Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 18 of 27
Found at i:2829573 original size:11 final size:11
Alignment explanation
Indices: 2829559--2829593 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2829549 ATTTTTTTCA
2829559 TGTTGTTTTTT
1 TGTTGTTTTTT
2829570 TGTTGTTTTTAT
1 TGTTGTTTTT-T
*
2829582 TTTTGTTTTTT
1 TGTTGTTTTTT
2829593 T
1 T
2829594 TACTTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (11 bp):
TGTTGTTTTTT
Found at i:2829584 original size:15 final size:15
Alignment explanation
Indices: 2829566--2829595 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2829556 TCATGTTGTT
2829566 TTTTTGTTGTTTTTA
1 TTTTTGTTGTTTTTA
*
2829581 TTTTTGTTTTTTTTA
1 TTTTTGTTGTTTTTA
2829596 CTTCTTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTTTGTTGTTTTTA
Found at i:2834397 original size:26 final size:27
Alignment explanation
Indices: 2834368--2834421 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2834358 TAATTTTTTG
2834368 TTGAA-AAATGGGGTTGGAGTATCCCC
1 TTGAAGAAATGGGGTTGGAGTATCCCC
* *
2834394 TTGAAGGAATGGGGTTGGAGTGTCCCC
1 TTGAAGAAATGGGGTTGGAGTATCCCC
2834421 T
1 T
2834422 GACAATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (27 bp):
TTGAAGAAATGGGGTTGGAGTATCCCC
Found at i:2836620 original size:20 final size:22
Alignment explanation
Indices: 2836595--2836646 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2836585 ACCTAGAATA
2836595 TATCGATACAA-TG-AGAA-ATG
1 TATCGATACAATTGTA-AACATG
2836615 TATCGATACAATTGTAAACATG
1 TATCGATACAATTGTAAACATG
2836637 TATCGATACA
1 TATCGATACA
2836647 TTTCCTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.38
21 4 0.14
22 14 0.48
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (22 bp):
TATCGATACAATTGTAAACATG
Found at i:2837097 original size:120 final size:120
Alignment explanation
Indices: 2836935--2837178 Score: 380
Period size: 120 Copynumber: 2.0 Consensus size: 120
2836925 CCAATCTTCG
* * *
2836935 TCCCCACACATCTCCAATCCTCCATCTACAAGGTAGGCCTCAAGTTGTCGGAAATTGGCCTGGAC
1 TCCCCACACATCTCCAATCCTCCATCTACAAGGTAGGCCTCAAGTTGTCGAAAATTGACCCGGAC
* **
2837000 AAAATGAGATGTCCACAATATTACATAGGTGTCAGTAAAATATTGAAGTTTAACT
66 AAAATGAGATGTCCACAATATTACATAGGTGTCAATAAAATATCAAAGTTTAACT
* * * *
2837055 TCCCCACACATCTCCAATCCTCCATTTACTAGGTAGGCCTCAAGTTGTTGAAAATTGACCCGGAT
1 TCCCCACACATCTCCAATCCTCCATCTACAAGGTAGGCCTCAAGTTGTCGAAAATTGACCCGGAC
* *
2837120 AAAATGAGATGTCCACAATATTACATAGGTGTTAATAAAATATCAAAGTTTATCT
66 AAAATGAGATGTCCACAATATTACATAGGTGTCAATAAAATATCAAAGTTTAACT
2837175 TCCC
1 TCCC
2837179 AAAATTTAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (120 bp):
TCCCCACACATCTCCAATCCTCCATCTACAAGGTAGGCCTCAAGTTGTCGAAAATTGACCCGGAC
AAAATGAGATGTCCACAATATTACATAGGTGTCAATAAAATATCAAAGTTTAACT
Found at i:2837748 original size:41 final size:41
Alignment explanation
Indices: 2837703--2837859 Score: 145
Period size: 41 Copynumber: 3.8 Consensus size: 41
2837693 GACTGAGATG
*
2837703 AAACCATATGAATCAACGAATGAGAAAAGTTGACCAGGACA
1 AAACCATATGAATCAACGAAAGAGAAAAGTTGACCAGGACA
* * ***
2837744 AAACCATATGAGA-CAAAGAAAGGGAAAAGTTGATTGGGACA
1 AAACCATATGA-ATCAACGAAAGAGAAAAGTTGACCAGGACA
* * * ** * *
2837785 AAACCATACGAGTTAACGAATTAGAAAATTTGACCAGGATA
1 AAACCATATGAATCAACGAAAGAGAAAAGTTGACCAGGACA
* * * *
2837826 AAACCATATGAGTTAATGAAAGGGAAAAGTTGAC
1 AAACCATATGAATCAACGAAAGAGAAAAGTTGAC
2837860 AAGATGACAT
Statistics
Matches: 90, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
41 89 0.99
42 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.18
Consensus pattern (41 bp):
AAACCATATGAATCAACGAAAGAGAAAAGTTGACCAGGACA
Found at i:2837829 original size:82 final size:82
Alignment explanation
Indices: 2837703--2837858 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 82
2837693 GACTGAGATG
*
2837703 AAACCATATGAATCAACGAATGAGAAAAGTTGACCAGGACAAAACCATATGAGACAAAGAAAGGG
1 AAACCATACGAATCAACGAATGAGAAAAGTTGACCAGGACAAAACCATATGAGACAAAGAAAGGG
2837768 AAAAGTTGATTGGGACA
66 AAAAGTTGATTGGGACA
* * * * * ** *
2837785 AAACCATACGAGTTAACGAATTAGAAAATTTGACCAGGATAAAACCATATGAGTTAATGAAAGGG
1 AAACCATACGAATCAACGAATGAGAAAAGTTGACCAGGACAAAACCATATGAGACAAAGAAAGGG
2837850 AAAAGTTGA
66 AAAAGTTGA
2837859 CAAGATGACA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.18
Consensus pattern (82 bp):
AAACCATACGAATCAACGAATGAGAAAAGTTGACCAGGACAAAACCATATGAGACAAAGAAAGGG
AAAAGTTGATTGGGACA
Found at i:2837992 original size:42 final size:42
Alignment explanation
Indices: 2837931--2838080 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 42
2837921 TCACCAAGGT
* *
2837931 AAAATCTATAAAGTCAACTAAATGTAAAAGAGTTGACCAGGC
1 AAAATCAATAAAGTCAACTAAAGGTAAAAGAGTTGACCAGGC
* *
2837973 AAAATCGATAAAGTTAACTAAAGGT-AAAGAAGTTGACCAGGGC
1 AAAATCAATAAAGTCAACTAAAGGTAAAAG-AGTTGACCA-GGC
* * * * *
2838016 GAAACCAATAAAATCAACTAAGGGTAAAAGAGTTGACCAAGGA
1 AAAATCAATAAAGTCAACTAAAGGTAAAAGAGTTGACC-AGGC
*
2838059 AAAATTAATAAAGTCAACTAAA
1 AAAATCAATAAAGTCAACTAAA
2838081 TATGACTAGG
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
41 4 0.04
42 31 0.35
43 49 0.55
44 5 0.06
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.19
Consensus pattern (42 bp):
AAAATCAATAAAGTCAACTAAAGGTAAAAGAGTTGACCAGGC
Found at i:2838144 original size:67 final size:63
Alignment explanation
Indices: 2838041--2838276 Score: 208
Period size: 64 Copynumber: 3.6 Consensus size: 63
2838031 AACTAAGGGT
* * *
2838041 AAAAGAGTTGACCAAGGAAAAATTAATAAAGTCAACTAAATATGACTAGGACAAACCTAAAGTAA
1 AAAAG-GTTGGCCAAGGCAAAACTAATAAAGTCAACTAAATATGACTAGGACAAACCT-AAGTAA
* * * *
2838106 AAAATGGTATTGGCTAAGGCAAAA-TCGATAAAGTCAACTAAAGATGACTACGACAAAACCTAAG
1 AAAA-GG--TTGGCCAAGGCAAAACT-AATAAAGTCAACTAAATATGACTAGGAC-AAACCTAAG
*
2838170 TCA
61 TAA
** * * *
2838173 AAAAGGTTGGCCAAGGTTAAACTAATAAAGTCAAGTAAATGTGACTAGGATGAAACCTAAGTCAA
1 AAAAGGTTGGCCAAGGCAAAACTAATAAAGTCAACTAAATATGACTAGGA-CAAACCTAAGT-AA
* * *
2838238 AAAAGG-TGGACCAAGGCGAAAGC-GATAAAGTTAACTAAA
1 AAAAGGTTGG-CCAAGGC-AAAACTAATAAAGTCAACTAAA
2838277 GGTGACTGGT
Statistics
Matches: 138, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
64 47 0.34
65 32 0.23
66 7 0.05
67 46 0.33
68 6 0.04
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (63 bp):
AAAAGGTTGGCCAAGGCAAAACTAATAAAGTCAACTAAATATGACTAGGACAAACCTAAGTAA
Found at i:2838879 original size:76 final size:75
Alignment explanation
Indices: 2838706--2838969 Score: 239
Period size: 76 Copynumber: 3.5 Consensus size: 75
2838696 ATTAAGAAAC
* * * * * * * *
2838706 ATGTGGTTTCTTCAATTTCCATTAATAGCCGAAACAAACCGATAACAAGCT--GAAGAAGAATAT
1 ATGTAGTTTCTACAATTTCCATCAATAGCCGAAACAAACTGAAAATAAGCTAAAAAGAAGAACAT
2838769 GATAGGGAA-
66 GATAGGGAAT
* * * *
2838778 ATGTGGTTTTTACAATTTTCCATCAATAGCCAAAACAAACTGAAAATAAGCTAAAAAAGAAAAAC
1 ATGTAGTTTCTACAA-TTTCCATCAATAGCCGAAACAAACTGAAAATAAGCT-AAAAAGAAGAAC
*
2838843 ATGATGGGGAAT
64 ATGATAGGGAAT
* * **
2838855 ATTTAGTTTCTACAATTTCCATCAACAGTTGAAACAAACT-AATAATAAGCTGAAAAAGAAGAAC
1 ATGTAGTTTCTACAATTTCCATCAATAGCCGAAACAAACTGAA-AATAAGCT-AAAAAGAAGAAC
*
2838919 AAGATAGGGAAT
64 ATGATAGGGAAT
* * * * * *
2838931 ATGTGGTTTCCAAAATCTCCCATCAATGGTCGAAACAAA
1 ATGTAGTTTCTACAAT-TTCCATCAATAGCCGAAACAAA
2838970 TTGACAAGAG
Statistics
Matches: 155, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
72 13 0.08
73 31 0.20
75 2 0.01
76 79 0.51
77 30 0.19
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (75 bp):
ATGTAGTTTCTACAATTTCCATCAATAGCCGAAACAAACTGAAAATAAGCTAAAAAGAAGAACAT
GATAGGGAAT
Found at i:2839184 original size:59 final size:60
Alignment explanation
Indices: 2839109--2839415 Score: 182
Period size: 60 Copynumber: 5.2 Consensus size: 60
2839099 AGACCGCACT
* * *
2839109 AGAAACCTACAA-AATGATTTGGGCAAAACCAAAACTCAAAGGAATGGCCTGGATGAGACC
1 AGAAACCTA-AATAATGATTTGGGCAAAACCAAAACTCAAAGAAATAGCCTGGATGAAACC
** * * * *
2839169 A-AAACCTAAATAATGATTTGGGTGAAACTAAGATTCAATGAAATAGCCTGGATGAAACC
1 AGAAACCTAAATAATGATTTGGGCAAAACCAAAACTCAAAGAAATAGCCTGGATGAAACC
* * * * ** * * **
2839228 AGAAAACTAAATAATGACTTGGCCAAAACCAAAGCTCAACTAAAT-GACTTGAAAAAAACC
1 AGAAACCTAAATAATGATTTGGGCAAAACCAAAACTCAAAGAAATAG-CCTGGATGAAACC
* * * * * * * * *
2839288 AAAAACCTAAACAATGACTTAGGCAAAACCAAGATTCAATGAAAT-GGCTCAGAT-AGAACC
1 AGAAACCTAAATAATGATTTGGGCAAAACCAAAACTCAAAGAAATAGCCT-GGATGA-AACC
* * ** * * * *
2839348 AGATATC-AAGA-AATGGCTTAGCCAAAACCAAAACTCAAAGAAATGGCCTAGATGAAA-C
1 AGAAACCTAA-ATAATGATTTGGGCAAAACCAAAACTCAAAGAAATAGCCTGGATGAAACC
2839406 A-AAACCTAAA
1 AGAAACCTAAA
2839416 AATTAACTAC
Statistics
Matches: 188, Mismatches: 50, Indels: 21
0.73 0.19 0.08
Matches are distributed among these distances:
57 4 0.02
58 6 0.03
59 86 0.46
60 92 0.49
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (60 bp):
AGAAACCTAAATAATGATTTGGGCAAAACCAAAACTCAAAGAAATAGCCTGGATGAAACC
Found at i:2839257 original size:30 final size:28
Alignment explanation
Indices: 2839223--2839319 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 28
2839213 AGCCTGGATG
2839223 AAACCAGAAAACTAAATAATGACTTGGCCA
1 AAACCA-AAAACTAAATAATGACTTGG-CA
* * **
2839253 AAACC-AAAGCTCAACTAAATGACTTGAAAA
1 AAACCAAAAACT-AAAT-AATGACTTG-GCA
*
2839283 AAACCAAAAACCTAAACAATGACTTAGGCA
1 AAACCAAAAA-CTAAATAATGACTT-GGCA
2839313 AAACCAA
1 AAACCAA
2839320 GATTCAATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
28 5 0.10
29 3 0.06
30 36 0.69
31 6 0.12
32 2 0.04
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.14
Consensus pattern (28 bp):
AAACCAAAAACTAAATAATGACTTGGCA
Found at i:2839348 original size:120 final size:119
Alignment explanation
Indices: 2839169--2839385 Score: 260
Period size: 120 Copynumber: 1.8 Consensus size: 119
2839159 GGATGAGACC
* * * ** * *
2839169 AAAACCTAAATAATGATTTGGGTGAAACTAAGATTCAATGAAATAGCCTGGATGAAACCAGAAAA
1 AAAACCTAAACAATGACTTAGGCAAAACCAAGATTCAATGAAATAGCCTAGATGAAACCAGAAAA
* *
2839234 CTAA-ATAATGACTTGGCCAAAACCAAAGCTCAACTAAATGACTTGAAAAAAACCA
66 C-AAGA-AATGACTTAGCCAAAACCAAAACTCAACTAAATGACTTGAAAAAAACCA
* *
2839289 AAAACCTAAACAATGACTTAGGCAAAACCAAGATTCAATGAAAT-GGCTCAGAT-AGAACCAGAT
1 AAAACCTAAACAATGACTTAGGCAAAACCAAGATTCAATGAAATAGCCT-AGATGA-AACCAGAA
* *
2839352 ATCAAGAAATGGCTTAGCCAAAACCAAAACTCAA
64 AACAAGAAATGACTTAGCCAAAACCAAAACTCAA
2839386 AGAAATGGCC
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
119 30 0.37
120 51 0.63
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (119 bp):
AAAACCTAAACAATGACTTAGGCAAAACCAAGATTCAATGAAATAGCCTAGATGAAACCAGAAAA
CAAGAAATGACTTAGCCAAAACCAAAACTCAACTAAATGACTTGAAAAAAACCA
Found at i:2839376 original size:29 final size:29
Alignment explanation
Indices: 2839300--2839399 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 29
2839290 AAACCTAAAC
* *
2839300 AATGACTTAGGCAAAACCAAGAT-TCAATGA
1 AATGGCTTAGACAAAACC-AGATATCAA-GA
* * *
2839330 AATGGCTCAGATAGAACCAGATATCAAGA
1 AATGGCTTAGACAAAACCAGATATCAAGA
* *
2839359 AATGGCTTAGCCAAAACCA-AAACTCAAAGA
1 AATGGCTTAGACAAAACCAGATA-TC-AAGA
*
2839389 AATGGCCTAGA
1 AATGGCTTAGA
2839400 TGAAACAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
28 2 0.04
29 23 0.42
30 30 0.55
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.17
Consensus pattern (29 bp):
AATGGCTTAGACAAAACCAGATATCAAGA
Found at i:2840743 original size:112 final size:109
Alignment explanation
Indices: 2840545--2840862 Score: 304
Period size: 112 Copynumber: 2.9 Consensus size: 109
2840535 ACTTCAGTTT
* * ** * *
2840545 AAAAATTTCAAAACTAATAGGATAAAAGCCCTATTTTTCGAGGCACGAATGGATCGA-ATTGTAT
1 AAAAATTTCAAAACTAATAGGATACATGCCCTATTTCCCCAGGCACGAATGGATC-ATGTTGTAT
* * * * *
2840609 AAAATATGAACTTATTTAAAAATCAGACAAACTTGATGTTGTTGGCTA
65 AAAACATGAATTTCTTTGAAAATCAGACAAA-TT--TGTTATTGGCTA
* * * * * *
2840657 AAAAATTTCAAAATTGATAGGATACATGTCCC-ATTTCCCTAGGCATGAATGGATCTTGTTGTAC
1 AAAAATTTCAAAACTAATAGGATACATG-CCCTATTTCCCCAGGCACGAATGGATCATGTTGTAT
* *
2840721 AAAACATGAATTTCTTTGAAAATTAGACAAATTTGTTATTGGCTC
65 AAAACATGAATTTCTTTGAAAATCAGACAAATTTGTTATTGGCTA
* * * * * *
2840766 AAAGATTTCTAAACCAATAGGATACATGCCCTATTTCCCCAGACACAAATGCATCATGTTGTATA
1 AAAAATTTCAAAACTAATAGGATACATGCCCTATTTCCCCAGGCACGAATGGATCATGTTGTATA
*
2840831 TAACAT-AATTTCCTTTG-AAATCAAGA-AAATTT
66 AAACATGAATTT-CTTTGAAAATC-AGACAAATTT
2840863 AATGTTCTTT
Statistics
Matches: 169, Mismatches: 32, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
108 18 0.11
109 72 0.43
111 2 0.01
112 74 0.44
113 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (109 bp):
AAAAATTTCAAAACTAATAGGATACATGCCCTATTTCCCCAGGCACGAATGGATCATGTTGTATA
AAACATGAATTTCTTTGAAAATCAGACAAATTTGTTATTGGCTA
Found at i:2841496 original size:17 final size:18
Alignment explanation
Indices: 2841474--2841507 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2841464 GGCATTGTCG
2841474 TAATTTT-TTAAAAATTT
1 TAATTTTATTAAAAATTT
2841491 TAATTTTATTAAAAATT
1 TAATTTTATTAAAAATT
2841508 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTTTATTAAAAATTT
Found at i:2843880 original size:216 final size:217
Alignment explanation
Indices: 2843498--2843938 Score: 733
Period size: 216 Copynumber: 2.0 Consensus size: 217
2843488 ACTTGTTTGT
*
2843498 CTTAAGGATATGCATGCATCAATTTGTCATCACCATGGATTTTTTTCTCATGAAATATGTCATCT
1 CTTAAGGATATGCATGCATCAATTTGTCATCACCATGGATTTTTTTCTCATGAAAAATGTCATCT
*
2843563 TGGTTTATGCATATGTGTTCTCCATGTTCTATATTGTGTTTGTTGCATTTGGCTTGTTTTAAGAT
66 TGGTTTATGCATATGTGTTCTCCATGTTCTATATTGTGTTTGTTGCATTTGGCTTGTGTTAAGAT
** *
2843628 GCTTGCTTGTGTGCTAAAAATCTAGTTT-TGAAAAAAATCCCCAAGTCAAGTTCATGTTACCTCC
131 GCTTGCTTGTGTGCTAAAAATCTAGTTTCAAAAAAAAATCCCCAAGTCAAGTTCATATTACCTCC
**
2843692 CATG-TATAGGGAATAACATGGA
196 CATGCT-TAGAAAATAACATGGA
*
2843714 CTTAAGGATATGCATGCATCAATTTGTCATCAGCATGGATTTTTTTCTCATGAAAAATGTCATCT
1 CTTAAGGATATGCATGCATCAATTTGTCATCACCATGGATTTTTTTCTCATGAAAAATGTCATCT
* * *
2843779 TGGTTTTTGCGTATGTGTTCTCCATGTTCTATATTGTGTTTGTTGCATTTTGCTTGTGTTAAGAT
66 TGGTTTATGCATATGTGTTCTCCATGTTCTATATTGTGTTTGTTGCATTTGGCTTGTGTTAAGAT
* *
2843844 GCTTGCTTGTGTGCTAAATATCTGGTTTCAAAAAAAAAATCCCCAAGTCAAGTTCATATTACCTC
131 GCTTGCTTGTGTGCTAAAAATCTAGTTTC-AAAAAAAAATCCCCAAGTCAAGTTCATATTACCTC
2843909 CCATGCTTAGAAAATAACATGGA
195 CCATGCTTAGAAAATAACATGGA
2843932 CTTAAGG
1 CTTAAGG
2843939 TTTTCAGAGA
Statistics
Matches: 209, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
216 150 0.72
218 58 0.28
219 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (217 bp):
CTTAAGGATATGCATGCATCAATTTGTCATCACCATGGATTTTTTTCTCATGAAAAATGTCATCT
TGGTTTATGCATATGTGTTCTCCATGTTCTATATTGTGTTTGTTGCATTTGGCTTGTGTTAAGAT
GCTTGCTTGTGTGCTAAAAATCTAGTTTCAAAAAAAAATCCCCAAGTCAAGTTCATATTACCTCC
CATGCTTAGAAAATAACATGGA
Found at i:2857101 original size:6 final size:6
Alignment explanation
Indices: 2857092--2857118 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2857082 AAAAAAAATG
2857092 AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAA
2857119 GGAACAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:2858633 original size:32 final size:31
Alignment explanation
Indices: 2858328--2859569 Score: 671
Period size: 31 Copynumber: 40.3 Consensus size: 31
2858318 TAAAAAGCAA
* * *
2858328 GACATTTTCTTTCTTTGTCCTAAAAAAGCAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * *
2858359 GACATTTTCATTT-TTTGTCCTTAAA-AGCAA
1 GACATTTTC-TTTCTTTGTCCTCAAAGAGTAG
** * ** * *
2858389 GATGTTTTCTTCCTTCATCCTCAAAGAGCAA
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * * * *
2858420 GACGTTTTCTTTTTTTGTTCTTAAAGAGCAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
**** * * *
2858451 GATGCGTTCTTTCATTGTCCTCAAAGAGCAA
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
*
2858482 GACATTTTCTTTCTCTGTCCTCAAAGAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
2858513 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * *
2858544 GACAATTTC-TTCTTTTATCCTTAAAGAGTAG
1 GACATTTTCTTTC-TTTGTCCTCAAAGAGTAG
** * ** * *
2858575 GACGGTTTCTTTTTCTTAACCCCAAAGAGTAA
1 GACATTTTCTTTCT-TTGTCCTCAAAGAGTAG
*
2858607 GACATTTTCCTTTCTTTATCCTCAAAGAGTAG
1 GACATTTT-CTTTCTTTGTCCTCAAAGAGTAG
* * *
2858639 GACAATTTCCTTCTTTTTCCTCAAAGAGTA-
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * *
2858669 -AAATTTT-TTTCTTTATCCTTAAAGAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * * *
2858698 GACA--TT-TTT-TTTATCTTCAAAGAGCAA
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
** * * *
2858725 GACGCTTTCTTTGTTTGTCTTCAAAGAGTAT
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * ** * *
2858756 GACGTTTTTCTTTCTTTATTTTCAAAGAGAAA
1 GAC-ATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * * *
2858788 AACATTTTCTTTCTTTGTCGTTAAAGAGTAA
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
** * ** * *
2858819 GATGTTTTCTTCCTTTGTTTTAAAAAAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * * * * *
2858850 GATGC-CTTCCTCT-TTTGTCTTCAAGGAGCA-
1 GA--CATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * * * *
2858880 -AGA-TGT-TTTCTTTG-CTTCAAAGGGCAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* *
2858907 GACATTTT-TCTTCTTTTGTCTTTAAAGAGTAG
1 GACATTTTCT-TTC-TTTGTCCTCAAAGAGTAG
** * * *
2858939 GACGCTTTCCTTCTTTGTCCTAAAAAAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
** * * *
2858970 GATGTTTT-TCTCCTTTATCCTCAAAGA-TCAA
1 GACATTTTCT-TTCTTTGTCCTCAAAGAGT-AG
* *
2859001 GAGATTTTCTTTCTTTGTCCTCAAAGAGCA-
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * **
2859031 -AAATGTTTCTTTTTTTTTTGTATTCAAAGAGTAG
1 GACAT-TTTC---TTTCTTTGTCCTCAAAGAGTAG
** * **
2859065 GACATTTTCTTTCCATGTTCTCAAAGAACAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
** * * *
2859096 GATGTTTTCTTTCTTTGTCTTCAAAAAGCAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
** *
2859127 GATGTTTTTCTTTCTTCGTCCTCAAAGA-TAAG
1 GA-CATTTTCTTTCTTTGTCCTCAAAGAGT-AG
** * * * *
2859159 GATGTTTCCTTTATTTGTCCTCAAAGAGAAA
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * *
2859190 GACATTTTCCTTTCTTTATCCTCAAAGAGAAA
1 GACATTTT-CTTTCTTTGTCCTCAAAGAGTAG
*
2859222 GACATTTTCCTTTCTTTATCCTCAAAGAGTA-
1 GACATTTT-CTTTCTTTGTCCTCAAAGAGTAG
2859253 GATCATTTTCCTTTCTTTGTCCTCAAAGAGTAG
1 GA-CATTTT-CTTTCTTTGTCCTCAAAGAGTAG
** * * *
2859286 GATGTTTT-TTTCTTTGTTCTTAAAAAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
*
2859316 GACATTTT-TCTCTTTTGTCCTCAAAGAGTAG
1 GACATTTTCTTTC-TTTGTCCTCAAAGAGTAG
* * *
2859347 GATATTTTCTTTCTTTATCCTCAAAGAGCAAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAG-TAG
* * *
2859379 AAAATTTTCTTTCTTTGTCCTCAAAGAGCAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* * *
2859410 GACATTTTTCTCCTTTCTTTATCTTCAAAGACTAG
1 GACA--TTT-T-CTTTCTTTGTCCTCAAAGAGTAG
** * * *
2859445 GATGTTTT-TCTTCTTTGTCCTCCAAGAGCAA
1 GACATTTTCT-TTCTTTGTCCTCAAAGAGTAG
2859476 GACA-----TTT-TTT-TCCTCAAAGAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
* *
2859500 GACATTTTCTTTCTTTGTCCTCAGAGAGCAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
*** *
2859531 GATGCTTTCTTTCTTTTTCCTCAAAGAGTAG
1 GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
2859562 GACATTTT
1 GACATTTT
2859570 TCCTTTCTGT
Statistics
Matches: 936, Mismatches: 219, Indels: 112
0.74 0.17 0.09
Matches are distributed among these distances:
24 15 0.02
25 3 0.00
26 14 0.01
27 23 0.02
28 25 0.03
29 19 0.02
30 68 0.07
31 480 0.51
32 230 0.25
33 30 0.03
34 5 0.01
35 24 0.03
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (31 bp):
GACATTTTCTTTCTTTGTCCTCAAAGAGTAG
Found at i:2858660 original size:126 final size:122
Alignment explanation
Indices: 2858472--2858700 Score: 343
Period size: 126 Copynumber: 1.8 Consensus size: 122
2858462 TCATTGTCCT
* * *
2858472 CAAAGAGCAAGACATTTTCTTTCTCTGTCCTCAAAGAGTAGGACATTTTCTTTCTTTGTCCTCAA
1 CAAAGAGCAAGACATTTTCTTTCTCTATCCTCAAAGAGTAGGACAATTTCCTTCTTTGTCCTCAA
2858537 AGAGTAGGACAATTTCTTCT-TTTATCCTTAAAGAGTAGGACGGTTTCTTTTTCTTAACCC
66 AGAGTA--A-AATTT-TTCTCTTTATCCTTAAAGAGTAGGACGGTTTCTTTTTCTTAACCC
* * *
2858597 CAAAGAGTAAGACATTTTCCTTTCTTTATCCTCAAAGAGTAGGACAATTTCCTTCTTTTTCCTCA
1 CAAAGAGCAAGACATTTT-CTTTCTCTATCCTCAAAGAGTAGGACAATTTCCTTCTTTGTCCTCA
*
2858662 AAGAGTAAAATTTTTTTCTTTATCCTTAAAGAGTAGGAC
65 AAGAGTAAAATTTTTCTCTTTATCCTTAAAGAGTAGGAC
2858701 ATTTTTTTTA
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
122 3 0.03
123 26 0.27
124 1 0.01
125 17 0.18
126 48 0.51
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (122 bp):
CAAAGAGCAAGACATTTTCTTTCTCTATCCTCAAAGAGTAGGACAATTTCCTTCTTTGTCCTCAA
AGAGTAAAATTTTTCTCTTTATCCTTAAAGAGTAGGACGGTTTCTTTTTCTTAACCC
Found at i:2858783 original size:63 final size:62
Alignment explanation
Indices: 2858707--2858839 Score: 151
Period size: 63 Copynumber: 2.1 Consensus size: 62
2858697 GGACATTTTT
* * * * * * *
2858707 TTTATCTTCAAAGAGCAAGACGCTTTCTTTGTTTGTC-TTCAAAGAGTATGACGTTTTTCTTTC
1 TTTATTTTCAAAGAGAAAAACACTTTCTTTCTTTGTCGTT-AAAGAGTAAGACG-TTTTCTTCC
* *
2858770 TTTATTTTCAAAGAGAAAAACATTTTCTTTCTTTGTCGTTAAAGAGTAAGATGTTTTCTTCC
1 TTTATTTTCAAAGAGAAAAACACTTTCTTTCTTTGTCGTTAAAGAGTAAGACGTTTTCTTCC
*
2858832 TTTGTTTT
1 TTTATTTT
2858840 AAAAAAGTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
62 15 0.25
63 42 0.71
64 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (62 bp):
TTTATTTTCAAAGAGAAAAACACTTTCTTTCTTTGTCGTTAAAGAGTAAGACGTTTTCTTCC
Found at i:2859002 original size:120 final size:120
Alignment explanation
Indices: 2858792--2859012 Score: 268
Period size: 120 Copynumber: 1.8 Consensus size: 120
2858782 GAGAAAAACA
* * **
2858792 TTTTCTTTCTTTGTCGTTAAAGAGTAAGATGTTTTCTTCCTTTGTTTTAAAAAAGTAGGATGCCT
1 TTTTCTTTCTTTGTCGTTAAAGAGTAAGACGTTTCCTTCCTTTGTCCTAAAAAAGTAGGATGCCT
* * * *
2858857 TCCTCTTTTGTCTTCAAGGAGCAAGATG-TTTTCTTTGCTTCAAAGGGCAGGACAT
66 TCCTCCTTTATCCTCAAAGAGCAAGA-GATTTTCTTTGCTTCAAAGGGCAGGACAT
* * *
2858912 TTTTC-TTCTTTTGTCTTTAAAGAGTAGGACGCTTTCCTT-CTTTGTCCTAAAAAAGTAGGATGT
1 TTTTCTTTC-TTTGTCGTTAAAGAGTAAGACG-TTTCCTTCCTTTGTCCTAAAAAAGTAGGATGC
* * *
2858975 TTTTCTCCTTTATCCTCAAAGATCAAGAGATTTTCTTT
64 CTTCCTCCTTTATCCTCAAAGAGCAAGAGATTTTCTTT
2859013 CTTTGTCCTC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
119 4 0.05
120 74 0.88
121 6 0.07
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (120 bp):
TTTTCTTTCTTTGTCGTTAAAGAGTAAGACGTTTCCTTCCTTTGTCCTAAAAAAGTAGGATGCCT
TCCTCCTTTATCCTCAAAGAGCAAGAGATTTTCTTTGCTTCAAAGGGCAGGACAT
Found at i:2859495 original size:24 final size:25
Alignment explanation
Indices: 2859462--2859512 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2859452 TTCTTCTTTG
*
2859462 TCCTCCAAGAGCAAGACATTTT-TT
1 TCCTCAAAGAGCAAGACATTTTCTT
* *
2859486 TCCTCAAAGAGTAGGACATTTTCTT
1 TCCTCAAAGAGCAAGACATTTTCTT
2859511 TC
1 TC
2859513 TTTGTCCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (25 bp):
TCCTCAAAGAGCAAGACATTTTCTT
Found at i:2859552 original size:86 final size:89
Alignment explanation
Indices: 2859396--2859570 Score: 207
Period size: 86 Copynumber: 2.0 Consensus size: 89
2859386 TCTTTCTTTG
* *
2859396 TCCTCAAAGAGCAGGACATTTTTCTCCTTTCTTTATCTTCAAAGACTAGGATGTTTTTCTTCTTT
1 TCCTCAAAGAGCAGGACA-TTTTCTCCTTTCTTTATCCTCAAAGACTAGGATGTTTCTCTTCTTT
*
2859461 GTCCTCCAAGAGCAAGACATTTTTT
65 GTCCTCAAAGAGCAAGACATTTTTT
* * *
2859486 TCCTCAAAGAGTAGGACA-TTT-T-CTTTCTTTGTCCTCAGAGAGC-AGGATGCTTTCT-TTCTT
1 TCCTCAAAGAGCAGGACATTTTCTCCTTTCTTTATCCTCAAAGA-CTAGGATG-TTTCTCTTCTT
* * *
2859546 TTTCCTCAAAGAGTAGGACATTTTT
64 TGTCCTCAAAGAGCAAGACATTTTT
2859571 CCTTTCTGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
86 48 0.65
87 6 0.08
88 3 0.04
90 17 0.23
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (89 bp):
TCCTCAAAGAGCAGGACATTTTCTCCTTTCTTTATCCTCAAAGACTAGGATGTTTCTCTTCTTTG
TCCTCAAAGAGCAAGACATTTTTT
Found at i:2860259 original size:111 final size:114
Alignment explanation
Indices: 2860053--2860288 Score: 325
Period size: 111 Copynumber: 2.1 Consensus size: 114
2860043 TTCCATGTGT
* * *
2860053 AGTATCAATACATGAAGGCTTGGTATTGATACCCAAGGTGTGTATATCGATACCTAGTGTGATTG
1 AGTATCGATACATGAAGGCTTGGTATCGATACCCAAGGTGTGTATATCAATACCTAGTGTGATTG
* * * **
2860118 TATCGATACAAGCCTTAGCAGTGGCTAAAATTTGATTTT-TGGATAGCA
66 TATCGATACAAGCCTTAGCAATAGCTAAAATTAGATTTTCTAAATAGCA
* * * *
2860166 AGTATTGATACGTGAAGGCTTGGTATCGATACCC-AGGTGTG-GTATCAATACTTAGTGTGATTG
1 AGTATCGATACATGAAGGCTTGGTATCGATACCCAAGGTGTGTATATCAATACCTAGTGTGATTG
* *
2860229 TATTGATACAAGCCTTGGCAATAGCTAAAATTAGATTTTCTAAATAGCA
66 TATCGATACAAGCCTTAGCAATAGCTAAAATTAGATTTTCTAAATAGCA
2860278 AGTATCGATAC
1 AGTATCGATAC
2860289 TCAAGTAATT
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
111 53 0.50
112 24 0.22
113 30 0.28
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (114 bp):
AGTATCGATACATGAAGGCTTGGTATCGATACCCAAGGTGTGTATATCAATACCTAGTGTGATTG
TATCGATACAAGCCTTAGCAATAGCTAAAATTAGATTTTCTAAATAGCA
Found at i:2863780 original size:20 final size:19
Alignment explanation
Indices: 2863738--2863824 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 19
2863728 CTACCACTGT
* *
2863738 TTGTATCGATGCATGGTACA
1 TTGTATCGATACATGATA-A
2863758 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGAT-AA
*
2863778 TTGTATAGATAC------A
1 TTGTATCGATACATGATAA
2863791 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGAT-AA
2863811 TTGTATCGATACAT
1 TTGTATCGATACAT
2863825 TGCTTATAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
13 12 0.22
20 42 0.76
21 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGATAA
Found at i:2863796 original size:33 final size:33
Alignment explanation
Indices: 2863754--2863826 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
2863744 CGATGCATGG
2863754 TACATTGTATCGATACATGATGAATTGTATAGA
1 TACATTGTATCGATACATGATGAATTGTATAGA
*
2863787 TACATTGTATCGATACATGATGAATTGTATCGA
1 TACATTGTATCGATACATGATGAATTGTATAGA
2863820 TACATTG
1 TACATTG
2863827 CTTATAACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (33 bp):
TACATTGTATCGATACATGATGAATTGTATAGA
Found at i:2872283 original size:19 final size:19
Alignment explanation
Indices: 2872240--2872312 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
2872230 CACACCCAGA
*
2872240 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
2872260 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
2872279 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
*
2872299 TGTATAGATACATG
1 TGTATCGATACATG
2872313 AAACTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:2872366 original size:20 final size:20
Alignment explanation
Indices: 2872341--2872394 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2872331 CTACCACTGT
*
2872341 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
2872361 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGATGAA
2872381 TTGTATCGATACAT
1 TTGTATCGATACAT
2872395 TGCTTATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:2874757 original size:20 final size:20
Alignment explanation
Indices: 2874715--2874764 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2874705 ACAATTTGTT
2874715 TCGATACAATAAGGTAATATA
1 TCGATAC-ATAAGGTAATATA
*
2874736 TCGATACATAA-GTGAATGTA
1 TCGATACATAAGGT-AATATA
2874756 TCGATACAT
1 TCGATACAT
2874765 GCTAGAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 18 0.67
21 7 0.26
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TCGATACATAAGGTAATATA
Found at i:2890097 original size:19 final size:18
Alignment explanation
Indices: 2890073--2890129 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
2890063 CGTATGTGGT
2890073 GATACATAAGTGTTGTATC
1 GATACATAAGT-TTGTATC
2890092 GATAC--AA---TGTATC
1 GATACATAAGTTTGTATC
*
2890105 GATGCATAAGTTTTGTATC
1 GATACATAAG-TTTGTATC
2890124 GATACA
1 GATACA
2890130 ATGTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 10 0.33
15 2 0.07
17 2 0.07
19 16 0.53
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (18 bp):
GATACATAAGTTTGTATC
Found at i:2890190 original size:13 final size:13
Alignment explanation
Indices: 2890172--2890196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2890162 ATTACTCAAA
2890172 TGTATCGATACAT
1 TGTATCGATACAT
2890185 TGTATCGATACA
1 TGTATCGATACA
2890197 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2890250 original size:52 final size:52
Alignment explanation
Indices: 2890205--2890333 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
2890195 CACTGATCTT
*
2890205 TGTATCGATACATTCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2890257 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2890309 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2890334 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2904193 original size:21 final size:19
Alignment explanation
Indices: 2904167--2904294 Score: 91
Period size: 20 Copynumber: 6.4 Consensus size: 19
2904157 TGCATCCTCC
*
2904167 ACAAAAAAAAAACCAAATAA
1 ACAAAAAAAAAAACAAA-AA
*
2904187 ACAAAAAAAAAGAA-AGAAGA
1 ACAAAAAAAAA-AACA-AAAA
*
2904207 A-AAAAACAAAAACAAAAAA
1 ACAAAAAAAAAAAC-AAAAA
2904226 ACAAAAAACAAAAA-ACAAAA
1 ACAAAAAA-AAAAACA-AAAA
*
2904246 ACAAAAAAAACAAAGAAAAA
1 ACAAAAAAAA-AAACAAAAA
* *
2904266 AGAAACAACAAAAACAACAACA
1 ACAAA-AAAAAAAACAA-AA-A
2904288 ACAAAAA
1 ACAAAAA
2904295 GGGTCTGGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.02
19 15 0.17
20 48 0.55
21 17 0.20
22 5 0.06
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (19 bp):
ACAAAAAAAAAAACAAAAA
Found at i:2904219 original size:6 final size:6
Alignment explanation
Indices: 2904208--2904288 Score: 63
Period size: 6 Copynumber: 12.3 Consensus size: 6
2904198 GAAAGAAGAA
* *
2904208 AAAAAC AAAAAC AAAAAAAC AAAAAAC AAAAAAC AAAAAC AAAAAA AACAAAGA
1 AAAAAC AAAAAC --AAAAAC -AAAAAC -AAAAAC AAAAAC AAAAAC AA-AAA-C
* *
2904262 AAAAAG AAACAAC AAAAAC AACAAC AA
1 AAAAAC AAA-AAC AAAAAC AAAAAC AA
2904289 CAAAAAGGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
6 32 0.48
7 25 0.38
8 9 0.14
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:2904223 original size:14 final size:14
Alignment explanation
Indices: 2904191--2904294 Score: 97
Period size: 15 Copynumber: 7.4 Consensus size: 14
2904181 AAATAAACAA
* *
2904191 AAAAAAAGAAAGAAG
1 AAAAAAACAAA-AAC
2904206 AAAAAAACAAAAAC
1 AAAAAAACAAAAAC
2904220 AAAAAAACAAAAA-
1 AAAAAAACAAAAAC
2904233 ACAAAAAACAAAAAC
1 A-AAAAAACAAAAAC
*
2904248 AAAAAAAACAAAGA-
1 -AAAAAAACAAAAAC
* *
2904262 AAAAAGA-AACAAC
1 AAAAAAACAAAAAC
*
2904275 AAAAACAACAACAAC
1 AAAAA-AACAAAAAC
2904290 AAAAA
1 AAAAA
2904295 GGGTCTGGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.04
13 12 0.16
14 28 0.37
15 32 0.42
16 1 0.01
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAC
Found at i:2904265 original size:39 final size:37
Alignment explanation
Indices: 2904171--2904294 Score: 117
Period size: 39 Copynumber: 3.2 Consensus size: 37
2904161 TCCTCCACAA
* * *
2904171 AAAAAAAACCAAATAAACAAAAAA-AAAGAAAGAAGAAAA
1 AAAAAAAA-CAAAAAAACAAAAAACAAA-AAACAA-AAAC
2904210 AAACAAAAACAAAAAAACAAAAAACAAAAAACAAAAAC
1 AAA-AAAAACAAAAAAACAAAAAACAAAAAACAAAAAC
* *
2904248 AAAAAAAACAAAGAAAA-AAGAAACAACAAAAACAACAAC
1 AAAAAAAACAAA-AAAACAAAAAAC-A-AAAAACAAAAAC
*
2904287 AACAAAAA
1 AAAAAAAA
2904295 GGGTCTGGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
37 15 0.20
38 11 0.15
39 40 0.54
40 8 0.11
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (37 bp):
AAAAAAAACAAAAAAACAAAAAACAAAAAACAAAAAC
Found at i:2904279 original size:1 final size:1
Alignment explanation
Indices: 2904169--2904266 Score: 61
Period size: 1 Copynumber: 98.0 Consensus size: 1
2904159 CATCCTCCAC
** * * * * * * * *
2904169 AAAAAAAAAACCAAATAAACAAAAAAAAAGAAAGAAGAAAAAAACAAAAACAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
2904234 CAAAAAACAAAAACAAAAAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2904267 GAAACAACAA
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.01
Consensus pattern (1 bp):
A
Found at i:2904290 original size:9 final size:9
Alignment explanation
Indices: 2904206--2904291 Score: 67
Period size: 9 Copynumber: 9.9 Consensus size: 9
2904196 AAGAAAGAAG
2904206 AAAAA-AAC
1 AAAAACAAC
2904214 AAAAACAA-
1 AAAAACAAC
2904222 AAAAAC-A-
1 AAAAACAAC
*
2904229 AAAAACAAA
1 AAAAACAAC
*
2904238 AAACAAAAAC
1 AAA-AACAAC
*
2904248 AAAAAAAAC
1 AAAAACAAC
2904257 AAAGAA-AA-
1 AAA-AACAAC
2904265 AAGAAACAAC
1 AA-AAACAAC
2904275 AAAAACAAC
1 AAAAACAAC
*
2904284 AACAACAA
1 AAAAACAA
2904292 AAAGGGTCTG
Statistics
Matches: 67, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
7 7 0.10
8 16 0.24
9 33 0.49
10 11 0.16
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAACAAC
Found at i:2904291 original size:33 final size:33
Alignment explanation
Indices: 2904167--2904292 Score: 114
Period size: 33 Copynumber: 3.8 Consensus size: 33
2904157 TGCATCCTCC
* *
2904167 ACAAAAAA-AAAACCAAATA-AACAAA-AAAAA
1 ACAAAAAACAAAAACAAAAACAACAAACAAAAA
* * *
2904197 AGAAAGAAGAAAAAAACAAAAACAAAAAAACAAAAA
1 ACAAA-AA-ACAAAAACAAAAAC-AACAAACAAAAA
* *
2904233 ACAAAAAACAAAAACAAAAAAAACAAAGAAAAA
1 ACAAAAAACAAAAACAAAAACAACAAACAAAAA
* * *
2904266 AGAAACAACAAAAACAACAACAACAAA
1 ACAAAAAACAAAAACAAAAACAACAAA
2904293 AAGGGTCTGG
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
30 4 0.05
31 2 0.03
32 1 0.01
33 42 0.55
34 12 0.16
35 7 0.09
36 9 0.12
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (33 bp):
ACAAAAAACAAAAACAAAAACAACAAACAAAAA
Found at i:2905831 original size:58 final size:57
Alignment explanation
Indices: 2905727--2906580 Score: 695
Period size: 58 Copynumber: 14.5 Consensus size: 57
2905717 TCCTCACCAT
*
2905727 TTTCAAAAGCCCACAAGTCAGTGGCACCATTTTTCAAAGCCCACAAGTCAGTGGCAACC
1 TTTC-AAAGCCCACAAGTCAGTGGCACC-CTTTTCAAAGCCCACAAGTCAGTGGCAACC
*
2905786 -TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCTAAAGCCCACAAGTCAGTGGC-ACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-C-AAAGCCCACAAGTCAGTGGCAAC-C
* * *
2905844 TTTTTCAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAACCCACAAGTCAGTGGCAACC
1 --TTTCAAAGCCCACAAGTCAGTGGCACCCTT-T-TCAAAGCCCACAAGTCAGTGGCAACC
* * * * *
2905905 -TTCAAAAGCTCACAAATCAGTGGCACCCTTCTCCCAAAGCCCACAACTCAGGGGCAACC
1 TTTC-AAAGCCCACAAGTCAGTGGCACCCTT-T-TCAAAGCCCACAAGTCAGTGGCAACC
* * * *
2905964 -TTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAATCAATGGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCAC-CCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * *
2906022 TTCTCCCAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAATCAGTGGCACCC
1 TT-T--CAAAGCCCACAAGTCAGTGGCACCCTTTTC-AAAGCCCACAAGTCAGTGGCAACC
* * *
2906081 TTCTCCCAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAATCAGTGGCACCC
1 TT-T--CAAAGCCCACAAGTCAGTGGCACCCTTTTC-AAAGCCCACAAGTCAGTGGCAACC
* * * *
2906140 TTCTCCCAAAGCCCACAAGTCAGTGGCAACC--TTCAAGGCCCACAAATCAGTGGCACCC
1 TT-T--CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACC
*
2906198 TTTTCCCAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAGTCAGTGGC-ACTC
1 -TTT--CAAAGCCCACAAGTCAGTGGCACCCTTTTC-AAAGCCCACAAGTCAGTGGCAAC-C
* * * *
2906257 TTTTTCAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGCCCA-TAGTTAGTGGCAACC
1 --TTTCAAAGCCCACAAGTCAGTGGCACCCTT-T-TCAAAGCCCACAAGTCAGTGGCAACC
* * * *
2906317 -TTCAAAAGCCCACAAGTCAGTGGCACCCCTTTCCAAAGCCCATAAGTCAGT-GTATCC
1 TTTC-AAAGCCCACAAGTCAGTGGCA-CCCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * * * *
2906374 CTTCAAAAGCCCACTAGTCAGTGGCACTCTTTTTCAAAGCCCACAAATTAGTGGC-ACC
1 TTTC-AAAGCCCACAAGTCAGTGGCAC-CCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * * *
2906432 TTTCTCCCAAAGCCCAAAAGTCAGTGGCAACC--TTCAAAAGCCCATAAGTCAGTGGCACCC
1 -TT-T--CAAAGCCCACAAGTCAGTGGCACCCTTTTC-AAAGCCCACAAGTCAGTGGCAACC
* * * * * * * *
2906492 TTTTCCAAAGCCCATAAGTCAGTGCCAACC-TTTAAAAGCCCACAAGTTAGTGGTATCT
1 -TTT-CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACC
*
2906550 TTTCAGAAGCCCACAAGTCAGTGGCAACCTT
1 TTTCA-AAGCCCACAAGTCAGTGGCACCCTT
2906581 CAAAAGCACA
Statistics
Matches: 695, Mismatches: 60, Indels: 81
0.83 0.07 0.10
Matches are distributed among these distances:
56 6 0.01
57 67 0.10
58 248 0.36
59 241 0.35
60 26 0.04
61 100 0.14
62 7 0.01
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.20
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACC
Found at i:2905936 original size:59 final size:58
Alignment explanation
Indices: 2905727--2906621 Score: 770
Period size: 59 Copynumber: 15.3 Consensus size: 58
2905717 TCCTCACCAT
* *
2905727 TTTCAAAAGCCCACAAGTCAGTGGCACCATTTTTCAAAGCCCACAAGTCAGTGGCAACC
1 TTTCAAAAGCCCACAAGTCAGTGGCACC-CTTTCCAAAGCCCACAAGTCAGTGGCAACC
*
2905786 -TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCTAAAGCCCACAAGTCAGTGGC-ACTC
1 TTTCAAAAGCCCACAAGTCAGTGGCACCC-TTTCC-AAAGCCCACAAGTCAGTGGCAAC-C
* *
2905844 TTTTTC-AAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAACCCACAAGTCAGTGGCAACC
1 --TTTCAAAAGCCCACAAGTCAGTGGCACCCTT-T-CCAAAGCCCACAAGTCAGTGGCAACC
* * * *
2905905 -TTCAAAAGCTCACAAATCAGTGGCACCCTTCTCCCAAAGCCCACAACTCAGGGGCAACC
1 TTTCAAAAGCCCACAAGTCAGTGGCACCCTT-T-CCAAAGCCCACAAGTCAGTGGCAACC
* * * * *
2905964 -TTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAATCAATGGCACCC
1 TTTCAAAAGCCCACAAGTCAGTGGCAC-CCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * *
2906022 TTCTCCCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAATCAGTGGCACCC
1 TT-T-CAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * *
2906081 TTCTCCCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAATCAGTGGCACCC
1 TT-T-CAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * *
2906140 TTCTCCCAAAGCCCACAAGTCAGTGGCAACC-TT-CAAGGCCCACAAATCAGTGGCACCC
1 TT-T-CAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * *
2906198 TTTTCCCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGC-ACTC
1 -TTT-CAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAAC-C
* * *
2906257 TTTTTC-AAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGCCCA-TAGTTAGTGGCAACC
1 --TTTCAAAAGCCCACAAGTCAGTGGCACCCTT-T-CCAAAGCCCACAAGTCAGTGGCAACC
* * *
2906317 -TTCAAAAGCCCACAAGTCAGTGGCACCCCTTTCCAAAGCCCATAAGTCAGT-GTATCC
1 TTTCAAAAGCCCACAAGTCAGTGGCA-CCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * * *
2906374 CTTCAAAAGCCCACTAGTCAGTGGCACTCTTTTTCAAAGCCCACAAATTAGTGGC-ACC
1 TTTCAAAAGCCCACAAGTCAGTGGCAC-CCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * * *
2906432 TTTCTCCCAAAGCCCAAAAGTCAGTGGCAACC-TTCAAAAGCCCATAAGTCAGTGGCACCC
1 -TT-T-CAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * * * * * *
2906492 TTTTCCAAAGCCCATAAGTCAGTGCCAACCTTT-AAAAGCCCACAAGTTAGTGGTATCT
1 -TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * **
2906550 TTTCAGAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCACACAAGTTGGT-GCAACCC
1 TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAA-CC
*
2906607 TATCAAAAGCCCACA
1 TTTCAAAAGCCCACA
2906622 CAAGTTGGTG
Statistics
Matches: 725, Mismatches: 76, Indels: 72
0.83 0.09 0.08
Matches are distributed among these distances:
56 4 0.01
57 101 0.14
58 240 0.33
59 246 0.34
60 29 0.04
61 101 0.14
62 4 0.01
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (58 bp):
TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
Found at i:2906005 original size:148 final size:148
Alignment explanation
Indices: 2905730--2906575 Score: 628
Period size: 148 Copynumber: 5.7 Consensus size: 148
2905720 TCACCATTTT
* *
2905730 CAAAAGCCCACAAGTCAGTGGC-ACCATTTTTC-AAAGCCCACAAGTCAGTGGCAACC-T-T--C
1 CAAAA-CCCACAAGTCAGTGGCAACC----TTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCC
* *
2905789 AAAGCCCACAAATCAGTGGCACCCTTTTCCTAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAG
61 AAAGCCCACAAATCAGTGGCAACC--TT-CAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAG
2905854 CCCACAAATCAGTGGCACCCTTCTCC
123 CCCACAAATCAGTGGCACCCTTCTCC
*
2905880 CAAAACCCACAAGTCAGTGGCAACCTTCAAAAGCTCACAAATCAGTGGCACCCTTCTCCCAAAGC
1 CAAAACCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGC
* *
2905945 CCACAACTCAGGGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAA
66 CCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAA
*
2906010 TCAATGGCACCCTTCTCC
131 TCAGTGGCACCCTTCTCC
*
2906028 CAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGC
1 CAAAACCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGC
* * * **
2906093 CCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGCCCACAA
66 CCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACTCTT-TTTCAAAGCCCACAA
* *
2906158 GTCAGTGGCAACC-T-T--
130 ATCAGTGGCACCCTTCTCC
** * * * * * *
2906173 CAAGGCCCACAAATCAGTGGCACCCTTTTCCCAAAGCCCACAAGTCAGTGGCAACC-T-T-CAAA
1 CAAAACCCACAAGTCAGTGGCAACC--TT-CAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAA
* * * **
2906235 AGCCCACAAGTCAGTGGC-ACTCTTTTTC-AAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAG
63 AGCCCACAAATCAGTGGCAAC-C---TTCAAAAGCCCACAAGTCAGTGGCACTCTT-TTTCAAAG
* * * *
2906298 CCCA-TAGTTAGTGGCAACC-T-T--
123 CCCACAAATCAGTGGCACCCTTCTCC
* * * * * *
2906319 CAAAAGCCCACAAGTCAGTGGCACCCCTTTCCAAAGCCCATAAGTCAGT-GTATCCC-T-T-CAA
1 CAAAA-CCCACAAGTCAGTGGCA-ACC-TTCAAAAGCCCACAAATCAGTGGCA-CCCTTCTCCCA
* * * * *
2906380 AAGCCCACTAGTCAGTGGC-ACTCTTTTTC-AAAGCCCACAAATTAGTGGCAC-CTTTCTCCCAA
62 AAGCCCACAAATCAGTGGCAAC-C---TTCAAAAGCCCACAAGTCAGTGGCACTCTTT-T-TCAA
*
2906442 AGCCCA-AAAGTCAGTGGCAACC-T-T--
121 AGCCCACAAA-TCAGTGGCACCCTTCTCC
* * * * * * * *
2906466 CAAAAGCCCATAAGTCAGTGGCACCCTTTTCCAAAGCCCATAAGTCAGTGCCAACCTT-T--AAA
1 CAAAA-CCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAA
* * * * * *
2906528 AGCCCACAAGTTAGTGGTATCTTTTCAGAAGCCCACAAGTCAGTGGCA
63 AGCCCACAAATCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCA
2906576 ACCTTCAAAA
Statistics
Matches: 619, Mismatches: 52, Indels: 54
0.85 0.07 0.07
Matches are distributed among these distances:
144 3 0.00
145 52 0.08
146 128 0.21
147 160 0.26
148 204 0.33
149 42 0.07
150 8 0.01
151 22 0.04
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (148 bp):
CAAAACCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGC
CCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAA
TCAGTGGCACCCTTCTCC
Found at i:2906468 original size:89 final size:85
Alignment explanation
Indices: 2905721--2906595 Score: 751
Period size: 89 Copynumber: 9.9 Consensus size: 85
2905711 AGACATTCCT
* * * *
2905721 CACCATTTTCAAAAGCCCACAAGTCAGTGGCACCATTTTTCAAAGCCCACAAGTCAGTGGCAACC
1 CACC-TTTTCCAAAGCCCAAAAGTCAGTGGCACC-CTTTCCAAAGCCCACAAGTCAGTGGCAACC
*
2905786 TTCAAAGCCCACAAATCAGTGG
64 TTCAAAGCCCACAAGTCAGTGG
* * * * *
2905808 CACCCTTTTCCTAAAGCCCACAAGTCAGTGGCACTCTTTTTCAAAGCCCACAAATCAGTGGCACC
1 CA-CCTTTTCC-AAAGCCCAAAAGTCAGTGGCAC-CCTTTCCAAAGCCCACAAGTCAGTGGCAAC
*
2905873 CTTCTCCCAAAACCCACAAGTCAGTGG
63 C-T-T--CAAAGCCCACAAGTCAGTGG
* * * *
2905900 CAACC--TTCAAAAGCTCACAAA-TCAGTGGCACCCTTCTCCCAAAGCCCACAACTCAGGGGCAA
1 C-ACCTTTTCCAAAGCCCA-AAAGTCAGTGGCACCCTT-T-CCAAAGCCCACAAGTCAGTGGCAA
2905962 CCTTCAAAAGCCCACAAGTCAGTGG
62 CCTTC-AAAGCCCACAAGTCAGTGG
* *
2905987 CACTCTTTTTCAAAGCCCACAAA-TCAATGGCACCCTTCTCCCAAAGCCCACAAGTCAGTGGCAA
1 CAC-CTTTTCCAAAGCCCA-AAAGTCAGTGGCACCCTT-T-CCAAAGCCCACAAGTCAGTGGCAA
*
2906051 CCTTCAAAAGCCCACAAATCAGTGG
62 CCTTC-AAAGCCCACAAGTCAGTGG
* * * * * *
2906076 CACCCTTCTCCCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAATCAGTGGCACCC
1 CA-CCTT-TTCCAAAGCCCAAAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
2906140 TTCTCCCAAAGCCCACAAGTCAGTGG
64 -T-T--CAAAGCCCACAAGTCAGTGG
*
2906166 CAACC--TT-CAAGGCCCACAAA-TCAGTGGCACCCTTTTCCCAAAGCCCACAAGTCAGTGGCAA
1 C-ACCTTTTCCAAAGCCCA-AAAGTCAGTGGCACCC-TTT-CCAAAGCCCACAAGTCAGTGGCAA
2906227 CCTTCAAAAGCCCACAAGTCAGTGG
62 CCTTC-AAAGCCCACAAGTCAGTGG
* * *
2906252 CACTCTTTTTCAAAGCCCACAAA-TCAGTGGCACCCTTCTCCCAAAGCCCA-TAGTTAGTGGCAA
1 CAC-CTTTTCCAAAGCCCA-AAAGTCAGTGGCACCCTT-T-CCAAAGCCCACAAGTCAGTGGCAA
2906315 CCTTCAAAAGCCCACAAGTCAGTGG
62 CCTTC-AAAGCCCACAAGTCAGTGG
* * * * *
2906340 CACCCCTTTCCAAAGCCCATAAGTCAGT-GTATCCC-TTCAAAAGCCCACTAGTCAGTGGC-ACT
1 CA-CCTTTTCCAAAGCCCAAAAGTCAGTGGCA-CCCTTTCCAAAGCCCACAAGTCAGTGGCAAC-
* *
2906402 CTTTTTCAAAGCCCACAAATTAGTGG
63 C---TTCAAAGCCCACAAGTCAGTGG
* * * *
2906428 CACCTTTCTCCCAAAGCCCAAAAGTCAGTGGCAACC-TTCAAAAGCCCATAAGTCAGTGGCACCC
1 CACCTTT-T-CCAAAGCCCAAAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACC
* *
2906492 TTTTCCAAAGCCCATAAGTCAGTGC
64 --TT-CAAAGCCCACAAGTCAGTGG
* * * * * *
2906517 CAACC-TTT-AAAAGCCCACAAGTTAGTGGTA-TCTTTTCAGAAGCCCACAAGTCAGTGGCAACC
1 C-ACCTTTTCCAAAGCCCAAAAGTCAGTGGCACCCTTTCCA-AAGCCCACAAGTCAGTGGCAACC
*
2906579 TTCAAAAGCACACAAGT
64 TTC-AAAGCCCACAAGT
2906596 TGGTGCAACC
Statistics
Matches: 668, Mismatches: 70, Indels: 102
0.80 0.08 0.12
Matches are distributed among these distances:
84 1 0.00
85 28 0.04
86 76 0.11
87 84 0.13
88 149 0.22
89 230 0.34
90 76 0.11
91 2 0.00
92 21 0.03
93 1 0.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.20
Consensus pattern (85 bp):
CACCTTTTCCAAAGCCCAAAAGTCAGTGGCACCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTT
CAAAGCCCACAAGTCAGTGG
Found at i:2906615 original size:29 final size:28
Alignment explanation
Indices: 2906551--2906631 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
2906541 GTGGTATCTT
* **
2906551 TTCAGAAGCC-CACAAGTCAGTGGCAACC
1 TTCAAAAGCCACACAAGTTGGT-GCAACC
2906579 TTCAAAAG-CACACAAGTTGGTGCAACCC
1 TTCAAAAGCCACACAAGTTGGTGCAA-CC
2906607 TATCAAAAGCCCACACAAGTTGGTG
1 T-TCAAAAG-CCACACAAGTTGGTG
2906632 GCATCTTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.11
28 19 0.42
29 7 0.16
31 14 0.31
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (28 bp):
TTCAAAAGCCACACAAGTTGGTGCAACC
Found at i:2906625 original size:31 final size:27
Alignment explanation
Indices: 2906573--2906631 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 27
2906563 CAAGTCAGTG
2906573 GCAACCTTCAAAAGCACACAAGTTGGT
1 GCAACCTTCAAAAGCACACAAGTTGGT
2906600 GCAACCCTATCAAAAGCCCACACAAGTTGGT
1 GCAA-CCT-TCAAAAG--CACACAAGTTGGT
2906631 G
1 G
2906632 GCATCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.14
28 3 0.11
29 7 0.25
31 14 0.50
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (27 bp):
GCAACCTTCAAAAGCACACAAGTTGGT
Found at i:2906701 original size:49 final size:49
Alignment explanation
Indices: 2906641--2906820 Score: 227
Period size: 49 Copynumber: 3.7 Consensus size: 49
2906631 GGCATCTTCT
*
2906641 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
2906690 TTTAAGACCAATGTCGTTGGCCTTGAATTAGCACT-TTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCA-TATTGGCACCTTCATC
** * * *
2906739 TTTAAGTCCGGTATCGCTAGCTTTGAATCAGCATATTGGCACCTTGATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
2906788 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
2906821 CATTAGCATT
Statistics
Matches: 107, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
48 1 0.01
49 105 0.98
50 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:2906810 original size:98 final size:96
Alignment explanation
Indices: 2906630--2906821 Score: 276
Period size: 98 Copynumber: 2.0 Consensus size: 96
2906620 CACAAGTTGG
*
2906630 TGGCATCTTCTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAA
1 TGGCATCTTCTTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCGTCATCTTTAA
* * *
2906695 GACCAATGTCGTTGGCCTTGAATTAGCACTT
66 GACCAATGTAGCTGGCCTTGAATCAGCACTT
** * * *
2906726 TGGCATCTTCATCTTTAAGTCCGGTATCGCTAGCTTTGAATCAGCATATTGGCACCTTGATCTTT
1 TGGCATCTTC-T-TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCGTCATCTTT
*
2906791 AAGTCCAATGTAGCTGGCCTTGAATCAGCAC
64 AAGACCAATGTAGCTGGCCTTGAATCAGCAC
2906822 ATTAGCATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 10 0.12
97 1 0.01
98 73 0.87
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (96 bp):
TGGCATCTTCTTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCGTCATCTTTAA
GACCAATGTAGCTGGCCTTGAATCAGCACTT
Found at i:2907556 original size:13 final size:13
Alignment explanation
Indices: 2907538--2907594 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2907528 CATAAAGTGT
2907538 TGTATCGATACAA
1 TGTATCGATACAA
2907551 TGTATCGATACATAA
1 TGTATCGATAC--AA
2907566 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2907583 TGTATCGATACA
1 TGTATCGATACA
2907595 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2907573 original size:32 final size:32
Alignment explanation
Indices: 2907518--2907618 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
2907508 TTTAACGATT
2907518 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
2907551 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2907583 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2907615 TGTA
1 TGTA
2907619 AGCTACTACC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 54 0.81
33 13 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2907575 original size:19 final size:18
Alignment explanation
Indices: 2907516--2907613 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
2907506 ATTTTAACGA
2907516 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
2907535 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2907551 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2907567 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2907583 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2907599 TTTTGTATCGATACA
1 -TTTGTATCGATACA
2907614 ATGTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:2907639 original size:65 final size:65
Alignment explanation
Indices: 2907518--2907646 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 65
2907508 TTTAACGATT
* ***
2907518 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTAGCGATACATAAGAAATGTATCGATACAA
* *
2907583 TGTATCGATACAT-AAGTTTTGTATCGATACAATGTAAGCTACTACCA-AA-AAATGTATCGATA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGT-AGCGA-TA-CATAAGAAATGTATCGATA
2907645 CA
63 CA
2907647 TTACTCAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
64 21 0.38
65 28 0.51
66 4 0.07
67 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (65 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAATGTAGCGATACATAAGAAATGTATCGATACAA
Found at i:2907674 original size:13 final size:13
Alignment explanation
Indices: 2907656--2907680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2907646 ATTACTCAAA
2907656 TGTATCGATACAT
1 TGTATCGATACAT
2907669 TGTATCGATACA
1 TGTATCGATACA
2907681 CTATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2907695 original size:33 final size:34
Alignment explanation
Indices: 2907635--2907701 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
2907625 TACCAAAAAA
* *
2907635 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACACTACTAAAATGTATCGATACAT
2907669 TGTATCGATACACTA-TAAAATGTATCGATACAT
1 TGTATCGATACACTACTAAAATGTATCGATACAT
2907702 GCAGGCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (34 bp):
TGTATCGATACACTACTAAAATGTATCGATACAT
Found at i:2907738 original size:52 final size:52
Alignment explanation
Indices: 2907669--2907869 Score: 357
Period size: 52 Copynumber: 3.9 Consensus size: 52
2907659 ATCGATACAT
2907669 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2907721 TGTATTGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCTAGA
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
2907773 TGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2907825 TGTATCGATACACTATGAAATGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
2907870 TCATATTTTG
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 143 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2911002 original size:20 final size:20
Alignment explanation
Indices: 2910977--2911090 Score: 158
Period size: 20 Copynumber: 5.7 Consensus size: 20
2910967 TTTTAACTAG
2910977 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
2910997 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
*
2911017 AGGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
* *
2911037 ATGTATCGATACATTCGTA-C
1 ATGTATCGATACATT-GAAGA
*
2911057 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAGA
**
2911077 ATACATCGATACAT
1 ATGTATCGATACAT
2911091 GTGGGTACTT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.02
20 80 0.95
21 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:2911878 original size:48 final size:48
Alignment explanation
Indices: 2911826--2911947 Score: 208
Period size: 48 Copynumber: 2.5 Consensus size: 48
2911816 CAATGTACCA
* *
2911826 ATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATGGACAATGTGCTG
*
2911874 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATGGACAATGTGCTG
*
2911922 ATTCAAGGCCAGGGACATTGAGCTAA
1 ATTCAAGGCCAGCGACATTGAGCTAA
2911948 TAAAGGTGCC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (48 bp):
ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATGGACAATGTGCTG
Found at i:2912126 original size:32 final size:30
Alignment explanation
Indices: 2912051--2912184 Score: 97
Period size: 28 Copynumber: 4.7 Consensus size: 30
2912041 GGCTTTTAAA
* *
2912051 AAAAGGTGCCACTAACTTATGTGGGCT-T-
1 AAAAGGTACCACTAACTTGTGTGGGCTCTG
*
2912079 TAAA---ACCACTAACTTGTGTGGGCTCTG
1 AAAAGGTACCACTAACTTGTGTGGGCTCTG
* * *
2912106 AAAGGGGATACCACTGAC-T-TGTGGGCTTTG
1 AAA-AGG-TACCACTAACTTGTGTGGGCTCTG
* *
2912136 AAAAGGTACCACTAAC-T-TGTGGACTGTG
1 AAAAGGTACCACTAACTTGTGTGGGCTCTG
* *
2912164 AAAGGGTGCCACTAACTTGTG
1 AAAAGGTACCACTAACTTGTG
2912185 GGCTTTAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
25 18 0.21
26 1 0.01
27 2 0.02
28 36 0.43
29 3 0.04
30 15 0.18
31 1 0.01
32 8 0.10
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (30 bp):
AAAAGGTACCACTAACTTGTGTGGGCTCTG
Found at i:2912154 original size:28 final size:28
Alignment explanation
Indices: 2912116--2912514 Score: 399
Period size: 28 Copynumber: 13.8 Consensus size: 28
2912106 AAAGGGGATA
*
2912116 CCACTGACTTGTGGGCTTTGAAAAGGTA
1 CCACTGACTTGTGGGCTTTGAAAAGGTG
* * * *
2912144 CCACTAACTTGTGGACTGTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGGTG
* * *
2912172 CCACTAACTTGTGGGCTTTAAAAAGATG
1 CCACTGACTTGTGGGCTTTGAAAAGGTG
*
2912200 CCACTGACTTGTGGGCTTTAAAAAGAGTG
1 CCACTGACTTGTGGGCTTTGAAAAG-GTG
2912229 CCACTGACTTGTGGGCTTTG-AAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAAGG-TG
* *
2912257 TCATTGACTTGTGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTGAAAAG-G-TG
* *
2912287 CCACCGACTCGTGGGCTTTG-AAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAAGG-TG
*
2912315 CCACTGACTGGTGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTGAAAAG-G-TG
**
2912345 CCACCAACTCGTGTGGGACTTTGAAAAGAGTTG
1 CCACTGACT--TGTGGG-CTTTGAAAAG-G-TG
** *
2912378 CCACCAACTCGTGTGGGCTTTGAAAGGAGTG
1 CCACTGACT--TGTGGGCTTTGAAAAG-GTG
* **
2912409 CCACTGACTTATGGGCTTTGAATGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGGTG
*
2912437 CCACTGACTTATGGGCTTTG-AAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAAGG-TG
*
2912465 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGGTG
* *
2912493 CCACTAACTTGTGGACTTTGAA
1 CCACTGACTTGTGGGCTTTGAA
2912515 GAGATGAACT
Statistics
Matches: 322, Mismatches: 38, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.01
28 181 0.56
29 51 0.16
30 29 0.09
31 9 0.03
32 16 0.05
33 32 0.10
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAAGGTG
Found at i:2912368 original size:33 final size:32
Alignment explanation
Indices: 2912266--2912412 Score: 191
Period size: 33 Copynumber: 4.8 Consensus size: 32
2912256 GTCATTGACT
*
2912266 TGTGGGCTTTGAAAAGAGTTGCCACCGACTC-
1 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCG
* **
2912297 -GTGGGCTTTG-AAAG-GATGCCACTGACT-G
1 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCG
2912325 -GTGGGCTTTGAAAAGAGTTGCCACCAACTCG
1 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCG
2912356 TGTGGGACTTTGAAAAGAGTTGCCACCAACTCG
1 TGTGGG-CTTTGAAAAGAGTTGCCACCAACTCG
*
2912389 TGTGGGCTTTGAAAGGAG-TGCCAC
1 TGTGGGCTTTGAAAAGAGTTGCCAC
2912413 TGACTTATGG
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
28 21 0.20
29 8 0.08
30 20 0.19
31 7 0.07
32 16 0.15
33 32 0.31
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (32 bp):
TGTGGGCTTTGAAAAGAGTTGCCACCAACTCG
Found at i:2913495 original size:20 final size:19
Alignment explanation
Indices: 2913470--2913542 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
2913460 CTGCCAGTTT
**
2913470 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
2913490 CATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
*
2913509 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
2913530 -ATGTATCGATACA
1 CATGTATCGATACA
2913543 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2913514 original size:19 final size:20
Alignment explanation
Indices: 2913470--2913523 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2913460 CTGCCAGTTT
**
2913470 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
2913490 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
2913509 CATGTATCGATACAA
1 CATGTATCGATACAA
2913524 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2923714 original size:1 final size:1
Alignment explanation
Indices: 2923700--2923785 Score: 55
Period size: 1 Copynumber: 86.0 Consensus size: 1
2923690 TCTGGACCCC
* * ** ** * ** * *
2923700 TTTTTGTTTGTTTTTTTTTAATTTTTTTAATTTTTTTTGTTTTTTGGTTTTTTGTTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
2923765 TATTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
2923786 GGGTATGAAG
Statistics
Matches: 65, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.06, C:0.01, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:2923742 original size:9 final size:9
Alignment explanation
Indices: 2923700--2923782 Score: 64
Period size: 10 Copynumber: 8.9 Consensus size: 9
2923690 TCTGGACCCC
2923700 TTTTTGTTTG
1 TTTTT-TTTG
2923710 TTTTTTTT-
1 TTTTTTTTG
*
2923718 TAATTTTTTTAA
1 T--TTTTTTT-G
2923730 TTTTTTTTG
1 TTTTTTTTG
*
2923739 -TTTTTTGG
1 TTTTTTTTG
2923747 TTTTTTGTT-
1 TTTTTT-TTG
*
2923756 TTTTTTTTC
1 TTTTTTTTG
2923765 TATTTTTTTG
1 T-TTTTTTTG
2923775 TTTTTTTT
1 TTTTTTTT
2923783 TTTGGGTATG
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
8 10 0.16
9 22 0.36
10 28 0.46
12 1 0.02
ACGTcount: A:0.06, C:0.01, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:2923757 original size:21 final size:20
Alignment explanation
Indices: 2923733--2923787 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
2923723 TTTTTAATTT
2923733 TTTTTGTTTTTTGGTTTTTTG
1 TTTTT-TTTTTTGGTTTTTTG
**
2923754 TTTTTTTTTTCTATTTTTTTG
1 TTTTTTTTTT-TGGTTTTTTG
2923775 TTTTTTTTTTTGG
1 TTTTTTTTTTTGG
2923788 GTATGAAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTTTGGTTTTTTG
Found at i:2925951 original size:33 final size:33
Alignment explanation
Indices: 2925909--2925977 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2925899 CCATTAAAAG
2925909 CAATGTATCAATACAAT-TCATCATGTATCGATA
1 CAATGTATCAATACAATGT-ATCATGTATCGATA
* *
2925942 CAATGTATCACTATAATGTATCATGTATCGATA
1 CAATGTATCAATACAATGTATCATGTATCGATA
2925975 CAA
1 CAA
2925978 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (33 bp):
CAATGTATCAATACAATGTATCATGTATCGATA
Found at i:2926045 original size:13 final size:13
Alignment explanation
Indices: 2926027--2926053 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2926017 ACAATTGTCC
2926027 ATGTATCGATACA
1 ATGTATCGATACA
2926040 ATGTATCGATACA
1 ATGTATCGATACA
2926053 A
1 A
2926054 AAGTATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2930042 original size:16 final size:17
Alignment explanation
Indices: 2930004--2930043 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2929994 AGATTTATCC
* *
2930004 ACATTTTTTCTATTAAA
1 ACATTTTTTCAATCAAA
2930021 ACATTTTTTCAATCAAA
1 ACATTTTTTCAATCAAA
2930038 A-ATTTT
1 ACATTTT
2930044 AAAAGCCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
ACATTTTTTCAATCAAA
Found at i:2947795 original size:20 final size:19
Alignment explanation
Indices: 2947770--2947843 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
2947760 AAAAGACAGG
*
2947770 ATGTATCGATATATTGAAGA
1 ATGTATCGATACATTGAA-A
* *
2947790 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGA-AA
2947810 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTG-AAA
2947830 ATGTATCGATACAT
1 ATGTATCGATACAT
2947844 CGAGTACTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:2949704 original size:154 final size:153
Alignment explanation
Indices: 2949263--2949704 Score: 428
Period size: 155 Copynumber: 2.9 Consensus size: 153
2949253 AGTTCAAGAA
* * * ** ** ** *
2949263 AAATTACGAAAATGCCTCTAAGGGATACTTTTGATGTAAAAGTACCCAACACCCCTAAA-GAATA
1 AAATTATGAAAATTCC-CTTAGGGATACTTTTGACATAAAAGTAAACAGTACCCCTAAAGGACT-
** ** * *
2949327 TAAAAAGGATTTTAAAAGGGATGAATTTATCCTAAATGCCCACCTTTAACATGAAAACG-GACCC
64 TAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCTACCTTTAGCAT-AAAA-GAGACCC
* * * *
2949391 AGTGACAACCTAGGACTCGATTTTAAG
127 GGTGACAACCTAAGACTCAATTCTAAG
* * **
2949418 AAATTATGAAAA-TGCCTCTAGGGAATACTTTTGACATAAAA--AAACCTGGTACTACTAAAGGA
1 AAATTATGAAAATTCCCT-TAGGG-ATACTTTTGACATAAAAGTAAA-C-AGTACCCCTAAAGGA
* * *
2949480 CTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCTA-CTTTCGGCATAAAAACAAAC
62 CTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCTACCTTT-AGCAT-AAAAGAGAC
* * * *
2949544 CTGGTGACAACCTAAGATTTAATTCTAGG
125 CCGGTGACAACCTAAGACTCAATTCTAAG
*
2949573 AAATTATGAAAATTCCCTTAGGGATACCTTTGACATAAAAGTAAACAGTACCCCTAAAGGACTTA
1 AAATTATGAAAATTCCCTTAGGGATACTTTTGACATAAAAGTAAACAGTACCCCTAAAGGACTTA
* * *
2949638 AAAAGGATTTTAAAAGGGATAAACCTAGCATAAATATCTACCTTTAGCATAAAAGTAGACCCGGT
66 AAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCTACCTTTAGCATAAAAG-AGACCCGGT
2949703 GA
130 GA
2949705 TTTTGTAAGA
Statistics
Matches: 231, Mismatches: 44, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
153 7 0.03
154 92 0.40
155 122 0.53
156 10 0.04
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (153 bp):
AAATTATGAAAATTCCCTTAGGGATACTTTTGACATAAAAGTAAACAGTACCCCTAAAGGACTTA
AAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCTACCTTTAGCATAAAAGAGACCCGGTG
ACAACCTAAGACTCAATTCTAAG
Found at i:2951040 original size:21 final size:24
Alignment explanation
Indices: 2951014--2951065 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
2951004 AGTTTTCTAA
2951014 TTTTTCACTC-TATTTCT-T-TTC
1 TTTTTCACTCTTATTTCTCTCTTC
* *
2951035 TTTTTCTCTCTTTTTTCTCTCTTC
1 TTTTTCACTCTTATTTCTCTCTTC
2951059 TTTTTCA
1 TTTTTCA
2951066 GCTGAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.36
22 6 0.24
23 1 0.04
24 9 0.36
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTCACTCTTATTTCTCTCTTC
Found at i:2951062 original size:13 final size:13
Alignment explanation
Indices: 2951032--2951064 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
2951022 TCTATTTCTT
2951032 TTCTTTTTCTCTC
1 TTCTTTTTCTCTC
2951045 -T-TTTTTCTCTC
1 TTCTTTTTCTCTC
2951056 TTCTTTTTC
1 TTCTTTTTC
2951065 AGCTGAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.56
12 2 0.11
13 6 0.33
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTTTTTCTCTC
Found at i:2951714 original size:166 final size:165
Alignment explanation
Indices: 2951376--2951814 Score: 503
Period size: 166 Copynumber: 2.6 Consensus size: 165
2951366 TAAGACATAC
* * * * *
2951376 AAAAAATTTAAAATTTATG-AAATAAATTTAATTTTTCAAAACTAATTTAAT-GGGAGTTAAATA
1 AAAAAATTTAAAACTCATGCAAATAAA-TAAATTTTTGAAAACTAATTTAATAGTGA-TTAAATA
* * * * * * *
2951439 ACA-ATATTAGATGAATTTTAAAAATTTTCAATCAAGAAAAATCTCTCCGAAAATACTTACAGAG
64 A-ATATATTTGATGAATTTTAAAAATTTTAAACCAAG-AAAATCCCCCCAAAAATACTTACAAAG
* *
2951503 TAGAAAACTCGGTTTTTCAAAAATAAAAAAATTTCAAGG
127 TAAAAAACTCGGTTTTTCAAAAACAAAAAAATTTCAAGG
2951542 AAAAAATTTAAAACTCATGCAAATAAATAAATTTTTGAAAACTAATTTAATAGTGATTAAATAAA
1 AAAAAATTTAAAACTCATGCAAATAAATAAATTTTTGAAAACTAATTTAATAGTGATTAAATAAA
** ** *
2951607 TATATTTGATCTATTTTAAAAATTAGAAACCAAGAAAATCCCCCCAAAAATATTTACAAAGTAAA
66 TATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAATCCCCCCAAAAATACTTACAAAGTAAA
* ** * *
2951672 AAATTTC-GTATTTT-GGAAACAAGAGAATTTCAAGG
131 AAA-CTCGGT-TTTTCAAAAACAAAAAAATTTCAAGG
* * *
2951707 AAAAAAATTTAAAACTCATGCAAATAAATGAATTTTTGAAAAGTAATTTAATAATGATTAAAT-A
1 -AAAAAATTTAAAACTCATGCAAATAAATAAATTTTTGAAAACTAATTTAATAGTGATTAAATAA
*
2951771 ATAATATTTGATGAATTTTAAAAATTTTTAAACCATGAAAATCC
65 AT-ATATTTGATGAATTTTAAAAA-TTTTAAACCAAGAAAATCC
2951815 TCTTGAAAAA
Statistics
Matches: 233, Mismatches: 32, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
165 50 0.21
166 157 0.67
167 26 0.11
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (165 bp):
AAAAAATTTAAAACTCATGCAAATAAATAAATTTTTGAAAACTAATTTAATAGTGATTAAATAAA
TATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAATCCCCCCAAAAATACTTACAAAGTAAA
AAACTCGGTTTTTCAAAAACAAAAAAATTTCAAGG
Found at i:2956178 original size:25 final size:25
Alignment explanation
Indices: 2956140--2956226 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
2956130 CTGTGGCTAC
2956140 TGTTGTTGGTTGCTGCTGCCATTGGT
1 TGTTG-TGGTTGCTGCTGCCATTGGT
* * *
2956166 TGTTGTGGCTGCTGTTG---TTGGG
1 TGTTGTGGTTGCTGCTGCCATTGGT
* * * *
2956188 TGCTGTTGTTGCTACTACCATTGGT
1 TGTTGTGGTTGCTGCTGCCATTGGT
2956213 TGTTGTGGTTGCTG
1 TGTTGTGGTTGCTG
2956227 TTGTTGCTTG
Statistics
Matches: 45, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
22 15 0.33
25 25 0.56
26 5 0.11
ACGTcount: A:0.05, C:0.14, G:0.36, T:0.46
Consensus pattern (25 bp):
TGTTGTGGTTGCTGCTGCCATTGGT
Found at i:2956179 original size:47 final size:47
Alignment explanation
Indices: 2956128--2956227 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
2956118 TGGTGTTGGT
* * *
2956128 TGCTGTGGCT-ACTGTTGTTGGTTGCTGCTGCCATTGGTTGTTGTGGC
1 TGCTGTGGCTGACTGCTGTT-GTTGCTACTACCATTGGTTGTTGTGGC
* * ** *
2956175 TGCTGTTGTTGGGTGCTGTTGTTGCTACTACCATTGGTTGTTGTGGT
1 TGCTGTGGCTGACTGCTGTTGTTGCTACTACCATTGGTTGTTGTGGC
2956222 TGCTGT
1 TGCTGT
2956228 TGTTGCTTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 38 0.86
48 6 0.14
ACGTcount: A:0.05, C:0.15, G:0.35, T:0.45
Consensus pattern (47 bp):
TGCTGTGGCTGACTGCTGTTGTTGCTACTACCATTGGTTGTTGTGGC
Found at i:2956193 original size:13 final size:15
Alignment explanation
Indices: 2956164--2956198 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
2956154 GCTGCCATTG
2956164 GTTGTTGTGGCTGCT
1 GTTGTTGTGGCTGCT
2956179 GTTGTTG-GG-TGCT
1 GTTGTTGTGGCTGCT
2956192 GTTGTTG
1 GTTGTTG
2956199 CTACTACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.00, C:0.09, G:0.43, T:0.49
Consensus pattern (15 bp):
GTTGTTGTGGCTGCT
Found at i:2956286 original size:13 final size:13
Alignment explanation
Indices: 2956268--2956317 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
2956258 ACTGCTTGGT
2956268 GTTGCTGTTGTTG
1 GTTGCTGTTGTTG
*
2956281 GTTGC---TATT-
1 GTTGCTGTTGTTG
*
2956290 GTTGCTGCTGTTG
1 GTTGCTGTTGTTG
2956303 GTTGCTGTTGTTG
1 GTTGCTGTTGTTG
2956316 GT
1 GT
2956318 GCCTGGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
12 3 0.10
13 19 0.63
ACGTcount: A:0.02, C:0.10, G:0.36, T:0.52
Consensus pattern (13 bp):
GTTGCTGTTGTTG
Found at i:2956292 original size:22 final size:22
Alignment explanation
Indices: 2956267--2956315 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2956257 CACTGCTTGG
*
2956267 TGTTGCTGTTGTTGGTTGCTAT
1 TGTTGCTGCTGTTGGTTGCTAT
*
2956289 TGTTGCTGCTGTTGGTTGCTGT
1 TGTTGCTGCTGTTGGTTGCTAT
2956311 TGTTG
1 TGTTG
2956316 GTGCCTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.35, T:0.53
Consensus pattern (22 bp):
TGTTGCTGCTGTTGGTTGCTAT
Found at i:2956906 original size:3 final size:3
Alignment explanation
Indices: 2956900--2956943 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2956890 TTTTTATTTT
2956900 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2956944 TTGTTCTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2957938 original size:165 final size:166
Alignment explanation
Indices: 2957757--2958139 Score: 392
Period size: 167 Copynumber: 2.3 Consensus size: 166
2957747 TTATAAACCA
* * * * *
2957757 TAAAAATCATCAAATATTATTATTTAGTTCACATTAAATCAGTTTTGAAAATTCCTTTTA-ATTC
1 TAAAATTCATCAAATATTATTATTTAATTCACAGTAAATCACTTTTGAAAATTCCATTTATATTC
*
2957821 ATATTTTTTTCA-TTTTTTCTTTGAAATTC-CTT-TGTTTTCG-AAATACGAAATTTTCTACTTC
66 ATA-TGTTTTCATTTTTTTCTTTGAAATTCTCTTAT-TTTT-GAAAATACG-AATTTTCTA-TTC
* *
2957882 -GTAAATGTTTTCAG-GGGGATTTTTCTTGG-TTTATAATTTTT
126 TGTAAATATTTT-AGAGGGGATTTTTC-TGGATTT-CAATTTTT
* * * * * *
2957923 T-AAATTCATCAAATATCATCATTTAATTCATAGTAAATTACTTTTGAAAATTTCATTTATTTTC
1 TAAAATTCATCAAATATTATTATTTAATTCACAGTAAATCACTTTTGAAAATTCCATTTATATTC
* * *
2957987 ATATGTTTTCATTTTTTTCTTTGAAATTCTCTTATTTTTGAAAAATTCGAGTTTTTTATTCTGTA
66 ATATGTTTTCATTTTTTTCTTTGAAATTCTCTTATTTTTG-AAAATACGAATTTTCTATTCTGTA
*
2958052 AATATTTTTGAGGGGATTTTTCTGGATTTCAATTTTT
130 AATATTTTAGAGGGGATTTTTCTGGATTTCAATTTTT
* * * *
2958089 TAAAATTCATTAAATATTTTTATTAAATTC-CTAGTAAGTCA-TTTTGTAAAA
1 TAAAATTCATCAAATATTATTATTTAATTCAC-AGTAAATCACTTTTG-AAAA
2958140 ATTTAATTTA
Statistics
Matches: 179, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
165 55 0.31
166 45 0.25
167 72 0.40
168 7 0.04
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (166 bp):
TAAAATTCATCAAATATTATTATTTAATTCACAGTAAATCACTTTTGAAAATTCCATTTATATTC
ATATGTTTTCATTTTTTTCTTTGAAATTCTCTTATTTTTGAAAATACGAATTTTCTATTCTGTAA
ATATTTTAGAGGGGATTTTTCTGGATTTCAATTTTT
Found at i:2958091 original size:166 final size:166
Alignment explanation
Indices: 2957757--2958105 Score: 383
Period size: 165 Copynumber: 2.1 Consensus size: 166
2957747 TTATAAACCA
* * * * * * *
2957757 TAAAAATCATCAAATATTATTATTTAGTTCACATTAAATCAGTTTTGAAAATTCCTTTTAATTCA
1 TAAAATTCATCAAATATCATCATTTAATTCACAGTAAATCACTTTTGAAAATTCCATTTAATTCA
*
2957822 TATTTTTTTCATTTTTTCTTTGAAATTCCTTTGTTTTCGAAATACGAAATTTTCTACTTCGTAAA
66 TATTGTTTTCATTTTTTCTTTGAAATTCCTTTGTTTTCGAAATACGAAATTTTCTACTTCGTAAA
*
2957887 TGTTTTCAGGGGGATTTTTCTTGGTTTATAATTTTT
131 TGTTTTCAGGGGGATTTTTCTTGGTTTACAATTTTT
* * * *
2957923 T-AAATTCATCAAATATCATCATTTAATTCATAGTAAATTACTTTTGAAAATTTCATTTATTTTC
1 TAAAATTCATCAAATATCATCATTTAATTCACAGTAAATCACTTTTGAAAATTCCATTTA-ATTC
* * *
2957987 ATA-TGTTTTCATTTTTTTCTTTGAAATTCTCTTAT-TTTT-GAAAAATTCG-AGTTTTTTA-TT
65 ATATTGTTTTCA-TTTTTTCTTTGAAATTC-CTT-TGTTTTCG--AAATACGAAATTTTCTACTT
* *
2958047 CTGTAAATATTTT-TGAGGGGATTTTTC-TGGATTT-CAATTTTT
125 C-GTAAATGTTTTCAG-GGGGATTTTTCTTGG-TTTACAATTTTT
*
2958089 TAAAATTCATTAAATAT
1 TAAAATTCATCAAATAT
2958106 TTTTATTAAA
Statistics
Matches: 154, Mismatches: 19, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
165 55 0.36
166 40 0.26
167 52 0.34
168 7 0.05
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (166 bp):
TAAAATTCATCAAATATCATCATTTAATTCACAGTAAATCACTTTTGAAAATTCCATTTAATTCA
TATTGTTTTCATTTTTTCTTTGAAATTCCTTTGTTTTCGAAATACGAAATTTTCTACTTCGTAAA
TGTTTTCAGGGGGATTTTTCTTGGTTTACAATTTTT
Found at i:2960124 original size:153 final size:152
Alignment explanation
Indices: 2959861--2960162 Score: 407
Period size: 153 Copynumber: 2.0 Consensus size: 152
2959851 ATTTTATTAG
*
2959861 ATCGAGTCTTAGGTTGTCATCGGATCCACTTTTTGTGCCGAAGGTGGGTATTTAGGATAGGTTCA
1 ATCGAGTCTTAGGTTGT-ATCCGATCCACTTTTTGT-CCGAAGGTGGGTATTTAGGATAGGTTCA
* * * * *
2959926 TCCTATCTACTCCTTTTTAAGTCTTTAGGGGTATCAGGCACTTCTAAGTC-AAAGTATCCCCTAG
64 TCCCATCTAATCCTTTTTAAGTCTTTAGGGGTATCAGACACTTCTAAGTCGAAAATATCACCTA-
2959990 AG-GTATTTTCGTAATTTTTCCAAA
128 AGTGTATTTTCGTAATTTTTCCAAA
*
2960014 ATCGAGTCTTAGGTTGT-TCCGAGTCTACTTTTATGT-CGAAGGTGGGTATTTAGGATA-GTTCA
1 ATCGAGTCTTAGGTTGTATCCGA-TCCACTTTT-TGTCCGAAGGTGGGTATTTAGGATAGGTTCA
* *
2960076 TCCCATCTATAATCTTTTTTAAGTCCTTTAGGGGTATCAGACATTTCTAAGTCGAAAATATCACC
64 TCCCATC--TAATCCTTTTTAAGT-CTTTAGGGGTATCAGACACTTCTAAGTCGAAAATATCACC
*
2960141 TAAGTGTATTTTTGTAATTTTT
126 TAAGTGTATTTTCGTAATTTTT
2960163 TTAGATTCAA
Statistics
Matches: 132, Mismatches: 10, Indels: 13
0.85 0.06 0.08
Matches are distributed among these distances:
150 11 0.08
151 25 0.19
152 21 0.16
153 48 0.36
154 27 0.20
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (152 bp):
ATCGAGTCTTAGGTTGTATCCGATCCACTTTTTGTCCGAAGGTGGGTATTTAGGATAGGTTCATC
CCATCTAATCCTTTTTAAGTCTTTAGGGGTATCAGACACTTCTAAGTCGAAAATATCACCTAAGT
GTATTTTCGTAATTTTTCCAAA
Found at i:2962334 original size:13 final size:13
Alignment explanation
Indices: 2962316--2962343 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2962306 GCTAAAACTC
2962316 ACATTGTATCGAT
1 ACATTGTATCGAT
2962329 ACATTGTATCGAT
1 ACATTGTATCGAT
2962342 AC
1 AC
2962344 TGTCTTTACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2963456 original size:79 final size:79
Alignment explanation
Indices: 2963324--2963492 Score: 241
Period size: 79 Copynumber: 2.1 Consensus size: 79
2963314 GGGGCTTGAG
* *
2963324 TATCCCCGATTATGGAAAATCGGTGTTGTGAAAATAAAATCGGGGTTGAAGTATCCCCTTCG-AA
1 TATCCCCGATTATAGAAAATCGGTATTGTGAAAATAAAATCGGGGTTGAAGTATCCCC-TCGAAA
2963388 ATAACAAGGTTGGAA
65 ATAACAAGGTTGGAA
* * * * *
2963403 TATCCCTGATTATAGAAGATCGGTATTTTGAAAATAAAATCGGGGTTGGAGTATTCCCTCGAAAA
1 TATCCCCGATTATAGAAAATCGGTATTGTGAAAATAAAATCGGGGTTGAAGTATCCCCTCGAAAA
* *
2963468 TAACGAGGTTGGAG
66 TAACAAGGTTGGAA
2963482 TATCCCCGATT
1 TATCCCCGATT
2963493 GTGAAAAATC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 3 0.04
79 76 0.96
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (79 bp):
TATCCCCGATTATAGAAAATCGGTATTGTGAAAATAAAATCGGGGTTGAAGTATCCCCTCGAAAA
TAACAAGGTTGGAA
Found at i:2963518 original size:79 final size:79
Alignment explanation
Indices: 2963321--2963515 Score: 236
Period size: 79 Copynumber: 2.5 Consensus size: 79
2963311 AACGGGGCTT
*
2963321 GAGTATCCCCGATTATGGAAAATCGGTG-TTGTGAAAATAAAATCGGGGTTGAAGTATCCCCTTC
1 GAGTATCCCCGATTATGAAAAATCGGTGATT-TGAAAATAAAATCGGGGTTGAAGTATCCCCTTC
2963385 GAAATAACAAGGTTG
65 GAAATAACAAGGTTG
* * * * *
2963400 GAATATCCCTGATTAT-AGAAGATCGGT-ATTTTGAAAATAAAATCGGGGTTGGAGTATTCCC-T
1 GAGTATCCCCGATTATGA-AAAATCGGTGA-TTTGAAAATAAAATCGGGGTTGAAGTATCCCCTT
*
2963462 CGAAAATAACGAGGTTG
64 CG-AAATAACAAGGTTG
* *
2963479 GAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAA
1 GAGTATCCCCGATTATGAAAAATCGGTGATTT-GAAA
2963516 TAAGGCTGGG
Statistics
Matches: 97, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
78 3 0.03
79 86 0.89
80 8 0.08
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (79 bp):
GAGTATCCCCGATTATGAAAAATCGGTGATTTGAAAATAAAATCGGGGTTGAAGTATCCCCTTCG
AAATAACAAGGTTG
Found at i:2963586 original size:51 final size:51
Alignment explanation
Indices: 2963475--2963590 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 51
2963465 AAATAACGAG
* * * * *
2963475 GTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAGGCTGGG
1 GTTGGAGTATCCCCGATTGTGAAAAACCAATGATTTAGAAATAAAGCCGGA
** * * *
2963526 GTTAAAGTATCCCTGATTGTGAGAAACCAAT-ATTTTGGAAATAAAGCCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAACCAATGA-TTTAGAAATAAAGCCGGA
2963577 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2963591 TCGGAAATAA
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAACCAATGATTTAGAAATAAAGCCGGA
Found at i:2963612 original size:28 final size:28
Alignment explanation
Indices: 2963577--2963645 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
2963567 TAAAGCCGGA
** *
2963577 GTTGGAGTATCCCCTCGGAAATAACAGG
1 GTTGGAGTATCCCCGAGAAAATAACAGG
* *
2963605 GTTGGAGTATCCCCGATAAAATAACGGG
1 GTTGGAGTATCCCCGAGAAAATAACAGG
2963633 GTTGGAGTATCCC
1 GTTGGAGTATCCC
2963646 TGATTGTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (28 bp):
GTTGGAGTATCCCCGAGAAAATAACAGG
Found at i:2963626 original size:158 final size:156
Alignment explanation
Indices: 2963445--2963776 Score: 400
Period size: 158 Copynumber: 2.1 Consensus size: 156
2963435 AATAAAATCG
2963445 GGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATT
1 GGGTTGGAGTA-TCCC-CGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATT
** * * *
2963510 TAGAAAT-AAGGCTGGGGTTAAAGTATCC-CTGATTGT-GAGAAACCAATATTTTGGAAATAAAG
64 TAGAAATAAAATC-GGAGTTAAAGTATCCTC-GATTGTGGA-AAACCAATATTTTAGAAATAAAA
2963572 CCGGAGTTGGAGTATCCCCTCGGAAATAACA
126 CCGGAGTTGGAGTATCCCCTCGGAAATAACA
* * * * *
2963603 GGGTTGGAGTATCCCCGATAAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTT
1 GGGTTGGAGTATCCCCG--AAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATT
* ** **** *
2963668 TGGAAATAAAATCGGAGTTGGAGTATCCTCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCG
64 TAGAAATAAAATCGGAGTTAAAGTATCCTCGATTGTGGAAAACCAATATTTTAGAAATAAAACCG
* *
2963733 GGGTTGGAGTATCCCCTCGGAAATGACA
129 GAGTTGGAGTATCCCCTCGGAAATAACA
2963761 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
2963777 AATTGTGAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
156 2 0.01
157 4 0.03
158 137 0.92
159 6 0.04
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (156 bp):
GGGTTGGAGTATCCCCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTA
GAAATAAAATCGGAGTTAAAGTATCCTCGATTGTGGAAAACCAATATTTTAGAAATAAAACCGGA
GTTGGAGTATCCCCTCGGAAATAACA
Found at i:2963702 original size:51 final size:51
Alignment explanation
Indices: 2963633--2963747 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
2963623 AAATAACGGG
* *
2963633 GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGGA
* *
2963684 GTTGGAGTAT-CCTCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCT-GATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGGA
2963735 GTTGGAGTATCCC
1 GTTGGAGTATCCC
2963748 CTCGGAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 3 0.05
51 53 0.91
52 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGGA
Found at i:2963928 original size:78 final size:79
Alignment explanation
Indices: 2963689--2963984 Score: 398
Period size: 79 Copynumber: 3.8 Consensus size: 79
2963679 TCGGAGTTGG
* * * *
2963689 AGTATCCTCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
* *
2963754 AATGACAGGG-TTGG
66 AATAAC-GGGATTGA
* * * * * * * *
2963768 AGTATCCCCAATTGTGAAAAACTGGTGTTTTGGGAATAAAATCGGGTTTGGAGTATCCCCTCGGA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
*
2963833 AATAACGGGATTAA
66 AATAACGGGATTGA
* **
2963847 AGTATCCCTGATTATGAAATTTTGATGTTTTAGAAATAAAA-CGGGGTTGGAGTATCCCCTCGGA
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
2963911 AATAACGGGATTGA
66 AATAACGGGATTGA
*
2963925 AGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCC
1 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
2963985 GAGATGAAGA
Statistics
Matches: 189, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
78 75 0.40
79 114 0.60
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (79 bp):
AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGA
AATAACGGGATTGA
Found at i:2969935 original size:17 final size:17
Alignment explanation
Indices: 2969902--2969934 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2969892 TAGGCCGTTC
*
2969902 ATTTTTTTTTACTTTTT
1 ATTTTTTTGTACTTTTT
2969919 ATTTTTTTGTA-TTTTT
1 ATTTTTTTGTACTTTTT
2969935 TGTCTCTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
ATTTTTTTGTACTTTTT
Found at i:2970339 original size:28 final size:28
Alignment explanation
Indices: 2970302--2971028 Score: 604
Period size: 28 Copynumber: 25.8 Consensus size: 28
2970292 CAATGACTTG
*
2970302 TGTGGGCTTTGAAAGGATGCTACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
2970330 TGTGGGCTTTGAAAAGATGCCATTTACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
2970358 TGTGAGCTTT-AAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTAACT
* *
2970386 TGTGGGCTTTAAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
2970414 TATGGGCTTTGAAAGG-TACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
2970441 TGTGGGCTTTGAAAGGATGCCA-TAGACT
1 TGTGGGCTTTGAAAGGATGCCACTA-ACT
* * *
2970469 TGTGGGCTTTGAGAATG-TGTCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTAACT
* * * *
2970497 TGTGGGCTTTAAAAAAGGTTGCCATTGACT
1 TGTGGGCTTT--GAAAGGATGCCACTAACT
* *
2970527 TGTGGGCTTTGAAAAGATACCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
2970555 TATGGGCTTTGAGAAGG-TGCCTCTAACT
1 TGTGGGCTTTGA-AAGGATGCCACTAACT
* * *
2970583 TGTGGGCTTTGAAAAAAGTTGCCACTGACT
1 TGTGGGCTTTG--AAAGGATGCCACTAACT
* * *
2970613 TGTGAGCTTTGAAAAGATACCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
2970641 TATGGGTTTTGAGAAGG-TGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTAACT
* *
2970669 TGTGGACTTTGACAAGGGTTGCCACTAACT
1 TGTGGGCTTTGA-AA-GGATGCCACTAACT
* *
2970699 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
2970727 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
2970755 TGTGGGTTTTGAGAAGG-TGGCACTTACT
1 TGTGGGCTTTGA-AAGGATGCCACTAACT
* * * *
2970783 TATAGGCTTTGAAAAGTG-TGCCATTGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTAACT
*
2970812 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
** *
2970839 TGTGGGCTTT-AAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
2970866 TGTGGGCTTTGAAA-AATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * **
2970893 TATGGGCTTTGAAAAGAGTGCCACCGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTAACT
* *
2970922 TGTGGGCTCTGAAATGGTTGCCAGCT-ACTT
1 TGTGGGCTTTGAAA-GGATGCCA-CTAAC-T
* * *
2970952 GTGTGGGCTTT-CAAGGATGCCACAAAGT
1 -TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
2970980 TGT-GGATTTCAAAGGATGCCA-TGAAGT
1 TGTGGGCTTTGAAAGGATGCCACT-AACT
* *
2971007 TGTGGAC-TTAAAAGGATGCCAC
1 TGTGGGCTTTGAAAGGATGCCAC
2971029 GGAGTTGTGG
Statistics
Matches: 573, Mismatches: 94, Indels: 64
0.78 0.13 0.09
Matches are distributed among these distances:
26 8 0.01
27 131 0.23
28 274 0.48
29 85 0.15
30 66 0.12
31 9 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTAACT
Found at i:2970561 original size:86 final size:85
Alignment explanation
Indices: 2970302--2970929 Score: 650
Period size: 86 Copynumber: 7.4 Consensus size: 85
2970292 CAATGACTTG
* * * * * * *
2970302 TGTGGGCTTTGA-AAGGATGCTACTAACTTGTGGGCTTT-GAAAAGATGCCATTTACTTGTGAGC
1 TGTGGGCTTTGAGAAGG-TGCCACTGACTTGTGGGCTTTAAAAAAGGTGCCACTGACTTGTGGGC
2970365 TTT-AAAAGAGTGCCACTAACT
65 TTTGAAAAGA-TGCCACTAACT
* * * * * * *
2970386 TGTGGGCTTTAAAAAGATGCCACTAACTTATGGGCTTT--GAAAGGTACCACTGACTTGTGGGCT
1 TGTGGGCTTTGAGAAGGTGCCACTGACTTGTGGGCTTTAAAAAAGGTGCCACTGACTTGTGGGCT
*
2970449 TTGAAAGGATGCCA-TAGACT
66 TTGAAAAGATGCCACTA-ACT
* * *
2970469 TGTGGGCTTTGAGAATGTGTCACTGACTTGTGGGCTTTAAAAAAGGTTGCCATTGACTTGTGGGC
1 TGTGGGCTTTGAGAAGGTGCCACTGACTTGTGGGCTTTAAAAAAGG-TGCCACTGACTTGTGGGC
*
2970534 TTTGAAAAGATACCACTAACT
65 TTTGAAAAGATGCCACTAACT
* * * * *
2970555 TATGGGCTTTGAGAAGGTGCCTCTAACTTGTGGGCTTTGAAAAAAGTTGCCACTGACTTGTGAGC
1 TGTGGGCTTTGAGAAGGTGCCACTGACTTGTGGGCTTT-AAAAAAGGTGCCACTGACTTGTGGGC
*
2970620 TTTGAAAAGATACCACTAACT
65 TTTGAAAAGATGCCACTAACT
* * * * * * *
2970641 TATGGGTTTTGAGAAGGTGCCACTGACTTGTGGACTTTGACAAGGGTTGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAGAAGGTGCCACTGACTTGTGGGCTTTAAAAAAGG-TGCCACTGACTTGTGGGC
* * *
2970706 TTTGAAAGGATGCCACTGATT
65 TTTGAAAAGATGCCACTAACT
* ** * * * * *
2970727 TGTGGGCTTTGA-AAGGGTGCCACTAACTTGTGGG-TTTTGAGAAGGTGGCACTTACTTATAGGC
1 TGTGGGCTTTGAGAA-GGTGCCACTGACTTGTGGGCTTTAAAAAAGGTGCCACTGACTTGTGGGC
* * *
2970790 TTTGAAAAGTGTGCCATTGACT
65 TTTGAAAAG-ATGCCACTAACT
2970812 TGTGGGCTTTGA-AAGGTGCCACTGACTTGTGGGCTTTAAAAAA--TGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAGAAGGTGCCACTGACTTGTGGGCTTTAAAAAAGGTGCCACTGACTTGTGGGCT
2970874 TTGAAAA-ATGCCACTAACT
66 TTGAAAAGATGCCACTAACT
* * *
2970893 TATGGGCTTTGAAAAGAGTGCCACCGACTTGTGGGCT
1 TGTGGGCTTTGAGAAG-GTGCCACTGACTTGTGGGCT
2970930 CTGAAATGGT
Statistics
Matches: 455, Mismatches: 75, Indels: 29
0.81 0.13 0.05
Matches are distributed among these distances:
81 20 0.04
82 5 0.01
83 101 0.22
84 75 0.16
85 49 0.11
86 196 0.43
87 9 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (85 bp):
TGTGGGCTTTGAGAAGGTGCCACTGACTTGTGGGCTTTAAAAAAGGTGCCACTGACTTGTGGGCT
TTGAAAAGATGCCACTAACT
Found at i:2971054 original size:28 final size:27
Alignment explanation
Indices: 2970964--2971404 Score: 506
Period size: 27 Copynumber: 16.1 Consensus size: 27
2970954 GTGGGCTTTC
** * *
2970964 AAGGATGCCACAAAGTTGTGGATTTCA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* *
2970991 AAGGATGCCATGAAGTTGTGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
2971018 AAGGATGCCACGGAGTTGTGGACTTTAA
1 AAGGATGCCACGGAGTTGTGGAC-TTAA
** **
2971046 ATTGATGCCATAGAGTTGTGGAC-TAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* * *
2971072 AATGATGCCACGTAGTGGTGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
*
2971099 AAGGATGCCACGGAGTTATGGACTTTAA
1 AAGGATGCCACGGAGTTGTGGAC-TTAA
*
2971127 AAGGATGCCACAGAGTTGTGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* *
2971154 AAGGATGCCATGAAGTTGTGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* *
2971181 AAGGATGCCACGGAGTTATAGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* * **
2971208 AAGAATGCTATAGAGTTGTGGACTTTAA
1 AAGGATGCCACGGAGTTGTGGAC-TTAA
**
2971236 AAGGATGCCATAGAGTTGTGGACTTTAA
1 AAGGATGCCACGGAGTTGTGGAC-TTAA
*
2971264 AAGGATGCCACGGAGTTATGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* * *
2971291 AAGGATGCTAAGGAGTTGTGGACTTGA
1 AAGGATGCCACGGAGTTGTGGACTTAA
* *
2971318 AAGGGTGCCACGGAGCTGTGGACCTTAA
1 AAGGATGCCACGGAGTTGTGGA-CTTAA
* *
2971346 AAGGGGTGCCACGGAGTTGTGAACTTAA
1 AA-GGATGCCACGGAGTTGTGGACTTAA
* *
2971374 AAGGGTGCCACGGAGTTGTGGACTTTA
1 AAGGATGCCACGGAGTTGTGGACTTAA
2971401 AAGG
1 AAGG
2971405 TTGCTGTCGC
Statistics
Matches: 356, Mismatches: 52, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
26 21 0.06
27 206 0.58
28 111 0.31
29 18 0.05
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (27 bp):
AAGGATGCCACGGAGTTGTGGACTTAA
Found at i:2971063 original size:82 final size:82
Alignment explanation
Indices: 2970964--2971404 Score: 543
Period size: 82 Copynumber: 5.4 Consensus size: 82
2970954 GTGGGCTTTC
* * *
2970964 AAGGATGCCACAAAGTTGTGGATTTCAAAGGATGCCATGAAGTTGTGGACTTAAAAGGATGCCAC
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGACTTAAAAGGATGCCAC
*
2971029 GGAGTTGTGGACTTTAA
66 GGAGTTATGGACTTTAA
** * * * * *
2971046 ATTGATGCCATAGAGTTGTGGAC-TAAAATGATGCCACGTAGTGGTGGACTTAAAAGGATGCCAC
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGACTTAAAAGGATGCCAC
2971110 GGAGTTATGGACTTTAA
66 GGAGTTATGGACTTTAA
2971127 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGACTTAAAAGGATGCCAC
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGACTTAAAAGGATGCCAC
*
2971192 GGAGTTATAGAC-TTAA
66 GGAGTTATGGACTTTAA
* * *
2971208 AAGAATGCTATAGAGTTGTGGACTTTAAAAGGATGCCAT-AGAGTTGTGGACTTTAAAAGGATGC
1 AAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCATGA-AGTTGTGGAC-TTAAAAGGATGC
2971272 CACGGAGTTATGGAC-TTAA
63 CACGGAGTTATGGACTTTAA
* * * * * * *
2971291 AAGGATGCTA-AGGAGTTGTGGACTTGAAAGGGTGCCACGGAGCTGTGGACCTTAAAAGGGGTGC
1 AAGGATGCCACA-GAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGA-CTTAAAA-GGATGC
* *
2971355 CACGGAGTTGTGAAC-TTAA
63 CACGGAGTTATGGACTTTAA
* * *
2971374 AAGGGTGCCACGGAGTTGTGGACTTTAAAGG
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGG
2971405 TTGCTGTCGC
Statistics
Matches: 314, Mismatches: 36, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
81 97 0.31
82 118 0.38
83 99 0.32
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (82 bp):
AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGACTTAAAAGGATGCCAC
GGAGTTATGGACTTTAA
Found at i:2971152 original size:55 final size:54
Alignment explanation
Indices: 2970964--2971404 Score: 492
Period size: 55 Copynumber: 8.1 Consensus size: 54
2970954 GTGGGCTTTC
* * * * *
2970964 AAGGATGCCACAAAGTTGTGGATTTCAAAGGATGCCATGAAGTTGTGGACTTAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAA
* ** **
2971018 AAGGATGCCACGGAGTTGTGGACTTTAAATTGATGCCATAGAGTTGTGGAC-TAA
1 AAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAA
* * *
2971072 AATGATGCCAC-GTAGTGGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTTAA
1 AAGGATGCCACAG-AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAA
* *
2971127 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGACTTAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAA
* * * * * **
2971181 AAGGATGCCACGGAGTTATAGACTTAAAAGAATGCTATAGAGTTGTGGACTTTAA
1 AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAA
* *
2971236 AAGGATGCCATAGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTATGGACTTAA
1 AAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAA
* * * *
2971291 AAGGATGCTA-AGGAGTTGTGGACTTGAAAGGGTGCCACGGAGCTGTGGACCTTAA
1 AAGGATGCCACA-GAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGA-CTTAA
* * * * *
2971346 AAGGGGTGCCACGGAGTTGTGAACTTAAAAGGGTGCCACGGAGTTGTGGACTTTA
1 AA-GGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAA
2971401 AAGG
1 AAGG
2971405 TTGCTGTCGC
Statistics
Matches: 328, Mismatches: 48, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
53 23 0.07
54 114 0.35
55 128 0.39
56 63 0.19
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (54 bp):
AAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAA
Found at i:2980859 original size:21 final size:21
Alignment explanation
Indices: 2980833--2980888 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
2980823 TTTCAATATC
2980833 TATAAATGTTTTAGAG-TTATA
1 TATAAATGTTTTAGAGCTT-TA
*
2980854 TATAAATGTTTTCGAGCTTTA
1 TATAAATGTTTTAGAGCTTTA
*
2980875 AATCAAATGTTTTA
1 TAT-AAATGTTTTA
2980889 AGTAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
TATAAATGTTTTAGAGCTTTA
Found at i:2981019 original size:20 final size:21
Alignment explanation
Indices: 2980996--2981089 Score: 81
Period size: 20 Copynumber: 4.6 Consensus size: 21
2980986 CATACCCAGA
2980996 TGTATCGATACATAATGCT-T
1 TGTATCGATACATAATGCTAT
*
2981016 TGTATCGATAGATAATGCTCAT
1 TGTATCGATACATAATGCT-AT
* * *
2981038 TGTATCAATACAT-GTTC-AT
1 TGTATCGATACATAATGCTAT
* *
2981057 TGTATTGATACATGAA--CAAT
1 TGTATCGATACAT-AATGCTAT
2981077 TGTATCGATACAT
1 TGTATCGATACAT
2981090 GAAACTGGCA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 14 0.23
20 32 0.53
21 2 0.03
22 12 0.20
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATAATGCTAT
Found at i:2982800 original size:12 final size:12
Alignment explanation
Indices: 2982777--2982810 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2982767 ACCATTAAAG
*
2982777 ATAATGAAGATA
1 ATAATGATGATA
*
2982789 ATGATGATGATA
1 ATAATGATGATA
2982801 ATAATGATGA
1 ATAATGATGA
2982811 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (12 bp):
ATAATGATGATA
Found at i:2983827 original size:99 final size:99
Alignment explanation
Indices: 2983679--2983884 Score: 358
Period size: 99 Copynumber: 2.1 Consensus size: 99
2983669 CTAAAGGAAT
* * *
2983679 CAAGACTTCGAATAATGGAATAACGAAATGGATTCCAAAAGGATCAAAAGTATTAAACATTAACG
1 CAAGACTTCGAATAATGAAATAACAAAATGGATTCCAAAAGGATCAAAAGTATTAAACACTAACG
* *
2983744 AAAAAGGACCAAAGAAAATTTGGGTACCTAAAAC
66 AAAAAAGACCAAAGAAAAATTGGGTACCTAAAAC
2983778 CAAGACTTCGAATAATGAAATAACAAAATGGATTCCAAAAGGATCAAAAGTATTAAACACTAACG
1 CAAGACTTCGAATAATGAAATAACAAAATGGATTCCAAAAGGATCAAAAGTATTAAACACTAACG
*
2983843 AAAAAAGACCCAAGAAAAATTGGGTACCTAAAAC
66 AAAAAAGACCAAAGAAAAATTGGGTACCTAAAAC
2983877 CAAGACTT
1 CAAGACTT
2983885 GTTCTTTATG
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (99 bp):
CAAGACTTCGAATAATGAAATAACAAAATGGATTCCAAAAGGATCAAAAGTATTAAACACTAACG
AAAAAAGACCAAAGAAAAATTGGGTACCTAAAAC
Found at i:2987432 original size:13 final size:13
Alignment explanation
Indices: 2987414--2987449 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2987404 ATGTTCTTTA
* *
2987414 TATCGATATATTG
1 TATCGATACAATG
2987427 TATCGATACAATG
1 TATCGATACAATG
2987440 TATCGATACA
1 TATCGATACA
2987450 TGGGTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:2989824 original size:20 final size:20
Alignment explanation
Indices: 2989782--2989874 Score: 82
Period size: 20 Copynumber: 4.6 Consensus size: 20
2989772 ACCCTTGAAA
* *
2989782 GTATCGATACAT-ATCCAGAT
1 GTATCGATACATAATGCA-TT
*
2989802 GTATCGATACATAATGCTTT
1 GTATCGATACATAATGCATT
*
2989822 GTATCGATAGATAATGTTCATT
1 GTATCGATACATAATG--CATT
* * *
2989844 GTATCAATACCT-ATTCATT
1 GTATCGATACATAATGCATT
2989863 GTATCGATACAT
1 GTATCGATACAT
2989875 GCACAATTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 14 0.24
20 28 0.47
21 5 0.08
22 12 0.20
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
GTATCGATACATAATGCATT
Found at i:2991893 original size:9 final size:10
Alignment explanation
Indices: 2991879--2991923 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
2991869 CAGGCCACTC
2991879 ATTTTTTT-T
1 ATTTTTTTGT
2991888 ATTTTTTTGT
1 ATTTTTTTGT
*
2991898 ATTTTTTTCT
1 ATTTTTTTGT
*
2991908 CTCTTTTTTGT
1 AT-TTTTTTGT
2991919 ATTTT
1 ATTTT
2991924 ATTATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 8 0.27
10 14 0.47
11 8 0.27
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (10 bp):
ATTTTTTTGT
Found at i:3001026 original size:12 final size:12
Alignment explanation
Indices: 3001009--3001061 Score: 88
Period size: 12 Copynumber: 4.3 Consensus size: 12
3000999 TTTGCTTGTA
3001009 TTACATACATGC
1 TTACATACATGC
3001021 TTACATACATGC
1 TTACATACATGC
3001033 TTACATACATGC
1 TTACATACATGC
*
3001045 ATACATACATGC
1 TTACATACATGC
3001057 ATTAC
1 -TTAC
3001062 TTTCGTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
12 35 0.92
13 3 0.08
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (12 bp):
TTACATACATGC
Found at i:3001902 original size:11 final size:11
Alignment explanation
Indices: 3001886--3001912 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3001876 TGGATTTTCA
3001886 AAAAACAAAAC
1 AAAAACAAAAC
3001897 AAAAACAAAAC
1 AAAAACAAAAC
3001908 AAAAA
1 AAAAA
3001913 AGAAAAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:3002299 original size:13 final size:13
Alignment explanation
Indices: 3002266--3002310 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
3002256 AATGAGAAAC
*
3002266 AAAAGAAAAGAAAA
1 AAAAGAAAA-AAGA
*
3002280 GAAAAGAAAAATGA
1 -AAAAGAAAAAAGA
3002294 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
3002307 AAAA
1 AAAA
3002311 AAGCATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
14 2 0.07
15 9 0.33
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:3002303 original size:6 final size:6
Alignment explanation
Indices: 3002266--3002310 Score: 51
Period size: 5 Copynumber: 7.7 Consensus size: 6
3002256 AATGAGAAAC
3002266 AAAAG- AAAAG- AAAAG- AAAAGA AAAATGA AAAAGAA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAA-GA AAAAG-A AAAAGA AAAA
3002311 AAGCATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.41
6 10 0.27
7 12 0.32
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:3002307 original size:30 final size:30
Alignment explanation
Indices: 3002266--3002331 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
3002256 AATGAGAAAC
*
3002266 AAAAGAAAAGAA-AAGAAAAG-A-AAAATGA
1 AAAAGAAAA-AAGAAAAAAAGCATAAAATGA
*
3002294 AAAAGAAAAAAGAAAAAAAGCATGAAATGA
1 AAAAGAAAAAAGAAAAAAAGCATAAAATGA
3002324 AAAAGAAA
1 AAAAGAAA
3002332 GTACAGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 16 0.48
29 1 0.03
30 14 0.42
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (30 bp):
AAAAGAAAAAAGAAAAAAAGCATAAAATGA
Found at i:3002311 original size:7 final size:7
Alignment explanation
Indices: 3002266--3002311 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
3002256 AATGAGAAAC
3002266 AAAAGAA
1 AAAAGAA
3002273 AAGAA-AA
1 AA-AAGAA
3002280 GAAAAGAA
1 -AAAAGAA
*
3002288 AAATG-A
1 AAAAGAA
3002294 AAAAGAA
1 AAAAGAA
3002301 AAAAGAA
1 AAAAGAA
3002308 AAAA
1 AAAA
3002312 AGCATGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 5 0.15
7 22 0.67
8 6 0.18
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:3004253 original size:89 final size:88
Alignment explanation
Indices: 3004088--3004342 Score: 283
Period size: 89 Copynumber: 2.9 Consensus size: 88
3004078 GGGAGAACAA
* *
3004088 CCCATACATTCCTAATCATATCCCCTCACTCAACTAATAGATGGTATTGATGCATCACAAAGCCT
1 CCCACACATTCCTAATCATATCCCCTCACTCAACCAATAGATGGTATTGATGCATCACAAAGCCT
* **
3004153 GATTTGCTTGGGGCAAGGTTTAG
66 AATTTGCTTGGGGCAAGGTGCAG
* * * *
3004176 CCTACACATTCCCAATCATATCCCCTTTACTCAACCACTAGATGGTATTGATGCATCACAAAGCC
1 CCCACACATTCCTAATCATATCCCC-TCACTCAACCAATAGATGGTATTGATGCATCACAAAGCC
*
3004241 TAATTT-CTTTGGGGCATGGTGCAG
65 TAATTTGC-TTGGGGCAAGGTGCAG
* *
3004265 CCCACACATTCCTAATCATATTCCCATCACT-AGACC-----ATGGT-TTGATGCACCACAAAGC
1 CCCACACATTCCTAATCATA-TCCCCTCACTCA-ACCAATAGATGGTATTGATGCATCACAAAGC
* * *
3004323 CAAATTTCCTTGGGGTAAGG
64 CTAATTTGCTTGGGGCAAGG
3004343 ATATCCCAAC
Statistics
Matches: 144, Mismatches: 18, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
83 31 0.22
84 6 0.04
88 24 0.17
89 79 0.55
90 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (88 bp):
CCCACACATTCCTAATCATATCCCCTCACTCAACCAATAGATGGTATTGATGCATCACAAAGCCT
AATTTGCTTGGGGCAAGGTGCAG
Found at i:3006966 original size:32 final size:32
Alignment explanation
Indices: 3006925--3006989 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3006915 GTCACGAACA
*
3006925 ATGTCTAGAAAGATAAAGAAAGCGAGGTTGGG
1 ATGTCTAGAAAGATAAAAAAAGCGAGGTTGGG
*
3006957 ATGTCTAGAAAGATAAAAAAAGTGAGGTTGGG
1 ATGTCTAGAAAGATAAAAAAAGCGAGGTTGGG
3006989 A
1 A
3006990 CGATGATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.05, G:0.32, T:0.20
Consensus pattern (32 bp):
ATGTCTAGAAAGATAAAAAAAGCGAGGTTGGG
Found at i:3019785 original size:13 final size:13
Alignment explanation
Indices: 3019767--3019805 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3019757 ACATTTTTCT
3019767 TTGTATCGATACA
1 TTGTATCGATACA
3019780 TTGTATCGATACA
1 TTGTATCGATACA
*
3019793 CTGTATCGATACA
1 TTGTATCGATACA
3019806 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3024228 original size:24 final size:20
Alignment explanation
Indices: 3024211--3024276 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
3024201 TTTTACCTAG
3024211 ATGTATTGATACATTTTTCA
1 ATGTATTGATACATTTTTCA
* * *
3024231 ATGTATTGATACATGTATGA
1 ATGTATTGATACATTTTTCA
**
3024251 ATGTATCAATACATTCTTT-A
1 ATGTATTGATACATT-TTTCA
3024271 ATGTAT
1 ATGTAT
3024277 CGACACATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 36 0.95
21 2 0.05
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (20 bp):
ATGTATTGATACATTTTTCA
Found at i:3024277 original size:20 final size:20
Alignment explanation
Indices: 3024250--3024287 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3024240 TACATGTATG
*
3024250 AATGTATCAATACATTCTTT
1 AATGTATCAACACATTCTTT
*
3024270 AATGTATCGACACATTCT
1 AATGTATCAACACATTCT
3024288 GTCTCTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
AATGTATCAACACATTCTTT
Found at i:3024315 original size:91 final size:90
Alignment explanation
Indices: 3024160--3024331 Score: 283
Period size: 91 Copynumber: 1.9 Consensus size: 90
3024150 TTTTACCAAG
* * * *
3024160 ATGTATCAATACATTTTTCATTGTATCGATACATTCTGTCTTTTTACCTAGATGTATTGATACAT
1 ATGTATCAATACATTTTTCAATGTATCGACACATTCTGTCTCTTTACCCAGATGTATTGATACAT
3024225 TTTTCAATGTATTGATACATGTATGA
66 TTTT-AATGTATTGATACATGTATGA
3024251 ATGTATCAATACATTCTTT-AATGTATCGACACATTCTGTCTCTTTACCCAGATGTATTGATACA
1 ATGTATCAATACATT-TTTCAATGTATCGACACATTCTGTCTCTTTACCCAGATGTATTGATACA
3024315 TTTTTAATGTATTGATA
65 TTTTTAATGTATTGATA
3024332 TATCTAGTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
90 12 0.16
91 61 0.80
92 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (90 bp):
ATGTATCAATACATTTTTCAATGTATCGACACATTCTGTCTCTTTACCCAGATGTATTGATACAT
TTTTAATGTATTGATACATGTATGA
Found at i:3025234 original size:20 final size:21
Alignment explanation
Indices: 3025195--3025234 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3025185 TAGTCTTTGA
*
3025195 CCATGCATTTTTTACTATGTT
1 CCATGCATTTTTAACTATGTT
3025216 CCATGCATTTTTAAC-ATGT
1 CCATGCATTTTTAACTATGT
3025235 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (21 bp):
CCATGCATTTTTAACTATGTT
Found at i:3031881 original size:78 final size:78
Alignment explanation
Indices: 3031609--3031942 Score: 341
Period size: 79 Copynumber: 4.2 Consensus size: 78
3031599 TTTTTCATTG
* * *
3031609 GGGATACTCTAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAATACCA
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTC-AAAATACCG
3031674 ATTTTTCACAAT-A
65 ATTTTTCACAATCA
* * * ** * *
3031687 GGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTTCAA-CCCTAGCCTTATTTCTAAATCAT
1 -GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGA-TTTTATTTCAAAAT-AC
*
3031751 CGATTTTTCACAATCG
63 CGATTTTTCACAATCA
* * *
3031767 GGGAAACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTCATTTTCAAAATACCG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTA-TTTCAAAATACCG
*
3031832 ATTTTT-ATAATCA
65 ATTTTTCACAATCA
* * * * * ** * *
3031845 AGGATACTCGAACTCTGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTCTGGAACACCA
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTC-AAAATACCG
* * *
3031910 ATTTTCCATAATCG
65 ATTTTTCACAATCA
*
3031924 GGGATACTCCAGCCCCGTT
1 GGGATACTCCAACCCCGTT
3031943 GTTATCTCCA
Statistics
Matches: 206, Mismatches: 42, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
77 4 0.02
78 66 0.32
79 124 0.60
80 12 0.06
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCAAAATACCGA
TTTTTCACAATCA
Found at i:3031924 original size:157 final size:158
Alignment explanation
Indices: 3031608--3031942 Score: 410
Period size: 157 Copynumber: 2.1 Consensus size: 158
3031598 ATTTTTCATT
* *
3031608 GGGGATACTCTAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAATACC
1 GGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTCATTTCTAAAATACC
* *
3031673 AATTTTTCACAATAGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTTCAACCCTAGCCTT
66 AATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTAGCCTT
* * *
3031738 ATTTCTAAATCATCGATTTTTCACAATC
131 ATTTCTAAATCACCAATTTTCCACAATC
* * *
3031766 GGGGAAACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTCATTT-TCAAAATAC
1 GGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTCATTTCT-AAAATAC
* * * * * * *
3031830 CGATTTTT-ATAATCA-AGGATACTCGAACTCTGTTATTTCCGAGGGGATACTCCAACCCT-GAT
65 CAATTTTTCACAAT-AGAGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTAG-C
* * *
3031892 TTTATTTCTGGAA-CACCAATTTTCCATAATC
128 CTTATTTCT-AAATCACCAATTTTCCACAATC
*
3031923 GGGGATACTCCAGCCCCGTT
1 GGGGATACTCCAACCCCGTT
3031943 GTTATCTCCA
Statistics
Matches: 151, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
156 1 0.01
157 83 0.55
158 67 0.44
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTCATTTCTAAAATACC
AATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTAGCCTT
ATTTCTAAATCACCAATTTTCCACAATC
Found at i:3044295 original size:1 final size:1
Alignment explanation
Indices: 3044291--3044378 Score: 50
Period size: 1 Copynumber: 88.0 Consensus size: 1
3044281 ATTCTTTTTC
* ** * * * * * ** *
3044291 AAAAAAAAAAACAAAAGCAACAAAAAAAACAAAAAACAAAAAAAAACAAAAACAAAAAACTAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
3044356 AAAGAAAAAAGAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
3044379 GAAGAATCTA
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.01
Consensus pattern (1 bp):
A
Found at i:3044317 original size:17 final size:17
Alignment explanation
Indices: 3044292--3044349 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
3044282 TTCTTTTTCA
*
3044292 AAAAAAAAAACAAAAGC
1 AAAAAAAAAACAAAAAC
3044309 AACAAAAAAAACAAAAA-
1 AA-AAAAAAAACAAAAAC
3044326 ACAAAAAAAAACAAAAAC
1 A-AAAAAAAAACAAAAAC
3044344 AAAAAA
1 AAAAAA
3044350 CTAAACAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 22 0.59
18 15 0.41
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Done.