Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 64 of 208
Found at i:18419998 original size:21 final size:23
Alignment explanation
Indices: 18419974--18420017 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18419964 TCTTATGGTT
18419974 TTCTT-AACATCAC-ATTTATAC
1 TTCTTAAACATCACAATTTATAC
18419995 TTCTTACAACATCACAATTTATA
1 TTCTTA-AACATCACAATTTATA
18420018 TAAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCTTAAACATCACAATTTATAC
Found at i:18420709 original size:28 final size:28
Alignment explanation
Indices: 18420677--18420734 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
18420667 AAACATGTCC
*
18420677 TTAGTTTAATCGAAAATGAGCAAATTAA
1 TTAGTCTAATCGAAAATGAGCAAATTAA
* *
18420705 TTAGTCTAATTGGAAATGAGCAAATTAA
1 TTAGTCTAATCGAAAATGAGCAAATTAA
18420733 TT
1 TT
18420735 GAAAGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (28 bp):
TTAGTCTAATCGAAAATGAGCAAATTAA
Found at i:18428713 original size:13 final size:13
Alignment explanation
Indices: 18428697--18428728 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18428687 TAGTGTGTAT
18428697 ATTTAAACCTAAA
1 ATTTAAACCTAAA
*
18428710 ATTTAAACCTTAA
1 ATTTAAACCTAAA
18428723 ATTTAA
1 ATTTAA
18428729 TATTAATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTAAACCTAAA
Found at i:18440792 original size:72 final size:72
Alignment explanation
Indices: 18440702--18440841 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
18440692 AATAGGTAAA
* * *
18440702 AAAAAATCTGGTAAGTTAATTTATTGAAAACAATATTAAATTTAAAAGAGTTCTAAAATTCTTAA
1 AAAAAATCTGCTAAGTTAATTTATTGAAAACAAAATTAAATCTAAAAGAGTTCTAAAATTCTTAA
18440767 AAAAGGT
66 AAAAGGT
* * * *
18440774 AAAAAATCTGCTATGTTAATTTATTGAAAACAAAATTATATCTAAAAGAGTTTTCAAATTCTTAA
1 AAAAAATCTGCTAAGTTAATTTATTGAAAACAAAATTAAATCTAAAAGAGTTCTAAAATTCTTAA
18440839 AAA
66 AAA
18440842 GAAAATAGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.34
Consensus pattern (72 bp):
AAAAAATCTGCTAAGTTAATTTATTGAAAACAAAATTAAATCTAAAAGAGTTCTAAAATTCTTAA
AAAAGGT
Found at i:18448843 original size:29 final size:30
Alignment explanation
Indices: 18448811--18448873 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
18448801 AGCTTTGGCT
18448811 ATCGATT-ATGAAAAGGGATGGTGACAACC
1 ATCGATTAATGAAAAGGGATGGTGACAACC
* *
18448840 ATCGATTAATGAAAAGGGATGGTTACCACC
1 ATCGATTAATGAAAAGGGATGGTGACAACC
18448870 ATCG
1 ATCG
18448874 TTTAGCACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (30 bp):
ATCGATTAATGAAAAGGGATGGTGACAACC
Found at i:18459076 original size:26 final size:26
Alignment explanation
Indices: 18459018--18459083 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
18459008 ACCATAACAC
*
18459018 AAATCAGTCATTTACCCACGAAGAGCA
1 AAAT-AGTCATTTACCCACCAAGAGCA
* *
18459045 AAATAGTCATTTACCCTCCAAGGGCA
1 AAATAGTCATTTACCCACCAAGAGCA
**
18459071 TTATAGTCATTTA
1 AAATAGTCATTTA
18459084 ACAACCTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 30 0.88
27 4 0.12
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (26 bp):
AAATAGTCATTTACCCACCAAGAGCA
Found at i:18468903 original size:2 final size:2
Alignment explanation
Indices: 18468896--18468932 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18468886 AGTATGGTTG
18468896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18468933 GAGTTTAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18475637 original size:27 final size:27
Alignment explanation
Indices: 18475584--18475897 Score: 377
Period size: 27 Copynumber: 11.7 Consensus size: 27
18475574 GGTATAACAG
*
18475584 TCATTTTACCCTAT-G-GGGTATTACGA
1 TCATTTTACCC-ATCGAGGGTATTTCGA
* *
18475610 TCATTTTATCCTTCGAGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTCGA
*
18475637 TCGTTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGA
*
18475663 GTCATTTTACACATCGAGGGTATTTCGA
1 -TCATTTTACCCATCGAGGGTATTTCGA
* *
18475691 TCATTTTACCCATCGAGGGTATCTCGG
1 TCATTTTACCCATCGAGGGTATTTCGA
* * *
18475718 TAATTTTACCCATCAAGGGTATTTTGA
1 TCATTTTACCCATCGAGGGTATTTCGA
*
18475745 TTATTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGA
* *
18475771 GTGATTTTATCCATCGAGGGTATTTCGA
1 -TCATTTTACCCATCGAGGGTATTTCGA
* * *
18475799 TCATTTTACCCATCGAAGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTCGA
* * *
18475826 TCATTTTACCCATTGAGGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTCGA
18475853 TCATTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGA
*
18475879 GTCATTTTACCCATTGAGG
1 -TCATTTTACCCATCGAGG
18475898 TTGTTTCAGT
Statistics
Matches: 249, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
25 1 0.00
26 13 0.05
27 233 0.94
28 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCATCGAGGGTATTTCGA
Found at i:18484280 original size:28 final size:28
Alignment explanation
Indices: 18484245--18484360 Score: 151
Period size: 28 Copynumber: 4.1 Consensus size: 28
18484235 CATGTAGTAG
* * **
18484245 CAGTGTGGGCCTGAGCCCTATACAGCAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
18484273 CGGTGTGGGCCTTAGCCCAACACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
*
18484301 CAGTGTAGGCCTTAGCCCAATACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
18484329 CAGTGTGGGCCTTAGCCAAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
18484357 CAGT
1 CAGT
18484361 ACAATGCAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 76 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAATAA
Found at i:18484725 original size:27 final size:27
Alignment explanation
Indices: 18484691--18485129 Score: 470
Period size: 27 Copynumber: 16.3 Consensus size: 27
18484681 GAATATAACA
*
18484691 GTCATTTTACCCTATAG-GGGTATTTTG
1 GTCATTTTACCC-ATCGAGGGTATTTTG
* * * **
18484718 GTTATTTTACCCTTCGGGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
18484745 ATCATTTTACCCATGGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
*
18484772 ATCATTTTACCCATCGAGGGTATTTCT-
1 GTCATTTTACCCATCGAGGGTATTT-TG
* *
18484799 GTCATTTTATCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
*
18484826 ATCATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
18484853 GTCATTTTAACCATTGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
* * *
18484880 GTCATTTAACCCATCAAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
* * **
18484907 ATCATTTTATCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTTG
* * * * * **
18484934 ATTATTTTACCAATTGATGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTTG
* * *
18484961 GTCATTTTATCCATCGAGGGAATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
18484988 ATCATTTTACCCATCGAAGGTATTTCT-
1 GTCATTTTACCCATCGAGGGTATTT-TG
* *
18485015 ATTATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
18485042 GTCATTTTATCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
18485069 ATCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
*
18485096 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
18485123 GTCATTT
1 GTCATTT
18485130 GCCCATGAAT
Statistics
Matches: 348, Mismatches: 59, Indels: 10
0.83 0.14 0.02
Matches are distributed among these distances:
26 3 0.01
27 344 0.99
28 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTTG
Found at i:18484755 original size:54 final size:54
Alignment explanation
Indices: 18484692--18485129 Score: 522
Period size: 54 Copynumber: 8.1 Consensus size: 54
18484682 AATATAACAG
* * * * * * *
18484692 TCATTTTACCCTATAG-GGGTATTTTGGTTATTTTACCCTTCGGGGGTATTTCAA
1 TCATTTTACCC-ATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* *
18484746 TCATTTTACCCATGGAGGGTATTTTGATCATTTTACCCATCGAGGGTATTTCTG-
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTC-GA
* * *
18484800 TCATTTTATCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * * * *
18484854 TCATTTTAACCATTGAGGGTATTTTGGTCATTTAACCCATCAAGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * * * *
18484908 TCATTTTATCCATCGAGGGTATTTCAATTATTTTACCAATTGATGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * *
18484961 GTCATTTTATCCATCGAGGGAATTTCGATCATTTTACCCATCGAAGGTATTTCTA
1 -TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * *
18485016 TTATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* *
18485070 TCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCGG
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
18485124 TCATTT
1 TCATTT
18485130 GCCCATGAAT
Statistics
Matches: 332, Mismatches: 47, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.02
54 326 0.98
55 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (54 bp):
TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
Found at i:18484806 original size:81 final size:81
Alignment explanation
Indices: 18484692--18485129 Score: 576
Period size: 81 Copynumber: 5.4 Consensus size: 81
18484682 AATATAACAG
* * * * * *
18484692 TCATTTTACCCTATAG-GGGTATTTTGGTTATTTTACCCTTCGGGGGTATTTCAATCATTTTACC
1 TCATTTTACCC-ATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACC
*
18484756 CATGGAGGGTATTTTGA
65 CATCGAGGGTATTTTGA
18484773 TCATTTTACCCATCGAGGGTATTTCT-GTCATTTTATCCATCGAGGGTATTTCGATCATTTTACC
1 TCATTTTACCCATCGAGGGTATTT-TGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACC
*
18484837 CATCGAGGGTATTTTGG
65 CATCGAGGGTATTTTGA
* * * * * *
18484854 TCATTTTAACCATTGAGGGTATTTTGGTCATTTAACCCATCAAGGGTATTTCGATCATTTTATCC
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
**
18484919 ATCGAGGGTATTTCAA
66 ATCGAGGGTATTTTGA
* * * * ** *
18484935 TTATTTTACCAATTGATGGTATTTCAGTCATTTTATCCATCGAGGGAATTTCGATCATTTTACCC
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
*
18485000 ATCGAAGGTATTTCT-A
66 ATCGAGGGTATTT-TGA
*
18485016 TTATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
* *
18485081 ATCGAGGGTATTTCGG
66 ATCGAGGGTATTTTGA
*
18485097 TCATTTTACCCATCGAGGGTATTTCGGTCATTT
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTT
18485130 GCCCATGAAT
Statistics
Matches: 311, Mismatches: 41, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.01
81 306 0.98
82 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
ATCGAGGGTATTTTGA
Found at i:18488973 original size:21 final size:23
Alignment explanation
Indices: 18488947--18488988 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
18488937 CAGAGATGCT
*
18488947 CTCTTAGTTTT-GTGT-TTTGTG
1 CTCTTAATTTTGGTGTGTTTGTG
18488968 CTCTTAATTTTGGTGTGTTTG
1 CTCTTAATTTTGGTGTGTTTG
18488989 AAGTGTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.07, C:0.10, G:0.24, T:0.60
Consensus pattern (23 bp):
CTCTTAATTTTGGTGTGTTTGTG
Found at i:18495781 original size:51 final size:51
Alignment explanation
Indices: 18495587--18495771 Score: 196
Period size: 51 Copynumber: 3.6 Consensus size: 51
18495577 GAAGTTGCTA
* * *
18495587 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG-GATGAAAAT
* * * ** ***
18495637 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCACAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAAT
* * * *
18495687 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACCTGTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAAT
18495739 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
18495772 TGTGAATCGG
Statistics
Matches: 108, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 2 0.02
50 37 0.34
51 67 0.62
52 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAAT
Found at i:18514086 original size:14 final size:15
Alignment explanation
Indices: 18514064--18514140 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
18514054 CAATCAAACA
18514064 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
18514078 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
18514093 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
18514113 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
18514127 ACAGAAAA-CATTTT
1 CCAGAAAATCATTTT
18514141 ACTGGCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 23 0.45
15 14 0.27
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:18514105 original size:20 final size:20
Alignment explanation
Indices: 18514080--18514119 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18514070 AATATTTTCC
*
18514080 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
18514100 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
18514120 TCATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:18514125 original size:34 final size:35
Alignment explanation
Indices: 18514068--18514134 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
18514058 CAAACACCAG
*
18514068 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
18514103 AAAACATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
18514135 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:18514141 original size:14 final size:14
Alignment explanation
Indices: 18514103--18514142 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
18514093 ACAGAAAAGT
*
18514103 AAAACATTTTCCAG
1 AAAACATTTTACAG
*
18514117 AAATCATTTTACAG
1 AAAACATTTTACAG
18514131 AAAACATTTTAC
1 AAAACATTTTAC
18514143 TGGCAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:18528764 original size:27 final size:27
Alignment explanation
Indices: 18528734--18529207 Score: 476
Period size: 27 Copynumber: 17.7 Consensus size: 27
18528724 TCATCTCTTA
** *
18528734 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
18528761 GGGGTATTTCGGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
**
18528788 AAGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* ** **
18528815 GGGTTATTTTGGTCATTCAACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
18528842 GGGTTATTTCGGTTATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
18528869 AGGGTATTTCAATCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
18528895 GGGGTATTTCAGTCAATTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * * *
18528922 AGGGTATTTCGGTCATTTTATCTTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
*
18528949 GGGGTA-TTCCGATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
18528976 GGGGTATTTTAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
18529003 AGGGTATTTCAGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
18529029 GGGGTATTTCAGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
*
18529055 GGGGTATTTCAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
18529082 GGGGTATTTCGGTCATTTTACCTTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
18529109 AGGGTATTT-TGATTATTTTGCCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
18529136 GGGGTATTTCGGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
18529163 GGAGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*** *
18529190 AATGTATTTCGGTCATTT
1 GGGGTATTTCAGTCATTT
18529208 ATCGACCTCT
Statistics
Matches: 374, Mismatches: 63, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
26 80 0.21
27 288 0.77
28 6 0.02
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:18528854 original size:81 final size:79
Alignment explanation
Indices: 18528734--18529207 Score: 542
Period size: 81 Copynumber: 5.9 Consensus size: 79
18528724 TCATCTCTTA
** * *
18528734 GGGGTATAACAGTCATTTTACCTTATGGGGGTATTTCGGTTATTTTACCCTATGAAGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGAAGGTATTTCG
18528799 ATCATTTTACCCTAT
65 ATCATTTTACCCTAT
** ** *
18528814 GGGGTTATTTTGGTCATTCAACCCTATGGGGTTATTTCGGTTATTTTACCCTAT-AAGGGTATTT
1 GGGG-TATTTCAGTCATTTTACCCTATGGGG-TATTTCGGTCATTTTACCCTATGAA-GGTATTT
*
18528878 CAATCATTTTACCCTAT
63 CGATCATTTTACCCTAT
* * * * * *
18528895 GGGGTATTTCAGTCAATTTATCCTATGAGGGTATTTCGGTCATTTTATCTTAT-AGGGGTATTCC
1 GGGGTATTTCAGTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGA-AGGTATTTC
18528959 GATCATTTTACCCTAT
64 GATCATTTTACCCTAT
* * *
18528975 GGGGGTATTTTAGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATG-GGGTATTTC
1 -GGGGTATTTCAGTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATGAAGGTATTTC
18529039 -AGTCATTTTACCCTAT
64 GA-TCATTTTACCCTAT
* * * *
18529055 GGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCTTACGAGGGTATTTTG
1 GGGGTATTTCAGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGAAGGTATTTCG
* *
18529120 ATTATTTTGCCCTAT
65 ATCATTTTACCCTAT
* * * *
18529135 GGGGGTATTTCGGTCATTTTATCCTATGGGAGTATTTCGATCATTTTACCCTATGAATGTATTTC
1 -GGGGTATTTCAGTCATTTTACCCTATGGG-GTATTTCGGTCATTTTACCCTATGAAGGTATTTC
*
18529200 GGTCATTT
64 GATCATTT
18529208 ATCGACCTCT
Statistics
Matches: 337, Mismatches: 44, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
79 49 0.15
80 115 0.34
81 173 0.51
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (79 bp):
GGGGTATTTCAGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGAAGGTATTTCGA
TCATTTTACCCTAT
Found at i:18530492 original size:11 final size:11
Alignment explanation
Indices: 18530473--18530503 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
18530463 TCCTCCCAAC
18530473 AACTCCATTCA
1 AACTCCATTCA
*
18530484 AATTCCATTCA
1 AACTCCATTCA
18530495 AACTCCATT
1 AACTCCATT
18530504 GACCTGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (11 bp):
AACTCCATTCA
Found at i:18537084 original size:25 final size:25
Alignment explanation
Indices: 18537039--18537089 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
18537029 ACTCTTCCTA
* *
18537039 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTATTC
*
18537064 TCTCTTCATTTCCCT-TCCATTATTC
1 TCTCTTCACTTCCCTCT-CATTATTC
18537089 T
1 T
18537090 TAATTCCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTATTC
Found at i:18538908 original size:21 final size:21
Alignment explanation
Indices: 18538884--18538935 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
18538874 AGTGTGTTCC
*
18538884 TTTTATGTTGATTG-TTTTAG
1 TTTTATGTTGAATGCTTTTAG
*
18538904 ATTTTCTTGTTGAATGCTTTTAG
1 -TTTT-ATGTTGAATGCTTTTAG
*
18538927 TTTCATGTT
1 TTTTATGTT
18538936 ATTTAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.15, C:0.06, G:0.17, T:0.62
Consensus pattern (21 bp):
TTTTATGTTGAATGCTTTTAG
Found at i:18542119 original size:139 final size:139
Alignment explanation
Indices: 18541869--18542141 Score: 510
Period size: 139 Copynumber: 2.0 Consensus size: 139
18541859 TAAGAACTAA
**
18541869 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAATGGGTTTATAG
1 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
18541934 CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
66 CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
18541999 AGTTGTGAC
131 AGTTGTGAC
18542008 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
1 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
* *
18542073 CCTGACGGGTCATGTCACGGGTCGAGCAAAAATTATAGATTTTCGCAGTGATGTCGCAACACAGG
66 CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
18542138 AGTT
131 AGTT
18542142 TTGTGTCACA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.32
Consensus pattern (139 bp):
TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
AGTTGTGAC
Found at i:18546437 original size:25 final size:25
Alignment explanation
Indices: 18546409--18546465 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
18546399 ACCTTATCAA
18546409 AGTCCTCA-TACTCAAGCAACATGTT
1 AGTCCTCACT-CTCAAGCAACATGTT
18546434 AGTCCTCACTCTCAAGCAACATGTT
1 AGTCCTCACTCTCAAGCAACATGTT
18546459 AGTCCTC
1 AGTCCTC
18546466 CCTTAGGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (25 bp):
AGTCCTCACTCTCAAGCAACATGTT
Found at i:18548451 original size:20 final size:20
Alignment explanation
Indices: 18548426--18548522 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 20
18548416 CTTATACTGG
18548426 TTGCACTTCAGTGCCCCTGA
1 TTGCACTTCAGTGCCCCTGA
* **
18548446 TTGCAC-TCTAGTGCCCTTTT
1 TTGCACTTC-AGTGCCCCTGA
* *
18548466 TTACACTTTAGTG-CCCT-A
1 TTGCACTTCAGTGCCCCTGA
18548484 TTTGCACTTC-GATGCCCCTGA
1 -TTGCACTTCAG-TGCCCCTGA
*
18548505 TTGCA-TTCTGGTGCCCCT
1 TTGCACTTC-AGTGCCCCT
18548523 ATTCAGCACT
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
18 1 0.02
19 17 0.28
20 39 0.65
21 3 0.05
ACGTcount: A:0.13, C:0.32, G:0.18, T:0.37
Consensus pattern (20 bp):
TTGCACTTCAGTGCCCCTGA
Found at i:18550458 original size:11 final size:11
Alignment explanation
Indices: 18550442--18550478 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
18550432 TAACAATAAC
18550442 AATATTAAAAT
1 AATATTAAAAT
18550453 AATATTAAAAT
1 AATATTAAAAT
18550464 AATA--AAAAT
1 AATATTAAAAT
18550473 AATATT
1 AATATT
18550479 TGTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:18551189 original size:28 final size:28
Alignment explanation
Indices: 18551137--18551206 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
18551127 AAATTAAAAA
*
18551137 TTACCAAAATGT-TATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
18551164 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
18551192 TTACCAAAATATATA
1 TTACCAAAATATATA
18551207 AAAAAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 11 0.27
28 30 0.73
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:18551302 original size:28 final size:27
Alignment explanation
Indices: 18551260--18551367 Score: 162
Period size: 27 Copynumber: 4.0 Consensus size: 27
18551250 ACTCCCTGGG
*
18551260 ACAAGGGAACACTGTTGGCGGCACCCAA
1 ACAAGGGAACCCTGTTGGCGGCA-CCAA
18551288 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
18551315 ACAAGGGTTCCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
18551342 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
18551368 CTCGTGTTAT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 55 0.71
28 22 0.29
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:18551327 original size:27 final size:27
Alignment explanation
Indices: 18551271--18551367 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
18551261 CAAGGGAACA
**
18551271 CTGTTGGCGGCACCCAAACAAGGGAACC
1 CTGTTGGCGGCA-CCAAACAAGGGTTCC
18551299 CTGTTGGCGGCACCAAACAAGGGTTCC
1 CTGTTGGCGGCACCAAACAAGGGTTCC
18551326 CTGTTGGCGGCACCAAACAAGGGTTCC
1 CTGTTGGCGGCACCAAACAAGGGTTCC
18551353 CTGTTGGCGGCACCA
1 CTGTTGGCGGCACCA
18551368 CTCGTGTTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 55 0.82
28 12 0.18
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (27 bp):
CTGTTGGCGGCACCAAACAAGGGTTCC
Found at i:18554076 original size:18 final size:18
Alignment explanation
Indices: 18554050--18554087 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18554040 ATCCAAATGA
* *
18554050 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
18554068 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
18554086 TC
1 TC
18554088 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:18554094 original size:18 final size:18
Alignment explanation
Indices: 18554053--18554094 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
18554043 CAAATGATCG
* *
18554053 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
18554071 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
18554089 CCACCA
1 CCACCA
18554095 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:18554832 original size:3 final size:3
Alignment explanation
Indices: 18554824--18554864 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18554814 AGTGACATCT
18554824 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18554865 CTATAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18555223 original size:27 final size:27
Alignment explanation
Indices: 18555150--18555229 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
18555140 ATAACACGAG
**
18555150 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
18555177 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
18555204 TGGTGCCGCCAACAGTGTTCCCTTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
18555230 CCCAGGGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:18555282 original size:18 final size:17
Alignment explanation
Indices: 18555256--18555292 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
18555246 ATCAGTCCAG
18555256 TTTTTTTTTTCTGTTTT
1 TTTTTTTTTTCTGTTTT
*
18555273 TTTTTGTTTTTTTGTTTT
1 TTTTT-TTTTTCTGTTTT
18555291 TT
1 TT
18555293 ATATATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTTCTGTTTT
Found at i:18555322 original size:27 final size:28
Alignment explanation
Indices: 18555292--18555362 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
18555282 TTTTGTTTTT
18555292 TATATATTTTGGTAAATAAAAAAAT-TA
1 TATATATTTTGGTAAATAAAAAAATATA
* *
18555319 TATATTTTTTGGTAAATAAAAAAATATT
1 TATATATTTTGGTAAATAAAAAAATATA
*
18555347 TATAACATTTTGGTAA
1 TAT-ATATTTTGGTAA
18555363 TTTTTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 24 0.63
28 4 0.11
29 10 0.26
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAATATA
Found at i:18556001 original size:9 final size:10
Alignment explanation
Indices: 18555987--18556011 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18555977 AGAAAAGTTA
18555987 TAAAAAATAT
1 TAAAAAATAT
18555997 TAAAAAATAT
1 TAAAAAATAT
18556007 TAAAA
1 TAAAA
18556012 TTTTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:18556302 original size:13 final size:13
Alignment explanation
Indices: 18556284--18556315 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18556274 AAATGTCACA
18556284 TTTATTTATATTT
1 TTTATTTATATTT
*
18556297 TTTATTTTTATTT
1 TTTATTTATATTT
18556310 TTTATT
1 TTTATT
18556316 ACACCTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTATATTT
Found at i:18556781 original size:17 final size:17
Alignment explanation
Indices: 18556761--18556806 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
18556751 AGATTAATTA
*
18556761 TATAAATTATTTAATAT
1 TATAAATTATTTAAAAT
* *
18556778 TATAAAATAATTAAAAT
1 TATAAATTATTTAAAAT
*
18556795 TACAAATTATTT
1 TATAAATTATTT
18556807 TATAAATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAAATTATTTAAAAT
Found at i:18556855 original size:11 final size:10
Alignment explanation
Indices: 18556841--18556888 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
18556831 TTTTTATGTT
18556841 ATTTTCTATAA
1 ATTTTCTAT-A
18556852 ATTTTTCTATA
1 A-TTTTCTATA
* *
18556863 TTTTTTTATA
1 ATTTTCTATA
18556873 ATATTTCTATA
1 AT-TTTCTATA
18556884 ATTTT
1 ATTTT
18556889 TAATAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 12 0.39
11 11 0.35
12 8 0.26
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTCTATA
Found at i:18556864 original size:21 final size:21
Alignment explanation
Indices: 18556840--18556895 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
18556830 ATTTTTATGT
*
18556840 TATTTTCTATA-AATTTTTCTA
1 TATTTT-TATATAATATTTCTA
*
18556861 TATTTTTTTATAATATTTCTA
1 TATTTTTATATAATATTTCTA
18556882 TAATTTTTA-ATAAT
1 T-ATTTTTATATAAT
18556896 CAATCAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTATATAATATTTCTA
Found at i:18556867 original size:22 final size:22
Alignment explanation
Indices: 18556842--18556889 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18556832 TTTTATGTTA
*
18556842 TTTTCTATAAATTTTTCTAT-AT
1 TTTTCTAT-AATATTTCTATAAT
*
18556864 TTTTTTATAATATTTCTATAAT
1 TTTTCTATAATATTTCTATAAT
18556886 TTTT
1 TTTT
18556890 AATAATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCTATAATATTTCTATAAT
Found at i:18565120 original size:20 final size:20
Alignment explanation
Indices: 18565086--18565127 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
18565076 AACTATTTAA
** *
18565086 ATAATATTACTTGAATAGTT
1 ATAATATTAAATGAATAATT
18565106 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
18565126 AT
1 AT
18565128 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:18567816 original size:17 final size:17
Alignment explanation
Indices: 18567796--18567828 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18567786 AAAATAAATA
*
18567796 AAGACATAAAAAATAAC
1 AAGAAATAAAAAATAAC
18567813 AAGAAATAAAAAATAA
1 AAGAAATAAAAAATAA
18567829 AAATAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAGAAATAAAAAATAAC
Found at i:18567918 original size:4 final size:4
Alignment explanation
Indices: 18567909--18567942 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
18567899 AAAAGGGAGT
*
18567909 AATA AATA AATA AATG AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
18567943 ATTTGTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:18571592 original size:42 final size:42
Alignment explanation
Indices: 18571462--18571599 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 42
18571452 GTGGATTCAG
* *
18571462 CACTTAGCAACCACC-ATAAATTCAGTGATACGAGGAATCAA
1 CACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAA
* *
18571503 CACATAGCAACC-CCTTTCACAATTAAG-GATTA-GGTGGAATCAA
1 CACTTAGCAACCACCTTT-A-AATTCAGTGA-TACGG-GGAATCAA
* *
18571546 CACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAG
1 CACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAA
18571588 CACTTAGCAACC
1 CACTTAGCAACC
18571600 CCTCGGGGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
40 2 0.02
41 12 0.15
42 30 0.37
43 32 0.40
44 5 0.06
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (42 bp):
CACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAA
Found at i:18571613 original size:26 final size:26
Alignment explanation
Indices: 18571577--18571626 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
18571567 TTCAGTGATA
18571577 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACTTAGCAACCCCT
18571603 CGGGGAATCAGCACTTAGCAACCC
1 CGGGGAATCAGCACTTAGCAACCC
18571627 TTTTAGAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.24, T:0.14
Consensus pattern (26 bp):
CGGGGAATCAGCACTTAGCAACCCCT
Found at i:18571665 original size:67 final size:67
Alignment explanation
Indices: 18571538--18571698 Score: 241
Period size: 67 Copynumber: 2.4 Consensus size: 67
18571528 AGGATTAGGT
* * * * * *
18571538 GGAATCAACACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACTTAGCAACCCCT
1 GGAATCAGCACTTAGCAACC-CTTTTAGAGTCAATAATACGGGGAATCAGCACTTAGCAACCCCT
18571603 CGG
65 CGG
* *
18571606 GGAATCAGCACTTAGCAACCCTTTTAGAGTCAATAATTCGTGGAATCAGCACTTAGCAACCCCTC
1 GGAATCAGCACTTAGCAACCCTTTTAGAGTCAATAATACGGGGAATCAGCACTTAGCAACCCCTC
18571671 GG
66 GG
18571673 GGAATCAGCACTTAGCAACCCTTTTA
1 GGAATCAGCACTTAGCAACCCTTTTA
18571699 TATTCAGTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 66 0.78
68 19 0.22
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (67 bp):
GGAATCAGCACTTAGCAACCCTTTTAGAGTCAATAATACGGGGAATCAGCACTTAGCAACCCCTC
GG
Found at i:18572787 original size:11 final size:12
Alignment explanation
Indices: 18572759--18572791 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18572749 GCCCAAATGT
18572759 CGAAATTTTCGAA
1 CGAAATTTTC-AA
18572772 CGAAATTTTC-A
1 CGAAATTTTCAA
18572783 CGAAATTTT
1 CGAAATTTT
18572792 TCCGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:18577109 original size:43 final size:41
Alignment explanation
Indices: 18577021--18577250 Score: 198
Period size: 43 Copynumber: 5.5 Consensus size: 41
18577011 CTCGGTGGAT
* *
18577021 TCAGCACTTAGCAACCACC-ATA-AATTC-AGTGATACAGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAA-TCAAG-GATACGGGGAA
* * *
18577062 TCAGCACATAGCAACCCCTTTCACAATTAAGGATTCGGTGGAA
1 TCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG-GGAA
* *
18577105 TCAGCACTTAGCAACCACCTTTATATTC-AGTGATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAG-GATACGGGGAA
* *
18577147 TCAGCACTTAGCAACCCCTTTCACAATCAAAGATACGGTGGGA
1 TCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG-GGAA
* * * ** **
18577190 TCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAGGATACGGGGAA
18577232 TCAGCACTTAGCAACCCCT
1 TCAGCACTTAGCAACCCCT
18577251 CGGGGAATCA
Statistics
Matches: 155, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.01
41 24 0.15
42 58 0.37
43 61 0.39
44 10 0.06
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
TCAGCACTTAGCAACCCCTTTACAATCAAGGATACGGGGAA
Found at i:18577154 original size:42 final size:42
Alignment explanation
Indices: 18577021--18577247 Score: 221
Period size: 42 Copynumber: 5.4 Consensus size: 42
18577011 CTCGGTGGAT
* *
18577021 TCAGCACTTAGCAACCACC-ATAAATTCAGTGATACAGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
* * *
18577062 TCAGCACATAGCAACC-CCTTTCACAATTAAG-GATTCGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-A-AATTCAGTGATACGG-GGAA
*
18577105 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
** *
18577147 TCAGCACTTAGCAACC-CCTTTCACAA-TCAAAGATACGGTGGGA
1 TCAGCACTTAGCAACCACCTTT-A-AATTCAGTGATACGG-GGAA
* * * * * **
18577190 TCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
18577232 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
18577248 CCTCGGGGAA
Statistics
Matches: 154, Mismatches: 21, Indels: 21
0.79 0.11 0.11
Matches are distributed among these distances:
40 2 0.01
41 21 0.14
42 61 0.40
43 60 0.39
44 10 0.06
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
Found at i:18577159 original size:85 final size:85
Alignment explanation
Indices: 18577012--18577250 Score: 327
Period size: 85 Copynumber: 2.8 Consensus size: 85
18577002 TATCCGTTAC
* * * *
18577012 TCGGTGGATTCAGCACTTAGCAACCACC-ATAAATTCAGTGATACAGGGAATCAGCACATAGCAA
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
* *
18577076 CCCCTTTCACAATTAAGGAT
66 CCCCTTTCACAATCAAAGAT
*
18577096 TCGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACTTAGCAA
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
18577161 CCCCTTTCACAATCAAAGAT
66 CCCCTTTCACAATCAAAGAT
* * * * * * * **
18577181 ACGGTGGGATCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAA
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
18577246 CCCCT
66 CCCCT
18577251 CGGGGAATCA
Statistics
Matches: 138, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 27 0.20
85 111 0.80
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (85 bp):
TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
CCCCTTTCACAATCAAAGAT
Found at i:18577255 original size:26 final size:26
Alignment explanation
Indices: 18577226--18577276 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
18577216 TCAATAATTT
18577226 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACTTAGCAACCCCTC
18577252 GGGGAATCAGCACTTAGCAACCCCT
1 GGGGAATCAGCACTTAGCAACCCCT
18577277 TTAGAGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTC
Found at i:18577299 original size:67 final size:67
Alignment explanation
Indices: 18577189--18577348 Score: 275
Period size: 67 Copynumber: 2.4 Consensus size: 67
18577179 ATACGGTGGG
* *
18577189 ATCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAACCCCTCGG
1 ATCAGCACTTAGCAACC-CCTTTAGAGTCAATAATTCGGGGAATCAGCACTTAGCAACCCCTCGG
18577254 GGA
65 GGA
*
18577257 ATCAGCACTTAGCAACCCCTTTAGAGTCAATAATTCGTGGAATCAGCACTTAGCAACCCCTCGGG
1 ATCAGCACTTAGCAACCCCTTTAGAGTCAATAATTCGGGGAATCAGCACTTAGCAACCCCTCGGG
18577322 GA
66 GA
*
18577324 ATCAGCACTTAGCAACCCTTTTAGA
1 ATCAGCACTTAGCAACCCCTTTAGA
18577349 TTCAGTATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 72 0.82
68 16 0.18
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (67 bp):
ATCAGCACTTAGCAACCCCTTTAGAGTCAATAATTCGGGGAATCAGCACTTAGCAACCCCTCGGG
GA
Found at i:18578392 original size:11 final size:12
Alignment explanation
Indices: 18578364--18578396 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18578354 GCCCAAACGT
18578364 CGAAATTTTCGAA
1 CGAAATTTTC-AA
18578377 CGAAATTTTC-A
1 CGAAATTTTCAA
18578388 CGAAATTTT
1 CGAAATTTT
18578397 TCTGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:18581736 original size:17 final size:17
Alignment explanation
Indices: 18581696--18581728 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18581686 GCAAAAGAGA
18581696 AAATCAAATAAGAAATC
1 AAATCAAATAAGAAATC
18581713 AAATCAAATAAGAAAT
1 AAATCAAATAAGAAAT
18581729 TGAGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.09, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATCAAATAAGAAATC
Found at i:18585794 original size:24 final size:24
Alignment explanation
Indices: 18585762--18585811 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
18585752 AAAGCATGTG
18585762 TTGAGAATCTTTAATTATTTGATA
1 TTGAGAATCTTTAATTATTTGATA
* *
18585786 TTGAGAATCTTTGATTATTTTATA
1 TTGAGAATCTTTAATTATTTGATA
18585810 TT
1 TT
18585812 ATTAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (24 bp):
TTGAGAATCTTTAATTATTTGATA
Found at i:18590781 original size:27 final size:27
Alignment explanation
Indices: 18590729--18590781 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
18590719 GCTCACATGA
*
18590729 GCTTCCCATTATATGGCTCGAGAGAGG
1 GCTTCCCATTATATGGCTCGAAAGAGG
* *
18590756 GCTTCCCTATTATGT-GCTCTAAAGAG
1 GCTTCCC-ATTATATGGCTCGAAAGAG
18590782 CACTCTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (27 bp):
GCTTCCCATTATATGGCTCGAAAGAGG
Found at i:18591417 original size:25 final size:25
Alignment explanation
Indices: 18591370--18591432 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
18591360 TATTTATCTC
*
18591370 TTATGAGCTTCCCGATACTTGGCTT
1 TTATGAGCTTCCCGATACATGGCTT
* *
18591395 TTATGAGCTTCCTGATTA-ATGGCTC
1 TTATGAGCTTCCCGA-TACATGGCTT
* *
18591420 GTAGGAGCTTCCC
1 TTATGAGCTTCCC
18591433 AATATTTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (25 bp):
TTATGAGCTTCCCGATACATGGCTT
Found at i:18591431 original size:50 final size:50
Alignment explanation
Indices: 18591374--18591504 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
18591364 TATCTCTTAT
* ** *
18591374 GAGCTTCCCGATACTTGGCTTTTATGAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCCCAATACTTGGCTCGTAAGAGCTTCCT-ATTACATGGCTCGTAG
* ** *
18591424 GAGCTTCCCAATATTTGGCTCGTAAGAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCAATACTTGGCTCGTAAGAGCTTCCTATTACATGGCTCGTAG
* *
18591474 GAGCTTCCCATTA-TATGGCTCGAAAGAGCTT
1 GAGCTTCCCAATACT-TGGCTCGTAAGAGCTT
18591505 TTCGATTACA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 5 0.07
50 64 0.93
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (50 bp):
GAGCTTCCCAATACTTGGCTCGTAAGAGCTTCCTATTACATGGCTCGTAG
Found at i:18591467 original size:25 final size:25
Alignment explanation
Indices: 18591399--18591504 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
18591389 TGGCTTTTAT
* *
18591399 GAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCC-CATTATATGGCTCGTAA
* *
18591424 GAGCTTCCCAATATTTGGCTCGTAA
1 GAGCTTCCCATTATATGGCTCGTAA
* * ** *
18591449 GAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCATTATATGGCTCGTAA
*
18591474 GAGCTTCCCATTATATGGCTCGAAA
1 GAGCTTCCCATTATATGGCTCGTAA
18591499 GAGCTT
1 GAGCTT
18591505 TTCGATTACA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
24 3 0.05
25 61 0.95
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGCTCGTAA
Found at i:18591521 original size:50 final size:50
Alignment explanation
Indices: 18591424--18591523 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
18591414 TGGCTCGTAG
* * * *
18591424 GAGCTTCCCAATATTTGGCTCGTAAGAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCAATATATGGCTCGAAAGAGCTTCCGATTACATGACTCACAT
* *
18591474 GAGCTTCCCATTATATGGCTCGAAAGAGCTTTTCGATTACAT-ACTCACAT
1 GAGCTTCCCAATATATGGCTCGAAAGAGC-TTCCGATTACATGACTCACAT
18591524 AGGCATACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 33 0.77
51 10 0.23
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (50 bp):
GAGCTTCCCAATATATGGCTCGAAAGAGCTTCCGATTACATGACTCACAT
Found at i:18599278 original size:32 final size:29
Alignment explanation
Indices: 18599240--18599303 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 29
18599230 TTTATTATAT
* *
18599240 AAACAATTTTTAAAATATAGTATATCAAATTG
1 AAACAATTCTTAAAATA-A-TA-AACAAATTG
18599272 AAACAATTCTTAAAATAATAAACAAATTG
1 AAACAATTCTTAAAATAATAAACAAATTG
18599301 AAA
1 AAA
18599304 ATACAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 11 0.37
30 2 0.07
31 1 0.03
32 16 0.53
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (29 bp):
AAACAATTCTTAAAATAATAAACAAATTG
Found at i:18599419 original size:23 final size:23
Alignment explanation
Indices: 18599393--18599449 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
18599383 TCTACAATAT
*
18599393 CCAAATAATATTATAAACGACAA
1 CCAAATAATATTAAAAACGACAA
*
18599416 CCAAATAATATTAAAAAGGACAA
1 CCAAATAATATTAAAAACGACAA
* *
18599439 CGAAACAATAT
1 CCAAATAATAT
18599450 AATAGCTGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.58, C:0.16, G:0.07, T:0.19
Consensus pattern (23 bp):
CCAAATAATATTAAAAACGACAA
Found at i:18599640 original size:3 final size:3
Alignment explanation
Indices: 18599632--18599695 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
18599622 AACATCGTCC
18599632 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
18599680 TCA TCA TTC- TCA TCA T
1 TCA TCA -TCA TCA TCA T
18599696 TCCTGAACCA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:18606341 original size:18 final size:18
Alignment explanation
Indices: 18606318--18606355 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18606308 CAAGGGTTTC
18606318 TCAATTGGTACTTATCAA
1 TCAATTGGTACTTATCAA
18606336 TCAATTGGTACTTATCAA
1 TCAATTGGTACTTATCAA
18606354 TC
1 TC
18606356 GCATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (18 bp):
TCAATTGGTACTTATCAA
Found at i:18606868 original size:17 final size:17
Alignment explanation
Indices: 18606848--18606894 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
18606838 ATCTCTTAAA
*
18606848 AGAGTTCATCAAACCCT
1 AGAGTTCACCAAACCCT
*
18606865 AGAGTTCACCAAACCTT
1 AGAGTTCACCAAACCCT
*
18606882 AGAGTTCGCCAAA
1 AGAGTTCACCAAA
18606895 TGAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (17 bp):
AGAGTTCACCAAACCCT
Found at i:18611041 original size:22 final size:23
Alignment explanation
Indices: 18611016--18611066 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
18611006 CACGTATATT
*
18611016 TTAAAAT-ATATCAAACATTT-CA
1 TTAAAATGA-ATCAAACATTTGAA
*
18611038 TTAAAATGAGTCAAACATTTGAA
1 TTAAAATGAATCAAACATTTGAA
18611061 TTAAAA
1 TTAAAA
18611067 CCATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (23 bp):
TTAAAATGAATCAAACATTTGAA
Found at i:18611073 original size:22 final size:21
Alignment explanation
Indices: 18611025--18611074 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
18611015 TTTAAAATAT
* **
18611025 ATCAAACATTTCATTAAAATG
1 ATCAAACATTTAATTAAAACC
18611046 AGTCAAACATTTGAATTAAAACC
1 A-TCAAACATTT-AATTAAAACC
18611069 ATCAAA
1 ATCAAA
18611075 ATTGATGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (21 bp):
ATCAAACATTTAATTAAAACC
Found at i:18612708 original size:50 final size:50
Alignment explanation
Indices: 18612653--18612880 Score: 258
Period size: 50 Copynumber: 4.4 Consensus size: 50
18612643 CAATGTCATA
* * * ** * * * *
18612653 TCCCAGATATAGTCTTACATGAGAGTTCTCATATCGGTGCCCATGTCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
18612703 TCCCAGACATGGTCTTACGTGGGACCTCTTATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
18612753 TCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* * *
18612803 TCCCAGACATGGTTTTACATAGGACCTCTCATGATCTCAAGGATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAACGCCATG
*
18612859 TCCCAGACATGGTTTTACATGG
1 TCCCAGACATGGTCTTACATGG
18612881 AATCTCTTTA
Statistics
Matches: 153, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 114 0.75
53 4 0.03
55 2 0.01
56 33 0.22
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
Found at i:18615466 original size:28 final size:28
Alignment explanation
Indices: 18615435--18615538 Score: 79
Period size: 28 Copynumber: 3.8 Consensus size: 28
18615425 TAAAAAATAA
*
18615435 AATAAACATACATTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACTATCTT
* ** ** ** *
18615463 AATACACA-ATTCTAATAATTCTA-CTAA
1 AATAAACATACACTACCAAAACTATCT-T
*
18615490 AATAAACATGCACTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACTATCTT
*
18615518 AATAAGCATACACTA-CAAAAC
1 AATAAACATACACTACCAAAAC
18615539 AAACATACAT
Statistics
Matches: 53, Mismatches: 20, Indels: 7
0.66 0.25 0.09
Matches are distributed among these distances:
26 2 0.04
27 21 0.40
28 28 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAAACATACACTACCAAAACTATCTT
Found at i:18615677 original size:19 final size:19
Alignment explanation
Indices: 18615650--18615686 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18615640 CTAAAGAAAA
18615650 TTTTAACACAAATCTAAAT
1 TTTTAACACAAATCTAAAT
*
18615669 TTTTGACACAAATCTAAA
1 TTTTAACACAAATCTAAA
18615687 CTAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTTAACACAAATCTAAAT
Found at i:18617226 original size:19 final size:19
Alignment explanation
Indices: 18617202--18617238 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18617192 TCATTTAAAA
18617202 ATTTTAAAAAATAAAAATC
1 ATTTTAAAAAATAAAAATC
* *
18617221 ATTTTAGAAAATTAAAAT
1 ATTTTAAAAAATAAAAAT
18617239 TATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTTTAAAAAATAAAAATC
Found at i:18622085 original size:29 final size:30
Alignment explanation
Indices: 18622020--18622085 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
18622010 TACAAACTCC
*
18622020 ACTTGATTGCATTAATATAAGTAAATTATT
1 ACTTGATTGCATTAATATAAATAAATTATT
** *
18622050 TGTTGATTGTATTAATATAAAT-AATTATT
1 ACTTGATTGCATTAATATAAATAAATTATT
18622079 ACTTGAT
1 ACTTGAT
18622086 AGACGTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (30 bp):
ACTTGATTGCATTAATATAAATAAATTATT
Found at i:18623034 original size:18 final size:19
Alignment explanation
Indices: 18623013--18623059 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
18623003 GTCATTTATA
18623013 AAAATATTTTAATT-CAAT
1 AAAATATTTTAATTACAAT
18623031 AAAA-ATATTTAATTACAAT
1 AAAATAT-TTTAATTACAAT
*
18623050 GAAAT-TTTTA
1 AAAATATTTTA
18623060 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.60
19 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATATTTTAATTACAAT
Found at i:18623034 original size:19 final size:19
Alignment explanation
Indices: 18623010--18623049 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
18623000 AAAGTCATTT
18623010 ATAAAAATATTTTAATT-CA
1 ATAAAAATA-TTTAATTACA
18623029 ATAAAAATATTTAATTACA
1 ATAAAAATATTTAATTACA
18623048 AT
1 AT
18623050 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATATTTAATTACA
Found at i:18628107 original size:16 final size:16
Alignment explanation
Indices: 18628086--18628124 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
18628076 AAAACCTACT
18628086 CACCACGTTGGCACAA
1 CACCACGTTGGCACAA
18628102 CACCACGTTGGCACAA
1 CACCACGTTGGCACAA
18628118 CTACCAC
1 C-ACCAC
18628125 TACCAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.13
Consensus pattern (16 bp):
CACCACGTTGGCACAA
Found at i:18631425 original size:31 final size:31
Alignment explanation
Indices: 18631380--18631446 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
18631370 TAATAAAGGT
*
18631380 AAAATTATATTTTAA-CTTTCTCTAAAAA-TATA
1 AAAATTATAATTTAATC-TT-T-TAAAAATTATA
18631412 AAAATT-TAATTTAATCTTTTAAAAATTATA
1 AAAATTATAATTTAATCTTTTAAAAATTATA
18631442 AAAAT
1 AAAAT
18631447 ATTGACTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 6 0.19
30 10 0.31
31 9 0.28
32 7 0.22
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (31 bp):
AAAATTATAATTTAATCTTTTAAAAATTATA
Found at i:18632183 original size:9 final size:9
Alignment explanation
Indices: 18632171--18632238 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
18632161 ATTTAGACTA
18632171 TTTTTATAT
1 TTTTTATAT
18632180 TTTTTATAT
1 TTTTTATAT
18632189 TTCTTT-T-T
1 TT-TTTATAT
*
18632197 TTTTTGTAATT
1 TTTTTAT-A-T
* *
18632208 TTTTTAAAA
1 TTTTTATAT
*
18632217 TTTTAACTAT
1 TTTTTA-TAT
18632227 TTTTTATAT
1 TTTTTATAT
18632236 TTT
1 TTT
18632239 GAAATATACA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 23 0.50
10 10 0.22
11 6 0.13
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTTTATAT
Found at i:18633270 original size:23 final size:24
Alignment explanation
Indices: 18633218--18633272 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
18633208 ATGATATTTT
*
18633218 TTAAAATATATATATTTTTATAAG
1 TTAAAATATATATATTTATATAAG
* *
18633242 TATAAAATATTTATATTTATATCA-
1 T-TAAAATATATATATTTATATAAG
18633266 TTAAAAT
1 TTAAAAT
18633273 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 2 0.07
25 19 0.70
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAAATATATATATTTATATAAG
Found at i:18633509 original size:9 final size:9
Alignment explanation
Indices: 18633495--18633525 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18633485 GTTAAACGAA
18633495 TCGAGTTAT
1 TCGAGTTAT
*
18633504 TCGAGTTAA
1 TCGAGTTAT
18633513 TCGAGTTAT
1 TCGAGTTAT
18633522 TCGA
1 TCGA
18633526 ATCAAATCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18633594 original size:9 final size:9
Alignment explanation
Indices: 18633577--18633613 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
18633567 TGAGTTTTCG
18633577 AATTCGAAT
1 AATTCGAAT
*
18633586 AACTCGAAT
1 AATTCGAAT
18633595 AATTCGAAT
1 AATTCGAAT
18633604 AATTCGAAT
1 AATTCGAAT
18633613 A
1 A
18633614 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:18633865 original size:30 final size:31
Alignment explanation
Indices: 18633830--18633889 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
18633820 AAACCTTTTA
*
18633830 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
18633860 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
18633890 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:18635505 original size:67 final size:68
Alignment explanation
Indices: 18635391--18635525 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 68
18635381 CGGACGAGGG
18635391 ACACCTGGTTTCAGCTGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCTT
1 ACACCTGGTTTCAGCTGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCTT
18635456 TTA
66 TTA
18635459 ACACC-GGTTTCAG-TGGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCT
1 ACACCTGGTTTCAGCT-GTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCT
18635522 TTTA
65 TTTA
18635526 CCTTTTACTT
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
66 1 0.02
67 60 0.91
68 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (68 bp):
ACACCTGGTTTCAGCTGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCTT
TTA
Found at i:18644914 original size:28 final size:30
Alignment explanation
Indices: 18644883--18644944 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
18644873 TTCAAAAATT
18644883 AAATAACATA-TTTAAT-ATGTAAAA-ATAA
1 AAATAACATATTTTAATAATG-AAAATATAA
*
18644911 AAAT-ATATATTTTAATAATGAAAATATAA
1 AAATAACATATTTTAATAATGAAAATATAA
18644940 AAATA
1 AAATA
18644945 TGTGGTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 4 0.14
28 14 0.48
29 11 0.38
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATAACATATTTTAATAATGAAAATATAA
Found at i:18645157 original size:9 final size:9
Alignment explanation
Indices: 18645143--18645173 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18645133 GTTAAACGAA
18645143 TCGAGTTAT
1 TCGAGTTAT
*
18645152 TCGAGTTAA
1 TCGAGTTAT
18645161 TCGAGTTAT
1 TCGAGTTAT
18645170 TCGA
1 TCGA
18645174 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18645243 original size:9 final size:9
Alignment explanation
Indices: 18645226--18645262 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
18645216 TGAGTTTTCG
18645226 AATTCGAAT
1 AATTCGAAT
*
18645235 AACTCGAAT
1 AATTCGAAT
18645244 AATTCGAAT
1 AATTCGAAT
18645253 AATTCGAAT
1 AATTCGAAT
18645262 A
1 A
18645263 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:18669255 original size:44 final size:43
Alignment explanation
Indices: 18669189--18669354 Score: 163
Period size: 44 Copynumber: 3.8 Consensus size: 43
18669179 GGAAATGGTG
18669189 AATCTTATCTCCCTGATGTTACAGTGGAGCAGATTGAAGCTAAA
1 AATCTTATCTCCCTGA-GTTACAGTGGAGCAGATTGAAGCTAAA
* * **
18669233 AATCTTATCTCCATGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAG-TTACAGTGGAGCAGATTGAAGCTAAA
* ** **
18669277 AATCCTATCTCCCTGAGGTTACAGTGGAGTGGATT-AAAATAAA
1 AATCTTATCTCCCTGA-GTTACAGTGGAGCAGATTGAAGCTAAA
* * * *
18669320 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 -AATCTTATCTCCCTG-AGTTACAGTGGAGCAGAT
18669355 CGCAGCAGAT
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
43 5 0.05
44 93 0.93
45 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTGAGTTACAGTGGAGCAGATTGAAGCTAAA
Found at i:18680772 original size:86 final size:85
Alignment explanation
Indices: 18680624--18680792 Score: 230
Period size: 86 Copynumber: 2.0 Consensus size: 85
18680614 TAAGGTCTTT
* * * **
18680624 CCTTTTAGAGTCTTGCCACAAAGCCATCATTTAAGAGGTTCACCGCAAAGGTTTACCCTTCCAGA
1 CCTTCTAGAGTCTTGCCACAAAGCCATCATTTAACAGGTTCACCACAAAGGCCTACCCTTCCAGA
*
18680689 GTTTTGGCACAAAGGTTTAC
66 GTTTTGCCACAAAGGTTTAC
* ** * *
18680709 CCTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAGGTTCACCACAAAGGCCTACCTTTCCAG
1 CCTTCTAGAGTCTTGCCACAAA-GCCATCATTTAACAGGTTCACCACAAAGGCCTACCCTTCCAG
18680774 AGTTTTGCCACAAAGGTTT
65 AGTTTTGCCACAAAGGTTT
18680793 TCCTTTAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
85 20 0.28
86 52 0.72
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (85 bp):
CCTTCTAGAGTCTTGCCACAAAGCCATCATTTAACAGGTTCACCACAAAGGCCTACCCTTCCAGA
GTTTTGCCACAAAGGTTTAC
Found at i:18680776 original size:57 final size:57
Alignment explanation
Indices: 18680696--18680896 Score: 258
Period size: 57 Copynumber: 3.5 Consensus size: 57
18680686 AGAGTTTTGG
* * * * * *
18680696 CACAAAGGTTTACCCTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAGGTTCAC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
*
18680753 CACAAAGGCCTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
* * ** * **
18680810 TACAAAGACTTACCTTTCTTGAGTTTTTCCACAAAGGTTTTCCTTTAATAGGTTTGC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
* *
18680867 CACAAAGGCTTACCTTTCCAAAATTTTGCC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCC
18680897 TAAACTCACA
Statistics
Matches: 122, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 122 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (57 bp):
CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
Found at i:18680797 original size:29 final size:29
Alignment explanation
Indices: 18680669--18680896 Score: 142
Period size: 29 Copynumber: 8.0 Consensus size: 29
18680659 AGGTTCACCG
* * *
18680669 CAAAGGTTTACCCTTCCAGAGTTTTGGCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* * *
18680698 CAAAGGTTTACCCTTCTAGAGTTTTGCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* **
18680727 CAAAGGCTGT-CCTTTAACAG-G-TTCACCA
1 CAAAGGCT-TACCTTT-CCAGAGTTTTGCCA
*
18680755 CAAAGGCCTACCTTTCCAGAGTTTTGCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* * * * * ** *
18680784 CAAAGGTTTTCCTTT-AATAGGTTCACTA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* ** *
18680812 CAAAGACTTACCTTTCTTGAGTTTTTCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* * * * *
18680841 CAAAGGTTTTCCTTT-AATAGGTTTGCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* *
18680869 CAAAGGCTTACCTTTCCAAAATTTTGCC
1 CAAAGGCTTACCTTTCCAGAGTTTTGCC
18680897 TAAACTCACA
Statistics
Matches: 147, Mismatches: 45, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
27 4 0.03
28 58 0.39
29 82 0.56
30 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (29 bp):
CAAAGGCTTACCTTTCCAGAGTTTTGCCA
Found at i:18680874 original size:28 final size:28
Alignment explanation
Indices: 18680720--18680883 Score: 123
Period size: 28 Copynumber: 5.8 Consensus size: 28
18680710 CTTCTAGAGT
*
18680720 TTTGCCACAAAGGCTGT-CCTTTAACAGG
1 TTTGCCACAAAGGCT-TACCTTTAATAGG
** * * * *
18680748 TTCACCACAAAGGCCTACCTTTCCAGAGT
1 TTTGCCACAAAGGCTTACCTTT-AATAGG
* *
18680777 TTTGCCACAAAGGTTTTCCTTTAATAGG
1 TTTGCCACAAAGGCTTACCTTTAATAGG
** * * ** *
18680805 TTCACTACAAAGACTTACCTTTCTTGAGT
1 TTTGCCACAAAGGCTTACCTTTAAT-AGG
* * *
18680834 TTTTCCACAAAGGTTTTCCTTTAATAGG
1 TTTGCCACAAAGGCTTACCTTTAATAGG
18680862 TTTGCCACAAAGGCTTACCTTT
1 TTTGCCACAAAGGCTTACCTTT
18680884 CCAAAATTTT
Statistics
Matches: 98, Mismatches: 35, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
27 1 0.01
28 58 0.59
29 39 0.40
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (28 bp):
TTTGCCACAAAGGCTTACCTTTAATAGG
Found at i:18683678 original size:10 final size:10
Alignment explanation
Indices: 18683663--18683697 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
18683653 TGTTAACAAT
18683663 TAAATATATA
1 TAAATATATA
18683673 TAAATATATA
1 TAAATATATA
*
18683683 TATATATATGA
1 TAAATATAT-A
18683694 TAAA
1 TAAA
18683698 GTAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
TAAATATATA
Found at i:18683803 original size:13 final size:13
Alignment explanation
Indices: 18683771--18683805 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
18683761 GAAACAGGGG
*
18683771 AAAGGAAAGAAGA
1 AAAGGAAAAAAGA
18683784 AAA-GAAAAAAGA
1 AAAGGAAAAAAGA
18683796 AAAGGAAAAA
1 AAAGGAAAAA
18683806 CTAGGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAAAGA
Found at i:18691627 original size:20 final size:20
Alignment explanation
Indices: 18691578--18691616 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18691568 TGGAGCAGGA
*
18691578 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
18691598 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
18691617 AGTATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:18693618 original size:6 final size:6
Alignment explanation
Indices: 18693607--18693657 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
18693597 AATTAAATAA
* * *
18693607 AATATT AATATT AATATT AA-ATA AAAATAA ATATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATAT-T A-ATATT AATATT AATATT
18693656 AA
1 AA
18693658 ATAAAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
5 4 0.10
6 29 0.74
7 3 0.08
8 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AATATT
Found at i:18693642 original size:25 final size:24
Alignment explanation
Indices: 18693598--18693661 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
18693588 ATTTAATTTA
*
18693598 ATTAAATAAAATATTAATATTAAT
1 ATTAAATAAAATAATAATATTAAT
18693622 ATTAAATAAAAATAA-ATATATTAAT
1 ATTAAAT-AAAATAATA-ATATTAAT
*
18693647 ATTAATATTAAATAA
1 ATTAA-ATAAAATAA
18693662 AAAAGTGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 8 0.23
25 25 0.71
26 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTAAATAAAATAATAATATTAAT
Found at i:18693646 original size:31 final size:30
Alignment explanation
Indices: 18693601--18693664 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 30
18693591 TAATTTAATT
18693601 AAATAAAATATTAATATTAATATTAAATAA
1 AAATAAAATATTAATATTAATATTAAATAA
18693631 AAATAAATATATTAATATTAATATTAAATAA
1 AAATAAA-ATATTAATATTAATATTAAATAA
18693662 AAA
1 AAA
18693665 AGTGGTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATAAAATATTAATATTAATATTAAATAA
Found at i:18700170 original size:31 final size:31
Alignment explanation
Indices: 18700095--18700170 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
18700085 GATATGAAAT
* *
18700095 ATTACAGGGTATGAAAATGAAAATGTGAATC
1 ATTACAGGGTGTGAAAATGAAAACGTGAATC
* * * * *
18700126 ATTATAGGATGTGAAAATGCAAACGTGACTG
1 ATTACAGGGTGTGAAAATGAAAACGTGAATC
18700157 ATTACAGGGTGTGA
1 ATTACAGGGTGTGA
18700171 TATGTAGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (31 bp):
ATTACAGGGTGTGAAAATGAAAACGTGAATC
Found at i:18700686 original size:183 final size:185
Alignment explanation
Indices: 18700360--18700720 Score: 474
Period size: 183 Copynumber: 2.0 Consensus size: 185
18700350 GACAGGTTAA
* * * **
18700360 ATCAAGATCTAGCATTTTTTTTGCAGATCATCGAGTATTATTTGTCTCTATGGAGACTTTTTTTG
1 ATCAAGATCTAGCA-TTTTGTTGCAGATCATCGAGTACTATTTGTCTCTATGAAGACTTTTGGTG
* * * * *
18700425 TGGTGGAGGGATGTAATTGAAAATTTTTAAACATTTGATGTCTACGGGTTTTACACTTAGATACC
65 TAGTAGAGGGATGTAATTGAAAATGTTTAAACATTTGATGTCTACAGGCTTTACACTTAGATACC
* * *
18700490 TTGGTGCGGTGTAGTTTAAGCTCGTACGAGTTATTTAGTATGGTGTAGTGGAGGAT
130 TTGGTACGGTGTAGTTTAAGCTCATACGAGCTATTTAGTATGGTGTAGTGGAGGAT
*
18700546 ATCAAGATCTAGCA-TTTGTTGCGGATCATCGAGTACTATTTGTCTCTATGAAGAC-TTTGGTGT
1 ATCAAGATCTAGCATTTTGTTGCAGATCATCGAGTACTATTTGTCTCTATGAAGACTTTTGGTGT
* * * * * * *
18700609 AGTAGAGGGGTTTAATTGAAAATGTTTAAATATTTGATGTCTACAGGCTTTACATTTTGGTGCCT
66 AGTAGAGGGATGTAATTGAAAATGTTTAAACATTTGATGTCTACAGGCTTTACACTTAGATACCT
* * * *
18700674 TGGTATGGTGTAGTTTACGCTCATACGAGCTATTTGGTGTGGTGTAG
131 TGGTACGGTGTAGTTTAAGCTCATACGAGCTATTTAGTATGGTGTAG
18700721 CTCACCCATG
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
183 99 0.66
184 37 0.25
186 14 0.09
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (185 bp):
ATCAAGATCTAGCATTTTGTTGCAGATCATCGAGTACTATTTGTCTCTATGAAGACTTTTGGTGT
AGTAGAGGGATGTAATTGAAAATGTTTAAACATTTGATGTCTACAGGCTTTACACTTAGATACCT
TGGTACGGTGTAGTTTAAGCTCATACGAGCTATTTAGTATGGTGTAGTGGAGGAT
Found at i:18720337 original size:12 final size:13
Alignment explanation
Indices: 18720313--18720341 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18720303 GGGCTATAAC
18720313 TATTTCATTTATT
1 TATTTCATTTATT
18720326 TATTTC-TTTATT
1 TATTTCATTTATT
18720338 TATT
1 TATT
18720342 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTCATTTATT
Found at i:18729523 original size:27 final size:27
Alignment explanation
Indices: 18729493--18729560 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
18729483 TATAGAGTAA
* *
18729493 GCCACCAAGGCATTCCATTCAGAATTT
1 GCCACAAAGGAATTCCATTCAGAATTT
* * *
18729520 GCCACAAAGGAATTCCTTTTAGAGTTT
1 GCCACAAAGGAATTCCATTCAGAATTT
18729547 GCCACAAAGGAATT
1 GCCACAAAGGAATT
18729561 TCTTAACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (27 bp):
GCCACAAAGGAATTCCATTCAGAATTT
Found at i:18737701 original size:66 final size:66
Alignment explanation
Indices: 18737620--18737748 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
18737610 GGAATGTCGA
* *
18737620 AGTTTTGTTATGTTGGTGTATAGTATTCGCCTATGTGACACACCTTTGGCATATTGAGTTTGTTA
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
18737685 G
66 G
*
18737686 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATATTGAGTTTGT
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGT
18737749 CTCAGTTTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.43
Consensus pattern (66 bp):
AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
G
Found at i:18737756 original size:66 final size:66
Alignment explanation
Indices: 18737620--18737764 Score: 229
Period size: 66 Copynumber: 2.2 Consensus size: 66
18737610 GGAATGTCGA
* *
18737620 AGTTTTGTTATGTTGGTGTATAGTATTCGCCTATGTGACACACCTTTGGCATATTGAGTTTGTTA
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
*
18737685 G
66 C
*
18737686 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATATTGAGTTTGTCT
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGT-T
18737751 -C
65 AC
18737752 AGTTTTGTATATG
1 AGTTTTGT-TATG
18737765 CCATTGGGCA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
66 68 0.93
67 5 0.07
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.44
Consensus pattern (66 bp):
AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
C
Found at i:18739429 original size:33 final size:33
Alignment explanation
Indices: 18739389--18739547 Score: 143
Period size: 33 Copynumber: 4.7 Consensus size: 33
18739379 TTGAATATGA
18739389 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATT
1 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATT
* *
18739422 AGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATAT
1 AGGGGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CAT-T
18739462 AAAGGGGGTTGCTAAGTGCTGATT-CCC--C-CA--
1 --A-GGGGTTGCTAAGTGCTGATTCCCCGACTCATT
*
18739492 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATT
1 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATT
18739525 -GGTGGTTGCTAAGTGCTGATTCC
1 AGG-GGTTGCTAAGTGCTGATTCC
18739548 ACCGTATCTT
Statistics
Matches: 104, Mismatches: 5, Indels: 34
0.73 0.03 0.24
Matches are distributed among these distances:
27 20 0.19
28 4 0.04
31 2 0.02
32 2 0.02
33 43 0.41
34 3 0.03
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
40 1 0.01
41 2 0.02
42 2 0.02
43 19 0.18
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (33 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGACTCATT
Found at i:18739570 original size:103 final size:103
Alignment explanation
Indices: 18739388--18739590 Score: 370
Period size: 103 Copynumber: 2.0 Consensus size: 103
18739378 ATTGAATATG
18739388 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
18739453 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
18739491 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
18739556 TTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCC
18739591 TCGAATGATT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:18739584 original size:76 final size:76
Alignment explanation
Indices: 18739491--18739703 Score: 327
Period size: 76 Copynumber: 2.8 Consensus size: 76
18739481 TGATTCCCCC
*
18739491 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
18739556 TTTAAATTTGA
66 TTTAAATGTGA
* * * * * *
18739567 AGGGGGTTGCTAAGTGCTGATTCCTCGAATGATTGGTGGTTGCTACGTGTTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
18739632 TTTGAATGTGA
66 TTTAAATGTGA
* *
18739643 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
18739704 ATAACGGTTA
Statistics
Matches: 120, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 120 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATGTGA
Found at i:18752720 original size:29 final size:29
Alignment explanation
Indices: 18752685--18752751 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
18752675 ATTTTGCTTC
18752685 AATAAAAAATATATGTAGTGTATTTTAAA
1 AATAAAAAATATATGTAGTGTATTTTAAA
* *
18752714 CATAAAAAATATCTGTAGTGTATTTTAAA
1 AATAAAAAATATATGTAGTGTATTTTAAA
18752743 AATAAAAAA
1 AATAAAAAA
18752752 AAATTAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (29 bp):
AATAAAAAATATATGTAGTGTATTTTAAA
Found at i:18752869 original size:21 final size:21
Alignment explanation
Indices: 18752845--18752897 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
18752835 CATTGTTTCT
*
18752845 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
18752866 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
18752887 AATCTCACCGC
1 AATCTCACCGC
18752898 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:18759321 original size:67 final size:65
Alignment explanation
Indices: 18759139--18759351 Score: 216
Period size: 68 Copynumber: 3.2 Consensus size: 65
18759129 AGGAGGTTTA
* * * *
18759139 AGGTGTAAGACCATAGCTTGATTATGACAATTAATATAGTCTGCCAGGACATTAAACATGGGGTT
1 AGGTGTAAGACCATAGCTCGA-TATGACAA-CAATAGATTCTGCCAGGACATTAAACATGGGGTT
*
18759204 AT
64 AC
* *
18759206 A-ATAAGTAAGACCATAGCTCGGATATGACAAC-ATAGGGAGTT-TGCCAGGATATTAAACATGG
1 AGGT--GTAAGACCATAGCTC-GATATGACAACAATA--GA-TTCTGCCAGGACATTAAACATGG
18759268 GGTTAC
60 GGTTAC
* *
18759274 AGGTGTAAGACCATATCTCGACTATGATAACCAATAGATTCTGCCAGGACATTAAACATGGGGGT
1 AGGTGTAAGACCATAGCTCGA-TATGACAA-CAATAGATTCTGCCAGGACATTAAACAT-GGGGT
18759339 TAC
63 TAC
*
18759342 AAGTGTAAGA
1 AGGTGTAAGA
18759352 ATATAGCTTG
Statistics
Matches: 122, Mismatches: 12, Indels: 23
0.78 0.08 0.15
Matches are distributed among these distances:
66 8 0.07
67 41 0.34
68 66 0.54
69 7 0.06
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (65 bp):
AGGTGTAAGACCATAGCTCGATATGACAACAATAGATTCTGCCAGGACATTAAACATGGGGTTAC
Found at i:18759394 original size:68 final size:67
Alignment explanation
Indices: 18759141--18759419 Score: 178
Period size: 68 Copynumber: 4.1 Consensus size: 67
18759131 GAGGTTTAAG
* * * * ** * * * *
18759141 GTGTAAGACCATAGCTTGATTATGACAATTAATATAGTCTGCCAGGACATTAAACATGGGGTTAT
1 GTGTAAGAACATAGCTCGACTATGATAACCAATAAATTCTGCCAGAACATTAAACATGGGGTTAC
18759206 AA
66 AA
* * * * *
18759208 -TAAGTAAGACCATAGCTCGGA-TATGACAA-C-ATAGGGAGTT-TGCCAGGATATTAAACATGG
1 GT--GTAAGAACATAGCTC-GACTATGATAACCAATA---AATTCTGCCAGAACATTAAACATGG
*
18759268 GGTTACAG
60 GGTTACAA
* * * *
18759276 GTGTAAGACCATATCTCGACTATGATAACCAATAGATTCTGCCAGGACATTAAACATGGGGGTTA
1 GTGTAAGAACATAGCTCGACTATGATAACCAATAAATTCTGCCAGAACATTAAACAT-GGGGTTA
18759341 CAA
65 CAA
* * * * *
18759344 GTGTAAGAATATAGCTTGACTATGGA-AACTAATAAAGTT-TGTCCA-AACATTAAACATGAGAT
1 GTGTAAGAACATAGCTCGACTAT-GATAACCAATAAA-TTCTG-CCAGAACATTAAACATGGGGT
18759406 TACAA
63 TACAA
18759411 TGTGTAAGA
1 -GTGTAAGA
18759420 CTATGGATCG
Statistics
Matches: 173, Mismatches: 23, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
66 8 0.05
67 46 0.27
68 105 0.61
69 14 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (67 bp):
GTGTAAGAACATAGCTCGACTATGATAACCAATAAATTCTGCCAGAACATTAAACATGGGGTTAC
AA
Found at i:18762087 original size:12 final size:13
Alignment explanation
Indices: 18762070--18762105 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
18762060 CGAAAGAAGG
18762070 AAAAATGGAAA-A
1 AAAAATGGAAATA
18762082 AAAAATGGAGAATA
1 AAAAATGGA-AATA
18762096 AAAAATGGAA
1 AAAAATGGAA
18762106 GCAACTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 3 0.14
14 10 0.45
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.11
Consensus pattern (13 bp):
AAAAATGGAAATA
Found at i:18764419 original size:43 final size:43
Alignment explanation
Indices: 18764337--18764451 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
18764327 TTTTCGGAAA
**
18764337 GTGTTTTTGTGTAAGACCACGTCTGGGACGTTGGTATCGA-CTT
1 GTGTTTTTGTGTAAGACCACGTCTGGGACGTTGACATCGATC-T
18764380 GTGTTTTTGTGTAAGACC-CTGTCTGGGACAG-TGACATCGATCT
1 GTGTTTTTGTGTAAGACCAC-GTCTGGGAC-GTTGACATCGATCT
*** *
18764423 GTGTTTACATGTAAGACCACGTCTAGGAC
1 GTGTTTTTGTGTAAGACCACGTCTGGGAC
18764452 ATTGGCATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
42 1 0.02
43 58 0.94
44 3 0.05
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (43 bp):
GTGTTTTTGTGTAAGACCACGTCTGGGACGTTGACATCGATCT
Found at i:18764677 original size:28 final size:29
Alignment explanation
Indices: 18764636--18764692 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
18764626 TTAAATTATA
18764636 AATGTGAACTATGTGTATACATATGTGGT
1 AATGTGAACTATGTGTATACATATGTGGT
* * *
18764665 AATGT-AATTATGTGTATGCATATTTGGT
1 AATGTGAACTATGTGTATACATATGTGGT
18764693 GATGCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (29 bp):
AATGTGAACTATGTGTATACATATGTGGT
Found at i:18766984 original size:19 final size:18
Alignment explanation
Indices: 18766962--18767000 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18766952 AATATAATAT
18766962 AAAACAAATAAATAAAAGA
1 AAAACAAAT-AATAAAAGA
* *
18766981 AAAAGAAATAGTAAAAGA
1 AAAACAAATAATAAAAGA
18766999 AA
1 AA
18767001 CAAGATAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAACAAATAATAAAAGA
Found at i:18767032 original size:13 final size:12
Alignment explanation
Indices: 18767014--18767051 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
18767004 GATAGAAACG
18767014 AAACAGAAAGGAA
1 AAACAGAAA-GAA
18767027 AAACAGAAAGAA
1 AAACAGAAAGAA
*
18767039 AAA-GGAAAGAA
1 AAACAGAAAGAA
18767050 AA
1 AA
18767052 GGAGAAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.38
12 6 0.25
13 9 0.38
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (12 bp):
AAACAGAAAGAA
Found at i:18768050 original size:40 final size:40
Alignment explanation
Indices: 18767929--18768068 Score: 137
Period size: 40 Copynumber: 3.5 Consensus size: 40
18767919 GACTTTGAGT
* *
18767929 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTTATT
1 CGATGAGACACTAGGTGTCAAATTATTACTTC-GATTTATC
** * * * *
18767970 CGATGAGGTAGTAGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
*
18768007 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
18768047 CGATGATG-CACT-GGCTGTCAAA
1 CGATGA-GACACTAGG-TGTCAAA
18768069 CTGGTGTGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
37 19 0.24
38 10 0.13
39 4 0.05
40 32 0.41
41 14 0.18
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
Found at i:18771623 original size:24 final size:26
Alignment explanation
Indices: 18771596--18771647 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
18771586 CTCGTTAAGT
18771596 GCTCTTTG-GAGCTACCCGATA-TAA
1 GCTCTTTGTGAGCTACCCGATATTAA
* *
18771620 GCTCTTTGTGAGCTTCCCGTTATTAA
1 GCTCTTTGTGAGCTACCCGATATTAA
18771646 GC
1 GC
18771648 CCAGATAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 11 0.46
26 5 0.21
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (26 bp):
GCTCTTTGTGAGCTACCCGATATTAA
Found at i:18778498 original size:26 final size:26
Alignment explanation
Indices: 18778463--18778520 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 26
18778453 TTCAGTAGAA
18778463 ATAAAATTTTA-A-TTATTATTTAATT
1 ATAAAATTTTATAGTTATTATTTAA-T
18778488 ATAACAATTTTATATGTTATTATTTAAT
1 ATAA-AATTTTATA-GTTATTATTTAAT
18778516 ATAAA
1 ATAAA
18778521 TCTAATACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.14
26 7 0.24
27 2 0.07
28 5 0.17
29 11 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATAAAATTTTATAGTTATTATTTAAT
Found at i:18778995 original size:14 final size:13
Alignment explanation
Indices: 18778976--18779005 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
18778966 TTCAAAACTT
18778976 AATTTTTTAAAATA
1 AATTTTTTAAAA-A
18778990 AATTTTTTAAAAA
1 AATTTTTTAAAAA
18779003 AAT
1 AAT
18779006 AAACTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTTTTAAAAA
Done.