGAGCTGAACGAAAAACC-ATAAGGTTTAAACAGAAACTCAA
52985396 AA
1 AA
52985398 ATGCTAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 29 0.76
43 9 0.24
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.15
Consensus pattern (42 bp):
AAGAGCTGAACGAAAAACCATAAGGTTTAAACAGAAACTCAA
Found at i:52985411 original size:42 final size:43
Alignment explanation
Indices: 52985331--52985411 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 43
52985321 ACGAAAAATC
*
52985331 ATAAGGTTTAAACAAAAGCTCAAAAGAGCTGAACGGAAACCCA
1 ATAAGGTTTAAACAAAAGCTCAAAAGAGCTAAACGGAAACCCA
* *
52985374 ATAAGG-TTAAATAGAAA-CTCAAAA-ATGCTAAATGGAAA
1 ATAAGGTTTAAACA-AAAGCTCAAAAGA-GCTAAACGGAAA
52985412 GAAAACACGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
41 1 0.03
42 23 0.70
43 9 0.27
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (43 bp):
ATAAGGTTTAAACAAAAGCTCAAAAGAGCTAAACGGAAACCCA
Found at i:52987427 original size:10 final size:11
Alignment explanation
Indices: 52987403--52987458 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
52987393 TTATATACTA
52987403 AATAAAATAAT
1 AATAAAATAAT
52987414 AATAAAAT-AT
1 AATAAAATAAT
* *
52987424 AATAAAAAAACA
1 AATAAAATAA-T
* *
52987436 AATCAAATATT
1 AATAAAATAAT
*
52987447 AATAAACTAAT
1 AATAAAATAAT
52987458 A
1 A
52987459 TTTATTTATT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
10 9 0.26
11 18 0.53
12 7 0.21
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:52991423 original size:6 final size:6
Alignment explanation
Indices: 52991412--52991447 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
52991402 GTTTCTTTTC
*
52991412 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT CTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
52991448 GGTGTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:53003491 original size:15 final size:15
Alignment explanation
Indices: 53003443--53003494 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
53003433 TAACTCAGAT
53003443 ATTTA-TAATATTTATA
1 ATTTATTAAT-TTTA-A
*
53003459 ATTAATTTAATTTT-A
1 ATTTA-TTAATTTTAA
53003474 ATTTATTAATTTTAA
1 ATTTATTAATTTTAA
53003489 ATTTAT
1 ATTTAT
53003495 ATTATCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 8 0.26
15 12 0.39
16 4 0.13
17 3 0.10
18 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTAATTTTAA
Found at i:53006557 original size:23 final size:22
Alignment explanation
Indices: 53006531--53006573 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
53006521 AAAGAATATA
53006531 TACGTA-ACTAATAATATGAGAAG
1 TACGTACA-TAAT-ATATGAGAAG
53006554 TACGTACATAATATATGAGA
1 TACGTACATAATATATGAGA
53006574 TTGTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 10 0.53
24 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (22 bp):
TACGTACATAATATATGAGAAG
Found at i:53006572 original size:22 final size:23
Alignment explanation
Indices: 53006531--53006573 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
53006521 AAAGAATATA
53006531 TACGTAACTAATAATATGAGAAG
1 TACGTAACTAATAATATGAGAAG
53006554 TACGT-ACATAAT-ATATGAGA
1 TACGTAAC-TAATAATATGAGA
53006574 TTGTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (23 bp):
TACGTAACTAATAATATGAGAAG
Found at i:53006772 original size:20 final size:20
Alignment explanation
Indices: 53006747--53006793 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
53006737 ATAGCATTAA
53006747 GAACATAATGAAGAATATAC
1 GAACATAATGAAGAATATAC
53006767 GAACATAATGAAGAATATAC
1 GAACATAATGAAGAATATAC
*
53006787 GTACATA
1 GAACATA
53006794 TATAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (20 bp):
GAACATAATGAAGAATATAC
Found at i:53006941 original size:3 final size:3
Alignment explanation
Indices: 53006927--53006977 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
53006917 AAACATAAAC
* *
53006927 TAA TACA TAA TAA TAT TAA TAA TAA TAA -AA TTAA TAA T-A TAA AAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
53006972 TAA TAA
1 TAA TAA
53006978 GAGTATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53006959 original size:15 final size:15
Alignment explanation
Indices: 53006927--53006977 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
53006917 AAACATAAAC
*
53006927 TAATACATAATAATAT
1 TAATA-ATAATAAAAT
53006943 TAATAATAATAAAAT
1 TAATAATAATAAAAT
*
53006958 TAATAAT-ATAAAAA
1 TAATAATAATAAAAT
53006972 TAATAA
1 TAATAA
53006978 GAGTATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.36
15 16 0.48
16 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATAATAAAAT
Found at i:53008167 original size:16 final size:16
Alignment explanation
Indices: 53008146--53008177 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53008136 TTTTGTGTAA
*
53008146 TGGGCTGTTAGTTTAG
1 TGGGCTGGTAGTTTAG
53008162 TGGGCTGGTAGTTTAG
1 TGGGCTGGTAGTTTAG
53008178 GTTATTGGGC
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:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (16 bp):
TGGGCTGGTAGTTTAG
Found at i:53008416 original size:16 final size:18
Alignment explanation
Indices: 53008379--53008417 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
53008369 AATTAATTGA
53008379 AAAATGTAATAAAATATT
1 AAAATGTAATAAAATATT
*
53008397 AAAAT-TAATAAGAT-TT
1 AAAATGTAATAAAATATT
53008413 AAAAT
1 AAAAT
53008418 AAAAATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAATGTAATAAAATATT
Found at i:53020821 original size:20 final size:20
Alignment explanation
Indices: 53020792--53020841 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
53020782 ATGCAAAAAT
* *
53020792 AATATTTTAATATATATATA
1 AATATATTAATATAAATATA
* * *
53020812 CATATCTTAATGTAAATATA
1 AATATATTAATATAAATATA
53020832 AATATATTAA
1 AATATATTAA
53020842 ACTTAATTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (20 bp):
AATATATTAATATAAATATA
Found at i:53032970 original size:7 final size:7
Alignment explanation
Indices: 53032958--53032987 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53032948 AAACATACTC
53032958 AATATCA
1 AATATCA
53032965 AATATCA
1 AATATCA
53032972 AATATCA
1 AATATCA
53032979 AATATCA
1 AATATCA
53032986 AA
1 AA
53032988 ACTATTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (7 bp):
AATATCA
Found at i:53033848 original size:20 final size:21
Alignment explanation
Indices: 53033810--53033848 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53033800 TCATGATATC
*
53033810 AATCTCATTCATATGTTATTT
1 AATCTCATTCACATGTTATTT
*
53033831 AATCT-ATTCACATTTTAT
1 AATCTCATTCACATGTTAT
53033849 AACTCTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (21 bp):
AATCTCATTCACATGTTATTT
Found at i:53033998 original size:43 final size:42
Alignment explanation
Indices: 53033921--53034060 Score: 138
Period size: 43 Copynumber: 3.3 Consensus size: 42
53033911 CTAGCATCAC
** * * *
53033921 AGTGCATCATCGGATAAACCGAAGGAAATATACTGGTACACA
1 AGTGCATCATCGGACGAACCAAAGCAAATGTACTGGTACACA
* * * *
53033963 TAGTGCTTCATCGGAC-AAGTCAAAGCAATTGTACTGGCACACA
1 -AGTGCATCATCGGACGAA-CCAAAGCAAATGTACTGGTACACA
* * *
53034006 AGGTGCATCATCTGACGAACCAAAGCAAATGTAATGGTACATA
1 A-GTGCATCATCGGACGAACCAAAGCAAATGTACTGGTACACA
53034049 AGTGCATCATCG
1 AGTGCATCATCG
53034061 AATTAACCGA
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
42 13 0.17
43 63 0.81
44 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (42 bp):
AGTGCATCATCGGACGAACCAAAGCAAATGTACTGGTACACA
Found at i:53034074 original size:42 final size:41
Alignment explanation
Indices: 53033921--53034147 Score: 141
Period size: 42 Copynumber: 5.3 Consensus size: 41
53033911 CTAGCATCAC
* * *
53033921 AGTGCATCATCGGATAAACCGAAGGAAATATACTGGTACACA
1 AGTGCATCATC-GATTAACCGAAGCAAATATACTGGTACATA
* * * * * * * *
53033963 TAGTGCTTCATCGGA-CAAGTCAAAGCAATTGTACTGGCACACA
1 -AGTGCATCATC-GATTAA-CCGAAGCAAATATACTGGTACATA
** * * *
53034006 AGGTGCATCATCTGACGAACCAAAGCAAATGTAATGGTACATA
1 A-GTGCATCATC-GATTAACCGAAGCAAATATACTGGTACATA
* **
53034049 AGTGCATCATCGAATTAACCGAAGCAAATATATTGACACATA
1 AGTGCATCATCG-ATTAACCGAAGCAAATATACTGGTACATA
* * * *
53034091 AGTGCACCATCGGTTAAATCGAAGTAAATATACTGGTACACATA
1 AGTGCATCATCGATT-AACCGAAGCAAATATACTGGT--ACATA
*
53034135 AGTGCATTATCGA
1 AGTGCATCATCGA
53034148 CTAAACTGAA
Statistics
Matches: 144, Mismatches: 33, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
41 3 0.02
42 62 0.43
43 62 0.43
44 17 0.12
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (41 bp):
AGTGCATCATCGATTAACCGAAGCAAATATACTGGTACATA
Found at i:53034159 original size:44 final size:42
Alignment explanation
Indices: 53034044--53034160 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 42
53034034 ATGTAATGGT
* * * *
53034044 ACATAAGTGCATCATCGAATTAACCGAAGCAAATATATTGAC
1 ACATAAGTGCATCATCGAATAAACTGAAGTAAATATATGGAC
* **
53034086 ACATAAGTGCACCATCGGTTAAA-TCGAAGTAAATATACTGGTAC
1 ACATAAGTGCATCATCGAATAAACT-GAAGTAAATATA-TGG-AC
* *
53034130 ACATAAGTGCATTATCGACTAAACTGAAGTA
1 ACATAAGTGCATCATCGAATAAACTGAAGTA
53034161 TAAACCCATT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 30 0.50
43 2 0.03
44 27 0.45
45 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (42 bp):
ACATAAGTGCATCATCGAATAAACTGAAGTAAATATATGGAC
Found at i:53036162 original size:20 final size:21
Alignment explanation
Indices: 53036131--53036169 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
53036121 ATAATATCAA
53036131 ATAAATCTGAATTTTCATTGT
1 ATAAATCTGAATTTTCATTGT
53036152 ATAAA-CTGAATTTTCATT
1 ATAAATCTGAATTTTCATT
53036170 AATATCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (21 bp):
ATAAATCTGAATTTTCATTGT
Found at i:53039871 original size:9 final size:9
Alignment explanation
Indices: 53039845--53039887 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
53039835 GGTATTTTTC
*
53039845 GGTAATTCA
1 GGTAATTCG
*
53039854 GTTAATTCG
1 GGTAATTCG
*
53039863 GTTAATTCG
1 GGTAATTCG
53039872 GGTAATTCG
1 GGTAATTCG
53039881 GGTAATT
1 GGTAATT
53039888 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (9 bp):
GGTAATTCG
Found at i:53053956 original size:14 final size:12
Alignment explanation
Indices: 53053936--53053977 Score: 59
Period size: 11 Copynumber: 3.4 Consensus size: 12
53053926 TTACCCTTTG
53053936 TTTTTTGTTCTT
1 TTTTTTGTTCTT
53053948 TATTATTTGTTCTT
1 T-TT-TTTGTTCTT
53053962 TTTTTT-TTCTT
1 TTTTTTGTTCTT
53053973 TTTTT
1 TTTTT
53053978 GTGCTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.36
12 4 0.14
13 4 0.14
14 10 0.36
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (12 bp):
TTTTTTGTTCTT
Found at i:53056488 original size:178 final size:179
Alignment explanation
Indices: 53056188--53056518 Score: 529
Period size: 178 Copynumber: 1.9 Consensus size: 179
53056178 TCAAAATAAT
* * * * *
53056188 ATTGTAAAAATAGGTAGTCATAAATCCTAAATATGAACCATAAATTAGATATGTATTAAGAAAAC
1 ATTGTAAAAATAGGTAATCATAAACCCCAAATATGAACCATAAATTAAAGATGTATTAAGAAAAC
* *
53056253 ACATAAACTTGAACTATTATTTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGATATTGT
66 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
* *
53056318 TAGGAGGAATAGTTATGAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
131 TAGGAGGAACAGTTATAAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
* * * *
53056367 ATTGTAAAAATAGGTAATTATGAACCCCAAATATGAACTATAAATTAAAGATGTATT-AGTAAAC
1 ATTGTAAAAATAGGTAATCATAAACCCCAAATATGAACCATAAATTAAAGATGTATTAAGAAAAC
53056431 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
66 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
*
53056496 TAGGAGGGACAGTTATAAACCCC
131 TAGGAGGAACAGTTATAAACCCC
53056519 AAATTTGAAC
Statistics
Matches: 138, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
178 89 0.64
179 49 0.36
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (179 bp):
ATTGTAAAAATAGGTAATCATAAACCCCAAATATGAACCATAAATTAAAGATGTATTAAGAAAAC
ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
TAGGAGGAACAGTTATAAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
Found at i:53057779 original size:13 final size:13
Alignment explanation
Indices: 53057743--53057781 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
53057733 TCGAGTCATA
53057743 AATTATATTTAATT
1 AATTAT-TTTAATT
*
53057757 AATATATTTTTATT
1 AAT-TATTTTAATT
53057771 AATTATTTTAA
1 AATTATTTTAA
53057782 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 7 0.32
14 12 0.55
15 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTATTTTAATT
Found at i:53060485 original size:19 final size:20
Alignment explanation
Indices: 53060446--53060493 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53060436 TTAAATTTTG
**
53060446 TTAATTTTAATAATGTTAAA
1 TTAATTTTTTTAATGTTAAA
*
53060466 TTTATTTTTTTAAT-TTAAA
1 TTAATTTTTTTAATGTTAAA
53060485 TTAATTTTT
1 TTAATTTTT
53060494 ATTGTGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATTTTTTTAATGTTAAA
Found at i:53062683 original size:9 final size:9
Alignment explanation
Indices: 53062666--53062702 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53062656 TGAGTTTTCG
53062666 AATTCGAAT
1 AATTCGAAT
*
53062675 AACTCGAAT
1 AATTCGAAT
53062684 AATTCGAAT
1 AATTCGAAT
53062693 AATTCGAAT
1 AATTCGAAT
53062702 A
1 A
53062703 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53067447 original size:20 final size:20
Alignment explanation
Indices: 53067422--53067459 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53067412 TGGATCAATG
*
53067422 ATTTAATATATATAATTATT
1 ATTTAACATATATAATTATT
53067442 ATTTAACATATATAATTA
1 ATTTAACATATATAATTA
53067460 GTATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAACATATATAATTATT
Found at i:53073676 original size:20 final size:19
Alignment explanation
Indices: 53073647--53073686 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
53073637 AAGAGAATAG
*
53073647 AAGAAAAAAAAGAAAGTTAA
1 AAGAAAAAAAA-AAAATTAA
*
53073667 AAGAACAAAAAAAAATTAA
1 AAGAAAAAAAAAAAATTAA
53073686 A
1 A
53073687 TTACTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (19 bp):
AAGAAAAAAAAAAAATTAA
Found at i:53079254 original size:10 final size:10
Alignment explanation
Indices: 53079239--53079269 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
53079229 CCCCCCCCCC
53079239 AAAAAAA-AA
1 AAAAAAAGAA
53079248 AAAAAAAGAA
1 AAAAAAAGAA
53079258 AAAAAAAGAA
1 AAAAAAAGAA
53079268 AA
1 AA
53079270 GAGACTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:53079261 original size:15 final size:15
Alignment explanation
Indices: 53079241--53079271 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53079231 CCCCCCCCAA
53079241 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
53079256 AAAAAAAAAGAAAAG
1 AAAAAAAAAAAAAAG
53079271 A
1 A
53079272 GACTCTGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:53081223 original size:24 final size:24
Alignment explanation
Indices: 53081193--53081261 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
53081183 GCAATGTTGA
53081193 TTTTTGTAGATTTACGTTGGATTT
1 TTTTTGTAGATTTACGTTGGATTT
* * * *
53081217 TTTTTGTAAATTCATGGTGGATTT
1 TTTTTGTAGATTTACGTTGGATTT
*
53081241 TTTTT-TGAGATTTACTTTGGA
1 TTTTTGT-AGATTTACGTTGGA
53081262 CTTTAGAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.19, C:0.04, G:0.20, T:0.57
Consensus pattern (24 bp):
TTTTTGTAGATTTACGTTGGATTT
Found at i:53086058 original size:11 final size:11
Alignment explanation
Indices: 53086017--53086066 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
53086007 AATTGACCAA
53086017 AACAAAACAAG
1 AACAAAACAAG
*
53086028 AAC-TAACACAG
1 AACAAAACA-AG
53086039 ATA-AAAACAAG
1 A-ACAAAACAAG
53086050 AACAAAACAA-
1 AACAAAACAAG
53086060 AACAAAA
1 AACAAAA
53086067 AATCATTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 12 0.36
11 16 0.48
12 5 0.15
ACGTcount: A:0.72, C:0.18, G:0.06, T:0.04
Consensus pattern (11 bp):
AACAAAACAAG
Found at i:53086695 original size:13 final size:13
Alignment explanation
Indices: 53086677--53086708 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
53086667 CTGGGCGGCC
53086677 CGGCCCGGCCTGA
1 CGGCCCGGCCTGA
53086690 CGGCCCGGCCTGA
1 CGGCCCGGCCTGA
53086703 CGGCCC
1 CGGCCC
53086709 ACTCGAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.50, G:0.38, T:0.06
Consensus pattern (13 bp):
CGGCCCGGCCTGA
Found at i:53086945 original size:25 final size:26
Alignment explanation
Indices: 53086894--53086955 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
53086884 TTTAAAATAC
* *
53086894 TTTTAAAATAATTTTTTTTATTTTTTAT
1 TTTTAAAATAA--TTTTTTAATGTTTAT
53086922 TTTTAAAATAA-TTTTTAATGTTTAT
1 TTTTAAAATAATTTTTTAATGTTTAT
*
53086947 TTTAAAAAT
1 TTTTAAAAT
53086956 GGGCCGGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.65
28 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTAATGTTTAT
Found at i:53097188 original size:29 final size:29
Alignment explanation
Indices: 53097152--53097219 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
53097142 GGTTAATTGT
*
53097152 GTTGTGTGGGTCATATGGGCGTGTGT-AA
1 GTTGTGTGGGTCATACGGGCGTGTGTGAA
53097180 GGTTGTGTGGGTCATACGGGCGTGTGTGAA
1 -GTTGTGTGGGTCATACGGGCGTGTGTGAA
*
53097210 GTCGTGTGGG
1 GTTGTGTGGG
53097220 CCACCTGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.12, C:0.09, G:0.47, T:0.32
Consensus pattern (29 bp):
GTTGTGTGGGTCATACGGGCGTGTGTGAA
Found at i:53100764 original size:17 final size:17
Alignment explanation
Indices: 53100742--53100774 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53100732 GGCATACGGT
53100742 CATGTGG-TTCACACGAC
1 CATGTGGCTT-ACACGAC
53100759 CATGTGGCTTACACGA
1 CATGTGGCTTACACGA
53100775 TTTGTTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (17 bp):
CATGTGGCTTACACGAC
Found at i:53104559 original size:34 final size:34
Alignment explanation
Indices: 53104521--53104590 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
53104511 ATTGTTTACC
* *
53104521 ACTGTATTGTTTTGTTA-AAGACATATTAAATGCT
1 ACTGTATTGATCTGTTACAAG-CATATTAAATGCT
* *
53104555 ACTGTATTGATCTGTTACATGCATATTAATTGCT
1 ACTGTATTGATCTGTTACAAGCATATTAAATGCT
53104589 AC
1 AC
53104591 CATTTGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
ACTGTATTGATCTGTTACAAGCATATTAAATGCT
Found at i:53105725 original size:4 final size:4
Alignment explanation
Indices: 53105713--53105747 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
53105703 TAAAATTAGT
53105713 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
53105748 AAAGGATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:53106149 original size:31 final size:31
Alignment explanation
Indices: 53106056--53106151 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
53106046 GGCAAATTAC
*
53106056 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53106087 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
53106119 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53106150 AA
1 AA
53106152 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:53109233 original size:31 final size:32
Alignment explanation
Indices: 53109206--53109265 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
53109196 GCTTTTTGTT
53109206 TTTTTTTTGTGCTTTGTACTCT-TTTTTTGCG
1 TTTTTTTTGTGCTTTGTACTCTCTTTTTTGCG
*
53109237 TTTTTTTTGTGCTTTTTACTCTCTTTTTT
1 TTTTTTTTGTGCTTTGTACTCTCTTTTTT
53109266 TAACGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.03, C:0.13, G:0.12, T:0.72
Consensus pattern (32 bp):
TTTTTTTTGTGCTTTGTACTCTCTTTTTTGCG
Found at i:53109263 original size:22 final size:20
Alignment explanation
Indices: 53109228--53109295 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 20
53109218 TTTGTACTCT
53109228 TTTTTTGCGT-TTTTTTTGTGC
1 TTTTTTGC-TCTTTTTTT-TGC
*
53109249 TTTTTACT-CTCTTTTTTTAACGC
1 TTTTT--TGCTCTTTTTTT--TGC
53109272 TTTTTTGCTCTTTTTTTTGC
1 TTTTTTGCTCTTTTTTTTGC
53109292 TTTT
1 TTTT
53109296 ATTTAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
20 6 0.15
21 7 0.18
22 18 0.46
23 8 0.21
ACGTcount: A:0.04, C:0.15, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTTTTGCTCTTTTTTTTGC
Found at i:53109276 original size:33 final size:31
Alignment explanation
Indices: 53109208--53109286 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 31
53109198 TTTTTGTTTT
* * *
53109208 TTTTTTGTGCTTTGTACTCTTTTTTTGCGTT
1 TTTTTTGTGCTTTTTACTCTTTTTTTACGTC
53109239 TTTTTTGTGCTTTTTACTCTCTTTTTTTAACG-C
1 TTTTTTGTGCTTTTTA--CTCTTTTTTT-ACGTC
53109272 TTTTTTGCT-CTTTTT
1 TTTTTTG-TGCTTTTT
53109287 TTTGCTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 15 0.37
33 23 0.56
34 3 0.07
ACGTcount: A:0.05, C:0.15, G:0.11, T:0.68
Consensus pattern (31 bp):
TTTTTTGTGCTTTTTACTCTTTTTTTACGTC
Found at i:53109943 original size:31 final size:31
Alignment explanation
Indices: 53109853--53109946 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
53109843 AAATTACAAG
* *
53109853 AGTAATTGAATCCTAATAAAACTCTTTCAAG
1 AGTAATTGAATCCTAATAAAACTCTTTAAAA
53109884 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
1 AGTAATTGAATCCTAAT-AAAACTCTTTAAAA
53109916 AGTAATTGAATCCTAATAAAACTCTTTAAAA
1 AGTAATTGAATCCTAATAAAACTCTTTAAAA
53109947 TTATCTAAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (31 bp):
AGTAATTGAATCCTAATAAAACTCTTTAAAA
Found at i:53112904 original size:24 final size:25
Alignment explanation
Indices: 53112857--53112906 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
53112847 TTTATAGTTA
* *
53112857 AATAGATATTTACTCAAAATTGAAT
1 AATAGATATTTACTAAAAAATGAAT
*
53112882 AATAGATATTT-TTAAAAAATGAAT
1 AATAGATATTTACTAAAAAATGAAT
53112906 A
1 A
53112907 GTGTTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (25 bp):
AATAGATATTTACTAAAAAATGAAT
Found at i:53134323 original size:42 final size:40
Alignment explanation
Indices: 53134269--53134363 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 40
53134259 TTAAAATTAT
*
53134269 TTATATTAAAAAAACACTACCATAAATATAATAAATGA-TTTA
1 TTATATTAAAAAAACAC-A-AATAAATATAATAAAT-ATTTTA
53134311 TTATATT-AAAAAACACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAAACACAAATAAATATAATAAATATTTTA
*
53134350 TTTTATTAAAAAAA
1 TTATATTAAAAAAA
53134364 TTTAAATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
38 1 0.02
39 25 0.51
40 7 0.14
41 9 0.18
42 7 0.14
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (40 bp):
TTATATTAAAAAAACACAAATAAATATAATAAATATTTTA
Found at i:53135099 original size:20 final size:20
Alignment explanation
Indices: 53135071--53135108 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53135061 TTATATATTC
53135071 TTTACAATTTTTTTAAAAAA
1 TTTACAATTTTTTTAAAAAA
*
53135091 TTTATAATTTTTTTAAAA
1 TTTACAATTTTTTTAAAA
53135109 TATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTACAATTTTTTTAAAAAA
Found at i:53135166 original size:11 final size:12
Alignment explanation
Indices: 53135144--53135177 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
53135134 TATTTAAATT
53135144 TTTTGAAATTTA
1 TTTTGAAATTTA
53135156 TTTTG-AATTTA
1 TTTTGAAATTTA
*
53135167 TTTTGTAATTT
1 TTTTGAAATTT
53135178 TTTATGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (12 bp):
TTTTGAAATTTA
Found at i:53144860 original size:3 final size:3
Alignment explanation
Indices: 53144852--53144892 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
53144842 AATCATTAAA
* * *
53144852 AAT AAT AAT AAT AAT TAT ATT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53144893 AATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:53145697 original size:5 final size:5
Alignment explanation
Indices: 53145689--53145723 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
53145679 TTTTTTTCTT
*
53145689 ATATA ATATA ATACA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
53145724 TAAAACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:53145861 original size:13 final size:13
Alignment explanation
Indices: 53145843--53145869 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53145833 ACACAACTAG
53145843 TCTAATAATTATT
1 TCTAATAATTATT
53145856 TCTAATAATTATT
1 TCTAATAATTATT
53145869 T
1 T
53145870 TCGAACTCAA
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:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTAATAATTATT
Found at i:53153866 original size:6 final size:6
Alignment explanation
Indices: 53153855--53153887 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
53153845 TTTTACATCG
53153855 ATAAAT ATAAAT ATAAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT AT
53153888 TCTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:53153873 original size:13 final size:13
Alignment explanation
Indices: 53153857--53153884 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53153847 TTACATCGAT
53153857 AAATATAAATATA
1 AAATATAAATATA
53153870 AAATATAAATATA
1 AAATATAAATATA
53153883 AA
1 AA
53153885 TATTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAATATA
Found at i:53158275 original size:7 final size:7
Alignment explanation
Indices: 53158265--53158292 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
53158255 CACTGCTGAA
53158265 CTCCTCC
1 CTCCTCC
53158272 CTCCTCC
1 CTCCTCC
53158279 CTCCTCC
1 CTCCTCC
53158286 CTCCTCC
1 CTCCTCC
53158293 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCCTCC
Found at i:53159214 original size:6 final size:6
Alignment explanation
Indices: 53159203--53159244 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
53159193 CGGTAACGGA
* *
53159203 TTGCTG TTGCTG TTGCTG TTGCTG TTGTTG TTGCTG CTGCTG
1 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG
53159245 ATGGTGAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.17, G:0.33, T:0.50
Consensus pattern (6 bp):
TTGCTG
Found at i:53164979 original size:17 final size:16
Alignment explanation
Indices: 53164957--53164990 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53164947 ACATGTGACA
*
53164957 AAAAAATTATAAATAAT
1 AAAAAATAATAAA-AAT
53164974 AAAAAATAATAAAAAT
1 AAAAAATAATAAAAAT
53164990 A
1 A
53164991 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATAATAAAAAT
Found at i:53164989 original size:19 final size:19
Alignment explanation
Indices: 53164967--53165071 Score: 58
Period size: 19 Copynumber: 5.7 Consensus size: 19
53164957 AAAAAATTAT
53164967 AAATAATAAAAAATAATAA
1 AAATAATAAAAAATAATAA
* ***
53164986 AAATATTAAATTTTAATAA
1 AAATAATAAAAAATAATAA
* *
53165005 AAAT-ATAAAATAT-TTAA
1 AAATAATAAAAAATAATAA
* * *
53165022 AATTTACTAAAAAATAAAAA
1 AA-ATAATAAAAAATAATAA
* *
53165042 AAAT-AT-AAGAATCAT-A
1 AAATAATAAAAAATAATAA
*
53165058 AAATAATTAAAAAT
1 AAATAATAAAAAAT
53165072 TTGTAAAATT
Statistics
Matches: 62, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
16 5 0.08
17 13 0.21
18 13 0.21
19 27 0.44
20 4 0.06
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.30
Consensus pattern (19 bp):
AAATAATAAAAAATAATAA
Found at i:53164995 original size:26 final size:26
Alignment explanation
Indices: 53164958--53165047 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
53164948 CATGTGACAA
53164958 AAAAAT-TATAAATAATAAAAAATAAT
1 AAAAATAT-TAAATAATAAAAAATAAT
** *
53164984 AAAAATATTAAATTTTAATAAA-AAT
1 AAAAATATTAAATAATAAAAAATAAT
* *
53165009 ATAAAATATTTAAAATTTACTAAAAAATAAA
1 A-AAAATA-TT-AAA--TAATAAAAAATAAT
53165040 AAAAATAT
1 AAAAATAT
53165048 AAGAATCATA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.08
26 23 0.46
27 3 0.06
28 3 0.06
29 1 0.02
30 13 0.26
31 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAATATTAAATAATAAAAAATAAT
Found at i:53165006 original size:27 final size:27
Alignment explanation
Indices: 53164970--53165041 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
53164960 AAATTATAAA
* *
53164970 TAATAAAAAATAATAAAAATATTAAATTT
1 TAATAAAAAATAA-AAATAT-TTAAAATT
53164999 TAAT-AAAAATATAAAATATTTAAAATT
1 TAATAAAAAATA-AAAATATTTAAAATT
*
53165026 TACTAAAAAATAAAAA
1 TAATAAAAAATAAAAA
53165042 AAATATAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 14 0.37
28 19 0.50
29 5 0.13
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (27 bp):
TAATAAAAAATAAAAATATTTAAAATT
Found at i:53165006 original size:28 final size:29
Alignment explanation
Indices: 53164970--53165047 Score: 99
Period size: 27 Copynumber: 2.8 Consensus size: 29
53164960 AAATTATAAA
*
53164970 TAATAAAAAATAATAAAAATATTAAATTT
1 TAATAAAAAATAATAAAAATATTAAAATT
53164999 TAAT-AAAAAT-AT-AAAATATTTAAAATT
1 TAATAAAAAATAATAAAAATA-TTAAAATT
* *
53165026 TACTAAAAAATAAAAAAAATAT
1 TAATAAAAAATAATAAAAATAT
53165048 AAGAATCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.14
27 12 0.29
28 12 0.29
29 6 0.14
30 6 0.14
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (29 bp):
TAATAAAAAATAATAAAAATATTAAAATT
Found at i:53172186 original size:36 final size:36
Alignment explanation
Indices: 53172134--53172206 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
53172124 AACTTAACTT
* * *
53172134 AAAAAATGAACGATAGGTTGATATTTATGTTTGATA
1 AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
53172170 AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
1 AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
53172206 A
1 A
53172207 TATCGATAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (36 bp):
AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
Found at i:53175081 original size:14 final size:15
Alignment explanation
Indices: 53175054--53175082 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53175044 CGTGGCATCC
53175054 TTCTTATATCTTTTT
1 TTCTTATATCTTTTT
53175069 TTCTTAT-TCTTTTT
1 TTCTTATATCTTTTT
53175083 ATTTCCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTATATCTTTTT
Found at i:53178207 original size:132 final size:138
Alignment explanation
Indices: 53178046--53178324 Score: 401
Period size: 144 Copynumber: 2.0 Consensus size: 138
53178036 CCTGTGTTCC
*
53178046 ATTCAAACCGAAATCCAATTCAATGTTATAATTCCAACAACAATT-C-AT-TTC---CAACAATA
1 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACAACAATTACAATATTCATACAACAATA
*
53178105 GAATAAATAAATAATACCATTCATCAATTTATACAAAA-TATTAAATTTTAACTGTAAGAACTTA
66 GAAAAAATAAATAATACCATTCATCAATTTATA-AAAATTATTAAATTTTAACTGTAAGAACTTA
53178169 CCTGGCTAA
130 CCTGGCTAA
* * *
53178178 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACTATAATTCCAACAATAATTCATTTCCA
1 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACAACAATT---ACAAT-ATTCA--TACA
53178243 ACAATAGAAAAAATAAATAATACCATTCATCAATTTATAAAAATTATTAAATTTTAACTGTAAGA
60 ACAATAGAAAAAATAAATAATACCATTCATCAATTTATAAAAATTATTAAATTTTAACTGTAAGA
53178308 ACTTACCTGGCTAA
125 ACTTACCTGGCTAA
53178322 ATT
1 ATT
53178325 GCAGAAACAT
Statistics
Matches: 130, Mismatches: 4, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
132 42 0.32
136 1 0.01
137 2 0.02
139 3 0.02
143 4 0.03
144 78 0.60
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (138 bp):
ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACAACAATTACAATATTCATACAACAATA
GAAAAAATAAATAATACCATTCATCAATTTATAAAAATTATTAAATTTTAACTGTAAGAACTTAC
CTGGCTAA
Found at i:53178221 original size:12 final size:12
Alignment explanation
Indices: 53178204--53178235 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
53178194 AATTCAATAT
53178204 TATAATTCCAAC
1 TATAATTCCAAC
53178216 TATAATTCCAAC
1 TATAATTCCAAC
*
53178228 AATAATTC
1 TATAATTC
53178236 ATTTCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (12 bp):
TATAATTCCAAC
Found at i:53180932 original size:23 final size:23
Alignment explanation
Indices: 53180906--53180963 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
53180896 CTTAATAGTG
**
53180906 ATCATATAACCAGAATGACACAA
1 ATCATATAACCAGAACAACACAA
*
53180929 ATCACATAACCAGAACAACACAA
1 ATCATATAACCAGAACAACACAA
*
53180952 ATCGTATAACCA
1 ATCATATAACCA
53180964 AAAGAGAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.16
Consensus pattern (23 bp):
ATCATATAACCAGAACAACACAA
Found at i:53183275 original size:21 final size:21
Alignment explanation
Indices: 53183249--53183302 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
53183239 GCCCGCCTGT
53183249 AAAAAAATCAAA-TCAAAATAA
1 AAAAAAATCAAAGTCAAAA-AA
* *
53183270 AAAAAATTTAAAGTTCAAAAAA
1 AAAAAAATCAAAG-TCAAAAAA
*
53183292 AAAAACATCAA
1 AAAAAAATCAA
53183303 TCCAATTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 10 0.38
22 10 0.38
23 6 0.23
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAAAATCAAAGTCAAAAAA
Found at i:53184569 original size:21 final size:22
Alignment explanation
Indices: 53184525--53184571 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53184515 AAATTTAGTA
*
53184525 TATTTTAAATTTATTACAATAT
1 TATTTTAAATTTATAACAATAT
53184547 TATTTT-AATATTATAAC-ATAT
1 TATTTTAAAT-TTATAACAATAT
53184568 TATT
1 TATT
53184572 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATAACAATAT
Found at i:53186082 original size:12 final size:12
Alignment explanation
Indices: 53186061--53186184 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 12
53186051 AAAAACGAAA
*
53186061 TGATTAAAAACT
1 TGATGAAAAACT
* *
53186073 TGATGGAAAATT
1 TGATGAAAAACT
*
53186085 TTATGAAAAGACT
1 TGATGAAAA-ACT
53186098 TGATGAAAAACT
1 TGATGAAAAACT
* *
53186110 TTA-AAAAGAACT
1 TGATGAAA-AACT
* * *
53186122 TGCTGCAAAACG
1 TGATGAAAAACT
*
53186134 TGATAAAAAAACT
1 TGAT-GAAAAACT
*
53186147 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
53186162 TGATAAAAGAACT
1 TGATGAAA-AACT
*
53186175 AGATGAAAAA
1 TGATGAAAAA
53186185 TACTTGAAGA
Statistics
Matches: 82, Mismatches: 22, Indels: 16
0.68 0.18 0.13
Matches are distributed among these distances:
11 3 0.04
12 39 0.48
13 28 0.34
14 2 0.02
15 8 0.10
16 2 0.02
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:53186102 original size:25 final size:24
Alignment explanation
Indices: 53186066--53186112 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
53186056 CGAAATGATT
* *
53186066 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTTGATGAAAAACTTTATG
53186090 AAAAGACTTGATGAAAAACTTTA
1 AAAA-ACTTGATGAAAAACTTTA
53186113 AAAAGAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (24 bp):
AAAAACTTGATGAAAAACTTTATG
Found at i:53186209 original size:20 final size:20
Alignment explanation
Indices: 53186180--53186218 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53186170 GAACTAGATG
*
53186180 AAAAATACTTGAA-GAAAGAA
1 AAAAACACTT-AATGAAAGAA
53186200 AAAAACACTTAATGAAAGA
1 AAAAACACTTAATGAAAGA
53186219 CTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAAACACTTAATGAAAGAA
Found at i:53188429 original size:11 final size:11
Alignment explanation
Indices: 53188413--53188438 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53188403 TAAATAAATA
53188413 AAAATATAAAC
1 AAAATATAAAC
53188424 AAAATATAAAC
1 AAAATATAAAC
53188435 AAAA
1 AAAA
53188439 ACTTCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATATAAAC
Found at i:53192360 original size:2 final size:2
Alignment explanation
Indices: 53192353--53192387 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
53192343 GGAGATATAA
53192353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
53192388 GGAATCTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53197874 original size:24 final size:24
Alignment explanation
Indices: 53197847--53197898 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53197837 TTAGTAAGTC
*
53197847 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53197871 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53197895 AAAT
1 AAAT
53197899 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53199844 original size:24 final size:24
Alignment explanation
Indices: 53199817--53199868 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53199807 TTAGTAAGTC
*
53199817 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53199841 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53199865 AAAT
1 AAAT
53199869 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53217353 original size:21 final size:22
Alignment explanation
Indices: 53217329--53217369 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53217319 CAGGTGGACA
*
53217329 GATTTTATAAT-TTTTATTTTT
1 GATTTTATAATAATTTATTTTT
*
53217350 GATTTTTTAATAATTTATTT
1 GATTTTATAATAATTTATTT
53217370 GCTTTGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
GATTTTATAATAATTTATTTTT
Found at i:53219491 original size:45 final size:45
Alignment explanation
Indices: 53219393--53219580 Score: 247
Period size: 45 Copynumber: 4.2 Consensus size: 45
53219383 AATAATAACA
* * * *
53219393 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* * *
53219436 GATACTCGGTGGAATCAGCACATAGCAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
53219481 -AGTACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
**
53219526 GATACCTAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
53219571 GGTACCCGGT
1 GATACCCGGT
53219581 ACACGTAATA
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 11 0.09
44 14 0.11
45 101 0.80
46 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
Found at i:53243250 original size:21 final size:21
Alignment explanation
Indices: 53243189--53243250 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
53243179 TTTTATAAAG
* *
53243189 TTGTAAAAAATATTA-AAAAAA
1 TTGTAAAAGA-ATTATAAAAAT
*
53243210 TTGT-AAAGAAATAT-AAAAT
1 TTGTAAAAGAATTATAAAAAT
53243229 TTGTAAAAGAATTATAAAAAT
1 TTGTAAAAGAATTATAAAAAT
53243250 T
1 T
53243251 ATCATATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.32
20 13 0.38
21 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (21 bp):
TTGTAAAAGAATTATAAAAAT
Found at i:53243317 original size:9 final size:9
Alignment explanation
Indices: 53243269--53243318 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
53243259 AAAATAAGTA
53243269 TTTTATAAT
1 TTTTATAAT
*
53243278 ATTTCTATGAT
1 -TTT-TATAAT
53243289 TTTTATAGAT
1 TTTTATA-AT
53243299 TTTTAT--T
1 TTTTATAAT
53243306 TTTTATAAT
1 TTTTATAAT
53243315 TTTT
1 TTTT
53243319 CGCCACATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 7 0.21
9 8 0.24
10 14 0.41
11 5 0.15
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53243448 original size:10 final size:10
Alignment explanation
Indices: 53243435--53243574 Score: 56
Period size: 9 Copynumber: 14.7 Consensus size: 10
53243425 CTTTTTGATG
53243435 ATTTTATAAT
1 ATTTTATAAT
53243445 A-TTTATAA-
1 ATTTTATAAT
53243453 ATTTT-TACA-
1 ATTTTATA-AT
* *
53243462 ATTTTTTTAT
1 ATTTTATAAT
*
53243472 ATTTTTATACT
1 A-TTTTATAAT
*
53243483 ATTTTTATATT
1 A-TTTTATAAT
*
53243494 TTTTTCA-AAT
1 ATTTT-ATAAT
53243504 -TTTTAGTAA-
1 ATTTTA-TAAT
53243513 ATTTTA-AAT
1 ATTTTATAAT
53243522 ATTTT-T-AT
1 ATTTTATAAT
53243530 ATTTTTATTAA-
1 A-TTTTA-TAAT
*
53243541 A-GTT-TAAT
1 ATTTTATAAT
53243549 ATTTTATAAT
1 ATTTTATAAT
*
53243559 -TTTTATAAA
1 ATTTTATAAT
53243568 ATTTTAT
1 ATTTTAT
53243575 TTTTATAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 38
0.68 0.07 0.26
Matches are distributed among these distances:
7 3 0.03
8 10 0.10
9 42 0.42
10 26 0.26
11 19 0.19
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:53243475 original size:19 final size:19
Alignment explanation
Indices: 53243436--53243536 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 19
53243426 TTTTTGATGA
* * *
53243436 TTTTATAATATTTATAAAT
1 TTTTACAATATTTTTATAT
*
53243455 TTTTACAATTTTTTTATAT
1 TTTTACAATATTTTTATAT
* *
53243474 TTTTATACTATTTTTATATT
1 TTTTACAATATTTTTATA-T
* *
53243494 TTTTTCAA-ATTTTTAGTAAA
1 TTTTACAATATTTTTA-T-AT
53243514 TTTTA-AATATTTTTATAT
1 TTTTACAATATTTTTATAT
53243532 TTTTA
1 TTTTA
53243537 TTAAAGTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
18 6 0.09
19 40 0.62
20 18 0.28
21 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTACAATATTTTTATAT
Found at i:53243571 original size:19 final size:19
Alignment explanation
Indices: 53243435--53243574 Score: 58
Period size: 19 Copynumber: 7.4 Consensus size: 19
53243425 CTTTTTGATG
*
53243435 ATTTTATAATATTTATAAA
1 ATTTTATAATTTTTATAAA
* * * *
53243454 TTTTTACAATTTTTTTATA
1 ATTTTATAATTTTTATAAA
* **
53243473 TTTTTATACTATTTTTATATT
1 ATTTTATA--ATTTTTATAAA
*
53243494 TTTTTCA-AATTTTTAGT-AA
1 ATTTT-ATAATTTTTA-TAAA
*
53243513 ATTTTA-AATATTTT-TATA
1 ATTTTATAAT-TTTTATAAA
* ** *
53243531 TTTTTATTAA-AGTT-TAAT
1 ATTTTA-TAATTTTTATAAA
53243549 ATTTTATAATTTTTATAAA
1 ATTTTATAATTTTTATAAA
53243568 ATTTTAT
1 ATTTTAT
53243575 TTTTATAAAT
Statistics
Matches: 90, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
17 4 0.04
18 21 0.23
19 46 0.51
20 3 0.03
21 15 0.17
22 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTTATAATTTTTATAAA
Found at i:53243588 original size:10 final size:10
Alignment explanation
Indices: 53243436--53243574 Score: 68
Period size: 10 Copynumber: 14.6 Consensus size: 10
53243426 TTTTTGATGA
53243436 TTTTAT-AAT
1 TTTTATAAAT
*
53243445 ATTTATAAAT
1 TTTTATAAAT
*
53243455 TTTTA-CAAT
1 TTTTATAAAT
* *
53243464 TTTTTTATAT
1 TTTTATAAAT
*
53243474 TTTTATACTAT
1 TTTTATA-AAT
53243485 TTTTAT--AT
1 TTTTATAAAT
*
53243493 TTTTTTCAAAT
1 TTTTAT-AAAT
53243504 TTTTAGTAAA-
1 TTTTA-TAAAT
53243514 TTTTA-AATAT
1 TTTTATAA-AT
53243524 TTTTAT--AT
1 TTTTATAAAT
53243532 TTTTATTAAA-
1 TTTTA-TAAAT
* *
53243542 GTTTA-ATA-
1 TTTTATAAAT
53243550 TTTTAT-AAT
1 TTTTATAAAT
*
53243559 TTTTATAAAA
1 TTTTATAAAT
53243569 TTTTAT
1 TTTTAT
53243575 TTTTATAAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
8 23 0.23
9 20 0.20
10 37 0.37
11 19 0.19
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:53243588 original size:16 final size:16
Alignment explanation
Indices: 53243557--53243587 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53243547 ATATTTTATA
53243557 ATTTTTATAAAATTTT
1 ATTTTTATAAAATTTT
53243573 ATTTTTAT-AAATTTT
1 ATTTTTATAAAATTTT
53243588 TTTGTCACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTTATAAAATTTT
Found at i:53243589 original size:27 final size:27
Alignment explanation
Indices: 53243501--53243588 Score: 92
Period size: 26 Copynumber: 3.3 Consensus size: 27
53243491 ATTTTTTTCA
* *
53243501 AATTTTTAGTAAATTTTAAATATTTT-T
1 AATTTTTATTAAAATTT-AATATTTTAT
*
53243528 ATATTTTTATTAAAGTTTAATATTTTAT
1 A-ATTTTTATTAAAATTTAATATTTTAT
*
53243556 AATTTTTA-TAAAATTTTAT-TTTTAT
1 AATTTTTATTAAAATTTAATATTTTAT
53243581 AAATTTTT
1 -AATTTTT
53243589 TTGTCACATG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
25 6 0.11
26 16 0.30
27 16 0.30
28 16 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
AATTTTTATTAAAATTTAATATTTTAT
Found at i:53252256 original size:25 final size:25
Alignment explanation
Indices: 53252218--53252286 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
53252208 TCTTTCGAGC
* *
53252218 CATATAACAAGAAGCTCATGTGAGT
1 CATATAACAGGAAGCTCATCTGAGT
* * * *
53252243 CATGTAACGGGAAGCTTATCTGGGT
1 CATATAACAGGAAGCTCATCTGAGT
*
53252268 TATATAACAGGAAGCTCAT
1 CATATAACAGGAAGCTCAT
53252287 AAGAGCCATA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (25 bp):
CATATAACAGGAAGCTCATCTGAGT
Found at i:53252359 original size:25 final size:24
Alignment explanation
Indices: 53252271--53252359 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 24
53252261 TCTGGGTTAT
**
53252271 ATAACAGGAAGCTCATAAGAGCC-
1 ATAACAGGAAGCTCCGAAGAGCCA
* **
53252294 ATAATTAGGAAGCT-CGTGCGAGCCA
1 ATAA-CAGGAAGCTCCG-AAGAGCCA
*
53252319 ATAACAGGTAGCTCCGAAGAGCCA
1 ATAACAGGAAGCTCCGAAGAGCCA
* *
53252343 TTAATCAGGAAGTTCCG
1 ATAA-CAGGAAGCTCCG
53252360 GATAGTCATA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 4 0.08
24 29 0.59
25 16 0.33
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (24 bp):
ATAACAGGAAGCTCCGAAGAGCCA
Found at i:53252474 original size:26 final size:26
Alignment explanation
Indices: 53252409--53252483 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
53252399 GAAACTCCAG
*
53252409 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* *
53252435 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
*
53252461 AGAGCCA-TATATCAGGATGCTCA
1 AGAGCCATTA-ATCAGGAAGCTCA
53252484 TAAGAGCTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:53258394 original size:13 final size:13
Alignment explanation
Indices: 53258360--53258400 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
53258350 TATGAATCAT
53258360 AAAATG-AATATAA
1 AAAATGAAAT-TAA
53258373 AAAAT-AAATTAA
1 AAAATGAAATTAA
*
53258385 AAAATGAAATGAA
1 AAAATGAAATTAA
53258398 AAA
1 AAA
53258401 GGAGAAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (13 bp):
AAAATGAAATTAA
Found at i:53259950 original size:4 final size:4
Alignment explanation
Indices: 53259941--53259969 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
53259931 GGTACTATAC
53259941 TAGA TAGA TAGA TAGA TAGA TAGA T-GA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
53259970 TACTAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (4 bp):
TAGA
Found at i:53262540 original size:59 final size:59
Alignment explanation
Indices: 53262448--53262562 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
53262438 AAAGCTATGA
*
53262448 TCCTCTTGAAGTCTTCCCTTAATACAACTGCAACATTCAATTCCAAACGAAAAAGATTT
1 TCCTCTTGAAGTCTTCCCTTAATACAACTGCAACATTCAATTCCAAACAAAAAAGATTT
53262507 TCCTCTTGAAGTCTTCCCTTAATACAACTGCAACATTCAATTCCAAACAAAAAAGA
1 TCCTCTTGAAGTCTTCCCTTAATACAACTGCAACATTCAATTCCAAACAAAAAAGA
53262563 ATTGAAAATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (59 bp):
TCCTCTTGAAGTCTTCCCTTAATACAACTGCAACATTCAATTCCAAACAAAAAAGATTT
Done.