Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 155 of 335
Found at i:45466275 original size:100 final size:100
Alignment explanation
Indices: 45466097--45466277 Score: 310
Period size: 100 Copynumber: 1.8 Consensus size: 100
45466087 TATTGTGTGG
* *
45466097 TCACCTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATTATTGGTCGCATGTGCAGTACT
1 TCACCTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACATGTGCAGTACT
45466162 AAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
* *
45466197 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCGGATAATTGGTCACATGTGTAGTAC
1 TCACCTGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-GGATAATTGGTCACATGTGCAGTAC
45466261 TAAGTGCAGGCTACTAT
65 TAAGTGCAGGCTACTAT
45466278 AGGTACCAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
99 1 0.01
100 75 0.99
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (100 bp):
TCACCTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACATGTGCAGTACT
AAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
Found at i:45469785 original size:20 final size:20
Alignment explanation
Indices: 45469762--45469805 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
45469752 TGAACTGAAC
*
45469762 AGAGCAGAACAAAATAAAAT
1 AGAGCAGAACAAAACAAAAT
*
45469782 AGAGCAGAACAGAACAAAAT
1 AGAGCAGAACAAAACAAAAT
45469802 AGAG
1 AGAG
45469806 GATGTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.61, C:0.11, G:0.20, T:0.07
Consensus pattern (20 bp):
AGAGCAGAACAAAACAAAAT
Found at i:45486838 original size:22 final size:22
Alignment explanation
Indices: 45486810--45486853 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
45486800 GGTGCAAGAA
45486810 AGAATGAAAAACATGGACATGG
1 AGAATGAAAAACATGGACATGG
45486832 AGAATGAAAAACATGGACATGG
1 AGAATGAAAAACATGGACATGG
45486854 CTTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.27, T:0.14
Consensus pattern (22 bp):
AGAATGAAAAACATGGACATGG
Found at i:45493207 original size:23 final size:23
Alignment explanation
Indices: 45493181--45493225 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
45493171 TGGGTATGTG
*
45493181 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
45493204 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
45493226 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:45497788 original size:29 final size:32
Alignment explanation
Indices: 45497748--45497823 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
45497738 CAATTTGATG
*
45497748 CATG-AACTTTG-ATT-TGGTGCA-ATTGTATA
1 CATGAAACTTTGAATTGTGGTGCATA-TATATA
*
45497777 CATGAAAC-TTGAATTGTGGTTCATATATATA
1 CATGAAACTTTGAATTGTGGTGCATATATATA
*
45497808 CATGAAATTTTGAATT
1 CATGAAACTTTGAATT
45497824 ACACATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.18
30 6 0.15
31 18 0.46
32 8 0.21
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (32 bp):
CATGAAACTTTGAATTGTGGTGCATATATATA
Found at i:45499519 original size:2 final size:2
Alignment explanation
Indices: 45499512--45499536 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45499502 CCAATTATCA
45499512 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
45499537 ATTTTTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45502581 original size:26 final size:26
Alignment explanation
Indices: 45502544--45502601 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
45502534 TGATACAAAT
45502544 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
45502570 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
45502596 TGATAA
1 TGATAA
45502602 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:45504321 original size:27 final size:26
Alignment explanation
Indices: 45504217--45504331 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
45504207 TGGAGGAAGC
* * *
45504217 GTTCTGGTGGCTATGCCACAAATATTT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
45504244 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
45504271 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* * *
45504298 GTATCTGGTGACTCTGTCATATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
45504325 GTTCTGG
1 GTTCTGG
45504332 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 55 0.71
28 16 0.21
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:45504324 original size:54 final size:54
Alignment explanation
Indices: 45504217--45504331 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
45504207 TGGAGGAAGC
* *
45504217 GTTCTGGTGGCTATGCCACAAATATTTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * * *
45504271 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCATAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
45504325 GTTCTGG
1 GTTCTGG
45504332 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:45504417 original size:19 final size:22
Alignment explanation
Indices: 45504393--45504432 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
45504383 CTCCCCACAC
45504393 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
45504412 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
45504433 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:45506026 original size:14 final size:15
Alignment explanation
Indices: 45506007--45506037 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
45505997 ACGTCCCAAA
45506007 AAAAAAAAGAAA-AG
1 AAAAAAAAGAAAGAG
45506021 AAAAAAAAGAAAGAG
1 AAAAAAAAGAAAGAG
45506036 AA
1 AA
45506038 GAGTGGGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAGAG
Found at i:45506027 original size:18 final size:18
Alignment explanation
Indices: 45506004--45506039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45505994 AGAACGTCCC
45506004 AAAAAAAAAAAGAAAAGA
1 AAAAAAAAAAAGAAAAGA
* *
45506022 AAAAAAAGAAAGAGAAGA
1 AAAAAAAAAAAGAAAAGA
45506040 GTGGGACCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAGA
Found at i:45518589 original size:2 final size:2
Alignment explanation
Indices: 45518584--45518609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45518574 ACTTGTTTTA
45518584 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
45518610 CACTCATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45520813 original size:48 final size:45
Alignment explanation
Indices: 45520712--45521072 Score: 193
Period size: 47 Copynumber: 7.7 Consensus size: 45
45520702 TTTGTGTGCC
* * * *
45520712 AGTGTAAGACATGTCTGGGACATGCTTCGGC--CACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATC-CA-GA-GAGGGCT
*
45520758 AGTGTAAGACCATGTCTGGGGCATGGCATCGGCATCCAGACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCCAGA-GAGGGCT
* * * *
45520806 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATA-GCCT
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCAT-CCA-GAGAGGGCT
*
45520853 -GTGTAAGACCATGTCTGGGACATGACATCGGCA--CAGAGATGAGTGCC
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCATCCAGAGA-G-G-GCT
* * ** *
45520900 AATGTAAGACATGTCTGGGACATGCATCGGTC-TCGATAGAGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CATC--CAGAGAGGGCT
* * * * * *
45520947 AGTGTAAGACGTGTCTGGGACACGCATTGGC-T-AAGAGTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATCCAGAG-AGGGCT
* * * * * *
45520991 AGTGTAAGACATGTCCGGGACATGCATCAGCA-CGCTTATATAAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATC-C--AGA-GAGGGCT
45521039 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
45521073 ATAGATCCCA
Statistics
Matches: 245, Mismatches: 42, Indels: 52
0.72 0.12 0.15
Matches are distributed among these distances:
43 7 0.03
44 29 0.12
46 31 0.13
47 97 0.40
48 50 0.20
49 17 0.07
50 14 0.06
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATCCAGAGAGGGCT
Found at i:45520882 original size:94 final size:94
Alignment explanation
Indices: 45520707--45521072 Score: 381
Period size: 94 Copynumber: 3.9 Consensus size: 94
45520697 GGTGATTTGT
* * * * *
45520707 GTGCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCACAT-TATGAGAGCCAGTGTAAGACCAT
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGCATATATGAGAGCCAGTGTAAGACCAT
* *
45520771 GTCTGGGGCATGGCATCGGCATCCAGACGA
66 GTCTGGGACATGGCATCGGCATCAAGA-GA
* * *
45520801 GGGCTAGTGTAAGACATGTCTGGGACATGCATCAG-C-CATACTATGATAGCCTGTGTAAGACCA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGCATA-TATGAGAGCCAGTGTAAGACCA
*
45520864 TGTCTGGGACATGACATCGGCA-CAGAGATGA
65 TGTCTGGGACATGGCATCGGCATCA-AGA-GA
* * * * * * * *
45520895 GTGCCAATGTAAGACATGTCTGGGACATGCATCGGTCTCGATAGA-GATAGCCAGTGTAAGA-CG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGC-ATATATGAGAGCCAGTGTAAGACCA
* * *
45520958 TGTCTGGGACA-CGCATTGGC-T-AAGAGTT
65 TGTCTGGGACATGGCATCGGCATCAAGAG-A
* * *
45520986 GTGCTAGTGTAAGACATGTCCGGGACATGCATCAGCACGCTTATATAAGAGCCAGTGTAAGACCA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-ACGCATATATGAGAGCCAGTGTAAGACCA
45521051 TGTCTGGGACATGGCATCGGCA
65 TGTCTGGGACATGGCATCGGCA
45521073 ATAGATCCCA
Statistics
Matches: 225, Mismatches: 34, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
90 1 0.00
91 37 0.16
92 20 0.09
93 20 0.09
94 126 0.56
95 16 0.07
96 2 0.01
97 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (94 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGCATATATGAGAGCCAGTGTAAGACCAT
GTCTGGGACATGGCATCGGCATCAAGAGA
Found at i:45520966 original size:141 final size:140
Alignment explanation
Indices: 45520713--45521072 Score: 351
Period size: 141 Copynumber: 2.6 Consensus size: 140
45520703 TTGTGTGCCA
* ** *
45520713 GTGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGG
1 GTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAATGTAAGACCATGTCTGGG
* * * *
45520778 GCATGGCATCGGCATCCAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACT
66 ACATGGCATCGGCATCCAGACGAGAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCCATACT
45520843 ATGATAGCCT
131 ATGATAGCCT
*
45520853 GTGTAAGACCATGTCTGGGACATGACATCGG-CACAGAGATGAGTGCCAATGTAAGA-CATGTCT
1 GTGTAAGA-CATGTCTGGGACATG-CATCGGCCACA-AGATGAGAGCCAATGTAAGACCATGTCT
* * * **
45520916 GGGACAT-GCATCGGTC-TCGATAGA-GATAGCCAGTGTAAGACGTGTCTGGGACACGCATTGGC
63 GGGACATGGCATCGG-CATC--CAGACGAGAGCCAGTGTAAGACATGTCTGGGACACGCATCAGC
* * *
45520978 TAAGAGT-TG-T-G-CT
125 -CATACTATGATAGCCT
* * * * * * *
45520991 AGTGTAAGACATGTCCGGGACATGCATCAGCACGCTTATATAAGAGCCAGTGTAAGACCATGTCT
1 -GTGTAAGACATGTCTGGGACATGCATCGGC-CAC-AAGATGAGAGCCAATGTAAGACCATGTCT
45521056 GGGACATGGCATCGGCA
63 GGGACATGGCATCGGCA
45521073 ATAGATCCCA
Statistics
Matches: 181, Mismatches: 25, Indels: 27
0.78 0.11 0.12
Matches are distributed among these distances:
137 5 0.03
138 16 0.09
139 27 0.15
140 33 0.18
141 73 0.40
142 27 0.15
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (140 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAATGTAAGACCATGTCTGGG
ACATGGCATCGGCATCCAGACGAGAGCCAGTGTAAGACATGTCTGGGACACGCATCAGCCATACT
ATGATAGCCT
Found at i:45529516 original size:6 final size:6
Alignment explanation
Indices: 45529505--45529535 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
45529495 ACAAATCCGA
*
45529505 AACAGT AACAGT AACAGT AACGGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
45529536 TTCAACACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:45530664 original size:5 final size:5
Alignment explanation
Indices: 45530654--45530723 Score: 90
Period size: 5 Copynumber: 14.0 Consensus size: 5
45530644 TTTCTTTTAT
* *
45530654 ATATA ATATA ATATA ATAT- ATATA ATATA ATATA ATATA AGA-A TATAAGA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA
45530704 ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA
45530724 CTTAATTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
4 5 0.09
5 49 0.84
6 3 0.05
7 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:45530706 original size:26 final size:24
Alignment explanation
Indices: 45530654--45530719 Score: 96
Period size: 26 Copynumber: 2.7 Consensus size: 24
45530644 TTTCTTTTAT
* *
45530654 ATATAATATAATATAATATATATA
1 ATATAATATAATATAAAATATAGA
45530678 ATATAATATAATATAAGAATATAAGA
1 ATATAATATAATATAA-AATAT-AGA
45530704 ATATAATATAATATAA
1 ATATAATATAATATAA
45530720 TATACTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 16 0.42
25 4 0.11
26 18 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
ATATAATATAATATAAAATATAGA
Found at i:45530719 original size:31 final size:32
Alignment explanation
Indices: 45530663--45530723 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
45530653 TATATAATAT
*
45530663 AATATAATATATATAATATAATATAATATAAG
1 AATATAAGATATATAATATAATATAATATAAG
45530695 AATATAAGA-ATATAATATAATATAATATA
1 AATATAAGATATATAATATAATATAATATA
45530724 CTTAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
AATATAAGATATATAATATAATATAATATAAG
Found at i:45537174 original size:43 final size:43
Alignment explanation
Indices: 45537113--45537329 Score: 294
Period size: 43 Copynumber: 5.0 Consensus size: 43
45537103 TATATGTGAT
* *
45537113 ATCGATATGTGATTACGTGTAAGAACACGTCTGGGATGTTGGA
1 ATCGATATGTGATTACGTGTAAGACCACGTCTGGGATGTTGGC
*
45537156 ATCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGC
1 ATCGATATGTGATTACGTGTAAGACCACGTCTGGGATGTTGGC
* *
45537199 ATCGATATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGC
1 ATCGATATGTGATTACGTGTAAGACCACGTCTGGGATGTTGGC
* * *
45537242 ATCGATATGTGTTTATGAGTAAGACC-CTGTCTGGGATAG-TGGC
1 ATCGATATGTGATTACGTGTAAGACCAC-GTCTGGGAT-GTTGGC
* * * *
45537285 ATCGATATGAGGTTACATGTAAGACCACATCTGGGATGTTGGC
1 ATCGATATGTGATTACGTGTAAGACCACGTCTGGGATGTTGGC
45537328 AT
1 AT
45537330 TGTATGATAT
Statistics
Matches: 155, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
42 2 0.01
43 151 0.97
44 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (43 bp):
ATCGATATGTGATTACGTGTAAGACCACGTCTGGGATGTTGGC
Found at i:45546555 original size:27 final size:27
Alignment explanation
Indices: 45546437--45546557 Score: 93
Period size: 27 Copynumber: 4.5 Consensus size: 27
45546427 ATAGTCTGCA
* * * **
45546437 ACAGTAAACACGGGGTAGTCTATTGGG
1 ACAGTAAACATGGGATAGTCCACCGGG
*
45546464 ACAGTAAACACAGGG-TAGTCCGA-CGGG
1 ACAGTAAACA-TGGGATAGTCC-ACCGGG
* * ** *
45546491 GCAGTAAACATAGGATAGTCTGCTGGG
1 ACAGTAAACATGGGATAGTCCACCGGG
*
45546518 TCAGTAAACATGGGATAGTCCACCGGG
1 ACAGTAAACATGGGATAGTCCACCGGG
*
45546545 ACAGTATACATGG
1 ACAGTAAACATGG
45546558 AACAGTTTGT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
26 2 0.03
27 68 0.92
28 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.19
Consensus pattern (27 bp):
ACAGTAAACATGGGATAGTCCACCGGG
Found at i:45548192 original size:20 final size:20
Alignment explanation
Indices: 45548150--45548195 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
45548140 TAATTATAAA
*
45548150 AAATATTTCATAAAAAAATT
1 AAATATTTCATAAAAAAACT
* **
45548170 AAATATTTTATAAAATGACT
1 AAATATTTCATAAAAAAACT
45548190 AAATAT
1 AAATAT
45548196 AAATAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATATTTCATAAAAAAACT
Found at i:45548663 original size:18 final size:17
Alignment explanation
Indices: 45548642--45548702 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
45548632 TAATTTTAAT
45548642 TTTTTATAAAATGTATAA
1 TTTTTATAAAAT-TATAA
*
45548660 TTTTTTTAAAATTTATAAA
1 TTTTTATAAAA-TTAT-AA
*
45548679 TTTTT-TAAAA-TATAT
1 TTTTTATAAAATTATAA
45548694 TTTTTATAA
1 TTTTTATAA
45548703 TTTTTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 6 0.16
16 6 0.16
18 18 0.47
19 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTTATAAAATTATAA
Found at i:45549641 original size:20 final size:19
Alignment explanation
Indices: 45549616--45549697 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
45549606 TAAAATATAT
45549616 AAATTTATAAAAGTAATTAA
1 AAATTTATAAAA-TAATTAA
* *
45549636 AAATTTCTAAAACT--CTAA
1 AAATTTATAAAA-TAATTAA
* *
45549654 AAATATTATAAAAATTATGAA
1 AAAT-TTAT-AAAATAATTAA
*
45549675 AAATTTCTAAAATAA-TAA
1 AAATTTATAAAATAATTAA
45549693 AAATT
1 AAATT
45549698 AAAAAGTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
18 14 0.29
19 10 0.20
20 19 0.39
21 6 0.12
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTTATAAAATAATTAA
Found at i:45549694 original size:39 final size:37
Alignment explanation
Indices: 45549606--45549697 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 37
45549596 AAATAATATT
* * *
45549606 TAAAATATATAAATTTATAAAAGTAATTAAAAATTTC
1 TAAAATATAAAAATTTATAAAAATAATGAAAAATTTC
* *
45549643 TAAAACTCTAAAAATATTATAAAAATTATGAAAAATTTC
1 TAAAA-TATAAAAAT-TTATAAAAATAATGAAAAATTTC
45549682 TAAAATAATAAAAATT
1 TAAAAT-ATAAAAATT
45549698 AAAAAGTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 5 0.11
38 9 0.20
39 32 0.70
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (37 bp):
TAAAATATAAAAATTTATAAAAATAATGAAAAATTTC
Found at i:45551130 original size:13 final size:13
Alignment explanation
Indices: 45551106--45551150 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
45551096 CCAAATTTAA
*
45551106 TTTTTATGTAATT
1 TTTTTATATAATT
*
45551119 TTTTTTTATAATT
1 TTTTTATATAATT
*
45551132 TTGTTATATAATT
1 TTTTTATATAATT
*
45551145 GTTTTA
1 TTTTTA
45551151 ACTCACATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTTATATAATT
Found at i:45554909 original size:115 final size:116
Alignment explanation
Indices: 45554783--45555036 Score: 411
Period size: 116 Copynumber: 2.2 Consensus size: 116
45554773 AATGCTTGAT
* *
45554783 CTTTAGTGGCG-TTTTTCAAAAAACGCCGCAAAAGAATTTTGCAAAATGACGTCGTTTTGTATTA
1 CTTTAGCGGCGCTTTTTTAAAAAACGCCGCAAAAGAATTTTGCAAAATGACGTCGTTTTGTATTA
* *
45554847 AGCTTTTAGTGGCTTTAGCGGCGCTTTTCAAAAACGTCGCTATAAGTACAC
66 AGCTTTTAATGGCTTTAGCGGCGCTTTTCAAAAACGCCGCTATAAGTACAC
* * * *
45554898 CTTTAGCGGCGTTTTTTTTAAAAACGCCGTAAAAGAATTTTGCAAGATGACGTCGTTTTGTATTA
1 CTTTAGCGGCGCTTTTTTAAAAAACGCCGCAAAAGAATTTTGCAAAATGACGTCGTTTTGTATTA
45554963 AGCTTTTAATGGCTTTAGCGGCGCTTTTCAAAAACGCCGCTATAAGTACAC
66 AGCTTTTAATGGCTTTAGCGGCGCTTTTCAAAAACGCCGCTATAAGTACAC
* *
45555014 CTTCAGCTGCGCTTTTTTAAAAA
1 CTTTAGCGGCGCTTTTTTAAAAA
45555037 CACCGCTAAT
Statistics
Matches: 127, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
115 10 0.08
116 117 0.92
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (116 bp):
CTTTAGCGGCGCTTTTTTAAAAAACGCCGCAAAAGAATTTTGCAAAATGACGTCGTTTTGTATTA
AGCTTTTAATGGCTTTAGCGGCGCTTTTCAAAAACGCCGCTATAAGTACAC
Found at i:45555026 original size:155 final size:155
Alignment explanation
Indices: 45554866--45555312 Score: 546
Period size: 156 Copynumber: 2.9 Consensus size: 155
45554856 TGGCTTTAGC
* * * * *
45554866 GGCGC-TTTTCAAAAACGTCGCTATAAGTACACCTTTAGCGGCGTTTTTTTTAAAAACGCCGTAA
1 GGCGCTTTTTTAAAAACGCCGCTATAAGTACACCTTTAGTGGCG-TTTTTTAAAAAACGCCGCAA
* * *
45554930 AAGAATTTTGCAAGATGACGTCGTTTTGTATTAAGCTTTTAATGGCTTTAGCGGCGCTTTTCAAA
65 AAGAATTTTGCAAAATGACGTCGTTTTGTATTGAGCTTTTAGTGGCTTTAGCGGCGCTTTTCAAA
*
45554995 AACGCCGCTATAAG-TAC-ACCT-TCAGC
130 AACGCCGCTA-AAGAT-CGA-CTATCAGA
* * * * * *
45555021 TGCGCTTTTTTAAAAACACCGCTA-ATGCATA-ATCTTTAGTGGCGTTTTTCAAAAAACGCTGCA
1 GGCGCTTTTTTAAAAACGCCGCTATAAG--TACACCTTTAGTGGCGTTTTTTAAAAAACGCCGCA
* * * *
45555084 AAATAATTTTTCAAAACGACGTCGTTTTGTATTGAGCTTTTAGTGACTTTAGCGGCGCTTTTCAA
64 AAAGAATTTTGCAAAATGACGTCGTTTTGTATTGAGCTTTTAGTGGCTTTAGCGGCGCTTTTCAA
* *
45555149 AAACGCCGCTAAAGATCGAGTATTAGA
129 AAACGCCGCTAAAGATCGACTATCAGA
* * * *
45555176 GGCACTTTTTTAAGAAACGCCGCTATAAGTACACCTTTAATGGTGCTTTTTAAAAAACGCCGCAA
1 GGCGCTTTTTTAA-AAACGCCGCTATAAGTACACCTTTAGTGGCGTTTTTTAAAAAACGCCGCAA
*
45555241 AAGAATTTTGCAAAATGACGTCGTTTTGTATTGAGCTTTTAGTGGCTTTAGCGGCGCTTTTTGAA
65 AAGAATTTTGCAAAATGACGTCGTTTTGTATTGAGCTTTTAGTGGCTTTAGCGGCGC-TTTTCAA
45555306 AAACGCC
129 AAACGCC
45555313 ACAAGAAATG
Statistics
Matches: 246, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
154 5 0.02
155 108 0.44
156 116 0.47
157 17 0.07
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (155 bp):
GGCGCTTTTTTAAAAACGCCGCTATAAGTACACCTTTAGTGGCGTTTTTTAAAAAACGCCGCAAA
AGAATTTTGCAAAATGACGTCGTTTTGTATTGAGCTTTTAGTGGCTTTAGCGGCGCTTTTCAAAA
ACGCCGCTAAAGATCGACTATCAGA
Found at i:45555546 original size:15 final size:15
Alignment explanation
Indices: 45555526--45555556 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45555516 ACTATCTTAA
*
45555526 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
45555541 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
45555556 G
1 G
45555557 TTGTAGCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:45558269 original size:14 final size:14
Alignment explanation
Indices: 45558252--45558306 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
45558242 TGGTTCAAGG
*
45558252 TTTATGTTTTAGGA
1 TTTATGGTTTAGGA
45558266 TTTATGGTTTAGGA
1 TTTATGGTTTAGGA
* *
45558280 TTTAGGGATTAGGA
1 TTTATGGTTTAGGA
*
45558294 GTTTAGGGTTTAG
1 -TTTATGGTTTAG
45558307 ATTAGTTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
TTTATGGTTTAGGA
Found at i:45558415 original size:7 final size:7
Alignment explanation
Indices: 45558403--45558435 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
45558393 TATCATTATA
45558403 GTTTAGG
1 GTTTAGG
45558410 GTTTAGG
1 GTTTAGG
45558417 GTTTAGG
1 GTTTAGG
45558424 GTTTAGG
1 GTTTAGG
45558431 GTTTA
1 GTTTA
45558436 AAGTGTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:45559098 original size:22 final size:22
Alignment explanation
Indices: 45559064--45559118 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
45559054 TTAATGGTTA
* *
45559064 GGGATTAGAGGTTAAGTGTTAAG
1 GGGA-TAGGGGTTAAGCGTTAAG
*
45559087 GGGATAGGGGTTAGGCGTTAAG
1 GGGATAGGGGTTAAGCGTTAAG
45559109 GGGATAGGGG
1 GGGATAGGGG
45559119 ATAGGGGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.49, T:0.24
Consensus pattern (22 bp):
GGGATAGGGGTTAAGCGTTAAG
Found at i:45559123 original size:22 final size:22
Alignment explanation
Indices: 45559081--45559132 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
45559071 GAGGTTAAGT
*
45559081 GTTAAGGGGATAGGGGTTAGGC
1 GTTAAGGGGATAGGGGATAGGC
*
45559103 GTTAAGGGGATAGGGGATAGGG
1 GTTAAGGGGATAGGGGATAGGC
45559125 GTT-AGGGG
1 GTTAAGGGG
45559133 TTTATGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.23, C:0.02, G:0.54, T:0.21
Consensus pattern (22 bp):
GTTAAGGGGATAGGGGATAGGC
Found at i:45559133 original size:7 final size:7
Alignment explanation
Indices: 45559045--45559134 Score: 65
Period size: 7 Copynumber: 12.7 Consensus size: 7
45559035 GGTGGTTTAA
45559045 GGGTT-G
1 GGGTTAG
*
45559051 GGGTTAA
1 GGGTTAG
*
45559058 TGGTTAG
1 GGGTTAG
*
45559065 GGATTAG
1 GGGTTAG
* *
45559072 AGGTTAA
1 GGGTTAG
*
45559079 GTGTTAAG
1 GGGTT-AG
*
45559087 GGGATAG
1 GGGTTAG
45559094 GGGTTAG
1 GGGTTAG
*
45559101 GCGTTAAG
1 GGGTT-AG
*
45559109 GGGATAG
1 GGGTTAG
*
45559116 GGGATAG
1 GGGTTAG
45559123 GGGTTAG
1 GGGTTAG
45559130 GGGTT
1 GGGTT
45559135 TATGGTTTAT
Statistics
Matches: 63, Mismatches: 18, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
6 5 0.08
7 49 0.78
8 9 0.14
ACGTcount: A:0.22, C:0.01, G:0.49, T:0.28
Consensus pattern (7 bp):
GGGTTAG
Found at i:45559199 original size:21 final size:21
Alignment explanation
Indices: 45559175--45559214 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45559165 ATGGATTATT
* *
45559175 GTTTAGGGATTATGTGTTAGG
1 GTTTAAGGATTAGGTGTTAGG
*
45559196 GTTTAAGGTTTAGGTGTTA
1 GTTTAAGGATTAGGTGTTA
45559215 TGTGTTAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (21 bp):
GTTTAAGGATTAGGTGTTAGG
Found at i:45559215 original size:28 final size:29
Alignment explanation
Indices: 45559175--45559236 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
45559165 ATGGATTATT
45559175 GTTTAGGGATTATGTGTT-AGGGTTTAAG
1 GTTTAGGGATTATGTGTTAAGGGTTTAAG
*
45559203 GTTTAGGTG-TTATGTGTTAAGGGTTTAGG
1 GTTTAGG-GATTATGTGTTAAGGGTTTAAG
45559232 GTTTA
1 GTTTA
45559237 AAGGTTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (29 bp):
GTTTAGGGATTATGTGTTAAGGGTTTAAG
Found at i:45559232 original size:36 final size:35
Alignment explanation
Indices: 45559191--45559281 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 35
45559181 GGATTATGTG
*
45559191 TTAGGGTTTAAGGTTTAGGTGTTAT-GTGTTAAGGGT
1 TTAGGGTTTAAGGTTTAGG-GATATAG-GTTAAGGGT
* *
45559227 TTAGGGTTTAAAGGTTAAGGGATATAGGTTATGGGT
1 TTAGGGTTT-AAGGTTTAGGGATATAGGTTAAGGGT
*
45559263 TTAAGGTTT-AGGATTTAGG
1 TTAGGGTTTAAGG-TTTAGG
45559282 ATTTAAGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
34 3 0.06
35 5 0.11
36 29 0.62
37 10 0.21
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (35 bp):
TTAGGGTTTAAGGTTTAGGGATATAGGTTAAGGGT
Found at i:45559322 original size:7 final size:7
Alignment explanation
Indices: 45559191--45559322 Score: 65
Period size: 7 Copynumber: 18.6 Consensus size: 7
45559181 GGATTATGTG
45559191 TTAGGGT
1 TTAGGGT
*
45559198 TTAAGGT
1 TTAGGGT
45559205 TTA-GGT
1 TTAGGGT
*
45559211 GTTATGTGT
1 -TTA-GGGT
*
45559220 TAAGGGT
1 TTAGGGT
45559227 TTAGGGT
1 TTAGGGT
*
45559234 TTAAAGGT
1 TT-AGGGT
*
45559242 TAAGGGAT
1 TTAGGG-T
*
45559250 ATA-GG-
1 TTAGGGT
45559255 TTATGGGT
1 TTA-GGGT
*
45559263 TTAAGGT
1 TTAGGGT
*
45559270 TTAGGAT
1 TTAGGGT
*
45559277 TTAGGAT
1 TTAGGGT
* *
45559284 TTAAGAT
1 TTAGGGT
*
45559291 TTAGGGG
1 TTAGGGT
*
45559298 TAAGGG-
1 TTAGGGT
45559304 TTAGAGGT
1 TTAG-GGT
45559312 TTAGGGT
1 TTAGGGT
45559319 TTAG
1 TTAG
45559323 ATTAATTAGT
Statistics
Matches: 95, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
5 2 0.02
6 6 0.06
7 69 0.73
8 16 0.17
9 2 0.02
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (7 bp):
TTAGGGT
Found at i:45564582 original size:15 final size:15
Alignment explanation
Indices: 45564562--45564595 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
45564552 TAATTTGATG
*
45564562 TTTGGATGTTCCATT
1 TTTGGATGTACCATT
45564577 TTTGGATGTACCATT
1 TTTGGATGTACCATT
45564592 TTTG
1 TTTG
45564596 TTCATCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.53
Consensus pattern (15 bp):
TTTGGATGTACCATT
Found at i:45569377 original size:136 final size:137
Alignment explanation
Indices: 45569133--45569407 Score: 507
Period size: 136 Copynumber: 2.0 Consensus size: 137
45569123 TTGGGCTTCA
45569133 GGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
* *
45569198 CAGATAACAGTATGGCCCATAGGCCTATTTCAGAATACATGCAACATCAAT-AACATATGCAAGC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGC
45569262 CCATTTG
131 CCATTTG
*
45569269 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
*
45569334 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGC
45569399 CCATTTG
131 CCATTTG
45569406 GG
1 GG
45569408 GAGACTACTC
Statistics
Matches: 134, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 112 0.84
137 22 0.16
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
GGTAACAGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGC
CCATTTG
Found at i:45571223 original size:26 final size:26
Alignment explanation
Indices: 45571187--45571296 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
45571177 CATGAATTTC
*
45571187 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
45571213 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
45571239 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
45571265 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
45571291 TTATCA
1 TTATCA
45571297 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:45572231 original size:7 final size:7
Alignment explanation
Indices: 45572219--45572253 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
45572209 ATTCTTTTCA
45572219 ACTCAAT
1 ACTCAAT
45572226 ACTCAAT
1 ACTCAAT
45572233 ACTCAAT
1 ACTCAAT
*
45572240 CCTCAAT
1 ACTCAAT
*
45572247 CCTCAAT
1 ACTCAAT
45572254 TTTCATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (7 bp):
ACTCAAT
Found at i:45572301 original size:14 final size:14
Alignment explanation
Indices: 45572220--45572302 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
45572210 TTCTTTTCAA
* *
45572220 CTCAATACTCAATA
1 CTCAATTCTCAATC
*
45572234 CTCAATCCTCAATC
1 CTCAATTCTCAATC
* * *
45572248 CTCAATTTTCATTT
1 CTCAATTCTCAATC
* *
45572262 CTTATTTCT-AGATC
1 CTCAATTCTCA-ATC
45572276 CTCAA-TCTTCAATC
1 CTCAATTC-TCAATC
45572290 CTCAATTCTCAAT
1 CTCAATTCTCAAT
45572303 TATATTCTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
13 3 0.06
14 46 0.88
15 3 0.06
ACGTcount: A:0.29, C:0.30, G:0.01, T:0.40
Consensus pattern (14 bp):
CTCAATTCTCAATC
Found at i:45572484 original size:7 final size:7
Alignment explanation
Indices: 45572473--45572534 Score: 81
Period size: 7 Copynumber: 8.9 Consensus size: 7
45572463 TTCATTTCAA
*
45572473 CTCAATA
1 CTCAATC
45572480 CTCAATC
1 CTCAATC
*
45572487 CTTAATC
1 CTCAATC
45572494 CTCAAAT-
1 CTC-AATC
*
45572501 TTCAATC
1 CTCAATC
45572508 CTCAATC
1 CTCAATC
45572515 CTCAATC
1 CTCAATC
45572522 CTCAATC
1 CTCAATC
45572529 CTCAAT
1 CTCAAT
45572535 TTTCAATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 3 0.06
7 42 0.88
8 3 0.06
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (7 bp):
CTCAATC
Found at i:45572540 original size:7 final size:7
Alignment explanation
Indices: 45572530--45572563 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
45572520 TCCTCAATCC
45572530 TCAATTT
1 TCAATTT
45572537 TCAATTT
1 TCAATTT
45572544 TCAATTT
1 TCAATTT
45572551 TCAATTT
1 TCAATTT
45572558 TCAATT
1 TCAATT
45572564 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (7 bp):
TCAATTT
Found at i:45572540 original size:14 final size:14
Alignment explanation
Indices: 45572490--45572562 Score: 65
Period size: 14 Copynumber: 5.2 Consensus size: 14
45572480 CTCAATCCTT
*
45572490 AATCCTCAAATTTC
1 AATCCTCAATTTTC
**
45572504 AATCCTCAATCCTC
1 AATCCTCAATTTTC
**
45572518 AATCCTCAATCCTC
1 AATCCTCAATTTTC
**
45572532 AATTTTCAATTTTC
1 AATCCTCAATTTTC
**
45572546 AATTTTCAATTTTC
1 AATCCTCAATTTTC
45572560 AAT
1 AAT
45572563 TATTTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 52 1.00
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (14 bp):
AATCCTCAATTTTC
Found at i:45572540 original size:21 final size:21
Alignment explanation
Indices: 45572502--45572562 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
45572492 TCCTCAAATT
**
45572502 TCAATCCTCAATCCTCAATCC
1 TCAATCCTCAATTTTCAATCC
**
45572523 TCAATCCTCAATTTTCAATTT
1 TCAATCCTCAATTTTCAATCC
**
45572544 TCAATTTTCAATTTTCAAT
1 TCAATCCTCAATTTTCAAT
45572563 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (21 bp):
TCAATCCTCAATTTTCAATCC
Found at i:45572609 original size:20 final size:20
Alignment explanation
Indices: 45572586--45572623 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45572576 CTTTTTCTGA
*
45572586 ATTTTATTCTCTT-TAATTTT
1 ATTTCATTC-CTTATAATTTT
45572606 ATTTCATTCCTTATAATT
1 ATTTCATTCCTTATAATT
45572624 GTGAAATGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTCATTCCTTATAATTTT
Found at i:45574685 original size:93 final size:93
Alignment explanation
Indices: 45574575--45574747 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
45574565 CGTCCATAAG
* *
45574575 CGAACTTGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
45574640 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACAAGCTCGGATGCCTAGTTACATCTCA
* * *
45574668 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCTGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
45574733 ACAAGTTCGGATGCC
66 ACAAGCTCGGATGCC
45574748 CAAATATCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGCTCGGATGCCTAGTTACATCTCA
Found at i:45574740 original size:46 final size:46
Alignment explanation
Indices: 45574567--45574743 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
45574557 ATGTAACCCG
* * *
45574567 TCCATAAGCGAACTTGAACTCAACTCAACGAGCTCGGGCGTTCGCA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCA
* *
45574613 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCA
* *
45574663 T-C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCA
* * * *
45574706 TCCATAAGTGAACTCTGACTCAACTCAACAAGTTCGGA
1 TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
45574744 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
TCCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCA
Found at i:45582996 original size:93 final size:93
Alignment explanation
Indices: 45582889--45583060 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
45582879 GCCCATAAGT
*
45582889 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACGCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACGCAACTCAA
45582954 CGAGCTCGGATGCCTAGTTACATCTTAC
66 CGAGCTCGGATGCCTAGTTACATCTTAC
* * *
45582982 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACGCAACTCAA
* *
45583047 TGAGTTCGGATGCC
66 CGAGCTCGGATGCC
45583061 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACGCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTTAC
Found at i:45583056 original size:46 final size:46
Alignment explanation
Indices: 45582881--45583056 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
45582871 TGTAACCCGC
* *
45582881 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
45582927 CCATAAGTGAACTCGGACGCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* * *
45582977 -C-TTA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
45583020 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
45583057 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 63 0.58
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:45588838 original size:12 final size:13
Alignment explanation
Indices: 45588821--45588858 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
45588811 TTCCTGGACT
45588821 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
45588833 ATTAAGAACACATA
1 ATTAAGAACA-AGA
45588847 ATTAAGAACAAG
1 ATTAAGAACAAG
45588859 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:45595645 original size:11 final size:11
Alignment explanation
Indices: 45595629--45595664 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
45595619 ATATTTCACA
45595629 ATTCCATTTCC
1 ATTCCATTTCC
45595640 ATTCCATTTCC
1 ATTCCATTTCC
* *
45595651 ATTTCATATCC
1 ATTCCATTTCC
45595662 ATT
1 ATT
45595665 TATTATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTCCATTTCC
Found at i:45595652 original size:17 final size:17
Alignment explanation
Indices: 45595630--45595665 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
45595620 TATTTCACAA
45595630 TTCCATTTCCAT-TCCAT
1 TTCCATTT-CATATCCAT
45595647 TTCCATTTCATATCCAT
1 TTCCATTTCATATCCAT
45595664 TT
1 TT
45595666 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCCATTTCATATCCAT
Found at i:45598611 original size:3 final size:3
Alignment explanation
Indices: 45598596--45598639 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
45598586 TCAGTAAAAC
*
45598596 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45598640 ATTTTCAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45599150 original size:16 final size:17
Alignment explanation
Indices: 45599117--45599150 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
45599107 GCTATTAATA
45599117 ATTTTAATTTATTTATG
1 ATTTTAATTTATTTATG
45599134 ATTTTAATTTA-TTATG
1 ATTTTAATTTATTTATG
45599150 A
1 A
45599151 ATTCGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
ATTTTAATTTATTTATG
Found at i:45599791 original size:18 final size:18
Alignment explanation
Indices: 45599770--45599819 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
45599760 AAAATAACTT
*
45599770 TTAAAATTTA-TAGAAAAA
1 TTAAAAATTATTA-AAAAA
45599788 TTAAAAATTATTAAAAAA
1 TTAAAAATTATTAAAAAA
45599806 TATAAAAA-TATTAA
1 T-TAAAAATTATTAA
45599820 TAAGTTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TTAAAAATTATTAAAAAA
Found at i:45599794 original size:19 final size:20
Alignment explanation
Indices: 45599772--45599814 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
45599762 AATAACTTTT
45599772 AAAATTTA-TAGAAAAAT-TA
1 AAAATTTATTA-AAAAATATA
45599791 AAAA-TTATTAAAAAATATA
1 AAAATTTATTAAAAAATATA
45599810 AAAAT
1 AAAAT
45599815 ATTAATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATTTATTAAAAAATATA
Found at i:45599831 original size:38 final size:38
Alignment explanation
Indices: 45599789--45599890 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
45599779 ATAGAAAAAT
45599789 TAAAAATTATTAAAAAATATAAAAATATTAATAAG-TTG
1 TAAAAATTATTAAAAAATATAAAAATATTAA-AAGATTG
* * * *
45599827 TAAAAATTATCATAAAATTTAACAA-ATTAAAAGATTG
1 TAAAAATTATTAAAAAATATAAAAATATTAAAAGATTG
* *
45599864 TGAAAATCATTAAATAAA-ATTAAAAAT
1 TAAAAATTATTAAA-AAATA-TAAAAAT
45599891 TGTAAAATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
36 3 0.06
37 18 0.36
38 29 0.58
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (38 bp):
TAAAAATTATTAAAAAATATAAAAATATTAAAAGATTG
Found at i:45601920 original size:20 final size:20
Alignment explanation
Indices: 45601883--45601921 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45601873 AATATGACAA
*
45601883 GGTATGTATGTACGTATATG
1 GGTATGTATGTACATATATG
* *
45601903 GGTATGTTTGTATATATAT
1 GGTATGTATGTACATATAT
45601922 ATACCCCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (20 bp):
GGTATGTATGTACATATATG
Found at i:45610200 original size:17 final size:17
Alignment explanation
Indices: 45610178--45610220 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
45610168 TCGTGTGGGC
45610178 CCACACGCCTGTGTGGT
1 CCACACGCCTGTGTGGT
45610195 CCACACGCCTGTGTGGT
1 CCACACGCCTGTGTGGT
45610212 CCACACGCC
1 CCACACGCC
45610221 CAATTTGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.42, G:0.26, T:0.19
Consensus pattern (17 bp):
CCACACGCCTGTGTGGT
Found at i:45610860 original size:8 final size:8
Alignment explanation
Indices: 45610823--45610916 Score: 61
Period size: 8 Copynumber: 11.6 Consensus size: 8
45610813 TGTATAATAT
45610823 ATATATTA
1 ATATATTA
*
45610831 ATA-CTTA
1 ATATATTA
*
45610838 GTAT-TTA
1 ATATATTA
* *
45610845 AGAAATTA
1 ATATATTA
45610853 ATATATTA
1 ATATATTA
45610861 ATATATTA
1 ATATATTA
*
45610869 ATATAAT-
1 ATATATTA
45610876 ATA-ATATA
1 ATATAT-TA
45610884 ATATAATATA
1 ATAT-AT-TA
45610894 ATATAATATA
1 ATAT-AT-TA
*
45610904 ATATAATA
1 ATATATTA
45610912 ATATA
1 ATATA
45610917 AAACAAATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
6 1 0.01
7 13 0.19
8 36 0.51
9 1 0.01
10 19 0.27
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (8 bp):
ATATATTA
Found at i:45610917 original size:5 final size:5
Alignment explanation
Indices: 45610851--45610911 Score: 94
Period size: 5 Copynumber: 13.0 Consensus size: 5
45610841 TTTAAGAAAT
45610851 TAATA T-AT- TAATA T-AT- TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
45610897 TAATA TAATA TAATA
1 TAATA TAATA TAATA
45610912 ATATAAAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.04
4 8 0.15
5 42 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:45616027 original size:18 final size:18
Alignment explanation
Indices: 45616004--45616038 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45615994 GCTGTATCAG
45616004 AATAGGAGCCTAAGTCAA
1 AATAGGAGCCTAAGTCAA
*
45616022 AATAGGAGCCTGAGTCA
1 AATAGGAGCCTAAGTCA
45616039 GAACAGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
AATAGGAGCCTAAGTCAA
Found at i:45621389 original size:12 final size:12
Alignment explanation
Indices: 45621372--45621396 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45621362 ATGGTCGAAT
45621372 CCGGAAGCGTAA
1 CCGGAAGCGTAA
45621384 CCGGAAGCGTAA
1 CCGGAAGCGTAA
45621396 C
1 C
45621397 ATAAAATGAG
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:0.32, C:0.28, G:0.32, T:0.08
Consensus pattern (12 bp):
CCGGAAGCGTAA
Found at i:45631356 original size:2 final size:2
Alignment explanation
Indices: 45631349--45631390 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
45631339 GCGTATTCAG
45631349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45631391 TAAAATTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45633763 original size:2 final size:2
Alignment explanation
Indices: 45633758--45633792 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45633748 AGTAAAATAA
45633758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45633793 ATAGGTTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45637939 original size:56 final size:56
Alignment explanation
Indices: 45637873--45637983 Score: 154
Period size: 56 Copynumber: 2.0 Consensus size: 56
45637863 TGAGTATAGT
45637873 GATTGGTAGTATTCCGCATA-AGTTGCAGACTA-CCGTAGCTCTATGTGAGCATCGAG
1 GATTGGTAGTATTCCGCATATA-TTGCAGACTATCC-TAGCTCTATGTGAGCATCGAG
** * *
45637929 GATTGGTAGTATTCCGCATATATTGTGGACTATTCTAGCTCTGTGTGAGCATCGA
1 GATTGGTAGTATTCCGCATATATTGCAGACTATCCTAGCTCTATGTGAGCATCGA
45637984 AGCTTACGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 47 0.96
57 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (56 bp):
GATTGGTAGTATTCCGCATATATTGCAGACTATCCTAGCTCTATGTGAGCATCGAG
Found at i:45641131 original size:46 final size:46
Alignment explanation
Indices: 45641076--45641255 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
45641066 TAGGATGGTT
45641076 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
45641122 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
45641168 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
45641215 GAACGCCCGAGCTCG-TGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45641256 GCGGGTTGGT
Statistics
Matches: 115, Mismatches: 12, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
43 4 0.03
45 28 0.24
46 44 0.38
47 33 0.29
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:45644220 original size:15 final size:15
Alignment explanation
Indices: 45644200--45644268 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
45644190 GTATCTTGGG
45644200 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
45644215 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
45644230 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
45644245 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
45644260 TTTCTTTAT
1 TTTCTTTAT
45644269 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:45644269 original size:30 final size:30
Alignment explanation
Indices: 45644191--45644278 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
45644181 CATAGTATCG
* * * *
45644191 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
45644221 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
45644251 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
45644279 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:45646699 original size:46 final size:46
Alignment explanation
Indices: 45646644--45646824 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
45646634 TAGGATGGTT
45646644 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
45646690 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
45646736 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
45646783 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45646825 GCGGGTTATG
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:45646805 original size:93 final size:93
Alignment explanation
Indices: 45646646--45646816 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
45646636 GGATGGTTGA
* *
45646646 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
45646711 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
45646739 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
45646804 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
45646817 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:45652260 original size:48 final size:48
Alignment explanation
Indices: 45652191--45652430 Score: 408
Period size: 48 Copynumber: 5.0 Consensus size: 48
45652181 AGATAAATAT
45652191 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
45652239 ATATATGTGTGATATGTATATGCGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
45652287 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
45652335 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
45652383 ATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
45652431 TGTTGTAACA
Statistics
Matches: 180, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 180 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:45652567 original size:36 final size:37
Alignment explanation
Indices: 45652483--45652616 Score: 216
Period size: 37 Copynumber: 3.6 Consensus size: 37
45652473 ATTCCAGGTG
* *
45652483 AGACCCGATGACTACGTGTGGAGATTACGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGAATATGTCCGGGTA
45652520 AGACCCGATGACTACGTGTGGAGAATATGTCCGGGT-
1 AGACCCGATGACTACGTGTGGAGAATATGTCCGGGTA
*
45652556 AGACCCGATGACTACATGTGGAGAATATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGAATATGTCCGGGTA
* *
45652593 AGACCCGATAACTTCGTGTGGAGA
1 AGACCCGATGACTACGTGTGGAGA
45652617 TTTCATCTGA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 35 0.39
37 55 0.61
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGAATATGTCCGGGTA
Found at i:45653954 original size:40 final size:40
Alignment explanation
Indices: 45653888--45654159 Score: 436
Period size: 40 Copynumber: 6.8 Consensus size: 40
45653878 GAGAATTGAG
* * * * *
45653888 AGTGATATGTCCGGGCTAAATCCCGAAGAGCATTCATGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
45653928 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
**
45653968 AGTGATGTATCCGGACTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
45654008 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
45654048 AGTGATGTATCCGGACTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
45654088 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
45654128 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCA
45654160 ATCATGCTGG
Statistics
Matches: 219, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
Found at i:45662873 original size:143 final size:140
Alignment explanation
Indices: 45662665--45662958 Score: 552
Period size: 143 Copynumber: 2.1 Consensus size: 140
45662655 TGAGTTAAAT
*
45662665 TTCGGCCATGCATGTTGTTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
45662730 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAA-TTTGTGCCATTGAGTTCTTGTTGTTA--TGTGT
45662795 GTGTGCATGAGTA
128 GTGTGCATGAGTA
45662808 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
45662873 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGTG
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGTG
45662938 TGCATGAGTA
131 TGCATGAGTA
45662948 TTCGGCCATGC
1 TTCGGCCATGC
45662959 TATAGAATTT
Statistics
Matches: 150, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
140 29 0.19
142 26 0.17
143 95 0.63
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (140 bp):
TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGTG
TGCATGAGTA
Found at i:45663632 original size:29 final size:29
Alignment explanation
Indices: 45663599--45663732 Score: 169
Period size: 29 Copynumber: 4.6 Consensus size: 29
45663589 GTGACGAGAT
*
45663599 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
45663628 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
45663657 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
45663686 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
45663715 CGGCACTGGGTGTGCGTG
1 TGGCACTAAGTGTGCGTG
45663733 GCAGCGTGCG
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:45665693 original size:13 final size:13
Alignment explanation
Indices: 45665675--45665700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45665665 CAGAGAGTTT
45665675 TTTTTTTATATAA
1 TTTTTTTATATAA
45665688 TTTTTTTATATAA
1 TTTTTTTATATAA
45665701 ACAACAGTTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTATATAA
Found at i:45670263 original size:26 final size:26
Alignment explanation
Indices: 45670228--45670277 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
45670218 CCAGTGCCGT
*
45670228 ATTTTTCCAGCTTGCACACATAGTTC
1 ATTTTTCCAGCATGCACACATAGTTC
*
45670254 ATTTTTCCAGCATGCACACTTAGT
1 ATTTTTCCAGCATGCACACATAGT
45670278 GCCTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (26 bp):
ATTTTTCCAGCATGCACACATAGTTC
Found at i:45670299 original size:29 final size:29
Alignment explanation
Indices: 45670257--45670339 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 29
45670247 ATAGTTCATT
* *
45670257 TTTCCAGCATGCACACTTAGTGCCTTATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
45670286 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
45670315 TTTCCAGCACGCACACTTAGTGCCA
1 TTTCCAGCACGCACACTTAGTGCCA
45670340 ATCTCGTCAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCATATA
Found at i:45671172 original size:142 final size:141
Alignment explanation
Indices: 45670983--45671276 Score: 554
Period size: 143 Copynumber: 2.1 Consensus size: 141
45670973 AAATTCTATA
45670983 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCC-TTT
1 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
45671047 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
45671112 GAAGACAACAT
131 GAAAACAACAT
45671123 GCATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
1 GCATGGCCGAATACTCATG--CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
45671188 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
64 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
45671253 AGGAAAACAACAT
129 AGGAAAACAACAT
45671266 GCATGGCCGAA
1 GCATGGCCGAA
45671277 ATTTAACTCA
Statistics
Matches: 150, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
140 19 0.13
142 42 0.28
143 89 0.59
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (141 bp):
GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAAACAACAT
Found at i:45678196 original size:29 final size:29
Alignment explanation
Indices: 45678164--45678298 Score: 146
Period size: 29 Copynumber: 4.7 Consensus size: 29
45678154 ATACCCTTCG
** *
45678164 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* * ** *
45678193 AGCTTGCACACATAGTATCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
45678222 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCGTATATTTCC
* *
45678251 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
45678280 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
45678299 AATCTCGTCA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 91 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:45678299 original size:29 final size:29
Alignment explanation
Indices: 45678217--45678299 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 29
45678207 GTATCGTATT
* *
45678217 TTTCCAGCATGCACACTTAGTGCCTTATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
45678246 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
45678275 TTTCCAGCACGCACACTTAGTGCCA
1 TTTCCAGCACGCACACTTAGTGCCA
45678300 ATCTCGTCAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCATATA
Found at i:45679133 original size:143 final size:141
Alignment explanation
Indices: 45678943--45679237 Score: 563
Period size: 143 Copynumber: 2.1 Consensus size: 141
45678933 AAATTCTATA
45678943 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
45679008 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
45679073 GAAGACAACAT
131 GAAAACAACAT
45679084 GCATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
1 GCATGGCCGAATACTCATG--CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
45679149 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
64 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
45679214 AGGAAAACAACAT
129 AGGAAAACAACAT
45679227 GCATGGCCGAA
1 GCATGGCCGAA
45679238 ATTTAACTCA
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
141 19 0.13
143 132 0.87
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (141 bp):
GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAAACAACAT
Found at i:45682926 original size:6 final size:7
Alignment explanation
Indices: 45682909--45682934 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
45682899 ATTTCTTCTT
45682909 TTTTTCC
1 TTTTTCC
45682916 TTTTTCC
1 TTTTTCC
45682923 TTTTTCC
1 TTTTTCC
45682930 TTTTT
1 TTTTT
45682935 AATTGTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:45683607 original size:61 final size:61
Alignment explanation
Indices: 45683488--45683683 Score: 243
Period size: 61 Copynumber: 3.2 Consensus size: 61
45683478 TGAACGACCC
* *
45683488 TGTAACTCACTGTTCATTATATAAAACCACATGGCCAGGGACACGGGCGTGTGCCCAGGCCG
1 TGTAACTCACTGTTCATTGTATAAAACCACATGGCCAGGGACACGGGC-TGTGGCCAGGCCG
* *
45683550 TGTAACTCACTGTTCATTGTAT-AAACCACACGACCAGGGACACGGGCATGTGGCCAGGCCG
1 TGTAACTCACTGTTCATTGTATAAAACCACATGGCCAGGGACACGGGC-TGTGGCCAGGCCG
* * * * * *
45683611 TGAAACTCATTATTCATAGTATAAAACCATATGGCCAGGGACA-TGGCTGTGTGCCCAGGCCG
1 TGTAACTCACTGTTCATTGTATAAAACCACATGGCCAGGGACACGGGCTGTG-G-CCAGGCCG
*
45683673 TGTGACTCACT
1 TGTAACTCACT
45683684 TTTTGTACTT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
60 4 0.03
61 57 0.50
62 54 0.47
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (61 bp):
TGTAACTCACTGTTCATTGTATAAAACCACATGGCCAGGGACACGGGCTGTGGCCAGGCCG
Found at i:45684837 original size:39 final size:39
Alignment explanation
Indices: 45684783--45684861 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
45684773 TCGATGAGGA
45684783 AGACATGAAAATGATGATAATAACTTTTATCTTTATTTT
1 AGACATGAAAATGATGATAATAACTTTTATCTTTATTTT
*
45684822 AGACATGAAAATGATGATAATAACTTTTATTTTTATTTT
1 AGACATGAAAATGATGATAATAACTTTTATCTTTATTTT
45684861 A
1 A
45684862 TTTAATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.44
Consensus pattern (39 bp):
AGACATGAAAATGATGATAATAACTTTTATCTTTATTTT
Found at i:45692179 original size:27 final size:26
Alignment explanation
Indices: 45692144--45692252 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 26
45692134 AGCATGGCTG
* *
45692144 CCAGAACAGAAAATGTGACAGAGTCA
1 CCAGAACAGAAAATGTGGCAGAGCCA
*
45692170 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGAAAAT-GTGGCAGAGCCA
*
45692198 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGA-AAATGTGGCAGAGCCA
* * *
45692225 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGA-AAATGTGGCAGAGCCA
45692252 C
1 C
45692253 TAGGACGCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
26 5 0.07
27 49 0.69
28 17 0.24
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGAAAATGTGGCAGAGCCA
Found at i:45692204 original size:54 final size:54
Alignment explanation
Indices: 45692144--45692252 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
45692134 AGCATGGCTG
*
45692144 CCAGAACAGA-AAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
45692198 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
45692252 C
1 C
45692253 TAGGACGCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 30 0.61
55 19 0.39
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATAAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:45693510 original size:25 final size:25
Alignment explanation
Indices: 45693482--45693543 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
45693472 TTCCTTGATT
*
45693482 TTCTCCCCTTTTCAGCTCCTAAATC
1 TTCTCCCCTTATCAGCTCCTAAATC
45693507 TTCTCCCCTTATCAGCTCCTAAATC
1 TTCTCCCCTTATCAGCTCCTAAATC
45693532 TTCT-CCCTTATC
1 TTCTCCCCTTATC
45693544 CCCTCCTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 8 0.22
25 28 0.78
ACGTcount: A:0.16, C:0.40, G:0.03, T:0.40
Consensus pattern (25 bp):
TTCTCCCCTTATCAGCTCCTAAATC
Found at i:45693549 original size:24 final size:25
Alignment explanation
Indices: 45693482--45693550 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
45693472 TTCCTTGATT
* *
45693482 TTCTCCCCTTTTCAGCTCCTAAATC
1 TTCTCCCCTTATCACCTCCTAAATC
*
45693507 TTCTCCCCTTATCAGCTCCTAAATC
1 TTCTCCCCTTATCACCTCCTAAATC
*
45693532 TTCT-CCCTTATCCCCTCCT
1 TTCTCCCCTTATCACCTCCT
45693551 TACTCAATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 13 0.32
25 28 0.68
ACGTcount: A:0.14, C:0.43, G:0.03, T:0.39
Consensus pattern (25 bp):
TTCTCCCCTTATCACCTCCTAAATC
Found at i:45705116 original size:43 final size:43
Alignment explanation
Indices: 45705062--45705234 Score: 228
Period size: 43 Copynumber: 4.0 Consensus size: 43
45705052 ATATCATACA
*
45705062 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACAG-GGTCTTACATGTAATCACATATCG
* *
45705105 ATGCCACTGTCCTAGACAGGGTCTTACACGTAATCACATATCG
1 ATGCCACTGTCCCAGACAGGGTCTTACATGTAATCACATATCG
*
45705148 ATGCCACTGTCCCAGACAGGGTCTTACATGTAATTACATATCG
1 ATGCCACTGTCCCAGACAGGGTCTTACATGTAATCACATATCG
* *
45705191 ATGCCAAC-GTCCCAGA-TGTGGTCTTACATG-AGAACACATATCG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGTA-ATCACATATCG
45705234 A
1 A
45705235 AAATCCTATG
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
42 2 0.02
43 112 0.96
44 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACAGGGTCTTACATGTAATCACATATCG
Found at i:45705789 original size:28 final size:27
Alignment explanation
Indices: 45705741--45705793 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
45705731 TACATTTCAT
*
45705741 TTATTTTACATTTTAGGCCCTCAATTTA
1 TTATTTTACAATTTAGGCCCT-AATTTA
45705769 TTATCTTTACAATTTA-GCCCTAATT
1 TTAT-TTTACAATTTAGGCCCTAATT
45705794 ACTCAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 9 0.39
29 10 0.43
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (27 bp):
TTATTTTACAATTTAGGCCCTAATTTA
Found at i:45708306 original size:26 final size:28
Alignment explanation
Indices: 45708276--45708340 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
45708266 ATCGATGAAT
*
45708276 GAAAAGGGATAG-TT-GCTATTGAATAC
1 GAAAAGGGATAGCTTAGCTATCGAATAC
* *
45708302 GAAAAGGGATAGCTTTAGCTATCGATTAT
1 GAAAAGGGATAGC-TTAGCTATCGAATAC
45708331 GAAAAGGGAT
1 GAAAAGGGAT
45708341 GGTGACGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.36
28 2 0.06
29 19 0.58
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (28 bp):
GAAAAGGGATAGCTTAGCTATCGAATAC
Found at i:45708380 original size:29 final size:29
Alignment explanation
Indices: 45708325--45708381 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
45708315 TTTAGCTATC
* *
45708325 GATTATGAAAAGGGATGGTGACGACCATA
1 GATTATGAAAAAGGATGGTGACAACCATA
*
45708354 GATTATGAAAAAGGATGGTGATAACCAT
1 GATTATGAAAAAGGATGGTGACAACCAT
45708382 CGAACTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (29 bp):
GATTATGAAAAAGGATGGTGACAACCATA
Found at i:45708391 original size:30 final size:29
Alignment explanation
Indices: 45708328--45708394 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
45708318 AGCTATCGAT
* * *
45708328 TATGAAAAGGGATGGTGACGACCATAGAT
1 TATGAAAAAGGATGGTGACAACCATAGAC
* *
45708357 TATGAAAAAGGATGGTGATAACCATCGAAC
1 TATGAAAAAGGATGGTGACAACCATAG-AC
45708387 TATGAAAA
1 TATGAAAA
45708395 GGTGGATGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.21
Consensus pattern (29 bp):
TATGAAAAAGGATGGTGACAACCATAGAC
Found at i:45708416 original size:32 final size:31
Alignment explanation
Indices: 45708380--45708458 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 31
45708370 GGTGATAACC
***
45708380 ATCGAACTATGAAAAGGTGGATGTGTTCGGCT
1 ATCGAACTATGAAAAGG-GGATAACTTCGGCT
45708412 ATCGAA-TCATGAAAA-GGGATAACTTCGGCT
1 ATCGAACT-ATGAAAAGGGGATAACTTCGGCT
* *
45708442 ATCAAACTATGCAAAGG
1 ATCGAACTATGAAAAGG
45708459 AATGGTGACG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 22 0.56
31 4 0.10
32 13 0.33
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (31 bp):
ATCGAACTATGAAAAGGGGATAACTTCGGCT
Found at i:45722726 original size:40 final size:40
Alignment explanation
Indices: 45722681--45722847 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
45722671 CGGAATATAA
*
45722681 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
45722721 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
45722761 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
45722801 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
45722840 CCGGATAT
1 CCGGATAT
45722848 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:45730371 original size:44 final size:42
Alignment explanation
Indices: 45730323--45730479 Score: 151
Period size: 44 Copynumber: 3.7 Consensus size: 42
45730313 TATGTTATCG
*
45730323 TGTAAGACCACGTCTGGGACATTGGCATCGACTTATAATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TTAT-ATTTACA
*
45730367 TGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATTT-CA
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ATTAT-ATTTACA
* * * *
45730409 TGTAAGACC-CTGTCTGGGATAGTGGCATC-AATATTTGGTTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGATTATAT--TTACA
* *
45730452 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
45730480 TGTATGAGAC
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
40 3 0.03
41 1 0.01
42 28 0.30
43 29 0.31
44 32 0.34
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTATATTTACA
Found at i:45730458 original size:43 final size:42
Alignment explanation
Indices: 45730323--45730479 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 42
45730313 TATGTTATCG
* * * * *
45730323 TGTAAGACCACGTCTGGGACATTGGCATCGACT-TATAATTTACG
1 TGTAAGACCATGTCTGGGACAGTGGCATC-A-TATTTGA-TTACA
* * *
45730367 TGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTTCA
1 TGTAAGACCATGTCTGGGACAGTGGCATCATATTTGATTACA
* * *
45730409 TGTAAGACCCTGTCTGGGATAGTGGCATCAATATTTGGTTACA
1 TGTAAGACCATGTCTGGGACAGTGGCATC-ATATTTGATTACA
* *
45730452 TGTAAGACCACGTCTAGGAC-GTTGGCAT
1 TGTAAGACCATGTCTGGGACAG-TGGCAT
45730480 TGTATGAGAC
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 31 0.33
43 35 0.37
44 28 0.30
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCATATTTGATTACA
Found at i:45730705 original size:21 final size:17
Alignment explanation
Indices: 45730662--45730694 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
45730652 AAATAAAATA
45730662 CAAATAAACTTATCATT
1 CAAATAAACTTATCATT
45730679 CAAATAAACTTATCAT
1 CAAATAAACTTATCAT
45730695 GTAATCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (17 bp):
CAAATAAACTTATCATT
Found at i:45732282 original size:47 final size:45
Alignment explanation
Indices: 45732217--45732337 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 45
45732207 TTTGTGTGCT
*
45732217 AGTGTAAGACATGTCTGGGACATGCATTGGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCA-T-ACCACATTGATGAGAGCC
* *
45732263 AGTGTAAGACCATGTCTGGGACATGGCA-ACGACATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATACCACATT--GATGAGAGCC
45732311 AGTGTAAGACATGTCTGGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
45732338 CGACCTAGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
45 6 0.09
46 12 0.18
47 28 0.42
48 20 0.30
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATACCACATTGATGAGAGCC
Found at i:45732365 original size:46 final size:46
Alignment explanation
Indices: 45732217--45732371 Score: 179
Period size: 46 Copynumber: 3.3 Consensus size: 46
45732207 TTTGTGTGCT
* * * *
45732217 AGTGTAAGACATGTCTGGGACATGCATTGGCC-ACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTAGA-GATGAGAGCC
* * * *
45732263 AGTGTAAGACCATGTCTGGGACATGGCAACGACATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTAGAGATGAGAGCC
*
45732311 AGTGTAAGACATGTCTGGGACATGCATCGACCTAGAGATGTA-AACC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTAGAGATG-AGAGCC
45732357 AGTGTAAGACATGTC
1 AGTGTAAGACATGTC
45732372 AGCTACAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
46 40 0.43
47 29 0.32
48 22 0.24
49 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCTAGAGATGAGAGCC
Found at i:45737755 original size:25 final size:25
Alignment explanation
Indices: 45737727--45737774 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
45737717 TTATACCATG
* * *
45737727 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
45737752 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
45737775 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:45737843 original size:20 final size:20
Alignment explanation
Indices: 45737818--45737874 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
45737808 TAAATATGGT
45737818 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
45737838 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
45737858 ATGTATGATATGCACAT
1 ATGTATGATATGCACAT
45737875 AATCATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:45737858 original size:11 final size:11
Alignment explanation
Indices: 45737822--45737874 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
45737812 TATGGTATGT
45737822 ATGATATGCAC
1 ATGATATGCAC
* *
45737833 ATGACATG--T
1 ATGATATGCAC
45737842 ATGATATGCAC
1 ATGATATGCAC
*
45737853 ATGATATG--T
1 ATGATATGCAC
45737862 ATGATATGCAC
1 ATGATATGCAC
45737873 AT
1 AT
45737875 AATCATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.47
11 17 0.53
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:45737951 original size:11 final size:11
Alignment explanation
Indices: 45737935--45737960 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45737925 AGAAAAGGGC
45737935 TTATGCCCCAG
1 TTATGCCCCAG
45737946 TTATGCCCCAG
1 TTATGCCCCAG
45737957 TTAT
1 TTAT
45737961 CAAAAGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (11 bp):
TTATGCCCCAG
Found at i:45738024 original size:45 final size:46
Alignment explanation
Indices: 45737946--45738077 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 46
45737936 TATGCCCCAG
45737946 TTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTATCAAA-AGC
1 TTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATCAAAGAGC
* *
45737991 TTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTGAAAGGGC
1 TTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTA-TCAAAGAGC
* *
45738038 TTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 TTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
45738078 ATGATAAAGC
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
44 13 0.17
45 23 0.30
46 4 0.05
47 15 0.19
48 12 0.16
49 10 0.13
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (46 bp):
TTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAGAGC
Found at i:45738073 original size:25 final size:24
Alignment explanation
Indices: 45737946--45738077 Score: 166
Period size: 24 Copynumber: 5.6 Consensus size: 24
45737936 TATGCCCCAG
*
45737946 TTATGCCCCAGTTATCAAAAGGGC
1 TTATGCCCCAGTTATTAAAAGGGC
*
45737970 TTATG-CCCAGTTATCAAAA--GC
1 TTATGCCCCAGTTATTAAAAGGGC
45737991 TTATGCCCCAGTTA-TAAAAGGGC
1 TTATGCCCCAGTTATTAAAAGGGC
*
45738014 TTATGCCCCAGTTATTGAAAGGGC
1 TTATGCCCCAGTTATTAAAAGGGC
*
45738038 TTTTGCCCCAGTTATTAAAAGAGGC
1 TTATGCCCCAGTTATTAAAAG-GGC
*
45738063 -TAGGCCTCCAGTTAT
1 TTATGCC-CCAGTTAT
45738078 ATGATAAAGC
Statistics
Matches: 96, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.11
22 8 0.08
23 30 0.31
24 36 0.38
25 11 0.11
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (24 bp):
TTATGCCCCAGTTATTAAAAGGGC
Found at i:45744528 original size:25 final size:25
Alignment explanation
Indices: 45744500--45744547 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
45744490 TTATACCTTG
* *
45744500 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
45744525 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
45744548 GTTTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:45744616 original size:20 final size:20
Alignment explanation
Indices: 45744591--45744674 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
45744581 TAAATATGGT
*
45744591 ATGTATGATATGCGCATGAC
1 ATGTATGATATGCACATGAC
45744611 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
45744631 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
45744651 ATGTATGATATGCACATGAG
1 ATGTATGATATGCACATGAC
45744671 ATGT
1 ATGT
45744675 TCATAAATGC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:45744651 original size:11 final size:11
Alignment explanation
Indices: 45744615--45744669 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
45744605 CATGACATGT
45744615 ATGATATGCAC
1 ATGATATGCAC
* *
45744626 ATGACATG--T
1 ATGATATGCAC
45744635 ATGATATGCAC
1 ATGATATGCAC
*
45744646 ATGATATG--T
1 ATGATATGCAC
45744655 ATGATATGCAC
1 ATGATATGCAC
45744666 ATGA
1 ATGA
45744670 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:45744751 original size:23 final size:23
Alignment explanation
Indices: 45744721--45744887 Score: 262
Period size: 23 Copynumber: 7.1 Consensus size: 23
45744711 AGGAAGTGCA
45744721 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
45744744 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
45744767 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
45744791 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
* *
45744815 AAAGGGCTTATGCCCCAGCTATA
1 AAAGGGCTTATGCCCCAGTTATT
45744838 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
45744861 GAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
45744885 AAA
1 AAA
45744888 AGAGGCTAGG
Statistics
Matches: 137, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
23 70 0.51
24 67 0.49
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:45744799 original size:24 final size:23
Alignment explanation
Indices: 45744720--45744909 Score: 265
Period size: 24 Copynumber: 8.0 Consensus size: 23
45744710 GAGGAAGTGC
45744720 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
45744743 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
45744766 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
45744789 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
45744813 CAAAAGGGCTTATGCCCCAGCTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
45744837 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* *
45744861 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
45744885 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
45744909 A
1 A
45744910 TGATAAAGCA
Statistics
Matches: 154, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
23 66 0.43
24 78 0.51
25 10 0.06
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:45744812 original size:47 final size:46
Alignment explanation
Indices: 45744721--45744908 Score: 270
Period size: 47 Copynumber: 4.0 Consensus size: 46
45744711 AGGAAGTGCA
*
45744721 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
*
45744767 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT-T
*
45744815 AAAGGGCTTATGCCCCAGCTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
* *
45744861 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 -AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
45744909 ATGATAAAGC
Statistics
Matches: 129, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
46 22 0.17
47 64 0.50
48 32 0.25
49 11 0.09
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:45745135 original size:31 final size:31
Alignment explanation
Indices: 45745100--45745163 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
45745090 CGTTTACAGT
45745100 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
45745131 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
45745162 AA
1 AA
45745164 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:45749994 original size:43 final size:43
Alignment explanation
Indices: 45749927--45750093 Score: 146
Period size: 42 Copynumber: 4.0 Consensus size: 43
45749917 ATAGGTCGTA
* *
45749927 CAATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCATAT
1 CAATGCCAATATCCCAGATATGGTCTTACACGAAATCTCATAT
* *
45749969 CAATGCCAATAGT-CCAGCTATGGTCTTACACGAAATTTCATAT
1 CAATGCCAATA-TCCCAGATATGGTCTTACACGAAATCTCATAT
* * * * * * *
45750012 CGATGCC-ATGTCCCAAACATAGTCTTACACGTAATATCATA-
1 CAATGCCAATATCCCAGATATGGTCTTACACGAAATCTCATAT
* * * *
45750053 CTGATGTC-ATATCCCAGATATGGTCTTACACGTATTCTCAT
1 C-AATGCCAATATCCCAGATATGGTCTTACACGAAATCTCAT
45750094 CTCGATAACC
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.02
42 64 0.63
43 35 0.34
44 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.32
Consensus pattern (43 bp):
CAATGCCAATATCCCAGATATGGTCTTACACGAAATCTCATAT
Done.