Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 73
Found at i:3113149 original size:11 final size:11
Alignment explanation
Indices: 3113082--3113143 Score: 90
Period size: 11 Copynumber: 5.7 Consensus size: 11
3113072 AACAAACTAA
*
3113082 TAATAACAAAA
1 TAATAACAAAC
*
3113093 TAATAACAAGC
1 TAATAACAAAC
3113104 TAATAACAAAC
1 TAATAACAAAC
*
3113115 -CATAACAAAC
1 TAATAACAAAC
3113125 TAATAACAAAC
1 TAATAACAAAC
3113136 TAATAACA
1 TAATAACA
3113144 CTCTAACATT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
10 9 0.20
11 36 0.80
ACGTcount: A:0.63, C:0.18, G:0.02, T:0.18
Consensus pattern (11 bp):
TAATAACAAAC
Found at i:3114699 original size:14 final size:14
Alignment explanation
Indices: 3114682--3114710 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3114672 CCAACAAACC
3114682 ATAACAAACTAATA
1 ATAACAAACTAATA
3114696 ATAACAAACTAATA
1 ATAACAAACTAATA
3114710 A
1 A
3114711 CAAGCTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAACAAACTAATA
Found at i:3114708 original size:11 final size:11
Alignment explanation
Indices: 3114694--3114744 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
3114684 AACAAACTAA
3114694 TAATAACAAAC
1 TAATAACAAAC
*
3114705 TAATAACAAGC
1 TAATAACAAAC
3114716 TAATAACAAAC
1 TAATAACAAAC
*
3114727 -CATAACAAAC
1 TAATAACAAAC
3114737 TAATAACA
1 TAATAACA
3114745 CTCTAACACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.18
Consensus pattern (11 bp):
TAATAACAAAC
Found at i:3119193 original size:12 final size:12
Alignment explanation
Indices: 3119178--3119215 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3119168 AAACGTTCGT
3119178 AAAAAA-AAAGA
1 AAAAAAGAAAGA
*
3119189 AAAAAAGAAGGA
1 AAAAAAGAAAGA
*
3119201 AAAACAGAAAGA
1 AAAAAAGAAAGA
3119213 AAA
1 AAA
3119216 GCAGAGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:3121935 original size:25 final size:25
Alignment explanation
Indices: 3121897--3121944 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3121887 TAAATGCATG
*
3121897 TGAACTAGAGATCATGTGGTTAGTT
1 TGAACTAGAGATCAAGTGGTTAGTT
*
3121922 TGAACTAGATATCAAGTGGTTAG
1 TGAACTAGAGATCAAGTGGTTAG
3121945 GGTTTTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.33
Consensus pattern (25 bp):
TGAACTAGAGATCAAGTGGTTAGTT
Found at i:3124653 original size:24 final size:24
Alignment explanation
Indices: 3124623--3124723 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 24
3124613 TTTTATCTTT
3124623 GTATTTTAGTTTAAATAGGTTTTA
1 GTATTTTAGTTTAAATAGGTTTTA
*
3124647 GTATTTTA-ATT-AAT---TTTTA
1 GTATTTTAGTTTAAATAGGTTTTA
* * * * **
3124666 GGATATTATTTTTATATTTGTTTTA
1 GTATTTTA-GTTTAAATAGGTTTTA
*
3124691 GGTATTTTAGTTGAAATAGGTTTTA
1 -GTATTTTAGTTTAAATAGGTTTTA
*
3124716 GTGTTTTA
1 GTATTTTA
3124724 ATTAGGATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
19 11 0.19
21 2 0.04
22 5 0.09
23 2 0.04
24 15 0.26
25 16 0.28
26 6 0.11
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (24 bp):
GTATTTTAGTTTAAATAGGTTTTA
Found at i:3124676 original size:75 final size:69
Alignment explanation
Indices: 3124587--3124791 Score: 170
Period size: 69 Copynumber: 3.0 Consensus size: 69
3124577 CAAACTCAAG
* *
3124587 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTT-AACATT-TATTTTA----GGTATTTTAGTTGAAATAGGTTTTAGTATT
3124652 TTAATTAATT
60 TTAATTAATT
* * * * *
3124662 TTTAGGATATTATTTTTATATTTGTTTTAGGTATTTTAGTTGAAATAGGTTTTAGTGTTTTAATT
1 TTTAGGATAATATTTTAACATTTATTTTAGGTATTTTAGTTGAAATAGGTTTTAGTATTTTAATT
***
3124727 AGGA
66 AATT
* ** * *
3124731 TTT---ATAATATTATATTA-TT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAAT
1 TTTAGGATAATATTTTAACATTTATTTTAGGTATTTTAGTTGAAATAGGTTTT-AGTATTTTAAT
3124790 TA
65 TA
3124792 TGATTTAAGA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 5 0.04
64 35 0.31
65 2 0.02
66 10 0.09
69 37 0.32
73 6 0.05
74 4 0.04
75 15 0.13
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (69 bp):
TTTAGGATAATATTTTAACATTTATTTTAGGTATTTTAGTTGAAATAGGTTTTAGTATTTTAATT
AATT
Found at i:3124826 original size:64 final size:64
Alignment explanation
Indices: 3124677--3124798 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
3124667 GATATTATTT
*
3124677 TTATATT-TGTTTTAGGTATTTTAGTTGAAATAGGTTTTAGTGTTTTAATTAGGATTTATAATA
1 TTATATTATTTTTTAGGTATTTTAGTTGAAATAGGTTTTAGTGTTTTAATTAGGATTTATAATA
* *
3124740 TTATATTATTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTATGATTTA
1 TTATATTATTTTTTAGGTATTTTAGTTGAAATAGGTTTT-AGTGTTTTAATTAGGATTTA
3124799 AGATGTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 12 0.22
64 42 0.78
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.57
Consensus pattern (64 bp):
TTATATTATTTTTTAGGTATTTTAGTTGAAATAGGTTTTAGTGTTTTAATTAGGATTTATAATA
Found at i:3128908 original size:20 final size:20
Alignment explanation
Indices: 3128883--3128926 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3128873 TTATTAAGGA
3128883 CTTTTCGAAGATAGCACAAC
1 CTTTTCGAAGATAGCACAAC
3128903 CTTTTCGAAGATAGCACAAC
1 CTTTTCGAAGATAGCACAAC
3128923 CTTT
1 CTTT
3128927 ATGCAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (20 bp):
CTTTTCGAAGATAGCACAAC
Found at i:3130841 original size:5 final size:5
Alignment explanation
Indices: 3130822--3130894 Score: 71
Period size: 5 Copynumber: 14.8 Consensus size: 5
3130812 ATATTTTTGC
* * * *
3130822 TTTTA TTTTCG TTTTA TTTTCA TTCTA -TTTA TTTCA TTTCA -TTTA TTTTA
1 TTTTA TTTT-A TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3130872 -TTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
3130895 TCTCTGAACA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
4 10 0.18
5 39 0.68
6 8 0.14
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:3130858 original size:14 final size:13
Alignment explanation
Indices: 3130834--3130893 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 13
3130824 TTATTTTCGT
3130834 TTTATTTTCATTCTA
1 TTTA-TTTCATT-TA
3130849 TTTATTTCATTTCA
1 TTTATTTCATTT-A
*
3130863 TTTATTTTATTTA
1 TTTATTTCATTTA
*
3130876 TTTTATTTTATTTTA
1 -TTTATTTCA-TTTA
3130891 TTT
1 TTT
3130894 TTCTCTGAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
13 2 0.05
14 31 0.76
15 8 0.20
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTCATTTA
Found at i:3130863 original size:19 final size:18
Alignment explanation
Indices: 3130834--3130893 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
3130824 TTATTTTCGT
3130834 TTTATTTTCATTCTA-TTTA
1 TTTA-TTTCATT-TATTTTA
3130853 TTTCATTTCATTTATTTTA
1 TTT-ATTTCATTTATTTTA
*
3130872 TTTATTTTATTTTATTTTA
1 TTTATTTCA-TTTATTTTA
3130891 TTT
1 TTT
3130894 TTCTCTGAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 7 0.19
19 29 0.78
20 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTCATTTATTTTA
Found at i:3130887 original size:10 final size:10
Alignment explanation
Indices: 3130822--3130894 Score: 71
Period size: 9 Copynumber: 7.4 Consensus size: 10
3130812 ATATTTTTGC
*
3130822 TTTTATTTTCG
1 TTTTATTTT-A
3130833 TTTTATTTTCA
1 TTTTATTTT-A
*
3130844 TTCTA-TTTA
1 TTTTATTTTA
* *
3130853 TTTCATTTCA
1 TTTTATTTTA
3130863 -TTTATTTTA
1 TTTTATTTTA
3130872 -TTTATTTTA
1 TTTTATTTTA
3130881 TTTTATTTTA
1 TTTTATTTTA
3130891 TTTT
1 TTTT
3130895 TCTCTGAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
9 20 0.38
10 19 0.36
11 14 0.26
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:3132609 original size:69 final size:63
Alignment explanation
Indices: 3132536--3132711 Score: 210
Period size: 64 Copynumber: 2.7 Consensus size: 63
3132526 TTTTATCTTT
* *
3132536 GTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTAGGAAATTATTTTTATATT-TGT
1 GTATTTTAGTTTAAATAG-TTTTAGTGTTTTAATTAAGATTTA-G-AA-TA---TTATATTATGT
3132600 TTTAG
59 TTTAG
* * *
3132605 GTATTTTAGTTAAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
1 GTATTTTAGTTTAAATA-GTTTTAGTGTTTTAATTAAGATTTAGAATATTATATTATGTTTTAG
*
3132669 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGTTTT-AGTGTTTTAATTAAGATTTA
3132712 AGATGTTTTA
Statistics
Matches: 98, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
63 12 0.12
64 43 0.44
66 2 0.02
67 2 0.02
68 1 0.01
69 37 0.38
70 1 0.01
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.55
Consensus pattern (63 bp):
GTATTTTAGTTTAAATAGTTTTAGTGTTTTAATTAAGATTTAGAATATTATATTATGTTTTAG
Found at i:3134913 original size:12 final size:12
Alignment explanation
Indices: 3134898--3134923 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3134888 TATGACAATT
3134898 ATGAAAATTTGA
1 ATGAAAATTTGA
3134910 ATGAAAATTTGA
1 ATGAAAATTTGA
3134922 AT
1 AT
3134924 TTACTAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGAAAATTTGA
Found at i:3135776 original size:20 final size:19
Alignment explanation
Indices: 3135735--3135776 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3135725 AAAGTTTAAA
* *
3135735 TTAAGATTTATCTTTGTTT
1 TTAAGAATTATCTTTATTT
3135754 TTAAGAATTATCTTTTATTT
1 TTAAGAATTATC-TTTATTT
3135774 TTA
1 TTA
3135777 GGATTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (19 bp):
TTAAGAATTATCTTTATTT
Found at i:3139524 original size:10 final size:10
Alignment explanation
Indices: 3139509--3139548 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
3139499 CGTTCGCTTA
3139509 ATTTTTATTT
1 ATTTTTATTT
3139519 ATTTTTATTTT
1 ATTTTTA-TTT
3139530 CATTTTTTATTT
1 -A-TTTTTATTT
3139542 ATTTTTA
1 ATTTTTA
3139549 ATGTGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 13 0.48
11 4 0.15
12 4 0.15
13 6 0.22
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:3142078 original size:19 final size:20
Alignment explanation
Indices: 3142030--3142072 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3142020 AAAGTTTAAA
* **
3142030 TTAAGATTTATCTTTGTTTT
1 TTAAGAATTATCTTTCATTT
3142050 TTAAGAATTATCTTTCATTT
1 TTAAGAATTATCTTTCATTT
3142070 TTA
1 TTA
3142073 GGATTAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (20 bp):
TTAAGAATTATCTTTCATTT
Found at i:3142886 original size:12 final size:12
Alignment explanation
Indices: 3142871--3142896 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3142861 ATTTTCATCT
3142871 TTACTTTCTTTA
1 TTACTTTCTTTA
3142883 TTACTTTCTTTA
1 TTACTTTCTTTA
3142895 TT
1 TT
3142897 GTATTTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (12 bp):
TTACTTTCTTTA
Found at i:3146513 original size:55 final size:55
Alignment explanation
Indices: 3146454--3146576 Score: 183
Period size: 55 Copynumber: 2.2 Consensus size: 55
3146444 TATGGAACTT
* * * * *
3146454 GAACAATTTTCAACCATCATGTCTGCTCTCTATTCCTTCAGAGAGTATGAGACTC
1 GAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATAAGACTC
* *
3146509 GAACAGTCTTCAACAATCATGTATGCTCCCTATTTCTTCAGAGAGTATAAGACTC
1 GAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATAAGACTC
3146564 GAACAATCTTCAA
1 GAACAATCTTCAA
3146577 ACGGGTTCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (55 bp):
GAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATAAGACTC
Found at i:3146646 original size:51 final size:52
Alignment explanation
Indices: 3146560--3147724 Score: 1163
Period size: 51 Copynumber: 22.3 Consensus size: 52
3146550 AGAGTATAAG
*
3146560 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
3146612 ACTCGAA-AATCTTCAAACGGGCTCGCTCCTTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
3146663 ACTCGAA-AATCTTTAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* ** * * *
3146714 ACTTGGACATCTTCTTCAAACGGGTTCGCACCCTCTTTCT-TCAGGAAGTATAGA
1 AC-TCGA-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* *
3146768 ACTCCAATAA-CTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
3146819 ACTCGAA-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** **
3146870 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGGAAGTATAAA
1 ACTC-GA-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGG-AGTATGGA
** * *
3146925 ACTCGGAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTC-G-AATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * * *
3146979 ACTCCAATAA-CTTCACACGGGTTCACTCCCTCTTTCTCTAGGGAATATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
3147030 ACTCGAA-CATCTTCAAAAGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** * * * *
3147081 ACTCGAACATCTTCTTCAAATGGGTTCACTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTCG-A-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
** * *
3147135 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTC-GA-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * * *
3147189 ACTCCAATAA-CCTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAATATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
3147240 ACTCGAA-CATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** * * * *
3147291 ACTCGAACATCTTCTTCAAACGGGCTCGCTCCCTCTTTCT-TCAAGAAGTATAGA
1 ACTCG-A-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * * * * * *
3147345 ACTCCAATAA-CTTCACACGGGTTTGTTCCCTCTTTCTCTAGGGAATACGAA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
3147396 ACTC-AA-ACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAA
1 ACTCGAATA-ATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** * * *
3147447 ACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTCG-A-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
** * *
3147501 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTC-GA-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * *
3147555 ACTCCAATAA-CTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAATATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
3147606 ACTCGAA-CATCTTTAAATGGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** * * *
3147657 ACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTCG-A-ATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
3147711 ACTCGAAT-ATCTTC
1 ACTCGAATAATCTTC
3147725 TTCCTCTTCA
Statistics
Matches: 961, Mismatches: 112, Indels: 81
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.00
50 8 0.01
51 498 0.52
52 33 0.03
53 17 0.02
54 352 0.37
55 51 0.05
56 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (52 bp):
ACTCGAATAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:3146748 original size:156 final size:156
Alignment explanation
Indices: 3146570--3147724 Score: 1242
Period size: 156 Copynumber: 7.4 Consensus size: 156
3146560 ACTCGAACAA
* *
3146570 TCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAAAATCTTCAAACGGGC
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCAAACGGGT
* *
3146634 TCGCTCCTTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTTAAACGGGTTCGCTCCCTCTTTC
65 TCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCCTCTTTC
3146699 TTCAGGAAGTATAGAACTTGGACATCT
130 TTCAGGAAGTATAGAACTTGGACATCT
* * * *
3146726 TCTTCAAACGGGTTCGCACCCTCTTTCTTCAGGAAGTATAGAACTCCAATAA-CTTCACACGGGT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCAAACGGGT
*
3146790 TCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTC
65 TCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCCTCTTTC
* * *
3146855 -TCTAGGGAGTATGGAACTCGGACATCT
130 TTC-AGGAAGTATAGAACTTGGACATCT
* *
3146882 TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAAGTATAAAACTCGGAAATCTTCTTCAAACG
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGG-AGTATAGAACTC-GAAA--ATCTTCAAACG
* * * * * * * *
3146947 GGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCACTCCCTC
62 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCCTC
* * *
3147011 TTTC-TCTAGGGAA-TATGGAAC-TCGA-A-CA
126 TTTCTTC-A-GGAAGTATAGAACTTGGACATCT
* * * * *
3147039 TCTTCAAAAGGGTTCACTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCTTCAAATG
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAA-A--ATCTTCAAACG
* * * *
3147103 GGTTCACTCCCTCTTTCT-TCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCC
62 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATC-T-TT-AAACGGGTTCGCTCC
** *
3147167 CTCTTTCTTCAGGAAGTATAGAAC-TCCA-AT-A
123 CTCTTTCTTCAGGAAGTATAGAACTTGGACATCT
* * * * * * *
3147198 ACCTCACACGGGTTCGCTCCCTCTTTC-TCTAGGGAATATGGAACTCGAACATCTTCAAATGGGT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCAAACGGGT
*
3147262 TCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGCTCGCTCCCTCT
65 TCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATC-T-TT-AAACGGGTTCGCTCCCTCT
* ** *
3147327 TTCTTCAAGAAGTATAGAAC-TCCA-AT-A
127 TTCTTCAGGAAGTATAGAACTTGGACATCT
* * * *
3147354 ACTTCACACGGGTTTGTTCCCTCTTTC-TCTAGGGA--ATACGAAACTC-AAACATCTTCAAACG
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATA-G-AACTCGAAA-ATCTTCAAACG
* *
3147415 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATCTTCTTCAAATGGGTTCGCTCCC
62 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATC-T-TT-AAACGGGTTCGCTCCC
*
3147480 TCTTTCTTCAGGAAGTATAGAACTCGGACATCT
124 TCTTTCTTCAGGAAGTATAGAACTTGGACATCT
* * *
3147513 TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAATAA-CTTCACACGGGT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCAAACGGGT
* * *
3147577 TCGCTCCCTCTTTCTCTAGGGAATATGGAACTCGAACATCTTTAAATGGGTTCGTTCCCTCTTTC
65 TCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCCTCTTTC
* * * *
3147642 -TCTAGGGAGTATGGAACTCGAACATCT
130 TTC-AGGAAGTATAGAACTTGGACATCT
* * *
3147669 TCTTCAAATGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAATATCTTC
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTC
3147725 TTCCTCTTCA
Statistics
Matches: 880, Mismatches: 87, Indels: 64
0.85 0.08 0.06
Matches are distributed among these distances:
154 2 0.00
155 11 0.01
156 551 0.63
157 51 0.06
158 11 0.01
159 160 0.18
160 87 0.10
161 7 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (156 bp):
TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTT
CGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCCTCTTTCT
TCAGGAAGTATAGAACTTGGACATCT
Found at i:3147231 original size:210 final size:209
Alignment explanation
Indices: 3146533--3147727 Score: 1612
Period size: 210 Copynumber: 5.7 Consensus size: 209
3146523 AATCATGTAT
* *
3146533 GCTCCCTATTTCTTCA-GAGAGTATA-AGACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTTCAGGA-AGTATAGA-ACTCCAACAA-CTTCAAACGGGTTCGCTCCCTCTTT
* * * *
3146596 CTCTAGGGAGTATGGAACTCGAAAATCTTCAAACGGGCTCGCTCCTTCTTTCTCTAGGGAGTATG
63 CTCTAGGGAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG
* *
3146661 GAACTCGAAAATC-T-TT-AAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTTGGACA
128 GAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGA-A
3146723 TCTTCTTCAAACGGGTTC
192 TCTTCTTCAAACGGGTTC
* * *
3146741 GCACCCTCTTTCTTCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAACAACTTCAAACGGGTTCGCTCCCTCTTTCTC
*
3146806 TAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
66 TAGGGAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
* *
3146871 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAAGTATAAAACTCGGAAATC
131 CTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCA-GGAAGTATAGAACTCGG-AATC
3146936 TTCTTCAAACGGGTTC
194 TTCTTCAAACGGGTTC
* * *
3146952 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAATAACTTCACACGGGTTCACTCCCTCTTTCTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAACAACTTCAAACGGGTTCGCTCCCTCTTTCTC
* * *
3147017 TAGGGAATATGGAACTCGAACATCTTCAAAAGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAA
66 TAGGGAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
* *
3147082 CTCGAACATCTTCTTCAAATGGGTTCACTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCT
131 CTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGA-ATCT
3147147 TCTTCAAACGGGTTC
195 TCTTCAAACGGGTTC
* * *
3147162 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAATAACCTCACACGGGTTCGCTCCCTCTTTCTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAACAACTTCAAACGGGTTCGCTCCCTCTTTCTC
*
3147227 TAGGGAATATGGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
66 TAGGGAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
* * * **
3147292 CTCGAACATCTTCTTCAAACGGGCTCGCTCCCTCTTTCTTCAAGAAGTATAGAACTC-CAAT-AA
131 CTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGAATCTT
* *
3147355 CTTCACACGGGTTT
196 CTTCAAACGGGTTC
* * * *
3147369 GTTCCCTCTTTC-TCTAGGGAA-TA-CGAAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTTC-A-GGAAGTATAG-AACTCCAACAACTTCAAACGGGTTCGCTCCCTCTTT
* *
3147431 CTCTAGGGAGTATGAAACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAG
63 CTCTAGGGAGTATGGAACTCGAACA---TCTTCAAATGGGTTCGCTCCCTCTTTCTCT-AGGGAG
* *
3147495 TATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-
124 TATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCG
* ** *
3147559 CAAT-AACTTCACACGGGTTC
189 GAATCTTCTTCAAACGGGTTC
* * * * * *
3147579 GCTCCCTCTTTC-TCTAGGGAA-TATGGAACTCGAACATCTTTAAATGGGTTCGTTCCCTCTTTC
1 GCTCCCTCTTTCTTC-A-GGAAGTATAGAACTCCAACAACTTCAAACGGGTTCGCTCCCTCTTTC
*
3147642 TCTAGGGAGTATGGAACTCGAACATCTTCTTCAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAGT
64 TCTAGGGAGTATGGAACTCGAACA---TCTTCAAATGGGTTCGCTCCCTCTTTCTCT-AGGGAGT
* *
3147706 ATAGAACTCGAATATCTTCTTC
125 ATGGAACTCGAACATCTTCTTC
3147728 CTCTTCACTA
Statistics
Matches: 913, Mismatches: 58, Indels: 30
0.91 0.06 0.03
Matches are distributed among these distances:
206 3 0.00
207 177 0.19
208 35 0.04
209 8 0.01
210 490 0.54
211 199 0.22
212 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (209 bp):
GCTCCCTCTTTCTTCAGGAAGTATAGAACTCCAACAACTTCAAACGGGTTCGCTCCCTCTTTCTC
TAGGGAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
CTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGAATCTT
CTTCAAACGGGTTC
Found at i:3149040 original size:10 final size:10
Alignment explanation
Indices: 3149015--3149061 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
3149005 AAACCTCCTT
3149015 TTCTTTCTTT-
1 TTCTTT-TTTG
3149025 TT-TTTTTTG
1 TTCTTTTTTG
3149034 TTCTTTTTTG
1 TTCTTTTTTG
3149044 TTCTTTTTTG
1 TTCTTTTTTG
3149054 TT-TTTTTT
1 TTCTTTTTT
3149062 CTTTTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.09
9 11 0.31
10 21 0.60
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:3149047 original size:25 final size:26
Alignment explanation
Indices: 3149019--3149067 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3149009 CTCCTTTTCT
3149019 TTCTTTTTT-TTTTTGTTCTTTTTTG
1 TTCTTTTTTGTTTTTGTTCTTTTTTG
*
3149044 TTCTTTTTTGTTTTTTTTCTTTTT
1 TTCTTTTTTGTTTTTGTTCTTTTT
3149068 CATTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (26 bp):
TTCTTTTTTGTTTTTGTTCTTTTTTG
Found at i:3149067 original size:10 final size:10
Alignment explanation
Indices: 3149013--3149075 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
3149003 TGAAACCTCC
*
3149013 TTTTCTTTCT
1 TTTTCTTTTT
3149023 TTTT-TTTTT
1 TTTTCTTTTT
*
3149032 TGTTCTTTTT
1 TTTTCTTTTT
*
3149042 TGTTCTTTTT
1 TTTTCTTTTT
*
3149052 TGTTTTTTTTCT
1 T-TTTCTTTT-T
3149064 TTTTCATTTTT
1 TTTTC-TTTTT
3149075 T
1 T
3149076 CATCTTCAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.16
10 20 0.45
11 11 0.25
12 6 0.14
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.84
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:3149073 original size:16 final size:15
Alignment explanation
Indices: 3149018--3149075 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
3149008 CCTCCTTTTC
3149018 TTTCTTTTTTTT-TT
1 TTTCTTTTTTTTCTT
3149032 TGTTCTTTTTTGTTCTTT
1 T-TTCTTTTTT-TTC-TT
*
3149050 TTTGTTTTTTTTCTT
1 TTTCTTTTTTTTCTT
3149065 TTTCATTTTTT
1 TTTC-TTTTTT
3149076 CATCTTCAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 1 0.03
15 14 0.38
16 11 0.30
17 8 0.22
18 3 0.08
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:3157008 original size:21 final size:20
Alignment explanation
Indices: 3156984--3157041 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
3156974 ATTATCCAAT
3156984 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
3157005 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
*
3157026 CAACTTGAACTCCATA
1 AAACTTGAA-TCCATA
3157042 TCTAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.21
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Found at i:3165466 original size:41 final size:41
Alignment explanation
Indices: 3165406--3165717 Score: 347
Period size: 41 Copynumber: 7.6 Consensus size: 41
3165396 ATGACAATTA
* * * *
3165406 CGGTGCTTGGTATTAAAATGCCACTAAAGTACGAGTCTTTAG
1 CGGTG-TTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
* * * *
3165448 CGGTATTTGTATAAAAATGCCACTAAAGCACGAGTCTTTAG
1 CGGTGTTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
* * * *
3165489 CGATGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTAAAG
1 CGGTGTTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
* * *
3165530 CGGCGTTTGTAAACACAAATGCCACTAAAGTATAAGTCTATAG
1 CGGTGTTTGTATA-A-AAATGCCACTAAAGTATGAGTCTATAG
** *
3165573 CGACGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATAG
1 CGGTGTTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
* **
3165614 CGGTGCTT-TATAAAAACCCCACTAAAGTATGAGTCTATAG
1 CGGTGTTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
* * * * *
3165654 CGATGTTTGTGTAAAAATGTCACGAAAGTATGAGTCTTTAG
1 CGGTGTTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
*
3165695 CGGCGTTTGTATAAAAATGCCAC
1 CGGTGTTTGTATAAAAATGCCAC
3165718 AACAGCGATT
Statistics
Matches: 230, Mismatches: 37, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
40 37 0.16
41 153 0.67
42 6 0.03
43 34 0.15
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (41 bp):
CGGTGTTTGTATAAAAATGCCACTAAAGTATGAGTCTATAG
Found at i:3165657 original size:165 final size:164
Alignment explanation
Indices: 3165415--3165717 Score: 410
Period size: 165 Copynumber: 1.8 Consensus size: 164
3165405 ACGGTGCTTG
* * * * **
3165415 GTATTAAAATGCCACTAAAGTACGAGTCTTTAGCGGTATTTGTATAAAAATGCCACTAAAGCACG
1 GTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGTACTTGTATAAAAACCCCACTAAAGCACG
* *
3165480 AGTCTTTAGCGATGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTAAAGCGGCGTTTGTAAACA
66 AGTCTATAGCGATGTTTGTATAAAAAAGCCACGAAAGTACGAGTCTAAAGCGGCGTTTGTAAA-A
3165545 CAAATGCCACTAAAGTATAAGTCTATAGCGACGTTT
130 -AAATGCCACTAAAGTATAAGTCTATAGCGACGTTT
* * * *
3165581 GTATAAAAACGCCACTAAAGTATGAGTCTATAGCGGTGCTT-TATAAAAACCCCACTAAAGTATG
1 GTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGTACTTGTATAAAAACCCCACTAAAGCACG
* * * * ** *
3165645 AGTCTATAGCGATGTTTGTGTAAAAATGTCACGAAAGTATGAGTCTTTAGCGGCGTTTGTATAAA
66 AGTCTATAGCGATGTTTGTATAAAAAAGCCACGAAAGTACGAGTCTAAAGCGGCGTTTGTAAAAA
3165710 AATGCCAC
131 AATGCCAC
3165718 AACAGCGATT
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
163 9 0.08
164 1 0.01
165 73 0.62
166 35 0.30
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (164 bp):
GTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGTACTTGTATAAAAACCCCACTAAAGCACG
AGTCTATAGCGATGTTTGTATAAAAAAGCCACGAAAGTACGAGTCTAAAGCGGCGTTTGTAAAAA
AATGCCACTAAAGTATAAGTCTATAGCGACGTTT
Found at i:3169224 original size:2 final size:2
Alignment explanation
Indices: 3169217--3169241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3169207 GTGAAATTTG
3169217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3169242 AGGCTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3171529 original size:20 final size:20
Alignment explanation
Indices: 3171504--3171552 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3171494 CCCATGGGTA
3171504 TCGATACCCAAAGAAAAGTG
1 TCGATACCCAAAGAAAAGTG
3171524 TCGATACCCAAAGAAAAGTG
1 TCGATACCCAAAGAAAAGTG
*
3171544 TTGATACCC
1 TCGATACCC
3171553 TATGAACAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
TCGATACCCAAAGAAAAGTG
Found at i:3172779 original size:21 final size:21
Alignment explanation
Indices: 3172741--3172781 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3172731 ATAGTATTGA
*
3172741 TTTTCATGGTATTAATATTAG
1 TTTTCATGATATTAATATTAG
3172762 TTTTCATGAT-TTACATATTA
1 TTTTCATGATATTA-ATATTA
3172782 TATCTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTTCATGATATTAATATTAG
Found at i:3174487 original size:17 final size:18
Alignment explanation
Indices: 3174458--3174496 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
3174448 AAATTTAAGA
3174458 AAATGAGAGAAAA-ACGAG
1 AAATGAGAGAAAATA-GAG
3174476 AAATGA-AGAAAATAGAG
1 AAATGAGAGAAAATAGAG
3174493 AAAT
1 AAAT
3174497 AGATGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.64, C:0.03, G:0.23, T:0.10
Consensus pattern (18 bp):
AAATGAGAGAAAATAGAG
Found at i:3187539 original size:358 final size:360
Alignment explanation
Indices: 3186830--3187546 Score: 1341
Period size: 358 Copynumber: 2.0 Consensus size: 360
3186820 GGCAGCATTA
3186830 TTATGGAAGATATCAATCTTTAGTCATTGAAAAAAAAAGATACACTTGAAAATCAAGTTATGACA
1 TTATGGAAGATATCAATCTTTAGTCATTGAAAAAAAAAGATACACTTGAAAATCAAGTTATGACA
3186895 TTTTGTGAAAAGGGTGGGGGAACTCAAAAAGAAAAAAGTCAATGAAAAAAATAAGTGAAAATAAA
66 TTTTGTGAAAAGGGTGGGGGAACTCAAAAAGAAAAAAGTCAATGAAAAAAATAAGTGAAAATAAA
* *
3186960 AGAGTTCATGGTTATAAAAGCCAAAAGAATAATGACCCACAGGGGGTAAGCGAACCTAATTGTGA
131 AGAGTTCATGGTTACAAAAGCCAAAAGAATAATGACCCACAGGGGGTAAGCGAAACTAATTGTGA
3187025 GAAGAATAGAGTGATTCAAAATACATATGTGAGCACAAAAAAATTGAGAGAGAATATTCTACATA
196 GAAGAATAGAGTGATTCAAAATACATATGTGAGCACAAAAAAATTGAGAGAGAATATTCTACATA
*
3187090 AAGAGCCTTGCATTCTTGTCCACTTTAGACAACTACTAGTTTCGATTTCTAATGTTAACACTATC
261 AAGAGCCTTGCATTCTTGTCCACTTTAGACAACTACTAGTTTCGATTTCTAATGATAACACTATC
3187155 TTGCCTAGTGTGTTTGTTCATTTTTTACAGAGTTG
326 TTGCCTAGTGTGTTTGTTCATTTTTTACAGAGTTG
* *
3187190 TTATGGAAGATATCAGTCTTTAGTCATTGAAAACAAAAGATACACTTGAAAATCAAGTTATGACA
1 TTATGGAAGATATCAATCTTTAGTCATTGAAAAAAAAAGATACACTTGAAAATCAAGTTATGACA
*
3187255 TTTTGTGAAAAGGTTGGGGGAACTCAAAAAG-AAAAAGTCAATG-AAAAAATAAGTGAAAATAAA
66 TTTTGTGAAAAGGGTGGGGGAACTCAAAAAGAAAAAAGTCAATGAAAAAAATAAGTGAAAATAAA
3187318 AGAGTTCATGGTTACAAAAGCCAAAAGAATAATGACCCACAGGGGGTAAGCGAAACTAATTGTGA
131 AGAGTTCATGGTTACAAAAGCCAAAAGAATAATGACCCACAGGGGGTAAGCGAAACTAATTGTGA
3187383 GAAGAATAGAGTGATTCAAAATACATATGTGAGCAC-AAAAAATTGAGAGAGAATATTCTACATA
196 GAAGAATAGAGTGATTCAAAATACATATGTGAGCACAAAAAAATTGAGAGAGAATATTCTACATA
3187447 AAGAGCCTTGCATTCTTGTCCACTTTAGACAACTACTAGTTTCGATTTCTAATGATAACACTATC
261 AAGAGCCTTGCATTCTTGTCCACTTTAGACAACTACTAGTTTCGATTTCTAATGATAACACTATC
*
3187512 TTGCCTAGTGTGTTTGTTTATTTTTTTACAGAGTT
326 TTGCCTAGTGTGTTTGTTCA-TTTTTTACAGAGTT
3187547 CAAATGGTGT
Statistics
Matches: 349, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
357 111 0.32
358 133 0.38
359 12 0.03
360 93 0.27
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (360 bp):
TTATGGAAGATATCAATCTTTAGTCATTGAAAAAAAAAGATACACTTGAAAATCAAGTTATGACA
TTTTGTGAAAAGGGTGGGGGAACTCAAAAAGAAAAAAGTCAATGAAAAAAATAAGTGAAAATAAA
AGAGTTCATGGTTACAAAAGCCAAAAGAATAATGACCCACAGGGGGTAAGCGAAACTAATTGTGA
GAAGAATAGAGTGATTCAAAATACATATGTGAGCACAAAAAAATTGAGAGAGAATATTCTACATA
AAGAGCCTTGCATTCTTGTCCACTTTAGACAACTACTAGTTTCGATTTCTAATGATAACACTATC
TTGCCTAGTGTGTTTGTTCATTTTTTACAGAGTTG
Found at i:3195642 original size:18 final size:18
Alignment explanation
Indices: 3195621--3195668 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3195611 GTCTTAATTG
3195621 TAAAAATTTAAATTTAAA
1 TAAAAATTTAAATTTAAA
**
3195639 TAAAAATAAAAATTTAAA
1 TAAAAATTTAAATTTAAA
3195657 TAAAAATTTAAA
1 TAAAAATTTAAA
3195669 ACATTGATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATTTAAATTTAAA
Found at i:3195645 original size:12 final size:12
Alignment explanation
Indices: 3195621--3195668 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3195611 GTCTTAATTG
3195621 TAAAAATTTAAA
1 TAAAAATTTAAA
** **
3195633 TTTAAATAAAAA
1 TAAAAATTTAAA
3195645 TAAAAATTTAAA
1 TAAAAATTTAAA
3195657 TAAAAATTTAAA
1 TAAAAATTTAAA
3195669 ACATTGATCT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAAATTTAAA
Found at i:3195945 original size:37 final size:37
Alignment explanation
Indices: 3195893--3196285 Score: 221
Period size: 37 Copynumber: 10.7 Consensus size: 37
3195883 TTTTTCAACA
* * *
3195893 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGT
1 GAAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
* * ** *
3195930 GAAACTGTCTCAAGTGAGA-CAAAAATTATTTCAAGG
1 GAAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
* * *
3195966 GAAAAC-ATCTCAAGTGAGATGTAATTTTGTTTCGAGT
1 G-AAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
* * ** * **
3196003 GAAATTATATTGAGTGAGAAGAAA-AGT-TTTCAAGG
1 GAAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
* *
3196038 GAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGG
1 GAAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
* * *
3196075 AAAAACTGTCTCGAGTGAGATGAAA--TTG-TTCAAGG
1 -GAAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
* *
3196110 GAAACTATCTCAAGTAAGATGCAATTTTTGTTTCAA-G
1 GAAACTATCTCAAGTGAGATG-AAATTTTGTTTCAAGG
* * * * * **
3196147 GAGATTGTCTCAAGTGATATGAAATTTGTTTTTTTGAGG
1 GAAACTATCTCAAGTGAGATGAAA-TT-TTGTTTCAAGG
* * * * * *
3196186 AAAACAATCTCAAGTGAGATAAAAAATTTATTTCAAGA
1 GAAACTATCTCAAGTGAGAT-GAAATTTTGTTTCAAGG
* * * ** * * *
3196224 AAAACTGTGTTGAGTTCA-ACG-AATTTTGTTTTAAGG
1 GAAACTATCTCAAG-TGAGATGAAATTTTGTTTCAAGG
* *
3196260 AAAACTATCTCAAGTGAGATAAAATT
1 GAAACTATCTCAAGTGAGATGAAATT
3196286 GGTATTTCGA
Statistics
Matches: 255, Mismatches: 84, Indels: 34
0.68 0.23 0.09
Matches are distributed among these distances:
34 17 0.07
35 35 0.14
36 56 0.22
37 79 0.31
38 47 0.18
39 18 0.07
40 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.32
Consensus pattern (37 bp):
GAAACTATCTCAAGTGAGATGAAATTTTGTTTCAAGG
Found at i:3196176 original size:72 final size:71
Alignment explanation
Indices: 3195881--3196173 Score: 302
Period size: 73 Copynumber: 4.1 Consensus size: 71
3195871 AGTGAGACAT
** *
3195881 AATTTTTCAACAGAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGTGAAACTGTCTCAAGTG
1 AATTTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGTGAAACTGTCTCAAGTG
*
3195946 AGACAAA
66 AGA-AGA
* * * * * * **
3195953 AATTATTTCAAGGGAAAACATCTCAAGTGAGATGTAATTTTGTTTCGAGTGAAATTATATTGAGT
1 AATT-TTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGTGAAACTGTCTCAAGT
3196018 GAGAAGAA
65 GAGAAG-A
* * *
3196026 AAGTTTTCAAGGGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAG-GAAAAACTGTCTCGAG
1 AATTTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGTG--AAACTGTCTCAAG
*
3196090 TGAGATGA
64 TGAGAAGA
* * * * * *
3196098 AATTGTTCAAGGGAAACTATCTCAAGTAAGATGCAATTTTTGTTTCAAG-GAGATTGTCTCAAGT
1 AATTTTTCAAGGGAAAATATCTCAAGTGAGATG-AAATTTTGTTTCAAGTGAAACTGTCTCAAGT
* *
3196162 GATATGA
65 GAGAAGA
3196169 AATTT
1 AATTT
3196174 GTTTTTTTGA
Statistics
Matches: 185, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
71 22 0.12
72 74 0.40
73 89 0.48
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (71 bp):
AATTTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGTGAAACTGTCTCAAGTG
AGAAGA
Found at i:3196477 original size:15 final size:15
Alignment explanation
Indices: 3196457--3196491 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3196447 AACTTTTTGG
3196457 AAACAAAATTTAATA
1 AAACAAAATTTAATA
*
3196472 AAACAAAATTTAATG
1 AAACAAAATTTAATA
3196487 AAACA
1 AAACA
3196492 TCAAGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.23
Consensus pattern (15 bp):
AAACAAAATTTAATA
Found at i:3213044 original size:16 final size:16
Alignment explanation
Indices: 3213025--3213060 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3213015 AGTGCAAAAG
3213025 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
* *
3213041 AAAATACTACAAAATA
1 AAAATAATAAAAAATA
3213057 AAAA
1 AAAA
3213061 AGGGTCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAATAAAAAATA
Found at i:3215082 original size:16 final size:16
Alignment explanation
Indices: 3215061--3215105 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
3215051 GTCTGACCCA
3215061 TTGACTTTGACCAGGG
1 TTGACTTTGACCAGGG
3215077 TTGACTTTGACCAGGG
1 TTGACTTTGACCAGGG
3215093 TTGACTTTGACCA
1 TTGACTTTGACCA
3215106 AAAAGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (16 bp):
TTGACTTTGACCAGGG
Found at i:3238048 original size:20 final size:20
Alignment explanation
Indices: 3238023--3238078 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
3238013 AGTGAGGAAT
*
3238023 AGATTTATCTTACCGAGGGA
1 AGATTTATCTTACAGAGGGA
*
3238043 AGATTTATCTTGCAGAGGGA
1 AGATTTATCTTACAGAGGGA
*
3238063 AGATTTATCTTGCAGA
1 AGATTTATCTTACAGA
3238079 TCTAACATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.32
Consensus pattern (20 bp):
AGATTTATCTTACAGAGGGA
Found at i:3239163 original size:18 final size:19
Alignment explanation
Indices: 3239135--3239177 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
3239125 TGAACCCAAC
3239135 ACTTTTAATTGCCTTAATA
1 ACTTTTAATTGCCTTAATA
*
3239154 A-TTTTGATTGCCTTAATA
1 ACTTTTAATTGCCTTAATA
3239172 ACTTTT
1 ACTTTT
3239178 CGCCTTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (19 bp):
ACTTTTAATTGCCTTAATA
Found at i:3239261 original size:120 final size:120
Alignment explanation
Indices: 3239048--3239282 Score: 416
Period size: 120 Copynumber: 2.0 Consensus size: 120
3239038 TTAGACATAG
*
3239048 AATAACTTTTCACCTTAGAAAAACCAACATAAGTGCTCCGTAAATAAGTATGTCTGTGTGTGGTT
1 AATAACTTTTCACCTTAGAAAAACCAACATAAGTGCTCCGTAAAGAAGTATGTCTGTGTGTGGTT
3239113 TTTTGAATATATTGAACCCAACACTTTTAATTGCCTTAATAATTTTGATTGCCTT
66 TTTTGAATATATTGAACCCAACACTTTTAATTGCCTTAATAATTTTGATTGCCTT
* * * * *
3239168 AATAACTTTTCGCCTTAGCAAACCCAACATAAGTGCTCTGTAAAGAAGTCTGTCTGTGTGTGGTT
1 AATAACTTTTCACCTTAGAAAAACCAACATAAGTGCTCCGTAAAGAAGTATGTCTGTGTGTGGTT
3239233 TTTTGAATATATTGAACCCAACACTTTTAATTGCCTTAATAATTTTGATT
66 TTTTGAATATATTGAACCCAACACTTTTAATTGCCTTAATAATTTTGATT
3239283 CATTTACTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (120 bp):
AATAACTTTTCACCTTAGAAAAACCAACATAAGTGCTCCGTAAAGAAGTATGTCTGTGTGTGGTT
TTTTGAATATATTGAACCCAACACTTTTAATTGCCTTAATAATTTTGATTGCCTT
Found at i:3241397 original size:18 final size:18
Alignment explanation
Indices: 3241361--3241398 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3241351 GAGCTTTATA
*
3241361 TCTTCCTTTATCTTCTTC
1 TCTTCATTTATCTTCTTC
3241379 TCTTCATTT-TCTTCATTC
1 TCTTCATTTATCTTC-TTC
3241397 TC
1 TC
3241399 ATTTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTCATTTATCTTCTTC
Found at i:3245249 original size:29 final size:30
Alignment explanation
Indices: 3245186--3245251 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
3245176 AAATTATCAA
*
3245186 TTTGGTACTTAAACTTTACCAAAGTTTATAC
1 TTTGGTACTTAAACTTTA-CAAAGTTTACAC
* *
3245217 TTTGGTAACTT-AACTTT-CAAATTTTACAT
1 TTTGGT-ACTTAAACTTTACAAAGTTTACAC
3245246 TTTGGT
1 TTTGGT
3245252 CACTATCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 15 0.48
31 12 0.39
32 4 0.13
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTGGTACTTAAACTTTACAAAGTTTACAC
Found at i:3252504 original size:14 final size:14
Alignment explanation
Indices: 3252485--3252511 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3252475 CTCTGGATTA
3252485 TGATATTTGGTTTC
1 TGATATTTGGTTTC
3252499 TGATATTTGGTTT
1 TGATATTTGGTTT
3252512 TTGAGCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.22, T:0.59
Consensus pattern (14 bp):
TGATATTTGGTTTC
Found at i:3258792 original size:21 final size:21
Alignment explanation
Indices: 3258766--3258806 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3258756 ATTATCCAAT
*
3258766 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
3258787 AAACTTGAAATCCATAACAA
1 AAACTTGAAATCCATAACAA
3258807 TAAATCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:3260224 original size:81 final size:80
Alignment explanation
Indices: 3260116--3260321 Score: 233
Period size: 81 Copynumber: 2.6 Consensus size: 80
3260106 GGAATATAGT
* * * *
3260116 GGCGTTTCTACAT-AAGCCACTAAAGTACACATTTTTAGC-G-GTTTTTACAAAAAATGGC-ACT
1 GGCGTTTTTACATAAAGCCACTAAAGTACACATTTTTAGCGGCGTGTTCAC-AAAAA-CGCTACT
** *
3260177 ATATATTTGGCTACAGC
64 ATATATCCGACTACAGC
* *
3260194 GGTGTTTTTTACATAAACGCCACTAAAGTACACATTGTT-GCGGCGTGTTCACAAAAACGCTACT
1 GGCG-TTTTTACATAAA-GCCACTAAAGTACACATTTTTAGCGGCGTGTTCACAAAAACGCTACT
3260258 ATATATCCGACTACAGC
64 ATATATCCGACTACAGC
*
3260275 GGCGTTTTCACATAAAATGCCACTAAAGTACACATTTTTAGCGGCGT
1 GGCGTTTTTACAT-AAA-GCCACTAAAGTACACATTTTTAGCGGCGT
3260322 TTATCCAAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.03
79 8 0.07
80 14 0.13
81 69 0.64
82 13 0.12
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (80 bp):
GGCGTTTTTACATAAAGCCACTAAAGTACACATTTTTAGCGGCGTGTTCACAAAAACGCTACTAT
ATATCCGACTACAGC
Found at i:3260252 original size:40 final size:41
Alignment explanation
Indices: 3260204--3260321 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 41
3260194 GGTGTTTTTT
*
3260204 ACAT-AAACGCCACTAAAGTACACATTGTTGCGGCGTGTTC
1 ACATAAAACGCCACTAAAGTACACATTATTGCGGCGTGTTC
* * * ** *
3260244 ACA-AAAACGCTACTATA-TATC-CGACTACAGCGGCGTTTTC
1 ACATAAAACGCCACTAAAGTA-CAC-ATTATTGCGGCGTGTTC
* *
3260284 ACATAAAATGCCACTAAAGTACACATTTTTAGCGGCGT
1 ACATAAAACGCCACTAAAGTACACATTATT-GCGGCGT
3260322 TTATCCAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
39 3 0.05
40 30 0.53
41 14 0.25
42 10 0.18
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
ACATAAAACGCCACTAAAGTACACATTATTGCGGCGTGTTC
Found at i:3262389 original size:25 final size:26
Alignment explanation
Indices: 3262337--3262389 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
3262327 AAACATAAAA
*
3262337 TTATAAATAATAAAAAATATACATGT
1 TTATAAATAATAAAAAATATACAAGT
* * *
3262363 TTATAATTAATTAAAAATA-CCAAGT
1 TTATAAATAATAAAAAATATACAAGT
3262388 TT
1 TT
3262390 CTTTTAACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
TTATAAATAATAAAAAATATACAAGT
Found at i:3262503 original size:31 final size:31
Alignment explanation
Indices: 3262468--3262548 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
3262458 ATAGAAGAAT
*
3262468 AATGATTGAATTGATAGAATT-TTTATATATG
1 AATGATTGAATTGATAGAATTATTT-TAAATG
* * * *
3262499 AATGATTAAATTTATTGAATTATTTTAAATT
1 AATGATTGAATTGATAGAATTATTTTAAATG
*
3262530 AA-GACTGAATTGATAGAAT
1 AATGATTGAATTGATAGAAT
3262549 ATATAAAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 13 0.32
31 24 0.60
32 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (31 bp):
AATGATTGAATTGATAGAATTATTTTAAATG
Found at i:3266626 original size:173 final size:170
Alignment explanation
Indices: 3266273--3266589 Score: 498
Period size: 173 Copynumber: 1.8 Consensus size: 170
3266263 TTATATATAT
3266273 TATATATAACATATGGGCTGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
1 TATATATAACATATGGGCTGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
3266338 TTAAACCAAAATCAATATAATTAATTAAAAAAATTATATAAAATTTTTTTATTTTATAATTATAT
66 TTAAACCAAAATCAATATAATTAATTAAAAAAATTATATAAAA--TTTTTATTTTATAATTATAT
*
3266403 ATTAAATTAATTGTAAACAGTTTTTTAATTAAAAATTAAATA
129 ATTAAATTAATTATAAACAGTTTTTTAATTAAAAATTAAATA
3266445 TATATATAAC-TATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA-TTAAGATCCAATAA
1 TATATATAACATATGGGCT--GCCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAA
* * * *
3266508 CTTTTAAACC-TAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TTTTATTTTATAATTAT
64 C-TTTAAACCAAAATCAATA-TAATTAATTAAAAAAATTATATAAAATTTTTATTTTATAATTAT
3266571 ATATTCAAATTAATTATAA
127 ATATT-AAATTAATTATAA
3266590 TTTTTTTTGA
Statistics
Matches: 135, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
170 22 0.16
171 20 0.15
172 33 0.24
173 60 0.44
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (170 bp):
TATATATAACATATGGGCTGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAACT
TTAAACCAAAATCAATATAATTAATTAAAAAAATTATATAAAATTTTTATTTTATAATTATATAT
TAAATTAATTATAAACAGTTTTTTAATTAAAAATTAAATA
Found at i:3266747 original size:31 final size:30
Alignment explanation
Indices: 3266688--3266747 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3266678 CCGAAATTTA
* *
3266688 TTCAGTTTGATTAATATGTTCGAAAAAAAG
1 TTCAGTTTGATTAATAGGTTAGAAAAAAAG
3266718 TTCAGTTTGATTAAT-GGTTAAAGAAAAAAA
1 TTCAGTTTGATTAATAGGTT--AGAAAAAAA
3266748 AAGTTCGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 15 0.58
31 8 0.31
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (30 bp):
TTCAGTTTGATTAATAGGTTAGAAAAAAAG
Found at i:3289640 original size:39 final size:40
Alignment explanation
Indices: 3289565--3289643 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
3289555 AGTGTTTTCG
*
3289565 CATAAGGTTGTGTCGACCCTTTTTGCACCAAAGTGCTTACA
1 CATAAGGCTGTGTCGACCC-TTTTGCACCAAAGTGCTTACA
*
3289606 CATAAGGCTGTGTCGATCC-TTTGCACCAAAGTGCTTAC
1 CATAAGGCTGTGTCGACCCTTTTGCACCAAAGTGCTTAC
3289644 CCAATATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 19 0.53
41 17 0.47
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (40 bp):
CATAAGGCTGTGTCGACCCTTTTGCACCAAAGTGCTTACA
Found at i:3295789 original size:81 final size:81
Alignment explanation
Indices: 3295654--3295815 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 81
3295644 TCAACATCAA
3295654 ATCTTTGGTTGTATGACTGATTGGATGCTCTAGTCACAAACAACTAGCAAATGAAGGCAAAGGGG
1 ATCTTTGGTTGTATGACTGATTGGATGCTCTAGTCACAAACAACTAGCAAATGAAGGCAAAGGGG
*
3295719 TGCACACATCGAATTT
66 AGCACACATCGAATTT
** * *
3295735 ATCTTTGGTTGTATGGTTGGTTGGATGCTTTAGTCACAAACAACTAGCAAATGAAGGCAAAGGGG
1 ATCTTTGGTTGTATGACTGATTGGATGCTCTAGTCACAAACAACTAGCAAATGAAGGCAAAGGGG
3295800 AGCACACATCGAATTT
66 AGCACACATCGAATTT
3295816 GTGTGGAACT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (81 bp):
ATCTTTGGTTGTATGACTGATTGGATGCTCTAGTCACAAACAACTAGCAAATGAAGGCAAAGGGG
AGCACACATCGAATTT
Found at i:3299783 original size:21 final size:21
Alignment explanation
Indices: 3299759--3299802 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3299749 AAACTCAAAT
* *
3299759 AACTCTAATTCAAATTTTATA
1 AACTCGAATACAAATTTTATA
* *
3299780 AACTCGAATAGAAATTTTTTA
1 AACTCGAATACAAATTTTATA
3299801 AA
1 AA
3299803 TAAAATTTGA
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:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (21 bp):
AACTCGAATACAAATTTTATA
Found at i:3300935 original size:25 final size:25
Alignment explanation
Indices: 3300902--3300985 Score: 100
Period size: 25 Copynumber: 3.4 Consensus size: 25
3300892 ACAAATTTAA
*
3300902 ATATTTTTAAAGATCATAATATTTG
1 ATATCTTTAAAGATCATAATATTTG
* * *
3300927 ATATCTTT-AATATCAGAA-ATTTAA
1 ATATCTTTAAAGATCATAATATTT-G
*
3300951 ATATTTTTAAAGATCATAATATTTG
1 ATATCTTTAAAGATCATAATATTTG
3300976 ATATCTTTAA
1 ATATCTTTAA
3300986 TATCAGTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
23 4 0.09
24 15 0.32
25 24 0.51
26 4 0.09
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (25 bp):
ATATCTTTAAAGATCATAATATTTG
Found at i:3300947 original size:49 final size:49
Alignment explanation
Indices: 3300894--3300991 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
3300884 AAAATAATAC
3300894 AAATTTAAATATTTTTAAAGATCATAATATTTGATATCTTTAATATCAG
1 AAATTTAAATATTTTTAAAGATCATAATATTTGATATCTTTAATATCAG
3300943 AAATTTAAATATTTTTAAAGATCATAATATTTGATATCTTTAATATCAG
1 AAATTTAAATATTTTTAAAGATCATAATATTTGATATCTTTAATATCAG
3300992 TTATAATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (49 bp):
AAATTTAAATATTTTTAAAGATCATAATATTTGATATCTTTAATATCAG
Found at i:3301125 original size:3 final size:3
Alignment explanation
Indices: 3301112--3301173 Score: 115
Period size: 3 Copynumber: 20.3 Consensus size: 3
3301102 AAGTGGCATA
3301112 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3301158 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
3301174 TAGGATGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3303035 original size:25 final size:26
Alignment explanation
Indices: 3302982--3303035 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
3302972 TTAACTAAAG
*
3302982 TAAAAAATATATATTAATCTTAACTT
1 TAAAAAATATATATTAATCTTAACAT
* *
3303008 TAAAAAATATA-ATTTATCTTTACAT
1 TAAAAAATATATATTAATCTTAACAT
3303033 TAA
1 TAA
3303036 CTTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAAAATATATATTAATCTTAACAT
Found at i:3303137 original size:33 final size:32
Alignment explanation
Indices: 3303100--3303172 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
3303090 ATATTTATTA
*
3303100 AAAATAAAACAAAAAATATAAATATAAAATTTT
1 AAAATAAAACAAAAAATAGAAA-ATAAAATTTT
* * *
3303133 AAAAT-AAATAAAAAATAGAAAATATATTTTT
1 AAAATAAAACAAAAAATAGAAAATAAAATTTT
*
3303164 AAATTAAAA
1 AAAATAAAA
3303173 TAAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 12 0.35
32 17 0.50
33 5 0.15
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (32 bp):
AAAATAAAACAAAAAATAGAAAATAAAATTTT
Found at i:3303164 original size:31 final size:29
Alignment explanation
Indices: 3303063--3303232 Score: 157
Period size: 29 Copynumber: 5.6 Consensus size: 29
3303053 TATTATTACA
* *
3303063 ATATTTTAAAATTAATATAAAAAT--AAT
1 ATATTTTTAAATTAAAATAAAAATAAAAT
* *
3303090 ATATTTATTAAAAATAAAACAAAAAATATAAAT
1 ATATTT-TT-AAATTAAAA-TAAAAATA-AAAT
* *
3303123 ATAAAATTTTAAAAT-AAATAAAAAATAGAAAAT
1 AT--ATTTTTAAATTAAAAT-AAAAAT--AAAAT
*
3303156 ATATTTTTAAATTAAAATAAGAATAAAAT
1 ATATTTTTAAATTAAAATAAAAATAAAAT
*
3303185 ATATTTTTAAATTAAAATAAGAATAAAAT
1 ATATTTTTAAATTAAAATAAAAATAAAAT
3303214 ATATATTTTAAATTAAAAT
1 ATAT-TTTTAAATTAAAAT
3303233 TATAAAAATA
Statistics
Matches: 121, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
27 6 0.05
28 1 0.01
29 45 0.37
30 20 0.17
31 14 0.12
32 13 0.11
33 16 0.13
34 3 0.02
35 3 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (29 bp):
ATATTTTTAAATTAAAATAAAAATAAAAT
Found at i:3303225 original size:30 final size:30
Alignment explanation
Indices: 3303063--3303395 Score: 153
Period size: 30 Copynumber: 11.0 Consensus size: 30
3303053 TATTATTACA
* * *
3303063 ATATTTTAAAATTAATATAAAAATAATATAT
1 ATATTTT-AAATTAAAATAAGAATAAAATAT
* * * * *
3303094 TTA-TTAAAAATAAAACAAAAAATATAAATAT
1 ATATTTTAAATTAAAA-TAAGAATA-AAATAT
* * *
3303125 AAAATTTTAAAAT-AAATAAAAAATAGAAA-AT
1 -ATATTTTAAATTAAAAT-AAGAATA-AAATAT
3303156 ATATTTTTAAATTAAAATAAGAATAAAATAT
1 ATA-TTTTAAATTAAAATAAGAATAAAATAT
3303187 AT-TTTTAAATTAAAATAAGAATAAAATAT
1 ATATTTTAAATTAAAATAAGAATAAAATAT
* *
3303216 ATATTTTAAATTAAAATTA-TA-AAAATA-
1 ATATTTTAAATTAAAATAAGAATAAAATAT
* * ** *
3303243 ATACTTAATAATTTAAGGTAAGAATAGAATAT
1 ATA-TT-TTAAATTAAAATAAGAATAAAATAT
* ** ** *
3303275 AT-TTAATACTTTAAGTTAAGAATATAATAT
1 ATATT-TTAAATTAAAATAAGAATAAAATAT
* ** * * *
3303305 ATGTAATAAGTTAATATAACAATAAAATAT
1 ATATTTTAAATTAAAATAAGAATAAAATAT
* * *
3303335 A-CTTTAAAAGTTAAGATAAGAATAAACTATAT
1 ATATTTTAAA-TTAAAATAAGAATAAA--ATAT
* * * *
3303367 ATTTTTTAATTTAAGATAAGATTAAAATA
1 ATATTTTAAATTAAAATAAGAATAAAATA
3303396 GTTTGTTAGT
Statistics
Matches: 239, Mismatches: 44, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
27 3 0.01
28 8 0.03
29 49 0.21
30 94 0.39
31 33 0.14
32 40 0.17
33 12 0.05
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (30 bp):
ATATTTTAAATTAAAATAAGAATAAAATAT
Found at i:3303728 original size:23 final size:23
Alignment explanation
Indices: 3303698--3303751 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
3303688 AATAATTTCG
3303698 TCTTTATGGCACGCCATCTTCTA
1 TCTTTATGGCACGCCATCTTCTA
** *
3303721 TCTTTATGGCACGTTATCTTCTG
1 TCTTTATGGCACGCCATCTTCTA
3303744 TCTTTATG
1 TCTTTATG
3303752 ACACTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (23 bp):
TCTTTATGGCACGCCATCTTCTA
Found at i:3305758 original size:14 final size:14
Alignment explanation
Indices: 3305741--3305781 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3305731 TCACTAAATC
3305741 GGTCTACCTAAACT
1 GGTCTACCTAAACT
** *
3305755 GGTCTGTCTGAACT
1 GGTCTACCTAAACT
3305769 GGTCTACCTAAAC
1 GGTCTACCTAAAC
3305782 CTGTCTGCTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (14 bp):
GGTCTACCTAAACT
Found at i:3305787 original size:28 final size:28
Alignment explanation
Indices: 3305740--3305801 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
3305730 ATCACTAAAT
3305740 CGGTCTACCTAAACTGGTCTG-TCTGAAC
1 CGGTCTACCTAAACTGGTCTGCT-TGAAC
*
3305768 TGGTCTACCTAAACCT-GTCTGCTTGAAC
1 CGGTCTACCTAAA-CTGGTCTGCTTGAAC
3305796 CGGTCT
1 CGGTCT
3305802 GCCAAAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (28 bp):
CGGTCTACCTAAACTGGTCTGCTTGAAC
Found at i:3305904 original size:23 final size:23
Alignment explanation
Indices: 3305852--3305905 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3305842 CAAACCAAAT
*
3305852 TTAACTTTGACTGACTCGAATTG
1 TTAACTTTGACTGACTCGAATCG
* *
3305875 TTGACTTTGACTGAC-CTAACTCG
1 TTAACTTTGACTGACTCGAA-TCG
3305898 TTAACTTT
1 TTAACTTT
3305906 TCTTGACCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (23 bp):
TTAACTTTGACTGACTCGAATCG
Found at i:3306679 original size:43 final size:43
Alignment explanation
Indices: 3306576--3306700 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
3306566 TTCATTTCTT
* * **
3306576 TGATTCTGCATGAGATCCTCTATGGAGGACATCATCCCCATTT
1 TGATTCTGCATAAGATCCTCTATGGAGGGCATCATCCCCATCC
* * * * * *
3306619 TGATACAGTATAGGATCCTCTACGGAGGGCATCATCCCCGTCC
1 TGATTCTGCATAAGATCCTCTATGGAGGGCATCATCCCCATCC
* *
3306662 TGATTCTGCATAAGATCCTATATGGAGGGCATCACCCCC
1 TGATTCTGCATAAGATCCTCTATGGAGGGCATCATCCCC
3306701 TGATTCTATT
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (43 bp):
TGATTCTGCATAAGATCCTCTATGGAGGGCATCATCCCCATCC
Found at i:3308069 original size:13 final size:13
Alignment explanation
Indices: 3308051--3308084 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3308041 TAAGATTTTC
*
3308051 TTTGAAAATCATT
1 TTTGAAAATCAAT
3308064 TTTG-AAATCAAT
1 TTTGAAAATCAAT
3308076 TTTGAAAAT
1 TTTGAAAAT
3308085 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:3309826 original size:12 final size:13
Alignment explanation
Indices: 3309809--3309841 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3309799 ATGGGCAACA
*
3309809 TTTGAAAACTAT-
1 TTTGAAAACAATG
3309821 TTTGAAAACAATG
1 TTTGAAAACAATG
3309834 TTTGAAAA
1 TTTGAAAA
3309842 ATCATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:3318610 original size:45 final size:45
Alignment explanation
Indices: 3318554--3318924 Score: 519
Period size: 45 Copynumber: 8.2 Consensus size: 45
3318544 ATTGTTCATT
* * *
3318554 ATTTTCATTTATGGCATCCTTTCATGTCTATAATGCACCGTTATAC
1 ATTTT-ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
3318600 ATTTTATTTATGGTATCCTTTCAT-ACTTGTAATACAACGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTT-TAATGCACCGTTATGC
* *
3318645 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
3318690 ATTTTATTTATGGCATCATTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
3318735 ATTTCATTTATGACATCTTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
3318780 ATTTTATTTATGGCATTCTTTCATGCCTTTAATGTACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
3318825 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCTTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
** *
3318870 ATTTCCTTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
3318915 ATTTTATTTA
1 ATTTTATTTA
3318925 GGTGCATCGA
Statistics
Matches: 287, Mismatches: 36, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
44 2 0.01
45 277 0.97
46 8 0.03
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (45 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:3319423 original size:96 final size:96
Alignment explanation
Indices: 3319278--3319467 Score: 263
Period size: 96 Copynumber: 2.0 Consensus size: 96
3319268 CCCATACCAT
* * * * *
3319278 AGTATCGATACTTCTATACTATGGTACCGATACACCCTTTCAGTATCGATACCATTTCGGCATTC
1 AGTAACGATACTTCTATACTATAGTACCGATACACCATTACAGTATCGATACCATTTAGGCATTC
*
3319343 TGTAAATTAATGGTATCGATACCTTCCTCTC
66 TGTAAATCAATGGTATCGATACCTTCCTCTC
* * * * * * *
3319374 AGTAACGATACTTCTGTATTATAGTACCGATACTCTATTACGGTATCGATACCATTTATGCATTT
1 AGTAACGATACTTCTATACTATAGTACCGATACACCATTACAGTATCGATACCATTTAGGCATTC
3319439 TGTAAATCAATGGTATCGATACCTTCCTC
66 TGTAAATCAATGGTATCGATACCTTCCTC
3319468 ATGGTATCCA
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (96 bp):
AGTAACGATACTTCTATACTATAGTACCGATACACCATTACAGTATCGATACCATTTAGGCATTC
TGTAAATCAATGGTATCGATACCTTCCTCTC
Found at i:3325643 original size:45 final size:45
Alignment explanation
Indices: 3325587--3325866 Score: 337
Period size: 45 Copynumber: 6.2 Consensus size: 45
3325577 TATTCATTAT
* *
3325587 TTTCATTTATGGCATCCTTTCATGCCTGTAATGCACCATTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
* * * * * *
3325632 ATTCATTTATGGGAATCCTTTAATG-CTTGTAATGCACCGTTCTACA
1 TTTCATTTAT-GGCATCCTTTCATGCCTT-TAATGCACCATTATGCA
* ** *
3325678 TTTCATTTAAGGCATCCTTTCATATCTTTAATGTACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
* * * *
3325723 TTTTATTTATGGCATCATTTCATACCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
3325768 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
* * * * *
3325813 TTTCCTTTATGTCATCCTTCCATGCCTTTAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
*
3325858 TTTTATTTA
1 TTTCATTTA
3325867 GGTGCATCGA
Statistics
Matches: 200, Mismatches: 32, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
45 162 0.81
46 38 0.19
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
Found at i:3325776 original size:24 final size:22
Alignment explanation
Indices: 3325661--3325821 Score: 57
Period size: 24 Copynumber: 7.1 Consensus size: 22
3325651 TTAATGCTTG
*
3325661 TAATGCACCGTTCTACATTTCATT
1 TAATGCACCATT-T-CATTTCATT
* *
3325685 TAAGGCATCC-TTTCATATC-TT
1 TAATGCA-CCATTTCATTTCATT
* *
3325706 TAATGTACCATTATGCATTTTATT
1 TAATGCACCATT-T-CATTTCATT
* * *
3325730 T-ATGGCATCATTTCA-TACCTT
1 TAAT-GCACCATTTCATTTCATT
*
3325751 TAATGCACCGTTATGCATTTCATT
1 TAATGCACCATT-T-CATTTCATT
* *
3325775 T-ATGGCATCC-TTTCA-TGCCTT
1 TAAT-GCA-CCATTTCATTTCATT
*
3325796 TAATGCACCATTATGCATTTCCTT
1 TAATGCACCATT-T-CATTTCATT
3325820 TA
1 TA
3325822 TGTCATCCTT
Statistics
Matches: 102, Mismatches: 18, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
20 4 0.04
21 29 0.28
22 16 0.16
23 15 0.15
24 34 0.33
25 4 0.04
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (22 bp):
TAATGCACCATTTCATTTCATT
Found at i:3325797 original size:21 final size:21
Alignment explanation
Indices: 3325773--3325842 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
3325763 ATGCATTTCA
3325773 TTTATGGCATCCTTTCATGCC
1 TTTATGGCATCCTTTCATGCC
*
3325794 TTTAAT-GCA-CCATTATGCATTTCC
1 TTT-ATGGCATCC-TT-T-CA-TGCC
* *
3325818 TTTATGTCATCCTTCCATGCC
1 TTTATGGCATCCTTTCATGCC
3325839 TTTA
1 TTTA
3325843 ATGCACCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 2 0.05
21 15 0.39
22 5 0.13
23 4 0.11
24 10 0.26
25 2 0.05
ACGTcount: A:0.19, C:0.27, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTATGGCATCCTTTCATGCC
Found at i:3326449 original size:18 final size:18
Alignment explanation
Indices: 3326423--3326468 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
3326413 CTTCCTCATG
*
3326423 GTATAGATACACACCTAA
1 GTATCGATACACACCTAA
*
3326441 GTATCGATACCCACCTAA
1 GTATCGATACACACCTAA
3326459 GTATCGATAC
1 GTATCGATAC
3326469 TAATTGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (18 bp):
GTATCGATACACACCTAA
Found at i:3337679 original size:40 final size:41
Alignment explanation
Indices: 3337634--3337715 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
3337624 TTCATTCTCA
3337634 TTCTCTTTAATTCCAACGTTTTCATCACCAATTA-TTTGTC
1 TTCTCTTTAATTCCAACGTTTTCATCACCAATTATTTTGTC
3337674 TTCTCTTTAATTCCAACGTTTTCATCACCAATTATTTTGTC
1 TTCTCTTTAATTCCAACGTTTTCATCACCAATTATTTTGTC
3337715 T
1 T
3337716 CTTCACAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 34 0.83
41 7 0.17
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.49
Consensus pattern (41 bp):
TTCTCTTTAATTCCAACGTTTTCATCACCAATTATTTTGTC
Found at i:3338568 original size:19 final size:19
Alignment explanation
Indices: 3338544--3338582 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3338534 GGAACGAACT
*
3338544 AACCGGTTGGACCAGTCTG
1 AACCGGCTGGACCAGTCTG
*
3338563 AACCGGCTGGACCGGTCTG
1 AACCGGCTGGACCAGTCTG
3338582 A
1 A
3338583 GTCGAGCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (19 bp):
AACCGGCTGGACCAGTCTG
Found at i:3338639 original size:10 final size:10
Alignment explanation
Indices: 3338624--3338685 Score: 88
Period size: 10 Copynumber: 6.0 Consensus size: 10
3338614 AAGCCACCTA
3338624 GTCGTTGACC
1 GTCGTTGACC
3338634 GTCGTTGACC
1 GTCGTTGACC
*
3338644 GCCGTTGACC
1 GTCGTTGACC
*
3338654 GTCGTTGATCG
1 GTCGTTGA-CC
3338665 GATCGTTGACC
1 G-TCGTTGACC
3338676 GTCGTTGACC
1 GTCGTTGACC
3338686 TGCCATTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
10 35 0.76
11 4 0.09
12 7 0.15
ACGTcount: A:0.11, C:0.29, G:0.31, T:0.29
Consensus pattern (10 bp):
GTCGTTGACC
Found at i:3342371 original size:21 final size:21
Alignment explanation
Indices: 3342345--3342385 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3342335 GACCAGACCA
* *
3342345 TTGACCGCCGTTGATCGGCCG
1 TTGACCACCATTGATCGGCCG
3342366 TTGACCACCATTGATCGGCC
1 TTGACCACCATTGATCGGCC
3342386 ATTTTTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (21 bp):
TTGACCACCATTGATCGGCCG
Found at i:3343207 original size:32 final size:32
Alignment explanation
Indices: 3343163--3343233 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
3343153 CACGGGAACC
3343163 TTGGAATCATCGAATTAAATTCCAGATCTATA
1 TTGGAATCATCGAATTAAATTCCAGATCTATA
*
3343195 TTTGAATCATCGAATTAAATTCCAGATCTATA
1 TTGGAATCATCGAATTAAATTCCAGATCTATA
3343227 TTGGAAT
1 TTGGAAT
3343234 TATAGAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TTGGAATCATCGAATTAAATTCCAGATCTATA
Found at i:3346905 original size:17 final size:17
Alignment explanation
Indices: 3346883--3346944 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
3346873 CTTGTAATCT
*
3346883 TGAATGAACTAGTTTGA
1 TGAATGAACTAGTTTAA
*
3346900 TGAATGAGCTAGTTTAA
1 TGAATGAACTAGTTTAA
3346917 TGAATGAACTAGTTTAA
1 TGAATGAACTAGTTTAA
*
3346934 TCAATGAACTA
1 TGAATGAACTA
3346945 CTTAGTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (17 bp):
TGAATGAACTAGTTTAA
Found at i:3346956 original size:17 final size:17
Alignment explanation
Indices: 3346936--3346981 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
3346926 TAGTTTAATC
* *
3346936 AATGAACTACTTAGTTA
1 AATGAACTACATAGCTA
* *
3346953 AATGAAGTGCATAGCTA
1 AATGAACTACATAGCTA
3346970 AATGAACTACAT
1 AATGAACTACAT
3346982 GTTTAAATGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (17 bp):
AATGAACTACATAGCTA
Found at i:3348295 original size:165 final size:165
Alignment explanation
Indices: 3348023--3348351 Score: 487
Period size: 165 Copynumber: 2.0 Consensus size: 165
3348013 AGTGTGAGAG
* **
3348023 CCTCCTCTATTTATAGGCTAGAGGAATCAAACTTTACTTAATAAAATTGCTCCAAATGTTGAGTG
1 CCTCCTCTATTTATAGGCTAGAGGAATCAAACTTCACCCAATAAAATTGCTCCAAATGTTGAGTG
* * * **
3348088 AAATGTCATCAATTAACAATTGCCCAGCCAGTTGTCCCATTCTAGAAAATTCCAATAATTACCTG
66 AAATGTCACCAATTAACAATTACCCAGCCAGCTGTCCCATTCTAGAAAATTCCAATAACCACCTG
* *
3348153 TGACATCAGTAATTGTTTCCATCTATACAGAACGT
131 TGACATCAGCAATTGTTTCCATCTATACACAACGT
* **
3348188 CCTCCTCTATTTATAGGCTAGAGTAATCAAACTTCACCCAATAAAATTGCTCCACGTGTTGAGTG
1 CCTCCTCTATTTATAGGCTAGAGGAATCAAACTTCACCCAATAAAATTGCTCCAAATGTTGAGTG
* * ** *
3348253 AAATGTCGCCAATTAACAGTTACCCAGCTTGCTGTCCCATTCTAGAAAATTCCAATAACCGCCTG
66 AAATGTCACCAATTAACAATTACCCAGCCAGCTGTCCCATTCTAGAAAATTCCAATAACCACCTG
*
3348318 TGACATTAGCAATTGTTTCCATCTATACACAACG
131 TGACATCAGCAATTGTTTCCATCTATACACAACG
3348352 CCTGAGCTAG
Statistics
Matches: 145, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
165 145 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (165 bp):
CCTCCTCTATTTATAGGCTAGAGGAATCAAACTTCACCCAATAAAATTGCTCCAAATGTTGAGTG
AAATGTCACCAATTAACAATTACCCAGCCAGCTGTCCCATTCTAGAAAATTCCAATAACCACCTG
TGACATCAGCAATTGTTTCCATCTATACACAACGT
Found at i:3353052 original size:24 final size:24
Alignment explanation
Indices: 3353007--3353056 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3352997 TGGTGGTTGG
*
3353007 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
3353031 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
3353055 TT
1 TT
3353057 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:3356280 original size:17 final size:18
Alignment explanation
Indices: 3356248--3356282 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3356238 GTCGTGAGTG
*
3356248 TTTGTTTGTTTATTTTTA
1 TTTGTTTGTATATTTTTA
3356266 TTTGTTT-TATATTTTTA
1 TTTGTTTGTATATTTTTA
3356283 GTTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTGTTTGTATATTTTTA
Found at i:3358654 original size:24 final size:24
Alignment explanation
Indices: 3358609--3358658 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3358599 TGGTGGTTGG
*
3358609 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
3358633 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
3358657 TT
1 TT
3358659 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:3374121 original size:24 final size:24
Alignment explanation
Indices: 3374077--3374122 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3374067 AACATTTTTT
**
3374077 AATCTTACTTTTCAACGGTAATTC
1 AATCTTACTTTTCAAAAGTAATTC
3374101 AATCTTACTTTTCAAAAGTAAT
1 AATCTTACTTTTCAAAAGTAAT
3374123 ACCAAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (24 bp):
AATCTTACTTTTCAAAAGTAATTC
Found at i:3374952 original size:27 final size:25
Alignment explanation
Indices: 3374894--3374979 Score: 99
Period size: 27 Copynumber: 3.5 Consensus size: 25
3374884 TTCGGTTTGC
*
3374894 AAAAAAACCGGATTTTTT-T-CGGAT
1 AAAAAAACCGG-TTTTTTATCCGGTT
3374918 -AAAAAACCGGTTTTTTATCCGGTTT
1 AAAAAAACCGGTTTTTTATCCGG-TT
*
3374943 GAAAAAAACCGGTTTTTAATCCGG-T
1 -AAAAAAACCGGTTTTTTATCCGGTT
3374968 AAAAAAACCGGT
1 AAAAAAACCGGT
3374980 CGTTCAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.11
23 11 0.20
24 15 0.27
25 2 0.04
27 21 0.38
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (25 bp):
AAAAAAACCGGTTTTTTATCCGGTT
Found at i:3374976 original size:24 final size:23
Alignment explanation
Indices: 3374894--3374979 Score: 86
Period size: 24 Copynumber: 3.5 Consensus size: 23
3374884 TTCGGTTTGC
*
3374894 AAAAAAACCGGATTTTT-TTCGG-
1 AAAAAAACCGG-TTTTTATCCGGT
3374916 ATAAAAAACCGGTTTTTTATCCGGTTT
1 A-AAAAAACCGG-TTTTTATCCGG--T
3374943 GAAAAAAACCGGTTTTTAATCCGGT
1 -AAAAAAACCGGTTTTT-ATCCGGT
3374968 AAAAAAACCGGT
1 AAAAAAACCGGT
3374980 CGTTCAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.02
23 15 0.27
24 16 0.29
25 1 0.02
26 5 0.09
27 16 0.29
28 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (23 bp):
AAAAAAACCGGTTTTTATCCGGT
Found at i:3376942 original size:16 final size:16
Alignment explanation
Indices: 3376923--3376974 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3376913 AAAGAGAAAT
3376923 AAATAAAAAATGAAGA
1 AAATAAAAAATGAAGA
*** * *
3376939 AAATGTTAAATTAAAA
1 AAATAAAAAATGAAGA
3376955 AAAT-AAAAATGAAGA
1 AAATAAAAAATGAAGA
3376970 AAATA
1 AAATA
3376975 TTAATTTCTA
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAATAAAAAATGAAGA
Found at i:3377008 original size:34 final size:34
Alignment explanation
Indices: 3376923--3377031 Score: 122
Period size: 34 Copynumber: 3.3 Consensus size: 34
3376913 AAAGAGAAAT
*
3376923 AAATAAAAAATGAAGAAAATGTTAAA--TTAAAA-
1 AAAT-AAAAATGAAGAAAATATTAAATTTTAAAAG
3376955 AAATAAAAATGAAGAAAATATT-AATTTCTAAAAG
1 AAATAAAAATGAAGAAAATATTAAATTT-TAAAAG
*
3376989 AAATAAAAA-GCAA-AGAAATATTAAATTTTAGAAG
1 AAATAAAAATG-AAGA-AAATATTAAATTTTAAAAG
3377023 AAATAAAAA
1 AAATAAAAA
3377032 ATAATATTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
30 2 0.03
31 17 0.25
32 5 0.07
33 7 0.10
34 32 0.47
35 5 0.07
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (34 bp):
AAATAAAAATGAAGAAAATATTAAATTTTAAAAG
Found at i:3377740 original size:24 final size:24
Alignment explanation
Indices: 3377694--3377769 Score: 89
Period size: 24 Copynumber: 3.0 Consensus size: 24
3377684 AAAGCCTCAA
*
3377694 GCTTTGTTTATTTTTTTGCTTTTGGTT
1 GCTTTGTTTA--TTTTT-ATTTTGGTT
3377721 GCTTTGTTTATTTTTATTTTGGTT
1 GCTTTGTTTATTTTTATTTTGGTT
* *
3377745 GCTTTGCTTATTTTTACTTTCGGTT
1 GCTTTGTTTATTTTTA-TTTTGGTT
3377770 TGTGGCTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
24 23 0.51
25 12 0.27
27 10 0.22
ACGTcount: A:0.07, C:0.09, G:0.17, T:0.67
Consensus pattern (24 bp):
GCTTTGTTTATTTTTATTTTGGTT
Found at i:3377769 original size:25 final size:25
Alignment explanation
Indices: 3377706--3377769 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
3377696 TTTGTTTATT
* *
3377706 TTTTTGCTTTTGGTTGCTTTGTTTA
1 TTTTTACTTTTGGTTGCTTTGCTTA
3377731 TTTTTA-TTTTGGTTGCTTTGCTTA
1 TTTTTACTTTTGGTTGCTTTGCTTA
*
3377755 TTTTTACTTTCGGTT
1 TTTTTACTTTTGGTT
3377770 TGTGGCTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.06, C:0.09, G:0.17, T:0.67
Consensus pattern (25 bp):
TTTTTACTTTTGGTTGCTTTGCTTA
Found at i:3378298 original size:5 final size:5
Alignment explanation
Indices: 3378274--3378606 Score: 195
Period size: 5 Copynumber: 66.6 Consensus size: 5
3378264 CAAAAACAAA
**
3378274 ATAAT A-AAT A-AAT A-AAT ATAAT ATATAT AATAAT ATAAT AT-AT ATGTT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT ATAAT
*
3378322 ATAA- ATAA- ATTAT A-ATAT ATAAT AT-AT A-ATAT ATAAT AT-AT ATACTAT
1 ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATA-AT ATAAT ATAAT ATA--AT
* * * *
3378370 ATAAT ATAAT ATATAT ATATAT ATACT ACAAT ACAAA ATAAAT ATAAT
1 ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT AT-AAT ATAAT
* *
3378418 AT-AT ATATAT ATTAT ATAAAT ATAGT ATAACT -T-AT AATAAT ATAAT
1 ATAAT ATA-AT ATAAT AT-AAT ATAAT ATAA-T ATAAT -ATAAT ATAAT
* * *
3378464 ATAAT ATATATT ATATT ATAAT ATAAAT ATACT ATAGT AT-AT AATAAT
1 ATAAT ATA-A-T ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT -ATAAT
*
3378512 ATAAT ATAAT ATAAT AT-AT ATTATAT ATAAT ATAAAT ATACT ATAAT
1 ATAAT ATAAT ATAAT ATAAT A-TA-AT ATAAT AT-AAT ATAAT ATAAT
* *
3378559 AT-AT AATAA- ATAA- ATAAT ATAAT AT-AT ATACT ATATT AT-AT A-AAT
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
3378604 ATA
1 ATA
3378607 CATAAAAACT
Statistics
Matches: 266, Mismatches: 25, Indels: 74
0.73 0.07 0.20
Matches are distributed among these distances:
3 1 0.00
4 58 0.22
5 144 0.54
6 48 0.18
7 15 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:3378301 original size:2 final size:2
Alignment explanation
Indices: 3378289--3378625 Score: 190
Period size: 2 Copynumber: 182.5 Consensus size: 2
3378279 AAATAAATAA
* *
3378289 AT AT A- AT AT AT AT A- AT A- AT AT A- AT AT AT AT GT -T AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3378326 AT AA AT -T AT A- AT AT AT A- AT AT AT A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3378363 AT ACT AT AT A- AT AT A- AT AT AT AT AT AT AT AT ACT AC A- AT AC
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
3378404 A- AA AT AA AT AT A- AT AT AT AT AT AT AT -T AT AT AA AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
3378444 AT A- ACT -T AT A- AT A- AT AT A- AT AT A- AT AT AT AT -T AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3378480 -T AT A- AT AT AA AT AT ACT AT AGT AT AT A- AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT
*
3378519 A- AT AT A- AT AT AT AT -T AT AT AT A- AT AT AA AT AT ACT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
3378557 AT AT AT A- AT AA AT AA AT A- AT AT A- AT AT AT AT ACT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
3378596 AT AT AA AT AT AC AT AA AA ACT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A
3378626 ATAAAAAAAG
Statistics
Matches: 263, Mismatches: 26, Indels: 92
0.69 0.07 0.24
Matches are distributed among these distances:
1 37 0.14
2 211 0.80
3 15 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:3378360 original size:7 final size:7
Alignment explanation
Indices: 3378274--3378606 Score: 206
Period size: 7 Copynumber: 47.4 Consensus size: 7
3378264 CAAAAACAAA
*
3378274 ATAATAA
1 ATAATAT
3378281 ATAA-AT
1 ATAATAT
3378287 A-AATAT
1 ATAATAT
3378293 A-ATATAT
1 ATA-ATAT
3378300 ATAATAAT
1 ATAAT-AT
3378308 ATAATAT
1 ATAATAT
*
3378315 AT-ATGTT
1 ATAAT-AT
3378322 ATAA-AT
1 ATAATAT
3378328 A-AAT-T
1 ATAATAT
3378333 ATAATAT
1 ATAATAT
3378340 ATAATAT
1 ATAATAT
3378347 ATAATAT
1 ATAATAT
3378354 ATAATAT
1 ATAATAT
3378361 ATATACTAT
1 ATA-A-TAT
3378370 ATAATAT
1 ATAATAT
3378377 AATATATAT
1 -ATA-ATAT
3378386 ATATATAT
1 ATA-ATAT
3378394 ACTACA-AT
1 A-TA-ATAT
*
3378402 ACAA-A-
1 ATAATAT
3378407 ATAA-AT
1 ATAATAT
3378413 ATAATAT
1 ATAATAT
3378420 AT-ATAT
1 ATAATAT
*
3378426 ATATTAT
1 ATAATAT
3378433 ATAA-AT
1 ATAATAT
*
3378439 ATAGTAT
1 ATAATAT
*
3378446 A-ACT-T
1 ATAATAT
3378451 ATAATAAT
1 ATAAT-AT
3378459 ATAATAT
1 ATAATAT
3378466 A-ATATAT
1 ATA-ATAT
*
3378473 ATTATATT
1 ATAATA-T
3378481 ATAATAT
1 ATAATAT
3378488 A-AATAT
1 ATAATAT
3378494 ACTATAGTAT
1 A-TA-A-TAT
3378504 ATAATA-
1 ATAATAT
3378510 AT-ATAAT
1 ATAAT-AT
3378517 ATAATAT
1 ATAATAT
3378524 A-ATATAT
1 ATA-ATAT
*
3378531 ATTATAT
1 ATAATAT
3378538 ATAATAT
1 ATAATAT
*
3378545 AAATATACT
1 ATA-ATA-T
3378554 ATAATAT
1 ATAATAT
*
3378561 ATAATAA
1 ATAATAT
3378568 ATAAATAAT
1 AT-AAT-AT
3378577 ATAATAT
1 ATAATAT
3378584 AT-ATACT
1 ATAATA-T
*
3378591 ATATTAT
1 ATAATAT
3378598 ATAA-AT
1 ATAATAT
3378604 ATA
1 ATA
3378607 CATAAAAACT
Statistics
Matches: 266, Mismatches: 21, Indels: 79
0.73 0.06 0.22
Matches are distributed among these distances:
5 14 0.05
6 53 0.20
7 117 0.44
8 56 0.21
9 22 0.08
10 4 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:3378621 original size:37 final size:36
Alignment explanation
Indices: 3378280--3378625 Score: 120
Period size: 37 Copynumber: 9.6 Consensus size: 36
3378270 CAAAATAATA
*
3378280 AATAAATAAAT-ATAATATATATAATAATATAATATAT
1 AATAAATAAATAAT-ATATATAT-ATACTATAATATAT
*
3378317 ATGTTATAAATAAATTATA-ATATATAATA-TATAATATAT
1 A----ATAAATAAATAATATATATAT-ATACTATAATATAT
* *
3378356 AATATATATACT-ATATAATATAATATA-TATATATATAT
1 AATAAATA-AATAATAT-ATAT-ATATACTATA-ATATAT
* *
3378394 ACTACAATACAA-AATAAATATA-ATA-TATATATATATT
1 AATA-AATA-AATAATATATATATATACTATA-ATATA-T
*
3378431 ATATAAATATAGTATAACT-TATAATAATATAATATAATATAT
1 A-ATAAATA-A--ATAA-TATAT-AT-ATATACTATAATATAT
* * * *
3378473 ATTATAT-TATAATATA-A-ATATACTATAGTATAT
1 AATAAATAAATAATATATATATATACTATAATATAT
3378506 AATAATATAATATAATATA-ATATATA-T-T-ATATAT
1 AATAA-ATAA-ATAATATATATATATACTATAATATAT
*
3378540 AAT--ATAAAT-ATA-CTATA-ATA-TAT-A-ATA-
1 AATAAATAAATAATATATATATATACTATAATATAT
*
3378567 AATAAAT-AAT-ATA-ATATATATACTATATTATAT
1 AATAAATAAATAATATATATATATACTATAATATAT
3378600 AAATATACATAAA-AACTATATATATA
1 -AATA-A-ATAAATAA-TATATATATA
3378626 ATAAAAAAAG
Statistics
Matches: 244, Mismatches: 22, Indels: 84
0.70 0.06 0.24
Matches are distributed among these distances:
27 3 0.01
28 17 0.07
29 13 0.05
30 5 0.02
31 4 0.02
32 3 0.01
33 17 0.07
34 14 0.06
35 12 0.05
36 28 0.11
37 34 0.14
38 19 0.08
39 26 0.11
40 14 0.06
41 18 0.07
42 5 0.02
43 8 0.03
44 4 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (36 bp):
AATAAATAAATAATATATATATATACTATAATATAT
Found at i:3378631 original size:17 final size:19
Alignment explanation
Indices: 3378597--3378632 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3378587 TACTATATTA
3378597 TATAAATATACATAAAAAC
1 TATAAATATACATAAAAAC
*
3378616 TATATATATA-ATAAAAA
1 TATAAATATACATAAAAA
3378633 AAGATAGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
TATAAATATACATAAAAAC
Found at i:3379397 original size:201 final size:201
Alignment explanation
Indices: 3379034--3379397 Score: 514
Period size: 201 Copynumber: 1.8 Consensus size: 201
3379024 AATCGTATTC
* * *
3379034 AACCTTGGTATTCTTATTGGCTTAAAGACCTCGGTTTTAAATTCAACCGAAAAGTAGTTCCTTGC
1 AACCTAGGTATTCTTATTGGCTTAAAGACCTCGGTTTAAAATTCAACCGAAAAGTAGTTCCATGC
*
3379099 TGCTACCATGCGGTTGATATGCCATCGAGATAAATGGAATCAAACTCGAAAGTATTCATTGACAG
66 TGCTACCATGCAGTTGATATGCCATCGAGATAAATGGAATCAAACTCGAAAGTATTCATTGACAG
** **
3379164 ATAACTTTTCTCGACTTAAGCTATGTTGTAAATTAGTCTGGGAGATAGTTTCTTGTTGCTAAATT
131 ATAACCCTTCTCGACTTAAGCTATACTGTAAATTAGTCTGGGAGATAGTTTCTTGTTGCTAAATT
3379229 GCAGCT
196 GCAGCT
* * * * *
3379235 AACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGGTTTAAAATTCAACTGGAAAGTAGTTTCATGC
1 AACCTAGGTATTCTTATTGGCTTAAAGACCTCGGTTTAAAATTCAACCGAAAAGTAGTTCCATGC
* * * * * *
3379300 TGCTACCATGCAGTTGATATGCCATTGAGCTGAATGGAAT-ATAACTCGAAATTTTTCGTTGACA
66 TGCTACCATGCAGTTGATATGCCATCGAGATAAATGGAATCA-AACTCGAAAGTATTCATTGACA
* * *
3379364 TATAACCCTTCTCGCCTTGAGCTATACTGTAAAT
130 GATAACCCTTCTCGACTTAAGCTATACTGTAAAT
3379398 GGTTCCTCTA
Statistics
Matches: 140, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
200 1 0.01
201 139 0.99
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (201 bp):
AACCTAGGTATTCTTATTGGCTTAAAGACCTCGGTTTAAAATTCAACCGAAAAGTAGTTCCATGC
TGCTACCATGCAGTTGATATGCCATCGAGATAAATGGAATCAAACTCGAAAGTATTCATTGACAG
ATAACCCTTCTCGACTTAAGCTATACTGTAAATTAGTCTGGGAGATAGTTTCTTGTTGCTAAATT
GCAGCT
Found at i:3385489 original size:3 final size:3
Alignment explanation
Indices: 3385481--3385517 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3385471 AGTTAGTAAG
*
3385481 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3385518 AAAATTCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3392906 original size:42 final size:46
Alignment explanation
Indices: 3392818--3392922 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 46
3392808 AGGATCAGAT
*
3392818 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAG-TTA
1 TTATTATTTTATTAGGAATTAA-G--GGGTTAAAAC-A-ATGTTTAGTTTA
3392868 TTATTATTTTATTAGGAATT-A-GGGTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGGGTTAAAACAATGTTTAGTTTA
3392911 TTA-TATTTTATT
1 TTATTATTTTATT
3392923 CTTTAGTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
42 16 0.30
43 6 0.11
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.51
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGGGTTAAAACAATGTTTAGTTTA
Found at i:3394402 original size:25 final size:26
Alignment explanation
Indices: 3394348--3394403 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
3394338 TAGAAAAGGT
*
3394348 TAAA-TTAAGAAATAAAAAATAAAAA
1 TAAAGTTAAGAAATAAAAAAGAAAAA
* * *
3394373 CAAAGTTAAGATA-AAAAAAGAATAA
1 TAAAGTTAAGAAATAAAAAAGAAAAA
3394398 TAAAGT
1 TAAAGT
3394404 GAAATAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (26 bp):
TAAAGTTAAGAAATAAAAAAGAAAAA
Found at i:3395739 original size:2 final size:2
Alignment explanation
Indices: 3395734--3395882 Score: 108
Period size: 2 Copynumber: 78.5 Consensus size: 2
3395724 AAATAAATAA
* *
3395734 AT AT AT AT AT AT AT AT ACT AT AT A- AT AT AA AT AT ACT AT A- AC
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT
* *
3395776 AT AT A- AT AT AT AT TT AT AT AT -T AT AT A- AT AT AA AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
3395816 AT A- AT AT AT A- AT -T A- AT AA AT A- AT AT -T AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3395851 AT ACT AT AT -T AT AT AA AT AT ACT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT A
3395883 AAAATAAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 36
0.72 0.07 0.22
Matches are distributed among these distances:
1 13 0.11
2 95 0.81
3 10 0.08
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3395795 original size:45 final size:45
Alignment explanation
Indices: 3395736--3395882 Score: 171
Period size: 45 Copynumber: 3.3 Consensus size: 45
3395726 ATAAATAAAT
3395736 ATATATATATATATACTATATAATATAAATATACTATAACATATA
1 ATATATATATATATACTATATAATATAAATATACTATAACATATA
* * *
3395781 ATATATATTTATATATTATATAATATAAATATACTATAATATATA
1 ATATATATATATATACTATATAATATAAATATACTATAACATATA
* **
3395826 AT-TA-ATA-A-ATAATATTATAATAT--ATATACTATATTATATAA
1 ATATATATATATATACTA-TATAATATAAATATACTATAACATAT-A
3395867 ATATACTATATATATA
1 ATATA-TATATATATA
3395883 AAAATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
40 15 0.17
41 8 0.09
42 11 0.12
43 2 0.02
44 5 0.06
45 45 0.51
46 3 0.03
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (45 bp):
ATATATATATATATACTATATAATATAAATATACTATAACATATA
Found at i:3396485 original size:36 final size:36
Alignment explanation
Indices: 3396438--3396509 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3396428 GTTGCTCACA
3396438 GATCATCGTCAGCGAGGACTGAGATGGCCGAGATCT
1 GATCATCGTCAGCGAGGACTGAGATGGCCGAGATCT
3396474 GATCATCGTCAGCGAGGACTGAGATGGCCGAGATCT
1 GATCATCGTCAGCGAGGACTGAGATGGCCGAGATCT
3396510 AAACCAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.19
Consensus pattern (36 bp):
GATCATCGTCAGCGAGGACTGAGATGGCCGAGATCT
Found at i:3396495 original size:20 final size:20
Alignment explanation
Indices: 3396438--3396495 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
3396428 GTTGCTCACA
3396438 GATCATCGTCAGCGAGGACT
1 GATCATCGTCAGCGAGGACT
* *
3396458 GA-GAT-GGC--CGA-GATCT
1 GATCATCGTCAGCGAGGA-CT
3396474 GATCATCGTCAGCGAGGACT
1 GATCATCGTCAGCGAGGACT
3396494 GA
1 GA
3396496 GATGGCCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
15 2 0.07
16 7 0.25
17 2 0.07
18 4 0.14
19 2 0.07
20 9 0.32
21 2 0.07
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (20 bp):
GATCATCGTCAGCGAGGACT
Found at i:3397576 original size:13 final size:13
Alignment explanation
Indices: 3397560--3397585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3397550 AGCTTTGTGT
3397560 AATGGGTGAAGGA
1 AATGGGTGAAGGA
3397573 AATGGGTGAAGGA
1 AATGGGTGAAGGA
3397586 TGAATGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.46, T:0.15
Consensus pattern (13 bp):
AATGGGTGAAGGA
Found at i:3399375 original size:86 final size:86
Alignment explanation
Indices: 3399171--3399381 Score: 241
Period size: 86 Copynumber: 2.4 Consensus size: 86
3399161 TGACGCTAAA
* * *
3399171 CCAACTCCTTATGTGATGGAATCGATCAAAAAGGGAATGATGATCCATCTCCATCTGTTATTGAA
1 CCAACTCCTTATGTGATGGAATCTAGCAAAAAGGGAATGATGATCCATCTCCATCTG-TATAGAA
**
3399236 TCAAATAAAATTTGATGATGAT
65 TCAAATAAAAGCTGATGATGAT
* * * * *
3399258 CCAACTCCTTATGTTATGGAATATAGTAAAAAAGGGAATGTTGATCC-GCATCC-TAC-G-ATAG
1 CCAACTCCTTATGTGATGGAATCTAG-CAAAAAGGGAATGATGATCCATC-TCCAT-CTGTATAG
*
3399319 AATCAAATAAAAGGCTGATGTTGAT
63 AATCAAATAAAA-GCTGATGATGAT
*
3399344 CCAACTCCTTATGTGATGAAATCTAGCAAAAAGGGAAT
1 CCAACTCCTTATGTGATGGAATCTAGCAAAAAGGGAAT
3399382 ATTTATCCAT
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
85 26 0.25
86 32 0.30
87 25 0.24
88 22 0.21
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (86 bp):
CCAACTCCTTATGTGATGGAATCTAGCAAAAAGGGAATGATGATCCATCTCCATCTGTATAGAAT
CAAATAAAAGCTGATGATGAT
Found at i:3401013 original size:40 final size:39
Alignment explanation
Indices: 3400958--3401034 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 39
3400948 TTCAAACGAC
* *
3400958 TGAAAGAATTTTATAAAACAAGTTGATTTCCCTTACTTAT
1 TGAAAGAATTTTATAAAACAAGATGA-TCCCCTTACTTAT
3400998 TGAAAGAATTTTATAAAACAAGATGATCCCCTTACTT
1 TGAAAGAATTTTATAAAACAAGATGATCCCCTTACTT
3401035 CAGGCTCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 10 0.29
40 25 0.71
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (39 bp):
TGAAAGAATTTTATAAAACAAGATGATCCCCTTACTTAT
Found at i:3401565 original size:51 final size:51
Alignment explanation
Indices: 3401508--3401630 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
3401498 TTGGACTACA
* * *
3401508 TAAACTCATTATCATCATTTTTACCTTAACCTTAGGCATTATCACCTTTAT
1 TAAACTCATAATCATCATTTTTACCTCAACCTTAGACATTATCACCTTTAT
* * * **
3401559 TAAACTCATCATCATCATTTTTACGTCACCCTTAGACATTATTGCCTTTAT
1 TAAACTCATAATCATCATTTTTACCTCAACCTTAGACATTATCACCTTTAT
* *
3401610 TGAACTCATAATCATTATTTT
1 TAAACTCATAATCATCATTTT
3401631 CTCATTTCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (51 bp):
TAAACTCATAATCATCATTTTTACCTCAACCTTAGACATTATCACCTTTAT
Found at i:3404833 original size:47 final size:45
Alignment explanation
Indices: 3404740--3404865 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
3404730 GTAAGCATAT
* *
3404740 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
* * *
3404784 AAATAAGCTTACGAGCTTATAGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
3404831 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
3404866 GGATTTTATA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 22 0.30
45 11 0.15
46 1 0.01
47 39 0.53
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:3406233 original size:27 final size:27
Alignment explanation
Indices: 3406203--3406264 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
3406193 AATATGTGAA
3406203 AATGAATTGTCCAACTTTCCATGCTTC
1 AATGAATTGTCCAACTTTCCATGCTTC
3406230 AATGAATTGTCCAACTTTCCATGCTTC
1 AATGAATTGTCCAACTTTCCATGCTTC
3406257 AATGAATT
1 AATGAATT
3406265 ATTGTTTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (27 bp):
AATGAATTGTCCAACTTTCCATGCTTC
Found at i:3407726 original size:17 final size:17
Alignment explanation
Indices: 3407704--3407768 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
3407694 TATATATTAT
3407704 AAGAAGAAAAAAAACAG
1 AAGAAGAAAAAAAACAG
*
3407721 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAACAG
*
3407738 AAAAAGAAAATGAAAAC-G
1 AAGAAGAAAA--AAAACAG
3407756 AAGAAGAAAAAAA
1 AAGAAGAAAAAAA
3407769 TTGAAAATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 3 0.07
17 25 0.60
18 10 0.24
19 4 0.10
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (17 bp):
AAGAAGAAAAAAAACAG
Found at i:3407745 original size:6 final size:6
Alignment explanation
Indices: 3407707--3407766 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
3407697 ATATTATAAG
* * * *
3407707 AAGAAA AA-AAA CAGAAG AAGAAA AA-AAA TAGAAA AAGAAA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
3407753 ACGAAG AAGAAA AA
1 AAGAAA AAGAAA AA
3407767 AATTGAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:3407746 original size:34 final size:33
Alignment explanation
Indices: 3407707--3407819 Score: 115
Period size: 33 Copynumber: 3.3 Consensus size: 33
3407697 ATATTATAAG
3407707 AAGAAAAAAAACAGAAGAAGAAAAAAAATAGAAA
1 AAGAAAAAAAACAGAAGAAGAAAAAAAAT-GAAA
*
3407741 AAGAAAATGAAAAC-GAAGAAGAAAAAAATTGAAA
1 AAGAAAA--AAAACAGAAGAAGAAAAAAAATGAAA
* *
3407775 ATGAGAAAGAAA-AGATAG-AGAAAAAAAATGAGAA
1 AAGA-AAAAAAACAGA-AGAAGAAAAAAAATGA-AA
*
3407809 ATGAAAAAAAA
1 AAGAAAAAAAA
3407820 AATATTTCAC
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 23 0.34
34 22 0.32
35 18 0.26
36 5 0.07
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (33 bp):
AAGAAAAAAAACAGAAGAAGAAAAAAAATGAAA
Found at i:3407761 original size:35 final size:34
Alignment explanation
Indices: 3407707--3407809 Score: 115
Period size: 34 Copynumber: 3.0 Consensus size: 34
3407697 ATATTATAAG
3407707 AAGAAAA-AAAACAGAAGAAGAAAAAAAATAGAAA
1 AAGAAAAGAAAAC-GAAGAAGAAAAAAAATAGAAA
*
3407741 AAGAAAATGAAAACGAAGAAG-AAAAAAATTGAAA
1 AAGAAAA-GAAAACGAAGAAGAAAAAAAATAGAAA
*
3407775 ATGAGAAAGAAAA-GATAG-AGAAAAAAAATGAGAAA
1 AAGA-AAAGAAAACGA-AGAAGAAAAAAAAT-AGAAA
3407810 TGAAAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
33 4 0.07
34 37 0.62
35 14 0.23
36 5 0.08
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (34 bp):
AAGAAAAGAAAACGAAGAAGAAAAAAAATAGAAA
Found at i:3407781 original size:21 final size:20
Alignment explanation
Indices: 3407719--3407787 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
3407709 GAAAAAAAAC
*
3407719 AGAAGAAGAAAA--AAAAT-
1 AGAAGAAAAAAATGAAAATG
*
3407736 AGAA-AAAGAAAATGAAAACG
1 AGAAGAAA-AAAATGAAAATG
3407756 AAGAAGAAAAAAATTGAAAATG
1 -AGAAGAAAAAAA-TGAAAATG
3407778 AGAAAGAAAA
1 AG-AAGAAAA
3407788 GATAGAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.05
17 8 0.20
19 4 0.10
21 10 0.24
22 17 0.41
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.07
Consensus pattern (20 bp):
AGAAGAAAAAAATGAAAATG
Done.