Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 131 of 135
Found at i:42450352 original size:31 final size:29
Alignment explanation
Indices: 42450297--42450367 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
42450287 AAAGTTTGAA
*
42450297 TTAATTTTAAATTCATTTTTAAATTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
42450326 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
42450357 TTAAATTTAAA
1 TTAAATTTAAA
42450368 CTTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:42450364 original size:11 final size:11
Alignment explanation
Indices: 42450295--42450365 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
42450285 TTAAAGTTTG
*
42450295 AATTAATTTTA
1 AATTTATTTTA
*
42450306 AATTCATTTTTA
1 AATTTA-TTTTA
*
42450318 AATTTATCTTA
1 AATTTATTTTA
*
42450329 AATTTAAATTT-
1 AATTT-ATTTTA
*
42450340 -ACTTA-TTTA
1 AATTTATTTTA
42450349 AATTTATTTTA
1 AATTTATTTTA
42450360 AATTTA
1 AATTTA
42450366 AACTTAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.15
11 24 0.50
12 13 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:42450376 original size:17 final size:17
Alignment explanation
Indices: 42450344--42450378 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42450334 AAATTTACTT
* *
42450344 ATTTAAATTTATTTTAA
1 ATTTAAACTTAATTTAA
42450361 ATTTAAACTTAATTTAA
1 ATTTAAACTTAATTTAA
42450378 A
1 A
42450379 ATAATATTAA
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:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAACTTAATTTAA
Found at i:42450483 original size:29 final size:28
Alignment explanation
Indices: 42450417--42450489 Score: 128
Period size: 28 Copynumber: 2.5 Consensus size: 28
42450407 CAATGTTCGT
42450417 TTACAAAAAAGGCCCAAATTAAAGGCCCGA
1 TTAC-AAAAA-GCCCAAATTAAAGGCCCGA
42450447 TTACAAAAAGCCCAAATTAAAGGCCCGA
1 TTACAAAAAGCCCAAATTAAAGGCCCGA
42450475 TTACAAAAAGCCCAA
1 TTACAAAAAGCCCAA
42450490 TTGGGCTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 34 0.79
29 5 0.12
30 4 0.09
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.14
Consensus pattern (28 bp):
TTACAAAAAGCCCAAATTAAAGGCCCGA
Found at i:42451026 original size:29 final size:29
Alignment explanation
Indices: 42450916--42451034 Score: 114
Period size: 30 Copynumber: 4.0 Consensus size: 29
42450906 GACAGGTACA
* * *
42450916 TTCAAAAATTATATTTTGAACCCAAAATTT
1 TTCAAAAATTACATTTTGACCCCAAAA-CT
* *
42450946 TTCCAAAATTACATTTTGACTCCAAAACTT
1 TTCAAAAATTACATTTTGACCCCAAAAC-T
* * * *
42450976 TTCTAAAATTATACTTTAACCCCAAAACT
1 TTCAAAAATTACATTTTGACCCCAAAACT
*
42451005 TTCAAAAATTACCATTTT-ACCCCCAAACT
1 TTCAAAAATTA-CATTTTGACCCCAAAACT
42451034 T
1 T
42451035 CCCTAAATCC
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
29 22 0.30
30 51 0.70
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (29 bp):
TTCAAAAATTACATTTTGACCCCAAAACT
Found at i:42451041 original size:59 final size:60
Alignment explanation
Indices: 42450920--42451041 Score: 142
Period size: 59 Copynumber: 2.0 Consensus size: 60
42450910 GGTACATTCA
* * * * **
42450920 AAAATTATATTTTGAACCCAAAATTTTTCCAAAATTACATTTTGACTCCAAAACTTTTCT
1 AAAATTATACTTTGAACCCAAAATCTTTCAAAAATTACATTTTGACCCCAAAACTTCCCT
*
42450980 AAAATTATACTTT-AACCCCAAAA-CTTTCAAAAATTACCATTTT-ACCCCCAAACTTCCCT
1 AAAATTATACTTTGAA-CCCAAAATCTTTCAAAAATTA-CATTTTGACCCCAAAACTTCCCT
42451039 AAA
1 AAA
42451042 TCCCATTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
59 28 0.53
60 25 0.47
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAATTATACTTTGAACCCAAAATCTTTCAAAAATTACATTTTGACCCCAAAACTTCCCT
Found at i:42451070 original size:59 final size:58
Alignment explanation
Indices: 42451007--42451201 Score: 185
Period size: 59 Copynumber: 3.3 Consensus size: 58
42450997 CCAAAACTTT
* *
42451007 CAAAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCCTGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCTGATTTCAC
* *** * * * * * * **
42451066 CAAAACTTACCGCCTTGCCTCCAAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCTGATTTCAC
* * * * *
42451125 CAAAATTTACCATTTTATTCCCCAAACTTTTCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA-CCCCCAAACTTTCCAAATTCCATTTTTAACCCTGATTTCAC
42451183 CAAAAATTACCATTTTACC
1 CAAAAATTACCATTTTACC
42451202 ACTAAAAACC
Statistics
Matches: 102, Mismatches: 33, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
57 1 0.01
58 16 0.16
59 74 0.73
60 11 0.11
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTCCATTTTTAACCCTGATTTCAC
Found at i:42460367 original size:17 final size:18
Alignment explanation
Indices: 42460322--42460376 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
42460312 ATCTTAATTC
*
42460322 TAAAAAATTAAAAATGTA
1 TAAAAAATTAAAAATATA
***
42460340 TAAAGTTTTAAAAAT-TA
1 TAAAAAATTAAAAATATA
42460357 TAAAAAATTAAAAATATA
1 TAAAAAATTAAAAATATA
42460375 TA
1 TA
42460377 TATAAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
TAAAAAATTAAAAATATA
Found at i:42471094 original size:4 final size:4
Alignment explanation
Indices: 42471087--42471116 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
42471077 ACACACACAC
42471087 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
42471117 CTTCATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:42475046 original size:315 final size:312
Alignment explanation
Indices: 42474477--42475108 Score: 1183
Period size: 315 Copynumber: 2.0 Consensus size: 312
42474467 AAATAATTTT
42474477 AATTTCTACGCTAACATGTCTAATTAGTAATTTAATTAAACTATAATACAATGAATCCTAAGGTG
1 AATTTCTACGCTAACATGTCTAATTAGTAATTTAATTAAACTATAATACAATGAATCCTAAGGTG
42474542 ACGAAAAATCATATTTTATAAAAATAAATAAAAAGCATAAAAACAAAGGGGAAACAAATTGCAGA
66 ACGAAAAATCATATTTTATAAAAATAAATAAAAAGCATAAAAACAAAGGGGAAACAAATTGCAGA
*
42474607 TTTTATCAAATCTAAGGACAAAAGATTAACTTACTTTGGTGGTCATAACTAACTTCTATTTTGGG
131 TTTTATCAAATCTAAGGACAAAAGATTAACTTACTTTGGTGGTCATAACTAACTTCTATTTCGGG
42474672 TTCTATCCAATCAACTAATCATTAACCTATTATGATCTCTCGATATTCCATTAAACTAATGAGTC
196 TTCTATCCAATCAACTAATCATTAACCTATTATGATCTCTCGATATTCCATTAAACTAATGAGTC
* *
42474737 GACAATAACTACTTATCTCTCGACCTCACAGTCCAAAGCGAATTGAGGTACC
261 GACAATAACTACTTATCTCTCGACCTCACAATCCAAACCGAATTGAGGTACC
42474789 AATTTCTACGCTAACATGTCTAATTAGTAATTTAATTAAACTATAATACAATGAATCCTAAGGTG
1 AATTTCTACGCTAACATGTCTAATTAGTAATTTAATTAAACTATAATACAATGAATCCTAAGGTG
42474854 ACGAAAAATCATATTTTATAAAAATAAATAAAAAGCATAAAAACAAAGAAGGGGAAACAAATTGC
66 ACGAAAAATCATATTTTATAAAAATAAATAAAAAGCATAAAAAC--A-AAGGGGAAACAAATTGC
*
42474919 AGATTTTATCAAATCTAAGGACAAAAGATTAACTTGCTTTGGTGGTCATAACTAACTTCTATTTC
128 AGATTTTATCAAATCTAAGGACAAAAGATTAACTTACTTTGGTGGTCATAACTAACTTCTATTTC
42474984 GGGTTCTATCCAATCAACTAATCATTAACCTATTATGATCTCTCGATATTCCATTAAACTAATGA
193 GGGTTCTATCCAATCAACTAATCATTAACCTATTATGATCTCTCGATATTCCATTAAACTAATGA
* *
42475049 GTCGGCAATAACTACTTATCTCTCGACCTCACAATCCAGACCGAATTGAGGTACC
258 GTCGACAATAACTACTTATCTCTCGACCTCACAATCCAAACCGAATTGAGGTACC
42475104 AATTT
1 AATTT
42475109 TAGGATCATT
Statistics
Matches: 311, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
312 109 0.35
314 1 0.00
315 201 0.65
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (312 bp):
AATTTCTACGCTAACATGTCTAATTAGTAATTTAATTAAACTATAATACAATGAATCCTAAGGTG
ACGAAAAATCATATTTTATAAAAATAAATAAAAAGCATAAAAACAAAGGGGAAACAAATTGCAGA
TTTTATCAAATCTAAGGACAAAAGATTAACTTACTTTGGTGGTCATAACTAACTTCTATTTCGGG
TTCTATCCAATCAACTAATCATTAACCTATTATGATCTCTCGATATTCCATTAAACTAATGAGTC
GACAATAACTACTTATCTCTCGACCTCACAATCCAAACCGAATTGAGGTACC
Found at i:42487466 original size:37 final size:37
Alignment explanation
Indices: 42487423--42487499 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
42487413 ACTTGATCCA
42487423 AGAAAAGCTCAAACTCAATTAACAAGATCAACACAAG
1 AGAAAAGCTCAAACTCAATTAACAAGATCAACACAAG
*
42487460 AGAAAAGCTCAAACTCAATTAACAAGATCAACACGAG
1 AGAAAAGCTCAAACTCAATTAACAAGATCAACACAAG
42487497 AGA
1 AGA
42487500 TGTTTGCCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (37 bp):
AGAAAAGCTCAAACTCAATTAACAAGATCAACACAAG
Found at i:42488923 original size:31 final size:32
Alignment explanation
Indices: 42488887--42488955 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
42488877 TTATAAAACG
*
42488887 GTCACTAAACTATTCGAAAGTTTTCA-TTTAA
1 GTCACTAAACTACTCGAAAGTTTTCATTTTAA
* * *
42488918 GTCACTGAATTACTCGAAAGTTTTTATTTTAA
1 GTCACTAAACTACTCGAAAGTTTTCATTTTAA
42488950 -TCACTA
1 GTCACTA
42488956 GGCTGTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (32 bp):
GTCACTAAACTACTCGAAAGTTTTCATTTTAA
Found at i:42492800 original size:43 final size:43
Alignment explanation
Indices: 42492704--42492847 Score: 134
Period size: 43 Copynumber: 3.3 Consensus size: 43
42492694 CGTTTATAAA
* * *
42492704 AAAAACGCCGCAAAAGAAC-ATGATCTTTAGCGGCGCTTTACCT
1 AAAAACGCCGCTAAAG-ACTATGTTCTTTAGCGGCGCTTTACCC
*
42492747 ACAAACGCCGCTAAAGACTATGTTCTTTAGCGGCGC-TTACTCC
1 AAAAACGCCGCTAAAGACTATGTTCTTTAGCGGCGCTTTAC-CC
* * **
42492790 AAAAATGCCGCTATAA-A-TAGTGTTCTTTAGCGGCGTTTTTTCC
1 AAAAACGCCGCTA-AAGACTA-TGTTCTTTAGCGGCGCTTTACCC
* *
42492833 ACAAACGTCGCTAAA
1 AAAAACGCCGCTAAA
42492848 ATTAACAGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
42 10 0.12
43 70 0.83
44 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACTATGTTCTTTAGCGGCGCTTTACCC
Found at i:42498952 original size:22 final size:20
Alignment explanation
Indices: 42498894--42498957 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 20
42498884 GATTATTTTT
42498894 AATAATTAAATATTTAATTA
1 AATAATTAAATATTTAATTA
*
42498914 AATAAGTAAATA--TAATTA
1 AATAATTAAATATTTAATTA
42498932 AATAATTAAATATTTTGAATTA
1 AATAATTAAATA-TTT-AATTA
42498954 AATA
1 AATA
42498958 TTTGGGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 17 0.45
20 11 0.29
21 1 0.03
22 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AATAATTAAATATTTAATTA
Found at i:42499044 original size:34 final size:33
Alignment explanation
Indices: 42498988--42499306 Score: 214
Period size: 34 Copynumber: 9.6 Consensus size: 33
42498978 TAAATAAATA
* * *
42498988 AATAAATAATTAATTAATTAATTGGATTGATTT
1 AATAATTAAATAATTAATTAATTGGGTTGATTT
* *
42499021 AACTAATTAAATAATTAAGTAATTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTG-ATTT
* *
42499056 AATAATTAAATATTTAATTAA--------A-TA
1 AATAATTAAATAATTAATTAATTGGGTTGATTT
*
42499080 AATAATTAATTAATTAATTAATTGGGTTGATTT
1 AATAATTAAATAATTAATTAATTGGGTTGATTT
* *
42499113 AACTAATTAAATAATTAAGTAATTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTG-ATTT
* * ** **
42499148 AATAATTAAATATTTAATTAAAT-AATT-AAAT
1 AATAATTAAATAATTAATTAATTGGGTTGATTT
* *
42499179 -ATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTT
1 AATAATTAAATA-ATT-AATT--A-A-TTGGGTTG-ATTT
* *
42499218 AATATTTATATAATTAATTAATTGGGTTGATTT
1 AATAATTAAATAATTAATTAATTGGGTTGATTT
* * *
42499251 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTG-ATTT
42499286 AATAATTAAAT-ATATAATTAA
1 AATAATTAAATAAT-TAATTAA
42499307 ATAATTAAAT
Statistics
Matches: 220, Mismatches: 40, Indels: 51
0.71 0.13 0.16
Matches are distributed among these distances:
24 20 0.09
30 11 0.05
31 4 0.02
32 5 0.02
33 14 0.06
34 129 0.59
35 17 0.08
36 2 0.01
37 2 0.01
38 4 0.02
39 3 0.01
40 9 0.04
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.47
Consensus pattern (33 bp):
AATAATTAAATAATTAATTAATTGGGTTGATTT
Found at i:42499089 original size:4 final size:4
Alignment explanation
Indices: 42499054--42499102 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
42499044 TGGGTTGTTT
* * * *
42499054 TTAA -TAA TTAA ATAT TTAA TTAA ATAA ATAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
42499101 TT
1 TT
42499103 GGGTTGATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:42499095 original size:92 final size:92
Alignment explanation
Indices: 42498972--42499186 Score: 376
Period size: 92 Copynumber: 2.3 Consensus size: 92
42498962 GGTTATTTTT
* *
42498972 AATATTTAAATAAATAAATAAATAATTAATTAATTAATTGGATTGATTTAACTAATTAAATAATT
1 AATATTTAATTAAATAAATAATTAATTAATTAATTAATTGGATTGATTTAACTAATTAAATAATT
42499037 AAGTAATTGGGTTGTTTTTAATAATTA
66 AAGTAATTGGGTTGTTTTTAATAATTA
*
42499064 AATATTTAATTAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAATAATT
1 AATATTTAATTAAATAAATAATTAATTAATTAATTAATTGGATTGATTTAACTAATTAAATAATT
42499129 AAGTAATTGGGTTGTTTTTAATAATTA
66 AAGTAATTGGGTTGTTTTTAATAATTA
*
42499156 AATATTTAATTAAATAATTAAATATAATTAA
1 AATATTTAATTAAATAAAT-AAT-TAATTAA
42499187 ATATTTTGAA
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
92 107 0.91
93 3 0.03
94 7 0.06
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (92 bp):
AATATTTAATTAAATAAATAATTAATTAATTAATTAATTGGATTGATTTAACTAATTAAATAATT
AAGTAATTGGGTTGTTTTTAATAATTA
Found at i:42499173 original size:20 final size:18
Alignment explanation
Indices: 42499148--42499189 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
42499138 GGTTGTTTTT
42499148 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
42499168 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
42499186 AATA
1 AATA
42499190 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:42499220 original size:70 final size:69
Alignment explanation
Indices: 42499125--42499546 Score: 300
Period size: 70 Copynumber: 5.9 Consensus size: 69
42499115 CTAATTAAAT
* * *
42499125 AATTAAGTAATTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATAATTAAATA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAATTAAATAATT-AATATAATTAAATA
42499190 TTTTG
65 TTTTG
* * * ** * * * *
42499195 AATTAAATATTTGGGTTGTTTTTAATATTTATATAATTAATTAATTGGGTTGATTTAACTAATTA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAATTAAAT-AATTAATATAATTAAATA
**
42499260 -AAT-
65 TTTTG
*
42499263 AATTAAGTATTTGGGTTGTTTTTAATAATTAAAT-ATATAATTAAATAATTAAATATAATTAAAT
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATAAT-TAATTAAATAATT-AATATAATTAAAT
42499327 ATTTTG
64 ATTTTG
* * * * *
42499333 AATTAAATATTTGAGTTGTTTTTCATATTTATATAATTAATTAATTAATTAAT-TAATTAATTGG
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAATTAAATAATTAATATAATTAA----
*
42499397 GTTGATTTAACT-
62 -AT-ATTT---TG
* ** ** * * *
42499409 AATTAAATAATTAAGTAT-TTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATAT
1 AATTAAATATTTGGGT-TGTT---TT-TAATAATTAAAT--A-A-TTAATTAAATAATT-AATAT
42499473 AATTAAATATTTTG
56 AATTAAATATTTTG
* * *
42499487 AATTAAATATTTGGGTTGTTTTTAATATTTATATAATTAATTAATTAATTAAT-TAATTAA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAATTAAATAATTAATATAATTAA
42499547 TTGTGTTGAT
Statistics
Matches: 269, Mismatches: 55, Indels: 58
0.70 0.14 0.15
Matches are distributed among these distances:
67 4 0.01
68 63 0.23
69 8 0.03
70 104 0.39
71 5 0.02
72 1 0.00
73 1 0.00
74 9 0.03
75 2 0.01
76 16 0.06
77 4 0.01
78 15 0.06
79 2 0.01
80 9 0.03
81 1 0.00
82 1 0.00
83 1 0.00
84 13 0.05
85 3 0.01
86 7 0.03
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (69 bp):
AATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAATTAAATAATTAATATAATTAAATAT
TTTG
Found at i:42499231 original size:104 final size:103
Alignment explanation
Indices: 42499058--42499268 Score: 250
Period size: 104 Copynumber: 2.0 Consensus size: 103
42499048 TTGTTTTTAA
* *
42499058 TAATTAAATATTTAATTAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAA
1 TAATTAAATATTAAATTAAATAAATAATT-ATTAATTAAATAATTGGGTTGATTTAACTAATTAA
* *
42499123 ATAATTAAGTAATTGGGTTGTTTTTAA-TAATTAAATATT
65 ATAATTAAGTAATTGGGTTG-ATTTAACTAATTAAATAAT
* * * *
42499162 TAATTAAATAATTAAATATAATTAAAT-ATT-TTGAATTAAATATTTGGGTTGTTTTTAA-TATT
1 TAATTAAAT-ATTAAAT-TAAATAAATAATTATT-AATTAAATAATTGGGTTG-ATTTAACTAAT
* *
42499224 TATATAATTAATTAATTGGGTTGATTTAACTAATTAAATAAT
62 TAAATAATTAAGTAATTGGGTTGATTTAACTAATTAAATAAT
42499266 TAA
1 TAA
42499269 GTATTTGGGT
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
103 7 0.08
104 63 0.68
105 14 0.15
106 8 0.09
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.47
Consensus pattern (103 bp):
TAATTAAATATTAAATTAAATAAATAATTATTAATTAAATAATTGGGTTGATTTAACTAATTAAA
TAATTAAGTAATTGGGTTGATTTAACTAATTAAATAAT
Found at i:42499311 original size:20 final size:18
Alignment explanation
Indices: 42499286--42499327 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 18
42499276 GGTTGTTTTT
42499286 AATAATTAAATATATAATTA
1 AATAATT-AA-ATATAATTA
42499306 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
42499324 AATA
1 AATA
42499328 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:42499375 original size:4 final size:4
Alignment explanation
Indices: 42499366--42499394 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
42499356 CATATTTATA
42499366 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
42499395 GGGTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:42499411 original size:154 final size:154
Alignment explanation
Indices: 42499228--42499920 Score: 1085
Period size: 154 Copynumber: 4.5 Consensus size: 154
42499218 AATATTTATA
42499228 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
1 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
* *
42499293 AAATATATAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTGTTTTTCA
66 AAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTGTTTTTAA
*
42499358 TATTTATATAATTAATTAATTAAT
131 TATTTATATAATTAAATAATTAAT
42499382 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
1 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
*
42499447 AAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTTAA
66 AAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTGTTTTTAA
*
42499512 TATTTATATAATTAATTAATTAAT
131 TATTTATATAATTAAATAATTAAT
*
42499536 TAATTAATTAATTGTGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
1 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
42499601 AAATATTTAATTAAATAATTAAATATAATTAAATAATTAAATATATTGAATTAAATATTTGAGTT
66 AAATATTTAATTAAATAATTAAATATAATT--A-AA-T--AT-T-TTGAATTAAATATTTGAGTT
* * *
42499666 ATTTTAAATA-TT-TA-AA-TAAATAAATAAT
123 GTTTTTAATATTTATATAATTAAATAATTAAT
* * *
42499694 TAATTAATTAATTAGGTTGATTTAAATAATTAAATAATTCAGTATTTGGGTTGTTTTTAATAATT
1 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
*
42499759 AAATATTTAATTAAATAATT-AA-ATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTTAA
66 AAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTGTTTTTAA
* *
42499822 TATTTAAATAAATAAATAATTAAT
131 TATTTATATAATTAAATAATTAAT
* * **
42499846 TAATTAATTAATTGGGTTGATTTAAGTAATTAAATAATGAAGTATTTGGGTTGTTTTTTCTAATT
1 TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAA-T
42499911 TAAA-ATTTAA
65 TAAATATTTAA
42499921 AAAAAATTCA
Statistics
Matches: 502, Mismatches: 24, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
148 27 0.05
149 3 0.01
150 3 0.01
151 2 0.00
152 75 0.15
153 7 0.01
154 246 0.49
156 7 0.01
157 4 0.01
158 92 0.18
159 2 0.00
160 4 0.01
161 3 0.01
162 27 0.05
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (154 bp):
TAATTAATTAATTGGGTTGATTTAACTAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATT
AAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTGTTTTTAA
TATTTATATAATTAAATAATTAAT
Found at i:42499420 original size:34 final size:34
Alignment explanation
Indices: 42499388--42499460 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
42499378 TAATTAATTA
42499388 ATTAATTGGGTTG-ATTTAACTAATTAAATAATTA
1 ATTAATTGGGTTGTATTTAA-TAATTAAATAATTA
* * * *
42499422 AGTATTTGGGTTGTTTTTAATAATTAAATATTTA
1 ATTAATTGGGTTGTATTTAATAATTAAATAATTA
42499456 ATTAA
1 ATTAA
42499461 ATAATTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.48
Consensus pattern (34 bp):
ATTAATTGGGTTGTATTTAATAATTAAATAATTA
Found at i:42499465 original size:20 final size:18
Alignment explanation
Indices: 42499440--42499481 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
42499430 GGTTGTTTTT
42499440 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
42499460 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
42499478 AATA
1 AATA
42499482 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:42499529 original size:4 final size:4
Alignment explanation
Indices: 42499520--42499548 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
42499510 AATATTTATA
42499520 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
42499549 GTGTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:42499566 original size:34 final size:34
Alignment explanation
Indices: 42499542--42499614 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
42499532 TAATTAATTA
*
42499542 ATTAATTGTGTTG-ATTTAACTAATTAAATAATTA
1 ATTAATTGGGTTGTATTTAA-TAATTAAATAATTA
* * * *
42499576 AGTATTTGGGTTGTTTTTAATAATTAAATATTTA
1 ATTAATTGGGTTGTATTTAATAATTAAATAATTA
42499610 ATTAA
1 ATTAA
42499615 ATAATTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.49
Consensus pattern (34 bp):
ATTAATTGGGTTGTATTTAATAATTAAATAATTA
Found at i:42499652 original size:22 final size:21
Alignment explanation
Indices: 42499594--42499657 Score: 91
Period size: 18 Copynumber: 3.2 Consensus size: 21
42499584 GGTTGTTTTT
42499594 AATAATTAAATAT-TTAATTA
1 AATAATTAAATATATTAATTA
42499614 AATAATT-AA-ATA-TAATTA
1 AATAATTAAATATATTAATTA
42499632 AATAATTAAATATATTGAATTA
1 AATAATTAAATATATT-AATTA
42499654 AATA
1 AATA
42499658 TTTGAGTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
18 15 0.38
19 4 0.10
20 10 0.26
21 1 0.03
22 9 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAATTAAATATATTAATTA
Found at i:42499768 original size:8 final size:8
Alignment explanation
Indices: 42499766--42499791 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
42499756 ATTAAATATT
42499766 TAATTAAA
1 TAATTAAA
42499774 TAATTAAA
1 TAATTAAA
42499782 TAATTAAA
1 TAATTAAA
42499790 TA
1 TA
42499792 TTTTGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:42499771 original size:12 final size:12
Alignment explanation
Indices: 42499754--42499808 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 12
42499744 TTGTTTTTAA
42499754 TAATTAAATATT
1 TAATTAAATATT
42499766 TAATTAAATAATT
1 TAATTAAAT-ATT
42499779 AAATAATTAAATATTT
1 ---TAATTAAATA-TT
42499795 TGAATTAAATATT
1 T-AATTAAATATT
42499808 T
1 T
42499809 GGGTTGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.24
13 7 0.19
14 9 0.24
15 1 0.03
16 11 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:42499864 original size:50 final size:47
Alignment explanation
Indices: 42499772--42499882 Score: 125
Period size: 50 Copynumber: 2.3 Consensus size: 47
42499762 TATTTAATTA
* * *
42499772 AATAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTT
1 AATAATTAAATAAATAAATATTTTGAATTAAATAATTGGGTTG-ATTT
* *
42499820 AATATTTAAATAAATAAATAATTAATT-AATTAATTAATTGGGTTGATTT
1 AATAATTAAATAAATAAAT-ATT--TTGAATTAAATAATTGGGTTGATTT
42499869 AAGTAATTAAATAA
1 AA-TAATTAAATAA
42499883 TGAAGTATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
48 17 0.32
49 8 0.15
50 26 0.49
51 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (47 bp):
AATAATTAAATAAATAAATATTTTGAATTAAATAATTGGGTTGATTT
Found at i:42502245 original size:24 final size:24
Alignment explanation
Indices: 42502218--42502291 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
42502208 CTTTTCCATA
42502218 AGCGCCGCTATTGCTTAGACTTTT
1 AGCGCCGCTATTGCTTAGACTTTT
* * *
42502242 AGCGGCGCT-TT--TT---C-ATA
1 AGCGCCGCTATTGCTTAGACTTTT
42502259 AGCGCCGCTATTGCTTAGACTTTT
1 AGCGCCGCTATTGCTTAGACTTTT
*
42502283 AGCGGCGCT
1 AGCGCCGCT
42502292 TTTCCATATG
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
20 2 0.06
21 2 0.06
23 3 0.08
24 17 0.47
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (24 bp):
AGCGCCGCTATTGCTTAGACTTTT
Found at i:42502259 original size:41 final size:41
Alignment explanation
Indices: 42502197--42502480 Score: 244
Period size: 41 Copynumber: 6.9 Consensus size: 41
42502187 AATGTAAAAA
*
42502197 TTTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCT-TAGAC
1 TTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTCT-GAC
42502238 TTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCT-TAGAC
1 TTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTCT-GAC
* * *
42502279 TTTTAGCGGCGCTTTTCCATATGCGCCGCTATTGATCTGA-
1 TTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTCTGAC
* * * *
42502319 TCTTTAGCGGTG-TTTATCGAAAAGCGCCGCTATTTCT-TGGA-
1 T-TTTAGCGGCGCTTTTTC-ATAAGCGCCGCTATTGCTCT-GAC
* * * * *
42502360 TCTTTAGCGGCGCTTTTACAAAAGCGTCACTAATT-CTCTTAC
1 T-TTTAGCGGCGCTTTTTCATAAGCGCCGCT-ATTGCTCTGAC
* * *
42502402 CTTTAGCGGCGC-TTTTCAATAAACGCCGCTAATT-CTCTTAC
1 TTTTAGCGGCGCTTTTTC-ATAAGCGCCGCT-ATTGCTCTGAC
* ** *
42502443 CTTTAGCGGCGCTTTTAAATAAACGCCGCTATTGCTCT
1 TTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTCT
42502481 ATCTTTTGTG
Statistics
Matches: 207, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
40 13 0.06
41 182 0.88
42 12 0.06
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTCTGAC
Found at i:42502470 original size:123 final size:123
Alignment explanation
Indices: 42502198--42502478 Score: 295
Period size: 123 Copynumber: 2.3 Consensus size: 123
42502188 ATGTAAAAAT
** * *
42502198 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTTAGACTTTTAGCGGCGCTTTTTCATAAGCG
1 TTTAGCGGCGCTTTTAAATAAGCGCCGCTATTGCTTAGACTTTTAGCGGCGCTTTTACAAAAGCG
* * * ** *
42502263 CCGCTATTGCTTAGACTTTTAGCGGCGCTTTTCCATATGCGCCGCTATTGATCTGATC
66 CCACTATTGCTTAGACCTTTAGCGGCGCTTTTCAATAAACGCCGCTATTGATCTGACC
* * * *
42502321 TTTAGCGGTG-TTTATCGAA-AAGCGCCGCTATTTCTTGGA-TCTTTAGCGGCGCTTTTACAAAA
1 TTTAGCGGCGCTTT-T-AAATAAGCGCCGCTATTGCTTAGACT-TTTAGCGGCGCTTTTACAAAA
* * * *
42502383 GCGTCACTAATT-CTCT-TACCTTTAGCGGCGCTTTTCAATAAACGCCGCTAATT-CTCTTACC
63 GCGCCACT-ATTGCT-TAGACCTTTAGCGGCGCTTTTCAATAAACGCCGCT-ATTGATCTGACC
*
42502444 TTTAGCGGCGCTTTTAAATAAACGCCGCTATTGCT
1 TTTAGCGGCGCTTTTAAATAAGCGCCGCTATTGCT
42502479 CTATCTTTTG
Statistics
Matches: 129, Mismatches: 21, Indels: 16
0.78 0.13 0.10
Matches are distributed among these distances:
122 6 0.05
123 112 0.87
124 11 0.09
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (123 bp):
TTTAGCGGCGCTTTTAAATAAGCGCCGCTATTGCTTAGACTTTTAGCGGCGCTTTTACAAAAGCG
CCACTATTGCTTAGACCTTTAGCGGCGCTTTTCAATAAACGCCGCTATTGATCTGACC
Found at i:42511801 original size:15 final size:15
Alignment explanation
Indices: 42511781--42511832 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
42511771 ACTGCAAAAC
42511781 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
42511796 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
42511815 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
42511830 ATT
1 ATT
42511833 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:42517837 original size:13 final size:13
Alignment explanation
Indices: 42517821--42517845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42517811 TCCTTTAATT
42517821 TCTTCTTTTTGTC
1 TCTTCTTTTTGTC
42517834 TCTTCTTTTTGT
1 TCTTCTTTTTGT
42517846 TTTCCAATTT
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:0.00, C:0.20, G:0.08, T:0.72
Consensus pattern (13 bp):
TCTTCTTTTTGTC
Found at i:42518899 original size:40 final size:40
Alignment explanation
Indices: 42518820--42518935 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
42518810 CACTCAATGA
*
42518820 ACACCTTTTGAAGAGTCACAATCC-TTTCAAATTGGATGG
1 ACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGATGG
*
42518859 ACACCTTTTGAAGAGTCACAACCCTTTTCACATTGGATGG
1 ACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGATGG
*
42518899 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA
1 ACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGA
42518936 CATACCTCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 23 0.32
40 50 0.68
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (40 bp):
ACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGATGG
Found at i:42523861 original size:40 final size:40
Alignment explanation
Indices: 42523806--42523886 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
42523796 TATGTACTTA
*
42523806 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAAACCTTTTCATATTGG
42523846 ATGGACACCTTTTGAAGAGTCACAAACCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAAACCTTTTCATATTGG
42523886 A
1 A
42523887 CATACCTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAAACCTTTTCATATTGG
Found at i:42525180 original size:16 final size:18
Alignment explanation
Indices: 42525143--42525180 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
42525133 GATGTTATGT
*
42525143 ATTTGATTTGATATATAT
1 ATTTGATTTGATATATAG
42525161 ATTTG-TTTGA-ATATAG
1 ATTTGATTTGATATATAG
42525177 ATTT
1 ATTT
42525181 ATTAGTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (18 bp):
ATTTGATTTGATATATAG
Found at i:42550684 original size:58 final size:58
Alignment explanation
Indices: 42550598--42550848 Score: 285
Period size: 58 Copynumber: 4.3 Consensus size: 58
42550588 AAAATCGAGA
* * **
42550598 TCAAAAATAAAATTTTTGGACATCTAGGGGT-AAAATGGTAATTTTTATAAGTTTCGGGG
1 TCAAAAATGAAATTTTTGGA-ATTTAGGGGTAAAAAT-GTAATTTTTGGAAGTTTCGGGG
*
42550657 T-AAAAATGAAATTTTTGGAATTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGG
1 TCAAAAATGAAATTTTTGGAA-TTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCGGGG
* ** *
42550715 TCAAAAATGGAATTTTTGGAAGTTTCAGGTTTAAAAATGAAATTTTTGGAAG-TTCGAGGG
1 TCAAAAATGAAATTTTTGGAA-TTT-AGGGGTAAAAATGTAATTTTTGGAAGTTTCG-GGG
* * **
42550775 T-AAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGAAATTTTTGGAATTTAG-GGGTAAAAATGTAATTTTTGGAAGTTTCGGGG
42550833 TCAAAAATGTAAATTT
1 TCAAAAATG-AAATTT
42550849 GGAGAAGTTC
Statistics
Matches: 164, Mismatches: 19, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 72 0.44
59 57 0.35
60 33 0.20
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (58 bp):
TCAAAAATGAAATTTTTGGAATTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCGGGG
Found at i:42550723 original size:30 final size:29
Alignment explanation
Indices: 42550624--42550888 Score: 250
Period size: 29 Copynumber: 9.0 Consensus size: 29
42550614 TGGACATCTA
**
42550624 GGGGT-AAAATGGTAATTTTTATAAGTTTC
1 GGGGTAAAAAT-GTAATTTTTGGAAGTTTC
* * *
42550653 GGGGTAAAAATGAAATTTTTGGAATTTTA
1 GGGGTAAAAATGTAATTTTTGGAAGTTTC
*
42550682 GGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGTAATTTTTGGAAGTTTC
*
42550711 GGGGTCAAAAATGGAATTTTTGGAAGTTTC
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTC
** *
42550741 AGGTTTAAAAATGAAATTTTTGGAAG-TTC
1 -GGGGTAAAAATGTAATTTTTGGAAGTTTC
*
42550770 GAGGGTAAAAATGAAATTTTTGGAAG-TTC
1 G-GGGTAAAAATGTAATTTTTGGAAGTTTC
*
42550799 GAGGGTAAAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGTAATTTTTGGAAGTTTC
* * *
42550829 AGGGTCAAAAATGTAAATTTGGAGAAG-TTC
1 GGGGT-AAAAATGTAATTTTTG-GAAGTTTC
* ** *
42550859 GGGAGTCAAAATACAATTTATGGACAGTTT
1 GGG-GTAAAAATGTAATTTTTGGA-AGTTT
42550889 AGGGACCTCT
Statistics
Matches: 198, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
28 1 0.01
29 108 0.55
30 78 0.39
31 11 0.06
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTC
Found at i:42550856 original size:89 final size:89
Alignment explanation
Indices: 42550600--42550859 Score: 266
Period size: 89 Copynumber: 2.9 Consensus size: 89
42550590 AATCGAGATC
* * * ** *
42550600 AAAAATAAAATTTTTGGACA-TCTAGGGGT--AAAATGGTAATTTTTATAAGTTTCGGGGT-AAA
1 AAAAATGAAATTTTTGGA-AGTTTCGGGGTCAAAAATGG-AATTTTTGGAAGTTTCAGGGTCAAA
* **
42550661 AATGAAATTTTTGGAA-TTTTAGGGGT
64 AATGAAATTTTGGGAAGTTCGA-GGGT
* * * *
42550687 AAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTCAGGTTTAAAAA
1 AAAAATGAAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAA
*
42550752 TGAAATTTTTGGAAGTTCGAGGGT
66 TGAAATTTTGGGAAGTTCGAGGGT
* *
42550776 AAAAATGAAATTTTTGGAAG-TTCGAGGGT-AAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAA
1 AAAAATGAAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTTTGGAAGTTTCAGGGTCAAAA
42550839 ATGTAAA-TTTGGAGAAGTTCG
65 ATG-AAATTTTGG-GAAGTTCG
42550860 GGAGTCAAAA
Statistics
Matches: 148, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
86 1 0.01
87 23 0.16
88 57 0.39
89 64 0.43
90 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (89 bp):
AAAAATGAAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAA
TGAAATTTTGGGAAGTTCGAGGGT
Found at i:42550877 original size:60 final size:56
Alignment explanation
Indices: 42550654--42550892 Score: 205
Period size: 60 Copynumber: 4.1 Consensus size: 56
42550644 ATAAGTTTCG
* * * *
42550654 GGGT-AAAAATGAAATTTTTGGAATTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTG
1 GGGTCAAAAATGAAA-TTTTGGAA-GTTCGGGGTAAAAAT-AAATTTTTGGAAGTTTTA
* ** **
42550712 GGGTCAAAAATGGAATTTTTGGAAGTTTCAGGTTTAAAAATGAAATTTTTGGAAGTTCGA
1 GGGTCAAAAAT-GAAATTTTGGAAG-TTC-GGGGTAAAAAT-AAATTTTTGGAAGTTTTA
*
42550772 GGGT-AAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTA
1 GGGTCAAAAATGAAA-TTTTGGAAGTTCG-GGGTAAAAAT-AAATTTTTGGAAGTTTTA
* * *
42550830 GGGTCAAAAATGTAAATTTGGAGAAGTTCGGGAGTCAAAATACAATTTATGGACAG-TTTA
1 GGGTCAAAAATG-AAATTTTG-GAAGTTCGGG-GTAAAAATA-AATTTTTGGA-AGTTTTA
42550890 GGG
1 GGG
42550893 ACCTCTAGGA
Statistics
Matches: 150, Mismatches: 19, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
57 1 0.01
58 38 0.25
59 44 0.29
60 65 0.43
61 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (56 bp):
GGGTCAAAAATGAAATTTTGGAAGTTCGGGGTAAAAATAAATTTTTGGAAGTTTTA
Found at i:42552098 original size:21 final size:21
Alignment explanation
Indices: 42552050--42552100 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
42552040 CTTCGATTTC
42552050 TTTTATT-ATTATTATTAAAA
1 TTTTATTAATTATTATTAAAA
* * * *
42552070 TATCATTAATTATTATTATAT
1 TTTTATTAATTATTATTAAAA
42552091 TTTTATTAAT
1 TTTTATTAAT
42552101 GTCATTTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATTAATTATTATTAAAA
Found at i:42552726 original size:25 final size:26
Alignment explanation
Indices: 42552698--42552753 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
42552688 TTTGGTTTGT
42552698 TTTGGACCTTTTGTGATT-GGGTCC-A
1 TTTGGACCTTTTG-GATTCGGGTCCAA
* *
42552723 TTTGGGCCTTTTGGTTTCGGGTCCAA
1 TTTGGACCTTTTGGATTCGGGTCCAA
42552749 TTTGG
1 TTTGG
42552754 GTTTGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 3 0.11
25 18 0.67
26 6 0.22
ACGTcount: A:0.09, C:0.16, G:0.30, T:0.45
Consensus pattern (26 bp):
TTTGGACCTTTTGGATTCGGGTCCAA
Found at i:42552835 original size:6 final size:6
Alignment explanation
Indices: 42552824--42552880 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
42552814 TCAAATTTAG
** * *
42552824 TTAAAT TTAAAT TTAAAT TTAAA- ACAAAT CTAAAT TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
42552871 ATAAAT TTAA
1 TTAAAT TTAA
42552881 GGTCAATCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
5 3 0.07
6 38 0.93
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:42552857 original size:23 final size:23
Alignment explanation
Indices: 42552826--42552870 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
42552816 AAATTTAGTT
*
42552826 AAATTTAAATTTAAATTTAAAAC
1 AAATCTAAATTTAAATTTAAAAC
42552849 AAATCTAAATTTAAATTTAAAA
1 AAATCTAAATTTAAATTTAAAA
42552871 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATCTAAATTTAAATTTAAAAC
Found at i:42552889 original size:35 final size:35
Alignment explanation
Indices: 42552824--42552909 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
42552814 TCAAATTTAG
* *
42552824 TTAAATTTAAATTTAAATTTAAAACAAATCTAAAT
1 TTAAATTTAAAATTAAATTTAAAACAAATCTAAAA
* **
42552859 TTAAATTTAAAAATAAATTTAAGGTC-AATCTAAAA
1 TTAAATTTAAAATTAAATTTAA-AACAAATCTAAAA
42552894 TT-AATTTAAAATTAAA
1 TTAAATTTAAAATTAAA
42552910 ATTTTATCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 13 0.30
35 30 0.68
36 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (35 bp):
TTAAATTTAAAATTAAATTTAAAACAAATCTAAAA
Found at i:42553591 original size:206 final size:206
Alignment explanation
Indices: 42553225--42554234 Score: 1307
Period size: 206 Copynumber: 4.9 Consensus size: 206
42553215 TCTGGTTTCA
* * * **
42553225 TTGATTTGGCCGTCTTCTCGGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTT
* * * * * *
42553290 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAGGCTAACCAC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
42553355 TTTATTGCTTCGACCTACTTCTCGGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
42553420 CGAGCGTGAGT
196 CGAGCGTGAGT
* * * ** **
42553431 TTGATTTGGTCTTCTTCTCAATACCTTATCAGGAAGATGACCGCATCACTTGTTTTGATGTACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTT
* * * * * * * *
42553496 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAAGAAGTTAACTAC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * *
42553561 TTTATTGCTTCGACTTGCTTCTCAGTATCTCAACAGGAAGTTGAGGTTCGAAGATTTGCTCATGT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
42553626 CGAGCGTGAGT
196 CGAGCGTGAGT
* * **
42553637 TTGATTTGATCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTT
*
42553702 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
42553767 TTTATTGCTTCGATCTGCTTCTCAGTATCTCATCAGGAAGCT-AGGGTTCGAATATTTGCTCATG
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGA-GGTTCGAAGATTTGCTCATA
*
42553831 TCGAGCGTGAAT
195 TCGAGCGTGAGT
* * * ** *
42553843 TTGATTTGATCTTCTTCTCAGTATCTAATCAGGAATATGACCGCATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTT
* * * *
42553908 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* ** * *
42553973 TTTATTGCTTCGACCTGCTTCTCAGCATCTCATCAAAAAGCT-AGGGTTCGAAGATTTACTCGTA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGA-GGTTCGAAGATTTGCTCATA
42554037 TCGAGC----G-
195 TCGAGCGTGAGT
* * * * * * * *
42554044 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCACCTCACTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTT
* *
42554109 CTCTGTATCTCATCAAGAAGACGAATTTGG-TCTACTTCTCAGTATCTCATCAAGAAGCTAACCA
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * *
42554173 TTTTATTGCTTCAACCTGCTTCTTAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTC
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTC
42554235 GCATTGAGCG
Statistics
Matches: 717, Mismatches: 84, Indels: 11
0.88 0.10 0.01
Matches are distributed among these distances:
200 1 0.00
201 164 0.23
205 1 0.00
206 551 0.77
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
CGAGCGTGAGT
Found at i:42554821 original size:92 final size:92
Alignment explanation
Indices: 42554550--42555190 Score: 1086
Period size: 92 Copynumber: 7.0 Consensus size: 92
42554540 TGTAACTTGA
* * * * * * **
42554550 ATCCATCTTCACTGCATCTTCATGAAGATAGGATTTGATG-TCGAAGCTTCATCTTGCTCTTACT
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
* * * *
42554614 GCAACTTTAGAGAGATGAAGATTTGCT
66 ACAACTTCAGAGAGATAAAGACTTGCT
42554641 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAAAGCTTCATCTTGCTCTTAC
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATG-TTTAAAGCTTCATCTTGCTCTTAC
42554706 TACAACTTCAGAGAGATAAAGACTTGCT
65 TACAACTTCAGAGAGATAAAGACTTGCT
* *
42554734 ATCCAACTTTACTGCATCTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCCTACT
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
42554799 ACAACTTCAGAGAGATAAAGACTTGCT
66 ACAACTTCAGAGAGATAAAGACTTGCT
*
42554826 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTTATCTTGCTCTTACT
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
42554891 ACAACTTCAGAGAGATAAAGACTTGCT
66 ACAACTTCAGAGAGATAAAGACTTGCT
*
42554918 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCCTACT
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
* *
42554983 ACAACTTTATAGAGATAAAGACTTGCT
66 ACAACTTCAGAGAGATAAAGACTTGCT
* *
42555010 ATCCAACTTTACTGCAACTTTAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCCTACT
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
42555075 ACAACTTCAGAGAGATAAAGACTTGCT
66 ACAACTTCAGAGAGATAAAGACTTGCT
42555102 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
1 ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
42555167 ACAACTTCAGAGAGATAAAGACTT
66 ACAACTTCAGAGAGATAAAGACTT
42555191 TTCCCTTTTG
Statistics
Matches: 522, Mismatches: 26, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
91 34 0.07
92 404 0.77
93 84 0.16
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (92 bp):
ATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACT
ACAACTTCAGAGAGATAAAGACTTGCT
Found at i:42554844 original size:40 final size:39
Alignment explanation
Indices: 42554795--42554943 Score: 109
Period size: 40 Copynumber: 3.4 Consensus size: 39
42554785 ATCTTGCTCC
42554795 TACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTT
1 TACTACAACTTCA-AGAGATAAAGACTTGCTATCCAACTT
* * ***
42554835 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTTATCTTGCTCT
1 TACTACAACTTCAAGA-GATA--AA--GA--CTT---GC--TATCCAACT-T
42554887 TACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTT
1 TACTACAACTTCA-AGAGATAAAGACTTGCTATCCAACTT
*
42554927 TACTGCAACTTCAAGAG
1 TACTACAACTTCAAGAG
42554944 GATAGGAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 29
0.68 0.09 0.23
Matches are distributed among these distances:
39 7 0.08
40 29 0.35
41 6 0.07
42 2 0.02
43 2 0.02
44 2 0.02
46 4 0.05
48 2 0.02
49 2 0.02
50 2 0.02
51 6 0.07
52 17 0.20
53 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (39 bp):
TACTACAACTTCAAGAGATAAAGACTTGCTATCCAACTT
Found at i:42556319 original size:6 final size:6
Alignment explanation
Indices: 42556304--42556379 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
42556294 CGACCTCTCA
* * *
42556304 TTTTCAT TTTTCT TTTT-T TTCTT-T TTTCTTT TTTTCT TTTTAT TTTTGT
1 TTTTC-T TTTTCT TTTTCT TT-TTCT TTT-TCT TTTTCT TTTTCT TTTTCT
*
42556353 TTTTCT TCTTCT TTTT-T CTTTTCT TTT
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTT
42556380 ATTCATTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.09
6 43 0.74
7 10 0.17
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:42556320 original size:7 final size:7
Alignment explanation
Indices: 42556304--42556374 Score: 54
Period size: 7 Copynumber: 9.3 Consensus size: 7
42556294 CGACCTCTCA
42556304 TTTTCATT
1 TTTTC-TT
*
42556312 TTTCTTTT
1 TTT-TCTT
42556320 TTTTCTT
1 TTTTCTT
42556327 TTTTCTTT
1 TTTTC-TT
42556335 TTTTCTT
1 TTTTCTT
42556342 TTTAT-TT
1 TTT-TCTT
*
42556349 TTGTTTTT
1 TT-TTCTT
42556357 CTTCTTCTT
1 -TT-TTCTT
42556366 TTTTCTT
1 TTTTCTT
42556373 TT
1 TT
42556375 CTTTTATTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
7 25 0.47
8 21 0.40
9 7 0.13
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:42556342 original size:24 final size:25
Alignment explanation
Indices: 42556310--42556379 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
42556300 CTCATTTTCA
42556310 TTTTTCTTTTTTTTCTTTTTTCTT-
1 TTTTTCTTTTTTTTCTTTTTTCTTC
*
42556334 TTTTTCTTTTTATTTTTGTTTTTCTTC
1 TTTTTCTTTTT-TTTCT-TTTTTCTTC
*
42556361 TTCTTT-TTTCTTTTCTTTT
1 TT-TTTCTTTTTTTTCTTTT
42556380 ATTCATTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 11 0.28
25 7 0.18
26 12 0.31
27 6 0.15
28 3 0.08
ACGTcount: A:0.01, C:0.13, G:0.01, T:0.84
Consensus pattern (25 bp):
TTTTTCTTTTTTTTCTTTTTTCTTC
Found at i:42556349 original size:36 final size:36
Alignment explanation
Indices: 42556304--42556379 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
42556294 CGACCTCTCA
* *
42556304 TTTTCATTTTTCTTTTTTTTCTT-TTTTCTTTTTTTC
1 TTTTCATTTTTCTTTTTCTTCTTCTTTT-TTCTTTTC
* *
42556340 TTTTTATTTTTGTTTTTCTTCTTCTTTTTTCTTTTC
1 TTTTCATTTTTCTTTTTCTTCTTCTTTTTTCTTTTC
42556376 TTTT
1 TTTT
42556380 ATTCATTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (36 bp):
TTTTCATTTTTCTTTTTCTTCTTCTTTTTTCTTTTC
Found at i:42560069 original size:85 final size:85
Alignment explanation
Indices: 42559926--42560095 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
42559916 CTTCACTTCA
*
42559926 AGCAAATAAGGTAAGTCTCTATAATCCTGATGAAACATCTGCCTCATCTCGTTATTCCATTGTCC
1 AGCAAATAAGGTAAGTCTCCATAATCCTGATGAAACATCTGCCTCATCTCGTTATTCCATTGTCC
42559991 CCAGATTTCTCTTAACTCTT
66 CCAGATTTCTCTTAACTCTT
42560011 AGCAAATAAGGTAAGTCTCCATAATCCTGATGAAACATCTGCCTCATCTCGTTATTCCATTGTCC
1 AGCAAATAAGGTAAGTCTCCATAATCCTGATGAAACATCTGCCTCATCTCGTTATTCCATTGTCC
42560076 CCAGATTTCTCTTAACTCTT
66 CCAGATTTCTCTTAACTCTT
42560096 GTAGATTATT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (85 bp):
AGCAAATAAGGTAAGTCTCCATAATCCTGATGAAACATCTGCCTCATCTCGTTATTCCATTGTCC
CCAGATTTCTCTTAACTCTT
Found at i:42562106 original size:30 final size:30
Alignment explanation
Indices: 42562070--42562219 Score: 139
Period size: 30 Copynumber: 5.0 Consensus size: 30
42562060 GGACATCCAT
*
42562070 GGTTAAAATGGTAATTTTTAGAAGTTTC-GG
1 GGTTAAAAT-GTAATTTTTGGAAGTTTCAGG
* * *
42562100 GGTTAAAAATGCAACTTTTGGAAG-TTCAGA
1 GGTT-AAAATGTAATTTTTGGAAGTTTCAGG
* *
42562130 GGTAAAAATGTAATTTTTGGAAGTTTTA-G
1 GGTTAAAATGTAATTTTTGGAAGTTTCAGG
* * *
42562159 GGTCAAAATATAATTTTTGAGAAG-TTCGGG
1 GGTTAAAATGTAATTTTTG-GAAGTTTCAGG
*
42562189 GGTTAAAATATAATTTTTGGACAGTTT-AGG
1 GGTTAAAATGTAATTTTTGGA-AGTTTCAGG
42562219 G
1 G
42562220 ACCTTCAGGG
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
29 41 0.42
30 50 0.51
31 7 0.07
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTTGGAAGTTTCAGG
Found at i:42562166 original size:29 final size:29
Alignment explanation
Indices: 42562074--42562219 Score: 127
Period size: 29 Copynumber: 4.9 Consensus size: 29
42562064 ATCCATGGTT
* *
42562074 AAAATGGTAATTTTTAGAAGTTTCGGGGTTA
1 AAAAT-GTAATTTTTGGAAGTTTCAGGG-TA
* *
42562105 AAAATGCAACTTTTGGAAG-TTCAGAGGTA
1 AAAATGTAATTTTTGGAAGTTTCAG-GGTA
* *
42562134 AAAATGTAATTTTTGGAAGTTTTAGGGTC
1 AAAATGTAATTTTTGGAAGTTTCAGGGTA
* * *
42562163 AAAATATAATTTTTGAGAAG-TTCGGGGGTT
1 AAAATGTAATTTTTG-GAAGTTTC-AGGGTA
*
42562193 AAAATATAATTTTTGGACAGTTT-AGGG
1 AAAATGTAATTTTTGGA-AGTTTCAGGG
42562220 ACCTTCAGGG
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
29 47 0.49
30 42 0.44
31 7 0.07
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTCAGGGTA
Found at i:42562183 original size:59 final size:58
Alignment explanation
Indices: 42562074--42562219 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 58
42562064 ATCCATGGTT
* ** *
42562074 AAAATGGTAATTTTTAGAAGTTTCGGGGTTAAAAATGCAACTTTTGGAAGTTCAGAGGTA
1 AAAAT-GTAATTTTTGGAAGTTTTAGGGTCAAAAAT-CAACTTTTGGAAGTTCAGAGGTA
* * * *
42562134 AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAATAT-AATTTTTGAGAAGTTCGGGGGTT
1 AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAA-ATCAACTTTTG-GAAGTTCAGAGGTA
*
42562193 AAAATATAATTTTTGGACAG-TTTAGGG
1 AAAATGTAATTTTTGGA-AGTTTTAGGG
42562220 ACCTTCAGGG
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
58 7 0.09
59 58 0.78
60 9 0.12
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATCAACTTTTGGAAGTTCAGAGGTA
Found at i:42564053 original size:25 final size:25
Alignment explanation
Indices: 42564008--42564059 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
42563998 TTGGTTTGTT
*
42564008 TTGGACCTTTTGTGATTGGGTGCAA
1 TTGGACCTTTTGTGATTGGGTCCAA
* *
42564033 TTGGGCCTTTTG-GTTTCGGGTCCAA
1 TTGGACCTTTTGTGATT-GGGTCCAA
42564058 TT
1 TT
42564060 TGGGTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.12, C:0.15, G:0.31, T:0.42
Consensus pattern (25 bp):
TTGGACCTTTTGTGATTGGGTCCAA
Found at i:42564144 original size:6 final size:6
Alignment explanation
Indices: 42564133--42564184 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
42564123 TCAAATTTAG
** * *
42564133 TTAAAT TTAAAT TTAAA- ACAAAT CTAAAT TTAAAT TTAAAA TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
42564180 TTAAA
1 TTAAA
42564185 ATCAATCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:42564206 original size:11 final size:11
Alignment explanation
Indices: 42564142--42564211 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
42564132 GTTAAATTTA
**
42564142 AATTTAAAACA
1 AATTTAAAATT
* *
42564153 AATCTAAATTT
1 AATTTAAAATT
42564164 AAATTTAAAATT
1 -AATTTAAAATT
*
42564176 AAATTTAAAATC
1 -AATTTAAAATT
* *
42564188 AATCTAAACTT
1 AATTTAAAATT
42564199 AATTTAAAATT
1 AATTTAAAATT
42564210 AA
1 AA
42564212 AATTTGATCC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 26 0.57
12 20 0.43
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:42564216 original size:35 final size:35
Alignment explanation
Indices: 42564133--42564212 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
42564123 TCAAATTTAG
* *
42564133 TTAAATTTAAATTTAAAACAAATCTAAATTTAAAT
1 TTAAAATTAAATTTAAAACAAATCTAAACTTAAAT
42564168 TTAAAATTAAATTTAAAATC-AATCTAAACTT-AAT
1 TTAAAATTAAATTTAAAA-CAAATCTAAACTTAAAT
42564202 TTAAAATTAAA
1 TTAAAATTAAA
42564213 ATTTGATCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
34 14 0.33
35 27 0.64
36 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (35 bp):
TTAAAATTAAATTTAAAACAAATCTAAACTTAAAT
Found at i:42565437 original size:59 final size:58
Alignment explanation
Indices: 42565302--42565558 Score: 249
Period size: 59 Copynumber: 4.4 Consensus size: 58
42565292 TTTTGTTTAC
* * * * * *
42565302 TCGAGGGTAAAATGGTAATTTTAGGAAATTTAGGG-TTAAAAAT-GAAATTTTAG-ACGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAA-ATCGGGATCAAAAATAG-AATTTTCGAACAT
** *
42565359 TCGAGGGTAAAATCATAATTTTTGGAAAGATCGGGATC-AAAATCGAAATTTTCGAACAT
1 TCGAGGGTAAAATGGTAATTTTTGGAAA-ATCGGGATCAAAAATAG-AATTTTCGAACAT
* * * *
42565418 TCGGGGGTAAAATGGTAATTTTTTGAAAAATCAAGG-TCAAAAATAGAATTTTTGAA-AGT
1 TCGAGGGTAAAATGGTAA-TTTTTGGAAAATC-GGGATCAAAAATAGAATTTTCGAACA-T
*
42565477 TCGAGGGTAAAAAT-GTAATTTTTAGAGAAATCGGGATCAAAAATAGAATTTTCGAACAT
1 TCGAGGGT-AAAATGGTAATTTTTGGA-AAATCGGGATCAAAAATAGAATTTTCGAACAT
*
42565536 CCGAGGGTAAAATGGTAATTTTT
1 TCGAGGGTAAAATGGTAATTTTT
42565559 AAAAGTTCGG
Statistics
Matches: 166, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
57 34 0.20
58 24 0.14
59 85 0.51
60 23 0.14
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.31
Consensus pattern (58 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAAATCGGGATCAAAAATAGAATTTTCGAACAT
Found at i:42565468 original size:30 final size:30
Alignment explanation
Indices: 42565434--42565528 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
42565424 GTAAAATGGT
*
42565434 AATTTTTTGAAAAATCAAGGTCAAAAATAG
1 AATTTTTTGAAAAATCAGGGTCAAAAATAG
**
42565464 AA-TTTTTGAAAGTTCGAGGGT-AAAAAT-G
1 AATTTTTTGAAAAATC-AGGGTCAAAAATAG
* *
42565492 TAATTTTTAGAGAAATC-GGGATCAAAAATAG
1 -AATTTTTTGAAAAATCAGGG-TCAAAAATAG
42565523 AATTTT
1 AATTTT
42565529 CGAACATCCG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
28 4 0.08
29 20 0.38
30 27 0.52
31 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (30 bp):
AATTTTTTGAAAAATCAGGGTCAAAAATAG
Found at i:42565472 original size:29 final size:29
Alignment explanation
Indices: 42565437--42565528 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
42565427 AAATGGTAAT
*
42565437 TTTTTGAAAAATCAAGGTCAAAAATAGAA
1 TTTTTGAAAAATCAGGGTCAAAAATAGAA
**
42565466 TTTTTGAAAGTTCGAGGGT-AAAAAT-GTAA
1 TTTTTGAAAAATC-AGGGTCAAAAATAG-AA
*
42565495 TTTTTAGAGAAATC-GGGATCAAAAATAGAA
1 TTTTT-GAAAAATCAGGG-TCAAAAATAGAA
42565525 TTTT
1 TTTT
42565529 CGAACATCCG
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 4 0.08
29 25 0.49
30 21 0.41
31 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.33
Consensus pattern (29 bp):
TTTTTGAAAAATCAGGGTCAAAAATAGAA
Found at i:42565510 original size:118 final size:117
Alignment explanation
Indices: 42565303--42565559 Score: 317
Period size: 118 Copynumber: 2.2 Consensus size: 117
42565293 TTTGTTTACT
* * * * * *
42565303 CGAGGGTAAAATGGTAA-TTTTAGGAAATTTAGGGTTAAAAATGAAATTTTAGACGTTCGAGGGT
1 CGAGGGTAAAATGGTAATTTTTAGAAAAATCAAGGTCAAAAATGAAATTTTAGAAGTTCGAGGGT
* * *
42565367 AAAATCATAATTTTTGGAAAGATCGGGATC-AAAATCGAAATTTTCGAACATT
66 AAAATCATAATTTTTAGAAAGATCGGGATCAAAAATAG-AATTTTCGAACATC
* * *
42565419 CGGGGGTAAAATGGTAATTTTTTGAAAAATCAAGGTCAAAAAT-AGAATTTTTGAAAGTTCGAGG
1 CGAGGGTAAAATGGTAATTTTTAGAAAAATCAAGGTCAAAAATGA-AATTTTAG-AAGTTCGAGG
*
42565483 GTAAAAAT-GTAATTTTTAGAGAA-ATCGGGATCAAAAATAGAATTTTCGAACATC
64 GT-AAAATCATAATTTTTAGA-AAGATCGGGATCAAAAATAGAATTTTCGAACATC
42565537 CGAGGGTAAAATGGTAATTTTTA
1 CGAGGGTAAAATGGTAATTTTTA
42565560 AAAGTTCGGG
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
116 17 0.14
117 26 0.22
118 64 0.53
119 13 0.11
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (117 bp):
CGAGGGTAAAATGGTAATTTTTAGAAAAATCAAGGTCAAAAATGAAATTTTAGAAGTTCGAGGGT
AAAATCATAATTTTTAGAAAGATCGGGATCAAAAATAGAATTTTCGAACATC
Found at i:42565592 original size:28 final size:29
Alignment explanation
Indices: 42565540--42565798 Score: 157
Period size: 29 Copynumber: 8.9 Consensus size: 29
42565530 GAACATCCGA
** *
42565540 GGGT-AAAATGGTAATTTTTAAAAGTTCGG
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTGG
*
42565569 GGGT-AAAATGTAATTTTTGGAAGTTTTG
1 GGGTAAAAATGTAATTTTTGGAAGTTTGG
* * * * *
42565597 GGGTCAAAATGGAATTGTAGGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGG
*
42565626 GGG-AAAATTGTAA-TTTTGGAAGTTTTGG
1 GGGTAAAAATGTAATTTTTGGAAG-TTTGG
* ** * **
42565654 GGTTAAAAATGTAATTTGGGGAAATTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGG
* * * **
42565683 AGGTCAAAAATGGAATTTTTGGGAGTTCAG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTGG
* * * * *
42565713 GGGCAAAAATGGAATTTTTGAAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGG
* * **
42565742 GGGTAAAAAAGTAATTTTTGCAAGTTTCA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGG
* *
42565771 AGGTCAAAAATGTAATTTTGGAGAAGTT
1 GGGT-AAAAATGTAATTTTTG-GAAGTT
42565799 CGGATGTCAA
Statistics
Matches: 175, Mismatches: 48, Indels: 12
0.74 0.20 0.05
Matches are distributed among these distances:
27 7 0.04
28 32 0.18
29 92 0.53
30 39 0.22
31 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTGG
Found at i:42565619 original size:29 final size:27
Alignment explanation
Indices: 42565540--42565670 Score: 113
Period size: 28 Copynumber: 4.6 Consensus size: 27
42565530 GAACATCCGA
** **
42565540 GGGTAAAATGGTAATTTTTAAAAGTTCGG
1 GGGTAAAAT-GTAA-TTTTGGAAGTTTTG
42565569 GGGTAAAATGTAATTTTTGGAAGTTTTG
1 GGGTAAAATGTAA-TTTTGGAAGTTTTG
* *
42565597 GGGTCAAAATGGAATTGTAGGAAG-TTTG
1 GGGT-AAAATGTAATT-TTGGAAGTTTTG
42565625 AGGG-AAAATTGTAATTTTGGAAGTTTTG
1 -GGGTAAAA-TGTAATTTTGGAAGTTTTG
42565653 GGGTTAAAAATGTAATTT
1 GGG-T-AAAATGTAATTT
42565671 GGGGAAATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
27 13 0.15
28 35 0.41
29 34 0.40
30 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (27 bp):
GGGTAAAATGTAATTTTGGAAGTTTTG
Found at i:42565751 original size:59 final size:60
Alignment explanation
Indices: 42565688--42565800 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 60
42565678 TTTTAAGGTC
* ** * *
42565688 AAAAATGGAATTTTTGGGAG-TTCAGGGGCAAAAATGGAATTTTTGA-AAGTTCGAGGGT
1 AAAAAAGGAATTTTTGCAAGTTTCAAGGGCAAAAATGGAATTTTGGAGAAGTTCGAGGGT
* * *
42565746 AAAAAAGTAATTTTTGCAAGTTTCAAGGTCAAAAATGTAATTTTGGAGAAGTTCG
1 AAAAAAGGAATTTTTGCAAGTTTCAAGGGCAAAAATGGAATTTTGGAGAAGTTCG
42565801 GATGTCAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
58 16 0.36
59 22 0.49
60 7 0.16
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (60 bp):
AAAAAAGGAATTTTTGCAAGTTTCAAGGGCAAAAATGGAATTTTGGAGAAGTTCGAGGGT
Found at i:42566577 original size:17 final size:16
Alignment explanation
Indices: 42566555--42566597 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
42566545 AAGGTAAAAC
*
42566555 TTCTTTTCTTTTCTTAT
1 TTCTTTTCTTTTC-CAT
*
42566572 TTCTTTCCTTTTCCAT
1 TTCTTTTCTTTTCCAT
42566588 TT-TTTTCTTT
1 TTCTTTTCTTT
42566598 AAAACTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 12 0.52
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTTTCTTTTCCAT
Found at i:42566932 original size:39 final size:39
Alignment explanation
Indices: 42566889--42566976 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
42566879 GTTGATGATG
*
42566889 ATCTGCCCTAGGCTCGGGGAAAGAGATCAAATGGCTTCA
1 ATCTGCCCCAGGCTCGGGGAAAGAGATCAAATGGCTTCA
* * *
42566928 ATCTGCCCCAGGCTCGGGGTAAGAGATCGAATGGCTGT-T
1 ATCTGCCCCAGGCTCGGGGAAAGAGATCAAATGGCT-TCA
42566967 ATCTGCCCCA
1 ATCTGCCCCA
42566977 AACTCGAGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 43 0.98
40 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGAAAGAGATCAAATGGCTTCA
Found at i:42566988 original size:39 final size:39
Alignment explanation
Indices: 42566909--42566995 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
42566899 GGCTCGGGGA
** *
42566909 AAGAGATCAAATGGCTTCAATCTGCCCCAGGCTCGGGGT
1 AAGAGATCAAATGGCTTCAATCTGCCCCAAACTCGAGGT
* *
42566948 AAGAGATCGAATGGCTGT-TATCTGCCCCAAACTCGAGGT
1 AAGAGATCAAATGGCT-TCAATCTGCCCCAAACTCGAGGT
*
42566987 AAAAGATCA
1 AAGAGATCA
42566996 GGATCTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (39 bp):
AAGAGATCAAATGGCTTCAATCTGCCCCAAACTCGAGGT
Found at i:42567210 original size:92 final size:92
Alignment explanation
Indices: 42567104--42568150 Score: 1733
Period size: 92 Copynumber: 11.4 Consensus size: 92
42567094 CCGAAGCTTT
42567104 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
*
42567169 AGGATAGGAATTGATGTTTGAAGCTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
* *
42567196 ATCTTACTCTTACTACAACTTCAGA-AGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
42567260 AGGATAGGAATTGATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
*
42567287 ATCTTGCTCTTACTATAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
*
42567352 AGGATAGGAAATGATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
* * * *
42567379 ATTTTTCTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCATCTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
42567444 AGGATAGGAATTGATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
* * *
42567471 ATCTTGCTCTTACTATAACTTCAGAGAGATAAAGACTTACTATCCATCTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
*
42567536 AGGATAGGAATTTATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
*
42567563 ATCTTGCTCTTACTAAAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
42567628 AGGATAGGAATTGATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
* * *
42567655 ATCTTTCTCTTACTACAACTTCAGAAAGATAAAGACTTTCTATCCAACTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
* *
42567720 AGGATAAGAATTGATGTTTGAAATTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
* * * *
42567747 ATCTTACTCTTATTACAACTTCAGAGAGTTAAAGACTTGCTATCCAACATTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
* * *
42567812 AGAATAGGGATTGATGTTTGAAGCTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
42567839 ATCTTGCTCTTACTACAACTTCAGAGAG--AAAGACTTGCTATCCAACTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
*
42567902 AGGATAAGAATTGATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
* * *
42567929 ATCTTACTCTTACTACAACTTTAGAGGGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
* *
42567994 GGGATAAGG-ATTGATGTTTGAAGCTTC
66 AGGAT-AGGAATTGATGTTTGAAACTTC
* *
42568021 ATCTTGCTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTTAAG
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
*
42568086 AGGATAGGAAATGATGTTTGAAACTTC
66 AGGATAGGAATTGATGTTTGAAACTTC
*
42568113 ATCTTTCTCTTACTACAACTTCAGAGAGATAAAGACTT
1 ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTT
42568151 TTGCCTTTTG
Statistics
Matches: 889, Mismatches: 61, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
90 82 0.09
91 90 0.10
92 715 0.80
93 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (92 bp):
ATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAG
AGGATAGGAATTGATGTTTGAAACTTC
Found at i:42568248 original size:50 final size:50
Alignment explanation
Indices: 42568159--42568354 Score: 155
Period size: 51 Copynumber: 3.9 Consensus size: 50
42568149 TTTTGCCTTT
* * * * *
42568159 TGTCTTTTTGCGGTAC-TGGATTCGCCGTTGCGGTCTTAGATCTTTCTCGTCG
1 TGTC-TTTTGAGGTACATGG-TCCGCCGTTGC-GACTTAGACCTTTCTCGTCA
* * * * **
42568211 TGTCTTCTGAGGTACATGGTCCGCTGTTACGACTTAGACCTTTTTC-TTT
1 TGTCTTTTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTTCTCGTCA
* * * * *
42568260 TGTCTTTTTGTGGTAC-TGGATCCACCGTTGCGGTCTTAGATCTTTCCCGTCA
1 TGTC-TTTTGAGGTACATGG-TCCGCCGTTGC-GACTTAGACCTTTCTCGTCA
* *
42568312 TGTCTTTTAAGGTACACGGTCCGCCGTTGCGACTTAGACCTTT
1 TGTCTTTTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTT
42568355 TTTTTGTCTT
Statistics
Matches: 111, Mismatches: 27, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
49 8 0.07
50 41 0.37
51 48 0.43
52 14 0.13
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.40
Consensus pattern (50 bp):
TGTCTTTTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTTCTCGTCA
Found at i:42568299 original size:51 final size:51
Alignment explanation
Indices: 42568155--42568426 Score: 193
Period size: 50 Copynumber: 5.4 Consensus size: 51
42568145 AGACTTTTGC
* * *
42568155 CTTTTGTCTTTTTGCGGTACTGGATTCGCCGTTGCGGTCTTAGATCTTTCT
1 CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGACTTAGATCTTTCT
** * * * * * *
42568206 CGTCGTGTC-TTCTGAGGTACATGG-TCCGCTGTTAC-GACTTAGACCTTTTT
1 C-TTTTGTCTTTTTGTGGTAC-TGGATCCGCCGTTGCGGACTTAGATCTTTCT
* * *
42568256 CTTTTGTCTTTTTGTGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCC
1 CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGACTTAGATCTTTCT
** ** * *
42568307 CGTCATGTC-TTTTAAGGTACACGG-TCCGCCGTTGC-GACTTAGACCTTT-T
1 C-TTTTGTCTTTTTGTGGTAC-TGGATCCGCCGTTGCGGACTTAGATCTTTCT
** * * *
42568356 -TTTTGTCTTTACGTGGTACTAGATCCGCCGTCGCGG-CTTAGATCTTTCC
1 CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGACTTAGATCTTTCT
* **
42568405 CTTGTGTCTTTGCGTGGTACTG
1 CTTTTGTCTTTTTGTGGTACTG
42568427 AGACCTATAG
Statistics
Matches: 165, Mismatches: 44, Indels: 25
0.71 0.19 0.11
Matches are distributed among these distances:
47 6 0.04
48 27 0.16
49 9 0.05
50 59 0.36
51 49 0.30
52 15 0.09
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (51 bp):
CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGACTTAGATCTTTCT
Found at i:42568333 original size:101 final size:100
Alignment explanation
Indices: 42568155--42568405 Score: 353
Period size: 101 Copynumber: 2.5 Consensus size: 100
42568145 AGACTTTTGC
* * * * *
42568155 CTTTTGTCTTTTTGCGGTACTGGATTCGCCGTTGCGGTCTTAGATCTTTCTCGTCGTGTCTTCTG
1 CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTCTA
* *
42568220 AGGTACATGGTCCGCTGTTACGACTTAGACCTTTTT
66 AGGTACACGGTCCGCCGTTACGACTTAGACC-TTTT
* *
42568256 CTTTTGTCTTTTTGTGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTTTA
1 CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTCTA
*
42568321 AGGTACACGGTCCGCCGTTGCGACTTAGACCTTTT
66 AGGTACACGGTCCGCCGTTACGACTTAGACCTTTT
** * *
42568356 -TTTTGTCTTTACGTGGTACTAGATCCGCCGTCGCGG-CTTAGATCTTTCCC
1 CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCC
42568406 TTGTGTCTTT
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
98 14 0.10
99 31 0.23
100 4 0.03
101 86 0.64
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (100 bp):
CTTTTGTCTTTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTCTA
AGGTACACGGTCCGCCGTTACGACTTAGACCTTTT
Found at i:42568383 original size:48 final size:49
Alignment explanation
Indices: 42568331--42568425 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 49
42568321 AGGTACACGG
* * *
42568331 TCCGCCGTTGCGACTTAGACCTTT-TTTTTGTCTTTACGTGGTACTAGA
1 TCCGCCGTCGCGACTTAGACCTTTCCTTGTGTCTTTACGTGGTACTAGA
* * *
42568379 TCCGCCGTCGCGGCTTAGATCTTTCCCTTGTGTCTTTGCGTGGTACT
1 TCCGCCGTCGCGACTTAGACCTTT-CCTTGTGTCTTTACGTGGTACT
42568426 GAGACCTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 21 0.54
50 18 0.46
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (49 bp):
TCCGCCGTCGCGACTTAGACCTTTCCTTGTGTCTTTACGTGGTACTAGA
Found at i:42569663 original size:21 final size:20
Alignment explanation
Indices: 42569634--42569688 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
42569624 TCACCTCAAC
42569634 CTCTCTTTTTTTTAGGTTTTTT
1 CTCT-TTTTTTTTA-GTTTTTT
42569656 CTCTTTTTTTTTAGTTTTTT
1 CTCTTTTTTTTTAGTTTTTT
* *
42569676 TTCTTTTCTTTTA
1 CTCTTTTTTTTTA
42569689 TTCATTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.58
21 9 0.29
22 4 0.13
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (20 bp):
CTCTTTTTTTTTAGTTTTTT
Found at i:42575050 original size:96 final size:96
Alignment explanation
Indices: 42574875--42575067 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
42574865 AAATTTTGGA
* * ** * *
42574875 TAAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTC
1 TAAGGATATTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGGAAGTTAAGGCGCAAATTTTC
42574940 ATAATCGAAGAT-AAAGAAACATTGCCTCGAT
66 ATAATCGAAGATAAAAG-AACATTGCCTCGAT
* *
42574971 TAAGGGTATTCGATTATTTCGATTTAAAGAAAAATCGCACCTAGGAAGTTAAGGCGCAAAATTTT
1 TAAGGATATTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGGAAGTTAAGGCGC-AAATTTT
* * *
42575036 GA-AACTCGAA-ATAAAAGAATATTGCCTTGAT
65 CATAA-TCGAAGATAAAAGAACATTGCCTCGAT
42575067 T
1 T
42575068 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 66 0.80
97 17 0.20
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (96 bp):
TAAGGATATTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGGAAGTTAAGGCGCAAATTTTC
ATAATCGAAGATAAAAGAACATTGCCTCGAT
Found at i:42575413 original size:58 final size:58
Alignment explanation
Indices: 42575351--42575513 Score: 211
Period size: 58 Copynumber: 2.8 Consensus size: 58
42575341 ATTTAGGGTT
** * * * *
42575351 AAAAATAAAATTTT-GGATGTTCTGGGGTAAAATGGTAATTTTTGGAAAGATCGGGATC
1 AAAAATAAAATTTTCGGACATCCGGGGGT-AAATGGTAATTTTTAGAAAAATCGGGATC
** *
42575409 AAAAACGAAATTTTCGGACATCCGGGGGTAAATGGTAATTTTTAGAAAAATCGGGATG
1 AAAAATAAAATTTTCGGACATCCGGGGGTAAATGGTAATTTTTAGAAAAATCGGGATC
* *
42575467 AAAAATAGAATTTTCGAACATCCGGGGGTAAATGGTAATTTTTAGAA
1 AAAAATAAAATTTTCGGACATCCGGGGGTAAATGGTAATTTTTAGAA
42575514 GTTCGGGGGT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 81 0.89
59 10 0.11
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (58 bp):
AAAAATAAAATTTTCGGACATCCGGGGGTAAATGGTAATTTTTAGAAAAATCGGGATC
Found at i:42575451 original size:29 final size:29
Alignment explanation
Indices: 42575419--42575526 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 29
42575409 AAAAACGAAA
*
42575419 TTTTCGGACATCCGGGGGTAAATGGTAAT
1 TTTTCGAACATCCGGGGGTAAATGGTAAT
* * ** *
42575448 TTTTAGAAAAAT-CGGGATGAAAAATAG-AA-
1 TTTTCG-AACATCCGGG--GGTAAATGGTAAT
42575477 TTTTCGAACATCCGGGGGTAAATGGTAAT
1 TTTTCGAACATCCGGGGGTAAATGGTAAT
* * *
42575506 TTTTAGAA-GTTCGGGGGTAAA
1 TTTTCGAACATCCGGGGGTAAA
42575527 AATGTAATTT
Statistics
Matches: 59, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
27 6 0.10
28 17 0.29
29 25 0.42
30 5 0.08
31 6 0.10
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (29 bp):
TTTTCGAACATCCGGGGGTAAATGGTAAT
Found at i:42575533 original size:29 final size:29
Alignment explanation
Indices: 42575489--42575690 Score: 135
Period size: 29 Copynumber: 6.9 Consensus size: 29
42575479 TTCGAACATC
42575489 CGGGGGT--AAATGGTAATTTTTAGAAGTT
1 CGGGGGTAAAAAT-GTAATTTTTAGAAGTT
42575517 CGGGGGTAAAAATGTAATTTTT-GAAAGTT
1 CGGGGGTAAAAATGTAATTTTTAG-AAGTT
** * ** *
42575546 TTGAGGTAAAAAATGTAATTTTGGGAAATT
1 CGGGGGT-AAAAATGTAATTTTTAGAAGTT
*** * * *
42575576 TTAGGGTCAAAAATGGAATTTTTGGGAGTT
1 CGGGGGT-AAAAATGTAATTTTTAGAAGTT
* * * *
42575606 CGAGGGCAAAAATGGAATTTTTAAAAGTT
1 CGGGGGTAAAAATGTAATTTTTAGAAGTT
* *
42575635 CGAGGGTAAAAATATAATTTTT-GAAAGTT
1 CGGGGGTAAAAATGTAATTTTTAG-AAGTT
*
42575664 TGGGGGCTCAAAAATGTAA-TTTTAGAA
1 CGGGGG-T-AAAAATGTAATTTTTAGAA
42575691 AAGTTTAGGG
Statistics
Matches: 140, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
28 8 0.06
29 65 0.46
30 56 0.40
31 11 0.08
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
CGGGGGTAAAAATGTAATTTTTAGAAGTT
Found at i:42575558 original size:30 final size:30
Alignment explanation
Indices: 42575524--42575718 Score: 150
Period size: 30 Copynumber: 6.5 Consensus size: 30
42575514 GTTCGGGGGT
* *
42575524 AAAAATGTAATTTTTGAAAGTTTTGAGGTA
1 AAAAATGTAATTTTTGAAAGTTTCGAGGTC
* * *
42575554 AAAAATGTAATTTTGGGAAATTTTAG-GGTC
1 AAAAATGTAATTTT-TGAAAGTTTCGAGGTC
* ** *
42575584 AAAAATGGAATTTTTGGGAG-TTCGAGGGC
1 AAAAATGTAATTTTTGAAAGTTTCGAGGTC
* *
42575613 AAAAATGGAATTTTTAAAAG-TTCGAGGGT-
1 AAAAATGTAATTTTTGAAAGTTTCGA-GGTC
* * *
42575642 AAAAATATAATTTTTGAAAGTTTGGGGGCTC
1 AAAAATGTAATTTTTGAAAGTTTCGAGG-TC
* *
42575673 AAAAATGTAATTTTAGAAAAGTTTAG-GGTTC
1 AAAAATGTAATTTTTG-AAAGTTTCGAGG-TC
*
42575704 -AAAATATAATTTTTG
1 AAAAATGTAATTTTTG
42575719 GATAGTTTAG
Statistics
Matches: 132, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.02
29 46 0.35
30 49 0.37
31 26 0.20
32 8 0.06
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAAATGTAATTTTTGAAAGTTTCGAGGTC
Found at i:42575625 original size:89 final size:89
Alignment explanation
Indices: 42575496--42575690 Score: 218
Period size: 89 Copynumber: 2.2 Consensus size: 89
42575486 ATCCGGGGGT
* * * * *
42575496 AAATGGTAATTTTTAGAAGTTCGGGGGTAAAAATGTAATTTTTGAAAGTTTTGA-GGTAAAAAAT
1 AAATGG-AATTTTTAGAAGTTCGAGGGCAAAAATGGAATTTTTAAAAG-TTCGAGGGT-AAAAAT
* *
42575560 GTAATTTTGGGAAA-TTTTAGGG-TCAA
63 ATAATTTT-GGAAAGTTTGAGGGCTCAA
* *
42575586 AAATGGAATTTTTGGGAGTTCGAGGGCAAAAATGGAATTTTTAAAAGTTCGAGGGTAAAAATATA
1 AAATGGAATTTTTAGAAGTTCGAGGGCAAAAATGGAATTTTTAAAAGTTCGAGGGTAAAAATATA
* *
42575651 ATTTTTGAAAGTTTGGGGGCTCAA
66 ATTTTGGAAAGTTTGAGGGCTCAA
*
42575675 AAATGTAA-TTTTAGAA
1 AAATGGAATTTTTAGAA
42575691 AAGTTTAGGG
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
87 4 0.05
88 29 0.33
89 49 0.56
90 6 0.07
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (89 bp):
AAATGGAATTTTTAGAAGTTCGAGGGCAAAAATGGAATTTTTAAAAGTTCGAGGGTAAAAATATA
ATTTTGGAAAGTTTGAGGGCTCAA
Found at i:42577736 original size:17 final size:19
Alignment explanation
Indices: 42577714--42577760 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
42577704 TAAATTTAAT
42577714 TAAATTTAAACTTAA-AG-
1 TAAATTTAAACTTAATAGA
* *
42577731 TAAATTGAAATTTAATTAGA
1 TAAATTTAAACTTAA-TAGA
42577751 TAAATTTAAA
1 TAAATTTAAA
42577761 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 13 0.54
19 2 0.08
20 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (19 bp):
TAAATTTAAACTTAATAGA
Found at i:42581480 original size:121 final size:121
Alignment explanation
Indices: 42581266--42581506 Score: 473
Period size: 121 Copynumber: 2.0 Consensus size: 121
42581256 TCTATTAGTG
42581266 TAATTGTCAATTCAAGTGTTAAATATAAGTTGTCCGTAGCTTAGATTTTAAATTTGCCTTTGTTT
1 TAATTGTCAATTCAAGTGTTAAATATAAGTTGTCCGTAGCTTAGATTTTAAATTTGCCTTTGTTT
42581331 CAATCCGGTCTTTCTGTCGTCTAGCTACCAATTTAGGTGTTAATGTTAGCATGTAA
66 CAATCCGGTCTTTCTGTCGTCTAGCTACCAATTTAGGTGTTAATGTTAGCATGTAA
*
42581387 TAATTGTCAATTCAGGTGTTAAATATAAGTTGTCCGTAGCTTAGATTTTAAATTTGCCTTTGTTT
1 TAATTGTCAATTCAAGTGTTAAATATAAGTTGTCCGTAGCTTAGATTTTAAATTTGCCTTTGTTT
42581452 CAATCCGGTCTTTCTGTCGTCTAGCTACCAATTTAGGTGTTAATGTTAGCATGTA
66 CAATCCGGTCTTTCTGTCGTCTAGCTACCAATTTAGGTGTTAATGTTAGCATGTA
42581507 GATCATATGG
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (121 bp):
TAATTGTCAATTCAAGTGTTAAATATAAGTTGTCCGTAGCTTAGATTTTAAATTTGCCTTTGTTT
CAATCCGGTCTTTCTGTCGTCTAGCTACCAATTTAGGTGTTAATGTTAGCATGTAA
Found at i:42584298 original size:44 final size:44
Alignment explanation
Indices: 42584235--42584319 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
42584225 ATCCAAAAAT
42584235 AAATTTAACACCTTACACCGAATATAATTAATAAATTAGGCATC
1 AAATTTAACACCTTACACCGAATATAATTAATAAATTAGGCATC
*
42584279 AAATTTAATACCTTACACCGAATATAATTAATAAATTAGGC
1 AAATTTAACACCTTACACCGAATATAATTAATAAATTAGGC
42584320 CAAAATTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (44 bp):
AAATTTAACACCTTACACCGAATATAATTAATAAATTAGGCATC
Found at i:42584309 original size:23 final size:23
Alignment explanation
Indices: 42584239--42584311 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
42584229 AAAAATAAAT
*
42584239 TTAACACCTTACACCGAATATAA
1 TTAATACCTTACACCGAATATAA
** *
42584262 TTAATAAATTAGGCATC-AA-AT--
1 TTAATACCTTA--CACCGAATATAA
42584283 TTAATACCTTACACCGAATATAA
1 TTAATACCTTACACCGAATATAA
42584306 TTAATA
1 TTAATA
42584312 AATTAGGCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 11 0.30
23 16 0.43
24 2 0.05
25 3 0.08
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (23 bp):
TTAATACCTTACACCGAATATAA
Found at i:42588647 original size:20 final size:20
Alignment explanation
Indices: 42588624--42588662 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42588614 CATAAAATAT
42588624 TTATAAAATTTATAAAAAAA
1 TTATAAAATTTATAAAAAAA
* * *
42588644 TTATTAATTTTTTAAAAAA
1 TTATAAAATTTATAAAAAA
42588663 CGGTTAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATAAAATTTATAAAAAAA
Found at i:42588735 original size:30 final size:29
Alignment explanation
Indices: 42588670--42588735 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
42588660 AAACGGTTAG
***
42588670 AAATTAATTAAAACCATAAAATTTTAAAA
1 AAATTAATTAAAACCATAAAAAAGTAAAA
*
42588699 ATAATTAATTAAAAACCATAAAAAAGTATAA
1 A-AATTAATT-AAAACCATAAAAAAGTAAAA
42588730 AAATTA
1 AAATTA
42588736 TTAGAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 13 0.42
31 17 0.55
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.29
Consensus pattern (29 bp):
AAATTAATTAAAACCATAAAAAAGTAAAA
Found at i:42588753 original size:21 final size:21
Alignment explanation
Indices: 42588701--42588767 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
42588691 TTTTAAAAAT
*
42588701 AATTAATTAAAAAC-CATAAA
1 AATTAATTAAAAACTTATAAA
* *
42588721 AA--AGTATAAAAA-TTATTAGA
1 AATTAAT-TAAAAACTTA-TAAA
42588741 AATTAATTAAAAACTTATAAA
1 AATTAATTAAAAACTTATAAA
42588762 AATTAA
1 AATTAA
42588768 AATATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.06
19 7 0.19
20 7 0.19
21 15 0.42
22 5 0.14
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (21 bp):
AATTAATTAAAAACTTATAAA
Found at i:42594672 original size:22 final size:20
Alignment explanation
Indices: 42594646--42594705 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 20
42594636 TAAAAATAAT
*
42594646 AAAATTTTAATTTAATCATTTA
1 AAAATTATAATTTAATCA--TA
42594668 AAAATTATAATTTTACTATCATA
1 AAAATTATAA-TTTA--ATCATA
42594691 AAAATTATAATTTAA
1 AAAATTATAATTTAA
42594706 CTTCATCGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 1 0.03
22 13 0.38
23 16 0.47
25 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATAATTTAATCATA
Found at i:42594711 original size:22 final size:23
Alignment explanation
Indices: 42594666--42594711 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
42594656 TTTAATCATT
*
42594666 TAAAAATTATAATTTTACTATCA
1 TAAAAATTATAATTTAACTATCA
42594689 TAAAAATTATAATTTAACT-TCA
1 TAAAAATTATAATTTAACTATCA
42594711 T
1 T
42594712 CGTCTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAAATTATAATTTAACTATCA
Found at i:42600928 original size:11 final size:11
Alignment explanation
Indices: 42600912--42600985 Score: 52
Period size: 11 Copynumber: 7.0 Consensus size: 11
42600902 TAAATCCATT
42600912 TTTTAAATTTA
1 TTTTAAATTTA
42600923 TTTT-AA---A
1 TTTTAAATTTA
*
42600930 -TTTAAATTTG
1 TTTTAAATTTA
42600940 TTTTAAATTTAA
1 TTTTAAATTT-A
*
42600952 ATTT-AATTTAA
1 TTTTAAATTT-A
*
42600963 GTTTAAATTTA
1 TTTTAAATTTA
42600974 TTTTTAAATTTA
1 -TTTTAAATTTA
42600986 AAATTATTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
10 2 0.04
11 24 0.48
12 18 0.36
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:42600933 original size:6 final size:6
Alignment explanation
Indices: 42600913--42601005 Score: 79
Period size: 6 Copynumber: 16.2 Consensus size: 6
42600903 AAATCCATTT
* **
42600913 TTTAAA TTT-AT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
42600958 TTTAAG TTTAAA TTTATT TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
42601005 T
1 T
42601006 AAATAAAAGC
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 49 0.73
7 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:42600935 original size:17 final size:17
Alignment explanation
Indices: 42600913--42601005 Score: 132
Period size: 17 Copynumber: 5.4 Consensus size: 17
42600903 AAATCCATTT
42600913 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
42600930 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* *
42600947 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
42600964 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
42600982 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
42600999 TTTAAAT
1 TTTAAAT
42601006 AAATAAAAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
17 52 0.79
18 14 0.21
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:42600954 original size:23 final size:23
Alignment explanation
Indices: 42600924--42600985 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
42600914 TTAAATTTAT
42600924 TTTAAATTTAAATTT-GTTTTAAA
1 TTTAAATTTAAATTTAG-TTTAAA
42600947 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
**
42600970 TTTATTTTTAAATTTA
1 TTTAAATTTAAATTTA
42600986 AAATTATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.15
23 23 0.68
24 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:42602809 original size:29 final size:29
Alignment explanation
Indices: 42602764--42602936 Score: 181
Period size: 29 Copynumber: 5.9 Consensus size: 29
42602754 TCCAAAAGGT
* *
42602764 CCCTAAACTTTCTAAAAATTACATTTTAC
1 CCCTAAACTTTCCAAAAATTACATTTTAA
* *
42602793 CCCTGAAC-TTCCAAAAATTCCATTTTTAA
1 CCCTAAACTTTCCAAAAATTACA-TTTTAA
* * *
42602822 CCCT-AGCTTTTCCAAAAATTTCATTTTTA
1 CCCTAAAC-TTTCCAAAAATTACATTTTAA
*
42602851 CCCTTAAA-TTTCCAAAAATTCCATTTTAA
1 CCC-TAAACTTTCCAAAAATTACATTTTAA
*
42602880 CCCTAAACTTTCCAAAAATTACATTTTGA
1 CCCTAAACTTTCCAAAAATTACATTTTAA
* * *
42602909 CCTTGAACTTTCCAAAAATCACAATTTT
1 CCCTAAACTTTCCAAAAATTAC-ATTTT
42602937 CCCCCCAAGT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
28 18 0.15
29 84 0.69
30 19 0.16
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTAA
Found at i:42602878 original size:58 final size:59
Alignment explanation
Indices: 42602764--42602927 Score: 210
Period size: 58 Copynumber: 2.8 Consensus size: 59
42602754 TCCAAAAGGT
* * * *
42602764 CCCTAAACTTTCTAAAAATTACA-TTTTACCCCTGAACTTCCAAAAATTCCATTTTTAA
1 CCCTAAACTTTCCAAAAATTACATTTTTACCCTTAAATTTCCAAAAATTCCATTTTTAA
* *
42602822 CCCT-AGCTTTTCCAAAAATTTCATTTTTACCCTTAAATTTCCAAAAATTCCA-TTTTAA
1 CCCTAAAC-TTTCCAAAAATTACATTTTTACCCTTAAATTTCCAAAAATTCCATTTTTAA
* *
42602880 CCCTAAACTTTCCAAAAATTACATTTTGA-CCTTGAACTTTCCAAAAAT
1 CCCTAAACTTTCCAAAAATTACATTTTTACCCTT-AAATTTCCAAAAAT
42602928 CACAATTTTC
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.07
58 59 0.64
59 27 0.29
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.37
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAAATTACATTTTTACCCTTAAATTTCCAAAAATTCCATTTTTAA
Found at i:42602923 original size:87 final size:88
Alignment explanation
Indices: 42602767--42602927 Score: 211
Period size: 87 Copynumber: 1.8 Consensus size: 88
42602757 AAAAGGTCCC
* * * * *
42602767 TAAACTTTCTAAAAATTACATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTAGCTTT
1 TAAACTTTCCAAAAATTACATTTTAACCCTAAACTTCCAAAAATTACATTTTTAACCCTAACTTT
42602832 TCCAAAAATTTCATTTTTACCCT
66 TCCAAAAATTTCATTTTTACCCT
* * *
42602855 TAAA-TTTCCAAAAATTCCATTTTAACCCTAAACTTTCCAAAAATTACA-TTTTGACCTTGAAC-
1 TAAACTTTCCAAAAATTACATTTTAACCCTAAAC-TTCCAAAAATTACATTTTTAACCCT-AACT
42602917 TTTCCAAAAAT
64 TTTCCAAAAAT
42602928 CACAATTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
87 44 0.70
88 19 0.30
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (88 bp):
TAAACTTTCCAAAAATTACATTTTAACCCTAAACTTCCAAAAATTACATTTTTAACCCTAACTTT
TCCAAAAATTTCATTTTTACCCT
Found at i:42602955 original size:87 final size:87
Alignment explanation
Indices: 42602774--42602966 Score: 192
Period size: 87 Copynumber: 2.2 Consensus size: 87
42602764 CCCTAAACTT
* * * * *
42602774 TCTAAAAATTACATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTAGCTTTTCCAAAA
1 TCTAAAAATTCCATTTTAACCCTAAACTTCCAAAAATTACATTTTTAACCCTAACTTTTCCAAAA
** * ** *
42602839 ATTTCATTTTTACCCTTAAATT
66 ATCACAATTTTACCCCCAAATG
* * *
42602861 TCCAAAAATTCCATTTTAACCCTAAACTTTCCAAAAATTACA-TTTTGACCTTGAAC-TTTCCAA
1 TCTAAAAATTCCATTTTAACCCTAAAC-TTCCAAAAATTACATTTTTAACCCT-AACTTTTCCAA
* *
42602924 AAATCACAATTTTCCCCCCAAGTG
64 AAATCACAATTTTACCCCCAAATG
*
42602948 TCTAAAAATTACCTTTTTA
1 TCTAAAAATT-CCATTTTA
42602967 CCCACGAACC
Statistics
Matches: 85, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
87 63 0.74
88 22 0.26
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (87 bp):
TCTAAAAATTCCATTTTAACCCTAAACTTCCAAAAATTACATTTTTAACCCTAACTTTTCCAAAA
ATCACAATTTTACCCCCAAATG
Found at i:42603105 original size:18 final size:17
Alignment explanation
Indices: 42603075--42603127 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
42603065 CATACTTAGA
42603075 TTTTAATTATTATTATTT
1 TTTTAATT-TTATTATTT
*
42603093 TTTTGTATTTTA-TATTT
1 TTTT-AATTTTATTATTT
*
42603110 TATTAATTTT-TTATTT
1 TTTTAATTTTATTATTT
42603126 TT
1 TT
42603128 GTTTATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 11 0.38
17 8 0.28
18 7 0.24
19 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTAATTTTATTATTT
Found at i:42603112 original size:25 final size:25
Alignment explanation
Indices: 42603074--42603121 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
42603064 CCATACTTAG
*
42603074 ATTTTAATTATTATTATTTTTTTGT
1 ATTTTAATTATTATTAATTTTTTGT
42603099 ATTTTATATT-TTATTAATTTTTT
1 ATTTTA-ATTATTATTAATTTTTT
42603122 ATTTTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (25 bp):
ATTTTAATTATTATTAATTTTTTGT
Found at i:42606641 original size:3 final size:3
Alignment explanation
Indices: 42606633--42606676 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
42606623 AAAATTCCAA
*
42606633 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42606677 CCAAAATGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42607746 original size:7 final size:7
Alignment explanation
Indices: 42607734--42607814 Score: 87
Period size: 7 Copynumber: 11.9 Consensus size: 7
42607724 TTTTGAAAAA
42607734 GTCAACG
1 GTCAACG
42607741 GTCAACG
1 GTCAACG
* *
42607748 ATCAATG
1 GTCAACG
42607755 GTCAACG
1 GTCAACG
*
42607762 GTCAA-A
1 GTCAACG
42607768 GTC-ACTG
1 GTCAAC-G
42607775 GTCAACG
1 GTCAACG
*
42607782 GTCAAAG
1 GTCAACG
42607789 GTCAACG
1 GTCAACG
42607796 GTCAA-G
1 GTCAACG
42607802 GTCAACG
1 GTCAACG
*
42607809 ATCAAC
1 GTCAAC
42607815 TTGGTTTGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
5 1 0.02
6 9 0.15
7 49 0.80
8 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:42607778 original size:34 final size:33
Alignment explanation
Indices: 42607731--42607814 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 33
42607721 GTTTTTTGAA
*
42607731 AAAGTCAACGGTCAACGATCAATGGTCAACGGTC
1 AAAGTC-ACGGTCAACGATCAAAGGTCAACGGTC
*
42607765 AAAGTCACTGGTCAACGGTCAAAGGTCAACGGTC
1 AAAGTCAC-GGTCAACGATCAAAGGTCAACGGTC
* *
42607799 AAGGTCAACGATCAAC
1 AAAGTC-ACGGTCAAC
42607815 TTGGTTTGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 2 0.05
34 40 0.91
35 2 0.05
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (33 bp):
AAAGTCACGGTCAACGATCAAAGGTCAACGGTC
Found at i:42617625 original size:209 final size:209
Alignment explanation
Indices: 42617251--42617943 Score: 1039
Period size: 209 Copynumber: 3.3 Consensus size: 209
42617241 TACGATTATC
* * * *
42617251 CAAAACAA-CGAGGTGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATGAAACCA
1 CAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCA
*
42617315 AGCTCAAAGTGAGTGAATCTTCGAACCCCAGCTTCCTTATGAGATACTGAGAAGCGGGTCGAAGC
66 AGCTCAAAGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCGGGTCGAAGC
* *
42617380 AATAAAGCGGTTACCTTCCAGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCTTGATGAGAC
131 AATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
42617445 ACAGAGAAGTGGAT
196 ACAGAGAAGTGGAT
* * *
42617459 CAAAACAAGTGAGGCGGTCATCTTCTTGGTGAGATACAGAGAAGTATACCAACTCAATGAAACCA
1 CAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCA
* * * *
42617524 AGCTCAAAGTGAGTGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCGGGTTGAAGT
66 AGCTCAAAGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCGGGTCGAAGC
*
42617589 AATAAAGCGGTTACCTTCCTGATGCGATACAGAGAAGTGAACCAGATCC-TCCTTCCTGATGAGA
131 AATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGT-CTTCCTGATGAGA
* *
42617653 CATACAGAAGTGGAT
195 CACAGAGAAGTGGAT
* * * * * *
42617668 CAAAACAAGTGATGTGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACTA
1 CAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCA
* * * *
42617733 GGCTCAAAGTGAGCGAATCTTCGAACCCCTGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGC
66 AGCTCAAAGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCGGGTCGAAGC
* * *
42617798 AATAAAGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAAATTCGTCTTCCTGATGAGAC
131 AATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
42617863 ACAGAGAAGTGGAT
196 ACAGAGAAGTGGAT
* * * * *
42617877 CAAAAACAAGTGATGCGGTCATATTCCTTATGAGATACTGAGAAGTAAACCAAATCAATGAAACC
1 C-AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACC
42617942 AA
65 AA
42617944 AGTGTCCATT
Statistics
Matches: 437, Mismatches: 44, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
208 9 0.02
209 369 0.84
210 59 0.14
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (209 bp):
CAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCA
AGCTCAAAGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCGGGTCGAAGC
AATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
ACAGAGAAGTGGAT
Found at i:42619682 original size:30 final size:29
Alignment explanation
Indices: 42619646--42619987 Score: 253
Period size: 30 Copynumber: 11.6 Consensus size: 29
42619636 ACCCCCGAAC
42619646 TTCCAAAAATTCCATTTTAACCCATAAAAT
1 TTCCAAAAATTCCATTTTAACCC-TAAAAT
** * ** *
42619676 TTCCAAAAATTAAATTTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTAACCCTAAAAT
* *
42619705 TTCTAAAAATTCCATTTTTAACCCT-TAAT
1 TTCCAAAAATTCCA-TTTTAACCCTAAAAT
* **
42619734 TTCCAAAAATTGCATTTTTAAACCC-CGAAT
1 TTCCAAAAATTCCA-TTTT-AACCCTAAAAT
** * *
42619764 GCCCAAAAATTCCATTTTGACCCT-AACT
1 TTCCAAAAATTCCATTTTAACCCTAAAAT
* * *
42619792 TTCTAAAAATTATCATTTT-ACCCTAAGAT
1 TTCCAAAAATT-CCATTTTAACCCTAAAAT
* *
42619821 TTCCAAAAATTCCATTTTTAACACTAAATT
1 TTCCAAAAATTCCA-TTTTAACCCTAAAAT
* * * *
42619851 TTCCAAAAACTGCATTTTTACCCTTAAAT
1 TTCCAAAAATTCCATTTTAACCCTAAAAT
* *
42619880 TTCCAAAAATTCCATTTTTGA-CCTCAAACT
1 TTCCAAAAATTCCA-TTTTAACCCT-AAAAT
* * *
42619910 TTCCAAAAATTACATTTTTACCCTCAAAT
1 TTCCAAAAATTCCATTTTAACCCTAAAAT
* * * *
42619939 GTCCAAAAATTCCATTTTTAACCTTGAACT
1 TTCCAAAAATTCCA-TTTTAACCCTAAAAT
*
42619969 TTCCAAAAATCACCATTTT
1 TTCCAAAAAT-TCCATTTT
42619988 TCCCTCAAGT
Statistics
Matches: 244, Mismatches: 55, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
28 21 0.09
29 105 0.43
30 115 0.47
31 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTAACCCTAAAAT
Found at i:42619976 original size:29 final size:29
Alignment explanation
Indices: 42619646--42619988 Score: 241
Period size: 29 Copynumber: 11.7 Consensus size: 29
42619636 ACCCCCGAAC
* *
42619646 TTCCAAAAATTCCA-TTTTAACCCATAAAAT
1 TTCCAAAAATTCCATTTTTAA-CC-TTAACT
** * *
42619676 TTCCAAAAATTAAATTTTTACCCTCGAAC-
1 TTCCAAAAATTCCATTTTTAACCT-TAACT
*
42619705 TTCTAAAAATTCCATTTTTAACCCTTAA-T
1 TTCCAAAAATTCCATTTTTAA-CCTTAACT
* **
42619734 TTCCAAAAATTGCATTTTTAAACCCCGAA-T
1 TTCCAAAAATTCCATTTTT-AA-CCTTAACT
** * *
42619764 GCCCAAAAATTCCA-TTTTGACCCTAACT
1 TTCCAAAAATTCCATTTTTAACCTTAACT
* * * *
42619792 TTCTAAAAATTATCA-TTTT-ACCCTAAGAT
1 TTCCAAAAATT-CCATTTTTAACCTTAA-CT
* *
42619821 TTCCAAAAATTCCATTTTTAACACTAAATT
1 TTCCAAAAATTCCATTTTTAAC-CTTAACT
* * * *
42619851 TTCCAAAAACTGCATTTTTACCCTTAAAT
1 TTCCAAAAATTCCATTTTTAACCTTAACT
* *
42619880 TTCCAAAAATTCCATTTTTGACCTCAAACT
1 TTCCAAAAATTCCATTTTTAACCT-TAACT
* * * *
42619910 TTCCAAAAATTACATTTTTACCCTCAAAT
1 TTCCAAAAATTCCATTTTTAACCTTAACT
*
42619939 GTCCAAAAATTCCATTTTTAACCTTGAACT
1 TTCCAAAAATTCCATTTTTAACCTT-AACT
*
42619969 TTCCAAAAATCACCATTTTT
1 TTCCAAAAAT-TCCATTTTT
42619989 CCCTCAAGTG
Statistics
Matches: 247, Mismatches: 52, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
27 5 0.02
28 19 0.08
29 111 0.45
30 96 0.39
31 16 0.06
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTAACCTTAACT
Found at i:42619994 original size:59 final size:59
Alignment explanation
Indices: 42619647--42620008 Score: 359
Period size: 59 Copynumber: 6.2 Consensus size: 59
42619637 CCCCCGAACT
* * * *
42619647 TCCAAAAATTCCA-TTTTAACCCATAAAATTTCCAAAAATTAAATTTTTACCCTCGAACT-
1 TCCAAAAATTCCATTTTTAA-CCTTAAACTTTCCAAAAATTACATTTTTACCCTC-AAATG
* * *
42619706 TCTAAAAATTCCATTTTTAACCCTT-AA-TTTCCAAAAATTGCATTTTTAAACCC-CGAATG
1 TCCAAAAATTCCATTTTTAA-CCTTAAACTTTCCAAAAATTACATTTTT--ACCCTCAAATG
* * * * *
42619765 CCCAAAAATTCCA-TTTTGACCCT-AACTTTCTAAAAATTATCA-TTTTACCCT-AAGATT
1 TCCAAAAATTCCATTTTTAACCTTAAACTTTCCAAAAATTA-CATTTTTACCCTCAA-ATG
* * * * *
42619822 TCCAAAAATTCCATTTTTAACAC-TAAATTTTCCAAAAACTGCATTTTTACCCTTAAATT
1 TCCAAAAATTCCATTTTTAAC-CTTAAACTTTCCAAAAATTACATTTTTACCCTCAAATG
* *
42619881 TCCAAAAATTCCATTTTTGACCTCAAACTTTCCAAAAATTACATTTTTACCCTCAAATG
1 TCCAAAAATTCCATTTTTAACCTTAAACTTTCCAAAAATTACATTTTTACCCTCAAATG
* * *
42619940 TCCAAAAATTCCATTTTTAACCTTGAACTTTCCAAAAATCACCATTTTT-CCCTCAAGTG
1 TCCAAAAATTCCATTTTTAACCTTAAACTTTCCAAAAATTA-CATTTTTACCCTCAAATG
*
42619999 TCTAAAAATT
1 TCCAAAAATT
42620009 ATCGTTTTAC
Statistics
Matches: 255, Mismatches: 33, Indels: 30
0.80 0.10 0.09
Matches are distributed among these distances:
56 5 0.02
57 19 0.07
58 50 0.20
59 158 0.62
60 23 0.09
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTAACCTTAAACTTTCCAAAAATTACATTTTTACCCTCAAATG
Found at i:42620017 original size:59 final size:59
Alignment explanation
Indices: 42619675--42620049 Score: 253
Period size: 59 Copynumber: 6.4 Consensus size: 59
42619665 ACCCATAAAA
* * * *
42619675 TTTCCAAAAATTA-AATTTTTACCCTCGAACT-TCTAAAAATTCCATTTTTAACC-CTTAA-
1 TTTCCAAAAATTACCATTTTTACCCTC-AAATGTCCAAAAATT-CATTTTTAACCGC-GAAC
* * * * *
42619733 TTTCCAAAAATT-GCATTTTTAAACCC-CGAATGCCCAAAAATTCCA-TTTTGACC-CTAAC
1 TTTCCAAAAATTACCATTTTT--ACCCTCAAATGTCCAAAAATT-CATTTTTAACCGCGAAC
* * * ** *
42619791 TTTCTAAAAATTATCA-TTTTACCCT-AAGATTTCCAAAAATTCCATTTTTAACAC-TAAAT
1 TTTCCAAAAATTACCATTTTTACCCTCAA-ATGTCCAAAAATT-CATTTTTAAC-CGCGAAC
* * * * * * *
42619850 TTTCCAAAAACT-GCATTTTTACCCTTAAATTTCCAAAAATTCCATTTTTGACCTCAAAC
1 TTTCCAAAAATTACCATTTTTACCCTCAAATGTCCAAAAATT-CATTTTTAACCGCGAAC
**
42619909 TTTCCAAAAATTA-CATTTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCTTGAAC
1 TTTCCAAAAATTACCATTTTTACCCTCAAATGTCCAAAAATT-CATTTTTAACCGCGAAC
* * * *
42619968 TTTCCAAAAATCACCATTTTT-CCCTCAAGTGTCTAAAAATT-ATCGTTTTACCCGCGAAC
1 TTTCCAAAAATTACCATTTTTACCCTCAAATGTCCAAAAATTCAT--TTTTAACCGCGAAC
*
42620027 CTT-CAAAAATTACCA-TTTTACCC
1 TTTCCAAAAATTACCATTTTTACCC
42620050 CTTAAGCATC
Statistics
Matches: 264, Mismatches: 35, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
56 5 0.02
57 23 0.09
58 66 0.25
59 157 0.59
60 13 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
TTTCCAAAAATTACCATTTTTACCCTCAAATGTCCAAAAATTCATTTTTAACCGCGAAC
Found at i:42620175 original size:23 final size:24
Alignment explanation
Indices: 42620125--42620176 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
42620115 TACATACTTA
*
42620125 GATTTTAATTATTATTTTTTTCGT
1 GATTTTAATTATTATTTATTTCGT
42620149 -ATTTTATATT-TTATTTATTT-GT
1 GATTTTA-ATTATTATTTATTTCGT
42620171 GATTTT
1 GATTTT
42620177 TGTGTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 20 0.80
24 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (24 bp):
GATTTTAATTATTATTTATTTCGT
Found at i:42631719 original size:3 final size:3
Alignment explanation
Indices: 42631711--42631735 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42631701 TTGGATACTA
42631711 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
42631736 AACCTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:42640162 original size:4 final size:4
Alignment explanation
Indices: 42640138--42640186 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
42640128 TACTTCTAGA
* * *
42640138 TATG TATG AATG CATG CATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
42640185 TA
1 TA
42640187 AATGAAGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:42640181 original size:23 final size:23
Alignment explanation
Indices: 42640141--42640186 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42640131 TTCTAGATAT
42640141 GTATGAATGCATGCATGTATGTA
1 GTATGAATGCATGCATGTATGTA
* * *
42640164 GTATGTATGTATGTATGTATGTA
1 GTATGAATGCATGCATGTATGTA
42640187 AATGAAGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.41
Consensus pattern (23 bp):
GTATGAATGCATGCATGTATGTA
Found at i:42640266 original size:4 final size:4
Alignment explanation
Indices: 42640259--42640366 Score: 83
Period size: 4 Copynumber: 27.2 Consensus size: 4
42640249 ATATGCATGC
* ** *
42640259 ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGC ATGT ACAT ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * ** * * * * *
42640306 ATGC ATGC ATGT ACAT ATGT ACGT ATGT GTGT ATGT ATTT ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
42640354 ATGC ATGT ATGT A
1 ATGT ATGT ATGT A
42640367 ATGAAGGTTT
Statistics
Matches: 83, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
3 3 0.04
4 80 0.96
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (4 bp):
ATGT
Found at i:42640279 original size:15 final size:15
Alignment explanation
Indices: 42640259--42640287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42640249 ATATGCATGC
42640259 ATGTATGTATGTATT
1 ATGTATGTATGTATT
42640274 ATGTATGTATGTAT
1 ATGTATGTATGTAT
42640288 GCATGTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
ATGTATGTATGTATT
Found at i:42640362 original size:24 final size:24
Alignment explanation
Indices: 42640249--42640366 Score: 112
Period size: 24 Copynumber: 5.0 Consensus size: 24
42640239 ATACTTTTAG
*
42640249 ATATGCATGCATGTATGTATGTA-
1 ATATGTATGCATGTATGTATGTAC
* * *
42640272 TTATGTATGTATGTATGCATGTAC
1 ATATGTATGCATGTATGTATGTAC
* *
42640296 ATATGTATGCATGCATGCATGTAC
1 ATATGTATGCATGTATGTATGTAC
* * * *
42640320 ATATGTACGTATGTGTGTATGTAT
1 ATATGTATGCATGTATGTATGTAC
* * *
42640344 TTATGCATGCATGCATGTATGTA
1 ATATGTATGCATGTATGTATGTA
42640367 ATGAAGGTTT
Statistics
Matches: 75, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
23 19 0.25
24 56 0.75
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (24 bp):
ATATGTATGCATGTATGTATGTAC
Found at i:42640524 original size:97 final size:97
Alignment explanation
Indices: 42640358--42640543 Score: 302
Period size: 97 Copynumber: 1.9 Consensus size: 97
42640348 GCATGCATGC
* *
42640358 ATGTATGTAATGAAGGTTTCATAGGTCCCATACATTTAGTATAATGCTGTTTTCCCAAACATTCT
1 ATGTATGTAATGAAGGTTTCATAGGTCCAATACATATAGTATAATGCTGTTTTCCCAAACATTCT
* *
42640423 TGAGGTTTTATGCAACTTGCAAATATGTATGT
66 TGAGGTCTTATGCAACTTACAAATATGTATGT
* *
42640455 ATGTATGTAAATGAAGGTTTCATAGGTCCAATAC-TATAGTATAATGCTGTTTTCCTATACATTC
1 ATGTATGT-AATGAAGGTTTCATAGGTCCAATACATATAGTATAATGCTGTTTTCCCAAACATTC
42640519 TTGAGGTCTTATGCAACTTACAAAT
65 TTGAGGTCTTATGCAACTTACAAAT
42640544 GCTTTTAGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 58 0.71
98 24 0.29
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (97 bp):
ATGTATGTAATGAAGGTTTCATAGGTCCAATACATATAGTATAATGCTGTTTTCCCAAACATTCT
TGAGGTCTTATGCAACTTACAAATATGTATGT
Done.