Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 94 of 318
Found at i:28408083 original size:5 final size:5
Alignment explanation
Indices: 28408075--28408102 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28408065 TAAGATGAGA
28408075 CGATG CGATG CGATG CGATG CGATG CGA
1 CGATG CGATG CGATG CGATG CGATG CGA
28408103 GAACGTACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.39, T:0.18
Consensus pattern (5 bp):
CGATG
Found at i:28414287 original size:33 final size:33
Alignment explanation
Indices: 28414247--28414310 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
28414237 ATTTATAAAG
28414247 TTATTAGATAAGTAAATTGAATTTTGGATAATA
1 TTATTAGATAAGTAAATTGAATTTTGGATAATA
28414280 TTATTAGATAAGTAAATTGAATTTTGGATAA
1 TTATTAGATAAGTAAATTGAATTTTGGATAA
28414311 GTAATTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (33 bp):
TTATTAGATAAGTAAATTGAATTTTGGATAATA
Found at i:28414311 original size:20 final size:20
Alignment explanation
Indices: 28414253--28414314 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
28414243 AAAGTTATTA
28414253 GATAAGTAAATTGAATTTTG
1 GATAAGTAAATTGAATTTTG
*
28414273 GATAA-T--ATT--A--TTA
1 GATAAGTAAATTGAATTTTG
28414286 GATAAGTAAATTGAATTTTG
1 GATAAGTAAATTGAATTTTG
28414306 GATAAGTAA
1 GATAAGTAA
28414315 TTTAGTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 1 0.03
16 3 0.09
17 3 0.09
18 1 0.03
19 1 0.03
20 16 0.48
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.39
Consensus pattern (20 bp):
GATAAGTAAATTGAATTTTG
Found at i:28428182 original size:54 final size:54
Alignment explanation
Indices: 28428115--28428248 Score: 232
Period size: 54 Copynumber: 2.5 Consensus size: 54
28428105 GTCATTGAAA
*
28428115 GGGATTTAGCCTGGACTGTTAATCCCGACATTGCTCTATTAGTTAATACTACAG
1 GGGATTTAGCCTGGACTGGTAATCCCGACATTGCTCTATTAGTTAATACTACAG
* *
28428169 GGGATTTAGCCTGGACTGGTAATCCTGACATTGCTCTATTAGTTAATACTACGG
1 GGGATTTAGCCTGGACTGGTAATCCCGACATTGCTCTATTAGTTAATACTACAG
*
28428223 GGGATTTAGCCTAGACTGGTAATCCC
1 GGGATTTAGCCTGGACTGGTAATCCC
28428249 ACCGTAAGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (54 bp):
GGGATTTAGCCTGGACTGGTAATCCCGACATTGCTCTATTAGTTAATACTACAG
Found at i:28435151 original size:20 final size:19
Alignment explanation
Indices: 28435128--28435166 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
28435118 ATGAAATAAG
*
28435128 AAAAAATAAATTTAAATGAA
1 AAAAAAT-AATATAAATGAA
28435148 AAAAAATAATATAAATGAA
1 AAAAAATAATATAAATGAA
28435167 TTGAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAATAATATAAATGAA
Found at i:28435215 original size:29 final size:30
Alignment explanation
Indices: 28435173--28435233 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
28435163 TGAATTGAGA
28435173 AAAAATTTAAATTTACAAGG-AAGATATAT
1 AAAAATTTAAATTTACAAGGAAAGATATAT
28435202 AAAAATTTAAATTTACAAGGAAAGATATAT
1 AAAAATTTAAATTTACAAGGAAAGATATAT
28435232 AA
1 AA
28435234 TTTAAATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (30 bp):
AAAAATTTAAATTTACAAGGAAAGATATAT
Found at i:28435230 original size:28 final size:29
Alignment explanation
Indices: 28435173--28435240 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
28435163 TGAATTGAGA
*
28435173 AAAAATTTAAATTTACAAGGAAGATATAT
1 AAAAATTTAAATTTACAAGGAAGAGATAT
28435202 AAAAATTTAAATTTACAAGGAA-AGATAT
1 AAAAATTTAAATTTACAAGGAAGAGATAT
*
28435230 -ATAATTTAAAT
1 AAAAATTTAAAT
28435241 GAAATGAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 10 0.27
28 5 0.14
29 22 0.59
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (29 bp):
AAAAATTTAAATTTACAAGGAAGAGATAT
Found at i:28435262 original size:27 final size:26
Alignment explanation
Indices: 28435232--28435494 Score: 135
Period size: 27 Copynumber: 10.8 Consensus size: 26
28435222 AAAGATATAT
28435232 AATTTAAATGAAATGAGAATAAAATTA
1 AATTTAAATGAAATGAGAA-AAAATTA
** * *
28435259 AATTTGCATGGAA--AG-ATAAA-T-
1 AATTTAAATGAAATGAGAAAAAATTA
*
28435280 AATGTAAATGAAATGAGAAAAAATATA
1 AATTTAAATGAAATGAGAAAAAAT-TA
28435307 AATTTAAATGAAATGAGGAAAAAATTA
1 AATTTAAATGAAATGA-GAAAAAATTA
* * *
28435334 AATTTAAATAAAATTAGAAAAAAATTG
1 AATTTAAATGAAATGAG-AAAAAATTA
** * *
28435361 AATTTGCAT-AGAA--AG-ATAGA-T-
1 AATTTAAATGA-AATGAGAAAAAATTA
28435382 AATTTAAATGAAATGAGGAAAAAATTA
1 AATTTAAATGAAATGA-GAAAAAATTA
* *
28435409 AA-TTAAA--ATA-G-GAAGATAGA-TA
1 AATTTAAATGAAATGAGAA-A-AAATTA
*
28435431 AA-TTATATGAAATGAGAAAAAATTA
1 AATTTAAATGAAATGAGAAAAAATTA
*
28435456 AATTTAAAT----TGA-AAAAAAAT-
1 AATTTAAATGAAATGAGAAAAAATTA
28435476 AATTTAAATGAAATG-GAAA
1 AATTTAAATGAAATGAGAAA
28435495 TGGAAATGAC
Statistics
Matches: 179, Mismatches: 28, Indels: 61
0.67 0.10 0.23
Matches are distributed among these distances:
20 9 0.05
21 28 0.16
22 15 0.08
23 12 0.07
24 17 0.09
25 13 0.07
26 17 0.09
27 60 0.34
28 8 0.04
ACGTcount: A:0.59, C:0.01, G:0.14, T:0.27
Consensus pattern (26 bp):
AATTTAAATGAAATGAGAAAAAATTA
Found at i:28435272 original size:48 final size:47
Alignment explanation
Indices: 28435202--28435494 Score: 270
Period size: 48 Copynumber: 6.1 Consensus size: 47
28435192 GAAGATATAT
* *
28435202 AAAAATTTAAATTTACAA-GGAAAGATATATAATTTAAATGAAATGAG
1 AAAAAATTAAATTTA-AATGGAAAGATAAATAATTTAAATGAAATGAG
** *
28435249 AATAAAATTAAATTTGCATGGAAAGATAAATAATGTAAATGAAATGAG
1 AA-AAAATTAAATTTAAATGGAAAGATAAATAATTTAAATGAAATGAG
* * * *
28435297 AAAAAATATAAATTTAAATGAAATGAGGAAAAAATTAAATTTAAATAAAATTAG
1 AAAAAAT-TAAATTTAAATGGAA--A-G-ATAAA-T-AATTTAAATGAAATGAG
* ** * *
28435351 AAAAAAATTGAATTTGCATAGAAAGATAGATAATTTAAATGAAATGAGG
1 -AAAAAATTAAATTTAAATGGAAAGATAAATAATTTAAATGAAATGA-G
* * * *
28435400 AAAAAATTAAATTAAAATAGG-AAGATAGATAAATTATATGAAATGAG
1 AAAAAATTAAATTTAAAT-GGAAAGATAAATAATTTAAATGAAATGAG
* *
28435447 AAAAAATTAAATTTAAATTGAAA-AAAAATAATTTAAATGAAATG-G
1 AAAAAATTAAATTTAAATGGAAAGATAAATAATTTAAATGAAATGAG
28435492 AAA
1 AAA
28435495 TGGAAATGAC
Statistics
Matches: 199, Mismatches: 34, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
45 4 0.02
46 18 0.09
47 28 0.14
48 103 0.52
49 3 0.02
50 4 0.02
51 2 0.01
52 5 0.03
53 1 0.01
54 24 0.12
55 7 0.04
ACGTcount: A:0.58, C:0.01, G:0.13, T:0.27
Consensus pattern (47 bp):
AAAAAATTAAATTTAAATGGAAAGATAAATAATTTAAATGAAATGAG
Found at i:28435376 original size:150 final size:152
Alignment explanation
Indices: 28435141--28435484 Score: 385
Period size: 150 Copynumber: 2.3 Consensus size: 152
28435131 AAATAAATTT
* * * *
28435141 AAATGA-AAAAAA-AT-AATATAAATGAATTGAGAAAAAATTTAAATTTACAAGGAAGATATATA
1 AAATGAGAAAAAATATAAATTTAAATGAAATGAGAAAAAATTTAAATTTACAAGGAAAATATAAA
* * ***
28435203 AAAATTTAAATTTACAAGGAAAGATATATAATTTAAATGAAATGA-GAATAAAATTAAATTTGCA
66 AAAAATTAAATTTACAAGGAAAGATAGATAATTTAAATGAAATGAGGAA-AAAATTAAATTAAAA
28435267 T-GGAAAGATAAAT-AATGTAAATG
130 TAGG-AAGATAAATAAAT-TAAATG
*
28435290 AAATGAGAAAAAATATAAATTTAAATGAAATGAGGAAAAAA-TTAAATTTA-AA-TAAAAT-TAG
1 AAATGAGAAAAAATATAAATTTAAATGAAATGA-GAAAAAATTTAAATTTACAAGGAAAATATA-
* *
28435351 AAAAAAATTGAATTTGCATA-GAAAGATAGATAATTTAAATGAAATGAGGAAAAAATTAAATTAA
64 AAAAAAATTAAATTTACA-AGGAAAGATAGATAATTTAAATGAAATGAGGAAAAAATTAAATTAA
* *
28435415 AATAGGAAGATAGATAAATTATATG
128 AATAGGAAGATAAATAAATTAAATG
28435440 AAATGAGAAAAAAT-TAAATTTAAATTGAAA--A-AAAATAATTTAAAT
1 AAATGAGAAAAAATATAAATTTAAA-TGAAATGAGAAAA-AATTTAAAT
28435485 GAAATGGAAA
Statistics
Matches: 169, Mismatches: 14, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
146 4 0.02
147 2 0.01
148 7 0.04
149 18 0.11
150 95 0.56
151 13 0.08
152 23 0.14
153 7 0.04
ACGTcount: A:0.59, C:0.01, G:0.12, T:0.28
Consensus pattern (152 bp):
AAATGAGAAAAAATATAAATTTAAATGAAATGAGAAAAAATTTAAATTTACAAGGAAAATATAAA
AAAAATTAAATTTACAAGGAAAGATAGATAATTTAAATGAAATGAGGAAAAAATTAAATTAAAAT
AGGAAGATAAATAAATTAAATG
Found at i:28435469 original size:75 final size:75
Alignment explanation
Indices: 28435141--28435469 Score: 240
Period size: 75 Copynumber: 4.4 Consensus size: 75
28435131 AAATAAATTT
* * * *
28435141 AAATGA-AAAAAA-AT-AATATAAATGAATTGA-GAAAAAATTTAAATTTACA-AGGAAGATATA
1 AAATGAGAAAAAATATAAATTTAAATGAAATGAGGAAAAAA-TTAAATTTAAATAGGAAGATAGA
* *
28435201 TAAA-AAT-TT
65 TAAATTATATG
* * **
28435210 AAATTTACAAGGAAAGATATATAATTTAAATGAAATGA-GAATAAAATTAAATTTGCAT-GGAAA
1 AAA-TGAGAA--AAA-ATATA-AATTTAAATGAAATGAGGAA-AAAATTAAATTTAAATAGG-AA
* *
28435273 GATAAAT-AATGTAAATG
59 GATAGATAAAT-TATATG
28435290 AAATGAGAAAAAATATAAATTTAAATGAAATGAGGAAAAAATTAAATTTAAATA--AA-ATTAGA
1 AAATGAGAAAAAATATAAATTTAAATGAAATGAGGAAAAAATTAAATTTAAATAGGAAGA-TAGA
**
28435352 -AAAAAAT-TG
65 TAAATTATATG
* * * * *
28435361 AATTTGCATAGAAAGATAGATAATTTAAATGAAATGAGGAAAAAATTAAATTAAAATAGGAAGAT
1 AA-ATG-AGA-AAAAATATA-AATTTAAATGAAATGAGGAAAAAATTAAATTTAAATAGGAAGAT
28435426 AGATAAATTATATG
62 AGATAAATTATATG
28435440 AAATGAGAAAAAAT-TAAATTTAAATTGAAA
1 AAATGAGAAAAAATATAAATTTAAA-TGAAA
28435470 AAAAATAATT
Statistics
Matches: 205, Mismatches: 27, Indels: 50
0.73 0.10 0.18
Matches are distributed among these distances:
69 3 0.01
70 2 0.01
71 6 0.03
72 4 0.02
73 12 0.06
74 16 0.08
75 74 0.36
76 13 0.06
77 42 0.20
78 20 0.10
79 9 0.04
80 4 0.02
ACGTcount: A:0.58, C:0.01, G:0.13, T:0.27
Consensus pattern (75 bp):
AAATGAGAAAAAATATAAATTTAAATGAAATGAGGAAAAAATTAAATTTAAATAGGAAGATAGAT
AAATTATATG
Found at i:28435502 original size:12 final size:11
Alignment explanation
Indices: 28435481--28435527 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
28435471 AAAATAATTT
28435481 AAAT-GAAATGG
1 AAATGGAAAT-G
28435492 AAATGGAAATG
1 AAATGGAAATG
28435503 ACAATGGAAATG
1 A-AATGGAAATG
28435515 AAATTGG-AATG
1 AAA-TGGAAATG
28435526 AA
1 AA
28435528 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 14 0.42
12 19 0.58
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (11 bp):
AAATGGAAATG
Found at i:28435510 original size:18 final size:16
Alignment explanation
Indices: 28435481--28435518 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
28435471 AAAATAATTT
28435481 AAATGAAATGGAAATGG
1 AAATGAAATGGAAAT-G
28435498 AAATGACAATGGAAATG
1 AAATGA-AATGGAAATG
28435515 AAAT
1 AAAT
28435519 TGGAATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.18
Consensus pattern (16 bp):
AAATGAAATGGAAATG
Found at i:28440071 original size:2 final size:2
Alignment explanation
Indices: 28440011--28440051 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
28440001 TAATTTCATA
*
28440011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
28440052 CATCACACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28443192 original size:90 final size:87
Alignment explanation
Indices: 28442981--28443223 Score: 247
Period size: 89 Copynumber: 2.7 Consensus size: 87
28442971 AGAAATTGAC
* * **
28442981 AAATTAAATTTACAGACACAATAAAATACAAACATTCTAAAATATTAATACAAAAAAATATAAAA
1 AAATTAAATTTAAAGACACAAAAAAATACAAACATTCTAAAA-ATTAATACACGAAAATATAAAA
*
28443046 TTCAAACAAAAATAATATGCACT
65 TTCAAACAAAAATAATAAGCACT
* * * * * * * *
28443069 AAATTAAATTTAAACACCCAACAAACTATAAACATATGGGT-AAAATTAATACACGAAAATTTTA
1 AAATTAAATTTAAAGACACAAAAAAATACAAACAT-T--CTAAAAATTAATACACGAAAATATAA
* * *
28443133 AATTTAAACTACATATAATACAG-ACT
63 AATTCAAAC-AAAAATAATA-AGCACT
* *
28443159 AAATTAAATTTATAGATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTAAAGACACAAAAAAATACAAACATTCTAA-AAATTAATACACGAAAATATAAAA
28443224 AATGAATCCT
Statistics
Matches: 123, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
87 1 0.01
88 30 0.24
89 48 0.39
90 42 0.34
91 2 0.02
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.26
Consensus pattern (87 bp):
AAATTAAATTTAAAGACACAAAAAAATACAAACATTCTAAAAATTAATACACGAAAATATAAAAT
TCAAACAAAAATAATAAGCACT
Found at i:28444084 original size:50 final size:53
Alignment explanation
Indices: 28443959--28444099 Score: 198
Period size: 50 Copynumber: 2.7 Consensus size: 53
28443949 CACAAAAAAG
* * *
28443959 TACTCTAGTGCCGGCAAATATGTGCCCAGCACCCAAAAAATTTAAATTTGTTTT
1 TACTCTAGTGCCGGCCAATAAGTGCCCAGCACCCAAAAAATATAAA-TTGTTTT
* **
28444013 TACTCTGGTGCAAGCCAATAAGTGCCCAGCACCCAAAAAA-ATAAA-T-TTTT
1 TACTCTAGTGCCGGCCAATAAGTGCCCAGCACCCAAAAAATATAAATTGTTTT
28444063 TACTCTAGTGCCGGCCAATAAGTGCCCAGCACCCAAA
1 TACTCTAGTGCCGGCCAATAAGTGCCCAGCACCCAAA
28444100 TTTTTTTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
50 38 0.49
51 1 0.01
53 4 0.05
54 35 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (53 bp):
TACTCTAGTGCCGGCCAATAAGTGCCCAGCACCCAAAAAATATAAATTGTTTT
Found at i:28445400 original size:27 final size:26
Alignment explanation
Indices: 28445363--28445477 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
28445353 AGCATGGCTG
* *
28445363 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28445389 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28445417 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
28445444 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
28445471 CCAGAAC
1 CCAGAAC
28445478 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28445422 original size:54 final size:54
Alignment explanation
Indices: 28445363--28445477 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
28445353 AGCATGGCTG
*
28445363 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
28445417 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
28445471 CCAGAAC
1 CCAGAAC
28445478 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:28447123 original size:26 final size:26
Alignment explanation
Indices: 28447087--28447196 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
28447077 CATGAAATTC
28447087 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28447113 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28447139 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
28447165 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
28447191 TTATCA
1 TTATCA
28447197 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28451184 original size:27 final size:27
Alignment explanation
Indices: 28451153--28451258 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
28451143 CTGCCAGAAT
*
28451153 AGATAATGTGACAGAGTCACCAGATAC
1 AGATAATGTGACAGAGCCACCAGATAC
*
28451180 AGATAATCGTGTCAGAGCCACCAGA-AC
1 AGATAAT-GTGACAGAGCCACCAGATAC
*
28451207 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGACAGAGCCACCAGATAC
* * *
28451234 AGATATTTGTGGCATAGCCACCAGA
1 AGATA-ATGTGACAGAGCCACCAGA
28451259 ACGCTTCCTC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
27 54 0.76
28 17 0.24
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
AGATAATGTGACAGAGCCACCAGATAC
Found at i:28451205 original size:54 final size:54
Alignment explanation
Indices: 28451146--28451260 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
28451136 AGCATGGCTG
* * *
28451146 CCAGAATAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGTCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
28451200 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
28451254 CCAGAAC
1 CCAGAAC
28451261 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:28452908 original size:26 final size:26
Alignment explanation
Indices: 28452872--28452981 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
28452862 CATGAAATTC
28452872 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28452898 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28452924 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
28452950 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
28452976 TTATCA
1 TTATCA
28452982 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28454253 original size:21 final size:23
Alignment explanation
Indices: 28454212--28454253 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28454202 GAAGTCGTTA
*
28454212 TATATTTGTATTATGAATTTGTG
1 TATATTTGTATAATGAATTTGTG
28454235 TATATTTG-ATAAT-AATTTG
1 TATATTTGTATAATGAATTTG
28454254 AATTGTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (23 bp):
TATATTTGTATAATGAATTTGTG
Found at i:28458491 original size:48 final size:48
Alignment explanation
Indices: 28458413--28458539 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 48
28458403 ATTGTGGGCT
* * * *
28458413 AGTGTAAGA-CATGCCTGGGACATGGCATCGGCCAT-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCC-TCATGATGAGAACC
* * * *
28458460 AGTGTAAGACCTTGTCTAGGATATGGCATCGGCCTCGGTGATGATAACC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTC-ATGATGAGAACC
28458509 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGACCATGTCTAGGACATGGCATCG
28458540 ACAACTTGCC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
47 10 0.15
48 20 0.30
49 37 0.55
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCATGATGAGAACC
Found at i:28465805 original size:46 final size:44
Alignment explanation
Indices: 28465752--28465920 Score: 155
Period size: 46 Copynumber: 3.7 Consensus size: 44
28465742 ATTGTGGGCT
*
28465752 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TATTA-GAGAGCA
*
28465798 AGTGTAAGACCATGTCTGGGACATGGCATCGG--TATTGAGACGAGTACT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTATT-AGA-GAG--CA
* * * **
28465846 AGTGTAAGACATATCAGGGACATGCATCAGCCT-TGGGACGTAAGCA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTATTAGA-G--AGCA
28465892 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
28465921 ACTACGGAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
45 6 0.06
46 50 0.49
47 27 0.26
48 20 0.19
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTATTAGAGAGCA
Found at i:28467382 original size:30 final size:29
Alignment explanation
Indices: 28467346--28467656 Score: 152
Period size: 30 Copynumber: 10.4 Consensus size: 29
28467336 GGTTGTCACC
*
28467346 ATCCCTTTTCATAATCTGATAGCTGAAGAT
1 ATCCCTTTTCATAAT-TGATAGCTGAAGCT
**
28467376 ATCCCTTTTCATAATTTGAT-TTTCGAAGCT
1 ATCCCTTTTCATAA-TTGATAGCT-GAAGCT
** * * * *
28467406 ATCTATTTTCATAATCCGAT-GTTCGTCA-CC
1 ATCCCTTTTCATAAT-TGATAGCT-G-AAGCT
* ** *
28467436 ATCCCTTTTCATAATTCGGTAGCCAAAGAT
1 ATCCCTTTTCATAATT-GATAGCTGAAGCT
*
28467466 ATCCCTTTTCATAATTCGATAGCCGAAGCT
1 ATCCCTTTTCATAATT-GATAGCTGAAGCT
* * *
28467496 ATCCCTTTTCATAATTTGAT-GGTCGTCA-CC
1 ATCCCTTTTCATAA-TTGATAGCT-G-AAGCT
* * *
28467526 ATCCCTTTTCATAATTGAT-GGTCGTTA-CC
1 ATCCCTTTTCATAATTGATAGCT-G-AAGCT
* * *
28467555 ATCCATTTTCATAATTTGATAGTTGAAGTT
1 ATCCCTTTTCATAA-TTGATAGCTGAAGCT
* * *
28467585 ATCCCTTTTCATTATTCAATAGTTGAAGCT
1 ATCCCTTTTCATAATT-GATAGCTGAAGCT
* * *
28467615 ATTCATTTTCATAATTCGATAG-TCGTAGCT
1 ATCCCTTTTCATAATT-GATAGCT-GAAGCT
28467645 ATCCCTTTTCAT
1 ATCCCTTTTCAT
28467657 TGGCCAGTGA
Statistics
Matches: 223, Mismatches: 43, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
29 35 0.16
30 180 0.81
31 8 0.04
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (29 bp):
ATCCCTTTTCATAATTGATAGCTGAAGCT
Found at i:28467493 original size:90 final size:91
Alignment explanation
Indices: 28467327--28467541 Score: 283
Period size: 90 Copynumber: 2.4 Consensus size: 91
28467317 CACGAAGTAA
**
28467327 AATCACGATGGTT-GTCACCATCCCTTTTCATAA-TCTGATAGCTGAAGATATCCCTTTTCATAA
1 AATC-CGAT-GTTCGTCACCATCCCTTTTCATAATTCTGATAGCCAAAGATATCCCTTTTCATAA
* *** *
28467390 TTTGATTTTCGAAGCTATCTATTTTCAT
64 TTCGATAGCCGAAGCTATCCATTTTCAT
*
28467418 AATCCGATGTTCGTCACCATCCCTTTTCATAATTC-GGTAGCCAAAGATATCCCTTTTCATAATT
1 AATCCGATGTTCGTCACCATCCCTTTTCATAATTCTGATAGCCAAAGATATCCCTTTTCATAATT
*
28467482 CGATAGCCGAAGCTATCCCTTTTCAT
66 CGATAGCCGAAGCTATCCATTTTCAT
** *
28467508 AATTTGATGGTCGTCACCATCCCTTTTCATAATT
1 AATCCGATGTTCGTCACCATCCCTTTTCATAATT
28467542 GATGGTCGTT
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
89 3 0.03
90 101 0.92
91 6 0.05
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (91 bp):
AATCCGATGTTCGTCACCATCCCTTTTCATAATTCTGATAGCCAAAGATATCCCTTTTCATAATT
CGATAGCCGAAGCTATCCATTTTCAT
Found at i:28467555 original size:29 final size:29
Alignment explanation
Indices: 28467496--28467570 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
28467486 AGCCGAAGCT
28467496 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAA-TTGATGGTCGTCACC
*
28467526 ATCCCTTTTCATAATTGATGGTCGTTACC
1 ATCCCTTTTCATAATTGATGGTCGTCACC
*
28467555 ATCCATTTTCATAATT
1 ATCCCTTTTCATAATT
28467571 TGATAGTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 29 0.67
30 14 0.33
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.43
Consensus pattern (29 bp):
ATCCCTTTTCATAATTGATGGTCGTCACC
Found at i:28467657 original size:60 final size:60
Alignment explanation
Indices: 28467346--28467656 Score: 231
Period size: 60 Copynumber: 5.2 Consensus size: 60
28467336 GGTTGTCACC
* * * **
28467346 ATCCCTTTTCATAA-TCTGATAG-CTGAAGATATCCCTTTTCATAATTTGATTTTCGAAGCT
1 ATCCCTTTTCATAATTC-GATAGTC-GAAGCTATCCATTTTCATAATTCGATAGTCGAAGCT
** * * * * * * * *
28467406 ATCTATTTTCATAATCCGAT-GTTCGTCA-CCATCCCTTTTCATAATTCGGTAGCCAAAGAT
1 ATCCCTTTTCATAATTCGATAG-TCG-AAGCTATCCATTTTCATAATTCGATAGTCGAAGCT
* * * * * *
28467466 ATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCGTCA-CC
1 ATCCCTTTTCATAATTCGATAGTCGAAGCTATCCATTTTCATAATTCGATAGTCG-AAGCT
* * * * * *
28467526 ATCCCTTTTCATAATT-GATGGTCGTTA-CCATCCATTTTCATAATTTGATAGTTGAAGTT
1 ATCCCTTTTCATAATTCGATAGTCG-AAGCTATCCATTTTCATAATTCGATAGTCGAAGCT
* * * * *
28467585 ATCCCTTTTCATTATTCAATAGTTGAAGCTATTCATTTTCATAATTCGATAGTCGTAGCT
1 ATCCCTTTTCATAATTCGATAGTCGAAGCTATCCATTTTCATAATTCGATAGTCGAAGCT
28467645 ATCCCTTTTCAT
1 ATCCCTTTTCAT
28467657 TGGCCAGTGA
Statistics
Matches: 192, Mismatches: 48, Indels: 22
0.73 0.18 0.08
Matches are distributed among these distances:
58 1 0.01
59 47 0.24
60 139 0.72
61 5 0.03
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (60 bp):
ATCCCTTTTCATAATTCGATAGTCGAAGCTATCCATTTTCATAATTCGATAGTCGAAGCT
Found at i:28473222 original size:29 final size:29
Alignment explanation
Indices: 28473189--28473319 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
28473179 TGACGAGATC
*
28473189 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
28473218 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
28473247 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
28473276 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
28473305 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
28473320 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:28481184 original size:29 final size:29
Alignment explanation
Indices: 28481151--28481281 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
28481141 TGACGAGATC
*
28481151 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
28481180 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
28481209 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
28481238 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
28481267 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
28481282 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:28485833 original size:42 final size:43
Alignment explanation
Indices: 28485727--28485843 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 43
28485717 TACCGTGTCA
* * * *
28485727 ATGCCATATCCCGGATATGGTCTTACATGAAAT-ATCATATCG
1 ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
* * * *
28485769 ATTCCATGT-CCTGACATGGTCTTATACGAAATCAT-ATACCG
1 ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
*
28485810 ATGCCATATCCCAGATATGGTCTTATACGGAATC
1 ATGCCATATCCCAGATATGGTCTTATACGAAATC
28485844 TCGGTAGTCC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 31 0.51
42 30 0.49
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (43 bp):
ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
Found at i:28489905 original size:43 final size:43
Alignment explanation
Indices: 28489851--28489971 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
28489841 ATCGAGATGT
* **
28489851 GATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TATTGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTA-AAA
*
28489894 GATTACGTGTAAGACCATGTCTAGGACATTGGCATTGTTAAAA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAAAA
* * *
28489937 GATTTCGTGTAAGATCC-TGTCTGGGATAGTGGCAT
1 GATTACGTGTAAGA-CCATGTCTGGGACATTGGCAT
28489972 CGATGTGTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 64 0.94
44 4 0.06
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAAAA
Found at i:28494669 original size:40 final size:39
Alignment explanation
Indices: 28494504--28494687 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
28494494 AAATTGAATG
* * *
28494504 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
28494544 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
28494584 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
28494624 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
28494663 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
28494688 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:28494712 original size:80 final size:81
Alignment explanation
Indices: 28494544--28494732 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
28494534 GCTGGAAATT
* * * *
28494544 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
28494609 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
28494625 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
28494688 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
28494704 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
28494733 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:28511507 original size:40 final size:39
Alignment explanation
Indices: 28511342--28511525 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
28511332 AAATTGAATG
* * *
28511342 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
28511382 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
28511422 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
28511462 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
28511501 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
28511526 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:28511550 original size:80 final size:81
Alignment explanation
Indices: 28511382--28511570 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
28511372 GCTGGAAATT
* * * *
28511382 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
28511447 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
28511463 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
28511526 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
28511542 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
28511571 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:28514181 original size:46 final size:46
Alignment explanation
Indices: 28514114--28514289 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
28514104 TGTAACCCGC
*
28514114 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
28514160 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
28514210 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
28514253 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28514290 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:28514229 original size:93 final size:93
Alignment explanation
Indices: 28514121--28514292 Score: 326
Period size: 93 Copynumber: 1.8 Consensus size: 93
28514111 CGCCCATAAG
*
28514121 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28514186 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28514214 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28514279 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28514293 TCAACCATCC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28518089 original size:28 final size:28
Alignment explanation
Indices: 28518024--28518124 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28518014 ATAGTGAATC
*
28518024 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
28518053 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28518081 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
28518111 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28518125 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28524458 original size:93 final size:93
Alignment explanation
Indices: 28524346--28524517 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
28524336 CGCCCATAAG
*
28524346 CGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
28524410 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
28524439 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28524504 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28524518 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
93 74 0.97
94 2 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28524513 original size:46 final size:47
Alignment explanation
Indices: 28524339--28524514 Score: 220
Period size: 46 Copynumber: 3.8 Consensus size: 47
28524329 TGTAACCCGC
* *
28524339 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
* *
28524385 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCAT
*
28524435 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
*
28524478 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28524515 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.54
47 31 0.28
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
Found at i:28529526 original size:50 final size:50
Alignment explanation
Indices: 28529369--28529602 Score: 321
Period size: 50 Copynumber: 4.7 Consensus size: 50
28529359 GGTGCCAACA
* * * * * **
28529369 CCATGTCCCGGACATGGTCTTACACTAGCTCACACA--TCAAAGTTGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGATGCCGATG
* * * *
28529417 CCATGTCCCAGAAATGGTCTTACACTAGCTCTTAT-TATCGGTGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGATGCCGATG
*
28529466 CCATGTCCCAGATATGGTCTTACACTAGCTCTCATATCTCGATGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGATGCCGATG
* *
28529516 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCCAATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGATGCCGATG
28529566 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT
28529603 ATCCCTAGCA
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
48 30 0.18
49 40 0.24
50 96 0.58
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGATGCCGATG
Found at i:28535985 original size:50 final size:50
Alignment explanation
Indices: 28535875--28536044 Score: 199
Period size: 50 Copynumber: 3.4 Consensus size: 50
28535865 GGTGCCAACA
* * * **
28535875 CCATGTCCCGGACATGGTCTTACACTGGCTCACTC-ATC-AAACTCGATG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCTCTATCGAGGCTCGATG
*
28535923 CCATGTCCCAGACATGGTCTTACACTGACTCTCGCATATCGAGGCT-GATG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCTC-TATCGAGGCTCGATG
*
28535973 CCATGTCCCAGACATGGTCTTACACT-AGCTCTTATCTATCG-GTG-TCGATG
1 CCATGTCCCAGACATGGTCTTACACTGA-CTC-TCTCTATCGAG-GCTCGATG
28536023 CCATGTCCCAGACATGGTCTTA
1 CCATGTCCCAGACATGGTCTTA
28536045 TACTAGCTCT
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
48 31 0.29
49 3 0.03
50 68 0.64
51 5 0.05
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACACTGACTCTCTCTATCGAGGCTCGATG
Found at i:28536062 original size:100 final size:98
Alignment explanation
Indices: 28535875--28536062 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 98
28535865 GGTGCCAACA
* *
28535875 CCATGTCCCGGACATGGTCTTACACTGGCTCACTCATCAAACTCGATGCCATGTCCCAGACATGG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACTCATCAAACTCGATGCCATGTCCCAGACATGG
*
28535940 TCTTACACTGACTCTCGCATATCGAGGCTGATG
66 TCTTACACTGACTCTCACATATCGAGGCTGATG
****
28535973 CCATGTCCCAGACATGGTCTTACACTAGCTCTTA-TCTATCGGTGTCGATGCCATGTCCCAGACA
1 CCATGTCCCAGACATGGTCTTACACTAGCTC--ACTC-ATCAAACTCGATGCCATGTCCCAGACA
* *
28536037 TGGTCTTATACT-AGCTCTCATATATC
63 TGGTCTTACACTGA-CTCTCACATATC
28536063 CCTAGCATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
98 29 0.38
99 3 0.04
100 45 0.58
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (98 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCACTCATCAAACTCGATGCCATGTCCCAGACATGG
TCTTACACTGACTCTCACATATCGAGGCTGATG
Found at i:28539478 original size:47 final size:47
Alignment explanation
Indices: 28539409--28539502 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
28539399 TAAAGTGCTT
*
28539409 AATTGCCATGACTTGTTAAATGAAAGGTCCTTATGTTGTAATTAGAC
1 AATTGCCATGACTTATTAAATGAAAGGTCCTTATGTTGTAATTAGAC
28539456 AATTGCCATGACTTATTAAATGAAAGGTCCTTATGTTGTAATTAGAC
1 AATTGCCATGACTTATTAAATGAAAGGTCCTTATGTTGTAATTAGAC
28539503 CATGGATAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (47 bp):
AATTGCCATGACTTATTAAATGAAAGGTCCTTATGTTGTAATTAGAC
Found at i:28540556 original size:43 final size:43
Alignment explanation
Indices: 28540449--28540570 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
28540439 ACATTGGGTT
* * *
28540449 ATCGAGATGTGATTACATGTAAGACCATGTCTGTGACATTGGC
1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACAGTGGC
* * * *
28540492 ATC-ATTAAT-AGATTTCGTGTAAGACCCTGTCTGGGACAGTGGC
1 ATCGA-T-ATGTGATTACATGTAAGACCATGTCTGGGACAGTGGC
* *
28540535 ATCGATATGTGATAACATGTAAGACCATATCTGGGA
1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGA
28540571 TATGGAATTG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
42 3 0.05
43 56 0.90
44 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (43 bp):
ATCGATATGTGATTACATGTAAGACCATGTCTGGGACAGTGGC
Found at i:28545355 original size:15 final size:15
Alignment explanation
Indices: 28545337--28545395 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
28545327 ATATTTAATG
28545337 ATATAATATATAAAA
1 ATATAATATATAAAA
*
28545352 ATAT-ATTTATAAGAA
1 ATATAATATATAA-AA
28545367 CA-ATAATTATATAAAA
1 -ATATAA-TATATAAAA
*
28545383 ATATAAAATATAA
1 ATATAATATATAA
28545396 TGGTTTAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 7 0.19
15 15 0.42
16 8 0.22
17 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATATAATATATAAAA
Found at i:28545357 original size:17 final size:17
Alignment explanation
Indices: 28545337--28545394 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
28545327 ATATTTAATG
28545337 ATATAATATATAAAAAT
1 ATATAATATATAAAAAT
* *
28545354 ATAT--T-TATAAGAAC
1 ATATAATATATAAAAAT
28545368 A-ATAATTATATAAAAAT
1 ATATAA-TATATAAAAAT
*
28545385 ATAAAATATA
1 ATATAATATA
28545395 ATGGTTTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
13 2 0.06
14 8 0.26
15 1 0.03
16 1 0.03
17 16 0.52
18 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
ATATAATATATAAAAAT
Found at i:28545705 original size:23 final size:23
Alignment explanation
Indices: 28545691--28545812 Score: 88
Period size: 25 Copynumber: 4.9 Consensus size: 23
28545681 AAATGACATA
28545691 ATAATATAAAATAAATATAATAT
1 ATAATATAAAATAAATATAATAT
*
28545714 ATAATATAAAAGTATATATGTGAA-A-
1 ATAATATAAAA-TA-A-ATAT-AATAT
28545739 ATAATATAATATATATAA-ATAATAT
1 ATAATATAA-A-ATA-AATATAATAT
28545764 GAGTAATATATAAAATAATTATATAATAT
1 -A-T-A-ATATAAAATAA--ATATAATAT
*
28545793 ATAATATAAAATAAAAATAA
1 ATAATATAAAATAAATATAA
28545813 AGCAAATAAC
Statistics
Matches: 81, Mismatches: 3, Indels: 30
0.71 0.03 0.26
Matches are distributed among these distances:
23 18 0.22
24 4 0.05
25 22 0.27
26 12 0.15
27 8 0.10
28 4 0.05
29 13 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAATATAAAATAAATATAATAT
Found at i:28545774 original size:20 final size:18
Alignment explanation
Indices: 28545660--28545801 Score: 89
Period size: 20 Copynumber: 7.4 Consensus size: 18
28545650 CAATATATAG
*
28545660 ATAAA-AATATTTAATAGT
1 ATAAATAATATATAATA-T
28545678 ATAAAATGACATA-ATAATAT
1 AT-AAAT-A-ATATATAATAT
28545698 A-AAATAA-ATATAATAT
1 ATAAATAATATATAATAT
*
28545714 ATAATATAAAAGTAT-ATAT
1 ATAA-ATAATA-TATAATAT
*
28545733 GTGAAAATAATATA-ATATAT
1 AT--AAATAATATATA-ATAT
28545753 ATAAATAATATGAGTAATAT
1 ATAAATAATAT-A-TAATAT
28545773 ATAAAATAATTATATAATAT
1 AT-AAATAA-TATATAATAT
28545793 ATAATATAA
1 ATAA-ATAA
28545802 AATAAAAATA
Statistics
Matches: 101, Mismatches: 4, Indels: 36
0.72 0.03 0.26
Matches are distributed among these distances:
15 1 0.01
16 9 0.09
17 3 0.03
18 19 0.19
19 14 0.14
20 33 0.33
21 16 0.16
22 6 0.06
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (18 bp):
ATAAATAATATATAATAT
Found at i:28548127 original size:205 final size:205
Alignment explanation
Indices: 28547768--28548145 Score: 693
Period size: 205 Copynumber: 1.8 Consensus size: 205
28547758 AAATCTGCTT
*
28547768 CTTCGATTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
28547833 ATGAAAGCCAAATCAACTATGTCTTCGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 ATGAAAGCCAAATCAACTATGTCTTCGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
*
28547898 GGATCTCCTTCAGTATAAACATCTGAAGGTGAGATCTGCTATGTATTTGCTCCCTGTCGAAGTGG
131 GGATCTCCTTCAGTATAAACATCTGAAGGTGAGATCCGCTATGTATTTGCTCCCTGTCGAAGTGG
28547963 AGATGCTAGA
196 AGATGCTAGA
*
28547973 CTTCGATTTGTTCTCTGACGATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
28548038 GTGAAAGCCAAATCAGCTATGTCTTCGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 ATGAAAGCCAAATCAACTATGTCTTCGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* *
28548103 GGATCTTCTTCAGTATAGACATCTGAAGGTGAGATCCGCTATG
131 GGATCTCCTTCAGTATAAACATCTGAAGGTGAGATCCGCTATG
28548146 CTGCGGTCTA
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
205 166 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
ATGAAAGCCAAATCAACTATGTCTTCGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTCCTTCAGTATAAACATCTGAAGGTGAGATCCGCTATGTATTTGCTCCCTGTCGAAGTGG
AGATGCTAGA
Found at i:28550755 original size:20 final size:20
Alignment explanation
Indices: 28550727--28550772 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
28550717 TAAGCTTCGA
*
28550727 TAATTGCATGTGAATTTAGT
1 TAATAGCATGTGAATTTAGT
28550747 TAATAGCATGTGAATTTAGT
1 TAATAGCATGTGAATTTAGT
28550767 TAATAG
1 TAATAG
28550773 GACTTATGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (20 bp):
TAATAGCATGTGAATTTAGT
Found at i:28553344 original size:47 final size:47
Alignment explanation
Indices: 28553291--28554241 Score: 1645
Period size: 47 Copynumber: 20.3 Consensus size: 47
28553281 ACAAGGTATG
* * * *
28553291 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
* *
28553338 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553385 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553432 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
*
28553479 TATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
* *
28553526 TATATGTGATAAGGCCGAAT-GCCAACGTGATGAATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553572 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553619 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553666 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553713 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553760 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553807 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553854 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28553901 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
*
28553948 TATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
* *
28553995 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
28554042 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
* * *
28554089 TATATGTGATAAGGCCGAATGGCCAATGTGATGAACGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
* * * * * * * *
28554136 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
* * *
28554183 TATATGTGATAAGGCCGAAT-GCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
*
28554229 TAAATGTGATAAG
1 TATATGTGATAAG
28554242 TCCCGAAGGG
Statistics
Matches: 875, Mismatches: 28, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
46 80 0.09
47 795 0.91
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTA
Found at i:28556164 original size:40 final size:40
Alignment explanation
Indices: 28555907--28556155 Score: 403
Period size: 40 Copynumber: 6.2 Consensus size: 40
28555897 AGTTATATAG
* *
28555907 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTGATGT--TATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCT-A-GTAATGTAT
28555947 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
*
28555987 CCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
28556027 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
*
28556067 CTGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
* *
28556107 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
*
28556147 CCAGGCTAA
1 CCGGGCTAA
28556156 ACCTCGAAGG
Statistics
Matches: 198, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 195 0.98
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
Found at i:28556268 original size:29 final size:28
Alignment explanation
Indices: 28556187--28556286 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
28556177 GAGTGATGAG
* * * *
28556187 GCACTGTGTGTGCAAGTTCTTCAACTGA
1 GCACTATGTGTGCGAGTTCTTTAATTGA
* **
28556215 GCACTATGCGTGCGAGATT-GGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTTAATTGA
*
28556243 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTCTTTAATTGA
28556272 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
28556287 AATCAGTCAG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 35 0.60
29 23 0.40
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGTTCTTTAATTGA
Found at i:28558366 original size:2 final size:2
Alignment explanation
Indices: 28558359--28558385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28558349 GTTAATGCTG
28558359 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28558386 CAACGATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28559650 original size:22 final size:22
Alignment explanation
Indices: 28559622--28559697 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
28559612 AAGTGTATAT
28559622 ATGTGATAAGGCTGAGTGGCCA
1 ATGTGATAAGGCTGAGTGGCCA
* ***
28559644 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCTG--AGTGGCCA
*
28559668 TATGTGATAAGGCCGAGTGGCCA
1 -ATGTGATAAGGCTGAGTGGCCA
28559691 ATGTGAT
1 ATGTGAT
28559698 GAATGTGAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 16 0.40
23 8 0.20
24 8 0.20
25 8 0.20
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCTGAGTGGCCA
Found at i:28559660 original size:47 final size:47
Alignment explanation
Indices: 28559584--28560195 Score: 999
Period size: 47 Copynumber: 13.0 Consensus size: 47
28559574 AAGGCCTAAT
*
28559584 GGCCGATTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
28559631 GGCTGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
28559678 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
28559725 GGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
28559772 GGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
28559819 GGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
28559866 GGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
28559913 GGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
28559960 GGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * *
28560007 GGCCGAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * *
28560054 GGCCGAATGACCGATGTGATGAATGTGAAAGTGTATATATGAGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * * * *
28560101 GACCTAATGGCCGATGTGATGGATGTGAAGGTGTATATATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * *
28560148 GGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATAAATGTGATAA
1 GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
28560195 G
1 G
28560196 TCCCGAAGGG
Statistics
Matches: 543, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 543 1.00
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (47 bp):
GGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:28560026 original size:22 final size:22
Alignment explanation
Indices: 28559998--28560073 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
28559988 AAGTGTATAT
28559998 ATGTGATAAGGCCGAATGACCG
1 ATGTGATAAGGCCGAATGACCG
* * ***
28560020 ATGTGATGAATG-TGAAAGTGTATAT
1 ATGTGAT-AAGGCCG-AA-TG-ACCG
28560045 ATGTGATAAGGCCGAATGACCG
1 ATGTGATAAGGCCGAATGACCG
28560067 ATGTGAT
1 ATGTGAT
28560074 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 16 0.41
23 7 0.18
24 7 0.18
25 9 0.23
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGACCG
Found at i:28571145 original size:23 final size:23
Alignment explanation
Indices: 28571131--28571251 Score: 86
Period size: 24 Copynumber: 4.9 Consensus size: 23
28571121 AAATGACATA
28571131 ATAATATAAAATAAATATAATAT
1 ATAATATAAAATAAATATAATAT
* *
28571154 ATAATATAAAGTATATATGTGAA-A-
1 ATAATATAAA--ATAAATAT-AATAT
28571178 ATAATATAATATATATAA-ATAATAT
1 ATAATATAA-A-ATA-AATATAATAT
28571203 GAGTAATATATAAATAATTATATAATAT
1 -A-TAATATA-AAATAA--ATATAATAT
*
28571231 ATAATATAAAAATAAAAATAA
1 ATAATAT-AAAATAAATATAA
28571252 AGCAAATAAC
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
23 12 0.15
24 20 0.25
25 10 0.13
26 18 0.23
27 11 0.14
28 8 0.10
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAATATAAAATAAATATAATAT
Found at i:28577501 original size:40 final size:40
Alignment explanation
Indices: 28577447--28577524 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
28577437 CGGATGTAAC
28577447 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
28577487 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATA
28577525 TTCTTTTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (40 bp):
AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:28580049 original size:15 final size:15
Alignment explanation
Indices: 28580029--28580059 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28580019 TTATTTAAAG
28580029 AAGGGCTATATCTGA
1 AAGGGCTATATCTGA
28580044 AAGGGCTATATCTGA
1 AAGGGCTATATCTGA
28580059 A
1 A
28580060 TTATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
AAGGGCTATATCTGA
Found at i:28582706 original size:2 final size:2
Alignment explanation
Indices: 28582658--28582689 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
28582648 ATATTTATTT
28582658 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
28582690 CAAAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28595054 original size:40 final size:40
Alignment explanation
Indices: 28594995--28595199 Score: 200
Period size: 40 Copynumber: 5.2 Consensus size: 40
28594985 CAATTGAATG
* * * *
28594995 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * *
28595035 ATATCCGGGTTAAGACCCGAAGGCA-TTGTGCTAGTGA--
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
** * **
28595072 CCATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
28595112 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
28595152 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
28595192 ATATCCGG
1 ATATCCGG
28595200 TTGTATTCCG
Statistics
Matches: 138, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
37 22 0.16
38 8 0.06
39 10 0.07
40 98 0.71
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:28595091 original size:77 final size:80
Alignment explanation
Indices: 28594997--28595184 Score: 229
Period size: 77 Copynumber: 2.4 Consensus size: 80
28594987 ATTGAATGAT
* * * * * *
28594997 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCA-T
1 ATCCGGGCTAAGACCCGAAGGCATTCATGCAAGTAATTAAATCCGGGCTAAGACCCGAAGGCATT
*
28595061 TGTGCTAGT-G-ACC
66 TGTGCAAGTCGTACC
* ** *
28595074 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCATGCAAGTAATTAAATCCGGGCTAAGACCCGAAGGCATT
* *
28595139 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGTACC
*
28595154 ATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 ATCCGGGCTAAGACCCGAAGGCATTCATGCA
28595185 TGTGGTTATA
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
77 53 0.56
78 9 0.09
79 1 0.01
80 32 0.34
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCATGCAAGTAATTAAATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGTACC
Found at i:28603142 original size:79 final size:80
Alignment explanation
Indices: 28603059--28603210 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
28603049 CCGGGTTAAG
* *
28603059 ACCCGAAGGCAATTGTGCTAGT-GACCCATCCGGGCTAAG-ACTCGAAGGCATTCGTGCAAGTTG
1 ACCCGAAGGCAATTGTGCAAGTCGACCCATCCGGGCTAAGAAC-CGAAGGCATTCGTGCAAGTGG
28603122 TTAAATCCGAGCTAAT
65 TTAAATCCGAGCTAAT
* ** * *
28603138 ACCCGAAGGCATTTGTGCAAGTCGTTCTATCCGGGCTAAGAACCGAAGGCATTCGTGCATGTGGT
1 ACCCGAAGGCAATTGTGCAAGTCGACCCATCCGGGCTAAGAACCGAAGGCATTCGTGCAAGTGGT
*
28603203 TATATCCG
66 TAAATCCG
28603211 GTTGTATTCC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 20 0.32
80 41 0.65
81 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ACCCGAAGGCAATTGTGCAAGTCGACCCATCCGGGCTAAGAACCGAAGGCATTCGTGCAAGTGGT
TAAATCCGAGCTAAT
Found at i:28603145 original size:40 final size:40
Alignment explanation
Indices: 28603007--28603211 Score: 173
Period size: 40 Copynumber: 5.2 Consensus size: 40
28602997 ATTGAATGAC
* * ** **
28603007 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAA-TAATTAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGC-AAGTCGTTAT
* * ****
28603047 ATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGT-GACCC
1 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTCGTTAT
* * *
28603086 ATCCGGGCTAAGACTCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAT
* * * *
28603126 ATCCGAGCTAATACCCGAAGGCATTTGTGCAAGTCGTTCT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAT
* * *
28603166 ATCCGGGCTAAGAACCGAAGGCATTCGTGCATGTGGTTAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAT
28603206 ATCCGG
1 ATCCGG
28603212 TTGTATTCCG
Statistics
Matches: 130, Mismatches: 31, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
38 3 0.02
39 28 0.22
40 96 0.74
41 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAT
Found at i:28604658 original size:47 final size:47
Alignment explanation
Indices: 28604581--28604696 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 47
28604571 GGGTGTTACA
* * *
28604581 GAAAGTGTATATATGAGATAAGACCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGACCGAATGGCCAATGTGATGAATGT
* *
28604628 GAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGT
1 GAAAGTGTATATATGTGATAAGACCGAATGGCCAATGTGATGAATGT
28604675 GAAAGTGTATA-AGTGTGATAAG
1 GAAAGTGTATATA-TGTGATAAG
28604697 TCCCGAAGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.02
47 62 0.98
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGACCGAATGGCCAATGTGATGAATGT
Found at i:28607661 original size:3 final size:3
Alignment explanation
Indices: 28607653--28607686 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28607643 CTAATTGAAT
28607653 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
28607687 ATTCTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:28610112 original size:17 final size:17
Alignment explanation
Indices: 28610090--28610123 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28610080 ATTAACAAGT
28610090 GACACACGGCCGTGTGC
1 GACACACGGCCGTGTGC
28610107 GACACACGGCCGTGTGC
1 GACACACGGCCGTGTGC
28610124 TTCATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12
Consensus pattern (17 bp):
GACACACGGCCGTGTGC
Found at i:28612133 original size:39 final size:39
Alignment explanation
Indices: 28612079--28612194 Score: 205
Period size: 39 Copynumber: 3.0 Consensus size: 39
28612069 TTCAATGATG
*
28612079 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
28612118 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* *
28612157 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
28612195 ATATGTCCAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:28612221 original size:39 final size:39
Alignment explanation
Indices: 28612079--28612231 Score: 130
Period size: 39 Copynumber: 3.9 Consensus size: 39
28612069 TTCAATGATG
* ** * * *
28612079 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
** * * *
28612118 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
* *
28612157 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
* * *
28612196 TATGTCCAGG-C-TAAAGTCCCACAGGCTTCGAGCTGG
1 TATATCC-GGACTTAAAGT-CCACAGGCTACGTGCTGG
28612232 TATTATACCG
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.05
39 96 0.93
40 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCACAGGCTACGTGCTGGAAA
Found at i:28612221 original size:78 final size:78
Alignment explanation
Indices: 28612079--28612222 Score: 184
Period size: 78 Copynumber: 1.8 Consensus size: 78
28612069 TTCAATGATG
* * * ** *
28612079 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGC
1 TATATCCGAACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCACAGGC
28612144 TATGTGCTGGAAT
66 TATGTGCTGGAAT
* *
28612157 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCAGG-C-TAAAGTCCCACAG
1 TATATCCGAACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTTAAAGT-CCACAG
28612220 GCT
64 GCT
28612223 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
77 4 0.07
78 50 0.89
79 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (78 bp):
TATATCCGAACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCACAGGC
TATGTGCTGGAAT
Found at i:28612231 original size:78 final size:78
Alignment explanation
Indices: 28612079--28612242 Score: 183
Period size: 78 Copynumber: 2.1 Consensus size: 78
28612069 TTCAATGATG
* * * * ** *
28612079 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGC
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCACAGGC
*
28612144 TATGTGCTGGAAT
66 TATGAGCTGGAAT
*
28612157 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCAGG-C-TAAAGTCCCACAG
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTTAAAGT-CCACAG
*
28612220 GCT-TCGAGCTGGTAT
64 GCTAT-GAGCTGGAAT
28612235 TATA-CCGG
1 TATATCCGG
28612243 GTTTAAATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
77 9 0.12
78 62 0.85
79 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (78 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCACAGGC
TATGAGCTGGAAT
Found at i:28615940 original size:25 final size:27
Alignment explanation
Indices: 28615903--28615955 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28615893 TCAAACATGC
28615903 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
28615929 ATTTTGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
28615955 A
1 A
28615956 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:28617470 original size:26 final size:26
Alignment explanation
Indices: 28617440--28617547 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28617430 TGAAATGCCC
28617440 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28617466 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28617492 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28617518 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28617544 ATCA
1 ATCA
28617548 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28621841 original size:39 final size:39
Alignment explanation
Indices: 28621787--28621898 Score: 197
Period size: 39 Copynumber: 2.9 Consensus size: 39
28621777 TTCAGTGATG
*
28621787 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
28621826 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* *
28621865 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCT
28621899 AGAAATATGT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:28621928 original size:39 final size:39
Alignment explanation
Indices: 28621787--28621930 Score: 139
Period size: 39 Copynumber: 3.7 Consensus size: 39
28621777 TTCAGTGATG
* * * * * *
28621787 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTGAAGGTCCGCAGGCTACGTGCTAGAAA
* * * * *
28621826 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTGAAGGTCCGCAGGCTACGTGCTAGAAA
*
28621865 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTAGAAA
1 TATATCCGGACTGAAGGTCCGCAGGCTACGTGCTAGAAA
*
28621904 TATGTCCAGG-CTGAA-GTCCTGCAGGCT
1 TATATCC-GGACTGAAGGTCC-GCAGGCT
28621931 TCGAGCTGGT
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
38 4 0.04
39 90 0.94
40 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTGAAGGTCCGCAGGCTACGTGCTAGAAA
Found at i:28621928 original size:78 final size:78
Alignment explanation
Indices: 28621787--28621930 Score: 184
Period size: 78 Copynumber: 1.8 Consensus size: 78
28621777 TTCAGTGATG
* * * * * *
28621787 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGC
1 TATATCCGAACTTAAGGTCCGCAGGCTACGTGCTAGAAATATATCCGGACTGAGAGTCCGCAGGC
28621852 TATGTGCTGGAAT
66 TATGTGCTGGAAT
* *
28621865 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTAGAAATATGTCCAGG-CTGA-AGTCCTGCAG
1 TATATCCGAACTTAAGGTCCGCAGGCTACGTGCTAGAAATATATCC-GGACTGAGAGTCC-GCAG
28621928 GCT
64 GCT
28621931 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
77 4 0.07
78 50 0.89
79 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (78 bp):
TATATCCGAACTTAAGGTCCGCAGGCTACGTGCTAGAAATATATCCGGACTGAGAGTCCGCAGGC
TATGTGCTGGAAT
Found at i:28621939 original size:78 final size:78
Alignment explanation
Indices: 28621787--28621950 Score: 183
Period size: 78 Copynumber: 2.1 Consensus size: 78
28621777 TTCAGTGATG
* * * * * * *
28621787 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGC
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTAGAAATATATCCGGACTGAGAGTCCGCAGGC
*
28621852 TATGTGCTGGAAT
66 TATGAGCTGGAAT
*
28621865 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTAGAAATATGTCCAGG-CTGA-AGTCCTGCAG
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTAGAAATATATCC-GGACTGAGAGTCC-GCAG
*
28621928 GCT-TCGAGCTGGTAT
64 GCTAT-GAGCTGGAAT
28621943 TATA-CCGG
1 TATATCCGG
28621951 GTTTAAATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
77 9 0.12
78 62 0.85
79 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (78 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTAGAAATATATCCGGACTGAGAGTCCGCAGGC
TATGAGCTGGAAT
Found at i:28626512 original size:31 final size:31
Alignment explanation
Indices: 28626474--28626571 Score: 146
Period size: 31 Copynumber: 3.2 Consensus size: 31
28626464 ATTTTCGTGT
28626474 ATCCGATAATATTCCAAGTGTTCAATGGGTA
1 ATCCGATAATATTCCAAGTGTTCAATGGGTA
* *
28626505 ATCCGATAATATTCCAATTGTTCAACT-TGT-
1 ATCCGATAATATTCCAAGTGTTCAA-TGGGTA
*
28626535 ATCCGATAATATTCCAAGTGTTCAACGGGTA
1 ATCCGATAATATTCCAAGTGTTCAATGGGTA
28626566 ATCCGA
1 ATCCGA
28626572 AGAGTATGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 26 0.44
31 32 0.54
32 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (31 bp):
ATCCGATAATATTCCAAGTGTTCAATGGGTA
Found at i:28626541 original size:30 final size:31
Alignment explanation
Indices: 28626470--28626560 Score: 141
Period size: 30 Copynumber: 3.0 Consensus size: 31
28626460 AAAAATTTTC
28626470 GTGTATCCGATAATATTCCAAGTGTTCAA-T
1 GTGTATCCGATAATATTCCAAGTGTTCAACT
* *
28626500 GGGTAATCCGATAATATTCCAATTGTTCAACT
1 GTGT-ATCCGATAATATTCCAAGTGTTCAACT
28626532 -TGTATCCGATAATATTCCAAGTGTTCAAC
1 GTGTATCCGATAATATTCCAAGTGTTCAAC
28626561 GGGTAATCCG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
30 28 0.51
31 26 0.47
32 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (31 bp):
GTGTATCCGATAATATTCCAAGTGTTCAACT
Found at i:28633368 original size:48 final size:48
Alignment explanation
Indices: 28633310--28633407 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
28633300 GTGGCTTGGG
*
28633310 ACATGCCCGTGTGGGCAGGCTGTGTGGTCACACACGCCCGTGTCCCTA
1 ACATGCCCGTGTGGGCAGGCCGTGTGGTCACACACGCCCGTGTCCCTA
**
28633358 ACATGCCCGTGTGGGCAGGCCGTGTGGTCGTACACGCCCGTGTCCCTA
1 ACATGCCCGTGTGGGCAGGCCGTGTGGTCACACACGCCCGTGTCCCTA
28633406 AC
1 AC
28633408 CCATGTAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.14, C:0.34, G:0.32, T:0.20
Consensus pattern (48 bp):
ACATGCCCGTGTGGGCAGGCCGTGTGGTCACACACGCCCGTGTCCCTA
Found at i:28636525 original size:21 final size:21
Alignment explanation
Indices: 28636479--28636525 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
28636469 GTATTTAAAT
* *
28636479 TTTTAATGATAGATCATGAAG
1 TTTTAATGATAAATCATCAAG
*
28636500 GTTTAATGATAAAT-ATACAAG
1 TTTTAATGATAAATCAT-CAAG
28636521 TTTTA
1 TTTTA
28636526 TAAAGTGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTTAATGATAAATCATCAAG
Found at i:28637232 original size:22 final size:22
Alignment explanation
Indices: 28637172--28637258 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
28637162 GCTTACTTTT
* * *
28637172 TTCAGCTCATTGGAGCTTACCG
1 TTCAGCTCAATAGAGCTTACAG
* *
28637194 TTTTAGCTC-GTATGAGCTTACAG
1 -TTCAGCTCAATA-GAGCTTACAG
* *
28637217 TTCAGCTTAATAGAGCTTACTG
1 TTCAGCTCAATAGAGCTTACAG
*
28637239 TTCAGCTCGATAGAGCTTAC
1 TTCAGCTCAATAGAGCTTAC
28637259 CGTTTTGACT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
22 34 0.65
23 18 0.35
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (22 bp):
TTCAGCTCAATAGAGCTTACAG
Found at i:28640052 original size:14 final size:14
Alignment explanation
Indices: 28640022--28640447 Score: 196
Period size: 14 Copynumber: 30.4 Consensus size: 14
28640012 GATAATTTGT
*
28640022 ATCTATGAACTTC-C
1 ATCTATGAA-TCCAC
*
28640036 ATCTATGATTCCAC
1 ATCTATGAATCCAC
28640050 ATCTATGAAT-CAGC
1 ATCTATGAATCCA-C
* **
28640064 ATGTA-GAAATTTAC
1 ATCTATG-AATCCAC
28640078 ATCTATGAATCCAC
1 ATCTATGAATCCAC
**
28640092 ATCTATGAATCTGC
1 ATCTATGAATCCAC
*
28640106 ATATATGAATCCAC
1 ATCTATGAATCCAC
* **
28640120 GTCTATGAATCTGC
1 ATCTATGAATCCAC
* *
28640134 ATATATGAATCTAC
1 ATCTATGAATCCAC
* * *
28640148 GTGTATGAATCCAT
1 ATCTATGAATCCAC
* ***
28640162 ATCTATTAATCTGT
1 ATCTATGAATCCAC
*
28640176 ATCTATGAGTCCAC
1 ATCTATGAATCCAC
* *
28640190 ATCTATGCATCCTC
1 ATCTATGAATCCAC
* * *
28640204 ATGTATGAATTCTC
1 ATCTATGAATCCAC
* *
28640218 ATCTATAAATCTAC
1 ATCTATGAATCCAC
* ***
28640232 ATATATGAATTTGC
1 ATCTATGAATCCAC
***
28640246 ATCTATGAATCTGT
1 ATCTATGAATCCAC
28640260 ATCTATGAATCCAC
1 ATCTATGAATCCAC
**
28640274 ATCTATGAATCCGT
1 ATCTATGAATCCAC
* *
28640288 A-CGTATAAATTCAC
1 ATC-TATGAATCCAC
**
28640302 ATCTATGAATCCGT
1 ATCTATGAATCCAC
*
28640316 A-CGTATGAATTCAC
1 ATC-TATGAATCCAC
***
28640330 ATCTATGAATCTGT
1 ATCTATGAATCCAC
* *
28640344 ATCTATGAATTCGC
1 ATCTATGAATCCAC
* *
28640358 ATCTATGAATCTAT
1 ATCTATGAATCCAC
* * *
28640372 AACTATGAACCCGC
1 ATCTATGAATCCAC
** * *
28640386 AAGTATGAATTCGC
1 ATCTATGAATCCAC
***
28640400 ATCTATGAATCTGT
1 ATCTATGAATCCAC
**
28640414 ATCTATGAATCTGC
1 ATCTATGAATCCAC
* *
28640428 ATCAATGAATTCAC
1 ATCTATGAATCCAC
*
28640442 TTCTAT
1 ATCTAT
28640448 TAGTTCACAT
Statistics
Matches: 304, Mismatches: 99, Indels: 18
0.72 0.24 0.04
Matches are distributed among these distances:
13 7 0.02
14 293 0.96
15 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (14 bp):
ATCTATGAATCCAC
Found at i:28640182 original size:28 final size:28
Alignment explanation
Indices: 28640151--28640447 Score: 217
Period size: 28 Copynumber: 10.6 Consensus size: 28
28640141 AATCTACGTG
* * *
28640151 TATGAATCCATATCTATTAATCTGTATC
1 TATGAATTCACATCTATGAATCTGTATC
* * * * *
28640179 TATGAGTCCACATCTATGCATCCT-CATG
1 TATGAATTCACATCTATGAAT-CTGTATC
* * ** *
28640207 TATGAATTCTCATCTATAAATCTACATA
1 TATGAATTCACATCTATGAATCTGTATC
**
28640235 TATGAATTTGCATCTATGAATCTGTATC
1 TATGAATTCACATCTATGAATCTGTATC
* *
28640263 TATGAATCCACATCTATGAATCCGTA-C
1 TATGAATTCACATCTATGAATCTGTATC
* *
28640290 GTATAAATTCACATCTATGAATCCGTA-C
1 -TATGAATTCACATCTATGAATCTGTATC
28640318 GTATGAATTCACATCTATGAATCTGTATC
1 -TATGAATTCACATCTATGAATCTGTATC
* * *
28640347 TATGAATTCGCATCTATGAATCTATAAC
1 TATGAATTCACATCTATGAATCTGTATC
** * ** *
28640375 TATGAACCCGCAAGTATGAAT-TCGCATC
1 TATGAATTCACATCTATGAATCT-GTATC
** *
28640403 TATGAA-TCTGTATCTATGAATCTGCATC
1 TATGAATTC-ACATCTATGAATCTGTATC
* *
28640431 AATGAATTCACTTCTAT
1 TATGAATTCACATCTAT
28640448 TAGTTCACAT
Statistics
Matches: 217, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
27 5 0.02
28 206 0.95
29 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (28 bp):
TATGAATTCACATCTATGAATCTGTATC
Found at i:28644275 original size:50 final size:50
Alignment explanation
Indices: 28644219--28644317 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
28644209 GTAAATGATA
*
28644219 ATGGGTGTATTATGATTTTAACCATATGATTTGGTTTGAATTTGGCATGG
1 ATGGGTGTATTATGATTTTAACCATATGATTTGGTTTGAATTTGACATGG
* *
28644269 ATGGGTGTATTATGATTTTACCCATATGATTTGTTTTGAATTTGACATG
1 ATGGGTGTATTATGATTTTAACCATATGATTTGGTTTGAATTTGACATG
28644318 TTTTACTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.45
Consensus pattern (50 bp):
ATGGGTGTATTATGATTTTAACCATATGATTTGGTTTGAATTTGACATGG
Found at i:28645654 original size:38 final size:38
Alignment explanation
Indices: 28645593--28645671 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
28645583 AACCTTTATT
*
28645593 ACACCGGCAATAAGCCTGCTAGGCACTAA-GCCTGAATA
1 ACACCGGCAATAAGCCTGCTAGGCAC-AAGGCCAGAATA
* *
28645631 ACACTGGCACTAAGCCTGCTAGGCACAAGGCCAGAATA
1 ACACCGGCAATAAGCCTGCTAGGCACAAGGCCAGAATA
28645669 ACA
1 ACA
28645672 TCATGATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (38 bp):
ACACCGGCAATAAGCCTGCTAGGCACAAGGCCAGAATA
Found at i:28646452 original size:19 final size:20
Alignment explanation
Indices: 28646430--28646468 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28646420 TTATTTTTCT
*
28646430 TTACTTAATT-TCATTTTAA
1 TTACCTAATTATCATTTTAA
*
28646449 TTACCTATTTATCATTTTAA
1 TTACCTAATTATCATTTTAA
28646469 CCTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (20 bp):
TTACCTAATTATCATTTTAA
Found at i:28650519 original size:31 final size:31
Alignment explanation
Indices: 28650473--28650552 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
28650463 GCAATCTAGA
**
28650473 TCGAATAATGCAATGA-TGTAAATAAAAACTT
1 TCGAATAATTTAATGACT-TAAATAAAAACTT
* *
28650504 TTGAATAATTTAATGACTTAAATGAAAACTT
1 TCGAATAATTTAATGACTTAAATAAAAACTT
*
28650535 TCGAATAGTTTAATGACT
1 TCGAATAATTTAATGACT
28650553 ATTTTGTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TCGAATAATTTAATGACTTAAATAAAAACTT
Found at i:28652281 original size:5 final size:5
Alignment explanation
Indices: 28652271--28652303 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
28652261 ATTTGTGTTC
28652271 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
28652304 TCATAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:28655834 original size:96 final size:96
Alignment explanation
Indices: 28655670--28655861 Score: 330
Period size: 96 Copynumber: 2.0 Consensus size: 96
28655660 TGCAGTAGGA
* * *
28655670 TATCTCATGTATGCTATGGTTTGTTCATGTCTAGATTTATCATATGTAGTCAGTGTAGTTAGCAG
1 TATCTCATGTATGCTATGGTTTGTTCATGTCCAGATTTATCATATGCAGTCAGTGCAGTTAGCAG
** *
28655735 ATACATGGTGAATCTCTGTAAAGAACACTGG
66 ATACATGGCAAATCCCTGTAAAGAACACTGG
28655766 TATCTCATGTATGCTATGGTTTGTTCATGTCCAGATTTATCATATGCAGTCAGTGCAGTTAGCAG
1 TATCTCATGTATGCTATGGTTTGTTCATGTCCAGATTTATCATATGCAGTCAGTGCAGTTAGCAG
28655831 ATACATGGCAAATCCCTGTAAAGAACACTGG
66 ATACATGGCAAATCCCTGTAAAGAACACTGG
28655862 AAAGCAGTTC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (96 bp):
TATCTCATGTATGCTATGGTTTGTTCATGTCCAGATTTATCATATGCAGTCAGTGCAGTTAGCAG
ATACATGGCAAATCCCTGTAAAGAACACTGG
Found at i:28657944 original size:2 final size:2
Alignment explanation
Indices: 28657937--28657962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28657927 GTTTGAGAAT
28657937 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28657963 CTCGGTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28659171 original size:32 final size:32
Alignment explanation
Indices: 28659135--28659229 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 32
28659125 AAATTTTCTG
28659135 TTTGTGGTTGAATATATATGAAATTATCATGT
1 TTTGTGGTTGAATATATATGAAATTATCATGT
* *
28659167 TTTGT-CTT---TAT-TCATGAAATTTTC-TG-
1 TTTGTGGTTGAATATAT-ATGAAATTATCATGT
*
28659193 TTTGTGGTTGAATATATAT-AGAATTATCATCT
1 TTTGTGGTTGAATATATATGA-AATTATCATGT
28659225 TTTGT
1 TTTGT
28659230 CTTTATTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
26 5 0.10
27 5 0.10
28 13 0.27
29 1 0.02
30 11 0.22
31 4 0.08
32 10 0.20
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (32 bp):
TTTGTGGTTGAATATATATGAAATTATCATGT
Found at i:28659218 original size:58 final size:58
Alignment explanation
Indices: 28659125--28659241 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
28659115 TATTTGTTTT
*
28659125 AAATTTTCTGTTTGTGGTTGAATATATATGAAATTATCATGTTTTGTCTTTATTCATG
1 AAATTTTCTGTTTGTGGTTGAATATATATGAAATTATCATCTTTTGTCTTTATTCATG
28659183 AAATTTTCTGTTTGTGGTTGAATATATAT-AGAATTATCATCTTTTGTCTTTATTCATG
1 AAATTTTCTGTTTGTGGTTGAATATATATGA-AATTATCATCTTTTGTCTTTATTCATG
28659241 A
1 A
28659242 TGAATTATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 1 0.02
58 56 0.98
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (58 bp):
AAATTTTCTGTTTGTGGTTGAATATATATGAAATTATCATCTTTTGTCTTTATTCATG
Found at i:28659584 original size:15 final size:15
Alignment explanation
Indices: 28659564--28659594 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28659554 TTATTATAAT
28659564 TGTGTATATATATTA
1 TGTGTATATATATTA
28659579 TGTGTATATATATTA
1 TGTGTATATATATTA
28659594 T
1 T
28659595 ATGCATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (15 bp):
TGTGTATATATATTA
Found at i:28659597 original size:17 final size:17
Alignment explanation
Indices: 28659550--28659597 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
28659540 GTATTATTTT
28659550 TATAT-TATTATAATTGTG
1 TATATATATTAT-A-TGTG
28659568 TATATATA-T-TATGTG
1 TATATATATTATATGTG
28659583 TATATATATTATATG
1 TATATATATTATATG
28659598 CATATCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.44
16 2 0.07
17 5 0.19
18 6 0.22
19 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (17 bp):
TATATATATTATATGTG
Found at i:28659602 original size:15 final size:15
Alignment explanation
Indices: 28659569--28659602 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28659559 ATAATTGTGT
* *
28659569 ATATATATTATGTGT
1 ATATATATTATATGC
28659584 ATATATATTATATGC
1 ATATATATTATATGC
28659599 ATAT
1 ATAT
28659603 CAAAGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (15 bp):
ATATATATTATATGC
Found at i:28661713 original size:60 final size:60
Alignment explanation
Indices: 28661646--28661765 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
28661636 TGACATCACT
28661646 TTTGACTTCTTTGATGTTTATAAAGTATAATGGTCAAGGAAATTCTAAGTAATCTATGGG
1 TTTGACTTCTTTGATGTTTATAAAGTATAATGGTCAAGGAAATTCTAAGTAATCTATGGG
28661706 TTTGACTTCTTTGATGTTTATAAAGTATAATGGTCAAGGAAATTCTAAGTAATCTATGGG
1 TTTGACTTCTTTGATGTTTATAAAGTATAATGGTCAAGGAAATTCTAAGTAATCTATGGG
28661766 CTATGAGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (60 bp):
TTTGACTTCTTTGATGTTTATAAAGTATAATGGTCAAGGAAATTCTAAGTAATCTATGGG
Found at i:28664328 original size:35 final size:34
Alignment explanation
Indices: 28664205--28664330 Score: 83
Period size: 35 Copynumber: 3.5 Consensus size: 34
28664195 CACAATCATC
* * **
28664205 GGTTTATCCAACTAGTGCTGGGCACAAACACAGTT
1 GGTTTATCCAACTAGAGCTGGG-TCAAACATTGTT
* * * *
28664240 GGTTCATCCAACTAGAGCTGGCTCATATTTATTATTGTC
1 GGTTTATCCAACTAGAGCTGGGTCA-A---A-CATTGTT
* *
28664279 GGTATT-TCCGACTAGCGCTGGGTGCAAACATTGTT
1 GGT-TTATCCAACTAGAGCTGGGT-CAAACATTGTT
28664314 GGTTTATCCAACTAGAG
1 GGTTTATCCAACTAGAG
28664331 TTAGGCTTAC
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
34 4 0.06
35 37 0.55
36 1 0.01
38 1 0.01
39 21 0.31
40 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (34 bp):
GGTTTATCCAACTAGAGCTGGGTCAAACATTGTT
Found at i:28665990 original size:8 final size:9
Alignment explanation
Indices: 28665954--28665988 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
28665944 TTAAAAATAC
28665954 TTTTTATAAT
1 TTTTTA-AAT
28665964 TTTTTAAAT
1 TTTTTAAAT
28665973 TTTTTAAAT
1 TTTTTAAAT
*
28665982 TGTTTAA
1 TTTTTAA
28665989 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:28672751 original size:21 final size:21
Alignment explanation
Indices: 28672726--28672769 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28672716 ATGAGTGTGA
28672726 TGAGTACCCTGAATCTGGTGG
1 TGAGTACCCTGAATCTGGTGG
** * *
28672747 TGAGTGTCTTGACTCTGGTGG
1 TGAGTACCCTGAATCTGGTGG
28672768 TG
1 TG
28672770 TGAGAGAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.36, T:0.34
Consensus pattern (21 bp):
TGAGTACCCTGAATCTGGTGG
Found at i:28677036 original size:43 final size:42
Alignment explanation
Indices: 28676988--28677137 Score: 203
Period size: 43 Copynumber: 3.5 Consensus size: 42
28676978 CTATTTAAAA
* * *
28676988 AAACGCCGTTAAAGATCATGATCTTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGC-TTTTCCAC
*
28677031 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTCCCTAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCC-AC
* *
28677074 AAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCTCAA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTC-CAC
28677117 AAACGCCGCTAAA-AGTCATGA
1 AAACGCCGCTAAAGA-TCATGA
28677138 AATTCAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
42 6 0.06
43 89 0.93
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCAC
Found at i:28677191 original size:20 final size:20
Alignment explanation
Indices: 28677145--28677192 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
28677135 TGAAATTCAA
*
28677145 AAAAAAATATTACAAAATAT
1 AAAAAAATATGACAAAATAT
* *
28677165 TATAAAATCATGA-AAAATAT
1 AAAAAAAT-ATGACAAAATAT
28677185 AAAAAAAT
1 AAAAAAAT
28677193 TTAAAATTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAATATGACAAAATAT
Found at i:28681968 original size:19 final size:19
Alignment explanation
Indices: 28681941--28681985 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28681931 CTAATCTCTA
*
28681941 TTTTATATTTTATTTTTAT
1 TTTTATATTTCATTTTTAT
*
28681960 TTTTTTATTTCATTTTTAT
1 TTTTATATTTCATTTTTAT
28681979 TTGTTAT
1 TT-TTAT
28681986 CAATGTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATATTTCATTTTTAT
Found at i:28682356 original size:21 final size:21
Alignment explanation
Indices: 28682327--28682366 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28682317 ATATAAACCA
*
28682327 TTAACCCCTAACCCTTAAATT
1 TTAAACCCTAACCCTTAAATT
28682348 TTAAACCCTAACCCTTAAA
1 TTAAACCCTAACCCTTAAA
28682367 CCATAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.30
Consensus pattern (21 bp):
TTAAACCCTAACCCTTAAATT
Found at i:28682432 original size:14 final size:14
Alignment explanation
Indices: 28682406--28682444 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28682396 TCATAAACCT
*
28682406 TAAACCCTCAATCA
1 TAAACCCTAAATCA
* *
28682420 TATACCCTAAATCG
1 TAAACCCTAAATCA
28682434 TAAACCCTAAA
1 TAAACCCTAAA
28682445 CTATAATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:28682729 original size:40 final size:40
Alignment explanation
Indices: 28682673--28682838 Score: 156
Period size: 41 Copynumber: 4.0 Consensus size: 40
28682663 GCAAAAATTG
**
28682673 TAAAACACAGAGCAATAGCGGCGTTTTTGCTAAAACGCATC
1 TAAAA-ACAGAGCAATAGCGGCGTTTTTGCTAAAACGCCGC
* * * *
28682714 TAAAAACCGAGCAATAGAGGCGTTTTTTGTTAAAATGCCGC
1 TAAAAACAGAGCAATAGCGGCG-TTTTTGCTAAAACGCCGC
* * *
28682755 TAAAAACAGAGCATTAGCGGCACTTTTGGC-AAAACGCCGC
1 TAAAAACAGAGCAATAGCGGC-GTTTTTGCTAAAACGCCGC
* * *
28682795 TAAAGACCAGAGCATTAGCGGCGCTTTT-CTAAGAAACGCCGC
1 TAAA-AACAGAGCAATAGCGGCGTTTTTGCT-A-AAACGCCGC
28682837 TA
1 TA
28682839 TAAGTACACA
Statistics
Matches: 102, Mismatches: 17, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 31 0.30
41 59 0.58
42 11 0.11
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGTTTTTGCTAAAACGCCGC
Found at i:28683115 original size:21 final size:21
Alignment explanation
Indices: 28683069--28683120 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
28683059 TTAATTATCA
* *
28683069 TTATAGTTTAGGGTTTATGGT
1 TTATGGTTAAGGGTTTATGGT
*
28683090 ATATGGTTAAGGGTTTAAT-GT
1 TTATGGTTAAGGGTTT-ATGGT
28683111 TTATGAGTTA
1 TTATG-GTTA
28683121 CTATTTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (21 bp):
TTATGGTTAAGGGTTTATGGT
Found at i:28683168 original size:15 final size:15
Alignment explanation
Indices: 28683132--28683164 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28683122 TATTTTAAGT
*
28683132 TTTATGGATTATGGG
1 TTTAGGGATTATGGG
28683147 TTTAGGGATTAT-GG
1 TTTAGGGATTATGGG
28683161 TTTA
1 TTTA
28683165 AGGGTGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (15 bp):
TTTAGGGATTATGGG
Found at i:28683234 original size:23 final size:23
Alignment explanation
Indices: 28683208--28683254 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
28683198 GTGTTAGGAG
28683208 TTAGGGGTTTAGGGGTTTA-GTTT
1 TTAGGGGTTTA-GGGTTTATGTTT
*
28683231 TTAGGGGTTTATGGTTTATGTTT
1 TTAGGGGTTTAGGGTTTATGTTT
28683254 T
1 T
28683255 AGTAGTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.34, T:0.53
Consensus pattern (23 bp):
TTAGGGGTTTAGGGTTTATGTTT
Found at i:28683277 original size:7 final size:7
Alignment explanation
Indices: 28683183--28683299 Score: 60
Period size: 7 Copynumber: 16.1 Consensus size: 7
28683173 TTAAAGGTTG
28683183 GGGTTTA
1 GGGTTTA
*
28683190 AGGTTTA
1 GGGTTTA
28683197 -GGTGTTA
1 GGGT-TTA
28683204 GGAG-TTA
1 GG-GTTTA
28683211 GGGGTTTA
1 -GGGTTTA
28683219 GGGGTTTA
1 -GGGTTTA
**
28683227 GTTTTTA
1 GGGTTTA
28683234 GGGGTTTA
1 -GGGTTTA
*
28683242 TGGTTTA
1 GGGTTTA
* *
28683249 TGTTTTA
1 GGGTTTA
*
28683256 GTAG-TTA
1 G-GGTTTA
*
28683263 TGGTTTA
1 GGGTTTA
28683270 GGGTTTA
1 GGGTTTA
**
28683277 GGGACTA
1 GGGTTTA
28683284 GGAGTTTA
1 GG-GTTTA
28683292 GGGTTTA
1 GGGTTTA
28683299 G
1 G
28683300 ATTAATTAGT
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
6 4 0.05
7 55 0.65
8 24 0.29
9 1 0.01
ACGTcount: A:0.18, C:0.01, G:0.38, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Found at i:28683415 original size:14 final size:14
Alignment explanation
Indices: 28683398--28683436 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
28683388 ATCATTATAG
28683398 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
* *
28683412 TTTAGGATTTATGT
1 TTTAGGGTTTATGA
28683426 TTTAGGGTTTA
1 TTTAGGGTTTA
28683437 AAGTGTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:28684278 original size:27 final size:27
Alignment explanation
Indices: 28684189--28684291 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 27
28684179 AAATCAAAAT
28684189 CCCGACCCATCT-CTGCATCG-C--CAGA
1 CCCGA-CCATCTGCTGCATCGTCGTC-GA
*
28684214 CCCGACCATATGCTGCATCGTCG--GA
1 CCCGACCATCTGCTGCATCGTCGTCGA
*
28684239 CCCGACCATCTGCTGCATCGCCGTCGA
1 CCCGACCATCTGCTGCATCGTCGTCGA
** *
28684266 CTTGACCATCTGCTGCGTCGTCGTCG
1 CCCGACCATCTGCTGCATCGTCGTCG
28684292 CGCTGCTCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
24 5 0.08
25 36 0.55
26 1 0.02
27 24 0.36
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (27 bp):
CCCGACCATCTGCTGCATCGTCGTCGA
Found at i:28687839 original size:24 final size:23
Alignment explanation
Indices: 28687812--28687876 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
28687802 TAGGGGTATA
* *
28687812 GTTTAAGGGTTAAGTTTTTTTAAG
1 GTTTAAGAGTTAAG-TGTTTTAAG
*
28687836 GTTTAAGAGTTTAGTGTTTTAAG
1 GTTTAAGAGTTAAGTGTTTTAAG
*
28687859 GATTATAGA-TT-AGTGTTT
1 GTTTA-AGAGTTAAGTGTTT
28687877 ATGATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.19
23 14 0.39
24 15 0.42
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (23 bp):
GTTTAAGAGTTAAGTGTTTTAAG
Found at i:28687874 original size:22 final size:22
Alignment explanation
Indices: 28687829--28687876 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
28687819 GGTTAAGTTT
*
28687829 TTTTAAGGTTTAAGAGTTTAGTG
1 TTTTAAGGATTAAGAG-TTAGTG
28687852 TTTTAAGGATTATAGA-TTAGTG
1 TTTTAAGGATTA-AGAGTTAGTG
28687874 TTT
1 TTT
28687877 ATGATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (22 bp):
TTTTAAGGATTAAGAGTTAGTG
Found at i:28687974 original size:41 final size:40
Alignment explanation
Indices: 28687917--28688093 Score: 282
Period size: 41 Copynumber: 4.4 Consensus size: 40
28687907 GTTATATGAC
*
28687917 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGAT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCG-T
28687958 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCC-GT
* * *
28687999 TTTTAGAGGCGTTTTACCAAAAGCGCCGCTATTGCTCCGG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCGT
* *
28688039 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCGT
28688079 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
28688094 TGGTAAAACG
Statistics
Matches: 128, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 53 0.41
41 74 0.58
42 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCGT
Found at i:28688123 original size:81 final size:81
Alignment explanation
Indices: 28687917--28688124 Score: 240
Period size: 81 Copynumber: 2.6 Consensus size: 81
28687907 GTTATATGAC
* * * * * *
28687917 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGATTTTTAGCGGCGTTTTACCAAAAGC
1 TTTTAGAGGCGTTTTACCAAAAGCGCCACTATTGCTCAG-GTTTTAGCGGCGTTTTACCAAAAGC
28687982 GCCGCTAATGCTCCGGT
65 GCCGCTAATGCTCCGGT
* *
28687999 TTTTAGAGGCGTTTTACCAAAAGCGCCGCTATTGCTCCGGTTTTAGCGGCGTTTTACCAAAAGCG
1 TTTTAGAGGCGTTTTACCAAAAGCGCCACTATTGCTCAGGTTTTAGCGGCGTTTTACCAAAAGCG
* *
28688064 CCGCTATTGCT-CTGT
66 CCGCTAATGCTCCGGT
* *** *
28688079 TTTTAGCGGCGTTTTTGGTAAAA-CGCCACTATTGCTCTATGTTTTA
1 TTTTAGAGGCG-TTTTACCAAAAGCGCCACTATTGCTC-AGGTTTTA
28688125 CAATTTTTGT
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
80 26 0.23
81 49 0.44
82 36 0.32
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (81 bp):
TTTTAGAGGCGTTTTACCAAAAGCGCCACTATTGCTCAGGTTTTAGCGGCGTTTTACCAAAAGCG
CCGCTAATGCTCCGGT
Done.