Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 174 of 203
Found at i:55319195 original size:29 final size:29
Alignment explanation
Indices: 55319145--55319278 Score: 182
Period size: 29 Copynumber: 4.7 Consensus size: 29
55319135 TTTTAGAGTC
*
55319145 TCACCACAAAGGCGTT-C-TTTAAAAGAGA
1 TCACCACAAAGGC-TTCCTTTTAACAGAGA
** * *
55319173 TTGCCTCAAAGGCTTCCTTTTAACAGATA
1 TCACCACAAAGGCTTCCTTTTAACAGAGA
*
55319202 TCACCACAAAGGCTTTCTTTTAACAGAGA
1 TCACCACAAAGGCTTCCTTTTAACAGAGA
*
55319231 TCACCATAAAGGCTTCCTTTTAACAGAGA
1 TCACCACAAAGGCTTCCTTTTAACAGAGA
55319260 TCACCACAAAGGCTTCCTT
1 TCACCACAAAGGCTTCCTT
55319279 ACAGAAACTG
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
27 2 0.02
28 11 0.12
29 78 0.86
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (29 bp):
TCACCACAAAGGCTTCCTTTTAACAGAGA
Found at i:55322800 original size:193 final size:193
Alignment explanation
Indices: 55322471--55322855 Score: 734
Period size: 193 Copynumber: 2.0 Consensus size: 193
55322461 AGGTAGACTT
55322471 TACCTATTTCATGGTTTCCATGATTCAACTAGCCCTTTTTGCATAAATAGCACAATTTATGAAAG
1 TACCTATTTCATGGTTTCCATGATTCAACTAGCCCTTTTTGCATAAATAGCACAATTTATGAAAG
*
55322536 TGATTAACCATCCCCATGGCCAATCCTTGTAAAGCATATCCACACCAAATGATTATAACATTGTA
66 TGATTAACCATCCCCATGGCCAATCCTTGTAAAGCATATCCACACCAAATGATTATAACATTATA
55322601 CTCAAACACATATAAGCCATTTTCGCATGGCTATCCAAAATTATACAAGTCCAAAGGGTCCAC
131 CTCAAACACATATAAGCCATTTTCGCATGGCTATCCAAAATTATACAAGTCCAAAGGGTCCAC
*
55322664 TACCTATTTCATGGTTTCCATGATTCAACTAGCCCTTTTTGCATAAATAGCACAATTTATGATAG
1 TACCTATTTCATGGTTTCCATGATTCAACTAGCCCTTTTTGCATAAATAGCACAATTTATGAAAG
* *
55322729 TGATTAACCATTCCCATGGCCAATCCTTGTCAAGCATATCCACACCAAATGATTATAACATTATA
66 TGATTAACCATCCCCATGGCCAATCCTTGTAAAGCATATCCACACCAAATGATTATAACATTATA
55322794 CTCAAACACATATAAGCCATTTTCGCATGGCTATCCAAAATTATACAAGTCCAAAGGGTCCA
131 CTCAAACACATATAAGCCATTTTCGCATGGCTATCCAAAATTATACAAGTCCAAAGGGTCCA
55322856 TGACCCACAA
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 188 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (193 bp):
TACCTATTTCATGGTTTCCATGATTCAACTAGCCCTTTTTGCATAAATAGCACAATTTATGAAAG
TGATTAACCATCCCCATGGCCAATCCTTGTAAAGCATATCCACACCAAATGATTATAACATTATA
CTCAAACACATATAAGCCATTTTCGCATGGCTATCCAAAATTATACAAGTCCAAAGGGTCCAC
Found at i:55323465 original size:79 final size:81
Alignment explanation
Indices: 55323363--55323547 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 81
55323353 GCTCCTCGTT
* * *
55323363 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGTACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
* *
55323425 CGGATTTAGTAAC-TCGCA
63 CGGATATAGTAACTTAGCA
** *
55323443 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCTGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
55323507 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
55323523 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55323548 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
78 5 0.06
79 51 0.57
80 34 0.38
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:55323480 original size:39 final size:40
Alignment explanation
Indices: 55323363--55323547 Score: 193
Period size: 40 Copynumber: 4.7 Consensus size: 40
55323353 GCTCCTCGTT
* *
55323363 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
55323403 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
55323443 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* * * * *
55323482 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ATC-TCGCA
55323523 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55323548 CATCATTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.02
39 34 0.28
40 73 0.59
41 14 0.11
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:55324663 original size:40 final size:39
Alignment explanation
Indices: 55324472--55324663 Score: 246
Period size: 39 Copynumber: 4.8 Consensus size: 39
55324462 CAAGCTTACA
55324472 ATCTCAGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGT
1 ATCTC-GCACAAATGCCTTCGGGCTTAGCCCGGAATTAGT
*
55324512 ATCTCGCACAAATGCCTTCGGGCTTAGCTCGGAATTAGT
1 ATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGT
* *
55324551 ATCTCGCACAAATGCCTTCGGGCTTAGCTCGGATTTAGT
1 ATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGT
* * *
55324590 ATCTCGCACAAATGCCTTCGGATCTTGGTCCGGATATT-GT
1 ATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT
*
55324630 CA-CTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 -ATC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGA
55324664 CATCATTCAA
Statistics
Matches: 136, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
39 92 0.68
40 33 0.24
41 11 0.08
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (39 bp):
ATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGT
Found at i:55335756 original size:20 final size:20
Alignment explanation
Indices: 55335731--55335769 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
55335721 TACTTTCTTC
55335731 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
55335751 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
55335770 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:55336099 original size:56 final size:50
Alignment explanation
Indices: 55335972--55336115 Score: 166
Period size: 50 Copynumber: 2.8 Consensus size: 50
55335962 TGATAAAAAC
* *
55335972 ATGCCAAAGCCATGTCCCAGACATGGTCTTACG-GAGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTG-GGACCTCTCATCTTA
*
55336022 GTGCCAACT-CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATA
1 ATGCCAA-TGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CT---TA
*
55336078 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
55336116 TTTCATTCCC
Statistics
Matches: 80, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
50 41 0.51
51 1 0.01
53 2 0.03
55 1 0.01
56 35 0.44
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTA
Found at i:55338831 original size:17 final size:17
Alignment explanation
Indices: 55338809--55338850 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
55338799 ATACCATTTT
55338809 GTTTTATTTTTGTTTAA
1 GTTTTATTTTTGTTTAA
55338826 GTTTTA--TTTGTTTAA
1 GTTTTATTTTTGTTTAA
55338841 -TTATTATTTT
1 GTT-TTATTTT
55338851 ACCCTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
17 8 0.36
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (17 bp):
GTTTTATTTTTGTTTAA
Found at i:55341170 original size:41 final size:41
Alignment explanation
Indices: 55341091--55341381 Score: 350
Period size: 41 Copynumber: 7.1 Consensus size: 41
55341081 CATAGGTACT
* *
55341091 ATTCAGGGGTACCGAAGT-CAAACAGGGTGGCACATATGTGCA
1 ATTCAGGGGTACCAAAGTACAAACA-GG-GGCACGTATGTGCA
* * *
55341133 ATTCAGTGGTATCAAAGTATAAACAGGGGCACGTATGTGCA
1 ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
* * * *
55341174 ATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGTA
1 ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
**
55341215 ATTCAGGGGTACCAAAGTACAAACAGGGGCACACATGTGCA
1 ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
* * * * *
55341256 ATTCAAGGGTATCGAAGTACAAAAAGGGGCACGTATATGCA
1 ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
* * * *
55341297 ATTTAGGGGTACCAAAGTATAAACTGGGACACGTATGTGCA
1 ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
* * *
55341338 ATTCAGGGGTATCGAAGTACAAACAGGGGCATGTATGTGCA
1 ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
55341379 ATT
1 ATT
55341382 TAGGAAATAA
Statistics
Matches: 209, Mismatches: 39, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
41 187 0.89
42 17 0.08
43 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (41 bp):
ATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
Found at i:55341376 original size:123 final size:123
Alignment explanation
Indices: 55341091--55341381 Score: 388
Period size: 123 Copynumber: 2.4 Consensus size: 123
55341081 CATAGGTACT
*
55341091 ATTCAGGGGTACCGAAGT-CAAACAGGGTGGCACATATGTGCAATTCAGTGGTATCAAAGTATAA
1 ATTCAGGGGTACCGAAGTACAAACA-GG-GGCACATATGTGCAATTCAGTGGTATCAAAGTACAA
* * * * *
55341155 ACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGTA
64 AAAGGGGCACGTATATGCAATTCAAGGGTACCAAAGTACAAACAGGGACACATATGTGCA
* * *
55341215 ATTCAGGGGTACCAAAGTACAAACAGGGGCACACATGTGCAATTCAAG-GGTATCGAAGTACAAA
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTC-AGTGGTATCAAAGTACAAA
* * * * *
55341279 AAGGGGCACGTATATGCAATTTAGGGGTACCAAAGTATAAACTGGGACACGTATGTGCA
65 AAGGGGCACGTATATGCAATTCAAGGGTACCAAAGTACAAACAGGGACACATATGTGCA
* **
55341338 ATTCAGGGGTATCGAAGTACAAACAGGGGCATGTATGTGCAATT
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATT
55341382 TAGGAAATAA
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
123 119 0.82
124 21 0.14
125 6 0.04
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (123 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAGTGGTATCAAAGTACAAAA
AGGGGCACGTATATGCAATTCAAGGGTACCAAAGTACAAACAGGGACACATATGTGCA
Found at i:55341385 original size:82 final size:82
Alignment explanation
Indices: 55341091--55341381 Score: 395
Period size: 82 Copynumber: 3.5 Consensus size: 82
55341081 CATAGGTACT
* * *
55341091 ATTCAGGGGTACCGAAGT-CAAACAGGGTGGCACATATGTGCAATTCAGTGGTATCAAAGTATAA
1 ATTCAAGGGTACCGAAGTACAAACA-GG-GGCACATATGTGCAATTCAGGGGTACCAAAGTATAA
55341155 ACAGGGGCACGTATGTGCA
64 ACAGGGGCACGTATGTGCA
* *
55341174 ATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGTAATTCAGGGGTACCAAAGTACAAAC
1 ATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACCAAAGTATAAAC
**
55341239 AGGGGCACACATGTGCA
66 AGGGGCACGTATGTGCA
* * * * *
55341256 ATTCAAGGGTATCGAAGTACAAAAAGGGGCACGTATATGCAATTTAGGGGTACCAAAGTATAAAC
1 ATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACCAAAGTATAAAC
* *
55341321 TGGGACACGTATGTGCA
66 AGGGGCACGTATGTGCA
* * **
55341338 ATTCAGGGGTATCGAAGTACAAACAGGGGCATGTATGTGCAATT
1 ATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATT
55341382 TAGGAAATAA
Statistics
Matches: 185, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
82 160 0.86
83 19 0.10
84 6 0.03
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (82 bp):
ATTCAAGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACCAAAGTATAAAC
AGGGGCACGTATGTGCA
Found at i:55346749 original size:26 final size:27
Alignment explanation
Indices: 55346720--55346787 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
55346710 ATTTTCCATG
55346720 TCATATTTTA-GTATATCAA-ATAATT
1 TCATATTTTATGTATATCAAGATAATT
* *
55346745 ATCAT-TTCTATGTATTTCAAGTATAATT
1 -TCATATTTTATGTATATCAAG-ATAATT
55346773 TCATGATTTTATGTA
1 TCAT-ATTTTATGTA
55346788 ATTATCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 12 0.35
27 4 0.12
28 6 0.18
29 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (27 bp):
TCATATTTTATGTATATCAAGATAATT
Found at i:55347019 original size:67 final size:67
Alignment explanation
Indices: 55346911--55347042 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
55346901 TTTTCAATTC
* * * *
55346911 AGAGAGGACACTCCTGCGAACCTCATTTCTTACAGCGGGATTACCAGTCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAATCTAGGCTAAATCCCCTG
55346976 CA
66 CA
*
55346978 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGTAGGATTACCAATCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAATCTAGGCTAAATCCCCTG
55347043 TAATATAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAATCTAGGCTAAATCCCCTG
CA
Found at i:55351079 original size:43 final size:43
Alignment explanation
Indices: 55351010--55351103 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
55351000 ACCTATATGG
*
55351010 GACACACGACTATGTCGAATGACCGTGTGTCACACACAATTGA
1 GACACACGACTATGTCAAATGACCGTGTGTCACACACAATTGA
* * *
55351053 GACACACGACTGTGTCAAATGGCCGTGTGTCACACACAGTTGA
1 GACACACGACTATGTCAAATGACCGTGTGTCACACACAATTGA
55351096 GACACACG
1 GACACACG
55351104 CCCGTATCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (43 bp):
GACACACGACTATGTCAAATGACCGTGTGTCACACACAATTGA
Found at i:55362639 original size:61 final size:61
Alignment explanation
Indices: 55362544--55362667 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
55362534 AGTTTCTCAC
55362544 CTTGGGGTGCACCAGTATTGTTCGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATTGA
1 CTTGGGGTGCACCAGTATTGTTCGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATTGA
*
55362605 CTTGGGGTGTACCAGTATTGTTCGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATTGA
1 CTTGGGGTGCACCAGTATTGTTCGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATTGA
55362666 CT
1 CT
55362668 ATCGTCAACT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (61 bp):
CTTGGGGTGCACCAGTATTGTTCGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATTGA
Found at i:55366930 original size:28 final size:28
Alignment explanation
Indices: 55366892--55367073 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
55366882 TAAATTGTAC
*
55366892 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55366920 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55366948 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55366976 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55367004 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55367032 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55367059 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55367074 GAATTAATAT
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
27 24 0.16
28 123 0.84
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:55375725 original size:41 final size:41
Alignment explanation
Indices: 55375650--55375835 Score: 230
Period size: 41 Copynumber: 4.5 Consensus size: 41
55375640 AGTGTAAGCA
* *
55375650 GGCACGTACGTGCTATTTAGGGGGTACCGAAGTACAAACAGG
1 GGCACGTATGTGCAATTTA-GGGGTACCGAAGTACAAACAGG
* * *
55375692 GGCACATATGTGCAATTTAGGGGTACTGAAGTACAAATAGG
1 GGCACGTATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
* * *
55375733 GACACGTATGTGCAATTCAGGGGTACCGAAGTACAAA-AAG
1 GGCACGTATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
* * * * *
55375773 GGAATGTATGTGTAATTTAGGGGTATCAAAGTACAAACAGG
1 GGCACGTATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
*
55375814 GGCACGTATGTACAATTTAGGG
1 GGCACGTATGTGCAATTTAGGG
55375836 AATAGTTAAG
Statistics
Matches: 121, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
40 32 0.26
41 73 0.60
42 16 0.13
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (41 bp):
GGCACGTATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
Found at i:55375792 original size:81 final size:82
Alignment explanation
Indices: 55375652--55375835 Score: 228
Period size: 81 Copynumber: 2.2 Consensus size: 82
55375642 TGTAAGCAGG
* * * *
55375652 CACGTACGTGCTATTTAGGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTTAGGGGTA
1 CACGTATGTGCAATTTA-GGGGTACCGAAGTACAAACAAGGGAACATATGTGCAATTTAGGGGTA
* *
55375717 -CTGAAGTACAAATAGGGA
65 TC-AAAGTACAAACAGGGA
* ** *
55375735 CACGTATGTGCAATTCAGGGGTACCGAAGTACAAA-AAGGGAATGTATGTGTAATTTAGGGGTAT
1 CACGTATGTGCAATTTAGGGGTACCGAAGTACAAACAAGGGAACATATGTGCAATTTAGGGGTAT
*
55375799 CAAAGTACAAACAGGGG
66 CAAAGTACAAACAGGGA
*
55375816 CACGTATGTACAATTTAGGG
1 CACGTATGTGCAATTTAGGG
55375836 AATAGTTAAG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 54 0.62
82 19 0.22
83 14 0.16
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (82 bp):
CACGTATGTGCAATTTAGGGGTACCGAAGTACAAACAAGGGAACATATGTGCAATTTAGGGGTAT
CAAAGTACAAACAGGGA
Found at i:55375984 original size:32 final size:32
Alignment explanation
Indices: 55375943--55376006 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
55375933 CTAGAGCGTA
55375943 AAACTACGATCATGCTAATCCGTAATTTTCGC
1 AAACTACGATCATGCTAATCCGTAATTTTCGC
55375975 AAACTACGATCATGCTAATCCGTAATTTTCGC
1 AAACTACGATCATGCTAATCCGTAATTTTCGC
55376007 CTTTCCTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (32 bp):
AAACTACGATCATGCTAATCCGTAATTTTCGC
Found at i:55378787 original size:25 final size:25
Alignment explanation
Indices: 55378752--55378816 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
55378742 ATACCCTCAA
55378752 AGGGTAAAATAACCAAAATACCCCT
1 AGGGTAAAATAACCAAAATACCCCT
* *
55378777 GGGGTAAAATAACCAAAATACCTCT
1 AGGGTAAAATAACCAAAATACCCCT
* *
55378802 AGGATAAAATTACCA
1 AGGGTAAAATAACCA
55378817 TTTTACCCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (25 bp):
AGGGTAAAATAACCAAAATACCCCT
Found at i:55412579 original size:140 final size:140
Alignment explanation
Indices: 55412349--55412623 Score: 388
Period size: 140 Copynumber: 2.0 Consensus size: 140
55412339 GGCTCGGCCA
* * * * * *
55412349 TGTGACCCAAGTCAGAGAGTTACATGGGCACGGACACAGGCTGGGACACGGTTGTTTGTCCCTAC
1 TGTGACCAAAGTCAGAAAGTTACATGGGCACAGACACAGCCTGGGACACGGTCGTTTGTCCATAC
* * * * *
55412414 TTCGAATACCTACACGGCTTGAGACATGAGCATGTGTCTCAGCCGTGTGAGTCACACGGCCTGGC
66 TTCGAATACCCACACGGCCTGAGACATGAGCATGTATCTCAGCCATGTAAGTCACACGGCCTGGC
55412479 CACATAGCTT
131 CACATAGCTT
* *
55412489 TGTGACCAAAGTTAGAAAGTTACATGGGCACAGACATAGCCTGGGACACGGTCGTTTGTCCATAC
1 TGTGACCAAAGTCAGAAAGTTACATGGGCACAGACACAGCCTGGGACACGGTCGTTTGTCCATAC
* * * * *
55412554 TTCGAATGCCCACACTGCCTGAGACATGGGCATGTATTTCAGCCATGTAAGTCACACGGCTTGGC
66 TTCGAATACCCACACGGCCTGAGACATGAGCATGTATCTCAGCCATGTAAGTCACACGGCCTGGC
55412619 CACAT
131 CACAT
55412624 GGCCGTGTAA
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
140 117 1.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (140 bp):
TGTGACCAAAGTCAGAAAGTTACATGGGCACAGACACAGCCTGGGACACGGTCGTTTGTCCATAC
TTCGAATACCCACACGGCCTGAGACATGAGCATGTATCTCAGCCATGTAAGTCACACGGCCTGGC
CACATAGCTT
Found at i:55419320 original size:15 final size:15
Alignment explanation
Indices: 55419272--55419323 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
55419262 GGCCGTGTGT
55419272 CACACACAGTTGAGA
1 CACACACAGTTGAGA
* *** * *
55419287 CACACGCCCATGTGT
1 CACACACAGTTGAGA
55419302 CACACACAGTTGAGA
1 CACACACAGTTGAGA
55419317 CACACAC
1 CACACAC
55419324 CCGTGTCTCA
Statistics
Matches: 25, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.35, G:0.17, T:0.13
Consensus pattern (15 bp):
CACACACAGTTGAGA
Found at i:55419594 original size:12 final size:13
Alignment explanation
Indices: 55419568--55419600 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
55419558 TTCACTCAAG
55419568 AAATACCTAATCA
1 AAATACCTAATCA
55419581 AAATACCT-ATCA
1 AAATACCTAATCA
55419593 AAGATACC
1 AA-ATACC
55419601 ACAATCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (13 bp):
AAATACCTAATCA
Found at i:55421782 original size:13 final size:13
Alignment explanation
Indices: 55421764--55421791 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55421754 ACTTTAGTGC
55421764 ATCTGTACTTTTA
1 ATCTGTACTTTTA
55421777 ATCTGTACTTTTA
1 ATCTGTACTTTTA
55421790 AT
1 AT
55421792 TATTGGTAGA
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:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (13 bp):
ATCTGTACTTTTA
Found at i:55423061 original size:98 final size:98
Alignment explanation
Indices: 55422890--55423086 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
55422880 GTGCAATAAA
* *
55422890 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGAGCACAATT
*
55422955 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACACGGAATATTTCCTTT
55422988 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGAGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGAGCACAATT
*
55423053 CCTTTAAAATCCCAAACACGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACACGGAATATTTCCTTT
55423086 A
1 A
55423087 TTATTTTTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGAGCACAATT
CCTCTAAAATCCCAAACACGGAATATTTCCTTT
Found at i:55423287 original size:205 final size:205
Alignment explanation
Indices: 55423032--55423969 Score: 1824
Period size: 205 Copynumber: 4.6 Consensus size: 205
55423022 GAAATCACAC
* * * * *
55423032 CCAATACGTTAGAGCACAATT-CCTTTAAAATCCCAAACACGGAATATTTCCTTTATTATTTTTA
1 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
55423096 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
66 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
55423161 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
131 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
55423226 AAATCGGAAT
196 AAATCGGAAT
55423236 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
1 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
55423301 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
66 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
55423366 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
131 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
55423431 AAATCGGAAT
196 AAATCGGAAT
55423441 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
1 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
55423506 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
66 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
55423571 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
131 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
55423636 AAATCGGAAT
196 AAATCGGAAT
55423646 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
1 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
55423711 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
66 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
55423776 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
131 TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
55423841 AAATCGGAAT
196 AAATCGGAAT
55423851 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
1 CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
55423916 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACAT
66 AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACAT
55423970 CACTTTCTGC
Statistics
Matches: 728, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
204 19 0.03
205 709 0.97
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (205 bp):
CCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTTTA
AAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACATTACGTGTTGAA
TTCCCAATAATGAATTCTTATTTTTTGATTAAAAAGAAATGCTCGATTATTGGATTTAACAAAGA
AAATCGGAAT
Found at i:55424942 original size:44 final size:44
Alignment explanation
Indices: 55424869--55425208 Score: 222
Period size: 44 Copynumber: 7.8 Consensus size: 44
55424859 ACTTGCTTCA
* *
55424869 TTAATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAGGGTT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGGTT
* * * *
55424912 TTAATCCGCTCCACTACAACTTCAGGGAGATAGGAT-TATCGGTT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTA-GGGTT
* * * * **
55424956 TTAATTTGCTCCACTGTAACTTTAGGGAAATAAGAT-TAGCCATT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAG-GGTT
* * *
55425000 TTCAGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGA-CT-TGCTT
1 TT-AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTAGGGTT
* * *
55425043 ACTTAGTCTGCTCCACTGCCACTTCAGGGAGATAAGA-CTA--GAT
1 --TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGGTT
*** ** * * *
55425086 GCGATCTGCT-CTTTGCAACTTCAGAGAGGTAAGATCT-GAGATT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAG-GGTT
* * * *
55425129 TTAATCCGCTCCACTGCAACTTCAGGAAGATAGGAT-T-GTTGGCT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAG--GGTT
55425173 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
55425209 TTGCCATCTT
Statistics
Matches: 225, Mismatches: 54, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
40 19 0.08
41 8 0.04
43 23 0.10
44 146 0.65
45 29 0.13
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (44 bp):
TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAGGGTT
Found at i:55425277 original size:217 final size:217
Alignment explanation
Indices: 55424872--55425277 Score: 543
Period size: 217 Copynumber: 1.9 Consensus size: 217
55424862 TGCTTCATTA
*
55424872 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAGGGTTTTAATCCGCTCCACTACAACTTCAG
1 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAGGATTTTAATCCGCTCCACTACAACTTCAG
* * * * * *
55424937 GGAGATAGGATTATCGGTTTTAATTTGCTCCACTGTAACTTTAGGGAAATAAGATTAGCCATTTT
66 GAAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTAGCCATCTT
* ** * *
55425002 CAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCCACTT
131 CAGTCTGCCTCACTACAACTTCAGGAGGATAAGACTTGAATACTTAATCTACTCCACTGCCACTT
55425067 CAGGGAGATAAGACTAGATGCG
196 CAGGGAGATAAGACTAGATGCG
* * *
55425089 ATCTGCTCTTTGCAACTTCAGAGAGGTAAGATCT-GAGATTTTAATCCGCTCCACTGCAACTTCA
1 ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAG-GATTTTAATCCGCTCCACTACAACTTCA
* * * *
55425153 GGAAGATAGGATTGTTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCT
65 GGAAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTAGCCATCT
* *
55425218 TCAGTCTGCCTCACTACTACTT-AGG-GAGATAAGA-TCTGAA-ATCTTCAATCTATTCCACTG
130 TCAGTCTGCCTCACTACAACTTCAGGAG-GATAAGACT-TGAATA-CTT-AATCTACTCCACTG
55425278 TTGTCCAGGG
Statistics
Matches: 163, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
215 3 0.02
216 16 0.10
217 144 0.88
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (217 bp):
ATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAGGATTTTAATCCGCTCCACTACAACTTCAG
GAAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTAGCCATCTT
CAGTCTGCCTCACTACAACTTCAGGAGGATAAGACTTGAATACTTAATCTACTCCACTGCCACTT
CAGGGAGATAAGACTAGATGCG
Found at i:55425797 original size:132 final size:132
Alignment explanation
Indices: 55425211--55425783 Score: 886
Period size: 132 Copynumber: 4.3 Consensus size: 132
55425201 GATAAGATTT
*
55425211 GCCATCTT-CAGTCTGC-CTCACTACTACTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCC
1 GCCATCTTCCA-TCTGCTC-CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCC
* * *
55425274 ACTGTTGTCCAGGGAAGTAGAGTTACTGGCTTCAATGTACTCCACTGTAACCATAGGGAGGTAAA
64 ACTGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAA
55425339 ATCC
129 ATCC
* * *
55425343 GCCATCTTCGATCTGCTCCACTACTGTTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCAC
1 GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
* * * *
55425408 T-TTTTTCCAGGAAAGTATAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAA
66 TGTTGTT-CAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA
*
55425472 TCT
130 TCC
* *
55425475 GCCATCTTCGATCTGCCCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
1 GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
*
55425540 TGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTATTCCACTGTAACCACAGGGAGGTAAAAT
66 TGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT
55425605 CC
131 CC
** * *
55425607 GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATTTTC--CCTGATTTCC
1 GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCT-A-TTCC
*
55425670 ACTGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTATTCCACTGTAACCACAGGGAGGTAAA
64 ACTGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAA
55425735 ATCC
129 ATCC
55425739 GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
1 GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
55425784 CTATTTTCAC
Statistics
Matches: 408, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
130 2 0.00
131 4 0.01
132 396 0.97
133 6 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
GCCATCTTCCATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAC
TGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT
CC
Found at i:55429436 original size:24 final size:24
Alignment explanation
Indices: 55429408--55429453 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
55429398 ATCATTTTTT
* *
55429408 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
55429432 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
55429454 GGATTGTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:55431456 original size:205 final size:205
Alignment explanation
Indices: 55431076--55432143 Score: 2016
Period size: 205 Copynumber: 5.2 Consensus size: 205
55431066 AAGAAATCAC
* * *
55431076 ACCCAATACGTTAGGGCACGATT-CCTCT-AAAATCCCAAACT-CGGAATATTTCCTTTATTATT
1 ACCCAATACGTTAGGGCTCAATTCCCT-TGAAAATCCTAAA-TACGGAATATTTCCTTTATTATT
55431138 TTTAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGT
64 TTTAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGT
55431203 TGAATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACA
129 TGAATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACA
55431268 AAGAAAATCAGA
194 AAGAAAATCAGA
55431280 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
1 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
55431345 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
66 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
55431410 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
131 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
55431475 GAAAATCAGA
196 GAAAATCAGA
55431485 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
1 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
55431550 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
66 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
55431615 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
131 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
55431680 GAAAATCAGA
196 GAAAATCAGA
55431690 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
1 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
55431755 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
66 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
55431820 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
131 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
55431885 GAAAATCAGA
196 GAAAATCAGA
55431895 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
1 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
* *
55431960 TAAAAGAAATCTTCATTACGAGAAATCAATGCGTCACATCCAAAACGTTAGGACACAACGTGTTG
66 TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
*
55432025 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTAGATTTAACAAA
131 AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
*
55432090 GAAAATCGGA
196 GAAAATCAGA
* *
55432100 ACCCAATACTTTAGGGCTTAATTCCCTTGAAAATCCTAAATACG
1 ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACG
55432144 AGCATTATCT
Statistics
Matches: 852, Mismatches: 9, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
204 23 0.03
205 829 0.97
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (205 bp):
ACCCAATACGTTAGGGCTCAATTCCCTTGAAAATCCTAAATACGGAATATTTCCTTTATTATTTT
TAAAAGAAATCTTCATTTCGAGAAATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTG
AATTCCCAATAATGAATTCTTATTTTTTGATTAAAGAGAAATGCTCGATTATTGGATTTAACAAA
GAAAATCAGA
Found at i:55432633 original size:58 final size:53
Alignment explanation
Indices: 55432481--55432657 Score: 155
Period size: 58 Copynumber: 3.2 Consensus size: 53
55432471 ATAAAGAAAA
* *
55432481 ATATATATAGAAATTATAAAAATATGGGTAGAAAGTATAATATATATATACGTAC
1 ATATATATATAAATTAT-AAAATAT-GATAGAAAGTATAATATATATATACGTAC
* * * * **
55432536 ATATATATGTAAATTA-ATAAATATAGACCATAAAG-ATAATGATTGCATATATATGTGT
1 ATATATATATAAATTATA-AAATAT-GA-TAGAAAGTATAAT-A-T--ATATATACGTAC
*
55432594 GTATATATATAAATTATAAAATATGTATAGAAAGTAT-A-ATATATATACGTAC
1 ATATATATATAAATTATAAAATATG-ATAGAAAGTATAATATATATATACGTAC
55432646 ATATATATATAA
1 ATATATATATAA
55432658 GGTAACAAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 21
0.72 0.13 0.16
Matches are distributed among these distances:
52 20 0.21
53 1 0.01
54 13 0.14
55 21 0.22
56 1 0.01
57 7 0.07
58 32 0.33
59 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.36
Consensus pattern (53 bp):
ATATATATATAAATTATAAAATATGATAGAAAGTATAATATATATATACGTAC
Found at i:55432700 original size:112 final size:113
Alignment explanation
Indices: 55432482--55432700 Score: 291
Period size: 112 Copynumber: 1.9 Consensus size: 113
55432472 TAAAGAAAAA
* *
55432482 TATATATAGAAATTATAAAAATATGGGTAGAAAGTATAATATATATATACGTACATATATATGTA
1 TATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATATA
* * * * * *
55432547 AATTAATAAATATAGACCATAAAGATAATGATTGCATATATATGTGTG
66 AAGTAACAAATATAGACCATAAACATAATAATTACACATATATGTGTG
* *
55432595 TATATATATAAATTAT-AAAATATGTATAGAAAGTAT-A-ATATATATACGTACATATATATATA
1 TATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATATA
* *
55432657 AGGTAACAAATATATACATCATAAACATAATAATTACACATATA
66 AAGTAACAAATATAGAC--CATAAACATAATAATTACACATATA
55432701 AGCTTAAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
110 37 0.40
111 1 0.01
112 39 0.42
113 15 0.16
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (113 bp):
TATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATATA
AAGTAACAAATATAGACCATAAACATAATAATTACACATATATGTGTG
Found at i:55437276 original size:13 final size:13
Alignment explanation
Indices: 55437258--55437312 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
55437248 AGCACACATG
*
55437258 AAACATATCTTTA
1 AAACATATCTTGA
* *
55437271 AAACATAACTTAA
1 AAACATATCTTGA
*
55437284 AAAAATATCTTGA
1 AAACATATCTTGA
*
55437297 AAATATATCTTGA
1 AAACATATCTTGA
55437310 AAA
1 AAA
55437313 TAGACTATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.31
Consensus pattern (13 bp):
AAACATATCTTGA
Found at i:55437804 original size:23 final size:18
Alignment explanation
Indices: 55437754--55437802 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
55437744 TTCTTGTCGA
55437754 AAAATAATTAAATATTAT
1 AAAATAATTAAATATTAT
55437772 AAAATAATTAAATATTAT
1 AAAATAATTAAATATTAT
55437790 AAAATAATTAAAT
1 AAAATAATTAAAT
55437803 TATGTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAATTAAATATTAT
Found at i:55438628 original size:20 final size:20
Alignment explanation
Indices: 55438603--55438640 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55438593 ACGAAGAACG
*
55438603 GAGAAATTAGTCAAGCCATA
1 GAGAAATCAGTCAAGCCATA
55438623 GAGAAATCAGTCAAGCCA
1 GAGAAATCAGTCAAGCCA
55438641 CGAAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (20 bp):
GAGAAATCAGTCAAGCCATA
Found at i:55446903 original size:12 final size:10
Alignment explanation
Indices: 55446878--55446917 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
55446868 GAACATGATG
55446878 AATTTTAATT
1 AATTTTAATT
55446888 AATTTTATAGTT
1 AATTTTA-A-TT
*
55446900 AATTTTGATT
1 AATTTTAATT
55446910 AATTTTAA
1 AATTTTAA
55446918 CTATTTTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (10 bp):
AATTTTAATT
Found at i:55448095 original size:7 final size:7
Alignment explanation
Indices: 55448085--55448117 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
55448075 TTTTTTTTTT
55448085 TTTTGCA
1 TTTTGCA
55448092 TTTTGCA
1 TTTTGCA
55448099 TTTTGCA
1 TTTTGCA
55448106 TTTTGCA
1 TTTTGCA
55448113 TTTTG
1 TTTTG
55448118 GTGAAGTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (7 bp):
TTTTGCA
Found at i:55452694 original size:20 final size:20
Alignment explanation
Indices: 55452669--55452708 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55452659 AATATTTTCC
*
55452669 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55452689 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55452709 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55452714 original size:34 final size:35
Alignment explanation
Indices: 55452657--55452723 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55452647 CAAACAGCAG
*
55452657 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55452692 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55452724 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55452715 original size:14 final size:14
Alignment explanation
Indices: 55452692--55452731 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55452682 ACAGAAAAGT
*
55452692 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
55452706 AAATCATTTTACGG
1 AAAACATTTTACAG
55452720 AAAACATTTTAC
1 AAAACATTTTAC
55452732 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:55453796 original size:20 final size:20
Alignment explanation
Indices: 55453771--55453828 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
55453761 TTTATATATT
*
55453771 TAAAATTATTATTTTTAATC
1 TAAAATTATTATTTTTAAAC
*
55453791 TAAAATT-TTAGTTTTCAAAC
1 TAAAATTATTA-TTTTTAAAC
55453811 -AAAATTATAATATTTTTA
1 TAAAATTAT--TATTTTTA
55453829 GGAATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 9 0.29
20 15 0.48
21 5 0.16
22 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TAAAATTATTATTTTTAAAC
Found at i:55455302 original size:11 final size:11
Alignment explanation
Indices: 55455288--55455337 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
55455278 TCAATTATTT
55455288 TCTCAATTTCC
1 TCTCAATTTCC
* *
55455299 TCTCAAATTGC
1 TCTCAATTTCC
55455310 TCTCAATTTCC
1 TCTCAATTTCC
*
55455321 TTCTAAATTT-C
1 -TCTCAATTTCC
55455332 TCTCAA
1 TCTCAA
55455338 ATCTATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 5 0.16
11 19 0.59
12 8 0.25
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:55455316 original size:22 final size:22
Alignment explanation
Indices: 55455288--55455337 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
55455278 TCAATTATTT
55455288 TCTCAATTTCC-TCTCAAATTGC
1 TCTCAATTTCCTTCT-AAATTGC
*
55455310 TCTCAATTTCCTTCTAAATTTC
1 TCTCAATTTCCTTCTAAATTGC
55455332 TCTCAA
1 TCTCAA
55455338 ATCTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (22 bp):
TCTCAATTTCCTTCTAAATTGC
Found at i:55455398 original size:51 final size:51
Alignment explanation
Indices: 55455299--55455398 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
55455289 CTCAATTTCC
*
55455299 TCTCAAATTGCTCTCAATTTCCTTCTAAATTTCTCTCAAATCTATATTTAA
1 TCTCAAATTGCTCTCAATTTCCTTCTAAATTTCTCTCAAATCCATATTTAA
* *
55455350 TCTC-AATCTGCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAAT-TGCTCTCAATTTCCTTC-TAAATTTCTCTCAAATCCATATTT
55455399 TTAATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 5 0.11
51 39 0.89
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTCCTTCTAAATTTCTCTCAAATCCATATTTAA
Found at i:55457239 original size:1 final size:1
Alignment explanation
Indices: 55457198--55457230 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
55457188 CTTGGATAAC
55457198 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
55457231 GAGCAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55461034 original size:20 final size:21
Alignment explanation
Indices: 55460993--55461047 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
55460983 AATAATAGTG
* *
55460993 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTGGATACTGTA
55461014 GCGGTGAGATTGGAT-CTGTA
1 GCGGTGAGATTGGATACTGTA
*
55461034 GCGATGAGATTGGA
1 GCGGTGAGATTGGA
55461048 AAGAATGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTGGATACTGTA
Found at i:55464655 original size:39 final size:39
Alignment explanation
Indices: 55464601--55464720 Score: 240
Period size: 39 Copynumber: 3.1 Consensus size: 39
55464591 ATGCAATCGA
55464601 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
55464640 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
55464679 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
55464718 TTT
1 TTT
55464721 TCACTTTATT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (39 bp):
TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
Found at i:55465081 original size:30 final size:30
Alignment explanation
Indices: 55465038--55465366 Score: 490
Period size: 30 Copynumber: 10.9 Consensus size: 30
55465028 TACACTATAT
55465038 ATATATATTTTTTATTTTTAAAATACACTAC
1 ATATAT-TTTTTTATTTTTAAAATACACTAC
55465069 ATATATTTTTTTATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
*
55465099 ATATATATTTTTATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
55465129 ATATATTTTTTTATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
55465159 --ATATTTTTTTA-TTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
*
55465186 ATATATATATTTTATTTTTAAAATACACTAC
1 ATATAT-TTTTTTATTTTTAAAATACACTAC
* * *
55465217 A-A-ATATATATATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
55465245 ATATATATATTTTTTATTTTTAAAATACACTTA-
1 --ATATAT-TTTTTTATTTTTAAAATACAC-TAC
55465278 ATATATTTTTTTTATTTTTAAAATACACTAC
1 ATATA-TTTTTTTATTTTTAAAATACACTAC
*
55465309 ATATATTTTTTTATTTTTAGAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
55465339 ATATATATTTTTTATTTTTAAAATACAC
1 ATATAT-TTTTTTATTTTTAAAATACAC
55465367 AAATACAATG
Statistics
Matches: 273, Mismatches: 12, Indels: 26
0.88 0.04 0.08
Matches are distributed among these distances:
27 16 0.06
28 31 0.11
29 6 0.02
30 122 0.45
31 75 0.27
32 3 0.01
33 18 0.07
34 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.51
Consensus pattern (30 bp):
ATATATTTTTTTATTTTTAAAATACACTAC
Found at i:55465268 original size:92 final size:90
Alignment explanation
Indices: 55465038--55465366 Score: 499
Period size: 92 Copynumber: 3.6 Consensus size: 90
55465028 TACACTATAT
55465038 ATATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATAT
1 ATATAT-TTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATAT
55465103 ATATTTTTATTTTTAAAATACACTAC
65 ATATTTTTATTTTTAAAATACACTAC
55465129 ATATATTTTTTTATTTTTAAAATACACTAC--ATATTTTTTTA-TTTTAAAATACACTACATATA
1 ATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATA
55465191 TATATTTTATTTTTAAAATACACTAC
66 TAT-TTTTATTTTTAAAATACACTAC
* * *
55465217 A-A-ATATATATATTTTTAAAATACACTACATATATATATTTTTTATTTTTAAAATACACTTA-A
1 ATATATTTTTTTATTTTTAAAATACACTAC--ATATAT-TTTTTTATTTTTAAAATACAC-TACA
*
55465279 TATATTTTTTTTATTTTTAAAATACACTAC
62 TATA-TATTTTTATTTTTAAAATACACTAC
*
55465309 ATATATTTTTTTATTTTTAGAATACACTACATATATATTTTTTATTTTTAAAATACAC
1 ATATATTTTTTTATTTTTAAAATACACTACATATAT-TTTTTTATTTTTAAAATACAC
55465367 AAATACAATG
Statistics
Matches: 219, Mismatches: 8, Indels: 21
0.88 0.03 0.08
Matches are distributed among these distances:
86 23 0.11
87 25 0.11
88 34 0.16
90 28 0.13
91 13 0.06
92 69 0.32
93 5 0.02
94 22 0.10
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.51
Consensus pattern (90 bp):
ATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATA
TATTTTTATTTTTAAAATACACTAC
Found at i:55465319 original size:61 final size:60
Alignment explanation
Indices: 55465038--55465366 Score: 490
Period size: 61 Copynumber: 5.5 Consensus size: 60
55465028 TACACTATAT
55465038 ATATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC
1 ATATAT-TTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC
*
55465099 ATATATATTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC
*
55465159 --ATATTTTTTTA-TTTTAAAATACACTACATATATATATTTTATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTACATATAT-TTTTTTATTTTTAAAATACACTAC
* * *
55465217 A-A-ATATATATATTTTTAAAATACACTACATATATATATTTTTTATTTTTAAAATACACTTA-
1 ATATATTTTTTTATTTTTAAAATACACTAC--ATATAT-TTTTTTATTTTTAAAATACAC-TAC
*
55465278 ATATATTTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAGAATACACTAC
1 ATATA-TTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC
55465339 ATATATATTTTTTATTTTTAAAATACAC
1 ATATAT-TTTTTTATTTTTAAAATACAC
55465367 AAATACAATG
Statistics
Matches: 246, Mismatches: 11, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
57 22 0.09
58 39 0.16
59 17 0.07
60 56 0.23
61 80 0.33
62 9 0.04
63 1 0.00
64 22 0.09
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.51
Consensus pattern (60 bp):
ATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC
Found at i:55465479 original size:17 final size:17
Alignment explanation
Indices: 55465457--55465491 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55465447 CCATTCCCAT
*
55465457 TTCCCCACTTCTACCGA
1 TTCCCCACTTCCACCGA
*
55465474 TTCCCCTCTTCCACCGA
1 TTCCCCACTTCCACCGA
55465491 T
1 T
55465492 CAAAGTCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.49, G:0.06, T:0.31
Consensus pattern (17 bp):
TTCCCCACTTCCACCGA
Found at i:55465513 original size:79 final size:79
Alignment explanation
Indices: 55465398--55465584 Score: 302
Period size: 79 Copynumber: 2.4 Consensus size: 79
55465388 TCCCTATCTT
* *
55465398 CCCTCTTCTACCGATCAAAGTCCCAAACCCTATGCCCTCATCCCATTTCCCATTCCCATTTCCCC
1 CCCTCTTCCACCGATCAAAGTCCCAAACCCCATGCCCTCATCCCATTTCCCATTCCCATTTCCCC
55465463 ACTTCTACCGATTC
66 ACTTCTACCGATTC
* *
55465477 CCCTCTTCCACCGATCAAAGTCCCAAACCCCGTGCCCTCCTCCCATTTCCCATTCCCATTTCCCC
1 CCCTCTTCCACCGATCAAAGTCCCAAACCCCATGCCCTCATCCCATTTCCCATTCCCATTTCCCC
* * **
55465542 TCTTTTATTGATTC
66 ACTTCTACCGATTC
55465556 CCCTCTTCCACCGATCAAAGTCCCAAACC
1 CCCTCTTCCACCGATCAAAGTCCCAAACC
55465585 TCGTTCCTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 100 1.00
ACGTcount: A:0.20, C:0.46, G:0.06, T:0.28
Consensus pattern (79 bp):
CCCTCTTCCACCGATCAAAGTCCCAAACCCCATGCCCTCATCCCATTTCCCATTCCCATTTCCCC
ACTTCTACCGATTC
Found at i:55465636 original size:21 final size:19
Alignment explanation
Indices: 55465612--55465650 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
55465602 AATTGAAAAG
*
55465612 CATTTGTTTTCTTGTCATGGC
1 CATTTCTTTT-TTG-CATGGC
55465633 CATTTCTTTTTTGCATGG
1 CATTTCTTTTTTGCATGG
55465651 ATTTCCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.54
Consensus pattern (19 bp):
CATTTCTTTTTTGCATGGC
Found at i:55467653 original size:17 final size:17
Alignment explanation
Indices: 55467619--55467670 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
55467609 AAATCCCAGA
*
55467619 TTTTGATATCCA-ATCT
1 TTTTGATACCCATATCT
55467635 TTTTGATACCCATATCT
1 TTTTGATACCCATATCT
*
55467652 TTCTGATACCCATATCT
1 TTTTGATACCCATATCT
55467669 TT
1 TT
55467671 GACTTTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
16 11 0.33
17 22 0.67
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (17 bp):
TTTTGATACCCATATCT
Found at i:55471226 original size:17 final size:17
Alignment explanation
Indices: 55471201--55471253 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
55471191 AAATCCCAGA
*
55471201 TTTTGATACCCATATCT
1 TTTTTATACCCATATCT
55471218 TTTTTATACCCATATCT
1 TTTTTATACCCATATCT
*
55471235 TTCTTATACCCATATCT
1 TTTTTATACCCATATCT
55471252 TT
1 TT
55471254 GACTTTCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTTATACCCATATCT
Found at i:55472755 original size:21 final size:21
Alignment explanation
Indices: 55472731--55472812 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
55472721 AAGAACAAAG
* *
55472731 CAAAAAGGGGGGAGAAACCAA
1 CAAAAACGAGGGAGAAACCAA
*
55472752 CAAAAACGAGGGACAAACCAA
1 CAAAAACGAGGGAGAAACCAA
* * *
55472773 TAAGAACAAGGGAGAAACCAA
1 CAAAAACGAGGGAGAAACCAA
* *
55472794 CAAGAACAAGGGGAGAAAC
1 CAAAAACGA-GGGAGAAAC
55472813 TGTTGGTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 43 0.83
22 9 0.17
ACGTcount: A:0.55, C:0.17, G:0.27, T:0.01
Consensus pattern (21 bp):
CAAAAACGAGGGAGAAACCAA
Found at i:55476381 original size:54 final size:51
Alignment explanation
Indices: 55476256--55476438 Score: 154
Period size: 54 Copynumber: 3.5 Consensus size: 51
55476246 GGTGGTAACG
* * * * * * *
55476256 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGGTTACA
1 TGTGTACTACTATGTGCAGGCTACTATGCGTACCAGATAGTAAT-GATCACA
* * **
55476306 TGTGTAGTACTATGGGCAGGCTACTATGCGTACCAGATAGTTTTGATCACA
1 TGTGTACTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGATCACA
* * * * * *
55476357 TGTGTGGTACTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACA
1 --TGT-GTACTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGATCACA
*
55476411 TGTGTAGTACTATGTGCAGGCTACTATG
1 TGTGTACTACTATGTGCAGGCTACTATG
55476439 TGAACTGAAC
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
50 33 0.31
51 29 0.27
52 5 0.05
53 3 0.03
54 38 0.35
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
TGTGTACTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGATCACA
Found at i:55486933 original size:31 final size:30
Alignment explanation
Indices: 55486896--55486964 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
55486886 ATGTTAATGG
* *
55486896 GTGACTGATTTGTCACTTTTTGATAATGTT-A
1 GTGACTGATTTGTCA-TTTTTCA-AAAGTTGA
* *
55486927 GTGACTGTTTTGTTATTTTTCAAAAGTTGA
1 GTGACTGATTTGTCATTTTTCAAAAGTTGA
55486957 GTGACTGA
1 GTGACTGA
55486965 ATTGAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.16
30 14 0.44
31 13 0.41
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46
Consensus pattern (30 bp):
GTGACTGATTTGTCATTTTTCAAAAGTTGA
Found at i:55486946 original size:173 final size:174
Alignment explanation
Indices: 55486657--55486971 Score: 436
Period size: 173 Copynumber: 1.8 Consensus size: 174
55486647 AGTTAATTAA
* *
55486657 CCACATTAGCTAATTTATTGGCCACGTCACCTGTCTCATTAGGCCAGTAACGGAAAATGTTAATG
1 CCACATTAGCTAATTAATTGGCCACGTCACCTGTCTCATTAGGCCAGTAACAGAAAATGTTAATG
* * * * **
55486722 GATGATTGATTTGTCTCTTTTCGGTAACGTTAGTGATTGATTAGCTATTTTTTTAAAGTTAAGTG
66 GATGACTGATTTGTCACTTTTCGATAACGTTAGTGACTGATTAGCTATTTTTCAAAAGTTAAGTG
55486787 ACTGAATTGAAACTTTGCCTCGACCAGCGTGACAAGTTAACTGG
131 ACTGAATTGAAACTTTGCCTCGACCAGCGTGACAAGTTAACTGG
* * * *
55486831 CCACGTTAGCTAGTTAATTGGCCACGTCACCT-TC-CTGTTAGGCCCGTAACAGAAAATGTTAAT
1 CCACATTAGCTAATTAATTGGCCACGTCACCTGTCTC-ATTAGGCCAGTAACAGAAAATGTTAAT
* * * * * * *
55486894 GGGTGACTGATTTGTCACTTTTTGATAATGTTAGTGACTGTTTTGTTATTTTTCAAAAGTTGAGT
65 GGATGACTGATTTGTCACTTTTCGATAACGTTAGTGACTGATTAGCTATTTTTCAAAAGTTAAGT
55486959 GACTGAATTGAAA
130 GACTGAATTGAAA
55486972 ATAGAGTGAC
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
172 1 0.01
173 91 0.75
174 29 0.24
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (174 bp):
CCACATTAGCTAATTAATTGGCCACGTCACCTGTCTCATTAGGCCAGTAACAGAAAATGTTAATG
GATGACTGATTTGTCACTTTTCGATAACGTTAGTGACTGATTAGCTATTTTTCAAAAGTTAAGTG
ACTGAATTGAAACTTTGCCTCGACCAGCGTGACAAGTTAACTGG
Found at i:55490336 original size:23 final size:23
Alignment explanation
Indices: 55490310--55490381 Score: 119
Period size: 23 Copynumber: 3.1 Consensus size: 23
55490300 TAAGTGCCAT
55490310 ACTGATATGTAGCCGAAGCTACC
1 ACTGATATGTAGCCGAAGCTACC
55490333 ACTGATATGTAGCC-ATAGCTACC
1 ACTGATATGTAGCCGA-AGCTACC
*
55490356 ACTGAAATGTAGCCGAAGCTACC
1 ACTGATATGTAGCCGAAGCTACC
55490379 ACT
1 ACT
55490382 AATTAATAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 1 0.02
23 44 0.96
24 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (23 bp):
ACTGATATGTAGCCGAAGCTACC
Found at i:55507889 original size:23 final size:21
Alignment explanation
Indices: 55507836--55507890 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
55507826 AATATTTGAC
*
55507836 ATGTTATTATT-TGGTTAAAT
1 ATGTTATTGTTATGGTTAAAT
*
55507856 -TGATATTGTTATGAGTTAAATT
1 ATGTTATTGTTATG-GTTAAA-T
55507878 ATGTTATTGTTAT
1 ATGTTATTGTTAT
55507891 TATTGGTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.29
20 2 0.07
21 6 0.21
22 1 0.04
23 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATGTTATTGTTATGGTTAAAT
Found at i:55511101 original size:50 final size:50
Alignment explanation
Indices: 55511020--55511155 Score: 155
Period size: 50 Copynumber: 2.7 Consensus size: 50
55511010 TATTGAGGTT
* * * * *
55511020 ATGAAAGGTCCCACGTAAGACCATGCCTGGGATATGGCGTTGGCATCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATGGGCACCGAG
* * * *
55511070 ATGAGAGGTCCCCCGTAAGACCATGTGTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATGGGCACCGAG
** * *
55511120 ATGAGAACTCCCATGTAAGACCATATCTGGGATATG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATG
55511156 ACATTGGAAG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATGGGCACCGAG
Found at i:55511441 original size:20 final size:20
Alignment explanation
Indices: 55511416--55511464 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
55511406 TGAGTTATTT
*
55511416 AAGTAAGCAAGTAGGTAAAG
1 AAGTAAGCAAGTAAGTAAAG
55511436 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAG
55511456 AAG-AAGCAA
1 AAGTAAGCAA
55511465 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.55, C:0.04, G:0.29, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAG
Found at i:55525022 original size:21 final size:21
Alignment explanation
Indices: 55524996--55525037 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55524986 GACGAGAAGT
55524996 CTACTTAAGCCCATAGATGAA
1 CTACTTAAGCCCATAGATGAA
*
55525017 CTACTTAAGCCCGTAGATGAA
1 CTACTTAAGCCCATAGATGAA
55525038 GTTCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
CTACTTAAGCCCATAGATGAA
Found at i:55527300 original size:56 final size:56
Alignment explanation
Indices: 55527214--55527669 Score: 894
Period size: 56 Copynumber: 8.1 Consensus size: 56
55527204 ACAAGGGATG
*
55527214 ATGGGCAAAACAAGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527270 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527326 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527382 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527438 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527494 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527550 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
*
55527606 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
55527662 ATGGGCAA
1 ATGGGCAA
55527670 TAAACTAATA
Statistics
Matches: 398, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 398 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.24
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGATTAAAATAAGAAGC
Found at i:55528898 original size:39 final size:40
Alignment explanation
Indices: 55528798--55528982 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
55528788 TCGAATGATG
* * *
55528798 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
55528837 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
55528878 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
55528917 TCCGAGTTAAGTCCCGAAGGCATTTTTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
55528956 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
55528983 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:55529005 original size:79 final size:79
Alignment explanation
Indices: 55528851--55529015 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
55528841 GGACTAAGAT
** **
55528851 CCGAAGGCATTTGTGCGAGTTACTAATTTCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
55528916 ATCCGAGTTAAGTC
66 ATCCGAGTTAAATC
* * *
55528930 CCGAAGGCATTTTTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
55528993 TATATCCG-GTTAAATT
63 TAAATCCGAGTTAAATC
55529009 CCGAAGG
1 CCGAAGG
55529016 TACATGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGAGTTAAATC
Found at i:55531514 original size:32 final size:32
Alignment explanation
Indices: 55531471--55531535 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
55531461 CCAGCTCCTG
*
55531471 CTGAAGAGGCAGTGCCGACTGAAAACTGACCT
1 CTGAAGAGGCAGTGCCGACTAAAAACTGACCT
* * *
55531503 CTGAAGGGGCAGTGTCGACTAAAAATTGACCT
1 CTGAAGAGGCAGTGCCGACTAAAAACTGACCT
55531535 C
1 C
55531536 CTACTGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (32 bp):
CTGAAGAGGCAGTGCCGACTAAAAACTGACCT
Found at i:55539399 original size:40 final size:40
Alignment explanation
Indices: 55539282--55539402 Score: 233
Period size: 40 Copynumber: 3.0 Consensus size: 40
55539272 TACTAACGCT
*
55539282 CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCATG
1 CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCGTG
55539322 CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCGTG
1 CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCGTG
55539362 CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCGTG
1 CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCGTG
55539402 C
1 C
55539403 TTACATTGGC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (40 bp):
CCTAGTACCTTTATGCGTTTAATGAACCATGTTCTTCGTG
Found at i:55541628 original size:40 final size:40
Alignment explanation
Indices: 55541547--55541767 Score: 304
Period size: 40 Copynumber: 5.6 Consensus size: 40
55541537 CAACCAAGTA
** * * *
55541547 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
55541586 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAACTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
55541626 CCTTCGGGACTTGGCCCGGTTATAGTAACTCACACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
55541666 CCTTCGGGACTTGGCCCGGTTATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
55541706 CCTTCAGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
55541746 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
55541768 CAATCCGAAT
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 27 0.16
40 137 0.84
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:55549434 original size:39 final size:39
Alignment explanation
Indices: 55549341--55549443 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 39
55549331 CCCAACCAAG
* * * *
55549341 TGCCTTCAGGGTTTAG-CCGGATATAGCTACTCGCTCGAA
1 TGCCTTCA-GGCTTAGCCCGGTTATAGCTACTCGCACAAA
**
55549380 TGCCTTTGGGACTTAGCCCGGTTATAG-TAACTCGCACAAA
1 TGCCTTCAGG-CTTAGCCCGGTTATAGCT-ACTCGCACAAA
55549420 TGCCTTCAGGCTTAGCCCGGTTAT
1 TGCCTTCAGGCTTAGCCCGGTTAT
55549444 CAATCCAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.04
39 25 0.47
40 26 0.49
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.29
Consensus pattern (39 bp):
TGCCTTCAGGCTTAGCCCGGTTATAGCTACTCGCACAAA
Found at i:55553424 original size:22 final size:20
Alignment explanation
Indices: 55553392--55553440 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
55553382 GTTGAATTTA
55553392 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
55553415 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
55553435 TGAACA
1 TGAACA
55553441 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:55554207 original size:11 final size:11
Alignment explanation
Indices: 55554191--55554231 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
55554181 TATACAAGTA
55554191 AAAAAAATTCG
1 AAAAAAATTCG
*
55554202 AAAAAAATTCAA
1 AAAAAAATTC-G
55554214 AAAAAAATTCG
1 AAAAAAATTCG
55554225 AAAAAAA
1 AAAAAAA
55554232 AATCTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:55554207 original size:12 final size:12
Alignment explanation
Indices: 55554190--55554245 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
55554180 TTATACAAGT
55554190 AAAAAAAATTCG
1 AAAAAAAATTCG
*
55554202 -AAAAAAATTCA
1 AAAAAAAATTCG
55554213 AAAAAAAATTCG
1 AAAAAAAATTCG
*
55554225 AAAAAAAAATCTG
1 AAAAAAAATTC-G
55554238 AAAAAAAA
1 AAAAAAAA
55554246 GTGTTTAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.26
12 20 0.51
13 9 0.23
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:55554208 original size:13 final size:13
Alignment explanation
Indices: 55554190--55554245 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
55554180 TTATACAAGT
55554190 AAAAAAAATTCG-
1 AAAAAAAATTCGA
55554202 -AAAAAAATTC-A
1 AAAAAAAATTCGA
55554213 AAAAAAAATTCGA
1 AAAAAAAATTCGA
55554226 AAAAAAAA-TCTGA
1 AAAAAAAATTC-GA
55554239 AAAAAAA
1 AAAAAAA
55554246 GTGTTTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.25
12 12 0.30
13 18 0.45
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:55555164 original size:9 final size:10
Alignment explanation
Indices: 55555157--55555213 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
55555147 AAGAGAAAAC
55555157 AAAGAAAAGA
1 AAAGAAAAGA
55555167 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
55555179 AAAGAAGA-A
1 AAAGAAAAGA
*
55555188 AAAGAAAATA
1 AAAGAAAAGA
*
55555198 AAATAAAAAGA
1 AAA-GAAAAGA
55555209 AAAGA
1 AAAGA
55555214 GAGGTGTGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
9 8 0.21
10 9 0.24
11 16 0.42
12 5 0.13
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:55555180 original size:21 final size:20
Alignment explanation
Indices: 55555146--55555211 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
55555136 ACATTCTTGT
55555146 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
55555167 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
*
55555188 AAAGAAAATAAAATAAAAAGAA
1 AAAGAAAA-ACAA-AAAAAGAA
55555210 AA
1 AA
55555212 GAGAGGTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.21
21 20 0.53
22 10 0.26
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:55555181 original size:6 final size:5
Alignment explanation
Indices: 55555157--55555213 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
55555147 AAGAGAAAAC
* * *
55555157 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATA AAATAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA
55555204 AAAGA AAAGA
1 AAAGA AAAGA
55555214 GAGGTGTGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.60
6 14 0.33
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:55555206 original size:25 final size:25
Alignment explanation
Indices: 55555161--55555209 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
55555151 GAAAACAAAG
55555161 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAAGAAGA
*
55555187 AAAAGAAAATAAAATA-AAAAGAA
1 AAAAGAAAAGAAAA-ACAAAAGAA
55555210 AAGAGAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAGAAGA
Found at i:55556955 original size:40 final size:40
Alignment explanation
Indices: 55556900--55557037 Score: 190
Period size: 40 Copynumber: 3.5 Consensus size: 40
55556890 TGGATGATAA
*
55556900 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
55556940 CCGGGCTAACTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
55556980 CCGAGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
55557020 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55557038 TACTTGGCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 14 0.16
40 73 0.84
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55557512 original size:89 final size:89
Alignment explanation
Indices: 55557411--55557588 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
55557401 GGACTCGGGA
55557411 GTGTCGAAGTCGAAGTCGCCCACACTATCAAAGCCCTTTGGTACACTTTTGGTTGAACTTTGAAA
1 GTGTCGAAGTCGAAGTCGCCCACACTATCAAAGCCCTTTGGTACACTTTTGGTTGAACTTTGAAA
55557476 TGGCATGTATAGGACTACCCTTTT
66 TGGCATGTATAGGACTACCCTTTT
55557500 GTGTCGAAGTCGAAGTCGCCCACACTATCAAAGCCCTTTGGTACACTTTTGGTTGAACTTTGAAA
1 GTGTCGAAGTCGAAGTCGCCCACACTATCAAAGCCCTTTGGTACACTTTTGGTTGAACTTTGAAA
55557565 TGGCATGTATAGGACTACCCTTTT
66 TGGCATGTATAGGACTACCCTTTT
55557589 TGATGTTGGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (89 bp):
GTGTCGAAGTCGAAGTCGCCCACACTATCAAAGCCCTTTGGTACACTTTTGGTTGAACTTTGAAA
TGGCATGTATAGGACTACCCTTTT
Found at i:55558569 original size:12 final size:12
Alignment explanation
Indices: 55558561--55558585 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55558551 TTTGAAAAGA
55558561 AAAAAGAAAATG
1 AAAAAGAAAATG
55558573 AAAAAGAAAATG
1 AAAAAGAAAATG
55558585 A
1 A
55558586 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:55558595 original size:30 final size:31
Alignment explanation
Indices: 55558561--55558642 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
55558551 TTTGAAAAGA
*
55558561 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
55558591 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
55558621 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
55558643 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:55558797 original size:19 final size:19
Alignment explanation
Indices: 55558773--55558811 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55558763 TCCTAGAAGT
55558773 TTGTGCGACCAATTCCATC
1 TTGTGCGACCAATTCCATC
55558792 TTGTGCGACCAATTCCATC
1 TTGTGCGACCAATTCCATC
55558811 T
1 T
55558812 ACATTACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (19 bp):
TTGTGCGACCAATTCCATC
Found at i:55562063 original size:27 final size:28
Alignment explanation
Indices: 55561979--55562076 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
55561969 CATGAGATTG
* * * *
55561979 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
55562008 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
55562036 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55562063 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
55562077 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55562087 original size:27 final size:27
Alignment explanation
Indices: 55562007--55562089 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
55561997 TAAATTGTAC
* *
55562007 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55562035 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
55562062 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
55562089 A
1 A
55562090 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:55562090 original size:29 final size:27
Alignment explanation
Indices: 55561979--55562090 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
55561969 CATGAGATTG
** * *
55561979 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
55562008 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
55562036 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
55562063 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
55562091 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:55572256 original size:37 final size:37
Alignment explanation
Indices: 55572206--55572284 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
55572196 TTATTACGAA
* * *
55572206 GTCTTACCCGGACATAA-TCTCCACATGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
55572243 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
55572280 GTCTT
1 GTCTT
55572285 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:55572481 original size:47 final size:47
Alignment explanation
Indices: 55572403--55572577 Score: 233
Period size: 47 Copynumber: 3.6 Consensus size: 47
55572393 CCCTTCGGGA
* * * * * *
55572403 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55572450 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55572497 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55572544 CTTATCACATATATATATACACTTTCACATTCAT
1 CTTATCAC----ATATATACACTTTCACATTCAT
55572578 TCAAATATAC
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
47 91 0.81
51 21 0.19
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55575766 original size:25 final size:25
Alignment explanation
Indices: 55575698--55575766 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
55575688 TGCACATGTA
*
55575698 TGCTCACACGA-ACTGTGAATCAGAT
1 TGCTCACATGAGA-TGTGAATCAGAT
* *
55575723 TGCTCACATGAGATATGAATTAGAT
1 TGCTCACATGAGATGTGAATCAGAT
*
55575748 TGCTCACATGAGTTGTGAA
1 TGCTCACATGAGATGTGAA
55575767 AATGGGCTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (25 bp):
TGCTCACATGAGATGTGAATCAGAT
Found at i:55576509 original size:30 final size:32
Alignment explanation
Indices: 55576473--55576546 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
55576463 TTCTACAGCT
*
55576473 TTTAATTATGCCTTG-TTTATT-ATATACATC
1 TTTAATTATGCCTTGCATTATTAATATACATC
* *
55576503 TTTAATTAATGTCTTGCATTATTAATCTACATC
1 TTTAATT-ATGCCTTGCATTATTAATATACATC
55576536 TTCTAATTATG
1 TT-TAATTATG
55576547 ACAAGCACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 7 0.19
31 7 0.19
32 5 0.14
33 13 0.35
34 5 0.14
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (32 bp):
TTTAATTATGCCTTGCATTATTAATATACATC
Found at i:55576697 original size:52 final size:51
Alignment explanation
Indices: 55576565--55576697 Score: 187
Period size: 50 Copynumber: 2.6 Consensus size: 51
55576555 TATCTATTCT
* * *
55576565 TCATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCA
1 TCATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCA
* * *
55576616 TCA-TAAATTATGACATGCATTATGCAACTCCCATGTTAGTTAAAGTTTGCA
1 TCATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTT-AAGTTTGCA
*
55576667 TCATTAAATTAAGTCATGCATTAAGTAACTC
1 TCATTAAATTAAGTCATGCATTATGTAACTC
55576698 ATTTGTTCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 32 0.46
51 15 0.21
52 23 0.33
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (51 bp):
TCATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCA
Found at i:55586714 original size:28 final size:28
Alignment explanation
Indices: 55586683--55586745 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
55586673 TTGATATTTT
55586683 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
55586711 GCACACTAAGTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
55586739 GTACACT
1 GCACACT
55586746 GAGTACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:55588334 original size:21 final size:21
Alignment explanation
Indices: 55588310--55588357 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
55588300 GAGTATTTTG
*
55588310 ATGTTTAATGATAGATTATG-A
1 ATGTTTAATGACAG-TTATGCA
*
55588331 ATGTTTGATGACAGTTATGCA
1 ATGTTTAATGACAGTTATGCA
55588352 A-GTTTA
1 ATGTTTA
55588358 TTTTAAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (21 bp):
ATGTTTAATGACAGTTATGCA
Found at i:55590208 original size:25 final size:25
Alignment explanation
Indices: 55590179--55590404 Score: 162
Period size: 25 Copynumber: 9.1 Consensus size: 25
55590169 AAACCAAACC
55590179 AAGCCTTTATGGTGAGTTATCTTGA
1 AAGCCTTTATGGTGAGTTATCTTGA
*
55590204 AAGCCTTTGTGGTGAGTTATCTAT-A
1 AAGCCTTTATGGTGAGTTATCT-TGA
*
55590229 AAGCCTTTATGGTGAATTATC-TGA
1 AAGCCTTTATGGTGAGTTATCTTGA
* *
55590253 GAAGTCTTTATGGCGAGTTAT-TTGTA
1 -AAGCCTTTATGGTGAGTTATCTTG-A
* *
55590279 AAGCCTTTGTGGCGAGTTATC-TGTA
1 AAGCCTTTATGGTGAGTTATCTTG-A
* * ** *
55590304 AAGCTTTTGTGGCAAATTAT-TTGTA
1 AAGCCTTTATGGTGAGTTATCTTG-A
* *
55590329 AAACCTTTATGGTGAATTATC-TGAA
1 AAGCCTTTATGGTGAGTTATCTTG-A
* **
55590354 AAGCTTTTATGGCAAGTTATCTGTG-
1 AAGCCTTTATGGTGAGTTATCT-TGA
* * *
55590379 AAGTCTTTGTGGTGAATTATC-TGA
1 AAGCCTTTATGGTGAGTTATCTTGA
55590403 AA
1 AA
55590405 CATCTTTGTG
Statistics
Matches: 162, Mismatches: 28, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.02
24 3 0.02
25 152 0.94
26 2 0.01
27 2 0.01
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (25 bp):
AAGCCTTTATGGTGAGTTATCTTGA
Found at i:55590233 original size:50 final size:49
Alignment explanation
Indices: 55590179--55590404 Score: 236
Period size: 50 Copynumber: 4.5 Consensus size: 49
55590169 AAACCAAACC
* * *
55590179 AAGCCTTTATGGTGAGTTATCTTGAAAGCCTTTGTGGTGAGTTATCTATA
1 AAGCCTTTATGGTGAATTATC-TGAAAGCCTTTGTGGCGAGTTATCTGTA
* * *
55590229 AAGCCTTTATGGTGAATTATCTGAGAAGTCTTTATGGCGAGTTATTTGTA
1 AAGCCTTTATGGTGAATTATCTGA-AAGCCTTTGTGGCGAGTTATCTGTA
* * * * * * *
55590279 AAGCCTTTGTGGCGAGTTATCTGTAAAGCTTTTGTGGCAAATTATTTGTA
1 AAGCCTTTATGGTGAATTATCTG-AAAGCCTTTGTGGCGAGTTATCTGTA
* * * * *
55590329 AAACCTTTATGGTGAATTATCTGAAAAGCTTTTATGGCAAGTTATCTGTG
1 AAGCCTTTATGGTGAATTATCTG-AAAGCCTTTGTGGCGAGTTATCTGTA
* *
55590379 AAGTCTTTGTGGTGAATTATCTGAAA
1 AAGCCTTTATGGTGAATTATCTGAAA
55590405 CATCTTTGTG
Statistics
Matches: 148, Mismatches: 26, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
49 6 0.04
50 141 0.95
51 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (49 bp):
AAGCCTTTATGGTGAATTATCTGAAAGCCTTTGTGGCGAGTTATCTGTA
Found at i:55590271 original size:75 final size:75
Alignment explanation
Indices: 55590182--55590404 Score: 254
Period size: 75 Copynumber: 3.0 Consensus size: 75
55590172 CCAAACCAAG
* * *
55590182 CCTTTATGGTGAGTTATCTTG-AAAGCCTTTGTGGTGAGTTATCTATAAAGCCTTTATGGTGAAT
1 CCTTTATGGTGAGTTATCTTGAAAAGCCTTTGTGGCGAGTTATCTGTAAAGCCTTTGTGGTGAAT
*
55590246 TATCTGAGAAG
66 TATCTGA-AAA
* * * * **
55590257 TCTTTATGGCGAGTTAT-TTGTAAAGCCTTTGTGGCGAGTTATCTGTAAAGCTTTTGTGGCAAAT
1 CCTTTATGGTGAGTTATCTTGAAAAGCCTTTGTGGCGAGTTATCTGTAAAGCCTTTGTGGTGAAT
*
55590321 TATTTGTAAAA
66 TATCTG-AAAA
* * * * * *
55590332 CCTTTATGGTGAATTATC-TGAAAAGCTTTTATGGCAAGTTATCTGTGAAGTCTTTGTGGTGAAT
1 CCTTTATGGTGAGTTATCTTGAAAAGCCTTTGTGGCGAGTTATCTGTAAAGCCTTTGTGGTGAAT
55590396 TATCTGAAA
66 TATCTGAAA
55590405 CATCTTTGTG
Statistics
Matches: 122, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
74 6 0.05
75 115 0.94
76 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (75 bp):
CCTTTATGGTGAGTTATCTTGAAAAGCCTTTGTGGCGAGTTATCTGTAAAGCCTTTGTGGTGAAT
TATCTGAAAA
Found at i:55592856 original size:37 final size:37
Alignment explanation
Indices: 55592808--55592878 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
55592798 TTGTGGCTCT
55592808 CCCCTCCTCTCCTCTCCTTTACCTTCACTCTCTTTCC
1 CCCCTCCTCTCCTCTCCTTTACCTTCACTCTCTTTCC
* *
55592845 CCCCTCTTCTCCTTTCCTTTACCTTCACTCTCTT
1 CCCCTCCTCTCCTCTCCTTTACCTTCACTCTCTT
55592879 GCCCTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.06, C:0.51, G:0.00, T:0.44
Consensus pattern (37 bp):
CCCCTCCTCTCCTCTCCTTTACCTTCACTCTCTTTCC
Found at i:55600624 original size:18 final size:18
Alignment explanation
Indices: 55600599--55600646 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
55600589 AAATAAAAGT
55600599 AAAG-TATAAAAAGTATA
1 AAAGATATAAAAAGTATA
* *
55600616 AAAGATATAACAAGTATT
1 AAAGATATAAAAAGTATA
* *
55600634 ATATATATAAAAA
1 AAAGATATAAAAA
55600647 TACTAATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.27
Consensus pattern (18 bp):
AAAGATATAAAAAGTATA
Found at i:55601816 original size:16 final size:16
Alignment explanation
Indices: 55601795--55601829 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55601785 ATATTTTAGC
55601795 TTTTATCGTATTAAAA
1 TTTTATCGTATTAAAA
* *
55601811 TTTTATTGTATTAGAA
1 TTTTATCGTATTAAAA
55601827 TTT
1 TTT
55601830 GTGTAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (16 bp):
TTTTATCGTATTAAAA
Found at i:55602165 original size:18 final size:18
Alignment explanation
Indices: 55602142--55602180 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
55602132 CATTTACCTA
55602142 TGATTTCACTATTGTGAG
1 TGATTTCACTATTGTGAG
55602160 TGATTTCACTATTGTGAG
1 TGATTTCACTATTGTGAG
55602178 TGA
1 TGA
55602181 AGTGTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (18 bp):
TGATTTCACTATTGTGAG
Found at i:55603456 original size:27 final size:27
Alignment explanation
Indices: 55603423--55603496 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
55603413 TTCAAATTTT
55603423 GCCACAAAGGCTTTTCTTTCATATTAC
1 GCCACAAAGGCTTTTCTTTCATATTAC
* * *
55603450 GCTACAAAGTCTTTCCTTTCATATTAC
1 GCCACAAAGGCTTTTCTTTCATATTAC
55603477 GCCACAAAGGCTTTTCTTTC
1 GCCACAAAGGCTTTTCTTTC
55603497 CTAACGTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (27 bp):
GCCACAAAGGCTTTTCTTTCATATTAC
Found at i:55605637 original size:26 final size:26
Alignment explanation
Indices: 55605608--55605664 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
55605598 GCACTCTCTC
*
55605608 GAGCCATGAAACATGAAACTCACAAA
1 GAGCCATGAAACAGGAAACTCACAAA
* * * *
55605634 GAGCCTTTAATCAGGAAGCTCACAAA
1 GAGCCATGAAACAGGAAACTCACAAA
55605660 GAGCC
1 GAGCC
55605665 TATCGGGAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (26 bp):
GAGCCATGAAACAGGAAACTCACAAA
Found at i:55605665 original size:26 final size:26
Alignment explanation
Indices: 55605626--55605795 Score: 87
Period size: 25 Copynumber: 6.9 Consensus size: 26
55605616 AAACATGAAA
55605626 CTCACAAAGAGCCTTTAATCAGGAAG
1 CTCACAAAGAGCCTTTAATCAGGAAG
*
55605652 CTCACAAAGAGCC--T-ATCGGGAAG
1 CTCACAAAGAGCCTTTAATCAGGAAG
* * *
55605675 CTTATC--CG-GGCTATATAA-CAGGAAG
1 CTCA-CAAAGAGCCT-T-TAATCAGGAAG
* * *
55605700 CTCACATAGAGCC-ATAATCAGAAAG
1 CTCACAAAGAGCCTTTAATCAGGAAG
* * * *
55605725 CTCACATAGAACTTTTAATCAAGAAG
1 CTCACAAAGAGCCTTTAATCAGGAAG
* *
55605751 CTCACGAAGAG-CTTTAA-AAGGGAAG
1 CTCACAAAGAGCCTTTAATCA-GGAAG
*
55605776 CTCAC---GAGCCATTAATCAGG
1 CTCACAAAGAGCCTTTAATCAGG
55605796 GGCTCCGGAT
Statistics
Matches: 107, Mismatches: 23, Indels: 31
0.66 0.14 0.19
Matches are distributed among these distances:
21 2 0.02
22 4 0.04
23 18 0.17
24 8 0.07
25 41 0.38
26 32 0.30
27 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (26 bp):
CTCACAAAGAGCCTTTAATCAGGAAG
Found at i:55616248 original size:40 final size:40
Alignment explanation
Indices: 55616188--55616300 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
55616178 TATTCGGATG
*
55616188 ATATTCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* *
55616228 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTATT
1 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* ** *
55616268 ATAACCGGGTTAAG-TCCCGAAGGCATTCGTGCT
1 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCT
55616301 GGTTGTTACA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 63 0.98
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (40 bp):
ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
Found at i:55619923 original size:26 final size:27
Alignment explanation
Indices: 55619894--55619965 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
55619884 CCCTGGCTTA
*** *
55619894 TAAAATTACCGAAATATTGTTGA-TTG
1 TAAAATTACCGAAATACCCTCGATTTG
*
55619920 TAAAATTACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTCGATTTG
55619947 TAAAA-TACCGAAATACCCT
1 TAAAATTACCGAAATACCCT
55619966 TGTAGGGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 31 0.79
27 8 0.21
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGATTTG
Found at i:55619986 original size:27 final size:27
Alignment explanation
Indices: 55619949--55620303 Score: 399
Period size: 27 Copynumber: 13.1 Consensus size: 27
55619939 TCGATTTGTA
55619949 AAATACCGAAATACCCTTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
*
55619976 AAATACTGAAATA-CCTCTGTAGGGTAG
1 AAATACCGAAATACCCT-TGTAGGGTAG
* * *
55620003 AATTACTGAAATACCCCTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* *
55620030 AATTACCAAAATACCCTTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
*
55620057 AAATACCGAAATATCCTTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* *
55620084 AAATACCGAAATACCCCTATAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* * ** * * * *
55620111 GATTATTGAAATACCCCTATAGGATTG
1 AAATACCGAAATACCCTTGTAGGGTAG
* *
55620138 AAATACCAAAATAACCTTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* *
55620165 AAATATCGAAATACCCCTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* * * *
55620192 AATTACTGAAATACCCCCTGTAGGATAG
1 AAATACCGAAATA-CCCTTGTAGGGTAG
* *
55620220 AATTATCGAAATACCCTTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
*
55620247 AAATACCGAAATACCCCTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* * *
55620274 AATTACCGAGATACCCTTGTGGGGTA-
1 AAATACCGAAATACCCTTGTAGGGTAG
55620300 AAAT
1 AAAT
55620304 TACCATTTTG
Statistics
Matches: 277, Mismatches: 48, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
26 6 0.02
27 245 0.88
28 26 0.09
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (27 bp):
AAATACCGAAATACCCTTGTAGGGTAG
Found at i:55620053 original size:81 final size:80
Alignment explanation
Indices: 55619952--55620303 Score: 463
Period size: 81 Copynumber: 4.3 Consensus size: 80
55619942 ATTTGTAAAA
* * *
55619952 TACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCTCTGTAGGGTAGAATTACTGAAATAC
1 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCT-TGTAGGGTAGAAATACCGAAATAC
55620017 CCCTGTAGGGTAGAAT
65 CCCTGTAGGGTAGAAT
*
55620033 TACCAAAATACCCTTGTAGGGTAGAAATACCGAAATATCCTTGTAGGGTAGAAATACCGAAATAC
1 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATA-CCTTGTAGGGTAGAAATACCGAAATAC
* *
55620098 CCCTATAGGGTAGGAT
65 CCCTGTAGGGTAGAAT
** * * * * * *
55620114 TATTGAAATACCCCTATAGGATTGAAATACCAAAATAACCTTGTAGGGTAGAAATATCGAAATAC
1 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAAT-ACCTTGTAGGGTAGAAATACCGAAATAC
55620179 CCCTGTAGGGTAGAAT
65 CCCTGTAGGGTAGAAT
* * * * *
55620195 TACTGAAATACCCCCTGTAGGATAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAAATA
1 TACCGAAATA-CCCTTGTAGGGTAGAAATACCGAAATA-CCTTGTAGGGTAGAAATACCGAAATA
55620260 CCCCTGTAGGGTAGAAT
64 CCCCTGTAGGGTAGAAT
* *
55620277 TACCGAGATACCCTTGTGGGGTA-AAAT
1 TACCGAAATACCCTTGTAGGGTAGAAAT
55620304 TACCATTTTG
Statistics
Matches: 237, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
80 3 0.01
81 159 0.67
82 75 0.32
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (80 bp):
TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCTTGTAGGGTAGAAATACCGAAATACC
CCTGTAGGGTAGAAT
Found at i:55620768 original size:22 final size:22
Alignment explanation
Indices: 55620740--55620799 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
55620730 GCCTTCTAAT
*
55620740 TATGGCTTTGTGCCAACCT-ACA
1 TATGGCTCTGTGCCAACCTGA-A
*
55620762 TATGGCTCTGTGCCAACCTGAT
1 TATGGCTCTGTGCCAACCTGAA
*
55620784 TATGGCTGTGTGCCAA
1 TATGGCTCTGTGCCAA
55620800 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
TATGGCTCTGTGCCAACCTGAA
Found at i:55620994 original size:26 final size:26
Alignment explanation
Indices: 55620958--55621037 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
55620948 ATTCTGTTAA
* *
55620958 GTGGCTTTGCCACATTATCTATTCTG
1 GTGGCTCTGCCACAATATCTATTCTG
* *
55620984 GTGGCTCTGCCACAATATCTGTATCTA
1 GTGGCTCTGCCACAATATCTAT-TCTG
* * *
55621011 GTGACTCTGTCACAATATCTTTTCTG
1 GTGGCTCTGCCACAATATCTATTCTG
55621037 G
1 G
55621038 AAGCCATGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
26 23 0.51
27 22 0.49
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTATTCTG
Found at i:55621164 original size:6 final size:6
Alignment explanation
Indices: 55621155--55621248 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
55621145 TTGCATTCAC
*
55621155 ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * * *
55621204 -TCACCTG ATTCTG ATTCTA ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
55621249 AATGTTTCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
5 4 0.06
6 58 0.82
7 7 0.10
8 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:55621186 original size:25 final size:25
Alignment explanation
Indices: 55621158--55621227 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
55621148 CATTCACATT
*
55621158 CTGATTCTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGATTCTGTCAC
*
55621183 CTGATACTGATTCTGATTCTGTCAC
1 CTGATTCTGATTCTGATTCTGTCAC
*
55621208 CTGATTCTGATTCTAATTCT
1 CTGATTCTGATTCTGATTCT
55621228 CATTTTGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGATTCTGTCAC
Found at i:55632873 original size:47 final size:47
Alignment explanation
Indices: 55632715--55633995 Score: 2292
Period size: 47 Copynumber: 27.1 Consensus size: 47
55632705 GAAATGATAG
* *
55632715 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
55632764 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATACGTGA
*
55632815 TAAGGCCTAATGGCCGATGTGATGAATGTAAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55632862 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55632909 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55632956 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633003 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633050 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633097 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633144 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633191 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633238 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633285 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633332 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633379 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633426 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633473 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633520 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633567 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633614 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633661 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
* *
55633708 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
55633755 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
55633804 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
55633851 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
* *
55633898 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
* * * * * * * * *
55633945 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
55633992 TAAG
1 TAAG
55633996 TCCCGAAGGG
Statistics
Matches: 1205, Mismatches: 23, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
47 1079 0.90
49 80 0.07
51 46 0.04
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
Found at i:55634170 original size:37 final size:37
Alignment explanation
Indices: 55634114--55634192 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
55634104 CCGAGCTCTA
* * *
55634114 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
55634151 AAGACCCGATAACTTCGTGTGGAGATTATGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55634188 AAGAC
1 AAGAC
55634193 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55636592 original size:40 final size:39
Alignment explanation
Indices: 55636498--55636642 Score: 173
Period size: 40 Copynumber: 3.6 Consensus size: 39
55636488 TACTCGAATG
*
55636498 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCT-AGCGACT
* * *
55636539 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCTAGCGACT
* * *
55636579 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCTAGCGACT
*
55636619 ATATCCGGGTTAAGGCCCGAAGGC
1 ATATCCGGGCTAA-GCCCGAAGGC
55636643 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 61 0.68
41 29 0.32
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55639100 original size:25 final size:24
Alignment explanation
Indices: 55639066--55639114 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
55639056 TTGATACTCC
*
55639066 AAATACCAATTCATA-ACAAGCATAT
1 AAATAACAATT-ATACACAA-CATAT
55639091 AAATAACAATTATACACAACATAT
1 AAATAACAATTATACACAACATAT
55639115 CCAAAGGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATAACAATTATACACAACATAT
Found at i:55640749 original size:13 final size:14
Alignment explanation
Indices: 55640721--55640751 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55640711 CCATGTTATT
55640721 TTTATTTTACTTAA
1 TTTATTTTACTTAA
55640735 TTTATTTTA-TTAA
1 TTTATTTTACTTAA
55640748 TTTA
1 TTTA
55640752 CACTTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATTTTACTTAA
Found at i:55642819 original size:43 final size:43
Alignment explanation
Indices: 55642800--55642973 Score: 251
Period size: 43 Copynumber: 4.1 Consensus size: 43
55642790 AAAGCACTGT
* *
55642800 TAAAAGTCATGGCCTTTAGTGGCGTTTGTGGGGGAAGCGCCGG
1 TAAAAGTCATGGCCTTTAGCGGCGTTTGTGGGGGAAGCGCCGC
** * * *
55642843 TAAAAGTCACAGCTTTTAGCGGCATTTGTGGGGGAAGCGTCGC
1 TAAAAGTCATGGCCTTTAGCGGCGTTTGTGGGGGAAGCGCCGC
*
55642886 TAAAAGTCATGGCCTTTAGCGGCGTTTGTGGGGGAATCGCCGC
1 TAAAAGTCATGGCCTTTAGCGGCGTTTGTGGGGGAAGCGCCGC
* *
55642929 TAAAAGTCATGGCCTTTAGCGGTGTTTGT-GGGGAAGTGCCGC
1 TAAAAGTCATGGCCTTTAGCGGCGTTTGTGGGGGAAGCGCCGC
55642971 TAA
1 TAA
55642974 TTTTGGCTGA
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 14 0.12
43 101 0.88
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.26
Consensus pattern (43 bp):
TAAAAGTCATGGCCTTTAGCGGCGTTTGTGGGGGAAGCGCCGC
Found at i:55643062 original size:31 final size:32
Alignment explanation
Indices: 55643027--55643107 Score: 103
Period size: 31 Copynumber: 2.5 Consensus size: 32
55643017 TTTCTACATT
*
55643027 AAATCCAACCAAAAACA-ACAAATATAGCAT-G
1 AAATCCAACCAAAAACAGA-AAATATAGCATAA
*
55643058 AAATCCAACCAAAAACAGAAAATGTAGCATAAA
1 AAATCCAACCAAAAACAGAAAATATAGCAT-AA
*
55643091 AAATACAACCAAAAACA
1 AAATCCAACCAAAAACA
55643108 TTAAATCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 27 0.61
32 1 0.02
33 16 0.36
ACGTcount: A:0.62, C:0.21, G:0.06, T:0.11
Consensus pattern (32 bp):
AAATCCAACCAAAAACAGAAAATATAGCATAA
Done.