Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 173 of 250
Found at i:55343567 original size:16 final size:17
Alignment explanation
Indices: 55343539--55343575 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
55343529 ATTTTATTTT
55343539 AATAATAAATTTTAAAA
1 AATAATAAATTTTAAAA
*
55343556 AATAAT-AATTTTAAAT
1 AATAATAAATTTTAAAA
55343572 AATA
1 AATA
55343576 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAATAAATTTTAAAA
Found at i:55345625 original size:29 final size:31
Alignment explanation
Indices: 55345577--55345640 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
55345567 TTTATAGTTA
*
55345577 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
55345608 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
55345637 TTTA
1 TTTA
55345641 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:55345629 original size:8 final size:8
Alignment explanation
Indices: 55345618--55345642 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
55345608 TTTAATAAGA
55345618 TATTTTAT
1 TATTTTAT
55345626 TATTTTAT
1 TATTTTAT
55345634 TATTTTAT
1 TATTTTAT
55345642 T
1 T
55345643 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:55353577 original size:19 final size:18
Alignment explanation
Indices: 55353540--55353583 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
55353530 ATACATGCAG
55353540 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
55353557 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
55353576 TACTAATT
1 TAATAATT
55353584 AATATATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:55355433 original size:28 final size:27
Alignment explanation
Indices: 55355335--55355433 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 27
55355325 GTGTTAACTA
* *
55355335 GGCCTTAGCCCATATCAATATTAATCTG
1 GGCC-TAGCCCATATCAGTATCAATCTG
* *
55355363 GGCCATAGCCCCT-TACAGTATCAGAGTATATTG
1 GGCC-TAGCCCATAT-CAGTATC--A--AT-CTG
55355396 GGCCTAGCCCATATCAGTATCAATCTG
1 GGCCTAGCCCATATCAGTATCAATCTG
55355423 GGCCGTAGCCC
1 GGCC-TAGCCC
55355434 TATTACAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 24 0.43
30 2 0.04
32 16 0.29
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (27 bp):
GGCCTAGCCCATATCAGTATCAATCTG
Found at i:55355466 original size:60 final size:59
Alignment explanation
Indices: 55355335--55355469 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 59
55355325 GTGTTAACTA
* * *
55355335 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATATTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATACTG
* *
55355396 GGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATACTG
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATACTG
* *
55355456 GGTCTTGCCCATAT
1 GGCCTAGCCCATAT
55355470 TAACATAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 4 0.06
60 51 0.80
61 9 0.14
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTATACTG
Found at i:55355836 original size:27 final size:26
Alignment explanation
Indices: 55355806--55355871 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
55355796 GTCAAAATTA
*
55355806 ACCTTAGGGGTATAACGGTCATTTTGC
1 ACCTTAGGGGTATAACGGTAATTTT-C
* * *
55355833 ACC-TAGGGATAAAATGGTAATTTTC
1 ACCTTAGGGGTATAACGGTAATTTTC
*
55355858 ATACTTAGGGGTAT
1 A-CCTTAGGGGTAT
55355872 TTTATTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
25 2 0.07
26 18 0.60
27 10 0.33
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (26 bp):
ACCTTAGGGGTATAACGGTAATTTTC
Found at i:55361307 original size:28 final size:28
Alignment explanation
Indices: 55361275--55361338 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
55361265 TTTTCAGTGT
55361275 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATTTATCAGTTTCATTTAGTAA
55361303 CATTCAATTTATCAGTTTCATTTAGTAA
1 CATTCAATTTATCAGTTTCATTTAGTAA
*
55361331 CACTCAAT
1 CATTCAAT
55361339 CATTCAGTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (28 bp):
CATTCAATTTATCAGTTTCATTTAGTAA
Found at i:55361345 original size:28 final size:28
Alignment explanation
Indices: 55361278--55361346 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
55361268 TCAGTGTCAT
* *
55361278 TCAATTTATCAGTTTCATTTAGTAACAT
1 TCAATATATCAGTTTCATTTAGTAACAC
*
55361306 TCAATTTATCAGTTTCATTTAGTAACAC
1 TCAATATATCAGTTTCATTTAGTAACAC
55361334 TCAATCAT-TCAGT
1 TCAAT-ATATCAGT
55361347 AGCAATTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.43
Consensus pattern (28 bp):
TCAATATATCAGTTTCATTTAGTAACAC
Found at i:55361381 original size:18 final size:18
Alignment explanation
Indices: 55361360--55361406 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55361350 AATTAGTTGT
*
55361360 TCAGCAACAATCATTTAC
1 TCAGCAACAATCAGTTAC
* * *
55361378 TCAGTAGCAATCAGTTAT
1 TCAGCAACAATCAGTTAC
55361396 TCAGCAACAAT
1 TCAGCAACAAT
55361407 AACAGCCAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (18 bp):
TCAGCAACAATCAGTTAC
Found at i:55362799 original size:19 final size:18
Alignment explanation
Indices: 55362777--55362823 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
55362767 TATTCTGTTA
55362777 CTTTGTTTCTTTTCTATTT
1 CTTTGTTTCTTTT-TATTT
*
55362796 CTTTATTTCTTTTTATTT
1 CTTTGTTTCTTTTTATTT
55362814 CATTTGTTTC
1 C-TTTGTTTC
55362824 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTGTTTCTTTTTATTT
Found at i:55362867 original size:21 final size:21
Alignment explanation
Indices: 55362837--55362877 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55362827 TATTTTATAA
*
55362837 TAATATTATAATAATATAATT
1 TAATAATATAATAATATAATT
* *
55362858 TAATAATATACTTATATAAT
1 TAATAATATAATAATATAAT
55362878 AAATATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAATATAATAATATAATT
Found at i:55362876 original size:13 final size:13
Alignment explanation
Indices: 55362833--55362878 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
55362823 CATTTATTTT
55362833 ATAATAATATTATA
1 ATAAT-ATATTATA
55362847 ATAATATAATT-TA
1 ATAATAT-ATTATA
55362860 ATAATATACTTAT-
1 ATAATATA-TTATA
55362873 ATAATA
1 ATAATA
55362879 AATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 19 0.66
14 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATATTATA
Found at i:55362981 original size:25 final size:25
Alignment explanation
Indices: 55362953--55363000 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
55362943 ATTTAGTTAA
55362953 ATATTACATAA-TAATATAATATAAT
1 ATATTACATAATTAA-ATAATATAAT
**
55362978 ATATTTTATAATTAAATAATATA
1 ATATTACATAATTAAATAATATA
55363001 TTTAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTACATAATTAAATAATATAAT
Found at i:55362998 original size:20 final size:22
Alignment explanation
Indices: 55362963--55363003 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
55362953 ATATTACATA
55362963 ATAATATAATATAATATATTTT
1 ATAATATAATATAATATATTTT
55362985 ATAAT-TAA-ATAATATATTT
1 ATAATATAATATAATATATTT
55363004 AAAACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATAATATAATATATTTT
Found at i:55363188 original size:20 final size:21
Alignment explanation
Indices: 55363140--55363192 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
55363130 TAATCCTTAT
*
55363140 ACCTAATTAACCTTAATTTAA
1 ACCTAATTAACCTTAATTAAA
*
55363161 A-CTAAATTCA-CTTAATTAAA
1 ACCT-AATTAACCTTAATTAAA
55363181 ACCTAATTAACC
1 ACCTAATTAACC
55363193 ACTCGATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (21 bp):
ACCTAATTAACCTTAATTAAA
Found at i:55363531 original size:16 final size:16
Alignment explanation
Indices: 55363510--55363541 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55363500 AAAATAAACT
55363510 CAATTAAACAATGAAA
1 CAATTAAACAATGAAA
55363526 CAATTAAACAATGAAA
1 CAATTAAACAATGAAA
55363542 ATATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
CAATTAAACAATGAAA
Found at i:55365094 original size:14 final size:14
Alignment explanation
Indices: 55365075--55365103 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55365065 AACTCGAAGG
55365075 ATTGAACATTGGAT
1 ATTGAACATTGGAT
55365089 ATTGAACATTGGAT
1 ATTGAACATTGGAT
55365103 A
1 A
55365104 ATCTTTTTAT
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:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (14 bp):
ATTGAACATTGGAT
Found at i:55368151 original size:15 final size:14
Alignment explanation
Indices: 55368133--55368163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
55368123 TTAATTTATT
55368133 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
55368148 TAATAATAATCTAA
1 TAATAATAATCTAA
55368162 TA
1 TA
55368164 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:55368174 original size:21 final size:20
Alignment explanation
Indices: 55368150--55368218 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
55368140 AATGCTAATA
55368150 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
55368171 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
55368190 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
55368211 ATAATAAT
1 ATAATAAT
55368219 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:55373261 original size:16 final size:16
Alignment explanation
Indices: 55373227--55373283 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 16
55373217 TGCAATATAT
*
55373227 ATATAAATAATTTA-AA
1 ATATAAA-AATTTATTA
55373243 ATATAAAAATTTATTA
1 ATATAAAAATTTATTA
55373259 ATATGTATATAAATTTATTA
1 ATA--TA-A-AAATTTATTA
55373279 ATATA
1 ATATA
55373284 TGTAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
18 4 0.11
19 1 0.03
20 13 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATAAAAATTTATTA
Found at i:55373284 original size:22 final size:20
Alignment explanation
Indices: 55373244--55373292 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
55373234 TAATTTAAAA
55373244 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
55373264 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
55373284 TGTAAAAAT
1 TATAAAAAT
55373293 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:55375168 original size:17 final size:17
Alignment explanation
Indices: 55375143--55375185 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
55375133 GGACCCTAAA
*
55375143 AATACTTTTACACGAGT
1 AATAATTTTACACGAGT
* *
55375160 AATAATTTTTACATGGGT
1 AATAA-TTTTACACGAGT
55375178 AATAATTT
1 AATAATTT
55375186 ATCTCCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAATTTTACACGAGT
Found at i:55375171 original size:18 final size:18
Alignment explanation
Indices: 55375148--55375185 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55375138 CTAAAAATAC
55375148 TTTTACACGAGTAATAAT
1 TTTTACACGAGTAATAAT
* *
55375166 TTTTACATGGGTAATAAT
1 TTTTACACGAGTAATAAT
55375184 TT
1 TT
55375186 ATCTCCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (18 bp):
TTTTACACGAGTAATAAT
Found at i:55404547 original size:3 final size:3
Alignment explanation
Indices: 55404539--55404564 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55404529 ATCACATGTT
55404539 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
55404565 TGTGTGTAAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55404751 original size:73 final size:74
Alignment explanation
Indices: 55404569--55404751 Score: 350
Period size: 74 Copynumber: 2.5 Consensus size: 74
55404559 ATTATTTGTG
*
55404569 TGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
55404634 TTAAGTGGA
66 TTAAGTGGA
55404643 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA-TT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
55404707 TTAAGTGGA
66 TTAAGTGGA
55404716 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
55404752 GTCAAGTTGT
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 47 0.44
74 61 0.56
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (74 bp):
TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
TTAAGTGGA
Found at i:55409163 original size:73 final size:74
Alignment explanation
Indices: 55408981--55409163 Score: 350
Period size: 74 Copynumber: 2.5 Consensus size: 74
55408971 ATTATTTGGG
*
55408981 TGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
55409046 TTAAGTGGA
66 TTAAGTGGA
55409055 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA-TT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
55409119 TTAAGTGGA
66 TTAAGTGGA
55409128 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
55409164 GTCAAGTTGT
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 47 0.44
74 61 0.56
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (74 bp):
TGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTATTT
TTAAGTGGA
Found at i:55428125 original size:46 final size:47
Alignment explanation
Indices: 55428051--55428161 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 47
55428041 GTACCCATAC
* * * *
55428051 CATGGCCCCGTAGCCAAATCAATGTAACT-TATCCGAAGAACTATTAT
1 CATGG-CCCGAAGCCAAATCAATATAACTCCATCCGAAGAACTAATAT
** **
55428098 CATGGCCCGAAGCCAAATCGGTATAACTCGCATCCGAAGTGCTAATAT
1 CATGGCCCGAAGCCAAATCAATATAACTC-CATCCGAAGAACTAATAT
*
55428146 CATGGCCTGAAGCCAA
1 CATGGCCCGAAGCCAA
55428162 CTCTACTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
46 19 0.36
47 5 0.09
48 29 0.55
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (47 bp):
CATGGCCCGAAGCCAAATCAATATAACTCCATCCGAAGAACTAATAT
Found at i:55430007 original size:26 final size:26
Alignment explanation
Indices: 55429970--55430027 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
55429960 TAATACAAAT
55429970 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
55429996 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
55430022 TGATAA
1 TGATAA
55430028 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:55451061 original size:28 final size:28
Alignment explanation
Indices: 55451025--55451081 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
55451015 CTGAAATCAG
*
55451025 AGTAAGCATCAGAAAGTCTAGACACAGA
1 AGTAAGCATCAGAAAGTCTAAACACAGA
55451053 AGTAAGCATCAGAAAGTCTAAACACAGA
1 AGTAAGCATCAGAAAGTCTAAACACAGA
55451081 A
1 A
55451082 CTCCATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (28 bp):
AGTAAGCATCAGAAAGTCTAAACACAGA
Found at i:55459184 original size:19 final size:19
Alignment explanation
Indices: 55459160--55459199 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
55459150 ATTATTTTTG
55459160 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
55459179 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
55459198 AT
1 AT
55459200 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:55473453 original size:21 final size:21
Alignment explanation
Indices: 55473427--55473467 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55473417 ACAAGTACGA
55473427 ATACTTACCGTAAGCAAAATT
1 ATACTTACCGTAAGCAAAATT
*
55473448 ATACTTACCTTAAGCAAAAT
1 ATACTTACCGTAAGCAAAAT
55473468 ATAAACAAAT
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:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (21 bp):
ATACTTACCGTAAGCAAAATT
Found at i:55474864 original size:18 final size:18
Alignment explanation
Indices: 55474846--55475039 Score: 217
Period size: 18 Copynumber: 10.8 Consensus size: 18
55474836 TTAGTATTAA
* *
55474846 TCAGTTATTCAGTAATAA
1 TCAGTTATTCAGTAACAG
*
55474864 TCATTTATTCAGTAACAG
1 TCAGTTATTCAGTAACAG
* *
55474882 TCATTTATTCAGTCACAG
1 TCAGTTATTCAGTAACAG
* * * *
55474900 TCAATTATCCAGTAATAA
1 TCAGTTATTCAGTAACAG
*
55474918 TCAGTTATTCAGTAATAG
1 TCAGTTATTCAGTAACAG
* *
55474936 TCATTTATTCAGTCACAG
1 TCAGTTATTCAGTAACAG
* * *
55474954 TCATTTATTCAGTAATAA
1 TCAGTTATTCAGTAACAG
55474972 TCAGTTATTCAGTAACAG
1 TCAGTTATTCAGTAACAG
*
55474990 TCATTTATTCAGTAACAG
1 TCAGTTATTCAGTAACAG
* * *
55475008 TTAATTATTCAGTAGCAG
1 TCAGTTATTCAGTAACAG
55475026 TCAGTTATTCAGTA
1 TCAGTTATTCAGTA
55475040 CCTTTATTTT
Statistics
Matches: 149, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 149 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
TCAGTTATTCAGTAACAG
Found at i:55474916 original size:54 final size:54
Alignment explanation
Indices: 55474850--55475039 Score: 299
Period size: 54 Copynumber: 3.5 Consensus size: 54
55474840 TATTAATCAG
*
55474850 TTATTCAGTAATAATCATTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
* * *
55474904 TTATCCAGTAATAATCAGTTATTCAGTAATAGTCATTTATTCAGTCACAGTCAT
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
* *
55474958 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTAACAGTTAA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
** *
55475012 TTATTCAGTAGCAGTCAGTTATTCAGTA
1 TTATTCAGTAATAATCAGTTATTCAGTA
55475040 CCTTTATTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 124 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (54 bp):
TTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAGTCAA
Found at i:55475466 original size:17 final size:18
Alignment explanation
Indices: 55475432--55475466 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55475422 TCAGCTAATC
*
55475432 ATATATATTTTCAGTTCA
1 ATATATATTTTCAATTCA
55475450 ATATATA-TTTCAATTCA
1 ATATATATTTTCAATTCA
55475467 CTTTACATTA
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:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATATATTTTCAATTCA
Found at i:55476305 original size:8 final size:8
Alignment explanation
Indices: 55476287--55476328 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
55476277 AATCCCAATT
55476287 TTTCCTT-
1 TTTCCTTC
55476294 TTTCCTTC
1 TTTCCTTC
55476302 TTTCCTTTC
1 TTTCC-TTC
55476311 TTTTTCCTTC
1 --TTTCCTTC
55476321 TTTCCTTC
1 TTTCCTTC
55476329 CCCTGTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.23
8 13 0.42
9 3 0.10
10 3 0.10
11 5 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTCCTTC
Found at i:55476315 original size:19 final size:19
Alignment explanation
Indices: 55476291--55476327 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
55476281 CCAATTTTTC
55476291 CTTTTTCCTTCTTTCCTTT
1 CTTTTTCCTTCTTTCCTTT
55476310 CTTTTTCCTTCTTTCCTT
1 CTTTTTCCTTCTTTCCTT
55476328 CCCCTGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTTTCCTTCTTTCCTTT
Found at i:55478837 original size:13 final size:13
Alignment explanation
Indices: 55478819--55478843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55478809 CTTAATGGGT
55478819 AATTGAACTTGAA
1 AATTGAACTTGAA
55478832 AATTGAACTTGA
1 AATTGAACTTGA
55478844 TATCGAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:55479057 original size:392 final size:391
Alignment explanation
Indices: 55478321--55479114 Score: 1387
Period size: 392 Copynumber: 2.0 Consensus size: 391
55478311 AAGTGATTTT
55478321 TGGAAAAA-T-TAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
1 TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
55478384 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTAAACTTGAAAATTGAACC
66 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTAAACTTGAAAATTGAACC
* *
55478449 TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTTGAATCAA
131 TGATATCAAAATTTGGGACCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
* * *
55478514 GTCTGGTACATGAAACTAGGCTTGGACTAGACCGATCGGACCTTCACTAGGCTTGGATTGAATCG
196 GTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCTTGGATCGAATCG
*
55478579 GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGTACCTGCGATGGCACCACCGGACACG
261 GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCGATGGCACCACCGGACACG
** *
55478644 ATGGTGACGGCGATGACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
326 ACAGTGACGGCGATAACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
55478709 G
391 G
* * *
55478710 TGGAAAATTTATAATATTGATCAAGTAAAATTAAATCAATCAAATTAATTACAATTAATATGATA
1 TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
* *
55478775 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTTAATGGGTAATTGAACTTGAAAATTGAAC
66 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAAT-GGTAATTAAACTTGAAAATTGAAC
* * *
55478840 TTGATATCGAAATTTGGGACCAAGAACCCAAAATCGAGATCGATACCTAAAAACTAGTCGAATCA
130 CTGATATCAAAATTTGGGACCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCA
*
55478905 AGTCTGGTACGTGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCTTGGATCGAATC
195 AGTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCTTGGATCGAATC
55478970 GGCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCGATGGCACCACCGGACAC
260 GGCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCGATGGCACCACCGGACAC
55479035 GACAGTG-CTGGCGATAACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAG
325 GACAGTGAC-GGCGATAACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAG
55479099 CAG
389 CAG
55479102 TGGAAAAATTATA
1 TGGAAAAATTATA
55479115 CTCTTACCAG
Statistics
Matches: 382, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
389 7 0.02
390 1 0.00
391 92 0.24
392 282 0.74
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (391 bp):
TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTAAACTTGAAAATTGAACC
TGATATCAAAATTTGGGACCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
GTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCTTGGATCGAATCG
GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCGATGGCACCACCGGACACG
ACAGTGACGGCGATAACGATGACAGCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
G
Found at i:55481373 original size:20 final size:21
Alignment explanation
Indices: 55481340--55481380 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
55481330 ATAAAAGTAC
55481340 AATAGGTATCGATACTTTTTG
1 AATAGGTATCGATACTTTTTG
*
55481361 AATA-GTATTGATACTTTTTG
1 AATAGGTATCGATACTTTTTG
55481381 CTTTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (21 bp):
AATAGGTATCGATACTTTTTG
Found at i:55497282 original size:12 final size:12
Alignment explanation
Indices: 55497265--55497291 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55497255 TTGTCTCTTA
55497265 AGTTTATTCATT
1 AGTTTATTCATT
55497277 AGTTTATTCATT
1 AGTTTATTCATT
55497289 AGT
1 AGT
55497292 ATTTAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (12 bp):
AGTTTATTCATT
Found at i:55497735 original size:13 final size:13
Alignment explanation
Indices: 55497719--55497743 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55497709 TGTTATGGAA
55497719 AAGTGCTTTTGAG
1 AAGTGCTTTTGAG
55497732 AAGTGCTTTTGA
1 AAGTGCTTTTGA
55497744 AAATTTTAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
AAGTGCTTTTGAG
Found at i:55497745 original size:26 final size:26
Alignment explanation
Indices: 55497685--55497746 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
55497675 TTTGGCAATA
*
55497685 CTTTTGAAAAGTGTTTTTAAAAAGTG
1 CTTTTGAAAAGTGCTTTTAAAAAGTG
* * *
55497711 -TTATGGAAAAGTGCTTTTGAGAAGTG
1 CTT-TTGAAAAGTGCTTTTAAAAAGTG
55497737 CTTTTGAAAA
1 CTTTTGAAAA
55497747 TTTTAGGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.07
26 25 0.86
27 2 0.07
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (26 bp):
CTTTTGAAAAGTGCTTTTAAAAAGTG
Found at i:55499359 original size:24 final size:23
Alignment explanation
Indices: 55499321--55499375 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
55499311 AATACATGTT
*
55499321 CATAATAT-ATATAAAACGTATA
1 CATAATATAATATAAAACATATA
* *
55499343 TATAATATAATATTAAAACATTTA
1 CATAATATAATA-TAAAACATATA
55499367 CATAATATA
1 CATAATATA
55499376 TACACATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 7 0.26
23 3 0.11
24 17 0.63
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CATAATATAATATAAAACATATA
Found at i:55499452 original size:21 final size:18
Alignment explanation
Indices: 55499408--55499452 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
55499398 AAAAACATAT
55499408 TAATATTAATAATAATAC
1 TAATATTAATAATAATAC
55499426 TAATATTACATAAATATATAC
1 TAATATTA-AT-AATA-ATAC
*
55499447 TTATAT
1 TAATAT
55499453 ATATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 4 0.17
21 9 0.39
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATTAATAATAATAC
Found at i:55499972 original size:3 final size:3
Alignment explanation
Indices: 55499964--55500028 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
55499954 GAGTACATAC
* *
55499964 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA GAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
55500011 TCAA TAA T-A TAA AAA TAA
1 T-AA TAA TAA TAA TAA TAA
55500029 CAAGGATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.08
3 47 0.89
4 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:55501860 original size:45 final size:44
Alignment explanation
Indices: 55501796--55501895 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
55501786 TTCTTTTGCG
** * * *
55501796 ACTTCAGAAAGACAAGATTTG-ATATCCTTGATCAGCTCCCCTGCA
1 ACTTCAGGGAGACAAGATTTGCA-A-CCTTGACCAGCTCCACTACA
* *
55501841 ACTTCAGGGAGACAAGATTTGCAACTTTGACCTGCTCCACTACA
1 ACTTCAGGGAGACAAGATTTGCAACCTTGACCAGCTCCACTACA
55501885 ACTTCAGGGAG
1 ACTTCAGGGAG
55501896 GCCAAATCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
44 26 0.55
45 20 0.43
46 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
ACTTCAGGGAGACAAGATTTGCAACCTTGACCAGCTCCACTACA
Found at i:55502163 original size:14 final size:14
Alignment explanation
Indices: 55502140--55502170 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55502130 AGTTGATTTA
*
55502140 AAAAATATAAATTG
1 AAAAACATAAATTG
55502154 AAAAACATAAATTG
1 AAAAACATAAATTG
55502168 AAA
1 AAA
55502171 TTACCTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAAACATAAATTG
Found at i:55502338 original size:82 final size:82
Alignment explanation
Indices: 55502189--55502339 Score: 198
Period size: 82 Copynumber: 1.8 Consensus size: 82
55502179 GCGTGCCCCG
* * * * * **
55502189 AGGCTCAACTCACCTCTCACAATATGAGTTGGTCTTTTTGAAACTTAATTTGAAAAGTAGATTTT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGGTATTTTTGAAACATAAATTAAAAAGCAGAAATT
55502254 GAAAAACAGAAATTAAA
66 GAAAAACAGAAATTAAA
*
55502271 AGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAGCATAAATTAAAAAGCAGAAA
1 AGGCTCAACTCACCTCTCACAATATGAGTTGGTATTTTTG-AAA-CATAAATTAAAAAGCAGAAA
55502334 TTGAAA
64 TTGAAA
55502340 TTACCTCAGC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 6 0.10
81 4 0.07
82 49 0.83
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (82 bp):
AGGCTCAACTCACCTCTCACAATATGAGTTGGTATTTTTGAAACATAAATTAAAAAGCAGAAATT
GAAAAACAGAAATTAAA
Found at i:55502381 original size:87 final size:88
Alignment explanation
Indices: 55502000--55502400 Score: 405
Period size: 87 Copynumber: 4.6 Consensus size: 88
55501990 AAAAGTAGAT
* * * * *
55502000 CTCAGCGTGCCCCGAGGCTTAACTTACCTCTCGTAATATGAGTTGATTTTTGAAAAATATAGATT
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
*
55502065 GGAAAAAAGCAGAAATTGAAAATAC
66 -G-AAAAAGCAGAAATTGAAATTAC
** * * *
55502090 CTCAGCGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTAAAAAATATAAATT
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
*
55502153 GAAAAA-CATAAATTGAAATTAC
66 GAAAAAGCAGAAATTGAAATTAC
* * * *
55502175 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGGTCTTTTTG--AAACTTAAT
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAACATAAA
* **
55502238 TTG-AAAAGTAGATTTTGAAA--A-
64 TTGAAAAAGCAGAAATTGAAATTAC
* ** **** *
55502259 -ACAGAAAT--TAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCATAAAT
1 CTCAG-CGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAAT
55502321 T-AAAAAGCAGAAATTGAAATTAC
65 TGAAAAAGCAGAAATTGAAATTAC
* *
55502344 CTCAGCGTGCCCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
55502401 AAATGGAATT
Statistics
Matches: 249, Mismatches: 47, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
80 6 0.02
81 1 0.00
82 51 0.20
83 3 0.01
84 2 0.01
85 56 0.22
86 13 0.05
87 59 0.24
88 15 0.06
89 3 0.01
90 40 0.16
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (88 bp):
CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
GAAAAAGCAGAAATTGAAATTAC
Found at i:55505954 original size:11 final size:12
Alignment explanation
Indices: 55505937--55505967 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
55505927 TAAATGATAT
55505937 TTTATTATTTTA
1 TTTATTATTTTA
55505949 -TTATTATTTTA
1 TTTATTATTTTA
55505960 TTTATTAT
1 TTTATTAT
55505968 ATATAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:55508162 original size:46 final size:46
Alignment explanation
Indices: 55508109--55508428 Score: 421
Period size: 46 Copynumber: 7.0 Consensus size: 46
55508099 GCTCTCTGAA
* *
55508109 ATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
55508155 ATGAAATGTA-TAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATG-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
55508201 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** ** * *
55508247 GGGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
55508293 ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACTTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
55508339 ATGAAAAG-GATAAGACCATGGTTGAAAAATACCATGGCAACATGAC
1 ATGAAATGAG-TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
55508385 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
55508429 TCAAAGATAA
Statistics
Matches: 243, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.00
46 241 0.99
47 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:55519237 original size:16 final size:15
Alignment explanation
Indices: 55519213--55519264 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
55519203 AATTAAGACC
55519213 TTTTAAAATTTAAAAA
1 TTTT-AAATTTAAAAA
* *
55519229 TTATTAAATATATAAA
1 TT-TTAAATTTAAAAA
*
55519245 TTTTAAAATTATAAAA
1 TTTTAAATTTA-AAAA
55519261 TTTT
1 TTTT
55519265 TATTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 7 0.24
16 20 0.69
17 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAATTTAAAAA
Found at i:55530592 original size:38 final size:37
Alignment explanation
Indices: 55530550--55530626 Score: 88
Period size: 38 Copynumber: 2.0 Consensus size: 37
55530540 AATTTGAATC
55530550 AATAT-TAAACTAATA-AAATATTATTATT-AATTTTATAA
1 AATATATAAA-TAATAGAAA-ATTATT-TTAAATTTT-TAA
55530588 AATATATAAATAATATGAAAATTATTTTAAATTTTTAA
1 AATATATAAATAATA-GAAAATTATTTTAAATTTTTAA
55530626 A
1 A
55530627 TGATAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
38 16 0.46
39 16 0.46
40 3 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
AATATATAAATAATAGAAAATTATTTTAAATTTTTAA
Found at i:55532309 original size:11 final size:12
Alignment explanation
Indices: 55532279--55532311 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
55532269 CGACCCGCCA
55532279 ATATTAATTTTT
1 ATATTAATTTTT
55532291 ATATTAATTTTT
1 ATATTAATTTTT
55532303 ATA-TAATTT
1 ATATTAATTT
55532312 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:55532469 original size:30 final size:30
Alignment explanation
Indices: 55532435--55532497 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
55532425 ATTTAACAAG
55532435 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
55532465 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
55532495 CAA
1 CAA
55532498 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:55532582 original size:22 final size:22
Alignment explanation
Indices: 55532535--55532584 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
55532525 TAATAACAAC
* *
55532535 AAAATACTAGCAACATAATAGT
1 AAAATACTAGCAAAATAAGAGT
*
55532557 AAAATAGTAGCAAAATAAGGAG-
1 AAAATACTAGCAAAATAA-GAGT
55532579 AAAATA
1 AAAATA
55532585 ACAAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.60, C:0.08, G:0.14, T:0.18
Consensus pattern (22 bp):
AAAATACTAGCAAAATAAGAGT
Found at i:55533160 original size:15 final size:14
Alignment explanation
Indices: 55533136--55533171 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
55533126 ATAAGAGTAT
55533136 AATAAAATATTTAA
1 AATAAAATATTTAA
55533150 AATATAAATATTTAA
1 AATA-AAATATTTAA
55533165 AATAAAA
1 AATAAAA
55533172 ATGCGTAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAAATATTTAA
Found at i:55533337 original size:6 final size:6
Alignment explanation
Indices: 55533326--55533359 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
55533316 ACGAGTCATG
*
55533326 AACCTA AACCTA AACCTA AACCTA GACCTA AACC
1 AACCTA AACCTA AACCTA AACCTA AACCTA AACC
55533360 GAACTGGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.35, G:0.03, T:0.15
Consensus pattern (6 bp):
AACCTA
Found at i:55535609 original size:17 final size:19
Alignment explanation
Indices: 55535576--55535610 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
55535566 TAGGATCGTG
55535576 TATTTCTCTAGTAATTTTT
1 TATTTCTCTAGTAATTTTT
55535595 TATTT-TCTA-TAATTTT
1 TATTTCTCTAGTAATTTT
55535611 AAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (19 bp):
TATTTCTCTAGTAATTTTT
Found at i:55538105 original size:22 final size:20
Alignment explanation
Indices: 55538080--55538133 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
55538070 TTTCTTTTTG
55538080 AAAAATAAAATTAATTATATAA
1 AAAAATAAAATTAATT-T-TAA
* *
55538102 AAAAGTAAATTTAATTTTAA
1 AAAAATAAAATTAATTTTAA
55538122 AAAATATAAAAT
1 AAAA-ATAAAAT
55538134 GAGTTATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAATAAAATTAATTTTAA
Found at i:55538131 original size:21 final size:20
Alignment explanation
Indices: 55538075--55538131 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
55538065 CAAGTTTTCT
*
55538075 TTTTGAAAAATA-AAATTAA
1 TTTTAAAAAATATAAATTAA
*
55538094 TTATATAAAAAAGTA-AATTTAA
1 TT-T-TAAAAAA-TATAAATTAA
55538116 TTTTAAAAAATATAAA
1 TTTTAAAAAATATAAA
55538132 ATGAGTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 7 0.23
22 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
TTTTAAAAAATATAAATTAA
Found at i:55544964 original size:18 final size:19
Alignment explanation
Indices: 55544934--55544971 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
55544924 TTTTATTGTA
55544934 TTCTATAATATAATAATAG
1 TTCTATAATATAATAATAG
*
55544953 TTCTAT-ATATAATAGTAG
1 TTCTATAATATAATAATAG
55544971 T
1 T
55544972 ACATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
TTCTATAATATAATAATAG
Found at i:55545218 original size:20 final size:20
Alignment explanation
Indices: 55545151--55545236 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
55545141 ATATTATGTA
* *
55545151 ATATTATATATTTTATTATAAT
1 ATATAATATAGTTTATTAT--T
* *
55545173 ATATAATATAATAATAGTTA-T
1 ATATAATATAGT-TTA-TTATT
55545194 ATATAATAGTAGTTT-TTATT
1 ATATAATA-TAGTTTATTATT
* *
55545214 ATATATTATTGTTTATTATT
1 ATATAATATAGTTTATTATT
55545234 ATA
1 ATA
55545237 CTGATTGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
19 8 0.15
20 16 0.31
21 10 0.19
22 13 0.25
23 2 0.04
24 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATATAATATAGTTTATTATT
Found at i:55545287 original size:240 final size:238
Alignment explanation
Indices: 55544904--55545674 Score: 745
Period size: 240 Copynumber: 3.2 Consensus size: 238
55544894 ATATAATGCC
* * *
55544904 ATATAATGTAATACTATATATTTTATTGTATTCTATAATATAATAATAGTTCTATATATAATAGT
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAG-T-TATATATAATAGT
** ** * * * *
55544969 AG--TACA-T-TAT-TTATTAATTATTATTATATTAGTTGAAATATGTTTTAAGTCCCTATATTT
64 AGTTTTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTT
* *
55545029 TTC-ATACATTTGAAAGTTAACCCTCCTACTATATTATATAATGCTATATCACATCATATAGTAT
129 TTCGA-ACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATA-TAT
*
55545093 ATAATATAGTAATAGTTTATATATATGTATATATGATTGAACATTATA
192 ATAATATA-TAATAGTTTATATATATGTATATATGATTAAACATTATA
* * *
55545141 ATATTATGTAATATTATATATTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAG
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAG
* * *
55545206 TTTTTATTATATATTATTGTTTATTATTATACTGATTGAAATATGCTGTAAGTCCCTATACTATT
66 TTTTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTT
*
55545271 CGAACATTTAAAAGTTAACGCTCCTACTATATTATATAATGCTATATCATATC--ATATAT-TAA
131 CGAACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATATATATAA
* * * * * *
55545333 TA-AT--T--TATATATATACGCATAAATTATTAAATATTATA
196 TATATAATAGTTTATATATATGTATATATGATTAAACATTATA
* * * * *
55545371 ATAGCATGTAATTCTATCTCTTTTATTATAATCTATATTATAATAATAGTTACT-TATAATAGTA
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTA-TATATAATAGTA
55545435 GTACATTATATATTACTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAG
65 G---------T-TT--TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAG
* * * * * * *
55545500 TCCCTATAGTTTTCGTACATTTAAAAATTAGCCCTCCTAC--T-GTATCTAATGCCATATCATAT
118 TCCCTATACTTTTCGAACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATAT
* * * *
55545562 TATCATATA-AT-ATATATTAATAGTTTATATATATATATGCATCGATGACTAAACATTACA
183 CAT-ATATATATAATATA-TAATAGTTTATATATATGTAT--AT--ATGATTAAACATTATA
* * * * * *
55545622 ATATCAAGTAACACTATATCTTTTATTATGATCTATATTTTAATAATAGTTAT
1 ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTAT
55545675 GTATGTATTA
Statistics
Matches: 439, Mismatches: 62, Indels: 53
0.79 0.11 0.10
Matches are distributed among these distances:
230 81 0.18
231 1 0.00
232 1 0.00
234 1 0.00
235 16 0.04
236 6 0.01
237 49 0.11
238 4 0.01
239 22 0.05
240 94 0.21
241 4 0.01
242 88 0.20
243 1 0.00
245 1 0.00
247 11 0.03
249 1 0.00
250 1 0.00
251 57 0.13
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (238 bp):
ATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAG
TTTTTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTT
CGAACATTTAAAAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATATATATAA
TATATAATAGTTTATATATATGTATATATGATTAAACATTATA
Found at i:55545443 original size:16 final size:17
Alignment explanation
Indices: 55545407--55545444 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
55545397 TATAATCTAT
55545407 ATTATAATAATAGTTAC
1 ATTATAATAATAGTTAC
*
55545424 -TTATAATAGTAG-TAC
1 ATTATAATAATAGTTAC
55545439 ATTATA
1 ATTATA
55545445 TATTACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTATAATAATAGTTAC
Found at i:55545492 original size:242 final size:248
Alignment explanation
Indices: 55545209--55545673 Score: 604
Period size: 242 Copynumber: 1.9 Consensus size: 248
55545199 ATAGTAGTTT
*
55545209 TTATTATATATTATTGTTTATTATTATACTGATTGAAATATGCTGTAAGTCCCTATACTATTCGA
1 TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTGTAAGTCCCTATACTATTCGA
* *
55545274 ACATTTAAAAGTTAACGCTCCTACTATAT-T-AT-ATAATGC-TA-TATCATAT-CATATATTAA
66 ACATTTAAAAATTAACCCTCCTACTATATCTAATCAT-AT-CATATTATCATATACATATATTAA
* * * * * ** *
55545333 TA-ATT-TATATATATACGCATAAATTATTAAATATTATAATAGCATGTAATTCTATCTCTTTTA
129 TAGATTATATATATATACGCATAAATGACTAAACATTACAATAGCAAGTAACACTATATCTTTTA
55545396 TTATAATCTATATTATAATAATAGTTACTTATAATAGTAGTACATTATATATTAC
194 TTATAATCTATATTATAATAATAGTTACTTATAATAGTAGTACATTATATATTAC
* * * *
55545451 TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATAGTTTTCGT
1 TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTGTAAGTCCCTATACTATTCGA
* * *
55545516 ACATTTAAAAATTAGCCCTCCTACTGTATCTAATGCCATATCATATTATCATATAATATATATTA
66 ACATTTAAAAATTAACCCTCCTACTATATCTAAT--CATATCATATTATCATAT-ACATATATTA
* * ** *
55545581 ATAGTTTATATATATATATGCATCGATGACTAAACATTACAATATCAAGTAACACTATATCTTTT
128 ATAGATTATATATATATACGCATAAATGACTAAACATTACAATAGCAAGTAACACTATATCTTTT
* *
55545646 ATTATGATCTATATTTTAATAATAGTTA
193 ATTATAATCTATATTATAATAATAGTTA
55545674 TGTATGTATT
Statistics
Matches: 187, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
242 85 0.45
243 1 0.01
244 2 0.01
245 1 0.01
246 4 0.02
247 10 0.05
249 11 0.06
250 2 0.01
251 71 0.38
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (248 bp):
TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTGTAAGTCCCTATACTATTCGA
ACATTTAAAAATTAACCCTCCTACTATATCTAATCATATCATATTATCATATACATATATTAATA
GATTATATATATATACGCATAAATGACTAAACATTACAATAGCAAGTAACACTATATCTTTTATT
ATAATCTATATTATAATAATAGTTACTTATAATAGTAGTACATTATATATTAC
Found at i:55545699 original size:30 final size:26
Alignment explanation
Indices: 55545657--55545733 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 26
55545647 TTATGATCTA
* *
55545657 TATTTTAATAATAGTTATGTATGTATT
1 TATTTTAGTAATAGTTATATAT-TATT
55545684 AATATTTTTAGTAATAGTTATATATTATT
1 --TA-TTTTAGTAATAGTTATATATTATT
*
55545713 TATTTTATGTAATAGTAATAT
1 TATTTTA-GTAATAGTTATAT
55545734 TCTAATTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 5 0.12
27 14 0.33
29 6 0.14
30 18 0.42
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (26 bp):
TATTTTAGTAATAGTTATATATTATT
Found at i:55545724 original size:27 final size:29
Alignment explanation
Indices: 55545655--55545733 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 29
55545645 TATTATGATC
* *
55545655 TATATTTTA-ATAATAGTTATGTATGTAT
1 TATATTTTATGTAATAGTTATATATGTAT
55545683 TAATATTTT-TAGTAATAGTTATATAT-TAT
1 T-ATATTTTAT-GTAATAGTTATATATGTAT
*
55545712 T-TATTTTATGTAATAGTAATAT
1 TATATTTTATGTAATAGTTATAT
55545734 TCTAATTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 18 0.41
28 2 0.05
29 11 0.25
30 13 0.30
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (29 bp):
TATATTTTATGTAATAGTTATATATGTAT
Found at i:55545871 original size:23 final size:25
Alignment explanation
Indices: 55545822--55545871 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
55545812 CATTAAAGTT
* *
55545822 TAATTTTATATATTTTAATAATTAA
1 TAATTTTATATAGTTTAATAATAAA
*
55545847 TAATTTTATAT-GTTT-ATTATAAA
1 TAATTTTATATAGTTTAATAATAAA
55545870 TA
1 TA
55545872 TATAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TAATTTTATATAGTTTAATAATAAA
Found at i:55550912 original size:17 final size:16
Alignment explanation
Indices: 55550892--55550937 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
55550882 AAAGTAAAAC
*
55550892 AAAAGAAAAAGAGATAG
1 AAAAGAAACAGAGAT-G
55550909 AAAAGAAACAGA-ATG
1 AAAAGAAACAGAGATG
*
55550924 AAACGAAACAGAGA
1 AAAAGAAACAGAGA
55550938 GCAAGGAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 12 0.46
16 3 0.12
17 11 0.42
ACGTcount: A:0.67, C:0.07, G:0.22, T:0.04
Consensus pattern (16 bp):
AAAAGAAACAGAGATG
Found at i:55552768 original size:18 final size:18
Alignment explanation
Indices: 55552747--55552923 Score: 135
Period size: 18 Copynumber: 9.7 Consensus size: 18
55552737 TAACTGATTA
55552747 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
55552765 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
* * * *
55552783 TTACTGAATAACTAAATA
1 TTACTGAATAATTGACTG
55552801 TTACTGAATAATTGA-TCG
1 TTACTGAATAATTGACT-G
* *
55552819 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
* *
55552837 TCACTGAACGAA-TGACTG
1 TTACTGAA-TAATTGACTG
* * *
55552855 TTATTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
* *
55552874 TTACTGAATACCTCCTGA-TT
1 TTACTGAATA-AT--TGACTG
55552894 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
55552912 TTACTGGATAAT
1 TTACTGAATAAT
55552924 CGATCAATTG
Statistics
Matches: 123, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
17 6 0.05
18 86 0.70
19 18 0.15
20 11 0.09
21 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:55552843 original size:54 final size:54
Alignment explanation
Indices: 55552735--55552844 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
55552725 AAAGGTATAA
* * * * *
55552735 AATAACTGATTATTACTGAATAATTGACTGTTACCGGATAATTGACTGTTACTG
1 AATAACTAAATATTACTGAATAATTGACTGTTACCGAATAACTGACTGTCACTG
* *
55552789 AATAACTAAATATTACTGAATAATTGA-TCGTTACTGAATAACTGATTGTCACTG
1 AATAACTAAATATTACTGAATAATTGACT-GTTACCGAATAACTGACTGTCACTG
55552843 AA
1 AA
55552845 CGAATGACTG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 47 0.98
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (54 bp):
AATAACTAAATATTACTGAATAATTGACTGTTACCGAATAACTGACTGTCACTG
Found at i:55552985 original size:22 final size:22
Alignment explanation
Indices: 55552942--55552992 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
55552932 TGATCGATAC
** *
55552942 TGAATAACTGGTTATTATTGAA
1 TGAATAACTGACTATTACTGAA
*
55552964 TGAATAACTGACTGTTACTGAA
1 TGAATAACTGACTATTACTGAA
*
55552986 TAAATAA
1 TGAATAA
55552993 TTGTTCTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (22 bp):
TGAATAACTGACTATTACTGAA
Found at i:55554931 original size:28 final size:28
Alignment explanation
Indices: 55554893--55554989 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
55554883 TCCCCTATCT
*
55554893 TTTAGATTTTATAGTATTGCTCATGTTC
1 TTTAGATTTTATAGTTTTGCTCATGTTC
* * *
55554921 TTTAGATTTTACAGTTTTGCCCTCCTATT-
1 TTTAGATTTTATAGTTTTG--CTCATGTTC
* *
55554950 TTTCAAATTTTATAGTTTTGCTCTTGTTC
1 TTT-AGATTTTATAGTTTTGCTCATGTTC
*
55554979 TTCAGATTTTA
1 TTTAGATTTTA
55554990 CAATTTCTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
28 30 0.55
29 5 0.09
30 20 0.36
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (28 bp):
TTTAGATTTTATAGTTTTGCTCATGTTC
Found at i:55555014 original size:27 final size:26
Alignment explanation
Indices: 55554982--55555140 Score: 140
Period size: 27 Copynumber: 5.7 Consensus size: 26
55554972 CTTGTTCTTC
55554982 AGATTTTACAATTTCT-CCCTAGTTTTT
1 AGATTTTACAATTT-TACCCTA-TTTTT
*
55555009 AGATTTTACAATTTTACCTCTATTCTTC
1 AGATTTTACAATTTTACC-CTATT-TTT
* * *
55555037 AAATTTTACAGTTTTGCCCCTATTTTT
1 AGATTTTACAATTTT-ACCCTATTTTT
* *
55555064 AAATTTTACAATTTTGCCCATATTTTTTT
1 AGATTTTACAATTTTACCC-TA--TTTTT
*
55555093 ATATTTTACAATTTTACCCCTATTTTT
1 AGATTTTACAATTTTA-CCCTATTTTT
*
55555120 CAGATTTGACAATTTTGACCC
1 -AGATTTTACAATTTT-ACCC
55555141 AAAATTTTAT
Statistics
Matches: 111, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.04
27 41 0.37
28 39 0.35
29 24 0.22
30 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (26 bp):
AGATTTTACAATTTTACCCTATTTTT
Found at i:55555043 original size:55 final size:55
Alignment explanation
Indices: 55554976--55555141 Score: 176
Period size: 55 Copynumber: 2.9 Consensus size: 55
55554966 TTTGCTCTTG
*
55554976 TTCTTCAGATTTTACAA-TTTCTCCCTAGTTTTTAGATTTTACAATTTTACCTC-TA-
1 TTCTTCAAATTTTACAATTTTC-CCCTA-TTTTTAGATTTTACAATTTTACC-CATAT
* * *
55555031 TTCTTCAAATTTTACAGTTTTGCCCCTATTTTTAAATTTTACAATTTTGCCCATAT
1 TTCTTCAAATTTTACAATTTT-CCCCTATTTTTAGATTTTACAATTTTACCCATAT
* * * *
55555087 TTTTTTATATTTTACAATTTTACCCCTATTTTTCAGATTTGACAATTTTGACCCA
1 TTCTTCAAATTTTACAATTTT-CCCCTATTTTT-AGATTTTACAATTTT-ACCCA
55555142 AAATTTTATA
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
54 1 0.01
55 38 0.41
56 36 0.39
57 14 0.15
58 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.51
Consensus pattern (55 bp):
TTCTTCAAATTTTACAATTTTCCCCTATTTTTAGATTTTACAATTTTACCCATAT
Found at i:55555051 original size:28 final size:26
Alignment explanation
Indices: 55554926--55555135 Score: 109
Period size: 28 Copynumber: 7.5 Consensus size: 26
55554916 TGTTCTTTAG
*
55554926 ATTTTACAGTTTTGCCCTCCTATTTTTCAA
1 ATTTTACAATTTT--CCT-CTA-TTTTCAA
* * * * *
55554956 ATTTTATAGTTTTGCTCTTGTTCTTCAG
1 ATTTTACAATTTTCCTC-TATT-TTCAA
* *
55554984 ATTTTACAATTTCTCC-CTAGTTTTTAG
1 ATTTTACAATTT-TCCTCTA-TTTTCAA
55555011 ATTTTACAATTTTACCTCTATTCTTCAA
1 ATTTTACAATTTT-CCTCTATT-TTCAA
* * *
55555039 ATTTTACAGTTTTGCCCCTATTTTTAA
1 ATTTTACAATTTT-CCTCTATTTTCAA
* *
55555066 ATTTTACAATTTTGCC-CATATTTTTTTAT
1 ATTTTACAATTTT-CCTC-TA--TTTTCAA
* *
55555095 ATTTTACAATTTTACCCCTATTTTTCAG
1 ATTTTACAATTTT-CCTCTA-TTTTCAA
*
55555123 ATTTGACAATTTT
1 ATTTTACAATTTT
55555136 GACCCAAAAT
Statistics
Matches: 148, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.01
27 45 0.30
28 63 0.43
29 25 0.17
30 13 0.09
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (26 bp):
ATTTTACAATTTTCCTCTATTTTCAA
Found at i:55555116 original size:84 final size:83
Alignment explanation
Indices: 55554921--55555136 Score: 238
Period size: 84 Copynumber: 2.6 Consensus size: 83
55554911 GCTCATGTTC
* * * * * * *
55554921 TTTAGATTTTACAGTTTTGCCCTCCTATTTTTCAAATTTTATAGTTTTGCTCTTGTTCTTCAGAT
1 TTTAGATTTTACAATTTT-ACC-CCTATTTTTCAAATTTTACAGTTTTGCCCCTATTCTTCAAAT
55554986 TTTACAATTTCTCCCTAGTT
64 TTTACAATTTCTCCCTAGTT
* * *
55555006 TTTAGATTTTACAATTTTACCTCTATTCTTCAAATTTTACAGTTTTGCCCCTATT-TTTAAATTT
1 TTTAGATTTTACAATTTTACCCCTATTTTTCAAATTTTACAGTTTTGCCCCTATTCTTCAAATTT
*
55555070 TACAATTT-TGCCCATATTTT
66 TACAATTTCT-CCC-TA-GTT
* * * *
55555090 TTTATATTTTACAATTTTACCCCTATTTTTCAGATTTGACAATTTTG
1 TTTAGATTTTACAATTTTACCCCTATTTTTCAAATTTTACAGTTTTG
55555137 ACCCAAAATT
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 18 0.16
83 30 0.27
84 45 0.41
85 17 0.15
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.53
Consensus pattern (83 bp):
TTTAGATTTTACAATTTTACCCCTATTTTTCAAATTTTACAGTTTTGCCCCTATTCTTCAAATTT
TACAATTTCTCCCTAGTT
Found at i:55555149 original size:56 final size:56
Alignment explanation
Indices: 55555039--55555151 Score: 140
Period size: 56 Copynumber: 2.0 Consensus size: 56
55555029 TATTCTTCAA
* * * **
55555039 ATTTTACAGTTTTGCCCCTATTTTTAAATTTTACAATTTTGCCCATATTTTTTTAT
1 ATTTTACAATTTTACCCCTATTTTTAAATTTGACAATTTTGCCCATATAATTTTAT
*
55555095 ATTTTACAATTTTACCCCTATTTTTCAGATTTGACAATTTTGACCCA-A-AATTTTAT
1 ATTTTACAATTTTACCCCTATTTTT-AAATTTGACAATTTTG-CCCATATAATTTTAT
55555151 A
1 A
55555152 GATTGACCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 30 0.61
57 15 0.31
58 4 0.08
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.50
Consensus pattern (56 bp):
ATTTTACAATTTTACCCCTATTTTTAAATTTGACAATTTTGCCCATATAATTTTAT
Found at i:55555678 original size:20 final size:20
Alignment explanation
Indices: 55555653--55555690 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55555643 AATGTTGTTT
55555653 TTAAAATTATAAAAAAATAA
1 TTAAAATTATAAAAAAATAA
* *
55555673 TTAAAATTTTATAAAAAT
1 TTAAAATTATAAAAAAAT
55555691 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAATTATAAAAAAATAA
Found at i:55555698 original size:20 final size:20
Alignment explanation
Indices: 55555655--55555698 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
55555645 TGTTGTTTTT
*
55555655 AAAATTATAAAAAAATAATT
1 AAAATTATAAAAAAATAATA
* * *
55555675 AAAATTTTATAAAAATTATA
1 AAAATTATAAAAAAATAATA
55555695 AAAA
1 AAAA
55555699 AATAAAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTATAAAAAAATAATA
Found at i:55557660 original size:22 final size:22
Alignment explanation
Indices: 55557635--55557676 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55557625 GTAATTACAC
* * *
55557635 ATAAAATATATATTATATTAAA
1 ATAAAAAATAGATTAAATTAAA
55557657 ATAAAAAATAGATTAAATTA
1 ATAAAAAATAGATTAAATTA
55557677 TATGTAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAAAATAGATTAAATTAAA
Found at i:55563047 original size:26 final size:27
Alignment explanation
Indices: 55562992--55563055 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
55562982 AATAAATTAT
*
55562992 TTATTATATACTATAAATATAAAAACA
1 TTATTATATAATATAAATATAAAAACA
* *
55563019 TTATTA-ATAATATAATTTATAAGAA-A
1 TTATTATATAATATAA-ATATAAAAACA
55563045 TTATATATATA
1 TTAT-TATATA
55563056 CTAAATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 13 0.42
27 15 0.48
28 3 0.10
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (27 bp):
TTATTATATAATATAAATATAAAAACA
Found at i:55568091 original size:46 final size:43
Alignment explanation
Indices: 55568041--55568129 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
55568031 CGCTGTAATG
55568041 GAATAGAACTGTAATAAGTAATTCAATTG-TTTGGTTGAATGAAATA
1 GAATAGAACTGTAAT-AGT-ATTC--TTGATTTGGTTGAATGAAATA
*
55568087 GAATAGAACTGTAATGGTATTCTTGTATTTGGTTGAATGAAAT
1 GAATAGAACTGTAATAGTATTCTTG-ATTTGGTTGAATGAAAT
55568130 GATGTTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 3 0.08
44 20 0.50
45 2 0.05
46 15 0.38
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (43 bp):
GAATAGAACTGTAATAGTATTCTTGATTTGGTTGAATGAAATA
Found at i:55568305 original size:16 final size:18
Alignment explanation
Indices: 55568236--55568299 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 18
55568226 ATTATTATTA
55568236 AATTTAATA-ATAAATAAT
1 AATTTAATACATAAAT-AT
55568254 AATTTAATCACATTTAAATAT
1 AATTTAAT-ACA--TAAATAT
*
55568275 AA-TTATTAC-TAAATAT
1 AATTTAATACATAAATAT
55568291 AATTTAATA
1 AATTTAATA
55568300 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 9 0.23
17 5 0.13
18 8 0.21
19 3 0.08
20 5 0.13
21 4 0.10
22 5 0.13
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAATACATAAATAT
Found at i:55569737 original size:63 final size:63
Alignment explanation
Indices: 55569638--55569763 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
55569628 CATGGAGATT
* *
55569638 TTCTTATCACATCAAGAATGAGGCGCATCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
1 TTCTTATCACATCAAGAAGGAGGCGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
* *
55569701 TTCTTATCACATCGAGAAGGAGGTGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
1 TTCTTATCACATCAAGAAGGAGGCGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
55569764 AATTAGGTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (63 bp):
TTCTTATCACATCAAGAAGGAGGCGCAGCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
Found at i:55572036 original size:21 final size:22
Alignment explanation
Indices: 55571992--55572042 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
55571982 TTTCCTGCAT
55571992 TTAAACACATTAAATTGAACTTA
1 TTAAACACATTAAA-TGAACTTA
* *
55572015 TTAAACACATTTAA-GCACTTA
1 TTAAACACATTAAATGAACTTA
*
55572036 TTGAACA
1 TTAAACA
55572043 TGCACTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (22 bp):
TTAAACACATTAAATGAACTTA
Found at i:55575257 original size:24 final size:24
Alignment explanation
Indices: 55575222--55575283 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
55575212 CACTTTTTCC
55575222 TTTC-TTTT-TTTTTCAAT-TTTT
1 TTTCTTTTTCTTTTTCAATCTTTT
*
55575243 TTGTCTTTTTCTTTTTCACTCTTTT
1 TT-TCTTTTTCTTTTTCAATCTTTT
* *
55575268 TTTCTTGTACTTTTTC
1 TTTCTTTTTCTTTTTC
55575284 TTTCACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 4 0.12
24 20 0.59
25 6 0.18
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.74
Consensus pattern (24 bp):
TTTCTTTTTCTTTTTCAATCTTTT
Found at i:55581164 original size:41 final size:41
Alignment explanation
Indices: 55581064--55581196 Score: 117
Period size: 41 Copynumber: 3.2 Consensus size: 41
55581054 TAGCGGCGTT
* * * ** * *
55581064 TGCAAAAGGTCAAGCATTAGCAATGTTTATGAAAAAAAATGC
1 TGCAAAAGATCAAACATTAGCGACATTTATG-ATAAAAACGC
* * * * * *
55581106 CGC-AAAGGTCAAGCATTAGCGGCGTTTATGATAAAAGCGAC
1 TGCAAAAGATCAAACATTAGCGACATTTATGATAAAAACG-C
55581147 -GCAAAAGATCAAACATTAGCGACATTTATGATAAAAACGC
1 TGCAAAAGATCAAACATTAGCGACATTTATGATAAAAACGC
55581187 TGCAAAAGAT
1 TGCAAAAGAT
55581197 ACATTGCAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
40 9 0.12
41 65 0.86
42 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (41 bp):
TGCAAAAGATCAAACATTAGCGACATTTATGATAAAAACGC
Found at i:55581598 original size:21 final size:21
Alignment explanation
Indices: 55581574--55581626 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
55581564 CAGTTGAGGA
* *
55581574 TTTATGATTTATGATTTAGAG
1 TTTAGGATTTAAGATTTAGAG
*
55581595 TTTAGGGTTTAAGATTTAGAG
1 TTTAGGATTTAAGATTTAGAG
* *
55581616 TTCAGGCTTTA
1 TTTAGGATTTA
55581627 GGGTTTAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (21 bp):
TTTAGGATTTAAGATTTAGAG
Found at i:55581633 original size:21 final size:21
Alignment explanation
Indices: 55581581--55581626 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
55581571 GGATTTATGA
* * *
55581581 TTTATGATTTAGAGTTTAGGG
1 TTTAAGATTTAGAGTTCAGGC
55581602 TTTAAGATTTAGAGTTCAGGC
1 TTTAAGATTTAGAGTTCAGGC
55581623 TTTA
1 TTTA
55581627 GGGTTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (21 bp):
TTTAAGATTTAGAGTTCAGGC
Found at i:55583058 original size:23 final size:24
Alignment explanation
Indices: 55583031--55583077 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
55583021 TTCCCCCTAT
*
55583031 TCTTCCATA-ATACTCTTT-CTTTC
1 TCTT-CATATATAATCTTTACTTTC
55583054 TCTTCATATATAATCTTTACTTTC
1 TCTTCATATATAATCTTTACTTTC
55583078 AAGCACCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 12 0.57
24 5 0.24
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (24 bp):
TCTTCATATATAATCTTTACTTTC
Found at i:55584543 original size:9 final size:9
Alignment explanation
Indices: 55584529--55584715 Score: 121
Period size: 9 Copynumber: 20.9 Consensus size: 9
55584519 TTCTTTAAAA
55584529 TTACATAAC
1 TTACATAAC
*
55584538 TTACATACC
1 TTACATAAC
55584547 TTACATAA-
1 TTACATAAC
* * *
55584555 ATATATATC
1 TTACATAAC
*
55584564 ATATCATAAC
1 TTA-CATAAC
*
55584574 TTACATACC
1 TTACATAAC
*
55584583 TCACATAAC
1 TTACATAAC
* *
55584592 ATACCTAAC
1 TTACATAAC
*
55584601 TTACGTAAC
1 TTACATAAC
55584610 TTACATAA-
1 TTACATAAC
55584618 -TACATAA-
1 TTACATAAC
* * *
55584625 ATATATATC
1 TTACATAAC
* *
55584634 ATATCATAAA
1 TTA-CATAAC
55584644 TGTACATAAC
1 T-TACATAAC
*
55584654 TTACATAAT
1 TTACATAAC
*
55584663 TTAAATAAC
1 TTACATAAC
*
55584672 TTACATAAT
1 TTACATAAC
*
55584681 TTTCATAAC
1 TTACATAAC
* *
55584690 TTACATTAT
1 TTACATAAC
55584699 TTACATAAC
1 TTACATAAC
*
55584708 TGACATAA
1 TTACATAA
55584716 ATAAATGCCA
Statistics
Matches: 135, Mismatches: 37, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
7 7 0.05
8 10 0.07
9 101 0.75
10 15 0.11
11 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:55584573 original size:36 final size:36
Alignment explanation
Indices: 55584532--55584661 Score: 140
Period size: 36 Copynumber: 3.6 Consensus size: 36
55584522 TTTAAAATTA
55584532 CATAACTTACATACCTTACATAAATATATATCATAT
1 CATAACTTACATACCTTACATAAATATATATCATAT
* ** * *
55584568 CATAACTTACATACCTCACATAACATACCTAACTTA-
1 CATAACTTACATACCTTACATAA-ATATATATCATAT
* *
55584604 CGTAACTTACATA--ATACATAAATATATATCATAT
1 CATAACTTACATACCTTACATAAATATATATCATAT
* *
55584638 CATAAATGTACATAACTTACATAA
1 CATAACT-TACATACCTTACATAA
55584662 TTTAAATAAC
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
33 8 0.11
34 11 0.15
35 6 0.08
36 34 0.46
37 15 0.20
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (36 bp):
CATAACTTACATACCTTACATAAATATATATCATAT
Found at i:55586421 original size:12 final size:12
Alignment explanation
Indices: 55586404--55586439 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
55586394 AAGATCGATG
*
55586404 GATGAATCTGAT
1 GATGAATCTAAT
55586416 GATGAATCTAAT
1 GATGAATCTAAT
55586428 GATGAATCTAAT
1 GATGAATCTAAT
55586440 AAAGAGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (12 bp):
GATGAATCTAAT
Found at i:55587194 original size:21 final size:20
Alignment explanation
Indices: 55587170--55587208 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
55587160 AATGCACATG
*
55587170 ATATTAAACATGATAATAATA
1 ATATTAAACACGA-AATAATA
55587191 ATATTAAACACGAAATAA
1 ATATTAAACACGAAATAA
55587209 AATCATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (20 bp):
ATATTAAACACGAAATAATA
Found at i:55587394 original size:14 final size:12
Alignment explanation
Indices: 55587367--55587438 Score: 65
Period size: 14 Copynumber: 5.7 Consensus size: 12
55587357 ATATGTACAT
55587367 AATATATATAAA
1 AATATATATAAA
55587379 AATATAGTATTAAA
1 AATATA-TA-TAAA
* *
55587393 AATATATA-CAT
1 AATATATATAAA
*
55587404 AATATAAACTTAAA
1 AATATATA--TAAA
55587418 AATAATATATAAA
1 AAT-ATATATAAA
55587431 AATATATA
1 AATATATA
55587439 CATAATATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 8 0.17
12 11 0.23
13 11 0.23
14 14 0.29
15 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (12 bp):
AATATATATAAA
Found at i:55587437 original size:38 final size:37
Alignment explanation
Indices: 55587345--55587446 Score: 136
Period size: 37 Copynumber: 2.7 Consensus size: 37
55587335 AGGTGCATTA
* * *
55587345 ATAGTATTGAAAATATGTACATAATATATATAAAAAT
1 ATAGTATTAAAAATATATACATAATATAAATAAAAAT
55587382 ATAGTATTAAAAATATATACATAATATAAACTTAAAAAT
1 ATAGTATTAAAAATATATACATAATATAAA--TAAAAAT
55587421 A-A-TATATAAAAATATATACATAATAT
1 ATAGTAT-TAAAAATATATACATAATAT
55587447 CTATTAAAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
37 30 0.51
38 21 0.36
39 8 0.14
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (37 bp):
ATAGTATTAAAAATATATACATAATATAAATAAAAAT
Found at i:55587607 original size:3 final size:3
Alignment explanation
Indices: 55587579--55587751 Score: 54
Period size: 3 Copynumber: 57.0 Consensus size: 3
55587569 AAGCTAAAAC
* * *
55587579 TAA TAC TAA TAA TAG TAA AAA CTAA TAA T-A TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
55587622 T-A TAA T-A TAA AAA TAAA GAA GTAA TAG TAA TAA T-A TGAA GAT TAA
1 TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA
* * * * * * *
55587667 TAA TAG TAA TAG TAA CAA TAA TGA TAA TATA TATG TACA TGAA TAG TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TA-A T-AA TAA TAA
* **
55587716 TAA TAA TAA TAC TAA -AA TAA TTAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
55587752 AGTAATTAAA
Statistics
Matches: 120, Mismatches: 36, Indels: 28
0.65 0.20 0.15
Matches are distributed among these distances:
2 14 0.12
3 86 0.72
4 19 0.16
5 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55587613 original size:5 final size:5
Alignment explanation
Indices: 55587603--55587631 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
55587593 GTAAAAACTA
55587603 ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
55587632 AAATAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:55587740 original size:21 final size:21
Alignment explanation
Indices: 55587716--55587760 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55587706 TGAATAGTAC
*
55587716 TAATAATAATACTAAAATAAT
1 TAATAATAATAATAAAATAAT
** *
55587737 TAATTTTAATAATAAAGTAAT
1 TAATAATAATAATAAAATAAT
55587758 TAA
1 TAA
55587761 AAAAGGATCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATAATAATAATAAAATAAT
Found at i:55588673 original size:21 final size:22
Alignment explanation
Indices: 55588634--55588674 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
55588624 TAGGTATTGA
* *
55588634 GTTATGGGTTTAAGTGTAATGG
1 GTTACGGGTTTAAGGGTAATGG
55588656 GTTACGGG-TTAAGGGTAAT
1 GTTACGGGTTTAAGGGTAAT
55588675 TAGTTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (22 bp):
GTTACGGGTTTAAGGGTAATGG
Found at i:55592846 original size:43 final size:43
Alignment explanation
Indices: 55592775--55592944 Score: 205
Period size: 43 Copynumber: 4.0 Consensus size: 43
55592765 TGCCAAAGTT
* * * *
55592775 AGCGACGTTTGTGGTAAAAGCGCCGCTAAAGATCATGTTCTTC
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
* * *
55592818 AACGGCGTTTGCAATAAAAGCGCTGCTAAAGGTCATGTTCTTC
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
* * * *
55592861 AGCGGCGTTTGCGATAAAAGTGCCGTTAAAGGTCATGTTATTT
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
* * * *
55592904 AGCGGCGTTTGTGATAAAAGTGCCGCTAAAAGTTATGTTCT
1 AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCT
55592945 AATAGTTTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 108 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
AGCGGCGTTTGCGATAAAAGCGCCGCTAAAGGTCATGTTCTTC
Found at i:55593798 original size:24 final size:22
Alignment explanation
Indices: 55593771--55593820 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
55593761 AATTCTTTTA
55593771 TTTTCCTTTTTTACATTATTTC-TC
1 TTTTCC-TTTTT-CATT-TTTCTTC
*
55593795 TTTTTCTTTTTCATTTTTCTTC
1 TTTTCCTTTTTCATTTTTCTTC
55593817 TTTT
1 TTTT
55593821 ATATTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 5 0.21
24 5 0.21
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCCTTTTTCATTTTTCTTC
Found at i:55593804 original size:22 final size:22
Alignment explanation
Indices: 55593779--55593820 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55593769 TATTTTCCTT
55593779 TTTTACATTATTTC-TCTTTTTC
1 TTTTACATT-TTTCTTCTTTTTC
*
55593801 TTTTTCATTTTTCTTCTTTT
1 TTTTACATTTTTCTTCTTTT
55593821 ATATTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTACATTTTTCTTCTTTTTC
Found at i:55594614 original size:31 final size:30
Alignment explanation
Indices: 55594542--55594599 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
55594532 ATATTTTATA
*
55594542 TATCATTATATTAATAATTTAAATATCATT
1 TATCATTATATTAAAAATTTAAATATCATT
55594572 TATCATTATATTAAAAATTTAAA-ATCAT
1 TATCATTATATTAAAAATTTAAATATCAT
55594600 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (30 bp):
TATCATTATATTAAAAATTTAAATATCATT
Found at i:55598367 original size:16 final size:18
Alignment explanation
Indices: 55598342--55598382 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55598332 TTTTAAAAAC
*
55598342 ATTTTGTAA-TTA-TATT
1 ATTTTTTAATTTATTATT
55598358 ATTTTTTAATTTATTATT
1 ATTTTTTAATTTATTATT
55598376 ATTTTTT
1 ATTTTTT
55598383 TGAAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTAATTTATTATT
Found at i:55599578 original size:18 final size:18
Alignment explanation
Indices: 55599552--55599595 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
55599542 AATAGAAGTG
*
55599552 ATAAGTATACATTTAAA-A
1 ATAATTATA-ATTTAAATA
*
55599570 ATAATTATAATTTAAATT
1 ATAATTATAATTTAAATA
55599588 ATAATTAT
1 ATAATTAT
55599596 TAGTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAATTATAATTTAAATA
Found at i:55600836 original size:47 final size:47
Alignment explanation
Indices: 55600761--55600921 Score: 162
Period size: 47 Copynumber: 3.4 Consensus size: 47
55600751 CTGCTTGTGT
* * * * *
55600761 TTGTGGATGAACCACTAGTTGAGCAGATGACTGCCAACTGAAATACA
1 TTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAAAATACA
* * * **
55600808 TTGTGGATAAATCACTGGTCGAGTAGATGACTAG-TGACTAAAATATG
1 TTGTGGATAAACCACTGGTCGAGCAGATGACT-GCCGACTAAAATACA
* * * * * *
55600855 CTGTAGATAAACTACTGGTCGAGCAGATGTCTACCGATTAAAATACA
1 TTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAAAATACA
55600902 TTGTGGATAAACCACTGGTC
1 TTGTGGATAAACCACTGGTC
55600922 AAGAAGATAA
Statistics
Matches: 88, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
47 87 0.99
48 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (47 bp):
TTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAAAATACA
Found at i:55613232 original size:24 final size:26
Alignment explanation
Indices: 55613187--55613239 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
55613177 ATATATACAC
*
55613187 ATAATGTATGAAAATACGTATACAAT
1 ATAATGTATGAAAACACGTATACAAT
* *
55613213 ATAATGT-T-AAAACACTTATATAAT
1 ATAATGTATGAAAACACGTATACAAT
55613237 ATA
1 ATA
55613240 TACATACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 1 0.04
26 7 0.29
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (26 bp):
ATAATGTATGAAAACACGTATACAAT
Found at i:55613858 original size:24 final size:24
Alignment explanation
Indices: 55613814--55613861 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55613804 ACGCATAAAT
*
55613814 AAATAAAATATAATAATAATACTA
1 AAATAAAATATAATAAAAATACTA
*
55613838 AAATAAAGTA-AATAAAAAATACTA
1 AAATAAAATATAAT-AAAAATACTA
55613862 TATATAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (24 bp):
AAATAAAATATAATAAAAATACTA
Found at i:55614355 original size:13 final size:13
Alignment explanation
Indices: 55614339--55614410 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
55614329 AATATTAGCA
55614339 AATATATGTACAT
1 AATATATGTACAT
* *
55614352 AATATATATATAT
1 AATATATGTACAT
* * *
55614365 AAAAAATATACAT
1 AATATATGTACAT
* *
55614378 AATATA-GTATTAA
1 AATATATGTA-CAT
55614391 AATATATGTACAT
1 AATATATGTACAT
55614404 AATATAT
1 AATATAT
55614411 ACTTATTAGA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
12 2 0.04
13 40 0.89
14 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
AATATATGTACAT
Found at i:55614376 original size:26 final size:25
Alignment explanation
Indices: 55614338--55614411 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
55614328 TAATATTAGC
* *
55614338 AAATATATGTACATAATATATATATA
1 AAATAAATATACATAATATATAT-TA
55614364 TAAA-AAATATACATAATATAGTATTA
1 -AAATAAATATACATAATATA-TATTA
* *
55614390 AAATATATGTACATAATATATA
1 AAATAAATATACATAATATATA
55614412 CTTATTAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 5 0.12
26 30 0.73
27 6 0.15
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
AAATAAATATACATAATATATATTA
Found at i:55615005 original size:11 final size:11
Alignment explanation
Indices: 55614991--55615024 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
55614981 AAGAAAAAAA
55614991 GAAGAGAGAAG
1 GAAGAGAGAAG
55615002 GAAGAGAGAAG
1 GAAGAGAGAAG
*
55615013 GGAGAGAGAAG
1 GAAGAGAGAAG
55615024 G
1 G
55615025 GTGGGGAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAG
Found at i:55615461 original size:26 final size:26
Alignment explanation
Indices: 55615432--55615540 Score: 191
Period size: 26 Copynumber: 4.2 Consensus size: 26
55615422 TGGTACAAAT
55615432 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
55615458 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55615484 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
55615510 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55615536 TGATA
1 TGATA
55615541 GGCATTTCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:55617571 original size:137 final size:137
Alignment explanation
Indices: 55617325--55617885 Score: 1041
Period size: 137 Copynumber: 4.1 Consensus size: 137
55617315 GAGTAGTCTC
55617325 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
55617390 TGTTATCTGAATAAAGGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
55617455 ACTGTTA
131 ACTGTTA
55617462 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
55617527 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
*
55617592 ACTTTTA
131 ACTGTTA
*
55617599 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTCTGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
55617664 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
55617729 ACTGTTA
131 ACTGTTA
*
55617736 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTAAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
55617801 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACA
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
55617866 ACTGTTA
131 ACTGTTA
**
55617873 CCTGAATGGGCTT
1 CCCAAATGGGCTT
55617886 AGGCCCAATG
Statistics
Matches: 413, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 413 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:55619859 original size:18 final size:18
Alignment explanation
Indices: 55619823--55619869 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
55619813 AATGTTATTG
55619823 GCCCAATATATTAGATAA
1 GCCCAATATATTAGATAA
* *
55619841 GTCCAATATGTTACG-TAA
1 GCCCAATATATTA-GATAA
*
55619859 GCCCAAAATAT
1 GCCCAATATAT
55619870 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (18 bp):
GCCCAATATATTAGATAA
Found at i:55633495 original size:21 final size:21
Alignment explanation
Indices: 55633466--55633535 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
55633456 TTTTAATTTG
*
55633466 ATTTGAAATTTTTTCGAATCA
1 ATTTCAAATTTTTTCGAATCA
* * * *
55633487 ATTTCAAATCTTATCCTAATTCG
1 ATTTCAAAT-TTTTTCGAA-TCA
* *
55633510 ATTTGAAATTCTTTCGAATCA
1 ATTTCAAATTTTTTCGAATCA
55633531 ATTTC
1 ATTTC
55633536 GAATCAAGAC
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
21 14 0.40
22 11 0.31
23 10 0.29
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (21 bp):
ATTTCAAATTTTTTCGAATCA
Found at i:55633841 original size:20 final size:20
Alignment explanation
Indices: 55633799--55633850 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
55633789 AAAATTTGAA
*
55633799 TTTTTTATATATTATTTAGAAT
1 TTTTTTA-AAATT-TTTAGAAT
55633821 TTTATTTAAAATTTTTA-AAT
1 TTT-TTTAAAATTTTTAGAAT
55633841 TTTTTTAAAA
1 TTTTTTAAAA
55633851 AATAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 4 0.14
22 7 0.25
23 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTAAAATTTTTAGAAT
Done.