Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 8 of 150
Found at i:2162916 original size:18 final size:16
Alignment explanation
Indices: 2162884--2162924 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 16
2162874 TAACATTGAA
2162884 TGAAAGAAAGAAATAC
1 TGAAAGAAAGAAATAC
2162900 TGAAATGAAAGGAAATAC
1 TGAAA-GAAA-GAAATAC
2162918 TGAAAGA
1 TGAAAGA
2162925 CTGAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 6 0.26
18 12 0.52
ACGTcount: A:0.59, C:0.05, G:0.22, T:0.15
Consensus pattern (16 bp):
TGAAAGAAAGAAATAC
Found at i:2166609 original size:8 final size:8
Alignment explanation
Indices: 2166598--2166624 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2166588 TTTTTATTAA
2166598 TTTAAAAT
1 TTTAAAAT
2166606 TTTAAAAT
1 TTTAAAAT
2166614 TTTAAAAT
1 TTTAAAAT
2166622 TTT
1 TTT
2166625 GTCATTTTAG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAAAAT
Found at i:2167280 original size:11 final size:11
Alignment explanation
Indices: 2167260--2167297 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2167250 GGCCCGGTCC
2167260 ATATTAAATAT
1 ATATTAAATAT
*
2167271 ATATTTAATAT
1 ATATTAAATAT
*
2167282 ATATAAAATAT
1 ATATTAAATAT
2167293 ATATT
1 ATATT
2167298 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:2167313 original size:24 final size:22
Alignment explanation
Indices: 2167265--2167326 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
2167255 GGTCCATATT
* *
2167265 AAATATATATTTAATATATATA
1 AAATATATATTTAATAAAAATA
*
2167287 AAATATATATTTGATTAAAAATAA
1 AAATATATATTT-AATAAAAAT-A
*
2167311 AAAAATATATTTAATA
1 AAATATATATTTAATA
2167327 TATAATTCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 12 0.36
23 9 0.27
24 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATATTTAATAAAAATA
Found at i:2172926 original size:17 final size:17
Alignment explanation
Indices: 2172904--2172944 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2172894 AATATAGACT
*
2172904 CAAAAAATGAGTTTGGA
1 CAAAAAATGAGTTTAGA
*
2172921 CAAAAAATGGGTTTAGA
1 CAAAAAATGAGTTTAGA
*
2172938 TAAAAAA
1 CAAAAAA
2172945 ATGAAGTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.22
Consensus pattern (17 bp):
CAAAAAATGAGTTTAGA
Found at i:2174569 original size:19 final size:19
Alignment explanation
Indices: 2174541--2174654 Score: 147
Period size: 19 Copynumber: 5.8 Consensus size: 19
2174531 AATTTTTGAG
*
2174541 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
2174560 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
2174579 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
2174600 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
2174619 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
2174638 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
2174655 GATTTAATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
19 55 0.65
20 12 0.14
21 18 0.21
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2174594 original size:40 final size:39
Alignment explanation
Indices: 2174541--2174640 Score: 168
Period size: 40 Copynumber: 2.6 Consensus size: 39
2174531 AATTTTTGAG
2174541 GATATA-CAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATATCAATCTTAGATATGATATGCAATCCTAGATAT
*
2174579 GATATATGCAATCTTAGATATGATATGCAATCTTAGATAT
1 GATATAT-CAATCTTAGATATGATATGCAATCCTAGATAT
2174619 GATATAT-AATCTTAGATATGAT
1 GATATATCAATCTTAGATATGAT
2174641 TTTGTAATCT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
38 21 0.36
40 38 0.64
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (39 bp):
GATATATCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:2174635 original size:59 final size:58
Alignment explanation
Indices: 2174541--2174654 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
2174531 AATTTTTGAG
*
2174541 GATATACAATCTTAGATATGATATGCAATCCTAGATATGATATATGCAATCTTAGATAT
1 GATATACAATCTTAGATATGATATACAATCCTAGATATGAT-TATGCAATCTTAGATAT
* * * * *
2174600 GATATGCAATCTTAGATATGATATATAATCTTAGATATGATTTTGTAATCTTAGA
1 GATATACAATCTTAGATATGATATACAATCCTAGATATGATTATGCAATCTTAGA
2174655 GATTTAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 12 0.24
59 37 0.76
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (58 bp):
GATATACAATCTTAGATATGATATACAATCCTAGATATGATTATGCAATCTTAGATAT
Found at i:2176125 original size:98 final size:98
Alignment explanation
Indices: 2175951--2176143 Score: 341
Period size: 98 Copynumber: 2.0 Consensus size: 98
2175941 TTAAAAATAA
* *
2175951 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
2176016 TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
* *
2176049 TAAAGGAAATATTCCGAGTTTGGGATTCTAGATGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
2176114 TTAAATCTTGGATAAGTGGATGTTCTTTTA
66 TTAAATATTGGATAAGTGGATGTTCTTTTA
2176144 CAGTTTCATT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATATTGGATAAGTGGATGTTCTTTTAAAG
Found at i:2187012 original size:24 final size:25
Alignment explanation
Indices: 2186976--2187029 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2186966 ATGTTATTGG
*
2186976 ATTATTGATTTAATATAAAT-ATATA
1 ATTATTGATTTAACATAAATAAT-TA
*
2187001 ATTATT-ATTTAACATATATAATTA
1 ATTATTGATTTAACATAAATAATTA
2187025 ATTAT
1 ATTAT
2187030 AATATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTATTGATTTAACATAAATAATTA
Found at i:2189455 original size:25 final size:26
Alignment explanation
Indices: 2189400--2189456 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2189390 GAATGTATTG
*
2189400 TGTATTAAACGAATAAAACTAAATCAA
1 TGTATTAAAAGAATAAAACTAAA-CAA
2189427 -GTATTAAAAGAAT-AAACTGAAA-AA
1 TGTATTAAAAGAATAAAACT-AAACAA
2189451 TGTATT
1 TGTATT
2189457 TAGTATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.07
25 10 0.37
26 15 0.56
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (26 bp):
TGTATTAAAAGAATAAAACTAAACAA
Found at i:2190412 original size:11 final size:11
Alignment explanation
Indices: 2190373--2190421 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
2190363 TAAACATTAA
2190373 AAAATTATTTT
1 AAAATTATTTT
2190384 AAAA--A-TTT
1 AAAATTATTTT
2190392 AATAATTATTTT
1 AA-AATTATTTT
*
2190404 AAAAGTATTTT
1 AAAATTATTTT
2190415 AAAATTA
1 AAAATTA
2190422 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
11 19 0.59
12 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:2196025 original size:35 final size:35
Alignment explanation
Indices: 2195986--2196062 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
2195976 TATCCTATCT
*
2195986 TTAAGGGTTTGACTTTATCTTATTTGAAAGCTAAG
1 TTAAGGATTTGACTTTATCTTATTTGAAAGCTAAG
*
2196021 TTAAGGATTTGACTTTATCTTATTTGAAAGCTAGG
1 TTAAGGATTTGACTTTATCTTATTTGAAAGCTAAG
*
2196056 TTGAGGA
1 TTAAGGA
2196063 GTTTCTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (35 bp):
TTAAGGATTTGACTTTATCTTATTTGAAAGCTAAG
Found at i:2204508 original size:14 final size:14
Alignment explanation
Indices: 2204489--2204518 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2204479 ATTTCTTTAG
2204489 TTTATTTTACTTAC
1 TTTATTTTACTTAC
*
2204503 TTTATTTTATTTAC
1 TTTATTTTACTTAC
2204517 TT
1 TT
2204519 AATAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTTACTTAC
Found at i:2204677 original size:21 final size:21
Alignment explanation
Indices: 2204653--2204693 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2204643 CAAATAATAA
2204653 TATT-ACAAATGTACATATATT
1 TATTGACAAATGTACA-ATATT
*
2204674 TATTGATAAATGTACAATAT
1 TATTGACAAATGTACAATAT
2204694 CATCTCTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (21 bp):
TATTGACAAATGTACAATATT
Found at i:2210873 original size:30 final size:30
Alignment explanation
Indices: 2210839--2210902 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
2210829 TCAAGTAGGG
*
2210839 TTAAATCCAAT-TATTATAATTCTATATTTT
1 TTAAATCC-ATGTATGATAATTCTATATTTT
* *
2210869 TTAAATGCATGTATGATAATTCTATTTTTT
1 TTAAATCCATGTATGATAATTCTATATTTT
2210899 TTAA
1 TTAA
2210903 TAAAACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (30 bp):
TTAAATCCATGTATGATAATTCTATATTTT
Found at i:2215918 original size:63 final size:63
Alignment explanation
Indices: 2215798--2215922 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
2215788 GGTCAACTCT
* * **
2215798 AGGACTTTCCTGGCATGTTCTCATACCAATGTCCACCACAAATTATGTTTAGGAACTACTTCC
1 AGGACTTTCCTGGCATGTTCTCATACCAATGTCCACCACAAATTATCTTGACCAACTACTTCC
** *
2215861 AGGACTTTCCTGGCATGTTCTCATGTCAATGTCCACCGCAAATTATCTTGACCAACTACTTC
1 AGGACTTTCCTGGCATGTTCTCATACCAATGTCCACCACAAATTATCTTGACCAACTACTTC
2215923 TCAGTAACCT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (63 bp):
AGGACTTTCCTGGCATGTTCTCATACCAATGTCCACCACAAATTATCTTGACCAACTACTTCC
Found at i:2216183 original size:30 final size:30
Alignment explanation
Indices: 2216138--2216210 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2216128 ATTAATGATA
* * *
2216138 AATAAAATATTTTAAA-AACTTAAATATAAT
1 AATAAATTATATTAAATAA-TTAAATACAAT
*
2216168 AATAAATTATATTAAATAATTTAATACAAT
1 AATAAATTATATTAAATAATTAAATACAAT
*
2216198 GATAAATTATATT
1 AATAAATTATATT
2216211 TATATAATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
AATAAATTATATTAAATAATTAAATACAAT
Found at i:2216381 original size:55 final size:55
Alignment explanation
Indices: 2216315--2216428 Score: 185
Period size: 55 Copynumber: 2.1 Consensus size: 55
2216305 TTTAAGTAGA
* *
2216315 AAAACAATTTTTCACCGTAGTTTTGACCCCAAAATTCAATTAT-CTTTCTAGGTGT
1 AAAACAATTTTTCACCGTAGTTTTAACCCCAAAAATCAATTATAC-TTCTAGGTGT
*
2216370 AAAACAATTTTTCACCGTAGTTTTAACCCCAAAAATCAGTTATACTTCTAGGTGT
1 AAAACAATTTTTCACCGTAGTTTTAACCCCAAAAATCAATTATACTTCTAGGTGT
2216425 AAAA
1 AAAA
2216429 GCACTTTTGG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 54 0.98
56 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (55 bp):
AAAACAATTTTTCACCGTAGTTTTAACCCCAAAAATCAATTATACTTCTAGGTGT
Found at i:2218759 original size:195 final size:195
Alignment explanation
Indices: 2218521--2218917 Score: 767
Period size: 195 Copynumber: 2.0 Consensus size: 195
2218511 TTGGGAGTCG
* *
2218521 TCTTTATTGGGCTTATTCTTTGCTATACATAGTTGATTGATTGCTAAGCAGGAGAAATACATAAT
1 TCTTTCTTGGGCTTATTCTTTGCCATACATAGTTGATTGATTGCTAAGCAGGAGAAATACATAAT
2218586 TTTTTGTTAATGATTTTGATGCATATATTACGGTCTGTTGGTTATCAGGGTTATAATCTCCGCCT
66 TTTTTGTTAATGATTTTGATGCATATATTACGGTCTGTTGGTTATCAGGGTTATAATCTCCGCCT
2218651 TTAGGAAAGTTTGCCACTTTTTACTTATTTTGATATGTCTGACTGCTGTATGTTGTTATGTGACT
131 TTAGGAAAGTTTGCCACTTTTTACTTATTTTGATATGTCTGACTGCTGTATGTTGTTATGTGACT
2218716 TCTTTCTTGGGCTTATTCTTTGCCATACATAGTTGATTGATTGCTAAGCAGGAGAAATACATAAT
1 TCTTTCTTGGGCTTATTCTTTGCCATACATAGTTGATTGATTGCTAAGCAGGAGAAATACATAAT
*
2218781 TTTTTGTTAATGATTTTGATGCATATATTTCGGTCTGTTGGTTATCAGGGTTATAATCTCCGCCT
66 TTTTTGTTAATGATTTTGATGCATATATTACGGTCTGTTGGTTATCAGGGTTATAATCTCCGCCT
2218846 TTAGGAAAGTTTGCCACTTTTTACTTATTTTGATATGTCTGACTGCTGTATGTTGTTATGTGACT
131 TTAGGAAAGTTTGCCACTTTTTACTTATTTTGATATGTCTGACTGCTGTATGTTGTTATGTGACT
2218911 TCTTTCT
1 TCTTTCT
2218918 CTTTTCTCTT
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 199 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (195 bp):
TCTTTCTTGGGCTTATTCTTTGCCATACATAGTTGATTGATTGCTAAGCAGGAGAAATACATAAT
TTTTTGTTAATGATTTTGATGCATATATTACGGTCTGTTGGTTATCAGGGTTATAATCTCCGCCT
TTAGGAAAGTTTGCCACTTTTTACTTATTTTGATATGTCTGACTGCTGTATGTTGTTATGTGACT
Found at i:2222244 original size:15 final size:15
Alignment explanation
Indices: 2222208--2222261 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2222198 TAAATTCAAT
*
2222208 ACTTAA-TTTTTAAT
1 ACTTAATTTTTTAAC
2222222 ACTT-ATTTTTTAAC
1 ACTTAATTTTTTAAC
*
2222236 ACTTAATTTTTTGAC
1 ACTTAATTTTTTAAC
2222251 ACTTAATTTTT
1 ACTTAATTTTT
2222262 CAATCTATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 1 0.03
14 15 0.42
15 20 0.56
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (15 bp):
ACTTAATTTTTTAAC
Found at i:2222260 original size:13 final size:14
Alignment explanation
Indices: 2222208--2222261 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
2222198 TAAATTCAAT
*
2222208 ACTTAATTTTTAAT
1 ACTTAATTTTTAAC
*
2222222 ACTTATTTTTTAAC
1 ACTTAATTTTTAAC
*
2222236 ACTTAATTTTTTGAC
1 ACTTAA-TTTTTAAC
2222251 ACTTAATTTTT
1 ACTTAATTTTT
2222262 CAATCTATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (14 bp):
ACTTAATTTTTAAC
Found at i:2227964 original size:11 final size:11
Alignment explanation
Indices: 2227947--2227989 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2227937 CAAAATAGTG
2227947 AAAAAAATAAC
1 AAAAAAATAAC
* *
2227958 AAGAAAATAGC
1 AAAAAAATAAC
* *
2227969 AACAAAATAAT
1 AAAAAAATAAC
2227980 AAAAAAATAA
1 AAAAAAATAA
2227990 ATATTTTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAATAAC
Found at i:2241891 original size:6 final size:6
Alignment explanation
Indices: 2241880--2241913 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2241870 AGAATTAGGG
2241880 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
2241914 TATGAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:2248271 original size:24 final size:24
Alignment explanation
Indices: 2248229--2248280 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2248219 AATCAAAGTC
** *
2248229 AAATATATTATGCTAATAAATGCT
1 AAATATATTATAATAATAAATACT
*
2248253 AAATATATTATAATCATAAATACT
1 AAATATATTATAATAATAAATACT
2248277 AAAT
1 AAAT
2248281 CTTCTAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATAATAATAAATACT
Found at i:2250631 original size:110 final size:110
Alignment explanation
Indices: 2250233--2250782 Score: 870
Period size: 110 Copynumber: 5.0 Consensus size: 110
2250223 GAAATTCAAG
* * * *
2250233 AGGATATTTGGCTATTCGGTTAAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* * *
2250298 GAATTT-TCAAATGCAAAACATTGCCTTATTTTAAAATTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
*
2250342 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
*
2250407 GAATTTCCCAAATGCAAAAACATTGCCTTATTTCGAAAATTCTTTAAA
66 GAATTTCCCAAACGC-AAAACATTGCCTTATTT-GAAAATT-TTTAAA
* * * * *
2250455 AGGATATTGGAGGCATTTGGTTGAACGAGAAAAAGCGACACCCAGCACCTTAGGGCACGTTCTCT
1 AGGATATT-TAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCT
* *
2250520 CGAATTTCCCAAACGCAAAACGTTGCCTTATTTTAAAATTTTTAAA
65 CGAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
*
2250566 AGGATATTTAGCCAGTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
*
2250631 GAATTTCTCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
*
2250676 AGGATATTTAGCCATTTGGTTGAATGAGAGAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
2250741 GAATTTCCCAAACGCCAAAA-ATTGCCTTATTTGAAAATTTTT
66 GAATTTCCCAAACG-CAAAACATTGCCTTATTTGAAAATTTTT
2250783 GTTTTTGATA
Statistics
Matches: 409, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
109 66 0.16
110 198 0.48
111 36 0.09
112 12 0.03
113 30 0.07
114 67 0.16
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
Found at i:2250921 original size:18 final size:17
Alignment explanation
Indices: 2250890--2250925 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2250880 ATATATAATG
*
2250890 AAAAGAAATCAACAAAT
1 AAAAGAAATAAACAAAT
2250907 AAAAGTAAATAAACAAAT
1 AAAAG-AAATAAACAAAT
2250925 A
1 A
2250926 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAGAAATAAACAAAT
Found at i:2251291 original size:22 final size:21
Alignment explanation
Indices: 2251247--2251293 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
2251237 TGTGTGTAAG
* *
2251247 TATATAAAAAAAATATATGTA
1 TATATAAAAAAAACATATATA
*
2251268 TATATATAAAAAAACGTATATA
1 TATATA-AAAAAAACATATATA
2251290 TATA
1 TATA
2251294 AGGGCAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
TATATAAAAAAAACATATATA
Found at i:2251385 original size:3 final size:3
Alignment explanation
Indices: 2251303--2251365 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
2251293 AAGGGCAATT
*
2251303 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
**
2251351 GCA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
2251366 TTATTATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2252443 original size:13 final size:14
Alignment explanation
Indices: 2252425--2252458 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2252415 CTTTTGGGGG
*
2252425 ATTTGGGCTCT-AA
1 ATTTGGGCTATAAA
2252438 ATTTGGGCTATAAA
1 ATTTGGGCTATAAA
2252452 ATTTGGG
1 ATTTGGG
2252459 TTAGGCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (14 bp):
ATTTGGGCTATAAA
Found at i:2253600 original size:24 final size:24
Alignment explanation
Indices: 2253585--2253638 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2253575 AATTAAAGTC
2253585 AAATATATTATGCTAATAAATACT
1 AAATATATTATGCTAATAAATACT
* * *
2253609 AAATATATTATACTCATAAGTACT
1 AAATATATTATGCTAATAAATACT
2253633 AAATAT
1 AAATAT
2253639 TCTAGAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATACT
Found at i:2255556 original size:16 final size:17
Alignment explanation
Indices: 2255535--2255570 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2255525 TATTAAAAAA
2255535 TATATTTT-ATAATTTT
1 TATATTTTAATAATTTT
*
2255551 TATATTTTAATTATTTT
1 TATATTTTAATAATTTT
2255568 TAT
1 TAT
2255571 GTGGATCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTTAATAATTTT
Found at i:2263519 original size:24 final size:24
Alignment explanation
Indices: 2263487--2263532 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2263477 GGTCTATTCA
2263487 TTTTATTTTAAAAATTAAAAATTT
1 TTTTATTTTAAAAATTAAAAATTT
*
2263511 TTTTTTTTTAAAAATTAAAAAT
1 TTTTATTTTAAAAATTAAAAAT
2263533 CTTAATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTATTTTAAAAATTAAAAATTT
Found at i:2265227 original size:2 final size:2
Alignment explanation
Indices: 2265220--2265266 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2265210 GTTGGGAAGA
2265220 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2265262 AG AG A
1 AG AG A
2265267 ANNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2271300 original size:89 final size:89
Alignment explanation
Indices: 2271172--2271352 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
2271162 AAATTATATA
*
2271172 AAGTAGTAGTGATATTGATGAAGGAAACTTGATAAGAAAAATAATGCACATATCCACTATGATGT
1 AAGTAGTAGTGATATTGATGAAGGAAACTTGATAAGAAAAATAATGCACATATCCACAATGATGT
2271237 TTAGGTAAATCATATACTATAGTG
66 TTAGGTAAATCATATACTATAGTG
*
2271261 AAGTAGTAGTGATATTGATGAAGGAAACTTGATAAGAAAAATAATGCACATATCCACAATGCTGT
1 AAGTAGTAGTGATATTGATGAAGGAAACTTGATAAGAAAAATAATGCACATATCCACAATGATGT
2271326 TTAGGTAAATCATATACTATAGTG
66 TTAGGTAAATCATATACTATAGTG
2271350 AAG
1 AAG
2271353 CAAATCGCAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (89 bp):
AAGTAGTAGTGATATTGATGAAGGAAACTTGATAAGAAAAATAATGCACATATCCACAATGATGT
TTAGGTAAATCATATACTATAGTG
Found at i:2275123 original size:22 final size:22
Alignment explanation
Indices: 2275095--2275175 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
2275085 GGATGCCTAA
2275095 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
2275117 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
2275139 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
2275161 CATGAGAGCTTAGTA
1 CATGAGAGCTTAGTA
2275176 ATCTCACAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:2277769 original size:6 final size:6
Alignment explanation
Indices: 2277758--2277795 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
2277748 AACTATATAA
*
2277758 TATATG TATATG TATATG TATACG TATATG TATATG TA
1 TATATG TATATG TATATG TATATG TATATG TATATG TA
2277796 CCTGCAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:2289726 original size:113 final size:111
Alignment explanation
Indices: 2289605--2289807 Score: 273
Period size: 112 Copynumber: 1.8 Consensus size: 111
2289595 AAAAAAAAAA
*
2289605 TTTACTGTACTGGGTATCAGCCATTGACAGGCC-AGCACCCAAAAAAAATTTCTTTTTTACTTTT
1 TTTACTGTACTGGGTACCAGCCATTGACA-GCCTAGCA-CCAAAAAAAATTTCTTTTTTACTTTT
* * *
2289669 TTTTGTACTCTGGTGCCTGCCATTGACAAACCAAAACTCGAAATTTTTT
64 TTTCGTACT-GGGTGCCGGCCATTGACAAACCAAAACTCGAAATTTTTT
* * * ** * *
2289718 TTTACTGTACTGGGTGCCGGCCATTGACAGCCTAGCACCTAAAAATTTTTTTTTTTTCCTTTTTT
1 TTTACTGTACTGGGTACCAGCCATTGACAGCCTAGCACCAAAAAAAATTTCTTTTTTACTTTTTT
2289783 TCGTACTGGGTGCCGGCCATTGACA
66 TCGTACTGGGTGCCGGCCATTGACA
2289808 GGCCAGCACC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
111 16 0.21
112 32 0.41
113 30 0.38
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (111 bp):
TTTACTGTACTGGGTACCAGCCATTGACAGCCTAGCACCAAAAAAAATTTCTTTTTTACTTTTTT
TCGTACTGGGTGCCGGCCATTGACAAACCAAAACTCGAAATTTTTT
Found at i:2293546 original size:2 final size:2
Alignment explanation
Indices: 2293539--2293567 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2293529 TTATTAATAG
2293539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2293568 TAACTATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2307463 original size:97 final size:97
Alignment explanation
Indices: 2307297--2307492 Score: 374
Period size: 97 Copynumber: 2.0 Consensus size: 97
2307287 TGATTTATAT
*
2307297 TTATGCAACAAATACTTAGTTTCTTGTTCTCAATTATGTGTGCTTAATGTTTGGTTTAATATATC
1 TTATGCAACAAATACTTAGTTTCTTGTTCTCAATTATGTGTGCTTAATATTTGGTTTAATATATC
2307362 TAGATTAATGATCAATATTTGATATGCTCAAA
66 TAGATTAATGATCAATATTTGATATGCTCAAA
2307394 TTATGCAACAAATACTTAGTTTCTTGTTCTCAATTATGTGTGCTTAATATTTGGTTTAATATATC
1 TTATGCAACAAATACTTAGTTTCTTGTTCTCAATTATGTGTGCTTAATATTTGGTTTAATATATC
*
2307459 TAGATTAATGATCAATATTTGATGTGCTCAAA
66 TAGATTAATGATCAATATTTGATATGCTCAAA
2307491 TT
1 TT
2307493 GGTGGTTGAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (97 bp):
TTATGCAACAAATACTTAGTTTCTTGTTCTCAATTATGTGTGCTTAATATTTGGTTTAATATATC
TAGATTAATGATCAATATTTGATATGCTCAAA
Found at i:2309870 original size:43 final size:43
Alignment explanation
Indices: 2309814--2309899 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
2309804 AAACAAGAGT
*
2309814 TAGTGGGCGGACACAAAGCAGATGATATCATTCGAAGAACAAC
1 TAGTGGGCAGACACAAAGCAGATGATATCATTCGAAGAACAAC
2309857 TAGTGGGCAGACACAAAGCAGATGATATCATTCGAAGAACAAC
1 TAGTGGGCAGACACAAAGCAGATGATATCATTCGAAGAACAAC
2309900 ATTCAACCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (43 bp):
TAGTGGGCAGACACAAAGCAGATGATATCATTCGAAGAACAAC
Found at i:2314779 original size:16 final size:15
Alignment explanation
Indices: 2314730--2314780 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2314720 ATAATTTTTT
2314730 TAAATAATCAAAACC
1 TAAATAATCAAAACC
*
2314745 TAAATAAATTCAAGA-C
1 TAAAT-AA-TCAAAACC
*
2314761 TAACCTAATCAAAACC
1 TAA-ATAATCAAAACC
2314777 TAAA
1 TAAA
2314781 ATAAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 10 0.36
16 12 0.43
17 6 0.21
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAATAATCAAAACC
Found at i:2315054 original size:21 final size:22
Alignment explanation
Indices: 2315012--2315056 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2315002 TTCTAGACAT
*
2315012 AAAAAAAGTGAAATTAACATTA
1 AAAAAAAGGGAAATTAACATTA
2315034 AAAAAAAGGGAGAA-TAA-ATTA
1 AAAAAAAGGGA-AATTAACATTA
2315055 AA
1 AA
2315057 TCCACATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 13 0.62
23 2 0.10
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.18
Consensus pattern (22 bp):
AAAAAAAGGGAAATTAACATTA
Found at i:2315151 original size:18 final size:19
Alignment explanation
Indices: 2315128--2315165 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2315118 CTAGACCTCC
*
2315128 ACGTTACACAAAAA-ATTT
1 ACGTTAAACAAAAATATTT
2315146 ACGTTAAACAAAAATATTT
1 ACGTTAAACAAAAATATTT
2315165 A
1 A
2315166 AATAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (19 bp):
ACGTTAAACAAAAATATTT
Found at i:2317515 original size:19 final size:20
Alignment explanation
Indices: 2317472--2317515 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2317462 AAAAAGTAAC
* *
2317472 GATTTCAACTTTTTAGTGTA
1 GATTTCAACGTTTTAGGGTA
*
2317492 TATTTCAA-GTTTTAGGGTA
1 GATTTCAACGTTTTAGGGTA
2317511 GATTT
1 GATTT
2317516 GACAAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (20 bp):
GATTTCAACGTTTTAGGGTA
Found at i:2317956 original size:18 final size:18
Alignment explanation
Indices: 2317930--2317966 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2317920 AACCAGAAAT
*
2317930 TAAAATTAACTTGAAAAC
1 TAAAATTAAATTGAAAAC
*
2317948 TAAATTTAAATTGAAAAC
1 TAAAATTAAATTGAAAAC
2317966 T
1 T
2317967 TATAACGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAAATTAAATTGAAAAC
Found at i:2322795 original size:19 final size:18
Alignment explanation
Indices: 2322735--2322797 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
2322725 ATCTTTTAAA
2322735 TATAAAAAATT-TGAAAA-
1 TATAAAAAATTAT-AAAAC
* *
2322752 AAT-AAAAAGTATAAAAC
1 TATAAAAAATTATAAAAC
* *
2322769 TATTAAAAATTATAAAGAT
1 TATAAAAAATTATAAA-AC
2322788 TATAAAAAAT
1 TATAAAAAAT
2322798 ATTTTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 10 0.28
17 5 0.14
18 11 0.31
19 10 0.28
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
TATAAAAAATTATAAAAC
Found at i:2322814 original size:21 final size:20
Alignment explanation
Indices: 2322773--2322816 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2322763 TAAAACTATT
*
2322773 AAAAATTATAAAGATTATAA
1 AAAAATTATAAAAATTATAA
* *
2322793 AAAATATTTTAAAAATTTTAA
1 AAAA-ATTATAAAAATTATAA
2322814 AAA
1 AAA
2322817 TTAAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATTATAAAAATTATAA
Found at i:2324843 original size:3 final size:3
Alignment explanation
Indices: 2324835--2324892 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
2324825 TTATACCATC
2324835 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2324883 ATA ATA ATA A
1 ATA ATA ATA A
2324893 ACCTTTAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2326069 original size:2 final size:2
Alignment explanation
Indices: 2326056--2326092 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2326046 ATATGTTGTC
*
2326056 TG TG TT TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2326093 AAATATGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:2332903 original size:3 final size:3
Alignment explanation
Indices: 2332891--2332966 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
2332881 ATTTAAAGGT
2332891 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2332938 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2332967 TTCAACCAGC
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2333285 original size:80 final size:80
Alignment explanation
Indices: 2333152--2333313 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
2333142 TAAATCAAAT
2333152 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
1 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
2333217 AAAAAGAAAAGAAAA
66 AAAAAGAAAAGAAAA
2333232 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
1 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
2333297 AAAAAGAAAAGAAAA
66 AAAAAGAAAAGAAAA
2333312 TG
1 TG
2333314 AAAATGAAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (80 bp):
TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
AAAAAGAAAAGAAAA
Found at i:2340316 original size:16 final size:17
Alignment explanation
Indices: 2340291--2340325 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2340281 TTTCGTCTCT
2340291 TTTTTCTTTTAGTTTTA
1 TTTTTCTTTTAGTTTTA
*
2340308 TTTTT-TTTTATTTTTA
1 TTTTTCTTTTAGTTTTA
2340324 TT
1 TT
2340326 GAAAAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTAGTTTTA
Found at i:2342659 original size:68 final size:67
Alignment explanation
Indices: 2342527--2342659 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 67
2342517 TTACAATACT
* * * **
2342527 AATAGCTTATAAATTACCACAAATGTCCTAAAGGCTAAAGCAAAATAGTAATACTAACTTACAAG
1 AATACCTTATAAATTACCAAAAATGTCCTAAAGGCTAAAGCAAAAGAGTAATACT-ACCAACAAG
2342592 ACC
65 ACC
* *
2342595 AATACCTTATAAGTTACCAAAAATGTCCTAAAGGCTAAAGCAAAAGGATTAATTACT-CCAACAA
1 AATACCTTATAAATTACCAAAAATGTCCTAAAGGCTAAAGCAAAA-GAGTAA-TACTACCAACAA
2342659 G
64 G
2342660 TGAGATGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 48 0.86
69 4 0.07
70 4 0.07
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (67 bp):
AATACCTTATAAATTACCAAAAATGTCCTAAAGGCTAAAGCAAAAGAGTAATACTACCAACAAGA
CC
Found at i:2343753 original size:46 final size:46
Alignment explanation
Indices: 2343633--2343756 Score: 185
Period size: 46 Copynumber: 2.7 Consensus size: 46
2343623 TTTATTTTAG
* *
2343633 TTATTTTTATAATTTTGAAATTATAAGTCAATACGATGATAAAATT
1 TTATTTTTATAATTTTAAAATTATAAGTTAATACGATGATAAAATT
* * * * *
2343679 ATATTTTTGTAATTTTCAATTTATAAGTTAGTACGATGATAAAATT
1 TTATTTTTATAATTTTAAAATTATAAGTTAATACGATGATAAAATT
2343725 TTATTTTTATAATTTTAAAATTATAAGTTAAT
1 TTATTTTTATAATTTTAAAATTATAAGTTAAT
2343757 CTTTTTATAC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (46 bp):
TTATTTTTATAATTTTAAAATTATAAGTTAATACGATGATAAAATT
Found at i:2344330 original size:6 final size:6
Alignment explanation
Indices: 2344319--2344347 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2344309 TTTCATTGGG
2344319 ATTATA ATTATA ATTATA ATTATA ATTAT
1 ATTATA ATTATA ATTATA ATTATA ATTAT
2344348 TGCTTCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:2345398 original size:24 final size:22
Alignment explanation
Indices: 2345340--2345394 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
2345330 ATAGCCTCTT
*
2345340 TTTTATATATATATTTAAAATAA
1 TTTTATAT-TATATATAAAATAA
*
2345363 TTTTCATTATTATATATAATATAA
1 TTTT-A-TATTATATATAAAATAA
2345387 TATTTATA
1 T-TTTATA
2345395 ATTAATAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.22
24 15 0.56
25 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATATTATATATAAAATAA
Found at i:2348588 original size:2 final size:2
Alignment explanation
Indices: 2348583--2348615 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2348573 TTATATAAAA
*
2348583 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2348616 GAAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2348589 original size:10 final size:10
Alignment explanation
Indices: 2348574--2348611 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2348564 TTTTAGACAT
*
2348574 TATATAAAAA
1 TATATATAAA
2348584 TATATATAAA
1 TATATATAAA
*
2348594 TATATATATA
1 TATATATAAA
2348604 TATATATA
1 TATATATA
2348612 TATAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATATAAA
Found at i:2348591 original size:12 final size:12
Alignment explanation
Indices: 2348574--2348623 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
2348564 TTTTAGACAT
2348574 TATATAAAAATA
1 TATATAAAAATA
*
2348586 TATATAAATATA
1 TATATAAAAATA
* *
2348598 TATATATATATA
1 TATATAAAAATA
2348610 TATATAGAAAATA
1 TATATA-AAAATA
2348623 T
1 T
2348624 TTGGTACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
12 28 0.85
13 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:2349090 original size:13 final size:14
Alignment explanation
Indices: 2349067--2349098 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2349057 TACTTTTAAA
2349067 AATATTAAAATATT
1 AATATTAAAATATT
2349081 AATA-TAAAATATT
1 AATATTAAAATATT
2349094 -ATATT
1 AATATT
2349099 TTTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:2349132 original size:21 final size:21
Alignment explanation
Indices: 2349106--2349155 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2349096 ATTTTTTAAT
2349106 ATTATTAAACATACATATTTA
1 ATTATTAAACATACATATTTA
2349127 ATTATTAAACATACATATTTA
1 ATTATTAAACATACATATTTA
2349148 ATTATTAA
1 ATTATTAA
2349156 TATAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATTAAACATACATATTTA
Found at i:2350780 original size:19 final size:19
Alignment explanation
Indices: 2350745--2350783 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2350735 TCTTGTGTCA
*
2350745 TTTTTCTATTTTTGTTGCT
1 TTTTTCTATTTTAGTTGCT
2350764 TTTTTC-ATTTTAAGTTGCT
1 TTTTTCTATTTT-AGTTGCT
2350783 T
1 T
2350784 CCACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTTCTATTTTAGTTGCT
Found at i:2352389 original size:34 final size:35
Alignment explanation
Indices: 2352331--2352397 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2352321 CAAACACCAG
2352331 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
2352366 AAAATATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
2352398 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2359345 original size:12 final size:12
Alignment explanation
Indices: 2359330--2359354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2359320 TATTACTATT
2359330 TTAATTTAATTA
1 TTAATTTAATTA
2359342 TTAATTTAATTA
1 TTAATTTAATTA
2359354 T
1 T
2359355 GTTTTATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATTTAATTA
Found at i:2377863 original size:29 final size:29
Alignment explanation
Indices: 2377812--2377867 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2377802 ATAGTAACCT
**
2377812 GATCAAACTAGTCCTTTTACTATTAAATG
1 GATCAAACTAGTCCTCGTACTATTAAATG
* *
2377841 GATCAATCTAGTCCTCGTGCTATTAAA
1 GATCAAACTAGTCCTCGTACTATTAAA
2377868 AAGAATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (29 bp):
GATCAAACTAGTCCTCGTACTATTAAATG
Found at i:2378131 original size:29 final size:31
Alignment explanation
Indices: 2378099--2378161 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2378089 ACAGTATAAT
2378099 GACTAAATTAATC-AA-TTTAATAATAAAGG
1 GACTAAATTAATCTAATTTTAATAATAAAGG
* * * *
2378128 GACTAATTTGATCTAATTTTTATAATATAGG
1 GACTAAATTAATCTAATTTTAATAATAAAGG
2378159 GAC
1 GAC
2378162 CTCCTAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.39
30 2 0.07
31 15 0.54
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37
Consensus pattern (31 bp):
GACTAAATTAATCTAATTTTAATAATAAAGG
Found at i:2382519 original size:13 final size:13
Alignment explanation
Indices: 2382501--2382528 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2382491 ACATGTGCTC
2382501 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
2382514 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
2382527 TT
1 TT
2382529 TAAAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:2383676 original size:20 final size:20
Alignment explanation
Indices: 2383638--2383676 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2383628 TCCGTCTATA
* *
2383638 CCCAAGGTGCTCTCTGAAGG
1 CCCAAGGTGCTCACAGAAGG
2383658 CCCAAGGTGCTCACAGAAG
1 CCCAAGGTGCTCACAGAAG
2383677 TGAGATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (20 bp):
CCCAAGGTGCTCACAGAAGG
Found at i:2385561 original size:19 final size:18
Alignment explanation
Indices: 2385526--2385596 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 18
2385516 ATTTGACAAA
2385526 AAAAATC-ATAAAA-TAT
1 AAAAATCAATAAAATTAT
2385542 AAAAATCAATAAAAGTTAT
1 AAAAATCAATAAAA-TTAT
* *
2385561 AAAAATTATTAAAATTTAAT
1 AAAAATCAATAAAA-TT-AT
*
2385581 AAAAATATAATAAAAT
1 AAAAAT-CAATAAAAT
2385597 ATTTAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.15
17 6 0.13
19 17 0.37
20 9 0.20
21 7 0.15
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAAATCAATAAAATTAT
Found at i:2385562 original size:9 final size:9
Alignment explanation
Indices: 2385526--2385670 Score: 75
Period size: 10 Copynumber: 15.6 Consensus size: 9
2385516 ATTTGACAAA
*
2385526 AAAAATCAT
1 AAAAATTAT
2385535 -AAAA-TAT
1 AAAAATTAT
*
2385542 AAAAATCAAT
1 AAAAAT-TAT
*
2385552 AAAAGTTAT
1 AAAAATTAT
2385561 AAAAATTATT
1 AAAAATTA-T
*
2385571 AAAATTTAAT
1 AAAAATT-AT
2385581 AAAAATATAAT
1 AAAAAT-T-AT
2385592 AAAATATT-T
1 AAAA-ATTAT
*
2385601 AAAATTTACT
1 AAAAATTA-T
* *
2385611 AATAA-TAG
1 AAAAATTAT
2385619 AAAAA-TAT
1 AAAAATTAT
*
2385627 AAAAATAGTAA
1 AAAAAT--TAT
*
2385638 AAAAATCAT
1 AAAAATTAT
2385647 AAAAAATTAT
1 -AAAAATTAT
*
2385657 AAAAAGTAT
1 AAAAATTAT
2385666 AAAAA
1 AAAAA
2385671 AAAACCCTTT
Statistics
Matches: 105, Mismatches: 18, Indels: 26
0.70 0.12 0.17
Matches are distributed among these distances:
7 2 0.02
8 21 0.20
9 30 0.29
10 32 0.30
11 18 0.17
12 2 0.02
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2385633 original size:19 final size:18
Alignment explanation
Indices: 2385611--2385670 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
2385601 AAAATTTACT
2385611 AATAATAGAAAAATATAAA
1 AATAATA-AAAAATATAAA
*
2385630 AATAGTAAAAAAATCATAAAA
1 AATAAT-AAAAAAT-AT-AAA
* *
2385651 AATTATAAAAAGTATAAA
1 AATAATAAAAAATATAAA
2385669 AA
1 AA
2385671 AAAACCCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 9 0.26
21 7 0.21
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (18 bp):
AATAATAAAAAATATAAA
Found at i:2385641 original size:11 final size:10
Alignment explanation
Indices: 2385619--2385672 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
2385609 CTAATAATAG
2385619 AAAAATAT--
1 AAAAATATAA
2385627 AAAAATAGTAA
1 AAAAATA-TAA
2385638 AAAAATCATAA
1 AAAAAT-ATAA
*
2385649 AAAATTAT-A
1 AAAAATATAA
*
2385658 AAAAGTATAA
1 AAAAATATAA
2385668 AAAAA
1 AAAAA
2385673 AACCCTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 7 0.18
9 9 0.24
10 7 0.18
11 14 0.37
12 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (10 bp):
AAAAATATAA
Found at i:2385883 original size:20 final size:20
Alignment explanation
Indices: 2385822--2385888 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
2385812 TAGTATGATA
*
2385822 ATTTTTATAACTCTT-TTACG
1 ATTTTTATAA-TTTTCTTACG
* *
2385842 AATTTTAT-A-TTTCTTTA-T
1 ATTTTTATAATTTTC-TTACG
2385860 ATTTTTATAATTTTCTTACG
1 ATTTTTATAATTTTCTTACG
2385880 A-TTTTATAA
1 ATTTTTATAA
2385889 AATTATATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
17 2 0.05
18 7 0.19
19 16 0.43
20 12 0.32
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.60
Consensus pattern (20 bp):
ATTTTTATAATTTTCTTACG
Found at i:2385944 original size:19 final size:19
Alignment explanation
Indices: 2385822--2385946 Score: 53
Period size: 19 Copynumber: 6.6 Consensus size: 19
2385812 TAGTATGATA
*
2385822 ATTTTTATAACTCTTTTACG
1 ATTTTTATAAAT-TTTTACG
* * *
2385842 AATTTTAT-ATTTCTTTA-T
1 ATTTTTATAAATT-TTTACG
*
2385860 ATTTTTATAATTTTCTTACG
1 ATTTTTATAAATTT-TTACG
* * *
2385880 A-TTTTATAAAATTATATTG
1 ATTTTTATAAATTTTTA-CG
* * * *
2385899 -TTTTTCTATATTTCTA-T
1 ATTTTTATAAATTTTTACG
*
2385916 ATATTATATAAATTTTTACG
1 AT-TTTTATAAATTTTTACG
2385936 ATTTTTATAAA
1 ATTTTTATAAA
2385947 AATATACAAC
Statistics
Matches: 76, Mismatches: 20, Indels: 19
0.66 0.17 0.17
Matches are distributed among these distances:
18 12 0.16
19 54 0.71
20 10 0.13
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTTTTATAAATTTTTACG
Found at i:2385961 original size:58 final size:58
Alignment explanation
Indices: 2385847--2385961 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 58
2385837 TTACGAATTT
* * * * ***
2385847 TATATTTCTTTATATTTTTATAATTTTCTTACGATTTTATAAAATTATATTGTTTTTC
1 TATATTTCTATATATTTATATAAATTTCTTACGATTTTATAAAAATATAAACTTTTTC
2385905 TATATTTCTATATA-TTATATAAATTT-TTACGATTTTTATAAAAATATACAACTTTTT
1 TATATTTCTATATATTTATATAAATTTCTTACGA-TTTTATAAAAATATA-AACTTTTT
2385962 TATGTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
56 6 0.12
57 24 0.50
58 18 0.38
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (58 bp):
TATATTTCTATATATTTATATAAATTTCTTACGATTTTATAAAAATATAAACTTTTTC
Found at i:2386021 original size:27 final size:27
Alignment explanation
Indices: 2385990--2386043 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2385980 TTATAATCTT
2385990 TTTCTAAATTTTAATAAAAATTAAATA
1 TTTCTAAATTTTAATAAAAATTAAATA
* * * *
2386017 TTTCTTATTTTTAATTAAAATTTAATA
1 TTTCTAAATTTTAATAAAAATTAAATA
2386044 AATTTAGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTCTAAATTTTAATAAAAATTAAATA
Found at i:2390916 original size:22 final size:22
Alignment explanation
Indices: 2390863--2390918 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2390853 TTATTTACTT
2390863 TTAA-ATAATCTTAATAATCTTA
1 TTAATATAAT-TTAATAATCTTA
*
2390885 TTAAATATAATTTAATAA-CATTC
1 TT-AATATAATTTAATAATC-TTA
2390908 TTAATATAATT
1 TTAATATAATT
2390919 CTCAAGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 12 0.40
23 13 0.43
24 5 0.17
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATATAATTTAATAATCTTA
Found at i:2393280 original size:9 final size:8
Alignment explanation
Indices: 2393244--2393279 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2393234 TTCGGTCACC
2393244 AAAAGAAA
1 AAAAGAAA
* *
2393252 AACAGAAG
1 AAAAGAAA
2393260 AAAAGAAA
1 AAAAGAAA
2393268 AAAAGAAA
1 AAAAGAAA
2393276 AAAA
1 AAAA
2393280 ACTTTGCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:2397057 original size:30 final size:30
Alignment explanation
Indices: 2397021--2397079 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2397011 AGTTAATATA
* * *
2397021 ATGATAAAATTATATTTTGGTCCTTACAAG
1 ATGATAAAATTATAGTTTAGTCCCTACAAG
*
2397051 ATGATAAAATTCTAGTTTAGTCCCTACAA
1 ATGATAAAATTATAGTTTAGTCCCTACAA
2397080 AAAATCCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (30 bp):
ATGATAAAATTATAGTTTAGTCCCTACAAG
Found at i:2400513 original size:2 final size:2
Alignment explanation
Indices: 2400506--2400545 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2400496 ACTTGAGGTA
2400506 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2400545 A
1 A
2400546 GAGAGAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2407708 original size:12 final size:12
Alignment explanation
Indices: 2407688--2407738 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2407678 TTGTTTAATA
*
2407688 TTCACGAACATG
1 TTCATGAACATG
2407700 TTCATGAACAT-
1 TTCATGAACATG
* *
2407711 ATAATTGAACATG
1 TTCA-TGAACATG
2407724 TTCATGAACAATG
1 TTCATGAAC-ATG
2407737 TT
1 TT
2407739 AATAAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 22 0.71
13 7 0.23
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:2409287 original size:5 final size:5
Alignment explanation
Indices: 2409279--2409312 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
2409269 ATTATATTAC
2409279 AAATT AAATT AAAATT AAATT AAAATT AAATT AA
1 AAATT AAATT -AAATT AAATT -AAATT AAATT AA
2409313 TTCAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 17 0.63
6 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AAATT
Found at i:2409295 original size:11 final size:11
Alignment explanation
Indices: 2409268--2409312 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
2409258 AAAATTTCGT
*
2409268 AATTATATTACA
1 AATTAAATTA-A
2409280 AATTAAATTAA
1 AATTAAATTAA
2409291 AATTAAATTAA
1 AATTAAATTAA
2409302 AATTAAATTAA
1 AATTAAATTAA
2409313 TTCAAGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTAAATTAA
Found at i:2409325 original size:16 final size:16
Alignment explanation
Indices: 2409279--2409326 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2409269 ATTATATTAC
*
2409279 AAATTAAATTAAAATT
1 AAATTAAAATAAAATT
*
2409295 AAATTAAAATTAAATT
1 AAATTAAAATAAAATT
*
2409311 -AATTCAAGATAAAATT
1 AAATT-AAAATAAAATT
2409327 TCTAATGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATTAAAATAAAATT
Found at i:2412561 original size:15 final size:16
Alignment explanation
Indices: 2412541--2412577 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2412531 TAATCTCCTG
2412541 TTGAAACACATA-A-AT
1 TTGAAAC-CATATATAT
2412556 TTGAAACCATATATAT
1 TTGAAACCATATATAT
2412572 TTGAAA
1 TTGAAA
2412578 AATTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 8 0.40
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (16 bp):
TTGAAACCATATATAT
Found at i:2412763 original size:18 final size:19
Alignment explanation
Indices: 2412740--2412777 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2412730 ATTTTTTAAA
2412740 TTATAAA-ATT-TGAAATTT
1 TTATAAATATTCTG-AATTT
2412758 TTATAAATATTCTGAATTT
1 TTATAAATATTCTGAATTT
2412777 T
1 T
2412778 AAAATCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 9 0.50
20 2 0.11
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATAAATATTCTGAATTT
Found at i:2414095 original size:13 final size:13
Alignment explanation
Indices: 2414058--2414097 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2414048 TTTAAACCAA
*
2414058 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
*
2414071 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
2414084 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
2414097 A
1 A
2414098 ATAAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:2416068 original size:31 final size:32
Alignment explanation
Indices: 2416033--2416096 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
2416023 GTTTCACGTG
* *
2416033 TATAATT-ACATCAAATTAAAATTTATATATA
1 TATAATTAACATCAAATCAAAATTCATATATA
*
2416064 TATAATTACACATTAAATCAAAATTCATATATA
1 TATAATTA-ACATCAAATCAAAATTCATATATA
2416097 ATTTCGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.25
33 21 0.75
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (32 bp):
TATAATTAACATCAAATCAAAATTCATATATA
Found at i:2424589 original size:25 final size:25
Alignment explanation
Indices: 2424529--2424589 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
2424519 GCAAACGAAC
** * *
2424529 GACGGTGGTCACTTGGTGGATGCCA
1 GACGGTGGTGGCTTAGTGGATACCA
* * *
2424554 AATGGTAGTGGCTTAGTGGATACCA
1 GACGGTGGTGGCTTAGTGGATACCA
2424579 GACGGTGGTGG
1 GACGGTGGTGG
2424590 GTGTGTTGAG
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.25
Consensus pattern (25 bp):
GACGGTGGTGGCTTAGTGGATACCA
Found at i:2424896 original size:14 final size:15
Alignment explanation
Indices: 2424877--2424909 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2424867 CACCACATAA
2424877 TTTAAA-AACATTTT
1 TTTAAATAACATTTT
*
2424891 TTTAAATAACCTTTT
1 TTTAAATAACATTTT
2424906 TTTA
1 TTTA
2424910 TATTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAATAACATTTT
Found at i:2429004 original size:31 final size:31
Alignment explanation
Indices: 2428969--2429044 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
2428959 AAAAAAACTT
*
2428969 AATAGTCCAATGACTTAAATAAAAACTTTCA
1 AATAGTTCAATGACTTAAATAAAAACTTTCA
*
2429000 AATAGTTCAATGACTTAAATGAAAACTTTCA
1 AATAGTTCAATGACTTAAATAAAAACTTTCA
*
2429031 AATAATTCAATGAC
1 AATAGTTCAATGAC
2429045 CATTTTGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.30
Consensus pattern (31 bp):
AATAGTTCAATGACTTAAATAAAAACTTTCA
Found at i:2441134 original size:22 final size:22
Alignment explanation
Indices: 2441109--2441151 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2441099 AAATTTAGTC
*
2441109 TTTA-TCCTTTTATTTCTAAAAA
1 TTTAGTCCTTCTATTT-TAAAAA
2441131 TTTAGTCCTTCTATTTTAAAA
1 TTTAGTCCTTCTATTTTAAAA
2441152 TTCAAGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAGTCCTTCTATTTTAAAAA
Found at i:2441747 original size:9 final size:10
Alignment explanation
Indices: 2441724--2441748 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2441714 AAGGGTCAAA
2441724 TTTTTCCTTC
1 TTTTTCCTTC
2441734 TTTTTCCTTC
1 TTTTTCCTTC
2441744 TTTTT
1 TTTTT
2441749 ATAAGGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCCTTC
Found at i:2446339 original size:16 final size:16
Alignment explanation
Indices: 2446293--2446339 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2446283 GAAAAATATT
2446293 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
2446310 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
2446326 TATATTTTTTATTT
1 TATATTTTTTATTT
2446340 ATTGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:2447319 original size:30 final size:30
Alignment explanation
Indices: 2447284--2447347 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2447274 GAATTTGATT
* * *
2447284 AAAATTTGAAGGTTAGGAGTTAAAATGACA
1 AAAATTTAAAAGTTAGGAGCTAAAATGACA
*
2447314 AAAATTTAAAAGTTAGGAGCTAAAGTGACA
1 AAAATTTAAAAGTTAGGAGCTAAAATGACA
2447344 AAAA
1 AAAA
2447348 GAAGTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (30 bp):
AAAATTTAAAAGTTAGGAGCTAAAATGACA
Found at i:2449271 original size:93 final size:93
Alignment explanation
Indices: 2449107--2449294 Score: 351
Period size: 93 Copynumber: 2.0 Consensus size: 93
2449097 GAATTAATAG
*
2449107 GAAAACTAATACAGCTATATTTCATTTCAAGGGTTGTTAGATATTTTATCATAAATTTGGATGTT
1 GAAAACTAATACAGCTATATTTCATTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATGTT
2449172 TTTTTTTTTCATTAATTGATTTATGCTT
66 TTTTTTTTTCATTAATTGATTTATGCTT
2449200 GAAAACTAATACAGCTATATTTCATTTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATG-
1 GAAAACTAATACAGCTATATTTCA-TTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATGT
2449264 TTTTTTTTTTCATTAATTGATTTATGCTT
65 TTTTTTTTTTCATTAATTGATTTATGCTT
2449293 GA
1 GA
2449295 TGGATCTACT
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
93 55 0.59
94 38 0.41
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (93 bp):
GAAAACTAATACAGCTATATTTCATTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATGTT
TTTTTTTTTCATTAATTGATTTATGCTT
Found at i:2450559 original size:14 final size:15
Alignment explanation
Indices: 2450540--2450568 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2450530 CAATTGACCC
2450540 TGAAATTT-AAAATT
1 TGAAATTTGAAAATT
2450554 TGAAATTTGAAAATT
1 TGAAATTTGAAAATT
2450569 AAAAAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TGAAATTTGAAAATT
Found at i:2450619 original size:30 final size:31
Alignment explanation
Indices: 2450562--2450619 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
2450552 TTTGAAATTT
* *
2450562 GAAAATTAAAAAGTAAAGAGGCTAAATTCTA
1 GAAAAATAAAAAGTAAAGAGACTAAATTCTA
*
2450593 GAAAAATAAAAA-TATAGAGACTAAATT
1 GAAAAATAAAAAGTAAAGAGACTAAATT
2450620 ATAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (31 bp):
GAAAAATAAAAAGTAAAGAGACTAAATTCTA
Found at i:2452139 original size:25 final size:24
Alignment explanation
Indices: 2452102--2452152 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
2452092 TTTTGAACAA
2452102 TTTAAATTTTTTCTTTTATATTCT
1 TTTAAATTTTTTCTTTTATATTCT
* * *
2452126 TTTAACTTTCTTTCTTTTTTCTTCT
1 TTTAAATTT-TTTCTTTTATATTCT
2452151 TT
1 TT
2452153 ATTTTCCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTAAATTTTTTCTTTTATATTCT
Found at i:2453673 original size:21 final size:20
Alignment explanation
Indices: 2453647--2453688 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2453637 TTATGAAAAA
2453647 TGGGTTTTTCATCTTCTTTTT
1 TGGG-TTTTCATCTTCTTTTT
* *
2453668 TGGGTTTTCTTTTTCTTTTT
1 TGGGTTTTCATCTTCTTTTT
2453688 T
1 T
2453689 CTTTAGGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.02, C:0.12, G:0.14, T:0.71
Consensus pattern (20 bp):
TGGGTTTTCATCTTCTTTTT
Found at i:2455983 original size:11 final size:11
Alignment explanation
Indices: 2455967--2455991 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2455957 ATTTTTTTAA
2455967 TTTAAAATACT
1 TTTAAAATACT
2455978 TTTAAAATACT
1 TTTAAAATACT
2455989 TTT
1 TTT
2455992 TTAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:2455998 original size:24 final size:26
Alignment explanation
Indices: 2455967--2456028 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
2455957 ATTTTTTTAA
*
2455967 TTTAAAATACTTTTAAA-AT-ACTTT
1 TTTAAAATACTTTTAAATATAAATTT
*
2455991 TTTAAAAT--TTTTAAATTTAAATTT
1 TTTAAAATACTTTTAAATATAAATTT
2456015 TTTAAAATACTTTT
1 TTTAAAATACTTTT
2456029 TTAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 7 0.22
23 1 0.03
24 20 0.62
26 4 0.12
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAAAATACTTTTAAATATAAATTT
Found at i:2456011 original size:15 final size:15
Alignment explanation
Indices: 2455991--2456020 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2455981 AAAATACTTT
2455991 TTTAAAATTTTTAAA
1 TTTAAAATTTTTAAA
*
2456006 TTTAAATTTTTTAAA
1 TTTAAAATTTTTAAA
2456021 ATACTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAAATTTTTAAA
Found at i:2456038 original size:36 final size:37
Alignment explanation
Indices: 2455954--2456070 Score: 161
Period size: 36 Copynumber: 3.2 Consensus size: 37
2455944 CCGAATATAA
*
2455954 TAAATTTTTTTAATTTAAAATACTTTTAAAATACTTTTT
1 TAAATTTTTTAAATTT-AAATA-TTTTAAAATACTTTTT
* *
2455993 TAAAATTTTTAAATTTAAATTTTTTAAAATACTTTTT
1 TAAATTTTTTAAATTTAAATATTTTAAAATACTTTTT
2456030 T-AATTTTTTAAATTTAAATATTTT-AAATAC--TTT
1 TAAATTTTTTAAATTTAAATATTTTAAAATACTTTTT
2456063 TAAATTTT
1 TAAATTTT
2456071 GTTTTAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
33 4 0.06
34 6 0.08
35 6 0.08
36 21 0.29
37 17 0.24
38 4 0.06
39 14 0.19
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (37 bp):
TAAATTTTTTAAATTTAAATATTTTAAAATACTTTTT
Found at i:2459802 original size:25 final size:25
Alignment explanation
Indices: 2459754--2459804 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2459744 TGAATGTTGG
**
2459754 TACTTAAACCAACATTAATTTTAAA
1 TACTTAAACCAACATTAAAATTAAA
**
2459779 TACTTAAATTAACATTAAAATTAAA
1 TACTTAAACCAACATTAAAATTAAA
2459804 T
1 T
2459805 TCAAGGACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (25 bp):
TACTTAAACCAACATTAAAATTAAA
Found at i:2464682 original size:14 final size:16
Alignment explanation
Indices: 2464658--2464691 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2464648 TTGAAACAAA
2464658 AAAAAAGTT-AAAAAG
1 AAAAAAGTTAAAAAAG
2464673 AAAAAA-TTAAAAAAG
1 AAAAAAGTTAAAAAAG
2464688 AAAA
1 AAAA
2464692 CCCTATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAAGTTAAAAAAG
Found at i:2471952 original size:28 final size:27
Alignment explanation
Indices: 2471852--2471953 Score: 75
Period size: 28 Copynumber: 3.7 Consensus size: 27
2471842 TTAATTTAAC
* * *
2471852 ATTTGGTACTTAAATTTAATTTTTTTCTA
1 ATTTGGTACCTAACTTT--TTTTTTCCTA
* **
2471881 ATTTAGTACCTAAACTTTTTTTGGCCTA
1 ATTTGGTACCT-AACTTTTTTTTTCCTA
*
2471909 ATTTGGTA-C--ACATTTTTTTTCCTA
1 ATTTGGTACCTAACTTTTTTTTTCCTA
*
2471933 ATTTGGCACCTAAGCTTTTTT
1 ATTTGGTACCTAA-CTTTTTT
2471954 AGGTTCAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
24 19 0.34
25 1 0.02
27 2 0.04
28 20 0.36
29 9 0.16
30 5 0.09
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.52
Consensus pattern (27 bp):
ATTTGGTACCTAACTTTTTTTTTCCTA
Found at i:2472410 original size:31 final size:31
Alignment explanation
Indices: 2472369--2472504 Score: 89
Period size: 31 Copynumber: 4.4 Consensus size: 31
2472359 AAAAAAGATT
*
2472369 AGGTATCAAATTAGGAAAAAGAGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAGAGTCAAGTTC
**** **
2472400 AGGTACCAAATT-GGATCCCGA-AAAAGATT-
1 AGGTACCAAATTAGGAAAAAGAGTCAAG-TTC
* * * * *
2472429 AAGTACCAACTTAAGAAGAAAAATGTCAAGTTT
1 AGGTACCAAATTAGGAA-AAAGA-GTCAAGTTC
* * *
2472462 AAGTATCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAGAGTCAAGTTC
2472493 AGGTACCAAATT
1 AGGTACCAAATT
2472505 GGATCCCGAA
Statistics
Matches: 74, Mismatches: 25, Indels: 12
0.67 0.23 0.11
Matches are distributed among these distances:
29 13 0.18
30 9 0.12
31 30 0.41
32 5 0.07
33 17 0.23
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (31 bp):
AGGTACCAAATTAGGAAAAAGAGTCAAGTTC
Found at i:2472478 original size:93 final size:93
Alignment explanation
Indices: 2472371--2472600 Score: 415
Period size: 93 Copynumber: 2.5 Consensus size: 93
2472361 AAAAGATTAG
*
2472371 GTATCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
1 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
2472436 AACTTAAGAAGAAAAATGTCAAGTTTAA
66 AACTTAAGAAGAAAAATGTCAAGTTTAA
2472464 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
1 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
2472529 AACTTAAGAAGAAAAATGTCAAGTTTAA
66 AACTTAAGAAGAAAAATGTCAAGTTTAA
* ** *
2472557 GTATCAAATTAGGAAAAAGTGTCAAATTTGGGTATCAAATTGGA
1 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGA
2472601 CCAAAAAATG
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 132 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (93 bp):
GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
AACTTAAGAAGAAAAATGTCAAGTTTAA
Found at i:2472592 original size:31 final size:30
Alignment explanation
Indices: 2472446--2472597 Score: 83
Period size: 31 Copynumber: 4.9 Consensus size: 30
2472436 AACTTAAGAA
*
2472446 GAAAAATGTCAAGTTTAAGTATCAAATTAG
1 GAAAAATGTCAAATTTAAGTATCAAATTAG
* * * *
2472476 GAAAAAGTGTCAAGTTCAGGTACCAAATT-G
1 GAAAAA-TGTCAAATTTAAGTATCAAATTAG
**** ** * * *
2472506 G-ATCCCGAAAAAGATTAAGTACCAACTTAAG
1 GAAAAATGTCAAA-TTTAAGTATCAAATT-AG
*
2472537 AAGAAAAATGTCAAGTTTAAGTATCAAATTAG
1 --GAAAAATGTCAAATTTAAGTATCAAATTAG
**
2472569 GAAAAAGTGTCAAATTTGGGTATCAAATT
1 GAAAAA-TGTCAAATTTAAGTATCAAATT
2472598 GGACCAAAAA
Statistics
Matches: 87, Mismatches: 27, Indels: 15
0.67 0.21 0.12
Matches are distributed among these distances:
28 3 0.03
29 12 0.14
30 14 0.16
31 39 0.45
32 2 0.02
33 13 0.15
34 4 0.05
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (30 bp):
GAAAAATGTCAAATTTAAGTATCAAATTAG
Found at i:2473350 original size:17 final size:17
Alignment explanation
Indices: 2473320--2473354 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2473310 CATTTAACTT
2473320 TTGTAAAAAATATTTAA
1 TTGTAAAAAATATTTAA
* *
2473337 TTGTATAAATTATTTAA
1 TTGTAAAAAATATTTAA
2473354 T
1 T
2473355 ATGCCGGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTGTAAAAAATATTTAA
Found at i:2478976 original size:31 final size:32
Alignment explanation
Indices: 2478922--2478985 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
2478912 TAAAGTTTCA
2478922 TGTATATATTTGAACCATAATCAAAATTTGATG
1 TGTATATATTTGAACCATAATCAAAATTT-ATG
*
2478955 TGTATA-ATTT-ACACCA-AATCAATATTTATG
1 TGTATATATTTGA-ACCATAATCAAAATTTATG
2478985 T
1 T
2478986 ATCAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.14
31 11 0.38
32 8 0.28
33 6 0.21
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (32 bp):
TGTATATATTTGAACCATAATCAAAATTTATG
Found at i:2482917 original size:90 final size:90
Alignment explanation
Indices: 2482794--2483012 Score: 210
Period size: 95 Copynumber: 2.4 Consensus size: 90
2482784 TAAATTTTTA
* * * * **
2482794 TTTTTTT-ACTTAATTGGATATTTAAATTTTCAAAATACATTAAAAAGGCCCTTAAA-TTTTTTT
1 TTTTTTTCACTTAATTGGATACTTGAACTTTCAAAATACATCAAAAAGGCCCACAAATTTTTTTT
* * *
2482857 AAGAAA-AGTAATTAAACCATTGCTT
66 AA-AAAGAGCAATTAAACCACTGATT
* * *
2482882 TTTTTTTCCACTTAATTGGGTACTTGAACTTTCAAAATATATCAAAAAGGCTCACAAACTTTTTT
1 TTTTTTT-CACTTAATTGGATACTTGAACTTTCAAAATACATCAAAAAGGCCCACAAA----TTT
*
2482947 TTTTTAAAAAGAGCAATTAAATCACTGATT
61 TTTTTAAAAAGAGCAATTAAACCACTGATT
* * *
2482977 TTTTTTTGCACTCAATTGGTTACTTGAACTATCAAA
1 TTTTTTT-CACTTAATTGGATACTTGAACTTTCAAA
2483013 TGCTTCAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
88 7 0.07
90 40 0.38
94 3 0.03
95 56 0.53
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (90 bp):
TTTTTTTCACTTAATTGGATACTTGAACTTTCAAAATACATCAAAAAGGCCCACAAATTTTTTTT
AAAAAGAGCAATTAAACCACTGATT
Found at i:2483207 original size:9 final size:9
Alignment explanation
Indices: 2483130--2483225 Score: 70
Period size: 9 Copynumber: 10.4 Consensus size: 9
2483120 CATGTGGCAA
2483130 AAAAATTAT
1 AAAAATTAT
2483139 AAAAA--AT
1 AAAAATTAT
*
2483146 AAAAATCAAT
1 AAAAAT-TAT
*
2483156 AAAAGTTAT
1 AAAAATTAT
*
2483165 AACAATTAT
1 AAAAATTAT
* *
2483174 TAAATTATATT
1 AAAAAT-TA-T
* *
2483185 AAAAAATAG
1 AAAAATTAT
2483194 AAAAATTTAT
1 AAAAA-TTAT
*
2483204 AAAAATCAT
1 AAAAATTAT
2483213 AAAAATTAT
1 AAAAATTAT
2483222 AAAA
1 AAAA
2483226 TGCATAAAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
7 7 0.11
9 37 0.56
10 18 0.27
11 4 0.06
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2483208 original size:19 final size:19
Alignment explanation
Indices: 2483184--2483225 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2483174 TAAATTATAT
2483184 TAAAAAAT-AGAAAAATT-
1 TAAAAAATCAGAAAAATTA
*
2483201 TATAAAAATCATAAAAATTA
1 TA-AAAAATCAGAAAAATTA
2483221 TAAAA
1 TAAAA
2483226 TGCATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.10
18 6 0.29
19 11 0.52
20 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAAATCAGAAAAATTA
Found at i:2483231 original size:18 final size:19
Alignment explanation
Indices: 2483194--2483235 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
2483184 TAAAAAATAG
2483194 AAAAATTTATAAAAATCAT
1 AAAAATTTATAAAAATCAT
2483213 AAAAA-TTAT-AAAATGCAT
1 AAAAATTTATAAAAAT-CAT
2483231 AAAAA
1 AAAAA
2483236 ATGTCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 12 0.55
19 5 0.23
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTTATAAAAATCAT
Found at i:2483235 original size:19 final size:19
Alignment explanation
Indices: 2483182--2483237 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
2483172 ATTAAATTAT
*
2483182 ATTA-AAAAAT-AGAAAAA
1 ATTATAAAAATCATAAAAA
*
2483199 TTTATAAAAATCAT-AAAA
1 ATTATAAAAATCATAAAAA
2483217 ATTAT-AAAATGCATAAAAA
1 ATTATAAAAAT-CATAAAAA
2483236 AT
1 AT
2483238 GTCATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.25
18 17 0.53
19 7 0.22
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (19 bp):
ATTATAAAAATCATAAAAA
Found at i:2483446 original size:19 final size:20
Alignment explanation
Indices: 2483424--2483467 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2483414 TAAATATATT
2483424 TTTACAAATTTTAT-ATTTC
1 TTTACAAATTTTATAATTTC
** *
2483443 TTTACATTTTTTATAATTTT
1 TTTACAAATTTTATAATTTC
2483463 TTTAC
1 TTTAC
2483468 GACTTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTACAAATTTTATAATTTC
Found at i:2483484 original size:29 final size:29
Alignment explanation
Indices: 2483451--2483512 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
2483441 TCTTTACATT
2483451 TTTTATAATTTTTTTACGA-CTTTATAAAA
1 TTTTATAA-TTTTTTACGATCTTTATAAAA
* *
2483480 TTTTATAATTTTTTATGATTTTTATAAAA
1 TTTTATAATTTTTTACGATCTTTATAAAA
2483509 TTTT
1 TTTT
2483513 TACGATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTTATAATTTTTTACGATCTTTATAAAA
Done.