Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 154 of 193
Found at i:47865048 original size:32 final size:33
Alignment explanation
Indices: 47864986--47865074 Score: 126
Period size: 32 Copynumber: 2.7 Consensus size: 33
47864976 ATCAAATAAT
47864986 TATTTCAAATATAATTATTAGTTTTATATGTAAAA
1 TATTTCAAATATAATTA-TA-TTTTATATGTAAAA
* *
47865021 TATTTCAAATATCATTAT-TTTTATATGTGAAA
1 TATTTCAAATATAATTATATTTTATATGTAAAA
*
47865053 TATTTCAAATATTATTATATTT
1 TATTTCAAATATAATTATATTT
47865075 CACCTACATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 30 0.60
33 3 0.06
34 1 0.02
35 16 0.32
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (33 bp):
TATTTCAAATATAATTATATTTTATATGTAAAA
Found at i:47871177 original size:10 final size:10
Alignment explanation
Indices: 47871155--47871188 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
47871145 TTTTGAGAAA
47871155 TTTAATTTTT
1 TTTAATTTTT
*
47871165 TTTTATGTTTT
1 TTTAAT-TTTT
47871176 TTTAATTTTT
1 TTTAATTTTT
47871186 TTT
1 TTT
47871189 TTGCTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:47871199 original size:21 final size:21
Alignment explanation
Indices: 47871155--47871199 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
47871145 TTTTGAGAAA
*
47871155 TTTAATTTTTTTTTATGTTTT
1 TTTAATTTTTTTTTATGTTCT
47871176 TTTAATTTTTTTTT-TGCTTCT
1 TTTAATTTTTTTTTATG-TTCT
47871197 TTT
1 TTT
47871200 TTTGTTTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTAATTTTTTTTTATGTTCT
Found at i:47871611 original size:15 final size:15
Alignment explanation
Indices: 47871591--47871641 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
47871581 ACAACTTGTT
47871591 AACGTAAGTGATTAA
1 AACGTAAGTGATTAA
*
47871606 AACGTAA-T-ATTTCA
1 AACGTAAGTGA-TTAA
*
47871620 AACATAAGTGATTAA
1 AACGTAAGTGATTAA
*
47871635 AATGTAA
1 AACGTAA
47871642 CTTGAGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 16 0.57
16 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (15 bp):
AACGTAAGTGATTAA
Found at i:47871834 original size:21 final size:21
Alignment explanation
Indices: 47871803--47871859 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
47871793 TATAAAGTTT
*
47871803 ATTTATATTTTAATTAATCATG
1 ATTTA-ATTTTAATTAATCATA
* * *
47871825 ATTTAATTTTTATCAATCTTA
1 ATTTAATTTTAATTAATCATA
47871846 ATTT-A-TTTAATTAA
1 ATTTAATTTTAATTAA
47871860 GCTTAATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.24
20 1 0.03
21 16 0.55
22 5 0.17
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTAATTTTAATTAATCATA
Found at i:47871906 original size:14 final size:14
Alignment explanation
Indices: 47871887--47871913 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47871877 TACATTAGGG
47871887 AATATAAATTTATA
1 AATATAAATTTATA
47871901 AATATAAATTTAT
1 AATATAAATTTAT
47871914 GTTTATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAAATTTATA
Found at i:47878016 original size:59 final size:59
Alignment explanation
Indices: 47877942--47878247 Score: 357
Period size: 59 Copynumber: 5.2 Consensus size: 59
47877932 TTTTACTTCT
* * * * *
47877942 AGGGTAAAAAT-GTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTAGAAAGTTCG
1 AGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
47878001 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTGAAAATGGGATTTTGGAAAGTTT-
1 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * * *
47878059 AGGGGTAAAATGGTAATTTATGGTAAAATCAAGGTTGAAAATGAAATTTTGGAAAGTTTG
1 A-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
47878119 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAGAGTTTG
1 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
* ** * * * *
47878178 GGGGTAAAATGGTAAGCTTTAGTGAAA-CTGGGGTCAAAAATGAAATTTTGGAAAGTTTG
1 AGGGTAAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTTG
*
47878237 GGGGTCAAAAT
1 AGGGT-AAAAT
47878248 ATAATTTATG
Statistics
Matches: 216, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
58 7 0.03
59 204 0.94
60 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.31
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:47878077 original size:29 final size:29
Alignment explanation
Indices: 47877978--47878192 Score: 99
Period size: 28 Copynumber: 7.3 Consensus size: 29
47877968 ACCGGGGTTA
* *
47877978 AAAATGG-AATTTTAGAAAG-TTCGAGGGT
1 AAAATGGTAATTTTGGAAAGTTTAG-GGGT
** *
47878006 AAAATGGTAATTTTTGGTGAAA-TCGA-GGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTAGGGGT
*
47878036 GAAAATGG-GATTTTGGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTAGGGGT
* * * *
47878065 AAAATGGTAATTTATGGTAAA-ATCAAGGTT
1 AAAATGGTAATTT-TGG-AAAGTTTAGGGGT
* *
47878095 GAAAAT-GAAATTTTGGAAAGTTTGGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTAGGGGT
** *
47878124 AAAATGGTAATTTTTGGTGAAA-TCGA-GGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTAGGGGT
* *
47878154 AAAAATGG-AATTTTGGAGAGTTTGGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTAGGGGT
47878183 AAAATGGTAA
1 AAAATGGTAA
47878193 GCTTTAGTGA
Statistics
Matches: 136, Mismatches: 30, Indels: 41
0.66 0.14 0.20
Matches are distributed among these distances:
27 7 0.05
28 34 0.25
29 32 0.24
30 31 0.23
31 24 0.18
32 8 0.06
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTAGGGGT
Found at i:47878157 original size:30 final size:30
Alignment explanation
Indices: 47877946--47878167 Score: 108
Period size: 30 Copynumber: 7.5 Consensus size: 30
47877936 ACTTCTAGGG
* * * *
47877946 TAAAAATGTAATTTTTGATGAAACCGGGGT
1 TAAAAATGGAATTTTTGGTGAAATCGAGGT
* *
47877976 TAAAAATGGAA-TTTT--AGAAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGTGAAA--TCGAGGT
47878005 T-AAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAAATGG-AATTTTTGGTGAAATCGAGGT
* * ** *
47878035 TGAAAATGGGA-TTTT-G-GAAAGTTTAGGGG
1 TAAAAATGGAATTTTTGGTGAAA-TCGA-GGT
* * *
47878064 T-AAAATGGTAATTTATGGTAAAATCAAGGT
1 TAAAAATGG-AATTTTTGGTGAAATCGAGGT
* * * * *
47878094 TGAAAAT-GAAATTTT-G-GAAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGTGAAA--TCGAGGT
47878123 T-AAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAAATGG-AATTTTTGGTGAAATCGAGGT
47878153 TAAAAATGGAATTTT
1 TAAAAATGGAATTTT
47878168 GGAGAGTTTG
Statistics
Matches: 143, Mismatches: 28, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
27 11 0.08
28 23 0.16
29 29 0.20
30 46 0.32
31 23 0.16
32 11 0.08
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (30 bp):
TAAAAATGGAATTTTTGGTGAAATCGAGGT
Found at i:47879367 original size:3 final size:3
Alignment explanation
Indices: 47879361--47879399 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
47879351 AATATCATAA
47879361 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47879400 AAATAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:47880101 original size:17 final size:17
Alignment explanation
Indices: 47880079--47880141 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
47880069 ATTTAATTTA
47880079 AAATTTAAATTTATAAT
1 AAATTTAAATTTATAAT
*
47880096 AAATTTAAATTT-TATAC
1 AAATTTAAATTTATA-AT
* *
47880113 AAATTTAAATTCAAAAT
1 AAATTTAAATTTATAAT
*
47880130 AAATCTAAATTT
1 AAATTTAAATTT
47880142 TAAAACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 2 0.05
17 35 0.92
18 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTAAATTTATAAT
Found at i:47880117 original size:34 final size:34
Alignment explanation
Indices: 47880079--47880143 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
47880069 ATTTAATTTA
* * *
47880079 AAATTTAAATTTATAATAAATTTAAATTTTATAC
1 AAATTTAAATTCAAAATAAATCTAAATTTTATAC
47880113 AAATTTAAATTCAAAATAAATCTAAATTTTA
1 AAATTTAAATTCAAAATAAATCTAAATTTTA
47880144 AAACTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (34 bp):
AAATTTAAATTCAAAATAAATCTAAATTTTATAC
Found at i:47880505 original size:8 final size:8
Alignment explanation
Indices: 47880492--47880519 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
47880482 CAAATGCATG
47880492 TTGTAATA
1 TTGTAATA
47880500 TTGTAATA
1 TTGTAATA
47880508 TTGTAATA
1 TTGTAATA
47880516 TTGT
1 TTGT
47880520 GCATGTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (8 bp):
TTGTAATA
Found at i:47880693 original size:26 final size:26
Alignment explanation
Indices: 47880658--47880717 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
47880648 AAAATTGGTA
* * *
47880658 AAAAAAAATTTAAACCCTTTAAAATT
1 AAAAAAAATTGAAACCCTTAAAAACT
* *
47880684 AAAAAAAATTGAATCTCTTAAAAACT
1 AAAAAAAATTGAAACCCTTAAAAACT
47880710 AAAAAAAA
1 AAAAAAAA
47880718 AATTATATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAAAAATTGAAACCCTTAAAAACT
Found at i:47883664 original size:20 final size:21
Alignment explanation
Indices: 47883641--47883679 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
47883631 TTAAAACTAT
47883641 TTATATAATTTTAT-AAAATC
1 TTATATAATTTTATCAAAATC
* *
47883661 TTATGTATTTTTATCAAAA
1 TTATATAATTTTATCAAAA
47883680 AAATAAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (21 bp):
TTATATAATTTTATCAAAATC
Found at i:47884046 original size:19 final size:20
Alignment explanation
Indices: 47884018--47884063 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
47884008 ATTATAATTT
47884018 ATTT-TTTTAAAAA-ATAAA
1 ATTTATTTTAAAAAGATAAA
47884036 ATTTATTTTAAAAAGTATAAA
1 ATTTATTTTAAAAAG-ATAAA
*
47884057 AATTATT
1 ATTTATT
47884064 AATTGCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
21 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTATTTTAAAAAGATAAA
Found at i:47885795 original size:12 final size:13
Alignment explanation
Indices: 47885772--47885800 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
47885762 CAACAGATCA
47885772 AAATTCATATATT
1 AAATTCATATATT
47885785 AAATT-ATATATT
1 AAATTCATATATT
47885797 AAAT
1 AAAT
47885801 CAAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTCATATATT
Found at i:47891617 original size:17 final size:17
Alignment explanation
Indices: 47891587--47891626 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
47891577 TGAAATTTGG
*
47891587 TTTATAATAGATAATAT
1 TTTATAATAAATAATAT
*
47891604 TTTATGATAAATAATAT
1 TTTATAATAAATAATAT
*
47891621 CTTATA
1 TTTATA
47891627 TGGACTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (17 bp):
TTTATAATAAATAATAT
Found at i:47892746 original size:4 final size:4
Alignment explanation
Indices: 47892737--47892765 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
47892727 TTGTGTGCAA
47892737 GATT GATT GATT GATT GATT GATT GATT G
1 GATT GATT GATT GATT GATT GATT GATT G
47892766 CTGAATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GATT
Found at i:47893520 original size:43 final size:43
Alignment explanation
Indices: 47893456--47893598 Score: 261
Period size: 43 Copynumber: 3.3 Consensus size: 43
47893446 GCGTTTTCCA
**
47893456 ATAAAATAA-ATAAATCAATTTCCACTTGATGAAGTTATTTTC
1 ATAAAATAAGATTCATCAATTTCCACTTGATGAAGTTATTTTC
47893498 ATAAAATAAGATTCATCAATTTCCACTTGATGAAGTTATTTTC
1 ATAAAATAAGATTCATCAATTTCCACTTGATGAAGTTATTTTC
47893541 ATAAAATAAGATTCATCAATTTCCACTTGATGAAGTTATTTTC
1 ATAAAATAAGATTCATCAATTTCCACTTGATGAAGTTATTTTC
47893584 ATAAAATAAGATTCA
1 ATAAAATAAGATTCA
47893599 GAAAATACAG
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
42 9 0.09
43 89 0.91
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (43 bp):
ATAAAATAAGATTCATCAATTTCCACTTGATGAAGTTATTTTC
Found at i:47896770 original size:2 final size:2
Alignment explanation
Indices: 47896765--47896811 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47896755 TATATATATA
47896765 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
47896807 TG TG T
1 TG TG T
47896812 AATAAGGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:47898386 original size:26 final size:27
Alignment explanation
Indices: 47898314--47898390 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
47898304 CGTTCTTTAT
*
47898314 ATATTCTTTA-AAAT-TTTTAAATTTTT
1 ATATT-TTTATAAATATTTTAAATTTTG
* *
47898340 ATAATTTTT-TAAA-AATATAAATTTTG
1 AT-ATTTTTATAAATATTTTAAATTTTG
47898366 AT-TTTTTATAAATATTTTAAATTTT
1 ATATTTTTATAAATATTTTAAATTTT
47898391 AAAAATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 5 0.12
25 4 0.10
26 29 0.71
27 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
ATATTTTTATAAATATTTTAAATTTTG
Found at i:47898390 original size:19 final size:19
Alignment explanation
Indices: 47898320--47898410 Score: 54
Period size: 18 Copynumber: 5.2 Consensus size: 19
47898310 TTATATATTC
47898320 TTTA-AAAT-TTTTAAATT
1 TTTATAAATATTTTAAATT
*
47898337 TTTAT-AATTTTTTAAA--
1 TTTATAAATATTTTAAATT
** * *
47898353 AATAT-AA-ATTTTGATTT
1 TTTATAAATATTTTAAATT
47898370 TTTATAAATATTTTAAA-T
1 TTTATAAATATTTTAAATT
* *
47898388 TTTAAAAATTATTTTTAATT
1 TTTATAAA-TATTTTAAATT
47898408 TTT
1 TTT
47898411 GAAATTTATT
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
15 5 0.09
16 5 0.09
17 10 0.18
18 17 0.31
19 14 0.25
20 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTATAAATATTTTAAATT
Found at i:47898396 original size:18 final size:19
Alignment explanation
Indices: 47898369--47898409 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47898359 AATTTTGATT
*
47898369 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
47898387 TTTTAAAAATTATTTTTAA
1 TTTTAAAAATTATTTTAAA
47898406 TTTT
1 TTTT
47898410 TGAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:47898429 original size:21 final size:20
Alignment explanation
Indices: 47898380--47898432 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
47898370 TTTATAAATA
* *
47898380 TTTTAAATTTTAAAAATTAT
1 TTTTAATTTTTGAAAATTAT
*
47898400 TTTTAATTTTTGAAATTTAT
1 TTTTAATTTTTGAAAATTAT
47898420 TTTGTAATTTTTG
1 TTT-TAATTTTTG
47898433 TTTAGAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTAATTTTTGAAAATTAT
Found at i:47898430 original size:20 final size:19
Alignment explanation
Indices: 47898369--47898430 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
47898359 AATTTTGATT
* *
47898369 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTTAA
47898387 TTTTAAAAATTATTTTTAA
1 TTTTAAAAATTATTTTTAA
* *
47898406 TTTTTGAAATTTATTTTGTAA
1 -TTTTAAAAATTATTTT-TAA
47898427 TTTT
1 TTTT
47898431 TGTTTAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 18 0.49
21 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTAAAAATTATTTTTAA
Found at i:47900567 original size:2 final size:2
Alignment explanation
Indices: 47900560--47900591 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47900550 CCACCAATTG
*
47900560 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47900592 CACACACACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47919210 original size:27 final size:26
Alignment explanation
Indices: 47919180--47919243 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
47919170 TAATCTTCCA
47919180 TTATTTTTTATAACTTTT-ATCTAATTT
1 TTATTTTTTAT-ACTTTTAAT-TAATTT
* * *
47919207 TTATATTTTATATTTTTAATTCATTT
1 TTATTTTTTATACTTTTAATTAATTT
47919233 TATATTTTTTA
1 T-TATTTTTTA
47919244 AATGATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.69
Consensus pattern (26 bp):
TTATTTTTTATACTTTTAATTAATTT
Found at i:47919261 original size:20 final size:19
Alignment explanation
Indices: 47919211--47919262 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
47919201 TAATTTTTAT
*
47919211 ATTTTAT-ATTTTTAATTC
1 ATTTTATAATTTTTAAATC
* *
47919229 ATTTTATATTTTTTAAATG
1 ATTTTATAATTTTTAAATC
47919248 ATTTTCATAATTTTT
1 ATTTT-ATAATTTTT
47919263 TTATAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 7 0.25
19 13 0.46
20 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTATAATTTTTAAATC
Found at i:47919302 original size:18 final size:18
Alignment explanation
Indices: 47919275--47919325 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
47919265 ATAACTTTTA
*
47919275 ATAATATATTTATATAATT
1 ATAATTTATTTATAT-ATT
* *
47919294 -TAATTTATTTGTATTTT
1 ATAATTTATTTATATATT
*
47919311 ATAATTTATTAATAT
1 ATAATTTATTTATAT
47919326 GAAATGTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATAATTTATTTATATATT
Found at i:47924772 original size:15 final size:15
Alignment explanation
Indices: 47924752--47924797 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
47924742 ATTCATCAAC
47924752 ATTTATTTAATTAAA
1 ATTTATTTAATTAAA
47924767 ATTTATTTAATTAAAA
1 ATTTATTTAATT-AAA
*
47924783 ATTAATTATAATTAA
1 ATTTATT-TAATTAA
47924798 CAAGGTTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 12 0.43
16 11 0.39
17 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTTAATTAAA
Found at i:47926615 original size:29 final size:28
Alignment explanation
Indices: 47926583--47926669 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 28
47926573 AGAAAGTTCA
47926583 AGGGTGAAATGGTAATTTTTGGTGAAATT
1 AGGGTGAAATGGTAATTTTT-GTGAAATT
* *
47926612 AGGGTCAAAAAT-G-AAATTTTG-GAAAGTTT
1 AGGGT--GAAATGGTAATTTTTGTGAAA--TT
47926641 AGGGGTGAAATGGTAATTTTTTGTGAAAT
1 A-GGGTGAAATGGTAA-TTTTTGTGAAAT
47926670 CGAGGTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 17
0.68 0.06 0.26
Matches are distributed among these distances:
27 4 0.09
28 5 0.11
29 15 0.33
30 8 0.18
31 9 0.20
32 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.36
Consensus pattern (28 bp):
AGGGTGAAATGGTAATTTTTGTGAAATT
Found at i:47926768 original size:59 final size:58
Alignment explanation
Indices: 47926523--47926778 Score: 269
Period size: 59 Copynumber: 4.3 Consensus size: 58
47926513 TTGGACTTGT
* * * * * **
47926523 GGGGGCAAAATAGTAATTTTTGGTAAAATCGGGACTTAAAATGGAATTTAAGAAAGTTC
1 GGGGGCAAAATGGTAATTTTTGGTGAAATCGGGTC-AAAAATGAAATTTTGGAAAGTTC
** ** * *
47926582 AAGGGTGAAATGGTAATTTTTGGTGAAATTAGGGTCAAAAATGAAATTTTGGAAAGTTT
1 GGGGGCAAAATGGTAATTTTTGGTGAAA-TCGGGTCAAAAATGAAATTTTGGAAAGTTC
* ** * * *
47926641 AGGGGTGAAATGGTAATTTTTTGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTT
1 GGGGGCAAAATGGTAATTTTTGGTGAAATCG-GGTCAAAAATGAAATTTTGGAAAGTTC
* * *
47926700 GGGGACAAAATGGTGATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTC
1 GGGGGCAAAATGGTAATTTTTGGTGAAATC-GGGTCAAAAATGAAATTTTGGAAAGTTC
*
47926759 GGGGGCAAAATGGTGATTTT
1 GGGGGCAAAATGGTAATTTT
47926779 GGAAAGTTTG
Statistics
Matches: 167, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.01
59 159 0.95
60 6 0.04
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (58 bp):
GGGGGCAAAATGGTAATTTTTGGTGAAATCGGGTCAAAAATGAAATTTTGGAAAGTTC
Found at i:47926807 original size:29 final size:28
Alignment explanation
Indices: 47926613--47926894 Score: 110
Period size: 29 Copynumber: 9.6 Consensus size: 28
47926603 GGTGAAATTA
*
47926613 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
1 GGGTC-AAAATGTAATTTTGGAAAGTTT-G
* *
47926643 GGGT-GAAATGGTAATTTTTTGTGAAA--TCG
1 GGGTCAAAAT-GTAA--TTTTG-GAAAGTTTG
* * *
47926672 AGGTTAAAAATGAAATTTTGGAAAGTTTG
1 -GGGTCAAAATGTAATTTTGGAAAGTTTG
* * **
47926701 GGGACAAAATGGTGATTTTTGGTGAAA--TCA
1 GGGTCAAAAT-GT-AATTTT-G-GAAAGTTTG
* *
47926731 GGGTCAAAAATGGAATTTTGGAAAGTTCG
1 GGGTC-AAAATGTAATTTTGGAAAGTTTG
* *
47926760 GGGGCAAAATGGTGATTTTGGAAAGTTTG
1 GGGTCAAAAT-GTAATTTTGGAAAGTTTG
* **
47926789 TGGTCAAAATGTAATTTTTAAAAAGTTTTG
1 GGGTCAAAATGTAA-TTTTGGAAAG-TTTG
* * * * *
47926819 GGGT-TAAATATAATTTTAGAGAATTTTAA
1 GGGTCAAAATGTAATTTTGGA-AAGTTT-G
* *
47926848 GGGTC-AAATGTAATTTTTAGAAAGTTTTA
1 GGGTCAAAATGTAA-TTTTGGAAAG-TTTG
* *
47926877 GGGTTAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
47926895 AAAGAATTTT
Statistics
Matches: 191, Mismatches: 37, Indels: 49
0.69 0.13 0.18
Matches are distributed among these distances:
27 8 0.04
28 34 0.18
29 80 0.42
30 46 0.24
31 15 0.08
32 8 0.04
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
GGGTCAAAATGTAATTTTGGAAAGTTTG
Found at i:47926857 original size:58 final size:60
Alignment explanation
Indices: 47926790--47926915 Score: 193
Period size: 59 Copynumber: 2.1 Consensus size: 60
47926780 GAAAGTTTGT
* *
47926790 GGTCAAAATGTAATTTTTAAAAAGTTTTGGGGTT-AAATATAATTTTAGAGAATTTTAAG
1 GGTCAAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATATAATTTTAAAGAATTTTAAG
* *
47926849 GGTC-AAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTAAAGAATTTTAGG
1 GGTCAAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATATAATTTTAAAGAATTTTAAG
*
47926908 GGTTAAAA
1 GGTCAAAA
47926916 CATTTTTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
58 27 0.45
59 30 0.50
60 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (60 bp):
GGTCAAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATATAATTTTAAAGAATTTTAAG
Found at i:47926911 original size:30 final size:30
Alignment explanation
Indices: 47926794--47926915 Score: 112
Period size: 29 Copynumber: 4.1 Consensus size: 30
47926784 GTTTGTGGTC
*
47926794 AAAATGTAATTTTTAAAAAGTTTT-GGGGTT
1 AAAATATAATTTTTAAAAA-TTTTAGGGGTT
* *
47926824 -AAATATAA-TTTTAGAGAATTTTAAGGG-T
1 AAAATATAATTTTTA-AAAATTTTAGGGGTT
* * *
47926852 CAAATGTAATTTTTAGAAAGTTTTA-GGGTT
1 AAAATATAATTTTTA-AAAATTTTAGGGGTT
47926882 AAAATATAA-TTTTAAAGAATTTTAGGGGTT
1 AAAATATAATTTTTAAA-AATTTTAGGGGTT
47926912 AAAA
1 AAAA
47926916 CATTTTTTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
28 12 0.16
29 34 0.45
30 30 0.39
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.40
Consensus pattern (30 bp):
AAAATATAATTTTTAAAAATTTTAGGGGTT
Found at i:47927942 original size:86 final size:85
Alignment explanation
Indices: 47927803--47928046 Score: 337
Period size: 86 Copynumber: 2.8 Consensus size: 85
47927793 ATTTGGCCTT
* * * * * * *
47927803 CTTCTCCGTGTCTCATCAGGAAGATGACTGCGTCA-TCTATTTCAATCCGCTTCTCTGTATCTCA
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACT-TGTTTTAATTCGCTTCTCTG-ATCTCC
47927867 TCAGGAAGACGAATTTGATCCA
64 TCAGGAAGACGAATTTGATCCA
* *
47927889 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCACTTCTCTAGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCT-GATCTCCT
* *
47927954 TAGGAAGACGAATTTGGTCCA
65 CAGGAAGACGAATTTGATCCA
*
47927975 CTTCACAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCT-GATCTCCT
47928040 CAGGAAG
65 CAGGAAG
47928047 CTGGGGTTCG
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
86 138 0.99
87 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (85 bp):
CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGATCTCCTC
AGGAAGACGAATTTGATCCA
Found at i:47928297 original size:205 final size:206
Alignment explanation
Indices: 47927889--47928458 Score: 860
Period size: 207 Copynumber: 2.8 Consensus size: 206
47927879 ATTTGATCCA
* *
47927889 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCACTTCTCTAGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
* * * * *
47927954 TAGGAAGACGAATTTGGTCCACTTCACAGTGTCTCATCAGGAAGATGACCGCA-TCACTTG-TTT
66 TAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCT-AAC-CATTTA-TTGCTTC
* ** * * * *
47928017 TAATTCGCTTCTCTG-GATCTCCTCAGGAAGCTGGGGTTCGAAGATTTGCTCCTATTTGAGCGTG
128 GACCT-GCTTCTCAGTG-TCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATATTTGAGCGTG
47928081 GGTTTGATTTGGTCTT
191 GGTTTGATTTGGTCTT
* * *
47928097 CTTCTCTGTGTCTCATCAGGAAGATGACCGCA-CACTTGTTTTAATTCGCTTCTTTGGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
*
47928161 TAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATTAGGAAGCTAACCATTTATTGCTTCGAC
66 TAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTATTGCTTCGAC
47928226 CTGCTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATATTTGAGCGTGGGTTT
131 CTGCTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATATTTGAGCGTGGGTTT
47928291 GATTTGGTCTT
196 GATTTGGTCTT
47928302 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
* * *
47928367 CAGAAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTGCTTCGA
66 TAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACC-ATTTATTGCTTCGA
*
47928432 CCTGCTTCTCAGTATCTCATCAGGAAG
130 CCTGCTTCTCAGTGTCTCATCAGGAAG
47928459 ATGACCGCCT
Statistics
Matches: 331, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
205 104 0.31
206 86 0.26
207 111 0.34
208 30 0.09
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (206 bp):
CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
TAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTATTGCTTCGAC
CTGCTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATATTTGAGCGTGGGTTT
GATTTGGTCTT
Found at i:47928987 original size:97 final size:98
Alignment explanation
Indices: 47928886--47929079 Score: 293
Period size: 97 Copynumber: 2.0 Consensus size: 98
47928876 GATCCGCTGT
* *
47928886 CGCGGCTTAGATCTTTCTCTTCATATCTTAGTGGTACTGGATCCACCGTTGCGGCTTAGAT-TTT
1 CGCGGCTTAGATCTTTCCCTTCATATCTTAGTGGTACTAGATCCACCGTTGCGGCTTAGATCTTT
*
47928950 TCTCTTG-TATCTTCGTGGTACTGGATCCGTCGA
66 CCT-TTGATATCTTCGTGGTACTGGATCCGTCGA
* * * *
47928983 CGCGGCTTAGATCTTTCCCTTCATGTCTTCGTGGTACTAGATTCATCGTTGCGGCTTAGATCTTT
1 CGCGGCTTAGATCTTTCCCTTCATATCTTAGTGGTACTAGATCCACCGTTGCGGCTTAGATCTTT
*
47929048 CCTTTGATGTCTTCGTGGTACTGGATCCGTCG
66 CCTTTGATATCTTCGTGGTACTGGATCCGTCG
47929080 TTACGACTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
97 58 0.67
98 29 0.33
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.39
Consensus pattern (98 bp):
CGCGGCTTAGATCTTTCCCTTCATATCTTAGTGGTACTAGATCCACCGTTGCGGCTTAGATCTTT
CCTTTGATATCTTCGTGGTACTGGATCCGTCGA
Found at i:47929081 original size:49 final size:50
Alignment explanation
Indices: 47928855--47929098 Score: 248
Period size: 49 Copynumber: 5.0 Consensus size: 50
47928845 AAACCTTTCA
* * * * *
47928855 CTTCAAATCTTTGTGATATTGGATCCG-CTGTCGCGGCTTAGATCTTT-CT
1 CTTCATATCTTCGTGGTACTGGATCCGTC-GTTGCGGCTTAGATCTTTCCT
* ** *
47928904 CTTCATATCTTAGTGGTACTGGATCCACCGTTGCGGCTTAGAT-TTTTCT
1 CTTCATATCTTCGTGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCCT
* **
47928953 CTT-GTATCTTCGTGGTACTGGATCCGTCGACGCGGCTTAGATCTTTCC-
1 CTTCATATCTTCGTGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCCT
* * * *
47929001 CTTCATGTCTTCGTGGTACTAGATTCATCGTTGCGGCTTAGATCTTTCCT
1 CTTCATATCTTCGTGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCCT
* * * * *
47929051 -TTGATGTCTTCGTGGTACTGGATCCGTCGTTACGACTTAGACCTTTCC
1 CTTCATATCTTCGTGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCC
47929099 CTTTTGTCTT
Statistics
Matches: 163, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
48 39 0.24
49 123 0.75
50 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (50 bp):
CTTCATATCTTCGTGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCCT
Found at i:47931400 original size:58 final size:59
Alignment explanation
Indices: 47931296--47931610 Score: 483
Period size: 59 Copynumber: 5.4 Consensus size: 59
47931286 GGACTCGCGA
* * * * **
47931296 GGGGCAAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
47931355 GAGGTAAAATGGTAA-TTTTGGTGAAATCG-GTGTTAAAAATAGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAG-GTTAAAAATGGAATTTTGGAAAGTTTG
*
47931413 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
47931472 GGGGTAAAATGGTAATTTTTGGTAAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
*
47931531 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TAAAAATGGAATTTTGAAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
*
47931589 GGGGTAAAATGGTAATCTTTGG
1 GGGGTAAAATGGTAATTTTTGG
47931611 AAATCCAAAG
Statistics
Matches: 235, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
57 1 0.00
58 95 0.40
59 138 0.59
60 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:47931478 original size:117 final size:117
Alignment explanation
Indices: 47931296--47931610 Score: 490
Period size: 117 Copynumber: 2.7 Consensus size: 117
47931286 GGACTCGCGA
* * * * * *
47931296 GGGGCAAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGGTTCAGAGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
* *
47931361 AAATGGTAATTTTGGTGAAATC-GGTGTTAAAAATAGAATTTTGGAAAGTTTG
66 AAATGGTAATTTTGGTAAAATCAAG-GTTAAAAATAGAATTTTGGAAAGTTTG
47931413 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
*
47931478 AAATGGTAATTTTTGGTAAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTG
66 AAATGGTAA-TTTTGGTAAAATCAAGGTTAAAAATAGAATTTTGGAAAGTTTG
* *
47931531 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TAAAAATGGAATTTTGAAAAGTTTGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
47931595 AAATGGTAATCTTTGG
66 AAATGGTAAT-TTTGG
47931611 AAATCCAAAG
Statistics
Matches: 184, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
116 1 0.01
117 111 0.60
118 71 0.39
119 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
AAATGGTAATTTTGGTAAAATCAAGGTTAAAAATAGAATTTTGGAAAGTTTG
Found at i:47932580 original size:13 final size:13
Alignment explanation
Indices: 47932551--47932594 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
47932541 TTAATATTGA
* *
47932551 TATTAATTATAAA
1 TATTAATTATTAT
47932564 TATTAATTATTAT
1 TATTAATTATTAT
*
47932577 TATTTATTATTAT
1 TATTAATTATTAT
*
47932590 AATTA
1 TATTA
47932595 TTACTAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTAATTATTAT
Found at i:47933391 original size:6 final size:6
Alignment explanation
Indices: 47933382--47933450 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
47933372 TTAATATTAT
**
47933382 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAGA --TAAA TTTAAA AATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
*
47933427 TTTAAA ATT-AA TTTAAA CTTTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA
47933451 AAATCAAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
4 3 0.06
5 11 0.22
6 29 0.58
7 7 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:47933391 original size:17 final size:16
Alignment explanation
Indices: 47933382--47933450 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 16
47933372 TTAATATTAT
47933382 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
*
47933398 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-TTAAA
47933415 TTTAAA---AA-TAAA
1 TTTAAATTTAATTAAA
*
47933427 TTTAAAATTAATTTAAA
1 TTTAAATTTAA-TTAAA
47933444 CTTTAAA
1 -TTTAAA
47933451 AAATCAAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
12 10 0.22
14 2 0.04
15 2 0.04
16 11 0.24
17 14 0.31
18 6 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:47933425 original size:12 final size:11
Alignment explanation
Indices: 47933400--47933443 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
47933390 TAATTAAATT
*
47933400 TAAATTTAAGA
1 TAAATTTAAAA
47933411 TAAATTTAAAAA
1 TAAATTT-AAAA
47933423 TAAATTTAAAA
1 TAAATTTAAAA
*
47933434 TTAATTTAAA
1 TAAATTTAAA
47933444 CTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:47933431 original size:29 final size:30
Alignment explanation
Indices: 47933394--47933452 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
47933384 TAAATTTAAT
*
47933394 TAAATTTAAATTTAAGATAAA-TTTAAAAA
1 TAAATTTAAAATTAAGATAAACTTTAAAAA
**
47933423 TAAATTTAAAATTAATTTAAACTTTAAAAA
1 TAAATTTAAAATTAAGATAAACTTTAAAAA
47933453 ATCAAAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAATTTAAAATTAAGATAAACTTTAAAAA
Found at i:47934046 original size:6 final size:6
Alignment explanation
Indices: 47934037--47934102 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
47934027 CGTCCTCTCC
* * * *
47934037 TTTTCT TTTTCTTT TTTTCCT TTTTCCT TTTTGT TTTTGT TTTTCT TCTTGT
1 TTTTCT TTTTC--T TTTT-CT TTTT-CT TTTTCT TTTTCT TTTTCT TTTTCT
47934089 TTTTC- TTTTCT TTT
1 TTTTCT TTTTCT TTT
47934103 ATTCATTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 5 0.10
6 27 0.54
7 12 0.24
8 5 0.10
9 1 0.02
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:47934088 original size:18 final size:19
Alignment explanation
Indices: 47934045--47934097 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
47934035 CCTTTTCTTT
47934045 TTCTT-TTTTTCCTTTTTCC
1 TTCTTGTTTTT-CTTTTTCC
* *
47934064 TTTTTGTTTTTGTTTTT-C
1 TTCTTGTTTTTCTTTTTCC
47934082 TTCTTGTTTTTCTTTT
1 TTCTTGTTTTTCTTTT
47934098 CTTTTATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 15 0.52
19 9 0.31
20 5 0.17
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (19 bp):
TTCTTGTTTTTCTTTTTCC
Found at i:47939749 original size:59 final size:59
Alignment explanation
Indices: 47939686--47939859 Score: 233
Period size: 59 Copynumber: 2.9 Consensus size: 59
47939676 TTCGAGGGCA
** * * *
47939686 AAATGGTAATTTTTTAT-ATAATCGAGGTTTAAAATGGAATTTTAGAAAGTTTGGGGGTG
1 AAATGGTAATTTTTGGTGA-AATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTG
* * *
47939745 AAATGGTAATTTTTGGTGAAATAGAGGTCAAAAATAGAATTTTGGAAAGTTCGGGGGTG
1 AAATGGTAATTTTTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTG
* * *
47939804 AAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGAAATTTTGGAAAGGTTGGGG
1 AAATGGTAATTTTTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGG
47939860 TCAAAATATA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 99 0.99
60 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (59 bp):
AAATGGTAATTTTTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTG
Found at i:47939891 original size:59 final size:60
Alignment explanation
Indices: 47939828--47939984 Score: 189
Period size: 59 Copynumber: 2.6 Consensus size: 60
47939818 GGTGAAATTG
47939828 AGGTTAAAAATGA-AATTTTGGA-AAGGTT-GGGGTCAAAATATAATTTTCAAAAAGTTTTA
1 AGGTTAAAAAT-ATAATTTTGGAGAA-GTTCGGGGTCAAAATATAATTTTCAAAAAGTTTTA
* * *
47939887 AGGTT-AAAATATAATTTTGGAGAAGTTCGGGGTCAAAATGTAATTTTTAGAAAGTTTT-
1 AGGTTAAAAATATAATTTTGGAGAAGTTCGGGGTCAAAATATAATTTTCAAAAAGTTTTA
* * * *
47939945 AGGGTCAAAATATAATTTTAGAGAATTTCGGGAGTCAAAA
1 AGGTTAAAAATATAATTTTGGAGAAGTTCGGG-GTCAAAA
47939985 CTTTATTTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
57 1 0.01
58 21 0.24
59 58 0.67
60 7 0.08
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (60 bp):
AGGTTAAAAATATAATTTTGGAGAAGTTCGGGGTCAAAATATAATTTTCAAAAAGTTTTA
Found at i:47939897 original size:30 final size:30
Alignment explanation
Indices: 47939857--47939963 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
47939847 GGAAAGGTTG
47939857 GGGTCAAAATATAATTTTCAAAAAGTTTTA
1 GGGTCAAAATATAATTTTCAAAAAGTTTTA
* * ** * **
47939887 AGGTTAAAATATAATTTTGGAGAAG-TTCG
1 GGGTCAAAATATAATTTTCAAAAAGTTTTA
* * *
47939916 GGGTCAAAATGTAATTTTTAGAAAGTTTTA
1 GGGTCAAAATATAATTTTCAAAAAGTTTTA
47939946 GGGTCAAAATATAATTTT
1 GGGTCAAAATATAATTTT
47939964 AGAGAATTTC
Statistics
Matches: 59, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
29 20 0.34
30 39 0.66
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTCAAAAAGTTTTA
Found at i:47939941 original size:29 final size:28
Alignment explanation
Indices: 47939841--47939984 Score: 110
Period size: 30 Copynumber: 4.9 Consensus size: 28
47939831 TTAAAAATGA
*
47939841 AATTTTGGAAAGGTT-GGGGTCAAAATAT
1 AATTTTAGAAA-GTTCGGGGTCAAAATAT
* *** *
47939869 AATTTTCAAAAAGTTTTAAGGTTAAAATAT
1 AATTTT-AGAAAG-TTCGGGGTCAAAATAT
* *
47939899 AATTTTGGAGAAGTTCGGGGTCAAAATGT
1 AATTTTAGA-AAGTTCGGGGTCAAAATAT
**
47939928 AATTTTTAGAAAGTTTTAGGGTCAAAATAT
1 AA-TTTTAGAAAG-TTCGGGGTCAAAATAT
*
47939958 AATTTTAGAGAATTTCGGGAGTCAAAA
1 AATTTTAGA-AAGTTCGGG-GTCAAAA
47939985 CTTTATTTTT
Statistics
Matches: 89, Mismatches: 19, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
28 7 0.08
29 33 0.37
30 49 0.55
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.35
Consensus pattern (28 bp):
AATTTTAGAAAGTTCGGGGTCAAAATAT
Found at i:47940809 original size:20 final size:18
Alignment explanation
Indices: 47940784--47940834 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
47940774 GATCTAGGAA
47940784 TTTAAAATCATTTCATTTTT-
1 TTTAAAATC-TTT--TTTTTG
47940804 TTTAAACATCTTTTTTTTG
1 TTTAAA-ATCTTTTTTTTG
47940823 TTTAAAA-CTTTT
1 TTTAAAATCTTTT
47940835 GATTTTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 6 0.21
20 9 0.31
21 3 0.10
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTAAAATCTTTTTTTTG
Found at i:47941070 original size:18 final size:19
Alignment explanation
Indices: 47941037--47941081 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
47941027 TTATTACTAT
47941037 TTATTATTATTTAAAAAAA
1 TTATTATTATTTAAAAAAA
*
47941056 TTATTATTA-TTAAAATAA
1 TTATTATTATTTAAAAAAA
*
47941074 TAATTATT
1 TTATTATT
47941082 GCTATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTATTATTTAAAAAAA
Found at i:47941830 original size:12 final size:11
Alignment explanation
Indices: 47941805--47941859 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
47941795 ACATAAATTC
47941805 AAATTTAAAAT
1 AAATTTAAAAT
*
47941816 AAATTTAAACCT
1 AAATTTAAA-AT
* *
47941828 AAA-ATAAATTT
1 AAATTTAAA-AT
47941839 AAATTTAAAAT
1 AAATTTAAAAT
47941850 AAA-TTAAAAT
1 AAATTTAAAAT
47941860 TTTAAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 7 0.19
11 21 0.58
12 8 0.22
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:47941859 original size:23 final size:23
Alignment explanation
Indices: 47941815--47941872 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
47941805 AAATTTAAAA
*
47941815 TAAATTTAAACCTAAAATAAA-TT
1 TAAATTTAAA-ATAAAATAAATTT
*
47941838 TAAATTTAAAATAAATTAAAATTT
1 TAAATTTAAAATAAAAT-AAATTT
*
47941862 TAAAATTAAAA
1 TAAATTTAAAA
47941873 ATTAGATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 13 0.43
24 12 0.40
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATTTAAAATAAAATAAATTT
Found at i:47941861 original size:17 final size:17
Alignment explanation
Indices: 47941783--47941867 Score: 98
Period size: 17 Copynumber: 4.9 Consensus size: 17
47941773 AATATTAAAC
* * *
47941783 AATTTTAATTCAACATA
1 AATTTAAATTTAAAATA
*
47941800 AATTCAAATTTAAAATA
1 AATTTAAATTTAAAATA
**
47941817 AATTTAAACCTAAAATA
1 AATTTAAATTTAAAATA
47941834 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
47941851 AATTAAAATTTTAAAAT
1 AATTTAAA-TTTAAAAT
47941868 TAAAAATTAG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
17 49 0.86
18 8 0.14
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:47942237 original size:11 final size:11
Alignment explanation
Indices: 47942223--47942290 Score: 55
Period size: 11 Copynumber: 5.8 Consensus size: 11
47942213 TATTTTAATC
47942223 TTAAATTTATT
1 TTAAATTTATT
*
47942234 TTAAATTCAATT
1 TTAAATT-TATT
* *
47942246 TTAATTTTAAT
1 TTAAATTTATT
* *
47942257 TTGAATTTAAT
1 TTAAATTTATT
47942268 TTAAATTTAATAT
1 TTAAATTT-AT-T
47942281 TATAAATTTA
1 T-TAAATTTA
47942291 AAAAAGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 25 0.56
12 10 0.22
13 3 0.07
14 7 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:47942248 original size:17 final size:16
Alignment explanation
Indices: 47942203--47942274 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 16
47942193 AACCATTTGA
*
47942203 AAATTAAATTTATTTT
1 AAATTCAATTTATTTT
* *
47942219 AATCTTAAATTTATTTT
1 AA-ATTCAATTTATTTT
47942236 AAATTCAATTTTAATTTT
1 AAATTCAA-TTT-ATTTT
* * *
47942254 AATTTGAATTTAATTT
1 AAATTCAATTTATTTT
47942270 AAATT
1 AAATT
47942275 TAATATTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 14 0.30
17 21 0.46
18 11 0.24
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (16 bp):
AAATTCAATTTATTTT
Found at i:47942254 original size:23 final size:23
Alignment explanation
Indices: 47942223--47942275 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
47942213 TATTTTAATC
* *
47942223 TTAAATTTATTTTAAATTCAATT
1 TTAATTTTAATTTAAATTCAATT
* *
47942246 TTAATTTTAATTTGAATTTAATT
1 TTAATTTTAATTTAAATTCAATT
*
47942269 TAAATTT
1 TTAATTT
47942276 AATATTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTAATTTTAATTTAAATTCAATT
Found at i:47942276 original size:6 final size:6
Alignment explanation
Indices: 47942206--47942292 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
47942196 CATTTGAAAA
* * * *
47942206 TTAAAT TT--AT TTTAAT CTTAAAT TT-ATT TTAAA- TTCAAT TTTAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
47942251 TTTAAT TTGAAT TT-AAT TTAAAT TTAATAT TATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT T-TAAAT TTAAA
47942293 AAAGAAAAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.06
5 13 0.19
6 36 0.54
7 11 0.16
8 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:47943083 original size:12 final size:12
Alignment explanation
Indices: 47943066--47943096 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
47943056 TGAAATATTA
*
47943066 AATAATATTAGT
1 AATAATATTAAT
47943078 AATAATATTAAT
1 AATAATATTAAT
47943090 AATAATA
1 AATAATA
47943097 AACATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:47944045 original size:162 final size:159
Alignment explanation
Indices: 47943847--47944212 Score: 511
Period size: 162 Copynumber: 2.3 Consensus size: 159
47943837 AGTTTTCAAT
* * * *
47943847 TTAATCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGTTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACTAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
* * * *
47943912 TTTAGTCCCTGACATTTTTAATTTTTTTTAATTTAATCCCTAAATTAACTTTTATTTAATTACAA
66 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAACTACAA
* *
47943977 AATTGGCCCAAGAATTTTTCAAGGTTTATAAA
131 AATTGGCCC---AATTTTTCAAGATTTACAAA
* * *
47944009 TTAGTCCTTTGACTGTTTGACTGCACTAGGGGCTGCCACATGTCATTTTTTGGCTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACTAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
*
47944074 TTTAGTCTCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAACTACAA
66 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAACTACAA
*
47944139 AATTGGCCCAATTTTTCAAGATTTACAAT
131 AATTGGCCCAATTTTTCAAGATTTACAAA
* * * *
47944168 TTAATCCCTTGACTGCTGGA-TGC-CTGTGGGGCTGCCACGTGTCAC
1 TTAATCCTTTGACTGTTTGACTGCACT-AGGGGCTGCCACGTGTCAC
47944213 CAACTCTTTG
Statistics
Matches: 181, Mismatches: 22, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
157 2 0.01
158 19 0.10
159 33 0.18
162 127 0.70
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (159 bp):
TTAATCCTTTGACTGTTTGACTGCACTAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAACTACAA
AATTGGCCCAATTTTTCAAGATTTACAAA
Found at i:47944286 original size:29 final size:29
Alignment explanation
Indices: 47944254--47944331 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
47944244 CAAATAATCC
*
47944254 AGAAATTGCATTTTGACCCCAAAATTTCA
1 AGAAATTACATTTTGACCCCAAAATTTCA
* * *
47944283 AGAAATTACATTCTGACCTCGAAACTTTCA
1 AGAAATTACATTTTGACC-CCAAAATTTCA
47944313 A-AAATTACCATTTT-ACCCC
1 AGAAATTA-CATTTTGACCCC
47944332 CGAACCTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 25 0.61
30 15 0.37
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (29 bp):
AGAAATTACATTTTGACCCCAAAATTTCA
Found at i:47944376 original size:59 final size:59
Alignment explanation
Indices: 47944311--47944742 Score: 534
Period size: 59 Copynumber: 7.4 Consensus size: 59
47944301 TCGAAACTTT
* * * *
47944311 CAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTTCATTTTTAACCCCGGTTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
47944370 TAAAAATTACCATTTTACTCCCGAACTTTCCAAAACTCCA-TTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
47944428 CAGAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
47944487 CTAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAA-CCCTATTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* *
47944544 CAAAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCCTGATTTCAT
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
** * * * *
47944602 TGAAAATTACCATTTTACCCCTGAACTTTCTAAAATACCATTTTTAACCCCGGTTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * * * * ** *
47944661 CAAAAATTATCGTTTTATCCCCGAACTCTCAAAAATTTTATTTTTTAACCCTGACTTT-AC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTTAACCCCGA-TTTCAC
*
47944721 C-ATAATTACCATTTTACCCCCG
1 CAAAAATTACCATTTTACCCCCG
47944743 GGTGTCCAAA
Statistics
Matches: 318, Mismatches: 49, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
56 13 0.04
57 39 0.12
58 89 0.28
59 160 0.50
60 14 0.04
61 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:47944472 original size:117 final size:114
Alignment explanation
Indices: 47944311--47944740 Score: 533
Period size: 117 Copynumber: 3.7 Consensus size: 114
47944301 TCGAAACTTT
* * * *
47944311 CAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTTCATTTTTAACCCCGGTTTCACTAAAAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACT-AAAA
47944376 TTACCATTTTACTCCCGAACTTTCCAAAACTCCATTTTAACCCCGATTTCAC
65 TTACCATTTTAC-CCCGAACTTTCCAAAA-TCCATTTTAACCCCGATTTCAC
* * *
47944428 CAGAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCTAAAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CTAAAA
*
47944493 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAA-CCCTATTTCAC
65 TTACCATTTTACCC-CGAACTTTCCAAAA-TCCATTTTAACCCCGATTTCAC
* *
47944544 CAAAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCCTGATTTCATTGAAAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACT-AAAA
* *
47944608 TTACCATTTTACCCCTGAACTTTCTAAAATACCATTTTTAACCCCGGTTTCAC
65 TTACCATTTTACCCC-GAACTTTCCAAAAT-CCA-TTTTAACCCCGATTTCAC
* * * * * ** * * *
47944661 CAAAAATTATCGTTTTATCCCCGAACTCTCAAAAATTTTATTTTTTAACCCTGACTTT-ACCATA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTTAACCCCGA-TTTCACTAAA
47944725 ATTACCATTTTACCCC
64 ATTACCATTTTACCCC
47944741 CGGGTGTCCA
Statistics
Matches: 276, Mismatches: 27, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
114 3 0.01
115 62 0.22
116 42 0.15
117 123 0.45
118 29 0.11
119 14 0.05
120 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (114 bp):
CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACTAAAAT
TACCATTTTACCCCGAACTTTCCAAAATCCATTTTAACCCCGATTTCAC
Found at i:47944570 original size:174 final size:174
Alignment explanation
Indices: 47944311--47944742 Score: 550
Period size: 174 Copynumber: 2.5 Consensus size: 174
47944301 TCGAAACTTT
* * ** *
47944311 CAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTTCATTTTTAACCCCGGTTTCACTAAAAA
1 CAAAAATTACCATTTTA-CCCCGAACTTTCAAAAATTTCATTTTTAA-CCCTATTTCACCAAAAA
*
47944376 TTACCATTTTACTCCCGAACTTTCCAAAACTCCA-TTTTAACCCCGATTTCACCAG-AAATTACC
64 TTACCATTTTACCCCCGAAC-TTCCAAAACTCCATTTTTAACCCCGATTTCA-CAGAAAATTACC
* *
47944439 ATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
127 ATTTTACCCCTGAACTTTCCAAAATACCATTTTTAACCCCGATTTCAC
* * *
47944487 CTAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCTATTTCACCAAAAAT
1 CAAAAATTACCATTTTACCC-CGAACTTTCAAAAATTTCATTTTTAACCCTATTTCACCAAAAAT
* * **
47944551 TACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCTGATTTCATTGAAAATTACCATT
65 TACCATTTTACCCCCGAACTTCCAAAACTCCATTTTTAACCCCGATTTCACAGAAAATTACCATT
* *
47944616 TTACCCCTGAACTTTCTAAAATACCATTTTTAACCCCGGTTTCAC
130 TTACCCCTGAACTTTCCAAAATACCATTTTTAACCCCGATTTCAC
* * * * *
47944661 CAAAAATTATCGTTTTATCCCCGAACTCTCAAAAATTTTATTTTTTAACCCTGACTTT-ACC-AT
1 CAAAAATTACCATTTTA-CCCCGAACTTTCAAAAATTTCA-TTTTTAACCCT-A-TTTCACCAAA
47944724 AATTACCATTTTACCCCCG
62 AATTACCATTTTACCCCCG
47944743 GGTGTCCAAA
Statistics
Matches: 224, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
173 13 0.06
174 130 0.58
175 12 0.05
176 62 0.28
177 4 0.02
178 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (174 bp):
CAAAAATTACCATTTTACCCCGAACTTTCAAAAATTTCATTTTTAACCCTATTTCACCAAAAATT
ACCATTTTACCCCCGAACTTCCAAAACTCCATTTTTAACCCCGATTTCACAGAAAATTACCATTT
TACCCCTGAACTTTCCAAAATACCATTTTTAACCCCGATTTCAC
Found at i:47957109 original size:76 final size:76
Alignment explanation
Indices: 47956824--47957564 Score: 996
Period size: 76 Copynumber: 9.9 Consensus size: 76
47956814 TCAGACCAAA
* * * *
47956824 CAAGATCATTTCCTATCTGCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTCATCTCTGAAAT
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
* *
47956888 TGAAGTAGGGG
66 TGAAGTAAGAG
* * * * * *
47956899 CAAAGATCTTTTCCTGA-CTGCTTGAAATTGAATTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 C-AAGATCATTTCCT-ATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAA
47956963 ATTGAAGTAAGAG
64 ATTGAAGTAAGAG
* *
47956976 C-A-A-C--GT-C-ATCCGCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
*
47957034 TGAAGTAATAG
66 TGAAGTAAGAG
*
47957045 CAACG-TCATTTCCTATCCGCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAA
1 CAA-GATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAA
*
47957109 TTGAAATAAGAG
65 TTGAAGTAAGAG
* * *
47957121 C-A-A-C--GT-C-ATCCGCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATGTCTGAAAT
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
47957179 TGAAGTAAGAG
66 TGAAGTAAGAG
* * *
47957190 CAACG-TCATTTCCTATCAGCTTGAAATTGAAGTAAAGTTGGATATTAAGTTTTTATCTCTGAAA
1 CAA-GATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAA
*
47957254 TTGAAGTAAGAA
65 TTGAAGTAAGAG
*
47957266 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
47957331 TGAAGTAAGAG
66 TGAAGTAAGAG
* * *
47957342 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
*
47957407 TGAAGTAAGAA
66 TGAAGTAAGAG
* *
47957418 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
47957483 TGAAGTAAGAG
66 TGAAGTAAGAG
* * *
47957494 CAAGATCATTTCCTATCCTCTTGAAATTGAGGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAA
1 CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTA--TCTCTGAA
47957559 ATTGAA
64 ATTGAA
47957565 AGATGAAGCA
Statistics
Matches: 600, Mismatches: 42, Indels: 45
0.87 0.06 0.07
Matches are distributed among these distances:
68 1 0.00
69 115 0.19
70 4 0.01
71 2 0.00
72 2 0.00
73 2 0.00
74 3 0.00
75 6 0.01
76 415 0.69
77 36 0.06
78 14 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (76 bp):
CAAGATCATTTCCTATCCGCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:47957899 original size:11 final size:11
Alignment explanation
Indices: 47957883--47957938 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
47957873 CATTTGAAAA
*
47957883 TTAAATTTATT
1 TTAAATTTAAT
*
47957894 TTAAATTCAAT
1 TTAAATTTAAT
*
47957905 TTTAATTTGAAT
1 TTAAATTT-AAT
*
47957917 TTGAATTTAAT
1 TTAAATTTAAT
47957928 TTAAATTTAAT
1 TTAAATTTAAT
47957939 ATTATTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:47958747 original size:12 final size:12
Alignment explanation
Indices: 47958730--47958759 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
47958720 TGAAATATTA
*
47958730 AATAATATTAGT
1 AATAATATTAAT
47958742 AATAATATTAAT
1 AATAATATTAAT
47958754 AATAAT
1 AATAAT
47958760 TAACATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:47959701 original size:162 final size:162
Alignment explanation
Indices: 47959519--47959857 Score: 516
Period size: 162 Copynumber: 2.1 Consensus size: 162
47959509 AGTTTTCAAT
* * * *
47959519 TTAATCCTTTGACTGTTTGACTGTACCAGAGGCTGCCATGTGTCACTTTTTGGTTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTACCACGTGTCACTTTTTGGCTTATTTATGCA
* *
47959584 TTTAGTCCCTAACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TTCAGTCCCTAACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTACAA
* *
47959649 AATTGGCCCAAGAATTTTTCAAGGTTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
* * *
47959681 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTACCACGTGTCATTTTTTGGCTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTACCACGTGTCACTTTTTGGCTTATTTATGCA
* * ** *
47959746 TTCAGTCTCTGACATTTTTAATTTGTTTTAATTTAATCTTTAAATCAACTTTTACTTAATTACGA
66 TTCAGTCCCTAACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTACAA
*
47959811 AATTGGCCCAAGAATTTTTCAAGATTTACAAT
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
47959843 TTAATCCCTTGACTG
1 TTAATCCTTTGACTG
47959858 CTGGATGCCT
Statistics
Matches: 158, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 158 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTACCACGTGTCACTTTTTGGCTTATTTATGCA
TTCAGTCCCTAACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:47960019 original size:30 final size:30
Alignment explanation
Indices: 47959960--47960088 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 30
47959950 AAATTTTAAG
* *
47959960 AAATTA-CATTCTGACCCCGAAAC-TTCCAA
1 AAATTACCATT-TTACCCCCAAACTTTCCAA
47959989 AAATTACCATTTTACCCCCAAACTTTCC-A
1 AAATTACCATTTTACCCCCAAACTTTCCAA
* *
47960018 AAATT-CCATTTTTAACCCC-GA-TTTCACCAA
1 AAATTACCA-TTTTACCCCCAAACTTT--CCAA
** *
47960048 AAATTACCATTTTACCCCTGAACTTT-CTA
1 AAATTACCATTTTACCCCCAAACTTTCCAA
47960077 AAA-TACCATTTT
1 AAATTACCATTTT
47960089 TAACCTTGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
27 3 0.04
28 13 0.16
29 38 0.46
30 22 0.27
31 4 0.05
32 3 0.04
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
AAATTACCATTTTACCCCCAAACTTTCCAA
Found at i:47960048 original size:59 final size:59
Alignment explanation
Indices: 47959985--47960220 Score: 260
Period size: 59 Copynumber: 4.0 Consensus size: 59
47959975 CCCGAAACTT
*
47959985 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * **
47960044 CCAAAAATTACCATTTTACCCCTGAACTTTCTAAAATACCATTTTTAACCTTGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * ** *
47960103 CCAAAAATTACCGTTTTACCCCCGAACTCTCAAAAATTCTATTTTTTAACTTCGACTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTTAACCCCGATTTCA
* * ** * * *
47960163 CC-ATAATTACCATTTTGCCCCCG-GGTGTCCAAAATTCTCATTTTCAATCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-CATTTTTAACCCCGATTTCA
47960221 TCATTTTTTC
Statistics
Matches: 147, Mismatches: 28, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
58 23 0.16
59 107 0.73
60 17 0.12
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:47960089 original size:29 final size:28
Alignment explanation
Indices: 47959960--47960140 Score: 97
Period size: 29 Copynumber: 6.2 Consensus size: 28
47959950 AAATTTTAAG
* *
47959960 AAATTA-CATTCTGACCCCGAAACTTCCAA
1 AAATTACCATT-TTACCCCG-AACTTTCAA
* *
47959989 AAATTACCATTTTACCCCCAAACTTTCCA
1 AAATTACCATTTTA-CCCCGAACTTTCAA
47960018 AAATT-CCATTTTTAACCCCG-A-TTTCACCAA
1 AAATTACCA-TTTT-ACCCCGAACTTT---CAA
*
47960048 AAATTACCATTTTACCCCTGAACTTTCTA
1 AAATTACCATTTTACCCC-GAACTTTCAA
**
47960077 AAA-TACCATTTTTAACCTTG-A-TTTCACCAA
1 AAATTACCA-TTTT-ACCCCGAACTTT---CAA
* *
47960107 AAATTACCGTTTTACCCCCGAACTCTCAA
1 AAATTACCATTTTA-CCCCGAACTTTCAA
47960136 AAATT
1 AAATT
47960141 CTATTTTTTA
Statistics
Matches: 118, Mismatches: 14, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
27 6 0.05
28 10 0.08
29 52 0.44
30 36 0.31
31 9 0.08
32 5 0.04
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (28 bp):
AAATTACCATTTTACCCCGAACTTTCAA
Found at i:47960120 original size:30 final size:30
Alignment explanation
Indices: 47960017--47960120 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 30
47960007 CAAACTTTCC
*
47960017 AAAATT-CCATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTTAACCCTGATTTCACCA
* *
47960047 AAAATTACCATTTTACCCCTGAACTTT---CT
1 AAAATTACCATTTTAACCCTG-A-TTTCACCA
*
47960076 AAAA-TACCATTTTTAACCTTGATTTCACCA
1 AAAATTACCA-TTTTAACCCTGATTTCACCA
*
47960106 AAAATTACCGTTTTA
1 AAAATTACCATTTTA
47960121 CCCCCGAACT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 3 0.05
28 6 0.10
29 14 0.24
30 25 0.42
31 8 0.14
32 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCTGATTTCACCA
Found at i:47962581 original size:29 final size:29
Alignment explanation
Indices: 47962549--47962844 Score: 130
Period size: 29 Copynumber: 10.1 Consensus size: 29
47962539 GGTGAAATCA
47962549 GGGTTAAAATGGAATTTTGGAAAGTTT-G
1 GGGTTAAAATGGAATTTTGGAAAGTTTCG
* *
47962577 GGGGTAAAATGGTAATTTTCAGTGAAA---TCA
1 GGGTTAAAATGG-AATTTT--G-GAAAGTTTCG
* *
47962607 GGGTTAAAAATGGAATTTT-AAAAGATTCG
1 GGGTT-AAAATGGAATTTTGGAAAGTTTCG
* *
47962636 GGGGTAAAATGGTAATTTTTGGTAAA--ATCG
1 GGGTTAAAATGG-AA-TTTTGG-AAAGTTTCG
47962666 GGGTTAAAAATGGAATTTTGGAAAG-TTCAG
1 GGGTT-AAAATGGAATTTTGGAAAGTTTC-G
47962696 GGG-T-AAATGGTAATTTTTGGTGAAA---TCG
1 GGGTTAAAATGG-AA-TTTT-G-GAAAGTTTCG
* * *
47962724 AGGTTAAAAATGGAATTTT-AAAAGATTCG
1 GGGTT-AAAATGGAATTTTGGAAAGTTTCG
*
47962753 GGGGTAAAATGGTAATTTTTGATGAAA---TCG
1 GGGTTAAAATGG-AA-TTTTG--GAAAGTTTCG
* *
47962783 GGGTTAAAAATGGAATTTTAG-AAGATTCG
1 GGGTT-AAAATGGAATTTTGGAAAGTTTCG
47962812 AGGG-T-AAATGGTAATTTTTGG-AAGTTTCG
1 -GGGTTAAAATGG-AA-TTTTGGAAAGTTTCG
47962841 GGGT
1 GGGT
47962845 CAGAATGTAG
Statistics
Matches: 210, Mismatches: 19, Indels: 77
0.69 0.06 0.25
Matches are distributed among these distances:
26 8 0.04
27 13 0.06
28 38 0.18
29 63 0.30
30 46 0.22
31 32 0.15
32 7 0.03
33 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (29 bp):
GGGTTAAAATGGAATTTTGGAAAGTTTCG
Found at i:47962639 original size:59 final size:58
Alignment explanation
Indices: 47962525--47962829 Score: 406
Period size: 59 Copynumber: 5.2 Consensus size: 58
47962515 ACCCGAGGGC
* *
47962525 AAAATGGTAATTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAG-TTTGGGGGT
1 AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTT-AAAAGATTCGGGGGT
*
47962582 AAAATGGTAATTTTCAGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGTAATTTT-GGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* * * *
47962641 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCAGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTT-AAAAGATTCGGGGGT
47962700 -AAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* * * *
47962758 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGAGGGT
1 AAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
47962817 -AAATGGTAATTTT
1 AAAATGGTAATTTT
47962830 TGGAAGTTTC
Statistics
Matches: 225, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
57 23 0.10
58 75 0.33
59 118 0.52
60 9 0.04
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
Found at i:47962741 original size:117 final size:116
Alignment explanation
Indices: 47962525--47962832 Score: 471
Period size: 117 Copynumber: 2.6 Consensus size: 116
47962515 ACCCGAGGGC
* *
47962525 AAAATGGTAA-TTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGT-AAATG
**
47962588 GTAATTTTCAGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
64 GTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
*
47962641 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAATGG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC-GGGGTAAATGG
47962706 TAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
65 TAATTTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* *
47962758 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATTCGAGGGTAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCG-GGGTAAATG
47962822 GTAATTTTTGG
64 GTAATTTTTGG
47962833 AAGTTTCGGG
Statistics
Matches: 178, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
116 15 0.08
117 139 0.78
118 24 0.13
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (116 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAATGGT
AATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
Found at i:47962844 original size:28 final size:27
Alignment explanation
Indices: 47962731--47962829 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 27
47962721 TCGAGGTTAA
* *
47962731 AAATGGAATTTTAAAAGATTCGGGGGT
1 AAATGGAATTTTAGAAGATTCGAGGGT
* * *
47962758 AAAATGGTAATTTTTGATGAAATCG-GGGTT
1 -AAATGG-AATTTTAGAAG-ATTCGAGGG-T
47962788 AAAAATGGAATTTTAGAAGATTCGAGGGT
1 --AAATGGAATTTTAGAAGATTCGAGGGT
47962817 AAATGGTAATTTT
1 AAATGG-AATTTT
47962830 TGGAAGTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
27 6 0.10
28 12 0.21
29 16 0.28
30 17 0.29
31 7 0.12
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (27 bp):
AAATGGAATTTTAGAAGATTCGAGGGT
Found at i:47964004 original size:20 final size:19
Alignment explanation
Indices: 47963957--47964005 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
47963947 CTTTTTTATT
47963957 TATTTATTATTAATATTAA
1 TATTTATTATTAATATTAA
* *
47963976 TAATCATTACTTAATATTAA
1 TATTTATTA-TTAATATTAA
*
47963996 TGTTTATTAT
1 TATTTATTAT
47964006 AACTGTCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTTATTATTAATATTAA
Found at i:47964767 original size:17 final size:16
Alignment explanation
Indices: 47964747--47964806 Score: 84
Period size: 17 Copynumber: 3.6 Consensus size: 16
47964737 AATTTTTATT
*
47964747 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
47964763 GTAAATTTAAATTTAAAA
1 -TAAATTTAAATTT-AAA
47964781 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
47964797 TAAAATTAAA
1 TAAATTTAAA
47964807 AATCAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
16 12 0.30
17 25 0.62
18 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:47964773 original size:6 final size:6
Alignment explanation
Indices: 47964721--47964797 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
47964711 TTTTTTAATG
* * ** * *
47964721 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
47964769 TTAAAT TTAAA- ATAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
47964798 AAAATTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
5 7 0.12
6 45 0.80
7 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:47964774 original size:23 final size:23
Alignment explanation
Indices: 47964744--47964797 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
47964734 TTTAATTTTT
*
47964744 ATTTAAATTTAAATTCAAA-GTAA
1 ATTTAAATTTAAAAT-AAATGTAA
*
47964767 ATTTAAATTTAAAATAAATTTAA
1 ATTTAAATTTAAAATAAATGTAA
47964790 ATTTAAAT
1 ATTTAAAT
47964798 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTAAATTTAAAATAAATGTAA
Found at i:47964824 original size:28 final size:28
Alignment explanation
Indices: 47964771--47964825 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
47964761 AAGTAAATTT
* *
47964771 AAATTTAAAATAAATTTAAATTTAAATA
1 AAATTAAAAATAAATTTAAATCTAAATA
* *
47964799 AAATTAAAAATCAATTTAACTCTAAAT
1 AAATTAAAAATAAATTTAAATCTAAAT
47964826 TAAACGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATTAAAAATAAATTTAAATCTAAATA
Found at i:47964835 original size:28 final size:28
Alignment explanation
Indices: 47964777--47964835 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
47964767 ATTTAAATTT
* **
47964777 AAAATAAATTTAAATTTAAATAAAATTA
1 AAAATAAATTTAAATCTAAATAAAACGA
* * *
47964805 AAAATCAATTTAACTCTAAATTAAACGA
1 AAAATAAATTTAAATCTAAATAAAACGA
47964833 AAA
1 AAA
47964836 GTCTAAGCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAATAAATTTAAATCTAAATAAAACGA
Found at i:47965302 original size:68 final size:69
Alignment explanation
Indices: 47965154--47965779 Score: 884
Period size: 68 Copynumber: 9.0 Consensus size: 69
47965144 AGGATAGGAA
* * *
47965154 ATGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
47965219 GAGG
66 GAGG
* * * * *
47965223 ATGACGTTGCTCTTACTTCAATTTCACAGATAAAGACTTGATATGC-TCTCTACTTCAATTTTAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
*
47965287 GGGG
66 GAGG
* * *
47965291 ATGGCATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
47965356 GAGG
66 GAGG
* *
47965360 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
*
47965424 GGGG
66 GAGG
*
47965428 ATGA-GATTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCA
1 ATGACG-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCA
47965492 AGAGG
65 AGAGG
* *
47965497 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
*
47965561 GGGG
66 GAGG
* * * * *
47965565 ATGACGTTGCTCTTACTTCAATTTCAGAGAAAAAGACGTGATATCCAATTTTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
47965630 GAGG
66 GAGG
* *
47965634 ATAGGAAACGATGTTACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCA
1 AT--G--AC---GTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCA
*
47965698 ATTTCAAGGGG
59 ATTTCAAGAGG
*
47965709 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
*
47965774 GCGG
66 GAGG
47965778 AT
1 AT
47965780 TGAAAATGAT
Statistics
Matches: 496, Mismatches: 48, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
67 1 0.00
68 223 0.45
69 206 0.42
70 1 0.00
71 3 0.01
73 3 0.01
75 21 0.04
76 38 0.08
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (69 bp):
ATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAA
GAGG
Found at i:47965411 original size:137 final size:137
Alignment explanation
Indices: 47965163--47965779 Score: 991
Period size: 137 Copynumber: 4.5 Consensus size: 137
47965153 AATGATGTTA
47965163 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
* * * * * *
47965228 GTTGCTCTTACTTCAATTTCACAGATAAAGACTTGATATGCTCTCTACTTCAATTTTAAGGGGAT
66 GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
*
47965293 GGCATTG
131 GACATTG
47965300 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
*
47965365 GTTGCTCTTACTTCAATTTCAGAGATAAGGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
66 GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
*
47965430 GAGATTG
131 GACATTG
47965437 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
*
47965502 GTTGCTCTTACTTCAATTTCAGAGATAAGGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
66 GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
*
47965567 GACGTTG
131 GACATTG
** * * * *
47965574 CTCTTACTTCAATTTCAGAGAAAAAGACGTGATATCCAATTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT--G
*
47965639 AAACGATGTTACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
64 --AC---GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
*
47965704 AGGGGATGACGTTG
124 AGGGGATGACATTG
*
47965718 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
1 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
47965780 TGAAAATGAT
Statistics
Matches: 447, Mismatches: 26, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
137 319 0.71
139 1 0.00
141 2 0.00
144 125 0.28
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (137 bp):
CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
GACATTG
Found at i:47972649 original size:18 final size:19
Alignment explanation
Indices: 47972623--47972661 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
47972613 TACTTTTATT
* *
47972623 AATTTAAAATTTAAA-AAA
1 AATTAAAAACTTAAATAAA
47972641 AATTAAAAACTTAAATAAA
1 AATTAAAAACTTAAATAAA
47972660 AA
1 AA
47972662 ATTTCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AATTAAAAACTTAAATAAA
Found at i:47978762 original size:11 final size:11
Alignment explanation
Indices: 47978742--47978781 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
47978732 AATTTTTATG
*
47978742 ATATATAAATT
1 ATATAAAAATT
47978753 ATATAAAAATT
1 ATATAAAAATT
*
47978764 ATA-AAAAATC
1 ATATAAAAATT
47978774 ATATAAAA
1 ATATAAAA
47978782 TATAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:47978763 original size:44 final size:42
Alignment explanation
Indices: 47978690--47978772 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 42
47978680 TATGAAAACA
*
47978690 AAATTTTAATATATAAAAATTTATTAAATT-CAAAAAATTTG
1 AAATTTTAATATATAAAAATTTATAAAATTACAAAAAATTTG
* * *
47978731 AAATTTTTATGATATATAAATTATATAAAAATTATAAAAAAT
1 AAATTTTAAT-ATATAAAAATT-TAT-AAAATTACAAAAAAT
47978773 CATATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 9 0.26
42 10 0.29
43 3 0.09
44 5 0.15
45 7 0.21
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (42 bp):
AAATTTTAATATATAAAAATTTATAAAATTACAAAAAATTTG
Found at i:47978787 original size:19 final size:21
Alignment explanation
Indices: 47978748--47978789 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
47978738 TATGATATAT
*
47978748 AAATTATATAAAAATTATAAA
1 AAATCATATAAAAATTATAAA
47978769 AAATCATAT-AAAA-TATAAA
1 AAATCATATAAAAATTATAAA
47978788 AA
1 AA
47978790 CTCAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATCATATAAAAATTATAAA
Found at i:47982258 original size:31 final size:32
Alignment explanation
Indices: 47982199--47982258 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
47982189 TCATAACCCT
*
47982199 TCCATACCCACTATTCAAAAGGAAAAAATCTA
1 TCCACACCCACTATTCAAAAGGAAAAAATCTA
*
47982231 TCCACACCCACTTTTCAAAA-GAAAAAAT
1 TCCACACCCACTATTCAAAAGGAAAAAAT
47982259 ATGTTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.47, C:0.27, G:0.05, T:0.22
Consensus pattern (32 bp):
TCCACACCCACTATTCAAAAGGAAAAAATCTA
Found at i:47984180 original size:10 final size:10
Alignment explanation
Indices: 47984165--47984192 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
47984155 TATATTAATT
47984165 TAAATTTTCA
1 TAAATTTTCA
47984175 TAAATTTTCA
1 TAAATTTTCA
47984185 TAAATTTT
1 TAAATTTT
47984193 AAAAGATCAA
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:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (10 bp):
TAAATTTTCA
Found at i:47986095 original size:58 final size:58
Alignment explanation
Indices: 47985944--47986253 Score: 297
Period size: 58 Copynumber: 5.3 Consensus size: 58
47985934 AAGACGGGAT
* * * ** *
47985944 AAAATGCAATTTTTGGAAATTCAAGGGTAAAATAGTAATTTTTGAAAAAATCGAGGTT
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGAAAAGTTCGAGGTC
* * ** *
47986002 AAAATTAGAATTTTTAGAAGTT-TGGAGGTAAAATGGCAATTTTTGAAAAGTTCGAGGTC
1 AAAA-TGGAATTTTTGGAAGTTCAAG-GGTAAAATGGTAATTTTTGAAAAGTTCGAGGTC
** * * *
47986061 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTAG-TAAGTT-TAGGGTC
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGAAAAGTTCGA-GGTC
* * * *
47986118 AAAAAAGGAATTTTTGGGAGTTCAAGGGTAAAATGGTAATTTTGGCAAAA-ATCGAGGTC
1 -AAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTG-AAAAGTTCGAGGTC
* * * *
47986177 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAAT-ATAATTTTTGAAAAGTTTAGGGGTT
1 AAAATGGAATTTTTGGAAGTTCAAGGGT-AAAATGGTAATTTTTGAAAAG-TTCGAGGTC
*
47986236 AAAATGTAATTTTTGGAA
1 AAAATGGAATTTTTGGAA
47986254 AGTTTAGGGG
Statistics
Matches: 206, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.00
57 13 0.06
58 110 0.53
59 79 0.38
60 3 0.01
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGAAAAGTTCGAGGTC
Found at i:47986121 original size:29 final size:28
Alignment explanation
Indices: 47985943--47986253 Score: 164
Period size: 29 Copynumber: 10.7 Consensus size: 28
47985933 GAAGACGGGA
* *
47985943 TAAAATGCAATTTTTGGAAATTCAAGGG
1 TAAAATGGAATTTTTGGAAGTTCAAGGG
* * ** * *
47985971 TAAAATAGTAATTTTTGAAAAAATCGAGGT
1 TAAAAT-GGAATTTTTG-GAAGTTCAAGGG
* * **
47986001 TAAAATTAGAATTTTTAGAAGTT-TGGAGG
1 TAAAA-TGGAATTTTTGGAAGTTCAAG-GG
* *
47986030 TAAAATGGCAATTTTTGAAAAGTTCGA-GG
1 TAAAATGG-AATTTTTG-GAAGTTCAAGGG
**
47986059 TCAAAATGGAATTTTTGGAAGTTCGGGGG
1 T-AAAATGGAATTTTTGGAAGTTCAAGGG
* * *
47986088 TAAAATGGTAATTTTAGTAAGTT-TAGGG
1 TAAAATGG-AATTTTTGGAAGTTCAAGGG
* *
47986116 TCAAAAAAGGAATTTTTGGGAGTTCAAGGG
1 T--AAAATGGAATTTTTGGAAGTTCAAGGG
** *
47986146 TAAAATGGTAA-TTTTGGCAAAAATCGA-GG
1 TAAAATGG-AATTTTTGG--AAGTTCAAGGG
47986175 TCAAAATGGAATTTTTGGAAGTTCAAGGG
1 T-AAAATGGAATTTTTGGAAGTTCAAGGG
** * * *
47986204 TAAAAATATAATTTTTGAAAAGTTTAGGGG
1 T-AAAATGGAATTTTTG-GAAGTTCAAGGG
*
47986234 TTAAAATGTAATTTTTGGAA
1 -TAAAATGGAATTTTTGGAA
47986254 AGTTTAGGGG
Statistics
Matches: 216, Mismatches: 46, Indels: 41
0.71 0.15 0.14
Matches are distributed among these distances:
28 44 0.20
29 87 0.40
30 83 0.38
31 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGAAGTTCAAGGG
Found at i:47986279 original size:31 final size:31
Alignment explanation
Indices: 47986184--47986293 Score: 138
Period size: 30 Copynumber: 3.6 Consensus size: 31
47986174 GTCAAAATGG
* *
47986184 AATTTTTGG-AAGTTCAAGGG-TAAAAATAT
1 AATTTTTGGAAAGTTTAGGGGTTAAAAATAT
* *
47986213 AATTTTTGAAAAGTTTAGGGGTT-AAAATGT
1 AATTTTTGGAAAGTTTAGGGGTTAAAAATAT
47986243 AATTTTTGGAAAGTTTAGGGGTTAAAAATAT
1 AATTTTTGGAAAGTTTAGGGGTTAAAAATAT
*
47986274 GATTTTTGGATAA-TTTAGGG
1 AATTTTTGGA-AAGTTTAGGG
47986294 ACCTTCAGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
29 8 0.11
30 37 0.53
31 23 0.33
32 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (31 bp):
AATTTTTGGAAAGTTTAGGGGTTAAAAATAT
Found at i:47988265 original size:29 final size:31
Alignment explanation
Indices: 47988216--47988283 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
47988206 TGGACATTCG
*
47988216 GGGGT-AAAAATGTAATTTTTAGA-AGTTTT
1 GGGGTCAAAAATGTAATTTTTAGAGAATTTT
47988245 GGGGTCAAAAATGTAA-TTTTAGAGAATTTT
1 GGGGTCAAAAATGTAATTTTTAGAGAATTTT
*
47988275 AGGGTCAAA
1 GGGGTCAAA
47988284 TATAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (31 bp):
GGGGTCAAAAATGTAATTTTTAGAGAATTTT
Found at i:47988293 original size:29 final size:29
Alignment explanation
Indices: 47988217--47988293 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
47988207 GGACATTCGG
* * *
47988217 GGGTAAAAATGTAATTTTTAGAAGTTTTG
1 GGGTCAAAATGTAATTTTTAGAAATTTTA
47988246 GGGTCAAAAATGTAA-TTTTAGAGAATTTTA
1 GGGTC-AAAATGTAATTTTTAGA-AATTTTA
*
47988276 GGGTC-AAATATAATTTTT
1 GGGTCAAAATGTAATTTTT
47988294 GGACAGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 7 0.17
29 15 0.37
30 19 0.46
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTAGAAATTTTA
Found at i:47990198 original size:6 final size:6
Alignment explanation
Indices: 47990178--47990244 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
47990168 TAAATACAAT
* *
47990178 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAGA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
47990221 TTTAAA TTTAAA AATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
47990245 ACCAATTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 5 0.10
5 8 0.17
6 35 0.73
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:47990199 original size:16 final size:16
Alignment explanation
Indices: 47990178--47990232 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
47990168 TAAATACAAT
47990178 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
*
47990194 TTTAAATTTAAAGTAAA
1 TTTAAATTT-AATTAAA
* *
47990211 TTTAGA-TAAATTTAAA
1 TTTAAATTTAA-TTAAA
47990227 TTTAAA
1 TTTAAA
47990233 AATAAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 19 0.59
17 11 0.34
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:47990210 original size:27 final size:27
Alignment explanation
Indices: 47990180--47990243 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 27
47990170 AATACAATTT
*
47990180 TAAATTTAATTAAATTTAAATTT-AAAG
1 TAAATTTAA-TAAATTTAAATTTAAAAA
47990207 TAAATTTAGATAAATTTAAATTTAAAAA
1 TAAATTTA-ATAAATTTAAATTTAAAAA
47990235 TAAATTTAA
1 TAAATTTAA
47990244 AACCAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
TAAATTTAATAAATTTAAATTTAAAAA
Found at i:47990991 original size:6 final size:6
Alignment explanation
Indices: 47990977--47991046 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
47990967 GTTTAAAACC
*
47990977 ATTTCAA ATTTAA A-TTAA A-TTAA ATTTAA A-CTAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** * *
47991023 A-ACAA ATTTAA ACTTAA AATTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
47991047 AAGTTTGATC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
5 17 0.33
6 31 0.60
7 4 0.08
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (6 bp):
ATTTAA
Found at i:47991005 original size:11 final size:12
Alignment explanation
Indices: 47990977--47991046 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 12
47990967 GTTTAAAACC
47990977 ATTTCAAATTTAA
1 ATTT-AAATTTAA
47990990 A-TTAAA-TTAA
1 ATTTAAATTTAA
*
47991000 ATTTAAA-CTAA
1 ATTTAAATTTAA
47991011 ATTTAAATTTAA
1 ATTTAAATTTAA
**
47991023 A-ACAAATTTAA
1 ATTTAAATTTAA
* *
47991034 ACTTAAAATTAA
1 ATTTAAATTTAA
47991046 A
1 A
47991047 AAGTTTGATC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
10 5 0.11
11 27 0.57
12 14 0.30
13 1 0.02
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:47991018 original size:17 final size:17
Alignment explanation
Indices: 47990977--47991040 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
47990967 GTTTAAAACC
*
47990977 ATTTCAAATTTAAATTAA
1 ATTT-AAATTTAAACTAA
47990995 A-TTAAATTTAAACTAA
1 ATTTAAATTTAAACTAA
47991011 ATTTAAATTTAAAAC-AA
1 ATTTAAATTT-AAACTAA
*
47991028 ATTTAAACTTAAA
1 ATTTAAATTTAAA
47991041 ATTAAAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 16 0.38
17 21 0.50
18 5 0.12
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAACTAA
Found at i:47991041 original size:17 final size:18
Alignment explanation
Indices: 47990992--47991046 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
47990982 AAATTTAAAT
*
47990992 TAAA-TTAAA-TTTAAAC
1 TAAATTTAAACTTAAAAC
*
47991008 TAAATTTAAATTTAAAAC
1 TAAATTTAAACTTAAAAC
*
47991026 -AAATTTAAACTTAAAAT
1 TAAATTTAAACTTAAAAC
47991043 TAAA
1 TAAA
47991047 AAGTTTGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 4 0.12
17 20 0.61
18 9 0.27
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTTAAACTTAAAAC
Found at i:47993873 original size:59 final size:58
Alignment explanation
Indices: 47993782--47994153 Score: 471
Period size: 59 Copynumber: 6.3 Consensus size: 58
47993772 TGGGTACTCG
*
47993782 GGGGCAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTT-GGAAAGTTTA
* * **
47993840 GGGGTAAGATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGT-TAAAATGGAATTTTGGAAAGTT-TA
* * * *
47993900 GGGGTAAAAGGGTAATTTTTGGTGAAATTGAGGTCAAAAATGGAATTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGT-TAAAATGGAATTTTGGAAAGTTTA
* *
47993958 GAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG-TTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTTA
* * * *
47994017 GGGGGTAAAATAGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAATTTG
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTTA
* * * *
47994077 GGGGTAAAATGGTAATTTTTGATGAAACCGAGGTTAAAACGGAATTTTGGAAACTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTA
*
47994135 AGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
47994154 CGGACAGTCC
Statistics
Matches: 281, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
58 52 0.19
59 161 0.57
60 68 0.24
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTA
Found at i:47994151 original size:29 final size:26
Alignment explanation
Indices: 47993787--47994153 Score: 155
Period size: 29 Copynumber: 12.5 Consensus size: 26
47993777 ACTCGGGGGC
* *
47993787 AAAATGGTAATTTTGGTGAAATCGAGGTT
1 AAAATGG-AATTTT-G-GAAATTGAGGGT
*
47993816 AAAATGGAATTTTGGGAAAGTTTAGGGGT
1 AAAATGGAATTTT-GGAAA-TTGA-GGGT
* *
47993845 AAGATGGTAATTTTTGGTGAAATCGA-GGT
1 AAAATGG-AA-TTTT-G-GAAATTGAGGGT
*
47993874 CAAAAATGGAATTTTGGAAAGTTCGGGGGGT
1 --AAAATGGAATTTTGGAAA-TT--GAGGGT
*
47993905 AAAAGGGTAATTTTTGGTGAAATTGA-GGT
1 AAAATGG-AA-TTTT-G-GAAATTGAGGGT
47993934 CAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 --AAAATGGAATTTTGGAAA-TT-GAGGGT
47993964 AAAATGGTAATTTTTGGTGAAATTG-GGGTT
1 AAAATGG-AA-TTTT-G-GAAATTGAGGG-T
*
47993994 AAAAATGGAATTTTGGAAAGTTAGGGGGT
1 -AAAATGGAATTTTGGAAA-TT-GAGGGT
* * *
47994023 AAAATAGTAATTTTTGATGAAATCGAGGTT
1 AAAAT-GGAA-TTTTG--GAAATTGAGGGT
*
47994053 AAAAATGGAATTTTGGAAAATTTGGGGGT
1 -AAAATGGAATTTTGG-AAA-TTGAGGGT
** *
47994082 AAAATGGTAATTTTTGATGAAACCGAGGTT
1 AAAATGG-AA-TTTTG--GAAATTGAGGGT
* *
47994112 AAAACGGAATTTTGGAAACTTTAAGGGT
1 AAAATGGAATTTTGGAAA--TTGAGGGT
47994140 AAAATGGTAATTTT
1 AAAATGG-AATTTT
47994154 CGGACAGTCC
Statistics
Matches: 265, Mismatches: 30, Indels: 86
0.70 0.08 0.23
Matches are distributed among these distances:
26 4 0.02
27 17 0.06
28 55 0.21
29 72 0.27
30 51 0.19
31 46 0.17
32 16 0.06
33 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (26 bp):
AAAATGGAATTTTGGAAATTGAGGGT
Found at i:47995233 original size:18 final size:20
Alignment explanation
Indices: 47995170--47995240 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
47995160 ATATTAAATA
47995170 TTATTATT-TTAAAAGTAGT-T
1 TTATTATTATTAAAA-TA-TAT
*
47995190 ATTATCATTATTAAAATATAT
1 -TTATTATTATTAAAATATAT
*
47995211 TTATTATTATTAAAA-CT-T
1 TTATTATTATTAAAATATAT
47995229 TTATTATTATTA
1 TTATTATTATTA
47995241 TTATTATCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
18 13 0.29
19 1 0.02
20 15 0.33
21 10 0.22
22 6 0.13
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTATTATTAAAATATAT
Found at i:47995648 original size:24 final size:24
Alignment explanation
Indices: 47995615--47995663 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
47995605 TGAGTGTTTA
47995615 AATTTCCAGAACAGGGGTCGTATT
1 AATTTCCAGAACAGGGGTCGTATT
* * *
47995639 AATTTTCAGAATAGGGTTCGTATT
1 AATTTCCAGAACAGGGGTCGTATT
47995663 A
1 A
47995664 GAATAGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (24 bp):
AATTTCCAGAACAGGGGTCGTATT
Found at i:47996515 original size:38 final size:38
Alignment explanation
Indices: 47996423--47996907 Score: 247
Period size: 38 Copynumber: 12.8 Consensus size: 38
47996413 TCGAGGCTTC
* **
47996423 ATCTTGCTCTTACGTCAATTTCAGAGAGATAAAGACTTG
1 ATCTTGCTCTTACTTCAATTTCA-AGAGATAAAGAAATG
* * *
47996462 --CTAT-C-C-AACTTCAATTTCACGAGGAT-AGGAAATG
1 ATCT-TGCTCTTACTTCAATTTCAAGA-GATAAAGAAATG
**
47996496 ATCTTGCTCTTACTTCAATTTC-AGAGATAAAGACTTG
1 ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
* * * * *
47996533 AT-ATCCAACTTTACTTCAATTTCAAGAGGAT-AGGAAATA
1 ATCTTGC-TC-TTACTTCAATTTCAAGA-GATAAAGAAATG
* **
47996572 ATCTTGCTCTTACTTCAATTTC-GGAGATAAAGACTTG
1 ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
** * *
47996609 ATATCCAGGT-TTACTTCAATTTCAAGAGGAT-AGGAAATG
1 --ATCTTGCTCTTACTTCAATTTCAAGA-GATAAAGAAATG
**
47996648 ATCTTGCTCTTACTTCAATTTC-AGAGATAAAGACTTG
1 ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
*** * *
47996685 TTATCCAACTC-TACTTCAATTTCAAGAGGAT-AGGAAATA
1 --ATCTTGCTCTTACTTCAATTTCAAGA-GATAAAGAAATG
* * **
47996724 ATCTTACTCTTACTTCAATTTC-GGAGATAAAGACTTG
1 ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
*** **
47996761 TTATCCAACTC-TACTTCAATTTCAAGAGATAAAGACTTG
1 --ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
** * *
47996800 ATATCCAGCT-TTACTTCAATTTCAAGAGGAT-AGGAAATA
1 --ATCTTGCTCTTACTTCAATTTCAAGA-GATAAAGAAATG
**
47996839 ATCTTGCTCTTACTTCAATTTC-AGAGATAAAGACTTG
1 ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
**
47996876 ATATCCAGCT-TTACTTCAATTTCAAGATGATA
1 --ATCTTGCTCTTACTTCAATTTCAAGA-GATA
47996908 GGAAAATGAT
Statistics
Matches: 339, Mismatches: 70, Indels: 73
0.70 0.15 0.15
Matches are distributed among these distances:
34 7 0.02
35 15 0.04
36 21 0.06
37 59 0.17
38 126 0.37
39 93 0.27
40 18 0.05
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (38 bp):
ATCTTGCTCTTACTTCAATTTCAAGAGATAAAGAAATG
Found at i:47996576 original size:76 final size:76
Alignment explanation
Indices: 47996423--47996788 Score: 553
Period size: 76 Copynumber: 4.9 Consensus size: 76
47996413 TCGAGGCTTC
* * *
47996423 ATCTTGCTCTTACGTCAATTTCAGAGAGATAAAGACTTGCTATCC-A----ACTTCAATTTCACG
1 ATCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAG
*
47996483 AGGATAGGAAATG
64 AGGATAGGAAATA
*
47996496 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
47996561 GATAGGAAATA
66 GATAGGAAATA
* ** *
47996572 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAGGTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
47996637 GATAGGAAATG
66 GATAGGAAATA
*
47996648 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
47996713 GATAGGAAATA
66 GATAGGAAATA
* * *
47996724 ATCTTACTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
47996789 ATAAAGACTT
Statistics
Matches: 272, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
71 20 0.07
72 1 0.00
73 21 0.08
76 230 0.85
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAATA
Found at i:48008960 original size:59 final size:59
Alignment explanation
Indices: 48008846--48009274 Score: 544
Period size: 59 Copynumber: 7.3 Consensus size: 59
48008836 TGGGTACTCG
* * * *
48008846 GGGGTAAAATGGTAA-TTTTGGTCAAATCAAGGTC-AAAATGGAATTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCA
* *
48008903 GGGGTAAGATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCA
* ** * *
48008962 GGGATAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGTTATTTTGGAATGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCA
* * * * *
48009021 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAAATGGAATTTTAGAAAGTTAA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TCAAAAATGGAATTTTGGAAAGTTCA
* * *
48009081 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCA
* * * * *
48009140 GGGGTAAAATGGTAATTTTTGATAAAATCGGGGT-TAAAATGGAATTTTGGAAAATTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCA
* * * *
48009198 GGCGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAACA--GAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAA-ATGGAATTTTGGAAAGTTCA
*
48009256 GGGGTAAAATGATAATTTT
1 GGGGTAAAATGGTAATTTT
48009275 CGAATAGTTC
Statistics
Matches: 324, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
57 14 0.04
58 100 0.31
59 160 0.49
60 50 0.15
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCA
Found at i:48009010 original size:30 final size:30
Alignment explanation
Indices: 48008914--48009010 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
48008904 GGGTAAGATG
48008914 GTAATTTTTGGTGAAATCGAGGTCAAAAAT
1 GTAATTTTTGGTGAAATCGAGGTCAAAAAT
* ** *
48008944 GGAA-TTTT-G-GAAAGTTTAGG-GATAAAAT
1 GTAATTTTTGGTGAAA-TCGAGGTCA-AAAAT
48008972 GGTAATTTTTGGTGAAATCGAGGTCAAAAAT
1 -GTAATTTTTGGTGAAATCGAGGTCAAAAAT
*
48009003 GTTATTTT
1 GTAATTTT
48009011 GGAATGTTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
27 5 0.10
28 10 0.20
29 7 0.14
30 14 0.27
31 10 0.20
32 5 0.10
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
GTAATTTTTGGTGAAATCGAGGTCAAAAAT
Found at i:48009038 original size:29 final size:29
Alignment explanation
Indices: 48008843--48009274 Score: 178
Period size: 29 Copynumber: 14.8 Consensus size: 29
48008833 TTTTGGGTAC
*
48008843 TCGGGGGTAAAATGGTAATTTTGGTCAAA-
1 TCGGGGGTAAAATGGTAATTTTGG-AAAAT
** * *
48008872 TC-AAGGTCAAAATGG-AATTTTGGGAAGT
1 TCGGGGGT-AAAATGGTAATTTTGGAAAAT
** * *
48008900 TTAGGGGTAAGATGGTAATTTTTGGTGAAA-
1 TCGGGGGTAAAATGGTAA-TTTTGG-AAAAT
* *
48008930 TC-GAGGTCAAAAATGG-AATTTTGGAAAGT
1 TCGGGGGT--AAAATGGTAATTTTGGAAAAT
** * *
48008959 TTAGGGATAAAATGGTAATTTTTGGTGAAA-
1 TCGGGGGTAAAATGGTAA-TTTTGG-AAAAT
* * **
48008989 TC-GAGGTCAAAAAT-GTTATTTTGGAATGT
1 TCGGGGGT--AAAATGGTAATTTTGGAAAAT
*
48009018 TCGGGGGTAAAATGGTAATTTTTGGTGAAAT
1 TCGGGGGTAAAATGGTAA-TTTTGG-AAAAT
* * *
48009049 T-GGGGTTAAAAAATGG-AATTTTAGAAAGT
1 TCGGGGGT--AAAATGGTAATTTTGGAAAAT
**
48009078 TAAGGGGTAAAATGGTAATTTTTGGTAAAA-
1 TCGGGGGTAAAATGGTAA-TTTTGG-AAAAT
* * *
48009108 TC-GAGGTCAAAAAT-GAAATTTTGGAAAGT
1 TCGGGGGT--AAAATGGTAATTTTGGAAAAT
* *
48009137 TCGGGGGTAAAATGGTAATTTTTGATAAAA
1 TCGGGGGTAAAATGGTAATTTTGGA-AAAT
*
48009167 TCGGGGTTAAAATGG-AATTTTGGAAAAT
1 TCGGGGGTAAAATGGTAATTTTGGAAAAT
* * *
48009195 TCAGGCGTAAAATGGTAATTTTTGATGAAA-
1 TCGGGGGTAAAATGGTAATTTTGGA--AAAT
* * ** *
48009225 TCGAGGTTAAAACAG-AATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTGGAAAAT
** *
48009253 TTAGGGGTAAAATGATAATTTT
1 TCGGGGGTAAAATGGTAATTTT
48009275 CGAATAGTTC
Statistics
Matches: 296, Mismatches: 70, Indels: 74
0.67 0.16 0.17
Matches are distributed among these distances:
27 4 0.01
28 71 0.24
29 98 0.33
30 84 0.28
31 32 0.11
32 7 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGAAAAT
Found at i:48010368 original size:18 final size:19
Alignment explanation
Indices: 48010326--48010375 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
48010316 AAAGTAGTTA
*
48010326 TTATCATTATTAAAATACAT
1 TTATTATTATT-AAATACAT
*
48010346 TTATTATTATTAAA-ACCT
1 TTATTATTATTAAATACAT
48010364 TTATTATTATTA
1 TTATTATTATTA
48010376 TTATCATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
19 3 0.11
20 10 0.36
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTATTATTAAATACAT
Found at i:48011229 original size:6 final size:6
Alignment explanation
Indices: 48011214--48011288 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
48011204 TTAAATTTCA
* * * *
48011214 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAGTGAA- TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* *
48011261 ATAAAT TTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
48011289 ACCCATTTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
5 15 0.29
6 34 0.65
8 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:48011237 original size:11 final size:10
Alignment explanation
Indices: 48011221--48011288 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 10
48011211 TCATTAAACT
48011221 TAAATTTAAA
1 TAAATTTAAA
48011231 GTAAATTTAAA
1 -TAAATTTAAA
* * *
48011242 T-AAGTGAAT
1 TAAATTTAAA
48011251 TAAATTTAAAA
1 TAAATTT-AAA
48011262 TAAATTTAAA
1 TAAATTTAAA
*
48011272 T---TTAAAA
1 TAAATTTAAA
48011279 TAAATTTAAA
1 TAAATTTAAA
48011289 ACCCATTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
7 6 0.14
9 6 0.14
10 13 0.30
11 19 0.43
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:48011240 original size:17 final size:17
Alignment explanation
Indices: 48011215--48011288 Score: 84
Period size: 17 Copynumber: 4.6 Consensus size: 17
48011205 TAAATTTCAT
* *
48011215 TAAACTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
*
48011232 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
*
48011246 TGAA-TTAAATTTAAAA
1 TAAATTTAAATTTAAAA
48011262 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
48011279 TAAATTTAAA
1 TAAATTTAAA
48011289 ACCCATTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 2 0.04
16 5 0.10
17 31 0.63
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:48011310 original size:28 final size:28
Alignment explanation
Indices: 48011248--48011310 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
48011238 TAAATAAGTG
* *
48011248 AATTAAATTTAAAATAAATTTAAATTTA
1 AATTAAATTTAAAACAAATTTAAACTTA
* ** *
48011276 AAATAAATTTAAAACCCATTTAAACTTC
1 AATTAAATTTAAAACAAATTTAAACTTA
48011304 AATTAAA
1 AATTAAA
48011311 ACCAAAGGCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTAAATTTAAAACAAATTTAAACTTA
Done.