Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015199.1 Kokia drynarioides strain JFW-HI SEQ_130243, whole genome shotgun sequence
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: 887795
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 743 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1227 original size:48 final size:50
Alignment explanation
Indices: 1162--1260 Score: 175
Period size: 48 Copynumber: 2.0 Consensus size: 50
1152 ATAAAACGTC
*
1162 TATATCTTCCTATTTAAATGTTAGGAAAGAGTTATAAATAGTTTTAGGCA
1 TATATCTTCCTATTTAAATGTTAGGAAAAAGTTATAAATAGTTTTAGGCA
1212 TATAT-TT-CTATTTAAATGTTAGGAAAAAGTTATAAATAGTTTTAGGCA
1 TATATCTTCCTATTTAAATGTTAGGAAAAAGTTATAAATAGTTTTAGGCA
1260 T
1 T
1261 TGAATAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 41 0.85
49 2 0.04
50 5 0.10
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.41
Consensus pattern (50 bp):
TATATCTTCCTATTTAAATGTTAGGAAAAAGTTATAAATAGTTTTAGGCA
Found at i:9852 original size:23 final size:23
Alignment explanation
Indices: 9838--9952 Score: 140
Period size: 23 Copynumber: 5.0 Consensus size: 23
9828 GTTTTCTGTT
9838 ATTAGCACTATGTGTGCTCTCTG
1 ATTAGCACTATGTGTGCTCTCTG
9861 ATTAGCACTATGTGTGCTCTCTG
1 ATTAGCACTATGTGTGCTCTCTG
*
9884 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTATGTGTGCTCTCTG
** * *
9907 ATTAATACTTTGTGTACTCTCTG
1 ATTAGCACTATGTGTGCTCTCTG
* * * **
9930 TTTATCATTGCGTGTGCTCTCTG
1 ATTAGCACTATGTGTGCTCTCTG
9953 TTGCCCAGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (23 bp):
ATTAGCACTATGTGTGCTCTCTG
Found at i:15125 original size:25 final size:23
Alignment explanation
Indices: 15028--15119 Score: 84
Period size: 23 Copynumber: 4.0 Consensus size: 23
15018 ATGGAACAAA
* *
15028 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
15049 CAGAGAGCACA-TAAGTGCTGGGCAAT
1 CAGAGAGCACACAAAGTGCT----AAT
15075 -AGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
15097 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
15120 AACAGAAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
21 15 0.26
22 3 0.05
23 21 0.36
25 12 0.21
26 7 0.12
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:15131 original size:23 final size:23
Alignment explanation
Indices: 15082--15131 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
15072 AATAGAGAGC
* * **
15082 ACACAAAGTGCTAATCAGAGAGC
1 ACACAAAGTGCTAATAACAGAAA
*
15105 ACACATAGTGCTAATAACAGAAA
1 ACACAAAGTGCTAATAACAGAAA
15128 ACAC
1 ACAC
15132 GAGACGTGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.22, G:0.16, T:0.14
Consensus pattern (23 bp):
ACACAAAGTGCTAATAACAGAAA
Found at i:20666 original size:11 final size:10
Alignment explanation
Indices: 20645--20672 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20635 GGACATTGTG
20645 AAAAAATAAA
1 AAAAAATAAA
20655 AAAAAATAAA
1 AAAAAATAAA
20665 AAAAAATA
1 AAAAAATA
20673 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:24024 original size:27 final size:27
Alignment explanation
Indices: 23994--24088 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
23984 ACAAGGGCAA
* *
23994 TTCCTTCAAGGTTCGCCAAGAATACCG
1 TTCCTTCAAAGTTCGCCAAGAATATCG
* *
24021 TTCCTTCAAAACTT-GCCAAGAATATTG
1 TTCCTTC-AAAGTTCGCCAAGAATATCG
* *
24048 TTCCTTCAAAGCTCACCAAGAATATCG
1 TTCCTTCAAAGTTCGCCAAGAATATCG
*
24075 TTCCTTCAGAGTTC
1 TTCCTTCAAAGTTC
24089 ACCATAAAGG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.07
27 48 0.86
28 4 0.07
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (27 bp):
TTCCTTCAAAGTTCGCCAAGAATATCG
Found at i:24246 original size:27 final size:27
Alignment explanation
Indices: 24180--24246 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
24170 TCGCCATAGT
24180 GGCTATTCCTTTCAAGATTCACCACAAA
1 GGCT-TTCCTTTCAAGATTCACCACAAA
* *
24208 GGC-TTCTGTTTCATGATTCACCACAAA
1 GGCTTTC-CTTTCAAGATTCACCACAAA
24235 GGCTTTCCTTTC
1 GGCTTTCCTTTC
24247 CTATCGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 25 0.74
28 6 0.18
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.34
Consensus pattern (27 bp):
GGCTTTCCTTTCAAGATTCACCACAAA
Found at i:26125 original size:13 final size:13
Alignment explanation
Indices: 26107--26145 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
26097 AAAATCTTGA
26107 TAATTAATTTAAC
1 TAATTAATTTAAC
*
26120 TAATTAATTCAAC
1 TAATTAATTTAAC
26133 TCAAATTAATTTA
1 T--AATTAATTTA
26146 TTTACACCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 13 0.59
15 9 0.41
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATTAATTTAAC
Found at i:38442 original size:20 final size:20
Alignment explanation
Indices: 38417--38455 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
38407 AAACCTACCT
38417 AATATATCATATCA-ATAAAC
1 AATATA-CATATCATATAAAC
38437 AATATACATATCATATAAA
1 AATATACATATCATATAAA
38456 TAAATAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATACATATCATATAAAC
Found at i:53773 original size:52 final size:53
Alignment explanation
Indices: 53696--53805 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 53
53686 CTACAGATTA
* * *
53696 TTAACTGTTCTAAATAGTGTTTTTCTCATGTAA-ACCTGTTCTGCTCTTATTG
1 TTAACTGTTCTAAATAGTGTTTTTCTCAAGTAATACCAGTTCTACTCTTATTG
*
53748 TTAACT-TTCTAAATAGT-TCTATTTCTCAAGTAATAGCAGTTCTACTCTTATTG
1 TTAACTGTTCTAAATAGTGT-T-TTTCTCAAGTAATACCAGTTCTACTCTTATTG
53801 TTAAC
1 TTAAC
53806 CATAGTACTG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
50 1 0.02
51 12 0.24
52 17 0.33
53 21 0.41
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (53 bp):
TTAACTGTTCTAAATAGTGTTTTTCTCAAGTAATACCAGTTCTACTCTTATTG
Found at i:53863 original size:51 final size:52
Alignment explanation
Indices: 53789--53887 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
53779 AATAGCAGTT
* *
53789 CTACTCTTATTGTTAACCATAGT-ACTGATGCTTTTTCTCATGTAACACCAA
1 CTACTCCTATTGTTAACCATAGTAACTGATGCCTTTTCTCATGTAACACCAA
* * *
53840 CTACTCCTATTTTTAACCTTAGTAACTGGTGCCTTTTCTCATGTAACA
1 CTACTCCTATTGTTAACCATAGTAACTGATGCCTTTTCTCATGTAACA
53888 GCTGTATTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 20 0.48
52 22 0.52
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.40
Consensus pattern (52 bp):
CTACTCCTATTGTTAACCATAGTAACTGATGCCTTTTCTCATGTAACACCAA
Found at i:64164 original size:84 final size:84
Alignment explanation
Indices: 64023--64193 Score: 306
Period size: 84 Copynumber: 2.0 Consensus size: 84
64013 GTAATTGTAA
64023 TGATAGACTAGATCACTAAATAACTCTATACAGAAATTAATAATGGATGAATGATAATCTTATCA
1 TGATAGACTAGATCACTAAATAACTCTATACAGAAATTAATAATGGATGAATGATAATCTTATCA
64088 AATCAAATGTCAATTTGAT
66 AATCAAATGTCAATTTGAT
* * *
64107 TGATAGACTAGGTCACTATATAACTCTATACAGAAATTAATAATGGATGAATGATAATCTTATTA
1 TGATAGACTAGATCACTAAATAACTCTATACAGAAATTAATAATGGATGAATGATAATCTTATCA
*
64172 AGTCAAATGTCAATTTGAT
66 AATCAAATGTCAATTTGAT
64191 TGA
1 TGA
64194 AACAGATGAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (84 bp):
TGATAGACTAGATCACTAAATAACTCTATACAGAAATTAATAATGGATGAATGATAATCTTATCA
AATCAAATGTCAATTTGAT
Found at i:66316 original size:21 final size:22
Alignment explanation
Indices: 66292--66341 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
66282 TAGTGCAAAT
66292 TGAAATTAATAAAAT-TTTGAC
1 TGAAATTAATAAAATATTTGAC
* * *
66313 TGAAATCAATTATATATTTGAC
1 TGAAATTAATAAAATATTTGAC
*
66335 TTAAATT
1 TGAAATT
66342 TTGTAAATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (22 bp):
TGAAATTAATAAAATATTTGAC
Found at i:70591 original size:3 final size:3
Alignment explanation
Indices: 70583--70609 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
70573 GCAATCGAGA
70583 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
70610 TGGTTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:83794 original size:18 final size:18
Alignment explanation
Indices: 83771--83824 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 18
83761 AATATATAAA
83771 AAATTCATAAAAATATAT
1 AAATTCATAAAAATATAT
*
83789 AAATTCTAGAAAAAAAATATAT
1 AAATTC----ATAAAAATATAT
83811 AAATT-ATAAAAATA
1 AAATTCATAAAAATA
83825 AAATTTACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
17 8 0.27
18 6 0.20
22 16 0.53
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AAATTCATAAAAATATAT
Found at i:83821 original size:20 final size:22
Alignment explanation
Indices: 83779--83828 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
83769 AAAAATTCAT
83779 AAAAATATATAAATTCTAGAAA
1 AAAAATATATAAATTCTAGAAA
*
83801 AAAAATATATAAATTATA-AAA
1 AAAAATATATAAATTCTAGAAA
83822 ATAAAAT
1 A-AAAAT
83829 TTACAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAATATATAAATTCTAGAAA
Found at i:84189 original size:11 final size:11
Alignment explanation
Indices: 84175--84199 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
84165 TTTTTTAGTT
84175 TTTTTTTATAA
1 TTTTTTTATAA
84186 TTTTTTTATAA
1 TTTTTTTATAA
84197 TTT
1 TTT
84200 ATATGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:84723 original size:16 final size:15
Alignment explanation
Indices: 84702--84733 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
84692 AGAATATAGT
84702 AAATTAAAAAAACAAA
1 AAATTAAAAAAA-AAA
84718 AAATTAAAAAAAAAA
1 AAATTAAAAAAAAAA
84733 A
1 A
84734 GATACATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (15 bp):
AAATTAAAAAAAAAA
Found at i:92345 original size:40 final size:40
Alignment explanation
Indices: 92301--92612 Score: 279
Period size: 40 Copynumber: 7.8 Consensus size: 40
92291 AAAAGATTGT
** * * *
92301 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGAACGGTC
1 TTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATGGTC
** **
92341 TTCAATCTTTCCTTTGATTAGGGTAAAAGATTGGATGGTC
1 TTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATGGTC
* * *
92381 TTCAATCTGCCCTC-TGATTAAGGTAAAAGATTGGATAGTT
1 TTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGATGGTC
* * * *
92421 TTCAATTTGTCCCATGATCAGGGTAAGAGATTGGATGGTC
1 TTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATGGTC
**
92461 TTCAATCTGCCCTTTGATTAGGGTAAAAGATTGGATGGTC
1 TTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATGGTC
* * * ** *
92501 CTCAATCTGCCCTC-TAATTAGGGTAAAAGGTTGGATAATT
1 TTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGATGGTC
** * * **
92541 TTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATAATC
1 TTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATGGTC
* * *
92581 TTCAATCTACCCTC-TGGTTAGGGTAAGAGATT
1 TTCAATCTGCCC-CATGATTAGGGTAAAAGATT
92613 AAAGGTTGTA
Statistics
Matches: 219, Mismatches: 48, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
39 2 0.01
40 216 0.99
41 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (40 bp):
TTCAATCTGCCCCATGATTAGGGTAAAAGATTGGATGGTC
Found at i:92481 original size:120 final size:120
Alignment explanation
Indices: 92300--92612 Score: 455
Period size: 120 Copynumber: 2.6 Consensus size: 120
92290 TAAAAGATTG
* * **
92300 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGAACGGTCTTCAATCTTTCCTTTGATTAGGGT
1 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTACCCTTTGATTAGGGT
* * *
92365 AAAAGATTGGATGGTCTTCAATCTGCCCTCTGATTAAGGTAAAAGATTGGATAGT
66 AAAAGATTGGATGGTCCTCAATCTGCCCTCTAATTAAGGTAAAAGATTGGATAAT
* * * *
92420 TTTCAATTTGTCCCATGATCAGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGATTAGGGT
1 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTACCCTTTGATTAGGGT
* *
92485 AAAAGATTGGATGGTCCTCAATCTGCCCTCTAATTAGGGTAAAAGGTTGGATAAT
66 AAAAGATTGGATGGTCCTCAATCTGCCCTCTAATTAAGGTAAAAGATTGGATAAT
* ** * *
92540 TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATAATCTTCAATCTACCCTCTGGTTAGGGT
1 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTACCCTTTGATTAGGGT
*
92605 AAGAGATT
66 AAAAGATT
92613 AAAGGTTGTA
Statistics
Matches: 171, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 171 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (120 bp):
TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTACCCTTTGATTAGGGT
AAAAGATTGGATGGTCCTCAATCTGCCCTCTAATTAAGGTAAAAGATTGGATAAT
Found at i:92691 original size:50 final size:49
Alignment explanation
Indices: 92637--92794 Score: 149
Period size: 50 Copynumber: 3.2 Consensus size: 49
92627 CACTTCATTT
* *
92637 CAGCTTCAGGAATATAAGATTCTTCC-TTGTGATTTCAATCTGCCCCTCTA
1 CAGCTTTAGGAATATGAGATT-TTCCATTG-GATTTCAATCTGCCCCTCTA
* * * * *
92687 CAGCTTTAGGTGA-ATGAGATTTGCCATTGCAGCTTCATTCTGCCCCTCTA
1 CAGCTTTAGG-AATATGAGATTTTCCATTGGA-TTTCAATCTGCCCCTCTA
** * * *
92737 CAGCTTTAGGTGTATGAGATTTTCCATTGCGGTTTCAATCTGCACCTCCA
1 CAGCTTTAGGAATATGAGATTTTCCATTG-GATTTCAATCTGCCCCTCTA
92787 CAGCTTTA
1 CAGCTTTA
92795 AGGGTAAAAG
Statistics
Matches: 87, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
49 4 0.05
50 82 0.94
51 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (49 bp):
CAGCTTTAGGAATATGAGATTTTCCATTGGATTTCAATCTGCCCCTCTA
Found at i:97879 original size:12 final size:12
Alignment explanation
Indices: 97862--97891 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
97852 TCATTAAAAT
97862 TGTTCGTGAACA
1 TGTTCGTGAACA
97874 TGTTCGTGAACA
1 TGTTCGTGAACA
97886 TGTTCG
1 TGTTCG
97892 ATTAAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (12 bp):
TGTTCGTGAACA
Found at i:100907 original size:8 final size:9
Alignment explanation
Indices: 100891--100920 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
100881 AATTTGGTTG
100891 AATTTTTTT
1 AATTTTTTT
100900 AATTTTTTT
1 AATTTTTTT
100909 AATTTTTTT
1 AATTTTTTT
100918 AAT
1 AAT
100921 CATCGATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
AATTTTTTT
Found at i:101414 original size:17 final size:17
Alignment explanation
Indices: 101388--101422 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
101378 TAAATTAAAC
*
101388 TTCTTCTCTTTCTTTCT
1 TTCTTCTCTTTCCTTCT
*
101405 TTCTTTTCTTTCCTTCT
1 TTCTTCTCTTTCCTTCT
101422 T
1 T
101423 CTCCCGTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTCTCTTTCCTTCT
Found at i:103880 original size:27 final size:27
Alignment explanation
Indices: 103838--103944 Score: 115
Period size: 27 Copynumber: 4.0 Consensus size: 27
103828 GTACAAGGGT
**
103838 GGTGCCTATTTGACAGGCGGCACCAAA
1 GGTGCCTACCTGACAGGCGGCACCAAA
* * * **
103865 GGTGCCTACCTAACAGGAGGCACTAGT
1 GGTGCCTACCTGACAGGCGGCACCAAA
*
103892 GGTGCCTACCTGCCAGGCGGCACCAAA
1 GGTGCCTACCTGACAGGCGGCACCAAA
* * *
103919 GGTGCCTATCTGGCAGGCTGCACCAA
1 GGTGCCTACCTGACAGGCGGCACCAA
103945 CCCCAAATTA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (27 bp):
GGTGCCTACCTGACAGGCGGCACCAAA
Found at i:107291 original size:26 final size:26
Alignment explanation
Indices: 107242--107291 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
107232 TCTGTTCAAA
**
107242 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
107268 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
107292 GCAAATAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:107379 original size:12 final size:12
Alignment explanation
Indices: 107359--107393 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
107349 ATATGCATAC
107359 ATAAACATAAAT
1 ATAAACATAAAT
107371 A-AGAACATAAAT
1 ATA-AACATAAAT
107383 ATAAACATAAA
1 ATAAACATAAA
107394 CATATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.05
12 19 0.90
13 1 0.05
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.20
Consensus pattern (12 bp):
ATAAACATAAAT
Found at i:109251 original size:29 final size:28
Alignment explanation
Indices: 109209--109529 Score: 324
Period size: 29 Copynumber: 11.0 Consensus size: 28
109199 GGAGGTCCCT
* *
109209 AAACTGTCTAAAAATTACATTTTTACACCC
1 AAACT-TCCAAAAATTCCATTTTTAC-CCC
109239 AAACTTCCAAAAA-TCTCATTTTTACCCC
1 AAACTTCCAAAAATTC-CATTTTTACCCC
*
109267 GAAACTTCCAAAAATTCCGTTTTTACCCC
1 -AAACTTCCAAAAATTCCATTTTTACCCC
* *
109296 GAACTTCCAAAAA-TCTCATTTTTAACCTCG
1 AAACTTCCAAAAATTC-CATTTTT-ACC-CC
* *
109326 AAACCTCTAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCC
*
109355 AAACTTCCAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCC
* *
109384 AAAAGTTCCAAAAGTTCCATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCC-C
* * *
109414 GAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACC-CC
*
109444 AAACTTCCAAAAGTTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCC-C
* *
109473 GAACTTCCAAAAATCCCATTTTTTACCCC
1 AAACTTCCAAAAATTCCA-TTTTTACCCC
109502 GAAACTTCCAAAAATTACCA-TTTTACCC
1 -AAACTTCCAAAAATT-CCATTTTTACCC
109530 TCGGATGTCC
Statistics
Matches: 244, Mismatches: 30, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.01
28 23 0.09
29 119 0.49
30 94 0.39
31 6 0.02
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTTACCCC
Found at i:109553 original size:59 final size:59
Alignment explanation
Indices: 109209--109532 Score: 422
Period size: 59 Copynumber: 5.5 Consensus size: 59
109199 GGAGGTCCCT
* * * *
109209 AAACTGTCTAAAAATTACATTTTTACACC-CAAACTTCCAAAAATCTCATTTTT-ACCCCG
1 AAACT-TCCAAAAATTCCATTTTTAC-CCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * *
109268 AAACTTCCAAAAATTCCGTTTTTACCC-CGAACTTCCAAAAATCTCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * *
109326 AAACCTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * *
109385 AAAGTTCCAAAAGTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* *
109444 AAACTTCCAAAAGTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
109503 AAACTTCCAAAAATTACCA-TTTTACCCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCTCG
109533 GATGTCCGAA
Statistics
Matches: 237, Mismatches: 25, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
57 25 0.11
58 46 0.19
59 163 0.69
60 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
Found at i:109573 original size:118 final size:115
Alignment explanation
Indices: 109209--109573 Score: 425
Period size: 118 Copynumber: 3.1 Consensus size: 115
109199 GGAGGTCCCT
* * *
109209 AAACTGTCTAAAAATTACATTTTTACACCCAAACTTCCAAAAATCTCA-TTTTTACCCCGAAACT
1 AAACTCTC-AAAAATTCCATTTTTAC-CCCAAACTTCCAAAAATCCCATTTTTTACCCCGAAACT
* *
109273 TCCAAAAATTCCGTTTTTACCC-CGAACTTCCAAAAATCTCATTTTTAACCTCG
64 TCCAAAAATTCC-ATTTTACCCTCGAACTTCCAAAAATC-CATTTTTGACCTCG
* * *
109326 AAAC-CTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAAGT
1 AAACTCTC-AAAAATTCCATTTTTA-CCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAAACT
* *
109390 TCCAAAAGTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
64 TCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAAT-CCATTTTTGACCTCG
* *
109444 AAACT-TCCAAAAGTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAACT
1 AAACTCT-CAAAAATTCCATTTTTACCC-CAAACTTCCAAAAATCCCATTTTTTACCCCGAAACT
* * * *
109508 TCCAAAAATTACCATTTTACCCTCGGA-TGTCCGAAGACTCCATTTTCGACCTCG
64 TCCAAAAATT-CCATTTTACCCTCGAACT-TCC-AAAAATCCATTTTTGACCTCG
*
109562 ACACTCTCAAAA
1 AAACTCTCAAAA
109574 TTACCCTTTT
Statistics
Matches: 214, Mismatches: 22, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
116 38 0.18
117 41 0.19
118 125 0.58
119 10 0.05
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (115 bp):
AAACTCTCAAAAATTCCATTTTTACCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAAACTTC
CAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCATTTTTGACCTCG
Found at i:110844 original size:56 final size:56
Alignment explanation
Indices: 110758--110869 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
110748 CAATATAATT
110758 GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
1 GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
* * *
110814 GTACTTTTCATACTTGTCAAATTTTGAACCAATCCTATATCTTTGTTATATCGACC
1 GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
110870 TAAAAGTCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (56 bp):
GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
Found at i:118321 original size:30 final size:30
Alignment explanation
Indices: 118271--118355 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
118261 NNNNNNNNNN
* *
118271 TTCCAAAAGTTCCATTTTTACCCTCG-AAC
1 TTCCAAAAATACCATTTTTACCCTCGAAAC
*
118300 TTCCAAAAATCCCATTTTTTACCC-CGAAAC
1 TTCCAAAAATACCA-TTTTTACCCTCGAAAC
118330 TTCCAAAAATTACCA-TTTTACCCTCG
1 TTCCAAAAA-TACCATTTTTACCCTCG
118356 GATGTCCGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 22 0.45
30 23 0.47
31 4 0.08
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.33
Consensus pattern (30 bp):
TTCCAAAAATACCATTTTTACCCTCGAAAC
Found at i:119667 original size:56 final size:56
Alignment explanation
Indices: 119581--119692 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
119571 CAATATAATT
119581 GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
1 GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
* * *
119637 GTACTTTTCATACTTGTCAAATTTTGAACCAATCCTATATCTTTGTTATATCGACC
1 GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
119693 TAAAAGTCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (56 bp):
GTACTTTTCATACATGTCAAATTTTGAACCAATCCTACATCTTTGTCATATCGACC
Found at i:137363 original size:2 final size:2
Alignment explanation
Indices: 137358--137403 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
137348 TAAAAAAAAA
137358 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
137400 AT AT
1 AT AT
137404 TTGTAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137609 original size:23 final size:23
Alignment explanation
Indices: 137555--137609 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
137545 TAAGAGGGGT
*
137555 CAAAATT-AAATTATAATTTTTA
1 CAAAATTAAAAATATAATTTTTA
** * *
137577 TGATAGTAAAAATATAATTTTTA
1 CAAAATTAAAAATATAATTTTTA
137600 CAAAATTAAA
1 CAAAATTAAA
137610 TCAAAATTTT
Statistics
Matches: 23, Mismatches: 9, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
CAAAATTAAAAATATAATTTTTA
Found at i:138824 original size:37 final size:37
Alignment explanation
Indices: 138774--138848 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
138764 AAATTAAATA
138774 GAAGACAAGTTCTCAACTAGCCCACCGCACCCACATG
1 GAAGACAAGTTCTCAACTAGCCCACCGCACCCACATG
138811 GAAGACAAGTTCTCAACTAGCCCACCGCACCCACATG
1 GAAGACAAGTTCTCAACTAGCCCACCGCACCCACATG
138848 G
1 G
138849 TCACCACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.37, G:0.17, T:0.13
Consensus pattern (37 bp):
GAAGACAAGTTCTCAACTAGCCCACCGCACCCACATG
Found at i:139211 original size:29 final size:29
Alignment explanation
Indices: 139147--139218 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
139137 GCACATTAAC
* * *
139147 TAATAATTTAAAAAATATTAAAATATTCA
1 TAATAATTAAAAAAAAATTAAAATAATCA
*
139176 -AACAATTAAAAACAAAATTAAAA-AATCA
1 TAATAATTAAAAA-AAAATTAAAATAATCA
139204 TAATAATTAAAAAAA
1 TAATAATTAAAAAAA
139219 TTAACATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 16 0.44
29 20 0.56
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (29 bp):
TAATAATTAAAAAAAAATTAAAATAATCA
Found at i:140150 original size:32 final size:32
Alignment explanation
Indices: 140109--140175 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
140099 ACTACATATT
140109 AATCTCAATGCATTATTGTTGTCCAAGCCCAC
1 AATCTCAATGCATTATTGTTGTCCAAGCCCAC
140141 AATCTCAATGCATTATTGTTGTCCAAGCCCAC
1 AATCTCAATGCATTATTGTTGTCCAAGCCCAC
140173 AAT
1 AAT
140176 AATACTTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (32 bp):
AATCTCAATGCATTATTGTTGTCCAAGCCCAC
Found at i:142010 original size:16 final size:16
Alignment explanation
Indices: 141977--142020 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
141967 TGGTACATGA
*
141977 AAAATTTATAAAATTTT
1 AAAATTTA-AATATTTT
141994 AAAATTTAAATATTTT
1 AAAATTTAAATATTTT
* *
142010 ATAATTAAAAT
1 AAAATTTAAAT
142021 TCAATAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATTTAAATATTTT
Found at i:151007 original size:49 final size:48
Alignment explanation
Indices: 150946--151244 Score: 292
Period size: 49 Copynumber: 6.1 Consensus size: 48
150936 AATCCTATAG
* *
150946 AGATGTGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAA
1 AGATGTG-AGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
* * * *
150995 AGATGTAGAGGGAAAGGTTAAAGCCGTAACGACGAACCTTATACCCTAA
1 AGATGT-GAGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
* * * * * *
151044 AGATGTGGAGGGAAAGGTTGAAGCTGTAATGGCAAACCTTATACCCTAG
1 AGATGT-GAGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
* * * * * * *
151093 AGATATGAAGGGAAAAATTGAAGGCATAACGGTGAATCTTATAACCTAG
1 AGATGTG-AGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
* ** * * *
151142 AGATGTAGAGGGAAAGGTTGAAGCCGTAACGATGAACCTTATACCTTAG
1 AGATGT-GAGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
* * *
151191 AGATGTGAAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCCAA
1 AGATGTG-AGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
151240 AGATG
1 AGATG
151245 AGGAGAAGCA
Statistics
Matches: 206, Mismatches: 40, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
48 2 0.01
49 202 0.98
50 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.20
Consensus pattern (48 bp):
AGATGTGAGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAA
Found at i:151123 original size:98 final size:98
Alignment explanation
Indices: 150946--151249 Score: 358
Period size: 98 Copynumber: 3.1 Consensus size: 98
150936 AATCCTATAG
* * * * *
150946 AGATGTGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAAAGATGT-AGAGGGAAA
1 AGATGTGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTATACCCTAGAGATGTGA-AGGGAAA
* * *
151010 GGTTAAAGCCGTAACGACGAACCTTATACCCTAA
65 GATTGAAGCCGTAACGACGAATCTTATACCCTAA
* * * *
151044 AGATGTGGAGGGAAAGGTTGAAGCTGTAATGGCAAACCTTATACCCTAGAGATATGAAGGGAAAA
1 AGATGTGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTATACCCTAGAGATGTGAAGGGAAAG
* * ** * *
151109 ATTGAAGGCATAACGGTGAATCTTATAACCTAG
66 ATTGAAGCCGTAACGACGAATCTTATACCCTAA
* * ** *
151142 AGATGTAGAGGGAAAGGTTGAAGCCGTAACGATGAACCTTATACCTTAGAGATGTGAAGGGAAAG
1 AGATGTGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTATACCCTAGAGATGTGAAGGGAAAG
* *
151207 ATTGAAGCCGCAACGACGAATCTTATACCCCAA
66 ATTGAAGCCGTAACGACGAATCTTATACCCTAA
*
151240 AGATGAGGAG
1 AGATGTGGAG
151250 AAGCAAATTG
Statistics
Matches: 168, Mismatches: 37, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
98 167 0.99
99 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (98 bp):
AGATGTGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTATACCCTAGAGATGTGAAGGGAAAG
ATTGAAGCCGTAACGACGAATCTTATACCCTAA
Found at i:151212 original size:147 final size:147
Alignment explanation
Indices: 150943--151214 Score: 409
Period size: 147 Copynumber: 1.9 Consensus size: 147
150933 TCGAATCCTA
* * * * *
150943 TAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAAAGATGTAGAGGGA
1 TAGAGATATGAAGGGAAAAATTGAAGCCACAACGGCGAATCTTATAACCTAAAGATGTAGAGGGA
* *
151008 AAGGTTAAAGCCGTAACGACGAACCTTATACCCTAAAGATGTGGAGGGAAAGGTTGAAGCTGTAA
66 AAGGTTAAAGCCGTAACGACGAACCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCTGTAA
151073 TGGCAAACCTTATACCC
131 TGGCAAACCTTATACCC
* * * *
151090 TAGAGATATGAAGGGAAAAATTGAAGGCATAACGGTGAATCTTATAACCTAGAGATGTAGAGGGA
1 TAGAGATATGAAGGGAAAAATTGAAGCCACAACGGCGAATCTTATAACCTAAAGATGTAGAGGGA
* * * *
151155 AAGGTTGAAGCCGTAACGATGAACCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGC
66 AAGGTTAAAGCCGTAACGACGAACCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGC
151215 CGCAACGACG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
147 110 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (147 bp):
TAGAGATATGAAGGGAAAAATTGAAGCCACAACGGCGAATCTTATAACCTAAAGATGTAGAGGGA
AAGGTTAAAGCCGTAACGACGAACCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCTGTAA
TGGCAAACCTTATACCC
Found at i:151278 original size:147 final size:147
Alignment explanation
Indices: 150951--151278 Score: 396
Period size: 147 Copynumber: 2.2 Consensus size: 147
150941 TATAGAGATG
* * *
150951 TGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAAAGATGTAGAGGGAAAGGTTAA
1 TGAAGGGAAAAATTGAAGCCGCAAAGGCGAATCTTATAACCTAAAGATGTAGAGGGAAAGGTTAA
* * * * * *
151016 AGCCGTAACGACGAACCTTATACCCTAAAGATGTGGAGGGAAAGGTTGAAGCTGTAATGGCAAAC
66 AGCCGTAACGACGAACCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCGCAACGACAAAC
* *
151081 CTTATACCCTAGAGATA
131 CTTATACCCCAGAGAGA
* *
151098 TGAAGGGAAAAATTGAAG--GCATAACGGTGAATCTTATAACCTAGAGATGTAGAGGGAAAGGTT
1 TGAAGGGAAAAATTGAAGCCGCA-AA-GGCGAATCTTATAACCTAAAGATGTAGAGGGAAAGGTT
* * * * *
151161 GAAGCCGTAACGATGAACCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGACGA
64 AAAGCCGTAACGACGAACCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCGCAACGACAA
*
151226 ATCTTATACCCCA-A-AGA
129 ACCTTATACCCCAGAGAGA
*
151243 TG-AGGAGAAGCAAATTGAAGCCGCAAAGGCAAATCT
1 TGAAGG-GAA--AAATTGAAGCCGCAAAGGCGAATCT
151279 CAAGACTGTA
Statistics
Matches: 153, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
144 3 0.02
145 10 0.07
146 2 0.01
147 133 0.87
148 2 0.01
149 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (147 bp):
TGAAGGGAAAAATTGAAGCCGCAAAGGCGAATCTTATAACCTAAAGATGTAGAGGGAAAGGTTAA
AGCCGTAACGACGAACCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCGCAACGACAAAC
CTTATACCCCAGAGAGA
Found at i:151320 original size:42 final size:42
Alignment explanation
Indices: 151247--151362 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 42
151237 CAAAGATGAG
* * **
151247 GAGAAGCAAATTGAAGCCGCAAAGGCAAATCTC-AAGACTGTA
1 GAGAAGCAGATTGAAGTCGCAAAGGTGAATCTCAAAG-CTGTA
* * *
151289 GAGAAGCAGATTAAAGTCACAAAGGTGAATCTTAAAGCTGTA
1 GAGAAGCAGATTGAAGTCGCAAAGGTGAATCTCAAAGCTGTA
* *
151331 AAG-AGCTAGATTGAAGTTGCAAAGGTGAATCT
1 GAGAAGC-AGATTGAAGTCGCAAAGGTGAATCT
151363 TACGTCCCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
41 3 0.05
42 55 0.90
43 3 0.05
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (42 bp):
GAGAAGCAGATTGAAGTCGCAAAGGTGAATCTCAAAGCTGTA
Found at i:152119 original size:3 final size:3
Alignment explanation
Indices: 152111--152142 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
152101 CGGGTTACTT
152111 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
152143 GCCGAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:154907 original size:19 final size:19
Alignment explanation
Indices: 154872--154922 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
154862 AGTATAATTA
* *
154872 TAATTAATATTTGATAATC
1 TAATTAACATTTAATAATC
*
154891 TAATTAA-ATTTCAATAATT
1 TAATTAACATTT-AATAATC
154910 TATATTAACATTT
1 TA-ATTAACATTT
154923 TTAAGGTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 5 0.19
21 4 0.15
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (19 bp):
TAATTAACATTTAATAATC
Found at i:156913 original size:24 final size:23
Alignment explanation
Indices: 156873--156931 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
156863 ATGAATTTAT
156873 TTTTTATAA-TTTAATTTGATCAA
1 TTTTTA-AATTTTAATTTGATCAA
* ** *
156896 TTTTTAATTTTTATATTTTTTTAA
1 TTTTTAAATTTTA-ATTTGATCAA
156920 TTTTTAAATTTT
1 TTTTTAAATTTT
156932 GATTATCACC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 18 0.62
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTTAAATTTTAATTTGATCAA
Found at i:156918 original size:17 final size:17
Alignment explanation
Indices: 156896--156931 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
156886 ATTTGATCAA
*
156896 TTTTTAATTTTTATATT
1 TTTTTAATTTTTAAATT
156913 TTTTTAATTTTTAAATT
1 TTTTTAATTTTTAAATT
156930 TT
1 TT
156932 GATTATCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTAATTTTTAAATT
Found at i:172404 original size:21 final size:21
Alignment explanation
Indices: 172368--172415 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
172358 TTTTCATTTA
172368 TTTTATTTTATATTATTT-CC
1 TTTTATTTTATATTATTTACC
172388 TTTTATTTT-TCACTTATTTACC
1 TTTTATTTTAT-A-TTATTTACC
172410 TTTTAT
1 TTTTAT
172416 GTCTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 6 0.24
22 8 0.32
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATTTTATATTATTTACC
Found at i:176427 original size:33 final size:33
Alignment explanation
Indices: 176380--176445 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
176370 CAAGAATTAT
*
176380 AGTTGGTATTGATATCTTAAATAAAATCGATAC
1 AGTTGGTATCGATATCTTAAATAAAATCGATAC
176413 AGTTGGTATCGATATCTTAAATAAAATCGATAC
1 AGTTGGTATCGATATCTTAAATAAAATCGATAC
176446 CAAACTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (33 bp):
AGTTGGTATCGATATCTTAAATAAAATCGATAC
Found at i:185462 original size:20 final size:21
Alignment explanation
Indices: 185431--185469 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
185421 AGTTACGGAT
185431 TTAAATACACAACAAATTTCA
1 TTAAATACACAACAAATTTCA
185452 TTAAA-ACACAACAAATTT
1 TTAAATACACAACAAATTT
185470 TTATTCTAAC
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:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAAATACACAACAAATTTCA
Found at i:186100 original size:18 final size:19
Alignment explanation
Indices: 186061--186100 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
186051 TACTAAGTTC
186061 CTTTCCTAGAAATCTCTCA
1 CTTTCCTAGAAATCTCTCA
* *
186080 CTTTCTTAGACATCT-TCA
1 CTTTCCTAGAAATCTCTCA
186098 CTT
1 CTT
186101 AATATTGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42
Consensus pattern (19 bp):
CTTTCCTAGAAATCTCTCA
Found at i:189840 original size:16 final size:16
Alignment explanation
Indices: 189819--189863 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
189809 TTTGATTCAC
*
189819 TGTAATGGAATAAAGT
1 TGTAATAGAATAAAGT
* *
189835 TGTAATACAATAGAGT
1 TGTAATAGAATAAAGT
189851 TGTAATAGAATAA
1 TGTAATAGAATAA
189864 GACTGTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (16 bp):
TGTAATAGAATAAAGT
Found at i:189886 original size:16 final size:16
Alignment explanation
Indices: 189827--189888 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
189817 ACTGTAATGG
*
189827 AATAAAGTTGTAATAC
1 AATAGAGTTGTAATAC
*
189843 AATAGAGTTGTAATAG
1 AATAGAGTTGTAATAC
*
189859 AATA-AGACTGTAATTA-
1 AATAGAG-TTGTAA-TAC
189875 AATAGAGTTGTAAT
1 AATAGAGTTGTAAT
189889 CAGTAATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.08
16 32 0.82
17 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (16 bp):
AATAGAGTTGTAATAC
Found at i:194103 original size:3 final size:3
Alignment explanation
Indices: 194091--194161 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
194081 TATTATTATT
*
194091 ATG ATT ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
194139 ATG ATG ATG AT- ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG
194162 TTCTCTAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:199241 original size:23 final size:22
Alignment explanation
Indices: 199213--199257 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
199203 TTCAATTTGA
199213 TATTTGAT-CTTAACAATTTTTTT
1 TATTTGATACTT-A-AATTTTTTT
*
199236 TATTTGGTACTTAAATTTTTTT
1 TATTTGATACTTAAATTTTTTT
199258 GGACCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 8 0.40
24 3 0.15
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (22 bp):
TATTTGATACTTAAATTTTTTT
Found at i:199268 original size:58 final size:59
Alignment explanation
Indices: 199180--199317 Score: 142
Period size: 58 Copynumber: 2.4 Consensus size: 59
199170 TATATTTTTA
* * * *
199180 ATTTGATATCTAAATTTTTTTGATTCAATTT-GATATTTGATCTTAACAATTTTTT-TT-
1 ATTTGGTATCTAAATTTTTTTGACTCAATTTAG-TACTTGAACTTAACAATTTTTTCTTG
* *
199237 ATTTGGTA-CTTAAATTTTTTTGGAC-CTAATTTAGTACTTGAACTTGACATTTTTTTCTTG
1 ATTTGGTATC-TAAATTTTTTT-GACTC-AATTTAGTACTTGAACTTAACAATTTTTTCTTG
*
199297 ATTTGGTATCTAAGTTTTTTT
1 ATTTGGTATCTAAATTTTTTT
199318 TTTTTTAAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
56 1 0.01
57 19 0.28
58 25 0.37
59 3 0.04
60 18 0.27
61 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.56
Consensus pattern (59 bp):
ATTTGGTATCTAAATTTTTTTGACTCAATTTAGTACTTGAACTTAACAATTTTTTCTTG
Found at i:199599 original size:31 final size:31
Alignment explanation
Indices: 199561--199622 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
199551 TACCAACCTA
199561 AAAAAAAAGTGTCAAGTTTAAGTATCAAATT
1 AAAAAAAAGTGTCAAGTTTAAGTATCAAATT
199592 AAAAAAAAGTGTCAAGTTTAAGTATCAAATT
1 AAAAAAAAGTGTCAAGTTTAAGTATCAAATT
199623 GGACTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (31 bp):
AAAAAAAAGTGTCAAGTTTAAGTATCAAATT
Found at i:199766 original size:22 final size:23
Alignment explanation
Indices: 199715--199776 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 23
199705 TAGGGGGTCG
* *
199715 AAATTAAATTATAATTTTTATGA
1 AAATTAAAATATAATTTTTATAA
* *
199738 TAA-TAAAATGTAATTTTTA-AA
1 AAATTAAAATATAATTTTTATAA
* *
199759 AAATTAAATTAAAATTTT
1 AAATTAAAATATAATTTT
199777 ATCATTTTAG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (23 bp):
AAATTAAAATATAATTTTTATAA
Found at i:201853 original size:22 final size:21
Alignment explanation
Indices: 201817--201858 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
201807 TTGACTCGTT
*
201817 TTATGTTTTTAATATTTTATA
1 TTATGTTTTTAATATATTATA
*
201838 TTATGTTTTTTTATATATTAT
1 TTATG-TTTTTAATATATTAT
201859 GTAATTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TTATGTTTTTAATATATTATA
Found at i:204815 original size:104 final size:105
Alignment explanation
Indices: 204533--204840 Score: 329
Period size: 109 Copynumber: 2.9 Consensus size: 105
204523 TTTAAATGAA
* * * *
204533 ATATTCGATTACTTAGGTTCAAGGCAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAG-T
1 ATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTT
* * * * *
204597 CCTCGAAAATAATAGAATATTGAGCATTAATTGGTTCCGAATAGG
66 CC-CTAAAATAAAAGAACATT--GCCTCAATT--TTCCGAATAGG
* * * ** *
204642 ATATTCAATTATTTAGGTTCAAACAAAAATCATACCCAACACGTTAG-GACATAAATCCTCGATT
1 ATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACACGTTAGAG-CACAATTTTTCGAGT
* *
204706 TCCCTAAAATAAAAGAACATTGCCTCGATTTT-TGAATAGG
65 TCCCTAAAATAAAAGAACATTGCCTCAATTTTCCGAATAGG
* * * *
204746 ATATTCAATTATTTAGGTTCAAAGAAAAATCGTACCCAATATGTTTGAGCACAATTTTTCGAGTT
1 ATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTT
204811 CCCT-AAAT-AAAGAAACATTGCCTCAATTTT
66 CCCTAAAATAAAAG-AACATTGCCTCAATTTT
204841 GAAAATATTT
Statistics
Matches: 167, Mismatches: 28, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
102 4 0.02
103 20 0.12
104 64 0.38
105 3 0.02
107 6 0.04
108 1 0.01
109 66 0.40
110 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (105 bp):
ATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACACGTTAGAGCACAATTTTTCGAGTT
CCCTAAAATAAAAGAACATTGCCTCAATTTTCCGAATAGG
Found at i:205352 original size:30 final size:30
Alignment explanation
Indices: 205271--205387 Score: 121
Period size: 30 Copynumber: 3.9 Consensus size: 30
205261 AAAGGAGGTC
*
205271 AAATCAAAATTTT-GAAAAGTTTAGGGGTTA
1 AAATCAAATTTTTAG-AAAGTTTAGGGGTTA
* * * *
205301 AAATGAAATTCTCAAAAAGTTTAGGGGTTA
1 AAATCAAATTTTTAGAAAGTTTAGGGGTTA
* * *
205331 AAATCAAATTTTTAGATAGTTTGGGGGTCA
1 AAATCAAATTTTTAGAAAGTTTAGGGGTTA
205361 AAATCAAATTTTTA-AGAAGTTTGAGGG
1 AAATCAAATTTTTAGA-AAGTTT-AGGG
205388 TGAAATTCAA
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
29 1 0.01
30 66 0.94
31 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (30 bp):
AAATCAAATTTTTAGAAAGTTTAGGGGTTA
Found at i:205381 original size:60 final size:61
Alignment explanation
Indices: 205271--205387 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 61
205261 AAAGGAGGTC
* *
205271 AAATCAAAATTTTGAAAAGTTTAGGGGTTAAAATGAAATTCTCAAAAAGTTT-AGGGGTTA
1 AAATCAAAATTTTGAAAAGTTTAGGGGTCAAAATCAAATTCTCAAAAAGTTTGAGGGGTTA
* * * * * *
205331 AAATC-AAATTTTTAGATAGTTTGGGGGTCAAAATCAAATTTTTAAGAAGTTTGAGGG
1 AAATCAAAATTTTGA-AAAGTTTAGGGGTCAAAATCAAATTCTCAAAAAGTTTGAGGG
205388 TGAAATTCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 8 0.17
60 35 0.74
61 4 0.09
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (61 bp):
AAATCAAAATTTTGAAAAGTTTAGGGGTCAAAATCAAATTCTCAAAAAGTTTGAGGGGTTA
Found at i:205399 original size:29 final size:30
Alignment explanation
Indices: 205325--205408 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
205315 AAAAGTTTAG
* *
205325 GGGTTAAAATCAAATTTTTAGATAGTTTGG
1 GGGTCAAAATCAAATTTTTAGATAGTTTGA
205355 GGGTCAAAATCAAATTTTTAAGA-AGTTTGA
1 GGGTCAAAATCAAATTTTT-AGATAGTTTGA
* * * *
205385 GGGTGAAATTCAATTTTTTGGATA
1 GGGTCAAAATCAAATTTTTAGATA
205409 AAACAAGGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.04
30 41 0.89
31 3 0.07
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATCAAATTTTTAGATAGTTTGA
Found at i:205403 original size:60 final size:60
Alignment explanation
Indices: 205271--205408 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 60
205261 AAAGGAGGTC
* * * * *
205271 AAATCAAAATTTT-GAAAAGTTTAGGGGTTAAAATGAAATTCTCAAAAAGTTTAGGGGTTA
1 AAATCAAATTTTTAG-ATAGTTTAGGGGTCAAAATCAAATTCTCAAAAAGTTTAGGGGTGA
* * * *
205331 AAATCAAATTTTTAGATAGTTTGGGGGTCAAAATCAAATTTTTAAGAAGTTT-GAGGGTGA
1 AAATCAAATTTTTAGATAGTTTAGGGGTCAAAATCAAATTCTCAAAAAGTTTAG-GGGTGA
* * *
205391 AATTCAATTTTTTGGATA
1 AAATCAAATTTTTAGATA
205409 AAACAAGGGC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.02
60 62 0.97
61 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (60 bp):
AAATCAAATTTTTAGATAGTTTAGGGGTCAAAATCAAATTCTCAAAAAGTTTAGGGGTGA
Found at i:207324 original size:39 final size:39
Alignment explanation
Indices: 207234--208052 Score: 239
Period size: 38 Copynumber: 20.7 Consensus size: 39
207224 ACTACAATCT
* * *
207234 GCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATTT
1 GCCCTATGATCAGGGTAAGAGATTGGATGATG---TCAATTC
* *
207276 G-CCTCATGATCAAGGTAAGAGATTGGATGATGTCAATAC
1 GCCCT-ATGATCAGGGTAAGAGATTGGATGATGTCAATTC
* * * *
207315 GCCCTATGATTAGGGTACGAGATTGGATGCT-TCAATTT
1 GCCCTATGATCAGGGTAAGAGATTGGATGATGTCAATTC
* * * *
207353 GCCCCATGATCGGGGTAAGAGATTGGATTG-TCTTCAATCC
1 GCCCTATGATCAGGGTAAGAGATTGGA-TGAT-GTCAATTC
* * * **
207393 GCCCTCTGATTAGGGTAAGAGATTAGATTCT-TCAA-TC
1 GCCCTATGATCAGGGTAAGAGATTGGATGATGTCAATTC
* ** * *
207430 TG-TCTAATGATTGGGGTAAGAAATTGGATGCT-TCAA-TC
1 -GCCCT-ATGATCAGGGTAAGAGATTGGATGATGTCAATTC
* * *
207468 TG-CCTCATGATCATGGTAAGAGATTAGAT--TGTCTTAAATC
1 -GCCCT-ATGATCAGGGTAAGAGATTGGATGATGTC--AATTC
* * * ** *
207508 TGCCCTCTGATTAGGGTAAGAGATTGAATTCT-TCAATTT
1 -GCCCTATGATCAGGGTAAGAGATTGGATGATGTCAATTC
* * *
207547 GCCCCATGATCTA-GGTAAGAGATTGGATGCT-TCAATTT
1 GCCCTATGATC-AGGGTAAGAGATTGGATGATGTCAATTC
* * *
207585 GCCCCATAATCGGGGTAAGAGATTGG-TG-TGTCTTCAA-TC
1 GCCCTATGATCAGGGTAAGAGATTGGATGATG---TCAATTC
* * * * *
207624 TGCCCTCT-AACTAGGGTAAAAGATTAGATG-TTTCAA-TC
1 -GCCCTATGATC-AGGGTAAGAGATTGGATGATGTCAATTC
* *
207662 TGCCCCATGAT-TGAGGTAAGAGATTGG-TG-TGTCTTCAA-TC
1 -GCCCTATGATCAG-GGTAAGAGATTGGATGATG---TCAATTC
* * * **
207702 TGCCCT-TTAACTAGGGTAAGAGATTGAATTCT-TCAA-TC
1 -GCCCTATGATC-AGGGTAAGAGATTGGATGATGTCAATTC
207740 TGTCCC-ATGATC-GAGGTAAGAGATTGGAT--TGTCTTTAA-TC
1 -G-CCCTATGATCAG-GGTAAGAGATTGGATGATGTC---AATTC
* * * *
207780 TTCCCTTTGATGAGGGTAAGAGATTGGATGATTGT-AATTT
1 -GCCCTATGATCAGGGTAAGAGATTGGATGA-TGTCAATTC
* * ** *
207820 GCCCTATGATCGGGGTAAGAGATTTGAT-AACT-ATAGTC
1 GCCCTATGATCAGGGTAAGAGATTGGATGATGTCA-ATTC
*
207858 TG-CCTCATGATCGGGGTAAGAGATTGGATGATGGCTGCAA-TC
1 -GCCCT-ATGATCAGGGTAAGAGATTGGATGAT-G-T-CAATTC
* * *
207900 TGCCCCATGATCGGGGTAGGAGATTGGATGATGGCTGCAA-TC
1 -GCCCTATGATCAGGGTAAGAGATTGGATGAT-G-T-CAATTC
*
207942 TG-CCTCATGATC-GAGGTAAGATATTGGATGATGGCTGCAA-TC
1 -GCCCT-ATGATCAG-GGTAAGAGATTGGATGAT-G-T-CAATTC
* * *
207984 TGCCCCATGATCGGGGTAAGAGATTGGATGGT-TGCAA-TC
1 -GCCCTATGATCAGGGTAAGAGATTGGATGATGT-CAATTC
**
208023 TGCCCTATGATTGGGGTAAGAGATTGGATG
1 -GCCCTATGATCAGGGTAAGAGATTGGATG
208053 GTGATGTAAC
Statistics
Matches: 617, Mismatches: 101, Indels: 121
0.74 0.12 0.14
Matches are distributed among these distances:
36 3 0.00
37 16 0.03
38 188 0.30
39 135 0.22
40 123 0.20
41 16 0.03
42 126 0.20
43 9 0.01
44 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (39 bp):
GCCCTATGATCAGGGTAAGAGATTGGATGATGTCAATTC
Found at i:207427 original size:78 final size:79
Alignment explanation
Indices: 207228--208053 Score: 599
Period size: 78 Copynumber: 10.5 Consensus size: 79
207218 TAGATAACTA
** * * * **
207228 CAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGATGTCTTCAATTTGCCTCATGATCAAGGT
1 CAATCTGCCCTC-TGATTAGGGTAAGAGATT--A-GATGGCTTCAATCTGCCCCATGATCGGGGT
*
207292 AAGAGATTGGA-TGAT-GT
62 AAGAGATTGGATTG-TCTT
* * * *
207309 CAATAC-GCCCTATGATTAGGGTACGAGATTGGAT-GCTTCAATTTGCCCCATGATCGGGGTAAG
1 CAAT-CTGCCCTCTGATTAGGGTAAGAGATTAGATGGCTTCAATCTGCCCCATGATCGGGGTAAG
207372 AGATTGGATTGTCTT
65 AGATTGGATTGTCTT
* * * ** *
207387 CAATCCGCCCTCTGATTAGGGTAAGAGATTAGAT-TCTTCAATCTGTCTAATGATTGGGGTAAGA
1 CAATCTGCCCTCTGATTAGGGTAAGAGATTAGATGGCTTCAATCTGCCCCATGATCGGGGTAAGA
*
207451 AATTGGA-TG-CTT
66 GATTGGATTGTCTT
* * * * **
207463 CAATCTG-CCTCATGATCATGGTAAGAGATTAGATTGTCTTAAATCTGCCCTC-TGATTAGGGTA
1 CAATCTGCCCTC-TGATTAGGGTAAGAGATTAGA-TGGCTTCAATCTGCCC-CATGATCGGGGTA
*
207526 AGAGATT-GAAT-TCTT
63 AGAGATTGGATTGTCTT
* * * *
207541 CAATTTGCCC-CATGATCTA-GGTAAGAGATTGGAT-GCTTCAATTTGCCCCATAATCGGGGTAA
1 CAATCTGCCCTC-TGAT-TAGGGTAAGAGATTAGATGGCTTCAATCTGCCCCATGATCGGGGTAA
207603 GAGATTGG-TGTGTCTT
64 GAGATTGGAT-TGTCTT
* * * * * *
207619 CAATCTGCCCTCTAACTAGGGTAAAAGATTAGAT-GTTTCAATCTGCCCCATGATTGAGGTAAGA
1 CAATCTGCCCTCTGATTAGGGTAAGAGATTAGATGGCTTCAATCTGCCCCATGATCGGGGTAAGA
207683 GATTGG-TGTGTCTT
66 GATTGGAT-TGTCTT
* * * * * *
207697 CAATCTGCCCTTTAACTAGGGTAAGAGATT-GAAT-TCTTCAATCTGTCCCATGATCGAGGTAAG
1 CAATCTGCCCTCTGATTAGGGTAAGAGATTAG-ATGGCTTCAATCTGCCCCATGATCGGGGTAAG
207760 AGATTGGATTGTCTT
65 AGATTGGATTGTCTT
* * * * * * * * *
207775 TAATCTTCCCTTTGATGAGGGTAAGAGATTGGAT-GATTGTAATTTGCCCTATGATCGGGGTAAG
1 CAATCTGCCCTCTGATTAGGGTAAGAGATTAGATGGCTT-CAATCTGCCCCATGATCGGGGTAAG
* **
207839 AGATTTGA-TAACTAT
65 AGATTGGATTGTCT-T
* ** *
207854 -AGTCTG-CCTCATGATCGGGGTAAGAGATTGGATGATGGCTGCAATCTGCCCCATGATCGGGGT
1 CAATCTGCCCTC-TGATTAGGGTAAGAGATT--A-GATGGCTTCAATCTGCCCCATGATCGGGGT
* * *
207917 AGGAGATTGGATGATGGCTG
62 AAGAGATTGGAT--TGTCTT
* * *
207937 CAATCTG-CCTCATGA-TCGAGGTAAGATATTGGATGATGGCTGCAATCTGCCCCATGATCGGGG
1 CAATCTGCCCTC-TGATTAG-GGTAAGAGATT--A-GATGGCTTCAATCTGCCCCATGATCGGGG
* *
208000 TAAGAGATTGGATGGT-TG
61 TAAGAGATTGGATTGTCTT
* * *
208018 CAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
1 CAATCTGCCCTCTGATTAGGGTAAGAGATTAGATGG
208054 TGATGTAACT
Statistics
Matches: 612, Mismatches: 97, Indels: 75
0.78 0.12 0.10
Matches are distributed among these distances:
75 5 0.01
76 54 0.09
77 49 0.08
78 313 0.51
79 34 0.06
81 76 0.12
82 9 0.01
83 1 0.00
84 71 0.12
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (79 bp):
CAATCTGCCCTCTGATTAGGGTAAGAGATTAGATGGCTTCAATCTGCCCCATGATCGGGGTAAGA
GATTGGATTGTCTT
Found at i:207464 original size:116 final size:115
Alignment explanation
Indices: 207228--208052 Score: 602
Period size: 116 Copynumber: 7.0 Consensus size: 115
207218 TAGATAACTA
* * *
207228 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATTTG-CCTCATGATCAAGGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGAT--TGTCTTCAATCTGCCCTC-TGATTAGGGT
* ** * *
207292 AAGAGATTGGATGATGTCAATAC-GCCCTATGATTAGGGTACGAGATTGGATGCTT
63 AAGAGATTAGATTCT-TCAAT-CTG-CCTATGATTGGGGTAAGAGATTGGATGCTT
* *
207347 CAATTTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCCGCCCTCTGATTAGGGTAAG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAG
* *
207412 AGATTAGATTCTTCAATCTGTCTAATGATTGGGGTAAGAAATTGGATGCTT
66 AGATTAGATTCTTCAATCTGCCT-ATGATTGGGGTAAGAGATTGGATGCTT
* ** * *
207463 CAATCTGCCTCATGATCATGGTAAGAGATTAGATTGTCTTAAATCTGCCCTCTGATTAGGGTAAG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAG
* * *
207528 AGATT-GAATTCTTCAATTTGCCCCATGATCT-AGGTAAGAGATTGGATGCTT
66 AGATTAG-ATTCTTCAATCTG-CCTATGAT-TGGGGTAAGAGATTGGATGCTT
* * * *
207579 CAATTTGCCCCATAATCGGGGTAAGAGATTGG-TGTGTCTTCAATCTGCCCTCTAACTAGGGTAA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-TGTCTTCAATCTGCCCTCTGATTAGGGTAA
* * * *
207643 AAGATTAGATGT-TTCAATCTGCCCCATGATTGAGGTAAGAGATTGGTGTGTCTT
65 GAGATTAGAT-TCTTCAATCTG-CCTATGATTGGGGTAAGAGATTGG-ATG-CTT
* * * * * * *
207697 CAATCTG-CCCTTTAACTAGGGTAAGAGATT-GAAT-TCTTCAATCTGTCCC-ATGA-TCGAGGT
1 CAATCTGCCCCATGATC-GGGGTAAGAGATTGGATTGTCTTCAATCTG-CCCTCTGATTAG-GGT
* * * * *
207757 AAGAGATTGGATTGTCTTTAATCTTCCCTTTGA-TGAGGGTAAGAGATTGGATGATT
63 AAGAGATTAGA-T-TCTTCAATC-TGCCTATGATTG-GGGTAAGAGATTGGATGCTT
* * * * ** * **
207813 GTAATTTGCCCTATGATCGGGGTAAGAGATTTGA-TAACTAT-AGTCTG-CCTCATGATCGGGGT
1 -CAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCT-TCAATCTGCCCTC-TGATTAGGGT
* * * * * *
207875 AAGAGATTGGATGATGGCTGCAATCTGCCCCATGATCGGGGTAGGAGATTGGATGATGGCTG
63 AAGAGATT--A-GAT-TCTTCAATCTG-CCTATGATTGGGGTAAGAGATT-G--GAT-GCTT
* * * * * **
207937 CAATCTGCCTCATGATCGAGGTAAGATATTGGATGATGGCTGCAATCTGCCC-CATGATCGGGGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGAT--TGTCTTCAATCTGCCCTC-TGATTAGGGT
* **
208001 AAGAGATTGGATGGTTGCAATCTGCCCTATGATTGGGGTAAGAGATTGGATG
63 AAGAGATTAGATTCTT-CAATCTG-CCTATGATTGGGGTAAGAGATTGGATG
208053 GTGATGTAAC
Statistics
Matches: 569, Mismatches: 94, Indels: 86
0.76 0.13 0.11
Matches are distributed among these distances:
115 8 0.01
116 248 0.44
117 73 0.13
118 77 0.14
119 38 0.07
120 27 0.05
121 4 0.01
122 3 0.01
123 59 0.10
124 2 0.00
126 28 0.05
127 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (115 bp):
CAATCTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAG
AGATTAGATTCTTCAATCTGCCTATGATTGGGGTAAGAGATTGGATGCTT
Found at i:207566 original size:194 final size:192
Alignment explanation
Indices: 207207--208052 Score: 667
Period size: 194 Copynumber: 4.3 Consensus size: 192
207197 TTGATTTTAG
* * * * * *
207207 GGGTAAAAGATTAGATAACTACAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCA
1 GGGTAAGAGATTAGATATCTTCAATCTG-CCTATGATTGGGGTAAGAAATT-G--GATG-CTTCA
* *
207272 ATTTGCCTCATGATCAAGGTAAGAGATTGGATGATGTC--AATAC-GCCCTATGATTAGGGTACG
61 ATCTGCCTCATGATC-AGGTAAGAGATT-GATG-TGTCTTAAT-CTGCCCTATGATTAGGGTAAG
* * * *
207334 AGATTGGATGCTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATTGTCTTCAATCCGCCCTC
122 AGATTGAATTCTTCAATTTGCCCCATGATCGAGGTAAGAGATTGGATTGTCTTCAATCTGCCCTC
*
207399 TGATTA
187 TGATCA
*
207405 GGGTAAGAGATTAGAT-TCTTCAATCTGTCTAATGATTGGGGTAAGAAATTGGATGCTTCAATCT
1 GGGTAAGAGATTAGATATCTTCAATCTGCCT-ATGATTGGGGTAAGAAATTGGATGCTTCAATCT
*
207469 GCCTCATGATCATGGTAAGAGATTAGAT-TGTCTTAAATCTGCCCTCTGATTAGGGTAAGAGATT
65 GCCTCATGATCA-GGTAAGAGATT-GATGTGTCTT-AATCTGCCCTATGATTAGGGTAAGAGATT
* * *
207533 GAATTCTTCAATTTGCCCCATGATCTAGGTAAGAGATTGGA-TG-CTTCAATTTGCCC-CATAAT
127 GAATTCTTCAATTTGCCCCATGATCGAGGTAAGAGATTGGATTGTCTTCAATCTGCCCTC-TGAT
*
207595 CG
191 CA
* * * * * * * * *
207597 GGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAACTAGGGTAA-AAGATTAGATGTTTCAAT
1 GGGTAAGAGATTAG-ATATCTTCAATCTG-CCTATGATTGGGGTAAGAA-ATTGGATGCTTCAAT
* * * * * *
207661 CTGCCCCATGATTGAGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTTTAACTAGGGTAAGAGAT
63 CTGCCTCATGA-TCAGGTAAGAGATTGATGTGTCTT-AATCTGCCCTATGATTAGGGTAAGAGAT
* * * * *
207726 TGAATTCTTCAATCTGTCCCATGATCGAGGTAAGAGATTGGATTGTCTTTAATCTTCCCTTTGAT
126 TGAATTCTTCAATTTGCCCCATGATCGAGGTAAGAGATTGGATTGTCTTCAATCTGCCCTCTGAT
*
207791 GA
191 CA
* * * * * *
207793 GGGTAAGAGATTGGATGAT-TGT-AATTTGCCCTATGATCGGGGTAAGAGATTTGATAACTAT-A
1 GGGTAAGAGATTAGAT-ATCT-TCAATCTG-CCTATGATTGGGGTAAGAAATTGGAT-GCT-TCA
* * * * * ** *
207855 GTCTGCCTCATGATCGGGGTAAGAGATTGGATGATGGCTGCAATCTGCCCCATGATCGGGGTAGG
61 ATCTGCCTCATGATC-AGGTAAGAGATT-GATG-TGTCT-TAATCTGCCCTATGATTAGGGTAAG
* * * * * * *
207920 AGATTGGATGATGGCTGCAATCTGCCTCATGATCGAGGTAAGATATTGGATGATGGCTGCAATCT
122 AGATT-GA--AT-TCTTCAATTTGCCCCATGATCGAGGTAAGAGATTGGAT--TGTCTTCAATCT
*
207985 GCCC-CATGATCG
181 GCCCTC-TGATCA
* * * *
207997 GGGTAAGAGATTGGATGGT-TGCAATCTGCCCTATGATTGGGGTAAGAGATTGGATG
1 GGGTAAGAGATTAGAT-ATCTTCAATCTG-CCTATGATTGGGGTAAGAAATTGGATG
208053 GTGATGTAAC
Statistics
Matches: 525, Mismatches: 90, Indels: 61
0.78 0.13 0.09
Matches are distributed among these distances:
191 5 0.01
192 28 0.05
193 41 0.08
194 190 0.36
195 32 0.06
196 56 0.11
197 30 0.06
198 41 0.08
199 2 0.00
201 2 0.00
202 33 0.06
204 65 0.12
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (192 bp):
GGGTAAGAGATTAGATATCTTCAATCTGCCTATGATTGGGGTAAGAAATTGGATGCTTCAATCTG
CCTCATGATCAGGTAAGAGATTGATGTGTCTTAATCTGCCCTATGATTAGGGTAAGAGATTGAAT
TCTTCAATTTGCCCCATGATCGAGGTAAGAGATTGGATTGTCTTCAATCTGCCCTCTGATCA
Found at i:208315 original size:99 final size:99
Alignment explanation
Indices: 208145--208512 Score: 481
Period size: 99 Copynumber: 3.7 Consensus size: 99
208135 CGTTATGGCT
* * * *
208145 TCAATCCTTCTCAT--CATGTTCCTAAGGT-ATCGGGTTCGCCTTTGCGACCTCTACCTTTCCCA
1 TCAATCCTTCCCATCACATCTT-CTAAGGTAAT-GGGTTCGCCATTGCGACCTCAACCTTTCCCA
* * * *
208207 TCACATCTTCATGGTATCAGATTCACCATTGCAACC
64 TCACATCTTCATGGTACCGGATTCACCGTTGCGACC
* * * * *
208243 TCAATCCTTCCCATCACATCTTGTAAGGTAATGGGTTTGCCATTGCGGCCTCAACCTTTCTCTTC
1 TCAATCCTTCCCATCACATCTTCTAAGGTAATGGGTTCGCCATTGCGACCTCAACCTTTCCCATC
**
208308 ATGTCTTCATGGTACCGGATTCACCGTTGCGACC
66 ACATCTTCATGGTACCGGATTCACCGTTGCGACC
* * * *
208342 TCAATCCTTCCCATCACATCTTCTAAGGTATTGGGTTCGTCATTTCGGCCTCAACCTTTCCCATC
1 TCAATCCTTCCCATCACATCTTCTAAGGTAATGGGTTCGCCATTGCGACCTCAACCTTTCCCATC
*
208407 ACATCTTCATGGTACCGGATTCACCGTTGCGGCC
66 ACATCTTCATGGTACCGGATTCACCGTTGCGACC
** * *
208441 TCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGATCTCAACCTTTCCCATC
1 TCAATCCTTCCCATCACATCTTCTAAGGTAATGGGTTCGCCATTGCGACCTCAACCTTTCCCATC
208506 ACATCTT
66 ACATCTT
208513 TTAAGGTATC
Statistics
Matches: 235, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
98 13 0.06
99 215 0.91
100 7 0.03
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (99 bp):
TCAATCCTTCCCATCACATCTTCTAAGGTAATGGGTTCGCCATTGCGACCTCAACCTTTCCCATC
ACATCTTCATGGTACCGGATTCACCGTTGCGACC
Found at i:208403 original size:50 final size:50
Alignment explanation
Indices: 208166--208552 Score: 356
Period size: 50 Copynumber: 7.8 Consensus size: 50
208156 CATCATGTTC
* *
208166 CTAAGGTATCGGGTTCGCCTTTGCGACCTCTACCTTTCCCATCACATCTT
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTT
* * * * * *
208216 C-ATGGTATCAGATTCACCATTGCAACCTCAATCC-TTCCCATCACATCTT
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAA-CCTTTCCCATCACATCTT
* * * * * * **
208265 GTAAGGTAAT-GGGTTTGCCATTGCGGCCTCAACCTTTCTCTTCATGTCTT
1 CTAAGGT-ATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTT
* * * *
208315 C-ATGGTACCGGATTCACCGTTGCGACCTCAATCC-TTCCCATCACATCTT
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAA-CCTTTCCCATCACATCTT
* * * * *
208364 CTAAGGTATTGGGTTCGTCATTTCGGCCTCAACCTTTCCCATCACATCTT
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTT
* * * * *
208414 C-ATGGTACCGGATTCACCGTTGCGGCCTCAATCC-TTCCCATCACATCTT
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAA-CCTTTCCCATCACATCTT
* *
208463 CTAAGGTACCGGGTTCGCCGTTGCGATCTCAACCTTTCCCATCACATCTT
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTT
* * * * *
208513 TTAAGGTATCGAGTTCGCCGTTACGGCCTCAACTTTTCCC
1 CTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCC
208553 TTCATATTTT
Statistics
Matches: 266, Mismatches: 60, Indels: 22
0.76 0.17 0.06
Matches are distributed among these distances:
48 1 0.00
49 115 0.43
50 148 0.56
51 2 0.01
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (50 bp):
CTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTT
Found at i:209163 original size:105 final size:107
Alignment explanation
Indices: 208998--209194 Score: 263
Period size: 105 Copynumber: 1.9 Consensus size: 107
208988 AACCACTAAC
* * * * * *
208998 CGTTATTTTAAATGCAAAAATGCTTGAATCAAGGTTGTAAGGTGGATGAAACTGAATTTTATTGA
1 CGTTATTTTAAATGCAAAAATGCTTGAAACAAGGTTGCAAGGAGAATAAAACTGAATTTTATCGA
**
209063 AGGCAAAGCTTGCATGAATGAAAAGATCATTGGTTCATTAAT
66 AGGCAAAGCTCACATGAATGAAAAGATCATTGGTTCATTAAT
* * * *
209105 CGTTATTTT-GATGCAAAAATGCTT-AAACATGGTTGCAAGGAGAATAAAATTGAATTTTATCGG
1 CGTTATTTTAAATGCAAAAATGCTTGAAACAAGGTTGCAAGGAGAATAAAACTGAATTTTATCGA
*
209168 AGGTAAAGCTCACATGAATGAAAAGAT
66 AGGCAAAGCTCACATGAATGAAAAGAT
209195 TAAAAATGAC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 54 0.70
106 14 0.18
107 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (107 bp):
CGTTATTTTAAATGCAAAAATGCTTGAAACAAGGTTGCAAGGAGAATAAAACTGAATTTTATCGA
AGGCAAAGCTCACATGAATGAAAAGATCATTGGTTCATTAAT
Found at i:209529 original size:12 final size:11
Alignment explanation
Indices: 209512--209545 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
209502 GACCTCTCCC
209512 TTTTCTTTTTT
1 TTTTCTTTTTT
209523 GTTTTCTTTTTT
1 -TTTTCTTTTTT
209535 TCTTTCTTTTT
1 T-TTTCTTTTT
209546 CTTCCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 20 0.95
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:209556 original size:21 final size:20
Alignment explanation
Indices: 209512--209569 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
209502 GACCTCTCCC
*
209512 TTTTCTTTTTTGTTTTCTTT
1 TTTTCTTTTTTGTTTTCCTT
209532 TTTTCTTTCTTT-TTCTTCCTT
1 TTTTCTTT-TTTGTT-TTCCTT
*
209553 TTTTCCTTTTTTATTTT
1 TTTT-CTTTTTTGTTTT
209570 TTTGGGTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 10 0.30
21 17 0.52
22 6 0.18
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTCTTTTTTGTTTTCCTT
Found at i:214429 original size:104 final size:103
Alignment explanation
Indices: 214147--214454 Score: 246
Period size: 109 Copynumber: 2.9 Consensus size: 103
214137 TTTAAATGAA
* * * * * **
214147 ATATTCGATTACTTAGGTTCAAGGC-AAAATCATACCCAACACGTTAGGGCACAATTTTTCGAGT
1 ATATTCAATTACTTAGGTTCAA-ACAAAAATCATAACCAACACGTTAGGACACAAATCCTCGAGT
* * * * * *
214211 CCTCCAAAATAACAG-AATATTGAGCATTAATTGGTTCCGAATAGG
65 TC-CCTAAATAA-AGAAACATT--GCCTCAATT--TT-TGAATAGG
* * * *
214256 ATATTCAATTATTTAGGTTCAAACAAAAATCATACCCAACACGTTAGGACATAAATCCTCGATTT
1 ATATTCAATTACTTAGGTTCAAACAAAAATCATAACCAACACGTTAGGACACAAATCCTCGAGTT
*
214321 CCCTAAAATAAA-AGAACATTGCCTCGATTTTTGAATAGG
66 CCCT-AAATAAAGA-AACATTGCCTCAATTTTTGAATAGG
* * * * * * * **
214360 ATATTCAATTACTTAGGTTCGAAGAAAAATCGTAATCAATACGTT-TGAGCACAATTTTTCGAGT
1 ATATTCAATTACTTAGGTTCAAACAAAAATCATAACCAACACGTTAGGA-CACAAATCCTCGAGT
214424 TCCCTAAATAAAGAAACATTGCCTCAATTTT
65 TCCCTAAATAAAGAAACATTGCCTCAATTTT
214455 GAAAATATTT
Statistics
Matches: 163, Mismatches: 30, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
103 25 0.15
104 61 0.37
105 2 0.01
107 6 0.04
108 4 0.02
109 65 0.40
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (103 bp):
ATATTCAATTACTTAGGTTCAAACAAAAATCATAACCAACACGTTAGGACACAAATCCTCGAGTT
CCCTAAATAAAGAAACATTGCCTCAATTTTTGAATAGG
Found at i:214973 original size:60 final size:59
Alignment explanation
Indices: 214898--215012 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
214888 GGTCAAATAG
* *
214898 AAATTTTAGTAAGTTTAGGGGTCAAAATGT-AATTTTCAAAAAATTTGAGGGTCAAAATCA
1 AAATTTTAGTAAGTTTAAGGGCCAAAAT-TAAATTTTCAAAAAATTTG-GGGTCAAAATCA
* * *
214958 AAATTTTAG-ACAGTTTAAGGGCCAAAATTAAATTTTTAGAAAGTTTGGGGTCAAA
1 AAATTTTAGTA-AGTTTAAGGGCCAAAATTAAATTTTCAAAAAATTTGGGGTCAAA
215013 TTTGAGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
59 10 0.21
60 38 0.79
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (59 bp):
AAATTTTAGTAAGTTTAAGGGCCAAAATTAAATTTTCAAAAAATTTGGGGTCAAAATCA
Found at i:214984 original size:30 final size:30
Alignment explanation
Indices: 214898--215003 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
214888 GGTCAAATAG
* * * *
214898 AAATTTTAGTAAGTTTAGGGGTCAAAAT-G
1 AAATTTTAGAAAGTTTAAGGGCCAAAATCA
* * * * *
214927 TAATTTTCAAAAAATTTGAGGGTCAAAATCA
1 AAATTTT-AGAAAGTTTAAGGGCCAAAATCA
* *
214958 AAATTTTAGACAGTTTAAGGGCCAAAATTA
1 AAATTTTAGAAAGTTTAAGGGCCAAAATCA
*
214988 AATTTTTAGAAAGTTT
1 AAATTTTAGAAAGTTT
215004 GGGGTCAAAT
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
29 6 0.10
30 47 0.80
31 6 0.10
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (30 bp):
AAATTTTAGAAAGTTTAAGGGCCAAAATCA
Found at i:217012 original size:45 final size:45
Alignment explanation
Indices: 216948--217037 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
216938 GAGATAAGTT
* *
216948 AGATATAAAGGCTCTATCCACAATTCAATTATGTTTAACAAATAA
1 AGATAAAAAGGCTCTATCCACAATTCAATTATGTCTAACAAATAA
**
216993 AGATAAAAAGGCTCTATCCATGATTCAATTATGTCTAACAAATAA
1 AGATAAAAAGGCTCTATCCACAATTCAATTATGTCTAACAAATAA
217038 TGTATTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (45 bp):
AGATAAAAAGGCTCTATCCACAATTCAATTATGTCTAACAAATAA
Found at i:219606 original size:51 final size:50
Alignment explanation
Indices: 219546--219765 Score: 127
Period size: 51 Copynumber: 4.4 Consensus size: 50
219536 AAATCACTAC
* *
219546 TTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAT
1 TTTATTTAAAAATCTAAACTTTT-TTTCGAAATAATTAAAAAAATCAAAAT
* * * ** * *
219597 TTTATTTAAAATTTTAATCTTTTTCTTTAAAATAACT-AAAAAA-CAAATT
1 TTTATTTAAAAATCTAAACTTTTT-TTCGAAATAATTAAAAAAATCAAAAT
** **
219646 TTTATTTTTAAAAAAATAAACTTTCTCTTT-----T--TTAAAGAAAATCACTAT
1 TTTA--TTTAAAAATCTAAACTTT-T-TTTCGAAATAATTAAA-AAAATCAAAAT
* * * *
219694 TTTACTTAAAAATCCAAACTTTTGTTTCGAAATAATTTAAAAAATCAAAAC
1 TTTATTTAAAAATCTAAACTTTT-TTTCGAAATAATTAAAAAAATCAAAAT
*
219745 TTTGTTTAAAAAAT-TAAACTT
1 TTTATTT-AAAAATCTAAACTT
219766 AAAAAAAAAA
Statistics
Matches: 124, Mismatches: 29, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
45 5 0.04
46 16 0.13
47 5 0.04
48 7 0.06
49 9 0.07
50 8 0.06
51 60 0.48
52 13 0.10
53 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (50 bp):
TTTATTTAAAAATCTAAACTTTTTTTCGAAATAATTAAAAAAATCAAAAT
Found at i:219622 original size:154 final size:148
Alignment explanation
Indices: 219375--219861 Score: 486
Period size: 148 Copynumber: 3.3 Consensus size: 148
219365 TTTCTTTCGA
* * ***
219375 TTAAA-AAAATCACTACTTTACTTCAAAATAAAAAAAAATTATTTCGAAATAGTTAAAAAAAT-A
1 TTAAAGAAAATCACTACTTTACTTAAAAAT-CAAAACTTTTATTTCGAAATAGTTAAAAAAATCA
*
219438 AGAACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATCACTAAAAAACAGAA-TTTTATTTTTT
65 A-AACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACA-AATTTTTA-TTTTT
** *
219502 AAAAATCTAAACTTTCTTTTTTTTTTT
127 AAAAAAATAAACTTTC-----TCTTTT
* * *
219529 TTGATGAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAA
1 TTAAAGAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAA
* * *
219594 AATTTTATTTAAAATTTTAATCTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAAAA
66 AACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAAAA
219659 AAATAAACTTTCTCTTTT
131 AAATAAACTTTCTCTTTT
* * * * *
219677 TTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTGTTTCGAAATAATTTAAAAAATCAA
1 TTAAAGAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAA
** *
219742 AACTTTGTTTAAAAAATTAAA------C-TT--AA-AA--AAAAAACAGATTTTTA-TTTTAAAA
66 AACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAAAA
* ** *
219794 AATCTAAACACTCACTTTT
131 AA-ATAAACTTTCTCTTTT
* *
219813 TTAAAGAAAATCATTATTTTACTTAAAAAAT-AAAAGCTTTTATTTCGAA
1 TTAAAGAAAATCACTACTTTACTT-AAAAATCAAAA-CTTTTATTTCGAA
219862 TTAAAAAAAA
Statistics
Matches: 292, Mismatches: 35, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
135 10 0.03
136 53 0.18
137 18 0.06
138 2 0.01
139 2 0.01
141 2 0.01
142 1 0.00
148 79 0.27
153 21 0.07
154 79 0.27
155 25 0.09
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.40
Consensus pattern (148 bp):
TTAAAGAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAA
AACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAAAA
AAATAAACTTTCTCTTTT
Found at i:219872 original size:136 final size:136
Alignment explanation
Indices: 219634--219883 Score: 337
Period size: 136 Copynumber: 1.8 Consensus size: 136
219624 TAAAATAACT
** *
219634 AAAAAACAAATTTTTATTTTTAAAAAAATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTAC
1 AAAAAACAAATTTTTATTTTTAAAAAAATAAACACTCACTTTTTTAAAGAAAATCACTATTTTAC
* * * *
219699 TTAAAAATCCAAACTTTTGTTTCGAAATAATTTAAAAAATCAAAA-CTTTGTTTAAAAAATTAAA
66 TTAAAAATCAAAACTTTTATTTCGAAATAA-TAAAAAAAACAAAAGCTTTGTTTAAAAAATTAAA
219763 CTTAAAA
130 CTTAAAA
* * *
219770 AAAAAACAGATTTTTA-TTTTAAAAAATCTAAACACTCACTTTTTTAAAGAAAATCATTATTTTA
1 AAAAAACAAATTTTTATTTTTAAAAAA-ATAAACACTCACTTTTTTAAAGAAAATCACTATTTTA
*
219834 CTTAAAAAAT-AAAAGCTTTTATTTCGAATTAA-AAAAAAAACAAAAGCTTT
65 CTT-AAAAATCAAAA-CTTTTATTTCGAAATAATAAAAAAAACAAAAGCTTT
219884 TCCCAAAATC
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
135 21 0.21
136 57 0.58
137 21 0.21
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (136 bp):
AAAAAACAAATTTTTATTTTTAAAAAAATAAACACTCACTTTTTTAAAGAAAATCACTATTTTAC
TTAAAAATCAAAACTTTTATTTCGAAATAATAAAAAAAACAAAAGCTTTGTTTAAAAAATTAAAC
TTAAAA
Found at i:220760 original size:42 final size:42
Alignment explanation
Indices: 220706--221172 Score: 585
Period size: 42 Copynumber: 11.1 Consensus size: 42
220696 TTTAATTGCA
* * * * *
220706 ATGAAAAGTAAATGGACCTCCACACTTGCGCCTCTAAAGGCA
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* * **
220748 ACGAAAAGTAAATGGGCCTCCACACTTGGGCCTCTAAATGAA
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* *
220790 ACGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCA
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* * * **
220832 ATGAAAAGTAAGTAGGCCTCCACACTTGGGCCTCTAAATATG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* * * **
220874 ATGAAAAGTAAATGGGCCTCTACACCTGAGCCTCTGAATATG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* *
220916 ATGAAAAGTAAATGGGCCTCCACACATGGGCCT-TCGAATGCG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCT-AAATGCG
* * *
220958 ATGAAAAGTAAATGAGCCTCTACACTTGGGCCTCTAAATGCG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* *
221000 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTGAATGTG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* * *
221042 ATGAAAAGTAAATGAGCCTCCACACTTGGGCCTCTAAATACG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
* * *
221084 ATGAAAAGTAAATGGGTCTCCACACCTGAGCCTCTGAATGCG
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
** *
221126 ATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTAAATGCA
1 ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
221168 ATGAA
1 ATGAA
221173 TACTTTCCTT
Statistics
Matches: 372, Mismatches: 51, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
41 1 0.00
42 370 0.99
43 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (42 bp):
ATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCG
Found at i:221539 original size:17 final size:17
Alignment explanation
Indices: 221519--221569 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
221509 CTCTTTTGTA
221519 AGATTACGTCTTAAAGT
1 AGATTACGTCTTAAAGT
* *
221536 AGA-TA-TTCTTCAA--
1 AGATTACGTCTTAAAGT
221549 AGATTACGTCTTAAAGT
1 AGATTACGTCTTAAAGT
221566 AGAT
1 AGAT
221570 ATTCTTCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 3 0.12
14 2 0.08
15 12 0.46
16 2 0.08
17 7 0.27
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (17 bp):
AGATTACGTCTTAAAGT
Found at i:221554 original size:30 final size:30
Alignment explanation
Indices: 221518--221578 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
221508 GCTCTTTTGT
221518 AAGATTACGTCTTAAAGTAGATATTCTTCA
1 AAGATTACGTCTTAAAGTAGATATTCTTCA
221548 AAGATTACGTCTTAAAGTAGATATTCTTCA
1 AAGATTACGTCTTAAAGTAGATATTCTTCA
221578 A
1 A
221579 TATAGTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (30 bp):
AAGATTACGTCTTAAAGTAGATATTCTTCA
Found at i:221624 original size:10 final size:10
Alignment explanation
Indices: 221604--221645 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
221594 TTTCTCTCTC
221604 TTTCTATTTTT
1 TTTCTA-TTTT
221615 TTTCTATTTT
1 TTTCTATTTT
*
221625 TCT-TATTTT
1 TTTCTATTTT
*
221634 TTTGTATTTT
1 TTTCTATTTT
221644 TT
1 TT
221646 ATTCTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.29
10 14 0.50
11 6 0.21
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:229114 original size:24 final size:24
Alignment explanation
Indices: 229087--229135 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
229077 CAACTTATTC
229087 AATATTTTATCATTACTCCGATTT
1 AATATTTTATCATTACTCCGATTT
229111 AATATTTTATCATTACTCCGATTT
1 AATATTTTATCATTACTCCGATTT
229135 A
1 A
229136 CTTGTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (24 bp):
AATATTTTATCATTACTCCGATTT
Found at i:230560 original size:4 final size:4
Alignment explanation
Indices: 230551--230575 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
230541 ACTTTGTTTC
230551 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
230576 GAAAATCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:230691 original size:167 final size:165
Alignment explanation
Indices: 230407--230722 Score: 422
Period size: 167 Copynumber: 1.9 Consensus size: 165
230397 TGACTAAAAC
*
230407 AAAATCACTACTTTACTTTAAAACCAAAACTTTTATTTCGAAATAGTTAAAAAAAAAATCAAAAT
1 AAAATCACTACTTTACTTTAAAACCAAAACTTTTATTTCGAAATAGTT-AAAAAAAAATCAAAAC
* *
230472 TTTATTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACATATTTTTATTTTTTAAAAAT
65 TTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTT-AAAAT
*
230537 CTAAACTTTGTTTCTTTATTTATTTATTTATTTATTTATG
129 ATAAA-TTT-TTTCTTT-TTTATTTATTTATTTATTTATG
* ***** *
230577 AAAATCACTATTTTACTTTAAAATTTGGACTTTTATTTCGAAATAG-T-AAAAAGAATCAAAACT
1 AAAATCACTACTTTACTTTAAAACCAAAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAACT
* * **
230640 TTATTTAAAAA-TTAGAATTTTTTCTTTAAAATAACTAGAAATTAGATTTTTATTTTTTAAAATA
66 TTATTTAAAAATTTA-AACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAATA
230704 TAAATTTTTTCTTTTTTAT
130 TAAATTTTTTCTTTTTTAT
230723 AGAGAATAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
163 5 0.04
164 7 0.05
165 3 0.02
166 12 0.09
167 62 0.48
169 1 0.01
170 40 0.31
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.47
Consensus pattern (165 bp):
AAAATCACTACTTTACTTTAAAACCAAAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAACT
TTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAATAT
AAATTTTTTCTTTTTTATTTATTTATTTATTTATG
Found at i:231359 original size:3 final size:3
Alignment explanation
Indices: 231351--231421 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
231341 ATGAAACCCT
* *
231351 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC TAC AAC TAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
*
231399 TAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AA
231422 TGATGATGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.63, C:0.32, G:0.00, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:232789 original size:15 final size:15
Alignment explanation
Indices: 232771--232808 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
232761 AATTGATCGT
*
232771 CAATGAAGCGCCGGC
1 CAATGAAGCGCCAGC
232786 CAATGAAGCGCCAGC
1 CAATGAAGCGCCAGC
232801 CAATGAAG
1 CAATGAAG
232809 AGCCTATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.29, G:0.29, T:0.08
Consensus pattern (15 bp):
CAATGAAGCGCCAGC
Found at i:236062 original size:9 final size:9
Alignment explanation
Indices: 236050--236111 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
236040 TTTCTATATA
236050 TTTTATAAT
1 TTTTATAAT
*
236059 TTTTATTAT
1 TTTTATAAT
*
236068 TTTTATAAAA
1 TTTTAT-AAT
* *
236078 TTTAATAAA
1 TTTTATAAT
*
236087 TTTTATAAC
1 TTTTATAAT
*
236096 TTTTATTGAT
1 TTTTA-TAAT
236106 TTTTAT
1 TTTTAT
236112 TTCTTTTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 30 0.70
10 13 0.30
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:236109 original size:19 final size:18
Alignment explanation
Indices: 236050--236111 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
236040 TTTCTATATA
*
236050 TTTTATAATTTTTATTAT
1 TTTTATAAATTTTATTAT
* * *
236068 TTTTATAAAATTTAATAAA
1 TTTTAT-AAATTTTATTAT
*
236087 TTTTATAACTTTTATTGAT
1 TTTTATAAATTTTATT-AT
236106 TTTTAT
1 TTTTAT
236112 TTCTTTTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATAAATTTTATTAT
Found at i:236361 original size:89 final size:85
Alignment explanation
Indices: 236189--236367 Score: 216
Period size: 86 Copynumber: 2.1 Consensus size: 85
236179 TTAGGGGTGA
* * *
236189 TTCAAGTACTCAATTGAGTGCAAAAAACATAGGGACTTAATTGCTTTTCTTGAAAAGTCTGAGTC
1 TTCAAGTACCCAATTGAATGCAAAAAAAATAGGGACTTAATTGCTTTTCTTGAAAAGTCTGAGTC
236254 TTTTTTATGTATTTTGAAAC
66 TTTTTTATGTATTTTGAAAC
** ** * *
236274 TTCAAGTACCCAATTGAATGCAAAAAAAAATAGGGGTTTAATTTTTTTTTTTGAAAAAGTTTGAG
1 TTCAAGTACCCAATTGAATGC-AAAAAAAATAGGGACTTAATTGCTTTTCTTG-AAAAGTCTGA-
*
236339 GGTCTTTTTTAT-TCATTTTGAAAG
63 -GTCTTTTTTATGT-ATTTTGAAAC
236363 TTCAA
1 TTCAA
236368 CTATATAAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
85 19 0.24
86 25 0.32
87 9 0.11
88 1 0.01
89 25 0.32
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (85 bp):
TTCAAGTACCCAATTGAATGCAAAAAAAATAGGGACTTAATTGCTTTTCTTGAAAAGTCTGAGTC
TTTTTTATGTATTTTGAAAC
Found at i:241909 original size:90 final size:90
Alignment explanation
Indices: 241747--241985 Score: 302
Period size: 90 Copynumber: 2.7 Consensus size: 90
241737 GTGACCGAAA
* * ** * * *
241747 ACCGAAGCGATGGTTGAGGTATTGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGTAGCATCG
1 ACCGAATCGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGATCGTGTGAGCAGCATCG
241812 TTAGGGAA-AATTTATATGCACAGAT
66 TTAGGGAACAA-TTATATGCACAGAT
* * * *
241837 ACTGAATCGATGGTTGGGGTACCGCATATTTTGCGAGTCCTTGACAGATTGTGT-ATGCAGCATC
1 ACCGAATCGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGATCGTGTGA-GCAGCATC
*
241901 GTTGGGGAACAATTATATGCACAGAT
65 GTTAGGGAACAATTATATGCACAGAT
* ** *
241927 ACCGTATCGATGACTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCA
1 ACCGAATCGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGATCGTGTGAGCA
241986 TTATCATATA
Statistics
Matches: 126, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
89 1 0.01
90 122 0.97
91 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (90 bp):
ACCGAATCGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGATCGTGTGAGCAGCATCG
TTAGGGAACAATTATATGCACAGAT
Found at i:242138 original size:120 final size:120
Alignment explanation
Indices: 241925--242164 Score: 356
Period size: 120 Copynumber: 2.0 Consensus size: 120
241915 ATATGCACAG
**
241925 ATACCGTATCGATGACTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCATTAT
1 ATACCGTATCGATGACTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCAT
* * *
241990 CATATACTAGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGACTATAGC
66 CATAGACTAGTAACAGAGTTGATACAGACATAAGAATGAAATTCTAGACTATAGC
* * *
242045 ATACCGTATCGATGGCTGGGGTACCGTATATGTTGCGGGTCCTCGACAGAC-CGTGTGAGCAGCA
1 ATACCGTATCGATGACTGGGGTACCGCATATGTTGCGAGTCCTCGACAG-CTCGTGTGAGCAGCA
* * * *
242109 TCGTAGACTAGTAACAGAGTTGATGCAGACATAAGGATGAAATTCTAGATTATAGC
65 TCATAGACTAGTAACAGAGTTGATACAGACATAAGAATGAAATTCTAGACTATAGC
242165 TTGTGGAAGC
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
120 106 0.99
121 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (120 bp):
ATACCGTATCGATGACTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCAT
CATAGACTAGTAACAGAGTTGATACAGACATAAGAATGAAATTCTAGACTATAGC
Found at i:244125 original size:39 final size:39
Alignment explanation
Indices: 244082--244180 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
244072 TTAATTTGTC
* *
244082 TCAAACTTAGACACCTTAAAAACAACTATTAAATATATA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATATA
* *
244121 TCAAAATAAGACACATTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATATA
244160 TCAAACTAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
244181 CCCTATTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.25
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATATA
Found at i:247355 original size:31 final size:28
Alignment explanation
Indices: 247320--247376 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
247310 TTCATATTTT
*
247320 TCTTTTCTCTCTTTCTTTTCACTTTCTTTGC
1 TCTTTTCTCTC-AT-TTTTC-CTTTCTTTGC
247351 TCTTTTCTCTCATTTTTCCTTTCTTT
1 TCTTTTCTCTCATTTTTCCTTTCTTT
247377 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 5 0.20
30 1 0.04
31 11 0.44
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (28 bp):
TCTTTTCTCTCATTTTTCCTTTCTTTGC
Found at i:247377 original size:21 final size:20
Alignment explanation
Indices: 247351--247399 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
247341 CTTTCTTTGC
*
247351 TCTTTTCTCTCATTTTTCCTT
1 TCTTTT-TCTCAATTTTCCTT
* *
247372 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTCTCAATTTTCCTT
247392 TCTTTTTC
1 TCTTTTTC
247400 ATTCTCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTTCTCAATTTTCCTT
Found at i:249522 original size:24 final size:25
Alignment explanation
Indices: 249477--249523 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
249467 ACTAGCCTTC
249477 TTTTTTTTTATACTTTCGAAACTCT
1 TTTTTTTTTATACTTTCGAAACTCT
249502 TTTTTTTTTAATA-TTTC-AAACT
1 TTTTTTTTT-ATACTTTCGAAACT
249524 TTGCACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTTTTTATACTTTCGAAACTCT
Found at i:252800 original size:31 final size:28
Alignment explanation
Indices: 252765--252821 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
252755 TTCATATTTT
*
252765 TCTTTTCTCTCTTTCTTTTCACTTTCTTTGC
1 TCTTTTCTCTC-AT-TTTTC-CTTTCTTTGC
252796 TCTTTTCTCTCATTTTTCCTTTCTTT
1 TCTTTTCTCTCATTTTTCCTTTCTTT
252822 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 5 0.20
30 1 0.04
31 11 0.44
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (28 bp):
TCTTTTCTCTCATTTTTCCTTTCTTTGC
Found at i:252822 original size:21 final size:20
Alignment explanation
Indices: 252796--252844 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
252786 CTTTCTTTGC
*
252796 TCTTTTCTCTCATTTTTCCTT
1 TCTTTT-TCTCAATTTTCCTT
* *
252817 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTCTCAATTTTCCTT
252837 TCTTTTTC
1 TCTTTTTC
252845 ATTCTCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTTCTCAATTTTCCTT
Found at i:254967 original size:24 final size:25
Alignment explanation
Indices: 254922--254968 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
254912 ACTAGCCTTC
254922 TTTTTTTTTATACTTTCGAAACTCT
1 TTTTTTTTTATACTTTCGAAACTCT
254947 TTTTTTTTTAATA-TTTC-AAACT
1 TTTTTTTTT-ATACTTTCGAAACT
254969 TTGCACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTTTTTATACTTTCGAAACTCT
Found at i:255753 original size:10 final size:10
Alignment explanation
Indices: 255740--255772 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
255730 AATTAAGTAA
255740 GGAGCTGAAT
1 GGAGCTGAAT
255750 GGAGCTGAAT
1 GGAGCTGAAT
255760 GGAGCTGAAT
1 GGAGCTGAAT
255770 GGA
1 GGA
255773 CTAGGCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.42, T:0.18
Consensus pattern (10 bp):
GGAGCTGAAT
Found at i:256184 original size:39 final size:39
Alignment explanation
Indices: 256141--256239 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
256131 TTAATTTGTC
* * *
256141 TCAAACTTAGACACCTTAAAAATAACTATTAAATATATA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATATA
* * *
256180 TCAAAATAAGAGACATTAAAAACAACTATTAAATATGTA
1 TCAAACTAAGACACATTAAAAACAACTATTAAATATATA
256219 TCAAACTAAGACACATTAAAA
1 TCAAACTAAGACACATTAAAA
256240 CCCTATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (39 bp):
TCAAACTAAGACACATTAAAAACAACTATTAAATATATA
Found at i:256807 original size:20 final size:20
Alignment explanation
Indices: 256784--256850 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
256774 TGATGTAACT
256784 TGGTTTATATTGTGGTGTTA
1 TGGTTTATATTGTGGTGTTA
* *
256804 TGGTTTCATA-TG-GATGTAA
1 TGGTTT-ATATTGTGGTGTTA
256823 CTTGGTTTATATTGTGGTGTTA
1 --TGGTTTATATTGTGGTGTTA
256845 TGGTTT
1 TGGTTT
256851 GTTATGGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 5 0.13
20 17 0.45
21 11 0.29
22 5 0.13
ACGTcount: A:0.16, C:0.03, G:0.28, T:0.52
Consensus pattern (20 bp):
TGGTTTATATTGTGGTGTTA
Found at i:256828 original size:21 final size:21
Alignment explanation
Indices: 256774--256834 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
256764 TAAGAATGAT
256774 TGATGTAACTTGGTTTATATTG
1 TGATGTAACTTGGTTTATA-TG
* *
256796 TGGTGTTA--TGGTTTCATATG
1 TGATGTAACTTGGTTT-ATATG
256816 -GATGTAACTTGGTTTATAT
1 TGATGTAACTTGGTTTATAT
256835 TGTGGTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.16
20 12 0.38
21 9 0.28
22 6 0.19
ACGTcount: A:0.21, C:0.05, G:0.25, T:0.49
Consensus pattern (21 bp):
TGATGTAACTTGGTTTATATG
Found at i:262914 original size:36 final size:36
Alignment explanation
Indices: 262858--262984 Score: 139
Period size: 36 Copynumber: 3.5 Consensus size: 36
262848 ATTTACCCCC
* * *
262858 TGTTGACCTAAAGGTCATGATGCTCGTTTAACTTCA
1 TGTTAACCCAAAGGTCATGATGCTCGTTTAACTCCA
* * * *
262894 TGTTAACTCAAAGGTCATGATGCTCATTTGACTCCC
1 TGTTAACCCAAAGGTCATGATGCTCGTTTAACTCCA
*
262930 TGTTAACCCAAAGGTCATGATGCTCAGTTT-ACTCCT
1 TGTTAACCCAAAGGTCATGATGCTC-GTTTAACTCCA
* * *
262966 TGCTGACCTAAAGGTCATG
1 TGTTAACCCAAAGGTCATG
262985 CCTGTTACCC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
36 74 0.96
37 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTTAACCCAAAGGTCATGATGCTCGTTTAACTCCA
Found at i:263289 original size:20 final size:20
Alignment explanation
Indices: 263249--263290 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
263239 CGTTTCTATC
* **
263249 TTTCTCGTTTCCAATCGTCA
1 TTTCTCATTTCCAATAATCA
263269 TTTCTCATTTCCAATAATCA
1 TTTCTCATTTCCAATAATCA
263289 TT
1 TT
263291 AGAAAGGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTCTCATTTCCAATAATCA
Found at i:269223 original size:15 final size:15
Alignment explanation
Indices: 269203--269256 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
269193 ACAAAAGAGT
269203 AAGAGAAGAAGGAGA
1 AAGAGAAGAAGGAGA
*
269218 AAGAGAAGAAGAGGGA
1 AAGAGAAGAAG-GAGA
*
269234 AA-AGAAG-AGAAGA
1 AAGAGAAGAAGGAGA
269247 AAGAAGAAGA
1 AAG-AGAAGA
269257 GTTTGCCCCG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 21 0.66
16 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
AAGAGAAGAAGGAGA
Found at i:269244 original size:17 final size:18
Alignment explanation
Indices: 269203--269247 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
269193 ACAAAAGAGT
269203 AAGAGAAGAAGGAGAAAG
1 AAGAGAAGAAGGAGAAAG
*
269221 -AGAAGAAGAGGGA-AAAG
1 AAG-AGAAGAAGGAGAAAG
269238 AAGAGAAGAA
1 AAGAGAAGAA
269248 AGAAGAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
AAGAGAAGAAGGAGAAAG
Found at i:270268 original size:16 final size:16
Alignment explanation
Indices: 270247--270304 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
270237 GCCTAGGAAT
270247 AAAAGAAAAGCTGATA
1 AAAAGAAAAGCTGATA
* *
270263 AAAAGAAATG-TAATAA
1 AAAAGAAAAGCTGAT-A
* *
270279 AGAAATAAAAGCTGGTA
1 A-AAAGAAAAGCTGATA
270296 AAAAGAAAA
1 AAAAGAAAA
270305 AAAAATTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
15 3 0.09
16 18 0.56
17 9 0.28
18 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAAGAAAAGCTGATA
Found at i:282188 original size:15 final size:16
Alignment explanation
Indices: 282156--282192 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
282146 CAGTCATTTG
*
282156 AAAA-AAAAAATGAGA
1 AAAAGAAAAAAGGAGA
282171 AAAAGAAAAAAGGA-A
1 AAAAGAAAAAAGGAGA
282186 AAAAGAA
1 AAAAGAA
282193 GAAGAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGGAGA
Found at i:295156 original size:22 final size:22
Alignment explanation
Indices: 295106--295149 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
295096 TGTACTTGCT
* * *
295106 AGAGAAGATAAATAGAGGGGAG
1 AGAGAAGATAAAAAAAGAGGAG
295128 AGAGAAGATAAAAAAAGAGGAG
1 AGAGAAGATAAAAAAAGAGGAG
295150 GAGGAAGCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (22 bp):
AGAGAAGATAAAAAAAGAGGAG
Found at i:301897 original size:23 final size:25
Alignment explanation
Indices: 301859--301912 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
301849 TCATTATAAT
*
301859 TTTTCTATTTACTTCTATAT-TTTA-
1 TTTTCTATTTAATTCTAT-TCTTTAG
301883 TTTTCT-TTTAATTCTATTCTTTAG
1 TTTTCTATTTAATTCTATTCTTTAG
301907 TTTTCT
1 TTTTCT
301913 GCAGGAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 14 0.52
24 12 0.44
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTCTATTTAATTCTATTCTTTAG
Found at i:303166 original size:18 final size:17
Alignment explanation
Indices: 303139--303174 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
303129 ACTATCGAAG
*
303139 AAAGAGAAAGGCAAGGA
1 AAAGAGAAAGACAAGGA
303156 AAAGAAGAAAGACAAGGA
1 AAAG-AGAAAGACAAGGA
303174 A
1 A
303175 TCCCATCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.64, C:0.06, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAGAAAGACAAGGA
Found at i:303689 original size:19 final size:17
Alignment explanation
Indices: 303654--303692 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
303644 GGGTGTTGAG
*
303654 GAAGAGGAGGAAGAAGA
1 GAAGAGGAAGAAGAAGA
303671 GAAGAGAGAAGAAGCAAGA
1 GAAGAG-GAAGAAG-AAGA
303690 GAA
1 GAA
303693 AAAAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.56, C:0.03, G:0.41, T:0.00
Consensus pattern (17 bp):
GAAGAGGAAGAAGAAGA
Found at i:312936 original size:17 final size:18
Alignment explanation
Indices: 312914--312947 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
312904 CTAGTGATAT
312914 TTGGTTTT-TTTGTGTTG
1 TTGGTTTTGTTTGTGTTG
312931 TTGGTTTTGTTTGTGTT
1 TTGGTTTTGTTTGTGTT
312948 TTCTCCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (18 bp):
TTGGTTTTGTTTGTGTTG
Found at i:334670 original size:26 final size:25
Alignment explanation
Indices: 334607--334672 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
334597 AGTAATTATA
334607 GCTCTTACGAGCTCAATCAGTAAGTT
1 GCTCTTACGAGC-CAATCAGTAAGTT
* * **
334633 G-TTTCTATGAGCCAATACAGTATTTT
1 GCTCT-TACGAGCCAAT-CAGTAAGTT
334659 GCTCTTACGAGCCA
1 GCTCTTACGAGCCA
334673 GTATTGCTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
25 6 0.19
26 23 0.74
27 2 0.06
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (25 bp):
GCTCTTACGAGCCAATCAGTAAGTT
Found at i:334676 original size:21 final size:21
Alignment explanation
Indices: 334650--334696 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
334640 TGAGCCAATA
334650 CAGTATTTTGCTCTTA-CGAGC
1 CAGTATTTTGCTC-TAGCGAGC
334671 CAGTA--TTGCTCTAGCGAGC
1 CAGTATTTTGCTCTAGCGAGC
334690 CAGTATT
1 CAGTATT
334697 GCTCAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
21 5 0.22
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (21 bp):
CAGTATTTTGCTCTAGCGAGC
Found at i:334681 original size:19 final size:19
Alignment explanation
Indices: 334657--334721 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
334647 ATACAGTATT
334657 TTGCTCTTACGAGCCAGTA
1 TTGCTCTTACGAGCCAGTA
334676 TTGCTC-TAGCGAGCCAGTA
1 TTGCTCTTA-CGAGCCAGTA
** *
334695 TTGCTCAAACAAGCCAGTA
1 TTGCTCTTACGAGCCAGTA
*
334714 TTGTTCTT
1 TTGCTCTT
334722 CCTTCCGAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 2 0.05
19 36 0.92
20 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (19 bp):
TTGCTCTTACGAGCCAGTA
Done.