Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 171 of 203
Found at i:54209688 original size:13 final size:14
Alignment explanation
Indices: 54209664--54209692 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54209654 ATTGGTTGAA
54209664 TTGAATTTGGTCAT
1 TTGAATTTGGTCAT
54209678 TTGAA-TTGGTCAT
1 TTGAATTTGGTCAT
54209691 TT
1 TT
54209693 TATGCATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (14 bp):
TTGAATTTGGTCAT
Found at i:54216862 original size:27 final size:27
Alignment explanation
Indices: 54216832--54217059 Score: 196
Period size: 27 Copynumber: 8.4 Consensus size: 27
54216822 TATAACAGTC
*
54216832 ATTTTACCCTAT-GGGGGTATTTTAGTA
1 ATTTTACCC-ATCGAGGGTATTTTAGTA
** * * *
54216859 ATTTTATACTTCAAAGGTATTTT-GATA
1 ATTTTACCCATCGAGGGTATTTTAG-TA
* *
54216886 ATTTTAACCATCGAGGGTA-TTTCGATA
1 ATTTTACCCATCGAGGGTATTTTAG-TA
* * *
54216913 ATTTTATCCATTGAGGGTATTTTAATA
1 ATTTTACCCATCGAGGGTATTTTAGTA
* **
54216940 ATTTTACCCATCAAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTTAGTA
* *
54216967 ATTTTACCTATCGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTTAGTA
** *
54216994 ATTTTATGCATTGAGGGTA--TTACGATA
1 ATTTTACCCATCGAGGGTATTTTA-G-TA
*
54217021 ATTTTACCCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTTAGTA
54217048 ATTTTACCCATC
1 ATTTTACCCATC
54217060 AGAGTTATTT
Statistics
Matches: 160, Mismatches: 33, Indels: 16
0.77 0.16 0.08
Matches are distributed among these distances:
25 2 0.01
26 6 0.04
27 146 0.91
28 4 0.03
29 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTTAGTA
Found at i:54216959 original size:81 final size:81
Alignment explanation
Indices: 54216846--54217082 Score: 273
Period size: 81 Copynumber: 2.9 Consensus size: 81
54216836 TACCCTATGG
* ** * *
54216846 GGGTATTTTAGTAATTTTATACTTCAAAGGTATTTTGATAATTTTAACCATCGAGGGTATTTCGA
1 GGGTATTTTAATAATTTTACCCATCAAGGGTATTTTGATAATTTTAACCATCGAGGGTATTTCGA
54216911 TAATTTTATCCATTGA
66 TAATTTTATCCATTGA
* * *
54216927 GGGTATTTTAATAATTTTACCCATCAAGGGTATTTCGGTAATTTT-ACCTATCGAGGGTATTTTG
1 GGGTATTTTAATAATTTTACCCATCAAGGGTATTTTGATAATTTTAACC-ATCGAGGGTATTTCG
* *
54216991 GTAATTTTATGCATTGA
65 ATAATTTTATCCATTGA
*** * * * *
54217008 GGGTATTACGATAATTTTACCCATCGAGGGTA-TTTCAGTAATTTTACCCATC-AGAGTTATTTC
1 GGGTATTTTAATAATTTTACCCATCAAGGGTATTTTGA-TAATTTTAACCATCGAG-GGTATTTC
54217071 GATAATTTTATC
64 GATAATTTTATC
54217083 GAGGGTATTA
Statistics
Matches: 130, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
80 7 0.05
81 121 0.93
82 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (81 bp):
GGGTATTTTAATAATTTTACCCATCAAGGGTATTTTGATAATTTTAACCATCGAGGGTATTTCGA
TAATTTTATCCATTGA
Found at i:54217068 original size:27 final size:27
Alignment explanation
Indices: 54216874--54217080 Score: 238
Period size: 27 Copynumber: 7.7 Consensus size: 27
54216864 ATACTTCAAA
* *
54216874 GGTATTTTGATAATTTTAACCATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
* *
54216901 GGTATTTCGATAATTTTATCCATTGAG
1 GGTATTTCGATAATTTTACCCATCGAG
** *
54216928 GGTATTTTAATAATTTTACCCATCAAG
1 GGTATTTCGATAATTTTACCCATCGAG
* *
54216955 GGTATTTCGGTAATTTTACCTATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
* * ** *
54216982 GGTATTTTGGTAATTTTATGCATTGAG
1 GGTATTTCGATAATTTTACCCATCGAG
*
54217009 GGTATTACGATAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCATCGAG
54217036 GGTATTTC-AGTAATTTTACCCATC-AG
1 GGTATTTCGA-TAATTTTACCCATCGAG
*
54217062 AGTTATTTCGATAATTTTA
1 -GGTATTTCGATAATTTTA
54217081 TCGAGGGTAT
Statistics
Matches: 151, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.02
27 147 0.97
28 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.42
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCCATCGAG
Found at i:54217510 original size:22 final size:21
Alignment explanation
Indices: 54217464--54217513 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
54217454 CATTACGGCT
*
54217464 ATAAAAAGCCATTGAAATACT
1 ATAAAAAGCCATTGAAATACA
*
54217485 ATAAAAAGGCATTGAGAA-ATCA
1 ATAAAAAGCCATTGA-AATA-CA
54217507 ATAAAAA
1 ATAAAAA
54217514 ACTGAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (21 bp):
ATAAAAAGCCATTGAAATACA
Found at i:54218526 original size:20 final size:21
Alignment explanation
Indices: 54218489--54218529 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
54218479 TATGTAATCA
54218489 TTATTTTCATAATCTATATAT
1 TTATTTTCATAATCTATATAT
54218510 TTATTTT-ATAA-CTTATATAT
1 TTATTTTCATAATC-TATATAT
54218530 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 11 0.58
21 7 0.37
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATCTATATAT
Found at i:54218667 original size:98 final size:98
Alignment explanation
Indices: 54218554--54218749 Score: 383
Period size: 98 Copynumber: 2.0 Consensus size: 98
54218544 TTATATTTTT
*
54218554 AATACATATTTTATAATCTATATATATATTTATATATTTTTCTTTATTTTCATCAATGCATTATA
1 AATAAATATTTTATAATCTATATATATATTTATATATTTTTCTTTATTTTCATCAATGCATTATA
54218619 TATTTTATTAAATTCATAACCCATAATCGTATA
66 TATTTTATTAAATTCATAACCCATAATCGTATA
54218652 AATAAATATTTTATAATCTATATATATATTTATATATTTTTCTTTATTTTCATCAATGCATTATA
1 AATAAATATTTTATAATCTATATATATATTTATATATTTTTCTTTATTTTCATCAATGCATTATA
54218717 TATTTTATTAAATTCATAACCCATAATCGTATA
66 TATTTTATTAAATTCATAACCCATAATCGTATA
54218750 TATCAATCCA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (98 bp):
AATAAATATTTTATAATCTATATATATATTTATATATTTTTCTTTATTTTCATCAATGCATTATA
TATTTTATTAAATTCATAACCCATAATCGTATA
Found at i:54222112 original size:39 final size:41
Alignment explanation
Indices: 54222017--54222200 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
54222007 TTGAATGATG
*
54222017 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
54222056 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
54222096 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
54222135 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
54222175 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54222201 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:54222152 original size:79 final size:81
Alignment explanation
Indices: 54222017--54222200 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
54222007 TTGAATGATG
54222017 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
54222080 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
54222095 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
54222156 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
54222175 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54222201 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:54222222 original size:79 final size:79
Alignment explanation
Indices: 54222069--54222233 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
54222059 GGACTAAGAT
* ** *
54222069 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
54222134 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
54222148 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* * *
54222210 CTATAT-CTGGTTAAATT
62 CTAAATCCGGGTTAAATC
54222227 CCGAAGG
1 CCGAAGG
54222234 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 47 0.64
80 23 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:54227936 original size:23 final size:22
Alignment explanation
Indices: 54227896--54227939 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
54227886 AAATTATAAA
*
54227896 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
54227918 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
54227940 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:54228075 original size:36 final size:36
Alignment explanation
Indices: 54228035--54228110 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
54228025 TGAAACATAG
*
54228035 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
54228071 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
54228108 AAA
1 AAA
54228111 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:54228666 original size:22 final size:21
Alignment explanation
Indices: 54228631--54228688 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
54228621 AAAGGATATC
* *
54228631 TACAAATTAAATCTCTAAAAT
1 TACAAATCATATCTCTAAAAT
*
54228652 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAAAT
* *
54228675 TGCATATCATATCT
1 TACAAATCATATCT
54228689 TGATAGAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:54246146 original size:14 final size:15
Alignment explanation
Indices: 54246127--54246155 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54246117 TAATTTTGCA
54246127 TTTTGGT-TTATTTT
1 TTTTGGTGTTATTTT
54246141 TTTTGGTGTTATTTT
1 TTTTGGTGTTATTTT
54246156 AGGTGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.76
Consensus pattern (15 bp):
TTTTGGTGTTATTTT
Found at i:54248849 original size:28 final size:27
Alignment explanation
Indices: 54248792--54248943 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
54248782 TAAATTGTGC
*
54248792 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
54248819 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
54248847 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
54248874 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
54248902 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
54248929 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54248944 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:54248856 original size:55 final size:55
Alignment explanation
Indices: 54248792--54248943 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
54248782 TAAATTGTGC
*
54248792 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
54248847 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
54248902 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
54248944 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:54273387 original size:13 final size:13
Alignment explanation
Indices: 54273369--54273394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54273359 TGAAATCATA
54273369 ATTATAATAATTT
1 ATTATAATAATTT
54273382 ATTATAATAATTT
1 ATTATAATAATTT
54273395 CAGTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:54274295 original size:35 final size:35
Alignment explanation
Indices: 54274246--54274314 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
54274236 CAATGAGAAT
* *
54274246 ACTTTGTCATCAATCAACTGCACATTAGTCTCAAC
1 ACTTTGTCACCAATCAACTACACATTAGTCTCAAC
*
54274281 ACTTTGTCACCAATCACCTACACATTAGTCTCAA
1 ACTTTGTCACCAATCAACTACACATTAGTCTCAA
54274315 TGCATTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.30
Consensus pattern (35 bp):
ACTTTGTCACCAATCAACTACACATTAGTCTCAAC
Found at i:54289724 original size:19 final size:18
Alignment explanation
Indices: 54289678--54289725 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
54289668 GATAGAATTT
*
54289678 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
54289697 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
54289715 TTGTATTAAAA
1 TTGTA-TAAAA
54289726 ATTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:54289784 original size:20 final size:21
Alignment explanation
Indices: 54289740--54289787 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
54289730 GAACATGTTC
54289740 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
54289762 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
54289782 ATTTTT
1 ATTTTT
54289788 GACAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:54291334 original size:5 final size:5
Alignment explanation
Indices: 54291324--54291356 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
54291314 GCATTAGAAC
*
54291324 TTTAT TTTAT TTTAT TTTAT TTTAC TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
54291357 CTAGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:54300363 original size:23 final size:23
Alignment explanation
Indices: 54300330--54300391 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
54300320 CGGTTTTGGG
* **
54300330 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATACGA
*
54300353 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATACGA
54300376 TTTGGTACGAAATGGT
1 TTTGGTACGAAATGGT
54300392 TATGGTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATACGA
Found at i:54323046 original size:21 final size:22
Alignment explanation
Indices: 54323001--54323046 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
54322991 AGAGAAAAAT
*
54323001 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
54323023 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
54323044 AAA
1 AAA
54323047 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:54326965 original size:119 final size:120
Alignment explanation
Indices: 54326763--54327037 Score: 353
Period size: 119 Copynumber: 2.3 Consensus size: 120
54326753 TTAGGGATAG
* * * * *
54326763 CGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGATATCGAAGTACAAATACGGGCACGTATG
1 CGAAGTACAAACAGGGGCAAGTATGTGCATTCAGGGATATCAAAGTACAAACACGGGCACATATG
* *
54326828 TGTATTCAGGGGTATTGAAGTACAAATAGGGGCA-ATATATGCATTTAGAGG-TAC
66 TGCATTCAGGGGTATTGAAGTACAAATAGGGGCATATATATGCATTCAG-GGCTAC
*
54326882 CGAAGTACAAACAGGGGCAAGTATGTGCATTCAGAGG-TAAT-AAAGTACAAACAGGGGCACATA
1 CGAAGTACAAACAGGGGCAAGTATGTGCATTCAG-GGAT-ATCAAAGTACAAACACGGGCACATA
* * *
54326945 TGTGCATTCAGGGGTTTTGAAGTACAAATAGGGGCATGTATGTGCATTCAGGGCTAC
64 TGTGCATTCAGGGGTATTGAAGTACAAATAGGGGCATATATATGCATTCAGGGCTAC
** *
54327002 TAAAGTGA-AAACAGGGGCATGTATGTGCATTCAGGG
1 CGAAGT-ACAAACAGGGGCAAGTATGTGCATTCAGGG
54327038 GTGCCGAAGT
Statistics
Matches: 137, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
119 89 0.65
120 47 0.34
121 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (120 bp):
CGAAGTACAAACAGGGGCAAGTATGTGCATTCAGGGATATCAAAGTACAAACACGGGCACATATG
TGCATTCAGGGGTATTGAAGTACAAATAGGGGCATATATATGCATTCAGGGCTAC
Found at i:54326987 original size:80 final size:79
Alignment explanation
Indices: 54326765--54327039 Score: 320
Period size: 80 Copynumber: 3.5 Consensus size: 79
54326755 AGGGATAGCG
* * * * *
54326765 AAGTACAAACAAGGGCACGTATGTGCATTCAGGGATATCGAAGTACAAATACGGGCACGTATGTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAATAGGGGCAAGTATGTG
* * *
54326830 TATTCAGGGGTATTG
66 CATTCA-GGGTAATA
* * * * * *
54326845 AAGTACAAATAGGGGCA-ATATATGCATTTAGAGGTACCGAAGTACAAACAGGGGCAAGTATGTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAATAGGGGCAAGTATGTG
54326909 CATTCAGAGGTAATA
66 CATTCAG-GGTAATA
* * *
54326924 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTTTTGAAGTACAAATAGGGGCATGTATGTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAATAGGGGCAAGTATGTG
*
54326989 CATTCAGGGCTACTA
66 CATTCAGGG-TAATA
**
54327004 AAGTGA-AAACAGGGGCATGTATGTGCATTCAGGGGT
1 AAGT-ACAAACAGGGGCACATATGTGCATTCAGGGGT
54327040 GCCGAAGTGA
Statistics
Matches: 165, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
78 1 0.01
79 66 0.40
80 97 0.59
81 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (79 bp):
AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTATCGAAGTACAAATAGGGGCAAGTATGTG
CATTCAGGGTAATA
Found at i:54326997 original size:20 final size:20
Alignment explanation
Indices: 54326974--54327038 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
54326964 AAGTACAAAT
54326974 AGGGGCATGTATGTGCATTC
1 AGGGGCATGTATGTGCATTC
* * * **
54326994 A-GGGCTACT-AAAGTGAAAAC
1 AGGGGC-A-TGTATGTGCATTC
54327014 AGGGGCATGTATGTGCATTC
1 AGGGGCATGTATGTGCATTC
54327034 AGGGG
1 AGGGG
54327039 TGCCGAAGTG
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (20 bp):
AGGGGCATGTATGTGCATTC
Found at i:54327054 original size:40 final size:40
Alignment explanation
Indices: 54326763--54327047 Score: 286
Period size: 40 Copynumber: 7.2 Consensus size: 40
54326753 TTAGGGATAG
* * *
54326763 CGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGATAT
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
* * * *
54326803 CGAAGTACAAATACGGGCACGTATGTGTATTCAGGGGTAT
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
* * * * * *
54326843 TGAAGTACAAATAGGGGCA-ATATATGCATTTAGAGGTAC
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
* * *
54326882 CGAAGTACAAACAGGGGCAAGTATGTGCATTCAGAGGTAA
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
** * **
54326922 TAAAGTACAAACAGGGGCACATATGTGCATTCAGGGGTTT
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
* * * *
54326962 TGAAGTACAAATAGGGGCATGTATGTGCATTCAGGGCTAC
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
** * *
54327002 TAAAGTGA-AAACAGGGGCATGTATGTGCATTCAGGGGTGC
1 CGAAGT-ACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
54327042 CGAAGT
1 CGAAGT
54327048 GAAAACACAA
Statistics
Matches: 205, Mismatches: 38, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
39 31 0.15
40 173 0.84
41 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.23
Consensus pattern (40 bp):
CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTAC
Found at i:54338527 original size:25 final size:25
Alignment explanation
Indices: 54338498--54338574 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 25
54338488 GCCACAACTG
54338498 GTGAGAGCATACCGATTTATAGCTC
1 GTGAGAGCATACCGATTTATAGCTC
* *
54338523 TTGAGAGCATACCGATCTATAGCTC
1 GTGAGAGCATACCGATTTATAGCTC
* * * *
54338548 GAGTGAGCATACCGATTCACAGCTC
1 GTGAGAGCATACCGATTTATAGCTC
54338573 GT
1 GT
54338575 ATGAGTATAC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
GTGAGAGCATACCGATTTATAGCTC
Found at i:54338579 original size:25 final size:25
Alignment explanation
Indices: 54338502--54338584 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
54338492 CAACTGGTGA
* *
54338502 GAGCATACCGATTTATAGCTCTTGA-
1 GAGCATACCGATTCATAGCTCGT-AT
54338527 GAGCATACCGA-TCTATAGCTCG-AGT
1 GAGCATACCGATTC-ATAGCTCGTA-T
*
54338552 GAGCATACCGATTCACAGCTCGTAT
1 GAGCATACCGATTCATAGCTCGTAT
*
54338577 GAGTATAC
1 GAGCATAC
54338585 ATGTACATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 44 0.90
26 3 0.06
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (25 bp):
GAGCATACCGATTCATAGCTCGTAT
Found at i:54347014 original size:148 final size:142
Alignment explanation
Indices: 54346712--54347149 Score: 428
Period size: 138 Copynumber: 3.0 Consensus size: 142
54346702 TTTTATATTA
* * *
54346712 ATAAATTCGATAAAATATATGCAATTAATATTTTTTATGAATCAAATTCATATATTAATTATATT
1 ATAAATTC-AT-ACATATATACAATTAATA--TTATATGAAT-AAATTCATATATTAATTATATT
* * * * *
54346777 CTTTCCAAAA-AATATTAATTTCCATTTATTTTGTA-TTTGACCT-AATTTAATTAATATAACTA
61 CTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGA-CTGAAATTAATTAATATAACTG
* ** *
54346839 TTTATACTACTGTTTATATTA
125 TTTATACTA--ATAAAT-TTG
*
54346860 ATAAATTCAGTATTATATATACAATTAATATCCTATATGAATAAGATTCATATATTAATTATATT
1 ATAAATTCA-TA-CATATATACAATTAATAT--TATATGAATAA-ATTCATATATTAATTATATT
* * *
54346925 CTTTCAAAAAGAATATTAATTTTCATGTCTTTTATATTTTGTCTGAAATTAATTAATATAACTGT
61 CTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAATATAACTGT
* *
54346990 TTACATTAATAAATTTG
126 TTATACTAATAAATTTG
* * * *
54347007 GTCAAATTTATACA-AT-TAAAATT--T-TGA-ATGAATAAAATTCATATATTAATTATATTCTT
1 AT-AAATTCATACATATATACAATTAATATTATATGAAT-AAATTCATATATTAATTATATTCTT
* *
54347066 TCCAAAAGAATATTAATTTCCATGTCTTTAATATATTT-ACCGAAATTAATTAATATAACTGTTT
64 TCCAAAAGAATATTAATTTCCATGTCTTTTATAT-TTTGACTGAAATTAATTAATATAACTGTTT
*
54347130 ATAGTAATAAATTTG
128 ATACTAATAAATTTG
54347145 ATAAA
1 ATAAA
54347150 ATATATACAA
Statistics
Matches: 249, Mismatches: 30, Indels: 33
0.80 0.10 0.11
Matches are distributed among these distances:
137 3 0.01
138 98 0.39
139 6 0.02
141 1 0.00
142 1 0.00
144 6 0.02
145 2 0.01
146 2 0.01
147 9 0.04
148 70 0.28
149 23 0.09
150 28 0.11
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (142 bp):
ATAAATTCATACATATATACAATTAATATTATATGAATAAATTCATATATTAATTATATTCTTTC
CAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAATATAACTGTTTATA
CTAATAAATTTG
Found at i:54355116 original size:28 final size:28
Alignment explanation
Indices: 54355057--54355116 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
54355047 AAGTACTTTG
*
54355057 AATTGATCATTTTATGATCGTATGTGAT
1 AATTGATCATTTAATGATCGTATGTGAT
*
54355085 AATTGATGCGATTTAATGATTGT-TGTGA-
1 AATTGAT-C-ATTTAATGATCGTATGTGAT
54355113 AATT
1 AATT
54355117 ATGTGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 11 0.39
29 6 0.21
30 11 0.39
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (28 bp):
AATTGATCATTTAATGATCGTATGTGAT
Found at i:54355431 original size:24 final size:23
Alignment explanation
Indices: 54355404--54355481 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
54355394 TTTGCTGCGA
54355404 TATTGAGTGGCTTCGCCACAACAT
1 TATTGAGTGGCTT-GCCACAACAT
* *
54355428 TATTAAGTGGCTTGTCCACAACGT
1 TATTGAGTGGCTTG-CCACAACAT
*
54355452 TATT-ACGTGACTTGGCCACAACAT
1 TATTGA-GTGGCTT-GCCACAACAT
54355476 TATTGA
1 TATTGA
54355482 TTAGTTTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.04
24 42 0.91
25 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (23 bp):
TATTGAGTGGCTTGCCACAACAT
Found at i:54356438 original size:12 final size:12
Alignment explanation
Indices: 54356421--54356445 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54356411 GGGTTACAAA
54356421 ATGAGCCAATTG
1 ATGAGCCAATTG
54356433 ATGAGCCAATTG
1 ATGAGCCAATTG
54356445 A
1 A
54356446 CACCAAAATC
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:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGAGCCAATTG
Found at i:54360137 original size:24 final size:24
Alignment explanation
Indices: 54360110--54360203 Score: 143
Period size: 24 Copynumber: 3.9 Consensus size: 24
54360100 CTTACTGCAA
*
54360110 TATTGAGTGGCTTGACCCCAACGT
1 TATTGAGTGGCTTGACCACAACGT
* *
54360134 TATTGAGTGGCTTGGCCACAACGC
1 TATTGAGTGGCTTGACCACAACGT
* *
54360158 TATTGAGTGGCTTGTCCACAATGT
1 TATTGAGTGGCTTGACCACAACGT
54360182 TATTGAGTGGCTTGACCACAAC
1 TATTGAGTGGCTTGACCACAAC
54360204 AATGTAGTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAACGT
Found at i:54361678 original size:27 final size:27
Alignment explanation
Indices: 54361648--54361717 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
54361638 ATCTAGTCAG
54361648 AGTACGCCACAAAGGCGATCCATACAA
1 AGTACGCCACAAAGGCGATCCATACAA
** * *
54361675 AGTACGCCACAAAGATGATTCATACAG
1 AGTACGCCACAAAGGCGATCCATACAA
* *
54361702 AGTATGCAACAAAGGC
1 AGTACGCCACAAAGGC
54361718 TGACAAAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.14
Consensus pattern (27 bp):
AGTACGCCACAAAGGCGATCCATACAA
Found at i:54375950 original size:15 final size:15
Alignment explanation
Indices: 54375915--54375943 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54375905 TGTAAGGAGG
54375915 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
54375930 AAGAAATACAGTGT
1 AAGAAATACAGTGT
54375944 GAGGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:54376206 original size:21 final size:20
Alignment explanation
Indices: 54376159--54376200 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
54376149 ACTTGTAGTG
54376159 TATTTTAAAAATAAAAAATA
1 TATTTTAAAAATAAAAAATA
54376179 TATTTTAAAAATAAAAAA-A
1 TATTTTAAAAATAAAAAATA
54376198 TAT
1 TAT
54376201 GGTTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAATA
Found at i:54380671 original size:14 final size:14
Alignment explanation
Indices: 54380652--54380678 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54380642 ATAGACATGG
54380652 CTATTTTAAATATT
1 CTATTTTAAATATT
54380666 CTATTTTAAATAT
1 CTATTTTAAATAT
54380679 AAAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
CTATTTTAAATATT
Found at i:54383047 original size:2 final size:2
Alignment explanation
Indices: 54383040--54383080 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
54383030 TGTTTCCTCC
*
54383040 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
54383081 AAGTCTCAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:54383219 original size:5 final size:5
Alignment explanation
Indices: 54383166--54383217 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
54383156 TACGGTTGCC
* * * *
54383166 CACCT CACCT CAACT CACCT CAACT CACCC CACCT CACCT CACCT CATCT
1 CACCT CACCT CACCT CACCT CACCT CACCT CACCT CACCT CACCT CACCT
54383216 CA
1 CA
54383218 TCATTTTCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.25, C:0.56, G:0.00, T:0.19
Consensus pattern (5 bp):
CACCT
Found at i:54384340 original size:30 final size:30
Alignment explanation
Indices: 54384279--54384340 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
54384269 GGAGGGGAGG
* * **
54384279 GGAGTAAAAGTTTTGGGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
54384309 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
54384339 GG
1 GG
54384341 TTTGGGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
Found at i:54384974 original size:13 final size:14
Alignment explanation
Indices: 54384956--54384984 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54384946 AATTCGAATC
54384956 AGCTAGCTA-ACTT
1 AGCTAGCTAGACTT
54384969 AGCTAGCTAGACTT
1 AGCTAGCTAGACTT
54384983 AG
1 AG
54384985 ACATCTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (14 bp):
AGCTAGCTAGACTT
Found at i:54389346 original size:21 final size:21
Alignment explanation
Indices: 54389301--54389346 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54389291 CTAAGATGTG
*
54389301 AATTGGATTAAATTGAATATG
1 AATTGGATTAAATTGAATATA
*
54389322 AATTGTATTAAATTG-ATATTA
1 AATTGGATTAAATTGAATA-TA
54389343 AATT
1 AATT
54389347 CATTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (21 bp):
AATTGGATTAAATTGAATATA
Found at i:54393260 original size:19 final size:20
Alignment explanation
Indices: 54393222--54393260 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54393212 AATGAATATA
54393222 TTGGAAATTACTGAAAGTGC
1 TTGGAAATTACTGAAAGTGC
*
54393242 TTGGAAATTA-TGGAAGTGC
1 TTGGAAATTACTGAAAGTGC
54393261 CTTTGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (20 bp):
TTGGAAATTACTGAAAGTGC
Found at i:54397684 original size:50 final size:50
Alignment explanation
Indices: 54397573--54397819 Score: 212
Period size: 50 Copynumber: 4.8 Consensus size: 50
54397563 ATTTGGGTAA
* * *
54397573 AGAGATCCCATGCAAGACCATGTCTGGGACTTGGCATTGGCATCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CA--GA---CATG
* * * * *
54397629 AGAGGTCCCATGTAAGACCATGTCTTGAACATGGCGTTGGCACAGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGACATG
* ** * * *
54397679 AGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCA-ATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CAGACATG
* * * *
54397729 AGAAATCCCATGTAAGACCATATCTGGGATATGGCATTGG--CAGTACAGG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAG-ACATG
* * *
54397778 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
54397820 TGTTATTATC
Statistics
Matches: 158, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.01
49 38 0.24
50 76 0.48
51 2 0.01
53 2 0.01
55 2 0.01
56 36 0.23
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGACATG
Found at i:54399303 original size:27 final size:26
Alignment explanation
Indices: 54399273--54399323 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
54399263 AATTTTTGAT
*
54399273 ATTTTTATATTTGGTAAAATTTTAACG
1 ATTTTTAT-TCTGGTAAAATTTTAACG
*
54399300 ATTTTTCTTCTGGTAAAATTTTAA
1 ATTTTTATTCTGGTAAAATTTTAA
54399324 GAAAATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (26 bp):
ATTTTTATTCTGGTAAAATTTTAACG
Found at i:54399475 original size:15 final size:15
Alignment explanation
Indices: 54399455--54399486 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54399445 CATTTCACTA
*
54399455 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
54399470 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
54399485 TT
1 TT
54399487 TGCATACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:54403031 original size:24 final size:25
Alignment explanation
Indices: 54402981--54403031 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
54402971 TTTTTGGAAA
* *
54402981 AAATTAATTTTGATAAAGTAAAATT
1 AAATTAATTTAGATAAACTAAAATT
*
54403006 AAATTAA-TTAGATTAACTAAAATT
1 AAATTAATTTAGATAAACTAAAATT
54403030 AA
1 AA
54403032 TATGATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
AAATTAATTTAGATAAACTAAAATT
Found at i:54403494 original size:48 final size:48
Alignment explanation
Indices: 54403428--54403525 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
54403418 TATTCCAAAA
* *
54403428 TAATATTATTTTAATAATTTAATATTAAATTAAATTTAATACTTATCT
1 TAATAGTAGTTTAATAATTTAATATTAAATTAAATTTAATACTTATCT
* * **
54403476 TAATAGTAGTTTATTAATTTAATATTAAATTGAATTTAATGTTTATCT
1 TAATAGTAGTTTAATAATTTAATATTAAATTAAATTTAATACTTATCT
54403524 TA
1 TA
54403526 TAGATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (48 bp):
TAATAGTAGTTTAATAATTTAATATTAAATTAAATTTAATACTTATCT
Found at i:54403538 original size:43 final size:46
Alignment explanation
Indices: 54403438--54403538 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 46
54403428 TAATATTATT
*
54403438 TTAATAATTTAATATTAAATTAAATTTAATACTTATCTTAATAGTA
1 TTAAAAATTTAATATTAAATTAAATTTAATACTTATCTTAATAGTA
** * **
54403484 GTTTATTAATTTAATATTAAATTGAATTTAATGTTTATCTT-ATAG-A
1 --TTAAAAATTTAATATTAAATTAAATTTAATACTTATCTTAATAGTA
54403530 -TAAAAATTT
1 TTAAAAATTT
54403539 TATTATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
43 7 0.15
46 1 0.02
47 4 0.09
48 35 0.74
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (46 bp):
TTAAAAATTTAATATTAAATTAAATTTAATACTTATCTTAATAGTA
Found at i:54408185 original size:257 final size:257
Alignment explanation
Indices: 54407729--54408242 Score: 1019
Period size: 257 Copynumber: 2.0 Consensus size: 257
54407719 TATAGCTTGG
54407729 CTGGCCACCCTTATGGATGATATATTGAATTCAGATTTTTTTTGTGGAGTGAAAACTCTCTTTGA
1 CTGGCCACCCTTATGGATGATATATTGAATTCAGATTTTTTTTGTGGAGTGAAAACTCTCTTTGA
54407794 GTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTATTTTTAACAATATTTTTGATTGTGG
66 GTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTATTTTTAACAATATTTTTGATTGTGG
54407859 GTGCCATCTTCAACCTTCTTCTTGCCGTGTTTTTACATTGGAGGGAAGATTAGAGCCGTTTGAAG
131 GTGCCATCTTCAACCTTCTTCTTGCCGTGTTTTTACATTGGAGGGAAGATTAGAGCCGTTTGAAG
54407924 GGAGTTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTATCCATCTTTTTTGCTAT
196 GGAGTTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTATCCATCTTTTTTGCTAT
54407986 CTGGCCACCCTTATGGATGATATATTGAATTCAGATTTTTTTTGTGGAGTGAAAACTCTCTTTGA
1 CTGGCCACCCTTATGGATGATATATTGAATTCAGATTTTTTTTGTGGAGTGAAAACTCTCTTTGA
*
54408051 GTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTATTTTTAACAATCTTTTTGATTGTGG
66 GTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTATTTTTAACAATATTTTTGATTGTGG
54408116 GTGCCATCTTCAACCTTCTTCTTGCCGTGTTTTTACATTGGAGGGAAGATTAGAGCCGTTTGAAG
131 GTGCCATCTTCAACCTTCTTCTTGCCGTGTTTTTACATTGGAGGGAAGATTAGAGCCGTTTGAAG
54408181 GGAGTTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTATCCATCTTTTTTGCTAT
196 GGAGTTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTATCCATCTTTTTTGCTAT
54408243 TTGTTCTTTT
Statistics
Matches: 256, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
257 256 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (257 bp):
CTGGCCACCCTTATGGATGATATATTGAATTCAGATTTTTTTTGTGGAGTGAAAACTCTCTTTGA
GTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTATTTTTAACAATATTTTTGATTGTGG
GTGCCATCTTCAACCTTCTTCTTGCCGTGTTTTTACATTGGAGGGAAGATTAGAGCCGTTTGAAG
GGAGTTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTATCCATCTTTTTTGCTAT
Found at i:54414404 original size:29 final size:29
Alignment explanation
Indices: 54414370--54414442 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
54414360 TTAGATATTA
* *
54414370 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
54414399 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
54414428 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
54414443 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:54417740 original size:27 final size:26
Alignment explanation
Indices: 54417702--54417787 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 26
54417692 CTTGCAGATT
54417702 TGTTTTGGTGAACTATGTTCACAAATG
1 TGTTTT-GTGAACTATGTTCACAAATG
*
54417729 TGTTTTGATGAACTATGTTCACAGATG
1 TGTTTTG-TGAACTATGTTCACAAATG
*
54417756 TGTTTTTGTGAACTACGTTCACAAATG
1 TG-TTTTGTGAACTATGTTCACAAATG
54417783 TGTTT
1 TGTTT
54417788 GTTAAGCTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.07
27 45 0.83
28 5 0.09
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (26 bp):
TGTTTTGTGAACTATGTTCACAAATG
Found at i:54420073 original size:56 final size:56
Alignment explanation
Indices: 54419986--54420096 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
54419976 AAGACAACAT
54419986 TTAGAACAATGTATGAGCATTATGAAATTTTGGTCATGCCCTTTGGATTAAAAAAA
1 TTAGAACAATGTATGAGCATTATGAAATTTTGGTCATGCCCTTTGGATTAAAAAAA
*
54420042 TTAGAACAATGTATGAGCATTATGAATTTTTGGTCATGCCCTTTGGATTAAAAAA
1 TTAGAACAATGTATGAGCATTATGAAATTTTGGTCATGCCCTTTGGATTAAAAAA
54420097 TTGCACGTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (56 bp):
TTAGAACAATGTATGAGCATTATGAAATTTTGGTCATGCCCTTTGGATTAAAAAAA
Found at i:54425551 original size:25 final size:25
Alignment explanation
Indices: 54425517--54425568 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
54425507 GATCTTGAGT
54425517 TAGCTTTAGAGCTTTCATAAGCTCG
1 TAGCTTTAGAGCTTTCATAAGCTCG
54425542 TAGCTTTAGAGCTTTCATAAGCTCG
1 TAGCTTTAGAGCTTTCATAAGCTCG
54425567 TA
1 TA
54425569 TAAGACCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (25 bp):
TAGCTTTAGAGCTTTCATAAGCTCG
Found at i:54426401 original size:43 final size:43
Alignment explanation
Indices: 54426354--54426458 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 43
54426344 AAATATGCTT
54426354 GCACACATAGTGCATCATC-G-GGCAAGCCGAAGAAATTATACTG
1 GCACACATAGTGCATCATCAGAGG-AA-CCGAAGAAATTATACTG
* * * *
54426397 GCACACGA-CGTGCATCATCAGATGAACTGAAGCAATTATACTG
1 GCACAC-ATAGTGCATCATCAGAGGAACCGAAGAAATTATACTG
**
54426440 GCACATGTAGTGCATCATC
1 GCACACATAGTGCATCATC
54426459 TGTAACAGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
43 46 0.90
44 4 0.08
45 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (43 bp):
GCACACATAGTGCATCATCAGAGGAACCGAAGAAATTATACTG
Found at i:54427726 original size:25 final size:24
Alignment explanation
Indices: 54427698--54427809 Score: 93
Period size: 25 Copynumber: 4.5 Consensus size: 24
54427688 ACTCGTACGG
* *
54427698 GCTTATCGATTTGCAGGTCGTGAGA
1 GCTTACCGATTT-CAGCTCGTGAGA
*
54427723 GCTTACTGATTCTCAGCTCGT-ATGA
1 GCTTACCGATT-TCAGCTCGTGA-GA
*
54427748 GCTTACCAATTTACAGCTCGTGAGA
1 GCTTACCGATTT-CAGCTCGTGAGA
* *
54427773 GCTTACCGATTCTCAACTCAT-ATGA
1 GCTTACCGATT-TCAGCTCGTGA-GA
*
54427798 GCTTACTGATTT
1 GCTTACCGATTT
54427810 ACTACTCGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
24 4 0.06
25 65 0.90
26 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (24 bp):
GCTTACCGATTTCAGCTCGTGAGA
Found at i:54427752 original size:50 final size:50
Alignment explanation
Indices: 54427686--54427834 Score: 156
Period size: 50 Copynumber: 3.0 Consensus size: 50
54427676 GGACACACCA
* * * * * * *
54427686 CAACTCGTACGGGCTTATCGATTTGCAGGTCGTGAGAGCTTACTGATTCT
1 CAACTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGCTTACCGATTCT
*
54427736 CAGCTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGCTTACCGATTCT
1 CAACTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGCTTACCGATTCT
* ** * * *
54427786 CAACTCATATGAGCTTACTGATTTACTA-CTCGTAAGAGCATACCAATTC
1 CAACTCGTATGAGCTTACCAATTTAC-AGCTCGTGAGAGCTTACCGATTC
54427835 ATATCTCATA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 82 0.99
51 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (50 bp):
CAACTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGCTTACCGATTCT
Found at i:54427816 original size:25 final size:25
Alignment explanation
Indices: 54427721--54427829 Score: 75
Period size: 25 Copynumber: 4.4 Consensus size: 25
54427711 CAGGTCGTGA
*
54427721 GAGCTTACTGA-TTCTCAGCTCGTAT
1 GAGCTTACCGATTTCT-AGCTCGTAT
*
54427746 GAGCTTACCAATTTAC-AGCTCGTGA-
1 GAGCTTACCGATTT-CTAGCTCGT-AT
* *
54427771 GAGCTTACCGA-TTCTCAACTCATAT
1 GAGCTTACCGATTTCT-AGCTCGTAT
* *
54427796 GAGCTTACTGATTTACTA-CTCGTAA
1 GAGCTTACCGATTT-CTAGCTCGTAT
*
54427821 GAGCATACC
1 GAGCTTACC
54427830 AATTCATATC
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
23 1 0.02
24 3 0.05
25 53 0.80
26 6 0.09
27 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGATTTCTAGCTCGTAT
Found at i:54427843 original size:50 final size:50
Alignment explanation
Indices: 54427731--54427849 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 50
54427721 GAGCTTACTG
* * * * *
54427731 ATTCTCAGCTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGCTTACCG
1 ATTCTCAACTCATATGAGCTTACCAATTTACAGCTCGTAAGAGCATACCA
**
54427781 ATTCTCAACTCATATGAGCTTACTGATTTACTA-CTCGTAAGAGCATACCA
1 ATTCTCAACTCATATGAGCTTACCAATTTAC-AGCTCGTAAGAGCATACCA
*
54427831 ATTCAT-ATCTCATATGAGC
1 ATTC-TCAACTCATATGAGC
54427850 ATACATGTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 57 0.97
51 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (50 bp):
ATTCTCAACTCATATGAGCTTACCAATTTACAGCTCGTAAGAGCATACCA
Found at i:54428013 original size:17 final size:17
Alignment explanation
Indices: 54427991--54428024 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54427981 TTACAGGTAT
54427991 AAAATGACATTACATGG
1 AAAATGACATTACATGG
54428008 AAAATGACATTACATGG
1 AAAATGACATTACATGG
54428025 CATATAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
AAAATGACATTACATGG
Found at i:54435319 original size:16 final size:16
Alignment explanation
Indices: 54435295--54435331 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
54435285 GTATGCGGAC
54435295 TTGAAAAGAAAAGAGA
1 TTGAAAAGAAAAGAGA
*
54435311 TTGAGAAGAAAAGAGA
1 TTGAAAAGAAAAGAGA
54435327 TTGAA
1 TTGAA
54435332 TTTCAAGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (16 bp):
TTGAAAAGAAAAGAGA
Found at i:54436856 original size:18 final size:17
Alignment explanation
Indices: 54436823--54436861 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54436813 TTGTATAAAT
54436823 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
54436841 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
54436858 TGTG
1 TGTG
54436862 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:54437114 original size:23 final size:23
Alignment explanation
Indices: 54437087--54437162 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
54437077 AGTGTTATTG
54437087 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
54437110 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54437133 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54437156 ATCAGTG
1 ATCAGTG
54437163 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:54439204 original size:42 final size:41
Alignment explanation
Indices: 54439089--54439234 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 41
54439079 AGGGGTGTTA
* *
54439089 CATCATCGGATAAACCAAAGCAATCATACTAGCACATAAATG
1 CATCATCGGATAAACCAAAGCAA-CATACTAGCACGTAAGTG
** * * * * *
54439131 CATCATTAGATAAATCGAAGTATTCATACTAGCACGTAAGTT
1 CATCATCGGATAAACCAAAGCA-ACATACTAGCACGTAAGTG
* *
54439173 CATCATTGGATAAACCAAAGCGAACAAACTAGCACGTAAGTG
1 CATCATCGGATAAACCAAAGC-AACATACTAGCACGTAAGTG
*
54439215 CATCATCGGCTAAACCAAAG
1 CATCATCGGATAAACCAAAG
54439235 TATAAACCCT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 83 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (41 bp):
CATCATCGGATAAACCAAAGCAACATACTAGCACGTAAGTG
Found at i:54442764 original size:30 final size:30
Alignment explanation
Indices: 54442721--54442783 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
54442711 ACTTATTTTA
*
54442721 TTGTTAATATTGTTTTTATTTTAAAGACAT
1 TTGTTAATATTGTTATTATTTTAAAGACAT
* * * *
54442751 TTGTTATTTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATATTGTTATTATTTTAAAGACAT
54442781 TTG
1 TTG
54442784 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATATTGTTATTATTTTAAAGACAT
Found at i:54448812 original size:23 final size:23
Alignment explanation
Indices: 54448782--54448827 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54448772 AGGATAGAAG
54448782 AGCTTATATACTTTGAAATCTCT
1 AGCTTATATACTTTGAAATCTCT
54448805 AGCTTATATACTTTGAAATCTCT
1 AGCTTATATACTTTGAAATCTCT
54448828 TTTACTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (23 bp):
AGCTTATATACTTTGAAATCTCT
Found at i:54453692 original size:34 final size:35
Alignment explanation
Indices: 54453634--54453700 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
54453624 CAAACACCAA
*
54453634 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
54453669 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
54453701 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:54455751 original size:29 final size:29
Alignment explanation
Indices: 54455674--54455762 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
54455664 AGGGTCTATT
* *
54455674 AGGCACTATGTGTCGGTGATTACATTTATC
1 AGGCACTTTGTGTCGGTG-TTACAGTTATC
* ** * *
54455704 AGGTACTTTGTACCAGTGTTACAGTTATG
1 AGGCACTTTGTGTCGGTGTTACAGTTATC
* * *
54455733 AGGCACTTTATGTCGGTGTTATATTTATC
1 AGGCACTTTGTGTCGGTGTTACAGTTATC
54455762 A
1 A
54455763 AGTACTATGT
Statistics
Matches: 44, Mismatches: 15, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 31 0.70
30 13 0.30
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (29 bp):
AGGCACTTTGTGTCGGTGTTACAGTTATC
Found at i:54458041 original size:34 final size:34
Alignment explanation
Indices: 54457974--54458041 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
54457964 TTAAATGATT
* **
54457974 AGCTTGACAATTGGAGTTCTCGAACAGTCTTGGA
1 AGCTTGACAATTGAAGTTCTCGAACAACCTTGGA
*
54458008 AGCTTGACACTTGAAGTTCTCGAA-AACCATTGGA
1 AGCTTGACAATTGAAGTTCTCGAACAACC-TTGGA
54458042 GTGGACTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (34 bp):
AGCTTGACAATTGAAGTTCTCGAACAACCTTGGA
Found at i:54459300 original size:36 final size:36
Alignment explanation
Indices: 54459245--54459328 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
54459235 AATCCTACCA
* * *
54459245 AAACACACCAGATGCTCATAAGAGCT-AGTCCATCTG
1 AAACACACCAAATGCTCATAAGACCTCA-TCCATCCG
*
54459281 AAACACACCAAATGTTCATAAGACCTCATCCATCCG
1 AAACACACCAAATGCTCATAAGACCTCATCCATCCG
54459317 AAACACACCAAA
1 AAACACACCAAA
54459329 ATAGAGAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.17
Consensus pattern (36 bp):
AAACACACCAAATGCTCATAAGACCTCATCCATCCG
Found at i:54473418 original size:30 final size:30
Alignment explanation
Indices: 54473384--54473440 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54473374 CCTCGACTCT
54473384 AACTTTTGA-AAAATTATGATTTTGCCCTTA
1 AACTTTT-ACAAAATTATGATTTTGCCCTTA
* *
54473414 AACTTTTACATAATTATGCTTTTGCCC
1 AACTTTTACAAAATTATGATTTTGCCC
54473441 CAAAGTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTATGATTTTGCCCTTA
Found at i:54480612 original size:23 final size:23
Alignment explanation
Indices: 54480585--54480706 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
54480575 AGTGTTATTG
*
54480585 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
54480608 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
54480631 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
54480654 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
54480677 AACAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54480700 ATCAGTG
1 ATCAGTG
54480707 TTGCACTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:54480640 original size:46 final size:46
Alignment explanation
Indices: 54480587--54480706 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
54480577 TGTTATTGAT
*
54480587 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGACTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACTACATAA
*
54480633 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACTACATAA
* *
54480679 CAGTGGTAGCTTCAGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
54480707 TTGCACTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGACTACATAA
Found at i:54489525 original size:41 final size:41
Alignment explanation
Indices: 54489463--54489638 Score: 307
Period size: 41 Copynumber: 4.3 Consensus size: 41
54489453 AATTTAACAT
* *
54489463 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
54489504 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
54489545 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
54489586 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
54489627 ATTCAGATCACC
1 ATTCAGATCACC
54489639 AATTCCAAAC
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:54495872 original size:9 final size:10
Alignment explanation
Indices: 54495852--54495889 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
54495842 ATTACGTGTT
54495852 TGAATAGAAA
1 TGAATAGAAA
54495862 TGAAT-GAAA
1 TGAATAGAAA
54495871 TGAATAGAAA
1 TGAATAGAAA
54495881 --AATAGAAA
1 TGAATAGAAA
54495889 T
1 T
54495890 AAGAAACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 9 0.35
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:54499338 original size:42 final size:42
Alignment explanation
Indices: 54499291--54499523 Score: 393
Period size: 42 Copynumber: 5.6 Consensus size: 42
54499281 GAGCATTGGA
54499291 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
54499333 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
54499375 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
54499417 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG--
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * *
54499457 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG--
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
54499497 ATATGTCCGGGTTAAGACCCGAAGGCA
1 ATATATCCGGGCTAAGACCCGAAGGCA
54499524 AATGTGTTTG
Statistics
Matches: 186, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 62 0.33
42 124 0.67
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (42 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:54509042 original size:11 final size:11
Alignment explanation
Indices: 54509026--54509050 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54509016 GTGTTTTATT
54509026 ATTGGAATTGA
1 ATTGGAATTGA
54509037 ATTGGAATTGA
1 ATTGGAATTGA
54509048 ATT
1 ATT
54509051 ATTATTGGTA
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (11 bp):
ATTGGAATTGA
Found at i:54521199 original size:22 final size:22
Alignment explanation
Indices: 54521136--54521209 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
54521126 CAGCAAAGCT
*
54521136 GCCAGTAACCAGAATGGCTAAGA
1 GCCA-TAAACAGAATGGCTAAGA
* * * **
54521159 GCCGTAAACAGGATAGCTATTA
1 GCCATAAACAGAATGGCTAAGA
*
54521181 GCTATAAACAGAATGGCTACA-A
1 GCCATAAACAGAATGGCTA-AGA
54521203 GCCATAA
1 GCCATAA
54521210 GTATAGTAAT
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
22 35 0.92
23 3 0.08
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (22 bp):
GCCATAAACAGAATGGCTAAGA
Found at i:54521255 original size:32 final size:32
Alignment explanation
Indices: 54521201--54521368 Score: 212
Period size: 32 Copynumber: 5.3 Consensus size: 32
54521191 GAATGGCTAC
* * *
54521201 AAGCCATAAGT-ATAGTAATATGATTGGCGCA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
54521232 AAGCCATCAGTAGTAATAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
54521264 CAGCCATCAGTAATAGTAGTATGATCAGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
54521296 AAGCCATCAATAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
54521328 CAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
54521360 AAGCCATCA
1 AAGCCATCA
54521369 ATAGCATCAT
Statistics
Matches: 114, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
31 10 0.09
32 104 0.91
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:54521316 original size:64 final size:64
Alignment explanation
Indices: 54521202--54521372 Score: 245
Period size: 64 Copynumber: 2.7 Consensus size: 64
54521192 AATGGCTACA
* ** * *
54521202 AGCCATAAGT-ATAGTAATATGATTGGCGCAAAGCCATCAGTAGTAATAATATGATCGGCACAC
1 AGCCATCAGTAATAGTAATATGATCAGCACAAAGCCATCAATAGTAATAATATGATCGGCACAC
* * *
54521265 AGCCATCAGTAATAGTAGTATGATCAGTACAAAGCCATCAATAGTAGTAATATGATCGGCACAC
1 AGCCATCAGTAATAGTAATATGATCAGCACAAAGCCATCAATAGTAATAATATGATCGGCACAC
* *
54521329 AGCCATCAGTAATGGTAATATGATCGGCACAAAGCCATCAATAG
1 AGCCATCAGTAATAGTAATATGATCAGCACAAAGCCATCAATAG
54521373 CATCATAGCA
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 9 0.09
64 86 0.91
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (64 bp):
AGCCATCAGTAATAGTAATATGATCAGCACAAAGCCATCAATAGTAATAATATGATCGGCACAC
Found at i:54521586 original size:24 final size:24
Alignment explanation
Indices: 54521543--54521652 Score: 139
Period size: 24 Copynumber: 4.6 Consensus size: 24
54521533 CCATGCATGG
**
54521543 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* * *
54521567 AATTAGTCATTTAAACCACAGATA
1 AATCAGTCATTTAAATCACAGACA
* *
54521591 AATTAGTCATTTAAATTACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
54521615 AATCAGCCATTTAAATTACAGACA
1 AATCAGTCATTTAAATCACAGACA
54521639 AATCAGTCATTTAA
1 AATCAGTCATTTAA
54521653 CCCCGAGGGG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.27
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:54521917 original size:27 final size:27
Alignment explanation
Indices: 54521671--54521925 Score: 336
Period size: 27 Copynumber: 9.4 Consensus size: 27
54521661 GGCAAAATAG
54521671 TCATTTTACCCTACAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* * ** *
54521698 TCATTTAACCCTATAGAAGTATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* *
54521725 CCATTTTACCCTACTGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
*
54521752 TCATTTTACCCTATAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* *
54521779 TCATTTTACCCTACAAGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
54521806 TCATTTTACCCTACAGGGGCATTAC-A
1 TCATTTTACCCTACAGGGGCATTACGA
*
54521832 GTCATTTTACCCTACAAGGGCATTAC-A
1 -TCATTTTACCCTACAGGGGCATTACGA
*
54521859 GTCATTTTACCCTACAAGGGCATTAC-A
1 -TCATTTTACCCTACAGGGGCATTACGA
* *
54521886 GTCATTTTACCCTACAGGGGAATTGCGA
1 -TCATTTTACCCTACAGGGGCATTACGA
54521914 TCATTTTACCCT
1 TCATTTTACCCT
54521926 TTGAGAGTAT
Statistics
Matches: 202, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
27 201 1.00
28 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGA
Found at i:54521946 original size:27 final size:27
Alignment explanation
Indices: 54521911--54521989 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
54521901 AGGGGAATTG
* *
54521911 CGATCATTTTACCCTTTGAGAGTATTC
1 CGATAATTTTACCCTTCGAGAGTATTC
* *
54521938 C-AGTAATTTTACCCTTCGAGGGTATTT
1 CGA-TAATTTTACCCTTCGAGAGTATTC
*
54521965 CGATAATTTTA-CCTTCGAGGGTATT
1 CGATAATTTTACCCTTCGAGAGTATT
54521990 TGAATGATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 15 0.33
27 30 0.65
28 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (27 bp):
CGATAATTTTACCCTTCGAGAGTATTC
Found at i:54521974 original size:81 final size:80
Alignment explanation
Indices: 54521671--54521977 Score: 309
Period size: 81 Copynumber: 3.8 Consensus size: 80
54521661 GGCAAAATAG
* * * * * *
54521671 TCATTTTACCCTACAGGGGCATTAC-GATCATTTAACCCTA-TAGAAGTATTACGACCATTTTAC
1 TCATTTTACCCTATA-GGGCATTACAG-TCATTTTACCCTACAAG-GGCATTACGATCATTTTAC
*
54521734 CCTACTGGGGCATTACGA
63 CCTACAGGGGCATTACGA
*
54521752 TCATTTTACCCTATAGGGGCATTAC-GATCATTTTACCCTACAAGGGCATTACGGTCATTTTACC
1 TCATTTTACCCTATA-GGGCATTACAG-TCATTTTACCCTACAAGGGCATTACGATCATTTTACC
54521816 CTACAGGGGCATTAC-A
64 CTACAGGGGCATTACGA
*
54521832 GTCATTTTACCCTACAAGGGCATTACAGTCATTTTACCCTACAAGGGCATTAC-AGTCATTTTAC
1 -TCATTTTACCCTA-TAGGGCATTACAGTCATTTTACCCTACAAGGGCATTACGA-TCATTTTAC
* *
54521896 CCTACAGGGGAATTGCGA
63 CCTACAGGGGCATTACGA
* * * * * * * * * *
54521914 TCATTTTACCCTTTGAGAGTATTCCAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACC
1 TCATTTTACCCTAT-AGGGCATTACAGTCATTTTACCCTACAAGGGCATTACGATCATTTTACC
54521978 TTCGAGGGTA
Statistics
Matches: 195, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
80 1 0.01
81 188 0.96
82 6 0.03
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (80 bp):
TCATTTTACCCTATAGGGCATTACAGTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCT
ACAGGGGCATTACGA
Found at i:54526332 original size:24 final size:25
Alignment explanation
Indices: 54526305--54526367 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
54526295 CTTGAAGAAC
*
54526305 GAAATAAAAACTAAACTTATAATT-
1 GAAATAAAAACTAAACTTACAATTA
*
54526329 GAAA-AGAAACATAAA-TTACAATTA
1 GAAATAAAAAC-TAAACTTACAATTA
54526353 GAAAT-AAAACTAAAC
1 GAAATAAAAACTAAAC
54526368 AAGAAATGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.22
Consensus pattern (25 bp):
GAAATAAAAACTAAACTTACAATTA
Found at i:54526338 original size:23 final size:24
Alignment explanation
Indices: 54526305--54526367 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
54526295 CTTGAAGAAC
*
54526305 GAAATAAAAACTAAACTTATAATT-
1 GAAAT-AAAACTAAACTTACAATTA
54526329 GAAA-AGAAACATAAA-TTACAATTA
1 GAAATA-AAAC-TAAACTTACAATTA
54526353 GAAATAAAACTAAAC
1 GAAATAAAACTAAAC
54526368 AAGAAATGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
22 1 0.03
23 15 0.45
24 16 0.48
25 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.22
Consensus pattern (24 bp):
GAAATAAAACTAAACTTACAATTA
Found at i:54534990 original size:23 final size:25
Alignment explanation
Indices: 54534945--54534990 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
54534935 GGTTTTAACC
*
54534945 TTTTAATTTGTTATTTATTTATTCT
1 TTTTAATTTGTTATTTATATATTCT
54534970 TTTTAA-TTGTT-TTTATATATT
1 TTTTAATTTGTTATTTATATATT
54534991 ATTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTAATTTGTTATTTATATATTCT
Found at i:54534999 original size:26 final size:26
Alignment explanation
Indices: 54534945--54535228 Score: 170
Period size: 26 Copynumber: 11.1 Consensus size: 26
54534935 GGTTTTAACC
*
54534945 TTTTAATTTGTTATT-TAT-TTATTCT-
1 TTTTAA-TTGTTTTTATATATTATT-TA
54534970 TTTTAATTGTTTTTATATATTATTTA
1 TTTTAATTGTTTTTATATATTATTTA
* * *
54534996 TTTTTAA-CGGTTTTATATTTTATTTA
1 -TTTTAATTGTTTTTATATATTATTTA
* *
54535022 TTTTAA---ATTTTATATATTATGTA
1 TTTTAATTGTTTTTATATATTATTTA
* * *
54535045 TATTAAAT-TATTT-TATATTATTTA
1 TTTTAATTGTTTTTATATATTATTTA
*
54535069 TTTTAAATT-TTTTCATATATTATTTA
1 TTTT-AATTGTTTTTATATATTATTTA
*
54535095 TTTTGAATTG-CTTTATATATTATTTTA
1 TTTT-AATTGTTTTTATATATTA-TTTA
54535122 TTTTAAACTAT-TTTTTATATATTATTTA
1 TTTT-AA-T-TGTTTTTATATATTATTTA
* * *
54535150 TTTTAGATT-TTTTCACATATTATTTC
1 TTTTA-ATTGTTTTTATATATTATTTA
* * * *
54535176 TATTAA-AGTGTTTTATGTATTGTTTA
1 TTTTAATTGT-TTTTATATATTATTTA
*
54535202 TTTTAAATTG-CTTTA-A-ATTATTTA
1 TTTT-AATTGTTTTTATATATTATTTA
54535226 TTT
1 TTT
54535229 CAAACAGTTT
Statistics
Matches: 206, Mismatches: 35, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
23 19 0.09
24 30 0.15
25 27 0.13
26 87 0.42
27 20 0.10
28 11 0.05
29 12 0.06
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (26 bp):
TTTTAATTGTTTTTATATATTATTTA
Found at i:54535069 original size:47 final size:50
Alignment explanation
Indices: 54535006--54535146 Score: 144
Period size: 50 Copynumber: 2.7 Consensus size: 50
54534996 TTTTTAACGG
54535006 TTTTATATTTTATTTATTTTAAA-TTTT-ATATATTATGTATATTAAATT-A
1 TTTTATA--TTATTTATTTTAAATTTTTCATATATTATGTATATTAAATTGA
* * * *
54535055 TTTTATATTATTTATTTTAAATTTTTTCATATATTATTTATTTTGAATTGC
1 TTTTATATTATTTATTTTAAA-TTTTTCATATATTATGTATATTAAATTGA
*
54535106 TTTATATATTATTTTATTTTAAACTATTTTTTATATATTAT
1 TTT-TATATTA-TTTATTTT-AA--ATTTTTCATATATTAT
54535147 TTATTTTAGA
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
47 14 0.18
49 11 0.14
50 18 0.23
51 3 0.04
52 7 0.09
53 8 0.10
54 2 0.03
55 14 0.18
56 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (50 bp):
TTTTATATTATTTATTTTAAATTTTTCATATATTATGTATATTAAATTGA
Found at i:54535070 original size:73 final size:77
Alignment explanation
Indices: 54534985--54535148 Score: 187
Period size: 73 Copynumber: 2.2 Consensus size: 77
54534975 ATTGTTTTTA
* *
54534985 TATATTATTTATTTTTAACGGTTTT-ATATTTTATTTATTTT-AAAT-TTTATATATTA-TGTAT
1 TATATTATTTATTTTTAAAGGTTTTCATATATTATTTATTTTGAAATCTTTATATATTATTGTAT
*
54535046 ATTAAATTATTT
66 ATTAAACTATTT
** * *
54535058 TATATTATTTA-TTTTAAATTTTTTCATATATTATTTATTTTGAATTGCTTTATATATTATTTTA
1 TATATTATTTATTTTTAAAGGTTTTCATATATTATTTATTTTGAAAT-CTTTATATATTATTGTA
*
54535122 TTTTAAACTATTT
65 TATTAAACTATTT
*
54535135 TTTA-TATATTATTT
1 TATATTAT-TTATTT
54535149 ATTTTAGATT
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
72 10 0.13
73 26 0.35
74 3 0.04
76 14 0.19
77 20 0.27
78 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (77 bp):
TATATTATTTATTTTTAAAGGTTTTCATATATTATTTATTTTGAAATCTTTATATATTATTGTAT
ATTAAACTATTT
Found at i:54535170 original size:55 final size:52
Alignment explanation
Indices: 54534969--54535228 Score: 177
Period size: 55 Copynumber: 5.1 Consensus size: 52
54534959 TTATTTATTC
* *** *
54534969 TTTTTAATTGTTTTTATATATTATTTATTTTTA-ACGGTTTT-ATATTTTATTTA
1 TTTTAAATT-TTTTTATATATTATTTA-TTTTAGATTATTTTAATATTAT-TTTA
* * *
54535022 TTTTAAA---TTTTATATATTATGTATATTAAATTATTTT-ATATTA-TTTA
1 TTTTAAATTTTTTTATATATTATTTATTTTAGATTATTTTAATATTATTTTA
* **
54535069 TTTTAAATTTTTTCATATATTATTTATTTT-GAATTGCTTTATATATTATTTTA
1 TTTTAAATTTTTTTATATATTATTTATTTTAG-ATTATTTTA-ATATTATTTTA
54535122 TTTTAAACTATTTTTTATATATTATTTATTTTAGATT-TTTTCACATATTATTTCTA
1 TTTTAAA-T-TTTTTTATATATTATTTATTTTAGATTATTTT-A-ATATTATTT-TA
* * * * * **
54535178 --TTAAAGTGTTTTATGTATTGTTTATTTTAAATTGCTTTAA-ATTA-TTTA
1 TTTTAAATTTTTTTATATATTATTTATTTTAGATTATTTTAATATTATTTTA
54535226 TTT
1 TTT
54535229 CAAACAGTTT
Statistics
Matches: 169, Mismatches: 22, Indels: 35
0.75 0.10 0.15
Matches are distributed among these distances:
47 11 0.07
48 6 0.04
49 27 0.16
50 28 0.17
51 1 0.01
52 30 0.18
53 20 0.12
54 9 0.05
55 34 0.20
56 3 0.02
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (52 bp):
TTTTAAATTTTTTTATATATTATTTATTTTAGATTATTTTAATATTATTTTA
Found at i:54535191 original size:81 final size:80
Alignment explanation
Indices: 54534979--54535208 Score: 215
Period size: 81 Copynumber: 3.0 Consensus size: 80
54534969 TTTTTAATTG
*** * * *
54534979 TTTTTATATATTATTTATTTTTAACGGTTTT-ATATTTTATTTATTTTAAA-T--TTTATATATT
1 TTTTTATATATTATTTA-TTTTAAATTTTTTCACATATTATTTATATTAAAGTGCTTTATATATT
* * *
54535040 ATGTATATT-AA--AT
65 GTTTATTTTAAACTAT
* * * * *
54535053 TATTT-TATATTATTTATTTTAAATTTTTTCATATATTATTTATTTTGAATTGCTTTATATATTA
1 TTTTTATATATTATTTATTTTAAATTTTTTCACATATTATTTATATTAAAGTGCTTTATATATT-
*
54535117 TTTTATTTTAAACTAT
65 GTTTATTTTAAACTAT
* * * *
54535133 TTTTTATATATTATTTATTTTAGATTTTTTCACATATTATTTCTATTAAAGTGTTTTATGTATTG
1 TTTTTATATATTATTTATTTTAAATTTTTTCACATATTATTTATATTAAAGTGCTTTATATATTG
54535198 TTTATTTTAAA
66 TTTATTTTAAA
54535209 TTGCTTTAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
72 10 0.08
73 28 0.22
74 5 0.04
76 10 0.08
77 6 0.05
78 2 0.02
80 17 0.13
81 50 0.39
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (80 bp):
TTTTTATATATTATTTATTTTAAATTTTTTCACATATTATTTATATTAAAGTGCTTTATATATTG
TTTATTTTAAACTAT
Found at i:54535403 original size:27 final size:27
Alignment explanation
Indices: 54535345--54535403 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
54535335 TATTTTAAAC
*
54535345 CTTTTTATATTATTTACTTTAAATTGT
1 CTTTGTATATTATTTACTTTAAATTGT
* * *
54535372 TTTTGTATATTATTTTA-TTTCATTTGT
1 CTTTGTATATTA-TTTACTTTAAATTGT
54535399 CTTTG
1 CTTTG
54535404 ATTATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (27 bp):
CTTTGTATATTATTTACTTTAAATTGT
Found at i:54541442 original size:44 final size:44
Alignment explanation
Indices: 54541396--54541706 Score: 184
Period size: 45 Copynumber: 7.0 Consensus size: 44
54541386 ATAAGGGAGG
* * * *
54541396 TTGAAGTTACGAGCCTTATCTCCTTTAAGTTGTAGTGGAACAGG
1 TTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTAGTGGAACAGA
* *
54541440 TTGAAGTTATGAGTTTTATCTCCCTGAAGTTGTAGTGGAACAGA
1 TTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTAGTGGAACAGA
* * * * * *
54541484 CTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAACAGA
1 TTGAAGTTA-CGAGTCTTATCTCCCTGAAGTTGTAGTGGAACAGA
* * * * * *
54541529 TTGAAGTTATAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
1 TTGAAG-------TTACGAGTCTTATCTCCCTGAAGTTGTAGTGGAACAGA
* * ** * *
54541580 -T-CA--TAGCAAACCTTATC-CCCTTGAAGTTGTAGTGG-GCAGG
1 TTGAAGTTA-CGAGTCTTATCTCCC-TGAAGTTGTAGTGGAACAGA
* * ** *
54541620 TTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAAA
1 TTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTAGTGGAACAGA
* * * *
54541664 CTGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGTGGAACA
1 TTGAAGTTA-CGAGTCTTATCTCCCTGAAGTTGTAGTGGAACA
54541707 AATTAAAGCT
Statistics
Matches: 207, Mismatches: 43, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
40 8 0.04
41 23 0.11
42 1 0.00
43 22 0.11
44 59 0.29
45 61 0.29
49 1 0.00
50 1 0.00
51 29 0.14
52 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (44 bp):
TTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTAGTGGAACAGA
Found at i:54541527 original size:45 final size:45
Alignment explanation
Indices: 54541455--54542022 Score: 225
Period size: 44 Copynumber: 12.5 Consensus size: 45
54541445 GTTATGAGTT
* *
54541455 TTATCTCCCTGAAGTTGTAGTGGAACAGACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
* * * *
54541500 TTATTTCCCTGAAGTTGCAGTGAAACAGATTGAAGTTATAAATTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAG--AT--A--GCAAATC
* * * * *
54541551 TTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
* * ** * *
54541592 TTATC-CCCTTGAAGTTGTAGTGG-GCAGGTTGAAGTTA-CAAGTC
1 TTATCTCCC-TGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
** * *
54541635 TTATCTCCCTGAAGTTGCAGTGGAGTAAACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
* * * * * *
54541680 TTATTTCCCTGAAGTTGTAGTGGAACAAATTAAAGCTATAAATTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAG--AT--A--GCAAATC
** * ** * *
54541731 TTATCTCTTTGAAGTTGCAGTAGAGTAGA-T---CATATCAAA-C
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
** * * *
54541771 TTCATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATA-AATCAATC
1 TT-ATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCA--AATC
* * *
54541818 TTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGACGGGCTA-CAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGA-----TAGCAAATC
* * * * ** *
54541867 TTATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGCCA-CAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
* * * * * ** * *
54541911 TTATTTTCTTAAAGTTGCAGTGGAGCAGGTTAAAGATA-CCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
* * * * * * * *
54541955 TTATATCTCTGAAGTTACAATGGAGCAGATTGAAGCTA-CTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
*
54541999 CTATCTCCCTGAAGTTGCAGTGGA
1 TTATCTCCCTGAAGTTGCAGTGGA
54542023 GTGGATTAAA
Statistics
Matches: 396, Mismatches: 94, Indels: 67
0.71 0.17 0.12
Matches are distributed among these distances:
40 9 0.02
41 48 0.12
42 1 0.00
43 24 0.06
44 107 0.27
45 71 0.18
46 31 0.08
47 7 0.02
49 38 0.10
50 2 0.01
51 58 0.15
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAAATC
Found at i:54541533 original size:89 final size:89
Alignment explanation
Indices: 54541422--54541706 Score: 294
Period size: 89 Copynumber: 3.2 Consensus size: 89
54541412 TATCTCCTTT
* * *
54541422 AAGTTGTAGTGGAACAGGTTGAAGTTATGAGTTTTATCTCCCTGAAGTTGTAGTGGAACAGACTG
1 AAGTTGTAGTGGAACAGGTTGAAGTTATAAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
54541487 AAGATAGCGAATCTTATTTCCCTG
66 AAGATAGCGAATCTTATTTCCCTG
* * * * * *
54541511 AAGTTGCAGTGAAACAGATTGAAGTTATAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAG
1 AAGTTGTAGTGGAACAGGTTGAAGTTAT-AAGT-----T-TTATCTCCCTGAAGTTGCAGTGGAG
* * * *
54541576 CAGA-T---CATAGCAAACCTTA-TCCCCTTG
59 CAGACTGAAGATAGCGAATCTTATTTCCC-TG
* * * * *
54541603 AAGTTGTAGTGG-GCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAAACTG
1 AAGTTGTAGTGGAACAGGTTGAAGTTATAAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
54541667 AAGATAGCGAATCTTATTTCCCTG
66 AAGATAGCGAATCTTATTTCCCTG
54541691 AAGTTGTAGTGGAACA
1 AAGTTGTAGTGGAACA
54541707 AATTAAAGCT
Statistics
Matches: 153, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
84 25 0.16
85 1 0.01
88 25 0.16
89 31 0.20
90 5 0.03
91 16 0.10
92 23 0.15
95 2 0.01
96 25 0.16
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (89 bp):
AAGTTGTAGTGGAACAGGTTGAAGTTATAAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
AAGATAGCGAATCTTATTTCCCTG
Found at i:54541642 original size:180 final size:181
Alignment explanation
Indices: 54541409--54541853 Score: 601
Period size: 180 Copynumber: 2.5 Consensus size: 181
54541399 AAGTTACGAG
* * ** * *
54541409 CCTTATCTCCTTTAAGTTGTAGTGGAACAGGTTGAAGTTATGAGTTTTATCTCCCTGAAGTTGTA
1 CCTTATCCCCTTGAAGTTGTAGTGGAACAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
* * * *
54541474 GTGGAACAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAACAGATTGAAGTTAT
66 GTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAACAAATTAAAGCTAT
54541539 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAA
131 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAA
*
54541590 CCTTATCCCCTTGAAGTTGTAGTGG-GCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 CCTTATCCCCTTGAAGTTGTAGTGGAACAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
* * * *
54541654 GTGGAGTAAACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGTGGAACAAATTAAAGCTAT
66 GTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAACAAATTAAAGCTAT
* * *
54541719 AAATTACAAATCTTATCTCTTTGAAGTTGCAGTAGAGTAGATCATATCAAA
131 AAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAA
* * * *
54541770 -CTTCATCTCCC-TGAAGTTGCAGTGGAACAGGTTAAAAATAAATCAA-TCTTATCTCCCTGAAG
1 CCTT-ATC-CCCTTGAAGTTGTAGTGGAACAGGTT-GAAGT-TA-CAAGTCTTATCTCCCTGAAG
* *
54541832 TTGCAATGGAGCAGATTGAAGA
61 TTGCAGTGGAGCAGACTGAAGA
54541854 CGGGCTACAA
Statistics
Matches: 231, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
179 3 0.01
180 155 0.67
181 32 0.14
182 3 0.01
183 35 0.15
184 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (181 bp):
CCTTATCCCCTTGAAGTTGTAGTGGAACAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAACAAATTAAAGCTAT
AAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAA
Found at i:54541970 original size:44 final size:44
Alignment explanation
Indices: 54541723--54542032 Score: 241
Period size: 44 Copynumber: 7.0 Consensus size: 44
54541713 AGCTATAAAT
** * * * *
54541723 TACAAATCTTATCTCTTTGAAGTTGCAGTAGAGTAGATCATA--
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * **
54541765 T-CAAA-CTTCATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAA
1 TACAAATCTT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* *
54541808 TAAATCAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGACGGGC
1 TACA--AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-A---GC
*
54541859 TACAAATCTTATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * * * * *
54541903 CACAAACCTTATTTTCTTAAAGTTGCAGTGGAGCAGGTTAAAGA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * * *
54541947 TACCAATCTTATATCTCTGAAGTTACAATGGAGCAGATTGAAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * **
54541991 TACTAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
54542033 ACAATGAATC
Statistics
Matches: 208, Mismatches: 48, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
40 3 0.01
41 28 0.13
42 1 0.00
43 1 0.00
44 102 0.49
46 28 0.13
47 6 0.03
48 3 0.01
49 33 0.16
51 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
Found at i:54541987 original size:137 final size:133
Alignment explanation
Indices: 54541783--54542032 Score: 340
Period size: 132 Copynumber: 1.8 Consensus size: 133
54541773 CATCTCCCTG
* * *
54541783 AAGTTGCAGTGGAACAGGTTAAAAATAAATCAATCTTATCTCCCTGAAGTTGCAATGGAGCAGAT
1 AAGTTGCAGTGGAACAGGTTAAAAAT-AACCAATCTTATATCCCTGAAGTTACAATGGAGCAGAT
*
54541848 TGAAGACGGGCTACAAATCTTATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGCCACAAACCTT
65 TG-A-A---GCTACAAATCCTATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGCCACAAACCTT
54541913 ATTTTCTTA
125 ATTTTCTTA
* * *
54541922 AAGTTGCAGTGGAGCAGGTTAAAGAT-ACCAATCTTATATCTCTGAAGTTACAATGGAGCAGATT
1 AAGTTGCAGTGGAACAGGTTAAAAATAACCAATCTTATATCCCTGAAGTTACAATGGAGCAGATT
* * **
54541986 GAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
66 GAAGCTACAAATCCTATCTCCCTGAAGCTGCAGTGGAGCAGATTAAA
54542033 ACAATGAATC
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
132 39 0.39
135 1 0.01
136 1 0.01
137 35 0.35
139 24 0.24
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (133 bp):
AAGTTGCAGTGGAACAGGTTAAAAATAACCAATCTTATATCCCTGAAGTTACAATGGAGCAGATT
GAAGCTACAAATCCTATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGCCACAAACCTTATTTTC
TTA
Found at i:54547255 original size:21 final size:21
Alignment explanation
Indices: 54547230--54547280 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
54547220 TAAAAAGAAA
*
54547230 GAGCTGAAATAAAGC-TAAGTT
1 GAGCTCAAATAAAGCTTAA-TT
*
54547251 GAGCTCAAA-CAAGCTTAATT
1 GAGCTCAAATAAAGCTTAATT
*
54547271 GAGCTTAAAT
1 GAGCTCAAAT
54547281 GAATTGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (21 bp):
GAGCTCAAATAAAGCTTAATT
Found at i:54563867 original size:18 final size:18
Alignment explanation
Indices: 54563846--54563885 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54563836 GATTGAGAGT
* * *
54563846 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
54563864 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
54563882 GAAA
1 GAAA
54563886 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:54568690 original size:107 final size:107
Alignment explanation
Indices: 54568544--54568867 Score: 441
Period size: 107 Copynumber: 3.0 Consensus size: 107
54568534 AAATTAGAAA
* * *
54568544 TTGCCGAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAGCTTTCGTTCATGTTAGTTTGAACC
1 TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
* * *
54568609 ATCATCCATAATTATATTGAATTAAGATTTGCATCAATTTTG
66 ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTG
* * * * * * *
54568651 TTTCCAAATGCTAGGGCAAGCTGAGCAAATAACTCTTGAAACTTTCTTTCTTATTAGTTTGAACT
1 TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
* *
54568716 GTCATCCTTAATTATACTGAATTAAGTTTTGCATCAATGTTG
66 ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTG
* * * **
54568758 CTTGCCAAATGCTAGAGCTAGCTGGGCAAATAACTTTTGAATCTTTCATTTGTGTTAGTTTGAAC
1 -TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAAC
* *
54568823 CATCCTCCTTAATTACATTGAATTAAGTTTTGCATCAATGTTG
65 CATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTG
54568866 TT
1 TT
54568868 AATAAGTTCC
Statistics
Matches: 187, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
107 95 0.51
108 92 0.49
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (107 bp):
TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTG
Found at i:54573130 original size:20 final size:21
Alignment explanation
Indices: 54573078--54573147 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
54573068 GAATATGTAG
* *
54573078 AATAAGAACCAAAGTGCAGAGT
1 AATAAGAACCGAAGTGC-GAAT
*
54573100 AGCATTAAGAACCGGAGTGC-AAT
1 A--A-TAAGAACCGAAGTGCGAAT
*
54573123 AATAAGAACTGAAGTGCGAAT
1 AATAAGAACCGAAGTGCGAAT
54573144 AATA
1 AATA
54573148 GTAAGCATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 13 0.33
21 8 0.21
22 1 0.03
23 3 0.08
24 1 0.03
25 13 0.33
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (21 bp):
AATAAGAACCGAAGTGCGAAT
Found at i:54575662 original size:16 final size:16
Alignment explanation
Indices: 54575641--54575688 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
54575631 GCTATCGCTG
54575641 TGCGAGCTCGTCAGTT
1 TGCGAGCTCGTCAGTT
* *
54575657 TGCGAGCTCGTTATTT
1 TGCGAGCTCGTCAGTT
* *
54575673 TGCTAGCTCATCAGTT
1 TGCGAGCTCGTCAGTT
54575689 CACCTTAGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (16 bp):
TGCGAGCTCGTCAGTT
Found at i:54587382 original size:40 final size:40
Alignment explanation
Indices: 54587327--54587516 Score: 362
Period size: 40 Copynumber: 4.8 Consensus size: 40
54587317 GAGCATTTGA
54587327 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
54587367 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
54587407 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
*
54587447 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTG
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
*
54587487 ATTTTATCCGGGCTAAGACCCGAAGGCATT
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATT
54587517 CGTGCGAGTT
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 148 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (40 bp):
ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
Found at i:54587549 original size:120 final size:119
Alignment explanation
Indices: 54587327--54587554 Score: 341
Period size: 120 Copynumber: 1.9 Consensus size: 119
54587317 GAGCATTTGA
* *
54587327 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAG
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAG
* * ** *
54587392 GCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTG
66 GCATTCATGCGAGT-ATGCTATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTG
54587447 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAG
1 ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAG
* *
54587512 GCATTCGTGCGAGT-TGCTATGCCCGGGTTAAGACCCGAAGGCA
66 GCATTCATGCGAGTATGCTAT--CCGGGCTAAGACCCGAAGGCA
54587555 ATTGTGCTTG
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
118 4 0.04
120 93 0.96
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (119 bp):
ATTTTATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAG
GCATTCATGCGAGTATGCTATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTG
Found at i:54587575 original size:120 final size:119
Alignment explanation
Indices: 54587331--54587581 Score: 326
Period size: 120 Copynumber: 2.1 Consensus size: 119
54587321 ATTTGAATTT
* *
54587331 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCAT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
* * ** * * * *
54587396 TTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
66 TCATGCGAGT-ATGCTATCCGGGCTAAGACCCGAAGGCAATTATGCTAGCGATTA
54587451 TATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
* * * * *
54587516 TCGTGCGAGT-TGCTATGCCCGGGTTAAGACCCGAAGGCAATTGTGCTTGCGGTTA
66 TCATGCGAGTATGCTAT--CCGGGCTAAGACCCGAAGGCAATTATGCTAGCGATTA
54587571 TATCC-GGCTAA
1 TATCCGGGCTAA
54587582 ATTTCGAAGA
Statistics
Matches: 114, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
118 4 0.04
119 6 0.05
120 104 0.91
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (119 bp):
TATCCGGGCTAAGTCCCGAAGGCATTTATACTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAT
TCATGCGAGTATGCTATCCGGGCTAAGACCCGAAGGCAATTATGCTAGCGATTA
Found at i:54589775 original size:20 final size:21
Alignment explanation
Indices: 54589737--54589840 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 21
54589727 TTGAAGTGAG
54589737 AACAGGGGCA-CGAATGTGCA
1 AACAGGGGCACCGAATGTGCA
* *
54589757 AGCAGGGGCACCGTA-GTGCA
1 AACAGGGGCACCGAATGTGCA
*
54589777 AACAGGGACACCGAAATGT--A
1 AACAGGGGCACCG-AATGTGCA
* * *
54589797 TACAGGGGAACCGAAAAGTGCA
1 AACAGGGGCACCG-AATGTGCA
**
54589819 AACAGAAGCACCGAA-GTGCA
1 AACAGGGGCACCGAATGTGCA
54589839 AA
1 AA
54589841 TCCCATACGA
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
20 48 0.73
21 6 0.09
22 12 0.18
ACGTcount: A:0.39, C:0.21, G:0.31, T:0.09
Consensus pattern (21 bp):
AACAGGGGCACCGAATGTGCA
Found at i:54593695 original size:99 final size:100
Alignment explanation
Indices: 54593577--54593775 Score: 355
Period size: 99 Copynumber: 2.0 Consensus size: 100
54593567 AAATCATGCA
*
54593577 TTGGAACATTTTTTCTTAGTTAAATTATTTAGTTAAGTTTTAGTTTTCATAACACTTTTTAATAT
1 TTGGAACATTTTTTCTTAGTTAAATTATTTAGTTAACTTTTAGTTTTCATAACACTTTTTAATAT
* * *
54593642 TAACATTTGTTTTCAACACCAAATTGTTTAAAGTT
66 CAACATTTGCTTTCAACACCAAATTGTTCAAAGTT
54593677 TTGGAACATTTTTT-TTAGTTAAATTATTTAGTTAACTTTTAGTTTTCATAACACTTTTTAATAT
1 TTGGAACATTTTTTCTTAGTTAAATTATTTAGTTAACTTTTAGTTTTCATAACACTTTTTAATAT
54593741 CAACATTTGCTTTCAACACCAAATTGTTCAAAGTT
66 CAACATTTGCTTTCAACACCAAATTGTTCAAAGTT
54593776 GCATTTTATA
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
99 81 0.85
100 14 0.15
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.49
Consensus pattern (100 bp):
TTGGAACATTTTTTCTTAGTTAAATTATTTAGTTAACTTTTAGTTTTCATAACACTTTTTAATAT
CAACATTTGCTTTCAACACCAAATTGTTCAAAGTT
Found at i:54596525 original size:13 final size:13
Alignment explanation
Indices: 54596507--54596531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54596497 AAAATGTAAT
54596507 GTCATGAAATCAA
1 GTCATGAAATCAA
54596520 GTCATGAAATCA
1 GTCATGAAATCA
54596532 GAATAAAATC
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
GTCATGAAATCAA
Found at i:54596791 original size:22 final size:22
Alignment explanation
Indices: 54596765--54596809 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
54596755 AGATCAACAC
54596765 AAATA-TAATCTCATACATATCA
1 AAATATTAATCTCA-ACATATCA
*
54596787 AAATATTAATCTCAACTTATCA
1 AAATATTAATCTCAACATATCA
54596809 A
1 A
54596810 TCATCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATTAATCTCAACATATCA
Found at i:54601954 original size:561 final size:561
Alignment explanation
Indices: 54600892--54602012 Score: 2233
Period size: 561 Copynumber: 2.0 Consensus size: 561
54600882 CACTTTAGTA
54600892 AGAATAATTCAGACATTTCTAGGTTATAGATACGATTTAATTTTTACTAATCTTTTCTTTTTGGG
1 AGAATAATTCAGACATTTCTAGGTTATAGATACGATTTAATTTTTACTAATCTTTTCTTTTTGGG
54600957 TTTAGTGTATGACTCATAGGAGGGGAACACTAGTAGAGCCAGTTACAGATTTTGAGAGAATAATT
66 TTTAGTGTATGACTCATAGGAGGGGAACACTAGTAGAGCCAGTTACAGATTTTGAGAGAATAATT
54601022 CAAAGAAATCATCGACAACAATAGTAGCAGGAGATGCATGATCCAGCACCACTTGCTGCCGGCAA
131 CAAAGAAATCATCGACAACAATAGTAGCAGGAGATGCATGATCCAGCACCACTTGCTGCCGGCAA
54601087 CGTACCATGCAAGAATCTGCTGTTCAATGAAGCTAATAATAATGCTTTAGAAGATCTACCAGCAC
196 CGTACCATGCAAGAATCTGCTGTTCAATGAAGCTAATAATAATGCTTTAGAAGATCTACCAGCAC
54601152 CACCGCAGCTACTGTAAATTTACATATGTCACATAATGAGAGAACCCTAAGAGAGCATACATTAC
261 CACCGCAGCTACTGTAAATTTACATATGTCACATAATGAGAGAACCCTAAGAGAGCATACATTAC
54601217 CAAGTCAGGACATGGTTCAAGAGAGCGTAACAAGGCCGACCATTATAGTGAACAACTTTGAGATC
326 CAAGTCAGGACATGGTTCAAGAGAGCGTAACAAGGCCGACCATTATAGTGAACAACTTTGAGATC
54601282 AAACTGACAATGATTCAGGTGATCCAGAATAATCTGCAATTTAGGGGTACAATGGTAGAGGTTCC
391 AAACTGACAATGATTCAGGTGATCCAGAATAATCTGCAATTTAGGGGTACAATGGTAGAGGTTCC
54601347 AAATCAACATTTAAAATAATTTTCCCAACTTTGTGATACTTTTCAGTATAATGGGGTCACTAATG
456 AAATCAACATTTAAAATAATTTTCCCAACTTTGTGATACTTTTCAGTATAATGGGGTCACTAATG
54601412 ACGCTATTCATCTTCAGTTGTTTCCCTTTTCTTTGATTGAG
521 ACGCTATTCATCTTCAGTTGTTTCCCTTTTCTTTGATTGAG
54601453 AGAATAATTCAGACATTTCTAGGTTATAGATACGATTTAATTTTTACTAATCTTTTCTTTTTGGG
1 AGAATAATTCAGACATTTCTAGGTTATAGATACGATTTAATTTTTACTAATCTTTTCTTTTTGGG
54601518 TTTAGTGTATGACTCATAGGAGGGGAACACTAGTAGAGCCAGTTACAGATTTTGAGAGAATAATT
66 TTTAGTGTATGACTCATAGGAGGGGAACACTAGTAGAGCCAGTTACAGATTTTGAGAGAATAATT
54601583 CAAAGAAATCATCGACAACAATAGTAGCAGGAGATGCATGATCCAGCACCACTTGCTGCCGGCAA
131 CAAAGAAATCATCGACAACAATAGTAGCAGGAGATGCATGATCCAGCACCACTTGCTGCCGGCAA
54601648 CGTACCATGCAAGAATCTGCTGTTCAATGAAGCTAATAATAATGCTTTAGAAGATCTACCAGCAC
196 CGTACCATGCAAGAATCTGCTGTTCAATGAAGCTAATAATAATGCTTTAGAAGATCTACCAGCAC
54601713 CACCGCAGCTACTGTAAATTTACATATGTCACATAATGAGAGAACCCTAAGAGAGCATACATTAC
261 CACCGCAGCTACTGTAAATTTACATATGTCACATAATGAGAGAACCCTAAGAGAGCATACATTAC
54601778 CAAGTCAGGACATGGTTCAAGAGAGCGTAACAAGGCCGACCATTATAGTGAACAACTTTGAGATC
326 CAAGTCAGGACATGGTTCAAGAGAGCGTAACAAGGCCGACCATTATAGTGAACAACTTTGAGATC
*
54601843 AAACTGACAATGATTCAGGTGATCCAGAATAATCTGTAATTTAGGGGTACAATGGTAGAGGTTCC
391 AAACTGACAATGATTCAGGTGATCCAGAATAATCTGCAATTTAGGGGTACAATGGTAGAGGTTCC
54601908 AAATCAACATTTAAAATAATTTTCCCAACTTTGTGATACTTTTCAGTATAATGGGGTCACTAATG
456 AAATCAACATTTAAAATAATTTTCCCAACTTTGTGATACTTTTCAGTATAATGGGGTCACTAATG
54601973 ACGCTATTCATCTTCAGTTGTTTCCCTTTTCTTTGATTGA
521 ACGCTATTCATCTTCAGTTGTTTCCCTTTTCTTTGATTGA
54602013 TAACGCTTTT
Statistics
Matches: 559, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
561 559 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (561 bp):
AGAATAATTCAGACATTTCTAGGTTATAGATACGATTTAATTTTTACTAATCTTTTCTTTTTGGG
TTTAGTGTATGACTCATAGGAGGGGAACACTAGTAGAGCCAGTTACAGATTTTGAGAGAATAATT
CAAAGAAATCATCGACAACAATAGTAGCAGGAGATGCATGATCCAGCACCACTTGCTGCCGGCAA
CGTACCATGCAAGAATCTGCTGTTCAATGAAGCTAATAATAATGCTTTAGAAGATCTACCAGCAC
CACCGCAGCTACTGTAAATTTACATATGTCACATAATGAGAGAACCCTAAGAGAGCATACATTAC
CAAGTCAGGACATGGTTCAAGAGAGCGTAACAAGGCCGACCATTATAGTGAACAACTTTGAGATC
AAACTGACAATGATTCAGGTGATCCAGAATAATCTGCAATTTAGGGGTACAATGGTAGAGGTTCC
AAATCAACATTTAAAATAATTTTCCCAACTTTGTGATACTTTTCAGTATAATGGGGTCACTAATG
ACGCTATTCATCTTCAGTTGTTTCCCTTTTCTTTGATTGAG
Found at i:54608363 original size:11 final size:11
Alignment explanation
Indices: 54608347--54608371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54608337 GTCAAAAAAT
54608347 TTATTTTATTA
1 TTATTTTATTA
54608358 TTATTTTATTA
1 TTATTTTATTA
54608369 TTA
1 TTA
54608372 CTCAAAGTTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:54608629 original size:23 final size:24
Alignment explanation
Indices: 54608602--54608656 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
54608592 TTTCAAGGCT
*
54608602 ATTAATTAAGG-TTAATTTAGTAA
1 ATTAATTAAGGATTAATATAGTAA
* *
54608625 TTTAAAT-AGGATTAATATAGTAA
1 ATTAATTAAGGATTAATATAGTAA
*
54608648 AATAATTAA
1 ATTAATTAA
54608657 AACAAAGATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
22 3 0.12
23 20 0.83
24 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (24 bp):
ATTAATTAAGGATTAATATAGTAA
Found at i:54611766 original size:14 final size:14
Alignment explanation
Indices: 54611747--54611775 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54611737 ACATACCAAA
54611747 TTATGTTCAAATGG
1 TTATGTTCAAATGG
54611761 TTATGTTCAAATGG
1 TTATGTTCAAATGG
54611775 T
1 T
54611776 CATAATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TTATGTTCAAATGG
Found at i:54616571 original size:8 final size:8
Alignment explanation
Indices: 54616558--54616583 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
54616548 GAATTCAATA
54616558 AATTAAAT
1 AATTAAAT
54616566 AATTAAAT
1 AATTAAAT
54616574 AATTAAAT
1 AATTAAAT
54616582 AA
1 AA
54616584 AATTGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTAAAT
Found at i:54617347 original size:30 final size:30
Alignment explanation
Indices: 54617290--54617347 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54617280 TGCCTTTGAA
* * * *
54617290 AATATTTGCAAAAAGAGACATCTAATTTCT
1 AATATTTACAAAAAGAGAAACCAAATTTCT
54617320 AATATTTACAAAAAGAGAAACCAAATTT
1 AATATTTACAAAAAGAGAAACCAAATTT
54617348 TGAAAATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (30 bp):
AATATTTACAAAAAGAGAAACCAAATTTCT
Found at i:54620394 original size:40 final size:40
Alignment explanation
Indices: 54620117--54620380 Score: 349
Period size: 40 Copynumber: 6.6 Consensus size: 40
54620107 CGAATGATGT
* * * *
54620117 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
54620157 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
54620197 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
54620235 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
54620276 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
54620316 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
54620356 CCGGGCTATGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54620381 AACGAGTAGC
Statistics
Matches: 201, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 33 0.16
40 158 0.79
41 10 0.05
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54620411 original size:159 final size:159
Alignment explanation
Indices: 54620117--54620413 Score: 379
Period size: 159 Copynumber: 1.9 Consensus size: 159
54620107 CGAATGATGT
*
54620117 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
* * ** *
54620182 TGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGAGTTAAGT
66 TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
54620247 CCCGAAGGCATTTGTGCGAGTTACTATAA
131 CCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
54620276 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATT
* * * *
54620339 TGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGCTATATCCG-GT
64 TGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-CTAAATCCGAGT
*
54620401 TAAATTCCGAAGG
126 TAAATCCCGAAGG
54620414 TACGTGATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
158 3 0.03
159 84 0.71
160 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (159 bp):
CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
CCCGAAGGCATTTGTGCGAGTTACTATAA
Done.