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 152 of 193
Found at i:47407748 original size:15 final size:17
Alignment explanation
Indices: 47407730--47407762 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
47407720 TATTTTTTAA
47407730 AAATTA-TAAA-AATAT
1 AAATTATTAAATAATAT
47407745 AAATTATTAAATAATAT
1 AAATTATTAAATAATAT
47407762 A
1 A
47407763 TTTATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTATTAAATAATAT
Found at i:47408412 original size:17 final size:17
Alignment explanation
Indices: 47408367--47408473 Score: 92
Period size: 17 Copynumber: 6.3 Consensus size: 17
47408357 CCCAAACCAT
* *
47408367 TTTAAATTTGCTTTGAAA
1 TTTAAATTT-ATTTTAAA
*
47408385 -TTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
47408401 TTCAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* **
47408418 TTTAAGTTTATTTTTGA
1 TTTAAATTTATTTTAAA
*
47408435 TTTAAATTTAATTTT-AG
1 TTTAAATTT-ATTTTAAA
* *
47408452 TTTGAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
47408469 TTTAA
1 TTTAA
47408474 TATTATGGTA
Statistics
Matches: 70, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
16 10 0.14
17 55 0.79
18 5 0.07
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:47408438 original size:23 final size:23
Alignment explanation
Indices: 47408412--47408472 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
47408402 TCAAATTTAT
* *
47408412 TTTAAATTTAAGTTTATTTTTG-A
1 TTTAAATTTAAATTTA-GTTTGAA
*
47408435 TTTAAATTTAATTTTAGTTTGAA
1 TTTAAATTTAAATTTAGTTTGAA
47408458 TTT-AATTTAAATTTA
1 TTTAAATTTAAATTTA
47408473 ATATTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTGAA
Found at i:47408447 original size:28 final size:28
Alignment explanation
Indices: 47408416--47408474 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
47408406 ATTTATTTTA
* *
47408416 AATTTAAGTTT-ATTTTTGATTTAAATTT
1 AATTTAAGTTTGA-ATTTAATTTAAATTT
*
47408444 AATTTTAGTTTGAATTTAATTTAAATTT
1 AATTTAAGTTTGAATTTAATTTAAATTT
47408472 AAT
1 AAT
47408475 ATTATGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (28 bp):
AATTTAAGTTTGAATTTAATTTAAATTT
Found at i:47408474 original size:11 final size:11
Alignment explanation
Indices: 47408399--47408473 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
47408389 GTTTATTTTA
*
47408399 AATTCAAATTT
1 AATTTAAATTT
*
47408410 ATTTTAAATTT
1 AATTTAAATTT
**
47408421 AAGTTTATTTTT
1 AA-TTTAAATTT
*
47408433 GATTTAAATTT
1 AATTTAAATTT
* *
47408444 AATTTTAGTTT
1 AATTTAAATTT
47408455 GAATTT-AATTT
1 -AATTTAAATTT
47408466 AAATTTAA
1 -AATTTAA
47408474 TATTATGGTA
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
11 34 0.71
12 14 0.29
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:47408487 original size:28 final size:28
Alignment explanation
Indices: 47408434--47408491 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
47408424 TTTATTTTTG
* * *
47408434 ATTTAAATTTAATTTTAGTTTGAATTTA
1 ATTTAAATTTAATATTAGTGTAAATTTA
47408462 ATTTAAATTTAATATTA-TGGTAAATTTA
1 ATTTAAATTTAATATTAGT-GTAAATTTA
47408490 AT
1 AT
47408492 GTCCACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTTAAATTTAATATTAGTGTAAATTTA
Found at i:47410093 original size:32 final size:33
Alignment explanation
Indices: 47410056--47410123 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
47410046 TTATTTCGCG
* *
47410056 TTTGGT-CCTTCCGTATTTTTTAATTA-TTTTAA
1 TTTGGTCCCTTCCATA-CTTTTAATTATTTTTAA
*
47410088 TTTGGTCCCTTTCATACTTTTAATTATTTTTAA
1 TTTGGTCCCTTCCATACTTTTAATTATTTTTAA
47410121 TTT
1 TTT
47410124 AGCCCGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.19, C:0.13, G:0.07, T:0.60
Consensus pattern (33 bp):
TTTGGTCCCTTCCATACTTTTAATTATTTTTAA
Found at i:47410443 original size:29 final size:29
Alignment explanation
Indices: 47410400--47410595 Score: 102
Period size: 29 Copynumber: 6.7 Consensus size: 29
47410390 TTAAACTATA
**
47410400 CAAAAATTATATTTTGACCCCTAAACTTTC
1 CAAAAATTCCATTTTGACCCCT-AACTTTC
* * *
47410430 C-AAAATTCCATTTTTA-ACCTCGA-TTTCAC
1 CAAAAATTCCATTTTGACCCCT-AACTTT--C
*
47410459 CAAAAATTACCATTTT-AGCCCCGAAC-TTC
1 CAAAAATT-CCATTTTGA-CCCCTAACTTTC
* * * * *
47410488 C-AAAATCCCATTTTTAACCCTGATTTCTC
1 CAAAAATTCCATTTTGACCCCTAACTT-TC
* * *
47410517 CAAAAAATACCATTTTGCCCCCAAACTTTC
1 C-AAAAATTCCATTTTGACCCCTAACTTTC
*
47410547 C-AAAATTCCATTTTGA-CCCTAATTTTAC
1 CAAAAATTCCATTTTGACCCCTAACTTT-C
* *
47410575 CAAAAATTACATTTTTACCCC
1 CAAAAATTCCATTTTGACCCC
47410596 CAAAAGTCAA
Statistics
Matches: 124, Mismatches: 27, Indels: 30
0.69 0.15 0.17
Matches are distributed among these distances:
27 22 0.18
28 26 0.21
29 32 0.26
30 14 0.11
31 28 0.23
32 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTGACCCCTAACTTTC
Found at i:47410473 original size:31 final size:29
Alignment explanation
Indices: 47410431--47410532 Score: 79
Period size: 30 Copynumber: 3.5 Consensus size: 29
47410421 TAAACTTTCC
47410431 AAAATT-CCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTTAACC-CGATTTC-CCA
* *
47410461 AAAATTACCA-TTTTAGCCCCGAACTT-CC-
1 AAAATTACCATTTTTA-ACCCG-ATTTCCCA
*
47410489 AAAA-TCCCATTTTTAACCCTGATTTCTCCA
1 AAAATTACCATTTTTAACCC-GATTTC-CCA
*
47410519 AAAAATACCATTTT
1 AAAATTACCATTTT
47410533 GCCCCCAAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
27 10 0.18
28 10 0.18
29 4 0.07
30 17 0.30
31 16 0.28
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTTAACCCGATTTCCCA
Found at i:47410523 original size:59 final size:59
Alignment explanation
Indices: 47410400--47410599 Score: 225
Period size: 58 Copynumber: 3.4 Consensus size: 59
47410390 TTAAACTATA
* * *
47410400 CAAAAATTA-TATTTTGACCCCTAAACTTTCCAAAATTCCATTTTTAA-CCTCGATTTCAC
1 CAAAAATTACCATTTTG-CCCCCAAACTTTCCAAAATTCCATTTTTAACCCT-GATTTCTC
* *
47410459 CAAAAATTACCATTTTAG-CCCCGAAC-TTCCAAAATCCCATTTTTAACCCTGATTTCTC
1 CAAAAATTACCATTTT-GCCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCTC
* * *
47410517 CAAAAAATACCATTTTGCCCCCAAACTTTCCAAAATTCCA-TTTTGACCCTAATTT-TAC
1 CAAAAATTACCATTTTGCCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCT-C
*
47410575 CAAAAATTA-CATTTTTACCCCCAAA
1 CAAAAATTACCA-TTTTGCCCCCAAA
47410600 AGTCAAAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
57 4 0.03
58 82 0.67
59 30 0.25
60 5 0.04
61 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTGCCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCTC
Found at i:47410557 original size:28 final size:27
Alignment explanation
Indices: 47410520--47410624 Score: 84
Period size: 28 Copynumber: 3.7 Consensus size: 27
47410510 ATTTCTCCAA
*
47410520 AAAATACCATTTTGCCCCCAAACTTTCC
1 AAAATTCCATTTTGCCCCCAAA-TTTCC
* * *
47410548 AAAATTCCATTTTGACCCTAATTTTACC
1 AAAATTCCATTTTGCCCCCAAATTT-CC
* * ** *
47410576 AAAAATTACATTTTTACCCCCAAAAGTCA
1 -AAAATTCCA-TTTTGCCCCCAAATTTCC
47410605 AAAATTACCATTTTGCCCCC
1 AAAATT-CCATTTTGCCCCC
47410625 GGGCATCCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
27 3 0.05
28 35 0.59
29 11 0.19
30 10 0.17
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAATTCCATTTTGCCCCCAAATTTCC
Found at i:47414066 original size:29 final size:29
Alignment explanation
Indices: 47414024--47414122 Score: 100
Period size: 28 Copynumber: 3.5 Consensus size: 29
47414014 GTTTGGGGGT
47414024 AAAATGGTAATTTTGGTGAAATCGAGGGCA
1 AAAATGGTAATTTTGGTGAAATCGAGGG-A
** *
47414054 AAAATGG-AATTTT--AAAAATTCGAGGGT
1 AAAATGGTAATTTTGGTGAAA-TCGAGGGA
47414081 AAAATGGTAATTTTGGTGAAATCG-GGGTA
1 AAAATGGTAATTTTGGTGAAATCGAGGG-A
*
47414110 AATATGG-AATTTT
1 AAAATGGTAATTTT
47414123 CAAAAATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
27 10 0.18
28 22 0.39
29 15 0.26
30 10 0.18
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGAGGGA
Found at i:47414084 original size:28 final size:29
Alignment explanation
Indices: 47414020--47414130 Score: 81
Period size: 28 Copynumber: 3.9 Consensus size: 29
47414010 GAAAGTTTGG
**
47414020 GGGT-AAAATGGTAATTTTGGTGAAA-TCGA
1 GGGTAAAAATGG-AATTTT-GAAAAATTCGA
*
47414049 GGGCAAAAATGGAATTTT-AAAAATTCGA
1 GGGTAAAAATGGAATTTTGAAAAATTCGA
**
47414077 GGGT-AAAATGGTAATTTTGGTGAAA-TCG-
1 GGGTAAAAATGG-AATTTT-GAAAAATTCGA
* *
47414105 GGGTAAATATGGAATTTTCAAAAATT
1 GGGTAAAAATGGAATTTTGAAAAATT
47414131 TTAGGGTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
27 13 0.20
28 24 0.37
29 18 0.28
30 10 0.15
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.31
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTGAAAAATTCGA
Found at i:47414137 original size:57 final size:57
Alignment explanation
Indices: 47413958--47414130 Score: 197
Period size: 57 Copynumber: 3.0 Consensus size: 57
47413948 TTTAGATACC
* * * * * * *
47413958 CGAGGGCAAAATGGTATTTTTGATGAAAT-TAGGGTTAAAAAATGGAACTTTAGAAAGTT
1 CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGG--CAAAAATGGAATTTTA-AAAATT
* *
47414017 TGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGGCAAAAATGGAATTTTAAAAATT
1 CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGGCAAAAATGGAATTTTAAAAATT
* *
47414074 CGAGGGTAAAATGGTAATTTTGGTGAAATCG-GGGTAAATATGGAATTTTCAAAAATT
1 CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGGCAAAAATGGAATTTT-AAAAATT
47414131 TTAGGGTTAA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
56 16 0.16
57 41 0.41
58 14 0.14
59 24 0.24
60 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.31
Consensus pattern (57 bp):
CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGGCAAAAATGGAATTTTAAAAATT
Found at i:47414159 original size:57 final size:57
Alignment explanation
Indices: 47413995--47414151 Score: 183
Period size: 57 Copynumber: 2.7 Consensus size: 57
47413985 ATTAGGGTTA
* * * * *
47413995 AAAAATGGAACTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGGC
1 AAAAATGGAATTTTA-AAAATTCGAGGGTAAAATGATAATTTTGGTGAAATCGAGGGC
* *
47414053 AAAAATGGAATTTTAAAAATTCGAGGGTAAAATGGTAATTTTGGTGAAATCG-GGGT
1 AAAAATGGAATTTTAAAAATTCGAGGGTAAAATGATAATTTTGGTGAAATCGAGGGC
* **
47414109 AAATATGGAATTTTCAAAAATTTTAGGGTTAAAAT-ATAATTTT
1 AAAAATGGAATTTT-AAAAATTCGAGGG-TAAAATGATAATTTT
47414152 AGAGAAATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
56 16 0.18
57 52 0.59
58 20 0.23
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (57 bp):
AAAAATGGAATTTTAAAAATTCGAGGGTAAAATGATAATTTTGGTGAAATCGAGGGC
Found at i:47414209 original size:60 final size:59
Alignment explanation
Indices: 47414133--47414301 Score: 241
Period size: 60 Copynumber: 2.8 Consensus size: 59
47414123 CAAAAATTTT
* * *
47414133 AGGGTTAAAATATAATTTTAGAGAAA-TTTAAGGGTTAAAATATAATTTTAGAGTAGTTTA
1 AGGGTTAAAATGTAATTTTA-A-AAAGTTTTAGGGTTAAAATATAATTTTAGAGAAGTTTA
*
47414193 AGGGTTAAAATGTAATTTTCAAAAAGTTTTAGGGTTAAAATATAATTTTAGAGAAGTTTT
1 AGGGTTAAAATGTAATTTT-AAAAAGTTTTAGGGTTAAAATATAATTTTAGAGAAGTTTA
* *
47414253 GGGGTTAAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATGTAATTTT
1 AGGGTTAAAATGTAA-TTTTAAAAAGTTTTAGGGTTAAAATATAATTTT
47414302 TGGATAGTCT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
59 3 0.03
60 92 0.92
61 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (59 bp):
AGGGTTAAAATGTAATTTTAAAAAGTTTTAGGGTTAAAATATAATTTTAGAGAAGTTTA
Found at i:47414235 original size:90 final size:89
Alignment explanation
Indices: 47414108--47414301 Score: 282
Period size: 90 Copynumber: 2.2 Consensus size: 89
47414098 GAAATCGGGG
*
47414108 TAAATATGGAATTTTCAAAAATTTTAGGGTTAAAATATAATTTTAGAGAAATTTAAGGGTTAAAA
1 TAAA-ATGTAATTTTCAAAAATTTTAGGGTTAAAATATAATTTTAGAGAAATTTAAGGGTTAAAA
**
47414173 TATAA-TTTTAGAGTAGTTTAAGGGT
65 TATAATTTTTA-AAAAGTTTAAGGGT
* **
47414198 TAAAATGTAATTTTCAAAAAGTTTTAGGGTTAAAATATAATTTTAGAGAAGTTTTGGGGTTAAAA
1 TAAAATGTAATTTTCAAAAA-TTTTAGGGTTAAAATATAATTTTAGAGAAATTTAAGGGTTAAAA
* *
47414263 TGTAATTTTTAAAAAGTTTTAGGGT
65 TATAATTTTTAAAAAGTTTAAGGGT
47414288 TAAAATGTAATTTT
1 TAAAATGTAATTTT
47414302 TGGATAGTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
89 15 0.16
90 74 0.79
91 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.41
Consensus pattern (89 bp):
TAAAATGTAATTTTCAAAAATTTTAGGGTTAAAATATAATTTTAGAGAAATTTAAGGGTTAAAAT
ATAATTTTTAAAAAGTTTAAGGGT
Found at i:47414302 original size:30 final size:31
Alignment explanation
Indices: 47414124--47414302 Score: 208
Period size: 30 Copynumber: 5.9 Consensus size: 31
47414114 TGGAATTTTC
* *
47414124 AAAAATTTTAGGGTTAAAATATAA-TTTTAG
1 AAAAGTTTTAGGGTTAAAATGTAATTTTTAG
* *
47414154 AGAAA-TTTAAGGGTTAAAATATAA-TTTTAG
1 A-AAAGTTTTAGGGTTAAAATGTAATTTTTAG
** * *
47414184 AGTAGTTTAAGGGTTAAAATGTAATTTTCA-
1 AAAAGTTTTAGGGTTAAAATGTAATTTTTAG
*
47414214 AAAAGTTTTAGGGTTAAAATATAA-TTTTAG
1 AAAAGTTTTAGGGTTAAAATGTAATTTTTAG
* *
47414244 AGAAGTTTTGGGGTTAAAATGTAATTTTTA-
1 AAAAGTTTTAGGGTTAAAATGTAATTTTTAG
47414274 AAAAGTTTTAGGGTTAAAATGTAATTTTT
1 AAAAGTTTTAGGGTTAAAATGTAATTTTT
47414303 GGATAGTCTA
Statistics
Matches: 129, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.04
30 112 0.87
31 12 0.09
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.41
Consensus pattern (31 bp):
AAAAGTTTTAGGGTTAAAATGTAATTTTTAG
Found at i:47421608 original size:32 final size:34
Alignment explanation
Indices: 47421537--47421613 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 34
47421527 TCTATTTACT
47421537 TAAAATAA-ATAATTTTAGTCAAAATAAAAATTAA
1 TAAAATAACA-AATTTTAGTCAAAATAAAAATTAA
* *
47421571 GAAAATAACAAA-TTTAGTCAAAA-CAAAATTAA
1 TAAAATAACAAATTTTAGTCAAAATAAAAATTAA
47421603 TAAAATAACAA
1 TAAAATAACAA
47421614 CCCATTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
32 18 0.46
33 11 0.28
34 9 0.23
35 1 0.03
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (34 bp):
TAAAATAACAAATTTTAGTCAAAATAAAAATTAA
Found at i:47421746 original size:17 final size:17
Alignment explanation
Indices: 47421720--47421802 Score: 103
Period size: 17 Copynumber: 4.9 Consensus size: 17
47421710 AACCATTTTG
* *
47421720 AATTTGTTTTAAAATTA
1 AATTTATTTTAAATTTA
47421737 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
47421754 AATTTAATTTAAATTTG
1 AATTTATTTTAAATTTA
* *
47421771 GATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
*
47421788 AATTTATTATAAATT
1 AATTTATTTTAAATT
47421803 CAAAGTCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:47421753 original size:6 final size:6
Alignment explanation
Indices: 47421727--47421793 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
47421717 TTGAATTTGT
* * **
47421727 TTTAAA ATTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAA TTTGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
47421773 TTT-AA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
47421794 TTATAAATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 13 0.25
6 38 0.75
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:47421762 original size:11 final size:12
Alignment explanation
Indices: 47421727--47421793 Score: 77
Period size: 11 Copynumber: 5.8 Consensus size: 12
47421717 TTGAATTTGT
*
47421727 TTTAAAATTAAA
1 TTTAAATTTAAA
*
47421739 TTT-ATTTTAAA
1 TTTAAATTTAAA
47421750 TTTAAATTT-AA
1 TTTAAATTTAAA
**
47421761 TTTAAATTTGGA
1 TTTAAATTTAAA
47421773 TTT-AATTTAAA
1 TTTAAATTTAAA
47421784 TTTAAATTTA
1 TTTAAATTTA
47421794 TTATAAATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
11 29 0.63
12 17 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:47423050 original size:27 final size:27
Alignment explanation
Indices: 47422988--47423053 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
47422978 CCGGACGGCG
*
47422988 GGCGCGTG--CGGCTGGGGGCAGGATC
1 GGCGCGTGACCGGCTGGAGGCAGGATC
*
47423013 GGAGCGTGACCGG-TGGAGGCAGGATGC
1 GGCGCGTGACCGGCTGGAGGCAGGAT-C
47423040 GGCGCGTGACCGGC
1 GGCGCGTGACCGGC
47423054 GACGCGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.21
26 11 0.32
27 16 0.47
ACGTcount: A:0.12, C:0.24, G:0.53, T:0.11
Consensus pattern (27 bp):
GGCGCGTGACCGGCTGGAGGCAGGATC
Found at i:47423089 original size:16 final size:18
Alignment explanation
Indices: 47423068--47423101 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
47423058 CGCTTTGGAC
47423068 GGCCGGCC-TGGT-AGGT
1 GGCCGGCCATGGTGAGGT
47423084 GGCCGGCCATGGTGAGGT
1 GGCCGGCCATGGTGAGGT
47423102 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.09, C:0.24, G:0.50, T:0.18
Consensus pattern (18 bp):
GGCCGGCCATGGTGAGGT
Found at i:47423743 original size:30 final size:30
Alignment explanation
Indices: 47423622--47423742 Score: 145
Period size: 30 Copynumber: 4.0 Consensus size: 30
47423612 CCCCAAACAA
* **
47423622 TCCAGAAATTGCATTTTAACCCTGAAACTTT
1 TCCA-AAATTACATTTTAACCCCAAAACTTT
* *
47423653 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
* *
47423683 TCCAAAATTAGATTTTGACCCCAAAAC-TT
1 TCCAAAATTACATTTTAACCCCAAAACTTT
*
47423712 TCAAAAAATTACATTTTAACCCCAAAACTTT
1 TC-CAAAATTACATTTTAACCCCAAAACTTT
47423743 CCTAAATCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 4 0.05
30 69 0.87
31 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTAACCCCAAAACTTT
Found at i:47423759 original size:30 final size:29
Alignment explanation
Indices: 47423634--47423764 Score: 120
Period size: 30 Copynumber: 4.4 Consensus size: 29
47423624 CAGAAATTGC
** **
47423634 ATTTTAACCCTGAAACTTTTCCAAAATTAT
1 ATTTTAACCCCAAAAC-TTTCCAAAATTCG
* *
47423664 ATTTTGACCCCAAAACTTTTCCAAAATTAG
1 ATTTTAACCCCAAAAC-TTTCCAAAATTCG
* *
47423694 ATTTTGACCCCAAAACTTTCAAAAAATTAC-
1 ATTTTAACCCCAAAACTTTC-CAAAATT-CG
*
47423724 ATTTTAACCCCAAAACTTTCCTAAATCTCG
1 ATTTTAACCCCAAAACTTTCCAAAAT-TCG
*
47423754 TTTTTAACCCC
1 ATTTTAACCCC
47423765 GATTTCACCG
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
29 9 0.10
30 78 0.90
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTTTAACCCCAAAACTTTCCAAAATTCG
Found at i:47423846 original size:29 final size:29
Alignment explanation
Indices: 47423755--47423846 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
47423745 TAAATCTCGT
*
47423755 TTTTAACCCCGATTTCACCGAAAATTACCA
1 TTTTAACCCCAATTTCACC-AAAATTACCA
* ** *
47423785 TTTT-ACCATCGAATCTT--TTAAAATT-CTA
1 TTTTAACC--CCAAT-TTCACCAAAATTACCA
47423813 TTTTTAACCCCAATTTCACCAAAATTACCA
1 -TTTTAACCCCAATTTCACCAAAATTACCA
47423843 TTTT
1 TTTT
47423847 GCCTCCCGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 17
0.63 0.13 0.24
Matches are distributed among these distances:
27 2 0.04
28 6 0.13
29 23 0.51
30 9 0.20
31 3 0.07
32 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTTAACCCCAATTTCACCAAAATTACCA
Found at i:47435861 original size:68 final size:69
Alignment explanation
Indices: 47435752--47437153 Score: 1906
Period size: 68 Copynumber: 19.9 Consensus size: 69
47435742 CTGCAGGTCT
*
47435752 CAACGTCATCCCCT-TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47435816 AGAG
66 AGAG
*
47435820 CAACGTCATCCCCTCAG-AATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGTTGAA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAA---TTGAA
47435884 GTAAGAG
63 GTAAGAG
*
47435891 CAACGTCATCCCCT-TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47435955 AGAG
66 AGAG
*
47435959 CAACGTCATCCCCT-TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47436023 AGAG
66 AGAG
* *
47436027 CAATGTCATCCCCTC-GAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47436091 AGAG
66 AGAG
*
47436095 CAACGTCATCCCCTC-GGAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTATTGAA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTG-AA--ATTGAA
47436159 GTAAGAG
63 GTAAGAG
* * *
47436166 CAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCTCTGAA
1 CAACG-TCA---TCC---CCTC-TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
47436230 ATTGAAGTAAGAG
57 ATTGAAGTAAGAG
*
47436243 CAACGTCATCCCCTC-GAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47436307 AGAG
66 AGAG
* *
47436311 CAACGTCATCCCCTC-GGAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTATTGAA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTG-AA--ATTGAA
47436375 GTAAGAG
63 GTAAGAG
* * *
47436382 CAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCTCTGAA
1 CAACG-TCA---TCC---CCTC-TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
47436446 ATTGAAGTAAGAG
57 ATTGAAGTAAGAG
* *
47436459 CAACGTCATCCCCT-TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTAAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47436523 AGAG
66 AGAG
*
47436527 CAACGTCATCCCCTC-GAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47436591 AGAG
66 AGAG
*
47436595 CAACGTCATCCCCTC-GGAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGTTGAA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAA---TTGAA
47436659 GTAAGAG
63 GTAAGAG
* * * *
47436666 CAAGGTCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCTCTGAAA
1 CAACGTCA---TCC---CCTC-TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAA
47436731 TTGAAGTAAGAG
58 TTGAAGTAAGAG
*
47436743 CAACGTCATCCCCTC-GAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47436807 AGAG
66 AGAG
*
47436811 CAACGTCATCCCCTC-GAAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTGAA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAA---TTGAA
47436875 GTAAGAG
63 GTAAGAG
* * *
47436882 CAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCTCTGAA
1 CAACG-TCA---TCC---CCTC-TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
47436946 ATTGAAGTAAGAG
57 ATTGAAGTAAGAG
*
47436959 CAACGTCATCCCCT-TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47437023 AGAG
66 AGAG
* * *
47437027 CAACGTCATCCCCTC-GAAATTGAAGTAGAGTGGATAACACATCTTTATCGCTGAAATTAAAGTA
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
47437091 AGAG
66 AGAG
* *
47437095 CAACGTCATCCCCTC-GGAACTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
1 CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
47437154 TTGAAGTAAA
Statistics
Matches: 1211, Mismatches: 61, Indels: 124
0.87 0.04 0.09
Matches are distributed among these distances:
68 732 0.60
69 63 0.05
70 4 0.00
71 149 0.12
74 24 0.02
77 87 0.07
78 3 0.00
79 57 0.05
80 92 0.08
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (69 bp):
CAACGTCATCCCCTCTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTA
AGAG
Found at i:47435917 original size:31 final size:31
Alignment explanation
Indices: 47435879--47436121 Score: 137
Period size: 31 Copynumber: 7.3 Consensus size: 31
47435869 TCTGAAATTG
47435879 TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
1 TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
** * **
47435910 TTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAA
1 TTGAAGTA-A---GAGCA-ACGTCATCCCCT-TGAAA
47435947 TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
1 TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
** * **
47435978 TTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAA
1 TTGAAGTA-A---GAGCA-ACGTCATCCCCT-TGAAA
* *
47436015 TTGAAGTAAGAGCAATGTCATCCCCTCGAAA
1 TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
* * * **
47436046 TTGAAGTAGAGTGGATAAC-ACATCTTTATCTCTGAAA
1 TTGAAGTA-AG-AG-CAACGTCATC---CCCT-TGAAA
* *
47436083 TTGAAGTAAGAGCAACGTCATCCCCTCGGAA
1 TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
47436114 TTGAAGTA
1 TTGAAGTA
47436122 GAGTGGATAA
Statistics
Matches: 156, Mismatches: 36, Indels: 40
0.67 0.16 0.17
Matches are distributed among these distances:
31 44 0.28
32 23 0.15
33 11 0.07
34 5 0.03
35 11 0.07
36 24 0.15
37 38 0.24
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (31 bp):
TTGAAGTAAGAGCAACGTCATCCCCTTGAAA
Found at i:47436262 original size:31 final size:31
Alignment explanation
Indices: 47436227--47436337 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 31
47436217 CTTCATCTCT
47436227 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
* * * **
47436258 GAAATTGAAGTAGAGTGGATAAC-ACATCTTTATCTC
1 GAAATTGAAGTA-AG-AG-CAACGTCATC---CCCTC
47436294 TGAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
*
47436326 GGAATTGAAGTA
1 GAAATTGAAGTA
47436338 GAGTAGATAA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
31 23 0.38
32 5 0.08
33 5 0.08
34 6 0.10
35 5 0.08
36 5 0.08
37 12 0.20
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (31 bp):
GAAATTGAAGTAAGAGCAACGTCATCCCCTC
Found at i:47436262 original size:216 final size:204
Alignment explanation
Indices: 47435752--47437153 Score: 1948
Period size: 216 Copynumber: 6.6 Consensus size: 204
47435742 CTGCAGGTCT
47435752 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
47435817 GAGCAACGTCATCCCCTC-AGAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGTT
66 GAGCAACGTCATCCCCTCGA-AATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAA---TT
* *
47435881 GAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAA
127 GAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAA
47435946 ATTGAAGTAAGAG
192 ATTGAAGTAAGAG
47435959 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
* *
47436024 GAGCAATGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAG
66 GAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
*
47436089 TAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTA
131 TAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTG-AA--A
47436154 TTGAAGTAAGAG
193 TTGAAGTAAGAG
*
47436166 CAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCTCTGAA
1 CAACG-TCA---TCC---C--CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAA
*
47436230 ATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCT
56 ATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCT
* *
47436295 GAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTAGATAACACGTCTTTATC
121 GAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATC
47436360 TCTGAAATTATTGAAGTAAGAG
186 TCTG-AA--ATTGAAGTAAGAG
*
47436382 CAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCTCTGAA
1 CAACG-TCA---TCC---C--CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAA
* *
47436446 ATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCT
56 ATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCT
* *
47436511 AAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATC
121 GAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATC
47436576 TCTGAAATTGAAGTAAGAG
186 TCTGAAATTGAAGTAAGAG
* * *
47436595 CAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGTTGAAG
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAA---TTGAAG
* * * *
47436660 TAAGAGCAAGGTCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATCT
63 TAAGAGCAACGTCA---TCC---C--CTCGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCT
*
47436725 CTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTA
119 CTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTA
47436790 TCTCTGAAATTGAAGTAAGAG
184 TCTCTGAAATTGAAGTAAGAG
* * *
47436811 CAACGTCATCCCCTCGAAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTGAAG
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAA---TTGAAG
* * *
47436876 TAAGAGCAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCATC
63 TAAGAGCAACG-TCA---TCC---C--CTCGAAATTGAAGTAGAG-TGGATAACACGTCTTTATC
* *
47436940 TCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTC
118 TCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTT
47437005 ATCTCTGAAATTGAAGTAAGAG
183 ATCTCTGAAATTGAAGTAAGAG
* * * * *
47437027 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCGCTGAAATTAAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
* *
47437092 GAGCAACGTCATCCCCTCGGAACTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
66 GAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
47437154 TTGAAGTAAA
Statistics
Matches: 1130, Mismatches: 36, Indels: 61
0.92 0.03 0.05
Matches are distributed among these distances:
204 115 0.10
205 31 0.03
206 1 0.00
207 160 0.14
208 1 0.00
210 12 0.01
213 38 0.03
214 2 0.00
215 37 0.03
216 733 0.65
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (204 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
TAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
AAGTAAGAG
Found at i:47436477 original size:31 final size:31
Alignment explanation
Indices: 47436442--47436621 Score: 110
Period size: 31 Copynumber: 5.4 Consensus size: 31
47436432 TCTTCATCTC
47436442 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
** * **
47436473 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT
*
47436509 CTAAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
* * * * **
47436541 CGAAATTGAAGTAGAGTGGATAAC-ACATCTTTATCT
1 TGAAATTGAAGTA-AG-AG-CAACGTCATC---CCCT
47436577 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
* *
47436609 CGGAATTGAAGTA
1 TGAAATTGAAGTA
47436622 GAGTGGATAA
Statistics
Matches: 109, Mismatches: 26, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
31 35 0.32
32 14 0.13
33 8 0.07
34 6 0.06
35 8 0.07
36 14 0.13
37 24 0.22
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCCCT
Found at i:47436684 original size:500 final size:500
Alignment explanation
Indices: 47435752--47437213 Score: 2692
Period size: 500 Copynumber: 2.9 Consensus size: 500
47435742 CTGCAGGTCT
* * *
47435752 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
* *
47435817 GAGCAACGTCATCCCCTCAGAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGTTG
66 GAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTG
*
47435882 AAGTAAGAGCAACG-TCA---TCC---C--CTTGAAATTGAAGTAGAG-TGGATAACACGTCTTC
131 AAGTAAGAGCAA-GATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTC
47435937 ATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTC
195 ATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTC
*
47436002 TTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACAC
260 TTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACAC
47436067 ATCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAA
325 ATCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAA
*
47436132 CACGTCTTTATCTCTGAAATTATTGAAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGA
390 CACGTCTTTATCTCTGAAATTGTTGAAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGA
47436197 AGTAAAGCTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
455 AGTAAAGCTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
47436243 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
*
47436308 GAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTATTG
66 GAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTG
47436373 AAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCA
131 AAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCA
47436438 TCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
196 TCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
47436503 TCATCTCTAAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACA
261 TCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACA
47436568 TCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAAC
326 TCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAAC
*
47436633 ACGTCTTTATCTCTGAAATTGTTGAAGTAAGAGCAAGGTCATTTTCCTATCTTCTTGAAATTGAA
391 ACGTCTTTATCTCTGAAATTGTTGAAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAA
47436698 GTAAAGCTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
456 GTAAAGCTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
47436743 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
*
47436808 GAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTG
66 GAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTG
47436873 AAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCA
131 AAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCA
47436938 TCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
196 TCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
47437003 TCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACA
261 TCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACA
* * *
47437068 TCTTTATCGCTGAAATTAAAGTAAGAGCAACGTCATCCCCTCGGAACTGAAGTAGAGTGGATAAC
326 TCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAAC
*
47437133 ACGTCTTTATCTCTGAAATTGTTGAAGTAAAAGCAAGATCATTTTCCTATCTTCTTGAAATTGAA
391 ACGTCTTTATCTCTGAAATTGTTGAAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAA
*
47437198 GTAAAGCTGGACAACA
456 GTAAAGCTGGATAACA
47437214 AGCCTTCGCC
Statistics
Matches: 941, Mismatches: 20, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
490 1 0.00
491 139 0.15
494 3 0.00
497 1 0.00
499 17 0.02
500 780 0.83
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (500 bp):
CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTAGATAACACGTCTTTATCTCTGAAATTGTTG
AAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACACGTCTTCA
TCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
TCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACA
TCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAAC
ACGTCTTTATCTCTGAAATTGTTGAAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAA
GTAAAGCTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG
Found at i:47436762 original size:31 final size:31
Alignment explanation
Indices: 47436727--47436837 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 31
47436717 CTTCATCTCT
47436727 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 GAAATTGAAGTAAGAGCAACGTCATCCCCTC
* * * **
47436758 GAAATTGAAGTAGAGTGGATAAC-ACATCTTTATCTC
1 GAAATTGAAGTA-AG-AG-CAACGTCATC---CCCTC
47436794 TGAAATTGAAGTAAGAGCAACGTCATCCCCTC
1 -GAAATTGAAGTAAGAGCAACGTCATCCCCTC
47436826 GAAATTGAAGTA
1 GAAATTGAAGTA
47436838 GAGTAGATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
31 24 0.39
32 5 0.08
33 5 0.08
34 6 0.10
35 5 0.08
36 5 0.08
37 12 0.19
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (31 bp):
GAAATTGAAGTAAGAGCAACGTCATCCCCTC
Found at i:47436977 original size:31 final size:31
Alignment explanation
Indices: 47436942--47437053 Score: 116
Period size: 31 Copynumber: 3.4 Consensus size: 31
47436932 TCTTCATCTC
47436942 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
** * **
47436973 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT
47437009 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
*
47437041 CGAAATTGAAGTA
1 TGAAATTGAAGTA
47437054 GAGTGGATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
31 25 0.39
32 10 0.16
33 3 0.05
35 3 0.05
36 10 0.16
37 13 0.20
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCCCT
Found at i:47437498 original size:17 final size:17
Alignment explanation
Indices: 47437472--47437554 Score: 103
Period size: 17 Copynumber: 4.9 Consensus size: 17
47437462 AACCATTTTG
* *
47437472 AATTTGTTTTAAAATTA
1 AATTTATTTTAAATTTA
47437489 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
47437506 AATTTAATTTAAATTTG
1 AATTTATTTTAAATTTA
* *
47437523 GATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
*
47437540 AATTTATTATAAATT
1 AATTTATTTTAAATT
47437555 CAAAGTCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:47437505 original size:6 final size:6
Alignment explanation
Indices: 47437479--47437545 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
47437469 TTGAATTTGT
* * **
47437479 TTTAAA ATTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAA TTTGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
47437525 TTT-AA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
47437546 TTATAAATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 13 0.25
6 38 0.75
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:47437514 original size:11 final size:12
Alignment explanation
Indices: 47437479--47437545 Score: 77
Period size: 11 Copynumber: 5.8 Consensus size: 12
47437469 TTGAATTTGT
*
47437479 TTTAAAATTAAA
1 TTTAAATTTAAA
*
47437491 TTT-ATTTTAAA
1 TTTAAATTTAAA
47437502 TTTAAATTT-AA
1 TTTAAATTTAAA
**
47437513 TTTAAATTTGGA
1 TTTAAATTTAAA
47437525 TTT-AATTTAAA
1 TTTAAATTTAAA
47437536 TTTAAATTTA
1 TTTAAATTTA
47437546 TTATAAATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
11 29 0.63
12 17 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:47437776 original size:15 final size:15
Alignment explanation
Indices: 47437756--47437786 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47437746 GCCTATGCTG
47437756 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
47437771 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
47437786 C
1 C
47437787 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:47438806 original size:27 final size:27
Alignment explanation
Indices: 47438744--47438809 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
47438734 CCGGACGGCG
*
47438744 GGCGCGTG--CGGCTGGGGGCAGGATC
1 GGCGCGTGACCGGCTGGAGGCAGGATC
*
47438769 GGAGCGTGACCGG-TGGAGGCAGGATGC
1 GGCGCGTGACCGGCTGGAGGCAGGAT-C
47438796 GGCGCGTGACCGGC
1 GGCGCGTGACCGGC
47438810 GACGCGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.21
26 11 0.32
27 16 0.47
ACGTcount: A:0.12, C:0.24, G:0.53, T:0.11
Consensus pattern (27 bp):
GGCGCGTGACCGGCTGGAGGCAGGATC
Found at i:47438845 original size:16 final size:18
Alignment explanation
Indices: 47438824--47438857 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
47438814 CGCTTTGGAC
47438824 GGCCGGCC-TGGT-AGGT
1 GGCCGGCCATGGTGAGGT
47438840 GGCCGGCCATGGTGAGGT
1 GGCCGGCCATGGTGAGGT
47438858 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.09, C:0.24, G:0.50, T:0.18
Consensus pattern (18 bp):
GGCCGGCCATGGTGAGGT
Found at i:47439417 original size:30 final size:30
Alignment explanation
Indices: 47439378--47439528 Score: 196
Period size: 30 Copynumber: 5.0 Consensus size: 30
47439368 CCCCAAACAA
* **
47439378 TCCAGAAATTGCATTTTGACCCTGAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
47439409 TCCAAAATTGCATTTTGACCCAAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
47439439 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
47439469 TCCAAAATTACATTTTGACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
47439498 TCAAAAAATTACATTTTAACCCCAGAACTTT
1 TC-CAAAATTACATTTTGACCCCAAAACTTT
47439529 CTTAAATCCC
Statistics
Matches: 109, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
29 4 0.04
30 99 0.91
31 6 0.06
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:47441550 original size:17 final size:17
Alignment explanation
Indices: 47441528--47441560 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
47441518 AAAAAGTTTT
47441528 TAATAAAGTGTTCAACC
1 TAATAAAGTGTTCAACC
47441545 TAATAAAGTGTTCAAC
1 TAATAAAGTGTTCAAC
47441561 TTTCTTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (17 bp):
TAATAAAGTGTTCAACC
Found at i:47454762 original size:157 final size:156
Alignment explanation
Indices: 47454473--47454784 Score: 423
Period size: 157 Copynumber: 2.0 Consensus size: 156
47454463 TAATTCAATA
* * * *
47454473 ATGTAAAACATGGCATTTTGTTTTAGTTAAACGATGCGGATAAGAGTTTAATAAAAACGGTGCGT
1 ATGTAAAACAGGGCATTTTATTTTAGTTAAACGAGGCGGATAAGAGTTTAATAAAAACGGCGCGT
* * * * *
47454538 AGAAAGGGAAGACAACGACTTGAGCTATTAATAGGCCAACTAACTTTTCAAACGGTTAATTACTT
66 AGAAAGAGAAGACAACGACCTGAGCTATCAATAGACCAACTAACTTTTCAAACGGCTAATTACTT
*
47454603 TCTTTTTAAGCACACCTTTGTTGTTGG
131 TCTTTTTAAGCACACCCTT-TTGTTGG
* * **
47454630 ATGTAAAACAGGGTATTTTATTTTAGTTAAACGGGGCGGATAAGAGTTTAATAAAAGTGATGCGC
1 ATGTAAAACAGGGCATTTTATTTTAGTTAAACGAGGCGGATAAGAGTTTAATAAAAACG--GCGC
* *
47454695 GTA-AAA-AGAATACAACGACCTGAGCTATCAATAGACTAACTAACTTTTCAAACGGCTAATT-C
64 GTAGAAAGAGAAGACAACGACCTGAGCTATCAATAGACCAACTAACTTTTCAAACGGCTAATTAC
47454757 ATTTCTTTTTAAGCACACCCTTTTGTTG
129 -TTTCTTTTTAAGCACACCCTTTTGTTG
47454785 AGCAGTTTCA
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
156 7 0.05
157 120 0.88
158 3 0.02
159 6 0.04
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (156 bp):
ATGTAAAACAGGGCATTTTATTTTAGTTAAACGAGGCGGATAAGAGTTTAATAAAAACGGCGCGT
AGAAAGAGAAGACAACGACCTGAGCTATCAATAGACCAACTAACTTTTCAAACGGCTAATTACTT
TCTTTTTAAGCACACCCTTTTGTTGG
Found at i:47456297 original size:178 final size:179
Alignment explanation
Indices: 47455991--47456339 Score: 565
Period size: 178 Copynumber: 1.9 Consensus size: 179
47455981 TTTTTTTTTG
*
47455991 GTGGATTTGATCTTTGGGACCTGTTCTTTTTTTTTTCTATAAAACCTTTGGTTTGATCAACATGT
1 GTGGATTTGATCTTTGGGACCTG-T-TTATTTTTTTCTATAAAACCTTTGGTTTGATCAACATGT
* * *
47456056 TTCGTTAGATTTGCATTTGTATTTCCCTGTGAGTTTGTGCTAAATATTTTAAGGTTCTACTTACA
64 TTCATTAGATTTGCATTTGTATTTCCCTGTGAGTTTGTGCTAAACATTTCAAGGTTCTACTTACA
* *
47456121 TTTGGCTTAGCAAAATGTTTTAGCAAAACAAGATTTTGTGTATGTGTGTGT
129 TTTAGCTTAGCAAAATGTTTTAGCAAAACAAGATTGTGTGTATGTGTGTGT
*
47456172 GTGGATTTGATCTTTGGGACCTG-TTATTTTTTTCTATAAAACCTTTGGTTTGATCAACTTGTTT
1 GTGGATTTGATCTTTGGGACCTGTTTATTTTTTTCTATAAAACCTTTGGTTTGATCAACATGTTT
* * *
47456236 CATTAGATTTGCATTTGTATTTCCCTGTGAGTTTGTGTTGAACATTTCAAGGTTTTACTTACATT
66 CATTAGATTTGCATTTGTATTTCCCTGTGAGTTTGTGCTAAACATTTCAAGGTTCTACTTACATT
* *
47456301 TAGCTTGGCAAAATGTTTTAGTAAAACAAGATTGTGTGT
131 TAGCTTAGCAAAATGTTTTAGCAAAACAAGATTGTGTGT
47456340 GTGAAGAATC
Statistics
Matches: 156, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
178 133 0.85
181 23 0.15
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (179 bp):
GTGGATTTGATCTTTGGGACCTGTTTATTTTTTTCTATAAAACCTTTGGTTTGATCAACATGTTT
CATTAGATTTGCATTTGTATTTCCCTGTGAGTTTGTGCTAAACATTTCAAGGTTCTACTTACATT
TAGCTTAGCAAAATGTTTTAGCAAAACAAGATTGTGTGTATGTGTGTGT
Found at i:47458917 original size:24 final size:24
Alignment explanation
Indices: 47458890--47458941 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
47458880 ACAAGAAGAA
47458890 AATGAAGATGATGATAG-TGATGCT
1 AATGAAGATGATGA-AGCTGATGCT
** *
47458914 AATGCTGATGCTGAAGCTGATGCT
1 AATGAAGATGATGAAGCTGATGCT
47458938 AATG
1 AATG
47458942 CTGAAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (24 bp):
AATGAAGATGATGAAGCTGATGCT
Found at i:47458922 original size:12 final size:12
Alignment explanation
Indices: 47458907--47458945 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
47458897 ATGATGATAG
47458907 TGATGCTAATGC
1 TGATGCTAATGC
47458919 TGATGCTGAA-GC
1 TGATGCT-AATGC
47458931 TGATGCTAATGC
1 TGATGCTAATGC
47458943 TGA
1 TGA
47458946 AGATAAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (12 bp):
TGATGCTAATGC
Found at i:47466830 original size:2 final size:2
Alignment explanation
Indices: 47466823--47466868 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
47466813 GGTAATTTAA
47466823 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
47466865 AG AG
1 AG AG
47466869 TTCACAATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47469737 original size:46 final size:46
Alignment explanation
Indices: 47469685--47469774 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
47469675 TGAAACCAGT
47469685 AGGATCATTAATATATAACGTGATAAAGAAGTACTTCTGCTTCCTA
1 AGGATCATTAATATATAACGTGATAAAGAAGTACTTCTGCTTCCTA
* * * *
47469731 AGGATCATTAATGTATAACGTGATATAGAATTATTTCTGCTTCC
1 AGGATCATTAATATATAACGTGATAAAGAAGTACTTCTGCTTCC
47469775 GAACAGAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (46 bp):
AGGATCATTAATATATAACGTGATAAAGAAGTACTTCTGCTTCCTA
Found at i:47470776 original size:11 final size:11
Alignment explanation
Indices: 47470760--47470788 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
47470750 TGAAGTACTA
47470760 GTGTTCAGCAC
1 GTGTTCAGCAC
47470771 GTGTTCAGCAC
1 GTGTTCAGCAC
47470782 GTGTTCA
1 GTGTTCA
47470789 ACACATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (11 bp):
GTGTTCAGCAC
Found at i:47472128 original size:17 final size:17
Alignment explanation
Indices: 47472095--47472127 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47472085 CAAATAAACA
47472095 AACAAAAATTTTATTTT
1 AACAAAAATTTTATTTT
*
47472112 AACAAAAGTTTT-TTTT
1 AACAAAAATTTTATTTT
47472128 TTATCATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AACAAAAATTTTATTTT
Found at i:47472531 original size:28 final size:27
Alignment explanation
Indices: 47472479--47472533 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
47472469 TATCTTAAAC
* *
47472479 AAAATTTAATAATTAAATCTGAATTTT
1 AAAATTTAAAAATTAAATCTCAATTTT
*
47472506 AAAATTTAAAAAATTAAATTTCAATTTT
1 AAAATTT-AAAAATTAAATCTCAATTTT
47472534 TCAAAGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAATTTAAAAATTAAATCTCAATTTT
Found at i:47473567 original size:11 final size:11
Alignment explanation
Indices: 47473526--47473556 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
47473516 CACAAGAATG
47473526 AGAAAAGAAGA
1 AGAAAAGAAGA
47473537 AGAAAAGAAGA
1 AGAAAAGAAGA
47473548 AGAAAAGAA
1 AGAAAAGAA
47473557 TGAGGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAGA
Found at i:47483872 original size:39 final size:40
Alignment explanation
Indices: 47483783--47483881 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
47483773 TGGGACAAGT
*
47483783 CTCTTCCAAAAGGTGTCCATCCAATATGAAAATGATTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
* *
47483824 CTTTTCAAAAGGTGTCCATCCAATATG-AAAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
47483863 CTCTTCAAAAGGTGTCCAT
1 CTCTTCAAAAGGTGTCCAT
47483882 TGAGTGCATA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 28 0.52
40 22 0.41
41 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
Found at i:47487450 original size:19 final size:19
Alignment explanation
Indices: 47487424--47487468 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
47487414 ACAGGGCTAT
47487424 AACGCAACTTGAGTATGCC
1 AACGCAACTTGAGTATGCC
*
47487443 AGCGCAACTTGAGTATGCC
1 AACGCAACTTGAGTATGCC
47487462 AACGCAA
1 AACGCAA
47487469 TTGGAAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (19 bp):
AACGCAACTTGAGTATGCC
Found at i:47488937 original size:48 final size:46
Alignment explanation
Indices: 47488882--47488999 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 46
47488872 CGAAGTACTG
47488882 AACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACAAAGTGCT-A-
1 AACAGAGAGCACA-AAGTGCT--G-AACAGAGAGCACACAAAGTGCTAAT
* * *
47488930 AACAGAGAGTACACAAAGTACTGATCAGAGAGCACACACAGTGCTAAT
1 AACAGAGAG--CACAAAGTGCTGAACAGAGAGCACACAAAGTGCTAAT
47488978 AACAGAGAGCACACACAGTGCT
1 AACAGAGAGCACA-A-AGTGCT
47489000 AATTAGAGAG
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
46 24 0.40
47 3 0.05
48 23 0.38
49 6 0.10
50 4 0.07
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (46 bp):
AACAGAGAGCACAAAGTGCTGAACAGAGAGCACACAAAGTGCTAAT
Found at i:47488938 original size:25 final size:23
Alignment explanation
Indices: 47488907--47489010 Score: 118
Period size: 23 Copynumber: 4.4 Consensus size: 23
47488897 AGTGCTGGGC
47488907 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
47488930 AACAGAGAGTACACAAAGTACTG
1 AACAGAGAGCACACAAAGTGCTA
* *
47488953 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
*
47488977 TAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCACACAAAGTGCTA
**
47489001 ATTAGAGAGC
1 AACAGAGAGC
47489011 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
23 46 0.68
24 1 0.01
25 21 0.31
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:47489008 original size:48 final size:46
Alignment explanation
Indices: 47488909--47489010 Score: 132
Period size: 48 Copynumber: 2.2 Consensus size: 46
47488899 TGCTGGGCAA
* *
47488909 CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTGAT
1 CAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * *
47488955 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCT-A-AACAGAGAGCACACAAAGTACTAAT
*
47489003 TAGAGAGC
1 CAGAGAGC
47489011 GCGCTAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 19 0.40
47 1 0.02
48 28 0.58
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.13
Consensus pattern (46 bp):
CAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:47489009 original size:71 final size:71
Alignment explanation
Indices: 47488860--47489001 Score: 191
Period size: 71 Copynumber: 2.0 Consensus size: 71
47488850 TAGACGGAAC
* * **
47488860 AAACAGA-AGTAC-CGAAGTACTGAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACAA
1 AAACAGAGAGTACACAAAGTACTGAACAGAGAGCACACAAGTGCTGAACAACAGAGAGCACACAA
47488923 AGTGCT
66 AGTGCT
* *
47488929 AAACAGAGAGTACACAAAGTACTGATCAGAGAGCACACACAGTGCT-AATAACAGAGAGCACACA
1 AAACAGAGAGTACACAAAGTACTGAACAGAGAGCACACA-AGTGCTGAACAACAGAGAGCACACA
*
47488993 CAGTGCT
65 AAGTGCT
47489000 AA
1 AA
47489002 TTAGAGAGCG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
69 7 0.11
70 5 0.08
71 45 0.71
72 6 0.10
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (71 bp):
AAACAGAGAGTACACAAAGTACTGAACAGAGAGCACACAAGTGCTGAACAACAGAGAGCACACAA
AGTGCT
Found at i:47491543 original size:39 final size:40
Alignment explanation
Indices: 47491456--47491554 Score: 148
Period size: 39 Copynumber: 2.5 Consensus size: 40
47491446 TGGGACAAGC
*
47491456 CTCTTCCAAAAGGTGTTCATACAATATGAGAAGGGTTGTGA
1 CTCTT-CAAAAGGTGTCCATACAATATGAGAAGGGTTGTGA
*
47491497 CTTTTCAAAAGGTGTCCAT-CTAATATGA-AAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCATAC-AATATGAGAAGGGTTGTGA
47491536 CTCTTCAAAAGGTGTCCAT
1 CTCTTCAAAAGGTGTCCAT
47491555 TGAGTGCATA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
39 30 0.56
40 20 0.37
41 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCATACAATATGAGAAGGGTTGTGA
Found at i:47492343 original size:17 final size:18
Alignment explanation
Indices: 47492304--47492345 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
47492294 TTTAAAAGTG
47492304 CTTTTGAGCCAAAAAGCA
1 CTTTTGAGCCAAAAAGCA
47492322 C-TTTG-GCTCAAAAA-CA
1 CTTTTGAGC-CAAAAAGCA
47492338 CTTTTGAG
1 CTTTTGAG
47492346 AAAAAGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.24
17 14 0.67
18 2 0.10
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (18 bp):
CTTTTGAGCCAAAAAGCA
Found at i:47497843 original size:2 final size:2
Alignment explanation
Indices: 47497836--47497861 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47497826 GTTCTTTTAC
47497836 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47497862 TTCTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47507172 original size:52 final size:52
Alignment explanation
Indices: 47507089--47507191 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
47507079 AAGATGCCAG
47507089 GATAGAAAGCAGGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGTT
1 GATAGAAAGCAGGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGTT
* * *
47507141 GATATAAAGCATGTGATTTGAAATTAACCTGACTTCATTAATAACAAATGT
1 GATAGAAAGCAGGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGT
47507192 AGATGTAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (52 bp):
GATAGAAAGCAGGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGTT
Found at i:47509275 original size:16 final size:18
Alignment explanation
Indices: 47509236--47509277 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
47509226 AAAATTTATA
47509236 ATATTT-TATATTATGAT
1 ATATTTATATATTATGAT
*
47509253 ATTTTTATATATTATG-T
1 ATATTTATATATTATGAT
47509270 A-ATTTATA
1 ATATTTATA
47509278 ACACATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATATTTATATATTATGAT
Found at i:47509405 original size:26 final size:27
Alignment explanation
Indices: 47509353--47509409 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
47509343 TAGAATGACT
* *
47509353 ATATAAAATATTTTAATAAATAAAATA
1 ATATAAAACATTTTAATAAAAAAAATA
47509380 ATAT-AAACATTTTAA-AAAAAATAATA
1 ATATAAAACATTTTAATAAAAAA-AATA
47509406 ATAT
1 ATAT
47509410 GAACGAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 5 0.19
26 18 0.67
27 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAAAACATTTTAATAAAAAAAATA
Found at i:47512687 original size:2 final size:2
Alignment explanation
Indices: 47512680--47512705 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47512670 CTTTTTCTTC
47512680 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47512706 GTCCTCAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47527876 original size:24 final size:24
Alignment explanation
Indices: 47527839--47527884 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
47527829 CCATTTCTCA
*
47527839 AGCCCTCTGTTGGGGATCGACTGG
1 AGCCCTCTGCTGGGGATCGACTGG
* *
47527863 AGCCCTTTGCTGGGGATTGACT
1 AGCCCTCTGCTGGGGATCGACT
47527885 CGTGTCGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.24, G:0.35, T:0.28
Consensus pattern (24 bp):
AGCCCTCTGCTGGGGATCGACTGG
Found at i:47529176 original size:29 final size:29
Alignment explanation
Indices: 47529091--47529181 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
47529081 CCGGGGGGGC
47529091 AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTGGTGAAATCGGGGTT
* * * *
47529120 AAAACGG-AATTCT--AGAAGCTTCGAGGG-T
1 AAAATGGTAATTTTGGTGAA--ATCG-GGGTT
47529148 AAAATGGTAATTTTCGGTGAAATCGGGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
47529178 AAAA
1 AAAA
47529182 ACGGGATTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
26 3 0.07
28 15 0.33
29 17 0.37
30 8 0.17
32 3 0.07
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTT
Found at i:47529228 original size:30 final size:30
Alignment explanation
Indices: 47529194--47529374 Score: 290
Period size: 30 Copynumber: 6.0 Consensus size: 30
47529184 GGGATTTAGG
* * *
47529194 AAAGTTCTGGGGTTAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
47529224 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
47529254 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
47529284 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
47529314 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
47529344 AAAGTTTCGGGGTCAAAATGCAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
47529375 TTGTTTGGGG
Statistics
Matches: 143, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
30 139 0.97
31 4 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:47529282 original size:19 final size:19
Alignment explanation
Indices: 47529258--47529312 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
47529248 TTTGGAAAAG
47529258 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
47529277 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
47529288 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
47529307 TTTTGG
1 TTTTGG
47529313 AAAAGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:47529635 original size:161 final size:162
Alignment explanation
Indices: 47529468--47529779 Score: 502
Period size: 162 Copynumber: 1.9 Consensus size: 162
47529458 ATTGTAAATT
* * *
47529468 TTGAAAACTTCTTGGGCCAATTTCGTAATT-GAATAAAAGTTGATTTGGG-ATTAAATTAAAACA
1 TTGAAAAATTATTGGGCCAATTTCGTAATTAAAAT-AAAGTTGATTTGGGAATTAAATTAAAACA
* *
47529531 AATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTCTGGTA
65 AATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTA
47529596 CAGTCAAACAGTCAAAGGACTAGTTTATAAACC
130 CAGTCAAACAGTCAAAGGACTAGTTTATAAACC
47529629 TTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGAATTAAATTAAAACAA
1 TTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGAATTAAATTAAAACAA
* *** * *
47529694 ATTAGAAATGTCAGGGACTAAATGCAGAAATGATCCAAAAAATGACACGTGGCAGCCTCTGGTAC
66 ATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTAC
47529759 AGTCAAACAGTCAAAGGACTA
131 AGTCAAACAGTCAAAGGACTA
47529780 AATTGAAAGC
Statistics
Matches: 138, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
161 42 0.30
162 96 0.70
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (162 bp):
TTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGAATTAAATTAAAACAA
ATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTAC
AGTCAAACAGTCAAAGGACTAGTTTATAAACC
Found at i:47530088 original size:16 final size:18
Alignment explanation
Indices: 47530057--47530090 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
47530047 TTTTCTCTCA
47530057 ACCTCACCATGGCCGGCC
1 ACCTCACCATGGCCGGCC
47530075 ACCT-ACCA-GGCCGGCC
1 ACCTCACCATGGCCGGCC
47530091 GTCCAAAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.18, C:0.50, G:0.24, T:0.09
Consensus pattern (18 bp):
ACCTCACCATGGCCGGCC
Found at i:47530131 original size:27 final size:26
Alignment explanation
Indices: 47530101--47530151 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
47530091 GTCCAAAGCG
47530101 CGTCGCCGGTCACGCGCCGCATCCTAC
1 CGTCGCCGGTCACGCGCCG-ATCCTAC
*
47530128 CGTCGCCGGTCACGCTCCGATCCT
1 CGTCGCCGGTCACGCGCCGATCCT
47530152 GCCCCCAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.10, C:0.47, G:0.25, T:0.18
Consensus pattern (26 bp):
CGTCGCCGGTCACGCGCCGATCCTAC
Found at i:47536480 original size:29 final size:29
Alignment explanation
Indices: 47536448--47536604 Score: 99
Period size: 29 Copynumber: 5.4 Consensus size: 29
47536438 TATGGATACC
*
47536448 CGGGGGCAAAATGGTAATTTTGGTAAAAT
1 CGGGGGTAAAATGGTAATTTTGGTAAAAT
* *
47536477 CGGGGTTAAAAATGG-AATTTT--AAAAGATT
1 CGGGGGT-AAAATGGTAATTTTGGTAAA-A-T
* *
47536506 CGGTGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGGTAATTTT-GGTAAAAT
* * * * * **
47536536 CGAGGTTAAAACGG-AATTCTAG-AAGCTT
1 CGGGGGTAAAATGGTAATTTTGGTAA-AAT
*
47536564 CGGGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGGTAATTTT-GGTAAAAT
*
47536594 CGGGGTTAAAA
1 CGGGGGTAAAA
47536605 ATGGGATTTA
Statistics
Matches: 92, Mismatches: 25, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
27 4 0.04
28 21 0.23
29 33 0.36
30 30 0.33
31 2 0.02
32 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTGGTAAAAT
Found at i:47536517 original size:58 final size:59
Alignment explanation
Indices: 47536448--47536643 Score: 240
Period size: 58 Copynumber: 3.4 Consensus size: 59
47536438 TATGGATACC
* *
47536448 CGGGGGCAAAATGGTAATTTT-GGTAAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * * * *
47536506 CGGTGGTAAAATGGTAATTTTCGGTGAAATCGAGGTT-AAAACGGAATTCTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
47536564 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGGA-TTTAGGAAAG-TT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTA--AAAGATT
*
47536623 CTGGGGTTAAAAT-GTAATTTT
1 C-GGGGGTAAAATGGTAATTTT
47536644 TTGAAAGTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
58 74 0.63
59 31 0.26
60 13 0.11
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:47536650 original size:30 final size:30
Alignment explanation
Indices: 47536617--47536815 Score: 247
Period size: 30 Copynumber: 6.6 Consensus size: 30
47536607 GGGATTTAGG
* * * *
47536617 AAAGTTCTGGGGTTAAAATGTAATTTTTTG-
1 AAAGTTTTGGGGTCAAAATATAA-TTTTGGA
* *
47536647 AAAGTTTTGGGGTCAAAATACAATTTTAGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
47536677 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* * *
47536707 AAAGTTTTAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
*
47536737 AAAGTTTTGGGGTCAAAATATAATTTTTGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* * *
47536767 AAAGTTTTAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
**
47536797 AAAGTTTCAGGGTCAAAAT
1 AAAGTTTTGGGGTCAAAAT
47536816 GCAATTTCTG
Statistics
Matches: 148, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
29 5 0.03
30 143 0.97
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATATAATTTTGGA
Found at i:47536720 original size:90 final size:91
Alignment explanation
Indices: 47536617--47536827 Score: 300
Period size: 90 Copynumber: 2.3 Consensus size: 91
47536607 GGGATTTAGG
* * *
47536617 AAAGTTCTGGGGTTAAAATGTAATTTTTTG-AAAGTTTTGGGGTCAAAATACAATTTTAGAAAAG
1 AAAGTTTTAGGGTTAAAATGTAATTTTTGGAAAAGTTTTGGGGTCAAAATACAATTTTAGAAAAG
*
47536681 TTTTGGGGTCAAAATATAATTTTGGA
66 TTTTAGGGTCAAAATATAATTTTGGA
* *
47536707 AAAGTTTTAGGGTTAAAATGTAA-TTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTTGAAAAG
1 AAAGTTTTAGGGTTAAAATGTAATTTTTGGAAAAGTTTTGGGGTCAAAATACAATTTTAGAAAAG
* *
47536771 TTTTAGGGTTAAAATGTAATTTTGGA
66 TTTTAGGGTCAAAATATAATTTTGGA
* * * *
47536797 AAAGTTTCAGGGTCAAAATGCAATTTCTGGA
1 AAAGTTTTAGGGTTAAAATGTAATTTTTGGA
47536828 TTGTTTGGGG
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
89 5 0.05
90 96 0.90
91 6 0.06
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (91 bp):
AAAGTTTTAGGGTTAAAATGTAATTTTTGGAAAAGTTTTGGGGTCAAAATACAATTTTAGAAAAG
TTTTAGGGTCAAAATATAATTTTGGA
Found at i:47536822 original size:60 final size:60
Alignment explanation
Indices: 47536617--47536815 Score: 283
Period size: 60 Copynumber: 3.3 Consensus size: 60
47536607 GGGATTTAGG
* * * * * ** *
47536617 AAAGTTCTGGGGTTAAAATGTAATTTTTTG-AAAGTTTTGGGGTCAAAATACAATTTTAGA
1 AAAGTTTTGGGGTCAAAATATAA-TTTTTGAAAAGTTTTAGGGTTAAAATGTAATTTTGGA
*
47536677 AAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTTGAAAAGTTTTAGGGTTAAAATGTAATTTTGGA
47536737 AAAGTTTTGGGGTCAAAATATAATTTTTGAAAAGTTTTAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTTGAAAAGTTTTAGGGTTAAAATGTAATTTTGGA
**
47536797 AAAGTTTCAGGGTCAAAAT
1 AAAGTTTTGGGGTCAAAAT
47536816 GCAATTTCTG
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 5 0.04
60 121 0.96
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (60 bp):
AAAGTTTTGGGGTCAAAATATAATTTTTGAAAAGTTTTAGGGTTAAAATGTAATTTTGGA
Found at i:47537099 original size:161 final size:162
Alignment explanation
Indices: 47536915--47537228 Score: 443
Period size: 162 Copynumber: 1.9 Consensus size: 162
47536905 GAATAAATTG
* * * * *
47536915 TAAATCTTGAAAACTTCTTGGGCCAATTTCGTAATTGAATA-AAAGTTGATTT-GGGATTAAATT
1 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATT-AAAAGAAAGTTGATTTGGGGATTAAATT
* *
47536978 AAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGACAACCT
65 AAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGACAACCT
*
47537043 CTGGTATAGTCAAACAATCAAAGGACTAGTTTA
130 CTGGTACAGTCAAACAATCAAAGGACTAGTTTA
47537076 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAAGAAAGTTGATTTGGGGATTAAATTA
1 TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAAGAAAGTTGATTTGGGGATTAAATTA
* *** * * * * *
47537141 AAACAAATTAGAAATGTCAGGGATTAAATGCAGAAATGATCCAAAAAATGACACGTGGCAGCCTC
66 AAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGACAACCTC
*
47537206 TGGTACAGTCAAACAGTCAAAGG
131 TGGTACAGTCAAACAATCAAAGG
47537229 CCTAAATTGA
Statistics
Matches: 133, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
160 3 0.02
161 43 0.32
162 87 0.65
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (162 bp):
TAAACCTTGAAAAATTATTGGGCCAATTTCATAATTAAAAGAAAGTTGATTTGGGGATTAAATTA
AAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGACAACCTC
TGGTACAGTCAAACAATCAAAGGACTAGTTTA
Found at i:47537592 original size:27 final size:26
Alignment explanation
Indices: 47537561--47537611 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
47537551 CAAAGAGCGT
47537561 CGCCGGTCACGCGCCGCATCCTGCCGC
1 CGCCGGTCACGCGCCG-ATCCTGCCGC
*
47537588 CGCCGGTCACGCTCCGATCCTGCC
1 CGCCGGTCACGCGCCGATCCTGCC
47537612 CCCAACCGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.08, C:0.51, G:0.27, T:0.14
Consensus pattern (26 bp):
CGCCGGTCACGCGCCGATCCTGCCGC
Found at i:47538906 original size:6 final size:6
Alignment explanation
Indices: 47538887--47538965 Score: 92
Period size: 6 Copynumber: 13.2 Consensus size: 6
47538877 ATGTTTAGTG
* *
47538887 TTTAAA TTTTAA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
47538936 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
47538966 CAATTTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 48 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:47538921 original size:11 final size:11
Alignment explanation
Indices: 47538897--47538958 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
47538887 TTTAAATTTT
*
47538897 AATTTAAATTTA
1 AATTTAAA-GTA
47538909 AATTTAAAGTA
1 AATTTAAAGTA
47538920 AATTTAAA-T-
1 AATTTAAAGTA
*
47538929 AA-TTAAATTTA
1 AATTTAAA-GTA
47538940 AATTT-AAGATA
1 AATTTAAAG-TA
47538951 AATTTAAA
1 AATTTAAA
47538959 TTTAAATCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 2 0.05
11 21 0.50
12 12 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AATTTAAAGTA
Found at i:47538921 original size:17 final size:17
Alignment explanation
Indices: 47538887--47538975 Score: 89
Period size: 17 Copynumber: 5.4 Consensus size: 17
47538877 ATGTTTAGTG
**
47538887 TTTAAATTTTAATTTAAA
1 TTTAAA-TTTAAAGTAAA
47538905 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAAGTAAA
*
47538922 TTTAAA--T-AATTAAA
1 TTTAAATTTAAAGTAAA
47538936 TTTAAATTT-AAGATAAA
1 TTTAAATTTAAAG-TAAA
*
47538953 TTTAAATTTAAA-TCAA
1 TTTAAATTTAAAGTAAA
47538969 TTTAAAT
1 TTTAAAT
47538976 CCAAATTGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
14 12 0.19
15 1 0.02
16 13 0.21
17 28 0.45
18 8 0.13
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAGTAAA
Found at i:47538937 original size:31 final size:31
Alignment explanation
Indices: 47538900--47538959 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
47538890 AAATTTTAAT
47538900 TTAAATTTAAATTTAA-AGTAAATTTAAATAA
1 TTAAATTTAAATTTAAGA-TAAATTTAAATAA
47538931 TTAAATTTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAATTTAAGATAAATTTAAAT
47538960 TTAAATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAAATTTAAATTTAAGATAAATTTAAATAA
Found at i:47539400 original size:24 final size:24
Alignment explanation
Indices: 47539384--47539452 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
47539374 AGTTTGACTC
*
47539384 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTA
47539408 AAACAAATAAACAGAGTTTAATTA
1 AAACAAATAAACAGAGTTTAATTA
*
47539432 AAACAATTAAACAGAGTTTAA
1 AAACAAATAAACAGAGTTTAA
47539453 CTGAAAGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTA
Found at i:47541134 original size:15 final size:16
Alignment explanation
Indices: 47541114--47541143 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47541104 TAATATCCAA
47541114 AAGTA-TATCATATTT
1 AAGTATTATCATATTT
47541129 AAGTATTATCATATT
1 AAGTATTATCATATT
47541144 CCCCCTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
AAGTATTATCATATTT
Found at i:47542356 original size:18 final size:16
Alignment explanation
Indices: 47542315--47542362 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
47542305 TTTCCTGGAC
47542315 AAAAAT-AAATAAATA
1 AAAAATAAAATAAATA
47542330 AATAAATAAAATAAGATA
1 AA-AAATAAAATAA-ATA
47542348 GAAAAATAAAATAAA
1 -AAAAATAAAATAAA
47542363 AATAATTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.07
16 4 0.14
17 7 0.24
18 14 0.48
19 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (16 bp):
AAAAATAAAATAAATA
Found at i:47543533 original size:21 final size:21
Alignment explanation
Indices: 47543507--47543546 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47543497 ATAGATGCCT
*
47543507 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
*
47543528 CAGTTTGCTTTTGGAAATC
1 CAGTTTGCTTTTGAAAATC
47543547 TATAGATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:47543556 original size:21 final size:21
Alignment explanation
Indices: 47543514--47543557 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
47543504 CCTCAGTTTT
*
47543514 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAGATTG
* * *
47543535 CTTTTGGAAATCTATAGATTG
1 CTTTTGAAAATCCACAGATTG
47543556 CT
1 CT
47543558 GCTGAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTTTGAAAATCCACAGATTG
Found at i:47545119 original size:21 final size:22
Alignment explanation
Indices: 47545095--47545141 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
47545085 CGATCTGAGG
*
47545095 AAAAATAGAAGAAA-TAGAATT
1 AAAAATAAAAGAAAGTAGAATT
*
47545116 AAAAATAAAAGAAAGTATAATT
1 AAAAATAAAAGAAAGTAGAATT
47545138 AAAA
1 AAAA
47545142 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATAAAAGAAAGTAGAATT
Found at i:47545156 original size:16 final size:16
Alignment explanation
Indices: 47545115--47545156 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
47545105 GAAATAGAAT
47545115 TAAAAATAAAAGAAAG
1 TAAAAATAAAAGAAAG
* *
47545131 TATAATTAAAAGAAA-
1 TAAAAATAAAAGAAAG
47545146 TAGAAAATAAA
1 TA-AAAATAAA
47545157 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAAGAAAG
Found at i:47545979 original size:19 final size:19
Alignment explanation
Indices: 47545955--47545997 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47545945 AAACATAAAT
47545955 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
47545974 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
47545993 TAAAT
1 TAAAT
47545998 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:47547863 original size:24 final size:24
Alignment explanation
Indices: 47547836--47547886 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
47547826 AGTTTGACTC
*
47547836 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGCTTAATTG
*
47547860 AAACAATTAAACAGAGCTTAATTG
1 AAACAAATAAACAGAGCTTAATTG
47547884 AAA
1 AAA
47547887 TATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGCTTAATTG
Found at i:47552633 original size:18 final size:18
Alignment explanation
Indices: 47552610--47552652 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
47552600 TAATAATTTT
47552610 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
47552628 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
47552646 TTAATTA
1 TTAATTA
47552653 CAACTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:47555906 original size:19 final size:20
Alignment explanation
Indices: 47555882--47555928 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
47555872 TAAATACTAA
*
47555882 ATTAAATAAA-AAGTTGAAT
1 ATTAAATAAAGAAGTTAAAT
*
47555901 ATTAAA-AAAGAATTTAAAT
1 ATTAAATAAAGAAGTTAAAT
47555920 ATTAAATAA
1 ATTAAATAA
47555929 TATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.79
20 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (20 bp):
ATTAAATAAAGAAGTTAAAT
Found at i:47560378 original size:19 final size:20
Alignment explanation
Indices: 47560341--47560381 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
47560331 TATCTTCTTT
47560341 ATCATCATCTTGAATCTATC
1 ATCATCATCTTGAATCTATC
47560361 ATCATCA-CTATG-ATCTATC
1 ATCATCATCT-TGAATCTATC
47560380 AT
1 AT
47560382 GTTAAGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (20 bp):
ATCATCATCTTGAATCTATC
Found at i:47562490 original size:73 final size:73
Alignment explanation
Indices: 47562407--47562554 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
47562397 CAAATACTAA
47562407 AAATTACATTTTTGATTATTATGTATTATATATATTATTTTTGGAAAAAGGTCGGATGTGTTTGT
1 AAATTACATTTTTGATTATTATGTATTATATATATTATTTTTGGAAAAAGGTCGGATGTGTTTGT
47562472 AAATAATT
66 AAATAATT
47562480 AAATTACATTTTTGATTATTATGTATTATATATATTATTTTTGGAAAAAGGTCGGATGTGTTTGT
1 AAATTACATTTTTGATTATTATGTATTATATATATTATTTTTGGAAAAAGGTCGGATGTGTTTGT
47562545 AAATAATT
66 AAATAATT
47562553 AA
1 AA
47562555 TATTTACGGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (73 bp):
AAATTACATTTTTGATTATTATGTATTATATATATTATTTTTGGAAAAAGGTCGGATGTGTTTGT
AAATAATT
Found at i:47569962 original size:3 final size:3
Alignment explanation
Indices: 47569954--47569994 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
47569944 TAAGTATGTT
*
47569954 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
47569995 TTACTTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:47570652 original size:16 final size:16
Alignment explanation
Indices: 47570610--47570652 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
47570600 CATACGCCAA
47570610 TATTTTATA-TATTTT
1 TATTTTATATTATTTT
47570625 TCATTTTA-ATTATTTT
1 T-ATTTTATATTATTTT
*
47570641 TATTATATATTA
1 TATTTTATATTA
47570653 ATCCTACCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTATATTATTTT
Found at i:47574406 original size:21 final size:22
Alignment explanation
Indices: 47574382--47574423 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
47574372 AAATATAAAT
*
47574382 TTAAATAATATAATT-AAGAAC
1 TTAAATAACATAATTCAAGAAC
*
47574403 TTAAATAGCATAATTCAAGAA
1 TTAAATAACATAATTCAAGAA
47574424 GAGAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
TTAAATAACATAATTCAAGAAC
Found at i:47579148 original size:41 final size:41
Alignment explanation
Indices: 47579103--47579229 Score: 106
Period size: 41 Copynumber: 3.1 Consensus size: 41
47579093 TCCACCATCC
47579103 TCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAAT
1 TCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAAT
** * * **
47579144 TCCTTCCCTTCCATACATCTAAACC---CCAATC-CACCA-T--CC
1 TCCTT--CAGCC-TACA-C-AATCCTTTCCATTCACACCAGTGAAT
47579183 TCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAAT
1 TCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAAT
47579224 TCCTTC
1 TCCTTC
47579230 CCTTCCATTA
Statistics
Matches: 62, Mismatches: 12, Indels: 24
0.63 0.12 0.24
Matches are distributed among these distances:
34 4 0.06
35 1 0.02
36 4 0.06
37 8 0.13
38 5 0.08
39 6 0.10
41 12 0.19
42 5 0.08
43 8 0.13
44 4 0.06
45 1 0.02
46 4 0.06
ACGTcount: A:0.25, C:0.41, G:0.05, T:0.29
Consensus pattern (41 bp):
TCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAAT
Found at i:47579211 original size:80 final size:80
Alignment explanation
Indices: 47579078--47579237 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
47579068 ACATGCACAA
47579078 ACATCTAAACCCCAATCCACCATCCTCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAA
1 ACATCTAAACCCCAATCCACCATCCTCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAA
47579143 TTCCTTCCCTTCCAT
66 TTCCTTCCCTTCCAT
47579158 ACATCTAAACCCCAATCCACCATCCTCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAA
1 ACATCTAAACCCCAATCCACCATCCTCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAA
47579223 TTCCTTCCCTTCCAT
66 TTCCTTCCCTTCCAT
47579238 TATGTTTTTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.26, C:0.42, G:0.04, T:0.28
Consensus pattern (80 bp):
ACATCTAAACCCCAATCCACCATCCTCCTTCAGCCTACACAATCCTTTCCATTCACACCAGTGAA
TTCCTTCCCTTCCAT
Found at i:47581056 original size:20 final size:20
Alignment explanation
Indices: 47581031--47581074 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
47581021 TATATATTAT
*
47581031 CATTGTTTATGACATGACCC
1 CATTGTTCATGACATGACCC
* *
47581051 CATTGTTCATTACTTGACCC
1 CATTGTTCATGACATGACCC
47581071 CATT
1 CATT
47581075 ATTTCTAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (20 bp):
CATTGTTCATGACATGACCC
Found at i:47581635 original size:4 final size:4
Alignment explanation
Indices: 47581618--47581662 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
47581608 TAGAATGCGC
* * *
47581618 TACA TGCA TGCA TACA TACA TACA TACA TACA TAAA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
47581663 GAACATGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:47585616 original size:47 final size:50
Alignment explanation
Indices: 47585520--47585616 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 50
47585510 GGGATCCATT
* * * *
47585520 TTTTTTTTAAACTTAAAAAATAAAATTACGTTGTTTTGATAAATGTTTAC
1 TTTTTTTTAAACTTAAAAAATAAAACTACGTTCTTTTGAGAAATATTTAC
* *
47585570 TTTTTTTT-AAGTT-AAAAATAAAACTA-TTTCTTTTGAGAAATATTTAC
1 TTTTTTTTAAACTTAAAAAATAAAACTACGTTCTTTTGAGAAATATTTAC
47585617 CCATTAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
47 17 0.41
48 12 0.29
49 4 0.10
50 8 0.20
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.48
Consensus pattern (50 bp):
TTTTTTTTAAACTTAAAAAATAAAACTACGTTCTTTTGAGAAATATTTAC
Found at i:47586617 original size:29 final size:28
Alignment explanation
Indices: 47586585--47586668 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
47586575 GGACTCTTGA
*
47586585 GGGGTAAAATGGCAATTTTGAGAAAATTT
1 GGGGTAAAATGGAAATTTT-AGAAAATTT
*
47586614 GGGGTTAAAATTGAAATTTTAG-AAATTT
1 GGGG-TAAAATGGAAATTTTAGAAAATTT
* * *
47586642 GAGGGCAAAACGGTAATTTTTAGAAAA
1 G-GGGTAAAATGG-AAATTTTAGAAAA
47586669 ATAAGGATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
28 12 0.27
29 17 0.38
30 16 0.36
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (28 bp):
GGGGTAAAATGGAAATTTTAGAAAATTT
Found at i:47586771 original size:59 final size:60
Alignment explanation
Indices: 47586643--47586780 Score: 179
Period size: 59 Copynumber: 2.3 Consensus size: 60
47586633 TAGAAATTTG
* * * *
47586643 AGGGCAAAACGGTAATTTTTAGAAAAATAAGGATCAAAAAACGGAATTTTCAAACATTCG
1 AGGGTAAAATGGTAATTTTTAGAAAAATAAGGATCAAAAAACGGAATTTTCAAACATCCA
* ** * **
47586703 GGGGTAAAATGGTAATTTTTAGAAAAATCGGGATC-AAAAACTGAATTTTCGGACATCCA
1 AGGGTAAAATGGTAATTTTTAGAAAAATAAGGATCAAAAAACGGAATTTTCAAACATCCA
47586762 AGGGTAAAATGGTAATTTT
1 AGGGTAAAATGGTAATTTT
47586781 GGATGTGTCG
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 37 0.55
60 30 0.45
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (60 bp):
AGGGTAAAATGGTAATTTTTAGAAAAATAAGGATCAAAAAACGGAATTTTCAAACATCCA
Found at i:47586859 original size:58 final size:59
Alignment explanation
Indices: 47586791--47586926 Score: 159
Period size: 58 Copynumber: 2.3 Consensus size: 59
47586781 GGATGTGTCG
** *
47586791 GGGTCAAAAATATGGTTTTCAGAAGTTTTAGGGTAAAAATGTAATTTTTAG-AAGTTTTA
1 GGGTCAAAAATATAATTTTCAGAAGTTTCAGGGTAAAAATGTAATTTTT-GTAAGTTTTA
** * * *
47586850 GGGTC-AAAATATAATTTTTGGAAGTTTCGGGGTCAAAATGTAATTTTTGTAAGTTTCA
1 GGGTCAAAAATATAATTTTCAGAAGTTTCAGGGTAAAAATGTAATTTTTGTAAGTTTTA
**
47586908 ACGTCAAAAATATAATTTT
1 GGGTCAAAAATATAATTTT
47586927 GGAAAAGTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 1 0.02
58 46 0.71
59 18 0.28
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (59 bp):
GGGTCAAAAATATAATTTTCAGAAGTTTCAGGGTAAAAATGTAATTTTTGTAAGTTTTA
Found at i:47586897 original size:29 final size:29
Alignment explanation
Indices: 47586812--47586970 Score: 153
Period size: 29 Copynumber: 5.4 Consensus size: 29
47586802 ATGGTTTTCA
* * * *
47586812 GAAGTTTTAGGGTAAAAATGTAATTTTTA
1 GAAGTTTCAGGGTCAAAATATAATTTTTG
*
47586841 GAAGTTTTAGGGTCAAAATATAATTTTTG
1 GAAGTTTCAGGGTCAAAATATAATTTTTG
* *
47586870 GAAGTTTCGGGGTCAAAATGTAATTTTTG
1 GAAGTTTCAGGGTCAAAATATAATTTTTG
* **
47586899 TAAGTTTCAACGTCAAAAATATAA-TTTTG
1 GAAGTTTCAGGGTC-AAAATATAATTTTTG
*
47586928 GAAAAG-TTCAGGGGTCAAAATACAATTTTTG
1 G--AAGTTTCA-GGGTCAAAATATAATTTTTG
47586959 GATAGTTT-AGGG
1 GA-AGTTTCAGGG
47586971 ACCTCTAGAG
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
29 71 0.66
30 23 0.21
31 14 0.13
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (29 bp):
GAAGTTTCAGGGTCAAAATATAATTTTTG
Found at i:47586927 original size:58 final size:57
Alignment explanation
Indices: 47586793--47586958 Score: 156
Period size: 58 Copynumber: 2.8 Consensus size: 57
47586783 ATGTGTCGGG
** * ** * * **
47586793 GTCAAAAATATGGTTTTCAGAAGTTTTAGGGTAAAAATGTAATTTTTAGAAGTTTTAGG
1 GTCAAAAATATAATTTT-GGAAGTTTCGGGGTCAAAATGTAATTTTT-GAAGTTTCAAC
47586852 GTC-AAAATATAATTTTTGGAAGTTTCGGGGTCAAAATGTAATTTTTGTAAGTTTCAAC
1 GTCAAAAATATAA-TTTTGGAAGTTTCGGGGTCAAAATGTAATTTTTG-AAGTTTCAAC
**
47586910 GTCAAAAATATAATTTTGGAAAAG-TTCAGGGGTCAAAATACAATTTTTG
1 GTCAAAAATATAATTTTGG--AAGTTTC-GGGGTCAAAATGTAATTTTTG
47586959 GATAGTTTAG
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 48 0.53
59 19 0.21
60 22 0.24
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (57 bp):
GTCAAAAATATAATTTTGGAAGTTTCGGGGTCAAAATGTAATTTTTGAAGTTTCAAC
Found at i:47586948 original size:30 final size:29
Alignment explanation
Indices: 47586774--47586970 Score: 120
Period size: 29 Copynumber: 6.7 Consensus size: 29
47586764 GGTAAAATGG
* *
47586774 TAATTTTGGATGTGTC-GGGGTCAAAAATA
1 TAATTTTGGAAGTTTCAGGGGTC-AAAATA
** * * * *
47586803 TGGTTTTCAGAAGTTTTA-GGGTAAAAATG
1 TAATTTT-GGAAGTTTCAGGGGTCAAAATA
* *
47586832 TAATTTTTAGAAGTTTTA-GGGTCAAAATA
1 TAA-TTTTGGAAGTTTCAGGGGTCAAAATA
*
47586861 TAATTTTTGGAAGTTTC-GGGGTCAAAATG
1 TAA-TTTTGGAAGTTTCAGGGGTCAAAATA
* **
47586890 TAATTTTTGTAAGTTTCA-ACGTCAAAAATA
1 TAA-TTTTGGAAGTTTCAGGGGTC-AAAATA
47586920 TAATTTTGGAAAAG-TTCAGGGGTCAAAATA
1 TAATTTTGG--AAGTTTCAGGGGTCAAAATA
*
47586950 CAATTTTTGGATAGTTT-AGGG
1 TAA-TTTTGGA-AGTTTCAGGG
47586971 ACCTCTAGAG
Statistics
Matches: 133, Mismatches: 23, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
29 80 0.60
30 39 0.29
31 14 0.11
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (29 bp):
TAATTTTGGAAGTTTCAGGGGTCAAAATA
Found at i:47588893 original size:28 final size:27
Alignment explanation
Indices: 47588878--47588963 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 27
47588868 TTACAATAAT
47588878 ATTAAATTTAAATTAAATTCAAACTTAA
1 ATTAAATTTAAATTAAATTCAAAC-TAA
*
47588906 ATTAAATTTAAATTAAATT-AAATTAAA
1 ATTAAATTTAAATTAAATTCAAACT-AA
* * *
47588933 ATTTAAA-ATAAATTTAATTTCAAAGTAA
1 A-TTAAATTTAAA-TTAAATTCAAACTAA
47588961 ATT
1 ATT
47588964 TTAAAATAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 12 0.24
28 33 0.66
29 4 0.08
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (27 bp):
ATTAAATTTAAATTAAATTCAAACTAA
Found at i:47588894 original size:11 final size:11
Alignment explanation
Indices: 47588879--47588949 Score: 83
Period size: 11 Copynumber: 6.4 Consensus size: 11
47588869 TACAATAATA
47588879 TTAAATTTAAA-
1 TTAAA-TTAAAT
*
47588890 TTAAATTCAAAC
1 TTAAATT-AAAT
47588902 TTAAATTAAAT
1 TTAAATTAAAT
47588913 TTAAATTAAA-
1 TTAAATTAAAT
47588923 TTAAATTAAAAT
1 TTAAATT-AAAT
*
47588935 TTAAAATAAAT
1 TTAAATTAAAT
47588946 TTAA
1 TTAA
47588950 TTTCAAAGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
10 9 0.17
11 32 0.59
12 13 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:47588895 original size:5 final size:5
Alignment explanation
Indices: 47588878--47588951 Score: 76
Period size: 5 Copynumber: 13.6 Consensus size: 5
47588868 TTACAATAAT
47588878 ATTAA ATTTAA ATTAA ATTCAA ACTTAA ATTAA ATTTAA ATTAA ATTAA
1 ATTAA A-TTAA ATTAA ATT-AA A-TTAA ATTAA A-TTAA ATTAA ATTAA
* *
47588927 ATTAAA ATTTAA AATAA ATTTA ATT
1 ATT-AA A-TTAA ATTAA ATTAA ATT
47588952 TCAAAGTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
5 34 0.57
6 22 0.37
7 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (5 bp):
ATTAA
Found at i:47588905 original size:17 final size:16
Alignment explanation
Indices: 47588878--47588946 Score: 84
Period size: 17 Copynumber: 4.2 Consensus size: 16
47588868 TTACAATAAT
*
47588878 ATTAAATTTAAATTAA
1 ATTAAAATTAAATTAA
*
47588894 ATTCAAACTTAAATTAA
1 ATT-AAAATTAAATTAA
*
47588911 ATTTAAATTAAATTAA
1 ATTAAAATTAAATTAA
*
47588927 ATTAAAATTTAAAATAA
1 ATTAAAA-TTAAATTAA
47588944 ATT
1 ATT
47588947 TAATTTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
16 20 0.43
17 26 0.57
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAAATTAAATTAA
Found at i:47588961 original size:17 final size:16
Alignment explanation
Indices: 47588860--47588964 Score: 75
Period size: 17 Copynumber: 6.2 Consensus size: 16
47588850 ATTAATGGAC
*
47588860 ATTTAAATTTACAATAA
1 ATTT-AATTTAAAATAA
* *
47588877 TATTAAATTTAAATTAA
1 -ATTTAATTTAAAATAA
* * *
47588894 ATTCAAACTTAAATTAA
1 ATT-TAATTTAAAATAA
* *
47588911 ATTTAAATTAAATTAA
1 ATTTAATTTAAAATAA
*
47588927 ATTAAAATTTAAAATAA
1 ATT-TAATTTAAAATAA
*
47588944 ATTTAATTTCAAAGTAA
1 ATTTAATTT-AAAATAA
47588961 ATTT
1 ATTT
47588965 TAAAATAGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
16 22 0.30
17 48 0.66
18 3 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
ATTTAATTTAAAATAA
Found at i:47589279 original size:3 final size:3
Alignment explanation
Indices: 47589273--47589309 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
47589263 TTTATTGAAA
47589273 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
47589310 AAAACATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47590290 original size:19 final size:20
Alignment explanation
Indices: 47590266--47590303 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
47590256 CCAAATTCAA
47590266 TTTAAATAATAAAA-ATATT
1 TTTAAATAATAAAATATATT
*
47590285 TTTAAATTATAAAATATAT
1 TTTAAATAATAAAATATAT
47590304 AAAATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATAATAAAATATATT
Found at i:47591702 original size:26 final size:26
Alignment explanation
Indices: 47591666--47591731 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
47591656 AATATATCAA
*
47591666 AATTGTTACATCATTTATTCGCCAAT
1 AATTGTTACATCATTTATTCACCAAT
47591692 AATTGTTACATCATTTATTCACCAAT
1 AATTGTTACATCATTTATTCACCAAT
47591718 AATTGTCT-CATCAT
1 AATTGT-TACATCAT
47591732 AATAAACAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.97
27 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (26 bp):
AATTGTTACATCATTTATTCACCAAT
Found at i:47592009 original size:23 final size:23
Alignment explanation
Indices: 47591975--47592019 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
47591965 ATTTTTATGA
*
47591975 TTAATATAATTTTTTACATAATT
1 TTAATATAATTTTATACATAATT
*
47591998 TTAATA-ATATTTTATATATAAT
1 TTAATATA-ATTTTATACATAAT
47592020 GTTGATGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATATAATTTTATACATAATT
Done.