Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 69 of 125
Found at i:21609093 original size:27 final size:27
Alignment explanation
Indices: 21609011--21609086 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
21609001 AGAATATAAA
21609011 TCATTTGAGCCCA-AAATAGAGTTTAGC
1 TCATTTGAGCCCAGAAA-AGAGTTTAGC
*
21609038 TCATTTGAGCTCAGAAAAGAGTTTAGC
1 TCATTTGAGCCCAGAAAAGAGTTTAGC
*
21609065 TCATTTGAGCCCAGAACAGAGT
1 TCATTTGAGCCCAGAAAAGAGT
21609087 AACGCTCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 42 0.93
28 3 0.07
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (27 bp):
TCATTTGAGCCCAGAAAAGAGTTTAGC
Found at i:21609196 original size:28 final size:28
Alignment explanation
Indices: 21609141--21609198 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
21609131 CATAGTGCAG
*
21609141 AGTTACGCTCTTACGAGCCAAAATACAA
1 AGTTACGCTCTTACGAGCCAAAACACAA
* * *
21609169 AGTTACGCTTTTACGAGCTAGAACACAA
1 AGTTACGCTCTTACGAGCCAAAACACAA
21609197 AG
1 AG
21609199 CATTTGCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (28 bp):
AGTTACGCTCTTACGAGCCAAAACACAA
Found at i:21611220 original size:15 final size:15
Alignment explanation
Indices: 21611182--21611226 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
21611172 AGTAAGTATG
*
21611182 TGTACTTTAGTTAAT
1 TGTACTTTAGTTACT
*
21611197 TGTATTTTAGTTACT
1 TGTACTTTAGTTACT
*
21611212 TTTACTTTAG-TACT
1 TGTACTTTAGTTACT
21611226 T
1 T
21611227 CAGTAAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.58
Consensus pattern (15 bp):
TGTACTTTAGTTACT
Found at i:21612806 original size:23 final size:20
Alignment explanation
Indices: 21612765--21612809 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 20
21612755 GGGTAGTGGG
21612765 GATTTGTTTTATTTTTATTT
1 GATTTGTTTTATTTTTATTT
21612785 GATTTGATTTTATTATTTTATTT
1 GATTTG-TTTTA-T-TTTTATTT
21612808 GA
1 GA
21612810 AATTATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 1 0.05
23 10 0.45
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (20 bp):
GATTTGTTTTATTTTTATTT
Found at i:21618036 original size:69 final size:69
Alignment explanation
Indices: 21617915--21618067 Score: 234
Period size: 69 Copynumber: 2.2 Consensus size: 69
21617905 GATACGCGGA
* * * *
21617915 TCTCTAACACACCAACACTAGACTTATAGAGTTGAAACATATCCCGTAAGTGAAGCATATAATCA
1 TCTCCAACACACCAACACTAGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAATCA
21617980 ACAC
66 ACAC
* * * *
21617984 TCTCCAACAGACCAATACTAGACTCATAGAGTCGAAACATATCTCATAAGTGAAGCATATAGTCA
1 TCTCCAACACACCAACACTAGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAATCA
21618049 ACAC
66 ACAC
21618053 TCTCCAACACACCAA
1 TCTCCAACACACCAA
21618068 ACATATCCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.22
Consensus pattern (69 bp):
TCTCCAACACACCAACACTAGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAATCA
ACAC
Found at i:21619044 original size:31 final size:33
Alignment explanation
Indices: 21619004--21619127 Score: 99
Period size: 31 Copynumber: 4.1 Consensus size: 33
21618994 AAGATTGAAT
* * *
21619004 AAAT-AAATAAAATTAAAGGGTT-AATTTTAAA
1 AAATAAAATAAAATAAAAAGATTAAATTTTAAA
*
21619035 AAA-AAAATAAAATAAAAATATTAAATTTT---
1 AAATAAAATAAAATAAAAAGATTAAATTTTAAA
* * *
21619064 -AA-AAAATAAAATAAAAGGACTAAA-TTTATA
1 AAATAAAATAAAATAAAAAGATTAAATTTTAAA
*
21619094 AAA-AAA-TAAAATAAAAGGATTAAATTTTAAA
1 AAATAAAATAAAATAAAAAGATTAAATTTTAAA
21619125 AAA
1 AAA
21619128 GAACAGAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.04
28 21 0.27
30 17 0.22
31 30 0.39
32 6 0.08
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (33 bp):
AAATAAAATAAAATAAAAAGATTAAATTTTAAA
Found at i:21619076 original size:28 final size:28
Alignment explanation
Indices: 21619036--21619127 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
21619026 AATTTTAAAA
**
21619036 AAAAAATAAAATAAAAATATTAAATTTT
1 AAAAAATAAAATAAAAGGATTAAATTTT
*
21619064 AAAAAATAAAATAAAAGGACTAAATTTAT
1 AAAAAATAAAATAAAAGGATTAAATTT-T
21619093 AAAAAAATAAAATAAAAGGATTAAATTTT
1 -AAAAAATAAAATAAAAGGATTAAATTTT
21619122 AAAAAA
1 AAAAAA
21619128 GAACAGAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 30 0.52
29 2 0.03
30 26 0.45
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (28 bp):
AAAAAATAAAATAAAAGGATTAAATTTT
Found at i:21619098 original size:30 final size:30
Alignment explanation
Indices: 21619002--21619127 Score: 150
Period size: 30 Copynumber: 4.3 Consensus size: 30
21618992 AAAAGATTGA
* * * *
21619002 ATAAATAAATAAAATTAAAGGGTTAATTTT
1 ATAAAAAAATAAAATAAAAGGATTAAATTT
* **
21619032 AAAAAAAAAATAAAATAAAAATATTAAATTT
1 -ATAAAAAAATAAAATAAAAGGATTAAATTT
*
21619063 -T-AAAAAATAAAATAAAAGGACTAAATTT
1 ATAAAAAAATAAAATAAAAGGATTAAATTT
21619091 ATAAAAAAATAAAATAAAAGGATTAAATTT
1 ATAAAAAAATAAAATAAAAGGATTAAATTT
21619121 -TAAAAAA
1 ATAAAAAA
21619128 GAACAGAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.30
29 8 0.10
30 26 0.32
31 23 0.28
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.28
Consensus pattern (30 bp):
ATAAAAAAATAAAATAAAAGGATTAAATTT
Found at i:21619116 original size:58 final size:59
Alignment explanation
Indices: 21619003--21619127 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 59
21618993 AAAGATTGAA
* ** * *
21619003 TAAATAAATAAAATTAAAGGGTTAATTTTAAAAAAAAAATAAAATAAAAATATTAAATTT
1 TAAA-AAATAAAATAAAAGGACTAAATTTAAAAAAAAAATAAAATAAAAAGATTAAATTT
* *
21619063 TAAAAAATAAAATAAAAGGACTAAATTT-ATAAAAAAATAAAATAAAAGGATTAAATTT
1 TAAAAAATAAAATAAAAGGACTAAATTTAAAAAAAAAATAAAATAAAAAGATTAAATTT
21619121 TAAAAAA
1 TAAAAAA
21619128 GAACAGAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 34 0.59
59 20 0.34
60 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.28
Consensus pattern (59 bp):
TAAAAAATAAAATAAAAGGACTAAATTTAAAAAAAAAATAAAATAAAAAGATTAAATTT
Found at i:21620941 original size:100 final size:99
Alignment explanation
Indices: 21620812--21621139 Score: 316
Period size: 100 Copynumber: 3.3 Consensus size: 99
21620802 AGCTTCACTC
21620812 CATTCCACTGTAACCTCAGGGACATTGAGATCTACTTTGTTGTTTTAACCTGACCCACTGTAACC
1 CATTCCACTGTAACCTCAGGGACATTGAGATCTACTTTGTTGTTTTAACCTGACCCACTGTAACC
21620877 ATAGAGGTATAGGATTTGGTGTTGTAATTTTACTT
66 ATAGAGGTATAGGATTTGGTGTTGTAA-TTTACTT
* * ** * * *
21620912 CATTCCACTGTAACCTCAGGGAGATTGAGATCT-GTTACTTGCTTTAATCC--ACTTCACCGTAA
1 CATTCCACTGTAACCTCAGGGACATTGAGATCTACTTTGTTGTTTTAA-CCTGAC-CCACTGTAA
* ** * * *
21620974 CTTCA-AGAAG-ATAGGATTTGAAGCT-TCA-CT-C-T
64 C--CATAGAGGTATAGGATTTGGTGTTGTAATTTACTT
** * * * *
21621006 -ATTCCACCCATAACCTCAGGGACATTGAGATCTGCTTTGTCGTTTTAATCTGACCCACTTTAAC
1 CATTCCA-CTGTAACCTCAGGGACATTGAGATCTACTTTGTTGTTTTAACCTGACCCACTGTAAC
* * *
21621070 CTTAGGGGTATAGGATTTGGTGTTGTAACTTTACTC
65 CATAGAGGTATAGGATTTGGTGTTGTAA-TTTACTT
*
21621106 CATTCCACTGTAACCTCAGGGAGATTGAGATCTA
1 CATTCCACTGTAACCTCAGGGACATTGAGATCTA
21621140 TTACTTGCTT
Statistics
Matches: 174, Mismatches: 38, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
93 7 0.04
94 28 0.16
95 29 0.17
96 5 0.03
98 5 0.03
99 31 0.18
100 61 0.35
101 8 0.05
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (99 bp):
CATTCCACTGTAACCTCAGGGACATTGAGATCTACTTTGTTGTTTTAACCTGACCCACTGTAACC
ATAGAGGTATAGGATTTGGTGTTGTAATTTACTT
Found at i:21621119 original size:194 final size:193
Alignment explanation
Indices: 21620731--21621216 Score: 738
Period size: 194 Copynumber: 2.5 Consensus size: 193
21620721 TCACAATATC
* *
21620731 ACCTCAGAGAGATTGAGATCTGTTACTTGTTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
1 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
** *
21620796 ATTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTACTTTGTTGTTTTAAC
66 ATTTGAAGCTTCACTCCATTCCACCATAACCTCAGGGACATTGAGATCTACTTTGTCGTTTTAAC
* *
21620861 CTGACCCACTGTAACCATAGAGGTATAGGATTTGGTGTTGTAATTTTACTTCATTCCACTGTA
131 CTGACCCACTGTAACCATAGAGGTATAGGATTTGGTGTTGTAACTTTACTCCATTCCACTGTA
* * *
21620924 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCACTTCACCGTAACTTCAAGAAGATAGG
1 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
* *
21620989 ATTTGAAGCTTCACTCTATTCCACCCATAACCTCAGGGACATTGAGATCTGCTTTGTCGTTTTAA
66 ATTTGAAGCTTCACTCCATTCCA-CCATAACCTCAGGGACATTGAGATCTACTTTGTCGTTTTAA
* * * *
21621054 TCTGACCCACTTTAACCTTAGGGGTATAGGATTTGGTGTTGTAACTTTACTCCATTCCACTGTA
130 CCTGACCCACTGTAACCATAGAGGTATAGGATTTGGTGTTGTAACTTTACTCCATTCCACTGTA
* * * * *
21621118 ACCTCAGGGAGATTGAGATCTATTACTTGCTTAAATCTGCTTCACTGCAACTTTAGGAAGATAGG
1 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
* * **
21621183 ATTTGAAGCTTTACTCCATCCCACTGTAACCTCA
66 ATTTGAAGCTTCACTCCATTCCACCATAACCTCA
21621217 TAGGTATAGG
Statistics
Matches: 263, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
193 91 0.35
194 172 0.65
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (193 bp):
ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
ATTTGAAGCTTCACTCCATTCCACCATAACCTCAGGGACATTGAGATCTACTTTGTCGTTTTAAC
CTGACCCACTGTAACCATAGAGGTATAGGATTTGGTGTTGTAACTTTACTCCATTCCACTGTA
Found at i:21624090 original size:28 final size:28
Alignment explanation
Indices: 21624060--21624182 Score: 139
Period size: 29 Copynumber: 4.5 Consensus size: 28
21624050 TTGAATAAAT
* * *
21624060 AAAAACAAAACAAAATGATTAAATTTTTA
1 AAAAATAAAATAAAAGGATTAAA-TTTTA
21624089 AAAAATAAAATAAAAGGATTAAATTTTAA
1 AAAAATAAAATAAAAGGATTAAATTTT-A
*
21624118 AAAAATAAAATAAAAGGACTAAATTTT-
1 AAAAATAAAATAAAAGGATTAAATTTTA
*
21624145 --AAA-AAAATAAAAGGATTAAA-TTAA
1 AAAAATAAAATAAAAGGATTAAATTTTA
*
21624169 AAAAATAGAATAAA
1 AAAAATAAAATAAA
21624183 GGGGCCAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.02
24 16 0.20
25 3 0.04
26 3 0.04
27 7 0.09
28 4 0.05
29 47 0.57
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (28 bp):
AAAAATAAAATAAAAGGATTAAATTTTA
Found at i:21624103 original size:29 final size:29
Alignment explanation
Indices: 21624060--21624156 Score: 149
Period size: 29 Copynumber: 3.3 Consensus size: 29
21624050 TTGAATAAAT
* * * *
21624060 AAAAACAAAACAAAATGATTAAATTTTTA
1 AAAAATAAAATAAAAGGATTAAATTTTAA
21624089 AAAAATAAAATAAAAGGATTAAATTTTAA
1 AAAAATAAAATAAAAGGATTAAATTTTAA
*
21624118 AAAAATAAAATAAAAGGACTAAATTTTAA
1 AAAAATAAAATAAAAGGATTAAATTTTAA
21624147 AAAAATAAAA
1 AAAAATAAAA
21624157 GGATTAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (29 bp):
AAAAATAAAATAAAAGGATTAAATTTTAA
Found at i:21624174 original size:22 final size:23
Alignment explanation
Indices: 21624124--21624175 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
21624114 TTAAAAAAAT
21624124 AAAATAAAAGGACTAAATTTTAAA
1 AAAATAAAAGGACTAAA-TTTAAA
*
21624148 AAAATAAAAGGATTAAA-TTAAA
1 AAAATAAAAGGACTAAATTTAAA
21624170 AAAATA
1 AAAATA
21624176 GAATAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 11 0.41
24 16 0.59
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (23 bp):
AAAATAAAAGGACTAAATTTAAA
Found at i:21624199 original size:51 final size:52
Alignment explanation
Indices: 21624095--21624200 Score: 142
Period size: 51 Copynumber: 2.0 Consensus size: 52
21624085 TTTAAAAAAT
* * *
21624095 AAAATAAAAGGATTAAATTTTAAAAAAATAAAATAAAAGGACTAAATTTTAAA
1 AAAATAAAAGGATTAAA-TTTAAAAAAATAAAATAAAAGGACCAAAATATAAA
* * *
21624148 AAAATAAAAGGATTAAA-TTAAAAAAATAGAATAAAGGGGCCAAAATATAAA
1 AAAATAAAAGGATTAAATTTAAAAAAATAAAATAAAAGGACCAAAATATAAA
21624199 AA
1 AA
21624201 TAAAATGGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 30 0.64
53 17 0.36
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.22
Consensus pattern (52 bp):
AAAATAAAAGGATTAAATTTAAAAAAATAAAATAAAAGGACCAAAATATAAA
Found at i:21625659 original size:23 final size:23
Alignment explanation
Indices: 21625633--21625742 Score: 166
Period size: 23 Copynumber: 4.8 Consensus size: 23
21625623 CATTATTATT
21625633 ACATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
21625656 ACATTAATATTTAAGTATAAATC
1 ACATTAATATTTAAGCACAAATC
*
21625679 ACATTAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
21625702 ATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
21625725 GCATTAATATTTAAGCAC
1 ACATTAATATTTAAGCAC
21625743 TTACACTCGG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (23 bp):
ACATTAATATTTAAGCACAAATC
Found at i:21625683 original size:46 final size:46
Alignment explanation
Indices: 21625633--21625742 Score: 184
Period size: 46 Copynumber: 2.4 Consensus size: 46
21625623 CATTATTATT
*
21625633 ACATTAATATTTAAGCACAAATCACATTAATATTTAAGTATAAATC
1 ACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATC
* *
21625679 ACATTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATC
*
21625725 GCATTAATATTTAAGCAC
1 ACATTAATATTTAAGCAC
21625743 TTACACTCGG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (46 bp):
ACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATC
Found at i:21627182 original size:22 final size:22
Alignment explanation
Indices: 21627156--21627197 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
21627146 TAAGGGGAAA
21627156 ACCTAGGGTTTTATAG-GAAATT
1 ACCTA-GGTTTTATAGAGAAATT
*
21627178 ACCTAGTTTTTATAGAGAAA
1 ACCTAGGTTTTATAGAGAAA
21627198 ACTTAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (22 bp):
ACCTAGGTTTTATAGAGAAATT
Found at i:21627234 original size:128 final size:133
Alignment explanation
Indices: 21626981--21627222 Score: 302
Period size: 129 Copynumber: 1.8 Consensus size: 133
21626971 TTTTTTTTTC
*
21626981 TTTTTTAGAATTAATTTCAATTTTTCTCATTACAAGGGAAGAGAAAACCTAGGGTTTTACAAGGA
1 TTTTTTAGAATTAATTTCAATTTTTCTCAATACAAGGG-AGAGAAAACCTAGGGTTTTACAAGGA
* * * **
21627046 ATTACCTGGATTTTTATTGGGAAAAACTTTAATTTTTGTTGAAAAACCAATTTATCTTTTTCATT
65 ATTACCTAGATTTTTATAGAGAAAAACTTTAATTTTTCATGAAAAACCAATTTATCTTTTTCATT
21627111 TCCA
130 TCCA
* * * *
21627115 TTTTTTAGAATTAATTTTAGTTTTT-TCAATATAA-GG-G-GAAAACCTAGGGTTTTA-TAGGAA
1 TTTTTTAGAATTAATTTCAATTTTTCTCAATACAAGGGAGAGAAAACCTAGGGTTTTACAAGG-A
21627175 ATTACCTAG-TTTTTATAGAG-AAAAC-TTAGATTTTTACATGAAAAACCA
65 ATTACCTAGATTTTTATAGAGAAAAACTTTA-ATTTTT-CATGAAAAACCA
21627223 TTTTTATTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
126 3 0.03
127 11 0.12
128 22 0.23
129 26 0.27
130 1 0.01
132 2 0.02
133 7 0.07
134 23 0.24
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (133 bp):
TTTTTTAGAATTAATTTCAATTTTTCTCAATACAAGGGAGAGAAAACCTAGGGTTTTACAAGGAA
TTACCTAGATTTTTATAGAGAAAAACTTTAATTTTTCATGAAAAACCAATTTATCTTTTTCATTT
CCA
Found at i:21651805 original size:28 final size:28
Alignment explanation
Indices: 21651769--21651832 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
21651759 GCAACTAGGA
*
21651769 AAGCCTTTATAGCTATCTTTATTAAAAG
1 AAGCCTTTATAGCTATCTCTATTAAAAG
* * *
21651797 AAGCCTTTATGGCTATCTCTGTTAAAGG
1 AAGCCTTTATAGCTATCTCTATTAAAAG
21651825 AACGCCTT
1 AA-GCCTT
21651833 CGTGGAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (28 bp):
AAGCCTTTATAGCTATCTCTATTAAAAG
Found at i:21662173 original size:12 final size:12
Alignment explanation
Indices: 21662156--21662219 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
21662146 TAACTTAATT
21662156 GAACATATTCAC
1 GAACATATTCAC
*
21662168 GAACAT-TTAAC
1 GAACATATTCAC
* * *
21662179 AAACATGTTCAT
1 GAACATATTCAC
*
21662191 GAACATA-TAAC
1 GAACATATTCAC
*
21662202 TGAACATGTTCAC
1 -GAACATATTCAC
21662215 GAACA
1 GAACA
21662220 AAGTTAATGG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
11 11 0.28
12 25 0.64
13 3 0.08
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (12 bp):
GAACATATTCAC
Found at i:21662177 original size:24 final size:23
Alignment explanation
Indices: 21662150--21662219 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
21662140 TTCATTTAAC
*
21662150 TTAATTGAACATATTCACGAACAT
1 TTAA-TGAACATGTTCACGAACAT
** *
21662174 TTAACAAACATGTTCATGAACAT
1 TTAATGAACATGTTCACGAACAT
*
21662197 ATAACTGAACATGTTCACGAACA
1 TTAA-TGAACATGTTCACGAACA
21662220 AAGTTAATGG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (23 bp):
TTAATGAACATGTTCACGAACAT
Found at i:21662183 original size:23 final size:24
Alignment explanation
Indices: 21662157--21662219 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
21662147 AACTTAATTG
* *
21662157 AACATATTCACGAACATTTAAC-A
1 AACATGTTCACGAACATATAACTA
* *
21662180 AACATGTTCATGAACATATAACTG
1 AACATGTTCACGAACATATAACTA
21662204 AACATGTTCACGAACA
1 AACATGTTCACGAACA
21662220 AAGTTAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (24 bp):
AACATGTTCACGAACATATAACTA
Found at i:21664112 original size:61 final size:61
Alignment explanation
Indices: 21664037--21664159 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
21664027 TTGGTTCAGG
21664037 GAGGTAGGACTGTGGCTGAGTATGAGTTGGAGTTTGTGCGACTCAGTCAGCATGCCCCGGA
1 GAGGTAGGACTGTGGCTGAGTATGAGTTGGAGTTTGTGCGACTCAGTCAGCATGCCCCGGA
21664098 GAGGTAGGACTGTGGCTGAGTATGAGTTGGAGTTTGTGCGACTCAGTCAGCATGCCCCGGA
1 GAGGTAGGACTGTGGCTGAGTATGAGTTGGAGTTTGTGCGACTCAGTCAGCATGCCCCGGA
21664159 G
1 G
21664160 TTGATTCACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.24
Consensus pattern (61 bp):
GAGGTAGGACTGTGGCTGAGTATGAGTTGGAGTTTGTGCGACTCAGTCAGCATGCCCCGGA
Found at i:21668054 original size:24 final size:24
Alignment explanation
Indices: 21668022--21668073 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
21668012 ACAAGTTCGT
*
21668022 TTTAAAAGCTCATTTATTGGCTTG
1 TTTAAAAGCTCATTTATTGACTTG
* *
21668046 TTTATAAGCTCGTTTATTGACTTG
1 TTTAAAAGCTCATTTATTGACTTG
21668070 TTTA
1 TTTA
21668074 CTCATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (24 bp):
TTTAAAAGCTCATTTATTGACTTG
Found at i:21668223 original size:23 final size:23
Alignment explanation
Indices: 21668165--21668234 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
21668155 TCATTAACAT
*
21668165 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
21668189 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
21668212 TGTTCGTAAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
21668235 GTTAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:21669626 original size:3 final size:3
Alignment explanation
Indices: 21669620--21669651 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
21669610 CCAAAATCAA
21669620 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21669652 GTAAATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21670753 original size:11 final size:11
Alignment explanation
Indices: 21670737--21670761 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21670727 GTCAACGGTC
21670737 GTCGGTCAACG
1 GTCGGTCAACG
21670748 GTCGGTCAACG
1 GTCGGTCAACG
21670759 GTC
1 GTC
21670762 TGACTTAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.20
Consensus pattern (11 bp):
GTCGGTCAACG
Found at i:21675387 original size:22 final size:22
Alignment explanation
Indices: 21675362--21675406 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21675352 TTTTTTTGCT
21675362 TTCTTCATTTTTCCACTTCTGG
1 TTCTTCATTTTTCCACTTCTGG
21675384 TTCTTCATTTTTCCACTTCTGG
1 TTCTTCATTTTTCCACTTCTGG
21675406 T
1 T
21675407 GGTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.27, G:0.09, T:0.56
Consensus pattern (22 bp):
TTCTTCATTTTTCCACTTCTGG
Found at i:21684340 original size:7 final size:7
Alignment explanation
Indices: 21684323--21684366 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
21684313 GAAGTGATAA
21684323 AAAGA-T
1 AAAGATT
21684329 AAAGATT
1 AAAGATT
21684336 AAAGATT
1 AAAGATT
21684343 AAAGATT
1 AAAGATT
21684350 AAAGATT
1 AAAGATT
21684357 AAAGATT
1 AAAGATT
21684364 AAA
1 AAA
21684367 TTTATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (7 bp):
AAAGATT
Found at i:21685095 original size:19 final size:19
Alignment explanation
Indices: 21685063--21685100 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21685053 TGATTAATTA
21685063 ATTTTAAATAATATATTTT
1 ATTTTAAATAATATATTTT
* *
21685082 ATTTTTAATTATATATTTT
1 ATTTTAAATAATATATTTT
21685101 GAAGCAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTAAATAATATATTTT
Found at i:21685845 original size:18 final size:18
Alignment explanation
Indices: 21685824--21685858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21685814 TATCATAAAG
21685824 CAGAAACATGCCACAAGA
1 CAGAAACATGCCACAAGA
* *
21685842 CAGAAGCGTGCCACAAG
1 CAGAAACATGCCACAAG
21685859 GCAAAAGCGT
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:0.43, C:0.29, G:0.23, T:0.06
Consensus pattern (18 bp):
CAGAAACATGCCACAAGA
Found at i:21685866 original size:18 final size:18
Alignment explanation
Indices: 21685832--21685879 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
21685822 AGCAGAAACA
* *
21685832 TGCCACAAGACAGAAGCG
1 TGCCACAAGGCAAAAGCG
21685850 TGCCACAAGGCAAAAGCG
1 TGCCACAAGGCAAAAGCG
* *
21685868 TGTCATAAGGCA
1 TGCCACAAGGCA
21685880 GAGAAAAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.25, G:0.27, T:0.10
Consensus pattern (18 bp):
TGCCACAAGGCAAAAGCG
Found at i:21685966 original size:23 final size:22
Alignment explanation
Indices: 21685915--21685967 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
21685905 ATAAAATTGG
21685915 AAAAAAACTAAAACATAAAAAA
1 AAAAAAACTAAAACATAAAAAA
*
21685937 AATAAAAACT-AAATATAAAAAA
1 AA-AAAAACTAAAACATAAAAAA
21685959 TTAAAAAAA
1 --AAAAAAA
21685968 ATACCGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 13 0.48
23 12 0.44
24 2 0.07
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAAAAACTAAAACATAAAAAA
Found at i:21686780 original size:20 final size:20
Alignment explanation
Indices: 21686755--21686794 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21686745 CACATTTATT
21686755 CAATTAAAATAACAAAAAAC
1 CAATTAAAATAACAAAAAAC
*
21686775 CAATTAAAATGACAAAAAAC
1 CAATTAAAATAACAAAAAAC
21686795 GTGATACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (20 bp):
CAATTAAAATAACAAAAAAC
Found at i:21687500 original size:3 final size:3
Alignment explanation
Indices: 21687487--21687515 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
21687477 AGAGCAAAGA
21687487 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21687516 GAGGGTGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21687655 original size:17 final size:17
Alignment explanation
Indices: 21687633--21687666 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21687623 TAAAAAATTC
*
21687633 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
21687650 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
21687667 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:21687919 original size:22 final size:23
Alignment explanation
Indices: 21687894--21687941 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
21687884 GCATTTTTTT
21687894 TTATCATTTTAAATTTATGAA-A
1 TTATCATTTTAAATTTATGAATA
* * *
21687916 TTATCTTTTTAATTTTTTGAATA
1 TTATCATTTTAAATTTATGAATA
21687939 TTA
1 TTA
21687942 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATCATTTTAAATTTATGAATA
Found at i:21693825 original size:26 final size:26
Alignment explanation
Indices: 21693796--21693845 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
21693786 AACCTTCTAT
*
21693796 TTCCTTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTTCTTCTTCAAAAATTTTGC
*
21693822 TTCCTTTTTTTCTTCAAAAATTTT
1 TTCCTTTTCTTCTTCAAAAATTTT
21693846 CTGTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (26 bp):
TTCCTTTTCTTCTTCAAAAATTTTGC
Found at i:21694545 original size:27 final size:27
Alignment explanation
Indices: 21694501--21694581 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
21694491 AAAATTCAGG
*
21694501 TTGGTGCCGCTTGACAGGAAGGCACCA
1 TTGGTGCCGCTTGACAGGTAGGCACCA
* *
21694528 TTGGTGCCGCCTGGCAGGTAGGCACCA
1 TTGGTGCCGCTTGACAGGTAGGCACCA
* * *
21694555 CTAGTGCCGCTTGTCAGGTAGGCACCA
1 TTGGTGCCGCTTGACAGGTAGGCACCA
21694582 CCCCTTGTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (27 bp):
TTGGTGCCGCTTGACAGGTAGGCACCA
Found at i:21697528 original size:9 final size:9
Alignment explanation
Indices: 21697514--21697538 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21697504 ACTAAAGCGC
21697514 GAATATTGT
1 GAATATTGT
21697523 GAATATTGT
1 GAATATTGT
21697532 GAATATT
1 GAATATT
21697539 ACTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (9 bp):
GAATATTGT
Found at i:21699860 original size:21 final size:21
Alignment explanation
Indices: 21699836--21699878 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
21699826 AGCAACTGTG
21699836 AAACAACA-ATAAAACAACACC
1 AAACAACATA-AAAACAACACC
21699857 AAACAACATAAAAACAACACC
1 AAACAACATAAAAACAACACC
21699878 A
1 A
21699879 TGCTGCACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.28, G:0.00, T:0.05
Consensus pattern (21 bp):
AAACAACATAAAAACAACACC
Found at i:21713134 original size:21 final size:21
Alignment explanation
Indices: 21713110--21713156 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21713100 CTTCCGTTCC
*
21713110 TCCTTGCG-TTACTTCTTCTTG
1 TCCTTGCGCTT-CCTCTTCTTG
*
21713131 TCCTTGCGCTTCCTCTTTTTG
1 TCCTTGCGCTTCCTCTTCTTG
21713152 TCCTT
1 TCCTT
21713157 TGAACCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.02, C:0.32, G:0.13, T:0.53
Consensus pattern (21 bp):
TCCTTGCGCTTCCTCTTCTTG
Found at i:21718262 original size:24 final size:23
Alignment explanation
Indices: 21718213--21718262 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
21718203 TAAAGTAGGT
* *
21718213 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
21718236 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
21718260 TAT
1 TAT
21718263 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:21718401 original size:58 final size:57
Alignment explanation
Indices: 21718240--21718406 Score: 203
Period size: 58 Copynumber: 2.9 Consensus size: 57
21718230 ATATTATATA
* * * *
21718240 TTATGATTTTTACTAATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTAT
1 TTATTATTTTTATTAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* *
21718300 ATATTA-TTTTATTGAATTGTATTTAATAATAATTATATTAAAATATAATTAAATTAT
1 TTATTATTTTTATT-AATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
21718357 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATT-AATTATATTTAATAATAAT-TATATTAAAATATAAT
21718407 AACAATAATC
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 21 0.22
58 56 0.60
59 9 0.10
60 8 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (57 bp):
TTATTATTTTTATTAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:21718587 original size:16 final size:16
Alignment explanation
Indices: 21718568--21718598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21718558 GATTATAGCC
*
21718568 CTATTTCATTACAGCT
1 CTATTCCATTACAGCT
21718584 CTATTCCATTACAGC
1 CTATTCCATTACAGC
21718599 GAACCAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (16 bp):
CTATTCCATTACAGCT
Found at i:21732382 original size:24 final size:24
Alignment explanation
Indices: 21732347--21732417 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
21732337 TTTCAGAAAT
* *
21732347 TTAGCTCATACGAGCCCATACAGG
1 TTAGCTCTTACGAGCCCAGACAGG
* *
21732371 TTAGCTCTTACGAGCCCAGATAAG
1 TTAGCTCTTACGAGCCCAGACAGG
21732395 TTAGCTCCTT-CGAGCCCAGACAG
1 TTAGCT-CTTACGAGCCCAGACAG
21732418 AGTTTAACCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
24 37 0.93
25 3 0.08
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGACAGG
Found at i:21732581 original size:82 final size:82
Alignment explanation
Indices: 21732432--21732582 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 82
21732422 TAACCAGTAT
* ** * *
21732432 ATGATGCTGCTCACACAAGCTGATGAGAATCCGTAACATATGCAGAAACTCAGCCATCGATATGG
1 ATGATGCTGCTCACACAAGCTAATGAGAATCCACAACATATGCAAAAACTCAGCCATCGATAGGG
21732497 TCCAGAATTACCCACTC
66 TCCAGAATTACCCACTC
* *
21732514 ATGATGCTGCTCACACAAGCTAATGAGAATCCACAACGTATGTAAAAACTCAGCCATCG-TAGGG
1 ATGATGCTGCTCACACAAGCTAATGAGAATCCACAACATATGCAAAAACTCAGCCATCGATA-GG
21732578 GTCCA
65 GTCCA
21732583 TATAATCAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 2 0.03
82 59 0.97
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (82 bp):
ATGATGCTGCTCACACAAGCTAATGAGAATCCACAACATATGCAAAAACTCAGCCATCGATAGGG
TCCAGAATTACCCACTC
Found at i:21742961 original size:24 final size:23
Alignment explanation
Indices: 21742934--21742980 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
21742924 GATGAAGAAG
* *
21742934 AAAAAGAAGAGAAAGAAATGAAAT
1 AAAAAGAAAAGAAAAAAAT-AAAT
21742958 AAAAAGAAAAGAAAAAAATAAAT
1 AAAAAGAAAAGAAAAAAATAAAT
21742981 TGAAGGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAAAATAAAT
Found at i:21742976 original size:19 final size:21
Alignment explanation
Indices: 21742940--21742979 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
21742930 GAAGAAAAAG
*
21742940 AAGAGAAAGAAATGAAATAAA
1 AAGAGAAAGAAATAAAATAAA
21742961 AAGA-AAAGAAA-AAAATAAA
1 AAGAGAAAGAAATAAAATAAA
21742980 TTGAAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (21 bp):
AAGAGAAAGAAATAAAATAAA
Found at i:21744438 original size:30 final size:30
Alignment explanation
Indices: 21744404--21744537 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 30
21744394 CTACTATATT
** *
21744404 TAAAAATGGTGTTTTGACCCCTAAACTTTC
1 TAAAAATTATGTTTTGACCACTAAACTTTC
* * *
21744434 TAAAAATTATGTTTTAACCATTAAATTTTC
1 TAAAAATTATGTTTTGACCACTAAACTTTC
* * *
21744464 CAAAAATTATATTTTGACCTCTAAACTTTC
1 TAAAAATTATGTTTTGACCACTAAACTTTC
** * *
21744494 TAAAAATTCAAATTTAG-CCCCTAAACTTTC
1 TAAAAATT-ATGTTTTGACCACTAAACTTTC
*
21744524 T-AAAATTTTGTTTT
1 TAAAAATTATGTTTT
21744538 AACCCCATTT
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
28 3 0.04
29 6 0.07
30 68 0.82
31 6 0.07
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (30 bp):
TAAAAATTATGTTTTGACCACTAAACTTTC
Found at i:21749782 original size:6 final size:6
Alignment explanation
Indices: 21749762--21749815 Score: 67
Period size: 6 Copynumber: 8.8 Consensus size: 6
21749752 GAGTGAAAAT
21749762 AAAAG- AAAAGA AAAAGGA AAAAGGA AAAA-A AAGAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAA-GA AAAA-GA AAAAGA AA-AAGA AAAAGA AAAAGA
21749811 AAAAG
1 AAAAG
21749816 GAGAGGTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
5 8 0.18
6 21 0.47
7 16 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:21750794 original size:49 final size:49
Alignment explanation
Indices: 21750738--21750921 Score: 217
Period size: 49 Copynumber: 3.8 Consensus size: 49
21750728 AATGACGAAT
* * * * **
21750738 CTTATACCTTAGAGATGTGATGGGAAAGGTTGAAGTCGTAACGGCAAAC
1 CTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCAAAC
* * *
21750787 CTTATACCTTAGTGATGTGAAGGGAAAGATTGAAGCCACAACGGCAAAT
1 CTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCAAAC
* * * * *
21750836 CTTATACCCTAAAGATG-AAGAGGGAAAGGTGGAAGCCACAACGGCGAAC
1 CTTATACCCTAGAGATGTGA-AGGGAAAGATTGAAGCCACAACGGCAAAC
*
21750885 CTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCC
1 CTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCC
21750922 GTGGCAACGA
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.01
49 111 0.98
50 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (49 bp):
CTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCAAAC
Found at i:21750837 original size:98 final size:98
Alignment explanation
Indices: 21750735--21750921 Score: 259
Period size: 98 Copynumber: 1.9 Consensus size: 98
21750725 CGCAATGACG
* * * * * ** *
21750735 AATCTTATACCTTAGAGATG-TGATGGGAAAGGTTGAAGTCGTAACGGCAAACCTTATACCTTAG
1 AATCTTATACCCTAAAGATGAAGA-GGGAAAGGTGGAAGCCACAACGGCAAACCTTATACCCTAG
*
21750799 TGATGTGAAGGGAAAGATTGAAGCCACAACGGCA
65 AGATGTGAAGGGAAAGATTGAAGCCACAACGGCA
* *
21750833 AATCTTATACCCTAAAGATGAAGAGGGAAAGGTGGAAGCCACAACGGCGAACCTTGTACCCTAGA
1 AATCTTATACCCTAAAGATGAAGAGGGAAAGGTGGAAGCCACAACGGCAAACCTTATACCCTAGA
21750898 GATGTGAAGGGAAAGATTGAAGCC
66 GATGTGAAGGGAAAGATTGAAGCC
21750922 GTGGCAACGA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 75 0.97
99 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (98 bp):
AATCTTATACCCTAAAGATGAAGAGGGAAAGGTGGAAGCCACAACGGCAAACCTTATACCCTAGA
GATGTGAAGGGAAAGATTGAAGCCACAACGGCA
Found at i:21750935 original size:98 final size:94
Alignment explanation
Indices: 21750732--21750955 Score: 241
Period size: 98 Copynumber: 2.3 Consensus size: 94
21750722 ATTCGCAATG
* * * * * ** *
21750732 ACGAATCTTATACCTTAGAGATGTGATGGGAAAGGTTGAAGTCGTAACGGCAAACCTTATACCTT
1 ACGAATCTTATACCCTAAAGATGAGA-GGGAAAGGTGGAAGCCACAACGGCAAACCTTATACCCT
*
21750797 AGTGATGTGAAGGGAAAGATTGAAGCCACA
65 AGAGATGTGAAGGGAAAGATTGAAGCCACA
* *
21750827 ACGGCAAATCTTATACCCTAAAGATGAAGAGGGAAAGGTGGAAGCCACAACGGCGAACCTTGTAC
1 AC-G--AATCTTATACCCTAAAGATG-AGAGGGAAAGGTGGAAGCCACAACGGCAAACCTTATAC
*
21750892 CCTAGAGATGTGAAGGGAAAGATTGAAGCCGTGGCA
62 CCTAGAGATGTGAAGGGAAAGATTGAAGCC---ACA
* *
21750928 ACGAATCTTATATCCTGAAGATGTAGAG
1 ACGAATCTTATACCCTAAAGATG-AGAG
21750956 AAGTAGATTG
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
95 2 0.02
96 1 0.01
98 97 0.91
99 2 0.02
100 1 0.01
101 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (94 bp):
ACGAATCTTATACCCTAAAGATGAGAGGGAAAGGTGGAAGCCACAACGGCAAACCTTATACCCTA
GAGATGTGAAGGGAAAGATTGAAGCCACA
Found at i:21751266 original size:42 final size:43
Alignment explanation
Indices: 21751199--21751393 Score: 164
Period size: 42 Copynumber: 4.5 Consensus size: 43
21751189 GAAGTTACAT
* * * *
21751199 CATCATCCAATCTTTCA-CCCTGACCATGGGGTAGATTGAAGA
1 CATCATCCAATCTTTTACCCCAGACAAAGGGGTAGATTGAAGA
* * * **
21751241 CATCATCCAATCTTTTACCCC-GACCACGGGGCAGATTGAACC
1 CATCATCCAATCTTTTACCCCAGACAAAGGGGTAGATTGAAGA
*
21751283 CATCATCCAATCTTTTACCCCTAAGTCAAAAGGGGTAGATTGAA-A
1 CATCATCCAATCTTTTACCCC--AGAC-AAAGGGGTAGATTGAAGA
* * * * *
21751328 CCATCATCTAATCTTTCACCCCTA-AGTAAAGGGGTAAATTGAAGC
1 -CATCATCCAATCTTTTACCCC-AGA-CAAAGGGGTAGATTGAAGA
*
21751373 CATAATCCAATCTTTTACCCC
1 CATCATCCAATCTTTTACCCC
21751394 TAAGTTAAGA
Statistics
Matches: 125, Mismatches: 20, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
42 54 0.43
43 3 0.02
44 33 0.26
45 3 0.02
46 32 0.26
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (43 bp):
CATCATCCAATCTTTTACCCCAGACAAAGGGGTAGATTGAAGA
Found at i:21751341 original size:46 final size:45
Alignment explanation
Indices: 21751226--21751418 Score: 207
Period size: 46 Copynumber: 4.3 Consensus size: 45
21751216 CCCTGACCAT
* * *
21751226 GGGGTAGATTGAAGA-CATCATCCAATCTTTTACCCC---GACCAC
1 GGGGTAGATTGAA-ACCATCATCCAATCTTTTACCCCTAAGTCAAA
* *
21751268 GGGGCAGATTGAACCCATCATCCAATCTTTTACCCCTAAGTCAAAA
1 GGGGTAGATTGAAACCATCATCCAATCTTTTACCCCTAAGTC-AAA
* *
21751314 GGGGTAGATTGAAACCATCATCTAATCTTTCACCCCTAAGT-AAA
1 GGGGTAGATTGAAACCATCATCCAATCTTTTACCCCTAAGTCAAA
* * * *
21751358 GGGGTAAATTGAAGCCATAATCCAATCTTTTACCCCTAAGTTAAGA
1 GGGGTAGATTGAAACCATCATCCAATCTTTTACCCCTAAGTCAA-A
* *
21751404 GGGGCAAATTGAAAC
1 GGGGTAGATTGAAAC
21751419 TATTATCTCA
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
42 33 0.26
44 39 0.30
45 4 0.03
46 52 0.41
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (45 bp):
GGGGTAGATTGAAACCATCATCCAATCTTTTACCCCTAAGTCAAA
Found at i:21751560 original size:74 final size:75
Alignment explanation
Indices: 21751446--21751609 Score: 258
Period size: 74 Copynumber: 2.2 Consensus size: 75
21751436 TGTAGTGGAG
* * * *
21751446 CAAAACAATGAAGTGGAGCTCAATGTGAGTGAAACTTCAAATCCCATCTT-CTGCTTAGATACAA
1 CAAAACAATGAAGCGGAGCTCAAAGTGAGTGAAACTTCAAACCCCATCTTACTGATTAGATACAA
21751510 AGAAGTGGGT
66 AGAAGTGGGT
* * *
21751520 CAAAACAATAAAGCGGAGTTCAAAGTGAGTGAAACTTCAAACCCCATCTTACTGATTAGATACAG
1 CAAAACAATGAAGCGGAGCTCAAAGTGAGTGAAACTTCAAACCCCATCTTACTGATTAGATACAA
21751585 AGAAGTGGGT
66 AGAAGTGGGT
21751595 CAAAACAATGAAGCG
1 CAAAACAATGAAGCG
21751610 ATCATCTTCT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 45 0.56
75 36 0.44
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (75 bp):
CAAAACAATGAAGCGGAGCTCAAAGTGAGTGAAACTTCAAACCCCATCTTACTGATTAGATACAA
AGAAGTGGGT
Found at i:21751629 original size:48 final size:47
Alignment explanation
Indices: 21751564--21751705 Score: 167
Period size: 48 Copynumber: 2.9 Consensus size: 47
21751554 CTTCAAACCC
* *
21751564 CATCTTACTGATTAGATACAGAGAAGTGGGTCAAAACAATGAAGCGAT
1 CATCTT-CTGATAAGATACAGAGAAGTGGATCAAAACAATGAAGCGAT
* * *
21751612 CATCTTCTTGATAAGATACAGAGAAGTGGATCAAAATAATGAAGTGGT
1 CATCTTC-TGATAAGATACAGAGAAGTGGATCAAAACAATGAAGCGAT
* * * *
21751660 CATCTTCCCGATGAGATACAGAGAAGTGGACCAAAAATAATGAAGC
1 CATCTT-CTGATAAGATACAGAGAAGTGGATC-AAAACAATGAAGC
21751706 AGAGCTCAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
47 1 0.01
48 68 0.83
49 13 0.16
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (47 bp):
CATCTTCTGATAAGATACAGAGAAGTGGATCAAAACAATGAAGCGAT
Found at i:21751840 original size:48 final size:48
Alignment explanation
Indices: 21751758--21751849 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
21751748 TCAAACCCCT
* * *
21751758 ATCTTCCTGATGAGAAATAGAGAGATGGATCAAAACAATGAAGCTGTC
1 ATCTTCCTGATGAGAAATAAAGAGATGAACCAAAACAATGAAGCTGTC
*
21751806 ATCTTCCTGATGAGATATAAAGA-AGTGAACCAAAACAATGAAGC
1 ATCTTCCTGATGAGAAATAAAGAGA-TGAACCAAAACAATGAAGC
21751850 GAAGCTCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.03
48 38 0.97
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (48 bp):
ATCTTCCTGATGAGAAATAAAGAGATGAACCAAAACAATGAAGCTGTC
Found at i:21751940 original size:123 final size:123
Alignment explanation
Indices: 21751743--21752438 Score: 716
Period size: 123 Copynumber: 5.5 Consensus size: 123
21751733 GGAGTAAAGT
* *
21751743 AAACTTCAAACCCCTATCTTCCTGATGAGAAATAGAG-AGATGGATCAAAACAATGAAGCTGTCA
1 AAACTTCAAACCCC-ATCTTCCTGATGAGATATAGAGAAG-TGGATCAAAACAATGAAGCGGTCA
* * * *
21751807 TCTTCCTGATGAGATATAAAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGTGAGAG
64 TCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTG
* * * * *
21751867 AAACTTCAAACTCCATCTTCTTGATGAGTTATAGAGAAATAGATCAAAACAATGAAGCGGTCATC
1 AAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATC
* * *
21751932 TTCTTGATGAGATACAGAGAAAG-GGATCAAAATAATGAAGC-AGAGCTCAACATCCTTAAGGTT
66 TTCCTGATGAGATACAGAG-AAGTGGACCAAAACAATGAAGCGA-AGCTC-A-A----T---G-T
*
21751995 ACAGTAG
119 -GAGT-G
** * *
21752002 AGTAGACTGAAACTTCAAACCCCCATCTTCCAGATGAGATACAGAGAAGTGGATCAAAACAATGA
1 A--A-ACTTCAA------A-CCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGA
* * * * * * * *
21752067 AGCGATCATCTTCCTGATGAGATACAAAGAAGTTGACAAAAACAATAAAGAGAAGCTCAATCTAA
56 AGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGA
21752132 GTG
121 GTG
* *
21752135 AAACTTCAAACCCCATCTTCCTAATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGATCATC
1 AAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATC
* *
21752200 TTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGTGAAGCTCAATGTGAGTG
66 TTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTG
*** * *
21752258 AAACTTCAAATTTCATCTTTCTGATGAGATATAGAGAAGTGGATCATAACAATGAAGCGGTCATC
1 AAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATC
* * * *
21752323 TTCCTTATGAGATACAGAGAAGTGGACCAAAATAATGAAACGAAGCTCAATAGAGAGTG
66 TTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAAT-GTGAGTG
* * * * *
21752382 AAACTTCAAACCCCATCTTCTTGATGACATACAGAGAAGTGGACCAAAA-GATGAAGC
1 AAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGC
21752439 TATAACACCA
Statistics
Matches: 474, Mismatches: 70, Indels: 57
0.79 0.12 0.09
Matches are distributed among these distances:
122 1 0.00
123 293 0.62
124 65 0.14
125 1 0.00
129 1 0.00
130 5 0.01
131 1 0.00
132 1 0.00
133 3 0.01
134 5 0.01
135 3 0.01
137 1 0.00
138 5 0.01
139 1 0.00
143 1 0.00
144 5 0.01
145 81 0.17
146 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (123 bp):
AAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATC
TTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTG
Found at i:21752017 original size:268 final size:267
Alignment explanation
Indices: 21751612--21752239 Score: 879
Period size: 268 Copynumber: 2.3 Consensus size: 267
21751602 ATGAAGCGAT
* * * * *
21751612 CATCTTCTTGATAAGATACAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCCGATGAGAT
1 CATCTTCTTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGAT
* *
21751677 ACAGAGAAGTGGACCAAAAATAATGAAGCAGAGCTCAACATCCCTGAAGTTACAGTGGAGTAAAG
66 ACAGAGAAGTGGACC-AAAATAATGAAGCAGAGCTCAACATCCCTGAAGTTACAGTAGAGTAAAC
* * *
21751742 TAAACTTCAAACCCCTATCTTCCTGATGAGAAATAGAG-AGATGGATCAAAACAATGAAGCTG-T
130 TAAACTTCAAACCCCCATCTTCCAGATGAGAAACAGAGAAG-TGGATCAAAACAATGAAGC-GAT
* * * * * *
21751805 CATCTTCCTGATGAGATATAAAGAAG-TGAACCAAAACAATGAAGCGAAGCTCAATGTGAGAGAA
193 CATCTTCCTGATGAGATACAAAGAAGTTG-ACAAAAACAATAAAGAGAAGCTCAATCTAAGAGAA
*
21751869 ACTTCAAACTC
257 ACTTCAAACCC
* * * *
21751880 CATCTTCTTGATGAGTTATAGAGAAATAGATCAAAACAATGAAGCGGTCATCTTCTTGATGAGAT
1 CATCTTCTTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGAT
* * *
21751945 ACAGAGAAAG-GGATCAAAATAATGAAGCAGAGCTCAACAT-CCTTAAGGTTACAGTAGAGTAGA
66 ACAGAG-AAGTGGACCAAAATAATGAAGCAGAGCTCAACATCCCTGAA-GTTACAGTAGAGTAAA
*
21752008 CTGAAACTTCAAACCCCCATCTTCCAGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGAT
129 CT-AAACTTCAAACCCCCATCTTCCAGATGAGAAACAGAGAAGTGGATCAAAACAATGAAGCGAT
*
21752073 CATCTTCCTGATGAGATACAAAGAAGTTGACAAAAACAATAAAGAGAAGCTCAATCTAAGTGAAA
193 CATCTTCCTGATGAGATACAAAGAAGTTGACAAAAACAATAAAGAGAAGCTCAATCTAAGAGAAA
21752138 CTTCAAACCC
258 CTTCAAACCC
* * * *
21752148 CATCTTCCTAATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGATCATCTTCCTAATGAGAT
1 CATCTTCTTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGAT
*
21752213 ACAGAGAAGTGGACCAAAACAATGAAG
66 ACAGAGAAGTGGACCAAAATAATGAAG
21752240 TGAAGCTCAA
Statistics
Matches: 317, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
266 5 0.02
267 44 0.14
268 261 0.82
269 7 0.02
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (267 bp):
CATCTTCTTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGAT
ACAGAGAAGTGGACCAAAATAATGAAGCAGAGCTCAACATCCCTGAAGTTACAGTAGAGTAAACT
AAACTTCAAACCCCCATCTTCCAGATGAGAAACAGAGAAGTGGATCAAAACAATGAAGCGATCAT
CTTCCTGATGAGATACAAAGAAGTTGACAAAAACAATAAAGAGAAGCTCAATCTAAGAGAAACTT
CAAACCC
Found at i:21752086 original size:48 final size:48
Alignment explanation
Indices: 21751880--21752112 Score: 145
Period size: 48 Copynumber: 4.8 Consensus size: 48
21751870 CTTCAAACTC
* * * * *
21751880 CATCTTCTTGATGAGTTATAGAGAAATAGATCAAAACAATGAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTAGATCAAAACAATGAAGCGAT
* * *
21751928 CATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAATAATGAAGCAGAGCT
1 CATCTTCCTGATGAGATACAGAG-AAGTAGATCAAAACAATGAAGC-GA--T
* * * * * * * * * ***
21751979 CAACATCCTTAAG-GTTACAGTAG-AGTAGA-CTGAAAC-TTCAAACCCC
1 CATCTTCCTGATGAGATACAG-AGAAGTAGATC-AAAACAATGAAGCGAT
* *
21752025 CATCTTCCAGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGAT
1 CATCTTCCTGATGAGATACAGAGAAGTAGATCAAAACAATGAAGCGAT
* *
21752073 CATCTTCCTGATGAGATACAAAGAAGTTGA-CAAAAACAAT
1 CATCTTCCTGATGAGATACAGAGAAGTAGATC-AAAACAAT
21752113 AAAGAGAAGC
Statistics
Matches: 135, Mismatches: 38, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
46 10 0.07
47 16 0.12
48 77 0.57
49 10 0.07
50 11 0.08
51 11 0.08
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGATCAAAACAATGAAGCGAT
Found at i:21752202 original size:48 final size:48
Alignment explanation
Indices: 21752148--21752239 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
21752138 CTTCAAACCC
* *
21752148 CATCTTCCTAATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGAT
1 CATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAT
21752196 CATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAG
1 CATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAG
21752240 TGAAGCTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (48 bp):
CATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAT
Found at i:21752360 original size:48 final size:48
Alignment explanation
Indices: 21752270--21752361 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
21752260 ACTTCAAATT
* * * *
21752270 TCATCTTTCTGATGAGATATAGAGAAGTGGATCATAACAATGAAGCGG
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGG
* *
21752318 TCATCTTCCTTATGAGATACAGAGAAGTGGACCAAAATAATGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAA
21752362 ACGAAGCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (48 bp):
TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGG
Found at i:21754105 original size:30 final size:30
Alignment explanation
Indices: 21754071--21754134 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
21754061 AAAAATGGTA
*
21754071 TTTTGACCCTCGAACTTTTC-AAAAATTATG
1 TTTTGA-CCTCGAAATTTTCTAAAAATTATG
**
21754101 TTTTGACCTTTAAATTTTCTAAAAATTATG
1 TTTTGACCTCGAAATTTTCTAAAAATTATG
21754131 TTTT
1 TTTT
21754135 AACACTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTTGACCTCGAAATTTTCTAAAAATTATG
Found at i:21754144 original size:30 final size:29
Alignment explanation
Indices: 21754086--21754156 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
21754076 ACCCTCGAAC
*
21754086 TTTTCAAAAATTATGTTTTGACCTTTAAA
1 TTTTCAAAAATTATGTTTTAACCTTTAAA
21754115 TTTTCTAAAAATTATGTTTTAACAC-TTAAA
1 TTTTC-AAAAATTATGTTTTAAC-CTTTAAA
*
21754145 TTTTCCAAAATT
1 TTTTCAAAAATT
21754157 TATACTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 11 0.29
30 26 0.68
31 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTTCAAAAATTATGTTTTAACCTTTAAA
Found at i:21754166 original size:30 final size:30
Alignment explanation
Indices: 21754110--21754187 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
21754100 GTTTTGACCT
* **
21754110 TTAAATTTTCTAAAAATTATGTTTTAACAC
1 TTAAATTTTCCAAAAATTATACTTTAACAC
* *
21754140 TTAAATTTTCCAAAATTTATACTTTAACCC
1 TTAAATTTTCCAAAAATTATACTTTAACAC
** *
21754170 CCAAACTTTCCAAAAATT
1 TTAAATTTTCCAAAAATT
21754188 TGAGTTTAGC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAATTTTCCAAAAATTATACTTTAACAC
Found at i:21756914 original size:20 final size:21
Alignment explanation
Indices: 21756891--21756930 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21756881 AATTAAACCT
*
21756891 AGCA-TCACTGAGTTAAAAAA
1 AGCAGTCACTAAGTTAAAAAA
*
21756911 AGCAGTTACTAAGTTAAAAA
1 AGCAGTCACTAAGTTAAAAA
21756931 TGCTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (21 bp):
AGCAGTCACTAAGTTAAAAAA
Found at i:21756948 original size:13 final size:13
Alignment explanation
Indices: 21756930--21756954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21756920 TAAGTTAAAA
21756930 ATGCTAAAAATGC
1 ATGCTAAAAATGC
21756943 ATGCTAAAAATG
1 ATGCTAAAAATG
21756955 ATAAAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:21757300 original size:11 final size:11
Alignment explanation
Indices: 21757284--21757332 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
21757274 AATATAAATA
21757284 TTTTTTTCTTT
1 TTTTTTTCTTT
21757295 TTTTTTTC--T
1 TTTTTTTCTTT
21757304 TTTTTTTCTTT
1 TTTTTTTCTTT
* *
21757315 TCTTCTTCTTT
1 TTTTTTTCTTT
21757326 TTTTTTT
1 TTTTTTT
21757333 ATAAATGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 9 0.28
11 23 0.72
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:21757309 original size:20 final size:20
Alignment explanation
Indices: 21757284--21757330 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21757274 AATATAAATA
* *
21757284 TTTTTTTCTTTTTTTTTTCT
1 TTTTTTTCTTTTCTTCTTCT
21757304 TTTTTTTCTTTTCTTCTTCT
1 TTTTTTTCTTTTCTTCTTCT
21757324 TTTTTTT
1 TTTTTTT
21757331 TTATAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTTTTTCTTTTCTTCTTCT
Found at i:21758415 original size:16 final size:18
Alignment explanation
Indices: 21758389--21758430 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21758379 CAGTAGGTTC
21758389 TTTCTTTCCTCCT-TC-TT
1 TTTC-TTCCTCCTCTCATT
21758406 TTTCTTCCTCCTCTCATT
1 TTTCTTCCTCCTCTCATT
21758424 TTTCTTC
1 TTTCTTC
21758431 TTTTTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 9 0.39
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCTTCCTCCTCTCATT
Found at i:21779842 original size:2 final size:2
Alignment explanation
Indices: 21779835--21779867 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21779825 ATTTTAATAA
21779835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21779868 CATAAAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21782023 original size:22 final size:22
Alignment explanation
Indices: 21781998--21782047 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
21781988 TAAAAATAAC
21781998 TTTAGTAAATAGTAA-AT-TTGAT
1 TTTAGTAAATA--AATATATTGAT
*
21782020 TTTA-TAAGTAAATATATTGAT
1 TTTAGTAAATAAATATATTGAT
21782041 TTTAGTA
1 TTTAGTA
21782048 TAATGGAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 14 0.58
22 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (22 bp):
TTTAGTAAATAAATATATTGAT
Found at i:21784951 original size:2 final size:2
Alignment explanation
Indices: 21784944--21784974 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21784934 ATTCTAAGAA
21784944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21784975 CATAAAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21794366 original size:52 final size:52
Alignment explanation
Indices: 21794303--21794574 Score: 400
Period size: 52 Copynumber: 5.2 Consensus size: 52
21794293 TGATAACACG
* * **
21794303 GTCATCAGACCTCACAATCCGTAAAATATTCATATACTCACGATGACACATA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
* * **
21794355 GTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCAAGATGACAGGTA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
* * * * *
21794407 GTCATTGGATCTCAAAATTCGTAAAGGATTCATATACTCACGATGACACGTA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
* *
21794459 GTCATCTGACCTCATAATCTGTAAAGGATTCATATACTCACGATGACACATA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
*
21794511 GTCATCGGACGTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
21794563 GTCATCGGACCT
1 GTCATCGGACCT
21794575 TTTACATTTA
Statistics
Matches: 194, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 194 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (52 bp):
GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATA
Found at i:21797711 original size:21 final size:21
Alignment explanation
Indices: 21797687--21797759 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
21797677 TAAACCCCAA
21797687 CTTAAACCTTAAATCCCGAAC
1 CTTAAACCTTAAATCCCGAAC
*
21797708 CTTAAACTTTAAATCCCGAAC
1 CTTAAACCTTAAATCCCGAAC
* * *
21797729 CTCAAACCATGAAAT-CCAAAC
1 CTTAAACC-TTAAATCCCGAAC
*
21797750 CATAAACCTT
1 CTTAAACCTT
21797760 GAACTCAAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
20 1 0.02
21 37 0.86
22 5 0.12
ACGTcount: A:0.41, C:0.32, G:0.04, T:0.23
Consensus pattern (21 bp):
CTTAAACCTTAAATCCCGAAC
Found at i:21797802 original size:20 final size:20
Alignment explanation
Indices: 21797745--21797803 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
21797735 CCATGAAATC
* *
21797745 CAAACCATAAACCTTGAACT
1 CAAACCCTAAACCTTGAATT
*
21797765 CAAACTCC-AAA-TTTGAATT
1 CAAAC-CCTAAACCTTGAATT
*
21797784 CGAACCCTAAACCTTGAATT
1 CAAACCCTAAACCTTGAATT
21797804 TTAAGGTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 15 0.48
21 1 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (20 bp):
CAAACCCTAAACCTTGAATT
Found at i:21800248 original size:24 final size:24
Alignment explanation
Indices: 21800211--21800256 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
21800201 TTTTATTTTA
21800211 TATTATAATATTTA-ATTTAATTGT
1 TATTATAATATTTATA-TTAATTGT
* *
21800235 TATTATTATTTTTATATTAATT
1 TATTATAATATTTATATTAATT
21800257 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTATAATATTTATATTAATTGT
Found at i:21803067 original size:21 final size:20
Alignment explanation
Indices: 21803042--21803083 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
21803032 ATTATTTTTC
21803042 ATATAAAAACAAATTTTAAAA
1 ATAT-AAAACAAATTTTAAAA
*
21803063 ATATAATACAAATTTTAAAA
1 ATATAAAACAAATTTTAAAA
21803083 A
1 A
21803084 ATACACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATAAAACAAATTTTAAAA
Found at i:21806586 original size:38 final size:38
Alignment explanation
Indices: 21806537--21806610 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
21806527 CTCCCTTAAA
21806537 AAATTTCGTCCTCGAAATTTTTACTTAGCAATACCTTT
1 AAATTTCGTCCTCGAAATTTTTACTTAGCAATACCTTT
21806575 AAATTTCGTCCTCGAAATTTTTACTTAGCAATACCT
1 AAATTTCGTCCTCGAAATTTTTACTTAGCAATACCT
21806611 CGAAATTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (38 bp):
AAATTTCGTCCTCGAAATTTTTACTTAGCAATACCTTT
Found at i:21807481 original size:11 final size:10
Alignment explanation
Indices: 21807473--21807557 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 10
21807463 TAAAATTAGG
21807473 TTTAAATTAA
1 TTTAAATTAA
21807483 TTTAAATTAA
1 TTTAAATTAA
21807493 TTTTAAATTTAAA
1 -TTTAAA-TT-AA
* *
21807506 TTTATCATAAA
1 TTTA-AATTAA
**
21807517 TTTATTTTAAA
1 TTTAAATT-AA
*
21807528 TTTAAATTTA
1 TTTAAATTAA
*
21807538 TCTTAAATTTAT
1 T-TTAAA-TTAA
21807550 TTTAAATT
1 TTTAAATT
21807558 TAAATTTATC
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
10 15 0.26
11 30 0.52
12 10 0.17
13 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTAAATTAA
Found at i:21807491 original size:21 final size:23
Alignment explanation
Indices: 21807456--21807501 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
21807446 GATTAAGCTT
*
21807456 TTAATTTTAAAATTAGGTTTAAA
1 TTAATTTTAAAATTAAGTTTAAA
*
21807479 TTAA-TTT-AAATTAATTTTAAA
1 TTAATTTTAAAATTAAGTTTAAA
21807500 TT
1 TT
21807502 TAAATTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAATTTTAAAATTAAGTTTAAA
Found at i:21807501 original size:17 final size:17
Alignment explanation
Indices: 21807481--21807621 Score: 70
Period size: 17 Copynumber: 7.9 Consensus size: 17
21807471 GGTTTAAATT
21807481 AATTTAAATTAATTTTA
1 AATTTAAATTAATTTTA
* **
21807498 AATTTAAATTTATCATA
1 AATTTAAATTAATTTTA
** *
21807515 AATTTATTTTAAATTTAA
1 AATTTAAATT-AATTTTA
*
21807533 ATTTATCTTAAATTTATTTTA
1 A---AT-TTAAATTAATTTTA
*
21807554 AATTTAAATTTATCCTTTTA
1 AATTTAAA-TTA--ATTTTA
***
21807574 AATTTAAATTTGCTTTA
1 AATTTAAATTAATTTTA
*
21807591 AATTTGAATTTAA--TTA
1 AATTT-AAATTAATTTTA
*
21807607 AATTTAAATTGATTT
1 AATTTAAATTAATTT
21807622 AAAAACTTGA
Statistics
Matches: 90, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
15 5 0.06
16 8 0.09
17 37 0.41
18 12 0.13
19 2 0.02
20 13 0.14
21 8 0.09
22 5 0.06
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTAAATTAATTTTA
Found at i:21807523 original size:28 final size:28
Alignment explanation
Indices: 21807485--21807567 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
21807475 TAAATTAATT
*
21807485 TAAATTAATTTTAAATTTAAATTTATCA
1 TAAATTTATTTTAAATTTAAATTTATCA
*
21807513 TAAATTTATTTTAAATTTAAATTTATCT
1 TAAATTTATTTTAAATTTAAATTTATCA
21807541 TAAATTTATTTTAAATTTAAATTTATC
1 TAAATTTATTTTAAATTTAAATTTATC
21807568 CTTTTAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (28 bp):
TAAATTTATTTTAAATTTAAATTTATCA
Found at i:21807558 original size:11 final size:11
Alignment explanation
Indices: 21807500--21807559 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
21807490 TAATTTTAAA
21807500 TTTAAATTTAT
1 TTTAAATTTAT
**
21807511 CATAAATTTAT
1 TTTAAATTTAT
21807522 TTT-AA---A-
1 TTTAAATTTAT
21807528 TTTAAATTTAT
1 TTTAAATTTAT
*
21807539 CTTAAATTTAT
1 TTTAAATTTAT
21807550 TTTAAATTTA
1 TTTAAATTTA
21807560 AATTTATCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
10 3 0.08
11 29 0.76
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:21807579 original size:6 final size:6
Alignment explanation
Indices: 21807473--21807616 Score: 87
Period size: 6 Copynumber: 25.3 Consensus size: 6
21807463 TAAAATTAGG
* *
21807473 TTTAAA -TT-AA TTTAAA -TTAAT TTTAAA TTTAAA TTT--A TCATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
* *
21807517 TTT-AT TTTAAA TTTAAA TTT--A TCTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
** ** *
21807562 TTTATCCT TTTAAA TTTAAA TTT-GC TTTAAA TTTGAA TTT-AA -TTAAA
1 TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
21807609 TTTAAA TT
1 TTTAAA TT
21807617 GATTTAAAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
4 8 0.08
5 26 0.25
6 63 0.60
7 4 0.04
8 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:21807592 original size:48 final size:47
Alignment explanation
Indices: 21807481--21807612 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 47
21807471 GGTTTAAATT
* * *
21807481 AATTTAAATTAATTTTAAATTTAAATTT-ATCATAAATTTA---TTTTA
1 AATTTAAATTTATCTTAAATTTGAATTTAAT--TAAATTTATCCTTTTA
*
21807526 AATTTAAATTTATCTTAAATTT-ATTTTAAATTTAAATTTATCCTTTTA
1 AATTTAAATTTATCTTAAATTTGAATTT-AA-TTAAATTTATCCTTTTA
*
21807574 AATTTAAATTT-GCTTTAAATTTGAATTTAATTAAATTTA
1 AATTTAAATTTATC-TTAAATTTGAATTTAATTAAATTTA
21807613 AATTGATTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
44 4 0.05
45 28 0.38
46 1 0.01
47 11 0.15
48 26 0.35
49 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (47 bp):
AATTTAAATTTATCTTAAATTTGAATTTAATTAAATTTATCCTTTTA
Found at i:21807621 original size:10 final size:11
Alignment explanation
Indices: 21807575--21807624 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
21807565 ATCCTTTTAA
21807575 ATTTAAATTTG
1 ATTTAAATTTG
*
21807586 CTTTAAATTTG
1 ATTTAAATTTG
**
21807597 AATTT-AATTAA
1 -ATTTAAATTTG
21807608 ATTTAAA-TTG
1 ATTTAAATTTG
21807618 ATTTAAA
1 ATTTAAA
21807625 AACTTGATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
10 12 0.39
11 16 0.52
12 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (11 bp):
ATTTAAATTTG
Found at i:21808517 original size:59 final size:60
Alignment explanation
Indices: 21808453--21808591 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 60
21808443 TAATTTCACC
* *
21808453 AAAAATTACCATTTTACCCCAGGATG-TCCAAAAATTTTATTTTTTGATCCCGA-TATTTCT
1 AAAAATTACCATTTTACCCCAGAATGCT-CAAAAATTTCA-TTTTTGATCCCGATTATTTCT
** * *
21808513 -AAAATTACCATTTTACCCTTGAATGCTTAAAAATTTCATTTTTGATCCCGATTTTTTCT
1 AAAAATTACCATTTTACCCCAGAATGCTCAAAAATTTCATTTTTGATCCCGATTATTTCT
* *
21808572 AAAAATTATCGTTTTACCCC
1 AAAAATTACCATTTTACCCC
21808592 TCGAGAGTCC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
58 13 0.19
59 37 0.55
60 17 0.25
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCCAGAATGCTCAAAAATTTCATTTTTGATCCCGATTATTTCT
Found at i:21818026 original size:42 final size:42
Alignment explanation
Indices: 21817948--21818671 Score: 896
Period size: 42 Copynumber: 17.2 Consensus size: 42
21817938 GAATCAATTG
* * **
21817948 ATGTATAAATGGAAGACTCGTGTCTCAGGACAAGCATGAGATT
1 ATGTTTAAA-GGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
21817991 ATGTTTAAAGGAAGACTCATGTATCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * *
21818033 ATGGTTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * *
21818075 ATGTTTAAAGAAAGACTCGTGACTCGAGATTAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
21818117 ATGTTTAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
** * *
21818159 ATGTTTAAAAAAAAGACCCGTGTCTTGGGATGAGCATGAGATT
1 ATGTTT-AAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
** * *
21818202 ATGTTTAAAAAAAAAGACCCGTGTCTTGGGATGAGCATGAGATT
1 ATGTTT--AAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
*
21818246 ATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * *
21818288 AGGTTTAAAGGAAGACTCCTGTCTCGAGATGAGCATGGGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * *
21818330 ATGTTTAAAGGAAGACTCGTGACTTGGGATGAGCAAGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
21818372 ATGTTTAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * *
21818414 ATGTTTAAAGAAAGACTCGTGTCTCAGGATGAGCATAAAATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * *
21818456 ATGTTTAATGGAAGACTCATGTCTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
** *
21818498 ATGTTTAAAGGAAGACTCGTAACTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * ** **
21818540 ATGTTTGAAGGAAGACTCGTGACTTAGGATGAGTGTGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
*
21818582 ATGGTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
** * * *
21818624 ATG-TTAAAGGAAGACTTATGTCTCAGTA-GAGCATAAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
21818664 -TGTTTAAA
1 ATGTTTAAA
21818672 AAGGAAGGCT
Statistics
Matches: 604, Mismatches: 74, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
39 2 0.00
40 16 0.03
41 21 0.03
42 478 0.79
43 44 0.07
44 43 0.07
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.28
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
Found at i:21821812 original size:36 final size:36
Alignment explanation
Indices: 21821765--21821860 Score: 147
Period size: 36 Copynumber: 2.7 Consensus size: 36
21821755 TAACAGGCAT
21821765 GACCTTTAGGTCAACAGGGAGTAAAATGAACATCAC
1 GACCTTTAGGTCAACAGGGAGTAAAATGAACATCAC
* * *
21821801 GACCTTTAGGTCAACAGGGAGTGAAATGAGCATCAT
1 GACCTTTAGGTCAACAGGGAGTAAAATGAACATCAC
* *
21821837 GACCTTTAGGTCAATAAGGAGTAA
1 GACCTTTAGGTCAACAGGGAGTAA
21821861 GCATGACCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (36 bp):
GACCTTTAGGTCAACAGGGAGTAAAATGAACATCAC
Found at i:21821876 original size:28 final size:28
Alignment explanation
Indices: 21821834--21821888 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
21821824 AAATGAGCAT
*
21821834 CATGACCTTTAGGTCAATAAGGAGTAAG
1 CATGACCTTTAGGTCAACAAGGAGTAAG
* *
21821862 CATGACCTTTGGGTCAACAGGGAGTAA
1 CATGACCTTTAGGTCAACAAGGAGTAA
21821889 ATCGGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (28 bp):
CATGACCTTTAGGTCAACAAGGAGTAAG
Found at i:21826201 original size:8 final size:8
Alignment explanation
Indices: 21826184--21826217 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
21826174 AAATTTATGT
*
21826184 TTAATGTA
1 TTAATATA
21826192 TTAATATA
1 TTAATATA
21826200 TTAATATA
1 TTAATATA
*
21826208 TTAATTTA
1 TTAATATA
21826216 TT
1 TT
21826218 TTAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (8 bp):
TTAATATA
Found at i:21828657 original size:142 final size:142
Alignment explanation
Indices: 21828235--21828708 Score: 598
Period size: 144 Copynumber: 3.3 Consensus size: 142
21828225 TGGTTAAAAC
* * *
21828235 AAAATTACTATTTTACCTT-AAAA-TCAAAACTTTTATTTCGAAATAGCTAAAAAAAATCAAAAC
1 AAAATCACTATTTTA-CTTAAAAATTC-AAACTTTTATTTCAAAATAG-TTAAAAAAATCAAAAC
* * * * *
21828298 TTTAATTAAAAATTTAAACTTTTTCTTTAAAATCATTAAAAATAAATTTTTATTTTTAAAAATCT
63 TTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAA-AAA-TATT-TTTTT-AAAATAT
**
21828363 AAACTTTCTCTTTTTAAAAAA
124 AAACTTTCTCTTTTT--TTAA
* * * *
21828384 AAAATTACTATTTTACTTAAAAATACAAACTTTTATTTCAAAACAGTT-AAAAAATAAAAACTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTT
* * *
21828448 ATTTAAAAATTTAAACTTTTTCCTTAAAATAACT-AAAAATATATTTTTTAAAAAAATATAAACT
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAAATATTTTTT--TAAAATATAAACT
21828512 TTCTCTTTTTTTAA
129 TTCTCTTTTTTTAA
* *
21828526 AAAATCACCATATTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTT
* *
21828591 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTTAAAATATAAATTTT
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAAATATTTTTTTAAAATATAAACTTT
21828656 CTCTTTTTTTAAA
131 CTCTTTTTTT-AA
21828669 GAAAATCACTATTTTACTTAAAAA-TCAAAACTTTTATTTC
1 -AAAATCACTATTTTACTTAAAAATTC-AAACTTTTATTTC
21828709 GAATTTTTTT
Statistics
Matches: 289, Mismatches: 27, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
142 68 0.24
143 56 0.19
144 72 0.25
145 2 0.01
146 4 0.01
147 45 0.16
148 4 0.01
149 37 0.13
150 1 0.00
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (142 bp):
AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTT
ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAAATATTTTTTTAAAATATAAACTTT
CTCTTTTTTTAA
Found at i:21829164 original size:3 final size:3
Alignment explanation
Indices: 21829156--21829184 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21829146 TGAAACCCTA
21829156 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
21829185 AATAATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:21830166 original size:28 final size:29
Alignment explanation
Indices: 21830105--21830177 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
21830095 ATTTGGCCTT
* *
21830105 TTTATTAATATAATATAAATAAAAAATTA
1 TTTACTAAAATAATATAAATAAAAAATTA
* *
21830134 ATTACTAAAATAATATAGAT-AAAAATTA
1 TTTACTAAAATAATATAAATAAAAAATTA
*
21830162 TTTACCAAAATAATAT
1 TTTACTAAAATAATAT
21830178 GTTTTGAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (29 bp):
TTTACTAAAATAATATAAATAAAAAATTA
Found at i:21834714 original size:25 final size:25
Alignment explanation
Indices: 21834680--21834749 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
21834670 ACACGTCAGG
21834680 AAAGAAAAGCCTTTGTGGCGAAATC
1 AAAGAAAAGCCTTTGTGGCGAAATC
* *
21834705 AAAGAAAAGCCTTTGTGCCTAAATC
1 AAAGAAAAGCCTTTGTGGCGAAATC
21834730 AAAGAAAAGCCTTTGTGGCG
1 AAAGAAAAGCCTTTGTGGCG
21834750 TTACACGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (25 bp):
AAAGAAAAGCCTTTGTGGCGAAATC
Found at i:21835705 original size:18 final size:19
Alignment explanation
Indices: 21835682--21835720 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21835672 TCATTTGTTT
21835682 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTGTA
21835700 TTATTAAATTTAAATTGTA
1 TTATTAAATTTAAATTGTA
21835719 TT
1 TT
21835721 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTGTA
Found at i:21839828 original size:44 final size:44
Alignment explanation
Indices: 21839772--21839859 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
21839762 AAAACCCAAC
21839772 CTAGTTGACTGGAGATACCAAGATCTAGGTTCAAAGGCCAACTT
1 CTAGTTGACTGGAGATACCAAGATCTAGGTTCAAAGGCCAACTT
21839816 CTAGTTGACTGGAGATACCAAGATCTAGGTTCAAAGGCCAACTT
1 CTAGTTGACTGGAGATACCAAGATCTAGGTTCAAAGGCCAACTT
21839860 ACTTGCATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
CTAGTTGACTGGAGATACCAAGATCTAGGTTCAAAGGCCAACTT
Found at i:21841234 original size:18 final size:19
Alignment explanation
Indices: 21841211--21841249 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21841201 TCATTTGTTT
21841211 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTGTA
21841229 TTATTAAATTTAAATTGTA
1 TTATTAAATTTAAATTGTA
21841248 TT
1 TT
21841250 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTGTA
Found at i:21843410 original size:28 final size:28
Alignment explanation
Indices: 21843367--21843572 Score: 191
Period size: 28 Copynumber: 7.4 Consensus size: 28
21843357 TTAGCATTTC
*
21843367 GGTGCTTACTGCTACGTGATTGCACTTT
1 GGTGCTTACTGTTACGTGATTGCACTTT
* *
21843395 GGTGCTTACTGTTACGTGATTACACTTC
1 GGTGCTTACTGTTACGTGATTGCACTTT
* * * *
21843423 GATGCTTATTGATACGTGAATGCACTTT
1 GGTGCTTACTGTTACGTGATTGCACTTT
* * *
21843451 AGTGCTTATTGTTACGTGATTGCACTTG
1 GGTGCTTACTGTTACGTGATTGCACTTT
* * ** *
21843479 GGTGCTTATTGCTACGCAAATGCACTTT
1 GGTGCTTACTGTTACGTGATTGCACTTT
* *
21843507 GGTGCTTA-TCATTACGTGATTGCACTTC
1 GGTGCTTACT-GTTACGTGATTGCACTTT
** * *
21843535 GGTGCTTACT-TCTACGCAAATGTACTTT
1 GGTGCTTACTGT-TACGTGATTGCACTTT
21843563 GGTGCTTACT
1 GGTGCTTACT
21843573 AATTAGCACT
Statistics
Matches: 144, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
27 2 0.01
28 141 0.98
29 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (28 bp):
GGTGCTTACTGTTACGTGATTGCACTTT
Found at i:21843440 original size:56 final size:55
Alignment explanation
Indices: 21843364--21843570 Score: 254
Period size: 56 Copynumber: 3.7 Consensus size: 55
21843354 AAATTAGCAT
* * *
21843364 TTCGGTGCTTACTGCTACGTGATTGCACTTTGGTGCTTACTGTTACGTGATTACAC
1 TTCGGTGCTTATTGCTACGTGAATGCACTTTGGTGCTTA-TGTTACGTGATTGCAC
* * *
21843420 TTCGATGCTTATTGATACGTGAATGCACTTTAGTGCTTATTGTTACGTGATTGCAC
1 TTCGGTGCTTATTGCTACGTGAATGCACTTTGGTGCTTA-TGTTACGTGATTGCAC
* ** *
21843476 TTGGGTGCTTATTGCTACGCAAATGCACTTTGGTGCTTATCATTACGTGATTGCAC
1 TTCGGTGCTTATTGCTACGTGAATGCACTTTGGTGCTTAT-GTTACGTGATTGCAC
** *
21843532 TTCGGTGCTTACTT-CTACGCAAATGTACTTTGGTGCTTA
1 TTCGGTGCTTA-TTGCTACGTGAATGCACTTTGGTGCTTA
21843571 CTAATTAGCA
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
55 1 0.01
56 130 0.98
57 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (55 bp):
TTCGGTGCTTATTGCTACGTGAATGCACTTTGGTGCTTATGTTACGTGATTGCAC
Found at i:21843586 original size:22 final size:22
Alignment explanation
Indices: 21843558--21843612 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
21843548 ACGCAAATGT
21843558 ACTTTGGTGCTTACTAAT-TAGC
1 ACTTTGGTGCTTA-TAATCTAGC
* **
21843580 ACTTTGGTACTTATTGTCTAGC
1 ACTTTGGTGCTTATAATCTAGC
21843602 ACTTTGGTGCT
1 ACTTTGGTGCT
21843613 CTTTGTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (22 bp):
ACTTTGGTGCTTATAATCTAGC
Found at i:21844668 original size:24 final size:24
Alignment explanation
Indices: 21844641--21844687 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21844631 TATTTTTTAT
21844641 AATTTTATATATTTTTA-AAATATA
1 AATTTTA-ATATTTTTATAAATATA
*
21844665 AATTTTAATTTTTTTATAAATAT
1 AATTTTAATATTTTTATAAATAT
21844688 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTTAATATTTTTATAAATATA
Found at i:21844715 original size:18 final size:18
Alignment explanation
Indices: 21844675--21844715 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21844665 AATTTTAATT
21844675 TTTTTATAAATATTTTGA
1 TTTTTATAAATATTTTGA
*
21844693 ATTTTA-AAATTATTTTGA
1 TTTTTATAAA-TATTTTGA
21844711 TTTTT
1 TTTTT
21844716 TTTTTGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTTATAAATATTTTGA
Found at i:21846037 original size:28 final size:29
Alignment explanation
Indices: 21845996--21846050 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
21845986 GCATCACATT
*
21845996 AAAAATAAACATCCATCTAAATATATCAG
1 AAAAATAAACATCCATCTAAAAATATCAG
* *
21846025 AAAAA-AAGCATCCATTTAAAAATATC
1 AAAAATAAACATCCATCTAAAAATATC
21846051 CTAAAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (29 bp):
AAAAATAAACATCCATCTAAAAATATCAG
Found at i:21846056 original size:28 final size:29
Alignment explanation
Indices: 21845995--21846056 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
21845985 CGCATCACAT
*
21845995 TAAAAATAAACATCCATCTAAATATATCA
1 TAAAAATAAACATCCATCTAAAAATATCA
* * * *
21846024 GAAAAA-AAGCATCCATTTAAAAATATCC
1 TAAAAATAAACATCCATCTAAAAATATCA
21846052 TAAAA
1 TAAAA
21846057 CTATGATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.24
Consensus pattern (29 bp):
TAAAAATAAACATCCATCTAAAAATATCA
Found at i:21854584 original size:22 final size:23
Alignment explanation
Indices: 21854550--21854593 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21854540 CTTTTTCTTT
*
21854550 TTTTTTTTCCTTT-TTATCTTCCA
1 TTTTTCTTCCTTTATTAT-TTCCA
21854573 TTTTTCTT-CTTTATTATTTCC
1 TTTTTCTTCCTTTATTATTTCC
21854594 TATCAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTCTTCCTTTATTATTTCCA
Found at i:21859432 original size:57 final size:56
Alignment explanation
Indices: 21859315--21859452 Score: 154
Period size: 57 Copynumber: 2.4 Consensus size: 56
21859305 TGATTCATAT
* * * * *
21859315 TTTAATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTGTA
1 TTTAATAAAAATTATATTAA-AATATGATTAAATTATATATTA-TCTATTAAATTATA
*
21859373 TTTAATAAAAATTATATTAAAATATGATTAAATTATTTATTA-CTATTAAATTTTATA
1 TTTAATAAAAATTATATTAAAATATGATTAAATTATATATTATCTATTAAA--TTATA
*
21859430 TTTAATAACAATCT-TATTAAAAT
1 TTTAATAAAAAT-TATATTAAAAT
21859453 TTAATAACAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
55 7 0.10
57 43 0.61
58 20 0.29
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (56 bp):
TTTAATAAAAATTATATTAAAATATGATTAAATTATATATTATCTATTAAATTATA
Found at i:21864839 original size:24 final size:24
Alignment explanation
Indices: 21864795--21864865 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
21864785 AAATAATCTC
*
21864795 TCAATTAAATTCTGATT-ATTTGTT
1 TCAATTAAATTCT-ATTAATTTATT
21864819 TCAATTAAATTCTATTAATTTATT
1 TCAATTAAATTCTATTAATTTATT
* * *
21864843 TTAATCAAAATTTTATTAATTTA
1 TCAAT-TAAATTCTATTAATTTA
21864866 AATTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
23 3 0.07
24 23 0.56
25 15 0.37
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.54
Consensus pattern (24 bp):
TCAATTAAATTCTATTAATTTATT
Found at i:21866168 original size:15 final size:16
Alignment explanation
Indices: 21866150--21866187 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
21866140 TATATTTTTA
21866150 ATTTATATAAA-ATAT
1 ATTTATATAAATATAT
21866165 ATTTAT-TAAATATAT
1 ATTTATATAAATATAT
21866180 ATTT-TATA
1 ATTTATATA
21866188 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATATAAATATAT
Found at i:21866180 original size:24 final size:24
Alignment explanation
Indices: 21866117--21866181 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 24
21866107 TAATAAGCAC
21866117 TTTAGTTAAATTATATAAAAATATA
1 TTTA-TTAAATTATATAAAAATATA
* *
21866142 TATTTTTAATTTATAT-AAAATATA
1 T-TTATTAAATTATATAAAAATATA
21866166 TTTATTAAATATATAT
1 TTTATTAAAT-TATAT
21866182 TTTATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.21
24 14 0.41
25 11 0.32
26 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATTAAATTATATAAAAATATA
Found at i:21867875 original size:2 final size:2
Alignment explanation
Indices: 21867868--21867897 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21867858 ACTAAAATTA
21867868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21867898 TTAACGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21869655 original size:2 final size:2
Alignment explanation
Indices: 21869648--21869696 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
21869638 TCCTTTCTAT
21869648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
21869690 GA TA TA T
1 TA TA TA T
21869697 TAATATTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21872464 original size:19 final size:19
Alignment explanation
Indices: 21872440--21872478 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21872430 GTACCTACGC
*
21872440 GTTAAAACAAATGCGTTAA
1 GTTAAAACAAACGCGTTAA
21872459 GTTAAAACAAACGCGTTAA
1 GTTAAAACAAACGCGTTAA
21872478 G
1 G
21872479 CCGGTGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (19 bp):
GTTAAAACAAACGCGTTAA
Found at i:21872697 original size:21 final size:21
Alignment explanation
Indices: 21872665--21872720 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 21
21872655 ATAAATGAAA
21872665 TTAACAGAAAGTACCAAAGTAC
1 TTAACAG-AAGTACCAAAGTAC
21872687 TT-ACTAGAAGTACCAAAGTAC
1 TTAAC-AGAAGTACCAAAGTAC
21872708 TTAACAGAAGTAC
1 TTAACAGAAGTAC
21872721 ATAACTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (21 bp):
TTAACAGAAGTACCAAAGTAC
Found at i:21872766 original size:22 final size:22
Alignment explanation
Indices: 21872735--21872789 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
21872725 CTGCTTGGGA
21872735 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
21872757 AATAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
21872779 AACAGAAGCAC
1 AACAGAAGCAC
21872790 GCTAGCGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.25, G:0.22, T:0.09
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:21876305 original size:21 final size:21
Alignment explanation
Indices: 21876273--21876328 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 21
21876263 ATAAATGAAA
21876273 TTAACAGAAAGTACCAAAGTAC
1 TTAACAG-AAGTACCAAAGTAC
21876295 TT-ACTAGAAGTACCAAAGTAC
1 TTAAC-AGAAGTACCAAAGTAC
21876316 TTAACAGAAGTAC
1 TTAACAGAAGTAC
21876329 ATAACTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (21 bp):
TTAACAGAAGTACCAAAGTAC
Done.