Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 90 of 295
Found at i:28418588 original size:10 final size:10
Alignment explanation
Indices: 28418573--28418601 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28418563 ATAAAATTCA
28418573 CATTCAATTT
1 CATTCAATTT
28418583 CATTCAATTT
1 CATTCAATTT
28418593 CATTCAATT
1 CATTCAATT
28418602 CACATCTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (10 bp):
CATTCAATTT
Found at i:28426837 original size:21 final size:20
Alignment explanation
Indices: 28426809--28426847 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28426799 ACCTTAAAAT
*
28426809 AGGGAACACGTCCGTGTGGA
1 AGGGAACACGCCCGTGTGGA
*
28426829 AGGGTAACATGCCCGTGTG
1 AGGG-AACACGCCCGTGTG
28426848 ACCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.23, C:0.21, G:0.38, T:0.18
Consensus pattern (20 bp):
AGGGAACACGCCCGTGTGGA
Found at i:28428010 original size:49 final size:48
Alignment explanation
Indices: 28427952--28428264 Score: 174
Period size: 46 Copynumber: 6.6 Consensus size: 48
28427942 GTAAAGTGTC
* *
28427952 GATGGCATGTCCCAGACATGGTCTCACACTGGCTATCATCTTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGA-GCT
* * * * ** *
28428001 GATGCCATGTCCCAGGCATGGTCTTACACTAGCTCTCA-CATAACCTTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATC-T--TCGAGCT
28428051 GATGCCATGTCCCAGACATGGTCTTACACTGGC-A-CATC-TCGTAGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCG-AGCT
** * * * *
28428097 GATG-CATGTCCCAGACA-CCTATTATACTGGCT-TACGTC-CCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-CATCTTCGA-GCT
*** * *
28428143 GATG-CATGTTTTAGACAT-GTCTTACACTAGC-ACTCATC-TCAATG-T
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTA-TCATCTTCGA-GCT
* * * * *
28428188 CGATGCCATGTCCGAGACATGGTCTTACACTGGGTCTCATAATGT-G-GCC
1 -GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-CT-TCGAGCT
28428237 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
28428265 AGCTCACACA
Statistics
Matches: 201, Mismatches: 43, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
44 10 0.05
45 16 0.08
46 57 0.28
47 25 0.12
48 23 0.11
49 35 0.17
50 33 0.16
51 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGAGCT
Found at i:28428227 original size:48 final size:44
Alignment explanation
Indices: 28428155--28428267 Score: 120
Period size: 48 Copynumber: 2.4 Consensus size: 44
28428145 TGCATGTTTT
*
28428155 AGACATGTCTTACACTAGCACTCATCTCAATGT-CGATGCCATGTCCG
1 AGACATGTCTTACACTAGCACTCA--T-AATGTGCGATG-CATGTCCC
* **
28428202 AGACATGGTCTTACACTGGGTCTCATAATGTGGCCGATGCATGTCCC
1 AGACAT-GTCTTACACTAGCACTCATAATGT-G-CGATGCATGTCCC
28428249 AGACATGTCTTACACTAGC
1 AGACATGTCTTACACTAGC
28428268 TCACACAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
45 5 0.09
46 12 0.21
47 19 0.34
48 20 0.36
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
AGACATGTCTTACACTAGCACTCATAATGTGCGATGCATGTCCC
Found at i:28431937 original size:34 final size:35
Alignment explanation
Indices: 28431849--28431938 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
28431839 CATAATAGCC
* *
28431849 AGTCCAACCAAAACACACCAATGCTCAAAAGGGCT
1 AGTCCAACCAAAACACACCAATACTCAAAAGAGCT
** *
28431884 AGTCCTTCCGAAACACACCAATACTCAAAAGAGCT
1 AGTCCAACCAAAACACACCAATACTCAAAAGAGCT
*
28431919 AGTCC-ACTAAAACACACCAA
1 AGTCCAACCAAAACACACCAA
28431939 ACAAAGAGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 12 0.26
35 35 0.74
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.13
Consensus pattern (35 bp):
AGTCCAACCAAAACACACCAATACTCAAAAGAGCT
Found at i:28433083 original size:46 final size:46
Alignment explanation
Indices: 28433030--28433120 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
28433020 TATATATACA
* * *
28433030 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGACTTTACCACATATC
* * *
28433076 CATCTCATACGCATTTCGCATTAGCCATTCGACTTTACCACATAT
1 CATCTCATACACATCTCACATTAGCCATTCGACTTTACCACATAT
28433121 ATACACTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGACTTTACCACATATC
Found at i:28433163 original size:22 final size:22
Alignment explanation
Indices: 28433137--28433447 Score: 88
Period size: 22 Copynumber: 13.3 Consensus size: 22
28433127 TTCCACGTTC
*
28433137 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGACCTT
*
28433159 ATCACATATGTG-CATGTTC-ACATT
1 ATCACAT-TG-GCCA--TTCGACCTT
28433183 CATCACATTGGCCATTCGACCTT
1 -ATCACATTGGCCATTCGACCTT
*
28433206 ATCACACATAT-G-CATGTTC-ACATTT
1 AT--CACAT-TGGCCA--TTCGAC-CTT
*
28433231 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGACCTT
* *** *
28433253 ATCACACATATTCATGTTC-ACATT
1 ATCACA-TTGGCCA--TTCGACCTT
* *
28433277 CGTCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
*
28433300 ATCACATATGTG-CATGTTC-ACATTT
1 ATCACAT-TG-GCCA--TTCGAC-CTT
*
28433325 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGACCTT
*
28433347 ATCACATATGTG-CATGTTC-ACATT
1 ATCACAT-TG-GCCA--TTCGACCTT
* * *
28433371 CGTCACATTGGACATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
*
28433394 ATCACATATGTG-CATGTTC-ACATT
1 ATCACAT-TG-GCCA--TTCGACCTT
* *
28433418 CGTCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
28433441 ATCACAT
1 ATCACAT
28433448 ATGTGCATGT
Statistics
Matches: 211, Mismatches: 36, Indels: 84
0.64 0.11 0.25
Matches are distributed among these distances:
22 63 0.30
23 46 0.22
24 46 0.22
25 56 0.27
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:28433165 original size:47 final size:47
Alignment explanation
Indices: 28433134--28433520 Score: 648
Period size: 47 Copynumber: 8.2 Consensus size: 47
28433124 CACTTCCACG
28433134 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* * *
28433181 TTCATCACATTGGCCATTCGACCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* * * *
28433228 TTTATCACATTGGCCATTCGGCCTTATCACACATATTCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28433275 TTCGTCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28433322 TTTATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* *
28433369 TTCGTCACATTGGACATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
*
28433416 TTCGTCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
* *
28433463 TTCGTCACATTGGTCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
28433510 TTCATCACATT
1 TTCATCACATT
28433521 AAATCCTAAA
Statistics
Matches: 321, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 321 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
Found at i:28441670 original size:49 final size:49
Alignment explanation
Indices: 28441581--28441803 Score: 223
Period size: 49 Copynumber: 4.5 Consensus size: 49
28441571 TCTATTGTGA
* * *
28441581 GGTCACGTGTGTAGTACTAAGTGTAGGATACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* ** * *
28441630 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTGTGCGTACCCGATAACTTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA--TT
* * * * * **
28441681 GATCACGTGTGTAGTACTAAGTTCAGGCTACTACGTGTATC-AAGTGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGA-TAATT
* * * *
28441730 AGGTCACGTGTGTAGTACTAAGTGCAAGCCACTACGTGTACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
*
28441780 GGTCGCATGTGTAGTACTAAGTGC
1 GGTCACATGTGTAGTACTAAGTGC
28441804 GGACGACTAT
Statistics
Matches: 139, Mismatches: 30, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
49 63 0.45
50 39 0.28
51 37 0.27
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:28459407 original size:54 final size:55
Alignment explanation
Indices: 28459326--28459598 Score: 132
Period size: 61 Copynumber: 4.7 Consensus size: 55
28459316 ATTATTTTTG
* *
28459326 TGTTTCTTTTTTTCCATTTGTTTTTTTTTTTTTGGTTTTTTTTTTGTT-TTGATTGTA
1 TGTTT-TTTTTTTTC-TTT-TTATTTTTTTTTTGGTTTTTTTTTTGTTATTGATTGTA
* * *
28459383 TGTTTTTTTTTTTCTTTTTATTTTTTGTTAATGTATTTTTTTTCATTGTTTATTGATT-TT
1 TGTTTTTTTTTTTCTTTTTATTTTTT-TT-TTG-GTTTTTTTT--TTG-TTATTGATTGTA
** * *
28459443 TGTTTCTTTGCTTTATTGTTGTATCCTTCTTCTTTTT--TTTTTATATTTTATTATTGACTTGT-
1 TGTTT-TTTTTTTTCTT-TT-TAT--TT-TT-TTTTTGGTTTTT-T-TTTTGTTATTGA-TTGTA
* * * *
28459505 T-TTTTTTTTTTTCTTTTTATTTTTTTTTT-TTTTTATTTTTTGTGTTTTTATTTTCA
1 TGTTTTTTTTTTTCTTTTTATTTTTTTTTTGGTTTT-TTTTTTGT-TATTGATTGT-A
*
28459561 TGTTCTTTTTCTTTT-TTGTTT-TTTTTTTTTTTGTTTTT
1 TGTT-TTTTT-TTTTCTT-TTTATTTTTTTTTTGGTTTTT
28459599 CAATCTCTTT
Statistics
Matches: 170, Mismatches: 18, Indels: 55
0.70 0.07 0.23
Matches are distributed among these distances:
54 21 0.12
55 16 0.09
56 14 0.08
57 15 0.09
58 21 0.12
59 16 0.09
60 16 0.09
61 24 0.14
62 12 0.07
63 5 0.03
64 2 0.01
65 3 0.02
66 4 0.02
67 1 0.01
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (55 bp):
TGTTTTTTTTTTTCTTTTTATTTTTTTTTTGGTTTTTTTTTTGTTATTGATTGTA
Found at i:28459418 original size:35 final size:36
Alignment explanation
Indices: 28459347--28459425 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
28459337 TTCCATTTGT
* * *
28459347 TTTTTTTTTTTTGGTTTTTTTTTTGTTTTGATTGTA
1 TTTTTTTTTTTTGCTTTTTTTTTTGTGTTGAATGTA
28459383 TGTTTTTTTTTTT-CTTTTTATTTTT-TGTT-AATGTA
1 T-TTTTTTTTTTTGCTTTTT-TTTTTGTGTTGAATGTA
28459418 TTTTTTTT
1 TTTTTTTT
28459426 CATTGTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
34 7 0.18
35 6 0.16
36 9 0.24
37 16 0.42
ACGTcount: A:0.08, C:0.01, G:0.10, T:0.81
Consensus pattern (36 bp):
TTTTTTTTTTTTGCTTTTTTTTTTGTGTTGAATGTA
Found at i:28459443 original size:22 final size:23
Alignment explanation
Indices: 28459417--28459460 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28459407 TTGTTAATGT
28459417 ATTTTT-TTTCATTG-TTTATTG
1 ATTTTTGTTTCATTGCTTTATTG
*
28459438 ATTTTTGTTTCTTTGCTTTATTG
1 ATTTTTGTTTCATTGCTTTATTG
28459461 TTGTATCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.70
Consensus pattern (23 bp):
ATTTTTGTTTCATTGCTTTATTG
Found at i:28459510 original size:1 final size:1
Alignment explanation
Indices: 28459504--28459598 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
28459494 TATTGACTTG
* * * * * * ** * *
28459504 TTTTTTTTTTTTTCTTTTTATTTTTTTTTTTTTTTATTTTTTGTGTTTTTATTTTCATGTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
28459569 TTCTTTTTTGTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28459599 CAATCTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.04, C:0.04, G:0.05, T:0.86
Consensus pattern (1 bp):
T
Found at i:28459635 original size:17 final size:15
Alignment explanation
Indices: 28459613--28459675 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
28459603 CTCTTTCTTA
28459613 TCTTTTTTTGTTTATT
1 TCTTTTTTTGTTT-TT
**
28459629 GTCTTTTTTAATTTTT
1 -TCTTTTTTTGTTTTT
28459645 TCTTTTTTTGTGTTTT
1 TCTTTTTTTGT-TTTT
* *
28459661 T-TTTTCTAGTTTTT
1 TCTTTTTTTGTTTTT
28459675 T
1 T
28459676 ATTGATTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 5 0.13
15 16 0.41
16 7 0.18
17 11 0.28
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.79
Consensus pattern (15 bp):
TCTTTTTTTGTTTTT
Found at i:28462934 original size:39 final size:39
Alignment explanation
Indices: 28462835--28462978 Score: 157
Period size: 40 Copynumber: 3.6 Consensus size: 39
28462825 CGAATGATAT
* * * *
28462835 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTATAA
* *
28462875 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTATA-A
*
28462915 CCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA
*
28462954 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGT-CCGAAGGCATTTG
28462979 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
39 36 0.40
40 46 0.51
41 8 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28462985 original size:79 final size:80
Alignment explanation
Indices: 28462834--28462985 Score: 184
Period size: 79 Copynumber: 1.9 Consensus size: 80
28462824 TCGAATGATA
*
28462834 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
28462899 GTGCGAGTTACTAAT
66 GAACGAGTTACTAAT
* * * * * *
28462914 TCCGGGTTAAGT-CCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
28462976 TTGAACGAGT
64 TTGAACGAGT
28462986 AGCTATATCC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAAT
Found at i:28462997 original size:79 final size:80
Alignment explanation
Indices: 28462831--28463001 Score: 183
Period size: 79 Copynumber: 2.2 Consensus size: 80
28462821 TATTCGAATG
* *
28462831 ATATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCA
**
28462896 TTTGTGCGAGTTACT
66 TTTGAACGAGTTACT
* * * * *
28462911 A-ATTCCGGGTTAAGT-CCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAG
1 ATA-TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAG
28462972 GCATTTGAACGAG-TAGCT
63 GCATTTGAACGAGTTA-CT
28462990 ATATCC-GGTTAA
1 ATATCCGGGTTAA
28463002 ATTCTGAAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
78 9 0.12
79 48 0.62
80 20 0.26
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (80 bp):
ATATCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCA
TTTGAACGAGTTACT
Found at i:28470048 original size:16 final size:16
Alignment explanation
Indices: 28470023--28470058 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
28470013 GCCTAAGATG
28470023 TAAA-ATGAATTCTAT
1 TAAATATGAATTCTAT
*
28470038 TAAATATGAATTGTAT
1 TAAATATGAATTCTAT
28470054 TAAAT
1 TAAAT
28470059 TCAAAGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (16 bp):
TAAATATGAATTCTAT
Found at i:28472236 original size:24 final size:24
Alignment explanation
Indices: 28472190--28472238 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28472180 TCTTACTTAT
*
28472190 TCGCACACATAGTGCAATGTTTTC
1 TCGCACACATAGTGCAATATTTTC
**
28472214 TCGCACACATAGTGCTGTATTTTC
1 TCGCACACATAGTGCAATATTTTC
28472238 T
1 T
28472239 TACCTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (24 bp):
TCGCACACATAGTGCAATATTTTC
Found at i:28486703 original size:29 final size:29
Alignment explanation
Indices: 28486668--28486741 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
28486658 GTTGTGAGAT
* *
28486668 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
28486697 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
28486726 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28486742 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:28495087 original size:29 final size:29
Alignment explanation
Indices: 28495052--28495125 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
28495042 GTTGTGAGAT
* *
28495052 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
28495081 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
28495110 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28495126 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:28497057 original size:35 final size:36
Alignment explanation
Indices: 28497000--28497071 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
28496990 TCTGTAAAAG
28497000 TAAAAAGGGTTTGGCTAGGCTTAAGATATGAATAAA
1 TAAAAAGGGTTTGGCTAGGCTTAAGATATGAATAAA
*
28497036 TAAAAAGGTTTTGGCTA-GCTTAAGATATGAATAAA
1 TAAAAAGGGTTTGGCTAGGCTTAAGATATGAATAAA
28497071 T
1 T
28497072 TCGATAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (36 bp):
TAAAAAGGGTTTGGCTAGGCTTAAGATATGAATAAA
Found at i:28497597 original size:48 final size:46
Alignment explanation
Indices: 28497489--28497652 Score: 172
Period size: 46 Copynumber: 3.5 Consensus size: 46
28497479 TTTGTGTGCT
* *
28497489 AGTGTAAGACATGTCTAGGACATGCATCAGCCATAGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAGAGTATGAGAGCC
* *
28497535 AGTGTAAGACATGTCTGGGACATGCATCAGCCCCGAGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CCAGAG-TA-TGAGAGCC
* * * ** *
28497583 AGTGTAAGATATGTCTGGGACATGAATC-GGCATTGAG-GCGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCA--GAGTATGAGAGCC
28497629 AGTGTAAGACATGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
28497653 GCGTCAGCTT
Statistics
Matches: 99, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 56 0.57
47 5 0.05
48 35 0.35
49 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCAGAGTATGAGAGCC
Found at i:28500478 original size:12 final size:12
Alignment explanation
Indices: 28500461--28500502 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
28500451 AATTTTTCTC
28500461 CCCTTT-CCTCTT
1 CCCTTTACC-CTT
28500473 CCCTTTACCCTT
1 CCCTTTACCCTT
*
28500485 CCCTTTGCCCTTT
1 CCCTTTACCC-TT
28500498 CCCTT
1 CCCTT
28500503 GGGTTGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.02, C:0.50, G:0.02, T:0.45
Consensus pattern (12 bp):
CCCTTTACCCTT
Found at i:28503397 original size:16 final size:17
Alignment explanation
Indices: 28503371--28503417 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
28503361 TGCTCAAACA
*
28503371 ATTTAAAATATAAATTT
1 ATTTAATATATAAATTT
28503388 ATTAATATATATATAAATTT
1 ATT--TA-ATATATAAATTT
28503408 A-TTAATATAT
1 ATTTAATATAT
28503418 GTAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
19 3 0.12
20 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAATATATAAATTT
Found at i:28503403 original size:20 final size:20
Alignment explanation
Indices: 28503378--28503417 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28503368 ACAATTTAAA
28503378 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
28503398 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
28503418 GTAAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:28503646 original size:14 final size:15
Alignment explanation
Indices: 28503619--28503648 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28503609 ATTGATATAG
28503619 AATATAATATTTTAA
1 AATATAATATTTTAA
28503634 AATATAA-ATTTTAA
1 AATATAATATTTTAA
28503648 A
1 A
28503649 TAATGGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATAATATTTTAA
Found at i:28505346 original size:98 final size:98
Alignment explanation
Indices: 28505177--28505371 Score: 390
Period size: 98 Copynumber: 2.0 Consensus size: 98
28505167 TAAAATTAGT
28505177 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAAATGATAAACG
1 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAAATGATAAACG
28505242 AGTTACAGACCTACAAAAAAATACAAGTAAGGA
66 AGTTACAGACCTACAAAAAAATACAAGTAAGGA
28505275 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAAATGATAAACG
1 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAAATGATAAACG
28505340 AGTTACAGACCTACAAAAAAATACAAGTAAGG
66 AGTTACAGACCTACAAAAAAATACAAGTAAGG
28505372 CCTTAGGAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (98 bp):
TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAAATGATAAACG
AGTTACAGACCTACAAAAAAATACAAGTAAGGA
Found at i:28506652 original size:4 final size:4
Alignment explanation
Indices: 28506645--28506676 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
28506635 ATACATACTT
28506645 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
28506677 ATATGAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:28513901 original size:25 final size:26
Alignment explanation
Indices: 28513873--28513927 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
28513863 TTAATTTATG
28513873 TTATATT-ATAACATATATTAA-CGTA
1 TTATATTAATAACATAT-TTAACCGTA
* *
28513898 TTAT-TTAATTACATATTTAACCTTA
1 TTATATTAATAACATATTTAACCGTA
28513923 TTATA
1 TTATA
28513928 AAATGTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (26 bp):
TTATATTAATAACATATTTAACCGTA
Found at i:28518928 original size:46 final size:46
Alignment explanation
Indices: 28518779--28518952 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
28518769 TGTAACCCGC
* * *
28518779 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28518825 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* *
28518870 ACATTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA-TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28518916 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28518953 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
45 34 0.31
46 65 0.60
47 1 0.01
48 4 0.04
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28518971 original size:46 final size:46
Alignment explanation
Indices: 28518787--28518971 Score: 152
Period size: 46 Copynumber: 4.0 Consensus size: 46
28518777 GCCCATAAGC
* ** * *
28518787 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCATAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-TAGT
* *
28518832 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCTAGT
* * * *
28518878 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCTAGT
28518924 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
28518970 GA
1 GA
28518972 CATGTCACTT
Statistics
Matches: 113, Mismatches: 13, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
44 10 0.09
45 29 0.26
46 64 0.57
47 1 0.01
48 4 0.04
49 5 0.04
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
Found at i:28521341 original size:14 final size:14
Alignment explanation
Indices: 28521322--28521399 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 14
28521312 CAAAGATAAC
*
28521322 AAGAAAACCGAATA
1 AAGAAATCCGAATA
*
28521336 AAGAAATCCAAGATA
1 AAGAAATCCGA-ATA
* *
28521351 GAGAAACCCGAATA
1 AAGAAATCCGAATA
28521365 AA-AAATCCAGAATA
1 AAGAAATCC-GAATA
* *
28521379 AAGAGATCCAGGATA
1 AAGAAATCC-GAATA
28521394 AAGAAA
1 AAGAAA
28521400 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 5 0.10
14 20 0.39
15 26 0.51
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (14 bp):
AAGAAATCCGAATA
Found at i:28521361 original size:29 final size:29
Alignment explanation
Indices: 28521322--28521408 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
28521312 CAAAGATAAC
*
28521322 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
28521351 GAGAAACCCGAATAAA-AAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
28521379 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
28521409 CGATACTATG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
27 2 0.04
28 12 0.26
29 23 0.49
30 8 0.17
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:28521389 original size:15 final size:15
Alignment explanation
Indices: 28521322--28521399 Score: 74
Period size: 14 Copynumber: 5.4 Consensus size: 15
28521312 CAAAGATAAC
*
28521322 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28521336 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28521351 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
28521365 AA-AAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28521379 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28521394 AAGAAA
1 AAGAAA
28521400 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 3 0.06
14 24 0.47
15 24 0.47
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28521408 original size:15 final size:15
Alignment explanation
Indices: 28521333--28521408 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
28521323 AGAAAACCGA
28521333 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
28521348 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
28521362 ATAAA-AAATCC-AG
1 ATAAAGAAATCCAAG
* *
28521375 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28521391 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28521406 ATA
1 ATA
28521409 CGATACTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
12 1 0.02
13 5 0.11
14 9 0.19
15 31 0.66
16 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28524464 original size:93 final size:93
Alignment explanation
Indices: 28524305--28524474 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
28524295 CCCATAAGCG
* * * *
28524305 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
28524370 GAGTTCGGATGCCTAGTTACATTTCACA
66 GAGTTCGGATGCCTAGTTACATTTCACA
*
28524398 AACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
28524463 GAGTTCGGATGC
66 GAGTTCGGATGC
28524475 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCACA
Found at i:28524471 original size:46 final size:46
Alignment explanation
Indices: 28524296--28524471 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
28524286 TGTAACCCGC
* * * *
28524296 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28524342 CCATAGGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCA-T
* * *
28524393 TCA-CA---AACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
28524435 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28524472 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 1 0.01
46 60 0.57
47 27 0.26
49 1 0.01
50 2 0.02
51 5 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28524490 original size:46 final size:45
Alignment explanation
Indices: 28524304--28524490 Score: 116
Period size: 46 Copynumber: 4.0 Consensus size: 45
28524294 GCCCATAAGC
* ** * *
28524304 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCATAGGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-C-TA-GT
* *
28524350 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AGT
* * * * * *
28524397 AAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCTAGT
28524443 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAGT
28524489 GA
1 GA
28524491 CATGTCACTT
Statistics
Matches: 109, Mismatches: 18, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
44 9 0.08
45 2 0.02
46 59 0.54
47 29 0.27
48 1 0.01
49 5 0.05
50 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAGT
Found at i:28532328 original size:16 final size:16
Alignment explanation
Indices: 28532307--28532337 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28532297 TATTTATCAT
28532307 AATAATCTACTTAGTA
1 AATAATCTACTTAGTA
28532323 AATAATCTACTTAGT
1 AATAATCTACTTAGT
28532338 CATACCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (16 bp):
AATAATCTACTTAGTA
Found at i:28539038 original size:55 final size:53
Alignment explanation
Indices: 28538909--28539040 Score: 131
Period size: 55 Copynumber: 2.4 Consensus size: 53
28538899 GGTTTAAGGA
* * * *
28538909 TAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTAGAAGGAAAGGAAATCATG
1 TAAGACCATG-CAAGGCATGGCATTGATAACTACTAGAAGGAAAGGAAACCATG
* * * **
28538963 TAAGATCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAA-GATCCCATG
1 TAAGACCATG-CAAGGCATGGCATTGAT-AACTACTAGAAGG-AAAGGAAACCATG
28539018 TAAGACCATGCGAAGGCATGGCA
1 TAAGACCATGC-AAGGCATGGCA
28539041 ATGGTGAGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
54 25 0.40
55 35 0.56
56 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (53 bp):
TAAGACCATGCAAGGCATGGCATTGATAACTACTAGAAGGAAAGGAAACCATG
Found at i:28539076 original size:53 final size:54
Alignment explanation
Indices: 28538909--28539103 Score: 196
Period size: 53 Copynumber: 3.6 Consensus size: 54
28538899 GGTTTAAGGA
* * * * * * *
28538909 TAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTAGAAGGAAAGGAAATCATG
1 TAAGACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGCAAGGATACCATG
* * * * * * *
28538963 TAAGATCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAAGATCCCATG
1 TAAGACCATGTCAAGACATGGCAATGGT-AAGTTCTATAAGGCAAGGATACCATG
* * *
28539018 TAAGACCATG-CGAAGGCATGGCAATGGTGAGTTC-ATAAGGCAAGGATACCACG
1 TAAGACCATGTC-AAGACATGGCAATGGTAAGTTCTATAAGGCAAGGATACCATG
*
28539071 TAAGACTATGTCAAGACATGGCAATGGTAAGTT
1 TAAGACCATGTCAAGACATGGCAATGGTAAGTT
28539104 TAAAAAGGAA
Statistics
Matches: 113, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
53 44 0.39
54 29 0.26
55 40 0.35
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (54 bp):
TAAGACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGCAAGGATACCATG
Found at i:28544441 original size:16 final size:17
Alignment explanation
Indices: 28544415--28544461 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
28544405 TGCTCAAACA
*
28544415 ATTTAAAATATAAATTT
1 ATTTAATATATAAATTT
28544432 ATTAATATATATATAAATTT
1 ATT--TA-ATATATAAATTT
28544452 A-TTAATATAT
1 ATTTAATATAT
28544462 GTAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
19 3 0.12
20 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAATATATAAATTT
Found at i:28544447 original size:20 final size:20
Alignment explanation
Indices: 28544422--28544461 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28544412 ACAATTTAAA
28544422 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
28544442 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
28544462 GTAAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:28544690 original size:14 final size:15
Alignment explanation
Indices: 28544663--28544692 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28544653 ATTGATATAG
28544663 AATATAATATTTTAA
1 AATATAATATTTTAA
28544678 AATATAA-ATTTTAA
1 AATATAATATTTTAA
28544692 A
1 A
28544693 TAATGGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATAATATTTTAA
Found at i:28546399 original size:97 final size:97
Alignment explanation
Indices: 28546219--28546412 Score: 370
Period size: 98 Copynumber: 2.0 Consensus size: 97
28546209 TAAAATTAGT
28546219 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAATGATAAACGA
1 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAATGATAAACGA
*
28546284 GTTACAGACCTACAAAAAAATACAAGTAAGGA
66 GTCACAGACCTACAAAAAAATACAAGTAAGGA
28546316 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAAATGATAAACG
1 TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTC-AAAAAAAATGATAAACG
28546381 AGTCACAGACCTACAAAAAAATACAAGTAAGG
65 AGTCACAGACCTACAAAAAAATACAAGTAAGG
28546413 CCTTAGGAAT
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
97 47 0.49
98 48 0.51
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.21
Consensus pattern (97 bp):
TATACAAAATATGTGGAGCTCCAGTATCATCGTATATCAAAATAGTCAAAAAAAATGATAAACGA
GTCACAGACCTACAAAAAAATACAAGTAAGGA
Found at i:28548151 original size:53 final size:54
Alignment explanation
Indices: 28547985--28548175 Score: 215
Period size: 53 Copynumber: 3.5 Consensus size: 54
28547975 TAAGGATAAT
* * * * * *
28547985 ACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAGGAAATCATGTAAG
1 ACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGCAAGGATACCATGTAAG
* * * * * *
28548039 ACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAAGATCCCATGTAAG
1 ACCATGTCAAGACATGGCAATGGT-AAGTTCTATAAGGCAAGGATACCATGTAAG
* * *
28548094 ACCATG-CGAAGGCATGGCAATGGTGAGTTC-ATAAGGCAAGGATACCACGTAAG
1 ACCATGTC-AAGACATGGCAATGGTAAGTTCTATAAGGCAAGGATACCATGTAAG
28548147 ACCATGTCAAGACATGGCAATGGTAAGTT
1 ACCATGTCAAGACATGGCAATGGTAAGTT
28548176 TAAAAAGGAA
Statistics
Matches: 113, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
53 45 0.40
54 26 0.23
55 42 0.37
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (54 bp):
ACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGCAAGGATACCATGTAAG
Found at i:28570116 original size:40 final size:40
Alignment explanation
Indices: 28570057--28570221 Score: 163
Period size: 39 Copynumber: 4.2 Consensus size: 40
28570047 ATTTGATGTG
*
28570057 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
* * *
28570097 TATCCGGGCTTAAAAACCCGCAGGCTATATGCTAGAATTA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
* * ** * *
28570137 TACCCAGACTT-AAGGTCCGCAGGCTATGTGTTGGAATTA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
* ** ** *
28570176 TAACCGGACTT-AAGGTCCGCAGGCTACGTGCTGGAAATA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
*
28570215 TGTCCGG
1 TATCCGG
28570222 GAAAAAGTCC
Statistics
Matches: 107, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 61 0.57
40 46 0.43
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (40 bp):
TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
Found at i:28572738 original size:11 final size:11
Alignment explanation
Indices: 28572722--28572747 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28572712 CGAAGCCCAC
28572722 ATCACAATAAT
1 ATCACAATAAT
28572733 ATCACAATAAT
1 ATCACAATAAT
28572744 ATCA
1 ATCA
28572748 TACGTACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:28573753 original size:16 final size:16
Alignment explanation
Indices: 28573703--28573747 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
28573693 GTAGCCAAAC
28573703 TTTCGGCTTTTCGACA
1 TTTCGGCTTTTCGACA
**
28573719 TTTTAGCTTTTCGACA
1 TTTCGGCTTTTCGACA
28573735 TTTCGGCTTTTCG
1 TTTCGGCTTTTCG
28573748 GGATTTGCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.49
Consensus pattern (16 bp):
TTTCGGCTTTTCGACA
Found at i:28576535 original size:13 final size:13
Alignment explanation
Indices: 28576513--28576545 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28576503 AAGCTACATC
*
28576513 AGTAGCGAGTGTT
1 AGTAGTGAGTGTT
28576526 AGTAGTGAGTGTT
1 AGTAGTGAGTGTT
28576539 AGTAGTG
1 AGTAGTG
28576546 TGAAAGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.39, T:0.33
Consensus pattern (13 bp):
AGTAGTGAGTGTT
Found at i:28578343 original size:31 final size:31
Alignment explanation
Indices: 28578308--28578369 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
28578298 CACCAGTGTT
*
28578308 AGTTCAGCTTGAGTCGGGTAAAGAATTCGTA
1 AGTTCAGATTGAGTCGGGTAAAGAATTCGTA
28578339 AGTTCAGATTGAGTCGGGTAAAGAATTCGTA
1 AGTTCAGATTGAGTCGGGTAAAGAATTCGTA
28578370 GTTTTCGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (31 bp):
AGTTCAGATTGAGTCGGGTAAAGAATTCGTA
Found at i:28584941 original size:42 final size:42
Alignment explanation
Indices: 28584895--28584990 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 42
28584885 GCACATGGGC
* **
28584895 GTGTGCCCAGGCCATGTGAGTCACACGGTTAAGGACACGGCT
1 GTGTGCCCAGGCCATGTGAGTCACACGGTCAAGGACACAACT
28584937 GTGTGCCCAGGCCATGTGAGTCACACGGTCAAGGACACAACT
1 GTGTGCCCAGGCCATGTGAGTCACACGGTCAAGGACACAACT
*
28584979 GTGTGTCCAGGC
1 GTGTGCCCAGGC
28584991 AGTGTAACTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (42 bp):
GTGTGCCCAGGCCATGTGAGTCACACGGTCAAGGACACAACT
Found at i:28593253 original size:42 final size:41
Alignment explanation
Indices: 28593206--28593341 Score: 115
Period size: 39 Copynumber: 3.3 Consensus size: 41
28593196 CTTGATATCA
28593206 CACACTAAGTGCCAATACATAGTCGAAGCTATTACAATCTCT-
1 CACACTAAGTGCCAATACATAGTCGAAGCTATT-CAATCT-TG
* * * * **
28593248 CACACTTAGCT-CC-TTAC--AGCCAAAGCTATCTCGGTCTTG
1 CACACTAAG-TGCCAATACATAGTCGAAGCTAT-TCAATCTTG
28593287 CACACTAAGTGCCAATACATAGTCGAAGCTATTCTGAATC--G
1 CACACTAAGTGCCAATACATAGTCGAAGCTATTC--AATCTTG
28593328 CACACTAAGTGCCA
1 CACACTAAGTGCCA
28593342 TATATATATC
Statistics
Matches: 73, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
38 2 0.03
39 24 0.33
40 4 0.05
41 20 0.27
42 20 0.27
43 3 0.04
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.25
Consensus pattern (41 bp):
CACACTAAGTGCCAATACATAGTCGAAGCTATTCAATCTTG
Found at i:28600893 original size:42 final size:42
Alignment explanation
Indices: 28600662--28600886 Score: 236
Period size: 42 Copynumber: 5.5 Consensus size: 42
28600652 AATACTCGAT
*
28600662 ATCTCGCACACTAAGTGCCAATACATAGCTGAAGCTATTAT-A
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTATT-TGA
*
28600704 ATCTCGCACAGTAAGTGCCAATACATAGCCGAAGCTATTAT-A
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTATT-TGA
* * * *
28600746 ATCTCGCACAGTAAGTTCC-TTACATAGCCGAAGCTATCTCG-
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAT-TTGA
* * **
28600787 GTCTCGCACACTAAGTGCC-ATATATAGCTAAAGCTATTTCGA
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTATTT-GA
*
28600829 A--TCGCACACTAAGTG-CAATATATAGCCGAAGCTATCTTGA
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAT-TTGA
28600869 AT-T-GCACACTAAGTGCCA
1 ATCTCGCACACTAAGTGCCA
28600887 TATATATATC
Statistics
Matches: 159, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
39 1 0.01
40 46 0.29
41 53 0.33
42 59 0.37
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTATTTGA
Found at i:28605536 original size:20 final size:20
Alignment explanation
Indices: 28605511--28605552 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
28605501 AAAATCGATG
*
28605511 GATATGCGATTTCTCGAAAT
1 GATATGCGATTTCCCGAAAT
*
28605531 GATATGTGATTTCCCGAAAT
1 GATATGCGATTTCCCGAAAT
28605551 GA
1 GA
28605553 ATGAGGTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
GATATGCGATTTCCCGAAAT
Found at i:28617788 original size:16 final size:18
Alignment explanation
Indices: 28617767--28617800 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28617757 CTTCAAGAAG
28617767 CTCAAG-TCT-GTTCTGA
1 CTCAAGCTCTAGTTCTGA
28617783 CTCAAGCTCTAGTTCTGA
1 CTCAAGCTCTAGTTCTGA
28617801 TACAGCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (18 bp):
CTCAAGCTCTAGTTCTGA
Found at i:28625800 original size:30 final size:30
Alignment explanation
Indices: 28625766--28625823 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
28625756 GGATATAAAT
28625766 GTCATGACATTAGGGTTATTTGAGTTTAAC
1 GTCATGACATTAGGGTTATTTGAGTTTAAC
28625796 GTCATGACATTAGGGTTATTTGAGTTTA
1 GTCATGACATTAGGGTTATTTGAGTTTA
28625824 CGTGTAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (30 bp):
GTCATGACATTAGGGTTATTTGAGTTTAAC
Found at i:28633084 original size:43 final size:45
Alignment explanation
Indices: 28633032--28633159 Score: 161
Period size: 51 Copynumber: 2.8 Consensus size: 45
28633022 TGTAGCATTC
*
28633032 GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGC-G-AGCATCT
1 GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAGTAACATCT
*
28633075 GAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGTGATTCATGTAACATCT
1 GAGCTCGTTGAGAGGTCCGAGTTCAT--T--ATG-GATGCA-GTAACATCT
*
28633126 GAGCTCGTTGAGAGGTTCGAGTTCATTATGGATG
1 GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
28633160 TGTTACATGT
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
43 26 0.36
45 1 0.01
46 3 0.04
47 6 0.08
48 4 0.05
49 1 0.01
50 1 0.01
51 31 0.42
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (45 bp):
GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAGTAACATCT
Found at i:28633147 original size:51 final size:51
Alignment explanation
Indices: 28633070--28633169 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
28633060 TGGATGCGAG
28633070 CATCTGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGTGATT-CATGTAA
1 CATCTGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGTG-TTACATGTAA
* *
28633121 CATCTGAGCTCGTTGAGAGGTTCGAGTTCATTATGGATGTGTTACATGT
1 CATCTGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGTGTTACATGT
28633170 TATGTGGTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 2 0.04
51 44 0.96
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (51 bp):
CATCTGAGCTCGTTGAGAGGTCCGAGTTCATGATGGATGTGTTACATGTAA
Found at i:28641410 original size:17 final size:18
Alignment explanation
Indices: 28641385--28641421 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28641375 TTGGCCAAAG
28641385 TGGGAATATGGG-CCACA
1 TGGGAATATGGGCCCACA
*
28641402 TGGGCATATGGGCCCACA
1 TGGGAATATGGGCCCACA
28641420 TG
1 TG
28641422 AGCAAGGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (18 bp):
TGGGAATATGGGCCCACA
Found at i:28642833 original size:43 final size:44
Alignment explanation
Indices: 28642751--28642834 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
28642741 CCAAGTTAAG
28642751 TCTCACTCTGTGCGATCCTTTGAGAGCATGAGCTATTGTGAGCA
1 TCTCACTCTGTGCGATCCTTTGAGAGCATGAGCTATTGTGAGCA
* * * *
28642795 TCTCACTCTGTGCGCTCC-TTGAGAGTATGGGCTTTTGTGA
1 TCTCACTCTGTGCGATCCTTTGAGAGCATGAGCTATTGTGA
28642835 TATTCGTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 19 0.53
44 17 0.47
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.35
Consensus pattern (44 bp):
TCTCACTCTGTGCGATCCTTTGAGAGCATGAGCTATTGTGAGCA
Found at i:28644786 original size:41 final size:41
Alignment explanation
Indices: 28644714--28644794 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
28644704 GTTTACTGAT
* * ** * *
28644714 TAATGTATATCTGATACTGTTACTCTGATGGGCTTAGGCCC
1 TAATGCATATCTAATACTGAAACTCTAATGGGCTAAGGCCC
*
28644755 TAATGCATATCTAATACTGAAACTTTAATGGGCTAAGGCC
1 TAATGCATATCTAATACTGAAACTCTAATGGGCTAAGGCC
28644795 TGAACTGCTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
TAATGCATATCTAATACTGAAACTCTAATGGGCTAAGGCCC
Found at i:28644904 original size:34 final size:34
Alignment explanation
Indices: 28644769--28644897 Score: 186
Period size: 34 Copynumber: 3.8 Consensus size: 34
28644759 GCATATCTAA
** *
28644769 TACTGAAACTTTAATGGGCTAAGGCCTGAACTGC
1 TACTGAAACTGAAATGGGCTAAGGCCCGAACTGC
*
28644803 TACTAAAACTGAAATGGGCTAAGGCCCGAACTGC
1 TACTGAAACTGAAATGGGCTAAGGCCCGAACTGC
* *
28644837 TACTGAAACTGAAATGGTCTAAAGCCCGAACTGC
1 TACTGAAACTGAAATGGGCTAAGGCCCGAACTGC
* *
28644871 TACTGAAACTGAAGTGGGCTTAGGCCC
1 TACTGAAACTGAAATGGGCTAAGGCCC
28644898 AGACTGCATT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 84 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (34 bp):
TACTGAAACTGAAATGGGCTAAGGCCCGAACTGC
Found at i:28652057 original size:34 final size:34
Alignment explanation
Indices: 28651926--28652050 Score: 171
Period size: 34 Copynumber: 3.7 Consensus size: 34
28651916 ATCTAATACC
28651926 GAAACT-ATAATGGGCTAAGGCCCGAACTGCTACT
1 GAAACTGA-AATGGGCTAAGGCCCGAACTGCTACT
**
28651960 GAAACTGAAATGGGCTAAGGATCGAACTGCTACT
1 GAAACTGAAATGGGCTAAGGCCCGAACTGCTACT
* *
28651994 AAAACTGAAATAGGCTAAGGCCCGAACTGCTACT
1 GAAACTGAAATGGGCTAAGGCCCGAACTGCTACT
* * *
28652028 GAAACCGAAGTGGGCTTAGGCCC
1 GAAACTGAAATGGGCTAAGGCCC
28652051 AGACTGCATT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 78 0.99
35 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (34 bp):
GAAACTGAAATGGGCTAAGGCCCGAACTGCTACT
Found at i:28654744 original size:11 final size:10
Alignment explanation
Indices: 28654730--28654795 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 10
28654720 ATTTATGATT
28654730 TGAATATGAAA
1 TGAA-ATGAAA
28654741 TGAAATTGAAA
1 TGAAA-TGAAA
28654752 TGAAAATGAAAA
1 TG-AAATG-AAA
* *
28654764 TAAGAATGATA
1 TGA-AATGAAA
28654775 TGAAAATGGAAA
1 TG-AAAT-GAAA
28654787 TGAAATGAA
1 TGAAATGAA
28654796 TTATAGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
10 4 0.09
11 24 0.53
12 17 0.38
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.23
Consensus pattern (10 bp):
TGAAATGAAA
Found at i:28654750 original size:6 final size:5
Alignment explanation
Indices: 28654730--28654795 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 5
28654720 ATTTATGATT
* *
28654730 TGAATA TGAAA TGAAA TTGAAA TGAAAA TGAAAA TAAGAA TGATA TGAAAA
1 TGAA-A TGAAA TGAAA -TGAAA TG-AAA TG-AAA TGA-AA TGAAA TG-AAA
28654781 TGGAAA TGAAA TGAA
1 T-GAAA TGAAA TGAA
28654796 TTATAGAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 20 0.39
6 30 0.59
7 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.23
Consensus pattern (5 bp):
TGAAA
Found at i:28654758 original size:17 final size:17
Alignment explanation
Indices: 28654729--28654762 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28654719 GATTTATGAT
28654729 TTGAATATGAAATGAAA
1 TTGAATATGAAATGAAA
28654746 TTGAA-ATGAAAATGAAA
1 TTGAATATG-AAATGAAA
28654763 ATAAGAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (17 bp):
TTGAATATGAAATGAAA
Found at i:28655470 original size:3 final size:3
Alignment explanation
Indices: 28655462--28655492 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28655452 GTTAGTTAGT
*
28655462 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28655493 TTGGTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28657678 original size:27 final size:26
Alignment explanation
Indices: 28657643--28657750 Score: 135
Period size: 27 Copynumber: 4.0 Consensus size: 26
28657633 AGCATGGCTG
* *
28657643 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28657669 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
28657697 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
28657724 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
28657751 TCAGGACGCT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 49 0.68
28 17 0.24
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28657735 original size:54 final size:54
Alignment explanation
Indices: 28657643--28657750 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
28657633 AGCATGGCTG
* *
28657643 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
28657697 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
28657751 TCAGGACGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 30 0.62
55 18 0.38
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:28659199 original size:24 final size:24
Alignment explanation
Indices: 28659172--28659242 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
28659162 CTAGATTTCC
**
28659172 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
28659196 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
28659220 TCCCTTATCAACTCTTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
28659243 CTCCTGCCAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.25, C:0.37, G:0.01, T:0.37
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:28669125 original size:8 final size:8
Alignment explanation
Indices: 28669112--28669136 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28669102 TCTCTACTAA
28669112 CGAGATGT
1 CGAGATGT
28669120 CGAGATGT
1 CGAGATGT
28669128 CGAGATGT
1 CGAGATGT
28669136 C
1 C
28669137 CTTGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (8 bp):
CGAGATGT
Found at i:28670370 original size:39 final size:39
Alignment explanation
Indices: 28670316--28670392 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
28670306 GGTAAGGTTG
*
28670316 AAACACCTTATTCAAATCAATATCAAACAAAGGAAGTAA
1 AAACACCTTATTCAAATCAATATCAAACAAAGAAAGTAA
*
28670355 AAACACCTTATTCAAATCAATATCAGACAAAGAAAGTA
1 AAACACCTTATTCAAATCAATATCAAACAAAGAAAGTA
28670393 CACTTCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.21
Consensus pattern (39 bp):
AAACACCTTATTCAAATCAATATCAAACAAAGAAAGTAA
Found at i:28672262 original size:22 final size:21
Alignment explanation
Indices: 28672229--28672269 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28672219 AAATGAAATA
*
28672229 AAAGAAATGAAAAAGAGAAAC
1 AAAGAAACGAAAAAGAGAAAC
*
28672250 AAAGCAAACGAAACAGAGAA
1 AAAG-AAACGAAAAAGAGAA
28672270 GAACAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.68, C:0.10, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAGAAACGAAAAAGAGAAAC
Found at i:28673392 original size:6 final size:6
Alignment explanation
Indices: 28673381--28673413 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
28673371 TGTGTACCGC
28673381 TACTGT TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TAC
28673414 CCTTACGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:28673419 original size:18 final size:18
Alignment explanation
Indices: 28673381--28673419 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28673371 TGTGTACCGC
**
28673381 TACTGTTACTGTTACTGT
1 TACTGTTACTGTTACCCT
28673399 TACTGTTACTGTTACCCT
1 TACTGTTACTGTTACCCT
28673417 TAC
1 TAC
28673420 GTGTATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.23, G:0.13, T:0.46
Consensus pattern (18 bp):
TACTGTTACTGTTACCCT
Found at i:28674878 original size:33 final size:33
Alignment explanation
Indices: 28674836--28674901 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28674826 GAAAAGGAGT
28674836 AAGCATAAAGCTTAGTAAGTTGCATATAAATAA
1 AAGCATAAAGCTTAGTAAGTTGCATATAAATAA
28674869 AAGCATAAAGCTTAGTAAGTTGCATATAAATAA
1 AAGCATAAAGCTTAGTAAGTTGCATATAAATAA
28674902 TTATACAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.27
Consensus pattern (33 bp):
AAGCATAAAGCTTAGTAAGTTGCATATAAATAA
Found at i:28675226 original size:47 final size:48
Alignment explanation
Indices: 28675155--28675368 Score: 187
Period size: 46 Copynumber: 4.6 Consensus size: 48
28675145 GGAGTAAGGT
28675155 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCA-A
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCT-ATCATCTCATA
* * * *
28675202 GTCAATGCCATGTCCCAGATATGGTCTTACACTGACTATCATCTTATA
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCATA
* * *
28675250 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACGTCTCGA-G
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-CATCTC-ATA
* * * *
28675296 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGC-ACTCGTCTCGAT-
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTA-TCATCTC-ATA
* **
28675342 GCCGATGCCATGTCTTAGACATGGTCT
1 GCCAATGCCATGTCCCAGACATGGTCT
28675369 GATGTATGCC
Statistics
Matches: 142, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
45 1 0.01
46 66 0.46
47 65 0.46
48 10 0.07
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCATA
Found at i:28675354 original size:93 final size:93
Alignment explanation
Indices: 28675154--28675364 Score: 216
Period size: 93 Copynumber: 2.3 Consensus size: 93
28675144 TGGAGTAAGG
* * *
28675154 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCAATGCCATGTCCCA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCAAGCCAATGCCATGTCCCA
* * *
28675219 GATATGGTCTTACACTGACTATCATCTTA
65 AACATGGTCTTACACTGACTATCATCTGA
* * * *
28675248 TAGCCGATG-CATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCGATG-CATGTCCC
1 T-GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTC-AAGCCAATGCCATGTCCC
*
28675311 AAACAT-GTCTTACACT-AGC-ACTCGTCTCGA
64 AAACATGGTCTTACACTGA-CTA-TCATCT-GA
**
28675341 TGCCGATGCCATGTCTTAGACATG
1 TGCCGATGCCATGTCCCAGACATG
28675365 GTCTGATGTA
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
91 2 0.02
92 23 0.23
93 46 0.47
94 21 0.21
95 6 0.06
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (93 bp):
TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAAGCCAATGCCATGTCCCAA
ACATGGTCTTACACTGACTATCATCTGA
Found at i:28681510 original size:29 final size:29
Alignment explanation
Indices: 28681478--28681546 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
28681468 CATTTTCGAG
28681478 TCTCCAAGAC-TTGGACAAATTTAAAACTT
1 TCTCCAA-ACTTTGGACAAATTTAAAACTT
28681507 TCT-CAAACTTATTGGACAAATTTAAAACTT
1 TCTCCAAAC-T-TTGGACAAATTTAAAACTT
28681537 TCT-CAAACTT
1 TCTCCAAACTT
28681547 ATCAACATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.05
28 4 0.11
29 4 0.11
30 27 0.73
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (29 bp):
TCTCCAAACTTTGGACAAATTTAAAACTT
Found at i:28681524 original size:30 final size:30
Alignment explanation
Indices: 28681488--28681548 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
28681478 TCTCCAAGAC
28681488 TTGGACAAATTTAAAACTTTCTCAAACTTA
1 TTGGACAAATTTAAAACTTTCTCAAACTTA
28681518 TTGGACAAATTTAAAACTTTCTCAAACTTA
1 TTGGACAAATTTAAAACTTTCTCAAACTTA
28681548 T
1 T
28681549 CAACATGTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (30 bp):
TTGGACAAATTTAAAACTTTCTCAAACTTA
Found at i:28682916 original size:47 final size:48
Alignment explanation
Indices: 28682845--28683070 Score: 202
Period size: 47 Copynumber: 4.8 Consensus size: 48
28682835 GGAGTAAGGT
* *
28682845 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCAT-ATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCAA
* * *
28682892 GTCGATGCCATGTCCCAGACATGGTCTTACACTAACT-ATCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-AA
* * *
28682940 GCCGATG-CATGTCCCA-AGCAT-GTCTTACATTAGCAC-TCGTCTCAA
1 GCCGATGCCATGTCCCAGA-CATGGTCTTACACTAGCTCATCATCTCAA
* * * * *
28682985 TGCCGATGCCATTTCTCAGACATGGTCTTACACTGGCTC-TCATAAT-ATG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCAT-CTCA-A
* *
28683034 GCCGATG-TATTTCCCAGACAT-GTCTTACACTAGCTCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCA
28683071 CAATAACCCA
Statistics
Matches: 146, Mismatches: 22, Indels: 22
0.77 0.12 0.12
Matches are distributed among these distances:
45 1 0.01
46 41 0.28
47 72 0.49
48 31 0.21
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCAA
Found at i:28683014 original size:94 final size:95
Alignment explanation
Indices: 28682845--28683018 Score: 237
Period size: 94 Copynumber: 1.8 Consensus size: 95
28682835 GGAGTAAGGT
* * *
28682845 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAG
28682910 ACATGGTCTTACACTAACTATCATCTCGTA
66 ACATGGTCTTACACTAACTATCATCTCGTA
* * * * *
28682940 GCCGATG-CATGTCCCAAGCAT-GTCTTACATTAGCAC-TCGTCTCAATGCCGATGCCATTTCTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACAT-ATCTCAA-GCCGATGCCATGTCCC
28683002 AGACATGGTCTTACACT
64 AGACATGGTCTTACACT
28683019 GGCTCTCATA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
92 1 0.01
93 18 0.26
94 43 0.62
95 7 0.10
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (95 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAACTATCATCTCGTA
Found at i:28683038 original size:94 final size:93
Alignment explanation
Indices: 28682845--28683067 Score: 227
Period size: 94 Copynumber: 2.4 Consensus size: 93
28682835 GGAGTAAGGT
* * * *
28682845 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAG
1 GCCGATG-CATGTCCCAAGCAT-GTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAG
* *
28682910 ACATGGTCTTACACTAACTATCATCTCGTA
64 ACATGGTCTTACACTAACTATCATATCATA
* * * *
28682940 GCCGATGCATGTCCCAAGCATGTCTTACATTAGCAC-TCGTCTCAATGCCGATGCCATTTCTCAG
1 GCCGATGCATGTCCCAAGCATGTCTTACACTAGCACAT-ATCTCAA-GCCGATGCCATGTCCCAG
** * *
28683004 ACATGGTCTTACACTGGCTCTCATAAT-ATG
64 ACATGGTCTTACACTAACTATCAT-ATCATA
* *
28683034 GCCGATGTATTTCCC-AGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAAG-CATGTCTTACACTAGC
28683068 TCACAATAAC
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
92 1 0.01
93 20 0.19
94 78 0.73
95 8 0.07
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (93 bp):
GCCGATGCATGTCCCAAGCATGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTAACTATCATATCATA
Found at i:28684861 original size:31 final size:31
Alignment explanation
Indices: 28684811--28684874 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28684801 TTACAAAATG
*
28684811 GTCACTAAACTACTGGAAAGTTTTCATTTAA
1 GTCACTAAACTACTCGAAAGTTTTCATTTAA
* *
28684842 GTCAGTAAACTATTCGAAAGTTTTCATTTAA
1 GTCACTAAACTACTCGAAAGTTTTCATTTAA
28684873 GT
1 GT
28684875 AATTGGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (31 bp):
GTCACTAAACTACTCGAAAGTTTTCATTTAA
Found at i:28685791 original size:12 final size:13
Alignment explanation
Indices: 28685769--28685801 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28685759 TTATTATAAA
*
28685769 TATTTTAATTAAT
1 TATTATAATTAAT
28685782 TA-TATAATTAAT
1 TATTATAATTAAT
28685794 TATTATAA
1 TATTATAA
28685802 AAATCTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATAATTAAT
Found at i:28686298 original size:26 final size:26
Alignment explanation
Indices: 28686258--28686323 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
28686248 AAGATATATA
*
28686258 TTTATA-TAAAATATTTTACATTAAT
1 TTTATATTTAAATATTTTACATTAAT
*
28686283 TTTATATTTAAATATTTTATATTAAT
1 TTTATATTTAAATATTTTACATTAAT
28686309 TTTATATTTAAATAT
1 TTTATATTTAAATAT
28686324 GAAATATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 6 0.16
26 32 0.84
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTATATTTAAATATTTTACATTAAT
Found at i:28686301 original size:15 final size:15
Alignment explanation
Indices: 28686281--28686323 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
28686271 TTTTACATTA
28686281 ATTTTATATTTAAAT
1 ATTTTATATTTAAAT
28686296 ATTTTATA-TT--A-
1 ATTTTATATTTAAAT
28686307 ATTTTATATTTAAAT
1 ATTTTATATTTAAAT
28686322 AT
1 AT
28686324 GAAATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
14 3 0.12
15 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATATTTAAAT
Found at i:28686330 original size:26 final size:26
Alignment explanation
Indices: 28686277--28686337 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
28686267 AATATTTTAC
***
28686277 ATTAATTTTATATTTAAATATTTTAT
1 ATTAATTTTATATTTAAATATGAAAT
28686303 ATTAATTTTATATTTAAATATGAAAT
1 ATTAATTTTATATTTAAATATGAAAT
*
28686329 ATTTATTTT
1 ATTAATTTT
28686338 TTAAATCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTAATTTTATATTTAAATATGAAAT
Found at i:28694716 original size:27 final size:27
Alignment explanation
Indices: 28694679--28694733 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28694669 AGACAGAATG
28694679 TGTGCAAATTTCTCTCATGTTTTCACA
1 TGTGCAAATTTCTCTCATGTTTTCACA
28694706 TGTGCAAATTTCTCTCATGTTTTCACA
1 TGTGCAAATTTCTCTCATGTTTTCACA
28694733 T
1 T
28694734 ACATATTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (27 bp):
TGTGCAAATTTCTCTCATGTTTTCACA
Found at i:28694741 original size:25 final size:26
Alignment explanation
Indices: 28694683--28694743 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
28694673 AGAATGTGTG
*
28694683 CAAATTTCTCTCATGTTTTCACATGTG
1 CAAATTTCTCTCATGTTTTCACA-GTA
28694710 CAAATTTCTCTCATGTTTTCACA-TA
1 CAAATTTCTCTCATGTTTTCACAGTA
*
28694735 CATATTTCT
1 CAAATTTCT
28694744 TTCTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 9 0.28
27 23 0.72
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.46
Consensus pattern (26 bp):
CAAATTTCTCTCATGTTTTCACAGTA
Found at i:28697117 original size:22 final size:23
Alignment explanation
Indices: 28697092--28697134 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28697082 ACCTAAATTT
28697092 TTAAA-TTAAAAAAATAAAAACA
1 TTAAATTTAAAAAAATAAAAACA
**
28697114 TTAAATTTCTAAAAATAAAAA
1 TTAAATTTAAAAAAATAAAAA
28697135 TATAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAAATTTAAAAAAATAAAAACA
Found at i:28697426 original size:10 final size:10
Alignment explanation
Indices: 28697406--28697452 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
28697396 GGATTTTACT
28697406 TAAATAAATTA
1 TAAA-AAATTA
28697417 TAAAAAATTA
1 TAAAAAATTA
*
28697427 TAAAAAGTTA
1 TAAAAAATTA
*
28697437 -AAAATATTA
1 TAAAAAATTA
28697446 CTAAAAA
1 -TAAAAA
28697453 TAGTAAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:28698791 original size:12 final size:12
Alignment explanation
Indices: 28698776--28698800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28698766 TATACTTTGA
28698776 TATATTGAAAAC
1 TATATTGAAAAC
28698788 TATATTGAAAAC
1 TATATTGAAAAC
28698800 T
1 T
28698801 TATGCATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TATATTGAAAAC
Found at i:28703995 original size:30 final size:30
Alignment explanation
Indices: 28703960--28704016 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
28703950 TTTCCGAGCC
*
28703960 TAGGGGCAAAATCATAATTTTGCAAAGGTT
1 TAGGGGCAAAATCATAATTTTGAAAAGGTT
**
28703990 TAGGGGCAAAATTGTAATTTTGAAAAG
1 TAGGGGCAAAATCATAATTTTGAAAAG
28704017 TTTGAGTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAATCATAATTTTGAAAAGGTT
Found at i:28704771 original size:47 final size:48
Alignment explanation
Indices: 28704645--28704802 Score: 130
Period size: 47 Copynumber: 3.4 Consensus size: 48
28704635 ATTGATGGTT
** * * * *
28704645 AAGGATACCATGTAAGACCATGTCAAGACATGACATTGG---TAAGGC
1 AAGGATACCATGTAAGACCAAATCAAGATATGGCATCGGCACTAAGAC
* * ** * *
28704690 AAGGATCCCGTGTAAGACCATGTCCAGATATGGCATCGGCA-T-TGAC
1 AAGGATACCATGTAAGACCAAATCAAGATATGGCATCGGCACTAAGAC
* *
28704736 TAAGGACT-CCATGTAAGACCAAATCAAGATGTGGCATTGGCACTAAGAC
1 -AAGGA-TACCATGTAAGACCAAATCAAGATATGGCATCGGCACTAAGAC
28704785 AAGGATACCATGTAAGAC
1 AAGGATACCATGTAAGAC
28704803 TATGTTTGGA
Statistics
Matches: 91, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
45 33 0.36
46 2 0.02
47 35 0.38
48 18 0.20
49 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (48 bp):
AAGGATACCATGTAAGACCAAATCAAGATATGGCATCGGCACTAAGAC
Found at i:28704905 original size:42 final size:42
Alignment explanation
Indices: 28704858--28704940 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
28704848 ACCATGCCAA
28704858 GGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTT
1 GGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTT
*
28704900 GGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGT
1 GGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGT
28704941 AAGACCATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (42 bp):
GGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTT
Found at i:28705039 original size:108 final size:108
Alignment explanation
Indices: 28704900--28705095 Score: 288
Period size: 108 Copynumber: 1.8 Consensus size: 108
28704890 AAATCATGTT
* * *
28704900 GGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATT
1 GGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACCATGTCAAGACATGGCAAT
28704965 GATAAGTT-AATATAAGGAAAAGGTCCCATGTAAGACCATGCCAA
66 GATAAGTTCAA-A-AAGGAAAAGGTCCCATGTAAGACCATGCCAA
* * * *
28705009 GGCATGGCATTGGTGAGTT-TATAAGGCAAGGATACCACGTAAGACCATGTCAAGAGATGGCAAT
1 GGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACCATGTCAAGACATGGCAAT
*
28705073 GGTAAGTTCAAAAAGGAAAAGGT
66 GATAAGTTCAAAAAGGAAAAGGT
28705096 TCCTGAGTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 11 0.14
108 48 0.62
109 19 0.24
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (108 bp):
GGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACCATGTCAAGACATGGCAAT
GATAAGTTCAAAAAGGAAAAGGTCCCATGTAAGACCATGCCAA
Found at i:28705055 original size:53 final size:54
Alignment explanation
Indices: 28704900--28705080 Score: 206
Period size: 53 Copynumber: 3.4 Consensus size: 54
28704890 AAATCATGTT
* * *
28704900 GGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGTCAA
1 GGCATGGCATTGATAAGTTATATAAGGCAAGGATACCATGTAAGACCATGTCAA
* * * *
28704954 GACATGGCATTGATAAGTTAATATAAGGAAAAGG-TCCCATGTAAGACCATGCCAA
1 GGCATGGCATTGATAAGTT-ATATAAGG-CAAGGATACCATGTAAGACCATGTCAA
* * *
28705009 GGCATGGCATTGGTGAGTT-TATAAGGCAAGGATACCACGTAAGACCATGTCAA
1 GGCATGGCATTGATAAGTTATATAAGGCAAGGATACCATGTAAGACCATGTCAA
* *
28705062 GAG-ATGGCAATGGTAAGTT
1 G-GCATGGCATTGATAAGTT
28705081 CAAAAAGGAA
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
52 4 0.04
53 40 0.37
54 19 0.18
55 40 0.37
56 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (54 bp):
GGCATGGCATTGATAAGTTATATAAGGCAAGGATACCATGTAAGACCATGTCAA
Found at i:28713018 original size:28 final size:29
Alignment explanation
Indices: 28712985--28713085 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28712975 TATAGTAAGT
* * *
28712985 CCGCACACTTAGTGTTATATAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
28713013 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
28713042 CCGCACACTTAGTGCTATACAATTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
28713071 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28713086 CAATTTCATG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTTGAAC
Found at i:28720839 original size:28 final size:29
Alignment explanation
Indices: 28720806--28720906 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28720796 TATAGTAAGT
* * *
28720806 CCGCACACTTAGTGTTATATAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
28720834 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
28720863 CCGCACACTTAGTGCTATACAATTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
28720892 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28720907 CAATTTCATG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTTGAAC
Found at i:28725276 original size:12 final size:13
Alignment explanation
Indices: 28725259--28725287 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28725249 CTCATACATG
28725259 AATAAATAAA-GC
1 AATAAATAAATGC
28725271 AATAAATAAATGC
1 AATAAATAAATGC
28725284 AATA
1 AATA
28725288 GTTATAGCCC
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:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:28730398 original size:15 final size:15
Alignment explanation
Indices: 28730362--28730409 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
28730352 GAAAACCAGG
*
28730362 TAAAGAAGTCCAAGA
1 TAAAGAAATCCAAGA
* *
28730377 CAGAGAAATCCAAGA
1 TAAAGAAATCCAAGA
28730392 TAAAGAAACTCCTAAGA
1 TAAAGAAA-TCC-AAGA
28730409 T
1 T
28730410 TCATAAATCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.15
Consensus pattern (15 bp):
TAAAGAAATCCAAGA
Found at i:28734627 original size:16 final size:16
Alignment explanation
Indices: 28734606--28734636 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28734596 AAATTGACTC
28734606 AAAATTATATTTTTGA
1 AAAATTATATTTTTGA
28734622 AAAATTATATTTTTG
1 AAAATTATATTTTTG
28734637 CCCCTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
AAAATTATATTTTTGA
Found at i:28747108 original size:21 final size:21
Alignment explanation
Indices: 28747084--28747123 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28747074 AAAGTTACGT
28747084 TGAAAAATTTTAACGTTTCAC
1 TGAAAAATTTTAACGTTTCAC
28747105 TGAAAAATTTTAACGTTTC
1 TGAAAAATTTTAACGTTTC
28747124 GATAGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAAAATTTTAACGTTTCAC
Found at i:28747867 original size:33 final size:32
Alignment explanation
Indices: 28747801--28747867 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
28747791 GCTTAGCCAG
* *
28747801 AATTTAATTTAAATAATAAAAAATATTATTTA
1 AATTTAATTTAAATAATAAAAAATATCAATTA
28747833 AATTTAATTATAAA-ATATAAAAAATATCAATTA
1 AATTTAATT-TAAATA-ATAAAAAATATCAATTA
28747866 AA
1 AA
28747868 AATATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 10 0.32
33 21 0.68
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AATTTAATTTAAATAATAAAAAATATCAATTA
Found at i:28757095 original size:16 final size:15
Alignment explanation
Indices: 28757070--28757099 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28757060 TTCTCAAAAT
28757070 ATTAATTAATTAATA
1 ATTAATTAATTAATA
28757085 ATTATATTAATTAAT
1 ATTA-ATTAATTAAT
28757100 TTTACACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATTAATTAATA
Found at i:28759165 original size:16 final size:17
Alignment explanation
Indices: 28759133--28759166 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28759123 GTGGATGTCA
28759133 TTTGTTTGATGTTTATT
1 TTTGTTTGATGTTTATT
*
28759150 TTTGTTTGGT-TTTATT
1 TTTGTTTGATGTTTATT
28759166 T
1 T
28759167 CATAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.74
Consensus pattern (17 bp):
TTTGTTTGATGTTTATT
Found at i:28762278 original size:21 final size:21
Alignment explanation
Indices: 28762254--28762294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28762244 TCAAAGGTGC
28762254 ATGATGGCAATATT-TTTAGAT
1 ATGATGG-AATATTCTTTAGAT
*
28762275 ATGATTGAATATTCTTTAGA
1 ATGATGGAATATTCTTTAGA
28762295 GGTTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (21 bp):
ATGATGGAATATTCTTTAGAT
Found at i:28764126 original size:22 final size:22
Alignment explanation
Indices: 28764093--28764159 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
28764083 TGAAGGACTC
*
28764093 ACACACCCGTGTGGTCCAAAGG
1 ACACGCCCGTGTGGTCCAAAGG
* *
28764115 ACACGCCTGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGTCCAAAGG
28764137 ACACGCCCGTGTGGTCC-AAGG
1 ACACGCCCGTGTGGTCCAAAGG
28764158 AC
1 AC
28764160 TCCTTTGGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 5 0.12
22 35 0.88
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.15
Consensus pattern (22 bp):
ACACGCCCGTGTGGTCCAAAGG
Found at i:28764923 original size:25 final size:25
Alignment explanation
Indices: 28764885--28764934 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28764875 GACTAGTAGA
28764885 TAGTGTGACGATGCTCCAGTGATCT
1 TAGTGTGACGATGCTCCAGTGATCT
28764910 TAGTGTGA-GAATGCTCCAGTGATCT
1 TAGTGTGACG-ATGCTCCAGTGATCT
28764935 CCAACCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (25 bp):
TAGTGTGACGATGCTCCAGTGATCT
Found at i:28765682 original size:25 final size:25
Alignment explanation
Indices: 28765644--28765694 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28765634 AATCGGGACT
*
28765644 TACCCTTTTATCATCATTTCAAGCA
1 TACCCCTTTATCATCATTTCAAGCA
*
28765669 TACCCCTTTGTCATCATTTCAAGCA
1 TACCCCTTTATCATCATTTCAAGCA
28765694 T
1 T
28765695 GTATTCAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.06, T:0.39
Consensus pattern (25 bp):
TACCCCTTTATCATCATTTCAAGCA
Found at i:28767774 original size:20 final size:20
Alignment explanation
Indices: 28767749--28767787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28767739 TGTATTCCTA
* *
28767749 AAATTTTAGAATTTTTCATC
1 AAATTTTAAAACTTTTCATC
28767769 AAATTTTAAAACTTTTCAT
1 AAATTTTAAAACTTTTCAT
28767788 TTTAGTCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATTTTAAAACTTTTCATC
Found at i:28788410 original size:42 final size:42
Alignment explanation
Indices: 28788351--28788431 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
28788341 TTTAGATACA
28788351 TAGCACAATAAGTTAATTTACACATGTATAGTATCAACACAT
1 TAGCACAATAAGTTAATTTACACATGTATAGTATCAACACAT
28788393 TAGCACAATAAGTTAATTTACACATGTATAGTATCAACA
1 TAGCACAATAAGTTAATTTACACATGTATAGTATCAACA
28788432 TATTTCAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (42 bp):
TAGCACAATAAGTTAATTTACACATGTATAGTATCAACACAT
Found at i:28793637 original size:18 final size:19
Alignment explanation
Indices: 28793614--28793651 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28793604 GTTCTCCCAA
* *
28793614 TATGATTCT-ATTTTATCT
1 TATGATACTCATTATATCT
28793632 TATGATACTCATTATATCT
1 TATGATACTCATTATATCT
28793651 T
1 T
28793652 CCTTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.55
Consensus pattern (19 bp):
TATGATACTCATTATATCT
Found at i:28800740 original size:34 final size:34
Alignment explanation
Indices: 28800702--28800766 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
28800692 CTTTTAATAG
*
28800702 CAGTAACAGTCT-GGGCCTAATCCCATTTCAGTAA
1 CAGTAACAGT-TGGGGCCTAAGCCCATTTCAGTAA
* *
28800736 CAGTAGCAGTTGGGGCCTTAGCCCATTTCAG
1 CAGTAACAGTTGGGGCCTAAGCCCATTTCAG
28800767 ACCAGTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (34 bp):
CAGTAACAGTTGGGGCCTAAGCCCATTTCAGTAA
Found at i:28813228 original size:21 final size:21
Alignment explanation
Indices: 28813204--28813244 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28813194 CAAAAAGGCC
* *
28813204 ATACGGGCTTGTCGCCTTTCT
1 ATACGAGCGTGTCGCCTTTCT
28813225 ATACGAGCGTGTCGCCTTTC
1 ATACGAGCGTGTCGCCTTTC
28813245 CACACGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.29, G:0.24, T:0.34
Consensus pattern (21 bp):
ATACGAGCGTGTCGCCTTTCT
Found at i:28822639 original size:19 final size:20
Alignment explanation
Indices: 28822602--28822639 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28822592 GTAAAGTTTG
* *
28822602 TAAAATAAATGGCACTTTTA
1 TAAAATAAATGGAAATTTTA
28822622 TAAAAT-AATGGAAATTTT
1 TAAAATAAATGGAAATTTT
28822640 GGGTTGCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (20 bp):
TAAAATAAATGGAAATTTTA
Found at i:28823170 original size:46 final size:46
Alignment explanation
Indices: 28823075--28823241 Score: 157
Period size: 46 Copynumber: 3.6 Consensus size: 46
28823065 TGATATGTGT
*
28823075 GCTAGTGTAAGACATGTCTGGGACATCCATCGGCGACATTATGAAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCGACATTATGAAA
*
28823121 GCTAGTGTAAGACATGTTTGGGACATGCATC-G-G-CATTGA-GACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCGACATT-ATGA--A-A
** * *
28823167 GCTAGTGTAAGACACATCTGGGACATGCATCAGCCTCGAGA-TAT-ACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-G--GCGACATTATGA-AA
*
28823215 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
28823242 GTGTCAGCTT
Statistics
Matches: 99, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 58 0.59
48 25 0.25
49 1 0.01
50 2 0.02
51 2 0.02
52 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCGACATTATGAAA
Done.