Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 38 of 322
Found at i:11399669 original size:34 final size:33
Alignment explanation
Indices: 11399595--11399707 Score: 124
Period size: 38 Copynumber: 3.3 Consensus size: 33
11399585 ATTATTTAAT
*
11399595 TAATAATTATCT-TTTACTT-AATAAATA-TAAA
1 TAATAAATATCTATTTACTTAAATAAA-AGTAAA
11399626 TAATAAATATCTATTTACTTAAATAAAAGTAATTAAA
1 TAATAAATATCTATTTACTTAAATAAAAG----TAAA
*
11399663 TAAATATATATCTATTTACTTAAATAAAAGTAAA
1 T-AATAAATATCTATTTACTTAAATAAAAGTAAA
11399697 TAAATAAATAT
1 T-AATAAATAT
11399708 ATCACAATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
31 11 0.15
32 8 0.11
33 6 0.08
34 14 0.20
37 5 0.07
38 27 0.38
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (33 bp):
TAATAAATATCTATTTACTTAAATAAAAGTAAA
Found at i:11399678 original size:38 final size:38
Alignment explanation
Indices: 11399621--11399709 Score: 153
Period size: 38 Copynumber: 2.4 Consensus size: 38
11399611 CTTAATAAAT
*
11399621 ATAAAT-AATAAATATCTATTTACTTAAATAAAAGTAA
1 ATAAATAAATATATATCTATTTACTTAAATAAAAGTAA
*
11399658 TTAAATAAATATATATCTATTTACTTAAATAAAAGTAA
1 ATAAATAAATATATATCTATTTACTTAAATAAAAGTAA
11399696 ATAAATAAATATAT
1 ATAAATAAATATAT
11399710 CACAATTGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 5 0.10
38 43 0.90
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.37
Consensus pattern (38 bp):
ATAAATAAATATATATCTATTTACTTAAATAAAAGTAA
Found at i:11399831 original size:15 final size:15
Alignment explanation
Indices: 11399786--11399831 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
11399776 ATTTATTTCA
*
11399786 TAATATAATATCAATT
1 TAATA-AATATCAAAT
* *
11399802 TAATAAAAATAAAAT
1 TAATAAATATCAAAT
11399817 TAATAAATATCAAAT
1 TAATAAATATCAAAT
11399832 ATAAAACCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAAATATCAAAT
Found at i:11400792 original size:125 final size:127
Alignment explanation
Indices: 11400538--11400773 Score: 300
Period size: 125 Copynumber: 1.9 Consensus size: 127
11400528 GAGTATGAGC
* *
11400538 TTGCCTTCTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATATTCGGATATTTAGAT
1 TTGCCTT-TATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAATCGGATACTTAGAT
** * ** *
11400603 CAAACGGAAAATCGAAACGCAATACGTTAGGGCACGACTACTCGAAGTTCTAGATACAAAATA
65 CAAACAAAAAATCGAAACGCAATACGTTAGGACACGACTACTAAAAGTTCAAGATACAAAATA
* *
11400666 TTGCCTTTATTTTATTTAAAACTCATGTATTTTAA-TTT-AAAAGGATAATC-GATTACTTAGAT
1 TTGCCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAATCGGA-TACTTAGAT
* * *
11400728 CAAACAAAAAATCGAAAC-CTAGTACGTTAGGACACGATTTCTAAAA
65 CAAACAAAAAATCGAAACGC-AATACGTTAGGACACGACTACTAAAA
11400774 TTTCCAAGTA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
124 3 0.03
125 55 0.59
126 3 0.03
127 26 0.28
128 7 0.07
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (127 bp):
TTGCCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAATCGGATACTTAGATC
AAACAAAAAATCGAAACGCAATACGTTAGGACACGACTACTAAAAGTTCAAGATACAAAATA
Found at i:11400798 original size:125 final size:127
Alignment explanation
Indices: 11400541--11400799 Score: 287
Period size: 125 Copynumber: 2.0 Consensus size: 127
11400531 TATGAGCTTG
* *
11400541 CCTTCTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATATTCGGATATTTAGATCAA
1 CCTT-TATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAATCGGATACTTAGATCAA
** * ** * *
11400606 ACGGAAAATCGAAACGCAATACGTTAGGGCACGACTACTCGAAGTTCTAGATACAAAATATTG
65 ACAAAAAATCGAAACGCAATACGTTAGGACACGACTACTAAAAGTTCAAGATACAAAATATTA
* *
11400669 CCTTTATTTTATTTAAAACTCATGTATTTTAA-TTT-AAAAGGATAATC-GATTACTTAGATCAA
1 CCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAATCGGA-TACTTAGATCAA
* * * * *
11400731 ACAAAAAATCGAAAC-CTAGTACGTTAGGACACGATTTCTAAAATTTCCAAG-TATC-GAATATT
65 ACAAAAAATCGAAACGC-AATACGTTAGGACACGACTACTAAAAGTT-CAAGATA-CAAAATATT
11400793 A
127 A
11400794 CCTTTA
1 CCTTTA
11400800 CTTGAAAAAT
Statistics
Matches: 111, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
124 3 0.03
125 71 0.64
126 7 0.06
127 26 0.23
128 4 0.04
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (127 bp):
CCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAATCGGATACTTAGATCAAA
CAAAAAATCGAAACGCAATACGTTAGGACACGACTACTAAAAGTTCAAGATACAAAATATTA
Found at i:11400837 original size:15 final size:16
Alignment explanation
Indices: 11400817--11400851 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11400807 AATCCAGGCA
*
11400817 AAAATAATA-ATAGAT
1 AAAATAATATAGAGAT
11400832 AAAATAATATAGAGAT
1 AAAATAATATAGAGAT
11400848 AAAA
1 AAAA
11400852 AATGGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
AAAATAATATAGAGAT
Found at i:11400984 original size:21 final size:21
Alignment explanation
Indices: 11400960--11401011 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
11400950 AATAGGATGG
*
11400960 ATAATAAAAATAATAGTAGTA
1 ATAATAAAAATAATAGTAATA
* *
11400981 ATAATAAATATAATGGTAATA
1 ATAATAAAAATAATAGTAATA
*
11401002 ATATTAAAAA
1 ATAATAAAAA
11401012 ATATATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (21 bp):
ATAATAAAAATAATAGTAATA
Found at i:11401072 original size:25 final size:25
Alignment explanation
Indices: 11401042--11401184 Score: 73
Period size: 24 Copynumber: 5.5 Consensus size: 25
11401032 AGTGTTAAAA
*
11401042 AATAATAATAATA-AACA-AACGAT
1 AATAATAATAATAGAAAATAACGAT
*
11401065 ATATTAATGATAATAGAAAATAACGAT
1 A-A-TAATAATAATAGAAAATAACGAT
**
11401092 AATAATAATGGAAGTAATGAAAATAATAAT
1 AATAATAAT--AA-T-A-GAAAATAACGAT
* *
11401122 AATAGA-AACAATAG-TAATAA-GAGT
1 AATA-ATAATAATAGAAAATAACGA-T
*
11401146 AATAATAA-AATAGAAAATAACAAT
1 AATAATAATAATAGAAAATAACGAT
*
11401170 GATACATTAATAATA
1 AATA-A-TAATAATA
11401185 ATATATGTGC
Statistics
Matches: 92, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
23 8 0.09
24 22 0.24
25 19 0.21
26 8 0.09
27 14 0.15
28 3 0.03
29 1 0.01
30 16 0.17
31 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.25
Consensus pattern (25 bp):
AATAATAATAATAGAAAATAACGAT
Found at i:11401098 original size:3 final size:3
Alignment explanation
Indices: 11401090--11401306 Score: 65
Period size: 3 Copynumber: 71.0 Consensus size: 3
11401080 GAAAATAACG
*
11401090 ATA ATA ATA ATGGA AGTA ATGA A-A ATA ATA ATA ATA GA-A ACA ATA
1 ATA ATA ATA AT--A A-TA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA
* * * * * *
11401135 GTA ATA AGA GTA ATA ATA A-A ATA GAAA ATA ACA ATG ATA CATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -A-TA ATA
* * * * ** *
11401182 ATA AT- ATA TGTG CTA ATA ATA ATA ACA ATA CGA A-A AAA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
11401226 CT- ATA TTA ATA AAA ATA ATA ATA GTA GGTTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA
* *
11401272 ATA AGGTA A-A A-A ATA ATA ATG A-A ATA ATA AAA ATA
1 ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11401307 CTATTGCGTT
Statistics
Matches: 156, Mismatches: 37, Indels: 42
0.66 0.16 0.18
Matches are distributed among these distances:
2 15 0.10
3 121 0.78
4 10 0.06
5 9 0.06
6 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:11401100 original size:28 final size:25
Alignment explanation
Indices: 11401042--11401101 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
11401032 AGTGTTAAAA
* *
11401042 AATAATAATAATAAACAAACGATAT
1 AATAATGATAATAAAAAAACGATAT
*
11401067 ATTAATGATAATAGAAAATAACGATAAT
1 AATAATGATAATA-AAAA-AACGAT-AT
11401095 AATAATG
1 AATAATG
11401102 GAAGTAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 11 0.39
26 3 0.11
27 6 0.21
28 8 0.29
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (25 bp):
AATAATGATAATAAAAAAACGATAT
Found at i:11401240 original size:23 final size:23
Alignment explanation
Indices: 11401214--11401271 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
11401204 TAACAATACG
*
11401214 AAAAA-AATAATACTATATTAAT
1 AAAAATAATAATACTAGATTAAT
* *
11401236 AAAAATAATAATAGTAGGTTAAT
1 AAAAATAATAATACTAGATTAAT
*
11401259 AATAATAATAATA
1 AAAAATAATAATA
11401272 ATAAGGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (23 bp):
AAAAATAATAATACTAGATTAAT
Found at i:11401302 original size:21 final size:23
Alignment explanation
Indices: 11401239--11401304 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
11401229 TATTAATAAA
* * * *
11401239 AATAATAATAGTAGGTTAATAAT
1 AATAATAATAATAAGTAAAAAAT
11401262 AATAATAATAATAAGGTAAAAAAT
1 AATAATAATAATAA-GTAAAAAAT
*
11401286 AATAATGA-AATAA-TAAAAA
1 AATAATAATAATAAGTAAAAA
11401305 TACTATTGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.16
23 17 0.46
24 14 0.38
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (23 bp):
AATAATAATAATAAGTAAAAAAT
Found at i:11401370 original size:3 final size:3
Alignment explanation
Indices: 11401362--11401393 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11401352 TAGTATATAG
11401362 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11401394 CATTCTGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11401874 original size:13 final size:13
Alignment explanation
Indices: 11401858--11401905 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
11401848 GGTGATGAAG
*
11401858 TTAGTGGGGTGGT
1 TTAGTGGGGTAGT
*
11401871 TTAGTGGGATAGT
1 TTAGTGGGGTAGT
*
11401884 TTAGT-GGTTAGT
1 TTAGTGGGGTAGT
11401896 TTAGTGGGGT
1 TTAGTGGGGT
11401906 GTTAATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.42
Consensus pattern (13 bp):
TTAGTGGGGTAGT
Found at i:11401897 original size:12 final size:12
Alignment explanation
Indices: 11401869--11401902 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11401859 TAGTGGGGTG
11401869 GTTTAGTGGGATA
1 GTTTAGT-GGATA
*
11401882 GTTTAGTGGTTA
1 GTTTAGTGGATA
11401894 GTTTAGTGG
1 GTTTAGTGG
11401903 GGTGTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (12 bp):
GTTTAGTGGATA
Found at i:11402182 original size:22 final size:22
Alignment explanation
Indices: 11402157--11402203 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
11402147 TAATCATTCC
*
11402157 AAATTTTTTCATCAAACAAACA
1 AAATTTTCTCATCAAACAAACA
*
11402179 AAATTTTCTCATCAAACAAATA
1 AAATTTTCTCATCAAACAAACA
11402201 AAA
1 AAA
11402204 GATAAACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATTTTCTCATCAAACAAACA
Found at i:11403958 original size:19 final size:19
Alignment explanation
Indices: 11403930--11403968 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
11403920 TTTACTTGAT
11403930 AAATATTAAT-TTTTCCAA
1 AAATATTAATATTTTCCAA
11403948 AAATCATTAATATTTTCCAA
1 AAAT-ATTAATATTTTCCAA
11403968 A
1 A
11403969 TATTTCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 9 0.47
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATTAATATTTTCCAA
Found at i:11404173 original size:27 final size:27
Alignment explanation
Indices: 11404132--11404196 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
11404122 ACAAATGGAC
*
11404132 CAATTGAACATATAAAATTAGACTCGAG
1 CAATTGCA-ATATAAAATTAGACTCGAG
11404160 CAATTGCAATATAAAATTAGACTCGAG
1 CAATTGCAATATAAAATTAGACTCGAG
11404187 CAATTGCAAT
1 CAATTGCAAT
11404197 TATGTCTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (27 bp):
CAATTGCAATATAAAATTAGACTCGAG
Found at i:11405403 original size:34 final size:33
Alignment explanation
Indices: 11405343--11405411 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 33
11405333 TAATTTCTAT
11405343 AATTTTGTAAATTTTTAATATATTTTATTTATAA
1 AATTTTGTAAA-TTTTAATATATTTTATTTATAA
* *
11405377 AATTTTAGTAAA-TTTAATAATTTTTTATTTTTAA
1 AATTTT-GTAAATTTTAAT-ATATTTTATTTATAA
11405411 A
1 A
11405412 TAAATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 6 0.19
34 20 0.65
35 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (33 bp):
AATTTTGTAAATTTTAATATATTTTATTTATAA
Found at i:11408161 original size:19 final size:19
Alignment explanation
Indices: 11408139--11408177 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11408129 ACTAGTTTTA
11408139 AAAATTATTAG-AAATTATT
1 AAAA-TATTAGAAAATTATT
11408158 AAAATATTAGAAAATTATT
1 AAAATATTAGAAAATTATT
11408177 A
1 A
11408178 GAAAATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAATATTAGAAAATTATT
Found at i:11408206 original size:10 final size:10
Alignment explanation
Indices: 11408136--11408231 Score: 69
Period size: 10 Copynumber: 10.0 Consensus size: 10
11408126 ATTACTAGTT
11408136 TTAAAAATTA
1 TTAAAAATTA
*
11408146 TTAGAAATTA
1 TTAAAAATTA
11408156 TT-AAAA-TA
1 TTAAAAATTA
11408164 TTAGAAAATTA
1 TTA-AAAATTA
11408175 TTAGAAAA-TA
1 TTA-AAAATTA
* **
11408185 GTAAATGTTA
1 TTAAAAATTA
*
11408195 TTAAAAAGTA
1 TTAAAAATTA
**
11408205 TTAAATGTTA
1 TTAAAAATTA
11408215 -TAAAAA-T-
1 TTAAAAATTA
11408222 TTAAAAATTA
1 TTAAAAATTA
11408232 CCACTCCTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
8 11 0.17
9 10 0.15
10 34 0.52
11 10 0.15
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:11408272 original size:11 final size:11
Alignment explanation
Indices: 11408258--11408293 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11408248 TATTATATTA
11408258 TTTTTATAATT
1 TTTTTATAATT
*
11408269 TTTTTAGAATT
1 TTTTTATAATT
*
11408280 TTTATATAATT
1 TTTTTATAATT
11408291 TTT
1 TTT
11408294 AAAAATCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:11408967 original size:26 final size:26
Alignment explanation
Indices: 11408938--11408988 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
11408928 ATATACATAT
11408938 AAATCTCGAGTCAAAAGTTGACTTAA
1 AAATCTCGAGTCAAAAGTTGACTTAA
* *
11408964 AAATTTGGAGTCAAAAGTTGACTTA
1 AAATCTCGAGTCAAAAGTTGACTTA
11408989 TTGATGACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (26 bp):
AAATCTCGAGTCAAAAGTTGACTTAA
Found at i:11410732 original size:30 final size:30
Alignment explanation
Indices: 11410696--11410757 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
11410686 CAACAAAATG
11410696 GAGAGGCTAGGGCATTGTTAAGGTTCAGCT
1 GAGAGGCTAGGGCATTGTTAAGGTTCAGCT
11410726 GAGAGGCTAGGGCATTGTTAAGGTTCAGCT
1 GAGAGGCTAGGGCATTGTTAAGGTTCAGCT
11410756 GA
1 GA
11410758 ATGAAGGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (30 bp):
GAGAGGCTAGGGCATTGTTAAGGTTCAGCT
Found at i:11412543 original size:127 final size:126
Alignment explanation
Indices: 11412310--11412632 Score: 468
Period size: 127 Copynumber: 2.5 Consensus size: 126
11412300 GAAAATTCCT
* * * *
11412310 TAAAACGAAGGCAATGTTTGATGTTTGAAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTTTG
1 TAAAAC-AAGGCAATGTTTAATGTTTGGAAATTCGAG-AATCGTGCCCTATCGTGCTGGGTTTCG
* *
11412375 ATTTCCCGTTTGTTCAAAATAATCGAATATTGCTTTAGAATTTTACTCGTGTTCTCCAAATTC
64 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTGTTCTCCAAATTC
* * *
11412438 TAAAACAAGGCAATATTCAATGTTTGGAAATTCAGAGAATCGTGCCCTATCGTGCTGGGTTTGGA
1 TAAAACAAGGCAATGTTTAATGTTTGGAAATTC-GAGAATCGTGCCCTATCGTGCTGGGTTTCGA
* * * *
11412503 TTTCCGGTTTGTTCAAAATAATTGAATATTCCTTTAGAATTTCACTCGTGTTTTCTAAATTC
65 TTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTGTTCTCCAAATTC
*
11412565 TAAAGCAAGGCAATGTTTAATGTTTGGAAATTCGAGGAATCGTGCCCTA-CTGTGCTGGGTTTCG
1 TAAAACAAGGCAATGTTTAATGTTTGGAAATTCGA-GAATCGTGCCCTATC-GTGCTGGGTTTCG
11412629 ATTT
64 ATTT
11412633 TTCGTTGAGC
Statistics
Matches: 176, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
126 3 0.02
127 165 0.94
128 8 0.05
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (126 bp):
TAAAACAAGGCAATGTTTAATGTTTGGAAATTCGAGAATCGTGCCCTATCGTGCTGGGTTTCGAT
TTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTGTTCTCCAAATTC
Found at i:11415927 original size:19 final size:19
Alignment explanation
Indices: 11415903--11415943 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11415893 GATGCCTCAT
*
11415903 TTACATT-CATGCATTTGCA
1 TTACATTACAT-CATATGCA
11415922 TTACATTACATCATATGCA
1 TTACATTACATCATATGCA
11415941 TTA
1 TTA
11415944 AAGGCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (19 bp):
TTACATTACATCATATGCA
Found at i:11418679 original size:27 final size:26
Alignment explanation
Indices: 11418639--11418750 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
11418629 AGCATGGCTG
* * *
11418639 CCAGAACATATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
11418665 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
11418693 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
11418720 CCAGATCAGATAATTGTGGCATATCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
11418747 CCAG
1 CCAG
11418751 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 51 0.69
28 17 0.23
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:11427518 original size:45 final size:45
Alignment explanation
Indices: 11427463--11427795 Score: 222
Period size: 45 Copynumber: 7.6 Consensus size: 45
11427453 AAGTAACAAG
* * * *
11427463 TCTTGTCTCCCTGAAGTTGTAGTGGAACAGACTAAAAATAGCAGA
1 TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
* * * *
11427508 TCTTGCCTCCCTAAAGTTGCAGCGGAGCAGA-T--CGA-AGCA-A
1 TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
*
11427548 GTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
1 -TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
* * * * * *
11427594 TCTTGTCTCCCTGAAGCTGCAATGGAACAGA-TCGAAG-TAAC-GA
1 TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACT-GAAGATAGCAGA
* * * *
11427637 GTCTTATCTTCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGTAGA
1 -TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
** * **
11427683 TCTTGTCTCCCTAAAGTTACAGTGGGGCAGA-TCGAAGCCA-C-GA
1 TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACT-GAAGATAGCAGA
* * * * * ** * *
11427726 TCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAG-TAACAAA
1 T-CTTGTCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
* *
11427771 TCTTGTCTCCCTGAAGTTGCAGTGG
1 TCTTGTCTCCCTAAAGTTGTAGTGG
11427796 GGCAAATCGA
Statistics
Matches: 224, Mismatches: 48, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
40 1 0.00
41 31 0.14
42 2 0.01
43 6 0.03
44 86 0.38
45 95 0.42
46 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (45 bp):
TCTTGTCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGA
Found at i:11427669 original size:89 final size:89
Alignment explanation
Indices: 11427452--11427842 Score: 407
Period size: 89 Copynumber: 4.4 Consensus size: 89
11427442 AGAGCGGGTT
* * * * *
11427452 GAAGTAACAAGTCTTGTCTCCCTGAAGTTGTAGTGGAACAGACTAAAAATAGCAGATCTTGCCTC
1 GAAGTAACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGTCTC
*
11427517 CCTAAAGTTGCAGCGGAGCAGATC
66 CCTAAAGTTGCAGTGGAGCAGATC
*
11427541 GAAG---CAAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGTCTC
1 GAAGTAACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGTCTC
* * * *
11427603 CCTGAAGCTGCAATGGAACAGATC
66 CCTAAAGTTGCAGTGGAGCAGATC
* * *
11427627 GAAGTAACGAGTCTTATCTTCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGTAGATCTTGTCTC
1 GAAGTAACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGTCTC
* *
11427692 CCTAAAGTTACAGTGGGGCAGATC
66 CCTAAAGTTGCAGTGGAGCAGATC
** * * * * ** * *
11427716 GAAGCCACGA-TCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAG-TAACAAATCTTGTCT
1 GAAGTAACAAGT-CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGTCT
* * *
11427779 CCCTGAAGTTGCAGTGGGGCAAATC
65 CCCTAAAGTTGCAGTGGAGCAGATC
** * * * *
11427804 GAAGCCACGA-TCCTTATCTCTCTGAAGTTGCAGTAGAGC
1 GAAGTAACAAGT-CTTATCTCCCTGAAGTTGTAGTGGAGC
11427843 GGGTTGAAAT
Statistics
Matches: 263, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
86 75 0.29
88 74 0.28
89 114 0.43
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (89 bp):
GAAGTAACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTGTCTC
CCTAAAGTTGCAGTGGAGCAGATC
Found at i:11427787 original size:44 final size:44
Alignment explanation
Indices: 11427450--11427943 Score: 280
Period size: 44 Copynumber: 11.2 Consensus size: 44
11427440 ATAGAGCGGG
* * * *
11427450 TTGAAGTAACAAGTCTTGTCTCCCTGAAGTTGTAGTGGAACAGA
1 TTGAAGTAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
** * * * ** * *
11427494 CTAAAAATAGCAGATCTTGCCTCCCTAAAGTTGCAGCGGAGCAGA
1 -TTGAAGTAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * * *
11427539 TCGAAG---CAAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGA
1 TTGAAGTAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * * * * * *
11427580 CTGAAGATAGCAGATCTTGTCTCCCTGAAGCTGCAATGGAACAGA
1 TTGAAG-TAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * * * *
11427625 TCGAAGTAACGAGTCTTATCTTCCTGAAGTTGTAGTGGAGCAGA
1 TTGAAGTAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* ** * * * * *
11427669 CTGAAGATAGTAGATCTTGTCTCCCTAAAGTTACAGTGGGGCAGA
1 TTGAAG-TAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* ** * * * *
11427714 TCGAAGCCAC-GATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
1 TTGAAGTAACAAAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * *
11427758 TTGAAGTAACAAATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAA
1 TTGAAGTAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* ** * * * * *
11427802 TCGAAGCCAC-GATCCTTATCTCTCTGAAGTTGCAGTAGAGCGGG
1 TTGAAGTAACAAAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * * * *
11427846 TTGAAATAACAAATCCGTATCTCTCTGAAGTTACAGTAGAGCAGGA
1 TTGAAGTAACAAAT-CTTATCTCCCTGAAGTTGCAGTGGAGCA-GA
** * * *
11427892 TAAAAATATGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG-
1 TTGAAGTA-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
*
11427936 TTGCAGTA
1 TTGAAGTA
11427944 GAGAAGATTA
Statistics
Matches: 328, Mismatches: 110, Indels: 23
0.71 0.24 0.05
Matches are distributed among these distances:
41 33 0.10
43 5 0.02
44 129 0.39
45 126 0.38
46 31 0.09
47 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
TTGAAGTAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
Found at i:11427920 original size:46 final size:46
Alignment explanation
Indices: 11427813--11427935 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 46
11427803 CGAAGCCACG
* **
11427813 ATCCTTATCTCTCTGAAGTTGCAGTAGAGC-GGGTTGAAATAACAA
1 ATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATAAAAATAACAA
* * *
11427858 ATCCGTATCTCTCTGAAGTTACAGTAGAGCAGGATAAAAATATGCAA
1 ATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATAAAAATA-ACAA
* *
11427905 A-CCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 ATCCTTATCTCTCTGAAGTTGCAGTAGAGCAG
11427936 TTGCAGTAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
45 28 0.42
46 34 0.52
47 4 0.06
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (46 bp):
ATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATAAAAATAACAA
Found at i:11430642 original size:127 final size:127
Alignment explanation
Indices: 11430465--11430783 Score: 435
Period size: 127 Copynumber: 2.5 Consensus size: 127
11430455 GAAAATTCCT
* ** * *
11430465 TAAAACGAAGGCAATGTTTGATGTTTGAAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTTCG
1 TAAAAC-AAGGCAATATTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCG
* *
11430530 ATTTCCCGTTTGTTCAAAATAATCGAATATTGCTTTAGAATTTCAC-ACGTGTTTTCCAAATTC
65 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTA-GTGTTTTCCAAATTA
* * *
11430593 TAAAACAAGGCAATATTCAATATTTGGAAATTCGGGGAATCGTGCCCTATCGTGTTGGGTTTGGA
1 TAAAACAAGGCAATATTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGA
* * * **
11430658 TTTTCGGTTTGTTCAAAATAATTGAATATTCCTTTAGAATTTCACTAGTGTTTTTTAAATTA
66 TTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTAGTGTTTTCCAAATTA
** *
11430720 TAAAGTAAGGCAATATTCAATGTTTGGAAATTCGAGGAATCGTGCCCTA-CTGTGCTGGGTTTCG
1 TAAAACAAGGCAATATTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATC-GTGCTGGGTTTCG
11430784 GTTTTTCGTT
Statistics
Matches: 168, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
126 1 0.01
127 160 0.95
128 7 0.04
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (127 bp):
TAAAACAAGGCAATATTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGA
TTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTAGTGTTTTCCAAATTA
Found at i:11431327 original size:18 final size:19
Alignment explanation
Indices: 11431290--11431326 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11431280 TTTTTTAAAA
11431290 TATAAA-ATTTGGAATTTT
1 TATAAATATTTGGAATTTT
11431308 TATAAATATTTGGAATTTT
1 TATAAATATTTGGAATTTT
11431327 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:11431332 original size:18 final size:20
Alignment explanation
Indices: 11431296--11431337 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11431286 AAAATATAAA
*
11431296 ATTTGGAATTTTTATAAA-T
1 ATTTGGAATTTTTAAAAATT
11431315 ATTTGGAA-TTTTAAAAATT
1 ATTTGGAATTTTTAAAAATT
11431334 ATTT
1 ATTT
11431338 TATATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTTGGAATTTTTAAAAATT
Found at i:11432109 original size:3 final size:3
Alignment explanation
Indices: 11432101--11432128 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11432091 ATAATATACT
11432101 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11432129 CTCTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11436026 original size:20 final size:20
Alignment explanation
Indices: 11436003--11436044 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
11435993 TTTAAAACTG
11436003 AGAAAATAGTAAAAAAATAT
1 AGAAAATAGTAAAAAAATAT
11436023 AGAAAATAGTAAAAAAATAT
1 AGAAAATAGTAAAAAAATAT
11436043 AG
1 AG
11436045 TGCTCATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (20 bp):
AGAAAATAGTAAAAAAATAT
Found at i:11436028 original size:10 final size:11
Alignment explanation
Indices: 11436005--11436041 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11435995 TAAAACTGAG
11436005 AAAATAGTAAA
1 AAAATAGTAAA
*
11436016 AAAATA-T-AG
1 AAAATAGTAAA
11436025 AAAATAGTAAA
1 AAAATAGTAAA
11436036 AAAATA
1 AAAATA
11436042 TAGTGCTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAATAGTAAA
Found at i:11439904 original size:21 final size:21
Alignment explanation
Indices: 11439859--11439904 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
11439849 AAAATGAATT
11439859 GTAATTGATTTGAATTATCTA
1 GTAATTGATTTGAATTATCTA
*
11439880 -TAATTGTTTTGAAATTAT-TA
1 GTAATTGATTTG-AATTATCTA
11439900 GTAAT
1 GTAAT
11439905 ACTCAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (21 bp):
GTAATTGATTTGAATTATCTA
Found at i:11443910 original size:14 final size:16
Alignment explanation
Indices: 11443891--11443924 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11443881 TCTTTTCTTC
11443891 TTTCG-TTCTT-TCTA
1 TTTCGTTTCTTCTCTA
11443905 TTTCGTTTCTTCTCTA
1 TTTCGTTTCTTCTCTA
11443921 TTTC
1 TTTC
11443925 TTTTTCTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 5 0.28
16 8 0.44
ACGTcount: A:0.06, C:0.24, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTCGTTTCTTCTCTA
Found at i:11443925 original size:26 final size:25
Alignment explanation
Indices: 11443874--11443927 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
11443864 ATTTCTCCTT
* * *
11443874 TTTCTTTTCTTTTCTTCTTTCGTTC
1 TTTCTTTTCGTTTCTTCTCTAGTTC
*
11443899 TTTCTATTTCGTTTCTTCTCTATTTC
1 TTTCT-TTTCGTTTCTTCTCTAGTTC
11443925 TTT
1 TTT
11443928 TTCTTGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTCTTTTCGTTTCTTCTCTAGTTC
Found at i:11444116 original size:3 final size:3
Alignment explanation
Indices: 11444108--11444138 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11444098 TTGATAAAAT
11444108 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11444139 GTAAATATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11444622 original size:18 final size:20
Alignment explanation
Indices: 11444591--11444627 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11444581 TTTTAAACTA
*
11444591 AATTTAACTCCCT-ATTTTC
1 AATTAAACTCCCTAATTTTC
11444610 AATTAAACT-CCTAATTTT
1 AATTAAACTCCCTAATTTT
11444628 TGAATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTAAACTCCCTAATTTTC
Found at i:11446658 original size:51 final size:51
Alignment explanation
Indices: 11446550--11446660 Score: 123
Period size: 51 Copynumber: 2.2 Consensus size: 51
11446540 ATGTATGTAA
* * *
11446550 GCTAAAATTGTTAAATCAAAACTAAAATGACAGAATATATAAATATTGAAG
1 GCTAAATTTGTTAAATCAAAAATAAAATGACAAAATATATAAATATTGAAG
** * * * * * *
11446601 ATTAAATTTGTTAAATCAAAAATAAATTGATAAAATATGTAAGTTTTGATG
1 GCTAAATTTGTTAAATCAAAAATAAAATGACAAAATATATAAATATTGAAG
11446652 GCTAAATTT
1 GCTAAATTT
11446661 ATTATACTAA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (51 bp):
GCTAAATTTGTTAAATCAAAAATAAAATGACAAAATATATAAATATTGAAG
Found at i:11447260 original size:16 final size:16
Alignment explanation
Indices: 11447241--11447295 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
11447231 TTTTATGATT
11447241 TTTTATATTTA-TAATA
1 TTTTA-ATTTATTAATA
11447257 TTTTGTAAATTTATTAAT-
1 -TTT-T-AATTTATTAATA
11447275 TTATTAATTTATTAATA
1 TT-TTAATTTATTAATA
11447292 TTTT
1 TTTT
11447296 TCATAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
16 13 0.39
17 8 0.24
18 7 0.21
19 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTAATTTATTAATA
Found at i:11447277 original size:8 final size:8
Alignment explanation
Indices: 11447264--11447290 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11447254 ATATTTTGTA
11447264 AATTTATT
1 AATTTATT
11447272 AATTTATT
1 AATTTATT
11447280 AATTTATT
1 AATTTATT
11447288 AAT
1 AAT
11447291 ATTTTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
AATTTATT
Found at i:11456221 original size:13 final size:13
Alignment explanation
Indices: 11456203--11456227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11456193 TATGTGATAT
11456203 GTGTGAAAATTTC
1 GTGTGAAAATTTC
11456216 GTGTGAAAATTT
1 GTGTGAAAATTT
11456228 TATTGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:11457049 original size:43 final size:43
Alignment explanation
Indices: 11456888--11457052 Score: 169
Period size: 43 Copynumber: 3.8 Consensus size: 43
11456878 CATAGGAATT
* *
11456888 TCGATATGT-ATTATCGTGTAAGACCACGTCTGGGA-TGTTGGCA
1 TCGATATTTGATTA-CGTGTAAGACCACGTCTGGGACAG-TGGCA
* * *
11456931 TCGAT-TTGTGATTTACGTGTAAGACCATGTCAGGGACATTGGCA
1 TCGATATT-TGA-TTACGTGTAAGACCACGTCTGGGACAGTGGCA
* *
11456975 TCG-TATCTGATTTCGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGATATTTGATTACGTGTAAGACCAC-GTCTGGGACAGTGGCA
* *
11457017 TCGATATTTGATTACATGTAAGACCACATCTGGGAC
1 TCGATATTTGATTACGTGTAAGACCACGTCTGGGAC
11457053 GTTGGTATTG
Statistics
Matches: 100, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
42 31 0.31
43 36 0.36
44 30 0.30
45 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGATATTTGATTACGTGTAAGACCACGTCTGGGACAGTGGCA
Found at i:11460753 original size:22 final size:23
Alignment explanation
Indices: 11460727--11460773 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
11460717 TAAAAGAAAT
11460727 AGAATAAAGAAAAGA-AACAAAA
1 AGAATAAAGAAAAGAGAACAAAA
* *
11460749 AGAATAGAGAAAAGAGAACAGAA
1 AGAATAAAGAAAAGAGAACAAAA
11460772 AG
1 AG
11460774 CATTCGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.04
Consensus pattern (23 bp):
AGAATAAAGAAAAGAGAACAAAA
Found at i:11460762 original size:27 final size:30
Alignment explanation
Indices: 11460718--11460772 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
11460708 TAAAGTAAAT
11460718 AAAAGAAATAGAATAAAGA-AA-AGAAACA
1 AAAAGAAATAGAATAAAGAGAACAGAAACA
11460746 AAAAG-AATAGAGA-AAAGAGAACAGAAA
1 AAAAGAAATAGA-ATAAAGAGAACAGAAA
11460773 GCATTCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (30 bp):
AAAAGAAATAGAATAAAGAGAACAGAAACA
Found at i:11462298 original size:23 final size:23
Alignment explanation
Indices: 11462272--11462346 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 23
11462262 AGGCACTTGA
11462272 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
11462295 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* * **
11462316 TGTGTC--ATTTTAGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
11462337 TGTGTCGTAT
1 TGTGTCGTAT
11462347 ACTGATCAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
21 32 0.73
23 11 0.25
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:11466306 original size:19 final size:19
Alignment explanation
Indices: 11466260--11466306 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 19
11466250 TCCAAGAATT
*
11466260 TGATAGAATTTTGAGAGGA
1 TGATAGAGTTTTGAGAGGA
11466279 T-AT-GAGTTTTGAGAGGA
1 TGATAGAGTTTTGAGAGGA
11466296 TGATAGAGTTT
1 TGATAGAGTTT
11466307 AGGTCACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 14 0.56
18 4 0.16
19 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (19 bp):
TGATAGAGTTTTGAGAGGA
Found at i:11469158 original size:13 final size:14
Alignment explanation
Indices: 11469140--11469173 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11469130 GAGAGATGTT
11469140 TAATTAGTT-AATA
1 TAATTAGTTAAATA
*
11469153 TAATTACTTAAATA
1 TAATTAGTTAAATA
11469167 TAATTAG
1 TAATTAG
11469174 ATAACAAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (14 bp):
TAATTAGTTAAATA
Found at i:11469227 original size:65 final size:67
Alignment explanation
Indices: 11469103--11469233 Score: 196
Period size: 65 Copynumber: 2.0 Consensus size: 67
11469093 CAACTTGAAG
11469103 AGATAACAAGACAAAAGCAAGGTCTGAGAGAGATGTTTAATTAGTTAATATAATTACTTAAATAT
1 AGATAACAAGACAAAAGCAAGGTCT--GAGAGATGTTTAATTAGTTAATATAATTACTTAAATAT
11469168 AATT
64 AATT
* *
11469172 AGATAACAAGACAAAAGCAAGGT-T-AG-TATTTTATAATTAGTTAATATAATTACTTAAATATA
1 AGATAACAAGACAAAAGCAAGGTCTGAGAGATGTT-TAATTAGTTAATATAATTACTTAAATATA
11469234 GCAACCTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
64 4 0.07
65 31 0.53
68 1 0.02
69 23 0.39
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (67 bp):
AGATAACAAGACAAAAGCAAGGTCTGAGAGATGTTTAATTAGTTAATATAATTACTTAAATATAA
TT
Found at i:11475596 original size:21 final size:21
Alignment explanation
Indices: 11475570--11475613 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
11475560 TTACTGCTTA
11475570 AACATGACAAATTTTCTAAGC
1 AACATGACAAATTTTCTAAGC
*
11475591 AACATGACAAGTTTTCTAAGC
1 AACATGACAAATTTTCTAAGC
11475612 AA
1 AA
11475614 ACAATACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (21 bp):
AACATGACAAATTTTCTAAGC
Found at i:11476394 original size:22 final size:23
Alignment explanation
Indices: 11476364--11476421 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
11476354 ATAAATTATT
*
11476364 ATAAAATAATAATATATG-T-TAA
1 ATAATATAATAATAT-TGTTATAA
11476386 ATAATATAATAA-ATTGTTGATAA
1 ATAATATAATAATATTGTT-ATAA
11476409 ATAATA-AATAATA
1 ATAATATAATAATA
11476422 AAAATATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.06
21 3 0.10
22 16 0.52
23 10 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
ATAATATAATAATATTGTTATAA
Found at i:11476414 original size:18 final size:17
Alignment explanation
Indices: 11476354--11476417 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 17
11476344 TAATTAAAAG
*
11476354 ATAAATTATTATAAAATA
1 ATAAATTGTTAT-AAATA
11476372 ATAATATATGTTAAATAATATA
1 ATAA-AT-TGTT--ATAA-ATA
11476394 ATAAATTGTTGATAAATA
1 ATAAATTGTT-ATAAATA
11476412 ATAAAT
1 ATAAAT
11476418 AATAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 13 0.33
19 6 0.15
20 7 0.18
21 4 0.10
22 9 0.23
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
ATAAATTGTTATAAATA
Found at i:11480718 original size:25 final size:24
Alignment explanation
Indices: 11480660--11480756 Score: 81
Period size: 25 Copynumber: 3.9 Consensus size: 24
11480650 ATTGGCTCGT
*
11480660 ATGAGCTTCCCGTTAATGGCTCTC
1 ATGAGCTTCCCGTTAATGGCTCAC
* * *
11480684 -CGAAGTTTCCTGTTACATGGCTCAC
1 ATG-AGCTTCCCGTTA-ATGGCTCAC
11480709 ATGAGCTTCCCGATTAATGGCTCGA-
1 ATGAGCTTCCCG-TTAATGGCTC-AC
* *
11480734 AAGAGCTTCCCGTTTATGTGCTC
1 ATGAGCTTCCCGTTAATG-GCTC
11480757 GTAAGAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.02
24 15 0.26
25 37 0.64
26 5 0.09
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (24 bp):
ATGAGCTTCCCGTTAATGGCTCAC
Found at i:11480757 original size:25 final size:25
Alignment explanation
Indices: 11480711--11480772 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
11480701 TGGCTCACAT
11480711 GAGCTTCCCGATTAATGGCTCGAAA
1 GAGCTTCCCGATTAATGGCTCGAAA
* *
11480736 GAGCTTCCCG-TTTATGTGCTCGTAA
1 GAGCTTCCCGATTAATG-GCTCGAAA
11480761 GAGCATTCCCGA
1 GAGC-TTCCCGA
11480773 ATATGAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 5 0.16
25 21 0.66
26 6 0.19
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCGAAA
Found at i:11480923 original size:17 final size:16
Alignment explanation
Indices: 11480889--11480927 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
11480879 TGAATTCGAA
11480889 ATGAATTATCATGGAT
1 ATGAATTATCATGGAT
* *
11480905 ATGAATTGTACATGTAT
1 ATGAATTAT-CATGGAT
11480922 ATGAAT
1 ATGAAT
11480928 ACATGACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (16 bp):
ATGAATTATCATGGAT
Found at i:11490078 original size:24 final size:25
Alignment explanation
Indices: 11490008--11490079 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
11489998 TAGCTCAAAA
* *
11490008 GAGCGTCCCGTTATTAGCTC-TCAT
1 GAGCTTCCCGTTATTAGCTCTTCAC
* * * *
11490032 GAGCTTTCCATTATATGGTTCTTC-C
1 GAGCTTCCCGTTAT-TAGCTCTTCAC
11490057 GAGCTTCCCGTTATTAGCTCTTC
1 GAGCTTCCCGTTATTAGCTCTTC
11490080 GGAGTATCCC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
24 18 0.50
25 16 0.44
26 2 0.06
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.39
Consensus pattern (25 bp):
GAGCTTCCCGTTATTAGCTCTTCAC
Found at i:11493538 original size:49 final size:51
Alignment explanation
Indices: 11493482--11493822 Score: 397
Period size: 51 Copynumber: 6.8 Consensus size: 51
11493472 TAGCCAAAGC
* *
11493482 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGA-CCAA-T
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
* * * ** *
11493531 TATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTTATCGAAGT
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
* * *
11493582 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGA-CCAA-T
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
* * * ** *
11493631 TATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTTATCGAAGT
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
* * *
11493682 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGA-CCAA-T
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
* * * ** *
11493731 TATCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTTATCGAAGT
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
*
11493782 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACG
1 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACG
11493823 TGACCTCACA
Statistics
Matches: 238, Mismatches: 48, Indels: 10
0.80 0.16 0.03
Matches are distributed among these distances:
49 111 0.47
50 15 0.06
51 112 0.47
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (51 bp):
TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGT
Found at i:11493625 original size:100 final size:100
Alignment explanation
Indices: 11493482--11493818 Score: 665
Period size: 100 Copynumber: 3.4 Consensus size: 100
11493472 TAGCCAAAGC
*
11493482 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
11493547 TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
66 TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
11493582 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
11493647 TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
66 TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
11493682 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
11493747 TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
66 TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
11493782 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACA
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACA
11493819 CACGTGACCT
Statistics
Matches: 236, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 236 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATCTGGTACACGTAG
TAGCTTGCACTTAGTACTACACACGTTATCGAAGT
Found at i:11498940 original size:26 final size:26
Alignment explanation
Indices: 11498902--11498983 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
11498892 TGATACAAAT
*
11498902 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11498928 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11498954 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11498980 TGAT
1 TGAT
11498984 TGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11505894 original size:26 final size:26
Alignment explanation
Indices: 11505865--11506726 Score: 1697
Period size: 26 Copynumber: 33.2 Consensus size: 26
11505855 TGATACAAAT
*
11505865 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11505891 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11505917 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
11505943 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11505969 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11505995 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506021 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506047 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506073 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506099 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506125 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506151 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506177 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506203 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506229 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506255 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506281 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506307 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506333 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506359 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506385 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506411 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506437 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506463 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506489 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506515 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506541 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506567 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506593 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506619 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506645 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506671 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
11506697 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11506723 TGAT
1 TGAT
11506727 TGGAATTTCA
Statistics
Matches: 832, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 832 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:11507162 original size:40 final size:41
Alignment explanation
Indices: 11507142--11507402 Score: 380
Period size: 41 Copynumber: 6.4 Consensus size: 41
11507132 CGTTCTAGAA
11507142 AAAACGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTTCAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
* * *
11507182 AAAACACCGATAAAAACCAGAGCATTAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
* *
11507223 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
* *
11507264 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCTCTTTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
* * *
11507305 AAAACACCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
* * * **
11507346 AAAACGCCGCTAAACACCAGAGCATCAGCGGCACTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
11507387 AAAACGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
11507403 TCTCATAACG
Statistics
Matches: 200, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
40 9 0.05
41 191 0.95
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCAT
Found at i:11507308 original size:123 final size:123
Alignment explanation
Indices: 11507142--11507402 Score: 427
Period size: 123 Copynumber: 2.1 Consensus size: 123
11507132 CGTTCTAGAA
11507142 AAAACGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTTCATAAAACACCG-ATAAAAACCAGAGC
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCATAAAACACCGCA-AAAAACCAGAGC
* *
11507205 ATTAGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
65 ATTAGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATCAGCGGCACTTTTCCT
* *
11507264 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCTCTTTTCCTAAAACACCGCAAAAAACCAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCATAAAACACCGCAAAAAACCAGAGCA
* * **
11507329 TTAGCGGCGCTTTTCGTAAAACGCCGCTAAACACCAGAGCATCAGCGGCACTTTTTGT
66 TTAGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATCAGCGGCACTTTTCCT
11507387 AAAACGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
11507403 TCTCATAACG
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
122 11 0.09
123 117 0.91
124 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (123 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCATAAAACACCGCAAAAAACCAGAGCA
TTAGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATCAGCGGCACTTTTCCT
Found at i:11507581 original size:14 final size:14
Alignment explanation
Indices: 11507559--11507598 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11507549 TTAATTATCA
* *
11507559 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
11507573 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
11507587 ATATGGTTTAAG
1 TTATGGTTTAAG
11507599 CATGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:11508561 original size:24 final size:24
Alignment explanation
Indices: 11508511--11508561 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
11508501 TATATGAGAT
* * *
11508511 AAATATATATAAAATATTATTTTA
1 AAATATATATAAAATATCATATGA
11508535 AAATATATAT-AAATATACATATGA
1 AAATATATATAAAATAT-CATATGA
11508559 AAA
1 AAA
11508562 GTGGTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATATAAAATATCATATGA
Found at i:11509564 original size:18 final size:18
Alignment explanation
Indices: 11509525--11509566 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11509515 TGATCTTAAT
*
11509525 GATGATGATGTTGATATT
1 GATGATGATGTTGATATC
* *
11509543 GATGTTGATGTTGATCTC
1 GATGATGATGTTGATATC
11509561 GATGAT
1 GATGAT
11509567 TATACCCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.43
Consensus pattern (18 bp):
GATGATGATGTTGATATC
Found at i:11510126 original size:61 final size:61
Alignment explanation
Indices: 11510013--11510193 Score: 344
Period size: 61 Copynumber: 3.0 Consensus size: 61
11510003 CCAAAATTTG
11510013 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGAT-TTTTTGTTCTGAAATGGAAAATTC
*
11510075 ATTTCTTTTTTGTTAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAATTC
11510136 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAA
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAA
11510194 ACTAGTTTGT
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
61 81 0.69
62 36 0.31
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56
Consensus pattern (61 bp):
ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAATTC
Found at i:11512811 original size:15 final size:15
Alignment explanation
Indices: 11512767--11512822 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
11512757 AACGACATGT
*
11512767 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
11512783 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
11512796 ATATTATTTAATTAA
1 ATATTATTTAATTAA
11512811 ATATTATTTAAT
1 ATATTATTTAAT
11512823 CCCACTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:11512967 original size:9 final size:9
Alignment explanation
Indices: 11512927--11513078 Score: 162
Period size: 9 Copynumber: 17.0 Consensus size: 9
11512917 TATTTGATAT
*
11512927 CATAATTTA
1 CATAACTTA
*
11512936 TATAACTTA
1 CATAACTTA
* *
11512945 CAAAACGTA
1 CATAACTTA
11512954 CATAACTTA
1 CATAACTTA
*
11512963 TATAACTTA
1 CATAACTTA
* *
11512972 GATAA-ATA
1 CATAACTTA
*
11512980 TATAACTTA
1 CATAACTTA
*
11512989 TATAACTTA
1 CATAACTTA
*
11512998 CATAACTCA
1 CATAACTTA
* *
11513007 TATAACATA
1 CATAACTTA
11513016 CATAACTTA
1 CATAACTTA
11513025 CATAACTTA
1 CATAACTTA
*
11513034 TATAACTTA
1 CATAACTTA
11513043 CATAACTTA
1 CATAACTTA
11513052 CATAACTTA
1 CATAACTTA
* *
11513061 TATCACTTA
1 CATAACTTA
11513070 CATAACTTA
1 CATAACTTA
11513079 TATGTTGTCA
Statistics
Matches: 117, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
8 6 0.05
9 111 0.95
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:11522863 original size:68 final size:64
Alignment explanation
Indices: 11522751--11522906 Score: 163
Period size: 68 Copynumber: 2.4 Consensus size: 64
11522741 TGGAACCACG
* * *
11522751 CATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACAT-AGTATCACC
1 CATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACAC-TCAGCATCACA
** *
11522815 CATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTAC-ACATGATGTGCACTCAGCAT
1 CATGCGACCTAGCTACAT-AT-A--TCCCGTAGCTCTCTTGT-CTACATGATGTACACTCAGCAT
*
11522879 CATA
61 CACA
*
11522883 CATGTGACCTAGCTACATACTATC
1 CATGCGACCTAGCTACATA-TATC
11522907 TGTATCATCC
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
64 18 0.23
65 4 0.05
66 1 0.01
67 3 0.04
68 50 0.65
69 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (64 bp):
CATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACTCAGCATCACA
Found at i:11535005 original size:49 final size:47
Alignment explanation
Indices: 11534828--11535006 Score: 250
Period size: 47 Copynumber: 3.8 Consensus size: 47
11534818 CCCTTCGGGA
* * * * * *
11534828 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
11534875 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11534922 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
11534969 CTTATCACATATATATACACTTTCACATTCACCACATC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATC
11535007 ACAATTATCC
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
47 90 0.77
49 27 0.23
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11542536 original size:44 final size:44
Alignment explanation
Indices: 11542488--11542731 Score: 132
Period size: 44 Copynumber: 5.5 Consensus size: 44
11542478 AGTCTGTTTC
* *
11542488 CTTGCTACCTCAGAAAGATAAGACTACAATCTTTAACCTGCTCT
1 CTTGCTACCTCAGAAAGATAAGACTACAATCTTCAATCTGCTCT
* ** ***** ** * *
11542532 CTTGCTACCTCAGATAGATAAGGTTGGTGGCTAAAATCTACTCC
1 CTTGCTACCTCAGAAAGATAAGACTACAATCTTCAATCTGCTCT
* ** * **
11542576 CCTGCTACCTTGGAAAGATAAGACTCACCATCTTTGATCTGCTC-
1 CTTGCTACCTCAGAAAGATAAGACT-ACAATCTTCAATCTGCTCT
* * * ** * *
11542620 CACTGTTATCTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCT-T
1 C-TTGCTACCTCAGAAAGATAAGA-CTACAATCTTCAATCTGCTCT
* * *
11542665 CCTTGCTACCTTAGGAAGATAAGACTACAATCTTCAACCTGCTCT
1 -CTTGCTACCTCAGAAAGATAAGACTACAATCTTCAATCTGCTCT
** * *
11542710 CTAACTACCTTAGAGAGATAAG
1 CTTGCTACCTCAGAAAGATAAG
11542732 GCTGGTGGCT
Statistics
Matches: 143, Mismatches: 51, Indels: 12
0.69 0.25 0.06
Matches are distributed among these distances:
44 85 0.59
45 55 0.38
46 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
CTTGCTACCTCAGAAAGATAAGACTACAATCTTCAATCTGCTCT
Found at i:11542552 original size:89 final size:89
Alignment explanation
Indices: 11542457--11542730 Score: 232
Period size: 89 Copynumber: 3.1 Consensus size: 89
11542447 ACTGCTTAGG
* *
11542457 GAGATAAAATCTTCAATCCTCAGTCTGTTTCCTTGCTACCTCAGAAAGATAAGACTACAATCTTT
1 GAGATAAAATCTTCAATCCTCAGTCTGCTTCCTTGCTACCTTAGAAAGATAAGACTACAATCTTT
11542522 AACCTGCTCTCTTGCTACCTCAGA
66 AACCTGCTCTCTTGCTACCTCAGA
* ** ** * * * * * * * *
11542546 TAGAT--AAGGTT-GGTGGCTAAAATCTACTCCCCTGCTACCTTGGAAAGATAAGACTCACCATC
1 GAGATAAAATCTTCAAT-CCT-CAGTCTGCTTCCTTGCTACCTTAGAAAGATAAGACT-ACAATC
* * * * * *
11542608 TTTGATCTGCTC-CACTGTTATCTCAGG
63 TTTAACCTGCTCTC-TTGCTACCTCAGA
* * * *
11542635 GAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATCTTC
1 GAGATAAAATCTTCAATCCTCAGTCTGCTTCCTTGCTACCTTAGAAAGATAAGACTACAATCTTT
** *
11542700 AACCTGCTCTCTAACTACCTTAGA
66 AACCTGCTCTCTTGCTACCTCAGA
11542724 GAGATAA
1 GAGATAA
11542731 GGCTGGTGGC
Statistics
Matches: 130, Mismatches: 47, Indels: 16
0.67 0.24 0.08
Matches are distributed among these distances:
86 1 0.01
87 6 0.05
88 29 0.22
89 59 0.45
90 30 0.23
91 4 0.03
92 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (89 bp):
GAGATAAAATCTTCAATCCTCAGTCTGCTTCCTTGCTACCTTAGAAAGATAAGACTACAATCTTT
AACCTGCTCTCTTGCTACCTCAGA
Found at i:11542697 original size:178 final size:176
Alignment explanation
Indices: 11542364--11542823 Score: 573
Period size: 178 Copynumber: 2.6 Consensus size: 176
11542354 CACTACAAAT
* * * *
11542364 TCAGGGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTACCTCAGGAAGATAAGATTCGCCA
1 TCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTGCTACCT-AGGAAGATAAGACTCACCA
* *
11542429 TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTTCAATCCTCAGTCTGTTTCCTTGCT
65 TTTTCGATCTGCTCCACTACTGCTCAGGGAGATAAAATCTTCAATCCTCAGTCTGCTTCCTTGCT
* **
11542494 ACCTCAGAAAGATAAGACTACAATCTTTAACCTGCTCTCTTGCTACC
130 ACCTCAGAAAGATAAGACTACAATCTTCAACCTGCTCTCTAACTACC
* * *
11542541 TCAGATAGATAAGGTTGGTGGCTAAAATCTACTCCCCTGCTACCTTGGAAAGATAAGACTCACCA
1 TCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTGCTACCTAGG-AAGATAAGACTCACCA
** * * *
11542606 TCTTT-GATCTGCTCCACTGTTATCTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTG
65 T-TTTCGATCTGCTCCACTACT-GCTCAGGGAGATAAAATCTTCAATCCTCAGTCTGCTTCCTTG
* *
11542670 CTACCTTAGGAAGATAAGACTACAATCTTCAACCTGCTCTCTAACTACC
128 CTACCTCAGAAAGATAAGACTACAATCTTCAACCTGCTCTCTAACTACC
* * * * * **
11542719 TTAGAGAGATAAGGCTGGTGGCTAAAATTTACTCCCCTTCTACCTCGGGAAGATAAGATTCGGCA
1 TCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTGCTACCT-AGGAAGATAAGACTCACCA
** * * *
11542784 TCCTCGATTTGCTCTACTACTGC-CTAGGGAGATAAGATCT
65 TTTTCGATCTGCTCCACTACTGCTC-AGGGAGATAAAATCT
11542824 GTAAATTCAC
Statistics
Matches: 242, Mismatches: 35, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
176 3 0.01
177 87 0.36
178 150 0.62
179 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (176 bp):
TCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTGCTACCTAGGAAGATAAGACTCACCAT
TTTCGATCTGCTCCACTACTGCTCAGGGAGATAAAATCTTCAATCCTCAGTCTGCTTCCTTGCTA
CCTCAGAAAGATAAGACTACAATCTTCAACCTGCTCTCTAACTACC
Found at i:11544105 original size:47 final size:47
Alignment explanation
Indices: 11544051--11544144 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
11544041 ATTTTATTGG
*
11544051 GTCTCAAAGCGCCCTTTGTGGGTTTTCACTTTGGCCTCTTTCTCTCT
1 GTCTCAAAGCGCCCTTTGTGGGTTTTCACTTTGGCCTCTTTCCCTCT
11544098 GTCTCAAAGCGCCCTTTGTGGGTTTTCACTTTGGCCTCTTTCCCTCT
1 GTCTCAAAGCGCCCTTTGTGGGTTTTCACTTTGGCCTCTTTCCCTCT
11544145 TCAAGTATAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.09, C:0.31, G:0.19, T:0.41
Consensus pattern (47 bp):
GTCTCAAAGCGCCCTTTGTGGGTTTTCACTTTGGCCTCTTTCCCTCT
Found at i:11556282 original size:35 final size:35
Alignment explanation
Indices: 11556157--11556309 Score: 116
Period size: 35 Copynumber: 4.3 Consensus size: 35
11556147 ACTCTCTGTT
* ** * *
11556157 TTGGTGTGTTTTGGTTGGACTAGCTCTTTTGAA-CA
1 TTGGTGTGTTTTAGAGGGATTAGCTCTTAT-AAGCA
* * *
11556192 TTGGTGTG-CTTCGAAGGGATTAACTCTTATAAGCA
1 TTGGTGTGTTTTAG-AGGGATTAGCTCTTATAAGCA
* *
11556227 TTTGTGTGTCTTTA-AGGGATTAGCTCTTATGAGCA
1 TTGGTGTGT-TTTAGAGGGATTAGCTCTTATAAGCA
* * *
11556262 TTGGTGTGTTTTAGATGGATTGGCT-TGTACAAGCA
1 TTGGTGTGTTTTAGAGGGATTAGCTCT-TATAAGCA
11556297 TCTGGTGTGTTTT
1 T-TGGTGTGTTTT
11556310 GGGTGGTTTG
Statistics
Matches: 94, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
34 10 0.11
35 71 0.76
36 11 0.12
37 2 0.02
ACGTcount: A:0.18, C:0.11, G:0.28, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTTAGAGGGATTAGCTCTTATAAGCA
Found at i:11559682 original size:43 final size:43
Alignment explanation
Indices: 11559561--11559714 Score: 172
Period size: 43 Copynumber: 3.6 Consensus size: 43
11559551 TGTGTTATCG
* *
11559561 TGTAATACCACGTCTGGGATGTTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACGTCTGGGATGTTGGCATCGA-TATTTGATTT-CA
* * *
11559605 TGTAAGACCATGTCTGGGATGTTGGCATTG-TATTTGATTTCG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGATATTTGATTTCA
* *
11559647 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGA-TGTTGGCATCGATATTTGATTTCA
*
11559690 TGTAAGACCACGTCTGGGACGTTGG
1 TGTAAGACCACGTCTGGGATGTTGG
11559715 TATTGTATGA
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
42 27 0.29
43 38 0.41
44 28 0.30
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGATATTTGATTTCA
Found at i:11559720 original size:85 final size:86
Alignment explanation
Indices: 11559558--11559722 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 86
11559548 ATATGTGTTA
* * *
11559558 TCGTGTAATACCACGTCTGGGATGTTGGCATCGACTTATGATTTACATGTAAGACCATGTCTGGG
1 TCGTGTAAGACCACGTCTGGGAAGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCTGGG
*
11559623 ATGTTGGCATTGTATTTGATT
66 ACGTTGGCATTGTATTTGATT
*
11559644 TCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATTTGA-TTACATGTAAGACCACGTCT
1 TCGTGTAAGACCAC-GTCTGGGA-AGTTGGCATCGACT-TATGATTTACATGTAAGACCACGTCT
*
11559705 GGGACGTTGGTATTGTAT
63 GGGACGTTGGCATTGTAT
11559723 GAGCTTTCTG
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
85 37 0.53
86 32 0.46
87 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (86 bp):
TCGTGTAAGACCACGTCTGGGAAGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCTGGG
ACGTTGGCATTGTATTTGATT
Found at i:11567139 original size:42 final size:43
Alignment explanation
Indices: 11567025--11567160 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 43
11567015 TATGTGTTAT
* *
11567025 CGTGTAAGACCACATCTGGGAC-GTTGGCATCG-ACTTATGATTTA
1 CGTGTAAGACCACGTCTAGGACAG-TGGCATCGTA-TT-TGATTTA
*
11567069 CGTGTAAGACCACGTCTAGGACATTGGCATCGTATTTGATTT-
1 CGTGTAAGACCACGTCTAGGACAGTGGCATCGTATTTGATTTA
* * *
11567111 CGTGTAAGATCC-TGTCTGGGATAGTGGCATCGATATTTGA-TTA
1 CGTGTAAGA-CCACGTCTAGGACAGTGGCATCG-TATTTGATTTA
*
11567154 CATGTAA
1 CGTGTAA
11567161 AACTACATCT
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
42 27 0.34
43 21 0.27
44 30 0.38
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTAGGACAGTGGCATCGTATTTGATTTA
Found at i:11567182 original size:43 final size:43
Alignment explanation
Indices: 11567025--11567183 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
11567015 TATGTGTTAT
*
11567025 CGTGTAAGACCACATCTGGGACGTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGA-TATTTGA-TTA
* * * *
11567069 CGTGTAAGACCACGTCTAGGACATTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGATATTTGATTA
** *
11567111 CGTGTAAGATCC-TGTCTGGGATAG-TGGCATCGATATTTGATTA
1 CGTGTAAGA-CCACATCTGGGA-CGTTGGCATCGATATTTGATTA
* * *
11567154 CATGTAAAACTACATCTGGGACGTTGGCAT
1 CGTGTAAGACCACATCTGGGACGTTGGCAT
11567184 TGTATAGGCT
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
42 29 0.31
43 35 0.38
44 29 0.31
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACATCTGGGACGTTGGCATCGATATTTGATTA
Found at i:11568423 original size:21 final size:21
Alignment explanation
Indices: 11568397--11568518 Score: 147
Period size: 21 Copynumber: 5.8 Consensus size: 21
11568387 AACAAGGATC
11568397 AGCTCTTATGAGCTTCTGTTA
1 AGCTCTTATGAGCTTCTGTTA
*
11568418 AGCTCTTATGAGCTTCTATTA
1 AGCTCTTATGAGCTTCTGTTA
* *
11568439 AGCTCTTTTGAGCTTTTGTTCA
1 AGCTCTTATGAGCTTCTGTT-A
* *
11568461 A-CTCTTATGAGCTTCTTTTC
1 AGCTCTTATGAGCTTCTGTTA
* * * *
11568481 AGGTCTTATAAGCTTTTGTTC
1 AGCTCTTATGAGCTTCTGTTA
11568502 AGCTCTTATGAGCTTCT
1 AGCTCTTATGAGCTTCT
11568519 ATTGGCGTGT
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
20 1 0.01
21 81 0.96
22 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTA
Found at i:11568466 original size:42 final size:42
Alignment explanation
Indices: 11568397--11568521 Score: 171
Period size: 42 Copynumber: 3.0 Consensus size: 42
11568387 AACAAGGATC
*
11568397 AGCTCTTATGAGCTTCTGTT-AAGCTCTTATGAGCTTCTATTA
1 AGCTCTTATGAGCTTTTGTTCAA-CTCTTATGAGCTTCTATTA
* * *
11568439 AGCTCTTTTGAGCTTTTGTTCAACTCTTATGAGCTTCTTTTC
1 AGCTCTTATGAGCTTTTGTTCAACTCTTATGAGCTTCTATTA
* * *
11568481 AGGTCTTATAAGCTTTTGTTCAGCTCTTATGAGCTTCTATT
1 AGCTCTTATGAGCTTTTGTTCAACTCTTATGAGCTTCTATT
11568522 GGCGTGTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 71 0.97
43 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.46
Consensus pattern (42 bp):
AGCTCTTATGAGCTTTTGTTCAACTCTTATGAGCTTCTATTA
Found at i:11569863 original size:30 final size:30
Alignment explanation
Indices: 11569827--11569917 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
11569817 TGTGTGGCCA
* * *
11569827 GCTCACACAAGCGTGTACCCAGCCTGTGTG
1 GCTCACACAAGCGTATGCCCAGCCCGTGTG
* *
11569857 GCTCACACGAGCATATGCCCAGCCCGTGTG
1 GCTCACACAAGCGTATGCCCAGCCCGTGTG
11569887 GCTCACACAAGCGTATGCCCAGCCCGTGTG
1 GCTCACACAAGCGTATGCCCAGCCCGTGTG
11569917 G
1 G
11569918 AAATGTCCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (30 bp):
GCTCACACAAGCGTATGCCCAGCCCGTGTG
Found at i:11571091 original size:106 final size:106
Alignment explanation
Indices: 11570778--11571091 Score: 382
Period size: 106 Copynumber: 3.0 Consensus size: 106
11570768 GTGTGTCCCT
* * *** *
11570778 TGTAGGTCCAAGGCATACCAGTCAGGCAGTTACATGGCCTAGCACAC-GGCCTGGCACATGGGCA
1 TGTAGGTTCAAGGCATACCAGTCAGGCAGTTACACGGCCTAGCACACAGG-CTGGCACACAAGCG
* * * * * *
11570842 TGTGAGGCCATTTCGAGGGTGACATGACTTGGCACATGGGCT
65 TGTAAGGCCATTTCGAGGGTGACACGGCCTGGCACACGGGCC
** * * *
11570884 TGTAGGTTCAAGGCATACCAACCAGGCAGTTACACGGCCTAGCA-AAAGGCTTGGTACACAAACG
1 TGTAGGTTCAAGGCATACCAGTCAGGCAGTTACACGGCCTAGCACACAGGC-TGGCACACAAGCG
* * * * *
11570948 TGTAAGGCCATTTCGAGGTTGACACAGACTAGTACACGGGCC
65 TGTAAGGCCATTTCGAGGGTGACACGGCCTGGCACACGGGCC
11570990 TGTAGGTTCAAGGCATACCAGTCAGGCAGTTACACGGCCTAGCACACAGG-TAGGCACACAAGCG
1 TGTAGGTTCAAGGCATACCAGTCAGGCAGTTACACGGCCTAGCACACAGGCT-GGCACACAAGCG
11571054 TGTAAGGCCATTTCGAGGGTGACACGGCCTGGCACACG
65 TGTAAGGCCATTTCGAGGGTGACACGGCCTGGCACACG
11571092 AGTGTGTGGC
Statistics
Matches: 172, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
105 3 0.02
106 165 0.96
107 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.19
Consensus pattern (106 bp):
TGTAGGTTCAAGGCATACCAGTCAGGCAGTTACACGGCCTAGCACACAGGCTGGCACACAAGCGT
GTAAGGCCATTTCGAGGGTGACACGGCCTGGCACACGGGCC
Found at i:11571273 original size:20 final size:20
Alignment explanation
Indices: 11571236--11571273 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11571226 CCTACAGACC
* *
11571236 AAAATTTTCAACTTTTTCCT
1 AAAATTTTCAAATATTTCCT
11571256 AAAATTTTCAAATATTTC
1 AAAATTTTCAAATATTTC
11571274 TGATTTAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTTTCAAATATTTCCT
Found at i:11574325 original size:143 final size:143
Alignment explanation
Indices: 11574058--11574327 Score: 441
Period size: 143 Copynumber: 1.9 Consensus size: 143
11574048 ACAAACTCTA
* *
11574058 TATGTGTCTTTAGGTGAAATAGAAGGTTTAACAGATAATGAGCAAGATGATGCATTGATCAAAGT
1 TATGTGTCTTTAGGTGAAATAGAAGGTTTAACAGATAATAAGCAAGATGATGCATTGATCAAAAT
* * * * *
11574123 TCCTAATCATCCAACGCAAATGCTCATTTTTCTAATTGTACCACCTTCTATGTGGTTAGCATAAT
66 TCCTAATCATCCAACGCAAATGCTCATTTTCCTAAGTCTACCACCTTCTAAGTGATTAGCATAAT
11574188 GGTAAAAAACCTC
131 GGTAAAAAACCTC
**
11574201 TATGTGTCTTTAGGTGAAATAGAAGGTTTAACAGATAATAAGTGAGATGATGCATTGATCAAAAT
1 TATGTGTCTTTAGGTGAAATAGAAGGTTTAACAGATAATAAGCAAGATGATGCATTGATCAAAAT
* *
11574266 TCCTAATCATCCAATGCAAATGCTCATTTTCCTTAGTCTACCACCTTCTAAGTGATTAGCAT
66 TCCTAATCATCCAACGCAAATGCTCATTTTCCTAAGTCTACCACCTTCTAAGTGATTAGCAT
11574328 GGGTGAAAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
143 116 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (143 bp):
TATGTGTCTTTAGGTGAAATAGAAGGTTTAACAGATAATAAGCAAGATGATGCATTGATCAAAAT
TCCTAATCATCCAACGCAAATGCTCATTTTCCTAAGTCTACCACCTTCTAAGTGATTAGCATAAT
GGTAAAAAACCTC
Found at i:11574483 original size:69 final size:68
Alignment explanation
Indices: 11574407--11574613 Score: 236
Period size: 69 Copynumber: 3.0 Consensus size: 68
11574397 TCATAGAGGG
* * *
11574407 TTGTCACTTTTTGCATGTGTAAATTGGTATGGTGGTGAACTAATATAGTTTTTTGTATGTAATTG
1 TTGTCACTTTTTGTATGTGTAAATTGGTGTGGTGGTG-ACTAATATAATTTTTTGTATGTAATTG
11574472 TAGA
65 TAGA
* * * * *
11574476 TTGTCACTTTTTGTATATGTAAATGGGTGTGGTGGTCGACTAATATCACTTTTTGTACGTAATTG
1 TTGTCACTTTTTGTATGTGTAAATTGGTGTGGTGGT-GACTAATATAATTTTTTGTATGTAATTG
*
11574541 TAGG
65 TAGA
* * * * *
11574545 TTGTTACTTTTCGTATGCGT-AATTGGGTGTGGTGATGGAGTAATATAATTTTTTTGTATGTAAT
1 TTGTCACTTTTTGTATGTGTAAATT-GGTGTGGTGGT-GACTAATATAA-TTTTTTGTATGTAAT
11574609 TGTAG
63 TGTAG
11574614 GATGATATAA
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
68 3 0.03
69 93 0.81
70 19 0.17
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.46
Consensus pattern (68 bp):
TTGTCACTTTTTGTATGTGTAAATTGGTGTGGTGGTGACTAATATAATTTTTTGTATGTAATTGT
AGA
Found at i:11581154 original size:33 final size:33
Alignment explanation
Indices: 11581112--11581177 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
11581102 GGAAGTAATC
11581112 AAGAGACCCACATCTAAAACACGCACCGCTCTT
1 AAGAGACCCACATCTAAAACACGCACCGCTCTT
*
11581145 AAGAGACCCACATCTAAAACACGCTCCGCTCTT
1 AAGAGACCCACATCTAAAACACGCACCGCTCTT
11581178 CATTCGGCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.36, G:0.12, T:0.17
Consensus pattern (33 bp):
AAGAGACCCACATCTAAAACACGCACCGCTCTT
Found at i:11585384 original size:21 final size:21
Alignment explanation
Indices: 11585351--11585396 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
11585341 ATACTAGTGG
11585351 TGTTACTAAAATGAAATATAA
1 TGTTACTAAAATGAAATATAA
* * *
11585372 TGTTATTATAATGGAATATAA
1 TGTTACTAAAATGAAATATAA
11585393 TGTT
1 TGTT
11585397 GGATATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (21 bp):
TGTTACTAAAATGAAATATAA
Found at i:11587953 original size:40 final size:40
Alignment explanation
Indices: 11587846--11588048 Score: 153
Period size: 41 Copynumber: 5.0 Consensus size: 40
11587836 TTAGTGTATC
11587846 GAGATAGCTTC-AGCTAT-ATAAAGCACTTAGTGTGCGA-AT
1 GAGATAGCTTCGA-CTATGA-AAAGCACTTAGTGTGCGAGAT
* * * * *
11587885 CAGAATAGCTTCGGCTA-CATATGACACTTAGTGTGCGAGAT
1 GAG-ATAGCTTCGACTATGAAAAG-CACTTAGTGTGCGAGAT
*
11587926 GAGATAGCTTCGACTATGAAAAGCACTTAGTGTGTGAGACT
1 GAGATAGCTTCGACTATGAAAAGCACTTAGTGTGCGAGA-T
* * * * *
11587967 GTGACAGCTTCGACTATGAAAGGCACTAAGTGTGAGAGAT
1 GAGATAGCTTCGACTATGAAAAGCACTTAGTGTGCGAGAT
* * * ****
11588007 TACAATAGTTTCGACTATGCTTTGGCACTTAGTGTGCGAGAT
1 GA-GATAGCTTCGACTATG-AAAAGCACTTAGTGTGCGAGAT
11588049 ATTGAGTATT
Statistics
Matches: 130, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
39 4 0.03
40 54 0.42
41 55 0.42
42 17 0.13
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (40 bp):
GAGATAGCTTCGACTATGAAAAGCACTTAGTGTGCGAGAT
Found at i:11596332 original size:38 final size:38
Alignment explanation
Indices: 11596289--11596419 Score: 136
Period size: 38 Copynumber: 3.2 Consensus size: 38
11596279 TTTCAAATTA
*
11596289 ACATGTATAACCGTGGCAAATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* *
11596327 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
* *
11596368 GAATCAATATATGTAACTGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
11596412 ACATGTAT
1 ACATGTAT
11596420 CAATATGTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
38 34 0.45
39 1 0.01
40 4 0.05
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 27 0.36
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:11596443 original size:48 final size:48
Alignment explanation
Indices: 11596334--11596467 Score: 191
Period size: 48 Copynumber: 2.8 Consensus size: 48
11596324 GTTACATGTT
* *
11596334 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACTGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
11596381 TAACTGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACTGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
11596429 TAATCT-TGGTATATCCACTTAGCACCATGTTACACGTAT
1 TAA-CTGTGGTATATCCACTTAGCACCACGTTACATGTAT
11596468 AACCGTGGTA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
47 30 0.38
48 46 0.59
49 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (48 bp):
TAACTGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:11599195 original size:28 final size:28
Alignment explanation
Indices: 11599142--11599213 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
11599132 TGAATAACAT
*
11599142 AGTCTGGGCCTAAGCCCAGGTTAGTAAC
1 AGTCTGGGCCTAAGCCCAGGTCAGTAAC
* * *
11599170 AGTCTGGGCCTTAGCCCTATG-CAGTAGC
1 AGTCTGGGCCTAAGCCC-AGGTCAGTAAC
* *
11599198 AGTGTGGGCCCAAGCC
1 AGTCTGGGCCTAAGCC
11599214 TAATGCAGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 34 0.94
29 2 0.06
ACGTcount: A:0.21, C:0.28, G:0.31, T:0.21
Consensus pattern (28 bp):
AGTCTGGGCCTAAGCCCAGGTCAGTAAC
Found at i:11599452 original size:27 final size:26
Alignment explanation
Indices: 11599392--11599472 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
11599382 CCAGAAACAG
* *
11599392 TAATGTGGCAAAGCCACCAATATCAA
1 TAATGTGGCATAGCCACCAGTATCAA
11599418 TAATTGTGGCATAGCCACCAGTAAT-AA
1 TAA-TGTGGCATAGCCACCAGT-ATCAA
* *
11599445 TGAATGTGACATAGTCACCAGT-TCAA
1 T-AATGTGGCATAGCCACCAGTATCAA
11599471 TA
1 TA
11599473 CTTCCTACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
25 2 0.04
26 6 0.13
27 35 0.74
28 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (26 bp):
TAATGTGGCATAGCCACCAGTATCAA
Found at i:11599639 original size:27 final size:27
Alignment explanation
Indices: 11599609--11599780 Score: 186
Period size: 27 Copynumber: 6.4 Consensus size: 27
11599599 GGCATAATCG
* *
11599609 TCATTTTACCCTACAGGGGTATAACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* ** * *
11599636 TCATTTTACCCTACAAGGGTTTTATGG
1 TCATTTTACCCTACAGGGGCATTACGA
*
11599663 TCATTTTACCCTACAAGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
*
11599690 TCATTTTACCCTACAGGGGCGTTAC-A
1 TCATTTTACCCTACAGGGGCATTACGA
* * *
11599716 GTCATTTTACCCTATAGGGGTATTACGG
1 -TCATTTTACCCTACAGGGGCATTACGA
* *
11599744 TTATTTTACTCTACAGGGGCATTAC-A
1 TCATTTTACCCTACAGGGGCATTACGA
11599770 GTCATTTTACC
1 -TCATTTTACC
11599781 TATTTTGGGG
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
26 1 0.01
27 119 0.99
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGA
Found at i:11599690 original size:54 final size:54
Alignment explanation
Indices: 11599608--11599780 Score: 220
Period size: 54 Copynumber: 3.2 Consensus size: 54
11599598 GGGCATAATC
* ** **
11599608 GTCATTTTACCCTACAGGGGTATAACGATCATTTTACCCTACAAGGGTTTTATG
1 GTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAAGGGCGTTACA
* * *
11599662 GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAGGGGCGTTACA
1 GTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAAGGGCGTTACA
* * * * * *
11599716 GTCATTTTACCCTATAGGGGTATTACGGTTATTTTACTCTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAAGGGCGTTACA
11599770 GTCATTTTACC
1 GTCATTTTACC
11599781 TATTTTGGGG
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (54 bp):
GTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAAGGGCGTTACA
Found at i:11599700 original size:81 final size:81
Alignment explanation
Indices: 11599596--11599780 Score: 223
Period size: 81 Copynumber: 2.3 Consensus size: 81
11599586 TACGGAACAT
* * *
11599596 AAGGGCATAATCG-TCATTTTACCCTACAGGGGTATAAC-GATCATTTTACCCTACAAGGGTTTT
1 AAGGGCATTA-CGATCATTTTACCCTACAGGGGCATAACAG-TCATTTTACCCTACAAGGGTATT
*
11599659 ATGGTCATTTTACCCTAC
64 ACGGTCATTTTACCCTAC
* * * *
11599677 AAGGGCATTACGATCATTTTACCCTACAGGGGCGTTACAGTCATTTTACCCTATAGGGGTATTAC
1 AAGGGCATTACGATCATTTTACCCTACAGGGGCATAACAGTCATTTTACCCTACAAGGGTATTAC
* *
11599742 GGTTATTTTACTCTAC
66 GGTCATTTTACCCTAC
*
11599758 AGGGGCATTAC-AGTCATTTTACC
1 AAGGGCATTACGA-TCATTTTACC
11599781 TATTTTGGGG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
80 3 0.03
81 86 0.96
82 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (81 bp):
AAGGGCATTACGATCATTTTACCCTACAGGGGCATAACAGTCATTTTACCCTACAAGGGTATTAC
GGTCATTTTACCCTAC
Found at i:11605530 original size:22 final size:22
Alignment explanation
Indices: 11605502--11605544 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
11605492 TACAAAGAGC
11605502 TTAGTAAGCCAAATACAATTGG
1 TTAGTAAGCCAAATACAATTGG
11605524 TTAGTAAGCCAAATACAATTG
1 TTAGTAAGCCAAATACAATTG
11605545 TTTTAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (22 bp):
TTAGTAAGCCAAATACAATTGG
Found at i:11612461 original size:26 final size:26
Alignment explanation
Indices: 11612432--11612539 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
11612422 TGGTACAAAT
11612432 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
11612458 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11612484 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11612510 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11612536 TGAT
1 TGAT
11612540 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11613211 original size:312 final size:312
Alignment explanation
Indices: 11612646--11613269 Score: 1239
Period size: 312 Copynumber: 2.0 Consensus size: 312
11612636 CTTTGTTCAC
11612646 CATAGCTGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAACTCTTAAATTTTCGGTCACTTGGGGA
1 CATAGCTGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAACTCTTAAATTTTCGGTCACTTGGGGA
11612711 AGAAAATTGAAGGTAAGTTCATGGTAGTTTGCTTCTATCTTGATGTTCATGAGTTCTTCTTGATT
66 AGAAAATTGAAGGTAAGTTCATGGTAGTTTGCTTCTATCTTGATGTTCATGAGTTCTTCTTGATT
11612776 CTACCTTAACTCTTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAGCATTTAGTCATGAATTAA
131 CTACCTTAACTCTTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAGCATTTAGTCATGAATTAA
11612841 AATGAAGGAAATGGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGC
196 AATGAAGGAAATGGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGC
11612906 CAAACAAATGAACATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAA
261 CAAACAAATGAACATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAA
11612958 CATAGCTGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAACTCTTAAATTTTCGGTCACTTGGGGA
1 CATAGCTGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAACTCTTAAATTTTCGGTCACTTGGGGA
11613023 AGAAAATTGAAGGTAAGTTCATGGTAGTTTGCTTCTATCTTGATGTTCATGAGTTCTTCTTGATT
66 AGAAAATTGAAGGTAAGTTCATGGTAGTTTGCTTCTATCTTGATGTTCATGAGTTCTTCTTGATT
11613088 CTACCTTAACTCTTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAGCATTTAGTCATGAATTAA
131 CTACCTTAACTCTTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAGCATTTAGTCATGAATTAA
11613153 AATGAAGGAAATGGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGC
196 AATGAAGGAAATGGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGC
*
11613218 CAAACAAATGAACATGCATGTGCCTTAGATGCTAAGGGGAAAAATCGGCTAA
261 CAAACAAATGAACATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAA
11613270 TATGTTGTGC
Statistics
Matches: 311, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
312 311 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (312 bp):
CATAGCTGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAACTCTTAAATTTTCGGTCACTTGGGGA
AGAAAATTGAAGGTAAGTTCATGGTAGTTTGCTTCTATCTTGATGTTCATGAGTTCTTCTTGATT
CTACCTTAACTCTTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAGCATTTAGTCATGAATTAA
AATGAAGGAAATGGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGC
CAAACAAATGAACATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAA
Found at i:11616603 original size:22 final size:23
Alignment explanation
Indices: 11616577--11616621 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
11616567 ACCTGATTAG
*
11616577 AATACGAAACAT-AAGTGCCTGA
1 AATACGAAACATAAAGCGCCTGA
*
11616599 AATACGACACATAAAGCGCCTGA
1 AATACGAAACATAAAGCGCCTGA
11616622 TCAGTAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (23 bp):
AATACGAAACATAAAGCGCCTGA
Found at i:11616822 original size:23 final size:23
Alignment explanation
Indices: 11616792--11616909 Score: 76
Period size: 28 Copynumber: 4.7 Consensus size: 23
11616782 GATTCCATCC
*
11616792 AAACACACCAAAAT-GTCCAACCA
1 AAACACACCAAAATAATCC-ACCA
* *
11616815 AAACACACCAATATAATCCTCCA
1 AAACACACCAAAATAATCCACCA
*
11616838 AAACACACCAGTATCATATAATCCTCCA
1 AAACACACCA--A--A-ATAATCCACCA
11616866 AAACACACCAGAATAATATAATCCATCCA
1 AAACACACC---A-AA-ATAATCCA-CCA
*
11616895 AAACACACCAGAATA
1 AAACACACCAAAATA
11616910 GCACAAAGTG
Statistics
Matches: 79, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
23 26 0.33
24 6 0.08
25 2 0.03
26 1 0.01
28 29 0.37
29 12 0.15
30 2 0.03
31 1 0.01
ACGTcount: A:0.50, C:0.31, G:0.03, T:0.15
Consensus pattern (23 bp):
AAACACACCAAAATAATCCACCA
Found at i:11616904 original size:29 final size:28
Alignment explanation
Indices: 11616824--11616909 Score: 145
Period size: 28 Copynumber: 3.0 Consensus size: 28
11616814 AAAACACACC
*
11616824 AATATAATCCTCCAAAACACACCAGTAT
1 AATATAATCCTCCAAAACACACCAGAAT
*
11616852 CATATAATCCTCCAAAACACACCAGAAT
1 AATATAATCCTCCAAAACACACCAGAAT
11616880 AATATAATCCATCCAAAACACACCAGAAT
1 AATATAATCC-TCCAAAACACACCAGAAT
11616909 A
1 A
11616910 GCACAAAGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 35 0.65
29 19 0.35
ACGTcount: A:0.49, C:0.29, G:0.03, T:0.19
Consensus pattern (28 bp):
AATATAATCCTCCAAAACACACCAGAAT
Found at i:11617950 original size:29 final size:29
Alignment explanation
Indices: 11617913--11617969 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
11617903 CACCTTGACA
* *
11617913 CGAATTCTCAACGAACAAGTTCTTCACCG
1 CGAACTCTCAACGAACAAGTTCTCCACCG
11617942 CGAACTCTCAACGAACAAGTTCTCCACC
1 CGAACTCTCAACGAACAAGTTCTCCACC
11617970 TCTTCCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.35, G:0.12, T:0.21
Consensus pattern (29 bp):
CGAACTCTCAACGAACAAGTTCTCCACCG
Found at i:11622365 original size:13 final size:13
Alignment explanation
Indices: 11622347--11622372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11622337 CAAAACCCAT
11622347 ACCAAAACAATCA
1 ACCAAAACAATCA
11622360 ACCAAAACAATCA
1 ACCAAAACAATCA
11622373 TAAAACATAT
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:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:11626053 original size:40 final size:40
Alignment explanation
Indices: 11626000--11626096 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 40
11625990 CTATCTCGGT
11626000 ATCGCACACTTAGTGCCTCA-TATAGCCGAAGCTATTCCAA
1 ATCGCACACTTAGTGCCT-ATTATAGCCGAAGCTATTCCAA
* * *
11626040 TTCGCACACTTAGTG-CTATTTTTAGCCGAAGCTATTTCAA
1 ATCGCACACTTAGTGCCTA-TTATAGCCGAAGCTATTCCAA
11626080 ATCGCACACTTAGTGCC
1 ATCGCACACTTAGTGCC
11626097 GATCATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 46 0.92
41 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (40 bp):
ATCGCACACTTAGTGCCTATTATAGCCGAAGCTATTCCAA
Found at i:11633564 original size:40 final size:40
Alignment explanation
Indices: 11633519--11633608 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
11633509 AGTATCACAC
*
11633519 ACTTAGTGCCTCA-TATAGCCGAAGCTATTGCAATTCGCAA
1 ACTTAGTGCCT-ATTATAGCCGAAGCTATTGCAAATCGCAA
* * *
11633559 ACTTAGTG-CTATTTTTAGCCGAAGCTATTTCAAATCGCAT
1 ACTTAGTGCCTA-TTATAGCCGAAGCTATTGCAAATCGCAA
11633599 ACTTAGTGCC
1 ACTTAGTGCC
11633609 AAACATAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 1 0.02
39 2 0.05
40 39 0.91
41 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (40 bp):
ACTTAGTGCCTATTATAGCCGAAGCTATTGCAAATCGCAA
Found at i:11638786 original size:28 final size:28
Alignment explanation
Indices: 11638749--11638802 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11638739 AATAATATCA
* *
11638749 TTAATTAAATTTATATTTTTAAATAATT
1 TTAATGAAATTTACATTTTTAAATAATT
11638777 TTAATGAAATTTACATTTTTAAATAA
1 TTAATGAAATTTACATTTTTAAATAA
11638803 AATAGGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TTAATGAAATTTACATTTTTAAATAATT
Found at i:11639737 original size:124 final size:124
Alignment explanation
Indices: 11639591--11639840 Score: 482
Period size: 124 Copynumber: 2.0 Consensus size: 124
11639581 GATACATTAA
*
11639591 ATTAAACTCTTTAAGGCTTGGTGATTTTCCTTAAAGAGCTTATTCTCAAGTATTTTTTGAATCTT
1 ATTAAACTCTTTAAGGCTTGGTGATTTTCCTTAAAGAGCTTATTCTCAAGTATTTTCTGAATCTT
11639656 TTTAATACTTTTTACAATTCTTATAATTTATTTTATATGTTAGTTTTTATTGCGTTTTC
66 TTTAATACTTTTTACAATTCTTATAATTTATTTTATATGTTAGTTTTTATTGCGTTTTC
*
11639715 ATTAAACTCTTTAAGGCTTGGTGATTTTCCTTAAAGAGCTTGTTCTCAAGTATTTTCTGAATCTT
1 ATTAAACTCTTTAAGGCTTGGTGATTTTCCTTAAAGAGCTTATTCTCAAGTATTTTCTGAATCTT
11639780 TTTAATACTTTTTACAATTCTTATAATTTATTTTATATGTTAGTTTTTATTGCGTTTTC
66 TTTAATACTTTTTACAATTCTTATAATTTATTTTATATGTTAGTTTTTATTGCGTTTTC
11639839 AT
1 AT
11639841 GCTTTTTAGA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.53
Consensus pattern (124 bp):
ATTAAACTCTTTAAGGCTTGGTGATTTTCCTTAAAGAGCTTATTCTCAAGTATTTTCTGAATCTT
TTTAATACTTTTTACAATTCTTATAATTTATTTTATATGTTAGTTTTTATTGCGTTTTC
Found at i:11651151 original size:12 final size:13
Alignment explanation
Indices: 11651128--11651165 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
11651118 TTAAATTTTA
11651128 ATTATATTAAGATT
1 ATTAT-TTAAGATT
11651142 ATT-TTTAAGATT
1 ATTATTTAAGATT
11651154 ATTATTT-AGATT
1 ATTATTTAAGATT
11651166 TAATTTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 16 0.70
13 4 0.17
14 3 0.13
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (13 bp):
ATTATTTAAGATT
Found at i:11656223 original size:35 final size:35
Alignment explanation
Indices: 11656156--11656223 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
11656146 CAACCTTTAA
*
11656156 AAAAAGATTAAGATAGACCCATATAAAGCAACCAT
1 AAAAAGATTAAGATAGACCCATATAAAACAACCAT
* * * *
11656191 AAAAAGGTTGAGATAGACCCGTCTAAAACAACC
1 AAAAAGATTAAGATAGACCCATATAAAACAACC
11656224 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.16
Consensus pattern (35 bp):
AAAAAGATTAAGATAGACCCATATAAAACAACCAT
Found at i:11656270 original size:39 final size:39
Alignment explanation
Indices: 11656191--11656271 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 39
11656181 AAGCAACCAT
* * * * *
11656191 AAAAAGGTTGAGATAGACCCGTCTAAAACAACCTTTAAA
1 AAAAAAGTTGAAATAAACCCGTCTAAAACAACATTAAAA
* **
11656230 AAAAAAGTTGAAATAAACCCGTTTAAGGCAACATTAAAA
1 AAAAAAGTTGAAATAAACCCGTCTAAAACAACATTAAAA
11656269 AAA
1 AAA
11656272 GTTAGGATCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.52, C:0.15, G:0.14, T:0.20
Consensus pattern (39 bp):
AAAAAAGTTGAAATAAACCCGTCTAAAACAACATTAAAA
Found at i:11659557 original size:15 final size:15
Alignment explanation
Indices: 11659537--11659567 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11659527 TTCAAATTCC
11659537 TGGCAACTTATACTT
1 TGGCAACTTATACTT
11659552 TGGCAACTTATACTT
1 TGGCAACTTATACTT
11659567 T
1 T
11659568 TAATGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
TGGCAACTTATACTT
Found at i:11669377 original size:37 final size:38
Alignment explanation
Indices: 11669322--11669399 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
11669312 CCAACCTCAT
*
11669322 CAGGCACTGGATCATTGTAAAATGCGCTAAGCCCCAGA
1 CAGGCACTGGATCATTGTAAAATCCGCTAAGCCCCAGA
** *
11669360 CAGG-ACTGGATCATTGTAATTTCCGCTAAGCCCCATA
1 CAGGCACTGGATCATTGTAAAATCCGCTAAGCCCCAGA
11669397 CAG
1 CAG
11669400 CCAAACCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (38 bp):
CAGGCACTGGATCATTGTAAAATCCGCTAAGCCCCAGA
Found at i:11671876 original size:43 final size:43
Alignment explanation
Indices: 11671828--11672050 Score: 216
Period size: 43 Copynumber: 5.2 Consensus size: 43
11671818 AGCACCACAA
* * * *
11671828 TGCATCATCAGATAAACCAAAGGAAATATAGTGGCACACATAG
1 TGCATCATCAGATAAACCGAAGCAATTATACTGGCACACATAG
** * ** *
11671871 TGCATCATTGGACAAGTCGAAGCAATTATATTGGCACACATAG
1 TGCATCATCAGATAAACCGAAGCAATTATACTGGCACACATAG
* * * * *
11671914 TGCATCATCAAACAAGCCAAAACAATTATACTGGCACACATAG
1 TGCATCATCAGATAAACCGAAGCAATTATACTGGCACACATAG
* * * * *
11671957 TGCATCATCAAATGAACTGAAGCAATTATATTGGCACACGTAG
1 TGCATCATCAGATAAACCGAAGCAATTATACTGGCACACATAG
* * *
11672000 TGCATCATC-GAATAAACCGAAGCAAATATACTTGCACATA-AG
1 TGCATCATCAG-ATAAACCGAAGCAATTATACTGGCACACATAG
11672042 TGCATCATC
1 TGCATCATC
11672051 GCCTATAAAG
Statistics
Matches: 147, Mismatches: 32, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
42 11 0.07
43 136 0.93
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (43 bp):
TGCATCATCAGATAAACCGAAGCAATTATACTGGCACACATAG
Found at i:11671979 original size:86 final size:86
Alignment explanation
Indices: 11671828--11672050 Score: 252
Period size: 86 Copynumber: 2.6 Consensus size: 86
11671818 AGCACCACAA
* * ** * *** *
11671828 TGCATCATCAGATAAACCAAAGGAAATATAGTGGCACACATAGTGCATCATTGGACAAGTCGAAG
1 TGCATCATCAAACAAACCAAAACAAATATACTGGCACACATAGTGCATCATCAAACAACTCGAAG
11671893 CAATTATATTGGCACACATAG
66 CAATTATATTGGCACACATAG
* * *
11671914 TGCATCATCAAACAAGCCAAAACAATTATACTGGCACACATAGTGCATCATCAAATGAACT-GAA
1 TGCATCATCAAACAAACCAAAACAAATATACTGGCACACATAGTGCATCATCAAA-CAACTCGAA
*
11671978 GCAATTATATTGGCACACGTAG
65 GCAATTATATTGGCACACATAG
* * * * * *
11672000 TGCATCATCGAATAAACCGAAGCAAATATACTTGCACATA-AGTGCATCATC
1 TGCATCATCAAACAAACCAAAACAAATATACTGGCACACATAGTGCATCATC
11672051 GCCTATAAAG
Statistics
Matches: 115, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
85 11 0.10
86 101 0.88
87 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (86 bp):
TGCATCATCAAACAAACCAAAACAAATATACTGGCACACATAGTGCATCATCAAACAACTCGAAG
CAATTATATTGGCACACATAG
Found at i:11673252 original size:31 final size:29
Alignment explanation
Indices: 11673188--11673252 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
11673178 ACAATAACGT
* *
11673188 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATTGCAAACAA
11673217 AAGTGACTAAAATGTAAC-TTGAGGCAAACAA
1 AAGTGACTAAAATGTAACATT---GCAAACAA
11673248 AAGTG
1 AAGTG
11673253 GCTATTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 18 0.58
31 11 0.35
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATTGCAAACAA
Done.