Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 35 of 199
Found at i:10831249 original size:12 final size:12
Alignment explanation
Indices: 10831232--10831257 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10831222 GCCACCAGCA
10831232 CCATCACACACC
1 CCATCACACACC
10831244 CCATCACACACC
1 CCATCACACACC
10831256 CC
1 CC
10831258 CATACCGTCT
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:0.31, C:0.62, G:0.00, T:0.08
Consensus pattern (12 bp):
CCATCACACACC
Found at i:10832126 original size:26 final size:26
Alignment explanation
Indices: 10832085--10832153 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
10832075 ATAAAATAAA
*
10832085 AAATAAAAAAGGGGAAAGTTGGTAATG
1 AAATAAAAAA-GGGAAAATTGGTAATG
10832112 AAATAAAAAAGGGAAAATTGGTAATG
1 AAATAAAAAAGGGAAAATTGGTAATG
* *
10832138 GAATAAAAAAAGGAAA
1 AAATAAAAAAGGGAAA
10832154 TTTTTTTGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 29 0.74
27 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (26 bp):
AAATAAAAAAGGGAAAATTGGTAATG
Found at i:10833051 original size:3 final size:3
Alignment explanation
Indices: 10833043--10833080 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
10833033 TCGATTTTAC
*
10833043 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
10833081 GTTTATGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:10833412 original size:27 final size:30
Alignment explanation
Indices: 10833382--10833441 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
10833372 TTTACACTAT
*
10833382 TATATAC-ATT-TTTCTA-ATATTATAT-TG
1 TATATACTATTGTTTATATATA-TATATGTG
10833409 TATATACTATTGTTTATATATATATATGTG
1 TATATACTATTGTTTATATATATATATGTG
10833439 TAT
1 TAT
10833442 GTATTTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 7 0.25
28 3 0.11
29 10 0.36
30 8 0.29
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (30 bp):
TATATACTATTGTTTATATATATATATGTG
Found at i:10834973 original size:23 final size:21
Alignment explanation
Indices: 10834941--10835015 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 21
10834931 GATGTTTATC
10834941 GTTGTAATTGAGGTGTATAAAT
1 GTTGTAATTGAGGTGT-TAAAT
10834963 GTTGTTAATTG-GGATGTTAAAGT
1 GTTG-TAATTGAGG-TGTTAAA-T
10834986 GTTGTAAGTTGAGGTGTTTAAAT
1 GTTGTAA-TTGAGGTG-TTAAAT
*
10835009 GCTGTAA
1 GTTGTAA
10835016 ACTGAAATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
22 13 0.28
23 26 0.57
24 7 0.15
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.41
Consensus pattern (21 bp):
GTTGTAATTGAGGTGTTAAAT
Found at i:10835026 original size:23 final size:23
Alignment explanation
Indices: 10834979--10835075 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 23
10834969 AATTGGGATG
* * *
10834979 TTAAAGTGTTGTAAGTTGAGGTGT
1 TTAAA-TGCTGTAAATTGAAGTGT
* *
10835003 TTAAATGCTGTAAACTGAAATGT
1 TTAAATGCTGTAAATTGAAGTGT
* * * *
10835026 TTAATTGCTATAAATTGAGGTGC
1 TTAAATGCTGTAAATTGAAGTGT
* *
10835049 TCAAATGATGTAAATTGAAGTGT
1 TTAAATGCTGTAAATTGAAGTGT
10835072 TTAA
1 TTAA
10835076 GTACTACAAA
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
23 50 0.91
24 5 0.09
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (23 bp):
TTAAATGCTGTAAATTGAAGTGT
Found at i:10835026 original size:46 final size:45
Alignment explanation
Indices: 10834924--10835077 Score: 132
Period size: 46 Copynumber: 3.4 Consensus size: 45
10834914 TAGTTGTTGG
* * *
10834924 AAATTGAGATGTTT-A-TCGTTGTAATTGAGGTGTATAAATGTTGT
1 AAATTGAAATGTTTAAGT-GTTGTAATTGAGGTGTTTAAATGATGT
* ** * *
10834968 TAATTGGGATGTTAAAGTGTTGTAAGTTGAGGTGTTTAAATGCTGT
1 AAATTGAAATGTTTAAGTGTTGTAA-TTGAGGTGTTTAAATGATGT
* * * * * *
10835014 AAACTGAAATGTTTAATTGCTATAAATTGAGGTGCTCAAATGATGT
1 AAATTGAAATGTTTAAGTGTTGT-AATTGAGGTGTTTAAATGATGT
*
10835060 AAATTGAAGTGTTTAAGT
1 AAATTGAAATGTTTAAGT
10835078 ACTACAAATT
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
44 11 0.13
45 8 0.09
46 66 0.76
47 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.40
Consensus pattern (45 bp):
AAATTGAAATGTTTAAGTGTTGTAATTGAGGTGTTTAAATGATGT
Found at i:10835087 original size:46 final size:45
Alignment explanation
Indices: 10834994--10835102 Score: 119
Period size: 46 Copynumber: 2.4 Consensus size: 45
10834984 GTGTTGTAAG
* * * * *
10834994 TTGAGGTGTTTAAATGCTGTAAACTGAAATGTTTAATTGCTATAAA
1 TTGAGGTG-TCAAATGATGTAAACTGAAATGTTTAAGTACTACAAA
* *
10835040 TTGAGGTGCTCAAATGATGTAAATTGAAGTGTTTAAGTACTACAAA
1 TTGAGGTG-TCAAATGATGTAAACTGAAATGTTTAAGTACTACAAA
*
10835086 TTGTGGTGTACAAATGA
1 TTGAGGTGT-CAAATGA
10835103 GTCTAAAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 1 0.02
46 52 0.98
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (45 bp):
TTGAGGTGTCAAATGATGTAAACTGAAATGTTTAAGTACTACAAA
Found at i:10835609 original size:29 final size:29
Alignment explanation
Indices: 10835576--10835633 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
10835566 TGTTATCTCC
10835576 ATGATTCAGACAGTTTCAATAATAAAAGA
1 ATGATTCAGACAGTTTCAATAATAAAAGA
10835605 ATGATTCAGACAGTTTCAATAATAAAAGA
1 ATGATTCAGACAGTTTCAATAATAAAAGA
10835634 GTGCAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (29 bp):
ATGATTCAGACAGTTTCAATAATAAAAGA
Found at i:10840799 original size:7 final size:7
Alignment explanation
Indices: 10840787--10840820 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
10840777 TCACCATATA
10840787 TCTTGAT
1 TCTTGAT
10840794 TCTTGAT
1 TCTTGAT
10840801 TCTTGAT
1 TCTTGAT
10840808 TCTTGAT
1 TCTTGAT
10840815 TCTTGA
1 TCTTGA
10840821 CTATTAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCTTGAT
Found at i:10842201 original size:3 final size:3
Alignment explanation
Indices: 10842193--10842218 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10842183 GAAGTTGACA
10842193 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10842219 CAACAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10843135 original size:14 final size:15
Alignment explanation
Indices: 10843118--10843149 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10843108 ATTTTCATTT
10843118 TATT-ATTTAAAATA
1 TATTAATTTAAAATA
10843132 TATTAATTTAAAATA
1 TATTAATTTAAAATA
10843147 TAT
1 TAT
10843150 ATATAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATTTAAAATA
Found at i:10844862 original size:44 final size:44
Alignment explanation
Indices: 10844799--10844888 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
10844789 CAGGGACTAA
10844799 AATTGTATTATACGTAAGTTAAACAGATTTAATTGCTATCGTTT
1 AATTGTATTATACGTAAGTTAAACAGATTTAATTGCTATCGTTT
10844843 AATTGTATTATACGTAAGTTAAACAGATTTAATTGCTATCGTTT
1 AATTGTATTATACGTAAGTTAAACAGATTTAATTGCTATCGTTT
10844887 AA
1 AA
10844889 CTTAACAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (44 bp):
AATTGTATTATACGTAAGTTAAACAGATTTAATTGCTATCGTTT
Found at i:10844899 original size:28 final size:30
Alignment explanation
Indices: 10844864--10844934 Score: 128
Period size: 28 Copynumber: 2.4 Consensus size: 30
10844854 ACGTAAGTTA
10844864 AACAGATTTAATTGCTATCGTTTAA-CT-T
1 AACAGATTTAATTGCTATCGTTTAAGCTAT
10844892 AACAGATTTAATTGCTATCGTTTAAGCTAT
1 AACAGATTTAATTGCTATCGTTTAAGCTAT
10844922 AACAGATTTAATT
1 AACAGATTTAATT
10844935 ACAAAATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 25 0.61
29 2 0.05
30 14 0.34
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (30 bp):
AACAGATTTAATTGCTATCGTTTAAGCTAT
Found at i:10855397 original size:2 final size:2
Alignment explanation
Indices: 10855390--10855415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10855380 AATTATGTAA
10855390 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10855416 GCATGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10855779 original size:3 final size:3
Alignment explanation
Indices: 10855771--10855806 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
10855761 AAGCATAAAC
10855771 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10855807 CATTGGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10855944 original size:3 final size:3
Alignment explanation
Indices: 10855930--10855980 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
10855920 ACACTAGTAT
* * * * *
10855930 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10855977 ATA A
1 ATA A
10855981 GGATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10875289 original size:19 final size:18
Alignment explanation
Indices: 10875265--10875300 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10875255 TTAATATTTT
10875265 ATTATTAAAATTAAATTAA
1 ATTATTAAAA-TAAATTAA
*
10875284 ATTATTAATATAAATTA
1 ATTATTAAAATAAATTA
10875301 GATATAGATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATTAAAATAAATTAA
Found at i:10875789 original size:2 final size:2
Alignment explanation
Indices: 10875782--10875806 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10875772 CATGCATGTG
10875782 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
10875807 CTTATTTTAA
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:10877996 original size:21 final size:21
Alignment explanation
Indices: 10877960--10878020 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
10877950 TTTTTAAAAA
*
10877960 TTAAAAATCATTAAAATTA-TT
1 TTAAAAAT-ATAAAAATTATTT
*
10877981 TTAAAAAGTATAAAAAATATTT
1 TTAAAAA-TATAAAAATTATTT
* *
10878003 TTTAAAATTTAAAAATTA
1 TTAAAAATATAAAAATTA
10878021 ATTAAATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 24 0.73
22 9 0.27
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAAAAATATAAAAATTATTT
Found at i:10881215 original size:86 final size:85
Alignment explanation
Indices: 10881070--10881232 Score: 222
Period size: 86 Copynumber: 1.9 Consensus size: 85
10881060 ATTTAAATCA
* * * *
10881070 TTTAAAAGATTATAAAGATATAAACTATTAAAATAGTAAATTTGCATTTTAACTTTTATAAATTA
1 TTTAAAAGATTATAAAGATATAAACTATTAAAATAGTAAAATTACATTTTAACTCTTATAAA-AA
10881135 TATACAACTTAATATCTGTGT
65 TATACAACTTAATATCTGTGT
* * *
10881156 TTTAAATA-ATTATAAATATATAAGCTATTAAAAT-GATAAAATTACATTTTAGCTCTTATAAAA
1 TTTAAA-AGATTATAAAGATATAAACTATTAAAATAG-TAAAATTACATTTTAACTCTTATAAAA
10881219 ATATACAACTTAAT
64 ATATACAACTTAAT
10881233 TCTACTTTGC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 15 0.22
86 52 0.76
87 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (85 bp):
TTTAAAAGATTATAAAGATATAAACTATTAAAATAGTAAAATTACATTTTAACTCTTATAAAAAT
ATACAACTTAATATCTGTGT
Found at i:10882490 original size:31 final size:31
Alignment explanation
Indices: 10882448--10882516 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
10882438 GTAACATTTC
*
10882448 ATAGTTAGGTGACCAAAAAAGAAATTTACTA
1 ATAGTTGGGTGACCAAAAAAGAAATTTACTA
*
10882479 ATAGTTGGGTGACTAAAAAAGAAATTTACTA
1 ATAGTTGGGTGACCAAAAAAGAAATTTACTA
10882510 ATAGTTG
1 ATAGTTG
10882517 ACTGACTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (31 bp):
ATAGTTGGGTGACCAAAAAAGAAATTTACTA
Found at i:10882523 original size:31 final size:31
Alignment explanation
Indices: 10882457--10882524 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
10882447 CATAGTTAGG
* **
10882457 TGACCAAAAAAGAAATTTACTAATAGTTGGG
1 TGACTAAAAAAGAAATTTACTAATAGTTGAC
10882488 TGACTAAAAAAGAAATTTACTAATAGTTGAC
1 TGACTAAAAAAGAAATTTACTAATAGTTGAC
10882519 TGACTA
1 TGACTA
10882525 CTAGTATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (31 bp):
TGACTAAAAAAGAAATTTACTAATAGTTGAC
Found at i:10882791 original size:16 final size:15
Alignment explanation
Indices: 10882750--10882792 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
10882740 ATTTTATTCT
10882750 AATTATAATTATTGA
1 AATTATAATTATTGA
*
10882765 AA-TATATATTATTTA
1 AATTATA-ATTATTGA
10882780 CAATTATAATTAT
1 -AATTATAATTAT
10882793 ATTTGTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 7 0.29
17 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AATTATAATTATTGA
Found at i:10890090 original size:32 final size:31
Alignment explanation
Indices: 10890040--10890101 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
10890030 CGTTTGTTCA
*
10890040 GGACTAAAATTTTAAAATTAAAAAAAGTACAT
1 GGACTAAAATTTAAAAATT-AAAAAAGTACAT
*
10890072 GGACT-AAATTTAACAAATTCAAAAAGTACA
1 GGACTAAAATTTAA-AAATTAAAAAAGTACA
10890102 GATACTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (31 bp):
GGACTAAAATTTAAAAATTAAAAAAGTACAT
Found at i:10890113 original size:32 final size:30
Alignment explanation
Indices: 10890061--10890126 Score: 71
Period size: 31 Copynumber: 2.1 Consensus size: 30
10890051 TTAAAATTAA
*
10890061 AAAAAGTACATGGACTAAATTTAACAAATT
1 AAAAAGTACATGGACTAAATTGAACAAATT
* *
10890091 CAAAAAGTACA-GATACTGAAATTGATCAAATT
1 -AAAAAGTACATG-GACT-AAATTGAACAAATT
10890123 AAAA
1 AAAA
10890127 TATAGGAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 1 0.03
31 17 0.57
32 12 0.40
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (30 bp):
AAAAAGTACATGGACTAAATTGAACAAATT
Found at i:10893000 original size:49 final size:50
Alignment explanation
Indices: 10892931--10893030 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 50
10892921 ACATGCCACC
*
10892931 CCCATATTCTGTATTGTAAC-ATATATATAGGATTTCAAGCAGAAAACCA
1 CCCATATTCTGTATTGTAACAATATATATAGGATTTCAAGCACAAAACCA
10892980 CCCATATTCTGTATTGTAACATATATATATAGGATTTCAAGCACAAAACCA
1 CCCATATTCTGTATTGTAACA-ATATATATAGGATTTCAAGCACAAAACCA
10893031 AAAATCTATC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 20 0.42
51 28 0.58
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (50 bp):
CCCATATTCTGTATTGTAACAATATATATAGGATTTCAAGCACAAAACCA
Found at i:10895088 original size:8 final size:9
Alignment explanation
Indices: 10895067--10895092 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10895057 GTGGTGGAAG
10895067 AAAAAGAAC
1 AAAAAGAAC
10895076 AAAAAGAAC
1 AAAAAGAAC
10895085 AAAAAGAA
1 AAAAAGAA
10895093 AATGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAGAAC
Found at i:10895106 original size:15 final size:15
Alignment explanation
Indices: 10895064--10895113 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
10895054 GTGGTGGTGG
*
10895064 AAGAAAAAGAACAAA
1 AAGAAAAAGAAGAAA
10895079 AAGAACAAA-AAGAAA
1 AAGAA-AAAGAAGAAA
* *
10895094 ATGAAAAAGAAGAAG
1 AAGAAAAAGAAGAAA
10895109 AAGAA
1 AAGAA
10895114 GCACATCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
16 3 0.10
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGAAGAAA
Found at i:10895114 original size:9 final size:9
Alignment explanation
Indices: 10895063--10895114 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
10895053 GGTGGTGGTG
10895063 GAAGAAAAA
1 GAAGAAAAA
*
10895072 GAACAAAAA
1 GAAGAAAAA
*
10895081 GAACAAAAA
1 GAAGAAAAA
10895090 GAAAATGAAAAA
1 G--AA-GAAAAA
*
10895102 GAAGAAGAA
1 GAAGAAAAA
10895111 GAAG
1 GAAG
10895115 CACATCCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 27 0.73
10 2 0.05
11 2 0.05
12 6 0.16
ACGTcount: A:0.73, C:0.04, G:0.21, T:0.02
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:10902722 original size:26 final size:26
Alignment explanation
Indices: 10902689--10902741 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
10902679 TAAATTTATA
*
10902689 TATAAAA-TAAATTAATATTTTTATTT
1 TATAAAATTAAAAT-ATATTTTTATTT
10902715 TATAAAATTAAAATATATTTTTATTT
1 TATAAAATTAAAATATATTTTTATTT
10902741 T
1 T
10902742 TATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATAAAATTAAAATATATTTTTATTT
Found at i:10902891 original size:16 final size:17
Alignment explanation
Indices: 10902866--10902907 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
10902856 TAATATATAT
10902866 TTTTTATTTTAT-CAAAG
1 TTTTT-TTTTATACAAAG
10902883 TTTTTTTTTATACAAAG
1 TTTTTTTTTATACAAAG
10902900 TTTTTTTT
1 TTTTTTTT
10902908 AATATGGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTTTTTTATACAAAG
Found at i:10904092 original size:18 final size:18
Alignment explanation
Indices: 10904052--10904108 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
10904042 ACAAGTAATA
*
10904052 ATTTTAAAATTCAAAAAATT
1 ATTTTAAAACT-AAAAAA-T
10904072 ATTTTAAAACTAAAAAAT
1 ATTTTAAAACTAAAAAAT
** *
10904090 ATTAAAAAAGTAAAAAAT
1 ATTTTAAAACTAAAAAAT
10904108 A
1 A
10904109 ATTAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 17 0.52
19 6 0.18
20 10 0.30
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
ATTTTAAAACTAAAAAAT
Found at i:10904093 original size:21 final size:20
Alignment explanation
Indices: 10904052--10904093 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
10904042 ACAAGTAATA
* *
10904052 ATTTTAAAATTCAAAAAATT
1 ATTTTAAAACTAAAAAAATT
10904072 ATTTTAAAACTAAAAAATATT
1 ATTTTAAAACTAAAAAA-ATT
10904093 A
1 A
10904094 AAAAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTTAAAACTAAAAAAATT
Found at i:10904112 original size:19 final size:18
Alignment explanation
Indices: 10904077--10904113 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
10904067 AAATTATTTT
10904077 AAAACTAAAAAATATTAA
1 AAAACTAAAAAATATTAA
*
10904095 AAAAGTAAAAAATAATTAA
1 AAAACTAAAAAAT-ATTAA
10904114 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAACTAAAAAATATTAA
Found at i:10910916 original size:31 final size:31
Alignment explanation
Indices: 10910849--10910916 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
10910839 TTAATAGCTC
* * * *
10910849 AGTGACTTAAATGAAAAGTTTTAAATAGTTT
1 AGTGATTTAAATGAAAACTTTCAAATAATTT
10910880 AGTGATTTAAATGAAAACTTTCAAATAATTT
1 AGTGATTTAAATGAAAACTTTCAAATAATTT
10910911 AGTGAT
1 AGTGAT
10910917 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (31 bp):
AGTGATTTAAATGAAAACTTTCAAATAATTT
Found at i:10913157 original size:16 final size:16
Alignment explanation
Indices: 10913136--10913185 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
10913126 ATATCTAATC
10913136 ATATAATAAATTATTA
1 ATATAATAAATTATTA
10913152 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
10913165 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
10913182 ATAT
1 ATAT
10913186 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:10913205 original size:14 final size:14
Alignment explanation
Indices: 10913196--10913225 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10913186 TTTAATTTTA
10913196 TTTTAATAATGTTT
1 TTTTAATAATGTTT
*
10913210 TTTTAATAATATTT
1 TTTTAATAATGTTT
10913224 TT
1 TT
10913226 CATATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTTAATAATGTTT
Found at i:10921513 original size:28 final size:28
Alignment explanation
Indices: 10921478--10921532 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
10921468 GATACTCAAA
10921478 CTTGGCTCCCTTGAGAAATAAAGCTCAG
1 CTTGGCTCCCTTGAGAAATAAAGCTCAG
* *
10921506 CTTGGCTCCTTTGAGAAATCAAGCTCA
1 CTTGGCTCCCTTGAGAAATAAAGCTCA
10921533 ACTTAACTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (28 bp):
CTTGGCTCCCTTGAGAAATAAAGCTCAG
Found at i:10933419 original size:24 final size:24
Alignment explanation
Indices: 10933374--10933419 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
10933364 CTAATTAAAT
* * *
10933374 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAAATTATTG
*
10933398 TTTAAAAATATTTAAAAATTAT
1 TTTAAAAATAATTAAAAATTAT
10933420 ATTTCATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTAAAAATAATTAAAAATTATTG
Found at i:10941469 original size:23 final size:21
Alignment explanation
Indices: 10941416--10941469 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 21
10941406 AAGAACTTCT
10941416 ATTTTATTAAAATATAAAATA
1 ATTTTATTAAAATATAAAATA
10941437 ATTTACTATTAAAATATTAAAATAA
1 ATTT--TATTAAAATA-TAAAAT-A
10941462 ATTTTATT
1 ATTTTATT
10941470 TTATTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.14
23 14 0.48
24 6 0.21
25 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTTATTAAAATATAAAATA
Found at i:10958214 original size:54 final size:52
Alignment explanation
Indices: 10958156--10958256 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 52
10958146 TGTGTTAATA
*
10958156 TCTAATTAAAATATT-TAATGATT-ATATTTATTATTTAAAATATAATTTATATAT
1 TCTAATT--AATATTATAATAATTAATATTTATTATTTAAAA-AT-ATTTATATAT
* *
10958210 TCTAATTAATTTTATAATAATTAATATTTATTGTTTAAAAATATTTA
1 TCTAATTAATATTATAATAATTAATATTTATTATTTAAAAATATTTA
10958257 AAATTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
52 10 0.24
53 9 0.21
54 23 0.55
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (52 bp):
TCTAATTAATATTATAATAATTAATATTTATTATTTAAAAATATTTATATAT
Found at i:10966288 original size:24 final size:22
Alignment explanation
Indices: 10966233--10966288 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 22
10966223 AAGAACTTCT
10966233 ATTTTATTAAAATATAAAAATA
1 ATTTTATTAAAATATAAAAATA
10966255 ATTTACTATTAAAATATTAAAAATAA
1 ATTT--TATTAAAATA-TAAAAAT-A
10966281 ATTTTATT
1 ATTTTATT
10966289 TTATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.13
24 14 0.47
25 7 0.23
26 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTATTAAAATATAAAAATA
Found at i:10966318 original size:29 final size:30
Alignment explanation
Indices: 10966241--10966319 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 30
10966231 CTATTTTATT
*
10966241 AAAATATAAAAATAATTTACTATTAAAATATT
1 AAAATATAAAAATAATTT--TATTAAAATATA
** *
10966273 AAAA-ATAAATTTTATTTTATT-AAATA-A
1 AAAATATAAAAATAATTTTATTAAAATATA
10966300 AACAATATAAAAATAATTTT
1 AA-AATATAAAAATAATTTT
10966320 TACAAATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 2 0.05
28 7 0.18
29 15 0.39
31 10 0.26
32 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAATATAAAAATAATTTTATTAAAATATA
Found at i:10968515 original size:30 final size:30
Alignment explanation
Indices: 10968481--10968545 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
10968471 ATTAATTAAA
10968481 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
*
10968511 GAGAGCTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
10968541 GAGAG
1 GAGAG
10968546 TTTTTTGCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.31, T:0.28
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAAGGAGAAATTT
Found at i:10981566 original size:188 final size:190
Alignment explanation
Indices: 10981247--10981652 Score: 495
Period size: 188 Copynumber: 2.1 Consensus size: 190
10981237 AGAAACGATG
* * * * *
10981247 AAAACAGTCACTATTTCGATCTTTTCTTTCCACTTTCTCGAATCCAGTGGAGAGAAAATAAAATC
1 AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCAG-GCAGAGAAAAGAAAATA
* * *
10981312 ATCAACTAAATACCGATCTAAAAAGTTCAAAACAGAGATAAAAACCCATAGCCACAACACAAAAT
65 ATCAACCAAATACCGATCTAAAAAGTTCAAAACAGAAATAAAAACCCATAGCCACAACAAAAAAT
* * * *
10981377 T-C-AAAAACCTCGGTAAGAAGTGATACTATATCG-ATATATATACAT-GAAAGCAGGATTA
130 TACAAAAAAACTCAGTAACAAGTGATACTATATCGAATATATATACATAG-AAGAAGGATTA
10981435 AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCA-GCA-AGTAAATAGAAAAT
1 AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCAGGCAGAG-AAA-AGAAAAT
* ** *
10981498 AAAATCAACCAAATACCGATCTAAAGAGTTCAAAAC-GCAAAT-AAATTCCGTAGCCACAACAAA
64 --AATCAACCAAATACCGATCTAAAAAGTTCAAAACAG-AAATAAAAACCCATAGCCACAACAAA
10981561 AAATTCAAAAGCAAAAAAACTCAGTAACAAGTGATACTATATCGATATATATATACATAGAAGAA
126 AAATT----A-CAAAAAAACTCAGTAACAAGTGATACTATATCGA-ATATATATACATAGAAGAA
10981626 GGATTA
185 GGATTA
10981632 AAAACAGTCGCTATTTCGATA
1 AAAACAGTCGCTATTTCGATA
10981653 GAAAAAAAAT
Statistics
Matches: 187, Mismatches: 16, Indels: 21
0.83 0.07 0.09
Matches are distributed among these distances:
185 2 0.01
186 5 0.03
187 6 0.03
188 67 0.36
189 34 0.18
194 1 0.01
195 28 0.15
197 43 0.23
198 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.25
Consensus pattern (190 bp):
AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCAGGCAGAGAAAAGAAAATAA
TCAACCAAATACCGATCTAAAAAGTTCAAAACAGAAATAAAAACCCATAGCCACAACAAAAAATT
ACAAAAAAACTCAGTAACAAGTGATACTATATCGAATATATATACATAGAAGAAGGATTA
Found at i:10985774 original size:24 final size:21
Alignment explanation
Indices: 10985729--10985774 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
10985719 TAATAAAATT
*
10985729 AACAATAAAACAATAGTTACA
1 AACAATAAAACAATAGTAACA
10985750 AACAATAACAACAAAATAGTAACA
1 AACAATAA-AAC--AATAGTAACA
10985774 A
1 A
10985775 TATAATAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
24 10 0.48
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.15
Consensus pattern (21 bp):
AACAATAAAACAATAGTAACA
Found at i:10992418 original size:31 final size:31
Alignment explanation
Indices: 10992380--10992448 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
10992370 TTGTGGTACC
*
10992380 AATGACTTAAATGAAAAATT-TCGAATAGTTT
1 AATGACTTAAAT-AAAAATTATCGAATAATTT
* *
10992411 AATGACTTGAATCAAAATTATCGAATAATTT
1 AATGACTTAAATAAAAATTATCGAATAATTT
*
10992442 GATGACT
1 AATGACT
10992449 ATTTAGTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTATCGAATAATTT
Found at i:10999531 original size:172 final size:176
Alignment explanation
Indices: 10999214--10999568 Score: 655
Period size: 172 Copynumber: 2.0 Consensus size: 176
10999204 ATCTTCATCT
10999214 ATTTTTACTGTTAAAAACTGGCATGACTAACAGAATAACCAAATAGTGACACGCGATGTGCCACA
1 ATTTTTACTGTTAAAAACTGGCATGACTAACAGAATAACCAAATAGTGACACGCGATGTGCCACA
*
10999279 TGTACCTCATGCTGACGTACAAGAGCCAATTTTTAACAGTAGAAATGGATAAAATTTTTAATAGA
66 TGTACCTCATGCTGACGTACAAGAGCCAATTTATAACAGTAGAAATGGATAAAATTTTTAATAGA
10999344 ATGATAGATTTACTCTTTGATCTAAGGTACAGGAGCAACTTTGCTC
131 ATGATAGATTTACTCTTTGATCTAAGGTACAGGAGCAACTTTGCTC
10999390 ATTTTTACTGTTAAAAACTGGCATGACTAA-AGAATAACCAAATAGTGACACGC-ATGTGCCACA
1 ATTTTTACTGTTAAAAACTGGCATGACTAACAGAATAACCAAATAGTGACACGCGATGTGCCACA
* *
10999453 TGTACCTCATGCT-ACGTACAAGGGCCAGTTTATAACAGTAGAAATGGAT-AAATTTTTAATAGA
66 TGTACCTCATGCTGACGTACAAGAGCCAATTTATAACAGTAGAAATGGATAAAATTTTTAATAGA
10999516 ATGATAGATTTACTCTTTGATCTAAGGTACAGGAGCAACTTTGCTC
131 ATGATAGATTTACTCTTTGATCTAAGGTACAGGAGCAACTTTGCTC
10999562 ATTTTTA
1 ATTTTTA
10999569 AGTGGAGAGG
Statistics
Matches: 176, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
172 67 0.38
173 33 0.19
174 23 0.13
175 23 0.13
176 30 0.17
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (176 bp):
ATTTTTACTGTTAAAAACTGGCATGACTAACAGAATAACCAAATAGTGACACGCGATGTGCCACA
TGTACCTCATGCTGACGTACAAGAGCCAATTTATAACAGTAGAAATGGATAAAATTTTTAATAGA
ATGATAGATTTACTCTTTGATCTAAGGTACAGGAGCAACTTTGCTC
Found at i:11000121 original size:39 final size:39
Alignment explanation
Indices: 11000046--11000124 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
11000036 GAATGTGAAT
*
11000046 ATCTTCAAATTTCATCATCTTATAGCTAGAAACTAGCTC
1 ATCTTCAAATTTCATCATCTTAAAGCTAGAAACTAGCTC
11000085 ATCTTCAAATTTCATCATCTTAAAGCTAGAAACTAGCTC
1 ATCTTCAAATTTCATCATCTTAAAGCTAGAAACTAGCTC
11000124 A
1 A
11000125 CCATAAAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (39 bp):
ATCTTCAAATTTCATCATCTTAAAGCTAGAAACTAGCTC
Found at i:11007154 original size:12 final size:12
Alignment explanation
Indices: 11007125--11007157 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
11007115 TAAATTTTTA
*
11007125 ATAAAAATAAAT
1 ATAAATATAAAT
11007137 -TAAATATAAAT
1 ATAAATATAAAT
11007148 ATAAATATAA
1 ATAAATATAA
11007158 GAAAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAATATAAAT
Found at i:11008019 original size:21 final size:18
Alignment explanation
Indices: 11007990--11008034 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 18
11007980 TTTTTTAAAA
11007990 TTTAAATTTTTATATAGTTT
1 TTTAAATTTTTATA-A-TTT
11008010 TTTAGAATTTTTATAATTT
1 TTTA-AATTTTTATAATTT
11008029 TTTAAA
1 TTTAAA
11008035 ATATAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 7 0.29
20 5 0.21
21 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTAAATTTTTATAATTT
Found at i:11008628 original size:7 final size:7
Alignment explanation
Indices: 11008616--11008671 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
11008606 ATTTATATTT
11008616 ATTATAA
1 ATTATAA
11008623 ATTATAA
1 ATTATAA
11008630 ATTATAA
1 ATTATAA
*
11008637 A-TATGA
1 ATTATAA
* *
11008643 TTTATAT
1 ATTATAA
11008650 ATT-TAA
1 ATTATAA
11008656 ATTA-AA
1 ATTATAA
11008662 ATATATAA
1 AT-TATAA
11008670 AT
1 AT
11008672 AATTTATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
6 13 0.33
7 22 0.56
8 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
ATTATAA
Found at i:11008635 original size:14 final size:14
Alignment explanation
Indices: 11008616--11008671 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
11008606 ATTTATATTT
11008616 ATTATAAATTATAA
1 ATTATAAATTATAA
*
11008630 ATTATAAA-TATGA
1 ATTATAAATTATAA
* *
11008643 TTTATATATT-TAA
1 ATTATAAATTATAA
11008656 ATTA-AAATATATAA
1 ATTATAAAT-TATAA
11008670 AT
1 AT
11008672 AATTTATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 3 0.09
13 16 0.48
14 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTATAAATTATAA
Found at i:11008680 original size:31 final size:32
Alignment explanation
Indices: 11008606--11008694 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 32
11008596 TTTGTCCCCT
11008606 ATTTATATTTATTATAAATTATAAATTATAAATATG
1 ATTTATA-TTATT-TAAATTA-AAATTATAAATA-G
11008642 ATTTATA-TATTTAAATTAAAATATATAAATA-
1 ATTTATATTATTTAAATTAAAAT-TATAAATAG
*
11008673 ATTTATATTAATT-AATTAAAAT
1 ATTTATATTATTTAAATTAAAAT
11008695 GCATTTAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
31 16 0.32
32 8 0.16
33 15 0.30
34 4 0.08
36 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
ATTTATATTATTTAAATTAAAATTATAAATAG
Found at i:11011125 original size:25 final size:24
Alignment explanation
Indices: 11011088--11011139 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
11011078 GCTGTTATAA
* *
11011088 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAA-AAATT
11011112 AAAATTACATAAATGAAAAAAAATT
1 AAAATTACA-AAATGAAAAAAAATT
11011137 AAA
1 AAA
11011140 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 11 0.46
26 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAAAATT
Found at i:11012411 original size:15 final size:18
Alignment explanation
Indices: 11012391--11012426 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
11012381 CTCCTGCAAC
11012391 AAACAA-CA-GCAAC-AG
1 AAACAACCACGCAACAAG
11012406 AAACAACCACGCAACAAG
1 AAACAACCACGCAACAAG
11012424 AAA
1 AAA
11012427 GATATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.33
16 2 0.11
17 5 0.28
18 5 0.28
ACGTcount: A:0.61, C:0.28, G:0.11, T:0.00
Consensus pattern (18 bp):
AAACAACCACGCAACAAG
Found at i:11013532 original size:29 final size:29
Alignment explanation
Indices: 11013469--11013534 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
11013459 ATTACAAACT
* * * *
11013469 TATATATATGTATATCTTTCAAATTTTTA
1 TATATATATATATATCTTTCAAACTGTAA
*
11013498 TGTATATATATATAT-TTTCAAAACTGTAA
1 TATATATATATATATCTTTC-AAACTGTAA
11013527 TATATATA
1 TATATATA
11013535 CATTTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (29 bp):
TATATATATATATATCTTTCAAACTGTAA
Found at i:11015484 original size:19 final size:19
Alignment explanation
Indices: 11015460--11015506 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11015450 AACGTCTCTT
*
11015460 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
11015479 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
11015498 TATGCATTA
1 TTTGCATTA
11015507 AACACCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:11019281 original size:45 final size:45
Alignment explanation
Indices: 11019229--11020130 Score: 1031
Period size: 45 Copynumber: 20.1 Consensus size: 45
11019219 TTGAAAATAA
* *
11019229 CAGATCTTGTCTTCCTGT-TCTGGCAGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATAT-TGGCAGCGAAGTAGATCAAAGATAG
* * * * * *
11019274 TAGATCTTATCTTCCTATATTGGTAGCGAAGTAGATCGAATATAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* *
11019319 CAGATATTGTCTTCCTATATTGGCAGCGAAGTAAATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* *
11019364 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* *
11019409 CAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* ** * * *
11019454 CAGATCTTGTCTTCCTATATTGGTAGTAAAATAGATCGAAGATAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * * * * *
11019499 CATATATTGTCTTCCTGTATTGGCACCGAAATAGATCAAATATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* ** * * * *
11019544 TAGATCTTGTCTTCCTATATTGATAGTGAAGTTGATCGAAGATAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * * *
11019589 CAGATATTGTATTCCTGTATTGACAGCGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * * * *
11019634 CAGATCTTATCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * *
11019679 TAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * * *
11019724 CAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * *
11019769 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGGTAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
*
11019814 CAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * * * ** *
11019859 TAGATTTTGTCTTCTTATATTGGTAGTAAAGTAGATCGAAGATA-
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * * * * * *
11019903 CCGAATCTTGTCTTCTTATATTGGTAGTGAAGTAAATCGAAGATAA
1 CAG-ATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * *
11019949 CGGATCTTGTCTTCCTGTATTGGCA-TGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * *
11019993 CAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* *
11020038 C-GAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAATATAG
1 CAG-ATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
* * *
11020083 CAGATCTTGTCTTTCTGTATTGGCAGTGAAGTAGATCGAAA-ATAG
1 CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC-AAAGATAG
11020128 CAG
1 CAG
11020131 CCTTATCTCC
Statistics
Matches: 726, Mismatches: 124, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
44 40 0.06
45 679 0.94
46 7 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (45 bp):
CAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAG
Found at i:11019329 original size:90 final size:90
Alignment explanation
Indices: 11019225--11020122 Score: 1237
Period size: 90 Copynumber: 10.0 Consensus size: 90
11019215 CGGGTTGAAA
* * *
11019225 ATAACAGATCTTGTCTTCCTGT-TCTGGCAGTGAAGTAGATCAAAGATAGTAGATCTTATCTTCC
1 ATAACAGATCTTGTCTTCCTGTAT-TGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCC
*
11019289 TATATTGGTAGCGAAGTAGATCGAAT
65 TATATTGGTAGCGAAGTAGATCGAAG
* * *
11019315 ATAACAGATATTGTCTTCCTATATTGGCAGCGAAGTAAATCAAAGATAGCAGATCTTGTCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
* * *
11019380 GTATTGGCAGCGAAGTAGATCAAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
*
11019405 ATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
** *
11019470 ATATTGGTAGTAAAATAGATCGAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
* * * * * *
11019495 ATAACATATATTGTCTTCCTGTATTGGCACCGAAATAGATCAAATATAGTAGATCTTGTCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
* * *
11019560 ATATTGATAGTGAAGTTGATCGAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
* * * *
11019585 ATAACAGATATTGTATTCCTGTATTGACAGCGAAGTAGATCAAAGATAGCAGATCTTATCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
11019650 ATATTGGTAGCGAAGTAGATCGAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
* * *
11019675 AAAATAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
11019740 ATATTGGTAGCGAAGTAGATCGAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
* * *
11019765 AAAATAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGGTAGCAGATCTTGTCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
*
11019830 ATATTGGTAGCGAAGTAGATCAAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
** * * * * ** * * *
11019855 ATAGTAGATTTTGTCTTCTTATATTGGTAGTAAAGTAGATCGAAGATA-CCGAATCTTGTCTTCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAG-ATCTTGTCTTCC
* *
11019919 TATATTGGTAGTGAAGTAAATCGAAG
65 TATATTGGTAGCGAAGTAGATCGAAG
* *
11019945 ATAACGGATCTTGTCTTCCTGTATTGGCA-TGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
1 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
* *
11020009 ATATTGGTAGTGAAGTAGATCAAAG
66 ATATTGGTAGCGAAGTAGATCGAAG
* *
11020034 ATAAC-GAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAATATAGCAGATCTTGTCTTTC
1 ATAACAG-ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCC
* * *
11020098 TGTATTGGCAGTGAAGTAGATCGAA
65 TATATTGGTAGCGAAGTAGATCGAA
11020123 AATAGCAGCC
Statistics
Matches: 717, Mismatches: 86, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
88 1 0.00
89 80 0.11
90 635 0.89
91 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (90 bp):
ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
ATATTGGTAGCGAAGTAGATCGAAG
Found at i:11020224 original size:88 final size:89
Alignment explanation
Indices: 11020080--11020245 Score: 194
Period size: 88 Copynumber: 1.9 Consensus size: 89
11020070 AGATCAAATA
* ** * *
11020080 TAGCAGATCTTGTCTTTCTGTATTGGCAGTGAAGTAGATCGAAAATAGCAGCCTTATCTCCCTG-
1 TAGCAGATCTTGTCTTCCTGTAACGACAGCGAAGTAGATCGAAAATAGCAGCCTTATCTCCCTGA
*
11020144 TGCAGTAGTGGAGTAGGTTGAAAG
66 AGCAGTAGTGGAGTAGGTTGAAAG
* * * *
11020168 TAGCAGATCTTGTCTTCCTGTAACGACAGCGAAGTAGGTTGAAGAA-A-CAAGTCTTATTTCCCT
1 TAGCAGATCTTGTCTTCCTGTAACGACAGCGAAGTAGATCGAA-AATAGC-AGCCTTATCTCCCT
*
11020231 GAAGTAGTAGTGGAG
64 GAAGCAGTAGTGGAG
11020246 CAGACAGAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
87 1 0.02
88 50 0.78
89 13 0.20
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (89 bp):
TAGCAGATCTTGTCTTCCTGTAACGACAGCGAAGTAGATCGAAAATAGCAGCCTTATCTCCCTGA
AGCAGTAGTGGAGTAGGTTGAAAG
Found at i:11022948 original size:31 final size:31
Alignment explanation
Indices: 11022913--11022971 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
11022903 AATAGCCTAG
*
11022913 TAACTTAAATAAAAACTTTCGAATAATTTAA
1 TAACTTAAATAAAAACTTTCAAATAATTTAA
* * *
11022944 TAACTTAAATGAAATCTTTTAAATAATT
1 TAACTTAAATAAAAACTTTCAAATAATT
11022972 CAATGACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (31 bp):
TAACTTAAATAAAAACTTTCAAATAATTTAA
Found at i:11031122 original size:15 final size:17
Alignment explanation
Indices: 11031104--11031139 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
11031094 TAATAAAAAT
11031104 AATTAAAT-ATA-TTAA
1 AATTAAATAATATTTAA
11031119 AATT-AATAATATTTAA
1 AATTAAATAATATTTAA
11031135 AATTA
1 AATTA
11031140 TCATATTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.17
15 7 0.39
16 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATAATATTTAA
Found at i:11033874 original size:18 final size:18
Alignment explanation
Indices: 11033851--11033892 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11033841 TTAAAATTAT
11033851 TATATAAATAAATATATA
1 TATATAAATAAATATATA
* *
11033869 TATATAAGTAAGTATATA
1 TATATAAATAAATATATA
*
11033887 CATATA
1 TATATA
11033893 CGTATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
TATATAAATAAATATATA
Found at i:11033971 original size:13 final size:13
Alignment explanation
Indices: 11033935--11033982 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
11033925 GTATAGGTAT
*
11033935 ATACATATATGAATC
1 ATACATATAT-AA-A
11033950 ATA-ATATATAAA
1 ATACATATATAAA
11033962 ATACATATATAAA
1 ATACATATATAAA
*
11033975 ATAGATAT
1 ATACATAT
11033983 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 3 0.10
13 18 0.60
14 6 0.20
15 3 0.10
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (13 bp):
ATACATATATAAA
Found at i:11034047 original size:25 final size:25
Alignment explanation
Indices: 11034004--11034052 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
11033994 AAGAATATGT
* **
11034004 AAATATATATATATTTATGAAAATA
1 AAATACATATATAGATATGAAAATA
*
11034029 AAATACATATATAGATATGTAAAT
1 AAATACATATATAGATATGAAAAT
11034053 GGATATGTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
AAATACATATATAGATATGAAAATA
Found at i:11034138 original size:3 final size:3
Alignment explanation
Indices: 11034130--11034154 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11034120 ATATAAAAGC
11034130 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
11034155 TGAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11038114 original size:12 final size:12
Alignment explanation
Indices: 11038097--11038155 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
11038087 TATACTAAAT
11038097 AAAATAATAATA
1 AAAATAATAATA
11038109 AAAATAATAATA
1 AAAATAATAATA
*
11038121 AAAAT-AT-TTA
1 AAAATAATAATA
*
11038131 AAAATCA-AATA
1 AAAATAATAATA
*
11038142 AAAATATTAATA
1 AAAATAATAATA
11038154 AA
1 AA
11038156 CTAATATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 7 0.17
11 10 0.25
12 23 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:11038133 original size:21 final size:21
Alignment explanation
Indices: 11038107--11038149 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11038097 AAAATAATAA
11038107 TAAAAATAATAATAAAAATATT
1 TAAAAATAA-AATAAAAATATT
*
11038129 TAAAAATCAAATAAAAATATT
1 TAAAAATAAAATAAAAATATT
11038150 AATAAACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATAAAATAAAAATATT
Found at i:11038161 original size:20 final size:21
Alignment explanation
Indices: 11038107--11038161 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
11038097 AAAATAATAA
*
11038107 TAAAAATAATAATAAAAATATT
1 TAAAAAT-CTAATAAAAATATT
*
11038129 TAAAAATCAAATAAAAATA-T
1 TAAAAATCTAATAAAAATATT
11038149 TAATAAA-CTAATA
1 TAA-AAATCTAATA
11038162 TTTATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 13 0.45
22 7 0.24
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATCTAATAAAAATATT
Found at i:11038634 original size:23 final size:23
Alignment explanation
Indices: 11038606--11038649 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
11038596 CTTTCTTACT
*
11038606 GTAGTAATTTTCGGGGTATTATA
1 GTAGTAATTTTCGGGATATTATA
11038629 GTAGTAATTTTCGGGATATTA
1 GTAGTAATTTTCGGGATATTA
11038650 CATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTATA
Found at i:11039241 original size:3 final size:3
Alignment explanation
Indices: 11039233--11039280 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
11039223 ACCTTGTTGC
11039233 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11039279 TT
1 TT
11039281 TGTATTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11039638 original size:29 final size:30
Alignment explanation
Indices: 11039598--11039729 Score: 89
Period size: 29 Copynumber: 4.6 Consensus size: 30
11039588 AAAACAAAAC
11039598 AAAA-TACATTTTAGCCCC-AAACTTTTTA
1 AAAATTACATTTTAGCCCCTAAACTTTTTA
* * *
11039626 AAAATTACATTTTA-ACCC-ATA-TTTTTT
1 AAAATTACATTTTAGCCCCTAAACTTTTTA
* * * * *
11039653 AAATTTACATCTTAACCCCTAATAATTTGT-
1 AAAATTACATTTTAGCCCCTAA-ACTTTTTA
** *
11039683 -AAATTACATTTGGGCCCCTAAACTTTCTA
1 AAAATTACATTTTAGCCCCTAAACTTTTTA
* *
11039712 GAAATTACATTTTGGCCC
1 AAAATTACATTTTAGCCC
11039730 TATATTTTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
27 17 0.21
28 17 0.21
29 26 0.32
30 17 0.21
31 4 0.05
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAGCCCCTAAACTTTTTA
Found at i:11039644 original size:28 final size:27
Alignment explanation
Indices: 11039598--11039670 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
11039588 AAAACAAAAC
*
11039598 AAAA-TACATTTTAGCCCCAAACTTTTTA
1 AAAATTACATTTTA-ACCCAAA-TTTTTA
* *
11039626 AAAATTACATTTTAACCCATATTTTTT
1 AAAATTACATTTTAACCCAAATTTTTA
* *
11039653 AAATTTACATCTTAACCC
1 AAAATTACATTTTAACCC
11039671 CTAATAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 21 0.54
28 9 0.23
29 9 0.23
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (27 bp):
AAAATTACATTTTAACCCAAATTTTTA
Found at i:11039929 original size:16 final size:16
Alignment explanation
Indices: 11039908--11039944 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
11039898 AAGGATTTAA
11039908 AAGAAGGAAAAAATAG
1 AAGAAGGAAAAAATAG
11039924 AAGAAGGAAAAAATAG
1 AAGAAGGAAAAAATAG
11039940 AAGAA
1 AAGAA
11039945 AGGGGGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (16 bp):
AAGAAGGAAAAAATAG
Found at i:11040124 original size:20 final size:19
Alignment explanation
Indices: 11040099--11040149 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
11040089 ACTAGGAAGT
11040099 AAAAAAAAAAAACAGCAAGGA
1 AAAAAAAAAAAACA--AAGGA
11040120 AAAAAAGAAAAAACAAAGGA
1 AAAAAA-AAAAAACAAAGGA
11040140 AAAAAGAAAA
1 AAAAA-AAAA
11040150 GAAAGGGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.46
21 7 0.25
22 8 0.29
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAACAAAGGA
Found at i:11040253 original size:4 final size:4
Alignment explanation
Indices: 11040244--11040312 Score: 76
Period size: 4 Copynumber: 18.2 Consensus size: 4
11040234 GAACGGGGAT
11040244 GAAA GAAA GAAA GAAA -AAGA GAAA -AAA GAAA GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* *
11040290 G-AA GAAA G-AA GGAA GAAA AAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
11040313 GAGATAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
3 14 0.25
4 40 0.71
5 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:11040273 original size:7 final size:7
Alignment explanation
Indices: 11040245--11040310 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
11040235 AACGGGGATG
11040245 AAAGAAA
1 AAAGAAA
11040252 GAAAGAAA
1 -AAAGAAA
11040260 AAGAGAAA
1 AA-AGAAA
11040268 AAAG---
1 AAAGAAA
11040272 AAAGAAA
1 AAAGAAA
11040279 AAAGAAA
1 AAAGAAA
*
11040286 GAAAGAAG
1 -AAAGAAA
*
11040294 AAAGAAG
1 AAAGAAA
*
11040301 GAAGAAA
1 AAAGAAA
11040308 AAA
1 AAA
11040311 AGGAGATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.08
7 25 0.51
8 20 0.41
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:11040304 original size:11 final size:11
Alignment explanation
Indices: 11040246--11040312 Score: 80
Period size: 11 Copynumber: 6.0 Consensus size: 11
11040236 ACGGGGATGA
11040246 AAGAAAGAAAG
1 AAGAAAGAAAG
* *
11040257 AAAAAGAGAAAA
1 AAGAA-AGAAAG
*
11040269 AAGAAAGAAAA
1 AAGAAAGAAAG
11040280 AAGAAAGAAAG
1 AAGAAAGAAAG
*
11040291 AAGAAAGAAGG
1 AAGAAAGAAAG
*
11040302 AAGAAAAAAAG
1 AAGAAAGAAAG
11040313 GAGATAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 39 0.81
12 9 0.19
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:11041051 original size:18 final size:18
Alignment explanation
Indices: 11041023--11041345 Score: 177
Period size: 17 Copynumber: 17.8 Consensus size: 18
11041013 CTTAAAAAAA
11041023 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
11041040 TCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTC--AAAAATTT
11041060 CTCGTG-TTTCAAAAAATTCCT
1 -TCGTGTTTTC-AAAAATT--T
* *
11041081 T-GTTTTTTAAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
11041098 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
11041116 CCATG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
11041133 TCGTGTTTTC-AAAA-TT
1 TCGTGTTTTCAAAAATTT
*
11041149 CCAGTG-TTTCAAAAATTT
1 TC-GTGTTTTCAAAAATTT
*
11041167 TCATGTTTTC-AAAATTT
1 TCGTGTTTTCAAAAATTT
* *
11041184 CCCGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTT
* *
11041203 CCGT-ATTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
* *
11041221 TCTTGTTTTCAAAAAAAAATT
1 TCGTGTTTTC---AAAAATTT
* *
11041242 CCGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTT
* * * * * *
11041259 CCATATTTTAAAAAAACTC
1 TCGTGTTTT-CAAAAATTT
*
11041278 TCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* *
11041295 TTGTGTTTTCAAAAAATTGA
1 TCGTGTTTTC-AAAAATT-T
* * *
11041315 CCGTG-ATTCATAAATTT
1 TCGTGTTTTCAAAAATTT
11041332 TCGTG-TTTCAAAAA
1 TCGTGTTTTCAAAAA
11041346 AGAATCCTTG
Statistics
Matches: 233, Mismatches: 49, Indels: 48
0.71 0.15 0.15
Matches are distributed among these distances:
16 7 0.03
17 74 0.32
18 68 0.29
19 44 0.19
20 23 0.10
21 17 0.07
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:11041236 original size:37 final size:36
Alignment explanation
Indices: 11041028--11041346 Score: 113
Period size: 36 Copynumber: 8.8 Consensus size: 36
11041018 AAAAATCGTG
* * *
11041028 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTCGTG
1 TTTCAAAAATTTTCTTGTTTTC-AAAAAA-TTCCCGTA
* * * ** *
11041066 TTTCAAAAAATTCCTTGTTTTTTAAAAAATTTTCGTGT
1 TTTCAAAAATTTTCTTG-TTTTCAAAAAATTCCCGT-A
** * ** *
11041104 TTTCAAAAATTCCCATG-TTTC-AAAAATTTTCGTGT
1 TTTCAAAAATTTTCTTGTTTTCAAAAAATTCCCGT-A
** * **
11041139 TTTC-AAAA--TTCCAGTGTTTCAAAAATTTTCATGT-
1 TTTCAAAAATTTTCTTGT-TTTCAAAAA-ATTCCCGTA
* *
11041173 TTTC-AAAATTTCCCGTGTTTTC-AAAAATTCCCGTA
1 TTTCAAAAATTT-TCTTGTTTTCAAAAAATTCCCGTA
*
11041208 TTTCAAAAAATTTTCTTGTTTTCAAAAAAAAATT-CCGTG
1 TTTC-AAAAATTTTCTTGTTTTC---AAAAAATTCCCGTA
* * * * * * * *
11041247 TTTCATAAATTTCCATATTTTAAAAAAACTCTCGTC
1 TTTCAAAAATTTTCTTGTTTTCAAAAAATTCCCGTA
*
11041283 TTTCAAAAATTTT-TGTGTTTTCAAAAAATTGACCGTGA
1 TTTCAAAAATTTTCT-TGTTTTCAAAAAATT-CCCGT-A
* *
11041321 -TTCATAAATTTTCGTG-TTTCAAAAAA
1 TTTCAAAAATTTTCTTGTTTTCAAAAAA
11041347 GAATCCTTGT
Statistics
Matches: 214, Mismatches: 46, Indels: 44
0.70 0.15 0.14
Matches are distributed among these distances:
32 2 0.01
34 21 0.10
35 37 0.17
36 56 0.26
37 32 0.15
38 47 0.22
39 12 0.06
40 7 0.03
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTCAAAAATTTTCTTGTTTTCAAAAAATTCCCGTA
Found at i:11041416 original size:16 final size:16
Alignment explanation
Indices: 11041395--11041429 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11041385 TTTCAAAAAC
*
11041395 AAATTTTGTGTTTTAA
1 AAATTTTGTGTTTCAA
11041411 AAATTTTGTGTTTCAA
1 AAATTTTGTGTTTCAA
11041427 AAA
1 AAA
11041430 GAAAATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (16 bp):
AAATTTTGTGTTTCAA
Found at i:11041436 original size:21 final size:21
Alignment explanation
Indices: 11041409--11041456 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
11041399 TTTGTGTTTT
*
11041409 AAAAATTTTGTG-TTTCAAAA
1 AAAAATTTCGTGTTTTCAAAA
11041429 AGAAAA-TTCGTGTTTTCAAAA
1 A-AAAATTTCGTGTTTTCAAAA
11041450 AAAAATT
1 AAAAATT
11041457 CGTATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAAATTTCGTGTTTTCAAAA
Found at i:11041443 original size:20 final size:19
Alignment explanation
Indices: 11041418--11041469 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
11041408 TAAAAATTTT
11041418 GTGTTTCAAAAAGAAAATTC
1 GTGTTTCAAAAA-AAAATTC
11041438 GTGTTTTCAAAAAAAAATTC
1 GTG-TTTCAAAAAAAAATTC
*
11041458 GTATTT-AAAAAA
1 GTGTTTCAAAAAA
11041470 TTTTCATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 6 0.20
19 3 0.10
20 12 0.40
21 9 0.30
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (19 bp):
GTGTTTCAAAAAAAAATTC
Found at i:11041534 original size:34 final size:35
Alignment explanation
Indices: 11041496--11041587 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 35
11041486 GGTACTTCTT
*
11041496 AAAAAAAATCGTGTTTCAAAATTTTTGT-GTTTTA
1 AAAAAAAATCGTGTTTCAAAATTCTTGTAGTTTTA
* * *
11041530 AAAAAAATTCGTGTTTCTAAAATTCTTGTATTTTTT
1 AAAAAAAATCGTGTTTC-AAAATTCTTGTAGTTTTA
* *
11041566 TAAAAAAATTGTGTTTTCAAAA
1 AAAAAAAATCGTG-TTTCAAAA
11041588 AAAGAAAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
34 16 0.33
35 10 0.21
36 18 0.38
37 4 0.08
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.45
Consensus pattern (35 bp):
AAAAAAAATCGTGTTTCAAAATTCTTGTAGTTTTA
Found at i:11046240 original size:5 final size:5
Alignment explanation
Indices: 11046230--11046255 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11046220 TGAGCATTTT
11046230 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
11046256 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:11047214 original size:21 final size:20
Alignment explanation
Indices: 11047175--11047214 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11047165 GGGGAAAGTG
* *
11047175 GGAAGAAGTAAAAGTTTTGA
1 GGAAAAAGTAAAAGGTTTGA
11047195 GGAAAAAGTAAAAAGGTTTG
1 GGAAAAAGT-AAAAGGTTTG
11047215 GGAGTTGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (20 bp):
GGAAAAAGTAAAAGGTTTGA
Found at i:11053170 original size:32 final size:32
Alignment explanation
Indices: 11053129--11053242 Score: 105
Period size: 32 Copynumber: 3.6 Consensus size: 32
11053119 CAAGATGATG
11053129 AAAGACTTTCGAGGAAAATCCTCCCGATACAA
1 AAAGACTTTCGAGGAAAATCCTCCCGATACAA
*
11053161 AAAGACTTTCGAGGAAAAT--TCCGCGA-AGGAGA
1 AAAGACTTTCGAGGAAAATCCTCC-CGATA-CA-A
* * *
11053193 ACTAGTAC--T-AAGAAAAATCCTCCCGATACAA
1 A-AAG-ACTTTCGAGGAAAATCCTCCCGATACAA
11053224 AAAGACTTTCGAGGAAAAT
1 AAAGACTTTCGAGGAAAAT
11053243 GGTCACCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
29 2 0.03
30 6 0.10
31 14 0.22
32 33 0.52
33 6 0.10
34 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (32 bp):
AAAGACTTTCGAGGAAAATCCTCCCGATACAA
Found at i:11054048 original size:27 final size:27
Alignment explanation
Indices: 11054018--11054071 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
11054008 TCCATTCCAC
11054018 ATCCTTAATATATATAACATGCTTATA
1 ATCCTTAATATATATAACATGCTTATA
11054045 ATCCTTAATATATATAACATGCTTATA
1 ATCCTTAATATATATAACATGCTTATA
11054072 TGTAACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (27 bp):
ATCCTTAATATATATAACATGCTTATA
Found at i:11055617 original size:9 final size:9
Alignment explanation
Indices: 11055599--11055630 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11055589 TATTATGCCT
11055599 AAAAAAAAC
1 AAAAAAAAC
*
11055608 AAACAAAAC
1 AAAAAAAAC
11055617 AAAAAAAAC
1 AAAAAAAAC
11055626 AAAAA
1 AAAAA
11055631 GGAAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:11055620 original size:14 final size:13
Alignment explanation
Indices: 11055599--11055662 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 13
11055589 TATTATGCCT
*
11055599 AAAAAAAACAAAC
1 AAAAAAAAAAAAC
11055612 AAAACAAAAAAAAC
1 AAAA-AAAAAAAAC
** *
11055626 AAAAAGGAAAAAG
1 AAAAAAAAAAAAC
* *
11055639 AAAAGGAAAAAAAG
1 AAAA-AAAAAAAAC
11055653 AAAAAAAAAA
1 AAAAAAAAAA
11055663 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 19 0.46
14 22 0.54
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:11055648 original size:25 final size:25
Alignment explanation
Indices: 11055600--11055667 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
11055590 ATTATGCCTA
* ** *
11055600 AAAAAAACAAACAAAACAAAAAAAAC
1 AAAAAAA-AAAGAAAAGGAAAAAAAG
11055626 AAAAAGGAAAAAGAAAAGGAAAAAAAG
1 AAAAA--AAAAAGAAAAGGAAAAAAAG
11055653 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
11055668 ATCAAGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 10 0.28
26 5 0.14
27 19 0.53
28 2 0.06
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAGAAAAGGAAAAAAAG
Found at i:11055663 original size:20 final size:19
Alignment explanation
Indices: 11055599--11055668 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
11055589 TATTATGCCT
* * *
11055599 AAAAAAAACAAACAAA-AC
1 AAAAAAAAGAAAAAAAGAA
* *
11055617 AAAAAAAA-CAAAAAGGAA
1 AAAAAAAAGAAAAAAAGAA
*
11055635 AAAGAAAAGGAAAAAAAGAA
1 AAA-AAAAAGAAAAAAAGAA
11055655 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
11055669 TCAAGATGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.10
18 12 0.29
19 14 0.34
20 11 0.27
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAGAA
Found at i:11056724 original size:78 final size:78
Alignment explanation
Indices: 11056517--11057091 Score: 662
Period size: 78 Copynumber: 7.3 Consensus size: 78
11056507 TTTCAAGAAA
* * * * *
11056517 TATTTTTCAATTTCTGTTTTGTTTTTAAAATCAATCAACTCATAATGCAAGAGGGGAGTTGAGCC
1 TATTTTTCAATTTCTG---T-TTTTCAAAA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
** * *
11056582 TCGGGTTGCATGCCGAGG
61 TCGGGTCACACGCTGAGG
* ** *
11056600 TATTCTTTTCAATTTTTACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTCG
1 TA-T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
**
11056665 GGTCGTACGCTGAGG
64 GGTCACACGCTGAGG
* * *
11056680 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTTATAATGCGAGAGGTGAGTTGAGCCTCGGA
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
11056745 TCACACGCTGAGG
66 TCACACGCTGAGG
*
11056758 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGCTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
11056823 TTACACACTGAGG
66 TCACACGCTGAGG
* *
11056836 TATTTTTTAAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG
1 TA-TTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
* *
11056899 GTCGCACACTGAGG
65 GTCACACGCTGAGG
*
11056913 TATTTCTTTTAAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
11056975 GAGT--CACG-TCGAGG
63 GGGTCACACGCT-GAGG
* * * * * *
11056989 TATTTTTCAATTTTTGGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAATTAAGCCTTGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
11057054 TCATATGCTGAGG
66 TCACACGCTGAGG
*
11057067 TATTTTTCAATTTCTATTTTTCAAA
1 TATTTTTCAATTTCTGTTTTTCAAA
11057092 GGTCAACTCA
Statistics
Matches: 432, Mismatches: 48, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
73 11 0.03
74 6 0.01
75 1 0.00
76 46 0.11
77 52 0.12
78 215 0.50
79 34 0.08
80 45 0.10
81 8 0.02
83 2 0.00
84 1 0.00
85 11 0.03
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (78 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
TCACACGCTGAGG
Found at i:11056959 original size:233 final size:230
Alignment explanation
Indices: 11056517--11057103 Score: 716
Period size: 233 Copynumber: 2.5 Consensus size: 230
11056507 TTTCAAGAAA
* * * * *
11056517 TATTTTTCAATTTCTGTTTTGTTTTTAAAATCAATCAACTCATAATGCAAGAGGGGAGTTGAGCC
1 TATTTTTCAATTTCTG---T-TTTTCAAAA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * * *
11056582 TCGGGTTGCATGCCGAGGTATTCTTTTCAATTTTTACTTTTCAAAAAAATCAACTCATATTGCGA
61 TCGGGTTACATGCTGAGGTATT-TTTTCAATTTCTATTTTTC--AAAAATCAACTCATATTGCGA
* * * *
11056647 GAGGTGAGTTGGGCCTCGGGTCGTACGCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAATCA
123 GAGGTGAGTTGAGCCTCGGGTCGCACACTGAGGTATTTTTAAATTTCTGTTTTTC-AAAAAATCA
*
11056712 ACTTATAATGCGAGAGGTGAGTTGAGCCTCG-GATCACACG-CTGAGG
187 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG-T--CACGTC-GAGG
*
11056758 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGCTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
** * *
11056823 TTACACACTGAGGTATTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
66 TTACATGCTGAGGTATTTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
*
11056888 TTGAGCCTTGGGTCGCACACTGAGGTATTTCTTTTAAATTTCTG-TTTTC-AAAAATCAACTCAT
131 TTGAGCCTCGGGTCGCACACTGAGGTA--T-TTTTAAATTTCTGTTTTTCAAAAAATCAACTCAT
*
11056951 ATTGCGAGAGGTGAGTTGAGCCTCGAGTCACGTCGAGG
193 AATGCGAGAGGTGAGTTGAGCCTCGAGTCACGTCGAGG
* * * * * *
11056989 TATTTTTCAATTTTTGGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAATTAAGCCTTGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * **
11057054 TCATATGCTGAGGTA-TTTTTCAATTTCTATTTTTCAAAGGTCAACTCATA
66 TTACATGCTGAGGTATTTTTTCAATTTCTATTTTTCAAAAATCAACTCATA
11057104 ATTTGAGAAG
Statistics
Matches: 305, Mismatches: 36, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
230 31 0.10
231 77 0.25
232 1 0.00
233 90 0.30
234 1 0.00
235 21 0.07
236 59 0.19
237 8 0.03
238 1 0.00
241 16 0.05
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (230 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
TTACATGCTGAGGTATTTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
TTGAGCCTCGGGTCGCACACTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATAAT
GCGAGAGGTGAGTTGAGCCTCGAGTCACGTCGAGG
Found at i:11056966 original size:155 final size:153
Alignment explanation
Indices: 11056517--11057091 Score: 626
Period size: 155 Copynumber: 3.7 Consensus size: 153
11056507 TTTCAAGAAA
* * *
11056517 TATTTTTCAATTTCTGTTTTGTTTTTAAAATCAATCAACTCATAATGCAAGAGGGGAGTTGAGCC
1 TATTTTTCAATTTCTG---T-TTTTCAAAA--AATCAACTCATAATGCGAGAGGTGAGTTGAGCC
* * * * *
11056582 TCGGGTTGCATGCCGAGGTATTCTTTTCAATTTTTACTTTTCAAAAAAATCAACTCATATTGCGA
60 TCGGGTCGCACGCTGAGGTATTCTTTTCAATTTCT-GTTTTC-AAAAAATCAACTCATATTGCGA
*
11056647 GAGGTGAGTTGGGCCTCGGG-TCGTACGCTGAGG
123 GAGGTGAGTTGAGCCTCGGGTTC--AC-CTGAGG
* *
11056680 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTTATAATGCGAGAGGTGAGTTGAGCCTCGGA
1 TATTTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* *
11056745 TCACACGCTGAGGTA-T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGCT
65 TCGCACGCTGAGGTATTCTTTTCAATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGAGAGGT
11056808 GAGTTGAGCCTCGGGTTACACACTGAGG
128 GAGTTGAGCCTCGGGTT-CAC-CTGAGG
* * *
11056836 TATTTTTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG
1 TA-TTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* *
11056900 TCGCACACTGAGGTATTTCTTTTAAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTG
65 TCGCACGCTGAGGTA-TTCTTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTG
* *
11056964 AGTTGAGCCTCGAG-TCACGTCGAGG
129 AGTTGAGCCTCGGGTTCACCT-GAGG
* * * * * * *
11056989 TATTTTTCAATTTTTGGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAATTAAGCCTTGGG
1 TATTTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
** * *
11057054 TCATATGCTGAGGTA-T-TTTTCAATTTCTATTTTTCAAA
65 TCGCACGCTGAGGTATTCTTTTCAATTTCT-GTTTTCAAA
11057092 GGTCAACTCA
Statistics
Matches: 362, Mismatches: 37, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
151 11 0.03
152 24 0.07
153 11 0.03
154 50 0.14
155 89 0.25
156 67 0.19
157 27 0.07
158 58 0.16
159 4 0.01
160 5 0.01
163 16 0.04
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (153 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
CGCACGCTGAGGTATTCTTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAG
TTGAGCCTCGGGTTCACCTGAGG
Found at i:11057440 original size:8 final size:8
Alignment explanation
Indices: 11057429--11057455 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11057419 AAAATTTAAA
11057429 AAAAAAAC
1 AAAAAAAC
11057437 AAAAAAAC
1 AAAAAAAC
11057445 AAAAAAAC
1 AAAAAAAC
11057453 AAA
1 AAA
11057456 TTACATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:11057968 original size:24 final size:22
Alignment explanation
Indices: 11057936--11057991 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
11057926 ACTAGGAAGT
11057936 AAAAAAAGAAAAAAAACATCAAGG
1 AAAAAAAGAAAAAAAACA--AAGG
11057960 AAAAAAAG-AAAAAAACAAAGG
1 AAAAAAAGAAAAAAAACAAAGG
11057981 -AAAAAAGAAAA
1 AAAAAAAGAAAA
11057992 GAAAGGGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.23
21 7 0.23
23 9 0.29
24 8 0.26
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAACAAAGG
Found at i:11057984 original size:20 final size:22
Alignment explanation
Indices: 11057936--11057991 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 22
11057926 ACTAGGAAGT
11057936 AAAAAAAGAAAAAAAACATCAAGG
1 AAAAAAAG-AAAAAAACA-CAAGG
11057960 AAAAAAAGAAAAAAACA-AAGG
1 AAAAAAAGAAAAAAACACAAGG
11057981 -AAAAAAGAAAA
1 AAAAAAAGAAAA
11057992 GAAAGGGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.34
21 4 0.12
23 9 0.28
24 8 0.25
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAAAACACAAGG
Found at i:11058093 original size:4 final size:4
Alignment explanation
Indices: 11058084--11058130 Score: 64
Period size: 4 Copynumber: 12.2 Consensus size: 4
11058074 CTGAACGGGG
11058084 AAGA AAGA AAGA AAGA AA-A AGAGA AA-A AAGA AAGA AA-A AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA AAGA
11058130 A
1 A
11058131 GGAAGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 8 0.21
4 29 0.74
5 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:11058115 original size:27 final size:27
Alignment explanation
Indices: 11058084--11058145 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
11058074 CTGAACGGGG
11058084 AAGAAAGAAAGAAAGAAA-AAGAGAA-AA
1 AAGAAAGAAA-AAAGAAAGAAG-GAAGAA
11058111 AAGAAAGAAAAAAGAAAGAAGGAAGAA
1 AAGAAAGAAAAAAGAAAGAAGGAAGAA
*
11058138 AAAAAAGA
1 AAGAAAGA
11058146 GATCAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAAAAGAAAGAAGGAAGAA
Found at i:11058121 original size:11 final size:11
Alignment explanation
Indices: 11058084--11058143 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
11058074 CTGAACGGGG
11058084 AAGAAAGAAAGA
1 AAGAAA-AAAGA
11058096 AAG-AAAAAG-
1 AAGAAAAAAGA
11058105 -AGAAAAAAGA
1 AAGAAAAAAGA
11058115 AAGAAAAAAGA
1 AAGAAAAAAGA
**
11058126 AAGAAGGAAGA
1 AAGAAAAAAGA
11058137 AA-AAAAA
1 AAGAAAAA
11058144 GAGATCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 2 0.05
9 6 0.15
10 7 0.17
11 23 0.56
12 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:11058121 original size:18 final size:18
Alignment explanation
Indices: 11058084--11058141 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
11058074 CTGAACGGGG
11058084 AAGAAAGAAAGAAAGAAAA
1 AAGAAA-AAAGAAAGAAAA
11058103 AGAGAAAAAAGAAAGAAAA
1 A-AGAAAAAAGAAAGAAAA
* *
11058122 AAGAAAGAAGGAAGAAAA
1 AAGAAAAAAGAAAGAAAA
11058140 AA
1 AA
11058142 AAGAGATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 17 0.47
19 14 0.39
20 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAGAAAGAAAA
Found at i:11058597 original size:16 final size:16
Alignment explanation
Indices: 11058557--11058597 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
11058547 TTTTAAGTAT
11058557 TTTTATTTTGTATTTA
1 TTTTATTTTGTATTTA
* * *
11058573 TGTTCTTTTTTATTTA
1 TTTTATTTTGTATTTA
11058589 TTTTATTTT
1 TTTTATTTT
11058598 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTATTTTGTATTTA
Found at i:11058920 original size:18 final size:18
Alignment explanation
Indices: 11058892--11059213 Score: 161
Period size: 17 Copynumber: 17.8 Consensus size: 18
11058882 CTTAAAAAAA
11058892 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
11058909 TCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTC--AAAAATTT
* *
11058929 CCCGTG-TTTCAAAAAATT
1 -TCGTGTTTTCAAAAATTT
* * * *
11058947 CCTTGTTTTTAAAAAAAAATT
1 TCGTG-TTTT--CAAAAATTT
*
11058968 T-GTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
11058985 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
11059002 TCGTGTTTTC-AAAA-TT
1 TCGTGTTTTCAAAAATTT
* *
11059018 CCAGTG-TTTCAAATATTT
1 TC-GTGTTTTCAAAAATTT
*
11059036 TCGTGTTTTC-AAGATTT
1 TCGTGTTTTCAAAAATTT
* *
11059053 CCCGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTT
* * *
11059072 CCGT-ATTTCGAAAATTT
1 TCGTGTTTTCAAAAATTT
* *
11059089 TCTTGTTTTCAAAAAAAAAAATT
1 TCGTGTTTTC-----AAAAATTT
*
11059112 TCGTG-TTTCATAAA-TT
1 TCGTGTTTTCAAAAATTT
**
11059128 TCTGTGTTTT-AAAAAAAT
1 TC-GTGTTTTCAAAAATTT
*
11059146 TCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
11059163 TCGTGTTTTCAAAAAATTGA
1 TCGTGTTTTC-AAAAATT-T
* *
11059183 CCGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTT
11059200 TCGTG-TTTCAAAAA
1 TCGTGTTTTCAAAAA
11059214 AAATCCTCGT
Statistics
Matches: 233, Mismatches: 43, Indels: 58
0.70 0.13 0.17
Matches are distributed among these distances:
16 13 0.06
17 96 0.41
18 57 0.24
19 23 0.10
20 18 0.08
21 12 0.05
22 4 0.02
23 10 0.04
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:11058934 original size:21 final size:19
Alignment explanation
Indices: 11058893--11058944 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
11058883 TTAAAAAAAT
*
11058893 CGTGTTTC--AAAAATTTT
1 CGTGTTTCAAAAAAATTTC
11058910 CGTGTTTTCAAAAAAATTTCC
1 CGTG-TTTCAAAAAAATTT-C
11058931 CGTGTTTCAAAAAA
1 CGTGTTTCAAAAAA
11058945 TTCCTTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 4 0.13
20 18 0.60
21 4 0.13
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
CGTGTTTCAAAAAAATTTC
Found at i:11059108 original size:110 final size:110
Alignment explanation
Indices: 11058994--11059228 Score: 243
Period size: 110 Copynumber: 2.2 Consensus size: 110
11058984 CTCATGTTTC
* ** * *
11058994 AAAAATCTTCGTGTTTTCA-AAATTCCAGTGTTTCAAATATTTTCGTGTTTTC-AAGATTTCCCG
1 AAAAATCTTCGTGTTTTCATAAATTCCAGTGTTTCAAAAAAATTCGT-CTTTCAAAAATTT-CCG
* *
11059057 TGTTTTC-AAAAATT-CCCGTATTTCGA-AAATTTTCTTGTTTTCAAAAAA
64 TGTTTTCAAAAAATTGACCGTATTTC-ATAAATTTTCGTG-TTTC--AAAA
* * * *
11059105 AAAAAT-TTCGTG-TTTCATAAATTTCTGTGTTTTAAAAAAATTCGTCTTTCAAAAATTTTCGTG
1 AAAAATCTTCGTGTTTTCATAAATTCCAGTGTTTCAAAAAAATTCGTCTTTCAAAAATTTCCGTG
*
11059168 TTTTCAAAAAATTGACCGTGTTTCATAAATTTTCGTGTTTC-AAA
66 TTTTCAAAAAATTGACCGTATTTCATAAATTTTCGTGTTTCAAAA
*
11059212 AAAAATCCTCGTGTTTT
1 AAAAATCTTCGTGTTTT
11059229 ATTTTTAGCA
Statistics
Matches: 104, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
107 9 0.09
108 5 0.05
109 21 0.20
110 45 0.43
111 24 0.23
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (110 bp):
AAAAATCTTCGTGTTTTCATAAATTCCAGTGTTTCAAAAAAATTCGTCTTTCAAAAATTTCCGTG
TTTTCAAAAAATTGACCGTATTTCATAAATTTTCGTGTTTCAAAA
Found at i:11059225 original size:37 final size:36
Alignment explanation
Indices: 11059102--11059227 Score: 127
Period size: 37 Copynumber: 3.5 Consensus size: 36
11059092 TGTTTTCAAA
*
11059102 AAAAAAAATTTCGTGTTTCATAAA-TTTCTGTGTTT-
1 AAAAAAAATCTCGTGTTTCATAAATTTTC-GTGTTTC
* * *
11059137 TAAAAAAAT-TCGTCTTTCAAAAATTTTCGTGTTTTC
1 AAAAAAAATCTCGTGTTTCATAAATTTTCGTG-TTTC
*
11059173 -AAAAAATTGAC-CGTGTTTCATAAATTTTCGTGTTTC
1 AAAAAAAAT--CTCGTGTTTCATAAATTTTCGTGTTTC
11059209 AAAAAAAATCCTCGTGTTT
1 AAAAAAAAT-CTCGTGTTT
11059228 TATTTTTAGC
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
34 15 0.20
35 22 0.29
36 5 0.07
37 33 0.44
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (36 bp):
AAAAAAAATCTCGTGTTTCATAAATTTTCGTGTTTC
Found at i:11059281 original size:15 final size:17
Alignment explanation
Indices: 11059267--11059344 Score: 52
Period size: 17 Copynumber: 4.3 Consensus size: 17
11059257 AAACAAATTT
*
11059267 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
*
11059284 GTGTTTCAAAAAAAAATTT-
1 GTGTTTC---AAAAATTTTC
11059303 GT-TTTCAAAAAAAAATTTTC
1 GTGTTTC---AA-AAATTTTC
*
11059323 GTGTTTCAAAAATTCTC
1 GTGTTTCAAAAATTTTC
11059340 GTGTT
1 GTGTT
11059345 AAATACGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
17 18 0.35
18 11 0.22
19 8 0.16
20 10 0.20
21 4 0.08
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
GTGTTTCAAAAATTTTC
Found at i:11059305 original size:17 final size:18
Alignment explanation
Indices: 11059248--11059334 Score: 72
Period size: 18 Copynumber: 4.7 Consensus size: 18
11059238 AAAATTTTTA
*
11059248 TGTTTTCAAAAACAAATT
1 TGTTTTCAAAAAAAAATT
* *
11059266 TGTGTTT---TAAAAATTT
1 TGT-TTTCAAAAAAAAATT
11059282 TCGTGTTTCAAAAAAAAATT
1 T-GT-TTTCAAAAAAAAATT
11059302 TGTTTTCAAAAAAAAATTT
1 TGTTTTCAAAAAAAAA-TT
11059321 TCGTGTTTCAAAAA
1 T-GT-TTTCAAAAA
11059335 TTCTCGTGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
16 7 0.12
17 6 0.11
18 16 0.29
19 8 0.14
20 10 0.18
21 9 0.16
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (18 bp):
TGTTTTCAAAAAAAAATT
Found at i:11059406 original size:36 final size:33
Alignment explanation
Indices: 11059359--11059451 Score: 125
Period size: 36 Copynumber: 2.7 Consensus size: 33
11059349 ACGGTACTTC
*
11059359 TTAAAAAAAATCGTGTTTCAAAATTTTCGTGTTTT
1 TTAAAAAAAATCGTGTTTCAAAATTTT--TGTATT
11059394 TTAAAAAAAAATCGTGTTTCTAAAATTTTTGTATT
1 TT-AAAAAAAATCGTGTTTC-AAAATTTTTGTATT
11059429 TT-AAAAAAATCGTGTTTTCAAAA
1 TTAAAAAAAATCGTG-TTTCAAAA
11059452 AAAGAAAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
33 16 0.30
34 4 0.07
35 9 0.17
36 17 0.31
37 8 0.15
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (33 bp):
TTAAAAAAAATCGTGTTTCAAAATTTTTGTATT
Found at i:11060489 original size:22 final size:23
Alignment explanation
Indices: 11060436--11060491 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
11060426 TTTAATTAAA
* * *
11060436 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
11060459 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
11060481 ATTAAAATTAA
1 ATTAAAATTAA
11060492 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:11060504 original size:16 final size:16
Alignment explanation
Indices: 11060467--11060506 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
11060457 TTAATAAAAT
* *
11060467 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
11060483 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
11060499 TAAAATTA
1 TAAAATTA
11060507 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:11060574 original size:66 final size:59
Alignment explanation
Indices: 11060509--11060628 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
11060499 TAAAATTATC
* * *
11060509 AAATTAT-TAATTTTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
11060567 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
11060626 AAA
1 AAA
11060629 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:11060734 original size:22 final size:24
Alignment explanation
Indices: 11060694--11060737 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
11060684 AAATAAACTT
11060694 AAAATAAAAAATTATTATATTTTA
1 AAAATAAAAAATTATTATATTTTA
11060718 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAATTATTATATTT
11060738 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATAAAAAATTATTATATTTTA
Found at i:11061221 original size:40 final size:42
Alignment explanation
Indices: 11061130--11061224 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 42
11061120 TCCCCTTACT
* *
11061130 TAAACTATAGATTTTTGCTAATTTGGTTGCATTTAAATTGAC
1 TAAACTATTGATTTTTGCTAATTTGGTTGCATATAAATTGAC
* * * *
11061172 -GAACAATTGATTTTTGCTAATTTTG-TGCATATAAGTTG-C
1 TAAACTATTGATTTTTGCTAATTTGGTTGCATATAAATTGAC
11061211 TAAACTATTGATTT
1 TAAACTATTGATTT
11061225 CCCAGATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.02
40 22 0.50
41 21 0.48
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (42 bp):
TAAACTATTGATTTTTGCTAATTTGGTTGCATATAAATTGAC
Found at i:11065509 original size:3 final size:3
Alignment explanation
Indices: 11065490--11065539 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
11065480 AATTTATGTC
* * *
11065490 ATA AT- ATA ATA ACA ATA ATA TTA ATA ATA ACA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11065536 ATA A
1 ATA A
11065540 AATGTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:11065518 original size:18 final size:18
Alignment explanation
Indices: 11065490--11065536 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
11065480 AATTTATGTC
11065490 ATAAT-ATAATAACAATA
1 ATAATAATAATAACAATA
*
11065507 ATATTAATAATAACAATA
1 ATAATAATAATAACAATA
11065525 ATAATAA-AATAA
1 ATAATAATAATAA
11065537 TAAAATGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAACAATA
Found at i:11069399 original size:30 final size:31
Alignment explanation
Indices: 11069365--11069430 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
11069355 GAACAAAAAC
* *
11069365 TTCAAGCCCTAATA-AGGAACAATTGCCTAG
1 TTCAAGCCCTAATATAGGAACAATTACCAAG
* *
11069395 TTCAAGCTCTAATATGGGAACAATTACCAAG
1 TTCAAGCCCTAATATAGGAACAATTACCAAG
11069426 TTCAA
1 TTCAA
11069431 TGATAAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (31 bp):
TTCAAGCCCTAATATAGGAACAATTACCAAG
Done.