Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 99 of 199
Found at i:30177158 original size:25 final size:25
Alignment explanation
Indices: 30177129--30177181 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
30177119 TTTTAATTTT
* *
30177129 ATTATCTAATTTTTTA-ATTTATTAA
1 ATTAT-TAATATTTTATATTAATTAA
30177154 ATTATTAATATTTTATATTAATTAA
1 ATTATTAATATTTTATATTAATTAA
30177179 ATT
1 ATT
30177182 TTTGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATTAATATTTTATATTAATTAA
Found at i:30181888 original size:42 final size:42
Alignment explanation
Indices: 30181829--30181913 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
30181819 TAAATAGACA
30181829 TAGTCTACTCTTGTAATCATCCGAATTCGACATAGTGAATTT
1 TAGTCTACTCTTGTAATCATCCGAATTCGACATAGTGAATTT
*
30181871 TAGTCTACTCTTGTAATCATTCGAATTCGACATAGTGAATTT
1 TAGTCTACTCTTGTAATCATCCGAATTCGACATAGTGAATTT
30181913 T
1 T
30181914 CTTCTTCTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (42 bp):
TAGTCTACTCTTGTAATCATCCGAATTCGACATAGTGAATTT
Found at i:30188893 original size:46 final size:47
Alignment explanation
Indices: 30188793--30188902 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 47
30188783 TATGAACCAT
*
30188793 CATAAAACCACATATACACAAGCCAACATGAAAACTAATTCATTAAC
1 CATAAAACCACATATACACAAGCCAACATGAAAACTAATTCATCAAC
* * * * *
30188840 CAAAAAACCACAT-T-TACAAGCCTAACAT-AATGACTATTTCATCAAG
1 CATAAAACCACATATACACAAGCC-AACATGAA-AACTAATTCATCAAC
*
30188886 CATAAAA-CACCTATACA
1 CATAAAACCACATATACA
30188903 TGCTATTATA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
45 13 0.26
46 24 0.48
47 13 0.26
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.21
Consensus pattern (47 bp):
CATAAAACCACATATACACAAGCCAACATGAAAACTAATTCATCAAC
Found at i:30189433 original size:29 final size:29
Alignment explanation
Indices: 30189296--30189524 Score: 162
Period size: 29 Copynumber: 7.9 Consensus size: 29
30189286 AGTGGAAAGA
* * *
30189296 TGATGGTCGTCACCATACCTTTTCGTAGT
1 TGATGGTCATCACCATCCCTTTTCATAGT
* * *
30189325 TGCTGGTCATCACCGTCCCTTTTCATAAT
1 TGATGGTCATCACCATCCCTTTTCATAGT
* * ** *
30189354 CGATAG-CCGCAACTATCCCTTTTCATA-T
1 TGATGGTCATC-ACCATCCCTTTTCATAGT
** *
30189382 TCGATGGTCATCACCATTGCTTTTCACAGT
1 T-GATGGTCATCACCATCCCTTTTCATAGT
* *
30189412 TGATGGTCATCACCATCCCTTTTAATA-A
1 TGATGGTCATCACCATCCCTTTTCATAGT
* * * * *
30189440 TCAGTAGTCGA--AGCTATCCCTTTTAATAAT
1 TGA-TGGTC-ATCA-CCATCCCTTTTCATAGT
* *
30189470 TGATGATCGTCACCATCCCTTTTCATAGT
1 TGATGGTCATCACCATCCCTTTTCATAGT
*
30189499 TGATGGTCGTCACCATCCCTTTTCAT
1 TGATGGTCATCACCATCCCTTTTCAT
30189525 TGGTCGATGA
Statistics
Matches: 152, Mismatches: 38, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
28 6 0.04
29 138 0.91
30 8 0.05
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (29 bp):
TGATGGTCATCACCATCCCTTTTCATAGT
Found at i:30189457 original size:87 final size:87
Alignment explanation
Indices: 30189296--30189521 Score: 287
Period size: 87 Copynumber: 2.6 Consensus size: 87
30189286 AGTGGAAAGA
* * * *
30189296 TGATGGTCGTCACCATACCTTTTCGTAGTTGCTGGTCATCACCGTCCCTTTTCATAATCGATAGC
1 TGATGGTCGTCACCATACCTTTTCATAGTTGATGGTCATCACCATCCCTTTTAATAATCGATAGC
*
30189361 CGCAACTATCCCTTTTCAT-AT
66 CGCAACTATCCCTTTTAATAAT
* ** *
30189382 TCGATGGTCATCACCATTGCTTTTCACAGTTGATGGTCATCACCATCCCTTTTAATAATC-AGTA
1 T-GATGGTCGTCACCATACCTTTTCATAGTTGATGGTCATCACCATCCCTTTTAATAATCGA-TA
*
30189446 GTCG-AAGCTATCCCTTTTAATAAT
64 GCCGCAA-CTATCCCTTTTAATAAT
* * *
30189470 TGATGATCGTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTT
1 TGATGGTCGTCACCATACCTTTTCATAGTTGATGGTCATCACCATCCCTTTT
30189522 CATTGGTCGA
Statistics
Matches: 120, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
86 4 0.03
87 113 0.94
88 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.37
Consensus pattern (87 bp):
TGATGGTCGTCACCATACCTTTTCATAGTTGATGGTCATCACCATCCCTTTTAATAATCGATAGC
CGCAACTATCCCTTTTAATAAT
Found at i:30192455 original size:22 final size:23
Alignment explanation
Indices: 30192412--30192455 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
30192402 GAAGATGAAT
*
30192412 AGGAAATATTCTCTGGCTAGAAC
1 AGGAAATATTCTCTGGCAAGAAC
30192435 AGGAAATATTC-CTGGCAAGAA
1 AGGAAATATTCTCTGGCAAGAA
30192456 AACACGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (23 bp):
AGGAAATATTCTCTGGCAAGAAC
Found at i:30192694 original size:15 final size:15
Alignment explanation
Indices: 30192676--30192714 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
30192666 AACTCGTTTC
30192676 TTCAAATTTTAAGTT
1 TTCAAATTTTAAGTT
*
30192691 TTCAAAAATTTAAGTT
1 TTC-AAATTTTAAGTT
*
30192707 TTTAAATT
1 TTCAAATT
30192715 ATTTTCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (15 bp):
TTCAAATTTTAAGTT
Found at i:30202072 original size:11 final size:12
Alignment explanation
Indices: 30202051--30202083 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
30202041 TACATGATAA
30202051 TAAACTAAAAAT
1 TAAACTAAAAAT
30202063 TAAA-TAAAAAT
1 TAAACTAAAAAT
*
30202074 TAAATTAAAA
1 TAAACTAAAA
30202084 GAGAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAACTAAAAAT
Found at i:30204595 original size:20 final size:21
Alignment explanation
Indices: 30204570--30204611 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30204560 CACATGGTAG
*
30204570 TGTGTTTGA-AAACCGTAACT
1 TGTGTTGGATAAACCGTAACT
30204590 TGTGTTGGATAAACCGTAACT
1 TGTGTTGGATAAACCGTAACT
30204611 T
1 T
30204612 CGCTTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (21 bp):
TGTGTTGGATAAACCGTAACT
Found at i:30210096 original size:31 final size:32
Alignment explanation
Indices: 30210037--30210101 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
30210027 GGCAAATTAC
*
30210037 AAGAGTAATTGAATCCTGATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
30210069 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
30210100 AA
1 AA
30210102 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:30220027 original size:28 final size:28
Alignment explanation
Indices: 30219987--30220060 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
30219977 AATACAGCGT
*
30219987 GGGCCTTAGCCCAATACAGTAACAATGC
1 GGGCCTTAGCCCAATACAGTAACAATAC
* *
30220015 GGGCCTTAGCCCAATATAGTAACAATAT
1 GGGCCTTAGCCCAATACAGTAACAATAC
30220043 GGGCCTTAGCCCAATACA
1 GGGCCTTAGCCCAATACA
30220061 ATATCGGTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (28 bp):
GGGCCTTAGCCCAATACAGTAACAATAC
Found at i:30220437 original size:27 final size:27
Alignment explanation
Indices: 30220407--30220521 Score: 122
Period size: 27 Copynumber: 4.3 Consensus size: 27
30220397 GGGTATAACA
* * *
30220407 GTCATTTTACCCTATGGGGGTATTTCT
1 GTCATTTTACCCTATGAGGGTAATTCG
* * *
30220434 GTCATTTTAACCGATTAGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
* *
30220461 GTCATTTTACCGTATAAGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
* * *
30220488 GTCATTTTATCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
*
30220515 ATCATTT
1 GTCATTT
30220522 ATTGACCTCT
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTAATTCG
Found at i:30235168 original size:27 final size:27
Alignment explanation
Indices: 30235124--30235340 Score: 258
Period size: 27 Copynumber: 8.1 Consensus size: 27
30235114 CACTATTGCA
* *
30235124 ACCGAAATCCCCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
** ** * *
30235151 ATTGAAATACCCTTATAGGGTAGAATA
1 ACCGAAATACCCCCATAGGGTAAAATG
30235178 ACCGAAATACCCCCATA-GGTGAAAATG
1 ACCGAAATACCCCCATAGGGT-AAAATG
*
30235205 ACCGAAACACCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* * *
30235232 ACCAAAATAGCCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
*
30235259 ACCAAAATA-CCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
30235285 ATCGAAATACCCCCATAGGGTAACATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
30235312 ATCGAAATACCCTCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
30235339 AC
1 AC
30235341 TGATATGACC
Statistics
Matches: 163, Mismatches: 24, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
26 26 0.16
27 134 0.82
28 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (27 bp):
ACCGAAATACCCCCATAGGGTAAAATG
Found at i:30235307 original size:80 final size:81
Alignment explanation
Indices: 30235124--30235340 Score: 287
Period size: 80 Copynumber: 2.7 Consensus size: 81
30235114 CACTATTGCA
* * * * * *
30235124 ACCGAAATCCCCCCATAGGGTAGAATGATTGAAATACCCTTATAGGGTAGAATAACCGAAATACC
1 ACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCTCATAGGGTAGAATGACCAAAATACC
30235189 CCCATAGGTGAAAATG
66 CCCATAGGTGAAAATG
* * *
30235205 ACCGAAACACCCCCATAGGGTAAAATGACCAAAATAGCCC-CATAGGGTAGAATGACCAAAATA-
1 ACCGAAATACCCCCATAGGGTAAAATGATCGAAATA-CCCTCATAGGGTAGAATGACCAAAATAC
30235268 CCCCATAGG-GTAAAATG
65 CCCCATAGGTG-AAAATG
* * *
30235285 ATCGAAATACCCCCATAGGGTAACATGATCGAAATACCCTCATAGGGTAAAATGAC
1 ACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCTCATAGGGTAGAATGAC
30235341 TGATATGACC
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
79 4 0.03
80 61 0.52
81 50 0.42
82 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (81 bp):
ACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCTCATAGGGTAGAATGACCAAAATACC
CCCATAGGTGAAAATG
Found at i:30235481 original size:26 final size:26
Alignment explanation
Indices: 30235451--30235513 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
30235441 TGGAGGAAGT
* *
30235451 ATACTGTTACTGGCAGATTTGCTGCG
1 ATACTGTTACTGGCAGATTAGCTACG
*
30235477 ATACTGTTACTGGCAGCTTAGCTACG
1 ATACTGTTACTGGCAGATTAGCTACG
*
30235503 ATACTATTACT
1 ATACTGTTACT
30235514 AGTAGCTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGATTAGCTACG
Found at i:30235526 original size:26 final size:25
Alignment explanation
Indices: 30235451--30235531 Score: 63
Period size: 26 Copynumber: 3.1 Consensus size: 25
30235441 TGGAGGAAGT
* * * *
30235451 ATACTGTTACTGGCAGATTTGCTGCG
1 ATACTATTACTAGCAG-CTTGCTACG
* *
30235477 ATACTGTTACTGGCAGCTTAGCTACG
1 ATACTATTACTAGCAGCTT-GCTACG
* *
30235503 ATACTATTACTAGTAGCTCTGCTATG
1 ATACTATTACTAGCAGCT-TGCTACG
30235529 ATA
1 ATA
30235532 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.04
26 44 0.94
27 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (25 bp):
ATACTATTACTAGCAGCTTGCTACG
Found at i:30245439 original size:16 final size:15
Alignment explanation
Indices: 30245400--30245438 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
30245390 AATATATATA
30245400 TATTTTTTTCATTCT
1 TATTTTTTTCATTCT
30245415 TATTTTTTTCA-TCT
1 TATTTTTTTCATTCT
30245429 CTATTTTTTT
1 -TATTTTTTT
30245439 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTTTTCATTCT
Found at i:30246096 original size:28 final size:28
Alignment explanation
Indices: 30246063--30246116 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
30246053 ACTTAAACAC
30246063 AAACAATAATTCAAGGGCTATATTGTAT
1 AAACAATAATTCAAGGGCTATATTGTAT
30246091 AAACAATAATTCAAGGGCTATATTGT
1 AAACAATAATTCAAGGGCTATATTGT
30246117 CTACGTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (28 bp):
AAACAATAATTCAAGGGCTATATTGTAT
Found at i:30246856 original size:20 final size:21
Alignment explanation
Indices: 30246814--30246861 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
30246804 TGCATGATAA
30246814 AATAAAATAAAAAACAAAAAC
1 AATAAAATAAAAAACAAAAAC
*
30246835 AA-AAAATAAAAATA-AAATAC
1 AATAAAATAAAAA-ACAAAAAC
30246855 AATAAAA
1 AATAAAA
30246862 GCAAAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (21 bp):
AATAAAATAAAAAACAAAAAC
Found at i:30246908 original size:6 final size:6
Alignment explanation
Indices: 30246892--30246940 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
30246882 AAAAATAAAC
30246892 AAATA- AAATAT AAATAT AAATAT AAATAT -AATAT AAA-ACT AAAT-T
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATA-T AAATAT
30246937 AAAT
1 AAAT
30246941 CACTTTGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 16 0.40
6 24 0.60
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:30246914 original size:12 final size:12
Alignment explanation
Indices: 30246892--30246940 Score: 61
Period size: 11 Copynumber: 4.3 Consensus size: 12
30246882 AAAAATAAAC
30246892 AAATA-AAATAT
1 AAATATAAATAT
30246903 AAATATAAATAT
1 AAATATAAATAT
30246915 AAATAT-AATAT
1 AAATATAAATAT
30246926 AAA-ACTAAAT-T
1 AAATA-TAAATAT
30246937 AAAT
1 AAAT
30246941 CACTTTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 18 0.53
12 15 0.44
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATAAATAT
Found at i:30254515 original size:158 final size:158
Alignment explanation
Indices: 30254222--30254538 Score: 589
Period size: 158 Copynumber: 2.0 Consensus size: 158
30254212 GATTGAACCC
*
30254222 ATAAGTTGGTGTTTAGGGGTTGTATAAGAGGTGTATTAATTAATTTCTATATTGATTTAAGTTAA
1 ATAAGTTGGTGTTTAGGGGTTGTATAAGAGGTGTATTAATTAATTTATATATTGATTTAAGTTAA
* *
30254287 TTTAATTTAATTTAGGTCTGTTTTAAAGTTTATTAAAAAACAACAAGATTCGCTAGTTTGCTGCG
66 TTTAATTTAATTTAGGTCTATTTTAAAGTTTATTAAAAAACAACAAGATTCGCTAGTGTGCTGCG
*
30254352 AAAGGGCGTAAATAATTTGTGGGTCTAA
131 AAAGGGCGTAAATAATGTGTGGGTCTAA
*
30254380 ATAATTTGGTGTTTAGGGGTTGTATAAGAGGTGTATTAATTAATTTATATATTGATTTAAGTTAA
1 ATAAGTTGGTGTTTAGGGGTTGTATAAGAGGTGTATTAATTAATTTATATATTGATTTAAGTTAA
30254445 TTTAATTTAATTTAGGTCTATTTTAAAGTTTATTAAAAAACAACAAGATTCGCTAGTGTGCTGCG
66 TTTAATTTAATTTAGGTCTATTTTAAAGTTTATTAAAAAACAACAAGATTCGCTAGTGTGCTGCG
30254510 AAAGGGCGTAAATAATGTGTGGGTCTAA
131 AAAGGGCGTAAATAATGTGTGGGTCTAA
30254538 A
1 A
30254539 CTCAAAACTT
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 154 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (158 bp):
ATAAGTTGGTGTTTAGGGGTTGTATAAGAGGTGTATTAATTAATTTATATATTGATTTAAGTTAA
TTTAATTTAATTTAGGTCTATTTTAAAGTTTATTAAAAAACAACAAGATTCGCTAGTGTGCTGCG
AAAGGGCGTAAATAATGTGTGGGTCTAA
Found at i:30264766 original size:5 final size:5
Alignment explanation
Indices: 30264756--30264780 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30264746 CAAACGGACC
30264756 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
30264781 CACTTTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:30269094 original size:25 final size:25
Alignment explanation
Indices: 30269048--30269110 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
30269038 CTGTCTTTGA
* *
30269048 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
* *
30269073 TAGTATATATTGAGACTACTATA--
1 TAGTATATACTGAAACTACTATAGG
30269096 TAG-ACTATACTGAAA
1 TAGTA-TATACTGAAA
30269111 ACACTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 1 0.03
23 11 0.35
25 19 0.61
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:30299439 original size:19 final size:20
Alignment explanation
Indices: 30299415--30299452 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
30299405 AAAAATAATA
30299415 TTTTATCTTAGTTT-CCAAT
1 TTTTATCTTAGTTTGCCAAT
30299434 TTTTATCTTAGTTTGCCAA
1 TTTTATCTTAGTTTGCCAA
30299453 GAAAGCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTTATCTTAGTTTGCCAAT
Found at i:30306667 original size:40 final size:41
Alignment explanation
Indices: 30306619--30306699 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
30306609 ATAATAGTTT
* *
30306619 GGGCCTTAGCCCATCTCAGTA-CAGTATCAAAT-ATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAGTAGC-AATCATGCAGTA
*
30306659 GGGCCTTAGCCCATCACTGTATCAGTAGCAATCATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
30306700 TTCAGTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 22 0.61
41 14 0.39
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
GGGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
Found at i:30307170 original size:17 final size:18
Alignment explanation
Indices: 30307137--30307170 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30307127 CCATGTTGTC
*
30307137 TGCCCGTGTGAGCCCACA
1 TGCCCATGTGAGCCCACA
30307155 TGCCCATGTG-GCCCAC
1 TGCCCATGTGAGCCCAC
30307171 TCGGCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (18 bp):
TGCCCATGTGAGCCCACA
Found at i:30311168 original size:18 final size:18
Alignment explanation
Indices: 30311134--30311168 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30311124 AATCTTTTCC
*
30311134 CTTTTACTTCTCCCAAAA
1 CTTTTACTTCTACCAAAA
*
30311152 CTTTTACTTCTAGCAAA
1 CTTTTACTTCTACCAAA
30311169 CCTCGCCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.40
Consensus pattern (18 bp):
CTTTTACTTCTACCAAAA
Found at i:30312710 original size:66 final size:66
Alignment explanation
Indices: 30312622--30312761 Score: 228
Period size: 66 Copynumber: 2.1 Consensus size: 66
30312612 AACATAAGTT
*
30312622 ATTGGAACATCTATCAGGGCAGCTTCATCAATGATTGGAACATCTATCGGGGC-AGTTTCATCAT
1 ATTGGAACATCTATCAGAGCAGCTTCATCAATGATTGGAACATCTATCGGGGCAAG-TTCATCAT
30312686 TG
65 TG
* *
30312688 ATTGGAATATCTATCAGAGCAGCTTCATCAATGATTGGAACATCTATCGGGGCAAGTTCATTATT
1 ATTGGAACATCTATCAGAGCAGCTTCATCAATGATTGGAACATCTATCGGGGCAAGTTCATCATT
30312753 G
66 G
*
30312754 ATTAGAAC
1 ATTGGAAC
30312762 TCCTATTGGG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
66 66 0.97
67 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (66 bp):
ATTGGAACATCTATCAGAGCAGCTTCATCAATGATTGGAACATCTATCGGGGCAAGTTCATCATT
G
Found at i:30312756 original size:33 final size:33
Alignment explanation
Indices: 30312622--30312741 Score: 186
Period size: 33 Copynumber: 3.6 Consensus size: 33
30312612 AACATAAGTT
30312622 ATTGGAACATCTATCAGGGCAGCTTCATCAATG
1 ATTGGAACATCTATCAGGGCAGCTTCATCAATG
* * *
30312655 ATTGGAACATCTATCGGGGCAGTTTCATCATTG
1 ATTGGAACATCTATCAGGGCAGCTTCATCAATG
* *
30312688 ATTGGAATATCTATCAGAGCAGCTTCATCAATG
1 ATTGGAACATCTATCAGGGCAGCTTCATCAATG
*
30312721 ATTGGAACATCTATCGGGGCA
1 ATTGGAACATCTATCAGGGCA
30312742 AGTTCATTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (33 bp):
ATTGGAACATCTATCAGGGCAGCTTCATCAATG
Found at i:30320804 original size:620 final size:618
Alignment explanation
Indices: 30319619--30321420 Score: 2972
Period size: 620 Copynumber: 2.9 Consensus size: 618
30319609 TTATTGTTTT
* * * *
30319619 TATTATAGGACAACACCATTGTGGATTTTATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
1 TATTGTAGGACAACACCATTGTGAACTTCATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
30319684 GGCTATTAAAATTTTCCAAACAAGGAAATTTTCTTGCAATTATGGTAATATTTCTAACAATTTTG
66 GGCTATTAAAATTTTCCAAACAAGGAAATTTTCTTGCAATTATGGTAATATTTCTAACAATTTTG
* *
30319749 GCCTCTTCCTCAATAGGTATGTCTTTGTCACTAACCTATTTAGGCATCTCTCCAATAATCGGT-A
131 GCCTCTTCCTCAATAGGTATGTCTTTGTCACTAACCTATTTAGGCATCTCTTCAATAATCGATAA
*
30319813 AAAAAAAAGGTATAAGCAATATGATGGGTTTGGTGACTTTTTTTTGTTTGTTGTTTTTAAAAATA
196 AAAAAAAAGGTATAAGCAATGTGATGGGTTTGGTGAC-TTTTTTTGTTTGTTGTTTTTAAAAATA
*
30319878 ATTTTGTACTCTTCTATCTACCAACAATTGTGCTAACTTATATTTTTTGCATTTTCATTACAAAA
260 ATATTGTACTCTTCTATCTACCAACAATTGTGCTAACTTATA-TTTTTGCATTTTCATTACAAAA
*
30319943 TAATATTTTATCTTAGTTTCATA-TTTTATATAAGAAAAAGAAATCTAGACAATAAACAAATTCA
324 TAATTTTTTATCTTAGTTTCATATTTTTATATAAGAAAAAGAAATCTAGACAATAAACAAATTCA
*
30320007 A-TTTTTTATCAAGATATTTAGGACAACATTGAGCTGTTATTCCAAATTAACTCAATCTTACTAT
389 ATTTTTTTATCAAGATATTTAGGACAACATTGAGCTGTTATTCCAAATTAACTCAATCTTAGTAT
*
30320071 AACTTATAAATAAAAAATGAAAAGAAAAAAGAAGAAGAAAAATTGTCTATATTATCAGCTATTCT
454 AACTTATAAATAAAAAATGAAAAGAAAAAAGAAGAAGAAAAATTGTCTATATTATCAACTATTCT
* *
30320136 AAACGAAGACTTATGTAATGATCTT-ATAATATTTGTAACAACAACATCAACAACAAGAAAAAAT
519 AAAAGAAGATTTATGTAATGAT-TTAATAATATTTGT---AACAACATCAACAACAAGAAAAAAT
30320200 ATAATGAGATATTATTAGACAACATAGATAAACGAGATA
580 ATAATGAGATATTATTAGACAACATAGATAAACGAGATA
30320239 TATTGTAGGACAACACCATTGTGAACTTCATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
1 TATTGTAGGACAACACCATTGTGAACTTCATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
* *
30320304 AGCTATTAAAATTTTCCAAATAAGGAAATTTTCTTGCAATTATGGTAATATTTCTAACAATTTTG
66 GGCTATTAAAATTTTCCAAACAAGGAAATTTTCTTGCAATTATGGTAATATTTCTAACAATTTTG
* * * *
30320369 GTCTCTTCCTCAATAGGAATGTCTTTGTCACTAACCTATTTAGCCCTCTCTTCAATAATCGATAA
131 GCCTCTTCCTCAATAGGTATGTCTTTGTCACTAACCTATTTAGGCATCTCTTCAATAATCGATAA
30320434 AAAAAAAAGGTATAAGCAATGTGATGGGTTTGGTGACATTTTTTTGTTTGTTGTTTTTAAAAATA
196 AAAAAAAAGGTATAAGCAATGTGATGGGTTTGGTGAC-TTTTTTTGTTTGTTGTTTTTAAAAATA
30320499 ATATTGTACTCTTCTATCTACCAACAATTGTGCTAACTTATATTTTTGCATTTTCATTACAAAAT
260 ATATTGTACTCTTCTATCTACCAACAATTGTGCTAACTTATATTTTTGCATTTTCATTACAAAAT
*
30320564 AATTTTTTATCTTAGTTTCATATTTTTTATTTAAGAAAAAGAAATCTAGACAATAAACAAATTCA
325 AATTTTTTATCTTAGTTTCATA-TTTTTATATAAGAAAAAGAAATCTAGACAATAAACAAATTCA
* *
30320629 ATTTTTTTATCAAGATATTTAGAACAACATTGAGCTGTTATTCCAAGTTAACTCAATCTTAGTAT
389 ATTTTTTTATCAAGATATTTAGGACAACATTGAGCTGTTATTCCAAATTAACTCAATCTTAGTAT
* * *
30320694 AACTTATAAATAAAAAATGAAAACAAAAAAGAAAAAGAAAAATTGTCTATATTATCAACTATTCA
454 AACTTATAAATAAAAAATGAAAAGAAAAAAGAAGAAGAAAAATTGTCTATATTATCAACTATTCT
*
30320759 AAAAGAAGATTTATGTAATGATTTAATAATATTTGTAACAACATCAACAACAAGAAAAATTATAA
519 AAAAGAAGATTTATGTAATGATTTAATAATATTTGTAACAACATCAACAACAAGAAAAAATATAA
*
30320824 TGAGATATTATTAGACAACATTGATAAACGAGATA
584 TGAGATATTATTAGACAACATAGATAAACGAGATA
* *
30320859 TATTGTAGGAGAACACCATTGCGAACTTCATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
1 TATTGTAGGACAACACCATTGTGAACTTCATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
* * *
30320924 GGTTATTAAAATTTTCCAAACAAGGAAATTTTCTTGCAATTATAGTAATATTTCTAAAAATTTTG
66 GGCTATTAAAATTTTCCAAACAAGGAAATTTTCTTGCAATTATGGTAATATTTCTAACAATTTTG
*
30320989 GCCTCTTCCTCAATAGGTATGTCTTTGTCACTAACCTATTTAGGCATCTC-TCTAATAATTGGTA
131 GCCTCTTCCTCAATAGGTATGTCTTTGTCACTAACCTATTTAGGCATCTCTTC-AATAA-TCG-A
* * *
30321053 AAAAAAAAAAAGGTATAAGTAATGTGATGGGTTTGGTGACTTTTTTTGTTTGATT-TTTCTTTAA
193 TAAAAAAAAAAGGTATAAGCAATGTGATGGGTTTGGTGACTTTTTTTGTTTG-TTGTTT-TTAAA
* *
30321117 AATAATATTGTACTCTTCTATCTACGAACAATTGTGCTAACTTATCTTTTTGCATTTTCATTACA
256 AATAATATTGTACTCTTCTATCTACCAACAATTGTGCTAACTTATATTTTTGCATTTTCATTACA
* * *
30321182 AAATAA-TTTTCATCTTAGTTTCATATTTTTATATAAGAAAAAGAAATCTAGACAGTAAACAACT
321 AAATAATTTTTTATCTTAGTTTCATATTTTTATATAAGAAAAAGAAATCTAGACAATAAACAAAT
* * *
30321246 TCAATTTTTTTATGAAGATATTTAGGACAACATTAAGCTGTTATTCTAAATTAACTCAATCTTAG
386 TCAATTTTTTTATCAAGATATTTAGGACAACATTGAGCTGTTATTCCAAATTAACTCAATCTTAG
* * * *
30321311 TATAACTTACAAATAAAAAATGAAAAGAAAAAA-AGGAAGAAAAATGGTTTATATTATCAACTAT
451 TATAACTTATAAATAAAAAATGAAAAGAAAAAAGAAGAAGAAAAATTGTCTATATTATCAACTAT
* * *
30321375 TCTAAAAGAAGATTTATGTGATGATCTATTAATATTTGTAACAACA
516 TCTAAAAGAAGATTTATGTAATGATTTAATAATATTTGTAACAACA
30321421 ACAAGAAAAT
Statistics
Matches: 1108, Mismatches: 64, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
619 71 0.06
620 588 0.53
621 140 0.13
622 157 0.14
623 152 0.14
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (618 bp):
TATTGTAGGACAACACCATTGTGAACTTCATTGTGAAAGGTATTCAACAGTAAATAATTCTTCTT
GGCTATTAAAATTTTCCAAACAAGGAAATTTTCTTGCAATTATGGTAATATTTCTAACAATTTTG
GCCTCTTCCTCAATAGGTATGTCTTTGTCACTAACCTATTTAGGCATCTCTTCAATAATCGATAA
AAAAAAAAGGTATAAGCAATGTGATGGGTTTGGTGACTTTTTTTGTTTGTTGTTTTTAAAAATAA
TATTGTACTCTTCTATCTACCAACAATTGTGCTAACTTATATTTTTGCATTTTCATTACAAAATA
ATTTTTTATCTTAGTTTCATATTTTTATATAAGAAAAAGAAATCTAGACAATAAACAAATTCAAT
TTTTTTATCAAGATATTTAGGACAACATTGAGCTGTTATTCCAAATTAACTCAATCTTAGTATAA
CTTATAAATAAAAAATGAAAAGAAAAAAGAAGAAGAAAAATTGTCTATATTATCAACTATTCTAA
AAGAAGATTTATGTAATGATTTAATAATATTTGTAACAACATCAACAACAAGAAAAAATATAATG
AGATATTATTAGACAACATAGATAAACGAGATA
Found at i:30325250 original size:2 final size:2
Alignment explanation
Indices: 30325243--30325267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30325233 TTATTCATTT
30325243 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 T
30325268 TTAACATGTG
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30327991 original size:19 final size:19
Alignment explanation
Indices: 30327963--30328002 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30327953 TAATACTAAC
* *
30327963 ATTAATATTAAAAATAAAG
1 ATTAAGATTAAAAACAAAG
*
30327982 ATTAAGATTAATAACAAAG
1 ATTAAGATTAAAAACAAAG
30328001 AT
1 AT
30328003 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (19 bp):
ATTAAGATTAAAAACAAAG
Found at i:30328022 original size:20 final size:20
Alignment explanation
Indices: 30327997--30328034 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30327987 GATTAATAAC
30327997 AAAGATAAAAATAAGAAATA
1 AAAGATAAAAATAAGAAATA
*
30328017 AAAGATAAAACTAAGAAA
1 AAAGATAAAAATAAGAAA
30328035 AGATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAGATAAAAATAAGAAATA
Found at i:30335661 original size:30 final size:30
Alignment explanation
Indices: 30335622--30335678 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
30335612 TTTTATAAAT
30335622 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
30335652 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
30335679 AACAATAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:30335904 original size:13 final size:13
Alignment explanation
Indices: 30335852--30335904 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
30335842 TTTAAACCAA
*
30335852 ACTTTTCAAAAGA
1 ACTTTTCAAAAGC
*
30335865 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
30335878 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
30335891 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
30335904 A
1 A
30335905 ATGAAGAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:30339828 original size:33 final size:34
Alignment explanation
Indices: 30339779--30339845 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
30339769 CATACAACAT
*
30339779 GCAGTAATAGTTTGGGCCTGAGCCCTATT-CAGTA
1 GCAGTAATAGTGTGGGCCTGAGCCC-ATTACAGTA
*
30339813 GCAGT-ATAGTGTGGGCCTTAGCCCATTACAGTA
1 GCAGTAATAGTGTGGGCCTGAGCCCATTACAGTA
30339846 ATAGTGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 3 0.10
33 22 0.73
34 5 0.17
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (34 bp):
GCAGTAATAGTGTGGGCCTGAGCCCATTACAGTA
Found at i:30339853 original size:28 final size:28
Alignment explanation
Indices: 30339814--30339905 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
30339804 TATTCAGTAG
*
30339814 CAGT-ATAGTGTGGGCCTTAGCCCATTA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
*
30339841 CAGTAATAGTGTGTGGGCCTTATCCCAATA
1 CAGTAATA--GTGTGGGCCTTAGCCCAATA
* *
30339871 CAGTAACAGTGTGAGCCTTAGCCCAATA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
30339899 CAGTAAT
1 CAGTAAT
30339906 CAGTACAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.07
28 27 0.48
30 25 0.45
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (28 bp):
CAGTAATAGTGTGGGCCTTAGCCCAATA
Found at i:30339857 original size:30 final size:29
Alignment explanation
Indices: 30339780--30339905 Score: 121
Period size: 28 Copynumber: 4.2 Consensus size: 29
30339770 ATACAACATG
* * * *
30339780 CAGTAATA-GTTTGGGCCTGAGCCCTATT
1 CAGTAATATGTGTGGGCCTTAGCCCAATA
*
30339808 CAGTAGCAGTATAGTGTGGGCCTTAGCCCATTA
1 CAGTA--A-TAT-GTGTGGGCCTTAGCCCAATA
*
30339841 CAGTAATAGTGTGTGGGCCTTATCCCAATA
1 CAGTAATA-TGTGTGGGCCTTAGCCCAATA
* *
30339871 CAGTAACA-GTGTGAGCCTTAGCCCAATA
1 CAGTAATATGTGTGGGCCTTAGCCCAATA
30339899 CAGTAAT
1 CAGTAAT
30339906 CAGTACAATG
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
28 29 0.36
30 28 0.35
31 4 0.05
33 20 0.25
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (29 bp):
CAGTAATATGTGTGGGCCTTAGCCCAATA
Found at i:30340385 original size:27 final size:27
Alignment explanation
Indices: 30340237--30340384 Score: 174
Period size: 27 Copynumber: 5.5 Consensus size: 27
30340227 AGGGCTATAA
* *
30340237 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTTTGAGGGTATTT
*
30340264 C-GATCATTTTACCCTTCGAGGGTATTT
1 CAG-TCATTTTACCCTTTGAGGGTATTT
* * **
30340291 CTGTTATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTTTGAGGGTATTT
* *
30340318 CGGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTTGAGGGTATTT
*
30340345 CAGTAATTTTA-CCTTTGAAGGGTATTT
1 CAGTCATTTTACCCTTTG-AGGGTATTT
30340372 CAGTCATTTTACC
1 CAGTCATTTTACC
30340385 TATAATTCAC
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
26 6 0.06
27 97 0.92
28 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTTTGAGGGTATTT
Found at i:30349427 original size:31 final size:31
Alignment explanation
Indices: 30349390--30349458 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
30349380 TCAAAATGAT
**
30349390 TATGAATTGTTACGGGATGTGTATTGAGAAA
1 TATGAATTGTTACGACATGTGTATTGAGAAA
30349421 TATGAATTGTTACGACATGTGTATTGAGAAA
1 TATGAATTGTTACGACATGTGTATTGAGAAA
30349452 TATGAAT
1 TATGAAT
30349459 ATATGTATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (31 bp):
TATGAATTGTTACGACATGTGTATTGAGAAA
Found at i:30350104 original size:34 final size:34
Alignment explanation
Indices: 30350060--30350127 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
30350050 GCACAGTTGA
* *
30350060 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
30350095 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
30350128 TCAAAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:30356826 original size:16 final size:16
Alignment explanation
Indices: 30356801--30356860 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
30356791 TTATTTACAC
*
30356801 AGTCTGTAGTTGTCTT
1 AGTCTATAGTTGTCTT
* *
30356817 AGTCTATAGTTTTTCAT
1 AGTCTATAG-TTGTCTT
* *
30356834 AGTCAATAGTTGTCTC
1 AGTCTATAGTTGTCTT
30356850 AGTCTATAGTT
1 AGTCTATAGTT
30356861 TCAAATATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 22 0.63
17 13 0.37
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (16 bp):
AGTCTATAGTTGTCTT
Found at i:30369265 original size:102 final size:102
Alignment explanation
Indices: 30369089--30369291 Score: 327
Period size: 102 Copynumber: 2.0 Consensus size: 102
30369079 ATTGAATATA
* * * * *
30369089 AAGGGGTTGCTAAGTGCTAATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGATAATTCTCCGAATCATTGGCGGTTGCTAAGTGCTGATCCCACCGTATC
*
30369154 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCC
*
30369191 AAGGGGTTGCTAAGTGATGATTC-CCGGAATCATTGGCGGTTGCTAAGTGCTGATCCCACCGTAT
1 AAGGGGTTGCTAAGTGATAATTCTCC-GAATCATTGGCGGTTGCTAAGTGCTGATCCCACCGTAT
30369255 CTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
65 CTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
30369292 GATTCGCTGG
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 2 0.02
102 91 0.98
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (102 bp):
AAGGGGTTGCTAAGTGATAATTCTCCGAATCATTGGCGGTTGCTAAGTGCTGATCCCACCGTATC
TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:30369314 original size:75 final size:76
Alignment explanation
Indices: 30369191--30369371 Score: 256
Period size: 75 Copynumber: 2.4 Consensus size: 76
30369181 TGATTCCCCC
* * * *
30369191 AAGGGGTTGCTAAGTGATGATTCCCGGAATCATTGGCGGTTGCTAAGTGCTGATCCCACCGTA-T
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCACTGGCGGTTGCTAAGTGCTGATCCCACCGTATT
30369255 CTTAAATGTGA
66 CTTAAATGTGA
* * *
30369266 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCGCTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCACTGGCGGTTGCTAAGTGCTGATCCCACCGTATT
* *
30369331 TTTGAATGTGA
66 CTTAAATGTGA
*
30369342 AAGGGGTTGCTAAGTGCTGAATCCACCGAT
1 AAGGGGTTGCTAAGTGCTGATTCC-CCGAT
30369372 AATGGATAAC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 56 0.60
76 33 0.35
77 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCACTGGCGGTTGCTAAGTGCTGATCCCACCGTATT
CTTAAATGTGA
Found at i:30371549 original size:24 final size:27
Alignment explanation
Indices: 30371499--30371563 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 27
30371489 TTCTTGATTT
30371499 ATATTATAAAAATATTATTTAATTAAA
1 ATATTATAAAAATATTATTTAATTAAA
* *
30371526 ATATTATAAAATATATTAATTAAAGTTAAT
1 ATATTATAAAA-ATATT-ATTTAA-TTAAA
30371556 ATATTATA
1 ATATTATA
30371564 TTATAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 11 0.33
28 5 0.15
29 5 0.15
30 12 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATTATAAAAATATTATTTAATTAAA
Found at i:30371556 original size:28 final size:26
Alignment explanation
Indices: 30371499--30371563 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 26
30371489 TTCTTGATTT
*
30371499 ATATTATAAAAATATTATTTAATTAAA
1 ATATTATAAAAATATTATTAAATT-AA
30371526 ATATTATAAAATATATTAATTAAAGTTAA
1 ATATTATAAAA-ATATT-ATTAAA-TTAA
30371555 TATATTATA
1 -ATATTATA
30371564 TTATAGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 11 0.33
28 5 0.15
29 7 0.21
30 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAAATTAA
Found at i:30372025 original size:10 final size:10
Alignment explanation
Indices: 30372007--30372048 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
30371997 AACATAAAGT
*
30372007 AAATAAAATA
1 AAATGAAATA
30372017 AAATGAAATA
1 AAATGAAATA
30372027 AAA-GAAAGT-
1 AAATGAAA-TA
30372036 AAATGAAATA
1 AAATGAAATA
30372046 AAA
1 AAA
30372049 GAAGGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAATGAAATA
Found at i:30373150 original size:22 final size:23
Alignment explanation
Indices: 30373092--30373152 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
30373082 TTCGTTGACT
*
30373092 AGGCACTTTATGTGCCGTACATC
1 AGGCACTTTATGTGTCGTACATC
*
30373115 AGGCACTTTATGTGTCGTACCTC
1 AGGCACTTTATGTGTCGTACATC
30373138 AGGCAC-TTATGTGTC
1 AGGCACTTTATGTGTC
30373153 ATATATTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 9 0.25
23 27 0.75
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.33
Consensus pattern (23 bp):
AGGCACTTTATGTGTCGTACATC
Found at i:30373359 original size:12 final size:12
Alignment explanation
Indices: 30373322--30373364 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
30373312 AGGAAATTTA
30373322 AAATTGTGGATTG
1 AAATTGT-GATTG
*
30373335 AAATTG-AATTG
1 AAATTGTGATTG
30373346 AAATTGTGATTG
1 AAATTGTGATTG
30373358 AAATTGT
1 AAATTGT
30373365 TTCATGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 10 0.37
12 11 0.41
13 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (12 bp):
AAATTGTGATTG
Found at i:30379778 original size:10 final size:10
Alignment explanation
Indices: 30379760--30379801 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
30379750 AACATAAAGT
*
30379760 AAATAAAATA
1 AAATGAAATA
30379770 AAATGAAATA
1 AAATGAAATA
30379780 AAA-GAAAGT-
1 AAATGAAA-TA
30379789 AAATGAAATA
1 AAATGAAATA
30379799 AAA
1 AAA
30379802 GAAGGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAATGAAATA
Found at i:30380888 original size:22 final size:23
Alignment explanation
Indices: 30380827--30380893 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
30380817 GGCTTTGCCG
*
30380827 ATCAGGCACTTTATGTGCCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
30380850 ATCAGGCACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
*
30380873 CTCAGGCAC-TTATGTGTCGTA
1 ATCAGGCACTTTATGTGTCGTA
30380894 TATTGATCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 12 0.29
23 30 0.71
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAC
Found at i:30381117 original size:12 final size:12
Alignment explanation
Indices: 30381060--30381115 Score: 76
Period size: 12 Copynumber: 4.6 Consensus size: 12
30381050 AGGAAATTTA
30381060 AAATTGTGGATTG
1 AAATTGT-GATTG
*
30381073 AAATTGAGATTG
1 AAATTGTGATTG
30381085 AAATTGTGATTG
1 AAATTGTGATTG
* *
30381097 AAATAGTTATTG
1 AAATTGTGATTG
30381109 AAATTGT
1 AAATTGT
30381116 TACACGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
12 32 0.84
13 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.39
Consensus pattern (12 bp):
AAATTGTGATTG
Found at i:30391006 original size:15 final size:15
Alignment explanation
Indices: 30390986--30391022 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
30390976 TTCATGCAAA
30390986 ATCTTATCAAATACT
1 ATCTTATCAAATACT
*
30391001 ATCTTATCAAATGCT
1 ATCTTATCAAATACT
*
30391016 AACTTAT
1 ATCTTAT
30391023 GCATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (15 bp):
ATCTTATCAAATACT
Found at i:30396372 original size:28 final size:28
Alignment explanation
Indices: 30396330--30396442 Score: 174
Period size: 28 Copynumber: 4.0 Consensus size: 28
30396320 CTATTCAGTA
*
30396330 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
30396357 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
30396385 ATAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
30396413 ACAGTAACAATGTGGACCTTGAACCCAAT
1 ACAGTAACAATGTGGGCCTT-AGCCCAAT
30396442 A
1 A
30396443 TCTCATACAC
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
27 5 0.06
28 66 0.84
29 8 0.10
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:30397729 original size:34 final size:28
Alignment explanation
Indices: 30397677--30397766 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
30397667 ATATAGTGTA
* * *
30397677 GGCCTTAGCCCAATACAATAGCAATATG
1 GGCCTTAGCCCAATACAGTAACAATGTG
30397705 GGCCTTAGCCCAATACAGTAACAATGTG
1 GGCCTTAGCCCAATACAGTAACAATGTG
* *
30397733 GGCGTTAGCCCAATACAGTAACAATTTG
1 GGCCTTAGCCCAATACAGTAACAATGTG
30397761 GGCCTT
1 GGCCTT
30397767 GAACCCAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (28 bp):
GGCCTTAGCCCAATACAGTAACAATGTG
Found at i:30398113 original size:24 final size:24
Alignment explanation
Indices: 30398081--30398129 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30398071 ATTATTCACA
30398081 TTTTTTTTCAAGGAACATTTCTAT
1 TTTTTTTTCAAGGAACATTTCTAT
30398105 TTTTTTTTCAAGGAACATTTCTAT
1 TTTTTTTTCAAGGAACATTTCTAT
30398129 T
1 T
30398130 ACAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTTTTTTCAAGGAACATTTCTAT
Found at i:30400625 original size:12 final size:12
Alignment explanation
Indices: 30400610--30400635 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30400600 GCATCTCTTT
30400610 AATAATTGGTCA
1 AATAATTGGTCA
30400622 AATAATTGGTCA
1 AATAATTGGTCA
30400634 AA
1 AA
30400636 AACTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (12 bp):
AATAATTGGTCA
Found at i:30405342 original size:25 final size:24
Alignment explanation
Indices: 30405314--30405372 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
30405304 AGCTCTTGCA
30405314 AGCTGAATATC-GTTAAGCTCAT-ACG
1 AGCTGAA-ATCAG-TAAGCTC-TCACG
30405339 AGCTGAGAATCAGTAAGCTCTCACG
1 AGCTGA-AATCAGTAAGCTCTCACG
30405364 AGCTGAAAT
1 AGCTGAAAT
30405373 AGGTAACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
24 4 0.13
25 25 0.81
26 2 0.06
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
AGCTGAAATCAGTAAGCTCTCACG
Found at i:30412772 original size:16 final size:17
Alignment explanation
Indices: 30412745--30412777 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
30412735 TTATTCATAT
30412745 TTCATATACATGTATCA
1 TTCATATACATGTATCA
30412762 TTCAT-TACATGTATCA
1 TTCATATACATGTATCA
30412778 ATATATCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (17 bp):
TTCATATACATGTATCA
Found at i:30412989 original size:26 final size:24
Alignment explanation
Indices: 30412951--30413017 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
30412941 TCCTATACAT
* *
30412951 GTATGCTCATACAAGCTCTTAAATCG
1 GTATGCTCTTACAAGCT-GT-AATCG
30412977 GTATGCTCTTACAAGCTGTAATCG
1 GTATGCTCTTACAAGCTGTAATCG
* *
30413001 GTAAGCTCTTTCAAGCT
1 GTATGCTCTTACAAGCT
30413018 AAGTAACTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 20 0.54
25 1 0.03
26 16 0.43
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (24 bp):
GTATGCTCTTACAAGCTGTAATCG
Found at i:30426320 original size:33 final size:33
Alignment explanation
Indices: 30426268--30426449 Score: 142
Period size: 33 Copynumber: 5.4 Consensus size: 33
30426258 TCCCCCAAAG
* *
30426268 GGTTACTAAGTACTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * *
30426301 GGTTGCTAAGTGCTAATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--AT-CAT-T---GGT
*
30426343 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
30426370 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
** *
30426403 TATTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
30426436 GGTTGCTAAGTGCT
1 GGTTGCTAAGTGCT
30426450 AAATCCACCG
Statistics
Matches: 118, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
27 22 0.19
28 2 0.02
31 2 0.02
32 2 0.02
33 59 0.50
34 3 0.03
35 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
41 2 0.02
42 21 0.18
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:30426412 original size:102 final size:102
Alignment explanation
Indices: 30426236--30426422 Score: 302
Period size: 102 Copynumber: 1.8 Consensus size: 102
30426226 ATTGAATATA
*
30426236 AAGGGGGTTGCTAAGTGTTGATTCCCCCAAAGGGTTACTAAGTACTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAAGGGTTACTAAGTACTGATTCCCCGAATCATTGGT
*
30426301 GGTTGCTAAGTGCTAATTCCACCGTATTTTAAATGTG
66 GATTGCTAAGTGCTAATTCCACCGTATTTTAAATGTG
* * * *
30426338 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAAGGGTTACTAAGTACTGATTCCCCGAATCATTGGT
* *
30426403 TATTGCTAAGTGCTGATTCC
66 GATTGCTAAGTGCTAATTCC
30426423 CCGAATCACT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAAGGGTTACTAAGTACTGATTCCCCGAATCATTGGT
GATTGCTAAGTGCTAATTCCACCGTATTTTAAATGTG
Found at i:30430963 original size:84 final size:84
Alignment explanation
Indices: 30430816--30430973 Score: 196
Period size: 84 Copynumber: 1.9 Consensus size: 84
30430806 AATTGCAGAT
* * *
30430816 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAG-
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGACAAATCTTATCTTCCCAAGCAGTAGT
30430880 GGAAGCAGATTTAAGCCAGC
66 GG-AGCAGATTTAAGCCAGC
* * ** *
30430900 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAA-ATTACAGATCTTATC-TCCCTAAGCAGTA
1 CTTATCTCCCTAAGCAGTAGTGGAGTA-GATCAAAGACGACAAATCTTATCTTCCC-AAGCAGTA
30430963 GTGGAGCAGAT
64 GTGGAGCAGAT
30430974 CGAAGATGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 4 0.06
84 52 0.83
85 7 0.11
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (84 bp):
CTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGACAAATCTTATCTTCCCAAGCAGTAGT
GGAGCAGATTTAAGCCAGC
Found at i:30430997 original size:128 final size:128
Alignment explanation
Indices: 30430769--30431025 Score: 460
Period size: 128 Copynumber: 2.0 Consensus size: 128
30430759 AGTGAAGACT
*
30430769 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
30430834 AGTGGAGTAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCC
66 AGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCC
30430897 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
* * * *
30430962 AGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCC
66 AGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCC
30431025 A
1 A
30431026 CAAACCCTAT
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (128 bp):
AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCC
Found at i:30431075 original size:172 final size:172
Alignment explanation
Indices: 30430897--30431380 Score: 824
Period size: 172 Copynumber: 2.8 Consensus size: 172
30430887 GATTTAAGCC
*
30430897 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
* * *
30430962 AGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
*
30431027 AAACCCTATCGCTCTGGACAGCAGTGGAATAGGTTGAAGACT
131 AAACCCTATCACTCTGGACAGCAGTGGAATAGGTTGAAGACT
* * *
30431069 AGCCTTATCTCCCTAAGTAGTAGTGGAGTAGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
*
30431134 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAAGAGTAGGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
* *
30431199 AAACCCTATCACTTTGGACATCAGTGGAATAGGTTGAAGACT
131 AAACCCTATCACTCTGGACAGCAGTGGAATAGGTTGAAGACT
* *
30431241 AGCCTTATCTCTCTAAGCATTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
* *
30431306 GGTGGAGCAGATCGAAGACAACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
*
30431371 AAACCTTATC
131 AAACCCTATC
30431381 TCCCTAAGCA
Statistics
Matches: 292, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
172 292 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (172 bp):
AGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
AAACCCTATCACTCTGGACAGCAGTGGAATAGGTTGAAGACT
Found at i:30431076 original size:128 final size:127
Alignment explanation
Indices: 30430774--30431096 Score: 373
Period size: 128 Copynumber: 2.5 Consensus size: 127
30430764 AGACTAGCCT
* * * * * *
30430774 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCGCCCTAAGCAGCAGTGGAATAGGTTGAAAACT-AAGACCTTATCTCCCTAAGCAGTAGTGG
* * *
30430839 AGTAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAGCCT
65 AGCAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAACCC
* * * * *
30430902 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCGCCCTAAGCAGCAGTGGAATAGGTTGAAAACTA-AGACCTTATCTCCCTAAGCAGTAGTGG
* * * *
30430967 AGCAGATCGAAGATGGCGAATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCCACAAACC
65 AGCAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAG-C-C-AACC
30431032 C
127 C
* * * *
30431033 TATCGCTCT-GGACAGCAGTGGAATAGGTTGAAGACT-AG-CCTTATCTCCCTAAGTAGTAGTGG
1 TATCGCCCTAAG-CAGCAGTGGAATAGGTTGAAAACTAAGACCTTATCTCCCTAAGCAGTAGTGG
30431095 AG
65 AG
30431097 TAGGTTAAAA
Statistics
Matches: 173, Mismatches: 17, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
128 138 0.80
129 3 0.02
130 2 0.01
131 30 0.17
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (127 bp):
TATCGCCCTAAGCAGCAGTGGAATAGGTTGAAAACTAAGACCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAACCC
Found at i:30431118 original size:128 final size:126
Alignment explanation
Indices: 30430774--30431145 Score: 349
Period size: 128 Copynumber: 2.9 Consensus size: 126
30430764 AGACTAGCCT
* * * * * *
30430774 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCGCCCTAAGCAGCAGTGGAATAGGTTGAAAACT-AAGACCTTATCTCCCTAAGCAGTAGTGG
* * * * *
30430839 AGTAGATCAAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAGCCT
65 AGTAGATCAAAGA-TGCAGATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCCAACCC
* * * * *
30430902 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCGCCCTAAGCAGCAGTGGAATAGGTTGAAAACTA-AGACCTTATCTCCCTAAGCAGTAGTGG
* *
30430967 AGCAGATCGAAGATGGC-GAATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCCACAAAC
65 AGTAGATCAAAGAT-GCAG-ATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAG-C-C-AAC
30431031 CC
125 CC
* * * *
30431033 TATCGCTCT-GGACAGCAGTGGAATAGGTTGAAGACT-AG-CCTTATCTCCCTAAGTAGTAGTGG
1 TATCGCCCTAAG-CAGCAGTGGAATAGGTTGAAAACTAAGACCTTATCTCCCTAAGCAGTAGTGG
* * * * * * *
30431095 AGTAGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGAT
65 AGTAGATCAAAGA-TGCAGATCTTATCTTCCTCAGGAGTAG-GGAAGCAGAT
30431146 CGAAGACGAC
Statistics
Matches: 208, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
128 169 0.81
129 7 0.03
130 2 0.01
131 30 0.14
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (126 bp):
TATCGCCCTAAGCAGCAGTGGAATAGGTTGAAAACTAAGACCTTATCTCCCTAAGCAGTAGTGGA
GTAGATCAAAGATGCAGATCTTATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCCAACCC
Found at i:30431403 original size:131 final size:131
Alignment explanation
Indices: 30431243--30431603 Score: 553
Period size: 131 Copynumber: 2.8 Consensus size: 131
30431233 TGAAGACTAG
* * *
30431243 CCTTATCTCTCTAAGCATTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTGG
1 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAG
*
30431308 TGGAGCAGATCGAAGACAACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAA
66 TGGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAA
30431373 A
131 A
* *
30431374 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCTTAAGCAATAG
1 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAG
* * * *
30431439 TGGAACAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAGTCACAA
66 TGGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAA
30431504 A
131 A
* ** * * ** *
30431505 CCTTATCTCCTTGTGCAGCAGTGGAGTAGGTTGAAAACTATAGATCTTATCTCCCTAAACAGTAG
1 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAG
30431570 TGGAGCAGATCGAAGACAGCGAATCTTA-CTTCCC
66 TGGAGCAGATCGAAGACAGCGAATCTTATCTTCCC
30431604 AGGTGATGCA
Statistics
Matches: 208, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
130 6 0.03
131 202 0.97
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (131 bp):
CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAA
A
Found at i:30431596 original size:44 final size:44
Alignment explanation
Indices: 30430772--30431597 Score: 304
Period size: 44 Copynumber: 19.1 Consensus size: 44
30430762 GAAGACTAGC
* * * **
30430772 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGC-AGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA-AT
* ** * *
30430816 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGGCAAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGAAT
* * * *
30430860 CTTATCTTCCC-CAGGAGTAG-GGAAGCAGATTTAAGCCAGC----
1 CTTATC-TCCCTAAGCAGTAGTGG-AGCAGATTGAAGACAGCGAAT
* * * *
30430900 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTA-C-AGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CAGCGA-AT
* **
30430944 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGAAT
* * * * * * *
30430988 CTTATCTTCCTCAGGAGTAG-GGAAGCAGATTTAAGCCA-CAAAC
1 CTTATCTCCCTAAGCAGTAGTGG-AGCAGATTGAAGACAGCGAAT
* * * * * ** *
30431031 CCTATCGCTCT-GGACAGCAGTGGAATAGGTTGAAGACTAGC----
1 CTTATCTCCCTAAG-CAGTAGTGGAGCAGATTGAAGAC-AGCGAAT
* * * * **
30431072 CTTATCTCCCTAAGTAGTAGTGGAGTAGGTT-AA-AAATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCG-A-AT
*
30431116 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-GACGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAG-CGAAT
* * * * *
30431160 CTTATCTTCCCCAAG-AGTAG-GGAAGCAGATTTAAGCCA-CAAAC
1 CTTATC-TCCCTAAGCAGTAGTGG-AGCAGATTGAAGACAGCGAAT
* * * ** ** *
30431203 CCTATC-ACTTTGGACA-TCAGTGGAATAGGTTGAAGACTAGC----
1 CTTATCTCCCTAAG-CAGT-AGTGGAGCAGATTGAAGAC-AGCGAAT
* * * * * **
30431244 CTTATCTCTCTAAGCATTAGTGGAGTAGGTTGAAAATTGC-AGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA-AT
* * *
30431288 CTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGACAACGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGAAT
* * * * * *
30431332 CTTATCTTCCC-CAGGAGTAG-GGAAGCAGATTTAAGCCA-CAAAC
1 CTTATC-TCCCTAAGCAGTAGTGG-AGCAGATTGAAGACAGCGAAT
* * * **
30431375 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGC-AGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGA-AT
* * * * *
30431419 CTTATCTCCTTAAGCAATAGTGGAACAGATCGAAGACGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGAAT
* * * * *
30431463 CTTATCTTCCCT-AGGAGTAG-GGAAGCAGATTTAAGTCA-CAAAC
1 CTTATC-TCCCTAAGCAGTAGTGG-AGCAGATTGAAGACAGCGAAT
* ** * * * * **
30431506 CTTATCTCCTTGTGCAGCAGTGGAGTAGGTTGAAAACTATAG-AT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC-AGCGAAT
* *
30431550 CTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACAGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGAAT
30431594 CTTA
1 CTTA
30431598 CTTCCCAGGT
Statistics
Matches: 563, Mismatches: 162, Indels: 114
0.67 0.19 0.14
Matches are distributed among these distances:
38 1 0.00
39 5 0.01
40 26 0.05
41 50 0.09
42 14 0.02
43 104 0.18
44 333 0.59
45 28 0.05
46 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCGAAT
Found at i:30436091 original size:5 final size:5
Alignment explanation
Indices: 30436081--30436105 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30436071 TTTGGCCGGA
30436081 GCCCG GCCCG GCCCG GCCCG GCCCG
1 GCCCG GCCCG GCCCG GCCCG GCCCG
30436106 AATATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.40, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:30436260 original size:20 final size:20
Alignment explanation
Indices: 30436235--30436281 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
30436225 CCGAGCCGGG
30436235 CTCGGGCTTATTATTTTTTT
1 CTCGGGCTTATTATTTTTTT
30436255 CTCGGGCTTATTATTTTTTT
1 CTCGGGCTTATTATTTTTTT
30436275 CTCGGGC
1 CTCGGGC
30436282 CGGGCCTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
CTCGGGCTTATTATTTTTTT
Found at i:30442968 original size:33 final size:33
Alignment explanation
Indices: 30442931--30443030 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
30442921 AGTCGAACAG
* *
30442931 AATGATGAAGCTGCCTCAATAGTTGTTCCAATC
1 AATGATGAAGCTGCCTCGATAGATGTTCCAATC
* *
30442964 AATGATGAAGCTGCCCCGATAGATGTTGCAATC
1 AATGATGAAGCTGCCTCGATAGATGTTCCAATC
* *
30442997 ATTGATGAAGCTGCCTTGATAGATGTTCCAATC
1 AATGATGAAGCTGCCTCGATAGATGTTCCAATC
30443030 A
1 A
30443031 CTTATGTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (33 bp):
AATGATGAAGCTGCCTCGATAGATGTTCCAATC
Found at i:30445258 original size:89 final size:90
Alignment explanation
Indices: 30445141--30445311 Score: 213
Period size: 90 Copynumber: 1.9 Consensus size: 90
30445131 CGATTTGGGA
* *
30445141 TTTATTCCCGCCGTTCAACGGATCTTATTCCATT-TTTTATTTTATTTCCAAATAG-GAAATTAA
1 TTTATTCCCGCCATTCAACGGATCTTATTCCATTAATTTATTTTATTTCCAAA-AGAGAAATTAA
*
30445204 AG-GTAATTAAAATCCGTTCAACAGAT
65 AGAG-AAATAAAATCCGTTCAACAGAT
* * * * * * *
30445230 TTTATTCTCGCCATTCAATGGATTTTATTCTATTAATTTGTTTTATTTTCAAACGAGAAATTAAA
1 TTTATTCCCGCCATTCAACGGATCTTATTCCATTAATTTATTTTATTTCCAAAAGAGAAATTAAA
30445295 GAGAAATAAAATCCGTT
66 GAGAAATAAAATCCGTT
30445312 TCAGGATTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
89 30 0.43
90 38 0.55
91 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (90 bp):
TTTATTCCCGCCATTCAACGGATCTTATTCCATTAATTTATTTTATTTCCAAAAGAGAAATTAAA
GAGAAATAAAATCCGTTCAACAGAT
Found at i:30445467 original size:79 final size:79
Alignment explanation
Indices: 30445298--30445765 Score: 491
Period size: 79 Copynumber: 5.9 Consensus size: 79
30445288 AATTAAAGAG
* * * ** * * * *
30445298 AAATAAAATCCGTTTCAGGATTGACTCCTACTGTTCAACGATTCTCTTCCAAAATTTTGA-TTTG
1 AAATAAAATCTGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCC-AAA-TTTGATTTTA
**
30445362 TTTCCAAAAACAAGTA
64 TTTCCAAAAATGAGTA
* ** *
30445378 AAATAAAATCTGTTTCGGGATTGATTCCCGCCATTCAACGATTTTATTTGAAATTTGGTTTTATT
1 AAATAAAATCTGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGATTTTATT
* *
30445443 TCCGAAAACGAGTA
66 TCCAAAAATGAGTA
* * * *
30445457 AAATAAAATCTGTTTCGAGATTGATTCCCGCTGTTCAATGATTTTATTCCAAATTTTATTTTATT
1 AAATAAAATCTGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGATTTTATT
*
30445522 TTCAAAAATGAAG-A
66 TCCAAAAATG-AGTA
* * *
30445536 AAATAAAATCCT-TTTCGAGATTGA-TCCTCGCTGTTCAACAATTTTATTCCAAATTTGATTTTA
1 AAATAAAAT-CTGTTTCGGGATTGATTCC-CGCCGTTCAACGATTTTATTCCAAATTTGATTTTA
30445599 TTTCCAAAAATGAGTA
64 TTTCCAAAAATGAGTA
** * * *
30445615 AAATAAAATCCATTTCGGGATTGATTCCCGCCGTTCAACGAATTTATTTCAAATTTTG-CTTTAT
1 AAATAAAATCTGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAA-TTTGATTTTAT
30445679 TTCCAAAAATGAGTA
65 TTCCAAAAATGAGTA
* * * * * *
30445694 AAATAAAACCTGTTTCGGGATTGATTCCTGCCATTCAAC-ATATTTATTAC-ATTTTGATTTTGT
1 AAATAAAATCTGTTTCGGGATTGATTCCCGCCGTTCAACGAT-TTTATTCCAAATTTGATTTTAT
*
30445757 TGCCAAAAA
65 TTCCAAAAA
30445766 CGAGAAATTA
Statistics
Matches: 330, Mismatches: 48, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
77 4 0.01
78 24 0.07
79 252 0.76
80 50 0.15
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (79 bp):
AAATAAAATCTGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGATTTTATT
TCCAAAAATGAGTA
Found at i:30445718 original size:237 final size:239
Alignment explanation
Indices: 30445293--30445721 Score: 625
Period size: 237 Copynumber: 1.8 Consensus size: 239
30445283 CGAGAAATTA
* *
30445293 AAGAGAAATAAAATCCGTTTCAGGATTGACTCCTACTGTTCAACGATTCTCTTCCAAAATTTTGA
1 AAGAGAAATAAAATCCGTTTCAGGATTGACTCCTACTGTTCAACAATTCTATTCCAAAATTTTGA
* ** *
30445358 TTTGTTTCCAAAAACAAGTAAAATAAAATCTGTTTCGGGATTGATTCCCGCCATTCAACGATTTT
66 TTTATTTCCAAAAACAAGTAAAATAAAATCCATTTCGGGATTGATTCCCGCCATTCAACGAATTT
* * * *
30445423 ATTTGAAATTTGGTTTTATTTCCGAAAACGAGTAAAATAAAATCTGTTTCGAGATTGATTCCCGC
131 ATTTCAAATTTGGCTTTATTTCCAAAAACGAGTAAAATAAAACCTGTTTCGAGATTGATTCCCGC
30445488 TGTTCAATGATTTTATTCCAAATTTTATTTTATTTTCAAAAATG
196 TGTTCAATGATTTTATTCCAAATTTTATTTTATTTTCAAAAATG
* * *
30445532 AAGA-AAATAAAATCCTTTTC-GAGATTGA-TCCTCGCTGTTCAACAATTTTATTCC-AAA-TTT
1 AAGAGAAATAAAATCCGTTTCAG-GATTGACTCCT-ACTGTTCAACAATTCTATTCCAAAATTTT
** *
30445592 GATTTTATTTCCAAAAATGAGTAAAATAAAATCCATTTCGGGATTGATTCCCGCCGTTCAACGAA
64 GA-TTTATTTCCAAAAACAAGTAAAATAAAATCCATTTCGGGATTGATTCCCGCCATTCAACGAA
* * *
30445657 TTTATTTCAAATTTTGCTTTATTTCCAAAAATGAGTAAAATAAAACCTGTTTCGGGATTGATTCC
128 TTTATTTCAAATTTGGCTTTATTTCCAAAAACGAGTAAAATAAAACCTGTTTCGAGATTGATTCC
30445722 TGCCATTCAA
Statistics
Matches: 168, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
236 5 0.03
237 121 0.72
238 38 0.23
239 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (239 bp):
AAGAGAAATAAAATCCGTTTCAGGATTGACTCCTACTGTTCAACAATTCTATTCCAAAATTTTGA
TTTATTTCCAAAAACAAGTAAAATAAAATCCATTTCGGGATTGATTCCCGCCATTCAACGAATTT
ATTTCAAATTTGGCTTTATTTCCAAAAACGAGTAAAATAAAACCTGTTTCGAGATTGATTCCCGC
TGTTCAATGATTTTATTCCAAATTTTATTTTATTTTCAAAAATG
Found at i:30445902 original size:86 final size:87
Alignment explanation
Indices: 30445746--30445916 Score: 209
Period size: 86 Copynumber: 2.0 Consensus size: 87
30445736 TTTATTACAT
* * *
30445746 TTTGATTTTGTTGCCAAAAACGAGAAATTAATTTAAATAAAATCTATTTCGAAATTTGTTCCCGC
1 TTTGATTTTGTTGCCAAAAACGAGAAATTAAATTAAATAAAATATATTTCGAAATTTATTCCCGC
**
30445811 CGTTTAGTAAGA-TTTATTTGA
66 CGTTTAACAAGATTTTATTTGA
** * * ** * *
30445832 TTTGATTTTGTTTTCAAAAATGAGAAATTAAATTAAATAAAATATGTTTCGGGATTTATTCTCGT
1 TTTGATTTTGTTGCCAAAAACGAGAAATTAAATTAAATAAAATATATTTCGAAATTTATTCCCGC
*
30445897 TGTTTAACAAGATTTTATTT
66 CGTTTAACAAGATTTTATTT
30445917 TGTTTCCAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
86 63 0.90
87 7 0.10
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (87 bp):
TTTGATTTTGTTGCCAAAAACGAGAAATTAAATTAAATAAAATATATTTCGAAATTTATTCCCGC
CGTTTAACAAGATTTTATTTGA
Found at i:30445956 original size:74 final size:76
Alignment explanation
Indices: 30445830--30445991 Score: 199
Period size: 74 Copynumber: 2.2 Consensus size: 76
30445820 AGATTTATTT
* * *
30445830 GATTTGATTTTGTTTTCAAAAATGAGAAATTAAATTAAATAAAATATGTTTCGGGATTTATT-CT
1 GATTTTATTTTGTTTTCAAAAATGAGAAATTAAATTAAATAAAATATATTTCGGGAGTTATTCCT
30445894 -CGTTGTTTAACAA
66 ACG--GTTTAA-AA
* * *
30445907 GATTTTATTTTG-TTTC-CAAATTAG-AATTAAATTAAATAAAATCTATTTCGGGAGTTATTCCT
1 GATTTTATTTTGTTTTCAAAAATGAGAAATTAAATTAAATAAAATATATTTCGGGAGTTATTCCT
*
30445969 ACGGTTTAATA
66 ACGGTTTAAAA
30445980 GATTTTATTTTG
1 GATTTTATTTTG
30445992 ATATAATTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
73 13 0.17
74 38 0.50
75 8 0.11
76 6 0.08
77 11 0.14
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (76 bp):
GATTTTATTTTGTTTTCAAAAATGAGAAATTAAATTAAATAAAATATATTTCGGGAGTTATTCCT
ACGGTTTAAAA
Found at i:30454380 original size:51 final size:51
Alignment explanation
Indices: 30454316--30454654 Score: 311
Period size: 51 Copynumber: 6.7 Consensus size: 51
30454306 TATTGATGAA
* * *
30454316 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * * * * *
30454367 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTG-GT
* * * *
30454418 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATTGGT
* * * * * *
30454469 TACATGTGTGGTACTAAGTGAAGGCTACTATG-GATACCGGA-AAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-TACC-GATAA-ATATTGGT
* *
30454520 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGATAAATA-TTGGT
* * * *
30454570 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AACTATAAA-ACTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
*
30454619 CACGTGTGTAGTACTATGTGAAGGCCACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
30454655 TCGAATGATG
Statistics
Matches: 232, Mismatches: 42, Indels: 29
0.77 0.14 0.10
Matches are distributed among these distances:
49 38 0.16
50 50 0.22
51 140 0.60
52 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:30454492 original size:102 final size:102
Alignment explanation
Indices: 30454316--30454657 Score: 385
Period size: 102 Copynumber: 3.4 Consensus size: 102
30454306 TATTGATGAA
* *
30454316 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTA
*
30454380 CTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCGAGAAGATTTGAG
* * * *
30454418 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTACATGTGTGGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
*
30454483 TAAGTGAAGGCTACTATG-GATACCG-GAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTG-TACCGAG-AAGATTTGAG
* * * * *
30454519 TCACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGT
1 -CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGT
* * * * * ** *
30454582 ACTATGTGAAGGCTACTACGTG-AACTATAA-AACTGAT
64 ACTAAGTGAAGGCTACTATGTGTACCGAGAAGATTTGAG
*
30454619 CACGTGTGTAGTACTATGTGAAGGCCACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
30454658 AATGATGAAA
Statistics
Matches: 204, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
99 34 0.17
100 6 0.03
101 37 0.18
102 126 0.62
103 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAGAAGATTTGAG
Found at i:30460902 original size:51 final size:51
Alignment explanation
Indices: 30460838--30461180 Score: 312
Period size: 51 Copynumber: 6.8 Consensus size: 51
30460828 TATCGATGAA
* *
30460838 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGT
* * * * * * *
30460889 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAACTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTG-GT
* * *
30460940 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TATTGGT
* * * * * * *
30460991 TACATGTGTGGTGCTAAGTGAAGGCTACTATG-GATATCGGA-AAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-TATC-GATAA-ATATTGGT
* * *
30461042 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-TCGATAAATA-TTGGT
* * *
30461092 CACGTGTGTAGGACTATGTGAAGGCTACTACGTG-AACTG-TAAA-ATTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GATAAATATTGGT
30461141 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
30461181 ATGATAAAAA
Statistics
Matches: 233, Mismatches: 44, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
49 40 0.17
50 51 0.22
51 138 0.59
52 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGT
Found at i:30461014 original size:102 final size:101
Alignment explanation
Indices: 30460838--30461179 Score: 369
Period size: 102 Copynumber: 3.4 Consensus size: 101
30460828 TATCGATGAA
* * *
30460838 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTGGTA
30460902 CTAAGTGAAGGCTACTATGTGTACCGAGAACTTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCGAGAAC-TTTGAG
* * * *
30460940 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTACATGTGTGGTGC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTGGTAC
*
30461005 TAAGTGAAGGCTACTATG-GATATCG-GAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTG-TACCGAG-AA-CTTTGAG
* * * * *
30461041 TCACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGG
1 -CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGT-GG
* * * * * *
30461104 -ACTATGTGAAGGCTACTACGTGAACTGTA-AA-ATTGAT
63 TACTAAGTGAAGGCTACTATGTGTACCG-AGAACTTTGAG
30461141 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
30461180 AATGATAAAA
Statistics
Matches: 203, Mismatches: 25, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
99 36 0.18
100 2 0.01
101 38 0.19
102 125 0.62
103 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTGGTAC
TAAGTGAAGGCTACTATGTGTACCGAGAACTTTGAG
Found at i:30466250 original size:27 final size:27
Alignment explanation
Indices: 30466209--30466276 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
30466199 ATAAAGGCAA
*
30466209 AAAATCTACCAAATAACATATAATGCGAT
1 AAAATC-ACC-AATAACATATAATACGAT
* * *
30466238 AAAATCATCAATATCATATAATATGAT
1 AAAATCACCAATAACATATAATACGAT
30466265 AAAATCACCAAT
1 AAAATCACCAAT
30466277 CCCCTCGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 26 0.76
28 2 0.06
29 6 0.18
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAATCACCAATAACATATAATACGAT
Found at i:30467146 original size:28 final size:28
Alignment explanation
Indices: 30467093--30467146 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
30467083 GTAACAAAAC
*
30467093 AATGTGGGCCTTAGCCCGATACAGTAAT
1 AATGTGGGCCTTAGCCCAATACAGTAAT
* *
30467121 AATGTGGGCCTTAGCTCAATATAGTA
1 AATGTGGGCCTTAGCCCAATACAGTA
30467147 TTAGAATCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (28 bp):
AATGTGGGCCTTAGCCCAATACAGTAAT
Found at i:30467477 original size:32 final size:32
Alignment explanation
Indices: 30467426--30467503 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
30467416 GAATGGCTAC
* * *
30467426 AAGCCATAAGTA-CAGTAATATGATTGGCATA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
*
30467457 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
*
30467489 CAGCCATCAGTAGCA
1 AAGCCATCAGTAGCA
30467504 TCGTAGCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 11 0.28
32 29 0.73
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGATCGGCACA
Found at i:30467672 original size:24 final size:24
Alignment explanation
Indices: 30467645--30467774 Score: 93
Period size: 24 Copynumber: 5.4 Consensus size: 24
30467635 CCATGCTCAG
30467645 AATCAATCATACAAATCACAGACA
1 AATCAATCATACAAATCACAGACA
** * *
30467669 AATCAGCCATACCAATCATAGACA
1 AATCAATCATACAAATCACAGACA
** *
30467693 AATCAATCATTTAAATCATAGACA
1 AATCAATCATACAAATCACAGACA
* ** * *
30467717 CATCGGTCACTTAC--ATCTCAAACA
1 AATCAATCA--TACAAATCACAGACA
** *
30467741 AATCAATCATTTACATCACAGACA
1 AATCAATCATACAAATCACAGACA
30467765 AATCAATCAT
1 AATCAATCAT
30467775 TTAACCCTGA
Statistics
Matches: 78, Mismatches: 24, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
22 1 0.01
24 76 0.97
26 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.23
Consensus pattern (24 bp):
AATCAATCATACAAATCACAGACA
Found at i:30467716 original size:48 final size:48
Alignment explanation
Indices: 30467645--30467769 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 48
30467635 CCATGCTCAG
** *
30467645 AATCAATCATACAAATCACAGACAAATCAG-C-CATACCAATCAT-AGACA
1 AATCAATCATTTAAATCACAGACAAATCAGTCACATA-C-ATC-TCAAACA
* * * *
30467693 AATCAATCATTTAAATCATAGACACATCGGTCACTTACATCTCAAACA
1 AATCAATCATTTAAATCACAGACAAATCAGTCACATACATCTCAAACA
*
30467741 AATCAATCATTTACATCACAGACAAATCA
1 AATCAATCATTTAAATCACAGACAAATCA
30467770 ATCATTTAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
47 1 0.02
48 57 0.90
49 2 0.03
50 3 0.05
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.22
Consensus pattern (48 bp):
AATCAATCATTTAAATCACAGACAAATCAGTCACATACATCTCAAACA
Found at i:30467775 original size:24 final size:24
Alignment explanation
Indices: 30467683--30467777 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
30467673 AGCCATACCA
* *
30467683 ATCATAGACAAATCAATCATTTAA
1 ATCACAGACAAATCAATCATTTAC
* * ** *
30467707 ATCATAGACACATCGGTCACTTAC
1 ATCACAGACAAATCAATCATTTAC
* *
30467731 ATCTCAAACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
30467755 ATCACAGACAAATCAATCATTTA
1 ATCACAGACAAATCAATCATTTA
30467778 ACCCTGAGGG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.27
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:30467814 original size:27 final size:27
Alignment explanation
Indices: 30467771--30468102 Score: 210
Period size: 27 Copynumber: 12.3 Consensus size: 27
30467761 GACAAATCAA
* * **
30467771 TCATTTAACCCT-GAGGGGCAAAACTG
1 TCATTTTACCCTATAGGGGCATTACTG
*
30467797 TCATTTTACCCTATAGGGGTATTACTG
1 TCATTTTACCCTATAGGGGCATTACTG
* * **
30467824 TCATTTTACCCTACAGGGGTATTACAA
1 TCATTTTACCCTATAGGGGCATTACTG
** * *
30467851 TCATTTTATAAC-ATAGGGGCATAACAG
1 TCATTTTA-CCCTATAGGGGCATTACTG
*** *
30467878 TCA-TTTAATGTCATAGGGGCATAACAT-
1 TCATTTTACCCT-ATAGGGGCATTAC-TG
*** *
30467905 TCA-TTTAATGTCATAGGGGCATAACAT-
1 TCATTTTACCCT-ATAGGGGCATTAC-TG
* *
30467932 TCATTTAACCCTATAGGGGTATTAC-G
1 TCATTTTACCCTATAGGGGCATTACTG
* * *
30467958 ATCATTTTACCTTATAGGGGCATAACGG
1 -TCATTTTACCCTATAGGGGCATTACTG
* * * *
30467986 TCACTTTACCCTACAGGGGTATTACGG
1 TCATTTTACCCTATAGGGGCATTACTG
* *
30468013 TTATTTTACCCTATAGGGGCATTACAG
1 TCATTTTACCCTATAGGGGCATTACTG
* ** *
30468040 TCATTTTACCCTACAAAGGCATTACGG
1 TCATTTTACCCTATAGGGGCATTACTG
* * *
30468067 TCATTTTACCCTATAGGGGTATGACGG
1 TCATTTTACCCTATAGGGGCATTACTG
30468094 TCATTTTAC
1 TCATTTTAC
30468103 AAATATTGGG
Statistics
Matches: 250, Mismatches: 47, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.00
26 15 0.06
27 228 0.91
28 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGCATTACTG
Found at i:30467856 original size:54 final size:54
Alignment explanation
Indices: 30467797--30468102 Score: 269
Period size: 54 Copynumber: 5.7 Consensus size: 54
30467787 GGCAAAACTG
* * * *
30467797 TCATTTTACCCTATAGGGGTATTACTGTCATTTTACCCTACAGGGGTATTACAA
1 TCATTTTACCCTATAGGGGCATAACAGTCATTTTACCCTACAGGGGTATTACGA
** *** * * *
30467851 TCATTTTATAAC-ATAGGGGCATAACAGTCA-TTTAATGTCATAGGGGCATAAC-A
1 TCATTTTA-CCCTATAGGGGCATAACAGTCATTTTACCCT-ACAGGGGTATTACGA
*** * * *
30467904 TTCA-TTTAATGTCATAGGGGCATAACATTCATTTAACCCTATAGGGGTATTACGA
1 -TCATTTTACCCT-ATAGGGGCATAACAGTCATTTTACCCTACAGGGGTATTACGA
* * * *
30467959 TCATTTTACCTTATAGGGGCATAACGGTCACTTTACCCTACAGGGGTATTACGG
1 TCATTTTACCCTATAGGGGCATAACAGTCATTTTACCCTACAGGGGTATTACGA
* * ** * *
30468013 TTATTTTACCCTATAGGGGCATTACAGTCATTTTACCCTACAAAGGCATTACGG
1 TCATTTTACCCTATAGGGGCATAACAGTCATTTTACCCTACAGGGGTATTACGA
* * *
30468067 TCATTTTACCCTATAGGGGTATGACGGTCATTTTAC
1 TCATTTTACCCTATAGGGGCATAACAGTCATTTTAC
30468103 AAATATTGGG
Statistics
Matches: 203, Mismatches: 41, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
52 1 0.00
53 10 0.05
54 181 0.89
55 11 0.05
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (54 bp):
TCATTTTACCCTATAGGGGCATAACAGTCATTTTACCCTACAGGGGTATTACGA
Found at i:30467881 original size:81 final size:81
Alignment explanation
Indices: 30467768--30468088 Score: 242
Period size: 81 Copynumber: 4.0 Consensus size: 81
30467758 ACAGACAAAT
* * * * * *
30467768 CAATCA-TTTAACCCT-GAGGGGCAAAACTGTCATTTTACCCTATAGGGGTATTACTGTCATTTT
1 CAATCATTTTAA-CCTATAGGGGCATAACAGTCATTTTACCCTATAGGGGCATAACGGTCATTTT
30467831 ACCCTACAGGGGTATTA
65 ACCCTACAGGGGTATTA
* *** **
30467848 CAATCATTTTATAAC-ATAGGGGCATAACAGTCA-TTTAATGTCATAGGGGCATAACATTCA-TT
1 CAATCATTTTA-ACCTATAGGGGCATAACAGTCATTTTACCCT-ATAGGGGCATAACGGTCATTT
*** * * *
30467910 TAATGTCATAGGGGCATAA
64 TACCCT-ACAGGGGTATTA
* * * * *
30467929 CATTCA-TTTAACCCTATAGGGGTATTAC-GATCATTTTACCTTATAGGGGCATAACGGTCACTT
1 CAATCATTTTAA-CCTATAGGGGCATAACAG-TCATTTTACCCTATAGGGGCATAACGGTCATTT
30467992 TACCCTACAGGGGTATTA
64 TACCCTACAGGGGTATTA
** * * * * ** *
30468010 CGGTTATTTTACCCTATAGGGGCATTACAGTCATTTTACCCTACAAAGGCATTACGGTCATTTTA
1 CAATCATTTTAACCTATAGGGGCATAACAGTCATTTTACCCTATAGGGGCATAACGGTCATTTTA
*
30468075 CCCTATAGGGGTAT
66 CCCTACAGGGGTAT
30468089 GACGGTCATT
Statistics
Matches: 185, Mismatches: 44, Indels: 23
0.73 0.17 0.09
Matches are distributed among these distances:
79 1 0.01
80 22 0.12
81 146 0.79
82 16 0.09
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (81 bp):
CAATCATTTTAACCTATAGGGGCATAACAGTCATTTTACCCTATAGGGGCATAACGGTCATTTTA
CCCTACAGGGGTATTA
Found at i:30468448 original size:12 final size:12
Alignment explanation
Indices: 30468431--30468461 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
30468421 CTTGGTTCAC
30468431 CACACGCACGAT
1 CACACGCACGAT
30468443 CACACGCACGAT
1 CACACGCACGAT
30468455 CACACGC
1 CACACGC
30468462 TCGTGTCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.45, G:0.16, T:0.06
Consensus pattern (12 bp):
CACACGCACGAT
Found at i:30471349 original size:43 final size:43
Alignment explanation
Indices: 30471288--30471579 Score: 237
Period size: 43 Copynumber: 6.9 Consensus size: 43
30471278 GATTGAATTA
* *
30471288 TTGATTCTAAAGGTGGTTGCTAAGTGCTGATTCCACCATATAT
1 TTGATTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAT
*
30471331 TTGATTGTGAAAGG-GGTTGCTAAGTGCTGATTCC-CCGAAT-T
1 TTGATTGT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAT
* * * * *
30471372 ATTGACTCTAAAGGTGGTTGCTAAGTGTTGATTCCACGGTATCT
1 -TTGATTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAT
*
30471416 TTGATTGTGAAAGG-GGTTGC-AATGTGTTGATTCC-CCGTATCA-
1 TTGATTGT-AAAGGTGGTTGCTAA-GTGCTGATTCCACCGTAT-AT
* * * * * *
30471458 CTAAATATAAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCT
1 TTGATTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAT
* * * *
30471501 TTGATTGTGAAAGG-GGCTGCTATGCGTTGATTCC-CCGTATCA-
1 TTGATTGT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTAT-AT
* * * *
30471543 CTGAAT-TAAAGGTGGTTGCTAAGTGTTGAATCCACCG
1 TTGATTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCG
30471580 AGTAACGGAT
Statistics
Matches: 198, Mismatches: 35, Indels: 33
0.74 0.13 0.12
Matches are distributed among these distances:
40 5 0.03
41 28 0.14
42 68 0.34
43 81 0.41
44 16 0.08
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (43 bp):
TTGATTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAT
Found at i:30471425 original size:85 final size:85
Alignment explanation
Indices: 30471293--30471579 Score: 389
Period size: 85 Copynumber: 3.4 Consensus size: 85
30471283 AATTATTGAT
* * *
30471293 TCTAAAGGTGGTTGCTAAGTGCTGATTCCACCATATATTTGATTGTGAAAGGGGTTGCTAAGTGC
1 TCTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTAAGTGT
* * *
30471358 TGATTCCCCGAATTATTGAC
66 TGATTCCCCGAATCACTGAA
* *
30471378 TCTAAAGGTGGTTGCTAAGTGTTGATTCCACGGTATCTTTGATTGTGAAAGGGGTTGC-AATGTG
1 TCTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTAA-GTG
* *
30471442 TTGATTCCCCGTATCACTAAA
65 TTGATTCCCCGAATCACTGAA
* * * * *
30471463 TATAAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCTTTGATTGTGAAAGGGGCTGCTATGCGT
1 TCTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTAAGTGT
*
30471528 TGATTCCCCGTATCACTGAA
66 TGATTCCCCGAATCACTGAA
* *
30471548 T-TAAAGGTGGTTGCTAAGTGTTGAATCCACCG
1 TCTAAAGGTGGTTGCTAAGTGCTGATTCCACCG
30471580 AGTAACGGAT
Statistics
Matches: 180, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
84 30 0.17
85 149 0.83
86 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (85 bp):
TCTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTAAGTGT
TGATTCCCCGAATCACTGAA
Found at i:30473845 original size:34 final size:33
Alignment explanation
Indices: 30473769--30473846 Score: 79
Period size: 34 Copynumber: 2.3 Consensus size: 33
30473759 ATCACAATGC
*
30473769 CAGTAATCAGTAGGGCCTTTGCCTAATTTCAGTAA
1 CAGT-ATCAGTAGGGCCTTAGCCTAA-TTCAGTAA
*
30473804 TAGTATCAGTAGGGCCTTAGCCCATAA-T-AGTAA
1 CAGTATCAGTAGGGCCTTAG-CC-TAATTCAGTAA
30473837 CAGATATCAG
1 CAG-TATCAG
30473847 ACATGTAGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 7 0.19
34 22 0.59
35 5 0.14
36 3 0.08
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (33 bp):
CAGTATCAGTAGGGCCTTAGCCTAATTCAGTAA
Found at i:30474349 original size:27 final size:27
Alignment explanation
Indices: 30474312--30474637 Score: 346
Period size: 27 Copynumber: 12.1 Consensus size: 27
30474302 TATAACAGTT
*
30474312 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
30474339 ATCTTATCCTATGGTGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
30474366 ATTCTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
30474393 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
30474420 ATTCTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
30474447 ATTCTACCCTATGGGGGTGTTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
** **
30474474 ATTTTACCCTATGAAGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
30474501 ATTTTACCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * ** *
30474528 ATTTTACCTTACGAAGGTACTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
30474555 ATTTTACCCTATGGGGGTATTCCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * * *
30474582 ATTCTACCTTATAGAGATATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * ** *
30474609 CTTTTACCCAATGAAGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
30474636 AT
1 AT
30474638 AATAGTGTAA
Statistics
Matches: 248, Mismatches: 51, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 248 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:30483304 original size:11 final size:11
Alignment explanation
Indices: 30483288--30483334 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
30483278 TTTAGTTTTA
30483288 TATTTTATATT
1 TATTTTATATT
30483299 TATTTTATATT
1 TATTTTATATT
* *
30483310 T-TTTTGTTTT
1 TATTTTATATT
*
30483320 TATTATAT-TT
1 TATTTTATATT
30483330 TATTT
1 TATTT
30483335 GGCACTGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 14 0.47
11 16 0.53
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TATTTTATATT
Found at i:30483312 original size:19 final size:19
Alignment explanation
Indices: 30483277--30483330 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
30483267 AAATTATTTC
30483277 ATTTAGTTTTATA-TTTTAT
1 ATTTA-TTTTATATTTTTAT
*
30483296 ATTTATTTTATATTTTTTT
1 ATTTATTTTATATTTTTAT
*
30483315 GTTT-TTATTATATTTT
1 ATTTATT-TTATATTTT
30483331 ATTTGGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
ATTTATTTTATATTTTTAT
Found at i:30483321 original size:21 final size:20
Alignment explanation
Indices: 30483285--30483335 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
30483275 TCATTTAGTT
* *
30483285 TTATATTTTATAT-TTATT-
1 TTATATTTTATTTGTTTTTA
30483303 TTATATTTT-TTTGTTTTTA
1 TTATATTTTATTTGTTTTTA
30483322 TTATATTTTATTTG
1 TTATATTTTATTTG
30483336 GCACTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 13 0.46
19 9 0.32
20 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (20 bp):
TTATATTTTATTTGTTTTTA
Found at i:30483518 original size:13 final size:13
Alignment explanation
Indices: 30483500--30483549 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
30483490 TATATTTATT
30483500 TTTTTGTTTTTGC
1 TTTTTGTTTTTGC
*
30483513 TTTTTGCTTTTGC
1 TTTTTGTTTTTGC
* *
30483526 -TTTTATTTTTAC
1 TTTTTGTTTTTGC
30483538 TTTTTTGTTTTT
1 -TTTTTGTTTTT
30483550 TATTTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 9 0.30
13 12 0.40
14 9 0.30
ACGTcount: A:0.04, C:0.08, G:0.10, T:0.78
Consensus pattern (13 bp):
TTTTTGTTTTTGC
Found at i:30491331 original size:30 final size:30
Alignment explanation
Indices: 30491295--30491357 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
30491285 AGCCCTAGTA
30491295 TGTGACACGCCTTGATTTTAAAATAAATAT
1 TGTGACACGCCTTGATTTTAAAATAAATAT
30491325 TGTGACACGCCTTGATTTTAAAATAAATAT
1 TGTGACACGCCTTGATTTTAAAATAAATAT
30491355 TGT
1 TGT
30491358 AAGGTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (30 bp):
TGTGACACGCCTTGATTTTAAAATAAATAT
Found at i:30496597 original size:31 final size:31
Alignment explanation
Indices: 30496510--30496618 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 31
30496500 TGTGCCAAGC
* * * **
30496510 CGTGTGAGCCACACGGTCTGAGCCAATAGGGC
1 CGTGTGGGCCACACGGCCT-AGCCAATTGGAA
* * * * * *
30496542 CATGTGGGCAACACAGCCTGGCCAATT-TATT
1 CGTGTGGGCCACACGGCCTAGCCAATTGGA-A
*
30496573 CGTGTGGGCCACACGGGCTAGCCAATTGGAA
1 CGTGTGGGCCACACGGCCTAGCCAATTGGAA
30496604 CGTGTGGGCCACACG
1 CGTGTGGGCCACACG
30496619 AGAGTCTAGG
Statistics
Matches: 58, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
31 43 0.74
32 15 0.26
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (31 bp):
CGTGTGGGCCACACGGCCTAGCCAATTGGAA
Found at i:30496780 original size:12 final size:12
Alignment explanation
Indices: 30496763--30496795 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30496753 CATACAGACC
30496763 ATTAAGCTT-AAA
1 ATTAAG-TTCAAA
30496775 ATTAAGTTCAAA
1 ATTAAGTTCAAA
30496787 ATTAAGTTC
1 ATTAAGTTC
30496796 CAAGGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 18 0.90
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (12 bp):
ATTAAGTTCAAA
Found at i:30500113 original size:27 final size:27
Alignment explanation
Indices: 30500083--30500134 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
30500073 GTGGAAGAAG
*
30500083 ACTTGAGAAAGATAAATGAATTTTAAA
1 ACTTGAAAAAGATAAATGAATTTTAAA
*
30500110 ACTTGAAAAAGATGAATGAATTTTA
1 ACTTGAAAAAGATAAATGAATTTTA
30500135 GGTTTTGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (27 bp):
ACTTGAAAAAGATAAATGAATTTTAAA
Found at i:30507097 original size:20 final size:20
Alignment explanation
Indices: 30507074--30507137 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
30507064 TACATACATG
30507074 CCCCTATTTGTACTTCAGTA
1 CCCCTATTTGTACTTCAGTA
* * * *
30507094 CCCCTCAATTGTACATAAGTG
1 CCCCT-ATTTGTACTTCAGTA
* *
30507115 CCTCTGTTTGTACTTCAGTA
1 CCCCTATTTGTACTTCAGTA
30507135 CCC
1 CCC
30507138 TTGAATTGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.36
Consensus pattern (20 bp):
CCCCTATTTGTACTTCAGTA
Found at i:30507125 original size:41 final size:41
Alignment explanation
Indices: 30507054--30507164 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 41
30507044 AGTTAATTAA
*
30507054 CCCTGAATTGTACATACA-TGCCCCTATTTGTACTTCAGTAC
1 CCCTGAATTGTACATA-AGTGCCCCTGTTTGTACTTCAGTAC
* *
30507095 CCCTCAATTGTACATAAGTGCCTCTGTTTGTACTTCAGTAC
1 CCCTGAATTGTACATAAGTGCCCCTGTTTGTACTTCAGTAC
* * *
30507136 CCTTGAATTGCACATACGTGCCCCTGTTT
1 CCCTGAATTGTACATAAGTGCCCCTGTTT
30507165 ACACTCCGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.02
41 60 0.98
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (41 bp):
CCCTGAATTGTACATAAGTGCCCCTGTTTGTACTTCAGTAC
Found at i:30510553 original size:50 final size:50
Alignment explanation
Indices: 30510444--30510740 Score: 319
Period size: 50 Copynumber: 5.8 Consensus size: 50
30510434 CATTTGGTAA
*
30510444 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
30510500 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* **
30510550 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *** * *
30510600 AGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * * *
30510650 GGAAATCCCATGTAAGACCATATCTGGGATATGGCATTTGTA--GTACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
30510699 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30510741 TGTTATTATC
Statistics
Matches: 207, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.00
49 38 0.18
50 121 0.58
53 3 0.01
55 2 0.01
56 42 0.20
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:30519464 original size:46 final size:46
Alignment explanation
Indices: 30519411--30519498 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
30519401 TATAAATGTG
*
30519411 TCACATGAGTCACATGAGTCAAATGAGAATGCTTGGAGATAACACA
1 TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAACACA
30519457 TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAA
1 TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAA
30519499 ATGAAAGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (46 bp):
TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAACACA
Found at i:30522285 original size:27 final size:27
Alignment explanation
Indices: 30522243--30522315 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
30522233 GCTACCATTT
*
30522243 AATGATTTTAGTTGAAGTGTTTCAACAC
1 AATGA-TTTAGATGAAGTGTTTCAACAC
30522271 AATGATTTAGATGAAGTGTTTCAACAC
1 AATGATTTAGATGAAGTGTTTCAACAC
30522298 AATGATTTAGATGAAGTG
1 AATGATTTAGATGAAGTG
30522316 ATACCAGATA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 39 0.89
28 5 0.11
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (27 bp):
AATGATTTAGATGAAGTGTTTCAACAC
Found at i:30524799 original size:20 final size:17
Alignment explanation
Indices: 30524776--30524825 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
30524766 TGCTAAAGTT
30524776 AAAAAAATCATAAATATCCA
1 AAAAAAAT-ATAAATAT--A
30524796 AAAATAAATATAAATATA
1 AAAA-AAATATAAATATA
30524814 AAAAAAAT-TAAA
1 AAAAAAATATAAA
30524826 GAAAACCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 5 0.17
20 12 0.41
21 4 0.14
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAAATATAAATATA
Found at i:30530869 original size:131 final size:131
Alignment explanation
Indices: 30530463--30531383 Score: 1592
Period size: 132 Copynumber: 7.0 Consensus size: 131
30530453 TTTTCAATCT
* **
30530463 ACTTCCTACCAATATAGGAAGACAGGACCCGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
*
30530528 ACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATT
66 ACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
30530593 C
131 C
* * * *
30530594 ACTTCCTACTAATATAAGAAGATAGGGCCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
*
30530659 ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTGTGGGAAGACAAGATCTGCATCTTCGAT
66 ACAAGATCTGC-TTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
30530724 CC
130 CC
*
30530726 ACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
*
30530791 ACAAGATCTGCTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
66 ACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
30530856 C
131 C
*
30530857 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAGG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
* *
30530922 ACAAGATCTGCTTCTTTGATCTACTTCGCCACCAGTATGGGAAAACAAGATCTGCATCTTCGATC
66 ACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
30530987 C
131 C
*
30530988 ACTTCCTACCAATATAGGAAGATAGGGACATGCTATC-TTGATCTACTTCACGCTAATACATGAA
1 ACTTCCTACCAATATAGGAAGATA-GGACATGCTATCTTTGATCTACTTCACGCCAATACATGAA
* *
30531052 GACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAGGACAAGATCTGCATCTTCGA
65 GACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGA
30531117 TCC
129 TCC
30531120 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
* *
30531185 ACAAGATCTGCTCTCTTCGATCTACTTTGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
66 ACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
30531250 CC
130 CC
*
30531252 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTTACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
* *
30531317 ATAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
66 ACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
30531382 CC
130 CC
30531384 GTTCTCTGGG
Statistics
Matches: 759, Mismatches: 27, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
131 326 0.43
132 433 0.57
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (131 bp):
ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
ACAAGATCTGCTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
C
Found at i:30530930 original size:263 final size:264
Alignment explanation
Indices: 30530463--30531383 Score: 1598
Period size: 263 Copynumber: 3.5 Consensus size: 264
30530453 TTTTCAATCT
* **
30530463 ACTTCCTACCAATATAGGAAGACAGGACCCGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
*
30530528 ACAAGATCTGCT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
66 ACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
* * * * *
30530592 TCACTTCCTACTAATATAAGAAGATAGGGCCTGCTATCTTTGATCTACTTCACGCCAATACATGA
131 CCACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGA
*
30530657 AGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTGTGGGAAGACAAGATCTGCATCTTCG
196 AGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCG
30530722 ATCC
261 ATCC
*
30530726 ACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
* *
30530791 ACAAGATCTGCT-TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
66 ACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
30530855 CCACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGA
131 CCACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGA
* * *
30530920 GGACAAGATCTGC-TTCTTTGATCTACTTCGCCACCAGTATGGGAAAACAAGATCTGCATCTTCG
196 AGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCG
30530984 ATCC
261 ATCC
*
30530988 ACTTCCTACCAATATAGGAAGATAGGGACATGCTATC-TTGATCTACTTCACGCTAATACATGAA
1 ACTTCCTACCAATATAGGAAGATA-GGACATGCTATCTTTGATCTACTTCACGCCAATACATGAA
*
30531052 GACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAGGACAAGATCTGCATCTTCGA
65 GACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
30531117 TCCACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATG
130 TCCACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATG
* * *
30531182 AAGACAAGATCTGCTCTCTTCGATCTACTTTGCCACCAATATGGGAAGACAAGATCTGCATCTTC
195 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTC
30531247 GATCC
260 GATCC
*
30531252 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTTACGCCAATACATGAAG
1 ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
*
30531317 ATAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
66 ACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
30531382 CC
131 CC
30531384 GTTCTCTGGG
Statistics
Matches: 627, Mismatches: 27, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
262 115 0.18
263 347 0.55
264 165 0.26
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (264 bp):
ACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGAAG
ACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
CCACTTCCTACCAATATAGGAAGATAGGACATGCTATCTTTGATCTACTTCACGCCAATACATGA
AGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCG
ATCC
Found at i:30538169 original size:12 final size:12
Alignment explanation
Indices: 30538139--30538171 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
30538129 GAAGTCTCTC
*
30538139 TGTGTTAGGCCT
1 TGTGTTGGGCCT
30538151 TGTGTTGGGCCT
1 TGTGTTGGGCCT
30538163 TGTGTTGGG
1 TGTGTTGGG
30538172 TTCTTGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.12, G:0.42, T:0.42
Consensus pattern (12 bp):
TGTGTTGGGCCT
Found at i:30544513 original size:24 final size:24
Alignment explanation
Indices: 30544484--30544537 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
30544474 TTTGACTGAA
30544484 TATTAATTATGAGCCTCCTTTTAT
1 TATTAATTATGAGCCTCCTTTTAT
30544508 TATTAATTATGAGCCTCCTTTTAT
1 TATTAATTATGAGCCTCCTTTTAT
30544532 TATTAA
1 TATTAA
30544538 ATAATTGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (24 bp):
TATTAATTATGAGCCTCCTTTTAT
Found at i:30552604 original size:73 final size:73
Alignment explanation
Indices: 30552485--30552630 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
30552475 AAACTTCTTA
*
30552485 AAACTGATTGGGTACATTGACAATGACTAGGTTGGATCAGTGGATGATATGCGAAGTACCTTTAG
1 AAACTGATTGGGTACATTGACAATGACTAGGTTGGATCAGTGGATGATATACGAAGTACCTTTAG
30552550 ATATTTCT
66 ATATTTCT
30552558 AAACTGATTGGGTACATTGACAATGACTAGGTTGGATCAGTGGATGATATACGAAGTACCTTTAG
1 AAACTGATTGGGTACATTGACAATGACTAGGTTGGATCAGTGGATGATATACGAAGTACCTTTAG
30552623 ATATTTCT
66 ATATTTCT
30552631 TCTCACTAAG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (73 bp):
AAACTGATTGGGTACATTGACAATGACTAGGTTGGATCAGTGGATGATATACGAAGTACCTTTAG
ATATTTCT
Found at i:30557631 original size:22 final size:22
Alignment explanation
Indices: 30557603--30557741 Score: 197
Period size: 22 Copynumber: 6.3 Consensus size: 22
30557593 TGTTGATAGT
*
30557603 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
30557625 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
30557647 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
30557669 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
30557691 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
30557713 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
30557735 ACGTACT
1 ACGTACT
30557742 TTTCAATGGT
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 105 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:30563284 original size:62 final size:62
Alignment explanation
Indices: 30563195--30563314 Score: 161
Period size: 62 Copynumber: 1.9 Consensus size: 62
30563185 AAGTGATTAC
** * * *
30563195 TTAATATTAAATTAAATTTAATGTTTATCTTG-TAGATAAACATTCTATTATTTTAATAAAAT
1 TTAATATTAAATTAAATCCAATATTTATCTTGATA-ATAAACATTATATTAATTTAATAAAAT
* *
30563257 TTAATATTAAATTTAATCCAATATTTATCTTGATAATAAATATTATATTAATTTAATA
1 TTAATATTAAATTAAATCCAATATTTATCTTGATAATAAACATTATATTAATTTAATA
30563315 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 48 0.96
63 2 0.04
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (62 bp):
TTAATATTAAATTAAATCCAATATTTATCTTGATAATAAACATTATATTAATTTAATAAAAT
Found at i:30564255 original size:21 final size:21
Alignment explanation
Indices: 30564216--30564255 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30564206 TATCTCATGA
30564216 TATATCTATTTTATAATTTTT
1 TATATCTATTTTATAATTTTT
*
30564237 TATAT-TATTTATATTATTT
1 TATATCTATTT-TATAATTT
30564256 AATGTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TATATCTATTTTATAATTTTT
Found at i:30573590 original size:11 final size:12
Alignment explanation
Indices: 30573559--30573591 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
30573549 ATAATAAAAA
30573559 TTAAAATAATTT
1 TTAAAATAATTT
30573571 TTAAAAATAA-TT
1 TT-AAAATAATTT
30573583 TTAAAATAA
1 TTAAAATAA
30573592 AAAAATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 6 0.30
13 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAAAATAATTT
Found at i:30573598 original size:16 final size:17
Alignment explanation
Indices: 30573572--30573604 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30573562 AAATAATTTT
*
30573572 TAAAAATAATTTTAAAA
1 TAAAAATAATTTCAAAA
30573589 TAAAAA-AATTTCAAAA
1 TAAAAATAATTTCAAAA
30573605 AGTGATAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAATAATTTCAAAA
Done.