Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 117 of 172
Found at i:38914466 original size:63 final size:63
Alignment explanation
Indices: 38914367--38914493 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
38914357 TCTTGTAGGG
* *
38914367 CCCTTCCTAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTTAATATTCCT
1 CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
*
38914430 CCCTTCCCAATTGGGATCTATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
1 CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
38914493 C
1 C
38914494 AAGACTAGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (63 bp):
CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
Found at i:38930235 original size:27 final size:27
Alignment explanation
Indices: 38930193--38930247 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
38930183 GTGTTTCGAA
*
38930193 GTTAAGAGATAGATCTTCAAACACCAT
1 GTTAAGAGATAAATCTTCAAACACCAT
*
38930220 GTTAAGAGATAAATCTTCAAACGCCAT
1 GTTAAGAGATAAATCTTCAAACACCAT
38930247 G
1 G
38930248 AAGACATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (27 bp):
GTTAAGAGATAAATCTTCAAACACCAT
Found at i:38939575 original size:23 final size:22
Alignment explanation
Indices: 38939536--38939580 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
38939526 TATTAAAATA
* * *
38939536 ATAAAATTATATTTTTACTTTC
1 ATAAAAATATATATTTAATTTC
38939558 ATAAAAATATATAATTTAATTTC
1 ATAAAAATATAT-ATTTAATTTC
38939581 GACCTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAAATATATATTTAATTTC
Found at i:38940212 original size:13 final size:13
Alignment explanation
Indices: 38940194--38940219 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38940184 AATTAATGTT
38940194 TTGATAGGGATAA
1 TTGATAGGGATAA
38940207 TTGATAGGGATAA
1 TTGATAGGGATAA
38940220 GTTTTCAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TTGATAGGGATAA
Found at i:38942862 original size:48 final size:49
Alignment explanation
Indices: 38942810--38942902 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
38942800 TTGTTTGAAC
*
38942810 ATTTGTGTTTGATATGCAAA-AAATGGAGAAAGTTAAATTTATATAAAA
1 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATATAAAA
38942858 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
1 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
38942903 CTACTTCCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 19 0.44
49 24 0.56
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (49 bp):
ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATATAAAA
Found at i:38952437 original size:5 final size:5
Alignment explanation
Indices: 38952427--38952456 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
38952417 CTATTGTGAA
*
38952427 TTGTG TTGTG TTGTG TTGTG TTATG TTGTG
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG
38952457 GGAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.37, T:0.60
Consensus pattern (5 bp):
TTGTG
Found at i:38954930 original size:27 final size:27
Alignment explanation
Indices: 38954888--38954982 Score: 140
Period size: 27 Copynumber: 3.6 Consensus size: 27
38954878 GTCACTAGAC
38954888 ACAGATAT-TGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
38954914 ACAGATATATGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
* * *
38954941 TCAGATA-ATTGTGGCATAGCCACCAGG
1 ACAGATATA-TGTGGCAGAGCCACCAGA
38954968 ACAGATATATGTGGC
1 ACAGATATATGTGGC
38954983 NGTGGCATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
26 9 0.15
27 52 0.84
28 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (27 bp):
ACAGATATATGTGGCAGAGCCACCAGA
Found at i:38956361 original size:26 final size:26
Alignment explanation
Indices: 38956331--38956405 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
38956321 CCCATGATGG
38956331 AACATTTACCTAACCCATTATCATGA
1 AACATTTACCTAACCCATTATCATGA
*
38956357 AACATTTACCTAACCCATTATCATGG
1 AACATTTACCTAACCCATTATCATGA
38956383 AACATTTACCTAACCCATTATCA
1 AACATTTACCTAACCCATTATCA
38956406 ATTTGTACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (26 bp):
AACATTTACCTAACCCATTATCATGA
Found at i:38969835 original size:17 final size:17
Alignment explanation
Indices: 38969815--38969862 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
38969805 TTTTACCCAT
*
38969815 TAAATTCTTTTAATTCA
1 TAAATTCTTCTAATTCA
*
38969832 TAAAATTC-ACTAATTCA
1 T-AAATTCTTCTAATTCA
*
38969849 AAAATTCTTCTAAT
1 TAAATTCTTCTAAT
38969863 GTCTTAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.24
17 13 0.52
18 6 0.24
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTCTTCTAATTCA
Found at i:38970360 original size:32 final size:32
Alignment explanation
Indices: 38970319--38970382 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
38970309 AAGCTTTAGG
38970319 GCCATTTATAACCTTGGAAACAAGAAATTGAC
1 GCCATTTATAACCTTGGAAACAAGAAATTGAC
*
38970351 GCCATTTATAACGTTGGAAACAAGAAATTGAC
1 GCCATTTATAACCTTGGAAACAAGAAATTGAC
38970383 TCTTACACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (32 bp):
GCCATTTATAACCTTGGAAACAAGAAATTGAC
Found at i:38983852 original size:51 final size:51
Alignment explanation
Indices: 38983763--38983868 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
38983753 AAACATCTGC
* *
38983763 TCATATGAAATAATAGTTCTTACCAAATGAAAACTCATGCAAAATAATAGT
1 TCATATGAAATAATAGTTCATACCAAATGAAAACTCATGCAAAATAAAAGT
* * *
38983814 TCATATGAAAT-ATCAGTTCATATCGAAT-AACAATTCATGCAAAATAAAAGT
1 TCATATGAAATAAT-AGTTCATACCAAATGAA-AACTCATGCAAAATAAAAGT
38983865 TCAT
1 TCAT
38983869 GCTCCATCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.08
51 44 0.92
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (51 bp):
TCATATGAAATAATAGTTCATACCAAATGAAAACTCATGCAAAATAAAAGT
Found at i:39007074 original size:14 final size:14
Alignment explanation
Indices: 39007055--39007084 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39007045 TATTTTCAAG
39007055 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
39007069 ATAGATTCACGCAT
1 ATAGATTAACGCAT
39007083 AT
1 AT
39007085 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:39015486 original size:21 final size:20
Alignment explanation
Indices: 39015457--39015511 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
39015447 AAAAACACTT
39015457 TAAC-TGATTGAAGAAAAGTC
1 TAACTTGATTGAA-AAAAGTC
** *
39015477 TAACTTGATTGAAACCATTC
1 TAACTTGATTGAAAAAAGTC
*
39015497 TAACTTGATTTAAAA
1 TAACTTGATTGAAAA
39015512 GTTGACTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
TAACTTGATTGAAAAAAGTC
Found at i:39018479 original size:10 final size:10
Alignment explanation
Indices: 39018464--39018494 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39018454 TAAATAAAAC
39018464 ATAACATAAA
1 ATAACATAAA
39018474 ATAACATAAA
1 ATAACATAAA
*
39018484 ATAAAATAAA
1 ATAACATAAA
39018494 A
1 A
39018495 CAAAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAACATAAA
Found at i:39018481 original size:15 final size:15
Alignment explanation
Indices: 39018461--39018492 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39018451 AATTAAATAA
*
39018461 AACATAACATAAAAT
1 AACATAAAATAAAAT
39018476 AACATAAAATAAAAT
1 AACATAAAATAAAAT
39018491 AA
1 AA
39018493 AACAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (15 bp):
AACATAAAATAAAAT
Found at i:39019339 original size:12 final size:14
Alignment explanation
Indices: 39019322--39019354 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39019312 TAAAGAAATA
39019322 ATAAATTG-AT-TG
1 ATAAATTGAATATG
39019334 ATAAATTGAATATG
1 ATAAATTGAATATG
39019348 ATAAATT
1 ATAAATT
39019355 ACAATTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 2 0.11
14 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (14 bp):
ATAAATTGAATATG
Found at i:39020020 original size:34 final size:34
Alignment explanation
Indices: 39019940--39020020 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
39019930 TTATAGTTTT
* * *
39019940 AATATTGGTGTGAAAGTCAATGATATATTTTAAG
1 AATATTGGTATGGAACTCAATGATATATTTTAAG
* * * *
39019974 CATATTGTTATGGAACTCAATGGTATGTTTTAAG
1 AATATTGGTATGGAACTCAATGATATATTTTAAG
39020008 AATATTGGTATGG
1 AATATTGGTATGG
39020021 TGATAGAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (34 bp):
AATATTGGTATGGAACTCAATGATATATTTTAAG
Found at i:39028375 original size:26 final size:26
Alignment explanation
Indices: 39028339--39028449 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
39028329 AGCCTGGCTG
* * *
39028339 CCAGAATAGATAATGTGACAAAGTCA
1 CCAGAATAGATAATGTGGCAGAGCCA
39028365 CCAGAATAGATAATCGTGGCAGAGCCA
1 CCAGAATAGATAAT-GTGGCAGAGCCA
*
39028392 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAATAGATA-ATGTGGCAGAGCCA
*
39028419 CCAG-ATCAGATAATTGTGGCATAGCCA
1 CCAGAAT-AGATAA-TGTGGCAGAGCCA
39028446 CCAG
1 CCAG
39028450 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 16 0.21
27 57 0.76
28 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAATAGATAATGTGGCAGAGCCA
Found at i:39029771 original size:140 final size:139
Alignment explanation
Indices: 39029589--39029867 Score: 522
Period size: 140 Copynumber: 2.0 Consensus size: 139
39029579 TCAAGTTTTC
39029589 GGGATTTCGGGATTTGAGGCAATCGGCTATAGTCTTAAAAATAATGGAAGGAAGGTGGTATAGAG
1 GGGATTTCGGGATTTGAGGCAATCGGCTATAGTCTTAAAAATAATGGAAGGAAGGTGGTATAGAG
* *
39029654 TAGGGTGGCTGAAGGATTCGGCTATGGGGAAAAGAAGAAGAAAAGAATAAGTGGATGGAGAGAAG
66 TAGGGTGGCTGAAAGATTCGACTATGGGGAAAAGAAGAAGAAAAGAATAAGTGGATGGAGAGAAG
39029719 AGAAAAAGA
131 AGAAAAAGA
39029728 NGGGATTTCGGGATTTGAGGCAATCGGCTATAGTCTTAAAAATAATGGAAGGAAGGTGGTATAGA
1 -GGGATTTCGGGATTTGAGGCAATCGGCTATAGTCTTAAAAATAATGGAAGGAAGGTGGTATAGA
*
39029793 GTAGGGTGGCTGAAAGATTCGACTATGGGGAAAAGAATAAGAAAAGAATAAGTGGATGGAGAGAA
65 GTAGGGTGGCTGAAAGATTCGACTATGGGGAAAAGAAGAAGAAAAGAATAAGTGGATGGAGAGAA
39029858 GAGAAAAAGA
130 GAGAAAAAGA
39029868 AAAGAAGAAG
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.20
Consensus pattern (139 bp):
GGGATTTCGGGATTTGAGGCAATCGGCTATAGTCTTAAAAATAATGGAAGGAAGGTGGTATAGAG
TAGGGTGGCTGAAAGATTCGACTATGGGGAAAAGAAGAAGAAAAGAATAAGTGGATGGAGAGAAG
AGAAAAAGA
Found at i:39030034 original size:24 final size:24
Alignment explanation
Indices: 39030007--39030077 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
39029997 CTAGATTTTC
**
39030007 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
39030031 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
39030055 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
39030078 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:39032174 original size:19 final size:18
Alignment explanation
Indices: 39032150--39032185 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39032140 TGATATATTT
39032150 TATTAATAAATAAAGTAAA
1 TATTAATAAAT-AAGTAAA
*
39032169 TATTAATTAATAAGTAA
1 TATTAATAAATAAGTAA
39032186 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TATTAATAAATAAGTAAA
Found at i:39033105 original size:38 final size:38
Alignment explanation
Indices: 39033053--39033132 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
39033043 TTTAATAAGT
* ** *
39033053 ATATGGATACATGAAATGGACCATGATTTGGATTAATG
1 ATATAGATACATGAAATAAACCATGATTTAGATTAATG
*
39033091 ATATAGATATATGAAATAAACCATGATTTAGATTAATG
1 ATATAGATACATGAAATAAACCATGATTTAGATTAATG
39033129 ATAT
1 ATAT
39033133 GGATTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (38 bp):
ATATAGATACATGAAATAAACCATGATTTAGATTAATG
Found at i:39036443 original size:21 final size:19
Alignment explanation
Indices: 39036405--39036452 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
39036395 AGATAGTTTT
*
39036405 CTTTATTTTATGTTTTAAC
1 CTTTATTTTATATTTTAAC
39036424 CTTTATTATTACTATTTTAAC
1 CTTTATT-TTA-TATTTTAAC
*
39036445 TTTTATTT
1 CTTTATTT
39036453 AACACATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 14 0.56
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (19 bp):
CTTTATTTTATATTTTAAC
Found at i:39046144 original size:42 final size:42
Alignment explanation
Indices: 39046084--39046195 Score: 170
Period size: 42 Copynumber: 2.7 Consensus size: 42
39046074 AATGCAGGGG
* ** *
39046084 ACACACGGCCAATCCACATGCCCATGTGCTAGGCCGTGTGTC
1 ACACACGGTCAAGACACATGCCCGTGTGCTAGGCCGTGTGTC
* *
39046126 ACACACGGTCAAGACACATGCCTGTGTGCTAGGTCGTGTGTC
1 ACACACGGTCAAGACACATGCCCGTGTGCTAGGCCGTGTGTC
39046168 ACACACGGTCAAGACACATGCCCGTGTG
1 ACACACGGTCAAGACACATGCCCGTGTG
39046196 TCTACCCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (42 bp):
ACACACGGTCAAGACACATGCCCGTGTGCTAGGCCGTGTGTC
Found at i:39052339 original size:31 final size:31
Alignment explanation
Indices: 39052296--39052357 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
39052286 GCTCGATCAC
39052296 TCAAAGAATACCCGTCCGGGCTAGATCCTTT
1 TCAAAGAATACCCGTCCGGGCTAGATCCTTT
*
39052327 TCAAGGAATACCCGTCCGGGCTAGATCCTTT
1 TCAAAGAATACCCGTCCGGGCTAGATCCTTT
39052358 CTATATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (31 bp):
TCAAAGAATACCCGTCCGGGCTAGATCCTTT
Found at i:39055174 original size:35 final size:35
Alignment explanation
Indices: 39055128--39055236 Score: 200
Period size: 35 Copynumber: 3.1 Consensus size: 35
39055118 GCTCAGGGCT
*
39055128 TTAACATAATAAAATTTTTATTTTAATATAAAAGG
1 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
39055163 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
1 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
*
39055198 TTAACATAATAAAATTTTTATTTTAATACAAGAGG
1 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
39055233 TTAA
1 TTAA
39055237 TGTTTATTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (35 bp):
TTAACATAATAAAATTTTTATTTTAATACAAAAGG
Found at i:39058520 original size:13 final size:13
Alignment explanation
Indices: 39058502--39058526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39058492 GCCAACCATT
39058502 TATAGATTTTTTC
1 TATAGATTTTTTC
39058515 TATAGATTTTTT
1 TATAGATTTTTT
39058527 TGTTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TATAGATTTTTTC
Found at i:39069263 original size:31 final size:31
Alignment explanation
Indices: 39069225--39069306 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
39069215 ATGGGGGTAG
* * ** *
39069225 GACACTGTATCTATTCTTATCTGTTTTGCAT
1 GACACTGTATTTATTCTGATCTACTCTGCAT
*
39069256 GACACTGTATTTGTTCTGATCTACTCTGCAT
1 GACACTGTATTTATTCTGATCTACTCTGCAT
39069287 GACACTGTATTTATTCTGAT
1 GACACTGTATTTATTCTGAT
39069307 ATGTTATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.45
Consensus pattern (31 bp):
GACACTGTATTTATTCTGATCTACTCTGCAT
Found at i:39082239 original size:20 final size:20
Alignment explanation
Indices: 39082214--39082260 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39082204 CTTCCAGACA
39082214 ACGTCGTGACATGATTTTTC
1 ACGTCGTGACATGATTTTTC
*
39082234 ACGTCGTGACGTGATTTTTC
1 ACGTCGTGACATGATTTTTC
39082254 ACGTCGT
1 ACGTCGT
39082261 CTCGGCATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ACGTCGTGACATGATTTTTC
Found at i:39090229 original size:27 final size:26
Alignment explanation
Indices: 39090199--39090278 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
39090189 GCACATAATT
39090199 AGGAAGCACTC-TCTCGAGCCATATAAC
1 AGGAAGC-CTCATCT-GAGCCATATAAC
* *
39090226 AGGAAG-CTCATGTGAGCCATATAAT
1 AGGAAGCCTCATCTGAGCCATATAAC
* *
39090251 AGGAAG-CTTATCCGAG-C-TATAAC
1 AGGAAGCCTCATCTGAGCCATATAAC
39090274 AGGAA
1 AGGAA
39090279 ACTTATAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
23 10 0.22
24 1 0.02
25 27 0.59
26 2 0.04
27 6 0.13
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
AGGAAGCCTCATCTGAGCCATATAAC
Found at i:39090277 original size:23 final size:25
Alignment explanation
Indices: 39090213--39090284 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
39090203 AGCACTCTCT
* *
39090213 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTTATC
* *
39090238 TGAGCCATATAATAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTTATC
*
39090263 CGAG-C-TATAACAGGAAACTTAT
1 CGAGCCATATAACAGGAAGCTTAT
39090285 AAGAGTTTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 24 0.60
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTTATC
Found at i:39093673 original size:56 final size:56
Alignment explanation
Indices: 39093606--39093718 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
39093596 TTATTTACTC
* *
39093606 TAACTTCCAGAAGAATGATGACATAAACATTTATCAAATCTCTGCAAGTGATCATT
1 TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTGCAAGTGATCATT
* *
39093662 TAACTTCCAGAAGAATAATGATATAAACATTTACCAAATCTCTTCAAGTGATCATT
1 TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTGCAAGTGATCATT
39093718 T
1 T
39093719 GAAAAACTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (56 bp):
TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTGCAAGTGATCATT
Found at i:39098713 original size:60 final size:54
Alignment explanation
Indices: 39098595--39098702 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
39098585 AAATTAACCA
* *
39098595 TGATAATGTATGATTATCATGATTTTGATTATTACATTATCTTTAAATAAAATT
1 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
*
39098649 TGATAATGTATGGTTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
1 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
39098703 GAACTGTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (54 bp):
TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
Found at i:39103676 original size:22 final size:22
Alignment explanation
Indices: 39103619--39103666 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
39103609 TCACTTGCCG
39103619 AGAAACACCTTCATATTGTAAT
1 AGAAACACCTTCATATTGTAAT
39103641 AGAAACACCTTCATATTGTAAT
1 AGAAACACCTTCATATTGTAAT
39103663 AGAA
1 AGAA
39103667 TTTCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (22 bp):
AGAAACACCTTCATATTGTAAT
Found at i:39107183 original size:15 final size:15
Alignment explanation
Indices: 39107163--39107192 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39107153 TAAAGCCTCC
39107163 TTTTAAACAATCATT
1 TTTTAAACAATCATT
39107178 TTTTAAACAATCATT
1 TTTTAAACAATCATT
39107193 GTTTCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTTAAACAATCATT
Found at i:39129675 original size:19 final size:19
Alignment explanation
Indices: 39129653--39129691 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39129643 ATTTTGCTAA
*
39129653 TTTTAGATTTTTATATATT
1 TTTTAGAATTTTATATATT
* *
39129672 TTTTTGAATTTTCTATATT
1 TTTTAGAATTTTATATATT
39129691 T
1 T
39129692 ATAAATTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTAGAATTTTATATATT
Found at i:39129681 original size:27 final size:28
Alignment explanation
Indices: 39129651--39129724 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
39129641 TAATTTTGCT
39129651 AATTTTAGATTTTTATATATT-TTTTTG
1 AATTTTAGATTTTTATATATTGTTTTTG
** * * *
39129678 AATTTTCTATATTTATAAATTGTTTTTT
1 AATTTTAGATTTTTATATATTGTTTTTG
*
39129706 ATTTTTATGATTTTTATAT
1 AATTTTA-GATTTTTATAT
39129725 TTATAAAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
27 17 0.49
28 10 0.29
29 8 0.23
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.66
Consensus pattern (28 bp):
AATTTTAGATTTTTATATATTGTTTTTG
Found at i:39129709 original size:37 final size:37
Alignment explanation
Indices: 39129634--39129731 Score: 107
Period size: 36 Copynumber: 2.7 Consensus size: 37
39129624 CATCATAATT
* *
39129634 TTTTTTTTAATTTTGCTA-ATTT-TAGATTTTTATATA
1 TTTTTTTGAATTTT-CTATATTTATAAATTTTTATATA
*
39129670 TTTTTTTGAATTTTCTATATTTATAAATTGTTT-TTTA
1 TTTTTTTGAATTTTCTATATTTATAAATT-TTTATATA
*
39129707 TTTTTATG-ATTTT-TATATTTATAAA
1 TTTTTTTGAATTTTCTATATTTATAAA
39129732 AAAATTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.27
36 22 0.40
37 15 0.27
38 3 0.05
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (37 bp):
TTTTTTTGAATTTTCTATATTTATAAATTTTTATATA
Found at i:39130777 original size:11 final size:11
Alignment explanation
Indices: 39130761--39130786 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39130751 TTAAAATATG
39130761 ATAAACAAATA
1 ATAAACAAATA
39130772 ATAAACAAATA
1 ATAAACAAATA
39130783 ATAA
1 ATAA
39130787 TAAAAACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAACAAATA
Found at i:39137765 original size:3 final size:3
Alignment explanation
Indices: 39137757--39137792 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39137747 TCCTGTTACC
39137757 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39137793 TCCAATTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39148567 original size:20 final size:19
Alignment explanation
Indices: 39148544--39148585 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39148534 AATAAATTTT
*
39148544 AAATTATTTTAAATATAATA
1 AAATAATTTT-AATATAATA
*
39148564 AAATAATTTTTATATAATA
1 AAATAATTTTAATATAATA
39148583 AAA
1 AAA
39148586 AATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATTTTAATATAATA
Found at i:39148589 original size:26 final size:27
Alignment explanation
Indices: 39148554--39148629 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
39148544 AAATTATTTT
*
39148554 AAATATAATAAAA-TAATTTTTATATA
1 AAATAAAATAAAATTAATTTTTATATA
*
39148580 ATAA-AAAATAAAATTAA-TTATATATA
1 A-AATAAAATAAAATTAATTTTTATATA
39148606 AAATAAAATAAAAATTAATTTTTA
1 AAATAAAAT-AAAATTAATTTTTA
39148630 AACATTCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.05
26 23 0.55
27 13 0.31
28 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATAAAATAAAATTAATTTTTATATA
Found at i:39148613 original size:27 final size:26
Alignment explanation
Indices: 39148560--39148626 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
39148550 TTTTAAATAT
* *
39148560 AATAAAA-TAATTTTTATATAATAAAA
1 AATAAAATTAATTTATATAAAAT-AAA
39148586 AATAAAATTAATTATATATAAAAT-AA
1 AATAAAATTAATT-TATATAAAATAAA
39148612 AATAAAAATTAATTT
1 AAT-AAAATTAATTT
39148627 TTAAACATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 13 0.36
27 15 0.42
28 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATTAATTTATATAAAATAAA
Found at i:39148922 original size:13 final size:14
Alignment explanation
Indices: 39148906--39148934 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39148896 ATTTTAGTCA
39148906 TTAATTTA-ATTTT
1 TTAATTTATATTTT
39148919 TTAATTTATATTTT
1 TTAATTTATATTTT
39148933 TT
1 TT
39148935 GTCAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTAATTTATATTTT
Found at i:39149581 original size:35 final size:35
Alignment explanation
Indices: 39149524--39149591 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
39149514 AAAGCCTACT
* * *
39149524 GAATCTTAATTTGATTAATATTAGTATAATTGTCA
1 GAATCTTAACTTAATTAATATTAGCATAATTGTCA
**
39149559 GAATCTTAACTTAATTTGTATTAGCATAATTGT
1 GAATCTTAACTTAATTAATATTAGCATAATTGT
39149592 TAATATAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (35 bp):
GAATCTTAACTTAATTAATATTAGCATAATTGTCA
Found at i:39150526 original size:14 final size:15
Alignment explanation
Indices: 39150507--39150535 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39150497 TGATTTTTCT
39150507 AAAAAAGAAA-TAAA
1 AAAAAAGAAACTAAA
39150521 AAAAAAGAAACTAAA
1 AAAAAAGAAACTAAA
39150536 CAATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAGAAACTAAA
Found at i:39155733 original size:30 final size:30
Alignment explanation
Indices: 39155697--39155756 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
39155687 AATAATCTTC
39155697 TAATTAAACTCTGTTTATTTGTTTCAATCA
1 TAATTAAACTCTGTTTATTTGTTTCAATCA
39155727 TAATTAAACTCTGTTTATTTGTTTCAATCA
1 TAATTAAACTCTGTTTATTTGTTTCAATCA
39155757 AACTCTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (30 bp):
TAATTAAACTCTGTTTATTTGTTTCAATCA
Found at i:39163537 original size:14 final size:15
Alignment explanation
Indices: 39163520--39163553 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39163510 TTAAATGCTG
39163520 AAAAAA-TAAATATT
1 AAAAAAGTAAATATT
*
39163534 AAAAAAGTAAGTATT
1 AAAAAAGTAAATATT
39163549 AAAAA
1 AAAAA
39163554 TTTAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAAAGTAAATATT
Found at i:39164508 original size:20 final size:20
Alignment explanation
Indices: 39164483--39164527 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39164473 ATACTTCATC
*
39164483 AAAATTAAAAAAAAATTATT
1 AAAATTAAAAAAAAATTATA
* * *
39164503 AAAATTCAAAAGAGATTATA
1 AAAATTAAAAAAAAATTATA
39164523 AAAAT
1 AAAAT
39164528 ATTAGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATTAAAAAAAAATTATA
Found at i:39166209 original size:37 final size:37
Alignment explanation
Indices: 39166156--39166240 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
39166146 GTTTATTTCC
*
39166156 TAAAATAAAATCTTTAAAAGATAATATAATATTAAAA
1 TAAAATAAAATATTTAAAAGATAATATAATATTAAAA
* *
39166193 TAAAATAAAATATTTAAAAGATAATATTATTTTAAAA
1 TAAAATAAAATATTTAAAAGATAATATAATATTAAAA
39166230 TAAAATAAAAT
1 TAAAATAAAAT
39166241 TTGAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (37 bp):
TAAAATAAAATATTTAAAAGATAATATAATATTAAAA
Found at i:39166236 original size:18 final size:18
Alignment explanation
Indices: 39166157--39166252 Score: 77
Period size: 18 Copynumber: 5.3 Consensus size: 18
39166147 TTTATTTCCT
*
39166157 AAAATAAAATCTTTAAAAG
1 AAAATATAAT-TTTAAAAG
* * *
39166176 ATAATATAATATTAAAAT
1 AAAATATAATTTTAAAAG
*
39166194 AAAATAAAATATTTAAAAG
1 AAAATATAAT-TTTAAAAG
* * *
39166213 ATAATATTATTTTAAAAT
1 AAAATATAATTTTAAAAG
* *
39166231 AAAATAAAATTTGAAAA-
1 AAAATATAATTTTAAAAG
39166248 AAAAT
1 AAAAT
39166253 CTGCATGTAA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
17 5 0.08
18 34 0.57
19 21 0.35
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAATATAATTTTAAAAG
Found at i:39170451 original size:5 final size:5
Alignment explanation
Indices: 39170440--39170501 Score: 74
Period size: 5 Copynumber: 12.6 Consensus size: 5
39170430 AAATAGAAAG
* * *
39170440 ATTTT GTTTT GTTTT ATTTT ATTTT ATTTT -TATT A-TTT ATATTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT
39170489 ATTTT ATTTT ATT
1 ATTTT ATTTT ATT
39170502 AATTTAGGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 6 0.12
5 39 0.78
6 5 0.10
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:39170485 original size:29 final size:29
Alignment explanation
Indices: 39170452--39170507 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
39170442 TTTGTTTTGT
39170452 TTTATTTTATTTTATTTTTATT-ATTTATA
1 TTTATTTTATTTTA-TTTTATTAATTTATA
39170481 TTTATTTTATTTTATTTTATTAATTTA
1 TTTATTTTATTTTATTTTATTAATTTA
39170508 GGTTAGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTATTTTATTTTATTTTATTAATTTATA
Found at i:39171360 original size:16 final size:16
Alignment explanation
Indices: 39171339--39171390 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
39171329 AAATCCCAAT
39171339 TTAATTTTTTATTTAG
1 TTAATTTTTTATTTAG
*
39171355 TTAATTATTTATCTTAG
1 TTAATTTTTTAT-TTAG
*
39171372 -CAATTTTAATTATTTAG
1 TTAATTTT--TTATTTAG
39171389 TT
1 TT
39171391 TCTACTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 16 0.57
17 8 0.29
18 4 0.14
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTTTTTATTTAG
Found at i:39174061 original size:20 final size:20
Alignment explanation
Indices: 39174036--39174079 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
39174026 TTAGTACTTA
39174036 TTTTTTTCTTCTT-TTTTTT
1 TTTTTTTCTTCTTCTTTTTT
39174055 CTTTTTTTCTTCTTCTTTTTT
1 -TTTTTTTCTTCTTCTTTTTT
39174076 TTTT
1 TTTT
39174080 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTTCTTCTTCTTTTTT
Found at i:39174067 original size:23 final size:23
Alignment explanation
Indices: 39174036--39174087 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
39174026 TTAGTACTTA
39174036 TTTTTTTCTTCTTTTTTTTCT-T
1 TTTTTTTCTTCTTTTTTTTCTAT
*
39174058 TTTTTCTTCTTCTTTTTTTTTTAT
1 TTTTT-TTCTTCTTTTTTTTCTAT
39174082 TTTTTT
1 TTTTTT
39174088 AAATTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 16 0.59
24 6 0.22
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.87
Consensus pattern (23 bp):
TTTTTTTCTTCTTTTTTTTCTAT
Found at i:39174377 original size:118 final size:118
Alignment explanation
Indices: 39174231--39174446 Score: 387
Period size: 118 Copynumber: 1.8 Consensus size: 118
39174221 TATTACCCAA
* * *
39174231 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
1 CACGTCACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGATTACTCAG
*
39174296 TCAGTCACGATTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
66 TCAGTCACAATTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
*
39174349 CACGTTACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGATTACTCAG
1 CACGTCACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGATTACTCAG
39174414 TCAGTCACAATTTGAGCCATACTCATAACCTCG
66 TCAGTCACAATTTGAGCCATACTCATAACCTCG
39174447 AAAAACATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (118 bp):
CACGTCACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGATTACTCAG
TCAGTCACAATTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
Found at i:39175292 original size:42 final size:42
Alignment explanation
Indices: 39175227--39175349 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
39175217 GGTTTTGGGG
* * *
39175227 ATTCTAAGGCTGAAATAGGACTGTTTGGCTGCA-GAGATATAGC
1 ATTCT-AGGCTGGAATAGAACTGTTTGGCAGCATG-GATATAGC
* *
39175270 ATTCTGGGCTGGAATAGAACTGTTTGGCAGCATGGATATGGC
1 ATTCTAGGCTGGAATAGAACTGTTTGGCAGCATGGATATAGC
* * * *
39175312 ATTTTAGGTTGGAATAGAACTGTTTGGTACCATGGATA
1 ATTCTAGGCTGGAATAGAACTGTTTGGCAGCATGGATA
39175350 GGGTTGTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 63 0.91
43 6 0.09
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (42 bp):
ATTCTAGGCTGGAATAGAACTGTTTGGCAGCATGGATATAGC
Found at i:39175458 original size:8 final size:8
Alignment explanation
Indices: 39175442--39175494 Score: 74
Period size: 8 Copynumber: 6.6 Consensus size: 8
39175432 TATTAATATT
39175442 TAAATATAA
1 TAAA-ATAA
39175451 TAAAATAA
1 TAAAATAA
39175459 TAAAATAA
1 TAAAATAA
39175467 TAAAATAA
1 TAAAATAA
39175475 T-AAATAA
1 TAAAATAA
39175482 T-AAATAAA
1 TAAAAT-AA
39175490 TAAAA
1 TAAAA
39175495 ATAAAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 11 0.26
8 24 0.57
9 7 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAAAATAA
Found at i:39175502 original size:23 final size:22
Alignment explanation
Indices: 39175444--39175504 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
39175434 TTAATATTTA
*
39175444 AATATAAT-AAAATAATAAAAT
1 AATAAAATAAAAATAATAAAAT
39175465 AATAAAATAATAAATAAT-AAAT
1 AATAAAATAA-AAATAATAAAAT
39175487 AAATAAAAATAAAAATAA
1 -AAT-AAAATAAAAATAA
39175505 AGATTAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 7 0.20
22 5 0.14
23 16 0.46
24 7 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
AATAAAATAAAAATAATAAAAT
Found at i:39182538 original size:6 final size:5
Alignment explanation
Indices: 39182505--39182556 Score: 59
Period size: 5 Copynumber: 9.6 Consensus size: 5
39182495 AAATAGAAAG
*
39182505 ATTTT ATTTT GTTTT ATTTT ATTATTT ATATTT ATATTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT A-T-TTT AT-TTT AT-TTT ATTTT ATTTT
39182554 ATT
1 ATT
39182557 AATTTAGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 25 0.58
6 14 0.33
7 4 0.09
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:39187292 original size:169 final size:169
Alignment explanation
Indices: 39186999--39187336 Score: 482
Period size: 169 Copynumber: 2.0 Consensus size: 169
39186989 CCTTCAATAG
* * * *
39186999 TAACCCACAAGACCCAAAAAACTACGGATCTTAAAAACGTTCCTAGGTTGTTTCTAATCAAGTAC
1 TAACCCACAAGACCCAAAAAAATACAGATCTTAAAAACGTTCCTAGGCTGTTTCTAATCAAGCAC
* * *
39187064 AGCCTCAATCTTTCTAGGATCAACTCAGATCTATTCAGCAAAAACTACGTACCCTAGAAATGTTA
66 AGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGCAAAAACTACGTACACTAGAAATGTTA
** * * *
39187129 TTTCCTGTAATCATAATTCACATTTGCTCAACTTAGCGT
131 TTTCCCATAACCAGAATTCACATTTACTCAACTTAGCGT
* * *
39187168 TAACCCGCAAGACCCAAAAAAATGCAGAT-TTCAAAAAGGTTCCTAGGCTGTTTCCT-ATCAAGC
1 TAACCCACAAGACCCAAAAAAATACAGATCTT-AAAAACGTTCCTAGGCTGTTT-CTAATCAAGC
* * *
39187231 ACGGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGTAGAAACTACGTACACTAGAAATGT
64 ACAGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGCAAAAACTACGTACACTAGAAATGT
39187296 TATTTCCCATAACCAGAATTCACATTTACTCAACTTAGCGT
129 TATTTCCCATAACCAGAATTCACATTTACTCAACTTAGCGT
39187337 AAAGCTACTT
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
168 2 0.01
169 145 0.97
170 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (169 bp):
TAACCCACAAGACCCAAAAAAATACAGATCTTAAAAACGTTCCTAGGCTGTTTCTAATCAAGCAC
AGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGCAAAAACTACGTACACTAGAAATGTTA
TTTCCCATAACCAGAATTCACATTTACTCAACTTAGCGT
Found at i:39188365 original size:27 final size:27
Alignment explanation
Indices: 39188335--39188397 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
39188325 ACGGATTAGT
*
39188335 ACAATAATCTCATCAGAAGTACACTCA
1 ACAATAATCTCACCAGAAGTACACTCA
* *
39188362 ACAATAATCTGACCGGAAGTACACTCA
1 ACAATAATCTCACCAGAAGTACACTCA
39188389 ACAATAATC
1 ACAATAATC
39188398 CCCAAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (27 bp):
ACAATAATCTCACCAGAAGTACACTCA
Found at i:39194879 original size:31 final size:31
Alignment explanation
Indices: 39194841--39194900 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39194831 TTAAGTGTAA
** *
39194841 AATCAAATAATTACGGTACAAATACATTAAG
1 AATCAAATAATTACAATACAAATAAATTAAG
*
39194872 AATCAAATTATTACAATACAAATAAATTA
1 AATCAAATAATTACAATACAAATAAATTA
39194901 TAAAGTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (31 bp):
AATCAAATAATTACAATACAAATAAATTAAG
Found at i:39201078 original size:211 final size:211
Alignment explanation
Indices: 39200714--39201134 Score: 770
Period size: 211 Copynumber: 2.0 Consensus size: 211
39200704 CTTGGGGTGC
39200714 ACCAGTATTGTTCGTGAAAGAAAAGGACGGAACCATGATATTGTGCATCGACTATCGTCAGTTGA
1 ACCAGTATTGTTCGTGAAAGAAAAGGACGGAACCATGATATTGTGCATCGACTATCGTCAGTTGA
39200779 ATAAAGTGACGATAAAGAATAAATATCCATTACCGCGTATTGATGATTTGTTTGATCAACTAAAG
66 ATAAAGTGACGATAAAGAATAAATATCCATTACCGCGTATTGATGATTTGTTTGATCAACTAAAG
39200844 GGAGCCTCAGTGTTTTCAAAGATAGATTTGAGATCGGGTTATTATCAGTTGCGAATTCGAGATTC
131 GGAGCCTCAGTGTTTTCAAAGATAGATTTGAGATCGGGTTATTATCAGTTGCGAATTCGAGATTC
*
39200909 GGATATACCCAAAACT
196 AGATATACCCAAAACT
39200925 ACCAGTATTGTTCGTGAAAGAAAAGGACGGAACCATGATATTGTGCATCGACTATCGTCAGTTGA
1 ACCAGTATTGTTCGTGAAAGAAAAGGACGGAACCATGATATTGTGCATCGACTATCGTCAGTTGA
* * *
39200990 ATAAAGTGACGATAAAGAATAAATATCCATTACCGCGTATTGATGATTTGTTTGATCAGCTGAAT
66 ATAAAGTGACGATAAAGAATAAATATCCATTACCGCGTATTGATGATTTGTTTGATCAACTAAAG
** *
39201055 GGAGTTTCAGTGTTTTCAAAGATAGATTTGAGATCGGGTTATTATCAGTTGCGAGTTCGAGATTC
131 GGAGCCTCAGTGTTTTCAAAGATAGATTTGAGATCGGGTTATTATCAGTTGCGAATTCGAGATTC
*
39201120 AGATATACCTAAAAC
196 AGATATACCCAAAAC
39201135 GGCTTTTGGA
Statistics
Matches: 202, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
211 202 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (211 bp):
ACCAGTATTGTTCGTGAAAGAAAAGGACGGAACCATGATATTGTGCATCGACTATCGTCAGTTGA
ATAAAGTGACGATAAAGAATAAATATCCATTACCGCGTATTGATGATTTGTTTGATCAACTAAAG
GGAGCCTCAGTGTTTTCAAAGATAGATTTGAGATCGGGTTATTATCAGTTGCGAATTCGAGATTC
AGATATACCCAAAACT
Found at i:39204634 original size:40 final size:39
Alignment explanation
Indices: 39204510--39204633 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
39204500 GCATGATACT
*
39204510 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
39204549 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
* * * * *
39204588 TGGAAATATATCCGGGCTTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAACATATCCGGACTTGAGGT-CCGCAGGCTATGTGC
*
39204628 TAGAAA
1 TGGAAA
39204634 TTGGACTCGG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 58 0.75
40 19 0.25
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
Found at i:39206122 original size:19 final size:19
Alignment explanation
Indices: 39206098--39206135 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39206088 TCTTTTGTAT
39206098 ATGATAATACTCTTTAACC
1 ATGATAATACTCTTTAACC
39206117 ATGATAATACTCTTTAACC
1 ATGATAATACTCTTTAACC
39206136 CTCCGGCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (19 bp):
ATGATAATACTCTTTAACC
Found at i:39207214 original size:117 final size:119
Alignment explanation
Indices: 39206949--39207222 Score: 392
Period size: 121 Copynumber: 2.3 Consensus size: 119
39206939 TAGAAAGGGA
* *
39206949 AAGTATCCAAAGTCCTAACAAAACATAATTATACAATTACAAGTCATGCACATCATCTAATATAG
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
* * *
39207014 GTAATGTATCCAAGAAAGGTTCAAAATATAATATTATCAAAGAAAGTTCAAAGAGG
66 GTAATGTA--CAAGAAAAGTTCAAAATATAATACTACCAAAGAAAGTTCAAAGAGG
* * *
39207070 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCATATCATCTCAGATTG
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
* *
39207135 GTAATGTA-AAGAAAAGTTC-AAATATAATACTACC-ATGAAAAGTTCAAAGATG
66 GTAATGTACAAGAAAAGTTCAAAATATAATACTACCAAAG-AAAGTTCAAAGAGG
* *
39207187 AAGTATTCAAAGTTCTAACAAAACCTAATTATACAA
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAA
39207223 AGCCCAAAAA
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
116 2 0.01
117 60 0.43
118 10 0.07
121 68 0.49
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (119 bp):
AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
GTAATGTACAAGAAAAGTTCAAAATATAATACTACCAAAGAAAGTTCAAAGAGG
Found at i:39212932 original size:12 final size:11
Alignment explanation
Indices: 39212915--39212945 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
39212905 ACAAATTAAA
39212915 AATAATAATATT
1 AATAATAATA-T
39212927 AATAATAATAT
1 AATAATAATAT
39212938 AATAATAA
1 AATAATAA
39212946 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAT
Found at i:39213005 original size:17 final size:17
Alignment explanation
Indices: 39212976--39213010 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39212966 TATATAAAAG
39212976 GATATAAATAAATAAAT
1 GATATAAATAAATAAAT
39212993 GATA-AAATAAAATAAAT
1 GATATAAAT-AAATAAAT
39213010 G
1 G
39213011 TACATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
GATATAAATAAATAAAT
Found at i:39216030 original size:20 final size:21
Alignment explanation
Indices: 39216007--39216045 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39215997 TGAGATTAAT
*
39216007 GAGGATT-TTTAAAATTTTGA
1 GAGGATTAATTAAAATTTTGA
*
39216027 GAGGCTTAATTAAAATTTT
1 GAGGATTAATTAAAATTTT
39216046 TTAAAATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (21 bp):
GAGGATTAATTAAAATTTTGA
Found at i:39216368 original size:21 final size:21
Alignment explanation
Indices: 39216342--39216384 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39216332 TTTCCAAGTA
39216342 TATTTA-CGGAAATGGACCGAT
1 TATTTACCGGAAA-GGACCGAT
*
39216363 TATTTACCGGAAAGGGCCGAT
1 TATTTACCGGAAAGGACCGAT
39216384 T
1 T
39216385 TTGGCAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (21 bp):
TATTTACCGGAAAGGACCGAT
Found at i:39216662 original size:21 final size:22
Alignment explanation
Indices: 39216638--39216680 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39216628 GTTTTACTAA
39216638 AATAATCTA-GGTTTAGAGTTT
1 AATAATCTAGGGTTTAGAGTTT
* *
39216659 AATAATTTAGGGTTTAGGGTTT
1 AATAATCTAGGGTTTAGAGTTT
39216681 TCTACAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.44
Consensus pattern (22 bp):
AATAATCTAGGGTTTAGAGTTT
Found at i:39216902 original size:121 final size:124
Alignment explanation
Indices: 39216678--39216939 Score: 372
Period size: 121 Copynumber: 2.1 Consensus size: 124
39216668 GGGTTTAGGG
*
39216678 TTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGTTTTTGAACAAAGAGTGTAAAAAAC
1 TTTTCTACAGTAGTTCCTAAAAAATAA-TTTGAGAAGACGTTTCTGAACAAAGAGTGTAAAAAAC
* * * *
39216743 GCTTTAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAATA-CTCCCACGTGGACACTAT
65 GCTTAAAGCAGAATCCACTGTCAGCAAAAGTACAGAAAAA-AGCTCCCACGTGGACACTAT
*
39216803 TTTTCTACAGTAGTTCCT-AAAAA-AA-TTGAGAAGACGTTTCTGAACAAATAGTGTAAAAAACG
1 TTTTCTACAGTAGTTCCTAAAAAATAATTTGAGAAGACGTTTCTGAACAAAGAGTGTAAAAAACG
* * * *
39216865 CTTCAAAG-AGAATCCACTGTCAGTAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCT
66 CTT-AAAGCAGAATCCACTGTCAGCAAAAGTACAGAAAAAAGCTCCCACGTGGACACTAT
39216924 TTTTCTACAGTAGTTC
1 TTTTCTACAGTAGTTC
39216940 ATGTTTGGCC
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
120 1 0.01
121 96 0.77
122 3 0.02
123 2 0.02
124 5 0.04
125 18 0.14
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (124 bp):
TTTTCTACAGTAGTTCCTAAAAAATAATTTGAGAAGACGTTTCTGAACAAAGAGTGTAAAAAACG
CTTAAAGCAGAATCCACTGTCAGCAAAAGTACAGAAAAAAGCTCCCACGTGGACACTAT
Found at i:39220340 original size:27 final size:27
Alignment explanation
Indices: 39220300--39220388 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
39220290 CCATCAACGA
*
39220300 TGGT-AATATAATCGGCACACAG-CAC
1 TGGTAAATATGATCGGCACACAGCCAC
* * *
39220325 TGGGTAAATATGATCGACACAGAGTCA-
1 T-GGTAAATATGATCGGCACACAGCCAC
* * *
39220352 TCGATAAATATGATAGGCACATAGCCAC
1 T-GGTAAATATGATCGGCACACAGCCAC
39220380 TGGTAAATA
1 TGGTAAATA
39220389 CGATTTGCAC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 43 0.86
28 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (27 bp):
TGGTAAATATGATCGGCACACAGCCAC
Found at i:39220850 original size:27 final size:26
Alignment explanation
Indices: 39220831--39220915 Score: 107
Period size: 27 Copynumber: 3.2 Consensus size: 26
39220821 GGTATTTTAG
*
39220831 TAATTTTACAAATTGAGGGTATTTCGA
1 TAATTTTACAAATCG-GGGTATTTCGA
*
39220858 TAATTTCACAAATCGGAGGTATTTCGA
1 TAATTTTACAAATCGG-GGTATTTCGA
* *
39220885 TAATTTTACAAACCGGGGGTATTTCAA
1 TAATTTTACAAATC-GGGGTATTTCGA
39220912 TAAT
1 TAAT
39220916 CTAAACAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 1 0.02
27 48 0.94
28 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (26 bp):
TAATTTTACAAATCGGGGTATTTCGA
Found at i:39221142 original size:18 final size:18
Alignment explanation
Indices: 39221121--39221156 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39221111 AAAGTTTGTC
39221121 ACTAATCGAGGATTTTAT
1 ACTAATCGAGGATTTTAT
39221139 ACTAATCGAGGATTTTAT
1 ACTAATCGAGGATTTTAT
39221157 CCGTGCGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
ACTAATCGAGGATTTTAT
Found at i:39222282 original size:24 final size:24
Alignment explanation
Indices: 39222254--39222317 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
39222244 CTCATTAAAT
*
39222254 CTCTCCATAAATCACTC-ATTGATT
1 CTCTCCATAAATCACTCTA-TGATA
* *
39222278 TTCTCC-TAATATCTCTCTATGATA
1 CTCTCCATAA-ATCACTCTATGATA
*
39222302 CACTCCATAAATCACT
1 CTCTCCATAAATCACT
39222318 TCAACCTCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
23 3 0.10
24 24 0.77
25 4 0.13
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (24 bp):
CTCTCCATAAATCACTCTATGATA
Found at i:39223429 original size:14 final size:14
Alignment explanation
Indices: 39223393--39223423 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39223383 TATTAGTTAT
*
39223393 ATACATAATACTAA
1 ATACAAAATACTAA
39223407 ATACAAAATACTAA
1 ATACAAAATACTAA
39223421 ATA
1 ATA
39223424 TGAAATGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (14 bp):
ATACAAAATACTAA
Found at i:39224384 original size:18 final size:19
Alignment explanation
Indices: 39224340--39224385 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
39224330 ACAGACTGTT
*
39224340 ATAAAAAATTATAAAATAC
1 ATAAATAATTATAAAATAC
* *
39224359 A-AATTAATTA-AAATTAC
1 ATAAATAATTATAAAATAC
39224376 ATAAATAATT
1 ATAAATAATT
39224386 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.32
18 14 0.64
19 1 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATAATTATAAAATAC
Found at i:39224605 original size:21 final size:21
Alignment explanation
Indices: 39224572--39224625 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
39224562 TAAAGAGAGT
** *
39224572 TTTGAGAAATTTAATAAGAAA
1 TTTGAGAGCTTTAAGAAGAAA
* *
39224593 TTTGAGAGCTTTAGGGAGAAA
1 TTTGAGAGCTTTAAGAAGAAA
39224614 TTTGAGAGCTTT
1 TTTGAGAGCTTT
39224626 TTTGTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (21 bp):
TTTGAGAGCTTTAAGAAGAAA
Found at i:39224953 original size:29 final size:30
Alignment explanation
Indices: 39224896--39224958 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 30
39224886 CGTTTTACCA
* *
39224896 AAATCGGCCCTTTCTGGTAAATAATGTT-G
1 AAATCAGCCCTTTCTGATAAATAATGTTGG
39224925 AAATCAGCCCATTTCT-ATAAAT-ATAGTTGG
1 AAATCAGCCC-TTTCTGATAAATAAT-GTTGG
39224955 AAAT
1 AAAT
39224959 GGACCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 2 0.07
29 17 0.59
30 10 0.34
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (30 bp):
AAATCAGCCCTTTCTGATAAATAATGTTGG
Found at i:39238680 original size:15 final size:15
Alignment explanation
Indices: 39238660--39238689 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39238650 TGTTAAAAAA
39238660 TGGATAATTTTGTTG
1 TGGATAATTTTGTTG
39238675 TGGATAATTTTGTTG
1 TGGATAATTTTGTTG
39238690 GTTCATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (15 bp):
TGGATAATTTTGTTG
Found at i:39238834 original size:17 final size:17
Alignment explanation
Indices: 39238791--39238833 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39238781 TATTTAATCT
* *
39238791 AATTCATTTGATATATTC
1 AATT-ATTTTATATATTA
39238809 AATTATTTTATATATTA
1 AATTATTTTATATATTA
39238826 AA-TATTTT
1 AATTATTTT
39238834 TTAAAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 13 0.57
18 4 0.17
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTATTTTATATATTA
Found at i:39245862 original size:17 final size:18
Alignment explanation
Indices: 39245840--39245880 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
39245830 ACTTTTATCT
*
39245840 TATTATAAT-TGTGTATA
1 TATTATAATGTGTATATA
*
39245857 TATTAT-GTGTGTATATA
1 TATTATAATGTGTATATA
39245874 TATTATA
1 TATTATA
39245881 TGCATATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
TATTATAATGTGTATATA
Found at i:39246913 original size:13 final size:13
Alignment explanation
Indices: 39246897--39246921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39246887 TTTAAACCAA
39246897 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39246910 ACTTTTCAAAAG
1 ACTTTTCAAAAG
39246922 TATTACCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39247650 original size:15 final size:17
Alignment explanation
Indices: 39247625--39247662 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
39247615 TCAATTACTT
*
39247625 CATACATATATTT-TTA
1 CATAAATATATTTATTA
39247641 -ATAAATATATTTATTA
1 CATAAATATATTTATTA
39247657 CATAAA
1 CATAAA
39247663 AAAAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
CATAAATATATTTATTA
Found at i:39252830 original size:33 final size:33
Alignment explanation
Indices: 39252775--39252884 Score: 80
Period size: 33 Copynumber: 3.3 Consensus size: 33
39252765 TAGTCCAACT
** * * *
39252775 ATGGTCTTACACATATATTGCCATGACCCTGCC
1 ATGGTCTTACATTTATAGTGCCATAACCCAGCC
* **
39252808 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTATAGTGCCATAACCCAGCC
* * * *
39252841 ATGGTCTTATCA-TTA-GGATGTCATAGCCCAGCT
1 ATGGTCTTA-CATTTATAG-TGCCATAACCCAGCC
39252874 ATGGTCTTACA
1 ATGGTCTTACA
39252885 CATATATTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
32 3 0.05
33 57 0.92
34 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACATTTATAGTGCCATAACCCAGCC
Found at i:39262325 original size:78 final size:75
Alignment explanation
Indices: 39262147--39262726 Score: 722
Period size: 78 Copynumber: 7.6 Consensus size: 75
39262137 GCGTGAGCTA
*
39262147 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCA
39262210 GCGTGTCCTG
66 GCGTGTCCTG
**
39262220 AGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTGAAAAAACAGAAATTGAAAATACCTC
* *
39262285 GGCGTGTGACCCG
65 AGCGTGT--CCTG
**
39262298 AGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTGAAAAAACAGAAATTGAAAATACCTC
* **
39262363 GGCGTGTGACCCA
65 AGCGTGT--CCTG
** *
39262376 AGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCCC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTGAAAAAACAGAAATTGAAAATACCTC
* *
39262441 GGCGTGTCTTG
65 AGCGTGTCCTG
*
39262452 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCA
39262515 GCGTGTCCTG
66 GCGTGTCCTG
*
39262525 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAAAAGGAATTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAA-A-ACA--G---A--AATTGA
* *
39262589 AAATACCTCAACGTGTCTTG
56 AAATACCTCAGCGTGTCCTG
*
39262609 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTG-AAAAGCAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAAACAGAAATTGAAAATACCTC
** *
39262673 AATGTGTCTTG
65 AGCGTGTCCTG
* *
39262684 AGGCTCAACTCACCTATCGTAATATGAGTTGATTTTTTCGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-GAAA
39262727 CAGAAATAAA
Statistics
Matches: 462, Mismatches: 25, Indels: 37
0.88 0.05 0.07
Matches are distributed among these distances:
73 99 0.21
74 8 0.02
75 69 0.15
76 63 0.14
77 3 0.01
78 151 0.33
79 1 0.00
80 1 0.00
82 2 0.00
83 1 0.00
84 58 0.13
85 3 0.01
86 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAATACCTCA
GCGTGTCCTG
Found at i:39262640 original size:84 final size:73
Alignment explanation
Indices: 39262583--39262720 Score: 222
Period size: 75 Copynumber: 1.9 Consensus size: 73
39262573 ATTGAAAAGG
39262583 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTT
1 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TT
*
39262648 GAAAAGCAGA
64 GAAAAACAGA
* * *
39262658 AATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
1 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
39262721 TCGAAACAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 2 0.03
74 3 0.05
75 55 0.92
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (73 bp):
AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
AAAACAGA
Found at i:39262660 original size:232 final size:225
Alignment explanation
Indices: 39262146--39262720 Score: 737
Period size: 232 Copynumber: 2.5 Consensus size: 225
39262136 CGCGTGAGCT
*
39262146 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCA
* **
39262210 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTG
66 GCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAACAGAAATTG
* *
39262275 AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAA
129 AAAATACCTCAGCGTGT-ACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGA-CTTTTTGAA
* **
39262340 AAAACAGAAATTGAAAATACCTCGGCGTGTGACCC
192 AAAAAAGAAATTGAAAATACCTCAACGTGT-ACCC
** *
39262375 AAGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCT
*
39262440 CGGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTG
64 CAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTG
* * *
39262504 AAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
129 AAAATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGACTTTTTG-AAA
**
39262567 ACATAAATTGAAAAGGAATTGAAAATACCTCAACGTGT-CTT
193 A-A-AAA--G---A--AATTGAAAATACCTCAACGTGTACCC
* *
39262608 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCTC
** * *
39262673 AATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
65 AGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
39262721 TCGAAACAGA
Statistics
Matches: 304, Mismatches: 28, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
225 6 0.02
226 4 0.01
227 34 0.11
228 2 0.01
229 60 0.20
230 7 0.02
231 6 0.02
232 129 0.42
233 36 0.12
235 20 0.07
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (225 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCA
GCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAA
AATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGACTTTTTGAAAAAA
AAGAAATTGAAAATACCTCAACGTGTACCC
Found at i:39274787 original size:22 final size:23
Alignment explanation
Indices: 39274762--39274826 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
39274752 TATTGAAAAT
*
39274762 ACATGTTCATAATATATA-TAAA
1 ACATATTCATAATATATATTAAA
39274784 ACATATAT-ATAATATAATATTAAA
1 ACATAT-TCATAATAT-ATATTAAA
*
39274808 ACATTTTACATAATATATA
1 ACATATT-CATAATATATA
39274827 CACATATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 12 0.33
23 5 0.14
24 12 0.33
25 7 0.19
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (23 bp):
ACATATTCATAATATATATTAAA
Found at i:39274820 original size:25 final size:23
Alignment explanation
Indices: 39274769--39274824 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
39274759 AATACATGTT
39274769 CATAATAT-ATATAAAACATATA
1 CATAATATAATATAAAACATATA
* *
39274791 TATAATATAATATTAAAACATTTTA
1 CATAATATAATA-TAAAACA-TATA
39274816 CATAATATA
1 CATAATATA
39274825 TACACATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.25
23 3 0.11
24 7 0.25
25 11 0.39
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
CATAATATAATATAAAACATATA
Found at i:39274902 original size:21 final size:23
Alignment explanation
Indices: 39274872--39274917 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
39274862 ATTAATAATA
39274872 ATACTAATAT-TACA-TAAAGAT
1 ATACTAATATATACATTAAAGAT
* *
39274893 ATACTTATATATATATTAAAGAT
1 ATACTAATATATACATTAAAGAT
39274916 AT
1 AT
39274918 GTGCATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (23 bp):
ATACTAATATATACATTAAAGAT
Found at i:39276498 original size:9 final size:9
Alignment explanation
Indices: 39276484--39276508 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39276474 TTGGACTTTA
39276484 TTTATTTGG
1 TTTATTTGG
39276493 TTTATTTGG
1 TTTATTTGG
39276502 TTTATTT
1 TTTATTT
39276509 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (9 bp):
TTTATTTGG
Found at i:39277030 original size:73 final size:74
Alignment explanation
Indices: 39276942--39277596 Score: 751
Period size: 78 Copynumber: 8.7 Consensus size: 74
39276932 ACGTGAGCTA
*
39276942 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
39277006 CGTGTCCTG
66 CGTGTCCTG
** *
39277015 AGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTG---AA-A-AAA---AAAATACCTTA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTGAAAAACAGAAATTGAAAATACCTCA
* *
39277072 GCGTGCCCCG
65 GCGTGTCCTG
* * * *
39277082 AAGCTCAACTCACCTCTCGCAATATGAGTTG-GTTTTTGAAAAATAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
39277146 CGTGTCCTG
66 CGTGTCCTG
*
39277155 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCTC
* *
39277220 GGCGTGTGACCCG
64 AGCGTGT--CCTG
*
39277233 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCTC
* *
39277298 GGCGTGTGACCCG
64 AGCGTGT--CCTG
*
39277311 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG--AAAAACAGAAATTGAAAATACCT
*
39277376 CGGCGTGTCCTG
63 CAGCGTGTCCTG
39277388 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAACAGGAATTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC----A--G---A--AATTGA
* *
39277452 AAATACCTCAACGTGTCTTG
55 AAATACCTCAGCGTGTCCTG
* *
39277472 AGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCTCA
** *
39277537 ATGTGTCTTG
65 GCGTGTCCTG
* *
39277547 AGGCTCAACTCACCTATCGTAATATGAGTTGATTTTTTCG--AAACAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-GAAAAACAGAAAT
39277597 AAAAACATCA
Statistics
Matches: 519, Mismatches: 33, Indels: 60
0.85 0.05 0.10
Matches are distributed among these distances:
65 6 0.01
67 45 0.09
68 2 0.00
69 1 0.00
70 6 0.01
71 1 0.00
72 2 0.00
73 91 0.18
74 2 0.00
75 77 0.15
76 28 0.05
77 36 0.07
78 121 0.23
79 33 0.06
80 1 0.00
82 2 0.00
84 54 0.10
85 3 0.01
86 8 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (74 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
CGTGTCCTG
Found at i:39277196 original size:140 final size:145
Alignment explanation
Indices: 39276942--39277583 Score: 704
Period size: 140 Copynumber: 4.3 Consensus size: 145
39276932 ACGTGAGCTA
*
39276942 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCAG
*
39277006 CGTGTCCTGAGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTG-AA-A-AAA-AAAATA
66 CGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAACAGAAATAAAATA
** *
39277067 CCTTAGCGTGCCCCG
131 CCTCGGCGTGACCCG
* * * *
39277082 AAGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTG-AAAAATAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCAG
39277146 CGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAACAGAAATTGA
66 CGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTG---AAACAGAAA-T-A
39277211 AAATACCTCGGCGTGTGACCCG
126 AAATACCTCGGC--GTGACCCG
*
39277233 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAACAGAAATTGAAAATACCTC
* *
39277298 GGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGAA
64 AGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTG----AAACAGAA
* *
39277363 ATTGAAAATACCTCGGCGTGTCCTG
123 A-T-AAAATACCTCGGCGTGACCCG
*
39277388 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGGAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG------A-AAA---AACAGAAATTGAA
* * * *
39277453 AATACCTCAACGTGTCTTGAGGCTCAATTCACCTCTCGCAATATGAGTTGAT-TTTCTTGAAAAG
56 AATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTT-TTG-AAA-
*** * **
39277517 CAGAAATTGAAAATACCTCAATGTGTCTTG
118 CAGAAA-T-AAAATACCTCGGCGTGACCCG
* *
39277547 AGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
39277584 TCGAAACAGA
Statistics
Matches: 443, Mismatches: 30, Indels: 39
0.87 0.06 0.08
Matches are distributed among these distances:
140 109 0.25
144 2 0.00
145 1 0.00
146 3 0.01
149 11 0.02
151 36 0.08
153 12 0.03
154 28 0.06
155 37 0.08
156 43 0.10
157 28 0.06
158 4 0.01
159 62 0.14
160 6 0.01
161 36 0.08
163 25 0.06
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (145 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCAG
CGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAACAGAAATAAAATA
CCTCGGCGTGACCCG
Found at i:39277497 original size:84 final size:75
Alignment explanation
Indices: 39277439--39277583 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 75
39277429 AACATAAATT
* *
39277439 GAACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA
1 GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
39277504 TTTTCTTGAAAA
66 -TTT-TTGAAAA
* * *
39277516 G--CAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGA
1 GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
39277579 TTTTT
66 TTTTT
39277584 TCGAAACAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
73 2 0.03
74 3 0.05
75 57 0.90
77 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (75 bp):
GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAAAA
Found at i:39277559 original size:159 final size:150
Alignment explanation
Indices: 39277061--39277583 Score: 629
Period size: 159 Copynumber: 3.4 Consensus size: 150
39277051 TTTGAAAAAA
* * * * * *
39277061 AAAATACCTTAGCGTGCCCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTG-AAAAA
1 AAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
* *
39277125 TAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCT
66 CAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCT
39277190 TTTTGAAAAAACAGAAATTG
131 TTTTGAAAAAACAGAAATTG
* * * *
39277210 AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAA
1 AAAATACCTC--AGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAA
* *
39277275 AAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAACATGAGT
62 AAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAACATGAGT
39277340 TGATCTTTTTGAAAAAAACAGAAATTG
125 TGATCTTTTTG-AAAAAACAGAAATTG
* *
39277367 AAAATACCTCGGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 AAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG------
* * * * *
39277432 ATAAATTGAACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAATTCACCTCTCGCAATAT
60 A-AAA---AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACAT
*
39277497 GAGTTGAT-TTTCTTG-AAAAGCAGAAATTG
121 GAGTTGATCTTT-TTGAAAAAACAGAAATTG
* * * *
39277526 AAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
1 AAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
39277584 TCGAAACAGA
Statistics
Matches: 325, Mismatches: 30, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
149 9 0.03
151 37 0.11
153 12 0.04
154 28 0.09
155 38 0.12
156 43 0.13
157 25 0.08
159 66 0.20
160 6 0.02
161 36 0.11
163 25 0.08
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (150 bp):
AAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
CAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCT
TTTTGAAAAAACAGAAATTG
Found at i:39281391 original size:11 final size:11
Alignment explanation
Indices: 39281375--39281415 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
39281365 GTTTGGAAAT
39281375 GATTCGACGAA
1 GATTCGACGAA
39281386 GATTCGACGAA
1 GATTCGACGAA
39281397 GATTCGACGAA
1 GATTCGACGAA
39281408 GATTCGAC
1 GATTCGAC
39281416 AGTTGGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (11 bp):
GATTCGACGAA
Found at i:39285454 original size:39 final size:36
Alignment explanation
Indices: 39285411--39285492 Score: 83
Period size: 39 Copynumber: 2.2 Consensus size: 36
39285401 GATGACTATA
*
39285411 TAAAAACTTTCAATAAAAAAATATAATTTTATTAAATAT
1 TAAAAACTAT-AATAAAAAAATAT-ATTTT-TTAAATAT
* * * *
39285450 TAAAATAGTATAATATAAATATATATTTTTTAAATTT
1 TAAAA-ACTATAATAAAAAAATATATTTTTTAAATAT
39285487 TAAAAA
1 TAAAAA
39285493 TAATATAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
36 1 0.03
37 12 0.32
38 5 0.14
39 16 0.43
40 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (36 bp):
TAAAAACTATAATAAAAAAATATATTTTTTAAATAT
Found at i:39286030 original size:33 final size:34
Alignment explanation
Indices: 39285950--39286036 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 34
39285940 TGACTATATA
* *
39285950 AAATTTACAATAAATAAAAAAATATAAAATTTTATT
1 AAATTTA-AA-AAATAATATAATATAAAATTTTATT
39285986 AAATATT--AAAATAATATAATAT-AAATATTT-TT
1 AAAT-TTAAAAAATAATATAATATAAAAT-TTTATT
39286018 AAATTTAAAAAATAATATA
1 AAATTTAAAAAATAATATA
39286037 TACGAGTCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 2 0.04
32 10 0.22
33 26 0.58
34 1 0.02
36 4 0.09
37 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATTTAAAAAATAATATAATATAAAATTTTATT
Found at i:39288305 original size:2 final size:2
Alignment explanation
Indices: 39288298--39288344 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
39288288 GTCTGTGTTC
* *
39288298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT TT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39288339 AT AT AT
1 AT AT AT
39288345 TTGCGATGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39289183 original size:9 final size:9
Alignment explanation
Indices: 39289171--39289213 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
39289161 AAATAATGCA
39289171 GTTAATTCG
1 GTTAATTCG
*
39289180 GTTAATTTG
1 GTTAATTCG
* *
39289189 GGTAATTCA
1 GTTAATTCG
39289198 GTTAATTCG
1 GTTAATTCG
39289207 GTTAATT
1 GTTAATT
39289214 TTATACTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (9 bp):
GTTAATTCG
Found at i:39289587 original size:9 final size:9
Alignment explanation
Indices: 39289575--39289617 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
39289565 AAATAATGCA
39289575 GTTAATTCG
1 GTTAATTCG
*
39289584 GTTAATTTG
1 GTTAATTCG
* *
39289593 GGTAATTCA
1 GTTAATTCG
39289602 GTTAATTCG
1 GTTAATTCG
39289611 GTTAATT
1 GTTAATT
39289618 TTATACTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (9 bp):
GTTAATTCG
Found at i:39289598 original size:404 final size:404
Alignment explanation
Indices: 39288849--39289656 Score: 1607
Period size: 404 Copynumber: 2.0 Consensus size: 404
39288839 TAACCGACCG
39288849 GATTCGGTTAATCGGTCTGTTAACCAAATTAATTCGATCAGGGGTCGGTTAATAATTTTTTGAGT
1 GATTCGGTTAATCGGTCTGTTAACCAAATTAATTCGATCAGGGGTCGGTTAATAATTTTTTGAGT
39288914 TTTCAGTTAACGGTTAATTCGGTTCGAAACCGGTCGGTTCACCGAATATTTTCGGTTTAACCGAA
66 TTTCAGTTAACGGTTAATTCGGTTCGAAACCGGTCGGTTCACCGAATATTTTCGGTTTAACCGAA
39288979 AATATTAATAAATAAATTTATAATATATAAATAGCCCACTATTTATTCAAATCCAATTCAACATA
131 AATATTAATAAATAAATTTATAATATATAAATAGCCCACTATTTATTCAAATCCAATTCAACATA
39289044 AACCCAAATACCCAATCTAATATATATTAACCCAAGCACCCAACCCAACCCAATTATAAAAATTA
196 AACCCAAATACCCAATCTAATATATATTAACCCAAGCACCCAACCCAACCCAATTATAAAAATTA
39289109 CAAATAATTTAATAAATAAAAATAAAAATAAAAAAAATATATAATTTTATACAAATAATGCAGTT
261 CAAATAATTTAATAAATAAAAATAAAAATAAAAAAAATATATAATTTTATACAAATAATGCAGTT
39289174 AATTCGGTTAATTTGGGTAATTCAGTTAATTCGGTTAATTTTATACTTATTTTAACCAAAAATAA
326 AATTCGGTTAATTTGGGTAATTCAGTTAATTCGGTTAATTTTATACTTATTTTAACCAAAAATAA
39289239 AAAATATATAATTT
391 AAAATATATAATTT
39289253 GATTCGGTTAATCGGTCTGTTAACCAAATTAATTCGATCAGGGGTCGGTTAATAATTTTTTGAGT
1 GATTCGGTTAATCGGTCTGTTAACCAAATTAATTCGATCAGGGGTCGGTTAATAATTTTTTGAGT
*
39289318 TTTCAGTTAACGGTTAATTCGGTTCGAAACCGGTCGGTTCACCGAATATTTTTGGTTTAACCGAA
66 TTTCAGTTAACGGTTAATTCGGTTCGAAACCGGTCGGTTCACCGAATATTTTCGGTTTAACCGAA
39289383 AATATTAATAAATAAATTTATAATATATAAATAGCCCACTATTTATTCAAATCCAATTCAACATA
131 AATATTAATAAATAAATTTATAATATATAAATAGCCCACTATTTATTCAAATCCAATTCAACATA
39289448 AACCCAAATACCCAATCTAATATATATTAACCCAAGCACCCAACCCAACCCAATTATAAAAATTA
196 AACCCAAATACCCAATCTAATATATATTAACCCAAGCACCCAACCCAACCCAATTATAAAAATTA
39289513 CAAATAATTTAATAAATAAAAATAAAAATAAAAAAAATATATAATTTTATACAAATAATGCAGTT
261 CAAATAATTTAATAAATAAAAATAAAAATAAAAAAAATATATAATTTTATACAAATAATGCAGTT
39289578 AATTCGGTTAATTTGGGTAATTCAGTTAATTCGGTTAATTTTATACTTATTTTAACCAAAAATAA
326 AATTCGGTTAATTTGGGTAATTCAGTTAATTCGGTTAATTTTATACTTATTTTAACCAAAAATAA
39289643 AAAATATATAATTT
391 AAAATATATAATTT
39289657 TCGGTTAATT
Statistics
Matches: 403, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
404 403 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (404 bp):
GATTCGGTTAATCGGTCTGTTAACCAAATTAATTCGATCAGGGGTCGGTTAATAATTTTTTGAGT
TTTCAGTTAACGGTTAATTCGGTTCGAAACCGGTCGGTTCACCGAATATTTTCGGTTTAACCGAA
AATATTAATAAATAAATTTATAATATATAAATAGCCCACTATTTATTCAAATCCAATTCAACATA
AACCCAAATACCCAATCTAATATATATTAACCCAAGCACCCAACCCAACCCAATTATAAAAATTA
CAAATAATTTAATAAATAAAAATAAAAATAAAAAAAATATATAATTTTATACAAATAATGCAGTT
AATTCGGTTAATTTGGGTAATTCAGTTAATTCGGTTAATTTTATACTTATTTTAACCAAAAATAA
AAAATATATAATTT
Found at i:39290999 original size:8 final size:8
Alignment explanation
Indices: 39290981--39291014 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
39290971 TTTGTTTTCT
39290981 TTATATATA
1 TTAT-TATA
39290990 TTATTATA
1 TTATTATA
39290998 TTATTATA
1 TTATTATA
39291006 TTACTTATA
1 TTA-TTATA
39291015 AAATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.62
9 9 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTATA
Found at i:39292894 original size:20 final size:21
Alignment explanation
Indices: 39292855--39292894 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39292845 TAATTAGATA
*
39292855 AATTGTTAAAAAATTGAAATG
1 AATTGTTAAAAAAATGAAATG
39292876 AATTGTTAAAAAAAT-AAAT
1 AATTGTTAAAAAAATGAAAT
39292895 TAGAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
AATTGTTAAAAAAATGAAATG
Found at i:39293552 original size:22 final size:22
Alignment explanation
Indices: 39293503--39293552 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
39293493 AAAATAGTAG
*
39293503 AAAAAATAGCGAGAAAATAACA
1 AAAAAATAGCGAGAAAACAACA
* *
39293525 AGAAAATAGC-AGTAAAACAATA
1 AAAAAATAGCGAG-AAAACAACA
39293547 AAAAAA
1 AAAAAA
39293553 AAGACAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.70, C:0.08, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAATAGCGAGAAAACAACA
Found at i:39299785 original size:14 final size:15
Alignment explanation
Indices: 39299766--39299805 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
39299756 CGAAATTTTT
39299766 ATAAAAAAAAT-AAA
1 ATAAAAAAAATAAAA
*
39299780 ATAAAATAAATAAAA
1 ATAAAAAAAATAAAA
39299795 ATAAATAAAAA
1 ATAAA-AAAAA
39299806 ATTTTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 8 0.36
16 4 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
ATAAAAAAAATAAAA
Found at i:39299805 original size:10 final size:9
Alignment explanation
Indices: 39299766--39299805 Score: 53
Period size: 10 Copynumber: 4.1 Consensus size: 9
39299756 CGAAATTTTT
39299766 ATAAAAAAA
1 ATAAAAAAA
39299775 ATAAAATAAA
1 ATAAAA-AAA
39299785 ATAAATAAAA
1 ATAAA-AAAA
39299795 ATAAATAAAA
1 ATAAA-AAAA
39299805 A
1 A
39299806 ATTTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.21
10 22 0.76
11 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:39300603 original size:143 final size:143
Alignment explanation
Indices: 39300346--39300605 Score: 321
Period size: 143 Copynumber: 1.8 Consensus size: 143
39300336 AGTTGCAAAC
* *
39300346 TTAGTCCTTATACTCTAATTTGGTTAATTTAATCCATGTACTCTTTTGAATTTTGAAATTTTAAT
1 TTAGTCCTTATACTCTAATTTGATCAATTTAATCCATGTACTCTTTTGAATTTTGAAATTTTAAT
* ** * * * * * * **
39300411 TATGACTTAAATGTTTATAGTTTAATTTGTTAGGTCAAAATTTGTTATTAGTTCATGTACTATGC
66 TATAACCCAAATGGTAACAATTAAATCTGTTAGGTCAAAATTTACTATTAGTTCATGTACTATGC
39300476 ATACATAGCATAA
131 ATACATAGCATAA
* *
39300489 TTAGTCTTTATACTCTAATTTGATCAATTTTAGTCCATGTA-T-TTTTCGAATTTTGAAATTTTA
1 TTAGTCCTTATACTCTAATTTGATCAA-TTTAATCCATGTACTCTTTT-GAATTTTGAAATTTTA
39300552 ATCT-TAACCCAAATGGTAACAATTAAATCTGTTAGGTC-AAATTCTACTATTAGT
64 AT-TATAACCCAAATGGTAACAATTAAATCTGTTAGGTCAAAATT-TACTATTAGT
39300606 CATTATATTA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
142 9 0.09
143 76 0.78
144 13 0.13
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (143 bp):
TTAGTCCTTATACTCTAATTTGATCAATTTAATCCATGTACTCTTTTGAATTTTGAAATTTTAAT
TATAACCCAAATGGTAACAATTAAATCTGTTAGGTCAAAATTTACTATTAGTTCATGTACTATGC
ATACATAGCATAA
Found at i:39301179 original size:13 final size:13
Alignment explanation
Indices: 39301161--39301186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39301151 GGCACGATTC
39301161 AATTTTTTATATT
1 AATTTTTTATATT
39301174 AATTTTTTATATT
1 AATTTTTTATATT
39301187 TTTTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTTTATATT
Found at i:39301225 original size:26 final size:29
Alignment explanation
Indices: 39301169--39301229 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
39301159 TCAATTTTTT
39301169 ATATTAATTTTTTATATTTTTTTAAATAAA
1 ATATTAATTTTTTATATTTTTTT-AATAAA
39301199 ATATT-ATTTTTT-TATTTTTATT-A-AAA
1 ATATTAATTTTTTATATTTTT-TTAATAAA
39301225 ATATT
1 ATATT
39301230 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.27
27 1 0.03
28 7 0.23
29 9 0.30
30 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATATTAATTTTTTATATTTTTTTAATAAA
Found at i:39302081 original size:27 final size:27
Alignment explanation
Indices: 39302051--39302120 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
39302041 CCTACCATTT
* *
39302051 GCGCCTCTGAGATAGGCACGATTAGTC
1 GCGCCTCTGAGATAGGCACAACTAGTC
* *
39302078 GCGCCTCTGAGAAAGGCTCAACTAGTC
1 GCGCCTCTGAGATAGGCACAACTAGTC
*
39302105 GCGCCTCTGACATAGG
1 GCGCCTCTGAGATAGG
39302121 TGCAACCTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (27 bp):
GCGCCTCTGAGATAGGCACAACTAGTC
Found at i:39305750 original size:146 final size:147
Alignment explanation
Indices: 39305502--39305770 Score: 362
Period size: 146 Copynumber: 1.8 Consensus size: 147
39305492 CTGAATTCGT
*
39305502 AAGGGATGAAAGAACGCTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGGCC
1 AAGGGATGAAAGAAC-CTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGACC
* * * *
39305567 TCATAGCACAATAGGACTATACTGAATGCACAGCTTCCAGGTTTCAACATAGTTATGCACATTAG
65 TCATAGCACAATAGGACTATACCGAATACACAGCTTCCAGATTTCAACATAATTATGCACATTAG
39305632 CATCGGACACCGACAGAC
130 CATCGGACACCGACAGAC
* * * *
39305650 AAGGGATGTAAGAA-CTCTGAGTCTCAAATTATGACATGAATGAGAGCAGAACATCGGAAGACCT
1 AAGGGATGAAAGAACCTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGACCT
** ** * * *
39305714 TGTAGCACGGTAGGATTATACCGAATATAC-GCCTTCCAGATTTCGACATAATTATGC
66 CATAGCACAATAGGACTATACCGAATACACAG-CTTCCAGATTTCAACATAATTATGC
39305771 CTTGAGCTAG
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
145 1 0.01
146 90 0.87
148 13 0.12
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (147 bp):
AAGGGATGAAAGAACCTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGACCT
CATAGCACAATAGGACTATACCGAATACACAGCTTCCAGATTTCAACATAATTATGCACATTAGC
ATCGGACACCGACAGAC
Found at i:39311329 original size:17 final size:17
Alignment explanation
Indices: 39311288--39311329 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
39311278 ATAAAATTAT
*
39311288 TGATAAATTAAATATTA
1 TGATAAATTAAATATCA
* *
39311305 TAAAAAATTAAATATCA
1 TGATAAATTAAATATCA
39311322 TGATAAAT
1 TGATAAAT
39311330 GATATTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
TGATAAATTAAATATCA
Found at i:39321949 original size:13 final size:13
Alignment explanation
Indices: 39321931--39321955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39321921 AAAAAATATT
39321931 AATTAATTAATTA
1 AATTAATTAATTA
39321944 AATTAATTAATT
1 AATTAATTAATT
39321956 TTAGTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTAATTA
Found at i:39322369 original size:14 final size:14
Alignment explanation
Indices: 39322326--39322397 Score: 65
Period size: 14 Copynumber: 4.9 Consensus size: 14
39322316 TGTGAAAATG
*
39322326 ATTAAAATAATATG
1 ATTAAAATAATATT
*
39322340 AATAAAATAATTTATT
1 ATTAAAATAA--TATT
39322356 ATTAAAATAATATT
1 ATTAAAATAATATT
*
39322370 AGTTCAAAATTA-ATT
1 A-TT-AAAATAATATT
*
39322385 ATTGAAATAATAT
1 ATTAAAATAATAT
39322398 GATGTGGGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
13 5 0.11
14 18 0.38
15 6 0.13
16 18 0.38
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (14 bp):
ATTAAAATAATATT
Found at i:39337285 original size:64 final size:64
Alignment explanation
Indices: 39337100--39337599 Score: 424
Period size: 64 Copynumber: 7.8 Consensus size: 64
39337090 AGTTTCAGGC
* * * * * ** *
39337100 TTTCAGCTAAAAGATAAAGCGATATAGCGTC-AAACTGAGTGAAAAAAACATAATGAAATTAAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
* * * * * *** *
39337163 TTTCAGCTAGAAGATAGAGCTGAATAGCATCAAAACCAAGTG--AAAAACATAAAAATTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
* * * *
39337225 TTTCAGATAAAACATAAA-CTAAATAGCGTAAAAAATGAGTGAAAAAAAACATAATGATTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTG-AAAAAAACATAAAGATTTTCAG
* * * *
39337289 TTTCAGCTAAAAGGTAAAGCTTAATAGCGTCAAAATTGAGTG-AAAAAACA-AAACGGTTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAA-GATTTTCAG
* * * * * ** * *
39337352 TTTCAGCTAAAAAGATAAAGCTAAATAGAGTCAAATTTTAGTTAAAAGTACATTAAGATTTACAG
1 TTTCAGAT-AAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
** *
39337417 TTTCAGATTTTCAGCTCAAAGATAAAGCTAAATAGCGTCAAAATTTTGTGGAAAAAA-ATAAAGA
1 TTTCAGA---T-A----AAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGA
39337481 TTTTCAG
58 TTTTCAG
* * * * *
39337488 -TACAGATAAAAGATAAAG-AAAATAGCATCAAAATTGAGTGAAAAAGACGTAAAGATTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
* * *
39337550 TTTCAGTTAAAAGATAAAGATAAATAACGTCAAAATTGAGTGGAAAAAAA
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGT-GAAAAAAA
39337600 TAATAAAATA
Statistics
Matches: 348, Mismatches: 69, Indels: 38
0.76 0.15 0.08
Matches are distributed among these distances:
61 40 0.11
62 54 0.16
63 65 0.19
64 87 0.25
65 46 0.13
66 3 0.01
67 1 0.00
68 2 0.01
70 5 0.01
71 12 0.03
72 33 0.09
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.25
Consensus pattern (64 bp):
TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
Done.