Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 177 of 198
Found at i:55442632 original size:37 final size:37
Alignment explanation
Indices: 55442591--55442702 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
55442581 GCTGAAGCTA
* **
55442591 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
55442628 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
55442665 CCACTTATCACGTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
55442702 C
1 C
55442703 TAAAACTACC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
Found at i:55447781 original size:11 final size:11
Alignment explanation
Indices: 55447767--55447808 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
55447757 GAAAAAAAGG
55447767 TTTTTT-TTTC
1 TTTTTTCTTTC
55447777 TTTTTTCTTTC
1 TTTTTTCTTTC
*
55447788 -TTTTTCATTC
1 TTTTTTCTTTC
*
55447798 TGTTTTCTTTC
1 TTTTTTCTTTC
55447809 CGACTCATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:55454955 original size:12 final size:13
Alignment explanation
Indices: 55454938--55454966 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55454928 GCCTATTTTT
55454938 AATAAATAAA-TA
1 AATAAATAAACTA
55454950 AATAAATAAACTA
1 AATAAATAAACTA
55454963 AATA
1 AATA
55454967 TATTGAGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAACTA
Found at i:55455491 original size:2 final size:2
Alignment explanation
Indices: 55455486--55455510 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55455476 TATATATATA
55455486 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
55455511 ATGATAAAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:55459130 original size:7 final size:7
Alignment explanation
Indices: 55459118--55459146 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
55459108 CATATTTTTG
55459118 TTTATTA
1 TTTATTA
55459125 TTTATTA
1 TTTATTA
55459132 TTTATTA
1 TTTATTA
55459139 TTTATTA
1 TTTATTA
55459146 T
1 T
55459147 CTTCGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:55463948 original size:72 final size:72
Alignment explanation
Indices: 55463797--55463938 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 72
55463787 TCTCGGATTT
* * *
55463797 AAAAAAGGGATTATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAAGGATTATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATAGTTTAAAA
55463862 CTTGAGA
66 CTTGAGA
*
55463869 AAAAAAAGGATTATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCTCGAGATAGTTTAAAA
1 AAAAAAAGGATTATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATAGTTTAAAA
55463934 CTTGA
66 CTTGA
55463939 ATTTGAAAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (72 bp):
AAAAAAAGGATTATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATAGTTTAAAA
CTTGAGA
Found at i:55464487 original size:3 final size:3
Alignment explanation
Indices: 55464479--55464518 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
55464469 TAAATGAGTA
55464479 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55464519 TCAAATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55465758 original size:7 final size:7
Alignment explanation
Indices: 55465735--55465771 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
55465725 GATTGGTATT
55465735 GGTTTTG
1 GGTTTTG
55465742 GGTATTTG
1 GGT-TTTG
55465750 GGTTTTG
1 GGTTTTG
55465757 GGTTTTG
1 GGTTTTG
*
55465764 AGTTTTG
1 GGTTTTG
55465771 G
1 G
55465772 TCCCCAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.05, C:0.00, G:0.41, T:0.54
Consensus pattern (7 bp):
GGTTTTG
Found at i:55468849 original size:7 final size:7
Alignment explanation
Indices: 55468837--55468871 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
55468827 GAATTACTCT
55468837 TCATAAA
1 TCATAAA
55468844 TCATAAA
1 TCATAAA
*
55468851 ACATAAA
1 TCATAAA
55468858 TCATAAA
1 TCATAAA
55468865 TCATAAA
1 TCATAAA
55468872 AGATAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (7 bp):
TCATAAA
Found at i:55468863 original size:21 final size:21
Alignment explanation
Indices: 55468837--55468878 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55468827 GAATTACTCT
55468837 TCATAAATCATAAAACATAAA
1 TCATAAATCATAAAACATAAA
*
55468858 TCATAAATCATAAAAGATAAA
1 TCATAAATCATAAAACATAAA
55468879 AGATAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (21 bp):
TCATAAATCATAAAACATAAA
Found at i:55472139 original size:20 final size:20
Alignment explanation
Indices: 55472101--55472138 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
55472091 TGTTTAGGAA
55472101 TGTTTTCTTAATCTCAAAAG
1 TGTTTTCTTAATCTCAAAAG
*
55472121 TGTTTT-TTTATCTCAAAA
1 TGTTTTCTTAATCTCAAAA
55472139 ATACTTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (20 bp):
TGTTTTCTTAATCTCAAAAG
Found at i:55472432 original size:6 final size:6
Alignment explanation
Indices: 55472423--55472450 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55472413 AATTTACCAC
55472423 AATTAT AATTAT AATTAT AATTAT AATT
1 AATTAT AATTAT AATTAT AATTAT AATT
55472451 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:55472460 original size:23 final size:23
Alignment explanation
Indices: 55472434--55472491 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
55472424 ATTATAATTA
55472434 TAATTATAATTATAATTTT-TTAT
1 TAATT-TAATTATAATTTTGTTAT
*
55472457 TAATTTAAATATAATTTTGTTAT
1 TAATTTAATTATAATTTTGTTAT
55472480 TAATTT-ATTATA
1 TAATTTAATTATA
55472492 TATATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TAATTTAATTATAATTTTGTTAT
Found at i:55472496 original size:28 final size:24
Alignment explanation
Indices: 55472436--55472493 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
55472426 TATAATTATA
55472436 ATTATAATTATAATTTTTTATTAAT
1 ATTATAA-TATAATTTTTTATTAAT
55472461 -TTA-AATATAATTTTGTTATTAAT
1 ATTATAATATAATTTT-TTATTAAT
*
55472484 -TTATTATATA
1 ATTATAATATA
55472494 TATTACCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.30
23 13 0.43
24 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTATAATATAATTTTTTATTAAT
Found at i:55477756 original size:22 final size:22
Alignment explanation
Indices: 55477716--55477757 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55477706 TATTTGTGCA
* *
55477716 TTATAATAATTTAATTATATGG
1 TTATAATAATTCAAATATATGG
*
55477738 TTATAATTATTCAAATATAT
1 TTATAATAATTCAAATATAT
55477758 ATTATTTATA
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:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTATAATAATTCAAATATATGG
Found at i:55479995 original size:16 final size:15
Alignment explanation
Indices: 55479970--55480009 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
55479960 AGTCTCTTAG
*
55479970 AATTATAAAATGTTA
1 AATTATAAAATGATA
55479985 AATTAATAAAATGATA
1 AATT-ATAAAATGATA
55480001 AATTTATAA
1 AA-TTATAA
55480010 TTCAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
AATTATAAAATGATA
Found at i:55482854 original size:3 final size:3
Alignment explanation
Indices: 55482848--55482887 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
55482838 TTATTTAACC
* *
55482848 TTA TTA TTG TTA TTA TTA TTA CTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
55482888 GTTTTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:55483983 original size:106 final size:108
Alignment explanation
Indices: 55483786--55483983 Score: 310
Period size: 109 Copynumber: 1.8 Consensus size: 108
55483776 GAAAATAATA
*
55483786 AAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGA-TTTTC
*
55483851 TCGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTACAAAAT
65 TCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTACAAAAT
* * *
55483895 AAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA-TTTCT
1 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCT
* *
55483958 CGTTTAACCAAATTGCCAAATATCCT
66 CGTTCAACCAAATAGCCAAATATCCT
55483984 CTTGAATTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
106 28 0.34
108 25 0.30
109 29 0.35
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (108 bp):
AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCT
CGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTACAAAAT
Found at i:55486204 original size:83 final size:84
Alignment explanation
Indices: 55486063--55486218 Score: 212
Period size: 83 Copynumber: 1.9 Consensus size: 84
55486053 ATTGGCTGAA
* *
55486063 ATTTTAAGTAAAATTTTAACTATTTCATATAAACAAGTCTATTAATTATAATTTATTAAATAAAA
1 ATTTTAAGTAAAATTTTAAC-ATTTCATATAAACAAATCTATTAATCATAATTTATTAAATAAAA
*
55486128 ATGATCTTAATTAAAATATT
65 ATAATCTTAATTAAAATATT
*
55486148 ATTTTAA-TAAAATGTTTAA-ATTTCATATGAAA-AAATCTATTAATCAT-ATTTGATTAAATGA
1 ATTTTAAGTAAAAT-TTTAACATTTCATAT-AAACAAATCTATTAATCATAATTT-ATTAAATAA
55486209 AAATAATCTT
63 AAATAATCTT
55486219 TAATGAGCGG
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
82 4 0.06
83 39 0.61
84 9 0.14
85 12 0.19
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (84 bp):
ATTTTAAGTAAAATTTTAACATTTCATATAAACAAATCTATTAATCATAATTTATTAAATAAAAA
TAATCTTAATTAAAATATT
Found at i:55488214 original size:21 final size:21
Alignment explanation
Indices: 55488153--55488238 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
55488143 GTGTTTTACT
* * *
55488153 TTCTGTTTAGCTCTTATGAAC
1 TTCTGTTCAGCTCTTACGAGC
* *
55488174 TTCTGATAAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
55488195 TTCTGTTCAGCTCTTACGAG-
1 TTCTGTTCAGCTCTTACGAGC
*
55488215 TTCCTATTCAGCTC-T-CGAGC
1 TT-CTGTTCAGCTCTTACGAGC
55488235 TTCT
1 TTCT
55488239 ATTGGCGTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 6 0.11
20 5 0.09
21 45 0.80
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:55492486 original size:86 final size:86
Alignment explanation
Indices: 55492315--55492486 Score: 276
Period size: 86 Copynumber: 2.0 Consensus size: 86
55492305 AAAAATTTAA
* *
55492315 GAATTAGGGTTTTCTATTAAATTTTTATGTATCCAAGGCTGTAAGATAACCTAGAATAATTAGAT
1 GAATTAGGGTTTTCTATTAAATTTTTATGTATCAAAGGCTGTAAAATAACCTAGAATAATTAGAT
* *
55492380 AAATTATTCTAATTATAAAGT
66 AAATTAGTCTAATTAAAAAGT
55492401 GAATTAGGGTTTTCTATTAAATTTTTATGTATCAAAGGCTGTAAAATAACCTAGAATAATTAGAT
1 GAATTAGGGTTTTCTATTAAATTTTTATGTATCAAAGGCTGTAAAATAACCTAGAATAATTAGAT
55492466 AAATT-GTC-AATTGAGAAAAGT
66 AAATTAGTCTAATT-A-AAAAGT
55492487 TAGTCCATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
84 4 0.05
85 3 0.04
86 73 0.91
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (86 bp):
GAATTAGGGTTTTCTATTAAATTTTTATGTATCAAAGGCTGTAAAATAACCTAGAATAATTAGAT
AAATTAGTCTAATTAAAAAGT
Found at i:55492990 original size:21 final size:21
Alignment explanation
Indices: 55492966--55493064 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 21
55492956 TGTTTTTGCT
* *
55492966 TTCAGTTTAGCTCTTATGGGC
1 TTCAGTTTAACTCTTATGAGC
* *
55492987 TTCAG-TTAACTCATATGAGT
1 TTCAGTTTAACTCTTATGAGC
* * * *
55493007 TTCAGTTTAACCCTTCTGGGT
1 TTCAGTTTAACTCTTATGAGC
* *
55493028 TTCAGTTTAGCTCTTCTGAGC
1 TTCAGTTTAACTCTTATGAGC
* *
55493049 TTCAGATTAACCCTTA
1 TTCAGTTTAACTCTTA
55493065 CGGGTTTCCA
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (21 bp):
TTCAGTTTAACTCTTATGAGC
Found at i:55493914 original size:25 final size:27
Alignment explanation
Indices: 55493857--55493915 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
55493847 TATTCATACC
*
55493857 TTATTTCACTATCTCAATTCCATTAGA
1 TTATTTCACTATCTCAATTCCAATAGA
55493884 TT-TTTCAC-ATCTC-ATTCCAATA-A
1 TTATTTCACTATCTCAATTCCAATAGA
55493907 TTCATTTCA
1 TT-ATTTCA
55493916 ATTCATATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 3 0.10
24 8 0.28
25 10 0.34
26 6 0.21
27 2 0.07
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.46
Consensus pattern (27 bp):
TTATTTCACTATCTCAATTCCAATAGA
Found at i:55495423 original size:14 final size:14
Alignment explanation
Indices: 55495387--55495426 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
55495377 AAAAACCCTA
55495387 TTTTTCCTT-TTTC
1 TTTTTCCTTCTTTC
*
55495400 -TTTTCTTTCTTTC
1 TTTTTCCTTCTTTC
55495413 TTTTTCCTTCTTTC
1 TTTTTCCTTCTTTC
55495427 CTCTCTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 12 0.52
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCCTTCTTTC
Found at i:55495654 original size:5 final size:5
Alignment explanation
Indices: 55495646--55495678 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
55495636 ATTTTACATA
55495646 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
55495679 TTTTACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:55495719 original size:28 final size:30
Alignment explanation
Indices: 55495656--55495719 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
55495646 ATAATATAAT
*
55495656 ATAATATAATATAATATAATATATTTTACAA
1 ATAA-ATAATATAATATAATATATTTTAAAA
*
55495687 TTAAATAATAT-AT-TAATATA-TTTAAAA
1 ATAAATAATATAATATAATATATTTTAAAA
55495714 CATAAA
1 -ATAAA
55495720 AATCTAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 6 0.21
28 11 0.38
29 2 0.07
30 7 0.24
31 3 0.10
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAATAATATAATATAATATATTTTAAAA
Found at i:55501003 original size:44 final size:44
Alignment explanation
Indices: 55500940--55501028 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
55500930 GTATATGGTT
*
55500940 GTTAACGGGTTGGATTATGGCAAATGATCAATTGTAGCTTTAAA
1 GTTAACAGGTTGGATTATGGCAAATGATCAATTGTAGCTTTAAA
* *
55500984 GTTAACAGGTTGGATTATGGTAAATGATCGATTGTAGCTTTAAA
1 GTTAACAGGTTGGATTATGGCAAATGATCAATTGTAGCTTTAAA
55501028 G
1 G
55501029 ACATCCATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (44 bp):
GTTAACAGGTTGGATTATGGCAAATGATCAATTGTAGCTTTAAA
Found at i:55507804 original size:17 final size:16
Alignment explanation
Indices: 55507778--55507823 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
55507768 ATCTTAAAAA
* *
55507778 ATTTATATATGTTTTTT
1 ATTTAAATAT-TTATTT
55507795 ATTTAAATATTTATTT
1 ATTTAAATATTTATTT
55507811 ATTTATAATATTT
1 ATTTA-AATATTT
55507824 TATATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTTAAATATTTATTT
Found at i:55508276 original size:24 final size:22
Alignment explanation
Indices: 55508245--55508326 Score: 78
Period size: 22 Copynumber: 3.6 Consensus size: 22
55508235 ATTTTCACAA
55508245 AAAAATTCAATATCAATATCC-TTC
1 AAAAATTC--TATCAAT-TCCGTTC
*
55508269 AAAAATTCTCTCAATTCCGTTC
1 AAAAATTCTATCAATTCCGTTC
* *
55508291 AAAAATTCTCTCAAATTCCTTTC
1 AAAAATTCTATC-AATTCCGTTC
*
55508314 -AAAATTCTCTCAA
1 AAAAATTCTATCAA
55508327 ACTCTCAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
21 5 0.09
22 32 0.59
23 9 0.17
24 8 0.15
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.35
Consensus pattern (22 bp):
AAAAATTCTATCAATTCCGTTC
Found at i:55508291 original size:22 final size:21
Alignment explanation
Indices: 55508257--55508326 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 21
55508247 AAATTCAATA
55508257 TCAATATCCTTCAAAAATTCTC
1 TCAAT-TCCTTCAAAAATTCTC
55508279 TCAATTCCGTTCAAAAATTCTC
1 TCAATTCC-TTCAAAAATTCTC
55508301 TCAAATTCCTTTC-AAAATTCTC
1 TC-AATTCC-TTCAAAAATTCTC
55508323 TCAA
1 TCAA
55508327 ACTCTCAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 5 0.11
22 31 0.69
23 9 0.20
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.37
Consensus pattern (21 bp):
TCAATTCCTTCAAAAATTCTC
Found at i:55508327 original size:22 final size:23
Alignment explanation
Indices: 55508266--55508327 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 23
55508256 ATCAATATCC
55508266 TTCAAAAATTCTCTC-AATTCCG
1 TTCAAAAATTCTCTCAAATTCCG
*
55508288 TTCAAAAATTCTCTCAAATTCCT
1 TTCAAAAATTCTCTCAAATTCCG
55508311 TTC-AAAATTCTCTCAAA
1 TTCAAAAATTCTCTCAAA
55508328 CTCTCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (23 bp):
TTCAAAAATTCTCTCAAATTCCG
Found at i:55508333 original size:30 final size:30
Alignment explanation
Indices: 55508298--55508356 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
55508288 TTCAAAAATT
* * *
55508298 CTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAAATTCATTCCAAAATCCTCTCAAA
55508328 CTCTCAAATTCATTCCAAAATCCTCTCAA
1 CTCTCAAATTCATTCCAAAATCCTCTCAA
55508357 TTTTCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCATTCCAAAATCCTCTCAAA
Found at i:55508463 original size:29 final size:28
Alignment explanation
Indices: 55508401--55508463 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
55508391 TAAATTTCAT
* *
55508401 TATTTTAAGAAAATTTTAAAATTTTTTA
1 TATTTTAAAAAAATTTTAAAATTTTTAA
*
55508429 TTTTTTAAAAATAATTTTAAAATTTTTAA
1 TATTTTAAAAA-AATTTTAAAATTTTTAA
55508458 TATTTT
1 TATTTT
55508464 CAACAATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TATTTTAAAAAAATTTTAAAATTTTTAA
Found at i:55508583 original size:14 final size:15
Alignment explanation
Indices: 55508554--55508587 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55508544 AAATTTTAAA
55508554 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
55508569 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
55508583 TTTTA
1 TTTTA
55508588 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:55510777 original size:28 final size:28
Alignment explanation
Indices: 55510732--55511252 Score: 477
Period size: 28 Copynumber: 19.7 Consensus size: 28
55510722 TTTTGACATT
* *
55510732 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
* *
55510760 ATATAATTAAAAACCCTAACTTAA-TTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
***** **
55510787 A---AAACCCTAA-CCTAATTTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
**
55510811 A-TT-A--AA-AACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
55510834 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
*
55510862 ATTTAATTAAAAATCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAATTTA
*
55510885 ATTTAATTAAAAATCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
55510913 ATTTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAATTTA
55510936 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
55510964 ATTTAATT-AAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
*
55510991 ATTTAATTAAAAA-CCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
* *
55511018 GTTTAATTAGAAACCCTAA-C----TTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
*
55511041 ACTTAATTAAAAA-CCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
* **
55511068 ATTTAATTAAAAACTCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
* **
55511096 ATTTAATTAAAATCCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAATTTA
55511125 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
*
55511153 ATTTAATTAAAAATCCTAACC-----TA
1 ATTTAATTAAAAACCCTAACCTAATTTA
* *
55511176 ATTTAATTAAAAATCATAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA
55511204 A-TTAA--AAACCCTAACCCTAACCTAATTTA
1 ATTTAATTAAA----AACCCTAACCTAATTTA
55511233 A-TTAATGTAAAAACCCTAAC
1 ATTTAAT-TAAAAACCCTAAC
55511253 ATAACTCAGC
Statistics
Matches: 414, Mismatches: 39, Indels: 80
0.78 0.07 0.15
Matches are distributed among these distances:
22 7 0.02
23 98 0.24
24 12 0.03
25 7 0.02
26 2 0.00
27 78 0.19
28 160 0.39
29 47 0.11
32 3 0.01
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAATTTA
Found at i:55510778 original size:23 final size:23
Alignment explanation
Indices: 55510751--55511218 Score: 269
Period size: 23 Copynumber: 18.3 Consensus size: 23
55510741 AAAACCCTAA
*
55510751 CCTAACTTAATATAATTAAAAAC
1 CCTAACTTAATTTAATTAAAAAC
55510774 CCTAACTTAA-TTAA--AAACCCTAA-
1 CCTAACTTAATTTAATTAAA----AAC
*
55510797 CCTAATTTAATTTAATTAAAAAC
1 CCTAACTTAATTTAATTAAAAAC
55510820 CCTAACCTAACCTAATTTAATTAAAAAC
1 CCTAA-CT----TAATTTAATTAAAAAC
*
55510848 CCTAACCTAATTTAATTTAATTAAAAAT
1 CCTAA-C----TTAATTTAATTAAAAAC
*
55510876 CCTAACATAATTTAATTAAAAATCC
1 CCTAACTTAATTTAATTAAAAA--C
*
55510901 TAACCTAATTTAATTTAATTAAAAAC
1 ---CCTAACTTAATTTAATTAAAAAC
*
55510927 CCTAACATAATTTAATTAAAAAC
1 CCTAACTTAATTTAATTAAAAAC
*
55510950 CCTAACCTAATTTAATTTAATTAAAAC
1 CCTAACTTAATTTAA-TT-A--AAAAC
55510977 CCTAACCTAATTTAATTTAATTAAAAAC
1 CCTAA-C----TTAATTTAATTAAAAAC
* * *
55511005 CTAACATAATTTAGTTTAATTAGAAAC
1 C---C-TAACTTAATTTAATTAAAAAC
*
55511032 CCTAACTTAACTTAATTAAAAACC
1 CCTAACTTAATTTAATTAAAAA-C
*
55511056 TAACCTAATTTAATTTAATTAAAAAC
1 ---CCTAACTTAATTTAATTAAAAAC
*
55511082 TCTAACCTAACCTAATTTAATTAAAATCCCTAAC
1 CCTAA-CT----TAATTTAATT-AAA-----AAC
*
55511116 CCTAACCTAATTTAATTAAAAAC
1 CCTAACTTAATTTAATTAAAAAC
*
55511139 CCTAACCTAATTTAATTTAATTAAAAAT
1 CCTAA-C----TTAATTTAATTAAAAAC
* *
55511167 CCTAACCTAATTTAATTAAAAAT
1 CCTAACTTAATTTAATTAAAAAC
* *
55511190 CATAACCTAATTTAATTAAAAAC
1 CCTAACTTAATTTAATTAAAAAC
55511213 CCTAAC
1 CCTAAC
55511219 CCTAACCTAA
Statistics
Matches: 359, Mismatches: 31, Indels: 110
0.72 0.06 0.22
Matches are distributed among these distances:
20 3 0.01
22 5 0.01
23 144 0.40
24 13 0.04
25 1 0.00
26 5 0.01
27 48 0.13
28 103 0.29
29 13 0.04
30 1 0.00
31 3 0.01
32 12 0.03
33 1 0.00
34 7 0.02
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (23 bp):
CCTAACTTAATTTAATTAAAAAC
Found at i:55510806 original size:19 final size:18
Alignment explanation
Indices: 55510763--55510803 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
55510753 TAACTTAATA
*
55510763 TAATTAAAAACCCTAACT
1 TAATTAAAAACCCTAACC
55510781 TAATTAAAAACCCTAACC
1 TAATTAAAAACCCTAACC
55510799 TAATT
1 TAATT
55510804 TAATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (18 bp):
TAATTAAAAACCCTAACC
Found at i:55514673 original size:125 final size:123
Alignment explanation
Indices: 55514453--55514718 Score: 408
Period size: 125 Copynumber: 2.1 Consensus size: 123
55514443 CCACGAGGGC
55514453 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
* * * * **
55514518 AATCGCGTCCATGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* *
55514576 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACC-ACTGTAG
1 GCGATTTGACACTATTTGCTCAG-AAACGTC--AAAAAAATTATTTCTTACATGACCAACTGTAG
55514640 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
63 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
**
55514701 GCGATTTCTCACTATTTG
1 GCGATTTGACACTATTTG
55514719 ACCAGATACA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
123 21 0.16
124 7 0.05
125 77 0.60
126 24 0.19
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (123 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
AATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:55529308 original size:30 final size:31
Alignment explanation
Indices: 55529269--55529328 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
55529259 GGAGGTGGGA
*
55529269 TGGGAAGGGAATAAAATTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
55529300 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
55529329 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:55529630 original size:9 final size:9
Alignment explanation
Indices: 55529613--55529643 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55529603 TTGAGTTGAT
55529613 TCGAATAAC
1 TCGAATAAC
*
55529622 TCGATTAAC
1 TCGAATAAC
55529631 TCGAATAAC
1 TCGAATAAC
55529640 TCGA
1 TCGA
55529644 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:55529879 original size:23 final size:23
Alignment explanation
Indices: 55529853--55529905 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
55529843 ATAAGTGCCA
*
55529853 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
55529876 CACTGATATGTAACCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
55529899 CACTGAT
1 CACTGAT
55529906 CAATAACACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAACCGAAGCTAC
Found at i:55531441 original size:25 final size:25
Alignment explanation
Indices: 55531425--55531500 Score: 127
Period size: 25 Copynumber: 3.0 Consensus size: 25
55531415 AGCGCTATCT
55531425 GATTATTAGCAAGTTAGTGCTCTCC
1 GATTATTAGCAAGTTAGTGCTCTCC
*
55531450 GATTATTAGCACGTTAGTGCTCTCC
1 GATTATTAGCAAGTTAGTGCTCTCC
55531475 GATTATTAGCATA-TTAGTGCTCTCC
1 GATTATTAGCA-AGTTAGTGCTCTCC
55531500 G
1 G
55531501 TTTAGCACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (25 bp):
GATTATTAGCAAGTTAGTGCTCTCC
Found at i:55531483 original size:50 final size:47
Alignment explanation
Indices: 55531425--55531520 Score: 131
Period size: 50 Copynumber: 2.0 Consensus size: 47
55531415 AGCGCTATCT
*
55531425 GATTATTAGCA-AGTTAGTGCTCTCCGATTATTAGCACGTTAGTGCTCTCC
1 GATTATTAGCATA-TTAGTGCTCTCCG--T-TTAGCACATTAGTGCTCTCC
*
55531475 GATTATTAGCATATTAGTGCTCTCCGTTTAGCACATTTGTGCTCTC
1 GATTATTAGCATATTAGTGCTCTCCGTTTAGCACATTAGTGCTCTC
55531521 TGTATGACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 17 0.40
48 1 0.02
50 24 0.56
51 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.39
Consensus pattern (47 bp):
GATTATTAGCATATTAGTGCTCTCCGTTTAGCACATTAGTGCTCTCC
Found at i:55531516 original size:22 final size:24
Alignment explanation
Indices: 55531428--55531542 Score: 114
Period size: 25 Copynumber: 4.9 Consensus size: 24
55531418 GCTATCTGAT
55531428 TATTAGCA-AGTTAGTGCTCTCCGA
1 TATTAGCACA-TTAGTGCTCTCCGA
*
55531452 TTATTAGCACGTTAGTGCTCTCCGA
1 -TATTAGCACATTAGTGCTCTCCGA
*
55531477 TTATTAGCATATTAGTGCTCTCCG-
1 -TATTAGCACATTAGTGCTCTCCGA
* *
55531501 T-TTAGCACATTTGTGCTCTCTG-
1 TATTAGCACATTAGTGCTCTCCGA
* *
55531523 TATGA-CACTTTAGTGCTCTC
1 TATTAGCACATTAGTGCTCTC
55531543 TGTTTAATAA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
22 32 0.41
23 3 0.04
25 44 0.56
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (24 bp):
TATTAGCACATTAGTGCTCTCCGA
Found at i:55531543 original size:22 final size:23
Alignment explanation
Indices: 55531488--55531546 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
55531478 TATTAGCATA
* *
55531488 TTAGTGCTCTCCGTTTAGCACAT
1 TTAGTGCTCTCTGTTGAGCACAT
55531511 TT-GTGCTCTCTGTATGA-CAC-T
1 TTAGTGCTCTCTGT-TGAGCACAT
55531532 TTAGTGCTCTCTGTT
1 TTAGTGCTCTCTGTT
55531547 TAATAATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 4 0.12
22 24 0.75
23 4 0.12
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (23 bp):
TTAGTGCTCTCTGTTGAGCACAT
Found at i:55532029 original size:13 final size:13
Alignment explanation
Indices: 55532011--55532048 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
55532001 AGTTTGGCAA
55532011 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
55532024 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
55532037 TGCTTTTGAAAA
1 TGCTTTTGAAAA
55532049 TTTTAGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:55540493 original size:23 final size:24
Alignment explanation
Indices: 55540444--55540496 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
55540434 TAATAAAAAA
*
55540444 AATAATACAACATAACTTTTAGGT
1 AATAATACAACATAACTTTTAGAT
*
55540468 AATAATACTA-ATAA-TTTTAGAAT
1 AATAATACAACATAACTTTTAG-AT
55540491 AATAAT
1 AATAAT
55540497 GCACAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 9 0.35
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (24 bp):
AATAATACAACATAACTTTTAGAT
Found at i:55541673 original size:51 final size:51
Alignment explanation
Indices: 55541586--55541733 Score: 170
Period size: 51 Copynumber: 2.9 Consensus size: 51
55541576 AAGCAAGTAG
* *
55541586 GTGGCAGCCTTGCCATAATTTGAACCGTGGCCATTGAGGCCACTATAGCAAC
1 GTGGCAGCCTTGCCATAA-CTGAACCGTGGCAATTGAGGCCACTATAGCAAC
** * * *
55541638 GTGGCAGCCTTGCCACCACTGAACCGTGGCAATTGAAGCCAGTATAGGAAC
1 GTGGCAGCCTTGCCATAACTGAACCGTGGCAATTGAGGCCACTATAGCAAC
* * ** * *
55541689 TTGGGAGCCTTGCCATTGCTGAACCGTGGCATTTGAGGCCGCTAT
1 GTGGCAGCCTTGCCATAACTGAACCGTGGCAATTGAGGCCACTAT
55541734 GGAGTCGTGG
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 64 0.80
52 16 0.20
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (51 bp):
GTGGCAGCCTTGCCATAACTGAACCGTGGCAATTGAGGCCACTATAGCAAC
Found at i:55544758 original size:4 final size:4
Alignment explanation
Indices: 55544749--55544841 Score: 159
Period size: 4 Copynumber: 23.2 Consensus size: 4
55544739 CATATTACAG
* * *
55544749 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAC GTAC GTAC
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
55544797 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
55544842 GGTTATTTGC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 87 1.00
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:55545428 original size:2 final size:2
Alignment explanation
Indices: 55545405--55545442 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
55545395 TATTTATAGG
* *
55545405 TA TA -A TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55545443 CAAAGCAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:55545654 original size:25 final size:23
Alignment explanation
Indices: 55545626--55545684 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
55545616 ACATTTTAAA
55545626 AAATGAATTAATTAATTTCATGAGT
1 AAATGAATTAATTAATTTCAT-A-T
* *
55545651 AAATATAATT-ATTTATTTCATAT
1 AAAT-GAATTAATTAATTTCATAT
55545674 AAATGTAATTA
1 AAATG-AATTA
55545685 TTGATTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
23 9 0.32
24 1 0.04
25 14 0.50
26 4 0.14
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (23 bp):
AAATGAATTAATTAATTTCATAT
Found at i:55545682 original size:23 final size:25
Alignment explanation
Indices: 55545626--55545691 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 25
55545616 ACATTTTAAA
55545626 AAATG-AATTAATTAATTTCATGAGT
1 AAATGTAATT-ATTAATTTCATGAGT
* *
55545651 AAATATAATTATTTATTTCAT-A-T
1 AAATGTAATTATTAATTTCATGAGT
*
55545674 AAATGTAATTATTGATTT
1 AAATGTAATTATTAATTT
55545692 ATGTGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.47
24 1 0.03
25 14 0.39
26 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (25 bp):
AAATGTAATTATTAATTTCATGAGT
Found at i:55549495 original size:15 final size:17
Alignment explanation
Indices: 55549474--55549515 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
55549464 TAACCTTCTA
55549474 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
55549490 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
55549506 AAAATTATAA
1 AAAATTATAA
55549516 TTTTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:55549507 original size:24 final size:23
Alignment explanation
Indices: 55549474--55549542 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
55549464 TAACCTTCTA
*
55549474 AAAATTATAAAAATATAAATTATT
1 AAAATAATAAAAATATAAATT-TT
*
55549498 AAAATAATAAAATTAT-AATTTT
1 AAAATAATAAAAATATAAATTTT
** *
55549520 ATTATCATAAAAATATATAATTT
1 AAAATAATAAAAATATA-AATTT
55549543 AATTTCAACC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 14 0.38
23 4 0.11
24 19 0.51
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATAATAAAAATATAAATTTT
Found at i:55549536 original size:22 final size:23
Alignment explanation
Indices: 55549474--55549536 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
55549464 TAACCTTCTA
*
55549474 AAAATTATAAAAATATAAATTATT
1 AAAATAATAAAAATAT-AATTATT
*
55549498 AAAATAATAAAATTATAATT-TT
1 AAAATAATAAAAATATAATTATT
** *
55549520 ATTATCATAAAAATATA
1 AAAATAATAAAAATATA
55549537 TAATTTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 4 0.12
24 14 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATAATAAAAATATAATTATT
Found at i:55551691 original size:11 final size:11
Alignment explanation
Indices: 55551675--55551699 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55551665 GTCAGATTCA
55551675 AATTTTAATTT
1 AATTTTAATTT
55551686 AATTTTAATTT
1 AATTTTAATTT
55551697 AAT
1 AAT
55551700 ATAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTAATTT
Found at i:55560506 original size:18 final size:19
Alignment explanation
Indices: 55560478--55560513 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
55560468 TTTCTCATCC
55560478 ATTTAAATATTTAATTTAA
1 ATTTAAATATTTAATTTAA
55560497 ATTT-AATATTTAATTTA
1 ATTTAAATATTTAATTTA
55560514 GTATCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATATTTAATTTAA
Found at i:55582579 original size:3 final size:3
Alignment explanation
Indices: 55582571--55582599 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55582561 CTAAAGCATG
55582571 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
55582600 GATGATGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55588806 original size:28 final size:28
Alignment explanation
Indices: 55588747--55588806 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
55588737 CTATTAATCT
* ** *
55588747 TATTTCTCAGTTTAGATGGCCATATTCT
1 TATTTCTCAGTTTAGATGGCCAAACACC
55588775 TATTTCTCAGTTTAGATGGCCAAACACC
1 TATTTCTCAGTTTAGATGGCCAAACACC
55588803 TATT
1 TATT
55588807 GTCGATGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (28 bp):
TATTTCTCAGTTTAGATGGCCAAACACC
Found at i:55588973 original size:31 final size:31
Alignment explanation
Indices: 55588938--55588996 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
55588928 CGTAGGAATA
*
55588938 GGAAATATATATAATATATTCCTAAATAAAT
1 GGAAAGATATATAATATATTCCTAAATAAAT
*
55588969 GGAAAGATATATAATTTATTCCTAAATA
1 GGAAAGATATATAATATATTCCTAAATA
55588997 TATGCCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (31 bp):
GGAAAGATATATAATATATTCCTAAATAAAT
Found at i:55589040 original size:13 final size:13
Alignment explanation
Indices: 55589022--55589046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55589012 ACGATAATAT
55589022 ATAATAATATCCC
1 ATAATAATATCCC
55589035 ATAATAATATCC
1 ATAATAATATCC
55589047 AAATCATGAG
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATATCCC
Found at i:55590272 original size:31 final size:31
Alignment explanation
Indices: 55590236--55590336 Score: 112
Period size: 31 Copynumber: 3.3 Consensus size: 31
55590226 CTACATCATT
* * *
55590236 AGTCACTAAACTATGGGTAAGTTTTCATTTT
1 AGTCACTAAACTATGCGAAAGTTTTCATTTA
* * * *
55590267 GGTCACTGAACTATTCGAAAGTTTTTATTTA
1 AGTCACTAAACTATGCGAAAGTTTTCATTTA
* * *
55590298 AGTCACTAAAGTATTCAAAAGTTTTCATTTA
1 AGTCACTAAACTATGCGAAAGTTTTCATTTA
55590329 AGTCACTA
1 AGTCACTA
55590337 GGTTGTTAAG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (31 bp):
AGTCACTAAACTATGCGAAAGTTTTCATTTA
Found at i:55594977 original size:20 final size:21
Alignment explanation
Indices: 55594952--55594995 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
55594942 TCAATTGAAT
55594952 AAATTA-TTAAAAAAATAAAA
1 AAATTATTTAAAAAAATAAAA
55594972 AAATTATTTAAAAAAATAAAA
1 AAATTATTTAAAAAAATAAAA
55594993 AAA
1 AAA
55594996 GATAGTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATTATTTAAAAAAATAAAA
Found at i:55600409 original size:29 final size:29
Alignment explanation
Indices: 55600375--55600430 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
55600365 TTTGATTCTT
* *
55600375 TTTAATATTACATGGATTAAATTGATCCA
1 TTTAATAATACAGGGATTAAATTGATCCA
* *
55600404 TTTAATAATAGAGGGATTAATTTGATC
1 TTTAATAATACAGGGATTAAATTGATC
55600431 AAATCCCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTAATAATACAGGGATTAAATTGATCCA
Found at i:55604273 original size:109 final size:108
Alignment explanation
Indices: 55604082--55604301 Score: 293
Period size: 109 Copynumber: 2.0 Consensus size: 108
55604072 AAAACCTCTT
* * * *
55604082 GAAGGATCCATGAACGGGAGTCAAGATCTGAAGAGCAGCATATCAATGAGAATTGGAGATCGGTT
1 GAAGGATCCATGAACGGGAGTCAAGATCTGAAGAGCAGCAGATCAAAGAGAATCGGAGATCGGAT
* * * *
55604147 CAAAGCATCGAAGCAGCTTCACTGATCGATACGAAGAGTGAGA
66 CAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
*
55604190 GAAGGATCCATTG-ACGGGAGTGAAGAGT-TCG-AGAGCAGCAGATCGAAAGAGAATCGGAGATC
1 GAAGGATCCA-TGAACGGGAGTCAAGA-TCT-GAAGAGCAGCAGATC-AAAGAGAATCGGAGATC
*
55604252 GGATCAAAGCATCGAAACAGCTTCACGGATCGATATAAAGAGTAAGA
62 GGATCAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
55604299 GAA
1 GAA
55604302 CCATGAATAC
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
108 35 0.36
109 63 0.64
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.17
Consensus pattern (108 bp):
GAAGGATCCATGAACGGGAGTCAAGATCTGAAGAGCAGCAGATCAAAGAGAATCGGAGATCGGAT
CAAAGCATCGAAACAGCTTCACGGATCGATACAAAGAGTAAGA
Found at i:55613944 original size:11 final size:11
Alignment explanation
Indices: 55613930--55613969 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
55613920 GTTTTCTCCT
55613930 TATTTTGCTAC
1 TATTTTGCTAC
* *
55613941 TATTTTACTAT
1 TATTTTGCTAC
*
55613952 TATGTTGCTAC
1 TATTTTGCTAC
55613963 TATTTTG
1 TATTTTG
55613970 TTGTTATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:55614046 original size:30 final size:30
Alignment explanation
Indices: 55614006--55614068 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
55613996 ATTTATTTTA
55614006 TTGTGAATTTTGTTATTATTTTAAAGGCAT
1 TTGTGAATTTTGTTATTATTTTAAAGGCAT
* *
55614036 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTGAATTTTGTTATTATTTTAAAGGCAT
55614066 TTG
1 TTG
55614069 CTTTTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.17, T:0.56
Consensus pattern (30 bp):
TTGTGAATTTTGTTATTATTTTAAAGGCAT
Found at i:55614204 original size:11 final size:11
Alignment explanation
Indices: 55614188--55614219 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
55614178 ATTATATATA
55614188 TATATAAAAAT
1 TATATAAAAAT
55614199 TATATAAAAAT
1 TATATAAAAAT
*
55614210 AATATAAAAA
1 TATATAAAAA
55614220 ATTAATACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TATATAAAAAT
Found at i:55614225 original size:13 final size:13
Alignment explanation
Indices: 55614187--55614226 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
55614177 TATTATATAT
55614187 ATATATAAAAATT-
1 ATATA-AAAAATTA
55614200 ATAT-AAAAA-TA
1 ATATAAAAAATTA
55614211 ATATAAAAAATTA
1 ATATAAAAAATTA
55614224 ATA
1 ATA
55614227 CGGGTAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
12 5 0.21
13 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATAAAAAATTA
Found at i:55614529 original size:12 final size:13
Alignment explanation
Indices: 55614458--55614531 Score: 60
Period size: 13 Copynumber: 5.4 Consensus size: 13
55614448 ATTTTTTTAA
55614458 TTTTAATTAAT-T
1 TTTTAATTAATAT
55614470 TTTTAATTAATAAAT
1 TTTTAATTAAT--AT
** *
55614485 TTATTGTTTTAAGTTT
1 TT-TT-AATTAA-TAT
*
55614501 TTTTAATTCATAT
1 TTTTAATTAATAT
55614514 TTTTAATTAATAT
1 TTTTAATTAATAT
55614527 TTTTA
1 TTTTA
55614532 TTTATATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
12 11 0.23
13 19 0.40
14 3 0.06
15 5 0.10
16 5 0.10
17 4 0.08
18 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (13 bp):
TTTTAATTAATAT
Found at i:55614586 original size:19 final size:22
Alignment explanation
Indices: 55614545--55614588 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
55614535 ATATAAATAA
*
55614545 AATAATAAATATGTCATTATAT
1 AATAATAAATATATCATTATAT
55614567 AATAA-AAATATAT-ATTTATAT
1 AATAATAAATATATCA-TTATAT
55614588 A
1 A
55614589 TATCATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AATAATAAATATATCATTATAT
Found at i:55616823 original size:14 final size:14
Alignment explanation
Indices: 55616804--55616830 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55616794 AAAAATTCAA
55616804 TTAAAATTAAAATT
1 TTAAAATTAAAATT
55616818 TTAAAATTAAAAT
1 TTAAAATTAAAAT
55616831 ATATATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAATTAAAATT
Found at i:55622812 original size:11 final size:12
Alignment explanation
Indices: 55622785--55622826 Score: 52
Period size: 11 Copynumber: 3.5 Consensus size: 12
55622775 TTTTCTTCCT
55622785 TAAATTTTTT-A
1 TAAATTTTTTAA
55622796 TAAATTTTTTAA
1 TAAATTTTTTAA
55622808 T-AATTTATTTAA
1 TAAATTT-TTTAA
55622820 TTAAATT
1 -TAAATT
55622827 AAACGAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 15 0.56
12 7 0.26
13 1 0.04
14 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTTTTAA
Found at i:55629126 original size:21 final size:23
Alignment explanation
Indices: 55629091--55629152 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 23
55629081 CCTAAAAATG
**
55629091 ATAAAAATTTGATTTAATCT-T-
1 ATAAAAATTACATTTAATCTATA
* *
55629112 TTAAAAATTACATTTTA-CTATA
1 ATAAAAATTACATTTAATCTATA
55629134 ATAAAAATTACAATTTAAT
1 ATAAAAATTAC-ATTTAAT
55629153 TTCAGCCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 14 0.45
22 10 0.32
23 5 0.16
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAAAATTACATTTAATCTATA
Found at i:55629900 original size:21 final size:22
Alignment explanation
Indices: 55629852--55629901 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
55629842 AAATATTTTA
*
55629852 ATTTTCCTTAATTTTCCCTTCT
1 ATTTTCCTCAATTTTCCCTTCT
* *
55629874 -TCTTCCTCAATTTTCTCTT-T
1 ATTTTCCTCAATTTTCCCTTCT
55629894 ATTTTCCT
1 ATTTTCCT
55629902 TGTCATTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTCCTCAATTTTCCCTTCT
Found at i:55637908 original size:33 final size:33
Alignment explanation
Indices: 55637869--55637934 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
55637859 AAAAACTAAA
55637869 AATAAAAGCACACTCGTAATAATATAATTTACT
1 AATAAAAGCACACTCGTAATAATATAATTTACT
55637902 AATAAAAGCACACTCGTAATAATATAATTTACT
1 AATAAAAGCACACTCGTAATAATATAATTTACT
55637935 TTATAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (33 bp):
AATAAAAGCACACTCGTAATAATATAATTTACT
Found at i:55645401 original size:19 final size:19
Alignment explanation
Indices: 55645364--55645411 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
55645354 AATATTTTGC
*
55645364 TCATAAAAATGATTAAAAAG
1 TCAT-AAAATGATTAAAAAA
55645384 TCATAAAAT-ATTATAAAAA
1 TCATAAAATGATTA-AAAAA
55645403 TCATAAAAT
1 TCATAAAAT
55645412 TATCGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (19 bp):
TCATAAAATGATTAAAAAA
Found at i:55645551 original size:21 final size:20
Alignment explanation
Indices: 55645516--55645573 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
55645506 TAAAAAATTA
* * *
55645516 ATAAAATATATTTAAAGTTTT
1 ATAAAAAATA-TTAAAATTCT
55645537 ATAAAAACATATTAAAATTCT
1 ATAAAAA-ATATTAAAATTCT
*
55645558 ATAAAAATTATTAAAA
1 ATAAAAAATATTAAAA
55645574 GTATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.25
21 21 0.66
22 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAAAATATTAAAATTCT
Found at i:55645569 original size:20 final size:18
Alignment explanation
Indices: 55645557--55645610 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
55645547 ATTAAAATTC
*
55645557 TATAAAAATTATTAAAA-G
1 TATAAAAATTA-TAAAACT
*
55645575 TATAAAAAATGATATAAACT
1 TAT-AAAAATTATA-AAACT
55645595 TATAAAAATTATAAAA
1 TATAAAAATTATAAAA
55645611 AAATCATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 8 0.27
19 19 0.63
20 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
TATAAAAATTATAAAACT
Found at i:55645582 original size:9 final size:9
Alignment explanation
Indices: 55645557--55645611 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
55645547 ATTAAAATTC
55645557 TATAAAAAT
1 TATAAAAAT
* *
55645566 TATTAAAAG
1 TATAAAAAT
55645575 TATAAAAAAT
1 TAT-AAAAAT
* *
55645585 GATATAAACT
1 TATA-AAAAT
55645595 TATAAAAAT
1 TATAAAAAT
55645604 TATAAAAA
1 TATAAAAA
55645612 AATCATAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 23 0.64
10 13 0.36
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
TATAAAAAT
Found at i:55645621 original size:10 final size:10
Alignment explanation
Indices: 55645480--55645622 Score: 55
Period size: 10 Copynumber: 14.2 Consensus size: 10
55645470 TTATAAAAAT
* *
55645480 AAATTTTAAT
1 AAATTATAAA
*
55645490 AAATTCTAAA
1 AAATTATAAA
55645500 AGAATT-TAAA
1 A-AATTATAAA
55645510 AAATTAATAAA
1 AAATT-ATAAA
55645521 ATATATT-TAAA
1 A-A-ATTATAAA
***
55645532 GTTTTATAAA
1 AAATTATAAA
*
55645542 AACA-TAT-TA
1 AA-ATTATAAA
*
55645551 AAATTCTATAA
1 AAATTATA-AA
*
55645562 AAATTAT-TA
1 AAATTATAAA
*
55645571 AAAGTATAAA
1 AAATTATAAA
* *
55645581 AAATGATATA
1 AAATTATAAA
*
55645591 AACTTAT-AA
1 AAATTATAAA
55645600 AAATTATAAAA
1 AAATTAT-AAA
*
55645611 AAATCATAAA
1 AAATTATAAA
55645621 AA
1 AA
55645623 CTTGAATTGG
Statistics
Matches: 97, Mismatches: 23, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
8 1 0.01
9 25 0.26
10 39 0.40
11 28 0.29
12 1 0.01
13 3 0.03
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (10 bp):
AAATTATAAA
Found at i:55645961 original size:9 final size:9
Alignment explanation
Indices: 55645947--55646004 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
55645937 GTTTTTTTAA
55645947 TTTAAAATT
1 TTTAAAATT
55645956 TTTAAAATT
1 TTTAAAATT
* *
55645965 TATAATATT
1 TTTAAAATT
55645974 TTT-AAATT
1 TTTAAAATT
*
55645982 TTTATAATT
1 TTTAAAATT
*
55645991 TTAATAAATT
1 TTTA-AAATT
55646001 TTTA
1 TTTA
55646005 TGAAAAAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
8 7 0.18
9 25 0.64
10 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:55645985 original size:19 final size:19
Alignment explanation
Indices: 55645953--55646005 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
55645943 TTAATTTAAA
*
55645953 ATTTTTAAA-ATTTATAAT
1 ATTTTTAAATTTTTATAAT
55645971 ATTTTTAAATTTTTATAAT
1 ATTTTTAAATTTTTATAAT
*
55645990 -TTTAATAAATTTTTAT
1 ATTT-TTAAATTTTTAT
55646006 GAAAAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTAAATTTTTATAAT
Found at i:55646002 original size:26 final size:26
Alignment explanation
Indices: 55645944--55646002 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
55645934 TAAGTTTTTT
*
55645944 TAATTTAAAATTTTTAAAATTTATAA
1 TAATTTTAAATTTTTAAAATTTATAA
* *
55645970 TATTTTTAAATTTTTATAATTT-TAA
1 TAATTTTAAATTTTTAAAATTTATAA
55645995 TAAATTTT
1 T-AATTTT
55646003 TATGAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TAATTTTAAATTTTTAAAATTTATAA
Found at i:55647898 original size:20 final size:21
Alignment explanation
Indices: 55647875--55647916 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
55647865 AAAAAAGTTT
55647875 AAAAAAAG-TAAA-AAAACAAA
1 AAAAAAAGTTAAATAAAA-AAA
55647895 AAAAAAAGTTAAATAAAAAAA
1 AAAAAAAGTTAAATAAAAAAA
55647916 A
1 A
55647917 TTTAACAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 8 0.40
22 4 0.20
ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAAAAAGTTAAATAAAAAAA
Found at i:55662566 original size:16 final size:16
Alignment explanation
Indices: 55662545--55662579 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55662535 ACCCTCACAC
*
55662545 TTTTTGGGCTTATATT
1 TTTTTGAGCTTATATT
*
55662561 TTTTTGAGTTTATATT
1 TTTTTGAGCTTATATT
55662577 TTT
1 TTT
55662580 GTCCAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (16 bp):
TTTTTGAGCTTATATT
Found at i:55662760 original size:25 final size:25
Alignment explanation
Indices: 55662732--55662816 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
55662722 GGTTGCCATT
55662732 CAATTTGCTTGGATATTATACCAAA
1 CAATTTGCTTGGATATTATACCAAA
* *** * *
55662757 CAATTCTTCTCCAATTACTATCTCCGAAGA
1 CAATT-TGCTTGGA-TATTAT-ACC-AA-A
*
55662787 CAATTTGCTTGGATATTACACCAAA
1 CAATTTGCTTGGATATTATACCAAA
55662812 CAATT
1 CAATT
55662817 CTTCTCCAAT
Statistics
Matches: 42, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
25 11 0.26
26 6 0.14
27 7 0.17
28 6 0.14
29 6 0.14
30 6 0.14
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (25 bp):
CAATTTGCTTGGATATTATACCAAA
Found at i:55662798 original size:55 final size:55
Alignment explanation
Indices: 55662732--55662839 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
55662722 GGTTGCCATT
* *
55662732 CAATTTGCTTGGATATTATACCAAACAATTCTTCTCCAATTACTATCTCCGAAGA
1 CAATTTGCTTGGATATTACACCAAACAATTCTTCTCCAATTACCATCTCCGAAGA
55662787 CAATTTGCTTGGATATTACACCAAACAATTCTTCTCCAATTACCATCTCCGAA
1 CAATTTGCTTGGATATTACACCAAACAATTCTTCTCCAATTACCATCTCCGAA
55662840 AAAGATGAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.33
Consensus pattern (55 bp):
CAATTTGCTTGGATATTACACCAAACAATTCTTCTCCAATTACCATCTCCGAAGA
Found at i:55664840 original size:2 final size:2
Alignment explanation
Indices: 55664827--55664857 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55664817 AAAACAAGTG
*
55664827 AT AT AC 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 AT AT AT A
55664858 AAAGTATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:55669506 original size:31 final size:31
Alignment explanation
Indices: 55669471--55669530 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
55669461 ACAAAATGGT
*
55669471 CATTGAACTATTTGAAAATTTTCATTTAAGC
1 CATTGAACTATTCGAAAATTTTCATTTAAGC
* * *
55669502 CATTGAATTATTCGAAAGTTTTTATTTAA
1 CATTGAACTATTCGAAAATTTTCATTTAA
55669531 ATCACTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (31 bp):
CATTGAACTATTCGAAAATTTTCATTTAAGC
Found at i:55675815 original size:19 final size:19
Alignment explanation
Indices: 55675791--55675828 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55675781 CCAGGCAGAT
55675791 CAACAAGATTTCACATCTA
1 CAACAAGATTTCACATCTA
55675810 CAACAAGATTTCACATCTA
1 CAACAAGATTTCACATCTA
55675829 ATATTGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
CAACAAGATTTCACATCTA
Found at i:55676797 original size:19 final size:19
Alignment explanation
Indices: 55676775--55676817 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
55676765 TTTTATATTA
*
55676775 TTAAAATATATTATTACCC
1 TTAAAATATATTATTAACC
*
55676794 TTAATATATATTATTAACC
1 TTAAAATATATTATTAACC
55676813 TTAAA
1 TTAAA
55676818 CTTAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAATATATTATTAACC
Found at i:55683843 original size:31 final size:30
Alignment explanation
Indices: 55683781--55683839 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
55683771 TTTGAAGAAA
* * *
55683781 TTTAATTTTGTACTTTTTAAATTTGTCAAT
1 TTTAATTTTATACTTTTAAAATTTGTAAAT
55683811 TTTAATTATTATACTTTTAAAATTT-TAAA
1 TTTAATT-TTATACTTTTAAAATTTGTAAA
55683840 ATTTCAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTAATTTTATACTTTTAAAATTTGTAAAT
Found at i:55696944 original size:2 final size:2
Alignment explanation
Indices: 55696937--55696975 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55696927 AGTAAGCTCC
55696937 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
55696976 CAATCTCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55705691 original size:6 final size:6
Alignment explanation
Indices: 55705680--55705704 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55705670 GATTATATAA
55705680 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
55705705 ATTTGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:55706876 original size:31 final size:31
Alignment explanation
Indices: 55706839--55706901 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
55706829 ACCACTTTTA
55706839 TTTTTTAATTTTAAAATACTTTTAAAATAAT
1 TTTTTTAATTTTAAAATACTTTTAAAATAAT
* *
55706870 TTTTTTATTTTTTAAATACTTTTAAAATAAT
1 TTTTTTAATTTTAAAATACTTTTAAAATAAT
55706901 T
1 T
55706902 ATGATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATACTTTTAAAATAAT
Found at i:55706910 original size:31 final size:31
Alignment explanation
Indices: 55706847--55706911 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
55706837 TATTTTTTAA
* **
55706847 TTTTAAAATACTTTTAAAATAATTTTTTTAT
1 TTTTAAAATACTTTTAAAATAATTATGATAT
*
55706878 TTTTTAAATACTTTTAAAATAATTATGATAT
1 TTTTAAAATACTTTTAAAATAATTATGATAT
55706909 TTT
1 TTT
55706912 CCTGGGCCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (31 bp):
TTTTAAAATACTTTTAAAATAATTATGATAT
Found at i:55708152 original size:2 final size:2
Alignment explanation
Indices: 55708145--55708172 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55708135 CAATACTTAA
55708145 AT 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 AT
55708173 TTCATATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55710758 original size:15 final size:14
Alignment explanation
Indices: 55710738--55710773 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
55710728 TAATATTTTA
55710738 TTTTTTTCTAGGTTT
1 TTTTTTTCTA-GTTT
55710753 TTTTTTTCTAGTTT
1 TTTTTTTCTAGTTT
55710767 TTTTTTT
1 TTTTTTT
55710774 TTTAATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTAGTTT
Found at i:55710774 original size:15 final size:15
Alignment explanation
Indices: 55710733--55710774 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
55710723 TGTCTTAATA
55710733 TTTTATTTTTTTCTAG
1 TTTT-TTTTTTTCTAG
*
55710749 GTTTTTTTTTTCTAG
1 TTTTTTTTTTTCTAG
55710764 TTTTTTTTTTT
1 TTTTTTTTTTT
55710775 TTAATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (15 bp):
TTTTTTTTTTTCTAG
Found at i:55712514 original size:22 final size:22
Alignment explanation
Indices: 55712489--55712531 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
55712479 GAACTTACCA
55712489 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
55712511 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
55712532 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:55720972 original size:22 final size:23
Alignment explanation
Indices: 55720945--55720991 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
55720935 TTTAGCGTAG
*
55720945 TTATAATTTTAAAAA-TATGTTT
1 TTATAATTTTAAAAATTATATTT
55720967 TTATAATTTTAAAAATTATATTT
1 TTATAATTTTAAAAATTATATTT
55720990 TT
1 TT
55720992 TTGGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATAATTTTAAAAATTATATTT
Found at i:55721114 original size:15 final size:16
Alignment explanation
Indices: 55721094--55721130 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
55721084 AATCATTCAA
55721094 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
55721109 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
55721125 AAATTA
1 AAATTA
55721131 CATAAATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:55723843 original size:5 final size:5
Alignment explanation
Indices: 55723833--55723880 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
55723823 TTGAAATTTT
* *
55723833 ATCGA ATCGA ATCGA GT-GA GATAGAA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA -ATCG-A ATCGA ATCGA ATCGA ATCGA AT
55723881 TATTTGTTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 30 0.81
6 4 0.11
7 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (5 bp):
ATCGA
Found at i:55726790 original size:22 final size:20
Alignment explanation
Indices: 55726742--55726784 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
55726732 AAATGTAGTG
*
55726742 TATTTTAAAAATAAAAAATA
1 TATTTTAAAAATAAAAAAAA
55726762 TATTTTAAAAATAAAAAAAA
1 TATTTTAAAAATAAAAAAAA
55726782 TAT
1 TAT
55726785 GGTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAA
Found at i:55727910 original size:22 final size:22
Alignment explanation
Indices: 55727881--55727929 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
55727871 CCTAGGCTGA
55727881 TTTGGGC-TAAGTGTAAT-TAGG
1 TTTGGGCTTAA-TGTAATCTAGG
55727902 TTTGAGGCTTAATGTAATCTAGG
1 TTTG-GGCTTAATGTAATCTAGG
55727925 TTTGG
1 TTTGG
55727930 ATGTAATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.16
22 10 0.40
23 11 0.44
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.41
Consensus pattern (22 bp):
TTTGGGCTTAATGTAATCTAGG
Found at i:55736328 original size:25 final size:25
Alignment explanation
Indices: 55736299--55736439 Score: 76
Period size: 25 Copynumber: 5.6 Consensus size: 25
55736289 AATAACGGGT
55736299 AGCTCCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * * * *
55736324 AGCTCTGGATAGCCA-CATATCGGGA
1 AGCTCCGAAGAGCCATTA-ATCAGGA
* * *
55736349 AG-TTC-AAGCGAGTCA-T-ATCGGGA
1 AGCTCCGAA--GAGCCATTAATCAGGA
* *
55736372 AGCTCCGGAGAGCCATTAATTAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * * *
55736397 AGCTTACAAAGAACCTTTAATCAGGA
1 AGC-TCCGAAGAGCCATTAATCAGGA
55736423 AGCTCACGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
55736440 ATAACGGGAC
Statistics
Matches: 81, Mismatches: 26, Indels: 17
0.65 0.21 0.14
Matches are distributed among these distances:
23 15 0.19
24 5 0.06
25 34 0.42
26 27 0.33
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Found at i:55736434 original size:26 final size:26
Alignment explanation
Indices: 55736369--55736439 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 26
55736359 AGTCATATCG
* * *
55736369 GGAAGCTC-CGGAGAGCCATTAATTA
1 GGAAGCTCACGAAGAACCATTAATCA
* * *
55736394 GGAAGCTTACAAAGAACCTTTAATCA
1 GGAAGCTCACGAAGAACCATTAATCA
*
55736420 GGAAGCTCACGAAGAGCCAT
1 GGAAGCTCACGAAGAACCAT
55736440 ATAACGGGAC
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
25 7 0.20
26 28 0.80
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (26 bp):
GGAAGCTCACGAAGAACCATTAATCA
Found at i:55744581 original size:35 final size:35
Alignment explanation
Indices: 55744535--55744631 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 35
55744525 CAGACAGTGA
55744535 TAGTTCCAATTGTGCTTCTCTATGATAGATAAAGT
1 TAGTTCCAATTGTGCTTCTCTATGATAGATAAAGT
* * *
55744570 TAGTTTCAATTGTGCTTCTTTTTGATAGATAAAGT
1 TAGTTCCAATTGTGCTTCTCTATGATAGATAAAGT
*
55744605 TAGTTCCAATTGTGCTTCTCTAGGATA
1 TAGTTCCAATTGTGCTTCTCTATGATA
55744632 AACAAATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (35 bp):
TAGTTCCAATTGTGCTTCTCTATGATAGATAAAGT
Found at i:55753101 original size:2 final size:2
Alignment explanation
Indices: 55753094--55753120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55753084 CCTTTTTCTT
55753094 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
55753121 TCCCTCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55777351 original size:10 final size:10
Alignment explanation
Indices: 55777338--55777362 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55777328 ACAAAAAAGT
55777338 ATAGAAAATG
1 ATAGAAAATG
55777348 ATAGAAAATG
1 ATAGAAAATG
55777358 ATAGA
1 ATAGA
55777363 TAGATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (10 bp):
ATAGAAAATG
Found at i:55777366 original size:4 final size:4
Alignment explanation
Indices: 55777357--55777386 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
55777347 GATAGAAAAT
55777357 GATA GATA GATA GATA GATA GATA GATA GA
1 GATA GATA GATA GATA GATA GATA GATA GA
55777387 GACCTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GATA
Found at i:55778813 original size:20 final size:20
Alignment explanation
Indices: 55778790--55778856 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
55778780 TTAGGTATCA
55778790 AAATTAAATTATAATTTTTT
1 AAATTAAATTATAATTTTTT
* *
55778810 AAATCAAAGTATAATTTTATTTT
1 AAATTAAATTATAA--TT-TTTT
* *
55778833 ATATTAATTTATAATTTTTT
1 AAATTAAATTATAATTTTTT
55778853 AAAT
1 AAAT
55778857 CAACTTGGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 19 0.51
21 2 0.05
22 2 0.05
23 14 0.38
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
AAATTAAATTATAATTTTTT
Found at i:55779881 original size:18 final size:18
Alignment explanation
Indices: 55779863--55779900 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
55779853 ATATTTTAAT
55779863 TTATTAATTAT-TTAAAA
1 TTATTAATTATATTAAAA
*
55779880 TTATTTATTATATT-AAA
1 TTATTAATTATATTAAAA
55779897 TTAT
1 TTAT
55779901 AAATATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTAATTATATTAAAA
Found at i:55779883 original size:17 final size:17
Alignment explanation
Indices: 55779858--55779900 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
55779848 TACAAATATT
*
55779858 TTAATTTATTAATTAT-
1 TTAAATTATTAATTATA
*
55779874 TTAAAATTATTTATTATA
1 TT-AAATTATTAATTATA
55779892 TTAAATTAT
1 TTAAATTAT
55779901 AAATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATTATTAATTATA
Found at i:55786499 original size:3 final size:3
Alignment explanation
Indices: 55786491--55786553 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
55786481 TCATAATGCC
55786491 TAA TAA TAA TAA 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 TAA TAA TAA TAA
55786539 TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA T
55786554 CTTTGCCCCT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55789761 original size:31 final size:31
Alignment explanation
Indices: 55789726--55789800 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
55789716 ATTTTTTGTT
55789726 TTATTTTTTTCTCATTT-TCCAATGAATGCAG
1 TTATTTTTTTCT-ATTTGTCCAATGAATGCAG
* *
55789757 TTATTTTTTTCTTTTTGTTCAATGAATGCAG
1 TTATTTTTTTCTATTTGTCCAATGAATGCAG
*
55789788 TTGATTTCTTTCT
1 TT-ATTTTTTTCT
55789801 TTGATCAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.08
31 27 0.69
32 9 0.23
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (31 bp):
TTATTTTTTTCTATTTGTCCAATGAATGCAG
Found at i:55795587 original size:2 final size:2
Alignment explanation
Indices: 55795582--55795629 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
55795572 CCGTACACAC
* *
55795582 AT AT AT CT AT CT AT AT 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 AT AT AT AT AT AT AT AT
55795624 AT AT AT
1 AT AT AT
55795630 TTTATGCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55801036 original size:14 final size:15
Alignment explanation
Indices: 55801010--55801043 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
55801000 AAATTCTTTG
*
55801010 TTTTTTCTGATTTTC
1 TTTTTTCTGATTTCC
55801025 TTTTTTCT-ATTTCC
1 TTTTTTCTGATTTCC
55801039 TTTTT
1 TTTTT
55801044 CTAGTTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTCTGATTTCC
Found at i:55801176 original size:7 final size:7
Alignment explanation
Indices: 55801166--55801202 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
55801156 TATTATTTAG
55801166 AAATATA
1 AAATATA
55801173 AAATATA
1 AAATATA
55801180 AAATATA
1 AAATATA
55801187 AAATATA
1 AAATATA
55801194 AAATATA
1 AAATATA
55801201 AA
1 AA
55801203 TATTAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Done.